@article{oliveira_druyan_uni_ashwell_ferket_2013, title={Metabolic profiling of late-term turkey embryos by microarrays}, volume={92}, ISSN={["1525-3171"]}, DOI={10.3382/ps.2012-02354}, abstractNote={The last stages of embryonic development are crucial for turkeys as their metabolism shifts to accommodate posthatch survival and growth. To better understand the metabolic change that occurs during the perinatal period, focused microarray methodology was used to identify changes in the expression of key genes that control metabolism of turkey embryos from 20 d of incubation (E) until hatch (E28). Gene expression patterns were evaluated in liver, pectoral muscle, and hatching muscle and were associated with measured embryonic growth and tissue glycogen concentration. Within the studied period, the expression of 60 genes significantly changed in liver, 53 in pectoral muscle, and 51 in hatching muscle. Genes related to lipid metabolism (enoyl-CoA hydratase, 3-hydroxyacyl-CoA dehydrogenase, 3-hydroxymethylglutaryl-CoA reductase, acetyl-CoA carboxylase, lipoprotein lipase, and thyroxine deiodinase) had reduced expression between E22 and E26, corresponding to the period of expected limited oxygen supply. In contrast, genes related to opposing pathways in carbohydrate metabolism, such as glycolysis and gluconeogenesis (hexokinases, glucose-6 phosphatase, phosphofructokinases, glucose 1-6 phosphatase, pyruvate kinase, and phosphoenolpyruvate carboxykinase), or glycogenesis and glycogenolysis (glycogen synthase and glycogen phosphorylase) had rather static expression patterns between E22 and E26, indicating their enzymatic activity must be under posttranscriptional control. Metabolic survey by microarray methodology brings new insights into avian embryonic development and physiology.}, number={4}, journal={POULTRY SCIENCE}, author={Oliveira, J. E. and Druyan, S. and Uni, Z. and Ashwell, C. M. and Ferket, P. R.}, year={2013}, month={Apr}, pages={1011–1028} }
 @article{de oliveira_druyan_uni_ashwell_ferket_2009, title={Prehatch intestinal maturation of turkey embryos demonstrated through gene expression patterns}, volume={88}, ISSN={0032-5791}, url={http://dx.doi.org/10.3382/ps.2008-00548}, DOI={10.3382/ps.2008-00548}, abstractNote={Some of the challenges faced by neonatal turkeys include weakness, reduced feed intake, impaired growth, susceptibility to disease, and mortality. These symptoms may be due to depleted energy reserves after hatch and an immature digestive system unable to replenish energy reserves from consumed feed. To better understand enteric development in turkeys just before hatch, a new method was used to identify the patterns of intestinal gene expression by utilizing a focused microarray. The duodenums of 24 turkey embryos were sampled on embryonic day (E)20, E24, E26, and hatch (E28). The RNA populations of 96 chosen genes were measured at each time point, from which 81 significantly changed (P < 0.01). These genes were clustered by gene expression pattern similarity into 4 groups. The expression pattern of hormone receptors revealed that intestinal tissues may be less responsive to growth hormone, insulin, glucagon, and triiodothyronine during the last 48 h before hatch, when developmental emphasis switches from cell proliferation to functional maturation. Based on gene expression patterns, we concluded that at hatch, poults should have the capacity to 1) digest disaccharides but not oligopeptides, due to increased expression of sucrase-isomaltase but decreased expression of aminopeptidases and 2) absorb monosaccharides and small peptides due to high expression of sodium-glucose cotransporter-4 and peptide transporter-1.}, number={12}, journal={Poultry Science}, publisher={Elsevier BV}, author={de Oliveira, J.E. and Druyan, S. and Uni, Z. and Ashwell, C.M. and Ferket, P.R.}, year={2009}, month={Dec}, pages={2600–2609} }
 @article{druyan_oliveira_ashwell_2008, title={Focused Microarrays as a Method to Evaluate Subtle Changes in Gene Expression}, volume={87}, ISSN={["1525-3171"]}, DOI={10.3382/ps.2007-00513}, abstractNote={Recent studies using microarray technologies for the chicken have reported information regarding the effects of specific experimental treatments on gene expression levels often resulting in large gene lists and limitations on the statistical significance levels detected. In most cases, with these limitations, along with thresholds of +/-2-fold differences in expression levels, that are used to create these gene lists, much of the biological information may have been overlooked. In this study, a focused 70-mer oligonucleotide microarray was developed to address the apparent limits of detection and issues with multiple testing resulting from the use of microarrays that include only a single spot (probe) for each gene. Gene expression was assayed across the development of the chicken embryonic heart from d 7 to 20 of incubation. When using a mixed-model approach and ANOVA with Bonferroni correction for multiple testing, including replicates within the focused array significantly increased the sensitivity with which differences could be detected across sample groups, as compared with single-spot data. By incorporating replication into the focused array, 50 genes were detected as being differentially expressed in the embryonic heart across the time points sampled. This compares with only 7 genes detected as being differentially expressed when a more typical, less statistically stringent single-spot analysis is conducted. Based on our observations, the use of focused microarrays allows for the thorough investigation of gene expression patterns, with detection of significant changes in gene expression of +/-7%. This limit of detection is far superior to that of real-time PCR, which is able to detect significant changes in expression from +/-33 to 55%, depending on the specific application. The ability to detect small differences in expression will allow investigators to identify subtle effects that have perhaps been overlooked in many prior assays, including single-spot arrays. Subtle shifts in gene expression are exactly those that occur during embryonic development, nutritional manipulation, and the initial stages of disease before clinical signs appear.}, number={11}, journal={POULTRY SCIENCE}, author={Druyan, S. and Oliveira, J. E. and Ashwell, C. M.}, year={2008}, month={Nov}, pages={2418–2429} }
 @article{druyan_cahaner_ashwell_2007, title={The expression patterns of hypoxia-inducing factor subunit alpha-1, heme oxygenase, hypoxia upregulated protein 1, and cardiac troponin T during development of the chicken heart}, volume={86}, ISSN={["1525-3171"]}, DOI={10.3382/ps.2007-00152}, abstractNote={Oxygen is one of the critical determinants of appropriate embryonic and fetal development, including cardiogenesis. When the demand of tissues for oxygen exceeds oxygen supply, hypoxic conditions develop. In the developing embryo, hypoxia is associated with increased fetal mortality, cerebrovascular anomalies, cardiovascular dysfunction, and altered angiogenesis. Tissue hypoxia may elicit a broad range of responses, many of which are dependent upon hypoxia-inducible transcription factors. Three genes that are stimulated by hypoxia-hypoxia-inducing factor subunit alpha-1, heme oxygenase, hypoxia upregulated protein 1, and cardiac troponin T, which is responsible for binding tropomyosin to regulate calcium binding and contractility of heart muscle-were examined in the embryonic heart of the chicken to determine if expression patterns were altered throughout development. On embryonic day (E) 7, all 3 hypoxic-induced genes were expressed at their highest levels, followed by a decrease from E7 to E19 followed by an increase between internal (E19) and external pipping (E20). The cardiac troponin T exhibited a similar expression level for E7 and E15 with a similar significant increase at E19 and E20. During these periods of development, significant changes in the primary gas exchange organs occur. Based on our observation of upregulation of these hypoxia response genes, it appears that tissue hypoxia is likely a normal component of embryonic development in the chicken based on the upregulation of hypoxia response genes.}, number={11}, journal={POULTRY SCIENCE}, author={Druyan, S. and Cahaner, A. and Ashwell, C. M.}, year={2007}, month={Nov}, pages={2384–2389} }