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    <title>Academic Publications and Presentations on MillironX</title>
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    <description>Recent content in Academic Publications and Presentations on MillironX</description>
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    <lastBuildDate>Thu, 19 Sep 2024 00:00:00 +0000</lastBuildDate>
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      <title>Genetic analysis of bovine papillomas</title>
      <link>http://localhost:1313/academia/bpv-genetics/</link>
      <pubDate>Thu, 19 Sep 2024 00:00:00 +0000</pubDate>
      <guid>http://localhost:1313/academia/bpv-genetics/</guid>
      <description>&lt;p&gt;Bovine papillomavirus (BPV) is a major cause of reproductive failure in cattle.&#xA;In bulls, penile papillomas caused by BPV may cause reluctance to breed, and is&#xA;always a cause to fail an animal on a breeding soundness exam. Historically, it&#xA;has been thought that BPV was transmitted via direct contact and could be&#xA;controlled by managing clinically presenting animals in the herd, but more&#xA;recent evidence suggests alternative modes of transmission. BPV has been found&#xA;repeatably in clinically healthy animals, and in non-cutaneous secretions&#xA;including milk, blood, urine and semen. Currently, no commercially available BPV&#xA;vaccine uses isolated viral particles and naturally occurring virus does not&#xA;produce cross-protective immunity. In order to develop a proper vaccine for&#xA;penile papillomas further studies are required to understand the epidemiology of&#xA;BPV in herds. While vulvar, cutaneous, and mammary papillomas have been&#xA;genotyped in recent years, this information is not available for penile&#xA;papillomas. In this study there were 31 submissions, collected from 7 states,&#xA;NE, KS, NY, TX, AL, MO and SD (14 different cattle operations) Samples were&#xA;collected between August of 2022 and April 2024. Twenty-two submissions were&#xA;penile papillomas and with pooling of samples represented over 50 penile&#xA;papillomas. Samples were metagenomically sequenced at the Kansas State&#xA;Veterinary Diagnostic Lab, and the genotype of each sample was determined using&#xA;the phylogenetic analysis. The clade of each sample was determined by aligning&#xA;consensus sequences of the L1 gene (used for both for phylogeny and as a vaccine&#xA;target) using MAFFT and a maximum-likelihood phylogeny generated in Mega X.&#xA;Analysis found that all penile papilloma submissions were composed of BPV type&#xA;2, with one sample showing co-infection with BPV type 1. Conversely, cutaneous&#xA;and teat papillomas had BPV genotypes that were more variable with genotypes of&#xA;1,2,7,12,14,29 and 40. These results indicate that BPV type 2 and type 1 provide&#xA;a unified target for bovine penile papilloma vaccine development.&lt;/p&gt;</description>
    </item>
    <item>
      <title>Got Warts? Bovine Papillomavirus Pathogenesis, Transmission, and Vaccination</title>
      <link>http://localhost:1313/academia/got-warts-naab/</link>
      <pubDate>Thu, 19 Sep 2024 00:00:00 +0000</pubDate>
      <guid>http://localhost:1313/academia/got-warts-naab/</guid>
      <description></description>
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    <item>
      <title>YAVSAP: versatile viral quasispecies analysis for veterinary samples</title>
      <link>http://localhost:1313/academia/yavsap/</link>
      <pubDate>Tue, 05 Mar 2024 00:00:00 +0000</pubDate>
      <guid>http://localhost:1313/academia/yavsap/</guid>
      <description>&lt;p&gt;Viral populations within an infected host are composed of viral particles with a&#xA;spectrum of genetic mutations rather than a unified genome. This phenomenon is&#xA;referred to as viral &amp;ldquo;quasispecies,&amp;rdquo; and has been useful for the understanding&#xA;of viral transmission and early detection of new viral variants. Next generation&#xA;sequencing (NGS) has enabled the study of these quasispecies for many viral&#xA;species, notably Influenza A and B, Human Immunodeficiency Virus (HIV), Foot and&#xA;Mouth Disease Virus (FMDV), and Severe Acute Respiratory Syndrome Coronavirus 2&#xA;(SARS CoV2), and established protocols and computer analysis tools have been&#xA;developed for these species. Some of the most important viruses, such as&#xA;emerging and exotic disease agents, however, do not have replicatable protocols&#xA;or software tools capable of producing valid output from their sequence data.&#xA;Here, we present Yet Another Viral Subspecies Analysis Pipeline (YAVSAP). YAVSAP&#xA;is a fully automated bioinformatic pipeline built from the ground up to identify&#xA;and analyze viral quasispecies of any arbitrary virus in human and veterinary&#xA;samples. YAVSAP provides reference-based genome mapping of both long- and&#xA;short-read sequencing reads to any reference genome that the user chooses,&#xA;identifies subconsensus variants and haplotypes, and assesses the phylogenies of&#xA;all viral sequences found within a sample. YAVSAP is written in Nextflow and&#xA;conforms to the nf-core initiative&amp;rsquo;s standards, which allows it to run on&#xA;low-end computers, high performance computing (HPC) clusters, or anything in&#xA;between with zero configuration. YAVSAP has been tested on viruses of interest&#xA;to veterinary medicine and public health, including Japanese Encephalitis Virus&#xA;(JEV), Influenza D Virus (IDV), Bovine Coronavirus (BCoV), SARS CoV2, and Rift&#xA;Valley Fever Virus (RVFV), and can correctly identify consensus genomes and&#xA;quasispecies within samples containing each of these viruses. This tool provides&#xA;a means for biologists with little bioinformatic experience to analyze deep&#xA;sequence data while correcting for many of the pitfalls associated with previous&#xA;and current analysis platforms. YAVSAP is open source software and is publicly&#xA;available at &lt;a&#xA;  href=&#34;https://github.com/ksumngs/yavsap&#34;&gt;https://github.com/ksumngs/yavsap&lt;/a&gt;.&lt;/p&gt;</description>
    </item>
    <item>
      <title>nf-core/taxprofiler: highly parallelised and flexible pipeline for metagenomic taxonomic classification and profiling</title>
      <link>http://localhost:1313/academia/taxprofiler/</link>
      <pubDate>Mon, 23 Oct 2023 00:00:00 +0000</pubDate>
      <guid>http://localhost:1313/academia/taxprofiler/</guid>
      <description>&lt;p&gt;Metagenomic classification tackles the problem of characterising the taxonomic&#xA;source of all DNA sequencing reads in a sample. A common approach to address the&#xA;differences and biases between the many different taxonomic classification tools&#xA;is to run metagenomic data through multiple classification tools and databases.&#xA;This, however, is a very time-consuming task when performed manually -&#xA;particularly when combined with the appropriate preprocessing of sequencing&#xA;reads before the classification. Here we present nf-core/taxprofiler, a highly&#xA;parallelised read-processing and taxonomic classification pipeline. It is&#xA;designed for the automated and simultaneous classification and/or profiling of&#xA;both short- and long-read metagenomic sequencing libraries against a 11&#xA;taxonomic classifiers and profilers as well as databases within a single&#xA;pipeline run. Implemented in Nextflow and as part of the nf-core initiative, the&#xA;pipeline benefits from high levels of scalability and portability, accommodating&#xA;from small to extremely large projects on a wide range of computing&#xA;infrastructure. It has been developed following best-practise software&#xA;development practises and community support to ensure longevity and adaptability&#xA;of the pipeline, to help keep it up to date with the field of metagenomics.&lt;/p&gt;</description>
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    <item>
      <title>Investigation of Hydronium Diffusion in Poly(vinyl alcohol) Hydrogels: A Critical First Step to Describe Acid Transport for Encapsulated Bioremediation</title>
      <link>http://localhost:1313/academia/hydronium-pva/</link>
      <pubDate>Fri, 02 Sep 2022 00:00:00 +0000</pubDate>
      <guid>http://localhost:1313/academia/hydronium-pva/</guid>
      <description>&lt;p&gt;Bioremediation of chlorinated aliphatic hydrocarbon-contaminated aquifers can be&#xA;hindered by high contaminant concentrations and acids generated during&#xA;remediation. Encapsulating microbes in hydrogels may provide a protective,&#xA;tunable environment from inhibiting compounds; however, current approaches to&#xA;formulate successful encapsulated systems rely on trial and error rather than&#xA;engineering approaches because fundamental information on mass-transfer&#xA;coefficients is lacking. To address this knowledge gap, hydronium ion&#xA;mass-transfer rates through two commonly used hydrogel materials, poly(vinyl&#xA;alcohol) and alginic acid, under two solidification methods (chemical and&#xA;cryogenic) were measured. Variations in hydrogel crosslinking conditions,&#xA;polymer composition, and solvent ionic strength were investigated to understand&#xA;how each influenced hydronium ion diffusivity. A three-way ANOVA indicated that&#xA;the ionic strength, membrane type, and crosslinking method significantly (&lt;em&gt;p&lt;/em&gt; &amp;lt;&#xA;0.001) contributed to changes in hydronium ion mass transfer. Hydronium ion&#xA;diffusion increased with ionic strength, counter to what is observed in&#xA;aqueous-only (no polymer) solutions. Co-occurring mechanisms correlated to&#xA;increased hydronium ion diffusion with ionic strength included an increased&#xA;water fraction within hydrogel matrices and hydrogel contraction. Measured&#xA;diffusion rates determined in this study provide first principal design&#xA;information to further optimize encapsulating hydrogels for bioremediation.&lt;/p&gt;</description>
    </item>
    <item>
      <title>Assessment of Porcine Rotavirus-associated virome variations in pigs with enteric disease</title>
      <link>http://localhost:1313/academia/rotavirus-virome/</link>
      <pubDate>Wed, 27 Apr 2022 00:00:00 +0000</pubDate>
      <guid>http://localhost:1313/academia/rotavirus-virome/</guid>
      <description>&lt;p&gt;Enteric disease is the predominant cause of morbidity and mortality in young&#xA;mammals including pigs. Viral species involved in porcine enteric disease&#xA;complex (PEDC) include rotaviruses, coronaviruses, picornaviruses, astroviruses&#xA;and pestiviruses among others. The virome of three groups of swine samples&#xA;submitted to the Kansas State University Veterinary Diagnostic Laboratory for&#xA;routine testing were assessed, namely, a Rotavirus A positive (RVA) group, a&#xA;Rotavirus co-infection (RV) group and a Rotavirus Negative (RV Neg) group. All&#xA;groups were designated by qRT-PCR results testing for Porcine Rotavirus A, B, C&#xA;and H such that samples positive for RVA only went in the RVA group, samples&#xA;positive for &amp;gt;1 rotavirus went in the RV group and samples negative for all were&#xA;grouped in the RVNeg group. All of the animals had clinical enteric disease&#xA;resulting in scours and swollen joints/lameness, enlarged heart and/or a cough.&#xA;All samples were metagenomic sequenced and analyzed for viral species&#xA;composition that identified 14 viral species and eight bacterial viruses/phages.&#xA;Sapovirus and Escherichia coli phages were found at a high prevalence in RVA and&#xA;RV samples but were found at low or no prevalence in the RV Neg samples.&#xA;Picobirnavirus was identified at a high proportion and prevalence in RV Neg and&#xA;RV samples but at a low prevalence in the RVA group. A sequence analysis of the&#xA;possible host of Picobirnaviruses revealed fungi as the most likely host.&#xA;Non-rotaviral diversity was highest in RVA samples followed by RV then RV Neg&#xA;samples. Various sequences were extracted from the sample reads and a&#xA;phylogenetic update was provided showing a high prevalence of G9 and P[23] RVA&#xA;genotypes. These data are important for pathogen surveillance and control&#xA;measures&lt;/p&gt;</description>
    </item>
    <item>
      <title>Polyoxometalate Incorporation and Effects on Proton Transport in Hydrogel Polymers</title>
      <link>http://localhost:1313/academia/thesis/</link>
      <pubDate>Fri, 07 Aug 2020 00:00:00 +0000</pubDate>
      <guid>http://localhost:1313/academia/thesis/</guid>
      <description>&lt;p&gt;Polyoxometalate clusters embedded into hydrogel biobeads may be able to solve&#xA;the challenges posed by free proton generation during remediation of&#xA;trichloroethylene by acting as buffers and reducing protons to hydrogen gas. In&#xA;this thesis, the challenges posed by systems that contain both diffusion and&#xA;reaction processes for protons are considered mathematically, and a computer&#xA;simulation to was developed to prove the relationship between diaphragm cell lag&#xA;period and reactive capabilities of membranes. Two polyoxometalate compounds,&#xA;sodium decavanadate and alumina sulfate, were successfully incorporated into a&#xA;poly(vinyl alcohol) hydrogel membrane, and the diffusivity changes associated&#xA;with each compound was determined. It was found that the diffusivity of protons&#xA;through an unmodified 10% w/v poly(vinyl alcohol) membrane was 1.76 ×&#xA;10&lt;sup&gt;-5&lt;/sup&gt;&#xA; cm&lt;sup&gt;2&lt;/sup&gt;&#xA; s&lt;sup&gt;-1&lt;/sup&gt;&#xA;, the diffusivity through a&#xA;10%/2% w/w/v poly(vinyl alcohol)/sodium decavanadate membrane was 3.10 ×&#xA;10&lt;sup&gt;-6&lt;/sup&gt;&#xA; cm&lt;sup&gt;2&lt;/sup&gt;&#xA; s&lt;sup&gt;-1&lt;/sup&gt;&#xA;, and the diffusivity through a&#xA;10%/2% w/w/v poly(vinyl alcohol)/alumina sulfate membrane was 3.32 ×&#xA;10&lt;sup&gt;-7&lt;/sup&gt;&#xA; cm&lt;sup&gt;2&lt;/sup&gt;&#xA; s&lt;sup&gt;-1&lt;/sup&gt;&#xA;. Through analysis of the&#xA;diaphragm cell lag period, it was found the incorporation of sodium decavanadate&#xA;did not increase the reactivity of a poly(vinyl alcohol) hydrogel, and&#xA;incorporation of alumina sulfate lowered the reactivity. These results indicate&#xA;that polyoxometalate integration into hydrogel membranes is feasible, but does&#xA;not provide any advantage to a bioremediation scenario.&lt;/p&gt;</description>
    </item>
    <item>
      <title>Metagenomic analysis of rumen populations in week-old calves as altered by maternal late gestational nutrition and mode of delivery</title>
      <link>http://localhost:1313/academia/metagenomics/</link>
      <pubDate>Wed, 12 Jun 2019 00:00:00 +0000</pubDate>
      <guid>http://localhost:1313/academia/metagenomics/</guid>
      <description>&lt;p&gt;Early colonization of the rumen microbiome is critical to host health and long&#xA;term performance. Factors that influence early colonization include maternal&#xA;factors such as gestational nutrition and mode of delivery. Therefore, we&#xA;hypothesized that late gestational nutrition and mode of delivery would&#xA;influence the calf rumen microbiome. Our objectives were to determine if&#xA;nutrient restriction during late gestation alters the calf rumen microbiome and&#xA;determine if ruminal microbiome composition differs in calves born vaginally&#xA;versus caesarean. Late gestating Angus cows were randomly allocated to one of&#xA;three treatment groups: control (&lt;strong&gt;CON&lt;/strong&gt;; n = 6), caesarean section (&lt;strong&gt;CS&lt;/strong&gt;; n =&#xA;4), and nutrient restricted (&lt;strong&gt;NR&lt;/strong&gt;; n = 5), where CON were fed DDGS and hay to&#xA;meet NRC requirements and calved naturally; CS were fed similarly to CON and&#xA;calves were born via caesarean section; and NR were fed at a level to reduce BCS&#xA;by 1.5-2.0 points over the last trimester compared to CON and calved naturally.&#xA;Rumen fluid was collected via oral lavage prior to partition from cows and at d&#xA;7 from calves. Microbial DNA was isolated from the rumen fluid and metagenomic&#xA;shotgun sequencing was performed using the Illumina HiSeq 2500 platform.&#xA;Sequence data were analyzed using Metaxa2 for taxonomic assignment followed by&#xA;QIIME1 and QIIME2 to determine differential abundance and alpha- and&#xA;beta-diversity differences. There were no significant differences in&#xA;alpha-diversity as measured by shannon index across treatment groups for cows&#xA;(&lt;em&gt;P&lt;/em&gt; = 0.239), but there were significant differences for calves (&lt;em&gt;P&lt;/em&gt; = 0.015).&#xA;Similarly, there were no significant differences in beta-diversity as measured&#xA;by the bray-curtis dissimilarity matrix for cows (&lt;em&gt;P&lt;/em&gt; = 0.059), but there were&#xA;significant differences for calves (&lt;em&gt;P&lt;/em&gt; = 0.007). Alpha-diversity differed (&lt;em&gt;P&lt;/em&gt;&#xA;&amp;lt; 0.001) between cows and calves, with cows having increased species richness&#xA;compared to calves. Beta-diversity also differed (&lt;em&gt;P&lt;/em&gt; = 0.001) between cows and&#xA;calves. At total of 410 taxa were differentially abundant (&lt;em&gt;P&lt;/em&gt; &amp;lt; 0.01) between&#xA;cows and calves. These results suggest that the mature rumen microbiome of cows&#xA;is able to withstand changes in feed intake, however the calf microbiome is&#xA;susceptible to alteration by maternal factors. These data also suggest that&#xA;there may be opportunities to develop management strategies during late&#xA;gestation that influence calf health and performance long-term.&lt;/p&gt;</description>
    </item>
    <item>
      <title>The ChemE Car that Cud: AIChE ChemE Car Engineering Design Proposal</title>
      <link>http://localhost:1313/academia/cheme-car/</link>
      <pubDate>Tue, 14 May 2019 00:00:00 +0000</pubDate>
      <guid>http://localhost:1313/academia/cheme-car/</guid>
      <description>&lt;p&gt;The ChemE Car That Cud showcases Wyoming&amp;rsquo;s dominant industries of agriculture&#xA;and mining by utilizing rumen fluid from a cannulated beef cow to generate&#xA;hydrogen to be used in a hydrogen fuel cell and radioactive cesium, a byproduct&#xA;of uranium that is often obtained from Wyoming&amp;rsquo;s mines, to time the car&amp;rsquo;s stop.&#xA;The concentration of cesium-137 source is measured using the radioactive decay&#xA;of cesium shielded by aluminum. The painted aluminum chassis was obtained from a&#xA;previous team at UW, and modified using plastic k&amp;rsquo;nex toys to adapt to the&#xA;current power source and stopping mechanism.&lt;/p&gt;</description>
    </item>
    <item>
      <title>Measuring Diffusion of Trichlorethylene Breakdown Products in Polyvinylalginate</title>
      <link>http://localhost:1313/academia/pva-aiche/</link>
      <pubDate>Mon, 29 Oct 2018 00:00:00 +0000</pubDate>
      <guid>http://localhost:1313/academia/pva-aiche/</guid>
      <description>&lt;p&gt;Trichloroethylene (TCE), a toxic and carcinogenic contaminant, presents unique&#xA;challenges for cleanup because of its water solubility, density, and volatility.&#xA;Bioremediation of TCE is a promising cleanup method; however, metabolism of TCE&#xA;results in acid generation that inhibits remediating microorganisms. Calcium&#xA;alginate(CA)-polyvinylalcohol (PVA) hydrogels show promise for protecting&#xA;remediating microbes, however diffusion of TCE or its byproducts through these&#xA;polymers is unknown. To measure the effective diffusion coefficient of TCE and&#xA;byproducts through hydrogel membranes, we used a modified diaphragm cell.&#xA;Measured effective diffusion coefficient of each species was (cm &lt;sup&gt;2&lt;/sup&gt;&#xA;/s&#xA;× 10&lt;sup&gt;6&lt;/sup&gt;&#xA;): 14.0 ± 1.91 for H&lt;sup&gt;&amp;#43;&lt;/sup&gt;&#xA; ions, 12.4 ± 1.64 for TCE,&#xA;7.83 ± 0.54 for cis-1,2-dichloroethylene (DCE), and 4.68 ± 4.14 for vinyl&#xA;chloride. These results aid in engineering biobeads and suggest that CA-PVA&#xA;hydrogel blends are effective in slowing diffusion of protons, buffering acids&#xA;produced by trichloroethylene metabolism, and remains suitable for encapsulation&#xA;of microorganisms involved in bioremediation.&lt;/p&gt;</description>
    </item>
    <item>
      <title>How to Build a Cow-Cud Fuel Cell</title>
      <link>http://localhost:1313/academia/how-to-build-a-cow-cud-fuel-cell/</link>
      <pubDate>Wed, 01 Aug 2018 00:00:00 +0000</pubDate>
      <guid>http://localhost:1313/academia/how-to-build-a-cow-cud-fuel-cell/</guid>
      <description></description>
    </item>
    <item>
      <title>Measuring diffusion of protons in polyvinyalginate</title>
      <link>http://localhost:1313/academia/pva-inbre/</link>
      <pubDate>Tue, 31 Jul 2018 00:00:00 +0000</pubDate>
      <guid>http://localhost:1313/academia/pva-inbre/</guid>
      <description>&lt;p&gt;Trichloroethylene (TCE) is a toxic and carcinogenic contaminant that presents&#xA;unique challenges for cleanup because of its density and volatility. Use of&#xA;microorganisms may be a promising remediation method, however metabolism of TCE&#xA;results in acid buildup, which consequently impedes the ability of&#xA;microorganisms to perform this remediation. Polyvinylalginate (PVA) shows&#xA;promise as a useful shield for microorganisms carrying out bioremediation of TCE&#xA;by surrounding them in a protective biofilm-like layer, however, key information&#xA;is missing which relates diffusion of TCE or its metabolic products through PVA.&#xA;To measure the effective diffusion coefficient of H&lt;sup&gt;&amp;#43;&lt;/sup&gt;&#xA; ions through&#xA;a PVA membrane cross-linked with boric acid and calcium ions, we used a modified&#xA;diaphragm cell. We found the effective diffusion coefficient to be 1.40 ×&#xA;10&lt;sup&gt;-5&lt;/sup&gt;&#xA; ± 1.91 × 10&lt;sup&gt;-6&lt;/sup&gt;&#xA; cm&lt;sup&gt;2&lt;/sup&gt;&#xA;s, a nearly&#xA;seven-fold decrease in diffusivity compared to protons in water, with an&#xA;unexpected significant but as of yet unquantified adsorption capacity. These&#xA;results suggest that polyvinylalginate is effective in slowing diffusion of&#xA;protons and buffering these acids produced by trichloroethylene metabolism, and&#xA;remains suitable for encapsulation of microorganisms involved in bioremediation.&lt;/p&gt;</description>
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