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https://www.readbyqxmd.com/read/29455155/newly-designed-11-gene-panel-reveals-first-case-of-hereditary-amyloidosis-captured-by-massive-parallel-sequencing
#1
Zuzana Chyra Kufova, Tereza Sevcikova, Jaroslav Januska, Petr Vojta, Arpad Boday, Pavla Vanickova, Jana Filipova, Katerina Growkova, Tomas Jelinek, Marian Hajduch, Roman Hajek
AIMS: Amyloidosis is caused by deposition of abnormal protein fibrils, leading to damage of organ function. Hereditary amyloidosis represents a monogenic disease caused by germline mutations in 11 amyloidogenic precursor protein genes. One of the important but non-specific symptoms of amyloidosis is hypertrophic cardiomyopathy. Diagnostics of hereditary amyloidosis is complicated and the real cause can remain overlooked. We aimed to design hereditary amyloidosis gene panel and to introduce new next-generation sequencing (NGS) approach to investigate hereditary amyloidosis in a cohort of patients with hypertrophic cardiomyopathy of unknown significance...
February 17, 2018: Journal of Clinical Pathology
https://www.readbyqxmd.com/read/29454215/effect-based-trigger-values-for-in-vitro-and-in-vivo-bioassays-performed-on-surface-water-extracts-supporting-the-environmental-quality-standards-eqs-of-the-european-water-framework-directive
#2
Beate I Escher, Selim Aїt-Aїssa, Peter A Behnisch, Werner Brack, François Brion, Abraham Brouwer, Sebastian Buchinger, Sarah E Crawford, David Du Pasquier, Timo Hamers, Karina Hettwer, Klára Hilscherová, Henner Hollert, Robert Kase, Cornelia Kienle, Andrew J Tindall, Jochen Tuerk, Ron van der Oost, Etienne Vermeirssen, Peta A Neale
Effect-based methods including cell-based bioassays, reporter gene assays and whole-organism assays have been applied for decades in water quality monitoring and testing of enriched solid-phase extracts. There is no common EU-wide agreement on what level of bioassay response in water extracts is acceptable. At present, bioassay results are only benchmarked against each other but not against a consented measure of chemical water quality. The EU environmental quality standards (EQS) differentiate between acceptable and unacceptable surface water concentrations for individual chemicals but cannot capture the thousands of chemicals in water and their biological action as mixtures...
February 14, 2018: Science of the Total Environment
https://www.readbyqxmd.com/read/29452767/uptake-and-distribution-of-organo-iodine-in-deep-sea-corals
#3
Nancy G Prouty, E Brendan Roark, Leslye M Mohon, Ching-Chih Chang
Understanding iodine concentration, transport, and bioavailability is essential in evaluating iodine's impact to the environment and its effectiveness as an environmental biogeotracer. While iodine and its radionuclides have proven to be important tracers in geologic and biologic studies, little is known about transport of this element to the deep sea and subsequent uptake in deep-sea coral habitats. Results presented here on deep-sea black coral iodine speciation and iodine isotope variability provides key information on iodine behavior in natural and anthropogenic environments, and its geochemical pathway in the Gulf of Mexico...
February 13, 2018: Journal of Environmental Radioactivity
https://www.readbyqxmd.com/read/29445889/clinical-significance-of-circulating-tumor-cells-from-lung-cancer-patients-using-microfluidic-chip
#4
Chen Qian, Shan Wu, Hongmei Chen, Xiaofen Zhang, Rongrong Jing, Lei Shen, Xudong Wang, Shaoqing Ju, Chunping Jia, Hui Cong
Circulating tumor cells (CTCs) exist in the peripheral blood and have an important role in the disease development, tumor metastasis and clinical surveillance, especially in the process of metastasis. However, the technology of detecting CTCs still had a large challenge since they were rare in the peripheral blood. Here, we developed a size-based microfluidic chip, which contained array and filter channel array that could enrich CTCs from blood samples more quickly and conveniently. Combined with clinical specimen, we analyzed CTCs in 200 lung cancer patients by this microfluidic chip...
February 14, 2018: Clinical and Experimental Medicine
https://www.readbyqxmd.com/read/29445826/genome-based-comparison-of-clostridioides-difficile-average-amino-acid-identity-analysis-of-core-genomes
#5
Adriana Cabal, Se-Ran Jun, Piroon Jenjaroenpun, Visanu Wanchai, Intawat Nookaew, Thidathip Wongsurawat, Mary J Burgess, Atul Kothari, Trudy M Wassenaar, David W Ussery
Infections due to Clostridioides difficile (previously known as Clostridium difficile) are a major problem in hospitals, where cases can be caused by community-acquired strains as well as by nosocomial spread. Whole genome sequences from clinical samples contain a lot of information but that needs to be analyzed and compared in such a way that the outcome is useful for clinicians or epidemiologists. Here, we compare 663 public available complete genome sequences of C. difficile using average amino acid identity (AAI) scores...
February 14, 2018: Microbial Ecology
https://www.readbyqxmd.com/read/29443895/correction-shelly-y-shih-et-al-applications-of-probe-capture-enrichment-next-generation-sequencing-for-whole-mitochondrial-genome-and-426-nuclear-snps-for-forensically-challenging-samples-genes-2018-9-49
#6
Shelly Y Shih, Nikhil Bose, Anna Beatriz R Gonçalves, Henry A Erlich, Cassandra D Calloway
The authors wish to make the following change to their paper [1][...].
February 14, 2018: Genes
https://www.readbyqxmd.com/read/29440596/multi-omics-driven-assembly-and-annotation-of-the-sandalwood-santalum-album-genome
#7
H B Mahesh, Pratigya Subba, Jayshree Advani, Meghana Deepak Shirke, Ramya Malarini Loganathan, S Chandana, S Shilpa, Oishi Chatterjee, Sneha M Pinto, Keshava Prasad, Malali Gowda
Santalum album (Indian sandalwood) is an important tropical evergreen tree, known for its fragrant heartwood-derived essential oil and its valuable carving wood. Here, we applied an integrated genomic, transcriptomic, and proteomic approach to assemble and annotate the Indian sandalwood genome. Our genome sequencing resulted in the establishment of a draft map of the smallest genome for any woody tree species to date (221 Mb). The genome annotation predicted 38,119 protein-coding genes and 27.42% repetitive DNA elements...
February 12, 2018: Plant Physiology
https://www.readbyqxmd.com/read/29430274/direct-enrichment-of-pathogens-from-physiological-samples-of-high-conductivity-and-viscosity-using-h-filter-and-positive-dielectrophoresis
#8
Dongyang Cai, Qiaolian Yi, Chaohua Shen, Ying Lan, Gerald Urban, Wenbin Du
The full potential of microfluidic techniques as rapid and accurate methods for the detection of disease-causing agents and foodborne pathogens is critically limited by the complex sample preparation process, which commonly comprises the enrichment of bacterial cells to detectable levels. In this manuscript, we describe a microfluidic device which integrates H-filter desalination with positive dielectrophoresis (pDEP) for direct enrichment of bacterial cells from physiological samples of high conductivity and viscosity, such as cow's milk and whole human blood...
January 2018: Biomicrofluidics
https://www.readbyqxmd.com/read/29426544/the-synthesis-of-a-smart-streptavidin-functionalized-poly-n-isopropylacrylamide-composite-and-its-application-in-the-separation-and-detection-of-virus-nucleic-acid
#9
Xinxin Wang, Mingyuan Du, Guobin Mao, Jiao Zheng, Jinyang Chen, Xinghu Ji, Zhike He
A new kind of polymeric material (PNIPAAm-co-SA) was prepared by conjugating a thermosensitive polymer, Poly (N-isopropylacrylamide) (PNIPAAm) with streptavidin (SA). This smart prepared composite displayed a controllable conformation change between an expanded and a collapsed form, below or above its lower critical solution temperature (LCST). Differential scanning calorimetry (DSC) analysis demonstrated that the PNIPAAm-co-SA bioconjugate showed the same LCST as the original synthetic polymer, PNIPAAm, which was also 32°C...
May 1, 2018: Talanta
https://www.readbyqxmd.com/read/29417725/whole-exome-sequencing-for-mutation-detection-in-pediatric-disorders-of-insulin-secretion-maturity-onset-diabetes-of-the-young-and-congenital-hyperinsulinism
#10
S R Johnson, P J Leo, A M McInerney-Leo, L K Anderson, M Marshall, I McGown, F Newell, M A Brown, L S Conwell, M Harris, E L Duncan
BACKGROUND: To assess the utility of whole-exome sequencing (WES) for mutation detection in maturity-onset diabetes of the young (MODY) and congenital hyperinsulinism (CHI). MODY and CHI are the two commonest monogenic disorders of glucose-regulated insulin secretion in childhood, with 13 causative genes known for MODY and 10 causative genes identified for CHI. The large number of potential genes makes comprehensive screening using traditional methods expensive and time-consuming. METHODS: Ten subjects with MODY and five with CHI with known mutations underwent WES using two different exome capture kits (Nimblegen SeqCap EZ Human v3...
February 8, 2018: Pediatric Diabetes
https://www.readbyqxmd.com/read/29416092/cd63-mhc-class-1-and-cd47-identify-subsets-of-extracellular-vesicles-containing-distinct-populations-of-noncoding-rnas
#11
Sukhbir Kaur, Abdel G Elkahloun, Anush Arakelyan, Lynn Young, Timothy G Myers, Francisco Otaizo-Carrasquero, Weiwei Wu, Leonid Margolis, David D Roberts
Extracellular vesicles (EVs) mediate the intercellular transfer of RNAs, which alter gene expression in target cells. EV heterogeneity has limited progress towards defining their physiological functions and utility as disease-specific biomarkers. CD63 and MHC1 are widely used as markers to purify EVs. CD47 is also present on EVs and alters their effects on target cells, suggesting that specific surface markers define functionally distinct EVs. This hypothesis was addressed by comparing Jurkat T cell EVs captured using CD47, CD63, and MHC1 antibodies...
February 7, 2018: Scientific Reports
https://www.readbyqxmd.com/read/29416036/a-transcriptomic-atlas-of-aged-human-microglia
#12
Marta Olah, Ellis Patrick, Alexandra-Chloe Villani, Jishu Xu, Charles C White, Katie J Ryan, Paul Piehowski, Alifiya Kapasi, Parham Nejad, Maria Cimpean, Sarah Connor, Christina J Yung, Michael Frangieh, Allison McHenry, Wassim Elyaman, Vlad Petyuk, Julie A Schneider, David A Bennett, Philip L De Jager, Elizabeth M Bradshaw
With a rapidly aging global human population, finding a cure for late onset neurodegenerative diseases has become an urgent enterprise. However, these efforts are hindered by the lack of understanding of what constitutes the phenotype of aged human microglia-the cell type that has been strongly implicated by genetic studies in the pathogenesis of age-related neurodegenerative disease. Here, we establish the set of genes that is preferentially expressed by microglia in the aged human brain. This HuMi_Aged gene set captures a unique phenotype, which we confirm at the protein level...
February 7, 2018: Nature Communications
https://www.readbyqxmd.com/read/29409446/exploring-the-potential-of-3d-zernike-descriptors-and-svm-for-protein-protein-interface-prediction
#13
Sebastian Daberdaku, Carlo Ferrari
BACKGROUND: The correct determination of protein-protein interaction interfaces is important for understanding disease mechanisms and for rational drug design. To date, several computational methods for the prediction of protein interfaces have been developed, but the interface prediction problem is still not fully understood. Experimental evidence suggests that the location of binding sites is imprinted in the protein structure, but there are major differences among the interfaces of the various protein types: the characterising properties can vary a lot depending on the interaction type and function...
February 6, 2018: BMC Bioinformatics
https://www.readbyqxmd.com/read/29408166/an-endoglycosidase-assisted-lc-ms-ms-based-strategy-for-the-analysis-of-site-specific-core-fucosylation-of-low-concentrated-glycoproteins-in-human-serum-using-prostate-specific-antigen-psa-as-example
#14
Robert Lang, Andreas Leinenbach, Johann Karl, Magdalena Swiatek-de Lange, Uwe Kobold, Michael Vogeser
Recently, site-specific fucosylation of glycoproteins has attracted attention as it can be associated with several types of cancers including prostate cancer. However, individual glycoproteins, which might serve as potential cancer markers, often are very low-concentrated in complex serum matrices and distinct glycan structures are hard to detect by immunoassays. Here, we present a mass spectrometry-based strategy for the simultaneous analysis of core-fucosylated and total prostate-specific antigen (PSA) in human serum in the low ng/ml concentration range...
January 26, 2018: Clinica Chimica Acta; International Journal of Clinical Chemistry
https://www.readbyqxmd.com/read/29398119/target-enriched-sequencing-of-chromosome-17q21-31-in-sporadic-tauopathies-reveals-no-candidate-variants
#15
Cristina Razquin, Sara Ortega-Cubero, Estefania Rojo-Bustamante, Monica Diez-Fairen, Elena Lorenzo, Elena Alonso, Mario Ezquerra, Owen A Ross, Maria Carcel, Oswaldo Lorenzo-Betancor, Alexandra I Soto, Jeremy D Burgess, Nilüfer Ertekin-Taner, Dennis W Dickson, Maria A Pastor, Eduard Tolosa, Pau Pastor
The main genetic risk factors for progressive supranuclear palsy (PSP) and corticobasal degeneration (CBD) are located at chromosome 17q21.31. The identification of risk H1 subhaplotypes suggests that disease-specific variants can be identified by resequencing the 17q21.31 region (1.4 Mb) in carriers of risk H1 subhaplotypes. We hypothesized that PSP/CBD H1 subhaplotype carriers could have undergone a mutational event absent among unaffected carriers leading to the disease risk. We performed this strategy in definite PSP subjects, definite CBD subjects, and healthy controls and tried to replicate the findings in a larger PSP/CBD case-control series...
January 11, 2018: Neurobiology of Aging
https://www.readbyqxmd.com/read/29395098/distinctive-molecular-signature-and-activated-signaling-pathways-in-aortic-smooth-muscle-cells-of-patients-with-myocardial-infarction
#16
Thidathip Wongsurawat, Chin Cheng Woo, Antonis Giannakakis, Xiao Yun Lin, Esther Sok Hwee Cheow, Chuen Neng Lee, Mark Richards, Siu Kwan Sze, Intawat Nookaew, Vladimir A Kuznetsov, Vitaly Sorokin
BACKGROUND AND AIMS: We aim to identify significant transcriptome alterations of vascular smooth muscle cells (VSMCs) in the aortic wall of myocardial infarction (MI) patients. Providing a robust transcriptomic signature, we aim to highlight the most likely aberrant pathway(s) in MI VSMCs. METHODS AND RESULTS: Laser-captured microdissection (LCM) was used to obtain VSMCs from aortic wall tissues harvested during coronary artery bypass surgery. Microarray gene analysis was applied to analyse VSMCs from 17 MI and 19 non-MI patients...
January 29, 2018: Atherosclerosis
https://www.readbyqxmd.com/read/29391471/detection-of-16s-rrna-and-kpc-genes-from-complex-matrix-utilizing-a-molecular-inversion-probe-assay-for-next-generation-sequencing
#17
Christopher P Stefan, Adrienne T Hall, Timothy D Minogue
Targeted sequencing promises to bring next-generation sequencing (NGS) into routine clinical use for infectious disease diagnostics. In this context, upfront processing techniques, including pathogen signature enrichment, must amplify multiple targets of interest for NGS to be relevant when applied to patient samples with limited volumes. Here, we demonstrate an optimized molecular inversion probe (MIP) assay targeting multiple variable regions within the 16S ribosomal gene for the identification of biothreat and ESKAPE pathogens in a process that significantly reduces complexity, labor, and processing time...
February 1, 2018: Scientific Reports
https://www.readbyqxmd.com/read/29389948/photocleavage-based-affinity-purification-of-biomarkers-from-serum-application-to-multiplex-allergy-testing
#18
Zhi Wan, Heather P Ostendorff, Ziying Liu, Lynda C Schneider, Kenneth J Rothschild, Mark J Lim
Multiplex serological immunoassays, such as implemented on microarray or microsphere-based platforms, provide greater information content and higher throughput, while lowering the cost and blood volume required. These features are particularly attractive in pediatric food allergy testing to facilitate high throughput multi-allergen analysis from finger- or heel-stick collected blood. However, the miniaturization and microfluidics necessary for creating multiplex assays make them highly susceptible to the "matrix effect" caused by interference from non-target agents in serum and other biofluids...
2018: PloS One
https://www.readbyqxmd.com/read/29386638/methylation-based-enrichment-facilitates-low-cost-noninvasive-genomic-scale-sequencing-of-populations-from-feces
#19
Kenneth L Chiou, Christina M Bergey
Obtaining high-quality samples from wild animals is a major obstacle for genomic studies of many taxa, particularly at the population level, as collection methods for such samples are typically invasive. DNA from feces is easy to obtain noninvasively, but is dominated by bacterial and other non-host DNA. The high proportion of non-host DNA drastically reduces the efficiency of high-throughput sequencing for host animal genomics. To address this issue, we developed an inexpensive capture method for enriching host DNA from noninvasive fecal samples...
January 31, 2018: Scientific Reports
https://www.readbyqxmd.com/read/29384072/vital-ex-vivo-tissue-labeling-and-pathology-guided-micropunching-to-characterize-cellular-heterogeneity-in-the-tissue-microenvironment
#20
Brian P Johnson, Ross A Vitek, Peter G Geiger, Wei Huang, David F Jarrard, Joshua M Lang, David J Beebe
Cellular heterogeneity within the tissue microenvironment may underlie chemotherapeutic resistance and response, enabling tumor evolution; however, this heterogeneity it is difficult to characterize. Here, we present a new approach-pathology-guided micropunching (PGM)-that enables identification and characterization of heterogeneous foci identified in viable human and animal model tissue slices. This technique consists of live-cell tissue labeling using fluorescent antibodies/small molecules to identify heterogeneous foci (e...
January 1, 2018: BioTechniques
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