Chlorurus sordidus
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REPOSITORIES: ENA
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Project description:The genomic DNAs of strains JPCM5 and 263 of L. infantum, strains LV39 and Friedlin of L. major and strains Parrot-TarII and S125 of L. tarentolae were used in comparative genomic hybridizations to reveal the intra-species and inter-species gene content, and to validate L. tarentolae Parrot-TarII genome sequencing results. Leishmania (Sauroleishmania) tarentolae was first isolated in the lizard Tarentola mauritanica. This species is not known to be pathogenic to humans but is often used as a model organism for molecular analyses or protein overproduction. The Leishmania tarentolae Parrot-TarII strain genome sequence was resolved by high-throughput sequencing technologies. The L. tarentolae genome was first assembled de novo and then aligned against the reference L. major Friedlin genome to facilitate contig positioning and annotation, providing a 23-fold coverage of the genome. This is the first non-pathogenic to humans kinetoplastid protozoan genome to be described, and it provides an opportunity for comparison with the completed genomes of the pathogenic Leishmania species. A high synteny was observed in de novo assembled contigs between all sequenced Leishmania species. A number of limited chromosomal regions diverged between L. tarentolae and L. infantum, while remaining syntenic with L. major. Globally, over 90% of the L. tarentolae gene content was shared with the other Leishmania species. There were 250 L. major genes absent from L. tarentolae, and interestingly these missing genes were primarily expressed in the intracellular amastigote stage of the pathogenic parasites. This implies that L. tarentolae may have impaired ability to survive as an intracellular parasite. In contrast to other Leishmania genomes, two gene families were expanded in L. tarentolae, namely the leishmanolysin (GP63) and a gene related to the promastigote surface antigen (PSA31C). Overall, L. tarentolae appears to have a gene content more adapted to the insect stage rather than the mammalian one. This may partly explain its inability to replicate within mammalian macrophages and its suspected preferred life style as promastigote in the lizards.
2011-10-21 | GSE27184 | GEO
Project description:The genomic DNAs of strains JPCM5 and 263 of L. infantum, strains LV39 and Friedlin of L. major and strains Parrot-TarII and S125 of L. tarentolae were used in comparative genomic hybridizations to reveal the intra-species and inter-species gene content, and to validate L. tarentolae Parrot-TarII genome sequencing results. Leishmania (Sauroleishmania) tarentolae was first isolated in the lizard Tarentola mauritanica. This species is not known to be pathogenic to humans but is often used as a model organism for molecular analyses or protein overproduction. The Leishmania tarentolae Parrot-TarII strain genome sequence was resolved by high-throughput sequencing technologies. The L. tarentolae genome was first assembled de novo and then aligned against the reference L. major Friedlin genome to facilitate contig positioning and annotation, providing a 23-fold coverage of the genome. This is the first non-pathogenic to humans kinetoplastid protozoan genome to be described, and it provides an opportunity for comparison with the completed genomes of the pathogenic Leishmania species. A high synteny was observed in de novo assembled contigs between all sequenced Leishmania species. A number of limited chromosomal regions diverged between L. tarentolae and L. infantum, while remaining syntenic with L. major. Globally, over 90% of the L. tarentolae gene content was shared with the other Leishmania species. There were 250 L. major genes absent from L. tarentolae, and interestingly these missing genes were primarily expressed in the intracellular amastigote stage of the pathogenic parasites. This implies that L. tarentolae may have impaired ability to survive as an intracellular parasite. In contrast to other Leishmania genomes, two gene families were expanded in L. tarentolae, namely the leishmanolysin (GP63) and a gene related to the promastigote surface antigen (PSA31C). Overall, L. tarentolae appears to have a gene content more adapted to the insect stage rather than the mammalian one. This may partly explain its inability to replicate within mammalian macrophages and its suspected preferred life style as promastigote in the lizards. Six strains of three Leishmania species were hybridizated to 12 microarrays, each with four biological replicates (independent cultures). Supplementary file: Represents final results obtained after statistical analysis of all replicates.
2011-10-20 | E-GEOD-27184 | biostudies-arrayexpress
Project description:Purpose: Examine the effect of the long non-coding RNA PARROT on the transcriptome in HeLa cells.
2017-02-10 | GSE69842 | GEO
Project description:Replacement of high-value fish species with cheaper varieties or mislabelling of food unfit for human consumption is a global problem violating both consumers’ rights and safety. For distinguishing fish species in pure samples, DNA approaches are available; however, authentication and quantification of fish species in mixtures remains a challenge. In the present study, a novel high-throughput shotgun DNA sequencing approach applying masked reference libraries was developed and used for authentication and abundance calculations of fish species in mixed samples. Results demonstrate that the analytical protocol presented here can discriminate and predict relative abundances of different fish species in mixed samples with high accuracy. In addition to DNA analyses, shotgun proteomics tools based on direct spectra comparisons were employed on the same mixture. Similar to the DNA approach, the identification of individual fish species and the estimation of their respective relative abundances in a mixed sample also were feasible. Furthermore, the data obtained indicated that DNA sequencing using masked libraries predicted species-composition of the fish mixture with higher specificity, while at a taxonomic family level, relative abundances of the different species in the fish mixture were predicted with slightly higher accuracy using proteomics tools. Taken together, the results demonstrate that both DNA and protein-based approaches presented here can be used to efficiently tackle current challenges in feed and food authentication analyses.
2021-03-09 | MSV000087017 | MassIVE
Project description:Interventions: CRC group:Nil;Healthy control group:Nil
Primary outcome(s): Identification of clostridium species
Study Design: Factorial
| 2697414 | ecrin-mdr-crc
Project description:Interventions: Tumor tissue group and tumor-adjacent tissue group:Nil
Primary outcome(s): Identification of clostridium species
Study Design: Factorial
| 2696605 | ecrin-mdr-crc
Project description:Aloe plant species have been used for centuries in traditional medicine and reported to be an important source of natural products. However, despite the large number of species within the Aloe genus, only a few of them have been investigated chemotaxonomically. A Molecular Network approach was used to highlight the different chemical classes characterizing the leaves of five Aloe species: Aloe macra, Aloe vera, Aloe tormentorii, Aloe ferox and Aloe purpurea. Aloe macra, A. tormentorii and A. purpurea are endemic from the Mascarene Islands comprising Reunion, Mauritius and Rodrigues. UHPLC-MS/MS analysis followed by a dereplication process allowed the characterization of 93 metabolites. The newly developed MolNotator algorithm was used as a tool for molecular networking and allowed a better exploration of the Aloe metabolome chemodiversity. The five species appeared to be rich in polyphenols (anthracene derivatives, flavonoids, phenolic acids). Therefore, total phenolic content and antioxidant activity of the five species were evaluated, and a DPPH-On-Line-HPLC assay was used to determine the metabolites responsible for the radical scavenging activity. The use of computational tools allowed a better description of the chemotaxonomy of five Aloe species, which showed differences in their metabolite composition, both qualitative and quantitative. Moreover, the molecular network approach allowed the identification of metabolites responsible for the antioxidant activity.
2022-06-17 | MSV000089679 | MassIVE
Project description:Viral metagenome in feces from different species of parrot
| PRJNA471756 | ENA
Project description:Ceramic vessels were used to cook fish/duck/black grouse, and proteomic studies were conducted on the ceramics to study how the choice of various database can affect the species identification and whether they can allow us to differentiate between fish and bird processing in ceramic vessels.
2022-11-11 | PXD027720 | Pride
Project description:Rainbow trout (Oncorhynchus mykiss) is an important aquaculture fish species that is farmed worldwide, and it is also the most widely cultivated cold water fish in China. This species, a member of the salmonidae family, is an ideal model organism for studying the immune system in fish. Two phenotypes of rainbow trout are widely cultured; wild-type rainbow trout with black skin (WR_S) and yellow mutant rainbow trout with yellow skin (YR_S). Fish skin is an important immune organ, however, little is known about the differences in skin immunity between WR_S and YR_S in a natural flowing water pond aquaculture environment, and very few studies were conducted to investigate the ceRNA mechanism for fish skin.
2021-08-17 | GSE181974 | GEO