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https://www.readbyqxmd.com/read/28944503/global-quantification-of-phosphoproteins-combining-metabolic-labeling-and-gel-based-proteomics-in-b-pumilus
#1
Christian Hentschker, Carolin Dewald, Andreas Otto, Knut Büttner, Michael Hecker, Dörte Becher
Differential proteomics targeting the protein abundance is commonly used to follow changes in biological systems. Differences in localization and degree of posttranslational modifications of proteins including phosphorylations are of tremendous interest due to the anticipated role in molecular regulatory processes. Because of their particular low abundance in prokaryotes, identification and quantification of protein phosphorylation is traditionally performed by either comparison of spot intensities on two-dimensional gels after differential phosphoprotein staining or gel-free by stable isotope labeling, sequential phosphopeptide enrichment and following LC-MS analysis...
September 25, 2017: Electrophoresis
https://www.readbyqxmd.com/read/28943950/apigenin-inhibits-growth-and-induces-apoptosis-in-human-cholangiocarcinoma-cells
#2
Pantipa Subhasitanont, Daranee Chokchaichamnankit, Khajeelak Chiablaem, Siriporn Keeratichamroen, Lukana Ngiwsara, N Monique Paricharttanakul, Kriengsak Lirdprapamongkol, Churat Weeraphan, Jisnuson Svasti, Chantragan Srisomsap
A promising nutraceutical, apigenin, was recently revealed to exhibit biological activity in inhibiting several types of cancer. The effects of apigenin on the growth inhibition and apoptosis of the cholangiocarcinoma HuCCA-1 cell line were investigated. Protein alterations subsequent to apigenin treatment were studied using a proteomic approach. The values of 20, 50 and 90% inhibition of cell growth (IC20, IC50 and IC90) were determined by MTT cell viability assay. Apoptotic cell death was detected using two different methods, a flow cytometric analysis (Muse Cell Analyzer) and DNA fragmentation assay...
October 2017: Oncology Letters
https://www.readbyqxmd.com/read/28941868/predicting-membrane-protein-types-using-various-decision-tree-classifiers-based-on-various-modes-of-general-pseaac-for-imbalanced-datasets
#3
E Siva Sankari, D Manimegalai
Predicting membrane protein types is an important and challenging research area in bioinformatics and proteomics. Traditional biophysical methods are used to classify membrane protein types. Due to large exploration of uncharacterized protein sequences in databases, traditional methods are very time consuming, expensive and susceptible to errors. Hence, it is highly desirable to develop a robust, reliable, and efficient method to predict membrane protein types. Imbalanced datasets and large datasets are often handled well by decision tree classifiers...
September 20, 2017: Journal of Theoretical Biology
https://www.readbyqxmd.com/read/28940772/enhancing-proteomic-throughput-in-capillary-electrophoresis-mass-spectrometry-by-sequential-sample-injection
#4
Klaus Faserl, Bettina Sarg, Laura Sola, Herbert H Lindner
In this study we demonstrate the potential of sequential injection of samples in capillary electrophoresis-mass spectrometry (CE-MS) for rapid and sensitive proteome characterization of human lymphoblastic T-cells (line CCRF-CEM). Proteins were extracted, enzymatically digested, and the resulting peptides fractionated by RP-HPLC. Twenty fractions were thereafter analyzed by CE-MS within a single MS analysis. The CE-MS method was designed that every 10 minutes a new fraction was injected into the CE system. Without any rinsing or equilibration steps we were able to generate a continuous stream of peptides feeding the mass analyzer...
September 20, 2017: Proteomics
https://www.readbyqxmd.com/read/28934434/high-sensitivity-assays-for-plasmodium-falciparum-infection-by-immuno-polymerase-chain-reaction-detection-of-pfideh-and-pfldh-antigens
#5
Jianbing Mu, John F Andersen, Jesus G Valenzuela, Thomas E Wellems
Background: Rapid diagnostic tests based on Plasmodium falciparum histidine-rich protein II (PfHRP-II) and P. falciparum lactate dehydrogenase (PfLDH) antigens are widely deployed for detection of P. falciparum infection; however, these tests often miss cases of low-level parasitemia, and PfHRP-II tests can give false-negative results when P. falciparum strains do not express this antigen. Methods: We screened proteomic data for highly expressed P. falciparum proteins and compared their features to those of PfHRP-II and PfLDH biomarkers...
September 15, 2017: Journal of Infectious Diseases
https://www.readbyqxmd.com/read/28934418/systems-biotechnology-for-protein-production-in-pichia-pastoris
#6
Richard J Zahrl, David A Peña, Diethard Mattanovich, Brigitte Gasser
The methylotrophic yeast Pichia pastoris (syn. Komagataella spp.) is one of the most important production systems for heterologous proteins. After the first genome sequences were published in 2009, tremendous effort was made to establish systems-level analytical methods. Methylotrophic lifestyle was one of the most thoroughly investigated topics, studied at the levels of transcriptome, proteome and metabolic flux. Also the responses of P. pastoris to environmental stress conditions experienced during high cell density production processes were studied...
November 1, 2017: FEMS Yeast Research
https://www.readbyqxmd.com/read/28934234/a-novel-feature-ranking-method-for-prediction-of-cancer-stages-using-proteomics-data
#7
Ehsan Saghapour, Saeed Kermani, Mohammadreza Sehhati
Proteomic analysis of cancers' stages has provided new opportunities for the development of novel, highly sensitive diagnostic tools which helps early detection of cancer. This paper introduces a new feature ranking approach called FRMT. FRMT is based on the Technique for Order of Preference by Similarity to Ideal Solution method (TOPSIS) which select the most discriminative proteins from proteomics data for cancer staging. In this approach, outcomes of 10 feature selection techniques were combined by TOPSIS method, to select the final discriminative proteins from seven different proteomic databases of protein expression profiles...
2017: PloS One
https://www.readbyqxmd.com/read/28933205/mass-spectrometry-methods-to-study-protein-metabolite-interactions
#8
Hongbo Guo, Hui Peng, Andrew Emili
To ​​​​understand and manipulate biochemical processes and signaling pathways, the knowledge of endogenous protein-metabolite interactions would be extremely helpful. Recent developments in precision mass spectrometry, high-throughput proteomics and sensitive metabolomic profiling are beginning to converge on a possible solution, heralding a new era of global metabolome-proteome 'interactome' studies that promise to change biomedical research and drug discovery. Areas covered: Here, we review innovative mass spectrometry-based methods and recent pioneering studies aimed at elucidating the physical associations of small molecule ligands with cellular proteins...
September 21, 2017: Expert Opinion on Drug Discovery
https://www.readbyqxmd.com/read/28932623/proteomics-technique-opens-new-frontiers-in-mobilome-research
#9
COMMENT
Andrew D Davidson, David A Matthews, Kevin Maringer
A large proportion of the genome of most eukaryotic organisms consists of highly repetitive mobile genetic elements. The sum of these elements is called the "mobilome," which in eukaryotes is made up mostly of transposons. Transposable elements contribute to disease, evolution, and normal physiology by mediating genetic rearrangement, and through the "domestication" of transposon proteins for cellular functions. Although 'omics studies of mobilome genomes and transcriptomes are common, technical challenges have hampered high-throughput global proteomics analyses of transposons...
2017: Mobile Genetic Elements
https://www.readbyqxmd.com/read/28932152/human-salivary-protein-extraction-from-rnapro%C3%A2-sal%C3%A2-pure%C3%A2-sal%C3%A2-and-passive-drooling-method
#10
Zohaib Khurshid, Syed Faraz Moin, Rabia Sannam Khan, Muhammad Atif Saleem Agwan, Abdullah Hamed Alwadaani, Muhammad Sohail Zafar
OBJECTIVE: The aim of the current study was to carry out a preliminary validation of devices for standardized collection of whole mouth fluid (WMF) in comparison to the passive drooling method for protein analysis in healthy subjects. MATERIALS AND METHODS: A carefully designed sample collection/pretreatment protocol is crucial to the success of any saliva proteomics project. In this study, WMF was collected from healthy volunteers (n = 10, ages: 18-26 years). Individuals with any oral disease were excluded from the study group...
July 2017: European Journal of Dentistry
https://www.readbyqxmd.com/read/28930563/mass-spectrometry-based-proteomic-analysis-of-the-dna-damage-response
#11
Matthew P Stokes, Yiying Zhu, Charles L Farnsworth
In response to DNA damage, cells have evolved mechanisms to halt cell cycle progression, activate repair, or initiate apoptosis. These DNA damage response (DDR) pathways are critical for cellular survival in response to genomic insult, and play important roles in growth, development, and disease. Historically, mediators of DNA damage response signaling have been studied one or a few proteins at a time. Advances in mass spectrometry instrumentation and enrichment methods now allow for more global analysis of the DDR in cells and tissues...
January 1, 2018: Frontiers in Bioscience (Landmark Edition)
https://www.readbyqxmd.com/read/28927943/laser-microdissection-a-powerful-tool-for-genomics-at-cell-level
#12
REVIEW
Claudia Bevilacqua, Bertrand Ducos
Laser microdissection (LM) has become considerably democratized over the last fifteen years. Instruments have evolved to offer more powerful and efficient lasers as well as new options for sample collection and preparation. Technological evolutions have also focused on the post-microdissection analysis capabilities, opening up investigations in all disciplines of experimental and clinical biology, thanks to the advent of new high-throughput methods of genome analysis, including RNAseq and proteomics, now globally known as microgenomics, i...
September 16, 2017: Molecular Aspects of Medicine
https://www.readbyqxmd.com/read/28927001/a-review-and-database-of-snake-venom-proteomes
#13
REVIEW
Theo Tasoulis, Geoffrey K Isbister
Advances in the last decade combining transcriptomics with established proteomics methods have made possible rapid identification and quantification of protein families in snake venoms. Although over 100 studies have been published, the value of this information is increased when it is collated, allowing rapid assimilation and evaluation of evolutionary trends, geographical variation, and possible medical implications. This review brings together all compositional studies of snake venom proteomes published in the last decade...
September 18, 2017: Toxins
https://www.readbyqxmd.com/read/28926970/proteomic-characterization-of-armillaria-mellea-reveals-oxidative-stress-response-mechanisms-and-altered-secondary-metabolism-profiles
#14
Cassandra Collins, Rachel Hurley, Nada Almutlaqah, Grainne O'Keeffe, Thomas M Keane, David A Fitzpatrick, Rebecca A Owens
Armillaria mellea is a major plant pathogen. Yet, the strategies the organism uses to infect susceptible species, degrade lignocellulose and other plant material and protect itself against plant defences and its own glycodegradative arsenal are largely unknown. Here, we use a combination of gel and MS-based proteomics to profile A. mellea under conditions of oxidative stress and changes in growth matrix. 2-DE and LC-MS/MS were used to investigate the response of A. mellea to H₂O₂ and menadione/FeCl₃ exposure, respectively...
September 17, 2017: Microorganisms
https://www.readbyqxmd.com/read/28926706/structural-and-kinetic-characterization-of-the-intrinsically-disordered-protein-sev-ntail-through-enhanced-sampling-simulations
#15
Mattia Bernetti, Matteo Masetti, Fabio Pietrucci, Martin Blackledge, Malene Ringkjøbing Jensen, Maurizio Recanatini, Luca Mollica, Andrea Cavalli
Intrinsically disordered proteins (IDPs) are emerging as an important class of the proteome. Being able to interact with different molecular targets, they participate in many physiological and pathological activities. However, due to their intrinsically heterogeneous nature, determining the equilibrium properties of IDPs is still a challenge for biophysics. Herein, we applied state-of-the-art enhanced sampling methods to Sev NTAIL, a test case of IDPs, and constructed a bin-based kinetic model to unveil the underlying kinetics...
September 19, 2017: Journal of Physical Chemistry. B
https://www.readbyqxmd.com/read/28925403/a-slow-cycling-subpopulation-of-melanoma-cells-with-highly-invasive-properties
#16
M Perego, M Maurer, J X Wang, S Shaffer, A C Müller, K Parapatics, L Li, D Hristova, S Shin, F Keeney, S Liu, X Xu, A Raj, J K Jensen, K L Bennett, S N Wagner, R Somasundaram, M Herlyn
Melanoma is a heterogeneous tumor with different subpopulations showing different proliferation rates. Slow-cycling cells were previously identified in melanoma, but not fully biologically characterized. Using the label-retention method, we identified a subpopulation of slow-cycling cells, defined as label-retaining cells (LRC), with strong invasive properties. We demonstrate through live imaging that LRC are leaving the primary tumor mass at a very early stage and disseminate to peripheral organs. Through global proteome analyses, we identified the secreted protein SerpinE2/protease nexin-1 as causative for the highly invasive potential of LRC in melanomas...
September 18, 2017: Oncogene
https://www.readbyqxmd.com/read/28925163/-proteomics-research-of-intervention-effect-of-qi-enriching-herbs-on-qi-deficiency-rats-based-on-technology-of-nanolc-ltq-orbitrap
#17
Yin-Fang Chen, Ying-Jun Fu, Chao Liu, Min Hou, Guo-Liang Xu, Ri-Yue Yu, Hong-Ning Liu, Li-Ping Huang
Proteomics method, based on NanoLC-LTQ-Orbitrap technology, was applied to explore the biological basis of intervention effect of "Qi enriching" herbs on "Qi deficiency" rats. The "Qi deficiency" rat model was established with caloric restriction combined with excessive swimming. Muscle proteins of vastus lateralis from the blank group, the model group and the ginseng group were detected by NanoLC-LTQ-Orbitrap system. The data were imported into Protein Discovery software to identify the proteins and all the raw datum were analyzed by SIEVE software...
October 2016: Zhongguo Zhong Yao za Zhi, Zhongguo Zhongyao Zazhi, China Journal of Chinese Materia Medica
https://www.readbyqxmd.com/read/28922838/comparative-genomics-of-a-drug-resistant-pseudomonas-aeruginosa-panel-and-the-challenges-of-antimicrobial-resistance-prediction-from-genomes
#18
J Jeukens, I Kukavica-Ibrulj, J G Emond-Rheault, L Freschi, R C Levesque
Antimicrobial resistance (AMR) is now recognized as a global threat to human health. The accessibility of microbial whole-genome sequencing offers an invaluable opportunity for resistance surveillance via the resistome, i.e. the genes and mutations underlying AMR. Unfortunately, AMR prediction from genomic data remains extremely challenging, especially for species with a large pan-genome. One such organism, for which multidrug-resistant (MDR) isolates are frequently encountered in the clinic, is Pseudomonas aeruginosa...
October 2, 2017: FEMS Microbiology Letters
https://www.readbyqxmd.com/read/28922600/ptml-model-for-proteome-mining-of-b-cell-epitopes-and-theoretic-experimental-study-of-bm86-protein-sequences-from-colima-mexico
#19
Saúl Gabriel Martínez, Esvieta Tenorio-Borroto, Alberto Barbabosa Pliego, Hector Diaz-Albiter, Juan C Vazquez-Chagoyan, Humbert Gonzalez-Diaz
In this work, we developed a general Perturbation Theory and Machine Learning (PTML) method for data mining of proteomes, in order to discover new B-cell epitopes useful for vaccine design. The method predicts the epitope activity εq(cqj) of one query peptide (q-peptide) in a set of experimental query conditions (cqj). The method uses as input the sequence of the q-peptide. The method also uses as input information about the sequence and epitope activity εr(crj) of a peptide of reference (r-peptide) assayed on similar experimental conditions (crj)...
September 18, 2017: Journal of Proteome Research
https://www.readbyqxmd.com/read/28922569/strategies-for-analysis-of-isomeric-peptides
#20
Erik T Jansson
This review presents an overview and recent progress of strategies for detecting isomerism in peptides, with focus on d/l epimerization and the various isomers that the presence of an aspartic acid residue may yield in a protein or peptide. While mass spectrometry has become a majorly used method of choice within proteomics, isomerism is inherently difficult to analyze because it is a modification that does not yield any change in mass of the analyte. Here, several techniques used for analysis of peptide isomerism are discussed, including enzymatic assays, liquid chromatography and capillary electrophoresis...
September 18, 2017: Journal of Separation Science
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