Molecular Characterization of Four ADF Genes Differentially Expressed in Cotton

Actin depolymerizing factor （ADF）, highly conserved in all eukaryotic cells, is a low molecular mass of actin-binding protein, which plays a key role in modulating the polymerizing and depolymerizing of the actin filaments. Four cDNAs （designated GhADF2, GhADF3, GhADF4, and GhADF5, respectively） encoding ADF proteins were isolated from cotton （Gossypium hirsutum） fiber cDNA library. GhADF2 cDNA is 705 bp in length and deduces a protein with 139 amino acids. GhADF3 cDNA is 819 bp in length and encodes a protein of 139 amino acids. GhADF4 cDNA is 804 bp in length and deduces a protein with 143 amino acids. GhADF5 cDNA is 644 bp in length and encodes a protein of 141 amino acids. The molecular evolutionary relationship of these genes was analyzed by means of bioinformatics. GhADF2 is closely related to GhADF3 （99% identity） and PetADF2 （89% identity）. GhADF4 is closely related to AtADF6 （78% identity）, and GhADF5 is closely related to AtADF5 （83% identity）. These results demonstrated that the plant ADF genes are highly conserved in structure. RT-PCR analysis showed that GhADF2 is predominantly expressed in fiber, whereas, GhADF5 is mainly expressed in cotyledons. On the other hand, it seems that GhADF3 and GhADF4 have no tissue specificity. Expression levels of different ADF genes may vary considerably in the same cell type, suggesting that they might be involved in regulating tissue development of cotton and the each ADF isoform may diverge to form the functional difference from the other ADFs during evolution.

Analysis of differential genes of ischemic stroke-induced heart tissue in mice based on GEO database

Objective:The differential genes of left ventricle in middle cerebral artery occlusion model(MCAO)mice and Sham mice(Sham)mice at 24h and 72h after ischemia were compared respectively,and the differential genes and their regulated functional pathways were analyzed at different time points after ischemic stroke,so as to analyze the mechanism of inducing cardiac dysfunction after ischemic stroke and provide evidence for its treatment.Methods:Gene-chip data from the left ventricle of MCAO mice and Sham mice were downloaded from the GEO database at the National Center for Biotechnology Information(NCBI).The differentially expressed genes were obtained by R language software programming.The GO functional enrichment and KEGG pathway enrichment analysis of the obtained differential genes were performed using DAVID 6.8 online analysis tool,and the Omicshare online analysis tool was used to visualize the enrichment analysis results.Results:At 24h after ischemia,187 differentially expressed genes were obtained,including 56 GO enrichment pathways and 5 KEGG enrichment pathways with significant significance.After 72h after ischemia,51 differentially expressed genes were obtained,14 GO enrichment pathways and 3 KEGG enrichment pathways with significant significance.The two time points involved Aplnr and Itgb6 gene targets and PI3K-Akt signaling pathway.Conclusion:①By analyzing the gene expression profile data,the differentially expressed genes and related pathways of cardiac dysfunction induced by ischemic stroke were obtained.②PI3K-AKT signaling pathway is closely related to the regulation of cardiac function,and regulation of PI3K-AKT signaling pathway may be an important direction for the treatment of cardiac dysfunction after ischemic stroke.

Identification of key genes and related pathways in hepatocarcinoma usingbioinformatics analysis

Objective Various treatments have greatly reduced the mortality of hepatocellular carcinoma （HCC）. However, few therapies could be performed in advanced HCC. Therefore, understanding the characteristics of HCC at the level of the whole transcriptome can help prevent the progression of HCC. Methods： The aim of this study was to identify differently expressed genes and potent pathways between normal liver and HCC tissues. The gene expression profiles of GSE104627 were downloaded from Gene Expression Omnibus database. The Gene Ontology and Kyoto Encyclopedia of Genes and Genomes pathway enrichment analyses were performed and protein-protein interaction network of the differentially expressed genes were constructed by Cytoscape software. Results： In total, 880 differently expressed genes were identified between normal and tumor tissues, including 554 up-regulated genes and 326 down-regulated genes. Gene Ontology analysis results showed that the up-regulated genes were significantly enriched in establishment of RNA localization, nucleic acid transport, RNA transport, RNA localization and nucleobase, nucleoside, nucleotide and nucleic acid transport. Kyoto Encyclopedia of Genes and Genomes pathway analysis showed the up-regulated genes were enriched in axon guidance, dorso-ventral axis formation and pathways in cancer. The top 10 hub genes were identified from the protein - protein interaction network, and sub-networks revealed these genes were involved in significant pathways, including G protein-coupled receptors signaling pathway, signaling pathway via MAPK and extracellular matrix organization. Conclusion： The present study described the differently expressed genes between normal tissues and HCC tissues from the level of gene transcription. The possible signaling pathways involved in the development of HCC and related molecules involved were analyzed. However, further laboratory and clinical validation is still needed.

Genes Expressing Differences in Upland Cotton Fiber Development Between 12 DPA and 16 DPA

Cotton is the major dominant natural fiber crop on the earth.Although some current cotton genetics and breeding programs had made great progresses in cotton lint yield increases and disease resistance(tolerance),fiber quality has little improvement.Global understanding genes expression

The first cavefish in the Dinaric Karst?Cave colonization made possible by phenotypic plasticity in Telestes karsticus

Cave animals are an excellent model system for studying adaptive evolution.At present,however,little is known about the mechanisms that enable surface colonizers to survive in the challenging environment of caves.One possibility is that these species have the necessary genetic background to respond with plastic changes to the pressures of underground habitats.To gain insight into this process,we conducted a comparative study with the fish species Telestes karsticus,which occurs in a hydrological system consisting of an interconnected stream and a cave.Results showed that T.karsticus resided year-round and spawned in Sušik cave,making it the first known cavefish in the Dinaric Karst.Cave and surface populations differed in morphological and physiological characteristics,as well as in patterns of gene expression without any evidence of genetic divergence.To test whether observed trait differences were plastic or genetic,we placed adult fish from both populations under light/dark or constant dark conditions.Common laboratory conditions erased all morphometric differences between the two morphs,suggesting phenotypic plasticity is driving the divergence of shape and size in wild fish.Lighter pigmentation and increased fat deposition exhibited by cave individuals were also observed in surface fish kept in the dark in the laboratory.Our study also revealed that specialized cave traits were not solely attributed to developmental plasticity,but also arose from adult responses,including acclimatization.Thus,we conclude that T.karsticus can adapt to cave conditions,with phenotypic plasticity playing an important role in the process of cave colonization.

Expression and analysis of zinc fi nger family gene in Lenzites gibbosa

Zinc finger transcription factors play significant roles in the growth and development of plant and animal,but their function remains obscure in fungi.Lenzites gibbosa mycelia were extracted and sequenced by transcriptome analysis after growing on sawdust at different times to support mycelial growth of L.gibbosa in a nutrient matrix.Data bases used for analysis were the Kyoto encyclopedia of genes and genomes(KEGG)annotation,the cluster of orthologous groups of proteins(COG)and gene ontology(GO)annotation.Zinc finger class genes related to the growth and development of L.gibbosa were screened.GO annotation and enrichment analysis of diff erentially expressed genes were carried out.A total of 114.55 Gb Clean Data were obtained from the L.gibbosa transcriptome.The average Clean Data in each sample was 6.16 Gb.The relative efficiency of reads between each sample and the reference genome was 88.5%to 91.4%.The COG analysis showed that most zinc finger protein genes were related to replication,recombination and repair function.GO enrichment analysis showed that the expressed genes involved in cellular process,cell part and binding.We identifi ed seventy-two expressed genes including seven up-regulated genes and sixty-five down-regulated genes by applying DESeq2 data analysis software.By comparing the significantly expressed genes with KEGG database,66 annotated sequences were obtained,and 35 primary metabolic pathways were annotated.Pathway enrichment analysis showed that differentially expressed genes were signifi cantly enriched in protein processing in endoplasmic reticulum and ubiquitin-mediated proteolysis pathways.Gene_11750 and gene_5266 are highly correlated with the growth and development of L.gibbosa and are closely related to protein processing in endoplasmic reticulum and ubiquitin-mediated proteolysis pathway.According to gene functional analysis,seven important differentially expressed genes related to the growth and development of L.gibbosa were identified.

Microarray Study of Mechanism of Trichostatin A Inducing Apoptosis of Molt-4 Cells

Histone deacetylase was overexpressed in a variety of cancers and was closely correlated with oncogenic factors. The histone deacetylase inhibitor, trichostatin A （TSA） was shown to induce apoptosis in many cancer cells. However, the mechanism of TSA on induction of cancer cells apoptosis is poorly understood. This study was designed to characterize the global gene expression profiles before and after treatment of human leukemia cell line Molt-4 with TSA. Flow cytometry, MTT and DNA ladder were used to observe the effect of TSA on the apoptosis of MOLT-4 cells and normal human peripheral blood mononuclear cells （PBMC）. Microarray, reverse transcription-polymerase chain reaction （RTopCR） and Western blotting were used to detect the difference of gene and protein expressions of Molt-4 cells after incubation of the cells with TSA. The results showed that TSA could induce Molt-4 apoptosis in dose- and time-dependent manners but spared PBMCs. Microarray analysis showed that after incubation with TSA for 9 h, 310 genes were upregulated and 313 genes were deregulated. These genes regulate the growth, differentiation and survival of cells. Among these genes, STATSA was down-regulated by 80.4% and MYC was down-regulated by 77.3%. It was concluded that TSA has definite growth-inhibiting and apoptosis-inducing effects on Molt-4 cells in time- and dose-dependent manners, with weak cytotoxic effects on PBMCs at the same time. The mechanism of TSA selectively inducing apoptosis and inhibiting growth may be ascribed to the changes of pro-proliferation genes and anti-apoptosis genes.

DIOXIN RECEPTOR GENE EXPRESSION IN DIFFERENT STAINS OF MICE

The aim of the present experiment is to find out whether there exist any differences in tissue expression of aryl