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https://www.readbyqxmd.com/read/29779489/rap1-downregulation-by-mir-320c-reduces-platelet-activation-in-ex-vivo-storage
#1
Chintamani Atreya, Neetu Dahiya
BACKGROUND: A small GTPase protein, the Ras-related protein 1 (RAP1), abundant in platelets is known to be activated following agonist induced platelet activation, suggesting that RAP1 downregulation could in turn reduce platelet activation in storage. Our objective of this study is to identify RAP1 regulating miRNAs and their role in platelet activation during storage. METHODS: We applied MS2-TRAP (tagged RNA affinity purification) methodology to enrich miRNAs that target the 3' untranslated region (3'UTR) of RAP1 mRNA in two mammalian cell lines followed by miRNA identification by microarray of total RNA samples enriched for miRNAs...
May 20, 2018: MicroRNA
https://www.readbyqxmd.com/read/29777514/a-modified-yeast-three-hybrid-system-enabling-both-positive-and-negative-selections
#2
Christopher P Wallis, Aleksandra Filipovska, Oliver Rackham
OBJECTIVE: To increase the reporter repertoire of the yeast three-hybrid system and introduce the option of negative selection. RESULTS: Two new versions of the yeast three-hybrid system were made by modifying the MS2 coat RNA-binding protein and fusing it to the Gal4 DNA-binding protein. This allows the use of Gal4 inducible reporters to measure RNA-protein interactions. We introduced two mutations, V29I and N55K into the tandem MS2 dimer and an 11 amino acid deletion to increase RNA-protein affinity and inhibit capsid formation...
May 18, 2018: Biotechnology Letters
https://www.readbyqxmd.com/read/29776535/multi-residue-analysis-of-pesticides-in-surface-water-by-liquid-chromatography-quadrupole-orbitrap-high-resolution-tandem-mass-spectrometry
#3
J Casado, D Santillo, P Johnston
A quantitative targeted screening method for the determination of residues of a broad group of more than 250 pesticides in surface water samples was developed and validated. Substances were isolated from the sample matrix by solid-phase extraction (SPE), using hydrophilic-lipophilic balanced polymeric sorbents (HLB), and analysed by reversed-phase liquid chromatography (LC) - Orbitrap high-resolution mass spectrometry (HRMS). Compounds were quantified in full scan acquisition mode, while accurate data dependant MS2 analysis was simultaneously triggered for the unambiguous identification of the targeted substances...
September 18, 2018: Analytica Chimica Acta
https://www.readbyqxmd.com/read/29776310/preparation-and-evaluation-of-ribonuclease-resistant-viral-hiv-rna-standards-based-on-armored-rna-technology
#4
Mohammad Gholami, Mehrdad Ravanshad, Kazem Baesi, Siamak M. Samiee, Negin Hosseini Rozbahani, Minoo Mohraz
BAckground: The human immunodeficiency virus type 1 (HIV-1) is an infectious viral agent that gradually extinguishes the immune system, resulting in acquired immune deficiency syndrome (AIDS). The aim of this study was to construct an RNA-positive control based on armored (AR) RNA technology, using HIV-1 RNA as a model. Methods: The MS2 maturase, a coat protein gene (at positions 1765 to 1787) and HIV-1 pol gene were cloned into pET-32a plasmid. The prepared plasmid was transformed into Escherichia coli strain BL2 (DE3), and the expression of the construct was induced by 1 mM of isopropyl-L-thio-D-galactopyranoside (IPTG) at 37 °C for 16 h to obtain the fabricated AR RNA...
May 19, 2018: Iranian Biomedical Journal
https://www.readbyqxmd.com/read/29763521/screening-and-investigation-of-triplex-dna-binders-from-stephania-tetrandra-s-moore-by-a-combination-of-peak-area-fading-uhplc-with-orbitrap-ms-and-optical-spectroscopies
#5
Hongmei Yang, Yihan Wang, Wenjing Yu, Lei Shi, Hongfeng Wang, Rui Su, Changbao Chen, Shuying Liu
The identification and screening of triplex DNA binders are important because these compounds, in many cases, are potential anticancer agents as well as promising drug candidates. Therefore, the ability to screen for these compounds in a high-throughput mode could dramatically improve the drug screening process. A method involving a combination of 96-well plate format and peak area-fading ultra high performance liquid chromatography coupled with Orbitrap mass spectrometry was employed for screening bioactive compounds binding to the triplex DNA from the extracts of Stephania tetrandra S...
May 15, 2018: Journal of Separation Science
https://www.readbyqxmd.com/read/29757646/inhibition-of-breast-cancer-cell-migration-by-cyclotides-isolated-from-pombalia-calceolaria
#6
Meri Emili F Pinto, Jhenny Z G Najas, Luma G Magalhães, Antonio F Bobey, Jacqueline N Mendonça, Norberto P Lopes, Flávia M Leme, Simone P Teixeira, Marcelo Trovó, Adriano D Andricopulo, Johannes Koehbach, Christian W Gruber, Eduardo Maffud Cilli, Vanderlan S Bolzani
Two new bracelet cyclotides from roots of Pombalia calceolaria with potential anticancer activity have been characterized in this work. The cyclotides Poca A and B (1 and 2) and the previously known CyO4 (3) were de novo sequenced by MALDI-TOF/TOF mass spectrometry (MS). The MS2 spectra were examined and the amino acid sequences were determined. The purified peptides were tested for their cytotoxicity and effects on cell migration of MDA-MB-231, a triple-negative breast cancer cell line. The isolated cyclotides reduced the number of cancer cells by more than 80% at 20 μM, and the concentration-related cytotoxic responses were observed with IC50 values of 1...
May 14, 2018: Journal of Natural Products
https://www.readbyqxmd.com/read/29749064/complementary-middle-down-and-intact-monoclonal-antibody-proteoform-characterization-by-capillary-zone-electrophoresis-mass-spectrometry
#7
Arseniy Mikhail Belov, Li Zang, Roberto Sebastiano, Marcia R Santos, David R Bush, Barry L Karger, Alexander R Ivanov
High resolution capillary zone electrophoresis - mass spectrometry (CZE-MS) has been of increasing interest for the analysis of biopharmaceuticals. In this work, a combination of middle-down and intact CZE-MS analyses has been implemented for the characterization of a biotherapeutic monoclonal antibody (mAb) with a variety of post-translational modifications (PTMs) and glycosylation structures. Middle-down and intact CZE separations were performed in an acidified methanol-water background electrolyte on a capillary with a positively-charged coating (M7C4I) coupled to an Orbitrap mass spectrometer using a commercial sheathless interface (CESI)...
May 11, 2018: Electrophoresis
https://www.readbyqxmd.com/read/29748384/balance-between-senescence-and-apoptosis-is-regulated-by-telomere-damage-induced-association-between-p16-and-caspase-3
#8
Shanmugam Panneer Selvam, Braden M Roth, Rose Nganga, Jisun Kim, Marion A Cooley, Kristi L Helke, Charles D Smith, Besim Ogretmen
Telomerase activation protects cells from telomere damage by delaying senescence and inducing cell immortalization, whereas telomerase inhibition mediates rapid senescence or apoptosis. However, the cellular mechanisms that determine telomere damage-dependent senescence versus apoptosis induction are largely unknown. Here, we demonstrate that telomerase instability mediated by silencing of sphingosine kinase 2 (SPHK2) and sphingosine 1-phosphate (S1P), which binds and stabilizes telomerase, induces telomere damage-dependent caspase-3 activation and apoptosis, but not senescence, in p16-deficient lung cancer cells or tumors...
May 10, 2018: Journal of Biological Chemistry
https://www.readbyqxmd.com/read/29748139/institutional-interventional-radiology-symposium-increases-medical-student-interest-and-identifies-target-recruitment-candidates
#9
Mina S Makary, Anand Rajan, Rose J Miller, Eric D Elliott, James W Spain, Gregory E Guy
OBJECTIVES: To assess and raise medical student interest in interventional radiology (IR); and to evaluate student response across gender, level of training, and surgical vs nonsurgical specialty interest. MATERIALS AND METHODS: All Ohio medical students were invited to an IR Symposium held by a large academic medical center in central Ohio. The program encompassed didactic lectures, hands-on simulation models, and a networking luncheon with faculty, trainees, and industry partners...
April 12, 2018: Current Problems in Diagnostic Radiology
https://www.readbyqxmd.com/read/29748090/non-targeted-glycosidic-profiling-of-international-wines-using-neutral-loss-high-resolution-mass-spectrometry
#10
C Barnaba, E Dellacassa, G Nicolini, T Nardin, M Serra, R Larcher
Many metabolites naturally occur as glycosides, since sugar moieties can be crucial for their biological activity and increase their water solubility. In the plant kingdom they may occur as glycosides or sugar esters, depending on precursor chemical structure, and in wine they have traditionally attracted attention due to their organoleptic properties, such as astringency and bitterness, and because they affect the colour and aroma of wines. A new approach directed at detailed description of glycosides in a large selection of monovarietal wines (8 samples each of Pinot Blanc, Muller Thurgau, Riesling, Traminer, Merlot, Pinot Noir and Cabernet Sauvignon) was developed by combining high performance liquid chromatography with high resolution tandem mass spectrometry...
May 4, 2018: Journal of Chromatography. A
https://www.readbyqxmd.com/read/29744561/selective-labeling-for-the-identification-and-semi-quantification-of-lipid-aldehydes-in-food-products
#11
Boudewijn Hollebrands, Eftychia Varvaki, Sonja Kaal, Hans-Gerd Janssen
Lipid oxidation reactions in foods rich in healthy unsaturated fatty acids result in the formation of a wide range of oxidation products that can have adverse effects on food quality and safety. To improve the understanding of oxidation reactions and methods for their inhibition, detailed information on the type and levels of the oxidation products formed is required. Accurate measurement of lipid oxidation products, especially of the non-volatile aldehyde products, has so far been a challenge due to the low sensitivity and limited specificity of most analytical methods...
May 10, 2018: Analytical and Bioanalytical Chemistry
https://www.readbyqxmd.com/read/29743190/ionstar-enables-high-precision-low-missing-data-proteomics-quantification-in-large-biological-cohorts
#12
Xiaomeng Shen, Shichen Shen, Jun Li, Qiang Hu, Lei Nie, Chengjian Tu, Xue Wang, David J Poulsen, Benjamin C Orsburn, Jianmin Wang, Jun Qu
Reproducible quantification of large biological cohorts is critical for clinical/pharmaceutical proteomics yet remains challenging because most prevalent methods suffer from drastically declined commonly quantified proteins and substantially deteriorated quantitative quality as cohort size expands. MS2-based data-independent acquisition approaches represent tremendous advancements in reproducible protein measurement, but often with limited depth. We developed IonStar, an MS1-based quantitative approach enabling in-depth, high-quality quantification of large cohorts by combining efficient/reproducible experimental procedures with unique data-processing components, such as efficient 3D chromatographic alignment, sensitive and selective direct ion current extraction, and stringent postfeature generation quality control...
May 9, 2018: Proceedings of the National Academy of Sciences of the United States of America
https://www.readbyqxmd.com/read/29738236/a-smartphone-based-in-gel-loop-mediated-isothermal-amplification-glamp-system-enables-rapid-coliphage-ms2-quantification-in-environmental-waters
#13
Xiao Huang, Xingyu Lin, Katharina Urmann, Lijie Li, Xing Xie, Sunny Jiang, Michael R Hoffmann
Model coliphages (e.g., ΦX174, MS2, and PRD1) have been widely used in place of pathogenic viruses to study their fate and transport in the environment and during wastewater treatment. Two groups of coliphages (F-specific and somatic) are being explored as indicators of viral fecal pollution in ambient water. However, the detection and quantification of coliphages still largely relies on time-consuming culture-based plaque assays. In this study, we developed an in-gel loop mediated isothermal amplification (gLAMP) system enabling coliphage MS2 quantification within 30 minutes using standard laboratory devices...
May 8, 2018: Environmental Science & Technology
https://www.readbyqxmd.com/read/29735998/boxcar-acquisition-method-enables-single-shot-proteomics-at-a-depth-of-10-000-proteins-in-100-minutes
#14
Florian Meier, Philipp E Geyer, Sebastian Virreira Winter, Juergen Cox, Matthias Mann
Great advances have been made in sensitivity and acquisition speed on the Orbitrap mass analyzer, enabling increasingly deep proteome coverage. However, these advances have been mainly limited to the MS2 level, whereas ion beam sampling for the MS1 scans remains extremely inefficient. Here we report a data-acquisition method, termed BoxCar, in which filling multiple narrow mass-to-charge segments increases the mean ion injection time more than tenfold as compared to that of a standard full scan. In 1-h analyses, the method provided MS1-level evidence for more than 90% of the proteome of a human cancer cell line that had previously been identified in 24 fractions, and it quantified more than 6,200 proteins in ten of ten replicates...
May 7, 2018: Nature Methods
https://www.readbyqxmd.com/read/29727953/profiling-the-decomposition-products-of-perfluorooctane-sulfonate-pfos-irradiated-using-an-electron-beam
#15
Tae-Hun Kim, Seungho Yu, Yeowool Choi, Tae-Yong Jeong, Sang Don Kim
Perfluorooctane sulfonate (PFOS) has been found in wastewater treatment plants (WWTPs) and in surface water as a result of domestic uses of textiles, electronics, and surfactants. The detection of PFOS in the aqueous environment has been linked to hazardous biological effects including estrogenicity and genotoxicity. To provide an alternative to conventional processes, one of the radical-based advanced oxidation and reduction processes being tested for treatment of refractory compounds in water, involves the use of an electron beam...
August 1, 2018: Science of the Total Environment
https://www.readbyqxmd.com/read/29726026/metabolic-profiles-of-neratinib-in-rat-by-using-ultra-high-performance-liquid-chromatography-coupled-with-diode-array-detector-and-q-exactive-orbitrap-tandem-mass-spectrometry
#16
Wen Liu, Sha Li, Yangke Wu, Xiao Yan, Y-M Zhu, J-H Huang, Zhuo Chen
Neratinib is a tyrosine kinase inhibitor that has been approved by FDA for the treatment of breast cancer. However, its metabolism remains unknown. This study was carried out to investigate the in vitro and in vivo metabolism of neratinib by using UHPLC-DAD-Q Exactive Orbitrap-MS instrument with dd-MS2 on-line data acquisition mode. The post-acquisition data was processed by MetWorks software. Under the current conditions, a total of 12 metabolites were detected and structurally identified based on their accurate masses, fragment ions and chromatographic retention times...
May 3, 2018: Biomedical Chromatography: BMC
https://www.readbyqxmd.com/read/29715646/effect-of-%C3%AE-m-fe-addition-mild-heat-and-solar-uv-on-sulfate-radical-mediated-inactivation-of-bacteria-viruses-and-micropollutant-degradation-in-water
#17
Miloch Marjanovic, Stefanos Giannakis, Dominique Grandjean, Luiz Felippe de Alencastro, Cesar Pulgarin
In this work, solar disinfection (SODIS) was enhanced by moderate addition of Fe and sodium peroxydisulfate (PDS), under solar light. A systematic assessment of the activating factors was performed, firstly isolated, then in pairs and concluded in the combined Fe/heat/solar UV-PDS activation process. Solar light was the most effective (single) activator, and its combination with Fe and heat (double activation) yielded high level of synergies (up to S = 2.13). The triple activation was able to reduce the bacterial load up to 6-log in less than 1 h, similarly to the photo-Fenton process done in comparison (SODIS alone: >5 h)...
April 26, 2018: Water Research
https://www.readbyqxmd.com/read/29694026/directed-evolution-of-heterologous-trnas-leads-to-reduced-dependence-on-post-transcriptional-modifications
#18
Kevin C Baldridge, Manasses Jora, Andre C Maranhao, Matthew M Quick, Balasubrahmanyam Addepalli, Jennifer S Brodbelt, Andrew D Ellington, Patrick A Limbach, Lydia M Contreras
Heterologous tRNA:aminoacyl tRNA synthetase pairs are often employed for noncanonical amino acid incorporation in the quest for an expanded genetic code. In this work, we investigated one possible mechanism by which directed evolution can improve orthogonal behavior for a suite of Methanocaldococcus jannaschii ( Mj) tRNATyr -derived amber suppressor tRNAs. Northern blotting demonstrated that reduced expression of heterologous tRNA variants correlated with improved orthogonality. We suspected that reduced expression likely minimized nonorthogonal interactions with host cell machinery...
April 25, 2018: ACS Synthetic Biology
https://www.readbyqxmd.com/read/29682972/parsing-and-quantification-of-raw-orbitrap-mass-spectrometer-data-using-rawquant
#19
Kevin A Kovalchik, Sophie Moggridge, David D Y Chen, Gregg B Morin, Christopher S Hughes
Effective analysis of protein samples by mass spectrometry (MS) requires careful selection and optimization of a range of experimental parameters. As the output from the primary detection device, the 'raw' MS data file can be used to gauge the success of a given sample analysis. However, the closed-source nature of the standard raw MS file can complicate effective parsing of the data contained within. To ease and increase the range of analyses possible, the RawQuant tool was developed to enable parsing of raw MS files derived from Thermo Orbitrap instruments to yield meta and scan data in an openly readable text format...
April 23, 2018: Journal of Proteome Research
https://www.readbyqxmd.com/read/29675740/identification-of-poly-n-acetyllactosamine-carrying-glycoproteins-from-hl-60-human-promyelocytic-leukemia-cells-using-a-site-specific-glycome-analysis-method-glyco-ridge
#20
Akira Togayachi, Azusa Tomioka, Mika Fujita, Masako Sukegawa, Erika Noro, Daisuke Takakura, Michiyo Miyazaki, Toshihide Shikanai, Hisashi Narimatsu, Hiroyuki Kaji
To elucidate the relationship between the protein function and the diversity and heterogeneity of glycans conjugated to the protein, glycosylation sites, glycan variation, and glycan proportions at each site of the glycoprotein must be analyzed. Glycopeptide-based structural analysis technology using mass spectrometry has been developed; however, complicated analyses of complex spectra obtained by multistage fragmentation are necessary, and sensitivity and throughput of the analyses are low. Therefore, we developed a liquid chromatography/mass spectrometry (MS)-based glycopeptide analysis method to reveal the site-specific glycome (Glycan heterogeneity-based Relational IDentification of Glycopeptide signals on Elution profile, Glyco-RIDGE)...
April 19, 2018: Journal of the American Society for Mass Spectrometry
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