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Nutrient genetic engineer

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https://www.readbyqxmd.com/read/28813680/antibiotics-disrupt-coordination-between-transcriptional-and-phenotypic-stress-responses-in-pathogenic-bacteria
#1
Paul A Jensen, Zeyu Zhu, Tim van Opijnen
Bacterial genes that change in expression upon environmental disturbance have commonly been seen as those that must also phenotypically matter. However, several studies suggest that differentially expressed genes are rarely phenotypically important. We demonstrate, for Gram-positive and Gram-negative bacteria, that these seemingly uncoordinated gene sets are involved in responses that can be linked through topological network analysis. However, the level of coordination is stress dependent. While a well-coordinated response is triggered in response to nutrient stress, antibiotics trigger an uncoordinated response in which transcriptionally and phenotypically important genes are neither linked spatially nor in their magnitude...
August 15, 2017: Cell Reports
https://www.readbyqxmd.com/read/28812299/conversion-of-the-high-yield-salinomycin-producer-streptomyces-albus-bk3-25-into-a-surrogate-host-for-polyketide-production
#2
Xiaojie Zhang, Chenyang Lu, Linquan Bai
An ideal surrogate host for heterologous production of various natural products is expected to have efficient nutrient utilization, fast growth, abundant precursors and energy supply, and a pronounced gene expression. Streptomyces albus BK3-25 is a high-yield industrial strain producing type-I polyketide salinomycin, with a unique ability of bean oil utilization. Its potential of being a surrogate host for heterologous production of PKS was engineered and evaluated herein. Firstly, introduction of a three-gene cassette for the biosynthesis of ethylmalonyl-CoA resulted in accumulation of ethylmalonyl-CoA precursor and salinomycin, and subsequent deletion of the salinomycin biosynthetic gene cluster resulted in a host with rich supplies of common polyketide precursors, including malonyl-CoA, methylmalonyl-CoA, and ethylmalonyl-CoA...
August 14, 2017: Science China. Life Sciences
https://www.readbyqxmd.com/read/28739822/stress-responsive-hilpda-is-necessary-for-thermoregulation-during-fasting
#3
Matthew J VandeKopple, Jinghai Wu, Lisa A Baer, Naresh C Bal, Santosh K Maurya, Anuradha Kalyanasundaram, Muthu Periasamy, Kristin I Stanford, Amato Giaccia, Nicholas Denko, Ioanna Papandreou
Hypoxia-Inducible Lipid-Droplet Associated protein (HILPDA) has been shown to localize to lipid droplets in nutrient responsive cell types such as hepatocytes and adipocytes. However, its role in the control of whole-body homeostasis is not known. We sought to measure cell-intrinsic and systemic stress responses in a mouse strain harboring whole body Hilpda deficiency. We generated a genetically engineered mouse model of whole body HILPDA deficiency by replacing the coding HILPDA exon with Luciferase. We subjected the knockout animals to environmental stresses and measured whole-animal metabolic and behavioral parameters...
July 24, 2017: Journal of Endocrinology
https://www.readbyqxmd.com/read/28718632/systematic-approaches-to-efficiently-produce-2-3-butanediol-in-a-marine-cyanobacterium
#4
Nicole E Nozzi, Anna E Case, Austin L Carroll, Shota Atsumi
Cyanobacteria have attracted significant interest as a platform for renewable production of fuel and feedstock chemicals from abundant atmospheric carbon dioxide by way of photosynthesis. While great strides have been made in developing this technology in freshwater cyanobacteria, logistical issues remain in scale-up. Use of the cyanobacterium Synechococcus sp. PCC 7002 (7002) as a chemical production chassis could address a number of these issues given the higher tolerance to salt, light, and heat as well as the fast growth rate of 7002 in comparison to traditional model cyanobacteria such as Synechococcus elongatus PCC 7942 and Synechocystis sp...
August 3, 2017: ACS Synthetic Biology
https://www.readbyqxmd.com/read/28717018/structure-and-properties-of-oil-bodies-in-diatoms
#5
REVIEW
Yoshiaki Maeda, Daisuke Nojima, Tomoko Yoshino, Tsuyoshi Tanaka
Diatoms accumulate triacylglycerols in spherical organelles called oil bodies when exposed to nutrient deprivation conditions. Oil body biology in diatoms has attracted significant attention due to the complexity of the intracellular organelles and the unique combination of genes generated by the evolutionary history of secondary endosymbiosis. The demand for biofuel production has further increased the interest in and importance of a better understanding of oil body biology in diatoms, because it could provide targets for genetic engineering to further enhance their promising lipid accumulation...
September 5, 2017: Philosophical Transactions of the Royal Society of London. Series B, Biological Sciences
https://www.readbyqxmd.com/read/28696049/increased-nutritional-value-in-food-crops
#6
Nieves Goicoechea, M Carmen Antolín
Modern agriculture and horticulture must combine two objectives that seem to be almost mutually exclusive: to satisfy the nutritional needs of an increasing human population and to minimize the negative impact on the environment. These two objectives are included in the Goal 2 of the 2030 Agenda for Sustainable Development of the United Nations: 'End hunger, achieve food security and improved nutrition and promote sustainable agriculture'. Enhancing the nutritional levels of vegetables would improve nutrient intake without requiring an increase in consumption...
July 11, 2017: Microbial Biotechnology
https://www.readbyqxmd.com/read/28636663/an-endophytic-basidiomycete-grammothele-lineata-isolated-from-corchorus-olitorius-produces-paclitaxel-that-shows-cytotoxicity
#7
Avizit Das, Mohammad Imtiazur Rahman, Ahlan Sabah Ferdous, Al- Amin, Mohammad Mahbubur Rahman, Nilufar Nahar, Md Aftab Uddin, Mohammad Riazul Islam, Haseena Khan
Grammothele lineata, an endophyte isolated in our laboratory from jute (Corchorus olitorius acc. 2015) was found to be a substantial paclitaxel producer. Taxol and its related compounds, produced by this endophyte were extracted by growing the fungus in simple nutrient media (potato dextrose broth, PDB). Taxol was identified and characterized by different analytical techniques (TLC, HPLC, FTIR, LC-ESI-MS/MS) following its extraction by ethyl acetate. In PDB media, this fungus was found to produce 382.2 μgL-1 of taxol which is about 7...
2017: PloS One
https://www.readbyqxmd.com/read/28628130/lipid-production-in-nannochloropsis-gaditana-is-doubled-by-decreasing-expression-of-a-single-transcriptional-regulator
#8
Imad Ajjawi, John Verruto, Moena Aqui, Leah B Soriaga, Jennifer Coppersmith, Kathleen Kwok, Luke Peach, Elizabeth Orchard, Ryan Kalb, Weidong Xu, Tom J Carlson, Kristie Francis, Katie Konigsfeld, Judit Bartalis, Andrew Schultz, William Lambert, Ariel S Schwartz, Robert Brown, Eric R Moellering
Lipid production in the industrial microalga Nannochloropsis gaditana exceeds that of model algal species and can be maximized by nutrient starvation in batch culture. However, starvation halts growth, thereby decreasing productivity. Efforts to engineer N. gaditana strains that can accumulate biomass and overproduce lipids have previously met with little success. We identified 20 transcription factors as putative negative regulators of lipid production by using RNA-seq analysis of N. gaditana during nitrogen deprivation...
July 2017: Nature Biotechnology
https://www.readbyqxmd.com/read/28582605/an-enzyme-coated-metal-organic-framework-shell-for-synthetically-adaptive-cell-survival
#9
Kang Liang, Joseph J Richardson, Christian J Doonan, Xavier Mulet, Yi Ju, Jiwei Cui, Frank Caruso, Paolo Falcaro
A bioactive synthetic porous shell was engineered to enable cells to survive in an oligotrophic environment. Eukaryotic cells (yeast) were firstly coated with a β-galactosidase (β-gal), before crystallization of a metal-organic framework (MOF) film on the enzyme coating; thereby producing a bioactive porous synthetic shell. The β-gal was an essential component of the bioactive shell as it generated nutrients (that is, glucose and galactose) required for cell viability in nutrient-deficient media (lactose-based)...
June 5, 2017: Angewandte Chemie
https://www.readbyqxmd.com/read/28576763/phylogenetic-and-functional-diversity-of-total-dna-and-expressed-rna-bacterial-communities-in-urban-green-infrastructure-bioswale-soils
#10
Aman S Gill, Angela Lee, Krista L McGuire
New York City (NYC) is pioneering green infrastructure with the use of bioswales and other engineered soil-based habitats to provide stormwater infiltration and other ecosystem functions. In addition to avoiding the environmental and financial costs of expanding traditional built infrastructure, green infrastructure is thought to generate cobenefits in the form of diverse ecological processes performed by its plant and microbial communities. Yet, although plant communities in these habitats are closely managed, we lack basic knowledge about how engineered ecosystems impact the distribution and functioning of soil bacteria...
August 15, 2017: Applied and Environmental Microbiology
https://www.readbyqxmd.com/read/28570535/visualization-and-quantitative-analysis-of-embryonic-angiogenesis-in-xenopus-tropicalis
#11
Jiyeon Ohk, Hosung Jung
Blood vessels supply oxygen and nutrients throughout the body, and the formation of the vascular network is under tight developmental control. The efficient in vivo visualization of blood vessels and the reliable quantification of their complexity are key to understanding the biology and disease of the vascular network. Here, we provide a detailed method to visualize blood vessels with a commercially available fluorescent dye, human plasma acetylated low density lipoprotein DiI complex (DiI-AcLDL), and to quantify their complexity in Xenopus tropicalis...
May 25, 2017: Journal of Visualized Experiments: JoVE
https://www.readbyqxmd.com/read/28526796/sulfide-induced-dissimilatory-nitrate-reduction-to-ammonium-supports-anammox-in-an-open-water-unit-process-wetland
#12
Zackary L Jones, Justin T Jasper, David L Sedlak, Jonathan O Sharp
Open-water unit process wetlands host a benthic diatomaceous and bacterial assemblage capable of nitrate removal from treated municipal wastewater with unexpected contributions from anammox processes. In exploring mechanistic drivers of anammox, 16S rRNA gene sequencing profiles of the biomat revealed significant microbial community shifts along the flow path and with depth. Notably there was an increasing abundance of sulfate reducers (Desulfococcus and other Deltaproteobacteria) and anammox microorganisms (Brocadiaceae) with depth...
May 19, 2017: Applied and Environmental Microbiology
https://www.readbyqxmd.com/read/28483713/safety-assessment-of-astaxanthin-derived-from-engineered-escherichia-coli-k-12-using-a-13-week-repeated-dose-oral-toxicity-study-and-a-prenatal-developmental-toxicity-study-in-rats
#13
Yin-Ju Lin, Jian-Yu Lin, Di-Sheng Wang, Chien-Hao Chen, Ming-Hsi Chiou
Astaxanthin is a natural carotenoid with strong antioxidant activity that has been used for decades as a nutrient/color additive and it has recently been marketed as a health supplement. Astaxanthin can be synthesized in a wide range of microalgae, yeast, and bacteria. As genes directing astaxanthin biosynthesis in various organisms have been cloned, this study assessed the safety of astaxanthin crystal produced by Escherichia coli K-12 harboring plasmids carrying astaxanthin biosynthetic genes. The astaxanthin crystal contains a total carotenoid content of 950 mg/g and an astaxanthin content of 795 mg/g...
May 5, 2017: Regulatory Toxicology and Pharmacology: RTP
https://www.readbyqxmd.com/read/28431252/engineered-regulatory-systems-modulate-gene-expression-of-human-commensals-in-the-gut
#14
Bentley Lim, Michael Zimmermann, Natasha A Barry, Andrew L Goodman
The gut microbiota is implicated in numerous aspects of health and disease, but dissecting these connections is challenging because genetic tools for gut anaerobes are limited. Inducible promoters are particularly valuable tools because these platforms allow real-time analysis of the contribution of microbiome gene products to community assembly, host physiology, and disease. We developed a panel of tunable expression platforms for the prominent genus Bacteroides in which gene expression is controlled by a synthetic inducer...
April 20, 2017: Cell
https://www.readbyqxmd.com/read/28235716/genomic-dissection-of-host-microbe-and-microbe-microbe-interactions-for-advanced-plant-breeding
#15
REVIEW
Samuel Kroll, Matthew T Agler, Eric Kemen
Agriculture faces many emerging challenges to sustainability, including limited nutrient resources, losses from diseases caused by current and emerging pathogens and environmental degradation. Microorganisms have great importance for plant growth and performance, including the potential to increase yields, nutrient uptake and pathogen resistance. An urgent need is therefore to understand and engineer plants and their associated microbial communities. Recent massive genomic sequencing of host plants and associated microbes offers resources to identify novel mechanisms of communal assembly mediated by the host...
February 21, 2017: Current Opinion in Plant Biology
https://www.readbyqxmd.com/read/28202725/stretchable-living-materials-and-devices-with-hydrogel-elastomer-hybrids-hosting-programmed-cells
#16
Xinyue Liu, Tzu-Chieh Tang, Eléonore Tham, Hyunwoo Yuk, Shaoting Lin, Timothy K Lu, Xuanhe Zhao
Living systems, such as bacteria, yeasts, and mammalian cells, can be genetically programmed with synthetic circuits that execute sensing, computing, memory, and response functions. Integrating these functional living components into materials and devices will provide powerful tools for scientific research and enable new technological applications. However, it has been a grand challenge to maintain the viability, functionality, and safety of living components in freestanding materials and devices, which frequently undergo deformations during applications...
February 28, 2017: Proceedings of the National Academy of Sciences of the United States of America
https://www.readbyqxmd.com/read/28097384/stress-response-physiology-of-thermophiles
#17
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...
April 2017: Archives of Microbiology
https://www.readbyqxmd.com/read/27965695/integration-of-plant-defense-traits-with-biological-control-of-arthropod-pests-challenges-and-opportunities
#18
REVIEW
Julie A Peterson, Paul J Ode, Camila Oliveira-Hofman, James D Harwood
Crop plants exhibit a wide diversity of defensive traits and strategies to protect themselves from damage by herbivorous pests and disease. These defensive traits may be naturally occurring or artificially selected through crop breeding, including introduction via genetic engineering. While these traits can have obvious and direct impacts on herbivorous pests, many have profound effects on higher trophic levels, including the natural enemies of herbivores. Multi-trophic effects of host plant resistance have the potential to influence, both positively and negatively, biological control...
2016: Frontiers in Plant Science
https://www.readbyqxmd.com/read/27965362/transport-and-homeostasis-of-potassium-and-phosphate-limiting-factors-for-sustainable-crop-production
#19
REVIEW
Mingda Luan, Ren-Jie Tang, Yumei Tang, Wang Tian, Congong Hou, Fugeng Zhao, Wenzhi Lan, Sheng Luan
Potassium (K) and phosphate (Pi) are both macronutrients essential for plant growth and crop production, but the unrenewable resources of phosphorus rock and potash have become limiting factors for food security. One critical measure to help solve this problem is to improve nutrient use efficiency (NUE) in plants by understanding and engineering genetic networks for ion uptake, translocation, and storage. Plants have evolved multiple systems to adapt to various nutrient conditions for growth and production...
December 12, 2016: Journal of Experimental Botany
https://www.readbyqxmd.com/read/27898053/microbial-mutualism-dynamics-governed-by-dose-dependent-toxicity-of-cross-fed-nutrients
#20
Breah LaSarre, Alexandra L McCully, Jay T Lennon, James B McKinlay
Microbial interactions, including mutualistic nutrient exchange (cross-feeding), underpin the flow of energy and materials in all ecosystems. Metabolic exchanges are difficult to assess within natural systems. As such, the impact of exchange levels on ecosystem dynamics and function remains unclear. To assess how cross-feeding levels govern mutualism behavior, we developed a bacterial coculture amenable to both modeling and experimental manipulation. In this coculture, which resembles an anaerobic food web, fermentative Escherichia coli and photoheterotrophic Rhodopseudomonas palustris obligately cross-feed carbon (organic acids) and nitrogen (ammonium)...
February 2017: ISME Journal
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