@article{brady_liu_hicks_long_porter_2023, title={Global gene expression analysis of the turkey hen hypothalamo-pituitary-gonadal axis during the preovulatory hormonal surge}, volume={102}, ISSN={["1525-3171"]}, DOI={10.1016/j.psj.2023.102547}, abstractNote={The preovulatory hormonal surge (PS) consists of elevated circulating luteinizing hormone (LH) and progesterone levels and serves as the primary trigger for ovarian follicle ovulation. Increased LH and progesterone, produced by the pituitary and the granulosa layer of the largest ovarian follicle (F1), respectively, result from hypothalamic stimulation and steroid hormone feedback on the hypothalamo-pituitary-gonadal (HPG) axis. The hypothalamus, pituitary, F1 granulosa, and granulosa layer of the fifth largest follicle (F5) were isolated from converter turkey hens outside and during the PS and subjected to RNA sequencing (n = 6 per tissue). Differentially expressed genes were subjected to functional annotation using DAVID and IPA. A total of 12, 250, 1235, and 1938 DEGs were identified in the hypothalamus, pituitary, F1 granulosa, and F5 granulosa respectively (q<0.05, |fold change|>1.5, FPKM>1). Gene Ontology (GO) analysis revealed key roles for metabolic processes, steroid hormone feedback, and hypoxia induced gene expression changes. Upstream analysis identified a total of 4, 42, 126, and 393 potential regulators of downstream gene expression in the hypothalamus, pituitary, F1G, and F5G respectively, with a total of 63 potential regulators exhibiting differential expression between samples collected outside and during the PS (|z-score|>2). The results from this study serve to increase the current knowledge base surrounding the regulation of the PS in turkey hens. Through GO analysis, downstream processes and functions associated with the PS were linked to identified DEGs, and through upstream analysis, potential regulators of DEGs were identified for further analysis. Linking upstream regulators to the downstream PS and ovulation events could allow for genetic selection or manipulation of ovulation frequencies in turkey hens.}, number={4}, journal={POULTRY SCIENCE}, author={Brady, Kristen and Liu, Hsiao-Ching and Hicks, Julie and Long, Julie A. and Porter, Tom E.}, year={2023}, month={Apr} }
 @article{pike_zhao_hicks_wang_hagen_liu_odle_lin_2023, title={Intestinal Carnitine Status and Fatty Acid Oxidation in Response to Clofibrate and Medium-Chain Triglyceride Supplementation in Newborn Pigs}, volume={24}, ISSN={["1422-0067"]}, url={https://doi.org/10.3390/ijms24076066}, DOI={10.3390/ijms24076066}, abstractNote={To investigate the role of peroxisome proliferator-activated receptor alpha (PPARα) in carnitine status and intestinal fatty acid oxidation in neonates, a total of 72 suckled newborn piglets were assigned into 8 dietary treatments following a 2 (±0.35% clofibrate) × 4 (diets with: succinate+glycerol (Succ), tri-valerate (TC5), tri-hexanoate (TC6), or tri-2-methylpentanoate (TMPA)) factorial design. All pigs received experimental milk diets with isocaloric energy for 5 days. Carnitine statuses were evaluated, and fatty acid oxidation was measured in vitro using [1-14C]-palmitic acid (1 mM) as a substrate in absence or presence of L659699 (1.6 µM), iodoacetamide (50 µM), and carnitine (1 mM). Clofibrate increased concentrations of free (41%) and/or acyl-carnitine (44% and 15%) in liver and plasma but had no effects in the intestine. The effects on carnitine status were associated with the expression of genes involved in carnitine biosynthesis, absorption, and transportation. TC5 and TMPA stimulated the increased fatty acid oxidation rate induced by clofibrate, while TC6 had no effect on the increased fatty acid oxidation induced by clofibrate (p > 0.05). These results suggest that dietary clofibrate improved carnitine status and increased fatty acid oxidation. Propionyl-CoA, generated from TC5 and TMPA, could stimulate the increased fatty acid oxidation rate induced by clofibrate as anaplerotic carbon sources.}, number={7}, journal={INTERNATIONAL JOURNAL OF MOLECULAR SCIENCES}, author={Pike, Brandon and Zhao, Jinan and Hicks, Julie A. and Wang, Feng and Hagen, Rachel and Liu, Hsiao-Ching and Odle, Jack and Lin, Xi}, year={2023}, month={Apr} }
 @article{hicks_pike_liu_2022, title={Alterations in hepatic mitotic and cell cycle transcriptional networks during the metabolic switch in broiler chicks}, volume={13}, ISSN={["1664-042X"]}, DOI={10.3389/fphys.2022.1020870}, abstractNote={During embryonic life, chicks mainly derive energy from hepatic oxidation of yolk lipids. After hatch, chicks must rely on carbohydrate-rich feed to obtain energy. This requires an abrupt and intensive switch of metabolic processes, particularly in the liver. We recently identified a number of transcriptional and post-transcriptional regulatory networks that work concordantly to tune metabolic processes during the metabolic switch. Here, we used delayed feeding post-hatch (48 h) to impede the metabolic switch in broilers. We used RNA-seq to identify hepatic transcriptome differences between late stage embryos (E18) and two-day-old chicks (D2), which were either fed-from-hatch (FED) or not fed (DLY). Between FED and E18, 2,430 genes were differentially expressed (fold-change≥ 2; FDR p-value 0.05), of these 1,237 were downregulated in FED birds and 1,193 were upregulated. Between DLY and E18, 1979 genes were differentially expressed, of these 1,043 were downregulated and 936 were upregulated in DLY birds. Between DLY and FED, 880 genes were differentially expressed, of these 543 were downregulated and 337 were upregulated in DLY birds. We found that in addition to disturbances in a number of metabolic pathways, unfed chicks had a widespread suppression of gene networks associated with cell proliferation, cell cycle progression and mitosis. Expression patterns suggest that hepatocytes of delayed-fed birds have abnormal mitosis and increased polyploidization. This suggests that post-hatch feed consumption maintains the rate and integrity of liver growth immediately, which in turn, likely helps facilitate the appropriate programming of hepatic metabolic networks.}, journal={FRONTIERS IN PHYSIOLOGY}, author={Hicks, Julie A. and Pike, Brandon E. and Liu, Hsiao-Ching}, year={2022}, month={Oct} }
 @article{wang_hicks_jiang_liu_2022, title={Transcriptome Analysis of Chicken Reveals the Impact of Herpesvirus of Turkeys on Bursa RNA Expression in Marek's Disease Virus Infections}, volume={100}, ISSN={["1525-3163"]}, DOI={10.1093/jas/skac247.392}, abstractNote={Abstract}, journal={JOURNAL OF ANIMAL SCIENCE}, author={Wang, Junjian and Hicks, Julie and Jiang, Jicai and Liu, Hsiao-Ching}, year={2022}, month={Oct}, pages={215–215} }
 @misc{hicks_liu_2021, title={Centennial Review: Metabolic microRNA- shifting gears in the regulation of metabolic pathways in poultry}, volume={100}, ISSN={["1525-3171"]}, DOI={10.1016/j.psj.2020.11.033}, abstractNote={Over 20 yr ago, a small noncoding class of RNA termed microRNA (miRNA) that was able to recognize sequences in mRNAs and inhibit their translation was discovered in Caenorhabditis elegans. In the intervening years, miRNA have been discovered in most eukaryotes and are now known to regulate the majority of protein-coding genes. It has been discovered that disruption of miRNA function often leads to the development of pathological conditions. One physiological system under extensive miRNA-mediated regulation is metabolism. Metabolism is one of the most dynamic of biological networks within multiple organs, including the liver, muscle, and adipose tissue, working in concert to respond to ever-changing nutritional cues and energy demands. Therefore, it is not surprising that miRNA regulate virtually all aspects of eukaryotic metabolism and have been linked to metabolic disorders, such as obesity, fatty liver diseases, and diabetes, just to name a few. Chickens, and birds in general, face their own unique metabolic challenges, particularly after hatching, when their metabolism must completely transform from using lipid-rich yolk to carbohydrate-rich feed as fuel in a very short period of time. Furthermore, commercial poultry breeds have undergone extensive selection over the last century for more desirable production traits, which has resulted in numerous metabolic consequences. Here, we review the current knowledge of miRNA-mediated regulation of metabolic development and function in chickens.}, number={3}, journal={POULTRY SCIENCE}, author={Hicks, Julie A. and Liu, Hsiao-Ching}, year={2021}, month={Mar} }
 @article{hicks_liu_2021, title={Expression Signatures of microRNAs and Their Targeted Pathways in the Adipose Tissue of Chickens during the Transition from Embryonic to Post-Hatch Development}, volume={12}, ISSN={["2073-4425"]}, DOI={10.3390/genes12020196}, abstractNote={As the chick transitions from embryonic to post-hatching life, its metabolism must quickly undergo a dramatic switch in its major energy source. The chick embryo derives most of its energy from the yolk, a lipid-rich/carbohydrate-poor source. Upon hatching, the chick’s metabolism must then be able to utilize a lipid-poor/carbohydrate-rich source (feed) as its main form of energy. We recently found that a number of hepatically-expressed microRNAs (miRNAs) help facilitate this shift in metabolic processes in the chick liver, the main site of lipogenesis. While adipose tissue was initially thought to mainly serve as a lipid storage site, it is now known to carry many metabolic, endocrine, and immunological functions. Therefore, it would be expected that adipose tissue is also an important factor in the metabolic switch. To that end, we used next generation sequencing (NGS) and real-time quantitative PCR (RT-qPCR) to generate miRNome and transcriptome signatures of the adipose tissue during the transition from late embryonic to early post-hatch development. As adipose tissue is well known to produce inflammatory and other immune factors, we used SPF white leghorns to generate the initial miRNome and transcriptome signatures to minimize complications from external factors (e.g., pathogenic infections) and ensure the identification of bona fide switch-associated miRNAs and transcripts. We then examined their expression signatures in the adipose tissue of broilers (Ross 708). Using E18 embryos as representative of pre-switching metabolism and D3 chicks as a representative of post-switching metabolism, we identified a group of miRNAs which work concordantly to regulate a diverse but interconnected group of developmental, immune and metabolic processes in the adipose tissue during the metabolic switch. Network mapping suggests that during the first days post-hatch, despite the consumption of feed, the chick is still heavily reliant upon adipose tissue lipid stores for energy production, and is not yet efficiently using their new energy source for de novo lipid storage. A number of core master regulatory pathways including, circadian rhythm transcriptional regulation and growth hormone (GH) signaling, likely work in concert with miRNAs to maintain an essential balance between adipogenic, lipolytic, developmental, and immunological processes in the adipose tissue during the metabolic switch.}, number={2}, journal={GENES}, author={Hicks, Julie A. and Liu, Hsiao-Ching}, year={2021}, month={Feb} }
 @article{brady_liu_hicks_long_porter_2021, title={Transcriptome Analysis During Follicle Development in Turkey Hens With Low and High Egg Production}, volume={12}, ISSN={["1664-8021"]}, DOI={10.3389/fgene.2021.619196}, abstractNote={Low and high egg producing hens exhibit gene expression differences related to ovarian steroidogenesis. High egg producing hens display increased expression of genes involved in progesterone and estradiol production, in the granulosa layer of the largest follicle (F1G) and small white follicles (SWF), respectively, whereas low egg producing hens display increased expression of genes related to progesterone and androgen production in the granulosa (F5G) and theca interna layer (F5I) of the fifth largest follicle, respectively. Transcriptome analysis was performed on F1G, F5G, F5I, and SWF samples from low and high egg producing hens to identify novel regulators of ovarian steroidogenesis. In total, 12,221 differentially expressed genes (DEGs) were identified between low and high egg producing hens across the four cell types examined. Pathway analysis implied differential regulation of the hypothalamo-pituitary-thyroid (HPT) axis, particularly thyroid hormone transporters and thyroid hormone receptors, and of estradiol signaling in low and high egg producing hens. The HPT axis showed up-regulation in high egg producing hens in less mature follicles but up-regulation in low egg producing hens in more mature follicles. Estradiol signaling exclusively exhibited up-regulation in high egg producing hens. Treatment of SWF cells from low and high egg producing hens with thyroid hormone in vitro decreased estradiol production in cells from high egg producing hens to the levels seen in cells from low egg producing hens, whereas thyroid hormone treatment did not impact estradiol production in cells from low egg producing hens. Transcriptome analysis of the major cell types involved in steroidogenesis inferred the involvement of the HPT axis and estradiol signaling in the regulation of differential steroid hormone production seen among hens with different egg production levels.}, journal={FRONTIERS IN GENETICS}, author={Brady, Kristen and Liu, Hsiao-Ching and Hicks, Julie A. and Long, Julie A. and Porter, Tom E.}, year={2021}, month={Mar} }
 @article{hicks_yoo_liu_2020, title={Transcriptional Immune Signatures of Alveolar Macrophages and the Impact of the NLRP3 Inflammasome on Porcine Reproductive and Respiratory Syndrome Virus (PRRSV) Replication}, volume={12}, ISSN={["1999-4915"]}, DOI={10.3390/v12111299}, abstractNote={Porcine Reproductive and Respiratory Syndrome (PRRS) is a contagious viral (PRRSV) disease in pigs characterized by poor reproductive health, increased mortality, and reductions in growth rates. PRRSV is known to implement immuno-antagonistic mechanisms to evade detection and mute host responses to infection. To better understand the cellular immunosignature of PRRSV we have undertaken transcriptome and immunomodulatory studies in PRRSV-infected porcine alveolar macrophages (PAMs). We first used genome-wide transcriptome profiling (RNA-seq) to elucidate PRRSV-induced changes in the PAM transcriptome in response to infection. We found a number of cellular networks were altered by PRRSV infection, including many associated with innate immunity, such as, the NLRP3 inflammasome. To further explore the role(s) of innate immune networks in PRRSV-infected PAMs, we used an NLRP3-specific inhibitor, MCC950, to identify the potential functionality of the inflammasome during PRRSV replication. We found that PRRSV does quickly induce expression of inflammasome-associated genes in PAMs. Treatment of PAMs with MCC950 suggests NLRP3 inflammasome activation negatively impacts viral replication. Treatment of PAMs with cell culture supernatants from macrophages subjected to NLRP3 inflammasome activation (via polyinosinic-polycytidylic acid (poly I:C) transfection), prior to PRRSV infection resulted in significantly reduced viral RNA levels compared to PAMs treated with cell culture supernatants from macrophages subjected to NLRP3 inflammasome inhibition (MCC950 treatment/poly I:C transfection). This further supports a role for NLRP3 inflammasome activation in the innate macrophagic anti-PRRSV immune response and suggests that PRRSV is sensitive to the effects of NLRP3 inflammasome activity. Taken together, these transcriptome and immunoregulatory data highlight the complex changes PRRSV infection induces in the molecular immune networks of its cellular host.}, number={11}, journal={VIRUSES-BASEL}, author={Hicks, Julie A. and Yoo, Dongwan and Liu, Hsiao-Ching}, year={2020}, month={Nov} }
 @article{brady_liu_hicks_long_porter_2020, title={Transcriptome analysis of the hypothalamus and pituitary of turkey hens with low and high egg production}, volume={21}, ISSN={["1471-2164"]}, DOI={10.1186/s12864-020-07075-y}, abstractNote={Abstract}, number={1}, journal={BMC GENOMICS}, author={Brady, Kristen and Liu, Hsiao-Ching and Hicks, Julie A. and Long, Julie A. and Porter, Tom E.}, year={2020}, month={Sep} }
 @article{hicks_trakooljul_liu_2019, title={Alterations in cellular and viral microRNA and cellular gene expression in Marek's disease virus-transformed T-cell lines treated with sodium butyrate}, volume={98}, ISSN={["1525-3171"]}, DOI={10.3382/ps/pey412}, abstractNote={ABSTRACT A shared feature of herpesviruses is their ability to enter a latent state following an initially lytic infection. Marek's disease virus serotype 1 (MDV‐1) is an oncogenic avian herpesvirus. Small RNA profiling studies have suggested that microRNAs (miRNAs) are involved in viral latency. Sodium butyrate treatment is known to induce herpesvirus reactivation. The present study was undertaken to determine transcriptome and miRNome changes induced by sodium butyrate in 2 MDV‐transformed cell lines, RP2 and CU115. In the first 24 h post‐treatment, microarray analysis of transcriptional changes in cell lines RP2 and CU115 identified 137 and 114 differentially expressed genes, respectively. Small RNA deep‐sequencing analysis identified 17 cellular miRNAs that were differentially expressed. The expression of MDV‐encoded miRNAs was also altered upon treatment. Many of the genes and miRNAs that are differentially expressed are involved in regulation of the cell cycle, mitosis, DNA metabolism, and lymphocyte differentiation.}, number={2}, journal={POULTRY SCIENCE}, author={Hicks, Julie A. and Trakooljul, Nares and Liu, Hsiao-Ching}, year={2019}, month={Feb}, pages={642–652} }
 @article{hicks_porter_sunny_liu_2019, title={Delayed Feeding Alters Transcriptional and Post-Transcriptional Regulation of Hepatic Metabolic Pathways in Peri-Hatch Broiler Chicks}, volume={10}, ISSN={["2073-4425"]}, DOI={10.3390/genes10040272}, abstractNote={Hepatic fatty acid oxidation of yolk lipoproteins provides the main energy source for chick embryos. Post-hatching these yolk lipids are rapidly exhausted and metabolism switches to a carbohydrate-based energy source. We recently demonstrated that many microRNAs (miRNAs) are key regulators of hepatic metabolic pathways during this metabolic switching. MiRNAs are small non-coding RNAs that post-transcriptionally regulate gene expression in most eukaryotes. To further elucidate the roles of miRNAs in the metabolic switch, we used delayed feeding for 48 h to impede the hepatic metabolic switch. We found that hepatic expression of several miRNAs including miR-33, miR-20b, miR-34a, and miR-454 was affected by delaying feed consumption for 48 h. For example, we found that delayed feeding resulted in increased miR-20b expression and conversely reduced expression of its target FADS1, an enzyme involved in fatty acid synthesis. Interestingly, the expression of a previously identified miR-20b regulator FOXO3 was also higher in delayed fed chicks. FOXO3 also functions in protection of cells from oxidative stress. Delayed fed chicks also had much higher levels of plasma ketone bodies than their normal fed counterparts. This suggests that delayed fed chicks rely almost exclusively on lipid oxidation for energy production and are likely under higher oxidative stress. Thus, it is possible that FOXO3 may function to both limit lipogenesis as well as to help protect against oxidative stress in peri-hatch chicks until the initiation of feed consumption. This is further supported by evidence that the FOXO3-regulated histone deacetylase (HDAC2) was found to recognize the FASN (involved in fatty acid synthesis) chicken promoter in a yeast one-hybrid assay. Expression of FASN mRNA was lower in delayed fed chicks until feed consumption. The present study demonstrated that many transcriptional and post-transcriptional mechanisms, including miRNA, form a complex interconnected regulatory network that is involved in controlling lipid and glucose molecular pathways during the metabolic transition in peri-hatch chicks.}, number={4}, journal={GENES}, author={Hicks, Julie A. and Porter, Tom E. and Sunny, Nishanth E. and Liu, Hsiao-Ching}, year={2019}, month={Apr} }
 @article{hicks_liu_2019, title={Impact of HVT Vaccination on Splenic miRNA Expression in Marek's Disease Virus Infections}, volume={10}, ISSN={["2073-4425"]}, DOI={10.3390/genes10020115}, abstractNote={Marek’s Disease is a lymphoproliferative disease of chickens caused by Marek’s Disease Virus. Similar to other herpesviruses, Marek’s Disease Virus (MDV) encodes its own small non-coding regulatory RNAs termed microRNAs (miRNAs). We previously found that the expression profile of these viral miRNAs is affected by vaccination with Herpesvirus of Turkeys (HVT). To further characterize miRNA-mediated gene regulation in MDV infections, in the current study we examine the impact of HVT vaccination on cellular miRNA expression in MDV-infected specific-pathogen-free (SPF) chickens. We used small RNA-seq to identify 24 cellular miRNAs that exhibited altered splenic expression in MDV infected chickens (42 dpi) compared to age-matched uninfected birds. We then used Real Time-quantitative PCR (RT-qPCR) to develop expression profiles of a select group of these host miRNAs in chickens receiving the HVT vaccine and in vaccinated chickens subsequently infected with MDV. As was seen with viral miRNA, host miRNAs had unique splenic expression profiles between chickens infected with HVT, MDV, or co-infected birds. We also discovered a group of transcription factors, using a yeast one-hybrid screen, which regulates immune responses and cell growth pathways and also likely regulates the expression of these cellular miRNAs. Overall, this study suggests cellular miRNAs are likely a critical component of both protection from and progression of Marek’s Disease.}, number={2}, journal={GENES}, author={Hicks, Julie A. and Liu, Hsiao-Ching}, year={2019}, month={Feb} }
 @article{hicks_porter_liu_2017, title={Identification of microRNAs controlling hepatic mRNA levels for metabolic genes during the metabolic transition from embryonic to posthatch development in the chicken}, volume={18}, ISSN={["1471-2164"]}, DOI={10.1186/s12864-017-4096-5}, abstractNote={The transition from embryonic to posthatch development in the chicken represents a massive metabolic switch from primarily lipolytic to primarily lipogenic metabolism. This metabolic switch is essential for the chick to successfully transition from the metabolism of stored egg yolk to the utilization of carbohydrate-based feed. However, regulation of this metabolic switch is not well understood. We hypothesized that microRNAs (miRNAs) play an important role in the metabolic switch that is essential to efficient growth of chickens. We used high-throughput RNA sequencing to characterize expression profiles of mRNA and miRNA in liver during late embryonic and early posthatch development of the chicken. This extensive data set was used to define the contributions of microRNAs to the metabolic switch during development that is critical to growth and nutrient utilization in chickens.We found that expression of over 800 mRNAs and 30 miRNAs was altered in the embryonic liver between embryonic day 18 and posthatch day 3, and many of these differentially expressed mRNAs and miRNAs are associated with metabolic processes. We confirmed the regulation of some of these mRNAs by miRNAs expressed in a reciprocal pattern using luciferase reporter assays. Finally, through the use of yeast one-hybrid screens, we identified several proteins that likely regulate expression of one of these important miRNAs.Integration of the upstream regulatory mechanisms governing miRNA expression along with monitoring the downstream effects of this expression will ultimately allow for the construction of complete miRNA regulatory networks associated with the hepatic metabolic switch in chickens. Our findings support a key role for miRNAs in controlling the metabolic switch that occurs between embryonic and posthatch development in the chicken.}, journal={BMC GENOMICS}, author={Hicks, Julie A. and Porter, Tom E. and Liu, Hsiao-Ching}, year={2017}, month={Sep} }
 @article{hicks_yoo_liu_2013, title={Characterization of the microRNAome in Porcine Reproductive and Respiratory Syndrome Virus Infected Macrophages}, volume={8}, ISSN={["1932-6203"]}, DOI={10.1371/journal.pone.0082054}, abstractNote={Porcine Reproductive and Respiratory Syndrome Virus (PRRSV), a member of the arterivirus family, is the causative agent of Porcine Reproductive and Respiratory Syndrome (PRRS). PRRS is characterized by late term abortions and respiratory disease, particularly in young pigs. Small regulatory RNAs termed microRNA (miRNA) are associated with gene regulation at the post-transcriptional level. MiRNAs are known to play many diverse and complex roles in viral infections. To discover the impact of PRRSV infections on the cellular miRNAome, Illumina deep sequencing was used to construct small RNA expression profiles from in vitro cultured PRRSV-infected porcine alveolar macrophages (PAMs). A total of forty cellular miRNAs were significantly differentially expressed within the first 48 hours post infection (hpi). The expression of six miRNAs, miR-30a-3p, miR-132, miR-27b*, miR-29b, miR-146a and miR-9-2, were altered at more than one time point. Target gene identification suggests that these miRNAs are involved in regulating immune signaling pathways, cytokine, and transcription factor production. The most highly repressed miRNA at 24 hpi was miR-147. A miR-147 mimic was utilized to maintain miR-147 levels in PRRSV-infected PAMs. PRRSV replication was negatively impacted by high levels of miR-147. Whether down-regulation of miR-147 is directly induced by PRRSV or if it is part of the cellular response and PRRSV indirectly benefits remains to be determined. No evidence could be found of PRRSV-encoded miRNAs. Overall, the present study has revealed that a large and diverse group of miRNAs are expressed in swine alveolar macrophages and that the expression of a subset of these miRNAs is altered in PRRSV infected macrophages.}, number={12}, journal={PLOS ONE}, author={Hicks, Julie A. and Yoo, Dongwan and Liu, Hsiao-Ching}, year={2013}, month={Dec} }
 @article{hicks_liu_2013, title={Current State of Marek's Disease Virus MicroRNA Research}, volume={57}, ISSN={["1938-4351"]}, DOI={10.1637/10355-090812-review.1}, abstractNote={SUMMARY.  MicroRNA (miRNA) is a major family of small RNAs that posttranscriptionally regulate gene expression. Small RNA profiling studies have revealed that some viruses, particularly large DNA viruses, such as Marek's disease virus (MDV), encode their own set of miRNAs. There are currently 406 viral miRNAs in miRBase, of which 392 are encoded by herpesviruses. To date, 26 MDV-1 miRNAs, 36 MDV-2 miRNAs, and 28 herpesvirus of turkeys miRNAs have been identified. Interestingly, herpesvirus miRNAs appear to have spatial conservation, located in clusters within repeat regions, but lack sequence conservation. Two clusters of MDV-1 miRNA have been identified, one located near the MEQ gene and one within the latency-associated transcript (LAT). miRNA profiling studies have shown that MDV miRNA are differentially expressed between strains and stages of infection. For example, mdv1-miR-M4 and mdv1-miR-M2-3p are three- and sixfold higher, expressed, respectively, in vv+ strains compared to vv strains. A recent study found that deletion or seed region mutation of mdv1-miR-M4 reduces viral oncogenicity, suggesting a link between mdv1-mir-M4 and lymphoma development in MDV-infected birds. Taken together, current research suggests that viral miRNAs are a key component of MDV pathogenesis. RESUMEN.  Estudio Recapitulativo—Estado actual de la investigación sobre micro ARN en la enfermedad de Marek. Las moléculas de micro ARN (miRNA) son una familia de moléculas pequeñas de ARN que regulan de manera postranscripcional la expresión de genes. Los estudios de los perfiles de moléculas pequeñas de ARN han revelado que algunos virus, particularmente virus ADN grandes como el virus de Marek codifican su propio conjunto de micro ARN. Actualmente existen 406 moléculas de micro ARN en la base de datos miRBase, de las cuales 392 están codificadas por herpesvirus. Hasta la fecha, se han identificado 26 moléculas de micro ARN del virus de Marek 1, 36 del virus de Marek 2 y 28 del herpesvirus de pavos. De manera interesante, las moléculas de micro ARN de los herpesvirus parecen ser conservadas de manera espacial, localizados en grupos dentro de regiones repetidas, pero carecen de secuencias conservadas. Dos grupos del virus de Marek 1 han sido identificados, uno se encuentra localizado cerca del gene MEQ y otro dentro del transcripto asociado con la latencia (LAT). Los estudios de perfiles de micro ARN han demostrado que las moléculas de micro ARN del virus de la enfermedad de Marek se expresan de manera diferente de acuerdo a las cepas o al estado de infección. Por ejemplo, las moléculas mdv1-miR-M4 y mdv1-miR-M2-3p se expresan de tres y seis veces más, respectivamente en las cepas muy virulentas plus en comparación con las cepas muy virulentas. Un estudio reciente demostró que la deleción o una mutación en la región de la semilla de mdv1-miR-M4 reduce la oncogénesis viral, lo que sugiere un vínculo entre mdv1-mir-M4 y el desarrollo de linfomas en las aves infectadas con Marek. Considerando todo, la investigación reciente sugiere que las moléculas de micro ARN virales son un componente clave en la patogénesis de la enfermedad de Marek.}, number={2}, journal={AVIAN DISEASES}, author={Hicks, Julie A. and Liu, Hsiao-Ching}, year={2013}, month={Jun}, pages={332–339} }
 @misc{hicks_liu_2013, title={Involvement of Eukaryotic Small RNA Pathways in Host Defense and Viral Pathogenesis}, volume={5}, ISSN={["1999-4915"]}, DOI={10.3390/v5112659}, abstractNote={Post-transcriptional gene regulation by small RNAs is now established as an important branch of the gene regulatory system. Many different classes of small RNAs have been discovered; among these are short interfering RNAs (siRNAs) and microRNA (miRNAs). Though differences in the processing and function of small RNAs exist between plants and animals, both groups utilize small RNA-mediated gene regulation in response to pathogens. Host encoded miRNAs and siRNAs are generated from viral RNA function in host defense and pathogenic resistance in plants. In animals, miRNAs are key regulators in both immune system development and in immune function. Pathogens, in particular viruses, have evolved mechanisms to usurp the host’s small RNA-mediated regulatory system. Overall, small RNAs are a major component of host defense and immunity in eukaryotes. The goal of this review is to summarize our current knowledge of the involvement of eukaryotic small RNA pathways in host defense and viral pathogenesis.}, number={11}, journal={VIRUSES-BASEL}, author={Hicks, Julie and Liu, Hsiao-Ching}, year={2013}, month={Nov}, pages={2659–2678} }
 @article{goher_hicks_liu_2013, title={The Interplay Between MDV and HVT Affects Viral miRNA Expression}, volume={57}, ISSN={["1938-4351"]}, DOI={10.1637/10440-110112-reg.1}, abstractNote={SUMMARY.  It is well established that herpesviruses encode numerous microRNAs (miRNAs) and that these virally encoded small RNAs play multiple roles in infection. The present study was undertaken to determine how co-infection of a pathogenic MDV serotype one (MDV1) strain (MD5) and a vaccine strain (herpesvirus of turkeys [HVT]) alters viral miRNA expression in vivo. We first used small RNA deep sequencing to identify MDV1-encoded miRNAs that are expressed in tumorigenic spleens of MDV1-infected birds. The expression patterns of these miRNAs were then further assessed at an early time point (7 days postinfection [dpi]) and a late time point (42 dpi) in birds with and without HVT vaccination using real-time PCR (RT-PCR). Additionally, the effect of MDV1 co-infection on HVT-encoded miRNAs was determined using RT-PCR. A diverse population of miRNAs was expressed in MDV-induced tumorigenic spleens at 42 dpi, with 18 of the 26 known mature miRNAs represented. Of these, both mdv1-miR-M4-5p and mdv1-miR-M2-3p were the most highly expressed miRNAs. RT-PCR analysis further revealed that nine MDV miRNAs were differentially expressed between 7 dpi and 42 dpi infected spleens. At 7 dpi, three miRNAs were differentially expressed between the spleens of birds co-infected with HVT and MD5 compared with birds singly infected with MD5, whereas at 42 dpi, nine miRNAs were differentially expressed. At 7 dpi, the expression of seven HVT-encoded miRNAs was affected in the spleens of co-infected birds compared with birds only receiving the HVT vaccine. At 42 dpi, six HVT-encoded miRNAs were differentially expressed between the two groups. Target prediction analysis suggests that these differentially expressed viral miRNAs are involved in regulating several cellular processes, including cell proliferation and the adaptive immune response. RESUMEN.  La interacción entre el virus de Marek y el herpesvirus de los pavos afecta a la expresión de micro ARN viral. Está bien establecido que los herpesvirus codifican numerosos micro ARN (con las siglas en inglés miRNAs) y que estas pequeñas moléculas de ARN codificadas viralmente juegan múltiples papeles en la infección. El presente estudio se realizó para determinar como la co-infección entre una cepa patógena (MD5) del virus de Marek serotipo 1 (MDV1) y una cepa vacunal (herpesvirus de los pavos [HVT]) altera la expresión de los genes micro ARN viral in vivo. Se utilizó por primera vez la secuenciación profunda de moléculas pequeñas de ARN para identificar micro ARN codificado por el virus de Marek serotipo 1 que se expresan en los bazos con tumores en las aves infectadas por el virus de Marek 1. Los patrones de expresión de micro ARN fueron valorados mediante PCR en tiempo real (RT-PCR), de manera temprana (7 días después de la infección) y tardíamente (42 días después de la infección) en las aves con y sin vacunación con el herpesvirus de los pavos. Además se determinó el efecto de la co-infección con el virus de Marek serotipo 1 sobre el micro ARN codificado por el herpesvirus de los pavos mediante PCR en tiempo real. Se expresó una población diversa de micro ARN en los bazos con tumores inducidos por el virus de Marek a los 42 días después de la infección, con 18 micro ARNs maduros representados de los 26. De éstos, tanto el mdv1-miR-M4-5p y el mdv1-miR-M2-3p fueron los micro ARN más expresados. El análisis por PCR en tiempo real reveló que nueve micro ARN del virus de Marek se expresan diferencialmente entre 7 y 42 días después de la infección en los bazos infectados. A los siete días después de la infección, tres micro ARN fueron expresados diferencialmente en los bazos de las aves co-infectadas con el herpesvirus de los pavos y la cepa MD5 en comparación con las aves infectadas con el virus MD5 por separado, mientras que a los 42 días después de la infección, nueve micro ARNs fueron expresados diferencialmente. A los siete días después, la expresión de siete micro ARNs codificados por el herpesvirus de los pavos se vio afectada en los bazos de las aves co-infectadas en comparación con las aves que sólo recibieron la vacuna con el herpesvirus de los pavos. A los 42 días después de la infección, seis micro ARNs codificados por el herpesvirus de los pavos fueron expresados diferencialmente entre los dos grupos. El análisis de predicción de moléculas blanco sugiere que estos micro ARNs virales expresados diferencialmente están involucrados en la regulación de varios procesos celulares, incluyendo la proliferación celular y la respuesta inmune adaptativa.}, number={2}, journal={AVIAN DISEASES}, author={Goher, Mohamed and Hicks, Julie A. and Liu, Hsiao-Ching}, year={2013}, month={Jun}, pages={372–379} }
 @article{trakooljul_hicks_liu_2012, title={Characterization of miR-10a mediated gene regulation in avian splenocytes}, volume={500}, ISSN={["1879-0038"]}, DOI={10.1016/j.gene.2012.03.028}, abstractNote={It is well established that microRNAs (miRNAs) are an important class of post-transcriptional regulators of gene expression. Although numerous miRNA expression profiles have been generated for many eukaryotic organisms, little is known about the specific functions of individual miRNAs in regulating gene expression. We previously reported that the miRNA, miR-10a, is highly expressed during spleen development in embryonic chicks. In this current study we have identified genes and potential pathways that are both directly and indirectly influenced by miR-10a expression. To achieve this goal, miRNA Real-Time (RT) PCR analysis was first utilized to examine miR-10a expression across tissues during both embryonic and post-hatch chick development. Next, microarray analysis was employed to determine alterations in global gene expression associated with miR-10a in embryonic chick splenocytes subjected to an in vitro miR-10a inhibitor treatment. Finally the miRNA target prediction algorithm miRanda was used to predict potential chicken genes directly targeted by miR-10a. A select group of potential miR-10a target genes was validated using an RCAS-miRNA expression based luciferase assay. Our results indicate that miR-10a is highly expressed in the avian spleen, lung, kidneys, and fat tissues. Functional analysis suggests that miR-10a is involved in regulating gene expression in pathways associated with Ras signaling, intracellular trafficking, and development of immune functions. Additionally, we confirmed that chicken HOXA1 is a miR-10a target gene, suggesting a conserved role for miR-10a in the regulation of hematopoiesis across vertebrates.}, number={1}, journal={GENE}, author={Trakooljul, Nares and Hicks, Julie A. and Liu, Hsiao-Ching}, year={2012}, month={May}, pages={107–114} }
 @article{trakooljul_hicks_liu_2012, title={Characterization of miR-10a mediated gene regulation in avian splenocytes (vol 500, pg 107, 2012)}, volume={504}, ISSN={["0378-1119"]}, DOI={10.1016/j.gene.2012.05.051}, number={2}, journal={GENE}, author={Trakooljul, Nares and Hicks, Julie A. and Liu, Hsiao-Ching}, year={2012}, month={Aug}, pages={315–316} }
 @article{hicks_trakooljul_liu_2010, title={Discovery of chicken microRNAs associated with lipogenesis and cell proliferation}, volume={41}, ISSN={["1531-2267"]}, DOI={10.1152/physiolgenomics.00156.2009}, abstractNote={The primary function of microRNA (miRNA, a class of small regulatory RNA) is to regulate gene expression. Studies of miRNA in mammals suggest that many liver-associated miRNAs are expressed, with a wide range of functions. To characterize miRNA expressed in the avian liver, we created two small RNA libraries from embryonic chick livers at embryonic day (E)15 and E20, a time at which the embryo begins to grow rapidly and so its energy demands increase. It is of interest to examine miRNAs expressed at these developmental stages because miRNAs involved in regulating metabolic pathways and cell proliferation are likely to be identified. The small RNA libraries were sequenced with 454 Life Sciences deep sequencing. Of the 49,937 sequences obtained, 29,390 represented known chicken miRNAs and 1,233 reads represented homologous miRNAs that have not been previously identified in chickens. Additionally, 1,032 reads represented 17 potential novel miRNAs not previously identified in any species. To further investigate the possible functions of avian liver miRNAs we identified the potential targets of two differentially expressed novel miRNAs, nc-miR-5 and nc-miR-33. These two miRNAs were predicted to target metabolic genes, including the lipid metabolism-associated gene fatty acid synthase ( FAS), and genes involved in the control of cell proliferation, such as peroxisome proliferator-activated binding protein ( Pparbp) and bone morphogenetic protein 4 ( BMP4). Our findings demonstrate that a diverse group of miRNAs are expressed in developing avian livers. In addition, some of the identified miRNAs have been suggested to play a key role(s) in regulating metabolic pathways.}, number={2}, journal={PHYSIOLOGICAL GENOMICS}, author={Hicks, Julie A. and Trakooljul, Nares and Liu, Hsiao-Ching}, year={2010}, month={Apr}, pages={185–193} }
 @article{trakooljul_hicks_liu_2010, title={Identification of target genes and pathways associated with chicken microRNA miR-143}, volume={41}, ISSN={["1365-2052"]}, DOI={10.1111/j.1365-2052.2009.02015.x}, abstractNote={Summary}, number={4}, journal={ANIMAL GENETICS}, author={Trakooljul, N. and Hicks, J. A. and Liu, H. -C.}, year={2010}, month={Aug}, pages={357–364} }
 @article{hansen_trakooljul_liu_hicks_ashwell_spears_2010, title={Proteins involved in iron metabolism in beef cattle are affected by copper deficiency in combination with high dietary manganese, but not by copper deficiency alone}, volume={88}, ISSN={["1525-3163"]}, DOI={10.2527/jas.2009-1846}, abstractNote={A 493-d study was conducted to determine the impact of a severe, long-term Cu deficiency on Fe metabolism in beef cattle. Twenty-one Angus calves were born to cows receiving one of the following treatments: 1) adequate Cu (+Cu), 2) Cu deficient (-Cu), and 3) Cu deficient plus high Mn (-Cu+Mn). Copper deficiency was induced through the addition of 2 mg of Mo/kg of DM. After weaning, calves remained on the same treatment as their dam through growing (basal diet analyzed 7 mg of Cu/kg of DM) and finishing (analyzed 4 mg of Cu/kg of DM) phases. Plasma Fe concentrations were positively correlated (P < 0.01; r = 0.49) with plasma Cu concentrations. Liver Fe concentrations were greater (P = 0.05) in -Cu vs. +Cu calves and further increased (P = 0.07) in -Cu+Mn vs. -Cu calves. There was a negative relationship (P < 0.01; r = -0.31) between liver Cu and Fe concentrations. This relationship is likely explained by less (P < 0.01) plasma ceruloplasmin activity in -Cu than +Cu calves. As determined by real-time reverse transcription-PCR, relative expression of hepatic hepcidin was significantly downregulated (>1.5 fold) in -Cu compared with +Cu calves (P = 0.03), and expression of hepatic ferroportin tended (P = 0.09) to be downregulated in -Cu vs. +Cu. In the duodenum, ferritin tended to be upregulated in -Cu. vs. +Cu calves (P < 0.06). No significant change (P > 0.2) due to Cu-deficiency was detected at the transcriptional level for either isoform of divalent metal transporter 1 (DMT1 mRNA with or without an iron responsive element; dmt1IRE and dmt1-nonIRE) in liver or intestine. Duodenal expression of hephaestin and ferroportin protein was not affected by dietary treatment (P > 0.20). However, duodenal expression of DMT1 protein was less (P = 0.04) in -Cu+Mn steers vs. -Cu steers. In summary, Cu deficiency alone did affect hepatic gene expression of hepcidin and ferroportin, but did not affect duodenal expression of proteins important in Fe metabolism. However, the addition of 500 mg of Mn/kg of DM to a diet low in Cu reduced duodenal expression of the Fe import protein DMT1.}, number={1}, journal={JOURNAL OF ANIMAL SCIENCE}, author={Hansen, S. L. and Trakooljul, N. and Liu, H. -C. S. and Hicks, J. A. and Ashwell, M. S. and Spears, J. W.}, year={2010}, month={Jan}, pages={275–283} }
 @article{hicks_tembhurne_liu_2009, title={Identification of microRNA in the developing chick immune organs}, volume={61}, ISSN={["1432-1211"]}, DOI={10.1007/s00251-009-0355-1}, abstractNote={MicroRNAs (miRNAs) are small (approximately 19-24 nt) noncoding RNAs that participate in posttranscriptionally regulating gene expression. MicroRNAs display very dynamic expression patterns with many being expressed in a temporal as well as a spatial manner. Immune genes have been shown to have a higher propensity for miRNA target sites compared to the rest of the genome, thus suggesting that miRNA are key regulators of the immune system. To better understand the involvement of miRNA in the immune system, a comprehensive profile of miRNA expression in the immune organs will be necessary. As a first step toward building such a profile, we pyrosequenced four small RNA libraries derived from the spleen and the bursa of Fabricius of embryonic chicks at days 15 and 20 of development. A total of 90,322 sequence reads were obtained, among which 44,387 reads represented known chicken miRNAs, 3,503 reads were not found in the Gallus gallus database but were homologs of miRBase miRNAs from other species, and 2,023 reads represented potentially novel chicken miRNAs that have not previously been identified. Many miRNAs identified in our work have been shown to be involved in regulating immune genes in other vertebrate species. For example, the miRNAs miR-221 and miR-222, which are known regulators of lymphocyte differentiation, were identified in our studies and appeared to be differentially expressed among the libraries. Overall, our results show that many of the identified miRNAs display dynamic expression patterns, suggesting that these miRNAs play diverse roles in the immune system.}, number={3}, journal={IMMUNOGENETICS}, author={Hicks, Julie A. and Tembhurne, Prabhakar A. and Liu, Hsiao-Ching}, year={2009}, month={Mar}, pages={231–240} }
 @article{hicks_tembhurne_liu_2008, title={MicroRNA Expression in Chicken Embryos}, volume={87}, ISSN={["1525-3171"]}, DOI={10.3382/ps.2008-00114}, abstractNote={MicroRNA (miRNA) are small single-stranded noncoding RNA that posttranscriptionally regulate gene expression. A major role of miRNA is the regulation of gene expression in developmental processes. In this study, we constructed a small RNA library from 11-d-old chick embryos and used this library to examine the miRNA expression profile of the embryos. This small RNA library was sequenced by using 454 Life Sciences pyrosequencing technology. A total of 10,466 sequences were obtained and annotated as either known chicken miRNA, miRNA that shared homology with other species, or novel miRNA. We identified the expression of 110 known chicken miRNA, 36 homologous chicken miRNA (previously unannotated in the chicken but conserved with miRNA from other species), and 14 novel chicken-specific miRNA not identified in any other species. We also demonstrated that some of the identified chicken embryonic miRNA are differentially expressed among the developing spleen, liver, or bursa. The current study demonstrates that a very diverse and dynamic set of miRNA is expressed in the embryonic chick at 11 d of incubation. The identification of miRNA present in the embryonic chicken will further aid in understanding the complexity of gene regulation during vertebrate development.}, number={11}, journal={POULTRY SCIENCE}, author={Hicks, J. A. and Tembhurne, P. and Liu, H. -C.}, year={2008}, month={Nov}, pages={2335–2343} }
 @article{liu_hicks_2007, title={Using proteomics to understand avian systems biology and infectious disease}, volume={86}, ISSN={["1525-3171"]}, DOI={10.1093/ps/86.7.1523}, abstractNote={The proteome is defined as the protein complement to the genome. Proteomics is the study of the proteome. Several techniques are frequently used in proteomics; these include 2-hybrid systems, 2-dimensional gel electrophoresis, and mass spectrometry. Systems biology is a scientific approach that takes into account the complex relationships among and between genes and proteins and determines how all of these interactions come together to form a functional organism. Proteomic tools can simultaneously probe the properties of numerous proteins and thus are a great aid to the emerging field of systems biology, in which the functional interactions of numerous proteins are studied instead of studying individual proteins as isolated entities. In the field of avian biology, proteomics has been used to study everything from the development and function of organs and systems to the interactions of infectious agents and the altered states that they induce in their hosts.}, number={7}, journal={POULTRY SCIENCE}, author={Liu, H.-C. S. and Hicks, J. A.}, year={2007}, month={Jul}, pages={1523–1529} }