Journal of proteomics & bioinformatics最新文献

{"title":"Proteomic Analysis Provides Insights into Arabidopsis thaliana Response Under Narrow-Wavelength LED of 595 nm light","authors":"N. Yavari, M. Lefsrud","doi":"10.35248/0974-276x.19.12.507","DOIUrl":"https://doi.org/10.35248/0974-276x.19.12.507","url":null,"abstract":"A growing body of evidence has highlighted that a wide range of plant processes including growth, photosynthesis, and stress response are regulated by 595 nm light. However, the molecular mechanisms underlying 595 nm-induced signals are not known. The aim of this work was to study the comparative proteomic changes in leaves of Arabidopsis thaliana Col-0 plants treated with narrow-wavelength 595 nm light or fluorescent light for 5 days. Harvested plant samples were analyzed using inline RP-SCX-RP liquid chromatography coupled with LTQ mass spectrometer, resulting in the identification of 1538 proteins. Linear regression modeling of proteins’ relative abundance revealed a total of 23 differentially abundant proteins (DAPs). Functional analysis of these DAPs demonstrated the role of several biological mechanisms in A. thaliana’s response to 595 nm light including stress response and metabolic processes. A network analysis of these DAPs revealed the importance of energy and redox regulation mechanisms. Further analyses determined potentially important roles for proteins associated with glycolysis, ATP synthase complex, cell wall modification, and thylakoid membrane that may modulate the plant’s adaptive response to 595 nm light. A significant enrichment of DAPs for PSII tolerance capacity, as well as associated Ca2+ and ROS signaling pathways were also identified. Collectively, this study provides an important insight into potential molecular pathways that sustain a plant’s response to 595 nm light.","PeriodicalId":73911,"journal":{"name":"Journal of proteomics & bioinformatics","volume":null,"pages":null},"PeriodicalIF":0.0,"publicationDate":"2019-01-01","publicationTypes":"Journal Article","fieldsOfStudy":null,"isOpenAccess":false,"openAccessPdf":"","citationCount":null,"resultStr":null,"platform":"Semanticscholar","paperid":"69961616","PeriodicalName":null,"FirstCategoryId":null,"ListUrlMain":null,"RegionNum":0,"RegionCategory":"","ArticlePicture":[],"TitleCN":null,"AbstractTextCN":null,"PMCID":"","EPubDate":null,"PubModel":null,"JCR":null,"JCRName":null,"Score":null,"Total":0}

{"title":"Redox Proteome Perturbation in Arabidopsis upon Pseudomonas syringae Infection","authors":"Pei Liu, Huoming Zhang, L. Xiong, Yiji Xia","doi":"10.4172/0974-276X.1000490","DOIUrl":"https://doi.org/10.4172/0974-276X.1000490","url":null,"abstract":"Oxidative burst is one of the earliest plant cellular responses triggered by pathogen infection. Reactive oxygen species can cause oxidative modifications of redox-sensitive proteins to mediate the defense responses. Identification and characterization of proteins that undergo oxidative modifications in these processes is an important step toward understanding molecular mechanisms of plant defense responses. In this study, an in vivo 15N metabolic labeling method combined with a cysteine-containing peptide enrichment technique was applied to identify and quantify proteins and their redox states in Arabidopsis in response to infection by Pseudomonas syringae pv tomato DC3000 (Pst). Changes of peptide redox states were compared and corrected with the changes of protein levels. A total of forty peptides representing thirty-six non-redundant proteins showed significantly redox state changes in response to the infection by the virulent Pst strain and the avirulent Pst strain (Pst avrRpm1), of which 23 had previously not been recognized to undergo oxidative PTMs. The differentially expressed redox-sensitive proteins are involved in cell wall organization, primary metabolism, photosynthesis and stress responses. Interestingly, proteins located at extracellular were more susceptible to be regulated on the redox PTMs level. These findings provide a foundation for further investigation into the redox signaling during plant defense responses.","PeriodicalId":73911,"journal":{"name":"Journal of proteomics & bioinformatics","volume":null,"pages":null},"PeriodicalIF":0.0,"publicationDate":"2019-01-01","publicationTypes":"Journal Article","fieldsOfStudy":null,"isOpenAccess":false,"openAccessPdf":"https://sci-hub-pdf.com/10.4172/0974-276X.1000490","citationCount":null,"resultStr":null,"platform":"Semanticscholar","paperid":"70907567","PeriodicalName":null,"FirstCategoryId":null,"ListUrlMain":null,"RegionNum":0,"RegionCategory":"","ArticlePicture":[],"TitleCN":null,"AbstractTextCN":null,"PMCID":"","EPubDate":null,"PubModel":null,"JCR":null,"JCRName":null,"Score":null,"Total":0}

{"title":"A Method for Isolation and Proteomic Analysis of Outer Membrane Vesicles from Fecal Samples by LC-MS/MS.","authors":"Jing Wu,&nbsp;Mingrui An,&nbsp;Jianhui Zhu,&nbsp;Zhijing Tan,&nbsp;Grace Y Chen,&nbsp;Ryan W Stidham,&nbsp;David M Lubman","doi":"10.4172/0974-276X.1000494","DOIUrl":"https://doi.org/10.4172/0974-276X.1000494","url":null,"abstract":"<p><p>Outer membrane vesicles (OMVs) are nanosized spheres secreted by bacteria that are similar to the vesicles known as exosomes, which are secreted by most mammalian cell types. In contrast to many studies focusing on optimizing methods for enriching exosomes from biological fluid, few studies have been conducted to investigate outer membrane vesicles from fecal samples. Herein, we have developed a pipeline comprised of membrane filtration and multiple cycles of ultracentrifugation (UC) to isolate OMVs from fecal samples for proteomics analysis, where multiple cycles of UC are required for removal of contaminants. By iTRAQ labeling quantitative proteomics analysis, different filter sizes (0.22 μm and 0.45 μm) were compared in terms of their performance in enriching OMVs and eliminating background fecal material. Using the 0.45 μm filter, a slightly higher protein yield was obtained but no additional contaminating proteins from bacteria were identified compared to those from the 0.22 μm filter. The 0.45 μm filter together with the multiple cycles of UC were thus used to isolate OMVs for proteomics analysis. To our knowledge, this is the first study profiling a large number of OMV proteins from fecal samples. Such capabilities may help provide valuable information in understanding the communication between the host and microbiota, which is critical in preventing cancer and disease development.</p>","PeriodicalId":73911,"journal":{"name":"Journal of proteomics & bioinformatics","volume":null,"pages":null},"PeriodicalIF":0.0,"publicationDate":"2019-01-01","publicationTypes":"Journal Article","fieldsOfStudy":null,"isOpenAccess":false,"openAccessPdf":"https://www.ncbi.nlm.nih.gov/pmc/articles/PMC6497448/pdf/","citationCount":null,"resultStr":null,"platform":"Semanticscholar","paperid":"37215487","PeriodicalName":null,"FirstCategoryId":null,"ListUrlMain":null,"RegionNum":0,"RegionCategory":"","ArticlePicture":[],"TitleCN":null,"AbstractTextCN":null,"PMCID":"OA","EPubDate":null,"PubModel":null,"JCR":null,"JCRName":null,"Score":null,"Total":0}

{"title":"Visual mass-spec share (vMS-Share): a new public web-based mass spectrometry visualization and data mining repository.","authors":"Niksa Blonder,&nbsp;Benjamin C Orsburn,&nbsp;Josip Blonder,&nbsp;Carlos A Gonzalez","doi":"10.4172/0974-276X.1000495","DOIUrl":"https://doi.org/10.4172/0974-276X.1000495","url":null,"abstract":"<p><p>Herein we introduce the Visual Mass-Spec Share (vMS-Share), a new public mass spectrometric (MS) repository and data mining website/resource freely accessible at https://vmsshare.nist.gov. vMS-Share is a web-based application developed for instant visualization of raw MS data with integrated display of metadata optimized for the sharing of proteomics and metabolomics experimental results. Each MS-based identification is linked to a given experiment and the entire experimental data can then be viewed using the link associated with a given peptide and/or small molecule. Interactive and user-friendly visualizations are provided to the user via variety of easily accessible search filters.</p>","PeriodicalId":73911,"journal":{"name":"Journal of proteomics & bioinformatics","volume":null,"pages":null},"PeriodicalIF":0.0,"publicationDate":"2019-01-01","publicationTypes":"Journal Article","fieldsOfStudy":null,"isOpenAccess":false,"openAccessPdf":"https://www.ncbi.nlm.nih.gov/pmc/articles/PMC6605085/pdf/nihms-1530821.pdf","citationCount":null,"resultStr":null,"platform":"Semanticscholar","paperid":"37399645","PeriodicalName":null,"FirstCategoryId":null,"ListUrlMain":null,"RegionNum":0,"RegionCategory":"","ArticlePicture":[],"TitleCN":null,"AbstractTextCN":null,"PMCID":"OA","EPubDate":null,"PubModel":null,"JCR":null,"JCRName":null,"Score":null,"Total":0}

{"title":"Engineering a Long Lasting Tethered, Multimeric Human Growth Hormone Protein to Improve Pharmacokinetic Half-Life and Potency","authors":"Tianxing Wang, Bin Zhao, E. Foehr","doi":"10.35248/0974-276x.19.12.497","DOIUrl":"https://doi.org/10.35248/0974-276x.19.12.497","url":null,"abstract":"Long-acting human growth hormone (hGH) is intended to improve compliance, adherence and efficacy for patients with growth hormone deficiency or other growth disorders. There is poor patient compliance with daily dosing and novel strategies for improving pharmacokinetic half-life and potency are under development. Subcutaneously and intramuscularly administered recombinant human growth hormone (aka somatropin) has a short half-life of just a few hours. Growth hormone is cleared by glomerular filtration based on its size and through receptor mediated uptake. By engineering a multimeric hGH, the clearance via glomerular filtration may be reduced and the receptor binding improved through multiple points of contact. A synthetic form of hGH was created by linking multiple hGH proteins together through bi-functional PEG linkers. In addition a recombinant form of hGH was created by expressing three hGH proteins tethered together by a repetitive amino acid linker sequence. These engineered proteins were evaluated for structure and function. The tethered hGH proteins were potent and increased weight gain in hypophysectomized rats.","PeriodicalId":73911,"journal":{"name":"Journal of proteomics & bioinformatics","volume":null,"pages":null},"PeriodicalIF":0.0,"publicationDate":"2019-01-01","publicationTypes":"Journal Article","fieldsOfStudy":null,"isOpenAccess":false,"openAccessPdf":"","citationCount":null,"resultStr":null,"platform":"Semanticscholar","paperid":"69960985","PeriodicalName":null,"FirstCategoryId":null,"ListUrlMain":null,"RegionNum":0,"RegionCategory":"","ArticlePicture":[],"TitleCN":null,"AbstractTextCN":null,"PMCID":"","EPubDate":null,"PubModel":null,"JCR":null,"JCRName":null,"Score":null,"Total":0}

{"title":"Neurocognitive Assessment Software for Enrichment Sensory Environments","authors":"Chatzichronis Stylianos, Alexiou Athanasios, Simou Panagiota, Mantzavinos Vasileios, Tsiamis Vasileios, Asma Perveen, G. Ashraf","doi":"10.4172/0974-276X.1000492","DOIUrl":"https://doi.org/10.4172/0974-276X.1000492","url":null,"abstract":"In cases with sensory processing dysfunctions like autism spectrum disorder (ASD) and cognitive decline like Alzheimer's disease (AD), optimistic neurological improvements have been recorded after systematic sensorimotor enrichment stimulation and art therapeutic procedures. While art therapy may offer a cognitive-behavioral breakthrough, several latest studies have explored the effectiveness of brain signals representations through audio and visual transformations of electroencephalography (EEG) measurements and the necessity of neurological evaluation of sensory integration therapies. In this technical report, new software based on the JAVA and processing programming language is presented, that detects, displays and analyzes EEG signals for individual or a group of patients. This neuroinformatics software offers a digital painting environment and a real time transformation of EEG signals into adjustable music volume and octave configuration per electrode, for the real time observation and evaluation of therapeutic procedures. The EEG acquisition is wireless, therefore, brain data can also be collected from the application of other sensory or sensorimotor therapeutic sessions as well. The Neurocognitive Assessment Software for Enrichment Sensory Environments (NASESE) includes two main functionalities, organized in five different modules. The first functionality includes recording, filtering and visualization of the EEG signals exported to a rotating 3D brain model and a real-time transformation of brain activity to sound sculptures, while the second functionality generates statistical tests and coherence calculation in a fully customizable computerized environment.","PeriodicalId":73911,"journal":{"name":"Journal of proteomics & bioinformatics","volume":null,"pages":null},"PeriodicalIF":0.0,"publicationDate":"2019-01-01","publicationTypes":"Journal Article","fieldsOfStudy":null,"isOpenAccess":false,"openAccessPdf":"","citationCount":null,"resultStr":null,"platform":"Semanticscholar","paperid":"70907813","PeriodicalName":null,"FirstCategoryId":null,"ListUrlMain":null,"RegionNum":0,"RegionCategory":"","ArticlePicture":[],"TitleCN":null,"AbstractTextCN":null,"PMCID":"","EPubDate":null,"PubModel":null,"JCR":null,"JCRName":null,"Score":null,"Total":0}

{"title":"Quantitative Proteomics Using Formalin-fixed, Paraffin-embedded Biopsy Tissues in Inflammatory Disease.","authors":"Abhimanyu Amarnani, Joseph R Capri, Puneet Souda, David A Elashoff, Ivan A Lopez, Julian P Whitelegge, Ram R Singh","doi":"10.35248/0974-276X.12.19.503","DOIUrl":"10.35248/0974-276X.12.19.503","url":null,"abstract":"<p><strong>Background: </strong>Investigations in human disease pathogenesis have been hampered due to paucity of access to fresh-frozen tissues (FFT) for use in global, data-driven methodologies. As an alternative, formalin-fixed, paraffin-embedded (FFPE) tissues are readily available in pathology banks. However, the use of formalin for fixation can lead to the loss of proteins that appear during inflammation, thus introducing an inherent sample bias. To address this, we compared FF and FFPE tissue proteomics to determine whether FFPE-tissue can be used effectively in inflammatory diseases.</p><p><strong>Methods: </strong>Adjacent kidney slices from lupus nephritic mice were processed as FFPE or FFTs. Their tissue lysates were run together using proteomics workflow involving filter-aided sample preparation, in-solution dimethyl isotope labeling, StageTip fractionation, and nano-LC MS/MS through an Orbitrap XL MS.</p><p><strong>Results: </strong>We report a >97% concordance in protein identification between adjacent FFPE and FFTs in murine lupus nephritic kidneys. Specifically, proteins representing pathways, namely, 'systemic lupus erythematosus', 'interferon-α', 'TGF-β', and 'extracellular matrix', were reproducibly quantified between FFPE and FFTs. However, 12%-29% proteins were quantified differently in FFPE compared to FFTs, but the differences were consistent across experiments. In particular, certain proteins represented in pathways, including 'inflammatory response' and 'innate immune system' were quantified less in FFPE than in FFTs. In a pilot study of human FFPE tissues, we identified proteins relevant to pathogenesis in lupus nephritic kidney biopsies compared to control kidneys.</p><p><strong>Conclusion: </strong>This is the first report of lupus nephritis kidney proteomics using FFPE tissue. We concluded that archived FFPE tissues can be reliably used for proteomic analyses in inflammatory diseases, with a caveat that certain proteins related to immunity and inflammation may be quantified less in FFPE than in FFTs.</p>","PeriodicalId":73911,"journal":{"name":"Journal of proteomics & bioinformatics","volume":null,"pages":null},"PeriodicalIF":0.0,"publicationDate":"2019-01-01","publicationTypes":"Journal Article","fieldsOfStudy":null,"isOpenAccess":false,"openAccessPdf":"https://www.ncbi.nlm.nih.gov/pmc/articles/PMC7236785/pdf/","citationCount":null,"resultStr":null,"platform":"Semanticscholar","paperid":"37954569","PeriodicalName":null,"FirstCategoryId":null,"ListUrlMain":null,"RegionNum":0,"RegionCategory":"","ArticlePicture":[],"TitleCN":null,"AbstractTextCN":null,"PMCID":"OA","EPubDate":null,"PubModel":null,"JCR":null,"JCRName":null,"Score":null,"Total":0}

{"title":"Interactive Web Tool for Standardizing Proteomics Workflow for Liquid Chromatography-Mass Spectrometry Data.","authors":"Sudhir Srivastava,&nbsp;Michael Merchant,&nbsp;Anil Rai,&nbsp;Shesh N Rai","doi":"","DOIUrl":"","url":null,"abstract":"<p><strong>Introduction: </strong>The proteomics experiments involve several steps and there are many choices available for each step in the workflow. Therefore, standardization of proteomics workflow is an essential task for design of proteomics experiments. However, there are challenges associated with the quantitative measurements based on liquid chromatography-mass spectrometry such as heterogeneity due to technical variability and missing values.</p><p><strong>Methods: </strong>We introduce a web application, Proteomics Workflow Standardization Tool (PWST) to standardize the proteomics workflow. The tool will be helpful in deciding the most suitable choice for each step of the experimentation. This is based on identifying steps/choices with least variability such as comparing Coefficient of Variation (CV). We demonstrate the tool on data with categorical and continuous variables. We have used the special cases of general linear model, analysis of covariance and analysis of variance with fixed effects to study the effects due to various sources of variability. We have provided various options that will aid in finding the contribution of sum of squares for each variable and the CV. The user can analyze the data variability at protein and peptide level even in the presence of missing values.</p><p><strong>Availability and implementation: </strong>The source code for \"PWST\" is written in R and implemented as shiny web application that can be accessed freely from https://ulbbf.shinyapps.io/pwst/.</p>","PeriodicalId":73911,"journal":{"name":"Journal of proteomics & bioinformatics","volume":null,"pages":null},"PeriodicalIF":0.0,"publicationDate":"2019-01-01","publicationTypes":"Journal Article","fieldsOfStudy":null,"isOpenAccess":false,"openAccessPdf":"https://www.ncbi.nlm.nih.gov/pmc/articles/PMC7059686/pdf/","citationCount":null,"resultStr":null,"platform":"Semanticscholar","paperid":"37716707","PeriodicalName":null,"FirstCategoryId":null,"ListUrlMain":null,"RegionNum":0,"RegionCategory":"","ArticlePicture":[],"TitleCN":null,"AbstractTextCN":null,"PMCID":"OA","EPubDate":null,"PubModel":null,"JCR":null,"JCRName":null,"Score":null,"Total":0}

{"title":"Proteomic Effects of Magnesium Stress on Biofilm Associated Proteins Isolated from Cellulolytic Bacillus licheniformis YNP5-TSU","authors":"Joshua A. OHair, Hui Li, M. Rangu, S. Thapa, Yong Yang, T. Fish, S. Bhatti, T. Thannhauser, Suping Zhou","doi":"10.35248/0974-276x.19.12.504","DOIUrl":"https://doi.org/10.35248/0974-276x.19.12.504","url":null,"abstract":"Optimization of cellulase activity is vital for synthesizing the end-products of second generation biofuel production. The slightest change in fermentation parameters can reduce the secretion of necessary enzymes to degrade cellulosic biomass. Determining the ecological effects of certain key media components is essential to understand how bacterial species will respond in a fluid environment. For our experiment a cellulosic media was designed to enhance the industrially important thermophile, Bacillus licheniformis YNP5-TSU. After several attempts to simplify the carboxymethylcellulose (CMC) media composition, impaired biofilm maturation and cellulase activity was noticed. This negative artifact occurred only when magnesium sulphate was removed from media. To analyze the shift in gene expression caused by magnesium stress, biofilm associated proteins were extracted from both control (4.0 mM MgSO4) and magnesium depleted (0.0 mM MgSO4) media at 24 hr and 48 hr incubation periods. These proteins were quantified through isobaric labeling and raw data generated from nanoLC-MS/MS identified over 2,000 proteins from the Bacillus licheniformis YNP5-TSU proteome (NCBI accession number MEDD00000000). After statistical normalization and false discovery rate were calculated, a total of 161 proteins from magnesium depleted media and 238 proteins from control media were deemed statistically relevant. A closer look through STRING interconnected webs, data mining, and NCBI annotations revealed several up/down regulated proteins that had linkage to biofilm formation and cellulase secretion. In this study we are able to provide significant evidence that; (1) biofilm maturation and cellulase production are highly correlated and (2), their optimization is dependent on the expression of several key proteins.","PeriodicalId":73911,"journal":{"name":"Journal of proteomics & bioinformatics","volume":null,"pages":null},"PeriodicalIF":0.0,"publicationDate":"2019-01-01","publicationTypes":"Journal Article","fieldsOfStudy":null,"isOpenAccess":false,"openAccessPdf":"","citationCount":null,"resultStr":null,"platform":"Semanticscholar","paperid":"69960896","PeriodicalName":null,"FirstCategoryId":null,"ListUrlMain":null,"RegionNum":0,"RegionCategory":"","ArticlePicture":[],"TitleCN":null,"AbstractTextCN":null,"PMCID":"","EPubDate":null,"PubModel":null,"JCR":null,"JCRName":null,"Score":null,"Total":0}

{"title":"In silico Mining of EST-SSRs from the Drought Tolerant ESTs in Safflower","authors":"C. Sudhakar, M. Thippeswamy, M. Sivakumar, O. Sudhakarbabu, Mangesh Y. Dudhe","doi":"10.35248/0974-276x.19.12.506","DOIUrl":"https://doi.org/10.35248/0974-276x.19.12.506","url":null,"abstract":"Drought stress is a major abiotic factor causing yield loss in safflower and limited studies have been carried out to dissect the molecular mechanism at EST-SSR level. In this study, a possible relationship between simple sequence repeats (SSRs) distribution and drought stress was studied using three EST libraries of safflower, Ct-D-EST, Ct-NEST and Co-EST. The Ct-D-EST was generated from drought tolerant safflower cultivar A-1; Ct-N-EST and Co-EST were the EST datasets of safflower and its wild progenitor C. oxycanthus, respectively. In total, 156 (45%), 1194 (5%) and 1550 (9%) EST-SSRs were mined from Ct-D-EST, Ct-N-EST and Co-EST libraries, respectively. Comparison of EST-SSRs from Ct-D-EST with that of SSRs from other two libraries showed reasonable differences for each class of repeats. Large variations were observed for dinucleotide repeats in all the libraries. In drought EST-SSRs, only one kind of amino acid was produced by repeat (ATG)14 which encodes met indicating the loci and repeat observed to be 100%. Since three ESTs with SSRs from Ct-D-EST, annotated to putative candidate genes, S-adenosylmethionine synthetase, one-helix protein and myo-inositol 1-phosphate synthetase, did not express with SSRs in the Ct-N-EST, these can be considered as potential candidate genes for drought tolerance. A trinuceotinde SSR, encoding met, was also found in the EST annotated to putative s-adenosylmethionine synthetase, hence, both can be considered as indices for drought tolerance. The genomic resources and the information generated in this study may be useful for the safflower breeders particularly for the development of drought tolerant cultivar.","PeriodicalId":73911,"journal":{"name":"Journal of proteomics & bioinformatics","volume":null,"pages":null},"PeriodicalIF":0.0,"publicationDate":"2019-01-01","publicationTypes":"Journal Article","fieldsOfStudy":null,"isOpenAccess":false,"openAccessPdf":"","citationCount":null,"resultStr":null,"platform":"Semanticscholar","paperid":"69961114","PeriodicalName":null,"FirstCategoryId":null,"ListUrlMain":null,"RegionNum":0,"RegionCategory":"","ArticlePicture":[],"TitleCN":null,"AbstractTextCN":null,"PMCID":"","EPubDate":null,"PubModel":null,"JCR":null,"JCRName":null,"Score":null,"Total":0}