scholarly journals Bioinformatics as a Tool for Assessing the Quality of Sub-Cellular Proteomic Strategies and Inferring Functions of Proteins: Plant Cell Wall Proteomics as a Test Case

2009 ◽  
Vol 3 ◽  
pp. BBI.S2065 ◽  
Author(s):  
Hélène San Clemente ◽  
Rafael Pont-Lezica ◽  
Elisabeth Jamet
Keyword(s):  
Cellular Localization ◽  
Protein Identification ◽  
Plant Cell Wall ◽  
Mass Spectrometry Data ◽  
Functional Domains ◽  
Test Case ◽  
Top Down ◽  
Proteomic Data ◽  
Cellular Compartments

Bioinformatics is used at three different steps of proteomic studies of sub-cellular compartments. First one is protein identification from mass spectrometry data. Second one is prediction of sub-cellular localization, and third one is the search of functional domains to predict the function of identified proteins in order to answer biological questions. The aim of the work was to get a new tool for improving the quality of proteomics of sub-cellular compartments. Starting from the analysis of problems found in databases, we designed a new Arabidopsis database named ProtAnnDB ( http://www.polebio.scsv.ups-tlse.fr/ProtAnnDB/ ). It collects in one page predictions of sub-cellular localization and of functional domains made by available software. Using this database allows not only improvement of interpretation of proteomic data (top-down analysis), but also of procedures to isolate sub-cellular compartments (bottom-up quality control).

TopPIC Gateway: A Web Gateway for Top-Down Mass Spectrometry Data Interpretation

2020 ◽  
Author(s):  
In Kwon Choi ◽  
Eroma Abeysinghe ◽  
Eric Coulter ◽  
Suresh Marru ◽  
Marlon Pierce ◽  
...  
Keyword(s):  
Mass Spectrometry ◽  
Data Interpretation ◽  
Mass Spectrometry Data ◽  
Top Down ◽  
Top Down Mass Spectrometry

scholarly journals Deeper Protein Identification Using Field Asymmetric Ion Mobility Spectrometry in Top-Down Proteomics

2021 ◽  
Author(s):  
Vincent R. Gerbasi ◽  
Rafael D. Melani ◽  
Susan E. Abbatiello ◽  
Michael W. Belford ◽  
Romain Huguet ◽  
...  
Keyword(s):  
Ion Mobility Spectrometry ◽  
Ion Mobility ◽  
Protein Identification ◽  
Top Down

scholarly journals Multiple cellular compartments engagement in Nicotiana benthamiana-peanut stunt virus-satRNA interactions revealed by systems biology approach

2021 ◽  
Author(s):  
Barbara Wrzesińska ◽  
Agnieszka Zmienko ◽  
Lam Dai Vu ◽  
Ive De Smet ◽  
Aleksandra Obrępalska-Stęplowska
Keyword(s):  
Virus Infection ◽  
Nicotiana Benthamiana ◽  
Cellular Localization ◽  
Plant Interactions ◽  
Satellite Rna ◽  
Functional Connections ◽  
Cell Compartments ◽  
Wide Range ◽  
Peanut Stunt Virus ◽  
Cellular Compartments

Abstract Key message PSV infection changed the abundance of host plant’s transcripts and proteins associated with various cellular compartments, including ribosomes, chloroplasts, mitochondria, the nucleus and cytosol, affecting photosynthesis, translation, transcription, and splicing. Abstract Virus infection is a process resulting in numerous molecular, cellular, and physiological changes, a wide range of which can be analyzed due to development of many high-throughput techniques. Plant RNA viruses are known to replicate in the cytoplasm; however, the roles of chloroplasts and other cellular structures in the viral replication cycle and in plant antiviral defense have been recently emphasized. Therefore, the aim of this study was to analyze the small RNAs, transcripts, proteins, and phosphoproteins affected during peanut stunt virus strain P (PSV-P)–Nicotiana benthamiana interactions with or without satellite RNA (satRNA) in the context of their cellular localization or functional connections with particular cellular compartments to elucidate the compartments most affected during pathogenesis at the early stages of infection. Moreover, the processes associated with particular cell compartments were determined. The ‘omic’ results were subjected to comparative data analyses. Transcriptomic and small RNA (sRNA)–seq data were obtained to provide new insights into PSV-P–satRNA–plant interactions, whereas previously obtained proteomic and phosphoproteomic data were used to broaden the analysis to terms associated with cellular compartments affected by virus infection. Based on the collected results, infection with PSV-P contributed to changes in the abundance of transcripts and proteins associated with various cellular compartments, including ribosomes, chloroplasts, mitochondria, the nucleus and the cytosol, and the most affected processes were photosynthesis, translation, transcription, and mRNA splicing. Furthermore, sRNA-seq and phosphoproteomic analyses indicated that kinase regulation resulted in decreases in phosphorylation levels. The kinases were associated with the membrane, cytoplasm, and nucleus components.

Protein kinase C-α and the regulation of diverse cell responses

2017 ◽  
Vol 8 (3-4) ◽  
pp. 143-153 ◽  
Author(s):  
Rishi Kant Singh ◽  
Sanjay Kumar ◽  
Pramod Kumar Gautam ◽  
Munendra Singh Tomar ◽  
Praveen Kumar Verma ◽  
...  
Keyword(s):  
Protein Kinase C ◽  
Protein Kinase ◽  
Cellular Localization ◽  
Cellular Transformation ◽  
Cell Types ◽  
Adapter Proteins ◽  
Cellular Functions ◽  
Cell Responses ◽  
Kinase C ◽  
Cellular Compartments

AbstractProtein kinase C (PKC) comprises a family of lipid-sensitive enzymes that have been involved in a broad range of cellular functions. PKC-α is a member of classical PKC with ubiquitous expression and different cellular localization. This unique PKC isoform is activated by various signals which evoke lipid hydrolysis, after activation it interacts with various adapter proteins and is localized to specific cellular compartments where it is devised to work. The universal expression and activation by various stimuli make it a perfect player in uncountable cellular functions including differentiation, proliferation, apoptosis, cellular transformation, motility, adhesion and so on. However, these functions are not intrinsic properties of PKC-α, but depend on cell types and conditions. The activities of PKC-α are managed by the various pharmacological activators/inhibitors and antisense oligonucleotides. The aim of this review is to elaborate the structural feature, and provide an insight into the mechanism of PKC-α activation and regulation of its key biological functions in different cellular compartments to develop an effective pharmacological approach to regulate the PKC-α signal array.

scholarly journals Empathy Measurement in Autistic and Nonautistic Adults: A COSMIN Systematic Literature Review

Assessment ◽  
2020 ◽  
pp. 107319112096456
Author(s):  
Jessica L. Harrison ◽  
Charlotte L. Brownlow ◽  
Michael J. Ireland ◽  
Adina M. Piovesana
Keyword(s):  
Empirical Support ◽  
Self Report ◽  
Group Differences ◽  
Test Case ◽  
Social Differences ◽  
Item Functioning ◽  
The Subject ◽  
Clinical Conditions ◽  
Psychometric Quality

Empathy is essential for social functioning and is relevant to a host of clinical conditions. This COSMIN review evaluated the empirical support for empathy self-report measures used with autistic and nonautistic adults. Given autism is characterized by social differences, it is the subject of a substantial proportion of empathy research. Therefore, this review uses autism as a lens through which to scrutinize the psychometric quality of empathy measures. Of the 19 measures identified, five demonstrated “High-Quality” evidence for “Insufficient” properties and cannot be recommended. The remaining 14 had noteworthy gaps in evidence and require further evaluation before use with either group. Without tests of measurement invariance or differential item functioning, the extent to which observed group differences represent actual trait differences remains unknown. Using autism as a test case highlights an alarming tendency for empathy measures to be used to characterize, and potentially malign vulnerable populations before sufficient validation.

scholarly journals Use of Expression Constructs to Dissect the Functional Domains of the CHS/Beige Protein: Identification of Multiple Phenotypes

Traffic ◽  
2003 ◽  
Vol 4 (6) ◽  
pp. 403-415 ◽  
Author(s):  
Diane McVey Ward ◽  
Shelly L. Shiflett ◽  
Dinh Huynh ◽  
Michael B Vaughn ◽  
Glenn Prestwich ◽  
...  
Keyword(s):  
Protein Identification ◽  
Functional Domains ◽  
Multiple Phenotypes

Proposal of Iterative Genetic Algorithm for Test Suite Generation

2021 ◽  
Vol 12 (1) ◽  
pp. 111-130
Author(s):  
Ankita Bansal ◽  
Abha Jain ◽  
Abhijeet Anand ◽  
Swatantra Annk
Keyword(s):  
Genetic Algorithm ◽  
Execution Time ◽  
Test Case Generation ◽  
Test Case ◽  
Test Cases ◽  
Computation Complexity ◽  
Test Suite Generation ◽  
Adaptive Nature ◽  
Efficiency And Reliability

Huge and reputed software industries are expected to deliver quality products. However, industry suffers from a loss of approximately $500 billion due to shoddy software quality. The quality of the product in terms of its accuracy, efficiency, and reliability can be revamped through testing by focusing attention on testing the product through effective test case generation and prioritization. The authors have proposed a test-case generation technique based on iterative listener genetic algorithm that generates test cases automatically. The proposed technique uses its adaptive nature and solves the issues like redundant test cases, inefficient test coverage percentage, high execution time, and increased computation complexity by maintaining the diversity of the population which will decrease the redundancy in test cases. The performance of the technique is compared with four existing test-case generation algorithms in terms of computational complexity, execution time, coverage, and it is observed that the proposed technique outperformed.

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