Project description:In this study two Viperidae species, living in two different habitats, the horned desert viper (Cerastes cerastes) native to the deserts in North Africa and in turn the mangrove pit viper (Cryptelytrops purpureomaculatus), which can be found in South/Southeast Asia, were studied in terms of the identification of the venom proteome.
Project description:Nasopharyngeal carcinoma (NPC) is an invasive cancer with particularly high incidence in Southeast Asia and Southern China. The pathogenic mechanisms of NPC, particularly those involving epigenetic dysregulation, remain largely elusive, hampering the clinical management of this malignancy. To identify novel druggable targets, we carried out an unbiased high-throughput chemical screening and observed that NPC cells were highly sensitive to cyclin-dependent kinases (CDKs) inhibitors, especially THZ1, a covalent inhibitor of CDK7. THZ1 demonstrated pronounced anti-neoplastic activities both in vitro and in vivo. An integrative analysis using both whole-transcriptome sequencing (RNA-Seq) and chromatin-immunoprecipitation sequencing (ChIP-Seq) pinpointed oncogenic transcriptional amplification mediated by Super-Enhancer (SE) as a key mechanism underlying the vulnerability of NPC cells to THZ1 treatment. Further characterization of SE-mediated network identified many novel SE-associated oncogenic transcripts, such as BCAR1, F3, LDLR, TBC1D2 and a long non-coding RNA, TP53TG1. These transcripts were highly and specifically expressed in NPC, and functionally promoted NPC malignant phenotypes. Moreover, DNA-binding motif analysis within the SE segments suggest that several transcription factors (including ETS2, MAFK and TEAD1) may help establish and maintain SE activity across the genome. Our data together established the landscape of SE-associated oncogenic transcriptional network in NPC, which can be exploited for the development of more effective therapeutic regimen for this disease.
Project description:To identify key genes in the regulation of salt tolerance in the mangrove plant Bruguiera gymnorhiza, the transcriptome profiling under salt stress was carried out. Main roots and lateral roots were collected from the mangrove plants at 0, 1, 3, 6, 12 and 24 h, 3 6 and 12 days after NaCl-treatment. Keywords: time course, stress response, root type comparison
Project description:If copy number variants (CNVs) are predominantly deleterious, we would expect them to be more efficiently purged from populations with a large effective population size (Ne) than from populations with a small Ne. Malaria parasites (Plasmodium falciparum) provide an excellent organism to examine this prediction, because this protozoan shows a broad spectrum of population structures within a single species, with large, stable, outbred populations in Africa, small unstable inbred populations in South America and with intermediate population characteristics in South East Asia. We characterized 122 single-clone parasites, without prior laboratory culture, from malaria-infected patients in 7 countries in Africa, SE Asia and S. America using a high density SNP/CNV microarray. We scored 134 high-confidence CNVs across the parasite exome, including 33 deletions and 102 amplifications, which ranged in size from <500bp to 59kb, as well as 10,107 flanking, biallelic SNPs. Overall, CNVs were rare, small and skewed towards low frequency variants, consistent with the deleterious model. Relative to African and SE Asian populations, CNVs were significantly more common in S. America, showed significantly less skew in allele frequencies, and were significantly larger. On this background of low frequency CNV, we also identified several high-frequency CNVs under putative positive selection using an FST outlier analysis. These included known adaptive CNVs containing rh2b and pfmdr1, and several other CNVs (e.g. DNA helicase, and 3 conserved proteins) that require further investigation. Our data are consistent with a significant impact of genetic structure on CNV burden in an important human pathogen.
2015-11-19 | GSE75137 | GEO
Project description:Mangrove sediment bacterial community (16S)
| PRJNA1019063 | ENA
Project description:Mangrove 16S and ITS metabarcoding
Project description:Nasopharyngeal carcinoma (NPC) is an invasive cancer with particularly high incidence in Southeast Asia and Southern China. The pathogenic mechanisms of NPC, particularly those involving epigenetic dysregulation, remain largely elusive, hampering the clinical management of this malignancy. To identify novel druggable targets, we carried out an unbiased high-throughput chemical screening and observed that NPC cells were highly sensitive to cyclin-dependent kinases (CDKs) inhibitors, especially THZ1, a covalent inhibitor of CDK7. THZ1 demonstrated pronounced anti-neoplastic activities both in vitro and in vivo. An integrative analysis using both whole-transcriptome sequencing (RNA-Seq) and chromatin-immunoprecipitation sequencing (ChIP-Seq) pinpointed oncogenic transcriptional amplification mediated by Super-Enhancer (SE) as a key mechanism underlying the vulnerability of NPC cells to THZ1 treatment. Further characterization of SE-mediated network identified many novel SE-associated oncogenic transcripts, such as BCAR1, F3, LDLR, TBC1D2 and a long non-coding RNA, TP53TG1. These transcripts were highly and specifically expressed in NPC, and functionally promoted NPC malignant phenotypes. Moreover, DNA-binding motif analysis within the SE segments suggest that several transcription factors (including ETS2, MAFK and TEAD1) may help establish and maintain SE activity across the genome. Our data together established the landscape of SE-associated oncogenic transcriptional network in NPC, which can be exploited for the development of more effective therapeutic regimen for this disease.
Project description:If copy number variants (CNVs) are predominantly deleterious, we would expect them to be more efficiently purged from populations with a large effective population size (Ne) than from populations with a small Ne. Malaria parasites (Plasmodium falciparum) provide an excellent organism to examine this prediction, because this protozoan shows a broad spectrum of population structures within a single species, with large, stable, outbred populations in Africa, small unstable inbred populations in South America and with intermediate population characteristics in South East Asia. We characterized 122 single-clone parasites, without prior laboratory culture, from malaria-infected patients in 7 countries in Africa, SE Asia and S. America using a high density SNP/CNV microarray. We scored 134 high-confidence CNVs across the parasite exome, including 33 deletions and 102 amplifications, which ranged in size from <500bp to 59kb, as well as 10,107 flanking, biallelic SNPs. Overall, CNVs were rare, small and skewed towards low frequency variants, consistent with the deleterious model. Relative to African and SE Asian populations, CNVs were significantly more common in S. America, showed significantly less skew in allele frequencies, and were significantly larger. On this background of low frequency CNV, we also identified several high-frequency CNVs under putative positive selection using an FST outlier analysis. These included known adaptive CNVs containing rh2b and pfmdr1, and several other CNVs (e.g. DNA helicase, and 3 conserved proteins) that require further investigation. Our data are consistent with a significant impact of genetic structure on CNV burden in an important human pathogen. SNP/CGH hybridisation of 175 malaria parasite samples