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Reproductive efficiency of a heifer is directly dependent on the health of reproductive system especially ovary and uterus. Current experiment was carried out to screen candidate genes related to reproductive traits and detect molecular mechanisms of DEGs by using RNA-sequencing (RNAseq) and Gene Set Enrichment Analysis (GSEA) to understand the environmental adaptability, molecular breeding and analyze the reproductive performance. Furthermore, Illumina II high throughput sequncing technology was utilized in the current experiment to sequence transcriptomes and analysis related to pathway of different genes between uterus and ovary in Xiangxi cattle. The total number of ovary assembled was compared to the reference genome sequence, DEGs analysis, GO and KEGG enrichment analysis and candidate gene screening were performed. Based on the transcriptome data, seven cDNA libraries were constructed by utilizing total RNA. Out of seven contracted cDNA libraries, in every sequencing library, raw reads reached >133 Mb, and >94% clean reads remained. After comparing the Xiangxi cattle ovaries with the uterus, a total of 3635 mRNAs were found, in which 1608 were significantly up-regulated expressed and 2027 were down-regulated expression mRNAs. The mRNA expression of ADCY3, ADCY4, ADCY9, FSHR, BMP15, LHCGR, INSR, CYP11A1, CYP17A1, CYP19A1, STAR and SCARB1 in ovary of Xiangxi Cattle were significant different in ovarian and uterus tissues. Through GSEA and PPI network, we found the ovarian steroidogenesis pathway played significant role in signal regulation during the development of the ovarian tissue of the Xiangxi cattle. [ABSTRACT FROM AUTHOR]

Salix psammophila is a desert shrub willow that has extraordinary adaptation to abiotic stresses and plays an important role in maintaining local ecosystems. Moreover, S. psammophila is regarded as a promising biomass feedstock because of its high biomass yields and short rotation coppice cycle. However, few suitable reference genes (RGs) for quantitative real-time polymerase chain reaction (qRT-PCR) constrain the study on normalization of gene expression in S. psammophila until now. Here, we investigated the expression stabilities of 14 candidate RGs across tissue types and under four abiotic stress treatments, including heat, cold, salt, and drought treatments. After calculation of PCR efficiencies, three different software, NormFinder, geNorm, and BestKeeper were employed to analyze systematically the qRT-PCR data, and the outputs were merged by RankAggreg software. The optimal RGs selected for gene expression analysis were EF1α (Elongation factor-1 alpha) and OTU (OTU-like cysteine protease family protein) for different tissue types, UBC (Ubiquitin-conjugating enzyme E2) and LTA4H (Leukotriene A-4 hydrolase homolog) for heat treatment, HIS (Histone superfamily protein H3) and ARF2 (ADP-ribosylation factor 2) for cold treatment, OTU and ACT7 (Actin 7) for salt treatment, UBC and LTA4H for drought treatment. The expression of UBC, ARF2, and VHAC (V-type proton ATPase subunit C) varied the least across tissue types and under abiotic stresses. Furthermore, the relative genes expression profiles of one tissue-specific gene WOX1a (WUSCHEL-related homeobox 1a), and four stress-inducible genes, including Hsf-A2 (Heat shock transcription factors A2), CBF3 (C-repeat binding factor 3), HKT1 (High-Affinity K+ Transporter 1), and GST (Glutathione S-transferase), were conducted to confirm the validity of the RGs in this study. These results provided an important RGs application guideline for gene expression characterization in S. psammophila. [ABSTRACT FROM AUTHOR]

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Background: Members of the heat shock protein 90 (Hsp90) class of proteins are evolutionarily conserved molecular chaperones. They are involved in protein folding, assembly, stabilization, activation, and degradation in many normal cellular processes and under stress conditions. Unlike many other well-characterized molecular chaperones, Hsp90s play key roles in signal transduction, cell-cycle control, genomic silencing, and protein trafficking. However, no systematic analysis of genome organization, gene structure, and expression compendium has been performed in the Populus model tree genus to date. Results: We performed a comprehensive analysis of the Populus Hsp90 gene family and identified 10 Populus Hsp90 genes, which were phylogenetically clustered into two major groups. Gene structure and motif composition are relatively conserved in each group. In Populus trichocarpa, we identified three paralogous pairs, among which the PtHsp90-5a/PtHsp90-5b paralogous pair might be created by duplication of a genome segment. Subcellular localization analysis shows that PtHsp90 members are localized in different subcellular compartments. PtHsp90-3 is localized both in the nucleus and in the cytoplasm, PtHsp90-5a and PtHsp90-5b are in chloroplasts, and PtHsp90-7 is in the endoplasmic reticulum (ER). Furthermore, microarray and semi-quantitative real-time RT-PCR analyses show that a number of Populus Hsp90 genes are differentially expressed upon exposure to various stresses. Conclusions: The gene structure and motif composition of PtHsp90s are highly conserved among group members, suggesting that members of the same group may also have conserved functions. Microarray and RT-PCR analyses show that most PtHsp90s were induced by various stresses, including heat stress. Collectively, these observations lay the foundation for future efforts to unravel the biological roles of PtHsp90 genes. [ABSTRACT FROM AUTHOR]

Aim: In an effort to identify patients with uveal melanoma at high risk of metastasis, the authors undertook correlation of gene expression profiles with histopathology data and tumour-related mortality. Methods: The RNA was isolated from 27 samples of uveal melanoma from patients who had consented to undergo enucleation, and transcripts profiled using a cDNA array comprised of sequence-verified cDNA clones representing approximately 4000 genes implicated in cancer development. Two multivariate data mining techniques-hierarchical cluster analysis and multidimensional scaling-were used to investigate the grouping structure in the gene expression data. Cluster analysis was performed with a subset of 10 000 randomly selected genes and the cumulative contribution of all the genes in making the correct grouping was recorded. Results: Hierarchical cluster analysis and multidimensional scaling revealed two distinct classes. When correlated with the data on metastasis, the two molecular classes corresponded very well to the survival data for the 27 patients. Thirty two discrete genes (corresponding to 44 probe sets) that correctly defined the molecular classes were selected. A single gene (ectonucleotide pyrophosphatase/phosphodiesterase 2; autotaxin) could classify the molecular types. The expression pattern was confirmed using real-time quantitative PCR. Conclusions: Gene expression profiling identifies two distinct prognostic classes of uveal melanoma. Underexpression of autotaxin in class 2 uveal melanoma with a poor prognosis needs to be explored further. [ABSTRACT FROM AUTHOR]

Identifies a gene expression fingerprint for heart failure. Statistical method to establish comprehensive cutoff point for identification of differentially-expressed genes; Differentiation of etiologies of heart failure by gene expression fingerprint; Gene clusters that show coordinated up- or downregulation in human heart failure.