University of Basel Seeks Professor of Paediatric Infectious and Emerging Diseases Modelling

University of Basel Seeks Professor of Paediatric Infectious and Emerging Diseases Modelling

visual: University of Basel, Mark Niedermann

 

The Faculty of Medicine of the University of Basel, Switzerland invites applications for a Tenure Track Assistant Professor, Associate or Full Professor of Paediatric Infectious and Emerging Diseases Modelling to be embedded in the BRCCH.

The BRCCH and its future Paediatric Digital Health Hub is a multi-disciplinary research centre creating new healthcare solutions for unmet medical needs related to communicable and non-communicable pathologies of significant burden to children and adolescents, irrespective of an individual's societal conditions.

Your position

The successful candidate will develop an internationally competitive research programme in Paediatric lnfectious and/or Emerging Diseases Modelling with an emphasis on clinical translation tailored for the special needs of children and adolescents. You will develop novel, integrative disease modelling approaches to investigate factors that influence disease development and outcomes in paediatric populations across different geographical and socio-economic settings, with special emphasis on low- and middle-income countries. Close collaborations are expected with clinical partners, scientists at the University of Basel and ETH Zurich in Basel, and within the Basel life sciences cluster.

The Master and Ph.D. programmes of the University's Medical and Sciences Faculties provide opportunities for teaching (in English).

Your profile

We expect from the candidate a genuine interest in interdisciplinary academic work and several years of experience in mathematical and computational modelling of health-related and epidemiological data. Experience with modelling of paediatric infectious and other emerging diseases is advantageous. Excellent academic performance and a proven record in acquiring competitive third-party funding relative to the applicant's career stage are essential qualifications. We expect a significant interest in student teaching and mentoring of junior scientists at different stages of their academic careers. Key personality traits include excellent social and communication skills and an open, engaging and collegial personality. The candidate's distinctive expertise, leadership, and outstanding communication skills place him/her in an ideal position to gain acceptance and trust. He/she is able to create an attractive work environment, inspire creative thinking that can be put into action, and encourage his/her employees.

The university offers you

  • A unique opportunity for interdisciplinary research in a highly innovative and translational research environment enabling access to patients and academic bioinformatics facilities
  • A challenging and varied job in a university and clinical environment
  • An innovative, interdisciplinary and open research environment
  • A responsible leadership role
  • A collaborative environment conducive to interdisciplinary research
  • Attractive employment conditions
  • Attractive startup package and endowment for research

The University of Basel stands for excellence through diversity and is committed to equal opportunities and family friendliness. In an effort to increase the proportion of women in professorships, the university is particularly interested in receiving applications from women.

Application / Contact

For further information, please contact the chair of the Academic Recruitment Committee, Prof. Ulrich Heininger (Email: ulrich.heininger@ukbb.ch) or the Scientific Coordinator of Academic Recruitment, Dr. Simone Neu Phone: (Email: berufungen-medizin@unibas.ch; Phone: +41 61 207 61 64).

Applications must be submitted by November 20, 2024.

We kindly ask you to apply exclusively via the online application platform of the University of Basel and as described in the application guidelines.

 

Dr. Na Cai appointed as BRCCH Professor of Computational Medical Genomics

Dr. Na Cai appointed as BRCCH Professor of Computational Medical Genomics

In February 2025, Dr. Na Cai will join the Basel Research Centre for Child Health (BRCCH) as an Assistant Professor of Computational Medical Genomics. She is currently leading a research group at Helmholtz Pioneer Campus at the Technical University of Munich, where she investigates the genetic bases of psychiatric disorders, particularly Major Depressive Disorder (MDD). This debilitating mental disorder manifests in a wide range of clinical symptoms, including depressed mood, anhedonia or sleep disturbance. In spite of its high prevalence worldwide, the strong polygenic nature of MDD and its heterogenous symptomatology hinder the identification of the biological factors causing this disease

 

Leveraging clinical and genomic datasets from biobanks and electronic health records, Dr. Na Cai and her group have developed a new computational and statistical approach to associate genetic variants with symptoms-based MDD subtypes (e.g. childhood depression vs late onset of MDD). In the future, she aims at developing new computational models to predict disease trajectories of MDD as well as examining the impact of MDD genetic factors in the context of other psychiatric disorders, such as attention-deficit/hyperactivity disorder, which often co-occurs with childhood MDD. Moreover, she will employ multi-omic approaches combined with machine learning methods to assess the impact of environmental risk factors such as childhood abuse or chronical social stress in individuals genetically predisposed to experience MDD.

 

Inaugural Lecture 25 November 2024 – Recent Advances in the Molecular Understanding and Diagnostics of Bone Tumours

Inaugural Lecture, 25 November 2024 - Recent Advances in the Molecular Understanding and Diagnostics of Bone Tumours

 

The BRCCH cordially invites you to the inaugural lecture of Prof Daniel Baumhoer of the University Hospital Basel, Switzerland. Prof Baumhoer will discuss recent advances in the molecular understanding and diagnosis of bone tumours.

When: Monday, 25th November 2024, 16:00 - 17:30 CET, to be followed by an apéro

Where: Hybrid Zoom / Zentrum für Lehre und Forschung, Kleiner Hörsaal, Universitätsspital Basel (Centre for Teaching and Learning, Small Lecture Theatre, University Hospital Basel), Hebelstrasse 20, 4031 Basel.

See map

Zoom Registration: HERE

In Person Registration: HERE

Schedule:

      • Welcome by Prof Georg Hollander, Director of the BRCCH
      • Lecture delivered by Prof Daniel Baumhoer, University Hospital Basel, Switzerland: "Recent advances in the molecular understanding and diagnostics of bone tumours"
      • Q&A and Closing
      • Networking Apéro

Speaker:

Prof Daniel Baumhoer

University Hospital Basel, Switzerland

Talk: "Recent Advances in the Molecular Understanding and Diagnostics of Bone Tumours"

Profile: Prof Dr Daniel Baumhoer is the BRCCH Professor in Bone and Soft Tissue Pathology. He is also a consultant pathologist with special expertise in bone and soft tissue, as well as head and neck pathology. At the University Hospital in Basel, he leads the Bone Tumour Reference Centre and the DÖSAK Reference Registry through which he receives 800-1000 consultation cases a year, mostly from Switzerland and Germany but also from other countries. Prof Baumhoer contributed to several fascicles of the WHO classification of tumours as the responsible first author and has contributed to more than 200 peer-reviewed publications. His research focuses on elucidating the molecular pathogenesis of bone and soft tissue tumours, with a particular focus on methylation classifiers.

 

Future of Paediatric Health Research Spotlight Day – Video Release

Future of Paediatric Health Research Spotlight Day - Video Release

 

On 19 April 2024 the BRCCH hosted its Future of Paediatric Health Research Spotlight Day in Basel, Switzerland. This one-day seminar and networking event brought together researchers across disciplines with a common focus on improving child and adolescent health.

This event included talks from BRCCH Postdoctoral Excellence Programme researchers about their paediatric health research progress over the last two years. Each of these fellows also invited an established researcher from their field to deliver a keynote address.

Videos of the day's presentations are now available to watch on YouTube. See the links below.

Speakers:

Dr Sarah Brüningk

BRCCH Postdoctoral Excellence Programme Researcher

ETH Zurich, Switzerland

Talk: "Harnessing Machine Learning and Mechanistic Modelling for Personalised Predictions for Paediatric Brain Tumour Patients"

View on YouTube

Dr Kanika Dheman

BRCCH Postdoctoral Excellence Programme Researcher

ETH Zurich, Switzerland

Talk: "Patch-IT: Multi-Sensor Sensor Nodes for Continuous Vital Sign Monitoring to Identify Novel Digital Biomarkers for Sepsis Detection in Neonatal Intensive Care"

View on YouTube

Dr Michele Magno

Head, Center for Project-Based Learning at the Department of Information Technology and Electrical Engineering

ETH Zurich, Switzerland

Talk: "AI-based Wearables and Noncontact Radars: Revolutionizing Neonatal and Infant Monitoring"

View on YouTube

Dr Gillian Levine

BRCCH Postdoctoral Excellence Programme Researcher

Swiss Tropical and Public Health Institute, Switzerland

Talk: "E-Helping Hands: Digital Clinical Decision Support Tools to Improve Care of Sick Young Infants"

View on YouTube

Dr Nigel Rollins

Medical Officer, Department of Maternal, Newborn, Child and Adolescent Health and Ageing

World Health Organization, Switzerland

Talk: "Translating the WHO Integrated Management of Childhood Illness into a Digital Tool for Use by Frontline Health Workers in Humanitarian Settings"

View on YouTube

Dr Nicole Zoratto

BRCCH Postdoctoral Excellence Programme Researcher

ETH Zurich, Switzerland

Talk: "Bioinspired, Low-Cost Device for Minimally Invasive Blood Sampling"

View on YouTube

Dr Nicole Stoffel

Lecturer, Department of Health Sciences and Technology

ETH Zurich, Switzerland

Talk: "The Effects of Iron Deficiency on Paediatric Vaccine Response"

View on YouTube

Prof Nissim Benvenisty

Herbert Cohn Chair in Cancer Research

Hebrew University, Israel

Talk: "The Essentialome of Human Development and Disease"

View on YouTube

ETH Zurich Seeks Assistant Professor (Tenure Track) for Biomolecular Engineering for Health

ETH Zurich Seeks Assistant Professor (Tenure Track) for Biomolecular Engineering for Health

 

The Department of Biosystems Science and Engineering (D-BSSE) at ETH Zurich invites applications for the above-mentioned position. D-BSSE is located in Basel, the heart of the BioValley area, providing excellent opportunities for collaboration within this strong life science research community at the academic, clinical and pharmaceutical industry levels. The main research focus of D-BSSE is the understanding, modeling, and engineering of biomolecular systems, including applications for medical translation. The Professorship will also be embedded within the newly established Basel Research Center for Child Health (BRCCH), which aims to provide innovative and translational solutions for child and adolescent health. Collaborations within the medical research communities in Basel and Zurich are highly encouraged.

This future Assistant Professor will bring unique multi-disciplinary expertise in engineering biomolecular systems for applications in translational medicine and health. She or he may use integrative and multi-disciplinary approaches involving biosystems engineering of molecular and cellular systems and/or synthetic biology to develop novel therapeutic and diagnostic solutions. While rooted in biomolecular systems engineering, the candidate is also expected to engage with the computational and systems biology groups in the department to advance therapeutic and health technologies. Key areas of interest are state-of-the-art molecular and cell biology and biomolecular systems engineering techniques (eg sequencing technologies, engineering proteins and protein networks), synthetic biology tools (eg RNA aptamers, DNA nanotechnology, CRISPR, synthetic circuits), in vitro-based systems (lab-on-a-chip, sensors, robots) coupled to quantitative biomolecular and cellular measurements, novel microscale or nanoscale technologies for biomolecular analysis (eg paper-based microfluidics, droplet systems, cellular systems), and digital -assisted tools and platforms for measuring biomolecular or physiological parameters (eg smartphone-based diagnostics). The candidate is expected to have a proven track record of publications in biomolecular and cellular systems engineering and/or synthetic biology. She or he should demonstrate a strong interest in clinical application and a clear ambition to pursue research that is directly relevant to childhood health and medicine. At the assistant professor level, commitment to teaching and the ability to lead a research group are expected.

Assistant professorships have been established to promote the careers of younger scientists. ETH Zurich implements a tenure track system equivalent to that of other top international universities.

ETH Zurich is an equal opportunity and family-friendly employer, values ​​diversity, and is responsive to the needs of dual-career couples.

Please apply online

Applications should include a curriculum vitae, a list of publications, a statement of future research and teaching interests, a description of the leadership philosophy, a description of the three most important achievements*, and a certificate of the highest degree. The letter of application should be addressed to the President of ETH Zurich, Prof. Dr. Joel Mesot. The closing date for applications is August 31, 2024.

*ETH Zurich attaches importance to a qualitative assessment of academic achievements. In this sense, you are asked to include a short description of your three most important achievements in your application (maximum half a page each). In addition to research results, these can also include special achievements in teaching and its further development, services for the benefit of the academic community or society, software developments, patents, knowledge and practice transfer, spin-offs and the like.

Launch of a New Global Research Centre in Switzerland

Launch of a New Global Research Centre in Switzerland

 

The Botnar Institute of Immune Engineering (BIIE) is a new independent research institute launching in Basel, Switzerland. Its mission is to develop computational tools and immune-based translational solutions for the diagnosis, treatment and prevention of disease. These shall address gaps in the healthcare of children and adolescents globally.

The Institute has been made possible by a one billion USD endowment over the next 15 years from Fondation Botnar, the main financial supporter of the BRCCH. Fondation Botnar is a Swiss philanthropic foundation working to improve the health and well-being of young people around the world.

With extensive knowledge of Fondation Botnar’s remit and research mission, BRCCH Director Prof Georg Holländer has been selected as the BIIE’s Global Engagement Director while continuing his engagement with the BRCCH. Former BRCCH Co-Director Prof Sai Reddy is the designated Scientific Director of the BIIE.

As a sister research centre, the BRCCH would like to congratulate everyone involved in bringing this vision to life. We look forward to seeing the immune engineering advances that result from this institute and are excited to collaborate with the BIIE in the future.

Read the full announcement from Fondation Botnar here.

Prof Daniel Müller Joins the Basel Research Centre for Child Health as Co-Director

Prof Daniel Müller Joins the Basel Research Centre for Child Health as Co-Director

The Basel Research Centre for Child Health (BRCCH) is pleased to share that Prof Daniel Müller is succeeding Prof Sai Reddy as Co-Director effective immediately. With the support of Director Prof Georg Holländer, Prof Müller will help guide the strategic orientation and initiatives of the BRCCH as it transitions to a digital health hub in Basel.

We want to sincerely thank Prof Sai Reddy for the time and expertise he dedicated to supporting the launch of the BRCCH and its initial scientific activities. Prof Reddy is an associate professor at ETH Zurich in the Department of Biosystems Science and Engineering and was the first Co-Director of the BRCCH, joining the organisation at its conception in 2018. During his tenure, Prof Reddy shaped the funding activities of the BRCCH while championing its mission to innovate solutions for the health and well-being of children and adolescents worldwide.

“Thank you, Sai, for your dedicated leadership of the BRCCH over the last five years,” says Prof Georg Holländer, BRCCH Director. “During your tenure, the BRCCH launched four funding calls that allowed us to support 80 scientists across 29 research projects. We appreciate your guidance during the initial activities of the BRCCH and in preparing for this next phase.”

As the BRCCH transitions into a digital health hub in Basel, Prof Reddy is passing his post to Prof Daniel Müller, a professor of biophysics at ETH Zurich in Basel. Prof Müller was involved in the initial conception and building of the BRCCH, was also formerly on the BRCCH Board as the previous Head of the Department of Biosystems Science and Engineering at ETH Zurich and actively participated in developing the BRCCH’s new strategic direction. As an expert in engineering biomolecular systems, his skills complement those of BRCCH Director Prof Georg Holländer, a paediatric researcher.

“I am delighted to begin my official role within the BRCCH,” says Prof Daniel Müller, BRCCH Co-Director. “As an organisation, the BRCCH has expanded the innovation potential in paediatric digital health in Switzerland. I look forward to concentrating this expertise in Basel during the BRCCH’s transition to a paediatric digital health hub and through the creation of one of the first institutes worldwide dedicated to this topic.”

The Power of Digital Pathology

The Power of Digital Pathology

Conversation with Prof Dr Daniel Baumhoer

In early 2024, Prof Daniel Baumhoer joined the Basel Research Centre for Child Health (BRCCH) as the first professor as part of the organisation’s transition to a digital health hub in Basel. Prof Dr Baumhoer will lead the Malignant and Bone and Soft Tissue Pathologies capacity-building platform. This resource will complement and support the work of the six appointed professors who will form the core of the new BRCCH. He is currently the Deputy Medical Director of the Institute of Medical Genetics and Pathology and Head of the Bone Tumour Reference Centre (BTRC) and DÖSAK (Swiss Austrian German Working Group on Maxillofacial Tumours) Registry at the University Hospital Basel.

Prof Dr Baumhoer grew up in Germany and attended medical school at the Georg-August University of Göttingen. He moved to Basel in 2004 to train in pathology and passed the pathology board exam in 2009. In 2014, he took over as the lead of the BTRC and DÖSAK registry, both at the University Hospital Basel providing second opinions on difficult-to-classify bone and soft tissue and maxillofacial tumours. Each year, the registries receive between 800 and 1,000 consultation requests from around the world.

“The Bone Tumor Reference Centre is something quite unique, I think, worldwide,” says Prof Dr Baumhoer. “Since it was founded in 1972, we have collected more than 22,000 bone tumours, mostly from children and adolescents, but also from adults.”

Since many of these tumours are rare, this large sample set provides an ideal setting to study these lesions and gain experience in their morphological and genetic spectrum. The team also uses elaborate molecular profiling techniques to analyse tissue samples. Available patient follow-up information makes this repository a powerful tool to drive innovative paediatric health research and informatics.

“I'm really looking forward to meeting the other experts within the BRCCH to foster collaboration and use the unique BTRC dataset to better understand the underlying pathogenesis of bone and soft tissue tumours,” shares Prof Dr Baumhoer.

Expediting Diagnosis Using Digital Pathology

Within the University Hospital Basel, Prof Dr Baumhoer has also been leading the transition to digital pathology. This process involves scanning histologic slides, which can then be assessed digitally. Integrating these digital slides into the hospital’s repository, which also contains radiologic images of patients, enables a more integrated approach as pathology findings can be provided to and assessed by all clinicians. Digital histology slides can also be easily shared and discussed with other experts, even internationally.

“From a scientific point of view, digital pathology makes it possible to share cases more easily, to use new techniques and algorithms to evaluate histologic patterns and to create a more holistic digital diagnostic approach by integrating other modalities, including radiology,” concludes Prof Dr Baumhoer.

One of the current challenges for the BTRC is that physical paraffin blocks of tissue must be sent to the registry in Basel by mail, a lengthy process prone to delays, sometimes customs-related. For patients waiting to start treatment, this is valuable time they can’t afford to waste. Digital pathology could help shorten this timeline by allowing clinicians to send histology images digitally. The physical tissue blocks will only be required for molecular testing.

“Using digital pathology would make these interactions more effective,” suggests Prof Dr Baumhoer. “I envision that there will be a lot more consultation cases in the future, but it will be easier and faster to assess and sign them out using digital pathology.”

The team has made great progress in transitioning to digital pathology at the University Hospital Basel over the last three years. All consult bone and soft tissue tumours are currently being digitised. It is expected that this platform will start being integrated into the routine diagnostic workflow in the coming months. Once digital pathology is implemented, it opens opportunities to incorporate automation for diagnostics into pathology workflows, accelerating the diagnostic process and getting information to clinicians and patients faster.

Diagnosing Bone and Soft Tissue Tumours Using Molecular Analysis

Outside of his clinical practice, Prof Dr Baumhoer studies the molecular profiles of bone and soft tissue tumours to better understand their pathogenesis. He started his career by investigating osteosarcoma, a highly aggressive type of bone cancer that is most common in adolescents and young adults. Different subtypes of osteosarcoma can be characterised by genetic pathway alterations, which could have therapeutic implications. With only 30 to 35 cases of this cancer type in Switzerland each year, it was challenging for Prof Dr Baumhoer to collect sufficient amounts of tissue samples needed to perform genetic profiling, a process that took several years. However, the results were worth the wait.

“We did a lot of sequencing on these samples and we found distinct genetic signatures which could be the basis of new and innovative treatment approaches,” illustrates Prof Dr Baumhoer.

His team was the first to define a specific genetic profile in osteosarcoma associated with deficiencies in DNA repair resembling breast and ovarian cancers with BRCA mutations (so-called BRCAness). To study how these tumours genetically evolve over time, Prof Dr Baumhoer sequentially investigated osteosarcoma samples from patients before and after treatment and following recurrence or metastatic spread.

“Most of the studies we conducted in recent years are included in the World Health Organisation (WHO) classification of tumours,” emphasises Prof Dr Baumhoer. “So, the results are diagnostically relevant.”

One example is the most common benign bone tumour called non-ossifying fibroma. This tumour affects 40 per cent of the population during skeletal growth and maturation. Since the vast majority of these lesions are incidental findings that undergo spontaneous regression, they were thought to be developmentally derived disorders and not regarded as true neoplasms. However, Prof Dr Baumhoer’s team was the first to show that, despite being completely benign, non-ossifying fibromas have recurrent mutations in common cancer pathways that can be used to confirm the diagnosis molecularly.

“It is really important to me to understand more about the molecular pathogenesis of bone tumours,” says Prof Dr Baumhoer. “If we identify recurrent driver gene alterations, these can be used to confirm a diagnosis, but potentially also to enable targeted treatment approaches. Understanding the mechanism of how tumours develop is a first and mandatory step to finding new and effective ways to treat patients.”

Prof Dr Baumhoer is now investigating the DNA methylation profiles of bone and soft tissue tumours. DNA methylation is involved in gene regulation and cellular differentiation. As a result, tumour cells often carry specific methylation patterns that differ between tumour subtypes, and also between normal and cancerous cells. By analysing the DNA of bone and soft tissue tumours, Prof Dr Baumhoer hopes to identify specific methylation patterns that could be used to better differentiate between tumour subtypes. Using new and innovative sequencing technologies, tumour classification could be possible in a few hours rather than the several days to weeks that molecular tests currently take.

“Identifying reliable diagnostic methylation signatures would have a huge impact on patient care since the treating clinicians could immediately start therapy without further delay,” proposes Prof Dr Baumhoer.

Welcoming Prof Dr Baumhoer to the BRCCH

As the first professor to join the BRCCH as a digital health hub, Prof Dr Baumhoer is enthusiastic about collaborating with other experts in paediatric digital health, bringing together his experience, data and diagnostic infrastructure.

“There will be experts in genetics and sequencing, in digitisation, and I think it will be very fruitful if different experts from different angles, but with the same aim, come together and join forces,” expresses Prof Dr Baumhoer. “I really hope we can develop innovative new ideas and projects together.”

19 April 2024 – Future of Paediatric Health Research Spotlight Day

19 April 2024 - Future of Paediatric Health Research Spotlight Day

 

Update: Thank you to all who attended.

The BRCCH cordially invites you to our Future of Paediatric Health Research Spotlight Day on 19 April 2024 in Basel, Switzerland. This one-day seminar and networking event will bring together researchers across disciplines with a common focus on improving child and adolescent health.

This event will include talks from BRCCH Postdoctoral Excellence Programme researchers about their paediatric health research progress over the last two years. Each of these fellows has also invited an established researcher from their field to deliver a keynote address. During the lunch break, attendees will have the opportunity to attend a workshop about nurturing research teams.

When: Friday, 19 April 2024, 9:00 - 17:30 CET, to be followed by an apéro

Where:  Hotel ODELYA, Missionstrasse 21a, 4055 Basel

Please Note: This event is taking place in person in Basel, Switzerland only and will not be accessible online.

In Person Registration: HERE

Schedule:

    • 9.00-9.30 – Arrival and coffee
    • 9.30-9.40 – Welcome by Daniel Müller, Co-Director, BRCCH
    • 9.40-12.15 – Talks by BRCCH Postdoctoral Excellence Programme researchers and their invited speakers on paediatric health
    • 12.15-12.45 – Lunch (Break until 14.00 if not attending the workshop)
    • 12.45-13.45 – Workshop: Nurturing Research Teams
    • 14.00-17.30 – Talks by BRCCH Postdoctoral Excellence Programme researchers and their invited speakers on paediatric health
    • 17:30-17:35 – Closing Remarks by Georg Holländer, Director, BRCCH
    • 17.35-18.00 – Networking & Apéro

Speakers:

Dr Sarah Brüningk

BRCCH Postdoctoral Excellence Programme Researcher

ETH Zurich, Switzerland

Talk: "Harnessing Machine Learning and Mechanistic Modelling for Personalised Predictions for Paediatric Brain Tumour Patients"

Prof Dr Ana Guerreiro Stücklin

SNF Eccellenza Professor for Pediatric Neurooncology

Kinderspital Zurich, Switzerland

Talk: "Dissecting the Role of Oncofusions in Brain Tumours in Infants"

Dr Kanika Dheman

BRCCH Postdoctoral Excellence Programme Researcher

ETH Zurich, Switzerland

Talk: "Patch-IT: Multi-Sensor Sensor Nodes for Continuous Vital Sign Monitoring to Identify Novel Digital Biomarkers for Sepsis Detection in Neonatal Intensive Care"

Dr Michele Magno

Head, Center for Project-Based Learning at the Department of Information Technology and Electrical Engineering

ETH Zurich, Switzerland

Talk: "AI-based Wearables and Noncontact Radars: Revolutionizing Neonatal and Infant Monitoring"

Dr Gillian Levine

BRCCH Postdoctoral Excellence Programme Researcher

Swiss Tropical and Public Health Institute, Switzerland

Talk: "E-Helping Hands: Digital Clinical Decision Support Tools to Improve Care of Sick Young Infants"

Dr Nigel Rollins

Medical Officer, Department of Maternal, Newborn, Child and Adolescent Health and Ageing

World Health Organization, Switzerland

Talk: "Translating the WHO Integrated Management of Childhood Illness into a Digital Tool for Use by Frontline Health Workers in Humanitarian Settings"

Dr Nicole Zoratto

BRCCH Postdoctoral Excellence Programme Researcher

ETH Zurich, Switzerland

Talk: "Bioinspired, Low-Cost Device for Minimally Invasive Blood Sampling"

Dr Nicole Stoffel

Lecturer, Department of Health Sciences and Technology

ETH Zurich, Switzerland

Talk: "The Effects of Iron Deficiency on Paediatric Vaccine Response"

Dr Keith Gunapala

BRCCH Postdoctoral Excellence Programme Researcher

University of Basel, Switzerland

Talk: "Novel Approaches to Treating Fragile X Syndrome"

Prof Nissim Benvenisty

Herbert Cohn Chair in Cancer Research

Hebrew University, Israel

Talk: "The Essentialome of Human Development and Disease"

Workshop: Nurturing Research Teams

Creativity, innovation and collaboration within research teams are prerequisites for knowledge creation and transfer, and for individual and team performance. Positive research leadership that encourages team productivity, motivation and development is crucial in fostering such conditions. But what does leadership mean and entail exactly? What makes a good leader? What leadership styles are there, and what type of leader are you?

This session offers an opportunity to learn, reflect and exchange perspectives on the skill- and mindset required to optimise dynamics and workflows within research teams, and to enable oneself and colleagues to fully develop and express their individual and collective potential.

Dr Maddalena Fumagalli

Seminar 21 March 2024 – Lessons from the Deceased to the Living and Back

Seminar 21 March 2024 - Lessons from the Deceased to the Living and Back

 

Update: Thank you to all who attended. For those who could not make it, the presentation videos are available for viewing below.

The BRCCH cordially invites you to join our seminar about the use of pathology during the COVID-19 pandemic to understand the interaction between the SARS-CoV-2 virus and the human body.

When: Thursday, 21st March 2024, 16:00 - 17:30 CET, to be followed by an apéro

Where: Hybrid Zoom / Seminarraum U1.197– Biozentrum, University of Basel, Spitalstrasse 41, 4056 Basel

Zoom Registration: HERE

In Person Registration: HERE
Directions and location information

Schedule:

      • Welcome by Prof Danny Jonigk (University Medical Center of RWTH Aachen University, Germany)
      • Keynote by Dr Jasmin Haslbauer (University Hospital Basel, Switzerland): "Cardiovascular Manifestations of COVID-19"
      • Keynote by Prof Maximilian Ackermann (RWTH University Clinics & Helios University Clinics, Germany): "COVID-19 – A Systemic Vasculo-inflammatory Disease"
      • Keynote by Prof Alexandar Tzankov (University Hospital Basel, Switzerland): "COVID-19 Insights from Non-Cardio-Pulmonary Organ Pathology"
      • Q&A and Closing
      • Networking Apéro

Speakers:

Prof Danny Jonigk

University Medical Center of RWTH Aachen University, Germany

Moderator

Profile

Prof Danny Jonigk is a surgical and molecular pathologist, the Chair of Pathology and the Head of the Department of the Institute of Pathology at the University Medical Center of RWTH Aachen University in Germany. Prof Jonigk received his doctoral degree from Hannover Medical School in Germany. He is also the Head and Founding Principal Investigator of the National Central Pathology Platform within the German Centre for Lung Research and the Head of the Pathology Platform at the German Centre for Lung Research. He is a Fellow of the Royal College of Pathologists, has received numerous research grants, including the first ERC consolidator grant to a pathologist and authored or co-authored 302 peer-reviewed papers.

Dr Jasmin Haslbauer

University Hospital Basel, Switzerland

Talk: "Cardiovascular Manifestations of COVID-19"

Profile

Dr Jasmin Haslbauer is a resident at the Institute of Medical Genetics and Pathology at University Hospital Basel (USB). She executes autopsies and is responsible for tissue collection, and also provides histopathological examinations, immunohistochemical examinations and data consolidation. She received her undergraduate medical degree from Johann Wolfgang Goethe Universität in Frankfurt am Main, Germany, and an MSc in molecular pathology and genomics from the Barts Cancer Institute at Queen Mary University of London, UK. Her current research deals with COVID-19-associated immunological and cardiovascular pathology.

Dr Haslbauer is a researcher on the BRCCH project: Lessons From the Deceased to the Living and Back. Read more here.

Watch the presentation on YouTube here.

Prof Maximilian Ackermann

RWTH University Clinics & Helios University Clinics, Germany

Talk: "COVID-19 – A Systemic Vasculo-inflammatory Disease"

Profile

Prof Maximilian Ackermann is a professor and pathologist within the Institute of Pathology at RWTH University Clinics and the Institute of Pathology and Molecular Pathology at Helios University Clinics in Germany. His research focuses on angiogenesis, inflammation and vascular remodelling in disease. PD Dr Ackermann received his medical and doctoral degrees from Johannes Gutenberg University of Mainz located in Germany. He has received a number of prestigious awards including the Rudolf-Virchow Award from the German Society of Pathology.

Watch the presentation on YouTube here.

Prof Alexandar Tzankov

University Hospital Basel, Switzerland

Talk: "COVID-19 Insights from Non-Cardio-Pulmonary Organ Pathology"

Profile

Prof Alexandar Tzankov is a surgical pathologist and Head of the Department of Histopathology and Autopsy at the Institute of Medical Genetics and Pathology at University Hospital Basel. He currently chairs the European Bone Marrow Working Group and is a joined expert in the field of pathology for the Swiss Accreditation Authority. His major interests and diagnostic expertise lie within haematopathology and mediastinal pathology. Alongside current intensive tissue-based research activity on the interaction between SARS-CoV-2 and the human body in COVID-19, his research group has long been involved in translational investigations and precision medicine of lymphomas and myeloid neoplasms. He has authored or co-authored more than 460 papers.

Prof Tzankov co-leads the BRCCH project: Lessons From the Deceased to the Living and Back. Read more here.

Watch the presentation on YouTube here.

The BRCCH Becomes the Basel Research Centre for Child Health

The BRCCH Becomes the Basel Research Centre for Child Health

 

The new name marks the BRCCH’s transition into a groundbreaking paediatric digital health research hub based in Basel

Today, the Botnar Research Centre for Child Health announces its new name effective immediately - the Basel Research Centre for Child Health (BRCCH). The Centre was originally named to recognise the generosity of Fondation Botnar, which has donated CHF 150 million to establish and support the paediatric health research activities of the BRCCH. The new name acknowledges the BRCCH’s transition to a paediatric digital health hub in Basel, as well as the city’s importance to the Centre’s past and present achievements.

The BRCCH was established in 2019 to drive outstanding and innovative paediatric health research that improves the health of children and young people, especially those living in low- and middle-income countries. Over the last four years, almost 80 researchers from the BRCCH’s partner institutions – the University of Basel, ETH Zurich, the University Children’s Hospital Basel (UKBB) and the Swiss Tropical and Public Health Institute (Swiss TPH) – have launched 29 interinstitutional research consortia aligned with this mission. Examples of project research topics include bioengineering bacteria to survey the gut microbiome, implementing digital health tools to enhance early childhood development in low- and middle-income countries and developing digital techniques to improve cleft lip and palate care.

The BRCCH is now transitioning into one of the first academic research centres in the world dedicated to interdisciplinary paediatric digital health research. At the core of this centre will be six newly appointed professors – three affiliated with the University of Basel and three affiliated with ETH Zurich – with expertise in biomolecular systems engineering, data analytics, systems developmental medicine, disease modelling, computational medical genomics and ethics and policy. These specialists will foster collaborations to address some of the biggest challenges facing paediatric health care today. An early career programme will also support emerging researchers to build global research capacity in this field.

“We are grateful to Fondation Botnar for their visionary philanthropy and the confidence they have shown in the work of the BRCCH to date,” says Professor Georg Holländer, Director of the BRCCH. “Through this transition and with this new name, we look forward to establishing Basel as an internationally recognised location for exceptional paediatric digital health research.”

ETH Zurich Seeks Assistant Professor (Tenure Track) of Ethics and Policy in Pediatric Digital Health

ETH Zurich Seeks Assistant Professor (Tenure Track) of Ethics and Policy in Pediatric Digital Health

 

The Department of Health Sciences and Technology at ETH Zurich invites applications for the above-​mentioned position at the Institute of Translational Medicine. As a leading international academic institution at the cutting edge of health sciences and technology, the aim of the Department of Health Sciences and Technology (D-​HEST) is to create the foundations for sustaining and improving the quality of life for people across the life span. The professorship will be physically embedded within the newly established Botnar Research Centre for Child Health (BRCCH) in Basel, which aims to provide innovative and translational solutions for child and adolescent health.

The successful candidate must have a proven track record in several of the following areas: research ethics, digital ethics, health policy, regulatory science, and law, with a focus on pediatric and adolescent health. She or he should demonstrate a strong interest in the application of ethics in clinical or public health-​related settings, expertise in the ethical, legal, and societal implications of translational research and a clear ambition to pursue research that is directly relevant to child and adolescent health. Experience in international organizations and / or global governance initiatives in relation to digital health and child and adolescent health would be an asset. This Assistant Professorship aims to set and pursue a research agenda that investigates ethical and policy challenges in the integration of digital health innovations in low-​ and middle-​income countries. The future Assistant Professor is expected to establish and lead a competitive research team, commit to teaching, interact with global health policy initiatives and contribute to the vibrant biomedical research environments at ETH Zurich and Basel.

Assistant professorships have been established to promote the careers of younger scientists. ETH Zurich implements a tenure track system equivalent to that of other top international universities.

ETH Zurich is an equal opportunity and family-​friendly employer, values diversity, and is responsive to the needs of dual-​career couples.

Please apply online.

Applications should include a curriculum vitae, a list of publications, a statement of future research and teaching interests, a description of the leadership philosophy, a description of the three most important achievements*, and a certificate of the highest degree. The letter of application should be addressed to the President of ETH Zurich, Prof. Dr. Joël Mesot. The closing date for applications is 15 Feburary 2024.

* ETH Zurich emphasizes qualitative assessment of academic accomplishments. This is why you are kindly asked to submit a short description of your three most important achievements (maximum a half page each). Besides research findings, these could also be extraordinary achievements in teaching and its further development, services in the benefit of the academic community or society, software development, patents, knowledge transfer and its practical application, spin-​​​​​​off companies or similar.

 

BRCCH 2023 Image Contest

BRCCH 2023 Image Contest

 

The BRCCH warmly invites all BRCCH Early Career Researchers involved in a BRCCH-supported project to participate in the third edition of the BRCCH Image Contest. Submit your images of your scientific work for a chance to win up to CHF 500 to attend a scientific conference or professional development event of your choice. 

Images should visually reflect the research done in your BRCCH project during 2023. They could, for example, show lab, clinical or field work, depict certain methods, visualise results or data, or show the goals of the project. Winning images will be selected based on aesthetics and alignment with the BRCCH scientific scope.

Please send us your image(s) by email to contact@brc.ch with a descriptive caption, a credit of the image(s) by Friday, 15 December 2023.

See the winners of the 2021 and 2022 contests.

Details and Conditions of 2023 Image Contest

Conditions of submission are addressed below, but please contact us at contact@brc.ch with any remaining questions.

BRCCH Image Contest’s conditions of submission:

  1. Early career researchers involved in BRCCH-funded projects are eligible to submit image entries.
  2. Several images can be submitted as a single entry.
  3. We welcome all types of images (e.g. photography, microscopy, computer-generated images, graphics).
  4. Minimal resolution of 300 dpi is required and any image file format (RAW, EPS, TIF, PNG, etc) can be submitted.
  5. If people are shown in the image and are identifiable, they must have given explicit consent to be photographed.
  6. Images should not show sensitive or confidential information or data.
  7. Images generated from BRCCH-funded photoshoots are not eligible.
  8. Images submitted to the BRCCH may be used for BRCCH communication projects (e.g., BRCCH Annual Report, flyers, website). Images will not be used for any commercial or for-profit purpose.
  9. Images remain the copyright of the researcher. BRCCH will credit the image accordingly.
  10. BRCCH will never share the images with third-parties (e.g., news media) without the explicit consent of the researcher.
  11. * Winners of contest receive support to attend a scientific conference or professional development event of their choice with justifiable costs reimbursable up to a maximum of 500 CHF.

Seminar 28 November 2023 – Evolving Perspectives in Improving Cleft Lip and Palate Care

Seminar 28 November 2023 - Evolving Perspectives in Improving Cleft Lip and Palate Care

Update: Thank you to all who attended. For those who could not make it, the presentation videos are available for viewing below.

The BRCCH cordially invites you to join our seminar about evolving perspectives in improving cleft lip and palate care. Prof Andreas Mueller (University Hospital Basel, Switzerland) and Dr Baran Gözcü (ETH Zurich, Switzerland) will share their BRCCH consortium’s research progress in developing a digital pipeline to reduce the treatment burden and cost of cleft lip and palate care. Assoc Prof David Chong (Royal Children's Hospital, Australia) will present his work pursuing the best way to treat children who require facial surgery for cleft lip and palate.

When: Tuesday, 28th November 2023, 16:00 - 17:30 CET, to be followed by an apéro

Where: Hybrid Zoom / Seminarraum U1.197– Biozentrum, University of Basel, Spitalstrasse 41, 4056 Basel

Zoom Registration: HERE

In Person Registration: HERE
Directions and location information

Schedule:

      • Welcome by Dr Adelita Sommacal (University Hospital Basel, Switzerland)
      • Keynote by Prof Andreas Mueller (University Hospital Basel, Switzerland): "Reducing the Burden in Cleft Care: The Knife is not Enough"
      • Keynote by Dr Baran Gözcü (ETH Zurich, Switzerland): "Cleft Care in the 21st Century: Can AI Revolutionize?"
      • Keynote by Assoc Prof David Chong (Royal Children's Hospital, Australia): "Global Cleft Care: A Personal Journey"
      • Q&A and Closing
      • Networking Apéro

Speakers:

Dr Adelita Sommacal

University Hospital Basel, Switzerland

Moderator

Prof Andreas Mueller

University Hospital Basel, Switzerland

Talk: "Reducing the Burden in Cleft Care: The Knife is not Enough"

Watch on YouTube

Dr Baran Gözcü

ETH Zurich, Switzerland

Talk: "Cleft Care in the 21st Century: Can AI Revolutionize"

Watch on YouTube

Assoc Prof David Chong

Royal Children's Hospital, Australia

Talk: "Global Cleft Care: A Personal Journey"

Watch on YouTube

Seminar 23 October 2023 – The Gut Microbiome as a Tool for Individualised Medicine

Seminar 23 October 2023 - The Gut Microbiome as a Tool for Individualised Medicine

 

Update: Thank you to all who attended. For those who could not make it, Dr Zimmermann's presentation is available for viewing below.

The BRCCH cordially invites you to join our seminar about the gut microbiome and individualised medicine. Prof Randall Platt (ETH Zurich, Switzerland) and Prof Andrew Macpherson (University Hospital Bern, Switzerland) will share their BRCCH consortium’s research progress in using engineered bacteria as a non-invasive diagnostic tool to survey the gastrointestinal tract and support child health worldwide. Dr Michael Zimmermann (EMBL - Heidelberg, Germany) will highlight his work investigating how interpersonal differences in the gut microbiome influence bacterial drug metabolism, activity and toxicity.

When: Monday, 23rd October 2023, 16:00 - 17:30 CET, to be followed by an apéro

Where: Hybrid Zoom / Seminarraum U1.197– Biozentrum, University of Basel, Spitalstrasse 41, 4056 Basel

Zoom Registration: HERE

In Person Registration: HERE
Directions and location information

Schedule:

      • Welcome by Dr Katie Guzzetta (ETH Zurich & BRCCH Postdoctoral Researcher)
      • Keynote by Prof Randall Platt (ETH Zurich & BRCCH Lead Researcher): "Living Microbial Diagnostics to Enable Individualised Child Health Interventions"
      • Keynote by Prof Andrew Macpherson (University Hospital Bern & BRCCH Lead Researcher): "An Update on the University of Zimbabwe Birth Cohort Study"
      • Keynote by Dr Michael Zimmermann (EMBL - Heidelberg): "Identifying Gut Microbiome Contributions to Drug Metabolism and Carcinogen Toxicity"
      • Q&A and Closing
      • Networking Apéro

Speakers:

Dr Katie Guzzetta

ETH Zurich, Switzerland

Moderator

Profile

Dr Katie Guzzetta is a postdoctoral fellow in the lab of Prof Randy Platt at ETH Zurich. Her research focuses on developing bacteria-based technologies to diagnose nutritional deficiencies and other health disruptions related to the gut microbiome. Prior to this, Katie completed her PhD in Neuroscience and Anatomy at the APC Microbiome Institute in Cork, Ireland, where she studied how the gut microbiota influences neurodevelopment and behavior under the mentorship of Prof John Cryan and Dr Olivia O’Leary. Outside of the lab, Katie enjoys spending time hiking and camping in the mountains, skiing, and exploring diverse countries and cultures.

Prof Randall Platt

ETH Zurich, Switzerland

Talk: "Living Microbial Diagnostics to Enable Individualised Child Health Interventions"

Profile

Prof Randall (Randy) Platt holds associate professorships at the Department of Biosystems Science and Engineering (D-BSSE) at ETH Zurich and the Department of Chemistry at the University of Basel. Prof Platt studied biomedical engineering and chemistry at the University of Utah in Salt Lake City, USA. In 2011, he obtained an MPhil in material science from Imperial College London, UK, and in 2016 he received a PhD in biological engineering from MIT, USA. After a joint postdoctoral fellowship between MIT, Harvard University, and the Broad Institute, he was appointed as a tenure-track assistant professor at ETH Zurich and the University of Basel in October 2016.

Prof Platt co-leads the BRCCH project: Living Microbial Diagnostics to Enable Individualised Child Health Interventions. Read more here.

Prof Andrew Macpherson

University Hospital Bern, Switzerland

Talk: "An Update on the University of Zimbabwe Birth Cohort Study"

Profile

Prof Andrew Macpherson is a Professor of Medicine at Inselspital Bern. His laboratory has worked on immune and non-immune mechanisms of host-microbial mutualism using animal models and translational work in human subjects. He has set up collaborations with Zimbabwean and Kenyan colleagues in order to address the problem of dysbiosis that triggers intestinal dysfunction and stunting in young children in low- and middle-income countries.

Prof Macpherson co-leads the BRCCH project: Living Microbial Diagnostics to Enable Individualised Child Health Interventions. Read more here.

Dr Michael Zimmermann

European Molecular Biology Laboratory (EMBL) Heidelberg, Germany

Talk: "Identifying Gut Microbiome Contributions to Drug Metabolism and Carcinogen Toxicity"

Profile

Michael Zimmermann is a group leader at the European Molecular Biology Laboratory (EMBL) in Heidelberg. Michael received his Bachelor’s degree in Pharmaceutical Sciences from Basel University and his Master’s degree in Biotechnology from the Ecole Supérieure de Biotechnologie (ESBS) in Strasbourg. Michael performed his PhD work at ETH Zurich in metabolomics and Systems Biology and he pursued his postdoctoral training at Yale University to investigate metabolic host-microbiome interactions. His research group at EMBL employs bacterial genetics, metabolomics, gnotobiotic mouse work, and mathematical modeling to systematically map metabolic microbiota-host interactions. Among several honors and scholarships, Michael was awarded the Daimler Benz Scholarship, Agilent’s Steve Berger Award, the 2021 FEBS Anniversary Prize, and an ERC Starting Grant.

3D Printed Plates for Cleft Lip and Palate Care in Less than Five Minutes

3D Printed Plates for Cleft Lip and Palate Care in Less than Five Minutes

The treatment of children born with cleft lip and palate typically includes the use of therapeutic intraoral plates before surgical closure of the cleft. The plate passively sits on the roof of the baby’s mouth and helps separate the nasal and oral regions. So far, these plates have mostly been fabricated manually, and the process for their production still leaves room for improvement. Now, computer science researchers from ETH Zurich have teamed up with clinical care researchers at the University Hospital Basel to create a digital pipeline that enables the automatic production of the plates. The research project has promising potential to facilitate wider access to presurgical cleft treatment, especially in low-income countries.

About 1 in 700 children worldwide are born with cleft lip and palate. Orofacial clefts are the most common craniofacial malformations in newborns, and there are no existing effective preventive measures. While children in high-income countries with this birth condition receive appropriate care, children from low-income countries often lack this opportunity because treatment is expensive and requires high levels of medical and/or technical expertise. In addition, hospitals are often far away or not sufficiently equipped.

These factors are especially relevant for the fabrication of presurgical orthopaedic plates, which are widely used for treating cleft lip and palate before surgery,” says Till Schnabel from ETH Zurich. Schnabel is a computer science doctoral researcher closely supervised by senior researchers Dr Baran Gözcü and Prof Barbara Solenthaler. They are part of ETH Zurich’s Computer Graphics Lab led by Prof Markus Gross. Schnabel and Gözcü are the first two authors of the research paper "Automated and data-driven plate computation for presurgical cleft lip and palate treatment" recently published in a special issue of the International Journal of Computer Assisted Radiology and Surgery. *

Within a few days after birth, a presurgical therapeutic plate designed to bridge the cleft space and to keep the baby from putting tongue pressure on the alveolar edges, i.e., the cleft opening is fitted to the baby’s mouth. The plate naturally facilitates the cleft opening becoming smaller after a few months, thus enabling a gentler repair surgery. The plate not only assists the infant in feeding but also fosters the baby’s development of early normal linguistic sounds.**

Conventionally, such a plate is fabricated using a plaster cast based on an imprint manually taken from the baby’s mouth. This intricate procedure requires highly trained specialists and carries some risk of the impression material entering the baby’s airways. More recently, handheld intraoral scanners have been introduced into practice to replace the imprint-taking, and – theoretically – to allow for fully digital workflows. However, most of these existing workflows and their 3D software are still too complex to be run in a non-specialised setting.

In contrast, the approach pursued by Schnabel and his colleagues at ETH Zurich, which was developed in collaboration with Andreas Mueller’s team at the University Hospital Basel, is as ambitious in development as it is straightforward in use: “Our aim has been to automate the whole process, which not only saves time but can also be done without an expert’s knowledge on site.

At its core, the project employs a deep learning model, which was trained on a dataset that Schnabel and Mueller’s team assembled for this specific purpose. “Collecting sufficient data is often the greatest challenge when it comes to machine learning, especially for digital health, because medical data are sensitive and have to be treated confidentially and with the proper data security protocols,” says Till Schnabel. Nevertheless, they were able to gather around 400 scans: about two-thirds of children affected with a one-sided cleft and the other one-third of children with double clefts. “We collected data from old plaster cast imprints, which we digitized via 3D scanning, and we combined it with new data from intraoral scans,” explains Till Schnabel.

The deep learning model trained on this data can automatically recognise and select the principal structures, so-called landmarks, on the digital 3D model of the palate. In the rest of the pipeline, Schnabel and colleagues implemented established methods, such as surface registration and smoothing algorithms. “With the help of the selected landmarks, one can more accurately register a 3D scan, i.e., determine a close correspondence between the template and the input scan.” This method also provides a 3D segmentation differentiating various areas on the intraoral scan. The final step is automated plate computation, which comprises filling the cleft palate area and volumizing the surface to be 3D-printed. In short, these algorithms ensure that the plate is customised to the individual geometry of the baby’s mouth, and mimics, as best as possible, a healthy closed palatal shape.

A baby wears the first palatal plate to be created entirely from the digital pipeline in Basel. As shown in the image, the plate is also fabricated with a small tab that nestles outside the mouth and helps to hold the plate in position. (Credit: Andreas Mueller and Benito Benitez). In the computer-generated rendering of the plate in the corner (Credit: Schnabel et al. 2023*), the palatal plate (translucent plastic) is shown overlaid on a baby’s intraoral scan of the unilateral cleft in the roof of the mouth. The plate effectively bridges the gap of the cleft and prevents the baby’s tongue from entering the intranasal region. View perspective is from the front of the baby’s mouth, gazing straight into the mouth towards the roof.

 

The pipeline has already been successfully implemented in the clinical routine in two hospitals, where 19 children have been treated with palatal plates that were produced with the digital pipeline. At the University Hospital Basel and Saveetha Medical College and Hospital, Chennai, India, digital intraoral scanning has already reduced the time necessary for conventional impression-taking from over 60 minutes to less than 20 minutes.

The biggest difference, though, became evident in plate fabrication,” says Till Schnabel. “Previously, it would take close to an hour to make a plate – with our pipeline, the plate was done in less than 5 minutes.” Moreover, it didn’t require a plate specialist to operate complex software but only a few clicks on the computer. In other words, the plates are potentially accessible anywhere, regardless of facility resources. “In India, the workflow was made even more accessible. Hospitals did not need to have the printing infrastructure on site, the pipeline can be decentralised and is compatible with remote printing,” recounts Till Schnabel. “It worked perfectly.

Schnabel is confident that the team’s automated pipeline will make a big difference in the treatment of cleft lip and palate, especially in low-income countries. “It has the potential to reduce the costs of cleft lip and palate care substantially,” he says, “making treatment accessible for those who might have been excluded so far.

And thus, one has to emphasise the potential impact of the research. It can reduce the burden of this condition and the devastating effects it can have on children and their families; it can enable more children to heal.

Background

Till Schnabel is an early career researcher in a BRCCH research project “Burden-Reduced Cleft Lip and Palate Care and Healing", which is co-led by Prof Barbara Solenthaler (ETH Zurich) and Prof Andreas Mueller (University Hospital Basel and University of Basel). His work and the project are part of the overarching programme: Multi-Investigator Programme.

Interview article: Irène Dietschi

*Research paper

SCHNABEL TN, GÖZCÜ B, GOTARDO P, LINGENS L, DORDA D, Vetterli F, Emhemmed A, NALABOTHU P, LILL Y, BENITEZ BK, MUELLER AA, GROSS M & SOLENTHALER B. 2023. “Automated and Data-Driven Plate Computation for Presurgical Cleft Lip and Palate Treatment.” International Journal of Computer Assisted Radiology and Surgery. https://doi.org/10.1007/S11548-023-02858-6

**Reference

NALABOTHU P, BENITEZ BK, Dalstra M, Verna C, MUELLER AA. 2020. “Three-Dimensional Morphological Changes of the True Cleft under Passive Presurgical Orthopaedics in Unilateral Cleft Lip and Palate: A Retrospective Cohort Study”. Journal of Clinical Medicine.  https://doi.org/10.3390/jcm9040962

Names in all caps indicate research contributions to the BRCCH consortium

Click here for a video abstract of the research paper

ETH Zurich Seeks Assistant Professor (Tenure Track) of Computational Medical Genomics

ETH Zurich Seeks Assistant Professor (Tenure Track) of Computational Medical Genomics

 

The Department of Biosystems Science and Engineering (D-​BSSE) at ETH Zurich invites applications for the above-​mentioned position. D-​BSSE is located in Basel, providing excellent opportunities for collaboration within this strong life science research community at the academic, clinical and pharmaceutical industry levels. The main research focus of the Department is the understanding, modeling, and engineering of systems for biomedical applications. The professorship will also be embedded within the newly established Botnar Research Centre for Child Health (BRCCH), which aims to provide innovative and translational solutions for child and adolescent health. Collaborations within the medical research communities in Basel and Zurich are highly encouraged.

The future Assistant Professor is expected to develop a strong and visible research program in the area of methods and tools development in computational biology and bioinformatics for medical applications. A candidate capable of advancing statistical and computational modeling of genomics data and translating models, methods, and findings into clinical applications is sought. Possible research topics include, but are not limited to, computational genomics and multi-​omics data integration, human genomics and rare diseases, medical genomics in clinical trials, and computational genomics for advanced therapies. The candidate should have a Ph.D. degree in Computational Biology, Medical Genomics, Computational Science, Data Science, or related disciplines, and demonstrated evidence of the ability to develop novel statistical and machine learning methods for genomic datasets. Further, a strong publication record reflecting innovative, interdisciplinary, translational, and collaborative approaches to important problems related to medical genomics is expected. She or he should demonstrate a strong interest in clinical applications and a clear ambition to pursue research that is directly relevant to childhood health and medicine. At the assistant professor level, commitment to teaching and the ability to lead a research group are expected.

Assistant professorships have been established to promote the careers of younger scientists. ETH Zurich implements a tenure track system equivalent to that of other top international universities.

ETH Zurich is an equal opportunity and family-​friendly employer, values diversity, and is responsive to the needs of dual-​career couples.

Please apply online

Applications should include a curriculum vitae, a list of publications, a statement of future research and teaching interests, a description of the leadership philosophy, a description of the three most important achievements*, and a certificate of the highest degree. The letter of application should be addressed to the President of ETH Zurich, Prof. Dr. Joël Mesot. The closing date for applications is 31 October 2023.

*ETH Zurich emphasizes qualitative assessment of academic accomplishments. This is why you are kindly asked to submit a short description of your three most important achievements (maximum a half page each). Besides research findings, these could also be extraordinary achievements in teaching and its further development, services in the benefit of the academic community or society, software development, patents, knowledge transfer and its practical application, spin-​​​​​​​​off companies or similar.

An Investment in More Research to Benefit Children and Adolescents

An Investment in More Research to Benefit Children and Adolescents

A family in the San Marcos region of Peru photographed by BRCCH researchers. Credit: Prof Günther Fink, BRCCH Researcher, Swiss Tropical and Public Health Institute

 

Fondation Botnar is donating an additional CHF 50 million to the University of Basel and ETH Zurich to expand the activities of the joint Botnar Research Centre for Child Health (BRCCH). This support will allow to create six new professorships with a research focus on paediatric digital health.

Launched in 2019, the Botnar Research Centre for Child Health (BRCCH) aims to drive innovative health research that benefits children and adolescents globally – especially those living in low- or middle-income countries. Within this centre, the University of Basel and ETH Zurich work in partnership with the University Children’s Hospital Basel (UKBB) and the Swiss Tropical and Public Health Institute (Swiss TPH).

Over the past four years, the BRCCH has supported around 80 researchers and 29 research projects worldwide. For example, researchers improved the treatment of cleft lip and palate and developed biotechnology to monitor paediatric gut health or digital tools that support healthy child development. To date, the BRCCH has been supported by Fondation Botnar with a total of 115 million Swiss francs.

“The BRCCH’s impressive achievements to date would not have been possible without the unique commitment of Fondation Botnar, the universities, their partnering institutions and the dedicated hard work done by the involved research community,” says Professor Georg Holländer, Director of the BRCCH.

New professorships for new expertise

Fondation Botnar’s latest funding will support the establishment of six new professorships – three at the University of Basel and three at ETH Zurich. "At 1.8 billion, young people make up a large part of the world's population, but their health and wellbeing are often overlooked in academic research. Since its inception, the BRCCH has driven innovative research in paediatrics and public health, and we hope that our additional investment will further advance this critical research," says Stefan Germann, CEO of Fondation Botnar.

The research areas of the newly appointed professors range from biomolecular diagnostics to the development, application and integration of state-of-the-art analytical methods and an exploration of ethics and politics in digitalised healthcare.

“The use of digital technologies in medicine and the public health system has the potential to transform global health care. However, technological progress must be accompanied by answers to central ethical questions,” says Professor Christian Wolfrum, ETH Vice President for Research. The breadth and the focus of the BRCCH’s new direction is in line with Fondation Botnar’s emphasis on the equitable use of artificial intelligence and digital technologies.

New building for more collaboration

In the coming years, these professorships and their respective research teams will work at a new, modern BRCCH research facility strategically located in the heart of the University of Basel Life Sciences Campus and adjacent to ETH’s Department of Biosystems Science and Engineering in Basel.The new building will serve as a synergistic digital health research hub and as an ideal location for interdisciplinary collaboration between individual institutions. “At the same time, we wish to emphasize that ETH and the University are determined to support the cutting-edge research at the BRCCH in the long-term,” says Professor Torsten Schwede, Vice President for Research at the University of Basel.

Contact

University of Basel: Matthias Geering, Head of Communications,
matthias.geering@unibas.ch, +41 61 207 35 75

ETH Zurich: Franziska Schmid, Spokesperson,
medienstelle@hk.ethz.ch, +41 44 632 41 41

Fondation Botnar: Kiara Jade Marvuglio, Engagement and Communication Lead, media@fondationbotnar.org, +41 61 201 04 82

BRCCH: Catherine Crawford-Brown, Communications Manager,
catherine.crawfordbrown@brc.ch, +41 78 250 48 82

Botnar Research Centre for Child Health (BRCCH)

The BRCCH, which works to better the health of young people, was founded in 2019. Since then, its team has grown to more than 400 participating scientists, including international colleagues from 26 countries. Researchers from the four institutions connected to BRCCH have launched some 29 multidisciplinary and interinstitutional projects, ranging from basic research to the implementation of such research in paediatrics and public health. The founding of the BRCCH was made possible by a CHF 100 million contribution from Fondation Botnar in Basel, which was donated to the University of Basel and the ETH Zurich Foundation.

More information: https://brc.ch/

Fondation Botnar

Fondation Botnar is a Swiss philanthropic foundation working to improve the health and wellbeing of young people living in cities around the world. Advocating for the inclusion of youth voices and the equitable use of AI and digital technology, the foundation invests in and supports innovative programs and research and brings together actors from across sectors to create dialogue and partnerships.

More information: www.fondationbotnar.org

Reaching and Supporting All Children with Digital Parenting Interventions

Reaching and Supporting All Children with Digital Parenting Interventions

Millions of children in low-income settings are at risk of missing their developmental potential in early life. One type of preventive measure is a home visiting programme, in which facilitators support parents with skills and knowledge related to early child development. Now, a collaborative study led by researchers of the Swiss Tropical and Public Health Institute, University of Basel, ETH Zurich, Universidad Peruana Cayetano Heredia (UPCH) and Harvard Graduate School of Education has examined whether families, instead of being visited physically, could also be reached digitally via an app. The study was conducted in remote areas in Peru – with promising results.

What if each parent, irrespective of income or location, had their own virtual tutor to help them take care of their little ones? A tutor that makes suggestions on how to stimulate the development of a young child with age-tailored activities? That’s the idea behind the start-up founded by Andreana Castellanos, Afinidata, a platform that uses artificial intelligence to support parents with care practices and knowledge about child development.

Afinidata uses channels like WhatsApp, Facebook Messenger and a mobile App to interact with parents of children aged 0-6 years. “Similar to facilitators that make home visits to parents, the virtual Afinidata tutor asks parents about the child’s well-being through messages and push notifications, and it suggests development-promoting activities that parents can do with their children,” explains Dr Lena Jäggi, a developmental psychologist of the Swiss Tropical and Public Health Institute (Swiss TPH) at the University of Basel and a researcher deeply involved in the pilot study. According to UNICEF there is “a large gap for effective, easy-to-access educational tools that are inclusive with lower-income families.” Digital tools such as Afinidata have the potential to close that gap. However: “There has been limited evidence on how feasible digital parenting interventions are in practice,” says Lena Jäggi, “especially in rural settings in low- and middle-income countries.

That’s where the study* published by the journal Archives of Disease in Childhood and first-authored by Lena Jäggi steps in. Lena Jäggi: “We wanted to find out whether Afinidata would work in a very remote area in Latin America, and if changes had to be made to adapt the platform to the local context.” The “local context” was the Cajamarca region in the north of Peru, in three provinces located in the Andes where the Swiss – Peruvian Health Research Platform of Swiss TPH and UPCH maintains a research station.

Milagros Alvarado Ilatance is also a developmental psychologist and one of the two study coordinators in Peru who together co-lead the training of local research team members and the collection of the field data. She explains how Afinidata had to be adapted to the context of Andean Peru: “For example, in order to facilitate ease and understandability for the parents, we had to rephrase some of the questions or change the vocabulary of the chatbot to a certain extent since we were working with a version that was originally intended for families in Guatemala.

In this mountainous region, stretching from 1900 to 3900 metres above sea level, the research team recruited families for their study. “The communities are small and thus representative of many rural settings in Andean South America, with a large share of low-income and remote households engaged in farming,” says Lena Jäggi.

Even so, almost 90 % of these households have access to at least one cell phone and the internet. For the pilot study, the research team enrolled 180 mothers with children aged between 2 and 24 months who either owned or had regular access to a smartphone. The field work was done by the Peruvian part of project team, consisting of the two study coordinators, Milagros Alvarado Ilatance and Maria Luisa Huaylinos Bustamante, from the Universidad Peruana Cayetano Heredia and about a dozen local facilitators who visited the mothers at their homes from February to July 2021.

Study coordinator Maria Luisa Huaylinos Bustamante discusses the digital parental intervention and the study with a mother and her children. Credit: Swiss-Peruvian Health Research Platform/Digital Support Systems to Improve Child Health and Development

 

During their first visit, the research team introduced the mothers to Afinidata, installed it on their smartphone and showed them how to navigate the app. After two months, the facilitators visited them again, interviewing and collecting detailed feedback. During their final visit five months from the start, the mothers were asked about their overall experience, satisfaction and use of the platform.

A mother participating in the study said that with the app, she was “jugar con mi niña, cantar…,a traves de la aplicación tenemos la actividad y nos dedicacabamos a ellos un momento, a veces hasta hacerla dormir”  "playing with my daughter, singing..., through the application we have the activity and we dedicate ourselves to them for a moment, sometimes until it puts her to sleep." From Jäggi et al. 2023, Supplemental Data 2 .

Another challenge was the availability of material for the parent-child activities. “Sometimes the mothers didn’t have the craft material at hand which the chatbot suggested,” adds fellow study coordinator Maria Luisa Huaylinos Bustamante. “With no supermarket nearby where they could have bought these things, the mothers would simply switch to alternatives they had in their house or created the toys themselves. They were amazingly flexible and creative,” says Huaylinos Bustamante.

The biggest challenge though was familiarizing the mothers with Afinidata so that they would feel confident and motivated to engage with the platform on a regular basis. “That’s one point we had clearly underestimated in the beginning,” says Milagros Alvarado Llatance. Through this pilot study, they found that the initial orientation to Afinidata during the first visit was not sufficient. “So to meet this need, we had to adapt. We created for them a physical, laminated booklet which detailed the app step by step that we will use in the main trial.

This point was one of the principal learnings of the pilot study for Lena Jäggi as well: “Just because people have access to a smartphone and the internet doesn’t mean they are automatically proficient in using digital health tools,” she says. The booklet, which will be implemented when the main trial begins, also includes general information on child development, sample activities and detailed instructions on how to self-enroll in case a phone got lost. “So we learned also to be flexible and creative and that this additional effort is important because ultimately, our goal is for the mothers to get the full benefit of the intervention,” says Lena Jäggi.

Even before adding this booklet, the results of the pilot study are very promising. After five months, 42 % of mothers were still active on the platform. One might argue that an adherence of less than half of the original participants is not very successful, but those 42 % have to be viewed within the larger frame, says Lena Jäggi: “Compliance is a big challenge in any kind of parental intervention, i.e. in home-visiting programmes too,” she says. “And as far as digital programmes resembling Afinidata are concerned, other studies have reported completion rates as low as 15 and 7 %.” Meaning that compared to similar interventions, a 42 % engagement with Afinidata at five months post-introduction was relatively high, “but more data on continued use over longer periods are needed.

Digital health tools like Afinidata stand not only to broaden the accessibility of interventions to families in remote regions but also to mitigate the consequences of sudden upheavals in the public healthcare system. This case in point: the field testing fell squarely in the COVID-19 pandemic, which hit Peru quite severely. In non-pandemic times, the Peruvian government offers families in areas of poverty and with children under 36 months a national visiting programme (Programa Nacional Cuna Más; PNCM) for early childhood and parental support. The PNCM, although only able to support the most vulnerable, is one of the largest of its kind in the world. During the COVID-19 pandemic, however, those services were shut down completely. So, digital parenting interventions actually filled a gap that was unforeseen.

These pilot study results are promising, but what the pilot study hasn’t assessed is the impact of the intervention on the mother’s or child’s outcome. Nor has cost-effectiveness been studied. These are follow-up research steps yet to be taken: A randomized-control study is already underway to address these aspects. Milagros Alvarado Ilatance: “I think this is a very important opportunity for the families in Cajamarca to have access to new strategies to improve their children’s development.

Background

Dr Lena Jäggi, Milagros Alvarado Llatance and Maria-Luisa Huaylinos Bustamante are researchers in a BRCCH research project "Digital Support Systems to Improve Child Health and Development in Low-Income Settings" and one of the activities of the Swiss – Peruvian Health Research Platform of Swiss TPH and UPCH. The research project is one of BRCCH’s cornerstone projects, within the overarching Multi-Investigator Programme.

Interview article: Irène Dietschi

*Research article

JÄGGI L, AGUILAR L, LLANTANCE ALVARADO M, CASTELLANOS A, FINK G, HINCKLEY K, BUSTAMANTE HUAYLINOS M-L, MCCOY DC, VERASTEGUI H, MÄUSEZAHL D & HARTINGER PENA SM. 2023. “Digital Tools to Improve Parenting Behaviour in Low-Income Settings: A Mixed-Methods Feasibility Study.” Archives of Disease in Childhood.  https://doi.org/10.1136/ARCHDISCHILD-2022-324964

University of Basel Seeks Professor of Paediatric Digital Health Data Analytics

University of Basel Seeks Professor of Paediatric Digital Health Data Analytics

visual: University of Basel, Mark Niedermann

**Update 1 September 2023: Applications for this position have now closed.**

The  Faculty of Medicine of the University of Basel, Switzerland invites applications for an open rank position of Professor in Paediatric Digital Health Data Analytics to be embedded in the BRCCH.

The BRCCH is a multi-disciplinary research centre creating new healthcare solutions for unmet medical needs related to communicable and non-communicable pathologies of significant burden to children and adolescents, irrespective of an individual's societal conditions. Bespoke solutions are designed and developed by BRCCH researchers to prevent, mitigate, or cure diseases.

Your position

The successful candidate will develop an internationally competitive research programme in Paediatric Digital Health Data Analytics with an emphasis on clinical translation and technology integration tailored for the special needs of children and adolescents. Close collaborations are expected with clinical partners, scientists at the University of Basel and the D-BSSE of ETH Zurich in Basel, and within the Basel life sciences cluster. The Master's and Ph.D. programmes of the University's Medical and Sciences Faculties provide opportunities for teaching (in English).

Your profile

The University of Basel expects from the candidate a genuine interest in interdisciplinary academic work and several years of experience in digital health and / or related fields including machine learning and artificial intelligence, medical informatics, measurement technologies, ideally with a wide variety of multi-modal medical data. Excellent academic performance or seniority relative to the applicant's career stage and a proven record in acquiring competitive third-party funding are essential qualifications. The university expects a strong interest in student teaching and mentoring of junior scientists at different stages of their academic careers. Key personality traits include excellent social and communication skills and an open, inquisitive, and collegial personality.

The university offers you

The university offers you a unique opportunity for interdisciplinary research in both theory and application of machine learning and related computational methods in (bio)medicine in a highly innovative and translational research environment enabling access to patients and academic bioinformatics facilities.

The University of Basel stands for excellence through diversity and is committed to equal opportunities and family friendliness. In an effort to increase the proportion of women in professorships, the University is particularly interested in receiving applications from women.

Application / Contact

For further information, please contact the Chair of the Academic Recruitment Committee, Prof. Georg Rauter (Phone: +41 61 207 54 70; e-mail: georg.rauter@unibas.ch) or the Scientific Coordinator of Academic Recruitment, Dr. Simone Neu (Phone: +41 61 207 61 64; e-mail: simone.neu@unibas.ch).

Applications must be submitted by July 28th, 2023.
The university kindly asks you to apply exclusively via the online platform and as described in the application guidelines.

 

 

ETH Zurich Seeks Assistant Professor of Data Science for Bioengineering and Biomedicine

ETH Zurich Seeks Assistant Professor of Data Science for Bioengineering and Biomedicine

visual: ETH Zurich / Gian Marco Castelberg

 

In an announcement by ETH Zurich, the Department of Biosystems Science and Engineering (D-BSSE) seeks outstanding candidates for the open faculty position of Assistant Professor (Tenure Track) of Data Science for Bioengineering and Biomedicine. The successful candidate will build a strong and visible research program in the development of data science methods and tools for heterogeneous data characterizing complex biosystems. A candidate capable of advancing statistical and computational modeling of large-​scale bioengineering and biomedical data and translating models, methods, and findings into clinical applications is sought. Possible research topics include, but are not limited to, sustainable data science for emerging bioengineering approaches, data integration and data fusion, and biomedical data science for advanced therapies. Candidates should have a doctoral degree in Data Science, Computational Science, Computational Biology, or related disciplines, and demonstrated evidence of the ability to develop novel statistical, computational, and machine learning methods for biomedical datasets. Successful candidates have a strong publication record reflecting innovative, interdisciplinary, translational, and collaborative approaches to important problems in biomedicine. Commitment to teaching and the ability to lead a research group are expected.

Read the full job announcement on ETH Zurich's website.

 

*Please note the above position is not associated with the BRCCH. Those interested in this position must apply through ETH Zurich's online faculty recruiting portal.

Swiss Tropical and Public Health Institute- Open House June 17

Swiss Tropical and Public Health Institute Invites the Public to New Headquarters

visual: Swiss TPH

 

The Swiss Tropical and Public Health Institute invites everyone to their public Open House of their new headquarters "Belo Horizonte" in Allschwil on Saturday, June 17th, 2023.

Among the exciting, family-friendly programme of activities and educational talks, BRCCH-supported research projects will showcase their work in a fun, interactive way.

See the full programme and event details on the Swiss TPH's website.

Open Position in the BRCCH Management Office

Open Position in the BRCCH Management Office

**update 15 June 2023: A sincere thank you to everyone for your interest to join the BRCCH management team. We have closed submission and will no longer accept applications.  We are currently processing applications. Thank you for your patience and understanding.**

The BRCCH seeks new talent for the position of Communications & Engagement Manager. A new colleague will join a core team to further the BRCCH mission: to drive scientifically outstanding research and innovation in paediatrics.

Open Position
BRCCH Communications & Engagement Manager
40%-60%, immediately or as per agreement

About Us
The Botnar Research Centre for Child Health (BRCCH) is physically located in Basel, Switzerland and supports researchers at its four partner institutions: University of Basel, ETH Zurich, University Children’s Hospital Basel and the Swiss Tropical and Public Health Institute. Generously funded by Fondation Botnar, the Centre drives innovative translational research addressing unmet medical needs of children and young people, especially those living in low- and middle-income countries, through funding programmes and professorial posts.

About the Position
As the BRCCH Communications and Engagement Manager, you lead activities, internally and externally, to ensure the visibility of scientific achievements of the BRCCH community and a cohesive BRCCH brand identity. You lead and coordinate activities to build community and engage stakeholders, and also contribute to the general activities of the BRCCH management office.

Your Role

  • Responsible for internal and external communications and engagement activities
  • Lead and implement workflow and tasks for a coherent communication strategy
  • Maintain BRCCH brand identity and its visibility by implementing and coordinating recurring communication mechanisms such as website updates/maintenance, newsletters, media releases, news announcements, LinkedIn, Twitter, as well as reports
  • Lead and support science communication and outreach activities by BRCCH and BRCCH-supported researchers
  • Lead BRCCH team efforts to foster community building and local network
  • First point of contact for external media inquiries to BRCCH or BRCCH-related research activities
  • Support the development and manage the implementation of early-career capacity-building programmes and dissemination events
  • Support the management and monitoring of the BRCCH research grant portfolio

Your Profile

  • You are passionate about communicating research and building community
  • You are a skilled practitioner, with experience (minimum 1-2 years) in communications and/or engagement in a scientific setting
  • You are experienced in planning and implementing events centred on science communications and/or outreach
  • You enjoy the hands-on approach to creating and producing communications and engagement activities
  • You are comfortable with social media and creative design platforms
  • You feel comfortable working independently as well as collaboratively in a small-team and enjoy a fast-paced, self-organising and dynamic setting
  • You enjoy a range of strategic and operational tasks
  • You are a positive, self-motivated and outcome-oriented person motivated to contribute to BRCCH’s mission and make an impact
  • Excellent or native fluency in written and spoken English are indispensable. Proficiency in German is desirable.
  • Further education, higher degree or equivalent work experience in biology, biotechnology, bioengineering or similar science-related field is desirable

We Offer
A responsible position within an energetic and internationally oriented research centre that is driven by a dedicated and collegial team. Conditions of employment in accordance with the personnel and salary regulations of the University of Basel including flexible working conditions and possibility of home-office. A fixed-term contract for 2 years with the possibility of extension. 

Application / Contact
Please send your application (CV, cover letter, certificates) in a single electronic document by 15 June 2023 to contact@brc.ch. For further questions about the position, please email maressa.takahashi@brc.ch (Scientific Officer and Communications Manager). For administrative and HR-related questions, please email greet.vanmalderen@brc.ch (acting General Manager BRCCH).

 

Modelling the Dynamics of SARS-CoV-2 in All of Its Twists and Turns

Modelling the Dynamics of SARS-CoV-2 in All of Its Twists and Turns

Prof Melissa Penny, Dr Andrew Shattock (Swiss Tropical and Public Health Institute, University of Basel) and colleagues have contributed to the understanding of SARS-CoV-2 dynamics and public health interventions for the pandemic. Their research has been relevant for the Swiss government and policy makers in other countries.

With a background in applied mathematics and public health, Prof Melissa Penny has long experience in modelling infectious diseases. At the Swiss Tropical and Public Health Institute (Swiss TPH), where she’s head of the Disease Modelling unit, a group of 22 researchers, she has been focusing on malaria for many years – developing analyses and different mathematical models to support product development and to assess vaccines and drugs for malaria.

A pandemic pivot

When SARS-CoV-2 emerged at the beginning of 2020, like other modelling scientists Melissa Penny and part of her team shifted their attention to COVID-19. She formed an especially close alliance with her colleague Dr Andrew Shattock from her unit at Swiss TPH. Dr Shattock, who has worked with more than 20 national governments on the control of HIV/AIDS, spent the early months of the pandemic collaborating with the European Centre for Disease Prevention and Control (ECDC) in Sweden.

Melissa Penny, on her part, became involved in the early stages of the Swiss National COVID-19 Science Taskforce, as a member of the data & modelling group. "Our first modelling steps were aimed at understanding the biology of the virus", says Penny, "but soon we turned to the dynamics of the disease itself, with data from the lab and from epidemiological studies."

In late 2020 and early 2021, one key scientific question the Swiss government turned to was the impact that vaccination against COVID-19 would have on the disease and hospitalisation burden of the pandemic, and how vaccination would possibly alter decisions on other, non-pharmaceutical interventions (NPIs) such as social distancing or the wearing of protective masks. In early 2021 Prof Penny conducted a study on this question* in close collaboration with Dr Shattock. They developed an individual-based transmission model of SARS-CoV-2 dynamics, comparing the impact of various vaccination and NPI strategies on the epidemic in Switzerland. "It was a key period in Switzerland ", Shattock says, "there was pressure to relax NPIs as vaccinations were only beginning to be rolled out." "Our findings stressed the importance of rapid vaccination scale up alongside a gradual relaxation of NPIs" says Penny. Their conclusion also confirmed that emerging viral variants of SARS-CoV-2 would have to be closely watched and responded to if public health officials wanted to keep control of the Swiss epidemic. The modelling was hence included in Cantonal documents as well as Taskforce documents.

New variants and the next twist

As so often happens in research, where answering one question leads to a brand new one, Penny and Shattock modelled the risk of new variants in a following study.* "The Delta variant was already present at that point", Penny recalls, "with Omicron increasing at the end of 2021." Engaging with the scientific community, the Swiss TPH team estimated the range of risks posed by Omicron or possible new variants, "depending on any change to disease severity with Omicron or new variants, or due to the variant’s ability to escape a person’s immune system, or if new variants have increased ability to transmit compared to Delta."  In their paper* they concluded that "increasing vaccination is projected to have the biggest public health benefit for mitigating highly infectious, severe variants to which the immune system is able to respond." However, they also emphasized that variants not controlled by any previously gained immunity, even less severe ones, would require alternative measures for control.

This graphical summary of the research paper* Le Rutte et al. 2022 shows the interplay between the potential infectivity, immune evasion and severity of future SARS-CoV-2 variants of concern (VOC) on its chances of becoming the next dominant variant, its associated public health burden, and the potential impact of interventions. Credit: the Swiss TPH COVID-19 modelling team of the group of Prof Melissa Penny.

 

A turn yet again

Meanwhile, in September 2021, the dynamics of COVID-19 had changed yet again, and the question public health officials raised was: Which vaccination strategies should we recommend to people, with immunity waning and possibly more transmissible variants of concern emerging? Or, to put it more simply: "How often do we vaccinate? Is it once a year? Twice a year? Is it just the high-risk population – or everyone?" Those were the scenarios which Melissa Penny and her colleagues examined in fall 2022.* They found that the most optimal scenario to reduce hospitalisations was to have a "well-timed" booster once a year, meaning three to four months ahead of a winter peak, whether or not new variants of concern emerge. That conclusion applied not just to the high-risk population, but to everyone eligible for vaccination. "The rationale was to allow some additional population-level immunity with the booster", explains Melissa Penny, "which is what most of the governments have recommended." The results were also shared with the ECDC, with Dr Andrew Shattock collaborating and supporting the EU agency. "Our findings really highlighted the societal effect of low-risk individuals getting an annual booster. Boosting your own immunity helps to protect those most at risk" Dr Shattock says.

A final twist?

In 2023, SARS-CoV-2 may be loosening its grip on the world. Even so, COVID-19 doesn’t belong to the past for many people. Cue the next question for Melissa Penny’s BRCCH project to investigate: "Now we are looking at therapeutic interventions for COVID-19 ", she says, "modelling different scenarios. Which treatment is effective in addition to high vaccination coverage to support those at higher risk of severe disease and beneficial to save health system costs?"

The COVID-19 pandemic has been characterized by several twists and unexpected turns and as yet still unanswered questions remain. In a scenario where new variants of the virus might emerge in the future, it is certainly good to know which treatments and adapted vaccines could help, and it remains crucial to have the mathematical tools to support evidence on new questions.

 

Background

Professor Melissa Penny leads the Disease Modelling Research Unit in the Epidemiology and Public Health department at Swiss TPH and is currently an assistant professor at the University of Basel. She leads a BRCCH research project "Using Model-based Evidence to Optimise Medical Intervention Profiles and Disease Management Strategies for COVID-19 Control." Her work, and that of her colleague Dr Shattock, is part of the overarching progamme: BRCCH’s Fast Track Call for COVID-19 Research.

Interview article: Irène Dietschi

*Research articles

SHATTOCK AJ, LE RUTTE EA, DÜNNER RP, Sen S, KELLY SL, CHITNIS N,  PENNY MA. 2022. "Impact of Vaccination and Non-pharmaceutical Interventions on SARS-CoV-2 Dynamics in Switzerland." Epidemics. https://doi.org/10.1016/J.EPIDEM.2021.100535

 

LE RUTTE EA, SHATTOCK AJ, CHITNIS N, KELLY SL, PENNY MA. 2022. "Modelling the Impact of Omicron and Emerging Variants on SARS-CoV-2 Transmission and Public Health Burden." Communications Medicine. https://doi.org/10.1038/s43856-022-00154-z

 

KELLY SL, LE RUTTE EA, Richter M, PENNY MA, SHATTOCK A. 2022. "COVID-19 Vaccine Booster Strategies in Light of Emerging Viral Variants: Frequency, Timing, and Target Groups." Infectious Diseases and Therapy. https://doi.org/10.1007/s40121-022-00683-z

 

Names in all caps indicate inclusion in BRCCH consortium

 

 

Seminar 27 Apr – Digital Support Tools for Paediatric Health

Seminar 27 Apr - Digital Support Tools for Paediatric Health

**Update May 22nd, 2023** Thank you to everyone that attended our hybrid seminar! We had a great turnout-- in case you missed the presentations or you would like to watch them again, you can now stream them below or on our YouTube channel.

Image: Daniel Mäusezahl and Stella Hartinger Peña

Image: Ebby Shaban and Magali Rochat/ DYNAMIC

    Description:  The BRCCH cordially invites you to join our seminar about advancing child health using digital health support tools and systems. Prof Günther Fink (Swiss TPH, Switzerland) will share his BRCCH consortium’s research progress on supporting the development of children in low-resource settings through the use of novel digital health technology. Prof Valérie D’Acremont (Unisanté, Switzerland) will highlight her work on an e-health system intervention aimed to improve paediatric clinical care, to promote sustainable resource use in a constrained setting and to enhance the detection of outbreaks.

    When: Thursday, 27th April 2023, 16:00 - 17:15 CET, to be followed by an apéro

    Where: Hybrid Zoom / Seminarraum U1.191– Biozentrum, University of Basel, Spitalstrasse 41, 4056 Basel

    Zoom Registration: HERE

    In-person Registration: HERE
    Directions and location information

    Schedule:

        • Welcome by Dr Gillian Levine (Swiss TPH & BRCCH PEP Fellow)
        • Keynote by Prof Günther Fink (Swiss TPH & BRCCH Lead Researcher): “Digital Support Systems to Improve Child Health and Development in Low-Income Settings”
        • Keynote by Prof Valérie D’Acremont (Unisanté): “DYNAMIC: An e-Health System Intervention to Improve Clinical Care for Children, Promote Sustainable Use of Resources and Enhance Outbreak Detection”
        • Q&A and Closing
        • Networking Apéro

    Speakers:

    Dr Gillian Levine

    Swiss TPH, Switzerland

    Welcome and Moderator

    Prof Günther Fink

    Swiss TPH, Switzerland

    Talk: “Digital Support Systems to Improve Child Health and Development in Low-Income Settings”

    Prof Valérie D’Acremont

    Unisanté Lausanne, Switzerland

    Talk: “DYNAMIC: An e-Health System Intervention to Improve Clinical Care for Children, Promote Sustainable Use of Resources and Enhance Outbreak Detection”.

    These seminars were recorded on April 27th, 2023 in Basel, Switzerland.

    BRCCH 2022 Image Contest Winners

    BRCCH Image Contest 2022 Winners

    The BRCCH was inspired by all the visuals submitted by BRCCH early career researchers to the second edition of the BRCCH Image Contest. We warmly thank everyone for participating.

    A range of excellent images visually reflected the hard work and research done in BRCCH projects ranging from lab, clinical, field and modelling activities. Three winning images were selected based on aesthetics and alignment with the BRCCH scientific scope.

    Marta S Palmierim (Swiss TPH) is working on a PII project. Her image shows a glimpse into a cross-sectional study conducted by her and her colleagues in the Kibaoni ward in Tanzania. Research assistants collected samples from participating children to check for different parasitic diseases such as soil-transmitted helminthiasis, schistosomiasis, intestinal protozoa infections, malaria and lymphatic filariasis. Dr Palmeirim is doing similar research in Uganda to study a combination drug treatment against soil transmitted helminths. Credit: MS Palmeirim

    Keith Gunapala (University of Basel) is working on a PEP project. His image shows a mass of human embryonic stem cells that form in vitro and develop some of the organizational and molecular properties of organs, i.e., an organ precursor in a petri dish. These so-called embryoid bodies are useful models for Dr Gunapala's work studying Fragile X Syndrome and investigating potential therapeutic approaches. Credit: Nissim Benvenisty Lab, Azrieli Center for Stem Cells and Genetic Research, Hebrew University of Jerusalem.

    Prasad Nalabothu (University Hospital Basel) is working on a MIP project. Here, he and a mother check the fit of orthopaedic palatal plate to treat the baby’s cleft lip and palate until surgery can be safely performed. During his research visit to the project’s partner, the Cleft and Craniofacial Centre at Saveetha Medical College and Hospital in Chennai, India, he and colleagues applied a digital workflow involving artificial intelligence to produce the palatal plate using a 3D printer. This process was developed by the MIP project and achieved the project’s early milestone of adoption outside of Switzerland. Credit: P Nalabothu and Dr Praveen Ganesh.

      About the 2022 Winners:

      Dr Prasad K. K. Nalabothu is a research scientist at the oral and maxillofacial surgery clinic at University Hospital Basel. His primary research background is in cleft and craniofacial orthodontics, which he specialized in during his training in Taipei, Taiwan. He did his master’s degree in lingual orthodontics at the University of Basel and his skill set is complemented by his PhD in smart implants for tissue expansion in cleft palate defects of newborns. He currently contributes his expertise to a Multi-Investigator Project.

      Dr Marta S Palmeirim has a MSc in medical parasitology and PhD in epidemiology. She has mainly focused on the control of soil-transmitted helminth infections, and has implemented drug and health education interventions. Additionally, she has investigated potential nutritional issues related to these infections. In general, her interests lie in the field of neglected tropical diseases (NTDs) and their control, elimination and eradication, among other public health issues. Her work has resulted in a total of 15 articles in the peer-reviewed literature, of which 11 are as first author. Currently, Dr Marta Palmeirim works in a BRCCH Principal Investigator Initiative project.

      Dr Keith Gunapala is a postdoctoral fellow in the lab of Prof Verdon Taylor at the Department of Biomedicine of the University of Basel. In the context of a Postdoctoral Excellence Programme project that he co-leads, his research interests lie in understanding human brain development using organotypic culturing and cerebral organoids. He aims to use these platforms to better understand normal human brain development, neurodevelopmental disorders, and find novel therapeutic strategies. He holds a PhD from the University of Basel in neurobiology.

      A New Approach to Understand Patients’ Incomplete Recovery from COVID-19

      A New Approach to Understand Patients’ Incomplete Recovery from COVID-19

      In a study* published in the journal Nature Immunology, Prof Christoph Hess (University of Basel and University of Cambridge, UK), Dr Hélène Ruffieux (University of Cambridge, UK), Dr Glenn R Bantug (University of Basel) and international collaborators present a new approach to understand incomplete recovery from SARS-CoV-2, including long COVID, based on biological features such as cellular and metabolic changes.

      Why do people react so differently to the SARS-CoV-2 virus, especially in the long term? How does the course of the immune response after infection relate to clinical sequelae i.e., the chronic effects following the disease’s initial acute phase? A team from the Cambridge Institute of Therapeutic Immunology and Infectious Diseases followed a group of 215 patients between late March 2020 and early August 2021 to study the dynamics of recovery from SARS-CoV-2 infection and the biology underlying patient-to-patient differences. The study cohort covered a spectrum of clinical severities: from hospitalized and ventilated patients, to patients with only mild or no symptoms. Uninfected healthy individuals also participated in the study, serving as controls.

      A patient-centric study design

      "We were primarily interested in collecting biological data, not at the level of the virus, but at the level of the host, i.e., the patients", says Prof Hess, senior author of the study. Specifically, the team wanted to investigate differences in cellular immunology, in inflammatory proteins and in metabolism over time at the patient level. “The goal of our work was to define the biological features characterizing patients with unfavourable outcomes, irrespective of demographic or clinical information”, explains Prof Hess.

      To evaluate how biological parameters encompass information about the extent and dynamics of recovery from infection, the research team deployed a statistical framework tailored to the longitudinal analysis of multiple related parameters. This allowed them to reconstruct the disease trajectories of individual patients, and to characterize differences in their immune and metabolic profiles over weeks to several months post infection. Based on parameters measured soon after disease onset, they then built a predictive model and thus identified an early biological signature, predictive of poor prognosis.

      New predictions based on the biological signature can be generated using their online tool (pictured above), designed to test the research findings prospectively. Not (yet) meant for clinical use! Image courtesy of Ruffieux et al. 2023

       

      Explore the tool yourself at http://shiny.mrc-bsu.cam.ac.uk/apps/covid-19-systemic-recovery-prediction-app/

      The biological markers of long COVID

      So which biological parameters are we talking about? Prof Hess explains:

      • There is – unsurprisingly – the aspect of inflammation: High and persistent inflammation correlated with long-term sequelae. In particular, the levels and dynamics of the C-reactive protein, an indicator of inflammation in the body, during the acute and convalescence phases were associated with the overall recovery profile of patients, months after infection.
      • The researchers also found strong predictive value of a measurement of a type of innate immune cells, the natural killer (NK) cells. Specifically, low NK cell numbers were associated with poor outcomes. How exactly NK cells contribute to the pathophysiology of SARS-CoV-2 remains to be defined.
      • Interlinked with the immune response, tryptophan metabolism has been implicated in the pathophysiology of long COVID. Tryptophan (an amino acid) is a precursor of the neurotransmitter serotonin, which regulates mood and other key bodily functions. However, tryptophan can also be funnelled into the kynurenine pathway. During inflammation, such as triggered by SARS-CoV-2 infection, this breakdown pathway is induced, diverting tryptophan away from the one leading to the formation of serotonin.

      Indeed, Prof Hess, Dr Ruffieux and their team did discover low serotonin levels in a subset of the patients they studied. At the same time, they found an accumulation of potentially neurotoxic metabolites, which are formed as degradation products of the tryptophan-degrading metabolic pathway.

      All this, says Prof Hess, coincides with one important clinical aspect of long COVID: "Key clinical elements of long COVID can be that patients experience a lack of concentration, patients tire quickly, and they may show signs and symptoms of depression. This fits with the excessive activation of the kynurenine pathway."

      Clinical relevance

      Prof Hess and his newly founded start-up company, Hornet Therapeutics, identified a drugable metabolic target that may affect serotonin levels, and aim to perform a clinical trial in patients with long COVID. If preventing depletion of serotonin indeed is effective to ameliorate the above-described symptoms, this would constitute a major step in the treatment of long COVID.

      Background

      Prof Christoph Hess leads the Immunobiology lab at the University of Basel and is the Professor of Experimental Medicine at the University of Cambridge, UK. Prof Hess’ research focuses on the translational aspects of lymphocyte function and its metabolic basis. The goal of his work is to improve our understanding of patients suffering from disorders of immunometabolic regulation.

      Read more about the BRCCH-supported research of Prof Hess and co-author Dr Glenn R Bantug- ISINC-19: Immune Senescence in COVID-19. This project is part of the BRCCH’s Fast Track Call for COVID-19 Research.

      Interview article: Irène Dietschi

      *Research Paper 

      Hélène Ruffieux, Aimee L Hanson, Samantha Lodge, Nathan G Lawler, Luke Whiley, Nicola Gray, Tui H Nolan, Laura Bergamaschi, Federica Mescia, Lorinda Turner, Aloka de Sa, Victoria S Pelly, The Cambridge Institute of Therapeutic Immunology and Infectious Disease-National Institute of Health Research (CITIID-NIHR) BioResource COVID-19 Collaboration, Prasanti Kotagiri, Nathalie Kingston, John R Bradley, Elaine Holmes, Julien Wist, Jeremy K Nicholson, Paul A Lyons, Kenneth GC Smith, Sylvia Richardson , Glenn R Bantug , Christoph Hess. 2023. A patient-centric modelling framework captures recovery from SARS-CoV-2 infection. Nature Immunology. https://www.nature.com/articles/s41590-022-01380-2

       

       

      Open Position in the BRCCH Management Office

      Open Position in the BRCCH Management Office

       

      **update 9 December 2022: A sincere thank you to everyone for your interest to join the BRCCH management team. We have closed submission and are currently processing applications. Thank you for your patience and understanding.**

      The BRCCH seeks new talent for the position of Scientific Officer  to join the management team based in Basel. A new colleague will join a core team to further the BRCCH mission: to drive scientifically outstanding research and innovation in paediatrics.

      Open Position
      Scientific Officer (Postdoctoral level)
      80%-100%, immediately or as per agreement

      About Us
      The Botnar Research Centre for Child Health (BRCCH) is physically located in Basel, Switzerland and supports researchers at its four partner institutions: University of Basel, ETH Zurich, University Children’s Hospital Basel and the Swiss Tropical and Public Health Institute. Generously funded by Fondation Botnar, the Centre drives innovative translational research addressing unmet medical needs of children and young people, especially those living in low- and middle-income countries, through funding programmes and professorial posts.

      Position
      The BRCCH management office seeks a dynamic and team-orientated colleague who will be responsible for:

      • Coordination and monitoring of the Centre’s research grant portfolio
      • Management of relationships with grantees
      • Management of the Centre’s key stakeholders, including its funding partners, partner institutions, governance boards and funded professors
      • Support of the Centre’s Directors
      • Support in the set-up of strategic activities related to academic research management and early-career capacity-building programmes
      • Support in the conceptualisation and organisation of scientific documents, meetings and dissemination events
      • Support of team members with scientific communications

      Your Profile & Competences
      You hold a doctoral degree in the domain of digital health, biomedicine or related health sciences. Proven experience in scientific communications, project management and stakeholder management are essential. Competency in strategic thinking and concise documentation preparation while ensuring precise, supporting operational processes, and the ability to adapt quickly between individual and team-based tasks, are required. Strong organisational and interpersonal skills as well as an ability to work efficiently in a busy, multi-stakeholder environment are a must. You enjoy working in small and efficient teams and are effective in taking up new challenges. Previous work experience in research and/or general management is an asset. Excellent analytical skills, and fluency in written and spoken English are indispensable. Proficiency in German is desirable. Proven competency in swiftly assimilating new knowledge and working with a high degree of independence is essential.

      We Offer
      A responsible position within a young and internationally oriented research centre that is driven by a dedicated and collegial team. Conditions of employment in accordance with the personnel and salary regulations of the University of Basel including flexible working conditions. A fixed-term contract for 3 years with the possibility of extension.

      Application / Contact
      Please send your application (CV, cover letter, certificates) in a single electronic document by 8 December 2022 to contact@brc.ch. For further information about the position, please contact tara.sugrue@brc.ch (Scientific Lead BRCCH). For administrative and HR-related questions, please contact greet.vanmalderen@brc.ch (acting General Manager BRCCH). For more information on the BRCCH, please see https://brc.ch

       

      ETH Zurich Seeks Assistant Professor of Methods and Technologies for Molecular and Cellular Systems Engineering

      ETH Zurich Seeks Assistant Professor of Methods and Technologies for Molecular and Cellular Systems Engineering

      visual: ETH Zurich / Gian Marco Castelberg

       

      **Update June 2023- Please note that this position is now closed. For more opportunities, refer to the ETH Zurich's online faculty recruiting portal.

      In an announcement by ETH Zurich, the Department of Biosystems Science and Engineering (D-BSSE) seeks outstanding candidates for the open faculty position of Assistant Professor (Tenure Track) of Methods and Technologies for Molecular and Cellular Systems Engineering. The successful candidate will develop innovative methods to advance biosystems science and engineering. Building upon current achievements in the field of living therapies, such as molecular, gene and cell therapies and tissue regeneration, the next generation of these therapeutic modalities will include the capacity to precisely manipulate individual cells, tissues, organs, and ultimately whole organisms. Such manipulation will be performed in a dynamic fashion in response to real-​time molecular and cellular cues and will possibly lead to fully personalized treatment strategies.

      Read the full job announcement on ETH Zurich's website.

       

      *Please note the above position is not associated with the BRCCH. Those interested in this position must apply through ETH Zurich's online faculty recruiting portal.

      Seminar 18 Nov – Importance of the Microbiome in Paediatric Health

      BRCCH Seminar 18 Nov - Importance of the Microbiome in Paediatric Health

      **Update December 12th, 2022** Thank you to everyone that attended our hybrid seminar! We had a great turnout-- in case you missed the presentations or you would like to watch them again, you can now stream them below or on our YouTube channel.

      Visual: Ronja Rappold

       

      Description:  The BRCCH cordially invites you to join our seminar addressing the importance of the microbiome in paediatric health. Prof Emma Slack (ETH Zurich, Switzerland) will share her work on the development of novel intervention strategies for inborn errors of metabolism and neonatal sepsis using advancements in microbiota bioengineering. Prof Mathias Hornef (University Hospital Aachen, Germany) will highlight his research on the postnatal microbiotic colonisation in the intestines and the development of the mucosal adaptive immune system after birth.

      When: Friday, November 18th, 2022 from 16:00-17:15 CET, to be followed by an apéro

      Where: Hybrid Zoom / Room HIL E7 – Hörsaal, ETH Zurich Hönggerberg Campus, Stefano-​​Franscini-​Platz 5, 8093 Zurich

      Zoom Registration: HERE

      In-person Registration: HERE
      Directions and location information

      Schedule:

          • Welcome by Prof Sai Reddy (Vice Director, BRCCH)
          • Prof Emma Slack (ETH Zurich): "Precision Microbiota Engineering for Child Health"
          • Prof Mathias Hornef (University Hospital Aachen, Germany): "Ontogeny of the Host-Microbial Interaction in the Intestine"
          • Q&A and Closing
          • Networking Apéro

      Keynote speakers:

      Prof Emma Slack

      ETH Zurich, Switzerland

      Talk: "Precision Microbiota Engineering for Child Health"

      Prof Mathias Hornef

      University Hospital Aachen, Germany

      Talk: "Ontology of the Host-Microbial Interaction in the Intestine."

      These seminars were recorded on November 18th, 2022 in Zurich, Switzerland.

      Insights into the University of Zimbabwe Birth Cohort study

      Insights into the University of Zimbabwe Birth Cohort study

      Prof Kerina Duri, associate professor in the Immunology Unit at the Faculty of Medicine and Health Science, University of Zimbabwe (UZ-FMHS), and her Master of Philosophy student Mr Arthur Mazhandu talk about their research studying mother-child health, focusing on HIV and its comorbidities in high-density residential areas in Harare, Zimbabwe. They are collaborating with the Department of Visceral Surgery and Medicine (University Hospital Bern) and Prof Randall Platt (ETH Zurich) on a BRCCH project entitled Living Microbial Diagnostics to Enable Individualised Child Health Interventions. This autumn, as part of this work, Prof Duri and Mr Mazhandu visited their Swiss collaborators, Prof Andrew Macpherson, Prof Benjamin Misselwitz and Prof Randall Platt, and the BRCCH took the opportunity to interview them.

       

      Prof Kerina Duri, Mr Arthur Mazhandu, thank you for your time. Prof Duri, could you tell us about your research interests?

      Kerina Duri (KD): My background is in biochemistry and biotechnology. I became interested and pursued my doctoral research in the field of viral immunology at the University of Norway, Oslo, and joined the University of Zimbabwe Faculty of Medicine and Health Sciences (UZ-FMHS) Parirenyatwa Teaching Hospital in 2010. At that time, we had some issues with high HIV prevalence. I worked hand-in-glove with paediatricians, who saw more and more HIV-uninfected babies born from HIV-infected mothers presenting with high mortality and morbidity, almost like HIV-infected babies.

      Using funding from the Wellcome Trust for my postdoctoral work, we established the University of Zimbabwe Birth Cohort Study (UZBCS) aiming to understand why these HIV-exposed but uninfected babies were at higher risk of dying. The hypothesis was that their immune system was impaired during foetal development due to maternal exposure to HIV and the baby’s exposure in utero, and/or during the breastfeeding period to the mother’s lifelong antiretroviral therapy (ART).

      We recruited 1200 pregnant women who were at least 20 weeks into gestation and followed up on three groups of babies: HIV-uninfected babies that were born to HIV-infected mothers, HIV-infected babies that were born to HIV-infected mothers, though this was a small number due to effective ART, and a healthy group of babies that were born to HIV-uninfected mothers. The main strengths of this study are the relatively large sample size and the simultaneous recruitment of HIV-infected pregnant women alongside HIV-uninfected pregnant women from the same community. Thus, all research participants reside in highly similar environmental conditions in high-density areas of Harare, resulting in an unusually homogenous study population.

      Mr Mazhandu, how did you become interested in this research?

      Arthur Mazhandu (AM): I am a biochemist currently working directly under Prof Duri in the Immunology Unit and working on my Master of Philosophy degree on Helicobacter pylori colonization in babies from birth until two years of age. I first met Prof Duri during an internship that was a requirement of my undergraduate studies in biochemistry. That is when I was introduced to her lab, her team and the work that she is doing. I caught the bug of being involved in clinical research.

      Prof Duri, you have a long-standing collaboration with Prof Andrew Macpherson (University Hospital Bern) and now with Prof Randall Platt (ETHZ). How did that relationship develop, and how did you decide to also collaborate on this BRCCH project?

      KD: We first met one of the researchers in Prof Andrew Macpherson’s lab, Prof Benjamin Misselwitz, when he visited UZ-FMHS in October 2018. At the time, they were and still are collaborating on inflammatory bowel disease (IBD) research in adults with Dr Leo Katsidzira in the Department of Medicine at UZ-FMHS, studying how diet and nutrition shape the microbiome profile in IBD patients. They thought to do a parallel study of the microbiome profiles in babies, since early life factors like low birth weight or the maternal microbiome impact infant microbiome colonization, and consequently their health and behaviour, even up to adulthood.

      At the same time, we wanted to expand our research horizon in the UZBCS to why these HIV-exposed but uninfected babies were getting sick. That is where the microbiome collaboration came in. We know that microbiome colonization in babies affects the development of their immune system, so it is important to understand how maternal HIV infection and the baby’s exposure to ART in utero and during breastfeeding moderate or modulate the microbiome profile and immunity. The Bern group were also interested in studying the impact of malnutrition, as malnutrition in babies is a problem in Zimbabwe. So, we also want to see how malnutrition impacts early-life microbiome colonization and health trajectories in children.

      There are a lot of synergies in this collaboration. We have an amazing biobank of samples from the cohorts of babies and their mothers including longitudinal paired mother-baby stool and breast milk samples, which is why we are here in Switzerland. We are adapting and applying Prof Platt’s technique, Record-seq, which was developed in mice exposed to gastrointestinal stresses. We want to gain a deeper understanding of Record-seq and to try to apply this technology to understand what happens in vivo in malnourished babies.

      Could you tell us more about the importance of this research in the local context? Why is it important to study the microbiome in mother-baby pairs in Zimbabwe? 

      KD: We want to apply this technology to understand the biological stress from HIV exposure that characterizes the HIV-exposed uninfected children. This is of public health importance because these babies are the future. This group is growing every year because with the advent of ART, more HIV-infected women are more willing to have babies since the risk of HIV transmission to their children has reduced (from 33% before the ART era to about 2.7% now1). In the future, these babies will probably constitute a large part of the population, but we don’t understand them; for example, how cognitive development and learning ability are impaired in school-aged children and how they fare when compared to healthy babies born to HIV-uninfected mothers remain elusive.

      AM: It is also important in the local context because the clinical findings we learn from this study could have a tangible effect on society now. For example, based on some of the UZBCS data, we have just submitted a paper on the factors responsible for women becoming anaemic in pregnancy. We publish that sort of information for the community. That is the biggest achievement we hope for with this research and these cohorts.

      What motivates the mothers to participate in your research?

      KD: The mothers want to contribute and have a sense of responsibility, duty and altruism. We explain to them that they themselves, or their children, might not benefit from this research, but we also explain to them, “If you decide to participate in this project, future mothers will benefit from the results of your participation, just as you now benefit from research done in the past and the participation of past mothers.” In addition, sick mothers and their babies are attended to by the clinicians for free. That is another benefit, because doctor visits can be expensive and 21% of the mothers are living under a dollar a day.2

      We have a lot of data that we initially obtained from index babies that we first enrolled at the inception of the project and followed for two years. As of 2022, we are including all subsequent pregnancies and babies from the same mothers who are interested in having their other children included. Thus, incredibly, we have a mother-siblings dataset that dampens down statistical noise and confounders associated with environmental differences and household variability.

      We are planning to provide the participating mothers with basic medication – paracetamol, analgesics and antipyretics – since currently local primary healthcare services are no longer providing these medicines. As part of our social corporate responsibility, we should give back to the community that is providing priceless, invaluable information that can benefit humankind.

      Has the team faced any challenges in this project? How are you overcoming them?

      KD: It is a challenge to motivate mothers to participate long-term in the project, especially during the COVID-19 pandemic. In addition, the national economic situation in Zimbabwe is concerning, such that some of the mothers are moving from the city back to their villages where life is relatively cheaper and less stressful. Some mothers now live 10 hours away, and some have even crossed the borders to neighbouring countries, especially South Africa. Now, after about five years, we have 600 mothers and babies actively participating in the study, which I think is still a phenomenal achievement given the circumstances.

      What do you hope to learn or advance from this work and collaboration?

      KR: We are grateful to our collaborators here for the technology transfer in 16S gene sequencing techniques. We are now writing a lot of papers and publishing profusely. Even today, we are supposed to submit a paper.

      The results from the UZBCS are impacting and will continue to impact policymakers and shape policy. Our main focus is HIV, but we also look at comorbidities: infections such viral hepatitis, cytomegalovirus, syphilis and latent tuberculosis and non-communicable diseases such as malnutrition and anaemia and their associated risk factors. For example, we also ask mothers how much they earn as a family or how much they spend on food to understand the factors influencing malnutrition. The data shows that spending less than $60 monthly per family (~3 people) on food predisposes mothers to anaemia. We can sit with the Ministry of Health and policymakers and engage with them about this information and with evidence to reduce inequalities and strengthen sustainable livelihood support for the vulnerable in order to reduce anaemia malnutrition and thereby, improve health outcomes for their children.

      We hope to continue this research because of the paucity of data on a very important growing population of HIV-exposed but uninfected babies. In the literature, most studies have only followed babies for one or two years. Our babies are already five years old. It is important to follow these babies to adolescence and, if resources permit, to establish a parallel rural group of mothers and babies to better understand the effects of different environments, microbial exposure and diets on these children’s health.

      AM: I am learning all aspects of the project, not just the biochemistry and lab. I am learning how to approach mothers about the study and answer their questions, to keep relationships with the mothers over time, process and analyse the samples and write papers.

      I also want to have an impact on my immediate surroundings. If I can continue my studies, I will continue to have great outputs, such as papers, that can also influence policy for the betterment of the community.

      KD: If I can comment: We do quite a lot with little resources, and the output is quite astronomical. That is because of these iconic students like Arthur and other members of my team currently at home, Mr Privilege Munjoma (pursuing a Doctorate of Philosophy) and Mr Panashe Chandiwana (pursuing a Master of Philosophy), who are also supported by the BRCCH. We depend on the motivated students who go above and beyond what is required of their studies to advance the UZBCS. I really commend them.

      We are coming to the end of our talk. Thank you again for sharing your insights. Are there any last thoughts that you would like to share?

      AM: Through this project, I have gained insights into the health system, especially from the perspective of children – how delicate they are and how much attention they need. For me, I can have a direct contribution to society. That has been really meaningful to me.

      KD: It is a passion for me. I want this project to work and continue like the famous Framingham Heart Study in the USA. We are doing everything, all the aspects involved in running and maintaining the study. And we depend on the students. We can do it for a certain time, but it is not sustainable as is. We work so hard, and the output is there, but we also want to put bread on the table and pay bills. We want to survive. We have children.

      It is about equity and survival and the unpredictable economic blips. That is our biggest challenge because we need a non-static adjustable living salary for these youngsters like Arthur in order for us to retain our students in Zimbabwe. If they can focus on their work,  we achieve much more and build capacity. I am getting old; I also want Arthur to take my lab to a higher level or to have his own, better lab in the future.

      This collaboration is really great, and I can see the exponential increase in tangible results clearly coming out of it. I think we are one of the few groups in Zimbabwe to work on the microbiome. I want to thank all the mothers and babies participating in the study, the students and support staff, and our collaborators Prof Andrew Macpherson, Prof Benjamin Misselwitz and Prof Randall Platt. Last but not least, I wish to sincerely thank the BRCCH for our research funding over the years. 

      Background:

      Prof Kerina Duri (PhD, MSc, BSc Hons) is an associate professor at the University of Zimbabwe in the Faculty of Medicine and Health Science. Her research interest is in understanding how maternal comorbidities such as HIV, Helicobacter pylori and intestinal helminths infections, malnutrition and mental health affect pregnancy outcomes, infant growth and health, immune development and immune dysregulation through gut microbiota profiles and composition from birth to adolescence, with a special focus on HIV-exposed but uninfected infants and children. She established a birth cohort of 1200 mother-infant pairs in urban Zimbabwe, from which there has been an incredible accumulation of data. The cohort study can be found at www.clinicaltrials.gov, under registration number NCT04087239.

      Within the context of the BRCCH, she is a Collaborator on the research project Living Microbial Diagnostics to Enable Individualised Child Health Interventions led by Prof Randall Platt (ETH Zurich). This project is part of the BRCCH’s Multi-Investigator Programme.

       

      References

      1. Duri K, Mataramvura H, Chandiwana P, Mazhandu AJ, Banhwa S, Munjoma PT, Mazengera LR and Gumbo FZ (2022). Mother-to-Child Transmission of HIV within 24 Months after Delivery in Women Initiating Lifelong Antiretroviral Therapy Pre/PostConception or Postnatally; Effects of Adolescent Girl and Young Woman Status and Plasma Viremia Late in Pregnancy. Frontiers in Virology. doi: 10.3389/fviro.2022.906271.
      2. Duri K, Munjoma PT, Mataramvura H, Mazhandu AJ, Marere T, Tabvuma T, Chandiwana P, Gumbo FZ and Mazengera LR (under review). Burden of Anaemia in Pregnancy: Associated Risk Factors and Adverse Birth Outcomes in a Resource-Limited Setting.

       

       

      Seminar 20 Oct – Malaria Prevention: Progress and Prospects

      BRCCH Seminar 20 Oct - Malaria Prevention: Progress and Prospects

      **Update Nov 9th, 2022** Thank you to everyone that attended our hybrid seminar! We had a great turnout-- in case you missed the presentations or you would like to watch them again, you can now stream them below or on our YouTube channel.

      Visual: Swiss TPH, fairpicture

       

      Description:  The BRCCH cordially invites you to join our seminar addressing the progress and prospects of malaria prevention. Prof Simon Draper (University of Oxford, UK) will highlight the challenges, successes and future developments of vaccine-based solutions. Then, Prof Melissa Penny (Swiss TPH) will share her work on data analytics and modelling as product development support. Finally, Prof Evelyn Korkor Ansah (University of Health and Allied Sciences, Ghana) will provide insights into vaccine implementation and equitable distribution.

      When: Thursday, October 20th, 2022 from 15:00-16:30 CET

      Where: Hybrid Zoom / Kollengienhaus, Hörsaal 116, Petersgraben 50, 4051 Basel

      Zoom Registration: HERE

      In-person Registration (encouraged but not mandatory): HERE

      Schedule:

          • Welcome by Prof Marcel Tanner (Swiss Academy of Arts and Sciences and Swiss TPH)
          • Prof Simon Draper (University of Oxford, UK): Malaria Vaccines – Recent Advances and Future Challenges (20 min)
          • Prof Melissa Penny (Swiss TPH): Data Analytics and Modelling Supporting Novel Malaria Prevention (20 min)
          • Prof Evelyn Korkor Ansah (University of Health and Allied Sciences, Ghana): Lessons from Malaria Vaccine Implementation in Ghana (20 min)
          • Q&A and Closing
          • Networking Apéro

      Keynote speakers:

      Prof Simon Draper
      University of Oxford, UK
      Talk: "Malaria Vaccines – Recent Advances and Future Challenges"

      Prof Melissa Penny
      Swiss TPH, Switzerland
      Talk: "Data Analytics and Modelling Supporting Novel Malaria Prevention"

      Prof Evelyn Korkor Ansah                                                                                      University of Health and Allied Sciences, Ghana
      Talk: "Lessons from Malaria Vaccine Implementation in Ghana"

      These seminars were recorded on October 20th, 2022 in Basel, Switzerland.

      Getting Ahead of Viral Evolution Using Artificial Intelligence

      Getting Ahead of Viral Evolution Using Artificial Intelligence

      It has been nearly three years since the emergence of SARS-CoV-2, and it is plainly apparent the world faces a future reality of an ever-changing virus that is here to stay. We now have diagnostics, vaccinations and therapies to fight COVID-19, but the continued emergence of new viral variants means that we too must continually assess, adapt and respond to these threats. Prof Sai Reddy (ETH Zurich and BRCCH) and his colleagues are doing just that by using artificial intelligence to prepare for future variants.

      Within the scope of the BRCCH’s Fast Track Call for COVID-19 research funding programme, Prof Reddy and his consortium have developed an artificial intelligence method, deep mutational learning, that predicts the ability of SARS-CoV-2 variants to bind to human cells and escape antibodies. This prediction for current and prospective variants may guide the future development of therapeutic antibody treatments and next-generation COVID-19 vaccines. The information can also be generated in real-time to aid faster public health decision-making. And from a global health perspective, the development of vaccines that protect against future variants improves their efficaciousness and may even help to address vaccine inequity.

      In this conversation, Prof Reddy joins BRCCH to discuss this exciting new method. He explains how this research came to be, “This work was enabled by the generous support of the Fondation Botnar to promote, in the very early stages of the pandemic, innovation to overcome the challenges that were known at the time of the peak of the pandemic. But at that time, new challenges, like variants, breakthrough infections and the evolution of SARS-Cov-2, were not necessarily anticipated.

      The Fondation’s early commitment to supporting the FTC programme enabled us to respond quickly to this changing pandemic landscape and actually to come up with a new strategy focused on SARS-CoV-2 specifically, instead of applying a band-aid approach using existing, and perhaps inadequate or outdated, methods.”

      In the journal Cell, Prof Reddy and his team published this new method called deep mutational learning, a machine learning-guided protein engineering technology that can help us understand how a new variant will affect vaccinated or previously infected people, potentially in real-time as the variant emerges in a population.

      Graphical abstract: "Selection and emergence of SARS-CoV-2 variants are driven in part by mutations within the viral spike protein and in particular the ACE2 receptor-binding domain (RBD), a primary target site for neutralizing antibodies. The researchers develop deep mutational learning (DML), a machine learning-guided protein engineering technology, which is used to interrogate a massive sequence space of combinatorial mutations, representing billions of RBD variants, by accurately predicting their impact on ACE2 binding and antibody escape. A highly diverse landscape of possible SARS-CoV-2 variants is identified that could emerge from a multitude of evolutionary trajectories. DML may be used for predictive profiling on current and prospective variants, including highly mutated variants such as Omicron, thus guiding the development of therapeutic antibody treatments and vaccines for COVID-19." -Taft et al. 2022

       

      The ability to make these predictions have big implications for how we may face the future of the pandemic. For example, researchers could use this method to identify therapeutic antibodies or develop next-generation vaccines that have the broadest coverage and the potential to be most effective against current and emergent variants. From a public health perspective, the method could be used to perform surveillance and a real-time assessment, so that governing bodies could leverage that wealth of information to guide public health decisions sooner and more effectively.

      “This method allows us to prospectively gather lots and lots of information about the potential evolutionary trajectories of any virus and that makes us a little bit more proactive, rather than always waiting and being a step behind the virus. This may even allow, someday, for us to get ahead of viral evolution.” - Prof Reddy

      Additionally, this technology has the potential for societal impact and improving vaccine inequity. In the current global health situation, countries differ greatly in access to vaccines. The inequity is exacerbated by time. The more time that passes between getting a vaccine and when it was designed, the higher the probability of it being less efficacious against variants that have since emerged. In other words, people who receive vaccinations later run the risk of not being protected against the newest variants and only being protected from older variants that are no longer circulating in the population.

      “Part of the importance of this method could be that we eventually can make vaccines that have broader coverage and have a longer shelf life of being useful. So even if populations do not get immediate access, they are still at least getting an effective vaccine. This is where there's an opportunity for us to make a difference in global and public health. Our research team cannot solve the problems with manufacturing, distribution and the economics of vaccinations, but we can at least contribute to the science behind the design of vaccines, which represents a highly important part of the science value chain on the path to global translation.” -Prof Reddy

      The science behind the technology is indeed innovative, as ETH News explains:

      Since viruses mutate randomly, no one can know exactly how SARS-CoV-2 will evolve in the coming months and years and which variants will dominate in the future. In theory, there is virtually no limit to the ways in which a virus could mutate. And this is the case even when considering a small region of the virus: the SARS-CoV-2 spike protein, which is important for infection and detection by the immune system. In this region alone there are tens of billions of theoretical possible mutations.

      That’s why the new method takes a comprehensive approach: for each variant in this multitude of potential viral variants, it predicts whether or not it is capable of infecting human cells and if it will be neutralized by antibodies produced by the immune system found in vaccinated and recovered persons. It is highly likely that hidden among all these potential variants is the one that will dominate the next stage of the COVID-19 pandemic.

      To establish their method, Reddy and his team used laboratory experiments to generate a large collection of mutated variants of the SARS-CoV-2 spike protein. The scientists did not produce or work with live virus, rather they produced only a part of the spike protein, and therefore there was no danger of a laboratory leak.

      The spike protein interacts with the ACE2 protein on human cells for infection, and antibodies from vaccination, infection or antibody therapy work by blocking this mechanism. Many of the mutations in SARS-CoV-2 variants occur in this region, which allows the virus to evade the immune system and continue to spread.

      Although the collection of mutated variants the researchers have analysed comprises only a small fraction of the several billion theoretically possible variants – which would be impossible to test in a laboratory setting – it does contain a million such variants. These carry different mutations or combinations of mutations.

      By performing high-throughput experiments and sequencing the DNA from these million variants, the researchers determined how successfully these variants interact with the ACE2 protein and with existing antibody therapies. This indicates how well the individual potential variants could infect human cells and how well they could escape from antibodies.

      The researchers used the collected data to train machine learning models, which are able to identify complex patterns and when given only the DNA sequence of a new variant could accurately predict whether it can bind to ACE2 for infection and escape from neutralizing antibodies. The final machine learning models can now be used to make these predictions for tens of billions of theoretically possible variants with single and combinatorial mutations and going far beyond the million that were tested in the laboratory. (Read full article)

      Background

      This research was developed by a BRCCH-supported multi-disciplinary consortium working together and as part of a larger BRCCH research programme, the Fast Track Call for COVID-19 research (FTC). The programme aims to enable research that will help mitigate medical and public health challenges and contribute tangible solutions to reduce global disease burden due to COVID-19. Lead investigator Sai Reddy is Vice Director of BRCCH and a professor in the Department of Biosystems Science and Engineering, ETH Zurich

      “This specific project was inspired and commenced as an extension of the original FTC project, which was initially based on developing a testing method for SARS-CoV-2 using a high throughput DNA sequencing method. As new variants emerged, such as Omicron this last winter, and the ensuing wave of breakthrough infections, we realised we could extend our work to develop technology and an approach where you could prospectively identify what combinations of mutations might escape from antibodies.” -Prof Reddy

       

      Research article:

      Taft JM, Weber CR, Gao B, Ehling RA, Han J, Frei L, Metcalfe SW, Overath M, Yermanos A, Kelton W, Reddy ST. 2022. "Deep Mutational Learning Predicts ACE2 Binding and Antibody Escape to Combinatorial Mutations in the SARS-CoV-2 Receptor Binding Domain." Cell. journal pre-proof. https://doi.org/10.1016/j.cell.2022.08.024

      Related articles:

      ETH News article "Preparing for Future Coronavirus Variants Using Artificial Intelligence"

      MORE about Prof Reddy’s FTC research DeepSARS

      MORE about the BRCCH-supported COVID-19 research

       

       

       

       

      BRCCH 2022 Image Contest

      BRCCH Image Contest

      **update 10 February 2023: Congratulations to the 2022 winners!

      The BRCCH warmly invites all BRCCH Early Career Researchers involved in a BRCCH-supported project to participate in the second edition of the BRCCH Image Contest. Submit your images of your scientific work for a chance to win a sponsorship* to attend a scientific conference of your choice. 

      Images should visually reflect the research done in your BRCCH project during 2022. They could, for example, show lab, clinical or field work, depict certain methods used, or visualise results or data, or show the goals of the project. Winning images will be selected based on aesthetics and alignment with the BRCCH scientific scope.

      Please send us your image(s) by email to contact@brc.ch with a descriptive caption and a credit of the image(s) by Friday, 2 December 2022.

      Details and conditions at bottom of page.

      Last year's winners

      The BRCCH received many stunning and inspiring entries in the 2021 contest. Here are the three winning entries.

      2021 contest winner Ronja Rappold (ETHZ) who is working on a MIP project. The image shows a mouse cross-section of cecal tissue with food content. It is stained with Hematoxylin and Eosin to visualise the nuclei and the extracellular matrix, respectively. Researchers use these stainings to assess the pathological state of tissues. Visual: Ronja Rappold

      2021 contest winner Keith Gunapala (University of Basel) who is working on a PEP project. In this image, human embryonic stem cells were engineered to have 23 chromosomes. These haploid embryonic stem cells can be used to more easily model human diseases and identify therapeutic approaches because having only one copy of a gene to work with makes the results of causation much easier to study. Blue shows DNA within a haploid cell, red indicates histones and green is the centromere of the chromosome. Visual: lab of Nissim Benvenisty

      2021 contest winner Michele Gregorini (University of Basel) who is working on a FTC project. In this image, BRCCH researchers are developing an affordable and accurate “rapid PCR test” with the goal of making advanced diagnostics available in point-of-care and resource-limited settings. Visual: Diaxxo AG

        About the 2021 Winners:

        Ronja Rappold, MSc, is a PhD student working with Prof Viola Vogel and Prof Emma Wetter Slack in the Department of Health Sciences and Technology (D-HEST) at ETH Zurich. She is highly interested in studying how mechanobiological cues affect cell signalling, more particularly the mechanobiological impact on intestinal inflammation. In a Multi-Investigator Project, she is investigating pathology-associated extracellular matrix changes occurring in the gastrointestinal tract and other disease-implicated organs. Using immunohistochemistry and histology techniques, high-resolution imaging and advanced image analysis, she is aiming to find mechanobiological readouts that could be used as early diagnostic markers in rare genetic disorders of metabolism.

        With her BRCCH Image Contest prize, Ronja attended the 2022 EMBL Symposium: Mechanobiology in development and disease in Heidelberg, Germany.

         

        Dr Michele Gregorini is a postdoctoral researcher at the Institute for Chemical and Bioengineering (ICB) at ETH Zurich. Dr Gregorini is a pioneer fellow of ETH Zurich and his PhD thesis focuses on the agile development of a variety of chemical devices. In a Fast Track Call for COVID-19 Research project, his main focus has been the development of hardware and software for the peakPCR platform, a series of thermocycling devices performing PCR analysis in a fraction of the usual time. Dr Gregorini obtained his PhD in Prof Wendelin Stark’s group after finishing his master’s degree in mechanical engineering at ETH Zurich.

         
        With his BRCCH Image Contest prize, Michele attended the 18th Münchner AIDS- und COVID-Tage in Munich, Germany.

        Dr Keith Gunapala is a postdoctoral fellow in the lab of Prof Verdon Taylor at the Department of Biomedicine of the University of Basel. In a Postdoctoral Excellence Programme project, His research interests lie in understanding human brain development using organotypic culturing and cerebral organoids. He aims to use these platforms to better understand normal human brain development, neurodevelopmental disorders, and find novel therapeutic strategies. He holds a PhD from the University of Basel in neurobiology.

        With his BRCCH Image Contest prize, Keith attended the International Society for Stem Cell Research (ISSCR) 2022 Annual Meeting in San Francisco, USA.

        Attending the ISSCR was a game changer for me. I was able to listen to cutting-edge unpublished work that widened my horizons but directly impacted my project as well. There was one talk about the epigenetics of FMR1 in stem cells which was highly relevant and made me turn my project to a different direction to find potential drug targets. Without the support of the BRCCH I would not have been able to broaden my project without the opportunity to hear that fantastic talk.” - Dr Keith Gunapala

        BRCCH Supports Travel Fellowships for the 7th World One Health Congress

        BRCCH Supports Travel Fellowships for the 7th World One Health Congress

         

        The BRCCH provides three travel fellowships (up to 5’000 SGD each / approximately 3'400 CHF) to PhD students and early career scientists aiming to attend the 7th World One Health Congress (WOHC 2022) taking place in Singapore on November 7-11, 2022. Early career researchers involved in paediatric health or medicine and residing in low- and middle-income countries are encouraged to apply.

        Apply by 31 July: More on the WOHC 2022 website. Submit application on the registration webpage.

        About the congress:

        The theme for the 7th World One Health Congress is Integrating Science, Policy and Clinical Practice: A One Health Imperative Post-COVID-19. To capture the multifaceted One Health paradigm, the WOHC 2022 will bring together five distinct tracks over five days: One Health Science, Pandemic Preparedness and Health Systems Resilience, Policy, Environment and Biosecurity, Impact on and Innovations in Clinical Practice, and Antimicrobial Resistance. The programme will feature renowned keynote speakers, plenary lectures from experts, scientific sessions with abstract presentations and panel discussions on urgent and emerging topics.

         

         

         

        Conversation with Prof Sai Reddy

        DeepSARS: Sequencing and testing at the same time

        A new scientific platform called DeepSARS, developed by Prof Sai Reddy, BRCCH Vice Director and Professor of Systems and Synthetic Immunology at ETH Zurich, could support viral testing and tracking for future pandemics: While current diagnostic testing and genomic surveillance methods are being done separately, DeepSARS is able to perform both tasks simultaneously. This allows for earlier detection of emerging variants and profiling mutations at the population level. In this conversation, Prof Reddy joins journalist Irène Dietschi to discuss the consortium’s exciting new findings.

        Graphical abstract: DeepSARS uses molecular barcodes (BCs) and multiplexed targeted deep sequencing (NGS) to enable simultaneous diagnostic detection and genomic surveillance of SARS-CoV-2. Image courtesy of Yermanos et al. 2022

         

        The ongoing COVID-19 pandemic remains a major global health concern with novel variants of SARS-CoV-2, such as alpha, beta, gamma, delta and omicron, that are continuously emerging and resulting in new waves of infection. Potentially exacerbating the situation, many of the masking and social distancing rules are relaxed around the world.

        The latest variant of SARS-CoV-2, omicron, with over 50 mutations is able to infect at a greater capacity than previous strains and often possesses substantial immune evasion, leading to many breakthrough infections in vaccinated or previously infected individuals. 

        Genomic surveillance of SARS-CoV-2 has been a vital component in the monitoring of the pandemic, providing valuable information for guiding public health decisions. However, despite the fact that the SARS-CoV-2 genomes from infected patients have been sequenced at unprecedented levels, they still represent a small fraction of the total number of global infections. And countries vary widely in how they prioritize viral genome sequencing. What makes it even more problematic is that in the countries with low sequencing rates, they also tend to have high infection rates and are therefore at an especially high risk for new mutations to evolve. They are hotspots for new variants.

        Key region: the receptor binding domain

        That is where DeepSARS comes into play. "A number of researchers have previously embraced the idea that sequencing could be used not just for genomic surveillance, but also for diagnostic testing", says immunology professor Sai Reddy, Vice Director of the BRCCH. Prof Reddy, who is the principal investigator of the Laboratory for Systems and Synthetic Immunology at ETH Zurich, has actually pursued this idea to a practical level. In a paper published recently in BMC Genomics, he, his team and collaborators have established a scientific concept which has proven that sequencing and testing can be done simultaneously. Their system is called DeepSARS.

        "One of the main challenges of the project was to determine which sites in the viral genome would yield maximum diagnostic and genomic information while maintaining sufficient coverage for each site", explains Prof Reddy. One region which is most associated with new variants is the spike protein of SARS-CoV-2, and within the spike protein it is particularly the so-called receptor binding domain – the site where the virus attaches itself to the host receptor ACE2 – where mutations most likely occur.

        This receptor binding domain also happens to be the target site of neutralizing antibodies, generated from either vaccination or previous infection. Mutations which emerge from this region can influence variants’ attachment to host cells, potentially making them more transmissible and are allowing them to escape from neutralizing antibodies. "Therefore, when we are developing sequencing tests, it is very important to get information about the receptor binding domain", says Prof Reddy. "It was a central part for the design of DeepSARS."

        Experimental protocol and ‘targeted deep sequencing’

        Once this was established, Sai Reddy and colleagues proceeded in a stepwise manner to develop the DeepSARS system. "First we elaborated an experimental protocol, which is in fact very similar to the protocol in which all PCR tests are performed", says Prof Reddy. "The main difference is that we added little personalized markers to each sample of the PCR, so that when you perform a genomic sequencing experiment you know which patient it came from." This procedure is called molecular barcoding.

        The second step the researchers undertook was to identify regions for what they call "targeted deep sequencing". Prof Reddy: "Targeted deep sequencing means reducing the viral genome from 30’000 RNA bases to about 20 percent of that number - 6000 bases. And it means identifying those 20 percent of sites which give us information that will likely track the evolution of the virus, as well as identify emerging variants." To achieve that, Reddy and colleagues performed an extensive computational analysis (i.e., computational phylogenetics). In this way they identified target candidates of the viral genome and then implemented them in the experimental protocol.

        Proof of concept on patients’ sample

        Next, they validated their data on synthetic RNA templates of SARS-CoV-2, based on genomic sequences recovered early in the pandemic. "That allowed us to do very precise experiments to detect the amount of viral material, which was as low as 10 copies of the virus per sample", Prof Reddy explains.

        The final step was testing DeepSARS on samples from patients. "We had samples from 30 patients, and we were able to show, based on nasal swabs or saliva, that the DeepSARS testing assay was very close to performing at the same level of diagnostic detection as a traditional PCR test", says Prof Reddy. And: "It was able to provide enough information about genomic surveillance to classify viral evolution, and whether there were any variants or not." In short: DeepSARS works. With the proof of concept, its science and technology may be regarded as well established.

        A solid foundation for future pandemics

        The exciting question is, could DeepSARS be applied at a larger scale? Could it even be deployed in the current COVID-19 pandemic? "DeepSARS certainly has a lot of potential", says Prof Reddy. "But right now, while we’re still in the COVID-19 pandemic, it wouldn’t make much sense to replace the current infrastructure for diagnostics and genomic surveillance with a new system." As Prof Reddy explains, that would implicate numerous changes in the logistics and regulations of the on-going pandemic, which, among other aspects, would be far too costly and require extensive regulatory approval.

        Yet Sai Reddy is collaborating with public health experts in Switzerland as well as with clinicians at University Hospital Basel and other partners, discussing future applications, including clinical testing of DeepSARS. The goal is to examine the system at a larger scale. "We have shown that DeepSARS can be rapidly adapted for identification of emerging variants and for profiling mutational changes at a small scale but for a pandemic, this requires population level implementation", says Prof Reddy. "Practically speaking, DeepSARS could be of immense benefit in for future pandemics or possibly as SARS-CoV-2 transitions to an endemic stage."

        Background

        DeepSARS was developed by a BRCCH-supported consortium where bioengineers, immunologists, computational biologists and clinical scientists work together and as part of a larger BRCCH research programme, the Fast Track Call for COVID-19 research (FTC). The programme aims to enable research that will help mitigate medical and public health challenges and contribute tangible solutions to reduce global disease burden due to COVID-19.

        This specific project aims for rapid transfer of these state-of-the art diagnostic methods across Switzerland and many other countries around the world, leading the way for innovative population level surveillance approaches of future variants and other disease outbreaks.

         

        Interview: Irène Dietschi

        Research article:

        https://bmcgenomics.biomedcentral.com/articles/10.1186/s12864-022-08403-0

        Yermanos A, Hong KL, Agrafiotis A, Han J, Nadeau S, Valenzuela C, Azizoglu A, Ehling R, Gao B, Spahr M, Neumeier D, Chang CH, Dounas A, Petrillo E, Nissen I, Burcklen E, Feldkamp M, Beisel C, Oxenius A, Savic M, Stadler T, Rudolf F & Reddy ST. 2022. "DeepSARS: simultaneous diagnostic detection and genomic surveillance of SARS-CoV-2." BMC Genomics. DOI:v10.1186/s12864-022-08403-0

        MORE about the BRCCH-supported COVID-19 research by Prof Sai Reddy and consortium.

         

         

         

        BRCCH Seminar 6 July: Refining Paediatric Treatments for All

        BRCCH Seminar 6 July: Refining Paediatric Treatments for All

        **Update July 19th, 2022** Thank you to everyone that attended our hybrid seminar! We had a great turnout-- in case you missed the presentations or you would like to watch them again, you can now stream them below or on our YouTube channel.

        Visual: Kiran Kuruvithadam

         

        Description:  The BRCCH cordially invites you to join our seminar looking at Refining Paediatric Treatments for All. This event will highlight the research progress of Prof Thomas Erb (UKBB) on how to reduce the risk associated with the use of mechanical ventilation in children, and the efforts to improve competence in paediatric anaesthesia in Switzerland. Then, Dr Marianne Schmid Daners (ETH Zurich) will provide an overview of the challenges of paediatric hydrocephalus treatment. Finally, Prof Kokila Lakhoo (University of Oxford) will present her work in low- and middle-income countries on providing surgical treatments to children in need.

        When: Wednesday, July 6th, 2022 from 16:00-17:30 CET

        Where: Hybrid Zoom / UKBB seminar room, Spitalstrasse 33, 4056 Basel

        Zoom Registration: HERE

        In-person Registration (encouraged but not mandatory): HERE

        Schedule:

            • Welcome by BRCCH Director Prof Georg Holländer
            • Prof Thomas Erb & his team (UKBB): "Safety first in children undergoing anaesthesia and sedation!" (25 min)
            • Dr Marianne Schmid Daners (ETH Zurich): "Challenges of paediatric hydrocephalus" (20 min)
            • Prof Kokila Lakhoo (University of Oxford): "Addressing the global health challenges for children with surgical needs in low- and middle-income countries" (40min, online)
            • Closing

        Seminar Archive

        Prof Thomas Erb (UKBB) presents "Safety first in children undergoing anaesthesia and sedation!" originally given on July 6th, 2022.

        Dr Marianne Schmid Daners (ETH Zurich) presents"Challenges of Paediatric Hydrocephalus"originally given on July 6th, 2022.

        Prof Kokila Lakhoo (University of Oxford) presents "Addressing the Global Health Challenges for Children with Surgical Needs in Low- and Middle-income Countries" originally given on July 6th, 2022.

        Keynote Speakers:

        Prof Kokila Lakhoo

        Nuffield Department of Surgical Sciences, University of Oxford

        Prof Kokila Lakhoo is a consultant paediatric surgeon at the Children’s Hospital in Oxford and the University of Oxford. She is also Chair of the International Forum for the British Association of Paediatric Surgeons and the President of the Global Initiative for Children’s Surgery (GICS). She is developing paediatric surgery through a link in Tanzania and has collaborative research projects in Malawi and South Africa. Besides general paediatric surgery and ambulatory surgery, her special interests are global health, fetal counselling, neonatal surgery, paediatric tumour surgery, paediatric thoracic surgery and specialist gastrointestinal surgery.

         

        Prof Thomas Erb

        University Children's Hospital Basel

        Prof Thomas Erb completed his medical training with board examinations in anaesthesiology and critical care. Subsequently, he moved to Durham, North Carolina, USA, where he worked in the Pediatric Cardiology Program at Duke University. There, he also obtained a master of health sciences in clinical research. Returning to Switzerland in 2000, Prof Erb started his clinical research programme in the Department of Anaesthesiology at the University of Basel and University Children’s Hospital Basel (UKBB). In 2010, he became Titular Professor of Anaesthesiology, and in 2011 he was made Head of the Division of Paediatric Anaesthesia at UKBB. His clinical interests and research are focused on the effects of anaesthetic conditions on airway and lung mechanics in children. He is currently leading the BRCCH-funded COVent project aiming to develop practical solutions that reduce the risks associated with the use of mechanical ventilation, especially those associated with low-cost/do-it-yourself ventilators and off-label use that are now available in many resource-limited settings.

         

         

        Dr Marianne Schmid Daners

        Institute of Design, Materials and Fabrication, ETH Zurich

        Dr Marianne Schmid Daners graduated from ETH Zurich as a mechanical engineer. She then completed her doctorate on the topic of “Adaptive Shunts for Cerebrospinal Fluid Control” at ETH Zurich’s Institute for Dynamic Systems and Control. Dr Schmid Daners heads the institute’s Biomedical Systems Group as a senior scientist. At the interdisciplinary interface of clinical research and engineering, her passion is the pathophysiological understanding of the dynamics of the intracranial and cardiovascular systems. Her research focuses on the modelling, control and testing of biological systems, as well as on the development and control of biomedical devices for the treatment of heart failure and hydrocephalus.

        Takeaways from Panel Discussion: Impact of COVID-19 on Global Paediatric Health

        Takeaways from Panel Discussion: Impact of COVID-19 on Global Paediatric Health

        On May 24th 2022, a panel of experts highlighted several important facets of the consequences that COVID-19 pandemic has on the global paediatric health situation:

        - decreased access to vital child healthcare services like newborn care and immunisation
        - increased poverty
        - more nutritional and physical activity deprivation
        - mental impairment
        - compromised learning and loss of a caregiver

        Moderator: Prof Julia Dratva, Zurich University of Applied Sciences (ZHAW) & University of Basel, Switzerland

        Panel members: Prof Yvonne Maldonado, Stanford University, USA; Prof Alan Stein, University of Oxford, UK; Dr Marc Birkhölzer, University of Basel, Switzerland; Prof Thomas Berger, Secretary and Chief Medical Advisor at NEO FOR NAMIBIA

        More about the event here.

        Find out more about our speakers and read about their takeaways below

         

        From left to right: Prof Julia Dratva, Dr Marc Birkhölzer, Prof Yvonne Maldonado, Prof Thomas Berger. (Prof Alan Stein joined remotely, not pictured)

         

         

        Prof Yvonne Maldonado

        Dr Marc Birkhölzer

        Prof Alan Stein

        Prof Thomas Berger

        Prof Julia Dratva

        Six Projects Selected for Principal Investigator Initiative

        Principal Investigator Initiative (PII)

        The Botnar Research Centre for Child Health (BRCCH) is pleased to announce six research projects within its new initiative, the Principal Investigator Initiative (PII). The PII aims to drive interdisciplinary research that addresses critical challenges in global paediatric health and medicine. BRCCH’s PII projects bring together researchers from its four partner institutions and international partners who will deliver step-changing innovations and intervention strategies across paediatric health diagnosis, disease treatment and prevention with global reach. Each project is supported with up to 1 million CHF for a duration of four years. Research activities will start in Summer 2022.

         

         

        The BRCCH supports the following projects:

        Visual Analysis of Long Lasting Insecticidal Nets to Maximise Universal Access

        Long-lasting insecticidal nets (LLINs) are the mainstay of malaria control. However, more than 50% of people living in endemic areas are currently unprotected because LLINs often develop holes and wear out sooner than their expected lifespan. The consortium led by Dr Sarah Moore, Dr Amanda Ross (Swiss TPH) and Prof Philippe Claude Cattin (UniBas) will develop a digital tool enabling national malaria control programs to improve planning for programmatic LLIN distribution, monitoring of LLIN quality and selection of the best product for use according to contextual settings. Increasing mosquito net lifespan will optimise resource use, increase the protection of children and reduce malaria transmission in LMICs.

        Team members: Dr Sarah Moore (Swiss Tropical and Public Health Institute), Prof Philippe Claude Cattin (University of Basel), Dr Robin Sandkühler (University of Basel), Dr Amanda Ross (Swiss Tropical and Public Health Institute); Sumaiyya Thawer (Swiss Tropical and Public Health Institute), Prof Fabrizio Tediosi (Swiss Tropical and Public Health Institute), Emmanuel Mbuba (Ifakara Health Institute, Tanzania), Dr Zawadi Mboma (Ifakara Health Institute, Tanzania), Frank Chacky (Ministry of Health, Tanzania).

         

        Alex: Design, Development and Evaluation of a Digital Health Assistant for Paediatric Asthma

        Poor adherence to medication and insufficient monitoring are key factors that contribute to inadequate asthma control in children and adolescents. The consortium led by adjunct Prof Edgar Delgado-Eckert (UKBB and UniBas), Prof Elgar Fleisch (ETH Zurich) and Dr Torsten Schmitz Cherdron (Swiss TPH) aims to improve asthma control in adolescents using a smartphone-based digital health assistant designed for regular and sustained remote disease monitoring and patient coaching. They will also harness digital and AI-based approaches to assess a patient’s health state passively, i.e., minimising the patient’s burden in the process of disease monitoring. Finally, the consortium will assess the feasibility and scalability of the digital health assistant in the socio-economic setting characteristic of low-to-middle income countries.

        Team members: Adjunct Prof Edgar Delgado-Eckert (University Children’s Hospital Basel and Department of Biomedical Engineering at University of Basel), Prof Elgar Fleisch (Center for Digital Health Interventions at ETH Zürich), Dr Torsten Schmitz Cherdron (Swiss Tropical and Public Health Institute), Prof Urs Frey (University Children’s Hospital Basel), Dr Filipe Barata (Center for Digital Health Interventions at ETH Zürich), Prof Nicole Probst-Hensch (Swiss Tropical and Public Health Institute), Prof Sorin Man (Emergency Clinical Hospital for Children, Romania).

         

        OptiThyDose: Intelligent Digital Decision Support Tool to Personalise Dosing for Children with Thyroid Diseases

        Hypo-/hyperthyroidism manifests at birth or during childhood. Prompt and adequate medical treatment is key to protecting cognitive and physiological development in affected children. Dose optimisation is complex as there is a wide spectrum of thyroid disease severity and activity, developmental pharmacology, and inter-individual variability in drug kinetics and response in these children. As such, there is frequent over- and under-dosing despite international treatment guidelines. The consortium led by Prof Gabor Szinnai and Prof Marc Pfister (UKBB) aims to develop an intelligent decision support tool - OptiThyDose - that optimises and computes personalised dosing for a given child afflicted with hypo- or hyperthyroidism. They will conduct international multi-centre studies to validate the clinical use of OptiThyDose in different socio-economic settings. This innovative research work is supporting families and caregivers with the ultimate goal to enhance cognitive and somatic outcomes in affected children, independent of socio-economic status.

        Team members: Prof Gabor Szinnai (PI, University Children’s Hospital Basel), Prof Marc Pfister (Co-PI, University Children’s Hospital Basel); Prof Michel Polak (Hôpital Necker-Enfants Malades, France), Prof Marco Cappa (Ospedale Pediatrico Bambino Gesù, Italy), Prof Lusine Navasardyan (Arabkir Medical Centre, Armenia), Prof Johannes Schropp (University of Konstanz, Germany).

         

        Investigating Early Signs and Developmental Course of Personality Disorders in Young People

        Personality disorders (PDs) are frequent mental illnesses that have devastating effects on both afflicted individuals and society. Until recently, PDs were primarily diagnosed in adulthood, although it is now well-established that their onset begins in childhood and adolescence. With the introduction of the Levels of Personality Functioning (LPF) in Section 3 of the DSM 5 in 2013 a new concept to diagnose PD was proposed. A very similar approach was adapted for the ICD 11, previous age restrictions for diagnosing PDs have been lifted. The consortium led by Dr Marc Birkhölzer (UniBas) aims to investigate if this new concept is valid and useful to diagnose and assess personality impairments in children and adolescents, in the same way as it does in adults. Through multi-site longitudinal studies, they will also develop approaches to investigate early signs and the progression of PDs in an equivalent way across different cultures, age groups and socio-economic settings.

        Team members: Dr Marc Birkhölzer (University of Basel), Dr Kirstin Goth (University of Basel), Prof Hojka Gregoric Kumperscak (University Medical Center Maribor, Slovenia), Prof Natalia Zvereva (Moscow State University, Russia), Prof Sylvia Kaaya (The Muhimbili University of Health and Allied Sciences, Tanzania), Dr Delia Birle (University of Oradea, Romania), Prof Rasa Barkauskiene (Vilnius University, Lithuania), Dr Moises Kassin (Universidad Iberoamericana Ciudad de México, Mexico), Prof Eva Möhler (Saarland University Hospital, Germany), Prof Carla Sharp (University of Houston, USA), Prof Diane Purper-Ouakil (University of Montpellier, France), Prof Kathrin Sevecke (Innsbruck University Clinic for Psychiatry, Austria), Dr Lea Sarrar (MSB Medical School Berlin, Germany), Dr Sefa Cosgun (Private Clinic Istanbul, Turkey), Dr Felix Euler (Juvenile Forensic Department, Zurich), Dr André Della Casa (Psychiatric University Clinic, Zurich).

         

        Feasibility and Economic Evaluation of Improved Child Deworming

        Parasitic worm infections are still very common, particularly among children living in areas with limited access to safe drinking water and adequate sanitation. Moreover, children are at the highest risk of morbidity associated with chronic worm infections. The consortium led by Prof Jennifer Keiser, Prof Fabrizio Tediosi and Prof Peter Steinmann (Swiss TPH) will evaluate the introduction of a new combination therapy for soil-transmitted helminth infections into routine neglected tropical disease control activities in Uganda. The consortium will assess the feasibility, acceptability and cost-effectiveness of this deworming treatment, develop delivery toolkits for effective child deworming tailored for local settings and support policy change at national and international levels. This project will contribute directly to the advancement of worm infection management affecting poor and marginalised children in LMICs.

        Team members: Jennifer Keiser (Swiss Tropical and Public Health Institute), Fabrizio Tediosi (Swiss Tropical and Public Health Institute), Peter Steinmann (Swiss Tropical and Public Health Institute); Adriko Moses (Ministry of Health, Uganda).

         

        New Tools for Early Diagnosis and Decentralised Treatment of Buruli Ulcer

        Buruli ulcer (BU) is a chronic necrotising skin disease, caused by Mycobacterium ulcerans. BU primarily affects children in West and Central Africa and most infections occur in remote, rural areas where patients have limited access to appropriate interventions. The consortium led by Prof Daniel H. Paris (Swiss TPH) and Prof Janos Vörös (ETH Zurich) aims to develop a simple point-of-care diagnostic test and a simplified, rapid treatment for BU that can be implemented at the primary healthcare and community levels. This project will enable rapid diagnosis and early treatment of BU, preventing long-term suffering, stigmatisation and permanent disabilities in afflicted children.

        Team members: Prof Daniel H. Paris (Swiss Tropical and Public Health Institute), Prof Janos Vörös (ETH Zürich), Prof Gerd Pluschke (Swiss Tropical and Public Health Institute), Dr Alexander Tanno (Hemetron AG).

        About the Call: The initial call for applications was launched in Summer 2021. 23 applications were submitted on November 5th 2021, with 53 (Co-) Investigators involved and a total requested budget of 20.2 million CHF. All applications were evaluated by an independent, international review panel. The panel recommended six projects for funding (success rate of ∼26%). The BRCCH Board approved these recommendations in Spring 2022.

        Archive Application Documents

        Impact of COVID-19 on Global Paediatric Health – Panel Discussion

        Impact of COVID-19 on Global Paediatric Health

        Join us during an interactive debate with a panel of experts on the topic: How the COVID-19 Pandemic has affected Global Paediatric Health. The discussion will mainly focus on: i) mental health in young people, ii) disruption to life-saving paediatric health services such as immunisation and antenatal care.

        Tuesday, May 24th 2022 (16.00-17.15 pm CET)

        Moderator: Prof Julia Dratva, Zurich University of Applied Sciences (ZHAW) & University of Basel, Switzerland

        Panel members: Prof Yvonne Maldonado, Stanford University, USA; Prof Alan Steiner, University of Oxford, UK; Dr Marc Birkhölzer, University of Basel, Switzerland; Prof Thomas Berger, Secretary and Chief Medical Advisor at NEO FOR NAMIBIA

        Find out more about our speakers below

        The event is taking place in a hybrid format:

        The number of seats at Basel Biozentrum is limited, please register here.

        Interested in joining virtually? Sign up here!

        For more information, contact Dr Amandine Bovay, BRCCH Scientific Officer and Development Manager (amandine.bovay@brc.ch)

        *Update 1 June 2022: In case you missed the event, you can read the discussion takeaways here.

        Programme Speakers:

        Prof Yvonne Maldonado
        Division of Infectious Diseases, Department of Pediatrics
        Department of Epidemiology and Population Health                                 Stanford University School of Medicine, USA

        Yvonne Maldonado is Professor of paediatrics, epidemiology, and population health, and Chief of the division of paediatric infectious diseases at the School of Medicine, Stanford University. She also currently serves as Stanford Medicine’s Senior Associate Dean of Faculty Development and Diversity. Prof Maldonado's research focuses on the epidemiology and prevention of viral infectious diseases such as paediatric HIV, polio, measles and Ebola. Her work on mother-to-child transmission of HIV in sub-Saharan Africa is credited for preventing hundreds of thousands of newborns from acquiring HIV. She also leads research on the development and implementation of vaccines in low- and middle-income countries.

        Visual: Stanford University

        Prof Julia Dratva
        Institute of Public Health, ZHAW Zurich University of Applied Sciences, Switzerland
        Medical Faculty, University of Basel, Switzerland

        Prof Julia Dratva is a public health expert with a focus on child and adolescent health and early life factors of health and disease. She is the Head of the Public Health Research Unit at the Zurich University of Applied Sciences (ZHAW) and an Assistant Professor in the Medical Faculty at the University of Basel.

        Prof Dratva is a medical doctor by training with a background in internal medicine. She also holds a Master degree in Public Health and a Specialist Certification (FMH) for "Prevention and Public Health". She has a particular interest in the life course approach to health and disease in research and teaching, addressing vulnerable groups and vulnerable time spans. She also has research interests in cardiovascular health, health monitoring, health literacy and digital health.

        Prof Alan Stein
        Department of Psychiatry, University of Oxford, UK

        Alan Stein is Professor of Child & Adolescent Psychiatry at the University of Oxford, Honorary Professor in the School of Public health at the University of Witwatersrand and a member of the faculty of the African Health Research Institute, South Africa. His main area of research concerns the development of children and adolescents in the face of adversity. Ultimately the priority is to develop interventions. He has led three Lancet series on: i) The mental health of internally displaced and refugee children, ii) Perinatal mental health, iii) The communication of life-threatening conditions to children.

        Prof Thomas Berger
        Secretary and Chief Medical Advisor at NEO FOR NAMIBIA - Helping Babies Survive

        Prof Thomas Berger is a paediatrician specialised in neonatology and intensive care. With more than 25 years of experience in neonatology in various high-income countries, he decided to share his knowledge with physicians and nurses in less privileged countries. Therefore, he and his wife founded the non-profit organisation NEO FOR NAMIBIA – Helping Babies Survive in 2017. The team has just launched their 14th mission in Rundu State Hospital to improve neonatal and paediatric care in Namibia.

        Dr Marc Birkhölzer
        Psychiatrist, University of Basel, Swizterland

        Dr Marc Birkhölzer is currently a senior physician at the Juvenile Forensic Department of the Psychiatric University Clinics of Basel (UPK). His research focuses on personality disorders. Over the years, he has built an extraordinary network of collaborators in countries all over the world.

        A New Frontier in Diagnosing Gut Health

        A New Frontier in Diagnosing Gut Health

        Every year, more than 200 million children worldwide do not reach their developmental potential. This is primarily due to infectious diseases as well as malnutrition and related disorders. Normal gut development and function are critical for determining a child’s development and health throughout life. Despite this, diagnostics that can measure the health status of the gut are severely lacking.  As part of the BRCCH’s Multi-Investigator funding programme, Prof Randall Platt (ETH Zürich), Prof Andrew Macpherson (University Hospital Bern) and fellow consortium members seek to develop a non-invasive, microbe-based diagnostic that is capable of sensing and recording the status of the gut.

        In a new groundbreaking study published in Science*, Prof Platt, Prof Macpherson and co-authors have achieved the first critical steps towards making this ambitious idea a reality.

        Behind this work is the innovative Record-seq technology pioneered by Prof Platt in 20181. The technology is based on CRISPR-engineered bacteria that can sense and create a molecular record of changes in their surrounding environment over time. These bacteria, or ''transcriptional recorders'' can then be analysed via sequencing approaches to reveal the history of events that they encountered. This technology holds enormous potential to provide real-time information on the status of the gut environment, which could then be harnessed to guide personalised therapeutic interventions.

        In this new study, the researchers first set out to understand how the transcriptional recorders behave in a real-life gut environment and what they are able to report on whilst travelling through the intestine. The team demonstrated that these bacteria survive and traverse through the gut of mice, and that they can be successfully collected from faecal samples for further analysis. Importantly, the study revealed that the transcriptional recorders are able to capture important biological information throughout all regions of the gut. This represents a major advance over current omics-based technologies that are used to study the gut, as they are unable to provide insights into intestinal regions that are more difficult to access, such as the proximal colon.

        The CRISPR-engineered bacteria (or transcriptional recorders) create molecular records of information about their surrounding environment as they transit through the gut. These bacteria can then be retrieved via faecal samples and their molecular records analysed through sequencing and computational methods. Image courtesy of Prof Randall Platt

         

        Following these exciting results, the team then embarked on testing if the transcriptional recorders can reliably report on two elements which are critical for determining gut health: nutrition and inflammation.

        To do this, mice were fed with different diets and the transcriptional recorders were collected from faecal samples over time. A Record-seq analysis revealed that these bacteria record unique molecular signatures that are diet-specific and are retained by the bacteria, even following a dietary switch. Therefore, not only are these transcriptional recorders capable of reporting on the real-time dietary status in vivo, these findings also suggest that they can provide a window into the nutritional history of the gut.

        The researchers then took one step further by studying the transcriptional recorders in a mouse model of gut inflammation, to mimic the local environment in the presence of gastrointestinal disease.  Remarkably, the team discovered that the molecular signatures recorded by the bacteria could be used to distinguish healthy mice from those with gastrointestinal inflammation. Moreover, they could also provide a read-out for measuring the severity and biological indicators of inflammation within the gut.

        Following this landmark work, we asked Prof Randall Platt about where the consortium plans to take Record-Seq from here:

        ''This highly collaborative and interdisciplinary project lays the groundwork towards realising the technology’s true potential for improving human health. The consortium is now focusing on translation, which primarily includes further rigorous testing in animal models of human conditions as well as ensuring robust safety and environmental containment of the genetically engineered bacteria''.

         

        *Read the paper: https://www.science.org/doi/10.1126/science.abm6038

        Schmidt F, Zimmermann J, Tanna T, Farouni R, Conway T, Macpherson AJ, Platt RJ: Noninvasive assessment of gut function using transcriptional recording sentinel cells. Science, 12 May 2022, doi: 10.1126/science.abm6038

        About the researchers 

        Professor Randall Platt is an Associate Professor at the Department of Biosystems Science and Engineering (D-BSSE) at ETH Zürich and the Department of Chemistry at the University of Basel.

        Professor Andrew Macpherson is Professor and Director of Gastroenterology at University Hospital Bern.

        Professors Platt and Macpherson, together with fellow consortium members, lead the BRCCH Multi-Investigator Project: Living Microbial Diagnostics to Enable Individualised Child Health Interventions.

        1 Related articles

        Recording device for cell history (ETH News 03.10.2018)

        Bacteria with recording function capture gut health status (ETH News 12.05.2022)

         

         

        BRCCH Early-Career Programme

        BRCCH's Early-Career Events 2021-2022

        The BRCCH endeavours to foster the development of aspiring young researchers who will pioneer the next frontiers in global paediatric medicine and health. The BRCCH’s Early Career Programme aims to provide unique opportunities for its community members to gain know-how in research areas at the heart of the Centre’s mission and to grow their global network.

        This upcoming year (late 2021-mid 2022), the BRCCH invites its early-career community members to join local and international speakers in a series of interactive workshops on topics across the Centre’s mandate.

        For more information and registration, contact Dr. Amandine Bovay, BRCCH Scientific Officer and Development Manager (amandine.bovay@brc.ch)

        Webinar: Community-based COVID-19 Testing in Lesotho and Zambia

        Webinar: Community-based COVID-19 Testing in Lesotho and Zambia

        Visual: SolidarMed & Swiss TPH

         

        Description:  The BRCCH cordially invites you to join us online for a webinar looking at Community-based COVID-19 testing in Lesotho and Zambia. This event will highlight research progress of the collaborative project between Dr Kwame Shanaube (Zambart) and Dr Klaus Reither (Swiss TPH) on the effects of community-led interventions in mitigating the COVID-19 epidemics in Lesotho and Zambia. The BRCCH and the European & Developing Countries Clinical Trials Partnership (EDCTP) partnered on a joint initiative to support multi-national collaborations for research to mitigate COVID-19, particularly in low- and middle-income countries.

        When: Wednesday, April 27th, 2022 from 15:30-17:00 CET

        Where: Online, Zoom seminar

        Registration: HERE

        Schedule:

            • Welcome by BRCCH Director Prof Georg Holländer
            • Keynote lecture by Dr Kwame Shanaube (Zambart), Dr Klaus Reither (Swiss TPH) & their research teams:
                    1. Overview of the joint BRCCH-EDCTP project: Improving Access to SARS-CoV-2 Screening and Testing through Community-based COVID-19 Case-Finding and the Use of Digital Solutions in Lesotho and Zambia
                    2. Comparing different approaches of community-based SARS-CoV-2 testing in Lesotho and Zambia
                    3. Barriers and facilitators to SARS-CoV-2 testing at community-based testing sites
                    4. Evaluation of SARS-CoV-2 tests and testing approaches
            • Plenary discussion
            • Closing

        Keynote Speakers:

         

         

        Dr Kwame Shanaube

        Zambart & School of Public Health, University of Zambia

        Dr Kwame Shanaube is Deputy Director of Research (Quantitative) at Zambart, a multidisciplinary research organisation that conducts a range of studies including clinical trials, epidemiological studies and laboratory-based diagnostic studies. She is a clinician with a Master’s degree in public health and a PhD in TB clinical epidemiology. She is also an honorary lecturer at the University of Zambia School of Public Health. Her research interests cover a wide range of disciplines, including TB/HIV epidemiology, community-based cluster randomised trials, operational research through evaluation of field diagnostics and adolescent health. She is also the country’s Principal Investigator for a large international TB consortium (the TREATS Project) and the overall Principal Investigator for the TREATS-COVID study, both funded by the EDCTP.

         

        Dr Klaus Reither

        Clinical Research Unit, Swiss Tropical and Public Health Institute

        Dr Klaus Reither is Head of the Clinical Research Unit and the leader of the Clinical TB Research Group at the Swiss Tropical and Public Health Institute (Swiss TPH). He oversees and coordinates clinical research projects conducted by Swiss TPH and his research responsibilities comprise the set-up, implementation, coordination and supervision of clinical research projects, with an emphasis on TB clinical trials at Swiss TPH’s international partner organisations such as the Ifakara Health Institute in Tanzania, the National Centre of Tuberculosis and Lung Diseases in Georgia and SolidarMed in Lesotho.

        Dr Reither is Lead Investigator of the BRCCH COVID-19 project: MistraL - Mitigation Strategies for Communities with COVID-19 Transmission in Lesotho Using Artificial Intelligence on Chest X-rays and Novel Rapid Diagnostic Tests. Together with Dr Kwame Shanaube, he also co-leads a BRCCH-EDCTP collaborative project on Improving Access to SARS-CoV-2 Screening and Testing through Community-based COVID-19 Case-Finding and the Use of Digital Solutions in Lesotho and Zambia.

         

        Conversation with Prof Alexandar Tzankov

        A Cell Fitness Marker for Predicting COVID-19 Outcomes

        COVID-19 is unpredictable. Identifying which COVID-19 patients are likely to develop severe disease versus those at lower risk of complications remains a major clinical challenge. In a recent collaborative study*, BRCCH-funded investigator Professor Alexandar Tzankov (University Hospital Basel) and co-authors discovered a novel biomarker that could be used to predict the prognosis of COVID-19 patients more accurately. In this conversation, Prof Tzankov joins journalist Irène Dietschi to discuss          the consortium’s exciting new findings.

         

        Assessing a patient’s risk of developing severe disease is difficult. Usually, individuals who test positive for SARS-CoV-2 are referred to their physician and sent home to isolate. Which patients will develop severe symptoms and require hospitalisation is largely unknown at this point. In a study published in EMBO Molecular Medicine, Prof Alexandar Tzankov and co-authors have now uncovered a means to predict the prognosis of COVID-19 patients more precisely: by using a genetic marker called hFwe-Lose, or simply Flower lose.

        Behind this discovery is a relatively recent finding: cells constantly compare their fitness with each other in the body. Collaborators of Prof Tzankov, Prof Eduardo Moreno (Champalimaud Centre for the Unknown, Portugal) and Prof Rajan Gogna (University of Copenhagen), previously identified that the human flower gene (hFwe) can be expressed in different forms, which mark cells as either winners or losers. Fit or 'winning' cells express a form of the flower gene called hFwe-Win, whereas unfit or 'losing' cells express hFwe-Lose. This allows the body to identify unhealthy cells that need to be eliminated.

        ''The balance of expression of these flower genes is very important physiologically'' says Alexandar Tzankov. ''Their correct expression is critical in embryo and organ development, as well as in diseases such as cancer. hFwe-Lose is a kind of lifetime document for the whole body.'' It can provide insights into how fit a person’s body is at a given moment: What a person’s biological age is, how much cumulative toxicity they have been exposed to during life, if they have pathological obesity, how well does their body handle high blood sugar and hypertension.

        In May 2020, Prof Tzankov had just published an autopsy study of 21 deceased COVID-19 patients, the first major observational cohort of its kind. Professors Morena and Gogna suspected that flower genes might play a role in the progression of COVID-19 and decided to reach out to Prof Tzankov. ''They suggested examining the tissues of deceased patients for hFwe-Lose, and that's what we did'' says Alexandar Tzankov. The team also examined hFwe-Lose in patients with co-morbidities such as hypertension, diabetes, obesity and chronic obstructive pulmonary disease (COPD). The results confirmed the researchers' original idea: ''In healthy lungs, the expression of hFwe-Lose is very low. In the lungs of patients with co-morbidities, its expression increases. In patients who died of COVID-19, it is very high'', Alexandar Tzankov explains.

        hFwe-Lose is a genetic marker than can be used to predict outcomes in COVID-19 patients. Source: EMBO Molecular Medicine (2021) 13:e13714; https://doi.org/10.15252/emmm.202013714

         

        The researchers then decided to go one step further: They analysed hFwe-Lose levels in nasopharyngeal swab samples collected from 283 COVID-19 -at that time unvaccinated - patients in Wisconsin, USA during the early waves of infection. The team discovered that the higher the hFwe-Lose level was in the nasal sample, the more likely the patient went on to develop severe disease and to undergo hospitalisation and/or die of COVID-19. Remarkably, using computational modelling, the team uncovered that hFwe-Lose levels could be used to predict the risk of hospitalisation and death with a high degree of accuracy. ''For about 85% of people for whom the level of hFwe-Lose predicted hospitalisation, they actually had to go to the hospital. For virtually no one who died, mathematical modelling predicted that they would not have died'' explains Alexandar Tzankov.

        hFwe-Lose is relatively straightforward to analyse via the same nasal swab used to test for SARS-CoV-2 infection. ''This makes hFwe-Lose a very useful biomarker for COVID-19 patients'' says Alexandar Tzankov. So what could this mean for clinicians? ''You could potentially identify at-risk COVID-19 patients early, instruct these patients to pay very close attention to symptoms and keep the threshold for hospitalisation lower. That way, emergency situations could possibly be avoided.''

        ''I admit that this is an optimistic scenario for the use of this marker - but it has the potential.''

         

        Interview: Irène Dietschi

        Research article: https://www.embopress.org/doi/10.15252/emmm.202013714

        MORE about the BRCCH-supported COVID-19 research by Prof Alexandar Tzankov and consortium.

        MORE about COVID-19 research by the pathology team at University Hospital Basel.

         

        Architecture Vision for BRCCH New Home

        Architecture Vision for BRCCH New Home

        visual: Guerra Clauss Garin Architekten

         

        In a press release by the City of Basel, the firm Guerra Clauss Garen Architekten is announced the winner of the anonymous project competition from a selection of 48 entries. The canton, over the course of the next few years, will restructure the building on the corner of Schanzenstrasse and Spitalstrasse in Basel. Located strategically next to the life sciences campus Schällemätteli, the building will be the home to 4-5 research groups of the BRCCH.

        Read the press release (in German) on Kanton Basel-Stadt's website.

        Webinar: Future of COVID-19 Research

        Webinar: Future of COVID-19 Research

        **Update October 28th, 2021 ** Thank you to everyone that attended our webinar! We had a great turnout-- in case you missed the presentations or you would like to watch them again, you can now stream them below or on our YouTube channel.

        visual: background image courtesy of National Institute of Allergy and Infectious Diseases

         

        Description: The BRCCH cordially invites you to join us online for a webinar looking at The Future of COVID-19 Research. This event will highlight significant research progress and the roadmap ahead related to immunology, epidemiology and bioengineering. Gain insights from our keynote speakers and engage with them during the Q&A panel discussion.

        When: Thursday, October 21st, 2021 from 15:00-17:00 CET

        Where: online, livestream Zoom seminar

        Schedule:
        Welcome by BRCCH Vice Director Prof Sai Reddy
        Keynote lecture by Prof Teresa Lambe OBE (University of Oxford)
             "Development and testing of the Oxford/AstraZeneca vaccine"
        Keynote lecture by Prof Benjamin Murrell (Karolinska Institutet)
             "Neutralizing SARS-CoV-2 variants"
        Keynote lecture by Prof Sai Reddy (ETH Zurich and BRCCH)
             "Identifying prospective variants of SARS-CoV-2 by deep mutational learning"
        Q&A Panel Discussion
        Closing

        Webinar Archive

        Prof Teresa Lambe OBE (University of Oxford) presents "Development and Testing of the ChAdOx1 nCoV-19/AZD1222 Vaccine" originally webcast on October 21st, 2021.

         

        Prof Benjamin Murrell (Karolinska Institutet) presents "Neutralizing SARS-CoV-2 Variants" originally webcast on October 21st, 2021.

         

        Prof Sai Reddy (ETH Zurich and BRCCH) presents "Identifying Prospective Variants of SARS-CoV-2 by Deep Mutational Learning" originally webcast on October 21st, 2021.

        Keynote Speakers:

        Prof Teresa Lambe OBE
        The Lambe Group for Emerging Pathogens
        The Oxford Vaccine Group and the Jenner Institute Laboratories
        Dept of Paediatrics, University of Oxford

        Assoc Prof Lambe will share her research insights into the immune response to SARS-CoV-2 and its vaccine. Her research group is part of the Covid-19 vaccine trial in the UK and has co-designed the vaccine and led the development and testing of the immune response after vaccination.

        Prof Lambe’s research investigates the establishment of protective immune responses following vaccination and the formation of adaptive immune memory. She is particularly interested in delineating the immune response post vaccination and also post natural infection to help develop vaccines and define correlates of protection. At the University of Oxford, her group uses platform technologies to develop vaccines against emerging and re-emerging pathogens. The group is currently developing vaccines against a number of outbreak pathogens including Crimean-Congo haemorrhagic fever virus, Lassa virus, Nipah virus, Influenza, Ebolavirus and coronaviruses.

        Visual: John Cairns/University of Oxford

        Prof Benjamin Murrell
        Department of Microbiology, Tumor and Cell Biology
        Karolinska Institutet

        Prof Murrell will speak about his work on the H2020 CoroNAb project, studying antibodies and isolating nanobodies against SARS-CoV-2.

        Prof Murrell's previous research interests surrounded the evolution of the HIV envelope protein, and antibodies against it. Recently, he has applied this expertise to SARS-CoV-2 and its variants. Together with colleagues, he has identified nanobodies from immunized alpacas that may be potential SARS-CoV-2 therapeutics, and has conducted preclinical immunization studies attempting to boost responses to SARS-CoV-2 variants. This work is part of the CoroNAb consortium research project, funded under Horizon2020 as part of the EU’s emergency funding call for COVID-19.

        Visual: Karolinska Institutet

        Prof Sai Reddy
        Laboratory for Systems and Synthetic Immunology
        Department of Biosystems Science and Engineering, ETH Zurich
        And Vice Director BRCCH

        Prof Reddy shares his recent work on developing a simultaneous diagnostic and genomic surveillance method for SARS-CoV-2 based on targeted deep sequencing. He will also present new data from his group related to identifying variants of SARS-CoV-2 using a novel method called deep mutational learning. 

        Prof Reddy’s research is focused on the emerging field of systems and synthetic immunology, with an aim towards developing technologies relevant to immunotherapy and biotechnology. He has developed a number of methods in systems immunology to improve our understanding of adaptive immunity, with a particular focus on immune repertoire sequencing. Recently, he founded two spin-off companies, deepCDR Biologics and Engimmune Therapeutics, which are both based on technologies developed in his research group on engineering antibodies or T cells.

        5 Early Career Researchers Selected for Postdoctoral Excellence Programme

        Postdoctoral Excellence Programme (PEP)

        The BRCCH announces five research projects within its new initiative, Postdoctoral Excellence Programme (PEP). The programme aims to foster the next generation of scientific leaders who will pursue interdisciplinary and step-changing research to address critical unmet needs and challenges in global paediatric health. Together with established Host Principal Investigators and Collaborators, PEP Fellows will implement highly translational and ambitious research proposals over the next three years.

        Patch-IT: Multi-Sensor Sensor Nodes for Continuous Vital Sign Monitoring to Identify Novel Digital Biomarkers for Sepsis Detection in Neonatal Intensive Care
        Neonatal sepsis has a high incidence globally and is a major cause of mortality worldwide. The project Patch-IT proposes a solution for improved neonatal sepsis monitoring and management. The team aims to develop a multi-sensor electronic epidermal system that incorporates wire-free, battery-free, non-invasive and autonomous monitoring of multiple vital signs continuously and in real time. The device will also employ in-sensor data analytics powered by state-of-the-art sensor-fusion algorithms to enable personalised patient monitoring. PEP Fellow Kanika Dheman (currently Department of Mechanical and Process Engineering, ETHZ) will join the lab of Dr Michele Magno (Department of Information Technology and Electrical Engineering, ETHZ).

        Developing Novel Drug Strategies for the Treatment of Fragile X by Functional Screening of Human Pluripotent Stem Cell Models
        Fragile X Syndrome (FXS) is the most common inherited cause of intellectual disability. FXS occurs due to epigenetic silencing, or non-expression, of a specific gene, FMR1. The goal of this project is to identify and test new drugs using human stem cells with the ability to induce re-expression of FMR1 and reverse FXS symptoms and effects. This proposal has 3 aims: 1. Establish baseline levels of FMR1 expression and downstream targets in normal and FXS stem cells 2. Screen novel categories of drug compounds and 3. Establish organoids, a type of tissue culture, from FXS stem cells to perform anatomical validation of drug efficacy. A PEP Fellow will conduct this work in the lab of Prof Verdon Taylor (Department of Biomedicine, University of Basel). The consortium also involves international collaboration with Prof Nissim Benvenisty (Department of Genetics, The Hebrew University of Jerusalem, Israel).

        Bioinspired, Low-Cost Device for Minimally Invasive Blood Sampling
        More than 70% of medical decisions depend on laboratory results and blood sampling is the most prevalent route for disease diagnosis and monitoring. The researchers propose to develop a versatile microsampling device for the collection of blood with minimal invasiveness, low manufacturing costs and sufficient volume retrieval for point-of-care tests or laboratory analysis. This device may be particularly suited for children where traditional blood draws using needles can cause distress. A prototype will be manufactured by 3D printing and validated pre-clinically ex vivo, in vivo and in combination with a commercially available point-of-care test for the detection of malaria. PEP Fellow Dr Nicole Zoratto (currently Department of Chemistry and Pharmaceutical Technologies, Sapienza University of Rome, Italy) will join the lab of Prof Jean-Christophe Leroux (Department of Chemistry and Applied Biosciences, ETHZ).

        Electronic Clinical Decision Support and Machine Learning to Improve Care Quality and Clinical Outcomes of Sick Young Infants in Low-Resource Settings
        Almost half of all deaths in children in the first five years of life occur in the neonatal and early infant period. Electronic Clinical Decision Support Algorithms (eCDSAs) can help guide health workers in appropriate and evidence-based patient evaluation and management, and have demonstrated benefit in improving clinical care for children. However, no such tool has been validated or tested for managing sick young infants in outpatient care settings in low- and middle-income countries (LMICs). The researchers will evaluate the effects of an eCDSA for neonates and young infants on the quality of care delivered and clinical outcomes among young infants in five LMICs. The investigators aim to enhance the prognostic and diagnostic performance of the algorithm using machine learning methods. PEP Fellow Dr Gillian Levine (currently Department of Epidemiology and Public Health, Household Economics and Health Systems Research Unit, Swiss TPH) will join the research group of Dr Tracy Glass (Department of Medicine, Swiss TPH).

        Harnessing Machine Learning and Mechanistic Modelling for Personalised Radiotherapy of Paediatric Diffuse Midline Glioma
        Diffuse midline glioma, a primary tumor within the most sensitive part of the brain, is a fatal disease primarily affecting children between 4-7 years of age. The project proposes to develop a digital health tool to guide doctors in designing optimal treatment strategies for affected children and their families. The overarching aim of this project is to build a treatment decision support platform facilitating personalised radiotherapy (RT) optimisation based on MRI for afflicted paediatric patients. The researchers will develop an analytical pipeline bridging mechanistic modelling and data-driven machine learning to refine patient stratification, discover imaging biomarkers, and inform RT scheduling and dosing by an individualised radiosensitivity score. PEP Fellow Dr Sarah Brüningk (currently Department of Biosystems Science and Engineering, ETHZ) will work with Prof Catherine Jutzeler (Department of Health Sciences and Technology, ETHZ), in collaboration with Prof Karsten Borgwardt (Max Planck Institute for Biochemistry) and Prof Javad Nazarian (DMG Research Center, University Children’s Hospital Zurich).

        image: Joachim Pelikan, SwissTPH

          About the Call: The initial call for applications was launched in Fall 2020. 15 proposals were submitted with a combined total requested budget of 5’010’747 CHF. Following an external evaluation by a committee of international experts, 5 projects were recommended for full funding. The BRCCH Board approved these recommendations in May 2021.

          BRCCH Supports Travel Fellowships for Computational Biology Conference

          BRCCH Supports Travel Fellowships for [BC]2 Basel Computational Biology Conference

           

          The BRCCH provides three travel fellowships (1’666 CHF each) to PhD students and early career scientists aiming to attend the [BC]2 Basel Computational Biology Conference. Early career researchers involved in paediatric research and those from low- and middle-income countries are encouraged to apply.

          More information and APPLY at the [BC]2 website.

          The [BC]2 Basel Computational Biology Conference, September 13-15, 2021, will be more interdisciplinary than ever this year, with sessions on cancer and precision medicine, machine learning, clinical population genomics, pathogens and immune system, single-cell biology, evolutionary biology and ecology.  

          The conference will offer many opportunities for interactivity including the ELIXIR Innovation and SME Forum to learn about solutions for preventive medicine and the whole learning ecosystem of health, as well as tutorials and workshops providing an informal setting to discover and discuss about the latest bioinformatics methods.  

           

           

          BRCCH Physical Home by 2025

          BRCCH Physical Home by 2025

          visual: Kanton Basel-Stadt

           

          In a press release by the City of Basel, the canton shares news of its plans to build a new research building next to the life sciences campus Schällemätteli. The building, which will be completed by 2025, will host 4-5 research groups of the BRCCH. There is now an open anonymous project competition for a general planning team.

          Read the full press release (in German) on Kanton Basel-Stadt's website.

          Conversation with the Directors

          "We want to be measured by impact in global child health."

          It’s only a little more than two years since the BRCCH started operations. Since then, the research centre has already achieved important milestones, launched major research initiatives and sharpened its focus. In this conversation about the first two years and the future of the BRCCH, the centre's two directors, Georg Holländer and Sai Reddy, talk with journalist Felix Müller.

           

          Georg Holländer and Sai Reddy, it’s only a little more than two years since the BRCCH started operations. What would you call your biggest achievement during this initial phase?

          Georg Holländer: I'm delighted that we succeeded in putting together and starting a couple of aspirational and important programmes. First and foremost, I’d like to mention the Multi Investigator Programmes – we call them MIPs. Under their umbrella, we managed to draw together highly competitive research groups from different institutes to work on questions that otherwise could not be addressed in this fashion. The second achievement is that within these first two years, we have been able to successfully engage with our two partner universities in creating paths toward professorial posts as well as defining new areas that would align with the Centre’s research focus and benefit from further academic strength.

          Indeed, you came out of the starting blocks very fast …

          Sai Reddy: … which was not self-evident at all! ETH Zurich, University of Basel and our two additional partners, UKBB and Swiss TPH, have different philosophies, perspectives and historical strengths. This could have been a challenge for us, but we were able to pull together a very broad coalition of researchers from both universities in this short time. In a lot of ways, it's an extremely constructive and balanced constellation; we truly feel both interdisciplinary and inter-institutional. Both universities have embraced us and we, likewise, feel embedded in them.

          GH: And, thanks to the openness of these two universities and all four partners, we can count on an ongoing dialogue to underpin what we're trying to achieve.

          If you are embedded within the universities though, what about your own identity as the BRCCH?

          SR: Yes, since our current projects come from existing research groups at both universities, we are really part of them. With the recruitment of new professorships, it will help to establish a more unique identity over time.

          GH: My wish is that we will always be understood as a partner of equal standing. And that this applies to all our partners.

          When the founding of the BRCCH was announced in autumn 2018, another partner played a prominent role – Fondation Botnar, the Centre’s main donor. Was there ever any confusion about who was who?

          GH: In the beginning, we sometimes received communications that were clearly addressed to and meant to be for the foundation rather than the BRCCH. But over time it became easier for people to differentiate between the two entities. Especially the local community has embraced our BRCCH identity and our role as an independent research centre.

          COVID-19 has disrupted many organisations. How did the pandemic affect your activities?

          SR: When Fondation Botnar contributed a significant sum to a BRCCH fast track call for COVID-19 research projects, in just two weeks we received almost 80 applications.

          Two weeks? That’s an incredibly short time span to come up with a scientific research proposal.

          SR: The speed was driven by the motivation of the science community to respond swiftly. Science can move quickly if people collaborate and pull together. It is really amazing to look at what has already been learned and the data gathered about the virus to date. While not directly related to child health research, it is nevertheless critical for global health – and that means it’s critical for children’s health as the pandemic impacts families and society. Because the BRCCH also has a keen interest in supporting global health in low- and middle-income countries, areas where COVID-19 is going to continue due to lack of vaccine supply, we aim to stay on top of this and remain involved.

          GH: We have also started to see that the disease changes its face and that the causative virus mutates under selective pressure. With emerging new variants new questions also arise. And we see more and more young people, amongst them children, being affected. This area of research will clearly keep us engaged and challenged for an extended period of time.

          Indeed child health is a broad field. How do you keep the BRCCH focused?

          GH: There is so much that could and should be done in child health. But the impact and the sustainability of the BRCCH will come from the fact that we can look at and focus on a number of very relevant issues in global child health. These we can analyse in depth. The first two years of the BRCCH have focused on areas where we think, collectively with our partners, substantial step-changing contributions can be made. Even with the very generous funding available to us, we will only effectively contribute to change if we don't spread our activity too broadly and thus too thinly. We know it is important to stick to an overall strategic plan in order to deliver on our remit, but that doesn't mean the programme pursued is static – as we've just seen with COVID-19 research. We need to regularly check whether our priorities are still the correct ones; we are currently undergoing our first evaluation process as part of such an effort. After two years, this is a good time for external experts to review our research strategy and structure.

          How exactly will the external evaluation support your activities?

          GH: I hope it will provide us with a critical reflection of the focal scientific areas we have chosen and where we believe we can make a difference. The evaluation is expected to enable us to go forward in the correct direction and in a focused manner to deliver on what is needed.

          SR: This is difficult to say since it is an independent evaluation. But feedback about how to ensure our work is sustainable would be welcome, about how to build a sustainable centre that can grow as well – not simply keep to our path, but how we can be creative and adapt to that path as it unfolds.

          “Focus”, too, is a word you emphasise. So what is the BRCCH’s focus for the rest of 2021?

          SR: Soon a decision will be made on applications for a postdoc excellence programme in support of young researchers who are trying to find, and make a transition to, independent careers in child and adolescent health research. We also plan to roll out a principal investigator initiative, which is funding related to slightly smaller projects than our MIPs. Furthermore, we hope to start recruiting for three, out of a total of six, planned professorships by the end of the year.

          In which fields are the professorships?

          GH: One is in molecular diagnostics, and affiliated primarily with ETH and the Department of Biosystems Science and Engineering. The second professorship is related to digital medicine and health at University of Basel, Faculty of Medicine. And then we have a third one that is going to look at the ethics of childhood digital health and data. It too will be hosted by ETH and associated with the Department of Health Sciences and Technology.

          If we look to the future, to the end of your first 10 years in 2028: What headline would you like to read about your work?

          SR: I would hope to see a headline that would relate to our early MIPs – these are the ones that have the longest possible time to achieve their goals and make a clinical or translational impact.

          GH: I fully agree. We want to be measured by impact. But more than that – in 10 years when we look back, I hope we can say it was a good idea to bring these two universities together in the context of the BRCCH, and that through this collaboration we could make real contributions to global child health and well-being.

          To make an impact requires collaboration on local and global level. What about your networks and their growth in the past two years?

          GH: Given the design of the Centre, we largely depended on the competencies and contributions of researchers based at our partner institutions. This meant drawing on a broad network via our partner institutions at the beginning. But as we move into new and paediatric-related domains, we need to broaden and establish additional networks to complement existent expertise locally. So it’s gratifying that after only two years, we have a research portfolio that involves international collaborators from 18 countries – this augurs well for future outreach.

          Sai, Georg – final words: What were your most uplifting moments during the past two years?

          SR: For me it’s been the positive support received from all stakeholders around us – especially all our partners, our Board, Scientific Advisory Board, and clearly Fondation Botnar. Each step of the way has been met with positivity and enthusiasm. The trust we’ve been given has been really great.

          GH: Since Sai looked outside and commented on the interface with our partners, let me look inside. I'm particularly delighted to have a very collegial, hard-working team that shares a set of core values and goals that we wish to collectively achieve. I am happy to say that we are all pulling on the same strings, and singing from the same hymn sheet. That makes our endeavour so much more fun because it demonstrates a very deep common understanding about what we want to achieve.

          Thanks for your time. All the best.

           

          Interview: Felix Müller

          BRCCH and EDCTP Start a New Joint Initiative

          The BRCCH and EDCTP
          Start a New Joint Initiative

          The BRCCH and the European & Developing Countries Clinical Trials Partnership (EDCTP) are to support three multi-institutional, multi-country collaborations for research to mitigate the impact of COVID-19. Three collaborative projects are responding to the COVID-19 pandemic with research to improve the surveillance and management of COVID-19. The projects are a result of a synergistic Collaboration Initiative by EDCTP and the BRCCH to drive interdisciplinary efforts to combat global health challenges amidst the COVID-19 pandemic.

          The Collaboration Initiative:

          In 2020, each organisation launched its own emergency mechanism to support research in COVID-19. The EDCTP mechanism focused on efforts in sub-Saharan Africa to manage and/or prevent the spread of COVID-19 and targeted four thematic research gaps: therapeutics, diagnostics, serological testing, and understanding of the natural history of infection. The BRCCH Fast Track Call initiative focused on research within diagnostics, immunology and medical interventions that will help mitigate medical and public health challenges in the short term, and to also contribute solutions that will lead to better preparedness and reduced global disease burden in the long term.

          Realising the potential for collaborative efforts, the EDCTP and the BRCCH initiated dialogues between Principal Investigators (PIs) in their respective programmes. BRCCH-EDCTP consortia that wished to pursue a potential future collaboration were then invited to submit formal applications for external peer-review. The applications underwent evaluation in November 2020.

          This joint BRCCH-EDCTP Collaboration Initiative will support three projects that range from immunology to diagnostics and health screening strategies for COVID-19 in low- and middle-income country (LMIC) settings. The projects, which are a complementary extension to the ongoing research activities being funded by BRCCH and EDCTP, will launch in early 2021 and will be supported with 900,000 CHF in total funding over a period of two years. Involved BRCCH researchers are based in the centre's partner institutions: ETH Zurich, Swiss Tropical and Public Health Institute and the University Hospital Basel.

          Researchers do community outreach in remote areas in Lesotho in order to increase access to essential health services. Image: SolidarMed & Swiss TPH

           

          The Research:

          Improving Access to SARS-CoV-2 Screening and Testing through Community-based COVID-19 Case-Finding and the Use of Digital Solutions in Lesotho and Zambia
          In a collaboration between teams in Lesotho and Zambia, Dr Klaus Reither (Swiss TPH, BRCCH grantee for the MistraL project) and Dr Kwame Shanaube (Zambart, EDCTP grantee for the TREATS-COVID project) will investigate the effects of community-led interventions, rapid point-of-care diagnostics and swab self-collection in mitigating the COVID-19 epidemic in these African nations. The project will be carried out by 14-member consortium, including collaborators based at  the London School of Hygiene and Tropical Medicine, SolidarMed, FIND and KNCV Tuberculosis Foundation.

          African-European Partnership for Development and Deployment of Rapid SARS-CoV-2 RNA and Antigen Detection Assays
          Prof Janos Vörös, Prof Wendelin Stark (both ETH Zurich, BRCCH grantee for a Rapid Diagnostic Test project and for the peakPCR project, respectively) and Dr Ahmed Abd El Wahed (University of Leipzig, EDCTP grantee for the Suitcaselab project) aim to advance novel and rapid COVID-19 diagnostic technologies tailored for poor-resource and emergency settings. Including partners in France and seven African countries, the 13-PI consortium will co-develop a rapid lateral flow diagnostic assay, a portable PCR device operated in a mobile suitcase lab for use in low- and middle-income countries (LMICs). The consortium includes collaborators from the Institut Pasteur de Paris, Institut Pasteur de Dakar, Institute Pasteur de Madagascar, KNUST, University of Ibadan, INRB, University of Khartoum and Makerere University.

          COVID-19 Antibody Repertoires in Infection and Vaccination
          The project co-led by Prof Andreas Moor (ETH Zurich, BRCCH grantee for a B-Cell Immunity project) and Dr Julie Fox (King’s College London, EDCTP grantee for the COVAB project) aims to investigate B cell-mediated immunity to SARS-CoV-2 infection in different health states. Specifically, the consortium will investigate and compare the effects of SARS-CoV-2 infection on the antibody repertoire in patients who contract the virus through natural means, in COVID-19 patients who also suffer from HIV and in vaccinated individuals. This consortium involves four researchers from institutions in the UK and Switzerland (in addition to the two named above, the University Hospital Basel).

            About EDCTP:

            The mission of the European & Developing Countries Clinical Trials Partnership (EDCTP) is to reduce the social and economic burden of poverty-related diseases in developing countries, in particular sub-Saharan Africa, by accelerating the clinical development of effective, safe, accessible, suitable, and affordable medical interventions for HIV/AIDS, tuberculosis, malaria, neglected infectious diseases, lower respiratory tract infections, diarrhoeal diseases and infectious diseases of epidemic potential, including Ebola and COVID-19 . EDCTP is supported by the European Union under Horizon 2020, its Framework Programme for Research and Innovation.

            BRCCH Brochure

            Just over 2 years ago the University of Basel and ETH Zurich, with the support of Fondation Botnar, founded the BRCCH. The Centre hit the ground running and established its identity as a collaborative research center. With this brochure, the BRCCH presents further information and insight into itself and its research areas.

            Webinar: Insights Into COVID-19 Research

            Webinar: Insights Into
            COVID-19 Research

            The BRCCH invites you to join us online for free webinars on COVID-19.

            **Update September 17th, 2020 ** Thank you to everyone that attended our webinars in September! We had a great turnout-- in case you missed the presentations or you would like to watch them again, you can now stream them below or on our YouTube channel

              Description: The pandemic is placing the world in a stress test that is unprecedented. In response, organizations across sectors from research to nonprofit are mobilizing resources and taking action. This 3-part webinar series will highlight the BRCCH's ongoing collaborative research efforts in Switzerland, as well as dip into the global conversation about the current challenges and latest developments in the race to respond to the pandemic, with a focus on low- and middle-income countries.

              Sept 2nd & 9th: We will take an in-depth look into recently launched research projects focused on diagnostics and the immunology of COVID-19, as well as others focused on novel medical interventions for COVID-19. The projects are part of our recent Fast Track Initiative for COVID-19.

              Sept 16th: During the panel discussion, we will hear first hand from international experts about the current landscape of public health and how technology and partnerships spanning borders could meet current challenges in the pandemic.

              Register: closed. In case you missed the webinars, you can now watch them here (scroll down) or on our Youtube channel
              More: Download our programme below for info on the talks and speakers

              Banner image: Produced by the National Institute of Allergy and Infectious Diseases (NIAID), this highly magnified, digitally colorized transmission electron microscopic (TEM) image reveals ultrastructural details exhibited by three, spherical shaped, Middle East respiratory syndrome coronavirus (MERS-CoV) virions.

              Webinar Archive

              Prof Janos Vörös (ETH Zurich) & PD Dr Michael Osthoff (University Hospital Basel) present "A mobile, rapid diagnostic test system for COVID-19 based on lateral flow assays diagnosing SARS-CoV-2 infections at point-of-need," originally webcast on Sep 2nd, 2020.

               

              Prof Andreas Moor (ETH Zurich) presents "B cell immunity in convalescent COVID-19 patients with the aim of identifying high-affinity antibodies against SARS-CoV-2" originally webcast on Sep 2nd, 2020.

               

              Prof Melissa Penny (Swiss TPH) & Prof Roland Regoes (ETH Zurich) present "Modelling and machine learning to optimise medical interventions and health strategies for emergency response to the pandemic" originally webcast on Sep 9th, 2020.

               

              Prof Thomas Erb (University Children's Hospital Basel) & Prof Mirko Meboldt (ETH Zurich) present "The challenge of ventilation in the COVID-19 pandemic - improved patient care with low-cost ventilators based on novel integrated pressure sensors" originally webcast on Sep 9th, 2020.

               

              International Panel Discussion
              Prof Alain Labrique (Global mHealth Initiative, Johns Hopkins University) &
              Dr Solomzi Makohliso (EssentialTech, EPFL) &
              Prof Marcel Tanner (Swiss Academy of Sciences | Fondation Botnar)  &
              Akhona Tshangela (Africa Centres for Disease Control and Prevention) &
              Moderated by Dr Maxine Mackintosh (One HealthTech | The Alan Turing Institute)

              11 Projects for COVID-19 Research

              Fast Track Call (FTC) for
              Acute Global Health Challenges

              The BRCCH is pleased to announce 11 COVID-19 research consortia: The mandate of the BRCCH is to drive the development of innovative and step-changing health solutions for those who are most in need. With the support of Fondation Botnar, the BRCCH launches a new research initiative to address several critical areas related to the ongoing COVID-19 pandemic. The Initiative’s objective is to both enable research that will help mitigate medical and public health challenges in the short-term, and to also contribute solutions that will lead to better preparedness and reduced global disease burden in the long-term.

              The BRCCH Board approved the FTC external evaluation committee’s recommendation to support 11 projects that seek to deliver immediate impact in the following research areas:

                Rapid and effective consortia among BRCCH’s four partner institutions, University of Basel including University Hospital Basel (USB), ETH Zurich, University Children’s Hospital Basel (UKBB) and the Swiss Tropical and Public Health Institute (Swiss TPH), and in collaboration with research teams worldwide, will aim to address urgent health needs. The following projects start activities this month.

                Each project is considerably supported for a duration of 2.5 years.

                About the Call: The initial call for the FTC circulated on March 27th, 2020. 73 research consortia submitted project proposals on April 8th, with more than 97 (Co-) Investigators involved and total requested budget of approximately CHF 84 million. Applications were evaluated by an external and international panel of reviewers. The panel recommended to support 11 projects (success rate of 15%), which were subsequently approved by the BRCCH Board. The FTC initiative is generously supported by Fondation Botnar.

                Inaugural BRCCH Spotlight Day

                The inaugural Spotlight Day of the BRCCH marked the start of our initiative to build a community, both locally and globally, around the central mission of improving the health and well-being of children and adolescents worldwide. This event was an opportunity for local and international community to meet, start new dialogues and enable fruitful collaborations.

                More than 200 visitors joined the BRCCH at the inaugural Spotlight Day on January 30, 2020 – a great turnout to the Centre's first public event. After inspiring welcome addresses by Andrea Schenker-Wicki and Detlef Günther, four new BRCCH Multi-Investigator Projects showcased their vision for the next 5 years. Three international keynote speakers gave new perspectives on how research can be applied and translated. With this event, the BRCCH welcomed our new research projects at the Centre and the start of their research activities at the BRCCH.

                Watch a summary of the event:

                 

                Artist Alex Hughes (Drawnalism) illustrated the event:

                   

                  The event programme:

                  4 Projects Launch in Multi-Investigator Programme

                  Multi-Investigator Programme (MIP)

                  The BRCCH is pleased to announce its Multi-Investigator Programme (MIP) projects for the 2019 Call, which establish the first cornerstones of the Centre's research portfolio to improve the health and well-being of children and adolescents worldwide. MIP projects bring together researchers from its four partner institutions and therefore represent collaborative and multi-institutional research consortia.  
                  The projects will start in early 2020 and will continue for five years. The Principal Investigators will introduce their projects on the inaugural Spotlight Day of the BRCCH on Thursday, 30 January 2020 at the Zentrum für Lehre und Forschung of the University Hospital Basel.

                  The BRCCH supports the following Multi-Investigator Projects:

                  Digital Support Systems to Improve Child Health and Development in Low-Income Settings
                  In many low- and middle-income countries, families living in remote areas often have insufficient access to healthcare and health-related services to adequately support their children in the first years of their life. As a result, children’s early development is often delayed compared to children who grow up without such adversity, limiting their potential to lead a healthy and prosperous life. To address this, a new project led by Professor Günther Fink and Professor Daniel Mäusezahl will assess the extent to which a mobile phone-based interactive app can support the well-being of infants and young children growing up in low-and middle-income countries. Together with the creator of the app, Afinidata, the team will assess this platform through a study involving 2,400 families with young children in San Marcos province, Peru.  Through this study, the research team will not only learn about the potential reach and impact of the app, but will also collect feedback from local communities to further improve the app’s ability to support children’s healthy development.

                       Team members: Professor Günther Fink and Professor Daniel Mäusezahl from the Swiss Tropical and Public Health Institute from Swiss TPH, Professor Ce Zhang from ETH Zürich, Professor Stella Hartinger-Peña from the Cayetano Heredia University (UPCH), Professor Dana McCoy from the Harvard Graduate School of Education, and Andreana Castellanos, CEO of Afinidata.

                  Burden-Reduced Cleft lip and palate Care and Healing
                  Dr Andreas Mueller and Dr Barbara Solenthaler aim to simplify and optimize the surgical treatment of cleft lip and palate with the use of machine learning algorithms, smartphone-based images of the malformation, and 3D-printing of tailor-made palatal orthopedic plates. Not only will this project leverage on cutting-edge technology, but it will also aim to reduce the burden of surgery from a multi-step to a single-step procedure. The applicability of the proposed research project is especially relevant for children in low-income settings because current treatments are relatively high in cost and burdensome for the patient and his/her family which, in addition, may face challenges in securing the funding for the multiple surgeries presently needed. The project goals also allow the social reintegration of children with cleft lip and palate.
                       Team members: Dr Andreas Mueller from the University Hospital and University Children’s Hospital Basel, Dr Barbara Solenthaler from ETH Zurich, Dr Srinivas Gosla Reddy from GSR Institute of Craniofacial Surgery, Hyderabad, India, Dr Andrzej Brudnicki from the Institute of Mother and Child, Warsaw and Cleft Lip and Palate Clinic Formmed, Warsaw and Prof. Markus Gross from Disney Research.

                  Living Microbial Diagnostics to Enable Individualized Child Health Interventions
                  Malnutrition, infectious diseases and inflammatory conditions remain leading causes of illness in children living in low-and-middle income countries. In times of sickness and chronic illness, our gut microbes undergo genetic and physiological changes in response to the effects of insults such as infection or disease on the human body. Therefore, the monitoring of the changes in the gut microbiome has the potential to serve as a functional readout of the status of our health. In this project, the team led by Professor Randall Platt aims to develop a CRISPR-based technology involving engineered bacteria which are capable of sensing, remembering, and reporting on the environment within the gut. These bacteria will be utilized to provide an assessment of the nutritional, infection, and inflammation status of the gut and thereby provide a basis for individualizing and improving medical and lifestyle interventions for children and adolescents in the future.
                       Team members: Professor Randall Platt and Professor Uwe Sauer from ETH Zurich, Professor Dirk Bumann from the University of Basel and Professor Andrew Macpherson from the University of Bern.

                  Precision Microbiota Engineering for Child Health
                  From shortly after birth, the large intestine is colonized by billions of bacteria, which make up the intestinal microbiota. We are only just beginning to understand the extent and the mechanisms by which these bacteria influence child health and development. However, current studies support causal roles of these bacteria in diseases as diverse as allergy and autism. Despite this knowledge, we still have no accurate medical intervention to “fix” the microbiota. This project headed by Professor  Emma Wetter Slack develops novel tools to engineer the microbiota of individuals with inborn errors of metabolism or necrotizing enterocolitis: these conditions currently have high mortality rates, long-term consequences for child development and limited treatment options. The project aims to replace “bad” bacteria in the microbiome of the gut by “desirable” ones. This modification will be achieved with the help of engineered antibodies, and the direct targeting of individual genes in intestine-resident bacteria by employing CRISPR-Cas9 methodology. Moreover, since microbiota engineering can be applied across a wide range of childhood diseases, this effort has far-reaching implications for the future of medicine.
                       Team members: Professor Emma Wetter Slack, Professor Viola Vogel, Professor Ferdinand von Meyenn, Professor Johannes Bohacek, and Professor Shinichi Sunagawa from ETH Zürich, and Professor Médéric Diard from the University of Basel, Professor Matthias Baumgartner, Professor Johannes Häberle and Dr Sean Froese from the University Children’s Hospital Zürich, Dr Johannes Trück from the University Children’s Hospital Zürich and University of Zürich, Professor Giancarlo Natalucci from the University Hospital Zürich, Professor Christian Wolfrum from ETH Zürich, Dr Martin Behe from the Paul Scherrer Institute and Professor Adrian Egli from the University Hospital Basel.

                  About the Call: The initial call for Multi-Investigator Projects circulated in Summer 2019. 28 applications were submitted, with more than 90 (co-) investigators involved and requested funding of approximately CHF 105 million. All submitted MIP applications were rigorously evaluated by an external and independent panel of reviewers. The first evaluation round was completed in September, the second round in October 2019. Applicants that  received positive assessments in both evaluation rounds were then invited to an interview-based workshop with our international Project Evaluation Board on 24 October 2019. On the basis of these presentations and all reviews, the evaluation board proposed four projects for funding, which the BRCCH Board accepted at its meeting on 6 December.

                  Please see more information on the evaluation process. We look forward to promoting innovative and bold research projects for the health and well-being of children and adolescents worldwide!

                  Archive Application Documents