bluuebunny/crossref_metadata_2025_split huggingface dataset:
72 The AG2pi Vision for Resources in Agricultural Genomics and Phenomics: How Asas Can Contribute
Authors: Tuggle Christopher K , Scott Nicole , Clarke Jennifer , Murdoch Brenda M , Dekkers Jack C M , Ertl David , Lyons Eric , Lawrence-Dill Carolyn J , Schnable Patrick S 
Published: November 2023

Abstract
To meet the challenges of an increasing global population and multiple environmental stressors on agricultural production, it is essential to better understand how genotype (G) and environment (E) influence phenotype for traits of economic importance in agriculture. To accomplish this requires interdisciplinary teams consisting of researchers from crop and livestock sciences, genetics, genomics, computational and data sciences, and engineering. Towards this end, in 2020, Congress established the Agricultural Genome to Phenome Initiative (AG2PI). An important objective of this presentation is to encourage strong participation of animal science researchers and industry in ongoing AG2PI activities. The purpose of the initial AG2PI project, awarded to Iowa State University and the Universities of Arizona, Idaho and Nebraska, was to assemble and prepare a community to conduct AG2P research across the plant and animal kingdoms. The AG2PI project aims to: a) identify research gaps and opportunities, b) foster community solutions to these challenges, and c) rapidly disseminate findings for community use. Training workshops, field days, conferences, community surveys, and seed grants have all contributed to these goals. Opinions and ideas from the crop and livestock genetics communities are key to advancing AG2P science and related work. AG2PI has used online community surveys and in-person conferences to gather these and to facilitate transdisciplinary communications. In September 2022, AG2PI held a conference titled “Thinking Big: Visualizing the Future of AG2PI”, in which attendees participated in focused small group discussions to identify which agricultural G2P-related topics are most critical for future R&D funding and which may be the most difficult to achieve. These discussions are summarized in a concept paper for the community, shared with USDA-NIFA, and submitted for publication. A follow-up conference was held June 14-15, 2023, in Kansas City, where people working in both the animal and plant genetics research communities and industry stakeholders attended. Outcomes from this conference will be summarized in this presentation, and requests for animal scientists to provide further input will be made. The future of agricultural genomics will be shaped by both the participants in AG2PI and the solutions developed by the AG2PI community. Funding for this work comes from USDA NIFA awards 2022-70412-38454, 2021-70412-35233, and 2020-70412-32615.
99 Noncoding Rnas Alter Our Interpretations of Genome to Phenome
Authors: Hagen Darren E , Goldkamp Anna K 
Published: November 2023

Abstract
Gene transcription and protein translation are core components in the process of gene expression. Previous research on the regulation of gene expression largely focuses on events prior to translation, including epigenetic regulation, transcription, and RNA processing. However, translation acts as an additional layer of regulation that plays an important role in gene expression and function. Highly expressed genes are thought to be codon-biased to support efficient translation, in which the encoded codons correspond to highly abundant tRNAs. Further, synonymous SNPs were once considered to be silent due to the degeneracy of the genetic code. However, synonymous SNPs may disturb protein abundance and function through alterations in translational efficiency and suboptimal pairing to lowly abundant tRNAs. Our previous study identified variation in tRNA expression within bovine liver and muscle tissue, suggesting tissue-specific modulation of translation. In addition, advances in sequencing technologies have recently permitted the study of the translatome, which refers to the entire population of mRNA associated with ribosomes for protein synthesis and can be investigated through ribosome profiling. Here, we applied Quantitative Mature tRNA sequencing (QuantM-tRNA-seq) and ribosome profiling to investigate the relationship between tRNA expression and translational stalling events. Moreover, we have identified translationally regulated genes underlying tissue-specific biological processes and found that many upregulated and downregulated genes coincided with high and low translational efficiency respectively. We have also successfully defined stalling sites that depict the regulatory information encoded within the coding sequence of transcripts, which could control translation rate and facilitate proper protein folding. This work offers an atlas of distinctive stalling sites across bovine tissues, which provides an opportunity to predict codon optimality and understand tissue-specific mechanisms of regulating protein synthesis.
154 Antibody and Cell-Mediated Responses Associated with Bvdv and Interferon-Gamma Expression in Reciprocal Angus-Brahman First Generation Crosses
Authors: Chapman MacKenzie G , Falkenberg Shollie M , Dassanayake Rohana P , Herring Andy D 
Published: November 2023

Abstract
The influence of sex and reciprocal cross type were evaluated in Brahman-sired (B × A) and Angus-sired (A × B) F1 cattle following modified-live viral vaccination regarding virus neutralization titers (VNT) and cell-mediated immune (CMI) responses following in vitro exposure to Bovine Viral Diarrhea Virus (BVDV) Type 1 (BVDV1) and Type 2 (BVDV2) genotypes. VNT against BVDV were based on virus neutralization assay, and CMI responses were measured using the PrimeFlow mRNA assay for determination of the frequency of BVDV and interferon-gamma (IFN-γ) positive cells. Mixed model procedures utilized individual calf ID as a random effect with fixed effects of F1 cross type, calf sex, evaluation date, and potential 2-way interactions; models for frequency of BVDV and IFN-γ positive cells, stimulation conditions (BVDV1, BVDV2, mitogen, none) and potential two-way and three-way interactions of fixed effects. Relationships of immune responses with calf birth weight and weaning weight and steer carcass traits were also investigated. This study found several CMI traits differed due to the type of cross and calf sex; however, no differences in VNT were attributed to these effects. Cells from B × A animals consistently ranked approximately 20% greater for BVDV positive cells (BVDV+) than those from A × B animals pre-MLV vaccination; however, post-MLV vaccination, cells from A × B animals ranked 20% greater (P &lt; 0.05) for CD2+, CD4+, and CD8+ cells. Post- MLV steers consistently had 30 to 35% greater (P &lt; 0.05) frequencies of BVDV+ cells following viral exposure; steers had greater frequencies (P &lt; 0.05) of CD4+ and CD335+ cells expressing IFN-γ and ranked greater for CD2+ and CD8+ cells when compared with heifers in both crosses. Only vaccination timing affected BVDV VNT. No significant correlations involving VNT and CMI responses were observed among A × B animals when stimulated with BVDV1, but among B × A animals, positive correlations were observed with IFN-γ in CD4+ (r = 0.406, P = 0.049) and CD335+ (r = 0.472, P = 0.020). When stimulated with BVDV2, positive correlations of 0.33 to 0.39 (P &lt; 0.05) were observed between BVDV and IFN-γ frequency within cell type; these were not significant when stimulated with BVDV1, except for CD335+ cells (r = 0.41, P = 0.003). No correlations for VNT and CMI responses were observed when stimulated with BVDV2. No major correlations between immune responses and weight or carcass traits were observed, and immune response category for BVDV or IFN-γ frequency did not influence birth weight or weaning weight. Differences in CMI responses involving reciprocal cross types and sex observed in this project may relate to widely reported reciprocal cross differences in birth weight in Bos indicus - Bos taurus crossbred cattle and warrant additional study.
162 Evaluating the Potential of a Thermal Imaging System to Identify Subclinical Mastitis in Dairy Cattle
Authors: Shrestha Bhuwan , Piñeiro Juan M , Paudyal Sushil 
Published: November 2023

Abstract
The objective was to evaluate the potential for the use of a thermal imaging system for the identification of subclinical mastitis in dairy cows. Multiparous Holstein dairy cows (n = 131) within 150 days in milk (DIM; range 65 to 155) were enrolled in the study at a commercial dairy farm in central Texas. Milk samples (10 mL) were collected from each quarter separately and evaluated for somatic cell counts (SCC; n*1000), fat (%), protein (%), lactose (%), SNF (%), BHBA (mM/L), acetone (mM/L), and milk urea nitrogen (MUN; mg/dL). A minimum of four thermal images per cow representing all four quarters were captured using a handheld infrared camera (Fluke TiS 75+) from approximately one-meter distance from the cow. All images were taken inside the milking parlor and after the morning milking during February 2023 to minimize the impact of daily ambient temperatures. Skin temperatures from each quarter (maximum, minimum, average) were extracted using Fluke Connect software. A total of 524 quarter-level milk samples and corresponding udder images were obtained, and 10 images were discarded from analyses due to the lack of appropriate resolution and focus. To prevent collinearity, a correlation matrix was developed using PROC CORR in SAS and variables with significant correlations were removed from the model. Subclinical mastitis was defined at the quarter level when SCC &gt; 250,000. Statistical analyses were performed using mixed linear regression models (PROC MIXED) with cow and DIM as random effects in the model, and logistic regression model (PROC LOGISTIC) was fitted to evaluate the probability of the disease based on temperature and milk variables. Maximum and average udder temperatures did not demonstrate a significant relationship with subclinical mastitis status whereas minimum udder temperature was greater in sick quarters (29.6 ± 0.52 vs 27.5 ± 0.45; P = 0.003). Increased minimum udder temperature was also associated with BHBA (P &lt; 0.0001), acetone (P &lt; 0.0004), and MUN (P &lt; 0.0007) concentrations in milk. Cows with subclinical mastitis had decreased BHBA (0.14 ± 0.037 vs 0.28 ± 0.031; P = 0.0036) and acetone (0.017 ± 0.003 vs 0.044 ± 0.003; P &lt; 0.001). Odds of subclinical mastitis were associated with MUN values in milk (OR 0.94; CI 0.89 - 0.98) but not with any udder surface temperature variables. We conclude that an increase in the minimum temperature of the udder could be used as an indicator of subclinical mastitis but studies with larger datasets and using advanced image analysis techniques are warranted to validate these results.
176 Relationships Among Early Life Weight and Growth Among Halfblood Bos Indicus Male Calves and Associations with Carcass Weight
Authors: Lake Steven Gunari , Riley David G , Herring Andy D 
Published: November 2023

Abstract
Nellore-Angus steers (n = 572) born in 2009-2013, 2015, and 2019 and Brahman-Angus reciprocal steers (n = 73) born in 2019 and 2020 were evaluated for calf and carcass weights (HCW). Calves were born and reared at the McGregor Research Center and included F2, F3, F4, and F5 Nellore-Angus and F1 Brahman-Angus. Calves were weighed at 4 approximate times: within 48 h of birth (BWT), 50 d age (spring-working, SWWT, not available for 2009-2010), 180 d age (pre-weaning, PRWWT), and approximately 210 d age (weaning, WWT). Animals born in the same year were managed similarly, and cow herds were managed together in most cases except during annual natural service, multi-sire breeding seasons. Animals born in the same year were managed as contemporaries post-weaning and for feedlot finishing. Mixed model analyses of variance for calf traits included genetic type (nested within calf birth year), calf birth year, age of dam category, and covariates of Julian birth date (BWT, SWWT) or calf age (PRWWT and WWT) as fixed effects. In each year at least 2 genetic types were present; however, because of imbalance across years, only genetic types produced in the same years were compared following significant F-tests. For these analyses cow age category did not affect calf BWT or SWWT, but showed influence for PRWWT (P = 0.006) and WWT (P &lt; 0.001); cow age category did not affect calf ADG. Differences in calf weights (P &lt; 0.001) and calf ADG (P &lt; 0.001) due to the genetic type were driven by reciprocal differences between Brahman-Angus crosses and potential maternal hybrid vigor advantages for F2 Nellore-Angus calves from F1 dams vs. other genetic types. Brahman-sired F1 (B × A) males were 12.7 to 14.1 kg heavier for BWT (P &lt; 0.001) and 14.9 to 19.2 kg heavier for SWWT (P &lt; 0.001) than Angus-sired F1 males (A × B), but persistence to weaning varied across years. It appears in these data that some genetic types may be more sensitive to individual year effects, but it is uncertain why. Correlations of calf weight traits with HCW were inconsistent across genetic types. No calf weight was associated with HCW in A × B crosses, and only PRWWT in B × A related to HCW (r = 0.44, P = 0.007). Among Nellore-Angus crosses, BWT showed small to moderate correlation to HCW (0.23 &lt; r &lt; 0.46); however, among the F4 and F5 calves, later weights (SSWT, PRWWT and WWT) had large correlations with HCW (0.50 &lt; r &lt; 0.79) whereas these correlations ranged from 0.24 to 0.37 in F2 and F3 steers. It appears animals of similar Bos indicus percentage may have quite different calf growth patterns related to HCW.
20 Methane Accounting and Its Importance to the Beef industry’s Implied Contribution to Climate Warming
Authors: Beck Matthew R , Thompson Logan 
Published: November 2023

Abstract
At 27% of U.S. methane (CH4) emissions (3% of U.S. total emissions), enteric CH4 emissions represent the largest source of U.S. CH4 emissions, surpassing natural gas systems according to the latest report from the Environmental Protection Agency (EPA). Total manure CH4 emissions represent 1% of total U.S. emissions. Enteric and manure CH4 emissions from the beef industry represent 2.1% and 0.03%, respectively, of U.S. total emissions. These contributions of CH4 emissions to total U.S. greenhouse gas emissions are determined by relating CH4 emissions to a carbon dioxide (CO2) equivalent basis (CO2-e) by multiplying the amount of CH4 emissions by its global warming potential (EPA uses 25 for CH4 on a 100-y basis; GWP100). The GWP100 method was adopted following the Kyoto Protocol in 1997, and ever since this time its appropriateness for short-lived climate forcers (SLCF; e.g., CH4 has a 12-y atmospheric lifespan) has been debated. This debate exists because GWP100 is a misnomer, as it is known to have no relationship with the contribution of a gas to warming. Since CH4 is a SLCF, when emission rates are decreasing there is a decreasing concentration of CH4 in the atmosphere. To account for SLCF, an alternative accounting methodology, termed GWP-star (GWP*), has been proposed to convert SLCF to a CO2-warming equivalence (CO2-we). The CO2-we values from GWP* methodology has been demonstrated to closely relate to warming contributions compared with the CO2-e value from the GWP100 method. Applying the GWP* metric to enteric and manure CH4 emissions from the beef industry reduces the implied contribution to climate warming of these emission sources by 92% and 62%, on average from 2010-2020, respectively, compared with the GWP100 methodology. There are currently promising mitigation technologies emerging for mitigating enteric CH4 emission. For example 3-nitrooxypropanol may reduce enteric CH4 by 30% and Asparagopsis seaweed may reduce it by 80%. We explored the effects of these technologies on CO2-we if they had 100% adoption by the beef industry and if these mitigation potentials were consistent across all production systems (admittedly a big assumption). Both technologies would result in negative CO2-we for 20-y, after which a new baseline would be achieved and the CH4 emissions would begin contributing to warming again (i.e., accumulating CH4 in the atmosphere). During the 20-y of net-cooling, a 30% and 80% reduction in enteric CH4 would result in -143 (3% of U.S. total CO2 emissions) and -461 (10% of U.S. total CO2 emissions) million metric tons of CO2-we/y, respectively. Ultimately, adopting GWP* not only provides estimates that actually relate to contributions to climate warming, therefore providing a more appropriate metric than what is currently used, but also provides a means for the beef industry to leverage mitigation strategies to be a solution for climate change.
91 Grazing management–Tools for Improving the Efficiency of Grazing Beef Production
Authors: Thompson Logan , Maciel Isabella , Beck Matthew R , Rowntree Jason E 
Published: November 2023

Abstract
The beef sector is facing mounting challenges related to its perceived impact on climate change and other negative ecological externalities that can occur from the rearing of beef cattle. This would include greenhouse gas emissions (GHG), soil degradation, eutrophication of water ways and a decrease in biodiversity, to name a few. Within the industry, the largest contributor of GHG comes from the grazing sector, predominantly in the form of enteric methane (CH4) produced during the reticulo-rumen fermentation process. This presents a unique challenge, as the grazing sector is one where animal scientists have low precision with respect to experimental design and data collection, and where producers assert a lower level of dietary control relative to confined operations. While enteric CH4 inhibitors are getting closer to regulatory approval, their ability to reduce emissions in grazing systems is still relatively unknown due to the “pulse” supplementation strategy being unstudied to date. Therefore, management decisions that improve the quality of the forage base are the most practical strategies to reduce enteric CH4 production. This would include strategies such as adaptive grazing management, inclusion of high-quality forages, and improved forage diversity as potential tools to reduce emissions, dependent on geographic location. Furthermore, how the human dimension influences soil-plant-animal interrelationships may lead to beneficial ecological outcomes such as carbon sequestration and soil health. Therefore, potential “win-win” outcomes may be achieved. However, climatic gradients, and more specifically moisture, can influence or limit outcomes and thus interpreting research should be done on a geographical and climatic specific basis. The objective of this presentation is to outline and examine how management decisions can influence the efficiency and environmental impact of U.S. beef production, and to identify potential limitations and knowledge gaps in need of future research.
190 The Nutrigenomic Effects of Dietary Choline and L-Carnitine on the Muscle and Liver of Lean and Overweight Cats
Authors: Fletcher Jess , Grapentine Sophie , Rankovic Alexandra , Brisson Brigitte , Sinclair Melissa , Shoveller Anna Kate K , Altom Eric K , Bakovic Marica , Verbrugghe Adronie 
Published: November 2023

Abstract
The objective of this study was to investigate the effects of dietary choline and L-carnitine on the lipotropic gene expression in the muscle and liver of overweight and lean cats, when fed for body weight (BW)maintenance. Overweight [n = 6, body fat percent (BF%): 33.2 ± 1.38] and lean (n = 6, BF%:18.4 ± 0.93), 1-2 year old, male, neutered cats received choline (378 mg/kg BW0.67), L-carnitine (200 mg/kg BW) and no supplementation (control) in a 3x3 Latin square design for 6 weeks, with a 2-week washout between treatments periods. Each treatment was offered with a commercial extruded diet; diet amount was provided to maintain current BW. Cats were anesthetized and quadriceps vastus lateralis (30-50 mg) and liver (30-50 mg) biopsies were harvested after each treatment period using an open muscle or laparoscopic biopsy technique respectively. Tissue RNA was isolated with TRIzol and sequenced using directional PolyA RNA-seq. The expressed genes were aligned using the reference genome, Felis_catus_9.0, Ensembl v.107. Differential gene expression was analyzed for 29,928 genes with SEQUIN, using edgeR and TMM normalization. Pathway analysis was performed using EnrichR databases, BioPlanet 2019 and KEGG 2021. Using a two-group comparison, global analysis revealed 92 and 759 differentially expressed genes in the liver and muscle, respectively of overweight cats compared with lean (P &lt; 0.05). Affected pathways included fat digestion and absorption, including peroxisome proliferator-activated receptor (PPAR) signaling in the liver, and immunity related pathways in muscle (P &lt; 0.05). Upon further analysis using a two-group comparison between overweight and lean cats for each treatment, 11 and 692 significant genes were found in choline treated liver samples and L-carnitine treated muscle samples, respectively (P &lt; 0.05). Similar to the global analysis, genes related to fat metabolism, including PPAR signaling, were significant in the choline treated liver samples, and immunity related genes were significant in the L-carnitine treated muscle samples (P &lt; 0.05). Based on preliminary data, supplemental dietary choline may be beneficial for overweight cats as it may increase fat metabolism in the liver, mitigating risks associated with feline hepatic lipidosis (FHL). Supplemental dietary L-carnitine may also be beneficial due to its effects on immunity related pathways, including pathogen defense. To investigate the full effects of choline and L-carnitine on gene expression, further studies are warranted including older, chronically obese cats, as well as confirmed cases of FHL. Acknowledgements: Natural Sciences and Engineering Council of Canada, Elmira Pet Products and Balchem Corp.