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Academic Publications and Presentations

Selected Presentations

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

Tyler Doerksen, Thomas A. Christensen II, Andrea Lu, Lance Noll, Jianfa Bai, Jamie Henningson, Rachel Palinski
Veterinary Microbiology: (27 Apr 2022)
Keywords: porcine rotavirus porcine enteric disease virome rotavirus

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. All groups were designated by qRT-PCR results testing for Porcine Rotavirus A, B, C and H such that samples positive for RVA only went in the RVA group, samples positive for >1 rotavirus went in the RV group and samples negative for all were grouped in the RVNeg group. All of the animals had clinical enteric disease resulting in scours and swollen joints/lameness, enlarged heart and/or a cough. All samples were metagenomic sequenced and analyzed for viral species composition that identified 14 viral species and eight bacterial viruses/phages. Sapovirus and Escherichia coli phages were found at a high prevalence in RVA and RV samples but were found at low or no prevalence in the RV Neg samples. Picobirnavirus was identified at a high proportion and prevalence in RV Neg and RV samples but at a low prevalence in the RVA group. A sequence analysis of the possible host of Picobirnaviruses revealed fungi as the most likely host. Non-rotaviral diversity was highest in RVA samples followed by RV then RV Neg samples. Various sequences were extracted from the sample reads and a phylogenetic update was provided showing a high prevalence of G9 and P[23] RVA genotypes. These data are important for pathogen surveillance and control measures

Polyoxometalate Incorporation and Effects on Proton Transport in Hydrogel Polymers

Thomas A. Christensen II
University of Idaho: Moscow, Idaho (07 Aug 2020)
Keywords: bioremediation polyoxometalate hydrogel polymers proton transport chemical engineering

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. Two polyoxometalate compounds, sodium decavanadate and alumina sulfate, were successfully incorporated into a poly(vinyl alcohol) hydrogel membrane, and the diffusivity changes associated with each compound was determined. It was found that the diffusivity of protons through an unmodified 10% w/v poly(vinyl alcohol) membrane was 1.76 × 10-5 cm2 s-1 , the diffusivity through a 10%/2% w/w/v poly(vinyl alcohol)/sodium decavanadate membrane was 3.10 × 10-6 cm2 s-1 , and the diffusivity through a 10%/2% w/w/v poly(vinyl alcohol)/alumina sulfate membrane was 3.32 × 10-7 cm2 s-1 . Through analysis of the diaphragm cell lag period, it was found the incorporation of sodium decavanadate did not increase the reactivity of a poly(vinyl alcohol) hydrogel, and incorporation of alumina sulfate lowered the reactivity. These results indicate that polyoxometalate integration into hydrogel membranes is feasible, but does not provide any advantage to a bioremediation scenario.

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

Thomas A. Christensen II, Kathy J. Austin, Kristi M. Cammack, Hannah C. Cunningham-Hollinger
Westion Section American Society of Animal Science Annual Meeting: Boise, Idaho (12 Jun 2019)
Keywords: gestation metagenomics microbiome rumen

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. Late gestating Angus cows were randomly allocated to one of three treatment groups: control (CON; n = 6), caesarean section (CS; n = 4), and nutrient restricted (NR; n = 5), where CON were fed DDGS and hay to meet NRC requirements and calved naturally; CS were fed similarly to CON and calves were born via caesarean section; and NR were fed at a level to reduce BCS by 1.5-2.0 points over the last trimester compared to CON and calved naturally. Rumen fluid was collected via oral lavage prior to partition from cows and at d 7 from calves. Microbial DNA was isolated from the rumen fluid and metagenomic shotgun sequencing was performed using the Illumina HiSeq 2500 platform. Sequence data were analyzed using Metaxa2 for taxonomic assignment followed by QIIME1 and QIIME2 to determine differential abundance and alpha- and beta-diversity differences. There were no significant differences in alpha-diversity as measured by shannon index across treatment groups for cows (P = 0.239), but there were significant differences for calves (P = 0.015). Similarly, there were no significant differences in beta-diversity as measured by the bray-curtis dissimilarity matrix for cows (P = 0.059), but there were significant differences for calves (P = 0.007). Alpha-diversity differed (P < 0.001) between cows and calves, with cows having increased species richness compared to calves. Beta-diversity also differed (P = 0.001) between cows and calves. At total of 410 taxa were differentially abundant (P < 0.01) between cows and calves. These results suggest that the mature rumen microbiome of cows is able to withstand changes in feed intake, however the calf microbiome is susceptible to alteration by maternal factors. These data also suggest that there may be opportunities to develop management strategies during late gestation that influence calf health and performance long-term.

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

Thomas A. Christensen II
University of Wyoming Honors Program: Laramie, Wyoming (14 May 2019)
Keywords: chemical engineering AIChE radiation rumen microbial electrolysis cells

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.

Other Presentations

Measuring Diffusion of Trichlorethylene Breakdown Products in Polyvinylalginate

Thomas A. Christensen II, Samuel R. Wolfe, Jonathan Counts, Mark F. Roll, Kristopher V. Waynant, James G. Moberly
AIChE Annual Meeting: Pittsburgh, Pennsylvania (29 Oct 2018)
Keywords: bioremediation polyoxometalate hydrogel polymers proton transport chemical engineering

How to Build a Cow-Cud Fuel Cell

Thomas A. Christensen II
Idaho INBRE Summer Research Conference: Moscow, Idaho (01 Aug 2018)

Measuring diffusion of protons in polyvinyalginate

Thomas A. Christensen II, Jonathan Counts, James G. Moberly
Idaho INBRE Summer Research Conference: Moscow, Idaho (31 Jul 2018)