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Thomas A. Christensen II

nf-core/taxprofiler: highly parallelised and flexible pipeline for metagenomic taxonomic classification and profiling

23 Oct 2023
Sofia Stamouli Moritz E. Beber Tanja Normark Thomas A. Christensen II Lili Andersson-Li Maxime Borry Mahwash Jamy nf-core community James A. Fellows Yate

Metagenomic classification tackles the problem of characterising the taxonomic source of all DNA sequencing reads in a sample. A common approach to address the differences and biases between the many different taxonomic classification tools is to run metagenomic data through multiple classification tools and databases. This, however, is a very time-consuming task when performed manually - particularly when combined with the appropriate preprocessing of sequencing reads before the classification. Here we present nf-core/taxprofiler, a highly parallelised read-processing and taxonomic classification pipeline. Read more »

Investigation of Hydronium Diffusion in Poly(vinyl alcohol) Hydrogels: A Critical First Step to Describe Acid Transport for Encapsulated Bioremediation

02 Sep 2022
Carson J. Silsby Jonathan R. Counts Thomas A. Christensen II Mark F. Roll Kristopher V. Waynant James G. Moberly

Bioremediation of chlorinated aliphatic hydrocarbon-contaminated aquifers can be hindered by high contaminant concentrations and acids generated during remediation. Encapsulating microbes in hydrogels may provide a protective, tunable environment from inhibiting compounds; however, current approaches to formulate successful encapsulated systems rely on trial and error rather than engineering approaches because fundamental information on mass-transfer coefficients is lacking. To address this knowledge gap, hydronium ion mass-transfer rates through two commonly used hydrogel materials, poly(vinyl alcohol) and alginic acid, under two solidification methods (chemical and cryogenic) were measured. Read more »

Assessment of Porcine Rotavirus-associated virome variations in pigs with enteric disease

27 Apr 2022
Tyler Doerksen Thomas A. Christensen II Andrea Lu Lance Noll Jianfa Bai Jamie Henningson Rachel Palinski

Enteric disease is the predominant cause of morbidity and mortality in young mammals including pigs. Viral species involved in porcine enteric disease complex (PEDC) include rotaviruses, coronaviruses, picornaviruses, astroviruses and pestiviruses among others. The virome of three groups of swine samples submitted to the Kansas State University Veterinary Diagnostic Laboratory for routine testing were assessed, namely, a Rotavirus A positive (RVA) group, a Rotavirus co-infection (RV) group and a Rotavirus Negative (RV Neg) group. Read more »

Polyoxometalate Incorporation and Effects on Proton Transport in Hydrogel Polymers

07 Aug 2020
Thomas A. Christensen II

Polyoxometalate clusters embedded into hydrogel biobeads may be able to solve the challenges posed by free proton generation during remediation of trichloroethylene by acting as buffers and reducing protons to hydrogen gas. In this thesis, the challenges posed by systems that contain both diffusion and reaction processes for protons are considered mathematically, and a computer simulation to was developed to prove the relationship between diaphragm cell lag period and reactive capabilities of membranes. Read more »

Metagenomic analysis of rumen populations in week-old calves as altered by maternal late gestational nutrition and mode of delivery

12 Jun 2019
Thomas A. Christensen II Kathy J. Austin Kristi M. Cammack Hannah C. Cunningham-Hollinger

Early colonization of the rumen microbiome is critical to host health and long term performance. Factors that influence early colonization include maternal factors such as gestational nutrition and mode of delivery. Therefore, we hypothesized that late gestational nutrition and mode of delivery would influence the calf rumen microbiome. Our objectives were to determine if nutrient restriction during late gestation alters the calf rumen microbiome and determine if ruminal microbiome composition differs in calves born vaginally versus caesarean. Read more »

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The ChemE Car that Cud: AIChE ChemE Car Engineering Design Proposal

14 May 2019
Thomas A. Christensen II

The ChemE Car That Cud showcases Wyoming’s dominant industries of agriculture and mining by utilizing rumen fluid from a cannulated beef cow to generate hydrogen to be used in a hydrogen fuel cell and radioactive cesium, a byproduct of uranium that is often obtained from Wyoming’s mines, to time the car’s stop. The concentration of cesium-137 source is measured using the radioactive decay of cesium shielded by aluminum. The painted aluminum chassis was obtained from a previous team at UW, and modified using plastic k’nex toys to adapt to the current power source and stopping mechanism. Read more »

Measuring Diffusion of Trichlorethylene Breakdown Products in Polyvinylalginate

29 Oct 2018
Thomas A. Christensen II Samuel R. Wolfe Jonathan Counts Mark F. Roll Kristopher V. Waynant James G. Moberly

Trichloroethylene (TCE), a toxic and carcinogenic contaminant, presents unique challenges for cleanup because of its water solubility, density, and volatility. Bioremediation of TCE is a promising cleanup method; however, metabolism of TCE results in acid generation that inhibits remediating microorganisms. Calcium alginate(CA)-polyvinylalcohol (PVA) hydrogels show promise for protecting remediating microbes, however diffusion of TCE or its byproducts through these polymers is unknown. To measure the effective diffusion coefficient of TCE and byproducts through hydrogel membranes, we used a modified diaphragm cell. Read more »

Measuring diffusion of protons in polyvinyalginate

31 Jul 2018
Thomas A. Christensen II Jonathan Counts James G. Moberly

Trichloroethylene (TCE) is a toxic and carcinogenic contaminant that presents unique challenges for cleanup because of its density and volatility. Use of microorganisms may be a promising remediation method, however metabolism of TCE results in acid buildup, which consequently impedes the ability of microorganisms to perform this remediation. Polyvinylalginate (PVA) shows promise as a useful shield for microorganisms carrying out bioremediation of TCE by surrounding them in a protective biofilm-like layer, however, key information is missing which relates diffusion of TCE or its metabolic products through PVA. Read more »