@article{bischoff_tsai_hardison_motsinger-reif_freking_nonneman_rohrer_piedrahita_2013, title={Differences in X-Chromosome Transcriptional Activity and Cholesterol Metabolism between Placentae from Swine Breeds from Asian and Western Origins}, volume={8}, ISSN={["1932-6203"]}, DOI={10.1371/journal.pone.0055345}, abstractNote={To gain insight into differences in placental physiology between two swine breeds noted for their dissimilar reproductive performance, that is, the Chinese Meishan and white composite (WC), we examined gene expression profiles of placental tissues collected at 25, 45, 65, 85, and 105 days of gestation by microarrays. Using a linear mixed model, a total of 1,595 differentially expressed genes were identified between the two pig breeds using a false-discovery rate q-value ≤0.05. Among these genes, we identified breed-specific isoforms of XIST, a long non-coding RNA responsible X-chromosome dosage compensation in females. Additionally, we explored the interaction of placental gene expression and chromosomal location by DIGMAP and identified three Sus scrofa X chromosomal bands (Xq13, Xq21, Xp11) that represent transcriptionally active clusters that differ between Meishan and WC during placental development. Also, pathway analysis identified fundamental breed differences in placental cholesterol trafficking and its synthesis. Direct measurement of cholesterol confirmed that the cholesterol content was significantly higher in the Meishan versus WC placentae. Taken together, this work identifies key metabolic pathways that differ in the placentae of two swine breeds noted for differences in reproductive prolificacy.}, number={1}, journal={PLOS ONE}, author={Bischoff, Steve R. and Tsai, Shengdar Q. and Hardison, Nicholas E. and Motsinger-Reif, Alison A. and Freking, Bradley A. and Nonneman, Dan J. and Rohrer, Gary A. and Piedrahita, Jorge A.}, year={2013}, month={Jan} }
 @article{koh_thomas_tsai_bischoff_lim_breen_olby_piedrahita_2013, title={Growth Requirements and Chromosomal Instability of Induced Pluripotent Stem Cells Generated from Adult Canine Fibroblasts}, volume={22}, ISSN={1547-3287 1557-8534}, url={http://dx.doi.org/10.1089/scd.2012.0393}, DOI={10.1089/scd.2012.0393}, abstractNote={In mice and humans, it has been shown that embryonic and adult fibroblasts can be reprogrammed into pluripotency by introducing 4 transcription factors, Oct3/4, Klf4, Sox2, and c-Myc (OKSM). Here, we report the derivation of induced pluripotent stem cells (iPSCs) from adult canine fibroblasts by retroviral OKSM transduction. The isolated canine iPSCs (ciPSCs) were expanded in 3 different culture media [fibroblast growth factor 2 (FGF2), leukemia inhibitory factor (LIF), or FGF2 plus LIF]. Cells cultured in both FGF2 and LIF expressed pluripotency markers [POU5F1 (OCT4), SOX2, NANOG, and LIN28] and embryonic stem cell (ESC)-specific genes (PODXL, DPPA5, FGF5, REX1, and LAMP1) and showed strong levels of alkaline phosphatase expression. In vitro differentiation by formation of embryoid bodies and by directed differentiation generated cell derivatives of all 3 germ layers as confirmed by mRNA and protein expression. In vivo, the ciPSCs created solid tumors, which failed to reach epithelial structure formation, but expressed markers for all 3 germ layers. Array comparative genomic hybridization and chromosomal fluorescence in situ hybridization analyses revealed that while retroviral transduction per se did not result in significant DNA copy number imbalance, there was evidence for the emergence of low-level aneuploidy during prolonged culture or tumor formation. In summary, we were able to derive ciPSCs from adult fibroblasts by using 4 transcription factors. The isolated iPSCs have similar characteristics to ESCs from other species, but the exact cellular mechanisms behind their unique co-dependency on both FGF2 and LIF are still unknown.}, number={6}, journal={Stem Cells and Development}, publisher={Mary Ann Liebert Inc}, author={Koh, Sehwon and Thomas, Rachael and Tsai, Shengdar and Bischoff, Steve and Lim, Ji-Hey and Breen, Matthew and Olby, Natasha J. and Piedrahita, Jorge A.}, year={2013}, month={Mar}, pages={951–963} }
 @article{chung_tsai_james_thames_shytle_piedrahita_2012, title={Lack of genomic imprinting of DNA primase, polypeptide 2 (PRIM2) in human term placenta and white blood cells}, volume={7}, ISSN={["1559-2294"]}, DOI={10.4161/epi.19777}, abstractNote={PRIM2, encoding a subunit of primase involved in DNA replication and transcription, is expressed in the placenta and is crucial for mammalian development and growth. Its role in placental function is not well understood. Recently, PRIM2 was reported as imprinted in human white blood cells (WBC). We report here our failure to confirm imprinting of the PRIM2 locus in human placenta or WBC. The discordance between our results and those of others are likely due to an incorrectly annotated PRIM2 pseudogene found in the human genome database.}, number={5}, journal={EPIGENETICS}, author={Chung, Jaewook and Tsai, Shengdar and James, Andra H. and Thames, Betty H. and Shytle, Stephanie and Piedrahita, Jorge A.}, year={2012}, month={May}, pages={429–431} }
 @article{tsai_hardison_james_motsinger-reif_bischoff_thames_piedrahita_2011, title={Transcriptional profiling of human placentas from pregnancies complicated by preeclampsia reveals disregulation of sialic acid acetylesterase and immune signalling pathways}, volume={32}, ISSN={["1532-3102"]}, DOI={10.1016/j.placenta.2010.11.014}, abstractNote={The placenta plays an important role as a regulator of fetal nutrition and growth throughout development and placental factors contribute to gestational abnormalities such as preeclampsia. This study describes the genome-wide gene expression profiles of a large (n = 60) set of human placentas in order to uncover gene expression patterns associated with preeclampsia. In addition to confirming changes in expression of soluble factors associated with preeclampsia such as sFLT1 (soluble fms-like tyrosine kinase-1), sENG (soluble endoglin), and INHA (inhibin alpha), we also find changes in immune-associated signaling pathways, offering a potential upstream explanation for the shallow trophoblast invasion and inadequate uterine remodeling typically observed in pathogenesis of preeclampsia. Notably, we also find evidence of preeclampsia-associated placental upregulation of sialic acid acetylesterase (SIAE), a gene functionally associated with autoimmune diseases.}, number={2}, journal={PLACENTA}, author={Tsai, S. and Hardison, N. E. and James, A. H. and Motsinger-Reif, A. A. and Bischoff, S. R. and Thames, B. H. and Piedrahita, J. A.}, year={2011}, month={Feb}, pages={175–182} }
 @article{bischoff_tsai_hardison_motsinger-reif_freking_nonneman_rohrer_piedrahita_2009, title={Characterization of Conserved and Nonconserved Imprinted Genes in Swine}, volume={81}, ISSN={["1529-7268"]}, DOI={10.1095/biolreprod.109.078139}, abstractNote={To increase our understanding of imprinted genes in swine, we carried out a comprehensive analysis of this gene family using two complementary approaches: expression and phenotypic profiling of parthenogenetic fetuses, and analysis of imprinting by pyrosequencing. The parthenote placenta and fetus were smaller than those of controls but had no obvious morphological differences at Day 28 of gestation. By Day 30, however, the parthenote placentas had decreased chorioallantoic folding, decreased chorionic ruggae, and reduction of fetal-maternal interface surface in comparison with stage-matched control fetuses. Using Affymetrix Porcine GeneChip microarrays and/or semiquantitative PCR, brain, fibroblast, liver, and placenta of Day 30 fetuses were profiled, and 25 imprinted genes were identified as differentially expressed in at least one of the four tissue types: AMPD3, CDKN1C, COPG2, DHCR7, DIRAS3, IGF2 (isoform specific), IGF2AS, IGF2R, MEG3, MEST, NAP1L5, NDN, NNAT, OSBPL1A, PEG3, APEG3, PEG10, PLAGL1, PON2, PPP1R9A, SGCE, SLC38A4, SNORD107, SNRPN, and TFPI2. For DIRAS3, PLAGL1, SGCE, and SLC38A4, tissue-specific differences were detected. In addition, we examined the imprinting status of candidate genes by quantitative allelic pyrosequencing. Samples were collected from Day 30 pregnancies generated from reciprocal crosses of Meishan and White Composite breeds, and single-nucleotide polymorphisms were identified in candidate genes. Imprinting was confirmed for DIRAS3, DLK1, H19, IGF2AS, NNAT, MEST, PEG10, PHLDA2, PLAGL1, SGCE, and SNORD107. We also found no evidence of imprinting in ASB4, ASCL2, CD81, COMMD1, DCN, DLX5, and H13. Combined, these results represent the most comprehensive survey of imprinted genes in swine to date.}, number={5}, journal={BIOLOGY OF REPRODUCTION}, author={Bischoff, Steve R. and Tsai, Shengdar and Hardison, Nicholas and Motsinger-Reif, Alison A. and Freking, Brad A. and Nonneman, Dan and Rohrer, Gary and Piedrahita, Jorge A.}, year={2009}, month={Nov}, pages={906–920} }
 @article{bischoff_tsai_hardison_york_freking_nonneman_rohrer_piedrahita_2008, title={Identification of SNPs and INDELS in swine transcribed sequences using short oligonucleotide microarrays}, volume={9}, ISSN={1471-2164}, url={http://dx.doi.org/10.1186/1471-2164-9-252}, DOI={10.1186/1471-2164-9-252}, abstractNote={Abstract}, number={1}, journal={BMC Genomics}, publisher={Springer Nature}, author={Bischoff, Steve R and Tsai, Shengdar and Hardison, Nicholas E and York, Abby M and Freking, Brad A and Nonneman, Dan and Rohrer, Gary and Piedrahita, Jorge A}, year={2008}, pages={252} }
 @article{estrada_collins_york_bischoff_sommer_tsai_petters_piedrahita_2008, title={Successful cloning of the Yucatan minipig using commercial/occidental breeds as oocyte donors and embryo recipients}, volume={10}, ISSN={["1536-2302"]}, DOI={10.1089/clo.2008.0005}, abstractNote={The widespread application of porcine SCNT to biomedical research is being hampered by the large adult size (300-600 lbs) of the commercial breeds commonly used for SCNT. The Yucatan minipig, in contrast, has an adult weight of 140-150 lbs and a long history of utility in biomedical research. In order to combine the wide availability of commercial swine with the biomedical value of the Yucatan minipig, we utilized SCNT using the Yucatan as nuclear donors and commercial swine as both oocyte donors and recipients. Of six recipient gilts receiving 631 SCNT embryos, three went to term and delivered seven piglets, four of which survived to adulthood. Additionally, we obtained fetal fibroblasts from a cloned Yucatan and used them for a second round of SCNT. Of three recipients receiving 315 reconstructed embryos, one went to term and delivered three piglets, one of which survived to adulthood. Both microsatellite and D-loop sequence analysis confirmed that all of the piglets generated were nuclear-mitochondrial hybrids carrying Yucatan nuclear DNA and commercial breed mitochondrial DNA. This report shows that it is possible to produce viable Yucatan SCNT clones and opens up the possibility of developing valuable biomedical models in this porcine breed.}, number={2}, journal={CLONING AND STEM CELLS}, author={Estrada, Jose L. and Collins, Bruce and York, Abby and Bischoff, Steve and Sommer, Jeff and Tsai, Shengdar and Petters, Robert M. and Piedrahita, Jorge A.}, year={2008}, month={Jun}, pages={287–296} }
 @article{tsai_cassady_freking_nonneman_rohrer_piedrahita_2006, title={Annotation of the Affymetrix(1) porcine genome microarray}, volume={37}, ISSN={["0268-9146"]}, DOI={10.1111/j.1365-2052.2006.01460.x}, abstractNote={Overview: The Affymetrix porcine genome microarray (http:// www.affymetrix.com/products/arrays/specific/porcine.affx) is minimally annotated. Less than 10% of the probe sets on this array are described with gene names, posing a challenge to biological interpretation of data. Lack of annotation is likely due to the limited availability of full-length porcine cDNA sequence. Presented here is a strategy for improving the annotation of this microarray.}, number={4}, journal={ANIMAL GENETICS}, author={Tsai, S. and Cassady, J. P. and Freking, B. A. and Nonneman, D. J. and Rohrer, G. A. and Piedrahita, J. A.}, year={2006}, month={Aug}, pages={423–424} }
 @article{tsai_mir_martin_estrada_bischoff_hsieh_cassady_freking_nonneman_rohrer_et al._2006, title={Detection of transcriptional difference of porcine imprinted genes using different microarray platforms}, volume={7}, journal={BMC Genomics}, author={Tsai, S. and Mir, B. and Martin, A. C. and Estrada, J. L. and Bischoff, S. R. and Hsieh, W. P. and Cassady, J. P. and Freking, B. A. and Nonneman, D. J. and Rohrer, G. A. and et al.}, year={2006} }