Scholarly Works, School of Animal Sciences

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Ablation of OCT4 function in cattle embryos by double electroporation of CRISPR-Cas for DNA and RNA targeting (CRISPR-DART)
Nix, Jada L.; Schettini, Gustavo P.; Speckhart, Savannah L.; Ealy, Alan D.; Biase, Fernando H. (Oxford University Press, 2023-11-01)
CRISPR-Cas ribonucleoproteins (RNPs) are important tools for gene editing in preimplantation embryos. However, the inefficient production of biallelic deletions in cattle zygotes has hindered mechanistic studies of gene function. In addition, the presence of maternal RNAs that support embryo development until embryonic genome activation may cause confounding phenotypes. Here, we aimed to improve the efficiency of biallelic deletions and deplete specific maternal RNAs in cattle zygotes using CRISPR-Cas editing technology. Two electroporation sessions with Cas9D10A RNPs targeting exon 1 and the promoter of OCT4 produced biallelic deletions in 91% of the embryos tested. In most cases, the deletions were longer than 1,000 nucleotides long. Electroporation of Cas13a RNPs prevents the production of the corresponding proteins. We electroporated Cas9D10A RNPs targeting exon 1, including the promoter region, of OCT4 in two sessions with inclusion of Cas13a RNPs targeting OCT4 mRNAs in the second session to ablate OCT4 function in cattle embryos. A lack of OCT4 resulted in embryos arresting development prior to blastocyst formation at a greater proportion (13%) than controls (31.6%, P < 0.001). The few embryos that developed past the morula stage did not form a normal inner cell mass. Transcriptome analysis of single blastocysts, confirmed to lack exon 1 and promoter region of OCT4, revealed a significant (False Discovery Rate, FDR < 0.1) reduction in transcript abundance of many genes functionally connected to stemness, including markers of pluripotency (CADHD1, DPPA4, GNL3, RRM2). The results confirm that OCT4 is a key regulator of genes that modulate pluripotency and is required to form a functional blastocyst in cattle.
Activity Dependent Protein Degradation Is Critical for the Formation and Stability of Fear Memory in the Amygdala
Jarome, Timothy J.; Werner, Craig T.; Kwapis, Janine L.; Helmstetter, Fred J. (PLOS, 2011-09)
Protein degradation through the ubiquitin-proteasome system [UPS] plays a critical role in some forms of synaptic plasticity. However, its role in memory formation in the amygdala, a site critical for the formation of fear memories, currently remains unknown. Here we provide the first evidence that protein degradation through the UPS is critically engaged at amygdala synapses during memory formation and retrieval. Fear conditioning results in NMDA-dependent increases in degradationspecific polyubiquitination in the amygdala, targeting proteins involved in translational control and synaptic structure and blocking the degradation of these proteins significantly impairs long-term memory. Furthermore, retrieval of fear memory results in a second wave of NMDA-dependent polyubiquitination that targets proteins involved in translational silencing and synaptic structure and is critical for memory updating following recall. These results indicate that UPS-mediated protein degradation is a major regulator of synaptic plasticity necessary for the formation and stability of long-term memories at amygdala synapses.
Acute heat stress activated inflammatory signaling in porcine oxidative skeletal muscle
Ganesan, Shanthi; Volodina, Olga; Pearce, Sarah C.; Gabler, Nicholas K.; Baumgard, Lance H.; Rhoads, Robert P.; Selsby, Joshua T. (2017-08)
Despite well-studied clinical manifestations, intracellular mechanisms of prolonged hyperthermic injury remain unclear, especially in skeletal muscle. Given muscle's large potential to impact systemic inflammation and metabolism, the response of muscle cells to heat-mediated injury warrants further investigation. We have previously reported increased activation of NF-κB signaling and increased NF-κB and AP-1-driven transcripts in oxidative skeletal muscle following 12 h of heat stress. The purpose of this investigation was to examine early heat stress-induced inflammatory signaling in skeletal muscle. We hypothesized that heat stress would increase NF-κB and AP-1 signaling in oxidative skeletal muscle. To address this hypothesis, 32 gilts were randomly assigned to one of four treatment groups (n = 8/group): control (0 h: 21°C) or exposed to heat stress conditions (37°C) for 2 h (n = 8), 4 h (n = 8), or 6 h (n = 8). Immediately following environmental exposure pigs were euthanized and the red portion of the semitendinosus muscle (STR) was harvested. We found evidence of NF-κB pathway activation as indicated by increased protein abundance of NF-κB activator IKK-α following 4 h and increased total NF-κB protein abundance following 6 h of heat stress. Heat stress also stimulated AP-1 signaling as AP-1 protein abundance was increased in nuclear fractions following 4 h of heat stress. Interleukin-6 protein abundance and activation of the JAK/STAT pathway were decreased in heat stressed muscle. These data indicate that heat stress activated inflammatory signaling in the porcine STR muscle via the AP-1 pathway and early activation of the NF-κB pathway.
Acute infection with Brachyspira hyodysenteriae affects mucin expression, glycosylation, and fecal MUC5AC
Lin, S.J.H.; Helm, E.T.; Gabler, N.K.; Burrough, E.R. (Frontiers, 2023-01-06)
Introduction: Infection with strongly β-hemolytic strains of Brachyspira hyodysenteriae leads to swine dysentery (SD), a production-limiting disease that causes mucohemorrhagic diarrhea and typhlocolitis in pigs. This pathogen has strong chemotactic activity toward mucin, and infected pigs often have a disorganized mucus layer and marked de novo expression of MUC5AC, which is not constitutively expressed in the colon. It has been shown that fucose is chemoattractant for B. hyodysenteriae, and a highly fermentable fiber diet can mitigate and delay the onset of SD. Methods: We used lectins targeting sialic acids in α-2,6 or α-2,3 linkages, N-acetylglucosamine (GlcNAc), α-linked L-fucose, and an immunohistochemical stain targeting N-glycolylneuraminic acid (NeuGc) to investigate the local expression of these mucin glycans in colonic tissues of pigs with acute SD. We used a commercial enzyme-linked immunosorbent assay (ELISA) to quantify fecal MUC5AC in infected pigs and assess its potential as a diagnostic monitoring tool and RNA in situ hybridization to detect IL-17A in the colonic mucosa. Results: Colonic mucin glycosylation during SD has an overall increase in fucose, a spatially different distribution of GlcNAc with more expression within the crypt lumens of the upper colonic mucosa, and decreased expression or a decreased trend of sialic acids in α-2,6 or α-2,3 linkages, and NeuGc compared to the controls. The degree of increased fucosylation was less in the colonic mucosa of pigs with SD and fed the highly fermentable fiber diet. There was a significant increase in MUC5AC in fecal and colonic samples of pigs with SD at the endpoint compared to the controls, but the predictive value for disease progression was limited. Discussion: Fucosylation and the impact of dietary fiber may play important roles in the pathogenesis of SD. The lack of predictive value for fecal MUC5AC quantification by ELISA is possibly due to the presence of other non-colonic sources of MUC5AC in the feces. The moderate correlation between IL-17A, neutrophils and MUC5AC confirms its immunoregulatory and mucin stimulatory role. Our study characterizes local alteration of mucin glycosylation in the colonic mucosa of pigs with SD after B. hyodysenteriae infection and may provide insight into host-pathogen interaction.
Additional Molecular Evidence that The Royal Palm is Probably a Turkey Breed
Smith, Edward J.; Xu, Jun; Adikari, J. (2019-07-09)
In earlier investigations, we reported the uniqueness of Royal Palm from other commonly raise heritage turkeys. Here, we provide evidence from screening using primers specific for the Melanocortin 1 (MC1R) Receptor gene (located on turkey chromosome 13, accession number NC_015023). Five heritage strains, including Broad Breasted Bronze (48), Blue Slate (40), Midget White (40), Royal Palm (45), and Spanish Black (48) were included in the analyses of approximately 3300 base pairs of the MC1R gene. Seven SNPs were identified and validated. Among the haplotypes identified, only Royal Palm had unique haplotypes. When combined with previous investigations, we believe that the Royal Palm may be a breed and not a strain. It may therefore be the most viable resource for introgression with a goal of genetic improvement.
Advancing livestock genomics education and research in developing countries using strategies from the Virginia Tech PREP and IMSD training programs
Smith, Edward J. (2019-07-11)
Our unique and impactful research and education program plan includes distinct activities that target three overlapping phases of each trainee’s tenure, which we define as the “moving in,” “moving through,” and “moving out” phases. During the “moving in” phase, 8 trainees “who need a PREP” will be recruited and assigned to mentors using our proven strategy that is “scholar-driven” and combines mentor qualities such as prior experience, which has resulted in a 98% retention for each of our 3 funding cycles. $409,537 annually or ~2.1 Million for five years. our successful interdisciplinary Initiative for Maximizing Student Development (IMSD) program for pre-doctoral (graduate) and pre-baccalaureate (undergraduate) students from groups underrepresented in careers in the biomedical and behavioral sciences. Our training program is a partnership with departments and interdisciplinary graduate programs which takes advantage of Virginia Tech’s (VT) history of excellence in Engineering and the Behavioral and Life Sciences. With lessons learned in the last eight years, we will continue to recruit across disciplines and from diverse geographic areas and institutions. From the first cycle, 2007-12, a total of 23 pre-doctoral students participated in the VT IMSD program. A total of 16 (or 69.5%) have completed and received the PhD degree; Total Year 1: $467,489.
Ag Commodities - VCE Showcasing Scholarship Poster
Arnold, Sandy; Baker, Karen (2017-02-22)
Youth are our future. Agriculture is our lifeline. Extension merges these two vital topics together through the 4-H Agriculture Commodities Tour, bringing awareness of the necessity for both to meet on an intimate real-life, out-of-classroom experience. Despite the continual and increasing demand for educated agriculturalists, interest and enrollment in agricultural fields of study has stagnated or declined. Lack of exposure, experience and familiarity with agricultural opportunities is likely a large contributor to this problem. By connecting across the state with Extension Agriculture State Specialists and Agents at the ARECs as part of the 2016 tour, 28 inner-city youth had the opportunity of a lifetime to explore agricultural lifestyles and potential careers. Providing more than basic agricultural information books can ever provide, these youths explored the importance of sustainability and stewardship across the state through talks, demonstrations and experiential hands-on learning opportunities. In addition, while learning how agriculture relates to their lives, this also gave them an awareness of career opportunities in agriculture that interest them. Studies demonstrate these interventions yield positive in attracting youth considering agricultural fields as viable career options (McCallister, Lee, & Mason, 2005; Shivy & Koehly, 2002; Esters, 2007; Ladany, Melincoff, Constantine, & Love, 1997). Although measuring the outcome of our youth and their future is beyond the scope of this initial investment, it is hoped that this tour has made a significant impact on the youth’s perception of agriculture outside of the classroom, and encourages them to seek further into this new world of possibilities.
AgroSeek: a system for computational analysis of environmental metagenomic data and associated metadata
Liang, Xiao; Akers, Kyle; Keenum, Ishi M.; Wind, Lauren L.; Gupta, Suraj; Chen, Chaoqi; Aldaihani, Reem; Pruden, Amy; Zhang, Liqing; Knowlton, Katharine F.; Xia, Kang; Heath, Lenwood S. (2021-03-10)
Background Metagenomics is gaining attention as a powerful tool for identifying how agricultural management practices influence human and animal health, especially in terms of potential to contribute to the spread of antibiotic resistance. However, the ability to compare the distribution and prevalence of antibiotic resistance genes (ARGs) across multiple studies and environments is currently impossible without a complete re-analysis of published datasets. This challenge must be addressed for metagenomics to realize its potential for helping guide effective policy and practice measures relevant to agricultural ecosystems, for example, identifying critical control points for mitigating the spread of antibiotic resistance. Results Here we introduce AgroSeek, a centralized web-based system that provides computational tools for analysis and comparison of metagenomic data sets tailored specifically to researchers and other users in the agricultural sector interested in tracking and mitigating the spread of ARGs. AgroSeek draws from rich, user-provided metagenomic data and metadata to facilitate analysis, comparison, and prediction in a user-friendly fashion. Further, AgroSeek draws from publicly-contributed data sets to provide a point of comparison and context for data analysis. To incorporate metadata into our analysis and comparison procedures, we provide flexible metadata templates, including user-customized metadata attributes to facilitate data sharing, while maintaining the metadata in a comparable fashion for the broader user community and to support large-scale comparative and predictive analysis. Conclusion AgroSeek provides an easy-to-use tool for environmental metagenomic analysis and comparison, based on both gene annotations and associated metadata, with this initial demonstration focusing on control of antibiotic resistance in agricultural ecosystems. Agroseek creates a space for metagenomic data sharing and collaboration to assist policy makers, stakeholders, and the public in decision-making. AgroSeek is publicly-available at https://agroseek.cs.vt.edu/ .
Allelic variation in rice Fertilization Independent Endosperm 1 contributes to grain width under high night temperature stress
Dhatt, Balpreet K.; Paul, Puneet; Sandhu, Jaspreet; Hussain, Waseem; Irvin, Larissa; Zhu, Feiyu; Adviento-Borbe, Maria Arlene; Lorence, Argelia; Staswick, Paul; Yu, Hongfeng; Morota, Gota; Walia, Harkamal (2020-10)
A higher minimum (night-time) temperature is considered a greater limiting factor for reduced rice yield than a similar increase in maximum (daytime) temperature. While the physiological impact of high night temperature (HNT) has been studied, the genetic and molecular basis of HNT stress response remains unexplored. We examined the phenotypic variation for mature grain size (length and width) in a diverse set of rice accessions under HNT stress. Genome-wide association analysis identified several HNT-specific loci regulating grain size as well as loci that are common for optimal and HNT stress conditions. A novel locus contributing to grain width under HNT conditions colocalized withFie1, a component of the FIS-PRC2 complex. Our results suggest that the allelic difference controlling grain width under HNT is a result of differential transcript-level response ofFie1in grains developing under HNT stress. We present evidence to support the role ofFie1in grain size regulation by testing overexpression (OE) and knockout mutants under heat stress. The OE mutants were either unaltered or had a positive impact on mature grain size under HNT, while the knockouts exhibited significant grain size reduction under these conditions.
Altered phosphorylation, electrophysiology, and behavior on attenuation of PDE4B action in hippocampus
Campbell, Susan L.; van Groen, Thomas; Kadish, Inga; Smoot, Lisa High Mitchell; Bolger, Graeme B. (BMC, 2017)
Background: PDE4 cyclic nucleotide phosphodiesterases regulate 3′, 5′ cAMP abundance in the CNS and thereby regulate PKA activity and phosphorylation of CREB, which has been implicated in learning and memory, depression and other functions. The PDE4 isoform PDE4B1 also interacts with the DISC1 protein, implicated in neural development and behavioral disorders. The cellular functions of PDE4B1 have been investigated extensively, but its function(s) in the intact organism remained unexplored. Results: To specifically disrupt PDE4B1, we developed mice that express a PDE4B1-D564A transgene in the hippocampus and forebrain. The transgenic mice showed enhanced phosphorylation of CREB and ERK1/2 in hippocampus. Hippocampal neurogenesis was increased in the transgenic mice. Hippocampal electrophysiological studies showed increased baseline synaptic transmission and enhanced LTP in male transgenic mice. Behaviorally, male transgenic mice showed increased activity in prolonged open field testing, but neither male nor female transgenic mice showed detectable anxiety-like behavior or antidepressant effects in the elevated plus-maze, tail-suspension or forced-swim tests. Neither sex showed any significant differences in associative fear conditioning or showed any demonstrable abnormalities in pre-pulse inhibition. Conclusions: These data support the use of an isoform-selective approach to the study of PDE4B1 function in the CNS and suggest a probable role of PDE4B1 in synaptic plasticity and behavior. They also provide additional rationale and a refined approach to the development of small-molecule PDE4B1-selective inhibitors, which have potential functions in disorders of cognition, memory, mood and affect.
Amino Acid Metabolomic Profiles in Bovine Mammary Epithelial Cells under Essential Amino Acid Restriction
López-Diez, Laura; Calle-Velásquez, Camilo; Hanigan, Mark D.; Ruiz-Cortés, Zulma Tatiana (MDPI, 2021-05-07)
Mammary epithelial cells (MECs) in culture are a useful model for elucidating mammary gland metabolism and changes that occur under different nutrient disponibility. MECs were exposed to different treatments: 100% EAA for 8 h and 24 h restriction (R); 2% EAA for 8 h and 24 h R; 2% EAA for 8 h and 24 h + 100% EAA for 8 h and 24 h restriction + re-feeding (R + RF). Western blotting and protein quantification was performed. The Kyoto Encyclopedia of Genes and Genomes (KEGG) software identified the amino acids (AAs) and signaling pathways. The chi-squared test, multiple classification analysis, and analysis of variance were used for the purification and identification of data. Intracellular casein levels were not affected. The KEGG analysis revealed that the important pathways of metabolism of AAs, which were involved in processes related to metabolism and biosynthesis of phenylalanine, tyrosine, and tryptophan (fumarate, acetyl-CoA, and tricarboxylic acid (TCA) cycle), were affected by both R and R + RF treatments, mainly through the glutamic-oxaloacetic transaminase-2 enzyme. Additionally, metabolic processes mediated by the mitochondrial malate dehydrogenase, S-adenosylmethionine synthetase, and asparagine synthase proteins positively regulated the carbohydrate pathway, pyruvate, and TCA cycles, as well as the metabolism of alanine, aspartate, and glutamate metabolism (carbohydrate and TCA cycle). We hypothesized that MECs have the capacity to utilize alternative pathways that ensure the availability of substrates for composing milk proteins.
AMP-Activated Protein Kinase Mediates the Effect of Leptin on Avian Autophagy in a Tissue-Specific Manner
Piekarski, Alissa; Nagarajan, Gurueswar; Ishola, Peter; Flees, Joshua; Greene, Elizabeth S.; Kuenzel, Wayne J.; Ohkubo, Takeshi; Maier, Helena; Bottje, Walter G.; Cline, Mark A.; Dridi, Sami (Frontiers, 2018-05-15)
Autophagy, a highly conserved intracellular self-digestion process, plays an integral role in maintaining cellular homeostasis. Although emerging evidence indicate that the endocrine system regulates autophagy in mammals, there is still a scarcity of information on autophagy in avian (non-mammalian) species. Here, we show that intracerebroventricular administration of leptin reduces feed intake, modulates the expression of feeding-related hypothalamic neuropeptides, activates leptin receptor and signal transducer and activator of transcription (Ob-Rb/STAT) pathway, and significantly increases the expression of autophagy-related proteins (Atg3, Atg5, Atg7, beclinl, and LC3B) in chicken hypothalamus, liver, and muscle. Similarly, leptin treatment activates Ob-Rb/STAT pathway and increased the expression of autophagy-related markers in chicken hypothalamic organotypic cultures, muscle (QM7) and hepatocyte (Sim-CEL) cell cultures as well as in Chinese Hamster Ovary (CHO-K1) cells-overexpressmg chicken Ob-Rb and STAT3. To define the downstream mediator(s) of leptin's effects on autophagy, we determined the role of the master energy sensor AMP-activated protein kinase (AMPK). Leptin treatment significantly increased the phosphorylated levels of AMPK alpha 1/2 at Thr172 site in chicken hypothalamus and liver, but not in muscle. Likewise, AMPK alpha 1/2 was activated by leptin in chicken hypothalamic organotypic culture and Sim-CEL, but not in QM7 cells. Blocking AMPK activity by compound C reverses the autophagy-inducing effect of leptin. Together, these findings indicate that AMPK mediates the effect of leptin on chicken autophagy in a tissue-specific manner.
Analytics in sustainable precision animal nutrition
Liebe, Douglas M.; White, Robin R. (Oxford University Press, 2019-04-01)
Animal welfare assessment of on-farm euthanasia methods for individual, heavy turkeys
Jacobs, Leonie; Bourassa, Dianna V.; Boyal, Ranjit S.; Harris, Caitlin E.; Josselson, L. Nicole Bartenfeld; Campbell, Andrew M.; Anderson, Gracie; Buhr, R. Jeff (2021-03)
On-farm euthanasia of poultry, including turkeys, may not be possible for most people as birds gain weight; thus alternative mechanical methods have been developed. Our objective was to compare mechanical cervical dislocation with the Koechner Euthanizing Device (KED), captive bolt euthanasia with the Turkey Euthanasia Device (TED), head-only CO2 euthanasia (CO2), and electric euthanasia as potential humane methods for euthanizing individual, heavy turkeys. We assessed their impact on loss of brain stem reflexes, acute distress (corticosterone, CORT), kill success, torn skin, and blood loss. Turkeys (n 5 174) were euthanized on 3 sampling days, while birds were restrained using a mobile bird euthanasia apparatus. Brain stem reflexes recorded were the cessation and return of induced nictitating membrane reflex (loss of consciousness and brain stem dysfunction), mouth gaping reflex (brain stem dysfunction), and musculoskeletal movements (spinal cord dysfunction). Overall, KED resulted in more frequent (at 4 min: KED 7 of 14; electric 0 of 13; TED 0 of 11; CO2 2 of 14 birds on day 1) and longer durations of the induced nictitating reflex compared to the other methods (means of day 2 and 3: KED 233; electric 15; TED 15; CO2 15 s). The mouth gaping reflex endured the longest after KED euthanasia (means of day 2 and 3: KED 197; electric 15; TED 51; CO2 15 s). Musculoskeletal movements endured longest after KED euthanasia (means of day 2 and 3: KED 235; electric 15; TED 219; CO2 15 s). Returning reflexes were more frequent after KED and TED compared to CO2 and electric euthanasia, where it was absent. CO2, electric, and TED euthanasia showed comparable kill success (success: CO2 42 out of 43; electric 44 of 45; TED 42 of 44), with KED resulting in most unsuccessful kills (unsuccessful: 8 out of 42). CORT responses were inconsistent. Torn skin and blood loss occurred more frequently after KED and TED compared to CO2 and electric applications. Therefore, we conclude that, based on a comparison of these 4 methods, the most discernibly humane was electric euthanasia, which consistently resulted in quick loss of consciousness within 15 s, no returning reflexes, and no torn skin or blood loss.
Animal welfare considerations for on-farm slaughter of poultry
Jacobs, Leonie (2018)
Animal Welfare Standards and Marketing
Jacobs, Leonie; Bovay, John; Pierce, Timothy (Virginia Cooperative Extension, 2021)
This handout provides an overview of animal welfare economics and the benefits to farmers from marketing their commitments to animal welfare.
Antibiotic resistance genes in the faeces of dairy cows following short-term therapeutic and prophylactic antibiotic administration
Feng, Xin; Chambers, Lindsey R.; Knowlton, Katharine F. (2019-12-06)
The objective of the research was to quantify three antibiotic resistance genes (tetQ, cfxA and mefA) in the faeces of dairy cows following therapeutic and prophylactic antibiotic treatments. Manure collected from dairy cows treated with either no antibiotic, pirlimycin hydrochloride (PIRL), ceftiofur crystalline free acid (CCFA) or cephapirin benzathine (CEPH) were submitted to quantitative PCR analysis. No treatment effects on the abundance of the tetQ and cfxA were observed. There was a trend for the abundance of the mefA to be increased in cows treated with PIRL (P = 0.07). Overall, the results showed no difference of measured three ARGs from cows receiving different antibiotics. Considering the limited scope of our investigation, further investigation is needed to provide more information on ARGs excretion from cows that received therapeutic and prophylactic antibiotic treatment.
ARGem: a new metagenomics pipeline for antibiotic resistance genes: metadata, analysis, and visualization
Liang, Xiao; Zhang, Jingyi; Kim, Yoonjin; Ho, Josh; Liu, Kevin; Keenum, Ishi M.; Gupta, Suraj; Davis, Benjamin; Hepp, Shannon L.; Zhang, Liqing; Xia, Kang; Knowlton, Katharine F.; Liao, Jingqiu; Vikesland, Peter J.; Pruden, Amy; Heath, Lenwood S. (Frontiers, 2023-09-15)
Antibiotic resistance is of crucial interest to both human and animal medicine. It has been recognized that increased environmental monitoring of antibiotic resistance is needed. Metagenomic DNA sequencing is becoming an attractive method to profile antibiotic resistance genes (ARGs), including a special focus on pathogens. A number of computational pipelines are available and under development to support environmental ARG monitoring; the pipeline we present here is promising for general adoption for the purpose of harmonized global monitoring. Specifically, ARGem is a user-friendly pipeline that provides full-service analysis, from the initial DNA short reads to the final visualization of results. The capture of extensive metadata is also facilitated to support comparability across projects and broader monitoring goals. The ARGem pipeline offers efficient analysis of a modest number of samples along with affordable computational components, though the throughput could be increased through cloud resources, based on the user’s configuration. The pipeline components were carefully assessed and selected to satisfy tradeoffs, balancing efficiency and flexibility. It was essential to provide a step to perform short read assembly in a reasonable time frame to ensure accurate annotation of identified ARGs. Comprehensive ARG and mobile genetic element databases are included in ARGem for annotation support. ARGem further includes an expandable set of analysis tools that include statistical and network analysis and supports various useful visualization techniques, including Cytoscape visualization of co-occurrence and correlation networks. The performance and flexibility of the ARGem pipeline is demonstrated with analysis of aquatic metagenomes. The pipeline is freely available at https://github.com/xlxlxlx/ARGem.
ASAS-NANP SYMPOSIUM: prospects for interactive and dynamic graphics in the era of data-rich animal science
Morota, Gota; Cheng, Hao; Cook, Dianne; Tanaka, Emi (2021-02)
Statistical graphics, and data visualization, play an essential but under-utilized, role for data analysis in animal science, and also to visually illustrate the concepts, ideas, or outputs of research and in curricula. The recent rise in web technologies and ubiquitous availability of web browsers enables easier sharing of interactive and dynamic graphics. Interactivity and dynamic feedback enhance humancomputer interaction and data exploration. Web applications such as decision support systems coupled with multimedia tools synergize with interactive and dynamic graphics. However, the importance of graphics for effectively communicating data, understanding data uncertainty, and the state of the field of interactive and dynamic graphics is underappreciated in animal science. To address this gap, we describe the current state of graphical methodology and technology that might be more broadly adopted. This includes an explanation of a conceptual framework for effective graphics construction. The ideas and technology are illustrated using publicly available animal datasets. We foresee that many new types of big and complex data being generated in precision livestock farming create exciting opportunities for applying interactive and dynamic graphics to improve data analysis and make data-supported decisions.
Assessing amino acid uptake and metabolism in mammary glands of lactating dairy cows intravenously infused with methionine, lysine, and histidine or leucine and isoleucine [Appendix]
Huang, Xinbei; Yoder, Peter; Teixeira, Izabelle; Hanigan, Mark D. (2020-12-02)
The objective of this study was to evaluate the effect of jugular infusions of 2 groups of AA on essential AA (EAA) transport and metabolism by mammary glands. Four Holstein cows in second lactation (66 ± 10 days in milk) were used in 4 x 4 Latin square design with a 2 x 2 factorial arrangement of treatments. Treatments were jugular infusions of saline; Met, Lys, and His (MKH); Ile and Leu (IL); or MKH plus IL (MKH+IL). Each period consisted of 8 d of no infusion followed by 8 d of jugular vein infusion of the treatment solutions. Amino acids were infused at rates of 21 g of Met, 38 g of Lys, 20 g of His, 50 g of Leu and 22 g of Ile per day. Cows were fed a basal diet consisting of 15.2% crude protein with adequate rumen degradable protein but 15% deficient in MP based on estimates by CNCPS (v6.5). On the last day of each period, 13C-AA derived from algae was infused into the jugular vein over 6 h, and blood and milk samples were collected before, during and after infusion. Plasma and milk samples were analyzed for AA isotopic enrichment, and a mammary compartmental model was fitted to the data to derive bidirectional transport and metabolism rates for individual EAA. Influx of Leu increased with IL, whereas influx of other EAA were not different among treatments. Cellular efflux of Met and Lys to venous plasma represented 12-34% of influx, while cellular efflux of Phe and BCAA represented 29-59% of influx. Increased efflux/influx ratios of Ile and Leu with IL but not Met and Lys with MKH demonstrated that increased Ile and Leu influx was mostly returned to plasma resulting in no change in net uptake or efficiency. The isotope results showed that mammary net uptake of Lys and Ile increased during MKH infusion. Net uptake of Met increased with MKH but only in the absence of IL. Catabolism of Lys and Met only increased with MKH alone resulting in decreased efficiency for milk protein, which demonstrated that Ile and Leu infusion can spare Lys and Met for milk protein synthesis. Total AA uptake to milk output was not different from 1 implying the catabolized Met and Lys contributed nitrogen to nonessential AA. Overall, EAA uptake and metabolism in mammary glands of dairy cows varied across individual EAA and responded differently to respective AA supplements. In addition, uptake, retention, and end use of amino acids by mammary tissue is variable and dependent on the mix of amino acids provided. This variability depending on the mix of AA absorbed will change the efficiency of utilization of individual AA at the mammary gland level and consequently the whole body level. Thus, it is inaccurate to use a fixed, constant efficiency within and across AA to represent tissue activity.

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