Back to the Past: Assessing the Genetic Composition of Cotton-Top Tamarins (Saguinus oedipus) Before Sweeping Anthropogenic Impact
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ABSTRACT:
PROVIDER: PRJEB59492 | ENA |
REPOSITORIES: ENA
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Project description:Genomic approaches to the discovery of promoters for sustained expression in cotton (Gossypium hirsutum L.) under field conditions: expression analysis in transgenic cotton and Arabidopsis of a Rubisco small subunit promoter identified using EST sequence analysis and cDNA microarrays. Keywords: Promoter Discovery
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Project description:This study introduced the use of cotton in 200µL tips, namely cotton HILIC as a convenient tool for enriching large-scale glycopeptides before MS analysis in this study. The optimal loading buffer for cotton HILIC was investigated by using mouse brain as a complex test sample. Subsequently, the performance of cotton HILIC was evaluated by comparing with other two commercial enrichment approaches, venusil HILIC and Oasis MAX in both mouse brain and seminal plasma. Moreover, capacity and recovery rate were evaluated using different milligram of cotton in 200µL tips. Thus, a simple, convenient, and cost-friendly cotton HILIC method was proposed to achieve highly selective intact glycopeptide profiling.
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Project description:Cotton fiber were used for the expression analysis at different developmental stages Affymetrix Cotton Genome array were used for the global profiling of gene expression of cotton fiber at different developmental stages
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Project description:Protein phosphorylation is one of the most common post-translational modifications (PTMs), which is involved in many important physiological functions. Understanding protein phosphorylation at molecular level is critical to decipher its relevant biological processes and signaling networks. Mass spectrometry (MS) has been proved to be a powerful tool in comprehensive characterization of protein phosphorylation. Yet the low abundance and poor ionization efficiency of phosphopeptides make its MS analysis challenging; an enrichment with high efficiency and selectivity is always necessary before MS analysis. In this study, we developed a phosphorylated cotton fiber-based Ti(IV)-IMAC material (termed as: Cotton Ti-IMAC) that can serve as a novel platform for phosphopeptide enrichment. The cotton fiber can be effectively grafted with phosphate groups in a single step, where the titanium ions can then be immobilized onto to capture phosphopeptides. The material can be prepared with cost-effective reagents within only 4 hours. Benefiting from the flexibility and filterability of cotton fibers, the material can be easily packed as a spin-tip and make the enrichment process more convenient. Cotton Ti-IMAC successfully enriched phosphopeptides from protein standard digests and exhibited a high selectivity (β-casein/BSA = 1:1000) and excellent sensitivity (0.1 fmol/µL). Moreover, 2354 phosphopeptides was identified in a single LC-MS/MS injection after enriching from only 100 µg HeLa cell digests, with an enrichment specificity up to 97.51%. Taken together, we believe Cotton Ti-IMAC is ready to serve as a widely applicable and robust platform for achieving large-scale phosphopeptide enrichment and expanding our knowledge of phosphoproteomics in complex biological systems.
2023-10-23 | PXD037549 | Pride
Project description:In response to infection, viral genomes are processed by Dicer-like (DCL) ribonuclease proteins into viral small RNAs (vsRNAs) of discrete sizes. vsRNAs are then used as guides for silencing the viral genome. The profile of vsRNAs produced during the infection process has been extensively studied for some group of viruses. However, nothing is known for members of the economically important family Luteoviridae, a group of phloem-restricted viruses. Here, the population of vsRNAs from cotton plants infected with Cotton leafroll dwarf virus (CLRDV), a member of the genus Polerovirus, family Luteoviridae, is characterized.Deep sequencing of small RNAs (sRNAs) from CLRDV-infected cotton leaves was performed. Results showed 21-nt to 24-nt long vsRNAs matching all the viral genome, with a higher frequency of matches in the 3â region. Equivalent amounts of sense and antisense vsRNAs were found, and the 22-nt long small RNA class was the most prominent one. Looking for cotton Dcl transcripts levels during infection, we could observe that Dcl4 seems to be up-regulated, while Dcl2 seems to be down-regulated.This is the first report on the profile of sRNAs coming from a plant infected with a member of the family Luteoviridae. Our sequence data strongly suggest that virus-derived double-stranded RNA functions as one of the main precursors of vsRNAsOur results indicate that secondary structures of the viral RNAs are not the main source of the viRNAs observed, as suggested for other viruses. Judging by the profiled size classes, all cotton DCLs might be working to silence the virus. The possible causes for the unexpected high accumulation of 22-nt viRNAvsRNAs are discussed. CLRDV is the causal agent of worldwide cotton pathology named Cotton blue disease. Our results are an important contribution for understanding the molecular mechanisms involved in this and related diseases.
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Project description:Roof top Crust Metagenome Metagenome
| PRJNA949969 | ENA