Open Access Publications

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Open access publications by faculty, postdocs, and graduate students in the Department of Animal and Food Sciences.

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Influence of an inoculant containing Lentilactobacillus hilgardii, Lentilactobacillus buchneri, and Pediococcus pentosaceus on the aerobic stability and nutrient degradability of whole-plant corn ensiled at different dry matter levels
(Animal Feed Science and Technology, 2025-12-08) Liu, X; Romero, N.; Cronin, S.K.; da Silva, E.B.; Kung Jr., L.; Gressley, T.F.
Two experiments were conducted to evaluate the effects of an inoculant containing Lentilactobacillus hilgardii CNCM-I-4785, Lentilactobacillus buchneri NCIMB 40788, Pediococcus pentosaceus NCIMB 12455, β-glucanase, and xylanase on the fermentation profile, aerobic stability, and nutrient degradability of whole-plant corn silage. In Experiment 1, a brown midrib corn hybrid was harvested at 35.4 % dry matter (DM) and ensiled for 14 and 90 d. In Experiment 2, a conventional corn hybrid was harvested at either a low DM content (26.2 %) or a high DM content (39.7 %) and ensiled for 30, 60, 120, and 180 d. In Experiment 1, inoculation increased acetic acid concentrations at both 14 and 90 d and markedly improved aerobic stability at 90 d (+ 360 h). In Experiment 2, inoculation increased acetic acid concentrations at 60, 120, and 180 d in both DM levels and at 30 d only in low DM. Inoculation improved aerobic stability at 30 (+ 30 h), 120 (+111 h), and 180 d (+ 89 h) across both DM levels. At 60 d, the increase in stability by inoculation was greater in low DM (+ 58 h) than in high DM silage (+ 36 h). Inoculation enhanced starch degradability by 9.8 %age points at 90 d in Experiment 1, and by 4.7 and 2.7 %age points at 120 and 180 d, respectively, in Experiment 2. Overall, the inoculant effectively enhanced aerobic stability and starch degradability across two hybrids and three distinct DM levels.
The swine IsoLoop model of the gut host-microbiota interface enables intra-animal treatment comparisons to advance 3R principles
(Gut Microbes, 2025-10-25) Bayne, Jenna; Charavaryamathc, Chandrashekhar; Hue, Yoonsung; Yousefie, Farnaz; Murphy, Morgan; Law, Andy; Michael, Alyona; Muyyarikkandy, Muhammed Shafeekh; Nibbering, Britt; Smits, Wiep Klaas; Kuijper, Ed; Opriessnig, Tanja; Sauerk, Mary; Scarial, Joy; Sponsellern, Brett; Ramirez, Alejandro; Mooyottu, Shankumar
Understanding gut–host microbiota interactions requires models that replicate human physiology while providing region-specific resolution, translational precision, and mini-mal animal use. To this end, we developed the IsoLoop model, a swine gut loop platform enabling intra-animal, multi-treatment comparisons. Microbiota-depleted ileal loops were surgically created in pigs, maintaining neurovascular integrity while isolating them from the anastomosed digestive tract. In Experiment 1, loops were inoculated with human fecal microbiota (HFM) or HFM combined with Peptacetobacter hiranonis. In Experiment 2, they were inoculated with Clostridioides difficile. Host–microbiota interactions were compared with respective controls in each experiment. The IsoLoop model reduced animal use by 75% compared to conventional whole-animal designs. Following antibiotic-induced depletion, loops re-established microbial diversity by day 5, despite reduced richness and loss of taxa, including Lactobacillus. HFM transplantation in microbiota-depleted loops induced robust tran-scriptomic recovery, enriched Akkermansia and Bifidobacterium, and restored specific metabolic pathways, although taxonomic and metabolic restoration remained incomplete and divergent. P. hiranonis promoted normal ileum-like metagenomic functional convergence, activated epithelial repair pathways, and increased specific secondary bile acids. C. difficile challenge recapitulated early infection pathology in IsoLoops. The IsoLoop model offers an ethical and precise platform for investigating host–microbiota crosstalk, localized enteric pathologies, and therapeutic interventions.
Impact of heat stress on the post-hatch growth, morphometrics, and allometry ofthe chicken (Gallus gallus)
(British Poultry Science, 2025-09-01) Schmidt, C J; Feinberg, A. J.; Brannick, E. M.
1. Heat stress negatively affects animal growth. This study examined the impact of heat stress on a modern broiler (Ross 708) chicken compared to a heritage meat-type chicken line (UIUC). 2. To mimic the effects of a heat wave, birds were exposed to daily, cyclic high ambient temperatures between post-hatch d 21-42, while control birds were maintained at thermoneutral temperature throughout this period. 3. On d 28 and 42 post-hatch, eight heat-stressed and eight control birds from both lines were weighed, necropsied and total organ masses were determined for the brain, breast muscle, liver, small intestine, and spleen. 4. Normalised tissue mass at d 42 under thermoneutral conditions for the Ross 708 breast muscle was 2.4-fold larger than that of the UIUC chickens. The cross-sectional area of the Ross 708 breast muscle cells was also twofold larger than that of the UIUC birds. In contrast, UIUC birds had larger heart, spleen, duodenum, jejunum, ileum and brain masses than the Ross 708 chickens when raised at the thermoneutral temperature. 5. These results indicated that heat-stress shifted growth resources away from immune, skeletal muscle, neuronal and hepatic systems to maintain the heart and small intestine.
Biological soil amendments can support survival of pathogenic and non-pathogenic Escherichia coli in soils and sporadic transfer to Romaine lettuce
(International Journal of Food Microbiology, 2025-03-07) Xiong, Zirui Ray; Gabriel, Ellen; Gutierrez, Alan; East, Cheryl; Kniel, Kalmia E.; Danyluk, Michelle D.; Jay-Russell, Michele; Sharma, Manan
Biological soil amendments (BSAs) are essential agricultural inputs that provide critical nutrients in organic leafy green production. Heat-treated poultry pellets (HTPP) and seabird guano (SBG), which have been treated to reduce microbial pathogen loads, are gaining popularity among growers. Using these BSAs in the process of side-dressing, providing nutrients to crops while growing, may provide opportunities for externally introduced bacterial pathogens to survive in soil. In this study, Romaine lettuce was grown in soils in a controlled environmental growth chamber. Soils were side-dressed twice with different combinations of treated BSAs: HTPP, SBG, and corn steep liquor (CSL). Soils were co-inoculated with non-pathogenic E. coli and two E. coli O157:H7 strains at the second of two side-dressing events. Survival of E. coli in soils over 28 days was evaluated. On day 28 post inoculation, two heads of Romaine lettuce from each planter were harvested, and the presence of E. coli on leaves was determined. Four nonlinear statistical models were fit to predict survival of E. coli in soils. In all soils regardless of BSA treatment, E. coli TVS 353 declined by 4.08–4.51 log CFU/g soil over 28 days, and E. coli O157:H7 declined by 2.77–4.3 log CFU/g soil over 28 days. E. coli TVS 353 and O157:H7 were recovered from 13.3 % (6/45) and 11.1 % (5/45) of plants, respectively. Transfer of E. coli from soils to Romaine lettuce was low, sporadic, and could not be measured quantitatively. Side-dressing with treated BSAs used in organic lettuce production supported but did not enhance survival of E. coli in side-dressed soils under controlled environmental conditions. Highlights • Soils were amended with BSAs to grow Romaine lettuce in environmental chambers. • Some treated BSAs facilitated a rapid decline of E. coli O157:H7 in soils. • Treated BSAs supported but did not enhance survival of E. coli in soils. • Transfer of E. coli from soils to lettuce was low and sporadic.
Fecal microbiota transplantation modulates jejunal host-microbiota interface in weanling piglets
(Microbiome, 2025-02-07) Mooyottu, Shankumar; Muyyarikkandy, Muhammed Shafeekh; Yousefi, Farnaz; Li, Ganwu; Sahin, Orhan; Burrough, Eric; Scaria, Joy; Sponseller, Brett; Ramirez, Alejandro
Background Weaning-associated enteric diseases are a major concern in the swine industry. This study investigates the effects of fecal microbiota transplantation (FMT) on the jejunum of weanling piglets, a segment of bowel less studied in terms of microbiomic changes despite its primary involvement in major post-weaning enteric diseases, including postweaning diarrhea (PWD). Thirty-two 3-week-old piglets were divided equally into two groups: Control and FMT. The FMT group received fecal microbiota preparation from 3-month-old healthy pigs on the 1st and 3rd day after weaning. Half of each group was inoculated with an enterotoxigenic E. coli (ETEC) isolate 10 days post-FMT. Piglets were euthanized in the third week (14th and 18th days post-FMT) after weaning to collect intestinal tissues and contents for microbiomic, metabolomic, and transcriptomic analyses. Results The jejunal microbiota showed a significant increase in alpha diversity in the third week post-FMT compared with the ileum and colon. FMT significantly enriched the jejunal microbiota composition, while multiple bacterial genera were specifically lacking in control weanling piglets. FMT was strongly associated with the enrichment of the genus Pseudoscardovia of the Bifidobacteriaceae family, which was found lacking in the jejunum of weanling control piglets and inversely associated with the abundance of the genus Bifidobacterium within the same family. Other genera associated with FMT included Solobacterium, Shuttleworthia, and Pseudoraminibacter, whereas bacteria such as Erysipelotrichaceae and Acidaminococcus were identified as most abundant in the control piglets. Metabolomic analysis revealed a significant modulatory effect of FMT on carbohydrate, amino acid, nucleotide, vitamin, and xenobiotic metabolisms, suggesting improved nutrient utilization. Transcriptomic analyses further confirmed the regulatory effects of FMT on gene expression associated with immune, metabolic, barrier, and neuroendocrine functions. Prior FMT treatment in the context of ETEC infection indicated a potential protective role, as evidenced by a significant shift in microbial diversity and metabolomic compositions and decreased diarrhea severity even though no effect on pathogen shedding was evident. Conclusions This study underscores the promise of FMT in enhancing jejunal health. In addition, the results suggest that FMT could be considered a potential strategy to address conditions associated with small intestinal dysbiosis in swine and other monogastric species with similar gut anatomy and physiology, such as humans. Video Abstract available at: https://doi.org/10.1186/s40168-025-02042-9
Ergotism in an organic sow herd and the impact on lactation performance and subsequent reproductive performance
(Journal of Swine Health and Production, 2025-01-16) Senatra, Katrina; Gaab, Tara; Pierdon, Meghann
Ergot alkaloids (EA) are produced by fungi, including Claviceps purpurea, which can lead to EA contamination of wheat and cereal grains and cause sow agalactia by inhibiting prolactin production. In this case of sow agalactia and increased piglet mortality, a diagnosis of ergotism was made based on clinical signs and feed analysis. The lactation diet had EA at 330 ppb and was fed to sows for 12 to 14 days resulting in 79% (50%) mean (SD) mortality in exposed litters. Ergot alkaloid levels as low as 0.33 mg/kg of feed (0.33 ppm) may result in clinical signs in lactating sows.
Understanding the liver under heat stress with statistical learning: an integrated metabolomics and transcriptomics computational approach
(BMC Genomics, 2019-06-17) Hubbard, Allen H.; Zhang, Xiaoke; Jastrebski, Sara; Singh, Abhyudai; Schmidt, Carl J.
Background We present results from a computational analysis developed to integrate transcriptome and metabolomic data in order to explore the heat stress response in the liver of the modern broiler chicken. Heat stress is a significant cause of productivity loss in the poultry industry, both in terms of increased livestock morbidity and its negative influence on average feed efficiency. This study focuses on the liver because it is an important regulator of metabolism, controlling many of the physiological processes impacted by prolonged heat stress. Using statistical learning methods, we identify genes and metabolites that may regulate the heat stress response in the liver and adaptations required to acclimate to prolonged heat stress. Results We describe how disparate systems such as sugar, lipid and amino acid metabolism, are coordinated during the heat stress response. Conclusions Our findings provide more detailed context for genomic studies and generates hypotheses about dietary interventions that can mitigate the negative influence of heat stress on the poultry industry.
Transcriptomic and metabolomic characterization of post-hatch metabolic reprogramming during hepatic development in the chicken
(BMC Genomics, 2021-05-24) Van Every, Heidi A.; Schmidt, Carl J.
Background Artificial selection of modern meat-producing chickens (broilers) for production characteristics has led to dramatic changes in phenotype, yet the impact of this selection on metabolic and molecular mechanisms is poorly understood. The first 3 weeks post-hatch represent a critical period of adjustment, during which the yolk lipid is depleted and the bird transitions to reliance on a carbohydrate-rich diet. As the liver is the major organ involved in macronutrient metabolism and nutrient allocatytion, a combined transcriptomics and metabolomics approach has been used to evaluate hepatic metabolic reprogramming between Day 4 (D4) and Day 20 (D20) post-hatch. Results Many transcripts and metabolites involved in metabolic pathways differed in their abundance between D4 and D20, representing different stages of metabolism that are enhanced or diminished. For example, at D20 the first stage of glycolysis that utilizes ATP to store or release glucose is enhanced, while at D4, the ATP-generating phase is enhanced to provide energy for rapid cellular proliferation at this time point. This work has also identified several metabolites, including citrate, phosphoenolpyruvate, and glycerol, that appear to play pivotal roles in this reprogramming. Conclusions At Day 4, metabolic flexibility allows for efficiency to meet the demands of rapid liver growth under oxygen-limiting conditions. At Day 20, the liver’s metabolism has shifted to process a carbohydrate-rich diet that supports the rapid overall growth of the modern broiler. Characterizing these metabolic changes associated with normal post-hatch hepatic development has generated testable hypotheses about the involvement of specific genes and metabolites, clarified the importance of hypoxia to rapid organ growth, and contributed to our understanding of the molecular changes affected by decades of artificial selection.
Transcriptome response to heat stress in a chicken hepatocellular carcinoma cell line
(Cell Stress and Chaperones, 2024-01-05) Sun, Liang; Lamont, Susan J.; Cooksey, Amanda M.; McCarthy, Fiona; Tudo, Catalina O.; Vijay-Shanker, K.; DeRita, Rachael M.; Rothschild, Max; Ashwell, Chris; Persia, Michael E.; Schmidt, Carl J.
Heat stress triggers an evolutionarily conserved set of responses in cells. The transcriptome responds to hyperthermia by altering expression of genes to adapt the cell or organism to survive the heat challenge. RNA-seq technology allows rapid identification of environmentally responsive genes on a large scale. In this study, we have used RNA-seq to identify heat stress responsive genes in the chicken male white leghorn hepatocellular (LMH) cell line. The transcripts of 812 genes were responsive to heat stress (p < 0.01) with 235 genes upregulated and 577 downregulated following 2.5 h of heat stress. Among the upregulated were genes whose products function as chaperones, along with genes affecting collagen synthesis and deposition, transcription factors, chromatin remodelers, and genes modulating the WNT and TGF-beta pathways. Predominant among the downregulated genes were ones that affect DNA replication and repair along with chromosomal segregation. Many of the genes identified in this study have not been previously implicated in the heat stress response. These data extend our understanding of the transcriptome response to heat stress with many of the identified biological processes and pathways likely to function in adapting cells and organisms to hyperthermic stress. Furthermore, this study should provide important insight to future efforts attempting to improve species abilities to withstand heat stress through genome-wide association studies and breeding.
Identifying mechanisms of regulation to model carbon flux during heat stress and generate testable hypotheses
(PLoS ONE, 2018-10-26) Hubbard, Allen H.; Zhang, Xiaoke; Jastrebski, Sara; Lamont, Susan J.; Singh, Abhyudai; Schmidt, Carl J.
Understanding biological response to stimuli requires identifying mechanisms that coordinate changes across pathways. One of the promises of multi-omics studies is achieving this level of insight by simultaneously identifying different levels of regulation. However, computational approaches to integrate multiple types of data are lacking. An effective systems biology approach would be one that uses statistical methods to detect signatures of relevant network motifs and then builds metabolic circuits from these components to model shifting regulatory dynamics. For example, transcriptome and metabolome data complement one another in terms of their ability to describe shifts in physiology. Here, we extend a previously described linear-modeling based method used to identify single nucleotide polymorphisms (SNPs) associated with metabolic changes. We apply this strategy to link changes in sulfur, amino acid and lipid production under heat stress by relating ratios of compounds to potential precursors and regulators. This approach provides integration of multi-omics data to link previously described, discrete units of regulation into functional pathways and identifies novel biology relevant to the heat stress response, in addition to generating hypotheses.
Comparison of a modern broiler line and a heritage line unselected since the 1950s
(Poultry Science, 2019-12-11) Schmidt, Carl J.; Persia, M.E.; Feierstein, E.; Kingham, B.; Saylor, W.W.
Selecting chicken for improved meat production has altered the relative growth of organs in modern broiler lines compared with heritage lines. In this study, we compared the growth and feed efficiency of a heritage line, UIUC, with a modern production line, Ross 708, for 5 wk posthatch. During this period, the BW and feed efficiency of the modern strain was higher than that of the heritage line, indicating that the Ross 708 birds were more efficient than the UIUC birds at converting feed to body mass. The relative growth of the breast, heart, liver, and intestine were also compared during these 5 wk. The breast muscle of the heritage line constituted 9% of the total body mass at 5 wk, whereas in the modern line, the breast muscle was 18% of the total mass of the bird. In contrast, the relative size of the heart decreased after d 14 in the modern line, suggesting that selection for increased breast muscle has translated into relatively less weight of the heart muscle. The liver matured earlier in modern lines, possibly improving nutrient utilization as the birds shift from lipid- to carbohydrate-rich feed. Finally, jejunal and ileal sections of the intestine were 20% longer in the modern line, perhaps allowing for increased nutrient absorption.
Chicken pituitary transcriptomic responses to acute heat stress
(Molecular Biology Reports, 2023-05-02) Pritchett, Elizabeth M.; Van Goor, Angelica; Schneider, Blair K.; Young, Meaghan; Lamont, Susan J.; Schmidt, Carl J.
Background Poultry production is vulnerable to increasing temperatures in terms of animal welfare and in economic losses. With the predicted increase in global temperature and the number and severity of heat waves, it is important to understand how chickens raised for food respond to heat stress. This knowledge can be used to determine how to select chickens that are adapted to thermal challenge. As neuroendocrine organs, the hypothalamus and pituitary provide systemic regulation of the heat stress response. Methods and Results Here we report a transcriptome analysis of the pituitary response to acute heat stress. Chickens were stressed for 2 h at 35 °C (HS) and transcriptomes compared with birds maintained in thermoneutral temperatures (25 °C). Conclusions The observations were evaluated in the context of ontology terms and pathways to describe the pituitary response to heat stress. The pituitaries of heat stressed birds exhibited responses to hyperthermia through altered expression of genes coding for chaperones, cell cycle regulators, cholesterol synthesis, transcription factors, along with the secreted peptide hormones, prolactin, and proopiomelanocortin.
Integrated Genomic Approaches to Characterize and Mitigate Heat Stress in Poultry
(Annual Review of Animal Biosciences, 2024-10-30) Schmidt, Carl J.; Lamont, Susan J.
With the burgeoning human population, climate change, and expansion of poultry production in hot climates, it is imperative to aid global food security by enhancing the resilience of thermally challenged poultry. As a complement to management approaches used to mitigate heat stress, we give selected examples of recent studies on heat stress in poultry using various omics technologies. An integrated analysis of positional and functional candidate genes is provided, highlighting the most prominent pathways involved in the heat stress response. We finish by discussing efficient strategies to enhance thermal tolerance of poultry by genomics approaches, advocating for preservation of biodiversity that may provide beneficial allelic variation, and identifying current and future challenges in producing climate-resilient poultry.
Transcriptome Analysis of Post-Hatch Breast Muscle in Legacy and Modern Broiler Chickens Reveals Enrichment of Several Regulators of Myogenic Growth
(PLoS ONE, 2015-03-30) Davis, Richard V. N.; Lamont, Susan J.; Rothschild, Max F.; Persia, Michael E.; Ashwell, Chris M.; Schmidt, Carl J.
Agriculture provides excellent model systems for understanding how selective pressure, as applied by humans, can affect the genomes of plants and animals. One such system is modern poultry breeding in which intensive genetic selection has been applied for meat production in the domesticated chicken. As a result, modern meat-type chickens (broilers) exhibit enhanced growth, especially of the skeletal muscle, relative to their legacy counterparts. Comparative studies of modern and legacy broiler chickens provide an opportunity to identify genes and pathways affected by this human-directed evolution. This study used RNA-seq to compare the transcriptomes of a modern and a legacy broiler line to identify differentially enriched genes in the breast muscle at days 6 and 21 post-hatch. Among the 15,945 genes analyzed, 10,841 were expressed at greater than 0.1 RPKM. At day 6 post-hatch 189 genes, including several regulators of myogenic growth and development, were differentially enriched between the two lines. The transcriptional profiles between lines at day 21 post-hatch identify 193 genes differentially enriched and still include genes associated with myogenic growth. This study identified differentially enriched genes that regulate myogenic growth and differentiation between the modern and legacy broiler lines. Specifically, differences in the ratios of several positive (IGF1, IGF1R, WFIKKN2) and negative (MSTN, ACE) myogenic growth regulators may help explain the differences underlying the enhanced growth characteristics of the modern broilers.
TransAtlasDB: an integrated database connecting expression data, metadata and variants
(Database: The Journal of Biological Databases and Curation, 2018-02-23) Adetunji, Modupeore O.; Lamont, Susan J.; Schmidt, Carl J.
High-throughput transcriptome sequencing (RNAseq) is the universally applied method for target-free transcript identification and gene expression quantification, generating huge amounts of data. The constraint of accessing such data and interpreting results can be a major impediment in postulating suitable hypothesis, thus an innovative storage solution that addresses these limitations, such as hard disk storage requirements, efficiency and reproducibility are paramount. By offering a uniform data storage and retrieval mechanism, various data can be compared and easily investigated. We present a sophisticated system, TransAtlasDB, which incorporates a hybrid architecture of both relational and NoSQL databases for fast and efficient data storage, processing and querying of large datasets from transcript expression analysis with corresponding metadata, as well as gene-associated variants (such as SNPs) and their predicted gene effects. TransAtlasDB provides the data model of accurate storage of the large amount of data derived from RNAseq analysis and also methods of interacting with the database, either via the command-line data management workflows, written in Perl, with useful functionalities that simplifies the complexity of data storage and possibly manipulation of the massive amounts of data generated from RNAseq analysis or through the web interface. The database application is currently modeled to handle analyses data from agricultural species, and will be expanded to include more species groups. Overall TransAtlasDB aims to serve as an accessible repository for the large complex results data files derived from RNAseq gene expression profiling and variant analysis.
Separation of Avian Preovulatory Follicle Granulosa and Theca Cell Layers for Downstream Applications
(Journal of Visualized Experiments, 2024-10-24) Kramer, Ashley E.; Ellwood, Kathryn M.; Brannick, Erin M.; Dutta, Aditya
Summary Here, we describe a protocol for separating yolk, granulosa cells, and theca cells in avian preovulatory follicles. This precision handling enables critical investigations into the role of these layers in reproductive function, aiding the understanding of follicular development, hormonal regulation, and disease research for enhanced agricultural yield and biomedical insights. Abstract Layer hens (egg-laying chickens) and broiler breeders (breeding stock for meat-producing chickens) are crucial to the world's food supply as a reliable source of protein. They are also an emerging animal model for the study of human reproductive disease. As the field of poultry research develops, the health and function of the layer hen and broiler breeder ovary will be an important point of study for both agricultural and biomedical researchers. One of the challenges presented by this emerging interest is the need for replicable techniques that all researchers can employ in ovarian specimen collection. In particular, a detailed visual process must be established to define the proper separation of the specialized granulosa and theca cell layers from hen follicles to achieve agreement and consistency among researchers. This study describes the extraction of preovulatory follicles and ovary tissue in white leghorn hens of prime reproductive age. The separation of these follicles is performed under cold, liquid conditions to congeal the yolk for easier manipulation and to prevent the follicle's own weight from tearing apart cell layers during the separation process. Once the separation is complete, the desired cell layers can be further digested for tissue culture approaches or can be cryopreserved for genomic and proteomic analyses.
Cross-species regulatory network analysis identifies FOXO1 as a driver of ovarian follicular recruitment
(Scientific Reports, 2024-12-28) Kramer, Ashley E.; Berral-González, Alberto; Ellwood, Kathryn M.; Ding, Shanshan; De Las Rivas, Javier; Dutta, Aditya
The transcriptional regulation of gene expression in the latter stages of follicular development in laying hen ovarian follicles is not well understood. Although differentially expressed genes (DEGs) have been identified in pre-recruitment and pre-ovulatory stages, the master regulators driving these DEGs remain unknown. This study addresses this knowledge gap by utilizing Master Regulator Analysis (MRA) combined with the Algorithm for the Reconstruction of Accurate Cellular Networks (ARACNe) for the first time in laying hen research to identify master regulators that are controlling DEGs in pre-recruitment and pre-ovulatory phases. The constructed ARACNe network included 10,466 nodes and 292,391 edges. The ARACNe network was then used in conjunction with the Virtual Inference of Protein-activity by Enriched Regulon (VIPER) for the MRA to identify top up- and down-regulated master regulators. VIPER analysis revealed FOXO1 as a master regulator, influencing 275 DEGs and impacting pathways related to apoptosis, proliferation, and hormonal regulation. Additionally, CLOCK, known as a crucial regulator of circadian rhythm, emerged as an upregulated master regulator in the pre-ovulatory stage. These findings provide new insights into the transcriptional landscape of laying hen ovarian follicles, offering a foundation for further exploration of follicle development and enhancing reproductive efficiency in avian species.
Transcriptomic data reveals MYC as an upstream regulator in laying hen follicular recruitment
(Poultry Science, 2024-11-24) Kramer, Ashley E.; Ellwood, Kathryn M.; Guarino, Nicole; Li, Cong-Jun; Dutta, Aditya
Understanding the mechanisms of follicular recruitment is essential for improving laying hen and broiler breeder productivity, as it directly influences egg production. Despite advancements in poultry breeding for enhanced egg production, the factors driving successful ovarian follicle maturation remain inadequately understood. This study investigates the genetic drivers mediating the transition of pre-recruitment follicles to the pre-ovulatory phase, a crucial stage before ovulation. Using RNA sequencing and bioinformatics approaches such as a differential gene expression analysis, we compared pre-recruitment follicles with the recently recruited F5 pre-ovulatory follicle to identify key genes and upstream regulators involved in this transition. Further validation through qRT-PCR confirmed these findings. Using Qiagen's Ingenuity Pathway Analysis we identified MYC proto-oncogene (C-Myc) as a pivotal upstream regulator, controlling genes essential for cell proliferation and differentiation. Additionally, TGFβ1 emerged as a key regulator, influencing pathways involving SMAD3, TNF, and TP53. The study highlights the intricate regulatory network involving MYC and other transcription factors such as CTNNB1, crucial for follicular development. These findings provide valuable insights into the molecular mechanisms governing follicular selection and maturation, which are essential for enhancing egg production efficiency. Future research should explore the roles of MYC, CTNNB1, and other driver genes in follicular development to further understand and improve reproductive efficiency in poultry.
The Meq Genes of Nigerian Marek’s Disease Virus (MDV) Field Isolates Contain Mutations Common to Both European and US High Virulence Strains
(Viruses, 2024-12-31) Patria, Joseph N.; Jwander, Luka; Mbachu, Ifeoma; Parcells, Levi; Ladman, Brian; Trimpert, Jakob; Kaufer, Benedikt B.; Tavlarides-Hontz, Phaedra; Parcells, Mark S.
Background: Marek’s disease (MD) is a pathology affecting chickens caused by Marek’s disease virus (MDV), an acute transforming alphaherpesvirus of the genus Mardivirus. MD is characterized by paralysis, immune suppression, and the rapid formation of T-cell (primarily CD4+) lymphomas. Over the last 50 years, losses due to MDV infection have been controlled worldwide through vaccination; however, these live-attenuated vaccines are non-sterilizing and potentially contributed to the virulence evolution of MDV field strains. Mutations common to field strains that can overcome vaccine protection were identified in the C-terminal proline-rich repeats of the oncoprotein Meq (Marek’s EcoRI-Q-encoded protein). These mutations in meq have been found to be distinct to their region of origin, with high virulence strains obtained in Europe differing from those having evolved in the US. The present work reports on meq mutations identified in MDV field strains in Nigeria, arising at farms employing different vaccination practices. Materials and Methods: DNA was isolated from FTA cards obtained at 12 farms affected by increased MD in the Plateau State, Nigeria. These sequences included partial whole genomes as well as targeted sequences of the meq oncogenes from these strains. Several of the meq genes were cloned for expression and their localization ability to interact with the chicken NF-IL3 protein, a putative Meq dimerization partner, were assessed. Results: Sequence analysis of the meq genes from these Nigerian field strains revealed an RB1B-like lineage co-circulating with a European Polen5-like lineage, as well as recombinants harboring a combination of these mutations. In a number of these isolates, Meq mutations accumulated in both N-terminal and C-terminal domains. Discussion: Our data, suggest a direct effect of the vaccine strategy on the selection of Meq mutations. Moreover, we posit the evolution of the next higher level of virulence MDVs, a very virulent plus plus pathotype (vv++).
Omics based technology application in poultry meat research
(Poultry Science, 2024-12-11) Zhou, Huaijun; Quach, Austin; Nair, Mahesh; Abasht, Behnam; Kong, Byungwhi; Bowker, Brian
Omics techniques, including genomics, transcriptomics, proteomics, metabolomics, and lipidomics, analyze entire sets of biological molecules to seek comprehensive knowledge on a particular phenotype. These approaches have been extensively utilized to identify both biomarkers and biological mechanisms for various physiological conditions in livestock and poultry. The purpose of this symposium was not only to focus on how recent omics technologies can be used to gather, integrate, and interpret data produced by various methodologies in poultry research, but also to highlight how omics and bioinformatics have increased our understanding of poultry meat quality problems and other complex traits. This Poultry Science Association symposium paper includes 5 sections that cover: 1) functional annotation of cis-regulatory elements in the genome informs genetic control of complex traits in poultry, 2) mass spectrometry for proteomics, metabolomics, and lipidomics, 3) proteomic approaches to investigate meat quality, 4) spatial transcriptomics and metabolomics studies of wooden breast disease, and 5) multiomics analyses on chicken meat quality and spaghetti meat. These topics provide insights into the molecular components that contribute to the structure, function, and dynamics of the underlying mechanisms influencing meat quality traits, including chicken breast myopathies. This information will ultimately contribute to improving the quality and composition of poultry products.

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