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https://www.readbyqxmd.com/read/29352615/gene-circuits-for-dynamically-regulating-metabolism
#1
Xiulai Chen, Liming Liu
Gene circuits are a functional innovation in synthetic biology for engineering cellular behavior. Recent advances have demonstrated that gene circuits can be exploited for dynamically controlling pathway redirection and pathway balance to produce valuable chemicals. The next frontier is to engineer robust, sensitive, and efficient circuits that adapt to changing conditions.
January 15, 2018: Trends in Biotechnology
https://www.readbyqxmd.com/read/29351298/construction-of-an-infectious-horsepox-virus-vaccine-from-chemically-synthesized-dna-fragments
#2
Ryan S Noyce, Seth Lederman, David H Evans
Edward Jenner and his contemporaries believed that his variolae vaccinae originated in horses and molecular analyses show that modern vaccinia virus (VACV) strains share common ancestry with horsepox virus (HPXV). Given concerns relating to the toxicity of modern VACV vaccines, we asked whether an HPXV-based vaccine might provide a superior alternative. Since HPXV may be extinct and the only specimen of HPXV that has been identified is unavailable for investigation, we explored whether HPXV could be obtained by large-scale gene synthesis...
2018: PloS One
https://www.readbyqxmd.com/read/29349573/mesencephalic-astrocyte-derived-neurotrophic-factor-manf-elevates-stimulus-evoked-release-of-dopamine-in-freely-moving-rats
#3
Juho-Matti Renko, Susanne Bäck, Merja H Voutilainen, T Petteri Piepponen, Ilkka Reenilä, Mart Saarma, Raimo K Tuominen
Neurotrophic factors (NTFs) hold potential as disease-modifying therapies for neurodegenerative disorders like Parkinson's disease. Glial cell line-derived neurotrophic factor (GDNF), cerebral dopamine neurotrophic factor (CDNF), and mesencephalic astrocyte-derived neurotrophic factor (MANF) have shown neuroprotective and restorative effects on nigral dopaminergic neurons in various animal models of Parkinson's disease. To date, however, their effects on brain neurochemistry have not been compared using in vivo microdialysis...
January 18, 2018: Molecular Neurobiology
https://www.readbyqxmd.com/read/29348803/synthesis-of-a-chloroalkene-dipeptide-isostere-containing-peptidomimetic-and-its-biological-application
#4
Takuya Kobayakawa, Yudai Matsuzaki, Kentaro Hozumi, Wataru Nomura, Motoyoshi Nomizu, Hirokazu Tamamura
The first rapid and efficient chemical synthesis of a cyclic Arg-Gly-Asp (RGD) peptide containing a chloroalkene dipeptide isostere (CADI) is reported. By a developed synthetic method, an N-tert-butylsulfonyl protected CADI was obtained utilizing diastereoselective allylic alkylation as a key reaction. This CADI was also transformed into an N-Fmoc protected CADI in a few steps. The CADI was used in Fmoc-based solid-phase peptide synthesis. The first synthesis of a CADI-containing cyclic RGD peptide was successful, and the synthesized CADI-containing peptidomimetic was found to be a more potent inhibitor against integrin-mediated cell attachment than the parent cyclic peptide...
January 11, 2018: ACS Medicinal Chemistry Letters
https://www.readbyqxmd.com/read/29347205/inferring-network-structure-from-cascades
#5
Sushrut Ghonge, Dervis Can Vural
Many physical, biological, and social phenomena can be described by cascades taking place on a network. Often, the activity can be empirically observed, but not the underlying network of interactions. In this paper we offer three topological methods to infer the structure of any directed network given a set of cascade arrival times. Our formulas hold for a very general class of models where the activation probability of a node is a generic function of its degree and the number of its active neighbors. We report high success rates for synthetic and real networks, for several different cascade models...
July 2017: Physical Review. E
https://www.readbyqxmd.com/read/29347182/propulsion-via-flexible-flapping-in-granular-media
#6
Zhiwei Peng, Yang Ding, Kyle Pietrzyk, Gwynn J Elfring, On Shun Pak
Biological locomotion in nature is often achieved by the interaction between a flexible body and its surrounding medium. The interaction of a flexible body with granular media is less understood compared with viscous fluids partially due to its complex rheological properties. In this work, we explore the effect of flexibility on granular propulsion by considering a simple mechanical model in which a rigid rod is connected to a torsional spring that is under a displacement actuation using a granular resistive force theory...
July 2017: Physical Review. E
https://www.readbyqxmd.com/read/29346868/effective-one-dimensional-approach-to-the-source-reconstruction-problem-of-three-dimensional-inverse-optoacoustics
#7
J Stritzel, O Melchert, M Wollweber, B Roth
The direct problem of optoacoustic signal generation in biological media consists of solving an inhomogeneous three-dimensional (3D) wave equation for an initial acoustic stress profile. In contrast, the more defiant inverse problem requires the reconstruction of the initial stress profile from a proper set of observed signals. In this article, we consider an effectively 1D approach, based on the assumption of a Gaussian transverse irradiation source profile and plane acoustic waves, in which the effects of acoustic diffraction are described in terms of a linear integral equation...
September 2017: Physical Review. E
https://www.readbyqxmd.com/read/29346730/2d-spectroscopy-is-being-used-to-address-core-scientific-questions-in-biology-and-materials-science
#8
Megan Petti, Justin P Lomont, Michał Maj, Martin T Zanni
Two-dimensional spectroscopy is a powerful tool for extracting structural and dynamic information from a wide range of chemical systems. We provide a brief overview of the ways in which two-dimensional visible and infrared spectroscopies are being applied to elucidate fundamental details of important processes in biological and materials science. The topics covered include amyloid proteins, photo-synthetic complexes, ion channels, photovoltaics, batteries, as well as a variety of promising new methods in two-dimensional spectroscopy...
January 18, 2018: Journal of Physical Chemistry. B
https://www.readbyqxmd.com/read/29346683/strigolactones-mediators-of-osmotic-stress-responses-with-a-potential-for-agrochemical-manipulation-of-crop-resilience
#9
Francesca Cardinale, Paolo Korwin Krukowski, Andrea Schubert, Ivan Visentin
After quickly touching upon general aspects of strigolactones biology and functions, including structure, synthesis and perception, this review focuses on the role and regulation of the strigolactone pathway during osmotic stress, in light of the most recent research developments. We discuss available data on organ-specific dynamics of strigolactone synthesis and interaction with abscisic acid in the acclimatization response, with emphasis on the ecophysiological implications of the effects on the stomatal closure process...
January 15, 2018: Journal of Experimental Botany
https://www.readbyqxmd.com/read/29346617/riboswitching-with-ciprofloxacin-development-and-characterization-of-a-novel-rna-regulator
#10
Florian Groher, Cristina Bofill-Bosch, Christopher Schneider, Johannes Braun, Sven Jager, Katharina Geißler, Kay Hamacher, Beatrix Suess
RNA molecules play important and diverse regulatory roles in the cell. Inspired by this natural versatility, RNA devices are increasingly important for many synthetic biology applications, e.g. optimizing engineered metabolic pathways, gene therapeutics or building up complex logical units. A major advantage of RNA is the possibility of de novo design of RNA-based sensing domains via an in vitro selection process (SELEX). Here, we describe development of a novel ciprofloxacin-responsive riboswitch by in vitro selection and next-generation sequencing-guided cellular screening...
January 13, 2018: Nucleic Acids Research
https://www.readbyqxmd.com/read/29346275/a-review-on-recent-advances-in-stabilizing-peptides-proteins-upon-fabrication-in-hydrogels-from-biodegradable-polymers
#11
REVIEW
Faisal Raza, Hajra Zafar, Ying Zhu, Yuan Ren, Aftab -Ullah, Asif Ullah Khan, Xinyi He, Han Han, Md Aquib, Kofi Oti Boakye-Yiadom, Liang Ge
Hydrogels evolved as an outstanding carrier material for local and controlled drug delivery that tend to overcome the shortcomings of old conventional dosage forms for small drugs (NSAIDS) and large peptides and proteins. The aqueous swellable and crosslinked polymeric network structure of hydrogels is composed of various natural, synthetic and semisynthetic biodegradable polymers. Hydrogels have remarkable properties of functionality, reversibility, sterilizability, and biocompatibility. All these dynamic properties of hydrogels have increased the interest in their use as a carrier for peptides and proteins to be released slowly in a sustained manner...
January 18, 2018: Pharmaceutics
https://www.readbyqxmd.com/read/29345976/synthetic-biology-immunotherapy-by-design
#12
Matthew J Brenner, Jang Hwan Cho, Nicole M L Wong, Wilson W Wong
Cellular immunotherapy holds great promise for the treatment of human disease. Clinical evidence suggests that T cell immunotherapies have the potential to combat cancers that evade traditional immunotherapy. Despite promising results, adverse effects leading to fatalities have left scientists seeking tighter control over these therapies, which is reflected in the growing body of synthetic biology literature focused on developing tightly controlled, context-independent parts. In addition, researchers are adapting these tools for other uses, such as for the treatment of autoimmune disease, HIV infection, and fungal interactions...
January 18, 2018: Annual Review of Biomedical Engineering
https://www.readbyqxmd.com/read/29345470/a-bioinspired-cascade-sequence-enables-facile-assembly-of-methanodibenzo-b-f-1-5-dioxocin-flavonoid-scaffold
#13
Hongxin Liu, Yu Wang, Xueying Guo, Luqiong Huo, Zhifang Xu, Weimin Zhang, Shengxiang Qiu, Bao Yang, Haibo Tan
A remarkable bioinspired EDDA-mediated method for the selective construction of biologically interesting and highly strained bridged methanodibenzo[b,f][1,5]dioxocin flavonoid scaffold was uncovered by starting from a variety of readily available acylphloroglucinol and 2-hydroxycinnamaldehyde substrates. This method merges a fascinating olefin isomerization/hemiacetallization/dehydration/[3 + 3]-type cycloaddition cascade reaction driven by an in situ generated chromenylium intermediate and provides a convenient and viable synthetic strategy for the efficient access of such flavonoid analogues...
January 18, 2018: Organic Letters
https://www.readbyqxmd.com/read/29345081/screening-for-latent-tuberculosis-infection-among-patients-with-rheumatoid-arthritis-in-the-era-of-biologics-and-targeted-synthetic-disease-modifying-anti-rheumatic-drugs-in-india-a-high-burden-tb-country-the-importance-of-mantoux-and-quantiferon-tb-gold-tests
#14
Anand N Malaviya, Vishal K Aggarwal, Roopa Rawat, Sadhana Baghel, Ravita Thakran, Qamar Zaheer, Shriram Garg, Sanjiv Kapoor
AIM: To test the validity of an augmented tuberculosis skin test (a-TST) combined with Quantiferon TB-gold® (QFTG) test for the screening of latent tuberculosis infection (LTBI) in patients with rheumatoid arthritis (RA) being considered for treatment with biologic disease-modifying anti-rheumatic drugs or targeted synthetic disease-modifying anti-rheumatic drugs. METHOD: Standard TST using 1 tuberculin unit (TU) of purified protein derivative (PPD, RT23 strain) was carried out...
January 17, 2018: International Journal of Rheumatic Diseases
https://www.readbyqxmd.com/read/29344916/the-acute-effects-of-erythromycin-and-oxytetracycline-on-enhanced-biological-phosphorus-removal-system-shift-in-bacterial-community-structure
#15
Zhetai Hu, Peide Sun, Jingyi Han, Ruyi Wang, Liang Jiao, Pengfei Yang, Jing Cai
Since extensive application, an increasing amount of antibiotics has been released into wastewater treatment plants. In this study, the enhanced biological phosphorus removal (EBPR) system was fed with synthetic wastewater containing erythromycin (ERY) and oxytetracycline (OTC) for 7 days to evaluate the variations of solution ortho-P (SOP), volatile fatty acid (VFA), poly-bhydroxyalkanoates (PHAs), specific oxygen uptake rater (SOUR), and microbial community in the EBPR system. The obtained results showed that the P-removal efficiency decreased to 0...
January 18, 2018: Environmental Science and Pollution Research International
https://www.readbyqxmd.com/read/29344593/biologically-inspired-oxidation-catalysis-using-metallopeptides
#16
Laia Vicens, Miquel Costas
The stereoselective oxidation of hydrocarbons is one of the most challenging reactions for synthetic chemists. However, this transformation is one of the most common reactions in nature. Metalloenzymes that catalyze this transformation are taken as inspiration for the development of new catalysts. There are several examples in the literature where either peptides or metal catalysts are used in the stereoselective oxidation reaction, but the synergistic combination of both systems is still a non-explored field...
January 18, 2018: Dalton Transactions: An International Journal of Inorganic Chemistry
https://www.readbyqxmd.com/read/29343759/incorporation-of-iloprost-in-phospholipase-resistant-phospholipid-scaffold-enhances-its-barrier-protective-effects-on-pulmonary-endothelium
#17
Olga Oskolkova, Nicolene Sarich, Yufeng Tian, Grzegorz Gawlak, Fanyong Meng, Valery N Bochkov, Evgeny Berdyshev, Anna A Birukova, Konstantin G Birukov
Correction of barrier dysfunction and inflammation in acute lung injury (ALI) represents an important problem. Previous studies demonstrate barrier-protective and anti-inflammatory effects of bioactive lipid prostacyclin and its stable analog iloprost (ILO). We generated a phospholipase resistant synthetic phospholipid with iloprost attached at the sn-2 position (ILO-PC) and investigated its biological effects. In comparison to free ILO, ILO-PC caused sustained endothelial cell (EC) barrier enhancement, linked to more prolonged activation of Rap1 and Rac1 GTPases and their cytoskeletal and cell junction effectors: cortactin, PAK1, p120-catenin and VE-cadherin...
January 17, 2018: Scientific Reports
https://www.readbyqxmd.com/read/29343191/thermophilic-xylanases-from-bench-to-bottle
#18
Abdul Basit, Junquan Liu, Kashif Rahim, Wei Jiang, Huiqiang Lou
Lignocellulosic biomass is a valuable raw material. As technology has evolved, industrial interest in new ways to take advantage of this raw material has grown. Biomass is treated with different microbial cells or enzymes under ideal industrial conditions to produce the desired products. Xylanases are the key enzymes that degrade the xylosidic linkages in the xylan backbone of the biomass, and commercial enzymes are categorized into different glycoside hydrolase families. Thermophilic microorganisms are excellent sources of industrially relevant thermostable enzymes that can withstand the harsh conditions of industrial processing...
January 17, 2018: Critical Reviews in Biotechnology
https://www.readbyqxmd.com/read/29343065/perfect-adaptation-and-optimal-equilibrium-productivity-in-a-simple-microbial-biofuel-metabolic-pathway-using-dynamic-integral-control
#19
Corentin Briat, Mustafa H Khammash
The production of complex biomolecules by genetically engineered organisms is one of the most promising applications of metabolic engineering and synthetic biology. To obtain processes with high productivity, it is therefore crucial to design and implement efficient dynamic in-vivo regulation strategies. We consider here the microbial biofuel production model of Dunlop et al. (2010) for which we demonstrate that an antithetic dynamic integral control strategy can achieve robust perfect adaptation for the intracellular biofuel concentration in presence of poorly known network parameters and implementation errors in certain rate parameters of the controller...
January 17, 2018: ACS Synthetic Biology
https://www.readbyqxmd.com/read/29341603/pokmt1-from-the-polyketomycin-biosynthetic-machinery-of-streptomyces-diastatochromogenes-t%C3%A3-6028-belongs-to-the-emerging-family-of-c-methyltransferases-that-act-on-coa-activated-aromatic-substrates
#20
Xun Guo, Ivana Crnovcic, Chin-Yuan Chang, Jun Luo, Jeremy R Lohman, Monica Papinski, Andreas Bechthold, Geoffrey P Horsman, Ben Shen
Recent biochemical characterizations of the MdpB2 CoA ligase and MdpB1 C-methyltransferase (C-MT) from the maduropeptin (MDP, 2) biosynthetic machinery revealed unusual pathway logic involving C-methylation occurring on a CoA-activated aromatic substrate. Here we confirmed this pathway logic for the biosynthesis of polyketomycin (POK, 3). Biochemical characterization unambiguously established that PokM3 and PokMT1 catalyze the sequential conversion of 6-methylsalicylic acid (6-MSA, 4) to form 3,6-dimethylsalicylyl-CoA (3,6-DMSA-CoA, 6), which serves as the direct precursor for the 3,6-dimethylsalicylic acid (3,6-DMSA) moiety in the biosynthesis of 3...
January 17, 2018: Biochemistry
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