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https://www.readbyqxmd.com/read/28527408/subcellular-localization-based-comparative-study-on-radioresistant-bacteria-a-novel-approach-to-mine-proteins-involve-in-radioresistance
#1
Divya Vishambra, Malay Srivastava, Kamal Dev, Varun Jaiswal
Radioresistant bacteria (RRB) are among the most radioresistant organisms and has a unique role in evolution. Along with the evolutionary role, radioresistant organisms play important role in paper industries, bioremediation, vaccine development and possibility in anti-aging and anti-cancer treatment. The study of radiation resistance in RRB was mainly focused on cytosolic mechanisms such as DNA repair mechanism, cell cleansing activity and high antioxidant activity. Although it was known that protein localized on outer areas of cell play role in resistance towards extreme condition but the mechanisms/proteins localized on the outer area of cells are not studied for radioresistance...
May 10, 2017: Computational Biology and Chemistry
https://www.readbyqxmd.com/read/28526880/prognostic-relevance-of-uch-l1-and-%C3%AE-internexin-in-pancreatic-neuroendocrine-tumors
#2
Yu-Li Song, Run Yu, Xin-Wei Qiao, Chun-Mei Bai, Chong-Mei Lu, Yu Xiao, Ding-Rong Zhong, Jie Chen, Yu-Pei Zhao, Tai-Ping Zhang, Tian-Tian Song, He-Li Gao, Ying-Hua Wan, Lin Shen, Jie Chen, Bin Lv, Jian-Jiang Hao, Ye Zhang, Laura Tang, Yuan-Jia Chen
Prognostic biomarkers for the pancreatic neuroendocrine tumors are needed. Proteomic study on insulinoma has been rarely reported. We identified the differential expression of proteins between insulinoma and their paired tissues by proteomic analysis, and evaluated the prognostic significance of specific proteins in pancreatic neuroendocrine tumors including insulinoma. The differential expression of select proteins was validated in more than 300 tumors using immunohistochemical staining and western blot. Methylation of UCH-L1 promoter in tumors was examined by methylation specific PCR and validated by sequencing...
May 19, 2017: Scientific Reports
https://www.readbyqxmd.com/read/28526873/role-of-s-palmitoylation-by-zdhhc13-in-mitochondrial-function-and-metabolism-in-liver
#3
Li-Fen Shen, Yi-Ju Chen, Kai-Ming Liu, Amir N Saleem Haddad, I-Wen Song, Hsiao-Yuh Roan, Li-Ying Chen, Jeffrey J Y Yen, Yu-Ju Chen, Jer-Yuarn Wu, Yuan-Tsong Chen
Palmitoyltransferase (PAT) catalyses protein S-palmitoylation which adds 16-carbon palmitate to specific cysteines and contributes to various biological functions. We previously reported that in mice, deficiency of Zdhhc13, a member of the PAT family, causes severe phenotypes including amyloidosis, alopecia, and osteoporosis. Here, we show that Zdhhc13 deficiency results in abnormal liver function, lipid abnormalities, and hypermetabolism. To elucidate the molecular mechanisms underlying these disease phenotypes, we applied a site-specific quantitative approach integrating an alkylating resin-assisted capture and mass spectrometry-based label-free strategy for studying the liver S-palmitoylome...
May 19, 2017: Scientific Reports
https://www.readbyqxmd.com/read/28526811/proteomic-analysis-of-cerebrospinal-fluid-from-children-with-central-nervous-system-tumors-identifies-candidate-proteins-relating-to-tumor-metastatic-spread
#4
Filippo Spreafico, Italia Bongarzone, Sara Pizzamiglio, Ruben Magni, Elena Taverna, Maida De Bortoli, Chiara M Ciniselli, Elena Barzanò, Veronica Biassoni, Alessandra Luchini, Lance A Liotta, Weidong Zhou, Michele Signore, Paolo Verderio, Maura Massimino
Central nervous system (CNS) tumors are the most common solid tumors in childhood. Since the sensitivity of combined cerebrospinal fluid (CSF) cytology and radiological neuroimaging in detecting meningeal metastases remains relatively low, we sought to characterize the CSF proteome of patients with CSF tumors to identify biomarkers predictive of metastatic spread. CSF samples from 27 children with brain tumors and 13 controls (extra-CNS non-Hodgkin lymphoma) were processed using core-shell hydrogel nanoparticles, and analyzed with reverse-phase liquid chromatography/electrospray tandem mass spectrometry (LC-MS/MS)...
May 3, 2017: Oncotarget
https://www.readbyqxmd.com/read/28526562/new-intracellular-activities-of-matrix-metalloproteinases-shine-in-the-moonlight
#5
REVIEW
Parker G Jobin, Georgina S Butler, ChristopherM Overall
Adaption of a single protein to perform multiple independent functions facilitates functional plasticity of the proteome allowing a limited number of protein-coding genes to perform a multitude of cellular processes. Multifunctionality is achievable by post-translational modifications and by modulating subcellular localization. Matrix metalloproteinases (MMPs), classically viewed as degraders of the extracellular matrix (ECM) responsible for matrix protein turnover, are more recently recognized as regulators of a range of extracellular bioactive molecules including chemokines, cytokines, and their binders...
May 16, 2017: Biochimica et Biophysica Acta
https://www.readbyqxmd.com/read/28526530/insights-into-the-early-stage-of-pinus-nigra-arn-somatic-embryogenesis-using-discovery-proteomics
#6
Katarína Klubicová, Lubica Uvácková, Maksym Danchenko, Peter Nemecek, Ludovít Skultéty, Ján Salaj, Terézia Salaj
The somatic embryogenesis in conifers represents a suitable model of plant regeneration system facilitating studies of fundamental aspects of an early development as well as in vitro micropropagation. The aim of our study was to deeper understand the somatic embryogenesis in the conifer tree Pinus nigra Arn. Comparative proteomic analysis based on 2D-PAGE in 1) proliferating embryogenic tissues (E) initiated from immature zygotic embryos, 2) non-embryogenic calli (NEC) initiated from cotyledons of somatic seedlings of the same genotypes, 3) embryogenic tissues that lost the maturation capacity (E-L) of two cell lines (E362, E366)...
May 16, 2017: Journal of Proteomics
https://www.readbyqxmd.com/read/28526399/evaluation-of-the-effectiveness-of-chronic-antidepressant-drug-treatments-in-the-hippocampal-mitochondria-a-proteomic-study-in-an-animal-model-of-depression
#7
Katarzyna Głombik, Aneta Stachowicz, Ewa Trojan, Rafał Olszanecki, Joanna Ślusarczyk, Maciej Suski, Katarzyna Chamera, Bogusława Budziszewska, Władysław Lasoń, Agnieszka Basta-Kaim
Several lines of evidence indicate that adverse experience in early life may be a triggering factor for disturbances in the brain mitochondrial proteins and lead to the development of depression in adulthood. On the other hand, little is known about the impact of chronic administration of various antidepressant drugs on the brain mitochondria, as a target for the pharmacotherapy of depression. The purpose of our study was to compare the impact of chronic treatment with two antidepressant drugs with different mechanisms of action, a tricyclic antidepressant (TCA), imipramine, and an antidepressant of the selective serotonin reuptake inhibitor (SSRI) class, fluoxetine, on the mitochondria-enriched subproteome profile in the hippocampus of 3-month-old male rats following a prenatal stress procedure (an animal model of depression)...
May 16, 2017: Progress in Neuro-psychopharmacology & Biological Psychiatry
https://www.readbyqxmd.com/read/28525970/the-immunoregulatory-role-of-alpha-enolase-in-dendritic-cell-function-during-chlamydia-infection
#8
Khamia Ryans, Yusuf Omosun, Danielle N McKeithen, Tankya Simoneaux, Camilla C Mills, Nathan Bowen, Francis O Eko, Carolyn M Black, Joseph U Igietseme, Qing He
BACKGROUND: We have previously reported that interleukin-10 (IL-10) deficient dendritic cells (DCs) are potent antigen presenting cells that induced elevated protective immunity against Chlamydia. To further investigate the molecular and biochemical mechanism underlying the superior immunostimulatory property of IL-10 deficient DCs we performed proteomic analysis on protein profiles from Chlamydia-pulsed wild-type (WT) and IL-10(-/-) DCs to identify differentially expressed proteins with immunomodulatory properties...
May 19, 2017: BMC Immunology
https://www.readbyqxmd.com/read/28525765/covalent-probe-finds-carboxylic-acid
#9
Alexander Jones, Xiaoyun Zhang, Xiaoguang Lei
In this issue of Cell Chemical Biology, Martín-Gago et al. (2017a) disclose a new strategy for the selective covalent targeting of binding site carboxylic acids within the proteome using the isoxazolium salt as a warhead. This discovery paves the way for developing new protein ligation methods as well as covalent drug candidates.
May 18, 2017: Cell Chemical Biology
https://www.readbyqxmd.com/read/28525741/in%C3%A2-vivo-ubiquitin-linkage-type-analysis-reveals-that-the-cdc48-rad23-dsk2-axis-contributes-to-k48-linked-chain-specificity-of-the-proteasome
#10
Hikaru Tsuchiya, Fumiaki Ohtake, Naoko Arai, Ai Kaiho, Sayaka Yasuda, Keiji Tanaka, Yasushi Saeki
Ubiquitin-binding domain (UBD) proteins regulate numerous cellular processes, but their specificities toward ubiquitin chain types in cells remain obscure. Here, we perform a quantitative proteomic analysis of ubiquitin linkage-type selectivity of 14 UBD proteins and the proteasome in yeast. We find that K48-linked chains are directed to proteasomal degradation through selectivity of the Cdc48 cofactor Npl4. Mutating Cdc48 results in decreased selectivity, and lacking Rad23/Dsk2 abolishes interactions between ubiquitylated substrates and the proteasome...
May 18, 2017: Molecular Cell
https://www.readbyqxmd.com/read/28525648/the-role-of-omics-in-the-application-of-adverse-outcome-pathways-for-chemical-risk-assessment
#11
Erica K Brockmeier, Geoff Hodges, Thomas H Hutchinson, Emma Butler, Markus Hecker, Knut Erik Tollefsen, Natalia Garcia-Reyero, Peter Kille, Dörthe Becker, Kevin Chipman, John Colbourne, Timothy W Collette, Andrew Cossins, Mark Cronin, Peter Graystock, Steve Gutsell, Dries Knapen, Ioanna Katsiadaki, Anke Lange, Stuart Marshall, Stewart F Owen, Edward J Perkins, Stewart Plaistow, Anthony Schroeder, Daisy Taylor, Mark Viant, Gerald Ankley, Francesco Falciani
In conjunction with the second International Environmental Omics Symposium (iEOS) conference, held at the University of Liverpool (UK) in September 2014, a workshop was held to bring together experts in toxicology and regulatory science from academia, government and industry. The purpose of the workshop was to review the specific roles that high-content omics datasets (e.g., transcriptomics, metabolomics, lipidomics, and proteomics) can hold within the adverse outcome pathway (AOP) framework for supporting ecological and human health risk assessments...
May 19, 2017: Toxicological Sciences: An Official Journal of the Society of Toxicology
https://www.readbyqxmd.com/read/28525563/omics-biomarkers-in-ophthalmology
#12
Susette Lauwen, Eiko K de Jong, Dirk J Lefeber, Anneke I den Hollander
"Omics" refers to high-throughput analyses of genes, proteins, or metabolites in a biological system, and is increasingly used for ophthalmic research. These system-based approaches can unravel disease-related processes and are valuable for biomarker discovery. Furthermore, potential therapeutic targets can be identified based on omics results, and targeted follow-up experiments can be designed to gain molecular understanding of the disease and to test new therapies. Here, we review the application of omics techniques in eye diseases, focusing on age-related macular degeneration (AMD), diabetic retinopathy (DR), retinal detachment (RD), myopia, glaucoma, Fuchs' corneal dystrophy (FCD), cataract, keratoconus, and dry eyes...
May 1, 2017: Investigative Ophthalmology & Visual Science
https://www.readbyqxmd.com/read/28525284/intrinsically-disordered-proteins-as-important-players-during-desiccation-stress-of-the-soybean-radicles
#13
Yun Liu, Jiahui Wu, Nan Sun, Chengjian Tu, Xiaoying Shi, Hua Cheng, Simu Liu, Shuiming Li, Yong Wang, Yizhi Zheng, Vladimir N Uversky
Intrinsically disordered proteins (IDPs) play a variety of important physiological roles in all living organisms. However, there is no comprehensive analysis of the abundance of IDPs associated with environmental stress in plants. Here, we show that a set of heat-stable proteins (i.e., proteins that do not denature after boiling at 100°C for 10 min) was present in R0mm and R15mm radicles (i.e., before the radicle emergence and the 15 mm long radicles) of soybean (Glycine max) seeds. This set of 795 iTRAQ-quantified heat-stable proteins contained a high proportion of wholly or highly disordered proteins (15%), which was significantly higher than that estimated for the whole soybean proteome containing 55,787 proteins (9%)...
May 19, 2017: Journal of Proteome Research
https://www.readbyqxmd.com/read/28524877/optimized-fragmentation-schemes-and-data-analysis-strategies-for-proteome-wide-cross-link-identification
#14
Fan Liu, Philip Lössl, Richard Scheltema, Rosa Viner, Albert J R Heck
We describe optimized fragmentation schemes and data analysis strategies substantially enhancing the depth and accuracy in identifying protein cross-links using non-restricted whole proteome databases. These include a novel hybrid data acquisition strategy to sequence cross-links at both MS2 and MS3 level and a new algorithmic design XlinkX v2.0 for data analysis. As proof-of-concept we investigated proteome-wide protein interactions in E. coli and HeLa cell lysates, respectively, identifying 1,158 and 3,301 unique cross-links at ∼1% false discovery rate...
May 19, 2017: Nature Communications
https://www.readbyqxmd.com/read/28524784/how-do-we-improve-treatments-for-patients-with-amyloidosis-using-proteomics
#15
Francesca Lavatelli, Giampaolo Merlini
No abstract text is available yet for this article.
May 19, 2017: Expert Review of Proteomics
https://www.readbyqxmd.com/read/28524762/exosomes-promote-restoration-after-an-experimental-animal-model-of-intracerebral-hemorrhage
#16
Laura Otero-Ortega, Mari Carmen Gómez de Frutos, Fernando Laso-García, Berta Rodríguez-Frutos, Esperanza Medina-Gutiérrez, Juan Antonio López, Jesús Vázquez, Exuperio Díez-Tejedor, María Gutiérrez-Fernández
Exosomes are gaining importance because they show great promise in therapeutic applications for several diseases. Particularly in stroke, exosomes derived from mesenchymal stem cell (MSC) therapy work as paracrine effectors responsible for promoting neurovascular remodeling and functional recovery. Adult male rats were subjected to intracerebral hemorrhage (ICH) by intrastriatal injection of collagenase type IV; 24 h after surgery, MSC-derived exosomes were administered through the tail vein. The rats were euthanized at 7 or 28 days after treatment...
January 1, 2017: Journal of Cerebral Blood Flow and Metabolism
https://www.readbyqxmd.com/read/28524624/pulmonary-arterial-hypertension-progress-in-understanding-the-disease-and-prioritizing-strategies-for-drug-development
#17
REVIEW
P Ghataorhe, C J Rhodes, L Harbaum, M Attard, J Wharton, M R Wilkins
Pulmonary arterial hypertension (PAH), at one time a largely overlooked disease, is now the subject of intense study in many academic and biotech groups. The availability of new treatments has increased awareness of the condition. This in turn has driven a change in the demographics of PAH, with an increase in the mean age at diagnosis. The diagnosis of PAH in more elderly patients has highlighted the need for careful phenotyping of patients and for further studies to understand how best to manage pulmonary hypertension associated with, for example, left heart disease...
May 19, 2017: Journal of Internal Medicine
https://www.readbyqxmd.com/read/28524240/potential-serum-biomarkers-associated-with-mild-and-severe-leptospirosis-infection-a-cohort-study-in-the-malaysian-population
#18
Tan Xue Ting, Fairuz Binti Amran, Ravindran Thayan, Norazah Ahmad, Roslinda Jaafar, Rahimah Haron, Rafidah Abdullah, Sazwan Reezal Bin Shamsuddin, Nor Suhaila Binti Md Riffin, Puteri Shafinaz Abdul-Rahman
Leptospirosis is an emerging zoonotic infectious disease in Malaysia. The symptoms of leptospirosis vary from mild non-specific flu-like illness to a severe condition which is usually associated with serious complication and fatality. To study the protein expression profile of mild and severe leptospirosis, fifteen paired sera were collected from the patients who were mildly infected and following that progressed to severe stage. The proteome profiles of mild and severe cases were studied using 2DE analysis in combination with LC-MS/MS...
May 19, 2017: Electrophoresis
https://www.readbyqxmd.com/read/28524200/isolation-of-a-novel-bioactive-protein-from-an-edible-mushroom-pleurotus-eryngii-and-its-anti-inflammatory-potential
#19
Biao Yuan, Liyan Zhao, Kanyasiri Rakariyatham, Yanhui Han, Zili Gao, Benard Muinde Kimatu, Qiuhui Hu, Hang Xiao
Edible mushrooms are rich sources of bioactive components. In this study, a bioactive protein, PEP, was isolated from an edible mushroom, Pleurotus eryngii, through (NH4)2SO4 precipitation and ion-exchange chromatography. Proteomic analysis by matrix assisted laser desorption ionization-time of flight mass spectrometry showed that PEP was a novel protein with a molecular weight of 40 kDa. PEP exhibited anti-inflammatory effects in LPS-stimulated RAW 264.7 macrophages by inhibiting the overproduction of pro-inflammatory mediators including nitric oxide (NO), cytokine IL-1β and IL-6...
May 19, 2017: Food & Function
https://www.readbyqxmd.com/read/28524115/label-free-quantitative-proteomic-analysis-of-chitosan-oligosaccharide-treated-rice-infected-with-southern-rice-black-streaked-dwarf-virus
#20
Anming Yang, Lu Yu, Zhuo Chen, Shanxue Zhang, Jing Shi, Xiaozhen Zhao, Yuanyou Yang, Deyu Hu, Baoan Song
Southern rice black-streaked dwarf virus (SRBSDV) has spread from thesouth of China to the north of Vietnam in the past few years and severelyinfluenced rice production. Its long incubation period and early symptoms are not evident; thus, controlling it is difficult. Chitosan oligosaccharide (COS) is a green plant immunomodulator. Early studies showed that preventing and controlling SRBSDV have a certain effect and reduce disease infection rate, but its underlying controlling and preventing mechanism is unclear...
May 18, 2017: Viruses
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