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proteomics pathway analysis

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https://www.readbyqxmd.com/read/27905125/gadd45%C3%AE-is-involved-in-the-apoptosis-of-lymphocytes-induced-by-riboflavin-and-ultraviolet-light
#1
Peng Yang, Huiqin Wen, Tao Zhong, Hailiang Hu, Bangqiang Zhu, Kang Xia, Mo Xu, Maohong Bian
BACKGROUND: Riboflavin plus ultraviolet (UV) pathogen reduction technology (RF-PRT) is an effective method for inactivating the residual white blood cells (WBCs) in blood components. The RF-PRT system for platelets is known to activate many signaling pathways, including p38 and NF-κB. Nevertheless, proteomic studies in WBCs after riboflavin plus UV treatment requires further analysis. STUDY DESIGN AND METHODS: ABO/D-matched lymphocytes were pooled, split, and treated with RF-PRT or UV light or left untreated...
December 1, 2016: Transfusion
https://www.readbyqxmd.com/read/27903906/eupathdb-the-eukaryotic-pathogen-genomics-database-resource
#2
Cristina Aurrecoechea, Ana Barreto, Evelina Y Basenko, John Brestelli, Brian P Brunk, Shon Cade, Kathryn Crouch, Ryan Doherty, Dave Falke, Steve Fischer, Bindu Gajria, Omar S Harb, Mark Heiges, Christiane Hertz-Fowler, Sufen Hu, John Iodice, Jessica C Kissinger, Cris Lawrence, Wei Li, Deborah F Pinney, Jane A Pulman, David S Roos, Achchuthan Shanmugasundram, Fatima Silva-Franco, Sascha Steinbiss, Christian J Stoeckert, Drew Spruill, Haiming Wang, Susanne Warrenfeltz, Jie Zheng
The Eukaryotic Pathogen Genomics Database Resource (EuPathDB, http://eupathdb.org) is a collection of databases covering 170+ eukaryotic pathogens (protists & fungi), along with relevant free-living and non-pathogenic species, and select pathogen hosts. To facilitate the discovery of meaningful biological relationships, the databases couple preconfigured searches with visualization and analysis tools for comprehensive data mining via intuitive graphical interfaces and APIs. All data are analyzed with the same workflows, including creation of gene orthology profiles, so data are easily compared across data sets, data types and organisms...
November 29, 2016: Nucleic Acids Research
https://www.readbyqxmd.com/read/27902743/itraq-based-quantitative-proteomic-analysis-of-spirulina-platensis-in-response-to-low-temperature-stress
#3
Qingye Li, Rong Chang, Yijun Sun, Bosheng Li
Low temperature (LT) is one of the most important abiotic stresses that can significantly reduce crop yield. To gain insight into how Spirulina responds to LT stress, comprehensive physiological and proteomic analyses were conducted in this study. Significant decreases in growth and pigment levels as well as excessive accumulation of compatible osmolytes were observed in response to LT stress. An isobaric tag for relative and absolute quantitation (iTRAQ)-based quantitative proteomics approach was used to identify changes in protein abundance in Spirulina under LT...
2016: PloS One
https://www.readbyqxmd.com/read/27899996/quantitative-label-free-mass-spectrometry-analysis-of-formalin-fixed-paraffin-embedded-tissue-representing-the-invasive-cutaneous-malignant-melanoma-proteome
#4
Paul Dowling, Benvon Moran, Edel McAuley, Paula Meleady, Michael Henry, Martin Clynes, Mairin McMenamin, Niamh Leonard, Mary Monks, Bairbre Wynne, Patrick Ormond, Annemarie Larkin
Understanding the events at a protein level that govern the progression from melanoma in situ to invasive melanoma are important areas of current research to be developed. Recent advances in the analysis of formalin-fixed, paraffin-embedded tissue by proteomics, particularly using the filter-aided sample preparation protocol, has opened up the possibility of studying vast archives of clinical material and associated medical records. In the present study, quantitative protein profiling was performed using tandem mass spectrometry, and the proteome differences between melanoma in situ and invasive melanoma were compared...
November 2016: Oncology Letters
https://www.readbyqxmd.com/read/27899558/pathdip-an-annotated-resource-for-known-and-predicted-human-gene-pathway-associations-and-pathway-enrichment-analysis
#5
Sara Rahmati, Mark Abovsky, Chiara Pastrello, Igor Jurisica
Molecular pathway data are essential in current computational and systems biology research. While there are many primary and integrated pathway databases, several challenges remain, including low proteome coverage (57%), low overlap across different databases, unavailability of direct information about underlying physical connectivity of pathway members, and high fraction of protein-coding genes without any pathway annotations, i.e. 'pathway orphans'. In order to address all these challenges, we developed pathDIP, which integrates data from 20 source pathway databases, 'core pathways', with physical protein-protein interactions to predict biologically relevant protein-pathway associations, referred to as 'extended pathways'...
November 28, 2016: Nucleic Acids Research
https://www.readbyqxmd.com/read/27898073/proteomic-analysis-of-the-postsynaptic-density-implicates-synaptic-function-and-energy-pathways-in-bipolar-disorder
#6
M Föcking, P Dicker, L M Lopez, M Hryniewiecka, K Wynne, J A English, G Cagney, D R Cotter
The postsynaptic density (PSD) contains a complex set of proteins of known relevance to neuropsychiatric disorders such as schizophrenia and bipolar disorder. We enriched for this anatomical structure in the anterior cingulate cortex of 16 bipolar disorder samples and 20 controls from the Stanley Medical Research Institute. Unbiased shotgun proteomics incorporating label-free quantitation was used to identify differentially expressed proteins. Quantitative investigation of the PSD identified 2033 proteins, among which 288 were found to be differentially expressed...
November 29, 2016: Translational Psychiatry
https://www.readbyqxmd.com/read/27898018/combating-ebola-with-repurposed-therapeutics-using-the-cando-platform
#7
Gaurav Chopra, Sashank Kaushik, Peter L Elkin, Ram Samudrala
Ebola virus disease (EVD) is extremely virulent with an estimated mortality rate of up to 90%. However, the state-of-the-art treatment for EVD is limited to quarantine and supportive care. The 2014 Ebola epidemic in West Africa, the largest in history, is believed to have caused more than 11,000 fatalities. The countries worst affected are also among the poorest in the world. Given the complexities, time, and resources required for a novel drug development, finding efficient drug discovery pathways is going to be crucial in the fight against future outbreaks...
November 25, 2016: Molecules: a Journal of Synthetic Chemistry and Natural Product Chemistry
https://www.readbyqxmd.com/read/27896924/detailed-tail-proteomic-analysis-of-axolotl-ambystoma-mexicanum-using-an-mrna-seq-reference-database
#8
Turan Demircan, Ilknur Keskin, Seda Nilgun Dumlu, Nilufer Ayturk, Mahmut Erhan Avsaroglu, Emel Akgun, Gurkan Ozturk, Ahmet Tarik Baykal
Salamander Axolotl has been emerging as an important model for stem cell research due to its powerful regenerative capacity. Several advantages, such as the high capability of advanced tissue, organ and appendages regeneration, promote Axolotl as an ideal model system to extend our current understanding on the mechanisms of regeneration. Acknowledging the common molecular pathways between amphibians and mammals, there is a great potential to translate the messages from Axolotl research to mammalian studies...
November 29, 2016: Proteomics
https://www.readbyqxmd.com/read/27896820/ppar%C3%AE-targeted-oral-cancer-treatment-and-additional-utility-of-genomics-analytic-techniques
#9
Nathan Handley, Jacob Eide, Randall Taylor, Beverly Wuertz, Patrick Gaffney, Frank Ondrey
OBJECTIVE: Peroxisome proliferator-activated receptor γ (PPARγ) agonists have been shown to have anti-proliferative, anti-angiogenic, and proapoptotic effects, leading to interest in their use as cancer therapeutics. Pioglitazone, a U.S. Food and Drug Administration-approved type II diabetes medication and PPARγ agonist, may have a role in adjuvant head-and-neck squamous cell carcinoma treatment or prevention. Therefore, the purpose of this study was: 1) to treat oral cavity cancer cells with the PPARγ activator, pioglitazone, to analyze gene expression changes; and 2) to compare those changes with our preexisting genomic data for development of hypothesis-driven additional basic and clinical studies...
November 29, 2016: Laryngoscope
https://www.readbyqxmd.com/read/27895910/proteomic-identification-of-cryostress-in-epididymal-spermatozoa
#10
Sung Jae Yoon, Md Saidur Rahman, Woo Sung Kwon, Do Yeal Ryu, Yoo Jin Park, Myung Geol Pang
BACKGROUND: Cryopreservation of epididymal spermatozoa is important in cases in which it is not possible to collect semen using normal methods, as the sudden death of an animal or a catastrophic injury. However, the freezing and thawing processes cause stress to spermatozoa, including cold shock, osmotic damage, and ice crystal formation, thereby reducing sperm quality. We assessed the motility (%), motion kinematics, capacitation status, and viability of spermatozoa using computer-assisted sperm analysis and Hoechst 33258/chlortetracycline fluorescence staining...
2016: Journal of Animal Science and Biotechnology
https://www.readbyqxmd.com/read/27895852/protein-protein-interaction-network-of-celiac-disease
#11
Mona Zamanian Azodi, Hassan Peyvandi, Mohammad Rostami-Nejad, Akram Safaei, Kamran Rostami, Reza Vafaee, Mohammadhossein Heidari, Mostafa Hosseini, Mohammad Reza Zali
AIM: The aim of this study is to investigate the Protein-Protein Interaction Network of Celiac Disease. BACKGROUND: Celiac disease (CD) is an autoimmune disease with susceptibility of individuals to gluten of wheat, rye and barley. Understanding the molecular mechanisms and involved pathway may lead to the development of drug target discovery. The protein interaction network is one of the supportive fields to discover the pathogenesis biomarkers for celiac disease...
2016: Gastroenterology and Hepatology From Bed to Bench
https://www.readbyqxmd.com/read/27895139/human-spermatozoa-quantitative-proteomic-signature-classifies-normo-and-asthenozoospermia
#12
Mayank Saraswat, Sakari Joenväärä, Tushar Jain, Anil Kumar Tomar, Ashima Sinha, Sarman Singh, Savita Yadav, Risto Renkonen
Scarcely understood defects lead to asthenozoospermia which results in poor fertility outcomes. Incomplete knowledge of these defects hinders the development of new therapies and reliance on interventional therapies, such as in vitro fertilization, increases. Sperm cells, being transcriptionally and translationally silent, necessitate the proteomic approach to study the sperm function. We have performed a differential proteomics analysis of human sperm and seminal plasma and identified and quantified 667 proteins in sperm and 429 proteins in seminal plasma dataset which were used for further analysis...
November 28, 2016: Molecular & Cellular Proteomics: MCP
https://www.readbyqxmd.com/read/27891174/combination-of-cisplatin-and-bromelain-exerts-synergistic-cytotoxic-effects-against-breast-cancer-cell-line-mda-mb-231-in-vitro
#13
Ahmad Zaim Mat Pauzi, Swee Keong Yeap, Nadiah Abu, Kian Lam Lim, Abdul Rahman Omar, Suraini Abdul Aziz, Adam Leow Thean Chow, Tamilselvan Subramani, Soon Guan Tan, Noorjahan Banu Alitheen
BACKGROUND: Bromelain, which is a cysteine endopeptidase commonly found in pineapple stems, has been investigated as a potential anti-cancer agent for the treatment of breast cancer. However, information pertaining to the effects of combining bromelain with existing chemotherapeutic drugs remains scarce. This study aimed to investigate the possible synergistic cytotoxic effects of using bromelain in combination with cisplatin on MDA-MB-231 human breast cancer cells. METHOD: MDA-MB-231 cells were treated with different concentrations (0...
2016: Chinese Medicine
https://www.readbyqxmd.com/read/27891143/comparative-physiological-and-proteomic-analysis-reveal-distinct-regulation-of-peach-skin-quality-traits-by-altitude
#14
Evangelos Karagiannis, Georgia Tanou, Martina Samiotaki, Michail Michailidis, Grigorios Diamantidis, Ioannis S Minas, Athanassios Molassiotis
The role of environment in fruit physiology has been established; however, knowledge regarding the effect of altitude in fruit quality traits is still lacking. Here, skin tissue quality characters were analyzed in peach fruit (cv. June Gold), harvested in 16 orchards located in low (71.5 m mean), or high (495 m mean) altitutes sites. Data indicated that soluble solids concentration and fruit firmness at commercial harvest stage were unaffected by alitute. Peach grown at high-altitude environment displayed higher levels of pigmentation and specific antioxidant-related activity in their skin at the commercial harvest stage...
2016: Frontiers in Plant Science
https://www.readbyqxmd.com/read/27890797/3-bromopyruvate-treatment-induces-alterations-of-metabolic-and-stress-related-pathways-in-glioblastoma-cells
#15
Davide Chiasserini, Magdalena Davidescu, Pier Luigi Orvietani, Federica Susta, Lara Macchioni, Maya Petricciuolo, Emilia Castigli, Rita Roberti, Luciano Binaglia, Lanfranco Corazzi
: Glioblastoma (GBM) is the most common and aggressive brain tumours of adults. The metabolic phenotype of GBM cells is highly dependent on glycolysis; therefore, therapeutic strategies aimed at interfering with glycolytic pathways are under consideration. 3-Bromopyruvate (3BP) is a potent antiglycolytic agent, with a variety of targets and possible effects on global cell metabolism. Here we analyzed the changes in protein expression on a GBM cell line (GL15 cells) caused by 3BP treatment using a global proteomic approach...
November 23, 2016: Journal of Proteomics
https://www.readbyqxmd.com/read/27889518/proteomic-analysis-provides-insights-into-changes-in-the-central-metabolism-of-the-cambium-during-dormancy-release-in-poplar
#16
Feng Jin, Jing Li, Qi Ding, Qing-Song Wang, Xin-Qiang He
Seasonal cycling of growth and dormancy is an important feature for the woody plants growing in temperate zone, and dormancy is an effective strategy for surviving the winter stress. But the mechanisms of dormancy maintenance and its release are still not clear, especially little information is available with regard to the changes of proteome during the process. A better understanding in the function of proteins and their related metabolic pathways would expand our knowledge of the mechanisms of dormancy maintenance and its release in trees...
November 16, 2016: Journal of Plant Physiology
https://www.readbyqxmd.com/read/27886551/reconsidering-azobenzene-as-a-component-of-small-molecule-hypoxia-mediated-cancer-drugs-a-theranostic-case-study
#17
Peter Verwilst, Jiyou Han, Jiyeong Lee, Sora Mun, Hee-Gyoo Kang, Jong Seung Kim
An azobenzene scaffold serves as both a fluorescence quencher and nitrogen mustard deactivator in a mitochondrial targeting unit bearing theranostic drug delivery system (DDS). The DDS exhibited a tissue selectivity for tumors with aggressive phenotypes, and the efficient in vitro and in vivo azoreduction under hypoxia conditions resulted in bright fluorescence at the tumor site as well as the in situ activation of the prodrug. In vivo therapeutic experiments demonstrated a significant reduction in tumor growth versus number of controls and ex vivo tissue analysis confirmed tissue normalization with strongly reduced angiogenic markers and suppressed cell proliferation...
November 16, 2016: Biomaterials
https://www.readbyqxmd.com/read/27886402/analysis-of-paracoccidioides-lutzii-mitochondria-a-proteomic-approach
#18
L Casaletti, P S Lima, L N Lima, C L Borges, S N Báo, A M Bailão, C M A Bailão
The genus Paracoccidioides is composed of thermal dimorphic fungi, causative agents of paracoccidioidomycosis, one of the most frequent systemic mycoses in Latin America. Mitochondria have sophisticated machinery for ATP production, which involves metabolic pathways such as citric acid and glyoxylate cycles, electron transport chain and oxidative phosphorylation. In addition, this organelle performs a variety of functions in the cell, working as an exceptional metabolic signaling center that contributes to cellular stress responses, as autophagy and apoptosis in eukaryotic organisms...
November 25, 2016: Yeast
https://www.readbyqxmd.com/read/27886127/viperid-envenomation-wound-exudate-contributes-to-increased-vascular-permeability-via-a-damps-tlr-4-mediated-pathway
#19
Alexandra Rucavado, Carolina A Nicolau, Teresa Escalante, Junho Kim, Cristina Herrera, José María Gutiérrez, Jay W Fox
Viperid snakebite envenomation is characterized by inflammatory events including increase in vascular permeability. A copious exudate is generated in tissue injected with venom, whose proteomics analysis has provided insights into the mechanisms of venom-induced tissue damage. Hereby it is reported that wound exudate itself has the ability to induce increase in vascular permeability in the skin of mice. Proteomics analysis of exudate revealed the presence of cytokines and chemokines, together with abundant damage associated molecular pattern molecules (DAMPs) resulting from both proteolysis of extracellular matrix and cellular lysis...
November 24, 2016: Toxins
https://www.readbyqxmd.com/read/27884752/quantitative-proteomic-analysis-reveals-that-proteins-required-for-fatty-acid-metabolism-may-serve-as-diagnostic-markers-for-gastric-cancer
#20
Zhen Jiang, Hongchun Shen, Bo Tang, Qin Yu, Xingli Ji, Li Wang
BACKGROUND: Gastric cancer is one of the leading causes of cancer-related deaths worldwide. The sensitivities and specificities of current biomarkers for gastric cancer are insufficient for clinical detection, and new diagnostic tests are therefore urgently required. METHODS: A discovery set of gastric cancer and adjacent normal tissues were analyzed for differentially expressed proteins by labeling of peptide digests with isobaric tag for relative and absolute quantitation (iTRAQ) reagents followed by liquid chromatography-electrospray ionization-tandem mass spectrometry...
November 21, 2016: Clinica Chimica Acta; International Journal of Clinical Chemistry
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