Dataset Information

Vibrio fluvialis A8 secretome nanoLC-MS/MS

ABSTRACT: Vibrio fluvialis A8 was a newly isolated strain that possessed a good agarase production ability. The Secretomic analysis using nanoLC-MS/MS was performed to study the molecular properties including molecular weight, pI and relative abundance of the agarases in the secretome of this strain.

INSTRUMENT(S): Q Exactive

ORGANISM(S): Vibrio Fluvialis

TISSUE(S): Cell Culture

SUBMITTER: Chunsheng Li

LAB HEAD: Chunsheng Li

PROVIDER: PXD019302 | Pride | 2020-07-30

REPOSITORIES: Pride

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Publications

Comparative Genomic and Secretomic Analysis Provide Insights Into Unique Agar Degradation Function of Marine Bacterium <i>Vibrio fluvialis</i> A8 Through Horizontal Gene Transfer.

Li Chunsheng C Li Chi C Li Laihao L Yang Xianqing X Chen Shengjun S Qi Bo B Zhao Yongqiang Y

Frontiers in microbiology 20200811

Agarose-oligosaccharide production from agar degradation by agarase exhibits lots of advantages and good application prospects. In this study, a novel agar-degrading bacterium <i>Vibrio</i> sp. A8 was isolated from a red algae in the South China Sea. The whole genome sequencing with comparative genomic and secretomic analysis were used to better understand its genetic components about agar degradation. This strain exhibited good agarase production in artificial seawater after culture optimizatio ...[more]

PMID: 32849481

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Project description:Background: With the growing availability of entire genome sequences, an increasing number of scientists can exploit oligonucleotide microarrays for genome-scale expression studies. While probe-design is a major research area, relatively little work has been reported on the optimization of microarray protocols. Results: As shown in this study, suboptimal conditions can have considerable impact on biologically relevant observations. For example, deviation from the optimal temperature by one degree Celsius lead to a loss of 44% of differentially expressed genes identified. While genes from thousands of Gene Ontology categories were affected, transcription factors and other low-copy-number regulators were disproportionately lost. Calibrated protocols are thus required in order to take full advantage of the large dynamic range of microarrays. For an objective optimization of protocols we introduce an approach that maximizes the amount of information obtained per experiment. A comparison of two typical samples is sufficient for this calibration. We ensure, however, that optimization results are independent of the samples and the specific measures used for calibration. Both simulations and spike-in experiments confirm an unbiased determination of generally optimal experimental conditions. Conclusions: Well calibrated hybridization conditions are thus easily achieved and necessary for the efficient detection of differential expression. They are essential for the sensitive profiling of low-copy-number molecules. This is particularly critical for studies of transcription factor expression, or the inference and study of regulatory networks. Supporting material, including source code and data, is available at http://bioinf.boku.ac.at/pub/optMA2010/. Optimization of hybridization temperature via an assessment of differential expression between two samples (male vs female Drosophila melanogaster) in 6 technical replicates (3 regular + 3 dye-swaps) for hybridizations at different temperatures (in two batches of 50, 52, 54, and 56; and 47, 49, 50, and 51 degree Celsius, with the repeated hybridization at 50 degree Celsius serving to demonstrate batch-to-batch stability).

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Dataset Information

Vibrio fluvialis A8 secretome nanoLC-MS/MS

Publications

Comparative Genomic and Secretomic Analysis Provide Insights Into Unique Agar Degradation Function of Marine Bacterium <i>Vibrio fluvialis</i> A8 Through Horizontal Gene Transfer.

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