content/academia/bpv-genetics.md

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----
-title: "Genetic analysis of bovine papillomas"
-date: 2024-09-19
-categories:
-  - poster
-people:
-  - Thomas A. Christensen II
-  - Rachel Palinski
-  - Bob Gentry
-journal:
-  "National Association of Animal Breeders Technical Conference Student Poster
-  session"
-location: "Middleton, Wisconsin"
----
-
-Bovine papillomavirus (BPV) is a major cause of reproductive failure in cattle.
-In bulls, penile papillomas caused by BPV may cause reluctance to breed, and is
-always a cause to fail an animal on a breeding soundness exam. Historically, it
-has been thought that BPV was transmitted via direct contact and could be
-controlled by managing clinically presenting animals in the herd, but more
-recent evidence suggests alternative modes of transmission. BPV has been found
-repeatably in clinically healthy animals, and in non-cutaneous secretions
-including milk, blood, urine and semen. Currently, no commercially available BPV
-vaccine uses isolated viral particles and naturally occurring virus does not
-produce cross-protective immunity. In order to develop a proper vaccine for
-penile papillomas further studies are required to understand the epidemiology of
-BPV in herds. While vulvar, cutaneous, and mammary papillomas have been
-genotyped in recent years, this information is not available for penile
-papillomas. In this study there were 31 submissions, collected from 7 states,
-NE, KS, NY, TX, AL, MO and SD (14 different cattle operations) Samples were
-collected between August of 2022 and April 2024. Twenty-two submissions were
-penile papillomas and with pooling of samples represented over 50 penile
-papillomas. Samples were metagenomically sequenced at the Kansas State
-Veterinary Diagnostic Lab, and the genotype of each sample was determined using
-the phylogenetic analysis. The clade of each sample was determined by aligning
-consensus sequences of the L1 gene (used for both for phylogeny and as a vaccine
-target) using MAFFT and a maximum-likelihood phylogeny generated in Mega X.
-Analysis found that all penile papilloma submissions were composed of BPV type
-2, with one sample showing co-infection with BPV type 1. Conversely, cutaneous
-and teat papillomas had BPV genotypes that were more variable with genotypes of
-1,2,7,12,14,29 and 40. These results indicate that BPV type 2 and type 1 provide
-a unified target for bovine penile papilloma vaccine development.

content/academia/got-warts-naab.md

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----
-title:
-  "Got Warts? Bovine Papillomavirus Pathogenesis, Transmission, and Vaccination"
-date: 2024-09-19
-featured: false
-categories:
-  - presentation
-people:
-  - Bob Gentry
-  - Thomas A. Christensen II
-journal:
-  "National Association of Animal Breeders Technical Conference Sponsor session"
-location: "Middleton, Wisconsin"
----

content/academia/yavsap/index.md

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----
-title: "YAVSAP: versatile viral quasispecies analysis for veterinary samples"
-date: 2024-03-05
-featured: false
-categories:
-  - presentation
-people:
-  - Thomas A. Christensen II
-  - Steven Stancic
-  - Andrea Lu
-  - Dana Mitzel
-  - William Wilson
-  - Rachel Palinski
-journal: "Phi Zeta Research Day"
-location: "Manhattan, Kansas"
-tags:
-  - virus
-  - quasispecies
-  - next-generation sequencing
-  - pipeline
-awards:
-  - "2nd Place Large Animal Applied Research Presentation"
-link: "/academia/yavsap/yavsap.pdf"
----
-
-Viral populations within an infected host are composed of viral particles with a
-spectrum of genetic mutations rather than a unified genome. This phenomenon is
-referred to as viral "quasispecies," and has been useful for the understanding
-of viral transmission and early detection of new viral variants. Next generation
-sequencing (NGS) has enabled the study of these quasispecies for many viral
-species, notably Influenza A and B, Human Immunodeficiency Virus (HIV), Foot and
-Mouth Disease Virus (FMDV), and Severe Acute Respiratory Syndrome Coronavirus 2
-(SARS CoV2), and established protocols and computer analysis tools have been
-developed for these species. Some of the most important viruses, such as
-emerging and exotic disease agents, however, do not have replicatable protocols
-or software tools capable of producing valid output from their sequence data.
-Here, we present Yet Another Viral Subspecies Analysis Pipeline (YAVSAP). YAVSAP
-is a fully automated bioinformatic pipeline built from the ground up to identify
-and analyze viral quasispecies of any arbitrary virus in human and veterinary
-samples. YAVSAP provides reference-based genome mapping of both long- and
-short-read sequencing reads to any reference genome that the user chooses,
-identifies subconsensus variants and haplotypes, and assesses the phylogenies of
-all viral sequences found within a sample. YAVSAP is written in Nextflow and
-conforms to the nf-core initiative's standards, which allows it to run on
-low-end computers, high performance computing (HPC) clusters, or anything in
-between with zero configuration. YAVSAP has been tested on viruses of interest
-to veterinary medicine and public health, including Japanese Encephalitis Virus
-(JEV), Influenza D Virus (IDV), Bovine Coronavirus (BCoV), SARS CoV2, and Rift
-Valley Fever Virus (RVFV), and can correctly identify consensus genomes and
-quasispecies within samples containing each of these viruses. This tool provides
-a means for biologists with little bioinformatic experience to analyze deep
-sequence data while correcting for many of the pitfalls associated with previous
-and current analysis platforms. YAVSAP is open source software and is publicly
-available at https://github.com/ksumngs/yavsap.