Fabini attended the Computational Microbial Ecology Workshop in Romulus, Michigan on November 2-4, 2015, hosted by Dr. Patrick Schloss of the University of Michigan. The workshop was geared towards people with interests in microbial ecology that would like to learn computer programming using the R language. It involved a blend of lecture/discussion and hands-on use of R with real data.
Learning R programming with Dr. Patrick Schloss
Yan and Fabini published a hypothesis paper entitled "The out-of-the-delta hypothesis: dense human populations in low-lying river deltas served as agents for the evolution of a deadly pathogen" in Frontiers in Microbiology. Dr. Munirul Alam, a collaborator from the International Centre for Diarrhoeal Disease Research, Bangladesh, is also co-author of the paper.
The authors propose that the unique human and physical geography of the Ganges Delta caused the naturally-occurring and nonpathogenic Vibrio cholerae to evolve into a deadly human pathogen. This is mainly due to the regular ingestion of V. cholerae through consumption of brackish water by the inhabitants of the Ganges Delta area and the subsequent release of V. cholerae back into the environment, therefore creating a continuous selection pressure for V. cholerae to adapt to life in the human gut.
The red and blue areas on the world map each house 5% of the world's population (from Boucher et al., 2015; map constructed by Max Galka, used with permission)
Members of the Boucher Lab recently published a paper, "The dynamics of genetic interactions between Vibrio metoecus and Vibrio cholerae, two close relatives co-occurring in the environment," in Genome Biology and Evolution. The known closest relative of V. cholerae is V. metoecus. The paper discusses the extent of gene exchange by horizontal gene transfer between the two species, suggesting that there is a strong bias in the direction of gene transfer from the former to the latter.
Yan, Fabini, and Paul are joined by Dr. Cheryl Tarr (Centers of Disease Control and Prevention), Raphaël Méheust (Université Pierre et Marie Curie), and Jed Barlow (Department of Computing Science) as co-authors. Jed is a former undergraduate student of the lab.
Whole genome BLAST atlas of various V. cholerae (Vc) and V. metoecus (Vm) strains (from Orata et al., 2015)
To celebrate lab members passing their candidacy exams and to welcome the new graduate students, Yan and Rebecca hosted a joint Boucher-Case lab barbecue party. Friends and family joined to celebrate as well.
Paul, Fabini, Tania, and Anna (of the Case Lab) are now official Ph.D. candidates after recently passing their candidacy exams. Tareq is the new Ph.D. student of the Boucher Lab. For the Case Lab, Yue just started his M.Sc. this month, and Albert will commence his Ph.D. in January.
Lab party!
Tareq Islam officially joins the Boucher Lab for his Ph.D.! He is originally from Dhaka, Bangladesh. He holds a B.Sc. and M.Sc. in Microbiology from the University of Dhaka. He worked as a Senior Research Officer in the Enteric and Food Microbiology Lab at the International Centre for Diarrhoeal Disease Research, Bangladesh (icddr,b) with Dr. Munirul Alam. He also worked as a visiting researcher in Dr. Rita Colwell-Dr. Anwar Huq's lab at the University of Maryland, College Park during his tenure at icddr,b. Back in the summer of 2014, Tareq assisted Yan and Tania during their field work in Bangladesh to isolate Vibrio cholerae from various regions of the Ganges Delta.
Tareq is the recipient of two awards – the University of Alberta Doctoral Recruitment Scholarship and the Alberta Innovates – Technology Futures Graduate Student Scholarship.
Welcome Tareq!
Tareq is ready for winter in Edmonton
Paul is excited to attend the Marine Biological Laboratory (MBL) Advanced Research Courses in Woods Hole, Massachusetts. He will join two courses: Workshop on Molecular Evolution (July 20-29, 2015) and Strategies and Techniques for Analyzing Microbial Population Structures (August 5-15, 2015).
In 2002, Yan attended the Microbial Biodiversity Course back when he was a Ph.D. student in Ford Doolittle's lab (Dalhousie University).
MBL is an affiliate of the University of Chicago. The workshop is supported by grants from the Howard Hughes Medical Institute, the Burroughs Wellcome Fund, and the National Institutes of Health.
Participants of the Workshop on Molecular Evolution (top) and Strategies and Techniques for Analyzing Microbial Population Structures (bottom) courses at the Marine Biological Laboratory in Woods Hole, Massachusetts
The Canadian Institute for Advanced Research (CIFAR) held its annual conference for members (and their students) of the Integrated Microbial Biodiversity (IMB) Program at the Westin Bear Mountain Golf Resort & Spa, Victoria, British Columbia on May 27-29, 2015.
Yan was accompanied by Paul. Yan gave a talk entitled "Interspecies genetic interaction in bacteria," and Paul presented a poster of his current work entitled "Ecological differentiation of Vibrio cholerae clonal complexes."
A new paper, "Ancient origin of the biosynthesis of lignin precursors," was published today in Biology Direct, with Ph.D. student Leen Labeeuw and Dr. Rebecca Case (Department of Biological Sciences) as lead and senior authors, respectively. The authors propose that the genes associated with the biosynthesis of p-coumaryl alcohol, the simplest lignin monomer, found in algal genomes likely evolved long before the transition of photosynthetic eukaryotes to land.
As co-authors, Yan contributed his expertise in phylogenetic analysis and was involved in the design of the experiment, and Dr. Patrick Martone (University of British Columbia) provided novel gene sequences for the study.
Major evolutionary events hypothesized in the evolution of the lignin biosynthetic pathway across the eukaryotic tree (from Labeeuw et al., 2015)
Tania is one of the recipients of the 2015 Graduate Student Teaching Award from the Faculty of Graduate Studies and Research (FGSR). Dr. Jonathan Schaeffer, Dean of the Faculty of Science, hosted a lunch get-together for all awardees at the Faculty Club. Congratulations!
Dr. Jonathan Schaeffer and Tania during the awarding ceremony
Congratulations to Tania and incoming Ph.D. student Tareq for receiving the Alberta Innovates – Technology Futures (AITF) Graduate Student Scholarships!
Tania is also currently a holder of the NSERC Postgraduate Scholarship – Doctoral award. Tareq will join the lab in the fall and is also the recipient of the University of Alberta Doctoral Recruitment Scholarship.
