keyword
MENU ▼
Read by QxMD icon Read
search

High throughput sequencing

keyword
https://www.readbyqxmd.com/read/28225773/whole-genome-duplication-and-molecular-evolution-in-cornus-l-cornaceae-insights-from-transcriptome-sequences
#1
Yan Yu, Qiuyun Xiang, Paul S Manos, Douglas E Soltis, Pamela S Soltis, Bao-Hua Song, Shifeng Cheng, Xin Liu, Gane Wong
The pattern and rate of genome evolution have profound consequences in organismal evolution. Whole-genome duplication (WGD), or polyploidy, has been recognized as an important evolutionary mechanism of plant diversification. However, in non-model plants the molecular signals of genome duplications have remained largely unexplored. High-throughput transcriptome data from next-generation sequencing have set the stage for novel investigations of genome evolution using new bioinformatic and methodological tools in a phylogenetic framework...
2017: PloS One
https://www.readbyqxmd.com/read/28225099/ultra-high-throughput-detection-1-million-droplets-per-second-of-fluorescent-droplets-using-a-cell-phone-camera-and-time-domain-encoded-optofluidics
#2
Venkata R Yelleswarapu, Heon-Ho Jeong, Sagar Yadavali, David Issadore
Droplet-based assays-in which ultra-sensitive molecular measurements are made by performing millions of parallel experiments in picoliter droplets-have generated enormous enthusiasm due to their single molecule resolution and robustness to reaction conditions. These assays have great untapped potential for point of care diagnostics but are currently confined to laboratory settings due to the instrumentation necessary to serially generate, control, and measure tens of millions of droplets. To address this challenge, we have developed the microdroplet megascale detector (μMD) that can generate and detect the fluorescence of millions of droplets per second (1000× faster than conventional approaches) using only a conventional cell phone camera...
February 22, 2017: Lab on a Chip
https://www.readbyqxmd.com/read/28224923/high-throughput-sequencing-reveals-modulation-of-micrornas-in-vigna-mungo-upon-mungbean-yellow-mosaic-india-virus-inoculation-highlighting-stress-regulation
#3
Anirban Kundu, Sujay Paul, Avishek Dey, Amita Pal
MicroRNAs (miRNAs) are 20-24 nucleotides long non-coding RNAs known to play important regulatory roles during biotic and abiotic stresses by controlling gene expression. Blackgram (Vigna mungo), an economically important grain legume is highly susceptible to pathogenic begomovirus Mungbean Yellow Mosaic India Virus (MYMIV) and resulting in high yield loss. In this study two different leaf-small-RNA libraries were prepared from the pooled RNA at three different time points of resistant V. mungo inbred line VM84 inoculated either with viruliferous or non-viruliferous whiteflies carrying MYMIV and performed high-throughput Illumina sequencing...
April 2017: Plant Science: An International Journal of Experimental Plant Biology
https://www.readbyqxmd.com/read/28224915/characterization-of-small-rna-populations-in-non-transgenic-and-aflatoxin-reducing-transformed-peanut
#4
Imana L Power, Phat M Dang, Victor S Sobolev, Valerie A Orner, Joseph L Powell, Marshall C Lamb, Renee S Arias
Aflatoxin contamination is a major constraint in food production worldwide. In peanut (Arachis hypogaea L.), these toxic and carcinogenic aflatoxins are mainly produced by Aspergillus flavus Link and A. parasiticus Speare. The use of RNA interference (RNAi) is a promising method to reduce or prevent the accumulation of aflatoxin in peanut seed. In this study, we performed high-throughput sequencing of small RNA populations in a control line and in two transformed peanut lines that expressed an inverted repeat targeting five genes involved in the aflatoxin-biosynthesis pathway and that showed up to 100% less aflatoxin B1 than the controls...
April 2017: Plant Science: An International Journal of Experimental Plant Biology
https://www.readbyqxmd.com/read/28224499/finding-rna-protein-interaction-sites-using-hmms
#5
Tao Wang, Jonghyun Yun, Yang Xie, Guanghua Xiao
RNA-binding proteins play important roles in the various stages of RNA maturation through binding to its target RNAs. Cross-linking immunoprecipitation coupled with high-throughput sequencing (CLIP-Seq) has made it possible to identify the targeting sites of RNA-binding proteins in various cell culture systems and tissue types on a genome-wide scale. Several Hidden Markov model-based (HMM) approaches have been suggested to identify protein-RNA binding sites from CLIP-Seq datasets. In this chapter, we describe how HMM can be applied to analyze CLIP-Seq datasets, including the bioinformatics preprocessing steps to extract count information from the sequencing data before HMM and the downstream analysis steps following peak-calling...
2017: Methods in Molecular Biology
https://www.readbyqxmd.com/read/28224496/computationally-tractable-multivariate-hmm-in-genome-wide-mapping-studies
#6
Hyungwon Choi, Debashis Ghosh, Zhaohui Qin
Hidden Markov model (HMM) is widely used for modeling spatially correlated genomic data (series data). In genomics, datasets of this kind are generated from genome-wide mapping studies through high-throughput methods such as chromatin immunoprecipitation coupled with massively parallel sequencing (ChIP-seq). When multiple regulatory protein binding sites or related epigenetic modifications are mapped simultaneously, the correlation between data series can be incorporated into the latent variable inference in a multivariate form of HMM, potentially increasing the statistical power of signal detection...
2017: Methods in Molecular Biology
https://www.readbyqxmd.com/read/28224060/twenty-microsatellite-markers-for-the-endangered-vatica-mangachapoi-dipterocarpaceae
#7
Jun-Jie Guo, Shuai-Bin Shang, Chun-Sheng Wang, Zhi-Gang Zhao, Jie Zeng
PREMISE OF THE STUDY: Microsatellite markers were developed for Vatica mangachapoi (Dipterocarpaceae), an endangered species indigenous to Southeast Asia and southern China. METHODS AND RESULTS: Twenty microsatellite markers, including 12 polymorphic markers, were identified from V. mangachapoi using high-throughput sequencing. Polymorphism at each marker was evaluated using 87 individuals from three natural populations. The number of alleles per polymorphic locus ranged from six to 15, and the observed and expected heterozygosity varied from 0...
February 2017: Applications in Plant Sciences
https://www.readbyqxmd.com/read/28223988/the-impact-of-genotyping-by-sequencing-pipelines-on-snp-discovery-and-identification-of-markers-associated-with-verticillium-wilt-resistance-in-autotetraploid-alfalfa-medicago-sativa-l
#8
Long-Xi Yu, Ping Zheng, Suresh Bhamidimarri, Xiang-Ping Liu, Dorie Main
Verticillium wilt (VW) of alfalfa is a soilborne disease causing severe yield loss in alfalfa. To identify molecular markers associated with VW resistance, we used an integrated framework of genome-wide association study (GWAS) with high-throughput genotyping by sequencing (GBS) to identify loci associated with VW resistance in an F1 full-sib alfalfa population. Phenotyping was performed using manual inoculation of the pathogen to cloned plants of each individual and disease severity was scored using a standard scale...
2017: Frontiers in Plant Science
https://www.readbyqxmd.com/read/28223683/metataxonomics-reveal-vultures-as-a-reservoir-for-clostridium-perfringens
#9
Xiangli Meng, Shan Lu, Jing Yang, Dong Jin, Xiaohong Wang, Xiangning Bai, Yumeng Wen, Yiting Wang, Lina Niu, Changyun Ye, Ramon Rosselló-Móra, Jianguo Xu
The Old World vulture may carry and spread pathogens for emerging infections since they feed on the carcasses of dead animals and participate in the sky burials of humans, some of whom have died from communicable diseases. Therefore, we studied the precise fecal microbiome of the Old World vulture with metataxonomics, integrating the high-throughput sequencing of almost full-length small subunit ribosomal RNA (16S rRNA) gene amplicons in tandem with the operational phylogenetic unit (OPU) analysis strategy...
February 22, 2017: Emerging Microbes & Infections
https://www.readbyqxmd.com/read/28223526/hypermutation-signature-reveals-a-slippage-and-realignment-model-of-translesion-synthesis-by-rev3-polymerase-in-cisplatin-treated-yeast
#10
Romulo Segovia, Yaoqing Shen, Scott A Lujan, Steven J M Jones, Peter C Stirling
Gene-gene or gene-drug interactions are typically quantified using fitness as a readout because the data are continuous and easily measured in high throughput. However, to what extent fitness captures the range of other phenotypes that show synergistic effects is usually unknown. Using Saccharomyces cerevisiae and focusing on a matrix of DNA repair mutants and genotoxic drugs, we quantify 76 gene-drug interactions based on both mutation rate and fitness and find that these parameters are not connected. Independent of fitness defects, we identified six cases of synthetic hypermutation, where the combined effect of the drug and mutant on mutation rate was greater than predicted...
February 21, 2017: Proceedings of the National Academy of Sciences of the United States of America
https://www.readbyqxmd.com/read/28223509/high-throughput-screening-of-rare-metabolically-active-tumor-cells-in-pleural-effusion-and-peripheral-blood-of-lung-cancer-patients
#11
Yin Tang, Zhuo Wang, Ziming Li, Jungwoo Kim, Yuliang Deng, Yan Li, James R Heath, Wei Wei, Shun Lu, Qihui Shi
Malignant pleural effusion (MPE), the presence of malignant cells in pleural fluid, is often the first sign of many cancers and occurs in patients with metastatic malignancies. Accurate detection of tumor cells in pleural fluid is crucial because the presence of MPE denotes an advanced stage of disease and directs a switch in clinical managements. Cytology, as a traditional diagnostic tool, has limited sensitivity especially when tumor cells are not abundant, and may be confounded by reactive mesothelial cells in the pleural fluid...
February 21, 2017: Proceedings of the National Academy of Sciences of the United States of America
https://www.readbyqxmd.com/read/28223504/transcriptome-wide-microrna-and-target-dynamics-in-the-fat-body-during-the-gonadotrophic-cycle-of-aedes-aegypti
#12
Xiufeng Zhang, Emre Aksoy, Thomas Girke, Alexander S Raikhel, Fedor V Karginov
The mosquito Aedes aegypti is a major vector of numerous viral diseases, because it requires a blood meal to facilitate egg development. The fat body, a counterpart of mammalian liver and adipose tissues, is the metabolic center, playing a key role in reproduction. Therefore, understanding of regulatory networks controlling its functions is critical, and the role of microRNAs (miRNAs) in the process is largely unknown. We aimed to explore miRNA expression and potential targets in the female fat body of Ae. aegypti, as well as their changes postblood meal (PBM)...
February 21, 2017: Proceedings of the National Academy of Sciences of the United States of America
https://www.readbyqxmd.com/read/28223254/issues-with-rna-seq-analysis-in-non-model-organisms-a-salmonid-example
#13
Arvind Sundaram, Torstein Tengs, Unni Grimholt
High throughput sequencing (HTS) is useful for many purposes as exemplified by the other topics included in this special issue. The purpose of this paper is to look into the unique challenges of using this technology in non-model organisms where resources such as genomes, functional genome annotations or genome complexity provide obstacles not met in model organisms. To describe these challenges, we narrow our scope to RNA sequencing used to study differential gene expression in response to pathogen challenge...
February 18, 2017: Developmental and Comparative Immunology
https://www.readbyqxmd.com/read/28223103/her2-amplification-and-cetuximab-efficacy-in-patients-with-metastatic-colorectal-cancer-harboring-wild-type-ras-and-braf
#14
Jae Ho Jeong, Jihun Kim, Yong Sang Hong, Dalyong Kim, Jeong Eun Kim, Sun Young Kim, Kyu-Pyo Kim, Young-Kwang Yoon, Deokhoon Kim, Sung-Min Chun, Yangsoon Park, Se Jin Jang, Tae Won Kim
BACKGROUND: Cetuximab has shown clinical benefit in patients with metastatic colorectal cancer (mCRC) harboring wild-type RAS. Human epidermal growth factor receptor 2 (HER2) amplification may be a mechanism of cetuximab resistance. We evaluated the association between HER2 amplification and cetuximab efficacy in patients with mCRC harboring wild-type RAS and BRAF. PATIENTS AND METHODS: Between December 2003 and June 2013, we identified 142 patients with mCRC whose tumors harbored both wild-type exons 2, 3, and 4 in KRAS and NRAS, and wild-type exon 15 in BRAF using high throughput sequencing (OncoMap version 4...
January 25, 2017: Clinical Colorectal Cancer
https://www.readbyqxmd.com/read/28223047/diversity-in-sequences-post-translational-modifications-and-expected-pharmacological-activities-of-toxins-from-four-conus-species-revealed-by-the-combination-of-cutting-edge-proteomics-transcriptomics-and-bioinformatics
#15
Michel Degueldre, Marion Verdenaud, Garikoitz Legarda, Rebeca Minambres, Sheila Zuniga, Mathieu Leblanc, Nicolas Gilles, Frederic Ducancel, Edwin De Pauw, Loic Quinton
Venomous animals have developed a huge arsenal of reticulated peptides for defense and predation. Based on various scaffolds, they represent a colossal pharmacological diversity, making them top candidates for the development of innovative drugs. Instead of relying on the classical, low-throughput bioassay-guided approach to identify innovative bioactive peptides, this work exploits a recent paradigm to access to venom diversity. This strategy bypasses the classical approach by combining high-throughput transcriptomics, proteomics and bioinformatics cutting-edge technologies to generate reliable peptide sequences...
February 18, 2017: Toxicon: Official Journal of the International Society on Toxinology
https://www.readbyqxmd.com/read/28222110/different-antibiotic-growth-promoters-induce-specific-changes-in-the-cecal-microbiota-membership-of-broiler-chicken
#16
Marcio C Costa, Jose A Bessegatto, Amauri A Alfieri, J Scott Weese, João A B Filho, Alexandre Oba
Antimicrobials are sometimes given to food animals at low doses in order to promote faster growth. However, the mechanisms by which those drugs improve performance are not fully understood. This study aimed to investigate the impact of zinc bacitracin (55g/ton), enramycin (10g/ton); halquinol® (30g/ton); virginiamycin (16,5g/ton) and avilamycin (10g/ton) on the cecal microbiota of broiler chicken, compared to a control group. Six hundred and twenty four chicks (Cobb 500) arriving to an experimental unit were randomly assigned into each treatment with four repetitions per treatment...
2017: PloS One
https://www.readbyqxmd.com/read/28221022/quantitative-13c-traces-of-glucose-fate-in-hepatitis-b-virus-infected-hepatocytes
#17
Qianfen Wan, Yulan Wang, Huiru Tang
Quantitative characterization of 13C-labeled metabolites is an important part of the stable isotope tracing method widely used in metabolic flux analysis. Due to long relaxation time and low sensitivity of 13C nuclei, direct measurement of 13C labeled metabolites using one dimensional 13C NMR often fails to meet the demand of metabolomics studies especially with large number of samples and metabolites having low abundance. Although HSQC-based 2D NMR methods have improved sensitivity with inversion detection, they are time-consuming thus unsuitable for high-throughput absolute quantification of 13C-labeled metabolites...
February 21, 2017: Analytical Chemistry
https://www.readbyqxmd.com/read/28220901/distinct-signatures-of-dental-plaque-metabolic-byproducts-dictated-by-periodontal-inflammatory-status
#18
Akito Sakanaka, Masae Kuboniwa, Ei Hashino, Takeshi Bamba, Eiichiro Fukusaki, Atsuo Amano
Onset of chronic periodontitis is associated with an aberrant polymicrobial community, termed dysbiosis. Findings regarding its etiology obtained using high-throughput sequencing technique suggested that dysbiosis holds a conserved metabolic signature as an emergent property. The purpose of this study was to identify robust biomarkers for periodontal inflammation severity. Furthermore, we investigated disease-associated metabolic signatures of periodontal microbiota using a salivary metabolomics approach. Whole saliva samples were obtained from adult subjects before and after removal of supragingival plaque (debridement)...
February 21, 2017: Scientific Reports
https://www.readbyqxmd.com/read/28220542/the-gut-microbiome-in-human-neurological-disease-a-review
#19
REVIEW
Helen Tremlett, Kylynda C Bauer, Silke Appel-Cresswell, Brett B Finlay, Emmanuelle Waubant
Almost half the cells and 1% of the unique genes found in our bodies are human, the rest are from microbes; predominantly bacteria, archaea, fungi, and viruses. These microorganisms collectively form the human microbiota, with most colonizing the gut. Recent technological advances, open access data-libraries, and application of high throughput sequencing have allowed these microbes to be identified and their contribution to neurological health examined. Emerging evidence links perturbations in the gut microbiota to neurological disease, including disease risk, activity, and progression...
February 21, 2017: Annals of Neurology
https://www.readbyqxmd.com/read/28220206/a-user-guide-to-the-brassica-60k-illumina-infinium%C3%A2-snp-genotyping-array
#20
REVIEW
Annaliese S Mason, Erin E Higgins, Rod J Snowdon, Jacqueline Batley, Anna Stein, Christian Werner, Isobel A P Parkin
The Brassica napus 60K Illumina Infinium™ SNP array has had huge international uptake in the rapeseed community due to the revolutionary speed of acquisition and ease of analysis of this high-throughput genotyping data, particularly when coupled with the newly available reference genome sequence. However, further utilization of this valuable resource can be optimized by better understanding the promises and pitfalls of SNP arrays. We outline how best to analyze Brassica SNP marker array data for diverse applications, including linkage and association mapping, genetic diversity and genomic introgression studies...
February 20, 2017: TAG. Theoretical and Applied Genetics. Theoretische und Angewandte Genetik
keyword
keyword
68065
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"