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Systems chemistry

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https://www.readbyqxmd.com/read/29776931/shuffling-the-neutral-drift-of-unspecific-peroxygenase-in-saccharomyces-cerevisiae
#1
Javier Martin-Diaz, Carmen Paret, Eva García-Ruiz, Patricia Molina-Espeja, Miguel Alcalde
Unspecific peroxygenase (UPO) is a highly promiscuous biocatalyst and its selective mono(per)oxygenase activity makes it useful for many synthetic chemistry applications. Among the broad repertory of library creation methods for directed enzyme evolution, genetic drift allows neutral mutations to be accumulated gradually within a polymorphic network of variants. In this study, we conducted a campaign of genetic drift with UPO in Saccharomyces cerevisiae so that neutral mutations were simply added and recombined in vivo With low mutational loading and an activity threshold of 45% of the parent's native function, mutant libraries enriched in folded and active UPO variants were generated...
May 18, 2018: Applied and Environmental Microbiology
https://www.readbyqxmd.com/read/29775595/the-neuropeptide-tac2-controls-a-distributed-brain-state-induced-by-chronic-social-isolation-stress
#2
Moriel Zelikowsky, May Hui, Tomomi Karigo, Andrea Choe, Bin Yang, Mario R Blanco, Keith Beadle, Viviana Gradinaru, Benjamin E Deverman, David J Anderson
Chronic social isolation causes severe psychological effects in humans, but their neural bases remain poorly understood. 2 weeks (but not 24 hr) of social isolation stress (SIS) caused multiple behavioral changes in mice and induced brain-wide upregulation of the neuropeptide tachykinin 2 (Tac2)/neurokinin B (NkB). Systemic administration of an Nk3R antagonist prevented virtually all of the behavioral effects of chronic SIS. Conversely, enhancing NkB expression and release phenocopied SIS in group-housed mice, promoting aggression and converting stimulus-locked defensive behaviors to persistent responses...
May 17, 2018: Cell
https://www.readbyqxmd.com/read/29774075/plectin-targeted-liposomes-enhance-the-therapeutic-efficacy-of-a-parp-inhibitor-in-the-treatment-of-ovarian-cancer
#3
Siva Sai Krishna Dasa, Galina Diakova, Ryo Suzuki, Anne M Mills, Michael F Gutknecht, Alexander L Klibanov, Jill K Slack-Davis, Kimberly A Kelly
Advances in genomics and proteomics drive precision medicine by providing actionable genetic alterations and molecularly targeted therapies, respectively. While genomic analysis and medicinal chemistry have advanced patient stratification with treatments tailored to the genetic profile of a patient's tumor, proteomic targeting has the potential to enhance the therapeutic index of drugs like poly(ADP-ribose) polymerase (PARP) inhibitors. PARP inhibitors in breast and ovarian cancer patients with BRCA1/2 mutations have shown promise...
2018: Theranostics
https://www.readbyqxmd.com/read/29773227/de1sign-of-synthetic-extracellular-matrices-for-probing-breast-cancer-cell-growth-using-robust-cyctocompatible-nucleophilic-thiol-yne-addition-chemistry
#4
Laura J Macdougall, Katherine L Wiley, April M Kloxin, Andrew P Dove
Controlled, three-dimensional (3D) cell culture systems are of growing interest for both tissue regeneration and disease, including cancer, enabling hypothesis testing about the effects of microenvironment cues on a variety of cellular processes, including aspects of disease progression. In this work, we encapsulate and culture in three dimensions different cancer cell lines in a synthetic extracellular matrix (ECM), using mild and efficient chemistry. Specifically, harnessing the nucleophilic addition of thiols to activated alkynes, we have created hydrogel-based materials with multifunctional poly(ethylene glycol) (PEG) and select biomimetic peptides...
May 7, 2018: Biomaterials
https://www.readbyqxmd.com/read/29771502/atmospheric-co2-enrichment-and-reactive-nitrogen-inputs-interactively-stimulate-soil-cation-losses-and-acidification
#5
Li Zhang, Yunpeng Qiu, Lei Cheng, Yi Wang, Lingli Liu, Cong Tu, Dan C Bowman, Kent O Burkey, Xinmin Bian, Weijian Zhang, Shuijin Hu
Reactive N inputs (Nr) may alleviate N-limitation of plant growth and are assumed to help sustain plant responses to the rising atmospheric CO2 (eCO2). However, Nr and eCO2 may elicit a cascade reaction that alters soil chemistry and nutrient availability, shifting the limiting factors of plant growth, particularly in acidic tropical and subtropical croplands with low organic matter and low nutrient cations. Yet, few have so far examined the interactive effects of Nr and eCO2 on the dynamics of soil cation nutrients and soil acidity...
May 17, 2018: Environmental Science & Technology
https://www.readbyqxmd.com/read/29771317/exon-skipping-advances-for-duchenne-muscular-dystrophy
#6
Lucía Echevarría, Philippine Aupy, Aurélie Goyenvalle
Duchenne muscular dystrophy (DMD) is a fatal genetic disorder characterized by progressive muscle wasting that has currently no cure. Exon-skipping strategy represents one of the most promising therapeutic approaches that aims to restore expression of a shorter but functional dystrophin protein. The antisense field has remarkably progress over the last years with recent accelerated approval of the first ASO-based therapy for DMD, Exondys 51, though the therapeutic benefit remains to be proven in patients. Despite clinical advances, the poor effective delivery to target all muscle remains the main hurdle for antisense drug therapy...
May 16, 2018: Human Molecular Genetics
https://www.readbyqxmd.com/read/29768999/essentials-and-perspectives-of-computational-modelling-assistance-for-cns-oriented-nanoparticle-based-drug-delivery-systems
#7
Joanna Kisała, Kinga I Heclik, Krzysztof Pogocki, Dariusz Pogocki
The blood-brain barrier (BBB) is a complex system controlling two-way substances traffic between circulatory (cardiovascular) system and central nervous system (CNS). It is almost perfectly crafted to regulate brain homeostasis and to permit selective transport of molecules that are essential for brain function. For potential drug candidates, the CNS-oriented neuropharmaceuticals as well as for those of primary targets in the periphery, the extent to which a substance in the circulation gains access to the CNS seems crucial...
May 16, 2018: Current Medicinal Chemistry
https://www.readbyqxmd.com/read/29768570/removal-of-synthetic-sex-hormones-by-hydrothermal-carbonization
#8
Ruiter L Morais, Mariângela F Santiago, Joachim W Zang, Warde A Fonseca-Zang, Fernando Schimidt
One of the most prominent fields of environmental chemistry is the study and the removal of micro-pollutants from aqueous matrices. Analytical techniques for their identification and quantification are becoming more sensitive and comprehensive and, as a result, an increasing number of drugs have been detected in environmental samples. However, the literature shows that conventional treatments for drinking water and wastewater are not sufficient for remove these compounds. This study aims to check whether the process of hydrothermal carbonization (CHT) is effective in removing the synthetic sex hormones: ethinyl estradiol, gestodene and cyproterone acetate from aqueous samples...
May 14, 2018: Anais da Academia Brasileira de Ciências
https://www.readbyqxmd.com/read/29768479/construction-of-a-tri-chromatic-reporter-cell-line-for-the-rapid-and-simple-screening-of-splice-switching-oligonucleotides-targeting-dmd-exon-51-using-high-content-screening
#9
Takenori Shimo, Keisuke Tachibana, Satoshi Obika
Splice-switching oligonucleotides (SSOs) that can modulate RNA splicing are used for the treatment of many genetic disorders. To enhance the efficacy of modulating splicing, it is important to optimize SSOs with regard to target sites, GC content, melting temperature (Tm value), chemistries, and lengths. Thus, in vitro assay systems that allow for the rapid and simple screening of SSOs are essential for optimizing SSO design. In this study, we established a novel tri-chromatic reporter cell line for SSO screening...
2018: PloS One
https://www.readbyqxmd.com/read/29767995/structure-activity-relationships-and-therapeutic-potentials-of-5-ht7-receptor-ligands-an-update
#10
Maria N Modica, Enza Lacivita, Sebastiano Intagliata, Loredana Salerno, Giuseppe Romeo, Valeria Pittala, Marcello Leopoldo
Serotonin 5-HT7 receptor (5-HT7R) has been the subject of intense research efforts because of its presence in brain areas such as hippocampus, hypothalamus, and cortex. Preclinical data link the 5-HT7R to a variety of central nervous system processes such as regulation of circadian rhythms, mood, cognitions, pain processing, and mechanisms of addiction. 5-HT7R blockade has antidepressant effects and may ameliorate cognitive deficits associated with schizophrenia. 5-HT7R has been recently shown to modulate neuronal morphology, excitability, and plasticity, thus contributing to shape brain networks during development and to remodel neuronal wiring in the mature brain...
May 16, 2018: Journal of Medicinal Chemistry
https://www.readbyqxmd.com/read/29767966/recent-advances-and-perspectives-on-nonadiabatic-mixed-quantum-classical-dynamics
#11
Rachel Crespo-Otero, Mario Barbatti
Nonadiabatic mixed quantum-classical (NA-MQC) dynamics methods form a class of computational theoretical approaches in quantum chemistry tailored to investigate the time evolution of nonadiabatic phenomena in molecules and supramolecular assemblies. NA-MQC is characterized by a partition of the molecular system into two subsystems: one to be treated quantum mechanically (usually but not restricted to electrons) and another to be dealt with classically (nuclei). The two subsystems are connected through nonadiabatic couplings terms to enforce self-consistency...
May 16, 2018: Chemical Reviews
https://www.readbyqxmd.com/read/29765806/formation-mechanisms-of-boron-oxide-films-fabricated-by-large-area-electron-beam-induced-deposition-of-trimethyl-borate
#12
Aiden A Martin, Philip J Depond
Boron-containing materials are increasingly drawing interest for the use in electronics, optics, laser targets, neutron absorbers, and high-temperature and chemically resistant ceramics. In this article, the first investigation into the deposition of boron-based material via electron beam-induced deposition (EBID) is reported. Thin films were deposited using a novel, large-area EBID system that is shown to deposit material at rates comparable to conventional techniques such as laser-induced chemical vapor deposition...
2018: Beilstein Journal of Nanotechnology
https://www.readbyqxmd.com/read/29765669/entrainment-in-the-master-equation
#13
Michael Margaliot, Lars Grüne, Thomas Kriecherbauer
The master equation plays an important role in many scientific fields including physics, chemistry, systems biology, physical finance and sociodynamics. We consider the master equation with periodic transition rates. This may represent an external periodic excitation like the 24 h solar day in biological systems or periodic traffic lights in a model of vehicular traffic. Using tools from systems and control theory, we prove that under mild technical conditions every solution of the master equation converges to a periodic solution with the same period as the rates...
April 2018: Royal Society Open Science
https://www.readbyqxmd.com/read/29765646/towards-the-fluorogenic-detection-of-peroxide-explosives-through-host-guest-chemistry
#14
Estefanía Almenar, Ana M Costero, Pablo Gaviña, Salvador Gil, Margarita Parra
Two dansyl-modified β-cyclodextrin derivatives ( 1 and 2 ) have been synthesized as host-guest sensory systems for the direct fluorescent detection of the peroxide explosives diacetone diperoxide (DADP) and triacetone triperoxide (TATP) in aqueous media. The sensing is based on the displacement of the dansyl moiety from the cavity of the cyclodextrin by the peroxide guest resulting in a decrease of the intensity of the fluorescence of the dye. Both systems showed similar fluorescent responses and were more sensitive towards TATP than DADP...
April 2018: Royal Society Open Science
https://www.readbyqxmd.com/read/29765604/deciphering-mineralogical-changes-and-carbonation-development-during-hydration-and-ageing-of-a-consolidated-ternary-blended-cement-paste
#15
Francis Claret, Sylvain Grangeon, Annick Loschetter, Christophe Tournassat, Wout De Nolf, Nicholas Harker, Faiza Boulahya, Stéphane Gaboreau, Yannick Linard, Xavier Bourbon, Alejandro Fernandez-Martinez, Jonathan Wright
To understand the main properties of cement, a ubiquitous material, a sound description of its chemistry and mineralogy, including its reactivity in aggressive environments and its mechanical properties, is vital. In particular, the porosity distribution and associated sample carbonation, both of which affect cement's properties and durability, should be quantified accurately, and their kinetics and mechanisms of formation known both in detail and in situ . However, traditional methods of cement mineralogy analysis ( e...
March 1, 2018: IUCrJ
https://www.readbyqxmd.com/read/29763318/on-the-peculiar-molecular-shape-and-size-dependence-of-the-dynamics-of-fluids-confined-in-a-small-pore-metal-organic-framework
#16
Ioannis Skarmoutsos, Mohamed Eddaoudi, Guillaume Maurin
Force field based-Molecular dynamics simulations were deployed to systematically explore the dynamics of confined molecules of different shapes and sizes, i.e. linear (CO2 and N2) and spherical (CH4) fluids, in a model small pore system, i.e. the Metal-Organic Framework SIFSIX-2-Cu-i. These computations unveil an unprecedented molecular symmetry dependence of the translational and rotational dynamics of fluids confined in channel-like nanoporous materials. In particular this peculiar behaviour is reflected by the extremely slow decay of the Legendre reorientational correlation functions of even-parity order for the linear fluids which is associated to jump-like orientation flips, while the spherical fluid shows a very fast decay taking place in a sub-picosecond time scale...
May 15, 2018: Journal of Physical Chemistry Letters
https://www.readbyqxmd.com/read/29763291/classics-in-neuroimaging-the-serotonergic-2a-receptor-system-from-discovery-to-modern-molecular-imaging
#17
Elina T L'Estrade, Hanne D Hansen, Maria Erlandsson, Tomas G Ohlsson, Gitte M Knudsen, Matthias M Herth
Already in 1953, Woolley and Shaw speculated that serotonin could be involved in a range of central nervous system (CNS) disorders. Lysergic acid diethylamide (LSD) displayed an important role in this respect. It was used not only to antagonize biological effects of serotonin and to study the system itself, but also to identify serotonergic subtype receptors. The 5-HT2A receptor was discovered in the 1970s and identified as the responsible receptor mediating psychedelic effects of LSD. The development of positron emission tomography (PET) allowed to study this receptor system in vivo...
May 15, 2018: ACS Chemical Neuroscience
https://www.readbyqxmd.com/read/29761432/quantification-of-low-abundant-phosphorylated-carbohydrates-using-hilic-qqq-ms-ms
#18
Tiago F Jorge, Carla António
Phosphorylated carbohydrates are central metabolites involved in key plant metabolic pathways, such as glycolysis and central carbon metabolism. Such pathways influence plant growth, development, and stress responses to environmental changes, and ultimately, reflect the plant's energy status. The high polarity of these metabolites, the variety of isomeric structures (e.g., glucose-1-phosphate (G1P)/fructose-6-phosphate (F6P)/mannose-6-phosphate (M6P)/G6P, sucrose-6-phosphate (S6P)/T6P), and rapid metabolic turnover makes their analysis particularly challenging...
2018: Methods in Molecular Biology
https://www.readbyqxmd.com/read/29760056/effects-of-the-hippopotamus-on-the-chemistry-and-ecology-of-a-changing-watershed
#19
Keenan Stears, Douglas J McCauley, Jacques C Finlay, James Mpemba, Ian T Warrington, Benezeth M Mutayoba, Mary E Power, Todd E Dawson, Justin S Brashares
Cross-boundary transfers of nutrients can profoundly shape the ecology of recipient systems. The common hippopotamus, Hippopotamus amphibius , is a significant vector of such subsidies from terrestrial to river ecosystems. We compared river pools with high and low densities of H. amphibius to determine how H. amphibius subsidies shape the chemistry and ecology of aquatic communities. Our study watershed, like many in sub-Saharan Africa, has been severely impacted by anthropogenic water abstraction reducing dry-season flow to zero...
May 14, 2018: Proceedings of the National Academy of Sciences of the United States of America
https://www.readbyqxmd.com/read/29760051/approach-to-classify-separate-and-enrich-objects-in-groups-using-ensemble-sorting
#20
Rebecca Turk-MacLeod, Alon Henson, Marc Rodriguez-Garcia, Graham M Gibson, Gerardo Aragon Camarasa, Dario Caramelli, Miles J Padgett, Leroy Cronin
The sorting of objects into groups is a fundamental operation, critical in the preparation and purification of populations of cells, crystals, beads, or droplets, necessary for research and applications in biology, chemistry, and materials science. Most of the efforts exploring such purification have focused on two areas: the degree of separation and the measurement precision required for effective separation. Conventionally, achieving good separation ultimately requires that the objects are considered one by one (which can be both slow and expensive), and the ability to measure the sorted objects by increasing sensitivity as well as reducing sorting errors...
May 14, 2018: Proceedings of the National Academy of Sciences of the United States of America
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