keyword
MENU ▼
Read by QxMD icon Read
search

Sequence library construction

keyword
https://www.readbyqxmd.com/read/27915271/changes-in-renal-gene-expression-associated-with-induced-ochratoxicosis-in-chickens-activation-and-deactivation-of-transcripts-after-varying-durations-of-exposure
#1
Cynthia P Zeferino, Kevin D Wells, Ana Silvia A M T Moura, George E Rottinghaus, David R Ledoux
Exposure to ochratoxin A (OTA) can lead to changes in global gene expression. This study investigated the individual expression of genes turned on and off in renal cells of chicks after different durations of exposure to dietary OTA. One hundred and eighty day-old male broiler chicks (Ross 308) were randomly assigned to a 3 × 3 factorial arrangement of treatments (3 levels of OTA: 0, 1 and 2 mg OTA/kg diet and 3 time periods: 7, 14 and 21 d). Birds were allocated to 36 pens (4 replicate pens of 5 birds each per treatment)...
December 3, 2016: Poultry Science
https://www.readbyqxmd.com/read/27907066/b-cell-based-seamless-engineering-of-antibody-fc-domains
#2
Koji Hashimoto, Kohei Kurosawa, Akiho Murayama, Hidetaka Seo, Kunihiro Ohta
Engineering of monoclonal antibodies (mAbs) enables us to obtain mAbs with additional functions. In particular, modifications in antibody's Fc (fragment, crystallizable) region can provide multiple benefits such as added toxicity by drug conjugation, higher affinity to Fc receptors on immunocytes, or the addition of functional modules. However, the generation of recombinant antibodies requires multiple laborious bioengineering steps. We previously developed a technology that enables rapid in vitro screening and isolation of specific mAb-expressing cells from the libraries constructed with chicken B-cell line DT40 (referred to as the 'ADLib system')...
2016: PloS One
https://www.readbyqxmd.com/read/27900680/construction-of-small-insert-and-large-insert-metagenomic-libraries
#3
Carola Simon, Rolf Daniel
The vast majority of the Earth's biological diversity is hidden in uncultured and yet uncharacterized microbial genomes. The construction of metagenomic libraries is a cultivation-independent molecular approach to assess this unexplored genetic reservoir. High numbers of novel biocatalysts have been identified by function-based or sequence-based screening of metagenomic libraries derived from various environments. Here, we describe detailed protocols for the construction of metagenomic small-insert and large-insert libraries in plasmids and fosmids, respectively, from environmental DNA...
2017: Methods in Molecular Biology
https://www.readbyqxmd.com/read/27899632/application-of-sorting-and-next-generation-sequencing-to-study-5-utr-influence-on-translation-efficiency-in-escherichia-coli
#4
Sergey A Evfratov, Ilya A Osterman, Ekaterina S Komarova, Alexandra M Pogorelskaya, Maria P Rubtsova, Timofei S Zatsepin, Tatiana A Semashko, Elena S Kostryukova, Andrey A Mironov, Evgeny Burnaev, Ekaterina Krymova, Mikhail S Gelfand, Vadim M Govorun, Alexey A Bogdanov, Petr V Sergiev, Olga A Dontsova
Yield of protein per translated mRNA may vary by four orders of magnitude. Many studies analyzed the influence of mRNA features on the translation yield. However, a detailed understanding of how mRNA sequence determines its propensity to be translated is still missing. Here, we constructed a set of reporter plasmid libraries encoding CER fluorescent protein preceded by randomized 5' untranslated regions (5'-UTR) and Red fluorescent protein (RFP) used as an internal control. Each library was transformed into Escherchia coli cells, separated by efficiency of CER mRNA translation by a cell sorter and subjected to next generation sequencing...
November 29, 2016: Nucleic Acids Research
https://www.readbyqxmd.com/read/27885197/a-thermostable-bilirubin-oxidizing-enzyme-from-activated-sludge-isolated-by-a-metagenomic-approach
#5
Nobutada Kimura, Yoichi Kamagata
A gene coding for a multicopper oxidase (BopA) was identified through the screening of a metagenomic library constructed from wastewater treatment activated sludge. The recombinant BopA protein produced in Escherichia coli exhibited oxidation activity toward 2,2'-azino-bis-(3-ethylbenzothiazoline-6-sulfonate) (ABTS) in the presence of copper, suggesting that BopA is laccase. A bioinformatic analysis of the bopA gene sequence indicated that it has a phylogenetically bacterial origin, possibly derived from a bacterium within the phylum Deinococcus-Thermus...
November 23, 2016: Microbes and Environments
https://www.readbyqxmd.com/read/27881076/clustering-of-disulfide-rich-peptides-provides-scaffolds-for-hit-discovery-by-phage-display-application-to-interleukin-23
#6
David T Barkan, Xiao-Li Cheng, Herodion Celino, Tran T Tran, Ashok Bhandari, Charles S Craik, Andrej Sali, Mark L Smythe
BACKGROUND: Disulfide-rich peptides (DRPs) are found throughout nature. They are suitable scaffolds for drug development due to their small cores, whose disulfide bonds impart extraordinary chemical and biological stability. A challenge in developing a DRP therapeutic is to engineer binding to a specific target. This challenge can be overcome by (i) sampling the large sequence space of a given scaffold through a phage display library and by (ii) panning multiple libraries encoding structurally distinct scaffolds...
November 23, 2016: BMC Bioinformatics
https://www.readbyqxmd.com/read/27877179/genome-wide-identification-of-micrornas-and-their-targets-in-the-leaves-and-fruits-of-eucommia-ulmoides-using-high-throughput-sequencing
#7
Lin Wang, Hongyan Du, Ta-Na Wuyun
MicroRNAs (miRNAs), a group of endogenous small non-coding RNAs, play important roles in plant growth, development, and stress response processes. Eucommia ulmoides Oliver (hardy rubber tree) is one of the few woody plants capable of producing trans-1, 4-polyisoprene (TPI), also known as Eu-rubber, which has been utilized as an industrial raw material and is extensively cultivated in China. However, the mechanism of TPI biosynthesis has not been identified in E. ulmoides. To characterize small RNAs and their targets with potential biological roles involved in the TPI biosynthesis in E...
2016: Frontiers in Plant Science
https://www.readbyqxmd.com/read/27876624/differences-in-structure-and-changes-in-gene-regulation-of-murrel-molecular-chaperone-hsp-family-during-epizootic-ulcerative-syndrome-eus-infection
#8
Akila Sathyamoorthy, Mukesh Kumar Chaurasia, Mariadhas Valan Arasu, Naif Abdullah Al-Dhabi, Ramasamy Harikrishnan, Jesu Arockiaraj
Heat shock proteins (HSPs) are immunogenic, ubiquitous class of molecular chaperones, which are induced in response to various environmental and microbial stressful conditions. It plays a vital role in maintaining cellular protein homeostasis in eukaryotic cells. In this study, we described a comprehensive comparative data by bioinformatics approach on three different full length cDNA sequences of HSP family at molecular level. The cDNA sequences of three HSPs were identified from constructed cDNA library of Channa striatus and named as CsCPN60, CsHSP60 and CsHSP70...
November 20, 2016: Fish & Shellfish Immunology
https://www.readbyqxmd.com/read/27875166/authoring-data-driven-videos-with-dataclips
#9
Fereshteh Amini, Nathalie Henry Riche, Bongshin Lee, Andres Monroy-Hernandez, Pourang Irani
Data videos, or short data-driven motion graphics, are an increasingly popular medium for storytelling. However, creating data videos is difficult as it involves pulling together a unique combination of skills. We introduce DataClips, an authoring tool aimed at lowering the barriers to crafting data videos. DataClips allows non-experts to assemble data-driven "clips" together to form longer sequences. We constructed the library of data clips by analyzing the composition of over 70 data videos produced by reputable sources such as The New York Times and The Guardian...
January 2017: IEEE Transactions on Visualization and Computer Graphics
https://www.readbyqxmd.com/read/27873261/functional-metagenomics-to-study-antibiotic-resistance
#10
Manish Boolchandani, Sanket Patel, Gautam Dantas
The construction and screening of metagenomic expression libraries has great potential to identify novel genes and their functions. Here, we describe metagenomic library preparation from fecal DNA, screening of libraries for antibiotic resistance genes (ARGs), massively parallel DNA sequencing of the enriched DNA fragments, and a computational pipeline for high-throughput assembly and annotation of functionally selected DNA.
2017: Methods in Molecular Biology
https://www.readbyqxmd.com/read/27873209/large-scale-interaction-profiling-of-protein-domains-through-proteomic-peptide-phage-display-using-custom-peptidomes
#11
Moon-Hyeong Seo, Satra Nim, Jouhyun Jeon, Philip M Kim
Protein-protein interactions are essential to cellular functions and signaling pathways. We recently combined bioinformatics and custom oligonucleotide arrays to construct custom-made peptide-phage libraries for screening peptide-protein interactions, an approach we call proteomic peptide-phage display (ProP-PD). In this chapter, we describe protocols for phage display for the identification of natural peptide binders for a given protein. We finally describe deep sequencing for the analysis of the proteomic peptide-phage display...
2017: Methods in Molecular Biology
https://www.readbyqxmd.com/read/27871234/a-genome-wide-bac-end-sequence-survey-provides-first-insights-into-sweetpotato-ipomoea-batatas-l-lam-genome-composition
#12
Zengzhi Si, Bing Du, Jinxi Huo, Shaozhen He, Qingchang Liu, Hong Zhai
BACKGROUND: Sweetpotato, Ipomoea batatas (L.) Lam., is an important food crop widely grown in the world. However, little is known about the genome of this species because it is a highly heterozygous hexaploid. Gaining a more in-depth knowledge of sweetpotato genome is therefore necessary and imperative. In this study, the first bacterial artificial chromosome (BAC) library of sweetpotato was constructed. Clones from the BAC library were end-sequenced and analyzed to provide genome-wide information about this species...
November 21, 2016: BMC Genomics
https://www.readbyqxmd.com/read/27866354/isolation-and-characterization-of-a-novel-glycosyl-hydrolase-family-74-gh74-cellulase-from-the-black-goat-rumen-metagenomic-library
#13
Yun-Hee Song, Kyung-Tai Lee, Jin-Young Baek, Min-Ju Kim, Mi-Ra Kwon, Young-Joo Kim, Mi-Rim Park, Haesu Ko, Jin-Sung Lee, Keun-Sung Kim
This study aimed to isolate and characterize a novel cellulolytic enzyme from black goat rumen by using a culture-independent approach. A metagenomic fosmid library was constructed from black goat rumen contents and screened for a novel cellulase. The KG37 gene encoding a protein of 858 amino acid residues (92.7 kDa) was isolated. The deduced protein contained a glycosyl hydrolase family 74 (GH74) domain and showed 77% sequence identity to two endo-1,4-β-glucanases from Fibrobacter succinogenes. The novel GH74 cellulase gene was overexpressed in Escherichia coli, and its protein product was functionally characterized...
November 19, 2016: Folia Microbiologica
https://www.readbyqxmd.com/read/27856695/multiplex-shrna-screening-of-germ-cell-development-by-in-vivo-transfection-of-mouse-testis
#14
Nicholas R Y Ho, Abul R Usmani, Yan Yin, Liang Ma, Donald F Conrad
Spermatozoa are one of the few mammalian cells types that cannot be fully derived in vitro, severely limiting the application of modern genomic techniques to study germ cell biology. The current gold standard approach of characterizing single gene knockout mice is slow as generation of each mutant line can take 6-9 months. Here, we describe an in vivo approach to rapid functional screening of germline genes based on a new non-surgical, non-viral in vivo transfection method to deliver nucleic acids into testicular germ cells...
November 16, 2016: G3: Genes—Genomes—Genetics
https://www.readbyqxmd.com/read/27855649/analysis-of-transcriptome-in-hickory-carya-cathayensis-and-uncover-the-dynamics-in-the-hormonal-signaling-pathway-during-graft-process
#15
Lingling Qiu, Bo Jiang, Jia Fang, Yike Shen, Zhongxiang Fang, Saravana Kumar Rm, Keke Yi, Chenjia Shen, Daoliang Yan, Bingsong Zheng
BACKGROUND: Hickory (Carya cathayensis), a woody plant with high nutritional and economic value, is widely planted in China. Due to its long juvenile phase, grafting is a useful technique for large-scale cultivation of hickory. To reveal the molecular mechanism during the graft process, we sequenced the transcriptomes of graft union in hickory. RESULTS: In our study, six RNA-seq libraries yielded a total of 83,676,860 clean short reads comprising 4.19 Gb of sequence data...
November 17, 2016: BMC Genomics
https://www.readbyqxmd.com/read/27854027/a-method-for-large-scale-screening-of-random-sequence-libraries-to-determine-the-function-of-unstructured-regions-from-essential-proteins
#16
Jean-François Millau, Benoit Guillemette, Luc Gaudreau
In this chapter we present a method allowing the screening of random sequences to discover essential aspects of unstructured protein regions in yeast. The approach can be applied to any protein with unstructured peptide sequences for which functions are difficult to decipher, for example the N-terminal tails of histones. The protocol first describes the building and preparation of a large library of random peptides in fusion with a protein of interest. Recent technical advances in oligonucleotide synthesis allow the construction of long random sequences up to 35 residues long...
2017: Methods in Molecular Biology
https://www.readbyqxmd.com/read/27852047/prognostic-gene-expression-profiling-in-esophageal-cancer-a-systematic-review
#17
REVIEW
Els Visser, Ingrid A Franken, Lodewijk A A Brosens, Jelle P Ruurda, Richard van Hillegersberg
BACKGROUND: Individual variability in prognosis of esophageal cancer highlights the need for advances in personalized therapy. This systematic review aimed at elucidating the prognostic role of gene expression profiles and at identifying gene signatures to predict clinical outcome. METHODS: A systematic search of the Medline, Embase and the Cochrane library databases (2000-2015) was performed. Articles associating gene expression profiles in patients with esophageal adenocarcinoma or squamous cell carcinoma to survival, response to chemo(radio)therapy and/or lymph node metastasis were identified...
November 12, 2016: Oncotarget
https://www.readbyqxmd.com/read/27835993/identification-of-interchangeable-cross-species-function-of-elongation-factor-1-alpha-promoters-in-babesia-bigemina-and-babesia-bovis
#18
Marta G Silva, Donald P Knowles, Carlos E Suarez
BACKGROUND: Tick-borne Babesia bigemina is responsible for acute and potentially lethal hemolytic disease in cattle. The development of genetic manipulation tools necessary to the better understanding of parasite biology is currently limited by the lack of a complete parasite genome and experimental tools such as transfection. Effective promoters, required to regulate expression of transgenes, such as the elongation factor-1 alpha (ef-1α), have been identified in other apicomplexans such as Babesia bovis and Plasmodium falciparum...
November 11, 2016: Parasites & Vectors
https://www.readbyqxmd.com/read/27835957/leaf-transcriptome-of-two-highly-divergent-genotypes-of-urochloa-humidicola-poaceae-a-tropical-polyploid-forage-grass-adapted-to-acidic-soils-and-temporary-flooding-areas
#19
Bianca Baccili Zanotto Vigna, Fernanda Ancelmo de Oliveira, Guilherme de Toledo-Silva, Carla Cristina da Silva, Cacilda Borges do Valle, Anete Pereira de Souza
BACKGROUND: Urochloa humidicola (Koronivia grass) is a polyploid (6x to 9x) species that is used as forage in the tropics. Facultative apospory apomixis is present in most of the genotypes of this species, although one individual has been described as sexual. Molecular studies have been restricted to molecular marker approaches for genetic diversity estimations and linkage map construction. The objectives of the present study were to describe and compare the leaf transcriptome of two important genotypes that are highly divergent in terms of their phenotypes and reproduction modes: the sexual BH031 and the aposporous apomictic cultivar BRS Tupi...
November 11, 2016: BMC Genomics
https://www.readbyqxmd.com/read/27830751/rapid-construction-of-a-whole-genome-transposon-insertion-collection-for-shewanella-oneidensis-by-knockout-sudoku
#20
Michael Baym, Lev Shaket, Isao A Anzai, Oluwakemi Adesina, Buz Barstow
Whole-genome knockout collections are invaluable for connecting gene sequence to function, yet traditionally, their construction has required an extraordinary technical effort. Here we report a method for the construction and purification of a curated whole-genome collection of single-gene transposon disruption mutants termed Knockout Sudoku. Using simple combinatorial pooling, a highly oversampled collection of mutants is condensed into a next-generation sequencing library in a single day, a 30- to 100-fold improvement over prior methods...
November 10, 2016: Nature Communications
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"