keyword
MENU ▼
Read by QxMD icon Read
search

Sequence library construction

keyword
https://www.readbyqxmd.com/read/28334828/flexible-crispr-library-construction-using-parallel-oligonucleotide-retrieval
#1
Abigail Read, Shaojian Gao, Eric Batchelor, Ji Luo
CRISPR/Cas9-based gene knockout libraries have emerged as a powerful tool for functional screens. We present here a set of pre-designed human and mouse sgRNA sequences that are optimized for both high on-target potency and low off-target effect. To maximize the chance of target gene inactivation, sgRNAs were curated to target both 5΄ constitutive exons and exons that encode conserved protein domains. We describe here a robust and cost-effective method to construct multiple small sized CRISPR library from a single oligo pool generated by array synthesis using parallel oligonucleotide retrieval...
March 16, 2017: Nucleic Acids Research
https://www.readbyqxmd.com/read/28334803/statistical-analysis-of-genetic-interactions-in-tn-seq-data
#2
Michael A DeJesus, Subhalaxmi Nambi, Clare M Smith, Richard E Baker, Christopher M Sassetti, Thomas R Ioerger
Tn-Seq is an experimental method for probing the functions of genes through construction of complex random transposon insertion libraries and quantification of each mutant's abundance using next-generation sequencing. An important emerging application of Tn-Seq is for identifying genetic interactions, which involves comparing Tn mutant libraries generated in different genetic backgrounds (e.g. wild-type strain versus knockout strain). Several analytical methods have been proposed for analyzing Tn-Seq data to identify genetic interactions, including estimating relative fitness ratios and fitting a generalized linear model...
February 22, 2017: Nucleic Acids Research
https://www.readbyqxmd.com/read/28330315/characterization-and-development-of-est-ssr-markers-in-sweet-potato-ipomoea-batatas-l-lam
#3
Jin-Hee Kim, Jun-Hoi Kim, Won-Sam Jo, Jeong-Gwan Ham, Il Kyung Chung, Kyung-Min Kim
In this study, a cDNA library was constructed from the total RNA of sweet potato leaves. A total of 789 copies of the cDNA were cloned in Escherichia coli by employing the pGEM-T Easy vector. Sequencing was carried out by Solgent Co. (Korea). As many as 579 expressed sequence tag-simple sequence repeat (EST-SSR) markers were designed (73.38%) from the known cDNA nucleotide base sequences. The lengths of the developed EST-SSR markers ranged from 100 to 499 bp (average length 238 bp). Their motif sequence types were varied, with most being dinucleotides and pentanucleotides, and the most commonly found motifs were CAGAAT (29...
December 2016: 3 Biotech
https://www.readbyqxmd.com/read/28330093/exploration-of-nifh-gene-through-soil-metagenomes-of-the-western-indian-himalayas
#4
Ravindra Soni, Deep Chandra Suyal, Santosh Sai, Reeta Goel
This group has previously highlighted the prevalence of Csp genes from cold Himalayan environments. However, this study has explored the uncultured diazotrophs from metagenomes of western Indian Himalayas. The metagenomic nifH gene clone library was constructed from the Temperate, Subtropical and Tarai soils of Western Himalaya, India followed by polymerase chain reaction (PCR) amplification. After preliminary screening, selected clones were sequenced. In silico analysis of the clones was done, which documented 83...
June 2016: 3 Biotech
https://www.readbyqxmd.com/read/28323250/the-atomic-simulation-environment-a-python-library-for-working-with-atoms
#5
Ask Larsen, Jens Mortensen, Jakob Blomqvist, Ivano Castelli, Rune Christensen, Marcin Dulak, Jesper Friis, Michael Groves, Bjork Hammer, Cory Hargus, Eric Hermes, Paul Jennings, Peter Jensen, James Kermode, John Kitchin, Esben Kolsbjerg, Joseph Kubal, Kristen Kaasbjerg, Steen Lysgaard, Jon Maronsson, Tristan Maxson, Thomas Olsen, Lars Pastewka, Andrew Peterson, Carsten Rostgaard, Jakob Schiøtz, Ole Schütt, Mikkel Strange, Kristian Thygesen, Tejs Vegge, Lasse Vilhelmsen, Michael Walter, Zhenhua Zeng, Karsten Wedel Jacobsen
The Atomic Simulation Environment (ASE) is a software package written in the Python programming language with the aim of setting up, steering, and analyzing atomistic simula- tions. In ASE, tasks are fully scripted in Python. The powerful syntax of Python combined with the NumPy array library make it possible to perform very complex simulation tasks. For example, a sequence of calculations may be performed with the use of a simple "for-loop" construction. Calculations of energy, forces, stresses and other quantities are performed through interfaces to many external electronic structure codes or force fields using a uniform interface...
March 21, 2017: Journal of Physics. Condensed Matter: An Institute of Physics Journal
https://www.readbyqxmd.com/read/28322330/distribution-of-bathyarchaeota-communities-across-different-terrestrial-settings-and-their-potential-ecological-functions
#6
Xing Xiang, Ruicheng Wang, Hongmei Wang, Linfeng Gong, Baiying Man, Ying Xu
High abundance and widespread distribution of the archaeal phylum Bathyarchaeota in marine environment have been recognized recently, but knowledge about Bathyarchaeota in terrestrial settings and their correlation with environmental parameters is fairly limited. Here we reported the abundance of Bathyarchaeota members across different ecosystems and their correlation with environmental factors by constructing 16S rRNA clone libraries of peat from the Dajiuhu Peatland, coupling with bioinformatics analysis of 16S rRNA data available to date in NCBI database...
March 21, 2017: Scientific Reports
https://www.readbyqxmd.com/read/28315209/recombinant-allergen-production-in-e-coli
#7
Changqi Liu, LeAnna N Willison, Shridhar K Sathe
Recombinant protein allergens have been used in allergy studies, allergy diagnosis, and epitope mapping. Messenger RNAs (mRNAs) are isolated from tissues of interest for complementary DNA (cDNA) library construction. Subsequently, the allergen gene is amplified by polymerase chain reaction (PCR) and sequenced. The amplified gene is then cloned into an expression vector, expressed in Escherichia coli cells, and purified from the cell lysate. This chapter describes the protocols for recombinant allergen production...
2017: Methods in Molecular Biology
https://www.readbyqxmd.com/read/28314725/a-genome-survey-and-postharvest-transcriptome-analysis-in-lentinula-edodes
#8
Yuichi Sakamoto, Keiko Nakade, Shiho Sato, Kentaro Yoshida, Kazuhiro Miyazaki, Satoshi Natsume, Naotake Konno
Lentinula edodes is a popular cultivated edible and medicinal mushroom. Lentinula edodes is susceptible to postharvest problems such as gill browning, fruiting body softening, and lentinan degradation. We constructed a de novo assembly draft genome sequence and performed gene prediction of Lentinula edodesDe novo assembly was carried out using short reads from paired-end and mate-paired libraries and long reads by PacBio, resulting in a contig number of 1951 and an N50 of 1 Mb. Further, we predicted genes by Augustus using RNA-seq data from the whole life cycle of Lentinula edodes, resulting in 12,959 predicted genes...
March 17, 2017: Applied and Environmental Microbiology
https://www.readbyqxmd.com/read/28303777/placental-up-regulation-of-leptin-and-arms2-is-associated-with-growth-discordance-in-monochorionic-diamniotic-twin-pregnancies
#9
Luming Sun, Jia Zhou, Kai Wang, Jian Wang, Ling Shang, Jianguang Zhang, Junqing Wu, David S Cram
Fetal growth discordance is a relatively common complication of monochorionic diamniotic (MCDA) twin pregnancies and is caused by a combination of maternal and placental factors. The aim of the study was to survey placental gene expression patterns and identify genes associated with growth discordance. Clinical samples comprised eight growth-discordant MCDA twin placentas (31+3-34+4 weeks gestational age) and six growth-concordant twin placentas (31+2-37 weeks gestational age). Gene expression libraries were constructed from placental biopsy samples and analyzed by RNA-sequencing...
April 2017: Twin Research and Human Genetics: the Official Journal of the International Society for Twin Studies
https://www.readbyqxmd.com/read/28299328/mir319-mir390-and-mir393-are-involved-in-aluminum-response-in-flax-linum-usitatissimum-l
#10
Alexey A Dmitriev, Anna V Kudryavtseva, Nadezhda L Bolsheva, Alexander V Zyablitsin, Tatiana A Rozhmina, Natalya V Kishlyan, George S Krasnov, Anna S Speranskaya, Anastasia A Krinitsina, Asiya F Sadritdinova, Anastasiya V Snezhkina, Maria S Fedorova, Olga Yu Yurkevich, Olga V Muravenko, Maxim S Belenikin, Nataliya V Melnikova
Acid soils limit agricultural production worldwide. Major reason of crop losses in acid soils is the toxicity of aluminum (Al). In the present work, we investigated expression alterations of microRNAs in flax (Linum usitatissimum L.) plants under Al stress. Flax seedlings of resistant (TMP1919 and G1071/4_k) and sensitive (Lira and G1071/4_o) to Al cultivars and lines were exposed to AlCl3 solution for 4 and 24 hours. Twelve small RNA libraries were constructed and sequenced using Illumina platform. In total, 97 microRNAs from 18 conserved families were identified...
2017: BioMed Research International
https://www.readbyqxmd.com/read/28291379/characterization-of-vdasp-f2-secretory-factor-from-verticillium-dahliae-by-a-fast-and-easy-gene-knockout-system
#11
Chengjian Xie, Qiaoling Li, Xingyong Yang
The vascular wilt fungus Verticillium dahliae produces persistent resting structures known as microsclerotia, which enable long-term survival of this plant pathogen in soil. The completed genome sequence of V. dahliae has facilitated large-scale investigations of individual gene functions using gene-disruption strategies based on Agrobacterium tumefaciens-mediated transformation (ATMT). However, the construction of gene-deletion vectors and screening of deletion mutants have remained challenging in V. dahliae...
March 14, 2017: Molecular Plant-microbe Interactions: MPMI
https://www.readbyqxmd.com/read/28282934/alternative-splicing-profile-and-sex-preferential-gene-expression-in-the-female-and-male-pacific-abalone-haliotis-discus-hannai
#12
Mi Ae Kim, Jae-Sung Rhee, Tae Ha Kim, Jung Sick Lee, Ah-Young Choi, Beom-Soon Choi, Ik-Young Choi, Young Chang Sohn
In order to characterize the female or male transcriptome of the Pacific abalone and further increase genomic resources, we sequenced the mRNA of full-length complementary DNA (cDNA) libraries derived from pooled tissues of female and male Haliotis discus hannai by employing the Iso-Seq protocol of the PacBio RSII platform. We successfully assembled whole full-length cDNA sequences and constructed a transcriptome database that included isoform information. After clustering, a total of 15,110 and 12,145 genes that coded for proteins were identified in female and male abalones, respectively...
March 9, 2017: Genes
https://www.readbyqxmd.com/read/28281773/b-cell-epitopes-of-african-horse-sickness-virus-serotype-4-recognised-by-immune-horse-sera
#13
Evans M Mathebula, Frederika E Faber, Wouter Van Wyngaardt, Antoinette Van Schalkwyk, Alri Pretorius, Jeanni Fehrsen
Identifying antigenic proteins and mapping their epitopes is important for the development of diagnostic reagents and recombinant vaccines. B-cell epitopes of African horse sickness virus (AHSV) have previously been mapped on VP2, VP5, VP7 and NS1, using mouse, rabbit and chicken monoclonal antibodies. A comprehensive study of the humoral immune response of five vaccinated horses to AHSV-4 antigenic peptides was undertaken. A fragmented-genome phage display library expressing a repertoire of AHSV-4 peptides spanning the entire genome was constructed...
February 24, 2017: Onderstepoort Journal of Veterinary Research
https://www.readbyqxmd.com/read/28280499/deep-sequencing-of-suppression-subtractive-hybridisation-drought-and-recovery-libraries-of-the-non-model-crop-trifolium-repens-l
#14
Maciej Bisaga, Matthew Lowe, Matthew Hegarty, Michael Abberton, Adriana Ravagnani
White clover is a short-lived perennial whose persistence is greatly affected by abiotic stresses, particularly drought. The aim of this work was to characterize its molecular response to water deficit and recovery following re-hydration to identify targets for the breeding of tolerant varieties. We created a white clover reference transcriptome of 16,193 contigs by deep sequencing (mean base coverage 387x) four Suppression Subtractive Hybridization (SSH) libraries (a forward and a reverse library for each treatment) constructed from young leaf tissue of white clover at the onset of the response to drought and recovery...
2017: Frontiers in Plant Science
https://www.readbyqxmd.com/read/28276654/a-family-13-thioesterase-isolated-from-an-activated-sludge-metagenome-insights-into-aromatic-compounds-metabolism
#15
Ayixon Sánchez-Reyez, Ramón Alberto Batista-García, Gilberto Valdés-García, Ernesto Ortiz, Lucía Perezgasga, Andrés Zárate-Romero, Nina Pastor, Jorge Luis Folch-Mallol
Activated sludge is produced during the treatment of sewage and industrial wastewaters. Its diverse chemical composition allows growth of a large collection of microbial phylotypes with very different physiologic and metabolic profiles. Thus, activated sludge is considered as an excellent environment to discover novel enzymes through functional metagenomics, especially activities related with degradation of environmental pollutants. Metagenomic DNA was isolated and purified from an activated sludge sample. Metagenomic libraries were subsequently constructed in Escherichia coli...
March 9, 2017: Proteins
https://www.readbyqxmd.com/read/28272485/construction-and-immunogenicity-of-a-recombinant-swinepox-virus-expressing-a-multi-epitope-peptide-for-porcine-reproductive-and-respiratory-syndrome-virus
#16
Huixing Lin, Zhe Ma, Xin Hou, Lei Chen, Hongjie Fan
To characterize neutralizing mimotopes, phages were selected from a 12-mer phage display library using three anti-porcine reproductive and respiratory syndrome virus (PRRSV) neutralizing monoclonal antibodies: (1) A1; (2) A2; and (3) A7. Of these, A2 and A7 recognize the mimotope, P2, which contains the SRHDHIH motif, which has conserved consensus sequences from amino acid positions 156 to 161 in the N-terminal ectodomain of GP3. The artificial multi-epitope gene, mp2, was designed by combining three repeats of the mimotope P2...
March 8, 2017: Scientific Reports
https://www.readbyqxmd.com/read/28270824/advances-of-community-level-plant-dna-barcoding-in-china
#17
Nancai Pei, Bufeng Chen, W J Kress
DNA barcoding is a commonly used bio-technology in multiple disciplines including biology, environmental science, forensics and inspection, etc. Forest dynamic plots provide a unique opportunity to carry out large-scale, comparative, and multidisciplinary research for plant DNA barcoding. The paper concisely reviewed four previous progresses in China; specifically, species discrimination, community phylogenetic reconstruction, phylogenetic community structure exploration, and biodiversity index evaluation. Further, we demonstrated three major challenges; specifically, building the impetus to generate DNA barcodes using multiple plant DNA markers for all woody species at forest community levels, analyzing massive DNA barcoding sequence data, and promoting theoretical innovation...
2017: Frontiers in Plant Science
https://www.readbyqxmd.com/read/28268049/application-of-an-esi-qtof-method-for-the-detailed-characterization-of-gsk-3%C3%AE-inhibitors
#18
Angela De Simone, Jessica Fiori, Marina Naldi, Annalisa D'Urzo, Vincenzo Tumiatti, Andrea Milelli, Vincenza Andrisano
The crucial role of Glycogen Synthase Kinase 3 (GSK-3β) as a pivotal player in Alzheimer's Disease (AD) has recently inspired significant attempts to design and synthesize potent kinase inhibitors. In fact GSK-3β is considered the main kinase which catalyzes the microtubule-associated protein tau hyper-phosphorylation and the neurofibrillary tangles (NFT) in vitro and in vivo, The first classes of GSK-3β inhibitors were classified as ATP-competitive and, therefore, they lack of an efficient degree of selectivity over other kinases...
February 27, 2017: Journal of Pharmaceutical and Biomedical Analysis
https://www.readbyqxmd.com/read/28267631/transcriptome-analysis-of-ruditapes-philippinarum-hepatopancreas-provides-insights-into-immune-signaling-pathways-under-vibrio-anguillarum-infection
#19
Yipeng Ren, Junli Xue, Huanhuan Yang, Baoping Pan, Wenjun Bu
The Manila clam, Ruditapes philippinarum, is one of the most economically important aquatic clams that are harvested on a large scale by the mariculture industry in China. However, increasing reports of bacterial pathogenic diseases have had a negative effect on the aquaculture industry of R. philippinarum. In the present study, the two transcriptome libraries of untreated (termed H) and challenged Vibrio anguillarum (termed HV) hepatopancreas were constructed and sequenced from Manila clam using an Illumina-based paired-end sequencing platform...
March 4, 2017: Fish & Shellfish Immunology
https://www.readbyqxmd.com/read/28264066/transcriptomes-of-three-species-of-tipuloidea-diptera-tipulomorpha-and-implications-for-phylogeny-of-tipulomorpha
#20
Zehui Kang, Xiao Zhang, Shuangmei Ding, Chufei Tang, Yuyu Wang, Herman de Jong, Stephen L Cameron, Mengqing Wang, Ding Yang
Tipulomorpha has long been a problematic taxon in terms of familial composition, phylogenetic relationships among families and position relative to other 'lower' Diptera. Whole-transcriptome shotgun sequencing provides a powerful basis for phylogenetic studies. We performed de novo transcriptome sequencing to produce the first transcriptome datasets representing the families Pediciidae, Limoniidae and Cylindrotomidae using high-throughput sequencing technologies. We assembled cDNA libraries for Pedicia vetusta (Alexander) (Pediciidae), Rhipidia sejuga Zhang, Li and Yang (Limoniidae) and Liogma simplicicornis Alexander (Cylindrotomidae)...
2017: PloS One
keyword
keyword
120786
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"