keyword
MENU ▼
Read by QxMD icon Read
search

proteomics analysis tools

keyword
https://www.readbyqxmd.com/read/28337740/proteome-comparison-for-discrimination-between-honeydew-and-floral-honeys-from-botanical-specie-mimosa-scabrella-bentham-by-principal-component-analysis
#1
Mônia Stremel Azevedo, Pedro Alexandre Valentim-Neto, Siluana Katia Tischer Seraglio, Cynthia Fernandes Pinto da Luz, Ana Carolina Maisonnave Arisi, Ana Carolina Oliveira Costa
BACKGROUND: Due to increasing valuation and appreciation of honeydew honey in many European countries and also to existing contamination among different kinds of honeys, the authentication is an important aspect of quality control and its regard with the origin guarantee in terms of source, honeydew or floral, needs to be determined. Furthermore, belonging to the minority composition of the honey, beyond of the importance of its physiological effects, proteins can differ according to these sources...
March 23, 2017: Journal of the Science of Food and Agriculture
https://www.readbyqxmd.com/read/28336332/how-to-use-and-integrate-bioinformatics-tools-to-compare-proteomic-data-from-distinct-conditions-a-tutorial-using-the-pathological-similarities-between-aortic-valve-stenosis-and-coronary-artery-disease-as-a-case-study
#2
Fábio Trindade, Rita Ferreira, Beatriz Magalhães, Adelino Leite-Moreira, Inês Falcão-Pires, Rui Vitorino
Nowadays we are surrounded by a plethora of bioinformatics tools, powerful enough to deal with the large amounts of data arising from proteomic studies, but whose application is sometimes hard to find. Therefore, we used a specific clinical problem - to discriminate pathophysiology and potential biomarkers between two similar cardiovascular diseases, aortic valve stenosis (AVS) and coronary artery disease (CAD) - to make a step-by-step guide through four bioinformatics tools: STRING, DisGeNET, Cytoscape and ClueGO...
March 20, 2017: Journal of Proteomics
https://www.readbyqxmd.com/read/28326926/potential-protein-biomarkers-for-burning-mouth-syndrome-discovered-by-quantitative-proteomics
#3
Eoon Hye Ji, Cynthia Diep, Tong Liu, Hong Li, Robert Merrill, Diana Messadi, Shen Hu
Burning mouth syndrome (BMS) is a chronic pain disorder characterized by severe burning sensation in normal looking oral mucosa. Diagnosis of BMS remains to be a challenge to oral healthcare professionals because the method for definite diagnosis is still uncertain. In this study, a quantitative saliva proteomic analysis was performed in order to identify target proteins in BMS patients' saliva that may be used as biomarkers for simple, non-invasive detection of the disease. By using isobaric tags for relative and absolute quantitation labeling and liquid chromatography-tandem mass spectrometry to quantify 1130 saliva proteins between BMS patients and healthy control subjects, we found that 50 proteins were significantly changed in the BMS patients when compared to the healthy control subjects ( p ≤ 0...
January 2017: Molecular Pain
https://www.readbyqxmd.com/read/28323242/investigation-of-the-indigenous-fungal-community-populating-barley-grains-secretomes-and-xylanolytic-potential
#4
Abida Sultan, Jens C Frisvad, Birgit Andersen, Birte Svensson, Christine Finnie
The indigenous fungal species populating cereal grains produce numerous plant cell wall-degrading enzymes including xylanases, which could play important role in plant-pathogen interactions and in adaptation of the fungi to varying carbon sources. To gain more insight into the grain surface-associated enzyme activity, members of the populating fungal community were isolated, and their secretomes and xylanolytic activities assessed. Twenty-seven different fungal species were isolated from grains of six barley cultivars over different harvest years and growing sites...
March 17, 2017: Journal of Proteomics
https://www.readbyqxmd.com/read/28322544/graphene-oxide-quantum-dots-as-novel-nanozymes-for-alcohol-intoxication
#5
Anqi Sun, Li Mu, Xiangang Hu
Alcohol overconsumption as a worldwide issue results in alcoholic liver disease (ALD), such as steatosis, alcoholic hepatitis and cirrhosis. The treatment of ALD has been widely investigated but remains challenging. In this work, the protective effects of graphene oxide quantum dots (GOQDs) as novel nanozymes against alcohol overconsumption are discovered, and the specific mechanisms underlying these effects are elucidated via omics analysis. GOQDs dramatically alleviate the reduction of cell viability induced by ethanol and can act as nanozymes to accelerate ethanol metabolism and avoid the accumulation of toxic intermediates in cells...
March 21, 2017: ACS Applied Materials & Interfaces
https://www.readbyqxmd.com/read/28320317/navigo-interactive-tool-for-visualization-and-functional-similarity-and-coherence-analysis-with-gene-ontology
#6
Qing Wei, Ishita K Khan, Ziyun Ding, Satwica Yerneni, Daisuke Kihara
BACKGROUND: The number of genomics and proteomics experiments is growing rapidly, producing an ever-increasing amount of data that are awaiting functional interpretation. A number of function prediction algorithms were developed and improved to enable fast and automatic function annotation. With the well-defined structure and manual curation, Gene Ontology (GO) is the most frequently used vocabulary for representing gene functions. To understand relationship and similarity between GO annotations of genes, it is important to have a convenient pipeline that quantifies and visualizes the GO function analyses in a systematic fashion...
March 20, 2017: BMC Bioinformatics
https://www.readbyqxmd.com/read/28317029/listeriomics-an-interactive-web-platform-for-systems-biology-of-listeria
#7
Christophe Bécavin, Mikael Koutero, Nicolas Tchitchek, Franck Cerutti, Pierre Lechat, Nicolas Maillet, Claire Hoede, Hélène Chiapello, Christine Gaspin, Pascale Cossart
As for many model organisms, the amount of Listeria omics data produced has recently increased exponentially. There are now >80 published complete Listeria genomes, around 350 different transcriptomic data sets, and 25 proteomic data sets available. The analysis of these data sets through a systems biology approach and the generation of tools for biologists to browse these various data are a challenge for bioinformaticians. We have developed a web-based platform, named Listeriomics, that integrates different tools for omics data analyses, i...
March 2017: MSystems
https://www.readbyqxmd.com/read/28314116/secretory-proteome-analysis-of-streptomycin-resistant-mycobacterium-tuberculosis-clinical-isolates
#8
Divakar Sharma, Deepa Bisht
Tuberculosis still remains one of the most fatal infectious diseases. Streptomycin (SM) is the drug of choice, especially for patients with multidrug-resistant tuberculosis or category II patients, because it targets the protein synthesis machinery by interacting with steps of translation. Several mechanisms have been proposed to explain the resistance, but our knowledge is inadequate. Secretome often plays an important role in pathogenesis and is considered an attractive reservoir for the development of novel diagnostic markers and targets...
March 1, 2017: SLAS Discov
https://www.readbyqxmd.com/read/28306751/peptidomic-and-transcriptomic-profiling-of-four-distinct-spider-venoms
#9
Vera Oldrati, Dominique Koua, Pierre-Marie Allard, Nicolas Hulo, Miriam Arrell, Wolfgang Nentwig, Frédérique Lisacek, Jean-Luc Wolfender, Lucia Kuhn-Nentwig, Reto Stöcklin
Venom based research is exploited to find novel candidates for the development of innovative pharmacological tools, drug candidates and new ingredients for cosmetic and agrochemical industries. Moreover, venomics, as a well-established approach in systems biology, helps to elucidate the genetic mechanisms of the production of such a great molecular biodiversity. Today the advances made in the proteomics, transcriptomics and bioinformatics fields, favor venomics, allowing the in depth study of complex matrices and the elucidation even of minor compounds present in minute biological samples...
2017: PloS One
https://www.readbyqxmd.com/read/28301937/tools-for-studying-glycans-recent-advances-in-chemoenzymatic-glycan-labeling
#10
Aime Lopez Aguilar, Jennie Grace Briard, Linette Yang, Ben Ovryn, Matthew Scott Macauley, Peng Wu
The study of cellular glycosylation presents many challenges due, in large part, to the nontemplated nature of glycan biosynthesis and glycans' structural complexity. Chemoenzymatic glycan labeling (CeGL) has emerged as a new technique to address the limitations of existing methods for glycan detection. CeGL combines glycosyltransferases and unnatural nucleotide sugar donors equipped with a bioorthogonal chemical tag to directly label specific glycan acceptor substrates in situ within biological samples. This article reviews the current CeGL strategies that are available to characterize cell-surface and intracellular glycans...
March 17, 2017: ACS Chemical Biology
https://www.readbyqxmd.com/read/28299940/epsilon-q-an-automated-analyzer-interface-for-mass-spectral-library-search-and-label-free-protein-quantification
#11
Jin-Young Cho, Hyoung-Joo Lee, Seul-Ki Jeong, Young-Ki Paik
Mass spectrometry (MS) is a widely used proteome analysis tool for biomedical science. In an MS-based bottom-up proteomic approach to protein identification, sequence database (DB) searching has been routinely used because of its simplicity and convenience. However, searching a sequence DB with multiple variables and modification options can increase processing time and false-positive errors in large and complicated MS datasets. Spectral library searching is an alternative solution, avoiding the limitations of sequence DB searching and allowing the detection of more peptides with high sensitivity...
March 16, 2017: Journal of Proteome Research
https://www.readbyqxmd.com/read/28299517/characterization-and-complete-genome-sequence-analysis-of-a-novel-virulent-siphoviridae-phage-against-staphylococcus-aureus-isolated-from-bovine-mastitis-in-xinjiang-china
#12
Qian Zhang, Shaozhen Xing, Qiang Sun, Guangqian Pei, Shi Cheng, Yannan Liu, Xiaoping An, Xianglilan Zhang, Yonggang Qu, Yigang Tong
Bovine mastitis is one of the most costly diseases in dairy cows worldwide. It can be caused by over 150 different microorganisms, where Staphylococcus aureus is the most frequently isolated and a major pathogen responsible for heavy economic losses in dairy industry. Although antibiotic therapy is most widely used, alternative treatments are necessary due to the increasing antibiotic resistance. Using phage for pathogen control is a promising tool in the fight against antibiotic resistance. Mainly using high-throughput sequencing, bioinformatics and our proposed phage termini identification method, we have isolated and characterized a novel virulent phage, designated as vB_SauS_IMEP5, from manure collected from dairy farms in Shihezi, Xinjiang, China, for use as a biocontrol agent against Staphylococcus aureus infections...
March 15, 2017: Virus Genes
https://www.readbyqxmd.com/read/28285496/maldi-tof-mass-spectrometry-as-a-useful-tool-for-identification-of-enterococcus-spp-from-wild-birds-and-differentiation-of-closely-related-species
#13
Dagmara Stępień-Pyśniak, Tomasz Hauschild, Paweł Różański, Agnieszka Marek
The aim of this study was to explore the accuracy and feasibility of Matrix-Assisted Laser Desorption Ionization Time-of-Flight Mass Spectrometry (MALDI-TOF MS) in identifying bacteria from environmental sources, as compared to rpoA gene sequencing, and to evaluate the occurrence of bacteria of the genus Enterococcus in wild birds. In addition, a phyloproteomic analysis of certain Enterococcus species with spectral relationships was performed. The enterococci were isolated from 25 species of wild birds in central Europe (Poland)...
March 13, 2017: Journal of Microbiology and Biotechnology
https://www.readbyqxmd.com/read/28283406/transcriptomic-insights-into-genetic-diversity-of-protein-coding-genes-in-x-laevis
#14
Virginia Savova, Esther J Pearl, Elvan Boke, Anwesha Nag, Ivan Adzhubei, Marko E Horb, Leonid Peshkin
We characterize the genetic diversity of Xenopus laevis strains using RNA-seq data and allele-specific analysis. This data provides a catalogue of coding variation, which can be used for improving the genomic sequence, as well as for better sequence alignment, probe design, and proteomic analysis. In addition, we paint a broad picture of the genetic landscape of the species by functionally annotating different classes of mutations with a well-established prediction tool (PolyPhen-2). Further, we specifically compare the variation in the progeny of four crosses: inbred genomic (J)-strain, outbred albino (B)-strain, and two hybrid crosses of J and B strains...
March 7, 2017: Developmental Biology
https://www.readbyqxmd.com/read/28282143/proteome-analysis-of-human-perilymph-using-an-intraoperative-sampling-method
#15
Heike Andrea Schmitt, Andreas Pich, Anke Schröder, Verena Scheper, Giorgio Lilli, Günter Reuter, Thomas Lenarz
The knowledge about the etiology and pathophysiology of sensorineural hearing loss (SNHL) is still very limited. The project aims at the improvement of understanding different types of SNHL by proteome analysis of human perilymph. Sampling of perilymph has been established during inner ear surgeries (cochlear implant and vestibular schwannoma surgeries) and safety of the sampling method was determined by pure tone audiometry. An in-depth shot-gun proteomics approach was performed to identify cochlear proteins and individual proteome in perilymph of patients...
March 10, 2017: Journal of Proteome Research
https://www.readbyqxmd.com/read/28263889/proteomic-analysis-of-chondromodulin-i-induced-differentiation-of-mesenchymal-stem-cells-into-chondrocytes
#16
Shuang-Chun Xing, Lian-Xin Du, Wei Zhou, Yu-Qiang Hu, Ya Feng, Hong-Feng Liang, Lin Sang, Min Qi, Li-Jie Zhai, Zhi-Qiang Wang
To identify novel proteins that might help clarify the molecular mechanisms underlying chondromodulin-I (ChM-I) induction of mesenchymal stem cells (MSCs) differentiate into chondrocytes. MSCs are triggered to differentiate into chondrocytes, which are recognized as important factors in cartilage tissue engineering. ChM-I is a glycoprotein that stimulates the growth of chondrocytes and inhibits angiogenesis in vitro. In this study, the proteomic approach was used to evaluate protein changes between undifferentiated MSCs and ChM-I-transfected MSCs...
March 2, 2017: Journal of Proteomics
https://www.readbyqxmd.com/read/28263070/param-medic-a-tool-for-improving-ms-ms-database-search-yield-by-optimizing-parameter-settings
#17
Damon H May, Kaipo Tamura, William S Noble
In shotgun proteomics analysis, user-specified parameters are critical to database search performance and therefore to the yield of confident peptide-spectrum matches (PSMs). Two of the most important parameters are related to the accuracy of the mass spectrometer. Precursor mass tolerance defines the peptide candidates considered for each spectrum. Fragment mass tolerance or bin size determines how close observed and theoretical fragments must be to be considered a match. For either of these two parameters, too wide a setting yields randomly high-scoring false PSMs, whereas too narrow a setting erroneously excludes true PSMs, in both cases, lowering the yield of peptides detected at a given false discovery rate...
March 13, 2017: Journal of Proteome Research
https://www.readbyqxmd.com/read/28259147/proteomodlr-for-functional-proteomic-analysis
#18
Paolo Cifani, Mojdeh Shakiba, Sagar Chhangawala, Alex Kentsis
BACKGROUND: High-accuracy mass spectrometry enables near comprehensive quantification of the components of the cellular proteomes, increasingly including their chemically modified variants. Likewise, large-scale libraries of quantified synthetic peptides are becoming available, enabling absolute quantification of chemically modified proteoforms, and therefore systems-level analyses of changes of their absolute abundance and stoichiometry. Existing computational methods provide advanced tools for mass spectral analysis and statistical inference, but lack integrated functions for quantitative analysis of post-translationally modified proteins and their modification stoichiometry...
March 4, 2017: BMC Bioinformatics
https://www.readbyqxmd.com/read/28255832/analysing-algorithms-and-data-sources-for-the-tissue-specific-reconstruction-of-liver-healthy-and-cancer-cells
#19
Jorge Ferreira, Sara Correia, Miguel Rocha
Genome-Scale Metabolic Models (GSMMs), mathematical representations of the cell metabolism in different organisms including humans, are resourceful tools to simulate metabolic phenotypes and understand associated diseases, such as obesity, diabetes and cancer. In the last years, different algorithms have been developed to generate tissue-specific metabolic models that simulate different phenotypes for distinct cell types. Hepatocyte cells are one of the main sites of metabolic conversions, mainly due to their diverse physiological functions...
March 2, 2017: Interdisciplinary Sciences, Computational Life Sciences
https://www.readbyqxmd.com/read/28255762/semax-an-analog-of-acth-4-7-regulates-expression-of-immune-response-genes-during-ischemic-brain-injury-in-rats
#20
Ekaterina V Medvedeva, Veronika G Dmitrieva, Svetlana A Limborska, Nikolay F Myasoedov, Lyudmila V Dergunova
Brain stroke continues to claim the lives of million people every year. To build the effective strategies for stroke treatment it is necessary to understand the neuroprotective mechanisms that are able to prevent the ischemic injury. Consisting of the ACTH(4-7) fragment and the tripeptide Pro-Gly-Pro (PGP), the synthetic peptide Semax effectively protects brain against ischemic stroke. However, the molecular mechanisms underlying its neuroprotection and participation of PGP in them are still needed to be clarified...
March 2, 2017: Molecular Genetics and Genomics: MGG
keyword
keyword
78635
1
2
Fetch more papers »
Fetching more papers... Fetching...
Read by QxMD. Sign in or create an account to discover new knowledge that matter to you.
Remove bar
Read by QxMD icon Read
×

Search Tips

Use Boolean operators: AND/OR

diabetic AND foot
diabetes OR diabetic

Exclude a word using the 'minus' sign

Virchow -triad

Use Parentheses

water AND (cup OR glass)

Add an asterisk (*) at end of a word to include word stems

Neuro* will search for Neurology, Neuroscientist, Neurological, and so on

Use quotes to search for an exact phrase

"primary prevention of cancer"
(heart or cardiac or cardio*) AND arrest -"American Heart Association"