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translational proteomics

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https://www.readbyqxmd.com/read/28929311/tbi-rehabilomics-research-an-exemplar-of-a-biomarker-based-approach-to-precision-care-for-populations-with-disability
#1
REVIEW
Amy K Wagner
PURPOSE OF REVIEW: The purpose of this review is to summarize how "-omics" technologies can inform rehabilitation-relevant outcomes for a range of populations with neurologically related disability by including outcome metrics linked to the World Health Organization's International Classification of Functioning, Disability, and Health (WHO-ICF) domains of impairments in body function, activity limitations, and participation restrictions. RECENT FINDINGS: To date, nearly every area of medicine uses biomarkers in some capacity to aid in understanding how personal biology informs clinical care...
September 19, 2017: Current Neurology and Neuroscience Reports
https://www.readbyqxmd.com/read/28928394/rna-localization-is-a-key-determinant-of-neurite-enriched-proteome
#2
Alessandra Zappulo, David van den Bruck, Camilla Ciolli Mattioli, Vedran Franke, Koshi Imami, Erik McShane, Mireia Moreno-Estelles, Lorenzo Calviello, Andrei Filipchyk, Esteban Peguero-Sanchez, Thomas Müller, Andrew Woehler, Carmen Birchmeier, Enrique Merino, Nikolaus Rajewsky, Uwe Ohler, Esteban O Mazzoni, Matthias Selbach, Altuna Akalin, Marina Chekulaeva
Protein subcellular localization is fundamental to the establishment of the body axis, cell migration, synaptic plasticity, and a vast range of other biological processes. Protein localization occurs through three mechanisms: protein transport, mRNA localization, and local translation. However, the relative contribution of each process to neuronal polarity remains unknown. Using neurons differentiated from mouse embryonic stem cells, we analyze protein and RNA expression and translation rates in isolated cell bodies and neurites genome-wide...
September 19, 2017: Nature Communications
https://www.readbyqxmd.com/read/28928079/polyglutamine-expansion-diseases-more-than-simple-repeats
#3
Alexandra Silva, Ana Viana de Almeida, Sandra Macedo-Ribeiro
Polyglutamine (polyQ) repeat-containing proteins are widespread in the human proteome but only nine of them are associated with highly incapacitating neurodegenerative disorders. The genetic expansion of the polyQ tract in disease-related proteins triggers a series of events resulting in neurodegeneration. The polyQ tract plays the leading role in the aggregation mechanism, but other elements modulate the aggregation propensity in the context of the full-length proteins, as implied by variations in the length of the polyQ tract required to trigger the onset of a given polyQ disease...
September 16, 2017: Journal of Structural Biology
https://www.readbyqxmd.com/read/28927812/bi-pssm-position-specific-scoring-matrix-based-intelligent-computational-model-for-identification-of-mycobacterial-membrane-proteins
#4
Muslim Khan, Maqsood Hayat, Sher Afzal Khan, Saeed Ahmad, Nadeem Iqbal
Mycobacterium is a pathogenic bacterium, which is a causative agent of tuberculosis (TB) and leprosy. These diseases are very crucial and become the cause of death of millions of people every year in the world. So, the characterize structure of membrane proteins of the protozoan play a vital role in the field of drug discovery because, without any knowledge about this Mycobacterium's membrane protein and their types, the scientists are unable to treat this pathogenic protozoan. So, an accurate and competitive computational model is needed to characterize this uncharacterized structure of mycobacterium...
September 16, 2017: Journal of Theoretical Biology
https://www.readbyqxmd.com/read/28925544/metaproteomics-of-marine-viral-concentrates-reveals-key-viral-populations-and-abundant-periplasmic-proteins-in-the-oligotrophic-deep-chlorophyll-maximum-of-the-south-china-sea
#5
Zhang-Xian Xie, Feng Chen, Shu-Feng Zhang, Ming-Hua Wang, Hao Zhang, Ling-Fen Kong, Min-Han Dai, Hua-Sheng Hong, Lin Lin, Da-Zhi Wang
Viral concentrates (VCs), containing bio-informative DNA and proteins, have been used to study viral diversity, viral metagenomics and virus-host interactions in natural ecosystems. Besides viruses, VCs also contain many non-cellular biological components including diverse functional proteins. Here, we used a shotgun proteomic approach to characterize the proteins of VCs collected from the oligotrophic deep chlorophyll maximum (DCM) of the South China Sea. Proteins of viruses infecting picophytoplankton, i...
September 19, 2017: Environmental Microbiology
https://www.readbyqxmd.com/read/28921609/biomarkers-for-equine-joint-injury-and-osteoarthritis
#6
REVIEW
C Wayne McIlwraith, Christopher E Kawcak, David D Frisbie, Christopher B Little, Peter D Clegg, Mandy J Peffers, Morten A Karsdal, Stina Ekman, Sheila Laverty, Richard A Slayden, Linda J Sandell, L Stefan Lohmander, Virginia B Kraus
We report the results of a symposium aimed at identifying validated biomarkers that can be used to complement clinical observations for diagnosis and prognosis of joint injury leading to equine osteoarthritis (OA). Biomarkers might also predict pre-fracture change that could lead to catastrophic bone failure in equine athletes. The workshop was attended by leading scientists in the fields of equine and human musculoskeletal biomarkers to enable cross-disciplinary exchange and improve knowledge in both. Detailed proceedings with strategic planning was written, added to, edited and referenced to develop this manuscript...
September 16, 2017: Journal of Orthopaedic Research: Official Publication of the Orthopaedic Research Society
https://www.readbyqxmd.com/read/28919899/emerging-roles-and-landscape-of-translating-mrnas-in-plants
#7
REVIEW
Gaurav Sablok, Jonathan J Powell, Kemal Kazan
Plants use a wide range of mechanisms to adapt to different environmental stresses. One of the earliest responses displayed under stress is rapid alterations in stress responsive gene expression that has been extensively analyzed through expression profiling such as microarrays and RNA-sequencing. Recently, expression profiling has been complemented with proteome analyses to establish a link between transcriptional and the corresponding translational changes. However, proteome profiling approaches have their own technical limitations...
2017: Frontiers in Plant Science
https://www.readbyqxmd.com/read/28918527/alterations-in-epididymal-proteomics-and-antioxidant-activity-of-mice-exposed-to-fluoride
#8
Zilong Sun, Sujuan Li, Yuxiang Yu, Hongyu Chen, Mohammad Mehdi Ommati, Ram Kumar Manthari, Ruiyan Niu, Jundong Wang
It is well known that high fluoride results in low fertility. Epididymis is the important place for spermatozoa maturation, which is essential for successful fertilization. In the previous studies, fluoride was reported to damage the epididymal structure of mouse and rabbit. However, the mechanism underlying sodium fluoride (NaF)-induced epididymal toxicity has not yet been well elucidated. The aim of this study is to explore the global protein alterations in epididymis of mice exposed to NaF using the iTRAQ technique...
September 16, 2017: Archives of Toxicology
https://www.readbyqxmd.com/read/28917266/urinary-biomarkers-in-prostate-cancer-detection-and-monitoring-progression
#9
REVIEW
Duojia Wu, Jie Ni, Julia Beretov, Paul Cozzi, Mark Willcox, Valerie Wasinger, Bradley Walsh, Peter Graham, Yong Li
Prostate cancer (CaP) is the most common cancer in men and the second leading cause of cancer deaths in males in Australia. Although serum prostate-specific antigen (PSA) has been the most widely used biomarker in CaP detection for decades, PSA screening has limitations such as low specificity and potential association with over-diagnosis. Current biomarkers used in the clinic are not useful for the early detection of CaP, or monitoring its progression, and have limited value in predicting response to treatment...
October 2017: Critical Reviews in Oncology/hematology
https://www.readbyqxmd.com/read/28916541/a-proteomic-atlas-of-insulin-signalling-reveals-tissue-specific-mechanisms-of-longevity-assurance
#10
Luke S Tain, Robert Sehlke, Chirag Jain, Manopriya Chokkalingam, Nagarjuna Nagaraj, Paul Essers, Mark Rassner, Sebastian Grönke, Jenny Froelich, Christoph Dieterich, Matthias Mann, Nazif Alic, Andreas Beyer, Linda Partridge
Lowered activity of the insulin/IGF signalling (IIS) network can ameliorate the effects of ageing in laboratory animals and, possibly, humans. Although transcriptome remodelling in long-lived IIS mutants has been extensively documented, the causal mechanisms contributing to extended lifespan, particularly in specific tissues, remain unclear. We have characterized the proteomes of four key insulin-sensitive tissues in a long-lived Drosophila IIS mutant and control, and detected 44% of the predicted proteome (6,085 proteins)...
September 15, 2017: Molecular Systems Biology
https://www.readbyqxmd.com/read/28914261/rsk2-is-a-new-pim2-target-with-pro-survival-functions-in-flt3-itd-positive-acute-myeloid-leukemia
#11
M-A Hospital, A Jacquel, F Mazed, E Saland, C Larrue, J Mondesir, R Birsen, A S Green, M Lambert, P Sujobert, E-F Gautier, V Salnot, M Le Gall, J Decroocq, L Poulain, N Jacque, M Fontenay, O Kosmider, C Récher, P Auberger, P Mayeux, D Bouscary, J-E Sarry, J Tamburini
Acute myeloid leukemia (AML) with the FLT3 internal tandem duplication (FLT3-ITD AML) accounts for 20-30% of AML cases. This subtype usually responds poorly to conventional therapies, and might become resistant to FLT3 tyrosine kinase inhibitors (TKIs) due to molecular bypass mechanisms. New therapeutic strategies focusing on resistance mechanisms are therefore urgently needed. Pim kinases are FLT3-ITD oncogenic targets that have been implicated in FLT3 TKI resistance. However, their precise biological function downstream of FLT3-ITD requires further investigation...
September 15, 2017: Leukemia: Official Journal of the Leukemia Society of America, Leukemia Research Fund, U.K
https://www.readbyqxmd.com/read/28912750/current-and-emerging-technologies-for-probing-molecular-signatures-of-traumatic-brain-injury
#12
REVIEW
Ari Ercole, Sandra Magnoni, Gloria Vegliante, Roberta Pastorelli, Jakub Surmacki, Sarah Elizabeth Bohndiek, Elisa R Zanier
Traumatic brain injury (TBI) is understood as an interplay between the initial injury, subsequent secondary injuries, and a complex host response all of which are highly heterogeneous. An understanding of the underlying biology suggests a number of windows where mechanistically inspired interventions could be targeted. Unfortunately, biologically plausible therapies have to-date failed to translate into clinical practice. While a number of stereotypical pathways are now understood to be involved, current clinical characterization is too crude for it to be possible to characterize the biological phenotype in a truly mechanistically meaningful way...
2017: Frontiers in Neurology
https://www.readbyqxmd.com/read/28912266/lysine-trimethylation-regulates-78-kda-glucose-regulated-protein-proteostasis-during-endoplasmic-reticulum-stress
#13
Jonas Sieber, Nicolas Wieder, Mauricio Ostrosky-Frid, Moran Dvela-Levitt, Ozan Aygün, Namrata D Udeshi, Steven A Carr, Anna Greka
The upregulation of chaperones such as the 78-kDa glucose-regulated protein (GRP78; also referred to as BiP or HSPA5) is part of the adaptive cellular response to endoplasmic reticulum (ER) stress. GRP78 is widely used as a marker of the unfolded protein response, associated with sustained ER stress. Here, we report the discovery of a proteostatic mechanism involving GRP78 trimethylation in the context of ER stress. Using mass spectrometry-based proteomics, we identified two GRP78 fractions, one homeostatic and one induced by ER stress...
September 14, 2017: Journal of Biological Chemistry
https://www.readbyqxmd.com/read/28900417/integrated-translatome-and-proteome-approach-for-accurate-portraying-of-widespread-multifunctional-aspects-of-trichoderma
#14
REVIEW
Vivek Sharma, Richa Salwan, P N Sharma, Arvind Gulati
Genome-wide studies of transcripts expression help in systematic monitoring of genes and allow targeting of candidate genes for future research. In contrast to relatively stable genomic data, the expression of genes is dynamic and regulated both at time and space level at different level in. The variation in the rate of translation is specific for each protein. Both the inherent nature of an mRNA molecule to be translated and the external environmental stimuli can affect the efficiency of the translation process...
2017: Frontiers in Microbiology
https://www.readbyqxmd.com/read/28899681/comparative-degradomics-of-porcine-and-human-wound-exudates-unravels-biomarker-candidates-for-assessment-of-wound-healing-progression-in-trauma-patients
#15
Fabio Sabino, Fabian E Egli, Simonas Savickas, Jörg Holstein, Daniela Kaspar, Mika Rollmann, Jayachandran N Kizhakkedathu, Tim Pohlemann, Hans Smola, Ulrich Auf dem Keller
Impaired cutaneous wound healing is a major complication in elderly people and patients suffering from diabetes with raising rates in industrialized countries. Heterogeneity of clinical manifestations hampers effective molecular diagnostics and decisions for appropriate therapeutic regimens. Using a customized positional quantitative proteomics workflow, we have established a time-resolved proteome and N-terminome resource from wound exudates in a clinically relevant pig wound model that we exploited as robust template to interpret a heterogeneous dataset from patients undergoing the same wound treatment...
September 9, 2017: Journal of Investigative Dermatology
https://www.readbyqxmd.com/read/28898539/plant-proteogenomics-improvements-to-the-grapevine-genome-annotation
#16
Brett Chapman, Matthew Bellgard
Grapevine is an important perennial fruit to the wine industry, and has implications for the health industry with some causative agents proven to reduce heart disease. Since the sequencing and assembly of grapevine cultivar Pinot Noir, several studies have contributed to its genome annotation. This new study further contributes towards genome annotation efforts by conducting a proteogenomics analysis using the latest genome annotation from CRIBI, legacy proteomics dataset from cultivar Cabernet Sauvignon and a large RNA-seq dataset...
September 12, 2017: Proteomics
https://www.readbyqxmd.com/read/28895440/unravelling-the-biology-of-chromatin-in-health-and-cancer-using-proteomic-approaches
#17
Cassandra G Eubanks, Gerald Dayebgadoh, Xingyu Liu, Michael P Washburn
Chromatin remodeling complexes play important roles in the control of genome regulation in both normal and diseased states, and are therefore critical components for the regulation of epigenetic states in cells. Given the role epigenetics plays in cancer, for example, chromatin remodeling complexes are routinely targeted for therapeutic intervention. Areas covered: Protein mass spectrometry and proteomics are powerful technologies used to study and understand chromatin remodeling. While impressive progress has been made in this area, there remain significant challenges in the application of proteomic technologies to the study of chromatin remodeling...
September 12, 2017: Expert Review of Proteomics
https://www.readbyqxmd.com/read/28893460/stress-activated-chaperones-a-first-line-of-defense
#18
REVIEW
Wilhelm Voth, Ursula Jakob
Proteins are constantly challenged by environmental stress conditions that threaten their structure and function. Especially problematic are oxidative, acid, and severe heat stress which induce very rapid and widespread protein unfolding and generate conditions that make canonical chaperones and/or transcriptional responses inadequate to protect the proteome. We review here recent advances in identifying and characterizing stress-activated chaperones which are inactive under non-stress conditions but become potent chaperones under specific protein-unfolding stress conditions...
September 8, 2017: Trends in Biochemical Sciences
https://www.readbyqxmd.com/read/28890846/prediction-of-endoplasmic-reticulum-resident-proteins-using-fragmented-amino-acid-composition-and-support-vector-machine
#19
Ravindra Kumar, Bandana Kumari, Manish Kumar
BACKGROUND: The endoplasmic reticulum plays an important role in many cellular processes, which includes protein synthesis, folding and post-translational processing of newly synthesized proteins. It is also the site for quality control of misfolded proteins and entry point of extracellular proteins to the secretory pathway. Hence at any given point of time, endoplasmic reticulum contains two different cohorts of proteins, (i) proteins involved in endoplasmic reticulum-specific function, which reside in the lumen of the endoplasmic reticulum, called as endoplasmic reticulum resident proteins and (ii) proteins which are in process of moving to the extracellular space...
2017: PeerJ
https://www.readbyqxmd.com/read/28889911/fpd-a-comprehensive-phosphorylation-database-in-fungi
#20
Youhuang Bai, Bin Chen, Mingzhu Li, Yincong Zhou, Silin Ren, Qin Xu, Ming Chen, Shihua Wang
Protein phosphorylation, one of the most classic post-translational modification, plays a critical role in diverse cellular processes including cell cycle, growth, and signal transduction pathways. However, the available information about phosphorylation in fungi is limited. Here, we provided a Fungi Phosphorylation Database (FPD) that comprises high-confidence in vivo phosphosites identified by MS-based proteomics in various fungal species. This comprehensive phosphorylation database contains 62 272 non-redundant phosphorylation sites in 11 222 proteins across eight organisms, including Aspergillus flavus, Aspergillus nidulans, Fusarium graminearum, Magnaporthe oryzae, Neurospora crassa, Saccharomyces cerevisiae, Schizosaccharomyces pombe, and Cryptococcus neoformans...
October 2017: Fungal Biology
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