bluuebunny/crossref_metadata_2025_split huggingface dataset:
403 Impact of lysine, methionine, and histidine deficiencies on gene expression and upstream transcriptional regulators in bovine mammary epithelial cells: An RNA-sequencing analysis
Authors: Li Boning , Innes David , Ribeiro Eduardo S , Burgos Sergio , Cant John 
Published: September 2024

Abstract
Essential (E) amino acids (AA) may alter bovine mammary epithelial cell functions by impacting mRNA expression of genes through their upstream transcription factors. The objective of this research was to study the impact of EAA deficiencies on gene expression and to identify upstream transcriptional factors mediating their effects in bovine mammary epithelial cells. Epithelial cells were collected from the mammary glands of lactating dairy cows and cultured in combined media of DMEM/F12 and Medium 170, differentiated for 5 d, and subsequently treated in triplicate for 60 h with a control medium containing all EAA at normal plasma concentrations for cows (CTL), or a medium with 20 μM Lys (LY), 5 μM Met (LM), or 10 μM His (LH), which are each 25% of normal concentration. RNA was isolated from the cells and sequenced on an Illumina NovaSeq 6000 producing 150 base pair paired-end reads with a minimum sequencing depth of 150 million reads. Reads were cleaned with ‘fastp’ (Chen et al., 2018), aligned to the bovine reference genome (ARS-UCD1.2) using ‘STAR’ aligner (Dobin et al., 2013), and genes counted using ‘featureCounts’ (Liao et al., 2014). Differential expression of genes between treatment pairs was determined using the ‘DESeq2’ package (Love et al., 2014) in R. Genes with an absolute log2 fold change ≥ 1 and a false discovery rate of &lt; 0.05 were considered differentially expressed. The number of differentially expressed genes relative to CTL was 780 for LY, 383 for LH, and 536 for LM. QIAGEN Ingenuity Pathway Analysis (IPA) identified four pathways consistently affected across LY, LM, and LH: kinetochore metaphase signaling, mitotic roles of polo-like kinase, cell cycle: G2/M DNA damage checkpoint regulation, and interferon signaling (Figure 1-3). Notably, the kinetochore metaphase signaling pathway was identified as the most significant across all treatments, suggesting a strong link to cell proliferation and apoptosis during EAA deficiency. The interferon signaling might be related to the Janus kinase 2/signal transducer and activator of transcription 5 (Jak2/STAT5) pathway which can promote the expression of genes encoding milk proteins such as β-casein and β-lactoglobulin. Furthermore, the IPA identified upstream transcription factors related to cell proliferation, apoptosis, autophagy, protein translation, endoplasmic reticulum biogenesis, and amino acid metabolism including NUPR1, FOXM1, MYC, CCND1, TP53, DDIT3, and ATF4 across all treatments. The findings suggest that AA deprivation regulates bovine mammary epithelial cell function by instigating amino acid response pathways and altering secretory cell number.
95 Temporal patterns of enteric gas production from cattle in response to ruminal infusions of synthetic bromoform
Authors: Muizelaar Wouter , Nichols Kelly , Taweel Hassan Z , van Laar Harmen , Dijkstra Jan , Martín-Tereso Javier 
Published: September 2024

Abstract
This dataset describes the temporal patterns of enteric gas production from cattle in response to ruminal infusions of synthetic bromoform (CHBr3). Four non-lactating, non-pregnant, rumen-fistulated Holstein-Friesian cows (12 yr of age, 781 ± 33 kg body weight) were infused via the rumen fistula with 592 mg CHBr3/d in an aqueous solution for 14 d. The daily dose was divided into 3 equal portions and infused every 8 h over a 24-h period (0545, 1345, and 2145 h). The 7 d following the infusion period served as a recovery period to describe the dynamics of enteric gas production after cessation of infusion. The Greenfeed system was used for enteric gas measurements. Animals had ad libitum access to grass hay and were supplemented with concentrate through the Greenfeed system for the infusion and recovery periods and for the 14-d adaptation period before the infusions. A two-way ANOVA was performed with phase (pre- and post-infusion) as fixed effect and animal as random effect to assess average differences. Preliminary results show a decrease in methane (CH4) production from on average 371 g/d before the infusions to 5 g/d after 14 d of infusions (P &lt; 0.01). Hydrogen (H2) production increased from on average 0.6 g/d before the infusions to 9.0 g/d after 14 d of infusions (P &lt; 0.01). Dry matter intake (DMI) decreased to on average 12.8 kg/d after 14 d of infusions compared with 16.9 kg/d before the infusions (P &lt; 0.01). A four-parameter logistic model was fitted for the response of CH4 (CH4-inf) and H2 (H2-inf) production in the 14 d after the first infusion, and separately for the response of CH4 (CH4-rec) and H2 (H2-rec) production in the 7 d after the last infusion (Table 1). Preliminary results indicate a 95% decrease in CH4-inf from the A-asymptote (small values of x) is reached after approximately 63 h, and a 95% increase in H2-inf from the B-asymptote (large values of x) is reached after approximately 49 h. After the last infusion, the 95% increase in CH4-rec from the B-asymptote is reached after approximately 109 h, and the 95% decrease in H2-rec from the A-asymptote is reached after approximately 112 h. When comparing the respective inflection points (xmid), the recovery of CH4 production took approximately 3 times longer than the decrease. In addition, after 7 d of recovery, CH4 production did not return to the initial levels before the infusion began. The reduced DMI can partially explain this difference in CH4 recovery; however, other factors cannot be excluded. In conclusion, our data suggest that ruminal infusion of 592 mg CHBr3/d for 14 d reduces CH4 production by &gt;95% and the recovery of CH4 production to pre-infusion levels might take longer than 7 d.
96 Using greenhouse gas flux to estimate forage dry matter intake in ad libitum fed replacement heifers
Authors: Briggs Emma A , Foote Andrew P , Beck Paul A , Reuter Ryan R , Rolf Megan M , Lalman David L 
Published: September 2024

Abstract
An accurate estimate of feed intake is a critical component in determining individual animal feed efficiency. However, existing feed intake measurement systems are not designed for unprocessed, dry forage diets. Open-circuit gas flux technology measures enteric gas emissions for cattle in a pasture-based setting. If a significant relationship exists between feed intake and gas emissions, this system could be used to rank grazing cattle for forage intake and forage utilization efficiency. Our objective was to develop prediction equations to estimate forage dry matter intake using gas flux and performance data. Angus and Angus x Hereford heifers [n = 71; initial body weight (BW) 329.5 ± 31.1 kg] were used over 3 yr to measure intake, gain, and gas flux. All heifers were subject to a 21-d adaptation and 71-d intake test using individual intake technology (SmartFeed; C-Lock Rapid City, SD) with a stocking rate of 3.3 heifers per feeder. Throughout the study, heifers were fed a long-stem, unprocessed, grass hay diet (≥ 10.8% CP, 2.0 Mcal ME, and 56% TDN) with ad libitum access to a salt/mineral supplement. The GreenFeed system (C-Lock Rapid City, SD) was used to monitor oxygen (O2) consumption (means ± SD; 3364.4 ± 374.8 g/d), methane (CH4; 181.4 ± 24.3 g/d) and carbon dioxide (CO2) production (4,965.3 ± 494.5 g/d). Body weights were collected every 14 d, and average daily gain (ADG) was calculated by regressing BW on day of study. The phenotypic correlations of forage DMI with CO2, CH4, O2, and heat production (HP) were 0.72, 0.66, 0.74, and 0.74, respectively. Average daily gain and midpoint metabolic BW combined with the estimate of daily HP, O2, or CO2 accounted for 60% of the variation in forage DMI. These results suggest that forage intake can be predicted using performance data in conjunction with the GreenFeed gas quantification system.
131 Effects of biochar type and inclusion level on in vitro gas production dynamics
Authors: Adams Jordan M , Gonzalez Daisy , Lee Eunsung , Brady Jeff A , Tedeschi Luis O 
Published: September 2024

Abstract
Biochar has been studied as a soil amendment for the storage of stable carbon in the soil, contributing to carbon capture and mitigation of greenhouse gas emissions. There may be potential for biochar use as a feed additive to reduce enteric methane (CH4) emissions from growing beef cattle, but it may be dependent on several factors, including biomass source, production methodology, biochar particle size, and several others. Thus, our objective was to determine the effects of 3 different biochars and their level of inclusion on in vitro gas production dynamics of bermudagrass (Cynodon dactylon) hay. Biochars included yellow pine wood (W, Waste to Energy Inc., Slocomb, AL), yellow pine wood modified with calcium hydroxide (CW), and dairy cattle manure (M, Ecochar, Heehugowaard, Netherlands). Air-dried bermudagrass hay with or without biochars was incubated for 48 h with fresh rumen inoculum collected from 4 ruminally cannulated steers. Biochars were investigated at 3 inclusion levels (IL; IL.5 = 0.5%, IL1 = 1.0%, and IL2 = 2.0% of DM). Four incubations were performed. Incubations were performed in an unbalanced, incomplete randomized block design as inclusion levels differed among incubations, with IL.5 only included in the first two incubations (Group1) and IL2 only included in the last two incubations (Group2), but IL1 was included in all four incubations, and it was used to scale the IL.5 and IL2 variables linearly. Enumeration of CH4 production was performed for all samples. Statistical analyses were performed using PROC GLIMMIX of SAS version 9.4 (SAS Institute Inc., Cary, NC). Data were evaluated by group, with biochar, IL, and biochar × IL included in the model, and incubation included as a random variable. There were no effects of biochar, IL, or biochar × IL for either group on any of the fermentation dynamics (P ≥ 0.05), including total gas production, fractional rate of gas production, and lag time before initiation of gas production, for either the exponential or log 2-pool functions. Additionally, there were no differences in grams of CH4 production (P ≥ 0.12) for either group. To compare biochars at all IL, relative CH4 production was explored after adjusting values for IL1 and IL2 in the last two incubations based on the difference in CH4 produced at IL1 in the first two incubations. In terms of relative CH4 production, the M biochar produced approximately 16 and 28% less CH4 than W and CW, respectively, at IL1. Our results indicate that M biochar may allow for reduced CH4 production from beef cattle, but several factors, including biomass source, production methodology, and particle size, should be considered to understand the differences better. Ultimately, further research is warranted to evaluate biochar in greater depth as a feed additive for growing beef cattle.
128 Bromoform metabolites from Asparagopsis taxiformis: Formation and impact on in vitro rumen fermentation parameters and microbial composition dynamics
Authors: Muizelaar Wouter , Sloth Jens J , Fromberg Arvid , Brask Maike J , Bruneel Brecht , Visker Marleen H P W , Dijkstra Jan 
Published: September 2024

Abstract
The aim of the experiment was to study the formation and impact of bromoform metabolites from Asparagopsis taxiformis on in vitro rumen fermentation parameters and microbial composition over time. Rumen fluid from three rumen fistulated lactating Holstein-Friesian dairy cows was collected and after buffering used as inoculum. Cows were fed a total mixed ration of grass silage, corn silage and concentrate. In total 0.5 g dry matter (DM) of substrate was incubated, consisting of either 0.3 g DM grass silage and 0.2 g DM corn silage (Control) or 0.295 g DM grass silage, 0.195 g DM corn silage and 0.01 g DM A. taxiformis (ASP). Substrates were incubated for 72 h. Total gas production (TGP) was measured continuously and methane (CH4) at 0, 1, 2, 4, 8, 12, 24, 36, 48, 60 and 72 h. After 72 h, volatile fatty acids (VFA), ammonia (NH3), and pH were determined. Substrates (Table 1) and contents of additional bottles at specific timepoints were analyzed for bromoform (CHBr3), dibromomethane (CH2Br2), bromomethane (CH3Br), dibromochloromethane (CHBr2Cl), arsenic (As), bromine (Br) and iodine (I). RNA was isolated and sequenced with specific primers for bacteria, archaea and protozoa. Data were averaged per inoculum and analyzed with an ANOVA to test for differences between treatments. Preliminary results revealed no difference between Control and ASP in TGP (mL/g organic matter; OM) after 72 h (P = 0.102), whereas CH4 (mL/g OM) was 78% less in ASP than in Control (P = 0.005). Total VFA (tVFA) did not differ between Control and ASP (P = 0.435). Acetate (% tVFA) was lower in ASP (49.2 vs 56.6; P = 0.011), and branched VFA (% tVFA) greater in ASP than in Control (5.8 vs 3.8; P = 0.001). At 72 h, NH3 (mg/L) and pH did not differ between ASP and Control (P = 0.183 and 0.519, respectively). After 1 h of incubation CHBr3 concentration was 118 ng/mL, rapidly decreasing below detection limit by 8 h of incubation. At 1 h of incubation CH2Br2 concentration was 22 ng/mL, reaching 40 ng/mL at 4 h of incubation and remained relatively stable thereafter. At any timepoint, CH3Br concentration was below detection limit. At 12 h of incubation CHBr2Cl concentration was 3.7 ng/mL and remained relatively stable. Mineral concentrations (As, I, Br) were constant throughout incubation. Addition of 2% DM A. taxiformis effectively reduced CH4 production without negative effects on TGP and tVFA in vitro. While CHBr3 disappeared quickly and CH2Br2 concentration increased, substantial formation of CH3Br in hydrogenation reactions by methanogens seemed absent. Levels of Br did not change, suggesting no substantial Br vaporization through secondary metabolites. Microbial composition data are pending analyses and will be presented at the symposium.
188 Prediction of individual grazing beef cattle dry matter intake
Authors: Blake Nathan , Walker Matthew , ArunKumar K E , Mata-Padrino Domingo , Holaskova Ida , Wilson Matthew E 
Published: September 2024

Abstract
Estimation of individual dry matter intake (DMI) of pastured beef cattle is critical to grassland management, genetic improvement of efficiency, and increasing the sustainability of animal agriculture. Currently, the only way to measure individual DMI of grazing cattle is through expensive, labor intensive, and spatially demanding research protocol. Very few options for assessment of individual DMI of grazing animals exist for cattle producers. We have developed a machine learning approach to predicting individual DMI of pastured beef cattle that requires only body weight (BW), water intake, and open-source climate variables. Training data were collected in Wardensville, WV at the West Virginia University Research, Outreach, and Education Center. Crossbred steers (n = 32) were phenotyped for Residual Feed Intake (RFI) in the barn. Animals were split into four groups of two low RFI and two high RFI. After a grazing acclimation period, animal groups were rotationally grazed concurrently through 0.05 ha plots for 7 d. Daily BW and water intake data were collected throughout the experiment using an RFID-equipped front-end scale and metered waterers. Beginning on d 2, animals were provided a bolus of Cr2O3 (10 g) at 0700 and 1900 h. Beginning on d 5, fecal samples were collected from each animal at 0700 and 1900 h. Samples were analyzed for Cr2O3 content and used in conjunction with forage digestibility from paired clipped samples to generate individual intakes. These data were used as ground truth data to assess model performance. We used our Repeated Measures Random Forest (RMRF) model to predict individual DMI of animals using daily BW, water intake, and climate variables. Intakes estimated by RMRF were compared with intakes estimated by NASEM equations. Our model outperformed NASEM predictions by 70%, indicating that our method achieves better results than the current most efficient approach. Though iterative model improvements will be made (collection of more training data, collection of more diverse training data, and use of first-differenced, moving average, and seasonally adjusted variables), our work demonstrates a novel, efficient method for researchers and producers to more accurately estimate DMI of individual pastured beef cattle.
190 Implementation of an updated beef energetics and body composition model in the Crop Livestock Enterprise Model (CLEM)
Authors: Dougherty James C H , Keogh Thomas , Liedloff Adam C , Thomas Dean T 
Published: September 2024

Abstract
The Crop Livestock Enterprise Model (CLEM) is a whole-farm bioeconomic model designed to simulate and explore ruminant performance across a wide range of production systems and management strategies. The model features a flexible, component-based structure that allows users to simulate multiple types of livestock production within the same system. Animals in the model are represented on an individual basis, allowing users to explore the effects of between-animal variation on a wide range of performance metrics at the animal and farm system levels. Recently, two new features were introduced to improve ability of CLEM to represent ruminant production systems: a user-defined timestep, and a new energetics model (based on the Australian ruminant feeding standards) that adds the ability to model changes in body composition in addition to existing predictions of body weight gain and feed intake. The change in timestep from monthly to daily was required to implement the new energetics model and allows for greater ability to compare CLEM results against field data, but other timesteps (e.g., weekly) can also be used depending on user preference. The Australian ruminant feeding standards were integrated with the existing CLEM modelling framework to create a revised energetics model for CLEM capable of predicting body composition, with additional updates to prediction of relative feed intake and the effect of diet type on feed quality. The energetics model was then evaluated for prediction of feed intake (DMI), final empty body weight (EBW), and fat and protein gain (Table 1) in feedlot cattle. The evaluation dataset consisted of treatment means (n = 29) from studies of Angus or British cross steers whose body composition (fat and protein) had been measured by serial slaughter. The updated model performed well for predicting final EBW, underpredicting by 2.35 kg on average (0.55% of the observed mean). Dry matter intake was underpredicted for 80% of treatments, with mean bias averaging 1.7 kg/d across all treatments and a root mean square prediction error (RMSPE, % of the observed mean) of 25%. Data on fat and protein gain was more variable than for EBW, and the model overpredicted protein gain and underpredicted fat gain in general, with mean bias of -51 g/d (RMSPE 42%) for protein and 270 g/d (RMSPE 58%) for fat. The addition of a daily timestep and a revised energetics model add to utility of CLEM by allowing for more in-depth exploration of the effects of feeding and management over time on intake, body weight gain, and body composition. The current version of CLEM can be downloaded from the APSIM Initiative website; and an upcoming update with additional options for prediction of intake and performance for both feedlot and grazing cattle will be made available.
251 Effect of diets containing soybean co-products formulated for developing heifers on reproductive efficiency
Authors: Midkiff Kirsten A , Kegley Elizabeth B , Cheek Robin A , Galloway Doug L , Reynolds Jana L , Harness Alexis , Looney Charles R , Littlejohn Brittni P , Powell Jeremy G 
Published: September 2024

Abstract
The objectives of this study were to determine the effects of including soybean oil in supplemental diets for developing heifers on reproductive tract scores, time of puberty and cyclicity, and successful artificial insemination. Angus crossbred heifers [n = 80; body weight (BW) = 248 ± 21 kg) were sorted randomly into one of eight pastures (n = 10 heifers/pasture) and pastures were assigned randomly to one of two treatment groups (n = 4 pastures/treatment), being: 1) control group fed an isonitrogenous and isocaloric grain supplement with no soy product (CON); and 2) treated group fed grain supplemented with soybean oil at 2% of estimated total diet dry matter intake (SBO). Heifers grazed 2.4 ha mixed grass pastures and when forage was limited heifers were offered bermudagrass hay for ad libitum intake. Supplements were offered beginning approximately 30 d after weaning and continued through the breeding season. Body weights, hair coat scores, and body condition scores (BCS) were recorded monthly. When heifers weighed &gt; 295 kg, rectal palpation was performed and an ultrasound used to determine ovary size, dominant follicle size (&gt; 10 mm), and follicular structures on the ovary (presence or absence of corpus luteum), and the tone and diameter of the uterine horns were determined (reproductive tract score; RTS). At 7-d intervals beginning on d 56, blood samples were collected via jugular venipuncture. Samples were used to measure serum progesterone concentrations to determine the percentage of heifers pubertal and cyclic. Heifers were classified as pubertal when serum progesterone concentrations were greater than 1 ng/mL. Heifers that maintained progesterone concentrations greater than 1 ng/mL for two consecutive samples were classified as cyclic. Cyclic heifers were not sampled further. Heifers were bred by artificial insemination (AI) at approximately 14 mo of age. Statistical analyses were performed using the MIXED and GLIMMIX procedures of SAS 9.4 (Cary, NC) to assess treatment effects. Treatment had no effect on hair coat shedding scores (P = 0.87), BCS (P = 0.13), and RTS (P = 0.27). Pubertal (P = 0.39) and cyclicity (P = 0.34) status were not affected by treatment. The percentage of females pubertal and cyclic by d 147 were numerically greater for the CON treatment (89.3% vs. 90.1%) than on the SBO treatment (80.5% and 75.2%). Heifers supplemented with SBO had numerically greater AI conception compared with CON supplemented heifers (52.6% vs. 42.5 %, respectively), but were not statistically different (P = 0.38). Further research is being performed to gather additional data for AI and overall pregnancy rates, effects of soybean co-product inclusion in supplements on uterine blood flow and corpus luteum perfusion, and resulting calf performance to AI-bred females.