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Genetic engineering

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https://www.readbyqxmd.com/read/28102666/a-simulation-approach-for-timing-analysis-of-genetic-logic-circuits
#1
Hasan Baig, Jan Madsen
Constructing genetic logic circuits is an application of synthetic biology, where parts of the DNA of a living cell are engineered to perform a dedicated Boolean function triggered by appropriate concentration levels of certain proteins or by different genetic components. These logic circuits work in a manner similar to electronic logic circuits, but are much more stochastic and hence much harder to characterize. In this paper, we introduce an approach to analyze the threshold value and timing of genetic logic circuits...
January 19, 2017: ACS Synthetic Biology
https://www.readbyqxmd.com/read/28102490/genome-engineering-of-stem-cell-organoids-for-disease-modeling
#2
REVIEW
Yingmin Sun, Qiurong Ding
Precision medicine emerges as a new approach that takes into account individual variability. Successful realization of precision medicine requires disease models that are able to incorporate personalized disease information and recapitulate disease development processes at the molecular, cellular and organ levels. With recent development in stem cell field, a variety of tissue organoids can be derived from patient specific pluripotent stem cells and adult stem cells. In combination with the state-of-the-art genome editing tools, organoids can be further engineered to mimic disease-relevant genetic and epigenetic status of a patient...
January 19, 2017: Protein & Cell
https://www.readbyqxmd.com/read/28102350/manipulation-of-auxin-response-factor-19-affects-seed-size-in-the-woody-perennial-jatropha-curcas
#3
Yanwei Sun, Chunming Wang, Ning Wang, Xiyuan Jiang, Huizhu Mao, Changxiang Zhu, Fujiang Wen, Xianghua Wang, Zhijun Lu, Genhua Yue, Zengfu Xu, Jian Ye
Seed size is a major determinant of seed yield but few is known about the genetics controlling of seed size in plants. Phytohormones cytokinin and brassinosteroid were known to be involved in the regulation of herbaceous plant seed development. Here we identified a homolog of Auxin Response Factor 19 (JcARF19) from a woody plant Jatropha curcas and genetically demonstrated its functions in controlling seed size and seed yield. Through Virus Induced Gene Silencing (VIGS), we found that JcARF19 was a positive upstream modulator in auxin signaling and may control plant organ size in J...
January 19, 2017: Scientific Reports
https://www.readbyqxmd.com/read/28102224/optimality-and-sub-optimality-in-a-bacterial-growth-law
#4
Benjamin D Towbin, Yael Korem, Anat Bren, Shany Doron, Rotem Sorek, Uri Alon
Organisms adjust their gene expression to improve fitness in diverse environments. But finding the optimal expression in each environment presents a challenge. We ask how good cells are at finding such optima by studying the control of carbon catabolism genes in Escherichia coli. Bacteria show a growth law: growth rate on different carbon sources declines linearly with the steady-state expression of carbon catabolic genes. We experimentally modulate gene expression to ask if this growth law always maximizes growth rate, as has been suggested by theory...
January 19, 2017: Nature Communications
https://www.readbyqxmd.com/read/28100647/marpodb-an-open-registry-for-marchantia-polymorpha-genetic-parts
#5
Mihails Delmans, Bernardo Pollak, Jim Haseloff
Marchantia polymorpha is an extant relative of the earliest terrestrial plants and has attracted a substantial interest as a model organism for evolutionary and developmental studies. Given its relatively simple genome, compact gene families, simple morphology, ease of propagation and transformation, M. polymorpha is becoming a promising platform for plant synthetic biology. Modular genetic parts have been essential for development of synthetic biology approaches, so we sought to design an engineering oriented database for M...
January 18, 2017: Plant & Cell Physiology
https://www.readbyqxmd.com/read/28100450/a-2-oxoglutarate-dependent-dioxygenase-mediates-the-biosynthesis-of-glucoraphasatin-in-radish
#6
Tomohiro Kakizaki, Hiroyasu Kitashiba, Zhongwei Zou, Feng Li, Nobuko Fukino, Takayoshi Ohara, Takeshi Nishio, Masahiko Ishida
Glucosinolates (GSLs) are secondary metabolites whose degradation products confer intrinsic flavors and aromas to Brassicaceae vegetables. Several structures of GSLs are known in the Brassicaceae, and the biosynthetic pathway and regulatory networks have been elucidated in Arabidopsis thaliana. GSLs are precursors of chemical defense substances against herbivorous pests. Specific GSLs can act as feeding blockers or stimulants, depending on the pest species. Natural selection has led to diversity in the GSL compositions even within individual species...
January 18, 2017: Plant Physiology
https://www.readbyqxmd.com/read/28100080/the-commercialization-of-genome-editing-technologies
#7
Katelyn Brinegar, Ali K Yetisen, Sun Choi, Emily Vallillo, Guillermo U Ruiz-Esparza, Anand M Prabhakar, Ali Khademhosseini, Seok-Hyun Yun
The emergence of new gene-editing technologies is profoundly transforming human therapeutics, agriculture, and industrial biotechnology. Advances in clustered regularly interspaced short palindromic repeats (CRISPR) have created a fertile environment for mass-scale manufacturing of cost-effective products ranging from basic research to translational medicine. In our analyses, we evaluated the patent landscape of gene-editing technologies and found that in comparison to earlier gene-editing techniques, CRISPR has gained significant traction and this has established dominance...
January 18, 2017: Critical Reviews in Biotechnology
https://www.readbyqxmd.com/read/28099196/use-of-engineered-exosomes-expressing-hla-and-costimulatory-molecules-to-generate-antigen-specific-cd8-t-cells-for-adoptive-cell-therapy
#8
Sueon Kim, Hyun-Jung Sohn, Hyun-Joo Lee, Dae-Hee Sohn, Seung-Joo Hyun, Hyun-Il Cho, Tai-Gyu Kim
Dendritic cell-derived exosomes (DEX) comprise an efficient stimulator of T cells. However, the production of sufficient DEX remains a barrier to their broad applicability in immunotherapeutic approaches. In previous studies, genetically engineered K562 have been used to generate artificial antigen presenting cells (AAPC). Here, we isolated exosomes from K562 cells (referred to as CoEX-A2s) engineered to express human leukocyte antigen (HLA)-A2 and costimulatory molecules such as CD80, CD83, and 41BBL. CoEX-A2s were capable of stimulating antigen-specific CD8 T cells both directly and indirectly via CoEX-A2 cross-dressed cells...
January 17, 2017: Journal of Immunotherapy
https://www.readbyqxmd.com/read/28099082/therapeutics-targeting-drivers-of-thoracic-aortic-aneurysms-and-acute-aortic-dissections-insights-from-predisposing-genes-and-mouse-models
#9
Dianna M Milewicz, Siddharth K Prakash, Francesco Ramirez
Thoracic aortic diseases, including aneurysms and dissections of the thoracic aorta, are a major cause of morbidity and mortality. Risk factors for thoracic aortic disease include increased hemodynamic forces on the ascending aorta, typically due to poorly controlled hypertension, and heritable genetic variants. The altered genes predisposing to thoracic aortic disease either disrupt smooth muscle cell (SMC) contraction or adherence to an impaired extracellular matrix, or decrease canonical transforming growth factor beta (TGF-β) signaling...
January 14, 2017: Annual Review of Medicine
https://www.readbyqxmd.com/read/28097384/stress-response-physiology-of-thermophiles
#10
REVIEW
Preeti Ranawat, Seema Rawat
Thermo (or hyperthermo) philic microorganisms are ubiquitous having a wide range of habitats from freshly fallen snow to pasteurized milk to geothermal areas like hot springs. The variations in physicochemical conditions, viz., temperature, pH, nutrient availability and light intensity in the habitats always pose stress conditions for the inhabitants leading to slow growth or cell death. The industrial processes used for harvesting secondary metabolites such as enzymes, toxins and organic acids also create stressed environments for thermophiles...
January 17, 2017: Archives of Microbiology
https://www.readbyqxmd.com/read/28097054/hydrogel-scaffolds-promote-neural-gene-expression-and-structural-reorganization-in-human-astrocyte-cultures
#11
V Bleu Knight, Elba E Serrano
Biomaterial scaffolds have the potential to enhance neuronal development and regeneration. Understanding the genetic responses of astrocytes and neurons to biomaterials could facilitate the development of synthetic environments that enable the specification of neural tissue organization with engineered scaffolds. In this study, we used high throughput transcriptomic and imaging methods to determine the impact of a hydrogel, PuraMatrix™, on human glial cells in vitro. Parallel studies were undertaken with cells grown in a monolayer environment on tissue culture polystyrene...
2017: PeerJ
https://www.readbyqxmd.com/read/28096221/efficient-crispr-cas9-assisted-gene-targeting-enables-rapid-and-precise-genetic-manipulation-of-mammalian-neural-stem-cells
#12
Raul Bardini Bressan, Pooran Singh Dewari, Maria Kalantzaki, Ester Gangoso, Mantas Matjusaitis, Claudia Garcia-Diaz, Carla Blin, Vivien Grant, Harry Bulstrode, Sabine Gogolok, William C Skarnes, Steven M Pollard
Mammalian neural stem (NS) cell lines provide a tractable model for discovery across stem cell and developmental biology, regenerative medicine and neuroscience. They can be derived from foetal or adult germinal tissues and continuously propagated in vitro as adherent monolayers. NS cells are clonally expandable, genetically stable, and easily transfectable - experimental attributes compatible with targeted genetic manipulations. However, gene targeting - so critical for functional studies of embryonic stem cells - has not been exploited to date in NS cells...
January 17, 2017: Development
https://www.readbyqxmd.com/read/28095718/key-players-associated-with-tuberization-in-potato-potential-candidates-for-genetic-engineering
#13
Som Dutt, Anshul Sharma Manjul, Pinky Raigond, Brajesh Singh, Sundaresha Siddappa, Vinay Bhardwaj, Prashant G Kawar, Virupakshagouda U Patil, Hemant Balasaheb Kardile
Tuberization in potato (Solanum tuberosum L.) is a complex biological phenomenon which is affected by several environmental cues, genetic factors and plant nutrition. Understanding the regulation of tuber induction is essential to devise strategies to improve tuber yield and quality. It is well established that short-day photoperiods promote tuberization, whereas long days and high-temperatures inhibit or delay tuberization. Worldwide research on this complex biological process has yielded information on the important bio-molecules (proteins, RNAs, plant growth regulators) associated with the tuberization process in potato...
January 18, 2017: Critical Reviews in Biotechnology
https://www.readbyqxmd.com/read/28095622/talens-and-crispr-cas9-fuel-genetically-engineered-clinically-relevant-xenopus-tropicalis-tumor-models
#14
REVIEW
Thomas Naert, Tom van Nieuwenhuysen, Kris Vleminckx
The targeted nuclease revolution (TALENs, CRISPR/Cas9) now allows Xenopus researchers to rapidly generate custom on-demand genetic knockout models. These novel methods to perform reverse genetics are unprecedented and are fueling a wide array of human disease models within the aquatic diploid model organism Xenopus tropicalis (X. tropicalis). This emerging technology review focuses on the tools to rapidly generate genetically engineered X. tropicalis models (GEXM), with a focus on establishment of genuine genetic and clinically relevant cancer models...
January 17, 2017: Genesis: the Journal of Genetics and Development
https://www.readbyqxmd.com/read/28095489/transgenic-expression-of-the-anti-parasitic-factor-tep1-in-the-malaria-mosquito-anopheles-gambiae
#15
Gloria Volohonsky, Ann-Katrin Hopp, Mélanie Saenger, Julien Soichot, Heidi Scholze, Jens Boch, Stéphanie A Blandin, Eric Marois
Mosquitoes genetically engineered to be resistant to Plasmodium parasites represent a promising novel approach in the fight against malaria. The insect immune system itself is a source of anti-parasitic genes potentially exploitable for transgenic designs. The Anopheles gambiae thioester containing protein 1 (TEP1) is a potent anti-parasitic protein. TEP1 is secreted and circulates in the mosquito hemolymph, where its activated cleaved form binds and eliminates malaria parasites. Here we investigated whether TEP1 can be used to create malaria resistant mosquitoes...
January 2017: PLoS Pathogens
https://www.readbyqxmd.com/read/28095316/rewiring-protein-synthesis-from-natural-to-synthetic-amino-acids
#16
REVIEW
Yongqiang Fan, Christopher R Evans, Jiqiang Ling
BACKGROUND: The protein synthesis machinery uses 22 natural amino acids as building blocks that faithfully decode the genetic information. Such fidelity is controlled at multiple steps and can be compromised in nature and in the laboratory to rewire protein synthesis with natural and synthetic amino acids. SCOPE OF REVIEW: This review summarizes the major quality control mechanisms during protein synthesis, including aminoacyl-tRNA synthetases, elongation factors, and the ribosome...
January 14, 2017: Biochimica et Biophysica Acta
https://www.readbyqxmd.com/read/28094982/bacterial-genome-editing-via-a-designed-toxin-antitoxin-cassette
#17
Jie Wu, Aihua Deng, Qinyun Sun, Hua Bai, Zhaopeng Sun, Xiuling Shang, Yun Zhang, Qian Liu, Yong Liang, Shuwen Liu, Yongsheng Che, Tingyi Wen
Manipulating the bacterial genomes in an efficient manner is essential to biological and biotechnological research. Despite usage of various modules for genomic editing with counter-selectable markers including the toxin genes, an easy-to-use and highly designable toxin-antitoxin (TA) cassette without causing any leakages is urgently needed for efficient genome editing of the Gram-positive bacteria. Here, we reprogramed the bacterial TA systems as a toxin counter-selectable cassette regulated by an antitoxin switch (TCCRAS) for genetic modifications in the extensively studied and utilized Gram-positive bacteria, B...
January 17, 2017: ACS Synthetic Biology
https://www.readbyqxmd.com/read/28094975/endoribonuclease-based-two-component-repressor-systems-for-tight-gene-expression-control-in-plants
#18
Yan Liang, Sarah M Richardson, Jingwei Yan, Veronica T Benites, Clarabelle Cheng-Yue, Thu Tran, Jenny Mortimer, Aindrila Mukhopadhyay, Jay D Keasling, Dominique Loque
Tight control and multifactorial regulation of gene expression are important challenges in genetic engineering and are critical for the development of regulatory circuits. Meeting these challenges will facilitate transgene expression regulation and support fine-tuning of metabolic pathways to avoid the accumulation of undesired intermediates. By employing the endoribonuclease Csy4 and its recognition sequence from Pseudomonas aeruginosa and manipulating 5'UTR of mRNA, we developed a two-component expression-repression system to tightly control synthesis of transgene products...
January 17, 2017: ACS Synthetic Biology
https://www.readbyqxmd.com/read/28094771/orphan-gpr182-suppresses-erk-mediated-intestinal-proliferation-during-regeneration-and-adenoma-formation
#19
Daniel O Kechele, R Eric Blue, Bailey Zwarycz, Scott T Espenschied, Amanda T Mah, Marni B Siegel, Charles M Perou, Shengli Ding, Scott T Magness, P Kay Lund, Kathleen M Caron
Orphan GPCRs provide an opportunity to identify potential pharmacological targets, yet their expression patterns and physiological functions remain challenging to elucidate. Here, we have used a genetically engineered knockin reporter mouse to map the expression pattern of the Gpr182 during development and adulthood. We observed that Gpr182 is expressed at the crypt base throughout the small intestine, where it is enriched in crypt base columnar stem cells, one of the most active stem cell populations in the body...
January 17, 2017: Journal of Clinical Investigation
https://www.readbyqxmd.com/read/28093767/progress-in-modification-of-sunflower-oil-to-expand-its-industrial-value
#20
REVIEW
Saeed Rauf, Nazia Jamil, Sultan Ali Tariq, Maria Khan, Maria Kausar, YalcinKaya
Increasing the sunflower seed oil content as well as improving its quality makes it compatible for industrial demands. This is an important breeding objective of sunflower which increases its market value and ensures high returns for the producers. The present review focuses on determining the progress of improving sunflower seed oil content and modifying its quality by empirical and advanced molecular breeding methods. It is known that the oil content and quality of sunflower oil have been altered through empirical selection methods and mutation breeding programs in various parts of the world...
January 17, 2017: Journal of the Science of Food and Agriculture
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