Gene expression regulating blastocyst formation

Development of embryos to the blastocyst stage is a critical event in the early lives of all eutherian mammalian species. Blastocyst formation is essential for implantation and is the principal morphological determinant of embryo quality prior to embryo transfer. The physiological events and roles of specific gene families that regulate blastocyst formation are subjects of intense research Recent findings have demonstrated that bovine embryos express multiple members of the Na/K-ATPase ion transporter gene family. Two members of this family have been co-localized to bovine trophectoderm, but each becomes largely confined to opposing cell membrane margins. Bovine blastocysts display a greater sensitivity to ouabain (potent inhibitor of the Na/K-ATPase) than murine blastocysts, and enzyme activity (ouabain sensitive 86Rb+ uptake) undergoes a 9-fold increase from the bovine morula to the blastocyst stage. Disruption of Na/K-ATPase gene expression by antisense oligodeoxynucleotide inhibition abolishes blastocyst formation. These results have implicated the Na/K-ATPase as a key regulator of bovine blastocyst formation and have provided insights necessary for the production of healthy bovine embryos by the application of in vitro maturation, in vitro fertilization and in vitro culture methods.     

Identification of genes associated with tumorigenesis of retinoblastoma by microarray analysis

There is no report on the gene expression profile of retinoblastoma (Rb). We analyzed the gene expression profile of Rb by the microarray technique. One thousand four genes were upregulated and 481 genes were downregulated. Microarray data were confirmed by semiquantitative RT-PCR for 5 genes in Rb samples: CDC25A, C17orf75, ERBB3, LATS2, and CHFR. Clusters of differentially expressed genes were identified on chromosomes 1, 16, and 17. Based on the expression profile, we hypothesized that the PI3K/AKT/mTOR (insulin signaling) pathway might be dysregulated in Rb. Our semiquantitative RT-PCR analysis of the PIK3CA, AKT1, FRAP1, and RPS6KB1 genes in Rb samples supported this hypothesis. We suggest that known inhibitors of this pathway could be evaluated for the treatment of Rb.     

Identification and antibiogram of microbes associated with bovine mastitis

An investigation of Mastitis in cattle was carried out in Anand city and in nearby villages of Gujarat state using California Mastitis Test (CMT) kit. The prevalence of clinical and subclinical mastitis was found to be 5.5% and 15.75%, respectively. Staphylococcus aureus was identified through strain specific polymerase chain reaction; the remaining isolates identified on the basis of molecular analysis by 16S rDNA sequencing and phylogenetic analysis were Staphylococcus species, B. pumilus, Staphylococcus chromogenes, Bacillus species, and Pseudomonas species. In vitro antimicrobial susceptibility pattern of all the isolates was checked against 13 different antibiotics using the agar disc diffusion method. Highest bacterial resistance was observed with penicillin G and oxacillin antibiotics. It was also observed that the patterns of bacterial resistance have not changed in India over the years. The data supports the decrease in the incidence of mastitis but the rate of decrease is minimal. More effective control strategies are required.     

Increasing the rate of blastocyst formation and hatching from in vitro-produced bovine zygotes

This study was designed to identify parameters that would facilitate early selection of superior embryos, as well as to define culture conditions that could increase the proportion of embryos proceeding to the blastocyst stage. In the first experiment, the developmental potential of bovine embryos that had reached different stages of development after 60 h of culture following insemination was assessed. No 2-cell embryos underwent further cleavage. Of the 4-cell embryos (n = 188) only 12.2% progressed to the blastocyst stage, while 62.5% of 8-cell embryos (n = 480) did so (P < 0.01). In a further experiment, the effects of conditioning the culture medium (TCM 199) either with Buffalo rat liver cells (BRLC) or bovine oviductal epithelial cells (BOEC) and the effects of co-culture with either of these 2 cell types were examined. The percentage of 8-cell embryos proceeding to the morula and blastocyst stages was independent of cell type and culture system. However, BOEC-conditioned medium supported significantly lower production of blastocysts than any of the other culture methods. Only 24.1% of the former proceeded to the blastocyst stage after the full 10 d of culture, and only 3% hatched, values that were significantly lower than in the other 3 groups (P < 0.01). Among the latter, 44% progressed to the blastocyst stage in BRLC-conditioned medium while 44 and 46% reached that endpoint after co-culture with BOEC or BRL cells, respectively. The percentages that hatched among these were 28.2, 31 and 28.5%, respectively.     

丽蝇蛹集金小蜂几丁质酶基因鉴定与表达分析

几丁质酶是降解几丁质的糖苷水解酶,参与昆虫蜕皮、器官发育、免疫等重要生理过程。目前,寄生蜂等膜翅目昆虫中几丁质酶的鉴定以及功能研究仍较少。本研究基于生物信息学分析,在丽蝇蛹集金小蜂Nasonia vitripennis基因组中鉴定到14个几丁质酶基因,氨基酸个数介于312~2 682之间。系统进化分析表明丽蝇蛹集金小蜂几丁质酶分为9个亚家族,其中Group Ⅳ、Ⅶ亚家族可能通过基因串联复制而发生基因家族扩增。qRT-PCR分析结果表明几丁质酶基因的表达具有多样性,其中NvCht1、NvCht5、NvCht6、NvCht7 4个基因在1.5 d幼虫表达量最高,NvCht3在5 d幼虫表达量最高,NvCht8在幼虫期高表达。此外,幼虫组织中的表达分析结果表明NvCht4、NvCht5、NvCht10、NvCht12在表皮中高表达,NvCht7、NvCht8、NvCht13在肠道中高表达,NvCht9在脂肪体和表皮中高表达,NvCht11在唾液腺中高表达。本研究为寄生蜂几丁质酶的进化分析以及功能研究提供理论基础。     

Identification and expression analysis of mical family genes in zebrafish

Mical(molecule interacting with CasL)represent a conserved family of cytosolic multidomain proteins that has been shown to be associated with a variety of cellular processes,including axon guidance,cell movement,cell-cell junction formation,vesicle trafficking and cancer cell metastasis.However,the expression and function of these genes during embryonic development have not been comprehensively characterized,especially in vertebrate species,although some limited in vivo studies have been carried out in neural and musculature systems of Drosophila and in neural systems of vertebrates.So far,no mica/family homologs have been reported in zebrafish,an ideal vertebrate model for the study of developmental processes.Here we report eight homologs of m/ca/family genes in zebrafish and their expression profiles during embryonic development.Consistent with the findings in Drosophila and mammals,most zebrafish mical family genes display expression in neural and musculature systems.In addition,five mica/homologs are detected in heart,and one,micall2a,in blood vessels.Our data established an important basis for further functional studies of mica/family genes in zebrafish,and suggest a possible role for mica/genes in cardiovascular development.     

Identification and expression analysis of candidate genes associated with stem gall disease in Coriander (Coriandrum sativum L.) cultivars

Molecular Biology Reports - Coriander (Coriandrum sativum L.) is a well-known spice and aromatic crop cultivated globally. Stem gall disease is one of the major constraints for its leaf and seed...     

Peptidomic analysis of blastocyst culture medium and the effect of peptide derived from blastocyst culture medium on blastocyst formation and viability

High‐quality in vitro human embryo culture medium can improve the blastocyst formation rate and blastocyst quality and be beneficial for the clinical application of single blastocyst transfer. Mammalian embryos can secrete protein products into the surrounding medium. As a group of bioactive molecules and degraded proteins, peptides have been shown to participate in various biological processes. Using liquid chromatography‐tandem mass spectrometry, we performed comparative peptidomic analysis of human culture medium in blastocyst formation and nonblastocyst‐formation groups. A total of 201 differentially expressed peptides originating from 157 precursor proteins were identified. Among these, a peptide derived from HERC2 (peptide derived from blastocyst culture medium [PDBCM]) passed through the zona pellucida, was distributed on the perivitelline space, was absent in arrest embryos and highly expressed in high‐quality blastocysts compared with low‐quality blastocysts, and significantly promoted blastocyst formation in a concentration‐dependent manner. These results indicate that PDBCM may be a novel biomarker for predicting blastocyst formation and viability. The mechanism remains unclear and needs to be explored in the future.     

Identification of genes associated with tumorigenesis of meibomian cell carcinoma by microarray analysis

Meibomian cell carcinoma (MCC) is a malignant tumor of the meibomian glands located in the eyelids. No information exists on the cytogenetic and genetic aspects of MCC. There is no report on the gene expression profile of MCC. Thus there is a need, for both scientific and clinical reasons, to identify genes and pathways that are involved in the development and progression of MCC. We analyzed the gene expression profile of MCC by the microarray technique. Forty-four genes were upregulated and 149 genes were downregulated in MCC. Differential expression data were confirmed for 5 genes by semiquantitative RT-PCR in MCC tumors: GTF2H4, RBM12, UBE2D3, DDX17, and LZTS1. We found dysregulation of two major pathways in MCC: MAPK and JAK/STAT. Clusters of genes on chromosomes 1, 12, and 19 were dysregulated in MCC. The data presented here will facilitate the identification of specific markers and therapeutic targets for the treatment of MCC patients.     

Identification of pathways and genes associated with cerebral palsy

Cerebral palsy (CP) is a non-progressive neurological disease, of which susceptibility is linked to genetic and environmental risk factors. More and more studies have shown that CP might be caused by multiple genetic factors, similar to other neurodevelopmental disorders. Due to the high genetic heterogeneity of CP, we focused on investigating related molecular pathways. Ten children with CP were collected for whole-exome sequencing by next-generation sequencing (NGS) technology. Customized processes were used to identify potential pathogenic pathways and variants. Three pathways (axon guidance, transmission across chemical synapses, protein–protein interactions at synapses) with twenty-three genes were identified to be highly correlated with CP. This study showed that the three pathways associated with CP might be the molecular mechanism of pathogenesis. These findings could provide useful clues for developing pathway-based pharmacotherapies. Further studies are required to confirm potential roles for these pathways in the pathogenesis of CP.     

Isolation of genes associated with developmental competency of bovine oocytes

Eggs differ widely in their ability to develop into an embryo. To address this characteristic, the concept of developmental competency has been coined, defined as the ability or potential of an oocyte to undergo maturation, fertilization and development to blastocyst stages or live offspring. Developmental competency is acquired progressively during folliculogenesis and is linked to follicular size. In an effort to understand the molecular changes underlying differences in competency we compared oocytes derived from large follicles (>or=5mm) to those from small follicles (相似文献   

Identification,characterization and expression analysis of lineage-specific genes within Triticeae

Lineage-specific genes (LSGs) are a set of genes in a given taxon without significant sequence similarity to genes and intergenic sequences of other taxa and are functional. The tribe Triticeae mainly includes species of different ploidy levels, such as staple food crops wheat (Triticum aestivum L.) and barley (Hordeum vulgare L.). This study is aimed at mining and characterizing the Triticeae-specific genes (TSGs) using expressed sequence data of wheat. A total of 3812 TSGs was identified and they were generally characterized by smaller size, fewer exons, shorter open reading frames and lower expression levels. Most TSGs were expressed with tissue preference and many of them were predominantly expressed in reproduction related tissues, especially in young stamen. Nearly one third of the TSGs were stress-responsive and inducible under abiotic and/or biotic stresses. A co-expression-based annotation supported the relevance of some TSGs with reproduction and stress responses, indicating their potential economic importance.     

Identification of optimal housekeeping genes for examination of gene expression in bovine corpus luteum

The selection of proper housekeeping genes for studies requiring genes expression normalization is an important step in the appropriate interpretation of results. The expression of housekeeping genes is regulated by many factors including age, gender, type of tissue or disease. The aim of the study was to identify optimal housekeeping genes in the corpus luteum obtained from cyclic or pregnant cows. The mRNA expression of thirteen housekeeping genes: C2orf29, SUZ12, TBP, TUBB2B, ZNF131, HPRT1, 18s RNA, GAPDH, SF3A1, SDHA, MRPL12, B2M and ACTB was measured by Real-time PCR. Range of cycle threshold (C_t) values of the tested genes varied between 12 and 30 cycles, and 18s RNA had the highest coefficient of variation, whereas C2orf29 had the smallest coefficient. GeNorm software demonstrated C2orf29 and TBP as the most stable and 18s RNA and B2M as the most unstable housekeeping genes. Using the proposed cut-off value (0.15), no more than two of the best GeNorm housekeeping genes are proposed to be used in studies requiring gene expression normalization. NormFinder software demonstrated C2orf29 and SUZ12 as the best and 18s RNA and B2M as the worst housekeeping genes. The study indicates that selection of housekeeping genes may essentially affect the quality of the gene expression results.     

Identification of pivotal genes associated with the prognosis of gastric carcinoma through integrated analysis

Purpose: Detecting and diagnosing gastric cancer (GC) during its early period remains greatly difficult. Our analysis was performed to detect core genes correlated with GC and explore their prognostic values.Methods: Microarray datasets from the Gene Expression Omnibus (GEO) ({"type":"entrez-geo","attrs":{"text":"GSE54129","term_id":"54129"}}GSE54129) and The Cancer Genome Atlas (TCGA)-stomach adenocarcinoma (STAD) datasets were applied for common differentially co-expressed genes using differential gene expression analysis and Weighted Gene Co-expression Network Analysis (WGCNA). Functional enrichment analysis and protein–protein interaction (PPI) network analysis of differentially co-expressed genes were performed. We identified hub genes via the CytoHubba plugin. Prognostic values of hub genes were explored. Afterward, Gene Set Enrichment Analysis (GSEA) was used to analyze survival-related hub genes. Finally, the tumor-infiltrating immune cell (TIC) abundance profiles were estimated.Results: Sixty common differentially co-expressed genes were found. Functional enrichment analysis implied that cell–cell junction organization and cell adhesion molecules were primarily enriched. Hub genes were identified using the degree, edge percolated component (EPC), maximal clique centrality (MCC), and maximum neighborhood component (MNC) algorithms, and serpin family E member 1 (SERPINE1) was highly associated with the prognosis of GC patients. Moreover, GSEA demonstrated that extracellular matrix (ECM) receptor interactions and pathways in cancers were correlated with SERPINE1 expression. CIBERSORT analysis of the proportion of TICs suggested that CD8⁺ T cell and T-cell regulation were negatively associated with SERPINE1 expression, showing that SERPINE1 may inhibit the immune-dominant status of the tumor microenvironment (TME) in GC.Conclusions: Our analysis shows that SERPINE1 is closely correlated with the tumorigenesis and progression of GC. Furthermore, SERPINE1 acts as a candidate therapeutic target and prognostic biomarker of GC.