Ontology highlight
ABSTRACT:
PROVIDER: PRJNA1097047 | ENA |
REPOSITORIES: ENA
Similar Datasets
Project description:Our data demonstrate the suitability of target capture technology for purifying very low quantities of Leptospira DNA from biological samples where the human genome is in vast excess. This enables deep sequencing of partial Leptospira genomes directly from clinical samples using next generation technologies and genotyping.
2022-05-23 | E-MTAB-11667 | biostudies-arrayexpress
Project description:Whole-genome sequences of Streptococcus suis isolated from humans in Thailand
| PRJNA691075 | ENA
Project description:Leptospira are emerging zoonotic pathogens transmitted from animals to humans typically through contaminated environmental sources of water and soil. Transcriptional regulation of pathogenic Leptospira spp. underlying the adaptive response to different hosts and environmental conditions remains elusive. In this study, we provide the first global Transcriptional Start Site (TSS) map of a Leptospira species. RNA was obtained from the pathogen Leptospira interrogans grown at 30° (optimal in vitro temperature) and 37°C (host temperature) and selectively enriched for 5' ends of native transcripts. Primary TSS (pTSS) was identified for 2,865 genes, accounting for 67% of the total genome. The majority of the TSSs were located between 0 to 10 nucleotides from the translational start site. Comparative dRNA-seq analysis revealed conservation of most pTSS at 30° and 37°C. Promoter prediction algorithms allow the identification of the binding sites of the alternative sigma factor sigma 54. However, other motifs were not identified indicating that Leptospira consensus promoter sequences are inherently different from the E. coli model. RNA sequencing also identified 277 and 226 putative small regulatory RNAs (sRNAs) at 30°C and 37°C, respectively, including 8 validated sRNAs by Northern blots. These results provide the first global view of transcriptional start sites and the repertoire of sRNAs in L. interrogans, and will establish a foundation for future experimental work on gene regulation under various environmental conditions including those in the host.
2017-01-23 | GSE92976 | GEO
Project description:Evolving resistance to artemisinin-based compounds in SE Asia threatens to derail attempts to control and eliminate malaria. Resistance has been confirmed in western Cambodia, has recently emerged in western Thailand, but is absent from neighboring Laos. Artemisinin resistance results in reduced parasite clearance rates (CR) from the blood following treatment. We used a two-phase approach to identify the genes underlying this ongoing selective event. Comparison of geographical differentiation and haplotype structure at 6,969 polymorphic SNPs in 91 parasites from western Cambodia, western Thailand and Laos identified 33 strongly selected genome regions. We screened SNPs and microsatellites within these genome regions in 718 parasites from western Thailand, and identified a 35kb region of chr 13 showing strong association (P=10-6 to 10-11) with slow CR. This region contains several compelling candidate loci, such as HSP70, for assessment by transfection. These results illustrate the efficacy of targeted association for identifying the genetic basis of adaptive traits.
2012-05-01 | GSE33002 | GEO
Project description:Leptospira, the causative agent of leptospirosis is known to have several proteases with potential to degrade extracellular matrix. However, a multipronged approach to identify, classify, characterize and elucidate their role has not been attempted. In this study, we carried out in-depth proteomic analysis of Triton X-114 fractions of Leptospira interrogans using high-resolution LC-MS/MS. Our analysis resulted in the identification of 104 of 130 proteases predicted by MEROPS. Approximately 3.5% of the Leptospira genome complements for proteases, which include catalytic types of metallo-, serine-, cysteine-, aspartic-, threonine- and asparagine- peptidases. Comparison of proteases from different serovars revealed that M04, M09B, M14A, M75, M28A, A01 and U73 protease families are exclusively present in pathogenic form. The M23 and S33 protease families are represented with more than 14 members in Leptospira. In silico prediction and characterization of the proteases revealed that several proteases are membrane anchored and secretory, classical as well as non-classical system. This study demonstrates the diversity and complexity of proteases, while maintaining conservation across the serovars in Leptospira and their differential expression under pathogenic conditions.
2018-04-18 | PXD009050 | Pride
Project description:The overall goal of these experiments was to determine how human endothelial cells respond to pathogenic Leptospira interrogans. Leptospira interrogans causes leptospirosis, the most widespread zoonotic infection in the world. A hallmark of leptospirosis is widespread endothelial damage, which in severe cases leads to hemorrhage. In these experiments, we infected two endothelial cell lines with pathogenic Leptospira interrogans serovar Canicola strain Ca12-005, and as controls, with the non-pathogenic Leptospira biflexa serovar Patoc strain Pfra. As additional controls, uninfected cells were also included in the analyses.
2010-07-27 | GSE23173 | GEO
Project description:The overall goal of these experiments was to determine how human endothelial cells respond to pathogenic Leptospira interrogans. Leptospira interrogans causes leptospirosis, the most widespread zoonotic infection in the world. A hallmark of leptospirosis is widespread endothelial damage, which in severe cases leads to hemorrhage. In these experiments, we infected two endothelial cell lines with pathogenic Leptospira interrogans serovar Canicola strain Ca12-005, and as controls, with the non-pathogenic Leptospira biflexa serovar Patoc strain Pfra. As additional controls, uninfected cells were also included in the analyses.
2010-07-27 | GSE23172 | GEO