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Sequence library construction

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https://www.readbyqxmd.com/read/28098189/global-identification-of-micrornas-associated-with-chlorantraniliprole-resistance-in-diamondback-moth-plutella-xylostella-l
#1
Bin Zhu, Xiuxia Li, Ying Liu, Xiwu Gao, Pei Liang
The diamondback moth (DBM), Plutella xylostella (L.), is one of the most serious cruciferous pests and has developed high resistance to most insecticides, including chlorantraniliprole. Previous studies have reported several protein-coding genes that involved in chlorantraniliprole resistance, but research on resistance mechanisms at the post-transcription level is still limited. In this study, a global screen of microRNAs (miRNAs) associated with chlorantraniliprole resistance in P. xylostella was performed...
January 18, 2017: Scientific Reports
https://www.readbyqxmd.com/read/28090264/drought-stress-induced-changes-of-micrornas-in-diploid-and-autotetraploid-paulownia-tomentosa
#2
Xibing Cao, Guoqiang Fan, Lin Cao, Minjie Deng, Zhenli Zhao, Suyan Niu, Zhe Wang, Yuanlong Wang
Drought stress adversely affects plant productivity. Growth and timber production of Paulownia trees are limited under drought stress. Changes in gene expression patterns and miRNA in different ploidy of Paulownia tomentosa have been investigated. However, the responses of P. tomentosa to drought stress at the microRNA (miRNA) level have not been reported so far. To identify miRNA candidates and their target genes involved in the drought stress response in diploid and tetraploid P. tomentosa, four small RNA and four degradome libraries from diploid and autotetraploid P...
2017: Genes & Genomics
https://www.readbyqxmd.com/read/28087649/identification-of-unique-essential-proteins-from-a-m-tuberculosis-f15-lam4-kzn-phage-secretome-library
#3
Thamsanqa Emmanuel Chiliza, Manormoney Pillay, Balakrishna Pillay
Mycobacterium tuberculosis (Mtb) is the causative agent of tuberculosis disease (TB), the leading cause of death from bacterial infection worldwide. Although treatable, the resurgence of multi- and extensively-drug resistance TB is a major setback for the fight against TB globally. Consequently, there is an urgent need for new Mtb derived biomarkers for use in the design of new drugs and rapid point-of-care diagnostic or prognostic tools for management of TB transmission. Therefore, the present study aimed to identify unique Mtb secreted proteins from the extensively drug resistant Mtb F15/LAM4/KZN phage secretome library...
January 12, 2017: Pathogens and Disease
https://www.readbyqxmd.com/read/28078489/identification-and-profiling-of-conserved-and-novel-micrornas-involved-in-oil-and-oleic-acid-production-during-embryogenesis-in-carya-cathayensis-sarg
#4
Zhengjia Wang, Ruiming Huang, Zhichao Sun, Tong Zhang, Jianqin Huang
MicroRNAs (miRNAs) are important regulators of plant development and fruit formation. Mature embryos of hickory (Carya cathayensis Sarg.) nuts contain more than 70% oil (comprising 90% unsaturated fatty acids), along with a substantial amount of oleic acid. To understand the roles of miRNAs involved in oil and oleic acid production during hickory embryogenesis, three small RNA libraries from different stages of embryogenesis were constructed. Deep sequencing of these three libraries identified 95 conserved miRNAs with 19 miRNA*s, 7 novel miRNAs (as well as their corresponding miRNA*s), and 26 potentially novel miRNAs...
January 11, 2017: Functional & Integrative Genomics
https://www.readbyqxmd.com/read/28066818/microbiome-helper-a-custom-and-streamlined-workflow-for-microbiome-research
#5
André M Comeau, Gavin M Douglas, Morgan G I Langille
Sequence-based approaches to study microbiomes, such as 16S rRNA gene sequencing and metagenomics, are uncovering associations between microbial taxa and a myriad of factors. A drawback of these approaches is that the necessary sequencing library preparation and bioinformatic analyses are complicated and continuously changing, which can be a barrier for researchers new to the field. We present three essential components to conducting a microbiome experiment from start to finish: first, a simplified and step-by-step custom gene sequencing protocol that requires limited lab equipment, is cost-effective, and has been thoroughly tested and utilized on various sample types; second, a series of scripts to integrate various commonly used bioinformatic tools that is available as a standalone installation or as a single downloadable virtual image; and third, a set of bioinformatic workflows and tutorials to provide step-by-step guidance and education for those new to the microbiome field...
January 2017: MSystems
https://www.readbyqxmd.com/read/28066712/de-novo-transcriptome-assembly-of-shrimp-palaemon-serratus
#6
Alejandra Perina, Ana M González-Tizón, Iago F Meilán, Andrés Martínez-Lage
: The shrimp Palaemon serratus is a coastal decapod crustacean with a high commercial value. It is harvested for human consumption. In this study, we used Illumina sequencing technology (HiSeq 2000) to sequence, assemble and annotate the transcriptome of P. serratus. RNA was isolated from muscle of adults individuals and, from a pool of larvae. A total number of 4 cDNA libraries were constructed, using the TruSeq RNA Sample Preparation Kit v2. The raw data in this study was deposited in NCBI SRA database with study accession number of SRP090769...
March 2017: Genomics Data
https://www.readbyqxmd.com/read/28064476/chemoselective-coupling-preserves-the-substrate-integrity-of-surface-immobilized-oligonucleotides-for-emulsion-pcr-based-gene-library-construction
#7
Marie L Malone, Valerie J Cavett, Brian M Paegel
Combinatorial bead libraries figure prominently in next-generation sequencing and are also important tools for in vitro evolution. The most common methodology for generating such bead libraries, emulsion PCR (emPCR), enzymatically extends bead-immobilized oligonucleotide PCR primers in emulsion droplets containing a single progenitor library member. Primers are almost always immobilized on beads via noncovalent biotin-streptavidin binding. Here, we describe covalent bead functionalization with primers (∼10(6) primers/2...
January 9, 2017: ACS Combinatorial Science
https://www.readbyqxmd.com/read/28062577/overlapping-specificity-of-duplicated-human-pancreatic-elastase-3-isoforms-and-archetypal-porcine-elastase-1-provides-clues-to-evolution-of-digestive-enzymes
#8
Eszter Boros, Katalin Zboray, Dávid Héja, Gábor Pál, Miklós Sahin-Tóth
Chymotrypsin-like elastases (CELAs) are pancreatic serine proteinases which digest dietary proteins. CELAs are typically expressed in multiple isoforms which can vary among different species. The human pancreas does not express CELA1 but secretes two CELA3 isoforms, CELA3A and CELA3B. The reason for the CELA3 duplication and the substrate preferences of the duplicated isoforms are unclear. Here, we tested whether CELA3A and CELA3B evolved unique substrate specificities to compensate for the loss of CELA1. We constructed a phage library displaying variants of the substrate-like Schistocerca gregaria proteinase inhibitor 2 (SGPI-2) to select reversible, high-affinity inhibitors of human CELA3A, CELA3B, and porcine CELA1...
January 6, 2017: Journal of Biological Chemistry
https://www.readbyqxmd.com/read/28061744/comprehensive-evaluation-of-extracellular-small-rna-isolation-methods-from-serum-in-high-throughput-sequencing
#9
Yan Guo, Kasey Vickers, Yanhua Xiong, Shilin Zhao, Quanhu Sheng, Pan Zhang, Wanding Zhou, Charles R Flynn
BACKGROUND: DNA and RNA fractions from whole blood, serum and plasma are increasingly popular analytes that are currently under investigation for their utility in the diagnosis and staging of disease. Small non-coding ribonucleic acids (sRNAs), specifically microRNAs (miRNAs) and their variant isoforms (isomiRs), and transfer RNA (tRNA)-derived small RNAs (tDRs) comprise a repertoire of molecules particularly promising in this regard. RESULTS: In this designed study, we compared the performance of various methods and kits for isolating circulating extracellular sRNAs (ex-sRNAs)...
January 7, 2017: BMC Genomics
https://www.readbyqxmd.com/read/28057818/dna-methylation-assessment-from-human-slow-and-fast-twitch-skeletal-muscle-fibers
#10
Gwenaelle Begue, Ulrika Raue, Bozena Jemiolo, Scott W Trappe
A new application of the Reduced Representation Bisulfite Sequencing method was developed using low-DNA input to investigate the epigenetic profile of human slow- and fast-twitch skeletal muscle fibers. Successful library construction was completed with as little as 15 ng of DNA and high quality sequencing data were obtained with 32 ng of DNA. Analysis identified 143,160 differentially methylated CpG-sites across 14,046 genes. In both fiber types, selected genes predominantly expressed in slow or fast fibers were hypomethylated, which was supported by the RNA-Seq analysis...
January 5, 2017: Journal of Applied Physiology
https://www.readbyqxmd.com/read/28045942/knock-down-of-whitefly-gut-gene-expression-and-mortality-by-orally-delivered-gut-gene-specific-dsrnas
#11
Meenal Vyas, Amir Raza, Muhammad Yousaf Ali, Muhammad Aleem Ashraf, Shahid Mansoor, Ahmad Ali Shahid, Judith K Brown
Control of the whitefly Bemisia tabaci (Genn.) agricultural pest and plant virus vector relies on the use of chemical insecticides. RNA-interference (RNAi) is a homology-dependent innate immune response in eukaryotes, including insects, which results in degradation of the corresponding transcript following its recognition by a double-stranded RNA (dsRNA) that shares 100% sequence homology. In this study, six whitefly 'gut' genes were selected from an in silico-annotated transcriptome library constructed from the whitefly alimentary canal or 'gut' of the B biotype of B...
2017: PloS One
https://www.readbyqxmd.com/read/28043598/investigation-of-isoniazid-and-ethionamide-cross-resistance-by-whole-genome-sequencing-and-association-with-poor-treatment-outcomes-of-multidrug-resistant-tuberculosis-patients-in-south-africa
#12
L Malinga, J Brand, C Jansen van Rensburg, G Cassell, M van der Walt
OBJECTIVE/BACKGROUND: Ethionamide (ETH) and isoniazid (INH) are part of the backbone regimen used for the treatment of multidrug-resistant tuberculosis (MDR-TB). Both ETH and INH are structurally similar and are activated by ethA and katG gene products. Resistance to INH among MDR-TB patients may cause ETH to be ineffective, as both target nicotinamide adenine dinucleotide-dependent enoyl-acyl carrier protein reductase inhA protein and mutations within inhA gene may lead to their cross-resistance...
December 2016: International Journal of Mycobacteriology
https://www.readbyqxmd.com/read/28043542/the-analysis-of-exosomal-micro-rnas-in-peripheral-blood-mononuclear-cell-derived-macrophages-after-infection-with-bacillus-calmette-gu%C3%A3-rin-by-rna-sequencing
#13
Esmaeil Mortaz, Shamila D Alipoor, Payam Tabarsi, Ian M Adcock, Johan Garssen, Ali Akbar Velayati
OBJECTIVE/BACKGROUND: Tuberculosis (TB) is a major global threat to human health, especially in low-income countries. The diagnosis of TB is challenging because of the limitations of specificity and sensitivity with the current diagnostics. Novel, selective biomarkers for TB would be of great practical value. Exosomes are bioactive vesicles with 30-100nm in diameter, which are secreted from almost all cell types and are found in virtually every human body fluid. Exosomes transport micro-RNAs (miRNAs), which are post-transcriptional regulators of gene expression, around the body and allow miRNAs to modulate biological pathways in target cells...
December 2016: International Journal of Mycobacteriology
https://www.readbyqxmd.com/read/28040784/genetic-analysis-of-the-lambda-spanins-rz-and-rz1-identification-of-functional-domains
#14
Jesse Cahill, Manoj Rajaure, Chandler O'Leary, Jordan Sloan, Armando Marrufo, Ashley Holt, Aneesha Kulkarni, Oscar Hernandez, Ry Young
Coliphage lambda proteins Rz and Rz1 are the inner membrane and outer membrane subunits of the spanin complex, a heterotetramer that bridges the periplasm and is essential for the disruption of the outer membrane during phage lysis. Recent evidence suggests the spanin complex functions by fusing the inner and outer membrane. Here we use a genetics approach to investigate and characterize determinants of spanin function. Because Rz1 is entirely embedded in the +1 reading frame of Rz, the genes were dis-embedded before using random mutagenesis to construct a library of lysis-defective alleles for both genes...
December 30, 2016: G3: Genes—Genomes—Genetics
https://www.readbyqxmd.com/read/28028549/ssunique-detecting-sequence-novelty-in-microbiome-surveys
#15
Michael D J Lynch, Josh D Neufeld
High-throughput sequencing of small-subunit (SSU) rRNA genes has revolutionized understanding of microbial communities and facilitated investigations into ecological dynamics at unprecedented scales. Such extensive SSU rRNA gene sequence libraries, constructed from DNA extracts of environmental or host-associated samples, often contain a substantial proportion of unclassified sequences, many representing organisms with novel taxonomy (taxonomic "blind spots") and potentially unique ecology. Indeed, these novel taxonomic lineages are associated with so-called microbial "dark matter," which is the genomic potential of these lineages...
November 2016: MSystems
https://www.readbyqxmd.com/read/28024146/genome-wide-mapping-of-autonomous-promoter-activity-in-human-cells
#16
Joris van Arensbergen, Vincent D FitzPatrick, Marcel de Haas, Ludo Pagie, Jasper Sluimer, Harmen J Bussemaker, Bas van Steensel
Previous methods to systematically characterize sequence-intrinsic activity of promoters have been limited by relatively low throughput and the length of the sequences that could be tested. Here we present 'survey of regulatory elements' (SuRE), a method that assays more than 10(8) DNA fragments, each 0.2-2 kb in size, for their ability to drive transcription autonomously. In SuRE, a plasmid library of random genomic fragments upstream of a 20-bp barcode is constructed, and decoded by paired-end sequencing...
December 26, 2016: Nature Biotechnology
https://www.readbyqxmd.com/read/28018366/identification-of-mirnas-affecting-the-establishment-of-brassica-alboglabra-seedling
#17
Rongfang Guo, Yanping Deng, Zhongkai Huang, Xiaodong Chen, Xu XuHan, Zhongxiong Lai
MicroRNAs (miRNAs) are important for plant development including seed formation, dormancy, and germination, as well as seedling establishment. The Brassica vegetable seedling establishment stage influences the development of high quality seedlings, but also affects the nutrient content of sprouts. Chinese kale (Brassica alboglabra) seedlings at different growth stages were used to construct two small-RNA (sRNA) libraries. We comprehensively analyzed the miRNAs in 2- and 9-day-old seedlings. An average of 11,722,490 clean reads were generated after removing low-quality reads and adapter contaminants...
2016: Frontiers in Plant Science
https://www.readbyqxmd.com/read/28008173/development-of-a-high-density-genetic-linkage-map-and-identification-of-flowering-time-qtls-in-adzuki-bean-vigna-angularis
#18
Changyou Liu, Baojie Fan, Zhimin Cao, Qiuzhu Su, Yan Wang, Zhixiao Zhang, Jing Tian
A high-density linkage map is crucial for the identification of quantitative trait loci (QTLs), positional cloning, and physical map assembly. Here, we report the development of a high-density linkage map based on specific length amplified fragment sequencing (SLAF-seq) for adzuki bean and the identification of flowering time-related QTLs. Through SLAF library construction and Illumina sequencing of a recombinant inbred line (RIL) population, a total of 4425 SLAF markers were developed and assigned to 11 linkage groups (LGs)...
December 23, 2016: Scientific Reports
https://www.readbyqxmd.com/read/28007941/registry-in-a-tube-multiplexed-pools-of-retrievable-parts-for-genetic-design-space-exploration
#19
Lauren B A Woodruff, Thomas E Gorochowski, Nicholas Roehner, Tarjei S Mikkelsen, Douglas Densmore, D Benjamin Gordon, Robert Nicol, Christopher A Voigt
Genetic designs can consist of dozens of genes and hundreds of genetic parts. After evaluating a design, it is desirable to implement changes without the cost and burden of starting the construction process from scratch. Here, we report a two-step process where a large design space is divided into deep pools of composite parts, from which individuals are retrieved and assembled to build a final construct. The pools are built via multiplexed assembly and sequenced using next-generation sequencing. Each pool consists of ∼20 Mb of up to 5000 unique and sequence-verified composite parts that are barcoded for retrieval by PCR...
December 21, 2016: Nucleic Acids Research
https://www.readbyqxmd.com/read/28004925/small-molecule-based-pattern-recognition-to-classify-rna-structure
#20
Christopher S Eubanks, Jordan E Forte, Gary J Kapral, Amanda E Hargrove
Three-dimensional RNA structures are notoriously difficult to determine, and the link between secondary structure and RNA conformation is only beginning to be understood. These challenges have hindered the identification of guiding principles for small molecule:RNA recognition. We herein demonstrate that the strong and differential binding ability of aminoglycosides to RNA structures can be used to classify five canonical RNA secondary structure motifs through principal component analysis (PCA). In these analyses, the aminoglycosides act as receptors, while RNA structures labeled with a benzofuranyluridine fluorophore act as analytes...
December 22, 2016: Journal of the American Chemical Society
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