Cleo is enrolled in the Masters of Biotechnology program at UPenn. As part of the molecular biology track within this program, Cleo is doing her independent study in the lab and is working with some of the bacterial isolates from our canine IBD study to try to set-up in vitro systems to study microbe-microbe interactions between bile acid producers and pathobionts.
Eman is senior at the University of the Sciences Philadelphia (USP), and is spending the Spring semester working in the lab on an independent study project. Eman is new to bench research and is getting acquainted with fundamental techniques in molecular microbiology.
Olivia is a PhD student in the Microbiology, Virology and Parasitology (MVP) Graduate group and spent her 2nd rotation with us. Olivia’s project is focused on the development of Selective Whole Genome Amplification (SWGA) to study the skin-dwelling parasite, Leishmania braziliensis. She will test whether specially designed primer sets are capable of selectively amplifying L. braziliensis DNA even in the presence of substantial human DNA contamination. If successful, this would constitute a breakthrough for the leishmania research field that would allow researchers to amplify whole L. braziliensis genomes directly from patient material to carry out population genetic studies of this important pathogen, without the need to culture or enrich parasites.
Wojtek joined the lab in November of 2019 as our first bona fide programmer. He came to us from the Sanger Institute, where he served as the primary developer of Wormbase paraSite. His role on our team is to advance our microbiomeDB project, and he works closely with the larger VEuPathDB team that is our partner in this effort. Wojtek has loaded large enteric disease datasets in microbiomeDB, and is currently working on developing private user workspaces and new tools for handling shotgun metagenomic data.
Camila initially came to spend a year in the lab as a PhD student participating in Brazil’s ‘sandwich’ program. During this time, she fell in love with bioinformatics and returned after her PhD to start a postdoc jointly between our lab and the laboratory of Phil Scott. Since she started her postdoc in January of 2018, she has taken the lead on advancing our understanding of the transcriptional response that drives skin pathology during cutaneous leishmaniasis. Her recent work identified key biomarkers that predict patient outcomes even before the first treatment has begun. Currently, she is working to integrate data from multiple tissues and assays generated from patients in Brazil, in an effort improve our understanding of disease development.
Alex completed his PhD in biology at UPenn, working in Dustin Brisson’s lab where he studied the population genetics of Trypanosoma cruzi in Peru. He joined us as a postdoc in August of 2018, and immediately began working on microbiome projects. He was the first to show that natural parasite infections are a dominant factor in shaping microbiome structure in humans and animals (preprint here), and he continues to advance microbiome projects that leverage veterinary animal models. In addition, Alex has played a key role in supporting and developing our transcriptomics course, and is currently writing up a manuscript that outlines a model for how this class could be broadly utilized for teaching transcriptomics to parasitology and immunology researchers in the US as well as in in lower- and middle-income countries.
Elise completed a dual Master’s degree in Biology and Design at Drexel University, and is interested in interdisciplinary science that incorporates elements of design. She joined us in July 2019 and is the primary person working with collaborators to plan, develop and manage high-throughput sequencing projects, ranging from transcriptome studies, single-cell seq, 16S rRNA profiling and shotgun metagenomics.
For nearly 20 years I have studied host-microbial interactions, with a primary focus on leveraging genomic and bioinformatic approaches to elucidate mechanisms that regulate inflammation and host defense during infection with zoonotic microbes. During my PhD in Judy Appleton’s lab at Cornell University’s Baker Institute for Animal Health, I studied the immune response during chronic infection with the parasitic helminth, Trichinella spiralis. This work led to the identification of the cytokines IL10 and TGF-β, and eosinophils, as critical regulators of inflammation and immunity to chronic helminth infection. As as postdoc in David Roos’ lab at UPenn, my work shifted from helminth to protozoan parasites, and I began to employ genome-wide transcriptional profiling and genetic screens to identify novel players involved signaling pathways that regulate both immunity and pathogenic inflammation. The results of these studies helped shed light on important immune effector mechanisms, ranging from IL27 signaling in Tregs, to identifying novel enhancers of STAT1 signaling, to reactive oxygen species production by infected monocytes, to TLR3-dependent type I interferon production. In January of 2013, I began a faculty position in the School of Veterinary Medicine at UPenn, were I Co-founded and continue to Co-direct the Center for Host-Microbial Interactions (CHMI). My primary research mission in this role is to develop interdisciplinary ‘One-health’ projects related to microbiology and infectious diseases. In parallel with my research program, I work to engage trainees at the University level in bioinformatics training for managing and analyzing genomic datasets.
Amanda is a PhD student in the Immunology Graduate Group (IGG) and spent her 1st rotation with us. The goal of Amanda’s project was to interrogate the host transcriptional response during infection-induced dysbiosis, and to identify the microbes or microbial factors associated with inflammation leading to sepsis. Amanda used an infection with Toxoplasma gondii to induce severe dysbiosis fand collected gut tissue, stool and created a microbial isolate collection from mice at 0, 2, 5, and 8 days post-infection. Amanda then worked to isolate RNA from these tissues and prepare sequence-ready libraries. The goal of this project is to try to use RNAseq to simultaneous profile host and microbial gene expression during dysbiosis. This data set will provide insight into microbial community structure AND function during dysbiosis, as well as profiling the host response…all from the same sample.
Jake is a PhD student in the Genomics and Computational Biology (GCB) graduate group and spent his 2nd rotation with us. He employed ‘hybrid’ (short + long read) genome assembly methods to generate one of the first complete genomes for Clostridium hiranonis, a bile-acid producing member of the gut microbiome that is implicated in maintaining gut health through the production of secondary bile acids. Jake then annotated this genome and used comparative genomic approaches to understand population genetics of C. hiranonis across animals and humans. Since there is only one other complete genome available for this organism, Jake turned to mining our shotgun metagenomic data from animal stool samples and identified ~20 samples for which the metagenomic reads provide at least 100x coverage of the C. hiranonis genome. He used contigs from the metagenome assembled genomes (MAGs) in his comparative analysis.