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Mass Spectrometric Proteomics

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ISBN: 9783038978268 9783038978275 Year: Pages: 192 DOI: 10.3390/books978-3-03897-827-5 Language: English
Publisher: MDPI - Multidisciplinary Digital Publishing Institute
Subject: Medicine (General) --- Therapeutics
Added to DOAB on : 2019-04-25 16:37:17
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As suggested by the title of this Special Issue, liquid chromatography-mass spectrometry plays a pivotal role in the field of proteomics. Indeed, the research and review articles  published in the Issue clearly evidence how the data produced by this sophisticated methodology may promote impressive advancements in this area. From among the topics discussed in the Issue, a few point to the development of  new procedures for the  optimization of the experimental conditions that should be applied  for the identification of proteins present in complex mixtures.  Other applications  described in these articles show  the huge potential of  these strategies in the protein profiling of organs and  range from  to the study of post-translational tissue modifications to the investigation of the molecular mechanisms behind human disorders and the identification of potential biomarkers of these diseases.

Plant Protein and Proteome Altlas--Integrated Omics Analyses of Plants under Abiotic Stresses

Authors: --- --- --- --- et al.
ISBN: 9783039219605 / 9783039219612 Year: Pages: 558 DOI: 10.3390/books978-3-03921-961-2 Language: eng
Publisher: MDPI - Multidisciplinary Digital Publishing Institute
Subject: Science (General) --- Biology --- Botany
Added to DOAB on : 2020-06-09 16:38:57
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Integrative omics of plants in response to stress conditions play more crucial roles in the post-genomic era. High-quality genomic data provide more deeper understanding of how plants to survive under environmental stresses. This book is focused on concluding the recent progress in the Protein and Proteome Atlas in plants under different stresses. It covers various aspects of plant protein ranging from agricultural proteomics, structure and function of proteins, and approaches for protein identification and quantification.

Keywords

proteomic --- postharvest freshness --- ATP synthase --- ATP synthase CF1 alpha subunit (chloroplast) --- chlorophyll fluorescence parameters --- photosynthetic parameters --- drought stress --- Triticum aestivum L. --- comparative proteomic analysis --- iTRAQ --- VIGS --- Jatropha curcas --- phosphoproteomics --- seedling --- chilling stress --- regulated mechanism --- Alternanthera philoxeroides --- proteomic --- stem --- potassium --- stress --- Salinity stress --- Dunaliella salina --- isobaric tags for relative and absolute quantitation --- differentially abundant proteins --- proteomics --- arbuscular mycorrhizal fungi --- salt stress --- E. angustifolia --- proteomics --- wheat --- root --- wood vinegar --- drought stress --- ROS --- ABA --- proteome --- maize --- AGPase --- phosphorylation --- brittle-2 --- phos-tagTM --- MIPS --- exon-intron structure diversity --- Gossypium hirsutum --- loss-of-function mutant --- root cell elongation --- CHA-SQ-1 --- cytomorphology --- pollen abortion --- proteomics --- wheat --- cotton --- somatic embryogenesis --- transdifferentiation --- quantitative proteomics --- regulation and metabolism --- molecular basis --- concerted network --- maize --- phosphoproteomics --- salt tolerance --- label-free quantification --- root and shoot --- sugar beet --- salt stress --- S-adenosylmethionine decarboxylase --- ROS --- antioxidant enzyme --- cotton --- somatic embryogenesis --- transdifferentiation --- widely targeted metabolomics --- purine metabolism --- flavonoid biosynthesis --- molecular and biochemical basis --- transcript-metabolite network --- leaf sheath --- maturation --- transcriptional dynamics --- transcriptome --- abiotic stress --- silicate limitation --- diatom --- iTRAQ --- proteomics --- photosynthesis --- carbon fixation --- natural rubber biosynthesis --- mass spectrometry --- rubber grass --- rubber latex --- shotgun proteomics --- Taraxacum kok-saghyz --- two-dimensional gel electrophoresis --- visual proteome map --- proteomics --- wheat --- drought --- leaf --- iTRAQ --- micro-exons --- constitutive splicing --- alternative splicing --- ancient genes --- domain --- radish --- heat stress --- transcriptome sequencing --- lncRNA --- miRNA --- physiological response --- Millettia pinnata --- woody oilseed plants --- seed development --- miRNA --- nitrogen fertilizer --- rice --- proteome --- cultivars --- nitrogen use efficiency (NUE) --- Nelumbo nucifera --- phylogeny --- genomics --- molecular mechanisms --- model plant --- proteomes --- iTRAQ --- filling kernel --- drought stress --- heat shock proteins --- Zea mays L. --- wucai --- low-temperature stress --- high-temperature stress --- proteomics --- redox homeostasis --- GLU1 --- glutathione --- heat response --- heat-sensitive spinach variety --- proteomics --- ROS scavenging --- inositol --- phosphatidylinositol --- phosphatase --- stress --- signaling pathway --- integrated omics --- plants under stress --- post-genomics era --- proteome atlas --- quantitative proteomics

Plant Proteomic Research 2.0

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ISBN: 9783039210626 9783039210633 Year: Pages: 594 DOI: 10.3390/books978-3-03921-063-3 Language: English
Publisher: MDPI - Multidisciplinary Digital Publishing Institute
Subject: Science (General) --- Biology --- Plant Sciences
Added to DOAB on : 2019-06-26 08:44:07
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Advancements in high-throughput “Omics” techniques have revolutionized plant molecular biology research. Proteomics offers one of the best options for the functional analysis of translated regions of the genome, generating a wealth of detailed information regarding the intrinsic mechanisms of plant stress responses. Various proteomic approaches are being exploited extensively for elucidating master regulator proteins which play key roles in stress perception and signaling, and these approaches largely involve gel-based and gel-free techniques, including both label-based and label-free protein quantification. Furthermore, post-translational modifications, subcellular localization, and protein–protein interactions provide deeper insight into protein molecular function. Their diverse applications contribute to the revelation of new insights into plant molecular responses to various biotic and abiotic stressors.

Keywords

Phalaenopsis --- petal --- pollination --- senescence --- 2-DE --- ROS --- Medicago sativa --- leaf cell wall proteome --- cadmium --- quantitative proteomics --- 2D DIGE --- chloroplast --- elevated CO2 --- heat stress --- nucleotide pyrophosphatase/phosphodiesterase --- (phospho)-proteomics --- photosynthesis --- protein phosphorylation --- 14-3-3 proteins --- Oryza sativa L. --- starch --- sucrose --- N utilization efficiency --- proteomics --- 2D --- protein phosphatase --- rice isogenic line --- SnRK1 --- 14-3-3 --- lettuce --- bolting --- proteome --- high temperature --- iTRAQ --- proteome profiling --- iTRAQ --- differentially abundant proteins (DAPs) --- drought stress --- physiological responses --- Zea mays L. --- GS3 --- ? subunit --- heterotrimeric G protein --- mass spectrometric analysis --- RGG3 --- rice --- western blotting --- Dn1-1 --- ?-subunit --- heterotrimeric G protein --- mass spectrometry analysis --- RGG4 --- rice --- western blotting --- Clematis terniflora DC. --- polyphenol oxidase --- virus induced gene silencing --- photosynthesis --- glycolysis --- Camellia sinensis --- chlorotic mutation --- chlorophyll deficiency --- weakening of carbon metabolism --- iTRAQ --- proteomics --- degradome --- wheat --- cultivar --- protease --- papain-like cysteine protease (PLCP) --- subtilase --- metacaspase --- caspase-like --- wheat leaf rust --- Puccinia recondita --- Stagonospora nodorum --- iTRAQ --- proteomics --- somatic embryogenesis --- pyruvate biosynthesis --- Zea mays --- chlorophylls --- LC-MS-based proteomics --- pea (Pisum sativum L.) --- proteome functional annotation --- proteome map --- seeds --- seed proteomics --- late blight disease --- potato proteomics --- Phytophthora infestans --- Sarpo Mira --- early and late disease stages --- Simmondsia chinensis --- cold stress --- proteomics --- leaf --- iTRAQ --- Ricinus communis L. --- cold stress --- seed imbibition --- iTRAQ --- proteomics --- Morus --- organ --- gel-free/label-free proteomics --- flavonoid --- antioxidant activity --- phosphoproteome --- barley --- seed dormancy --- germination --- imbibition --- after-ripening --- sugarcane --- Sporisorium scitamineum --- smut --- proteomics --- RT-qPCR --- ISR --- holm oak --- Quercus ilex --- 2-DE proteomics --- shotgun proteomics --- non-orthodox seed --- population variability --- stresses responses --- ammonium --- Arabidopsis thaliana --- carbon metabolism --- nitrogen metabolism --- nitrate --- proteomics --- root --- secondary metabolism --- proteomics --- wheat --- silver nanoparticles --- plant pathogenesis responses --- data-independent acquisition --- quantitative proteomics --- Pseudomonas syringae --- sweet potato plants infected by SPFMV --- SPV2 and SPVG --- sweet potato plants non-infected by SPFMV --- SPV2 and SPVG --- co-infection --- transcriptome profiling --- gene ontology --- pathway analysis --- lesion mimic mutant --- leaf spot --- phenylpropanoid biosynthesis --- proteomics --- isobaric tags for relative and absolute quantitation (iTRAQ) --- rice --- affinity chromatography --- ergosterol --- fungal perception --- innate immunity --- pattern recognition receptors --- plasma membrane --- proteomics --- proteomics --- maize --- plant-derived smoke --- shoot --- Solanum tuberosum --- patatin --- seed storage proteins --- vegetative storage proteins --- tuber phosphoproteome --- targeted two-dimensional electrophoresis --- B. acuminata petals --- MALDI-TOF/TOF --- GC-TOF-MS --- qRT-PCR --- differential proteins --- n/a

Neuroproteomics

Authors: ---
ISBN: 9783039281060 9783039281077 Year: Pages: 318 DOI: 10.3390/books978-3-03928-107-7 Language: English
Publisher: MDPI - Multidisciplinary Digital Publishing Institute
Subject: Medicine (General) --- Neurology
Added to DOAB on : 2020-04-07 23:07:08
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The Neuroproteomics Special Issue overviews the unique challenges that must be addressed to carry out meaningful MS/proteomics analyses on neural tissues and the technologies that are available to meet these challenges. The articles on Alzheimer’s disease, addiction, and schizophrenia illustrate how MS/proteomics technologies can be used to improve our ability to diagnose and understand the molecular basis for neurological diseases. Several articles will be of interest to investigators beyond the field of neurological disorders. The review on the discovery of biofluid biomarkers of neurodegenerative dementias will be of interest to investigators searching for other disease biomarkers. Similarly, the review on the role of neuroproteomics in elucidating mechanisms of drug addiction provides an overview of the utility of MS/proteomics approaches for addressing critical questions in addiction neuroscience that should be applicable to investigators involved in virtually any area of biomedical research. Likewise, the article on developing targeted MS approaches for quantifying postsynaptic density proteins will be useful for any investigator who wishes to design targeted assays for virtually any protein. Finally, the peroxidase-mediated proximity labeling technology, described in the article on mapping the proteome of the synaptic cleft, will be of interest to investigators interested in mapping other spatially restricted proteomes.

Keywords

proteomics --- basal ganglia --- synapses --- synapse specificity --- neuronal circuits --- axons --- dendrites --- neurodegeneration --- synapse --- postsynaptic --- proteome --- mass spectrometry --- protein interaction networks --- connectome --- neurodegeneration --- Alzheimer’s disease --- cerebrospinal fluid --- plasma --- serum --- proteomics --- biomarkers --- LC-MS/MS --- cocaine --- addiction --- cytokine --- neuroimmune --- ventral tegmental area --- peptidylglycine ?-amidating monooxygenase --- cilia --- mating --- signal peptide --- prohormone convertase --- carboxypeptidase --- matrix metalloproteinase --- subtilisin --- pherophorin --- morphine --- opioid receptors --- conformational antibody --- analgesia --- GPCR signaling --- phosphorylation --- AMPA receptor complex --- transmembrane AMPA receptor regulatory protein --- synaptic plasticity --- adolescence --- corticosterone --- proteomics --- yohimbine --- progressive ratio --- reinstatement --- ethanol --- nicotinic receptor --- CaMKII --- PKA --- quantitative phosphoproteomics --- mouse --- phosphorylation --- nicotine --- proteomics --- proteome --- mass spectrometry --- Alzheimer’s disease --- protein aggregation --- laser capture microdissection --- splicing --- U1 snRNP --- synapse --- synaptic cleft --- trans-synaptic adhesion --- proximity labeling --- SynCAM --- Cadm --- Receptor-type tyrosine-protein phosphatase zeta --- R-PTP-zeta --- Ptprz1 --- neuroproteome --- drug abuse --- neuropeptidomics --- phosphorylation --- interactome --- cell type --- neuroscience --- proteomics --- mass spectrometry --- neuron --- proximity labeling --- affinity chromatography --- neuroproteomics --- biotinylation --- amphetamine --- spinophilin --- protein phosphatase-1 --- dopamine --- striatum --- mass spectroscopy --- bioinformatics --- FGF14 --- voltage gated channels --- schizophrenia --- autism --- Alzheimer’s Disease --- sex-specific differences --- synaptic plasticity --- cognitive impairment --- excitatory/inhibitory tone --- n/a --- postsynaptic density --- PSD --- parallel reaction monitoring --- PRM --- targeted proteomics --- data-independent acquisition --- DIA --- quantitative mass spectrometry --- n/a

Marine Natural Products and Obesity

Authors: ---
ISBN: 9783039211913 9783039211920 Year: Pages: 194 DOI: 10.3390/books978-3-03921-192-0 Language: English
Publisher: MDPI - Multidisciplinary Digital Publishing Institute
Subject: Medicine (General) --- Internal medicine
Added to DOAB on : 2019-08-28 11:21:27
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Obesity and related co-morbidities are increasing worldwide and pose a serious health problem. Changes in lifestyle and diet would be the best remedies to fight obesity; however, many people will still rely on medical aid. Marine organisms have been prolific in the production of bioactive compounds for many diseases, e.g., cancer, and promise to be an excellent source for natural-derived molecules and novel nutraceuticals. Bioactive compounds with beneficial activities towards obesity have been described from diverse marine organism including marine algae, bacteria, sponges, fungi, crustaceans or fish. This Special Issue will highlight the progress in the following topics: Bioactive compounds for the treatment of obesity and obesity-related co-morbidities (diabetes, fatty liver, hyperlipidemia) from marine organisms; the isolation of novel compounds, the bioactivity screening of marine organisms and the elucidation of molecular mode of action of marine bioactive compounds.

Arthropod Venom Components and Their Potential Usage

Authors: ---
ISBN: 9783039285402 9783039285419 Year: Pages: 404 DOI: 10.3390/books978-3-03928-541-9 Language: English
Publisher: MDPI - Multidisciplinary Digital Publishing Institute
Subject: Public Health --- Medicine (General)
Added to DOAB on : 2020-04-07 23:07:09
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Thousands of arthropod species, ranging from arachnids (spiders and scorpions) to hymenopterans (ants, bees, and wasps) and myriapods (centipedes), are venomous and use their venoms for both defense and predation. These venoms are invariably harmful to humans, and some may cause serious injuries, e.g., those from scorpions, spiders, and wasps. Arthropods’ venoms are also known as rich sources of biologically active compounds and have attracted the attention of toxin researchers for years. In this century, venom component analysis has progressed considerable due to the advances in analytical techniques, in particular, mass spectrometry and next-generation deep (DNA and RNA) sequencing. As such, proteomic and peptidomic analyses using LC–MS have enabled the full analysis of venom components, revealing a variety of novel peptide and protein toxins sequences and scaffolds, potentially useful as pharmacological research tools and for the development of highly selective peptide ligands and therapeutic leads, like chlorotoxin. Due to their specificity for numerous ion-channel subtypes, including voltage- and ligand-gated ion channels, arthropod neurotoxins have been investigated to dissect and treat neurodegenerative diseases and control epileptic syndromes. This Special Issue collects information on such progress, encouraging contributions on the chemical and biological characterization of venom components, not only peptides and proteins, but also small molecules, their mechanisms of action, and the development of venom-derived peptide leads.

Keywords

ant --- venom --- mass spectrometry analysis --- pilosulin-like peptide --- phospholipases D --- metalloproteases --- Loxosceles spp. --- recombinant toxins --- hybrid immunogen --- neutralizing antibodies --- antivenoms --- LyeTxI-b --- Staphylococcus aureus --- keratitis --- AMP --- mastoparan --- Acinetobacter baumannii --- stent --- cantharidin --- blister beetle --- Berberomeloe majalis --- nematicide --- ixodicide --- antifeedant --- scorpion venom --- insecticidal peptide --- mass spectrometric analysis --- de novo sequencing --- Centruroides limpidus Karch --- proteome --- scorpion --- transcriptome --- venom toxicity --- brown spider --- venom --- Loxosceles --- toxins --- biotools --- drug targets --- novel therapeutics --- spider toxin --- directed disulfide bond formation --- Nav channel activity --- Nav1.7 --- pain target --- automated patch-clamp --- bee venom --- alternative treatment --- skin --- cutaneous disease --- mechanism --- chemotherapy --- cold allodynia --- mechanical allodynia --- melittin --- neuropathic pain --- oxaliplatin --- natural antibiotics --- piperidine heterocyclic amines --- industrial biotechnology --- LTQ Orbitrap Hybrid Mass Spectrometer --- myrmecology --- venom --- pain --- ants --- wasps --- bees --- Hymenoptera --- envenomation --- toxins --- peptides --- pharmacology --- Dinoponera quadriceps --- Formicidae --- Hymenoptera venom --- proteomics --- venom allergens --- ICK-like toxins --- melittin --- insect immune system --- apoptosis --- heart contractility --- Tenebrio molitor --- bee venom --- bioinformatics --- computational docking --- homology modelling --- ion channel structure --- protein–peptide interactions --- tertiapin --- venom peptides --- virtual screening --- small hive beetle --- solitary wasp --- venom --- antimicrobial peptide --- linear cationic ?-helical peptide --- amphipathic ?-helix structure --- channel-like pore-forming activity --- antimicrobial peptide --- venom --- arthropod --- malaria --- Chagas disease --- human African trypanosomiasis --- leishmaniasis --- toxoplasmosis --- venom peptides --- FMRF-amide --- insect neurotoxin --- protons --- pH regulation --- acid-sensing ion channels --- acid-gated currents --- chronic pain --- ICK peptide --- knottins --- NaV --- spider venom --- voltage-gated sodium channel --- n/a

Renal Cell Carcinoma

Author:
ISBN: 9783039286386 / 9783039286393 Year: Pages: 500 DOI: 10.3390/books978-3-03928-639-3 Language: eng
Publisher: MDPI - Multidisciplinary Digital Publishing Institute
Subject: Science (General) --- Biology
Added to DOAB on : 2020-06-09 16:38:57
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Renal cancer is a health problem of major concern worldwide. Although tyrosine kinase inhibitors and immune check-point blockade treatments, alone or in combination, are giving promising results, failures are quite frequent due to intratumor heterogeneity and to the acquisition of drug resistance. The spectrum of renal cell carcinoma subtypes is wide. Up to 70–80% of renal tumors are clear cell renal cell carcinomas, a clinically aggressive tumor subtype linked to VHL gene inactivation. Next in frequency, the papillary renal cell carcinoma category encompasses an intricate puzzle of classic and newly described entities with poorly defined limits, some of them pending definite clarification. Likewise, the chromophobe–oncocytoma duality, the so-called hybrid tumors and oncocytic neoplasms, remain to be well profiled. Finally, a growing list of very uncommon renal tumors linked to specific molecular signatures fulfill the current portrait of renal cell neoplasia. This Special Issue of Cancers regards RCC from very different perspectives, from the intimate basic mechanisms governing this disease to the clinical practice principles of their diagnoses and treatments. The interested reader will have the opportunity to contact with some of the most recent findings and will be updated with excellent reviews.

Keywords

ghrelin --- aurora A --- MMP10 --- invasion --- sarcomatoid --- RCC --- immunotherapy --- checkpoint inhibitors --- survival --- PD-L1 --- chronic kidney disease --- nephrectomy --- overall survival --- recurrence free survival --- renal cell carcinoma --- statins --- uric acid --- intratumour heterogeneity --- metastatic ccRCC --- copy number alteration --- mutation --- gene expression --- MiT family translocation renal cell carcinoma --- Xp11 translocation renal cell carcinoma --- t(6 --- 11) translocation renal cell carcinoma --- FISH --- TFE3 --- TFEB --- TFEB-amplified renal cell carcinoma --- renal cell carcinoma --- immune checkpoint inhibitors --- tyrosine kinase inhibitors --- efficacy --- toxicity --- cytoreductive nephrectomy --- Papillary renal cell carcinoma (pRCC) --- proteome profiling --- metabolome profiling --- glutathione metabolism --- metabolic reprogramming --- IL4R? --- IL13R?1 --- renal cell carcinoma --- JAK2 --- FOXO3 --- clear cell renal cell carcinoma --- identification of circular RNAs --- experimental validation of circular RNA --- diagnostic and prognostic markers --- circular RNAs in a clinico-genomic predictive model --- cancer-specific survival --- recurrence-free survival --- overall survival --- chromophobe renal cell carcinoma --- pale cell --- eosinophilic variant --- chromosomal loss --- copy number analysis --- renal cell carcinoma --- clear cell renal cell carcinoma --- AMP-activated protein kinases --- immunohistochemistry --- prognosis --- SMAD proteins --- transforming growth factor beta --- renal cell cancer --- microRNA --- metabolome --- proliferation --- PPP --- pentose phosphate pathway --- TCA cycle --- miR-155-5p --- miR-146a-5p --- TCGA --- renal cell carcinoma --- metastasis --- MTA2 --- MMP-9 --- miR-133b --- kidney cancer --- immunotherapy --- renal cell --- inflammation markers --- programmed death-ligand 1 --- immune checkpoint inhibitors --- prognostic factors --- predictive factors --- glutathione transferase omega 1 --- glutathione transferase omega 2 --- polymorphism --- PI3K/Akt/mTOR --- Raf/MEK/ERK --- IL-1? --- pro-IL-1? --- gene signature --- renal cancer --- survival prediction --- polybromo-1 --- PBRM1 --- renal cell carcinoma --- biomarker --- prognosis --- predictive role --- collecting duct carcinoma --- RNA sequencing --- solute carrier proteins --- kidney --- renal cell carcinoma --- molecular genetic features --- practical approach --- review --- renal cell carcinoma --- sarcomatoid --- immunotherapy --- renal cell carcinoma --- checkpoint inhibitors --- VEGF inhibitors --- mTOR inhibitors --- kidney --- emerging entity --- new entity --- oncocytic renal tumor --- unclassified renal cell carcinoma --- unclassified renal tumor --- anaplastic lymphoma kinase rearrangement --- ALK --- ESC --- HOT --- LOT --- drug sensitivity --- immune infiltration --- renal cancer --- targeted therapy --- tumor slice culture --- clear cell Renal Cell Carcinoma --- urine --- glycoproteomics --- N-glycomapping --- label-free --- glycomarkers --- everolimus --- EVI1 --- genetic association --- mTOR --- clear cell renal cell carcinoma --- curcumin --- renal cell cancer --- tumor adhesion --- tumor migration --- integrins --- NK cells --- kidney cancer --- renal cell carcinoma --- IL-2 --- cancer immunotherapy --- tumor microenvironment --- von Hippel–Lindau --- EMT like --- hyperosmolality --- chromophobe renal cell carcinoma --- copy number loss --- CDKN1A expression --- patient survival --- prognosis --- n/a

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