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https://www.readbyqxmd.com/read/28081159/osmoregulation-in-the-halophilic-bacterium-halomonas-elongata-a-case-study-for-integrative-systems-biology
#1
Viktoria Kindzierski, Silvia Raschke, Nicole Knabe, Frank Siedler, Beatrix Scheffer, Katharina Pflüger-Grau, Friedhelm Pfeiffer, Dieter Oesterhelt, Alberto Marin-Sanguino, Hans-Jörg Kunte
Halophilic bacteria use a variety of osmoregulatory methods, such as the accumulation of one or more compatible solutes. The wide diversity of compounds that can act as compatible solute complicates the task of understanding the different strategies that halophilic bacteria use to cope with salt. This is specially challenging when attempting to go beyond the pathway that produces a certain compatible solute towards an understanding of how the metabolic network as a whole addresses the problem. Metabolic reconstruction based on genomic data together with Flux Balance Analysis (FBA) is a promising tool to gain insight into this problem...
2017: PloS One
https://www.readbyqxmd.com/read/28078418/absolute-quantification-of-myosin-heavy-chain-isoforms-by-selected-reaction-monitoring-can-underscore-skeletal-muscle-changes-in-a-mouse-model-of-amyotrophic-lateral-sclerosis
#2
Caterina Peggion, Maria Lina Massimino, Giancarlo Biancotto, Roberto Angeletti, Carlo Reggiani, Maria Catia Sorgato, Alessandro Bertoli, Roberto Stella
Skeletal muscle fibers contain different isoforms of myosin heavy chain (MyHC) that define distinctive contractile properties. In light of the muscle capacity to adapt MyHC expression to pathophysiological conditions, a rapid and quantitative assessment of MyHC isoforms in small muscle tissue quantities would represent a valuable diagnostic tool for (neuro)muscular diseases. As past protocols did not meet these requirements, in the present study we applied a targeted proteomic approach based on selected reaction monitoring that allowed the absolute quantification of slow and fast MyHC isoforms in different mouse skeletal muscles with high reproducibility...
January 11, 2017: Analytical and Bioanalytical Chemistry
https://www.readbyqxmd.com/read/28064163/predicting-albuminuria-response-to-spironolactone-treatment-with-urinary-proteomics-in-patients-with-type-2-diabetes-and-hypertension
#3
Morten Lindhardt, Frederik Persson, Christina Oxlund, Ib A Jacobsen, Petra Zürbig, Harald Mischak, Peter Rossing, Hiddo J L Heerspink
BACKGROUND: The mineralocorticoid receptor antagonist spironolactone significantly reduces albuminuria in patients with diabetes. Prior studies have shown large between-patient variability in albuminuria treatment response. We previously developed and validated a urinary proteomic classifier that predicts onset and progression of chronic kidney disease. Here, we tested whether the proteomic classifier based on 273 urinary peptides (CKD273) predicts albuminuria response to spironolactone treatment...
January 7, 2017: Nephrology, Dialysis, Transplantation
https://www.readbyqxmd.com/read/28062376/a-biotin-enrichment-strategy-identifies-novel-carbonylated-amino-acids-in-proteins-from-human-plasma
#4
Jesper F Havelund, Katarzyna Wojdyla, Michael J Davies, Ole N Jensen, Ian Max Møller, Adelina Rogowska-Wrzesinska
: Protein carbonylation is an irreversible protein oxidation correlated with oxidative stress, various diseases and ageing. Here we describe a peptide-centric approach for identification and characterisation of up to 14 different types of carbonylated amino acids in proteins. The modified residues are derivatised with biotin-hydrazide, enriched and characterised by tandem mass spectrometry. The strength of the method lies in an improved elution of biotinylated peptides from monomeric avidin resin using hot water (95°C) and increased sensitivity achieved by reduction of analyte losses during sample preparation and chromatography...
January 3, 2017: Journal of Proteomics
https://www.readbyqxmd.com/read/28056027/quantitative-proteomics-reveals-ecophysiological-effects-of-light-and-silver-stress-on-the-mixotrophic-protist-poterioochromonas-malhamensis
#5
Daniela Beisser, Farnusch Kaschani, Nadine Graupner, Lars Grossmann, Manfred Jensen, Sabrina Ninck, Florian Schulz, Sven Rahmann, Jens Boenigk, Markus Kaiser
Aquatic environments are heavily impacted by human activities including climate warming and the introduction of xenobiotics. Due to the application of silver nanoparticles as bactericidal agent the introduction of silver into the environment strongly has increased during the past years. Silver ions affect the primary metabolism of algae, in particular photosynthesis. Mixotrophic algae are an interesting test case as they do not exclusively rely on photosynthesis which may attenuate the harmful effect of silver...
2017: PloS One
https://www.readbyqxmd.com/read/28049346/genoproteomics-assisted-improvement-of-andrographis-paniculata-toward-a-promising-molecular-and-conventional-breeding-platform-for-autogamous-plants-affecting-the-pharmaceutical-industry
#6
Alireza Valdiani, Daryush Talei, Surrinder K Lattoo, Rodomiro Ortiz, Søren Kjærsgaard Rasmussen, Jacqueline Batley, Mohd Yusop Rafii, Mahmood Maziah, Kallevettankuzhy K Sabu, Rambod Abiri, Suchirat Sakuanrungsirikul, Soon Guan Tan
Andrographis paniculata (Burm. f.) Wall. ex Nees. (AP) is a hermaphroditic, self-compatible, and habitual inbreeding plant. Its main bioactive component is andrographolide, which is capable of inducing autophagic cell death in some human cancer cells and helps fight HIV/AIDS. Increasing the andrographolide content by investigating the genetic mechanisms controlling its biosynthesis in order to improve and develop high-yielding cultivars are the main breeding targets for AP. However, there might exist some limitations or barriers for crossability within AP accessions...
January 3, 2017: Critical Reviews in Biotechnology
https://www.readbyqxmd.com/read/28045899/characterisation-of-antigen-b-protein-species-present-in-the-hydatid-cyst-fluid-of-echinococcus-canadensis-g7-genotype
#7
Ana Maite Folle, Eduardo S Kitano, Analía Lima, Magdalena Gil, Marcela Cucher, Gustavo Mourglia-Ettlin, Leo K Iwai, Mara Rosenzvit, Carlos Batthyány, Ana María Ferreira
The larva of cestodes belonging to the Echinococcus granulosus sensu lato (s.l.) complex causes cystic echinococcosis (CE). It is a globally distributed zoonosis with significant economic and public health impact. The most immunogenic and specific Echinococcus-genus antigen for human CE diagnosis is antigen B (AgB), an abundant lipoprotein of the hydatid cyst fluid (HF). The AgB protein moiety (apolipoprotein) is encoded by five genes (AgB1-AgB5), which generate mature 8 kDa proteins (AgB8/1-AgB8/5). These genes seem to be differentially expressed among Echinococcus species...
January 2017: PLoS Neglected Tropical Diseases
https://www.readbyqxmd.com/read/28045431/unraveling-massive-crocins-transport-and-accumulation-through-proteome-and-microscopy-tools-during-the-development-of-saffron-stigma
#8
Lourdes Gómez-Gómez, Verónica Parra-Vega, Alba Rivas-Sendra, Jose M Seguí-Simarro, Rosa Victoria Molina, Claudia Pallotti, Ángela Rubio-Moraga, Gianfranco Diretto, Alicia Prieto, Oussama Ahrazem
Crocins, the glucosides of crocetin, are present at high concentrations in saffron stigmas and accumulate in the vacuole. However, the biogenesis of the saffron chromoplast, the changes during the development of the stigma and the transport of crocins to the vacuole, are processes that remain poorly understood. We studied the process of chromoplast differentiation in saffron throughout stigma development by means of transmission electron microscopy. Our results provided an overview of a massive transport of crocins to the vacuole in the later developmental stages, when electron dense drops of a much greater size than plastoglobules (here defined "crocinoplast") were observed in the chromoplast, connected to the vacuole with a subsequent transfer of these large globules inside the vacuole...
January 1, 2017: International Journal of Molecular Sciences
https://www.readbyqxmd.com/read/28043501/comparative-proteomic-analysis-of-sequential-isolates-of-mycobacterium-tuberculosis-sensitive-and-resistant-beijing-type-from-a-patient-with-pulmonary-tuberculosis
#9
Amit Singh, Anil Kumar Gupta, Krishnamoorthy Gopinath, Divakar Sharma, Prashant Sharma, Deepa Bisht, Pawan Sharma, Sarman Singh
AIM & OBJECTIVE: In India, tuberculosis (TB) is a foremost health problem, and the emergence of multidrug-resistant (MDR) and extensively drug resistant (XDR) strains of Mycobacterium tuberculosis (M. tuberculosis) has further complicated the situation. Although various mechanisms have been proposed to elucidate the emergence of resistance, our knowledge remains insufficient. The formation of a very complex network and drugs of proteins are countered by their efflux/modification or target over-expression/modification...
December 2016: International Journal of Mycobacteriology
https://www.readbyqxmd.com/read/28039059/recent-advances-in-lipidomics-analytical-and-clinical-perspectives
#10
REVIEW
Sumit Sethi, Elisa Brietzke
Lipidomics or lipid-profiling is a lipid-targeted metabolomics approach aiming at comprehensive analysis of lipids in biological systems. The extent of information in the genomic and proteomic fields is greater than that in the lipidomics field, because of the complex nature of lipids and the limitations of tools for analysis. Modern technological advances in mass spectrometry and chromatography have greatly improved the developments and applications of metabolic profiling of diverse lipids in complex biological samples...
December 27, 2016: Prostaglandins & Other Lipid Mediators
https://www.readbyqxmd.com/read/28032943/mass-spectrometry-based-tools-to-characterize-dna-protein-cross-linking-by-bis-electrophiles
#11
Arnold Groehler, Amanda Degner, Natalia Y Tretyakova
DNA-protein cross-links (DPCs) are unusually bulky DNA adducts that form in cells as a result of exposure to endogenous and exogenous agents including reactive oxygen species, ultraviolet light, ionizing radiation, environmental agents (e.g. transition metals, formaldehyde, 1,2-dibromoethane, 1,3-butadiene) and common chemotherapeutic agents. Covalent DPCs are cytotoxic and mutagenic due to their ability to interfere with faithful DNA replication and prevent accurate gene expression. Key to our understanding of the biological significance of DPC formation is identifying the proteins most susceptible to forming these unusually bulky and complex lesions and quantifying the extent of DNA-protein cross-linking in cells and tissues...
December 29, 2016: Basic & Clinical Pharmacology & Toxicology
https://www.readbyqxmd.com/read/28025563/novel-structural-approaches-to-study-gpcr-regulation
#12
REVIEW
Marco A Alfonzo-Méndez, Rocío Alcántara-Hernández, J Adolfo García-Sáinz
BACKGROUND: Upon natural agonist or pharmacological stimulation, G protein-coupled receptors (GPCRs) are subjected to posttranslational modifications, such as phosphorylation and ubiquitination. These posttranslational modifications allow protein-protein interactions that turn off and/or switch receptor signaling as well as trigger receptor internalization, recycling or degradation, among other responses. Characterization of these processes is essential to unravel the function and regulation of GPCR...
December 23, 2016: International Journal of Molecular Sciences
https://www.readbyqxmd.com/read/28013236/comparing-genome-versus-proteome-based-identification-of-clinical-bacterial-isolates
#13
Valentina Galata, Christina Backes, Cédric Christian Laczny, Georg Hemmrich-Stanisak, Howard Li, Laura Smoot, Andreas Emanuel Posch, Susanne Schmolke, Markus Bischoff, Lutz von Müller, Achim Plum, Andre Franke, Andreas Keller
Whole-genome sequencing (WGS) is gaining importance in the analysis of bacterial cultures derived from patients with infectious diseases. Existing computational tools for WGS-based identification have, however, been evaluated on previously defined data relying thereby unwarily on the available taxonomic information.Here, we newly sequenced 846 clinical gram-negative bacterial isolates representing multiple distinct genera and compared the performance of five tools (CLARK, Kaiju, Kraken, DIAMOND/MEGAN and TUIT)...
December 24, 2016: Briefings in Bioinformatics
https://www.readbyqxmd.com/read/28008374/comparative-proteomics-analysis-of-human-osteosarcoma-by-2d-dige-with-maldi-tof-tof-ms
#14
Guoxiang Wang, Zhengyao Zhang, Maoguang Yang, Bo Xu, Qi Gao, Xiaoyu Yang
Osteosarcoma (OS) is the most common primary malignant tumor of bone and the third most common cancer in childhood and adolescence. However, controversy concerning the ideal combination of chemotherapy agents ensued throughout the last quarter of the 20th century because of conflicting and often nonrandomized data. Collaborative efforts to increase understanding of the biology of osteosarcoma and the use of preclinical models to test novel protein targets will be critical to identify the path toward improving outcomes for patients...
November 2016: Journal of Bone Oncology
https://www.readbyqxmd.com/read/28004338/network-analysis-identifies-disease-specific-pathways-for-parkinson-s-disease
#15
Chiara Monti, Ilaria Colugnat, Leonardo Lopiano, Adriano Chiò, Tiziana Alberio
Neurodegenerative diseases are characterized by the progressive loss of specific neurons in selected regions of the central nervous system. The main clinical manifestation (movement disorders, cognitive impairment, and/or psychiatric disturbances) depends on the neuron population being primarily affected. Parkinson's disease is a common movement disorder, whose etiology remains mostly unknown. Progressive loss of dopaminergic neurons in the substantia nigra causes an impairment of the motor control. Some of the pathogenetic mechanisms causing the progressive deterioration of these neurons are not specific for Parkinson's disease but are shared by other neurodegenerative diseases, like Alzheimer's disease and amyotrophic lateral sclerosis...
December 21, 2016: Molecular Neurobiology
https://www.readbyqxmd.com/read/28003327/identification-and-characterization-of-seed-coat-mucilage-proteins
#16
Allen Yi-Lun Tsai, Tadashi Kunieda, Jason Rogalski, Leonard J Foster, Brian E Ellis, George W Haughn
Plant cell wall proteins are important regulators of cell wall architecture and function. However, because cell wall proteins are difficult to extract and analyze, they are generally poorly understood. Here we describe the identification and characterization of proteins integral to the Arabidopsis (Arabidopsis thaliana) seed coat mucilage, a specialized layer of the extracellular matrix composed of plant cell wall carbohydrates that is used as a model for cell wall research. The proteins identified in mucilage include those previously identified by genetic analysis, and several mucilage proteins are reduced in mucilage-deficient mutant seeds, suggesting that these proteins are genuinely associated with the mucilage...
December 21, 2016: Plant Physiology
https://www.readbyqxmd.com/read/28003051/interaction-of-chiral-herbicides-with-soil-microorganisms-algae-and-vascular-plants
#17
REVIEW
Muhammad Asad Ullah Asad, Michel Lavoie, Hao Song, Yujian Jin, Zhengwei Fu, Haifeng Qian
Chiral herbicides are often used in agriculture as racemic mixtures, although studies have shown that the fate and toxicity of herbicide enantiomers to target and non-target plants can be enantioselective and that herbicide toxicity can be mediated by only one enantiomer. If one enantiomer is active against the target plant, the use of enantiomer-rich herbicide mixtures instead of racemic herbicides could decrease the amount of herbicide applied to a crop and the cost of herbicide application, as well as unintended toxic herbicide effects in the environment...
December 18, 2016: Science of the Total Environment
https://www.readbyqxmd.com/read/28000080/a-bioinformatics-pipeline-to-search-functional-motifs-within-whole-proteome-data-a-case-study-of-poxviruses
#18
Haitham Sobhy
Proteins harbor domains or short linear motifs, which facilitate their functions and interactions. Finding functional motifs in protein sequences could predict the putative cellular roles or characteristics of hypothetical proteins. In this study, we present Shetti-Motif, which is an interactive tool to (i) map UniProt and PROSITE flat files, (ii) search for multiple pre-defined consensus patterns or experimentally validated functional motifs in large datasets protein sequences (proteome-wide), (iii) search for motifs containing repeated residues (low-complexity regions, e...
December 20, 2016: Virus Genes
https://www.readbyqxmd.com/read/27998759/the-crispr-cas9-system-targeting-egfr-exon-17-abrogates-nf-%C3%AE%C2%BAb-activation-via-epigenetic-modulation-of-ubxn1-in-egfrwt-viii-glioma-cells
#19
Kai Huang, Chao Yang, Qi-Xue Wang, Yan-Sheng Li, Chuan Fang, Yan-Li Tan, Jian-Wei Wei, Yun-Fei Wang, Xin Li, Jun-Hu Zhou, Bing-Cong Zhou, Kai-Kai Yi, Kai-Liang Zhang, Jie Li, Chun-Sheng Kang
Worldwide, glioblastoma (GBM) is the most lethal and frequent intracranial tumor. Despite decades of study, the overall survival of GBM patients remains unchanged. epidermal growth factor receptor (EGFR) amplification and gene mutation are thought to be negatively correlated with prognosis. In this study, we used proteomics to determine that UBXN1 is a negative downstream regulator of the EGFR mutation vIII (EGFRvIII). Via bioinformatics analysis, we found that UBXN1 is a factor that can improve glioma patients' overall survival time...
December 18, 2016: Cancer Letters
https://www.readbyqxmd.com/read/27989939/high-resolution-mass-spectrometry-based-global-proteomic-analysis-of-probiotic-strains-lactobacillus-fermentum-ncdc-400-and-rs2
#20
Parijat Pragya, Gurjeet Kaur, Syed Azmal Ali, Shveta Bhatla, Preeti Rawat, Vaibhao Lule, Sudarshan Kumar, Ashok Kumar Mohanty, Pradip Behare
Lactobacillus fermentum strains NCDC 400 and RS2, previously isolated from dairy sources, exhibited excellent probiotic properties were studied for the global proteomic profile. A total of 1125 proteins were identified by a high-resolution mass spectrometer, ESI-qTOF (nano-LC-MS/MS) in the strains of L. fermentum. Kyoto Encyclopedia of Genes and Genomes (KEGG) pathway analysis resulted in 60.9% and 59.2% of the total proteins were functionally annotated for NCDC 400 and RS2 respectively. Simultaneously, a cluster of orthologous groups (COGs) and KEGG together revealed the presence of a significant number of proteins involved in transcription, translation, chaperones, peptidoglycan biosynthesis, nucleotide, amino acid and carbohydrate metabolism...
January 30, 2017: Journal of Proteomics
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