Denise Konetchy

IntroductionWildfire smoke degrades air quality across the United States, including major dairy-producing regions, largely through emissions of fine particulate matter (PM2.5). Although wildfire smoke is a well-recognized public health concern, its impacts on livestock health and productivity remain poorly characterized. This study evaluated respiratory function and immune and metabolic responses in lactating Holstein cows exposed to wildfire smoke.MethodsPrimiparous (n = 8) and multiparous (n = 13) cows housed in open-air freestall pens were monitored during the 2024 wildfire season (July-October). Sampling occurred opportunistically following naturally occurring wildfire smoke events. Environmental data, including PM2.5 concentration, air temperature, and relative humidity were obtained from a monitoring station located 5.7 km from the farm. Air temperature and relative humidity were used to calculate temperature-humidity index (THI). Daily milk yield (MY) was recorded. Blood, milk, and pulmonary function measurements, including tidal volume (VT), minute ventilation (VE), and respiratory rate (RR) were collected at three time points: 1 day after each of two separate 72-h wildfire smoke episodes (WF1 and WF2), and once two weeks later under low ambient PM conditions (LP). Blood hematology, metabolites, acute phase proteins, and milk composition were evaluated. At WF1 and LP, phagocytosis of granulocytes in whole blood was measured, and blood granulocytes and mononuclear cells were isolated for gene expression.ResultsWildfire smoke exposure altered breathing patterns, characterized by reduced VT and increased RR, while VE remained unchanged. Plasma haptoglobin concentration was greater at WF1 than at WF2 and LP. The proportion of phagocytosing granulocytes was higher at WF1 compared with LP, and expression of IL1B, CXCL8, TNF, and SELL was upregulated in circulating immune cell populations during WF1 relative to LP. Elevated PM2.5 interacted with THI to reduce MY on lag day 6 and 7. Milk fat percentage was lower at WF2 and LP, compared with WF1. Concentrations of plasma β-hydroxybutyrate and non-esterified fatty acids were greater at WF1 compared to WF2 and LP, whereas glucose concentration was reduced at WF1 relative to WF2 and LP.DiscussionAlthough stage of lactation likely contributed to some extent to these inflammatory and metabolic changes, the present findings demonstrate that even moderate wildfire-PM2.5 exposure is associated with altered pulmonary function and coordinated immune and metabolic responses in lactating dairy cows.

The objective of this study was to examine the effect of feeding colostrum once versus twice on growth and passive transfer immunity (PTI) of preweaning Hol-stein calves by measuring BW, withers height (WH), as well as serum total protein (STP) and Brix values.
On the day of birth (des-ignated as d 1), 70 Holstein calves were weighed and as-signed randomly to one of the colostrum feeding groups: 1-feeding, n = 34; or 2-feeding, n = 36. Both groups re-ceived 4 L of pasteurized high-quality first-milking colos-trum (Brix > 23%) between 2.5 and 3 h after birth. The 2-feeding group received an additional 2 L of first-milking colostrum 8 to 10 h after the first feeding. Thereafter, all calves were fed 3.5 L of pasteurized whole milk twice daily and provided ad libitum access to calf starter. Blood samples, WH, and BW were obtained on d 3 and 7. Also, WH and BW were measured on d 30 and 45. Health status was scored and recorded during the experiment. Serum Brix and STP were measured using digital and optical refractometers, respectively. The differences in Brix, STP, IgG, WH, and BW were analyzed by ANOVA, repeated measures.
Body weight, WH, and ADG (d 1 to 45) were not different in calves fed 2 doses of pasteurized colostrum or fed 1 dose of colostrum. Fur-thermore, during the first 45 d after birth, no mortality or morbidity were observed in the 2 groups. Mean STP and Brix were affected by treatment and feeding frequency by day interaction. On d 3, mean STP and Brix were greater in 2-feeding than 1-feeding (STP: 7.4 vs. 7.1 ± 0.1 g/dL; Brix: 10.9% vs. 10.3% ± 0.1%), respectively. Mean STP and Brix decreased in both groups by d 7, but tended to be greater in 2-feeding than 1-feeding (STP: 7.3 vs. 6.5 ± 0.2 g/dL; Brix: 10.7% vs. 9.8% ± 0.2%).
Well-established evidence supports the importance of colostrum quality, cleanliness, and timing for calf immunity, but the effects of feeding frequency on PTI and calf performance are in-consistent. Despite marginal differences in serum Brix and STP between the 1- and 2-feeding groups, both measures were above the recommended critical thresholds, sug-gesting that successful passive transfer of immunity was achieved with either 1 or 2 timely feedings of pasteurized high-quality colostrum. The colostrum frequency treat-ment did not influence the growth performance and health of preweaning calves.

Background
Establishing a comprehensive characterization of the regulatory landscapes of cattle tissues facilitates a better understanding of the biological mechanisms responsible for condition-dependent phenotypes that drive tissue-specific gene regulation, developmental processes, and responses to environmental or physiological cues. This can be achieved through the characterization of gene expression, transcript usage and open chromatin accessibility. While much of this work has been done in human and biomedical model species, there is a lack of research in cattle that jointly characterizes chromatin accessibility and transcript usage alongside gene expression to define tissue-specific regulatory landscapes in cattle. Samples of prefrontal cortex (PFC), liver (L), and gracilis skeletal muscle (SM) were collected from four 3-month-old Angus steers and subjected to ATAC-seq and RNA-seq analyses. Differential gene expression (DGE) and transcript usage (DTU) were quantified across the tissues and evaluated in PFC-L, PFC-SM, and L-SM pairwise comparisons.

Results
In total, 4,840, 4,151, and 3,663 genes were identified as differentially expressed, while 209, 236, and 154 genes exhibited differential transcript usage in PFC-L, PFC-SM, and L-SM comparisons, respectively. The genes CLTA, SLC25A3 and P2RX5 were highlighted for DTU between tissues, and further comparison of predicted protein sequences identified structural differences between CLTA and P2RX5 isoforms suggesting tissue-specific roles. Differential chromatin accessibility analysis revealed 2,576, 1,820, and 2,960 differential peaks in promoter regions across the same pairwise tissue comparisons. Functional enrichment revealed that PFC regulatory genes were associated with synaptic formation, myelination, and neurodevelopment, L genes with homeostatic regulation and lipid metabolism, and SM genes with muscle differentiation, myonuclear addition, and hypertrophy. These patterns aligned with ATF, HNF, and MEF2 motif enrichment in PFC, L, and SM promoter peaks, respectively. Furthermore, the integration of ATAC-seq and RNA-seq results revealed 62 genes in PFC, 93 genes in L, and 59 genes in SM as potential tissue-specific regulatory genes.

Conclusions
These findings provide insight into the complex regulatory mechanisms governing biological processes in the PFC, L, and SM of young Angus steers. This work integrates chromatin accessibility, transcript usage, and gene expression across multiple physiologically important cattle tissues, providing a comprehensive view of tissue-specific regulatory landscapes and generating a resource to support future studies in cattle genomics.

DNA 5-methylcytosine (5mC) and RNA N6-methyladenosine (m6A) methylation are prevalent modifications in eukaryotes, both playing crucial roles in gene regulation. Recent studies have explored their crosstalk and impact on transcription. However, the intricate relationships among 5mC, m6A, and gene expression remain incompletely elucidated.
We collect data on 5mC, m6A, and gene expression from samples from three tissues from each of four pregnant cattle and sheep. We construct a comprehensive genome-wide self-interaction (same gene) and across-interaction (across genes) network of 5mC and m6A within gene-bodies or promoters and gene expression in both species. Qualitative analysis identifies uniquely expressed genes with specific m6A methylation in each tissue from both species. A quantitative comparison of gene expression ratio between methylated and unmethylated genes for m6A within gene body and promoter, and 5mC within gene body and promoter confirms the positive effect of RNA methylation on gene expression. Importantly, the influence of RNA methylation on gene expression is stronger than that of DNA methylation. The predominant self- and across-interactions are between RNA methylation within gene bodies and gene expression, as well as between RNA methylation within promoters and gene expression in both species.
RNA methylation has a stronger effect on gene expression than does DNA methylation within gene bodies and promoters. DNA and RNA methylation in gene-bodies has a greater impact on gene expression than those in promoters. These findings deepen comprehension of the dynamics and complex relationships among the epigenome, epitranscriptome, and transcriptome, offering fresh insights for advancing epigenetics research.

Introduction: Health and performance of dairy calves can be influenced by the intra-uterine environment. Environmental stressors such as heat stress, maternal inflammatory status, and nutrient deficiencies have been shown to impair intra-uterine and postnatal development in dairy cattle, with implications for long-term productivity. Recent studies in primates have reported lower birth weights and altered infant inflammatory markers associated with maternal exposure to wildfire smoke particulate matter (wildfire-PM2.5) during pregnancy. However, the impact of intra-uterine exposure to wildfire-PM2.5 on dairy calf growth and health is unknown.
Methods: Holstein heifer calves were born to cows exposed (WFS, n = 17) or unexposed (CON, n = 26) to wildfire smoke during mid gestation. Calves were monitored from birth through 6 months of life to evaluate growth patterns, health, and basal metabolic and inflammatory markers.
Results: Although there was no difference detected between groups in gestation length or calf frame size at birth, WFS calves had lower birth weights compared with that of CON (36.87 ± 0.87 kg vs. 40.82 ± 0.80 kg). WFS calves had greater average daily gain in the pre-weaning period but lower gain in the post-weaning period compared with CON. WFS calves also had greater plasma glucose concentrations in the pre-weaning period, lower β-hydroxybutyrate concentrations in the early post-weaning period, and greater non-esterified fatty acid concentrations for much of the pre-weaning and the early post-weaning period relative to those for CON calves. In addition, WFS calves had lower white blood cell counts throughout the preweaning period, coupled with greater serum albumin and lower serum amyloid A through the study, as well as lower haptoglobin concentrations at approximately 3 months of age. All calves received adequate passive transfer of immunity, but WFS calves had greater serum IgG concentrations, yet no difference was detected in apparent efficiency of IgG absorption compared with that for CON. WFS calves had lower odds of lung consolidation throughout the study.
Discussion: Overall, these results indicate that prenatal exposure to wildfire particulates restricts fetal growth and programs postnatal calf metabolic and immune systems, which may have implications for future health and productivity.

Transportation can compromise health and production performance in young calves. Although widely accepted that the younger calves are, the greater the probability of negative outcomes, there still is a lack of evidence-based recommendations on the minimum age at transportation. Our objective was to evaluate the impact of transport age on growth performance, incidence of scours, and plasma metabolites over the first 28 d post-transport in Charolais × Holstein crossbred calves. Calves (n = 36) ages 2, 4, 8 and 14-d old were transported in summer from a commercial farm to an on-campus calf rearing facility (410 miles). Calf body weight (BW) was recorded before departure, on arrival and d 28 post-transport. Dry matter intake (DMI) and fecal scores were recorded daily. Blood samples collected prior to transportation, on arrival, and d 7 and 28 post-transport were used for targeted metabolomics analysis (Biocrates MxP Quant 500 kit). Growth performance and fecal score data were analyzed using PROC MIXED (SAS) whereas R was used for predictive modeling of metabolomics data. Over the 28-d period post-transport, DMI was greater (P < 0.01) for 14 d than 2 and 4 d old calves; however, it did not differ between 2, 4, and 8 d old calves. Average daily gain (ADG) and feed efficiency (FE) were also greater (P < 0.01) for 14 d than 2, 4, and 8 d old calves. During wk 1 post-transport, the total number of days calves had scours was least (P < 0.01) for 2 and 14 d, intermediate for 4 d, and greatest for 8 d old calves. During wk 2, the total number of days with scours was less (P < 0.01) for 8 and 14 d (average of 2 d) compared with 2 and 4 d old calves (5 d). Additionally, the total number of days calves had scours during the first 2 wk post-transport tended (P = 0.08) to be greater for 2, 4, and 8 d than 14 d old calves. However, during wk 3 and 4 post-transport, there were no differences (P ≥ 0.58) in the total number of days with scours across transport age. Arginine methylation, d 7 of measurements, carnitine uptake defect, phosphatidic acid 16:0:18:2, methylenetetrahydrofolate reductase, sodium, triglyceride 18:2:34:4, threonine, α-aminobutyric acid, and glycolithocholic acid 3-sulfate were the most important features in terms of predicting the occurrence of scours. Overall, DMI, ADG and FE were less for calves transported at 2, 4, and 8 d than at 14 d of age, which could partially be attributed to differences in the incidence rate of scours. In addition, several plasma metabolites could be good predictors of scours in transported calves.

The aim of this study was to determine the effect of the weaning calves at 2 ages (early vs. late) and 2 weaning paces (abrupt over 3 d vs. gradual over 14 d) on plasma oxylipids. Seventy-one dairy calves (38.8 ± 4.4 kg, body weight ± standard deviation), blocked by sex and body weight at birth, were randomly assigned in a 2 × 2 factorial arrangement of treatments. The factors were weaning age (early (6–7 weeks) vs. late (8–9 weeks)), and weaning pace (abrupt (3 weaning steps over 2 d) vs. gradual (7 weaning steps over 14 d)), generating 4 treatment groups: early-abrupt, early-gradual, late-abrupt, and late-gradual. Blood samples were collected from the jugular vein one day pre-weaning, and one day post-weaning. Oxylipids concentration was measured by liquid chromatography-tandem mass spectrometry. Fatty acid profile (including nonesterified fatty acids) was also assessed. Weaning pace, age, pace × age, body weight at birth, and sex were included as fixed effect and cohort was included as random effect in the model. Linoleic acid derivatives 13- oxooctadecadienoic (OxoODE) and 9-OxoODE had a greater concentration in calves abruptly weaned when compared with that for gradually weaned calves. Calves weaned gradually showed a greater concentration of 9- hydroxyoctadecadienoic (HODE), 13-HODE, 12,13- dihydroxyoctadecenoic (DiHOME), 9,10-DiHOME, all linoleic acid-derived compared with that for abruptly weaned calves. Anti-inflammatory oxylipid 17,18- dihydroxyeicosatrienoic (DiHETE), an eicosapentaenoic acid (EPA) derivative, was greater in calves abruptly weaned compared with gradual. Overall, pace of weaning affected the plasma concentration of oxylipids, demonstrating that weaning pace affects the oxylipids status involved in inflammation in dairy calves.

Mycoplasma ovipneumoniae is associated with respiratory disease in wild and domestic Caprinae globally, with wide variation in disease outcomes within and between host species. To gain insight into phylogenetic structure and mechanisms of pathogenicity for this bacterial species, we compared M. ovipneumoniae genomes for 99 samples from 6 countries (Australia, Bosnia and Herzegovina, Brazil, China, France and USA) and 4 host species (domestic sheep, domestic goats, bighorn sheep and caribou). Core genome sequences of M. ovipneumoniae assemblies from domestic sheep and goats fell into two well-supported phylogenetic clades that are divergent enough to be considered different bacterial species, consistent with each of these two clades having an evolutionary origin in separate host species. Genome assemblies from bighorn sheep and caribou also fell within these two clades, indicating multiple spillover events, most commonly from domestic sheep. Pangenome analysis indicated a high percentage (91.4 %) of accessory genes (i.e. genes found only in a subset of assemblies) compared to core genes (i.e. genes found in all assemblies), potentially indicating a propensity for this pathogen to adapt to within-host conditions. In addition, many genes related to carbon metabolism, which is a virulence factor for Mycoplasmas, showed evidence for homologous recombination, a potential signature of adaptation. The presence or absence of annotated genes was very similar between sheep and goat clades, with only two annotated genes significantly clade-associated. However, three M. ovipneumoniae genome assemblies from asymptomatic caribou in Alaska formed a highly divergent subclade within the sheep clade that lacked 23 annotated genes compared to other assemblies, and many of these genes had functions related to carbon metabolism. Overall, our results suggest that adaptation of M. ovipneumoniae has involved evolution of carbon metabolism pathways and virulence mechanisms related to those pathways. The genes involved in these pathways, along with other genes identified as potentially involved in virulence in this study, are potential targets for future investigation into a possible genomic basis for the high variation observed in disease outcomes within and between wild and domestic host species.

The objective of this study was to evaluate the effects of weaning age and pace on blood metabolites, cortisol concentration, and mRNA abundance of inflammation-related genes in Holstein dairy calves. Seventy-one day-old calves [38.8 ± 4.4 kg, body weight (BW) ± sd] blocked by gender and birth BW, were randomly assigned to a 2 × 2 factorial arrangement of treatments. The first factor was weaning age [6 weeks (early) vs. Eight weeks (late)], the second factor was weaning pace [abrupt (4 step-down over 3 d, the initial milk replacer was 7.6 L, which was reduced 1.9 L in each step-down) vs. gradual (7 step-down over 14 d, the initial milk replacer was 7.6 L, which was reduced 1.09 L in each step-down)], generating early-abrupt (EA), early-gradual (EG), late-abrupt (LA), and late-gradual (LG) treatments. All treatments had 10 female and 8 male calves, except EA that had 1 fewer male calf. Milk replacer (MR; 24% CP, 17% fat) was bottle-fed, up to 1,200 g/d, twice daily (0600h and 1800h). EA and EG calves received 46.2 kg MR while LA and LG calves received a total of 63 kg MR. The study had 2 cohorts (2020, n = 40; 2021, n = 31), and each cohort included all treatments. Blood was collected from the jugular vein at 0900h on d 3 and d 7 of age, a day before starting and a day after weaning completion; male calves were humanely killed a day post-weaning. Rumen, jejunum, large intestine, liver, omental adipose and perirenal adipose tissues were sampled to determine the mRNA abundance of inflammation-related genes. Weaning pace, age, and pace × age, birth BW, and sex were included as fixed and cohort was included as random effects in the model. Blood metabolites and cortisol were analyzed as repeated measure, and sampling day, pace × sampling day, and age × sampling day were also included as additional fixed effects. Significance were noted at P ≤ 0.05 and tendencies when 0.05