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Synthetic genetics

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https://www.readbyqxmd.com/read/28720784/snap-tagged-chikungunya-virus-replicons-improve-visualisation-of-non-structural-protein-3-by-fluorescence-microscopy
#1
Roland Remenyi, Grace C Roberts, Carsten Zothner, Andres Merits, Mark Harris
Chikungunya virus (CHIKV), a mosquito-borne alphavirus, causes febrile disease, muscle and joint pain, which can become chronic in some individuals. The non-structural protein 3 (nsP3) plays essential roles during infection, but a complete understanding of its function is lacking. Here we used a microscopy-based approach to image CHIKV nsP3 inside human cells. The SNAP system consists of a self-labelling enzyme tag, which catalyses the covalent linking of exogenously supplemented synthetic ligands. Genetic insertion of this tag resulted in viable replicons and specific labelling while preserving the effect of nsP3 on stress granule responses and co-localisation with GTPase Activating Protein (SH3 domain) Binding Proteins (G3BPs)...
July 18, 2017: Scientific Reports
https://www.readbyqxmd.com/read/28720677/synthetic-circulating-cell-free-dna-as-quality-control-materials-for-somatic-mutation-detection-in-liquid-biopsy-for-cancer
#2
Rui Zhang, Rongxue Peng, Ziyang Li, Peng Gao, Shiyu Jia, Xin Yang, Jiansheng Ding, Yanxi Han, Jiehong Xie, Jinming Li
BACKGROUND: Detection of somatic genomic alterations in tumor-derived cell-free DNA (cfDNA) in the plasma is challenging owing to the low concentrations of cfDNA, variable detection methods, and complex workflows. Moreover, no proper quality control materials are available currently. METHODS: We developed a set of synthetic cfDNA quality control materials (SCQCMs) containing spike-in cfDNA on the basis of micrococcal nuclease digestion carrying somatic mutations as simulated cfDNA and matched genomic DNA as genetic background to emulate paired tumor-normal samples in real clinical tests...
July 18, 2017: Clinical Chemistry
https://www.readbyqxmd.com/read/28718764/crispr-mediated-genetic-interaction-profiling-identifies-rna-binding-proteins-controlling-metazoan-fitness
#3
Adam D Norris, Xicotencatl Gracida, John Calarco
<span style="font-size: 12pt; font-family: 'Times';">Genetic interaction screens have aided our understanding of complex genetic traits,</span><span style="font-size: 11.000000pt; font-family: 'Calibri';"> </span><span style="font-size: 12pt; font-family: 'Times';">diseases, and biological pathways. However, approaches for synthetic genetic analysis with</span><span style="font-size: 11.000000pt; font-family: 'Calibri';"> </span><span style="font-size: 12pt; font-family: 'Times';">null-alleles in metazoans have not been feasible...
July 18, 2017: ELife
https://www.readbyqxmd.com/read/28718331/entinostat-for-the-treatment-of-breast-cancer
#4
Dario Trapani, Angela Esposito, Carmen Criscitiello, Luca Mazzarella, Marzia Locatelli, Ida Minchella, Saverio Minucci, Giuseppe Curigliano
Breast cancer accounts for 29% of malignant tumors. It is an heterogenous disease covering a spectrum of different molecular subtypes. Epigenetic aberrations may affect gene expression through DNA and histone proteins modifications thus promoting tumor progression and resistance to anti- tumor treatment. Area covered: This article explores the potential role of entinostat in the treatment of breast cancer. The clinical trials evaluating entinostat are discussed, highlighting preclinical data and early-phase clinical studies results...
July 18, 2017: Expert Opinion on Investigational Drugs
https://www.readbyqxmd.com/read/28715702/engineering-carbon-fixation-in-e-coli-from-heterologous-rubisco-expression-to-the-calvin-benson-bassham-cycle
#5
REVIEW
Niv Antonovsky, Shmuel Gleizer, Ron Milo
Carbon fixation is the gateway of inorganic carbon into the biosphere. Our ability to engineer carbon fixation pathways in living organisms is expected to play a crucial role in the quest towards agricultural and energetic sustainability. Recent successes to introduce non-native carbon fixation pathways into heterotrophic hosts offer novel platforms for manipulating these pathways in genetically malleable organisms. Here, we focus on past efforts and future directions for engineering the dominant carbon fixation pathway in the biosphere, the Calvin-Benson cycle, into the well-known model organism Escherichia coli...
July 14, 2017: Current Opinion in Biotechnology
https://www.readbyqxmd.com/read/28715701/synthetic-biological-approaches-to-optogenetically-control-cell-signaling
#6
REVIEW
Katja Kolar, Wilfried Weber
Precise spatial and temporal control of cellular processes is in life sciences a highly sought-after capability. In the recent years, this goal has become progressively achievable through the field of optogenetics, which utilizes light as a non-invasive means to control genetically encoded light-responsive proteins. The latest optogenetic systems, such as those for control of subcellular localization or cellular decision-making and tissue morphogenesis provide us with insights to gain a deeper understanding of the cellular inner workings...
July 14, 2017: Current Opinion in Biotechnology
https://www.readbyqxmd.com/read/28714313/artificial-metalloenzymes-reaction-scope-and-optimization-strategies
#7
Fabian Schwizer, Yasunori Okamoto, Tillmann Heinisch, Yifan Gu, Michela M Pellizzoni, Vincent Lebrun, Raphael Reuter, Valentin Köhler, Jared C Lewis, Thomas R Ward
The incorporation of a synthetic, catalytically competent metallocofactor into a protein scaffold to generate an artificial metalloenzyme (ArM) has been explored since the late 1970's. Progress in the ensuing years was limited by the tools available for both organometallic synthesis and protein engineering. Advances in both of these areas, combined with increased appreciation of the potential benefits of combining attractive features of both homogeneous catalysis and enzymatic catalysis, led to a resurgence of interest in ArMs starting in the early 2000's...
July 17, 2017: Chemical Reviews
https://www.readbyqxmd.com/read/28714256/a1s_2811-a-chea-y-like-hybrid-two-component-regulator-from-acinetobacter%C3%A2-baumannii-atcc17978-is-involved-in-surface-motility-and-biofilm-formation-in-this-bacterium
#8
Rong Chen, Ruichen Lv, Lisheng Xiao, Min Wang, Zongmin Du, Yafang Tan, Yujun Cui, Yanfeng Yan, Yanping Luo, Ruifu Yang, Yajun Song
Two-component systems in Acinetobacter baumannii are associated with its virulence, drug resistance, motility, biofilm formation, and other characteristics. In this study, we used RecAb , a genetic engineering method, to investigate the function of A1S_2811 in A. baumannii strain ATCC17978. A1S_2811, a hypothetical hybrid sensor histidine kinase/response regulator, has four histidine-containing phosphotransfer domains, a CheA-like regulatory domain, and a CheY-like receiver domain at its C terminus. Compared with the ATCC17978 strain, both surface motility and biofilm formation at the gas-liquid interface decreased significantly in the A1S_2811 knock-out strain...
July 17, 2017: MicrobiologyOpen
https://www.readbyqxmd.com/read/28713623/bistability-and-oscillations-in-co-repressive-synthetic-microbial-consortia
#9
Mehdi Sadeghpour, Alan Veliz-Cuba, Gábor Orosz, Krešimir Josić, Matthew R Bennett
Synthetic microbial consortia are conglomerations of multiple strains of genetically engineered microbes programmed to cooperatively bring about population-level phenotypes. By coordinating their activity, the constituent strains can display emergent behaviors that are difficult to engineer into isogenic populations. To do so, strains are engineered to communicate with one another through intercellular signaling pathways. As a result, the regulatory networks that control gene transcription throughout the population are sensitive to the extracellular concentration of the signaling molecules, and hence the relative densities of constituent strains...
March 2017: Quantitative Biology
https://www.readbyqxmd.com/read/28713567/genetically-engineered-bananas-resistant-to-xanthomonas-wilt-disease-and-nematodes
#10
REVIEW
Leena Tripathi, Howard Atkinson, Hugh Roderick, Jerome Kubiriba, Jaindra N Tripathi
Banana is an important staple food crop feeding more than 100 million Africans, but is subject to severe productivity constraints due to a range of pests and diseases. Banana Xanthomonas wilt caused by Xanthomonas campestris pv. musacearum is capable of entirely destroying a plantation while nematodes can cause losses up to 50% and increase susceptibility to other pests and diseases. Development of improved varieties of banana is fundamental in order to tackle these challenges. However, the sterile nature of the crop and the lack of resistance in Musa germplasm make improvement by traditional breeding techniques either impossible or extremely slow...
May 2017: Food and energy security
https://www.readbyqxmd.com/read/28712711/specificity-and-putative-mode-of-action-of-a-mosquito-larvicidal-toxin-from-the-bacterium-xenorhabdus-innexi
#11
Il-Hwan Kim, Jerald Ensign, Do-Young Kim, Hoe-Yune Jung, Na-Ri Kim, Bo-Hwa Choi, Sun-Min Park, Que Lan, Walter G Goodman
Reduction of mosquito-borne diseases relies, in part, on the use of synthetic pesticides to control pest mosquitoes. This reliance has led to genetic resistance, environmental contamination and the nondiscriminatory elimination of both pest and non-pest species. To expand our options for control, we screened entomopathogenic bacteria for potential larvicidal activity. A lipopeptide from the bacterium, Xenorhabdus innexi, was discovered that displayed potent larvicidal activity. The LC50s of the lipopeptide towards Aedes aegypti, Culex pipiens and Anopheles gambiae larvae were 1...
July 13, 2017: Journal of Invertebrate Pathology
https://www.readbyqxmd.com/read/28711856/rnaseq-based-transcriptome-comparison-of-saccharomyces-cerevisiae-strains-isolated-from-diverse-fermentative-environments
#12
Clara Ibáñez, Roberto Pérez-Torrado, Miguel Morard, Christina Toft, Eladio Barrio, Amparo Querol
Transcriptome analyses play a central role in unraveling the complexity of gene expression regulation in Saccharomyces cerevisiae. This species, one of the most important microorganisms for humans given its industrial applications, shows an astonishing degree of genetic and phenotypic variability among different strains adapted to specific environments. In order to gain novel insights into the Saccharomyces cerevisiae biology of strains adapted to different fermentative environments, we analyzed the whole transcriptome of three strains isolated from wine, flor wine or mezcal fermentations...
July 6, 2017: International Journal of Food Microbiology
https://www.readbyqxmd.com/read/28710849/long-distance-dispersal-of-fungi
#13
Jacob J Golan, Anne Pringle
Dispersal is a fundamental biological process, operating at multiple temporal and spatial scales. Despite an increasing understanding of fungal biodiversity, most research on fungal dispersal focuses on only a small fraction of species. Thus, any discussion of the dispersal dynamics of fungi as a whole is problematic. While abundant morphological and biogeographic data are available for hundreds of species, researchers have yet to integrate this information into a unifying paradigm of fungal dispersal, especially in the context of long-distance dispersal (LDD)...
July 2017: Microbiology Spectrum
https://www.readbyqxmd.com/read/28710008/identifying-synthetic-lethal-targets-using-crispr-cas9-system
#14
Jaspreet Kaur Dhanjal, Navaneethan Radhakrishnan, Durai Sundar
Synthetic lethality occurs when co-occurrence of two genetic events is unfavorable for the survival of the cell or organism. The conventional approach of high throughput screening of synthetic lethal targets using chemical compounds has been replaced by RNAi technology. CRISPR/Cas9, an RNA guided endonuclease system is the most recent technology for this work. Here, we have discussed the major considerations involved in designing a CRISPR/Cas9 based screening experiment for identification of synthetic lethal targets...
July 11, 2017: Methods: a Companion to Methods in Enzymology
https://www.readbyqxmd.com/read/28709120/advances-in-design-of-protein-folds-and-assemblies
#15
REVIEW
Ajasja Ljubetič, Helena Gradišar, Roman Jerala
Conceptual and computational advances triggered an explosion of designed protein structures in the recent years. Various protein fold geometries have been robustly designed with atomic accuracy, including protein folds unseen in nature. The same principles and tools have been extended to design multi-chain assemblies. By exploiting symmetry, mega-Dalton structures have been created with exciting potential applications for synthetic biology. In this review we focus on design of single chain and multi polypeptide chain assemblies of defined size and composition...
July 11, 2017: Current Opinion in Chemical Biology
https://www.readbyqxmd.com/read/28707298/melatonin-receptors-molecular-pharmacology-and-signaling-in-the-context-of-system-bias
#16
REVIEW
Erika Cecon, Atsuro Oishi, Ralf Jockers
Melatonin, N-acetyl-5-methoxytryptamine, an evolutionally old molecule, is produced by the pineal gland in vertebrates and it binds with high affinity to melatonin receptors, which are members of the G protein-coupled receptor family. Among the multiple effects attributed to melatonin we will focus here on those that are dependent on the activation of the two mammalian MT1 and MT2 melatonin receptors. We briefly summarize the latest developments on synthetic melatonin receptor ligands, including multi-target-directed ligands, and the characterization of signaling-biased ligands...
July 13, 2017: British Journal of Pharmacology
https://www.readbyqxmd.com/read/28705249/vector-control-with-driving-y-chromosomes-modelling-the-evolution-of-resistance
#17
Andrea Beaghton, Pantelis John Beaghton, Austin Burt
BACKGROUND: The introduction of new malaria control interventions has often led to the evolution of resistance, both of the parasite to new drugs and of the mosquito vector to new insecticides, compromising the efficacy of the interventions. Recent progress in molecular and population biology raises the possibility of new genetic-based interventions, and the potential for resistance to evolve against these should be considered. Here, population modelling is used to determine the main factors affecting the likelihood that resistance will evolve against a synthetic, nuclease-based driving Y chromosome that produces a male-biased sex ratio...
July 14, 2017: Malaria Journal
https://www.readbyqxmd.com/read/28705159/an-att-site-based-recombination-reporter-system-for-genome-engineering-and-synthetic-dna-assembly
#18
Michael J Bland, Magaly Ducos-Galand, Marie-Eve Val, Didier Mazel
BACKGROUND: Direct manipulation of the genome is a widespread technique for genetic studies and synthetic biology applications. The tyrosine and serine site-specific recombination systems of bacteriophages HK022 and ΦC31 are widely used for stable directional exchange and relocation of DNA sequences, making them valuable tools in these contexts. We have developed site-specific recombination tools that allow the direct selection of recombination events by embedding the attB site from each system within the β-lactamase resistance coding sequence (bla)...
July 14, 2017: BMC Biotechnology
https://www.readbyqxmd.com/read/28704034/unique-thermal-stability-of-unnatural-hydrophobic-ds-bases-in-double-stranded-dnas
#19
Michiko Kimoto, Ichiro Hirao
Genetic alphabet expansion technology, the introduction of unnatural bases or base pairs into replicable DNA, has rapidly advanced as a new synthetic biology area. A hydrophobic unnatural base pair between 7-(2-thienyl)imidazo[4,5-b]pyridine (Ds) and 2-nitro-4-propynylpyrrole (Px) exhibited high fidelity as a third base pair in PCR. SELEX methods using the Ds-Px pair enabled high-affinity DNA aptamer generation, and introducing a few Ds bases into DNA aptamers extremely augmented their affinities and selectivities to target proteins...
July 13, 2017: ACS Synthetic Biology
https://www.readbyqxmd.com/read/28702937/genetic-engineering-strategies-for-biotic-and-abiotic-stress-tolerance-and-quality-enhancement-in-horticultural-crops-a-comprehensive-review
#20
REVIEW
Nehanjali Parmar, Kunwar Harendra Singh, Deepika Sharma, Lal Singh, Pankaj Kumar, J Nanjundan, Yasin Jeshima Khan, Devendra Kumar Chauhan, Ajay Kumar Thakur
Genetic engineering technique offers myriads of applications in improvement of horticultural crops for biotic and abiotic stress tolerance, and produce quality enhancement. During last two decades, a large number of transgenic horticultural crops has been developed and more are underway. A number of genes including natural and synthetic Cry genes, protease inhibitors, trypsin inhibitors and cystatin genes have been used to incorporate insect and nematode resistance. For providing protection against fungal and bacterial diseases, various genes like chitinase, glucanase, osmotin, defensin and pathogenesis-related genes are being transferred to many horticultural crops world over...
August 2017: 3 Biotech
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