Project description:We sequenced and analyzed the genome of a highly inbred miniature Chinese pig strain, the Banna Minipig Inbred Line (BMI). we conducted whole genome screening using next generation sequencing (NGS) technology and performed SNP calling using Sus Scrofa genome assembly Sscrofa11.1.
Project description:Leishmania donovani WHO reference strain MHOM/IN/80/DD8 and Leptomonas seymouri isolates Ld 2001 and Ld39 were used for proteome analysis which were originally isolated from clinical cases of kala azar patients with different inherent antimonial sensitivities. Ld 2001 was Sb-S and Ld 39 was Sb-R. The genome sequencing of these isolates had confirmed co-infection with Leptomonas.
Project description:Candida lusitaniae is an emerging human opportunistic yeast, which can switch from yeast to pseudohyphae, and one of the rare Candida species capable of sexual reproduction. Its haploid genome and the genetic tools available make it a model of interest to study gene function. This study describes the consequences of DPP3 inactivation on cell morphology and mating, both altered in the dpp3Δ knock-out. Interestingly, reintroducing a wild-type copy of the DPP3 gene in the dpp3Δ mutant failed to restore the wild-type phenotypes. Proteomic analyses showed that about 150 proteins were statistically deregulated in the dpp3Δ mutant, and that most of them did not return to their wild-type level in the reconstituted DPP3 strain. The analysis of the segregation of the dpp3Δ mutation and the phenotypes in the progeny of a cross (between the dpp3Δ knock-out and a wild-type strain) showed that the phenotypes are not linked to dpp3Δ, but to a secondary mutation. Genome sequencing of the dpp3Δ mutant allowed us to identify this secondary mutation.
Project description:In Drosophila, siRNAs are classified as endo- or exo-siRNAs based on their origin. Both are processed from double-stranded RNA precursors by Dcr-2, then loaded into the Argonaute protein Ago2. While exo-siRNAs serve to defend the cell against viruses, endo-siRNAs restrict the spread of selfish DNA in somatic cells, analogous to piRNAs in the germ line. Endo- and exo-siRNAs display a differential requirement for double-stranded RNA binding domain proteins (dsRBPs): R2D2 is needed to load exo-siRNAs into Ago2 while the PD isoform of Loquacious (Loqs-PD) stimulates Dcr-2 during the nucleolytic processing of hairpin-derived endo-siRNAs. In cell culture assays, R2D2 antagonizes Loqs-PD in endo-siRNA silencing and Loqs-PD is an inhibitor of RNA interference. Loqs-PD can interact via the C-terminus unique to this isoform with the DExH/D-helicase domain of Drosophila Dcr-2, where binding of R2D2 has also been localized. Separation of the two pathways is not complete; rather, the dicing and Ago2-loading steps appear uncoupled, analogous to the corresponding steps in miRNA biogenesis. Analysis of deep sequencing data further demonstrates that in r2d2 mutant flies, siRNAs can be loaded into Ago2 but not all siRNA classes are equally proficient for this. Thus, the canonical Ago2-RISC loading complex can be bypassed under certain circumstances.
Project description:In Drosophila, the siRNA pathway is initiated when exogenous or endogenous double stranded RNA (dsRNA) is processed into siRNAs by Dicer-2 (Dcr-2) and a dsRNA-binding protein (dsRBP) cofactor called Loquacious (Loqs). The siRNAs are then loaded onto Argonaute-2 (Ago2) protein by the action of Dcr-2 with another dsRBP cofactor called R2D2. Loaded Ago2 executes the destruction of target RNAs that have sequence complementarity to the siRNA. Dcr-2, R2D2, and Ago2 have also been shown to be required for innate antiviral defense in Drosophila. However, the biogenesis of virus-derived siRNAs (vsiRNAs) and their targets in virus-infected cells remain unclear. Here, we analyzed the antiviral response in Drosophila by monitoring the replication of different RNA viruses and deep sequencing of small RNAs in infected animals. We show that vsiRNAs are generated by Dcr-2 processing of dsRNA formed during viral genome replication and transcription. These vsiRNAs then directly target viral transcripts but not genomes, to inhibit viral replication. The biogenesis of vsiRNAs was virtually independent of Loqs and R2D2. R2D2, however, was essential for sorting and loading of vsiRNAs onto Ago2 and effective silencing of viral RNA expression. Loqs was completely dispensable for silencing of viruses in contrast to its role in silencing of endogenous targets. Our results suggest the existence of a specific siRNA pathway triggered by viral infection independent of conserved dsRBP cofactors and separate from the endogenous pathway. Inhibition of virus replication resulting from direct injection of viral RNA into Drosophila embryos was also not dependent on Loqs, suggesting the distinction of the two pathways is not related to the mode of entry but recognition of intrinsic features of viral RNA or its mode of replication. We speculate that this unique framework might be necessary for a prompt and efficient antiviral response
Project description:Using an integrated systems approach, the expressed proteome of B. diazoefficiens strain 110scp4 was measured under i) normal, oxic growth, and ii) microoxic growth condtions. This included, as a first step, the sequencing and de novo assembly of the genome of this widely used rhizobial model strain, which turned out to harbor several deletions and insertions compared to the B. diazoefficiens USDA 110 NCBI reference genome. With this optimal basis in hand, a shotgun proteomics approach relying on a slightly adapated FASP protocol was carried out, allowing to identify 2900 (oxia) and 2826 (microoxia) proteins, respectively, thereby largely expanding the proteome known to be expressed under microoxic conditions.
Project description:The 791spin is the spinosad-selected strain derived from 791a, a laboratory strain derived from a multi-resistant field-collected sample of houseflies. The 791a strain proved highly resistant to pyrethroids and some anticholinesterases and showed some resistance to the chitin synthesis-disrupting larvicides.In order to understand the evolution of insecticide resistance, de novo assembly of a spinosad resistant housefly strain 791spin using 454 technology was initiated
Project description:Helicobacter pylori enhances the risk for ulcer disease and gastric cancer, yet only a minority of H. pylori-colonized individuals develop disease. We examined the ability of two H. pylori isolates to induce differential host responses in vivo or in vitro, and then used an H. pylori whole genome microarray to identify bacterial determinants related to pathogenesis. Gastric ulcer strain B128 induced more severe gastritis, proliferation, and apoptosis in gerbil mucosa than did duodenal ulcer strain G1.1, and gastric ulceration and atrophy occurred only in B128+ gerbils. In vitro, gerbil-passaged B128 derivatives significantly increased IL-8 secretion and apoptosis compared with G1.1 strains. DNA hybridization to the microarray identified several strain-specific differences in gene composition including a large deletion of the cag pathogenicity island in strain G1.1. Partial and complete disruption of the cag island in strain B128 attenuated induction of IL-8 in vitro and significantly decreased gastric inflammation in vivo. These results indicate that the ability of H. pylori to regulate epithelial cell responses related to inflammation depends on the presence of an intact cag pathogenicity island. Use of an H pylori whole genome microarray is an effective method to identify differences in gene content between H. pylori strains that induce distinct pathological outcomes in a rodent model of H. pylori infection. Set of arrays organized by shared biological context, such as organism, tumors types, processes, etc. Keywords: Logical Set