Project description:To further explore the molecular mechanisms of flowering regulation in pitaya, we used de novo RNA sequencing-based transcriptomic analysis for four stages of pitaya subjected to light induction. We assembled 68113 unigenes in total, of which 29782 unigenes with functional annotations in the Nr database, 20716 annotations in SwissProt, 18088 annotations in KOG, and 11059 annotations in Kegg
Project description:miRNA profiling of human H9-derived neural stem cells (H9-NSCs) comparing control human adult dermal fibroblasts (hDFs), SOX2-transduced human induced neural stem cells (hDF-iNSC (SOX2)), SOX2/HMGA2-transduced human induced neural stem cells (hDF-iNSC (SOX2/HMGA2)). Goal was to determine the global miRNA expression between the groups.
Project description:The genomic sequences of diverse varieties of many crop species continue to be produced at a frenetic pace. However, it remains challenging to develop complete annotations of functional genes and regulatory elements in these genomes. Here, we explore the potential to use DNA methylation profiles to develop more complete and refined annotations. Using leaf tissue in maize, we define ~100,000 unmethylated regions (UMRs) that account for 5.8% of the genome; 33,375 UMRs (1.3% of the genome) are found greater than 2 kilobase pairs from genes. UMRs are highly stable in multiple vegetative tissues and they capture the vast majority of accessible chromatin regions from leaf tissue. However, many UMRs are not accessible in leaf (leaf-iUMRs) and these represent a set of genomic regions with potential to become accessible in specific cell types or developmental stages. Leaf-iUMRs often occur near genes that are expressed in other tissues and are enriched for transcription factor (TF) binding sites of TFs that are also not expressed in leaf tissue. The leaf-iUMRs exhibit unique chromatin modification patterns and are enriched for chromatin interactions with nearby genes. The total UMRs space in four additional monocots ranges from 80-120 megabases, which is remarkably similar considering the range in genome size of 271 megabases to 4.8 gigabases. In summary, based on the profile from a single tissue, DNA methylation signatures pinpoint both accessible regions and regions poised to become accessible or expressed in other tissues. Thus, UMRs can provide powerful filters to distill large genomes down to the small fraction putative functional elements and facilitate the discovery of tens of thousands of novel candidate regulatory regions.
Project description:A marine bacterium M44 was separated from 30 m deep seawater in the East China Sea (26° 28.3' N 122° 29.0' E) in 2006. 16S rDNA gene sequence comparison showed that the strain M44 was a member of the genus Sulfitobacter and highly similar to KMM 3554(T). A series of experiments demonstrated that this strain M44 had many distinctive characteristics: its cells were gram-negative and mesophilic; its colonies were slightly yellowish, round, convex, and smooth; and it could grow at 10-28°C, pH 6.0-10.0, and in the presence of 0-12.5% (w/v) NaCl; the optimum growth conditions were 25°C and pH 7.0, and the optimum Na(+) concentration was 2.5%. In addition, strain M44 contained 18 : 1 ω7c, 11 methyl 18 : 1 ω7c and 16 : 0 fatty acids as major fatty acids, and the genomic DNA G+C content was 58.04 mol%. According to our results of the secondary metabolites, six cyclodipeptides were isolated from the strain M44, which were Cyclo (Val-Leu), Cyclo (Phe-Val), Cyclo (Phe-Leu), Cyclo (Leu-Ile), Cyclo (Phe-Ile), and Cyclo (Trp-Pro). It is the first study of secondary metabolites isolated from this genus.
Project description:To exploring the difference of microRNA expression between IA and MMA, we have employed microRNA array expression profiling as a discovery platform to identify genes between the IA and MMA. Futher functional analyses were performed based on the data.
Project description:Divergence of K-562 genomes through in vitro clonal evolution revealed by comparing three sublines. Comparison of three K-562 sublines
Project description:<p>Traveler's diarrhea (TD) is caused by enterotoxigenic Escherichia coli (ETEC), other pathogenic gram-negative pathogens, norovirus and some parasites. Nevertheless, standard diagnostic methods fail to identify pathogens in more than 30% of TD patients, so it is predicted that new pathogens or groups of pathogens may be causative agents of disease. A comprehensive metagenomic study of the fecal microbiomes from 23 TD patients and seven healthy travelers was performed, all of which tested negative for the known etiologic agents of TD in standard tests. Metagenomic reads were assembled and the resulting contigs were subjected to semi-manual binning to assemble independent genomes from metagenomic pools. Taxonomic and functional annotations were conducted to assist identification of putative pathogens. We extracted 560 draft genomes, 320 of which were complete enough to be enough characterized as cellular genomes and 160 of which were bacteriophage genomes. We made predictions of the etiology of disease in individual subjects based on the properties and features of the recovered cellular genomes. Three subtypes of samples were observed. First were four patients with low diversity metagenomes that were predominated by one or more pathogenic E. coli strains. Annotation allowed prediction of pathogenic type in most cases. Second, five patients were co-infected with E. coli and other members of the Enterobacteriaceae, including antibiotic resistant Enterobacter, Klebsiella, and Citrobacter. Finally, several samples contained genomes that represented dark matter. In one of these samples we identified a TM7 genome that phylogenetically clustered with a strain isolated from wastewater and carries genes encoding potential virulence factors. We also observed a very high proportion of bacteriophage reads in some samples. The relative abundance of phage was significantly higher in healthy travelers when compared to TD patients. Our results highlight that assembly-based analysis revealed that diarrhea is often polymicrobial and includes members of the Enterobacteriaceae not normally associated with TD and have implicated a new member of the TM7 phylum as a potential player in diarrheal disease. </p>