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intact cell protein profiling

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https://www.readbyqxmd.com/read/28910620/ctag-paperclip-reveals-alternative-polyadenylation-promotes-cell-type-specific-protein-diversity-and-shifts-araf-isoforms-with-microglia-activation
#1
Hun-Way Hwang, Yuhki Saito, Christopher Y Park, Nathalie E Blachère, Yoko Tajima, John J Fak, Ilana Zucker-Scharff, Robert B Darnell
Alternative polyadenylation (APA) is increasingly recognized to regulate gene expression across different cell types, but obtaining APA maps from individual cell types typically requires prior purification, a stressful procedure that can itself alter cellular states. Here, we describe a new platform, cTag-PAPERCLIP, that generates APA profiles from single cell populations in intact tissues; cTag-PAPERCLIP requires no tissue dissociation and preserves transcripts in native states. Applying cTag-PAPERCLIP to profile four major cell types in the mouse brain revealed common APA preferences between excitatory and inhibitory neurons distinct from astrocytes and microglia, regulated in part by neuron-specific RNA-binding proteins NOVA2 and PTBP2...
September 13, 2017: Neuron
https://www.readbyqxmd.com/read/28886250/dectin-2-is-a-c-type-lectin-receptor-that-recognizes-pneumocystis-and-participates-in-innate-immune-responses
#2
Theodore J Kottom, Deanne M Hebrink, Paige E Jenson, Paige L Marsolek, Marcel Wüthrich, Huafeng Wang, Bruce Klein, Sho Yamasaki, Andrew H Limper
Pneumocystis remains an important fungal pathogen causing life-threatening pneumonia in patients with AIDS and malignancy. Lung fungal pathogens are recognized by C-type Lectin Receptors (CLRs), which bind specific ligands and stimulate innate immune responses. Previously, a role for the CLR Dectin-1 has been shown to mediate immune responses to Pneumocystis spp. For this reason, we investigated a potential role for Dectin-2. Rats with Pneumocystis pneumonia (PCP) exhibited elevated Dectin-2 mRNA levels. Soluble Dectin-2 CRD fusions protein showed binding to intact Pneumocystis carinii (Pc) and to native Pneumocystis major surface glycoprotein/glycoprotein A (Msg/gpA)...
September 8, 2017: American Journal of Respiratory Cell and Molecular Biology
https://www.readbyqxmd.com/read/28866327/beyond-quality-control-the-role-of-nonsense-mediated-mrna-decay-nmd-in-regulating-gene-expression
#3
REVIEW
Sofia Nasif, Lara Contu, Oliver Mühlemann
Nonsense-mediated mRNA decay (NMD) has traditionally been described as a quality control system that rids cells of aberrant mRNAs with crippled protein coding potential. However, transcriptome-wide profiling of NMD deficient cells identified a plethora of seemingly intact mRNAs coding for functional proteins as NMD targets. This led to the view that NMD constitutes an additional post-transcriptional layer of gene expression control involved in the regulation of many different biological pathways. Here, we review our current knowledge about the role of NMD in embryonic development and tissue-specific cell differentiation...
September 1, 2017: Seminars in Cell & Developmental Biology
https://www.readbyqxmd.com/read/28860943/biochemical-and-histological-alterations-induced-by-the-smoke-of-allethrin-based-mosquito-coil-on-mice-model
#4
M Abdulla Al-Mamun, M Ataur Rahman, M Habibur Rahman, K M F Hoque, Z Ferdousi, Mohammad Nurul Matin, M Abu Reza
BACKGROUND: Mosquito coil (MC) emits insecticide upon burning which provides limited protection against lethal mosquito borne diseases. However, apart from killing the insect, toxicities associated with the inhalation of these insecticides poses severe health hazards. However, the use of MC is increasing day by day in third world countries in particular but, yet to receive enough attention of both policy maker and general public. The current study was aimed to assess the MC smoke induced damage of pulmonary and hepatic tissues along with observing the alterations of several blood biochemical parameters in mice model...
2017: BMC Clinical Pathology
https://www.readbyqxmd.com/read/28839250/pharmacological-profile-and-efficiency-in-vivo-of-diflapolin-the-first-dual-inhibitor-of-5-lipoxygenase-activating-protein-and-soluble-epoxide-hydrolase
#5
Ulrike Garscha, Erik Romp, Simona Pace, Antonietta Rossi, Veronika Temml, Daniela Schuster, Stefanie König, Jana Gerstmeier, Stefanie Liening, Markus Werner, Heiner Atze, Sandra Wittmann, Christina Weinigel, Silke Rummler, Gerhard K Scriba, Lidia Sautebin, Oliver Werz
Arachidonic acid (AA) is metabolized to diverse bioactive lipid mediators. Whereas the 5-lipoxygenase-activating protein (FLAP) facilitates AA conversion by 5-lipoxygenase (5-LOX) to pro-inflammatory leukotrienes (LTs), the soluble epoxide hydrolase (sEH) degrades anti-inflammatory epoxyeicosatrienoic acids (EETs). Accordingly, dual FLAP/sEH inhibition might be advantageous drugs for intervention of inflammation. We present the in vivo pharmacological profile and efficiency of N-[4-(benzothiazol-2-ylmethoxy)-2-methylphenyl]-N'-(3,4-dichlorophenyl)urea (diflapolin) that dually targets FLAP and sEH...
August 24, 2017: Scientific Reports
https://www.readbyqxmd.com/read/28771188/apigenin-impacts-the-growth-of-the-gut-microbiota-and-alters-the-gene-expression-of-enterococcus
#6
Minqian Wang, Jenni Firrman, Liqing Zhang, Gustavo Arango-Argoty, Peggy Tomasula, LinShu Liu, Weidong Xiao, Kit Yam
Apigenin is a major dietary flavonoid with many bioactivities, widely distributed in plants. Apigenin reaches the colon region intact and interacts there with the human gut microbiota, however there is little research on how apigenin affects the gut bacteria. This study investigated the effect of pure apigenin on human gut bacteria, at both the single strain and community levels. The effect of apigenin on the single gut bacteria strains Bacteroides galacturonicus, Bifidobacterium catenulatum, Lactobacillus rhamnosus GG, and Enterococcus caccae, was examined by measuring their anaerobic growth profiles...
August 3, 2017: Molecules: a Journal of Synthetic Chemistry and Natural Product Chemistry
https://www.readbyqxmd.com/read/28766291/comprehensive-identification-of-mrna-polyadenylation-sites-by-paperclip
#7
Hun-Way Hwang, Robert B Darnell
We discuss a newly developed method to profile mRNA polyadenylation (pA) sites in an unbiased manner, PAPERCLIP (Poly(A) binding Protein-mediated mRNA 3'End Retrieval by CrossLinking ImmunoPrecipitation). Based on the well-established CLIP (crosslinking immunoprecipitation) technique, PAPERCLIP utilizes the poly(A) binding protein (PABP) as a biological filter to selectively retrieve mRNA 3' end fragments by immunoprecipitation from ultraviolet (UV) irradiated tissues or cultured cells. The mRNA fragments are subsequently extracted from the immunoprecipitated PABP:RNA complexes to generate a cDNA library, which goes through two rounds of purification before the final amplification by real-time polymerase chain reaction (PCR)...
2017: Methods in Molecular Biology
https://www.readbyqxmd.com/read/28765873/classification-of-cancer-cell-lines-using-matrix-assisted-laser-desorption-ionization-time%C3%A2-of%C3%A2-flight-mass-spectrometry-and-statistical-analysis
#8
Vlad Serafim, Ajit Shah, Maria Puiu, Nicoleta Andreescu, Dorina Coricovac, Alexander Nosyrev, Demetrios A Spandidos, Aristides M Tsatsakis, Cristina Dehelean, Iulia Pinzaru
Over the past decade, matrix-assisted laser desorption/ionization time‑of‑flight mass spectrometry (MALDI‑TOF MS) has been established as a valuable platform for microbial identification, and it is also frequently applied in biology and clinical studies to identify new markers expressed in pathological conditions. The aim of the present study was to assess the potential of using this approach for the classification of cancer cell lines as a quantifiable method for the proteomic profiling of cellular organelles...
October 2017: International Journal of Molecular Medicine
https://www.readbyqxmd.com/read/28764802/mesenchymal-stem-cells-derived-from-inflamed-dental-pulpal-and-gingival-tissue-a-potential-application-for-bone-formation
#9
Laura Tomasello, Rodolfo Mauceri, Antonina Coppola, Maria Pitrone, Giuseppe Pizzo, Giuseppina Campisi, Giuseppe Pizzolanti, Carla Giordano
BACKGROUND: Chronic periodontal disease is an infectious disease consisting of prolonged inflammation of the supporting tooth tissue and resulting in bone loss. Guided bone regeneration procedures have become common and safe treatments in dentistry, and in this context dental stem cells would represent the ideal solution as autologous cells. In this study, we verified the ability of dental pulp mesenchymal stem cells (DPSCs) and gingival mesenchymal stem cells (GMSCs) harvested from periodontally affected teeth to produce new mineralized bone tissue in vitro, and compared this to cells from healthy teeth...
August 1, 2017: Stem Cell Research & Therapy
https://www.readbyqxmd.com/read/28744713/genome-wide-analysis-of-gene-expression-profiling-revealed-that-cop9-signalosome-is-essential-for-correct-expression-of-fe-homeostasis-genes-in-arabidopsis
#10
Seckin Eroglu, Emre Aksoy
In plant cells, either excess or insufficient iron (Fe) concentration triggers stress responses, therefore it is strictly controlled. Proteasome-mediated degradation through ubiquitination of Fe homeostasis proteins has just become the focus of research in recent years. Deactivating ubiquitin ligases, COP9 signalosome has a central importance in the translational control of various stress responses. The aim of the study was to investigate COP9 signalosome in Fe deficiency response of Strategy I plants. In silico analysis of a set of Fe-deficiency-responsive genes was conducted against the transcriptome of Arabidopsis csn mutant lines using Genevestigator software...
July 25, 2017: Biometals: An International Journal on the Role of Metal Ions in Biology, Biochemistry, and Medicine
https://www.readbyqxmd.com/read/28741179/activation-of-liver-x-receptor-inhibits-oct2-mediated-organic-cation-transport-in-renal-proximal-tubular-cells
#11
Teerasak Wongwan, Suticha Kittayaruksakul, Nithi Asavapanumas, Varanuj Chatsudthipong, Sunhapas Soodvilai
Liver X receptor (LXR) is transcriptional factor that plays an important role in the regulation of energy metabolism such as cholesterol, lipid, and glucose metabolism as well as membrane transporters and channels. Using both in vitro and in vivo models, LXR regulation of the expression and function of renal organic cation transporter 2 (OCT2) was observed. Synthetic LXR agonist (GW3965) and endogenous LXR agonist (22R-hydroxycholesterol) significantly reduced the uptake of (3)H-MPP(+), a prototypic substrate of OCT2, in both OCT2- Chinese hamster ovary K1 and human renal proximal tubular cells (RPTEC/TERT1)...
July 25, 2017: Pflügers Archiv: European Journal of Physiology
https://www.readbyqxmd.com/read/28693997/lectin-from-canavalia-villosa-seeds-a-glucose-mannose-specific-protein-and-a-new-tool-for-inflammation-studies
#12
Claudia F Lossio, Cleane G Moreira, Renata M F Amorim, Clareane S Nobre, Mayara T L Silva, Cornevile C Neto, Vanir R Pinto-Junior, Ivanice B Silva, Julia Campos, Ana Maria S Assreuy, Benildo S Cavada, Kyria S Nascimento
With important carbohydrate binding properties, lectins are proteins able to decipher the glycocode, and as such, they can be used in bioassays involving cell-cell communication, protein targeting, inflammation, and hypernociception, among others. In this study, a new glucose/mannose-specific lectin from Canavalia villosa seeds (Cvill) was isolated by a single affinity chromatography step in a Sephadex(®) G-50 column, with a purification yield of 19.35mg of lectin per gram of powdered seed. Analysis of intact protein by mass spectrometry showed the lectin is composed of three polypeptide chains, including a 25...
July 7, 2017: International Journal of Biological Macromolecules
https://www.readbyqxmd.com/read/28629195/candida-albicans-impairments-induced-by-peppermint-and-clove-oils-at-sub-inhibitory-concentrations
#13
Katarzyna Rajkowska, Anna Otlewska, Alina Kunicka-Styczyńska, Agnieszka Krajewska
Members of Candida species cause significant health problems, inducing various types of superficial and deep-seated mycoses in humans. In order to prevent from Candida sp. development, essential oils are more and more frequently applied, due to their antifungal activity, low toxicity if used appropriately, and biodegrability. The aim of the study was to characterize the early alterations in Candida albicans metabolic properties in relation to proteins and chromosomal DNA profiles, after treatment with peppermint and clove oils at sub-inhibitory concentrations...
June 19, 2017: International Journal of Molecular Sciences
https://www.readbyqxmd.com/read/28627464/analysis-of-protein-complexes-in-arabidopsis-leaves-using-size-exclusion-chromatography-and-label-free-protein-correlation-profiling
#14
Uma K Aryal, Zachary McBride, Donglai Chen, Jun Xie, Daniel B Szymanski
Protein complexes are fundamentally important for diverse cellular functions, and create functionalities that could never be achieved by a single polypeptide. Knowledge of the protein complex assemblies that exist in plant cells are limited. To close this gap, we applied an integrative proteomic approach that combines cell fractionation, protein chromatography and quantitative mass spectrometry (MS) to analyze the oligomerization state of thousands of proteins in a single experiment. Soluble extracts from intact Arabidopsis leaves were fractionated using size exclusion chromatography (SEC), and abundance profiles across the column fractions were quantified using label-free precursor ion (MS1) intensity...
June 13, 2017: Journal of Proteomics
https://www.readbyqxmd.com/read/28625888/combined-venom-profiling-and-cytotoxicity-screening-of-the-radde-s-mountain-viper-montivipera-raddei-and-mount-bulgar-viper-montivipera-bulgardaghica-with-potent-cytotoxicity-against-human-a549-lung-carcinoma-cells
#15
Ayse Nalbantsoy, Benjamin-Florian Hempel, Daniel Petras, Paul Heiss, Bayram Göçmen, Nasit Iğci, Mehmet Zülfü Yildiz, Roderich D Süssmuth
Here we report the first characterization of the endemic Mount Bulgar Viper (Montivipera bulgardaghica) and Radde's mountain viper (Montivipera raddei) venom by a combined approach using intact mass profiling and bottom-up proteomics. The cytotoxicity screening of crude venom as well as isolated serine proteases revealed a high activity against A549 human lung carcinoma cells. By means of intact mass profiling of native and reduced venom we observed basic and acidic phospholipases type A2. Moreover, the analysis revealed snake venom metalloproteases, cysteine-rich secretory proteins, disintegrins, snake venom serine proteases, C-type lectins, a vascular endothelial growth factor and an L-amino acid oxidase...
June 16, 2017: Toxicon: Official Journal of the International Society on Toxinology
https://www.readbyqxmd.com/read/28603764/data-on-endogenous-bovine-ovarian-follicular-cells-peptides-and-small-proteins-obtained-through-top-down-high-resolution-mass-spectrometry
#16
Valérie Labas, Ana-Paula Teixeira-Gomes, Laura Bouguereau, Audrey Gargaros, Lucie Spina, Aurélie Marestaing, Svetlana Uzbekova
The endogenous peptides and small proteins extracted from bovine ovarian follicular cells (oocytes, cumulus and granulosa cells) were identified by Top-down High Resolution Mass Spectrometry (TD-HR-MS/MS) in order to annotate peptido- and proteoforms detected using qualitative and quantitative profiling method based on ICM-MS (Intact Cell Matrix-Assisted Laser Desorption/Ionization Time-of-Flight Mass Spectrometry). The description and analysis of these Top-down MS data in the context of oocyte quality biomarkers research are available in the original research article of Labas et al...
August 2017: Data in Brief
https://www.readbyqxmd.com/read/28592538/identification-of-interleukin-27-il-27-il-27-receptor-subunit-alpha-as-a-critical-immune-axis-for-in-vivo-hiv-control
#17
M Ruiz-Riol, D Berdnik, A Llano, B Mothe, C Gálvez, S Pérez-Álvarez, B Oriol-Tordera, A Olvera, S Silva-Arrieta, M Meulbroek, F Pujol, J Coll, J Martinez-Picado, C Ganoza, J Sanchez, G Gómez, T Wyss-Coray, C Brander
Intact and broad immune cell effector functions and specific individual cytokines have been linked to HIV disease outcome, but their relative contribution to HIV control remains unclear. We asked whether the proteome of secreted cytokines and signaling factors in peripheral blood can be used to discover specific pathways critical for host viral control. A custom glass-based microarray, able to measure >600 plasma proteins involved in cell-to-cell communication, was used to measure plasma protein profiles in 96 HIV-infected, treatment-naive individuals with high (>50,000) or low (<10,000 HIV RNA copies/ml) viral loads...
August 15, 2017: Journal of Virology
https://www.readbyqxmd.com/read/28584155/capsid-assembly-modulators-have-a-dual-mechanism-of-action-in-primary-human-hepatocytes-infected-with-hepatitis-b-virus
#18
Jan Martin Berke, Pascale Dehertogh, Karen Vergauwen, Ellen Van Damme, Wendy Mostmans, Koen Vandyck, Frederik Pauwels
Hepatitis B virus (HBV) capsid assembly is a critical step in the propagation of the virus and is mediated by the core protein. Due to its multiple functions in the viral life cycle, core became an attractive target for new antiviral therapies. Capsid assembly modulators (CAMs) accelerate the kinetics of capsid assembly and prevent encapsidation of the polymerase-pregenomic RNA (Pol-pgRNA) complex, thereby blocking viral replication. CAM JNJ-632 is a novel and potent inhibitor of HBV replication in vitro across genotypes A to D...
August 2017: Antimicrobial Agents and Chemotherapy
https://www.readbyqxmd.com/read/28569190/single-cell-mrna-profiling-reveals-transcriptional-heterogeneity-among-pancreatic-circulating-tumour-cells
#19
Morten Lapin, Kjersti Tjensvoll, Satu Oltedal, Milind Javle, Rune Smaaland, Bjørnar Gilje, Oddmund Nordgård
BACKGROUND: Single-cell mRNA profiling of circulating tumour cells may contribute to a better understanding of the biology of these cells and their role in the metastatic process. In addition, such analyses may reveal new knowledge about the mechanisms underlying chemotherapy resistance and tumour progression in patients with cancer. METHODS: Single circulating tumour cells were isolated from patients with locally advanced or metastatic pancreatic cancer with immuno-magnetic depletion and immuno-fluorescence microscopy...
May 31, 2017: BMC Cancer
https://www.readbyqxmd.com/read/28510335/proteoforms-in-peripheral-blood-mononuclear-cells-as-novel-rejection-biomarkers-in-liver-transplant-recipients
#20
T K Toby, M Abecassis, K Kim, P M Thomas, R T Fellers, R D LeDuc, N L Kelleher, J Demetris, J Levitsky
Biomarker profiles of acute rejection in liver transplant recipients could enhance the diagnosis and management of recipients. Our aim was to identify diagnostic proteoform signatures of acute rejection in circulating immune cells, using an emergent "top-down" proteomics methodology. We prepared differentially processed and cryopreserved cell lysates from 26 nonviral liver transplant recipients by molecular weight-based fractionation and analyzed them by mass spectrometry of whole proteins in three steps: (i) Nanocapillary liquid chromatography coupled with high-resolution tandem mass spectrometry; (ii) database searching to identify and characterize intact proteoforms; (iii) data processing through a hierarchical linear model matching the study design to quantify proteoform fold changes in patients with rejection versus normal liver function versus acute dysfunction without rejection...
September 2017: American Journal of Transplantation
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