keyword
MENU ▼
Read by QxMD icon Read
search

Capture enrichment

keyword
https://www.readbyqxmd.com/read/28541485/histologically-defined-intratumoral-sequencing-uncovers-evolutionary-cues-into-conserved-molecular-events-driving-gliomagenesis
#1
Antony Prabhu, Pravin Kesarwani, Shiva Kant, Stewart F Graham, Prakash Chinnaiyan
BACKGROUND: Glioblastoma represents an archetypal example of a heterogeneous malignancy. To understand the diverse molecular consequences of this complex tumor ecology, we analyzed RNA-seq data generated from commonly identified intra-tumoral structures in glioblastoma enriched using laser capture microdissection. METHODS: Raw gene-level fragments per kilobase of transcript per million reads mapped (FPKM) values and the associated clinical data were acquired from the publically available Ivy GAP database and analyzed using MetaboAnalyst (v...
May 25, 2017: Neuro-oncology
https://www.readbyqxmd.com/read/28536309/development-and-validation-of-an-ultra-deep-next-generation-sequencing-assay-for-testing-of-plasma-cell-free-dna-from-patients-with-advanced-cancer
#2
Filip Janku, Shile Zhang, Jill Waters, Li Liu, Helen Huang, Vivek Subbiah, David S Hong, Daniel Karp, Siqing Fu, Xuyu Cai, Nishma M Ramzanali, Kiran Madwani, Goran Cabrilo, Debra D Andrews, Yue Zhao, Milind Javle, Scott Kopetz, Rajyalakshmi Luthra, Hyunsung J Kim, Sante Gnerre, Ravi Vijaya Satya, Han-Yu Chuang, Kristina M Kruglyak, Jonathan Toung, Chen Zhao, Richard Shen, John Heymach, Funda Meric-Bernstam, Gordon B Mills, Jian-Bing Fan, Neeraj S Salathia
Purpose: Tumor-derived cell-free DNA (cfDNA) in plasma can be used for molecular testing and provide an attractive alternative to tumor tissue. Commonly used PCR-based technologies can test for limited number of alterations at the time. Therefore, novel ultrasensitive technologies capable of testing for a broad spectrum of molecular alterations are needed to further personalized cancer therapy. <p>Experimental Design: We developed a highly sensitive ultra-deep next-generation sequencing (NGS) assay using reagents from TruSeq Nano library preparation and Nextera Rapid Capture target enrichment kits to generate plasma cfDNA sequencing libraries for mutational analysis in 61 cancer-related genes using common bioinformatics tools...
May 23, 2017: Clinical Cancer Research: An Official Journal of the American Association for Cancer Research
https://www.readbyqxmd.com/read/28534482/an-engineered-high-affinity-fbs1-carbohydrate-binding-protein-for-selective-capture-of-n-glycans-and-n-glycopeptides
#3
Minyong Chen, Xiaofeng Shi, Rebecca M Duke, Cristian I Ruse, Nan Dai, Christopher H Taron, James C Samuelson
A method for selective and comprehensive enrichment of N-linked glycopeptides was developed to facilitate detection of micro-heterogeneity of N-glycosylation. The method takes advantage of the inherent properties of Fbs1, which functions within the ubiquitin-mediated degradation system to recognize the common core pentasaccharide motif (Man3GlcNAc2) of N-linked glycoproteins. We show that Fbs1 is able to bind diverse types of N-linked glycomolecules; however, wild-type Fbs1 preferentially binds high-mannose-containing glycans...
May 23, 2017: Nature Communications
https://www.readbyqxmd.com/read/28532053/functionalized-fe3o4-graphene-oxide-nanocomposites-with-hairpin-aptamers-for-the-separation-and-preconcentration-of-trace-pb-2-from-biological-samples-prior-to-determination-by-icp-ms
#4
Mojtaba Shamsipur, Leila Farzin, Mahmoud Amouzadeh Tabrizi, Shahab Sheibani
Lead (Pb) as a topically poisonous metal represents a serious threat to the ecological environment and especially to human beings. Therefore, it is urgent to develop a rapid and reliable monitoring technique for this heavy metal in the environmental samples. In the present study, we have designed a selective and sensitive method for the determination of ultratrace contents of Pb(2+) in biological samples, based on the guanine (G)-quadruplex formed by the aptamer with hairpin structure and Pb(2+). For this purpose, Pb(2+) specific aptamer serving as affinity probe to capture and separate trace amounts of the analyte, was covalently linked to Fe3O4/graphene oxide (GO) surface by using a suitable cross-linking agent...
August 1, 2017: Materials Science & Engineering. C, Materials for Biological Applications
https://www.readbyqxmd.com/read/28514873/unpacking-community-mobility-a-preliminary-study-into-the-embodied-experiences-of-stroke-survivors
#5
Christa S Nanninga, Louise Meijering, Klaas Postema, Marleen C Schönherr, Ant T Lettinga
PURPOSE: To enrich the discussion on mobility in stroke rehabilitation by translating theoretical repertoires of mobility from the context of geography to rehabilitation. METHOD: Qualitative research methodology was applied, and included in-depth interviews with stroke survivors. RESULTS: This study revealed: (a) social and material differences in clinical, private and public places; (b) ambivalences and shifting tensions in bodily, family and community life; (c) differences in access to resources to be used for mobility...
May 17, 2017: Disability and Rehabilitation
https://www.readbyqxmd.com/read/28511992/rna-seq-analyses-reveal-that-cervical-spinal-cords-and-anterior-motor-neurons-from-amyotrophic-lateral-sclerosis-subjects-show-reduced-expression-of-mitochondrial-dna-encoded-respiratory-genes-and-rhtfam-may-correct-this-respiratory-deficiency
#6
Amy C Ladd, David G Brohawn, Ravindar R Thomas, Paula M Keeney, Stuart S Berr, Shaharyar M Khan, Francisco R Portell, Meiram Zh Shakenov, Patrick F Antkowiak, Bijoy Kundu, Nicholas Tustison, James P Bennett
Amyotrophic lateral sclerosis (ALS) is a generally fatal neurodegenerative disease of adults that produces weakness and atrophy due to dysfunction and death of upper and lower motor neurons. We used RNA-sequencing (RNA-seq) to analyze expression of all mitochondrial DNA (mtDNA)-encoded respiratory genes in ALS and CTL human cervical spinal cords (hCSC) and isolated motor neurons. We analyzed with RNA-seq mtDNA gene expression in human neural stem cells (hNSC) exposed to recombinant human mitochondrial transcription factor A (rhTFAM), visualized in 3-dimensions clustered gene networks activated by rhTFAM, quantitated their interactions with other genes and determined their gene ontology (GO) families...
May 13, 2017: Brain Research
https://www.readbyqxmd.com/read/28509371/quantitative-assessment-of-sialo-glycoproteins-and-n-glycans-during-cardiomyogenic-differentiation-of-human-induced-pluripotent-stem-cells
#7
Sarah Anna Konze, Samanta Cajic, Astrid Oberbeck, René Hennig, Andreas Pich, Erdmann Rapp, Falk Buettner
Human induced pluripotent stem cell-derived cardiomyocytes (hiPSC-CMs) may be used in regenerative medicine for individualized tissue transplants in future. For application in patients, the generated CMs have to be highly pure and well characterized. To overcome the prevalent scarcity of CM-specific markers, we quantitatively assessed cell surface exposed sialo-glycoproteins and N-glycans of hiPSCs, CM progenitors and CMs derived thereof. Applying a combination of metabolic labeling and specific sialo-glycoprotein capture, we could highly enrich and quantify membrane proteins during cardiomyogenic differentiation...
May 16, 2017: Chembiochem: a European Journal of Chemical Biology
https://www.readbyqxmd.com/read/28508363/glycoproteins-enrichment-and-lc-ms-ms-glycoproteomics-in-central-nervous-system-applications
#8
Rui Zhu, Ehwang Song, Ahmed Hussein, Firas H Kobeissy, Yehia Mechref
Proteins and glycoproteins play important biological roles in central nervous systems (CNS). Qualitative and quantitative evaluation of proteins and glycoproteins expression in CNS is critical to reveal the inherent biomolecular mechanism of CNS diseases. This chapter describes proteomic and glycoproteomic approaches based on liquid chromatography/tandem mass spectrometry (LC-MS or LC-MS/MS) for the qualitative and quantitative assessment of proteins and glycoproteins expressed in CNS. Proteins and glycoproteins, extracted by a mass spectrometry friendly surfactant from CNS samples, were subjected to enzymatic (tryptic) digestion and three down-stream analyses: (1) a nano LC system coupled with a high-resolution MS instrument to achieve qualitative proteomic profile, (2) a nano LC system combined with a triple quadrupole MS to quantify identified proteins, and (3) glycoprotein enrichment prior to LC-MS/MS analysis...
2017: Methods in Molecular Biology
https://www.readbyqxmd.com/read/28507606/transcription-and-chromatin-determinants-of-de-novo-dna-methylation-timing-in-oocytes
#9
Lenka Gahurova, Shin-Ichi Tomizawa, Sébastien A Smallwood, Kathleen R Stewart-Morgan, Heba Saadeh, Jeesun Kim, Simon R Andrews, Taiping Chen, Gavin Kelsey
BACKGROUND: Gametogenesis in mammals entails profound re-patterning of the epigenome. In the female germline, DNA methylation is acquired late in oogenesis from an essentially unmethylated baseline and is established largely as a consequence of transcription events. Molecular and functional studies have shown that imprinted genes become methylated at different times during oocyte growth; however, little is known about the kinetics of methylation gain genome wide and the reasons for asynchrony in methylation at imprinted loci...
2017: Epigenetics & Chromatin
https://www.readbyqxmd.com/read/28505584/development-of-a-gold-nanoparticle-based-universal-oligonucleotide-microarray-for-multiplex-and-low-cost-detection-of-foodborne-pathogens
#10
Xiaoqiang Wang, Sisi Ying, Xiaoguang Wei, Jun Yuan
Bacterial foodborne diseases remain major threats to food safety and public health, especially in developing countries. In this study a novel assay, combining gold nanoparticle (GNP)-based multiplex oligonucleotide ligation-PCR and universal oligonucleotide microarray technology, was developed for inexpensive, specific, sensitive, and multiplex detection of eight common foodborne pathogens, including Shigella spp., Campylobacter jejuni, Bacillus cereus, Escherichia coli O157:H7, Listeria monocytogenes, Salmonella enterica, Staphylococcus aureus, and Vibrio parahaemolyticus...
May 9, 2017: International Journal of Food Microbiology
https://www.readbyqxmd.com/read/28505563/ultrasensitive-magnetic-field-assisted-surface-plasmon-resonance-immunoassay-for-human-cardiac-troponin-i
#11
Qiong Wu, Ying Sun, Di Zhang, Shuo Li, Yue Zhang, Pinyi Ma, Yang Yu, Xinghua Wang, Daqian Song
An ultrasensitive surface plasmon resonance (SPR) immunoassay was developed for the specific detection of human cardiac troponin I (cTnI), a principle diagnostic marker for myocardial damage. The thin gold film evaporated on a glass slate, which was employed as the SPR sensing film, was modified by hollow gold nanoparticles (HGNPs) and polydopamine (PDA) sequentially, and then was immobilized with antibodies for specific recognition of target analyte. Electronic coupling of the surface plasmon waves originating from the HGNPs and the gold film leads to the remarkable amplification of SPR response...
May 12, 2017: Biosensors & Bioelectronics
https://www.readbyqxmd.com/read/28501997/using-laser-capture-microdissection-to-isolate-cortical-laminae-in-nonhuman-primate-brain
#12
Brian A Corgiat, Claudius Mueller
Laser capture microdissection (LCM) is a technique that allows procurement of an enriched cell population from a heterogeneous tissue sample under direct microscopic visualization. Fundamentally, laser capture microdissection consists of three main steps: (1) visualizing the desired cell population by microscopy, (2) melting a thermolabile polymer onto the desired cell populations using infrared laser energy to form a polymer-cell composite (capture method) or photovolatizing a region of tissue using ultraviolet laser energy (cutting method), and (3) removing the desired cell population from the heterogeneous tissue...
2017: Methods in Molecular Biology
https://www.readbyqxmd.com/read/28501193/immunoaffinity-chromatography-combined-with-tandem-mass-spectrometry-a-new-tool-for-the-selective-capture-and-analysis-of-brassinosteroid-plant-hormones
#13
Jana Oklestkova, Danuše Tarkowská, Luděk Eyer, Tomáš Elbert, Aleš Marek, Zora Smržová, Ondřej Novák, Milan Fránek, Vladimir N Zhabinskii, Miroslav Strnad
Brassinosteroids (BRs) are plant-specific steroid hormones that play essential roles in the regulation of many important physiological processes in plant life. Their extremely low concentrations (~pmoles/g FW) in plant tissue and huge differences in polarity of individual members within the BR family hamper their detection and quantification. To address this problem, an immunoaffinity sorbent with broad specificity and high capacity for different BR metabolites containing a monoclonal antibody (mAb) against a BR spacer (20S)-2α,3α-dihydroxy-7-oxa-7α-homo-5α-pregnane-6-one-20 carboxylic acid (BR4812) was used for the rapid and highly selective isolation of endogenous BRs containing a 2α,3α-diol in ring A from minute plant samples...
August 1, 2017: Talanta
https://www.readbyqxmd.com/read/28501172/combining-phagomagnetic-separation-with-immunoassay-for-specific-fast-and-sensitive-detection-of-staphylococcus-aureus
#14
Chenghui Yan, Yun Zhang, Hang Yang, Junping Yu, Hongping Wei
A Staphylococcus aureus (S. aureus)-specific lytic bacteriophage P-S. aureus-9, isolated from an environmental water sample, was assembled on magnetic beads for capturing S. aureus from samples through magnetic separation. Horseradish Peroxidase (HRP) labeled immunoglobulin (IgG) antibodies were used to detect the captured S. aureus by reacting with protein A on S. aureus followed by colorimetric signals, which were generated from the catalytic reaction between HRP and the substrate 3,3',5,5'-Tetramethylbenzidine (TMB)...
August 1, 2017: Talanta
https://www.readbyqxmd.com/read/28500854/systematic-analysis-of-coronary-artery-disease-datasets-revealed-the-potential-biomarker-and-treatment-target
#15
Yan Shi, Sijin Yang, Man Luo, Wei-Dong Zhang, Zun-Ping Ke
Coronary artery disease caused about 1 of every 7 deaths in the United States and early prevention was potential to decrease the incidence and mortality. We aimed to figure the genes involving in the coronary artery disease using meta-anlaysis. Five datasets of coronary heart disease from GEO series were retrieved and data preprocessing and quality control were carried out. Moderated t-test was used to decide the differentially expressed genes for a single dataset. And the combined p-value using systematic-analysis methods were conducted using MetaDE...
April 26, 2017: Oncotarget
https://www.readbyqxmd.com/read/28498481/comparison-of-three-different-methods-for-the-detection-of-circulating-tumor-cells-in-mice-with-lung-metastasis
#16
Weifeng Xu, Bing Wu, Lengxi Fu, Junying Chen, Zeng Wang, Fei Huang, Jinrong Chen, Mei Zhang, Zhenhuan Zhang, Jingan Lin, Ruilong Lan, Ruiqing Chen, Wei Chen, Long Chen, Jinsheng Hong, Weijian Zhang, Yuxiong Ding, Paul Okunieff, Jianhua Lin, Lurong Zhang
Circulating tumor cells (CTCs) represent the key step of cancer cell dissemination. The alteration of CTCs correlates with the treatment outcome and prognosis. To enrich and identify CTCs from billions of blood cells renders a very challenging task, which triggers development of several methods, including lysis of RBC plus negative or positive enrichment using antibodies, and filter membrane or spiral microfluidics to capture CTCs. To compare the advantages of different enrichment methods for CTCs, we utilized the 4T1 breast cancer cells transfected with both green fluorescent protein (GFP) and luciferase to trace CTCs in the experimental lung metastasis model...
May 2, 2017: Oncology Reports
https://www.readbyqxmd.com/read/28497690/a-novel-electrochemiluminescence-sensing-platform-for-precise-analysis-of-multiple-ltbi-markers
#17
Bin Zhou, Mingyao Zhu, Peihui Yang, Peihui Yang
Latent tuberculosis infection (LTBI) is one of the major contributing factors for the high incidence of tuberculosis (TB), and the low contents of LTBI markers in human serum presents a great challenge for the diagnosis of LTBI. Here we reported a novel electrochemiluminescence (ECL) sensing platform for the precise analysis of multiple LTBI markers, interferon-gamma (IFN-γ) and interleukin (IL)-2. In this approach, self-prepared carbon quantum dots (CQDs) and luminol were integrated onto gold nanoparticles (AuNPs), which were further enriched on the surface of magnetic bead (MB) to create two solid-phase ECL nanoprobes (MB@Au@CQDs and MB@Au@luminol) for improving the detection sensitivity efficiently...
May 12, 2017: ACS Applied Materials & Interfaces
https://www.readbyqxmd.com/read/28497531/exposure-enriched-outcome-dependent-designs-for-longitudinal-studies-of-gene-environment-interaction
#18
Zhichao Sun, Bhramar Mukherjee, Jason P Estes, Pantel S Vokonas, Sung Kyun Park
Joint effects of genetic and environmental factors have been increasingly recognized in the development of many complex human diseases. Despite the popularity of case-control and case-only designs, longitudinal cohort studies that can capture time-varying outcome and exposure information have long been recommended for gene-environment (G × E) interactions. To date, literature on sampling designs for longitudinal studies of G × E interaction is quite limited. We therefore consider designs that can prioritize a subsample of the existing cohort for retrospective genotyping on the basis of currently available outcome, exposure, and covariate data...
May 11, 2017: Statistics in Medicine
https://www.readbyqxmd.com/read/28497333/next-generation-sequencing-based-genomic-profiling-of-brain-metastases-of-primary-ovarian-cancer-identifies-high-number-of-brca-mutations
#19
S Balendran, S Liebmann-Reindl, A S Berghoff, T Reischer, N Popitsch, C B Geier, L Kenner, P Birner, B Streubel, M Preusser
Ovarian cancer represents the most common gynaecological malignancy and has the highest mortality of all female reproductive cancers. It has a rare predilection to develop brain metastases (BM). In this study, we evaluated the mutational profile of ovarian cancer metastases through Next-Generation Sequencing (NGS) with the aim of identifying potential clinically actionable genetic alterations with options for small molecule targeted therapy. Library preparation was conducted using Illumina TruSight Rapid Capture Kit in combination with a cancer specific enrichment kit covering 94 genes...
May 11, 2017: Journal of Neuro-oncology
https://www.readbyqxmd.com/read/28492983/target-enrichment-sequencing-in-cultivated-peanut-arachis-hypogaea-l-using-probes-designed-from-transcript-sequences
#20
Ze Peng, Wen Fan, Liping Wang, Dev Paudel, Dante Leventini, Barry L Tillman, Jianping Wang
Enabled by the next generation sequencing, target enrichment sequencing (TES) is a powerful method to enrich genomic regions of interest and to identify sequence variations. The objective of this study was to explore the feasibility of probe design from transcript sequences for TES application in calling sequence variants in peanut, an important allotetraploid crop with a large genome size. In this study, we applied an in-solution hybridization method to enrich DNA sequences of seven peanut genotypes. Our results showed that it is feasible to apply TES with probes designed from transcript sequences in polyploid peanut...
May 10, 2017: Molecular Genetics and Genomics: MGG
keyword
keyword
80593
1
2
Fetch more papers »
Fetching more papers... Fetching...
Read by QxMD. Sign in or create an account to discover new knowledge that matter to you.
Remove bar
Read by QxMD icon Read
×

Search Tips

Use Boolean operators: AND/OR

diabetic AND foot
diabetes OR diabetic

Exclude a word using the 'minus' sign

Virchow -triad

Use Parentheses

water AND (cup OR glass)

Add an asterisk (*) at end of a word to include word stems

Neuro* will search for Neurology, Neuroscientist, Neurological, and so on

Use quotes to search for an exact phrase

"primary prevention of cancer"
(heart or cardiac or cardio*) AND arrest -"American Heart Association"