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https://www.readbyqxmd.com/read/29161009/a-sensitive-microbead-based-organic-media-assisted-method-for-proteomics-sample-preparation-from-dilute-and-denaturing-solutions
#1
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/29158881/serum-proteomic-profiling-of-obsessive-compulsive-disorder-washing-subtype-a-preliminary-study
#2
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/29157807/a-comparative-proteomic-study-of-secretomes-in-kaempferitrin-treated-ctx-tna2-astrocytic-cells
#3
Wei-Chi Ku, Yi-Ling Chang, Sheng-Fa Wu, Hui-Nung Shih, Yew-Min Tzeng, Hui-Ru Kuo, Kai-Ming Chang, Dinesh Chandra Agrawal, Bing-Lan Liu, Chin-An Chang, Siendong Huang, Meng-Jen Lee
ETHNOPHARMACOLOGICAL RELEVANCE: Kaempferitrin is extracted in significantly high quantities from the leaves of Cinnamomum osmophloeum (C.O) and Bauhinia forficata, and are used as an antidiabetic herbal remedy in China and Brazil. Commercial product using dry Cinnamomum osmophloeum leaves has been sold locally in Taiwan. Oral administration of kaempferitrin reduced blood sugar in diabetic rats. AIM OF THE STUDY: Though previously demonstrated to activate the classical insulin signaling pathways, a mechanism for kaempferitrin is still not fully understood...
December 1, 2017: Phytomedicine: International Journal of Phytotherapy and Phytopharmacology
https://www.readbyqxmd.com/read/29157295/single-cell-multiplexed-cytokine-profiling-of-cd19-car-t-cells-reveals-a-diverse-landscape-of-polyfunctional-antigen-specific-response
#4
Qiong Xue, Emily Bettini, Patrick Paczkowski, Colin Ng, Alaina Kaiser, Timothy McConnell, Olja Kodrasi, Máire F Quigley, James Heath, Rong Fan, Sean Mackay, Mark E Dudley, Sadik H Kassim, Jing Zhou
BACKGROUND: It remains challenging to characterize the functional attributes of chimeric antigen receptor (CAR)-engineered T cell product targeting CD19 related to potency and immunotoxicity ex vivo, despite promising in vivo efficacy in patients with B cell malignancies. METHODS: We employed a single-cell, 16-plex cytokine microfluidics device and new analysis techniques to evaluate the functional profile of CD19 CAR-T cells upon antigen-specific stimulation. CAR-T cells were manufactured from human PBMCs transfected with the lentivirus encoding the CD19-BB-z transgene and expanded with anti-CD3/anti-CD28 coated beads...
November 21, 2017: Journal for Immunotherapy of Cancer
https://www.readbyqxmd.com/read/29155757/dissection-of-human-retina-and-rpe-choroid-for-proteomic-analysis
#5
Thiago Cabral, Marcus A Toral, Gabriel Velez, James E DiCarlo, Anuradha M Gore, MaryAnn Mahajan, Stephen H Tsang, Alexander G Bassuk, Vinit B Mahajan
The human retina is composed of the sensory neuroretina and the underlying retinal pigmented epithelium (RPE), which is firmly complexed to the vascular choroid layer. Different regions of the retina are anatomically and molecularly distinct, facilitating unique functions and demonstrating differential susceptibility to disease. Proteomic analysis of each of these regions and layers can provide vital insights into the molecular process of many diseases, including Age-Related Macular Degeneration (AMD), diabetes mellitus, and glaucoma...
November 12, 2017: Journal of Visualized Experiments: JoVE
https://www.readbyqxmd.com/read/29155430/engineering-peptide-ligase-specificity-by-proteomic-identification-of-ligation-sites
#6
Amy M Weeks, James A Wells
Enzyme-catalyzed peptide ligation is a powerful tool for site-specific protein bioconjugation, but stringent enzyme-substrate specificity limits its utility. We developed an approach for comprehensively characterizing peptide ligase specificity for N termini using proteome-derived peptide libraries. We used this strategy to characterize the ligation efficiency for >25,000 enzyme-substrate pairs in the context of the engineered peptide ligase subtiligase and identified a family of 72 mutant subtiligases with activity toward N-terminal sequences that were previously recalcitrant to modification...
November 20, 2017: Nature Chemical Biology
https://www.readbyqxmd.com/read/29155377/new-forensics-methods-looking-more-like-csi-rapid-dna-analysis-proteomics-and-new-technology-increasingly-impact-forensics-investigations
#7
Leslie Mertz
If CSI and those other police procedural TV shows are to be believed, criminals don't have a chance. A finger smudge on a light switch, a flake of skin, or a sweat-stained fiber is all the information an investigator needs to positively identify the perpetrator and put him or her behind bars.
November 2017: IEEE Pulse
https://www.readbyqxmd.com/read/29155263/identification-and-characterisation-of-the-epididymal-proteins-in-the-lizard-eutropis-carinata-reptilia-squamata-schneider-1801
#8
R Medini, M Bhagya, S Samson
Lizards are seasonal breeders. Cyclic reproductive nature makes lizard as a useful model for the study of the reproductively active protein secretions in the epididymis. During breeding season, the epididymides of the lizard secret proteins that mixes with the spermatozoa and create a favourable environment for sperm maturation. In this spectrum, the aim of this study is to identify and characterize proteins which are present in the lumen of the epididymis of the lizard, E. carinata during the active phase of reproduction...
November 16, 2017: General and Comparative Endocrinology
https://www.readbyqxmd.com/read/29154769/extracellular-lipids-accumulate-in-human-carotid-arteries-as-distinct-three-dimensional-structures-and-have-proinflammatory-properties
#9
Satu Lehti, Su D Nguyen, Ilya Belevich, Helena Vihinen, Hanna M Heikkilä, Rabah Soliymani, Reijo Käkelä, Jani Saksi, Matti Jauhiainen, Gregory A Grabowski, Outi Kummu, Sohvi Hörkkö, Marc Baumann, Perttu J Lindsberg, Eija Jokitalo, Petri T Kovanen, Katariina Öörni
Lipid accumulation is a key characteristic of advancing atherosclerotic lesions. Here we analyzed the ultrastructure of the accumulated lipids in endarterectomized human carotid atherosclerotic plaques using three-dimensional (3D) electron microscopy, a method never used in this context before. 3D-electron microscopy revealed intracellular lipid droplets and extracellular lipoprotein particles. The majority of the particles were aggregated and some connected to needle-shaped or sheet-like cholesterol crystals...
November 14, 2017: American Journal of Pathology
https://www.readbyqxmd.com/read/29154539/electrokinetic-removal-of-dodecyl-sulfate-micelles-from-digested-protein-samples-prior-to-electrospray-ionization-mass-spectrometry
#10
Ria Marni Tubaon, Paul Raymond Haddad, Joselito P Quirino
In proteomics, dodecyl sulfate (DS-) as sodium salt is commonly used in protein solubilization prior to tryptic digestion, but the presence of the DS- hampers the electrospray ionization mass spectrometric (ESI-MS) analysis. The development of DS- depletion techniques is therefore important especially when dealing with small samples where there could be poor sensitivity due to sample loss or dilution during sample preparation. Here, we present a simple and fast electrokinetic removal method of DS- from small volumes of peptide and digested protein samples prior to ESI-MS...
November 20, 2017: Analytical Chemistry
https://www.readbyqxmd.com/read/29154149/rar%C3%AE-2-dependent-signaling-represses-neuronal-differentiation-in-mouse-es-cells
#11
Sri L Kona, Amita Shrestha, Xiaoping Yi, Serenthia Joseph, Humberto Munoz Barona, Eduardo Martinez-Ceballos
Embryonic Stem (ES) cells are pluripotent cells that can be induced to differentiate into cells of all three lineages: mesoderm, endoderm, and ectoderm. In culture, ES cells can be differentiated into mature neurons by treatment with Retinoic Acid (RA) and this effect is mediated mainly through the activation of the RA nuclear receptors (RAR α, β, and γ), and their isoforms. However, little is known about the role played by specific RAR types on ES cell differentiation. Here, we found that treatment of ES cells with AC55649, an RARβ2 agonist, increased endodermal marker gene expression...
November 10, 2017: Differentiation; Research in Biological Diversity
https://www.readbyqxmd.com/read/29153204/proteomic-biomarkers-of-heart-failure
#12
REVIEW
Muhammad Zubair Israr, Liam M Heaney, Toru Suzuki
Heart failure (HF) is associated with significant morbidity and mortality. Biomarkers are used to assist clinicians with timely diagnosis, prognosis, and risk prediction of patients for personalized treatment. Using modern proteomic methods such as mass spectrometry, an increasing number of novel biomarkers have been identified that further aid clinicians in the early diagnosis and outcome prediction of HF. This article focuses on the array of common and novel protein-based biomarkers that provide diagnostic and prognostic information in HF...
January 2018: Heart Failure Clinics
https://www.readbyqxmd.com/read/29151793/plasma-protein-absolute-quantification-by-nano-lc-q-tof-udms-e-for-clinical-biomarker-verification
#13
Maria Ilies, Cristina Adela Iuga, Felicia Loghin, Vishnu Mukund Dhople, Elke Hammer
Background and aims: Proteome-based biomarker studies are targeting proteins that could serve as diagnostic, prognosis, and prediction molecules. In the clinical routine, immunoassays are currently used for the absolute quantification of such biomarkers, with the major limitation that only one molecule can be targeted per assay. The aim of our study was to test a mass spectrometry based absolute quantification method for the verification of plasma protein sets which might serve as reliable biomarker panels for the clinical practice...
2017: Clujul Medical (1957)
https://www.readbyqxmd.com/read/29150981/systematic-proteomic-analysis-of-protein-methylation-in-prokaryotes-and-eukaryotes-revealed-distinct-substrate-specificity
#14
Min Zhang, Jun-Yu Xu, Hao Hu, Bang-Ce Ye, Minjia Tan
The studies of protein methylation mainly focus on lysine and arginine residues due to their diverse roles in essential cellular processes from gene expression to signal transduction. Nevertheless, atypical protein methylation occurring on amino acid residues, such as glutamine and glutamic acid, was largely neglected until recently. In addition, the systematic analysis for the distribution of methylation on different amino acids in various species is still lacking, which hinders our understanding of its functional roles...
November 18, 2017: Proteomics
https://www.readbyqxmd.com/read/29150517/multi-omics-reveal-the-lifestyle-of-the-acidophilic-mineral-oxidizing-model-species-leptospirillum-ferriphilum-t
#15
Stephan Christel, Malte Herold, Sören Bellenberg, Mohamed El Hajjami, Antoine Buetti-Dinh, Igor V Pivkin, Wolfgang Sand, Paul Wilmes, Ansgar Poetsch, Mark Dopson
Leptospirillum ferriphilum plays a major role in acidic, metal rich environments where it represents one of the most prevalent iron oxidizers. These milieus include acid rock and mine drainage as well as biomining operations. Despite its perceived importance, no complete genome sequence of this model species' type strain is available, limiting the possibilities to investigate the strategies and adaptations Leptospirillum ferriphilum(T) applies to survive and compete in its niche. This study presents a complete, circular genome of Leptospirillum ferriphilum(T) DSM 14647 obtained by PacBio SMRT long read sequencing for use as a high quality reference...
November 17, 2017: Applied and Environmental Microbiology
https://www.readbyqxmd.com/read/29149817/high-density-lipoprotein-hdl-dysfunction-and-future-of-hdl
#16
Sibel Ertek
Although high density lipoprotein cholesterol (HDL-C) levels are inversely proportional to cardiovascular risk in many studies, recent pharmacological interventional studies with HDL-C raising strategies did not show a benefit in terms of vascular events. The HDL particle is heterogenous with anti-atherogenic functions and non-vascular effects. Many factors affect HDL components and may either cause compositional changes, post-translational modifications of proteins, or alter lipids and other cargo molecules; generally these factors cause more than one of these changes, resulting in functional differences...
November 16, 2017: Current Vascular Pharmacology
https://www.readbyqxmd.com/read/29148164/protein-profiling-of-non-model-plant-cuminum-cyminum-by-gel-based-proteomic-approach
#17
Uzma Zaman, Henning Urlaub, Atiya Abbasi
INTRODUCTION: Cumin (Cuminum cyminum), a popular spice has been widely used in traditional medicine to cure various ailments. Despite the existence of scientific literature about its pharmacological properties, no successful proteome profiling has yet been attempted. OBJECTIVE: To optimise extraction of cumin proteins and analyse its profile by shotgun proteomics, using one-dimensional electrophoresis coupled with nano-ESI-LC-MS/MS. METHODOLOGY: As a first step, we have compared three extraction protocols for total proteins extraction from cumin...
November 16, 2017: Phytochemical Analysis: PCA
https://www.readbyqxmd.com/read/29147916/integrative-analysis-of-proteomics-data-to-obtain-clinically-relevant-markers
#18
Nathan Salomonis
The analysis of proteomics data can be significantly challenging. Beyond the technical challenges of accurately identifying and quantifying peptides, identifying the most biologically coherent set of biomarkers can be a particularly daunting step. In this chapter, we will review a series of methods implemented in the software AltAnalyze that can be used to normalize proteomics peptide counts, identify a minimal set of the most distinguishing morbidity-associated biomarkers, and connect up these results to known pathways and interacting protein and regulatory networks...
November 18, 2017: Methods in Molecular Biology
https://www.readbyqxmd.com/read/29145449/estimation-of-the-proteomic-cancer-co-expression-sub-networks-by-using-association-estimators
#19
Cihat Erdoğan, Zeyneb Kurt, Banu Diri
In this study, the association estimators, which have significant influences on the gene network inference methods and used for determining the molecular interactions, were examined within the co-expression network inference concept. By using the proteomic data from five different cancer types, the hub genes/proteins within the disease-associated gene-gene/protein-protein interaction sub networks were identified. Proteomic data from various cancer types is collected from The Cancer Proteome Atlas (TCPA). Correlation and mutual information (MI) based nine association estimators that are commonly used in the literature, were compared in this study...
2017: PloS One
https://www.readbyqxmd.com/read/29145071/proteomic-analysis-reveals-that-tomato-interaction-with-plant-growth-promoting-bacteria-is-highly-determined-by-ethylene-perception
#20
Pablo Ibort, Hiroyuki Imai, Matsuo Uemura, Ricardo Aroca
Feeding an increasing global population as well as reducing environmental impact of crops is the challenge for the sustainable intensification of agriculture. Plant-growth-promoting bacteria (PGPB) management could represent a suitable method but elucidation of their action mechanisms is essential for a proper and effective utilization. Furthermore, ethylene is involved in growth and response to environmental stimuli but little is known about the implication of ethylene perception in PGPB activity. The ethylene-insensitive tomato never ripe and its isogenic wild-type cv...
November 10, 2017: Journal of Plant Physiology
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