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https://www.readbyqxmd.com/read/28822142/-prospects-of-molecular-breeding-in-medical-plants
#1
REVIEW
Xiao-Jun Ma, Chang-Ming Mo
The molecular-assisted breeding, transgenic breeding and molecular designing breeding are three development directions of plant molecular breeding. Base on these three development directions, this paper summarizes developing status and new tendency of research field of genetic linkage mapping, QTL mapping, association mapping, molecular-assisted selections, pollen-mediated transformations, agrobacterium-mediated transformations, particle gun-mediated transformations, genome editing technologies, whole-genome sequencing, transcriptome sequencing, proteome sequencing and varietal molecular designing...
June 2017: Zhongguo Zhong Yao za Zhi, Zhongguo Zhongyao Zazhi, China Journal of Chinese Materia Medica
https://www.readbyqxmd.com/read/28822126/dimethyl-labeling-based-quantification-of-the-lysine-acetylome-and-proteome-of-plants
#2
Ines Lassowskat, Markus Hartl, Fabian Hosp, Paul J Boersema, Matthias Mann, Iris Finkemeier
Photorespiratory enzymes in different cellular compartments have been reported to be posttranslational modified by phosphorylation, disulfide formation, S-nitrosylation, glutathionylation, and lysine acetylation. However, not much is known yet about the function of these modifications to regulate the activities, localizations, or interactions of the proteins in this metabolic pathway. Hence, it will be of great importance to study these modifications and their temporal and conditional occurrence in more detail...
2017: Methods in Molecular Biology
https://www.readbyqxmd.com/read/28821884/the-atopic-dermatitis-blood-signature-is-characterized-by-increases-in-inflammatory-and-cardiovascular-risk-proteins
#3
Patrick M Brunner, Mayte Suárez-Fariñas, Helen He, Kunal Malik, Huei-Chi Wen, Juana Gonzalez, Tom Chih-Chieh Chan, Yeriel Estrada, Xiuzhong Zheng, Saakshi Khattri, Nancy Dattola, James G Krueger, Emma Guttman-Yassky
Beyond classic "allergic"/atopic comorbidities, atopic dermatitis (AD) emerges as systemic disease with increased cardiovascular risk. To better define serum inflammatory and cardiovascular risk proteins, we used an OLINK high-throughput proteomic assay to analyze moderate-to-severe AD (n = 59) compared to psoriasis (n = 22) and healthy controls (n = 18). Compared to controls, 10 proteins were increased in serum of both diseases, including Th1 (IFN-γ, CXCL9, TNF-β) and Th17 (CCL20) markers. 48 proteins each were uniquely upregulated in AD and psoriasis...
August 18, 2017: Scientific Reports
https://www.readbyqxmd.com/read/28821844/n-glycosylation-triggers-a-dual-selection-pressure-in-eukaryotic-secretory-proteins
#4
Máximo Lopez Medus, Gabriela E Gomez, Lucía F Zacchi, Paula M Couto, Carlos A Labriola, María S Labanda, Rodrigo Corti Bielsa, Eugenia M Clérico, Benjamin L Schulz, Julio J Caramelo
Nearly one third of the eukaryotic proteome traverses the secretory pathway and most of these proteins are N-glycosylated in the lumen of the endoplasmic reticulum. N-glycans fulfill multiple structural and biological functions, and are crucial for productive folding of many glycoproteins. N-glycosylation involves the attachment of an oligosaccharide to selected asparagine residues in the sequence N-X-S/T (X ≠ P), a motif known as an N-glycosylation'sequon'. Mutations that create novel sequons can cause disease due to the destabilizing effect of a bulky N-glycan...
August 18, 2017: Scientific Reports
https://www.readbyqxmd.com/read/28821836/porv-is-an-outer-membrane-shuttle-protein-for-the-type-ix-secretion-system
#5
Michelle D Glew, Paul D Veith, Dina Chen, Dhana G Gorasia, Ben Peng, Eric C Reynolds
Porphyromonas gingivalis is a keystone pathogen associated with chronic periodontitis. Major virulence factors named gingipains (cysteine proteinases, RgpA, RgpB and Kgp) are secreted via the Type IX Secretion System (T9SS). These, together with approximately 30 other proteins, are secreted to the cell surface and anchored to the outer membrane by covalent modification to anionic lipopolysaccharide (A-LPS) via the novel Gram negative sortase, PorU. PorU is localised on the cell surface and cleaves the C-terminal domain signal (CTD) of T9SS substrates and conjugates their new C-termini to A-LPS...
August 18, 2017: Scientific Reports
https://www.readbyqxmd.com/read/28821815/epac1-deficient-mice-have-bleeding-phenotype-and-thrombocytes-with-decreased-gpib%C3%AE-expression
#6
Gyrid Nygaard, Lars Herfindal, Kathrine S Asrud, Ronja Bjørnstad, Reidun K Kopperud, Eystein Oveland, Frode S Berven, Lene Myhren, Erling A Hoivik, Turid Helen Felli Lunde, Marit Bakke, Stein O Døskeland, Frode Selheim
Epac1 (Exchange protein directly activated by cAMP 1) limits fluid loss from the circulation by tightening the endothelial barrier. We show here that Epac1(-/-) mice, but not Epac2(-/-) mice, have prolonged bleeding time, suggesting that Epac1 may limit fluid loss also by restraining bleeding. The Epac1(-/-) mice had deficient in vitro secondary hemostasis. Quantitative comprehensive proteomics analysis revealed that Epac1(-/-) mouse platelets (thrombocytes) had unbalanced expression of key components of the glycoprotein Ib-IX-V (GPIb-IX-V) complex, with decrease of GP1bβ and no change of GP1bα...
August 18, 2017: Scientific Reports
https://www.readbyqxmd.com/read/28821813/metabolomic-and-lipidomic-profiling-identifies-the-role-of-the-rna-editing-pathway-in-endometrial-carcinogenesis
#7
Tatiana Altadill, Tyrone M Dowdy, Kirandeep Gill, Armando Reques, Smrithi S Menon, Cristian P Moiola, Carlos Lopez-Gil, Eva Coll, Xavier Matias-Guiu, Silvia Cabrera, Angel Garcia, Jaume Reventos, Stephen W Byers, Antonio Gil-Moreno, Amrita K Cheema, Eva Colas
Endometrial cancer (EC) remains the most common malignancy of the genital tract among women in developed countries. Although much research has been performed at genomic, transcriptomic and proteomic level, there is still a significant gap in the metabolomic studies of EC. In order to gain insights into altered metabolic pathways in the onset and progression of EC carcinogenesis, we used high resolution mass spectrometry to characterize the metabolomic and lipidomic profile of 39 human EC and 17 healthy endometrial tissue samples...
August 18, 2017: Scientific Reports
https://www.readbyqxmd.com/read/28821744/exploring-the-sequence-based-prediction-of-folding-initiation-sites-in-proteins
#8
Daniele Raimondi, Gabriele Orlando, Rita Pancsa, Taushif Khan, Wim F Vranken
Protein folding is a complex process that can lead to disease when it fails. Especially poorly understood are the very early stages of protein folding, which are likely defined by intrinsic local interactions between amino acids close to each other in the protein sequence. We here present EFoldMine, a method that predicts, from the primary amino acid sequence of a protein, which amino acids are likely involved in early folding events. The method is based on early folding data from hydrogen deuterium exchange (HDX) data from NMR pulsed labelling experiments, and uses backbone and sidechain dynamics as well as secondary structure propensities as features...
August 18, 2017: Scientific Reports
https://www.readbyqxmd.com/read/28821634/lipidomic-and-proteomic-analysis-of-exosomes-from-mouse-cortical-collecting-duct-cells
#9
Viet D Dang, Kishore Kumar Jella, Ragy R T Ragheb, Nancy D Denslow, Abdel A Alli
Exosomes are endosome-derived nanovesicles that are involved in cellular communication and signaling. Exosomes are produced by epithelial cells and are found in biologic fluids including blood and urine. The packaged material within exosomes includes proteins and lipids, but the molecular comparison within exosome subtypes is largely unknown. The purpose of this study was to investigate differences between exosomes derived from the apical plasma membrane and basolateral plasma membrane of polarized murine cortical collecting duct principal cells...
August 16, 2017: FASEB Journal: Official Publication of the Federation of American Societies for Experimental Biology
https://www.readbyqxmd.com/read/28821611/the-proteasome-interacting-ecm29-protein-disassembles-the-26s-proteasome-in-response-to-oxidative-stress
#10
Xiaorong Wang, Ilan E Chemmama, Clinton Yu, Alexander Huszagh, Yue Xu, Rosa Viner, Sarah Ashley Block, Peter Cimermancic, Scott D Rychnovsky, Yihong Ye, Andrej Sali, Lan Huang
Oxidative stress has been implicated in multiple human neurological and other disorders. Proteasomes are multi-subunit proteases critical for the removal of oxidatively damaged proteins. To understand stress-associated human pathologies, it is important to uncover the molecular events underlying the regulation of proteasomes upon oxidative stress. To this end, we investigated H2O2 stress-induced molecular changes of the human 26S proteasome and determined that stress-induced 26S proteasome disassembly is conserved from yeast to human...
August 15, 2017: Journal of Biological Chemistry
https://www.readbyqxmd.com/read/28821603/a-simple-light-isotope-metabolic-labeling-slim-labeling-strategy-a-powerful-tool-to-address-the-dynamics-of-proteome-variations-in-vivo
#11
Thibaut Léger, Camille Garcia, Laetitia Collomb, Jean-Michel Camadro
Many quantitative proteomics strategies rely on in vivo metabolic incorporation of amino acids with modified stable isotope profiles into proteins. These methods give rise to multiple ions for each peptide, with possible distortion of the isotopolog distribution, making the overall analytical process complex. We validated an alternative strategy, simple light isotope metabolic labeling (SLIM-labeling), which alleviates many of these problems. SLIM-labeling is based on the in vivo reduction of the isotopic composition of proteins using metabolic precursors with a unique light isotope composition to label all amino acids...
August 18, 2017: Molecular & Cellular Proteomics: MCP
https://www.readbyqxmd.com/read/28821602/large-scale-proteomics-combined-with-transgenic-experiments-demonstrates-an-important-role-of-jasmonic-acid-nbsp-in-potassium-nbsp-deficiency-response-in-wheat-and-rice
#12
Gezi Li, Yufang Wu, Guoyu Liu, Xianghong Xiao, Pengfei Wang, Tian Gao, Mengjun Xu, Qiaoxia Han, Yonghua Wang, Tiancai Guo, Guozhang Kang
Potassium (K+) is the most abundant inorganic cation in plants, and molecular dissection of K+ deficiency has received considerable interest in order to minimize K+ fertilizer input and develop high quality K+-efficient crops. However, the molecular mechanism of plant responses to K+ deficiency is still poorly understood. In this study, two-week-old bread wheat seedlings grown hydroponically in Hoagland solution were transferred to K+-free conditions for 8 d, and their root and leaf proteome profiles were assessed using the iTRAQ proteome method...
August 18, 2017: Molecular & Cellular Proteomics: MCP
https://www.readbyqxmd.com/read/28821601/high-sensitivity-quantitative-proteomics-using-automated-multidimensional-nano-flow-chromatography-and-accumulated-ion-monitoring-on-quadrupole-orbitrap-linear-ion-trap-mass-spectrometer
#13
Paolo Cifani, Alex Kentsis
Quantitative proteomics using high-resolution and accuracy mass spectrometry promises to transform our understanding of biological systems and disease. Recent development of parallel reaction monitoring (PRM) using hybrid instruments substantially improved the specificity of targeted mass spectrometry. Combined with high-efficiency ion trapping, this approach also provided significant improvements in sensitivity. Here, we investigated the effects of ion isolation and accumulation on the sensitivity and quantitative accuracy of targeted proteomics using the recently developed hybrid quadrupole-Orbitrap-linear ion trap mass spectrometer...
August 18, 2017: Molecular & Cellular Proteomics: MCP
https://www.readbyqxmd.com/read/28821582/identification-of-%C3%AE-enolase-as-a-prognostic-and-diagnostic-precancer-biomarker-in-oral-submucous-fibrosis
#14
Swarnendu Bag, Debabrata Dutta, Amrita Chaudhary, Bidhan Chandra Sing, Mousumi Pal, Ajoy Kumar Ray, Rita Banerjee, Ranjan Rashmi Paul, Amit Basak, Amit Kumar Das, Jyotirmoy Chatterjee
AIMS: Diagnostic ambiguities regarding the malignant potentiality of oral submucous fibrosis (OSF), an oral precancerous condition having dysplastic and non-dysplastic isoforms are the major failure for early intervention of oral squamous cell carcinoma (OSCC) patients. Our goal is to identify proteomic signatures from biopsies that can be used as precancer diagnostic marker for patient suffering from OSF. METHODS: The high throughput techniques adopting de novo peptide sequencing (1D SDS-PAGE coupled nanoLC MALDI tandem mass spectrometry (MS/MS)-based peptide mass fingerprint), immunohistochemistry (IHC), Western blot (WB) and real-time PCR (RT-PCR) analysis are considered for such biomarker identification and multilevel validations...
August 18, 2017: Journal of Clinical Pathology
https://www.readbyqxmd.com/read/28820984/identification-of-m-tuberculosis-antigens-in-the-sera-of-tuberculosis-patients-using-biomimetic-affinity-chromatography-in-conjunction-with-esi-cid-ms-ms
#15
Guorong Ma, Jinting Pan, Jincheng Han, Lina Gao, Shulin Zhang, Rongxiu Li
The profiling of abnormally-expressed proteins in host cells using mass spectrometry (MS) analysis is a classical approach for screening disease-associated biomarkers in clinical diagnosis. However, few pathogen-specific antigens can currently be detected in serum using this proteomic approach, since these are very low-abundant proteins that are easily masked by host high-abundant proteins. Identification of pathogen-specific antigens in the sera of tuberculosis patients is crucial for the clinical diagnosis of this infectious disease, especially in immune-compromised patients...
July 31, 2017: Journal of Chromatography. B, Analytical Technologies in the Biomedical and Life Sciences
https://www.readbyqxmd.com/read/28820946/proteogenomic-investigation-of-strain-variation-in-clinical-mycobacterium-tuberculosis-isolates
#16
Tiaan Heunis, Anzaan Dippenaar, Robin M Warren, Paul D van Helden, Ruben G van der Merwe, Nicolaas C Gey van Pittius, Arnab Pain, Samantha L Sampson, David L Tabb
Mycobacterium tuberculosis consists of a large number of different strains that display unique virulence characteristics. Whole-genome sequencing has revealed substantial genetic diversity among clinical M. tuberculosis isolates, and elucidating the phenotypic variation encoded by this genetic diversity will be of utmost importance to fully understand M. tuberculosis biology and pathogenicity. In this study we integrated whole-genome sequencing and mass spectrometry (GeLC-MS/MS) to reveal strain-specific characteristics in the proteomes of two clinical M...
August 18, 2017: Journal of Proteome Research
https://www.readbyqxmd.com/read/28820493/marine-lipids-on-cardiovascular-diseases-and-other-chronic-diseases-induced-by-diet-an-insight-provided-by-proteomics-and-lipidomics
#17
REVIEW
Lucía Méndez, Gabriel Dasilva, Nùria Taltavull, Marta Romeu, Isabel Medina
Marine lipids, especially ω-3 polyunsaturated fatty acids (PUFAs) eicosapentaenoic acid (EPA) and docosahexaenoic acid (DHA), have largely been linked to prevention of diet-induced diseases. The anti-inflammatory and hypolipidemic properties of EPA and DHA supplementation have been well-described. However, there is still a significant lack of information about their particular mechanism of action. Furthermore, repeated meta-analyses have not shown conclusive results in support of their beneficial health effects...
August 18, 2017: Marine Drugs
https://www.readbyqxmd.com/read/28820483/a-microsomal-proteomics-view-of-h%C3%A2-o%C3%A2-and-aba-dependent-responses
#18
May Alqurashi, Ludivine Thomas, Chris Gehring, Claudius Marondedze
The plant hormone abscisic acid (ABA) modulates a number of plant developmental processes and responses to stress. In planta, ABA has been shown to induce reactive oxygen species (ROS) production through the action of plasma membrane-associated nicotinamide adenine dinucleotide phosphate (NADPH)-oxidases. Although quantitative proteomics studies have been performed to identify ABA- or hydrogen peroxide (H₂O₂)-dependent proteins, little is known about the ABA- and H₂O₂-dependent microsomal proteome changes...
August 18, 2017: Proteomes
https://www.readbyqxmd.com/read/28820294/k-deficiency-caused-defects-in-renal-tubular-cell-proliferation-oxidative-stress-response-tissue-repair-and-tight-junction-integrity-but-enhanced-energy-production-proteasome-function-and-cellular-k-uptake
#19
Chompunoot Kapincharanon, Visith Thongboonkerd
Hypokalemia is a common electrolyte disorder in hospitalized patients and those with chronic diseases and is associated with renal tubular injury. Our recent expression proteomics study revealed changes in levels of several proteins in renal tubular cells during K(+) deficiency. However, functional significance and mechanisms underlying such changes remained unclear. The present study, thus, aimed to investigate functional changes of renal tubular cells induced by K(+) deficiency. MDCK cells were maintained in normal-K(+) (ANK; [K(+)] = 5...
August 18, 2017: Cell Adhesion & Migration
https://www.readbyqxmd.com/read/28820289/recent-advances-in-quantitative-and-chemical-proteomics-for-autophagy-studies
#20
Yin-Kwan Wong, Jianbin Zhang, Zi-Chun Hua, Qingsong Lin, Han-Ming Shen, Jigang Wang
Macroautophagy/autophagy is an evolutionarily well-conserved cellular degradative process with important biological functions that is closely implicated in health and disease. In recent years, quantitative mass spectrometry-based proteomics and chemical proteomics have emerged as important tools for the study of autophagy, through large-scale unbiased analysis of the proteome or through highly specific and accurate analysis of individual proteins of interest. At present, a variety of approaches have been successfully applied, including (i) expression and interaction proteomics for the study of protein post-translational modifications, (ii) investigating spatio-temporal dynamics of protein synthesis and degradation, and (iii) direct determination of protein activity and profiling molecular targets in the autophagic process...
August 18, 2017: Autophagy
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