@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{brady_long_liu_porter_2021, title={Characterization of hypothalamo-pituitary-thyroid axis gene expression in the hypothalamus, pituitary gland, and ovarian follicles of turkey hens during the preovulatory surge and in hens with low and high egg production}, volume={100}, ISSN={["1525-3171"]}, DOI={10.1016/j.psj.2020.12.026}, abstractNote={Dysregulation of the preovulatory surge (PS) leads to lowered egg production. The hypothalamo–pituitary–thyroid (HPT) axis has been shown to influence plasma progesterone levels and follicle ovulation. The presence of thyroid hormone receptors (THR) in the reproductive axis suggests possible effects of thyroid hormone. To further understand the potential role of thyroid hormone on the PS, HPT axis plasma hormone concentrations and gene expression were characterized surrounding the PS in average egg producing hens (AEPH), low egg producing hens (LEPH), and high egg producing hens (HEPH) (n = 3 hens/group). Data were analyzed using the mixed models procedure of SAS, with significance indicated at P < 0.05. Average egg producing hens and HEPH displayed lower levels of triiodothyronine (T3) and higher levels of thyroxine (T4) inside of the PS, whereas LEPH showed inverse T3 and T4 levels relative to the PS. Expression of mRNA for hypothalamic thyrotropin-releasing hormone (TRH), pituitary thyrotropin (TSHB), and the main thyroid hormone metabolism enzyme (DIO2) were downregulated during the PS in AEPH and HEPH. Low egg producing hens displayed higher expression of mRNA for hypothalamic TRH as well as pituitary TSHB and DIO2 compared with HEPH. Average egg producing hens expression of THR mRNAs was upregulated during the PS in the hypothalamus but downregulated in the pituitary. High egg producing hens showed decreased expression of THR mRNAs in both the hypothalamus and pituitary when compared with LEPH. In ovarian follicles, THR mRNAs were more prevalent in the thecal layer of the follicle wall compared with the granulosa layer, and expression tended to decrease with follicle maturity. Minimal differences in follicular THR expression were seen between LEPH and HEPH, indicating that THR expression is unlikely to be responsible for steroid hormone production differences occurring between LEPH and HEPH. Generally, downregulation of the HPT axis was seen during the PS in AEPH and HEPH, whereas upregulation of the HPT axis was seen in LEPH. Further studies will be required to clarify the role of the HPT axis in the regulation of ovulation and egg production rates in turkey hens.}, number={4}, journal={POULTRY SCIENCE}, author={Brady, Kristen and Long, Julie A. and Liu, Hsiao-Ching and Porter, Tom E.}, year={2021}, month={Apr} }
 @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_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{zhu_lu_li_zhang_ji_lin_liu_odle_luo_2018, title={Effect of dietary manganese on antioxidant status and expressions of heat shock proteins and factors in tissues of laying broiler breeders under normal and high environmental temperatures (Retraction of Vol 114, Pg 1965, 2015)}, volume={119}, ISSN={["1475-2662"]}, url={http://www.scopus.com/inward/record.url?eid=2-s2.0-85041556249&partnerID=MN8TOARS}, DOI={10.1017/s0007114517003312}, abstractNote={Effect of dietary manganese on antioxidant status and expressions of heat shock proteins and factors in tissues of laying broiler breeders under normal and high environmental temperatures – RETRACTION - Volume 119 Issue 1}, number={1}, journal={BRITISH JOURNAL OF NUTRITION}, publisher={Cambridge University Press (CUP)}, author={Zhu, Yong-Wen and Lu, Lin and Li, Wen-Xiang and Zhang, Li-Yang and Ji, Cheng and Lin, Xi and Liu, Hsiao-Ching and Odle, Jack and Luo, Xu-Gang}, year={2018}, month={Jan}, pages={117–117} }
 @article{hicks_yoo_liu_2018, title={Interaction of porcine reproductive and respiratory syndrome virus major envelope proteins GP5 and M with the cellular protein Snapin}, volume={249}, ISSN={["1872-7492"]}, DOI={10.1016/j.virusres.2018.03.010}, abstractNote={Porcine reproductive and respiratory syndrome (PRRS) is characterized by abortions in pregnant sows and respiratory disease, particularly in young pigs. The causative agent is porcine reproductive and respiratory syndrome virus (PRRSV), a member of the arterivirus family. GP5 and M are the major envelope proteins encoded by PRRSV. To further characterize these two viral proteins, a yeast two-hybrid approach was utilized to identify interacting partners of PRRSV GP5 and M proteins. Interacting partners of PRRSV GP5 and M were identified using a porcine macrophage cDNA library yeast two-hybrid screen. Subsequently, the interactions between PRRSV GP5/M and the cellular protein Snapin were mapped using truncated versions of the GP5 and M proteins in a yeast two-hybrid assay to localize the interactions. The Snapin gene from the African green monkey kidney cell line MARC-145, which is permissive to PRRSV, was cloned and sequenced, and compared to porcine Snapin. Cellular Snapin expression was reduced in PRRSV-infected cells via Snapin-specific siRNA targeting. Here we show that the cellular Snap-Associated Protein (Snapin), an accessory protein of the SNARE membrane fusion network and also a member of the BLOC-1 complex, specifically interacts with GP5 and M. Inhibition of Snapin expression via siRNA targeting of Snapin results in the reduction of PRRSV replication. The PRRSV GP5 and M proteins are known to form a heterodimeric complex which is important for viral structure and infectivity, and both PRRSV proteins can interact with cellular Snapin. Snapin knock-down suggests these interactions could be important in the PRRSV lifecycle. GP5 and M proteins may interact with Snapin to exploit its roles in intracellular transport and membrane fusion.}, journal={VIRUS RESEARCH}, author={Hicks, Julie A. and Yoo, Dongwan and Liu, Hsiao-Ching}, year={2018}, month={Apr}, pages={85–92} }
 @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{zhu_li_lu_zhang_ji_lin_liu_odle_luo_2017, title={Impact of maternal heat stress in conjunction with dietary zinc supplementation on hatchability, embryonic development, and growth performance in offspring broilers}, volume={96}, ISSN={0032-5791}, url={http://dx.doi.org/10.3382/ps/pew481}, DOI={10.3382/ps/pew481}, abstractNote={&NA; The aim of this study was to investigate whether maternal dietary supplementations with different zinc (Zn) sources could reduce the deleterious effect of maternal heat stress on hatchability performance and progeny growth performance. A completely randomized design (n = 6) with 2 maternal environmental temperatures [normal 21 ± 1°C (NT) vs. high 32 ± 1°C (HT)] × 3 maternal dietary supplemental Zn levels [Zn‐unsupplemented control diet (CON), the control diet + 110 mg of Zn/kg of diet as either inorganic ZnSO4 (iZn) or organic Zn with a moderate chelation strength (oZn)] was used. HT decreased (P < 0.05) fertility, hatchability, chick hatch weight, and embryonic survival. HT also decreased (P ≤ 0.05) progeny BW, ADG, and ADFI at one to 21, 22 to 28, and 29 to 42 d of age as well as breast muscle ratio and plasma aspartate aminotransferase and creatine kinase activities at 42 d of age. Maternal dietary Zn supplementation with either iZn or oZn increased (P < 0.004) Zn contents in yolk and liver, non‐weak chick ratio, as well as progeny BW, ADFI, and survivability at one to 21 d of age. Notably, the addition of oZn increased (P < 0.05) hatchability and progeny thigh meat quality by reducing b* value. The progeny ADG at one to 21 d and 22 to 28 d of age and BW at 28 d of age from maternal NT were not affected (P > 0.46) by maternal dietary Zn supplementation, but the above 3 indices from HT‐iZn (P < 0.05) and HT‐oZn (P < 0.003) were higher than those from HT‐CON. Our results indicate that maternal heat stress impairs hatching performance, embryonic development, and progeny growth performance, inducing metabolic changes, while supplementation of Zn in maternal diets regardless of Zn sources improved hatch chick quality and survivability of offspring and alleviated the negative effect of maternal heat stress on growth performance of offspring during the starter period. In addition, maternal dietary supplementation with the organic Zn improved hatchability and progeny meat quality.}, number={7}, journal={Poultry Science}, publisher={Elsevier BV}, author={Zhu, Y.W. and Li, W.X. and Lu, L. and Zhang, L.Y. and Ji, C. and Lin, X. and Liu, H.C. and Odle, J. and Luo, X.G.}, year={2017}, month={Jul}, pages={2351–2359} }
 @article{zhu_lu_liao_li_zhang_ji_lin_liu_odle_luo_et al._2017, title={Maternal dietary manganese protects chick embryos against maternal heat stress via epigenetic-activated antioxidant and anti-apoptotic abilities}, volume={8}, ISSN={1949-2553}, url={http://dx.doi.org/10.18632/oncotarget.20804}, DOI={10.18632/oncotarget.20804}, abstractNote={Maternal heat stress induced the aberrant epigenetic patterns resulting in the abnormal development of offspring embryos. It is unclear whether maternal dietary manganese supplementation as an epigenetic modifier could protect the chick embryonic development against maternal heat stress via epigenetic mechanisms. To test this hypothesis using an avian model, a completely randomized design with a 2 (maternal normal and high environmental temperatures of 21 and 32°C, respectively) × 3 (maternal dietary manganese sources, the control diet without manganese supplementation and the control diet + 120 mg/kg as either inorganic or organic manganese) factorial arrangement was adopted. Maternal environmental hyperthermia increased mRNA expressions of heat shock proteins 90 and 70, cyclin-dependent kinase 6 and B-cell CLL/lymphoma 2-associated X protein displaying oxidative damage and apoptosis in the embryonic heart. Maternal environmental hyperthermia impaired the embryonic development associated with the alteration of epigenetic status, as evidenced by global DNA hypomethylation and histone 3 lysine 9 hypoacetylation in the embryonic heart. Maternal dietary manganese supplementation increased the heart anti-apoptotic gene B-cell CLL/lymphoma 2 expressions under maternal environmental hyperthermia and manganese superoxide dismutase enzyme activity in the embryonic heart. Maternal dietary organic Mn supplementation effectively eliminated the impairment of maternal environmental hyperthermia on the embryonic development. Maternal dietary manganese supplementation up-regulated manganese superoxide dismutase mRNA expression by reducing DNA methylation and increasing histone 3 lysine 9 acetylation of its promoter. It is suggested that maternal dietary manganese addition could protect the chick embryonic development against maternal heat stress via enhancing epigenetic-activated antioxidant and anti-apoptotic abilities.}, number={52}, journal={Oncotarget}, publisher={Impact Journals, LLC}, author={Zhu, Y. W. and Lu, L. and Liao, X. D. and Li, W. X. and Zhang, L. Y. and Ji, C. and Lin, X. and Liu, H. C. and Odle, J. and Luo, X. G. and et al.}, year={2017}, month={Sep}, pages={89665–89680} }
 @article{zhu_liao_lu_li_zhang_ji_lin_liu_odle_luo_et al._2017, title={Maternal dietary zinc supplementation enhances the epigenetic-activated antioxidant ability of chick embryos from maternal normal and high temperatures}, volume={8}, ISSN={1949-2553}, url={http://dx.doi.org/10.18632/oncotarget.15057}, DOI={10.18632/oncotarget.15057}, abstractNote={The role of maternal dietary zinc supplementation in protecting the embryos from maternal hyperthermia-induced negative effects via epigenetic mechanisms was examined using an avian model (Gallus gallus). Broiler breeder hens were exposed to two maternal temperatures (21°C and 32°C) × three maternal dietary zinc treatments (zinc-unsupplemented control diet, the control diet + 110 mg zinc/kg inorganic or organic zinc) for 8 weeks. Maternal hyperthermia increased the embryonic mortality and induced oxidative damage evidenced by the elevated mRNA expressions of heat shock protein genes. Maternal dietary zinc deficiency damaged the embryonic development associated with the global DNA hypomethylation and histone 3 lysine 9 hyperacetylation in the embryonic liver. Supplementation of zinc in maternal diets effectively eliminated the embryonic mortality induced by maternal hyperthermia and enhanced antioxidant ability with the increased mRNA and protein expressions of metallothionein IV in the embryonic liver. The increased metallothionein IV mRNA expression was due to the reduced DNA methylation and increased histone 3 lysine 9 acetylation of the metallothionein IV promoter regardless of zinc source. These data demonstrate that maternal dietary zinc addition as an epigenetic modifier could protect the offspring embryonic development against maternal heat stress via enhancing the epigenetic-activated antioxidant ability.}, number={12}, journal={Oncotarget}, publisher={Impact Journals, LLC}, author={Zhu, Y. W. and Liao, X. D. and Lu, L. and Li, W. X. and Zhang, L. Y. and Ji, C. and Lin, X. and Liu, H. C. and Odle, J. and Luo, X. and et al.}, year={2017}, month={Feb}, pages={19814–19824} }
 @article{zhu_lu_li_zhang_ji_lin_liu_odle_luo_2016, title={Effect of dietary manganese on antioxidant status and expressions of heat shock proteins and factors in tissues of laying broiler breeders under normal and high environmental temperatures}, volume={116}, ISSN={0007-1145 1475-2662}, url={http://dx.doi.org/10.1017/S0007114516003822}, DOI={10.1017/s0007114516003822}, abstractNote={Abstract}, number={11}, journal={British Journal of Nutrition}, publisher={Cambridge University Press (CUP)}, author={Zhu, Yong-Wen and Lu, Lin and Li, Wen-Xiang and Zhang, Li-Yang and Ji, Cheng and Lin, Xi and Liu, Hsiao-Ching and Odle, Jack and Luo, Xu-Gang}, year={2016}, month={Nov}, pages={1851–1860} }
 @article{zhang_huang_yang_gao_liu_tang_feng_2016, title={MicroRNA-30c Modulates Type I IFN Responses To Facilitate Porcine Reproductive and Respiratory Syndrome Virus Infection by Targeting JAK1}, volume={196}, ISSN={["1550-6606"]}, DOI={10.4049/jimmunol.1502006}, abstractNote={Abstract}, number={5}, journal={JOURNAL OF IMMUNOLOGY}, author={Zhang, Qiong and Huang, Chen and Yang, Qian and Gao, Li and Liu, Hsiao-Ching and Tang, Jun and Feng, Wen-hai}, year={2016}, month={Mar}, pages={2272–2282} }
 @article{zhu_lu_li_zhang_ji_lin_liu_odle_luo_2015, title={Effect of dietary manganese on antioxidant status and expression levels of heat-shock proteins and factors in tissues of laying broiler breeders under normal and high environmental temperatures (Retracted article. See vol. 119, pg. 117, 2018)}, volume={114}, ISSN={["1475-2662"]}, url={http://www.scopus.com/inward/record.url?eid=2-s2.0-84949319502&partnerID=MN8TOARS}, DOI={10.1017/s0007114515003803}, abstractNote={Abstract}, number={12}, journal={BRITISH JOURNAL OF NUTRITION}, publisher={Cambridge University Press (CUP)}, author={Zhu, Yong-Wen and Lu, Lin and Li, Wen-Xiang and Zhang, Li-Yang and Ji, Cheng and Lin, Xi and Liu, Hsiao-Ching and Odle, Jack and Luo, Xu-Gang}, year={2015}, month={Dec}, pages={1965–1974} }
 @article{xie_tang_lu_zhang_lin_liu_odle_luo_2015, title={Effects of acute and chronic heat stress on plasma metabolites, hormones and oxidant status in restrictedly fed broiler breeders}, volume={94}, ISSN={0032-5791}, url={http://dx.doi.org/10.3382/ps/pev105}, DOI={10.3382/ps/pev105}, abstractNote={Heat tolerance can be improved by feed restriction in broiler chickens. It is unknown whether the same is true for broiler breeders, which are restrictedly fed. Therefore, the current study was conducted to study the effects of heat stress on plasma metabolites, hormones, and oxidative status of restricted fed broiler breeders with special emphases on the temperature and latency of heat exposure. In trial 1, 12 broiler breeders were kept either in a thermoneutral chamber (21°C, control, n = 6) or in a chamber with a step-wise increased environmental temperature from 21 to 33°C (21, 25, 29, 33°C, heat-stressed, n = 6). Changes in plasma total cholesterol, glucose, and triiodothyronine (T3) were closely related to the environmental temperature. When the temperature reached 29°C, plasma T3 (P < 0.05) was significantly decreased in acute heat-stressed birds, whereas plasma glucose (P < 0.001) and cholesterol (P = 0.002) increased only when the temperature reached 33°C. Plasma triglyceride (P = 0.026) and creatine kinase (CK, P = 0.018) were lower in heat-stressed birds than controls regardless of the temperatures applied. In Trial 2, 24 broiler breeders were divided into 2 groups and raised under 21°C and 32°C for 8 weeks, respectively. Total cholesterol was increased in chronic heat-stressed broiler breeders after 4 weeks. Plasma lactate dehydrogenase (LDH, P = 0.047) and glutamic-oxaloacetic transaminase (GOT, P = 0.036) was up-regulated after 6 weeks of thermal treatment, whereas plasma CK (P = 0.009) was increased at the end of thermal treatment. Plasma malonaldehyde, protein carbonyl content, activity of total superoxide dismutase (SOD), and corticosterone content were not altered after acute and prolonged heat challenges. Taken together, acute heat stress primarily resulted in disturbance of plasma metabolites, whereas chronic heat stress caused tissue damage reflected by increased plasma LDA, GOT, and CK. During acute heat stress, plasma metabolites were minimally disturbed in broiler breeders until the environmental temperature reached 33°C.}, number={7}, journal={Poultry Science}, publisher={Elsevier BV}, author={Xie, Jingjing and Tang, Li and Lu, Lin and Zhang, Liyang and Lin, Xi and Liu, Hsiao-Ching and Odle, Jack and Luo, Xugang}, year={2015}, month={Jul}, pages={1635–1644} }
 @article{zhu_xie_li_lu_zhang_ji_lin_liu_odle_luo_2015, title={Effects of environmental temperature and dietary manganese on egg production performance, egg quality, and some plasma biochemical traits of broiler breeders}, volume={93}, ISSN={0021-8812 1525-3163}, url={http://dx.doi.org/10.2527/jas.2015-8956}, DOI={10.2527/jas.2015-8956}, abstractNote={An experiment was conducted to investigate the effects of environmental temperature and dietary Mn on egg production performance, egg quality, and some plasma biochemical traits of broiler breeders. A completely randomized factorial design involved 2 environmental temperatures (a normal temperature, 21 ± 1°C, and a high temperature, 32 ± 1°C) × 3 dietary Mn treatments (a Mn-unsupplemented corn–soybean meal basal diet or the basal diet supplemented with 120 mg of Mn/kg of diet as either MnSO4·H2O or manganese proteinate). There were 6 treatments with 6 replicates (4 birds per replicate). High temperature decreased egg weight (P < 0.0001), laying rate (P < 0.0001), egg yield (P < 0.0001), feed intake (P < 0.0001), egg:feed ratio (P < 0.0001), eggshell strength (P < 0.05) and thickness (P < 0.0001), plasma triiodothyronine level (P < 0.05), and alkaline phosphatase activity (P < 0.04) whereas it increased rectal temperature (P < 0.0001); plasma malondialdehyde level (P < 0.02); and activities (P < 0.002) of lactic dehydrogenase, aspartate aminotransferase, and creatine kinase. Broiler breeders fed the diets supplemented with Mn regardless of source had greater (P < 0.05) eggshell strength and lower (P ≤ 0.05) plasma triiodothyronine level and protein carbonyl content than those fed the control diet. The broiler breeders fed the diet supplemented with the organic Mn had greater (P < 0.01) eggshell thickness than those fed the control diet. There were interactions (P < 0.05) between environmental temperature and dietary Mn in laying rate, egg yield, feed intake, and egg:feed ratio. Under normal temperature, dietary Mn did not affect the above 4 parameters; however, under high temperature, broiler breeders fed the diet supplemented with the organic Mn showed greater (P < 0.03) improvements in these 4 parameters than those fed the control diet. The results from this study indicated that high temperature significantly impaired egg production performance and eggshell quality and induced lipid peroxidation and tissue damage whereas dietary supplementation of either organic or inorganic Mn improved eggshell strength and thermotolerance and reduced protein oxidation and that the organic Mn could alleviate the negative effect of high temperature on egg production performance of broiler breeders at the period of 32 to 45 wk of age.}, number={7}, journal={Journal of Animal Science}, publisher={Oxford University Press (OUP)}, author={Zhu, Y. W. and Xie, J. J. and Li, W. X. and Lu, L. and Zhang, L. Y. and Ji, C. and Lin, X. and Liu, H. C. and Odle, J. and Luo, X. G.}, year={2015}, month={Jul}, pages={3431–3440} }
 @article{zhu_lu_li_zhang_ji_lin_liu_odle_luo_2015, title={Effects of maternal dietary manganese and incubation temperature on hatchability, antioxidant status, and expression of heat shock proteins in chick embryos}, volume={93}, ISSN={0021-8812 1525-3163}, url={http://dx.doi.org/10.2527/jas.2015-9610}, DOI={10.2527/jas.2015-9610}, abstractNote={To investigate whether supplementing manganese (Mn) to the maternal diet could reduce the deleterious effect of heat stress on the developing embryo, the hatchability, antioxidant status, and expression of heat shock proteins (HSP) were evaluated in chick embryos under normal and high incubation temperatures. A completely randomized design ( = 6) with 2 maternal dietary Mn treatments (unsupplemented control basal diet versus the basal diet + 120 mg Mn/kg as inorganic Mn) × 2 incubation temperatures (normal, 37.8°C, versus high, 39.0°C) was used. High incubation temperature did not affect ( > 0.19) hatchability and embryo mortality and development but did increase ( < 0.05) activities of heart manganese superoxide dismutase (MnSOD) and liver copper zinc superoxide dismutase and liver MnSOD mRNA and protein levels in embryos. High incubation temperature also decreased ( < 0.003) HSP70 protein level in the heart but had no effects ( > 0.07) in the liver of embryos. Maternal diet with Mn supplementation not only increased ( < 0.05) the hatchability and Mn content ( < 0.001) in the yolk and embryonic tissues and the activity of MnSOD in the heart ( < 0.004) as well as relative liver weight ( < 0.05) under normal incubation temperature but also decreased ( ≤ 0.05) embryo mortality and HSP90 mRNA level in the liver and heart of embryos. Furthermore, under high incubation temperature, maternal diet Mn supplementation increased ( < 0.002) MnSOD protein expression in the liver of embryos but had no effect ( > 0.43) under normal incubation temperature. These results indicated that high incubation temperature induced self-protective responses of chick embryos with a modification of antioxidant status and a depression of HSP70 protein level. Maternal dietary supplementation of Mn could improve the hatchability as well as antioxidant ability to protect against heat challenge in embryos during incubation.}, number={12}, journal={Journal of Animal Science}, publisher={Oxford University Press (OUP)}, author={Zhu, Y. W. and Lu, L. and Li, W. X. and Zhang, L. Y. and Ji, C. and Lin, X. and Liu, H. C. and Odle, J. and Luo, X. G.}, year={2015}, month={Dec}, pages={5725–5734} }
 @article{xie_tang_lu_zhang_xi_liu_odle_luo_2014, title={Differential expression of heat shock transcription factors and heat shock proteins after acute and chronic heat stress in laying chickens (Gallus gallus)}, volume={9}, ISSN={1932-6203}, url={http://dx.doi.org/10.1371/journal.pone.0102204}, DOI={10.1371/journal.pone.0102204}, abstractNote={Heat stress due to high environmental temperature negatively influences animal performances. To better understand the biological impact of heat stress, laying broiler breeder chickens were subjected either to acute (step-wisely increasing temperature from 21 to 35°C within 24 hours) or chronic (32°C for 8 weeks) high temperature exposure. High temperature challenges significantly elevated body temperature of experimental birds (P<0.05). However, oxidation status of lipid and protein and expression of heat shock transcription factors (HSFs) and heat shock proteins (HSPs) 70 and 90 were differently affected by acute and chronic treatment. Tissue-specific responses to thermal challenge were also found among heart, liver and muscle. In the heart, acute heat challenge affected lipid oxidation (P = 0.05) and gene expression of all 4 HSF gene expression was upregulated (P<0.05). During chronic heat treatment, the HSP 70 mRNA level was increased (P<0.05) and HSP 90 mRNA (P<0.05) was decreased. In the liver, oxidation of protein was alleviated during acute heat challenge (P<0.05), however, gene expression HSF2, 3 and 4 and HSP 70 were highly induced (P<0.05). HSP90 expression was increased by chronic thermal treatment (P<0.05). In the muscle, both types of heat stress increased protein oxidation, but HSFs and HSPs gene expression remained unaltered. Only tendencies to increase were observed in HSP 70 (P = 0.052) and 90 (P = 0.054) gene expression after acute heat stress. The differential expressions of HSF and HSP genes in different tissues of laying broiler breeder chickens suggested that anti-heat stress mechanisms might be provoked more profoundly in the heart, by which the muscle was least protected during heat stress. In addition to HSP, HSFs gene expression could be used as a marker during acute heat stress.}, number={7}, journal={PLoS One}, publisher={Public Library of Science (PLoS)}, author={Xie, J. J. and Tang, L. and Lu, L. and Zhang, L. Y. and Xi, L. and Liu, H-C and Odle, J. and Luo, X. G.}, editor={Cotterill, SueEditor}, year={2014}, pages={e102204} }
 @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{chien_blackburn_liu_goshe_2012, title={Proteomic and Phosphoproteomic Analysis of Chicken Embryo Fibroblasts Infected with Cell Culture-Attenuated and Vaccine Strains of Marek's Disease Virus}, volume={11}, ISSN={["1535-3907"]}, DOI={10.1021/pr300471y}, abstractNote={Vaccination is an effective strategy to reduce the loss of chickens in the poultry industry caused by Marek's Disease (MD), an avian lymphoproliferative disease. The vaccines currently used are from attenuated serotype 1 Marek's disease virus (MDV) or naturally nononcogenic MDV strains. To prepare for future immunity breaks, functional genomic and proteomic studies have been used to better understand the underlying mechanisms of MDV pathogenicity and the effects induced by the vaccine viruses. In this study, a combined approach of quantitative GeLC-MSE and qualitative ERLIC/IMAC/LC-MS/MS analysis were used to identify abundance changes of proteins and the variations of phosphorylation status resulting from the perturbations due to infection with an attenuated oncogenic virus strain (Md11/75C) and several nononcogenic virus strains (CVI988, FC126 and 301B) in vitro. Using this combined approach, several signal transduction pathways mapped by the identified proteins were found to be altered at both the level of protein abundance and phosphorylation. On the basis of this study, a kinase-dependent pathway to regulate phosphorylation of 4E-BP1 to modulate assembly of the protein translation initiation complex was revealed. The differences of 4E-BP1 phosphorylation patterns as well as the measured abundance changes among several other proteins that regulate host transcriptional and translational activities across the virus strains used in this study provide new insight for future functional and biochemical characterization of specific proteins involved in MDV pathogenesis.}, number={12}, journal={JOURNAL OF PROTEOME RESEARCH}, author={Chien, Ko-yi and Blackburn, Kevin and Liu, Hsiao-Ching and Goshe, Michael B.}, year={2012}, month={Dec}, pages={5663–5677} }
 @article{chien_liu_goshe_2011, title={Development and Application of a Phosphoproteomic Method Using Electrostatic Repulsion-Hydrophilic Interaction Chromatography (ERLIC), IMAC, and LC-MS/MS Analysis to Study Marek's Disease Virus Infection}, volume={10}, ISSN={["1535-3893"]}, DOI={10.1021/pr2002403}, abstractNote={Marek's Disease (MD) is an avian neoplastic disease caused by Marek's Disease Virus (MDV). The mechanism of virus transition between the lytic and latent cycle is still being investigated; however, post-translational modifications, especially phosphorylation, have been thought to play an important role. Previously, our group has used strong cation exchange chromatography in conjunction with reversed-phase liquid chromatography-tandem mass spectrometry (LC-MS/MS) to study the changes in global proteomic expression upon MDV infection (Ramaroson , M. F.; Ruby, J.; Goshe, M. B.; Liu , H.-C. S. J. Proteome Res. 2008, 7, 4346-4358). Here, we extend our study by developing an effective separation and enrichment approach to investigate the changes occurring in the phosphoproteome using electrostatic repulsion-hydrophilic interaction chromatography (ERLIC) to fractionate peptides from chicken embryo fibroblast (CEF) digests and incorporating a subsequent IMAC enrichment step to selectively target phosphorylated peptides for LC-MS/MS analysis. To monitor the multidimensional separation between mock- and MDV-infected CEF samples, a casein phosphopeptide mixture was used as an internal standard. With LC-MS/MS analysis alone, no CEF phosphopeptides were detected, while with ERLIC fractionation only 1.2% of all identified peptides were phosphorylated. However, the incorporation of IMAC enrichment with ERLIC fractionation provided a 50-fold increase in the percentage of identified phosphopeptides. Overall, a total of 581 unique phosphopeptides were identified (p < 0.05) with those of the MDV-infected CEF sample containing nearly twice as many as the mock-infected control of which 11% were unique to MDV proteins. The changes in the phosphoproteome are discussed including the role that microtubule-associated proteins may play in MDV infection mechanisms.}, number={9}, journal={JOURNAL OF PROTEOME RESEARCH}, author={Chien, Ko-yi and Liu, Hsiao-Ching and Goshe, Michael B.}, year={2011}, month={Sep}, pages={4041–4053} }
 @article{hansen_trakooljul_spears_liu_2010, title={Age and Dietary Iron Affect Expression of Genes Involved in Iron Acquisition and Homeostasis in Young Pigs}, volume={140}, ISSN={["1541-6100"]}, DOI={10.3945/jn.109.112722}, abstractNote={To investigate the effects of dietary iron (Fe) and age on Fe metabolism, we used 36 weaned barrows in a 2 x 3 design with 2 concentrations of dietary Fe [97 (control) and 797 (high Fe) mg Fe/kg dry matter] and 3 time points of tissue collection (after 21, 42, or 63 d on diets). Pigs were weighed and bled on d 0, 20, 41, and 62. High Fe reduced feed efficiency but did not affect pig weight gain. Blood hemoglobin concentrations and Fe concentrations of liver, intestine, and heart were increased by high dietary Fe on all days. Concentrations of liver and heart Fe increased with age. As determined by quantitative real-time PCR, hepatic expression of hepcidin (HAMP) in pigs given the high-Fe diet was 6.25-fold that of control pigs. In the intestine, relative mRNA levels of ferroportin, divalent metal transporter 1, and transferrin receptor were downregulated by high Fe. Expression of an alternative route of Fe absorption, solute carrier family 39 member 14 (SLC39A14), was downregulated in the intestine of pigs fed high dietary Fe. Additionally, duodenal mRNA level of certain genes including scavenger receptor class A, member 5, and frataxin decreased with age of the animal. Our findings indicate new roles in Fe metabolism for several mineral metabolism-associated genes and that some of these genes, such as SLC39A14, may be regulated in response to dietary Fe in pigs. Additionally, the expression of some genes examined in this study was affected by age, suggesting age dependency of Fe metabolism in pigs.}, number={2}, journal={JOURNAL OF NUTRITION}, author={Hansen, Stephanie L. and Trakooljul, Nares and Spears, Jerry W. and Liu, Hsiao-Ching}, year={2010}, month={Feb}, pages={271–277} }
 @misc{liu_hicks_trakooljul_zhao_2010, title={Current knowledge of microRNA characterization in agricultural animals}, volume={41}, ISSN={["1365-2052"]}, DOI={10.1111/j.1365-2052.2009.01995.x}, abstractNote={Summary}, number={3}, journal={ANIMAL GENETICS}, author={Liu, H. -C. and Hicks, J. A. and Trakooljul, N. and Zhao, S. -H.}, year={2010}, month={Jun}, pages={225–231} }
 @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} }
 @misc{yoo_song_sun_du_kim_liu_2010, title={Modulation of host cell responses and evasion strategies for porcine reproductive and respiratory syndrome virus}, volume={154}, ISSN={["1872-7492"]}, DOI={10.1016/j.virusres.2010.07.019}, abstractNote={The immune surveillance system protects host cells from viral infection, and viruses have evolved to escape this system for efficient proliferation in the host. Host cells produce cytokines and chemokines in response to viral infection, and among such effector molecules, type I interferons are the principal antiviral cytokines and therefore effective targets for viruses to disarm host surveillance. Porcine reproductive and respiratory syndrome virus (PRRSV) expresses proteins that circumvent the IFN response and other cellular processes, and to compensate the small coding capacity of PRRSV, these proteins are multifunctional. To date, at least four viral proteins have been identified and studied as viral antagonists of host defenses: N as a structural protein and three non-structural proteins, Nsp1 (Nsp1α and Nsp1β), Nsp2, and Nsp11. Among these, N and Nsp1 are nuclear-cytoplasmic proteins distributed in both the nucleus and cytoplasm of cells. Nsp1 and Nsp2 are viral proteases while Nsp11 is an endoribonuclease. This review describes the current understanding of the role of these proteins in modulating the host innate immune responses. Blocking against virus-mediated inhibition of the innate response may lead to the future development of effective vaccines. The understanding of viral mechanisms modulating the normal cellular processes will be a key to the design of an effective control strategy for PRRS.}, number={1-2}, journal={VIRUS RESEARCH}, author={Yoo, Dongwan and Song, Cheng and Sun, Yan and Du, Yijun and Kim, Oekyung and Liu, Hsiao-Ching}, year={2010}, month={Dec}, pages={48–60} }
 @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{song_lu_bienzle_liu_yoo_2009, title={Interaction of the porcine reproductive and respiratory syndrome virus nucleocapsid protein with the inhibitor of MyoD family-a domain-containing protein}, volume={390}, ISSN={["1437-4315"]}, DOI={10.1515/BC.2009.028}, abstractNote={Abstract}, number={3}, journal={BIOLOGICAL CHEMISTRY}, author={Song, Cheng and Lu, Ray and Bienzle, Dorothee and Liu, Hsiao-Ching and Yoo, Dongwan}, year={2009}, month={Mar}, pages={215–223} }
 @article{hansen_trakooljul_liu_moeser_spears_2009, title={Iron Transporters Are Differentially Regulated by Dietary Iron, and Modifications Are Associated with Changes in Manganese Metabolism in Young Pigs}, volume={139}, ISSN={["1541-6100"]}, DOI={10.3945/jn.109.105866}, abstractNote={To investigate the effects of dietary iron (Fe) on manganese (Mn) metabolism, 24 weaned pigs (21 d old) were blocked by litter and weight and randomly assigned to the following treatments: 1) no supplemental Fe [low Fe (L-Fe)]; 2) 100 mg supplemental Fe/kg [adequate Fe (A-Fe)]; and 3) 500 mg supplemental Fe/kg [high Fe (H-Fe)]. The basal diet was analyzed to contain 20 mg Fe/kg. Tissues were harvested after 32 d of feeding. Daily gain (least square means +/- SEM) was greater in A-Fe pigs (328.3 +/- 29.9 g/d) than in L-Fe pigs (224.0 +/- 11.2 g/d). Hemoglobin concentrations on d 32 were lower in L-Fe pigs (62 +/- 3.5 g/L) than in A-Fe pigs (128 +/- 5.6 g/L) and did not differ between pigs fed A-Fe and H-Fe (133 +/- 12.0 g/L). Liver Fe increased with increasing dietary Fe. Relative hepatic hepcidin expression was greater in pigs fed A-Fe and H-Fe than in those fed L-Fe. Relative expressions of duodenal divalent metal transporter 1 (DMT1) and solute carrier family 39 member 14 (ZIP14) were increased in L-Fe pigs compared with H-Fe pigs. Liver copper (Cu) was higher in L-Fe (0.56 +/- 0.04 mmol/kg) and H-Fe (0.58 +/- 0.04 mmol/kg) pigs than in A-Fe pigs (0.40 +/- 0.04 mmol/kg). Liver Mn was lower in H-Fe pigs (0.15 +/- 0.01 mmol/kg) than in A-Fe (0.23 +/- 0.02 mmol/kg) or L-Fe pigs (0.20 +/- 0.02 mmol/kg). Duodenal Mn concentrations were greater in L-Fe pigs than in A-Fe or H-Fe pigs. Fe deficiency in pigs increased gene expression of duodenal metal transporters (DMT1 and ZIP14) and supplementation with H-Fe reduced expression of DMT1 and ZIP14, which may have decreased absorption of Mn.}, number={8}, journal={JOURNAL OF NUTRITION}, author={Hansen, Stephanie L. and Trakooljul, Nares and Liu, Hsiao-Ching and Moeser, Adam J. and Spears, Jerry W.}, year={2009}, month={Aug}, pages={1474–1479} }
 @article{ramaroson_ruby_goshe_liu_2008, title={Changes in the Gallus gallus proteorne induced by Marek's disease virus}, volume={7}, ISSN={["1535-3893"]}, DOI={10.1021/pr800268h}, abstractNote={Marek's disease virus (MDV) is a highly oncogenic avian herpesvirus. We have used a modified MudPIT analysis to examine the effect of MDV infection on the chicken proteome. We identified 3561 unique nonphosphorylated peptides, representing 1460 chicken proteins, in a mock-infected sample versus 4240 unique nonphosphorylated peptides, representing 1676 proteins, in an MDV-infected sample. Of these unique peptides, 59.1% from the mock- and 49.6% from the MDV-infected samples were detected in both samples, and for the represented proteins, 69.1% from the mock- and 60.2% from the MDV-infected samples were common to both samples. In terms of phosphorylation, 357 and 506 phosphopeptides, representing 342 and 483 proteins, were detected in the mock- and MDV-infected samples, respectively. At the phosphopeptide level, 10.1% from the mock- and 7.1% from the MDV-infected samples overlapped, and for the represented phosphoproteins, 12.0% from the mock- and 8.5% from the MDV-infected samples were common to both samples. There were no significant differences in the hydropathicity values and number of transmembrane domains of the identified protein sets. Subtle differences were observed for subcellular localizations of the identified proteins. These results suggest that MDV infection may alter host cell biochemistry by perturbing the host's proteomic composition.}, number={10}, journal={JOURNAL OF PROTEOME RESEARCH}, author={Ramaroson, Mialy F. and Ruby, James and Goshe, Michael B. and Liu, Hsiao-Ching}, year={2008}, month={Oct}, pages={4346–4358} }
 @article{legleiter_spears_liu_2008, title={Copper deficiency in the young bovine results in dramatic decreases in brain copper concentration but does not alter brain prion protein biology}, volume={86}, ISSN={["0021-8812"]}, DOI={10.2527/jas.2007-0403}, abstractNote={An Mn for Cu substitution on cellular prion proteins (PrP(c)) in the brain that results in biochemical changes to PrP(c) has been implicated in the pathogenesis of transmissible spongiform encephalopathies. Recent research in the mature bovine does not support this theory. The present study tested this hypothesis by using progeny from gestating cows receiving Cu-deficient diets or Cu-deficient diets coupled with high dietary Mn. Copper-adequate cows (n = 39) were assigned randomly to 1 of 3 treatments: 1) control (adequate in Cu and Mn), 2) Cu deficient (-Cu), or 3) Cu deficient plus high dietary Mn (-Cu+Mn). Cows assigned to treatments -Cu and -Cu+Mn received no supplemental Cu and were supplemented with Mo to further induce Cu deficiency. The -Cu+Mn treatment also received 500 mg of supplemental Mn/kg of dietary DM. Calves were weaned at 180 d and maintained on the same treatments as their respective dams for 260 d. Copper-deficient calves (-Cu and -Cu+Mn) had decreased (P = 0.001) brain (obex) Cu and tended to have increased (P = 0.09) obex Mn relative to control calves. Obex Mn:Cu ratios were substantially increased (P < 0.001) in calves receiving -Cu and -Cu+Mn treatments compared with control calves and were greater (P < 0.001) in -Cu+Mn calves than in -Cu calves. Obex prion protein characteristics, including proteinase K degradability, superoxide dismutase (SOD)-like activity, and glycoform distributions, were largely unaffected. Obex tissue antioxidant capacity was not compromised by perturbations in brain metals, but Cu-deficient calves tended to have decreased (P = 0.06) Cu:Zn SOD activity and increased (P = 0.06) Mn SOD activity. Although obex Cu was decreased because of Cu deficiency and Mn increased because of exposure to high dietary Mn, the obex metal imbalance had minimal effects on PrP(c) functional characteristics in the calves.}, number={11}, journal={JOURNAL OF ANIMAL SCIENCE}, author={Legleiter, L. R. and Spears, J. W. and Liu, H. C.}, year={2008}, month={Nov}, pages={3069–3078} }
 @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{legleiter_liu_lloyd_hansen_fry_spears_2007, title={Exposure to low dietary copper or low copper coupled with high dietary manganese for one year does not alter brain prion protein characteristics in the mature cow}, volume={85}, ISSN={["0021-8812"]}, DOI={10.2527/jas.2007-0215}, abstractNote={It is now widely accepted that abnormal prion proteins are the likely causative agent in bovine spongiform encephalopathy. Cellular prion proteins (PrP(c)) bind Cu, which appears to be required to maintain functional characteristics of the protein. The replacement of Cu on PrP(c) with Mn has resulted in loss of function and increased protease resistance. Twelve mature cows were used to determine the effects of Cu deficiency, alone and coupled with high dietary Mn, on brain Cu and Mn concentrations and on PrP(c) functional characteristics. Copper-adequate cows were randomly assigned to treatments: 1) control (adequate in Cu and Mn), 2) Cu-deficient (-Cu), and 3) Cu-deficient plus high dietary Mn (-Cu+Mn). Cows assigned to treatments -Cu and -Cu+Mn received no supplemental Cu and were supplemented with Mo to further induce Cu deficiency. After 360 d, Cu-deficient cows (-Cu and -Cu+Mn) tended to have lesser concentrations of Cu (P = 0.09) in the obex region of the brain stem. Brain Mn tended (P = 0.09) to be greater in -Cu+Mn cattle compared with -Cu cattle. Western blots revealed that PrP(c) relative optical densities, proteinase K degradability, elution profiles, molecular weights, and glycoform distributions were not different among treatments. The concentration of PrP(c), as determined by ELISA, was similar across treatment groups. Brain tissue (obex) Mn superoxide dismutase activity was greatest (P = 0.04) in cattle receiving -Cu+Mn, whereas immunopurified PrP(c) had similar superoxide dismutase-like activities among treatments. Immunopurified PrP(c) had similar Cu concentrations across treatments, whereas Mn was undetectable. We concluded that Cu deficiency, coupled with excessive Mn intake, in the bovine may decrease brain Cu and increase brain Mn. Copper deficiency, alone or coupled with high dietary Mn, did not cause detectable alterations in PrP(c) functional characteristics.}, number={11}, journal={JOURNAL OF ANIMAL SCIENCE}, author={Legleiter, L. R. and Liu, H. C. and Lloyd, K. E. and Hansen, S. L. and Fry, R. S. and Spears, J. W.}, year={2007}, month={Nov}, pages={2895–2903} }
 @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} }
 @article{liu_soderblom_goshe_2006, title={A mass spectrometry-based proteomic approach to study Marek's Disease Virus gene expression}, volume={135}, ISSN={0166-0934}, url={http://dx.doi.org/10.1016/j.jviromet.2006.02.001}, DOI={10.1016/j.jviromet.2006.02.001}, abstractNote={Marek's Disease Virus (MDV) is an avian herpesvirus that causes a lymphoproliferative disorder in chickens. MDV transitions between a lytic phase in which new viruses are produced and a latent phase in which the virus lays dormant. The mechanism controlling this lytic-to-latent switch remains unclear. To better understand the lytic phase of MDV infection, a mass spectrometry-based strategy was developed to identify viral proteins and to qualitatively examine their abundance in lytically infected chicken embryo fibroblast (CEF) cells. A combination of strong cation exchange chromatography (SCXC) and microcapillary reversed-phase liquid chromatography-tandem mass spectrometry (murpLC/MS/MS) was used to resolve peptides from tryptic digests of MDV-infected CEF cell lysates. Peptides were identified by searching the tandem mass spectra against a protein database containing both MDV proteins and all currently available Gallus gallus proteins using the SEQUEST algorithm. A total of 427 MDV peptides, corresponding to 82 unique proteins, were identified, with 56 of them detected with at least two unique peptides. Overall, nearly 80% of all putative MDV proteins expressed in infected CEF cells were identified. We anticipate that this approach will be a viable method for determining how viral and host proteome changes occurring in Marek's Disease pathogenesis regulate the switch between the lytic and latent phases of the MDV life cycle.}, number={1}, journal={Journal of Virological Methods}, publisher={Elsevier BV}, author={Liu, Hsiao-Ching S. and Soderblom, Erik J. and Goshe, Michael B.}, year={2006}, month={Jul}, pages={66–75} }