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      Quantitative Proteomics Study of Larval Settlement in the Barnacle Balanus amphitrite

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          Abstract

          Barnacles are major sessile components of the intertidal areas worldwide, and also one of the most dominant fouling organisms in fouling communities. Larval settlement has a crucial ecological effect not only on the distribution of the barnacle population but also intertidal community structures. However, the molecular mechanisms involved in the transition process from the larval to the juvenile stage remain largely unclear. In this study, we carried out comparative proteomic profiles of stage II nauplii, stage VI nauplii, cyprids, and juveniles of the barnacle Balanus amphitrite using label-free quantitative proteomics, followed by the measurement of the gene expression levels of candidate proteins. More than 700 proteins were identified at each stage; 80 were significantly up-regulated in cyprids and 95 in juveniles vs other stages. Specifically, proteins involved in energy and metabolism, the nervous system and signal transduction were significantly up-regulated in cyprids, whereas proteins involved in cytoskeletal remodeling, transcription and translation, cell proliferation and differentiation, and biomineralization were up-regulated in juveniles, consistent with changes associated with larval metamorphosis and tissue remodeling in juveniles. These findings provided molecular evidence for the morphological, physiological and biological changes that occur during the transition process from the larval to the juvenile stages in B. amphitrite.

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          Most cited references54

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          Empirical statistical model to estimate the accuracy of peptide identifications made by MS/MS and database search.

          We present a statistical model to estimate the accuracy of peptide assignments to tandem mass (MS/MS) spectra made by database search applications such as SEQUEST. Employing the expectation maximization algorithm, the analysis learns to distinguish correct from incorrect database search results, computing probabilities that peptide assignments to spectra are correct based upon database search scores and the number of tryptic termini of peptides. Using SEQUEST search results for spectra generated from a sample of known protein components, we demonstrate that the computed probabilities are accurate and have high power to discriminate between correctly and incorrectly assigned peptides. This analysis makes it possible to filter large volumes of MS/MS database search results with predictable false identification error rates and can serve as a common standard by which the results of different research groups are compared.
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            Absolute protein expression profiling estimates the relative contributions of transcriptional and translational regulation.

            We report a method for large-scale absolute protein expression measurements (APEX) and apply it to estimate the relative contributions of transcriptional- and translational-level gene regulation in the yeast and Escherichia coli proteomes. APEX relies upon correcting each protein's mass spectrometry sampling depth (observed peptide count) by learned probabilities for identifying the peptides. APEX abundances agree with measurements from controls, western blotting, flow cytometry and two-dimensional gels, as well as known correlations with mRNA abundances and codon bias, providing absolute protein concentrations across approximately three to four orders of magnitude. Using APEX, we demonstrate that 73% of the variance in yeast protein abundance (47% in E. coli) is explained by mRNA abundance, with the number of proteins per mRNA log-normally distributed about approximately 5,600 ( approximately 540 in E. coli) protein molecules/mRNA. Therefore, levels of both eukaryotic and prokaryotic proteins are set per mRNA molecule and independently of overall protein concentration, with >70% of yeast gene expression regulation occurring through mRNA-directed mechanisms.
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              Supply-side ecology and benthic marine assemblages.

              Many marine invertebrates have a planktonic stage of their life history during which widespread dispersal and much mortality occur. The numbers surviving to recruit into habitats occupied by adults are therefore very variable in time and space. Models for the structure and dynamics of benthic assemblages tend to focus on processes causing death - often assuming consistent arrivals of recruits. Supply-side ecology is a newly fashionable term to describe recent interest in the long-realized consequences of variations in recruitment. Such variations have important influences on theory and empirical research in these assemblages. Copyright © 1989. Published by Elsevier Ltd.
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                Author and article information

                Contributors
                Role: Editor
                Journal
                PLoS One
                PLoS ONE
                plos
                plosone
                PLoS ONE
                Public Library of Science (San Francisco, USA )
                1932-6203
                2014
                13 February 2014
                : 9
                : 2
                : e88744
                Affiliations
                [1 ]KAUST Global Collaborative Research Program, Division of Life Science, The Hong Kong University of Science and Technology, Hong Kong SAR, China
                [2 ]Bioscience Core Laboratory, King Abdullah University of Science and Technology, Thuwal, Kingdom of Saudi Arabia
                [3 ]Integrative Systems Biology Lab, King Abdullah University of Science and Technology, Thuwal, Kingdom of Saudi Arabia
                National Center for Biotechnology Information (NCBI), United States of America
                Author notes

                Competing Interests: Dr. Timothy Ravasi, one of the co-authors is an editor of PLOS ONE. This does not alter the authors' adherence to all the PLOS ONE policies on sharing data and materials.

                Conceived and designed the experiments: Z-FC HZ. Performed the experiments: Z-FC HZ HW. Analyzed the data: Z-FC HZ HW KM. Contributed reagents/materials/analysis tools: Z-FC HZ TR P-YQ. Wrote the paper: Z-FC HZ HW KM YHW P-YQ.

                Article
                PONE-D-13-46937
                10.1371/journal.pone.0088744
                3923807
                24551147
                de1fd43a-b245-4743-ae8c-3568ca45c1f7
                Copyright @ 2014

                This is an open-access article distributed under the terms of the Creative Commons Attribution License, which permits unrestricted use, distribution, and reproduction in any medium, provided the original author and source are credited.

                History
                : 8 November 2013
                : 8 January 2014
                Page count
                Pages: 19
                Funding
                This study was supported by grants from the Research Grants Council of the Hong Kong Special Administrative Region (GRF662413 and AoE/P-04/04-II) and an award from the King Abdullah University of Science and Technology (SA-C0040/UK-C0016) to P.-Y. Qian. The funders had no role in study design, data collection and analysis, decision to publish, or preparation of the manuscript.
                Categories
                Research Article
                Agriculture
                Animal management
                Animal genetics
                Biology
                Computational biology
                Molecular genetics
                Gene expression
                Ecology
                Marine biology
                Marine ecology
                Marine technology
                Molecular cell biology
                Gene expression
                Proteomics
                Protein abundance
                Earth sciences
                Marine and aquatic sciences
                Marine biology

                Uncategorized
                Uncategorized

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