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https://www.readbyqxmd.com/read/29161576/unraveling-physiological-biochemical-and-molecular-mechanisms-involved-in-olive-olea-europaea-l-cv-ch%C3%A3-toui-tolerance-to-drought-and-salt-stresses
#1
Mariem Ben Abdallah, Dalila Trupiano, Antonella Polzella, Elena De Zio, Mauro Sassi, Andrea Scaloni, Mokhtar Zarrouk, Nabil Ben Youssef, Gabriella Stefania Scippa
Olive (Olea europaea L.) is an economically important crop for the Mediterranean basin, where prolonged drought and soil salinization may occur. This plant has developed a series of mechanisms to tolerate and grow under these adverse conditions. By using an integrated approach, we described in Chétoui olive cultivar the changes in plant growth, oxidative damage and osmolyte accumulation in leaves, in combination with corresponding changes in physiological parameters and proteome. Our results showed, under both stress conditions, a greater growth reduction of the aboveground plant organs than of the underground counterparts...
November 10, 2017: Journal of Plant Physiology
https://www.readbyqxmd.com/read/29161511/a-customizable-flow-injection-system-for-automated-high-throughput-and-time-sensitive-ion-mobility-spectrometry-and-mass-spectrometry-measurements
#2
Daniel J Orton, Malak M Tfaily, Ronald J Moore, Brian L LaMarche, Xueyun Zheng, Thomas L Fillmore, Rosalie K Chu, Karl K Weitz, Matthew E Monroe, Ryan T Kelly, Richard D Smith, Erin Shammel Baker
To better understand disease conditions and environmental perturbations, multi-omic studies combining proteomic, lipidomic, and metabolomic analyses are vastly increasing in popularity. In a multi-omic study, a single sample is typically extracted in multiple ways and various analyses are performed using different instruments. Thus, one sample becomes many measurements, making high throughput and reproducible evaluations a necessity. One way to address the numerous samples and varying instrumental conditions is to utilize a flow injection analysis (FIA) system for rapid sample injection...
November 21, 2017: Analytical Chemistry
https://www.readbyqxmd.com/read/29161091/dealing-with-stress-defective-metabolic-adaptation-in-chronic-obstructive-pulmonary-disease-pathogenesis
#3
Charalambos Michaeloudes, Pankaj K Bhavsar, Sharon Mumby, Kian Fan Chung, Ian M Adcock
The mitochondrion is the main site of energy production and a hub of key signaling pathways. It is also central in stress-adaptive response due to its dynamic morphology and ability to interact with other organelles. In response to stress, mitochondria fuse into networks to increase bioenergetic efficiency and protect against oxidative damage. Mitochondrial damage triggers segregation of damaged mitochondria from the mitochondrial network through fission and their proteolytic degradation by mitophagy. Post-translational modifications of the mitochondrial proteome and nuclear cross-talk lead to reprogramming of metabolic gene expression to maintain energy production and redox balance...
November 2017: Annals of the American Thoracic Society
https://www.readbyqxmd.com/read/29161012/top-down-proteomics-ready-for-prime-time
#4
Bifan Chen, Kyle A Brown, Ziqing Lin, Ying Ge
In the post-genomics era, the study of proteins is critical for understanding cellular functions at the molecular level.1-5 Beyond the genetic code, the human proteome is greatly diversified by various genetic variations, alternative splicing of RNA transcripts, and post-translational modifi-cations (PTMs).6,7 In 2013, the term "proteoform" was designated to describe "all of the different molecular forms in which the protein product of a single gene can be found",6 clearing up the confusion in nomenclature and joining research efforts to develop methodologies for pro-teoform characterization...
November 21, 2017: Analytical Chemistry
https://www.readbyqxmd.com/read/29161009/a-sensitive-microbead-based-organic-media-assisted-method-for-proteomics-sample-preparation-from-dilute-and-denaturing-solutions
#5
Masato Taoka, Michihiko Fujii, Masahiro Tsuchiya, Takamasa Uekita, Tohru Ichimura
We developed a robust and sensitive sample preparation method for proteomics termed microbead-based and organic-media-assisted proteolysis strategy (BOPs). BOPs combine two advantages of current techniques, (1) unbiased binding of reversed-phase polymeric microbeads to any type of protein and (2) enhanced trypsin digestion efficiency in CH3CN-aqueous solvent systems, into a single-tube workflow. Compared with conventional techniques, this method effectively concentrates proteins and improves proteolytic digestion, and can be used with submicromolar protein samples in dilute and/or denaturing solutions such as 70 % formic acid, 8 M urea, or 7 M guanidine hydrochloride without any sample pretreatment...
November 21, 2017: ACS Applied Materials & Interfaces
https://www.readbyqxmd.com/read/29160079/a-comprehensive-mass-spectrometric-survey-of-streptococcus-pyogenes-subcellular-proteomes
#6
Laura Wilk, Lotta Happonen, Johan Malmström, Heiko Herwald
Streptococcus pyogenes is a major global health burden causing a wide variety of diseases. As a vaccine against this bacterium is still lacking, vaccine candidates or antimicrobial therapies are urgently needed. Here, we use an invasive and clinical relevant streptococcal M1 serotype in order to characterise the bacterial proteome in-depth. An elaborate fractionation technique is employed to separate the different cell fractions followed by shotgun mass spectrometry analysis, allowing us to confirm the expression of nearly two thirds (1022) of the 1690 open reading frames predicted for the streptococcal M1 reference proteome...
November 21, 2017: Journal of Proteome Research
https://www.readbyqxmd.com/read/29159954/unraveling-the-mechanistic-complexity-of-the-glomerulocystic-phenotype-in-dicer-conditional-ko-mice-by-2d-gel-electrophoresis-coupled-mass-spectrometry
#7
Claudia Vincenza Fiumara, Domenica Scumaci, Anna Iervolino, Angela Mena Perri, Antonio Concolino, Laura Tammè, Federica Petrillo, Giovambattista Capasso, Giovanni Cuda
PURPOSE: Dicer, an RNase III type endonuclease, is a key enzyme involved in miRNA biogenesis. It has been shown that this enzyme is essential for several aspects of postnatal kidney functions and homeostasis. In this study, we have examined conditional knockout (cKO) mice for Dicer in Pax8 (Paired-box gene 8) expressing cells to investigate the kidney protein profile. This specific model develops a glomerulocystic phenotype coupled with urinary concentration impairment, proteinuria and severe renal failure...
November 21, 2017: Proteomics. Clinical Applications
https://www.readbyqxmd.com/read/29159944/effect-of-iron-on-the-growth-of-phaeodactylum-tricornutum-via-photosynthesis
#8
Peipei Zhao, Wenhui Gu, Aiyou Huang, Songcui Wu, Changheng Liu, Li Huan, Shan Gao, Xiujun Xie, Guangce Wang
Iron is a limiting factor in the modern ocean, which is a major factor that controls the phytoplankton biomass of the ocean, and iron fertilization of the ocean could lead to blooms dominated by diatoms. Thus, iron plays an important role in controlling the distribution of diatoms. In this study, we measured the growth rate and photosynthetic activity of the model diatom Phaeodactylum tricornutum cultured under different iron concentrations and found that it grew more rapidly and had a much higher photosynthetic efficiency under higher iron concentrations...
November 21, 2017: Journal of Phycology
https://www.readbyqxmd.com/read/29159325/role-of-aramchol-in-steatohepatitis-and-fibrosis-in-mice
#9
Marta Iruarrizaga-Lejarreta, Marta Varela-Rey, David Fernández-Ramos, Ibon Martínez-Arranz, Teresa C Delgado, Jorge Simon, Virginia Gutiérrez-de Juan, Laura delaCruz-Villar, Mikel Azkargorta, José L Lavin, Rebeca Mayo, Sebastiaan M Van Liempd, Igor Aurrekoetxea, Xabier Buqué, Donatella Delle Cave, Arantza Peña, Juan Rodríguez-Cuesta, Ana M Aransay, Felix Elortza, Juan M Falcón-Pérez, Patricia Aspichueta, Liat Hayardeny, Mazen Noureddin, Arun J Sanyal, Cristina Alonso, Juan Anguita, María Luz Martínez-Chantar, Shelly C Lu, José M Mato
Nonalcoholic steatohepatitis (NASH) is the advanced form of nonalcoholic fatty liver disease (NAFLD) which sets the stage for further liver damage. The mechanism for the progression of NASH involves multiple parallel hits including oxidative stress, mitochondrial dysfunction, inflammation and others. Manipulation of any of these pathways may be an approach to prevent NASH development and progression. Aramchol (arachidyl-amido cholanoic acid) is presently in a phase IIb NASH study. The aim of this study was to investigate Aramchol's mechanism of action and its effect on fibrosis using the methionine- and choline-deficient (MCD) diet model of NASH...
November 2017: Hepatol Commun
https://www.readbyqxmd.com/read/29158881/serum-proteomic-profiling-of-obsessive-compulsive-disorder-washing-subtype-a-preliminary-study
#10
Mona Zamanian-Azodi, Mostafa Rezaei-Tavirani, Naser Nejadi, Afsaneh Arefi Oskouie, Faird Zayeri, Mostafa Hamdieh, Akram Safaei, Majid Rezaei-Tavirani, Alireza Ahmadzadeh, Alireza Amouzandeh-Nobaveh, Farshad Okhovatian
Introduction: Obsessive-Compulsive Disorder (OCD) is a disabling mental condition that its proteomic profiling is not yet investigated. Proteomics is a valuable tool to discover biomarker approaches. It can be helpful to detect protein expression changes in complex disorders such as OCD. Methods: Here, by the application of 2D gel electrophoresis (2DE), a pilot study of serum proteome profile of females with washing subtype of OCD was performed. Serum samples were obtained from females with washing subtype of OCD...
July 2017: Basic and Clinical Neuroscience
https://www.readbyqxmd.com/read/29158831/identification-and-validation-of-a-salivary-protein-panel-to-detect-heart-failure-early
#11
Xi Zhang, Terry Walsh, John J Atherton, Karam Kostner, Benjamin Schulz, Chamindie Punyadeera
BACKGROUND: Over 26 million people suffer from heart failure (HF) globally. Current diagnosis of HF relies on clinical evaluation, blood assays and imaging techniques. Our aim is to develop a diagnostic assay to detect HF in at risk individuals within the community using human saliva as a medium, potentially leading to a simple, safe early warning system. METHODS: Saliva samples were collected from healthy controls (n=36) and HF patients (n=75). Salivary proteome profiles were analysed by Sequential Window Acquisition of All Theoretical fragment ion spectra - Mass Spectrometry (SWATH-MS)...
2017: Theranostics
https://www.readbyqxmd.com/read/29158724/comparative-proteomic-analysis-between-nitrogen-supplemented-and-starved-conditions-in-magnaporthe-oryzae
#12
Yeonyee Oh, Suzanne L Robertson, Jennifer Parker, David C Muddiman, Ralph A Dean
Background: Fungi are constantly exposed to nitrogen limiting environments, and thus the efficient regulation of nitrogen metabolism is essential for their survival, growth, development and pathogenicity. To understand how the rice blast pathogen Magnaporthe oryzae copes with limited nitrogen availability, a global proteome analysis under nitrogen supplemented and nitrogen starved conditions was completed. Methods: M. oryzae strain 70-15 was cultivated in liquid minimal media and transferred to media with nitrate or without a nitrogen source...
2017: Proteome Science
https://www.readbyqxmd.com/read/29158562/highly-expressed-genes-evolve-under-strong-epistasis-from-a-proteome-wide-scan-in-e-coli
#13
Pouria Dasmeh, Éric Girard, Adrian W R Serohijos
Epistasis or the non-additivity of mutational effects is a major force in protein evolution, but it has not been systematically quantified at the level of a proteome. Here, we estimated the extent of epistasis for 2,382 genes in E. coli using several hundreds of orthologs for each gene within the class Gammaproteobacteria. We found that the average epistasis is ~41% across genes in the proteome and that epistasis is stronger among highly expressed genes. This trend is quantitatively explained by the prevailing model of sequence evolution based on minimizing the fitness cost of protein unfolding and aggregation...
November 20, 2017: Scientific Reports
https://www.readbyqxmd.com/read/29158489/yeast-display-biopanning-identifies-human-antibodies-targeting-glioblastoma-stem-like-cells
#14
Michael Zorniak, Paul A Clark, Benjamin J Umlauf, Yongku Cho, Eric V Shusta, John S Kuo
Glioblastoma stem-like cells (GSC) are hypothesized to evade current therapies and cause tumor recurrence, contributing to poor patient survival. Existing cell surface markers for GSC are developed from embryonic or neural stem cell systems; however, currently available GSC markers are suboptimal in sensitivity and specificity. We hypothesized that the GSC cell surface proteome could be mined with a yeast display antibody library to reveal novel immunophenotypes. We isolated an extensive collection of antibodies that were differentially selective for GSC...
November 20, 2017: Scientific Reports
https://www.readbyqxmd.com/read/29158431/salmonella-typhimurium-alters-the-extracellular-proteome-of-macrophages-and-leads-to-the-production-of-pro-inflammatory-exosomes
#15
Winnie W Hui, Kamil Hercik, Sayali Belsare, Navatha Alugubelly, Beata Clapp, Carlos Rinaldi, Mariola J Edelmann
Salmonella enterica serovar Typhimurium is a Gram-negative bacterium, which can invade and survive within macrophages. Pathogenic Salmonellae induce the secretion of specific cytokines from these phagocytic cells and interfere with the host secretory pathways. In this study, we describe the extracellular proteome of human macrophages infected with S. Typhimurium, followed by analysis of canonical pathways of proteins isolated from the extracellular milieu. We demonstrate that some of the proteins secreted by macrophages upon S...
November 20, 2017: Infection and Immunity
https://www.readbyqxmd.com/read/29158353/blood-pressure-control-by-a-secreted-fgfbp1-fibroblast-growth-factor-binding-protein
#16
Elena Tassi, En Yin Lai, Lingli Li, Glenn Solis, Yifan Chen, William E Kietzman, Patricio E Ray, Anna T Riegel, William J Welch, Christopher S Wilcox, Anton Wellstein
Fibroblast growth factors (FGFs) participate in organ development and tissue maintenance, as well as the control of vascular function. The paracrine-acting FGFs are stored in the extracellular matrix, and their release is controlled by a secreted FGF-binding protein (FGF-BP, FGFBP1, and BP1) that modulates FGF receptor signaling. A genetic polymorphism in the human FGFBP1 gene was associated with higher gene expression and an increased risk of familial hypertension. Here, we report on the effects of inducible BP1 expression in a transgenic mouse model...
November 20, 2017: Hypertension
https://www.readbyqxmd.com/read/29158290/a-comparative-proteome-profile-of-female-mouse-gonads-suggests-a-tight-link-between-the-electron-transport-chain-and-meiosis-initiation
#17
Cong Shen, Mingrui Li, Pan Zhang, Yueshuai Guo, Hao Zhang, Bo Zheng, Hui Teng, Tao Zhou, Xuejiang Guo, Ran Huo
Generation of haploid gametes by meiosis is a unique property of germ cells and is critical for sexual reproduction. Leaving mitosis and entering meiosis is a key step in germ cell development. Several inducers or intrinsic genes are known to be important for meiotic initiation, but the regulation of meiotic initiation, especially at the protein level, is still not well understood. We constructed a comparative proteome profile of female mouse fetal gonads at specific time points (11.5, 12.5, and 13.5 days post coitum), spanning a critical window for initiation of meiosis in female germ cells...
November 20, 2017: Molecular & Cellular Proteomics: MCP
https://www.readbyqxmd.com/read/29158248/pregnancy-increases-norbuprenorphine-clearance-in-mice-by-induction-of-hepatic-glucuronidation
#18
Michael Z Liao, Chunying Gao, Brian R Phillips, Naveen K Neradugomma, Lyrialle W Han, Deepak Kumar Bhatt, Bhagwat Prasad, Danny D Shen, Qingcheng Mao
Norbuprenorphine (NBUP) is the major active metabolite of buprenorphine (BUP) which is commonly used to treat opiate addiction during pregnancy; it possesses 25% of BUP's analgesic activity and 10 times BUP's respiratory depression effect. To optimize BUP's dosing regimen during pregnancy with better efficacy and safety, it is important to understand how pregnancy affects NBUP disposition. In this study, we examined the pharmacokinetics of NBUP in pregnant and non-pregnant mice by administering the same amount of NBUP through retro-orbital injection...
November 20, 2017: Drug Metabolism and Disposition: the Biological Fate of Chemicals
https://www.readbyqxmd.com/read/29158195/understanding-missing-proteins-a-functional-perspective
#19
REVIEW
Longjian Zhou, Limsoon Wong, Wilson Wen Bin Goh
A missing protein (MP) is an unconfirmed genetic sequence for which a protein product is not yet detected. Currently, MPs are tiered based on supporting evidence mainly in the form of protein existence (PE) classification. As we discuss here, this definition is overly restrictive because proteins go missing in day-to-day proteomics as a result of low abundance, lack of sequence specificity, splice variants, and so on. Thus, we propose a broader functional classification of MPs that complements PE classification, discuss major causes, and examine three corresponding solution tiers:...
November 17, 2017: Drug Discovery Today
https://www.readbyqxmd.com/read/29158163/identification-of-tissue-damage-extracellular-matrix-remodeling-and-bacterial-challenge-as-common-mechanisms-associated-with-high-risk-cutaneous-squamous-cell-carcinomas
#20
Melanie C Föll, Matthias Fahrner, Christine Gretzmeier, Käthe Thoma, Martin L Biniossek, Dimitra Kiritsi, Frank Meiss, Oliver Schilling, Alexander Nyström, Johannes S Kern
In this study we used a genetic extracellular matrix (ECM) disease to identify mechanisms associated with aggressive behavior of cutaneous squamous cell carcinoma (cSCC). cSCC is one of the most common malignancies and usually has a good prognosis. However, some cSCCs recur or metastasize and cause significant morbidity and mortality. Known factors that are associated with aggressiveness of cSCCs include tumor grading, size, localization and microinvasive behavior. To investigate molecular mechanisms that influence biologic behavior we used global proteomic and histologic analyses of formalin-fixed paraffin-embedded tissue of primary human cSCCs...
November 17, 2017: Matrix Biology: Journal of the International Society for Matrix Biology
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