Diversify your research skills with Peng Ye, intern at the Institut Pasteur in Paris

Ye Peng is year-3 PhD candidate at the HKU-Pasteur Research Pole, School of Public Health, LKS Faculty of Medicine. The topic of his current research is gut microbiota in health and disease.


He is a laureate of the HKU-Pasteur Research Pole Fellowship 2021 and is currently an intern at the Biological Image Analysis Laboratory under Dr Elisabeth Labruyère at the Institut Pasteur in Paris.


He shared with us his first feedbacks on pursuing his research project for 3 months at the Institut Pasteur in Paris!

What is your training background?


I received training in genetic engineering especially for synthetic biology in the first two years of my undergraduate study. From the third year of undergraduate to the end of my Master degree, I was trained as a bioinformatician specialized in metagenomics. Now in the HKU-Pasteur Research Pole, a joint laboratory between the University of Hong Kong and the Institut Pasteur, I receive training from my supervisor, Dr. Hein Min TUN, in microbiome studies using statistical, epidemiological, as well as experimental approaches. On the one hand, I study impacts of perinatal exposures on early-life programming of gut microbiota and associated health consequences. On the other hand of my research, I investigate the role of baseline gut microbiota in colonization resistance against opportunistic pathogens and in immune responses to vaccination.


Why did you choose the Institut Pasteur Biological Image Analysis Lab with Dr Elisabeth Labruyère for this research internship?


In the past few years, my research work was mostly bioinformatic and statistical analyses done on computers. As my projects progress, I identified gaps of experimental evidence to establish causality of my findings. Additionally, as a Ph.D. student, I gradually realised the need to diversify my skill set ranging from the desktop to the bench, so as to better generate and test hypotheses. I learned there is a cutting-edge “Gut-on-a-chip” technology implemented in Institut Pasteur, that mimics human guts physiology and can be colonised by complex microbiota. This technology interests me because it overcomes barriers to translating microbiota research findings from animal models to humans. Fortunately, my supervisor is in collaboration with Dr. Elisabeth Labruyère at BIA for a project named Mechabiome using this technology and advanced live imaging. So I chose this lab to learn these technologies, and to extend the original proposal and test hypotheses generated from my previous findings.


Can you tell us a little bit more about what you are doing on a daily basis at the laboratory?


My research program during these three months is commensal microbes colonizing in the gut-on-a-chip. This includes 1) experiment design and ad hoc adjustment; 2) chip preparation and cell culture; 3) bacteria culture and colonization on the chip; 4) image data acquisition and 5) image data analysis. The first four steps take one week. To maximize the number of experiments we can do to test my hypotheses, I do experiments in parallel, meaning preparing chip and cell culture for the next round while acquiring and analysing image data for the current round. Currently, as I am still green in this field, experiments in the lab are done with guidance/supervision of our collaborators to ensure security and quality.


How this new research environment can contribute to developing your ongoing research project?


I am learning mainly experiment design and image data analyses on organ-chips; I am also practicing cell culturing and chip preparation. These practices will lead to data generation for the current project. Dr. Elisabeth Labruyère, my hosting PI, shared with me an important note in experimental science, that is to think (carefully) before and after, but not during experiments. This is helpful to me because, in contrast to that in my previous bioinformatic analyses, I cannot do much ad hoc adjustment during the experiments. Beyond this project, the technologies and strategy will be applicable to and really useful for my future projects.


What has the most surprised you about this internship so far?


The most surprising part is the way people make things work out here. On the one hand, people plan their vacations long beforehand and do not let work interfere personal life. On the other hand, people work with efficiency and flexibility, and work together to progress. Members from the same lab and other labs are readily available to share their opinions and to help. Thus, questions can be answered and problems can be solved timely. The balance between work and life is well maintained, and so are energy, creativity and good mood, essential elements to advance science.


Is there any upcoming step / event in the research internship you are looking forward to?


The upcoming event I am looking forward to is the Departmental Retreat, which will be held in a Parc in holiday park in Normandy. There will be a scientific program including oral presentations, poster sections given by researchers and around table discussion. I expect to learn what are going on in the department and discuss with the presenters on interested projects. There will also be free time in between these sections for entertainments and sight-seeing in the nearby field and forest. I believe it would be a great chance to learn things and to relax.


HKU-Pasteur Fellowship Call for Application 2022 is now open: apply before December 20th!


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