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Capture enrichment

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https://www.readbyqxmd.com/read/29921228/laser-capture-microdissection-for-transcriptomic-profiles-in-human-skin-biopsies
#1
Silvia Santoro, Ignazio Diego Lopez, Raffaella Lombardi, Andrea Zauli, Ana Maria Osiceanu, Melissa Sorosina, Ferdinando Clarelli, Silvia Peroni, Daniele Cazzato, Margherita Marchi, Angelo Quattrini, Giancarlo Comi, Raffaele Adolfo Calogero, Giuseppe Lauria, Filippo Martinelli Boneschi
BACKGROUND: The acquisition of reliable tissue-specific RNA sequencing data from human skin biopsy represents a major advance in research. However, the complexity of the process of isolation of specific layers from fresh-frozen human specimen by laser capture microdissection, the abundant presence of skin nucleases and RNA instability remain relevant methodological challenges. We developed and optimized a protocol to extract RNA from layers of human skin biopsies and to provide satisfactory quality and amount of mRNA sequencing data...
June 19, 2018: BMC Molecular Biology
https://www.readbyqxmd.com/read/29913018/assessment-of-a-targeted-gene-panel-for-identification-of-genes-associated-with-movement-disorders
#2
Solveig Montaut, Christine Tranchant, Nathalie Drouot, Gabrielle Rudolf, Claire Guissart, Julien Tarabeux, Tristan Stemmelen, Amandine Velt, Cécile Fourrage, Patrick Nitschké, Bénédicte Gerard, Jean-Louis Mandel, Michel Koenig, Jamel Chelly, Mathieu Anheim
Importance: Movement disorders are characterized by a marked genotypic and phenotypic heterogeneity, complicating diagnostic work in clinical practice and molecular diagnosis. Objective: To develop and evaluate a targeted sequencing approach using a customized panel of genes involved in movement disorders. Design, Setting and Participants: We selected 127 genes associated with movement disorders to create a customized enrichment in solution capture array...
June 18, 2018: JAMA Neurology
https://www.readbyqxmd.com/read/29912191/adaptation-of-hybridization-capture-of-chromatin-associated-proteins-for-proteomics-to-mammalian-cells
#3
Hector Guillen-Ahlers, Prahlad K Rao, Danu S Perumalla, Maria J Montoya, Avinash Y L Jadhav, Michael R Shortreed, Lloyd M Smith, Michael Olivier
The hybridization capture of chromatin-associated proteins for proteomics (HyCCAPP) technology was initially developed to uncover novel DNA-protein interactions in yeast. It allows analysis of a target region of interest without the need for prior knowledge about likely proteins bound to the target region. This, in theory, allows HyCCAPP to be used to analyze any genomic region of interest, and it provides sufficient flexibility to work in different cell systems. This method is not meant to study binding sites of known transcription factors, a task better suited for Chromatin Immunoprecipitation (ChIP) and ChIP-like methods...
June 1, 2018: Journal of Visualized Experiments: JoVE
https://www.readbyqxmd.com/read/29912187/laser-capture-microdissection-of-highly-pure-trabecular-meshwork-from-mouse-eyes-for-gene-expression-analysis
#4
Caleb Sutherland, Yu Wang, Robert V Brown, Julie Foley, Beth Mahler, Kyathanahalli S Janardhan, Ramesh C Kovi, Anton M Jetten
Laser capture microdissection (LCM) has allowed gene expression analysis of single cells and enriched cell populations in tissue sections. LCM is a great tool for the study of the molecular mechanisms underlying cell differentiation and the development and progression of various diseases, including glaucoma. Glaucoma, which comprises a family of progressive optic neuropathies, is the most common cause of irreversible blindness worldwide. Structural changes and damage within the trabecular meshwork (TM) can result in increased intraocular pressure (IOP), which is a major risk factor for developing glaucoma...
June 3, 2018: Journal of Visualized Experiments: JoVE
https://www.readbyqxmd.com/read/29907032/theoretical-description-of-quantum-mechanical-permeation-of-graphene-membranes-by-charged-hydrogen-isotopes
#5
James W Mazzuca, Nathaniel K Haut
It has been recently shown that in the presence of an applied voltage, hydrogen and deuterium nuclei can be separated from one another using graphene membranes as a nuclear sieve, resulting in a 10-fold enhancement in the concentration of the lighter isotope. While previous studies, both experimental and theoretical, have attributed this effect mostly to differences in vibrational zero point energy (ZPE) of the various isotopes near the membrane surface, we propose that multi-dimensional quantum mechanical tunneling of nuclei through the graphene membrane influences this proton permeation process in a fundamental way...
June 14, 2018: Journal of Chemical Physics
https://www.readbyqxmd.com/read/29906255/helicobacter-pylori-nickel-storage-proteins-recognition-and-modulation-of-diverse-metabolic-targets
#6
Zachary Saylor, Robert Maier
Nickel metabolism and trafficking in Helicobacter pylori is complex, perhaps more so than in any other pathogen. Along with nickel enzymes and their associated nickel-binding maturation machinery, H. pylori contains nickel storage proteins, Hpn and Hpnl. Through a combined crosslinking and enrichment approach, we show that Hpn/Hpnl interact with a wide array of partners; over 100 proteins were captured, including known nickel-enzyme maturation proteins, and other proteins outside known H. pylori nickel-associated proteins...
June 15, 2018: Microbiology
https://www.readbyqxmd.com/read/29903469/a-sublimate-sorbent-for-stir-bar-sorptive-extraction-of-aqueous-endocrine-disruptor-pesticides-for-gas-chromatography-electron-capture-detection
#7
Yu-Wen Huang, Hua Kwang Lee, Hou-Kuang Shih, Jen-Fon Jen
A dumbbell-shaped magnetic stir-bar with sublimate sorbent was prepared for the stir bar sorptive extraction (SBSE) of pesticides in an aqueous sample prior to gas chromatography-micro-electron capture detection (GC-μECD). Cyclododecane (CDD) was coated onto a magnetic stir-bar surface as a sublimate sorbent, and steel balls were placed on both ends to form a dumbbell-shaped magnetic stir-bar for SBSE. Four EDC pesticides including chlorpyrifos, ethion, bromopropylate, and λ-cyhalothrin in aqueous samples were selected as model species to examine the proposed SBSE and the following desorption...
June 6, 2018: Journal of Chromatography. A
https://www.readbyqxmd.com/read/29902572/phylogenetics-of-moth-like-butterflies-papilionoidea-hedylidae-based-on-a-new-13-locus-target-capture-probe-set
#8
Akito Y Kawahara, Jesse W Breinholt, Marianne Espeland, Caroline Storer, David Plotkin, Kelly M Dexter, Emmanuel F A Toussaint, Ryan A St Laurent, Gunnar Brehm, Sergio Vargas, Dimitri Forero, Naomi E Pierce, David J Lohman
The Neotropical moth-like butterflies (Hedylidae) are perhaps the most unusual butterfly family. In addition to being species-poor, this family is predominantly nocturnal and has anti-bat ultrasound hearing organs. Evolutionary relationships among the 36 described species are largely unexplored. A 13-gene anchored hybrid enrichment probe set ('BUTTERFLY2.0'), that includes standard markers used in butterfly phylogenetics, captured sequences from decades-old museum specimens, and appears to be a cost-effective technique to infer phylogenetic relationships of the butterfly tree of life...
June 11, 2018: Molecular Phylogenetics and Evolution
https://www.readbyqxmd.com/read/29895565/chromatin-interaction-analysis-using-paired-end-tag-chia-pet-sequencing-in-tadpole-tissues
#9
Nicolas Buisine, Xiaoan Ruan, Yijun Ruan, Laurent M Sachs
Proper gene expression involves communication between the regulatory elements and promoters of genes. Today, chromosome conformation capture (3C)-based methods efficiently probe chromosome folding in the nucleus and thus provide a molecular description of physical proximity through DNA looping between enhancer(s) and their target promoter(s). One such method, chromatin interaction analysis using paired-end-tag (ChIA-PET) sequencing is a powerful high-throughput method for detection of genome-wide chromatin interactions...
June 12, 2018: Cold Spring Harbor Protocols
https://www.readbyqxmd.com/read/29895563/chromatin-immunoprecipitation-for-chromatin-interaction-analysis-using-paired-end-tag-chia-pet-sequencing-in-tadpole-tissues
#10
Nicolas Buisine, Xiaoan Ruan, Yijun Ruan, Laurent M Sachs
Proper gene expression involves communication between the regulatory elements and promoters of genes. Because regulatory elements can be located over a large range of genomic distances (from as close as a few hundred bp to as much as several Mb away), contact and communication between regulators and the core transcriptional machinery at promoters are mediated through DNA looping. Today, chromosome conformation capture (3C)-based methods efficiently probe chromosome folding in the nucleus and thus provide a molecular description of physical proximity between enhancer(s) and their target promoter(s)...
June 12, 2018: Cold Spring Harbor Protocols
https://www.readbyqxmd.com/read/29886988/metal-fractionation-in-marine-sediments-acidified-by-enrichment-of-co-2-a-risk-assessment
#11
Manoela Romanó de Orte, Estefanía Bonnail, Aguasanta M Sarmiento, Esther Bautista-Chamizo, M Dolores Basallote, Inmaculada Riba, Ángel DelValls, José Miguel Nieto
Carbon-capture and storage is considered to be a potential mitigation option for climate change. However, accidental leaks of CO2 can occur, resulting in changes in ocean chemistry such as acidification and metal mobilization. Laboratory experiments were performed to provide data on the effects of CO2 -related acidification on the chemical fractionation of metal(loid)s in marine-contaminated sediments using sequential extraction procedures. The results showed that sediments from Huelva estuary registered concentrations of arsenic, copper, lead, and zinc that surpass the probable biological effect level established by international protocols...
June 2018: Marine Pollution Bulletin
https://www.readbyqxmd.com/read/29885208/leveraging-digital-health-technologies-and-outpatient-sampling-in-clinical-drug-development-a-phase-1-exploratory-study
#12
Marissa F Dockendorf, Gowri Murthy, Kevin P Bateman, Prajakti A Kothare, Melanie Anderson, Iris Xie, Jeff R Sachs, Rubi Burlage, Andra Goldman, Matthew Moyer, Jyoti Shah, Rachel Ruba, Lisa Shipley, Jane Harrelson
Merck & Co., Inc. (Kenilworth, New Jersey) is investing in approaches to enrich clinical trial data and augment decision-making through utilization of digital health technologies, outpatient sampling, and real-time data access. As part of this strategy, a Phase 1 study was conducted to explore a few technologies of interest. In this fixed-sequence, two-period trial, 16 healthy subjects were administered 50-mg once-daily sitagliptin packaged in a bottle that electronically captured the date and time study medication was dispensed (Period 1) and in a traditional pharmacy bottle (Period 2)...
June 9, 2018: Clinical Pharmacology and Therapeutics
https://www.readbyqxmd.com/read/29884412/comparative-genomic-analysis-of-oral-versus-laryngeal-and-pharyngeal-cancer
#13
David M Vossen, Caroline V M Verhagen, Marcel Verheij, Lodewyk F A Wessels, Conchita Vens, Michiel W M van den Brekel
OBJECTIVE: Locally advanced oral squamous cell carcinoma (OSCC) shows lower locoregional control and disease specific survival rates than laryngeal and pharyngeal squamous cell carcinoma (L/P-SCC) after definitive chemoradiotherapy treatment. Despite clinical factors, this can point towards a different tumor biology that could impact chemoradiotherapy response rates. This prompted us to compare the mutational profiles of OSCC with L/P-SCC. METHODS: We performed target capture DNA sequencing on 111 HPV-negative HNSCC samples (NKI dataset), 55 oral and 56 laryngeal/pharyngeal, and identified somatic point mutations and copy number aberrations...
June 2018: Oral Oncology
https://www.readbyqxmd.com/read/29881994/transcriptome-pathology-correlation-identifies-interplay-between-tdp-43-and-the-expression-of-its-kinase-ck1e-in-sporadic-als
#14
Florian Krach, Ranjan Batra, Emily C Wheeler, Anthony Q Vu, Ruth Wang, Kasey Hutt, Stuart J Rabin, Michael W Baughn, Ryan T Libby, Sandra Diaz-Garcia, Jennifer Stauffer, Elaine Pirie, Shahram Saberi, Maria Rodriguez, Assael A Madrigal, Zacharias Kohl, Beate Winner, Gene W Yeo, John Ravits
Sporadic amyotrophic lateral sclerosis (sALS) is the most common form of ALS, however, the molecular mechanisms underlying cellular damage and motor neuron degeneration remain elusive. To identify molecular signatures of sALS we performed genome-wide expression profiling in laser capture microdissection-enriched surviving motor neurons (MNs) from lumbar spinal cords of sALS patients with rostral onset and caudal progression. After correcting for immunological background, we discover a highly specific gene expression signature for sALS that is associated with phosphorylated TDP-43 (pTDP-43) pathology...
June 7, 2018: Acta Neuropathologica
https://www.readbyqxmd.com/read/29877604/silica-based-magnetic-hybrid-nano-composite-for-the-extraction-and-pre-concentration-of-some-organophosphorus-pesticides-before-gas-chromatography
#15
Somayeh Koupaei Malek, Hamid Rashidi Nodeh, Behrouz Akbari-Adergani
The precise control of pesticide residues in foodstuffs depends thoroughly on the clean extraction of analytes using specifically designed separation methods. In this study, a one-pot sol-gel process was used for the preparation of a magnetic hybrid silica-gel tetraethylortho silicate-cyanopropyltriethoxy silane nano-composite. The prepared material was characterized using energy dispersive X-ray spectroscopy, Fourier transform infrared spectroscopy, single-point specific surface area and scanning electron microcopy...
June 7, 2018: Journal of Separation Science
https://www.readbyqxmd.com/read/29874767/a-novel-strategy-towards-sustainable-and-stable-nitritation-denitritation-in-an-a-b-process-for-mainstream-municipal-wastewater-treatment
#16
Jun Gu, Qin Yang, Yu Liu
The conventional activated sludge process is increasingly receiving concerns for its high energy consumption and excess sludge production. To cope with these issues, an A-B process for nitrogen removal via nitritation-denitritation was proposed in previous study which showed the possibility to achieve energy self-sufficient wastewater reclamation. However, nitritation-denitritation in such a process could not be sustained due to excessive COD capture at A-stage. In this study a novel A-B process configuration in which a portion of influent was directed to B-stage was developed for sustainable and stable nitrogen removal via nitrite shunt with minimal impacts on energy recovery...
February 2018: Chemosphere
https://www.readbyqxmd.com/read/29873705/a-systematic-approach-for-identifying-shared-mechanisms-in-epilepsy-and-its-comorbidities
#17
Charles Tapley Hoyt, Daniel Domingo-Fernández, Nora Balzer, Anka Güldenpfennig, Martin Hofmann-Apitius
Cross-sectional epidemiological studies have shown that the incidence of several nervous system diseases is more frequent in epilepsy patients than in the general population. Some comorbidities [e.g. Alzheimer's disease (AD) and Parkinson's disease] are also risk factors for the development of seizures; suggesting they may share pathophysiological mechanisms with epilepsy. A literature-based approach was used to identify gene overlap between epilepsy and its comorbidities as a proxy for a shared genetic basis for disease, or genetic pleiotropy, as a first effort to identify shared mechanisms...
January 1, 2018: Database: the Journal of Biological Databases and Curation
https://www.readbyqxmd.com/read/29873203/amorphous-porous-organic-polymers-based-on-schiff-base-chemistry-for-high-efficient-iodine-capture
#18
Zongxia Guo, Panli Sun, Jianbin Lin, Tong Shi, Shaofeng Liu, Abin Sun, Zhibo Li
Porous organic polymers (POPs) have been considered as prominent adsorbents for volatile iodine. So far, both crystalline and amorphous POPs have accomplished excellent Iodine capture capability. Considering the difficulty and challenging in preparing perfect crystalline POPs, it needs more explorations in developing versatile amorphous POPs. Herein, amorphous POPs based on Schiff-base reaction were designed and synthesized for volatile iodine removal. Four amorphous POPs products named as NDB-H, NDB-S, ADB-HS and ADB-S obtained under different solvothermal conditions were investigated in morphologies, porosity and their iodine enrichment performance in details...
June 5, 2018: Chemistry, An Asian Journal
https://www.readbyqxmd.com/read/29872146/somatic-mutations-in-benign-breast-disease-tissue-and-risk-of-subsequent-invasive-breast-cancer
#19
Thomas E Rohan, Christopher A Miller, Tiandao Li, Yihong Wang, Olivier Loudig, Mindy Ginsberg, Andrew Glass, Elaine Mardis
BACKGROUND: Insights into the molecular pathogenesis of breast cancer might come from molecular analysis of tissue from early stages of the disease. METHODS: We conducted a case-control study nested in a cohort of women who had biopsy-confirmed benign breast disease (BBD) diagnosed between 1971 and 2006 at Kaiser Permanente Northwest and who were followed to mid-2015 to ascertain subsequent invasive breast cancer (IBC); cases (n = 218) were women with BBD who developed subsequent IBC and controls, individually matched (1:1) to cases, were women with BBD who did not develop IBC in the same follow-up interval as that for the corresponding case...
June 6, 2018: British Journal of Cancer
https://www.readbyqxmd.com/read/29872131/the-prion-protein-is-embedded-in-a-molecular-environment-that-modulates-transforming-growth-factor-%C3%AE-and-integrin-signaling
#20
Farinaz Ghodrati, Mohadeseh Mehrabian, Declan Williams, Ondrej Halgas, Matthew E C Bourkas, Joel C Watts, Emil F Pai, Gerold Schmitt-Ulms
At times, it can be difficult to discern if a lack of overlap in reported interactions for a protein-of-interest reflects differences in methodology or biology. In such instances, systematic analyses of protein-protein networks across diverse paradigms can provide valuable insights. Here, we interrogated the interactome of the prion protein (PrP), best known for its central role in prion diseases, in four mouse cell lines. Analyses made use of identical affinity capture and sample processing workflows. Negative controls were generated from PrP knockout lines of the respective cell models, and the relative levels of peptides were quantified using isobaric labels...
June 5, 2018: Scientific Reports
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