Blog

Creating Prokaryotic Taxonomies with Whole Genomes

Contributed by Cory Schlesener, B.S. Historically it has been difficult to categorize prokaryotes into taxonomic units. Advances made have utilized DNA sequence identity to profile organisms at a higher resolution.  Older technologies based on genomic DNA hybridization, or sequence comparison of the 16s rDNA gene (PCR amplified), have greatly advanced our understanding of phylogeny, but […]

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Year Four

Contributed by DJ Darwin Bandoy, PhD Candidate I am now in my year four of my PhD studies in Integrative Pathobiology in UC Davis, still in the middle of the COVID-19 Pandemic. I presented in the lab meeting yesterday the theoretical framework of my epidemic modelling work from the UP Pandemic Response Team.  Understanding compartmental […]

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New Quality Control Program Optimized for Long Read Nucleotide Sequencing

Contributed by Cory Schlesener, B.S. DNA sequencing, in a high throughput process, generates errors in the reads, such as low confidence nucleotide based calling. Quality control is needed to evaluate the quality of the sequencing output and identify undesired features. The program FastQC (https://www.bioinformatics.babraham.ac.uk/projects/fastqc) has become one of the most popular tools for assessing quality […]

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Gut Microbiota and Unhealthy Aging

Contributed by Carol Huang, Sr. Research Specialist                      @BartWeimersLab The equilibrium of gut microbiota is fundamental to our health. The gut microbiota composition established at birth which changes with aging, diet, health condition and other factors.  As growing up the dynamic nature of gut microbiota getting […]

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Where is the metadata?

Contributed by DJ Darwin Bandoy, PhD Candidate One distinguishing feature of this pandemic is the rapid release of whole genome sequencing data. These sequences are usually uploaded in public databases with minimal accompanying metadata. While dates and geographic origin are useful for creation of phylogenetic analysis, further sophisticated analysis requires more metadata, particularly associated with […]

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Quantify Structural Similarity Comparisons of Genome Assemblies

Contributed by Cory Schlesener, B.S. One important component of a genome’s overall composition is the larger structure of how conserved blocks of genetic sequence are arranged. As segments of DNA recombine, sequences are introduced into new locations and/or orientations in a genome. However, this composition of large genetic blocks can artificially be rearranged in a constructed genome […]

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More on the Equine Microbiome

Contributed by Ashleigh Flores, M.S. Within the GI Tract, horses can host up to 1015 bacterial cells, with the highest population residing within the caecum. Recent studies have revealed that distinct individual ecosystems for each compartment of the equine gut exist, with adjacent compartments having the most similarities in microbiome composition. The upper GI tract […]

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Pandemic Status as of July 12, 2020

Contributed by DJ Darwin Bandoy, Ph.D. Candidate California is in full lockdown again after a surge in cases. This is a consequence of opening too early when the cases are not fully suppressed. This requires people to wear masks, practice physical distancing, and a reduction of unnecessary travel. Heterogeneous properties of infection indicate super-spreading events […]

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Professor Bart C. Weimer, Ph.D.

Professor, School of Veterinary Medicine,       UC Davis        Director, 100K Pathogen Genome Project  Publication Summary: 22 book chapters 4 books 159 manuscripts 6 patents awarded 13 invention disclosures 540 presentations Google Scholar, ResearchGate, Orcid, ReseacherID (Publons)  UCDavis Microbiome Special Research Program Leadership Experience: Chair; Department of Population Health and Reproduction. 2019 – present Director, founder; Genomes4Health. 2019 […]

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Horses and “Pigeon Fever”

Contributed by Ashleigh Flores, M.S. Corynebacterium pseudotuberculosis biovar equi is responsible for the highly contagious disease in horses commonly known as “Pigeon Fever”. Although flies act as the primary vector, soil serves as a reservoir for this robust microorganism. Research has shown that C. pseudotuberculosis can persist in soil for months at a time, particularly […]

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