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Synthetic genetics

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https://www.readbyqxmd.com/read/29045755/the-triforc-database-a-comprehensive-up-to-date-resource-of-plant-triterpene-biosynthesis
#1
Karel Miettinen, Sabrina Iñigo, Lukasz Kreft, Jacob Pollier, Christof De Bo, Alexander Botzki, Frederik Coppens, S Ren Bak, Alain Goossens
Triterpenes constitute a large and important class of plant natural products with diverse structures and functions. Their biological roles range from membrane structural components over plant hormones to specialized plant defence compounds. Furthermore, triterpenes have great potential for a variety of commercial applications such as vaccine adjuvants, anti-cancer drugs, food supplements and agronomic agents. Their biosynthesis is carried out through complicated, branched pathways by multiple enzyme types that include oxidosqualene cyclases, cytochrome P450s, and UDP-glycosyltransferases...
October 17, 2017: Nucleic Acids Research
https://www.readbyqxmd.com/read/29045151/dynamic-blue-light-inducible-t7-rna-polymerases-opto-t7rnaps-for-precise-spatiotemporal-gene-expression-control
#2
Armin Baumschlager, Stephanie K Aoki, Mustafa Khammash
Light has emerged as a control input for biological systems due to its precise spatiotemporal resolution. The limited toolset for light control in bacteria motivated us to develop a light-inducible transcription system that is independent from cellular regulation through the use of an orthogonal RNA polymerase. Here, we present our engineered blue light-responsive T7 RNA polymerases (Opto-T7RNAPs) that show properties such as low leakiness of gene expression in the dark state, high expression strength when induced with blue light, and an inducible range of more than 300-fold...
October 18, 2017: ACS Synthetic Biology
https://www.readbyqxmd.com/read/29043651/reporter-based-synthetic-genetic-array-analysis-a-functional-genomics-approach-for-investigating-transcript-or-protein-abundance-using-fluorescent-proteins-in-saccharomyces-cerevisiae
#3
Hendrikje Göttert, Mojca Mattiazzi Usaj, Adam P Rosebrock, Brenda J Andrews
Fluorescent reporter genes have long been used to quantify various cell features such as transcript and protein abundance. Here, we describe a method, reporter synthetic genetic array (R-SGA) analysis, which allows for the simultaneous quantification of any fluorescent protein readout in thousands of yeast strains using an automated pipeline. R-SGA combines a fluorescent reporter system with standard SGA analysis and can be used to examine any array-based strain collection available to the yeast community. This protocol describes the R-SGA methodology for screening different arrays of yeast mutants including the deletion collection, a collection of temperature-sensitive strains for the assessment of essential yeast genes and a collection of inducible overexpression strains...
2018: Methods in Molecular Biology
https://www.readbyqxmd.com/read/29043650/rewiring-the-budding-yeast-proteome-using-synthetic-physical-interactions
#4
Guðjón Ólafsson, Peter H Thorpe
Artificially tethering two proteins or protein fragments together is a powerful method to query molecular mechanisms. However, this approach typically relies upon a prior understanding of which two proteins, when fused, are most likely to provide a specific function and is therefore not readily amenable to large-scale screening. Here, we describe the Synthetic Physical Interaction (SPI) method to create proteome-wide forced protein associations in the budding yeast Saccharomyces cerevisiae. This method allows thousands of protein-protein associations to be screened for those that affect either normal growth or sensitivity to drugs or specific conditions...
2018: Methods in Molecular Biology
https://www.readbyqxmd.com/read/29043649/genome-wide-quantitative-fitness-analysis-qfa-of-yeast-cultures
#5
Eva-Maria Holstein, Conor Lawless, Peter Banks, David Lydall
We provide a detailed protocol for robot-assisted, genome-wide measurement of fitness in the model yeast Saccharomyces cerevisiae using Quantitative Fitness Analysis (QFA). We first describe how we construct thousands of double or triple mutant yeast strains in parallel using Synthetic Genetic Array (SGA) procedures. Strains are inoculated onto solid agar surfaces by liquid spotting followed by repeated photography of agar plates. Growth curves are constructed and the fitness of each strain is estimated. Robot-assisted QFA, can be used to identify genetic interactions and chemical sensitivity/resistance in genome-wide experiments, but QFA can also be used in smaller scale, manual workflows...
2018: Methods in Molecular Biology
https://www.readbyqxmd.com/read/29040384/selansi-a-toolbox-for-simulation-of-stochastic-gene-regulatory-networks
#6
Manuel Pájaro, Irene Otero-Muras, Carlos Vázquez, Antonio A Alonso
Motivation: Gene regulation is inherently stochastic. In many applications concerning Systems and Synthetic Biology such as the reverse engineering and the de novo design of genetic circuits, stochastic effects (yet potentially crucial) are often neglected due to the high computational cost of stochastic simulations. With advances in these fields there is an increasing need of tools providing accurate approximations of the stochastic dynamics of gene regulatory networks (GRNs) with reduced computational effort...
October 11, 2017: Bioinformatics
https://www.readbyqxmd.com/read/29038346/atr-is-a-therapeutic-target-in-synovial-sarcoma
#7
Samuel E Jones, Emmy D G Fleuren, Jessica Frankum, Asha Konde, Chris T Williamson, Dragomir B Krastev, Helen N Pemberton, James Campbell, Aditi Gulati, Richard Elliott, Malini Menon, Joanna L Selfe, Rachel Brough, Stephen J Pettitt, Wojciech Niedzwiedz, Winette T A van der Graaf, Janet Shipley, Alan Ashworth, Christopher J Lord
Synovial sarcoma (SS) is an aggressive soft-tissue malignancy characterised by expression of SS18-SSX fusions, where treatment options are limited. To identify therapeutically actionable genetic dependencies in SS, we performed a series of parallel, high-throughput small interfering RNA (siRNA) screens and compared genetic dependencies in SS tumor cells to those in >130 non-SS tumour cell lines. This approach revealed a reliance of SS tumor cells upon the DNA damage response serine/threonine protein kinase ATR...
October 16, 2017: Cancer Research
https://www.readbyqxmd.com/read/29035366/cytoplasmic-p53-couples-oncogene-driven-glucose-metabolism-to-apoptosis-and-is-a-therapeutic-target-in-glioblastoma
#8
Wilson X Mai, Laura Gosa, Veerle W Daniels, Lisa Ta, Jonathan E Tsang, Brian Higgins, W Blake Gilmore, Nicholas A Bayley, Mitra Dehghan Harati, Jason T Lee, William H Yong, Harley I Kornblum, Steven J Bensinger, Paul S Mischel, P Nagesh Rao, Peter M Clark, Timothy F Cloughesy, Anthony Letai, David A Nathanson
Cross-talk among oncogenic signaling and metabolic pathways may create opportunities for new therapeutic strategies in cancer. Here we show that although acute inhibition of EGFR-driven glucose metabolism induces only minimal cell death, it lowers the apoptotic threshold in a subset of patient-derived glioblastoma (GBM) cells. Mechanistic studies revealed that after attenuated glucose consumption, Bcl-xL blocks cytoplasmic p53 from triggering intrinsic apoptosis. Consequently, targeting of EGFR-driven glucose metabolism in combination with pharmacological stabilization of p53 with the brain-penetrant small molecule idasanutlin resulted in synthetic lethality in orthotopic glioblastoma xenograft models...
October 9, 2017: Nature Medicine
https://www.readbyqxmd.com/read/29034482/deep-reinforcement-learning-for-automated-radiation-adaptation-in-lung-cancer
#9
Huan-Hsin Tseng, Yi Luo, Sunan Cui, Jen-Tzung Chien, Randall K Ten Haken, Issam El Naqa
PURPOSE: To investigate deep reinforcement learning (DRL) based on historical treatment plans for developing automated radiation adaptation protocols for non-small cell lung cancer (NSCLC) patients that aim to maximize tumor local control at reduced rates of radiation pneumonitis grade 2 (RP2). METHODS: In a retrospective population of 114 NSCLC patients who received radiotherapy, a 3-component neural networks framework was developed for deep reinforcement learning (DRL) of dose fractionation adaptation...
October 16, 2017: Medical Physics
https://www.readbyqxmd.com/read/29032264/building-a-safer-and-faster-car-seatbelts-airbags-and-crispr
#10
REVIEW
Miguel-Angel Perales, Partow Kebriaei, Leslie S Kean, Michel Sadelain
Therapeutic T cell engineering has recently garnered widespread interest owing to the success of CD19 (Chimeric Antigen Receptor) CAR therapy. CARs are synthetic receptors for antigen that redirect the specificity and reprogram the function of the T cells in which they are genetically introduced. CARs targeting CD19, a cell surface molecule found in most leukemias and lymphomas, have yielded high remission rates in patients with chemorefractory, relapsed disease, including acute lymphoblastic leukemia, chronic lymphocytic leukemia and non-Hodgkin lymphoma...
October 12, 2017: Biology of Blood and Marrow Transplantation
https://www.readbyqxmd.com/read/29031852/inhibition-of-cdk5-rejuvenates-inhibitory-circuits-and-restores-experience-dependent-plasticity-in-adult-visual-cortex
#11
Yue Li, Laijian Wang, Xinxin Zhang, Mengyao Huang, Sitong Li, Xinxing Wang, Lin Chen, Bin Jiang, Yupeng Yang
Cyclin-dependent kinase 5 (Cdk5) acts as an essential modulator for neural development and neurological disorders. Here we show that Cdk5 plays a pivotal role in modulating GABAergic signaling and the maturation of visual system. In adult mouse primary visual cortex, Cdk5 formed complex with the GABA synthetic enzyme glutamate decarboxylase GAD67, but not with GAD65. In addition to enhancement in the surface level of NR2B-containing NMDA receptors, inhibition of Cdk5 reduced the protein levels of GADs and Otx2, while leaving intact the expression of vesicular GABA transporter and subunits of GABAA or AMPA receptors...
October 12, 2017: Neuropharmacology
https://www.readbyqxmd.com/read/29030416/genome-wide-identification-of-medicago-peptides-involved-in-macronutrient-responses-and-nodulation
#12
Thomas de Bang, Peter Knut Lundquist, Xinbin Dai, Clarissa Boschiero, Zhaohong Zhuang, Pooja Pant, Ivone Torres-Jerez, Sonali Roy, Joaquina Nogales, Vijaykumar Veerappan, Rebecca Dickstein, Michael K Udvardi, Patrick Xuechun Zhao, Wolf Scheible
Growing evidence indicates that small, secreted peptides (SSPs) play critical roles in legume growth and development, yet annotation of SSP-coding genes is far from complete. Systematic re-annotation of the Medicago truncatula genome identified 1,970 homologs of established SSP gene families and an additional 2,455 potential SSP genes. Expression patterns of known and putative SSP genes based on 144 RNA-seq datasets covering various stages of macronutrient deficiencies and symbiotic interactions with rhizobium and mycorrhiza were investigated...
October 13, 2017: Plant Physiology
https://www.readbyqxmd.com/read/29030023/on-universal-coding-events-in-protein-biogenesis
#13
REVIEW
Vladimir Kubyshkin, Carlos G Acevedo-Rocha, Nediljko Budisa
The complete ribosomal protein synthesis cycle and codon-amino acids associations are universally preserved in all life taxa on Earth. This process is accompanied by a set of hierarchically organized recognition and controlling events at different complexity levels. It starts with amino acid activation by aminoacyl tRNA synthetases (aaRS) followed by cellular matching with the acceptor units of their cognitive tRNAs ("operational RNA code") and ribosomal codon-anticodon pairing of messenger RNA ("triplet code")...
October 10, 2017: Bio Systems
https://www.readbyqxmd.com/read/29029158/genetic-interaction-network-as-an-important-determinant-of-gene-order-in-genome-evolution
#14
Yu-Fei Yang, Wenqing Cao, Shaohuan Wu, Wenfeng Qian
Although it is generally accepted that eukaryotic gene order is not random, the basic principles of gene arrangement on a chromosome remain poorly understood. Here, we extended existing population genetics theories that were based on two-locus models and proposed a hypothesis that genetic interaction networks drive the evolution of eukaryotic gene order. We predicted that genes with positive epistasis would move toward each other in evolution, during which a negative correlation between epistasis and gene distance formed...
October 3, 2017: Molecular Biology and Evolution
https://www.readbyqxmd.com/read/29027357/studies-on-the-aerobic-utilization-of-synthesis-gas-syngas-by-wild-type-and-recombinant-strains-of-ralstonia-eutropha-h16
#15
Daniel Heinrich, Matthias Raberg, Alexander Steinbüchel
The biotechnical platform strain Ralstonia eutropha H16 was genetically engineered to express a cox subcluster of the carboxydotrophic Oligotropha carboxidovoransOM5, including (i) the structural genes coxM, -S and -L, coding for an aerobic carbon monoxide dehydrogenase (CODH) and (ii) the genes coxD, -E, -F and -G, essential for the maturation of CODH. The coxOc genes expressed under control of the CO2 -inducible promoter PL enabled R. eutropha to oxidize CO to CO2 for the use as carbon source, as demonstrated by (13) CO experiments, but the recombinant strains remained dependent on H2 as external energy supply...
October 13, 2017: Microbial Biotechnology
https://www.readbyqxmd.com/read/29024819/a-modular-metabolic-engineering-approach-for-the-production-of-1-2-propanediol-from-glycerol-by-saccharomyces-cerevisiae
#16
Zia-Ul Islam, Mathias Klein, Maximilian R Aßkamp, Anders S R Ødum, Elke Nevoigt
Compared to sugars, a major advantage of using glycerol as a feedstock for industrial bioprocesses is the fact that this molecule is more reduced than sugars. A compound whose biotechnological production might greatly profit from the substrate's higher reducing power is 1,2-propanediol (1,2-PDO). Here we present a novel metabolic engineering approach to produce 1,2-PDO from glycerol in S. cerevisiae. Apart from implementing the heterologous methylglyoxal (MG) pathway for 1,2-PDO formation from dihydroxyacetone phosphate (DHAP) and expressing a heterologous glycerol facilitator, the employed genetic modifications included the replacement of the native FAD-dependent glycerol catabolic pathway by the `DHA pathway´ for delivery of cytosolic NADH and the reduction of triosephosphate isomerase (TPI) activity for increased precursor (DHAP) supply...
October 9, 2017: Metabolic Engineering
https://www.readbyqxmd.com/read/29023694/adaptive-self-organization-in-the-embryo-its-importance-to-adult-anatomy-and-to-tissue-engineering
#17
REVIEW
Jamie A Davies
The anatomy of healthy humans shows much minor variation, and twin-studies reveal at least some of this variation cannot be explained genetically. A plausible explanation is that fine-scale anatomy is not specified directly in a genetic programme, but emerges from self-organizing behaviours of cells that, for example, place a new capillary where it happens to be needed to prevent local hypoxia. Self-organizing behaviour can be identified by manipulating growing tissues (e.g. putting them under a spatial constraint) and observing an adaptive change that conserves the character of the normal tissue while altering its precise anatomy...
October 10, 2017: Journal of Anatomy
https://www.readbyqxmd.com/read/29022864/reverse-genetic-system-genetically-stable-reporter-viruses-and-packaged-subgenomic-replicon-based-on-a-brazilian-zika-virus-isolate
#18
Margit Mutso, Sirle Saul, Kai Rausalu, Olga Susova, Eva Žusinaite, Suresh Mahalingam, Andres Merits
Zika virus (ZIKV, genus Flavivirus) has emerged as a major mosquito-transmitted human pathogen, with recent outbreaks associated with an increased incidence of neurological complications, particularly microcephaly and the Guillain-Barré syndrome. Because the virus has only very recently emerged as an important pathogen, research is being hampered by a lack of reliable molecular tools. Here we report an infectious cDNA (icDNA) clone for ZIKV isolate BeH819015 from Brazil, which was selected as representative of South American ZIKV isolated at early stages of the outbreak...
October 12, 2017: Journal of General Virology
https://www.readbyqxmd.com/read/29020772/genetic-constructor-an-online-dna-design-platform
#19
Maxwell Bates, Joe Lachoff, Duncan Meech, Valentin Zulkower, Anais Moisy, Yisha Luo, Hille Tekotte, Cornelia Johanna Franziska Scheitz, Rupal Khilari, Florencio Mazzoldi, Deepak Chandran, Eli S Groban
Genetic Constructor is a cloud Computer Aided Design (CAD) application developed to support synthetic biologists from design intent through DNA fabrication and experiment iteration. The platform allows users to design, manage, and navigate complex DNA constructs and libraries, using a new visual language that focuses on functional parts abstracted from sequence. Features like combinatorial libraries and automated primer design allow the user to separate design from construction by focusing on functional intent, and design constraints aid iterative refinement of designs...
October 11, 2017: ACS Synthetic Biology
https://www.readbyqxmd.com/read/29020744/fastbma-scalable-network-inference-and-transitive-reduction
#20
Ling-Hong Hung, Kaiyuan Shi, Migao Wu, William Chad Young, Adrian E Raftery, Ka Yee Yeung
Inferring genetic networks from genome-wide expression data is extremely demanding computationally. We have developed fastBMA, a distributed, parallel, and scalable implementation of Bayesian model averaging (BMA) for this purpose. fastBMA also includes a computationally efficient module for eliminating redundant indirect edges in the network by mapping the transitive reduction to an easily solved shortest-path problem. We evaluated the performance of fastBMA on synthetic data and experimental genome-wide time series yeast and human datasets...
October 1, 2017: GigaScience
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