@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{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{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} }
 @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{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} }