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

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.

The Study on the Gene Expression of Preimplantation IVF Bovine Embryos

The cattle different stage embryos obtained from in vitro was studied using the technology of single preimplantation embryo mRNA different display:single 8-cell and blastocyst stage embryos were studied using technology of mRNA different display and one different fragment was found. The result suggested that this fragment displayed high homology (99%) to cattle mRNA for ribosomal protein L31. Then to detect the expression of RPL31mRNA in 8 cell and blastocyst stage embryos by real-time quantitative PCR,the result showed the relative amount of 8 cells was 3.2 times of blastocyst's.

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.

Combining QTL mapping and expression profile analysis to identify candidate genes of cold tolerance from Dongxiang common wild rice(Oryza rufipogon Griff.)

Rice（Oryza sativa L.）, a tropical and subtropical crop, is susceptible to low temperature stress during seedling, booting, and flowering stages, which leads to lower grain quality levels and decreasing rice yields. Cold tolerance is affected by multiple genetic factors in rice, and the complex genetic mechanisms associated with chilling stress tolerance remain unclear. Here, we detected seven quantitative trait loci（QTLs） for cold tolerance at booting stage and identified one cold tolerant line, SIL157, in an introgression line population derived from a cross between the indica variety Guichao 2, as the recipient, and Dongxiang common wild rice, as the donor. When compared with Guichao 2, SIL157 showed a stronger cold tolerance during different growth stages. Through an integrated strategy that combined QTL-mapping with expression profile analysis, six candidate genes, which were up-regulated under chilling stress at the seedling and booting developmental stages, were studied. The results may help in understanding cold tolerance mechanisms and in using beneficial alleles from wild rice to improve the cold tolerance of rice cultivars through molecular marker-assisted selection.

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.

Cloning and Sequence Analysis of SLC11A1 Gene Promoter of Three Cattle Breeds in Xinjiang

[Objective]Solute carrier family 11 member 1（SLC11A1）is a major natural resistance candidate gene,which contributes to defense mechanisms of a variety of intracellular bacteria.The SLC11A1 gene promoter sequence of Xinjiang Brown Cattle,Holstein and Simmental were cloned in the test,and promoter sequence difference was analyzed,in order to provide genetic marker-assisted selection for disease-resistant breeding of dairy cattle.[Method]The Genomic DNA was extracted from whole blood collected from three cattle breeds in Xinjiang,and the 5’ flanking region of SLC11A1 gene was amplified by PCR and sequenced.The sequence was analyzed by bioinformatics software CpGplot,RepeatMasker,TFSEARCH,WWW Signal Scan and dual luciferase assay system.[Result]The SLC11A1 gene promoter sequence of 1 463 bp was confirmed,which had promoter activity.No CpG islands were found on promoter sequence.There were four different sites in SLC11A1 gene promoter sequences between Angus from America and three cattle breeds in Xinjiang.Sequence analysis revealed 12 transcription factor binding sites including Sp1,NF1,RelA-p65,GKLF,and CPBP.In promoter region there was an enhancer region（-734- -740）and two short scattered repetitive elements BOV-tA2,MIR3,as well as repeated DNA element Charlie8.[Conclusion]The SLC11A1 gene promoter sequences of three breeds were obtained,which were different from that of Angus.The paper provided a theoretical basis for further studying the influence of SLC11A1 gene polymorphisms on resistance against intracellular bacteria infection.

Cultivar Mixture Cooperation(CMC)of rice varieties(lines) with different blast resistant gene

We studied Cultivar Mixture Cooperation(CMC)of rice varieties(lines)by screening mixture ofrice varieties which possess different genes,1983-1996.

The stability of E protein gene of the Japanese encephalitis live attenuated vaccine virus SA_(14)-14-2

The purpose of this study was to understand the stability and possibility of back mutation of Japanese encephalitis （JE） attenuated vaccine virus strain SA14-14-2 HKs on molecular level. The E genes of the SA14-14-2 HKs vaccine virus and its PHK cells passaged virus （SA14-14-2 HK17 ）, its mouse brain passaged virus （SA14-14-2 SM1 ） were sequenced and compared with the E gene of parental SAI4 virus. The total RNA was extracted from infected Vero cells and amplified by RT-PCR. The RT-PCR products were purified and cloned into T-vector. Positive clones were screened, identified and sequenced. There were twelve nucleotides and eight amino acids substitutions between SA14 parent virus and SA14-34-2 PHKs vaccine virus. The SA14-14-2 PHK17 virus showed two additional mutations （E-331 and E-398） which were not back mutations. Although five additional mutations were found in SA14-34-2 SMt virus, only one （E-307） was back mutation. Genetic characteristics of the attenuated vaccine virus SA14- 34-2 were stable when it was passaged 37 times on PHK cells or one time in mouse brains.

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.

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.

Relationship between FGF12 expression in high-grade gliomas and clinical features

Objective:gliomas are the most common intracranial tumors.Fibroblast growth factor-12(FGF12),which belongs to the fibroblast growth factor(FGFs)family,plays an important role in cell mitosis,as well as in other life functions,such as embryo development,tissue repair,cell proliferation,and tumor growth and invasion.The purpose of this study was to explore the potential value of FGF12 in high-grade gliomas and to predict its drug sensitivity.To provide a possible therapeutic target for glioma.Methods:high-grade glioma gene expression data and clinical information were downloaded from the gene expression omnibus(GEO)database,using the R language“impute”and“survival”survival analysis package.The FGF12 genes closely related to survival were screened,a survival curve was drawn,and clinical correlation analysis was conducted.The differentially expressed genes(DEGs)were defined as |logFC|>1,adj.PVal<0.05 as the standard.We used the David for Gene Ontology(GO)and Kyoto Encyclopedia of Genes and Genomes(KEGG)analysis,and constructed the protein-protein interactions(PPI)network.Then we used the Connectivity Map(CMAP)database for drug location,and the validation group was verified by the Chinese Glioma Genome Atlas(CGGA)database in the same way.Results:we found that high FGF12 expression was associated with a higher survival rate.The same validation was performed in the validation group through the CGGA database,and the survival curve showed the same trend.The expression level of FGF12 is an independent factor that affects the life time and status of the samples,and it is a low risk factor.GO enrichment analysis showed that differential genes were enriched in matrix transmembrane transporter activity,ion channels and calcium ion active channels.KEGG showed that DEGs were enriched in the phosphatidylinositol 3-kinase(PI3K)-protein kinase B(Akt)signaling pathway,dopaminergic synapse and cyclic adenosine monophosphate(cAMP)signaling pathway.Four seed genes,GRIA2,COLLA2,GRIA4 and HES6,were obtained by PPI network analysis.The cAMP was used to analyze and obtained 7 small molecule drugs,such as merbromin,naloxone,AH-2384&ticarcillin,vincamine,amoxicillin,azacyclonol,which may be helpful in the prognosis of high-grade gliomas.Conclusion:FGF12 and its pathway may serve as a biomarker or therapeutic target for high-grade gliomas.

Parameters inversion of high central core rockfill dams based on a novel genetic algorithm

Parameters identification of rockfill materials is a crucial issue for high rockfill dams. Because of the scale effect, random sampling and sample disturbance, it is difficult to obtain the actual mechanical properties of rockfill from laboratory tests. Parameters inversion based on in situ monitoring data has been proven to be an efficient method for identifying the exact parameters of the rockfill. In this paper, we propose a modified genetic algorithm to solve the high-dimension multimodal and nonlinear optimal parameters inversion problem. A novel crossover operator based on the sum of differences in gene fragments(So DX) is proposed, inspired by the cloning of superior genes in genetic engineering. The crossover points are selected according to the difference in the gene fragments, defining the adaptive length. The crossover operator increases the speed and accuracy of algorithm convergence by reducing the inbreeding and enhancing the global search capability of the genetic algorithm. This algorithm is compared with two existing crossover operators. The modified genetic algorithm is then used in combination with radial basis function neural networks(RBFNN) to perform the parameters back analysis of a high central earth core rockfill dam. The settlements simulated using the identified parameters show good agreement with the monitoring data, illustrating that the back analysis is reasonable and accurate. The proposed genetic algorithm has considerable superiority for nonlinear multimodal parameter identification problems.

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

cDNA representational difference analysis of differentially expressed cDNA sequences in human nasopharyngeal carcinoma

Objective To search differentially expressed sequences correlated with pathogenesis of human nasopharyngeal carcinoma (NPC), including the candidates of tumor suppressor genes Methods Representational difference analysis (RDA) was performed to isolate differentially expressed sequences between cDNA from normal human primary cultures of nasopharyngeal epithelial cells and cDNA from NPC cell line HNE1 The source of differentially expressed products were proved by Southern blot, Northern blot and in situ hybridization The fragments were cloned with pGEM T easy kit and sequenced by the chain termination reaction Results Four differentially expressed cDNA fragments were isolated in the fourth subtractive hybridization using cDNA from normal human nasopharyngeal epithelial cells as tester amplicon and cDNA from NPC cell line HNE1 as driver amplicon by cDNA RDA These differential cDNA fragments revealed that they really came from the tester amplicon and were not expressed or down regulated in the NPC HNE1 cells Some of the genes were expressed only in human nasopharyngeal epithelial cells but deleted or down regulated in the biopsies of NPC Of these obtained clones, some were the sequences of the human known genes including house keeping genes, the others represented novel gene sequences Conclusion The differentially expressed products including the candidates of tumor suppressor genes may be associated with the initiation of the NPC

Genome-wide analysis of differential DNA methylation in Silver-Russell syndrome

Silver-Russell Syndrome(SRS) is clinically heterogeneous disorder characterized by low birth weight, postnatal growth restriction, and variable dysmorphic features. Current evidence strongly implicates imprinted genes as an important etiology of SRS. Although almost half of the patients showed DNA hypomethylation at the H19/IGF2 imprinted domain, and approximately7%–10% of SRS patients have maternal uniparental disomy of chromosome 7(UPD(7) mat); the rest of the SRS patients shows unknown etiology. In this study, we investigate whether there are further DNA methylation defects in SRS patients. We measured DNA methylation in seven SRS patients and five controls at more than 485,000 CpG sites using DNA methylation microarrays. We analyzed methylation changes genome-wide and identified the differentially methylated regions(DMRs) using bisulfite sequencing and digital PCR. Our analysis identifies epimutations at the previously characterized domains of H19/IGF2,providing proof of principle that our methodology can detect the changes in DNA methylation at imprinted loci. In addition,our results showed a novel SRS associated imprinted gene OSBPL5 located on chromosome 11p14 with the probe cg25963939,which is hypomethylated in 4/7 patients(P=0.023, β=.0.243). We also report DMRs in other genes including TGFβ3, HSF1,GAP43, NOTCH4 and MYH14. These DMRs were found to be associated with SRS using GO pathway analysis. In this study,we identified the probe cg25963939, located at the 5′UTR of imprinted gene OSBPL5, as a novel DMR that is associated with SRS. This finding provides new insights into the mechanism of SRS etiology and aid the further stratification of SRS patients by molecular phenotypes.