Molecular investigations on grain filling rate under terminal heat ...

African Journals Online (AJOL)

Grain yield under post anthesis high temperature stress is largely influenced by grain filling rate (GFR). To investigate molecular basis of this trait, a set of 111 recombinant inbred lines (RILs) derived from Raj 4014, a heat sensitive genotype and WH 730, heat tolerant cultivar was phenotyped during 2009-2010 and ...

Mapping Hydrophobicity on the Protein Molecular Surface at Atom-Level Resolution

Science.gov (United States)

Nicolau Jr., Dan V.; Paszek, Ewa; Fulga, Florin; Nicolau, Dan V.

2014-01-01

A precise representation of the spatial distribution of hydrophobicity, hydrophilicity and charges on the molecular surface of proteins is critical for the understanding of the interaction with small molecules and larger systems. The representation of hydrophobicity is rarely done at atom-level, as this property is generally assigned to residues. A new methodology for the derivation of atomic hydrophobicity from any amino acid-based hydrophobicity scale was used to derive 8 sets of atomic hydrophobicities, one of which was used to generate the molecular surfaces for 35 proteins with convex structures, 5 of which, i.e., lysozyme, ribonuclease, hemoglobin, albumin and IgG, have been analyzed in more detail. Sets of the molecular surfaces of the model proteins have been constructed using spherical probes with increasingly large radii, from 1.4 to 20 Å, followed by the quantification of (i) the surface hydrophobicity; (ii) their respective molecular surface areas, i.e., total, hydrophilic and hydrophobic area; and (iii) their relative densities, i.e., divided by the total molecular area; or specific densities, i.e., divided by property-specific area. Compared with the amino acid-based formalism, the atom-level description reveals molecular surfaces which (i) present an approximately two times more hydrophilic areas; with (ii) less extended, but between 2 to 5 times more intense hydrophilic patches; and (iii) 3 to 20 times more extended hydrophobic areas. The hydrophobic areas are also approximately 2 times more hydrophobicity-intense. This, more pronounced “leopard skin”-like, design of the protein molecular surface has been confirmed by comparing the results for a restricted set of homologous proteins, i.e., hemoglobins diverging by only one residue (Trp37). These results suggest that the representation of hydrophobicity on the protein molecular surfaces at atom-level resolution, coupled with the probing of the molecular surface at different geometric resolutions

Computational Analysis of Molecular Interaction Networks Underlying Change of HIV-1 Resistance to Selected Reverse Transcriptase Inhibitors.

Science.gov (United States)

Kierczak, Marcin; Dramiński, Michał; Koronacki, Jacek; Komorowski, Jan

2010-12-12

Despite more than two decades of research, HIV resistance to drugs remains a serious obstacle in developing efficient AIDS treatments. Several computational methods have been developed to predict resistance level from the sequence of viral proteins such as reverse transcriptase (RT) or protease. These methods, while powerful and accurate, give very little insight into the molecular interactions that underly acquisition of drug resistance/hypersusceptibility. Here, we attempt at filling this gap by using our Monte Carlo feature selection and interdependency discovery method (MCFS-ID) to elucidate molecular interaction networks that characterize viral strains with altered drug resistance levels. We analyzed a number of HIV-1 RT sequences annotated with drug resistance level using the MCFS-ID method. This let us expound interdependency networks that characterize change of drug resistance to six selected RT inhibitors: Abacavir, Lamivudine, Stavudine, Zidovudine, Tenofovir and Nevirapine. The networks consider interdependencies at the level of physicochemical properties of mutating amino acids, eg,: polarity. We mapped each network on the 3D structure of RT in attempt to understand the molecular meaning of interacting pairs. The discovered interactions describe several known drug resistance mechanisms and, importantly, some previously unidentified ones. Our approach can be easily applied to a whole range of problems from the domain of protein engineering. A portable Java implementation of our MCFS-ID method is freely available for academic users and can be obtained at: http://www.ipipan.eu/staff/m.draminski/software.htm.

A Multi-step and Multi-level approach for Computer Aided Molecular Design

DEFF Research Database (Denmark)

. The problem formulation step incorporates a knowledge base for the identification and setup of the design criteria. Candidate compounds are identified using a multi-level generate and test CAMD solution algorithm capable of designing molecules having a high level of molecular detail. A post solution step...... using an Integrated Computer Aided System (ICAS) for result analysis and verification is included in the methodology. Keywords: CAMD, separation processes, knowledge base, molecular design, solvent selection, substitution, group contribution, property prediction, ICAS Introduction The use of Computer...... Aided Molecular Design (CAMD) for the identification of compounds having specific physic...

The thermodynamics of molecular cloud fragmentation : Star formation under non-Milky Way conditions

NARCIS (Netherlands)

Hocuk, S.; Spaans, M.

Context. Properties of candidate stars, forming out of molecular clouds, depend on the ambient conditions of the parent cloud. We present a series of 2D and 3D simulations of fragmentation of molecular clouds in starburst regions, as well as of clouds under conditions in dwarf galaxies, leading to

Low-molecular weight heparin increases circulating sFlt-1 levels and enhances urinary elimination.

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Henning Hagmann

Full Text Available RATIONALE: Preeclampsia is a devastating medical complication of pregnancy which leads to maternal and fetal morbidity and mortality. While the etiology of preeclampsia is unclear, human and animal studies suggest that excessive circulating levels of soluble fms-like tyrosine-kinase-1 (sFlt-1, an alternatively spliced variant of VEGF-receptor1, contribute to the signs and symptoms of preeclampsia. Since sFlt-1 binds to heparin and heparan sulfate proteoglycans, we hypothesized that the anticoagulant heparin, which is often used in pregnancy, may interfere with the levels, distribution and elimination of sFlt-1 in vivo. OBJECTIVE: We systematically determined serum and urine levels of angiogenic factors in preeclamptic women before and after administration of low molecular weight heparin and further characterized the interaction with heparin in biochemical studies. METHODS AND RESULTS: Serum and urine samples were used to measure sFlt-1 levels before and after heparin administration. Serum levels of sFlt-1 increased by 25% after heparin administration in pregnant women. The magnitude of the increase in circulating sFlt-1 correlated with initial sFlt-1 serum levels. Urinary sFlt-1 levels were also elevated following heparin administration and levels of elimination were dependent on the underlying integrity of the glomerular filtration barrier. Biochemical binding studies employing cation exchange chromatography revealed that heparin bound sFlt-1 had decreased affinity to negatively charged surfaces when compared to sFlt-1 alone. CONCLUSION: Low molecular weight heparin administration increased circulating sFlt1 levels and enhanced renal elimination. We provide evidence that both effects may be due to heparin binding to sFlt1 and masking the positive charges on sFlt1 protein.

Phase behaviour of macromolecular liquid crystalline materials. Computational studies at the molecular level

International Nuclear Information System (INIS)

Stimson, Lorna M.

2003-01-01

Molecular simulations provide an increasingly useful insight into the static and dynamic characteristics of materials. In this thesis molecular simulations of macro-molecular liquid crystalline materials are reported. The first liquid crystalline material that has been investigated is a side chain liquid crystal polymer (SCLCP). In this study semi-atomistic molecular dynamics simulations have been conducted at a range of temperatures and an aligning potential has been applied to mimic the effect of a magnetic field. In cooling the SCLCP from an isotropic melt, microphase separation was observed yielding a domain structure. The application of a magnetic field to this structure aligns the domains producing a stable smectic mesophase. This is the first study in which mesophases have been observed using an off-lattice model of a SCLCP. The second material that has been investigated is a dendrimer with terminal mesogenic functionalization. Here, a multi-scale approach has been taken with Monte Carlo studies of a single dendrimer molecule in the gas phase at the atomistic level, semi-atomistic molecular dynamics of a single molecule in liquid crystalline solvents and a coarse-grained molecular dynamics study of the dendrimer in the bulk. The coarse-grained model has been developed and parameterized using the results of the atomistic and semi-atomistic work. The single molecule studies showed that the liquid crystalline dendrimer was able to change its structure by conformational changes in the flexible chains that link the mesogenic groups to the core. Structural change was seen under the application of a mean field ordering potential in the gas phase, and in the presence of liquid crystalline solvents. No liquid crystalline phases were observed for the bulk phase studies of the coarse-grained model. However, when the length of the mesogenic units was increased there was some evidence for microphase separation in these systems. (author)

Fermi level alignment in molecular nanojunctions and its relation to charge transfer

DEFF Research Database (Denmark)

Stadler, Robert; Jacobsen, Karsten Wedel

2006-01-01

The alignment of the Fermi level of a metal electrode within the gap of the highest occupied molecular orbital (HOMO) and the lowest unoccupied molecular orbital (LUMO) of a molecule is a key quantity in molecular electronics, which can vary the electron transparency of a single-molecule junction...... by orders of magnitude. We present a quantitative analysis of the relation between this level alignment (which can be estimated from charging free molecules) and charge transfer for bipyridine and biphenyl dithiolate (BPDT) molecules attached to gold leads based on density functional theory calculations...... end of the gap in the transmission function for bipyridine and at its lower end for BPDT....

Post-learning molecular reactivation underlies taste memory consolidation

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Kioko eGuzman-Ramos

2011-09-01

Full Text Available It is considered that memory consolidation is a progressive process that requires post-trial stabilization of the information. In this regard, it has been speculated that waves of receptors activation, expression of immediate early genes and replenishment of receptor subunit pools occur to induce functional or morphological changes to maintain the information for longer periods. In this paper, we will review data related to neuronal changes in the post-acquisition stage of taste aversion learning that could be involved in further stabilization of the memory trace. In order to achieve such stabilization, evidence suggests that the functional integrity of the insular cortex (IC and the amygdala (AMY is required. Particularly the increase of extracellular levels of glutamate and activation of N-methyl-D-aspartate (NMDA receptors within the IC shows a main role in the consolidation process. Additionally the modulatory actions of the dopaminergic system in the IC appear to be involved in the mechanisms that lead to taste aversion memory consolidation through the activation of pathways related to enhancement of protein synthesis such as the Protein Kinase A pathway. In summary, we suggest that post-acquisition molecular and neuronal changes underlying memory consolidation are dependent on the interactions between the AMY and the IC.

Nanopore wall-liquid interaction under scope of molecular dynamics study: Review

Science.gov (United States)

Tsukanov, A. A.; Psakhie, S. G.

2017-12-01

The present review is devoted to the analysis of recent molecular dynamics based on the numerical studies of molecular aspects of solid-fluid interaction in nanoscale channels. Nanopore wall-liquid interaction plays the crucial role in such processes as gas separation, water desalination, liquids decontamination, hydrocarbons and water transport in nano-fractured geological formations. Molecular dynamics simulation is one of the most suitable tools to study molecular level effects occurred in such multicomponent systems. The nanopores are classified by their geometry to four groups: nanopore in nanosheet, nanotube-like pore, slit-shaped nanopore and soft-matter nanopore. The review is focused on the functionalized nanopores in boron nitride nanosheets as novel selective membranes and on the slit-shaped nanopores formed by minerals.

Evaluation of the molecular level visualisation approach for teaching and learning chemistry in Thailand

Science.gov (United States)

Phenglengdi, Butsari

This research evaluates the use of a molecular level visualisation approach in Thai secondary schools. The goal is to obtain insights about the usefulness of this approach, and to examine possible improvements in how the approach might be applied in the future. The methodology used for this research used both qualitative and quantitative approaches. Data were collected in the form of pre- and post-intervention multiple choice questions, open-ended-questions, drawing exercises, one-to-one interviews and video recordings of class activity. The research was conducted in two phases, involving a total of 261 students from the 11th Grade in Thailand. The use of VisChem animations in three studies was evaluated in Phase I. Study 1 was a pilot study exploring the benefits of incorporating VisChem animations to portray the molecular level. Study 2 compared test results between students exposed to these animations of molecular level events, and those not. Finally, in Study 3, test results were gathered from different types of schools (a rural school, a city school, and a university school). The results showed that students (and teachers) had misconceptions at the molecular level, and VisChem animations could help students understand chemistry concepts at the molecular level across all three types of schools. While the animation treatment group had a better score on the topic of states of water, the non-animation treatment group had a better score on the topic of dissolving sodium chloride in water than the animation group. The molecular level visualisation approach as a learning design was evaluated in Phase II. This approach involved a combination of VisChem animations, pictures, and diagrams together with the seven-step VisChem learning design. The study involved three classes of students, each with a different treatment, described as Class A - Traditional approach; Class B - VisChem animations with traditional approach; and Class C - Molecular level visualisation approach

Deciphering Molecular Mechanism Underlying Hypolipidemic Activity of Echinocystic Acid

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Li Han

2014-01-01

Full Text Available Our previous study showed that a triterpene mixture, consisting of echinocystic acid (EA and oleanolic acid (OA at a ratio of 4 : 1, dose-dependently ameliorated the hyperlipidemia and atherosclerosis in rabbits fed with high fat/high cholesterol diets. This study was aimed at exploring the mechanisms underlying antihyperlipidemic effect of EA. Molecular docking simulation of EA was performed using Molegro Virtual Docker (version: 4.3.0 to investigate the potential targets related to lipid metabolism. Based on the molecular docking information, isotope labeling method or spectrophotometry was applied to examine the effect of EA on the activity of 3-hydroxy-3-methylglutaryl coenzyme A (HMG-CoA reductase, acyl-CoA:cholesterol acyltransferase (ACAT, and diacylglycerol acyltransferase (DGAT in rat liver microsomes. Our results revealed a strong affinity of EA towards ACAT and DGAT in molecular docking analysis, while low binding affinity existed between EA and HMG-CoA reductase as well as between EA and cholesteryl ester transfer protein. Consistent with the results of molecular docking, in vitro enzyme activity assays showed that EA inhibited ACAT and DGAT, with IC50 values of 103 and 139 μM, respectively, and exhibited no significant effect on HMG-CoA reductase activity. The present findings suggest that EA may exert hypolipidemic effect by inhibiting the activity of ACAT and DGAT.

Simulation of aerosol flow interaction with a solid body on molecular level

Science.gov (United States)

Amelyushkin, Ivan A.; Stasenko, Albert L.

2018-05-01

Physico-mathematical models and numerical algorithm of two-phase flow interaction with a solid body are developed. Results of droplet motion and its impingement upon a rough surface in real gas boundary layer simulation on the molecular level obtained via molecular dynamics technique are presented.

Exploring the molecular mechanisms underlying the potentiation of exogenous growth hormone on alcohol-induced fatty liver diseases in mice

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Tian Ya-ping

2010-11-01

Full Text Available Abstract Background Growth hormone (GH is an essential regulator of intrahepatic lipid metabolism by activating multiple complex hepatic signaling cascades. Here, we examined whether chronic exogenous GH administration (via gene therapy could ameliorate liver steatosis in animal models of alcoholic fatty liver disease (AFLD and explored the underlying molecular mechanisms. Methods Male C57BL/6J mice were fed either an alcohol or a control liquid diet with or without GH therapy for 6 weeks. Biochemical parameters, liver histology, oxidative stress markers, and serum high molecular weight (HMW adiponectin were measured. Quantitative real-time PCR and western blotting were also conducted to determine the underlying molecular mechanism. Results Serum HMW adiponectin levels were significantly higher in the GH1-treated control group than in the control group (3.98 ± 0.71 μg/mL vs. 3.07 ± 0.55 μg/mL; P P P P P Conclusions GH therapy had positive effects on AFLD and may offer a promising approach to prevent or treat AFLD. These beneficial effects of GH on AFLD were achieved through the activation of the hepatic adiponectin-SIRT1-AMPK and PPARα-AMPK signaling systems.

Physiological and molecular alterations in plants exposed to high [CO2] under phosphorus stress.

Science.gov (United States)

Pandey, Renu; Zinta, Gaurav; AbdElgawad, Hamada; Ahmad, Altaf; Jain, Vanita; Janssens, Ivan A

2015-01-01

Atmospheric [CO2] has increased substantially in recent decades and will continue to do so, whereas the availability of phosphorus (P) is limited and unlikely to increase in the future. P is a non-renewable resource, and it is essential to every form of life. P is a key plant nutrient controlling the responsiveness of photosynthesis to [CO2]. Increases in [CO2] typically results in increased biomass through stimulation of net photosynthesis, and hence enhance the demand for P uptake. However, most soils contain low concentrations of available P. Therefore, low P is one of the major growth-limiting factors for plants in many agricultural and natural ecosystems. The adaptive responses of plants to [CO2] and P availability encompass alterations at morphological, physiological, biochemical and molecular levels. In general low P reduces growth, whereas high [CO2] enhances it particularly in C3 plants. Photosynthetic capacity is often enhanced under high [CO2] with sufficient P supply through modulation of enzyme activities involved in carbon fixation such as ribulose-1,5-bisphosphate carboxylase/oxygenase (Rubisco). However, high [CO2] with low P availability results in enhanced dry matter partitioning towards roots. Alterations in below-ground processes including root morphology, exudation and mycorrhizal association are influenced by [CO2] and P availability. Under high P availability, elevated [CO2] improves the uptake of P from soil. In contrast, under low P availability, high [CO2] mainly improves the efficiency with which plants produce biomass per unit P. At molecular level, the spatio-temporal regulation of genes involved in plant adaptation to low P and high [CO2] has been studied individually in various plant species. Genome-wide expression profiling of high [CO2] grown plants revealed hormonal regulation of biomass accumulation through complex transcriptional networks. Similarly, differential transcriptional regulatory networks are involved in P

Level crossing in a molecular Cr8 ring

International Nuclear Information System (INIS)

Affronte, M.; Guidi, T.; Caciuffo, R.; Carretta, S.; Amoretti, G.; Hinderer, J.; Sheikin, I.; Smith, A.A.; Winpenny, R.E.P.; Slageren, J. van; Gatteschi, D.

2004-01-01

The heat capacity of a molecular Cr 8 ring was measured as a function of temperature and magnetic field in order to follow the evolution of the Schottky anomaly through the first (S=0 to |1,-1>) level crossing occurring at B c1 =6.9 T. The results are interpreted within the framework of a spin Hamiltonian approach and they nicely fit the pattern of the energy levels derived by inelastic neutron spectroscopy. At B c1 , the Schottky anomaly almost vanishes suggesting that a true crossing occurs in Cr 8 in contrast to what was observed for ferric wheels

Molecular Bases Underlying the Hepatoprotective Effects of Coffee

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Federico Salomone

2017-01-01

Full Text Available Coffee is the most consumed beverage worldwide. Epidemiological studies with prospective cohorts showed that coffee intake is associated with reduced cardiovascular and all-cause mortality independently of caffeine content. Cohort and case-control studies reported an inverse association between coffee consumption and the degree of liver fibrosis as well as the development of liver cancer. Furthermore, the beneficial effects of coffee have been recently confirmed by large meta-analyses. In the last two decades, various in vitro and in vivo studies evaluated the molecular determinants for the hepatoprotective effects of coffee. In the present article, we aimed to critically review experimental evidence regarding the active components and the molecular bases underlying the beneficial role of coffee against chronic liver diseases. Almost all studies highlighted the beneficial effects of this beverage against liver fibrosis with the most solid results indicating a pivot role for both caffeine and chlorogenic acids. In particular, in experimental models of fibrosis, caffeine was shown to inhibit hepatic stellate cell activation by blocking adenosine receptors, and emerging evidence indicated that caffeine may also favorably impact angiogenesis and hepatic hemodynamics. On the other side, chlorogenic acids, potent phenolic antioxidants, suppress liver fibrogenesis and carcinogenesis by reducing oxidative stress and counteract steatogenesis through the modulation of glucose and lipid homeostasis in the liver. Overall, these molecular insights may have translational significance and suggest that coffee components need clinical evaluation.

Reconstructing genealogies of serial samples under the assumption of a molecular clock using serial-sample UPGMA.

Science.gov (United States)

Drummond, A; Rodrigo, A G

2000-12-01

Reconstruction of evolutionary relationships from noncontemporaneous molecular samples provides a new challenge for phylogenetic reconstruction methods. With recent biotechnological advances there has been an increase in molecular sequencing throughput, and the potential to obtain serial samples of sequences from populations, including rapidly evolving pathogens, is fast being realized. A new method called the serial-sample unweighted pair grouping method with arithmetic means (sUPGMA) is presented that reconstructs a genealogy or phylogeny of sequences sampled serially in time using a matrix of pairwise distances. The resulting tree depicts the terminal lineages of each sample ending at a different level consistent with the sample's temporal order. Since sUPGMA is a variant of UPGMA, it will perform best when sequences have evolved at a constant rate (i.e., according to a molecular clock). On simulated data, this new method performs better than standard cluster analysis under a variety of longitudinal sampling strategies. Serial-sample UPGMA is particularly useful for analysis of longitudinal samples of viruses and bacteria, as well as ancient DNA samples, with the minimal requirement that samples of sequences be ordered in time.

Elevated levels of high-molecular-weight adiponectin in type 1 diabetes

DEFF Research Database (Denmark)

Leth, H.; Andersen, K.K.; Frystyk, J.

2008-01-01

BACKGROUND: Several studies have shown that type 1 diabetic patients have elevated total levels of the adipocyte-derived adipocytokine adiponectin. However, adiponectin circulates in three different subforms, and the high-molecular-weight (HMW) subform is believed to be the primary biologically...... active form. The effects of the medium-molecular-weight (MMW) subform and the low-molecular-weight (LMW) subform are still unresolved. PURPOSE: The objective of the study was to investigate the distribution of the three molecular subforms of adiponectin in well-characterized groups of type 1 diabetics...... with varying degrees of nephropathy as well as in healthy control subjects. STUDY POPULATION: Two hundred seven individuals were included: 58 type 1 diabetics with normoalbuminuria, 46 with microalbuminuria, 46 with macroalbuminuria, and 57 matched controls. METHODS: The HMW, MMW, and LMW subforms were...

Effect of Internal Heteroatoms on Level Alignment at Metal/Molecular Monolayer/Si Interfaces

NARCIS (Netherlands)

Alon, Hadas; Garrick, Rachel; Pujari, Sidharam P.; Toledano, Tal; Sinai, Ofer; Kedem, Nir; Bendikov, Tatyana; Baio, Joe E.; Weidner, Tobias; Zuilhof, Han; Cahen, David; Kronik, Leeor; Sukenik, Chaim N.; Vilan, Ayelet

2018-01-01

Molecular monolayers at metal/semiconductor heterointerfaces affect electronic energy level alignment at the interface by modifying the interface's electrical dipole. On a free surface, the molecular dipole is usually manipulated by means of substitution at its external end. However, at an interface

Non-Newtonian behavior and molecular structure of Cooee bitumen under shear flow

DEFF Research Database (Denmark)

Lemarchand, Claire; Bailey, Nicholas; Daivis, Peter

2015-01-01

The rheology and molecular structure of a model bitumen (Cooee bitumen) under shear are investigated in the non-Newtonian regime using non-equilibrium molecular dynamics simulations. The shear viscosity, normal stress differences, and pressure of the bitumen mixture are computed at different shear...... rates and different temperatures. The model bitumen is shown to be a shear-thinning fluid at all temperatures. In addition, the Cooee model is able to reproduce experimental results showing the formation of nanoaggregates composed of stacks of flat aromatic molecules in bitumen. These nanoaggregates...

Molecular mechanism of catalase activity change under sodium dodecyl sulfate-induced oxidative stress in the mouse primary hepatocytes.

Science.gov (United States)

Wang, Jing; Wang, Jiaxi; Xu, Chi; Liu, Rutao; Chen, Yadong

2016-04-15

Sodium dodecyl sulfate (SDS) contributes to adverse effects of organisms probably because of its ability to induce oxidative stress via changing the activity of antioxidant enzyme catalase (CAT). But the underlying molecular mechanisms still remain unclear. This study characterized the harmful effects of SDS-induced oxidative stress on the mouse primary hepatocytes as well as the structure and function of CAT molecule and investigated the underlying molecular mechanism. After 12h SDS (0.1μM to 0.2mM) exposure, no significant change was observed in CAT activity of the hepatocytes. After 0.5 and 0.8mM SDS exposure, the state of oxidative stress stimulated CAT production in the hepatocytes. The inhibition of CAT activity induced by directly interacting with SDS was unable to catch the synthesis of CAT and therefore resulted in the increased activity and elevated ROS level. Further molecular experiments showed that SDS prefers to bind to the interface with no direct effect on the active site and the structure of heme groups of CAT molecule. When the sites in the interface is saturated, SDS interacts with VAL 73, HIS 74, ASN 147 and PHE 152, the key residues of the enzyme activity, and leads to the decrease of CAT activity. Copyright © 2015 Elsevier B.V. All rights reserved.

Molecular characteristics of stress overshoot for polymer melts under start-up shear flow.

Science.gov (United States)

Jeong, Sohdam; Kim, Jun Mo; Baig, Chunggi

2017-12-21

Stress overshoot is one of the most important nonlinear rheological phenomena exhibited by polymeric liquids undergoing start-up shear at sufficient flow strengths. Despite considerable previous research, the fundamental molecular characteristics underlying stress overshoot remain unknown. Here, we analyze the intrinsic molecular mechanisms behind the overshoot phenomenon using atomistic nonequilibrium molecular dynamics simulations of entangled linear polyethylene melts under shear flow. Through a detailed analysis of the transient rotational chain dynamics, we identify an intermolecular collision angular regime in the vicinity of the chain orientation angle θ ≈ 20° with respect to the flow direction. The shear stress overshoot occurs via strong intermolecular collisions between chains in the collision regime at θ = 15°-25°, corresponding to a peak strain of 2-4, which is an experimentally well-known value. The normal stress overshoot appears at approximately θ = 10°, at a corresponding peak strain roughly equivalent to twice that for the shear stress. We provide plausible answers to several basic questions regarding the stress overshoot, which may further help understand other nonlinear phenomena of polymeric systems.

Renormalized molecular levels in a Sc3N@C-80 molecular electronic device

DEFF Research Database (Denmark)

Larade, Brian; Taylor, Jeremy Philip; Zheng, Q. R.

2001-01-01

We address several general questions about quantum transport through molecular systems by an ab initio analysis of a scandium-nitrogen doped C-80 metallofullerene device. Charge transfer from the Sc3N is found to drastically change the current-voltage characteristics: the current through the Sc3N...... levels and main transmission features shift in energy corresponding to half the applied bias voltage. This is also consistent with our finding that the voltage drops by V-b/2 at each molecule/electrode contact....

Proteomic-Biostatistic Integrated Approach for Finding the Underlying Molecular Determinants of Hypertension in Human Plasma.

Science.gov (United States)

Gajjala, Prathibha R; Jankowski, Vera; Heinze, Georg; Bilo, Grzegorz; Zanchetti, Alberto; Noels, Heidi; Liehn, Elisa; Perco, Paul; Schulz, Anna; Delles, Christian; Kork, Felix; Biessen, Erik; Narkiewicz, Krzysztof; Kawecka-Jaszcz, Kalina; Floege, Juergen; Soranna, Davide; Zidek, Walter; Jankowski, Joachim

2017-08-01

Despite advancements in lowering blood pressure, the best approach to lower it remains controversial because of the lack of information on the molecular basis of hypertension. We, therefore, performed plasma proteomics of plasma from patients with hypertension to identify molecular determinants detectable in these subjects but not in controls and vice versa. Plasma samples from hypertensive subjects (cases; n=118) and controls (n=85) from the InGenious HyperCare cohort were used for this study and performed mass spectrometric analysis. Using biostatistical methods, plasma peptides specific for hypertension were identified, and a model was developed using least absolute shrinkage and selection operator logistic regression. The underlying peptides were identified and sequenced off-line using matrix-assisted laser desorption ionization orbitrap mass spectrometry. By comparison of the molecular composition of the plasma samples, 27 molecular determinants were identified differently expressed in cases from controls. Seventy percent of the molecular determinants selected were found to occur less likely in hypertensive patients. In cross-validation, the overall R 2 was 0.434, and the area under the curve was 0.891 with 95% confidence interval 0.8482 to 0.9349, P hypertensive patients were found to be -2.007±0.3568 and 3.383±0.2643, respectively, P hypertensives and normotensives. The identified molecular determinants may be the starting point for further studies to clarify the molecular causes of hypertension. © 2017 American Heart Association, Inc.

Quantum level structure of molecular magnets, Fe12 and V15

Energy Technology Data Exchange (ETDEWEB)

Ajiro, Y.; Inagaki, Y.; Itoh, H.; Asano, T.; Narumi, Y.; Kindo, K.; Sakon, T.; Nojiri, H.; Motokawa, M.; Cornia, A.; Gatteschi, D.; Mueller, A.; Barbara, B

2003-05-01

We review our recent work on molecular magnets, Fe12 and V15 with focus on the determination of low-lying quantum energy levels which have permanent importance in understanding their unique quantum magnetism.

Quantum level structure of molecular magnets, Fe12 and V15

International Nuclear Information System (INIS)

Ajiro, Y.; Inagaki, Y.; Itoh, H.; Asano, T.; Narumi, Y.; Kindo, K.; Sakon, T.; Nojiri, H.; Motokawa, M.; Cornia, A.; Gatteschi, D.; Mueller, A.; Barbara, B.

2003-01-01

We review our recent work on molecular magnets, Fe12 and V15 with focus on the determination of low-lying quantum energy levels which have permanent importance in understanding their unique quantum magnetism

PREFACE: International Symposium on Molecular Conductors: Novel Functions of Molecular Conductors under Extreme Conditions (ISMC 2008)

Science.gov (United States)

Takahashi, Toshihiro; Suzumura, Yoshikazu

2008-02-01

The International Symposium on Molecular Conductors 2008 (ISMC2008) was held as the second international symposium of the project entitled `Novel Functions of Molecular Conductors under Extreme Conditions', which was supported by the Grant-in-aid for Scientific Research on Priority Areas from the Ministry of Education, Culture, Sports, Science and Technology in Japan. The project lasted from September 2003 to March 2008, and was completed by this symposium held at Okazaki Conference Center, Institute for Molecular Science, Okazaki, Japan (23-25 July 2008), which about 100 scientists attended. During the symposium, five project teams gave summary talks and exciting talks were given on the topics developed recently not only by the members of the project but also by other scientists including invited speakers from abroad, who are doing active research on molecular conductors. It is expected that papers presented in the symposium will give valuable hints for the next step in the research of this field. Therefore the organizers of this symposium decided to publish this proceedings in order to demonstrate these activities, not only for the local community of the project, but also for the broad society of international scientists who are interested in molecular conductors. The editors, who are also the organizers of this symposium, believe that this proceedings provides a significant and relevant contribution to the field of molecular conductors since it is the first time we have published such a proceedings as an electronic journal. We note that all papers published in this volume of Journal of Physics: Conference Series have been peer reviewed by expert referees. Editors made every effort to satisfy the criterion of a proceedings journal published by IOP Publishing. Toshihiro Takahashi and Yoshikazu Suzumura Editors: Toshihiro Takahashi (Gakushuin University) (Chairman) Kazushi Kanoda (University of Tokyo) Seiichi Kagoshima (University of Tokyo) Takehiko Mori (Tokyo

Changes in permittivity and density of molecular liquids under high pressure.

Science.gov (United States)

Kiselev, Vladimir D; Kornilov, Dmitry A; Konovalov, Alexander I

2014-04-03

We collected and analyzed the density and permittivity of 57 nonpolar and dipolar molecular liquids at different temperatures (143 sets) and pressures (555 sets). No equation was found that could accurately predict the change to polar liquid permittivity by the change of its density in the range of the pressures and temperatures tested. Consequently, the influence of high hydrostatic pressure and temperature on liquid permittivity may be a more complicated process compared to density changes. The pressure and temperature coefficients of permittivity can be drastically larger than the pressure and temperature coefficients of density, indicating that pressure and particularly temperature significantly affect the structure of molecular liquids. These changes have less influence on the density change but can strongly affect the permittivity change. The clear relationship between the tangent and secant moduli of the permittivity curvatures under pressure for various molecular liquids at different temperatures was obtained, from which one can calculate the Tait equation coefficients from the experimental values of the pressure influence on the permittivity at ambient pressure.

Foundational Concepts and Underlying Theories for Majors in "Biochemistry and Molecular Biology"

Science.gov (United States)

Tansey, John T.; Baird, Teaster, Jr.; Cox, Michael M.; Fox, Kristin M.; Knight, Jennifer; Sears, Duane; Bell, Ellis

2013-01-01

Over the past two years, through an NSF RCN UBE grant, the ASBMB has held regional workshops for faculty members and science educators from around the country that focused on identifying: 1) core principles of biochemistry and molecular biology, 2) essential concepts and underlying theories from physics, chemistry, and mathematics, and 3)…

Level crossing in a molecular Cr{sub 8} ring

Energy Technology Data Exchange (ETDEWEB)

Affronte, M. E-mail: affronte@unimore.it; Guidi, T.; Caciuffo, R.; Carretta, S.; Amoretti, G.; Hinderer, J.; Sheikin, I.; Smith, A.A.; Winpenny, R.E.P.; Slageren, J. van; Gatteschi, D

2004-05-01

The heat capacity of a molecular Cr{sub 8} ring was measured as a function of temperature and magnetic field in order to follow the evolution of the Schottky anomaly through the first (S=0 to |1,-1>) level crossing occurring at B{sub c1}=6.9 T. The results are interpreted within the framework of a spin Hamiltonian approach and they nicely fit the pattern of the energy levels derived by inelastic neutron spectroscopy. At B{sub c1}, the Schottky anomaly almost vanishes suggesting that a true crossing occurs in Cr{sub 8} in contrast to what was observed for ferric wheels.

Deep level transient spectroscopic investigation of phosphorus-doped silicon by self-assembled molecular monolayers.

Science.gov (United States)

Gao, Xuejiao; Guan, Bin; Mesli, Abdelmadjid; Chen, Kaixiang; Dan, Yaping

2018-01-09

It is known that self-assembled molecular monolayer doping technique has the advantages of forming ultra-shallow junctions and introducing minimal defects in semiconductors. In this paper, we report however the formation of carbon-related defects in the molecular monolayer-doped silicon as detected by deep-level transient spectroscopy and low-temperature Hall measurements. The molecular monolayer doping process is performed by modifying silicon substrate with phosphorus-containing molecules and annealing at high temperature. The subsequent rapid thermal annealing drives phosphorus dopants along with carbon contaminants into the silicon substrate, resulting in a dramatic decrease of sheet resistance for the intrinsic silicon substrate. Low-temperature Hall measurements and secondary ion mass spectrometry indicate that phosphorus is the only electrically active dopant after the molecular monolayer doping. However, during this process, at least 20% of the phosphorus dopants are electrically deactivated. The deep-level transient spectroscopy shows that carbon-related defects are responsible for such deactivation.

Molecular dynamics for irradiation driven chemistry

DEFF Research Database (Denmark)

Sushko, Gennady B.; Solov'yov, Ilia A.; Solov'yov, Andrey V.

2016-01-01

A new molecular dynamics (MD) approach for computer simulations of irradiation driven chemical transformations of complex molecular systems is suggested. The approach is based on the fact that irradiation induced quantum transformations can often be treated as random, fast and local processes...... that describe the classical MD of complex molecular systems under irradiation. The proposed irradiation driven molecular dynamics (IDMD) methodology is designed for the molecular level description of the irradiation driven chemistry. The IDMD approach is implemented into the MBN Explorer software package...... involving small molecules or molecular fragments. We advocate that the quantum transformations, such as molecular bond breaks, creation and annihilation of dangling bonds, electronic charge redistributions, changes in molecular topologies, etc., could be incorporated locally into the molecular force fields...

A molecular perspective on the limits of life: Enzymes under pressure

Directory of Open Access Journals (Sweden)

Q. Huang

2016-03-01

Full Text Available From a purely operational standpoint, the existence of microbes that can grow under extreme conditions, or "extremophiles", leads to the question of how the molecules making up these microbes can maintain both their structure and function. While microbes that live under extremes of temperature have been heavily studied, those that live under extremes of pressure have been neglected, in part due to the difficulty of collecting samples and performing experiments under the ambient conditions of the microbe. However, thermodynamic arguments imply that the effects of pressure might lead to different organismal solutions than from the effects of temperature. Observationally, some of these solutions might be in the condensed matter properties of the intracellular milieu in addition to genetic modifications of the macromolecules or repair mechanisms for the macromolecules. Here, the effects of pressure on enzymes, which are proteins essential for the growth and reproduction of an organism, and some adaptations against these effects are reviewed and amplified by the results from molecular dynamics simulations. The aim is to provide biological background for soft matter studies of these systems under pressure.

Molecular Mechanisms Underlying γ-Aminobutyric Acid (GABA) Accumulation in Giant Embryo Rice Seeds.

Science.gov (United States)

Zhao, Guo-Chao; Xie, Mi-Xue; Wang, Ying-Cun; Li, Jian-Yue

2017-06-21

To uncover the molecular mechanisms underlying GABA accumulation in giant embryo rice seeds, we analyzed the expression levels of GABA metabolism genes and contents of GABA and GABA metabolic intermediates in developing grains and germinated brown rice of giant embryo rice 'Shangshida No. 5' and normal embryo rice 'Chao2-10' respectively. In developing grains, the higher GABA contents in 'Shangshida No. 5' were accompanied with upregulation of gene transcripts and intermediate contents in the polyamine pathway and downregulation of GABA catabolic gene transcripts, as compared with those in 'Chao2-10'. In germinated brown rice, the higher GABA contents in 'Shangshida No. 5' were parallel with upregulation of OsGAD and polyamine pathway gene transcripts and Glu and polyamine pathway intermediate contents and downregulation of GABA catabolic gene transcripts. These results are the first to indicate that polyamine pathway and GABA catabolic genes play a crucial role in GABA accumulation in giant embryo rice seeds.

Molecular Mechanistic Reasoning: Toward Bridging the Gap between the Molecular and Cellular Levels in Life Science Education

Science.gov (United States)

van Mil, Marc H. W.; Postma, Paulien A.; Boerwinkel, Dirk Jan; Klaassen, Kees; Waarlo, Arend Jan

2016-01-01

Although learning about DNA, RNA, and proteins is part of the upper secondary biology curriculum in most countries, many studies report that students fail to connect molecular knowledge to phenomena at the higher level of cells, organs, and organisms. As a result, many students use memorization and rote learning as a coping strategy when presented…

Flashing evaporation under different pressure levels

International Nuclear Information System (INIS)

Liao, Yixiang; Lucas, Dirk; Krepper, Eckhard; Rzehak, Roland

2013-01-01

Highlights: • CFD simulation based on two-fluid model for flashing boiling inside a vertical pipe. • Effect of pressure level on the maximum thermal energy available for evaporation. • Effect of presumed bubble size on the onset of flashing as well as evaporation rate. • Effect of pressure level on the critical bubble size that can start stable flashing. • Effect of pressure level on nucleation rate and mechanism. - Abstract: Flashing evaporation of water inside a vertical pipe under four pressure levels is investigated both experimentally and numerically. In the experiment depressurization is realized through a blow-off valve, and the evaporation rate is controlled by the opening rate and degree of the valve. In the CFD simulation phase change is assumed to be caused by thermal heat transfer between steam–water interface and the surrounding water. Consequently, the evaporation rate is determined by heat transfer coefficient, interfacial area density as well as liquid superheat degree. The simulated temporal course of cross-section averaged steam volume fraction is compared with the measured one. It is found that the increasing rate and maximum value of steam volume fraction is over-predicted under low-pressure conditions, which is mainly caused by the neglect of bubble growth in the mono-dispersed simulation. The agreement is notably improved by performing poly-dispersed simulations with the inhomogeneous MUSIG approach (IMUSIG). On the other hand an underestimation of the maximum steam volume fraction is observed in high-pressure cases, since the contribution of nucleation to the total steam generation rate becomes large as the system pressure increases. Reliable models for nucleation rate as well as bubble detachment size are indispensable for reliable predictions. An effect of the system pressure level on the nucleation mechanism is observed in the experiment

A new vibrational level of the H2+ molecular ion

International Nuclear Information System (INIS)

Carbonell, J.; Lazauskas, R.; Delande, D.; Hilico, L.; Kilic, S.; Hilico, L.; Kilic, S.

2003-01-01

A new vibrational level of the molecular ion H 2 + with binding energy of 1.09 x 10 -9 a.u. ∼ 30 neV below the first dissociation limit is predicted, using highly accurate numerical non-relativistic quantum calculations, which go beyond the Born-Oppenheimer approximation. It is the first-excited vibrational level v=1 of the 2pσ u electronic state, antisymmetric with respect to the exchange of the two protons, with orbital angular momentum L=0. It manifests itself as a huge p - H scattering length of a = 750 ± 5 Bohr radii. (authors)

A hypothesis regarding the molecular mechanism underlying dietary soy-induced effects on seizure propensity.

Directory of Open Access Journals (Sweden)

Cara Jean Westmark

2014-09-01

Full Text Available Numerous neurological disorders including fragile X syndrome, Down syndrome, autism and Alzheimer’s disease are comorbid with epilepsy. We have observed elevated seizure propensity in mouse models of these disorders dependent on diet. Specifically, soy-based diets exacerbate audiogenic-induced seizures in juvenile mice. We have also found potential associations between the consumption of soy-based infant formula and seizure incidence, epilepsy comorbidity and autism diagnostic scores in autistic children by retrospective analyses of medical record data. In total, these data suggest that consumption of high levels of soy protein during postnatal development may affect neuronal excitability. Herein, we present our theory regarding the molecular mechanism underlying soy-induced effects on seizure propensity. We hypothesize that soy phytoestrogens interfere with metabotropic glutamate receptor signaling through an estrogen receptor-dependent mechanism, which results in elevated production of key synaptic proteins and decreased seizure threshold.

Elucidating the molecular mechanisms underlying cellular response to biophysical cues using synthetic biology approaches

NARCIS (Netherlands)

Denning, Denise; Roos, Wouter H

2016-01-01

The use of synthetic surfaces and materials to influence and study cell behavior has vastly progressed our understanding of the underlying molecular mechanisms involved in cellular response to physicochemical and biophysical cues. Reconstituting cytoskeletal proteins and interfacing them with a

Deciphering molecular circuits from genetic variation underlying transcriptional responsiveness to stimuli.

Science.gov (United States)

Gat-Viks, Irit; Chevrier, Nicolas; Wilentzik, Roni; Eisenhaure, Thomas; Raychowdhury, Raktima; Steuerman, Yael; Shalek, Alex K; Hacohen, Nir; Amit, Ido; Regev, Aviv

2013-04-01

Individual genetic variation affects gene responsiveness to stimuli, often by influencing complex molecular circuits. Here we combine genomic and intermediate-scale transcriptional profiling with computational methods to identify variants that affect the responsiveness of genes to stimuli (responsiveness quantitative trait loci or reQTLs) and to position these variants in molecular circuit diagrams. We apply this approach to study variation in transcriptional responsiveness to pathogen components in dendritic cells from recombinant inbred mouse strains. We identify reQTLs that correlate with particular stimuli and position them in known pathways. For example, in response to a virus-like stimulus, a trans-acting variant responds as an activator of the antiviral response; using RNA interference, we identify Rgs16 as the likely causal gene. Our approach charts an experimental and analytic path to decipher the mechanisms underlying genetic variation in circuits that control responses to stimuli.

Turning randomness into meaning at the molecular level using Muller's morphs.

Science.gov (United States)

Henson, Kathleen; Cooper, Melanie M; Klymkowsky, Michael W

2012-04-15

While evolutionary theory follows from observable facts and logical inferences (Mayr, 1985), historically, the origin of novel inheritable variations was a major obstacle to acceptance of natural selection (Bowler, 1992; Bowler, 2005). While molecular mechanisms address this issue (Jablonka and Lamb, 2005), analysis of responses to the Biological Concept Inventory (BCI) (Klymkowsky et al., 2010), revealed that molecular biology majors rarely use molecular level ideas in their discourse, implying that they do not have an accessible framework within which to place evolutionary variation. We developed a "Socratic tutorial" focused on Muller's categorization of mutations' phenotypic effects (Muller, 1932). Using a novel vector-based method to analyzed students' essay responses, we found that a single interaction with this tutorial led to significant changes in thinking toward a clearer articulation of the effects of mutational change. We suggest that Muller's morphs provides an effective framework for facilitating student learning about mutational effects and evolutionary mechanisms.

Turning randomness into meaning at the molecular level using Muller's morphs

Directory of Open Access Journals (Sweden)

Kathleen Henson

2012-02-01

While evolutionary theory follows from observable facts and logical inferences (Mayr, 1985, historically, the origin of novel inheritable variations was a major obstacle to acceptance of natural selection (Bowler, 1992; Bowler, 2005. While molecular mechanisms address this issue (Jablonka and Lamb, 2005, analysis of responses to the Biological Concept Inventory (BCI (Klymkowsky et al., 2010, revealed that molecular biology majors rarely use molecular level ideas in their discourse, implying that they do not have an accessible framework within which to place evolutionary variation. We developed a “Socratic tutorial” focused on Muller's categorization of mutations' phenotypic effects (Muller, 1932. Using a novel vector-based method to analyzed students' essay responses, we found that a single interaction with this tutorial led to significant changes in thinking toward a clearer articulation of the effects of mutational change. We suggest that Muller's morphs provides an effective framework for facilitating student learning about mutational effects and evolutionary mechanisms.

ESCA and electron diffraction studies of InP surface heated under As molecular beam exposure

International Nuclear Information System (INIS)

Sugiura, Hideo; Yamaguchi, Masafumi; Shibukawa, Atsushi

1983-01-01

Chemical composition of InP substrate surface heattreated under As molecular beam exposure in an ultrahigh vacuum chamber was studied with ESCA, and surface reconstruction of the substrate was examined by in-situ electron diffraction. The InP substrate heated under the exposure of As molecular beam has mirror surface up to 590 0 C while the surface of InP heated above 400 0 C in vacuum is roughened. The ESCA study shows that thin InAs layer (thickness 0 C under the exposure of As. The electron diffraction study indicates that the InP is cleaned at about 500 0 C in As pressures of 10 -7 - 10 -5 Torr. The InP surface is prevented from thermally decomposing by the coverage of the InAs layer, which may be formed through the following process: 2InPO 4 + As 4 → 2InAs + P 2 O 5 + As 2 O 3 . (author)

Cerebrospinal fluid tau levels are a marker for molecular subtype in sporadic Creutzfeldt-Jakob disease.

Science.gov (United States)

Karch, André; Hermann, Peter; Ponto, Claudia; Schmitz, Matthias; Arora, Amandeep; Zafar, Saima; Llorens, Franc; Müller-Heine, Annika; Zerr, Inga

2015-05-01

The molecular subtype of sporadic Creutzfeldt-Jakob disease (sCJD) is an important prognostic marker for patient survival. However, subtype determination is not possible during lifetime. Because the rate of disease progression is associated with the molecular subtype, this study aimed at investigating if total tau, a marker of neuronal death, allows premortem diagnosis of molecular subtype when codon 129 genotype is known. Two hundred ninety-six sCJD patients were tested for their cerebrospinal fluid total tau level at the time of diagnosis and were investigated for their sCJD subtype postmortem. There was a significant association between tau levels and the prion protein type in patients with codon 129 MM (p disease. Copyright © 2015 Elsevier Inc. All rights reserved.

Improved Inhibition of Telomerase by Short Twisted Intercalating Nucleic Acids under Molecular Crowding Conditions

DEFF Research Database (Denmark)

Agarwal, Tani; Pradhan, Devranjan; Géci, Imrich

2012-01-01

Human telomeric DNA has the ability to fold into a 4-stranded G-quadruplex structure. Several G-quadruplex ligands are known to stabilize the structure and thereby inhibit telomerase activity. Such ligands have demonstrated efficient telomerase inhibition in dilute conditions, but under molecular...

Formation of neutrophil extracellular traps under low oxygen level

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Katja Branitzki-Heinemann

2016-11-01

Full Text Available Since their discovery, neutrophil extracellular traps (NETs have been characterized as a fundamental host innate immune defense mechanism. Conversely, excessive NET release may have a variety of detrimental consequences for the host. A fine balance between NET formation and elimination is necessary to sustain a protective effect during an infectious challenge. Our own recently published data revealed that stabilization of hypoxia inducible factor 1α (HIF-1α by the iron chelating HIF-1α-agonist desferoxamine or AKB-4924 enhanced the release of phagocyte extracellular traps. Since HIF-1α is a global regulator of the cellular response to low oxygen, we hypothesized that NET formation may be similarly increased under low oxygen conditions. Hypoxia occurs in tissues during infection or inflammation, mostly due to overconsumption of oxygen by pathogens and recruited immune cells. Therefore, experiments were performed to characterize the formation of NETs under hypoxic oxygen conditions compared to normoxia. Human blood-derived neutrophils were isolated and incubated under normoxic (21% oxygen level and compared to hypoxic (1% conditions. Dissolved oxygen levels were monitored in the primary cell culture using a Fibox4-PSt3 measurement system. The formation of NETs was quantified by fluorescence microscopy in response to the known NET-inducer phorbol 12-myristate 13-acetate (PMA or S. aureus wildtype and a nuclease-deficient mutant. In contrast to our hypothesis, spontaneous NET formation of neutrophils incubated under hypoxia was distinctly reduced compared to control neutrophils incubated under normoxia. Furthermore, neutrophils incubated under hypoxia showed significantly reduced formation of NETs in response to PMA. Gene expression analysis revealed that mRNA level of hif-1α as well as hif-1α target genes was not altered. However, in good correlation to the decreased NET formation under hypoxia, the cholesterol content of the neutrophils was

Unraveling the Root Proteome Changes and Its Relationship to Molecular Mechanism Underlying Salt Stress Response in Radish (Raphanus sativus L.

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Xiaochuan Sun

2017-07-01

Full Text Available To understand the molecular mechanism underlying salt stress response in radish, iTRAQ-based proteomic analysis was conducted to investigate the differences in protein species abundance under different salt treatments. In total, 851, 706, and 685 differential abundance protein species (DAPS were identified between CK vs. Na100, CK vs. Na200, and Na100 vs. Na200, respectively. Functional annotation analysis revealed that salt stress elicited complex proteomic alterations in radish roots involved in carbohydrate and energy metabolism, protein metabolism, signal transduction, transcription regulation, stress and defense and transport. Additionally, the expression levels of nine genes encoding DAPS were further verified using RT-qPCR. The integrative analysis of transcriptomic and proteomic data in conjunction with miRNAs was further performed to strengthen the understanding of radish response to salinity. The genes responsible for signal transduction, ROS scavenging and transport activities as well as several key miRNAs including miR171, miR395, and miR398 played crucial roles in salt stress response in radish. Based on these findings, a schematic genetic regulatory network of salt stress response was proposed. This study provided valuable insights into the molecular mechanism underlying salt stress response in radish roots and would facilitate developing effective strategies toward genetically engineered salt-tolerant radish and other root vegetable crops.

Molecular Mechanisms Underlying Abscisic Acid/Gibberellin Balance in the Control of Seed Dormancy and Germination in Cereals

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Pham A. Tuan

2018-05-01

Full Text Available Seed dormancy is an adaptive trait that does not allow the germination of an intact viable seed under favorable environmental conditions. Non-dormant seeds or seeds with low level of dormancy can germinate readily under optimal environmental conditions, and such a trait leads to preharvest sprouting, germination of seeds on the mother plant prior to harvest, which significantly reduces the yield and quality of cereal crops. High level of dormancy, on the other hand, may lead to non-uniform germination and seedling establishment. Therefore, intermediate dormancy is considered to be a desirable trait as it prevents the problems of sprouting and allows uniformity of postharvest germination of seeds. Induction, maintenance, and release of seed dormancy are complex physiological processes that are influenced by a wide range of endogenous and environmental factors. Plant hormones, mainly abscisic acid (ABA and gibberellin (GA, are the major endogenous factors that act antagonistically in the control of seed dormancy and germination; ABA positively regulates the induction and maintenance of dormancy, while GA enhances germination. Significant progress has been made in recent years in the elucidation of molecular mechanisms regulating ABA/GA balance and thereby dormancy and germination in cereal seeds, and this review summarizes the current state of knowledge on the topic.

Molecular Mechanisms Underlying Abscisic Acid/Gibberellin Balance in the Control of Seed Dormancy and Germination in Cereals

Science.gov (United States)

Tuan, Pham A.; Kumar, Rohit; Rehal, Pawanpuneet K.; Toora, Parneet K.; Ayele, Belay T.

2018-01-01

Seed dormancy is an adaptive trait that does not allow the germination of an intact viable seed under favorable environmental conditions. Non-dormant seeds or seeds with low level of dormancy can germinate readily under optimal environmental conditions, and such a trait leads to preharvest sprouting, germination of seeds on the mother plant prior to harvest, which significantly reduces the yield and quality of cereal crops. High level of dormancy, on the other hand, may lead to non-uniform germination and seedling establishment. Therefore, intermediate dormancy is considered to be a desirable trait as it prevents the problems of sprouting and allows uniformity of postharvest germination of seeds. Induction, maintenance, and release of seed dormancy are complex physiological processes that are influenced by a wide range of endogenous and environmental factors. Plant hormones, mainly abscisic acid (ABA) and gibberellin (GA), are the major endogenous factors that act antagonistically in the control of seed dormancy and germination; ABA positively regulates the induction and maintenance of dormancy, while GA enhances germination. Significant progress has been made in recent years in the elucidation of molecular mechanisms regulating ABA/GA balance and thereby dormancy and germination in cereal seeds, and this review summarizes the current state of knowledge on the topic. PMID:29875780

Immobilized enzymes: understanding enzyme - surface interactions at the molecular level.

Science.gov (United States)

Hoarau, Marie; Badieyan, Somayesadat; Marsh, E Neil G

2017-11-22

Enzymes immobilized on solid supports have important and industrial and medical applications. However, their uses are limited by the significant reductions in activity and stability that often accompany the immobilization process. Here we review recent advances in our understanding of the molecular level interactions between proteins and supporting surfaces that contribute to changes in stability and activity. This understanding has been facilitated by the application of various surface-sensitive spectroscopic techniques that allow the structure and orientation of enzymes at the solid/liquid interface to be probed, often with monolayer sensitivity. An appreciation of the molecular interactions between enzyme and surface support has allowed the surface chemistry and method of enzyme attachement to be fine-tuned such that activity and stability can be greatly enhanced. These advances suggest that a much wider variety of enzymes may eventually be amenable to immobilization as green catalysts.

Mechanisms of molecular electronic rectification through electronic levels with strong vibrational coupling

DEFF Research Database (Denmark)

Kuznetsov, A.M.; Ulstrup, Jens

2002-01-01

We present a new view and an analytical formalism of electron flow through a donor-acceptor molecule inserted between a pair of metal electrodes. The donor and acceptor levels are strongly coupled to an environmental nuclear continuum. The formalism applies to molecular donor-acceptor systems bot...

Energy level alignment and molecular conformation at rubrene/Ag interfaces: Impact of contact contaminations on the interfaces

Energy Technology Data Exchange (ETDEWEB)

Sinha, Sumona, E-mail: sumona.net.09@gmail.com [Saha Institute of Nuclear Physics, 1/AF, Bidhannagar, Kolkata 700064 (India); Wang, C.-H. [National Synchrotron Radiation Research Center, Hsinchu 30076, Taiwan (China); Mukherjee, M. [Saha Institute of Nuclear Physics, 1/AF, Bidhannagar, Kolkata 700064 (India)

2017-07-01

Highlights: • Impact of contact contaminations on the energy level alignment and molecular conformation at rubrene/Ag interfaces. • Adventitious contamination layer was acted as a spacer layer between Ag substrate surface and rubrene molecular layer. • Hole injection barrier height and interface dipole at rubrene/Ag interfaces depend on the cleanliness of Ag substrate. • Molecular conformation as well as orientation controlled by the cleanliness of Ag surface. • Resulted different surface morphology of rubrene thin films on unclean and clean Ag substrate. - Abstract: This paper addresses the impact of electrode contaminations on the interfacial energy level alignment, the molecular conformation, orientation and surface morphology deposited organic film at organic semiconductor/noble metal interfaces by varying of film thickness from sub-monolayer to multilayer, which currently draws significant attention with regard to its application in organic electronics. The UHV clean Ag and unclean Ag were employed as substrate whereas rubrene was used as an organic semiconducting material. The photoelectron spectroscopy (XPS and UPS) was engaged to investigate the evolution of interfacial energetics; polarization dependent near edge x-ray absorption fine structure spectroscopy (NEXAFS) was employed to understand the molecular conformation as well as orientation whereas atomic force microscopy (AFM) was used to investigate the surface morphologies of the films. The adventitious contamination layer was acted as a spacer layer between clean Ag substrate surface and rubrene molecular layer. As a consequence, hole injection barrier height, interface dipole as well as molecular-conformation, molecular-orientation and surface morphology of rubrene thin films were found to depend on the cleanliness of Ag substrate. The results have important inferences about the understanding of the impact of substrate contamination on the energy level alignment, the molecular conformation

Molecular mechanisms underlying formation of long-term reward memories and extinction memories in the honeybee (Apis mellifera)

Science.gov (United States)

2014-01-01

The honeybee (Apis mellifera) has long served as an invertebrate model organism for reward learning and memory research. Its capacity for learning and memory formation is rooted in the ecological need to efficiently collect nectar and pollen during summer to ensure survival of the hive during winter. Foraging bees learn to associate a flower's characteristic features with a reward in a way that resembles olfactory appetitive classical conditioning, a learning paradigm that is used to study mechanisms underlying learning and memory formation in the honeybee. Due to a plethora of studies on appetitive classical conditioning and phenomena related to it, the honeybee is one of the best characterized invertebrate model organisms from a learning psychological point of view. Moreover, classical conditioning and associated behavioral phenomena are surprisingly similar in honeybees and vertebrates, suggesting a convergence of underlying neuronal processes, including the molecular mechanisms that contribute to them. Here I review current thinking on the molecular mechanisms underlying long-term memory (LTM) formation in honeybees following classical conditioning and extinction, demonstrating that an in-depth analysis of the molecular mechanisms of classical conditioning in honeybees might add to our understanding of associative learning in honeybees and vertebrates. PMID:25225299

Stable Molecular Diodes Based on π-π Interactions of the Molecular Frontier Orbitals with Graphene Electrodes.

Science.gov (United States)

Song, Peng; Guerin, Sarah; Tan, Sherman Jun Rong; Annadata, Harshini Venkata; Yu, Xiaojiang; Scully, Micheál; Han, Ying Mei; Roemer, Max; Loh, Kian Ping; Thompson, Damien; Nijhuis, Christian A

2018-03-01

In molecular electronics, it is important to control the strength of the molecule-electrode interaction to balance the trade-off between electronic coupling strength and broadening of the molecular frontier orbitals: too strong coupling results in severe broadening of the molecular orbitals while the molecular orbitals cannot follow the changes in the Fermi levels under applied bias when the coupling is too weak. Here, a platform based on graphene bottom electrodes to which molecules can bind via π-π interactions is reported. These interactions are strong enough to induce electronic function (rectification) while minimizing broadening of the molecular frontier orbitals. Molecular tunnel junctions are fabricated based on self-assembled monolayers (SAMs) of Fc(CH 2 ) 11 X (Fc = ferrocenyl, X = NH 2 , Br, or H) on graphene bottom electrodes contacted to eutectic alloy of gallium and indium top electrodes. The Fc units interact more strongly with graphene than the X units resulting in SAMs with the Fc at the bottom of the SAM. The molecular diodes perform well with rectification ratios of 30-40, and they are stable against bias stressing under ambient conditions. Thus, tunnel junctions based on graphene with π-π molecule-electrode coupling are promising platforms to fabricate stable and well-performing molecular diodes. © 2018 WILEY-VCH Verlag GmbH & Co. KGaA, Weinheim.

Current state of molecular imaging research

International Nuclear Information System (INIS)

Grimm, J.; Wunder, A.

2005-01-01

The recent years have seen significant advances in both molecular biology, allowing the identification of genes and pathways related to disease, and imaging technologies that allow for improved spatial and temporal resolution, enhanced sensitivity, better depth penetration, improved image processing, and beneficial combinations of different imaging modalities. These advances have led to a paradigm shift in the scope of diagnostic imaging. The traditional role of radiological diagnostic imaging is to define gross anatomy and structure in order to detect pathological abnormalities. Available contrast agents are mostly non-specific and can be used to image physiological processes such as changes in blood volume, flow, and perfusion but not to demonstrate pathological alterations at molecular levels. However, alterations at the anatomical-morphological level are relatively late manifestations of underlying molecular changes. Using molecular probes or markers that bind specifically to molecular targets allows for the non-invasive visualization and quantitation of biological processes such as gene expression, apoptosis, or angiogenesis at the molecular level within intact living organisms. This rapidly evolving, multidisciplinary approach, referred to as molecular imaging, promises to enable early diagnosis, can provide improved classification of stage and severity of disease, an objective assessment of treatment efficacy, and a reliable prognosis. Furthermore, molecular imaging is an important tool for the evaluation of physiological and pathophysiological processes, and for the development of new therapies. This article comprises a review of current technologies of molecular imaging, describes the development of contrast agents and various imaging modalities, new applications in specific disease models, and potential future developments. (orig.)

Submicron particulate organic matter in the urban atmosphere: a new method for real-time measurement, molecular-level characterization and source apportionment

Science.gov (United States)

Müller, Markus; Eichler, Philipp; D'Anna, Barbara; Tan, Wen; Wisthaler, Armin

2017-04-01

We used a novel chemical analytical method for measuring submicron particulate organic matter in the atmosphere of three European cities (Innsbruck, Lyon, Valencia). Proton-Transfer-Reaction Time-of-Flight Mass Spectrometry (PTR-ToF-MS) was used in combination with the "chemical analysis of aerosol online" (CHARON) inlet for detecting particulate organic compounds on-line (i.e. without filter pre-collection), in real-time (1-min time resolution), at ng m-3 concentrations, with molecular-level resolution (i.e. obtaining molecular weight and elemental composition information). The CHARON-PTR-ToF-MS system monitored molecular tracers associated with different particle sources including levoglucosan from biomass combustion, PAHs from vehicular traffic, nicotine from cigarette smoking, and monoterpene oxidation products secondarily formed from biogenic emissions. The tracer information was used for interpreting positive matrix factorization (PMF) data which allowed us to apportion the sources of submicron particulate organic matter in the different urban environments. This work was funded through the PIMMS ITN, which was supported by the European Commission's 7th Framework Programme under grant agreement number 287382.

COPRED: prediction of fold, GO molecular function and functional residues at the domain level.

Science.gov (United States)

López, Daniel; Pazos, Florencio

2013-07-15

Only recently the first resources devoted to the functional annotation of proteins at the domain level started to appear. The next step is to develop specific methodologies for predicting function at the domain level based on these resources, and to implement them in web servers to be used by the community. In this work, we present COPRED, a web server for the concomitant prediction of fold, molecular function and functional sites at the domain level, based on a methodology for domain molecular function prediction and a resource of domain functional annotations previously developed and benchmarked. COPRED can be freely accessed at http://csbg.cnb.csic.es/copred. The interface works in all standard web browsers. WebGL (natively supported by most browsers) is required for the in-line preview and manipulation of protein 3D structures. The website includes a detailed help section and usage examples. pazos@cnb.csic.es.

Clinical and molecular sub-classification of hepatocellular carcinoma relative to alpha-fetoprotein level in an Asia-Pacific island cohort.

Science.gov (United States)

Nishioka, Scott T; Sato, Miles M; Wong, Linda L; Tiirikainen, Maarit; Kwee, Sandi A

2018-01-01

Increased serum alpha-fetoprotein (AFP) levels are associated with specific molecular sub-classes of hepatocellular carcinoma (HCC), supporting AFP as a predictive or therapeutic biomarker for precision treatment of this disease. Considering recent efforts to validate HCC molecular classification systems across different populations, we applied existing signature-based classification templates to Hawaii cohorts and examined whether associations between HCC molecular sub-class, AFP levels, and clinical features found elsewhere can also be found in Hawaii, a region with a unique demographic and risk factor profile for HCC. Whole-genome expression profiling was performed on HCC tumors collected from 40 patients following partial hepatectomy. Tumors underwent transcriptome-based categorization into 3 molecular sub-classes (S1, S2, and S3). Patient groups based on molecular sub-class and AFP level were then compared with regards to clinical features and survival. Differences associated with AFP level and other clinical parameters were also examined at the gene signature level by gene set enrichment analysis. Statistically confident (false discovery rate 400 ng/mL predicted significant tumor enrichment for genes corresponding to MYC target activation, high cell proliferation, poor clinical prognosis, and the S2 sub-class. AFP > 400 ng/mL and non-S3 tumor classification were found to be significant predictors of overall survival. Distinct sub-classes of HCC associated with different molecular features and survival outcomes can be detected with statistical confidence in a Pacific Island cohort. Molecular classification signatures and other predictive markers for HCC that are valid for all patient populations are needed to support multi-center efforts to develop targeted therapies for HCC.

Molecular dynamics study of radiation damage and microstructure evolution of zigzag single-walled carbon nanotubes under carbon ion incidence

Science.gov (United States)

Li, Huan; Tang, Xiaobin; Chen, Feida; Huang, Hai; Liu, Jian; Chen, Da

2016-07-01

The radiation damage and microstructure evolution of different zigzag single-walled carbon nanotubes (SWCNTs) were investigated under incident carbon ion by molecular dynamics (MD) simulations. The radiation damage of SWCNTs under incident carbon ion with energy ranging from 25 eV to 1 keV at 300 K showed many differences at different incident sites, and the defect production increased to the maximum value with the increase in incident ion energy, and slightly decreased but stayed fairly stable within the majority of the energy range. The maximum damage of SWCNTs appeared when the incident ion energy reached 200 eV and the level of damage was directly proportional to incident ion fluence. The radiation damage was also studied at 100 K and 700 K and the defect production decreased distinctly with rising temperature because radiation-induced defects would anneal and recombine by saturating dangling bonds and reconstructing carbon network at the higher temperature. Furthermore, the stability of a large-diameter tube surpassed that of a thin one under the same radiation environments.

Variations of serum testosterone levels in prostate cancer patients under LH-releasing hormone therapy: an open question.

Science.gov (United States)

Reis, Leonardo Oliveira

2012-06-01

The hypothesis 'the lower the better when achieving castration levels of testosterone' is based on the data from second-line hormonal manipulation and its molecular basis, and on better oncological results reported for lower castration levels in prostate cancer (PCa) patients, including those achieved with maximal androgen blockade. In this regard, the equivalence of surgical and different pharmacological castrations has been controversial. The modified amino acid structure that makes LH-releasing hormone (LHRH) analogs more potent than LHRH, and the method of delivering the analogs impacts on bioavailibility and potentially causes differences in androgen levels and in its final oncological efficacy. In addition to this, there is a myriad of circumstances, such as those related to ethnic variations and co-morbidities, which uniquely impact on the pharmacological approach in a highly heterogeneous population of castration-resistant prostate cancer (CRPC) patients. Ineffective testosterone suppression through hormonal escape is currently poorly recognized and may result in increased PCa mortality. Until now, the optimal serum testosterone level in patients under castration, and the impact of its variations in patients under LHRH therapy, remain open questions and have been merged to a broad spectra of patients who are highly heterogeneous. This heterogeneity relates to a number of mechanisms regarding response to treatment, which influences the biology of the relapsing tumor and the sensitivity to subsequent therapies in the individual patient. The rationale to achieve testosterone levels below 20-50 ng/dl warrant further investigation as these levels have recently rescued CRPC patients. In the last few years and months, important advancements in prostate cancer treatment have been achieved. Nevertheless, these advances are measured in a few months of additional survival and under high costs, not available to most of the world population, compared with the benefits

Surface Functionalization of g-C 3 N 4 : Molecular-Level Design of Noble-Metal-Free Hydrogen Evolution Photocatalysts

KAUST Repository

Chen, Yin

2015-06-12

A stable noble-metal-free hydrogen evolution photocatalyst based on graphite carbon nitride (g-C3N4) was developed by a molecular-level design strategy. Surface functionalization was successfully conducted to introduce a single nickel active site onto the surface of the semiconducting g-C3N4. This catalyst family (with less than 0.1 wt% of Ni) has been found to produce hydrogen with a rate near to the value obtained by using 3 wt% platinum as co-catalyst. This new catalyst also exhibits very good stability under hydrogen evolution conditions, without any evidence of deactivation after 24h. © 2015 WILEY-VCH Verlag GmbH & Co. KGaA, Weinheim.

Renormalization of Molecular Quasiparticle Levels at Metal-Molecule Interfaces: Trends across Binding Regimes

DEFF Research Database (Denmark)

Thygesen, Kristian Sommer; Rubio, Angel

2009-01-01

a microscopic model of the metal-molecule interface, we illustrate the basic features of this renormalization mechanism through systematic GW, Hartree-Fock, and Kohn-Sham calculations for the molecular energy levels as function of the model parameters. We identify two different polarization mechanisms: (i...

Evidence for systems-level molecular mechanisms of tumorigenesis

Directory of Open Access Journals (Sweden)

Capellá Gabriel

2007-06-01

Full Text Available Abstract Background Cancer arises from the consecutive acquisition of genetic alterations. Increasing evidence suggests that as a consequence of these alterations, molecular interactions are reprogrammed in the context of highly connected and regulated cellular networks. Coordinated reprogramming would allow the cell to acquire the capabilities for malignant growth. Results Here, we determine the coordinated function of cancer gene products (i.e., proteins encoded by differentially expressed genes in tumors relative to healthy tissue counterparts, hereafter referred to as "CGPs" defined as their topological properties and organization in the interactome network. We show that CGPs are central to information exchange and propagation and that they are specifically organized to promote tumorigenesis. Centrality is identified by both local (degree and global (betweenness and closeness measures, and systematically appears in down-regulated CGPs. Up-regulated CGPs do not consistently exhibit centrality, but both types of cancer products determine the overall integrity of the network structure. In addition to centrality, down-regulated CGPs show topological association that correlates with common biological processes and pathways involved in tumorigenesis. Conclusion Given the current limited coverage of the human interactome, this study proposes that tumorigenesis takes place in a specific and organized way at the molecular systems-level and suggests a model that comprises the precise down-regulation of groups of topologically-associated proteins involved in particular functions, orchestrated with the up-regulation of specific proteins.

The levels of processing effect under nitrogen narcosis.

Science.gov (United States)

Kneller, Wendy; Hobbs, Malcolm

2013-01-01

Previous research has consistently demonstrated that inert gas (nitrogen) narcosis affects free recall but not recognition memory in the depth range of 30 to 50 meters of sea water (msw), possibly as a result of narcosis preventing processing when learned material is encoded. The aim of the current research was to test this hypothesis by applying a levels of processing approach to the measurement of free recall under narcosis. Experiment 1 investigated the effect of depth (0-2 msw vs. 37-39 msw) and level of processing (shallow vs. deep) on free recall memory performance in 67 divers. When age was included as a covariate, recall was significantly worse in deep water (i.e., under narcosis), compared to shallow water, and was significantly higher in the deep processing compared to shallow processing conditions in both depth conditions. Experiment 2 demonstrated that this effect was not simply due to the different underwater environments used for the depth conditions in Experiment 1. It was concluded memory performance can be altered by processing under narcosis and supports the contention that narcosis affects the encoding stage of memory as opposed to self-guided search (retrieval).

Molecular sensors and molecular logic gates

International Nuclear Information System (INIS)

Georgiev, N.; Bojinov, V.

2013-01-01

Full text: The rapid grow of nanotechnology field extended the concept of a macroscopic device to the molecular level. Because of this reason the design and synthesis of (supra)-molecular species capable of mimicking the functions of macroscopic devices are currently of great interest. Molecular devices operate via electronic and/or nuclear rearrangements and, like macroscopic devices, need energy to operate and communicate between their elements. The energy needed to make a device work can be supplied as chemical energy, electrical energy, or light. Luminescence is one of the most useful techniques to monitor the operation of molecular-level devices. This fact determinates the synthesis of novel fluorescence compounds as a considerable and inseparable part of nanoscience development. Further miniaturization of semiconductors in electronic field reaches their limit. Therefore the design and construction of molecular systems capable of performing complex logic functions is of great scientific interest now. In semiconductor devices the logic gates work using binary logic, where the signals are encoded as 0 and 1 (low and high current). This process is executable on molecular level by several ways, but the most common are based on the optical properties of the molecule switches encoding the low and high concentrations of the input guest molecules and the output fluorescent intensities with binary 0 and 1 respectively. The first proposal to execute logic operations at the molecular level was made in 1988, but the field developed only five years later when the analogy between molecular switches and logic gates was experimentally demonstrated by de Silva. There are seven basic logic gates: AND, OR, XOR, NOT, NAND, NOR and XNOR and all of them were achieved by molecules, the fluorescence switching as well. key words: fluorescence, molecular sensors, molecular logic gates

Molecular medicine: a path towards a personalized medicine.

Science.gov (United States)

Miranda, Debora Marques de; Mamede, Marcelo; Souza, Bruno Rezende de; Almeida Barros, Alexandre Guimarães de; Magno, Luiz Alexandre; Alvim-Soares, Antônio; Rosa, Daniela Valadão; Castro, Célio José de; Malloy-Diniz, Leandro; Gomez, Marcus Vinícius; Marco, Luiz Armando De; Correa, Humberto; Romano-Silva, Marco Aurélio

2012-03-01

Psychiatric disorders are among the most common human illnesses; still, the molecular and cellular mechanisms underlying their complex pathophysiology remain to be fully elucidated. Over the past 10 years, our group has been investigating the molecular abnormalities in major signaling pathways involved in psychiatric disorders. Recent evidences obtained by the Instituto Nacional de Ciência e Tecnologia de Medicina Molecular (National Institute of Science and Technology - Molecular Medicine, INCT-MM) and others using behavioral analysis of animal models provided valuable insights into the underlying molecular alterations responsible for many complex neuropsychiatric disorders, suggesting that "defects" in critical intracellular signaling pathways have an important role in regulating neurodevelopment, as well as in pathophysiology and treatment efficacy. Resources from the INCT have allowed us to start doing research in the field of molecular imaging. Molecular imaging is a research discipline that visualizes, characterizes, and quantifies the biologic processes taking place at cellular and molecular levels in humans and other living systems through the results of image within the reality of the physiological environment. In order to recognize targets, molecular imaging applies specific instruments (e.g., PET) that enable visualization and quantification in space and in real-time of signals from molecular imaging agents. The objective of molecular medicine is to individualize treatment and improve patient care. Thus, molecular imaging is an additional tool to achieve our ultimate goal.

Molecular level in silico studies for oncology. Direct models review

Science.gov (United States)

Psakhie, S. G.; Tsukanov, A. A.

2017-09-01

The combination of therapy and diagnostics in one process "theranostics" is a trend in a modern medicine, especially in oncology. Such an approach requires development and usage of multifunctional hybrid nanoparticles with a hierarchical structure. Numerical methods and mathematical models play a significant role in the design of the hierarchical nanoparticles and allow looking inside the nanoscale mechanisms of agent-cell interactions. The current position of in silico approach in biomedicine and oncology is discussed. The review of the molecular level in silico studies in oncology, which are using the direct models, is presented.

When biomolecules meet graphene: from molecular level interactions to material design and applications.

Science.gov (United States)

Li, Dapeng; Zhang, Wensi; Yu, Xiaoqing; Wang, Zhenping; Su, Zhiqiang; Wei, Gang

2016-12-01

Graphene-based materials have attracted increasing attention due to their atomically-thick two-dimensional structures, high conductivity, excellent mechanical properties, and large specific surface areas. The combination of biomolecules with graphene-based materials offers a promising method to fabricate novel graphene-biomolecule hybrid nanomaterials with unique functions in biology, medicine, nanotechnology, and materials science. In this review, we focus on a summarization of the recent studies in functionalizing graphene-based materials using different biomolecules, such as DNA, peptides, proteins, enzymes, carbohydrates, and viruses. The different interactions between graphene and biomolecules at the molecular level are demonstrated and discussed in detail. In addition, the potential applications of the created graphene-biomolecule nanohybrids in drug delivery, cancer treatment, tissue engineering, biosensors, bioimaging, energy materials, and other nanotechnological applications are presented. This review will be helpful to know the modification of graphene with biomolecules, understand the interactions between graphene and biomolecules at the molecular level, and design functional graphene-based nanomaterials with unique properties for various applications.

Molecular Mechanisms Underlying the Epileptogenesis and Seizure Progression in Tuberous Sclerosis Complex 1 Deficient Mouse Models

Science.gov (United States)

2016-10-01

dysregulation in epileptogenesis in the developing brain? 2) What are the molecular mechanisms downstream of mTOR hyperactivation that trigger epileptogenesis...underlying epilepsy. Hopefully, a knowledge of these mechanisms will aid in a rational development of therapies. KEYWORDS Tuberous Sclerosis, Epilepsy

Dialkylthio Substitution: An Effective Method to Modulate the Molecular Energy Levels of 2D-BDT Photovoltaic Polymers.

Science.gov (United States)

Yao, Huifeng; Zhang, Hao; Ye, Long; Zhao, Wenchao; Zhang, Shaoqing; Hou, Jianhui

2016-02-17

Dialkylthio-substituted thienyl-benzodithiophene (BDT-DST) was designed and synthesized as a building block to modulate the molecular levels of the conjugated polymers, and three copolymers named PDST-BDD, PDST-TT and PDST-DPP were prepared and applied in polymer solar cells (PSCs). Theoretical calculations and electrochemical cyclic voltammetry (CV) measurement suggested that the dialkylthio group could decrease the molecular energy levels of the resulting polymers distinctly. The open-circuit voltage (VOC) of PSC devices based on PDST-BDD, PDST-TT, and PDST-DPP are as high as 1.0, 0.98, and 0.88 V, respectively, which are ∼0.15 V higher than those of the corresponding alky-substituted analogues. Moreover, the influence of the dialkylthio group on the absorption spectra, crystalline properties, hole mobilities, and blend morphologies of the polymers was also investigated. The results indicate that the dialkythio substitution is an effective method to modulate the molecular energy levels and that the BDT-DST unit has potential for constructing high-efficiency photovoltaic polymers.

Molecular-level mechanisms of vibrational frequency shifts in a polar liquid.

Science.gov (United States)

Morales, Christine M; Thompson, Ward H

2011-06-16

A molecular-level analysis of the origins of the vibrational frequency shifts of the CN stretching mode in neat liquid acetonitrile is presented. The frequency shifts and infrared spectrum are calculated using a perturbation theory approach within a molecular dynamics simulation and are in good agreement with measured values reported in the literature. The resulting instantaneous frequency of each nitrile group is decomposed into the contributions from each molecule in the liquid and by interaction type. This provides a detailed picture of the mechanisms of frequency shifts, including the number of surrounding molecules that contribute to the shift, the relationship between their position and relative contribution, and the roles of electrostatic and van der Waals interactions. These results provide insight into what information is contained in infrared (IR) and Raman spectra about the environment of the probed vibrational mode. © 2011 American Chemical Society

Cadmium toxicity studies under long term-low level exposure (LLE) conditions. I

International Nuclear Information System (INIS)

Sabbioni, E.; Marafante, E.; Amantini, L.; Ubertalli, L.; Pietra, R.

1978-01-01

A long term-low level exposure (LLE) experiment was conducted on rats to determine the metabolic patterns for realistic dietary levels of cadmium. Male rats fed with 61 ppb of cadmium ad libitum, 50 labelled with 109 Cd radiotracer as cadmium chloride via drinking mineral water and 11 unlabelled via food for 2 years. The diet was characterized in its metal content by neutron activation analysis to obtain the total dietary intake of different elements. The kidney was found to be the tissue with the major concentration of cadmium which accumulated continuously during the experiment. The variation of the accumulation pattern of Cd concentration in the liver and intestine indicated an initial rapid increase of Cd during the first 100 days. After this period an apparent equilibrium was attained in both these tissues until the end of the study. The intracellular distribution of cadmium in kidneys, liver, intestine and pancreas were similar, the cytosol fractions containing about 80% of the cellular cadmium. Dialysis experiments indicated that significant amounts of cadmium were able to be associated with cellular organelles, the mitochondria representing the most important organelle capable of binding cadmium. The cytoplasmatic Cd-profiles obtained at various stages of the experiment showed that the metal was only bound to a low-molecular-weight component, cadmium-binding protein (CdBP), which represents the specific cellular-binding component for cadmium under the long term-low level exposure (LLE) conditions. No significant variations in the concentrations of the elements in different organs were observed in animals supplemented with 109 Cd in respect to 109 Cd untreated controls. (Auth.)

Cardiovascular molecular imaging of apoptosis

International Nuclear Information System (INIS)

Wolters, S.L.; Reutelingsperger, C.P.M.; Corsten, M.F.; Hofstra, L.; Narula, J.

2007-01-01

Molecular imaging strives to visualise processes at the molecular and cellular level in vivo. Understanding these processes supports diagnosis and evaluation of therapeutic efficacy on an individual basis and thereby makes personalised medicine possible. Apoptosis is a well-organised mode of cell suicide that plays a role in cardiovascular diseases (CVD). Apoptosis is associated with loss of cardiomyocytes following myocardial infarction, atherosclerotic plaque instability, congestive heart failure and allograft rejection of the transplanted heart. Thus, apoptosis constitutes an attractive target for molecular imaging of CVD. Our current knowledge about the molecular players and mechanisms underlying apoptosis offers a rich palette of potential molecular targets for molecular imaging. However, only a few have been successfully developed so far. This review highlights aspects of the molecular machinery and biochemistry of apoptosis relevant to the development of molecular imaging probes. It surveys the role of apoptosis in four major areas of CVD and portrays the importance and future perspectives of apoptosis imaging. The annexin A5 imaging protocol is emphasised since it is the most advanced protocol to measure apoptosis in both preclinical and clinical studies. (orig.)

Cardiovascular molecular imaging of apoptosis

Energy Technology Data Exchange (ETDEWEB)

Wolters, S.L.; Reutelingsperger, C.P.M. [Maastricht University, Department of Biochemistry, Cardiovascular Research Institute Maastricht, Maastricht (Netherlands); Corsten, M.F.; Hofstra, L. [Maastricht University, Department of Cardiology, Cardiovascular Research Institute Maastricht, P.O. Box 616, Maastricht (Netherlands); Narula, J. [University of California Irvine, Department of Cardiology, Irvine (United States)

2007-06-15

Molecular imaging strives to visualise processes at the molecular and cellular level in vivo. Understanding these processes supports diagnosis and evaluation of therapeutic efficacy on an individual basis and thereby makes personalised medicine possible. Apoptosis is a well-organised mode of cell suicide that plays a role in cardiovascular diseases (CVD). Apoptosis is associated with loss of cardiomyocytes following myocardial infarction, atherosclerotic plaque instability, congestive heart failure and allograft rejection of the transplanted heart. Thus, apoptosis constitutes an attractive target for molecular imaging of CVD. Our current knowledge about the molecular players and mechanisms underlying apoptosis offers a rich palette of potential molecular targets for molecular imaging. However, only a few have been successfully developed so far. This review highlights aspects of the molecular machinery and biochemistry of apoptosis relevant to the development of molecular imaging probes. It surveys the role of apoptosis in four major areas of CVD and portrays the importance and future perspectives of apoptosis imaging. The annexin A5 imaging protocol is emphasised since it is the most advanced protocol to measure apoptosis in both preclinical and clinical studies. (orig.)

Molecular dynamics simulations of the melting curve of NiAl alloy under pressure

OpenAIRE

Wenjin Zhang; Yufeng Peng; Zhongli Liu

2014-01-01

The melting curve of B2-NiAl alloy under pressure has been investigated using molecular dynamics technique and the embedded atom method (EAM) potential. The melting temperatures were determined with two approaches, the one-phase and the two-phase methods. The first one simulates a homogeneous melting, while the second one involves a heterogeneous melting of materials. Both approaches reduce the superheating effectively and their results are close to each other at the applied pressures. By fit...

Thymic function in the regulation of T cells, and molecular mechanisms underlying the modulation of cytokines and stress signaling (Review).

Science.gov (United States)

Yan, Fenggen; Mo, Xiumei; Liu, Junfeng; Ye, Siqi; Zeng, Xing; Chen, Dacan

2017-11-01

The thymus is critical in establishing and maintaining the appropriate microenvironment for promoting the development and selection of T cells. The function and structure of the thymus gland has been extensively studied, particularly as the thymus serves an important physiological role in the lymphatic system. Numerous studies have investigated the morphological features of thymic involution. Recently, research attention has increasingly been focused on thymic proteins as targets for drug intervention. Omics approaches have yielded novel insights into the thymus and possible drug targets. The present review addresses the signaling and transcriptional functions of the thymus, including the molecular mechanisms underlying the regulatory functions of T cells and their role in the immune system. In addition, the levels of cytokines secreted in the thymus have a significant effect on thymic functions, including thymocyte migration and development, thymic atrophy and thymic recovery. Furthermore, the regulation and molecular mechanisms of stress‑mediated thymic atrophy and involution were investigated, with particular emphasis on thymic function as a potential target for drug development and discovery using proteomics.

Molecular Level Investigation of Staphylococci’s Resistance Mechanisms to Antibiotics

Directory of Open Access Journals (Sweden)

Lavinia Lorena PRUTEANU

2017-09-01

Full Text Available Polymerase chain reaction (PCR techniques development allows elaboration of many assays for identification of bacteria’s resistance mechanisms to antibiotics. Following this idea, the results of molecular level investigation of bacteria’s resistance mechanisms to antibiotics may give many opportunities to find more rapid methods for identifying the genes which are responsible for antibiotic resistance induction. The aim of this study was to investigate antibiotic resistance genes in Staphylococcus bacteria on molecular level. As classes of antibiotics it was used macrolides-lincosamides-streptogramin B (MLSB and beta-lactams. In the proposed study the bacterial strains are represented by 50 isolates of Staphylococcus. The bacterial strains were analyzed using polymerase chain reaction to identify the nuc, tuf, tst, sea, pathogenic activity genes. After this, the bacteria were tested for ermA, ermB, ermC genes and for mecA, femA which are involved in resistance to macrolides, lincosamides, streptogramin B and to beta-lactams, respectively. The presence or the absence of these genes confirms that tested strains are resistant to specific antibiotic or not. Bacteria pathogenic activity was emphasized by genes as follows: sea (enterotoxin which was found at all isolates, tst (toxic shock toxin gene was not detected in any of isolates and tuf gene (elongation factor was obtained with one pair of primers. Resistance to beta-lactams was evidenced by the presence of mecA in all isolates and femA in some strains. Each of ermC, ermA and ermB, macrolides-lincosamides-streptogramin B resistance genes, were detected.

Molecular basis for the regulation of hypoxia-inducible factor-1α levels by 2-deoxy-D-ribose.

Science.gov (United States)

Ikeda, Ryuji; Tabata, Sho; Tajitsu, Yusuke; Nishizawa, Yukihiko; Minami, Kentaro; Furukawa, Tatsuhiko; Yamamoto, Masatatsu; Shinsato, Yoshinari; Akiyama, Shin-Ichi; Yamada, Katsushi; Takeda, Yasuo

2013-09-01

The angiogenic factor, platelet-derived endothelial cell growth factor/thymidine phosphorylase (PD-ECGF/TP), stimulates the chemotaxis of endothelial cells and confers resistance to apoptosis induced by hypoxia. 2-Deoxy-D-ribose, a degradation product of thymidine generated by TP enzymatic activity, inhibits the upregulation of hypoxia-inducible factor (HIF) 1α, BNIP3 and caspase-3 induced by hypoxia. In the present study, we investigated the molecular basis for the suppressive effect of 2-deoxy-D-ribose on the upregulation of HIF-1α. 2-Deoxy-D-ribose enhanced the interaction of HIF-1α and the von Hippel-Lindau (VHL) protein under hypoxic conditions. It did not affect the expression of HIF-1α, prolyl hydroxylase (PHD)1/2/3 and VHL mRNA under normoxic or hypoxic conditions, but enhanced the interaction of HIF-1α and PHD2 under hypoxic conditions. 2-Deoxy-D-ribose also increased the amount of hydroxy-HIF-1α in the presence of the proteasome inhibitor MG-132. The expression levels of TP are elevated in many types of malignant solid tumors and, thus, 2-deoxy-D-ribose generated by TP in these tumors may play an important role in tumor progression by preventing hypoxia-induced apoptosis.

ORAC: a molecular dynamics simulation program to explore free energy surfaces in biomolecular systems at the atomistic level.

Science.gov (United States)

Marsili, Simone; Signorini, Giorgio Federico; Chelli, Riccardo; Marchi, Massimo; Procacci, Piero

2010-04-15

We present the new release of the ORAC engine (Procacci et al., Comput Chem 1997, 18, 1834), a FORTRAN suite to simulate complex biosystems at the atomistic level. The previous release of the ORAC code included multiple time steps integration, smooth particle mesh Ewald method, constant pressure and constant temperature simulations. The present release has been supplemented with the most advanced techniques for enhanced sampling in atomistic systems including replica exchange with solute tempering, metadynamics and steered molecular dynamics. All these computational technologies have been implemented for parallel architectures using the standard MPI communication protocol. ORAC is an open-source program distributed free of charge under the GNU general public license (GPL) at http://www.chim.unifi.it/orac. 2009 Wiley Periodicals, Inc.

Biosystems Study of the Molecular Networks Underlying Hippocampal Aging Progression and Anti-aging Treatment in Mice

Directory of Open Access Journals (Sweden)

Jiao Wang

2017-12-01

Full Text Available Aging progression is a process that an individual encounters as they become older, and usually results from a series of normal physiological changes over time. The hippocampus, which contributes to the loss of spatial and episodic memory and learning in older people, is closely related to the detrimental effects of aging at the morphological and molecular levels. However, age-related genetic changes in hippocampal molecular mechanisms are not yet well-established. To provide additional insight into the aging process, differentially-expressed genes of 3- versus 24- and 29-month old mice were re-analyzed. The results revealed that a large number of immune and inflammatory response-related genes were up-regulated in the aged hippocampus, and membrane receptor-associated genes were down-regulated. The down-regulation of transmembrane receptors may indicate the weaker perception of environmental exposure in older people, since many transmembrane proteins participate in signal transduction. In addition, molecular interaction analysis of the up-regulated immune genes indicated that the hub gene, Ywhae, may play essential roles in immune and inflammatory responses during aging progression, as well as during hippocampal development. Our biological experiments confirmed the conserved roles of Ywhae and its partners between human and mouse. Furthermore, comparison of microarray data between advanced-age mice treated with human umbilical cord blood plasma protein and the phosphate-buffered saline control showed that the genes that contribute to the revitalization of advanced-age mice are different from the genes induced by aging. These results implied that the revitalization of advanced-age mice is not a simple reverse process of normal aging progression. Our data assigned novel roles of genes during aging progression and provided further theoretic evidence for future studies exploring the underlying mechanisms of aging and anti-aging-related disease

Molecular-level architectural design using benzothiadiazole-based polymers for photovoltaic applications.

Science.gov (United States)

Viswanathan, Vinila N; Rao, Arun D; Pandey, Upendra K; Kesavan, Arul Varman; Ramamurthy, Praveen C

2017-01-01

A series of low band gap, planar conjugated polymers, P1 (PFDTBT), P2 (PFDTDFBT) and P3 (PFDTTBT), based on fluorene and benzothiadiazole, was synthesized. The effect of fluorine substitution and fused aromatic spacers on the optoelectronic and photovoltaic performance was studied. The polymer, derived from dithienylated benzothiodiazole and fluorene, P1 , exhibited a highest occupied molecular orbital (HOMO) energy level at -5.48 eV. Density functional theory (DFT) studies as well as experimental measurements suggested that upon substitution of the acceptor with fluorine, both the HOMO and lowest unoccupied molecular orbital (LUMO) energy levels of the resulting polymer, P2 , were lowered, leading to a higher open circuit voltage and short circuit current with an overall improvement of more than 110% for the photovoltaic devices. Moreover, a decrease in the torsion angle between the units was also observed for the fluorinated polymer P2 due to the enhanced electrostatic interaction between the fluorine substituents and sulfur atoms, leading to a high hole mobility. The use of a fused π-bridge in polymer P3 for the enhancement of the planarity as compared to the P1 backbone was also studied. This enhanced planarity led to the highest observed mobility among the reported three polymers as well as to an improvement in the device efficiency by more than 40% for P3 .

Molecular-level architectural design using benzothiadiazole-based polymers for photovoltaic applications

Science.gov (United States)

Viswanathan, Vinila N; Rao, Arun D; Pandey, Upendra K; Kesavan, Arul Varman

2017-01-01

A series of low band gap, planar conjugated polymers, P1 (PFDTBT), P2 (PFDTDFBT) and P3 (PFDTTBT), based on fluorene and benzothiadiazole, was synthesized. The effect of fluorine substitution and fused aromatic spacers on the optoelectronic and photovoltaic performance was studied. The polymer, derived from dithienylated benzothiodiazole and fluorene, P1, exhibited a highest occupied molecular orbital (HOMO) energy level at −5.48 eV. Density functional theory (DFT) studies as well as experimental measurements suggested that upon substitution of the acceptor with fluorine, both the HOMO and lowest unoccupied molecular orbital (LUMO) energy levels of the resulting polymer, P2, were lowered, leading to a higher open circuit voltage and short circuit current with an overall improvement of more than 110% for the photovoltaic devices. Moreover, a decrease in the torsion angle between the units was also observed for the fluorinated polymer P2 due to the enhanced electrostatic interaction between the fluorine substituents and sulfur atoms, leading to a high hole mobility. The use of a fused π-bridge in polymer P3 for the enhancement of the planarity as compared to the P1 backbone was also studied. This enhanced planarity led to the highest observed mobility among the reported three polymers as well as to an improvement in the device efficiency by more than 40% for P3. PMID:28546844

Elucidation of molecular mechanisms of physiological variations between bovine subcutaneous and visceral fat depots under different nutritional regimes.

Science.gov (United States)

Romao, Josue Moura; Jin, Weiwu; He, Maolong; McAllister, Tim; Guan, Le Luo

2013-01-01

Adipose tissue plays a critical role in energy homeostasis and metabolism. There is sparse understanding of the molecular regulation at the protein level of bovine adipose tissues, especially within different fat depots under different nutritional regimes. The objective of this study was to analyze the differences in protein expression between bovine subcutaneous and visceral fat depots in steers fed different diets and to identify the potential regulatory molecular mechanisms of protein expression. Subcutaneous and visceral fat tissues were collected from 16 British-continental steers (15.5 month old) fed a high-fat diet (7.1% fat, n=8) or a control diet (2.7% fat, n=8). Protein expression was profiled using label free quantification LC-MS/MS and expression of selected transcripts was evaluated using qRT-PCR. A total of 682 proteins were characterized and quantified with fat depot having more impact on protein expression, altering the level of 51.0% of the detected proteins, whereas diet affected only 5.3%. Functional analysis revealed that energy production and lipid metabolism were among the main functions associated with differentially expressed proteins between fat depots, with visceral fat being more metabolically active than subcutaneous fat as proteins associated with lipid and energy metabolism were upregulated. The expression of several proteins was significantly correlated to subcutaneous fat thickness and adipocyte size, indicating their potential as adiposity markers. A poor correlation (r=0.245) was observed between mRNA and protein levels for 9 genes, indicating that many proteins may be subjected to post-transcriptional regulation. A total of 8 miRNAs were predicted to regulate more than 20% of lipid metabolism proteins differentially expressed between fat depots, suggesting that miRNAs play a role in adipose tissue regulation. Our results show that proteomic changes support the distinct metabolic and physiological characteristics observed between

two-level inventory optimization under probability event chain

African Journals Online (AJOL)

Journal of Modeling, Design and Management of Engineering Systems ... The paper introduces the concept of effective inventory level, which is used to evaluate the impact of upstream shortage on downstream inventory, models the inventory at warehouse and retailer under random lead time and demand, and makes the ...

A study on EUV reticle surface molecular contamination under different storage conditions in a HVM foundry fab

Science.gov (United States)

Singh, SherJang; Yatzor, Brett; Taylor, Ron; Wood, Obert; Mangat, Pawitter

2017-03-01

The prospect of EUVL (Extreme Ultraviolet Lithography) insertion into HVM (High Volume Manufacturing) has never been this promising. As technology is prepared for "lab to fab" transition, it becomes important to comprehend challenges associated with integrating EUVL infrastructure within existing high volume chip fabrication processes in a foundry fab. The existing 193nm optical lithography process flow for reticle handling and storage in a fab atmosphere is well established and in-fab reticle contamination concerns are mitigated with the reticle pellicle. However EUVL reticle pellicle is still under development and if available, may only provide protection against particles but not molecular contamination. HVM fab atmosphere is known to be contaminated with trace amounts of AMC's (Atmospheric Molecular Contamination). If such contaminants are organic in nature and get absorbed on the reticle surface, EUV photon cause photo-dissociation resulting into carbon generation which is known to reduce multilayer reflectivity and also degrades exposure uniformity. Chemical diffusion and aggregation of other ions is also reported under the e-beam exposure of a EUV reticle which is known to cause haze issues in optical lithography. Therefore it becomes paramount to mitigate absorbed molecular contaminant concerns on EUVL reticle surface. In this paper, we have studied types of molecular contaminants that are absorbed on an EUVL reticle surface under HVM fab storage and handling conditions. Effect of storage conditions (gas purged vs atmospheric) in different storage pods (Dual pods, Reticle Clamshells) is evaluated. Absorption analysis is done both on ruthenium capping layer as well as TaBN absorber. Ru surface chemistry change as a result of storage is also studied. The efficacy of different reticle cleaning processes to remove absorbed contaminant is evaluated as well.

Molecular-level removal of proteinaceous contamination from model surfaces and biomedical device materials by air plasma treatment.

Science.gov (United States)

Banerjee, K K; Kumar, S; Bremmell, K E; Griesser, H J

2010-11-01

Established methods for cleaning and sterilising biomedical devices may achieve removal of bioburden only at the macroscopic level while leaving behind molecular levels of contamination (mainly proteinaceous). This is of particular concern if the residue might contain prions. We investigated at the molecular level the removal of model and real-life proteinaceous contamination from model and practical surfaces by air plasma (ionised air) treatment. The surface-sensitive technique of X-ray photoelectron spectroscopy (XPS) was used to assess the removal of proteinaceous contamination, with the nitrogen (N1s) photoelectron signal as its marker. Model proteinaceous contamination (bovine serum albumin) adsorbed on to a model surface (silicon wafer) and the residual proteinaceous contamination resulting from incubating surgical stainless steel (a practical biomaterial) in whole human blood exhibited strong N1s signals [16.8 and 18.5 atomic percent (at.%), respectively] after thorough washing. After 5min air plasma treatment, XPS detected no nitrogen on the sample surfaces, indicating complete removal of proteinaceous contamination, down to the estimated XPS detection limit 10ng/cm(2). Applying the same plasma treatment, the 7.7at.% nitrogen observed on a clinically cleaned dental bur was reduced to a level reflective of new, as-received burs. Contact angle measurements and atomic force microscopy also indicated complete molecular-level removal of the proteinaceous contamination upon air plasma treatment. This study demonstrates the effectiveness of air plasma treatment for removing proteinaceous contamination from both model and practical surfaces and offers a method for ensuring that no molecular residual contamination such as prions is transferred upon re-use of surgical and dental instruments. Crown Copyright © 2010. Published by Elsevier Ltd. All rights reserved.

ENVIROSUITE: USING STATE-OF-THE-ART SYNCHROTRON TECHNIQUES TO UNDERSTAND ENVIRONMENTAL REMEDIATION SCIENCE ISSUES AT THE MOLECULAR LEVEL.

Energy Technology Data Exchange (ETDEWEB)

FITTS,J.P.; KALB,P.D.; FRANCIS,A.J.; FUHRMANN,M.; DODGE,C.J.; GILLOW,J.B.

2004-03-01

Although DOE's Environmental Management program has made steady progress in cleaning up environmental legacies throughout the DOE complex, there are still significant remediation issues that remain to be solved. For example, DOE faces difficult challenges related to potential mobilization of radionuclides (e.g., actinides) and other hazardous contaminants in soils, removal and final treatment of high-level waste and residuals from leaking tanks, and the long-term stewardship of remediated sites and engineered disposal facilities, to name just a few. In some cases, new technologies and technology applications will be required based on current engineering expertise. In others, however, basic scientific research is needed to understand the mechanisms of how contaminants behave under specific conditions and how they interact with the environment, from which new engineering solutions can emerge. At Brookhaven National Laboratory (BNL) and Stony Brook University, scientists have teamed to use state-of-the-art synchrotron techniques to help understand the basic interactions of contaminants in the environment. Much of this work is conducted at the BNL National Synchrotron Light Source (NSLS), which is a user facility that provides high energy X-ray and ultraviolet photon beams to facilitate the examination of contaminants and materials at the molecular level. These studies allow us to determine how chemical speciation and structure control important parameters such as solubility, which in turn drive critical performance characteristics such as leaching. In one study for example, we are examining the effects of microbial activity on actinide contaminants under conditions anticipated at the Waste Isolation Pilot Plant. One possible outcome of this research is the identification of specific microbes that can trap uranium or other contaminants within the intracellular structure and help mitigate mobility. In another study, we are exploring the interaction of contaminants

ENVIROSUITE: USING STATE-OF-THE-ART SYNCHROTRON TECHNIQUES TO UNDERSTAND ENVIRONMENTAL REMEDIATION SCIENCE ISSUES AT THE MOLECULAR LEVEL

International Nuclear Information System (INIS)

FITTS, J.P.; KALB, P.D.; FRANCIS, A.J.; FUHRMANN, M.; DODGE, C.J.; GILLOW, J.B.

2004-01-01

Although DOE's Environmental Management program has made steady progress in cleaning up environmental legacies throughout the DOE complex, there are still significant remediation issues that remain to be solved. For example, DOE faces difficult challenges related to potential mobilization of radionuclides (e.g., actinides) and other hazardous contaminants in soils, removal and final treatment of high-level waste and residuals from leaking tanks, and the long-term stewardship of remediated sites and engineered disposal facilities, to name just a few. In some cases, new technologies and technology applications will be required based on current engineering expertise. In others, however, basic scientific research is needed to understand the mechanisms of how contaminants behave under specific conditions and how they interact with the environment, from which new engineering solutions can emerge. At Brookhaven National Laboratory (BNL) and Stony Brook University, scientists have teamed to use state-of-the-art synchrotron techniques to help understand the basic interactions of contaminants in the environment. Much of this work is conducted at the BNL National Synchrotron Light Source (NSLS), which is a user facility that provides high energy X-ray and ultraviolet photon beams to facilitate the examination of contaminants and materials at the molecular level. These studies allow us to determine how chemical speciation and structure control important parameters such as solubility, which in turn drive critical performance characteristics such as leaching. In one study for example, we are examining the effects of microbial activity on actinide contaminants under conditions anticipated at the Waste Isolation Pilot Plant. One possible outcome of this research is the identification of specific microbes that can trap uranium or other contaminants within the intracellular structure and help mitigate mobility. In another study, we are exploring the interaction of contaminants with

Thermodynamic properties by equation of state and from Ab initio molecular dynamics of liquid potassium under pressure

Science.gov (United States)

Li, Huaming; Tian, Yanting; Sun, Yongli; Li, Mo; Nonequilibrium materials; physics Team; Computational materials science Team

In this work, we apply a general equation of state of liquid and Ab initio molecular-dynamics method to study thermodynamic properties in liquid potassium under high pressure. Isothermal bulk modulus and molar volume of molten sodium are calculated within good precision as compared with the experimental data. The calculated internal energy data and the calculated values of isobaric heat capacity of molten potassium show the minimum along the isothermal lines as the previous result obtained in liquid sodium. The expressions for acoustical parameter and nonlinearity parameter are obtained based on thermodynamic relations from the equation of state. Both parameters for liquid potassium are calculated under high pressure along the isothermal lines by using the available thermodynamic data and numeric derivations. Furthermore, Ab initio molecular-dynamics simulations are used to calculate some thermodynamic properties of liquid potassium along the isothermal lines. Scientific Research Starting Foundation from Taiyuan university of Technology, Shanxi Provincial government (``100-talents program''), China Scholarship Council and National Natural Science Foundation of China (NSFC) under Grant No. 51602213.

Yield, Esterification Degree and Molecular Weight Evaluation of Pectins Isolated from Orange and Grapefruit Peels under Different Conditions

Science.gov (United States)

Sayah, Mohamed Yassine; Chabir, Rachida; Benyahia, Hamid; Rodi Kandri, Youssef; Ouazzani Chahdi, Fouad; Touzani, Hanan; Errachidi, Faouzi

2016-01-01

Orange (Citrus sinensis) and grapefruit (Citrus paradise) peels were used as a source of pectin, which was extracted under different conditions. The peels are used under two states: fresh and residual (after essential oil extraction). Organic acid (citric acid) and mineral acid (sulfuric acid) were used in the pectin extraction. The aim of this study is the evaluation the effect of extraction conditions on pectin yield, degree of esterification “DE” and on molecular weight “Mw”. Results showed that the pectin yield was higher using the residual peels. Moreover, both peels allow the obtainment of a high methoxyl pectin with DE >50%. The molecular weight was calculated using Mark-Houwink-Sakurada equation which describes its relationship with intrinsic viscosity. This later was determined using four equations; Huggins equation, kramer, Schulz-Blaschke and Martin equation. The molecular weight varied from 1.538 x1005 to 2.47x1005 g/mol for grapefruit pectin and from 1.639 x1005 to 2.471 x1005 g/mol for orange pectin. PMID:27644093

Time-Series Analyses of Transcriptomes and Proteomes Reveal Molecular Networks Underlying Oil Accumulation in Canola.

Science.gov (United States)

Wan, Huafang; Cui, Yixin; Ding, Yijuan; Mei, Jiaqin; Dong, Hongli; Zhang, Wenxin; Wu, Shiqi; Liang, Ying; Zhang, Chunyu; Li, Jiana; Xiong, Qing; Qian, Wei

2016-01-01

Understanding the regulation of lipid metabolism is vital for genetic engineering of canola ( Brassica napus L.) to increase oil yield or modify oil composition. We conducted time-series analyses of transcriptomes and proteomes to uncover the molecular networks associated with oil accumulation and dynamic changes in these networks in canola. The expression levels of genes and proteins were measured at 2, 4, 6, and 8 weeks after pollination (WAP). Our results show that the biosynthesis of fatty acids is a dominant cellular process from 2 to 6 WAP, while the degradation mainly happens after 6 WAP. We found that genes in almost every node of fatty acid synthesis pathway were significantly up-regulated during oil accumulation. Moreover, significant expression changes of two genes, acetyl-CoA carboxylase and acyl-ACP desaturase, were detected on both transcriptomic and proteomic levels. We confirmed the temporal expression patterns revealed by the transcriptomic analyses using quantitative real-time PCR experiments. The gene set association analysis show that the biosynthesis of fatty acids and unsaturated fatty acids are the most significant biological processes from 2-4 WAP and 4-6 WAP, respectively, which is consistent with the results of time-series analyses. These results not only provide insight into the mechanisms underlying lipid metabolism, but also reveal novel candidate genes that are worth further investigation for their values in the genetic engineering of canola.

Molecular pathways associated with blood pressure and hexadecanedioate levels.

Directory of Open Access Journals (Sweden)

Cristina Menni

Full Text Available The dicarboxylic acid hexadecanedioate is associated with increased blood pressure (BP and mortality in humans and feeding it to rats raises BP. Here we aim to characterise the molecular pathways that influence levels of hexadecanedioate linked to BP regulation, using genetic and transcriptomic studies. The top associations for hexadecanedioate in a genome-wide association scan (GWAS conducted on 6447 individuals from the TwinsUK and KORA cohorts were tested for association with BP and hypertension in the International Consortium for BP and in a GWAS of BP extremes. Transcriptomic analyses correlating hexadecanedioate with gene expression levels in adipose tissue in 740 TwinsUK participants were further performed. GWAS showed 242 SNPs mapping to two independent loci achieving genome-wide significance. In rs414056 in the SCLO1B1 gene (Beta(SE = -0.088(0.006P = 1.65 x 10-51, P < 1 x 10-51, the allele previously associated with increased risk of statin associated myopathy is associated with higher hexadecanedioate levels. However this SNP did not show association with BP or hypertension. The top SNP in the second locus rs6663731 mapped to the intronic region of CYP4Z2P on chromosome 1 (0.045(0.007, P = 5.49x10-11. Hexadecanedioate levels also correlate with adipose tissue gene-expression of the 3 out of 4 CYP4 probes (P<0.05 and of alcohol dehydrogenase probes (Beta(SE = 0.12(0.02; P = 6.04x10-11. High circulating levels of hexadecanedioate determine a significant effect of alcohol intake on BP (SBP: 1.12(0.34, P = 0.001; DBP: 0.70(0.22, P = 0.002, while no effect is seen in the lower hexadecanedioate level group. In conclusion, levels in fat of ADH1A, ADH1B and CYP4 encoding enzymes in the omega oxidation pathway, are correlated with hexadecanedioate levels. Hexadecanedioate appears to regulate the effect of alcohol on BP.

D2+ Molecular complex in non-uniform height quantum ribbon under crossed electric and magnetic fields

Science.gov (United States)

Suaza, Y. A.; Laroze, D.; Fulla, M. R.; Marín, J. H.

2018-05-01

The D2+ molecular complex fundamental properties in a uniform and multi-hilled semiconductor quantum ribbon under orthogonal electric and magnetic fields are theoretically studied. The energy structure is calculated by using adiabatic approximation combined with diagonalization procedure. The D2+ energy structure is more strongly controlled by the geometrical structural hills than the Coulomb interaction. The formation of vibrational and rotational states is discussed. Aharanov-Bohm oscillation patterns linked to rotational states as well as the D2+ molecular complex stability are highly sensitive to the number of hills while electric field breaks the electron rotational symmetry and removes the energy degeneration between low-lying states.

Comparative Phenotypical and Molecular Analyses of Arabidopsis Grown under Fluorescent and LED Light

Directory of Open Access Journals (Sweden)

Franka Seiler

2017-06-01

Full Text Available Comparative analyses of phenotypic and molecular traits of Arabidopsis thaliana grown under standardised conditions is still a challenge using climatic devices supplied with common light sources. These are in most cases fluorescent lights, which have several disadvantages such as heat production at higher light intensities, an invariable spectral output, and relatively rapid “ageing”. This results in non-desired variations of growth conditions and lowers the comparability of data acquired over extended time periods. In this study, we investigated the growth behaviour of Arabidopsis Col0 under different light conditions, applying fluorescent compared to LED lamps, and we conducted physiological as well as gene expression analyses. By changing the spectral composition and/or light intensity of LEDs we can clearly influence the growth behaviour of Arabidopsis and thereby study phenotypic attributes under very specific light conditions that are stable and reproducible, which is not necessarily given for fluorescent lamps. By using LED lights, we can also roughly mimic the sun light emission spectrum, enabling us to study plant growth in a more natural-like light set-up. We observed distinct growth behaviour under the different light regimes which was reflected by physiological properties of the plants. In conclusion, LEDs provide variable emission spectra for studying plant growth under defined, stable light conditions.

Thermal conductivity of graphene nanoribbons under shear deformation: A molecular dynamics simulation

Science.gov (United States)

Zhang, Chao; Hao, Xiao-Li; Wang, Cui-Xia; Wei, Ning; Rabczuk, Timon

2017-01-01

Tensile strain and compress strain can greatly affect the thermal conductivity of graphene nanoribbons (GNRs). However, the effect of GNRs under shear strain, which is also one of the main strain effect, has not been studied systematically yet. In this work, we employ reverse nonequilibrium molecular dynamics (RNEMD) to the systematical study of the thermal conductivity of GNRs (with model size of 4 nm × 15 nm) under the shear strain. Our studies show that the thermal conductivity of GNRs is not sensitive to the shear strain, and the thermal conductivity decreases only 12–16% before the pristine structure is broken. Furthermore, the phonon frequency and the change of the micro-structure of GNRs, such as band angel and bond length, are analyzed to explore the tendency of thermal conductivity. The results show that the main influence of shear strain is on the in-plane phonon density of states (PDOS), whose G band (higher frequency peaks) moved to the low frequency, thus the thermal conductivity is decreased. The unique thermal properties of GNRs under shear strains suggest their great potentials for graphene nanodevices and great potentials in the thermal managements and thermoelectric applications. PMID:28120921

Spin dynamics at level crossing in molecular AF rings probed by NMR

International Nuclear Information System (INIS)

Lascialfari, A.; Borsa, F.; Julien, M.-H.; Micotti, E.; Furukawa, Y.; Jang, Z.H.; Cornia, A.; Gatteschi, D.; Horvatic, M.; Van Slageren, J.

2004-01-01

The low-temperature spin dynamics in molecular rings with a finite number (N≤10) of magnetic ions was studied by means of 1 H NMR. When an external magnetic field (B) induces a crossing between energy levels, peaks are observed in the spin-lattice relaxation rate of protons, 1/T 1 (B), at constant temperature. We discuss similarities and differences in the data from three different rings: Fe10, Fe6:Li and Cr8

Influence of the molecular modifications on the properties of EPDM elastomers under irradiation

Energy Technology Data Exchange (ETDEWEB)

Davenas, J. E-mail: joel.davenas@univ-lyon1.fr; Stevenson, I.; Celette, N.; Vigier, G.; David, L

2003-08-01

The degradation of the mechanical behaviour of EPDM elastomers used as cable insulation materials has been investigated by mechanical spectroscopy and tensile tests for different formulations: unvulcanised EPDM, vulcanised and stabilised elastomer with an antioxidant. In all cases, {gamma}-irradiation of EPDM under oxygen leads to a reduction of the molecular mobility indicated by the shift of the glass transition relaxation temperature towards higher temperatures. Moreover, the molecular flow occurring above T{sub g} is suppressed after irradiation for the unvulcanised EPDM providing evidence of cross-linking. The competition between cross-linking and chain scissions is shown by the decrease of the storage modulus above the crystallites melting temperature ({approx}40 deg. C) at doses larger than 100 kGy. A strong increase of the Young modulus and reduction of the elongation at break of the non-vulcanised EPDM becoming more brittle are shown by stress/strain characterisations performed at 80 deg. C. At the opposite vulcanised EPDM exhibits higher elongation at break after crystallites melting. This evolution is interpreted by the competition between cross-linking and chain scissions, being hindered by the crystallites at room temperature. The intrinsic irradiation effects can be isolated after crystallite melting. The reduction of the molecular mobility can be explained by a chemi-crystallisation process assisted by chain scissions, leading to a more rigid phase upon irradiation.

Influence of the molecular modifications on the properties of EPDM elastomers under irradiation

International Nuclear Information System (INIS)

Davenas, J.; Stevenson, I.; Celette, N.; Vigier, G.; David, L.

2003-01-01

The degradation of the mechanical behaviour of EPDM elastomers used as cable insulation materials has been investigated by mechanical spectroscopy and tensile tests for different formulations: unvulcanised EPDM, vulcanised and stabilised elastomer with an antioxidant. In all cases, γ-irradiation of EPDM under oxygen leads to a reduction of the molecular mobility indicated by the shift of the glass transition relaxation temperature towards higher temperatures. Moreover, the molecular flow occurring above T g is suppressed after irradiation for the unvulcanised EPDM providing evidence of cross-linking. The competition between cross-linking and chain scissions is shown by the decrease of the storage modulus above the crystallites melting temperature (∼40 deg. C) at doses larger than 100 kGy. A strong increase of the Young modulus and reduction of the elongation at break of the non-vulcanised EPDM becoming more brittle are shown by stress/strain characterisations performed at 80 deg. C. At the opposite vulcanised EPDM exhibits higher elongation at break after crystallites melting. This evolution is interpreted by the competition between cross-linking and chain scissions, being hindered by the crystallites at room temperature. The intrinsic irradiation effects can be isolated after crystallite melting. The reduction of the molecular mobility can be explained by a chemi-crystallisation process assisted by chain scissions, leading to a more rigid phase upon irradiation

Competition between two wetland macrophytes under different levels of sediment saturation

Directory of Open Access Journals (Sweden)

Feng Li

2015-02-01

Full Text Available Plant-plant interactions have been widely studied under various environmental conditions. However, in wetland ecosystems how plant interactions change in response to variation in sediment saturation remains largely unclear, even though different levels of sediment saturation play important roles in determining plant growth performance in wetland ecosystems. To this end, a competition experiment with two typical wetland species, Carex brevicuspis (neighbor plant and Polygonum hydropiper (target plant, was conducted in a target-neighbor design. Two water levels (0 cm and -40 cm water levels representing waterlogged and drained sediments, respectively and three neighbor plant densities (0 plants m-2, 400 plants m-2, and 1600 plants m-2 were tested in a factorial design. Biomass accumulation of P. hydropiper decreased along with enhanced C. brevicuspis density in the waterlogged treatment. However, in the drained treatment, biomass accumulation did not change under two C. brevicuspis densities. Above-ground relative neighbor effect index (ARNE and relative neighbor effect index (RNE of C. brevicuspis on P. hydropiper increased along with enhanced C. brevicuspis density only under waterlogged conditions. The below-ground relative neighbor effect index (BRNE was not affected at the different water level and density treatments. The below-ground mass fraction of P. hydropiper was much higher in the waterlogged treatment than it was in the drained one, especially with no C. brevicuspis treatment. However, the leaf mass fraction displayed the opposite pattern. The longest root length of P. hydropiper was much shorter under waterlogged treatment than under the drained treatment. These results suggest that the competition intensity of C. brevicuspis to P. hydropiper increased along with increasing C. brevicuspis density only under waterlogged conditions. Moreover, this study also confirms that P. hydropiper can acclimate to water stress mainly through

A Molecular-Level View of the Physical Stability of Amorphous Solid Dispersions

Science.gov (United States)

Yuan, Xiaoda

Many pharmaceutical compounds being developed in recent years are poorly soluble in water. This has led to insufficient oral bioavailability of many compounds in vitro. The amorphous formulation is one of the promising techniques to increase the oral bioavailability of these poorly water-soluble compounds. However, an amorphous drug substance is inherently unstable because it is a high energy form. In order to increase the physical stability, the amorphous drug is often formulated with a suitable polymer to form an amorphous solid dispersion. Previous research has suggested that the formation of an intimately mixed drug-polymer mixture contributes to the stabilization of the amorphous drug compound. The goal of this research is to better understand the role of miscibility, molecular interactions and mobility on the physical stability of amorphous solid dispersions. Methods were developed to detect different degrees of miscibility on nanometer scale and to quantify the extent of hydrogen-bonding interactions between the drug and the polymer. Miscibility, hydrogen-bonding interactions and molecular mobility were correlated with physical stability during a six-month period using three model systems. Overall, this research provides molecular-level insights into many factors that govern the physical stability of amorphous solid dispersions which can lead to a more effective design of stable amorphous formulations.

Essential concepts and underlying theories from physics, chemistry, and mathematics for "biochemistry and molecular biology" majors.

Science.gov (United States)

Wright, Ann; Provost, Joseph; Roecklein-Canfield, Jennifer A; Bell, Ellis

2013-01-01

Over the past two years, through an NSF RCN UBE grant, the ASBMB has held regional workshops for faculty members from around the country. The workshops have focused on developing lists of Core Principles or Foundational Concepts in Biochemistry and Molecular Biology, a list of foundational skills, and foundational concepts from Physics, Chemistry, and Mathematics that all Biochemistry or Molecular Biology majors must understand to complete their major coursework. The allied fields working group created a survey to validate foundational concepts from Physics, Chemistry, and Mathematics identified from participant feedback at various workshops. One-hundred twenty participants responded to the survey and 68% of the respondents answered yes to the question: "We have identified the following as the core concepts and underlying theories from Physics, Chemistry, and Mathematics that Biochemistry majors or Molecular Biology majors need to understand after they complete their major courses: 1) mechanical concepts from Physics, 2) energy and thermodynamic concepts from Physics, 3) critical concepts of structure from chemistry, 4) critical concepts of reactions from Chemistry, and 5) essential Mathematics. In your opinion, is the above list complete?" Respondents also delineated subcategories they felt should be included in these broad categories. From the results of the survey and this analysis the allied fields working group constructed a consensus list of allied fields concepts, which will help inform Biochemistry and Molecular Biology educators when considering the ASBMB recommended curriculum for Biochemistry or Molecular Biology majors and in the development of appropriate assessment tools to gauge student understanding of how these concepts relate to biochemistry and molecular biology. © 2013 by The International Union of Biochemistry and Molecular Biology.

Recent progress in transition-metal-catalyzed reduction of molecular dinitrogen under ambient reaction conditions.

Science.gov (United States)

Nishibayashi, Yoshiaki

2015-10-05

This paper describes our recent progress in catalytic nitrogen fixation by using transition-metal-dinitrogen complexes as catalysts. Two reaction systems for the catalytic transformation of molecular dinitrogen into ammonia and its equivalent such as silylamine under ambient reaction conditions have been achieved by the molybdenum-, iron-, and cobalt-dinitrogen complexes as catalysts. Many new findings presented here may provide new access to the development of economical nitrogen fixation in place of the Haber-Bosch process.

Heat impact caused molecular level changes in solid and dissolved soil organic matter

Science.gov (United States)

Hofmann, Diana; Steffen, Bernhard; Eckhardt, Kai-Uwe; Leinweber, Peter

2015-04-01

resolution (used 400.000 at m/z 400 Da) and mass accuracy (≤ 1 ppm), simultaneously providing molecular level details of thousands of compounds. The characteristics and differences of the FTICR-MS spectra with as many as ten or more peaks at each nominal mass are discussed: heated samples showed considerable higher intensities of even numbered peaks. An in-house developed, automated post processing was used for further exploitation of the data with the aim of an unambiguous assignment of as many peaks as possible. Obtained mass lists were transformed for sorting and preparation/ interpretation of graphics like Kendrick and van Krevelen plots. The heat-treated solid samples show decreasing C/N ratios and the formation cyclic and N-heterocyclic compounds in good agreement among the various methods (Py-FIMS and C- and N-XANES). Detailed insight into the hot-water extracts by FTICR-MS showed clear qualitative as well as quantitative changes in the number and the intensity of nitrogen and nitrogen + sulfur containing compounds, respectively, which generally became enriched under soil heating. This demonstrates for the first time, that not only the bulk SOM is affected in structure by heat impact but also the more mobile DOM. We assume, that heat impact volatilizes and oxidizes parts of the organic substances is as expected but another part of the substances incorporates (further) nitrogen atom(s) similar to the generation of new compounds under the conditions of plasma etching in nitrogen atmosphere. This would explain to some extent, why soils are e.g. after fire clearing of vegetation are highly fertile for a short period (better plant acceptable compounds) but become more infertile in the long run, especially under tropical conditions with frequently heavy rain that would lead to an increased leaching of compounds with higher polarity.

Spin dynamics at level crossing in molecular AF rings probed by NMR

Energy Technology Data Exchange (ETDEWEB)

Lascialfari, A. E-mail: lascialfari@fisicavolta.unipv.it; Borsa, F.; Julien, M.-H.; Micotti, E.; Furukawa, Y.; Jang, Z.H.; Cornia, A.; Gatteschi, D.; Horvatic, M.; Van Slageren, J

2004-05-01

The low-temperature spin dynamics in molecular rings with a finite number (N{<=}10) of magnetic ions was studied by means of {sup 1}H NMR. When an external magnetic field (B) induces a crossing between energy levels, peaks are observed in the spin-lattice relaxation rate of protons, 1/T{sub 1}(B), at constant temperature. We discuss similarities and differences in the data from three different rings: Fe10, Fe6:Li and Cr8.

Selected materials of the international workshop on radiation risk and its origin at molecular and cellular level

International Nuclear Information System (INIS)

Pinak, Miroslav

2003-11-01

The workshop ''International Workshop on Radiation Risk and its Origin at Molecular and Cellular Level'' was held at The Tokai Research Establishment, Japan Atomic Energy Research Institute, on the 6th and 7th of February 2003. The Laboratory of Radiation Risk Analysis of JAERI organized it. This international workshop attracted scientists from several different scientific areas, including radiation physics, radiation biology, molecular biology, crystallography of biomolecules, modeling and bio-informatics. Several foreign and domestic keynote speakers addresses the very fundamental areas of radiation risk and tried to establish a link between the fundamental studies at the molecular and cellular level and radiation damages at the organism. The symposium consisted of 13 oral lectures, 10 poster presentations and panel discussion. The 108 participants attended the workshop. This publication comprises of proceedings of oral and poster presentations where available. For the rest of contributions the abstracts or/and selections of presentation materials are shown instead. The 5 papers are indexed individually. (J.P.N.)

MALDI-TOF mass spectrometry analysis of small molecular weight compounds (under 10 KDa) as biomarkers of rat hearts undergoing arecoline challenge.

Science.gov (United States)

Chen, Tung-Sheng; Chang, Mu-Hsin; Kuo, Wei-Wen; Lin, Yueh-Min; Yeh, Yu-Lan; Day, Cecilia Hsuan; Lin, Chien-Chung; Tsai, Fuu-Jen; Tsai, Chang-Hai; Huang, Chih-Yang

2013-04-01

Statistical and clinical reports indicate that betel nut chewing is strongly associated with progression of oral cancer because some ingredients in betel nuts are potential cancer promoters, especially arecoline. Early diagnosis for cancer biomarkers is the best strategy for prevention of cancer progression. Several methods are suggested for investigating cancer biomarkers. Among these methods, gel-based proteomics approach is the most powerful and recommended tool for investigating biomarkers due to its high-throughput. However, this proteomics approach is not suitable for screening biomarkers with molecular weight under 10 KDa because of the characteristics of gel electrophoresis. This study investigated biomarkers with molecular weight under 10 KDa in rats with arecoline challenge. The centrifuging vials with membrane (10 KDa molecular weight cut-off) played a crucial role in this study. After centrifuging, the filtrate (containing compounds with molecular weight under 10 KDa) was collected and spotted on a sample plate for MALDI-TOF mass spectrometry analysis. Compared to control, three extra peaks (m/z values were 1553.1611, 1668.2097 and 1740.1832, respectively) were found in sera and two extra peaks were found in heart tissue samples (408.9719 and 524.9961, respectively). These small compounds should play important roles and may be potential biomarker candidates in rats with arecoline. This study successfully reports a mass-based method for investigating biomarker candidates with small molecular weight in different types of sample (including serum and tissue). In addition, this reported method is more time-efficient (1 working day) than gel-based proteomics approach (5~7 working days).

Comparative Transcriptome Analysis of Latex Reveals Molecular Mechanisms Underlying Increased Rubber Yield in Hevea brasiliensis Self-Rooting Juvenile Clones.

Science.gov (United States)

Li, Hui-Liang; Guo, Dong; Zhu, Jia-Hong; Wang, Ying; Chen, Xiong-Ting; Peng, Shi-Qing

2016-01-01

Rubber tree (Hevea brasiliensis) self-rooting juvenile clones (JCs) are promising planting materials for rubber production. In a comparative trial between self-rooting JCs and donor clones (DCs), self-rooting JCs exhibited better performance in rubber yield. To study the molecular mechanism associated with higher rubber yield in self-rooting JCs, we sequenced and comparatively analyzed the latex of rubber tree self-rooting JCs and DCs at the transcriptome level. Total raw reads of 34,632,012 and 35,913,020 bp were obtained from the library of self-rooting JCs and DCs, respectively, by using Illumina HiSeq 2000 sequencing technology. De novo assemblies yielded 54689 unigenes from the library of self-rooting JCs and DCs. Among 54689 genes, 1716 genes were identified as differentially expressed between self-rooting JCs and DCs via comparative transcript profiling. Functional analysis showed that the genes related to the mass of categories were differentially enriched between the two clones. Several genes involved in carbohydrate metabolism, hormone metabolism and reactive oxygen species scavenging were up-regulated in self-rooting JCs, suggesting that the self-rooting JCs provide sufficient molecular basis for the increased rubber yielding, especially in the aspects of improved latex metabolisms and latex flow. Some genes encoding epigenetic modification enzymes were also differentially expressed between self-rooting JCs and DCs. Epigenetic modifications may lead to gene differential expression between self-rooting JCs and DCs. These data will provide new cues to understand the molecular mechanism underlying the improved rubber yield of H. brasiliensis self-rooting clones.

Comparison of atomic-level and coarse-grained models for liquid hydrocarbons from molecular dynamics configurational entropy estimates

NARCIS (Netherlands)

Baron, R; de Vries, AH; Hunenberger, PH; van Gunsteren, WF

2006-01-01

Molecular liquids can be modeled at different levels of spatial resolution. In atomic-level (AL) models, all (heavy) atoms can be explicitly simulated. In coarse-grained (CG) models, particles (beads) that represent groups of covalently bound atoms are used as elementary units. Ideally, a CG model

Molecular-Level Processes Governing the Interaction of Contaminants with Iron and Manganese Oxides - Final Report; FINAL

International Nuclear Information System (INIS)

Brown, G. E. Jr.; Chambers, S. A.

1999-01-01

Many of the inorganic and organic contaminants present in sediments at DOE sites can be altered or destroyed by reduction and oxidation (redox) reactions occurring at mineral surfaces. A fundamental understanding of such redox processes provided by molecular-level studies on structurally and compositionally well-defined mineral surfaces will lead to: (i) improved models of contaminant fate and transport in geochemical systems, and (ii) optimized manipulation of these processes for remediation purposes. To contribute to this understanding, we will study, both experimentally and theoretically, redox processes involving three important contaminants - chromate ion, carbon tetrachloride, and trichloroethene TCE, on the following iron and manganese oxides - hematite, magnetite, maghemite, and pyrolusite. These oxides and their hydroxylated analogs commonly occur as coatings on minerals or as interfaces in the subsurface environment. Single-crystal surfaces of these oxides will be synthesized in carefully controlled fashion by molecular beam epitaxy. These surfaces, as well as high surface are powdered samples of these oxides, will be used in spectroscopic and kinetic experiments in both aqueous and gas phases. Our goal is to identify products and to determine the kinetics and mechanisms of surface-catalyzed redox reaction of Cr(VI) and CR(III), and the reductive dechlorination of carbon tetrachloride and TCE. The combination of theory and experiment will provide the base information needed to scale from the molecular level to the microscopic grain level minerals

Upregulation of interleukin-1β/transforming growth factor-β1 and hypoxia relate to molecular mechanisms underlying immobilization-induced muscle contracture.

Science.gov (United States)

Honda, Yuichiro; Sakamoto, Junya; Nakano, Jiro; Kataoka, Hideki; Sasabe, Ryo; Goto, Kyo; Tanaka, Miho; Origuchi, Tomoki; Yoshimura, Toshiro; Okita, Minoru

2015-09-01

In this study we investigated the molecular mechanism underlying muscle contracture in rats. The rats were divided into immobilization and control groups, and soleus muscles of the right and left sides were selected for analyses. The levels of CD11b and α-SMA protein, IL-1β, and TGF-β1 mRNA, and type I and III collagen protein and mRNA were significantly greater in the immobilization group than in the control group at all time-points. HIF-1α mRNA levels were significantly higher in the immobilization group at 4 weeks. Moreover, HIF-1α, α-SMA, and type I collagen levels were significantly higher at 4 weeks than at 1 and 2 weeks in the immobilization group. In the early stages of immobilization, upregulation of IL-1β/TGF-β1 via macrophages may promote fibroblast differentiation that could affect muscle contracture. The soleus muscle became hypoxic in the later stages of immobilization, suggesting that hypoxia influences the progression of muscle contracture. © 2014 Wiley Periodicals, Inc.

Transcriptional profiling at whole population and single cell levels reveals somatosensory neuron molecular diversity

Science.gov (United States)

Chiu, Isaac M; Barrett, Lee B; Williams, Erika K; Strochlic, David E; Lee, Seungkyu; Weyer, Andy D; Lou, Shan; Bryman, Gregory S; Roberson, David P; Ghasemlou, Nader; Piccoli, Cara; Ahat, Ezgi; Wang, Victor; Cobos, Enrique J; Stucky, Cheryl L; Ma, Qiufu; Liberles, Stephen D; Woolf, Clifford J

2014-01-01

The somatosensory nervous system is critical for the organism's ability to respond to mechanical, thermal, and nociceptive stimuli. Somatosensory neurons are functionally and anatomically diverse but their molecular profiles are not well-defined. Here, we used transcriptional profiling to analyze the detailed molecular signatures of dorsal root ganglion (DRG) sensory neurons. We used two mouse reporter lines and surface IB4 labeling to purify three major non-overlapping classes of neurons: 1) IB4+SNS-Cre/TdTomato+, 2) IB4−SNS-Cre/TdTomato+, and 3) Parv-Cre/TdTomato+ cells, encompassing the majority of nociceptive, pruriceptive, and proprioceptive neurons. These neurons displayed distinct expression patterns of ion channels, transcription factors, and GPCRs. Highly parallel qRT-PCR analysis of 334 single neurons selected by membership of the three populations demonstrated further diversity, with unbiased clustering analysis identifying six distinct subgroups. These data significantly increase our knowledge of the molecular identities of known DRG populations and uncover potentially novel subsets, revealing the complexity and diversity of those neurons underlying somatosensation. DOI: http://dx.doi.org/10.7554/eLife.04660.001 PMID:25525749

Molecular-level insights into aging processes of skin elastin

DEFF Research Database (Denmark)

Mora Huertas, Angela C; Schmelzer, Christian E H; Hoehenwarter, Wolfgang

2016-01-01

Skin aging is characterized by different features including wrinkling, atrophy of the dermis and loss of elasticity associated with damage to the extracellular matrix protein elastin. The aim of this study was to investigate the aging process of skin elastin at the molecular level by evaluating...... the influence of intrinsic (chronological aging) and extrinsic factors (sun exposure) on the morphology and susceptibility of elastin towards enzymatic degradation. Elastin was isolated from biopsies derived from sun-protected or sun-exposed skin of differently aged individuals. The morphology of the elastin...... pronounced in sun-exposed tissue. Marker peptides were identified, which showed an age-related increase or decrease in their abundances and provide insights into the progression of the aging process of elastin fibers. Strong age-related cleavage occurs in hydrophobic tropoelastin domains 18, 20, 24 and 26...

Molecular phenology in plants: in natura systems biology for the comprehensive understanding of seasonal responses under natural environments.

Science.gov (United States)

Kudoh, Hiroshi

2016-04-01

Phenology refers to the study of seasonal schedules of organisms. Molecular phenology is defined here as the study of the seasonal patterns of organisms captured by molecular biology techniques. The history of molecular phenology is reviewed briefly in relation to advances in the quantification technology of gene expression. High-resolution molecular phenology (HMP) data have enabled us to study phenology with an approach of in natura systems biology. I review recent analyses of FLOWERING LOCUS C (FLC), a temperature-responsive repressor of flowering, along the six steps in the typical flow of in natura systems biology. The extensive studies of the regulation of FLC have made this example a successful case in which a comprehensive understanding of gene functions has been progressing. The FLC-mediated long-term memory of past temperatures creates time lags with other seasonal signals, such as photoperiod and short-term temperature. Major signals that control flowering time have a phase lag between them under natural conditions, and hypothetical phase lag calendars are proposed as mechanisms of season detection in plants. Transcriptomic HMP brings a novel strategy to the study of molecular phenology, because it provides a comprehensive representation of plant functions. I discuss future perspectives of molecular phenology from the standpoints of molecular biology, evolutionary biology and ecology. © 2015 The Author. New Phytologist © 2015 New Phytologist Trust.

Nanomaterials under extreme environments: A study of structural and dynamic properties using reactive molecular dynamics simulations

Science.gov (United States)

Shekhar, Adarsh

Nanotechnology is becoming increasingly important with the continuing advances in experimental techniques. As researchers around the world are trying to expand the current understanding of the behavior of materials at the atomistic scale, the limited resolution of equipment, both in terms of time and space, act as roadblocks to a comprehensive study. Numerical methods, in general and molecular dynamics, in particular act as able compliment to the experiments in our quest for understanding material behavior. In this research work, large scale molecular dynamics simulations to gain insight into the mechano-chemical behavior under extreme conditions of a variety of systems with many real world applications. The body of this work is divided into three parts, each covering a particular system: 1) Aggregates of aluminum nanoparticles are good solid fuel due to high flame propagation rates. Multi-million atom molecular dynamics simulations reveal the mechanism underlying higher reaction rate in a chain of aluminum nanoparticles as compared to an isolated nanoparticle. This is due to the penetration of hot atoms from reacting nanoparticles to an adjacent, unreacted nanoparticle, which brings in external heat and initiates exothermic oxidation reactions. 2) Cavitation bubbles readily occur in fluids subjected to rapid changes in pressure. We use billion-atom reactive molecular dynamics simulations on a 163,840-processor BlueGene/P supercomputer to investigate chemical and mechanical damages caused by shock-induced collapse of nanobubbles in water near amorphous silica. Collapse of an empty nanobubble generates high-speed nanojet, resulting in the formation of a pit on the surface. The pit contains a large number of silanol groups and its volume is found to be directly proportional to the volume of the nanobubble. The gas-filled bubbles undergo partial collapse and consequently the damage on the silica surface is mitigated. 3) The structure and dynamics of water confined in

Elucidation of molecular mechanisms of physiological variations between bovine subcutaneous and visceral fat depots under different nutritional regimes.

Directory of Open Access Journals (Sweden)

Josue Moura Romao

Full Text Available Adipose tissue plays a critical role in energy homeostasis and metabolism. There is sparse understanding of the molecular regulation at the protein level of bovine adipose tissues, especially within different fat depots under different nutritional regimes. The objective of this study was to analyze the differences in protein expression between bovine subcutaneous and visceral fat depots in steers fed different diets and to identify the potential regulatory molecular mechanisms of protein expression. Subcutaneous and visceral fat tissues were collected from 16 British-continental steers (15.5 month old fed a high-fat diet (7.1% fat, n=8 or a control diet (2.7% fat, n=8. Protein expression was profiled using label free quantification LC-MS/MS and expression of selected transcripts was evaluated using qRT-PCR. A total of 682 proteins were characterized and quantified with fat depot having more impact on protein expression, altering the level of 51.0% of the detected proteins, whereas diet affected only 5.3%. Functional analysis revealed that energy production and lipid metabolism were among the main functions associated with differentially expressed proteins between fat depots, with visceral fat being more metabolically active than subcutaneous fat as proteins associated with lipid and energy metabolism were upregulated. The expression of several proteins was significantly correlated to subcutaneous fat thickness and adipocyte size, indicating their potential as adiposity markers. A poor correlation (r=0.245 was observed between mRNA and protein levels for 9 genes, indicating that many proteins may be subjected to post-transcriptional regulation. A total of 8 miRNAs were predicted to regulate more than 20% of lipid metabolism proteins differentially expressed between fat depots, suggesting that miRNAs play a role in adipose tissue regulation. Our results show that proteomic changes support the distinct metabolic and physiological characteristics

Cognitive neuroepigenetics: the next evolution in our understanding of the molecular mechanisms underlying learning and memory?

Science.gov (United States)

Marshall, Paul; Bredy, Timothy W.

2016-07-01

A complete understanding of the fundamental mechanisms of learning and memory continues to elude neuroscientists. Although many important discoveries have been made, the question of how memories are encoded and maintained at the molecular level remains. So far, this issue has been framed within the context of one of the most dominant concepts in molecular biology, the central dogma, and the result has been a protein-centric view of memory. Here, we discuss the evidence supporting a role for neuroepigenetic mechanisms, which constitute dynamic and reversible, state-dependent modifications at all levels of control over cellular function, and their role in learning and memory. This neuroepigenetic view suggests that DNA, RNA and protein each influence one another to produce a holistic cellular state that contributes to the formation and maintenance of memory, and predicts a parallel and distributed system for the consolidation, storage and retrieval of the engram.

A molecular spin-photovoltaic device.

Science.gov (United States)

Sun, Xiangnan; Vélez, Saül; Atxabal, Ainhoa; Bedoya-Pinto, Amilcar; Parui, Subir; Zhu, Xiangwei; Llopis, Roger; Casanova, Fèlix; Hueso, Luis E

2017-08-18

We fabricated a C 60 fullerene-based molecular spin-photovoltaic device that integrates a photovoltaic response with the spin transport across the molecular layer. The photovoltaic response can be modified under the application of a small magnetic field, with a magnetophotovoltage of up to 5% at room temperature. Device functionalities include a magnetic current inverter and the presence of diverging magnetocurrent at certain illumination levels that could be useful for sensing. Completely spin-polarized currents can be created by balancing the external partially spin-polarized injection with the photogenerated carriers. Copyright © 2017 The Authors, some rights reserved; exclusive licensee American Association for the Advancement of Science. No claim to original U.S. Government Works.

Response of maize ( Zea mays L.) to varied moisture levels under ...

African Journals Online (AJOL)

Laboratory and glasshouse trials were used to determine the response of maize plants to varied moisture levels under Striga lutea infestation. Six moisture levels (1.5, 2.0, 2.5, 3.0, 3.5 and 4.0 ml) were applied to striga seed for germination count in the laboratory, while five moisture levels (300, 600, 900, 1200 and 1500 ml) ...

Molecular dynamics simulation on the elastoplastic properties of copper nanowire under torsion

Science.gov (United States)

Yang, Yong; Li, Ying; Yang, Zailin; Zhang, Guowei; Wang, Xizhi; Liu, Jin

2018-02-01

Influences of different factors on the torsion properties of single crystal copper nanowire are studied by molecular dynamics method. The length, torsional rate, and temperature of the nanowire are discussed at the elastic-plastic critical point. According to the average potential energy curve and shear stress curve, the elastic-plastic critical angle is determined. Also, the dislocation at elastoplastic critical points is analyzed. The simulation results show that the single crystal copper nanowire can be strengthened by lengthening the model, decreasing the torsional rate, and lowering the temperature. Moreover, atoms move violently and dislocation is more likely to occur with a higher temperature. This work mainly describes the mechanical behavior of the model under different states.

Molecular level biodegradation of phenol and its derivatives through dmp operon of Pseudomonas putida: A bio-molecular modeling and docking analysis.

Science.gov (United States)

Ray, Sujay; Banerjee, Arundhati

2015-10-01

Participation of Pseudomonas putida-derived methyl phenol (dmp) operon and DmpR protein in the biodegradation of phenol or other harmful, organic, toxic pollutants was investigated at a molecular level. Documentation documents that P. putida has DmpR protein which positively regulates dmp operon in the presence of inducers; like phenols. From the operon, phenol hydroxylase encoded by dmpN gene, participates in degrading phenols after dmp operon is expressed. For the purpose, the 3-D models of the four domains from DmpR protein and of the DNA sequences from the two Upstream Activation Sequences (UAS) present at the promoter region of the operon were demonstrated using discrete molecular modeling techniques. The best modeled structures satisfying their stereo-chemical properties were selected in each of the cases. To stabilize the individual structures, energy optimization was performed. In the presence of inducers, probable interactions among domains and then the two independent DNA structures with the fourth domain were perused by manifold molecular docking simulations. The complex structures were made to be stable by minimizing their overall energy. Responsible amino acid residues, nucleotide bases and binding patterns for the biodegradation, were examined. In the presence of the inducers, the biodegradation process is initiated by the interaction of phe50 from the first protein domain with the inducers. Only after the interaction of the last domain with the DNA sequences individually, the operon is expressed. This novel residue level study is paramount for initiating transcription in the operon; thereby leading to expression of phenol hydroxylase followed by phenol biodegradation. Copyright © 2015. Published by Elsevier B.V.

C sub 6 sub 0 fullerene and its molecular complexes under axial and shear deformation

CERN Document Server

Spitsina, N G; Bashkin, I V; Meletov, K P

2002-01-01

We have studied the pristine C sub 6 sub 0 and its molecular complexes with the organic donors bis(ethylenedithio) tetrathiafulvalene (BEDT-TTF or ET) and tetramethyltetraselenafulvalene (TMTSF) by means of ESR and Raman spectroscopy at high pressure. The important changes in the ESR signal of C sub 6 sub 0 were observed under axial pressure combined with shear deformation. It is shown that the treatment at a anisotropic pressure of 4 GPa results in a reduction in the symmetry of the C sub 6 sub 0 molecule and the formation of radicals. Treatment of the molecular complex of (ET) sub 2 centre dot C sub 6 sub 0 at a pressure of approx 4.5 GPa and a temperature of 150 deg. C leads to the formation of C sub 6 sub 0 dimers. The Raman spectra of the molecular complex C sub 6 sub 0 centre dot TMTSF centre dot 2(CS sub 2) were measured in situ at ambient temperature and pressures up to 9.5 GPa. The pressure behaviour of the Raman peaks reveals singularity at 5.0 +- 0.5 GPa related to the softening and splitting of so...

Molecular and Microbial Mechanisms Increasing Soil C Storage Under Future Rates of Anthropogenic N Deposition

Energy Technology Data Exchange (ETDEWEB)

Zak, Donald R. [Univ. of Michigan, Ann Arbor, MI (United States)

2017-11-17

A growing body of evidence reveals that anthropogenic N deposition can reduce the microbial decay of plant detritus and increase soil C storage across a wide range of terrestrial ecosystems. This aspect of global change has the potential to constrain the accumulation of anthropogenic CO₂ in the Earth’s atmosphere, and hence slow the pace of climate warming. The molecular and microbial mechanisms underlying this biogeochemical response are not understood, and they are not a component of any coupled climate-biogeochemical model estimating ecosystem C storage, and hence, the future climate of an N-enriched Earth. Here, we report the use of genomic-enabled approaches to identify the molecular underpinnings of the microbial mechanisms leading to greater soil C storage in response to anthropogenic N deposition, thereby enabling us to better anticipate changes in soil C storage.

A probe to study the toxic interaction of tartrazine with bovine hemoglobin at the molecular level.

Science.gov (United States)

Li, Yating; Wei, Haoran; Liu, Rutao

2014-03-01

Tartrazine is an artificial azo dye commonly used in food products, but tartrazine in the environment is potentially harmful. The toxic interaction between tartrazine and bovine hemoglobin (BHb) was investigated using fluorescence, synchronous fluorescence, UV-vis absorption, circular dichroism (CD) and molecular modeling techniques under simulated physiological conditions. The fluorescence data showed that tartrazine can bind with BHb to form a complex. The binding process was a spontaneous molecular interaction, in which van der Waals' forces and hydrogen bonds played major roles. Molecular docking results showed that the hydrogen bonds exist between the oxygen atoms at position 31 of tartrazine and the nitrogen atom NZ7 on Lys99, and also between the oxygen atoms at position 15 of tartrazine and the nitrogen atom NZ7 on Lys104, Lys105. The results of UV-vis and CD spectra revealed that tartrazine led to conformational changes in BHb, including loosening of the skeleton structure and decreasing α helix in the secondary structure. The synchronous fluorescence experiment revealed that tartrazine binds into the hemoglobin central cavity, and this was verified using a molecular modeling study. Copyright © 2013 John Wiley & Sons, Ltd.

Changing of Bacteria Catalase Activity Under the Influence of Electro-Magnetic Radiation on a Frequency of Nitric Oxide Absorption and Radiation Molecular Spectrum

Directory of Open Access Journals (Sweden)

G.M. Shub

2009-09-01

Full Text Available The dynamics of catalase activity degree changing in Staphylococcus aureus, Escherichia coli and Pseudomonas aeruginosa is described under the influence of electro-magnetic radiation on a frequency of nitric oxide absorption and radiation molecular spectrum. The panoramic spectrometric measuring complex, developed in Central Scientific Research Institute of measuring equipment Public corporation, Saratov, was used while carrying out the research. Electromagnetic vibrations of extremely high frequencies were stimulated in this complex imitating the structure of nitric oxide absorption and radiation molecular spectrum. The growth of activity of the mentioned enzyme of the strains under research was detected. The most significant changes were observed under 60-minutes exposure.

The molecular basis of low activity levels of coagulation factor VII: a Brazilian cohort.

Science.gov (United States)

Rabelo, F Y; Jardim, L L; Landau, M B; Gadelha, T; Corrêa, M F B; Pereira, I F M; Rezende, S M

2015-09-01

Inherited factor VII (FVII) deficiency is the most common among the rare bleeding disorders. It is transmitted as an autosomal recessive inheritance, due to mutations in the FVII gene (F7). Molecular studies of FVII deficiency are rare in non-Caucasian populations. The aim of the study was to evaluate the molecular basis behind low levels of FVII activity (FVII:C) levels in a cohort of Brazilian patients. A total of 34 patients with low FVII levels were clinically evaluated and submitted to laboratory tests, among these, prothrombin time and FVII:C, with different thromboplastins. All exons and intron/exon boundaries of F7 were amplified and sequenced. A total of 14 genetic alterations were identified, of which six were described previously, c.1091G>A, c.1151C>T, c.-323_-313insCCTATATCCT, c.285G>A, c.525C>T, c.1238G>A and eight (54.0%) and eight were new, c.128G>A, c.252C>T, c.348G>A, c.417G>A, c.426G>A, c.745_747delGTG, c.843G>A and c.805+52C>T. In addition to the mutation c.1091G>A, known as FVII Padua, the mutation c.1151C>T also presented discrepant FVII:C levels when tested with human and rabbit brain thromboplastin. There was no association between phenotype and genotype. Most of the identified genetic alterations found were polymorphisms. Low levels of FVII:C in this population were mostly related to polymorphisms in F7 and associated with a mild clinical phenotype. Mutation c.1151C>T was associated with discrepant levels of FVII:C using different thromboplastins, such as reported with FVII Padua. © 2015 John Wiley & Sons Ltd.

Rovibrational coupling in molecular nitrogen at high temperature: An atomic-level study

Energy Technology Data Exchange (ETDEWEB)

Valentini, Paolo, E-mail: vale0142@umn.edu; Norman, Paul, E-mail: norma198@umn.edu; Zhang, Chonglin, E-mail: zhang993@umn.edu; Schwartzentruber, Thomas E., E-mail: schwart@aem.umn.edu [Department of Aerospace Engineering and Mechanics, College of Science and Engineering, University of Minnesota, Minneapolis, Minnesota 55455 (United States)

2014-05-15

This article contains an atomic-level numerical investigation of rovibrational relaxation in molecular nitrogen at high temperature (>4000 K), neglecting dissociation. We conduct our study with the use of pure Molecular Dynamics (MD) and Classical Trajectory Calculations (CTC) Direct Simulation Monte Carlo (DSMC), verified to produce statistically identical results at the conditions of interest here. MD and CTC DSMC solely rely on the specification of a potential energy surface: in this work, the site-site Ling-Rigby potential. Additionally, dissociation is prevented by modeling the N–N bond either as a harmonic or an anharmonic spring. The selected molecular model was shown to (i) recover the shear viscosity (obtained from equilibrium pure MD Green-Kubo calculations) of molecular nitrogen over a wide range of temperatures, up to dissociation; (ii) predict well the near-equilibrium rotational relaxation behavior of N{sub 2}; (iii) reproduce vibrational relaxation times in excellent accordance with the Millikan-White correlation and previous semi-classical trajectory calculations in the low temperature range, i.e., between 4000 K and 10 000 K. By simulating isothermal relaxations in a periodic box, we found that the traditional two-temperature model assumptions become invalid at high temperatures (>10 000 K), due to a significant coupling between rotational and vibrational modes for bound states. This led us to add a modification to both the Jeans and the Landau-Teller equations to include a coupling term, essentially described by an additional relaxation time for internal energy equilibration. The degree of anharmonicity of the N{sub 2} bond determines the strength of the rovibrational coupling. Although neglecting N{sub 2} dissociation only provides a partial description of a nitrogen system at very high temperatures, high-energy trends for bound-bound transitions are essential to understand nonequilibrium gas flows, with possible implications on rovibration

Rovibrational coupling in molecular nitrogen at high temperature: An atomic-level study

International Nuclear Information System (INIS)

Valentini, Paolo; Norman, Paul; Zhang, Chonglin; Schwartzentruber, Thomas E.

2014-01-01

This article contains an atomic-level numerical investigation of rovibrational relaxation in molecular nitrogen at high temperature (>4000 K), neglecting dissociation. We conduct our study with the use of pure Molecular Dynamics (MD) and Classical Trajectory Calculations (CTC) Direct Simulation Monte Carlo (DSMC), verified to produce statistically identical results at the conditions of interest here. MD and CTC DSMC solely rely on the specification of a potential energy surface: in this work, the site-site Ling-Rigby potential. Additionally, dissociation is prevented by modeling the N–N bond either as a harmonic or an anharmonic spring. The selected molecular model was shown to (i) recover the shear viscosity (obtained from equilibrium pure MD Green-Kubo calculations) of molecular nitrogen over a wide range of temperatures, up to dissociation; (ii) predict well the near-equilibrium rotational relaxation behavior of N 2 ; (iii) reproduce vibrational relaxation times in excellent accordance with the Millikan-White correlation and previous semi-classical trajectory calculations in the low temperature range, i.e., between 4000 K and 10 000 K. By simulating isothermal relaxations in a periodic box, we found that the traditional two-temperature model assumptions become invalid at high temperatures (>10 000 K), due to a significant coupling between rotational and vibrational modes for bound states. This led us to add a modification to both the Jeans and the Landau-Teller equations to include a coupling term, essentially described by an additional relaxation time for internal energy equilibration. The degree of anharmonicity of the N 2 bond determines the strength of the rovibrational coupling. Although neglecting N 2 dissociation only provides a partial description of a nitrogen system at very high temperatures, high-energy trends for bound-bound transitions are essential to understand nonequilibrium gas flows, with possible implications on rovibration

Molecular Ecological Basis of Grasshopper (Oedaleus asiaticus) Phenotypic Plasticity under Environmental Selection

Science.gov (United States)

Qin, Xinghu; Hao, Kun; Ma, Jingchuan; Huang, Xunbing; Tu, Xiongbing; Ali, Md. Panna; Pittendrigh, Barry R.; Cao, Guangchun; Wang, Guangjun; Nong, Xiangqun; Whitman, Douglas W.; Zhang, Zehua

2017-01-01

While ecological adaptation in insects can be reflected by plasticity of phenotype, determining the causes and molecular mechanisms for phenotypic plasticity (PP) remains a crucial and still difficult question in ecology, especially where control of insect pests is involved. Oedaleus asiaticus is one of the most dominant pests in the Inner Mongolia steppe and represents an excellent system to study phenotypic plasticity. To better understand ecological factors affecting grasshopper phenotypic plasticity and its molecular control, we conducted a full transcriptional screening of O. asiaticus grasshoppers reared in four different grassland patches in Inner Mongolia. Grasshoppers showed different degrees of PP associated with unique gene expressions and different habitat plant community compositions. Grasshopper performance variables were susceptible to habitat environment conditions and closely associated with plant architectures. Intriguingly, eco-transcriptome analysis revealed five potential candidate genes playing important roles in grasshopper performance, with gene expression closely relating to PP and plant community factors. By linking the grasshopper performances to gene profiles and ecological factors using canonical regression, we first demonstrated the eco-transcriptomic architecture (ETA) of grasshopper phenotypic traits (ETAGPTs). ETAGPTs revealed plant food type, plant density, coverage, and height were the main ecological factors influencing PP, while insect cuticle protein (ICP), negative elongation factor A (NELFA), and lactase-phlorizin hydrolase (LCT) were the key genes associated with PP. Our study gives a clear picture of gene-environment interaction in the formation and maintenance of PP and enriches our understanding of the transcriptional events underlying molecular control of rapid phenotypic plasticity associated with environmental variability. The findings of this study may also provide new targets for pest control and highlight the

Molecular Ecological Basis of Grasshopper (Oedaleus asiaticus Phenotypic Plasticity under Environmental Selection

Directory of Open Access Journals (Sweden)

Xinghu Qin

2017-10-01

Full Text Available While ecological adaptation in insects can be reflected by plasticity of phenotype, determining the causes and molecular mechanisms for phenotypic plasticity (PP remains a crucial and still difficult question in ecology, especially where control of insect pests is involved. Oedaleus asiaticus is one of the most dominant pests in the Inner Mongolia steppe and represents an excellent system to study phenotypic plasticity. To better understand ecological factors affecting grasshopper phenotypic plasticity and its molecular control, we conducted a full transcriptional screening of O. asiaticus grasshoppers reared in four different grassland patches in Inner Mongolia. Grasshoppers showed different degrees of PP associated with unique gene expressions and different habitat plant community compositions. Grasshopper performance variables were susceptible to habitat environment conditions and closely associated with plant architectures. Intriguingly, eco-transcriptome analysis revealed five potential candidate genes playing important roles in grasshopper performance, with gene expression closely relating to PP and plant community factors. By linking the grasshopper performances to gene profiles and ecological factors using canonical regression, we first demonstrated the eco-transcriptomic architecture (ETA of grasshopper phenotypic traits (ETAGPTs. ETAGPTs revealed plant food type, plant density, coverage, and height were the main ecological factors influencing PP, while insect cuticle protein (ICP, negative elongation factor A (NELFA, and lactase-phlorizin hydrolase (LCT were the key genes associated with PP. Our study gives a clear picture of gene-environment interaction in the formation and maintenance of PP and enriches our understanding of the transcriptional events underlying molecular control of rapid phenotypic plasticity associated with environmental variability. The findings of this study may also provide new targets for pest control and

Designing automation for complex work environments under different levels of stress.

Science.gov (United States)

Sauer, Juergen; Nickel, Peter; Wastell, David

2013-01-01

This article examines the effectiveness of different forms of static and adaptable automation under low- and high-stress conditions. Forty participants were randomly assigned to one of four experimental conditions, comparing three levels of static automation (low, medium and high) and one level of adaptable automation, with the environmental stressor (noise) being varied as a within-subjects variable. Participants were trained for 4 h on a simulation of a process control environment, called AutoCAMS, followed by a 2.5-h testing session. Measures of performance, psychophysiology and subjective reactions were taken. The results showed that operators preferred higher levels of automation under noise than under quiet conditions. A number of parameters indicated negative effects of noise exposure, such as performance impairments, physiological stress reactions and higher mental workload. It also emerged that adaptable automation provided advantages over low and intermediate static automation, with regard to mental workload, effort expenditure and diagnostic performance. The article concludes that for the design of automation a wider range of operational scenarios reflecting adverse as well as ideal working conditions needs to be considered. Copyright © 2012 Elsevier Ltd and The Ergonomics Society. All rights reserved.

Water interactions with condensed organic phases: a combined experimental and theoretical study of molecular-level processes

Science.gov (United States)

Johansson, Sofia M.; Kong, Xiangrui; Thomson, Erik S.; Papagiannakopoulos, Panos; Pettersson, Jan B. C.; Lovrić, Josip; Toubin, Céline

2016-04-01

Water uptake on aerosol particles modifies their chemistry and microphysics with important implications for air quality and climate. A large fraction of the atmospheric aerosol consists of organic aerosol particles or inorganic particles with condensed organic components. Here, we combine laboratory studies using the environmental molecular beam (EMB) method1 with molecular dynamics (MD) simulations to characterize water interactions with organic surfaces in detail. The over-arching aim is to characterize the mechanisms that govern water uptake, in order to guide the development of physics-based models to be used in atmospheric modelling. The EMB method enables molecular level studies of interactions between gases and volatile surfaces at near ambient pressure,1 and the technique may provide information about collision dynamics, surface and bulk accommodation, desorption and diffusion kinetics. Molecular dynamics simulations provide complementary information about the collision dynamics and initial interactions between gas molecules and the condensed phase. Here, we focus on water interactions with condensed alcohol phases that serve as highly simplified proxies for systems in the environment. Gas-surface collisions are in general found to be highly inelastic and result in efficient surface accommodation of water molecules. As a consequence, surface accommodation of water can be safely assumed to be close to unity under typical ambient conditions. Bulk accommodation is inefficient on solid alcohol and the condensed materials appear to produce hydrophobic surface structures, with limited opportunities for adsorbed water to form hydrogen bonds with surface molecules. Accommodation is significantly more efficient on the dynamic liquid alcohol surfaces. The results for n-butanol (BuOH) are particularly intriguing where substantial changes in water accommodation taking place over a 10 K interval below and above the BuOH melting point.2 The governing mechanisms for the

First-principles studies of PETN molecular crystal vibrational frequencies under high pressure

Science.gov (United States)

Perger, Warren; Zhao, Jijun

2005-07-01

The vibrational frequencies of the PETN molecular crystal were calculated using the first-principles CRYSTAL03 program which employs an all-electron LCAO approach and calculates analytic first derivatives of the total energy with respect to atomic displacements. Numerical second derivatives were used to enable calculation of the vibrational frequencies at ambient pressure and under various states of compression. Three different density functionals, B3LYP, PW91, and X3LYP were used to examine the effect of the exchange-correlation functional on the vibrational frequencies. The pressure-induced shift of the vibrational frequencies will be presented and compared with experiment. The average deviation with experimental results is shown to be on the order of 2-3%, depending on the functional used.

Molecular Mechanisms Underlying Renin-Angiotensin-Aldosterone System Mediated Regulation of BK Channels

Directory of Open Access Journals (Sweden)

Zhen-Ye Zhang

2017-09-01

Full Text Available Large-conductance calcium-activated potassium channels (BK channels belong to a family of Ca2+-sensitive voltage-dependent potassium channels and play a vital role in various physiological activities in the human body. The renin-angiotensin-aldosterone system is acknowledged as being vital in the body's hormone system and plays a fundamental role in the maintenance of water and electrolyte balance and blood pressure regulation. There is growing evidence that the renin-angiotensin-aldosterone system has profound influences on the expression and bioactivity of BK channels. In this review, we focus on the molecular mechanisms underlying the regulation of BK channels mediated by the renin-angiotensin-aldosterone system and its potential as a target for clinical drugs.

Molecular Origin of the Vibrational Structure of Ice Ih.

Science.gov (United States)

Moberg, Daniel R; Straight, Shelby C; Knight, Christopher; Paesani, Francesco

2017-06-15

An unambiguous assignment of the vibrational spectra of ice I h remains a matter of debate. This study demonstrates that an accurate representation of many-body interactions between water molecules, combined with an explicit treatment of nuclear quantum effects through many-body molecular dynamics (MB-MD), leads to a unified interpretation of the vibrational spectra of ice I h in terms of the structure and dynamics of the underlying hydrogen-bond network. All features of the infrared and Raman spectra in the OH stretching region can be unambiguously assigned by taking into account both the symmetry and the delocalized nature of the lattice vibrations as well as the local electrostatic environment experienced by each water molecule within the crystal. The high level of agreement with experiment raises prospects for predictive MB-MD simulations that, complementing analogous measurements, will provide molecular-level insights into fundamental processes taking place in bulk ice and on ice surfaces under different thermodynamic conditions.

The molecular biology capstone assessment: a concept assessment for upper-division molecular biology students.

Science.gov (United States)

Couch, Brian A; Wood, William B; Knight, Jennifer K

2015-03-02

Measuring students' conceptual understandings has become increasingly important to biology faculty members involved in evaluating and improving departmental programs. We developed the Molecular Biology Capstone Assessment (MBCA) to gauge comprehension of fundamental concepts in molecular and cell biology and the ability to apply these concepts in novel scenarios. Targeted at graduating students, the MBCA consists of 18 multiple-true/false (T/F) questions. Each question consists of a narrative stem followed by four T/F statements, which allows a more detailed assessment of student understanding than the traditional multiple-choice format. Questions were iteratively developed with extensive faculty and student feedback, including validation through faculty reviews and response validation through student interviews. The final assessment was taken online by 504 students in upper-division courses at seven institutions. Data from this administration indicate that the MBCA has acceptable levels of internal reliability (α=0.80) and test-retest stability (r=0.93). Students achieved a wide range of scores with a 67% overall average. Performance results suggest that students have an incomplete understanding of many molecular biology concepts and continue to hold incorrect conceptions previously documented among introductory-level students. By pinpointing areas of conceptual difficulty, the MBCA can provide faculty members with guidance for improving undergraduate biology programs. © 2015 B. A. Couch et al. CBE—Life Sciences Education © 2015 The American Society for Cell Biology. This article is distributed by The American Society for Cell Biology under license from the author(s). It is available to the public under an Attribution–Noncommercial–Share Alike 3.0 Unported Creative Commons License (http://creativecommons.org/licenses/by-nc-sa/3.0).

Network-based integration of molecular and physiological data elucidates regulatory mechanisms underlying adaptation to high-fat diet

NARCIS (Netherlands)

Derous, D.; Kelder, T.; Schothorst, E.M. van; Erk, M. van; Voigt, A.; Klaus, S.; Keijer, J.; Radonjic, M.

2015-01-01

Health is influenced by interplay of molecular, physiological and environmental factors. To effectively maintain health and prevent disease, health-relevant relations need to be understood at multiple levels of biological complexity. Network-based methods provide a powerful platform for integration

Performance Evaluation of Three-Level Z-Source Inverters Under Semiconductor-Failure Conditions

DEFF Research Database (Denmark)

Gao, Feng; Loh, Poh Chiang; Blaabjerg, Frede

2009-01-01

This paper evaluates and proposes various compensation methods for three-level Z-source inverters under semiconductor-failure conditions. Unlike the fault-tolerant techniques used in traditional three-level inverters, where either an extra phase-leg or collective switching states are used......, the proposed methods for three-level Z-source inverters simply reconfigure their relevant gating signals so as to ride-through the failed semiconductor conditions smoothly without any significant decrease in their ac-output quality and amplitude. These features are partly attributed to the inherent boost...... under semiconductor-failure conditions. For verifying these described performance features, PLECS simulation and experimental testing were performed with some results captured and shown in a later section for visual confirmation....

Molecular Processes Studied at a Single-Molecule Level Using DNA Origami Nanostructures and Atomic Force Microscopy

Directory of Open Access Journals (Sweden)

Ilko Bald

2014-09-01

Full Text Available DNA origami nanostructures allow for the arrangement of different functionalities such as proteins, specific DNA structures, nanoparticles, and various chemical modifications with unprecedented precision. The arranged functional entities can be visualized by atomic force microscopy (AFM which enables the study of molecular processes at a single-molecular level. Examples comprise the investigation of chemical reactions, electron-induced bond breaking, enzymatic binding and cleavage events, and conformational transitions in DNA. In this paper, we provide an overview of the advances achieved in the field of single-molecule investigations by applying atomic force microscopy to functionalized DNA origami substrates.

Radiation damage at the molecular level: Nanodosimetry

International Nuclear Information System (INIS)

Blanco, F.; Munoz, A.; Lagares, J. I.; Nunez, L.; Garcia, G.

2013-01-01

One of the main practical use of the model is its use as a tool of nanodosimetry which basically consists in characterizing the effect of radiation on nano volumes (comparable to the DNA of volumes) in terms of link breaks and molecular dissociations. (Author)

Molecular basis of alcoholism.

Science.gov (United States)

Most, Dana; Ferguson, Laura; Harris, R Adron

2014-01-01

Acute alcohol intoxication causes cellular changes in the brain that last for hours, while chronic alcohol use induces widespread neuroadaptations in the nervous system that can last a lifetime. Chronic alcohol use and the progression into dependence involve the remodeling of synapses caused by changes in gene expression produced by alcohol. The progression of alcohol use, abuse, and dependence can be divided into stages, which include intoxication, withdrawal, and craving. Each stage is associated with specific changes in gene expression, cellular function, brain circuits, and ultimately behavior. What are the molecular mechanisms underlying the transition from recreational use (acute) to dependence (chronic)? What cellular adaptations result in drug memory retention, leading to the persistence of addictive behaviors, even after prolonged drug abstinence? Research into the neurobiology of alcoholism aims to answer these questions. This chapter will describe the molecular adaptations caused by alcohol use and dependence, and will outline key neurochemical participants in alcoholism at the molecular level, which are also potential targets for therapy. © 2014 Elsevier B.V. All rights reserved.

Identification of SSR and retrotransposon-based molecular markers linked to morphological characters in oily sunfl ower (Helianthus annuus L.) under natural and water-limited states.

Science.gov (United States)

Ali, Soleimani Gezeljeh; Darvishzadeh, Reza; Ebrahimi, Asa; Bihamta, Mohammad Reza

2018-03-01

Sunflower is an important source of edible oil. Drought is known as an important factor limiting the growth and productivity of field crops in most parts of the world. Agricultural biotechnology mainly aims at developing crops with higher tolerance to the challenging environmental conditions, such as drought. This study examined a number of morphological characters, along with relative water content (RWC) in 100 inbred sunflower lines. A 10 × 10 simple lattice design with two replications was employed to measure the mentioned parameters under natural and water-limited states during two successive years. In molecular trial, 30 simple sequence repeat (SSR) primer pairs, as well as 14 inter-retrotransposon amplified polymorphism (IRAP) and 14 retrotransposon-microsatellite amplified polymorphism (REMAP) primer combinations were used for DNA fingerprinting of the lines. Most of the examined characters had lower average values under water-limited than natural states. Maximum and minimum reductions were observed in the cases of yield and oil percentage, respectively. The broad-sense heritabilities for all the examined characters were 0.20-0.73 and 0.10-0.34 under natural and water-limited states, respectively. In the studied samples, 8.97% of the 435 possible locus pairs of the SSRs represented significant linkage disequilibrium (LD) levels. In the association analysis using SSR markers, 22 and 21 markers were identified (P ≤ 0.05) for the studied characters under natural and water-limited states, respectively. The corresponding values were 50 and 37 using retrotransposon-based molecular markers. Some detected markers were communal between the characters under water-limited and natural states. This was in line with the phenotypic correlations detected between the characters. Communal markers facilitate the simultaneous selection of several characters and can thus improve the efficacy of selection based on markers in the plant-breeding activities.

Explicit control of adaptive automation under different levels of environmental stress.

Science.gov (United States)

Sauer, Jürgen; Kao, Chung-Shan; Wastell, David; Nickel, Peter

2011-08-01

This article examines the effectiveness of three different forms of explicit control of adaptive automation under low- and high-stress conditions, operationalised by different levels of noise. In total, 60 participants were assigned to one of three types of automation design (free, prompted and forced choice). They were trained for 4 h on a highly automated simulation of a process control environment, called AutoCAMS. This was followed by a 4-h testing session under noise exposure and quiet conditions. Measures of performance, psychophysiology and subjective reactions were taken. The results showed that all three modes of explicit control of adaptive automation modes were able to attenuate the negative effects of noise. This was partly due to the fact that operators opted for higher levels of automation under noise. It also emerged that forced choice showed marginal advantages over the two other automation modes. Statement of Relevance: This work is relevant to the design of adaptive automation since it emphasises the need to consider the impact of work-related stressors during task completion. During the presence of stressors, different forms of operator support through automation may be required than under more favourable working conditions.

Hyperinsulinemic Hypoglycemia ? The Molecular Mechanisms

OpenAIRE

Nessa, Azizun; Rahman, Sofia A.; Hussain, Khalid

2016-01-01

Under normal physiological conditions, pancreatic β-cells secrete insulin to maintain fasting blood glucose levels in the range 3.5–5.5 mmol/L. In hyperinsulinemic hypoglycemia (HH), this precise regulation of insulin secretion is perturbed so that insulin continues to be secreted in the presence of hypoglycemia. HH may be due to genetic causes (congenital) or secondary to certain risk factors. The molecular mechanisms leading to HH involve defects in the key genes regulating insulin secretio...

Biomechanical and biophysical environment of bone from the macroscopic to the pericellular and molecular level.

Science.gov (United States)

Ren, Li; Yang, Pengfei; Wang, Zhe; Zhang, Jian; Ding, Chong; Shang, Peng

2015-10-01

Bones with complicated hierarchical configuration and microstructures constitute the load-bearing system. Mechanical loading plays an essential role in maintaining bone health and regulating bone mechanical adaptation (modeling and remodeling). The whole-bone or sub-region (macroscopic) mechanical signals, including locomotion-induced loading and external actuator-generated vibration, ultrasound, oscillatory skeletal muscle stimulation, etc., give rise to sophisticated and distinct biomechanical and biophysical environments at the pericellular (microscopic) and collagen/mineral molecular (nanoscopic) levels, which are the direct stimulations that positively influence bone adaptation. While under microgravity, the stimulations decrease or even disappear, which exerts a negative influence on bone adaptation. A full understanding of the biomechanical and biophysical environment at different levels is necessary for exploring bone biomechanical properties and mechanical adaptation. In this review, the mechanical transferring theories from the macroscopic to the microscopic and nanoscopic levels are elucidated. First, detailed information of the hierarchical structures and biochemical composition of bone, which are the foundations for mechanical signal propagation, are presented. Second, the deformation feature of load-bearing bone during locomotion is clarified as a combination of bending and torsion rather than simplex bending. The bone matrix strains at microscopic and nanoscopic levels directly induced by bone deformation are critically discussed, and the strain concentration mechanism due to the complicated microstructures is highlighted. Third, the biomechanical and biophysical environments at microscopic and nanoscopic levels positively generated during bone matrix deformation or by dynamic mechanical loadings induced by external actuators, as well as those negatively affected under microgravity, are systematically discussed, including the interstitial fluid flow

Allowances for evolving coastal flood risk under uncertain local sea-level rise

Science.gov (United States)

Buchanan, M. K.; Kopp, R. E.; Oppenheimer, M.; Tebaldi, C.

2015-12-01

Sea-level rise (SLR) causes estimates of flood risk made under the assumption of stationary mean sea level to be biased low. However, adjustments to flood return levels made assuming fixed increases of sea level are also inaccurate when applied to sea level that is rising over time at an uncertain rate. To accommodate both the temporal dynamics of SLR and their uncertainty, we develop an Average Annual Design Life Level (AADLL) metric and associated SLR allowances [1,2]. The AADLL is the flood level corresponding to a time-integrated annual expected probability of occurrence (AEP) under uncertainty over the lifetime of an asset; AADLL allowances are the adjustment from 2000 levels that maintain current risk. Given non-stationary and uncertain SLR, AADLL flood levels and allowances provide estimates of flood protection heights and offsets for different planning horizons and different levels of confidence in SLR projections in coastal areas. Allowances are a function primarily of local SLR and are nearly independent of AEP. Here we employ probabilistic SLR projections [3] to illustrate the calculation of AADLL flood levels and allowances with a representative set of long-duration tide gauges along U.S. coastlines. [1] Rootzen et al., 2014, Water Resources Research 49: 5964-5972. [2] Hunter, 2013, Ocean Engineering 71: 17-27. [3] Kopp et al., 2014, Earth's Future 2: 383-406.

42 CFR 435.236 - Individuals in institutions who are eligible under a special income level.

Science.gov (United States)

2010-10-01

... a special income level. 435.236 Section 435.236 Public Health CENTERS FOR MEDICARE & MEDICAID... in institutions who are eligible under a special income level. (a) If the agency provides Medicaid... not institutionalized; but (2) Have income below a level specified in the plan under § 435.722. (See...

Neutral molecular cluster formation of sulfuric acid–dimethylamine observed in real time under atmospheric conditions

CERN Document Server

Kürten, Andreas; Simon, Mario; Sipilä, Mikko; Sarnela, Nina; Junninen, Heikki; Adamov, Alexey; Almeida, João; Amorim, Antonio; Bianchi, Federico; Breitenlechner, Martin; Dommen, Josef; Donahue, Neil M; Duplissy, Jonathan; Ehrhart, Sebastian; Flagan, Richard C; Franchin, Alessandro; Hakala, Jani; Hansel, Armin; Heinritzi, Martin; Hutterli, Manuel; Kangasluoma, Juha; Kirkby, Jasper; Laaksonen, Ari; Lehtipalo, Katrianne; Leiminger, Markus; Makhmutov, Vladimir; Mathot, Serge; Onnela, Antti; Petäjä, Tuukka; Praplan, Arnaud P; Riccobono, Francesco; Rissanen, Matti P; Rondo, Linda; Schobesberger, Siegfried; Seinfeld, John H; Steiner, Gerhard; Tomé, António; Tröstl, Jasmin; Winkler, Paul M; Williamson, Christina; Wimmer, Daniela; Ye, Penglin; Baltensperger, Urs; Carslaw, Kenneth S; Kulmala, Markku; Worsnop, Douglas R; Curtius, Joachim

2014-01-01

For atmospheric sulfuric acid (SA) concentrations the presence of dimethylamine (DMA) at mixing ratios of several parts per trillion by volume can explain observed boundary layer new particle formation rates. However, the concentration and molecular composition of the neutral (uncharged) clusters have not been reported so far due to the lack of suitable instrumentation. Here we report on experiments from the Cosmics Leaving Outdoor Droplets chamber at the European Organization for Nuclear Research revealing the formation of neutral particles containing up to 14 SA and 16 DMA molecules, corresponding to a mobility diameter of about 2 nm, under atmospherically relevant conditions. These measurements bridge the gap between the molecular and particle perspectives of nucleation, revealing the fundamental processes involved in particle formation and growth. The neutral clusters are found to form at or close to the kinetic limit where particle formation is limited only by the collision rate of SA molecules. Even tho...

Studies on liposomes with Chlorophyll for monitoring the electromagnetic influence at molecular level

International Nuclear Information System (INIS)

Tugulea, Laura; Miclaus, Simona; Iacovache, Ioan

2001-01-01

The liposomes with Chlorophyll are excellent model membranes and could be successfully used to study the electromagnetic influence at molecular level. The strong visible absorption and fluorescence of Chlorophyll allow its use as sensor for the interactions at molecular level and as a fluorescence marker; it reflects certain aspects of the supramolecular structure of the lipid phase: fluidity, lipid and liposomes aggregation. The objective of our work was to evidence athermal effect of low level, pulsed microwave (MW) fields on liposomes and to evidence the possible mechanism of interaction at molecular level. Unilamellar liposomes were obtained from multilamellar vesicles by the hand-shaken method and sonication for 30 minutes. The multilamellar vesicles were prepared using Chla /lipid films with specific molar ratio (lipid/Chla 1/10 and 1/100) and different lipids (Dipalmitoyl phosphatidylcholine, Dimirystoyl Phosphatidylcholine and Dioleoyl Phosphatidylcholine-Sigma). The films were dispersed in buffer solutions of different pH (6.2 - 7.6). The Chlorophyll was freshly extracted from spinach leaves and separated by the chromatographic method. Portions of liposome suspension (0.6 ml) were inserted into Teflon cuvettes. The samples were irradiated in series, for periods of 5-30 minutes. The exposure system was: MW generator + adapted load (shortened rectangular waveguide) + Teflon cuvette filled with sample liquid. The effect of MW irradiation is not observable on multilamellar vesicles, but only on small unilamellar vesicles. The MW effect is athermal, verified by conventional heating in the same range of temperatures and results in enlarging the size of vesicles. The enlarging effect of MW is opposed to the effect of ultrasounds exposure. It is not clear if effects due to MW are proportional with exposure duration; it seems that this mostly depends on the type of lipid in vesicles. The UV and VIS spectra were recorded to observe the oxidation state of the

Molecular dynamics simulations of the structure evolutions of Cu-Zr metallic glasses under irradiation

Energy Technology Data Exchange (ETDEWEB)

Lang, Lin [College of Materials Science and Engineering, Hunan University, Changsha 410082 (China); Department of Applied Physics, School of Physics and Electronics, Hunan University, Changsha 410082 (China); Tian, Zean; Xiao, Shifang [Department of Applied Physics, School of Physics and Electronics, Hunan University, Changsha 410082 (China); Deng, Huiqiu, E-mail: hqdeng@hnu.edu.cn [Department of Applied Physics, School of Physics and Electronics, Hunan University, Changsha 410082 (China); Ao, Bingyun [Science and Technology on Surface Physics and Chemistry Laboratory, Mianyang 621907 (China); Chen, Piheng, E-mail: chenpiheng@caep.cn [Science and Technology on Surface Physics and Chemistry Laboratory, Mianyang 621907 (China); Hu, Wangyu [College of Materials Science and Engineering, Hunan University, Changsha 410082 (China)

2017-02-15

Highlights: • The structural evolution of Cu{sub 64.5}Zr{sub 35.5} MG under irradiation was studied. • The structure clusters were analyzed using the LSCA method. • Most of these radiation damages have been self-recovered quickly. - Abstract: Molecular dynamics simulations have been performed to investigate the structural evolution of Cu{sub 64.5}Zr{sub 35.5} metallic glasses under irradiation. The largest standard cluster analysis (LSCA) method was used to quantify the microstructure within the collision cascade regions. It is found that the majority of clusters within the collision cascade regions are full and defective icosahedrons. Not only the smaller structures (common neighbor subcluster) but also primary clusters greatly changed during the collision cascades; while most of these radiation damages self-recover quickly in the following quench states. These findings indicate the Cu-Zr metallic glasses have excellent irradiation-resistance properties.

Advances Towards Synthetic Machines at the Molecular and Nanoscale Level

Directory of Open Access Journals (Sweden)

Kristina Konstas

2010-06-01

Full Text Available The fabrication of increasingly smaller machines to the nanometer scale can be achieved by either a “top-down” or “bottom-up” approach. While the former is reaching its limits of resolution, the latter is showing promise for the assembly of molecular components, in a comparable approach to natural systems, to produce functioning ensembles in a controlled and predetermined manner. In this review we focus on recent progress in molecular systems that act as molecular machine prototypes such as switches, motors, vehicles and logic operators.

The role of stable α-synuclein oligomers in the molecular events underlying amyloid formation

DEFF Research Database (Denmark)

Lorenzen, Nikolai; Nielsen, Søren Bang; Buell, Alexander K.

2014-01-01

α-synuclein (αSN), whose aggregation is strongly implicated in the development of Parkinson’s disease (PD). The two types of oligomers are both formed under conditions where amyloid fibril formation is observed but differ in molecular weight by an order of magnitude. Both possess a degree of β......, either as precursors of fibrils or as species involved in the fibril elongation process or instead if they are associated with an aggregation process that is distinct from that generating mature fibrils. Here we describe and characterize in detail two well-defined oligomeric species formed by the protein...

Disintegration of Ar2+ molecular ions under collisions with electrons in a plasma

International Nuclear Information System (INIS)

Ivanov, V.A.

1992-01-01

A spectroscopic experiment is carried out for investigation of disintegration of Ar 2 + ions by plasma electrons. For the first time in the wide electron temperature range from the room one up to T e ∼ 2 eV is measured the process rate constant. At temperatures lower 0.4 eV the obtained values agree well with published data on the value and temperature dependence of the coefficient of dissociative recombination of Ar 2 + with electrons. When temperature increasing in the range of T e =0.5-2 eV is found substantial rise of the rate of molecular ions disintegration, conditioned by starting dissociation mechanism under collicions with plasma electrons

Developing State Level Approaches under the State Level Concept

International Nuclear Information System (INIS)

Budlong Sylvester, K.; Murphy, C.L.; Boyer, B.; Pilat, J.F.

2015-01-01

With the pursuit of the State-Level Concept (SLC), the IAEA has sought to further evolve the international safeguards system in a manner which maintains (or improves) the effectiveness of the system in an environment of expanding demands and limited resources. The IAEA must not remain static and should continuously examine its practices to ensure it can capture opportunities for cost reductions while adapting to, and staying ahead of, emerging proliferation challenges. Contemporary safeguards have been focused on assessing the nuclear programme of the State as a whole, rather than on the basis of individual facilities. Since the IAEA's integrated safeguards program, State-level Approaches (SLAs) have been developed that seek to optimally combine the measures provided for by the Additional Protocol with those of traditional safeguards. This process resulted in facility specific approaches that, while making use of a State's broader conclusion, were nonetheless prescriptive. Designing SLAs on a State-by-State basis would avoid the shortcomings of a one-size-fits-all system. It would also enable the effective use of the Agency's information analysis and State evaluation efforts by linking this analysis to safeguards planning efforts. Acquisition Path Analysis (APA), along with the State Evaluation process, can be used to prioritize paths in a State in terms of their attractiveness for proliferation. While taking advantage of all safeguards relevant information, and tailoring safeguards to individual characteristics of the State, paths of the highest priority in all States will necessarily meet the same standard of coverage. Similarly, lower priority paths will have lower performance targets, thereby promoting nondiscrimination. Such an approach would improve understanding of safeguards implementation under the SLC and the rational for safeguards resource allocation. The potential roles for APA and performance targets in SLA development will be reviewed

Solvent Clathrate Driven Dynamic Stereomutation of a Supramolecular Polymer with Molecular Pockets.

Science.gov (United States)

Kulkarni, Chidambar; Korevaar, Peter A; Bejagam, Karteek K; Palmans, Anja R A; Meijer, E W; George, Subi J

2017-10-04

Control over the helical organization of synthetic supramolecular systems is intensively pursued to manifest chirality in a wide range of applications ranging from electron spin filters to artificial enzymes. Typically, switching the helicity of supramolecular assemblies involves external stimuli or kinetic traps. However, efforts to achieve helix reversal under thermodynamic control and to understand the phenomena at a molecular level are scarce. Here we present a unique example of helix reversal (stereomutation) under thermodynamic control in the self-assembly of a coronene bisimide that has a 3,5-dialkoxy substitution on the imide phenyl groups (CBI-35CH), leading to "molecular pockets" in the assembly. The stereomutation was observed only if the CBI monomer possesses molecular pockets. Detailed chiroptical studies performed in alkane solvents with different molecular structures reveal that solvent molecules intercalate or form clathrates within the molecular pockets of CBI-35CH at low temperature (263 K), thereby triggering the stereomutation. The interplay among the helical assembly, molecular pockets, and solvent molecules is further unraveled by explicit solvent molecular dynamics simulations. Our results demonstrate how the molecular design of self-assembling building blocks can orchestrate the organization of surrounding solvent molecules, which in turn dictates the helical organization of the resulting supramolecular assembly.

Non-sensitized selective photochemical reduction of CO2 to CO under visible light with an iron molecular catalyst.

Science.gov (United States)

Rao, Heng; Bonin, Julien; Robert, Marc

2017-03-02

A substituted tetraphenyl iron porphyrin, bearing positively charged trimethylammonio groups at the para position of each phenyl ring, demonstrates its ability as a homogeneous molecular catalyst to selectively reduce CO 2 to CO under visible light irradiation in organic media without the assistance of a sensitizer and no competitive hydrogen evolution for several days.

Molecular dynamics simulations of elasto-hydrodynamic lubrication and boundary lubrication for automotive tribology

International Nuclear Information System (INIS)

Washizu, Hitoshi; Sanda, Shuzo; Hyodo, Shi-aki; Ohmori, Toshihide; Nishino, Noriaki; Suzuki, Atsushi

2007-01-01

Friction control of machine elements on a molecular level is a challenging subject in vehicle technology. We describe the molecular dynamics studies of friction in two significant lubrication regimes. As a case of elastohydrodynamic lubrication, we introduce the mechanism of momentum transfer related to the molecular structure of the hydrocarbon fluids, phase transition of the fluids under high pressure, and a submicron thickness simulation of the oil film using a tera-flops computer. For boundary lubrication, the dynamic behavior of water molecules on hydrophilic and hydrophobic silicon surfaces under a shear condition is studied. The dynamic structure of the hydrogen bond network on the hydrophilic surface is related to the low friction of the diamond-like carbon containing silicon (DLC-Si) coating

Identification of light absorbing oligomers from glyoxal and methylglyoxal aqueous processing: a comparative study at the molecular level

Science.gov (United States)

Finessi, Emanuela; Hamilton, Jacqueline; Rickard, Andrew; Baeza-Romero, Maria; Healy, Robert; Peppe, Salvatore; Adams, Tom; Daniels, Mark; Ball, Stephen; Goodall, Iain; Monks, Paul; Borras, Esther; Munoz, Amalia

2014-05-01

Numerous studies point to the reactive uptake of gaseous low molecular weight carbonyls onto atmospheric waters (clouds/fog droplets and wet aerosols) as an important SOA formation route not yet included in current models. However, the evaluation of these processes is challenging because water provides a medium for a complex array of reactions to take place such as self-oligomerization, aldol condensation and Maillard-type browning reactions in the presence of ammonium salts. In addition to adding to SOA mass, aqueous chemistry products have been shown to include light absorbing, surface-active and high molecular weight oligomeric species, and can therefore affect climatically relevant aerosol properties such as light absorption and hygroscopicity. Glyoxal (GLY) and methylglyoxal (MGLY) are the gaseous carbonyls that have perhaps received the most attention to date owing to their ubiquity, abundance and reactivity in water, with the majority of studies focussing on bulk physical properties. However, very little is known at the molecular level, in particular for MGLY, and the relative potential of these species as aqueous SOA precursors in ambient air is still unclear. We have conducted experiments with both laboratory solutions and chamber-generated particles to simulate the aqueous processing of GLY and MGLY with ammonium sulphate (AS) under typical atmospheric conditions and investigated their respective aging products. Both high performance liquid chromatography coupled with UV-Vis detection and ion trap mass spectrometry (HPLC-DAD-MSn) and high resolution mass spectrometry (FTICRMS) have been used for molecular identification purposes. Comprehensive gas chromatography with nitrogen chemiluminescence detection (GCxGC-NCD) has been applied for the first time to these systems, revealing a surprisingly high number of nitrogen-containing organics (ONs), with a large extent of polarities. GCxGC-NCD proved to be a valuable tool to determine overall amount and rates of

Enhanced mechanical properties of graphene/copper nanocomposites using a molecular-level mixing process.

Science.gov (United States)

Hwang, Jaewon; Yoon, Taeshik; Jin, Sung Hwan; Lee, Jinsup; Kim, Taek-Soo; Hong, Soon Hyung; Jeon, Seokwoo

2013-12-10

RGO flakes are homogeneously dispersed in a Cu matrix through a molecular-level mixing process. This novel fabrication process prevents the agglomeration of the RGO and enhances adhesion between the RGO and the Cu. The yield strength of the 2.5 vol% RGO/Cu nanocomposite is 1.8 times higher than that of pure Cu. The strengthening mechanism of the RGO is investigated by a double cantilever beam test using the graphene/Cu model structure. © 2013 WILEY-VCH Verlag GmbH & Co. KGaA, Weinheim.

Statistical inference on censored data for targeted clinical trials under enrichment design.

Science.gov (United States)

Chen, Chen-Fang; Lin, Jr-Rung; Liu, Jen-Pei

2013-01-01

For the traditional clinical trials, inclusion and exclusion criteria are usually based on some clinical endpoints; the genetic or genomic variability of the trial participants are not totally utilized in the criteria. After completion of the human genome project, the disease targets at the molecular level can be identified and can be utilized for the treatment of diseases. However, the accuracy of diagnostic devices for identification of such molecular targets is usually not perfect. Some of the patients enrolled in targeted clinical trials with a positive result for the molecular target might not have the specific molecular targets. As a result, the treatment effect may be underestimated in the patient population truly with the molecular target. To resolve this issue, under the exponential distribution, we develop inferential procedures for the treatment effects of the targeted drug based on the censored endpoints in the patients truly with the molecular targets. Under an enrichment design, we propose using the expectation-maximization algorithm in conjunction with the bootstrap technique to incorporate the inaccuracy of the diagnostic device for detection of the molecular targets on the inference of the treatment effects. A simulation study was conducted to empirically investigate the performance of the proposed methods. Simulation results demonstrate that under the exponential distribution, the proposed estimator is nearly unbiased with adequate precision, and the confidence interval can provide adequate coverage probability. In addition, the proposed testing procedure can adequately control the size with sufficient power. On the other hand, when the proportional hazard assumption is violated, additional simulation studies show that the type I error rate is not controlled at the nominal level and is an increasing function of the positive predictive value. A numerical example illustrates the proposed procedures. Copyright © 2013 John Wiley & Sons, Ltd.

Microendophenotypes of psychiatric disorders: phenotypes of psychiatric disorders at the level of molecular dynamics, synapses, neurons, and neural circuits.

Science.gov (United States)

Kida, S; Kato, T

2015-01-01

Psychiatric disorders are caused not only by genetic factors but also by complicated factors such as environmental ones. Moreover, environmental factors are rarely quantitated as biological and biochemical indicators, making it extremely difficult to understand the pathological conditions of psychiatric disorders as well as their underlying pathogenic mechanisms. Additionally, we have actually no other option but to perform biological studies on postmortem human brains that display features of psychiatric disorders, thereby resulting in a lack of experimental materials to characterize the basic biology of these disorders. From these backgrounds, animal, tissue, or cell models that can be used in basic research are indispensable to understand biologically the pathogenic mechanisms of psychiatric disorders. In this review, we discuss the importance of microendophenotypes of psychiatric disorders, i.e., phenotypes at the level of molecular dynamics, neurons, synapses, and neural circuits, as targets of basic research on these disorders.

A graph-clustering approach to search important molecular markers ...

African Journals Online (AJOL)

Here, we performed a comprehensive gene level assessment of Parkinson's disease using 16 colorectal cancer samples and nine normal samples. The results show that SLC6A3, SLC18A2, and EN1, etc., are related to Parkinson's disease. Besides, we further mined the underlying molecular mechanism within these ...

Estimating sea-level allowances for Atlantic Canada under conditions of uncertain sea-level rise

Directory of Open Access Journals (Sweden)

B. Greenan

2015-03-01

Full Text Available This paper documents the methodology of computing sea-level rise allowances for Atlantic Canada in the 21st century under conditions of uncertain sea-level rise. The sea-level rise allowances are defined as the amount by which an asset needs to be raised in order to maintain the same likelihood of future flooding events as that site has experienced in the recent past. The allowances are determined by combination of the statistics of present tides and storm surges (storm tides and the regional projections of sea-level rise and associated uncertainty. Tide-gauge data for nine sites from the Canadian Atlantic coast are used to derive the scale parameters of present sea-level extremes using the Gumbel distribution function. The allowances in the 21st century, with respect to the year 1990, were computed for the Intergovernmental Panel on Climate Change (IPCC A1FI emission scenario. For Atlantic Canada, the allowances are regionally variable and, for the period 1990–2050, range between –13 and 38 cm while, for the period 1990–2100, they range between 7 and 108 cm. The negative allowances in the northern Gulf of St. Lawrence region are caused by land uplift due to glacial isostatic adjustment (GIA.

Molecular spectrum of laterally coupled quantum rings under intense terahertz radiation.

Science.gov (United States)

Baghramyan, Henrikh M; Barseghyan, Manuk G; Laroze, David

2017-09-05

We study the influence of intense THz laser radiation and electric field on molecular states of laterally coupled quantum rings. Laser radiation shows the capability to dissociate quantum ring molecule and add 2-fold degeneracy to the molecular states at the fixed value of the overlapping size between rings. It is shown that coupled to decoupled molecular states phase transition points form almost a straight line with a slope equal to two. In addition, the electric field direction dependent energy spectrum shows unexpected oscillations, demonstrating strong coupling between molecular states. Besides, intraband absorption is considered, showing both blue and redshifts in its spectrum. The obtained results can be useful for the controlling of degeneracy of the discrete energy spectrum of nanoscale structures and in the tunneling effects therein.

FAMILY’S ECONOMIC LEVEL AND CULTURE CORRELATE WITH NUTRITIONAL STATUS OF CHILDREN UNDER FIVE YEARS

Directory of Open Access Journals (Sweden)

Abdul Muhith

2017-01-01

Full Text Available Introduction: Nutrition is an important thing for human life. Variety in family’s economic level and culture have effect on family’s eating habit. Family with higher economic status have big opportunity to met under fi ve year’s nutrition. Cultural diversity on each family has an impact on the difference of raw food selection, processing methods, and presentation of food. The purpose of this study was to determine the correlation between family’s economic level and culture with nutritional status of children under fi ve year. Method: Research design was observational analytic with cross sectional approach. The population were mother and their children under fi ve years at Desa Jatigono Kunir, Kabupaten Lumajang. Sampel were 184 respondents, taken by using cluster sampling. Independent variables were family’s economic level and culture. Dependent variable was nutritional status of children under fi ve years. Data were collected by using questionnaire and observational sheet. Then, data were analyzed by using Spearman Rho Test with α<0.05. Result: The results showed that 140 (76.1% respondents have low economic level, 105 (57.1% respondents have negative culture in children’s nutrition, and 89 (48% respondents have good nutritional status. The result of Spearman-rho test showed that family’s economic level (p=0.000 and culture (0.019 have correlated with nutritional status of children under five years. Discussion: It can be concluded that family’s economic level and culture have correlated with nutritional status of children under fi ve years. Nurses should develop health education and counseling to improve family’s knowledge about nutrition, so children will have good nutritional status. Keywords: economic level, family’s culture, nutritional status, children under five years

An Overview of Biomarkers and Molecular Signatures in HCC

Energy Technology Data Exchange (ETDEWEB)

Yim, Seon-Hee [Integrated Research Center for Genome Polymorphism, The Catholic University of Korea School of Medicine, 505 Banpo-dong, Seocho-gu, Seoul 137-701 (Korea, Republic of); Chung, Yeun-Jun, E-mail: yejun@catholic.ac.kr [Integrated Research Center for Genome Polymorphism, The Catholic University of Korea School of Medicine, 505 Banpo-dong, Seocho-gu, Seoul 137-701 (Korea, Republic of); Department of Microbiology, The Catholic University of Korea School of Medicine, 505 Banpo-dong, Seocho-gu, Seoul 137-701 (Korea, Republic of)

2010-05-07

Hepatocellular carcinoma (HCC) is the third most common cause of cancer mortality worldwide. Although most HCCs seem to originate from the accumulation of genetic abnormalities induced by various risk factors, underlying mechanisms of hepatocarcinogenesis remain unclear. Long-term survival of HCC patients is also poor, partly due to HCC recurrence. Although serum alpha-fetoprotein (AFP) level is a useful marker for the detection and monitoring of HCC, AFP levels may remain normal in the patients even with advanced HCC. To identify useful biomarkers for HCC, many studies have been conducted on molecular events such as genetic and epigenetic alterations, and gene expression. This review summarizes recent studies of potential molecular markers for diagnosis and monitoring metastasis or recurrence of HCC.

Asymptotic stability of a genetic network under impulsive control

International Nuclear Information System (INIS)

Li Fangfei; Sun Jitao

2010-01-01

The study of the stability of genetic network is an important motif for the understanding of the living organism at both molecular and cellular levels. In this Letter, we provide a theoretical method for analyzing the asymptotic stability of a genetic network under impulsive control. And the sufficient conditions of its asymptotic stability under impulsive control are obtained. Finally, an example is given to illustrate the effectiveness of the obtained method.

Molecular Level Investigation of CH ₄ and CO ₂ Adsorption in Hydrated Calcium–Montmorillonite

Energy Technology Data Exchange (ETDEWEB)

Lee, Mal-Soon [Physical; McGrail, B. Peter [Physical; Rousseau, Roger [Physical; Glezakou, Vassiliki-Alexandra [Physical

2017-11-17

We have studied the mechanism of intercalation and methane adsorption from a H2O/CH4/CO2 mixture on a prototypical shale component, Ca-montmorillonite. We employed ab initio molecular dynamics simulations at 323 K and 90 bar to obtain molecular level information of adsorption energetics, speciation, and structural and thermodynamic properties. Interaction of CH4 with surface Lewis acidic sites (Ca2+, surface OH) results in large induced dipoles (~1 D) that lead to relatively strong adsorption energies that level off once a full CH4 layer is formed. Intercalated CH4, also exhibits induced dipoles at low hydration levels, when the interaction with Ca2+ cations are less hindered. CO2 displaces CH4 in the coordination sphere of the cations (in the interlayer) or in the surface, thereby driving CH4 extraction. Our simulations indicate that there is a Goldilocks pressure range (~60-100 bar) where scCO2 –facilitated CH4 extraction will be maximized.

Molecular design of photovoltaic materials for polymer solar cells: toward suitable electronic energy levels and broad absorption.

Science.gov (United States)

Li, Yongfang

2012-05-15

Bulk heterojunction (BHJ) polymer solar cells (PSCs) sandwich a blend layer of conjugated polymer donor and fullerene derivative acceptor between a transparent ITO positive electrode and a low work function metal negative electrode. In comparison with traditional inorganic semiconductor solar cells, PSCs offer a simpler device structure, easier fabrication, lower cost, and lighter weight, and these structures can be fabricated into flexible devices. But currently the power conversion efficiency (PCE) of the PSCs is not sufficient for future commercialization. The polymer donors and fullerene derivative acceptors are the key photovoltaic materials that will need to be optimized for high-performance PSCs. In this Account, I discuss the basic requirements and scientific issues in the molecular design of high efficiency photovoltaic molecules. I also summarize recent progress in electronic energy level engineering and absorption spectral broadening of the donor and acceptor photovoltaic materials by my research group and others. For high-efficiency conjugated polymer donors, key requirements are a narrower energy bandgap (E(g)) and broad absorption, relatively lower-lying HOMO (the highest occupied molecular orbital) level, and higher hole mobility. There are three strategies to meet these requirements: D-A copolymerization for narrower E(g) and lower-lying HOMO, substitution with electron-withdrawing groups for lower-lying HOMO, and two-dimensional conjugation for broad absorption and higher hole mobility. Moreover, better main chain planarity and less side chain steric hindrance could strengthen π-π stacking and increase hole mobility. Furthermore, the molecular weight of the polymers also influences their photovoltaic performance. To produce high efficiency photovoltaic polymers, researchers should attempt to increase molecular weight while maintaining solubility. High-efficiency D-A copolymers have been obtained by using benzodithiophene (BDT), dithienosilole

Drugs meeting the molecular basis of diabetic kidney disease: bridging from molecular mechanism to personalized medicine.

Science.gov (United States)

Lambers Heerspink, Hiddo J; Oberbauer, Rainer; Perco, Paul; Heinzel, Andreas; Heinze, Georg; Mayer, Gert; Mayer, Bernd

2015-08-01

Diabetic kidney disease (DKD) is a complex, multifactorial disease and is associated with a high risk of renal and cardiovascular morbidity and mortality. Clinical practice guidelines for diabetes recommend essentially identical treatments for all patients without taking into account how the individual responds to the instituted therapy. Yet, individuals vary widely in how they respond to medications and therefore optimal therapy differs between individuals. Understanding the underlying molecular mechanisms of variability in drug response will help tailor optimal therapy. Polymorphisms in genes related to drug pharmacokinetics have been used to explore mechanisms of response variability in DKD, but with limited success. The complex interaction between genetic make-up and environmental factors on the abundance of proteins and metabolites renders pharmacogenomics alone insufficient to fully capture response variability. A complementary approach is to attribute drug response variability to individual variability in underlying molecular mechanisms involved in the progression of disease. The interplay of different processes (e.g. inflammation, fibrosis, angiogenesis, oxidative stress) appears to drive disease progression, but the individual contribution of each process varies. Drugs at the other hand address specific targets and thereby interfere in certain disease-associated processes. At this level, biomarkers may help to gain insight into which specific pathophysiological processes are involved in an individual followed by a rational assessment whether a specific drug's mode of action indeed targets the relevant process at hand. This article describes the conceptual background and data-driven workflow developed by the SysKid consortium aimed at improving characterization of the molecular mechanisms underlying DKD at the interference of the molecular impact of individual drugs in order to tailor optimal therapy to individual patients. © The Author 2015. Published by

Global plant-responding mechanisms to salt stress: physiological and molecular levels and implications in biotechnology.

Science.gov (United States)

Tang, Xiaoli; Mu, Xingmin; Shao, Hongbo; Wang, Hongyan; Brestic, Marian

2015-01-01

The increasing seriousness of salinization aggravates the food, population and environmental issues. Ameliorating the salt-resistance of plants especially the crops is the most effective measure to solve the worldwide problem. The salinity can cause damage to plants mainly from two aspects: hyperosmotic and hyperionic stresses leading to the restrain of growth and photosynthesis. To the adverse effects, the plants derive corresponding strategies including: ion regulation and compartmentalization, biosynthesis of compatible solutes, induction of antioxidant enzymes and plant hormones. With the development of molecular biology, our understanding of the molecular and physiology knowledge is becoming clearness. The complex signal transduction underlying the salt resistance is being illuminated brighter and clearer. The SOS pathway is the central of the cell signaling in salt stress. The accumulation of the compatible solutes and the activation of the antioxidant system are the effective measures for plants to enhance the salt resistance. How to make full use of our understanding to improve the output of crops is a huge challenge for us, yet the application of the genetic engineering makes this possible. In this review, we will discuss the influence of the salt stress and the response of the plants in detail expecting to provide a particular account for the plant resistance in molecular, physiological and transgenic fields.

Survival under stress: molecular mechanisms of metabolic rate ...

African Journals Online (AJOL)

Studies in my laboratory are analysing the molecular mechanisms and regulatory events that underlie transitions to and from hypometabolic states In systems including anoxia-tolerant turtles and molluscs, estivating snails and toads, hibernating small mammals, and freeze tolerant frogs and insects. Our newest research ...

Investigation of tribological properties of graphene oxide reinforced ultrahigh molecular weight polyethylene under artificial seawater lubricating condition

Science.gov (United States)

Pang, Wenchao; Ni, Zifeng; Wu, JiaLiang; Zhao, Yongwu

2018-03-01

A range of ultrahigh molecular weight polyethylene (UHMWPE)/graphene oxide (GO) nanocomposites were fabricated using liquid-phase ultrasonication mixing followed by hot-pressing. The wettability, water absorption and corrosion resistance of composites were studied to prove the composites were suitable for application in liquid environment. The tribological properties of composites under dry, deionized water and seawater lubricating condition were investigated. The results showed that the incorporation of GO decreased the wear rate of UHMWPE under different lubricating conditions and with the increase of GO addition, the wear rate of UHMWPE/GO composites decreased. UHMWPE/GO composites exhibited better tribological behaviors under seawater lubricating condition than other conditions, because good corrosion resistance and excellent wear resistance of UHMWPE/GO composites, and the lubricating effect of seawater is also indispensable.

Artificial molecular motors

NARCIS (Netherlands)

Kassem, Salma; van Leeuwen, Thomas; Lubbe, Anouk S.; Wilson, Miriam R.; Feringa, Ben L.; Leigh, David A.

2017-01-01

Motor proteins are nature's solution for directing movement at the molecular level. The field of artificial molecular motors takes inspiration from these tiny but powerful machines. Although directional motion on the nanoscale performed by synthetic molecular machines is a relatively new

Proton NMR for Measuring Quantum Level Crossing in the Magnetic Molecular Ring Fe10

International Nuclear Information System (INIS)

Julien, M.; Jang, Z.H.; Borsa, F.; Julien, M.; Lascialfari, A.; Borsa, F.; Horvatic, M.; Caneschi, A.; Gatteschi, D.

1999-01-01

The proton nuclear spin-lattice relaxation rate 1/T 1 has been measured as a function of temperature and magnetic field (up to 15thinspthinspT) in the molecular magnetic ring Fe 10 ( OCH 3 ) 20 (O 2 CCH 2 Cl) 10 (Fe10). Striking enhancement of 1/T 1 is observed around magnetic field values corresponding to a crossing between the ground state and the excited states of the molecule. We propose that this is due to a cross-relaxation effect between the nuclear Zeeman reservoir and the reservoir of the Zeeman levels of the molecule. This effect provides a powerful tool to investigate quantum dynamical phenomena at level crossing. copyright 1999 The American Physical Society

Assessing Flood Risk Under Sea Level Rise and Extreme Sea Levels Scenarios: Application to the Ebro Delta (Spain)

Science.gov (United States)

Sayol, J. M.; Marcos, M.

2018-02-01

This study presents a novel methodology to estimate the impact of local sea level rise and extreme surges and waves in coastal areas under climate change scenarios. The methodology is applied to the Ebro Delta, a valuable and vulnerable low-lying wetland located in the northwestern Mediterranean Sea. Projections of local sea level accounting for all contributions to mean sea level changes, including thermal expansion, dynamic changes, fresh water addition and glacial isostatic adjustment, have been obtained from regionalized sea level projections during the 21st century. Particular attention has been paid to the uncertainties, which have been derived from the spread of the multi-model ensemble combined with seasonal/inter-annual sea level variability from local tide gauge observations. Besides vertical land movements have also been integrated to estimate local relative sea level rise. On the other hand, regional projections over the Mediterranean basin of storm surges and wind-waves have been used to evaluate changes in extreme events. The compound effects of surges and extreme waves have been quantified using their joint probability distributions. Finally, offshore sea level projections from extreme events superimposed to mean sea level have been propagated onto a high resolution digital elevation model of the study region in order to construct flood hazards maps for mid and end of the 21st century and under two different climate change scenarios. The effect of each contribution has been evaluated in terms of percentage of the area exposed to coastal hazards, which will help to design more efficient protection and adaptation measures.

Dynamic coherence in excitonic molecular complexes under various excitation conditions

Energy Technology Data Exchange (ETDEWEB)

Chenu, Aurélia; Malý, Pavel; Mančal, Tomáš, E-mail: mancal@karlov.mff.cuni.cz

2014-08-17

Highlights: • Dynamic coherence does not improve energy transfer efficiency in natural conditions. • Photo-induced quantum jumps are discussed in classical context. • Natural time scale of a light excitation event is identified. • Coherence in FMO complex averages out under excitation by neighboring antenna. • This result is valid even in absence of dissipation. - Abstract: We investigate the relevance of dynamic quantum coherence in the energy transfer efficiency of molecular aggregates. We derive the time evolution of the density matrix for an open quantum system excited by light or by a neighboring antenna. Unlike in the classical case, the quantum description does not allow for a formal decomposition of the dynamics into sudden jumps in an observable quantity – an expectation value. Rather, there is a natural finite time-scale associated with the excitation process. We propose a simple experiment to test the influence of this time scale on the yield of photosynthesis. We demonstrate, using typical parameters of the Fenna–Matthews–Olson (FMO) complex and a typical energy transfer rate from the chlorosome baseplate, that dynamic coherences are averaged out in the complex even when the FMO model is completely free of all dissipation and dephasing.

Molecular phenotyping of multiple mouse strains under metabolic challenge uncovers a role for Elovl2 in glucose-induced insulin secretion

Directory of Open Access Journals (Sweden)

Céline Cruciani-Guglielmacci

2017-04-01

Conclusion: Our results suggest a role for Elovl2 in ensuring normal insulin secretory responses to glucose. Moreover, the large comprehensive dataset and integrative network-based approach provides a new resource to dissect the molecular etiology of β cell failure under metabolic stress.

Radio-adaptation: cellular and molecular features of a response to low levels of ionizing radiation

International Nuclear Information System (INIS)

Rigaud, O.

1998-01-01

It is well established that sublethal doses of DNA damaging agents induce protective mechanisms against a subsequent high dose treatment ; for instance, the phenomenon of radio-adaptation in the case of ionizing radiations. Since the early observation described in 1984, numerous studies have confirmed the radio-adaptive response in terms of reduction of chromosomal breaks for varied biological models in vitro and in vivo. Evidence for an adaptive response against the induction of gene mutations and the lethal effect is clearly demonstrated. This paper reviews the experimental results describing various aspects of these adaptive responses expressed on these different biological end-points. The molecular mechanism underlying radio-adaptation still remains nuclear. The development of this phenomenon requires de novo synthesis of transcripts and proteins during the time interval between the two doses. Some data are consistent with the hypotheses that these gene products would be involved in the activation of DNA repair pathways and antioxidant systems. However, a major question still remains unanswered; indeed, it is not clear whether or not the radio-adaptation could affect the estimation of cancer risk related with low level exposure to ionizing radiation, a major concern in radioprotection. Until such data are available, it is yet unwise to evoke the beneficial effects of radio-adaptation. (authors)

Molecular HIV screening.

Science.gov (United States)

Bourlet, Thomas; Memmi, Meriam; Saoudin, Henia; Pozzetto, Bruno

2013-09-01

Nuclear acid testing is more and more used for the diagnosis of infectious diseases. This paper focuses on the use of molecular tools for HIV screening. The term 'screening' will be used under the meaning of first-line HIV molecular techniques performed on a routine basis, which excludes HIV molecular tests designed to confirm or infirm a newly discovered HIV-seropositive patient or other molecular tests performed for the follow-up of HIV-infected patients. The following items are developed successively: i) presentation of the variety of molecular tools used for molecular HIV screening, ii) use of HIV molecular tools for the screening of blood products, iii) use of HIV molecular tools for the screening of organs and tissue from human origin, iv) use of HIV molecular tools in medically assisted procreation and v) use of HIV molecular tools in neonates from HIV-infected mothers.

Molecular characterisation of a calmodulin gene, VcCaM1, that is differentially expressed under aluminium stress in highbush blueberry.

Science.gov (United States)

Inostroza-Blancheteau, C; Aquea, F; Loyola, R; Slovin, J; Josway, S; Rengel, Z; Reyes-Díaz, M; Alberdi, M; Arce-Johnson, P

2013-11-01

Calmodulin (CaM), a small acidic protein, is one of the best characterised Ca(2+) sensors in eukaryotes. This Ca(2+) -regulated protein plays a critical role in decoding and transducing environmental stress signals by activating specific targets. Many environmental stresses elicit changes in intracellular Ca(2+) activity that could initiate adaptive responses under adverse conditions. We report the first molecular cloning and characterisation of a calmodulin gene, VcCaM1 (Vaccinium corymbosum Calmodulin 1), in the woody shrub, highbush blueberry. VcCaM1 was first identified as VCAL19, a gene induced by aluminium stress in V. corymbosum L. A full-length cDNA of VcCaM1 containing a 766-bp open reading frame (ORF) encoding 149 amino acids was cloned from root RNA. The sequence encodes four Ca(2+) -binding motifs (EF-hands) and shows high similarity (99%) with the isoform CaM 201 of Daucus carota. Expression analyses showed that following Al treatment, VcCaM1 message level decreased in roots of Brigitta, an Al-resistant cultivar, and after 48 h, was lower than in Bluegold, an Al-sensitive cultivar. VcCAM1 message also decreased in leaves of both cultivars within 2 h of treatment. Message levels in leaves then increased by 24 h to control levels in Brigitta, but not in Bluegold, but then decreased again by 48 h. In conclusion, VcCaM1 does not appear to be directly involved in Al resistance, but may be involved in improved plant performance under Al toxicity conditions through regulation of Ca(2+) homeostasis and antioxidant systems in leaves. © 2013 German Botanical Society and The Royal Botanical Society of the Netherlands.

Molecular environmental science and synchrotron radiation sources

Energy Technology Data Exchange (ETDEWEB)

Brown, G.E. Jr. [Stanford Univ., CA (United States)

1995-12-31

Molecular environmental science is a relatively new field but focuses on the chemical and physical forms of toxic and/or radioactive contaminants in soils, sediments, man-made waste forms, natural waters, and the atmosphere; their possible reactions with inorganic and organic compounds, plants, and organisms in the environment; and the molecular-level factors that control their toxicity, bioavailability, and transport. The chemical speciation of a contaminant is a major factor in determining its behavior in the environment, and synchrotron-based X-ray absorption fine structure (XAFS) spectroscopy is one of the spectroscopies of choice to quantitatively determine speciation of heavy metal contaminants in situ without selective extraction or other sample treatment. The use of high-flux insertion device beam lines at synchrotron sources and multi-element array detectors has permitted XAFS studies of metals such as Se and As in natural soils at concentration levels as low as 50 ppm. The X-ray absorption near edge structure of these metals is particularly useful in determining their oxidation state. Examples of such studies will be presented, and new insertion device beam lines under development at SSRL and the Advanced Photon Source for molecular environmental science applications will be discussed.

Molecular plasmonics: The role of rovibrational molecular states in exciton-plasmon materials under strong-coupling conditions

Science.gov (United States)

Sukharev, Maxim; Charron, Eric

2017-03-01

We extend the model of exciton-plasmon materials to include a rovibrational structure of molecules using wave-packet propagations on electronic potential energy surfaces. Our model replaces conventional two-level emitters with more complex molecules, allowing us to examine the influence of alignment and vibrational dynamics on strong coupling with surface plasmon-polaritons. We apply the model to a hybrid system comprising a thin layer of molecules placed on top of a periodic array of slits. Rigorous simulations are performed for two types of molecular systems described by vibrational bound-bound and bound-continuum electronic transitions. Calculations reveal new features in transmission, reflection, and absorption spectra, including the observation of significantly higher values of the Rabi splitting and vibrational patterns clearly seen in the corresponding spectra. We also examine the influence of anisotropic initial conditions on optical properties of hybrid materials, demonstrating that the optical response of the system is significantly affected by an initial prealignment of the molecules. Our work demonstrates that prealigned molecules could serve as an efficient probe for the subdiffraction characterization of the near-field near metal interfaces.

Phototoxicity and oxidative stress responses in Daphnia magna under exposure to sulfathiazole and environmental level ultraviolet B irradiation

Energy Technology Data Exchange (ETDEWEB)

Kim, Jungkon [School of Public Health, Seoul National University, Seoul, 110-799 (Korea, Republic of)], E-mail: koguma@snu.ac.kr; Park, Yena [School of Public Health, Seoul National University, Seoul, 110-799 (Korea, Republic of)], E-mail: elohim@snu.ac.kr; Choi, Kyungho [School of Public Health, Seoul National University, Seoul, 110-799 (Korea, Republic of)], E-mail: kyungho@snu.ac.kr

2009-01-18

Sulfonamide antibiotics frequently occur in aquatic environments. In this study, phototoxicity of sulfathiazole (STZ) and its mechanism of action were investigated using Daphnia magna. We evaluated the changes of molecular level stress responses by assessing gene expression, enzyme induction and lipid peroxidation, and the related organism-level effects in D. magna. In the presence of ultraviolet B (UV-B) light (continuous irradiation with 13.8 {+-} 1.0 {mu}W cm{sup -2} d{sup -1}), STZ (at the nominal concentration of 94.9 mg/L) caused a significant increase in reactive oxygen species (ROS) generation and lipid peroxidation. Catalase (CAT) and glutathione S-transferase (GST) showed concentration-dependent increases caused by the exposure. Exposure to STZ and UV-B light caused apparent up-regulation of {alpha}-esterase, hemoglobin, and vitellogenin mRNA. The survival of daphnids was significantly affected by the co-exposure to STZ and UV-B. The biochemical and molecular level observations in combination with organism-level effects suggest that the phototoxicity of STZ was mediated in part by ROS generated by oxidative stress in D. magna.

Phototoxicity and oxidative stress responses in Daphnia magna under exposure to sulfathiazole and environmental level ultraviolet B irradiation

International Nuclear Information System (INIS)

Kim, Jungkon; Park, Yena; Choi, Kyungho

2009-01-01

Sulfonamide antibiotics frequently occur in aquatic environments. In this study, phototoxicity of sulfathiazole (STZ) and its mechanism of action were investigated using Daphnia magna. We evaluated the changes of molecular level stress responses by assessing gene expression, enzyme induction and lipid peroxidation, and the related organism-level effects in D. magna. In the presence of ultraviolet B (UV-B) light (continuous irradiation with 13.8 ± 1.0 μW cm -2 d -1 ), STZ (at the nominal concentration of 94.9 mg/L) caused a significant increase in reactive oxygen species (ROS) generation and lipid peroxidation. Catalase (CAT) and glutathione S-transferase (GST) showed concentration-dependent increases caused by the exposure. Exposure to STZ and UV-B light caused apparent up-regulation of α-esterase, hemoglobin, and vitellogenin mRNA. The survival of daphnids was significantly affected by the co-exposure to STZ and UV-B. The biochemical and molecular level observations in combination with organism-level effects suggest that the phototoxicity of STZ was mediated in part by ROS generated by oxidative stress in D. magna

Surface Functionalization of g-C 3 N 4 : Molecular-Level Design of Noble-Metal-Free Hydrogen Evolution Photocatalysts

KAUST Repository

Chen, Yin; Lin, Bin; Yu, Weili; Yang, Yong; Bashir, Shahid M.; Wang, Hong; Takanabe, Kazuhiro; Idriss, Hicham; Basset, Jean-Marie

2015-01-01

A stable noble-metal-free hydrogen evolution photocatalyst based on graphite carbon nitride (g-C3N4) was developed by a molecular-level design strategy. Surface functionalization was successfully conducted to introduce a single nickel active site

Noncanonical structures and their thermodynamics of DNA and RNA under molecular crowding: beyond the Watson-Crick double helix.

Science.gov (United States)

Sugimoto, Naoki

2014-01-01

How does molecular crowding affect the stability of nucleic acid structures inside cells? Water is the major solvent component in living cells, and the properties of water in the highly crowded media inside cells differ from that in buffered solution. As it is difficult to measure the thermodynamic behavior of nucleic acids in cells directly and quantitatively, we recently developed a cell-mimicking system using cosolutes as crowding reagents. The influences of molecular crowding on the structures and thermodynamics of various nucleic acid sequences have been reported. In this chapter, we discuss how the structures and thermodynamic properties of nucleic acids differ under various conditions such as highly crowded environments, compartment environments, and in the presence of ionic liquids, and the major determinants of the crowding effects on nucleic acids are discussed. The effects of molecular crowding on the activities of ribozymes and riboswitches on noncanonical structures of DNA- and RNA-like quadruplexes that play important roles in transcription and translation are also described. © 2014 Elsevier Inc. All rights reserved.

Gas Exchange Characteristics in Tectona grandis L. Clones under Varying Concentrations of CO2 Levels

Directory of Open Access Journals (Sweden)

S. Saravanan

2014-08-01

Full Text Available The Institute of Forest Genetics and Tree Breeding, Coimbatore, India functioning under the Indian Council of Forestry Research and Education, Dehara Dun, has a long term systematic tree improvement program for Tectona grandis aimed to enhancing productivity and screening of clones for site specific. In the process, twenty clones of T. grandis L. were studied for the physiological parameters and water use efficiency with reference to the elevated CO2 levels. CO2 enrichment studies in special chambers help in understanding the changes at individual level, and also at physiological, biochemical and genetic level. It also provides valuable information for establishing plantations at different geographic locations. Considerable variations were observed when the selected 20 clones of T. grandis were subjected to physiological studies under elevated CO2 conditions (600 and 900 mol mol-1. Eight clones exhibited superior growth coupled with favorable physiological characteristics including high photosynthetic rate, carboxylation and water use efficiency under elevated CO2 levels. Clones with minimal variation in physiological characteristics under elevated levels of CO2 suggest their ability to overcome physiological stresses and adapt to varying climatic conditions.

Stability of large-area molecular junctions

NARCIS (Netherlands)

Akkerman, Hylke B.; Kronemeijer, Auke J.; Harkema, Jan; van Hal, Paul A.; Smits, Edsger C. P.; de Leeuw, Dago M.; Blom, Paul W. M.

The stability of molecular junctions is crucial for any application of molecular electronics. Degradation of molecular junctions when exposed to ambient conditions is regularly observed. In this report the stability of large-area molecular junctions under ambient conditions for more than two years

Global transcriptomic profiling of aspen trees under elevated [CO2] to identify potential molecular mechanisms responsible for enhanced radial growth.

Science.gov (United States)

Wei, Hairong; Gou, Jiqing; Yordanov, Yordan; Zhang, Huaxin; Thakur, Ramesh; Jones, Wendy; Burton, Andrew

2013-03-01

Aspen (Populus tremuloides) trees growing under elevated [CO(2)] at a free-air CO(2) enrichment (FACE) site produced significantly more biomass than control trees. We investigated the molecular mechanisms underlying the observed increase in biomass by producing transcriptomic profiles of the vascular cambium zone (VCZ) and leaves, and then performed a comparative study to identify significantly changed genes and pathways after 12 years exposure to elevated [CO(2)]. In leaves, elevated [CO(2)] enhanced expression of genes related to Calvin cycle activity and linked pathways. In the VCZ, the pathways involved in cell growth, cell division, hormone metabolism, and secondary cell wall formation were altered while auxin conjugation, ABA synthesis, and cytokinin glucosylation and degradation were inhibited. Similarly, the genes involved in hemicellulose and pectin biosynthesis were enhanced, but some genes that catalyze important steps in lignin biosynthesis pathway were inhibited. Evidence from systemic analysis supported the functioning of multiple molecular mechanisms that underpin the enhanced radial growth in response to elevated [CO(2)].

Atomistic simulations of highly conductive molecular transport junctions under realistic conditions

KAUST Repository

French, William R.; Iacovella, Christopher R.; Rungger, Ivan; Souza, Amaury Melo; Sanvito, Stefano; Cummings, Peter T.

2013-01-01

We report state-of-the-art atomistic simulations combined with high-fidelity conductance calculations to probe structure-conductance relationships in Au-benzenedithiolate (BDT)-Au junctions under elongation. Our results demonstrate that large increases in conductance are associated with the formation of monatomic chains (MACs) of Au atoms directly connected to BDT. An analysis of the electronic structure of the simulated junctions reveals that enhancement in the s-like states in Au MACs causes the increases in conductance. Other structures also result in increased conductance but are too short-lived to be detected in experiment, while MACs remain stable for long simulation times. Examinations of thermally evolved junctions with and without MACs show negligible overlap between conductance histograms, indicating that the increase in conductance is related to this unique structural change and not thermal fluctuation. These results, which provide an excellent explanation for a recently observed anomalous experimental result [Bruot et al., Nat. Nanotechnol., 2012, 7, 35-40], should aid in the development of mechanically responsive molecular electronic devices. © 2013 The Royal Society of Chemistry.

Molecular Force Spectroscopy on Cells

Science.gov (United States)

Liu, Baoyu; Chen, Wei; Zhu, Cheng

2015-04-01

Molecular force spectroscopy has become a powerful tool to study how mechanics regulates biology, especially the mechanical regulation of molecular interactions and its impact on cellular functions. This force-driven methodology has uncovered a wealth of new information of the physical chemistry of molecular bonds for various biological systems. The new concepts, qualitative and quantitative measures describing bond behavior under force, and structural bases underlying these phenomena have substantially advanced our fundamental understanding of the inner workings of biological systems from the nanoscale (molecule) to the microscale (cell), elucidated basic molecular mechanisms of a wide range of important biological processes, and provided opportunities for engineering applications. Here, we review major force spectroscopic assays, conceptual developments of mechanically regulated kinetics of molecular interactions, and their biological relevance. We also present current challenges and highlight future directions.

Molecular toxicity of nanomaterials.

Science.gov (United States)

Chang, Xue-Ling; Yang, Sheng-Tao; Xing, Gengmei

2014-10-01

With the rapid developments in the fields of nanoscience and nanotechnlogy, more and more nanomaterials and their based consumer products have been used into our daily life. The safety concerns of nanomaterials have been well recognized by the scientific community and the public. Molecular mechanism of interactions between nanomaterials and biosystems is the most essential topic and final core of the biosafety. In the last two decades, nanotoxicology developed very fast and toxicity phenomena of nanomaterials have been reported. To achieve better understanding and detoxication of nanomaterials, thorough studies of nanotoxicity at molecular level are important. The interactions between nanomaterials and biomolecules have been widely investigated as the first step toward the molecular nanotoxicology. The consequences of such interactions have been discussed in the literature. Besides this, the chemical mechanism of nanotoxicology is gaining more attention, which would lead to a better design of nontoxic nanomaterials. In this review, we focus on the molecular nanotoxicology and explore the toxicity of nanomaterials at molecular level. The molecular level studies of nanotoxicology are summarized and the published nanotoxicological data are revisited.

Molecular profiling of short-term and long-term surviving patients identifies CD34 mRNA level as prognostic for glioblastoma survival

DEFF Research Database (Denmark)

Michaelsen, Signe Regner; Urup, Thomas; Olsen, Lars Rønn

2018-01-01

Despite extensive treatment, overall survival (OS) for glioblastoma (GBM) remains poor. A small proportion of patients present long survival over 3 years, but the underlying molecular background separating these long-term survivors (LTS) from short-term survivors (STS) are insufficiently understood....... Accordingly, study aim was to identify independent prognostic biomarkers for survival. Study cohort consisted of 93 primary GBM patients treated with radiation-, chemo- and bevacizumab therapy, among which 14 STS (OS ≤ 12 months) and 6 LTS (OS ≥ 36 months) were identified, all confirmed being IDH wild......-type. RNA expression levels in diagnostic tumor specimen for 792 genes were analyzed by NanoString technology. While no differences were found with regard to GBM subtype between LTS versus STS, comparative analysis of individual genes identified 14 significantly differently expressed candidate genes...

Molecular and Cellular Signaling

CERN Document Server

Beckerman, Martin

2005-01-01

A small number of signaling pathways, no more than a dozen or so, form a control layer that is responsible for all signaling in and between cells of the human body. The signaling proteins belonging to the control layer determine what kinds of cells are made during development and how they function during adult life. Malfunctions in the proteins belonging to the control layer are responsible for a host of human diseases ranging from neurological disorders to cancers. Most drugs target components in the control layer, and difficulties in drug design are intimately related to the architecture of the control layer. Molecular and Cellular Signaling provides an introduction to molecular and cellular signaling in biological systems with an emphasis on the underlying physical principles. The text is aimed at upper-level undergraduates, graduate students and individuals in medicine and pharmacology interested in broadening their understanding of how cells regulate and coordinate their core activities and how diseases ...

Parental epigenetic difference in DNA methylation-level may play ...

African Journals Online (AJOL)

Parental epigenetic difference in DNA methylation-level may play contrasting roles for different agronomic traits related to yield heterosis in maize. ... or hybrid vigor has been exploited to nearly the fullest extent, the molecular and genetic basis underlying this remarkable biological phenomenon remains largely an enigma.

Controlling single-molecule junction conductance by molecular interactions

Science.gov (United States)

Kitaguchi, Y.; Habuka, S.; Okuyama, H.; Hatta, S.; Aruga, T.; Frederiksen, T.; Paulsson, M.; Ueba, H.

2015-01-01

For the rational design of single-molecular electronic devices, it is essential to understand environmental effects on the electronic properties of a working molecule. Here we investigate the impact of molecular interactions on the single-molecule conductance by accurately positioning individual molecules on the electrode. To achieve reproducible and precise conductivity measurements, we utilize relatively weak π-bonding between a phenoxy molecule and a STM-tip to form and cleave one contact to the molecule. The anchoring to the other electrode is kept stable using a chalcogen atom with strong bonding to a Cu(110) substrate. These non-destructive measurements permit us to investigate the variation in single-molecule conductance under different but controlled environmental conditions. Combined with density functional theory calculations, we clarify the role of the electrostatic field in the environmental effect that influences the molecular level alignment. PMID:26135251

Frontiers of controlling energy levels at interfaces

Science.gov (United States)

Koch, Norbert

The alignment of electron energy levels at interfaces between semiconductors, dielectrics, and electrodes determines the function and efficiency of all electronic and optoelectronic devices. Reliable guidelines for predicting the level alignment for a given material combination and methods to adjust the intrinsic energy landscape are needed to enable efficient engineering approaches. These are sufficiently understood for established electronic materials, e.g., Si, but for the increasing number of emerging materials, e.g., organic and 2D semiconductors, perovskites, this is work in progress. The intrinsic level alignment and the underlying mechanisms at interfaces between organic and inorganic semiconductors are discussed first. Next, methods to alter the level alignment are introduced, which all base on proper charge density rearrangement at a heterojunction. As interface modification agents we use molecular electron acceptors and donors, as well as molecular photochromic switches that add a dynamic aspect and allow device multifunctionality. For 2D semiconductors surface transfer doping with molecular acceptors/donors transpires as viable method to locally tune the Fermi-level position in the energy gap. The fundamental electronic properties of a prototypical 1D interface between intrinsic and p-doped 2D semiconductor regions are derived from local (scanning probe) and area-averaged (photoemission) spectroscopy experiments. Future research opportunities for attaining unsurpassed interface control through charge density management are discussed.

Molecular subgroups of medulloblastoma identification using noninvasive magnetic resonance spectroscopy.

Science.gov (United States)

Blüml, Stefan; Margol, Ashley S; Sposto, Richard; Kennedy, Rebekah J; Robison, Nathan J; Vali, Marzieh; Hung, Long T; Muthugounder, Sakunthala; Finlay, Jonathan L; Erdreich-Epstein, Anat; Gilles, Floyd H; Judkins, Alexander R; Krieger, Mark D; Dhall, Girish; Nelson, Marvin D; Asgharzadeh, Shahab

2016-01-01

Medulloblastomas in children can be categorized into 4 molecular subgroups with differing clinical characteristics, such that subgroup determination aids in prognostication and risk-adaptive treatment strategies. Magnetic resonance spectroscopy (MRS) is a widely available, noninvasive tool that is used to determine the metabolic characteristics of tumors and provide diagnostic information without the need for tumor tissue. In this study, we investigated the hypothesis that metabolite concentrations measured by MRS would differ between molecular subgroups of medulloblastoma and allow accurate subgroup determination. MRS was used to measure metabolites in medulloblastomas across molecular subgroups (SHH = 12, Groups 3/4 = 17, WNT = 1). Levels of 14 metabolites were analyzed to determine those that were the most discriminant for medulloblastoma subgroups in order to construct a multivariable classifier for distinguishing between combined Group 3/4 and SHH tumors. Medulloblastomas across molecular subgroups revealed distinct spectral features. Group 3 and Group 4 tumors demonstrated metabolic profiles with readily detectable taurine, lower levels of lipids, and high levels of creatine. SHH tumors showed prominent choline and lipid with low levels of creatine and little or no evidence of taurine. A 5-metabolite subgroup classifier inclusive of creatine, myo-inositol, taurine, aspartate, and lipid 13a was developed that could discriminate between Group 3/4 and SHH medulloblastomas with excellent accuracy (cross-validated area under the curve [AUC] = 0.88). The data show that medulloblastomas of Group 3/4 differ metabolically as measured using MRS when compared with SHH molecular subgroups. MRS is a useful and accurate tool to determine medulloblastoma molecular subgroups. © The Author(s) 2015. Published by Oxford University Press on behalf of the Society for Neuro-Oncology. All rights reserved. For permissions, please e-mail: journals.permissions@oup.com.

Progress on molecular imaging

International Nuclear Information System (INIS)

Chen Quan; Zhang Yongxue

2011-01-01

Molecular imaging is a new era of medical imaging,which can non-invasively monitor biological processes at the cellular and molecular level in vivo, including molecular imaging of nuclear medicine, magnetic resonance molecular imaging, ultrasound molecular imaging,optical molecular imaging and molecular imaging with X-ray. Recently, with the development of multi-subjects amalgamation, multimodal molecular imaging technology has been applied in clinical imaging, such as PET-CT and PET-MRI. We believe that with development of molecular probe and multi-modal imaging, more and more molecular imaging techniques will be applied in clinical diagnosis and treatment. (authors)

Molecular responses during cadmium-induced stress in Daphnia magna: Integration of differential gene expression with higher-level effects

Energy Technology Data Exchange (ETDEWEB)

Soetaert, Anneleen [Department of Biology, Laboratory for Ecophysiology, Biochemistry and Toxicology, University of Antwerp, Groenenborgerlaan 171, B-2020 Antwerp (Belgium)]. E-mail: anneleen.soetaert@ua.ac.be; Vandenbrouck, Tine [Department of Biology, Laboratory for Ecophysiology, Biochemistry and Toxicology, University of Antwerp, Groenenborgerlaan 171, B-2020 Antwerp (Belgium); Ven, Karlijn van der [Department of Biology, Laboratory for Ecophysiology, Biochemistry and Toxicology, University of Antwerp, Groenenborgerlaan 171, B-2020 Antwerp (Belgium); Maras, Marleen [Department of Biology, Laboratory for Ecophysiology, Biochemistry and Toxicology, University of Antwerp, Groenenborgerlaan 171, B-2020 Antwerp (Belgium); Remortel, Piet van [Department of Mathematics and Informatics, Intelligent Systems Laboratory, University of Antwerp, Middelheimlaan 1, B-2020 Antwerp (Belgium); Blust, Ronny [Department of Biology, Laboratory for Ecophysiology, Biochemistry and Toxicology, University of Antwerp, Groenenborgerlaan 171, B-2020 Antwerp (Belgium); Coen, Wim M. de [Department of Biology, Laboratory for Ecophysiology, Biochemistry and Toxicology, University of Antwerp, Groenenborgerlaan 171, B-2020 Antwerp (Belgium)

2007-07-20

DNA microarrays offer great potential in revealing insight into mechanistic toxicity of contaminants. The aim of the present study was (i) to gain insight in concentration- and time-dependent cadmium-induced molecular responses by using a customized Daphnia magna microarray, and (ii) to compare the gene expression profiles with effects at higher levels of biological organization (e.g. total energy budget and growth). Daphnids were exposed to three cadmium concentrations (nominal value of 10, 50, 100 {mu}g/l) for two time intervals (48 and 96 h). In general, dynamic expression patterns were obtained with a clear increase of gene expression changes at higher concentrations and longer exposure duration. Microarray analysis revealed cadmium affected molecular pathways associated with processes such as digestion, oxygen transport, cuticula metabolism and embryo development. These effects were compared with higher-level effects (energy budgets and growth). For instance, next to reduced energy budgets due to a decline in lipid, carbohydrate and protein content, we found an up-regulated expression of genes related to digestive processes (e.g. {alpha}-esterase, cellulase, {alpha}-amylase). Furthermore, cadmium affected the expression of genes coding for proteins involved in molecular pathways associated with immune response, stress response, cell adhesion, visual perception and signal transduction in the present study.

Optimal Retention Level for Infinite Time Horizons under MADM

Directory of Open Access Journals (Sweden)

Başak Bulut Karageyik

2016-12-01

Full Text Available In this paper, we approximate the aggregate claims process by using the translated gamma process under the classical risk model assumptions, and we investigate the ultimate ruin probability. We consider optimal reinsurance under the minimum ultimate ruin probability, as well as the maximum benefit criteria: released capital, expected profit and exponential-fractional-logarithmic utility from the insurer’s point of view. Numerical examples are presented to explain how the optimal initial surplus and retention level are changed according to the individual claim amounts, loading factors and weights of the criteria. In the decision making process, we use The Analytical Hierarchy Process (AHP and The Technique for Order of Preference by Similarity to ideal Solution (TOPSIS methods as the Multi-Attribute Decision Making methods (MADM and compare our results considering different combinations of loading factors for both exponential and Pareto individual claims.

RNA-Seq and molecular docking reveal multi-level pesticide resistance in the bed bug

Directory of Open Access Journals (Sweden)

Mamidala Praveen

2012-01-01

Full Text Available Abstract Background Bed bugs (Cimex lectularius are hematophagous nocturnal parasites of humans that have attained high impact status due to their worldwide resurgence. The sudden and rampant resurgence of C. lectularius has been attributed to numerous factors including frequent international travel, narrower pest management practices, and insecticide resistance. Results We performed a next-generation RNA sequencing (RNA-Seq experiment to find differentially expressed genes between pesticide-resistant (PR and pesticide-susceptible (PS strains of C. lectularius. A reference transcriptome database of 51,492 expressed sequence tags (ESTs was created by combining the databases derived from de novo assembled mRNA-Seq tags (30,404 ESTs and our previous 454 pyrosequenced database (21,088 ESTs. The two-way GLMseq analysis revealed ~15,000 highly significant differentially expressed ESTs between the PR and PS strains. Among the top 5,000 differentially expressed ESTs, 109 putative defense genes (cuticular proteins, cytochrome P450s, antioxidant genes, ABC transporters, glutathione S-transferases, carboxylesterases and acetyl cholinesterase involved in penetration resistance and metabolic resistance were identified. Tissue and development-specific expression of P450 CYP3 clan members showed high mRNA levels in the cuticle, Malpighian tubules, and midgut; and in early instar nymphs, respectively. Lastly, molecular modeling and docking of a candidate cytochrome P450 (CYP397A1V2 revealed the flexibility of the deduced protein to metabolize a broad range of insecticide substrates including DDT, deltamethrin, permethrin, and imidacloprid. Conclusions We developed significant molecular resources for C. lectularius putatively involved in metabolic resistance as well as those participating in other modes of insecticide resistance. RNA-Seq profiles of PR strains combined with tissue-specific profiles and molecular docking revealed multi-level insecticide

Sterically controlled mechanochemistry under hydrostatic pressure

Science.gov (United States)

Yan, Hao; Yang, Fan; Pan, Ding; Lin, Yu; Hohman, J. Nathan; Solis-Ibarra, Diego; Li, Fei Hua; Dahl, Jeremy E. P.; Carlson, Robert M. K.; Tkachenko, Boryslav A.; Fokin, Andrey A.; Schreiner, Peter R.; Galli, Giulia; Mao, Wendy L.; Shen, Zhi-Xun; Melosh, Nicholas A.

2018-02-01

Mechanical stimuli can modify the energy landscape of chemical reactions and enable reaction pathways, offering a synthetic strategy that complements conventional chemistry. These mechanochemical mechanisms have been studied extensively in one-dimensional polymers under tensile stress using ring-opening and reorganization, polymer unzipping and disulfide reduction as model reactions. In these systems, the pulling force stretches chemical bonds, initiating the reaction. Additionally, it has been shown that forces orthogonal to the chemical bonds can alter the rate of bond dissociation. However, these bond activation mechanisms have not been possible under isotropic, compressive stress (that is, hydrostatic pressure). Here we show that mechanochemistry through isotropic compression is possible by molecularly engineering structures that can translate macroscopic isotropic stress into molecular-level anisotropic strain. We engineer molecules with mechanically heterogeneous components—a compressible (‘soft’) mechanophore and incompressible (‘hard’) ligands. In these ‘molecular anvils’, isotropic stress leads to relative motions of the rigid ligands, anisotropically deforming the compressible mechanophore and activating bonds. Conversely, rigid ligands in steric contact impede relative motion, blocking reactivity. We combine experiments and computations to demonstrate hydrostatic-pressure-driven redox reactions in metal-organic chalcogenides that incorporate molecular elements that have heterogeneous compressibility, in which bending of bond angles or shearing of adjacent chains activates the metal-chalcogen bonds, leading to the formation of the elemental metal. These results reveal an unexplored reaction mechanism and suggest possible strategies for high-specificity mechanosynthesis.

First principles molecular dynamics of metal/water interfaces under bias potential

Science.gov (United States)

Pedroza, Luana; Brandimarte, Pedro; Rocha, Alexandre; Fernandez-Serra, Marivi

2014-03-01

Understanding the interaction of the water-metal system at an atomic level is extremely important in electrocatalysts for fuel cells, photocatalysis among other systems. The question of the interface energetics involves a detailed study of the nature of the interactions between water-water and water-substrate. A first principles description of all components of the system is the most appropriate methodology in order to advance understanding of electrochemically processes. In this work we describe, using first principles molecular dynamics simulations, the dynamics of a combined surface(Au and Pd)/water system both in the presence and absence of an external bias potential applied to the electrodes, as one would come across in electrochemistry. This is accomplished using a combination of density functional theory (DFT) and non-equilibrium Green's functions methods (NEGF), thus accounting for the fact that one is dealing with an out-of-equilibrium open system, with and without van der Waals interactions. DOE Early Career Award No. DE-SC0003871.

Musical molecules: the molecular junction as an active component in audio distortion circuits

International Nuclear Information System (INIS)

Bergren, Adam Johan; Zeer-Wanklyn, Lucas; Pekas, Nikola; Szeto, Bryan; McCreery, Richard L; Semple, Mitchell

2016-01-01

Molecular junctions that have a non-linear current–voltage characteristic consistent with quantum mechanical tunneling are demonstrated as analog audio clipping elements in overdrive circuits widely used in electronic music, particularly with electric guitars. The performance of large-area molecular junctions fabricated at the wafer level is compared to currently standard semiconductor diode clippers, showing a difference in the sound character. The harmonic distributions resulting from the use of traditional and molecular clipping elements are reported and discussed, and differences in performance are noted that result from the underlying physics that controls the electronic properties of each clipping component. In addition, the ability to tune the sound using the molecular junction is demonstrated. Finally, the hybrid circuit is compared to an overdriven tube amplifier, which has been the standard reference electric guitar clipped tone for over 60 years. In order to investigate the feasibility of manufacturing molecular junctions for use in commercial applications, devices are fabricated using a low-density format at the wafer level, where 38 dies per wafer, each containing two molecular junctions, are made with exceptional non-shorted yield (99.4%, representing 718 out of 722 tested devices) without requiring clean room facilities. (paper)

Musical molecules: the molecular junction as an active component in audio distortion circuits

Science.gov (United States)

Bergren, Adam Johan; Zeer-Wanklyn, Lucas; Semple, Mitchell; Pekas, Nikola; Szeto, Bryan; McCreery, Richard L.

2016-03-01

Molecular junctions that have a non-linear current-voltage characteristic consistent with quantum mechanical tunneling are demonstrated as analog audio clipping elements in overdrive circuits widely used in electronic music, particularly with electric guitars. The performance of large-area molecular junctions fabricated at the wafer level is compared to currently standard semiconductor diode clippers, showing a difference in the sound character. The harmonic distributions resulting from the use of traditional and molecular clipping elements are reported and discussed, and differences in performance are noted that result from the underlying physics that controls the electronic properties of each clipping component. In addition, the ability to tune the sound using the molecular junction is demonstrated. Finally, the hybrid circuit is compared to an overdriven tube amplifier, which has been the standard reference electric guitar clipped tone for over 60 years. In order to investigate the feasibility of manufacturing molecular junctions for use in commercial applications, devices are fabricated using a low-density format at the wafer level, where 38 dies per wafer, each containing two molecular junctions, are made with exceptional non-shorted yield (99.4%, representing 718 out of 722 tested devices) without requiring clean room facilities.

Extinction antagonizes olfactory memory at the subcellular level.

Science.gov (United States)

Schwaerzel, Martin; Heisenberg, Martin; Zars, Troy

2002-08-29

Memory loss occurs by diverse mechanisms, as different time constants of performance decrement and sensitivities to experimental manipulations suggest. While the phenomena of memory decay, interference, and extinction are well established behaviorally, little is known about them at the circuit or molecular level. In Drosophila, odorant memories lasting up to 3 hr can be localized to mushroom body Kenyon cells, a single neuronal level in the olfactory pathway. The plasticity underlying this memory trace can be induced without Kenyon cell synaptic output. Experimental extinction, i.e., presentation of the conditioned stimulus without the reinforcer, reduces memory performance and does so at the same circuit level as memory formation. Thus, unreinforced presentation of learned odorants antagonizes intracellularly the signaling cascade underlying memory formation.

Tear film lipid layer: A molecular level view

Czech Academy of Sciences Publication Activity Database

Cwiklik, Lukasz

2016-01-01

Roč. 1858, č. 10 (2016), s. 2421-2430 ISSN 0005-2736 R&D Projects: GA ČR GA15-14292S Institutional support: RVO:61388955 Keywords : tear film * tear film lipid layer * molecular dynamics simulations Subject RIV: CF - Physical ; Theoretical Chemistry Impact factor: 3.498, year: 2016

A comparison of nitrate level in spinach grown both under different densities in aquaponic system and under natural growth conditions

Directory of Open Access Journals (Sweden)

Ştefan Mihai PETREA

2013-12-01

Full Text Available As bio-integrated systems that link both plants and fish culture, inside aquaponic systems, the processes of ammonia-oxidizing and nitrification in nitrite and nitrate are essential for growth and development of both fish and plants culture biomass. Plants with nearly the same nutritional requirements during their life cycle, like spinach in our case, are recommended to be grown under aquaponic conditions. Although nitrates concentrations up to 200 – 250mg/l are reported to be acceptable for fish growth, in the last years the toxic effect of long term exposure to high nitrate levels on fish and plants cultured biomass were highlighted. The main goal of the present study is to compare the nitrate level of spinach, grown in an aquaponic system, under three plant densities (V1 - 59 plants/m2, V2 - 48plants/m2 and V3 – 39 plants/m2. The second objective is to compare the results obtained, in term of nitrate content, for spinach grown in the integrated rainbow trout – spinach aquaponic system with those of marketable spinach, grown under conventional condition, in the field. The experimental design consists in a recirculating aquaculture system with 12 growing units, mechanical and biological water treatment units and four aquaponic units. Fish were fed with two types of feed with 41% and 50% protein, using 3 different feeding regimes. The results show a higher nitrate level on spinach grown in aquaponic system, compared to the one derived from field culture. Differences were observed also among the three variants grown in aquaponic conditions, under different plant densities. As a conclusion, it can be said that considering the nitrate level, spinach grown in aquaponic system is marketable.

Molecular-level chemistry of model single-crystal oxide surfaces with model halogenated compounds

Science.gov (United States)

Adib, Kaveh

Synchrotron-based X-ray photoelectron spectroscopy (XPS), temperature-programmed desorption (TPD) and low energy electron diffraction (LEED) have been used to investigate, at a molecular level, the chemistry of different terminations of single crystal iron-oxide surfaces with probe molecules (CCl4 and D2O). Comparisons of the reactivity of these surfaces towards CCl4, indicate that the presence of an uncapped surface Fe cation (strong Lewis acid site) and an adjacent oxygen site capped by that cation can effect the C-Cl bond cleavage in CCl4, resulting in dissociatively adsorbed Cl-adatoms and carbon-containing fragments. If in addition to these sites, an uncapped surface oxygen (Lewis base) site is also available, the carbon-containing moiety can then move that site, coordinate itself with that uncapped oxygen, and stabilize itself. At a later step, the carbon-containing fragment may form a strong covalent bond with the uncapped oxygen and may even abstract that surface oxygen. On the other hand, if an uncapped oxygen is not available to stabilize the carbon-containing fragment, the surface coordination will not occur and upon the subsequent thermal annealing of the surface the Cl-adatoms and the carbon-containing fragments will recombine and desorb as CCl4. Finally, the presence of surface deuteroxyls blocking the strong Lewis acid and base sites of the reactive surface, passivates this surface. Such a deuteroxylated surface will be unreactive towards CCl 4. Such a molecular level understanding of the surface chemistry of metal-oxides will have applications in the areas of selective catalysis, including environmental catalysis, and chemical sensor technology.

Molecular dynamics simulation of ZnO wurtzite phase under high and low pressures and temperatures

Science.gov (United States)

Chergui, Y.; Aouaroun, T.; Hadley, M. J.; Belkada, R.; Chemam, R.; Mekki, D. E.

2017-11-01

Isothermal and isobaric ensembles behaviours of ZnO wurtzite phase have been investigated, by parallel molecular dynamics method and using Buckingham potential, which contains long-range Coulomb, repulsive exponential, and attractive dispersion terms. To conduct our calculations, we have used dl_poly 4 software, under which the method is implemented. We have examined the influence of the temperature and pressure on molar volume in the ranges of 300-3000 K and 0-200 GPa. Isothermal-isobaric relationships, fluctuations, standard error, equilibrium time, molar volume and its variation versus time are predicted and analyzed. Our results are close to available experimental data and theoretical results.

Short-term dynamics of North Sea bacterioplankton-dissolved organic matter coherence on molecular level

Directory of Open Access Journals (Sweden)

Judith eLucas

2016-03-01

Full Text Available Remineralisation and transformation of dissolved organic matter (DOM by marine microbes shape the DOM composition and thus, have large impact on global carbon and nutrient cycling. However, information on bacterioplankton-DOM interactions on a molecular level is limited. We examined the variation of bacterial community composition at Helgoland Roads (North Sea in relation to variation of molecular DOM composition and various environmental parameters on short-time scales. Surface water samples were taken daily over a period of twenty days. Bacterial community and molecular DOM composition were assessed via 16S rRNA gene tag sequencing and ultrahigh resolution Fourier-transform ion cyclotron resonance mass spectrometry (FT-ICR-MS, respectively. Environmental conditions were driven by a coastal water influx during the first half of the sampling period and the onset of a summer phytoplankton bloom towards the end of the sampling period. These phenomena led to a distinct grouping of bacterial communities and DOM composition which was particularly influenced by total dissolved nitrogen concentration, temperature and salinity, as revealed by distance-based linear regression analyses. Bacterioplankton-DOM interaction was demonstrated in strong correlations between specific bacterial taxa and particular DOM molecules, thus, suggesting potential specialization on particular substrates. We propose that a combination of high resolution techniques, as used in this study, may provide substantial information on substrate generalists and specialists and thus, contribute to prediction of bacterial community composition variation.

Molecular Dynamics Simulation of Damage to Coiled Carbon Nanotubes under C Ion Irradiation

International Nuclear Information System (INIS)

Zhou Bin; Zhang Wei; Gong Wen-Bin; Wang Song; Ren Cui-Lan; Wang Cheng-Bin; Zhu Zhi-Yuan; Huai Ping

2013-01-01

The stability of coiled carbon nanotubes under C ion irradiation is investigated by molecular dynamics simulations. The defect statistics shows that small curvature coiled carbon nanotubes have better radiation tolerance than normal straight carbon nanotubes. To understand the effect of the curvature on defect production, the threshold displacement energies for the upper and lower walls, as well as those for the side parts, are calculated. The results show that the lower wall has better radiation tolerance than the upper wall. For the upper wall, a small increase in the curvature of nanotube axis gives rise to an increase in the radiation tolerance and then a decrease with the curvature becomes larger. However, for the lower wall, as the curvature of the nanotube axis increases, the radiation tolerance increases as the bonds compressed slightly in our simulation

Thermal buckling behavior of defective CNTs under pre-load: A molecular dynamics study.

Science.gov (United States)

Mehralian, Fahimeh; Tadi Beni, Yaghoub; Kiani, Yaser

2017-05-01

Current study is concentrated on the extraordinary properties of defective carbon nanotubes (CNTs). The role of vacancy defects in thermal buckling response of precompressed CNTs is explored via molecular dynamics (MD) simulations. Defective CNTs are initially compressed at a certain ratio of their critical buckling strain and then undergo a uniform temperature rise. Comprehensive study is implemented on both armchair and zigzag CNTs with different vacancy defects including monovacancy, symmetric bivacancy and asymmetric bivacancy. The results reveal that defects have a pronounced impact on the buckling behavior of CNTs; interestingly, defective CNTs under compressive pre-load show higher resistance to thermal buckling than pristine ones. In the following, the buckling response of defective CNTs is shown to be dependent on the vacancy defects, location of defects and chirality. Copyright © 2017 Elsevier Inc. All rights reserved.

50 CFR 216.16 - Prohibitions under the General Authorization for Level B harassment for scientific research.

Science.gov (United States)

2010-10-01

... 50 Wildlife and Fisheries 7 2010-10-01 2010-10-01 false Prohibitions under the General Authorization for Level B harassment for scientific research. 216.16 Section 216.16 Wildlife and Fisheries... Prohibitions under the General Authorization for Level B harassment for scientific research. It shall be...

[Vulnerability assessment on the coastal wetlands in the Yangtze Estuary under sea-level rise].

Science.gov (United States)

Cui, Li-Fang; Wang, Ning; Ge, Zhen-Ming; Zhang, Li-Quan

2014-02-01

To study the response of coastal wetlands to climate change, assess the impacts of climate change on the coastal wetlands and formulate feasible and practical mitigation strategies are the important prerequisite for securing coastal ecosystems. In this paper, the possible impacts of sea level rise caused by climate change on the coastal wetlands in the Yangtze Estuary were analyzed by the Source-Pathway-Receptor-Consequence (SPRC) model and IPCC definition on the vulnerability. An indicator system for vulnerability assessment was established, in which sea-level rise rate, subsidence rate, habitat elevation, inundation threshold of habitat and sedimentation rate were selected as the key indicators. A quantitatively spatial assessment method based on the GIS platform was established by quantifying each indicator, calculating the vulnerability index and grading the vulnerability index for the assessment of coastal wetlands in the Yangtze Estuary under the scenarios of sea-level rise. The vulnerability assessments on the coastal wetlands in the Yangtze Estuary in 2030 and 2050 were performed under two sea-level rise scenarios (the present sea-level rise trend over recent 30 years and IPCC A1F1 scenario). The results showed that with the projection in 2030 under the present trend of sea-level rise (0.26 cm x a(-1)), 6.6% and 0.1% of the coastal wetlands were in the low and moderate vulnerabilities, respectively; and in 2050, 9.8% and 0.2% of the coastal wetlands were in low and moderate vulnerabilities, respectively. With the projection in 2030 under the A1F1 scenario (0.59 cm x a(-1)), 9.0% and 0.1% of the coastal wetlands were in the low and moderate vulnerabilities, respectively; and in 2050, 9.5%, 1.0% and 0.3% of the coastal wetlands were in the low, moderate and high vulnerabilities, respectively.

A Security Level Classification Method for Power Systems under N-1 Contingency

Directory of Open Access Journals (Sweden)

Zhigang Lu

2017-12-01

Full Text Available Security assessment is crucial for the reliable and secure operation of power systems. This paper proposes a security level classification (SLC method to analyze the security level of power systems both qualitatively and quantitatively. In this SLC method, security levels are graded according to a comprehensive safety index (CSI, which is defined by integrating the system margin index (SMI and load entropy. The SMI depends on the operating load and the total supply capacity (TSC under N-1 contingency, and the load entropy reflects the heterogeneity of load distribution calculated from entropy theory. In order to calculate the TSC under N-1 contingency considering both of the computational accuracy and speed, the TSC is converted into an extended conic quadratic programming (ECQP model. In addition, the load boundary vector (LBV model is established to obtain the capacity limit of each load bus, and thus detect potential risks of power systems. Finally, two modified practical power systems and the IEEE 118-bus test system are studied to validate the feasibility of the proposed SLC method.

An update on potential molecular mechanisms underlying the actions of snake venom L-amino acid oxidases (LAAOs).

Science.gov (United States)

Paloschi, Mauro Valentino; Pontes, Adriana Silva; Soares, Andreimar Martins; Zuliani, Juliana Pavan

2017-11-08

LAAOs (EC 1.4.3.2) are found in concentrations that vary according to each species of snakes; Viperidae, Crotalidae and Elapidae contain 1-9% of this enzyme in their venoms. This review focuses on an update on molecular mechanisms, platelet activities, antimicrobial, antiprotozoal, induction of apoptosis and inflammatory potential underlying the actions of SV-LAAOs. Snake venom LAAOs (SV-LAAOs) have become an interesting subject for pharmacological, structural and molecular studies. Although the mechanisms of action of these enzymes are not well understood they are a subject of a variety of studies, because LAAOs are multifunctional enzymes exhibiting a wide range of pharmacological effects, including the inhibition or induction of platelet aggregation, hemolysis and hemorrhage, in addition to the stimulation of apoptosis, the activation of leukocytes and the formation of edema. Moreover, SV-LAAOs play an important role in bactericidal, cytotoxic, anti-parasitic, anti-tumor, and antiviral activities. Copyright© Bentham Science Publishers; For any queries, please email at epub@benthamscience.org.

Nitrogen transformation under different dissolved oxygen levels by the anoxygenic phototrophic bacterium Marichromatium gracile.

Science.gov (United States)

Hong, Xuan; Chen, Zhongwei; Zhao, Chungui; Yang, Suping

2017-06-01

Marichromatium gracile: YL28 (M. gracile YL28) is an anoxygenic phototrophic bacterial strain that utilizes ammonia, nitrate, or nitrite as its sole nitrogen source during growth. In this study, we investigated the removal and transformation of ammonium, nitrate, and nitrite by M. gracile YL28 grown in a combinatorial culture system of sodium acetate-ammonium, sodium acetate-nitrate and sodium acetate-nitrite in response to different initial dissolved oxygen (DO) levels. In the sodium acetate-ammonium system under aerobic conditions (initial DO = 7.20-7.25 mg/L), we detected a continuous accumulation of nitrate and nitrite. However, under semi-anaerobic conditions (initial DO = 4.08-4.26 mg/L), we observed a temporary accumulation of nitrate and nitrite. Interestingly, under anaerobic conditions (initial DO = 0.36-0.67 mg/L), there was little accumulation of nitrate and nitrite, but an increase in nitrous oxide production. In the sodium acetate-nitrite system, nitrite levels declined slightly under aerobic conditions, and nitrite was completely removed under semi-anaerobic and anaerobic conditions. In addition, M. gracile YL28 was able to grow using nitrite as the sole nitrogen source in situations when nitrogen gas produced by denitrification was eliminated. Taken together, the data indicate that M. gracile YL28 performs simultaneous heterotrophic nitrification and denitrification at low-DO levels and uses nitrite as the sole nitrogen source for growth. Our study is the first to demonstrate that anoxygenic phototrophic bacteria perform heterotrophic ammonia-oxidization and denitrification under anaerobic conditions.

Performance of high level waste forms and engineered barriers under repository conditions

International Nuclear Information System (INIS)

1991-02-01

The IAEA initiated in 1977 a co-ordinated research programme on the ''Evaluation of Solidified High-Level Waste Forms'' which was terminated in 1983. As there was a continuing need for international collaboration in research on solidified high-level waste form and spent fuel, the IAEA initiated a new programme in 1984. The new programme, besides including spent fuel and SYNROC, also placed greater emphasis on the effect of the engineered barriers of future repositories on the properties of the waste form. These engineered barriers included containers, overpacks, buffer and backfill materials etc. as components of the ''near-field'' of the repository. The Co-ordinated Research Programme on the Performance of High-Level Waste Forms and Engineered Barriers Under Repository Conditions had the objectives of promoting the exchange of information on the experience gained by different Member States in experimental performance data and technical model evaluation of solidified high level waste forms, components of the waste package and the complete waste management system under conditions relevant to final repository disposal. The programme includes studies on both irradiated spent fuel and glass and ceramic forms as the final solidified waste forms. The following topics were discussed: Leaching of vitrified high-level wastes, modelling of glass behaviour in clay, salt and granite repositories, environmental impacts of radionuclide release, synroc use for high--level waste solidification, leachate-rock interactions, spent fuel disposal in deep geologic repositories and radionuclide release mechanisms from various fuel types, radiolysis and selective leaching correlated with matrix alteration. Refs, figs and tabs

Molecular evolution of multiple-level control of heme biosynthesis pathway in animal kingdom.

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Tzou, Wen-Shyong; Chu, Ying; Lin, Tzung-Yi; Hu, Chin-Hwa; Pai, Tun-Wen; Liu, Hsin-Fu; Lin, Han-Jia; Cases, Ildeofonso; Rojas, Ana; Sanchez, Mayka; You, Zong-Ye; Hsu, Ming-Wei

2014-01-01

Adaptation of enzymes in a metabolic pathway can occur not only through changes in amino acid sequences but also through variations in transcriptional activation, mRNA splicing and mRNA translation. The heme biosynthesis pathway, a linear pathway comprised of eight consecutive enzymes in animals, provides researchers with ample information for multiple types of evolutionary analyses performed with respect to the position of each enzyme in the pathway. Through bioinformatics analysis, we found that the protein-coding sequences of all enzymes in this pathway are under strong purifying selection, from cnidarians to mammals. However, loose evolutionary constraints are observed for enzymes in which self-catalysis occurs. Through comparative genomics, we found that in animals, the first intron of the enzyme-encoding genes has been co-opted for transcriptional activation of the genes in this pathway. Organisms sense the cellular content of iron, and through iron-responsive elements in the 5' untranslated regions of mRNAs and the intron-exon boundary regions of pathway genes, translational inhibition and exon choice in enzymes may be enabled, respectively. Pathway product (heme)-mediated negative feedback control can affect the transport of pathway enzymes into the mitochondria as well as the ubiquitin-mediated stability of enzymes. Remarkably, the positions of these controls on pathway activity are not ubiquitous but are biased towards the enzymes in the upstream portion of the pathway. We revealed that multiple-level controls on the activity of the heme biosynthesis pathway depend on the linear depth of the enzymes in the pathway, indicating a new strategy for discovering the molecular constraints that shape the evolution of a metabolic pathway.

Cardiovascular Molecular Imaging

International Nuclear Information System (INIS)

Lee, Kyung Han

2009-01-01

Molecular imaging strives to visualize processes in living subjects at the molecular level. Monitoring biochemical processes at this level will allow us to directly track biological processes and signaling events that lead to pathophysiological abnormalities, and help make personalized medicine a reality by allowing evaluation of therapeutic efficacies on an individual basis. Although most molecular imaging techniques emerged from the field of oncology, they have now gradually gained acceptance by the cardiovascular community. Hence, the availability of dedicated high-resolution small animal imaging systems and specific targeting imaging probes is now enhancing our understanding of cardiovascular diseases and expediting the development of newer therapies. Examples include imaging approaches to evaluate and track the progress of recent genetic and cellular therapies for treatment of myocardial ischemia. Other areas include in vivo monitoring of such key molecular processes as angiogenesis and apoptosis. Cardiovascular molecular imaging is already an important research tool in preclinical experiments. The challenge that lies ahead is to implement these techniques into the clinics so that they may help fulfill the promise of molecular therapies and personalized medicine, as well as to resolve disappointments and controversies surrounding the field

Accelerated uncertainty propagation in two-level probabilistic studies under monotony

International Nuclear Information System (INIS)

Limbourg, Philipp; Rocquigny, Etienne de; Andrianov, Guennadi

2010-01-01

Double-level probabilistic uncertainty models that separate aleatory and epistemic components enjoy significant interest in risk assessment. But the expensive computational costs associated with calculations of rare failure probabilities are still a large obstacle in practice. Computing accurately a risk lower than 10 -3 with 95% epistemic confidence usually requires 10 7 -10 8 runs in a brute-force double Monte Carlo. For single-level probabilistic studies, FORM (First Order Reliability Analysis) is a classical recipe allowing fast approximation of failure probabilities while MRM (Monotonous Reliability Method) recently proved an attractive robust alternative under monotony. This paper extends these methods to double-level probabilistic models through two novel algorithms designed to compute a set of failure probabilities or an aleatory risk level with an epistemic confidence quantile. The first, L2-FORM (level-2 FORM), allows a rapid approximation of the failure probabilities through a combination of FORM with new ideas to use similarity between computations. L2-MRM (level-2 MRM), a quadrature approach, provides 100%-guaranteed error bounds on the results. Experiments on three flood prediction problems showed that both algorithms approximate a set of 500 failure probabilities of 10 -3 -10 -2 or derived 95% epistemic quantiles with a total of only 500-1000 function evaluations, outperforming importance sampling, iterative FORM and regression splines metamodels.

A Fuzzy Max–Min Decision Bi-Level Fuzzy Programming Model for Water Resources Optimization Allocation under Uncertainty

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Chongfeng Ren

2018-04-01

Full Text Available Water competing conflict among water competing sectors from different levels should be taken under consideration during the optimization allocation of water resources. Furthermore, uncertainties are inevitable in the optimization allocation of water resources. In order to deal with the above problems, this study developed a fuzzy max–min decision bi-level fuzzy programming model. The developed model was then applied to a case study in Wuwei, Gansu Province, China. In this study, the net benefit and yield were regarded as the upper-level and lower-level objectives, respectively. Optimal water resource plans were obtained under different possibility levels of fuzzy parameters, which could deal with water competing conflict between the upper level and the lower level effectively. The obtained results are expected to make great contribution in helping local decision-makers to make decisions on dealing with the water competing conflict between the upper and lower level and the optimal use of water resources under uncertainty.

The comparison of naturally weathered oil and artificially photo-degraded oil at the molecular level by a combination of SARA fractionation and FT-ICR MS

International Nuclear Information System (INIS)

Islam, Ananna; Cho, Yunju; Yim, Un Hyuk; Shim, Won Joon; Kim, Young Hwan; Kim, Sunghwan

2013-01-01

Highlights: • Weathered oils from the Hebei Spirit oil spill and photo degraded oils are compared. • We investigate changes of polar species at the molecular level by 15T FT-ICR MS. • Significant reduction of sulfur class compounds in saturates fraction is observed. • The relative abundance of protonated compounds (presumably basic nitrogen compounds) increase after degradation. • Changes of polar compounds occurred by natural and photo degradation are similar. -- Abstract: Two sets of oil samples, one obtained from different weathering stages of the M/V Hebei Spirit oil spill site and the other prepared by an in vitro photo-degradation experiment, were analyzed and compared at the molecular level by atmospheric pressure photo-ionization coupled with Fourier transform ion cyclotron resonance mass spectrometry (FT-ICR MS). For a more detailed comparison at the molecular level, the oil samples were separated into saturate, aromatic, resin, and asphaltene (SARA) fractions before MS analysis. Gravimetric analysis of the SARA fractions revealed a decreased weight percentage of the aromatic fraction and an increased resin fraction in both sets of samples. Molecular-level investigations of the SARA fractions showed a significant reduction in the S 1 class in the saturate fraction and increase of S 1 O 1 class compounds with high DBE values in resin fraction. Levels of N 1 and N 1 O 1 class compounds resulting in protonated ions (presumably basic nitrogen compounds) increased after degradation compared to compounds generating molecular ions (presumably non-basic nitrogen compounds). This study revealed changes occurring in heteroatom polar species of crude oils such as sulfur and nitrogen containing compounds that have not been easily detected with conventional GC based techniques

The long Tramp from Cellular Pathology to Molecular Pathology

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Hans Guski

2017-05-01

Derivatives: The observation of principal identity of biological meaningful elements can be agglutinated to a ‘general theory of live’ and its manifestation. All of the investigated elements posses the same regularities, which are altered, destroyed or newly built by external influences such as disease, physical and psychological forces. Not all magnification levels that display with these elements are of the same significance. Already Virchow suggested that ‘smaller elements (molecules might be responsible for changes that are visible ‘in larger elements’ (at cellular level.  The reflection on these ideas can be associated with the implementation of molecular techniques which has been developed in the 20th century and are still ongoing today. Perspectives: Thus, cellular and molecular pathology can be integrated under one umbrella. This umbrella will lead to newly man-formed structures, such as artificial DNA and gene components or functional chip implantations.

Dissecting molecular stress networks: identifying nodes of divergence between life-history phenotypes.

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Schwartz, Tonia S; Bronikowski, Anne M

2013-02-01

The complex molecular network that underlies physiological stress response is comprised of nodes (proteins, metabolites, mRNAs, etc.) whose connections span cells, tissues and organs. Variable nodes are points in the network upon which natural selection may act. Thus, identifying variable nodes will reveal how this molecular stress network may evolve among populations in different habitats and how it might impact life-history evolution. Here, we use physiological and genetic assays to test whether laboratory-born juveniles from natural populations of garter snakes (Thamnophis elegans), which have diverged in their life-history phenotypes, vary concomitantly at candidate nodes of the stress response network, (i) under unstressed conditions and (ii) in response to an induced stress. We found that two common measures of stress (plasma corticosterone and liver gene expression of heat shock proteins) increased under stress in both life-history phenotypes. In contrast, the phenotypes diverged at four nodes both under unstressed conditions and in response to stress: circulating levels of reactive oxygen species (superoxide, H(2)O(2)); liver gene expression of GPX1 and erythrocyte DNA damage. Additionally, allele frequencies for SOD2 diverge from neutral markers, suggesting diversifying selection on SOD2 alleles. This study supports the hypothesis that these life-history phenotypes have diverged at the molecular level in how they respond to stress, particularly in nodes regulating oxidative stress. Furthermore, the differences between the life-history phenotypes were more pronounced in females. We discuss the responses to stress in the context of the associated life-history phenotype and the evolutionary pressures thought to be responsible for divergence between the phenotypes. © 2012 Blackwell Publishing Ltd.

Molecular simulations of hydrocarbon lubricants: Impact of molecular architecture on performance properties

Science.gov (United States)

Kioupis, Loukas I.

2000-07-01

With the increased power of modern computers, molecular modeling has been used widely and proven to be a valuable tool for elucidating the physical processes important in many industrial and engineering problems. Of particular interest to us is the rheology and physical chemistry of complex fluids, such as hydrocarbon lubricants and polymers. The goal is to provide qualitative and quantitative molecular-level explanations for the behavior of such fluids, and provide guidance in the development of new improved materials. For example, during the production of poly-α-olefin (PAO) synthetic lubricants, the number of the isomer skeletal structures that can be obtained is staggering. Which of the countless PAO isomers produce a lubricant with superior performance properties? How does it behave under different operational conditions of temperature, pressure, and shear rate? A fundamental understanding of the effect that molecular structure has on the oil's rheological and lubricant performance is first needed, in order to answer these questions. To serve this purpose, we have developed efficient molecular dynamics (MD) simulation programs, which utilize multiple time step algorithms and parallel computational techniques. This enables us to conduct simulations of typical PAO isomers and compute the viscosity, as well as several other dynamic and static properties, as a function of temperature, pressure, and shear rate. The key molecular mechanisms that determine important macroscopic properties, such as viscosity index, viscosity-pressure coefficient, traction coefficient, and shear thinning behavior are discussed. Based on this analysis, lubricant and traction fluid structures that have a high likelihood of having desirable properties are proposed. In addition, studies on simple alkane mixtures are presented, in an attempt to understand the more complex polydisperse lubricant fluids, their blends, and their interaction with additives.

Ab initio molecular dynamics simulation of structural transformation in zinc blende GaN under high pressure

International Nuclear Information System (INIS)

Xiao, H.Y.; Gao, Fei; Zu, X.T.; Weber, W.J.

2010-01-01

High-pressure induced zinc blende to rocksalt phase transition in GaN has been investigated by ab initio molecular dynamics method to characterize the transformation mechanism at the atomic level. It was shown that at 100 GPa GaN passes through tetragonal and monoclinic states before rocksalt structure is formed. The transformation mechanism is consistent with that for other zinc blende semiconductors obtained from the same method. Detailed structural analysis showed that there is no bond breaking involved in the phase transition.

Molecular Responses of Groundnut (Arachis hypogea L. to Zinc Stress

Directory of Open Access Journals (Sweden)

A. John De Britto

2013-08-01

Full Text Available Heavy metals are important environmental pollutants and their toxicity is a problem of increasing significance for ecological, evolutionary and environmental reasons. The interference of germination related proteins by heavy metals has not been well documented at the proteomic and genomic level. In the current study, molecular responses of germinating groundnut seeds were investigated under Zinc stress. The SDS-PAGE showed the preliminary changes in the polypeptides patterns under Zinc stress. Restriction digestion banding pattern of EcoRI and Hind III enzymes showed distinct banding pattern in the treated plants.

Molecular Pathogenesis and Diagnostic, Prognostic and Predictive Molecular Markers in Sarcoma.

Science.gov (United States)

Mariño-Enríquez, Adrián; Bovée, Judith V M G

2016-09-01

Sarcomas are infrequent mesenchymal neoplasms characterized by notable morphological and molecular heterogeneity. Molecular studies in sarcoma provide refinements to morphologic classification, and contribute diagnostic information (frequently), prognostic stratification (rarely) and predict therapeutic response (occasionally). Herein, we summarize the major molecular mechanisms underlying sarcoma pathogenesis and present clinically useful diagnostic, prognostic and predictive molecular markers for sarcoma. Five major molecular alterations are discussed, illustrated with representative sarcoma types, including 1. the presence of chimeric transcription factors, in vascular tumors; 2. abnormal kinase signaling, in gastrointestinal stromal tumor; 3. epigenetic deregulation, in chondrosarcoma, chondroblastoma, and other tumors; 4. deregulated cell survival and proliferation, due to focal copy number alterations, in dedifferentiated liposarcoma; 5. extreme genomic instability, in conventional osteosarcoma as a representative example of sarcomas with highly complex karyotype. Copyright © 2016 Elsevier Inc. All rights reserved.

General perspectives for molecular nuclear imaging

International Nuclear Information System (INIS)

Chung, June Key

2004-01-01

Molecular imaging provides a visualization of normal as well as abnormal cellular processes at a molecular or genetic level rather than at an anatomical level. Conventional medical imaging methods utilize the imaging signals produced by nonspecific physico-chemical interaction. However, molecular imaging methods utilize the imaging signals derived from specific cellular or molecular events. Because molecular and genetic changes precede anatomical change in the course of disease development, molecular imaging can detect early events in disease progression. In the near future, through molecular imaging we can understand basic mechanisms of disease, and diagnose earlier and, subsequently, treat earlier intractable disease such as cancer, neuro-degenerative diseases, and immunologic disorders. In beginning period, nuclear medicine started as a molecular imaging, and has had a leading role in the field of molecular imaging. But recently molecular imaging has been rapidly developed. Besides nuclear imaging, molecular imaging methods such as optical imaging, magnetic resonance imaging are emerging. Each imaging modalities have their advantages and weaknesses. The opportunities from molecular imaging look bright. We should try nuclear medicine continues to have a leading role in molecular imaging

Investigation of the molecular level interactions between mucins and food proteins: Spectroscopic, tribological and rheological studies

OpenAIRE

Celebioglu, Hilal Yilmaz; Chronakis, Ioannis S.; Lee, Seunghwan; Guðjónsdóttir, María

2017-01-01

The thesis investigated the structure and molecular-level interaction of β-lactoglobulin (BLG) and mucins, representing major components of the dairy products and saliva/digestion systems, respectively. Mucins are long glycoprotein molecules responsible for the gel nature of the mucous layer covers epithelial surfaces throughout the body. A literature review of the interactions of different mucin types and saliva mucins with several food proteins and food protein emulsions, as well as their f...

Multiplicity of Mathematical Modeling Strategies to Search for Molecular and Cellular Insights into Bacteria Lung Infection.

Science.gov (United States)

Cantone, Martina; Santos, Guido; Wentker, Pia; Lai, Xin; Vera, Julio

2017-01-01

Even today two bacterial lung infections, namely pneumonia and tuberculosis, are among the 10 most frequent causes of death worldwide. These infections still lack effective treatments in many developing countries and in immunocompromised populations like infants, elderly people and transplanted patients. The interaction between bacteria and the host is a complex system of interlinked intercellular and the intracellular processes, enriched in regulatory structures like positive and negative feedback loops. Severe pathological condition can emerge when the immune system of the host fails to neutralize the infection. This failure can result in systemic spreading of pathogens or overwhelming immune response followed by a systemic inflammatory response. Mathematical modeling is a promising tool to dissect the complexity underlying pathogenesis of bacterial lung infection at the molecular, cellular and tissue levels, and also at the interfaces among levels. In this article, we introduce mathematical and computational modeling frameworks that can be used for investigating molecular and cellular mechanisms underlying bacterial lung infection. Then, we compile and discuss published results on the modeling of regulatory pathways and cell populations relevant for lung infection and inflammation. Finally, we discuss how to make use of this multiplicity of modeling approaches to open new avenues in the search of the molecular and cellular mechanisms underlying bacterial infection in the lung.

Early molecular events involved in Pinus pinaster Ait. somatic embryo development under reduced water availability: transcriptomic and proteomic analyses.

Science.gov (United States)

Morel, Alexandre; Teyssier, Caroline; Trontin, Jean-François; Eliášová, Kateřina; Pešek, Bedřich; Beaufour, Martine; Morabito, Domenico; Boizot, Nathalie; Le Metté, Claire; Belal-Bessai, Leila; Reymond, Isabelle; Harvengt, Luc; Cadene, Martine; Corbineau, Françoise; Vágner, Martin; Label, Philippe; Lelu-Walter, Marie-Anne

2014-09-01

Maritime pine somatic embryos (SEs) require a reduction in water availability (high gellan gum concentration in the maturation medium) to reach the cotyledonary stage. This key switch, reported specifically for pine species, is not yet well understood. To facilitate the use of somatic embryogenesis for mass propagation of conifers, we need a better understanding of embryo development. Comparison of both transcriptome (Illumina RNA sequencing) and proteome [two-dimensional sodium dodecyl sulfate-polyacrylamide gel electrophoresis with mass spectrometry (MS) identification] of immature SEs, cultured on either high (9G) or low (4G) gellan gum concentration, was performed, together with analysis of water content, fresh and dry mass, endogenous abscisic acid (ABA; gas chromatography-MS), soluble sugars (high-pressure liquid chromatography), starch and confocal laser microscope observations. This multiscale, integrated analysis was used to unravel early molecular and physiological events involved in SE development. Under unfavorable conditions (4G), the glycolytic pathway was enhanced, possibly in relation to cell proliferation that may be antagonistic to SE development. Under favorable conditions (9G), SEs adapted to culture constraint by activating specific protective pathways, and ABA-mediated molecular and physiological responses promoting embryo development. Our results suggest that on 9G, germin-like protein and ubiquitin-protein ligase could be used as predictive markers of SE development, whereas protein phosphatase 2C could be a biomarker for culture adaptive responses. This is the first characterization of early molecular mechanisms involved in the development of pine SEs following an increase in gellan gum concentration in the maturation medium, and it is also the first report on somatic embryogenesis in conifers combining transcriptomic and proteomic datasets. © 2014 Scandinavian Plant Physiology Society.

Molecular Level Structure and Dynamics of Electrolytes Using 17O Nuclear Magnetic Resonance Spectroscopy

Energy Technology Data Exchange (ETDEWEB)

Murugesan, Vijayakumar; Han, Kee Sung; Hu, Jianzhi; Mueller, Karl T.

2017-03-19

Electrolytes help harness the energy from electrochemical processes by serving as solvents and transport media for redox-active ions. Molecular-level interactions between ionic solutes and solvent molecules – commonly referred to as solvation phenomena – give rise to many functional properties of electrolytes such as ionic conductivity, viscosity, and stability. It is critical to understand the evolution of solvation phenomena as a function of competing counterions and solvent mixtures to predict and design the optimal electrolyte for a target application. Probing oxygen environments is of great interest as oxygens are located at strategic molecular sites in battery solvents and are directly involved in inter- and intramolecular solvation interactions. NMR signals from 17O nuclei in battery electrolytes offer nondestructive bulk measurements of isotropic shielding, electric field gradient tensors, and transverse and longitudinal relaxation rates, which are excellent means for probing structure, bonding, and dynamics of both solute and solvent molecules. This article describes the use of 17O NMR spectroscopy in probing the solvation structures of various electrolyte systems ranging from transition metal ions in aqueous solution to lithium cations in organic solvent mixtures.

Different routes, same pathways: Molecular mechanisms under silver ion and nanoparticle exposures in the soil sentinel Eisenia fetida

International Nuclear Information System (INIS)

Novo, Marta; Lahive, Elma; Díez-Ortiz, María; Matzke, Marianne; Morgan, Andrew J.; Spurgeon, David J.; Svendsen, Claus; Kille, Peter

2015-01-01

Use of nanotechnology products is increasing; with silver (Ag) nanoparticles particularly widely used. A key uncertainty surrounding the risk assessment of AgNPs is whether their effects are driven through the same mechanism of action that underlies the toxic effects of Ag ions. We present the first full transcriptome study of the effects of Ag ions and NPs in an ecotoxicological model soil invertebrate, the earthworm Eisenia fetida. Gene expression analyses indicated similar mechanisms for both silver forms with toxicity being exerted through pathways related to ribosome function, sugar and protein metabolism, molecular stress, disruption of energy production and histones. The main difference seen between Ag ions and NPs was associated with potential toxicokinetic effects related to cellular internalisation and communication, with pathways related to endocytosis and cilia being significantly enriched. These results point to a common final toxicodynamic response, but initial internalisation driven by different exposure routes and toxicokinetic mechanisms. - Highlights: • Molecular effects underlying Ag ions and NPs exposure were studied in Eisenia fetida. • Full transcriptomic study of a genetically characterised lineage. • NPs and ions presented a similar toxicodynamic response. • Internalisation of the two Ag forms by different toxicokinetic mechanisms. - Transcriptomic analyses after exposure of earthworms to silver NPs or ions showed a final common toxicodynamic response, but internalisation by different toxicokinetic mechanisms

Factor VII deficiency: Unveiling the cellular and molecular mechanisms underlying three model alterations of the enzyme catalytic domain.

Science.gov (United States)

Chollet, Maria Eugenia; Andersen, Elisabeth; Skarpen, Ellen; Myklebust, Christiane F; Koehler, Christian; Morth, Jens Preben; Chuansumrit, Ampaiwan; Pinotti, Mirko; Bernardi, Francesco; Thiede, Bernd; Sandset, Per Morten; Skretting, Grethe

2018-03-01

Activated factor (F) VII is a vitamin K-dependent glycoprotein that initiates blood coagulation upon interaction with tissue factor. FVII deficiency is the most common of the rare congenital bleeding disorders. While the mutational pattern has been extensively characterized, the pathogenic molecular mechanisms of mutations, particularly at the intracellular level, have been poorly defined. Here, we aimed at elucidating the mechanisms underlying altered FVII biosynthesis in the presence of three mutation types in the catalytic domain: a missense change, a microdeletion and a frameshift/elongation, associated with severe or moderate to severe phenotypes. Using CHO-K1 cells transiently transfected with expression vectors containing the wild-type FVII cDNA (FVIIwt) or harboring the p.I289del, p.G420V or p.A354V-p.P464Hfs mutations, we found that the secretion of the FVII mutants was severely decreased compared to FVIIwt. The synthesis rate of the mutants was slower than the FVIIwt and delayed, and no degradation of the FVII mutants by proteasomes, lysosomes or cysteine proteases was observed. Confocal immunofluorescence microscopy studies showed that FVII variants were localized into the endoplasmic reticulum (ER) but were not detectable within the Golgi apparatus. These findings suggested that a common pathogenic mechanism, possibly a defective folding of the mutant proteins, was triggered by the FVII mutations. The misfolded state led to impaired trafficking of these proteins causing ER retention, which would explain the low to very low FVII plasma levels observed in patients carrying these mutations. Copyright © 2017 Elsevier B.V. All rights reserved.

Estuarine Response to River Flow and Sea-Level Rise under Future Climate Change and Human Development

Energy Technology Data Exchange (ETDEWEB)

Yang, Zhaoqing; Wang, Taiping; Voisin, Nathalie; Copping, Andrea E.

2015-04-01

Understanding the response of river flow and estuarine hydrodynamics to climate change, land-use/land-cover change (LULC), and sea-level rise is essential to managing water resources and stress on living organisms under these changing conditions. This paper presents a modeling study using a watershed hydrology model and an estuarine hydrodynamic model, in a one-way coupling, to investigate the estuarine hydrodynamic response to sea-level rise and change in river flow due to the effect of future climate and LULC changes in the Snohomish River estuary, Washington, USA. A set of hydrodynamic variables, including salinity intrusion points, average water depth, and salinity of the inundated area, were used to quantify the estuarine response to river flow and sea-level rise. Model results suggest that salinity intrusion points in the Snohomish River estuary and the average salinity of the inundated areas are a nonlinear function of river flow, although the average water depth in the inundated area is approximately linear with river flow. Future climate changes will shift salinity intrusion points further upstream under low flow conditions and further downstream under high flow conditions. In contrast, under the future LULC change scenario, the salinity intrusion point will shift downstream under both low and high flow conditions, compared to present conditions. The model results also suggest that the average water depth in the inundated areas increases linearly with sea-level rise but at a slower rate, and the average salinity in the inundated areas increases linearly with sea-level rise; however, the response of salinity intrusion points in the river to sea-level rise is strongly nonlinear.

Simulational nanoengineering: Molecular dynamics implementation of an atomistic Stirling engine.

Science.gov (United States)

Rapaport, D C

2009-04-01

A nanoscale-sized Stirling engine with an atomistic working fluid has been modeled using molecular dynamics simulation. The design includes heat exchangers based on thermostats, pistons attached to a flywheel under load, and a regenerator. Key aspects of the behavior, including the time-dependent flows, are described. The model is shown to be capable of stable operation while producing net work at a moderate level of efficiency.

Molecular modeling of the process of reversible dissolution of the collagen protein under the action of tissue-clearing agents

Science.gov (United States)

Dvoretsky, K. N.; Berezin, K. V.; Chernavina, M. L.; Likhter, A. M.; Shagautdinova, I. T.; Antonova, E. M.; Rybakov, A. V.; Grechukhina, O. N.; Tuchin, V. V.

2018-04-01

The interaction of glycerol immersion agent with collagen mimetic peptide ((GPH)9)3 and a fragment of the microfibril 5((GPH)12)3 was studied by the classical molecular dynamics method using the GROMACS software. The change in geometric parameters of collagen α-chains at various concentrations of an aqueous solution of glycerol is analyzed. It is shown that these changes nonlinearly depend on the concentration and are limited to a certain level, which correlates with the experimental data on optical clearing efficiency of human skin. A hypothesis on the cause of the decreased efficiency of optical skin clearing at high immersion agent concentrations is put forward. The molecular mechanism of immersion optical clearing of biological tissues is discussed.

Differentiation of molecular chain entanglement structure through laser Raman spectrum measurement of High strength PET fibers under stress

Science.gov (United States)

Go, D.; Takarada, W.; Kikutani, T.

2017-10-01

The aim of this study was to investigate the mechanism for the improvement of mechanical properties of poly(ethylene terephthalate) (PET) fibers based on the concept of controlling the state of molecular entanglement. For this purpose, five different PET fibers were prepared through either the conventional melt spinning and drawing/annealing process or the high-speed melt spinning process. In both cases, the melt spinning process was designed so as to realize different Deborah number conditions. The prepared fibers were subjected to the laser Raman spectroscopy measurement and the characteristics of the scattering peak at around 1616 cm-1, which corresponds to the C-C/C=C stretching mode of the aromatic ring in the main chain, were investigated in detail. It was revealed that the fibers drawn and annealed after the melt spinning process of lower Deborah number showed higher tensile strength as well as lower value of full width at half maximum (FWHM) in the laser Raman spectrum. Narrow FWHM was considered to represent the homogeneous state of entanglement structure, which may lead to the higher strength and toughness of fibers because individual molecular chains tend to bare similar level of tensile stress when the fiber is stretched. In case of high-speed spun fibers prepared with a high Deborah number condition, the FWHM was narrow presumably because much lower tensile stress in comparison with the drawing/annealing process was applied when the fiber structure was developed, however the value increased significantly upon applying tensile load to the fibers during the laser Raman spectrum measurement. From these results, it was concluded that the Laser Raman spectroscopy could differentiate molecular chain entanglement structure of various fiber samples, in that low FWHM, which corresponds to either homogeneous state of molecular entanglement or lower level of mean residual stress, and small increase of FWTH upon applying tensile stress are considered to be the key

EFNS guidelines for the molecular diagnosis of neurogenetic disorders: motoneuron, peripheral nerve and muscle disorders.

Science.gov (United States)

Burgunder, J-M; Schöls, L; Baets, J; Andersen, P; Gasser, T; Szolnoki, Z; Fontaine, B; Van Broeckhoven, C; Di Donato, S; De Jonghe, P; Lynch, T; Mariotti, C; Spinazzola, A; Tabrizi, S J; Tallaksen, C; Zeviani, M; Harbo, H F; Finsterer, J

2011-02-01

These EFNS guidelines on the molecular diagnosis of motoneuron disorders, neuropathies and myopathies are designed to summarize the possibilities and limitations of molecular genetic techniques and to provide diagnostic criteria for deciding when a molecular diagnostic work-up is indicated. To collect data about planning, conditions and performance of molecular diagnosis of these disorders, a literature search in various electronic databases was carried out and original papers, meta-analyses, review papers and guideline recommendations reviewed. The best level of evidence for genetic testing recommendation (B) can be found for the disorders with specific presentations, including familial amyotrophic lateral sclerosis, spinal and bulbar muscular atrophy, Charcot-Marie-Tooth 1A, myotonic dystrophy and Duchenne muscular dystrophy. For a number of less common disorders, a precise description of the phenotype, including the use of immunologic methods in the case of myopathies, is considered as good clinical practice to guide molecular genetic testing. These guidelines are provisional and the future availability of molecular-genetic epidemiological data about the neurogenetic disorders under discussion in this article will allow improved recommendation with an increased level of evidence. © 2010 The Author(s). European Journal of Neurology © 2010 EFNS.

MOLECULAR MECHANISMS OF FEAR LEARNING AND MEMORY

Science.gov (United States)

Johansen, Joshua P.; Cain, Christopher K.; Ostroff, Linnaea E.; LeDoux, Joseph E.

2011-01-01

Pavlovian fear conditioning is a useful behavioral paradigm for exploring the molecular mechanisms of learning and memory because a well-defined response to a specific environmental stimulus is produced through associative learning processes. Synaptic plasticity in the lateral nucleus of the amygdala (LA) underlies this form of associative learning. Here we summarize the molecular mechanisms that contribute to this synaptic plasticity in the context of auditory fear conditioning, the form of fear conditioning best understood at the molecular level. We discuss the neurotransmitter systems and signaling cascades that contribute to three phases of auditory fear conditioning: acquisition, consolidation, and reconsolidation. These studies suggest that multiple intracellular signaling pathways, including those triggered by activation of Hebbian processes and neuromodulatory receptors, interact to produce neural plasticity in the LA and behavioral fear conditioning. Together, this research illustrates the power of fear conditioning as a model system for characterizing the mechanisms of learning and memory in mammals, and potentially for understanding fear related disorders, such as PTSD and phobias. PMID:22036561

Molecular mechanisms of fear learning and memory.

Science.gov (United States)

Johansen, Joshua P; Cain, Christopher K; Ostroff, Linnaea E; LeDoux, Joseph E

2011-10-28

Pavlovian fear conditioning is a particularly useful behavioral paradigm for exploring the molecular mechanisms of learning and memory because a well-defined response to a specific environmental stimulus is produced through associative learning processes. Synaptic plasticity in the lateral nucleus of the amygdala (LA) underlies this form of associative learning. Here, we summarize the molecular mechanisms that contribute to this synaptic plasticity in the context of auditory fear conditioning, the form of fear conditioning best understood at the molecular level. We discuss the neurotransmitter systems and signaling cascades that contribute to three phases of auditory fear conditioning: acquisition, consolidation, and reconsolidation. These studies suggest that multiple intracellular signaling pathways, including those triggered by activation of Hebbian processes and neuromodulatory receptors, interact to produce neural plasticity in the LA and behavioral fear conditioning. Collectively, this body of research illustrates the power of fear conditioning as a model system for characterizing the mechanisms of learning and memory in mammals and potentially for understanding fear-related disorders, such as PTSD and phobias. Copyright © 2011 Elsevier Inc. All rights reserved.

Surface functionalization of SPR chip for specific molecular interaction analysis under flow condition

Directory of Open Access Journals (Sweden)

Tao Ma

2017-03-01

Full Text Available Surface functionalization of sensor chip for probe immobilization is crucial for the biosensing applications of surface plasmon resonance (SPR sensors. In this paper, we report a method circulating the dopamine aqueous solution to coat polydopamine film on sensing surface for surface functionalization of SPR chip. The polydopamine film with available thickness can be easily prepared by controlling the circulation time and the biorecognition elements can be immobilized on the polydopamine film for specific molecular interaction analysis. These operations are all performed under flow condition in the fluidic system, and have the advantages of easy implementation, less time consuming, and low cost, because the reagents and devices used in the operations are routinely applied in most laboratories. In this study, the specific absorption between the protein A probe immobilized on the sensing surface and human immunoglobulin G in the buffer is monitored based on this surface functionalization strategy to demonstrated its feasibility for SPR biosensing applications.

Quality in the pepper under different fertigation managements and levels of nitrogen and potassium

Directory of Open Access Journals (Sweden)

Francisco de Assis de Oliveira

Full Text Available ABSTRACTThe rational use of nutrients is of fundamental importance for obtaining high productivity of high nutritional quality. This work was developed with the aim of evaluating the quality of pepper fruit grown under different fertigation managements and different levels of nitrogen and potassium. The experimental design was of randomised blocks in a 3 x 6 factorial scheme with four replications. The treatments resulted from the combination of three fertigation managements (M1-based on the rate of absorption; M2-monitoring the conductivity of the soil solution; M3-monitoring concentrations of N and K ions in the soil solution with six levels of N and K (N0K0, N50K50, N100K100, N150K150, N200K200 and N300K300 as a percentage of the recommended dosage for the crop under conventional fertigation (M1 or hydroponics (M2 and M3. Fruit quality was evaluated for the following characteristics: pH, soluble solids, titratable acidity, vitamin C content and the ratio of soluble solids to titratable acidity. The different fertigation managements only affected the levels of soluble solids (SS and titratable acidity (TA, reducing the SS and TA. The variables under study were adjusted for the levels of N and K using quadratic models.

Multi-Scale Molecular Deconstruction of the Serotonin Neuron System.

Science.gov (United States)

Okaty, Benjamin W; Freret, Morgan E; Rood, Benjamin D; Brust, Rachael D; Hennessy, Morgan L; deBairos, Danielle; Kim, Jun Chul; Cook, Melloni N; Dymecki, Susan M

2015-11-18

Serotonergic (5HT) neurons modulate diverse behaviors and physiology and are implicated in distinct clinical disorders. Corresponding diversity in 5HT neuronal phenotypes is becoming apparent and is likely rooted in molecular differences, yet a comprehensive approach characterizing molecular variation across the 5HT system is lacking, as is concomitant linkage to cellular phenotypes. Here we combine intersectional fate mapping, neuron sorting, and genome-wide RNA-seq to deconstruct the mouse 5HT system at multiple levels of granularity-from anatomy, to genetic sublineages, to single neurons. Our unbiased analyses reveal principles underlying system organization, 5HT neuron subtypes, constellations of differentially expressed genes distinguishing subtypes, and predictions of subtype-specific functions. Using electrophysiology, subtype-specific neuron silencing, and conditional gene knockout, we show that these molecularly defined 5HT neuron subtypes are functionally distinct. Collectively, this resource classifies molecular diversity across the 5HT system and discovers sertonergic subtypes, markers, organizing principles, and subtype-specific functions with potential disease relevance. Copyright © 2015 Elsevier Inc. All rights reserved.

Molecular and physiological manifestations and measurement of aging in humans.

Science.gov (United States)

Khan, Sadiya S; Singer, Benjamin D; Vaughan, Douglas E

2017-08-01

Biological aging is associated with a reduction in the reparative and regenerative potential in tissues and organs. This reduction manifests as a decreased physiological reserve in response to stress (termed homeostenosis) and a time-dependent failure of complex molecular mechanisms that cumulatively create disorder. Aging inevitably occurs with time in all organisms and emerges on a molecular, cellular, organ, and organismal level with genetic, epigenetic, and environmental modulators. Individuals with the same chronological age exhibit differential trajectories of age-related decline, and it follows that we should assess biological age distinctly from chronological age. In this review, we outline mechanisms of aging with attention to well-described molecular and cellular hallmarks and discuss physiological changes of aging at the organ-system level. We suggest methods to measure aging with attention to both molecular biology (e.g., telomere length and epigenetic marks) and physiological function (e.g., lung function and echocardiographic measurements). Finally, we propose a framework to integrate these molecular and physiological data into a composite score that measures biological aging in humans. Understanding the molecular and physiological phenomena that drive the complex and multifactorial processes underlying the variable pace of biological aging in humans will inform how researchers assess and investigate health and disease over the life course. This composite biological age score could be of use to researchers seeking to characterize normal, accelerated, and exceptionally successful aging as well as to assess the effect of interventions aimed at modulating human aging. © 2017 The Authors. Aging Cell published by the Anatomical Society and John Wiley & Sons Ltd.

RNA sequencing of Populus x canadensis roots identifies key molecular mechanisms underlying physiological adaption to excess zinc.

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Andrea Ariani

Full Text Available Populus x canadensis clone I-214 exhibits a general indicator phenotype in response to excess Zn, and a higher metal uptake in roots than in shoots with a reduced translocation to aerial parts under hydroponic conditions. This physiological adaptation seems mainly regulated by roots, although the molecular mechanisms that underlie these processes are still poorly understood. Here, differential expression analysis using RNA-sequencing technology was used to identify the molecular mechanisms involved in the response to excess Zn in root. In order to maximize specificity of detection of differentially expressed (DE genes, we consider the intersection of genes identified by three distinct statistical approaches (61 up- and 19 down-regulated and validate them by RT-qPCR, yielding an agreement of 93% between the two experimental techniques. Gene Ontology (GO terms related to oxidation-reduction processes, transport and cellular iron ion homeostasis were enriched among DE genes, highlighting the importance of metal homeostasis in adaptation to excess Zn by P. x canadensis clone I-214. We identified the up-regulation of two Populus metal transporters (ZIP2 and NRAMP1 probably involved in metal uptake, and the down-regulation of a NAS4 gene involved in metal translocation. We identified also four Fe-homeostasis transcription factors (two bHLH38 genes, FIT and BTS that were differentially expressed, probably for reducing Zn-induced Fe-deficiency. In particular, we suggest that the down-regulation of FIT transcription factor could be a mechanism to cope with Zn-induced Fe-deficiency in Populus. These results provide insight into the molecular mechanisms involved in adaption to excess Zn in Populus spp., but could also constitute a starting point for the identification and characterization of molecular markers or biotechnological targets for possible improvement of phytoremediation performances of poplar trees.

Synthesis of core-shell molecularly imprinted polymer microspheres by precipitation polymerization for the inline molecularly imprinted solid-phase extraction of thiabendazole from citrus fruits and orange juice samples.

Science.gov (United States)

Barahona, Francisco; Turiel, Esther; Cormack, Peter A G; Martín-Esteban, Antonio

2011-01-01

In this work, the synthesis of molecularly imprinted polymer microspheres with narrow particle size distributions and core-shell morphology by a two-step precipitation polymerization procedure is described. Polydivinylbenzene (poly DVB-80) core particles were used as seed particles in the production of molecularly imprinted polymer shells by copolymerization of divinylbenzene-80 with methacrylic acid in the presence of thiabendazole (TBZ) and an appropriate porogen. Thereafter, polymer particles were packed into refillable stainless steel HPLC columns used in the development of an inline molecularly imprinted SPE method for the determination of TBZ in citrus fruits and orange juice samples. Under optimized chromatographic conditions, recoveries of TBZ within the range 81.1-106.4%, depending upon the sample, were obtained, with RSDs lower than 10%. This novel method permits the unequivocal determination of TBZ in the samples under study, according to the maximum residue levels allowed within Europe, in less than 20 min and without any need for a clean-up step in the analytical protocol. Copyright © 2011 WILEY-VCH Verlag GmbH & Co. KGaA, Weinheim.

Voltammetric determination of attomolar levels of a sequence derived from the genom of hepatitis B virus by using molecular beacon mediated circular strand displacement and rolling circle amplification.

Science.gov (United States)

Huang, Shan; Feng, Mengmeng; Li, Jiawen; Liu, Yi; Xiao, Qi

2018-03-03

The authors describe an electrochemical method for the determination of the single-stranded DNA (ssDNA) oligonucleotide with a sequence derived from the genom of hepatitis B virus (HBV). It is making use of circular strand displacement (CSD) and rolling circle amplification (RCA) strategies mediated by a molecular beacon (MB). This ssDNA hybridizes with the loop portion of the MB immobilized on the surface of a gold electrode, while primer DNA also hybridizes with the rest of partial DNA sequences of MB. This triggers the MB-mediated CSD. The RCA is then initiated to produce a long DNA strand with multiple tandem-repeat sequences, and this results in a significant increase of the differential pulse voltammetric response of the electrochemical probe Methylene Blue at a rather low working potential of -0.24 V (vs. Ag/AgCl). Under optimal experimental conditions, the assay displays an ultrahigh sensitivity (with a 2.6 aM detection limit) and excellent selectivity. Response is linear in the 10 to 700 aM DNA concentration range. Graphical abstract Schematic of a voltammetric method for the determination of attomolar levels of target DNA. It is based on molecular beacon mediated circular strand displacement and rolling circle amplification strategies. Under optimal experimental conditions, the assay displays an ultrahigh sensitivity with a 2.6 aM detection limit and excellent selectivity.

Molecular adaptation during adaptive radiation in the Hawaiian endemic genus Schiedea.

Directory of Open Access Journals (Sweden)

Maxim V Kapralov

2006-12-01

Full Text Available "Explosive" adaptive radiations on islands remain one of the most puzzling evolutionary phenomena. The rate of phenotypic and ecological adaptations is extremely fast during such events, suggesting that many genes may be under fairly strong selection. However, no evidence for adaptation at the level of protein coding genes was found, so it has been suggested that selection may work mainly on regulatory elements. Here we report the first evidence that positive selection does operate at the level of protein coding genes during rapid adaptive radiations. We studied molecular adaptation in Hawaiian endemic plant genus Schiedea (Caryophyllaceae, which includes closely related species with a striking range of morphological and ecological forms, varying from rainforest vines to woody shrubs growing in desert-like conditions on cliffs. Given the remarkable difference in photosynthetic performance between Schiedea species from different habitats, we focused on the "photosynthetic" Rubisco enzyme, the efficiency of which is known to be a limiting step in plant photosynthesis.We demonstrate that the chloroplast rbcL gene, encoding the large subunit of Rubisco enzyme, evolved under strong positive selection in Schiedea. Adaptive amino acid changes occurred in functionally important regions of Rubisco that interact with Rubisco activase, a chaperone which promotes and maintains the catalytic activity of Rubisco. Interestingly, positive selection acting on the rbcL might have caused favorable cytotypes to spread across several Schiedea species.We report the first evidence for adaptive changes at the DNA and protein sequence level that may have been associated with the evolution of photosynthetic performance and colonization of new habitats during a recent adaptive radiation in an island plant genus. This illustrates how small changes at the molecular level may change ecological species performance and helps us to understand the molecular bases of extremely

Molecular pathology and age estimation.

Science.gov (United States)

Meissner, Christoph; Ritz-Timme, Stefanie

2010-12-15

Over the course of our lifetime a stochastic process leads to gradual alterations of biomolecules on the molecular level, a process that is called ageing. Important changes are observed on the DNA-level as well as on the protein level and are the cause and/or consequence of our 'molecular clock', influenced by genetic as well as environmental parameters. These alterations on the molecular level may aid in forensic medicine to estimate the age of a living person, a dead body or even skeletal remains for identification purposes. Four such important alterations have become the focus of molecular age estimation in the forensic community over the last two decades. The age-dependent accumulation of the 4977bp deletion of mitochondrial DNA and the attrition of telomeres along with ageing are two important processes at the DNA-level. Among a variety of protein alterations, the racemisation of aspartic acid and advanced glycation endproducs have already been tested for forensic applications. At the moment the racemisation of aspartic acid represents the pinnacle of molecular age estimation for three reasons: an excellent standardization of sampling and methods, an evaluation of different variables in many published studies and highest accuracy of results. The three other mentioned alterations often lack standardized procedures, published data are sparse and often have the character of pilot studies. Nevertheless it is important to evaluate molecular methods for their suitability in forensic age estimation, because supplementary methods will help to extend and refine accuracy and reliability of such estimates. Copyright © 2010 Elsevier Ireland Ltd. All rights reserved.

Melting curves of molecular hydrogen and molecular deuterium under high pressures between 20 and 373 K

International Nuclear Information System (INIS)

Diatschenko, V.; Chu, C.W.; Liebenberg, D.H.; Young, D.A.; Ross, M.; Mills, R.L.

1985-01-01

We determined the melting curve of molecular hydrogen and molecular deuterium at closely spaced intervals from 20 to 373 K by two different techniques using high-pressure diamond cells. The cells were loaded with liquid at low temperature or with compressed gas at room temperature. Empirical functions for the melting curves were evaluated from least-squares fits of the data. Values of the compressibility and Debye temperature were computed at melting, and the results are compared with those calculated from various theoretical models. The good agreement shows that the models are generally valid, although small systematic deviations may point the way toward refinements in modeling. Our study also demonstrates the need to determine a one-piece intermolecular potential valid over a wide pressure range by refitting all experimental data, including the shock data recently made available

Molecular MR imaging

International Nuclear Information System (INIS)

Fleige, G.; Hamm, B.

2000-01-01

Basic medicobiological research in recent years has made rapid advances in the functional understanding of normal and pathological processes down to the molecular level. At the same time, various imaging modalities have developed from the depiction of organs to approaching the depiction of the cellular level and are about to make the visualization of molecular processes an established procedure. Besides other modalities like PET and near-infrared fluorescence, MR imaging offers some promising options for molecular imaging as well as some applications that have already been tested such as the visualization of enzyme activity, the depiction of the expression of certain genes, the visualization of surface receptors, or the specific demonstration of cells involved in the body's immune response. A major advantage of molecular magnetic resonance imaging (mMRI) over other more sensitive modalities is its high spatial resolution. However, the establishment of mMRI crucially relies on further improvements in resolution and the development of molecular markers for improving its sensitivity and specificity. The state of the art of mMRI is presented by giving a survey of the literature on experimental studies and reporting the results our study group obtained during investigation on gliomas. (orig.) [de

Structural phase transition and failure of nanographite sheets under high pressure: a molecular dynamics study

International Nuclear Information System (INIS)

Zhang Bin; Liang Yongcheng; Sun Huiyu

2007-01-01

Nanographite sheets under high compressive stresses at ambient temperature have been investigated through molecular dynamics simulations using the Tersoff-Brenner potential. Nanographite undergoes a soft to hard phase transition at a certain compressive stress, about 15 GPa. With increasing compressions, the bonding structures of nanographite are changed, interlayer sp 3 -bonds are formed, and nanographite transforms into a superhard carbon phase (SCP). Further compressions lead to the instabilities of the SCP. Although the detailed lattice structure of the SCP remains elusive, its compressive strength can approach 150 GPa, comparable to that of diamond. The maximum failure stresses of nanographite sheets are sensitive to the inter-and intra-layer interstices. Our results may explain paradoxical experimental results in the available literature

Light and redox switchable molecular components for molecular electronics.

Science.gov (United States)

Browne, Wesley R; Feringa, Ben L

2010-01-01

The field of molecular and organic electronics has seen rapid progress in recent years, developing from concept and design to actual demonstration devices in which both single molecules and self-assembled monolayers are employed as light-responsive components. Research in this field has seen numerous unexpected challenges that have slowed progress and the initial promise of complex molecular-based computers has not yet been realised. Primarily this has been due to the realisation at an early stage that molecular-based nano-electronics brings with it the interface between the hard (semiconductor) and soft (molecular) worlds and the challenges which accompany working in such an environment. Issues such as addressability, cross-talk, molecular stability and perturbation of molecular properties (e.g., inhibition of photochemistry) have nevertheless driven development in molecular design and synthesis as well as our ability to interface molecular components with bulk metal contacts to a very high level of sophistication. Numerous groups have played key roles in progressing this field not least teams such as those led by Whitesides, Aviram, Ratner, Stoddart and Heath. In this short review we will however focus on the contributions from our own group and those of our collaborators, in employing diarylethene based molecular components.

Interactions between proteins and carbon-based nanoparticles: exploring the origin of nanotoxicity at the molecular level.

Science.gov (United States)

Zuo, Guanghong; Kang, Seung-Gu; Xiu, Peng; Zhao, Yuliang; Zhou, Ruhong

2013-05-27

The widespread application of nanomaterials has spurred an interest in the study of interactions between nanoparticles and proteins due to the biosafety concerns of these nanomaterials. In this review, a summary is presented of some of the recent studies on this important subject, especially on the interactions of proteins with carbon nanotubes (CNTs) and metallofullerenols. Two potential molecular mechanisms have been proposed for CNTs' inhibition of protein functions. The driving forces of CNTs' adsorption onto proteins are found to be mainly hydrophobic interactions and the so-called π-π stacking between CNTs' carbon rings and proteins' aromatic residues. However, there is also recent evidence showing that endohedral metallofullerenol Gd@C82 (OH)22 can be used to inhibit tumor growth, thus acting as a potential nanomedicine. These recent findings have provided a better understanding of nanotoxicity at the molecular level and also suggested therapeutic potential by using nanoparticles' cytotoxicity against cancer cells. Copyright © 2013 WILEY-VCH Verlag GmbH & Co. KGaA, Weinheim.

The structure of molecular liquids. Neutron diffraction and molecular dynamics simulations

International Nuclear Information System (INIS)

Bianchi, L.

2000-05-01

Neutron diffraction (ND) measurements on liquid methanol (CD 3 OD, CD 3 O(H/D), CD 3 OH) under ambient conditions were performed to obtain the distinct (intra- + inter-molecular), G dist (r) and inter-molecular, G inter (r) radial distribution functions (rdfs) for the three samples. The H/D substitution on hydroxyl-hydrogen (Ho) has been used to extract the partial distribution functions, G XHo (r) (X=C, O, and H - a methyl hydrogen) and G XX (r) at both the distinct and inter-molecular levels from the difference techniques of ND. The O-Ho bond length, which has been the subject of controversy in the past, is found purely from the distinct partial distribution function, G XHo (r) to be 0.98 ± 0.01 A. The C-H distance obtained from the distinct G XX (r) partial is 1.08 ± 0.01 A. These distances determined by fitting an intra-molecular model to the total distinct structure functions are 0.961 ± 0.001 A and 1.096 ± 0.001 A, respectively. The inter-molecular G XX (r) function, dominated by contributions from the methyl groups, apart from showing broad oscillations extending up to ∼14 A is featureless, mainly because of cancellation effects from six contributing pairs. The Ho-Ho partial pair distribution function (pdf), g HoHo (r), determined from the second order difference, shows that only one other Ho atom can be found within a mean Ho-Ho separation of 2.36 A. The average position of the O-Ho hydrogen bond determined for the first time purely from experimental inter-molecular G XHo (r) partial distribution function is found to be at 1.75 ± 0.03 A. The experimental structural results at the partial distribution level are compared with those obtained from molecular dynamics (MD) simulations performed in NVE ensemble by using both 3- and 6-site force field models for the first time in this study. The MD simulations with both the models reproduce the ND rdfs rather well. However, discrepancies begin to appear between the simulated and the experimental partial

Modeling the Thiophene HDS reaction on a molecular level

NARCIS (Netherlands)

Diemann, E.; Weber, T.; Müller, A.

1994-01-01

The structure of MoS2/Al2O3 catalyst and the initial step of the hydrodesulfurization (HDS) reaction using an experimental model have been studied by in situ Raman-, infrared emission (IRE)-, inelastic electron tunneling (IET)-spectroscopy and thermal desorption measurements accompanied by molecular

Molecular fountain.

Energy Technology Data Exchange (ETDEWEB)

Strecker, Kevin E.; Chandler, David W.

2009-09-01

A molecular fountain directs slowly moving molecules against gravity to further slow them to translational energies that they can be trapped and studied. If the molecules are initially slow enough they will return some time later to the position from which they were launched. Because this round trip time can be on the order of a second a single molecule can be observed for times sufficient to perform Hz level spectroscopy. The goal of this LDRD proposal was to construct a novel Molecular Fountain apparatus capable of producing dilute samples of molecules at near zero temperatures in well-defined user-selectable, quantum states. The slowly moving molecules used in this research are produced by the previously developed Kinematic Cooling technique, which uses a crossed atomic and molecular beam apparatus to generate single rotational level molecular samples moving slowly in the laboratory reference frame. The Kinematic Cooling technique produces cold molecules from a supersonic molecular beam via single collisions with a supersonic atomic beam. A single collision of an atom with a molecule occurring at the correct energy and relative velocity can cause a small fraction of the molecules to move very slowly vertically against gravity in the laboratory. These slowly moving molecules are captured by an electrostatic hexapole guiding field that both orients and focuses the molecules. The molecules are focused into the ionization region of a time-of-flight mass spectrometer and are ionized by laser radiation. The new molecular fountain apparatus was built utilizing a new design for molecular beam apparatus that has allowed us to miniaturize the apparatus. This new design minimizes the volumes and surface area of the machine allowing smaller pumps to maintain the necessary background pressures needed for these experiments.

Uncovering molecular processes in crystal nucleation and growth by using molecular simulation.

Science.gov (United States)

Anwar, Jamshed; Zahn, Dirk

2011-02-25

Exploring nucleation processes by molecular simulation provides a mechanistic understanding at the atomic level and also enables kinetic and thermodynamic quantities to be estimated. However, whilst the potential for modeling crystal nucleation and growth processes is immense, there are specific technical challenges to modeling. In general, rare events, such as nucleation cannot be simulated using a direct "brute force" molecular dynamics approach. The limited time and length scales that are accessible by conventional molecular dynamics simulations have inspired a number of advances to tackle problems that were considered outside the scope of molecular simulation. While general insights and features could be explored from efficient generic models, new methods paved the way to realistic crystal nucleation scenarios. The association of single ions in solvent environments, the mechanisms of motif formation, ripening reactions, and the self-organization of nanocrystals can now be investigated at the molecular level. The analysis of interactions with growth-controlling additives gives a new understanding of functionalized nanocrystals and the precipitation of composite materials. Copyright © 2011 WILEY-VCH Verlag GmbH & Co. KGaA, Weinheim.

Assessment of molecular events during in vitro re-epithelialization under honey-alginate matrix ambience

Energy Technology Data Exchange (ETDEWEB)

Barui, Ananya [Centre for Healthcare Science and Technology, BESU, Shibpur, Howrah 711103, West Bengal (India); Mandal, Naresh [Dept. of Electronics and Telecommunication Engg., BESU, Shibpur, Howrah 711103, West Bengal (India); Majumder, Subhadipa [Department of Biochemistry, University of Calcutta Ballygunge, Circular Road, Kolkata 700 019, West Bengal (India); Das, Raunak Kumar [School of Medical Science and Technology, IIT, Kharagpur 721 302, West Bengal (India); Sengupta, Sanghamitra [Department of Biochemistry, University of Calcutta Ballygunge, Circular Road, Kolkata 700 019, West Bengal (India); Banerjee, Provas [School of Medical Science and Technology, IIT, Kharagpur 721 302, West Bengal (India); Ray, Ajoy Kumar; RoyChaudhuri, Chirosree [Dept. of Electronics and Telecommunication Engg., BESU, Shibpur, Howrah 711103, West Bengal (India); Chatterjee, Jyotirmoy, E-mail: jchatterjee@smst.iitkgp.ernet.in [School of Medical Science and Technology, IIT, Kharagpur 721 302, West Bengal (India)

2013-08-01

Re-epithelialization is one of the most important stages of cutaneous regeneration and its success requires supportive micro-ambience which may be provided with suitable bio-matrix. Biocompatibility and efficacy of such bio-matrix in re-epithelialization could be explored by multimodal analysis of structural and functional attributes of in vitro wound healing model including evaluation of prime molecular expressions of the epithelial cells during repair. Present study examines the influence of honey-alginate and alginate matrices on re-epithelialization in keratinocyte (HaCaT) population in a 2-D wound model. Cellular viability, proliferation and cell–cell adhesion status were assessed during wound closure using live/dead cell assay and by evaluating expressions of Ki67, p63 and E-cadherin along-with % change in cellular electrical impedance. Efficacy of honey-alginate matrix in comparison to only alginate one was demonstrated by a quicker reduction in wound gap, improved cellular viability, enhanced expressions of Ki67, p63 and its isoforms (TAp63, ΔNp63) as well as E-cadherin. Faster restoration of electrical attribute (% of impedance change) after wounding also indicated better impact of honey-alginate matrix in re-epithelialization. - Highlights: • Role of honey based matrix is evaluated in wound re-epithelialization. • Healing impact of matrix studied in 2D in vitro keratinocyte (HaCaT) wound model. • Faster impedance restoration indicated rapid healing rate of HaCaT under honey. • PCR observations showed faster initiation of cell proliferation under honey. • ICC study indicated better up-regulation of healing markers under honey matrix.

Assessment of molecular events during in vitro re-epithelialization under honey-alginate matrix ambience

International Nuclear Information System (INIS)

Barui, Ananya; Mandal, Naresh; Majumder, Subhadipa; Das, Raunak Kumar; Sengupta, Sanghamitra; Banerjee, Provas; Ray, Ajoy Kumar; RoyChaudhuri, Chirosree; Chatterjee, Jyotirmoy

2013-01-01

Re-epithelialization is one of the most important stages of cutaneous regeneration and its success requires supportive micro-ambience which may be provided with suitable bio-matrix. Biocompatibility and efficacy of such bio-matrix in re-epithelialization could be explored by multimodal analysis of structural and functional attributes of in vitro wound healing model including evaluation of prime molecular expressions of the epithelial cells during repair. Present study examines the influence of honey-alginate and alginate matrices on re-epithelialization in keratinocyte (HaCaT) population in a 2-D wound model. Cellular viability, proliferation and cell–cell adhesion status were assessed during wound closure using live/dead cell assay and by evaluating expressions of Ki67, p63 and E-cadherin along-with % change in cellular electrical impedance. Efficacy of honey-alginate matrix in comparison to only alginate one was demonstrated by a quicker reduction in wound gap, improved cellular viability, enhanced expressions of Ki67, p63 and its isoforms (TAp63, ΔNp63) as well as E-cadherin. Faster restoration of electrical attribute (% of impedance change) after wounding also indicated better impact of honey-alginate matrix in re-epithelialization. - Highlights: • Role of honey based matrix is evaluated in wound re-epithelialization. • Healing impact of matrix studied in 2D in vitro keratinocyte (HaCaT) wound model. • Faster impedance restoration indicated rapid healing rate of HaCaT under honey. • PCR observations showed faster initiation of cell proliferation under honey. • ICC study indicated better up-regulation of healing markers under honey matrix

Equations of states for an ionic liquid under high pressure: A molecular dynamics simulation study

International Nuclear Information System (INIS)

Ribeiro, Mauro C.C.; Pádua, Agílio A.H.; Gomes, Margarida F.C.

2014-01-01

Highlights: • We compare different equation of states, EoS, for an ionic liquid under high pressure. • Molecular dynamics, MD, simulations have been used to evaluate the best EoS. • MD simulations show that a group contribution model can be extrapolated to P ∼ 1.0 GPa. • A perturbed hard-sphere EoS also fits the densities calculated by MD simulations. - Abstract: The high-pressure dependence of density given by empirical equation of states (EoS) for the ionic liquid 1-butyl-3-methylimidazolium trifluoromethanesulfonate (or triflate), [C 4 C 1 im][TfO], is compared with results obtained by molecular dynamics (MD) simulations. Two EoS proposed for [C 4 C 1 im][TfO] in the pressure range of tens of MPa, which give very different densities when extrapolated to pressures beyond the original experiments, are compared with a group contribution model (GCM). The MD simulations provide support that one of the empirical EoS and the GCM is valid in the pressure range of hundreds of MPa. As an alternative to these EoS that are based on modified Tait equations, it is shown that a perturbed hard-sphere EoS based on the Carnahan–Starling–van der Waals equation also fits the densities calculated by MD simulations of [C 4 C 1 im][TfO] up to ∼1.0 GPa

Shuttlecock-Shaped Molecular Rectifier: Asymmetric Electron Transport Coupled with Controlled Molecular Motion.

Science.gov (United States)

Ryu, Taekhee; Lansac, Yves; Jang, Yun Hee

2017-07-12

A fullerene derivative with five hydroxyphenyl groups attached around a pentagon, (4-HOC 6 H 4 ) 5 HC 60 (1), has shown an asymmetric current-voltage (I-V) curve in a conducting atomic force microscopy experiment on gold. Such molecular rectification has been ascribed to the asymmetric distribution of frontier molecular orbitals over its shuttlecock-shaped structure. Our nonequilibrium Green's function (NEGF) calculations based on density functional theory (DFT) indeed exhibit an asymmetric I-V curve for 1 standing up between two Au(111) electrodes, but the resulting rectification ratio (RR ∼ 3) is insufficient to explain the wide range of RR observed in experiments performed under a high bias voltage. Therefore, we formulate a hypothesis that high RR (>10) may come from molecular orientation switching induced by a strong electric field applied between two electrodes. Indeed, molecular dynamics simulations of a self-assembled monolayer of 1 on Au(111) show that the orientation of 1 can be switched between standing-up and lying-on-the-side configurations in a manner to align its molecular dipole moment with the direction of the applied electric field. The DFT-NEGF calculations taking into account such field-induced reorientation between up and side configurations indeed yield RR of ∼13, which agrees well with the experimental value obtained under a high bias voltage.

Renal Effects and Underlying Molecular Mechanisms of Long-Term Salt Content Diets in Spontaneously Hypertensive Rats

Science.gov (United States)

Berger, Rebeca Caldeira Machado; Vassallo, Paula Frizera; Crajoinas, Renato de Oliveira; Oliveira, Marilene Luzia; Martins, Flávia Letícia; Nogueira, Breno Valentim; Motta-Santos, Daisy; Araújo, Isabella Binotti; Forechi, Ludimila; Girardi, Adriana Castello Costa; Santos, Robson Augusto Souza; Mill, José Geraldo

2015-01-01

Several evidences have shown that salt excess is an important determinant of cardiovascular and renal derangement in hypertension. The present study aimed to investigate the renal effects of chronic high or low salt intake in the context of hypertension and to elucidate the molecular mechanisms underlying such effects. To this end, newly weaned male SHR were fed with diets only differing in NaCl content: normal salt (NS: 0.3%), low salt (LS: 0.03%), and high salt diet (HS: 3%) until 7 months of age. Analysis of renal function, morphology, and evaluation of the expression of the main molecular components involved in the renal handling of albumin, including podocyte slit-diaphragm proteins and proximal tubule endocytic receptors were performed. The relationship between diets and the balance of the renal angiotensin-converting enzyme (ACE) and ACE2 enzymes was also examined. HS produced glomerular hypertrophy and decreased ACE2 and nephrin expressions, loss of morphological integrity of the podocyte processes, and increased proteinuria, characterized by loss of albumin and high molecular weight proteins. Conversely, severe hypertension was attenuated and renal dysfunction was prevented by LS since proteinuria was much lower than in the NS SHRs. This was associated with a decrease in kidney ACE/ACE2 protein and activity ratio and increased cubilin renal expression. Taken together, these results suggest that LS attenuates hypertension progression in SHRs and preserves renal function. The mechanisms partially explaining these findings include modulation of the intrarenal ACE/ACE2 balance and the increased cubilin expression. Importantly, HS worsens hypertensive kidney injury and decreases the expression nephrin, a key component of the slit diaphragm. PMID:26495970

Renal Effects and Underlying Molecular Mechanisms of Long-Term Salt Content Diets in Spontaneously Hypertensive Rats.

Directory of Open Access Journals (Sweden)

Rebeca Caldeira Machado Berger

Full Text Available Several evidences have shown that salt excess is an important determinant of cardiovascular and renal derangement in hypertension. The present study aimed to investigate the renal effects of chronic high or low salt intake in the context of hypertension and to elucidate the molecular mechanisms underlying such effects. To this end, newly weaned male SHR were fed with diets only differing in NaCl content: normal salt (NS: 0.3%, low salt (LS: 0.03%, and high salt diet (HS: 3% until 7 months of age. Analysis of renal function, morphology, and evaluation of the expression of the main molecular components involved in the renal handling of albumin, including podocyte slit-diaphragm proteins and proximal tubule endocytic receptors were performed. The relationship between diets and the balance of the renal angiotensin-converting enzyme (ACE and ACE2 enzymes was also examined. HS produced glomerular hypertrophy and decreased ACE2 and nephrin expressions, loss of morphological integrity of the podocyte processes, and increased proteinuria, characterized by loss of albumin and high molecular weight proteins. Conversely, severe hypertension was attenuated and renal dysfunction was prevented by LS since proteinuria was much lower than in the NS SHRs. This was associated with a decrease in kidney ACE/ACE2 protein and activity ratio and increased cubilin renal expression. Taken together, these results suggest that LS attenuates hypertension progression in SHRs and preserves renal function. The mechanisms partially explaining these findings include modulation of the intrarenal ACE/ACE2 balance and the increased cubilin expression. Importantly, HS worsens hypertensive kidney injury and decreases the expression nephrin, a key component of the slit diaphragm.

A multiscale simulation technique for molecular electronics: design of a directed self-assembled molecular n-bit shift register memory device

International Nuclear Information System (INIS)

Lambropoulos, Nicholas A; Reimers, Jeffrey R; Crossley, Maxwell J; Hush, Noel S; Silverbrook, Kia

2013-01-01

A general method useful in molecular electronics design is developed that integrates modelling on the nano-scale (using quantum-chemical software) and on the micro-scale (using finite-element methods). It is applied to the design of an n-bit shift register memory that could conceivably be built using accessible technologies. To achieve this, the entire complex structure of the device would be built to atomic precision using feedback-controlled lithography to provide atomic-level control of silicon devices, controlled wet-chemical synthesis of molecular insulating pillars above the silicon, and controlled wet-chemical self-assembly of modular molecular devices to these pillars that connect to external metal electrodes (leads). The shift register consists of n connected cells that read data from an input electrode, pass it sequentially between the cells under the control of two external clock electrodes, and deliver it finally to an output device. The proposed cells are trimeric oligoporphyrin units whose internal states are manipulated to provide functionality, covalently connected to other cells via dipeptide linkages. Signals from the clock electrodes are conveyed by oligoporphyrin molecular wires, and μ-oxo porphyrin insulating columns are used as the supporting pillars. The developed multiscale modelling technique is applied to determine the characteristics of this molecular device, with in particular utilization of the inverted region for molecular electron-transfer processes shown to facilitate latching and control using exceptionally low energy costs per logic operation compared to standard CMOS shift register technology. (paper)

A multiscale simulation technique for molecular electronics: design of a directed self-assembled molecular n-bit shift register memory device

Science.gov (United States)

Lambropoulos, Nicholas A.; Reimers, Jeffrey R.; Crossley, Maxwell J.; Hush, Noel S.; Silverbrook, Kia

2013-12-01

A general method useful in molecular electronics design is developed that integrates modelling on the nano-scale (using quantum-chemical software) and on the micro-scale (using finite-element methods). It is applied to the design of an n-bit shift register memory that could conceivably be built using accessible technologies. To achieve this, the entire complex structure of the device would be built to atomic precision using feedback-controlled lithography to provide atomic-level control of silicon devices, controlled wet-chemical synthesis of molecular insulating pillars above the silicon, and controlled wet-chemical self-assembly of modular molecular devices to these pillars that connect to external metal electrodes (leads). The shift register consists of n connected cells that read data from an input electrode, pass it sequentially between the cells under the control of two external clock electrodes, and deliver it finally to an output device. The proposed cells are trimeric oligoporphyrin units whose internal states are manipulated to provide functionality, covalently connected to other cells via dipeptide linkages. Signals from the clock electrodes are conveyed by oligoporphyrin molecular wires, and μ-oxo porphyrin insulating columns are used as the supporting pillars. The developed multiscale modelling technique is applied to determine the characteristics of this molecular device, with in particular utilization of the inverted region for molecular electron-transfer processes shown to facilitate latching and control using exceptionally low energy costs per logic operation compared to standard CMOS shift register technology.

A multiscale simulation technique for molecular electronics: design of a directed self-assembled molecular n-bit shift register memory device.

Science.gov (United States)

Lambropoulos, Nicholas A; Reimers, Jeffrey R; Crossley, Maxwell J; Hush, Noel S; Silverbrook, Kia

2013-12-20

A general method useful in molecular electronics design is developed that integrates modelling on the nano-scale (using quantum-chemical software) and on the micro-scale (using finite-element methods). It is applied to the design of an n-bit shift register memory that could conceivably be built using accessible technologies. To achieve this, the entire complex structure of the device would be built to atomic precision using feedback-controlled lithography to provide atomic-level control of silicon devices, controlled wet-chemical synthesis of molecular insulating pillars above the silicon, and controlled wet-chemical self-assembly of modular molecular devices to these pillars that connect to external metal electrodes (leads). The shift register consists of n connected cells that read data from an input electrode, pass it sequentially between the cells under the control of two external clock electrodes, and deliver it finally to an output device. The proposed cells are trimeric oligoporphyrin units whose internal states are manipulated to provide functionality, covalently connected to other cells via dipeptide linkages. Signals from the clock electrodes are conveyed by oligoporphyrin molecular wires, and μ-oxo porphyrin insulating columns are used as the supporting pillars. The developed multiscale modelling technique is applied to determine the characteristics of this molecular device, with in particular utilization of the inverted region for molecular electron-transfer processes shown to facilitate latching and control using exceptionally low energy costs per logic operation compared to standard CMOS shift register technology.

Intrinsic bacterial biodegradation of petroleum contamination demonstrated in situ using natural abundance, molecular-level 14C analysis

International Nuclear Information System (INIS)

Slater, G.F.; Nelson, R.K.; Kile, B.M.; Reddy, C.M.

2006-01-01

Natural abundance, molecular-level C 14 analysis was combined with comprehensive gas chromatography (GC x GC) to investigate, in situ, the role of intrinsic biodegradation in the loss of petroleum hydrocarbons from the rocky, inter-tidal zone impacted by the Bouchard 120 oil spill. GC x GC analysis indicated accelerated losses of n-alkane components of the residual petroleum hydrocarbons between day 40 and day 50 after the spill. 14 C analysis of bacterial phospholipid fatty acids (PLFA) from the impacted zone on day 44 showed that the polyunsaturated fatty acids attributed to the photoautotrophic component of the microbial community had the same ( 14 C as the local dissolved inorganic carbon (DIG), indicating that this DIG was their carbon source. In contrast there was significant (C depletion in the saturated and mono-unsaturated PLFA indicating incorporation of petroleum carbon. This correlation between the observed accelerated n-alkane losses and microbial incorporation of (C-depleted carbon directly demonstrated, in situ, that intrinsic biodegradation was affecting the petroleum. Since the majority of organic contaminants originate from petroleum feed-stocks, in situ molecular-level 14 C analysis of microbial PLFA can provide insights into the occurrence and pathways of biodegradation of a wide range of organic contaminants. (Author)

Transport in aluminized RDX under shock compression explored using molecular dynamics simulations

International Nuclear Information System (INIS)

Losada, M; Chaudhuri, S

2014-01-01

Shock response of energetic materials is controlled by a combination of mechanical response, thermal, transport, and chemical properties. How these properties interplay in condensed-phase energetic materials is of fundamental interest for improving predictive capabilities. Due to unknown nature of chemistry during the evolution and growth of high-temperature regions within the energetic material (so called hot spots), the connection between reactive and unreactive equations of state contain a high degree of empiricism. In particular, chemistry in materials with high degree of heterogeneity such as aluminized HE is of interest. In order to identify shock compression states and transport properties in high-pressure/temperature (HP-HT) conditions, we use molecular dynamics (MD) simulations in conjunction with the multi-scale shock technique (MSST). Mean square displacement calculations enabled us to track the diffusivity of stable gas products. Among decomposition products, H 2 O and CO 2 are found to be the dominant diffusing species under compression conditions. Heat transport and diffusion rates in decomposed RDX are compared and the comparison shows that around 2000 K, transport can be a major contribution during propagation of the reaction front.

Charge-leveling and proper treatment of long-range electrostatics in all-atom molecular dynamics at constant pH.

Science.gov (United States)

Wallace, Jason A; Shen, Jana K

2012-11-14

Recent development of constant pH molecular dynamics (CpHMD) methods has offered promise for adding pH-stat in molecular dynamics simulations. However, until now the working pH molecular dynamics (pHMD) implementations are dependent in part or whole on implicit-solvent models. Here we show that proper treatment of long-range electrostatics and maintaining charge neutrality of the system are critical for extending the continuous pHMD framework to the all-atom representation. The former is achieved here by adding forces to titration coordinates due to long-range electrostatics based on the generalized reaction field method, while the latter is made possible by a charge-leveling technique that couples proton titration with simultaneous ionization or neutralization of a co-ion in solution. We test the new method using the pH-replica-exchange CpHMD simulations of a series of aliphatic dicarboxylic acids with varying carbon chain length. The average absolute deviation from the experimental pK(a) values is merely 0.18 units. The results show that accounting for the forces due to extended electrostatics removes the large random noise in propagating titration coordinates, while maintaining charge neutrality of the system improves the accuracy in the calculated electrostatic interaction between ionizable sites. Thus, we believe that the way is paved for realizing pH-controlled all-atom molecular dynamics in the near future.

Level and determinants of infant and under-five mortality in Wad-Medani Town, Sudan

Directory of Open Access Journals (Sweden)

Huda M Haroun

2007-01-01

Full Text Available Aim: This study aimed to determine the level of infant and under-five mortality rates and to examine the effect of socioeconomic, demographic and environmental factors on the health status of the children under five years. Methods: The data for this study were collected by means of a questionnaire addressed to women in Wad-Medani, Sudan. Three hundred women in the reproductive age (15-49 years were chosen randomly for this study. The data were analyzed statistically using the Statistical Package for Social Sciences (SPSS. Frequency distributions and a statistical test based on Chi-square for independence was conducted. Results: Infant mortality rate was 77 per 100 and child mortality rate was 67 per 100. The results revealed that immunization, child order, child birth weight, birth interval and contraceptive use had a significant influence on the mortality of children under the age of five. The mother′s level of education is highly significant on the mortality of children under five years old. Conclusions: The Ministry of Health should give greater attention to improving immunization services and concentrate on health education campaigns for mothers and for the community.

Antihypertrophic Effects of Small Molecules that Maintain Mitochondrial ATP Levels Under Hypoxia

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Hiroaki Nagai

2017-10-01

Full Text Available Since impaired mitochondrial ATP production in cardiomyocytes is thought to lead to heart failure, a drug that protects mitochondria and improves ATP production under disease conditions would be an attractive treatment option. In this study, we identified small-molecule drugs, including the anti-parasitic agent, ivermectin, that maintain mitochondrial ATP levels under hypoxia in cardiomyocytes. Mechanistically, transcriptomic analysis and gene silencing experiments revealed that ivermectin increased mitochondrial ATP production by inducing Cox6a2, a subunit of the mitochondrial respiratory chain. Furthermore, ivermectin inhibited the hypertrophic response of human induced pluripotent stem cell-derived cardiomyocytes. Pharmacological inhibition of importin β, one of the targets of ivermectin, exhibited protection against mitochondrial ATP decline and cardiomyocyte hypertrophy. These findings indicate that maintaining mitochondrial ATP under hypoxia may prevent hypertrophy and improve cardiac function, providing therapeutic options for mitochondrial dysfunction.

Determination of low levels of krypton in helium by gas chromatography

International Nuclear Information System (INIS)

Evans, D.L.; Mukherji, A.K.

1980-01-01

Krypton-helium mixture was used as an adsorbate for surface area measurement--. The surface area measurements depend on the accuracy with which the krypton concentration is known. Generally gas tanks supplied by Union Carbide provide a nominal value of 0.1% krypton in helium. The surface area measurements require, however, that the krypton concentraion be known to +- 0.001% or better. A standard plot of krypton volume in microliters vs the area under the curve as measured by a planimeter using the helium detector and Molecular Sieve 5A column was obtained. Results with a thermal conductivity detector using Molecular Sieve 5A and Carbon Molecular Sieve are also given. Low levels of krypton in helium can be measured with precision using either a helium or a thermal conductivity detector with Molecular Sieve 5A or Carbon Molecular Sieve columns. 2 figures, 1 table

Unraveling the effect of the hydration level on the molecular mobility of nanolayered polymeric systems.

Science.gov (United States)

Borges, João; Caridade, Sofia G; Silva, Joana M; Mano, João F

2015-02-01

This work investigates the influence of the hydration level on the molecular mobility and glass transition dynamics of freestanding chitosan/alginate (CHT/ALG) nanolayered systems. Nonconventional dynamic mechanical analysis identifies two relaxation processes assigned to the α-relaxation of the two biopolymers, respectively, CHT and ALG, when immersed in water/ethanol mixtures. This phenomenon explains the shape memory properties of the multilayered systems induced by hydration, thus constituting promising smart materials that would be of paramount importance in a plethora of research fields, including in the biomedical and biotechnological fields. © 2015 WILEY-VCH Verlag GmbH & Co. KGaA, Weinheim.

Endurance of lead-free assembly under board level drop test and thermal cycling

Energy Technology Data Exchange (ETDEWEB)

Xia Yanghua [State Key Laboratory of Functional Materials for Informatics, Shanghai Institute of Microsystem and Information Technology, Chinese Academy of Sciences, Shanghai 200050 (China)], E-mail: xia_yanghua@hotmail.com; Xie Xiaoming [State Key Laboratory of Functional Materials for Informatics, Shanghai Institute of Microsystem and Information Technology, Chinese Academy of Sciences, Shanghai 200050 (China)

2008-06-12

The reliability of lead-free electronic assemblies under board level drop test and thermal cycling was investigated. TSOP (thin small outline package) devices with FeNi leads were reflow soldered on FR4 PCB (printed circuit board) with Sn3.0Ag0.5Cu (wt%) solder. The effects of different PCB finishes (organic solderability preservative (OSP) and electroless nickel immersion gold (ENIG)) on the reliability performance were studied. The results show that the assemblies with ENIG finishes reveal better reliability performance than its OSP counterparts under drop test, however, the OSP samples outperform those with ENIG finishes under thermal cycling. The failure mechanism is different under these two test conditions: the solder joints fracture into the intermetallic compounds (IMCs) layer under drop test, and cracks initiate in the bulk solder under thermal cycling. The surface finishes have an effect on the failure mode. The propagation of crack in the ENIG case is along the device/solder interface, while in the case of OSP, the crack extends parallel to the solder/PCB interface.

High accuracy results for the energy levels of the molecular ions H+2, D+2 and HD+, up to J = 2

International Nuclear Information System (INIS)

Karr, J Ph; Hilico, L

2006-01-01

We present a nonrelativistic calculation of the rotation-vibration levels of the molecular ions H + 2 , D + 2 and HD + , relying on the diagonalization of the exact three-body Hamiltonian in a variational basis. The J = 2 levels are obtained with a very high accuracy of 10 -14 au (for most levels) representing an improvement by five orders of magnitude over previous calculations. The accuracy is also improved for the J = 1 levels of H + 2 and D + 2 with respect to earlier works. Moreover, we have computed the sensitivities of the energy levels with respect to the mass ratios, allowing these levels to be used for metrological purposes

Photoinduced diffusion molecular transport

Energy Technology Data Exchange (ETDEWEB)

Rozenbaum, Viktor M., E-mail: vik-roz@mail.ru, E-mail: litrakh@gmail.com [Chuiko Institute of Surface Chemistry, National Academy of Sciences of Ukraine, Generala Naumova St. 17, Kiev 03164 (Ukraine); Dekhtyar, Marina L. [Institute of Organic Chemistry, National Academy of Sciences of Ukraine, Murmanskaya St. 5, Kiev 02094 (Ukraine); Lin, Sheng Hsien [Department of Applied Chemistry, National Chiao Tung University, 1001 Ta Hsuen Road, Hsinchu 300, Taiwan (China); Trakhtenberg, Leonid I., E-mail: vik-roz@mail.ru, E-mail: litrakh@gmail.com [Semenov Institute of Chemical Physics, Russian Academy of Sciences, Kosygin Street 4, Moscow 119991, Russia and Moscow Institute of Physics and Technology (State University), Institutskii Per. 9, Dolgoprudnyi, Moscow Region 141700 (Russian Federation)

2016-08-14

We consider a Brownian photomotor, namely, the directed motion of a nanoparticle in an asymmetric periodic potential under the action of periodic rectangular resonant laser pulses which cause charge redistribution in the particle. Based on the kinetics for the photoinduced electron redistribution between two or three energy levels of the particle, the time dependence of its potential energy is derived and the average directed velocity is calculated in the high-temperature approximation (when the spatial amplitude of potential energy fluctuations is small relative to the thermal energy). The thus developed theory of photoinduced molecular transport appears applicable not only to conventional dichotomous Brownian motors (with only two possible potential profiles) but also to a much wider variety of molecular nanomachines. The distinction between the realistic time dependence of the potential energy and that for a dichotomous process (a step function) is represented in terms of relaxation times (they can differ on the time intervals of the dichotomous process). As shown, a Brownian photomotor has the maximum average directed velocity at (i) large laser pulse intensities (resulting in short relaxation times on laser-on intervals) and (ii) excited state lifetimes long enough to permit efficient photoexcitation but still much shorter than laser-off intervals. A Brownian photomotor with optimized parameters is exemplified by a cylindrically shaped semiconductor nanocluster which moves directly along a polar substrate due to periodically photoinduced dipole moment (caused by the repetitive excited electron transitions to a non-resonant level of the nanocylinder surface impurity).

Study on the Variation of Groundwater Level under Time-varying Recharge

Science.gov (United States)

Wu, Ming-Chang; Hsieh, Ping-Cheng

2017-04-01

The slopes of the suburbs come to important areas by focusing on the work of soil and water conservation in recent years. The water table inside the aquifer is affected by rainfall, geology and topography, which will result in the change of groundwater discharge and water level. Currently, the way to obtain water table information is to set up the observation wells; however, owing to that the cost of equipment and the wells excavated is too expensive, we develop a mathematical model instead, which might help us to simulate the groundwater level variation. In this study, we will discuss the groundwater level change in a sloping unconfined aquifer with impermeable bottom under time-varying rainfall events. Referring to Child (1971), we employ the Boussinesq equation as the governing equation, and apply the General Integral Transforms Method (GITM) to analyzing the groundwater level after linearizing the Boussinesq equation. After comparing the solution with Verhoest & Troch (2000) and Bansal & Das (2010), we get satisfactory results. To sum up, we have presented an alternative approach to solve the linearized Boussinesq equation for the response of groundwater level in a sloping unconfined aquifer. The present analytical results combine the effect of bottom slope and the time-varying recharge pattern on the water table fluctuations. Owing to the limitation and difficulty of measuring the groundwater level directly, we develop such a mathematical model that we can predict or simulate the variation of groundwater level affected by any rainfall events in advance.

Production of tropical forage grasses under different shading levels

Directory of Open Access Journals (Sweden)

Francisco Eduardo Torres

2017-12-01

Full Text Available This study aimed to evaluate the forage production of three tropical forage grasses under different shading levels. The experiment was conducted in a greenhouse at Universidade Estadual de Mato Grosso do Sul, University Unit of Aquidauana (UEMS/UUA, in a soil classified as Ultisol sandy loam texture. The treatments consisted of three grasses species combinations (B. brizantha cv. Marandu, B. decumbens cv. Basilisck and Panicum maximum cv. Tanzania, submitted to four shading levels (0, 30, 50 and 75%, arranged in a completely randomized blocks design in a factorial 3 x 4, with eight replications. After harvest, the plants were separated into shoot and roots for determination of shoot fresh mass (SFM, shoot dry mass (SDM and roots dry mass production. After analysis of variance, the qualitative factor was subjected to comparison of averages by Tukey’s test, and the quantitative factor to analysis of polynomial regression, being interactions appropriately unfolded. It was verified that B. decumbens, by its linearly increasing production of forage and less decrease of root formation, is the most recommended for shading conditions compared to grasses Tanzania and Marandu.

SERS- and Electrochemically Active 3D Plasmonic Liquid Marbles for Molecular-Level Spectroelectrochemical Investigation of Microliter Reactions.

Science.gov (United States)

Koh, Charlynn Sher Lin; Lee, Hiang Kwee; Phan-Quang, Gia Chuong; Han, Xuemei; Lee, Mian Rong; Yang, Zhe; Ling, Xing Yi

2017-07-17

Liquid marbles are emergent microreactors owing to their isolated environment and the flexibility of materials used. Plasmonic liquid marbles (PLMs) are demonstrated as the smallest spectroelectrochemical microliter-scale reactor for concurrent spectro- and electrochemical analyses. The three-dimensional Ag shell of PLMs are exploited as a bifunctional surface-enhanced Raman scattering (SERS) platform and working electrode for redox process modulation. The combination of SERS and electrochemistry (EC) capabilities enables in situ molecular read-out of transient electrochemical species, and elucidate the potential-dependent and multi-step reaction dynamics. The 3D configuration of our PLM-based EC-SERS system exhibits 2-fold and 10-fold superior electrochemical and SERS performance than conventional 2D platforms. The rich molecular-level electrochemical insights and excellent EC-SERS capabilities offered by our 3D spectroelectrochemical system are pertinent in charge transfer processes. © 2017 Wiley-VCH Verlag GmbH & Co. KGaA, Weinheim.

Projected global ground-level ozone impacts on vegetation under different emission and climate scenarios

Directory of Open Access Journals (Sweden)

P. Sicard

2017-10-01

Full Text Available The impact of ground-level ozone (O3 on vegetation is largely under-investigated at the global scale despite large areas worldwide that are exposed to high surface O3 levels. To explore future potential impacts of O3 on vegetation, we compared historical and projected surface O3 concentrations simulated by six global atmospheric chemistry transport models on the basis of three representative concentration pathways emission scenarios (i.e. RCP2.6, 4.5, 8.5. To assess changes in the potential surface O3 threat to vegetation at the global scale, we used the AOT40 metric. Results point out a significant exceedance of AOT40 in comparison with the recommendations of UNECE for the protection of vegetation. In fact, many areas of the Northern Hemisphere show that AOT40-based critical levels will be exceeded by a factor of at least 10 under RCP8.5. Changes in surface O3 by 2100 worldwide range from about +4–5 ppb in the RCP8.5 scenario to reductions of about 2–10 ppb in the most optimistic scenario, RCP2.6. The risk of O3 injury for vegetation, through the potential O3 impact on photosynthetic assimilation, decreased by 61 and 47 % under RCP2.6 and RCP4.5, respectively, and increased by 70 % under RCP8.5. Key biodiversity areas in southern and northern Asia, central Africa and North America were identified as being at risk from high O3 concentrations.

Molecular mechanisms underlying memory consolidation of taste information in the cortex.

Science.gov (United States)

Gal-Ben-Ari, Shunit; Rosenblum, Kobi

2011-01-01

The senses of taste and odor are both chemical senses. However, whereas an organism can detect an odor at a relatively long distance from its source, taste serves as the ultimate proximate gatekeeper of food intake: it helps in avoiding poisons and consuming beneficial substances. The automatic reaction to a given taste has been developed during evolution and is well adapted to conditions that may occur with high probability during the lifetime of an organism. However, in addition to this automatic reaction, animals can learn and remember tastes, together with their positive or negative values, with high precision and in light of minimal experience. This ability of mammalians to learn and remember tastes has been studied extensively in rodents through application of reasonably simple and well defined behavioral paradigms. The learning process follows a temporal continuum similar to those of other memories: acquisition, consolidation, retrieval, relearning, and reconsolidation. Moreover, inhibiting protein synthesis in the gustatory cortex (GC) specifically affects the consolidation phase of taste memory, i.e., the transformation of short- to long-term memory, in keeping with the general biochemical definition of memory consolidation. This review aims to present a general background of taste learning, and to focus on recent findings regarding the molecular mechanisms underlying taste-memory consolidation in the GC. Specifically, the roles of neurotransmitters, neuromodulators, immediate early genes, and translation regulation are addressed.

Molecular mechanisms underlying memory consolidation of taste information in the cortex

Directory of Open Access Journals (Sweden)

Shunit eGal-Ben-Ari

2012-01-01

Full Text Available The senses of taste and odor are both chemical senses. However, whereas an organism can detect an odor at a relatively long distance from its source, taste serves as the ultimate proximate gatekeeper of food intake: it helps in avoiding poisons and consuming beneficial substances. The automatic reaction to a given taste has been developed during evolution and is well adapted to conditions that may occur with high probability during the lifetime of an organism. However, in addition to this automatic reaction, animals can learn and remember tastes, together with their positive or negative values, with high precision and in light of minimal experience. This ability of mammalians to learn and remember tastes has been studied extensively in rodents through application of reasonably simple and well defined behavioral paradigms. The learning process follows a temporal continuum similar to those of other memories: acquisition, consolidation, retrieval, relearning, and reconsolidation. Moreover, inhibiting protein synthesis in the gustatory cortex specifically affects the consolidation phase of taste memory, i.e., the transformation of short- to long-term memory, in keeping with the general biochemical definition of memory consolidation. This review aims to present a general background of taste learning, and to focus on recent findings regarding the molecular mechanisms underlying taste memory consolidation in the gustatory cortex. Specifically, the role of neurotransmitters, meuromodulators, immediate early genes, and translation regulation are addressed.

Modulation of Human Plasma Fibronectin Levels Following Exercise,

Science.gov (United States)

1988-01-01

forms of this large molecular weight (440 kilodaltons) glycoprotein,(17. While the tissue type is cell-associated and important to cell adhesion and...increased under conditions of pathology, such as in obesity (6). cancer (3). proteinuria (4). diabetic retinopathy (5). and preeclampsia (27). in the absence...Res. 1977: 22:709-716. 27. Stubbs. T.M.. Lazarchick. J.. and Horger. E.O. Plasma fibronectin levels in preeclampsia : A possible biochemical marker

Morphological and molecular features of some freshwater prawn species under genus Macrobrachium Spence Bate, 1868 (Crustacea: Decapoda: Palaemonidae) from Myanmar.

Science.gov (United States)

Mar, Win; Kang, Peng-Fei; Mao, Bin; Wang, Yu-Feng

2018-02-28

Myanmar is abundant in lakes and rivers, yet only a few investigations on the fauna of shrimps and prawns have been conducted and no molecular characteristics of prawn species have been described. This study reveals the morphologically identification of five freshwater prawn species under the genus Macrobrachium, including M. cavernicola, M. australiense, M. johnsoni, M. josephi and Macrobrachium sp.WMY-2017. As there was no previous record and information concerning with M. australiense, M. johnsoni, M. josephi and Macrobrachium sp. WMY-2017, they were regarded as the first record from Myanmar. A fragment of Mitochondrial Cytochrome Oxidase I Gene (COI) was amplified successfully from three studied species: M. australiense, M. josephi, and Macrobrachium sp.WMY-2017. The interspecific divergences of studied species varied from 0.01 to 0.15. The phylogenetic tree based on COI fragment sequences showed that M. australiense was closely related to M. rosenbergii, while Macrobrachium sp. WMY-2017 was closest to M. josephi. The results of molecular phylogeny has clarified the relationship within the genus Macrobrachium and represents the first step toward understanding the pattern of speciation base on molecular approach in Myanmar.

Experimental investigation of channel avulsion frequency on river deltas under rising sea levels

Science.gov (United States)

Silvestre, J.; Chadwick, A. J.; Steele, S.; Lamb, M. P.

2017-12-01

River deltas are low-relief landscapes that are socioeconomically important; they are home to over half a billion people worldwide. Many deltas are built by cycles of lobe growth punctuated by abrupt channel shifts, or avulsions, which often reoccur at a similar location and with a regular frequency. Previous experimental work has investigated the effect of hydrodynamic backwater in controlling channel avulsion location and timing on deltas under constant sea level conditions, but it is unclear how sea-level rise impacts avulsion dynamics. We present results from a flume experiment designed to isolate the role of relative sea-level rise on the evolution of a backwater-influenced delta. The experiment was conducted in the river-ocean facility at Caltech, where a 7m long, 14cm wide alluvial river drains into a 6m by 3m "ocean" basin. The experimental delta grew under subcritical flow, a persistent backwater zone, and a range of sea level rise rates. Without sea level rise, lobe progradation produced in-channel aggradation and periodic avulsions every 3.6 ± 0.9 hours, which corresponded to when channels aggraded to approximately one-half of their flow depth. With a modest rate of sea-level rise (0.25 mm/hr), we observed enhanced aggradation in the backwater zone, causing channels to aggrade more quickly and avulse more frequently (every 2.1 ± 0.6 hours). In future work, we expect further increases in the rate of relative sea-level rise to cause avulsion frequency to decrease as the delta drowns and the backwater zone retreats upstream. Experimental results can serve as tests of numerical models that are needed for hazard mitigation and coastal sustainability efforts on drowning deltas.

Electron Transport through Porphyrin Molecular Junctions

Science.gov (United States)

Zhou, Qi

The goal of this work is to study the properties that would affect the electron transport through a porphyrin molecular junction. This work contributes to the field of electron transport in molecular junctions in the following 3 aspects. First of all, by carrying out experiments comparing the conductance of the iron (III) porphyrin (protected) and the free base porphyrin (protected), it is confirmed that the molecular energy level broadening and shifting occurs for porphyrin molecules when coupled with the metal electrodes, and this level broadening and shifting plays an important role in the electron transport through molecular junctions. Secondly, by carrying out an in-situ deprotection of the acetyl-protected free base porphyrin molecules, it is found out that the presence of acetyl groups reduces the conductance. Thirdly, by incorporating the Matrix-assisted laser desorption/ionization (MALDI) spectrum and the in-situ deprotection prior to formation of molecular junctions, it allows a more precise understanding of the molecules involved in the formation of molecular junctions, and therefore allows an accurate analysis of the conductance histogram. The molecules are prepared by self-assembly and the junctions are formed using a Scanning Tunneling Microscopy (STM) molecular break junction technique. The porphyrin molecules are characterized by MALDI in solution before self-assembly to a gold/mica substrate. The self-assembled monolayers (SAMs) of porphyrins on gold are characterized by Ultraviolet-visible (UV-Vis) reflection spectroscopy to confirm that the molecules are attached to the substrate. The SAMs are then characterized by Angle-Resolved X-ray photoelectron spectroscopy (ARXPS) to determine the thickness and the average molecular orientation of the molecular layer. The electron transport is measured by conductance-displacement (G-S) experiments under a given bias (-0.4V). The conductance value of a single molecule is identified by a statistical analysis

Actinides and environmental interfaces: striving for molecular-level understanding

International Nuclear Information System (INIS)

Heino Nitsche

2005-01-01

Actinides can undergo a variety of complex chemical reactions in the environment. In addition to the formation of solid precipitates, colloids and dissolved solution species common to aqueous systems, actinide ions can interact with the surrounding geo and biomedia to change oxidation states or sorb on surfaces and colloids. The rate of migration is determined by aqueous solubility, and interactions with solid surfaces such as minerals, soils, natural organic matter, and soil microorganisms Sorption of aqueous actinide species on biological and geological matrices can be quantitatively described by a surface complexation or site-binding model. The disadvantage of this model is the difficulty in the experimental determination of the model parameters and surface reaction constants. Usually, a set of surface reactions and species are proposed based on knowledge of the solution speciation of the solute, and the reaction constants are usually derived by fitting computer-calculated absorption curves to experimental data. Because this process typically involves a large number of potentially adjustable parameters, it is likely to lead to non-unique parameter fitting and does not always result in a consistent set of parameters for the same systems. A fundamental molecular-level understanding of sorption processes of actinides on environmental surfaces is required to better understand and predict their transport behavior in nature. Several different surface spectroscopic techniques have been applied to the characterization of the adsorbed species and surface reactions and a direct determination of the sorbed species and surface reactions has become possible. The non-linear optical techniques of second harmonic and sum frequency generation (SHG and SFG) are ideally suited to study surfaces and interfaces of mineral oxides, biosurfactants and biopolymers, organic adlayers adsorbed on solid/mineral surfaces and soil organic matter, including humic and fulvic acids. Resonant

Opposite photo-induced deformations in azobenzene-containing polymers with different molecular architecture: Molecular dynamics study

International Nuclear Information System (INIS)

Ilnytskyi, Jaroslav M.; Neher, Dieter; Saphiannikova, Marina

2011-01-01

Photo-induced deformations in azobenzene-containing polymers (azo-polymers) are central to a number of applications, such as optical storage and fabrication of diffractive elements. The microscopic nature of the underlying opto-mechanical coupling is yet not clear. In this study, we address the experimental finding that the scenario of the effects depends on molecular architecture of the used azo-polymer. Typically, opposite deformations in respect to the direction of light polarization are observed for liquid crystalline and amorphous azo-polymers. In this study, we undertake molecular dynamics simulations of two different models that mimic these two types of azo-polymers. We employ hybrid force field modeling and consider only trans-isomers of azobenzene, represented as Gay-Berne sites. The effect of illumination on the orientation of the chromophores is considered on the level of orientational hole burning and emphasis is given to the resulting deformation of the polymer matrix. We reproduce deformations of opposite sign for the two models being considered here and discuss the relevant microscopic mechanisms in both cases.

Intrinsic work function of molecular films

International Nuclear Information System (INIS)

Ivančo, Ján

2012-01-01

The electronic properties of molecular films are analysed with the consideration of the molecular orientation. The study demonstrates that surfaces of electroactive oligomeric molecular films can be classified—analogously to the elemental surfaces—by their intrinsic work functions. The intrinsic work function of molecular films is correlated with their ionisation energies; again, the behaviour is analogous to the correlation existing between the first ionisation energy of elements and the work function of the corresponding elemental surfaces. The proposed intrinsic work-function concept suggests that the mechanism for the energy-level alignment at the interfaces associated with molecular films is virtually controlled by work functions of materials brought into the contact. - Highlights: ► Molecular films exhibit their own (intrinsic) work function. ► Intrinsic work function is correlated with ionisation energy of molecular films. ► Intrinsic work function determines dipole at interface with a particular surface. ► Surface vacuum-level change upon film growth does not relate to interfacial dipole.

Phylogenetic and Molecular Evolutionary Analysis of Mitophagy Receptors under Hypoxic Conditions

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Xiaomei Wu

2017-07-01

Full Text Available As animals evolved to use oxygen as the main strategy to produce ATP through the process of mitochondrial oxidative phosphorylation, the ability to adapt to fluctuating oxygen concentrations is a crucial component of evolutionary pressure. Three mitophagy receptors, FUNDC1, BNIP3 and NIX, induce the removal of dysfunctional mitochondria (mitophagy under prolonged hypoxic conditions in mammalian cells, to maintain oxygen homeostasis and prevent cell death. However, the evolutionary origins and structure-function relationships of these receptors remain poorly understood. Here, we found that FUN14 domain-containing proteins are present in archaeal, bacterial and eukaryotic genomes, while the family of BNIP3 domain-containing proteins evolved from early animals. We investigated conservation patterns of the critical amino acid residues of the human mitophagy receptors. These residues are involved in receptor regulation, mainly through phosphorylation, and in interaction with LC3 on the phagophore. Whereas FUNDC1 may be able to bind to LC3 under the control of post-translational regulations during the early evolution of vertebrates, BINP3 and NIX had already gained the ability for LC3 binding in early invertebrates. Moreover, FUNDC1 and BNIP3 each lack a layer of phosphorylation regulation in fishes that is conserved in land vertebrates. Molecular evolutionary analysis revealed that BNIP3 and NIX, as the targets of oxygen sensing HIF-1α, showed higher rates of substitution in fishes than in mammals. Conversely, FUNDC1 and its regulator MARCH5 showed higher rates of substitution in mammals. Thus, we postulate that the structural traces of mitophagy receptors in land vertebrates and fishes may reflect the process of vertebrate transition from water onto land, during which the changes in atmospheric oxygen concentrations acted as a selection force in vertebrate evolution. In conclusion, our study, combined with previous experimental results, shows that

Fatigue of graphite/epoxy /0/90/45/-45/s laminates under dual stress levels

Science.gov (United States)

Yang, J. N.; Jones, D. L.

1982-01-01

A model for the prediction of loading sequence effects on the statistical distribution of fatigue life and residual strength in composite materials is generalized and applied to (0/90/45/-45)s graphite/epoxy laminates. Load sequence effects are found to be caused by both the difference in residual strength when failure occurs (boundary effect) and the effect of previously applied loads (memory effect). The model allows the isolation of these two effects, and the estimation of memory effect magnitudes under dual fatigue loading levels. It is shown that the material memory effect is insignificant, and that correlations between predictions of the number of early failures agree with the verification tests, as do predictions of fatigue life and residual strength degradation under dual stress levels.

Molecular similarity measures.

Science.gov (United States)

Maggiora, Gerald M; Shanmugasundaram, Veerabahu

2011-01-01

Molecular similarity is a pervasive concept in chemistry. It is essential to many aspects of chemical reasoning and analysis and is perhaps the fundamental assumption underlying medicinal chemistry. Dissimilarity, the complement of similarity, also plays a major role in a growing number of applications of molecular diversity in combinatorial chemistry, high-throughput screening, and related fields. How molecular information is represented, called the representation problem, is important to the type of molecular similarity analysis (MSA) that can be carried out in any given situation. In this work, four types of mathematical structure are used to represent molecular information: sets, graphs, vectors, and functions. Molecular similarity is a pairwise relationship that induces structure into sets of molecules, giving rise to the concept of chemical space. Although all three concepts - molecular similarity, molecular representation, and chemical space - are treated in this chapter, the emphasis is on molecular similarity measures. Similarity measures, also called similarity coefficients or indices, are functions that map pairs of compatible molecular representations that are of the same mathematical form into real numbers usually, but not always, lying on the unit interval. This chapter presents a somewhat pedagogical discussion of many types of molecular similarity measures, their strengths and limitations, and their relationship to one another. An expanded account of the material on chemical spaces presented in the first edition of this book is also provided. It includes a discussion of the topography of activity landscapes and the role that activity cliffs in these landscapes play in structure-activity studies.

Aspects of two-level systems under external time-dependent fields

Energy Technology Data Exchange (ETDEWEB)

Bagrov, V.G.; Wreszinski, W.F. [Tomsk State University and Tomsk Institute of High Current Electronics (Russian Federation); Barata, J.C.A.; Gitman D.M. [Universidade de Sao Paulo, Instituto de Fisica (Brazil)]. E-mails: jbarata@fma.if.usp.br; gitman@fma.if.usp.br

2001-12-14

The dynamics of two-level systems in time-dependent backgrounds is under consideration. We present some new exact solutions in special backgrounds decaying in time. On the other hand, following ideas of Feynman et al, we discuss in detail the possibility of reducing the quantum dynamics to a classical Hamiltonian system. This, in particular, opens the possibility of directly applying powerful methods of classical mechanics (e.g. KAM methods) to study the quantum system. Following such an approach, we draw conclusions of relevance for 'quantum chaos' when the external background is periodic or quasi-periodic in time. (author)

Molecular orientation and electronic structure at organic heterojunction interfaces

Energy Technology Data Exchange (ETDEWEB)

Zhong, Shu [Department of Chemistry, National University of Singapore, 3 Science Drive 3, 117543 Singapore (Singapore); Zhong, Jian Qiang; Wee, Andrew T.S. [Department of Physics, National University of Singapore, 2 Science Drive 3, 117542 Singapore (Singapore); Chen, Wei, E-mail: phycw@nus.edu.sg [Department of Chemistry, National University of Singapore, 3 Science Drive 3, 117543 Singapore (Singapore); Department of Physics, National University of Singapore, 2 Science Drive 3, 117542 Singapore (Singapore); National University of Singapore (Suzhou) Research Institute, Suzhou (China)

2015-10-01

Highlights: • Molecular orientation at the organic heterojunction interfaces. • Energy level alignments at the organic heterojunction interfaces. • Gap-states mediated interfacial energy level alignment. - Abstract: Due to the highly anisotropic nature of π-conjugated molecules, the molecular orientation in organic thin films can significantly affect light absorption, charge transport, energy level alignment (ELA) and hence device performance. Synchrotron-based near-edge X-ray absorption fine structure (NEXAFS) spectroscopy represents a powerful technique for probing molecular orientation. The aim of this review paper is to provide a balanced assessment on the investigation of molecular orientation at the organic–organic heterojunction (OOH) interface by NEXAFS, as well as the gap-states mediated orientation dependent energy level alignment at OOH interfaces. We highlight recent progress in elucidating molecular orientation at OOH interfaces dominated by various interfacial interactions, gap-states controlled orientation dependent energy level alignments at OOH interfaces, and the manipulations of molecular orientation and ELA in OOH.

Local adaptation at the transcriptome level in brown trout: Evidence from early life history temperature genomic reaction norms

DEFF Research Database (Denmark)

Meier, Kristian; Hansen, Michael Møller; Normandeau, Eric

2014-01-01

Local adaptation and its underlying molecular basis has long been a key focus in evolutionary biology. There has recently been increased interest in the evolutionary role of plasticity and the molecular mechanisms underlying local adaptation. Using transcriptome analysis, we assessed differences....... These included genes involved in immune- and stress response. We observed less plasticity in the resident as compared to the anadromous populations, possibly reflecting that the degree of environmental heterogeneity encountered by individuals throughout their life cycle will select for variable level...... of phenotypic plasticity at the transcriptome level. Our study demonstrates the usefulness of transcriptome approaches to identify genes with different temperature reaction norms. The responses observed suggest that populations may vary in their susceptibility to climate change....

Charge transport through molecular rods with reduced pi-conjugation.

Science.gov (United States)

Lörtscher, Emanuel; Elbing, Mark; Tschudy, Meinrad; von Hänisch, Carsten; Weber, Heiko B; Mayor, Marcel; Riel, Heike

2008-10-24

A series of oligophenylene rods of increasing lengths is synthesized to investigate the charge-transport mechanisms. Methyl groups are attached to the phenyl rings to weaken the electronic overlap of the pi-subsystems along the molecular backbones. Out-of-plane rotation of the phenyl rings is confirmed in the solid state by means of X-ray analysis and in solution by using UV/Vis spectroscopy. The influence of the reduced pi-conjugation on the resonant charge transport is studied at the single-molecule level by using the mechanically controllable break-junction technique. Experiments are performed under ultra-high-vacuum conditions at low temperature (50 K). A linear increase of the conductance gap with increasing number of phenyl rings (from 260 meV for one ring to 580 meV for four rings) is revealed. In addition, the absolute conductance of the first resonant peaks does not depend on the length of the molecular wire. Resonant transport through the first molecular orbital is found to be dominated by charge-carrier injection into the molecule, rather than by the intrinsic resistance of the molecular wire length.

Molecular dynamics for irradiation driven chemistry: application to the FEBID process*

Science.gov (United States)

Sushko, Gennady B.; Solov'yov, Ilia A.; Solov'yov, Andrey V.

2016-10-01

A new molecular dynamics (MD) approach for computer simulations of irradiation driven chemical transformations of complex molecular systems is suggested. The approach is based on the fact that irradiation induced quantum transformations can often be treated as random, fast and local processes involving small molecules or molecular fragments. We advocate that the quantum transformations, such as molecular bond breaks, creation and annihilation of dangling bonds, electronic charge redistributions, changes in molecular topologies, etc., could be incorporated locally into the molecular force fields that describe the classical MD of complex molecular systems under irradiation. The proposed irradiation driven molecular dynamics (IDMD) methodology is designed for the molecular level description of the irradiation driven chemistry. The IDMD approach is implemented into the MBN Explorer software package capable to operate with a large library of classical potentials, many-body force fields and their combinations. IDMD opens a broad range of possibilities for modelling of irradiation driven modifications and chemistry of complex molecular systems ranging from radiotherapy cancer treatments to the modern technologies such as focused electron beam deposition (FEBID). As an example, the new methodology is applied for studying the irradiation driven chemistry caused by FEBID of tungsten hexacarbonyl W(CO)6 precursor molecules on a hydroxylated SiO2 surface. It is demonstrated that knowing the interaction parameters for the fragments of the molecular system arising in the course of irradiation one can reproduce reasonably well experimental observations and make predictions about the morphology and molecular composition of nanostructures that emerge on the surface during the FEBID process.

Molecular modeling of nucleic Acid structure: electrostatics and solvation.

Science.gov (United States)

Bergonzo, Christina; Galindo-Murillo, Rodrigo; Cheatham, Thomas E

2014-12-19

This unit presents an overview of computer simulation techniques as applied to nucleic acid systems, ranging from simple in vacuo molecular modeling techniques to more complete all-atom molecular dynamics treatments that include an explicit representation of the environment. The third in a series of four units, this unit focuses on critical issues in solvation and the treatment of electrostatics. UNITS 7.5 & 7.8 introduced the modeling of nucleic acid structure at the molecular level. This included a discussion of how to generate an initial model, how to evaluate the utility or reliability of a given model, and ultimately how to manipulate this model to better understand its structure, dynamics, and interactions. Subject to an appropriate representation of the energy, such as a specifically parameterized empirical force field, the techniques of minimization and Monte Carlo simulation, as well as molecular dynamics (MD) methods, were introduced as a way of sampling conformational space for a better understanding of the relevance of a given model. This discussion highlighted the major limitations with modeling in general. When sampling conformational space effectively, difficult issues are encountered, such as multiple minima or conformational sampling problems, and accurately representing the underlying energy of interaction. In order to provide a realistic model of the underlying energetics for nucleic acids in their native environments, it is crucial to include some representation of solvation (by water) and also to properly treat the electrostatic interactions. These subjects are discussed in detail in this unit. Copyright © 2014 John Wiley & Sons, Inc.

Discovery of molecular mechanism of a clinical herbal formula upregulating serum HDL-c levels in treatment of metabolic syndrome by in vivo and computational studies.

Science.gov (United States)

Chen, Meimei; Yang, Fafu; Kang, Jie; Gan, Huijuan; Lai, Xinmei; Gao, Yuxing

2018-01-15

Decreased HDL cholesterol (HDL-c) is considered as an independent risk factor of cardiovascular disease in metabolic syndrome (Mets). Wendan decoction (WDD), a famous clinical traditional Chinese medicine formula in Mets in China, which can obviously up-regulate serum HDL-c levels in Mets. However, till now, the molecular mechanism of up-regulation still remained unclear. In this study, an integrated approach that combined serum ABCA1 in vivo assay, QSAR modeling and molecular docking was developed to explore the molecular mechanism and chemical substance basis of WDD upregulating HDL-c levels. Compared with Mets model group, serum ABCA1 and HDL-c levels intervened by two different doses of WDD for two weeks were significantly up-regulated. Then, kohonen and LDA were applied to develop QSAR models for ABCA1 up-regulators based flavonoids. The derived QSAR model produced the overall accuracy of 100%, a very powerful tool for screening ABCA1 up-regulators. The QSAR model prediction revealed 67 flavonoids in WDD were ABCA1 up-regulators. Finally, they were subjected to the molecular docking to understand their roles in up-regulating ABCA1 expression, which led to discovery of 23 ABCA1 up-regulators targeting LXR beta. Overall, QSAR modeling and docking studies well accounted for the observed in vivo activities of ABCA1 affected by WDD. Copyright © 2017 Elsevier Ltd. All rights reserved.

GnRH mRNA levels in male three-spined sticklebacks, Gasterosteus aculeatus, under different reproductive conditions.

Science.gov (United States)

Shao, Yi Ta; Tseng, Yung Che; Chang, Chia-Hao; Yan, Hong Young; Hwang, Pung Pung; Borg, Bertil

2015-02-01

In vertebrates, reproduction is regulated by the brain-pituitary-gonad (BPG) axis, where the gonadotropin-releasing hormone (GnRH) is one of the key components. However, very little is known about the possible role of GnRH in the environmental and feedback control of fish reproduction. To investigate this, full-length gnrh2 (chicken GnRH II) and gnrh3 (salmon GnRH) sequences of male three-spined sticklebacks (Gasterosteus aculeatus), which are clustered with the taxa of the same GnRH type as other Euteleostei, were cloned and annotated. gnrh1 is absent in this species. The mRNA levels of gnrh2 and gnrh3 in the sticklebacks' brain were measured under breeding and post-breeding conditions as well as in castrated and sham-operated breeding fish and castrated/sham-operated fish kept under long-day (LD 16:8) and short-day (LD 8:16) conditions. Fully breeding males had considerably higher mRNA levels of gnrh2 and gnrh3 in the thalamus (Th) and in the telencephalon and preoptic area (T+POA), respectively, than post-breeding males. Sham-operated breeding males have higher gnrh3 mRNA levels than the corresponding castrated males. Moreover, higher gnrh2 mRNA levels in the Th and higher gnrh3 mRNA levels in the T+POA and hypothalamus (HypTh) were also found in long-day sham-operated males than in sham-operated fish kept under an inhibitory short day photoperiod. Nevertheless, gnrh2 and gnrh3 mRNA levels were not up-regulated in castrated males kept under long-day photoperiod, which suggests that positive feedbacks on the brain-pituitary-gonad axis are necessary for this response. Copyright © 2014 Elsevier Inc. All rights reserved.

Arsenate biotransformation by Microcystis aeruginosa under different nitrogen and phosphorus levels.

Science.gov (United States)

Che, Feifei; Du, Miaomiao; Yan, Changzhou

2018-04-01

The arsenate (As(V)) biotransformation by Microcystis aeruginosa in a medium with different concentrations of nitrogen (N) and phosphorus (P) has been studied under laboratory conditions. When 15μg/L As(V) was added, N and P in the medium showed effective regulation on arsenic (As) metabolism in M. aeruginosa, resulting in significant differences in the algal growth among different N and P treatments. Under 0.2mg/L P treatment, increases in N concentration (4-20mg/L) significantly stimulated the cell growth and therefore indirectly enhanced the production of dimethylarsinic acid (DMA), the main As metabolite, accounting for 71%-79% of the total As in the medium. Meanwhile, 10-20mg/L N treatments accelerated the ability of As metabolization by M. aeruginosa, leading to higher contents of DMA per cell. However, As(V) uptake by M. aeruginosa was significantly impeded by 0.5-1.0mg/L P treatment, resulting in smaller rates of As transformation in M. aeruginosa as well as lower contents of As metabolites in the medium. Our data demonstrated that As(V) transformation by M. aeruginosa was significantly accelerated by increasing N levels, while it was inhibited by increasing P levels. Overall, both P and N play key roles in As(V) biotransformation processes. Copyright © 2017. Published by Elsevier B.V.

Complex formation and vectorization of a phosphorothioate oligonucleotide with an amphipathic leucine- and lysine-rich peptide: study at molecular and cellular levels.

Science.gov (United States)

Boukhalfa-Heniche, Fatima-Zohra; Hernández, Belén; Gaillard, Stéphane; Coïc, Yves-Marie; Huynh-Dinh, Tam; Lecouvey, Marc; Seksek, Olivier; Ghomi, Mahmoud

2004-04-15

Optical spectroscopic techniques such as CD, Raman scattering, and fluorescence imaging allowed us to analyze the complex formation and vectorization of a single-stranded 20-mer phosphorothioate oligodeoxynucleotide with a 15-mer amphipathic peptide at molecular and cellular levels. Different solvent mixtures (methanol and water) and molecular ratios of peptide/oligodeoxynucleotide complexes were tested in order to overcome the problems related to solubility. Optimal conditions for both spectroscopic and cellular experiments were obtained with the molecular ratio peptide/oligodeoxynucleotide equal to 21:4, corresponding to a 7:5 ratio for their respective +/- charge ratio. At the molecular level, CD and Raman spectra were consistent with a alpha-helix conformation of the peptide in water or in a methanol-water mixture. The presence of methanol increased considerably the solubility of the peptide without altering its alpha-helix conformation, as evidenced by CD and Raman spectroscopies. UV absorption melting profile of the oligodeoxynucleotide gave rise to a flat melting profile, corresponding to its random structure in solution. Raman spectra of oligodeoxynucleotide/peptide complexes could only be studied in methanol/water mixture solutions. Drastic changes observed in Raman spectra have undoubtedly shown: (a) the perturbation occurred in the peptide secondary structure, and (b) possible interaction between the lysine residues of the peptide and the oligodeoxynucleotide. At the cellular level, the complex was prepared in a mixture of 10% methanol and 90% cell medium. Cellular uptake in optimal conditions for the oligodeoxynucleotide delivery with low cytotoxicity was controlled by fluorescence imaging allowing to specifically locate the compacted oligonucleotide labeled with fluorescein at its 5'-terminus with the peptide into human glioma cells after 1 h of incubation at 37 degrees C. Copyright 2004 Wiley Periodicals, Inc.

Molecular dynamics simulations of polyelectrolyte brushes under poor solvent conditions: origins of bundle formation.

Science.gov (United States)

He, Gui-Li; Merlitz, Holger; Sommer, Jens-Uwe

2014-03-14

Molecular dynamics simulations are applied to investigate salt-free planar polyelectrolyte brushes under poor solvent conditions. Starting above the Θ-point with a homogeneous brush and then gradually reducing the temperature, the polymers initially display a lateral structure formation, forming vertical bundles of chains. A further reduction of the temperature (or solvent quality) leads to a vertical collapse of the brush. By varying the size and selectivity of the counterions, we show that lateral structure formation persists and therefore demonstrate that the entropy of counterions being the dominant factor for the formation of the bundle phase. By applying an external compression force on the brush we calculate the minimal work done on the polymer phase only and prove that the entropy gain of counterions in the bundle state, as compared to the homogeneously collapsed state at the same temperature, is responsible for the lateral microphase segregation. As a consequence, the observed lateral structure formation has to be regarded universal for osmotic polymer brushes below the Θ-point.

Molecular ultrasound imaging: current status and future directions

International Nuclear Information System (INIS)

Deshpande, N.; Needles, A.; Willmann, J.K.

2010-01-01

Targeted contrast-enhanced ultrasound (molecular ultrasound) is an emerging imaging strategy that combines ultrasound technology with novel molecularly-targeted ultrasound contrast agents for assessing biological processes at the molecular level. Molecular ultrasound contrast agents are nano- or micro-sized particles that are targeted to specific molecular markers by adding high-affinity binding ligands onto the surface of the particles. Following intravenous administration, these targeted ultrasound contrast agents accumulate at tissue sites overexpressing specific molecular markers, thereby enhancing the ultrasound imaging signal. High spatial and temporal resolution, real-time imaging, non-invasiveness, relatively low costs, lack of ionising irradiation and wide availability of ultrasound systems are advantages compared to other molecular imaging modalities. In this article we review current concepts and future directions of molecular ultrasound imaging, including different classes of molecular ultrasound contrast agents, ongoing technical developments of pre-clinical and clinical ultrasound systems, the potential of molecular ultrasound for imaging different diseases at the molecular level, and the translation of molecular ultrasound into the clinic.

Characterization of majority and minority carrier deep levels in p-type GaN:Mg grown by molecular beam epitaxy using deep level optical spectroscopy

International Nuclear Information System (INIS)

Armstrong, A.; Caudill, J.; Ringel, S. A.; Corrion, A.; Poblenz, C.; Mishra, U. K.; Speck, J. S.

2008-01-01

Deep level defects in p-type GaN:Mg grown by molecular beam epitaxy were characterized using steady-state photocapacitance and deep level optical spectroscopy (DLOS). Low frequency capacitance measurements were used to alleviate dispersion effects stemming from the deep Mg acceptor. Use of DLOS enabled a quantitative survey of both deep acceptor and deep donor levels, the latter being particularly important due to the limited understanding of minority carrier states for p-type GaN. Simultaneous electron and hole photoemissions resulted in a convoluted deep level spectrum that was decoupled by emphasizing either majority or minority carrier optical emission through control of the thermal filling time conditions. In this manner, DLOS was able to resolve and quantify the properties of deep levels residing near both the conduction and valence bandedges in the same sample. Bandgap states through hole photoemission were observed at E v +3.05 eV, E v +3.22 eV and E v +3.26 eV. Additionally, DLOS revealed levels at E c -3.24 eV and E c -2.97 eV through electron emission to the conduction band with the former attributed to the Mg acceptor itself. The detected deep donor concentration is less than 2% of activated [Mg] and demonstrates the excellent quality of the film

Document authentication at molecular levels using desorption atmospheric pressure chemical ionization mass spectrometry imaging.

Science.gov (United States)

Li, Ming; Jia, Bin; Ding, Liying; Hong, Feng; Ouyang, Yongzhong; Chen, Rui; Zhou, Shumin; Chen, Huanwen; Fang, Xiang

2013-09-01

Molecular images of documents were obtained by sequentially scanning the surface of the document using desorption atmospheric pressure chemical ionization mass spectrometry (DAPCI-MS), which was operated in either a gasless, solvent-free or methanol vapor-assisted mode. The decay process of the ink used for handwriting was monitored by following the signal intensities recorded by DAPCI-MS. Handwritings made using four types of inks on four kinds of paper surfaces were tested. By studying the dynamic decay of the inks, DAPCI-MS imaging differentiated a 10-min old from two 4 h old samples. Non-destructive forensic analysis of forged signatures either handwritten or computer-assisted was achieved according to the difference of the contour in DAPCI images, which was attributed to the strength personalized by different writers. Distinction of the order of writing/stamping on documents and detection of illegal printings were accomplished with a spatial resolution of about 140 µm. A Matlab® written program was developed to facilitate the visualization of the similarity between signature images obtained by DAPCI-MS. The experimental results show that DAPCI-MS imaging provides rich information at the molecular level and thus can be used for the reliable document analysis in forensic applications. © 2013 The Authors. Journal of Mass Spectrometry published by John Wiley & Sons, Ltd.

The Importance of Interactions at the Molecular Level: A Spectroscopic Study of a New Composite Sorber Material.

Science.gov (United States)

Crocellà, Valentina; Groppo, Elena; Dani, Alessandro; Castellero, Alberto; Bordiga, Silvia; Zilio, Stefano; De Simone, Agnello; Vacca, Paolo

2017-10-01

The functional properties of a new composite material having water vapor getter properties have been investigated by a large arsenal of characterization techniques. The composite system is originated by combining two constituents having very different chemical natures, a magnesium perchlorate (Mg(ClO 4 ) 2 ) salt and a polymeric acrylic matrix. In particular, Fourier transform infrared (FT-IR) and Raman spectroscopy have been fundamental to understand the type of interactions between the salt and the matrix in different hydration conditions. It was found that in the anhydrous composite system the dispersed Mg(ClO 4 ) 2 salt retains its molecular structure, because Mg 2+ cations are still surrounded by their [ClO 4 ] - counter-anions; at the same time, the salt and the polymeric matrix chemically interact each other at the molecular level. These interactions gradually vanish in the presence of water, and disappear in the fully hydrated composite system, where the Mg 2+ cations are completely solvated by the water molecules.

Photon Upconversion and Molecular Solar Energy Storage by Maximizing the Potential of Molecular Self-Assembly.

Science.gov (United States)

Kimizuka, Nobuo; Yanai, Nobuhiro; Morikawa, Masa-Aki

2016-11-29

The self-assembly of functional molecules into ordered molecular assemblies and the fulfillment of potentials unique to their nanotomesoscopic structures have been one of the central challenges in chemistry. This Feature Article provides an overview of recent progress in the field of molecular self-assembly with the focus on the triplet-triplet annihilation-based photon upconversion (TTA-UC) and supramolecular storage of photon energy. On the basis of the integration of molecular self-assembly and photon energy harvesting, triplet energy migration-based TTA-UC has been achieved in varied molecular systems. Interestingly, some molecular self-assemblies dispersed in solution or organogels revealed oxygen barrier properties, which allowed TTA-UC even under aerated conditions. The elements of molecular self-assembly were also introduced to the field of molecular solar thermal fuel, where reversible photoliquefaction of ionic crystals to ionic liquids was found to double the molecular storage capacity with the simultaneous pursuit of switching ionic conductivity. A future prospect in terms of innovating molecular self-assembly toward molecular systems chemistry is also discussed.

Optimum conditions for producing Cs2 molecular condensates by stimulated Raman adiabatic passage

International Nuclear Information System (INIS)

Feng Zhifang; Li Weidong; Wang Lirong; Xiao Liantuan; Jia Suotang

2009-01-01

The optimum conditions for producing Cs 2 molecular condensates from Cs atomic condensates with high transfer efficiency by stimulated Raman adiabatic passage are presented. Under the extended 'two-photon' resonance condition, including the two-photon process, the mean-field correction, and the tunneling coupling between two upper excited molecular levels, a high and stable conversion efficiency is realized. The high conversion efficiency could be achieved by following two methods under experimentally less demanding conditions (relatively small effective Rabi frequency for pump laser pulse). One is adjusting the detuning difference between two laser pulses for same effective Rabi frequencies with up to 87.2% transfer efficiency. Another one is adjusting the effective Rabi frequency, the detuning of dump laser for given effective Rabi frequency, and the detuning of pump laser with up to 80.7% transfer efficiency.

Optimum conditions for producing Cs2 molecular condensates by stimulated Raman adiabatic passage

Science.gov (United States)

Feng, Zhifang; Li, Weidong; Wang, Lirong; Xiao, Liantuan; Jia, Suotang

2009-10-01

The optimum conditions for producing Cs2 molecular condensates from Cs atomic condensates with high transfer efficiency by stimulated Raman adiabatic passage are presented. Under the extended “two-photon” resonance condition, including the two-photon process, the mean-field correction, and the tunneling coupling between two upper excited molecular levels, a high and stable conversion efficiency is realized. The high conversion efficiency could be achieved by following two methods under experimentally less demanding conditions (relatively small effective Rabi frequency for pump laser pulse). One is adjusting the detuning difference between two laser pulses for same effective Rabi frequencies with up to 87.2% transfer efficiency. Another one is adjusting the effective Rabi frequency, the detuning of dump laser for given effective Rabi frequency, and the detuning of pump laser with up to 80.7% transfer efficiency.

Measurement of incident molecular temperature in the formation of organic thin films

Science.gov (United States)

Abe, Takahiro; Matsubara, Ryosuke; Hayakawa, Munetaka; Shimoyama, Akifumi; Tanaka, Takaaki; Tsuji, Akira; Takahashi, Yoshikazu; Kubono, Atsushi

2018-03-01

To investigate the effects of incident molecular temperature on organic-thin-film growth by vacuum evaporation, quantitative analysis of molecular temperature is required. In this study, we propose a method of determining molecular temperature based on the heat exchange between a platinum filament and molecular vapor. Molecular temperature is estimated from filament temperature, which remains unchanged even under molecular vapor supply. The results indicate that our method has sufficient sensitivity to evaluate the molecular temperature under the typical growth rate used for fabrication of functional organic thin films.

Source-sink interaction: a century old concept under the light of modern molecular systems biology.

Science.gov (United States)

Chang, Tian-Gen; Zhu, Xin-Guang; Raines, Christine

2017-07-20

Many approaches to engineer source strength have been proposed to enhance crop yield potential. However, a well-co-ordinated source-sink relationship is required finally to realize the promised increase in crop yield potential in the farmer's field. Source-sink interaction has been intensively studied for decades, and a vast amount of knowledge about the interaction in different crops and under different environments has been accumulated. In this review, we first introduce the basic concepts of source, sink and their interactions, then summarize current understanding of how source and sink can be manipulated through both environmental control and genetic manipulations. We show that the source-sink interaction underlies the diverse responses of crops to the same perturbations and argue that development of a molecular systems model of source-sink interaction is required towards a rational manipulation of the source-sink relationship for increased yield. We finally discuss both bottom-up and top-down routes to develop such a model and emphasize that a community effort is needed for development of this model. © The Author 2017. Published by Oxford University Press on behalf of the Society for Experimental Biology. All rights reserved. For permissions, please email: journals.permissions@oup.com.

Molecular dynamics simulations of ejecta production from sinusoidal tin surfaces under supported and unsupported shocks

Science.gov (United States)

Wu, Bao; Wu, FengChao; Zhu, YinBo; Wang, Pei; He, AnMin; Wu, HengAn

2018-04-01

Micro-ejecta, an instability growth process, occurs at metal/vacuum or metal/gas interface when compressed shock wave releases from the free surface that contains surface defects. We present molecular dynamics (MD) simulations to investigate the ejecta production from tin surface shocked by supported and unsupported waves with pressures ranging from 8.5 to 60.8 GPa. It is found that the loading waveforms have little effect on spike velocity while remarkably affect the bubble velocity. The bubble velocity of unsupported shock loading remains nonzero constant value at late time as observed in experiments. Besides, the time evolution of ejected mass in the simulations is compared with the recently developed ejecta source model, indicating the suppressed ejection of unmelted or partial melted materials. Moreover, different reference positions are chosen to characterize the amount of ejecta under different loading waveforms. Compared with supported shock case, the ejected mass of unsupported shock case saturates at lower pressure. Through the analysis on unloading path, we find that the temperature of tin sample increases quickly from tensile stress state to zero pressure state, resulting in the melting of bulk tin under decaying shock. Thus, the unsupported wave loading exhibits a lower threshold pressure causing the solid-liquid phase transition on shock release than the supported shock loading.

DNA under Force: Mechanics, Electrostatics, and Hydration

Directory of Open Access Journals (Sweden)

Jingqiang Li

2015-02-01

Full Text Available Quantifying the basic intra- and inter-molecular forces of DNA has helped us to better understand and further predict the behavior of DNA. Single molecule technique elucidates the mechanics of DNA under applied external forces, sometimes under extreme forces. On the other hand, ensemble studies of DNA molecular force allow us to extend our understanding of DNA molecules under other forces such as electrostatic and hydration forces. Using a variety of techniques, we can have a comprehensive understanding of DNA molecular forces, which is crucial in unraveling the complex DNA functions in living cells as well as in designing a system that utilizes the unique properties of DNA in nanotechnology.

Revealing Atomic-Level Mechanisms of Protein Allostery with Molecular Dynamics Simulations.

Directory of Open Access Journals (Sweden)

Samuel Hertig

2016-06-01

Full Text Available Molecular dynamics (MD simulations have become a powerful and popular method for the study of protein allostery, the widespread phenomenon in which a stimulus at one site on a protein influences the properties of another site on the protein. By capturing the motions of a protein's constituent atoms, simulations can enable the discovery of allosteric binding sites and the determination of the mechanistic basis for allostery. These results can provide a foundation for applications including rational drug design and protein engineering. Here, we provide an introduction to the investigation of protein allostery using molecular dynamics simulation. We emphasize the importance of designing simulations that include appropriate perturbations to the molecular system, such as the addition or removal of ligands or the application of mechanical force. We also demonstrate how the bidirectional nature of allostery-the fact that the two sites involved influence one another in a symmetrical manner-can facilitate such investigations. Through a series of case studies, we illustrate how these concepts have been used to reveal the structural basis for allostery in several proteins and protein complexes of biological and pharmaceutical interest.

Sustained High Levels of Both Total and High Molecular Weight Adiponectin in Plasma during the Convalescent Phase of Haemorrhagic Fever with Renal Syndrome Are Associated with Disease Severity

Directory of Open Access Journals (Sweden)

Kang Tang

2017-01-01

Full Text Available Haemorrhagic fever with renal syndrome (HFRS is characterised by an uncontrolled immune response that causes vascular leakage. Adiponectin (APN is an adipocytokine involved in prorevascularisation and immunomodulation. To investigate the possible effects of APN in the pathogenesis of HFRS, total and high molecular weight (HMW APN levels in the plasma of patients with HFRS were quantified using enzyme-linked immunosorbent assay (ELISA. Compared with those in healthy controls, the plasma total and HMW APN levels in patients were elevated to different degrees from the fever onset and remained high at the convalescent phase. Consistent with these results, western blot analysis additionally showed that low molecular weight (LMW, middle molecular weight (MMW, and HMW APN levels were all elevated and contributed to the elevation of the total APN level. Importantly, sustained high levels of total and HMW APN at the convalescent phase were significantly higher in patients with critical disease than those in patients with mild or moderate disease. Moreover, total and HMW APN levels negatively correlated with white blood cell count and positively correlated with platelet count and serum albumin level. These results may provide insights into understanding the roles of total and HMW APN in the pathogenesis of HFRS.

Interplay of intra-atomic and interatomic effects: An investigation of the 2p core level spectra of atomic Fe and molecular FeCl2

International Nuclear Information System (INIS)

Richter, T.; Wolff, T.; Zimmermann, P.; Godehusen, K.; Martins, M.

2004-01-01

The 2p photoabsorption and photoelectron spectra of atomic Fe and molecular FeCl 2 were studied by photoion and photoelectron spectroscopy using monochromatized synchrotron radiation and atomic or molecular beam technique. The atomic spectra were analyzed with configuration interaction calculations yielding excellent agreement between experiment and theory. For the analysis of the molecular photoelectron spectrum which shows pronounced interatomic effects, a charge transfer model was used, introducing an additional 3d 7 configuration. The resulting good agreement between the experimental and theoretical spectrum and the remarkable similarity of the molecular with the corresponding spectrum in the solid phase opens a way to a better understanding of the interplay of the interatomic and intra-atomic interactions in the 2p core level spectra of the 3d metal compounds

Echinococcus-Host Interactions at Cellular and Molecular Levels.

Science.gov (United States)

Brehm, K; Koziol, U

2017-01-01

The potentially lethal zoonotic diseases alveolar and cystic echinococcosis are caused by the metacestode larval stages of the tapeworms Echinococcus multilocularis and Echinococcus granulosus, respectively. In both cases, metacestode growth and proliferation occurs within the inner organs of mammalian hosts, which is associated with complex molecular host-parasite interactions that regulate nutrient uptake by the parasite as well as metacestode persistence and development. Using in vitro cultivation systems for parasite larvae, and informed by recently released, comprehensive genome and transcriptome data for both parasites, these molecular host-parasite interactions have been subject to significant research during recent years. In this review, we discuss progress in this field, with emphasis on parasite development and proliferation. We review host-parasite interaction mechanisms that occur early during an infection, when the invading oncosphere stage undergoes a metamorphosis towards the metacestode, and outline the decisive role of parasite stem cells during this process. We also discuss special features of metacestode morphology, and how this parasite stage takes up nutrients from the host, utilizing newly evolved or expanded gene families. We comprehensively review mechanisms of host-parasite cross-communication via evolutionarily conserved signalling systems and how the parasite signalling systems might be exploited for the development of novel chemotherapeutics. Finally, we point to an urgent need for the development of functional genomic techniques in this parasite, which will be imperative for hypothesis-driven analyses into Echinococcus stem cell biology, developmental mechanisms and immunomodulatory activities, which are all highly relevant for the development of anti-infective measures. Copyright © 2017 Elsevier Ltd. All rights reserved.

Molecular weights and molecular weight distributions of irradiated cellulose fibers by gel permeation chromatography

International Nuclear Information System (INIS)

Kusama, Y.; Kageyama, E.; Shimada, M.; Nakamura, Y.

1976-01-01

Radiation degradation of cellulose fibers was investigated by gel permeation chromatography (GPC). Scoured cotton of Mexican variety (cellulose I), Polynosic rayon (cellulose II), and their microcrystalline celluloses obtained by hydrolysis of the original fibers were irradiated by Co-60 γ-rays under vacuum or humid conditions. The irradiated samples were then nitrated under nondegradative conditions. The molecular weights and molecular weight distributions were measured by GPC using tetrahydrofuran as solvent. The relationship between molecular weight and elution count was obtained with cellulose trinitrate standards fractionated by preparative GPC. The degree of polymerization of the fibers decreased with increasing irradiation dose, but their microcrystalline celluloses were only slightly degraded by irradiation, especially in microcrystalline cellulose from cellulose I. Degradation of the fibers irradiated under humid conditions was less than that irradiated under vacuum. It was found that the G-values for main-chain scission for the irradiated cellulose I, cellulose II, microcrystalline cellulose I, and microcrystalline cellulose II were 2.8, 2.9, less than 1, and 2.9, respectively, but the G-value for main-chain scission for the irradiated cellulose II was increased to 11.2 at irradiation doses above 3 Mrad. Consequently, it is inferred that cellulose molecules in the amorphous regions are degraded more readily, and the well-aligned molecules in crystalline regions are not as easily degraded by irradiation

Cell cycle gene expression under clinorotation

Science.gov (United States)

Artemenko, Olga

2016-07-01

Cyclins and cyclin-dependent kinase (CDK) are main regulators of the cell cycle of eukaryotes. It's assumes a significant change of their level in cells under microgravity conditions and by other physical factors actions. The clinorotation use enables to determine the influence of gravity on simulated events in the cell during the cell cycle - exit from the state of quiet stage and promotion presynthetic phase (G1) and DNA synthesis phase (S) of the cell cycle. For the clinorotation effect study on cell proliferation activity is the necessary studies of molecular mechanisms of cell cycle regulation and development of plants under altered gravity condition. The activity of cyclin D, which is responsible for the events of the cell cycle in presynthetic phase can be controlled by the action of endogenous as well as exogenous factors, but clinorotation is one of the factors that influence on genes expression that regulate the cell cycle.These data can be used as a model for further research of cyclin - CDK complex for study of molecular mechanisms regulation of growth and proliferation. In this investigation we tried to summarize and analyze known literature and own data we obtained relatively the main regulators of the cell cycle in altered gravity condition.

Making molecular machines work

NARCIS (Netherlands)

Browne, Wesley R.; Feringa, Ben L.

2006-01-01

In this review we chart recent advances in what is at once an old and very new field of endeavour the achievement of control of motion at the molecular level including solid-state and surface-mounted rotors, and its natural progression to the development of synthetic molecular machines. Besides a

Linking metabolomics data to underlying metabolic regulation

Directory of Open Access Journals (Sweden)

Thomas eNägele

2014-11-01

Full Text Available The comprehensive experimental analysis of a metabolic constitution plays a central role in approaches of organismal systems biology.Quantifying the impact of a changing environment on the homeostasis of cellular metabolism has been the focus of numerous studies applying various metabolomics techniques. It has been proven that approaches which integrate different analytical techniques, e.g. LC-MS, GC-MS, CE-MS and H-NMR, can provide a comprehensive picture of a certain metabolic homeostasis. Identification of metabolic compounds and quantification of metabolite levels represent the groundwork for the analysis of regulatory strategies in cellular metabolism. This significantly promotes our current understanding of the molecular organization and regulation of cells, tissues and whole organisms.Nevertheless, it is demanding to elicit the pertinent information which is contained in metabolomics data sets.Based on the central dogma of molecular biology, metabolite levels and their fluctuations are the result of a directed flux of information from gene activation over transcription to translation and posttranslational modification.Hence, metabolomics data represent the summed output of a metabolic system comprising various levels of molecular organization.As a consequence, the inverse assignment of metabolomics data to underlying regulatory processes should yield information which-if deciphered correctly-provides comprehensive insight into a metabolic system.Yet, the deduction of regulatory principles is complex not only due to the high number of metabolic compounds, but also because of a high level of cellular compartmentalization and differentiation.Motivated by the question how metabolomics approaches can provide a representative view on regulatory biochemical processes, this article intends to present and discuss current metabolomics applications, strategies of data analysis and their limitations with respect to the interpretability in context of

The status of the safeguards implementation under the State-Level Approach at the HANARO

Energy Technology Data Exchange (ETDEWEB)

Kim, H. S.; Lee, B. D.; Kim, I. C.; Kim, H. J.; Jung, J. A.; Lee, S. H. [Korea Atomic Energy Research Institute, Daejeon (Korea, Republic of)

2016-10-15

The IAEA developed the SLA(State-Level Approach) for the States in order to maximize effectiveness of safeguards in an environment of constrained resources. The SLA has been implemented at KAERI-Daejeon site in the ROK since 2015. The ten nuclear facilities and one LOF(Location Outsides Facility) of the KAERI-Daejeon site are grouped into three categories under the SLA. The HANARO(High flux Advanced Neutron Application ReactOr) and PIEF(Post Irradiation Examination Facility) are involved in the category I “self-contained capability” facilities that have at least one significant quantity of suitable nuclear material and which could support undeclared plutonium production/separation activities without other supporting infrastructures. This paper described the status of the safeguards implementation at the HANARO involved in the category I under the SLA. The status of a model inventory management system for a research reactor developed in 2013 was also investigated. In this paper, the features and status of the safeguards implementation of the HANARO under the SLA were analyzed. Under the SLA, the monthly, quarterly and annual advanced facility operational information for the HANARO has been submitted to the IAEA in a timely manner. The IAEA inspection at HANARO has been successfully performed under the SLA. It is expected that the safeguards implementation work at HANARO under the SLA has the similar level with that under IS. Under the SLA, the data occurred from the surveillance cameras and other equipment installed at HANARO enables to transmit remotely to the IAEA. The IAEA is targeting 2017~2018 to upgrade them. In addition, the development status of a model inventory management system for a research reactor was investigated. It aims at controlling the material inventory for the nuclear material accounting work and the convenient facility operation. The major functions of it are to trace the transfer history of the nuclear materials and non-nuclear materials

The status of the safeguards implementation under the State-Level Approach at the HANARO

International Nuclear Information System (INIS)

Kim, H. S.; Lee, B. D.; Kim, I. C.; Kim, H. J.; Jung, J. A.; Lee, S. H.

2016-01-01

The IAEA developed the SLA(State-Level Approach) for the States in order to maximize effectiveness of safeguards in an environment of constrained resources. The SLA has been implemented at KAERI-Daejeon site in the ROK since 2015. The ten nuclear facilities and one LOF(Location Outsides Facility) of the KAERI-Daejeon site are grouped into three categories under the SLA. The HANARO(High flux Advanced Neutron Application ReactOr) and PIEF(Post Irradiation Examination Facility) are involved in the category I “self-contained capability” facilities that have at least one significant quantity of suitable nuclear material and which could support undeclared plutonium production/separation activities without other supporting infrastructures. This paper described the status of the safeguards implementation at the HANARO involved in the category I under the SLA. The status of a model inventory management system for a research reactor developed in 2013 was also investigated. In this paper, the features and status of the safeguards implementation of the HANARO under the SLA were analyzed. Under the SLA, the monthly, quarterly and annual advanced facility operational information for the HANARO has been submitted to the IAEA in a timely manner. The IAEA inspection at HANARO has been successfully performed under the SLA. It is expected that the safeguards implementation work at HANARO under the SLA has the similar level with that under IS. Under the SLA, the data occurred from the surveillance cameras and other equipment installed at HANARO enables to transmit remotely to the IAEA. The IAEA is targeting 2017~2018 to upgrade them. In addition, the development status of a model inventory management system for a research reactor was investigated. It aims at controlling the material inventory for the nuclear material accounting work and the convenient facility operation. The major functions of it are to trace the transfer history of the nuclear materials and non-nuclear materials

Molecularly Imprinted Membranes

Science.gov (United States)

Trotta, Francesco; Biasizzo, Miriam; Caldera, Fabrizio

2012-01-01

Although the roots of molecularly imprinted polymers lie in the beginning of 1930s in the past century, they have had an exponential growth only 40–50 years later by the works of Wulff and especially by Mosbach. More recently, it was also proved that molecular imprinted membranes (i.e., polymer thin films) that show recognition properties at molecular level of the template molecule are used in their formation. Different procedures and potential application in separation processes and catalysis are reported. The influences of different parameters on the discrimination abilities are also discussed. PMID:24958291

Molecular dynamics simulation of the local concentration and structure in multicomponent aerosol nanoparticles under atmospheric conditions.

Science.gov (United States)

Karadima, Katerina S; Mavrantzas, Vlasis G; Pandis, Spyros N

2017-06-28

Molecular dynamics (MD) simulations were employed to investigate the local structure and local concentration in atmospheric nanoparticles consisting of an organic compound (cis-pinonic acid or n-C 30 H 62 ), sulfate and ammonium ions, and water. Simulations in the isothermal-isobaric (NPT) statistical ensemble under atmospheric conditions with a prespecified number of molecules of the abovementioned compounds led to the formation of a nanoparticle. Calculations of the density profiles of all the chemical species in the nanoparticle, the corresponding radial pair distribution functions, and their mobility inside the nanoparticle revealed strong interactions developing between sulfate and ammonium ions. However, sulfate and ammonium ions prefer to populate the central part of the nanoparticle under the simulated conditions, whereas organic molecules like to reside at its outer surface. Sulfate and ammonium ions were practically immobile; in contrast, the organic molecules exhibited appreciable mobility at the outer surface of the nanoparticle. When the organic compound was a normal alkane (e.g. n-C 30 H 62 ), a well-organized (crystalline-like) phase was rapidly formed at the free surface of the nanoparticle and remained separate from the rest of the species.

Genetic architecture of vitamin B12 and folate levels uncovered applying deeply sequenced large datasets

DEFF Research Database (Denmark)

Grarup, Niels; Sulem, Patrick; Sandholt, Camilla H

2013-01-01

of the underlying biology of human traits and diseases. Here, we used a large Icelandic whole genome sequence dataset combined with Danish exome sequence data to gain insight into the genetic architecture of serum levels of vitamin B12 (B12) and folate. Up to 22.9 million sequence variants were analyzed in combined...... in serum B12 or folate levels do not modify the risk of developing these conditions. Yet, the study demonstrates the value of combining whole genome and exome sequencing approaches to ascertain the genetic and molecular architectures underlying quantitative trait associations....

Who regulates the disposal of low-level radioactive waste under the Low-Level Radioactive Waste Policy Act

International Nuclear Information System (INIS)

Mostaghel, D.M.

1988-01-01

The present existence of immense quantities of low-level nuclear waste, a federal law providing for state or regional control of such waste disposal, and a number of state disposal laws challenged on a variety of constitutional grounds underscore what currently may be the most serious problem in nuclear waste disposal: who is to regulate the disposal of low-level nuclear wastes. This problem's origin may be traced to crucial omissions in the Atomic Energy Act of 1946 and its 1954 amendments (AEA) that concern radioactive waste disposal. Although the AEA states that nuclear materials and facilities are affected with the public interest and should be regulated to provide for the public health and safety, the statute fails to prescribe specific guidelines for any nuclear waste disposal. The Low-Level Radioactive Waste Policy Act of 1980 (LLRWPA) grants states some control over radioactive waste disposal, an area from which they were previously excluded by the doctrine of federal preemption. This Comment discusses the question of who regulates low-level radioactive waste disposal facilities by examining the following: the constitutional doctrines safeguarding federal government authority; area of state authority; grants of specific authority delegations under the LLRWPA and its amendment; and finally, potential problems that may arise depending on whether ultimate regulatory authority is deemed to rest with single states, regional compacts, or the federal government

Salinity reduction benefits European eel larvae: Insights at the morphological and molecular level

DEFF Research Database (Denmark)

Politis, Sebastian Nikitas; Mazurais, David; Servili, Arianna

2018-01-01

. Moreover, larvae were able to keep energy metabolism related gene expression (atp6, cox1) at stable levels, irrespective of the salinity reduction. As such, when reducing salinity, an energy surplus associated to reduced osmoregulation demands and stress (lower nkcc, aqp and hsp expression), likely......European eel (Anguilla anguilla) is a euryhaline species, that has adapted to cope with both, hyper- and hypo-osmotic environments. This study investigates the effect of salinity, from a morphological and molecular point of view on European eel larvae reared from 0 to 12 days post hatch (dph......). Offspring reared in 36 practical salinity units (psu; control), were compared with larvae reared in six scenarios, where salinity was decreased on 0 or 3 dph and in rates of 1, 2 or 4 psu/day, towards iso-osmotic conditions. Results showed that several genes relating to osmoregulation (nkcc2α, nkcc2β, aqp1...

75 FR 340 - Approval for Expansion of Subzone 22F, Abbott Molecular, Inc. (Pharmaceutical and Molecular...

Science.gov (United States)

2010-01-05

... DEPARTMENT OF COMMERCE Foreign-Trade Zones Board [Order No. 1654] Approval for Expansion of Subzone 22F, Abbott Molecular, Inc. (Pharmaceutical and Molecular Diagnostic Products), Chicago, IL, Area Pursuant to its authority under the Foreign-Trade Zones Act of June 18, 1934, as amended (19 U.S.C. 81a-81u...

Molecular dynamics simulation of UO2 nanocrystals melting under isolated and periodic boundary conditions

International Nuclear Information System (INIS)

Boyarchenkov, A.S.; Potashnikov, S.I.; Nekrasov, K.A.; Kupryazhkin, A.Ya.

2012-01-01

Highlights: ► We perform MD simulation of UO 2 nanocrystals melting (in range of 768–49 152 ions). ► T(P) melting curves intersect zero near −20 GPa and saturate near 25 GPa. ► Reciprocal size dependences of nanocrystal melting point decrease nonlinearly. ► Linear and parabolic extrapolations to macroscopic values are considered. ► Melting point and density jump are reproduced, but heat of fusion is underestimated. - Abstract: Melting of uranium dioxide (UO 2 ) nanocrystals has been studied by molecular dynamics (MD) simulation. Ten recent and widely used sets of pair potentials were assessed in the rigid ion approximation. Both isolated (in vacuum) and periodic boundary conditions (PBC) were explored. Using barostat under PBC the pressure dependences of melting point were obtained. These curves intersected zero near −20 GPa, saturated near 25 GPa and increased nonlinearly in between. Using simulation of surface under isolated boundary conditions (IBC) recommended melting temperature and density jump were successfully reproduced. However, the heat of fusion is still underestimated. These melting characteristics were calculated for nanocrystals of cubic shape in the range of 768–49 152 particles (volume range of 10–1000 nm 3 ). The obtained reciprocal size dependences decreased nonlinearly. Linear and parabolic extrapolations to macroscopic values are considered. The parabolic one is found to be better suited for analysis of the data on temperature and heat of melting.

Molecular cardiovascular imaging

International Nuclear Information System (INIS)

Schaefers, M.

2007-01-01

Although huge and long-lasting research efforts have been spent on the development of new diagnostic techniques investigating cardiovascular diseases, still fundamental challenges exist; the main challenge being the diagnosis of a suspected or known coronary artery disease or its consequences (myocardial infarction, heart failure etc.). Beside morphological techniques, functional imaging modalities are available in clinical diagnostic algorithms, whereas molecular cardiovascular imaging techniques are still under development. This review summarizes clinical-diagnostical challenges of modern cardiovascular medicine as well as the potential of new molecular imaging techniques to face these. (orig.)

Noncovalent Molecular Electronics.

Science.gov (United States)

Gryn'ova, G; Corminboeuf, C

2018-05-03

Molecular electronics covers several distinctly different conducting architectures, including organic semiconductors and single-molecule junctions. The noncovalent interactions, abundant in the former, are also often found in the latter, i.e., the dimer junctions. In the present work, we draw the parallel between the two types of noncovalent molecular electronics for a range of π-conjugated heteroaromatic molecules. In silico modeling allows us to distill the factors that arise from the chemical nature of their building blocks and from their mutual arrangement. We find that the same compounds are consistently the worst and the best performers in the two types of electronic assemblies, emphasizing the universal imprint of the underlying chemistry of the molecular cores on their diverse charge transport characteristics. The interplay between molecular and intermolecular factors creates a spectrum of noncovalent conductive architectures, which can be manipulated using the design strategies based upon the established relationships between chemistry and transport.

STICK AND SLIP BEHAVIOR OF CONFINED OLIGOMER MELTS UNDER SHEAR - A MOLECULAR-DYNAMICS STUDY

NARCIS (Netherlands)

MANIAS, E; HADZIIOANNOU, G; BITSANIS, [No Value; TENBRINKE, G

1993-01-01

The flow behaviour of melts of short chains, confined in molecularly thin Couette flow geometries, is studied with molecular-dynamics simulations. The effect of wall attraction and confinement on the density and velocity profiles is analysed. In these highly inhomogeneous films, a strong correlation

Stress and its molecular consequences in cancer progression

Directory of Open Access Journals (Sweden)

Magdalena Surman

2017-06-01

Full Text Available Stress, caused by psychological, physiological and physical factors has an adverse impact on human body homeostasis. There are two kind of stress: short-term and chronic. Cancer patients usually live under chronic stress, caused by diagnosis-related strong emotional experience and depression, resulting from various difficulties associated with disease progression and treatment. At the molecular level, stress factors induce production and secretion of stress-related hormones, such as catecholamines, glucocorticoids and dopamine (as a part of adaptational body response, which influence both normal and transformed cells through their specific receptors. The particular effects exerted by these molecules on cancer cells have been also observed in in vitro cultures and include changes in proliferation, apoptosis susceptibility and migration/invasion potential. As a result, it has been suggested that stress hormones may be responsible for progression of malignancy and thus accelerate the metastasis formation in cancer patients. However, the clinical data on correlation between stress and the patients survival, as well as the molecular analysis of stress hormone receptors expression and action in cancer cell, have not yet provided an unequivocal answer. For this reason, extensive studies, on molecular and clinical level are needed to fully determine stress impact on cancerprogression and on the effectiveness of anti-cancer treatment. Nowadays, it seems reasonable that the personalization of anti-cancer therapy should also focus on mental state of cancer patients, and provide them with psychological tools or techniques for stress management.

Elucidation of molecular kinetic schemes from macroscopic traces using system identification.

Directory of Open Access Journals (Sweden)

Miguel Fribourg

2017-02-01

Full Text Available Overall cellular responses to biologically-relevant stimuli are mediated by networks of simpler lower-level processes. Although information about some of these processes can now be obtained by visualizing and recording events at the molecular level, this is still possible only in especially favorable cases. Therefore the development of methods to extract the dynamics and relationships between the different lower-level (microscopic processes from the overall (macroscopic response remains a crucial challenge in the understanding of many aspects of physiology. Here we have devised a hybrid computational-analytical method to accomplish this task, the SYStems-based MOLecular kinetic scheme Extractor (SYSMOLE. SYSMOLE utilizes system-identification input-output analysis to obtain a transfer function between the stimulus and the overall cellular response in the Laplace-transformed domain. It then derives a Markov-chain state molecular kinetic scheme uniquely associated with the transfer function by means of a classification procedure and an analytical step that imposes general biological constraints. We first tested SYSMOLE with synthetic data and evaluated its performance in terms of its rate of convergence to the correct molecular kinetic scheme and its robustness to noise. We then examined its performance on real experimental traces by analyzing macroscopic calcium-current traces elicited by membrane depolarization. SYSMOLE derived the correct, previously known molecular kinetic scheme describing the activation and inactivation of the underlying calcium channels and correctly identified the accepted mechanism of action of nifedipine, a calcium-channel blocker clinically used in patients with cardiovascular disease. Finally, we applied SYSMOLE to study the pharmacology of a new class of glutamate antipsychotic drugs and their crosstalk mechanism through a heteromeric complex of G protein-coupled receptors. Our results indicate that our methodology

On the widths of Stokes lines in Raman scattering from molecules adsorbed at metal surfaces and in molecular conduction junctions

Energy Technology Data Exchange (ETDEWEB)

Gao, Yi, E-mail: yig057@ucsd.edu; Galperin, Michael, E-mail: migalperin@ucsd.edu [Department of Chemistry and Biochemistry, University of California San Diego, La Jolla, California 92093 (United States); Nitzan, Abraham, E-mail: nitzan@post.tau.ac.il [Department of Chemistry, University of Pennsylvania, Philadelphia, Pennsylvania 19104, USA and School of Chemistry, Tel Aviv University, Tel Aviv 69978 (Israel)

2016-06-28

Within a generic model we analyze the Stokes linewidth in surface enhanced Raman scattering (SERS) from molecules embedded as bridges in molecular junctions. We identify four main contributions to the off-resonant Stokes signal and show that under zero voltage bias (a situation pertaining also to standard SERS experiments) and at low bias junctions only one of these contributions is pronounced. The linewidth of this component is determined by the molecular vibrational relaxation rate, which is dominated by interactions with the essentially bosonic thermal environment when the relevant molecular electronic energy is far from the metal(s) Fermi energy(ies). It increases when the molecular electronic level is close to the metal Fermi level so that an additional vibrational relaxation channel due to electron-hole (eh) exciton in the molecule opens. Other contributions to the Raman signal, of considerably broader linewidths, can become important at larger junction bias.

Comparative transcriptome analysis of the Asteraceae halophyte Karelinia caspica under salt stress.

Science.gov (United States)

Zhang, Xia; Liao, Maoseng; Chang, Dan; Zhang, Fuchun

2014-12-17

Much attention has been given to the potential of halophytes as sources of tolerance traits for introduction into cereals. However, a great deal remains unknown about the diverse mechanisms employed by halophytes to cope with salinity. To characterize salt tolerance mechanisms underlying Karelinia caspica, an Asteraceae halophyte, we performed Large-scale transcriptomic analysis using a high-throughput Illumina sequencing platform. Comparative gene expression analysis was performed to correlate the effects of salt stress and ABA regulation at the molecular level. Total sequence reads generated by pyrosequencing were assembled into 287,185 non-redundant transcripts with an average length of 652 bp. Using the BLAST function in the Swiss-Prot, NCBI nr, GO, KEGG, and KOG databases, a total of 216,416 coding sequences associated with known proteins were annotated. Among these, 35,533 unigenes were classified into 69 gene ontology categories, and 18,378 unigenes were classified into 202 known pathways. Based on the fold changes observed when comparing the salt stress and control samples, 60,127 unigenes were differentially expressed, with 38,122 and 22,005 up- and down-regulated, respectively. Several of the differentially expressed genes are known to be involved in the signaling pathway of the plant hormone ABA, including ABA metabolism, transport, and sensing as well as the ABA signaling cascade. Transcriptome profiling of K. caspica contribute to a comprehensive understanding of K. caspica at the molecular level. Moreover, the global survey of differentially expressed genes in this species under salt stress and analyses of the effects of salt stress and ABA regulation will contribute to the identification and characterization of genes and molecular mechanisms underlying salt stress responses in Asteraceae plants.

LevelScheme: A level scheme drawing and scientific figure preparation system for Mathematica

Science.gov (United States)

Caprio, M. A.

2005-09-01

LevelScheme is a scientific figure preparation system for Mathematica. The main emphasis is upon the construction of level schemes, or level energy diagrams, as used in nuclear, atomic, molecular, and hadronic physics. LevelScheme also provides a general infrastructure for the preparation of publication-quality figures, including support for multipanel and inset plotting, customizable tick mark generation, and various drawing and labeling tasks. Coupled with Mathematica's plotting functions and powerful programming language, LevelScheme provides a flexible system for the creation of figures combining diagrams, mathematical plots, and data plots. Program summaryTitle of program:LevelScheme Catalogue identifier:ADVZ Program obtainable from: CPC Program Library, Queen's University of Belfast, N. Ireland Program summary URL:http://cpc.cs.qub.ac.uk/summaries/ADVZ Operating systems:Any which supports Mathematica; tested under Microsoft Windows XP, Macintosh OS X, and Linux Programming language used:Mathematica 4 Number of bytes in distributed program, including test and documentation:3 051 807 Distribution format:tar.gz Nature of problem:Creation of level scheme diagrams. Creation of publication-quality multipart figures incorporating diagrams and plots. Method of solution:A set of Mathematica packages has been developed, providing a library of level scheme drawing objects, tools for figure construction and labeling, and control code for producing the graphics.

Molecular science solving global problems

International Nuclear Information System (INIS)

Dunning, T.H. Jr.; Stults, B.R.

1995-01-01

From the late 1940s to the late 1980s, the Department of Energy (DOE) had a critical role in the Cold War. Many sites were built to contribute to the nation's nuclear weapons effort. However, not enough attention was paid to how the waste generated at these facilities should be handled. As a result, a number of sites fouled the soil around them or dumped low-level radioactive waste into nearby rivers. A DOE laboratory is under construction with a charter to help. Called the Environmental Molecular Sciences Laboratory (EMSL), this national user facility will be located at DOE's Pacific Northwest Laboratory (PNL) in Richland, WA. This laboratory has been funded by DOE and Congress to play a major role as the nation confronts the enormous challenge of reducing environmental and human risks from hundreds of government and industrial waste sites in an economically viable manner. The original proposal for the EMSL took a number of twists and turns on its way to its present form, but one thing remained constant: the belief that safe, permanent, cost-effective solutions to many of the country's environmental problems could be achieved only by multidisciplinary teams working to understand and control molecular processes. The processes of most concern are those that govern the transport and transformation of contaminants, the treatment and storage of high-level mixed wastes, and the risks those contaminants ultimately pose to workers and the public

Molecular-level insights into aging processes of skin elastin.

Science.gov (United States)

Mora Huertas, Angela C; Schmelzer, Christian E H; Hoehenwarter, Wolfgang; Heyroth, Frank; Heinz, Andrea

2016-01-01

Skin aging is characterized by different features including wrinkling, atrophy of the dermis and loss of elasticity associated with damage to the extracellular matrix protein elastin. The aim of this study was to investigate the aging process of skin elastin at the molecular level by evaluating the influence of intrinsic (chronological aging) and extrinsic factors (sun exposure) on the morphology and susceptibility of elastin towards enzymatic degradation. Elastin was isolated from biopsies derived from sun-protected or sun-exposed skin of differently aged individuals. The morphology of the elastin fibers was characterized by scanning electron microscopy. Mass spectrometric analysis and label-free quantification allowed identifying differences in the cleavage patterns of the elastin samples after enzymatic digestion. Principal component analysis and hierarchical cluster analysis were used to visualize differences between the samples and to determine the contribution of extrinsic and intrinsic aging to the proteolytic susceptibility of elastin. Moreover, the release of potentially bioactive peptides was studied. Skin aging is associated with the decomposition of elastin fibers, which is more pronounced in sun-exposed tissue. Marker peptides were identified, which showed an age-related increase or decrease in their abundances and provide insights into the progression of the aging process of elastin fibers. Strong age-related cleavage occurs in hydrophobic tropoelastin domains 18, 20, 24 and 26. Photoaging makes the N-terminal and central parts of the tropoelastin molecules more susceptible towards enzymatic cleavage and, hence, accelerates the age-related degradation of elastin. Copyright © 2016 Elsevier B.V. and Société Française de Biochimie et Biologie Moléculaire (SFBBM). All rights reserved.

Metabolomics as a Powerful Tool for Molecular Quality Assessment of the Fish Sparus aurata

Science.gov (United States)

Picone, Gianfranco; Engelsen, Søren Balling; Savorani, Francesco; Testi, Silvia; Badiani, Anna; Capozzi, Francesco

2011-01-01

The molecular profiles of perchloric acid solutions extracted from the flesh of Sparus aurata fish specimens, produced according to different aquaculture systems, have been investigated. The 1H-NMR spectra of aqueous extracts are indicative of differences in the metabolite content of fish reared under different conditions that are already distinguishable at their capture, and substantially maintain the same differences in their molecular profiles after sixteen days of storage under ice. The fish metabolic profiles are studied by top-down chemometric analysis. The results of this exploratory investigation show that the fish metabolome accurately reflects the rearing conditions. The level of many metabolites co-vary with the rearing conditions and a few metabolites are quantified including glycogen (stress indicator), histidine, alanine and glycine which all display significant changes dependent on the aquaculture system and on the storage times. PMID:22254093

Deciphering the molecular mechanisms underlying sea urchin reversible adhesion: A quantitative proteomics approach.

Science.gov (United States)

Lebesgue, Nicolas; da Costa, Gonçalo; Ribeiro, Raquel Mesquita; Ribeiro-Silva, Cristina; Martins, Gabriel G; Matranga, Valeria; Scholten, Arjen; Cordeiro, Carlos; Heck, Albert J R; Santos, Romana

2016-04-14

Marine bioadhesives have unmatched performances in wet environments, being an inspiration for biomedical applications. In sea urchins specialized adhesive organs, tube feet, mediate reversible adhesion, being composed by a disc, producing adhesive and de-adhesive secretions, and a motile stem. After tube foot detachment, the secreted adhesive remains bound to the substratum as a footprint. Sea urchin adhesive is composed by proteins and sugars, but so far only one protein, Nectin, was shown to be over-expressed as a transcript in tube feet discs, suggesting its involvement in sea urchin adhesion. Here we use high-resolution quantitative mass-spectrometry to perform the first study combining the analysis of the differential proteome of an adhesive organ, with the proteome of its secreted adhesive. This strategy allowed us to identify 163 highly over-expressed disc proteins, specifically involved in sea urchin reversible adhesion; to find that 70% of the secreted adhesive components fall within five protein groups, involved in exocytosis and microbial protection; and to provide evidences that Nectin is not only highly expressed in tube feet discs but is an actual component of the adhesive. These results give an unprecedented insight into the molecular mechanisms underlying sea urchin adhesion, and opening new doors to develop wet-reliable, reversible, and ecological biomimetic adhesives. Sea urchins attach strongly but in a reversible manner to substratum, being a valuable source of inspiration for industrial and biomedical applications. Yet, the molecular mechanisms governing reversible adhesion are still poorly studied delaying the engineering of biomimetic adhesives. We used the latest mass spectrometry techniques to analyze the differential proteome of an adhesive organ and the proteome of its secreted adhesive, allowing us to uncover the key players in sea urchin reversible adhesion. We demonstrate, that Nectin, a protein previously pointed out as potentially

Enhanced decomposition of dimethyl phthalate via molecular oxygen activated by Fe-Fe{sub 2}O{sub 3}/AC under microwave irradiation

Energy Technology Data Exchange (ETDEWEB)

Chen, Yiling [Key Laboratory of Pesticide and Chemical Biology of Ministry of Education, College of Chemistry, Central China Normal University, Wuhan 430079 (China); Ai, Zhihui, E-mail: jennifer.ai@mail.ccnu.edu.cn [Key Laboratory of Pesticide and Chemical Biology of Ministry of Education, College of Chemistry, Central China Normal University, Wuhan 430079 (China); Zhang, Lizhi [Key Laboratory of Pesticide and Chemical Biology of Ministry of Education, College of Chemistry, Central China Normal University, Wuhan 430079 (China)

2012-10-15

Highlights: Black-Right-Pointing-Pointer Microwave irradiation induces the electrons transferring from AC to Fe-Fe{sub 2}O{sub 3} and reacts with molecular oxygen. Black-Right-Pointing-Pointer Microwave heating accelerates the electron transferring from AC to Fe-Fe{sub 2}O{sub 3} to generate reactive oxygen species. Black-Right-Pointing-Pointer This environmental remediation method is feasible for aqueous organic pollutants treatment. - Abstract: In this study, we demonstrate that the decomposition of dimethyl phthalate under microwave irradiation could be greatly enhanced over Fe-Fe{sub 2}O{sub 3} nanowires supported on activated carbon (Fe-Fe{sub 2}O{sub 3}/AC). The great enhanced decomposition of dimethyl phthalate could be attributed to a unique microwave induced molecular oxygen activation process. Upon microwave irradiation, electrons could be transferred from activated carbon to zero-valent iron, and then react with molecular oxygen to form O{sub 2}{center_dot}{sup -} and {center_dot}OH radicals for the decomposition of dimethyl phthalate. The deactivation and the regeneration of Fe-Fe{sub 2}O{sub 3}/AC catalyst were systematically studied. We also found that microwave heating could accelerate the electron transferring from AC to Fe-Fe{sub 2}O{sub 3} to generate more reactive oxygen species for the decomposition of DMP than conventional oil bath heating. This novel molecular oxygen activation approach may find applications for wastewater treatment and drinking water purification.

The fate of fertilizer nitrogen in winter wheat under different water and nitrogen levels

International Nuclear Information System (INIS)

Li Shijuan; Zhou Dianxi; Lan Linwang

2002-01-01

N uptake and the fate of fertilizer N were studied in the field under different water and nitrogen levels with 15 N technique. Results showed that (1) the total N uptake of economical N treatment under saving irrigation was higher than that under conventional irrigation. Under saving irrigation the total N uptake of conventional N was higher than that of economical N treatment, yet the NHI decreased; (2) compared with saving irrigation, the N loss of conventional irrigation increased and NUE and soil residue decreased. On the same water condition the NUE and soil residue of conventional N treatment was lower than that of economical treatment, and N loss increased; (3) for the same fertilizer amount, the loss of N applied all as basal fertilizer is lower than that of part as basal and part as top-dressing treatment

Enhanced abundance of tintinnids under elevated CO2 level from coastal Bay of Bengal

Digital Repository Service at National Institute of Oceanography (India)

Biswas, H.; Gadi, S.D.; Venkataramana, V.; Bharathi, M.D.; Priyan, R.K.; Manjari, D.T.; DileepKumar, M.

of marine plankton to increasing CO2 concentrations. Natural water samples from the coastal Bay of Bengal were incubated under the ambient condition and high CO2 levels (703-711 latm) for 5 days in May and June 2010. A significant negative correlation...

Serum vitamin D and IgE levels in infants and children under 2 years ...

African Journals Online (AJOL)

Ehab

Serum vitamin D and IgE levels in infants and children under 2 years of age with recurrent chest ... from 6-24 months, diagnosed to have recurrent wheeze (>3 attacks), recruited ... IgE and the development of allergic sensitization29. Hence this ...

Dynamic combinatorial libraries: from exploring molecular recognition to systems chemistry.

Science.gov (United States)

Li, Jianwei; Nowak, Piotr; Otto, Sijbren

2013-06-26

Dynamic combinatorial chemistry (DCC) is a subset of combinatorial chemistry where the library members interconvert continuously by exchanging building blocks with each other. Dynamic combinatorial libraries (DCLs) are powerful tools for discovering the unexpected and have given rise to many fascinating molecules, ranging from interlocked structures to self-replicators. Furthermore, dynamic combinatorial molecular networks can produce emergent properties at systems level, which provide exciting new opportunities in systems chemistry. In this perspective we will highlight some new methodologies in this field and analyze selected examples of DCLs that are under thermodynamic control, leading to synthetic receptors, catalytic systems, and complex self-assembled supramolecular architectures. Also reviewed are extensions of the principles of DCC to systems that are not at equilibrium and may therefore harbor richer functional behavior. Examples include self-replication and molecular machines.

Stability of multi-objective bi-level linear programming problems under fuzziness

Directory of Open Access Journals (Sweden)

Abo-Sinna Mahmoud A.

2013-01-01

Full Text Available This paper deals with multi-objective bi-level linear programming problems under fuzzy environment. In the proposed method, tentative solutions are obtained and evaluated by using the partial information on preference of the decision-makers at each level. The existing results concerning the qualitative analysis of some basic notions in parametric linear programming problems are reformulated to study the stability of multi-objective bi-level linear programming problems. An algorithm for obtaining any subset of the parametric space, which has the same corresponding Pareto optimal solution, is presented. Also, this paper established the model for the supply-demand interaction in the age of electronic commerce (EC. First of all, the study uses the individual objectives of both parties as the foundation of the supply-demand interaction. Subsequently, it divides the interaction, in the age of electronic commerce, into the following two classifications: (i Market transactions, with the primary focus on the supply demand relationship in the marketplace; and (ii Information service, with the primary focus on the provider and the user of information service. By applying the bi-level programming technique of interaction process, the study will develop an analytical process to explain how supply-demand interaction achieves a compromise or why the process fails. Finally, a numerical example of information service is provided for the sake of illustration.

High Molecular Weight Adiponectin Levels are Neither Influenced by Adiponectin Polymorphisms Nor Associated with Insulin Resistance in Mixed-Ancestry Hyperglycemic Subjects from South Africa

Directory of Open Access Journals (Sweden)

Zemlin Annalise E

2016-10-01

Full Text Available Background: High molecular weight (HMW adiponectin has antiatherogenic, antiinflammatory and antidiabetic properties and these effects have been linked to its effect on high density lipoprotein cholesterol (HDL-c. Single nucleotide polymorphisms (SNPs in the adiponectin gene influence adiponectin levels. We examined the relationship between HMW-adiponectin levels and cardiometabolic traits in normo- and hyperglycemic mixed ancestry South Africans and correlated these levels to two common polymorphisms.

Molecular-nuclear transitions

International Nuclear Information System (INIS)

Belyaev, V.B.; Miller, M.B.

2007-01-01

Full text: The spectra in some light nuclei have one interesting property. For example, in the closed vicinity of some resonance states of such nuclei as 5 He, 8 Be, 18 F, 18 Ne the thresholds exist for two- or three-body decay of those nuclei. Let us consider the lightest of the above nuclei, 5 He. The energy threshold for 5 He > d+t decay is ∼50 keV lower than the energy of 3/2 + state of 5 He nucleus. However, due to a rather large width of this state, ∼70 keV, the nuclear capture of deuterons by tritons in dtm-molecule is highly enhanced in comparison with the process of dd capture in the ddm molecule. The physical reason for the enhancement of the probability of the capture into the resonant state can be associated with a long tail of wave function of the resonant state and, accordingly, with the large value of the overlap integral determining in general the probability of the transition between two systems. Thus, one can expect the enhancement of the molecular-nuclear transitions, and this was indeed observed experimentally for the case of dtm molecule. Now, let us consider some other molecular-nuclear combinations: 18 Ne - H 2 O, 18 F - 17 OH, and 8 Be - 6 LiD molecule. With the high accuracy the energies of the above molecular systems coincide with the energies of the resonant states in the appropriate nuclei. Due to the uncertainty in the experimental nuclear data it is not known at present whether the energies of these thresholds are lower or higher of the corresponding energies of the nuclear resonances. Let us assume that the molecular energy is few keV over the energy of the nuclear resonance. Then, we will deal with a very interesting phenomenon: the molecular-nuclear complex constitutes a two level system, which in some sense is analogous to the two-level atomic system, as in a laser. The crucial difference between this one and the two-level atomic systems consists in a fact that in the molecular-nuclear case no special procedure of pumping up

Molecular dynamics simulations of ejecta production from sinusoidal tin surfaces under supported and unsupported shocks

Directory of Open Access Journals (Sweden)

Bao Wu

2018-04-01

Full Text Available Micro-ejecta, an instability growth process, occurs at metal/vacuum or metal/gas interface when compressed shock wave releases from the free surface that contains surface defects. We present molecular dynamics (MD simulations to investigate the ejecta production from tin surface shocked by supported and unsupported waves with pressures ranging from 8.5 to 60.8 GPa. It is found that the loading waveforms have little effect on spike velocity while remarkably affect the bubble velocity. The bubble velocity of unsupported shock loading remains nonzero constant value at late time as observed in experiments. Besides, the time evolution of ejected mass in the simulations is compared with the recently developed ejecta source model, indicating the suppressed ejection of unmelted or partial melted materials. Moreover, different reference positions are chosen to characterize the amount of ejecta under different loading waveforms. Compared with supported shock case, the ejected mass of unsupported shock case saturates at lower pressure. Through the analysis on unloading path, we find that the temperature of tin sample increases quickly from tensile stress state to zero pressure state, resulting in the melting of bulk tin under decaying shock. Thus, the unsupported wave loading exhibits a lower threshold pressure causing the solid-liquid phase transition on shock release than the supported shock loading.

Molecular mechanisms underlying the role of microRNAs in the chemoresistance of pancreatic cancer.

Science.gov (United States)

Garajová, Ingrid; Le Large, Tessa Y; Frampton, Adam E; Rolfo, Christian; Voortman, Johannes; Giovannetti, Elisa

2014-01-01

Pancreatic ductal adenocarcinoma (PDAC) is an extremely severe disease where the mortality and incidence rates are almost identical. This is mainly due to late diagnosis and limited response to current treatments. The tumor macroenvironment/microenvironment have been frequently reported as the major contributors to chemoresistance in PDAC, preventing the drugs from reaching their intended site of action (i.e., the malignant duct cells). However, the recent discovery of microRNAs (miRNAs) has provided new directions for research on mechanisms underlying response to chemotherapy. Due to their tissue-/disease-specific expression and high stability in tissues and biofluids, miRNAs represent new promising diagnostic and prognostic/predictive biomarkers and therapeutic targets. Furthermore, several studies have documented that selected miRNAs, such as miR-21 and miR-34a, may influence response to chemotherapy in several tumor types, including PDAC. In this review, we summarize the current knowledge on the role of miRNAs in PDAC and recent advances in understanding their role in chemoresistance through multiple molecular mechanisms.

Molecular Mechanisms Underlying the Role of MicroRNAs in the Chemoresistance of Pancreatic Cancer

Directory of Open Access Journals (Sweden)

Ingrid Garajová

2014-01-01

Full Text Available Pancreatic ductal adenocarcinoma (PDAC is an extremely severe disease where the mortality and incidence rates are almost identical. This is mainly due to late diagnosis and limited response to current treatments. The tumor macroenvironment/microenvironment have been frequently reported as the major contributors to chemoresistance in PDAC, preventing the drugs from reaching their intended site of action (i.e., the malignant duct cells. However, the recent discovery of microRNAs (miRNAs has provided new directions for research on mechanisms underlying response to chemotherapy. Due to their tissue-/disease-specific expression and high stability in tissues and biofluids, miRNAs represent new promising diagnostic and prognostic/predictive biomarkers and therapeutic targets. Furthermore, several studies have documented that selected miRNAs, such as miR-21 and miR-34a, may influence response to chemotherapy in several tumor types, including PDAC. In this review, we summarize the current knowledge on the role of miRNAs in PDAC and recent advances in understanding their role in chemoresistance through multiple molecular mechanisms.

Comparative Transcriptome Analysis of Latex Reveals Molecular Mechanisms Underlying Increased Rubber Yield in Hevea brasiliensis Self-Rooting Juvenile Clones

OpenAIRE

Li, Hui-Liang; Guo, Dong; Zhu, Jia-Hong; Wang, Ying; Chen, Xiong-Ting; Peng, Shi-Qing

2016-01-01

Rubber tree (Hevea brasiliensis) self-rooting juvenile clones (JCs) are promising planting materials for rubber production. In a comparative trial between self-rooting JCs and donor clones (DCs), self-rooting JCs exhibited better performance in rubber yield. To study the molecular mechanism associated with higher rubber yield in self-rooting JCs, we sequenced and comparatively analyzed the latex of rubber tree self-rooting JCs and DCs at the transcriptome level. Total raw reads of 34,632,012 ...

Detailed assessment of gene activation levels by multiple hypoxia-responsive elements under various hypoxic conditions.

Science.gov (United States)

Takeuchi, Yasuto; Inubushi, Masayuki; Jin, Yong-Nan; Murai, Chika; Tsuji, Atsushi B; Hata, Hironobu; Kitagawa, Yoshimasa; Saga, Tsuneo

2014-12-01

HIF-1/HRE pathway is a promising target for the imaging and the treatment of intractable malignancy (HIF-1; hypoxia-inducible factor 1, HRE; hypoxia-responsive element). The purposes of our study are: (1) to assess the gene activation levels resulting from various numbers of HREs under various hypoxic conditions, (2) to evaluate the bidirectional activity of multiple HREs, and (3) to confirm whether multiple HREs can induce gene expression in vivo. Human colon carcinoma HCT116 cells were transiently transfected by the constructs containing a firefly luciferase reporter gene and various numbers (2, 4, 6, 8, 10, and 12) of HREs (nHRE+, nHRE-). The relative luciferase activities were measured under various durations of hypoxia (6, 12, 18, and 24 h), O2 concentrations (1, 2, 4, 8, and 16 %), and various concentrations of deferoxamine mesylate (20, 40, 80, 160, and 320 µg/mL growth medium). The bidirectional gene activation levels by HREs were examined in the constructs (dual-luc-nHREs) containing firefly and Renilla luciferase reporter genes at each side of nHREs. Finally, to test whether the construct containing 12HRE and the NIS reporter gene (12HRE-NIS) can induce gene expression in vivo, SPECT imaging was performed in a mouse xenograft model. (1) gene activation levels by HREs tended to increase with increasing HRE copy number, but a saturation effect was observed in constructs with more than 6 or 8 copies of an HRE, (2) gene activation levels by HREs increased remarkably during 6-12 h of hypoxia, but not beyond 12 h, (3) gene activation levels by HREs decreased with increasing O2 concentrations, but could be detected even under mild hypoxia at 16 % O2, (4) the bidirectionally proportional activity of the HRE was confirmed regardless of the hypoxic severity, and (5) NIS expression driven by 12 tandem copies of an HRE in response to hypoxia could be visualized on in vivo SPECT imaging. The results of this study will help in the understanding and assessment of

Synthesis of one-dimensional metal-containing insulated molecular wire with versatile properties directed toward molecular electronics materials.

Science.gov (United States)

Masai, Hiroshi; Terao, Jun; Seki, Shu; Nakashima, Shigeto; Kiguchi, Manabu; Okoshi, Kento; Fujihara, Tetsuaki; Tsuji, Yasushi

2014-02-05

We report, herein, the design, synthesis, and properties of new materials directed toward molecular electronics. A transition metal-containing insulated molecular wire was synthesized through the coordination polymerization of a Ru(II) porphyrin with an insulated bridging ligand of well-defined structure. The wire displayed not only high linearity and rigidity, but also high intramolecular charge mobility. Owing to the unique properties of the coordination bond, the interconversion between the monomer and polymer states was realized under a carbon monoxide atmosphere or UV irradiation. The results demonstrated a high potential of the metal-containing insulated molecular wire for applications in molecular electronics.

Integrative Bioinformatic Analysis of Transcriptomic Data Identifies Conserved Molecular Pathways Underlying Ionizing Radiation-Induced Bystander Effects (RIBE

Directory of Open Access Journals (Sweden)

Constantinos Yeles

2017-11-01

Full Text Available Ionizing radiation-induced bystander effects (RIBE encompass a number of effects with potential for a plethora of damages in adjacent non-irradiated tissue. The cascade of molecular events is initiated in response to the exposure to ionizing radiation (IR, something that may occur during diagnostic or therapeutic medical applications. In order to better investigate these complex response mechanisms, we employed a unified framework integrating statistical microarray analysis, signal normalization, and translational bioinformatics functional analysis techniques. This approach was applied to several microarray datasets from Gene Expression Omnibus (GEO related to RIBE. The analysis produced lists of differentially expressed genes, contrasting bystander and irradiated samples versus sham-irradiated controls. Furthermore, comparative molecular analysis through BioInfoMiner, which integrates advanced statistical enrichment and prioritization methodologies, revealed discrete biological processes, at the cellular level. For example, the negative regulation of growth, cellular response to Zn2+-Cd2+, and Wnt and NIK/NF-kappaB signaling, thus refining the description of the phenotypic landscape of RIBE. Our results provide a more solid understanding of RIBE cell-specific response patterns, especially in the case of high-LET radiations, like α-particles and carbon-ions.

Tungsten polyoxometalate molecules as active nodes for dynamic carrier exchange in hybrid molecular/semiconductor capacitors

International Nuclear Information System (INIS)

Balliou, A.; Douvas, A. M.; Normand, P.; Argitis, P.; Glezos, N.; Tsikritzis, D.; Kennou, S.

2014-01-01

In this work we study the utilization of molecular transition metal oxides known as polyoxometalates (POMs), in particular the Keggin structure anions of the formula PW 12 O 40 3− , as active nodes for potential switching and/or fast writing memory applications. The active molecules are being integrated in hybrid Metal-Insulator/POM molecules-Semiconductor capacitors, which serve as prototypes allowing investigation of critical performance characteristics towards the design of more sophisticated devices. The charging ability as well as the electronic structure of the molecular layer is probed by means of electrical characterization, namely, capacitance-voltage and current-voltage measurements, as well as transient capacitance measurements, C (t), under step voltage polarization. It is argued that the transient current peaks observed are manifestations of dynamic carrier exchange between the gate electrode and specific molecular levels, while the transient C (t) curves under conditions of molecular charging can supply information for the rate of change of the charge that is being trapped and de-trapped within the molecular layer. Structural characterization via surface and cross sectional scanning electron microscopy as well as atomic force microscopy, spectroscopic ellipsometry, UV and Fourier-transform IR spectroscopies, UPS, and XPS contribute to the extraction of accurate electronic structure characteristics and open the path for the design of new devices with on-demand tuning of their interfacial properties via the controlled preparation of the POM layer.

Light-Triggered Soft Artificial Muscles: Molecular-Level Amplification of Actuation Control Signals.

Science.gov (United States)

Dicker, Michael P M; Baker, Anna B; Iredale, Robert J; Naficy, Sina; Bond, Ian P; Faul, Charl F J; Rossiter, Jonathan M; Spinks, Geoffrey M; Weaver, Paul M

2017-08-23

The principle of control signal amplification is found in all actuation systems, from engineered devices through to the operation of biological muscles. However, current engineering approaches require the use of hard and bulky external switches or valves, incompatible with both the properties of emerging soft artificial muscle technology and those of the bioinspired robotic systems they enable. To address this deficiency a biomimetic molecular-level approach is developed that employs light, with its excellent spatial and temporal control properties, to actuate soft, pH-responsive hydrogel artificial muscles. Although this actuation is triggered by light, it is largely powered by the resulting excitation and runaway chemical reaction of a light-sensitive acid autocatalytic solution in which the actuator is immersed. This process produces actuation strains of up to 45% and a three-fold chemical amplification of the controlling light-trigger, realising a new strategy for the creation of highly functional soft actuating systems.

Low Molecular Weight Fucoidan Inhibits Tumor Angiogenesis through Downregulation of HIF-1/VEGF Signaling under Hypoxia

Directory of Open Access Journals (Sweden)

Meng-Chuan Chen

2015-07-01

Full Text Available Activation of hypoxia-induced hypoxia-inducible factors-1 (HIF-1 plays a critical role in promoting tumor angiogenesis, growth and metastasis. Low molecular weight fucoidan (LMWF is prepared from brown algae, and exhibits anticancer activity. However, whether LMWF attenuates hypoxia-induced angiogenesis in bladder cancer cells and the molecular mechanisms involved remain unclear. This is the first study to demonstrate that LMWF can inhibit hypoxia-stimulated H2O2 formation, HIF-1 accumulation and transcriptional activity vascular endothelial growth factor (VEGF secretion, and the migration and invasion in hypoxic human bladder cancer cells (T24 cells. LMWF also downregulated hypoxia-activated phosphorylation of PI3K/AKT/mTOR/p70S6K/4EBP-1 signaling in T24 cells. Blocking PI3K/AKT or mTOR activity strongly diminished hypoxia-induced HIF-1α expression and VEGF secretion in T24 cells, supporting the involvement of PI3K/AKT/mTOR in the induction of HIF-1α and VEGF. Additionally, LMWF significantly attenuated angiogenesis in vitro and in vivo evidenced by reduction of tube formation of hypoxic human umbilical vascular endothelial cells and blood capillary generation in the tumor. Similarly, administration of LMWF also inhibited the HIF-1α and VEGF expression in vivo, accompanied by a reduction of tumor growth. In summary, under hypoxia conditions, the antiangiogenic activity of LMWF in bladder cancer may be associated with suppressing HIF-1/VEGF-regulated signaling pathway.

Cellular and molecular repair of X-ray-induced damage: dependence on oxygen tension and nutritional status

International Nuclear Information System (INIS)

Spiro, I.J.; Kennedy, K.A.; Stickler, R.; Ling, C.C.

1985-01-01

Cellular and molecular repair was studied at 23 0 C using split-dose recovery and alkaline elution techniques, respectively, as a function of cellular oxygen and nutrient conditions. Hypoxic cells in full medium showed a partial reduction in the level of sublethal damage (SLD) repair relative to aerated cells; the respective repair kinetics were similar with a common repair half-time of 30 min. Similarly, hypoxic cells showed a slight reduction in strand break rejoining capacity compared to aerated cells. Under nutrient deprivation, anoxic cells displayed no SLD repair or strand break repair, while aerated cells exhibited the same level of SLD and strand break repair as for well-fed cells. In addition, nutrient deprived cells at low O 2 levels displayed normal SLD and strand break repair capability. These results indicate that both nutrient and O 2 deprivation are necessary for complete inhibition of cellular and molecular repair, and low levels of O 2 can effectively reverse this inhibition

Mathematical modeling of the crack growth in linear elastic isotropic materials by conventional fracture mechanics approaches and by molecular dynamics method: crack propagation direction angle under mixed mode loading

Science.gov (United States)

Stepanova, Larisa; Bronnikov, Sergej

2018-03-01

The crack growth directional angles in the isotropic linear elastic plane with the central crack under mixed-mode loading conditions for the full range of the mixity parameter are found. Two fracture criteria of traditional linear fracture mechanics (maximum tangential stress and minimum strain energy density criteria) are used. Atomistic simulations of the central crack growth process in an infinite plane medium under mixed-mode loading using Large-scale Molecular Massively Parallel Simulator (LAMMPS), a classical molecular dynamics code, are performed. The inter-atomic potential used in this investigation is Embedded Atom Method (EAM) potential. The plane specimens with initial central crack were subjected to Mixed-Mode loadings. The simulation cell contains 400000 atoms. The crack propagation direction angles under different values of the mixity parameter in a wide range of values from pure tensile loading to pure shear loading in a wide diapason of temperatures (from 0.1 К to 800 К) are obtained and analyzed. It is shown that the crack propagation direction angles obtained by molecular dynamics method coincide with the crack propagation direction angles given by the multi-parameter fracture criteria based on the strain energy density and the multi-parameter description of the crack-tip fields.

Atomic level insights into realistic molecular models of dendrimer-drug complexes through MD simulations

Science.gov (United States)

Jain, Vaibhav; Maiti, Prabal K.; Bharatam, Prasad V.

2016-09-01

Computational studies performed on dendrimer-drug complexes usually consider 1:1 stoichiometry, which is far from reality, since in experiments more number of drug molecules get encapsulated inside a dendrimer. In the present study, molecular dynamic (MD) simulations were implemented to characterize the more realistic molecular models of dendrimer-drug complexes (1:n stoichiometry) in order to understand the effect of high drug loading on the structural properties and also to unveil the atomistic level details. For this purpose, possible inclusion complexes of model drug Nateglinide (Ntg) (antidiabetic, belongs to Biopharmaceutics Classification System class II) with amine- and acetyl-terminated G4 poly(amidoamine) (G4 PAMAM(NH2) and G4 PAMAM(Ac)) dendrimers at neutral and low pH conditions are explored in this work. MD simulation analysis on dendrimer-drug complexes revealed that the drug encapsulation efficiency of G4 PAMAM(NH2) and G4 PAMAM(Ac) dendrimers at neutral pH was 6 and 5, respectively, while at low pH it was 12 and 13, respectively. Center-of-mass distance analysis showed that most of the drug molecules are located in the interior hydrophobic pockets of G4 PAMAM(NH2) at both the pH; while in the case of G4 PAMAM(Ac), most of them are distributed near to the surface at neutral pH and in the interior hydrophobic pockets at low pH. Structural properties such as radius of gyration, shape, radial density distribution, and solvent accessible surface area of dendrimer-drug complexes were also assessed and compared with that of the drug unloaded dendrimers. Further, binding energy calculations using molecular mechanics Poisson-Boltzmann surface area approach revealed that the location of drug molecules in the dendrimer is not the decisive factor for the higher and lower binding affinity of the complex, but the charged state of dendrimer and drug, intermolecular interactions, pH-induced conformational changes, and surface groups of dendrimer do play an

Multishell structure formation in Ni nanowire under uniaxial strain along <0 0 1> crystallographic direction: A molecular dynamics simulation

Energy Technology Data Exchange (ETDEWEB)

Wang Li, E-mail: wanglihxf@sdu.edu.c [School of Mechanical and Electrical Engineering, Shandong University at Weihai, 180 Wenhuaxi Road, Weihai 264209 (China); Peng Chuanxiao [Key Laboratory of Liquid Structure and Heredity of Materials, Ministry of Education, Shandong University, Jinan 250061 (China); Gong Jianhong [School of Mechanical and Electrical Engineering, Shandong University at Weihai, 180 Wenhuaxi Road, Weihai 264209 (China)

2010-04-01

Molecular dynamics simulations based upon embedded-atom-method potential are employed to explore the fracture behavior of Ni nanowire along <0 0 1> crystallographic direction at temperature of 300 K. We find the formation of (5,5) multishell structure (MS), which is transformed from (6,5) MS at the necking region of nanowire under the strain rate of 0.02%ps{sup -1}. A reorientation transformation from <0 0 1> to <1 1 0> is first detected before formation of (6,5) MS. The formed (5,5) MS is more stable and can be tensioned longer as lower strain rate is loaded.

Effect of Magnesium on Gas Exchange and Photosynthetic Efficiency of Coffee Plants Grown under Different Light Levels

Directory of Open Access Journals (Sweden)

Kaio Gonçalves de Lima Dias

2017-09-01

Full Text Available The aim of the present study was to investigate the effects of magnesium on the gas exchange and photosynthetic efficiency of Coffee seedlings grown in nutrient solution under different light levels. The experiment was conducted under controlled conditions in growth chambers and nutrient solution at the Department of Plant Pathology of the Federal University of Lavras. The treatments consisted of five different Mg concentrations (0, 48, 96, 192 and 384 mg·L−1 and four light levels (80, 160, 240 and 320 µmol photon m−2·s−1. Both the Mg concentration and light levels affected gas exchange in the coffee plants. Photosynthesis increased linearly with the increasing light, indicating that the light levels tested were low for this crop. The highest CO2 assimilation rate, lowest transpiration, and highest water use efficiency were observed with 250 mg·Mg·L−1, indicating that this concentration was the optimal Mg supply for the tested light levels.

Molecular Combing of DNA: Methods and Applications

DEFF Research Database (Denmark)

Nazari, Zeniab Esmail; Gurevich, Leonid

2013-01-01

studies to nanoelectronics. While molecular combing has been applied in a variety of DNA-related studies, no comprehensive review has been published on different combing methods proposed so far. In this review, the underlying mechanisms of molecular combing of DNA are described followed by discussion...

Synthesis of molecularly imprinted polypyrrole/titanium dioxide nanocomposites and its selective photocatalytic degradation of rhodamine B under visible light irradiation

Directory of Open Access Journals (Sweden)

M. Q. He

2014-11-01

Full Text Available Highly selective molecularly imprinted nanocomposites MIPRhB-PPy/TiO2 were successfully prepared by surface molecular imprinting technique with rhodamine B (RhB as template molecule. The prepared MIPRhB-PPy/TiO2 coated with a thin imprinted layer could respond to visible light. The static and dynamic binding experiments revealed that MIPRhB-PPy/TiO2 possessed strong affinity, high adsorption capacity and fast adsorption rate for RhB. The selectivity experiments indicated that MIPRhB-PPy/TiO2 had excellent recognition selectivity for RhB. Selective photocatalytic degradation experiments indicated that the apparent rate constant (k for the photodegradation of RhB over MIPRhB-PPy/TiO2 is 0.0158 min–1, being 3.6 times of that over non-imprinted nanocomposites NIPRhB-PPy/TiO2 (0.0044 min–1. Compared with the NIPRhB-PPy/TiO2, MIPRhB-PPy/TiO2 showed higher photocatalytic selectivity toward RhB under visible light, which was attributed the introduction of the imprinted cavities on the surface of MIPRhB-PPy/TiO2. Moreover, MIPRhB-PPy/TiO2 exhibited high reusability and stability. The results indicate that molecularly imprinted nanocomposites MIPRhB-PPy/TiO2 have a promising perspective in industrial wastewater treatment.

Molecular Physiology of Root System Architecture in Model Grasses

Science.gov (United States)

Hixson, K.; Ahkami, A. H.; Anderton, C.; Veličković, D.; Myers, G. L.; Chrisler, W.; Lindenmaier, R.; Fang, Y.; Yabusaki, S.; Rosnow, J. J.; Farris, Y.; Khan, N. E.; Bernstein, H. C.; Jansson, C.

2017-12-01

Unraveling the molecular and physiological mechanisms involved in responses of Root System Architecture (RSA) to abiotic stresses and shifts in microbiome structure is critical to understand and engineer plant-microbe-soil interactions in the rhizosphere. In this study, accessions of Brachypodium distachyon Bd21 (C3 model grass) and Setaria viridis A10.1 (C4 model grass) were grown in phytotron chambers under current and elevated CO2 levels. Detailed growth stage-based phenotypic analysis revealed different above- and below-ground morphological and physiological responses in C3 and C4 grasses to enhanced CO2 levels. Based on our preliminary results and by screening values of total biomass, water use efficiency, root to shoot ratio, RSA parameters and net assimilation rates, we postulated a three-phase physiological mechanism, i.e. RootPlus, BiomassPlus and YieldPlus phases, for grass growth under elevated CO2 conditions. Moreover, this comprehensive set of morphological and process-based observations are currently in use to develop, test, and calibrate biophysical whole-plant models and in particular to simulate leaf-level photosynthesis at various developmental stages of C3 and C4 using the model BioCro. To further link the observed phenotypic traits at the organismal level to tissue and molecular levels, and to spatially resolve the origin and fate of key metabolites involved in primary carbohydrate metabolism in different root sections, we complement root phenotypic observations with spatial metabolomics data using mass spectrometry imaging (MSI) methods. Focusing on plant-microbe interactions in the rhizosphere, six bacterial strains with plant growth promoting features are currently in use in both gel-based and soil systems to screen root growth and development in Brachypodium. Using confocal microscopy, GFP-tagged bacterial systems are utilized to study the initiation of different root types of RSA, including primary root (PR), coleoptile node axile root (CNR

Molecular Evidence for Species-Level Distinctions in Clouded Leopards

OpenAIRE

Buckley-Beason, Valerie A.; Johnson, Warren E.; Nash, Willliam G.; Stanyon, Roscoe; Menninger, Joan C.; Driscoll, Carlos A.; Howard, JoGayle; Bush, Mitch; Page, John E.; Roelke, Melody E.; Stone, Gary; Martelli, Paolo P.; Wen, Ci; Ling, Lin; Duraisingam, Ratna K.

2006-01-01

Among the 37 living species of Felidae, the clouded leopard (Neofelis nebulosa) is generally classified as a monotypic genus basal to the Panthera lineage of great cats [1–5]. This secretive, mid-sized (16–23 kg) carnivore, now severely endangered, is traditionally subdivided into four southeast Asian subspecies (Figure 1A) [4–8]. We used molecular genetic methods to re-evaluate subspecies partitions and to quantify patterns of population genetic variation among 109 clouded leopards of known ...

Step-flow anisotropy of the m-plane GaN (1100) grown under nitrogen-rich conditions by plasma-assisted molecular beam epitaxy

International Nuclear Information System (INIS)

Sawicka, Marta; Siekacz, Marcin; Skierbiszewski, Czeslaw; Turski, Henryk; Krysko, Marcin; DziePcielewski, Igor; Grzegory, Izabella; Smalc-Koziorowska, Julita

2011-01-01

The homoepitaxial growth of m-plane (1100) GaN was investigated by plasma-assisted molecular beam epitaxy under nitrogen-rich conditions. The surface morphologies as a function of sample miscut were studied, providing evidence for a strong growth anisotropy that is a consequence of the anisotropy of Ga adatom diffusion barriers on the m-plane surface recently calculated ab initio[Lymperakis and Neugebauer, Phys. Rev. B 79, 241308(R) (2009)]. We found that substrate miscut toward [0001] implies a step flow toward while substrate miscut toward [0001] causes formation of atomic steps either perpendicular or parallel to the [0001] direction, under N-rich conditions at 730 deg C. We describe the growth conditions for achieving atomically flat m-plane GaN layers with parallel atomic steps.

Computational methods for molecular imaging

CERN Document Server

Shi, Kuangyu; Li, Shuo

2015-01-01

This volume contains original submissions on the development and application of molecular imaging computing. The editors invited authors to submit high-quality contributions on a wide range of topics including, but not limited to: • Image Synthesis & Reconstruction of Emission Tomography (PET, SPECT) and other Molecular Imaging Modalities • Molecular Imaging Enhancement • Data Analysis of Clinical & Pre-clinical Molecular Imaging • Multi-Modal Image Processing (PET/CT, PET/MR, SPECT/CT, etc.) • Machine Learning and Data Mining in Molecular Imaging. Molecular imaging is an evolving clinical and research discipline enabling the visualization, characterization and quantification of biological processes taking place at the cellular and subcellular levels within intact living subjects. Computational methods play an important role in the development of molecular imaging, from image synthesis to data analysis and from clinical diagnosis to therapy individualization. This work will bring readers fro...

The coherence lifetime-borrowing effect in vibronically coupled molecular aggregates under non-perturbative system-environment interactions.

Science.gov (United States)

Yeh, Shu-Hao; Engel, Gregory S.; Kais, Sabre

Recently it has been suggested that the long-lived coherences in some photosynthetic pigment-protein systems, such as the Fenna-Matthews-Olson complex, could be attributed to the mixing of the pigments' electronic and vibrational degrees of freedom. In order to verify whether this is the case and to understand its underlying mechanism, a theoretical model capable of including both the electronic excitations and intramolecular vibrational modes of the pigments is necessary. Our model simultaneously considers the electronic and vibrational degrees of freedom, treating the system-environment interactions non-perturbatively by implementing the hierarchical equations of motion approach. Here we report the simulated two-dimensional electronic spectra of vibronically coupled molecular dimers to demonstrate how the electronic coherence lifetimes can be extended by borrowing the lifetime from the vibrational coherences. Funded by Qatar National Research Fund and Qatar Environment and Energy Research Institute.

Molecular imaging and the unification of multilevel mechanisms and data in medical physics

International Nuclear Information System (INIS)

Nikiforidis, George C.; Sakellaropoulos, George C.; Kagadis, George C.

2008-01-01

Molecular imaging (MI) constitutes a recently developed approach of imaging, where modalities and agents have been reinvented and used in novel combinations in order to expose and measure biologic processes occurring at molecular and cellular levels. It is an approach that bridges the gap between modalities acquiring data from high (e.g., computed tomography, magnetic resonance imaging, and positron-emitting isotopes) and low (e.g., PCR, microarrays) levels of a biological organization. While data integration methodologies will lead to improved diagnostic and prognostic performance, interdisciplinary collaboration, triggered by MI, will result in a better perception of the underlying biological mechanisms. Toward the development of a unifying theory describing these mechanisms, medical physicists can formulate new hypotheses, provide the physical constraints bounding them, and consequently design appropriate experiments. Their new scientific and working environment calls for interventions in their syllabi to educate scientists with enhanced capabilities for holistic views and synthesis.

Excitation of high energy levels under laser exposure of suspensions of nanoparticles in liquids

Energy Technology Data Exchange (ETDEWEB)

Shafeev, G.A. [Wave Research Center of A.M. Prokhorov General Physics Institute, 38, Vavilov Street, 119991 Moscow (Russian Federation)], E-mail: shafeev@kapella.gpi.ru; Simakin, A.V. [Wave Research Center of A.M. Prokhorov General Physics Institute, 38, Vavilov Street, 119991 Moscow (Russian Federation); Bozon-Verduraz, F. [ITODYS, UMR CNRS 7086, Universite Paris 7-Denis Diderot, 2, place Jussieu, 75251 Paris cedex 05 (France); Robert, M. [Laboratoire d' Electrochimie Moleculaire, UMR CNRS 7591, Universite Paris 7 Denis Diderot, 2, place Jussieu, 75251 Paris cedex 05 (France)

2007-12-15

Laser exposure of suspensions of nanoparticles in liquids leads to excitation of high energy levels in both liquid and nanoparticle material. The emission spectrum of the colloidal solution under exposure of a suspension metallic nanoparticles in water to radiation of a Nd:YAG laser of a picosecond range of pulse duration is discussed. Excitation of nuclear energy levels and neutron release is experimentally studied on the model system of transmutation of Hg into Au that occurs under exposure of Hg nanodrops suspended in D{sub 2}O. The proposed mechanism involves: (i) emission of X-ray photons by Hg nanoparticles upon laser exposure, leading to neutron release from D{sub 2}O, (ii) initiation of Hg {yields} Au transmutation by the capture of neutrons. The effect of transmutation is more pronounced using {sup 196}Hg isotope instead of Hg of natural isotope composition. The influence of laser pulse duration on the degree of transmutation (from fs through ns range) is discussed.

Time Domains of the Hypoxic Ventilatory Response and Their Molecular Basis

Science.gov (United States)

Pamenter, Matthew E.; Powell, Frank L.

2016-01-01

Ventilatory responses to hypoxia vary widely depending on the pattern and length of hypoxic exposure. Acute, prolonged, or intermittent hypoxic episodes can increase or decrease breathing for seconds to years, both during the hypoxic stimulus, and also after its removal. These myriad effects are the result of a complicated web of molecular interactions that underlie plasticity in the respiratory control reflex circuits and ultimately control the physiology of breathing in hypoxia. Since the time domains of the physiological hypoxic ventilatory response (HVR) were identified, considerable research effort has gone toward elucidating the underlying molecular mechanisms that mediate these varied responses. This research has begun to describe complicated and plastic interactions in the relay circuits between the peripheral chemoreceptors and the ventilatory control circuits within the central nervous system. Intriguingly, many of these molecular pathways seem to share key components between the different time domains, suggesting that varied physiological HVRs are the result of specific modifications to overlapping pathways. This review highlights what has been discovered regarding the cell and molecular level control of the time domains of the HVR, and highlights key areas where further research is required. Understanding the molecular control of ventilation in hypoxia has important implications for basic physiology and is emerging as an important component of several clinical fields. PMID:27347896

Molecular-level characterization of elastin-like constructs and human aortic elastin

DEFF Research Database (Denmark)

Heinz, Andrea; Schräder, Christoph U; Baud, Stéphanie

2014-01-01

This study aimed to characterize the structures of two elastin-like constructs, one composed of a cross-linked elastin-like polypeptide and the other one of cross-linked tropoelastin, and native aortic elastin. The structures of the insoluble materials and human aortic elastin were investigated...... quantification revealed that the cross-linking degree of the two in vitro cross-linked materials was significantly lower than that of native elastin. Molecular dynamics simulations were performed, based on molecular species identified in the samples, to follow the formation of elastin cross-links. The results...... provide evidence for the significance of the GVGTP hinge region of domain 23 for the formation of elastin cross-links. Overall, this work provides important insight into structural similarities and differences between elastin-like constructs and native elastin. Furthermore, it represents a step toward...

Global Changes in Drought Conditions Under Different Levels of Warming

Science.gov (United States)

Naumann, G.; Alfieri, L.; Wyser, K.; Mentaschi, L.; Betts, R. A.; Carrao, H.; Spinoni, J.; Vogt, J.; Feyen, L.

2018-04-01

Higher evaporative demands and more frequent and persistent dry spells associated with rising temperatures suggest that drought conditions could worsen in many regions of the world. In this study, we assess how drought conditions may develop across the globe for 1.5, 2, and 3°C warming compared to preindustrial temperatures. Results show that two thirds of global population will experience a progressive increase in drought conditions with warming. For drying areas, drought durations are projected to rise at rapidly increasing rates with warming, averaged globally from 2.0 month/°C below 1.5°C to 4.2 month/°C when approaching 3°C. Drought magnitudes could double for 30% of global landmass under stringent mitigation. If contemporary warming rates continue, water supply-demand deficits could become fivefold in size for most of Africa, Australia, southern Europe, southern and central states of the United States, Central America, the Caribbean, north-west China, and parts of Southern America. In approximately 20% of the global land surface, drought magnitude will halve with warming of 1.5°C and higher levels, mainly most land areas north of latitude 55°N, but also parts of South America and Eastern and South-eastern Asia. A progressive and significant increase in frequency of droughts is projected with warming in the Mediterranean basin, most of Africa, West and Southern Asia, Central America, and Oceania, where droughts are projected to happen 5 to 10 times more frequent even under ambitious mitigation targets and current 100-year events could occur every two to five years under 3°C of warming.

Molecular selectivity of graphene-enhanced Raman scattering.

Science.gov (United States)

Huang, Shengxi; Ling, Xi; Liang, Liangbo; Song, Yi; Fang, Wenjing; Zhang, Jin; Kong, Jing; Meunier, Vincent; Dresselhaus, Mildred S

2015-05-13

Graphene-enhanced Raman scattering (GERS) is a recently discovered Raman enhancement phenomenon that uses graphene as the substrate for Raman enhancement and can produce clean and reproducible Raman signals of molecules with increased signal intensity. Compared to conventional Raman enhancement techniques, such as surface-enhanced Raman scattering (SERS) and tip-enhanced Raman scattering (TERS), in which the Raman enhancement is essentially due to the electromagnetic mechanism, GERS mainly relies on a chemical mechanism and therefore shows unique molecular selectivity. In this paper, we report graphene-enhanced Raman scattering of a variety of different molecules with different molecular properties. We report a strong molecular selectivity for the GERS effect with enhancement factors varying by as much as 2 orders of magnitude for different molecules. Selection rules are discussed with reference to two main features of the molecule, namely its molecular energy levels and molecular structures. In particular, the enhancement factor involving molecular energy levels requires the highest occupied molecular orbital (HOMO) and lowest unoccupied molecular orbital (LUMO) energies to be within a suitable range with respect to graphene's Fermi level, and this enhancement effect can be explained by the time-dependent perturbation theory of Raman scattering. The enhancement factor involving the choice of molecular structures indicates that molecular symmetry and substituents similar to that of the graphene structure are found to be favorable for GERS enhancement. The effectiveness of these factors can be explained by group theory and the charge-transfer interaction between molecules and graphene. Both factors, involving the molecular energy levels and structural symmetry of the molecules, suggest that a remarkable GERS enhancement requires strong molecule-graphene coupling and thus effective charge transfer between the molecules and graphene. These conclusions are further

Contributions to advances in blend pellet products (BPP) research on molecular structure and molecular nutrition interaction by advanced synchrotron and globar molecular (Micro)spectroscopy.

Science.gov (United States)

Guevara-Oquendo, Víctor H; Zhang, Huihua; Yu, Peiqiang

2018-04-13

To date, advanced synchrotron-based and globar-sourced techniques are almost unknown to food and feed scientists. There has been little application of these advanced techniques to study blend pellet products at a molecular level. This article aims to provide recent research on advanced synchrotron and globar vibrational molecular spectroscopy contributions to advances in blend pellet products research on molecular structure and molecular nutrition interaction. How processing induced molecular structure changes in relation to nutrient availability and utilization of the blend pellet products. The study reviews Utilization of co-product components for blend pellet product in North America; Utilization and benefits of inclusion of pulse screenings; Utilization of additives in blend pellet products; Application of pellet processing in blend pellet products; Conventional evaluation techniques and methods for blend pellet products. The study focus on recent applications of cutting-edge vibrational molecular spectroscopy for molecular structure and molecular structure association with nutrient utilization in blend pellet products. The information described in this article gives better insight on how advanced molecular (micro)spectroscopy contributions to advances in blend pellet products research on molecular structure and molecular nutrition interaction.

A new instrument of VUV laser desorption/ionization mass spectrometry imaging with micrometer spatial resolution and low level of molecular fragmentation.

Science.gov (United States)

Wang, Jia; Liu, Feng; Mo, Yuxiang; Wang, Zhaoying; Zhang, Sichun; Zhang, Xinrong

2017-11-01

Mass spectrometry imaging (MSI) has important applications in material research, biology, and medicine. The MSI method based on UV laser desorption/ionization (UVLDI) can obtain images of intact samples, but has a high level of molecular fragmentation. In this work, we report a new MSI instrument that uses a VUV laser (125.3 nm) as a desorption/ionization source to exploit its advantages of high single photon energy and small focus size. The new instrument was tested by the mass spectra of Nile red and FGB (Fibrinogen beta chain) samples and mass spectrometric images of a fly brain section. For the tested samples, the VUVDI method offers lower levels of molecular fragmentations and higher sensitivities than those of the UVLDI method and second ion mass spectrometry imaging method using a Bi 3 + beam. The ablation crater produced by the focused VUV laser on a quartz plate has an area of 10 μm 2 . The VUV laser is prepared based on the four-wave mixing method using three collimated laser beams and a heated Hg cell.

A new instrument of VUV laser desorption/ionization mass spectrometry imaging with micrometer spatial resolution and low level of molecular fragmentation

Science.gov (United States)

Wang, Jia; Liu, Feng; Mo, Yuxiang; Wang, Zhaoying; Zhang, Sichun; Zhang, Xinrong

2017-11-01

Mass spectrometry imaging (MSI) has important applications in material research, biology, and medicine. The MSI method based on UV laser desorption/ionization (UVLDI) can obtain images of intact samples, but has a high level of molecular fragmentation. In this work, we report a new MSI instrument that uses a VUV laser (125.3 nm) as a desorption/ionization source to exploit its advantages of high single photon energy and small focus size. The new instrument was tested by the mass spectra of Nile red and FGB (Fibrinogen beta chain) samples and mass spectrometric images of a fly brain section. For the tested samples, the VUVDI method offers lower levels of molecular fragmentations and higher sensitivities than those of the UVLDI method and second ion mass spectrometry imaging method using a Bi3+ beam. The ablation crater produced by the focused VUV laser on a quartz plate has an area of 10 μm2. The VUV laser is prepared based on the four-wave mixing method using three collimated laser beams and a heated Hg cell.

Molecular Structural Transformation of 2:1 Clay Minerals by a Constant-Pressure Molecular Dynamics Simulation Method

International Nuclear Information System (INIS)

Wang, J.; Gutierre, M.S.

2010-01-01

This paper presents results of a molecular dynamics simulation study of dehydrated 2:1 clay minerals using the Parrinello-Rahman constant-pressure molecular dynamics method. The method is capable of simulating a system under the most general applied stress conditions by considering the changes of MD cell size and shape. Given the advantage of the method, it is the major goal of the paper to investigate the influence of imposed cell boundary conditions on the molecular structural transformation of 2:1 clay minerals under different normal pressures. Simulation results show that the degrees of freedom of the simulation cell (i.e., whether the cell size or shape change is allowed) determines the final equilibrated crystal structure of clay minerals. Both the MD method and the static method have successfully revealed unforeseen structural transformations of clay minerals upon relaxation under different normal pressures. It is found that large shear distortions of clay minerals occur when full allowance is given to the cell size and shape change. A complete elimination of the interlayer spacing is observed in a static simulation. However, when only the cell size change is allowed, interlayer spacing is retained, but large internal shear stresses also exist.

Expression profiling of a genetic animal model of depression reveals novel molecular pathways underlying depressive-like behaviours.

Directory of Open Access Journals (Sweden)

Ekaterini Blaveri

2010-09-01

Full Text Available The Flinders model is a validated genetic rat model of depression that exhibits a number of behavioural, neurochemical and pharmacological features consistent with those observed in human depression.In this study we have used genome-wide microarray expression profiling of the hippocampus and prefrontal/frontal cortex of Flinders Depression Sensitive (FSL and control Flinders Depression Resistant (FRL lines to understand molecular basis for the differences between the two lines. We profiled two independent cohorts of Flinders animals derived from the same colony six months apart, each cohort statistically powered to allow independent as well as combined analysis. Using this approach, we were able to validate using real-time-PCR a core set of gene expression differences that showed statistical significance in each of the temporally distinct cohorts, representing consistently maintained features of the model. Small but statistically significant increases were confirmed for cholinergic (chrm2, chrna7 and serotonergic receptors (Htr1a, Htr2a in FSL rats consistent with known neurochemical changes in the model. Much larger gene changes were validated in a number of novel genes as exemplified by TMEM176A, which showed 35-fold enrichment in the cortex and 30-fold enrichment in hippocampus of FRL animals relative to FSL.These data provide significant insights into the molecular differences underlying the Flinders model, and have potential relevance to broader depression research.

Constraints on extra dimensions from precision molecular spectroscopy

NARCIS (Netherlands)

Salumbides, E.J.; Schellekens, A.N.; Gato-Rivera, B.; Ubachs, W.M.G.

2015-01-01

Accurate investigations of quantum-level energies in molecular systems are shown to provide a testing ground to constrain the size of compactified extra dimensions. This is made possible by recent progress in precision metrology with ultrastable lasers on energy levels in neutral molecular hydrogen

Molecular Dynamics Simulation and Analysis of Interfacial Water at Selected Sulfide Mineral Surfaces under Anaerobic Conditions

Energy Technology Data Exchange (ETDEWEB)

Jin, Jiaqi; Miller, Jan D.; Dang, Liem X.

2014-04-10

In this paper, we report on a molecular dynamics simulation (MDS) study of the behavior of interfacial water at selected sulfide mineral surfaces under anaerobic conditions. The study revealed the interfacial water structure and wetting characteristics of the pyrite (100) surface, galena (100) surface, chalcopyrite (012) surface, sphalerite (110) surface, and molybdenite surfaces (i.e., the face, armchair-edge, and zigzag-edge surfaces), including simulated contact angles, relative number density profiles, water dipole orientations, hydrogen-bonding, and residence times. For force fields of the metal and sulfur atoms in selected sulfide minerals used in the MDS, we used the universal force field (UFF) and another set of force fields optimized by quantum chemical calculations for interactions with interfacial water molecules at selected sulfide mineral surfaces. Simulation results for the structural and dynamic properties of interfacial water molecules indicate the natural hydrophobic character for the selected sulfide mineral surfaces under anaerobic conditions as well as the relatively weak hydrophobicity for the sphalerite (110) surface and two molybdenite edge surfaces. Part of the financial support for this study was provided by the U.S. Department of Energy (DOE) under Basic Science Grant No. DE-FG-03-93ER14315. The Division of Chemical Sciences, Geosciences, and Biosciences, Office of Basic Energy Sciences (BES), of the DOE, funded work performed by Liem X. Dang. Battelle operates Pacific Northwest National Laboratory for DOE. The calculations were carried out using computer resources provided by BES. The authors are grateful to Professor Tsun-Mei Chang for valuable discussions.

Molecularly targeted therapeutic radiopharmaceuticals

International Nuclear Information System (INIS)

Saw, M.M.

2007-01-01

Full text: It is generally agreed that current focus of nuclear medicine development should be on molecular imaging and therapy. Though, the widespread use of the terminology 'molecular imaging' is quite recent, nuclear medicine has used molecular imaging techniques for more than 20 years ago. A variety of radiopharmaceuticals have been introduced for the internal therapy of malignant and inflammatory lesions in nuclear medicine. In the field of bio/medical imaging, nuclear medicine is one of the disciplines which has the privilege of organized and well developed chemistry/ pharmacy section; radio-chemistry/radiopharmacy. Fundamental principles have been developed more than 40 years ago and advanced research is going well into postgenomic era. The genomic revolution and dramatically increased insight in the molecular mechanisms underlying pathology have led to paradigm shift in drug development. Likewise does in the nuclear medicine. Here, the author will present current clinical and pre-clinical therapeutic radiopharmaceuticals based on molecular targets such as membrane-bound receptors, enzymes, nucleic acids, sodium iodide symporter, etc, in correlation with fundamentals of radiopharmacy. (author)

Molecular methods for the study of signal transduction in plants

KAUST Repository

Irving, Helen R.

2013-09-03

Novel and improved analytical methods have led to a rapid increase in our understanding of the molecular mechanism underlying plant signal transduction. Progress has been made both at the level of single-component analysis and in vivo imaging as well as at the systems level where transcriptomics and particularly phosphoproteomics afford a window into complex biological responses. Here we review the role of the cyclic nucleotides cAMP and cGMP in plant signal transduction as well as the discovery and biochemical and biological characterization of an increasing number of complex multi-domain nucleotide cyclases that catalyze the synthesis of cAMP and cGMP from ATP and GTP, respectively. © Springer Science+Business Media New York 2013.

Molecular Technologies in Serbian Lowland Forestry under Climate Changes - Possibilities and Perspectives

Directory of Open Access Journals (Sweden)

Branislav Trudić

2014-12-01

Full Text Available Background and Purpose: Vojvodina province, the northern part of the Republic of Serbia, is predominantly lowland agricultural region with over 75% of arable land which in previous years, has been highly impacted by drought. The annual precipitation is lower than 700 mm and it is the limit for the growth and development of natural forest vegetation. Unfortunately, the atmospheric precipitation is still a major source of water for plant biodiversity. Taking these facts into account, it is highly recommended to primarily use the xerothermic tree species, which have a well-developed root system for “classical” afforestation. Some species from Salicaceae and Fagaceae like poplars, willows, oaks and beeches are surely the best option for afforestation in temperate zones strongly influenced by drought. Conclusions: In order to develop stress-based genomic information in Populus and the rest of woody plant species from Vojvodina, an integrated genetic research needs to be done. The aim of this particular paper is to analyse and summarize data regarding stress-based biotechnology perspectives in Vojvodina and to give recommendations for future forest tree breeding. Drought as a strong negative ecological factor must be carefully considered. In order to achieve sustainability, new forest management plans must consider wide approaches, from molecular to ecosystem level.

Impact of noise on molecular network inference.

Directory of Open Access Journals (Sweden)

Radhakrishnan Nagarajan

Full Text Available Molecular entities work in concert as a system and mediate phenotypic outcomes and disease states. There has been recent interest in modelling the associations between molecular entities from their observed expression profiles as networks using a battery of algorithms. These networks have proven to be useful abstractions of the underlying pathways and signalling mechanisms. Noise is ubiquitous in molecular data and can have a pronounced effect on the inferred network. Noise can be an outcome of several factors including: inherent stochastic mechanisms at the molecular level, variation in the abundance of molecules, heterogeneity, sensitivity of the biological assay or measurement artefacts prevalent especially in high-throughput settings. The present study investigates the impact of discrepancies in noise variance on pair-wise dependencies, conditional dependencies and constraint-based Bayesian network structure learning algorithms that incorporate conditional independence tests as a part of the learning process. Popular network motifs and fundamental connections, namely: (a common-effect, (b three-chain, and (c coherent type-I feed-forward loop (FFL are investigated. The choice of these elementary networks can be attributed to their prevalence across more complex networks. Analytical expressions elucidating the impact of discrepancies in noise variance on pairwise dependencies and conditional dependencies for special cases of these motifs are presented. Subsequently, the impact of noise on two popular constraint-based Bayesian network structure learning algorithms such as Grow-Shrink (GS and Incremental Association Markov Blanket (IAMB that implicitly incorporate tests for conditional independence is investigated. Finally, the impact of noise on networks inferred from publicly available single cell molecular expression profiles is investigated. While discrepancies in noise variance are overlooked in routine molecular network inference, the

Quantitative gene expression underlying 18f-fluorodeoxyglucose uptake in colon cancer

DEFF Research Database (Denmark)

Engelmann, Bodil E.; Binderup, Tina; Kjær, Andreas

2015-01-01

Background: Positron emission tomography (PET) with the glucose analogue 18F-fluorodeoxyglucose (FDG) is widely used in oncologic imaging. This study examines the molecular mechanism underlying the detection of colon cancer (CC) by FDG-PET. Methods: Pre-operative PET/CT scans and tissue samples....... Mean gene expression levels of GLUT1, HK2, ki67, HIF1α, VEGF and CaIX, but not HK1, were significantly higher in primary tumours than in surrounding normal colonic mucosa. Linear regressions pairing tumour SUVmax with gene expression levels showed significant correlations between SUVmax and HK2, ki67...

Molecular dynamics modeling on the role of initial void geometry in a thin aluminum film under uniaxial tension

International Nuclear Information System (INIS)

Cui, Yi; Chen, Zengtao

2015-01-01

The effect of initial void geometry on damage progression in a thin aluminum film under uniaxial load is studied via molecular dynamics (MD) method. The embedded voids are with different initial geometries regarding shape, porosity and intervoid ligament distance (ILD). Major simulations are run upon twelve MD geometries with each containing 8–27 million atoms. The corresponding stress–strain relation is monitored during the microstructure evolution of the specimens. The critical stress to trigger the dislocation emission is found in line with the prediction of the Lubarda model. The simulation results reveal that the initial void geometry has substantial impact on the stress–strain relation especially for a specimen with larger initial porosity. (paper)

Understanding the molecular mechanisms underlying the effects of light intensity on flavonoid production by RNA-seq analysis in Epimedium pseudowushanense B.L.Guo.

Science.gov (United States)

Pan, Junqian; Chen, Haimei; Guo, Baolin; Liu, Chang

2017-01-01

Epimedium pseudowushanense B.L.Guo, a light-demanding shade herb, is used in traditional medicine to increase libido and strengthen muscles and bones. The recognition of the health benefits of Epimedium has increased its market demand. However, its resource recycling rate is low and environmentally dependent. Furthermore, its natural sources are endangered, further increasing prices. Commercial culture can address resource constraints of it.Understanding the effects of environmental factors on the production of its active components would improve the technology for cultivation and germplasm conservation. Here, we studied the effects of light intensities on the flavonoid production and revealed the molecular mechanism using RNA-seq analysis. Plants were exposed to five levels of light intensity through the periods of germination to flowering, the flavonoid contents were measured using HPLC. Quantification of epimedin A, epimedin B, epimedin C, and icariin showed that the flavonoid contents varied with different light intensity levels. And the largest amount of epimedin C was produced at light intensity level 4 (I4). Next, the leaves under the treatment of three light intensity levels ("L", "M" and "H") with the largest differences in the flavonoid content, were subjected to RNA-seq analysis. Transcriptome reconstruction identified 43,657 unigenes. All unigene sequences were annotated by searching against the Nr, Gene Ontology, and Kyoto Encyclopedia of Genes and Genomes (KEGG) databases. In total, 4008, 5260, and 3591 significant differentially expressed genes (DEGs) were identified between the groups L vs. M, M vs. H and L vs. H. Particularly, twenty-one full-length genes involved in flavonoid biosynthesis were identified. The expression levels of the flavonol synthase, chalcone synthase genes were strongly associated with light-induced flavonoid abundance with the highest expression levels found in the H group. Furthermore, 65 transcription factors, including 31

Pressure effects on martensitic transformation under quenching process in a molecular dynamics model of NiAl alloy

International Nuclear Information System (INIS)

Kazanc, S.; Ozgen, S.; Adiguzel, O.

2003-01-01

The solid-solid phase transitions in NiAl alloys occur by the temperature changes and application of a pressure on the system. Both types of transitions are called martensitic transformation and have displacive and thermoelastic characters. Pressure effects on thermoelastic transformation in Ni 62.5 Al 37.5 alloy model have been studied by means of molecular dynamics method proposed by Parrinello-Rahman. Interaction forces between atoms in the model system were calculated by Lennard-Jones potential energy function. Thermodynamics and structural analysis of the martensitic transformations under hydrostatic pressure during the quenching processes have been performed. The simulation runs have been carried out in different hydrostatic pressures changing from zero to 40.65 GPa during the quenching process of the model alloy. At the zero and nonzero pressures, the system with B2-type ordered structure undergoes the product phase with L1 0 -type ordered structure by Bain distortion in the first step of martensitic transformation under the quenching process. The increase in hydrostatic pressure causes decrease in the formation time of the product phase, and twin-like lattice distortion is observed in low temperature L1 0 phase

Effect of Trichoderma harzianum on Wheat (Triticum aestivum L. Grain Yield under Different Levels of Cadmium Nitrate

Directory of Open Access Journals (Sweden)

F. Taghavi Ghasemkheyli

2014-12-01

Full Text Available A pot experiment was designed to evaluate the effect of Trichoderma spp. on yield and yield components of wheat (cv. N81 under different levels of cadmium nitrate. Experiment was arranged in factorial based on completely randomized design with three replicates. Trichoderma harzianum at two levels (with and without inoculation and four levels of cadmium nitrate (0, 50, 100, 150 mg l-1 were the treatment. Results of ANOVA and mean comparisons showed that inoculation of Trichoderma increased biological yield (46% and straw yield (30% as compared to control. Cadmium pollution has led to significant decrease in harvest index, grain number per spike and partitioning coefficient up to 5, 20, 24 and 38 percent compared to control, respectively. Furthermore, cadmium and fungus interaction were significant in terms of spike number, grain weight per spike, grain yield and tolerance index. Maximum grain yield and tolerance index were recorded in Trichoderma inoculation under cadmium-free plots which nearly increased 65 and 53 percent, respectively. In conclusion, using Trichoderma under cadmium pollution could improve wheat growth, yield and tolerance index

Molecular dynamics simulations of the melting curve of NiAl alloy under pressure

International Nuclear Information System (INIS)

Zhang, Wenjin; Peng, Yufeng; Liu, Zhongli

2014-01-01

The melting curve of B2-NiAl alloy under pressure has been investigated using molecular dynamics technique and the embedded atom method (EAM) potential. The melting temperatures were determined with two approaches, the one-phase and the two-phase methods. The first one simulates a homogeneous melting, while the second one involves a heterogeneous melting of materials. Both approaches reduce the superheating effectively and their results are close to each other at the applied pressures. By fitting the well-known Simon equation to our melting data, we yielded the melting curves for NiAl: 1783(1 + P/9.801) 0.298 (one-phase approach), 1850(1 + P/12.806) 0.357 (two-phase approach). The good agreement of the resulting equation of states and the zero-pressure melting point (calc., 1850 ± 25 K, exp., 1911 K) with experiment proved the correctness of these results. These melting data complemented the absence of experimental high-pressure melting of NiAl. To check the transferability of this EAM potential, we have also predicted the melting curves of pure nickel and pure aluminum. Results show the calculated melting point of Nickel agrees well with experiment at zero pressure, while the melting point of aluminum is slightly higher than experiment

Incorporation of Eu(III) into calcite under recrystallization conditions

International Nuclear Information System (INIS)

Hellebrandt, S.E.; Jordan, Norbert; Barkleit, Astrid; Schmidt, Moritz; Hofmann, S.

2017-01-01

The interaction of three calcite powders with Eu(III) under recrystallization conditions was studied on the molecular level using site-selective time-resolved laser fluorescence spectroscopy (TRLFS). Batch contact studies with reaction times from 1 week up to 3 years revealed that the speciation differs from that observed previously in co-precipitation experiments and is dominated by a newly identified species ''γ''. The speed of formation of this species was found to depend greatly on the recrystallization rate of the studied minerals.

Incorporation of Eu(III) into calcite under recrystallization conditions

Energy Technology Data Exchange (ETDEWEB)

Hellebrandt, S.E. [Helmholtz-Zentrum Dresden-Rossendorf e.V., Dresden (Germany). Inst. of Resource Ecology; Jordan, Norbert [Helmholtz-Zentrum Dresden-Rossendorf e.V., Dresden (Germany). Surface Processes; Barkleit, Astrid [Helmholtz-Zentrum Dresden-Rossendorf e.V., Dresden (Germany). Chemistry of the F-Elements; Schmidt, Moritz [Helmholtz-Zentrum Dresden-Rossendorf e.V., Dresden (Germany). HGF Young Investigator Group; Hofmann, S.

2017-06-01

The interaction of three calcite powders with Eu(III) under recrystallization conditions was studied on the molecular level using site-selective time-resolved laser fluorescence spectroscopy (TRLFS). Batch contact studies with reaction times from 1 week up to 3 years revealed that the speciation differs from that observed previously in co-precipitation experiments and is dominated by a newly identified species ''γ''. The speed of formation of this species was found to depend greatly on the recrystallization rate of the studied minerals.

Identification and analysis of evolutionary selection pressures acting at the molecular level in five forkhead subfamilies.

Science.gov (United States)

Fetterman, Christina D; Rannala, Bruce; Walter, Michael A

2008-09-24

Members of the forkhead gene family act as transcription regulators in biological processes including development and metabolism. The evolution of forkhead genes has not been widely examined and selection pressures at the molecular level influencing subfamily evolution and differentiation have not been explored. Here, in silico methods were used to examine selection pressures acting on the coding sequence of five multi-species FOX protein subfamily clusters; FoxA, FoxD, FoxI, FoxO and FoxP. Application of site models, which estimate overall selection pressures on individual codons throughout the phylogeny, showed that the amino acid changes observed were either neutral or under negative selection. Branch-site models, which allow estimated selection pressures along specified lineages to vary as compared to the remaining phylogeny, identified positive selection along branches leading to the FoxA3 and Protostomia clades in the FoxA cluster and the branch leading to the FoxO3 clade in the FoxO cluster. Residues that may differentiate paralogs were identified in the FoxA and FoxO clusters and residues that differentiate orthologs were identified in the FoxA cluster. Neutral amino acid changes were identified in the forkhead domain of the FoxA, FoxD and FoxP clusters while positive selection was identified in the forkhead domain of the Protostomia lineage of the FoxA cluster. A series of residues under strong negative selection adjacent to the N- and C-termini of the forkhead domain were identified in all clusters analyzed suggesting a new method for refinement of domain boundaries. Extrapolation of domains among cluster members in conjunction with selection pressure information allowed prediction of residue function in the FoxA, FoxO and FoxP clusters and exclusion of known domain function in residues of the FoxA and FoxI clusters. Consideration of selection pressures observed in conjunction with known functional information allowed prediction of residue function and

A Complex Approach for Unravelling Musaceae Phylogeny at Molecular Level

Czech Academy of Sciences Publication Activity Database

Němcová, Pavla; Hřibová, Eva; Valárik, Miroslav; Doležel, Jaroslav

2011-01-01

Roč. 897, SEP 14 (2011), s. 139-142 ISSN 0567-7572. [INTERNATIONAL ISHS-PROMUSA SYMPOSIUM ON GLOBAL PERSPECTIVES ON ASIAN CHALLENGES. Guangzhou, 14.08.2009-16.08.2009] R&D Projects: GA AV ČR IAA600380703 Institutional support: RVO:61389030 Keywords : DArT * low-copy genes * molecular phylogenetics Subject RIV: EF - Botanics http://www.actahort.org/books/897/897_14.htm

Adsorption properties of a molecular 5 A sieve for 85Kr

International Nuclear Information System (INIS)

Wardaszko, T.; Nidecka, J.

1978-01-01

The enrichment processes which are necessary at low-level 85 Kr determinations in the atmospheric air require the knowledge of adsorption properties of appropriate sorbing agents, such as a molecular 5A sieve. Following low-temperature adsorption, under specified conditions, of known amounts of 85 Kr diluted in the air, desorption was carried out and then the 85 Kr content in the temperature fraction as well as their total volume were determined. Distribution curves for the above quantities in fractions are presented. (author)

Bringing molecules back into molecular evolution.

Directory of Open Access Journals (Sweden)

Claus O Wilke

Full Text Available Much molecular-evolution research is concerned with sequence analysis. Yet these sequences represent real, three-dimensional molecules with complex structure and function. Here I highlight a growing trend in the field to incorporate molecular structure and function into computational molecular-evolution work. I consider three focus areas: reconstruction and analysis of past evolutionary events, such as phylogenetic inference or methods to infer selection pressures; development of toy models and simulations to identify fundamental principles of molecular evolution; and atom-level, highly realistic computational modeling of molecular structure and function aimed at making predictions about possible future evolutionary events.

Solutions for ecosystem-level protection of ocean systems under climate change.

Science.gov (United States)

Queirós, Ana M; Huebert, Klaus B; Keyl, Friedemann; Fernandes, Jose A; Stolte, Willem; Maar, Marie; Kay, Susan; Jones, Miranda C; Hamon, Katell G; Hendriksen, Gerrit; Vermard, Youen; Marchal, Paul; Teal, Lorna R; Somerfield, Paul J; Austen, Melanie C; Barange, Manuel; Sell, Anne F; Allen, Icarus; Peck, Myron A

2016-12-01

The Paris Conference of Parties (COP21) agreement renewed momentum for action against climate change, creating the space for solutions for conservation of the ocean addressing two of its largest threats: climate change and ocean acidification (CCOA). Recent arguments that ocean policies disregard a mature conservation research field and that protected areas cannot address climate change may be oversimplistic at this time when dynamic solutions for the management of changing oceans are needed. We propose a novel approach, based on spatial meta-analysis of climate impact models, to improve the positioning of marine protected areas to limit CCOA impacts. We do this by estimating the vulnerability of ocean ecosystems to CCOA in a spatially explicit manner and then co-mapping human activities such as the placement of renewable energy developments and the distribution of marine protected areas. We test this approach in the NE Atlantic considering also how CCOA impacts the base of the food web which supports protected species, an aspect often neglected in conservation studies. We found that, in this case, current regional conservation plans protect areas with low ecosystem-level vulnerability to CCOA, but disregard how species may redistribute to new, suitable and productive habitats. Under current plans, these areas remain open to commercial extraction and other uses. Here, and worldwide, ocean conservation strategies under CCOA must recognize the long-term importance of these habitat refuges, and studies such as this one are needed to identify them. Protecting these areas creates adaptive, climate-ready and ecosystem-level policy options for conservation, suitable for changing oceans. © 2016 John Wiley & Sons Ltd.

Alkynes as a versatile platform for construction of chemical molecular complexity and realization of molecular 3D printing

International Nuclear Information System (INIS)

Galkin, K I; Ananikov, V P

2016-01-01

The current level of scientific and technological development requires the formation of general tools and techniques. One of the most versatile technologies is 3D printing, which allows fast and efficient creation of materials and biological objects of desired shape and composition. Today, methods have been developed for 3D printing of macro- and nano-sized objects and for production of films and deposited materials with molecular precision but the most promising technology is printing at the molecular level (molecular 3D printing) for the purpose of direct construction of molecular complexity. This process is currently at the initial stage concerning selection of simple molecules to be used as building blocks possessing flexibility, availability and ease of modification. In this review, we examine the possible versatile synthons suitable for preparation of the main types of organic compounds using molecular 3D printing. The surveyed data strongly indicate that alkyne molecules may be used as a building material in a molecular 3D printer working on hydrocarbons. The bibliography includes 428 references

3D Multi-Level Non-LTE Radiative Transfer for the CO Molecule

Science.gov (United States)

Berkner, A.; Schweitzer, A.; Hauschildt, P. H.

2015-01-01

The photospheres of cool stars are both rich in molecules and an environment where the assumption of LTE can not be upheld under all circumstances. Unfortunately, detailed 3D non-LTE calculations involving molecules are hardly feasible with current computers. For this reason, we present our implementation of the super level technique, in which molecular levels are combined into super levels, to reduce the number of unknowns in the rate equations and, thus, the computational effort and memory requirements involved, and show the results of our first tests against the 1D implementation of the same method.

Effects of epigallocatechin gallate on lipid metabolism and its underlying molecular mechanism in broiler chickens.

Science.gov (United States)

Huang, J B; Zhang, Y; Zhou, Y B; Wan, X C; Zhang, J S

2015-08-01

The objective of this study was to investigate the effects of epigallocatechin gallate (EGCG) on fat metabolism and to establish the molecular mechanism of these effects in broilers. Seventy-two 28-day-old male Ross 308 broiler chickens were divided into three groups with different levels of EGCG supplementation for 4 weeks: normal control (NC) group, L-EGCG (a low-level supplement of EGCG, 40 mg/kg body weight daily) and H-EGCG (a high-level supplement of EGCG, 80 mg/kg body weight daily). After 4 weeks of oral administration, EGCG significantly reduced the level of abdominal fat deposition in broilers. The serum triglycerides and low-density lipoprotein cholesterol of chickens in H-EGCG group were also significantly decreased compared with the NC group, and the high-density lipoprotein cholesterol was notably increased at the same time. Moreover, the vital role of the liver and abdominal adipose tissue in lipid metabolism of poultry animals was examined through gene expression and enzyme activities related to fat anabolism and catabolism in these organs. Our data show that EGCG supplementation for 2 weeks significantly downregulated the expression of fatty acid synthesis and fat deposition-related genes, and upregulated the expression of genes involved in fatty acid β-oxidation and lipolysis genes. Simultaneously, the activities of hepatic fatty acid synthesis enzymes (fatty acid synthase and acetyl CoA carboxylase) were significantly decreased, and the activity of carnitine palmitoyl transferase-1 was notably elevated. The results suggest that EGCG could alleviate fat deposition in broilers through inhibiting fat anabolism and stimulating lipid catabolism in broilers. Journal of Animal Physiology and Animal Nutrition © 2014 Blackwell Verlag GmbH.

Circulating anti-Mullerian hormone levels in adult men are under a strong genetic influence.

Science.gov (United States)

Pietiläinen, Kirsi H; Kaprio, Jaakko; Vaaralahti, Kirsi; Rissanen, Aila; Raivio, Taneli

2012-01-01

The determinants of serum anti-Müllerian hormone (AMH) levels in adult men remain unclear. The objective of the study was to investigate the genetic and environmental components in determining postpubertal AMH levels in healthy men. Serum AMH levels, body mass index (BMI), and fat mass (dual energy x-ray absorptiometry) were measured in 64 healthy male (23 monozygotic and 41 dizygotic) twin pairs. Postpubertal AMH levels were highly genetically determined (broad sense heritability 0.92, 95% confidence interval 0.83-0.96). AMH correlated negatively with BMI (r = -0.26, P = 0.030) and fat mass (r = -0.23, P = 0.048). As AMH, BMI had a high heritability (0.68, 95% confidence interval 0.39-0.83), but no genetic correlation was observed between them. AMH levels in men after puberty are under a strong genetic influence. Twin modeling suggests that AMH and BMI are influenced by different sets of genes.

Ion-beam-induced aggregation in polystyrene: The influence of the molecular parameters

International Nuclear Information System (INIS)

Puglisi, O.; Licciardello, A.; Calcagno, L.; Foti, G.

1988-01-01

The formation of an insoluble gel under ion-beam bombardment is governed by ion-beam parameters and target parameters. Here reported is a study of the influence of the target molecular parameters on the sol--gel transition of ion-bombarded polystyrene with particular emphasis for the number-average molecular weight M-bar/sub n/. It is shown that the main parameter is the number of macromolcules of the film so that by adopting a ''corrected'' fluence F/n (ions per macromolecule), the different curves of the various polymers collapse in only one universal curve. The importance of the ''corrected'' fluence is shown also at molecular level and the MWD of the various polymers is similar at equal F/n values. An experimental model is outlined which explains the sol--gel transition on the basis of transition from an isolated-track regime to an overlap regime where the formation of insoluble giant macromolecules occurs

Radiation induced deep level defects in bipolar junction transistors under various bias conditions

International Nuclear Information System (INIS)

Liu, Chaoming; Yang, Jianqun; Li, Xingji; Ma, Guoliang; Xiao, Liyi; Bollmann, Joachim

2015-01-01

Bipolar junction transistor (BJT) is sensitive to ionization and displacement radiation effects in space. In this paper, 35 MeV Si ions were used as irradiation source to research the radiation damage on NPN and PNP bipolar transistors. The changing of electrical parameters of transistors was in situ measured with increasing irradiation fluence of 35 MeV Si ions. Using deep level transient spectroscopy (DLTS), defects in the bipolar junction transistors under various bias conditions are measured after irradiation. Based on the in situ electrical measurement and DLTS spectra, it is clearly that the bias conditions can affect the concentration of deep level defects, and the radiation damage induced by heavy ions.

20 CFR 666.130 - Under what conditions may a State or DOL request revisions to the State negotiated levels of...

Science.gov (United States)

2010-04-01

... a State or DOL request revisions to the State negotiated levels of performance? (a) The DOL guidelines describe when and under what circumstances a Governor may request revisions to negotiated levels... 20 Employees' Benefits 3 2010-04-01 2010-04-01 false Under what conditions may a State or DOL...

Thermophysical properties of liquid carbon dioxide under shock compressions: quantum molecular dynamic simulations.

Science.gov (United States)

Wang, Cong; Zhang, Ping

2010-10-07

Quantum molecular dynamics were used to calculate the equation of state, electrical, and optical properties of liquid carbon dioxide along the Hugoniot at shock pressures up to 74 GPa. The principal Hugoniot derived from the calculated equation of state is in good agreement with experimental results. Molecular dissociation and recombination are investigated through pair correlation functions and decomposition of carbon dioxide is found to be between 40 and 50 GPa along the Hugoniot, where nonmetal-metal transition is observed. In addition, the optical properties of shock compressed carbon dioxide are also theoretically predicted along the Hugoniot.

Cool C-shocks and high-velocity flows in molecular clouds

International Nuclear Information System (INIS)

Smith, M.D.; Brand, P.W.J.L.

1990-01-01

C-shocks can be driven through dense clouds when the neutrals and magnetic field interact weakly due to a paucity of ions. We develop a method for calculating C-shock properties with the aim of interpreting the observed high-velocity molecular hydrogen. A high Mach number approximation, corresponding to low temperatures, is employed. Under strong cooling conditions the flow is continuous even though a subsonic region may be present downstream. Analytic expressions for the maximum temperature, dissociation fraction, self-ionization level and J-shock transition are derived. (author)

Molecular Mechanisms of Preeclampsia

Directory of Open Access Journals (Sweden)

N. Vitoratos

2012-01-01

Full Text Available Preeclampsia is one of the leading causes of maternal morbidity/mortality. The pathogenesis of preeclampsia is still under investigation. The aim of this paper is to present the molecular mechanisms implicating in the pathway leading to preeclampsia.

Revisiting the four-level inverted-Y system under both Doppler-free and Doppler-broadened conditions: an analytical approach

International Nuclear Information System (INIS)

Ghosh, Arindam; Islam, Khairul; Bandyopadhyay, Amitava; Bhattacharyya, Dipankar

2016-01-01

We report the occurrence of electromagnetically induced transparency (EIT) in the simulated probe response signal for a four-level inverted-Y type system that is being acted upon by a weak coherent probe field, a strong coherent pump field and a coherent repump field. There are two ground energy levels, one intermediate energy level and one uppermost energy level. The weak probe field couples the lowest ground level to the intermediate level whereas the repump field connects the other ground level with the intermediate level. The strong control field couples the intermediate level with the uppermost energy level, thereby forming an inverted-Y type system. The density matrix based theoretical model has been developed and solved analytically for this four-level system and the probe response signal has been simulated at different values of the control and repump Rabi frequencies, control and repump frequency detunings and under both Doppler-free and Doppler-broadened conditions using the parameters of 87 Rb D 2 transition. Extremely low line width (few tens of kHz) for the EIT signal has been noticed under thermal averaging for copropagating probe, control and repump field configuration. The EIT signal is found to be immune to the variation in the control Rabi frequency. (paper)

Energy transformation in molecular electronic systems

International Nuclear Information System (INIS)

Kasha, M.

1985-01-01

Our new optical pumping spectroscopy (steady state, and double-laser pulse) allows the production and study of the unstable rare tautomer in its ground and excited states, including picosecond dynamic studies. Molecules under study here included 7-azaindole (model for biological purines), 3-hydroxyflavone (model for plant flavones), lumichrome, and other heterocyclics. New detailed molecular mechanisms for proton transfer are derived, especially with catalytic assisting molecules. A new proton-transfer laser of extraordinary efficiency has become a side dividend, possibly worth of industrial development. The excited and highly reactive singlet molecular oxygen species 1 Δ/sub g/) has proven to be ubiquitous in chemical peroxide systems and in physically excited sensitizer-oxygen systems. Hyperbaric oxygen mechanisms in biology probably involve singlet oxygen. We have undertaken a spectroscopic study of tris - dibenzoylmethane chelates of Al, Gd, Eu, and Yb trivalent ions. These chelates offer a variety of electronic behaviors, from Z-effects on π-electron spin-orbital coupling (Al, Gd) to Weissman intramolecular energy transfer to 4f mestable levels (Eu, Gd). Elegant new spectroscopic resolution at 77K permits separation of tautomeric, parasitic self-absorption, dissociation, and cage effects to be resolved. 18 refs., 4 figs

Molecular heterojunctions of oligo(phenylene ethynylene)s with linear to cruciform framework

DEFF Research Database (Denmark)

Wei, Zhongming; Hansen, Tim; Santella, Marco

2015-01-01

Electrical transport properties of molecular junctions are fundamentally affected by the energy alignment between molecular frontier orbitals (highest occupied molecular orbital (HOMO) or lowest unoccupied molecular orbital (LUMO)) and Fermi level (or work function) of electrode metals. Dithiaful......Electrical transport properties of molecular junctions are fundamentally affected by the energy alignment between molecular frontier orbitals (highest occupied molecular orbital (HOMO) or lowest unoccupied molecular orbital (LUMO)) and Fermi level (or work function) of electrode metals......-tetrathiafulvalene (TTF) can form good self-assembled monolayers (SAMs) on Au substrates. Molecular heterojunctions based on these SAMs are investigated using conducting probe-atomic force microscopy with different tips (Ag, Au, and Pt) and Fermi levels. The calibrated conductance values follow the sequence OPE3-TTF...... > OPE3-DTF > OPE3 irrespective of the tip metal. Rectification properties (or diode behavior) are observed in case of the Ag tip for which the work function is furthest from the HOMO levels of the OPE3s. Quantum chemical calculations of the transmission qualitatively agree with the experimental data...

Giant rectification in graphene nanoflake molecular devices with asymmetric graphene nanoribbon electrodes

International Nuclear Information System (INIS)

Ji, Xiao-Li; Xie, Zhen; Zuo, Xi; Zhang, Guang-Ping; Li, Zong-Liang; Wang, Chuan-Kui

2016-01-01

By applying density functional theory based nonequilibrium Green's function method, we theoretically investigate the electron transport properties of a zigzag-edged trigonal graphene nanoflake (ZTGNF) sandwiched between two asymmetric zigzag graphene nanoribbon (zGNR) and armchair graphene nanoribbon (aGNR) electrodes with carbon atomic chains (CACs) as the anchoring groups. Significant rectifying effects have been observed for these molecular devices in low bias voltage regions. Interestingly, the rectifying performance of molecular devices can be optimized by changing the width of the aGNR electrode and the number of anchoring CACs. Especially, the molecular device displays giant rectification ratios up to the order of 10"4 when two CACs are used as the anchoring group between the ZTGNF and the right aGNR electrode. Further analysis indicates that the asymmetric shift of the perturbed molecular energy levels and the spatial parity of the electron wavefunctions in the electrodes around the Fermi level play key roles in determining the rectification performance. And the spatial distributions of tunneling electron wavefunctions under negative bias voltages can be modified to be very localized by changing the number of anchoring CACs, which is found to be the origin of the giant rectification ratios. - Highlights: • The rectification properties of triangular Graphene nanoflakes are investigated. • The rectifying performance can be optimized by changing the width of the right arm-chaired GNR electrode. • The rectifying performance can also be tuned by varying the number of anchoring carbon atomic chains.

High-performance n-type organic semiconductors: incorporating specific electron-withdrawing motifs to achieve tight molecular stacking and optimized energy levels.

Science.gov (United States)

Yun, Sun Woo; Kim, Jong H; Shin, Seunghoon; Yang, Hoichang; An, Byeong-Kwan; Yang, Lin; Park, Soo Young

2012-02-14

Novel π–conjugated cyanostilbene-based semiconductors (Hex-3,5-TFPTA and Hex-4-TFPTA) with tight molecular stacking and optimized energy levels are synthesized. Hex-4-TFPTA exhibits high-performance n-type organic field-effect transistor (OFET) properties with electron mobilities as high as 2.14 cm2 V−1s−1 and on-off current ratios Copyright © 2012 WILEY-VCH Verlag GmbH & Co. KGaA, Weinheim.

Reverse engineering of an affinity-switchable molecular interaction characterized by atomic force microscopy single-molecule force spectroscopy.

Science.gov (United States)

Anselmetti, Dario; Bartels, Frank Wilco; Becker, Anke; Decker, Björn; Eckel, Rainer; McIntosh, Matthew; Mattay, Jochen; Plattner, Patrik; Ros, Robert; Schäfer, Christian; Sewald, Norbert

2008-02-19

Tunable and switchable interaction between molecules is a key for regulation and control of cellular processes. The translation of the underlying physicochemical principles to synthetic and switchable functional entities and molecules that can mimic the corresponding molecular functions is called reverse molecular engineering. We quantitatively investigated autoinducer-regulated DNA-protein interaction in bacterial gene regulation processes with single atomic force microscopy (AFM) molecule force spectroscopy in vitro, and developed an artificial bistable molecular host-guest system that can be controlled and regulated by external signals (UV light exposure and thermal energy). The intermolecular binding functionality (affinity) and its reproducible and reversible switching has been proven by AFM force spectroscopy at the single-molecule level. This affinity-tunable optomechanical switch will allow novel applications with respect to molecular manipulation, nanoscale rewritable molecular memories, and/or artificial ion channels, which will serve for the controlled transport and release of ions and neutral compounds in the future.