keyword
MENU ▼
Read by QxMD icon Read
search

Sequence library construction

keyword
https://www.readbyqxmd.com/read/28534478/complementary-information-derived-from-crispr-cas9-mediated-gene-deletion-and-suppression
#1
Joseph Rosenbluh, Han Xu, William Harrington, Stanley Gill, Xiaoxing Wang, Francisca Vazquez, David E Root, Aviad Tsherniak, William C Hahn
CRISPR-Cas9 provides the means to perform genome editing and facilitates loss-of-function screens. However, we and others demonstrated that expression of the Cas9 endonuclease induces a gene-independent response that correlates with the number of target sequences in the genome. An alternative approach to suppressing gene expression is to block transcription using a catalytically inactive Cas9 (dCas9). Here we directly compare genome editing by CRISPR-Cas9 (cutting, CRISPRc) and gene suppression using KRAB-dCas9 (CRISPRi) in loss-of-function screens to identify cell essential genes...
May 23, 2017: Nature Communications
https://www.readbyqxmd.com/read/28531277/genome-wide-discovery-of-viral-micrornas-based-on-phylogenetic-analysis-and-structural-evolution-of-various-human-papillomavirus-subtypes
#2
Shun-Long Weng, Kai-Yao Huang, Julia Tzu-Ya Weng, Fang-Yu Hung, Tzu-Hao Chang, Tzong-Yi Lee
In mammals, microRNAs (miRNAs) play key roles in controlling posttranscriptional regulation through binding to the mRNAs of target genes. Recently, it was discovered that viral miRNAs may be involved in human cancers and diseases. It is likely that viral miRNAs help viruses enter the latent phase of their life cycle and become undetected by the host's immune system, while increasing the host's risk for cancer development. Cervical cancer is typically related to the infection of human papillomavirus (HPV) through sexual transmission...
May 20, 2017: Briefings in Bioinformatics
https://www.readbyqxmd.com/read/28530391/single-bead-quantification-of-peptide-loading-distribution-for-one-bead-one-compound-library-synthesis-using-confocal-raman-spectroscopy
#3
Yuchen Tang, Yann Thillier, Ruiwu Liu, Xiaocen Li, Kit S Lam, Tingjuan Gao
We report an analytical method to determine peptide loading of "one-bead one-compound" (OBOC) combinatorial peptide libraries at single-bead level. The quantification is based on a linear relationship between the amount of N-terminal amino groups on individual peptide beads and the intensity of Raman signal obtained from a specifically designed reporter labeled on amino groups. Confocal Raman spectroscopy was employed to characterize peptide loading of beads with defined peptide sequences and from OBOC combinatorial peptide libraries...
May 22, 2017: Analytical Chemistry
https://www.readbyqxmd.com/read/28528024/structure-diverse-phylomer-libraries-as-a-rich-source-of-bioactive-hits-from-phenotypic-and-target-directed-screens-against-intracellular-proteins
#4
REVIEW
Paul M Watt, Nadia Milech, Shane R Stone
Phylomers are peptides derived from biodiverse protein fragments. Genetically encoded Phylomer libraries have been constructed, containing hundreds of billions of peptides derived from virtually all of the few thousand fold families found in the protein universe. They offer a rich source of high quality hits against diverse target sequences and have been used for three main purposes: firstly, to identify and validate targets in phenotypic screens; secondly, to block protein interactions with nanomolar potency binding affinities; thirdly as a source of more efficient cell penetrating peptides for the delivery of a wide range of biologics...
May 18, 2017: Current Opinion in Chemical Biology
https://www.readbyqxmd.com/read/28527015/a-genome-wide-association-study-identifies-the-genomic-region-associated-with-shell-color-in-yesso-scallop-patinopecten-yessoensis
#5
Liang Zhao, Yangping Li, Yajuan Li, Jiachen Yu, Huan Liao, Shuyue Wang, Jia Lv, Jun Liang, Xiaoting Huang, Zhenmin Bao
The shell color polymorphism widely exists in economic shellfish, which not only results in a better visual perception but also shows great value as an economic trait for breeding. Small numbers of reddish-orange shell Yesso scallops, Patinopecten yessoensis, were found in cultured populations compared to the brown majority. In this study, a genome-wide association study was conducted to understand the genetic basis of shell color. Sixty-six 2b-RAD libraries with equal numbers of reddish-orange and brown shell individuals were constructed and sequenced using the Illumina HiSeq 2000 platform...
May 19, 2017: Marine Biotechnology
https://www.readbyqxmd.com/read/28520717/modular-protein-expression-toolbox-mopet-a-standardized-assembly-system-for-defined-expression-constructs-and-expression-optimization-libraries
#6
Ernst Weber, Jörg Birkenfeld, Jürgen Franz, Uwe Gritzan, Lars Linden, Mark Trautwein
The design and generation of an optimal expression construct is the first and essential step in in the characterization of a protein of interest. Besides evaluation and optimization of process parameters (e.g. selection of the best expression host or cell line and optimal induction conditions and time points), the design of the expression construct itself has a major impact. However, the path to this final expression construct is often not straight forward and includes multiple learning cycles accompanied by design variations and retesting of construct variants, since multiple, functional DNA sequences of the expression vector backbone, either coding or non-coding, can have a major impact on expression yields...
2017: PloS One
https://www.readbyqxmd.com/read/28515773/building-a-multipurpose-insertional-mutant-library-for-forward-and-reverse-genetics-in-chlamydomonas
#7
Xi Cheng, Gai Liu, Wenting Ke, Lijuan Zhao, Bo Lv, Xiaocui Ma, Nannan Xu, Xiaoling Xia, Xuan Deng, Chunlei Zheng, Kaiyao Huang
BACKGROUND: The unicellular green alga, Chlamydomonas reinhardtii, is a classic model for studying flagella and biofuel. However, precise gene editing, such as Clustered Regularly Interspaced Short Palindromic Repeats (CRISPR) and CRISPR-associated protein (Cas9) system, is not widely used in this organism. Screening of random insertional mutant libraries by polymerase chain reaction provides an alternate strategy to obtain null mutants of individual gene. But building, screening, and maintaining such a library was time-consuming and expensive...
2017: Plant Methods
https://www.readbyqxmd.com/read/28506253/genome-wide-identification-of-lncrnas-associated-with-chlorantraniliprole-resistance-in-diamondback-moth-plutella-xylostella-l
#8
Bin Zhu, Manyu Xu, Haiyan Shi, Xiwu Gao, Pei Liang
BACKGROUND: Long noncoding RNAs (lncRNAs) are now considered important regulatory factors, with a variety of biological functions in many species including insects. Some lncRNAs have the ability to show rapid responses to diverse stimuli or stress factors and are involved in responses to insecticide. However, there are no reports to date on the characterization of lncRNAs associated with chlorantraniliprole resistance in Plutella xylostella. RESULTS: Nine RNA libraries constructed from one susceptible (CHS) and two chlorantraniliprole-resistant P...
May 15, 2017: BMC Genomics
https://www.readbyqxmd.com/read/28505436/control-of-heme-coordination-and-catalytic-activity-by-conformational-changes-in-peptide-amphiphile-assemblies
#9
Lee Andrew Solomon, Jacob Kronenberg, H Christopher Fry
Self-Assembling peptide materials have gained significant attention, due to well-demonstrated applications, but are functionally underutilized. To advance their utility, we use non-covalent interactions to incorporate the biological cofactor heme-B for catalysis. Heme-proteins achieve differing functions through structural and coordinative variations. Here, we replicate this phenomenon by highlighting changes in heme reactivity as a function of coordination, sequence, and morphology (micelles versus fibers) in a series of simple peptide-amphiphiles with the sequence c16-xyL3K3-CO2H...
May 15, 2017: Journal of the American Chemical Society
https://www.readbyqxmd.com/read/28505302/the-first-whole-genome-and-transcriptome-of-the-manila-clam-ruditapes-philippinarum-isolated-in-korea
#10
Seyoung Mun, Yun-Ji Kim, Kesavan Markkandan, Wonseok Shin, Sumin Oh, Jiyoung Woo, Jongsu Yoo, Hyesuck An, Kyudong Han
The manila clam, Ruditapes philippinarum, is an important bivalve species in worldwide aquaculture including Korea. The aquaculture production of R. philippinarum is under threat from diverse environmental factors including viruses, microorganisms, parasites, and water conditions with subsequently declining production. In spite of its importance as a marine resource, the reference genome of R. philippinarum for comprehensive genetic studies is largely unexplored. Here, we report the de novo whole-genome and transcriptome assembly of R...
May 13, 2017: Genome Biology and Evolution
https://www.readbyqxmd.com/read/28492527/single-cell-template-strand-sequencing-by-strand-seq-enables-the-characterization-of-individual-homologs
#11
Ashley D Sanders, Ester Falconer, Mark Hills, Diana C J Spierings, Peter M Lansdorp
The ability to distinguish between genome sequences of homologous chromosomes in single cells is important for studies of copy-neutral genomic rearrangements (such as inversions and translocations), building chromosome-length haplotypes, refining genome assemblies, mapping sister chromatid exchange events and exploring cellular heterogeneity. Strand-seq is a single-cell sequencing technology that resolves the individual homologs within a cell by restricting sequence analysis to the DNA template strands used during DNA replication...
June 2017: Nature Protocols
https://www.readbyqxmd.com/read/28489891/rna-seq-approach-to-analysis-of-gene-expression-profiles-in-dark-green-islands-and-light-green-tissues-of-cucumber-mosaic-virus-infected-nicotiana-tabacum
#12
Lijuan Chen, Chunyan Fei, Lin Zhu, Zhenpeng Xu, Wenshan Zou, Ting Yang, Honghui Lin, Dehui Xi
Dark green islands (DGIs) surrounded by light green tissues (LGTs) are common leaf symptoms of plants that are systemically infected by various viruses that induce leaf mosaic in infected plants. The inoculation of Cucumber mosaic virus (CMV) in Nicotiana tabacum produced a commonly occurring sequence of classic patterns of DGIs and LGTs. Previous studies confirmed that there are significant differences between DGIs and LGTs in terms of physiology, biochemistry and molecular biology, but the mechanisms by which DGIs form remain unclear...
2017: PloS One
https://www.readbyqxmd.com/read/28488082/genome-wide-identification-of-cucumber-green-mottle-mosaic-virus-responsive-micrornas-in-watermelon
#13
Yuyan Sun, Xiaowei Niu, Min Fan
Cucumber green mottle mosaic virus (CGMMV) is a damaging pathogen that attacks crop plants belonging to the family Cucurbitaceae. Little is known about the regulatory role of microRNAs (miRNAs) in response to CGMMV infection. To identify CGMMV-responsive miRNAs, two sRNA libraries from mock-inoculated and CGMMV-infected watermelon leaves were constructed and sequenced using Solexa sequencing technology. In total, 471 previously known and 1,809 novel miRNAs were obtained, of which 377 known and 246 novel miRNAs were found to be differentially expressed during CGMMV infection...
May 9, 2017: Archives of Virology
https://www.readbyqxmd.com/read/28486658/a-high-coverage-draft-genome-of-the-mycalesine-butterfly-bicyclus-anynana
#14
Reuben W Nowell, Ben Elsworth, Vicencio Oostra, Bas J Zwaan, Christopher W Wheat, Marjo Saastamoinen, Ilik J Saccheri, Arjen E Van't Hof, Bethany R Wasik, Heidi Connahs, Muhammad L Aslam, Sujai Kumar, Richard J Challis, Antónia Monteiro, Paul M Brakefield, Mark Blaxter
Background: The mycalesine butterfly Bicyclus anynana , the 'Squinting bush brown', is a model organism in the study of lepidopteran ecology, development and evolution. Here, we present a draft genome sequence for B. anynana to serve as a genomics resource for current and future studies of this important model species. Findings: Seven libraries with insert sizes ranging from 350 bp to 20 kb were constructed using DNA from an inbred female and sequenced using both Illumina and PacBio technology...
May 9, 2017: GigaScience
https://www.readbyqxmd.com/read/28476431/identification-and-characterization-of-known-and-novel-micrornas-in-three-tissues-of-chinese-giant-salamander-base-on-deep-sequencing-approach
#15
Yong Huang, Hong Tao Ren, Jian Li Xiong, Xiao Chan Gao, Xi Hong Sun
MicroRNAs (miRNAs) are a class of non-coding small RNAs that play important roles in the regulation of gene expression. Although animal miRNAs have been extensively studied in model systems, less is known in other animal with limited genome sequence data, including Chinese giant salamander (Andrias davidianus). The identification of the full repertoire of miRNAs expressed in the liver, spleen and muscle of A. davidianus would significantly increase our understanding for physiological function of A. davidianus, in this ancient and endangered urodele amphibian...
May 2, 2017: Genomics
https://www.readbyqxmd.com/read/28465712/a-novel-hairpin-library-based-approach-to-identify-nbs-lrr-genes-required-for-effector-triggered-hypersensitive-response-in-nicotiana-benthamiana
#16
Cyril Brendolise, Mirco Montefiori, Romain Dinis, Nemo Peeters, Roy D Storey, Erik H Rikkerink
BACKGROUND: PTI and ETI are the two major defence mechanisms in plants. ETI is triggered by the detection of pathogen effectors, or their activity, in the plant cell and most of the time involves internal receptors known as resistance (R) genes. An increasing number of R genes responsible for recognition of specific effectors have been characterised over the years; however, methods to identify R genes are often challenging and cannot always be translated to crop plants. RESULTS: We present a novel method to identify R genes responsible for the recognition of specific effectors that trigger a hypersensitive response (HR) in Nicotiana benthamiana...
2017: Plant Methods
https://www.readbyqxmd.com/read/28464062/ssr-marker-development-linkage-mapping-and-qtl-analysis-for-establishment-rate-in-common-bermudagrass
#17
Yuanwen Guo, Yanqi Wu, Jeff A Anderson, Justin Q Moss, Lan Zhu, Jinmin Fu
Common bermudagrass has been widely used as a major warm-season turf, forage, and soil stabilization grass in the southern United States. However, codominant marker development, linkage, and quantitative trait loci (QTL) mapping resources are limited in the important taxon. Accordingly, the objectives of this study were to develop simple sequence repeat (SSR) markers, construct a genetic map, and identify genomic regions associated with establishment rate. Five genomic SSR libraries were constructed, sequenced, and used in the development of 1003 validated SSR primer pairs (PPs)...
March 2017: Plant Genome
https://www.readbyqxmd.com/read/28463494/sort-seq-approach-to-engineering-a-formaldehyde-inducible-promoter-for-dynamically-regulated-escherichia-coli-growth-on-methanol
#18
Julia Rohlhill, Nicholas R Sandoval, Eleftherios T Papoutsakis
Tight and tunable control of gene expression is a highly desirable goal in synthetic biology for constructing predictable gene circuits and achieving preferred phenotypes. Elucidating the sequence-function relationship of promoters is crucial for manipulating gene expression at the transcriptional level, particularly for inducible systems dependent on transcriptional regulators. Sort-seq methods employing fluorescence-activated cell sorting (FACS) and high-throughput sequencing allow for the quantitative analysis of sequence-function relationships in a robust and rapid way...
May 9, 2017: ACS Synthetic Biology
https://www.readbyqxmd.com/read/28448969/synthetic-switchable-enzymes
#19
Vic Norris, Sergey N Krylov, Pratul K Agarwal, Glenn J White
The construction of switchable, radiation-controlled, aptameric enzymes - "swenzymes" - is, in principle, feasible. We propose a strategy to make such catalysts from 2 (or more) aptamers each selected to bind specifically to one of the substrates in, for example, a 2-substrate reaction. Construction of a combinatorial library of candidate swenzymes entails selecting a set of a million aptamers that bind one substrate and a second set of a million aptamers that bind the second substrate; the aptamers in these sets are then linked pairwise by a linker, thus bringing together the substrates...
2017: Journal of Molecular Microbiology and Biotechnology
https://www.readbyqxmd.com/read/28446605/crispr-cas9-mediated-gene-knockout-screens-and-target-identification-via-whole-genome-sequencing-uncover-host-genes-required-for-picornavirus-infection
#20
Heon Seok Kim, Kyungjin Lee, Sangsu Bae, Jeongbin Park, Chong-Kyo Lee, Meehyein Kim, Eunji Kim, Minju Kim, Seokjoong Kim, Chonsaeng Kim, Jin-Soo Kim
Several groups have used genome-wide libraries of lentiviruses encoding small-guide RNAs (sgRNAs) for genetic screens. In most cases, sgRNA expression cassettes are integrated into cells by using lentiviruses, and target genes are statistically estimated by the readout of sgRNA sequences after targeted sequencing. We present a new virus-free method for human gene-knockout screens using a genome-wide library of CRISPR/Cas9 sgRNAs based on plasmids, and target gene identification via whole-genome sequencing (WGS) confirming authentic mutations rather than statistical estimating through targeted amplicon sequencing...
April 26, 2017: Journal of Biological Chemistry
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"