ABSTRACT
BACKGROUND: Ischemic Stroke (IS) is a major disease which greatly threatens human health. Recent studies showed sex-specific outcomes and mechanisms of cerebral ischemic stroke. This study aimed to identify the key changes of gene expression between male and female IS in humans. METHODS: Gene expression dataset GSE22255, including peripheral blood samples, was downloaded from the Gene Expression Omnibus (GEO) dataset. Differentially Expressed Genes (DEGs) with a LogFC>1, and a P-value <0.05 were screened by BioConductor R package and grouped in female, male and overlap DEGs for further bioinformatic analysis. Gene Ontology (GO) functional annotation, Protein-Protein Interaction (PPI) network, "Molecular Complex Detection" (MCODE) modules, CytoNCA (cytoscape network centrality analysis) essential genes and Kyoto Encyclopedia of Genes and Genomes (KEGG) pathway interrelation analysis were performed. RESULTS: In a total of 54,665 genes, 185 (73 ups and 112 downs) DEGs in the female dataset, 461 DEGs (297 ups and 164 downs) in the male dataset, within which 118 DEGs overlapped (7 similar changes in female and male, 111 opposite changes in female and male) were obtained from the GSE22255 dataset. Female, male and overlapping DEGs enriched for similar cellular components and molecular function. Male DEGs enriched for divergent biological processes from female and overlapping DEGs. Sex-specific and overlapping DEGs were put into the PPI network. Overlapping genes such as IL6, presented opposite changes and were mainly involved in cytokine-cytokine receptor interactions, the TNF-signalling pathway, etc. CONCLUSION: The analysis of sex-specific DEGs from GEO human blood samples showed that not only specific but also opposite DEG alterations in the female and male stroke genome wide dataset. The results provided an overview of sex-specific mechanisms, which might provide insight into stroke and its biomarkers and lead to sex-specific prognosis and treatment strategies in future clinical practice.
Subject(s)
Protein Interaction Maps/genetics , Stroke/metabolism , Computational Biology/methods , Databases, Factual , Female , Gene Expression Profiling , Gene Expression Regulation , Gene Ontology , Humans , Male , Sex Factors , Stroke/blood , Stroke/pathologyABSTRACT
The voltage-dependent anion channel (VDAC) is the major transport protein in the outer membrane of mitochondria, and is involved in the formation of a permeable transition pore and metabolite transport. In this study, we explored the role of Arabidopsis thaliana VDAC2 (AtVDAC2) in the signal transduction pathway in Arabidopsis under salt stress. We investigated the germination rates of AtVDAC2 transgenic lines under salicylic acid (SA) treatment, and found that AtVDAC2 can affect the sensitivity of Arabidopsis to SA. Furthermore, the stomatal apertures of AtVDAC2 transgenic Arabidopsis were calculated. Results showed that the over-expression lines showed the obvious stomatal closure, while in the antisense lines, no obvious changes in stomatal apertures were found. In addition, we also detected the expression levels of salt stress and SA response-associated genes in transgenic plants and found that AtVDAC2 affected the expression of these genes. Our study investigated the role of AtVDAC2 in SA and salt stress response in Arabidopsis; our observations provide some helpful information for better understanding the direct and downstream functions of AtVDAC.
Subject(s)
Arabidopsis/genetics , Arabidopsis/metabolism , Signal Transduction , Stress, Physiological/genetics , Voltage-Dependent Anion Channel 2/genetics , Voltage-Dependent Anion Channel 2/metabolism , Arabidopsis/drug effects , Gene Expression Regulation, Plant , Germination/genetics , Plants, Genetically Modified , Salicylic Acid/pharmacology , Salt Tolerance/genetics , Sodium Chloride/pharmacologyABSTRACT
Maize (Zea mays L.) kernel width is one of the most important traits that is related to yield and appearance. To understand its genetic mechanisms more clearly, a recombinant inbred line (RIL) segregation population consisting of 239 RILs was used for quantitative trait locus (QTL) mapping for kernel width. We found four QTLs on chromosomes 3 (one), 5 (two), and 10 (one). The QTLs were close to their adjacent markers, with a range of 0-23.8 cM, and explained 6.2-19.7% of the phenotypic variation. The three QTLs on chromosomes 3 and 5 had positive additive effects, and to a certain extent increased kernel width, whereas the one on chromosome 10 exhibited negative additive effects and decreased kernel width. These results can be used for gene cloning and marker-assisted selection in maize-breeding programs.
Subject(s)
Chromosome Mapping , Quantitative Trait Loci/genetics , Zea mays/genetics , Breeding , Chromosomes, Plant , Phenotype , Zea mays/growth & developmentABSTRACT
Kernel thickness is one of the most important traits in kernel structure, and is related to yield. To ascertain its genetic information more clearly, an immortal recombinant inbred line segregation population was used to map the quantitative trait loci (QTLs) for kernel thickness. As a result, two QTLs were identified on chromosome 9; both of them had negative additive effects, and could decrease kernel thickness to some extent. The QTLs explained 25.8% of the total phenotypic variation. These results advance our understanding of the genetic basis of kernel thickness in maize-breeding programs.
Subject(s)
Quantitative Trait Loci , Quantitative Trait, Heritable , Zea mays/genetics , Chromosome Mapping , Chromosomes, Plant , Genetic Testing , Inbreeding , Lod Score , PhenotypeABSTRACT
Aloe (Aloe spp), containing abundant polysaccharides and numerous bioactive ingredients, has remarkable medical, ornamental, calleidic, and edible values. In the present study, the total RNA was extracted from aloe leaf tissue. The isolated high-quality RNA was further used to clone actin gene by using reverse transcription-polymerase chain reaction (RT-PCR). The result of sequence analysis for the amplified fragment revealed that the cloned actin gene was 1012 bp in length (GenBank accession No. KC751541.1) and contained a 924-bp coding region and encoded a protein consisting of 307 amino acids. Homologous alignment showed that it shared over 80 and 96% identity with the nucleotide and amino acid sequences of actin from other plants, respectively. In addition, the cloned gene was used for phylogenetic analyses based on the deduced amino acid sequences, and the results suggested that the actin gene is highly conserved in evolution. The findings of this study will be useful for investigating the expression patterns of other genes in Aloe.
Subject(s)
Actins/genetics , Aloe/genetics , Phylogeny , Plant Leaves/genetics , Plant Proteins/genetics , Actins/chemistry , Aloe/classification , Amino Acid Sequence , Base Sequence , Biological Evolution , Cloning, Molecular , Conserved Sequence , Gene Expression , Molecular Sequence Data , Plant Leaves/classification , Plant Proteins/chemistry , Recombinant Proteins/chemistry , Recombinant Proteins/genetics , Sequence AlignmentABSTRACT
Dioscorea opposita Thunb. has been used as health food and herbal medicinal ingredients in traditional Chinese medicine. In this study, the total DNA of D. opposita Thunb. was extracted using an improved cetyltrimethylammonium bromide (CTAB) method, and the extracted DNA was further used for random amplified polymorphic DNA (RAPD) reaction system by design of the L16 (4(4)) orthogonal diagram. The results showed that the improved CTAB method can be used to isolate high-quality and high-concentration DNA, and the optimized protocol can overcome the instability of RAPD reaction system. The knowledge stated here can be used to study the genetic diversity of D. opposita Thunb.