keyword
MENU ▼
Read by QxMD icon Read
search

Synthetic genetics

keyword
https://www.readbyqxmd.com/read/28820204/droplet-microfluidics-for-synthetic-biology
#1
REVIEW
Philip C Gach, Kosuke Iwai, Peter W Kim, Nathan J Hillson, Anup K Singh
Synthetic biology is an interdisciplinary field that aims to engineer biological systems for useful purposes. Organism engineering often requires the optimization of individual genes and/or entire biological pathways (consisting of multiple genes). Advances in DNA sequencing and synthesis have recently begun to enable the possibility of evaluating thousands of gene variants and hundreds of thousands of gene combinations. However, such large-scale optimization experiments remain cost-prohibitive to researchers following traditional molecular biology practices, which are frequently labor-intensive and suffer from poor reproducibility...
August 18, 2017: Lab on a Chip
https://www.readbyqxmd.com/read/28818368/review-metabolic-engineering-of-unusual-lipids-in-the-synthetic-biology-era
#2
REVIEW
Jose A Aznar-Moreno, Timothy P Durrett
The plant kingdom produces a variety of fatty acid structures, many of which possess functional groups useful for industrial applications. The species that produce these unusual fatty acids are often not suitable for large scale commercial production. The ability to create genetically modified plants, together with emerging synthetic biology approaches, offers the potential to develop alternative oil seed crops capable of producing high levels of modified lipids. In some cases, by combining genes from different species, non-natural lipids with a targeted structure can be conceived...
October 2017: Plant Science: An International Journal of Experimental Plant Biology
https://www.readbyqxmd.com/read/28815907/t7-rna-polymerase-driven-inducible-cell-lysis-for-dna-transfer-from-escherichia-coli-to-bacillus-subtilis
#3
Mario Juhas, James W Ajioka
The majority of the good DNA editing techniques have been developed in Escherichia coli; however, Bacillus subtilis is better host for a plethora of synthetic biology and biotechnology applications. Reliable and efficient systems for the transfer of synthetic DNA between E. coli and B. subtilis are therefore of the highest importance. Using synthetic biology approaches, such as streamlined lambda Red recombineering and Gibson Isothermal Assembly, we integrated genetic circuits pT7L123, Repr-ts-1 and pLT7pol encoding the lysis genes of bacteriophages MS2, ΦX174 and lambda, the thermosensitive repressor and the T7 RNA polymerase into the E...
August 16, 2017: Microbial Biotechnology
https://www.readbyqxmd.com/read/28812884/controlling-bdellovibrio-bacteriovorus-gene-expression-and-predation-using-synthetic-riboswitches
#4
Mohammed Dwidar, Yohei Yokobayashi
Bdellovibrio bacteriovorus is a predatory bacterium that feeds on Gram-negative bacteria including a wide range of pathogens and thus has potential applications as a biocontrol agent. Owing to its unique life cycle, however, there are limited tools that enable genetic manipulation of B. bacteriovorus. This work describes our first steps toward engineering the predatory bacterium for practical applications by developing basic genetic parts to control gene expression. Specifically, we evaluated four robust promoters that are active during the attack phase of B...
August 18, 2017: ACS Synthetic Biology
https://www.readbyqxmd.com/read/28811820/modified-mahalanobis-taguchi-system-for-imbalance-data-classification
#5
Mahmoud El-Banna
The Mahalanobis Taguchi System (MTS) is considered one of the most promising binary classification algorithms to handle imbalance data. Unfortunately, MTS lacks a method for determining an efficient threshold for the binary classification. In this paper, a nonlinear optimization model is formulated based on minimizing the distance between MTS Receiver Operating Characteristics (ROC) curve and the theoretical optimal point named Modified Mahalanobis Taguchi System (MMTS). To validate the MMTS classification efficacy, it has been benchmarked with Support Vector Machines (SVMs), Naive Bayes (NB), Probabilistic Mahalanobis Taguchi Systems (PTM), Synthetic Minority Oversampling Technique (SMOTE), Adaptive Conformal Transformation (ACT), Kernel Boundary Alignment (KBA), Hidden Naive Bayes (HNB), and other improved Naive Bayes algorithms...
2017: Computational Intelligence and Neuroscience
https://www.readbyqxmd.com/read/28809975/discovery-of-synthetic-small-molecules-that-enhance-the-number-of-stomata-c-h-functionalization-chemistry-for-plant-biology
#6
Asraa Ziadi, Naoyuki Uchida, Hiroe Kato, Rina Hisamatsu, Ayato Sato, Shinya Hagihara, Kenichiro Itami, Keiko U Torii
The increasing climate changes and global warming are leading to colossal agricultural problems such as abatement of food production and quality. As stomatal development is considered to play a key role in crop plant productivity and water-use efficiency, studying stomatal development is useful for understanding the productivity of plant systems for both natural and agricultural systems. Herein, we report the first-in-class synthetic small molecules enhancing the number of stomata in Arabidopsis thaliana that have been discovered by screening of the chemical library and further optimized by the Pd-catalyzed C-H arylation reaction...
August 15, 2017: Chemical Communications: Chem Comm
https://www.readbyqxmd.com/read/28808131/intercellular-communication-via-the-comx-inducing-peptide-xip-of-streptococcus-mutans
#7
Justin Kaspar, Simon A M Underhill, Robert C Shields, Adrian Reyes, Suzanne Rosenzweig, Stephen J Hagen, Robert A Burne
Gram-positive bacteria utilize exported peptides to coordinate genetic and physiological processes required for biofilm formation, stress responses and ecological competitiveness. One example is activation of natural genetic competence by ComR and the comX-inducing peptide (XIP) in Streptococcus mutans Although the competence pathway can be activated by addition of synthetic XIP in defined medium, the hypothesis that XIP is able to function as an intercellular signal molecule has not been rigorously tested...
August 14, 2017: Journal of Bacteriology
https://www.readbyqxmd.com/read/28808099/enhancing-crop-plant-photosynthesis-by-introducing-novel-genetic-diversity
#8
REVIEW
Marcel Dann, Dario Leister
Although some elements of the photosynthetic light reactions might appear to be ideal, the overall efficiency of light conversion to biomass has not been optimized during evolution. Because crop plants are depleted of genetic diversity for photosynthesis, efforts to enhance its efficiency with respect to light conversion to yield must generate new variation. In principle, three sources of natural variation are available: (i) rare diversity within extant higher plant species, (ii) photosynthetic variants from algae, and (iii) reconstruction of no longer extant types of plant photosynthesis...
September 26, 2017: Philosophical Transactions of the Royal Society of London. Series B, Biological Sciences
https://www.readbyqxmd.com/read/28807672/pharmacological-characterization-of-novel-synthetic-opioids-nso-found-in-the-recreational-drug-marketplace
#9
REVIEW
Michael H Baumann, Susruta Majumdar, Valerie Le Rouzic, Amanda Hunkele, Rajendra Uprety, Xi Ping Huang, Jin Xu, Bryan L Roth, Ying-Xian Pan, Gavril W Pasternak
Novel synthetic opioids (NSO) are increasingly encountered in illicit heroin and counterfeit pain pills. Many NSO are resurrected from older biomedical literature or patent applications, so limited information is available about their biological effects. Here we examined the pharmacology of three structurally-distinct NSO found in the recreational drug market: N-(1-(2-phenylethyl)-4-piperidinyl)-N-phenylbutyramide (butyrylfentanyl), 3,4-dichloro-N-[(1R,2R)-2-(dimethylamino)cyclohexyl]-N-methylbenzamide (U-47700) and 1-cyclohexyl-4-(1,2-diphenylethyl)piperazine (MT-45)...
August 11, 2017: Neuropharmacology
https://www.readbyqxmd.com/read/28806777/a-synthetic-sickness-screen-for-senescence-re-engagement-targets-in-mutant-cancer-backgrounds
#10
Claire J Cairney, Lauren S Godwin, Alan E Bilsland, Sharon Burns, Katrina H Stevenson, Lynn McGarry, John Revie, Jon D Moore, Ceri M Wiggins, Rebecca S Collinson, Clare Mudd, Elpida Tsonou, Mahito Sadaie, Dorothy C Bennett, Masashi Narita, Christopher J Torrance, W Nicol Keith
Senescence is a universal barrier to immortalisation and tumorigenesis. As such, interest in the use of senescence-induction in a therapeutic context has been gaining momentum in the past few years; however, senescence and immortalisation remain underserved areas for drug discovery owing to a lack of robust senescence inducing agents and an incomplete understanding of the signalling events underlying this complex process. In order to address this issue we undertook a large-scale morphological siRNA screen for inducers of senescence phenotypes in the human melanoma cell line A375P...
August 14, 2017: PLoS Genetics
https://www.readbyqxmd.com/read/28806522/development-of-a-recombinant-multifunctional-biomacromolecule-for-targeted-gene-transfer-to-prostate-cancer-cells
#11
Arash Hatefi, Zahra Karjoo, Alireza Nomani
The objective of this study was to genetically engineer a fully functional single chain fusion peptide composed of motifs from diverse biological and synthetic origins that can perform multiple tasks including DNA condensation, cell targeting, cell transfection, particle shielding from immune system and effective gene transfer to prostate tumors. To achieve the objective, a single chain biomacromolecule (vector) consisted of four repetative units of histone H2A peptide, fusogenic peptide GALA, short elastin-like peptide and PC-3 cell targeting peptide was designed...
August 14, 2017: Biomacromolecules
https://www.readbyqxmd.com/read/28804512/engineering-shewanella-oneidensis-enables-xylose-fed-microbial-fuel-cell
#12
Feng Li, Yuanxiu Li, Liming Sun, Xiaofei Li, Changji Yin, Xingjuan An, Xiaoli Chen, Yao Tian, Hao Song
BACKGROUND: The microbial fuel cell (MFC) is a green and sustainable technology for electricity energy harvest from biomass, in which exoelectrogens use metabolism and extracellular electron transfer pathways for the conversion of chemical energy into electricity. However, Shewanella oneidensis MR-1, one of the most well-known exoelectrogens, could not use xylose (a key pentose derived from hydrolysis of lignocellulosic biomass) for cell growth and power generation, which limited greatly its practical applications...
2017: Biotechnology for Biofuels
https://www.readbyqxmd.com/read/28803913/synthetic-rescue-couples-nadph-generation-to-metabolite-overproduction-in-saccharomyces-cerevisiae
#13
Siavash Partow, Patrick B Hyland, Radhakrishnan Mahadevan
Engineering the redox cofactor metabolism is known to be a key challenge in developing a platform strain for biosynthesis of valuable products. Hence, general strategies for manipulation of co-factor metabolism in industrially relevant hosts are of significance. Here, we demonstrate an improvement in α-ketoglutarate (AKG) production in S. cerevisiae using a novel approach based on synthetic rescue. Here, we first perturb the cytosolic NADPH metabolism via deletion of glucose-6-phosphate dehydrogenase (ZWF1)...
August 10, 2017: Metabolic Engineering
https://www.readbyqxmd.com/read/28803467/not-gate-genetic-circuits-to-control-gene-expression-in-cyanobacteria
#14
Arnaud Taton, Amy T Ma, Mizuho Ota, Susan Golden, James W Golden
To downregulate gene expression in cyanobacteria, we constructed NOT gate genetic circuits using orthogonal promoters and their cognate repressors regulated translationally by synthetic riboswitches. Four NOT gates were tested and characterized in five cyanobacterial strains using fluorescent reporter-gene assays. In comparison to alternative systems used to downregulate gene expression in cyanobacteria, these NOT gates performed well, reducing YFP reporter expression by 4 to 50-fold. We further evaluated these NOT gates by controlling the expression of the ftsZ gene, which encodes a prokaryotic tubulin homolog that is required for cell division and is essential for Synechococcus elongatus PCC 7942...
August 14, 2017: ACS Synthetic Biology
https://www.readbyqxmd.com/read/28801911/a-modular-approach-to-building-complex-synthetic-circuits
#15
Yinqing Li, Ron Weiss
Efficient assembly of genetic circuits is a critical element in synthetic biology for implementing complex gene expression systems. Here we present an assembly framework that integrates recent developments in DNA recombination technologies and unique nucleotide sequences for modular and reliable construction of complex genetic circuits. All relevant protocols are described in detail. Implementing these protocols relies on readily available reagents and basic molecular biology techniques without the need for specialized equipment...
2017: Methods in Molecular Biology
https://www.readbyqxmd.com/read/28801899/bioluminescence-monitoring-of-promoter-activity-in-vitro-and-in-vivo
#16
Juliette M K M Delhove, Rajvinder Karda, Kate E Hawkins, Lorna M FitzPatrick, Simon N Waddington, Tristan R McKay
The application of luciferase reporter genes to provide quantitative outputs for the activation of promoters is a well-established technique in molecular biology. Luciferase catalyzes an enzymatic reaction, which in the presence of the substrate luciferin produces photons of light relative to its molar concentration. The luciferase transgene can be genetically inserted at the first intron of a target gene to act as a surrogate for the gene's endogenous expression in cells and transgenic mice. Alternatively, promoter sequences can be excised and/or amplified from genomic sources or constructed de novo and cloned upstream of luciferase in an expression cassette transfected into cells...
2017: Methods in Molecular Biology
https://www.readbyqxmd.com/read/28799737/method-to-assemble-genomic-dna-fragments-or-genes-on-human-artificial-chromosome-with-regulated-kinetochore-using-a-multi-integrase-system
#17
Nicholas C O Lee, Jung-Hyun Kim, Nikolai Petrov, Hee-Sheung Lee, Hiroshi Masumoto, William C Earnshaw, Vladimir Larionov, Natalay Kouprina
The production of cells capable of carrying multiple transgenes to Mb-size genomic loci has multiple applications in biomedicine and biotechnology. In order to achieve this goal, three key steps are required: i) Cloning of large genomic segments; ii) Insertion of multiple DNA blocks at a precise location and iii) The capability to eliminate the assembled region from cells. In this study, we designed the Iterative Integration System (IIS) that utilizes recombinases Cre, ΦC31 and ΦBT1, and combined it with Human Artificial Chromosome (HAC) possessing a regulated kinetochore (alphoid(tetO)-HAC)...
August 11, 2017: ACS Synthetic Biology
https://www.readbyqxmd.com/read/28798914/rapid-characterization-of-bacterial-electrogenicity-using-a-single-sheet-paper-based-electrofluidic-array
#18
Yang Gao, Daniel J Hassett, Seokheun Choi
Electrogenicity, or bacterial electron transfer capacity, is an important application which offers environmentally sustainable advances in the fields of biofuels, wastewater treatment, bioremediation, desalination, and biosensing. Significant boosts in this technology can be achieved with the growth of synthetic biology that manipulates microbial electron transfer pathways, thereby potentially significantly improving their electrogenic potential. There is currently a need for a high-throughput, rapid, and highly sensitive test array to evaluate the electrogenic properties of newly discovered and/or genetically engineered bacterial species...
2017: Frontiers in Bioengineering and Biotechnology
https://www.readbyqxmd.com/read/28797087/a-comparison-of-monte-carlo-based-bayesian-parameter-estimation-methods-for-stochastic-models-of-genetic-networks
#19
Inés P Mariño, Alexey Zaikin, Joaquín Míguez
We compare three state-of-the-art Bayesian inference methods for the estimation of the unknown parameters in a stochastic model of a genetic network. In particular, we introduce a stochastic version of the paradigmatic synthetic multicellular clock model proposed by Ullner et al., 2007. By introducing dynamical noise in the model and assuming that the partial observations of the system are contaminated by additive noise, we enable a principled mechanism to represent experimental uncertainties in the synthesis of the multicellular system and pave the way for the design of probabilistic methods for the estimation of any unknowns in the model...
2017: PloS One
https://www.readbyqxmd.com/read/28796508/in-vivo-structure-activity-relationships-and-optimization-of-an-unnatural-base-pair-for-replication-in-a-semi-synthetic-organism
#20
Aaron W Feldman, Floyd E Romesberg
In an effort to expand the genetic alphabet and create semi-synthetic organisms (SSOs) that store and retrieve increased information, we have developed the unnatural base pairs (UBPs) dNaM and d5SICS or dTPT3 (dNaM-d5SICS and dNaM-dTPT3). The UBPs form based on hydrophobic and packing forces, as opposed to complementary hydrogen bonding, and while they are both retained within the in vivo environment of an Escherichia coli SSO, their development was based on structure-activity relationship (SAR) data generated in vitro...
August 10, 2017: Journal of the American Chemical Society
keyword
keyword
77443
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"