NE1834: Genetic Bases for Resistance and Immunity to Avian Diseases

(Multistate Research Project)

Status: Inactive/Terminating

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SAES-422 Reports

Annual/Termination Reports:

[11/29/2019] [11/10/2020] [11/18/2021] [10/11/2022] [10/12/2023]

Date of Annual Report: 11/29/2019

Report Information

Annual Meeting Dates: 09/28/2019 - 09/29/2019
Period the Report Covers: 09/01/2018 - 09/30/2019

Participants

Host: Ramesh Selvaraj (selvaraj.7@osu.edu); Chair: Lisa Bielke (bielke.1@osu.edu); Secretary: Yvonne Drechsler (ydrechsler@westernu.edu)

Technical committee participants
Confirmed technical committee or guest (g) attendance:
Bob Taylor, West Virginia University
Gisela Erf, University of Arkansas
Marites Sales, University of Arkansas
Ramesh Selvaraj, University of Georgia
Yvonne Drechsler, Western University
Lisa Bielke, Ohio State University
Ryan Arsenault, University of Delaware
Mark Parcells, University of Delaware
Cari Hearn, USDA ARS East Lansing
Robert Beckstead, North Carolina State University
Huaijun Zhou, UC Davis
Mohammad Heidari, USDA ARS Athens
Huanmin Zhang, USDA ARS Athens
Henk Parmentier, Wageningen University
Matt Koci, NC State
Keith Jaronsinski, University of Illinois
Kevin Bolek, Ascus Bioscience
Janet Fulton, Hyline
Christine Vuong, University of Arkansas
Muhammad Mortada, UGA
Ragini Reddivari, UGA
Gabriel Akerele, UGA
Noor Ramadan, UGA
Keila Acevedo, UGA
Jarred Oxford, UGA
PhD Students-Staff-Post doctoral scholars:
Katherine Cupo, North Carolina State University (Dr. Beckstead’s lab)
Missy Monson, Iowa State University (Dr. Lamont’s lab)
Theros Ng, UGA (Dr. Selvaraj’s lab)
Andrea DeRogatis, UC Davis (Dr. Klasing’s lab)
Absentees:
Dalloul, Rami, Virginia Tech
Calvin Keeler, U Delaware
Marcia Miller, City of Hope, CA
Rodrigo Gallardo UC Davis
Matukumalli, Lakshmi (USDA-NIFA)

Brief Summary of Minutes

Minutes Attachment:

NE summary and accomplishments.docx

Accomplishments

added with summary statement in previous section

Publications

Impact Statements

added with summary and accomplishments

Date of Annual Report: 11/10/2020

Report Information

Annual Meeting Dates: 10/13/2020 - 10/14/2020
Period the Report Covers: 10/01/2019 - 10/13/2020

Participants

Bob Taylor, West Virginia University
Gisela Erf, University of Arkansas
Ramesh Selvaraj, University of Georgia
Yvonne Drechsler, Western University
Lisa Bielke, Ohio State University
Ryan Arsenault, University of Delaware
Mark Parcells, University of Delaware
Robert Beckstead, North Carolina State University
Huaijun Zhou, UC Davis
Matt Koci, North Carolina State University
Keith Jaronsinski, University of Illinois
Janet Fulton, Hyline
Dalloul, Rami, University of Georgia
Marcia Miller, City of Hope, CA
Rodrigo Gallardo UC Davis
Kirk Klasing, UC Davis
Jiuzhou Song, University of Maryland
Sue Lamont, Iowa State
Chris Ashwell, North Carolina State University
Christi Swaggerty, USDA-ARS
Juan Carlos Rodriguez, Atlantic Veterinary College
Henk Parmentier, Wageningen University (did attend some of the time but did not give a presentation)
Muquarrab Qureshi USDA-ARS

Guest
Tina Dalgaard, Aarhus University Denmark

PhD Students-Staff-Post doctoral scholars:
Theros Ng, UGA (Dr. Drechsler’s lab)
Kaylin Chasser, M.S (Dr. Bielke’s lab)

Absentees:
Calvin Keeler, University of Delaware
Mohammad Heidari, USDA ARS Athens
Cari Hearn, USDA ARS East Lansing
Mark Berres, University of Wisconsin
Solomon O. Odemuyiwa,, University of Missouri

Brief Summary of Minutes

Minutes Attachment:

NE1834 Business Meeting Notes-Oct.14.2020.docx

Accomplishments

Erf Objective 2. A vitiligo treatment study, conducted in AR using the Smyth line autoimmune vitiligo model, revealed that the target tissue (the growing feather; GF) can be repeatedly microinjected without impact on GF growth and development. Examination of innate immunity in systemic sclerosis/scleroderma-prone UCD 200/206 chickens revealed altered responses to microbial components and poly-clonal T cell activators in UCD200/206 chickens. The GF-cutaneous test developed to examine local cellular/tissue responses to pulp-injection of test-materials was successfully adapted for use in young commercial broilers, yielding new knowledge on the local (GF) and systemic (blood) LPS-induced inflammatory response. Objective 3. Genetic stocks, 3 MHC-matched lines of the Smyth autoimmune vitiligo model, two lines (220 & 206) of the UCD chicken model for systemic sclerosis/scleroderma, and the Obese strain chicken model for Hashimoto’s thyroiditis, were maintained at AR for research. AR continued to refine and expand the growing feather as an in vivo test-tube system to study innate and adaptive immune responses in poultry.   Arsenault Objective 1: N/A Objective 2: We elucidated a potential mechanism of why we see differing prevalence of Salmonella serovars in poultry in the field. The serovars trade off infectivity/invasiveness for persistence. S. Enteritidis is more invasive and elicit a greater inflammatory response but may lead to greater clearance. S. Heidelberg is less invasive but may evade immunity better for longer-term infectivity. A combination of purified yeast cell wall fractions appears to be the better formulation for immune modulation and resistance to necrotic enteritis. They provide greater potency in addition to a synergistic effect. Our collaborations with the Mellata group at Iowa State and Johnson group at Minnesota showed that non-tradition probiotics, SFB, and host-adaptive probiotics have positive effects on poultry gut health and are promising preventative approaches in poultry production.    Beckstead Objective: To identify the SNP markers associated with genetic resistance to H. meleagridis infection in commercial.   Koci For 2020 we have not made any contributions to Objective 1. For Objective 2 we have characterized the expression of innate immune cells from turkey poults following infection with turkey astrovirus type-2 to better understand the nature of the immune suppression induced by this virus. We have also used machine learning to assist with our understanding of the differences in the immune responses of genetic lines of chickens selected for differences in their antibody responses. We have not made any contributions to Objective 3 for 2020.   Miller For Objective 1, we have made significant advances in defining the sequence of MHC-Y and the NOR regions on chicken Chromosome 16.  We have advanced understanding of the polymorphic nature of chicken MHC class I molecules revealing an unusual arrangement of polymorphic residues.  We have also contributed to efforts defining the function of MHC-Y in immune responses and bacterial colonization.  For Objective 2, we have provided the those interested in chicken genetics a sample means for defining MHC-Y genotypes in chickens.  This method is suitable for typing large numbers of birds in a short time.   Ashwell Objective 2   The NC/Ashwell group has increased the characterization of the adaptive immune functions and the influence of genetic and environmental factors contributing to these processes by studying lines of White Leghorn chickens, High Antibody Selected (HAS) and Low Antibody Selected (LAS), that have been continuously divergently selected for 5-day post-injection antibody titer to injection with sheep red blood cells (SRBC) for nearly 50 years. Differential gene expression was analyzed combining traditional statistics and machine learning to obtain signature gene lists for functional analysis, which revealed differences in energy production and cellular processes between lines and with SRBC injection.   Gallardo We have been able to generate good basic information in regards to resistance to IBV infections using MHC B haplotype chickens. This information allows us to have a working animal model that has been proven testing minerals as boosters of immune responses. In addition, we have been able to respond to pressing issues to the industry i.e. avian reovirus variants, IBV associated false layer syndrome and infectious coryza.   Dalloul Necrotic enteritis, is one of the major enteric diseases that negatively impacts the poultry industry.  The increasing ban on the use of antibiotic growth promoters in poultry production has resulted in higher incidence of necrotic enteritis outbreaks worldwide.  Our research demonstrated that supplementation of natural additives established a unique taxonomic and functional signature in the ileal microbiota, which was accompanied by better performance and reduced pathology of broilers.   Taylor Objective 1. DNA sequence and SNP analyses of samples from chickens with defined alloantigen genotypes revealed an association between alloantigen A and a chromosome 26 region from 2,420,000 to 2,890,000 bp. Among four possible candidate genes, high consistency between amino acid changing SNP and allelic differences identified the alloantigen A gene as C4BPA (complement component 4 binding protein alpha).  Alloantigen E, tightly linked to the A system received tentative identification as an unannotated locus, LOC101748581.  Objective 3. Genetic stocks consisting of two inbred lines, two congenic lines and five line crosses were maintained for research. Stocks are typed at the MHC and other alloantigen systems.   Bielke Objectives 2 and 3 – The role of pioneer colonization of the GIT in neonatal birds was shown to have age-related effects, especially with regards to immune tolerance and innate immune function. Generally, Gram negative bacteria decrease ability of birds to respond to inflammatory events and lactic acid bacteria promote colonization with segmented filamentous bacteria, which are thought to promote beneficial innate immune function. This has been demonstrated through other experiments in which early inoculation with Gram negative bacteria increased gut permeability and susceptibility to necrotic enteritis. Gram negative inoculation promoted dendritic cell migration to gut tissue, decreased HNF1-alpha, decrease pathways associated with D-glucose, and F-gamma receptor dependent phagocystosis. Conversely, lactic acid bacteria promoted gluconeogenesis, B cell receptor signaling, Class I MHC antigen processing, and IL-1 while downregulating heterophil degranulation and MHC Class II antigen presentation. These clearly demonstrate the role of colonizing bacteria in immune system function and maturation.   Lamont    Objective 1.  We characterized the splenic transcriptome of commercial brown-egg birds infected with NDV. We conducted a joint-tissue analysis of the transcriptomes of lung, trachea and Harderian gland of Leghorn and Fayoumi birds infected with NDV. We determined the expression of genes of the eIF2 family in spleen of Leghorn and Fayoumi birds infected with NDV. Objective 3.  We characterized the thymic transcriptome of birds exposed to heat, injected with LPS, or both. We defined the expression of 20 host defense peptides in chick embryo fibroblasts and bone-marrow-derived cell cultures after LPS or poly I:C exposure.  We maintained the eight ISU chicken genetic lines, and transferred them into a new building. We assessed cell-surface expression of MHC class I antigens on red blood cells of the ISU genetics lines.   Parmentier Hygienic conditions appear to determine the level of specific immune responses (specific antibodies), natural and natural auto antibodies, aswell as innate immunity (complement dependent lysis) in young growing broilers. In hygienic (clean) conditions immune responses were considerably lower. Behaviour was accompanied by levels of specific and natural antibodies. ‘Aggressive’ birds showed higher IgG levels compared to ‘passive’ birds that were characterized by higher IgM levels. This suggests that levels of immune parameters may be helpful as breeding goal against misbehaviour of poultry, but also point to the risk that breeding for high immunocompetence may result in enhanced misbehaviour.Birds (and mammals) show high contents of antibodies binding ‘self-antigens’, especially when these antigens are conjugated to danger signals such as phophoryl choline (PC). Innate immune cells show training (non-specific memory) when earlier challenged with non-related PAMP.   Rodriguez We have demonstrated that FA supplementation modulated B lymphocytes response and improved their innate immune antiviral and proinflammatory response pathways; their effect is evident when he have used a low virulent pathotype serotype I modified live IBDV vaccine that was able to trigger and mount an immune response in chickens B lymphocytes without affecting B-cell viability. Besides, we demonstrated the capacity of IBDV to trigger a potent innate immune response in chicken cells (DF-1, HD-11, and DT-40); we found the beneficial effect of Vit D supplementation as an immunomodulator.   Huaijun Zhou Objective 1: For Genomics to improve Poultry project, we conducted naïve natural vNDV exposure trials and estimated genetic parameters of different traits associated with disease resistance for genomic selection in African ecotypes. For epigenomic study, we functionally annotate regulatory elements in chicken bursa and identified regulatory elements changes associated with genes related cell cycle and receptor signaling of lymphocytes in chickens. Objective 2: For Salmonella infection, we found that perturbation in metabolic pathways related to arginine and proline metabolism as well as TCA cycle contributed to Salmonella persistence in chickens.   Drechsler Objective 3: Functional Annotation of the Chicken Genome: Yvonne Drechsler in collaboration with Dr. Hawkins at the University of Washington is funded to functionally annotate the chicken genome in several immune cells and tissues.  Tissues and cells have been collected and are in various processing stages. DNA sequencing is completed for most cells and tissues, RNA seq is mostly complete. ATAC seq and ChiP seq are in optimization stages. Resistance to respiratory pathogens, including coronavirus-induced infection and clinical illness in chickens has been correlated with the B (MHC) complex and differential ex vivo macrophage responses. RNA seq and ATAC seq have been analyzed in SPF chickens infected with IBV. Tissue and viral strain specific epigenetic changes have been observed. Final analysis is pending.   Song In allelic specific expressions of CD4+ T cells, we found some critical genes and CNV linked to T cell activation, T cell receptor (TCR), B cell receptor (BCR), ERK/MAPK, and PI3K/AKT-mTOR signaling pathways, which play potentially essential roles in MDV infection. However, the effects of parent-of-origin have not been detected on survival days after MDV infection. Moreover, an interaction between MDV infection and linc-GALMD1 was also observed. The lincRNA could repress MDV gene expression during MDV infection, which may help uncover the roles of linc-GALMD1 as a viral gene regulator and tumor suppression by regulating immune responses to MDV infection. Interestingly, we found that the adipoR1 mRNA expression level was significantly increased in MD-susceptible chickens after MDV infection.   Parcells This year we compared the ability of vaccine-associated exosomes (VEX) to increase the efficacy of HVT against an RB1B challenge. We found that injection of 5 x 109 exosomes at 10 days post-hatch increased the survival of chickens challenged at hatch after in ovo HVT vaccination (p<0.002), and that injection at 5 and 10 dph showed a trend of increasing survival (p<0.07), but that treatment at 5 dph alone did not positively affect survival. Conversely, we examined the effect of tumor-associated serum exosomes (TEX) on MD incidence and survival of HVT/SB1-vaccinated chickens (in ovo) and found no significant change in survival due to the severity of the low passage RB1B challenge. Role of Meq Splice Variants in Interactions with Polycomb Repressive Complex Proteins: The finding of interaction of Meq splice variant-derived proteins, proteins that accumulate as MDV establishes latency, with the Polycomb Repressive complex (PRCs), ties MDV latency directly to a pathway associated with cellular transformation and tumor progression. Modeling of MDV Evolution of Virulence: We have established the following NetLogo Agent-based models of: (1) Chicken spleen infection by MDV, (2) Model for MDV Reactivation from Latency, and (3) MDV Infection and Spread in chicken embryo fibroblasts (CEF).   Klasing Objective 1 - The effect of an enzyme blend (xylanase, amylase and protease; XAP) on intestinal histology, immunological response and performance of Cobb500 broilers following a mild coccidial challenge was examined. The challenged birds had increased pro-inflammatory cytokines (IL-6, IL-1β; P < 0.05) in the intestine and decrease growth and feed efficiency. XAP reduced inflammatory responses as measure by indices of the hepatic and systemic acute phase response and immunopathology and improved performance. Objective 2 - A chicken knockout line (KO) lacking B lymphocytes were examined for their resistance to a challenge with Salmonella enterica. When challenged the KO chickens lost less body weight than the controls, had similar mortality, but higher indices of intestinal inflammation.

Publications

Peer reviewed Alber, A., Morris, K.M., Bryson, K.J., Sutton, K., Monson, M.S., Chintoan-Uta, C., Borowska, D., Lamont, S.J., Schouler, C., Kaiser, P., Stevens, M., Vervelde, L. 2020. Avian pathogenic Escherichia coli (APEC) strain-dependent immunomodulation of respiratory granulocytes and mononuclear phagocytes in CSF1R-reporter transgenic chickens. Front. Immunol. <a href="https://doi.org/10.3389/fimmu.2019.03055">https://doi.org/10.3389/fimmu.2019.03055</a>   Bai H, He Y, Ding Y, Chang S, Zhang H, Chen J, Song J. Parent-of-origin has no detectable effect on survival days of Marek's disease virus infected White Leghorns. Poult Sci. 2019 98:4498-4503 doi: 10.3382/ps/pez209   Bai H, He Y, Ding Y, Chu Q, Lian L, Heifetz EM, Yang N, Cheng HH, Zhang H, Chen J, Song J. Genome-wide characterization of copy number variations in the host genome in genetic resistance to Marek's disease using next generation sequencing. BMC Genet. 2020 21:77. doi: 10.1186/s12863-020-00884-w.   Bai Y, Yuan, P., Zhang, H. Ramachandran, Yang, N. Song J. Adiponectin and its receptor genes expression in response to MDV infection of White, Leghorns. Poultry Science. doi: 10.1016/j.psj.2020.06.004   Bai, H.; He, Y.; Ding, Y.; Carrillo, J.A.; Selvaraj, R.K.; Zhang, H.; Chen, J.; Song, J. Allele-Specific Expression of CD4+ T Cells in Response to Marek’s Disease Virus Infection. Genes 2019, 10, 718. He Y, Han B, Ding Y, Zhang H, Chang S, Zhang L, Zhao C, Yang N, *Song J. Linc-GALMD1 Regulates Viral Gene Expression in the Chicken. Front Genet. 2019 10:1122. doi: 10.3389/fgene.2019.01122. eCollection 2019.   Beckstead RB, Anderson K and McDougald LR. 2020. Oviduct fluke (Prostagonimus macrorchis) found inside a chicken egg in North Carolina. Avian Diseases. 64: 352–353. https://doi.org/10.1637/aviandiseases-D-20-00021   Blakey, B. Crossley, A.P. Da Silva, D. Rejmanek, C. Jerry, R.A. Gallardo, S. Stoute. Infectious Bronchitis Virus Associated with Nephropathy in Diagnostic Cases from Commercial Broiler Chickens in California. Avian Diseases 2020 64:482-489 doi: 10.1637/0005-2086-64.4.482   Bolek, K., and K. Klasing. 2019. The effects of vaccination with keyhole limpet hemocyanin or oral administration of Salmonella enterica serovar Enteritidis on the growth performance of immunoglobulin knockout chickens. Poultry science 98(9):3504-3513.   Buttemer, W.A., B.A. Addison, and K.C. Klasing. 2020. The energy cost of feather replacement is not intrinsically inefficient. Journal of Zoology 98(2):142-148.   Calik A, Omara II, White MB, Evans NP, Karnezos TP, Dalloul RA. Dietary non-drug feed additive as an alternative for antibiotic growth promoters for broilers during a necrotic enteritis challenge. Microorganisms 7:257. 2019.   Calik A, Omara II, White MB, Li W, Dalloul RA. Effects of dietary direct fed microbial supplementation on performance, intestinal morphology and immune response of broiler chickens challenged with coccidiosis. Frontiers in Veterinary Science 6:463. 2019.   Chadwick EV, Beckstead RB. 2020. Two blackhead disease outbreaks in commercial turkey flocks were potentially exacerbated by poor poult quality and coccidiosis. Avian Diseases <a href="https://doi.org/10.1637/aviandiseases-D-20-00052">https://doi.org/10.1637/aviandiseases-D-20-00052</a>   Chadwick EV, Malheiros RD, Beckstead RB. Early inoculation with Histomonas meleagridis has limited effects on broiler breeder growth and egg production and quality. Poultry Science  2020 Sep;99(9):4242-4248. doi: 10.1016/j.psj.2020.05.020   Chadwick EV, Rahimi S, Grimes J, Pitts J and Beckstead RB. 2020. Sodium bisulfate feed additive aids broilers in growth and intestinal health during a coccidiosis challenge. Poultry Science 99:5324-5330   Chanthavixay, G., Kern, C., Wang, Y., Saelao, P., Lamont, S.J., Gallardo, R.A., Rincon, G. and Zhou, H., 2020. Integrated Transcriptome and Histone Modification Analysis Reveals NDV Infection Under Heat Stress Affects Bursa Development and Proliferation in Susceptible Chicken Line. Frontiers in Genetics, 11, p.1176.   Chanthavixay, G., Kern, C., Wang, Y., Saelao, P., Lamont, S.J., Gallardo, R.A., Rincon, G., Zhou, H. 2020. Integrated transcriptome and histone modification analysis reveals NDV infection under heat stress affects bursa development and proliferation in susceptible chicken line. Front. Genet. 11:567812. doi: 10.3389/fgene.2020.567812   Chu, Q.; Ding, Y.; Cai, W.; Liu, L.; Zhang, H.; Song, J. Marek’s Disease Virus Infection Induced Mitochondria Changes in Chickens. Int. J. Mol. Sci. 2019, 20, 3150 doi: 10.3390/ijms20133150   da Silva, A., Schat, K. A., & Gallardo, R. A. (2019). Cytokine responses in tracheas from MHC congenic chicken lines with distinct susceptibilities to infectious bronchitis virus. Avian Diseases. 2020 64:36-45. doi: 10.1637/0005-2086-64.1.36.   da Silva, A.P., Aston, E.J., Chiwanga, G.H., Birakos, A., Muhairwa, A.P., Kayang, B.B., Kelly, T., Zhou, H. and Gallardo, R.A., 2020. Molecular Characterization of Newcastle Disease Viruses Isolated from Chickens in Tanzania and Ghana. Viruses, 12(9), p.916.   Deist, M. S., Gallardo, R. A., Dekkers, J., Zhou, H., & Lamont, S. J. (2020). Novel combined tissue transcriptome analysis after lentogenic Newcastle disease virus challenge in inbred chicken lines of differential resistance. Frontiers in Genetics, 11, http://review.frontiersin.org/review/506097/18/453015#/tab/History   Deist, M.S., Gallardo, R.A., Dekkers, J.C.M., Zhou, H. Lamont, S.J. 2020. Novel combined tissue transcriptome analysis after lentogenic Newcastle disease virus challenge in inbred chicken lines of differential resistance. Frontiers Genet. 11:11. doi: 10.3389/fgene.2020.00011   Del Vesco, A.P., Kaiser, M.G., Monson, M.S., Zhou, H., Lamont, S.J.. 2020. Genetic responses of inbred chicken lines illustrate importance of eIF2 family and immune-related genes in resistance to Newcastle disease virus. Scientific Reports 10:6155. <a href="https://doi.org/10.1038/s41598-020-63074-9">https://doi.org/10.1038/s41598-020-63074-9</a>   Downs, C.J., N.A. Dochtermann, R. Ball, K.C. Klasing, and L.B. Martin. 2020. The effects of body mass on immune cell concentrations. The American Naturalist 195(1):107-114.   Echeveryy H, Alizadeh M, Yitbarek A, Slominsky B, Rodriguez-Lecompte, JC. 2020. Immune Response of Chicken B cells to Yeast-derived products treated with Lytic Enzyme. In press British Poult. Sci. 21:1-6. doi: 10.1080/00071668.2020.1817328   Elad O, Uribe-Diaz S, Losada-Medina D, Yitbarek A, Sharif S and Rodriguez-Lecompte JC. 2020.Epigenetic effect of folic acid (FA) on the gene proximal promoter area and mRNA expression of chicken B-cell as antigen presenting cell. Br Poult Sci. 2020 14:1-9. doi: 10.1080/ 000 71668.2020.1799332   Emami NK, Calik A, White MB, Kimminau EA, Dalloul RA. Effects of probiotics and multi-component feed additives on microbiome, gut barrier and immune responses in broiler chickens during subclinical necrotic enteritis. Frontiers in Veterinary Science. 2020 <a href="https://doi.org/10.3389/fvets.2020.572142">https://doi.org/10.3389/fvets.2020.572142</a>   Emami NK, Calik A, White MB, Young M, Dalloul RA. Necrotic enteritis: The role of tight junctions and mucosal immune responses in alleviating the effects of the disease. Microorganisms 7:231. 2019 doi: 10.3390/microorganisms7080231   Ferreira, H. L., Reilley, A. M., Goldenberg, D., Ortiz, I. R., Gallardo, R. A., & Suarez, D. L. (2020). Protection conferred by commercial NDV live attenuated and double recombinant HVT vaccines against virulent California 2018 Newcastle disease virus (NDV) in chickens. Vaccine, 38(34), 5507-5515.   Figueroa, T. Derksen, S. Biswas, A. Nazmi, D. Rejmanek, B. Crossley, P.Pandey, R.A. Gallardo. Persistence of LPAI and HPAI in Reused Poultry Litter, Effects of Litter Amendment Use and Composting Temperatures. J Appl. Poult. Res. 2020 in press   French, C. E., M. A. Sales, S. J. Rochell, A. Rodriguez, and G. F. Erf. 2020. Local and systemic inflammatory responses to lipopolysaccharide in broilers: new insights using a two-window approach. Poult. Sci. (in press).   Gallardo, R. A. Invited Review: Infectious bronchitis virus variants: Generation, Surveillance, Control and Prevention. Australian Journal of Veterinary Sciences. 2019. In press.   Gallardo, R. A., da Silva, A. P., & Rebollo, M. A. (2020). Effects of Amino acid-bound Zinc and Manganese Feed Additives on MHC Haplotype Chickens Challenged with Infectious Bronchitis Coronavirus. Avian Diseases. 2020 64:451-456. doi: 10.1637/aviandiseases-D-20-00031   Gallardo, R. A., Da Silva, A. P., Egaña-Labrin, S., Stoute, S., Kern, C., Zhou, H., ... & Corsiglia, C. (2020). Infectious Coryza: Persistence, Genotyping, and Vaccine Testing. Avian diseases, 64:157-165. https://www.aaapjournals.info/doi/abs/10.1637/aviandiseases-D-19-00184   Hassan, H.M., M. Mendoza, M. Rezvani, M. D. Koci, A. N. Dickey, and E. H. Scholl. 2020). Complete Genome Sequences of Lactobacillus strains, C25 and P38, Isolated from Chicken Cecum. Microbiol. Resour. Announc. Sep, 9 (39) e00501-20. DOI: 10.1128/MRA.00501-20.   Jaime J, Vargas-Bermúdez D.S., Yitbarek A., Reyes J, and Rodríguez-Lecompte JC. 2019. Differential immunomodulation effect of vitamin D (1,25 (OH)2 D3) on the innate immune response in different types of cells infected with IBDV. Poult. Sci. 99:4265-4277   Johnson, C.N., Hashim, M.M., Bailey, C.A., Byrd, J.A., Kogut, M.H., Arsenault, R.J. Feeding of yeast cell wall extracts during a necrotic enteritis challenge enhances cell growth/survival and immune signaling in the jejunum of broiler chickens. 2020. Poultry Science. 99, 2955-2966.   Kim, T.H., C. Kern, and H. Zhou. 2020. Knockout of IRF7 Highlights its Modulator Function of Host Response Against Avian Influenza Virus and the Involvement of MAPK and TOR Signaling Pathways in Chicken. Genes 11, 385; doi:10.3390/genes11040385   Krieter, A., N.P. Ponnuraj, and K.W. Jarosinski. 2020. Expression of the conserved herpesvirus protein kinase (CHPK) of Marek’s disease alphaherpesvirus in the skin reveals a mechanistic importance for CHPK during interindividual spread in chickens. J Virol. 94(5):e01522-19. https://doi.org/10.1128/JVI.01522-19   Liu L, Wang D, Mi S, Duan Z, Yang S, Song J, Xu G, Yang N, Yu Y. The different effects of viral and bacterial mimics maternal stimuli on ethology of hens and reproduction of their offspring. Poult Sci. 2019 98:4153-4160 doi: 10.3382/ps/pez189   Losada-Medina D, Yitbarek A, Uribe-Diaz S, Ahmed M and Rodríguez-Lecompte JC. 2020. Identification, tissue characterization and innate immune role of Angiogenin-4 expression in young broiler chickens. Poult. Sci. 99:2992-3000   Mon, K.Z., Y. Zhu, G. Chanthavixay, C. Kern and H. Zhou. 2020. Integrative analysis of gut microbiome and metabolites revealed novel mechanisms of intestinal Salmonella carriage in chicken. Sci Rep. 10:4809. <a href="http://www.nature.com/articles/s41598-020-60892-9">www.nature.com/articles/s41598-020-60892-9</a>   Mushi, G. Chiwanga, E. Amuzu-Aweh, M. Walugembe, R. Max, S.J. Lamont, T. Kelly, E. Mollel, P. Msoffe, J. Dekkers, R. A. Gallardo, H. Zhou, A. Muhairwa. Phenotypic variability and population structure analysis of Tanzanian free range local chickens. BMC Veterinary Research 16, 360 (2020). https://doi.org/10.1186/s12917-020-02541-x   Neerukonda SN, Katneni UK, Bhandari N, Parcells MS. Transcriptional Analyses of Innate and Acquired Immune Patterning Elicited by Marek's Disease Virus Vaccine Strains: Turkey Herpesvirus (HVT), Marek's Disease Virus 2 (strain SB1), and Bivalent Vaccines (HVT/SB1 and HVT-LT/SB1). Avian Dis. 2019 Dec;63(4):670-680. doi: 10.1637/aviandiseases-D-19-00117. PMID: 31865682.   Oxford, J. H., & Selvaraj, R. K. (n.d.). Effects of Glutamine Supplementation on Broiler Performance and Intestinal Immune Parameters During an Experimental Coccidiosis Infection. The Journal of Applied Poultry Research. doi:10.3382/japr/pfz095   Perry, F., Johnson, C.N., Aylward, B.A., Arsenault, R.J. The Differential Phosphorylation-Dependent Signaling and Glucose Immunometabolic Responses Induced during Infection by Salmonella Enteritidis and Salmonella Heidelberg in Chicken Macrophage-like cells. 2020. Microorganisms. 8(7), 1041.   Ponnuraj, N.P., Y.T. Tien, W. Vega Rodriguez, A. Krieter, and K.W. Jarosinski. 2019. The Herpesviridae conserved multifunctional infected cell protein 27 (ICP27) is important, but not required for replication and oncogenicity of Marek’s disease alphaherpesvirus (MDV). J Virol. 93(4); e01903-18. <a href="https://doi.org/10.1128/jvi.01903-18">https://doi.org/10.1128/jvi.01903-18</a>   Redweik, G.A.J., Kogut, M.H., Arsenault, R.J., and Mellata, M. Oral Treatment with Ileal Spores Triggers Immunometabolic Shifts in Chicken Gut. 2020. Frontiers in Veterinary Science. 7 (629) <a href="https://doi.org/10.3389/fvets.2020.00629">https://doi.org/10.3389/fvets.2020.00629</a>.   Selvaraj, R., Markazi, A., Shanmugasundaram, R., Murugesan, R., & Mohnl, M. (2019). Effects of acidifier supplementation in laying hens challenged with Salmonella. Journal of Applied Poultry Research, 28, 919-929   Selvaraj, R., Renu, S., Markazi, A., dhakal, S., Shanmugasundaram, R., & Gourapura, R. (2019). Oral deliverable mucoadhesive chitosan-Salmonella subunit nanovaccine for layer chickens. International Journal of Nanomedicine 2020; 15: 761–777   Selvaraj, R., Shanmugasundaram, R., Markazi, A., Mortada, M., Bielke, L., Applegate, T., & Murugesan, R. Effect of Synbiotic Supplementation on Caecal Clostridium perfringens load in Broiler Chickens with different Necrotic Enteritis Challenge Models. Poult. Sci. 99, 2020, 2452-2458   Shanmugasundaram, R., Morris, A., & Selvaraj, R. (2019). Effect of 25-hydroxycholecalciferol supplementation on turkey performance and immune cell parameters in a coccidial infection model. Poultry Science, 98, 1127-1133. Retrieved from http://dx.doi.org/10.3382/ps/pey480   Shanmugasundaram, R., Mortada, M., Cosby, D. E., Singh, M., Applegate, T. J., Syed, B., Selvaraj, R. K. (2019). Synbiotic supplementation to decrease Salmonella colonization in the intestine and carcass contamination in broiler birds.. PloS one, 14(10), e0223577. doi:10.1371/journal.pone.0223577   Swaggerty,C.L., Arsenault, R.J., Johnson, C., Piva, A., and Grilli, E. Dietary supplementation with a microencapsulated blend of organic acids and botanicals alters the kinome in the ileum and jejunum to enhance growth and feed efficiency in broilers. 2020. PLOS One. 15(7), e0236950.   Talghari M, Behnamifar A, Rahimi S, Torshizi MAK, Beckstead RB, Grimes JL. The effect of sodium bisulfate and coccidiostat on intestinal lesions and growth performance of Eimeria spp. challenged broilers. Poultry Science. 99:4769-4775   Taylor, R. L., Jr. 2020.  A Year of Change. Poult. Sci. 99:6291–6292 https://doi.org/10.1016/j.psj.2020.09.018   Uribe-Diaz S, A. Yitbarek A, Vallejo D, Losada-Medina D, Ahmed M and Rodríguez-Lecompte 2020. Effect of folic acid on the innate immune receptors in chicken B cells infected with IBDV. Veterinary Immunology and Immunopathology in press   Vega-Rodriguez, W., Ponnuraj, N.P., and K.W. Jarosinski. 2019. Marek’s disease alphaherpesvirus (MDV) RLORF4 is not required for expression of glycoprotein C and interindividual spread. Virology 534:108-113. <a href="https://doi.org/10.1016/j.virol.2019.06.008">https://doi.org/10.1016/j.virol.2019.06.008</a>   Walugembe, M., Amuzu-Aweh,E.N., Botchway, P.K., Naazie, A., Aning, G., Wang, Y., Saelao, P., Kelly, T., Gallardo, R.A., Zhou, H., Lamont, S.J., Kayang, B., Dekkers, J. 2020. Genetic Basis of Response of Ghanaian Local Chickens to Infection with a Lentogenic Newcastle Disease Virus, Frontiers Genetics <a href="https://doi.org/10.3389/fgene.2020.00739">https://doi.org/10.3389/fgene.2020.00739</a>   Wang, Y., Saelao, P., Kern, C., Jin, S., Gallardo, R.A., Kelly, T., Dekkers, J.M., Lamont, S.J. and Zhou, H., 2020. Liver Transcriptome Responses to Heat Stress and Newcastle Disease Virus Infection in Genetically Distinct Chicken Inbred Lines. Genes, 11(9), p.1067.   Wang, Y., Saelao, P., Kern, C., Jin, S., Gallardo, R.A., Kelly, T., Dekkers, J.M., Lamont, S.J., Zhou, H. 2020. Liver transcriptome responses to heat stress and Newcastle Disease virus infection in genetically distinct chicken inbred lines. Genes 11, 1067; doi:10.3390/genes11091067   Ward, T.L., Weber, B.P., Mendoza, K.M., Danzeisen, J.L., Llop, K., Lang, K., Clayton, J.B., Grace, E., Brannon, J., Radovic, I., Beauclaire, M., Heisel, T.J., Knights, D., Cardona, C., Kogut, M., Johnson, C., Noll, S.L., Arsenault, R., Reed, K.M., and Johnson, T.J. Antibiotics and host-tailored probiotics similarly modulate effects on the developing avian microbiome, mycobiome, and host gene expression. 2019. mBio. 10(5), 02171-19   Wilkinson, N. G., R. T. Kopulos, L. M. Yates, W. E. Briles, and R. L. Taylor, Jr. 2020.  Major histocompatibility (B) complex recombinant R13 antibody response against bovine red blood cells. Poult. Sci. 99:4804-4808 <a href="https://doi.org/10.1016/j.psj.2020.06.069">https://doi.org/10.1016/j.psj.2020.06.069</a>   You Z, Zhang Q, Liu C, Song J, Yang N, Lian L. Integrated analysis of lncRNA and mRNA repertoires in Marek's disease infected spleens identifies genes relevant to resistance. BMC Genomics. 2019 Mar 28;20(1):245. doi: 10.1186/s12864-019-5625-1.   Zhang, J. R. M. Goto and M. M. Miller.  2020.  A simple means for MHC-Y genotyping in chickens using short tandem repeat sequences.  Immunogenetics 72(5):325-332. doi: 10.1007/s00251-020-01166-6.   Zhang, J., Kaiser, M. G., Gallardo, R. A., Kelly, T. R., Dekkers, J., Zhou, H., & Lamont, S. J. (2020). Transcriptome analysis reveals inhibitory effects of lentogenic Newcastle disease virus on cell survival and immune function in spleen of commercial layer chicks. Genes, 11(9), 1003.   Zhang, J., Kaiser, M.G., Gallardo, R.A., Kelly, T. R., Dekkers, J.C.M., Zhou, H., Lamont, S.J. 2020. Transcriptome analysis reveals inhibitory effects of lentogenic Newcastle disease virus on cell survival and immune function in spleen of commercial layer chicks. Genes 11:1003; doi:10.3390/genes11091003   Non-peer reviewed, rapid communication Quinlan, B. D., H. Mou, L. Zhang, Y. Guo, W. He, A. Ojha, M. S. Parcells, G. Luo, W. Li, G. Zhong, H. Choe, and M. Farzan,, The SARS-CoV-2 Receptor-Binding Domain Elicits a Potent Neutralizing Response Without Antibody-Dependent Enhancement. doi: <a href="https://doi.org/10.1101/2020.04.10.036418">https://doi.org/10.1101/2020.04.10.036418</a>   Published Abstracts Arsenault, R.J. Immunometabolism: The Potential Cause of and Solution to our Most Pressing Poultry Problems in Health and Infectious Disease. Proceedings of the 2020 Animal Nutrition Conference of Canada. 2020. Animal Nutrition Association of Canada, Ottawa, Canada, pp 68-74   Arsenault, R.J. The Immunometabolic Responses of Heritage and Modern Broilers to Immune Challenge: Learning From the Past to Inform the Future. Symposium on Gut Health in Production of Food Animals; 2019 November 4-6; St. Louis, MO.   Boothe SM, Emami NK, White MB, Dalloul RA. In-house hatching and early feeding to improve chick performance during a necrotic enteritis challenge. International Poultry Scientific Forum (IPSF), SPSS and SCAD. Atlanta, GA. 2020.   Çalik A, Emami NK, White MB, Dalloul RA. The impact of dietary vitamin E and selenium on body composition, intestinal integrity and immunity of broilers subjected to heat stress. International Poultry Scientific Forum (IPSF), SPSS and SCAD. Atlanta, GA. 2020.   Chadwick, Elle Jesse Grimes, Shaban Rahimi, John Pitts, and Robert Beckstead Sodium bisulfate aids broilers in growth and intestinal health during a coccidiosis challenge. International Poultry Scientific Forum (IPSF), SPSS and SCAD. Atlanta, GA. 2020   Chadwick, Elle, Robert Beckstead. Dietary additives, coccidiosis and Fenbendazole treatment alter fecal moisture to various degrees in turkey poults. Poultry Science Association Annual Meeting, 2020   Chasser, Kaylin, Audrey F. Duff, Whitney Briggs, Kate McGovern, Johel Bielke, Lisa Bielke. Day of hatch exposure to Enterobacteriaceae and characterization of avian pathogenic E. coli on inflammation. Poultry Science Association Virtual Conference, July 2020.   Chasser, Kaylin, Kate McGovern, Audrey F. Duff, B D. Graham, Whitney Briggs, Denise Russi Rodrigues, Johel Bielke, and Lisa Bielke. Effect of day of hatch inoculation with Gram-negative bacteria on gastrointestinal inflammation. International Poultry Scientific Forum (IPSF), SPSS and SCAD. Atlanta, GA. 2020.   Cox, J. L., D. R. Rodrigues, A. F. Duff, K. M. Chasser, J. C. Bielke, D. Jeffrey, C. Risch, D. Shafer, L. R. Bielke. Characterization of intestinal microbiota of newly hatched ducklings. International Poultry Scientific Forum (IPSF), SPSS and SCAD. Atlanta, GA. 2020.   Cueva, Justin R., Nicholas Egan, Imane Assakhi, Phaedra Tavlarides-Hontz, and Mark S. Parcells. Sequential Interactions of Meq Proteins with Polycomb Repressive Complex Proteins in Marek’s Disease Virus Latency. Proceedings of the 92nd NECAD, Penn State University, September 15, 2020   Cupo, Katherine Catherine Fudge, Kelly Keen, and Robert Beckstead Development of a diagnostic PCR specific to the Cochlosoma anatis 28S ribosomal gene. International Poultry Scientific Forum (IPSF), SPSS and SCAD. Atlanta, GA. 2020   Dallakoti, Aksana, Eric Munoz, Matthew D. Huson, Shannon Modla and Mark S. Parcells. The Role of Exosomes in Marek’s Disease Virus Vaccine Responses. Proceedings of the 92nd NECAD, Penn State University, September 15, 2020   Drechsler Y, and Hawkins D. 2020. Infectious Bronchitis Virus Infection Affects Chromatin Accessibility and RNA Differential Expression in a Tissue-Specific Manner. Plant & Animal Genome XXVIII, San Diego, CA.   Duff, Audrey F., K. M. Chasser, W. N. Briggs, D. Russi-Rodrigues, L. R. Bielke. Age-Related Changes in Gut Permeability and Optimal Timing for Experimentally Induced Leaky Gut. International Poultry Scientific Forum (IPSF), SPSS and SCAD. Atlanta, GA. 2020.   Duff, Audrey F., Kaylin Chasser, Whitney Briggs, Johel Bielke, Shelby Ramirez, Antonia Tacconi, G. R. Murugesan, Lisa Bielke. Necrotic enteritis model to achieve mortality reflective of industry. Poultry Science Association Virtual Conference, July 2020   Emami NK, Boothe SM, White MB, Dalloul RA. Effects of a naturally occurring necrotic enteritis challenge on performance, lesion scores, and expression of tight junction proteins in broiler chickens. International Poultry Scientific Forum (IPSF), SPSS and SCAD. Atlanta, GA. 2020.   Erf, G. F., G. Le Pape, S. Rémy, and C. Denesvre. 2020. Vitiligo onset favors earlier HVT replication in feathers of Smyth chickens. 13th International Symposium on Marek’s disease and avian herpesviruses, June 14-17, 2020, Guelph, Ontario, Canada (in press).   Gogineni, Vivek, Huawei Wang, Kyle Moskowitz, Prasad Dhurjati, Joshua Miller, Benedikt Kaufer, and Mark S. Parcells. Agent-based Modeling of Marek’s Disease Virus Lytic Infection. 92nd Annual Northeastern Conference on Avian Diseases (NECAD) Penn State, virtual, Sept. 15 and 16, 2020.   Hawkins D. and Drechsler Y. 2020. Epigenomic annotation of candidate cis-regulatory elements in the chicken genome. Plant & Animal Genome XXVIII, San Diego, CA.   Koci, M. D., A. Ballou, X. Wei, L. Zhang, Z. Q. Liew, and R. Ali. 2020. Connecting the microbiome to host metabolites: understanding how the microbiome controls immune activity in birds. Experimental Biology 2020. San Diego, CA.   McGovern, Kate, K.M.Chasser, A.F.Duff, W.N.Briggs, D.R. Rodrigues, L.R.Bielke. Effect of Select Gram Negative Bacteria on Alpha-1-Acid-Glycoprotein and Ileal Histology. International Poultry Scientific Forum (IPSF), SPSS and SCAD. Atlanta, GA. 2020.   Miller, Joshua, Kyle Moskowitz, Samuel Keating, Abhyudai Singh, Prasad Dhurjati, Andelé Conradie, Benedikt B. Kaufer, Phaedra Travlarides-Hontz, Mark Parcells. The Development of Agent-based and Mathematical Models for Marek’s disease virus (MDV) Lytic and Latent Infections. Proceedings of the 92nd NECAD, Penn State University, September 15, 2020   Miller, M. M., J. Zhang, R. M. Goto, C. F. Honaker, P. B. Siegel, R. L. Taylor, Jr., and H. K. Parmentier. 2020.  Major advances in defining variability and function of chicken MHC-Y region genes. PAG XXVII https://plan.core-apps.com/pag_2020/abstract/66376fdb-aa85-4703-a8d0-b3a4372e75f2   Patria, Joseph, Nirajan Bhandari, Phaedra Travlarides-Hontz, Andelé Conradie, Benedikt B. Kaufer, and Mark S. Parcells. Mutations in the Meq oncoprotein of MDV may be selected based on innate immune and latent T-cell interactomes. Proceedings of the 92nd NECAD, Penn State University, September 15, 2020.   Rodrigues, D. R., J. L. Cox, A. Hysong, W. Briggs, A. Duff, K. Chasser, J. Bielke, K. Wilson, C. Risch, D. Jeffrey, D. Shafer, and L.Bielke. Strategies to manipulate early-life microbiota of poultry toward beneficial bacterial growth. International Poultry Scientific Forum (IPSF), SPSS and SCAD. Atlanta, GA. 2020.   Rodríguez-Lecompte JC, Jaime J, Vargas-Bermúdez DS, Yitbarek A , and Reyes J. 2019. Susceptibility and characterization of anti-viral innate immune responses in chicken B cells infected with infectious bursa diseases virus and supplemented with 1,25(OH)2 D3. AVMA Convention-AAAP, Washington, DC, August 2-6, 2019.   Rodríguez-Lecompte JC, Jaime J, Vargas-Bermúdez DS, Yitbarek A , and Reyes J. 2019. Effect of 1,25(OH)2 D3 on gene mRNA expression of innate immune toll-like receptors, proteins signal adapters, RIGI-like receptor, IFN type I, IFN-induced proteins, and proinflammatory cytokines on chicken fibroblast infected with IBDV. The Western Poultry Disease Conference-Association of Poultry Science Specialists (ANECA). Puerto Vallarta, Mexico, April 2-6, 2019.   Rodríguez-Lecompte JC, Jaime J, Vargas-Bermúdez DS, YitbarekA , and Reyes J. 2019. Chicken macrophages’ susceptibility and innate immune response to infectious bursal disease virus with the supplementation of 1,25(OH)2 D3. International Poultry Scientific Forum (IPSF), SPSS and SCAD. Atlanta, GA, February 11-14, 2019.   Rodríguez-Lecompte JC, Uribe-Diaz S, Martinez-Morales BC, Despres B, and J. Reyes. 2019. Pre- and post-challenge effects of essential oils (EO) on mRNA expression of antiviral and pro-inflammatory pathways genes on chicken macrophages infected with IBDV. International Poultry Scientific Forum (IPSF), SPSS and SCAD. Atlanta, GA, January 28-30, 2020.   Sigmon, Christina S., Alessandro Ferrarini, Robert Beckstead. The use of a direct ELISA to identify Blackhead resistant turkeys. Poultry Science Association Annual Meeting, 2020   Taylor, R. L., Jr., W. Drobik-Czwarno, and J. E. Fulton. 2020. Candidate gene for chicken alloantigen A. Poult. Sci. 99(E-Suppl. 1):45-46   Tracy, K., R. A. Gallardo, E. Aston, and H. Zhou. 2020. Role of Humoral Immunity in Clearance of Lentogenic Newcastle Disease Virus in Chickens. Plant & Animal Genome XXVIII, San Diego, CA.   Uribe-Diaz S, Pirateque JF, Despres B, Reyes J, and Rodríguez-Lecompte JC. 2019. Effect of essential oils (EO) on mRNA expression of antiviral and pro-inflammatory innate immunity genes on chicken macrophages infected with IBDV. PSA annual meeting. Montreal, QC, Canada, July 15-18, 2019.   Uribe-Diaz S, Yitbarek A, Vallejo D, Losada-Medina D, Ahmed M, and Rodríguez-Lecompte JC. 2020. Role of folic acid on the antiviral innate immune pathways in chicken B-lymphocytes infected with IBDV. PSA annual meeting. Online, July 15-18, 2020.   Uribe-Diaz S, Yitbarek A, Vallejo D, Losada-Medina D, Ahmed M, and Rodríguez-Lecompte JC. 2019. Effect of folic acid on the innate immune receptors in chicken B-lymphocytes infected with IBDV. International Poultry Scientific Forum (IPSF), SPSS and SCAD. Atlanta, GA, January 28-30, 2020.   Vignale-Pollock, Karen, Elle Chadwick, and Robert Beckstead. The effect of feeding encapsulated butyric acid and zinc on disease signs of turkeys challenged with histomonas meleagridis and coccidia. International Poultry Scientific Forum (IPSF), SPSS and SCAD. Atlanta, GA. 2020.   Wang Y., Chanthavixay K., C. Kern, Saelao, P., R. Gallardo, S.J. Lamont. N. Chubb, G. Rincon, Zhou, H. 2020. Identification of Active Promoters and Enhancers By H3K27ac Peaks in the Spleen Tissue of Two Inbred Chicken Lines Under NDV Infection and Heat Stress. Plant & Animal Genome XXVIII, San Diego, CA.   White MB, Boothe SM, Dalloul RA. Broiler response to a necrotic enteritis challenge after varying in ovo doses of commercial probiotics. International Poultry Scientific Forum (IPSF), SPSS and SCAD. Atlanta, GA. 2020.   Wisser-Parker, Kristy, Kristen Wooten, Phaedra Talverides-Hontz, and Mark S. Parcells. Assessment of the Role of IRG1 and Itaconate on Marek’s diseases virus (MDV) Infection. Proceedings of the 92nd NECAD, Penn State University, September 15, 2020   Undergraduate Research Symposium: Gogineni, Vivek, Huawei Wang, Kyle Moskowitz, Prasad Dhurjati, Joshua Miller, Benedikt Kaufer, and Mark S. Parcells. Agent-based Modeling of Marek’s Disease Virus Infection of Chicken Embryo Fibroblasts (CEF). University of Delaware Undergraduate Research Symposium August 13, 2020   Wang, Huawei, Vivek Gogineni, Kyle Moskowitz, Prasad Dhurjati, Joshua Miller, Benedikt Kaufer, and Mark S. Parcells. Agent-based Modeling of Marek’s Disease Virus Reactivation from Latency. University of Delaware Undergraduate Research Symposium August 13, 2020   Book Chapters: Cheng, H.H. and Lamont, S.J. 2020. Genetics of disease resistance. pp. 90-108. In: Diseases of Poultry. 14th ed. D.E. Swayne, M. Boulianne, C.M. Logue, L.R. McDougald, V. Nair, and D.L. Suarez, Eds. Wiley-Blackwell, Hoboken   Erf, G. F. Autoimmune diseases of poultry. in: Avian Immunology, Schat, K. A., Kaspers B. and, P. Kaiser, editors. Elsevier, Academic Press, San Diego, CA. 3rd edition of Avian Immunology in press.   Klasing, K.C., and D.R. Korver. 2020. Nutritional diseases. pp. 1255-1285. In: Diseases of Poultry. 14th ed. D.E. Swayne, M. Boulianne, C.M. Logue, L.R. McDougald, V. Nair, and D.L. Suarez, Eds. Wiley-Blackwell, Hoboken   Pinard-van der Laan, M.-H., J. Kaufman, A. Psifidi, H. Zhou, M. Fife. 2020. Genetics and genomics of immunity and disease traits in poultry species. In S. E. Aggrey, H. Zhou, M. Tixier-Boichard and D. D. Rhoads (Eds). 2020 Advances in poultry genetics and genomics. Burleigh Dodds Science Publishing ISBN:978-1-78676-324.   6.3 Thesis/Dissertation Aylward, Bridget. A Comparative Evaluation of the Gastrointestinal Immune Response of the Modern and Heritage Broiler Chicken. Ph.D. Dissertation. 2020. University of Delaware. Supervisor: Ryan J. Arsenault   Boothe, Siobhan M.  In-house hatching and early feeding to improve chick performance during a necrotic enteritis challenge.  MS Thesis, Virginia Tech. Supervisor: Rami A. Dalloul   Briggs, Whitney. Evaluation and optimization of quantitative analysis methods for C. perfringens detection in broiler intestinal samples to use with necrotic enteritis challenge models. M. S. thesis, 2020. Ohio State University. Supervisor: Lisa R. Bielke   Chadwick, Elle. The role of poultry parasites in gut health and production. PhD Dissertation, 2020. North Carolina State University. Supervisor: Robert B. Beckstead   Cox, Jeremiah. Characterization of intestinal microbiota of newly hatched ducklings. Undergraduate research thesis, 2020. Ohio State University. Supervisor: Lisa R. Bielke <a href="https://kb.osu.edu/handle/1811/91796">https://kb.osu.edu/handle/1811/91796</a>   Ellington, C. Effects of dietary copper, zinc and manganese source and level on the acute inflammatory response of broilers. MS Thesis, 2019. University of Arkansas, Fayetteville Supervisor: G. F. Erf   Tracy, Karen. The systemic immune response to Newcastle disease virus infection in chickens. PhD Dissertation, 2020. University of California-Davis. Supervisor: Rodrigo A. Gallardo   Emami, Nima K.  Managing poultry gut integrity, immunity and microbial balance during necrotic enteritis.  PhD Dissertation. 2020 Virginia Tech. Supervisor: Rami A. Dalloul

Impact Statements

Erf Objective 2. The autoimmune disease-prone Smyth, UCD-200/206 and Obese strain chickens are important genetic models to study the cause-effect relationship between genetic susceptibility, immune function, and environmental factors in multifactorial, non-communicable diseases. Objective 3. The development of the growing feather as a dermal test-site enables study of in vivo immune system and tissue responses initiated by injected test-material in a complex vascularized tissue. Arsenault Delaware Objective 2: The identification of pathogenesis between two serovars of Salmonella important to human food safety. The differences center on the timing and intensity of innate immune inflammatory responses, which may be important in how quickly or effectively birds do or do not clear Salmonella. We determined that a combination purified yeast cell wall fractions prevent NE better than crude YCW due to greater engagement of immune responses. The recommendation will be for at least two purified fractions to be included in feed, rather than crude YCW. SFB are a beneficial probiotic due to their activation of immune responses and enhancement of gut barrier function. Host-adapted probiotics are effective at improving gut health in a way similar to antibiotics. Beckstead Objective 1 Currently there are no treatments or vaccines available to treat or prevent histomoniasis. Data from this research will aid turkey genetics companies in selecting for pedigree lines that are resistant to the disease, thereby preventing the financial losses and animal welfare issues associated with histomoniasis. Koci Objective 2 The data reported for 2020 ad to our understanding of how gene expression regulates the immune response. Miller Objective 1. The genomic sequence determination for MHC-Y in the RJF reference genome will provide a base for further studies devoted to MHC-Y immunogenetics. Data are emerging supporting the hypothesis that genes within the highly polymorphic MHC-Y region are involve in guiding immune responses in chickens. Data are emerging suggesting that MHC-Y contributes to the genetics governing colonization of chickens by Campylobacter jejuni. Objective 3. There is now a much simpler method for MHC-Y genotyping that will make it possible to type large numbers of birds quickly. This will make it possible to far more easily compare sample sets across experimental challenge trials and different strains of chickens. NC- Ashwell Objective 1. The results of this work provide insight into energetic resource needs and allocations in response to genetic selection and antigen exposure in HAS and LAS which may help explain phenotypic differences observed in antibody response between lines. Gallardo Objective 1. Our work provides further insight into the increased susceptibility of 335/B19 birds to infectious bronchitis. In addition we have taken advantage of the MHC resistant / susceptible model to investigate the effect of Zn and Mn on the immunity of chickens as direct application of this model. In terms of infectious diseases affecting poultry we have understood the persistence, vaccine protection and bacterial genotyping for Avibacterium paragallinarum and we have understood the pathobiology and of IBV causing FLS and some of the repercussions of the use of vaccination to control this syndrome. Objective #2: We have proved that avian reovirus variants (ARV) are able to infect and cause lymphoid depletion in Bursa of Fabricius and thymus suggesting that this virus causes B and T cell immunodeficiency. Dalloul Objective 2. This work is of significant impact showing the possibility to control and modify the immune responses, microbial profile and metabolism of chickens by dietary supplementation of natural additives. By modifying such responses, this approach led to alleviating the negative impact of necrotic enteritis under filed-like research settings, which remains to be proved in commercial field conditions. Taylor Objective 1. Knowing alloantigen genes and gene products will assist in genetic improvement. Stakeholders benefit form knowledge of associations between alloantigen genes and characteristics with commercial value. Objective 3. Defined genetic stocks will enable further discovery of genes that affect traits having economic importance. Bielke Objective 2. Altogether, this research stresses the importance of early microbial colonization on immune function and inflammation of poultry. Gram negative bacteria, which possess lipopolysaccharides, appear to negatively influence susceptibility to disease and ability of broilers to respond to inflammatory events later in life. Conversely, results suggest that lactic acid bacteria promote a favorable bacterial environment and help control inflammation in the GIT. Some results presented here suggest that pioneer colonization can affect susceptibility of broilers to necrotic enteritis caused by co-infection with Eimeria and C. perfringens, further demonstrating the importance of hatchery and parent flock management. Parent flock and hatchery microbiology should be considered critical components to directing favorable colonization of production flocks. Lamont Objective 3. Maintenance of genetic resources enables future studies in immunogenetics in chickens. Identification of genes and pathways responding to infection with bacterial or viral pathogens, especially those differing between resistant and susceptible genetic lines, will aid our understanding of resistance mechanisms, and identify candidate genes for genetic selection to improve response. This will result in enhanced animal health and welfare, improved food safety, and better-informed management practices. Parmentier Objective 2. Hygienic conditions appear to determine the level of specific immune responses (specific antibodies), natural and natural auto antibodies, as well as innate immunity (complement dependent lysis) in young growing broilers. Modulation or management of the environment (housing) have a profound effect on immune responsiveness. Levels of immune parameters may be helpful as breeding goal against misbehaviour of poultry, but also point to the risk that breeding for high immunocompetence may result in enhanced misbehaviour. (lower) levels of these self-binding antibodies may predict upcoming metabolic diseases, and as such may act as a predictor. ‘Vaccination’ to enhance or maintain levels of these antibodies might add to prevent metabolic and inflammatory related diseases. Importance of hygienic conditions in housing and feed? Juan Carlos Rodriguez Objective 2. The chicken Ang4 might have a potential bactericidal effect against intestinal pathogenic microbes such Clostridium perfringens; however, independent of the modulating the intestinal microbiota and the innate immunity, their effect on angiogenesis and tissue repair need to be evaluated. Our work is contributing to the understanding of the activation pathways of innate immunity induced by IBDV. Zhou Objective 1: Identification of genes that are associated with resistance to heat stress and Newcastle disease virus and can be used to genetic enhancement of disease resistance of chicken in adaption to hot climate. Objective 2: Understanding the molecular mechanisms of Salmonella colonization in chickens could aid in development novel strategy in improving food safety in poultry industry. Drechsler Objective 1. Characterization of gene regulatory elements in the chicken genome will aid in the selection of markers for disease resistance in breeding. An ideal mechanism for controlling disease in poultry is to breed birds with natural resistance. We are identifying mechanisms for this resistance. Innate immune functions, particularly activation of macrophages, has consistently shown to be different in disease resistant versus susceptible birds. We are investigating the role of the host epigenome in immune evasion of viruses and disease resistance and susceptibility to develop a deeper understanding of the genetic processes involved. Song Objective 1. The role of adiponectin in chickens will help advance the understanding of lipid metabolism in response to herpesvirus infection. The first report on the relationship between virus infection and mitochondria in chickens will provide a unique clue in understanding pathogenesis and tumorigenesis due to viral infection. Parcells Objective 1. Role of polycomb repressive complex proteins: The finding of interaction of Meq splice variant-derived proteins, proteins that accumulate as MDV establishes latency, with the Polycomb Repressive complex, ties MDV latency directly to a pathway associated with cellular transformation and tumor progression. This work also connects MDV-induced lymphomagenesis to EBV-associated Hodgkin’s lymphoma, as well as other human leukemias and lymphomas. Meq mutations and innate selection: Our finding that mutations in the C-terminus of the Meq oncoprotein, which have been associated with the MDV virulence level, affect the innate sensing and signaling in infected cells. This is the first direct, causal association of meq mutation and a mechanism affecting one aspect of MDV virulence; namely, the evasion of the innate immune system. In follow up to this, we have submitted Meq immunoprecipitations from MDV-infected spleen cell lysates from an in vivo study, as well as tumor cell lines from JM10, RB-1B, RB-1B-based recombinants, and MK and TK strain-transformed T-cell lines to further characterize Meq-binding proteins during lytic and latent infections. Presence of MDV mRNAs in Exosomes of Vaccinated and Protected Chickens: Our finding that viral mRNAs, but not virus DNA, are present in serum exosomes in vaccinated and protected chickens suggests that these exosomes are conferring systemic immunity through CTL-priming by macrophages and dendritic cells that have taken up these exosomes and expressed these proteins. This observation, coupled with our small RNA transcriptomic analysis, may provide the very basis of systemic immune protection elicited by MD vaccines. The finding that we can, in fact, generate mature dendritic cells with IL4, GM-CSF, LPS and IFNpermits a careful and methodical analysis of the role exosomes play in mediating long-term, systemic CTL responses. Klasing Objective 1- The use of enzymes to lower the pathogenicity of coccidia will be a useful adjunct to vaccination approaches in the control of this disease. Objective 2- Understanding the importance of B lymphocytes relative to T lymphocytes in the protective response to SE challenges is important for the development of efficacious vaccines.

Date of Annual Report: 11/18/2021

Report Information

Annual Meeting Dates: 09/17/2021 - 09/19/2021
Period the Report Covers: 10/01/2020 - 09/30/2021

Participants

Robert Taylor, West Virginia University; Christopher Ashwell, West Virginia University; Gisela Erf, University of Arkansas; Ramesh Selvaraj, University of Georgia; Yvonne Drechsler, Western University; Lisa Bielke, Ohio State University; Ryan Arsenault, University of Delaware; Mark Parcells, University of Delaware; Calvin Keeler, University of Delaware; Matthew Koci, North Carolina State University; Keith Jaronsinski, University of Illinois; Janet Fulton, Hy-Line; Rami Dalloul, University of Georgia; Rodrigo Gallardo, UC Davis; Jiuzhou Song, University of Maryland; Shawna Weimer, University of Maryland; Susan Lamont, Iowa State University; Paul Cotter, Cotter Laboratory; Andrew Broadbent, University of Maryland; Mostafa Ghanem, University of Maryland, Ali Nazmi, Ohio State University; Billy Hargis, University of Arkansas.
Students-Staff-Post doctoral scholars: Audrey Duff, Ohio State University (presented Station Report, Dr. Bielke’s lab); Brandi Sparling, PhD student, Western University (presented Station Report, Dr. Drechsler’s lab); Sofia Egaña, UC Davis (presented part of the Station Report, Dr. Gallardo’s lab); Theros Ng, Western University (Dr. Drechsler’s lab).

Brief Summary of Minutes

Minutes Attachment:

2021_NE1834 BusinessMeetingMinutes.pdf

Accomplishments

Erf Objective 2. Evaluation of the local (GF-pulp) cellular- and systemic (blood)-antibody responses to autogenous Salmonella vaccines (SVs) revealed that heterophils and macrophages dominated both the local primary and secondary responses to pulp injection of SVs, with only minor participation of lymphocytes. These inflammatory leukocytes persisted longer during the recall than the primary response. The lymphocyte recruitment in response to vaccine vehicle was not observed when mixed with Salmonella bacteria or LPS. Pulp injection of SVs initiated T-dependent antibody responses as indicated by isotype switch from IgM to IgG, and a faster and higher increase in plasma IgG levels following the second compared to the first immunization. Objective 3. AR maintained and reproduced genetic lines that spontaneously develop autoimmune diseases. AR refined and expanded the use of the growing feather as an in vivo test-tube system to study innate and adaptive immune responses in poultry.   Arsenault Objective 2. We elucidated a potential mechanism of why we observe differing responses to cocci challenge in older genetic lines as compared to new. The difference centers on the HIF1 pathway and involves apoptosis and glycolysis metabolism shifts, increasing in ACRB with a challenge dose. With collaborators in Germany, we reported on the first model of a chicken methylation biological clock that reflects the inflammatory state of the bird. Finally, we elucidated the mechanism of action of two distinct and important potential antibiotic alternative feed additives. These mechanism of action results may inform rational feed regimes to prevent performance loss due to management or challenge issues.   Koci Objective 3. Our team at NCSU has worked to develop a new multiplex assay to allow for the assessment of gene expression levels of 50 targets, simultaneously, without the need to produce cDNA or perform RT-PCR. This system is based on the QuantiGene platform. This system uses a mixture of Luminex beads capable of producing 50 unique luminescent signals. Each unique bead is then complexed with capture oligos specific to a given target mRNA. This assay is designed to serve as an initial gene expression screening tool, to assist poultry scientists in identifying signaling pathways for further investigation. Validation of this assay is still ongoing and expected to be completed the following reporting cycle.   Gallardo Objective 1. We have generated additional information in regards to resistance to IBV infections using MHC B haplotype chickens. This information allows us to have a working animal model that has been proven testing minerals as boosters of immune responses. In addition, we have continued to respond to pressing field issues in the commercial industry including avian reovirus variants, IBV associated false layer syndrome, and infectious coryza. Further, we developed an antigenic cartography computational method that can be used to understand the antigenic and genetic relatedness of diverse pathogens.   Lamont Objective 1. A review of literature on genetics and APEC was published. Bioinformatic analyses of the splenic transcriptome revealed that innate immune pathways were differentially expressed and therefore could be potential targets to modulate resistance to APEC. Knockdown of OASL increased the amount of NDV viral RNA, and it also eliminated the difference in expression of interferon response and apoptosis-related genes between NDV-infected and noninfected cells, suggesting that OASL modulates response to NDV infection. Objective 3. Expression patterns of chicken HDPs were determined in resistant and susceptible chicken genetic lines. ISU chicken genetic lines were reproduced and maintained and shared.   Drechsler Objective 1: Developing new project on Immunglobulin-like receptors in the chicken (ChIR). Phylogenetic analysis and re-annotation of ChIR is in progress. Preliminary data with siRNA shows effects on ChIR-B. Objective 3: Continuation of functional annotation of chicken genome: 20 tissues/cells in progress. DNA methylome completed for reproductive and intestinal tissues/ peripheral immune cells. RNA seq completed for all tissues, peripheral blood cells. Pending: tissue macrophages. Some samples need repeating due to QC. ATAC seq completed for intestinal, reproductive tissues and peripheral immune cells. ChIP seq optimization is ongoing for several tissues/cells.   Taylor Objective 1: Individual and pooled samples from chickens with defined alloantigen genotypes underwent SNP analyses.  Alloantigen A was associated with a region from 2,420,000 to 2,890,000 bp on chromosome 26.  A candidate gene with high consistency between amino acid changing SNP and allelic differences identified the alloantigen A gene as C4BPM (complement component 4 binding protein membrane).  A second alloantigen, E, is tightly linked to the A system. It was originally identified as unannotated locus, LOC101748581, but has been annotated as FCAMR, Fc fragment of IgA and IgM receptor.  A similar approach was used to identify alloantigen D.  A chromosome 1 region between 128,600,000 to 128,850,000 bp was associated with allelic changes and SNP.  The candidate gene for alloantigen D is CD99.  Objective 3. Genetic stocks consisting of two inbred lines, four congenic lines and six line crosses are maintained for research. Stocks are typed at the MHC and other alloantigen systems.   Bielke Objectives 2 and 3: The role of pioneer colonization of the GIT in neonatal birds was shown to have age-related effects, especially with regards to immune tolerance and innate immune function. Generally, Gram negative bacteria decrease ability of birds to respond to inflammatory events and lactic acid bacteria promote colonization with segmented filamentous bacteria, which are thought to promote beneficial innate immune function. This has been demonstrated through other experiments in which early inoculation with Gram negative bacteria increased gut permeability and susceptibility to necrotic enteritis. Gram negative inoculation promoted dendritic cell migration to gut tissue, decreased HNF1-alpha, decrease pathways associated with D-glucose, and F-gamma receptor dependent phagocytosis. Conversely, lactic acid bacteria promoted gluconeogenesis, B cell receptor signaling, Class I MHC antigen processing, and IL-1 while downregulating heterophil degranulation and MHC Class II antigen presentation. These clearly demonstrate the role of colonizing bacteria in immune system function and maturation.   Song Objective 1: In allelic specific expressions of CD4+ T cells, we found some critical genes and CNV linked to T cell activation, T cell receptor (TCR), B cell receptor (BCR), ERK/MAPK, and PI3K/AKT-mTOR signaling pathways, which play potentially essential roles in MDV infection. Objective 3: We investigated the antibiotic resistance profiles of Escherichia coli found in poultry litter, as well as E. coli O serogroups, virulence genes, and antimicrobial resistance genes. In this context , we examined the prevalence of antimicrobial resistance and heavy metal genes detected among isolates and identified those with a high prevalence of copper and silver, tetracycline, aminoglycosides, gentamicin, and sulphonamides.   Parcells We cloned the chicken EZH2 gene (2 isoforms) and the chicken SATB1 and have found that these interact with Meq splice variant-encoded proteins. These data have direct implications regarding the suppression of MDV lytic gene expression, transformation and the Treg patterning of MDV-latently-infected cells. We found that the long form of Meq in CVI988 actually confers higher levels of oncogenicity to RB-1B, but that the short form of this same Meq is attenuating. We also found that Meq isoforms from higher virulence strains have increased interactions with DNA-repair proteins, suggesting that MDV evolution of virulence may involve increased somatic mutation. This year we found that serum exosomes are taken up by HD11 cells programmed to be DCs, suggesting that in vivo, serum exosomes may be important to systemic antigen presentation. We found that C4BP-A is not likely a determinant of Alloantigen A.   Jarosinski Objective 1: Identification and characterization of chicken complement receptor-like 1 (CR1L) or complement component 4 binding protein, GPI-anchored (C4BPG) showed differences in protein sequences between different chicken lines more resistant or susceptible to MD. Objective 2: We identified up- and down-regulation of purinergic receptors both during MDV infection, as well as between infected or transformed cells in vivo. Objective 3: We have cloned the putative chicken CR1L/C4BPG and developed monoclonal antibodies to this protein.   Swaggerty Objective 1: We evaluation the innate immune markers from chickens selected for high (HAS) and low (LAS) antibody responses to sheep red blood cells. Differences were observed in the mRNA expression levels of CXCL8 comparing males and females from the HAS line which held true for both PBL and spleen samples. Further, mRNA expression levels for IL6, CXCL8, and CCL4 were consistently higher in spleen samples compared to the PBL in the HAS line.   Selvaraj Objective 3: Conducted a study to identify the effects of Effects of Salmonella enterica ser. Enteritidis and Heidelberg on Host CD4+CD25+ Regulatory T Cell Suppressive Immune Responses in Chickens. S. Enteritidis and S. Heidelberg infection at 3 d of age induces a persistent infection through inducing CD4+CD25+ cells and altering the IL-10 mRNA transcription of CD4+CD25+  cell numbers and cytokine production in chickens between 3 to 32 dpi allowing chickens to become asymptomatic carriers of Salmonella after 18 dpi. A second study was conducted to identify if a Salmonella chitosan nanoparticle vaccine administration is protective against Salmonella Enteritidis in broiler birds. Chitosan nanoparticle vaccinated birds had 0.9 Log10 CFU/g decreased SE cecal loads (P<0.05) compared to control. The vaccine under study did not had any adverse effects on the bird’s BWG and FCR or the IL-1β, IL-10, IFN-γ, or iNOS mRNA expression levels. We concluded that the CNP vaccine, either as a first dose or as a booster vaccination, is an alternative vaccine candidate against Salmonella in poultry.   Cotter Objective 2: The demonstration of heterogeneity among plasmacyte series, cells known for antibody secretion is an important step in the understanding of the complexities of immune reactions.

Publications

<h2>Peer Reviewed Papers</h2> Akerele, G., N. Ramadan, S. Renu, R. Shanmugasundaram, G.J. Renukaradhya, and R.K. Selvaraj. 2020. In vitro characterization and Immunogenicity of chitosan nanoparticles loaded with native and inactivated extracellular proteins from a field strain of Clostridium perfringens associated with necrotic enteritis. Veterinary Immunology and Immunopathology 224:110059. Asfor, A., S. Nazki, V.R.A.P. Reddy, E. Campbell, K.L. Dulwich, E.S. Giotis, M.A. Skinner, and A.J. Broadbent. 2021. Transcriptomic analysis of inbred chicken lines reveals infectious bursal disease severity is associated with greater bursal inflammation in vivo and more rapid induction of pro-inflammatory responses in primary bursal cells stimulated ex vivo. Viruses 13:933. doi: 10.3390/v13050933 Aston, E., A. Nayaran, S. Egaña, M. Wallach, and R.A. Gallardo. Hyperimmunized chickens produce neutralizing antibodies against SARS-CoV-2. 2021. Scientific Reports. Submitted <a href="https://www.researchsquare.com/article/rs-515320/v1">https://www.researchsquare.com/article/rs-515320/v1</a> Aston, E., Y. Wang, K. Tracy, R.A. Gallardo, S.J. Lamont, and H. Zhou. 2021. Comparison of cellular immune responses to avian influenza in two genetically distinct , highly inbred chickens. Veterinary Immunology and Immunopathology 235:110233. https://www.sciencedirect.com/science/article/pii/S0165242721000519 Bai, H., Y. He, Y. Ding, Q. Chu, L. Lian, E.M. Heifetz, N. Yang, H.H. Cheng, H. Zhang, J. Chen, and J. Song. 2020. Genome-wide characterization of copy number variations in the host genome in genetic resistance to Marek's disease using next generation sequencing. BMC Genetics 21:77. doi: 10.1186/s12863-020-00884-w. Bai, Y., P. Yuan, H. Zhang, R. Ramachandran, N. Yang, and J. Song. 2020. Adiponectin and its receptor genes expression in response to MDV infection of White Leghorns. Poultry Science, doi: 10.1016/j.psj.2020.06.004 Bai, H., Y. He, Y. Lin, Q. Leng, J.A. Carrillo, J. Liu, F. Jiang, J. Chen, and J. Song. 2020. Identification of a novel differentially methylated region adjacent to ATG16L2 in lung cancer cells using methyl-CpG binding domain protein enriched genome sequencing. Genome, doi: 10.1139/gen-2020-0071 Bortoluzzi, C., Lahaye, L., Perry, F., Arsenault, R.J., Santin, E., Korver, D.R., and Kogut, M.H. 2021. A protected complex of biofactors and antioxidants improved growth performance and modulated the immunometabolic phenotype of broiler chickens undergoing early life stress. Poultry Science 101176. Chang, R., P. Pandey, Y. Li, C. Venkitasamy, Z Chen, R. Gallardo, B. Weimer, B. and J.M. Russell. 2020. Assessment of gaseous ozone treatment on Salmonella Typhimurium and Escherichia coli O157: H7 reductions in poultry litter. Waste Management, 117: 42-47. Chasser, K.M., K. McGovern, A.F. Duff, B.D. Graham, W.N. Briggs, D.R. Rodrigues, M. Trombetta, E. Winson, and L.R. Bielke. 2021. Evaluation of day of hatch exposure to various Enterobacteriaceae on inducing gastrointestinal inflammation in chicks through two weeks of age. Poultry Science 100:101193. Chasser, K.M., K. McGovern, A.F. Duff, M. Trombetta, B.D. Graham, L. Graham, W.N. Briggs, D.R. Rodrigues, and L.R. Bielke. 2021. Enteric permeability and inflammation associated with day of hatch Enterobacteriaceae inoculation. Poultry Science 100:101298. Conradie, A.M., L.D. Bertzbach, J. Trimpert, J.N. Patria, S. Murata, M.S. Parcells, and B.B. Kaufer. 2020. Distinct polymorphisms in a single herpesvirus gene are capable of enhancing virulence and mediating vaccinal resistance. PLoS Pathogens 16(12):e1009104, doi: 10.1371/journal.ppat.1009104. Cotter, P.F. 2021a. Erythroplastids of duck blood produced by cytokinesis, lysis, and amitosis Journal of World Poultry Research 11(2): 271-277, https://dx.doi.org/10.36380/jwpr.2021.32 Cotter, P.F. 2021b. Atypical hemograms of the commercial duck. Poultry Science100, doi: 10.1016/j.psj.2021.101248 da Silva, A.P. and R.A. Gallardo. 2020. Review: The Chicken MHC: Insights on genetic resistance, immunity and inflammation following infectious bronchitis virus infections. Viruses, https://www.mdpi.com/2076-393X/8/4/637 da Silva, A.P., R. Hauck, S.R.C Nociti, C. Kern, H.L. Shivaprasad, H. Zhou, and R.A. Gallardo. 2021. Molecular biology and pathological process of an infectious bronchitis virus with enteric tropism in commercial broilers. Viruses 13,1477. Respiratory Diseases Special Edition. <a href="https://www.mdpi.com/1999-4915/13/8/1477">https://www.mdpi.com/1999-4915/13/8/1477#</a> da Silva, A.P., C. Giroux, H.S. Sellers, A. Mendoza-Reilley, S. Stoute, and R.A. Gallardo. 2021. Characterization of an IBV isolated from commercial layers suffering from false layer syndrome. Avian Diseases. https://doi.org/10.1637/aviandiseases-D-21-00037 Del Vesco, A.P., H.J. Jang, M.S. Monson, and S.J. Lamont. 2021. Role of chicken oligoadenylate synthase like gene during in vitro Newcastle disease virus infection. Poultry Science, doi.org/10.1016/j.psj.2021.101067 Dulwich, K.L., A. Gray, A. Asfor, S. Giotis, M. Skinner, and AJ Broadbent. 2020. The stronger downregulation of in vitro and in vivo innate antiviral responses by a very virulent strain of infectious bursal disease virus (IBDV), compared to a classical strain, is mediated, in part, by the VP4 protein. Frontiers in Cellular and Infection Microbiology 10.315. doi: 10.3389/fcimb.2020.00315 Egaña-Labrin, S., C. Jerry, H.J. Roh, A.P. da Silva, C. Corsiglia, B. Crossley, D. Rejmanek, and R.A. Gallardo. 2021. Avian reoviruses of the same genotype induce different pathology in chickens. Avian Diseases, Accepted. Emami, N.K, and R.A. Dalloul. 2021. CENTENNIAL REVIEW: Recent developments in host-pathogen interactions during necrotic enteritis in poultry. Poultry Science 100:101330. Emami, N.K., A. Calik, A., M.B. White, E.A. Kimminau, and R.A. Dalloul. 2021.Managing broilers gut health with antibiotic-free diets during subclinical necrotic enteritis. Poultry Science 100:101055. Erf, G.F., G. Le Pape, S. Rémy, and C. Denesvre. 2020. Mardivirus infection and persistence in feathers of a chicken model harboring local autoimmune response. Microorganisms 8(10):1613. <a href="https://doi.org/10.3390/microorganisms8101613">https://doi.org/10.3390/microorganisms8101613</a> Felfoldi, B., H. Wang, N. Nuthalapati, R. L. Taylor, Jr., J. D. Evans, S. L. Branton, and G. T. Pharr. 2021. Expression of chicken leukocyte cell-derived chemotaxin 2 in the embryonic bursa of Fabricius. Int. J. Poult. Sci. 20: 43-47 https://doi.org/10.3923/ijps.2021.43.47 French, C.E., M.A. Sales, S.J. Rochell, A. Rodriguez, and G.F. Erf. 2020. Local and systemic inflammatory responses to lipopolysaccharide in broilers: new insights using a two-window approach. Poultry Science 99:6593-6605. <a href="https://doi.org/10.1016/j.psj.2020.09.078">https://doi.org/10.1016/j.psj.2020.09.078</a> Garcia, G., Jr, A. Sharma, A. Ramaiah, C. Sen, A. Purkayastha, D.B. Kohn, M.S. Parcells, S. Beck, H. Kim, M.A. Bakowski, M.G. Kirkpatrick, L. Riva, K.C. Wolff, B. Han, C. Yuen, Ulmert D, Purbey PK, Scumpia P, Beutler N, Rogers TF, Chatterjee AK, Gabriel G, Bartenschlager R, Gomperts B, C.N. Svendsen, U.A.K. Betz, R.D. Damoiseaux, and V. Arumugaswami. 2021. Antiviral drug screen identifies DNA-damage response inhibitor as potent blocker of SARS-CoV-2 replication. Cell Reports 35(1):108940. doi: 10.1016/j.celrep.2021.108940 Glenn, H., G.J. Mullenix, and G.F. Erf. 2021. Effect of low crude protein diet with and without Spirulina platensis inclusion on white blood cell profiles in broilers. Discovery 21:38-44. (Undergraduate Journal Publication) Gonzales-Viera, O., F. Carvallo-Chaigneau, E. Blair, D. Rejmanek, O. Erdogan-Bamac, K. Sverlow, A. Figueroa, R.A. Gallardo, and A. Mete. 2021. Infectious bronchitis virus prevalence, characterization and strain identification in California backyard chickens. Avian Diseases DOI: 10.1637/aviandiseases-d-20-00113 Guo, Y., W. He, H. Mou, L. Zhang, J. Chang, S. Peng, A. Ojha, R. Tavora, M.S. Parcells, G. Luo, W. Li, G. Zhong, H. Choe, M. Farzan, and B.D. Quinlan. 2021. An engineered receptor-binding domain improves the immunogenicity of multivalent SARS-CoV-2 vaccines. mBio 12(3):e00930-21, doi: 10.1128/mBio.00930-21 Han, Y., S. Renu, V. Patil, J. Schrock, N. Feliciano-Ruiz, R. Selvaraj, and G.J. Renukaradhya. 2020. Immune response to salmonella enteritidis infection in broilers immunized orally with chitosan-based salmonella subunit nanoparticle vaccine. Frontiers in immunology 11:935. Han, Y., S. Renu, J. Schrock, K.Y. Acevedo-Villanueva, B. Lester, R. Selvaraj ,and G.J. Renukaradhya. 2020.Temporal dynamics of innate and adaptive immune responses in broiler birds to oral delivered chitosan-based Salmonella subunit nanoparticle vaccine. Veterinary Immunology and Immunopathology, https://doi.org/10.1016/j.vetimm.2020.110111 Jang, H.-J., Monson, M., Kaiser., M., Lamont, S.J. 2020. Induction of chicken host defense peptides within disease-resistant and -susceptible lines. GENES 11:1195; doi:10.3390/genes11101195 Lee, A., G.C. Dal Pont, M. Battaglia, R. Arsenault, and M. Kogut. 2021. Role of JAK-STAT pathway in chicks fed with chestnut tannins. Animals 11(2):337. Lee, A., G.C. Dal Pont, M.B. Farnell, S. Jarvis, M. Battaglia, R. Arsenault, and M. Kogut. 2021. Supplementing chestnut tannins in the broiler diet mediates a metabolic phenotype of the ceca. Poultry Science 100:47-54. Mon, K.K.Z., C. Kern, G. Chanthavixay, Y. Wang, and H. Zhou. 2021. Tolerogenic immunoregulation towards Salmonella Enteritidis contribute to colonization persistence in young chicks. Infection and Immunity. doi: 10.1128/IAI.00736-20. Monson, M.S. and S.J. Lamont. 2021. Genetic resistance to avian pathogenic Escherichia coli (APEC): current status and opportunities. Avian Pathology, doi: 10.1080/03079457.2021.1879990 Monson, M.S., B.L. Bearson,, M.J. Sylte, T. Looft, S.J. Lamont, S.J., and S.M.D. Bearson. 2021.Transcriptional response of blood leukocytes from turkeys challenged with Salmonella enterica serovar Typhimurium UK1. Veterinary Immunology and Immunopathology 232: doi.org/10.1016/j.vetimm.2020.110181 Mortada, M., D.E. Cosby, R. Shanmugasundaram, and R.K. Selvaraj. 2020. In vivo and in vitro assessment of commercial probiotic and organic acid feed additives in broilers challenged with Campylobacter coli. Journal of Applied Poultry Research  29:435-446. doi:10.1016/j.japr.2020.02.001 Mullenix G. J, E.S. Greene, N.K. Emami, G. Tellez-Isaias, W.G. Bottje, G.F. Erf, M.T. Kidd, and S. Dridi. 2021. Spirulina platensis inclusion reverses circulating pro-inflammatory (chemo)cytokine profiles in broilers fed low-protein diets. Frontiers in Veterinary Science <a href="https://doi.org/10.3389/fvets.2021.640968">https://doi.org/10.3389/fvets.2021.640968</a> Mushi, J., G.H. Chiwanga, E. Mollel, M. Walugembe, R.A. Max, P. Msoffe, R.A. Gallardo, T. Kelly, S. Lamont, J. Dekkers, H. Zhou, and A. Muhairwa. 2021. Antibody response, viral load, viral clearance and growth rate in Tanzanian free-range local chickens infected with lentogenic Newcastle disease virus. 2021. Journal of Veterinary Medicine and Animal Health 13:98-105. Mushi, J., G.H. Chiwanga, E.N. Amuzu-Aweh, M. Walugembe, R.A. Max, S.J. Lamont, T.R. Kelly, E.L. Mollel, P.L. Msoffe, J. Dekkers, R. Gallardo, H. Zhou, and A.P. Muhairwa. 2020. Phenotypic variability and population structure analysis of Tanzanian free-range local chickens. BMC Veterinary Research 16:360. doi: 10.1186/s12917-020-02541-x. Neerukonda SN, N.A. Egan, J. Patria, I. Assakhi, P. Tavlarides-Hontz, S. Modla, E.R. Muñoz, M.B. Hudson, and M.S. Parcells. 2020. A comparison of exosome purification methods using serum of Marek's disease virus (MDV)-vaccinated and -tumor-bearing chickens. Heliyon 6(12):e05669. doi: 10.1016/j.heliyon.2020.e05669 Nuthalapati, N., T.A. Burks, R.L. Taylor, Jr., P.B. Siegel, and G. . Pharr. 2021. Protein tyrosine kinase gene expression profiles in the embryonic bursa of Fabricius of chicken lines selected for high and low antibody responses. International Journal of Poultry Science 20:173-178 <a href="https://doi.org/10.3923/ijps.2021.173.178">https://doi.org/10.3923/ijps.2021.173.178</a> Omara, I.I., C.M. Pender, M.B. White, and R.A. Dalloul. 2021. The modulating effect of dietary beta-glucan supplementation on expression of immune response genes of broilers during a coccidiosis challenge. Animals 11:151. Overbey, E.G., T.T. Ng, P. Catini, L.M. Griggs, P. Stewart, S. Tkalcic, R.D. Hawkins, and Y. Drechsler: 2021. Transcriptomes of an array of chicken ovary, intestinal, and immune cells and tissues. Frontiers in Genetics 12:664424. doi: 10.3389/fgene.2021.664424 Patel, R.T., B.M. Gallamoza, P. Kulkarni, M.L. Sherer, N.A. Haas, E. Lemanski, I. Malik, K. Hekmatyar, M.S. Parcells, and J.M. Schwarz. 2021. An examination of the long-term neurodevelopmental impact of prenatal zika virus infection in a rat model using a high resolution, longitudinal MRI approach. Viruses 13(6):1123. doi: 10.3390/v13061123 Raddatz, G., R.J. Arsenault, B. Aylward, R. Whelan, F. Böhl, and F. Lyko. 2021. A chicken DNA methylation clock for the prediction of broiler health. Communications Biology 4(1):1-8. Renu, S., Y. Han, S. Dhakal, Y.S. Lakshmanappa, S. Ghimire, N. Feliciano-Ruiz, S. Senapati, B. Narasimhan, R. Selvaraj, and G.J. Renukaradhya. 2020. Chitosan-adjuvanted Salmonella subunit nanoparticle vaccine for poultry delivered through drinking water and feed. Carbohydrate Polymers 243:116434. Saelao, P., Y. Wang, G. Chanthavixay, V. Yu, R.A. Gallardo, J. Dekkers, S.J. Lamont, T. Kelly, and H. Zhou. 2021. Distinct transcriptomic response to Newcastle disease virus infection during heat stress in chicken tracheal epithelial tissue. Scientific Reports 11:7450. <a href="https://www.nature.com/articles/s41598-021-86795-x.pdf">https://www.nature.com/articles/s41598-021-86795-x.pdf</a> Shanmugasundaram, R., A. Markazi, M. Mortada, T.T. Ng, T.J. Applegate, L.R. Bielke, and R.K. Selvaraj. 2020. Effect of synbiotic supplementation on caecal Clostridium perfringens load in broiler chickens with different necrotic enteritis challenge models. Poultry Science 99(5):2452-2458. doi:10.1016/j.psj.2019.10.081 Taylor, R.L., Jr. 2021. The 100 most cited papers from Poultry Science’s centennial. Poultry Science 100:, <a href="https://doi.org/10.1016/j.psj.2021.101256">https://doi.org/10.1016/j.psj.2021.101256</a> Taylor, R.L., Jr. and D. Jones. 2021. A century of progress 1921-2021. Poult. Sci. 100:101073 https://doi.org/10.1016/j.psj.2021.101073 Tong, Z.W.M., A.C. Karawita, C. Kern, H. Zhou, J.E. Sinclair, L. Yan, K.Y. Chew, S. Lowther, L. Trinidad, A. Challagulla, K.A. Schat, M.L. Baker, and K.R. Short. 2021. Primary chicken and duck endothelial cells display a differential response to infection with highly pathogenic avian influenza virus. Genes 12 (6):901. Troxell, B., M. Mendoza, R. Ali, M. Koci, and H. Hassan. 2020. The attenuated Salmonella enterica serovar Typhimurium, strain NC983, is immunogenic, and protective against virulent Typhimurium challenges in mice. Vaccines 8 (4), 646. https://doi.org/10.3390/vaccines8040646 Vega-Rodriguez, W., H. Xu, N. Ponnuraj, H. Akbar, T. Kim, and K.W. Jarosinski. 2021. The requirement of glycoprotein C (gC) for interindividual spread is a conserved function of gC for avian herpesviruses. Scientific Reports 11(1):7753. Vega-Rodriguez W., N. Ponnuraj, M. Garcia, and K.W. Jarosinski. 2021. The requirement of glycoprotein C for interindividual spread is functionally conserved within the Alphaherpesvirus genus (Mardivirus), but not the host (Gallid). Viruses 13(8):1419 Wilkinson, N.G., R.T. Kopulos, L.M. Yates, W.E. Briles, and R.L. Taylor, Jr. 2021. Research Note: Rous sarcoma growth differs among congenic lines containing major histocompatibility (B) complex recombinants.  Poultry Science 100: Zhang, L., X. Wei, R. Zhang, M. Koci, D. Si, B. Ahmad, and H. Guo. 2020. C-terminal amination of a cationic anti-inflammatory peptide improves bioavailability and inhibitory activity against LPS-induced inflammation. Frontiers in Immunology 15. doi 10.3389/fimmu.2020.618312 Zhao, C.F., X. Li, B. Han, L.J. Qu, C.J. Liu, J. Song, N. Yang, and L. Lian. 2020. Knockdown of the Meq gene in Marek's disease tumor cell line MSB1 might induce cell apoptosis and inhibit cell proliferation and invasion. Journal of Integrative Agriculture 19:2767-2774. doi.org/10.1016/S2095     <h2>Published Abstracts</h2> Arsenault, R.J. Strategic Modulation of Intestinal Microbiome: An Immunologist Perspective. Poultry Science Annual Meeting. 2021, July, Virtual Conference. Arsenault, R.J. Kinomics: Regulation of the Metabolome. Poultry Science Annual Meeting. 2021, July, Virtual Conference. Arsenault, R.J. The Immunometabolic Interface Between Host and Microbiota. Animal Nutrition Conference of Canada. 2021, May, Virtual Conference. Beck, C. N., J. Santamaria, M. A. Sales, and G. F. Erf. 2021. Primary and recall immune responses to autogenous Salmonella vaccine or Salmonella lipopolysaccharide administration in Light-brown Leghorn pullets. Poult. Sci. PSA Virtual Conference. Bielke, L.R.. A.F. Duff, K. M. Chasser, W.N. Briggs, and K.M. Wilson. “Modeling necrotic enteritis: Applying lessons learned.” Poultry Science Association Annual Meeting, Virtual Conference, July 2021. Blue, C.E.C., E.A. Kimminau, M.B. White, N.K. Emami, and R.A. Dalloul. 2021. Effects of a phytogenic feed additive on broilers during a necrotic enteritis challenge. International Poultry Scientific Forum (Virtual),  Atlanta, GA. Chasser, K.M., A.F. Duff, K.E. McGovern, M. Trombetta, and L.R. Bielke. “Comparison of chick quality, health, and inflammation from two hatchery environments.” Poultry Science Association Annual Meeting, Virtual Conference, July 2021. Cueva, Justin R., Nicholas Egan, Imane Assakhi, Phaedra Tavlarides-Hontz, and Mark S. Parcells. Sequential interactions of meq proteins with polycomb repressive complex proteins in marek’s disease virus latency. The 13th International Symposium on Marek’s Disease and Avian Herpesviruses, June 2021. Dallakoti, Aksana, Sabarinath Neerukonda, Phaedra Travlarides-Hontz, and Mark S. Parcells. Transcriptomic and proteomic analysis of exosomes released by Marek’s disease virus transformed t-cell lines. The 13th International Symposium on Marek’s Disease and Avian Herpesviruses, June 2021. Duff, A.F., K.M. Chasser, K.E. McGovern, M. Trombetta, and L.R. Bielke. Adaptation of cell culture assay measuring fluorescent quantification of β-D-Glucuronidase activity for assessment of ileal granulocyte degranulation in tissue scrapings. Poultry Science Association Annual Meeting, Virtual Conference, July 2021. Evans, R.D., J. Santamaria, and G.F. Erf. 2021. Evaluation of the toxigenicity of lipopolysaccharide associated with chicken hepatopathy. AAAP Virtual Conference. Koci, M. Connecting the Microbiome to Immune Function Through Metabolomics. 3rd Microbiome Movement – Animal Health & Nutrition. Online. October 2020 (International meeting). McGovern, K.E., J.C. Bielke, A.F. Duff, A. Calvert, K.M. Chasser, and L.R. Bielke. Measuring Eimeria oocysts viability via auto-fluorescence following anticoccidial treatment. Poultry Science Association Annual Meeting, Virtual Conference, July 2021. Miller, Joshua, Kyle Moskowitz, Samuel Keating, Abhyudai Singh, Prasad Dhurjati, Andelé Conradie, Benedikt B. Kaufer, Phaedra Travlarides-Hontz, and Mark Parcells. The development of agent-based and mathematical models for Marek’s disease virus (mdv) lytic and latent infections. The 13th International Symposium on Marek’s Disease and Avian Herpesviruses, June 2021. Parcells, Mark S., Joshua S. Miller, Erin Gollhardt, Aksana Dallakoti, Shannon Modla, Eric Muñoz, Matthew B. Hudson, and Ryan J. Arsenault. Effect of serum exosomes from vaccinated and protected and tumor-bearing chickens on immune function. The 13th International Symposium on Marek’s Disease and Avian Herpesviruses, June 2021. Patria, Joseph, Nirajan Bhandari, Phaedra Travlarides-Hontz, Andelé Conradie, Benedikt B. Kaufer, and Mark S. Parcells. Evaluation of the effect of Meq isoform on Marek’s disease virus (MDV) pathogenicity. The 13th International Symposium on Marek’s Disease and Avian Herpesviruses, June 2021. Santamaria, J., C.N. Beck, M.A. Sales, and G.F. Erf. 2021. Inflammatory and antibody responses to intradermally administered autogenous Salmonella vaccine isolates and content-matched Salmonella lipopolysaccharide. Poultry Science association Annual Conference (Virtual). Taylor, R.L., Jr., W. Drobik-Czwarno, A. Wolc, and J.E. Fulton. 2021. Candidate genes for A and E blood group systems in the chicken. Poultry Science 100(E-Suppl. 1):54. Trombetta, M., K.M. Chasser, A.F. Duff, K.E. McGovern, D.R. Rodrigues, D. Jeffery, D.J. Shafer, and L.R. Bielke. Effect of probiotics on early microbial colonization in day of hatch ducklings. Poultry Science Association Annual Meeting, Virtual Conference, July 2021. Wisser-Parker, Kristy, Kristen Wooten, Phaedra Talverides-Hontz, and Mark S. Parcells. Assessment of the role of IRG1 and itaconate on Marek’s disease virus (NDV) infection. The 13th International Symposium on Marek’s Disease and Avian Herpesviruses, June 2021.   <h2>Book Chapters:</h2> Erf, G.F. (in press). Autoimmune diseases of poultry. Pp. xxx-xxx. In: Avian Immunology, 3rd Ed.. K.A. Schat, B. Kaspers, T. Goebel, L. Vervelde, Eds., Elsevier, London, San Diego Lamont, S.J., J.C.M. Dekkers, A. Wolc, and H. Zhou. (in press). Immunogenetics and the mapping of immunological functions. Pp. xxx-xxx. In: Avian Immunology. K.A. Schat, B. Kaspers, T. Goebel, L. Vervelde, Eds., Elsevier, London, San Diego     <h2>6.3 Thesis/Dissertation</h2> Chasser, Kaylin. Effect of day of hatch inoculation with Enterobacteriaceae on inflammation and enteric permeability in broilers. Ph.D. dissertation, May 2021. Ohio State University. Supervisor: Lisa R. Bielke Johnson, Casey. A Kinomic Analysis of the Immunometabolic Effects of Antibiotic Alternatives in Necrotic Enteritis Disease Model. Ph.D. Dissertation. 2021. University of Delaware. Supervisor: Ryan J. Arsenault White, Mallory B. In ovo and feed application of probiotics or synbiotics and response of broiler chicks to post-hatch necrotic enteritis. PhD Dissertation. 2021  Virginia Tech. Supervisor: Rami A. Dalloul

Impact Statements

Erf Objective 2. The autoimmune disease-prone Smyth, UCD-200/206 and Obese strain chickens are important genetic models to study the cause-effect relationship between genetic susceptibility, immune function, and environmental factors in multifactorial, non-communicable diseases. Objective 3. The development of the growing feather as a dermal test-site enables study of in vivo immune system and tissue responses initiated by injected test-material in a complex vascularized tissue. Arsenault Objective 2: The results from the work comparing ACRB and modern broilers response to cocci challenge will allow us to better understand the changes to the modern broiler immune system due to selective pressures, this information will aid in formulating methods of modulating the immune response at key points in grow out to enhance the modern broiler’s resistance to disease. The chicken methylation clock provides insights into inflammatory effects on epigenetics. This can impact both growth performance of the bird as well as innate immune training and adaptive immune response. In addition, this provides another method of measuring the inflammatory status of broilers chickens, proving new insight into the resting and challenge state of the birds and their immune responses. The two collaborative feed additive mechanism of action studies both provide insight into antibiotic alternatives and alternative growth promoters. These results may serve as a target of intervention for specific inflammatory management conditions and challenges. Koci Objective 3. Once completed, this multiplex assay system will allow for members of the community to screen samples for changes in gene expression of 45 different targets, across 3 major systems (immunology, stress, and gut function). The data from these experiments will be useful in helping scientists determine the best complement of genes to assay for by RT-PCR, as well as identify experimental conditions best suited for RNAseq analysis. Gallardo Objective 1. Our recent work has provided a better understanding of 1) the primary and secondary immune response against IBV and the role of cell responses on resistance to the pathogen; 2) persistence and antigenic determinants in Avibacterium paragallinarum (AP); and 3) antigenic determinants in reovirus. Zhou Identification of genes that are associated with resistance to heat stress and Newcastle disease virus and can be used to genetic enhancement of disease resistance of chicken in adaption to hot climate; Elucidating underlying cellular mechanisms of genetic resistance to avian influenza virus in chickens could lay a great foundation for novel strategy in prevention; Understanding the molecular mechanisms of Salmonella colonization in chickens could aid in development novel strategy in improving food safety in poultry industry. Lamont Objective 1. A review paper provided access for scientists to a curated summary of literature associated with genetics and APEC response. Identification of structural and functional genetic variants associated with differential responses to pathogens laid the foundation for future studies, for rationale design of vaccines and for genetic selection to improve disease resistance in poultry. Objective 3. Information on expression of HDP in resistant and susceptible chicken lines may aid in understanding their function. Continued research with ISU chicken genetic lines was enabled. Drechsler Objective 1. Functionally annotating the chicken genome will benefit research in agricultural animals. Uncovering the location of regulatory elements and determining their interactions will provide the necessary framework to understand how regulatory networks govern gene expression and how genetic and environmental influences alter these networks to impact animal growth, health and disease susceptibility or resistance. Establishing the role of chicken immunoglobulin-like receptors will benefit agricultural and human research. Their role in immunity in chicken, and in human, association with MHC-I during disease remains unexplored. This study will further understanding of immunoglobulin-like receptors in disease resistance in MHC defined chickens, providing producers with genetic biomarkers for enhanced immunity against diseases through selective breeding. Taylor Objective 1. Genetic improvement will benefit from alloantigen gene and gene product identification. Associations between economic traits and specific alloantigen genes will be advantageous to stakeholders. Objective 3. WVU will continue producing specific MHC haplotypes and segregating alloantigen alleles in genetic stocks for collaborative studies. Bielke Altogether, this research at Ohio State U. stresses the importance of early microbial colonization on immune function and inflammation of poultry. Gram negative bacteria, which possess lipopolysaccharides, appear to negatively influence susceptibility to disease and ability of broilers to respond to inflammatory events later in life. Conversely, results suggest that lactic acid bacteria promote a favorable bacterial environment and help control inflammation in the GIT. Some results presented here suggest that pioneer colonization can affect susceptibility of broilers to necrotic enteritis caused by co-infection with Eimeria and C. perfringens, further demonstrating the importance of hatchery and parent flock management. Parent flock and hatchery microbiology should be considered critical components to directing favorable colonization of production flocks. Song Objective 1. In copy number variation analysis, we found some critical genes and CNV linked to T cell activation and key signaling pathways that which play potentially essential roles in MDV infection. Also, we found that the adipoR1 mRNA expression level was significantly increased in MD-susceptible chickens after MDV infection. The role of adiponectin in chickens will help advance the understanding of lipid metabolism in response to herpesvirus infection. Most importantly, we found that The Meq might affect the main features of tumorous cells, including proliferation, apoptosis, and invasion, suggesting that the Meq gene might play a crucial role in interfering with lymphomatous cell transformation. Parcells The identification of Meq proteins with the polycomb repressive complex and chickens SATB1 ties latency directly to cellular transformation, suggesting a very important and tractable model for Hogkin’s lymphoma. Uptake of exosomes by DC-patterned HD11 cells supports our hypothesis that serum exosomes may be important to systemic immunity. Jarosinski Objective 1: Differences in chCR1L/C4BPG between chicken lines suggest potential role of this protein in MD resistance. Objective 2: Specific purinergic receptors identified will be studied in genetic differences in chickens to MD induction or progression. Objective 3: The addition of mAbs against chCR1L/C4BPG will allow greater characterization of the immune response in chickens. Swaggerty Objective 1:. Immunological evaluation of lines of chickens selected for antibody responses provides insight into the interplay of innate and adaptive immune responses and could prove beneficial in identifying markers associated with robust immunological responsiveness. Selvaraj Objective 3: Identified a potential nanoparticle vaccine as an alternative vaccine candidate against Salmonella in poultry. Identified that S. Enteritidis and S. Heidelberg infection at 3 d of age induces a persistent infection through inducing CD4+CD25+ cells and altering the IL-10 mRNA transcription of CD4+CD25+ cell numbers and cytokine production in chickens between 3 to 32 dpi allowing chickens to become asymptomatic carriers of Salmonella after 18 dpi. Identified that a nanoparticle vaccine decreased necrotic enteritis lesions in broiler birds. Cotter Objective 2: The recognition of morphological differences among plasmacytes participating in “reactive plasmacytosis” and their similarity to multiple myeloma (MM) plasmacyte series should be of importance to those interested in basic immunological phenomena.

Date of Annual Report: 10/11/2022

Report Information

Annual Meeting Dates: 09/23/2022 - 09/25/2022
Period the Report Covers: 09/17/2021 - 09/23/2022

Participants

Ryan Arsenault, University of Delaware
Chris Ashwell, West Virginia University
Andrew Broadbent, University of Maryland
Paul Cotter, Cotter Laboratory
Rami Dalloul, University of Georgia
Gisela Erf, University of Arkansas
Janet Fulton, Hy-Line International
Keith Jarosinski, University of Illinois
Matt Koci, North Carolina State University
Sue Lamont, Iowa State University
Ali Nazmi, Ohio State University
Shelly Nolin, North Carolina State University
Mark Parcells, University of Delaware
Muquarrab Qureshi, USDA-ARS
Ramesh Selvaraj, University of Georgia
Jiuzhou Song, University of Maryland
Bob Taylor, West Virginia University
Huaijun Zhou, University of California Davis

Students-Staff-Post doctoral scholars
Sofia Egana-Labrin, University of Maryland
Famatta Perry, University of Delaware
Brandi Sparling, Western University of Health Sciences
Theros Ng, Western University of Health Sciences

Brief Summary of Minutes

Minutes Attachment:

NE 1834 Business meeting_2022.docx

Accomplishments

Cotter Objective 2. The demonstration of heterogeneity among plasmacyte series, cells known for antibody secretion, and the capacity to recognize differences among primitive PC and derived types is an important step in understanding the complexities of immune reactions. Recognition of Tϋrk cells as members of the avian proplasmacyte cell series adds to basic immune function.   Song Objective 1. Genome-wide characterization of copy number variations in the host genome in genetic resistance to Marek’s disease using next generation sequencing. Objective 3. The Epigenetics and Plasticity of CD4+ T Cells in Poultry Health   Broadbent Objective 1. Evaluation of how different inbred lines of chickens with different allelic variation respond to very virulent (vv) infectious bursal disease virus (IBDV) infection. Objective 2. Identify the molecular basis underpinning IBDV-mediated dysfunction and pathology of poultry immune system. Objective 3. Development of new tools for IBDV research.   Gallardo Objective 1. A comprehensive multilocus genomic analysis to compare DMV/1639 and QX strains. The role of maternal antibodies and early vaccination in the development of false layer syndrome. Testicular atrophy and epididymitis-orchitis associated with infectious bronchitis in broiler breeder roosters. Genotipic classification of avibacterium paragallinarum the causative agent of infectious coryza. Antigenic cartography as a tool to determine antigenic relatedness of avian reovirus variants.   Erf Objective 2. Evaluation of the local (GF-pulp) cellular- and systemic (blood) antibody-responses to a first and second administration of autogenous Salmonella vaccines and vaccine components revealed a heterophil dominated, Th17-like, primary and secondary responses at site of intradermal injection. Analysis of SE-specific antibody profiles revealed classic primary and secondary response, with isotype switching to IgG and memory phenotype. Studies on multifactorial, non-communicable disease using the Smyth, UCD200/206 and OS autoimmune disease models, provided new insights into autoimmune pathology and revealed aberrant innate immune responses in the UCD-scleroderma model. Objective 3. AR maintained and reproduced genetic lines that spontaneously develop autoimmune diseases. Refined and expanded the use of the growing feather as an in vivo test-tube system to study innate and adaptive immune responses in poultry.   Zhou Objective 1. Improving food security in Africa by enhancing resistance to Newcastle disease virus and heat stress in chickens Objective 2. Longitudinal Analysis of CD4 and CD8 T Cell Receptor Repertoires Associated with Newcastle Disease Virus Infection in Layer Birds   Jarosinski Objective 1: N/A. Objective 2: Identification and characterization of chicken complement receptor-like 1 (CR1L) or complement component 4 binding protein, GPI-anchored (C4BPG) showed MDV gC interacts with CR1L in co-localization and co-immunoprecipitation assays. Objective 3: We have cloned the putative chicken CR1, CR2, C3, and C4 with the goal of generating reagents such as mAbs.   Taylor Objective 1.  Individual and pooled samples from chickens with defined alloantigen genotypes underwent SNP analyses.  Alloantigen I was associated with a region on chromosome 23.  alloantigen I was identified as RHCE as this candidate gene had high consistency between amino acid changing SNP and allelic differences. Alloantigen frequencies for the A, E, B, D, and I alloantigen systems were tested in two pair of lines divergently selected for antibody response against sheep red blood cells. Wageningen lines from generation 32 were control (C), high antibody (HA) and low antibody. Virginia Tech lines from generation 48 were high antibody (HAS) and low antibody (LAS). Altered frequencies for alloantigens A, E, B, and D were found between both sets of high antibody (HA, HAS) lines versus their corresponding low antibody (LA, LAS) lines. The distribution for alloantigen I differed between the Virginia Tech HAS vs LAS lines only. Objective 3. Two inbred lines, four congenic lines and four line crosses typed at the major histocompatibility complex and other alloantigen systems are maintained for station research and collaboration.   Lamont Objective 1. Bioinformatic and laboratory analyses demonstrated an important role of RIP2 in cellular response to APEC in HD11 cells. Objective 3. ISU chicken genetic lines were reproduced and maintained and shared.   Drechsler Objective 1. Developing project on Cluster Homolog Immunoglobulin-like Receptors in the chicken (CHIR). Phylogenetic analysis and re-annotation of CHIR submitted to NCBI. Preliminary data with siRNA shows effects on ChIR-B. Single-cell sequencing of the shell gland show differences in cellular populations and CHIRs in B2 and B19 haplotypes. Objective 3: Continuation of functional annotation of the chicken genome: 20 tissues/cells in progress. DNA methylome completed for reproductive and intestinal tissues/ peripheral immune cells. RNA seq was completed for all tissues and peripheral blood cells. ATAC seq is ongoing with a new methodology for better quality and smaller cell populations due to issues with QC previously. ChIP seq with new methodology is ongoing for several tissues/cells.   Arsenault Objective 2. From our acute Salmonella study we determined a number of novel insights into bacterial pathology (1) Salmonella is recognized by both TLR and NOD receptors that initiated the innate immune response; (2) activation of the PPRs induced the production of chemokines CXCLi2 (IL-8) and cytokines IL-2, IL-6, IFN-α, and IFN-γ; (3) Salmonella infection targeted the JAK-STAT pathway as a means of evading the host response by targeting the dephosphorylation of JAK1 and TYK2 and STAT1,2,3,4, and 6; (4) apoptosis appears to be a host defense mechanism where the infection with Salmonella induced both the intrinsic and extrinsic apoptotic pathways; and (5) the T cell receptor signaling pathway activates the AP-1 and NF-κB transcription factor cascades, but not NFAT. In our butyrate study we identified a novel and potential key mechanism of host response alteration due to butyrate. OCR and ECAR measurements showed that treatment with butyrate followed by Salmonella infection no difference in OCR of uninfected cells treated with SB compared to control. The increase in ECAR in butyrate treated cells is a sign of a pro-inflammatory response. In the reserpine study, reserpine treatment led to phosphorylative changes in epidermal growth factor receptor (EGFR), mammalian target of rapamycin (mTOR), and the mitogen-associated protein kinase 2(MEK2). Exogenous norepinephrine treatment alone increased Salmonella resistance, and reserpine-induced antimicrobial responses were blocked using beta-adrenergic receptor inhibitors, suggesting norepinephrine signaling is crucial in this mechanism. Overall, this study demonstrated a central role for MEK1/2 activity in reserpine induced neuro-immunometabolic signaling and subsequent antimicrobial responses in the chicken intestine, providing a means of reducing bacterial colonization in chickens to improve food safety.   Nazmi Objective 3. Thus, the objective of this study is to characterize the intestinal intraepithelial lymphocytes (IELs) during the Eimeria infection. In the current study, at 14 day of age, SPF chicks were divided into 3 groups (n=30 each): non-infected control, and 2 infected groups (low-dose and high-dose). The low-dose group was challenged orally with 10000 oocysts/ml per bird, while the high-dose group was challenged with 20000 oocysts/ml per bird of Eimeria acervulina. A single cell suspension was prepared from duodenums collected from 8 bird/group at 2-days post-infection (dpi), 7dpi and 14dpi. Cells were stained with antibody cocktail and acquired with a flow cytometry. The number of IEL subpopulations including, TCRγδ, TCRβ, TCRneg, TCRβ+CD4+, TCRβ+CD4+CD8α+, TCRβ+CD8αβ+, TCRβ+CD8αα+, and iCD8α were significantly increased in the infected groups at 14dpi compared control group. However, there was no difference among groups at 2dpi and 7dpi. In addition, more challenge experiments with other Eimeria species will be tested.   Koci Objective 3. Our team has developed a novel reporter plasmid which will be used to create a series of reporter cell lines, each containing a different immune related transcriptional response element (TRE) derived from avian genes. Our initial work has characterized our new plasmid which contains 2 reporter proteins. One under the control of a constitutive promoter and will serve as a control. The second is under the control of different TREs, and who’s activity will be induced by pathway specific stimuli. We have demonstrated the function of the positive and negative control plasmids. Furthermore, we have developed and initially characterized inducible reporter activity using the avian specific interferon stimulated response element (ISRE) sequence. We are currently in the process of bioinformatically identifying avian consensus TREs for multiple immune related transcription factors. Specifically: NFkB, AP-1, GAS, T-bet, STAT4, STAT6, GATA3, STAT3, FOXP3 SMAD, and GRE.   Parcells Objective 2. We cloned the chicken EZH2 gene (2 isoforms) and the chicken SATB1 and have found that these interact with Meq splice variant-encoded proteins. These data have direct implications regarding the suppression of MDV lytic gene expression, transformation and the Treg patterning of MDV-latently-infected cells. We found that the long form of Meq in CVI988 actually confers higher levels of oncogenicity to RB-1B, but that the short form of this same Meq is attenuating. We also found that Meq isoforms from higher virulence strains have increased interactions with DNA-repair and transcriptional efficiency-regulating proteins, suggesting that MDV evolution of virulence may involve increased somatic mutation and or higher order chromatin structural regulation, as well as transcriptional regulation.   Hauck Objective 2. Coccidia are among the most important intestinal pathogens in chickens. ARV are one of the possible reasons of runting-stunting syndrome. ARV are also known to be immunosuppressive, most likely by causing lymphoid depletion of immune organs. There are indications that co-infections with coccidia and avian reoviruses act synergistically. We plaque purified an ARV isolated from clinical cases or arthritis tenosynovitis in broiler chickens. We used this isolate and a laboratory strain in an experiment to establish a model for oral infections of chickens with ARV testing two different doses of each isolate. Samples taken at different time points are currently processed to characterize the expression of a panel of immune genes, lesions in various organs and the intestinal microbiota.   Dalloul Objective 2.  Necrotic enteritis, is one of the major enteric diseases that negatively impacts the poultry industry.  The increasing ban on the use of antibiotic growth promoters in poultry production has resulted in higher incidence of necrotic enteritis outbreaks worldwide.  Previous research demonstrated that supplementation of natural additives led to unique microbiome signature accompanied by better performance and reduced pathology of broilers.  The current studies further dissected the host response during NE leading to new potential markers of disease progression that could be exploited in designing mitigation methods.  Objective 3. Histomoniasis (aka blackhead disease) is a perennial problem in the poultry industry particularly turkeys where it inflicts substantial losses in poults as well as in broiler breeders.  We established a unique research model that closely resembles commercial field conditions and affords a much-needed opportunity for conducting detailed research on histomoniasis.  The newly established lateral transmission model in floor pens is a key system to study this disease, its progression, and potential mitigation strategies.

Publications

Peer Reviewed Publications Asfor A, Nazki S, Reddy VRAP, Campbell E, Dulwich KL, Giotis ES, Skinner MA, Broadbent AJ. Transcriptomic Analysis of Inbred Chicken Lines Reveals Infectious Bursal Disease Severity Is Associated with Greater Bursal Inflammation In Vivo and More Rapid Induction of Pro-Inflammatory Responses in Primary Bursal Cells Stimulated Ex Vivo. Viruses, 2021, 13(5), 933; doi: 10.3390/v13050933 Aylward, B.A., Johnson, C.N., Perry, F., Whelan, R., Zhang, C., Arsenault, R.J. Broiler chickens with 1950s genetics display a more stable immune profile as measured by kinome, mRNA expression, microbiome and metabolism when stimulated early in life with CpG. 2022. Poultry Science. 101(5), p.101775. Bai H, He Y, Ding Y, Chu Q, Lian L, Heifetz EM, Yang N, Cheng HH, Zhang H, Chen J, *Song  Genome-wide characterization of copy number variations in the host genome in genetic resistance to Marek's disease using next-generation sequencing. BMC Genet. 2021 Jul 16;21(1):77. DOI: 10.1186/s12863-020-00884-w. Blue, C.E.C, N.K. Emami, M.B. White, O. Gutierrez, S. Cantley, and R.A. Dalloul. 2022. Inclusion of Clarity Q manages growth performance, immune response, and nutrient transports of broilers during subclinical necrotic enteritis. Under review. Blue, C.E.C, N.K. Emami, M.B. White, E. Kimminau, and R.A. Dalloul. 2022. Assessing the effects of a proprietary phytogenic feed additive on broilers during a necrotic enteritis challenge. Under review. Botchway ,P.K., Amuzu-Aweh, E.N., Naazie, A., Aning, G. K., Otsyina, H.R., Saelao, P., Wang, Y., Zhou, H., Walugembe, M., Dekkers, J., Lamont, S.J., Gallardo, R.A., Kelly, T.R., Bunn, D. and Kayang, B.B. 2022. Host response to successive challenges with lentogenic and velogenic Newcastle disease virus in local chickens of Ghana. Poultry Science 101:102138. doi.org/10.1016/j.psj.2022.102138 Campbell E, Reddy VRAP, Gray A, Skinner M, Jennifer Simpson, Pippa Hawes, Broadbent AJ. Discrete virus factories form in the cytoplasm of cells co-infected with two strains of the segmented dsRNA virus, infectious bursal disease virus (IBDV), that subsequently coalesce. Journal of Virology, 2020, Jun 16; 94 (13), e-02107-19, doi: 10.1128/JVI.02107-19. Coe, C., T. Boltz, R. Stearns, P. Foster, R. L. Taylor, Jr., J. S. Moritz, J. Jaczynski, A. Freshour, and C. Shen. 2022. Thermal inactivation of Salmonella typhimurium and the surrogate Enterococcus faecium in mash broiler feed in a laboratory scale circulated thermal bath. Poult. Sci. 101:101976 https://doi.org/10.1016/j.psj.2022.101976 Cotter, P. F., 2021a. Erythroplastids of duck blood produced by cytokinesis, lysis, and amitosis J. World Poult. Res. 11(2): 271-277. DOI: <a href="https://dx.doi.org/10.36380/jwpr.2021.32">https://dx.doi.org/10.36380/jwpr.2021.32</a> Cotter, P. F., 2021b. Atypical hemograms of the commercial duck, Poult. Sci.100:2021,101248, ISSN 0032-5791, <a href="https://doi.org/10.1016/j.psj.2021.101248">https://doi.org/10.1016/j.psj.2021.101248</a> Da Silva, A.P., R. Jude, R.A. Gallardo. Infectious bronchitis virus: A comprehensive multilocus genomic analysis to compare DMV/1639 and QX strains. Viruses. 2022. Dulwich KL, Gray A, Asfor A, Giotis S, Skinner M, Broadbent AJ. The stronger downregulation of in vitro and in vivo innate antiviral responses by a very virulent strain of infectious bursal disease virus (IBDV), compared to a classical strain, is mediated, in part, by the VP4 protein. Frontiers in Cellular and Infection Microbiology, 2020, June 9, 10.315. doi: 10.3389/fcimb.2020.00315 Egaña-Labrin, S., C. Jerry, H. J. Roh, A. P. da Silva, C. Corsiglia, B. Crossley, D. Rejmanek, R. A. Gallardo. Avian Reoviruses of the Same Genotype Induce Different Pathology in Chickens. Avian Diseases. 2022. Figueroa, A., E. Escobedo, M. Solis, C. Rivera, A. Ikelman and R.A. Gallardo. Outreach Efforts to Prevent Newcastle Disease Outbreaks in Southern California. Viruses. 2022 Emami, N.K., and R.A. Dalloul. 2021.  Centennial Review: Recent developments in host-pathogen interactions during necrotic enteritis in poultry. Poultry Science 100:101330. Emami, N.K., A.L. Fuller, and R.A. Dalloul. 2022.  Lateral transmission of Histomonas meleagridis in turkey poults raised on floor pens.  Poultry Science 101:101951. Fulton. J. E. W. Drobik-Czwarno, A. Wolc, A. M. McCarron, A.R. Lund, C. J. Schmidt and R. L. Taylor, Jr. 2022.  The chicken A and E blood group systems are due to variation in proteins encoded by genes within the chicken RCA syntenic gene region. J. Immunol. 209: 1-10 https://doi.org/10.4049/jimmunol.2101010 Gallardo, R.A. Molecular Characterization of Variant Avian Reoviruses and its Relationship with Antigenicity and Pathogenicity. Avian Diseases. 2022. Gallardo, R.A., and A.P. Da Silva. MHC B Complex Genetic Resistance and Immune Responses to Infectious Bronchitis Virus in Chickens. Avian Diseases. 2022. Gallardo, R.A., da Silva, A.P., Gilbert, R., Alfonso, M., Conley, A., Jones, K., Stayer, P.A. and Hoerr, F.J., 2022. Testicular Atrophy and Epididymitis-Orchitis Associated with Infectious Bronchitis Virus in Broiler Breeder Roosters. Avian Diseases, 66(1), pp.112-118. Gilbert, I. M, J. M. Santamaria, and G. F. Erf. 2022. Time-course investigation of dermal leukocyte response to lipoteichoic acid in chickens.  Discovery 22:44-50. Jiang J, Chen C, Cheng S, Yuan X, Jin J, Zhang C, Sun X, Song J, Zuo Q, Zhang Y, Chen G, Li B. Long Noncoding RNA LncPGCR Mediated by TCF7L2 Regulates Primordial Germ Cell Formation in Chickens. Animals (Basel). 2021 Jan 24;11(2):292. DOI: 10.3390/ani11020292. PMID: 33498947; PMCID: PMC7912682. Jing, Y., Yuan, Y., Monson, M. Wang, P., Mu, F., Zhang, Q., Na, W., Zhang, K., Wang, Y., Leng, L., Li, Y., Luan, P., Wang, N., Guo, R., Lamont, S., Li, H., and Yuan, H. 2022. Multi-omics association reveals the effects of intestinal microbiome-host interactions on fat deposition in broiler lines divergently selected for abdominal fat content. Frontiers in Microbiology 12:815538. doi: 10.3389/fmicb.2021.815538 Kaiser, M., Hsieh, J., Kaiser, P. and Lamont, S.J. 2022. Differential immunological response detected in mRNA expression profiles among diverse chicken lines in response to Salmonella challenge. Poultry Sci. 101: 101605 <a href="https://doi.org/10.1016/j.psj.2021.101605">https://doi.org/10.1016/j.psj.2021.101605</a> Kogut, M., Genovese, K.J., Byrd, J.A., Swaggerty, C., He, H., Farnell, Y., Arsenault, R. Chicken-Specific Kinome Analysis of Early Host Immune Signaling Pathways in the Cecum of Newly Hatched Chickens Infected with Salmonella enterica Serovar Enteritidis. 2022. Frontiers Cellular and Infection Microbiology. 857. Krieter A, Xu H, Akbar H, Kim T, Jarosinski KW*. 2022. The conserved Herpesviridae protein kinase (CHPK) of Gallid alphaherpesvirus 3 (GaHV3) in required for horizontal spread and natural infection in chickens. Viruses 14(3):586. https://doi.org/10.3390/v14030586 Meyer, M.M., Lamont, S.J., and Bobeck, E.A. 2022. Mitochondrial and glycolytic capacity of peripheral blood mononuclear cells isolated from diverse poultry genetic lines: optimization and assessment. Frontiers in Veterinary Sci. 8:815878. doi: 10.3389/fvets.2021.815878 Montine, P., T.R. Kelly, S. Stoute, A.P. da Silva, B. Crossley, C. Corsiglia, H.L. Shivaprasad, and R.A. Gallardo. Infectious Bronchitis Virus Surveillance in Broilers in California (2012-2020). Avian Diseases. 2022. Nguyen, Veronica, Asli Mete, Anibal Armien, Ana P. da Silva, Patrick Montine, Charles Corsiglia, VM Sadagopa Ramanujam, Karl E. Anderson, Ruediger Hauck, and Rodrigo A. Gallardo. Porphyrin Accumulation and Biliary Lithiasis Causing Diffusely Black Livers in Broiler Chickens. Avian Diseases 66, no. 2 (2022): 1-5. Reddy VRAP, Nazki S., Brodrick A.J., Asfor A., Urbaniec J., Morris Y., Broadbent A. J. Evaluating the breadth of neutralizing antibody responses elicited by infectious bursal disease virus (IBDV) genogroup A1 strains using a novel chicken B-cell rescue system and neutralization assay. Journal of Virology, 2022, Sep 7;e0125522.doi: 10.1128/jvi.01255-22 Reddy VRAP, Campbell EA, Wells J, Simpson J, Nazki S, Hawes PC, Broadbent AJ. Birnaviridae virus factories show features of liquid-liquid phase separation, and are distinct from paracrystalline arrays of virions observed by electron microscopy. Journal of Virology, 2022, Feb 9;jvi0202421. doi: 10.1128/jvi.02024-21. Redweik, G.A.J., Kogut, M.H., Arsenault, R.J., Lyte, M., Mellata, M. Reserpine improves Enterobacteriaceae resistance in chicken intestine via neuro-immunometabolic signaling and MEK1/2 activation. 2021. Communications Biology, 4(1), 1-11 Rocchi, A., J. Ruff, C. J. Maynard, A. J. Forga, R. Señas-Cuesta, E. S. Greene, J. D. Latorre, C. N. Vuong, B. D. Graham, X. Hernandez-Velasco, G. Tellez Jr., V. M. Petrone-Garcia, B. M. Hargis, G. F. Erf, C. M. Owens, and G. Tellez-Isaias. 2022. Cyclic heat stress model alters intestinal permeability, bone mineralization, and meat quality in broiler chickens. Animals 12:1273 doi: 10.3390/ani12101273. Sato J, Murata S, Yang Z, Kaufer BB, Fujisawa S, Seo H, Maekawa N, Okagawa T, Konnai S, Osterrieder N, Parcells MS, Ohashi K. Effect of Insertion and Deletion in the Meq Protein Encoded by Highly Oncogenic Marek's Disease Virus on Transactivation Activity and Virulence. Viruses. 2022 Feb 14;14(2):382. doi: 10.3390/v14020382. PMID: 35215975; PMCID: PMC8876991. Sherer ML, Lemanski EA, Patel RT, Wheeler SR, Parcells MS, Schwarz JM. A Rat Model of Prenatal Zika Virus Infection and Associated Long-Term Outcomes. Viruses. 2021 Nov 18;13(11):2298. doi: 10.3390/v13112298. PMID: 34835104; PMCID: PMC8624604. Song, J. He, Y, Ding, Y. Tian, F. Zhao, K., Zhang, H., Yu, Y., Yang, N., Lian, L., Luo, J., Mitra, A. The Epigenetics and Plasticity of CD4+ T Cells in Poultry Health, Journal of Animal Science, Volume 99, Issue Supplement_3, November 2021, Page 55, https://doi.org/10.1093/jas/skab235.098 Sorrick, J., W. Huett, K. A. Byrne, and G. F. Erf. 2022. Autoimmune activities in choroids of visually impaired Smyth chickens with autoimmune vitiligo. Front. Med. 9:846100. doi:10.3389/fmed.2022.846100. Sun C, Jin K, Zuo Q, Sun H, Song J, Zhang Y, Chen G, Li B. Characterization of Alternative Splicing (AS) Events during Chicken (Gallus gallus) Male Germ-Line Stem Cell Differentiation with Single-Cell RNA-seq. Animals (Basel). 2021 May 20;11(5):1469. doi: 10.3390/ani11051469. PMID: 34065391; PMCID: PMC8160964. Sun C, Jin K, Zhou J, Zuo Q, Song J, Yani Z, Chen G, Li B. Role and function of the Hintw in early sex differentiation in chicken (Gallus gallus) embryo. Anim Biotechnol. 2021 Jun 21:1-11. DOI: 10.1080/10495398.2021.1935981. Epub ahead of print. PMID: 34153202. Sun, H., Yang, Y., Cao, Y., Li, H., Qu, L., Lamont, S.J. 2022. Gene expression profiling of RIP2-knockdown in HD11 macrophages—elucidation of potential pathways (gene network) when challenged with avian pathogenic E. coli (APEC) BMC Genomics 23 (1), 1-20. doi.org/10.1186/s12864-022-08595-5 Sun, H., Li, N., Tan, J., Li, H., Zhang, J., Qu, L., Lamont, S.J. 2022. Transcriptional regulation of RIP2 gene by NFIB is associated with cellular immune and inflammatory response to APEC infection Int. J. Mol. Sci. 23(7):3814. doi.org/10.3390/ijms23073814 Swaggerty, C.L., Byrd, J.A., Arsenault, R.J.,  Perry, F., Johnson, C.N., Genovese, K.J., He, H., Kogut, M.H., Piva, A., and Grilli, E. A blend of microencapsulated organic acids and botanicals reduces necrotic enteritis via specific signaling pathways in broilers. 2022. Poultry Science. p.101753. Taylor, R. L., Jr. 2022.  Nunc Dimitis – Fred M. McCorkle, Jr. Poult. Sci. 101:101854 https://doi.org/10.1016/j.psj.2022.101854 Taylor, R. L., Jr. 2022.  The 50 most downloaded articles from Poultry Science in 2021. Poult. Sci. 101: 101818 https://doi.org/10.1016/j.psj.2022.101818 Tudeka, C.K., Aning, G.K., Naazie, A., Botchway, P.K., Amuzu-Aweh, E.N., Agbenyegah, G.K., Enyetornye, B., Fiadzomor, D., Saelao, P., Wang, Y., Kelly, T.R., Gallardo, R., Dekkers, J.C.M., Lamont, S.J., Zhou, H., and Kayang, B.B. 2022. Response of three local chicken ecotypes of Ghana to lentogenic and velogenic Newcastle disease virus challenge. Tropical Animal Health and Production 54:134. doi.org/10.1007/s11250-022-03124-8 Xu H, Krieter AL, Ponnuraj N, Tien YY, Kim T, Jarosinski KW*. 2022. Coinfection in the host can result in functional complementation between live vaccines and virulent virus. Virulence 13(1);980. <a href="https://doi.org/10.1080/21505594.2022.2082645">https://doi.org/10.1080/21505594.2022.2082645</a> Zhang, C., Zuo, Q., Wang, M., Chen, H., He, N., Jin, J., Li, T., Jiang, J., Yuan, X., Li, J., Shi, X., Zhang, M., Bai, H., Zhang, Y., Xu, Q., Cui, H., Chang, G., Song, J., Sun, H., Zhang, Y., Chen, G., and Li, B. (2021) Narrow H3K4me2 is required for chicken PGC formation. J Cell Physiol 236, 1391-1400 Zhang, J., R. M. Goto, C. F. Honaker, P. B. Siegel, R. L. Taylor, Jr., H. K. Parmentier, and M. M. Miller. 2022.  Association of MHCY genotypes in lines of chickens divergently selected for high or low antibody response to sheep red blood cells. Poult. Sci. 101:101621 https://doi.org/10.1016/j.psj.2021.101621 Zhang, J., R. M. Goto, A. Psifidi, M. P. Stevens, R. L. Taylor, Jr., and M. M. Miller. 2022. Research Note: MHCY haplotype and Campylobacter jejuni colonization in a (Line N x Line 61) x Line N backcross population.  Poult. Sci. 101:101654 <a href="https://doi.org/10.1016/j.psj.2021.101654">https://doi.org/10.1016/j.psj.2021.101654</a> Zhao R, Zuo Q, Yuan X, Jin K, Jin J, Ding Y, Zhang C, Li T, Jiang J, Li J, Zhang M, Shi X, Sun H, Zhang Y, Xu Q, Chang G, Zhao Z, Li B, Wu X, Zhang Y, Song J, Chen G, Li B. Production of viable chicken by allogeneic transplantation of primordial germ cells induced from somatic cells. Nat Commun. 2021 May 20;12(1):2989. DOI: 10.1038/s41467-021-23242-5. PMID: 34017000; PMCID: PMC8138025.   Abstracts Abraham, M., M. Erasmus, G. Fraley, G. F. Erf, and D. Karcher. 2022. Understanding stress and welfare of laying pullets using stock density and feeder space stressors. American Association of Pathologists. Beck, C. N., J. Santamaria, M. A. Sales, and G. F. Erf. 2022. Primary and secondary immune responses in Light-brown Leghorn pullets vaccinated with Salmonella vaccines. International Poultry Scientific Forum, Atlanta January 2022. accepted Beck, C. N., J. Santamaria, M. A. Sales, and G. F. Erf. 2022. Local mRNA expression of cytokines during the first seven days following the intradermal administration of autogenous Salmonella vaccines in previously vaccinated Light-brown Leghorn pullets. Poult. Sci. 101 (E-Suppl. 1). Beck, C. N., J. Santamaria, M. A. Sales, and G. F. Erf. 2022. Local cellular- and systemic humoral-responses to intradermal injection of killed autogenous Salmonella vaccines in immunized and non-immunized Light-brown Leghorn pullets. International Avian Immunology Research Group Meeting, September 26-29, 2022, Newark, DE. Blue CEC, Emami NK, White MB, Gutierrez O, Cantley S, and Dalloul RA. Effects of Quillaja saponaria extract on mRNA abundance of tight junction proteins and cellular metabolism genes during a necrotic enteritis challenge in broilers. International Poultry Scientific Forum. 2022. Blue CEC, Emami NK, Gutierrez O, Cantley S, and Dalloul RA. Effects of Clarity Q on mRNA abundance of nutrient transporters during a subclinical necrotic enteritis. Poultry Science Association Annual Meeting. 2022. Emami NK, and Dalloul RA. Comparison of two Clostridium perfringens strains for inducing subclinical necrotic enteritis in broiler chickens. International Poultry Scientific Forum. 2022. Emami NK, Fenster DA, Blue CEC, and Dalloul RA. Differential analysis of breast muscle and liver mRNA in broiler chickens challenged with Eimeria maxima with/without Clostridium perfringens. World Poultry Congress. 2022. Emami NK, Fuller AL, and Dalloul RA. Lateral Transmission of Histomonas meleagridis in turkey poults raised on floor pens. World Poultry Congress. 2022. Froebel LE, Emami NK, and Dalloul RA. Evaluation of circulatory mRNA abundance of pro-inflammatory and regulatory cytokines and receptors during a subclinical necrotic enteritis challenge. International Poultry Scientific Forum. 2022. Froebel LE, and Dalloul RA. Evaluating mRNA abundance of cytokines and chemokines in the modern broiler and heritage breed during a necrotic enteritis challenge. Poultry Science Association Annual Meeting. 2022. Fulton. J. E. W. Drobik-Czwarno, A. Wolc, C. Schmidt, and R. L. Taylor, Jr. 2022.  Identification of the Genes Responsible for the Chicken A and E Blood Group Systems. Plant and Animal Genome PAG PAG XXIX 2022 https://pag.confex.com/pag/xxix/meetingapp.cgi/Paper/45612 Ng, TT, Hawkins, RD, and Drechsler, Y. An update on transcriptome of an array of chicken ovary, intestinal, and immune cells and tissues. Poultry Science Association. July 11th to 14th, 2022. San Antonio, Texas. Patria, Joseph, Nirajan Bhandari, Phaedra Travlarides-Hontz, Benedikt B. Kaufer, and Mark S. Parcells. Marek’s disease virus (MDV) evolution of virulence: Investigating the selection for protein binding interfaces at the C-terminus of the Meq oncoprotein. Proceedings of 94th Annual Northeastern Conference on Avian Diseases (NECAD) Penn State University, Sept. 14 and 15, 2022  Parcells, M.S., Katneni, U.K., Neerukonda, S., Tavlarides-Hontz, P., Arsenault, R.J. Cell culture and In Vivo Examination of the Mechanism of Action of Victrio a DNA-Liposome-based Innate Immune Agonist. 18th International Conference on Production Diseases in Farm Animals; 2022 June 15–17; Madison, WI Perry, F., Bortoluzzi, C., Eyng, C., Aeschleman, L., Jones, E., Kogut, M., Arsenault, R., The immunometabolic effects of butyrate in chicken small intestines and macrophage-like cells. World Poultry Congress; 2022 August 8-11; Paris, France Perry, F., Bortoluzzi, C., Eyng, C., Kogut, M., Arsenault, R. The immunometabolic effects of sodium butyrate supplementation in the ileum of broiler chickens. Poultry Science Association Annual Meeting; 2022 July 1-14; San Antonio, TX. Perry F., Bortoluzzi, C., Lahaye, L., Santin, E., Johnson, C., Korver, D.R., Kogut, M.H., Arsenault R.J. Protected Biofactors and Antioxidants Reduce the Negative Consequences of Virus and Cold Challenge while Enhancing Performance by Modulating Immunometabolism through Cytoskeletal and Immune Signaling. Symposium on Gut Health in Production of Food Animals; 2021 November 1-3; St. Louis, MO. Runcharoon K, Emami NK, and Dalloul RA. Differential analysis of autophagy-related genes in broilers challenged with Eimeria maxima with or without Clostridium perfringens. Poultry Science Association Annual Meeting. 2022. Santamaria, J., C. N. Beck, M. A. Sales, and G. F. Erf. 2022. Local and systemic inflammatory and antibody responses to intradermal administration of killed Salmonella Vaccine in different vaccine vehicles. Poult. Sci. 101 (E-Suppl. 1). Shaimaa K. Hamad, Shuja Majeed, Ali Nazmi. Characterization of Intestinal Immune Responses to Coccidiosis in Chicken. 2022 Food for Health Discovery Annual Meeting. Columbus OH Sparling, B. and Drechsler, Y. Talk. An update on chicken transcriptome and epigenome annotation, factors involved in host resistance against IBV; and establishing Ig-like receptors' role in innate immunity. NE-1834 Genetic Bases for Resistance and Immunity to Avian Diseases. September 17-19, 2021. Baltimore, Maryland. Sparling, B. and Drechsler, Y. Talk. Identification of immunoglobulin-like receptors in the chicken genome that are associated with disease resistance. January 8, 2022. Plant and Animal Genome Conference. San Diego, CA. Sparling, B. and Drechsler, Y. Talk. Advances in identifying immunoglobulin-like receptors and their roles in immunity in the chicken. Western University of Health Sciences, College of Veterinary Medicine, 2022 CVM Research Day. March 28, 2022. Pomona, California. Sparling, B. and Drechsler, Y. Talk. Determining chicken immunoglobulin-like receptors (CHIRs) expression and their effect on immune response in a macrophage disease model. American Association of Immunologists. May 6-9, 2022. Portland, Oregon. Taylor, R. L., Jr., W. Drobik-Czwarno, and J. E. Fulton. 2022.  Chicken alloantigen D is CD99. Poult. Sci. 101: (E-Suppl 1) in press Taylor, R. L., Jr., W. Drobik-Czwarno, and J. E. Fulton. 2022.  Identifying chicken alloantigens A, E and D. AIRG meeting in press   Book Chapters Lamont, S.J., Dekkers, J.C.M., Wolc, A. and Zhou, H. 2022. Immunogenetics and the mapping of immunological functions. Pp. 277-297. In: Avian Immunology, 3rd ed. B. Kaspers, K.A. Schat, T. Goebel, L. Vervelde, Eds., Elsevier, London, San Diego, Cambridge, Oxford. Doi.org/10.1016/C2018-0-00454-5.   Thesis/Dissertation Ye Bi, M.S. Animal Biology. Longitudinal Analysis of CD4 and CD8 T Cell Receptor Repertoires Associated with Newcastle Disease Virus Infection in Layer Birds “The Regulation and Role of Glycoprotein C during Herpesvirus Pathogenesis.” Widaliz Vega Rodriguez, PhD Dissertation 2022. University of Illinois at Urbana-Champaign. Supervisor: Keith W. Jarosinski EVALUATING THE ROLE OF IRG1 AND ITACONATE ON MAREK’S DISEASE VIRUS INFECTION, Kristy Wisser-Parker, MS in Biological Sciences (defense date June xx, 2022) THE ROLE OF EXOSOMES IN MAREK’S DISEASE VIRUS VACCINE RESPONSE, Aksana Dallakoti, non-thesis MS in Bioinformatics (defense date August 22, 2022) INFECTION DYNAMICS OF A CHICKEN T-CELL LINE BY DIFFERENT PATHOTYPES OF MAREK’S DISEASE VIRUS (MDV), Joshua Miller, MS in Biological Sciences (defense date August 26, 2022) White, Mallory B.  In ovo and feed application of probiotics or synbiotics and response of broiler chicks to post-hatch necrotic enteritis. PhD Dissertation, August 2021. Froebel, Laney E.  Evaluating immune related genes in heritage and modern broiler breeds and macrophages in response to clostridium perfringens. MS, July 2022.

Impact Statements

Dalloul Objective 2. This work is of significant impact showing the possibility to control and modify the immune responses during disease progression, as well as identify unique markers that may provide timely intervention methods. By better understanding these responses, mitigation approaches could be developed and tested to alleviate the negative impact of necrotic enteritis. Objective 3. The newly established lateral transmission model of Histomonas meleagridis in floor pens is a key system to study this disease, its progression, and potential mitigation strategies. This research model closely resembles commercial field conditions and affords a much-needed opportunity for conducting detailed research on histomoniasis.

Date of Annual Report: 10/12/2023

Report Information

Annual Meeting Dates: 09/21/2023 - 09/23/2023
Period the Report Covers: 09/22/2022 - 09/23/2023

Participants

Ali Nazmi, The Ohio State University
Andrew Broadbent, University of Maryland
Brandi Sparling, Western University of Health Sciences
Calvin Keeler, University of Delaware
Chrysta Beck, University of Arkansas
Gisela Erf, University of Arkansas
Huaijun Zhou, University of California, Davis
Keith Jarosinski, University of Illinois
Lisa Bielke, North Carolina State University
Marcia Miller, Beckman Research Institute, COH
Mark Parcells, University of Delaware
Matt Koci, North Carolina State University
Michael Kaiser, Iowa State University
Ramesh Selvaraj, University of Georgia
Rami Dalloul, University of Georgia
Robert Taylor, University of West Virgina
Ruediger Hauck, Auburn University
Sue Lamont, Iowa State University
Theros T. Ng, Western University of Health Sciences
Yvonne Drechsler, Western University of Health Sciences

Brief Summary of Minutes

Summary of minutes is enclosed in the attached PDF.

Minutes Attachment:

NE-1834_meeting_minutes_2023.pdf

Accomplishments

Accomplishments Cotter Objective 3. Cotter Laboratory continues to expand descriptions of plasmacyte (PC) variation. In SPF chickens housed in isolators it is shown that PCs are able to attach to one another as an indication of reactivity/toxicity. PCs may be further differentiated into primitive (deep blue), intermediate (gray), and mature types (sky blue) cytoplasm. In ducklings PCs can form cell-to-cell associations “toroids” as an indication of reactivity. PCs of mature ducks can form “rosettes” by surrounding themselves with a wreath of RBCs. Giant (neoplastic) plasmacytoid cells have been recognized in experimental chickens infected with Marek’s virus. Lamont Objective 1.  Spleen transcriptome sequencing and overexpression in DF-1 cells demonstrated an important role of LncIRF1 in cellular response to ALV-J. Objective 3. ISU chicken genetic lines were reproduced and maintained and shared for collaborative research. Taylor Objective 1.  Ongoing chicken alloantigen research has identified genes responsible for multiple systems. Analyses of SNP from individual or pooled DNA having defined alloantigen genotypes, as well as inbred line sequences aided the identification of systems A, D, E, H, and I as C4BPM, CD99, FCAMR, CD146 (MCAM), and RHCE, respectively. Alloantigen allele frequencies differed significantly between lines selected for high or low antibody response against sheep red blood cells (SRBC). Virginia Tech high antibody (VT-HAS) and low antibody (VT-LAS) lines, generation 48, as well as Wageningen lines control (WUR-CON), high antibody (WUR-HA) and low antibody (WUR-LA), generation 32 were studied. Allele frequencies for alloantigens A, E, B, and D were altered in both high antibody (VT-HAS, WUR-HA) lines compared with their respective low antibody (VT-LAS, WUR-LA) lines. Alloantigen I allele frequencies differed in VT-HAS vs VT-LAS lines but not WUR-HA vs WUR-LA. The WUR selected lines allele frequencies differed from the WUR-CON except for the D system in WUR-LA. Selection for antibody titer impacts local and systemic cytokine profile in generation 48 of VT-HAS and VT-LAS lines. The anti-inflammatory cytokine, IL4, and pro-inflammatory chemokine, CXCL8, were significantly higher in VT-HAS spleen cells compared with those from VT-LAS. Pro-inflammatory IL6 cytokine was higher in VT-LAS peripheral blood leukocytes versus VT-HAS. Both IL6 and IL10 were higher in VT-LAS females compared with males from that line. Objective 3. West Virginia University maintained two inbred lines, four congenic lines and five line crosses station research and collaborative projects. Genetic stocks are typed at the MHC and other alloantigen systems. West Virginia University (WVU) held alloantisera produced by Dr. W. E. Briles at Northern Illinois University (NIU). The 243 alloantisera reacting against 74 different antigens, include most alloantigen systems. Selvaraj Objective 3. A study evaluated the efficacy of two killed Salmonella bacterin vaccine, administered intramuscularly- in layers. The first vaccine had 97% S. typhimurium and 3% Immune Plus® with preservatives and adjuvants. The second vaccine was synthesized with 77% S. typhimurium, 10% Klebsiella strain KP9580, 10% Klebsiella strain KPZBT01, and 3% Immune Plus® with preservatives and adjuvants. These results indicate that the killed bacterin vaccine produces an increase in serum antibody titer and could be a potential viable vaccine candidate against Salmonella infection in layers. A second study identified that synbioitcs improved the production performance by decreasing mid-gut lesions and enhancing protective immunity during necrotic enteritis infection. Erf Objective 2. Evaluation of the local (GF-pulp) cellular- and systemic (blood) antibody-responses to different formulations, preparations, and dosages of a first and second administration of killed Salmonella vaccines and vaccine components demonstrated heterophil dominated, T cell dependent, immune rersponses. Studies on multifactorial, non-communicable disease using the UCD200/206 and OS autoimmune disease models, provided new insights into autoimmune pathology and revealed aberrant innate immune responses in the UCD-scleroderma model. Objective 3. AR maintained and reproduced genetic lines that spontaneously develop autoimmune diseases. Refined and expanded the use of the growing feather as an in vivo test-tube system to study innate and adaptive immune responses in poultry. The combination of the in vivo test-tube with blood sampling proofed effective in evaluating effects of genetic selection and nutrition on innate immune system development and function. Song Objective 1. Transgenerational epigenetic inheritance and immunity in chickens that vary in Marek's disease resistance. Temporal Profiling of the Bursa Transcriptome in Marek's Disease Resistant and Susceptible Chickens. Broadbent Objective 2. Molecular characterization of infectious bursal disease virus (IBDV) in the Delmarva (DMV) region. Objective 3. Antigenic characterization of infectious bursal disease virus (IBDV) in the Delmarva (DMV) region. Zhou Objective 1. Improving food security in Africa by enhancing resistance to Newcastle disease virus and heat stress in chickens Hauck Objective 2. 1. Assess how infections with coccidia and avian reoviruses (ARV) interact with each other and the immune system Miller Objective 1. We conducted tests for a role of MHCY genetics in guiding immune responses.  We tested for the influence of MHCY genetics in the colonization of chickens by Campylobacter.  These studies became possible because of the STR-based typing system for MHCY we recently developed.  The results of these early tests indicate there is indeed a role of the polymorphic MHCY region in immunity and in the interactions of chickens with microbes.  In a genomic analysis, we expanded understanding of the genomic composition of MHCY by identifying many elements in the MHCY haplotype within the RJF reference genome.  The sequence has been annotated in detail.  We found evidence for the presence of multiple blocks of identical and near identical sequence duplicated within the sequence of this haplotype.  There are many copies of MHC class I genes within the sequence.  In addition, using mass spectrometry we found evidence that lysophospholipids are ligands bound by MHCY class I molecules.  The identification of lysophospholipids as ligands within these unusual MHC class I molecules is especially intriguing.  It appears that MHCY class I molecules with distinctively different amino acid sequences bind the same lysophospholipids.  These data support the possibility that MHCY variability among isoforms has more to do with receptor interactions than with ligand binding.  Further studies to define MHCY gene function fits well within the objectives of NE 1834 to characterize the function of genes in poultry to define their role in infectious disease.  Gallardo  Objective 3. Mitigation of False Layer Syndrome Through Maternal Antibodies Against Infectious Bronchitis Virus. Histopathological changes in different organs in chicks early challenged or vaccinated with IBV strains. Mimicking Maternally Derived Antibodies for Early Protection Against Infectious Bronchitis Virus in Chicks. Efficacy of a Trivalent Coryza Inactivated Vaccine Against Challenges with Wild Type Avibacterium paragallinarum Serovars A and C. Molecular Characterization of Newcastle Disease Virus obtained from Mawenzi Live Bird Market in Morogoro, Tanzania in 2020-2021. Arsenault Objective 2. a) Evidence indicated that Salmonella could reprogram the host metabolism to increase energy or metabolites available for intracellular replication. We found that infection by Salmonella enterica Enteritidis induced significant phosphorylation changes in many key proteins of the glycolytic pathway in chicken macrophage HD-11 cells, indicating a shift in glycolysis caused by Salmonella infection. The infection reduced glycolysis and enhanced OXPHOS in chicken macrophages as indicated by changes of ECAR and OCR. Salmonella strains differentially affected macrophage polarization and glycolysis. Our results suggested that downregulation of host cell glycolysis and increase of M2 polarization of macrophages may contribute to increased intracellular survival of S. Enteritidis. b) In comparing the effect of a microencapsulated thymol-based blend of botanicals (TBB) with commonly used in-feed antibiotics in broilers during a Salmonella Enteritidis challenge we found body weights remained stable until d35, when blend 1000 was significantly higher than all the other groups (+152 g compared to CTR). The trend of Salmonella counts in ceca for CTR, blend 500, and blend 1000 showed a peak at d14, followed by a progressive decrease until the bacteria at d35 were totally cleared. The thymol-based blend of botanicals at the highest dose had a positive effect on the final body weight. Furthermore, the blend at both doses was able to completely clear S. Enteritidis in broilers, while conventional antibiotics were not effective. c) Chicken enteroids can be an effective model of the chicken gut for screening and mechanistic purposes. Chicken enteroids were generated from chicken embryo crypts and were inoculated with Salmonella and/or treated with Gallinat+ (Gal). We then compared the proteome level changes in phosphorylation, thus the alteration in the underlying signaling pathways through the kinome peptide array technique. The goal is to understand the effects of the Salmonella and treatment on the enteroids as well as determine if the response is similar to that observed in a chicken gut. The Salmonella alone did not elicit an exceptionally strong response in the enteroids as measured by phosphorylation. However, the Gal product did moderate the Salmonella response and return signaling to a more baseline level, both metabolically and immunologically. For product alone the Gal at 0.25 mg/mL had a moderating effect more so than Gal at 0.5 mg/mL as compared to control. The enteroids appear to significantly alter pathways that have been observed in vivo as well, indicating a good model for Salmonella pathogenesis. Jarosinski Objective 1.  Determine how allelic variation influences the efficacy of innate and acquired immune functions. Objective 2. Identify factors and agents affecting poultry immune development, function, dysfunction and pathology. Objective 3. Develop and employ genetic stocks, methods, reagents and other tools to assess basic immune functions, characterize immune evolutionary processes, guide genetic selection, and increase resistance to or protection against avian diseases. Parcells Objective 2. After over a year of struggle, we seem to have a grasp on the use of CRISPR/Cas9 for targeted cleavage and gene insertion into the genome of herpesvirus of turkeys (HVT) using transfected RNPs and gene cassettes. We have generated several recombinant HVTs using this technology. In our analysis of the mechanism of MDV virulence evolution, we have found that the mutations in the Meq oncoprotein mediate increased transcription through the binding of an ATP-dependent DNA gyrase (SMARCA4/BRG-1). Through our study of MDV genome uptake, expression and replication using the CU91 cell model, we have concluded that strains of increased virulence express viral genes at a higher level from fewer genome copies and that this may be key to the increased efficiency of transmission scene with MDVs of increased virulence. In terms of MDV latency establishment, we found that a likely first step is methylation of histone 3 at K27 through interaction with EZH2. Suppression of EZH2 leads to the rapid induction of MDV from latency with an increase in MDV genomes and infectious virus. Koci Objective 2. Our group has continued to explore the various impacts of diet and nutritional supplementation on the chicken gut microbiome and how changes in the microbiome can influence host physiology and specifically immunity. Over the past year we have continued to analyze 16S DNA sequences from chickens fed two different starter diets with and without a commercial probiotic. These diets both met or exceeded the NCR recommendations for broiler chicks but were not identical did and did differ in terms of form (mash vs crumble). The goal of this experiment was to help understand how much two nutritionally adequate diets, formulated by different nutritionists, and produced in different mills could influence the taxa identified by 16S sequencing. Day old chicks were randomly assigned to one of four groups: Diet 1 control (D1C), diet 1 probiotic (D1P), diet 2 control (D2C), diet 2 probiotic (D2P). At the start of the experiment, samples of the probiotic premix, and feed were collected for DNA isolation. Chicks were fed ad libitum and 5 animals per group were euthanized at 28 days and digesta contents collected from the crop, gizzard, duodenum, jejunum, ileum, and cecum. DNA was isolated from all samples and subjected to 16S sequencing. Analysis of the 16S data demonstrated the basal diet induced a bigger difference in microbiomes than the probiotic. Additionally, the impact of the probiotic on the microbiome was larger in one diet as compared to the other. This is likely due, at least in part, to the higher levels of Lactobacillus found in the one diet, and Lactobacillus is the major constituent of the probiotic. Interestingly, while the impact the probiotic had on the microbiomes were diet dependent, probiotic induced changes to the immune system were found independent of diet. Collectively these results demonstrate, unsurprisingly, if not frustratingly, that the presence or absence of shifts in microbial taxa cannot be used solely as evidence of microbiome induced changes that can affect the host. Dalloul Objective 1. The role of blood system types in the chicken response to a coccidiosis challenge. Objective 2. Necrotic enteritis in broilers – disease development and host response: A) Assessing dietary phytogenic blends on response of broilers to NE; and B) In ovo administration and water supplementation of a postbiotic positively influence response of broilers to necrotic enteritis. Objective 3. Characterization and mitigation of blackhead disease in turkey poults using a lateral transmission model of Histom onas meleagridis. Drechsler and Ng Objective 1. Identification, Characterization, and Role of Cluster Homolog Immunoglobulin-like Receptors (CHIRs);  and Role of CHIR in the reproductive tract of B2/B2 and B19/B19 haplotypes; Characterizing CHIR in the intestinal tract after coccidia challenge. Objective 3. Functional Annotation of the Chicken Genome: In collaboration with Dr. Hawkins at the University of Washington, we have continued to optimize all assays to functionally annotate the chicken genome in several immune cells and tissues. A total of 20 cells/tissues will be profiled until the end of 2023 and will be combined with research looking at epigenetic regulation of differential immune responses in chickens of different genetic backgrounds. The investigators are mapping the cis-regulatory elements in macrophages, T-cells, B-cells, reproductive and intestinal tissues, bursa, thymus, and muscle in the Michigan 6x7 F1 line. Immune cells from tissues have been collected after optimizing procedures for maximum yields, such as liver, kidney, lung, and spleen macrophages/T cells. DNA methylation sequencing is completed, and RNA seq results were published of some cells/tissues in 2021, with the rest of the RNA samples being completed and the manuscript in preparation. ATAC seq, ChIP seq, and Hi-Seq samples were collected for the difficult samples and were cryopreserved with optimization of ATAC and CHiP seq being concluded and the procedure changed to use Cut and Tag as methodology, resulting in cleaner data on smaller cell numbers. HiChip optimization is still ongoing. Collaboration with Dr. Wes Warren at the University of Missouri. Single-cell data was distributed and a team of several collaborators at a variety of institutions is in the process of annotating subpopulations in the bursa, thymus, and spleen. Due to changes in annotations, subpopulations have been reclustered and re-annotated. Manuscript preparation is pending. Nazmi Objective 3. Characterize the intestinal intraepithelial lymphocytes (IELs) during the enteric diseases, such as coccidiosis, necrotic enteritis, and salmonellosis.

Publications

Publications Peer Reviewed Publications Cotter PF, 2023. Bone Marrow and Blood Pictures of Broilers with BCO. J Anim Res Vet Sci 2023, 7: 048 DOI: 10.24966/ARVS-3751/100048 Cotter PF, 2022. Cytogenetics of reactive bone marrow associated with a fungal infection (Hemomycetes avium) of ducklings. World J Vet Sci 4: 1018 Cotter PF, 2022. Stress assessment by the hemogram method - circulating cells complicating reliance on heterophil/lymphocyte (H/L) ratio. J Vet Med Res 9(1): 1224. DOI:10.47739/veterinarymedicine-1224 Cotter PF, 2022. A microscopic study of the morphology of reactive thrombocytes of the duckling. J. World Poult. Res. 12(3). https://dx.doi.org/10.36380/jwpr.2022.16 Cotter P, 2022. The Cytology of Resting and Reactive NK Cells of Chickens. Asian Journal of Research in Animal and Veterinary Sciences, 5(4), 329-338. <a href="https://journalajravs.com/index.php/AJRAVS/article/view/222">https://journalajravs.com/index.php/AJRAVS/article/view/222</a> Fries-Craft, K., Lamont, S.J., Bobeck, E.A. 2023. Implementing real-time immunometabolic assays and immune cell profiling to evaluate systemic immune response variations to Eimeria challenge in three novel layer genetic lines. Front. Vet. Sci.  DOI 10.3389/fvets.2023.1179198 Pritchett, E.,M., Van Goor, A., Schneider,  B.K., Young, M., Lamont, S.J., Schmidt, C.K. 2023. Chicken pituitary transcriptomic responses to acute heat stress. Mol. Biol. Rep. doi.org/10.1007/s11033-023-08464-8 Pacheco Santana, T., Gasparino, E., De Souza Khatlab, A., Favaro Elias Pereira, A.M., Teixeira Barbosa, L., Pereira Miranda Fernandes, R., Lamont, S.J., Del Vesco, A.P. 2023. Effects of maternal methionine supplementation on the response of Japanese quail (Coturnix coturnix japonica) chicks to heat stress. J Anim.Sci. doi.org/10.1093/jas/skad042 Warren, W.C., Rice, E.S., Meyer, A., Hearn, C.J., Steep, A., Hunt, H.D., Monson, M.S., Lamont, S.J., Cheng, H.H. 2023. The immune cell landscape and response of Marek’s disease resistant and susceptible chickens infected with Marek’s disease virus. Scientific Rep. 13:5355. doi.org/10.1038/s41598-023-32308-x Wang, Y., Saelao, P., Kern, C., Zhao, B., Gallardo, R.A., Kelly, T., Dekkers, J.M., Lamont, S.J., Zhou, H. 2023. Distinct Hypothalamus and Breast Muscle Transcriptomic Response to Heat Stress under Newcastle Disease Virus Infection.  Cytogenet. Genome Res. DOI.org/10.1159/000529376 Smith J., Alfieri, J.M., Anthony, N., Arensburger, P., Athrey, G.N., Balacco, J., Balic, A., Bardou, P., Barela, P., Bigot, Y., Blackmon, H., Borodin, P.M., Rachel Carroll, R., Casono, M.C., Charles, M., Cheng, H., Chiodi, M., Cigan, L., Coghill, L.M., Crooijmans, R., Neelabja Das, N., Davey, S., Davidian, A., Degalez, F., Dekkers, J.M., Derks, M., Diack, A.B., Djikeng, A., Drechsler, Y., Dyomin, A., Fedrigo, O., Fiddaman, S.R., Giulio Formenti, G., Frantz, L.A.F., Fulton, J.E., Gaginskaya, E., Galkina, S., Gallardo, R.A., Geibel, J., Gheyas, A., Godinez, C.J.P., Goodell, A., Graves, J.A.M., Griffin, D.K., Haase, B., Han, J.-L., Hanotte, O., Henderson, L.J., Hou, Z.-C., Howe, K., Huynh, L., Ilatsia, E., Jarvis, E., Johnson, S.M., Kaufman, J., Kelly, T., Kemp, S., Kern, C., Keroack, J.H., Klopp, C., Lagarrigue, S., Lamont, S.J., Lange, M., Lanke, A., Larkin, D., Larson, G., Layos, J.K.N., Lebrasseur, O., Malinovskaya, L.P., Martin, R.J., Martin Cerezo, M.L., Mason, A.S., McCarthy, F.M., McGrew, M.J., Mountcastle, J., Kamidi Muhonja, C., Muir, W., Muret, K.,  Murphy, T., Ng’ang’a, I., Nishibori, M., O’Connor, R.E., Ogugo, M., Okimoto, R., Ouko, O., Patel, H.R., Perini, F., María Pigozzi, M., Potter, K.C., Price, P.D., Reimer, C., Rice, E.S., Rocos, N., Rogers, T.F., Saelao, P., Schauer, J., Schnabel, R., Schneider, V., Simianer, H., Smith, A., Stevens, M.P., Stiers, K., Keambou Tiambo, C., Tixier-Boichard, M., Torgasheva, A.A., Tracey, A., Tregaskes, C.A., Vervelde, L., Wang, Y., Warren, W.C., Waters, P., Webb, D., Weigend, S., Wolc, A., Wright, A.E., Wright, D., Wu, Z., Yamagata, M., Yang, C., Yin, Z.-T., Young, M.C., Zhang, G., Zhao, B., Zhou, H.  2023. Fourth Report on Chicken Genes and Chromosomes 2022. Cytogenet. Genome Res. 162:405–527. DOI.org/10.1159/000529376 Walugembe, M., Naazie, A., Mushi, J.S., Akwoviah, G.A., Mollel, E., Mang'enya, J.A., Wang, Y., Chouicha, N., Kelly, T., Msoffe, P.L.M. Otsyina, H.R., Gallardo, R.A., Lamont, S., Muhairwa, A.P., Kayang, B.B., Zhou, H., Dekkers, J.C.M. 2022. Genetic analyses of response of local Ghanaian and Tanzanian chicken ecotypes to a natural challenge with velogenic Newcastle disease virus. Animals 12:2755. doi.org/10.3390/ani12202755 Fulton. J. E. W. Drobik-Czwarno, A. Wolc, A. M. McCarron, A.R. Lund, C. J. Schmidt and R. L. Taylor, Jr. 2023. CD99 and the chicken alloantigen D blood system. Genes 14:402 https://doi.org/10.3390/genes14020402 He, Y., R. L. Taylor, Jr., H. Bai, C. M. Ashwell, K. Zhao, Y. Li, G. Sun, H. Zhang, and J. Song. 2023. Transgenerational epigenetic inheritance and immunity in chickens that vary in Marek's disease resistance. Poult. Sci. 102: 103036 https://doi.org/10.1016/j.psj.2023.103036 Nolin, S. J., C. M. Ashwell, R. L. Taylor, Jr., P. B. Siegel, and F. W. Edens. 2023. Combining supervised machine learning with statistics reveals differential gene expression patterns related to energy metabolism in the jejuna of chickens divergently selected for antibody response to sheep red blood cells. Poult. Sci. 102:102751 https://doi.org/10.1016/j.psj.2023.102751 Taylor, R. L., Jr. and M. H. Kogut. 2023. Editorial: Poultry Science manuscript preparation. Poult. Sci. 102:1102732 https://doi.org/10.1016/j.psj.2023.102732 Taylor, R. L., Jr. and M. H. Kogut. 2023. Editorial: Poultry Science manuscript revision. Poult. Sci. 102:102982 https://doi.org/10.1016/j.psj.2023.102982 Cason, E. E., Al Hakeem, W. G., Adams, D., Shanmugasundaram, R., & Selvaraj, R. (2022). Effects of synbiotic supplementation as an antibiotic growth promoter replacement on cecal Campylobacter jejuni load in broilers challenged with C. jejuni. Journal of Applied Poultry Research, 100315. doi:10.1016/j.japr.2022.100315 Akerele, G., Al Hakeem, W. G., Lourenco, J., & Selvaraj, R. K. (2022). The Effect of Necrotic Enteritis Challenge on Production Performance, Cecal Microbiome, and Cecal Tonsil Transcriptome in Broilers. PATHOGENS, 11(8), 16 pages. doi:10.3390/pathogens11080839 Acevedo-Villanueva, K., Akerele, G., Al-Hakeem, W., Adams, D., Gourapura, R., & Selvaraj, R. (2022). Immunization of Broiler Chickens With a Killed Chitosan Nanoparticle Salmonella Vaccine Decreases Salmonella Enterica Serovar Enteritidis Load. FRONTIERS IN PHYSIOLOGY, 13, 18 pages. doi:10.3389/fphys.2022.920777 Fathima, S., Shanmugasundaram, R., Adams, D., & Selvaraj, R. K. (2022). Gastrointestinal Microbiota and Their Manipulation for Improved Growth and Performance in Chickens. FOODS, 11(10), 30 pages. doi:10.3390/foods11101401 Al Hakeem, W. G., Fathima, S., Shanmugasundaram, R., & Selvaraj, R. K. (n.d.). Campylobacter jejuni in Poultry: Pathogenesis and Control Strategies. Microorganisms, 10(11), 2134. doi:10.3390/microorganisms10112134 Fathima, S., Hakeem, W. G. A., Shanmugasundaram, R., & Selvaraj, R. K. (n.d.). Necrotic Enteritis in Broiler Chickens: A Review on the Pathogen, Pathogenesis, and Prevention. Microorganisms, 10(10), 1958. doi:10.3390/microorganisms10101958 Yanghua He, Robert L. Taylor, Hao Bai, Christopher M. Ashwell, Keji Zhao, Yaokun Li, Guirong Sun, Huanmin Zhang, Jiuzhou Song, Transgenerational epigenetic inheritance and immunity in chickens that vary in Marek's disease resistance, Poultry Science, 2023, 103036, ISSN 0032-5791, <a href="https://doi.org/10.1016/j.psj.2023.103036">https://doi.org/10.1016/j.psj.2023.103036</a> Pan Z, Y. Wang, M. Wang, Y. Wang, X. Zhu, S. Gu, C. Zhong, L. An, M. Shan , J. Damas, M. M. Halstead, D. Guan, N. Trakooljul, K. Wimmers, Y. Bi, S. Wu, M. E. Delany, X. Bai, H.H. Cheng, C. Sun, N. Yang, X. Hu, H. A Lewin,  L. Fang, H. Zhou. 2023. An atlas of regulatory elements in chicken: a resource for chicken genetics and genomics. Science Advances 9,eade1204(2023).DOI:10.1126/sciadv.ade1204. Zhang J, Goto RM, Miller MM.  2020.  A simple means for chicken MHC-Y genotyping using short tandem repeat sequences.  Immunogenetics 72:325-332. doi: 10.1007/s00251-020-01166-6.  PMID: 32488290. Zhang J, Goto RM, Honaker CF, Siegel PB, Taylor RL Jr, Parmentier HK, Miller MM.  2021a.  Association of MHCY genotypes in lines of chickens divergently selected for high or low antibody response to sheep red blood cells.  Poult Sci. 101(3):101621. doi: 10.1016/j.psj.2021.101621.  PMID: 34995879. Zhang J, Goto RM, Psifidi A, Stevens MP, Taylor RL Jr, Miller MM.  2021b.  Research Note: MHCY haplotype impacts Campylobacter jejuni colonization in a backcross [(Line 61 x Line N) x Line N] population.  Poult Sci. 101(3):101654. doi: 10.1016/j.psj.2021.101654.  PMID: 35007930. Goto RM, Warden CD, Shiina T, Hosomichi K, Zhang J, Kang TH, Wu X, Glass MC, Delany ME, Miller MM. 2022.  The Gallus gallus RJF reference genome reveals an MHCY haplotype organized in gene blocks that contain 107 loci including 45 specialized, polymorphic MHC class I loci, 41 C-type lectin-like loci, and other loci amid hundreds of transposable elements. G3 (Bethesda). 2022 Nov 4;12(11):jkac218. doi: 10.1093/g3journal/jkac218. PMID: 35997588. Gugiu GB, Goto RM, Bhattacharya S, Delgado MK, Dalton J, Balendiran V, Miller MM. Mass spectrometry defines lysophospholipids as ligands for chicken MHCY class I molecules. J Immunol. 2023 Jan 1;210(1):96-102. doi: 10.4049/jimmunol.2200066. PMID: 36427007. <ol start="2023"> <li>Buter, A. Feberwee, Sjaak de Wit, A. Heuvelink, A. P. da Silva, R. A. Gallardo, E. Soriano Vargas, J. Verwey, A. Jung, M. Tödte, R. Dijkman. Molecular characterization of the HMTp210 gene of Avibacterium paragallinarum and the proposition of a new genotyping method as alternative for classical serotyping. 2023. Avian Pathology. Accepted</li> <li>Jude*, B. Jordan*, A. Muller-Slay, R. Luciano, A. P da Silva, R. A. Gallardo*. Mitigation of False Layer Syndrome Through Maternal Antibodies Against Infectious Bronchitis Virus. 2023. Avian Diseases. Submitted</li> </ol> Botchway ,P.K., Amuzu-Aweh, E.N., Naazie, A., Aning, G. K., Otsyina, H.R., Saelao, P., Wang, Y., Zhou, H., Walugembe, M., Dekkers, J., Lamont, S.J., Gallardo, R.A., Kelly, T.R., Bunn, D. and Kayang, B.B. 2022. Host response to successive challenges with lentogenic and velogenic Newcastle disease virus in local chickens of Ghana. Poultry Science 101:102138. doi.org/10.1016/j.psj.2022.102138 J.B. Tsaxra, R.A. Gallardo*, C. Abolnik, A. Chengula, P. M. Msoffe, A. P. Muhairwa, T. Phiri, J.R. Mushi, N. Chouicha, E.L. Mollel, H. Zhou*, and T.R. Kelly. Spatio-temporal Patterns and Prevalence of Newcastle Disease Virus at Mawenzi Live Bird Market in Morogoro Municipality, Tanzania. Transboundary and emerging diseases. Submitted. 2023. J.B. Tsaxra, R.A. Gallardo*, C. Abolnik, R. Jude*, A. Chengula, P. M. Msoffe, A. P. Muhairwa, T. Phiri, J.R. Mushi, N. Chouicha, E.L. Mollel, H. Zhou*, and T.R. Kelly. Spatio-temporal Patterns and Prevalence of Newcastle Disease Virus at Mawenzi Live Bird Market in Morogoro Municipality, Tanzania. Tropical animal health and production. Submitted. 2023. <ol start="2023"> <li>Ramsubeik, S. Stoute, R.A. Gallardo*, B. Crossley, D. Rejmanek, R. Jude*, C. Jerry. Infectious bronchitis virus California variant CA1737 isolated from a commercial layer flock with cystic oviducts and poor external egg quality. Avian Diseases. 2023. Accepted</li> <li>Jude*, A.P. Da Silva, D. Rejmanek, H.L. Shivaprasad, S. Stoute, C. Jerry, R.A. Gallardo*. Whole genome sequence of a novel genotype VIII infectious bronchitis virus isolated from California layers in 2021. ASM Microbiology Resource Announcements. 2023. Submitted.</li> </ol> He, H., Genovese, K.J., Arsenault, R.J., Swaggerty, C.L., Johnson, C.N., Byrd, J.A., Kogut, M.H. M2 polarization and inhibition of host cell glycolysis contributes intracellular survival of Salmonella strains in chicken macrophage HD-11 cells. 2023. Microorganisms. 11 (7). Johnson, C.N., Arsenault, R.J., Piva, A., Grilli, E., and Swaggerty, C.L. A microencapsulated feed additive containing organic acids and botanicals has a distinct effect on proliferative and metabolic related signaling in the jejunum and ileum of broiler chickens. 2023. Frontiers in Physiology. 14, 474. Giovagnoni, G., Perry, F., Tugnoli, B., Piva, A., Grilli, E., Arsenault, R.J. A comparison of the immunometabolic effect of antibiotics and plant extracts in a chicken macrophage-like cell line during a Salmonella Enteritidis challenge. 2023. Antibiotics. 12(2), 357 Fries-Craft, K., Arsenault, R.J., & Bobeck, E. A. Basal diet composition contributes to differential performance, intestinal health, and immunological responses to a microalgae-based feed ingredient in broiler chickens. 2023. Poultry Science. 102(1), 102235. Perry, F., Lahaye, L., Santin, E., Johnson, C., Korver, D.R., Kogut, M.H., and Arsenault, R.J. Protected Biofactors and Antioxidants Reduce the Negative Consequences of Virus and Cold Challenge while Enhancing Performance by Modulating Immunometabolism through Cytoskeletal and Immune Signaling in the Jejunum. 2022. Poultry Science. 101(12), p 102172. Garcia G Jr, Irudayam JI, Jeyachandran AV, Dubey S, Chang C, Castillo Cario S, Price N, Arumugam S, Marquez AL, Shah A, Fanaei A, Chakravarty N, Joshi S, Sinha S, French SW, Parcells MS, Ramaiah A, Arumugaswami V. Innate immune pathway modulator screen identifies STING pathway activation as a strategy to inhibit multiple families of arbo and respiratory viruses. Cell Rep Med. 2023 May 16;4(5):101024. doi: 10.1016/j.xcrm.2023.101024. Epub 2023 Apr 28. PMID: 37119814; PMCID: PMC10213809. Garcia G Jr, Irudayam JI, Jeyachandran AV, Dubey S, Chang C, Cario SC, Price N, Arumugam S, Marquez AL, Shah A, Fanaei A, Chakravarty N, Joshi S, Sinha S, French SW, Parcells M, Ramaiah A, Arumugaswami V. Broad-spectrum antiviral inhibitors targeting pandemic potential RNA viruses. bioRxiv [Preprint]. 2023 Jan 20:2023.01.19.524824. doi: 10.1101/2023.01.19.524824. Update in: Cell Rep Med. 2023 May 16;4(5):101024. PMID: 36711787; PMCID: PMC9882367. Kaufer BB, Parcells MS, Bertzbach LD. A Special Issue on Marek's Disease Virus-The Editors' View. Microorganisms. 2023 Mar 21;11(3):805. doi: 10.3390/microorganisms11030805. PMID: 36985378; PMCID: PMC10057323. Blue CEC, Emami NK, White MB, Cantley S, and Dalloul RA. 2023. Inclusion of Clarity Q manages growth performance, immune response, and nutrient transports of broilers during subclinical necrotic enteritis. Microorganisms 11(8):1894. Henschen AE, Vinkler M, Langager MM, Rowley AA, Dalloul RA, Hawley DM, and Adelman JS. 2023. Rapid adaptation to a novel pathogen through disease tolerance in a wild songbird. PLoS Pathogens 19(6):e1011408. Emami, NK, Fuller AL, and Dalloul RA. 2022. Lateral transmission of Histomonas meleagridis in turkey poults raised on floor pens. Poultry Science 101(7):101951. Weitzman CL, Belden LK, May M, Langager MM, Dalloul RA, and Hawley DM. 2022. Antibiotic perturbation of gut bacteria does not significantly alter host responses to ocular disease in a songbird species. PeerJ 10:e13559. Brandi A. Sparling, Theros T. Ng, Anaid Carlo-Allende, Fiona M. McCarthy, Robert L. Taylor, Jr., Yvonne Drechsler: Immunoglobulin-like Receptors in Chickens: identification, functional characterization, and renaming to Cluster Homolog of Immunoglobulin-like Receptors. Poultry science. Submitted.     Abstracts Swaggerty, C. L., C. N. Johnson, C. F. Honaker, P. B. Siegel, C. M. Ashwell, and R. L. Taylor, Jr. 2023. Chickens selected for high and low antibody responses to sheep red blood cells exhibit different cytokine and chemokine expression in peripheral blood leukocytes and the spleen. Poult. Sci. 102(E-Suppl. 1): in press Taylor, R. L., Jr., P. B. Siegel, C. F. Honaker, H. Parmentier, A. Wolc, C. M. Ashwell, and J. E. Fulton. 2023. Selection for antibody response against sheep red blood cells (SRBC) altered alloantigen frequencies in Virginia and Wageningen genetic stocks. Poult. Sci. 102(E-Suppl. 1): in press Taylor, R. L., Jr.,W. Drobik-Czwarno, A. Wolc, and J. E. Fulton. 2022. Identifying chicken alloantigen candidate genes. Proc. Avian Immunology Research Group (AIRG) Meeting XVI, Newark, DE, p. 17 Taylor, R. L., Jr., W. Drobik-Czwarno, A. Wolc and J. E. Fulton. 2022. Chicken alloantigen D is CD99. Poult. Sci. 101(E-Suppl. 1):154-155 Al Hakeem, W., Lourenco, J., Cason, E., Adams, D., villanueva, K., Fathima, S., . . . Selvaraj, R. (2023). The effect of Campylobacter jejuni challenge on the ileal microbiota and short-chain fatty acids concentration in broilers. INTERNATIONAL POULTRY SCIENTIFIC FORUM Shah, B., Al Hakeem, W., Fathima, S., Shanmugasundaram, R., & Selvaraj, R. (2023). Effect of synbiotic supplementation on production performance and necrotic enteritis severity in broilers under an experimental necrotic enteritis challenge. International Poultry Science Forum Fathima, S., Al Hakeem, W., Shah, B., Shanmugasundaram, R., & Selvaraj, R. (2023). Effect of arginine supplementation on production performance and inflammatory response in broilers during necrotic enteritis challenge. International Poultry Science Forum Acevedo-Villanueva, K., Renu, S., Gourapura, R., & Selvaraj, R. (2022). Salmonella chitosan nanoparticle vaccine administration is protective against Salmonella Enteritidis in broiler birds. Poult. Sci. 100 (E-Suppl 1) Selvaraj, R., Shanmugasundaram, R., & Applegate, T. (2022). Effect of Bacillus subtilis and Bacillus licheniformis probiotic supplementation on performance and Campylobacter jejuni load in broilers challenged with C. jejuni. Poult. Sci. 100 (E-Suppl 1). Song, J. Temporal Expression of immune organs in Marek’s disease. XVI Avian Immunology Research Group Meeting University of Delaware, August 26-28, 2022 Egana-Labrin. Molecular characterization of infectious bursal disease virus (IBDV) circulating in the Delmarva region between 2019-2023. 2023 American Association of Avian Pathologists (AAAP) meeting, Jacksonville, Florida. Khalid Z, Pietruska A, Chowdhury E, Hauck R (2023): Influence of avian reovirus infection on the intestinal microbiome. In: Abstracts of the International Poultry Scientific Forum, Atlanta, GA. p 18. Khalid Z, Conrad S, Alvarez-Narvaez S, Harrell TL, Chowdhury E, Hauck R (2023): Systemic invasiveness and pathogenicity of an avian reovirus field isolate compared to a reference strain after oral inoculation. Presentation at the Meeting of the American Association of Avian Pathologists, Jacksonville, FL. Arsenault, R. J. Postbiotics: a metabolic and immune gut health feed additive. Poultry Federation Annual Nutrition Conference, 2023, August 29-31; Little Rock, AR. Giovagnoni, G., Perry, F., Tugnoli, B., Piva, A., Arsenault, R., Grilli, E. The immunometabolic role of a thymol-based blend of botanicals on chicken macrophage-like cells challenged with Salmonella Enteritidis. Poultry Science Association Annual Meeting; 2023 July 10-13; Philadelphia, PA. Arsenault, R.J. Unveiling the secrets of kinome analysis. Vetagro Satellite Symposium (ESPN 2023), 2023, June 21; Rimini, Italy. Johnson, C., Arsenault, R., Grilli, E., Piva, A., Swaggerty, C. A microencapsulated feed additive containing organic acids and botanicals has a distinct effect on proliferative and metabolic related signaling in the jejunum and ileum of broiler chickens. 23rd European Symposium on Poultry Nutrition; 2023 June 21-24; Rimini, Italy. Giovagnoni, G., Tugnoli, B., Johnson, C., Piva, A., Arsenault, R., Swaggerty, C., Grilli, E. A microencapsulated thymol-based blend of botanicals can clear Salmonella Enteritidis in contrast to common in-feed antibiotics in broilers. 23rd European Symposium on Poultry Nutrition; 2023 June 21-24; Rimini, Italy. Perry, F., Bortoluzzi, C., Elango, J.N., James, A., Jones, E., Eyng, C., Kogut, M., Arsenault, R. Butyrate affects chicken monocyte-like cell cycle progression. International Poultry Scientific Forum; 2023 January 23-34; Atlanta, GA. Arsenault, R.J. Determining immunometabolic markers of gut health and the mechanism of action for challenges and treatments using kinome and molecular analysis. Kemin Intestinal Health Symposium. 2022, October 12-14, Palm Springs, CA Giovagnoni, G., Perry, F., Anderson-Coughlin, B., Kniel, K., Tugnoli, B., Grilli, E., Arsenault, R. Digital PCR as a new highly sensitive method in chicken cytokine profiling. Avian Immunology Research Group Meeting; 2022 September 25-28; Newark, DE. Parcells, M.S., Katneni, U.K., Neerukonda, S., Tavlarides-Hontz, P., Arsenault, R.J. Cell culture and In Vivo Examination of the Mechanism of Action of Victrio®, a DNA-Liposome-based Innate Immune Agonist. Avian Immunology Research Group Meeting; 2022 September 25-28; Newark, DE. Parcells, M.S. Dallakoti, A., Tavlarides-Hontz, P., Pendarvis, K., Gollhardt, E., Perry, F., Arsenault, R.J. Proteomic analysis of the differentiation of chicken monocyte cell line HD11 into macrophages and dendritic cells. Avian Immunology Research Group Meeting; 2022 September 25-28; Newark, DE. Mark S. Parcells, Aksana Dallakoti, Sohee Lee, Yaw Kobia Dwomor, Eric Munoz, Matthew B. Hudson, Shannon Modla and Phaedra Tavlarides-Hontz. The Effect of Exosomes from the Serum of Chickens Vaccinated and Protected from Marek’s Disease Virus (MDV) Challenge and MDV-induced Tumor-bearing Chickens on the Proteomes of Chicken Macrophage Cell Line HD11. Proceedings of 95th Annual Northeastern Conference on Avian Diseases (NECAD), 2023, Penn State University. p. 81 Taxonomic and Metabolic Changes in the Animal. 5th Microbiome Movement – Animal Health & Nutrition. Raleigh, NC. October 2022 (International meeting). Blue CEC, Medina B, Wagner AL, Dalloul RA. Novel natural feed additive efficacy during a clinical necrotic enteritis challenge in broilers. International Poultry Scientific Forum. 2023. Dong B, Dalloul RA. Establishment of chicken apical-out three-dimensional enteroids. International Poultry Scientific Forum. 2023. Niraula A, Blue CEC, Fenster DA, Emami NK, Dalloul RA. Assessment of mRNA abundance of key cytokines during histomoniasis in turkey poults in a lateral transmission model. International Poultry Scientific Forum. 2023. Blue CEC, Froebel LE, Dalloul RA. Evaluating mRNA abundance of host defense peptide genes in heritage and modern broiler breeds during subclinical necrotic enteritis. International Poultry Scientific Forum. 2023. Niraula A, Fenster DA, Wagner AL, Medina B, Girard I, Fuller AL, and Dalloul RA. Protective effects of Alterna HTS in turkey poults raised in a floor pen lateral transmission model of Histomonas meleagridis. Poultry Science Association Annual Meeting. 2023. Blue CEC, Wagner AL, Medina B, Girard I, Dalloul RA. Assessment of phytogenic blends on performance and tight junction proteins in broiler chickens during a necrotic enteritis challenge. Poultry Science Association Annual Meeting. 2023. Dong B, Blue CEC, Regmi P, Ellestad LE, Dalloul RA. In ovo administration and water supplementation of a postbiotic positively influence response of broilers to necrotic enteritis. Poultry Science Association Annual Meeting. 2023. Marasini H, Dong B, Dalloul RA, Regmi P. Effect of experimental coccidiosis and necrotic enteritis on broiler behavior during open-field test. Poultry Science Association Annual Meeting. 2023. Fenster DA, Chaney WE, Dalloul RA. Effect of Diamond V Original XPC postbiotic on Salmonella Typhimurium colonization and growth performance in broilers. Poultry Science Association Annual Meeting. 2023.   Thesis/Dissertation Bikas Shah, Synbiotic supplementation as an replacement to antimicrobial growth promoters in broilers challenged with necrotic enteritis challenge. MS. University of Georgia. Determining the Role of the Conserved Herpesviridae Protein Kinase (CHPK) in Replication and Transmission of Avian Herpesviruses.” Andrea Krieter, PhD Dissertation 2023. University of Illinois at Urbana-Champaign. Supervisor: Keith W. Jarosinski Wang J, Fenster DA, Vaddu S, Bhumanapalli A, Dalloul RA, Leone C, Singh M, Thippareddi H. Translocation of Salmonella from the gastrointestinal tract to internal organs of broilers. Poultry Science Association Annual Meeting. 2023. Vaddu S, Singh A, Wang J, Koft B, Mallavarapu B, Subedi D, Bhumanapalli A, Patil P, Dalloul RA, Singh M, Thippareddi H. Effects of Salmonella co-infection with Eimeria maxima and Clostridium perfringens on growth performance and pathogen shedding in broilers. Poultry Science Association Annual Meeting. 2023. Carlo-Allende,A., Sparling, B., Drechsler, Y. Poster. RNA-interference: role of Ig-like receptor B in chicken macrophage response to AIV and Salmonella typhimurium. August 3rd to 5th, 2023. San Juan, Puerto Rico. <a href="https://www.aavmc.org/wp-content/uploads/2023/07/Abstracts_Rev_465.pdf">https://www.aavmc.org/wp-content/uploads/2023/07/Abstracts_Rev_465.pdf</a> Sparling, B. and Drechsler, Y. Talk and Conference Proceedings. The chicken cluster homolog of immunoglobulin-like receptor-B molecules plays a suppressive role during avian influenza infection in vitro. Proceedings of the 72nd Western Poultry Disease Conference. March 13-15, 2023. Sacramento, California. Available online at: <a href="https://static1.squarespace.com/static/6324cc48a5e67e5d682f1773/t/6400fba0dcae832ad0f98336/1677786028158/WPDC_2023_Proceedings.pdf">https://static1.squarespace.com/static/6324cc48a5e67e5d682f1773/t/6400fba0dcae832ad0f98336/1677786028158/WPDC_2023_Proceedings.pdf</a> Ng, T., Drechsler, Y. Cellular composition and Ig-like Receptors Expression in the Reproductive Tract of the B2B2 and B19B19 chickens. March 6th, 2023. Sparling, B., Ng, T., and Drechsler, Y. Poster. Improving the cluster homolog of immunoglobulin-like receptor annotation and their implications of expression in innate immune response in different chicken strains. Avian Immunology Research Group Meeting. September 25-28, 2022. Newark, Delaware. Majeed, S., L. Bielke, A. Nazmi. 2023. Natural Intraepithelial Lymphocytes are critical intestinal mucosal defense against Salmonella Typhimurium Infection in Broiler Chicken. Poultry Science Annual Meeting, Philadelphia, Pennsylvania, USA. Oral presentation Majeed, S., S.K. Hamad, L. Bielke, A. Nazmi. 2023. The role of Intraepithelial lymphocytes in chicken response to necrotic enteritis. Poultry Science Annual Meeting, Philadelphia, Pennsylvania, USA. Oral presentation Nazmi, A., S.K. Hamad, S. Majeed. 2023. The role of intestinal intraepithelial lymphocytes in resistance against coccidiosis in chickens. American Association of Immunologist Annual Meeting, Washington DC., USA. Poster presentation

Impact Statements

(Nazmi) Objective 3. Our results indicates that innate immune cells (iCD8a and non-T cells (CD3neg IEL) and innate-like immune cells (TCRgd and TCRabCD8aa IEL) play crucial role in protecting the mucosal barrier against NE induced by C. perfringens.