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intact cell protein profiling

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https://www.readbyqxmd.com/read/28771188/apigenin-impacts-the-growth-of-the-gut-microbiota-and-alters-the-gene-expression-of-enterococcus
#1
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
#2
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
#3
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...
July 27, 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
#4
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
#5
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
#6
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
#7
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
#8
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
#9
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
#10
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
#11
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
#12
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
#13
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
#14
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
#15
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...
May 16, 2017: American Journal of Transplantation
https://www.readbyqxmd.com/read/28481867/the-rb-il-6-axis-controls-self-renewal-and-endocrine-therapy-resistance-by-fine-tuning-mitochondrial-activity
#16
S Kitajima, A Yoshida, S Kohno, F Li, S Suzuki, N Nagatani, Y Nishimoto, N Sasaki, H Muranaka, Y Wan, T C Thai, N Okahashi, F Matsuda, H Shimizu, T Nishiuchi, Y Suzuki, K Tominaga, N Gotoh, M Suzuki, M E Ewen, D A Barbie, O Hirose, T Tanaka, C Takahashi
Retinoblastoma (RB) protein inactivation during tumor progression is often associated with acquisition of immature phenotypes and resistance to therapy. Determination of an RB inactivation signature in a context of gaining undifferentiated phenotype in a p53-null sarcoma system revealed a critical role for interleukin (IL)-6. Using a Gene Set Enrichment Analysis (GSEA), we discovered that poorly differentiated breast cancers are enriched for this RB inactivation signature. Accelerated IL-6 secretion following RB inactivation in an RB-intact luminal-type breast cancer cell line MCF-7 promoted a positive feed forward loop between IL-6 and STAT3 driving tumor growth and endocrine therapy resistance...
May 8, 2017: Oncogene
https://www.readbyqxmd.com/read/28412815/high-throughput-analysis-of-intact-human-proteins-using-uvpd-and-hcd-on-an-orbitrap-mass-spectrometer
#17
Timothy P Cleland, Caroline J DeHart, Ryan T Fellers, Alexandra J VanNispen, Joseph B Greer, Richard D LeDuc, W Ryan Parker, Paul M Thomas, Neil L Kelleher, Jennifer S Brodbelt
The analysis of intact proteins (top-down strategy) by mass spectrometry has great potential to elucidate proteoform variation, including patterns of post-translational modifications (PTMs), which may not be discernible by analysis of peptides alone (bottom-up approach). To maximize sequence coverage and localization of PTMs, various fragmentation modes have been developed to produce fragment ions from deep within intact proteins. Ultraviolet photodissociation (UVPD) has recently been shown to produce high sequence coverage and PTM retention on a variety of proteins, with increasing evidence of efficacy on a chromatographic time scale...
May 5, 2017: Journal of Proteome Research
https://www.readbyqxmd.com/read/28385661/intact-cell-maldi-tof-mass-spectrometry-on-single-bovine-oocyte-and-follicular-cells-combined-with-top-down-proteomics-a-novel-approach-to-characterise-markers-of-oocyte-maturation
#18
Valérie Labas, Ana-Paula Teixeira-Gomes, Laura Bouguereau, Audrey Gargaros, Lucie Spina, Aurélie Marestaing, Svetlana Uzbekova
Intact cell MALDI-TOF mass spectrometry (ICM-MS) was adapted to bovine follicular cells from individual ovarian follicles to obtain the protein/peptide signatures (<17kDa) of single oocytes, cumulus cells (CC) and granulosa cells (GC), which shared a total of 439 peaks. By comparing the ICM-MS profiles of single oocytes and CC before and after in vitro maturation (IVM), 71 different peaks were characterised, and their relative abundance was found to vary depending on the stage of oocyte meiotic maturation...
April 3, 2017: Journal of Proteomics
https://www.readbyqxmd.com/read/28369609/4-bromodiphenyl-ether-induces-germ-cell-apoptosis-by-induction-of-ros-and-dna-damage-in-caenorhabditis-elegans
#19
Xinyue You, Jing Xi, Yiyi Cao, Jinfu Zhang, Yang Luan
Polybrominated diphenyl ethers may affect male reproductive function; however, the underlying mechanism is still uncertain. By using Caenorhabditis elegans, a commonly used model to study basic biological processes in apoptosis, we investigated the toxic effects of 4-bromodiphenyl ether (BDE-3), the most fundamental mono-BDE generated from degradation of polybrominated diphenyl ethers in the environment. We found that BDE-3 treated worms exhibited decreased life spans, impaired fecundity and delayed egg laying...
June 1, 2017: Toxicological Sciences: An Official Journal of the Society of Toxicology
https://www.readbyqxmd.com/read/28291811/systematic-identification-and-characterization-of-long-non-coding-rnas-in-mouse-mature-sperm
#20
Xiaoning Zhang, Fengxin Gao, Jianbo Fu, Peng Zhang, Yuqing Wang, Xuhui Zeng
Increasing studies have shown that mature spermatozoa contain many transcripts including mRNAs and miRNAs. However, the expression profile of long non-coding RNAs (lncRNAs) in mammalian sperm has not been systematically investigated. Here, we used highly purified RNA to investigate lncRNA expression profiles in mouse mature sperm by stranded-specific RNA-seq. We identified 20,907 known and 4,088 novel lncRNAs transcripts, and the existence of intact lncRNAs was confirmed by RT-PCR and fluorescence in situ hybridization on two representative lncRNAs...
2017: PloS One
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