keyword
MENU ▼
Read by QxMD icon Read
search

Chip sequencing

keyword
https://www.readbyqxmd.com/read/28819973/mobile-platform-for-multiplexed-detection-and-differentiation-of-disease-specific-nucleic-acid-sequences-using-microfluidic-loop-mediated-isothermal-amplification-and-smartphone-detection
#1
Weili Chen, Hojeong Yu, Fu Sun, Akid Ornob, Ryan Brisbin, Anurup Ganguli, Vinay Kumar Vemuri, Piotr Strzebonski, Guangzhe Cui, Karen J Allen, Smit A Desai, Weiran Lin, David M Nash, David Hirschberg, Ian Brooks, Rashid Bashir, Brian T Cunningham
New tools are needed to enable rapid detection, identification, and reporting of infectious viral and microbial pathogens in a wide variety of point-of-care applications that impact human and animal health. We report the design, construction, and characterization of a platform for multiplexed analysis of disease-specific DNA sequences that utilizes a smartphone camera as the sensor in conjunction with a handheld "cradle" that interfaces the phone with a silicon-based microfluidic chip embedded within a credit card-sized cartridge...
August 18, 2017: Analytical Chemistry
https://www.readbyqxmd.com/read/28819310/genome-wide-target-enrichment-aided-chip-design-a-66%C3%A2-k-snp-chip-for-cashmere-goat
#2
Xian Qiao, Rui Su, Yang Wang, Ruijun Wang, Ting Yang, Xiaokai Li, Wei Chen, Shiyang He, Yu Jiang, Qiwu Xu, Wenting Wan, Yaolei Zhang, Wenguang Zhang, Jiang Chen, Bin Liu, Xin Liu, Yixing Fan, Duoyuan Chen, Huaizhi Jiang, Dongming Fang, Zhihong Liu, Xiaowen Wang, Yanjun Zhang, Danqing Mao, Zhiying Wang, Ran Di, Qianjun Zhao, Tao Zhong, Huanming Yang, Jian Wang, Wen Wang, Yang Dong, Xiaoli Chen, Xun Xu, Jinquan Li
Compared with the commercially available single nucleotide polymorphism (SNP) chip based on the Bead Chip technology, the solution hybrid selection (SHS)-based target enrichment SNP chip is not only design-flexible, but also cost-effective for genotype sequencing. In this study, we propose to design an animal SNP chip using the SHS-based target enrichment strategy for the first time. As an update to the international collaboration on goat research, a 66 K SNP chip for cashmere goat was created from the whole-genome sequencing data of 73 individuals...
August 17, 2017: Scientific Reports
https://www.readbyqxmd.com/read/28815002/a-comprehensive-method-for-identification-of-suitable-reference-genes-in-extracellular-vesicles
#3
Kenneth Gouin, Kiel Peck, Travis Antes, Jennifer Leigh Johnson, Chang Li, Sharon Denise Vaturi, Ryan Middleton, Geoff de Couto, Ann-Sophie Walravens, Luis Rodriguez-Borlado, Rachel Ruckdeschel Smith, Linda Marbán, Eduardo Marbán, Ahmed Gamal-Eldin Ibrahim
Reverse transcription-quantitative polymerase chain reaction (RT-qPCR) is one of the most sensitive, economical and widely used methods for evaluating gene expression. However, the utility of this method continues to be undermined by a number of challenges including normalization using appropriate reference genes. The need to develop tailored and effective strategies is further underscored by the burgeoning field of extracellular vesicle (EV) biology. EVs contain unique signatures of small RNAs including microRNAs (miRs)...
2017: Journal of Extracellular Vesicles
https://www.readbyqxmd.com/read/28811350/defining-the-dna-binding-site-recognized-by-the-fission-yeast-zn2cys6-transcription-factor-pho7-and-its-role-in-phosphate-homeostasis
#4
Beate Schwer, Ana M Sanchez, Angad Garg, Debashree Chatterjee, Stewart Shuman
Fission yeast phosphate homeostasis entails transcriptional induction of genes encoding phosphate-mobilizing proteins under conditions of phosphate starvation. Transcription factor Pho7, a member of the Zn2Cys6 family of fungal transcription regulators, is the central player in the starvation response. The DNA binding sites in the promoters of phosphate-responsive genes have not been defined, nor have any structure-function relationships been established for the Pho7 protein. Here we narrow this knowledge gap by (i) delineating an autonomous DNA-binding domain (DBD) within Pho7 that includes the Zn2Cys6 module, (ii) deploying recombinant Pho7 DBD in DNase I footprinting and electrophoretic mobility shift assays (EMSAs) to map the Pho7 recognition sites in the promoters of the phosphate-regulated pho1 and tgp1 genes to a 12-nucleotide sequence motif [5'-TCG(G/C)(A/T)xxTTxAA], (iii) independently identifying the same motif as a Pho7 recognition element via in silico analysis of available genome-wide ChIP-seq data, (iv) affirming that mutations in the two Pho7 recognition sites in the pho1 promoter efface pho1 expression in vivo, and (v) establishing that the zinc-binding cysteines and a pair of conserved arginines in the DBD are essential for Pho7 activity in vivoIMPORTANCE Fungi respond to phosphate starvation by inducing the transcription of a set of phosphate acquisition genes that comprise a phosphate regulon...
August 15, 2017: MBio
https://www.readbyqxmd.com/read/28811026/multiple-epitope-presentation-and-surface-density-control-enabled-by-chemoselective-immobilization-lead-to-enhanced-performance-in-ige-binding-fingerprinting-on-peptide-microarrays
#5
Alessandro Gori, Marina Cretich, Renzo Vanna, Laura Sola, Paola Gagni, Giulia Bruni, Marta Liprino, Furio Gramatica, Samuele Burastero, Marcella Chiari
Multiple ligand presentation is a powerful strategy to enhance the affinity of a probe for its corresponding target. A promising application of this concept lies in the analytical field, where surface immobilized probes interact with their corresponding targets in the context of complex biological samples. Here we investigate the effect of multiple epitope presentation (MEP) in the challenging context of IgE-detection in serum samples using peptide microarrays, and evaluate the influence of probes surface density on the assay results...
August 29, 2017: Analytica Chimica Acta
https://www.readbyqxmd.com/read/28809015/systems-biology-analyses-in-chicken-workflow-for-transcriptome-and-chip-seq-analyses-using-the-chicken-skin-paradigm
#6
Yung-Chih Lai, Randall B Widelitz, Cheng-Ming Chuong
With advances in molecular biology, various biological phenomena can now be explored at higher resolution using mRNA sequencing (RNA-Seq) and chromatin immunoprecipitation followed by high-throughput sequencing (ChIP-Seq), two powerful high-throughput next-generation sequencing (NGS) technologies. While methods are used widely in mouse, human, etc., less information is available in other animals, such as the chicken. Here we assemble a workflow of the RNA-Seq and ChIP-Seq analyses for the chicken studies using chicken skin appendage tissue as an example...
2017: Methods in Molecular Biology
https://www.readbyqxmd.com/read/28806091/sparsity-based-super-resolution-for-sem-images
#7
Shahar Tsiper, Or Dicker, Idan Kaizerman, Zeev Zohar, Mordechai Segev, Yonina C Eldar
The Scanning Electron Microscope (SEM) is an electron microscope that produces an image of a sample by scanning it with a focused beam of electrons. The electrons interact with the atoms in the sample, which emit secondary electrons that contain information about the surface topography and composition. The sample is scanned by the electron beam point by point, until an image of the surface is formed. Since its invention in 1942, the capabilities of SEMs have become paramount in the discovery and understanding of the nanometer world, and today it is extensively used for both research and in industry...
August 14, 2017: Nano Letters
https://www.readbyqxmd.com/read/28805661/the-foxn3-neat1-sin3a-repressor-complex-promotes-progression-of-hormonally-responsive-breast-cancer
#8
Wanjin Li, Zihan Zhang, Xinhua Liu, Xiao Cheng, Yi Zhang, Xiao Han, Yu Zhang, Shumeng Liu, Jianguo Yang, Bosen Xu, Lin He, Luyang Sun, Jing Liang, Yongfeng Shang
The pathophysiological function of the forkhead transcription factor FOXN3 remains to be explored. Here we report that FOXN3 is a transcriptional repressor that is physically associated with the SIN3A repressor complex in estrogen receptor-positive (ER+) cells. RNA immunoprecipitation-coupled high-throughput sequencing identified that NEAT1, an estrogen-inducible long noncoding RNA, is required for FOXN3 interactions with the SIN3A complex. ChIP-Seq and deep sequencing of RNA genomic targets revealed that the FOXN3-NEAT1-SIN3A complex represses genes including GATA3 that are critically involved in epithelial-to-mesenchymal transition (EMT)...
August 14, 2017: Journal of Clinical Investigation
https://www.readbyqxmd.com/read/28801897/chromatin-immunoprecipitation-and-quantitative-real-time-pcr-to-assess-binding-of-a-protein-of-interest-to-identified-predicted-binding-sites-within-a-promoter
#9
Jordan E Read
Chromatin immunoprecipitation (ChIP) has become a widely used methodology for assessment of protein/DNA interactions. The technique allows the analysis of direct binding of transcription factors to gene promoters, identification of histone modifications, and localization of DNA modifying enzymes. Antibodies conjugated to agarose beads can be utilized to immunoprecipitate specific proteins, cross-linked to sheared chromatin regions to which they are bound endogenously. With downstream applications including quantitative real-time polymerase chain reaction (qRT-PCR), genome-wide sequencing (ChIP-seq), microarray analysis (ChIP-chip), and mass spectrometry (ChIP-MS), the technique enables comprehensive assessment of protein/DNA interactions...
2017: Methods in Molecular Biology
https://www.readbyqxmd.com/read/28801691/a-new-data-processing-routine-facilitating-the-identification-of-surface-adhered-proteins-from-bacterial-conditioning-films-via-qcm-d-maldi-tof-ms
#10
Siegfried Hohmann, Anke Neidig, Boris Kühl, Frank Kirschhöfer, Jörg Overhage, Gerald Brenner-Weiß
Conditioning films are an important factor in the initiation and development of microbial biofilms, which are the leading cause of chronic infections associated with medical devices. Here, we analyzed the protein content of conditioning films formed after exposure to supernatants of cultures of the human pathogen Pseudomonas aeruginosa PAO1. Adhesion of substances from the supernatant was monitored using quartz crystal microbalance with dissipation monitoring (QCM-D) sensor chips modified with the commonly used implant material titanium dioxide (TiO2)...
August 11, 2017: Analytical and Bioanalytical Chemistry
https://www.readbyqxmd.com/read/28801683/regulation-of-tumour-related-genes-by-dynamic-epigenetic-alteration-at-enhancer-regions-in-gastric-epithelial-cells-infected-by-epstein-barr-virus
#11
Atsushi Okabe, Sayaka Funata, Keisuke Matsusaka, Hiroe Namba, Masaki Fukuyo, Bahityar Rahmutulla, Motohiko Oshima, Atsushi Iwama, Masashi Fukayama, Atsushi Kaneda
Epstein-Barr virus (EBV) infection is associated with tumours such as Burkitt lymphoma, nasopharyngeal carcinoma, and gastric cancer. We previously showed that EBV(+) gastric cancer presents an extremely high-methylation epigenotype and this aberrant DNA methylation causes silencing of multiple tumour suppressor genes. However, the mechanisms that drive EBV infection-mediated tumorigenesis, including other epigenomic alteration, remain unclear. We analysed epigenetic alterations induced by EBV infection especially at enhancer regions, to elucidate their contribution to tumorigenesis...
August 11, 2017: Scientific Reports
https://www.readbyqxmd.com/read/28801681/nrf1-and-zscan10-bind-to-the-promoter-region-of-the-six1-gene-and-their-effects-body-measurements-in-qinchuan-cattle
#12
Da-Wei Wei, Lin-Sheng Gui, Sayed Haidar Abbas Raza, Song Zhang, Rajwali Khan, Li Wang, Hong-Fang Guo, Lin-Sen Zan
The SIX1 homeobox gene belongs to the six homeodomain family and is widely thought to play a principal role in mediating of skeletal muscle development. In the present study, we determined that the bovine SIX1 gene was highly expressed in the longissimus thoracis and physiologically immature individuals. DNA sequencing of 428 individual Qinchuan cattle identified nine single nucleotide polymorphisms (SNPs) in the promoter region of the SIX1 gene. Using a series of 5' deletion promoter plasmid luciferase reporter assays and 5'-rapid amplification of cDNA end analysis (RACE), two of these SNPs were found to be located in the proximal minimal promoter region -216/-28 relative to the transcriptional start site (TSS)...
August 11, 2017: Scientific Reports
https://www.readbyqxmd.com/read/28800596/fungal-genome-and-mating-system-transitions-facilitated-by-chromosomal-translocations-involving-intercentromeric-recombination
#13
Sheng Sun, Vikas Yadav, R Blake Billmyre, Christina A Cuomo, Minou Nowrousian, Liuyang Wang, Jean-Luc Souciet, Teun Boekhout, Betina Porcel, Patrick Wincker, Joshua A Granek, Kaustuv Sanyal, Joseph Heitman
Species within the human pathogenic Cryptococcus species complex are major threats to public health, causing approximately 1 million infections globally annually. Cryptococcus amylolentus is the most closely known related species of the pathogenic Cryptococcus species complex, and it is non-pathogenic. Additionally, while pathogenic Cryptococcus species have bipolar mating systems with a single large mating type (MAT) locus that represents a derived state in Basidiomycetes, C. amylolentus has a tetrapolar mating system with 2 MAT loci (P/R and HD) located on different chromosomes...
August 11, 2017: PLoS Biology
https://www.readbyqxmd.com/read/28800138/phylogenetically-conserved-resource-partitioning-in-the-coastal-microbial-loop
#14
Samuel Bryson, Zhou Li, Francisco Chavez, Peter K Weber, Jennifer Pett-Ridge, Robert L Hettich, Chongle Pan, Xavier Mayali, Ryan S Mueller
Resource availability influences marine microbial community structure, suggesting that population-specific resource partitioning defines discrete niches. Identifying how resources are partitioned among populations, thereby characterizing functional guilds within the communities, remains a challenge for microbial ecologists. We used proteomic stable isotope probing (SIP) and NanoSIMS analysis of phylogenetic microarrays (Chip-SIP) along with 16S rRNA gene amplicon and metagenomic sequencing to characterize the assimilation of six (13)C-labeled common metabolic substrates and changes in the microbial community structure within surface water collected from Monterey Bay, CA...
August 11, 2017: ISME Journal
https://www.readbyqxmd.com/read/28789639/cipher-a-flexible-and-extensive-workflow-platform-for-integrative-next-generation-sequencing-data-analysis-and-genomic-regulatory-element-prediction
#15
Carlos Guzman, Iván D'Orso
BACKGROUND: Next-generation sequencing (NGS) approaches are commonly used to identify key regulatory networks that drive transcriptional programs. Although these technologies are frequently used in biological studies, NGS data analysis remains a challenging, time-consuming, and often irreproducible process. Therefore, there is a need for a comprehensive and flexible workflow platform that can accelerate data processing and analysis so more time can be spent on functional studies. RESULTS: We have developed an integrative, stand-alone workflow platform, named CIPHER, for the systematic analysis of several commonly used NGS datasets including ChIP-seq, RNA-seq, MNase-seq, DNase-seq, GRO-seq, and ATAC-seq data...
August 8, 2017: BMC Bioinformatics
https://www.readbyqxmd.com/read/28782042/polycomb-repressive-complex-1-modifies-transcription-of-active-genes
#16
Michelle Pherson, Ziva Misulovin, Maria Gause, Kathie Mihindukulasuriya, Amanda Swain, Dale Dorsett
This study examines the role of Polycomb repressive complex 1 (PRC1) at active genes. The PRC1 and PRC2 complexes are crucial for epigenetic silencing during development of an organism. They are recruited to Polycomb response elements (PREs) and establish silenced domains over several kilobases. Recent studies show that PRC1 is also directly recruited to active genes by the cohesin complex. Cohesin participates broadly in control of gene transcription, but it is unknown whether cohesin-recruited PRC1 also plays a role in transcriptional control of active genes...
August 2017: Science Advances
https://www.readbyqxmd.com/read/28780075/brca1-associated-protein-increases-invasiveness-of-esophageal-squamous-cell-carcinoma
#17
Yanjie Zhao, Lixuan Wei, Mingming Shao, Xudong Huang, Jiang Chang, Jian Zheng, Jiahui Chu, Qionghua Cui, Linna Peng, Yingying Luo, Wenle Tan, Wen Tan, Dongxin Lin, Chen Wu
BACKGROUND & AIMS: We performed a screen for genes whose expression correlates with invasiveness of esophageal squamous-cell carcinoma (ESCC) cells. We studied the effects of overexpression and knockdown of these genes in cell lines and expression levels in patient samples. METHODS: We selected genes for analysis from 11 loci associated with risk of ESCC. We analyzed the effects of knocking down expression of 47 of these genes using RNA interference on-chip analysis in ESCC cells and HeLa cells...
August 2, 2017: Gastroenterology
https://www.readbyqxmd.com/read/28777841/-genetic-analysis-of-three-families-affected-with-split-hand-split-foot-malformation
#18
Wenbin He, Ge Lin, Ping Liang, Dehua Cheng, Xiao Hu, Lihua Zhou, Bo Xiong, Yueqiu Tan, Guangxiu Lu, Wen Li
OBJECTIVE: To explore the genetic etiology of three families affected with split-hand/split-foot malformation (SHFM). METHODS: Peripheral venous blood samples from 21 members of pedigree 1, 2 members of pedigree 2, and 2 members of pedigree 3 were collected. PCR-Sanger sequencing, microarray chip, fluorescence in situ hybridization (FISH), real-time PCR, and next-generation sequencing were employed to screen the mutations in the 3 families. The effect of the identified mutations on the finger (toe) abnormality were also explored...
August 10, 2017: Zhonghua Yi Xue Yi Chuan Xue za Zhi, Zhonghua Yixue Yichuanxue Zazhi, Chinese Journal of Medical Genetics
https://www.readbyqxmd.com/read/28777348/genotyping-and-bio-sensing-chemosensory-proteins-in-insects
#19
REVIEW
Guoxia Liu, Philippe Arnaud, Bernard Offmann, Jean-François Picimbon
Genotyping is the process of determining differences in the genetic make-up of an individual and comparing it to that of another individual. Focus on the family of chemosensory proteins (CSPs) in insects reveals differences at the genomic level across various strains and biotypes, but none at the level of individuals, which could be extremely useful in the biotyping of insect pest species necessary for the agricultural, medical and veterinary industries. Proposed methods of genotyping CSPs include not only restriction enzymatic cleavage and amplification of cleaved polymorphic sequences, but also detection of retroposons in some specific regions of the insect chromosome...
August 4, 2017: Sensors
https://www.readbyqxmd.com/read/28776754/quantitative-two-dimensional-ultrashort-echo-time-magnetization-transfer-2d-ute-mt-imaging-of-cortical-bone
#20
Ya-Jun Ma, Anthony Tadros, Jiang Du, Eric Y Chang
PURPOSE: To investigate quantitative 2D ultrashort echo time magnetization transfer (UTE-MT) imaging in ex vivo bovine cortical bone and in vivo human tibial cortical bone. METHODS: Data were acquired from five fresh bovine cortical bone samples and five healthy volunteer tibial cortical bones using a 2D UTE-MT sequence on a clinical 3T scanner. The 2D UTE-MT sequence used four or five MT powers with five frequency offsets. Results were analyzed with a two-pool quantitative MT model, providing measurements of macromolecular fraction (f), macromolecular proton transverse relaxation times (T2m ), proton exchange rates from water/macromolecular to the macromolecular/water pool (RM0m /RM0w ), and spin-lattice relaxation rate of water pool (R1w )...
August 3, 2017: Magnetic Resonance in Medicine: Official Journal of the Society of Magnetic Resonance in Medicine
keyword
keyword
103069
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"