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Proceedings of the National Academy of Sciences of the United States of America

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https://www.readbyqxmd.com/read/30242137/first-principles-based-reaction-kinetics-from-reactive-molecular-dynamics-simulations-application-to-hydrogen-peroxide-decomposition
#1
Daniil V Ilyin, William A Goddard, Julius J Oppenheim, Tao Cheng
This paper presents our vision of how to use in silico approaches to extract the reaction mechanisms and kinetic parameters for complex condensed-phase chemical processes that underlie important technologies ranging from combustion to chemical vapor deposition. The goal is to provide an analytic description of the detailed evolution of a complex chemical system from reactants through various intermediates to products, so that one could optimize the efficiency of the reactive processes to produce the desired products and avoid unwanted side products...
September 21, 2018: Proceedings of the National Academy of Sciences of the United States of America
https://www.readbyqxmd.com/read/30242136/on-the-use-of-group-performance-and-rights-for-environmental-protection-and-resource-management
#2
Matthew J Kotchen, Kathleen Segerson
Environmental and natural resource (ENR) policies that focus on group outcomes are common but have received relatively less attention from economists than policies based on individual behavior. Existing research tends to focus on particular contexts, such as water or air quality, fisheries, or land use. This paper discusses unifying themes of group performance policies, along with their advantages and disadvantages. We discuss a range of specific policy instruments, including group-based taxes, subsidies, and fixed penalties...
September 21, 2018: Proceedings of the National Academy of Sciences of the United States of America
https://www.readbyqxmd.com/read/30242135/hypoxia-inducible-factor-1-dependent-expression-of-adenosine-receptor-2b-promotes-breast-cancer-stem-cell-enrichment
#3
Jie Lan, Haiquan Lu, Debangshu Samanta, Shaima Salman, You Lu, Gregg L Semenza
Breast cancer stem cells (BCSCs), which are characterized by a capacity for unlimited self-renewal and for generation of the bulk cancer cell population, play a critical role in cancer relapse and metastasis. Hypoxia is a common feature of the cancer microenvironment that stimulates the specification and maintenance of BCSCs. In this study, we found that hypoxia increased expression of adenosine receptor 2B (A2BR) in human breast cancer cells through the transcriptional activity of hypoxia-inducible factor 1...
September 21, 2018: Proceedings of the National Academy of Sciences of the United States of America
https://www.readbyqxmd.com/read/30242134/astn2-modulates-synaptic-strength-by-trafficking-and-degradation-of-surface-proteins
#4
Hourinaz Behesti, Taylor R Fore, Peter Wu, Zachi Horn, Mary Leppert, Court Hull, Mary E Hatten
Surface protein dynamics dictate synaptic connectivity and function in neuronal circuits. ASTN2 , a gene disrupted by copy number variations (CNVs) in neurodevelopmental disorders, including autism spectrum, was previously shown to regulate the surface expression of ASTN1 in glial-guided neuronal migration. Here, we demonstrate that ASTN2 binds to and regulates the surface expression of multiple synaptic proteins in postmigratory neurons by endocytosis, resulting in modulation of synaptic activity. In cerebellar Purkinje cells (PCs), by immunogold electron microscopy, ASTN2 localizes primarily to endocytic and autophagocytic vesicles in the cell soma and in subsets of dendritic spines...
September 21, 2018: Proceedings of the National Academy of Sciences of the United States of America
https://www.readbyqxmd.com/read/30242133/activation-of-autophagy-rescues-synaptic-and-cognitive-deficits-in-fragile-x-mice
#5
Jingqi Yan, Morgan W Porch, Brenda Court-Vazquez, Michael V L Bennett, R Suzanne Zukin
Fragile X syndrome (FXS) is the most frequent form of heritable intellectual disability and autism. Fragile X ( Fmr1 -KO) mice exhibit aberrant dendritic spine structure, synaptic plasticity, and cognition. Autophagy is a catabolic process of programmed degradation and recycling of proteins and cellular components via the lysosomal pathway. However, a role for autophagy in the pathophysiology of FXS is, as yet, unclear. Here we show that autophagic flux, a functional readout of autophagy, and biochemical markers of autophagy are down-regulated in hippocampal neurons of fragile X mice...
September 21, 2018: Proceedings of the National Academy of Sciences of the United States of America
https://www.readbyqxmd.com/read/30242132/movement-kinematics-drive-chain-selection-toward-intention-detection
#6
Marco Soriano, Andrea Cavallo, Alessandro D'Ausilio, Cristina Becchio, Luciano Fadiga
The ability to understand intentions based on another's movements is crucial for human interaction. This ability has been ascribed to the so-called motor chaining mechanism: anytime a motor chain is activated (e.g., grasp-to-drink), the observer attributes to the agent the corresponding intention (i.e., to drink) from the first motor act (i.e., the grasp). However, the mechanisms by which a specific chain is selected in the observer remain poorly understood. In the current study, we investigate the possibility that in the absence of discriminative contextual cues, slight kinematic variations in the observed grasp inform mapping to the most probable chain...
September 21, 2018: Proceedings of the National Academy of Sciences of the United States of America
https://www.readbyqxmd.com/read/30237288/phevamine-a-a-small-molecule-that-suppresses-plant-immune-responses
#7
Erinn M O'Neill, Tatiana S Mucyn, Jon B Patteson, Omri M Finkel, Eui-Hwan Chung, Joshua A Baccile, Elisabetta Massolo, Frank C Schroeder, Jeffery L Dangl, Bo Li
Bacterial plant pathogens cause significant crop damage worldwide. They invade plant cells by producing a variety of virulence factors, including small-molecule toxins and phytohormone mimics. Virulence of the model pathogen Pseudomonas syringae pv. tomato DC3000 ( Pto ) is regulated in part by the sigma factor HrpL. Our study of the HrpL regulon identified an uncharacterized, three-gene operon in Pto that is controlled by HrpL and related to the Erwinia hrp -associated systemic virulence ( hsv ) operon. Here, we demonstrate that the hsv operon contributes to the virulence of Pto on Arabidopsis thaliana and suppresses bacteria-induced immune responses...
September 20, 2018: Proceedings of the National Academy of Sciences of the United States of America
https://www.readbyqxmd.com/read/30237287/predicting-polymorphism-in-molecular-crystals-using-orientational-entropy
#8
Pablo M Piaggi, Michele Parrinello
We introduce a computational method to discover polymorphs in molecular crystals at finite temperature. The method is based on reproducing the crystallization process starting from the liquid and letting the system discover the relevant polymorphs. This idea, however, conflicts with the fact that crystallization has a timescale much longer than that of molecular simulations. To bring the process within affordable simulation time, we enhance the fluctuations of a collective variable by constructing a bias potential with well-tempered metadynamics...
September 20, 2018: Proceedings of the National Academy of Sciences of the United States of America
https://www.readbyqxmd.com/read/30237286/synchronized-mechanical-oscillations-at-the-cell-matrix-interface-in-the-formation-of-tensile-tissue
#9
David F Holmes, Ching-Yan Chloé Yeung, Richa Garva, Egor Zindy, Susan H Taylor, Yinhui Lu, Simon Watson, Nicholas S Kalson, Karl E Kadler
The formation of uniaxial fibrous tissues with defined viscoelastic properties implies the existence of an orchestrated mechanical interaction between the cytoskeleton and the extracellular matrix. This study addresses the nature of this interaction. The hypothesis is that this mechanical interplay underpins the mechanical development of the tissue. In embryonic tendon tissue, an early event in the development of a mechanically robust tissue is the interaction of the pointed tips of extracellular collagen fibrils with the fibroblast plasma membrane to form stable interface structures (fibripositors)...
September 20, 2018: Proceedings of the National Academy of Sciences of the United States of America
https://www.readbyqxmd.com/read/30237285/revised-m06-density-functional-for-main-group-and-transition-metal-chemistry
#10
Ying Wang, Pragya Verma, Xinsheng Jin, Donald G Truhlar, Xiao He
We present a hybrid metageneralized-gradient-approximation functional, revM06, which is based on adding Hartree-Fock exchange to the revM06-L functional form. Compared with the original M06 suite of density functionals, the resulting revM06 functional has significantly improved across-the-board accuracy for both main-group and transition-metal chemistry. The revM06 functional improves on the M06-2X functional for main-group and transition-metal bond energies, atomic excitation energies, isomerization energies of large molecules, molecular structures, and both weakly and strongly correlated atomic and molecular data, and it shows a clear improvement over M06 and M06-2X for noncovalent interactions, including smoother potential curves for rare-gas dimers...
September 20, 2018: Proceedings of the National Academy of Sciences of the United States of America
https://www.readbyqxmd.com/read/30237284/-let-7i-inhibition-enhances-progesterone-induced-functional-recovery-in-a-mouse-model-of-ischemia
#11
Trinh Nguyen, Chang Su, Meharvan Singh
Progesterone (P4) is a potent neuroprotectant and a promising therapeutic for stroke treatment. However, the underlying mechanism(s) remain unclear. Our laboratory recently reported that brain-derived neurotrophic factor (BDNF) is a critical mediator of P4's protective actions and that P4-induced BDNF release from cortical astrocytes is mediated by a membrane-associated progesterone receptor, Pgrmc1. Here, we report that the microRNA (miRNA) let-7i is a negative regulator of Pgrmc1 and BDNF in glia and that let-7i disrupts P4-induced BDNF release and P4's beneficial effects on cell viability and markers of synaptogenesis...
September 20, 2018: Proceedings of the National Academy of Sciences of the United States of America
https://www.readbyqxmd.com/read/30237283/energy-dependent-quenching-adjusts-the-excitation-diffusion-length-to-regulate-photosynthetic-light-harvesting
#12
Doran I G Bennett, Graham R Fleming, Kapil Amarnath
An important determinant of crop yields is the regulation of photosystem II (PSII) light harvesting by energy-dependent quenching (qE). However, the molecular details of excitation quenching have not been quantitatively connected to the fraction of excitations converted to chemical energy by PSII reaction centers (PSII yield), which determines flux to downstream metabolism. Here, we incorporate excitation dissipation by qE into a pigment-scale model of excitation transfer and trapping for a 200 × 200-nm patch of the grana membrane...
September 20, 2018: Proceedings of the National Academy of Sciences of the United States of America
https://www.readbyqxmd.com/read/30232266/repurposing-type-iii-polyketide-synthase-as-a-malonyl-coa-biosensor-for-metabolic-engineering-in-bacteria
#13
Dongsoo Yang, Won Jun Kim, Seung Min Yoo, Jong Hyun Choi, Shin Hee Ha, Mun Hee Lee, Sang Yup Lee
Malonyl-CoA is an important central metabolite for the production of diverse valuable chemicals including natural products, but its intracellular availability is often limited due to the competition with essential cellular metabolism. Several malonyl-CoA biosensors have been developed for high-throughput screening of targets increasing the malonyl-CoA pool. However, they are limited for use only in Escherichia coli and Saccharomyces cerevisiae and require multiple signal transduction steps. Here we report development of a colorimetric malonyl-CoA biosensor applicable in three industrially important bacteria: E...
September 19, 2018: Proceedings of the National Academy of Sciences of the United States of America
https://www.readbyqxmd.com/read/30232265/phosphoethanolamine-cellulose-enhances-curli-mediated-adhesion-of-uropathogenic-escherichia-coli-to-bladder-epithelial-cells
#14
Emily C Hollenbeck, Alexandra Antonoplis, Chew Chai, Wiriya Thongsomboon, Gerald G Fuller, Lynette Cegelski
Uropathogenic Escherichia coli (UPEC) are the major causative agents of urinary tract infections, employing numerous molecular strategies to contribute to adhesion, colonization, and persistence in the bladder niche. Identifying strategies to prevent adhesion and colonization is a promising approach to inhibit bacterial pathogenesis and to help preserve the efficacy of available antibiotics. This approach requires an improved understanding of the molecular determinants of adhesion to the bladder urothelium...
September 19, 2018: Proceedings of the National Academy of Sciences of the United States of America
https://www.readbyqxmd.com/read/30232264/chloride-regulates-dynamic-nlrp3-dependent-asc-oligomerization-and-inflammasome-priming
#15
Jack P Green, Shi Yu, Fátima Martín-Sánchez, Pablo Pelegrin, Gloria Lopez-Castejon, Catherine B Lawrence, David Brough
The NLRP3 inflammasome is an important regulator of inflammation and immunity. It is a multimolecular platform formed within cells that facilitates the activation of proinflammatory caspases to drive secretion of cytokines such as interleukin-1β (IL-1β). Knowledge of the mechanisms regulating formation of the NLRP3 inflammasome is incomplete. Here we report Cl- channel-dependent formation of dynamic ASC oligomers and inflammasome specks that remain inactive in the absence of K+ efflux. Formed after Cl- efflux exclusively, ASC specks are NLRP3 dependent, reversible, and inactive, although they further prime inflammatory responses, accelerating and enhancing release of IL-1β in response to a K+ efflux-inducing stimulus...
September 19, 2018: Proceedings of the National Academy of Sciences of the United States of America
https://www.readbyqxmd.com/read/30232263/differential-effects-of-partial-and-complete-loss-of-trem2-on-microglial-injury-response-and-tauopathy
#16
Faten A Sayed, Maria Telpoukhovskaia, Lay Kodama, Yaqiao Li, Yungui Zhou, David Le, Axel Hauduc, Connor Ludwig, Fuying Gao, Claire Clelland, Lihong Zhan, Yonatan A Cooper, Dimitrios Davalos, Katerina Akassoglou, Giovanni Coppola, Li Gan
Alzheimer's disease (AD), the most common form of dementia, is characterized by the abnormal accumulation of amyloid plaques and hyperphosphorylated tau aggregates, as well as microgliosis. Hemizygous missense variants in Triggering Receptor Expressed on Myeloid Cells 2 ( TREM2 ) are associated with elevated risk for developing late-onset AD. These variants are hypothesized to result in loss of function, mimicking TREM2 haploinsufficiency. However, the consequences of TREM2 haploinsufficiency on tau pathology and microglial function remain unknown...
September 19, 2018: Proceedings of the National Academy of Sciences of the United States of America
https://www.readbyqxmd.com/read/30232262/collusion-between-neutralizing-antibodies-and-other-immune-factions-in-the-destruction-of-adenoviral-vectors
#17
P J Klasse
No abstract text is available yet for this article.
September 19, 2018: Proceedings of the National Academy of Sciences of the United States of America
https://www.readbyqxmd.com/read/30232261/substance-p-and-il-33-administered-together-stimulate-a-marked-secretion-of-il-1%C3%AE-from-human-mast-cells-inhibited-by-methoxyluteolin
#18
Alexandra Taracanova, Irene Tsilioni, Pio Conti, Errol R Norwitz, Susan E Leeman, Theoharis C Theoharides
Mast cells are critical for allergic and inflammatory responses in which the peptide substance P (SP) and the cytokine IL-33 are involved. SP (0.01-1 μM) administered together with IL-33 (30 ng/mL) to human cultured LAD2 mast cells stimulates a marked increase ( P < 0.0001) in secretion of the proinflammatory cytokine IL-1β. Preincubation of LAD2 (30 min) with the SP receptor (NK-1) antagonists L-733,060 (10 μM) or CP-96345 (10 µM) inhibits ( P < 0.001) secretion of IL-1β stimulated by either SP (1 μM) or SP together with IL-33 (30 ng/mL)...
September 19, 2018: Proceedings of the National Academy of Sciences of the United States of America
https://www.readbyqxmd.com/read/30232260/structural-basis-for-cooperative-regulation-of-kix-mediated-transcription-pathways-by-the-htlv-1-hbz-activation-domain
#19
Ke Yang, Robyn L Stanfield, Maria A Martinez-Yamout, H Jane Dyson, Ian A Wilson, Peter E Wright
The human T cell leukemia virus I basic leucine zipper protein (HTLV-1 HBZ) maintains chronic viral infection and promotes leukemogenesis through poorly understood mechanisms involving interactions with the KIX domain of the transcriptional coactivator CBP and its paralog p300. The KIX domain binds regulatory proteins at the distinct MLL and c-Myb/pKID sites to form binary or ternary complexes. The intrinsically disordered N-terminal activation domain of HBZ (HBZ AD) deregulates cellular signaling pathways by competing directly with cellular and viral transcription factors for binding to the MLL site and by allosterically perturbing binding of the transactivation domain of the hematopoietic transcription factor c-Myb...
September 19, 2018: Proceedings of the National Academy of Sciences of the United States of America
https://www.readbyqxmd.com/read/30232259/phasic-locus-coeruleus-activity-regulates-cortical-encoding-of-salience-information
#20
Elena M Vazey, David E Moorman, Gary Aston-Jones
Phasic activation of locus coeruleus (LC)-norepinephrine (NE) neurons is associated with focused attention and behavioral responses to salient stimuli. We used cell-type-specific optogenetics and single-unit neurophysiology to identify how LC activity influences neural encoding of sensory information. We found that phasic, but not tonic, LC-NE photoactivation generated a distinct event-related potential (ERP) across cortical regions. Salient sensory stimuli (which innately trigger phasic LC activity) produced strong excitatory cortical responses during this ERP window...
September 19, 2018: Proceedings of the National Academy of Sciences of the United States of America
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