Oocyte Developmental Competence: Insights from Cross-Species Differential Gene Expression and Human Oocyte-Specific Functional Gene Networks

2017 ◽  
Vol 21 (3) ◽  
pp. 156-168 ◽  
Author(s):  
Fernando H. Biase
Keyword(s):  
Gene Expression ◽  
Differential Gene Expression ◽  
Gene Networks ◽  
Functional Gene ◽  
Developmental Competence ◽  
Human Oocyte ◽  
Oocyte Developmental Competence ◽  
Differential Gene

scholarly journals The Western Diet Regulates Hippocampal Microvascular Gene Expression: An Integrated Genomic Analyses in Female Mice

2019 ◽  
Vol 9 (1) ◽  
Author(s):  
Saivageethi Nuthikattu ◽  
Dragan Milenkovic ◽  
John Rutledge ◽  
Amparo Villablanca
Keyword(s):  
Gene Expression ◽  
Transcription Factors ◽  
Differential Expression ◽  
Differential Gene Expression ◽  
Gene Networks ◽  
Molecular Mechanisms ◽  
Western Diet ◽  
Protein Coding ◽  
Female Mice ◽  
Differential Gene

AbstractHyperlipidemia is a risk factor for dementia, and chronic consumption of a Western Diet (WD) is associated with cognitive impairment. However, the molecular mechanisms underlying the development of microvascular disease in the memory centers of the brain are poorly understood. This pilot study investigated the nutrigenomic pathways by which the WD regulates gene expression in hippocampal brain microvessels of female mice. Five-week-old female low-density lipoprotein receptor deficient (LDL-R−/−) and C57BL/6J wild type (WT) mice were fed a chow or WD for 8 weeks. Metabolics for lipids, glucose and insulin were determined. Differential gene expression, gene networks and pathways, transcription factors, and non-protein coding RNAs were evaluated by genome-wide microarray and bioinformatics analysis of laser captured hippocampal microvessels. The WD resulted in differential expression of 2,412 genes. The majority of differential gene expression was attributable to differential regulation of cell signaling proteins and their transcription factors, approximately 7% was attributable to differential expression of miRNAs, and a lesser proportion was due to other non-protein coding RNAs, primarily long non-coding RNAs (lncRNAs) and small nucleolar RNAs (snoRNAs) not previously described to be modified by the WD in females. Our findings revealed that chronic consumption of the WD resulted in integrated multilevel molecular regulation of the hippocampal microvasculature of female mice and may provide one of the mechanisms underlying vascular dementia.

scholarly journals Combined stress of ocean acidification and warming influence survival and drives differential gene expression patterns in the Antarctic pteropod, Limacina helicina antarctica

2020 ◽  
Vol 8 (1) ◽  
Author(s):  
Kevin M Johnson ◽  
Gretchen E Hofmann
Keyword(s):  
Gene Expression ◽  
Ocean Acidification ◽  
Differential Gene Expression ◽  
Gene Networks ◽  
Expression Patterns ◽  
Significant Degree ◽  
Change Factors ◽  
Limacina Helicina ◽  
Differential Gene ◽  
The Antarctic

Abstract The ecologically important thecosome pteropods in the Limacina spp. complex have recently been the focus of studies examining the impacts global change factors – e.g., ocean acidification (OA) and ocean warming (OW) – on their performance and physiology. This focus is driven by conservation concerns where the health of pteropod populations is threatened by the high susceptibility of their shells to dissolution in low aragonite saturation states associated with OA and how coupling of these stressors may push pteropods past the limits of physiological plasticity. In this manipulation experiment, we describe changes in the transcriptome of the Antarctic pteropod, Limacina helicina antarctica, to these combined stressors. The conditions used in the laboratory treatments met or exceeded those projected for the Southern Ocean by the year 2100. We made two general observations regarding the outcome of the data: (1) Temperature was more influential than pH in terms of changing patterns of gene expression, and (2) these Antarctic pteropods appeared to have a significant degree of transcriptomic plasticity to respond to acute abiotic stress in the laboratory. In general, differential gene expression was observed amongst the treatments; here, for example, transcripts associated with maintaining protein structure and cell proliferation were up-regulated. To disentangle the effects of OA and OW, we used a weighted gene co-expression network analysis to explore patterns of change in the transcriptome. This approach identified gene networks associated with OW that were enriched for transcripts proposed to be involved in increasing membrane fluidity at warmer temperatures. Together these data provide evidence that L.h.antarctica has a limited capacity to acclimate to the combined conditions of OA and OW used in this study. This reduced scope of acclimation argues for continued study of how adaptation to polar aquatic environments may limit the plasticity of present-day populations in responding to future environmental change.

280 INDISTINGUISHABLE TRANSCRIPTIONAL PROFILES BETWEEN IN VIVO- AND IN VITRO-PRODUCED BOVINE FETUSES

2010 ◽  
Vol 22 (1) ◽  
pp. 297
Author(s):  
L. Jiang ◽  
S. L. Marjani ◽  
M. Bertolini ◽  
H. A. Lewin ◽  
G. B. Anderson ◽  
...  
Keyword(s):  
Gene Expression ◽  
Differential Gene Expression ◽  
Expression Profiles ◽  
Subsequent Development ◽  
Blastocyst Stage ◽  
Developmental Competence ◽  
Differentially Expressed ◽  
Differential Gene

During the past several decades, in vitro fertilization (IVF) has been increasingly used in animal production and human infertility treatment. In vitro production (IVP) has been shown to cause reduced developmental competence, aberrant gene expression, and developmental abnormalities. Our objective was to determine how in vitro procedures influence global gene expression during fetal development. To this end, we analyzed the gene expression profiles of liver and placentome tissue samples (n = 18) from IVP and in vivo-derived fetuses at Days 90 and 180 of gestation (n = 5 IVP and n = 4 in vivo-derived pregnancies for each day of gestation). Standard in vitro maturation and fertilization protocols were employed. Putative zygotes were co-cultured with bovine oviductal epithelial cells to the blastocyst stage. In vivo embryos were collected 7 days after AI by nonsurgical uterine flushing. Blastocyst-stage IVP and in vivo embryos were transferred to synchronized recipients and monitored until collection at Day 90 or 180. The pregnancy rate at Day 90 was 12% and 27% for IVP and in vivo pregnancies, respectively (Bertolini et al. 2004 Reproduction 128, 341-354). To conduct expression profiling, total RNA from each tissue sample and a standard reference was indirectly labeled with Cy3 and Cy5, respectively, and hybridized in duplicate to custom, bovine 13 K oligonucleotide microarrays. After Loess normalization, a two-way (origin and day) ANOVA model (GeneSpring 7.3.1) was used to identify differentially expressed genes in each tissue. The P-values were adjusted for multiple comparisons using a 5% false discovery rate (FDR). The expression of 11 candidate genes was confirmed independently by quantitative RT-PCR. Surprisingly, in both the liver and placentome tissues, no differential gene expression was detected between the IVP and in vivo fetuses at Day 90 and 180. This was observed even when the FDR was relaxed to 10% and 20%. A total of 879 genes (523 genes ≥ 1.5-fold) were differentially expressed during liver development from 90 to 180 days of gestation. Conversely, no differential gene expression was detected in the placentomes during this developmental period. Our findings show that during early and mid gestation, surviving IVP fetuses had normal patterns of gene expression. It is possible that embryos with less severe perturbations may survive with their gene expression normalized as development proceeds. Additionally, initial changes in gene expression caused by IVP may affect subsequent development, but do not necessarily persist throughout gestation. Present addresses: L. Jiang, Columbia University, New York, NY, USA; S. L. Marjani, Yale University, New Haven, CT, USA; M. Bertolini, University of Fortaleza, CE, Brazil. This work was supported by USDA grants to X.Y, H.A.L., and X.C T.

Differential gene expression in liposarcoma: Insight into pathways for dedifferentiation?

2012 ◽  
Vol 30 (15_suppl) ◽  
pp. 10048-10048
Author(s):  
Dale Han ◽  
Gregory C Bloom ◽  
Marilyn M Bui ◽  
Steven Enkemann ◽  
Hideko Yamauchi ◽  
...  
Keyword(s):  
Gene Expression ◽  
Lipid Metabolism ◽  
Network Analysis ◽  
Differential Expression ◽  
Differential Gene Expression ◽  
Gene Networks ◽  
Expression Patterns ◽  
Differential Regulation ◽  
Gene Expression Patterns ◽  
Differential Gene

10048 Background: Liposarcoma (LPS) dedifferentiation signifies conversion to a clinically aggressive phenotype, but the biologic processes required for this change have not been determined. We describe differential gene expression patterns between well-differentiated (WD) and dedifferentiated (DD) tumors to determine pathways involved in LPS dedifferentiation. Methods: From 1999 to 2006, 121 fatty tumors were resected at a single institution. Twenty tumors, consisting of atypical lipomatous tumors (ALT), WD LPS or DD LPS, were randomly selected and clinicopathologic characteristics were retrospectively reviewed. Gene expression profiling was performed on extracted RNA using the Affymetrix GeneChip platform. Differentially expressed genes were obtained and gene network analysis was done using GeneGO by MetaCore. Results: Median age was 59 years and 70% of cases were male. WD tumors, consisting of 3 ALT and 6 WD LPS, were compared with 11 DD LPS. After a median follow-up of 64 months, 7 patients had died of whom 6 had DD LPS. DD histology was associated with lower overall survival (p<0.05). Significance Analysis of Microarrays for WD tumors vs. DD LPS using a 0% false discovery rate showed differential expression of 188 genes. Network analysis of genes from WD tumors vs. DD LPS showed significant (p<0.001) differential regulation of glucose-activated transcription factor ChREBP (carbohydrate response element binding protein), a key element involved in lipogenesis, gluconeogenesis and glycolysis. There was also significant differential regulation of insulin signaling, PI3K-dependent and PKA signal transduction pathways and of amino acid, fatty acid and glucose metabolism pathways (p<0.05). These pathways, based on Gene Ontology cellular processes, mapped to gene networks primarily involved in lipid metabolism (p<0.05). Conclusions: Differential expression of genes involved in lipid metabolism networks is seen in DD LPS and changes in lipid metabolism may be associated with dedifferentiation. These differential gene expression patterns may help identify fatty tumors potentially at risk for progressing to a malignant or DD state and provide prognostic factors and therapeutic targets for patients with LPS.

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