Development of the “Applied Proteomics” Concept for Biotechnology Applications in Microalgae: Example of the Proteome Data in Nannochloropsis gaditana

Most of the marine ecosystems on our planet are still unknown. Among these ecosystems, microalgae act as a baseline due to their role as primary producers. The estimated millions of species of these microorganisms represent an almost infinite source of potentially active biocomponents offering unlimited biotechnology applications. This review considers current research in microalgae using the “omics” approach, which today is probably the most important biotechnology tool. These techniques enable us to obtain a large volume of data from a single experiment. The specific focus of this review is proteomics as a technique capable of generating a large volume of interesting information in a single proteomics assay, and particularly the concept of applied proteomics. As an example, this concept has been applied to the study of Nannochloropsis gaditana, in which proteomics data generated are transformed into information of high commercial value by identifying proteins with direct applications in the biomedical and agri-food fields, such as the protein designated UCA01 which presents antitumor activity, obtained from N. gaditana.

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FLEXIQuant-LF to quantify protein modification extent in label-free proteomics data

eLife ◽

10.7554/elife.58783 ◽

2020 ◽

Vol 9 ◽

Author(s):

Christoph N Schlaffner ◽

Konstantin Kahnert ◽

Jan Muntel ◽

Ruchi Chauhan ◽

Bernhard Y Renard ◽

...

Keyword(s):

Protein Modification ◽

Large Scale ◽

Software Tool ◽

Label Free ◽

Anaphase Promoting Complex ◽

Proteomics Data ◽

Single Experiment ◽

Post Translational Modifications ◽

Data Independent Acquisition ◽

Modified Peptides

Improvements in LC-MS/MS methods and technology have enabled the identification of thousands of modified peptides in a single experiment. However, protein regulation by post-translational modifications (PTMs) is not binary, making methods to quantify the modification extent crucial to understanding the role of PTMs. Here, we introduce FLEXIQuant-LF, a software tool for large-scale identification of differentially modified peptides and quantification of their modification extent without knowledge of the types of modifications involved. We developed FLEXIQuant-LF using label-free quantification of unmodified peptides and robust linear regression to quantify the modification extent of peptides. As proof of concept, we applied FLEXIQuant-LF to data-independent-acquisition (DIA) data of the anaphase promoting complex/cyclosome (APC/C) during mitosis. The unbiased FLEXIQuant-LF approach to assess the modification extent in quantitative proteomics data provides a better understanding of the function and regulation of PTMs. The software is available at https://github.com/SteenOmicsLab/FLEXIQuantLF.

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Udoteaceae (Bryopsidales, Chlorophyta) no litoral do estado da Bahia, Brasil

SITIENTIBUS série Ciências Biológicas ◽

10.13102/scb436 ◽

2014 ◽

Vol 14 ◽

Author(s):

Gabriel Do Nascimento Santos ◽

José Marcos De Castro Nunes

Keyword(s):

Marine Ecosystems ◽

Primary Producers ◽

Distribution Maps ◽

Taxonomic Treatment ◽

Identification Keys

The Udoteaceae are ubiquitous and ecologically important in tropical marine ecosystems. Apart from primary producers, calcified representatives contribute to the construction and sedimentation of reefs. In this study, we present the taxonomic treatment of Udoteaceae from Bahia coast. Based on collected material and on material deposited in the main Brazilian herbaria, 10 taxa, distributed in three genera, were recognized: Boodleopsis (B. pusilla), Penicillus (P. capitatus, including three forms), and Udotea (4 species, 2 varieties, and 2 forms). Identification keys for the taxa are presented, along with descriptions, illustrations, comparisons with related taxa, and distribution maps for species in Bahia.

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Proteomics: The protein complement of the genome

The Biochemist ◽

10.1042/bio02501007 ◽

2003 ◽

Vol 25 (1) ◽

pp. 7-9

Author(s):

Hannes Ponstingl ◽

Janet M. Thornton

Keyword(s):

Messenger Rna ◽

Protein Separation ◽

Large Scale ◽

Protein Complexes ◽

Protein Isoforms ◽

Structural Proteomics ◽

Protein Markers ◽

Proteomics Data ◽

Single Experiment ◽

Large Sets

Recent advances in protein separation technology and mass spectrometry (MS) have enabled the systematic identification and quantification of large sets of proteins from an organelle, cell type or organism. In principle, protein isoforms, enzymically modified variants and protein complexes can be studied, for instance, at a certain stage in development or in response to stress or more subtle changes of the environment. An important pre-clinical application is the search for protein markers in body fluids for diagnostic purposes. Such proteomics studies can be performed increasingly at high-throughput rates that are reminiscent of those of genomic sequencing or the monitoring of messenger RNA levels. Thus, large sets of proteins can be monitored simultaneously in a single experiment. Proteomics data will increasingly be followed up by investigations of the three-dimensional structures of proteins and protein complexes at atomic detail in large-scale structural proteomics projects. We attempt in this article to give a flavour of what to us seem important experimental developments and to point to links with bioinformatics resources where appropriate.

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Using multivariate mixed-effects selection models for analyzing batch-processed proteomics data with non-ignorable missingness

Biostatistics ◽

10.1093/biostatistics/kxy022 ◽

2018 ◽

Vol 20 (4) ◽

pp. 648-665

Author(s):

Jiebiao Wang ◽

Pei Wang ◽

Donald Hedeker ◽

Lin S Chen

Keyword(s):

Breast Tumors ◽

Mixed Effects ◽

Amino Acid Sequences ◽

Protein Profiling ◽

Batch Effects ◽

Statistical Efficiency ◽

Proteomics Data ◽

Single Experiment ◽

Data Set ◽

Selection Models

Summary In quantitative proteomics, mass tag labeling techniques have been widely adopted in mass spectrometry experiments. These techniques allow peptides (short amino acid sequences) and proteins from multiple samples of a batch being detected and quantified in a single experiment, and as such greatly improve the efficiency of protein profiling. However, the batch-processing of samples also results in severe batch effects and non-ignorable missing data occurring at the batch level. Motivated by the breast cancer proteomic data from the Clinical Proteomic Tumor Analysis Consortium, in this work, we developed two tailored multivariate MIxed-effects SElection models (mvMISE) to jointly analyze multiple correlated peptides/proteins in labeled proteomics data, considering the batch effects and the non-ignorable missingness. By taking a multivariate approach, we can borrow information across multiple peptides of the same protein or multiple proteins from the same biological pathway, and thus achieve better statistical efficiency and biological interpretation. These two different models account for different correlation structures among a group of peptides or proteins. Specifically, to model multiple peptides from the same protein, we employed a factor-analytic random effects structure to characterize the high and similar correlations among peptides. To model biological dependence among multiple proteins in a functional pathway, we introduced a graphical lasso penalty on the error precision matrix, and implemented an efficient algorithm based on the alternating direction method of multipliers. Simulations demonstrated the advantages of the proposed models. Applying the proposed methods to the motivating data set, we identified phosphoproteins and biological pathways that showed different activity patterns in triple negative breast tumors versus other breast tumors. The proposed methods can also be applied to other high-dimensional multivariate analyses based on clustered data with or without non-ignorable missingness.

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Delayed herbivory and the assembly of marine benthic ecosystems

Paleobiology ◽

10.1666/0094-8373(2000)026<0419:dhatao>2.0.co;2 ◽

2000 ◽

Vol 26 (3) ◽

pp. 419-430 ◽

Cited By ~ 48

Author(s):

Geerat J. Vermeij ◽

David R. Lindberg

Keyword(s):

Phylogenetic Analysis ◽

Marine Ecosystems ◽

Evolutionary Tree ◽

Photic Zone ◽

Primary Producers ◽

Marine Plants ◽

Benthic Ecosystems

Phylogenetic analysis of the metazoan evolutionary tree as a whole, and of trees of component major clades, indicates that marine herbivores, defined here as macrophagous consumers of living multicellular attached marine plants, always occupy terminal positions at several scales of analysis. Nearly all living benthic marine herbivores are derived from microphages, detritivores, or predators, and most have post-Paleozoic origins. The derived nature of herbivory in the sea parallels the evolutionary situation among land animals. Pre-Mesozoic marine benthic ecosystems, characterized by relatively low rates of flow of energy and nutrients, may have relied even more heavily on decomposers for the transfer of carbon from primary producers to animals than do living marine ecosystems in the photic zone.

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The trophic roles of microzooplankton in marine systems

ICES Journal of Marine Science ◽

10.1093/icesjms/fsn013 ◽

2008 ◽

Vol 65 (3) ◽

pp. 325-331 ◽

Cited By ~ 164

Author(s):

Albert Calbet

Keyword(s):

Marine Ecosystems ◽

Size Class ◽

Grazing Impact ◽

Marine Science ◽

Primary Producers ◽

Marine Systems ◽

Final Remark ◽

Estuarine Systems

Abstract Calbet, A. 2008. The trophic roles of microzooplankton in marine systems. – ICES Journal of Marine Science, 65: 325–331. Microzooplankton (here defined as <200 µm grazers) are key components of marine foodwebs. Their grazing significantly affects primary producers and usually exceeds that of mesozooplankton. However, our knowledge of the detailed roles that microzooplankton taxa play in marine ecosystems is surprisingly limited. Here, I identify the main protists responsible for most of the grazing impact on phytoplankton in two contrasting marine ecosystems: oligotrophic waters and productive waters, such as upwelling systems, spring blooms, and other blooms in nearshore and estuarine systems. Evidence indicates that pico- and nano-sized flagellates, which are routinely included with the microzooplankton size class of protists, appear to be the main grazers of phytoplankton in oligotrophic habitats, whereas heterotrophic and mixotrophic dinoflagellates are candidates for the dominant grazing impact in upwelling and other productive ecosystems. Microzooplankton are also important contributors to mesozooplankton diet, especially in oligotrophic areas, although the strength of the mesozooplankton–microzooplankton link is traditionally overlooked in plankton studies. As a final remark, this review emphasizes the need to develop suitable methods for studying the role of microbial grazers in the dynamics of marine ecosystems.

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FLEXIQuant-LF: Robust Regression to Quantify Protein Modification Extent in Label-Free Proteomics Data

10.1101/2020.05.11.088492 ◽

2020 ◽

Author(s):

Konstantin Kahnert ◽

Christoph N. Schlaffner ◽

Jan Muntel ◽

Ruchi Chauhan ◽

Bernhard Y. Renard ◽

...

Keyword(s):

Protein Modification ◽

Large Scale ◽

Robust Regression ◽

Software Tool ◽

Label Free ◽

Anaphase Promoting Complex ◽

Proteomics Data ◽

Single Experiment ◽

Data Independent Acquisition ◽

Modified Peptides

AbstractImprovements in LC-MS/MS methods and technology have enabled the identification of thousands of modified peptides in a single experiment. However, protein regulation by post-translational modifications (PTMs) is not binary, making methods to quantify the modification extent crucial to understanding the role of PTMs. Here, we introduce FLEXIQuant-LF, a software tool for large-scale identification of differentially modified peptides and quantification of their modification extent without prior knowledge of the type of modification. We developed FLEXIQuant-LF using label-free quantification of unmodified peptides and robust linear regression to quantify the modification extent of peptides. As proof of concept, we applied FLEXIQuant-LF to data-independent-acquisition (DIA) data of the anaphase promoting complex/cyclosome (APC/C) during mitosis. The unbiased FLEXIQuant-LF approach to assess the modification extent in quantitative proteomics data provides a better understanding of the function and regulation of PTMs. The software is available at https://github.com/SteenOmicsLab/FLEXIQuantLF.

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Processing Metabolomics and Proteomics Data with Open Software

10.1039/9781788019880 ◽

2020 ◽

Keyword(s):

Proteomics Data

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Selected Abstracts of Recent Research in Stuttering

Perspectives on Fluency and Fluency Disorders ◽

10.1044/ffd9.1.5 ◽

1999 ◽

Vol 9 (1) ◽

pp. 5-6

Author(s):

Carrie Bain ◽

Nan Bernstein Ratner

Keyword(s):

Large Volume ◽

Clinical Relevance

Due to the large volume of fluency-related publications since the last column, we have chosen to highlight those articles of highest potential clinical relevance.

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