keyword
MENU ▼
Read by QxMD icon Read
search

translational proteomics

keyword
https://www.readbyqxmd.com/read/28336726/proteomic-signature-of-acute-liver-failure-from-discovery-and-verification-in-a-pig-model-to-confirmation-in-humans
#1
Jie Wang, Zeyu Sun, Jing Jiang, Daxian Wu, Xiaoli Liu, Zhongyang Xie, Ermei Chen, Danhua Zhu, Chao Ye, Xiaoqian Zhang, Wenqian Chen, Hongcui Cao, Lanjuan Li
Acute liver failure (ALF) is a fatal condition hallmarked by rapid development. The present study aimed to describe the dynamic alterations of serum proteins associated with ALF development, and to seek for novel biomarkers of ALF. Miniature pigs (n=30) were employed to establish ALF models by infusing D-galactosamine (GALN, 1.3g/kg). A total of 1589 serum proteins were compared in pooled serum samples (n=10) before and 36 hours after GALN administration through label-free quantitation (LFQ) based shotgun proteomics...
March 23, 2017: Molecular & Cellular Proteomics: MCP
https://www.readbyqxmd.com/read/28336331/are-neutral-loss-and-internal-product-ions-useful-for-top-down-protein-identification
#2
Kaijie Xiao, Fan Yu, Houqin Fang, Bingbing Xue, Yan Liu, Yunhui Li, Zhixin Tian
Neutral loss and internal product ions have been found to be significant in both peptide and protein tandem mass spectra and they have been proposed to be included in database search and for protein identification. In addition to common canonical b/y ions in collision-based dissociation or c/z ions in electron-based dissociation, inclusion of neutral loss and internal product ions would certainly make better use of tandem mass spectra data; however, their ultimate utility for protein identification with false discovery rate control remains unclear...
March 20, 2017: Journal of Proteomics
https://www.readbyqxmd.com/read/28336093/concurrent-methylation-and-demethylation-of-arsenic-by-fungi-and-their-differential-expression-in-the-protoplasm-proteome
#3
Shiming Su, Xibai Zeng, Lingyu Bai, Yanan Wang, Lili Zhang, Mansheng Li, Cuixia Wu
Microbial methylation and demethylation are central to arsenic's (As) biogeochemical cycling. Here, the transformations of monomethylarsonic acid (MMA(V)) (50 mg L(-1)) for 15 days in cells of As-methylating fungi, Fusarium oxysporum CZ-8F1, Penicillium janthinellum SM-12F4, and Trichoderma asperellum SM-12F1, were evaluated, and trace concentrations of As(III) and As(V) were observed in fungal cell extracts. Trace amounts of DMA(V) were also detected in MMA(V) and P. janthinellum SM-12F4 incubations. In situ X-ray absorption near edge structure (XANES) indicated that after exposure to MMA(V) (500 mg L(-1)) for 15 days, 28...
March 21, 2017: Environmental Pollution
https://www.readbyqxmd.com/read/28334050/improving-transcriptome-de-novo-assembly-by-using-a-reference-genome-of-a-related-species-translational-genomics-from-oil-palm-to-coconut
#4
Alix Armero, Luc Baudouin, Stéphanie Bocs, Dominique This
The palms are a family of tropical origin and one of the main constituents of the ecosystems of these regions around the world. The two main species of palm represent different challenges: coconut (Cocos nucifera L.) is a source of multiple goods and services in tropical communities, while oil palm (Elaeis guineensis Jacq) is the main protagonist of the oil market. In this study, we present a workflow that exploits the comparative genomics between a target species (coconut) and a reference species (oil palm) to improve the transcriptomic data, providing a proteome useful to answer functional or evolutionary questions...
2017: PloS One
https://www.readbyqxmd.com/read/28333336/comparative-sperm-proteomics-in-mouse-species-with-divergent-mating-systems
#5
Alberto Vicens, Kirill Borziak, Timothy L Karr, Eduardo R S Roldan, Steve Dorus
Sexual selection is the pervasive force underlying the dramatic divergence of sperm form and function. Although it has been demonstrated that testis gene expression evolves rapidly, exploration of the proteomic basis of sperm diversity is in its infancy. We have employed a whole-cell proteomics approach to characterize sperm divergence among closely related Mus species that experience different sperm competition regimes and exhibit pronounced variation in sperm energetics, motility and fertilization capacity...
February 25, 2017: Molecular Biology and Evolution
https://www.readbyqxmd.com/read/28330337/co-generating-synthetic-parts-toward-a-self-replicating-system
#6
Jun Li, Wilhelm Haas, Kirsten Jackson, Erkin Kuru, Michael C Jewett, Z Hugh Fan, Steven P Gygi, George M Church
To build replicating systems with new functions, the engineering of existing biological machineries requires a sensible strategy. Protein synthesis Using Recombinant Elements (PURE) system consists of the desired components for transcription, translation, aminoacylation and energy regeneration. PURE, might be the basis for a radically alterable, lifelike system after optimization. Here, we regenerated 54 E. coli ribosomal (r-) proteins individually from DNA templates in the PURE system. We show that using stable isotope labeling with amino acids, mass spectrometry based quantitative proteomics could detect 26 of the 33 50S and 20 of the 21 30S subunit r-proteins when co-expressed in batch format PURE system...
March 23, 2017: ACS Synthetic Biology
https://www.readbyqxmd.com/read/28330297/differential-expression-and-characterization-of-cypermethrin-degrading-potential-proteins-in-bacillus-thuringiensis-strain-sg4
#7
Pankaj, Geeta Negi, Saurabh Gangola, Priyanka Khati, Govind Kumar, Anjana Srivastava, Anita Sharma
A cypermethrin-degrading bacterium (SG4) was isolated from the pesticide-contaminated soil in the agricultural field of the crop research centre of the University, and characterized as Bacillus thuringiensis strain, SG4. The bacterium degraded 78.9 % of cypermethrin (50 ppm) in 15 days when grown in a minimal medium. To understand the functional proteins of cypermethrin degradation in Bacillus thuringiensis strain SG4, a comparative proteomic analysis was performed in the presence/absence of cypermethrin after 5 days of incubation in minimal medium...
December 2016: 3 Biotech
https://www.readbyqxmd.com/read/28329008/insulin-and-diet-induced-changes-in-the-ubiquitin-modified-proteome-of-rat-liver
#8
Shilpa R Nagarajan, Amanda E Brandon, Jessie A McKenna, Harrison C Shtein, Thinh Q Nguyen, Eurwin Suryana, Philip Poronnik, Gregory J Cooney, Darren N Saunders, Andrew J Hoy
Ubiquitin is a crucial post-translational modification regulating numerous cellular processes, but its role in metabolic disease is not well characterized. In this study, we identified the in vivo ubiquitin-modified proteome in rat liver and determined changes in this ubiquitome under acute insulin stimulation and high-fat and sucrose diet-induced insulin resistance. We identified 1267 ubiquitinated proteins in rat liver across diet and insulin-stimulated conditions, with 882 proteins common to all conditions...
2017: PloS One
https://www.readbyqxmd.com/read/28328971/mapping-the-n-linked-glycosites-of-rice-oryza-sativa-l-germinating-embryos
#9
Jiezheng Ying, Juan Zhao, Yuxuan Hou, Yifeng Wang, Jiehua Qiu, Zhiyong Li, Xiaohong Tong, Zhaomei Shi, Jun Zhu, Jian Zhang
Germination is a key event in the angiosperm life cycle. N-glycosylation of proteins is one of the most common post-translational modifications, and has been recognized to be an important regulator of the proteome of the germinating embryo. Here, we report the first N-linked glycosites mapping of rice embryos during germination by using a hydrophilic interaction chromatography (HILIC) glycopeptides enrichment strategy associated with high accuracy mass spectrometry identification. A total of 242 glycosites from 191 unique proteins was discovered...
2017: PloS One
https://www.readbyqxmd.com/read/28327990/estimating-the-total-number-of-phosphoproteins-and-phosphorylation-sites-in-eukaryotic-proteomes
#10
Panayotis Vlastaridis, Pelagia Kyriakidou, Anargyros Chaliotis, Yves Van de Peer, Stephen G Oliver, Grigoris D Amoutzias
Background: Phosphorylation is the most frequent post-translational modification made to proteins and may regulate protein activity as either a molecular digital switch or a rheostat. Despite the cornucopia of high-throughput (HTP) phosphoproteomic data in the last decade, it remains unclear how many proteins are phosphorylated and how many phosphorylation sites (p-sites) can exist in total within a eukaryotic proteome. We present the first reliable estimates of the total number of phosphoproteins and phosphorylation sites (p-sites), for four eukaryotes (human, mouse, Arabidopsis, and yeast)...
January 7, 2017: GigaScience
https://www.readbyqxmd.com/read/28326097/different-proteome-profiles-between-male-and-female-populus-cathayana-exposed-to-uv-b-radiation
#11
Yunxiang Zhang, Lihua Feng, Hao Jiang, Yuanbin Zhang, Sheng Zhang
With increasing altitude, solar UV-B radiation is enhanced. Based on the phenomenon of male-biased sex ratio of Populus cathayana Rehder in high altitude alpine area, we hypothesized that males have a faster and more sophisticated responsive mechanism to high UV-B radiation than that of females. Our previous studies have shown sexually different responses to high UV-B radiation were existed in P. cathayana at the morphological, physiological, and transcriptomic levels. However, the responses at the proteomic level remain unclear...
2017: Frontiers in Plant Science
https://www.readbyqxmd.com/read/28325629/towards-integrating-extracellular-matrix-and-immunological-pathways
#12
David F Boyd, Paul G Thomas
The extracellular matrix (ECM) is a complex and dynamic structure made up of an estimated 300 different proteins. The ECM is also a rich source of cytokines and growth factors in addition to numerous bioactive ECM degradation products that influence cell migration, proliferation, and differentiation. The ECM is constantly being remodeled during homeostasis and in a wide range of pathological contexts. Changes in the ECM modulate immune responses, which in turn regulate repair and regeneration of tissues. Here, we review the many components of the ECM, enzymes involved in ECM remodeling, and the signals that feed into immunological pathways in the context of a dynamic ECM...
March 18, 2017: Cytokine
https://www.readbyqxmd.com/read/28322794/involvement-of-vimentin-in-neurite-outgrowth-damage-induced-by-fipronil-in-sh-sy5y-cells
#13
Theetat Ruangjaroon, Daranee Chokchaichamnankit, Chantragan Srisomsap, Jisnuson Svasti, N Monique Paricharttanakul
Fipronil, a phenylpyrazole insecticide, is more selective in its potency towards insects than humans and is thus commonly used. In this study, we demonstrated that exposure to fipronil may pose a human health risk. We observed in vitro the shortening of neurite outgrowths of SH-SY5Y neuroblastoma cells upon treatment with fipronil, even at a non-cytotoxic concentration. Fipronil induced apoptosis involving caspase-6, which is an apoptotic effector highly implicated in neurodegenerative diseases. Moreover, at a concentration that did not induce apoptosis, mitochondrial dysfunction and autophagic vacuole formation were detected...
March 17, 2017: Biochemical and Biophysical Research Communications
https://www.readbyqxmd.com/read/28322451/genome-wide-association-studies-with-proteomics-data-reveal-genes-important-for-synthesis-transport-and-packaging-of-globulins-in-legume-seeds
#14
Christine Le Signor, Delphine Aimé, Amandine Bordat, Maya Belghazi, Valérie Labas, Jérôme Gouzy, Nevin D Young, Jean-Marie Prosperi, Olivier Leprince, Richard D Thompson, Julia Buitink, Judith Burstin, Karine Gallardo
Improving nutritional seed quality is an important challenge in grain legume breeding. However, the genes controlling the differential accumulation of globulins, which are major contributors to seed nutritional value in legumes, remain largely unknown. We combined a search for protein quantity loci with genome-wide association studies on the abundance of 7S and 11S globulins in seeds of the model legume species Medicago truncatula. Identified genomic regions and genes carrying polymorphisms linked to globulin variations were then cross-compared with pea (Pisum sativum), leading to the identification of candidate genes for the regulation of globulin abundance in this crop...
March 21, 2017: New Phytologist
https://www.readbyqxmd.com/read/28320318/encounter-a-parsing-tool-to-uncover-the-mature-n-terminus-of-organelle-targeted-proteins-in-complex-samples
#15
Willy Vincent Bienvenut, Jean-Pierre Scarpelli, Johan Dumestier, Thierry Meinnel, Carmela Giglione
BACKGROUND: Characterization of mature protein N-termini by large scale proteomics is challenging. This is especially true for proteins undergoing cleavage of transit peptides when they are targeted to specific organelles, such as mitochondria or chloroplast. Protein neo-N-termini can be located up to 100-150 amino acids downstream from the initiator methionine and are not easily predictable. Although some bioinformatics tools are available, they usually require extensive manual validation to identify the exact N-terminal position...
March 20, 2017: BMC Bioinformatics
https://www.readbyqxmd.com/read/28315242/profiling-of-protein-n-termini-and-their-modifications-in-complex-samples
#16
Fatih Demir, Stefan Niedermaier, Jayachandran N Kizhakkedathu, Pitter F Huesgen
Protein N termini are a unique window to the functional state of the proteome, revealing translation initiation sites, co-translation truncation and modification, posttranslational maturation, and further proteolytic processing into different proteoforms with distinct functions. As a direct readout of proteolytic activity, protein N termini further reveal proteolytic regulation of diverse biological processes and provide a route to determine specific substrates and hence the physiological functions for any protease of interest...
2017: Methods in Molecular Biology
https://www.readbyqxmd.com/read/28315241/silpronaq-a-convenient-approach-for-proteome-wide-analysis-of-protein-n-termini-and-n-terminal-acetylation-quantitation
#17
Willy V Bienvenut, Carmela Giglione, Thierry Meinnel
Protein N-terminal modifications have recently been involved in overall proteostasis through their impact on cell fate and protein life time. This explains the development of new approaches to characterize more precisely the N-terminal end of mature proteins. Although few approaches are available to perform N-terminal enrichment based on positive or negative discriminations, these methods are usually restricted to the enrichment in N-terminal peptides and their characterization by mass spectrometry. Recent investigation highlights both (1) the knowledge of the N-terminal acetylation status of most cytosolic proteins and (2) post-translational addition of this modification on the N-terminus of nuclear coded chloroplast proteins imported in the plastid and after the cleavage of the transit peptide...
2017: Methods in Molecular Biology
https://www.readbyqxmd.com/read/28314116/secretory-proteome-analysis-of-streptomycin-resistant-mycobacterium-tuberculosis-clinical-isolates
#18
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/28306143/mutant-eif2b-leads-to-impaired-mitochondrial-oxidative-phosphorylation-in-vanishing-white-matter-disease
#19
Gali Raini, Reut Sharet, Melisa Herrero, Andrea Atzmon, Anjana Shenoy, Tamar Geiger, Orna Elroy-Stein
Eukaryotic translation initiation factor 2B (eIF2B) is a master regulator of protein synthesis under normal and stress conditions. Mutations in any of the five genes encoding its subunits lead to Vanishing White Matter (VWM) disease, a recessive genetic deadly illness caused by progressive loss of white matter in the brain. In the current study we used fibroblasts, which are not involved in the disease, to demonstrate the involvement of eIF2B in mitochondrial function and abundance. Mass-spectrometry of total proteome of mouse embryonic fibroblasts (MEFs) isolated from Eif2b5(R132H/R132H) mice revealed unbalanced stoichiometry of proteins involved in oxidative phosphorylation and of mitochondrial translation machinery components, among others...
March 17, 2017: Journal of Neurochemistry
https://www.readbyqxmd.com/read/28299657/runx1-eto-leukemia
#20
Shan Lin, James C Mulloy, Susumu Goyama
AML1-ETO leukemia is the most common cytogenetic subtype of acute myeloid leukemia, defined by the presence of t(8;21). Remarkable progress has been achieved in understanding the molecular pathogenesis of AML1-ETO leukemia. Proteomic surveies have shown that AML-ETO forms a stable complex with several transcription factors, including E proteins. Genome-wide transcriptome and ChIP-seq analyses have revealed the genes directly regulated by AML1-ETO, such as CEBPA. Several lines of evidence suggest that AML1-ETO suppresses endogenous DNA repair in cells to promote mutagenesis, which facilitates acquisition of cooperating secondary events...
2017: Advances in Experimental Medicine and Biology
keyword
keyword
78229
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"