keyword
MENU ▼
Read by QxMD icon Read
search

Proteomic

keyword
https://www.readbyqxmd.com/read/28092651/long-lasting-antinociceptive-effects-of-green-light-in-acute-and-chronic-pain-in-rats
#1
Mohab M Ibrahim, Amol Patwardhan, Kerry B Gilbraith, Aubin Moutal, Xiaofang Yang, Lindsey A Chew, Tally Largent-Milnes, T Philip Malan, Todd W Vanderah, Frank Porreca, Rajesh Khanna
Treatments for chronic pain are inadequate, and new options are needed. Nonpharmaceutical approaches are especially attractive with many potential advantages including safety. Light therapy has been suggested to be beneficial in certain medical conditions such as depression, but this approach remains to be explored for modulation of pain. We investigated the effects of light-emitting diodes (LEDs), in the visible spectrum, on acute sensory thresholds in naive rats as well as in experimental neuropathic pain...
February 2017: Pain
https://www.readbyqxmd.com/read/28092479/prospects-for-proteomics-in-kidney-stone-disease
#2
Arada Vinaiphat, Visith Thongboonkerd
No abstract text is available yet for this article.
January 16, 2017: Expert Review of Proteomics
https://www.readbyqxmd.com/read/28092471/genomics-pipelines-and-data-integration-challenges-and-opportunities-in-the-research-setting
#3
Jeremy Davis-Turak, Sean M Courtney, E Starr Hazard, W Bailey Glen, Willian da Silveira, Timothy Wesselman, Larry P Harbin, Bethany J Wolf, Dongjun Chung, Gary Hardiman
The emergence and mass utilization of high-throughput (HT) technologies, including sequencing technologies (genomics) and mass spectrometry (proteomics, metabolomics, lipids), has allowed geneticists, biologists, and biostatisticians to bridge the gap between genotype and phenotype on a massive scale. These new technologies have brought rapid advances in our understanding of cell biology, evolutionary history, microbial environments, and are increasingly providing new insights and applications towards clinical care and personalized medicine...
January 16, 2017: Expert Review of Molecular Diagnostics
https://www.readbyqxmd.com/read/28092360/chemical-proteomics-reveals-adp-ribosylation-of-small-gtpases-during-oxidative-stress
#4
Nathan P Westcott, Joseph P Fernandez, Henrik Molina, Howard C Hang
ADP-ribosylation is a post-translational modification that is known to be involved in cellular homeostasis and stress but has been challenging to analyze biochemically. To facilitate the detection of ADP-ribosylated proteins, we show that an alkyne-adenosine analog, N(6)-propargyl adenosine (N(6)pA), is metabolically incorporated in mammalian cells and enables fluorescence detection and proteomic analysis of ADP-ribosylated proteins. Notably, our analysis of N(6)pA-labeled proteins that are upregulated by oxidative stress revealed differential ADP-ribosylation of small GTPases...
January 16, 2017: Nature Chemical Biology
https://www.readbyqxmd.com/read/28092104/quantitative-proteomic-analysis-of-gingival-crevicular-fluids-from-deciduous-and-permanent-teeth
#5
Yumi Moriya, Takashi Obama, Toshihiro Aiuchi, Tomomi Sugiyama, Yumiko Endo, Yoko Koide, Emiko Noguchi, Motonori Ishizuka, Mitsuko Inoue, Hiroyuki Itabe, Matsuo Yamamoto
AIM: Gingivitis commonly progresses to periodontitis in permanent dentition but rarely in deciduous teeth. Little is known about the biochemical differences between gingiva of deciduous and permanent teeth. Here we compared the protein profiles of gingival crevicular fluids (GCF) from the gingiva of deciduous and permanent teeth. MATERIALS AND METHODS: Forty children with mixed dentition (Hellman's dental age IIIA) were selected and GCF samples were collected from deciduous cuspids and central incisors in the maxilla...
January 16, 2017: Journal of Clinical Periodontology
https://www.readbyqxmd.com/read/28092050/microwestern-arrays-for-systems-level-analysis-of-sh2-domain-containing-proteins
#6
Mark F Ciaccio, Richard B Jones
The Microwestern Array (MWA) method combines the scalability and miniaturization afforded by the Reverse Phase Lysate Array (RPLA) approach with the electrophoretic separation characteristic of the Western blot. This technology emulates the creation of an array of small Western blots on a single sheet of nitrocellulose allowing for the sensitive and quantitative measurement of hundreds of proteins from hundreds of cell lysates with minimal cost and maximal accuracy, precision, and reproducibility. The MWA is a versatile technology that can be easily configured for purposes such as antibody screening, cell signaling network inference, protein modification/phenotype regression analysis, and genomic/proteomic relationships...
2017: Methods in Molecular Biology
https://www.readbyqxmd.com/read/28092047/analysis-of-the-global-changes-in-sh2-binding-properties-using-mass-spectrometry-supported-by-quantitative-stable-isotope-labeling-by-amino-acids-in-cell-culture-silac-technique
#7
Radoslaw M Sobota
Quantitative mass spectrometry (MS)-based proteomics enables fast and reliable analysis of protein complexes. Its robustness and sensitivity effectively substitute traditional antibody-based approaches. Here, we describe the combination of mass spectrometry and Stable Isotope Labeling by Amino acids in Cell culture (SILAC) in characterization of the SH2 domain binding capacity.
2017: Methods in Molecular Biology
https://www.readbyqxmd.com/read/28092045/sh2-domains-as-affinity-reagents-for-phosphotyrosine-protein-enrichment-and-proteomic-analysis
#8
Mi Ke, Bizhu Chu, Lin Lin, Ruijun Tian
Dynamic tyrosine phosphorylation is a key molecular modulation for many signal transduction events. Because of their low abundance and dynamic nature in cells, the detection and enrichment of phosphotyrosine proteins has long relied on specific antibodies, such as 4G10 and P-Tyr-100. Another well-established approach for phosphotyrosine proteins recognition and enrichment is by their specific binding domains, such as Src homology 2 (SH2) domains. In this chapter, we describe a typical analytical approach for purifying specific SH2 domains, enriching specific phosphotyrosine proteins from activated cells, mass spectrometry analysis, and related data analysis...
2017: Methods in Molecular Biology
https://www.readbyqxmd.com/read/28092035/functionally-altered-sh2-domains-for-biochemical-studies-loss-of-function-mutant-and-domain-concatenation
#9
Mari Ogiue-Ikeda, Kazuya Machida
Recombinant modular protein domains have been a convenient proteomics tool for deciphering protein-protein interactions and elucidating the role of protein modifications in cell signaling. To obtain reliable experimental data, these protein domain probes require sufficient specificity and sensitivity. Since naturally evolved protein domains do not always have optimal biochemical characteristics for in vitro assays, functional alterations such as improved affinity are sometimes needed. In this chapter, we describe preparation of loss-of-function and concatenated (tandem) SH2 domains that should be widely applicable to both high- and low-throughput phosphoproteomics studies...
2017: Methods in Molecular Biology
https://www.readbyqxmd.com/read/28092031/expression-and-production-of-sh2-domain-proteins
#10
Bernard A Liu, Mari Ogiue-Ikeda, Kazuya Machida
The Src Homology 2 (SH2) domain lies at the heart of phosphotyrosine signaling, coordinating signaling events downstream of receptor tyrosine kinases (RTKs), adaptors, and scaffolds. Over a hundred SH2 domains are present in mammals, each having a unique specificity which determines its interactions with multiple binding partners. One of the essential tools necessary for studying and determining the role of SH2 domains in phosphotyrosine signaling is a set of soluble recombinant SH2 proteins. Here we describe methods, based on a broad experience with purification of all SH2 domains, for the production of SH2 domain proteins needed for proteomic and biochemical-based studies such as peptide arrays, mass-spectrometry, protein microarrays, reverse-phase microarrays, and high-throughput fluorescence polarization (HTP-FP)...
2017: Methods in Molecular Biology
https://www.readbyqxmd.com/read/28092030/proteomic-clustering-analysis-of-sh2-domain-datasets
#11
Karl Jablonowski
Proteomic clustering analysis provides a means of identifying relationships and visualizing those relationships in an extremely complex field of study with many interacting parts. With recent high-throughput studies of Src Homology 2 (SH2) domains, many and varied datasets are being amassed. A strategy for analyzing patterns between these large datasets is required to transform the information into knowledge. The methods for creating neighbor-joining phylogenetic trees, pairs scatter plots, and two-dimensional hierarchical clustering heatmaps are just a few of the diverse methods available to a proteomic researcher...
2017: Methods in Molecular Biology
https://www.readbyqxmd.com/read/28092029/an-efficient-semi-supervised-learning-approach-to-predict-sh2-domain-mediated-interactions
#12
Kousik Kundu, Rolf Backofen
Src homology 2 (SH2) domain is an important subclass of modular protein domains that plays an indispensable role in several biological processes in eukaryotes. SH2 domains specifically bind to the phosphotyrosine residue of their binding peptides to facilitate various molecular functions. For determining the subtle binding specificities of SH2 domains, it is very important to understand the intriguing mechanisms by which these domains recognize their target peptides in a complex cellular environment. There are several attempts have been made to predict SH2-peptide interactions using high-throughput data...
2017: Methods in Molecular Biology
https://www.readbyqxmd.com/read/28092026/hidden-markov-models-for-protein-domain-homology-identification-and-analysis
#13
Karl Jablonowski
Protein domain identification and analysis are cornerstones of modern proteomics. The tools available to protein domain researchers avail a variety of approaches to understanding large protein domain families. Hidden Markov Models (HMM) form the basis for identifying and categorizing evolutionarily linked protein domains. Here I describe the use of HMM models for predicting and identifying Src Homology 2 (SH2) domains within the proteome.
2017: Methods in Molecular Biology
https://www.readbyqxmd.com/read/28092024/introduction-history-of-sh2-domains-and-their-applications
#14
Bernard A Liu, Kazuya Machida
The Src Homology 2 (SH2) domain is the prototypical protein interaction module that lies at the heart of phosphotyrosine signaling. Since its serendipitous discovery, there has been a tremendous advancement in technologies and an array of techniques available for studying SH2 domains and phosphotyrosine signaling. In this chapter, we provide a glimpse of the history of SH2 domains and describe many of the tools and techniques that have been developed along the way and discuss future directions for SH2 domain studies...
2017: Methods in Molecular Biology
https://www.readbyqxmd.com/read/28091899/proteomic-study-of-blood-serum-in-coronary-atherosclerosis
#15
E M Stakhneva, I A Meshcheryakova, E A Demidov, K V Starostin, Yu I Ragino, S E Peltek, M I Voevoda
Changes in the blood serum proteins were assessed in men with coronary atherosclerosis and without coronary heart disease. Proteins were separated by 2D-electrophoresis, protein fractions were identified by their peptide fingerprint by MALDI method; fractions with more than twofold increase in protein level were determined. In blood serum of patients with coronary atherosclerosis, the content of C4 complement protein increased and ceruloplasmin level decreased, which is typical of heart failure and coronary heart disease...
January 14, 2017: Bulletin of Experimental Biology and Medicine
https://www.readbyqxmd.com/read/28091625/mplex-a-method-for-simultaneous-pathogen-inactivation-and-extraction-of-samples-for-multi-omics-profiling
#16
Kristin E Burnum-Johnson, Jennifer E Kyle, Amie J Eisfeld, Cameron P Casey, Kelly G Stratton, Juan F Gonzalez, Fabien Habyarimana, Nicholas M Negretti, Amy C Sims, Sadhana Chauhan, Larissa B Thackray, Peter J Halfmann, Kevin B Walters, Young-Mo Kim, Erika M Zink, Carrie D Nicora, Karl K Weitz, Bobbie-Jo M Webb-Robertson, Ernesto S Nakayasu, Brian Ahmer, Michael E Konkel, Vladimir Motin, Ralph S Baric, Michael S Diamond, Yoshihiro Kawaoka, Katrina M Waters, Richard D Smith, Thomas O Metz
The continued emergence and spread of infectious agents is of great concern, and systems biology approaches to infectious disease research can advance our understanding of host-pathogen relationships and facilitate the development of new therapies and vaccines. Molecular characterization of infectious samples outside of appropriate biosafety containment can take place only subsequent to pathogen inactivation. Herein, we describe a modified Folch extraction using chloroform/methanol that facilitates the molecular characterization of infectious samples by enabling simultaneous pathogen inactivation and extraction of proteins, metabolites, and lipids for subsequent mass spectrometry-based multi-omics measurements...
January 16, 2017: Analyst
https://www.readbyqxmd.com/read/28091549/urinary-proteomics-can-define-distinct-diagnostic-inflammatory-arthritis-subgroups
#17
Stefan Siebert, Duncan Porter, Caron Paterson, Rosie Hampson, Daniel Gaya, Agnieszka Latosinska, Harald Mischak, Joost Schanstra, William Mullen, Iain McInnes
Current diagnostic tests applied to inflammatory arthritis lack the necessary specificity to appropriately categorise patients. There is a need for novel approaches to classify patients with these conditions. Herein we explored whether urinary proteomic biomarkers specific for different forms of arthritis (rheumatoid arthritis (RA), psoriatic arthritis (PsA), osteoarthritis (OA)) or chronic inflammatory conditions (inflammatory bowel disease (IBD)) can be identified. Fifty subjects per group with RA, PsA, OA or IBD and 50 healthy controls were included in the study...
January 16, 2017: Scientific Reports
https://www.readbyqxmd.com/read/28091410/molecular-mechanisms-of-increased-heart-rate-in-shenxianshengmai-treated-bradycardia-rabbits
#18
Zhou-Ying Liu, Jian Huang, Na-Na Liu, Min Zheng, Tao Zhao, Bu-Chang Zhao, Yi-Min Wang, Jie-Lin Pu
BACKGROUND: The molecular mechanisms of Shenxianshengmai (SXSM), a traditional Chinese medicine, on bradycardia have been incompletely understood. The study tried to investigate the gene expression profile and proteomics of bradycardia rabbits' hearts after SXSM treatment. METHODS: Twenty-four adult rabbits were randomly assigned in four groups: sham, model, model plus SXSM treatment, and sham plus SXSM treatment groups. Heart rate was recorded in all rabbits. Then, total RNA of atria and proteins of ventricle were isolated and quantified, respectively...
2017: Chinese Medical Journal
https://www.readbyqxmd.com/read/28090302/three-dimensional-micro-computed-tomography-analysis-of-the-lung-vasculature-and-differential-adipose-proteomics-in-the-sugen-hypoxia-rat-model-of-pulmonary-arterial-hypertension
#19
Kelly J Shields, Kostas Verdelis, Michael J Passineau, Erin M Faight, Lee Zourelias, Changgong Wu, Rong Chong, Raymond L Benza
Pulmonary arterial hypertension (PAH) is a rare disease characterized by significant vascular remodeling. The obesity epidemic has produced great interest in the relationship between small visceral adipose tissue depots producing localized inflammatory conditions, which may link metabolism, innate immunity, and vascular remodeling. This study used novel micro computed tomography (microCT) three-dimensional modeling to investigate the degree of remodeling of the lung vasculature and differential proteomics to determine small visceral adipose dysfunction in rats with severe PAH...
December 2016: Pulmonary Circulation
https://www.readbyqxmd.com/read/28089894/determining-the-cleavage-site-for-the-mature-antimicrobial-peptide-of-nile-tilapia-%C3%AE-defensin-using-2d-electrophoresis-western-blot-and-mass-spectrometry-analysis
#20
Chin-I Chang, Li-Hao Chen, Yeh-Fang Hu, Chia-Che Wu, Jyh-Ming Tsai
Several proteomic techniques were used to determine the cleavage site of the mature antimicrobial peptide of Nile tilapia β-defensin. The computer-predicted Nile tilapia β-defensin ((25)ASFPWSCLSLSGVCRKVCLPTELFFGPLGCGKGSLCCVSHFL(66)) composed of 42 amino acids was chemically synthesized and prepared to produce an antibody for Western blotting. Total proteins from the skin of the Nile tilapia were separated on two-dimensional electrophoresis, and the spot of Nile tilapia β-defensin was recognized using Western blot analysis...
January 9, 2017: Fish & Shellfish Immunology
keyword
keyword
15931
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"