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https://www.readbyqxmd.com/read/29149596/rational-design-of-evolutionarily-stable-microbial-kill-switches
#1
Finn Stirling, Lisa Bitzan, Samuel O'Keefe, Elizabeth Redfield, John W K Oliver, Jeffrey Way, Pamela A Silver
The evolutionary stability of synthetic genetic circuits is key to both the understanding and application of genetic control elements. One useful but challenging situation is a switch between life and death depending on environment. Here are presented "essentializer" and "cryodeath" circuits, which act as kill switches in Escherichia coli. The essentializer element induces cell death upon the loss of a bi-stable cI/Cro memory switch. Cryodeath makes use of a cold-inducible promoter to express a toxin. We employ rational design and a toxin/antitoxin titering approach to produce and screen a small library of potential constructs, in order to select for constructs that are evolutionarily stable...
November 16, 2017: Molecular Cell
https://www.readbyqxmd.com/read/29149055/exploration-for-the-salinity-tolerance-related-genes-from-xero-halophyte-atriplex-canescens-exploiting-yeast-functional-screening-system
#2
Gang Yu, Jingtao Li, Xinhua Sun, Yanzhi Liu, Xueliang Wang, Hao Zhang, Hongyu Pan
Plant productivity is limited by salinity stress, both in natural and agricultural systems. Identification of salt stress-related genes from halophyte can provide insights into mechanisms of salt stress tolerance in plants. Atriplex canescens is a xero-halophyte that exhibits optimum growth in the presence of 400 mM NaCl. A cDNA library derived from highly salt-treated A. canescens plants was constructed based on a yeast expression system. A total of 53 transgenic yeast clones expressing enhanced salt tolerance were selected from 10⁵ transformants...
November 17, 2017: International Journal of Molecular Sciences
https://www.readbyqxmd.com/read/29148054/transcriptome-analysis-unravels-an-ethylene-response-factor-involved-in-regulating-fruit-ripening-in-pear
#3
Ping-Ping Hao, Guo-Ming Wang, Hai-Yan Cheng, Ya-Qi Ke, Kai-Jie Qi, Chao Gu, Shao-Ling Zhang
Ethylene response factor (ERF) has been widely studied in regulating fruit ripening in tomato, apple, banana and kiwifruit, but little is known in pear. In this study 1-methylcyclopropene (1-MCP) treatment, an inhibitor of ethylene perception, was conducted at approximately 30 days before harvest to delay fruit ripening in a climacteric white pear cultivar Yali. Transcriptome libraries were constructed and sequenced in pre-ripening, ripening, and 1-MCP treated fruits. Data analysis showed that 73 candidate genes related to fruit ripening were induced by 1-MCP, among which two were positively related, namely 1-aminocyclopropane-1-carboxyla oxidase and an ERF gene (designated as ACO54 and ERF24)...
November 16, 2017: Physiologia Plantarum
https://www.readbyqxmd.com/read/29144011/a-gold-catalyzed-domino-cyclization-enabling-rapid-construction-of-diverse-polyheterocyclic-frameworks
#4
Erik Van der Eycken, Yi He, Zhenghua Li, Koen Robeyns, Luc Van Meervelt
We report herein an efficient gold(I)-catalyzed post-Ugi domino dearomatization/ipso-cyclization/Michael sequence that enables access to libraries of diverse (hetero)arene-annulated tricyclic heterocycles. This process affords novel complex polycyclic scaffolds in moderate to good yields from readily available acyclic precursors with excellent chemo-, regio-, and diastereo-selectivity. The power of this strategy has been demonstrated by the rapid synthesis of 40 highly functionalized polyheterocycles bearing indole, pyrrole, (benzo)furan, (benzo)thiophene, pyrazole and electron-rich arenes in two-operational steps...
November 16, 2017: Angewandte Chemie
https://www.readbyqxmd.com/read/29139094/investigating-the-therapeutic-potential-and-mechanism-of-curcumin-in-breast-cancer-based-on-rna-sequencing-and-bioinformatics-analysis
#5
Rong Wang, Jinbin Li, Yulan Zhao, Yapeng Li, Ling Yin
BACKGROUND: Breast cancer is a prevalent cancer in female. This study aims to investigate the therapeutic potential and mechanism of curcumin in breast cancer. METHODS: After cultivation, human breast cancer cells (MCF-7 cells) were treated with 0.1% (v/v) 15 µmol/ml curcumin-dimethylsulfoxide solution and 0.1% (v/v) dimethylsulfoxide, respectively, at 37 °C and 5% CO2 for 48 h. Total RNA was extracted, cDNA library was constructed, and cDNAs were amplified and sequenced...
November 14, 2017: Breast Cancer: the Journal of the Japanese Breast Cancer Society
https://www.readbyqxmd.com/read/29138304/refactoring-the-genetic-code-for-increased-evolvability
#6
Gur Pines, James D Winkler, Assaf Pines, Ryan T Gill
The standard genetic code is robust to mutations during transcription and translation. Point mutations are likely to be synonymous or to preserve the chemical properties of the original amino acid. Saturation mutagenesis experiments suggest that in some cases the best-performing mutant requires replacement of more than a single nucleotide within a codon. These replacements are essentially inaccessible to common error-based laboratory engineering techniques that alter a single nucleotide per mutation event, due to the extreme rarity of adjacent mutations...
November 14, 2017: MBio
https://www.readbyqxmd.com/read/29136547/natural-products-used-as-a-chemical-library-for-protein-protein-interaction-targeted-drug-discovery
#7
Xuemei Jin, Kyungro Lee, Nam Hee Kim, Hyun Sil Kim, Jong In Yook, Jiwon Choi, Kyoung Tai No
Protein-protein interactions (PPIs), which are essential for cellular processes, have been recognized as attractive therapeutic targets. Therefore, the construction of a PPI-focused chemical library is an inevitable necessity for future drug discovery. Natural products have been used as traditional medicines to treat human diseases for millennia; in addition, their molecular scaffolds have been used in diverse approved drugs and drug candidates. The recent discovery of the ability of natural products to inhibit PPIs led us to use natural products as a chemical library for PPI-targeted drug discovery...
October 27, 2017: Journal of Molecular Graphics & Modelling
https://www.readbyqxmd.com/read/29134700/comparative-analysis-of-ovarian-transcriptomes-between-prolific-and-non-prolific-goat-breeds-via-high-throughput-sequencing
#8
X-D Zi, J-Y Lu, H Zhou, L Ma, W Xia, X-R Xiong, D-L Lan, X-H Wu
To increase the current understanding of the gene expression in the pre-ovulatory ovary and identify the key genes involved in the regulation of ovulation rate, we compared the transcriptomes of ovaries from the prolific Jintang black goat (JTG) and the non-prolific Tibetan goat (TBG) during the follicular phase using the Illumina RNA-Seq method. Three ovarian libraries were constructed for each breed. On average, we obtained approximately 49.2 and 45.9 million reads for each individual ovary of TBGs and JTGs, respectively, of which 79...
November 14, 2017: Reproduction in Domestic Animals, Zuchthygiene
https://www.readbyqxmd.com/read/29131846/how-many-species-and-under-what-names-using-dna-barcoding-and-genbank-data-for-west-central-african-amphibian-conservation
#9
Jessica L Deichmann, Daniel G Mulcahy, Hadrien Vanthomme, Elie Tobi, Addison H Wynn, Breda M Zimkus, Roy W McDiarmid
Development projects in west Central Africa are proceeding at an unprecedented rate, often with little concern for their effects on biodiversity. In an attempt to better understand potential impacts of a road development project on the anuran amphibian community, we conducted a biodiversity assessment employing multiple methodologies (visual encounter transects, auditory surveys, leaf litter plots and pitfall traps) to inventory species prior to construction of a new road within the buffer zone of Moukalaba-Doudou National Park, Gabon...
2017: PloS One
https://www.readbyqxmd.com/read/29131830/transcriptome-profiling-and-digital-gene-expression-analysis-of-sweet-potato-for-the-identification-of-putative-genes-involved-in-the-defense-response-against-fusarium-oxysporum-f-sp-batatas
#10
Yuli Lin, Weikun Zou, Shiqiang Lin, Dennis Onofua, Zhijian Yang, Haizhou Chen, Songliang Wang, Xuanyang Chen
Sweet potato production is constrained by Fusarium wilt, which is caused by Fusarium oxysporum f. sp. batatas (Fob). The identification of genes related to disease resistance and the underlying mechanisms will contribute to improving disease resistance via sweet potato breeding programs. In the present study, we performed de novo transcriptome assembly and digital gene expression (DGE) profiling of sweet potato challenged with Fob using Illumina HiSeq technology. In total, 89,944,188 clean reads were generated from 12 samples and assembled into 101,988 unigenes with an average length of 666 bp; of these unigenes, 62,605 (61...
2017: PloS One
https://www.readbyqxmd.com/read/29130184/generation-of-high-sensitivity-monoclonal-antibodies-specific-for-homoserine-lactones
#11
Soumya Palliyil
A number of bacteria use a class of chemical compounds called acyl-homoserine lactones (AHLs) as quorum sensing (QS) signals to coordinate their behavior at the population level, including pathogens like Pseudomonas aeruginosa. Blocking QS using antibodies is an attractive strategy for infection control as this process takes a central role in P. aeruginosa infections. Here the methods involved in the generation of high sensitivity anti-QS monoclonal antibodies from an immunized sheep phage display antibody library are described...
2018: Methods in Molecular Biology
https://www.readbyqxmd.com/read/29127298/sub-genome-anchored-physical-frameworks-of-the-allotetraploid-upland-cotton-gossypium-hirsutum-l-genome-and-an-approach-toward-reference-grade-assemblies-of-polyploids
#12
Christopher A Saski, Brian E Scheffler, Amanda M Hulse-Kemp, Bo Liu, Qingxin Song, Atsumi Ando, David M Stelly, Jodi A Scheffler, Jane Grimwood, Don C Jones, Daniel G Peterson, Jeremy Schmutz, Z Jeffery Chen
Like those of many agricultural crops, the cultivated cotton is an allotetraploid and has a large genome (~2.5 gigabase pairs). The two sub genomes, A and D, are highly similar but unequally sized and repeat-rich, which pose significant challenges for accurate genome reconstruction using standard approaches. Here we report the development of BAC libraries, sub genome specific physical maps, and a new-generation sequencing approach that will lead to a reference-grade genome assembly for Upland cotton. Three BAC libraries were constructed, fingerprinted, and integrated with BAC-end sequences (BES) to produce a de novo whole-genome physical map...
November 10, 2017: Scientific Reports
https://www.readbyqxmd.com/read/29126180/replong-de-novo-repeat-identification-using-long-read-sequencing-data
#13
Rui Guo, Yan-Ran Li, Shan He, Le Ou-Yang, Yiwen Sun, Zexuan Zhu
Motivation: The identification of repetitive elements is important in genome assembly and phylogenetic analyses. The existing de novo repeat identification methods exploiting the use of short reads are impotent in identifying long repeats. Since long reads are more likely to cover repeat regions completely, using long reads is more favorable for recognizing long repeats. Summary: In this study, we propose a novel de novo repeat elements identification method namely RepLong based on PacBio long reads...
November 6, 2017: Bioinformatics
https://www.readbyqxmd.com/read/29122012/drug-target-ontology-to-classify-and-integrate-drug-discovery-data
#14
Yu Lin, Saurabh Mehta, Hande Küçük-McGinty, John Paul Turner, Dusica Vidovic, Michele Forlin, Amar Koleti, Dac-Trung Nguyen, Lars Juhl Jensen, Rajarshi Guha, Stephen L Mathias, Oleg Ursu, Vasileios Stathias, Jianbin Duan, Nooshin Nabizadeh, Caty Chung, Christopher Mader, Ubbo Visser, Jeremy J Yang, Cristian G Bologa, Tudor I Oprea, Stephan C Schürer
BACKGROUND: One of the most successful approaches to develop new small molecule therapeutics has been to start from a validated druggable protein target. However, only a small subset of potentially druggable targets has attracted significant research and development resources. The Illuminating the Druggable Genome (IDG) project develops resources to catalyze the development of likely targetable, yet currently understudied prospective drug targets. A central component of the IDG program is a comprehensive knowledge resource of the druggable genome...
November 9, 2017: Journal of Biomedical Semantics
https://www.readbyqxmd.com/read/29118030/large-scale-low-cost-ngs-library-preparation-using-a-robust-tn5-purification-and-tagmentation-protocol
#15
Bianca P Hennig, Lars Velten, Ines Racke, Chelsea Szu Tu, Matthias Thoms, Vladimir Rybin, Hüseyin Besir, Kim Remans, Lars M Steinmetz
Efficient preparation of high quality sequencing libraries that represent well the biological sample is a key step for using next-generation sequencing in research. Tn5 enables fast, robust, and highly efficient processing of limited input material while scaling to the parallel processing of hundreds of samples. Here, we present a robust Tn5 transposase purification strategy based on an N-terminal His6-Sumo3 tag. We demonstrate that libraries prepared with our in-house Tn5 are of the same quality as those processed with a commercially available kit (Nextera XT), while they reduce the cost of large-scale experiments dramatically...
November 8, 2017: G3: Genes—Genomes—Genetics
https://www.readbyqxmd.com/read/29116524/epitope-mapping-by-phage-display
#16
Gustavo Marçal Schmidt Garcia Moreira, Viola Fühner, Michael Hust
Among the molecules of the immune system, antibodies, particularly monoclonal antibodies (mAbs), have been shown to be interesting for many biological applications. Due to their ability to recognize only a unique part of their target, mAbs are usually very specific. These targets can have many different compositions, but the most common ones are proteins or peptides that are usually from outside the host, although self-proteins can also be targeted in autoimmune diseases, or in some types of cancer. The parts of a mAb that interact with its target compose the paratope, while the recognized parts of the target compose the epitope...
2018: Methods in Molecular Biology
https://www.readbyqxmd.com/read/29116518/antibody-affinity-and-stability-maturation-by-error-prone-pcr
#17
Tobias Unkauf, Michael Hust, André Frenzel
Antibodies are the fastest growing class of pharmaceutical proteins and essential tools for research and diagnostics. Often antibodies do show a desirable specificity profile but lack sufficient affinity for the desired application. Here, we describe a method to increase the affinity of recombinant antibody fragments based on the construction of mutagenized phage display libraries.After the construction of a mutated antibody gene library by error-prone PCR, selection of high-affinity variants is either performed by panning in solution or on immobilized antigen with washing conditions optimized for off-rate-dependent selection...
2018: Methods in Molecular Biology
https://www.readbyqxmd.com/read/29116508/construction-of-a-synthetic-antibody-gene-library-for-the-selection-of-intrabodies-and-antibodies
#18
Déborah Caucheteur, Gautier Robin, Vincent Parez, Pierre Martineau
Libraries of antibody fragments displayed on filamentous phages have proved their value to generate human antibodies against virtually any target. We describe here a simple protocol to make large and diverse libraries based on a single or a limited number of frameworks. The approach is flexible enough to be used with any antibody format, either single-chain (scFv, VHH) or multi-chain (Fv, Fab, (Fab')2), and to target in a single step the six complementarity-determining regions-or any other part-of the antibody molecule...
2018: Methods in Molecular Biology
https://www.readbyqxmd.com/read/29116507/construction-and-selection-of-affilin-%C3%A2-phage-display-libraries
#19
Florian Settele, Madlen Zwarg, Sebastian Fiedler, Daniel Koscheinz, Eva Bosse-Doenecke
Affilin(®) molecules represent a new class of so-called scaffold proteins. The concept of scaffold proteins is to use stable and versatile protein structures which can be endowed with de novo binding properties and specificities by introducing mutations in surface exposed amino acid residues. Complex variations and combinations are generated by genetic methods of randomization resulting in large cDNA libraries. The selection for candidates binding to a desired target can be executed by display methods, especially the very robust and flexible phage display...
2018: Methods in Molecular Biology
https://www.readbyqxmd.com/read/29116506/construction-of-chicken-antibody-libraries
#20
Jeanni Fehrsen, Susan Wemmer, Wouter van Wyngaardt
Recombinant antibody libraries based on chicken immunoglobulin genes are potentially valuable sources of phage displayed scFvs for use in veterinary diagnostics and research. The libraries described in this chapter are based on chicken variable heavy and light chain immunoglobulin genes joined by a short flexible linker cloned in the phagemid vector pHEN1. The resulting phagemids produce either scFvs displayed on the surface of the fusion phage subsequent to co-infection with helper phage, or soluble scFvs following IPTG induction...
2018: Methods in Molecular Biology
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