keyword
MENU ▼
Read by QxMD icon Read
search

Library construction

keyword
https://www.readbyqxmd.com/read/27910178/snape-a-versatile-method-to-generate-multiplexed-protein-fusions-using-synthetic-linker-peptides-for-in-vitro-applications
#1
Veronika Ulrich, Max J Cryle
Understanding the structure and function of protein complexes and multi-domain proteins is highly important in biology, although the in vitro characterization of these systems is often complicated by their size or the transient nature of protein/protein interactions. To assist in the characterization of such protein complexes, we have developed a modular approach to fusion protein generation that relies upon Sortase-mediated and Native chemical ligation using synthetic Peptide linkers (SNaPe) to link two separately expressed proteins...
December 2, 2016: Journal of Peptide Science: An Official Publication of the European Peptide Society
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/27905930/combinatory-optimization-of-chromosomal-integrated-mevalonate-pathway-for-%C3%AE-carotene-production-in-escherichia-coli
#3
Lijun Ye, Chunzhi Zhang, Changhao Bi, Qingyan Li, Xueli Zhang
BACKGROUND: Plasmid expression is a popular method in studies of MVA pathway for isoprenoid production in Escherichia coli. However, heterologous gene expression with plasmid is often not stable and might burden growth of host cells, decreases cell mass and product yield. In this study, MVA pathway was divided into three modules, and two heterologous modules were integrated into the E. coli chromosome. These modules were individually modulated with regulatory parts to optimize efficiency of the pathway in terms of downstream isoprenoid production...
December 1, 2016: Microbial Cell Factories
https://www.readbyqxmd.com/read/27900696/activity-based-screening-of-metagenomic-libraries-for-hydrogenase-enzymes
#4
Nicole Adam, Mirjam Perner
Here we outline how to identify hydrogenase enzymes from metagenomic libraries through an activity-based screening approach. A metagenomic fosmid library is constructed in E. coli and the fosmids are transferred into a hydrogenase deletion mutant of Shewanella oneidensis (ΔhyaB) via triparental mating. If a fosmid exhibits hydrogen uptake activity, S. oneidensis' phenotype is restored and hydrogenase activity is indicated by a color change of the medium from yellow to colorless. This new method enables screening of 48 metagenomic fosmid clones in parallel...
2017: Methods in Molecular Biology
https://www.readbyqxmd.com/read/27900683/constructing-and-screening-a-metagenomic-library-of-a-cold-and-alkaline-extreme-environment
#5
Mikkel A Glaring, Jan K Vester, Peter Stougaard
Natural cold or alkaline environments are common on Earth. A rare combination of these two extremes is found in the permanently cold (less than 6 °C) and alkaline (pH above 10) ikaite columns in the Ikka Fjord in Southern Greenland. Bioprospecting efforts have established the ikaite columns as a source of bacteria and enzymes adapted to these conditions. They have also highlighted the limitations of cultivation-based methods in this extreme environment and metagenomic approaches may provide access to novel extremophilic enzymes from the uncultured majority of bacteria...
2017: Methods in Molecular Biology
https://www.readbyqxmd.com/read/27900682/construction-and-screening-of-marine-metagenomic-large-insert-libraries
#6
Nancy Weiland-Bräuer, Daniela Langfeldt, Ruth A Schmitz
The marine environment covers more than 70 % of the world's surface. Marine microbial communities are highly diverse and have evolved during extended evolutionary processes of physiological adaptations under the influence of a variety of ecological conditions and selection pressures. They harbor an enormous diversity of microbes with still unknown and probably new physiological characteristics. In the past, marine microbes, mostly bacteria of microbial consortia attached to marine tissues of multicellular organisms, have proven to be a rich source of highly potent bioactive compounds, which represent a considerable number of drug candidates...
2017: Methods in Molecular Biology
https://www.readbyqxmd.com/read/27900680/construction-of-small-insert-and-large-insert-metagenomic-libraries
#7
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
#8
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/27895718/consensus-diversity-plots-a-global-diversity-analysis-of-chemical-libraries
#9
Mariana González-Medina, Fernando D Prieto-Martínez, John R Owen, José L Medina-Franco
BACKGROUND: Measuring the structural diversity of compound databases is relevant in drug discovery and many other areas of chemistry. Since molecular diversity depends on molecular representation, comprehensive chemoinformatic analysis of the diversity of libraries uses multiple criteria. For instance, the diversity of the molecular libraries is typically evaluated employing molecular scaffolds, structural fingerprints, and physicochemical properties. However, the assessment with each criterion is analyzed independently and it is not straightforward to provide an evaluation of the "global diversity"...
2016: Journal of Cheminformatics
https://www.readbyqxmd.com/read/27889445/mindfulness-training-for-health-profession-students-the-effect-of-mindfulness-training-on-psychological-well-being-learning-and-clinical-performance-of-health-professional-students-a-systematic-review-of-randomized-and-non-randomized-controlled-trials
#10
REVIEW
Janet McConville, Rachael McAleer, Andrew Hahne
BACKGROUND: High levels of stress have been identified in medical students and increasingly in other health profession student population groups. As stress can affect psychological well-being and interfere with learning and clinical performance, there is a clear argument for universities to include health professional student well-being as an outcome in core curriculum. Mindfulness training is a potential construct to manage stress and enhance academic success. OBJECTIVES: The aims of this systematic review were to assess the effectiveness of mindfulness training in medical and other health professional student population groups and to compare the effectiveness of the different mindfulness-based programs...
October 24, 2016: Explore: the Journal of Science and Healing
https://www.readbyqxmd.com/read/27889295/novel-t7-like-expression-systems-used-for-halomonas
#11
Han Zhao, Haoqian M Zhang, Xiangbin Chen, Teng Li, Qiong Wu, Qi Ouyang, Guo-Qiang Chen
To engineer non-model organisms, suitable genetic parts must be available. However, biological parts are often host strain sensitive. It is therefore necessary to develop genetic parts that are functional regardless of host strains. Here we report several novel phage-derived expression systems used for transcriptional control in non-model bacteria. Novel T7-like RNA polymerase-promoter pairs were obtained by mining phage genomes, followed by in vivo characterization in non-model strains Halomonas spp TD01 and Pseudomonas entomophila...
November 24, 2016: Metabolic Engineering
https://www.readbyqxmd.com/read/27887869/a-highly-diverse-and-functional-na%C3%A3-ve-ubiquitin-variant-library-for-generation-of-intracellular-affinity-reagents
#12
Isabel Leung, Nick Jarvik, Sachdev Sidhu
We report the design, construction and validation of a highly diverse phage-displayed naïve ubiquitin variant (Ubv) library. We first conducted a mutation tolerance scan of 27 residues and confirmed that 24 of these could be substituted by chemically diverse amino acids without compromising the display of Ubvs on phage. Subsequently, we constructed a library containing 6.8×10(10) unique members in which these 24 positions were diversified with a degenerate codon that encodes for six amino acids that are prevalent in protein interaction sites...
November 22, 2016: Journal of Molecular Biology
https://www.readbyqxmd.com/read/27885927/the-quest-for-industrial-enzymes-from-microorganisms
#13
Shotaro Yamaguchi
Satoshi Ōmura, Professor Emeritus at Kitasato University, was awarded the Nobel Prize for his discovery of a substance of tremendous value to mankind from a microorganism. As a researcher who regularly deals with enzymes produced by microorganisms and a person engaged in microorganism-based business, Professor Ōmura's Nobel Prize fills me with great pride and joy. It is perhaps not surprising that this Nobel Prize-winning research would emerge from Asia, specifically Japan, where people live in harmony with nature rather than try to conquer it...
January 2017: Bioscience, Biotechnology, and Biochemistry
https://www.readbyqxmd.com/read/27885197/a-thermostable-bilirubin-oxidizing-enzyme-from-activated-sludge-isolated-by-a-metagenomic-approach
#14
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/27881142/ethnoagroforestry-integration-of-biocultural-diversity-for-food-sovereignty-in-mexico
#15
Ana Isabel Moreno-Calles, Alejandro Casas, Alexis Daniela Rivero-Romero, Yessica Angélica Romero-Bautista, Selene Rangel-Landa, Roberto Alexander Fisher-Ortíz, Fernando Alvarado-Ramos, Mariana Vallejo-Ramos, Dídac Santos-Fita
BACKGROUND: Documenting the spectrum of ecosystem management, the roles of forestry and agricultural biodiversity, TEK, and human culture for food sovereignty, are all priority challenges for contemporary science and society. Ethnoagroforestry is a research approach that provides a theoretical framework integrating socio-ecological disciplines and TEK. We analyze in this study general types of Agroforestry Systems of México, in which peasants, small agriculturalist, and indigenous people are the main drivers of AFS and planning of landscape diversity use...
November 23, 2016: Journal of Ethnobiology and Ethnomedicine
https://www.readbyqxmd.com/read/27881076/clustering-of-disulfide-rich-peptides-provides-scaffolds-for-hit-discovery-by-phage-display-application-to-interleukin-23
#16
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/27879679/hydrostatin-tl1-an-anti-inflammatory-active-peptide-from-the-venom-gland-of-hydrophis-cyanocinctus-in-the-south-china-sea
#17
Ningyuan Wang, Yan Huang, An Li, Hailong Jiang, Jie Wang, Jianzhong Li, Lei Qiu, Ka Li, Yiming Lu
Tumor necrosis factor (TNF)-α is a pleiotropic cytokine with intense pro-inflammatory and immunomodulatory properties, and anti-TNF-α biologics are effective therapies for various inflammatory diseases such as inflammatory bowel disease (IBD) and sepsis. Snake venom, as a traditional Chinese medicine, has been used in the treatment of inflammatory diseases in China for centuries. In this research, we constructed a venom gland T7 phage display library of the sea snake Hydrophis cyanocinctus to screen bioactive compounds that antagonize TNF-α and identified a novel nine-amino-acid peptide, termed hydrostatin-TL1 (H-TL1)...
November 22, 2016: International Journal of Molecular Sciences
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
#18
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
#19
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
#20
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
keyword
keyword
52573
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"