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https://www.readbyqxmd.com/read/27920755/finding-potential-therapeutic-targets-against-shigella-flexneri-through-proteome-exploration
#1
Mohammad Uzzal Hossain, Md Arif Khan, Abu Hashem, Md Monirul Islam, Mohammad Neaz Morshed, Chaman Ara Keya, Md Salimullah
Background:Shigella flexneri is a gram negative bacteria that causes the infectious disease "shigellosis." S. flexneri is responsible for developing diarrhea, fever, and stomach cramps in human. Antibiotics are mostly given to patients infected with shigella. Resistance to antibiotics can hinder its treatment significantly. Upon identification of essential therapeutic targets, vaccine and drug could be effective therapy for the treatment of shigellosis. Methods: The study was designed for the identification and qualitative characterization for potential drug targets from S...
2016: Frontiers in Microbiology
https://www.readbyqxmd.com/read/27920753/neuroproteomics-and-systems-biology-approach-to-identify-temporal-biomarker-changes-post-experimental-traumatic-brain-injury-in-rats
#2
Firas H Kobeissy, Joy D Guingab-Cagmat, Zhiqun Zhang, Ahmed Moghieb, Olena Y Glushakova, Stefania Mondello, Angela M Boutté, John Anagli, Richard Rubenstein, Hisham Bahmad, Amy K Wagner, Ronald L Hayes, Kevin K W Wang
Traumatic brain injury (TBI) represents a critical health problem of which diagnosis, management, and treatment remain challenging. TBI is a contributing factor in approximately one-third of all injury-related deaths in the United States. The Centers for Disease Control and Prevention estimate that 1.7 million people suffer a TBI in the United States annually. Efforts continue to focus on elucidating the complex molecular mechanisms underlying TBI pathophysiology and defining sensitive and specific biomarkers that can aid in improving patient management and care...
2016: Frontiers in Neurology
https://www.readbyqxmd.com/read/27908670/proteome-of-the-rete-testis-fluid-from-tropically-adapted-morada-nova-rams
#3
Mauricio Fraga van Tilburg, Solange Damasceno Sousa, Révila Bianca Ferreira de Melo, Frederico B Moreno, Ana Cristina Monteiro-Moreira, Renato A Moreira, Arlindo de Alencar Moura
The rete testis has a close relationship with sperm development and may have other functions besides serving as an intercalated channel. The aim of this study was to identify and characterize the proteins of rete testis fluid (RTF) from tropically-adapted Morada Nova rams. Testicles obtained from six Morada Nova rams were dissected and the head of the epididymis was separated to access the efferent ducts. Rete testis fluid was obtained by gentle massage of the testis. The fluid was centrifuged to remove cell debris and sperm...
November 22, 2016: Animal Reproduction Science
https://www.readbyqxmd.com/read/27903906/eupathdb-the-eukaryotic-pathogen-genomics-database-resource
#4
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/27899614/suba4-the-interactive-data-analysis-centre-for-arabidopsis-subcellular-protein-locations
#5
Cornelia M Hooper, Ian R Castleden, Sandra K Tanz, Nader Aryamanesh, A Harvey Millar
The SUBcellular location database for Arabidopsis proteins (SUBA4, http://suba.live) is a comprehensive collection of manually curated published data sets of large-scale subcellular proteomics, fluorescent protein visualization, protein-protein interaction (PPI) as well as subcellular targeting calls from 22 prediction programs. SUBA4 contains an additional 35 568 localizations totalling more than 60 000 experimental protein location claims as well as 37 new suborganellar localization categories. The experimental PPI data has been expanded to 26 327 PPI pairs including 856 PPI localizations from experimental fluorescent visualizations...
November 28, 2016: Nucleic Acids Research
https://www.readbyqxmd.com/read/27899155/comparative-sequence-analysis-of-cyclospora-cayetanensis-apicoplast-genomes-originating-from-diverse-geographical-regions
#6
Hediye Nese Cinar, Yvonne Qvarnstrom, Yuping Wei-Pridgeon, Wen Li, Fernanda S Nascimento, Michael J Arrowood, Helen R Murphy, AhYoung Jang, Eunje Kim, RaeYoung Kim, Alexandre da Silva, Gopal R Gopinath
BACKGROUND: Cyclospora cayetanensis is an emerging coccidian parasite that causes endemic and epidemic diarrheal disease called cyclosporiasis, and this infection is associated with consumption of contaminated produce or water in developed and developing regions. Food-borne outbreaks of cyclosporiasis have occurred almost every year in the USA since the 1990s. Investigations of these outbreaks are currently hampered due to lack of molecular epidemiological tools for trace back analysis...
November 29, 2016: Parasites & Vectors
https://www.readbyqxmd.com/read/27897190/versatile-sensitive-liquid-chromatography-mass-spectrometry-implementation-of-10%C3%A2-%C3%AE-m-ot-columns-suitable-for-small-molecules-peptides-and-proteins
#7
T Vehus, H Roberg-Larsen, J Waaler, S Aslaksen, S Krauss, S R Wilson, E Lundanes
We have designed a versatile and sensitive liquid chromatographic (LC) system, featuring a monolithic trap column and a very narrow (10 μm ID) fused silica open tubular liquid chromatography (OTLC) separation column functionalized with C18-groups, for separating a wide range of molecules (from small metabolites to intact proteins). Compared to today's capillary/nanoLC approaches, our system provides significantly enhanced sensitivity (up to several orders) with matching or improved separation efficiency, and highly repeatable chromatographic performance...
November 29, 2016: Scientific Reports
https://www.readbyqxmd.com/read/27896960/on-the-power-and-limits-of-sequence-similarity-based-clustering-of-proteins-into-families
#8
Christian Wiwie, Richard Röttger
Over the last decades, we have observed an ongoing tremendous growth of available sequencing data fueled by the advancements in wet-lab technology. The sequencing information is only the beginning of the actual understanding of how organisms survive and prosper. It is, for instance, equally important to also unravel the proteomic repertoire of an organism. A classical computational approach for detecting protein families is a sequence-based similarity calculation coupled with a subsequent cluster analysis. In this work we have intensively analyzed various clustering tools on a large scale...
2016: Pacific Symposium on Biocomputing
https://www.readbyqxmd.com/read/27895543/proteome-analysis-of-excretory-secretory-proteins-of-entamoeba-histolytica-hm1-imss-via-lc-esi-ms-ms-and-lc-maldi-tof-tof
#9
Jorim Anak Ujang, Soon Hong Kwan, Mohd Nazri Ismail, Boon Huat Lim, Rahmah Noordin, Nurulhasanah Othman
BACKGROUND: Excretory-secretory (ES) proteins of E. histolytica are thought to play important roles in the host invasion, metabolism, and defence. Elucidation of the types and functions of E. histolytica ES proteins can further our understanding of the disease pathogenesis. Thus, the aim of this study is to use proteomics approach to better understand the complex ES proteins of the protozoa. METHODS: E. histolytica ES proteins were prepared by culturing the trophozoites in protein-free medium...
2016: Clinical Proteomics
https://www.readbyqxmd.com/read/27891114/comparative-analysis-of-two-helicobacter-pylori-strains-using-genomics-and-mass-spectrometry-based-proteomics
#10
Roger Karlsson, Kaisa Thorell, Shaghayegh Hosseini, Diarmuid Kenny, Carina Sihlbom, Åsa Sjöling, Anders Karlsson, Intawat Nookaew
Helicobacter pylori, a gastroenteric pathogen believed to have co-evolved with humans over 100,000 years, shows significant genetic variability. This motivates the study of different H. pylori strains and the diseases they cause in order to identify determinants for disease evolution. In this study, we used proteomics tools to compare two H. pylori strains. Nic25_A was isolated in Nicaragua from a patient with intestinal metaplasia, and P12 was isolated in Europe from a patient with duodenal ulcers. Differences in the abundance of surface proteins between the two strains were determined with two mass spectrometry-based methods, label-free quantification (MaxQuant) or the use of tandem mass tags (TMT)...
2016: Frontiers in Microbiology
https://www.readbyqxmd.com/read/27885863/progress-and-pitfalls-in-finding-the-missing-proteins-from-the-human-proteome-map
#11
Victor Segura, Alba Garin-Muga, Elizabeth Guruceaga, Fernando J Corrales
The Human Proteome Project was launched with two main goals: the comprehensive and systematic definition of the human proteome map and the development of ready to use analytical tools to measure relevant proteins in their biological context in health and disease. Despite the great progress in this endeavour, there is still a group of reluctant proteins with no, or scarce, experimental evidence supporting their existence. These are called the 'missing proteins' and represent one of the biggest challenges to complete the human proteome map...
December 2, 2016: Expert Review of Proteomics
https://www.readbyqxmd.com/read/27878450/mass-spectrometry-based-proteomics-profiling-of-human-monocytes
#12
Yong Zeng, Fei-Yan Deng, Wei Zhu, Lan Zhang, Hao He, Chao Xu, Qing Tian, Ji-Gang Zhang, Li-Shu Zhang, Hong-Gang Hu, Hong-Wen Deng
Human monocyte is an important cell type which is involved in various complex human diseases. To better understand the biology of human monocytes and facilitate further studies, we developed the first comprehensive proteome knowledge base specifically for human monocytes by integrating both in vivo and in vitro datasets. The top 2000 expressed genes from in vitro datasets and 779 genes from in vivo experiments were integrated into this study. Altogether, a total of 2237 unique monocyte-expressed genes were cataloged...
November 22, 2016: Protein & Cell
https://www.readbyqxmd.com/read/27865793/multiplexed-mass-spectrometry-monitoring-of-biomarker-candidates-for-osteoarthritis
#13
Patricia Fernández-Puente, Valentina Calamia, Lucía González-Rodríguez, Lucía Lourido, María Camacho-Encina, Natividad Oreiro, Cristina Ruiz-Romero, Francisco J Blanco
: The methods currently available for the diagnosis and monitoring of osteoarthritis (OA) are very limited and lack sensitivity. Being the most prevalent rheumatic disease, one of the most disabling pathologies worldwide and currently untreatable, there is a considerable interest pointed in the verification of specific biological markers for improving its diagnosis and disease progression studies. Considering the remarkable development of targeted proteomics methodologies in the frame of the Human Proteome Project, the aim of this work was to develop and apply a MRM-based method for the multiplexed analysis of a panel of 6 biomarker candidates for OA encoded by the Chromosome 16, and another 8 proteins identified in previous shotgun studies as related with this pathology, in specimens derived from the human joint and serum...
November 16, 2016: Journal of Proteomics
https://www.readbyqxmd.com/read/27862981/standardization-of-sample-homogenization-for-mosquito-identification-using-an-innovative-proteomic-tool-based-on-protein-profiling
#14
Amira Nebbak, Alexandra C Willcox, Idir Bitam, Didier Raoult, Philippe Parola, Lionel Almeras
The rapid spread of vector-borne diseases demands the development of an innovative strategy for arthropod monitoring. The emergence of MALDI-TOF MS as a rapid, low-cost and accurate tool for arthropod identification is revolutionizing medical entomology. However, as MS spectra from an arthropod can vary according to the body part selected, the sample homogenization method used and the mode and duration of sample storage, standardization of protocols is indispensable prior to the creation and sharing of an MS reference spectra database...
November 12, 2016: Proteomics
https://www.readbyqxmd.com/read/27860399/toxin-a-of-the-nosocomial-pathogen-clostridium-difficile-induces-primary-effects-in-the-proteome-of-hep-2-cells
#15
Johannes Junemann, Gurbet Birgin, Jelena Erdmann, Anke Schröder, Ingo Just, Ralf Gerhard, Andreas Pich
PURPOSE: This study was carried out to investigate the impact of high concentrations of Clostridium difficile toxin A (TcdA) on the proteome of human cells. It should also be examined whether a catalytically deficient mutant (TcdANXN ) has an effect on target cells. EXPERIMENTAL DESIGN: Proteome changes were investigated after treatment of HEp-2 cells with 20 nM TcdA for 8 h using a triplex SILAC labeling method and shotgun proteomics. Proteins from differently labeled and treated cells were combined for analysis using an HPLC coupled to an Orbitrap mass spectrometer...
November 10, 2016: Proteomics. Clinical Applications
https://www.readbyqxmd.com/read/27858266/reverse-phase-protein-arrays-enable-glioblastoma-molecular-subtyping
#16
Gregor Hutter, Martin Sailer, Tej Deepak Azad, André O von Bueren, Peter Nollau, Stephan Frank, Cristobal Tostado, Durga Sarvepalli, Arkasubhra Ghosh, Marie-Françoise Ritz, Jean-Louis Boulay, Luigi Mariani
In the present study we investigated the phosphorylation status of the 12 most important signaling cascades in glioblastomas. More than 60 tumor and control biopsies from tumor center and periphery (based on neuronavigation) were subjected to selective protein expression analysis using reverse-phase protein arrays (RPPA) incubated with antibodies against posttranslationally modified cancer pathway proteins. The ratio between phosphorylated (or modified) and non-phosphorylated protein was assessed. All samples were histopathologically validated and proteomic profiles correlated with clinical and survival data...
November 17, 2016: Journal of Neuro-oncology
https://www.readbyqxmd.com/read/27858106/bioavailability-and-toxicity-of-copper-manganese-and-nickel-in-paronychiurus-kimi-collembola-and-biomarker-discovery-for-their-exposure
#17
Jino Son, Yun-Sik Lee, Sung-Eun Lee, Key-Il Shin, Kijong Cho
Bioavailability and toxicity of Cu, Mn, and Ni in Paronychiurus kimi were investigated after 28 days of exposure to OECD artificial soil spiked with these metals. Uptake and effect of Cu, Mn, and Ni on the reproduction of P. kimi were related to different metal fractions (water-soluble, 0.01 M CaCl2-extractable or porewater metal concentrations). Cu and Mn concentrations in P. kimi increased with increasing Cu and Mn concentrations in the soil, while Ni contents in P. kimi reached a plateau at a concentration higher than 200 mg/kg in soil...
November 17, 2016: Archives of Environmental Contamination and Toxicology
https://www.readbyqxmd.com/read/27856224/tid-standalone-software-for-mining-putative-drug-targets-from-bacterial-proteome
#18
Reena Gupta, Dibyabhaba Pradhan, Arun Kumar Jain, Chandra Shekhar Rai
TiD is a standalone application, which relies on basic assumption that a protein must be essential for pathogens survival and non-homologous with host to qualify as putative target. With an input bacterial proteome, TiD removes paralogous proteins, picks essential ones, and excludes proteins homologous with host organisms. The targets illustrate non-homology with at least 40 out of 84 gut microbes, considered safe for human. TiD classifies proposed targets as known, novel and virulent. Users can perform pathway analysis, choke point analysis, interactome analysis, subcellular localization and functional annotations through web servers cross-referenced with the application...
November 14, 2016: Genomics
https://www.readbyqxmd.com/read/27853253/generation-of-metastatic-melanoma-specific-antibodies-by-affinity-purification
#19
Birgit Schütz, Anita Koppensteiner, David Schörghofer, Katharina Kinslechner, Gerald Timelthaler, Robert Eferl, Markus Hengstschläger, Albert Missbichler, Harald Hundsberger, Mario Mikula
Melanoma is the most aggressive type of skin cancer and one of the most frequent tumours in young adults. Identification of primary tumours prone to develop metastasis is of paramount importance for further patient stratification. However, till today, no markers exist that are routinely used to predict melanoma progression. To ameliorate this problem, we generated antiserum directed against metastatic melanoma tissue lysate and applied a novel approach to purify the obtained serum via consecutive affinity chromatography steps...
November 17, 2016: Scientific Reports
https://www.readbyqxmd.com/read/27846722/-utilization-of-hydrogen-deuterium-exchange-in-biopharmaceutical-industry
#20
D Coufalová, B Vojtěšek, L Hernychova
BACKGROUND: The development of biopharmaceutics is the fastest growing segment of the present pharmaceutical industry. The analysis of proteins therapeutics is a challenging task due to their large size and complexity of spatial structure. Any changes in the primary, secondary, tertiary or quaternary protein structure can have huge impact on their function, efficiency and toxicity. Mass spectrometry proved itself to be a powerful tool for analysis of primary protein structure (amino acid sequence) and thanks to the development of new techniques in last years it is able to analyse higher order protein structures...
2016: Klinická Onkologie: Casopis Ceské a Slovenské Onkologické Spolecnosti
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