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translational proteomics

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https://www.readbyqxmd.com/read/29785401/rheumatoid-arthritis-and-mirnas-a-critical-review-through-a-functional-view
#1
REVIEW
Maria Cristina Moran-Moguel, Stefania Petarra-Del Rio, Evangelina E Mayorquin-Galvan, Maria G Zavala-Cerna
Rheumatoid arthritis (RA) is a systemic autoimmune disease with severe joint inflammation and destruction associated with an inflammatory environment. The etiology behind RA remains to be elucidated; most updated concepts include the participation of environmental, proteomic, epigenetic, and genetic factors. Epigenetic is considered the missing link to explain genetic diversification among RA patients. Within epigenetic factors participating in RA, miRNAs are defined as small noncoding molecules with a length of approximately 22 nucleotides, capable of gene expression modulation, either negatively through inhibition of translation and degradation of the mRNA or positively through increasing the translation rate...
2018: Journal of Immunology Research
https://www.readbyqxmd.com/read/29783951/the-transcriptomic-and-proteomic-responses-of-daphnia-pulex-to-changes-in-temperature-and-food-supply-comprise-environment-specific-and-clone-specific-elements
#2
Dörthe Becker, Yann Reydelet, Jacqueline A Lopez, Craig Jackson, John K Colbourne, Susan Hawat, Michael Hippler, Bettina Zeis, Rüdiger J Paul
BACKGROUND: Regulatory adjustments to acute and chronic temperature changes are highly important for aquatic ectotherms because temperature affects their metabolic rate as well as the already low oxygen concentration in water, which can upset their energy balance. This also applies to severe changes in food supply. Thus, we studied on a molecular level (transcriptomics and/or proteomics) the immediate responses to heat stress and starvation and the acclimation to different temperatures in two clonal isolates of the model microcrustacean Daphnia pulex from more or less stressful environments, which showed a higher (clone M) or lower (clone G) tolerance to heat and starvation...
May 21, 2018: BMC Genomics
https://www.readbyqxmd.com/read/29782891/review-article-a-translational-view-of-cells-secretome-analysis-from-untargeted-proteomic-to-potential-circulating-biomarkers
#3
REVIEW
Sandra I Anjo, Bruno Manadas
The identification of circulating biomarkers capable of being used as routine for diagnosis, prognosis, risk stratification and therapeutic monitoring is still the major aim at clinical proteomics. However, the direct search in blood samples or other clinical relevant biofluids is frequently associated with technical limitations that makes the biomarker discovery process extremely difficult when using these types of samples. In this sense, the use of different approaches, such as the analysis of cells' secretomes, can be an important and promising complementary method for the identification and pre-selection of potential circulating biomarkers...
May 18, 2018: Biochimie
https://www.readbyqxmd.com/read/29782494/ubiquitin-dependent-proteolysis-of-cxcl7-leads-to-posterior-longitudinal-ligament-ossification
#4
Michiyo Tsuru, Atsushi Ono, Hideaki Umeyama, Masahiro Takeuchi, Kensei Nagata
Ossification of the posterior longitudinal ligament (OPLL), a spinal ligament, reduces the range of motion in limbs. No treatment is currently available for OPLL, which is why therapies are urgently needed. OPLL occurs in obesity, is more common in men, and has an onset after 40 years of age. The mechanisms underlying OPLL remain unclear. In this study, we performed a serum proteomic analysis in both OPLL patients and healthy subjects to identify factors potentially involved in the development of OPLL, and found reduced levels of a protein that might underlie the pathology of OPLL...
2018: PloS One
https://www.readbyqxmd.com/read/29781997/antimicrobial-peptides-produced-by-selective-pressure-incorporation-of-non-canonical-amino-acids
#5
Jessica H Nickling, Tobias Baumann, Franz-Josef Schmitt, Maike Bartholomae, Oscar P Kuipers, Thomas Friedrich, Nediljko Budisa
Nature has a variety of possibilities to create new protein functions by modifying the sequence of the individual amino acid building blocks. However, all variations are based on the 20 canonical amino acids (cAAs). As a way to introduce additional physicochemical properties into polypeptides, the incorporation of non-canonical amino acids (ncAAs) is increasingly used in protein engineering. Due to their relatively short length, the modification of ribosomally synthesized and post-translationally modified peptides by ncAAs is particularly attractive...
May 4, 2018: Journal of Visualized Experiments: JoVE
https://www.readbyqxmd.com/read/29777870/profiling-modifications-for-glioblastoma-proteome-using-ultra-tolerant-database-search-are-the-peptide-mass-shifts-biologically-relevant-or-chemically-induced
#6
Irina A Tarasova, Peter M Chumakov, Sergei A Moshkovskii, Mikhail V Gorshkov
Peptide mass shifts were profiled using ultra-tolerant database search strategy for shotgun proteomics data sets of human glioblastoma cell lines demonstrating strong response to the type I interferon (IFNα-2b) treatment. The main objective of this profiling was revealing the cell response to IFN treatment at the level of protein modifications. To achieve this objective, statistically significant changes in peptide mass shift profiles between IFN treated and untreated glioblastoma samples were analyzed. Detailed analysis of MS/MS spectra allowed further interpretation of the observed mass shifts and differentiation between post-translational and artifact modifications...
May 16, 2018: Journal of Proteomics
https://www.readbyqxmd.com/read/29775578/c-terminal-end-directed-protein-elimination-by-crl2-ubiquitin-ligases
#7
Hsiu-Chuan Lin, Chi-Wei Yeh, Yen-Fu Chen, Ting-Ting Lee, Pei-Yun Hsieh, Domnita V Rusnac, Sung-Ya Lin, Stephen J Elledge, Ning Zheng, Hsueh-Chi S Yen
The proteolysis-assisted protein quality control system guards the proteome from potentially detrimental aberrant proteins. How miscellaneous defective proteins are specifically eliminated and which molecular characteristics direct them for removal are fundamental questions. We reveal a mechanism, DesCEND (destruction via C-end degrons), by which CRL2 ubiquitin ligase uses interchangeable substrate receptors to recognize the unusual C termini of abnormal proteins (i.e., C-end degrons). C-end degrons are mostly less than ten residues in length and comprise a few indispensable residues along with some rather degenerate ones...
May 17, 2018: Molecular Cell
https://www.readbyqxmd.com/read/29773844/identification-of-differentially-accumulated-proteins-involved-in-regulating-independent-and-combined-osmosis-and-cadmium-stress-response-in-brachypodium-seedling-roots
#8
Ziyan Chen, Dong Zhu, Jisu Wu, Zhiwei Cheng, Xing Yan, Xiong Deng, Yueming Yan
In this study, we aimed to identify differentially accumulated proteins (DAPs) involved in PEG mock osmotic stress, cadmium (Cd2+ ) stress, and their combined stress responses in Brachypodium distachyon seedling roots. The results showed that combined PEG and Cd2+ stresses had more significant effects on Brachypodium seedling root growth, physiological traits, and ultrastructures when compared with each individual stress. Totally, 106 DAPs were identified that are responsive to individual and combined stresses in roots...
May 17, 2018: Scientific Reports
https://www.readbyqxmd.com/read/29773679/comparative-proteomic-analysis-reveals-the-regulatory-network-of-the-vea-gene-during-asexual-and-sexual-spore-development-of-aspergillus-cristatus
#9
Hui Liu, Shilei Sang, Hui Wang, Xiyi Ren, Yumei Tan, Wei Chen, Zuoyi Liu, Yongxiang Liu
Aspergillus cristatus belongs to the homothallic fungal group that undergoes a sexual stage without asexual conidiation under hypotonic conditions, while hypertonic medium induces initiation of the asexual stage and completely blocks sexual development. However, the veA deletion mutant only produces conidia in hypotonic medium after a 24 h culture, but both asexual and sexual spores are observed after 72 h. To elucidate the molecular mechanism of how VeA regulates asexual and sexual spore development in A. cristatus , two dimensional electrophoresis combined with matrix-assisted laser desorption/ionization-tandem time of flight mass spectrometry analysis were applied to identify 173 differentially expressed proteins (DEPs) by comparing the agamotype (24 h) and teleomorph (72 h) with wild-type A...
May 17, 2018: Bioscience Reports
https://www.readbyqxmd.com/read/29773508/comparative-proteomic-analyses-of-hyphozyma-roseonigra-atcc-20624-in-response-to-sclareol
#10
Xiuwen Wang, Xiaohua Zhang, Qingshou Yao, Dongliang Hua, Jiayang Qin
Sclareol is an important intermediate for ambroxide synthesis industries. Hyphozyma roseonigra ATCC 20624 was the only reported strain capable of degrading sclareol to the main product of sclareol glycol, which is the precursor of ambroxide. To date, knowledge is lacking about the effects of sclareol on cells and the proteins involved in sclareol metabolism. Comparative proteomic analyses were conducted on the strain H. roseonigra ATCC 20624 by using sclareol or glucose as the sole carbon source. A total of 79 up-regulated protein spots with a >2...
April 24, 2018: Brazilian Journal of Microbiology: [publication of the Brazilian Society for Microbiology]
https://www.readbyqxmd.com/read/29772557/high-density-lipoprotein-carbamylation-and-dysfunction-in-vascular-disease
#11
Jeans Miguel Santana, Clinton Douglas Brown
High-density lipoprotein (HDL) is cardioprotective because of its anti-atherogenic properties. Nevertheless, our goal to optimize HDL cholesterol (HDL-C) levels have had little effects on the atherothrombotic burden and suggests a closer look be taken at HDL function and dysfunction. HDL is a group of complex macromolecules composed of a lipid- and proteome that work in synergy to execute its anti-inflammatory, anti-atherogenic, and anti-thrombotic effects. However, throughout its life-span in circulation, HDL undergoes significant modification...
June 1, 2018: Frontiers in Bioscience (Landmark Edition)
https://www.readbyqxmd.com/read/29768530/ns1-codon-usage-adaptation-to-humans-in-pandemic-zika-virus
#12
Caio César de Melo Freire, Giuseppe Palmisano, Carla T Braconi, Fernanda R Cugola, Fabiele B Russo, Patricia Cb Beltrão-Braga, Atila Iamarino, Daniel Ferreira de Lima Neto, Amadou Alpha Sall, Livia Rosa-Fernandes, Martin R Larsen, Paolo Marinho de Andrade Zanotto
BACKGROUND: Zika virus (ZIKV) was recognised as a zoonotic pathogen in Africa and southeastern Asia. Human infections were infrequently reported until 2007, when the first known epidemic occurred in Micronesia. After 2013, the Asian lineage of ZIKV spread along the Pacific Islands and Americas, causing severe outbreaks with millions of human infections. The recent human infections of ZIKV were also associated with severe complications, such as an increase in cases of Guillain-Barre syndrome and the emergence of congenital Zika syndrome...
May 10, 2018: Memórias do Instituto Oswaldo Cruz
https://www.readbyqxmd.com/read/29762088/an-updated-taxonomy-and-a-graphical-summary-tool-for-optimal-classification-and-comprehension-of-omics-research
#13
Nina Pirih, Tanja Kunej
The volume of publications and the type of research approaches used in omics system sciences are vast and continue to expand rapidly. This increased complexity and heterogeneity of omics data are challenging data extraction, sensemaking, analyses, knowledge translation, and interpretation. An extended and dynamic taxonomy for the classification and summary of omics studies are essential. We present an updated taxonomy for classification of omics research studies based on four criteria: (1) type and number of genomic loci in a research study, (2) number of species and biological samples, (3) the type of omics technology (e...
May 2018: Omics: a Journal of Integrative Biology
https://www.readbyqxmd.com/read/29760587/the-role-of-adipokines-in-skeletal-muscle-inflammation-and-insulin-sensitivity
#14
REVIEW
Thomas Nicholson, Chris Church, David J Baker, Simon W Jones
Background: There is currently an unmet clinical need to develop better pharmacological treatments to improve glucose handling in Type II Diabetes patients with obesity. To this end, determining the effect of obesity-associated adipokines on skeletal muscle insulin sensitivity has emerged as an important area of drug discovery research. This review draws together the data on the functional role of adipokines on skeletal muscle insulin signalling, highlights several understudied novel adipokines and provides a perspective on the direction of future research...
2018: Journal of Inflammation
https://www.readbyqxmd.com/read/29760453/evolutionary-instability-of-cug-leu-in-the-genetic-code-of-budding-yeasts
#15
Tadeusz Krassowski, Aisling Y Coughlan, Xing-Xing Shen, Xiaofan Zhou, Jacek Kominek, Dana A Opulente, Robert Riley, Igor V Grigoriev, Nikunj Maheshwari, Denis C Shields, Cletus P Kurtzman, Chris Todd Hittinger, Antonis Rokas, Kenneth H Wolfe
The genetic code used in nuclear genes is almost universal, but here we report that it changed three times in parallel during the evolution of budding yeasts. All three changes were reassignments of the codon CUG, which is translated as serine (in 2 yeast clades), alanine (1 clade), or the 'universal' leucine (2 clades). The newly discovered Ser2 clade is in the final stages of a genetic code transition. Most species in this clade have genes for both a novel tRNASer (CAG) and an ancestral tRNALeu (CAG) to read CUG, but only tRNASer (CAG) is used in standard growth conditions...
May 14, 2018: Nature Communications
https://www.readbyqxmd.com/read/29759483/induction-of-the-immunoproteasome-subunit-lmp7-links-proteostasis-and-immunity-in-%C3%AE-synuclein-aggregation-disorders
#16
Scott Ugras, Malcolm J Daniels, Hossein Fazelinia, Neal S Gould, Anastasia K Yocum, Kelvin C Luk, Esteban Luna, Hua Ding, Chris McKennan, Steven Seeholzer, Dan Martinez, Perry Evans, Daniel Brown, John E Duda, Harry Ischiropoulos
Accumulation of aggregated α-synuclein into Lewy bodies is thought to contribute to the onset and progression of dopaminergic neuron degeneration in Parkinson's disease (PD) and related disorders. Although protein aggregation is associated with perturbation of proteostasis, how α-synuclein aggregation affects the brain proteome and signaling remains uncertain. In a mouse model of α-synuclein aggregation, 6% of 6215 proteins and 1.6% of 8183 phosphopeptides changed in abundance, indicating conservation of proteostasis and phosphorylation signaling...
May 11, 2018: EBioMedicine
https://www.readbyqxmd.com/read/29759185/a-fast-sample-processing-strategy-for-large-scale-profiling-of-human-urine-phosphoproteome-by-mass-spectrometry
#17
Xinyuan Zhao, Wanjun Zhang, Tong Liu, Hangyan Dong, Junjie Huang, Changqing Sun, Guangshun Wang, Xiaohong Qian, Weijie Qin
Liquid biopsies using body fluids have gained much attention in recent years due to their multiple advantages in clinical diagnosis, such as less/non-invasive collection, suitability for longitudinal disease monitoring, and better representation of tumor heterogeneity. As an attractive choice for liquid biopsy, urine proteins and their post-translational modifications (PTMs) have the potential to offer significant insights into physiological variations and pathological changes in the human body. However, due to the intrinsically large variability of urine proteins and their PTMs among different individuals, there is a high demand for strategies for high-throughput analysis of a large number of samples to obtain a comprehensive view and a reliable reference interval of the urine proteome...
August 1, 2018: Talanta
https://www.readbyqxmd.com/read/29758068/differentially-abundant-proteins-associated-with-heterosis-in-the-primary-roots-of-popcorn
#18
Mathias F Rockenbach, Caio C G Corrêa, Angelo S Heringer, Ismael L J Freitas, Claudete Santa-Catarina, Antônio T do Amaral-Júnior, Vanildo Silveira
Although heterosis has significantly contributed to increases in worldwide crop production, the molecular mechanisms regulating this phenomenon are still unknown. In the present study, we used a comparative proteomic approach to explore hybrid vigor via the proteome of both the popcorn L54 ♀ and P8 ♂ genotypes and the resultant UENF/UEM01 hybrid cross. To analyze the differentially abundant proteins involved in heterosis, we used the primary roots of these genotypes to analyze growth parameters and extract proteins...
2018: PloS One
https://www.readbyqxmd.com/read/29757393/snpnexus-assessing-the-functional-relevance-of-genetic-variation-to-facilitate-the-promise-of-precision-medicine
#19
Abu Z Dayem Ullah, Jorge Oscanoa, Jun Wang, Ai Nagano, Nicholas R Lemoine, Claude Chelala
Broader functional annotation of genetic variation is a valuable means for prioritising phenotypically-important variants in further disease studies and large-scale genotyping projects. We developed SNPnexus to meet this need by assessing the potential significance of known and novel SNPs on the major transcriptome, proteome, regulatory and structural variation models. Since its previous release in 2012, we have made significant improvements to the annotation categories and updated the query and data viewing systems...
May 11, 2018: Nucleic Acids Research
https://www.readbyqxmd.com/read/29756027/translatome-regulation-in-neuronal-injury-and-axon-regrowth
#20
Meir Rozenbaum, Marek Rajman, Ida Rishal, Indrek Koppel, Sandip Koley, Katalin F Medzihradszky, Juan A Oses-Prieto, Riki Kawaguchi, Paul S Amieux, Alma L Burlingame, Giovanni Coppola, Mike Fainzilber
Transcriptional events leading to outgrowth of neuronal axons have been intensively studied, but the role of translational regulation in this process is not well understood. Here, we use translatome analyses by ribosome pull-down and protein synthesis characterization by metabolic isotopic labeling to study nerve injury and axon outgrowth proteomes in rodent dorsal root ganglia (DRGs) and sensory neurons. We identify over 1600 gene products that are primarily translationally regulated in DRG neurons after nerve injury, many of which contain a 5'UTR cytosine-enriched regulator of translation (CERT) motif, implicating the translation initiation factor Eif4e in the injury response...
March 2018: ENeuro
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