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intact cell protein profiling

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https://www.readbyqxmd.com/read/29341427/lc-ms-based-intact-igg-and-released-glycan-analysis-for-bioprocessing-applications
#1
Tianhua Wang, Kong Meng Hoi, Henning Stöckmann, Corrine Wan, Lyn Chiin Sim, Noor Hayati Bte Kamari, Shi Jie Tay, Ce Huang Poo, Susanto Woen, Yuangsheng Yang, Peiqing Zhang, Pauline M Rudd
Robust plate based antibody glycan analysis platforms are urgently needed for biopharmaceutical development and manufacturing as well as for clinical biomarker research. A 96-well plate based workflow has been developed to analyze both intact IgG antibodies and released N-glycans using an Orbitrap Fusion Mass Spectrometer and an LC/MS method on the Waters UNIFI platform. Here we describe such a workflow including protein A purification, PNGaseF digestion, 2-AB labeling and SPE clean-up. The measured IgG glycan profile is consistent with that obtained from non-plate based method and commercial kit and has the advantage of less hands-on time...
January 17, 2018: Biotechnology Journal
https://www.readbyqxmd.com/read/29321630/engineered-mesenchymal-stem-cell-sheets-patches-prevents-postoperative-pancreatic-leakage-in-a-rat-model
#2
Seong-Ryong Kim, Hye-Jin Yi, Yu Na Lee, Ji Yoon Park, Robert M Hoffman, Teruo Okano, In Kyong Shim, Song Cheol Kim
Post-operative pancreatic fistula (POPF) following pancreatic resection is a life-threatening surgical complication. Cell sheets were prepared and harvested using temperature-responsive culture dishes and transplanted as patches to seal POPF. Two different mesenchymal stem cell (MSC) sheets were compared in terms of the preventative ability for pancreatic leakage in a rat model. Both rat adipose-derived stem cell (rADSC) and bone marrow-derived stem cell (rBMSC) sheets were transplanted. Those rADSC and rBMSC sheets are created without enzymes and thus maintained their cell-cell junctions and adhesion proteins with intact fibronectin on the basal side, as well as characteristics of MSCs...
January 10, 2018: Scientific Reports
https://www.readbyqxmd.com/read/29301241/comparative-venomics-of-the-vipera-ammodytes-transcaucasiana-and-vipera-ammodytes-montandoni-from-turkey-provides-insights-into-kinship
#3
Benjamin-Florian Hempel, Maik Damm, Bayram Göçmen, Mert Karis, Mehmet Anıl Oguz, Ayse Nalbantsoy, Roderich D Süssmuth
The Nose-horned Viper (Vipera ammodytes) is one of the most widespread and venomous snakes in Europe, which causes high frequent snakebite accidents. The first comprehensive venom characterization of the regional endemic Transcaucasian Nose-horned Viper (Vipera ammodytes transcaucasiana) and the Transdanubian Sand Viper (Vipera ammodytes montandoni) is reported employing a combination of intact mass profiling and bottom-up proteomics. The bottom-up analysis of both subspecies identified the major snake protein families of viper venoms...
January 1, 2018: Toxins
https://www.readbyqxmd.com/read/29217487/genistein-and-daidzein-treatments-differently-affect-uterine-homeostasis-in-the-ovary-intact-middle-aged-rats
#4
Ivana Jarić, Jasmina Živanović, Marko Miler, Vladimir Ajdžanović, Duško Blagojević, Nataša Ristić, Verica Milošević, Nataša Nestorović
This study aimed to investigate the effects of soy isoflavones, genistein (GEN) and daidzein, (DAI) on the uterine function in ovary-intact middle-aged rats. GEN and DAI (35mg/kg) were subcutaneously administrated to acyclic (12-month-old) Wistar females, daily, for 4weeks. Control group received either vehicle (olive oil and ethanol, 9:1) or remained intact. We found that GEN and DAI differently affect uterine morphophysiology. GEN significantly increased the uterine wet weight which was associated with hyperplastic changes, revealed by stereological and histomorphometrical analyses...
December 5, 2017: Toxicology and Applied Pharmacology
https://www.readbyqxmd.com/read/29211351/application-of-fourier-transform-infrared-spectroscopy-to-biomolecular-profiling-of-cultured-fibroblast-cells-from-gaucher-disease-patients-a-preliminary-investigation
#5
Nasit Igci, Parisa Sharafi, Duygu Ozel Demiralp, Cemil Ozerk Demiralp, Aysel Yuce, Serap Dokmeci Emre
BACKGROUND: Gaucher disease (GD) is defined as an autosomal recessive disorder resulting from the deficiency of glucocerebrosidase (E.C. 3.2.1.45). Glucocerebrosidase is responsible for the degradation of glucosylceramide into ceramide and glucose. The deficiency of this enzyme results in the accumulation of undegraded glucosylceramide, almost exclusively in macrophages. With Fourier transform infrared (FTIR) spectroscopy, the complete molecular diversity of the samples can be studied comparatively and the amount of the particular materials can be determined...
October 2017: Advances in Clinical and Experimental Medicine: Official Organ Wroclaw Medical University
https://www.readbyqxmd.com/read/29198584/aptamers-targeting-cell-surface-proteins
#6
REVIEW
Masaki Takahashi
High affinity binders targeting specific cell surface proteins are vital for developing basic and applied biosciences. However, despite sustained efforts to generate such binders by chemicals and antibodies, there are still many cell surface proteins that lack high affinity binders. Nucleic acids, referred to as aptamers, appear to be potential binders to capture cell surface proteins because single-strand DNA/RNA can form distinct structures of high affinity and specificity to a wide range of targets. Aptamers are isolated from large combinatorial libraries using a unique iterative selection-amplification process known as systematic evolution of ligands by exponential enrichment (SELEX)...
November 30, 2017: Biochimie
https://www.readbyqxmd.com/read/29196970/endocannabinoid-hydrolases-in-avian-hd11-macrophages-identified-by-chemoproteomics-inactivation-by-small-molecule-inhibitors-and-pathogen-induced-downregulation-of-their-activity
#7
Jung Hwa Lee, Xiang Hou, Evangel Kummari, Abdolsamad Borazjani, Mariola J Edelmann, Matthew K Ross
The endocannabinoids (eCBs) are endogenous arachidonoyl-containing lipid mediators with important roles in host defense. Macrophages are first-line defenders of the innate immune system and biosynthesize large amounts of eCBs when activated. The cellular levels of eCBs are controlled by the activities of their biosynthetic enzymes and catabolic enzymes, which include members of the serine hydrolase (SH) superfamily. The physiologic activity of SHs can be assessed in a class-specific way using chemoproteomic activity-based protein profiling (ABPP) methods...
December 1, 2017: Molecular and Cellular Biochemistry
https://www.readbyqxmd.com/read/29082417/vibrational-spectroscopy-combined-with-transcriptomic-analysis-for-investigation-of-bacterial-responses-towards-acid-stress
#8
Mya M Hlaing, Bayden R Wood, Don McNaughton, Julian I Rood, Edward M Fox, Mary Ann Augustin
The ability of bacteria to tolerate acid stress plays an important role in their growth and survival. In particular, aciduric bacteria have several survival systems that prevent cell damage from acid stress. In this study, the effect of the bacterial stress induced by pre-adaptation at different pH values on the cellular macromolecules of Lactobacillus plantarum was investigated using Raman spectroscopy and Fourier transform infrared spectroscopy. The expression of key genes was also quantified to provide understanding of the transcriptional response of the cells to lethal acid stress conditions...
October 29, 2017: Applied Microbiology and Biotechnology
https://www.readbyqxmd.com/read/29075180/evaluating-the-autonomy-of-the-drosophila-circadian-clock-in-dissociated-neuronal-culture
#9
Virginie Sabado, Ludovic Vienne, Emi Nagoshi
Circadian behavioral rhythms offer an excellent model to study intricate interactions between the molecular and neuronal mechanisms of behavior. In mammals, pacemaker neurons in the suprachiasmatic nucleus (SCN) generate rhythms cell-autonomously, which are synchronized by the network interactions within the circadian circuit to drive behavioral rhythms. However, whether this principle is universal to circadian systems in animals remains unanswered. Here, we examined the autonomy of the Drosophila circadian clock by monitoring transcriptional and post-transcriptional rhythms of individual clock neurons in dispersed culture with time-lapse microscopy...
2017: Frontiers in Cellular Neuroscience
https://www.readbyqxmd.com/read/29052189/cell-type-specific-profiling-of-chromatin-modifications-and-associated-proteins
#10
Ana Karina Morao, Erwann Caillieux, Vincent Colot, François Roudier
Progression of a cell along a differentiation path is characterized by changes in gene expression profiles. Alterations of these transcriptional programs result from cell type-specific transcription factors that act in a dynamic chromatin environment. Understanding the precise contribution of these molecular factors during the differentiation process requires accessing specific cell types within a developing organ. This chapter describes a streamlined and alternative version of INTACT, a method enabling the isolation of specific cell populations by affinity-purification of tagged nuclei and the subsequent analysis of gene expression, transcription factor binding profiles, as well as chromatin state at a genome-wide scale...
2018: Methods in Molecular Biology
https://www.readbyqxmd.com/read/29046457/hiv-1-infection-of-primary-cd4-t-cells-regulates-the-expression-of-specific-herv-k-hml-2-elements
#11
George R Young, Sandra N Terry, Lara Manganaro, Alvaro Cuesta-Dominguez, Gintaras Deikus, Dabeiba Bernal-Rubio, Laura Campisi, Ana Fernandez-Sesma, Robert Sebra, Viviana Simon, Lubbertus C F Mulder
Endogenous retroviruses (ERVs) occupy extensive regions of the human genome. Although many of these retroviral elements have lost their ability to replicate, those whose insertion took place more recently, such as the HML-2 group of HERV-K elements, still retain intact open reading frames and the capacity to produce certain viral RNA and/or proteins. Transcription of these ERVs is, however, tightly regulated by dedicated epigenetic control mechanisms. Nonetheless, it has been reported that some pathologic states, such as viral infections and certain cancers, coincide with ERV expression suggesting transcriptional reawakening is possible...
October 18, 2017: Journal of Virology
https://www.readbyqxmd.com/read/29030127/a-method-for-the-isolation-and-enrichment-of-purified-bovine-milk-exosomes
#12
Kanchan Vaswani, Yong Qin Koh, Fatema B Almughlliq, Hassendrini N Peiris, Murray D Mitchell
Exosomes are nanovesicles that play important roles in intercellular communication as they carry information to target cells. Isolation of high purity exosomes will aid in studying the exosomal cargo and quantity as well as how cell-specific messages are carried. We describe a new method incorporating size exclusion chromatography (SEC) to enrich milk-derived exosomes from extracellular vesicles (EVs). This involved the initial isolation of EVs from bovine milk via milk processing and ultracentrifugation; followed by a new method to enrich exosomes using SEC...
October 10, 2017: Reproductive Biology
https://www.readbyqxmd.com/read/28960179/effects-of-orally-ingested-arsenic-on-respiratory-epithelial-permeability-to-bacteria-and-small-molecules-in-mice
#13
Michael W Henderson, Jennifer H Madenspacher, Gregory S Whitehead, Seddon Y Thomas, Jim J Aloor, Kymberly M Gowdy, Michael B Fessler
BACKGROUND: Arsenic exposure via drinking water impacts millions of people worldwide. Although arsenic has been associated epidemiologically with increased lung infections, the identity of the lung cell types targeted by peroral arsenic and the associated immune mechanisms remain poorly defined. OBJECTIVES: We aimed to determine the impact of peroral arsenic on pulmonary antibacterial host defense. METHODS: Female C57BL/6 mice were administered drinking water with 0, 250 ppb, or 25 ppm sodium arsenite for 5 wk and then challenged intratracheally with Klebsiella pneumoniae, Streptococcus pneumoniae, or lipopolysaccharide...
September 28, 2017: Environmental Health Perspectives
https://www.readbyqxmd.com/read/28956755/nuclear-transcriptomes-at-high-resolution-using-retooled-intact
#14
Mauricio Reynoso, Germain Pauluzzi, Kaisa Kajala, Sean Cabanlit, Joel Velasco, Jérémie Bazin, Roger Deal, Neelima Sinha, Siobhan M Brady, Julia Bailey-Serres
Isolated nuclei provide access to early steps in gene regulation involving chromatin as well as transcript production and processing. Here we describe transfer of the Isolation of Nuclei from TAgged specific Cell Types (INTACT) to the monocot rice (Oryza sativa L.). The purification of biotinylated nuclei was redesigned by replacing the outer nuclear envelope-targeting domain of the Nuclear Tagging Fusion (NTF) protein with an outer nuclear envelope-anchored domain. This modified NTF was combined with codon optimized E...
September 27, 2017: Plant Physiology
https://www.readbyqxmd.com/read/28910620/ctag-paperclip-reveals-alternative-polyadenylation-promotes-cell-type-specific-protein-diversity-and-shifts-araf-isoforms-with-microglia-activation
#15
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
#16
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
#17
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
#18
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
#19
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
#20
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
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