scholarly journals Pyntheon: A Functional Analysis Framework for Protein Modifications and Mutations of 83 Model Organisms

2019 ◽  
Author(s):  
Ahmed Arslan
Keyword(s):  
Posttranslational Modifications ◽  
Protein Modification ◽  
Model Organisms ◽  
Analysis Framework ◽  
Proteomics Data ◽  
Functional Protein ◽  
Protein Modifications ◽  
Community Of Researchers ◽  
Protein Mutations ◽  
The Impact

AbstractMotivationPosttranslational modifications (PTMs) modulate proteins activity depending on the dynamics of cellular conditions, in the highly regulated processes that control the reversible nature of these modifications and a cellular state. Due to the unique importance of PTMs, a number of resources are available to analyze the protein modification data for different organisms. These databases are quite informative on a limited number of popular organisms, mostly human and yeast. However there has not been a single database to date that makes it possible to analyze the modified protein residue data for up to 83 model organisms. Moreover, there are limited resources that rely on both protein mutations and modifications in evaluating a phenotype.ResultsI am presenting a comprehensive python tool Pyntheon that enables users to analyze protein modifications and mutations data. This resource can be used in different ways to know: (i) if the proteins of interest have modifications and (ii) if the modified residues overlap with mutated sites. Additional functions include, analyzing if a PTM-site is present in a functional protein region, like domain and structural regions. In summary, Pyntheon makes it possible for a larger community of researchers to evaluate their curated proteomics data and interpret the impact of mutations on phenotypes.ConclusionPyntheon has multifold functions that can help analyzing the protein mutations impact on the modified residues for a large number of popular model organisms.Code-Availabilityhttps://github.com/AhmedArslan/[email protected]

scholarly journals The Plant PTM Viewer, a central resource exploring plant protein modifications. From site-seeing to protein function

2018 ◽  
Author(s):  
Patrick Willems ◽  
Alison Horne ◽  
Sofie Goormachtig ◽  
Ive De Smet ◽  
Alexander Botzki ◽  
...  
Keyword(s):  
Mass Spectrometry ◽  
Posttranslational Modifications ◽  
Protein Function ◽  
Protein Sequences ◽  
Specific Protein ◽  
Specific Information ◽  
Active Site Residues ◽  
Functional Protein ◽  
Protein Modifications ◽  
Modern Mass

SUMMARYPosttranslational modifications (PTMs) of proteins are central in any kind of cellular signaling. Modern mass spectrometry technologies enable comprehensive identification and quantification of various PTMs. Given the increased number and types of mapped protein modifications, a database is necessary that simultaneouly integrates and compares site-specific information for different PTMs, especially in plants for which the available PTM data are poorly catalogued. Here, we present the Plant PTM Viewer (http://www.psb.ugent.be/PlantPTMViewer), an integrative PTM resource that comprises approximately 200,000 PTM sites for 17 types of protein modifications in plant proteins from five different species. The Plant PTM Viewer provides the user with a protein sequence overview in which the experimentally evidenced PTMs are highlighted together with functional protein domains or active site residues. The PTM sequence search tool can query PTM combinations in specific protein sequences, whereas the PTM BLAST tool searches for modified protein sequences to detect conserved PTMs in homologous sequences. Taken together, these tools facilitate to assume the role and potential interplay of PTMs in specific proteins or within a broader systems biology context. The Plant PTM Viewer is an open repository that allows submission of mass spectrometry-based PTM data to remain at pace with future PTM plant studies.

scholarly journals Development of the Circular Bioeconomy: Drivers and Indicators

2021 ◽  
Vol 13 (1) ◽  
pp. 413
Author(s):  
Maximilian Kardung ◽  
Kutay Cingiz ◽  
Ortwin Costenoble ◽  
Roel Delahaye ◽  
Wim Heijman ◽  
...  
Keyword(s):  
Circular Economy ◽  
Food Production ◽  
Conceptual Analysis ◽  
Green Economy ◽  
Political Agenda ◽  
Analysis Framework ◽  
Stakeholder Consultation ◽  
Time Period ◽  
The Impact ◽  
The Eu

The EU’s 2018 Bioeconomy Strategy Update and the European Green Deal recently confirmed that the bioeconomy is high on the political agenda in Europe. Here, we propose a conceptual analysis framework for quantifying and analyzing the development of the EU bioeconomy. The bioeconomy has several related concepts (e.g., bio-based economy, green economy, and circular economy) and there are clear synergies between these concepts, especially between the bioeconomy and circular economy concepts. Analyzing the driving factors provides important information for monitoring activities. We first derive the scope of the bioeconomy framework in terms of bioeconomy sectors and products to be involved, the needed geographical coverage and resolution, and time period. Furthermore, we outline a set of indicators linked to the objectives of the EU’s bioeconomy strategy. In our framework, measuring developments will, in particular, focus on the bio-based sectors within the bioeconomy as biomass and food production is already monitored. The selected indicators commit to the EU Bioeconomy Strategy objectives and conform with findings from previous studies and stakeholder consultation. Additionally, several new indicators have been suggested and they are related to measuring the impact of changes in supply, demand drivers, resource availability, and policies on sustainability goals.

scholarly journals Ageratina adenophora Inhibits Spleen Immune Function in Rats via the Loss of the FRC Network and Th1–Th2 Cell Ratio Elevation

Toxins ◽  
2021 ◽  
Vol 13 (5) ◽  
pp. 309
Author(s):  
Zhihua Ren ◽  
Pei Gao ◽  
Samuel Kumi Okyere ◽  
Yujing Cui ◽  
Juan Wen ◽  
...  
Keyword(s):  
Protein Expression ◽  
Immune Function ◽  
Tissue Sample ◽  
Th2 Cells ◽  
Sample Collection ◽  
Functional Protein ◽  
Th2 Cell ◽  
Ageratina Adenophora ◽  
Mrna And Protein Expression ◽  
The Impact

The objective of this study was to determine the impact of Ageratina adenophora (A. adenophora) on splenic immune function in a rat model. Rats were fed with 10 g/100 g normal feed and an experimental feed, which was composed of 3:7 A. adenophora powder and normal feed for 60 days. On days 14, 28, and 60, subsets of rats (n = 8 rats/group/time point) were selected for blood and spleen tissue sample collection. The results showed that the proportion of CD3+ T cells in the spleen was decreased at day 60 (vs. control). Also, mRNA and protein expression of chemokines CCL21 and CCL19 and functional protein gp38 in spleen decreased significantly versus the control at day 60. In addition, ER-TR7 antigen protein expression was also decreased at day 60. Levels of T-helper (Th)1 cells significantly increased, whereas those of Th2 cells decreased significantly versus the control at day 60 in spleen. The finding revealed that A. adenophora could affect splenic immune function in rats by altering the fibroblast reticulocyte (FRC) network, as well as by causing an imbalance in Th1/Th2 cell ratios. This research provides new insights into potential mechanisms of spleen immunotoxicity due to exposures to A. Adenophora.

Decline of contractility during ischemia-reperfusion injury: actin glutathionylation and its effect on allosteric interaction with tropomyosin

2006 ◽  
Vol 290 (3) ◽  
pp. C719-C727 ◽  
Author(s):  
Frank C. Chen ◽  
Ozgur Ogut
Keyword(s):  
Reperfusion Injury ◽  
Posttranslational Modifications ◽  
Actin Polymerization ◽  
Time Course ◽  
Troponin I ◽  
Ischemia Reperfusion Injury ◽  
Ischemia Reperfusion ◽  
High Concentration ◽  
Cross Sectional ◽  
The Impact

The severity and duration of ischemia-reperfusion injury is hypothesized to play an important role in the ability of the heart subsequently to recover contractility. Permeabilized trabeculae were prepared from a rat model of ischemia-reperfusion injury to examine the impact on force generation. Compared with the control perfused condition, the maximum force (Fmax) per cross-sectional area and the rate of tension redevelopment of Ca2+-activated trabeculae fell by 71% and 44%, respectively, during ischemia despite the availability of a high concentration of ATP. The reduction in Fmax with ischemia was accompanied by a decline in fiber stiffness, implying a drop in the absolute number of attached cross bridges. However, the declines during ischemia were largely recovered after reperfusion, leading to the hypothesis that intrinsic, reversible posttranslational modifications to proteins of the contractile filaments occur during ischemia-reperfusion injury. Examination of thin-filament proteins from ischemic or ischemia-reperfused hearts did not reveal proteolysis of troponin I or T. However, actin was found to be glutathionylated with ischemia. Light-scattering experiments demonstrated that glutathionylated G-actin did not polymerize as efficiently as native G-actin. Although tropomyosin accelerated the time course of native and glutathionylated G-actin polymerization, the polymerization of glutathionylated G-actin still lagged native G-actin at all concentrations of tropomyosin tested. Furthermore, cosedimentation experiments demonstrated that tropomyosin bound glutathionylated F-actin with significantly reduced cooperativity. Therefore, glutathionylated actin may be a novel contributor to the diverse set of posttranslational modifications that define the function of the contractile filaments during ischemia-reperfusion injury.

scholarly journals ProMoST (Protein Modification Screening Tool): a web-based tool for mapping protein modifications on two-dimensional gels

2004 ◽  
Vol 32 (Web Server) ◽  
pp. W638-W644 ◽  
Author(s):  
B. D. Halligan ◽  
V. Ruotti ◽  
W. Jin ◽  
S. Laffoon ◽  
S. N. Twigger ◽  
...  
Keyword(s):  
Protein Modification ◽  
Screening Tool ◽  
Two Dimensional ◽  
Web Based ◽  
Protein Modifications

scholarly journals Conformational entropy of a single peptide controlled under force governs protease recognition and catalysis

2018 ◽  
Vol 115 (45) ◽  
pp. 11525-11530 ◽  
Author(s):  
Marcelo E. Guerin ◽  
Guillaume Stirnemann ◽  
David Giganti
Keyword(s):  
Single Molecule ◽  
Conformational Dynamics ◽  
Conformational Sampling ◽  
Enzymatic Reactions ◽  
Sequence Specificity ◽  
Proteomics Data ◽  
Conformational Entropy ◽  
Substrate Peptide ◽  
The Impact

An immense repertoire of protein chemical modifications catalyzed by enzymes is available as proteomics data. Quantifying the impact of the conformational dynamics of the modified peptide remains challenging to understand the decisive kinetics and amino acid sequence specificity of these enzymatic reactions in vivo, because the target peptide must be disordered to accommodate the specific enzyme-binding site. Here, we were able to control the conformation of a single-molecule peptide chain by applying mechanical force to activate and monitor its specific cleavage by a model protease. We found that the conformational entropy impacts the reaction in two distinct ways. First, the flexibility and accessibility of the substrate peptide greatly increase upon mechanical unfolding. Second, the conformational sampling of the disordered peptide drives the specific recognition, revealing force-dependent reaction kinetics. These results support a mechanism of peptide recognition based on conformational selection from an ensemble that we were able to quantify with a torsional free-energy model. Our approach can be used to predict how entropy affects site-specific modifications of proteins and prompts conformational and mechanical selectivity.

GEMPROT: visualization of the impact on the protein of the genetic variants found on each haplotype

2018 ◽  
Vol 35 (14) ◽  
pp. 2492-2494
Author(s):  
Tania Cuppens ◽  
Thomas E Ludwig ◽  
Pascal Trouvé ◽  
Emmanuelle Genin
Keyword(s):  
Genetic Variants ◽  
Protein Sequence ◽  
Sequence Data ◽  
Protein Sequences ◽  
Supplementary Information ◽  
Analysis Tool ◽  
Functional Protein ◽  
Key Players ◽  
On Line ◽  
The Impact

Abstract Summary When analyzing sequence data, genetic variants are considered one by one, taking no account of whether or not they are found in the same individual. However, variant combinations might be key players in some diseases as variants that are neutral on their own can become deleterious when associated together. GEMPROT is a new analysis tool that allows, from a phased vcf file, to visualize the consequences of the genetic variants on the protein. At the level of an individual, the program shows the variants on each of the two protein sequences and the Pfam functional protein domains. When data on several individuals are available, GEMPROT lists the haplotypes found in the sample and can compare the haplotype distributions between different sub-groups of individuals. By offering a global visualization of the gene with the genetic variants present, GEMPROT makes it possible to better understand the impact of combinations of genetic variants on the protein sequence. Availability and implementation GEMPROT is freely available at https://github.com/TaniaCuppens/GEMPROT. An on-line version is also available at http://med-laennec.univ-brest.fr/GEMPROT/. Supplementary information Supplementary data are available at Bioinformatics online.

scholarly journals POLA KONSENTRASI SPASIAL INDUSTRI KECIL MENENGAH DI PROVINSI NUSA TENGGARA BARAT

GANEC SWARA ◽  
2021 ◽  
Vol 15 (1) ◽  
pp. 858
Author(s):  
CHANDRADITYA BAGASKARA ◽  
PUTU KARISMAWAN ◽  
FIRMANSYAH FIRMANSYAH
Keyword(s):  
Concentration Ratio ◽  
Production Cost ◽  
Location Theory ◽  
Ratio Analysis ◽  
Analysis Framework ◽  
Economic Activities ◽  
Systematic Analysis ◽  
Power Sources ◽  
The Right ◽  
The Impact

      Location Theory gives systematic analysis framework  of selecting location of economic adn social activities. Chosing of the right location  thrifts reduce the transportation and production cost that drives efficient in production and marketing. The impact of efficiency is the higest profit and concentration of economic activities. There are many factor afecting the concentration of economic activities, such as wages, man power sources and productivity. Based on Concentration Ratio analysis that Small-medium  industries cosentrated in Mataram City and Central Lombok distric. Based on concentration Index of Man power  shows that the concentration of man power  are in Sumbawa district, North Lombok, Central Lombok, Bima City, Bima district and West Lombok district. Based on those  result that concentration spatial of Small-Medium Industries in each district of West Nusa Tenggara are not equal . Based on Regresioan analysis with Randomeffect Model that concentration of small-medium industries in West Nusa Tenggara siginificanly corelated with amount of man power and productivity, neither than wages.

scholarly journals Responses to Developmental Temperature Fluctuation in Life History Traits of Five Drosophila Species (Diptera: Drosophilidae) from Different Thermal Niches

Insects ◽  
2021 ◽  
Vol 12 (10) ◽  
pp. 925
Author(s):  
Tommaso Manenti ◽  
Anders Kjærsgaard ◽  
Toke Munk Schou ◽  
Cino Pertoldi ◽  
Neda N. Moghadam ◽  
...  
Keyword(s):  
Thermal Resistance ◽  
Temperature Fluctuation ◽  
Developmental Time ◽  
Drosophila Species ◽  
Model Organisms ◽  
Wing Size ◽  
Multiple Traits ◽  
Biochemical Processes ◽  
Developmental Temperature ◽  
The Impact

Temperature has profound effects on biochemical processes as suggested by the extensive variation in performance of organisms across temperatures. Nonetheless, the use of fluctuating temperature (FT) regimes in laboratory experiments compared to constant temperature (CT) regimes is still mainly applied in studies of model organisms. We investigated how two amplitudes of developmental temperature fluctuation (22.5/27.5 °C and 20/30 °C, 12/12 h) affected several fitness-related traits in five Drosophila species with markedly different thermal resistance. Egg-to-adult viability did not change much with temperature except in the cold-adapted D. immigrans. Developmental time increased with FT among all species compared to the same mean CT. The impact of FT on wing size was quite diverse among species. Whereas wing size decreased quasi-linearly with CT in all species, there were large qualitative differences with FT. Changes in wing aspect ratio due to FT were large compared to the other traits and presumably a consequence of thermal stress. These results demonstrate that species of the same genus but with different thermal resistance can show substantial differences in responses to fluctuating developmental temperatures not predictable by constant developmental temperatures. Testing multiple traits facilitated the interpretation of responses to FT in a broader context.

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