scholarly journals Inverting proteomics analysis provides powerful insight into the peptide/protein conundrum

2015 ◽  
Author(s):  
Wilson Wen Bin Goh ◽  
Limsoon Wong
Keyword(s):  
Proteomic Profiling ◽  
Proteomics Analysis ◽  
Spectra Analysis ◽  
Rule Based ◽  
Cancer Data ◽  
Class Separation ◽  
Protein Splice ◽  
Bin Method ◽  
Splice Forms ◽  
Insight Into

In proteomics, a large proportion of mass spectrometry (MS) data is ignored due to the lack of, or insufficient statistical evidence for mappable peptides. In reality, only a small fraction of features are expected to be differentially relevant anyway. Mapping spectra to peptides and subsequently, proteins, produces uncertainty at several levels. We propose it is better to analyze proteomic profiling data directly at MS level, and then relate these features to peptides/proteins. In a renal cancer data comprising 12 normal and 12 cancer subjects, we demonstrate that a simple rule-based binning approach can give rise to informative features. We note that the peptides associated with significant spectral bins gave rise to better class separation than the corresponding proteins, suggesting a loss of signal in the peptide-to-protein transition. Additionally, the binning approach sharpens focus on relevant protein splice forms rather than just canonical sequences. Taken together, the inverted raw spectra analysis paradigm, which is realised by the MZ-Bin method described in this article, provides new possibilities and insights, in how MS-data can be interpreted.

scholarly journals Comparative Proteomics Analysis of Mouse Habu Nephritis Models with and without Unilateral Nephrectomy

2016 ◽  
Vol 39 (5) ◽  
pp. 1761-1776 ◽  
Author(s):  
Lei Chen ◽  
Yang Lu ◽  
Jun Wen ◽  
Xu Wang ◽  
Lingling Wu ◽  
...  
Keyword(s):  
Renal Injury ◽  
Quantitative Proteomics ◽  
Mesangial Cells ◽  
Unilateral Nephrectomy ◽  
Label Free ◽  
Proteomics Analysis ◽  
Single Kidney ◽  
Regulation Of Actin Cytoskeleton ◽  
Insight Into

Background/Aims: Individuals possessing a single kidney are at greater risk of renal injury upon exposure to harmful stimuli. This study aimed to explore the pathogenesis of renal injury in glomerulonephritis with versus without unilateral nephrectomy (UNX). Methods: Histological analysis and label-free quantitative proteomics were performed on two models—the Habu snake venom-induced glomerulonephritis model with versus without UNX (HabuU and Habu models, respectively). The role of villin 1, a differentially expressed protein (DEP) in mouse mesangial cells, was investigated. Results: Persistent mesangiolysis and focal hypercellularity together with reduced activation of cell proliferation in the HabuU model induced more serious renal injury compared with that in the Habu model. The DEPs between the two models were identified by label-free liquid chromatography-mass spectrometry. The KEGG pathway results indicated that regulation of actin cytoskeleton and focal adhesion were specifically enriched in the HabuU model. The cytoskeleton regulation protein villin 1 was downregulated in the HabuU model, but unchanged in the Habu model. Knockdown of villin 1 promoted apoptosis and inhibited the proliferation of mouse mesangial cells, suggesting villin 1 to be involved in qlomerular lesion self-repair insufficiency. Conclusion: By assessing the proteomic profiles of the two models, this study identified several important differences, particularly villin 1 expression, in regulatory mechanisms between the two models. Our findings provide novel insight into the mechanism of serious renal injury in glomerulonephritis with UNX.

scholarly journals The Arabidopsis thaliana PeptideAtlas; harnessing world-wide proteomics data for a comprehensive community proteomics resource

2021 ◽  
Author(s):  
Klaas Jan van Wijk ◽  
Eric W Deutsch ◽  
Qi Sun ◽  
Zhi Sun ◽  
Tami Leppert ◽  
...  
Keyword(s):  
Splice Variants ◽  
Community Resources ◽  
Proteomics Data ◽  
Post Translational Modifications ◽  
Arabidopsis Proteome ◽  
Metadata Annotation ◽  
Protein Properties ◽  
Specific Proteins ◽  
Protein Splice ◽  
Splice Forms

We developed a new resource, the Arabidopsis PeptideAtlas (www.peptideatlas.org/builds/arabidopsis/), to solve central questions about the Arabidopsis proteome, such as the significance of protein splice forms, post-translational modifications (PTMs), or simply obtain reliable information about specific proteins. PeptideAtlas is based on published mass spectrometry (MS) analyses collected through ProteomeXchange and reanalyzed through a uniform processing and metadata annotation pipeline. All matched MS-derived peptide data are linked to spectral, technical and biological metadata. Nearly 40 million out of ~143 million MSMS spectra were matched to the reference genome Araport11, identifying ~0.5 million unique peptides and 17858 uniquely identified proteins (only isoform per gene) at the highest confidence level (FDR 0.0004; 2 non-nested peptides ≥ 9 aa each), assigned canonical proteins, and 3543 lower confidence proteins. Physicochemical protein properties were evaluated for targeted identification of unobserved proteins. Additional proteins and isoforms currently not in Araport11 were identified, generated from pseudogenes, alternative start, stops and/or splice variants and sORFs; these features should be considered for updates to the Arabidopsis genome. Phosphorylation can be inspected through a sophisticated PTM viewer. This new PeptideAtlas is integrated with community resources including TAIR, tracks in JBrowse, PPDB and UniProtKB. Subsequent PeptideAtlas builds will incorporate millions more MS data.

Morphological generalization in heritage speakers: The Turkish aorist

2021 ◽  
pp. 026765832110592
Author(s):  
Serkan Uygun ◽  
Lara Schwarz ◽  
Harald Clahsen
Keyword(s):  
Language Production ◽  
Formal Model ◽  
Inflectional Morphology ◽  
Heritage Speakers ◽  
Rule Based ◽  
Production Experiment ◽  
Insight Into ◽  
The Way

Heritage speakers (HS) have been shown to experience difficulties with inflectional morphology (particularly with irregular morphology) and to frequently overapply regular morphology. The present study seeks to get further insight into the inflectional processes of HS by investigating how these are generalized to nonce words in language production, the first study of this kind for heritage Turkish. We specifically examined morphological generalization processes in the Turkish aorist which – unusual for this language – includes both regular and irregular forms. A written elicited-production experiment containing nonce verbs with varying degrees of similarity to existing verbs was administered to Turkish HS and native monolingually-raised Turkish speakers (MS). We also explored how well a formal model that was trained on a large lexical corpus of Turkish matches the human speakers’ performance. Our main finding is that HS employ both similarity-based and rule-based mechanisms for morphological generalization of the Turkish aorist, with subtle differences to the way these mechanisms are applied by Turkish MS.

scholarly journals Smart Techniques in Urban Planning: An Insight to Ruled-Based Design

2019 ◽  
Vol 12 (1) ◽  
pp. 114
Author(s):  
Carlo Pisano ◽  
Giuseppe De Luca ◽  
Ahmadreza Shirvani Dastgerdi
Keyword(s):  
Urban Planning ◽  
Implementation Process ◽  
Rule Based ◽  
The North ◽  
Research Findings ◽  
And Performance ◽  
The City ◽  
Insight Into ◽  
Significant Factors ◽  
Design Techniques

In the last decades, the ideology of managing the city form and performance through pre-determined plans has gradually lost its validity. Some contemporary urban planning theories suggest the application of smart design techniques for managing urban complexity. However, the proposed approach has partially been experienced in practice, and more research on how to integrate them into urban planning is needed. This study aims to present an insight into the rule-based design as a smart design technique for a shift from pre-determined urban plans to design rules. The methodology is based on a comparative analysis between the experiments of some cases in the north of Europe. Research findings highlight that the capacity to deliver variety with harmony, the distinction between the roles of code writer and building designer, the potential to support the implementation process and to prescribe specific qualities, both for the spatial and organizational purposes, are significant factors for the integration of smart design techniques to urban planning.

scholarly journals Multidimensional Proteomics Analysis of Amniotic Fluid to Provide Insight into the Mechanisms of Idiopathic Preterm Birth

PLoS ONE ◽  
2008 ◽  
Vol 3 (4) ◽  
pp. e2049 ◽  
Author(s):  
Irina A. Buhimschi ◽  
Guomao Zhao ◽  
Victor A. Rosenberg ◽  
Sonya Abdel-Razeq ◽  
Stephen Thung ◽  
...  
Keyword(s):  
Preterm Birth ◽  
Amniotic Fluid ◽  
Proteomics Analysis ◽  
Insight Into

scholarly journals Comparative proteomics analysis provide novel insight into laminitis in Chinese Holstein cows

2015 ◽  
Vol 11 (1) ◽  
Author(s):  
Shu-Wei Dong ◽  
Shi-Dong Zhang ◽  
Dong-Sheng Wang ◽  
Hui Wang ◽  
Xiao-Fei Shang ◽  
...  
Keyword(s):  
Comparative Proteomics ◽  
Holstein Cows ◽  
Proteomics Analysis ◽  
Chinese Holstein ◽  
Chinese Holstein Cows ◽  
Insight Into

scholarly journals Hybrid bat-ant colony optimization algorithm for rule-based feature selection in health care

2020 ◽  
Vol 10 (6) ◽  
pp. 6655
Author(s):  
Rafid Sagban ◽  
Haydar A. Marhoon ◽  
Raaid Alubady
Keyword(s):  
Health Care ◽  
Cervical Cancer ◽  
Feature Selection ◽  
Ant Colony Optimization ◽  
Diagnostic Methods ◽  
Ant Colony ◽  
Ant Colony Optimization Algorithm ◽  
Data Set ◽  
Rule Based ◽  
Cancer Data

Rule-based classification in the field of health care using artificial intelligence provides solutions in decision-making problems involving different domains. An important challenge is providing access to good and fast health facilities. Cervical cancer is one of the most frequent causes of death in females. The diagnostic methods for cervical cancer used in health centers are costly and time-consuming. In this paper, bat algorithm for feature selection and ant colony optimization-based classification algorithm were applied on cervical cancer data set obtained from the repository of the University of California, Irvine to analyze the disease based on optimal features. The proposed algorithm outperforms other methods in terms of comprehensibility and obtains better results in terms of classification accuracy.

Proteomic Profiling of Zebrafish Challenged by Spring Viremia of Carp Virus Provides Insight into Skin Antiviral Response

Zebrafish ◽  
2020 ◽  
Vol 17 (2) ◽  
pp. 91-103 ◽  
Author(s):  
Rongrong Liu ◽  
Xiucai Hu ◽  
Aijun Lü ◽  
Yajiao Song ◽  
Zhengyi Lian ◽  
...  
Keyword(s):  
Antiviral Response ◽  
Proteomic Profiling ◽  
Insight Into

Novel localizations and interactions of intercellular bridge proteins revealed by proteomic profiling†

2020 ◽  
Vol 102 (5) ◽  
pp. 1134-1144 ◽  
Author(s):  
Tokuko Iwamori ◽  
Naoki Iwamori ◽  
Masaki Matsumoto ◽  
Hiroyuki Imai ◽  
Etsuro Ono
Keyword(s):  
Germ Cells ◽  
Small Rnas ◽  
Protein Complexes ◽  
Proteomic Profiling ◽  
Intercellular Bridge ◽  
Proteomics Analysis ◽  
Meiotic Chromosomes ◽  
Junction Protein ◽  
Associated Proteins ◽  
Ectoplasmic Specialization

Abstract Intercellular bridges (ICBs) connecting germ cells are essential for spermatogenesis, and their deletion causes male infertility. However, the functions and component factors of ICBs are still unknown. We previously identified novel ICB-associated proteins by proteomics analysis using ICB enrichment. Here, we performed immunoprecipitation–proteomics analyses using antibodies specific to known ICB proteins MKLP1, RBM44, and ectoplasmic specialization-associated protein KIAA1210 and predicted protein complexes in the ICB cores. KIAA1210, its binding protein topoisomerase2B (TOP2B), and tight junction protein ZO1 were identified as novel ICB proteins. On the other hand, as well as KIAA1210 and TOP2B, MKLP1 and RBM44, but not TEX14, were localized at the XY body of spermatocytes, suggesting that there is a relationship between ICB proteins and meiotic chromosomes. Moreover, small RNAs interacted with an ICB protein complex that included KIAA1210, RBM44, and MKLP1. These results indicate dynamic movements of ICB proteins and suggest that ICB proteins could be involved not only in the communication between germ cells but also in their epigenetic regulation. Our results provide a novel perspective on the function of ICBs and could be helpful in revealing the biological function of the ICB.

Sign in / Sign up

Export Citation Format

Share Document