Synthesis and characterization of poly-3-((2,5-hydroquinone)vinyl)-1H-pyrrole: investigation on backbone/pendant interactions in a conducting redox polymer.

PubMed

Huang, Hao; Karlsson, Christoffer; Strømme, Maria; Gogoll, Adolf; Sjödin, Martin

2017-04-19

We herein report the synthesis and electrochemical characterization of poly-3-((2,5-hydroquinone)vinyl)-1H-pyrrole, consisting of a polypyrrole backbone derivatized at the beta position by a vinyl-hydroquinone pendant group. The structure of the polymer was characterized by solid state NMR spectroscopy. The interactions between the polypyrrole backbone and the oxidized quinone or reduced hydroquinone pendant groups are probed by several in situ methods. In situ attenuated total reflectance-Fourier transform infrared spectroscopy shows a spectroscopic response from both the doping of the polymer backbone and the redox activity of the pendant groups. Using an in situ Electrochemical Quartz Crystal Microbalance we reveal that the polymer doping is unaffected by the pendant group redox chemistry, as opposed to previous reports. Despite the continuous doping the electrochemical conversion from the hydroquinone state to the quinone state results in a significant conductance drop, as observed by in situ conductivity measurements using an Interdigitated Array electrode set-up. Twisting of the conducting polymer backbone as a result of a decreased separation between pendant groups due to π-π stacking in the oxidized state is suggested as the cause of this conductance drop.

Folding of a helix is critically stabilized by polarization of backbone hydrogen bonds: study in explicit water.

PubMed

Duan, Li L; Gao, Ya; Mei, Ye; Zhang, Qing G; Tang, Bo; Zhang, John Z H

2012-03-15

Multiple single-trajectory molecular dynamics (MD) simulation at room temperature (300 K) in explicit water was carried out to study the folding dynamics of an α-helix (PDB 2I9M ) using a polarized charge scheme that includes electronic polarization of backbone hydrogen bonds. Starting from an extended conformation, the 17-residue peptide was successfully folded into the native structure (α-helix) between 80 and 130 ns with a root-mean-square deviation of ~1.0 Å. Analysis of the time-dependent trajectories revealed that helix formation of the peptide started at the terminals and progressed toward the center of the peptide. For comparison, MD trajectories generated under various versions of standard AMBER force fields failed to show any significant or stable helix formation in our simulation. Our result shows clear evidence that the electronic polarization of backbone hydrogen bonds energetically stabilizes the helix formation and is critical to the stable folding of the short helix structure. © 2012 American Chemical Society

Computation-Guided Backbone Grafting of a Discontinuous Motif onto a Protein Scaffold

DOE Office of Scientific and Technical Information (OSTI.GOV)

Azoitei, Mihai L.; Correia, Bruno E.; Ban, Yih-En Andrew

2012-02-07

The manipulation of protein backbone structure to control interaction and function is a challenge for protein engineering. We integrated computational design with experimental selection for grafting the backbone and side chains of a two-segment HIV gp120 epitope, targeted by the cross-neutralizing antibody b12, onto an unrelated scaffold protein. The final scaffolds bound b12 with high specificity and with affinity similar to that of gp120, and crystallographic analysis of a scaffold bound to b12 revealed high structural mimicry of the gp120-b12 complex structure. The method can be generalized to design other functional proteins through backbone grafting.

Observation of Water-Protein Interaction Dynamics with Broadband Two-Dimensional Infrared Spectroscopy

NASA Astrophysics Data System (ADS)

De Marco, Luigi; Haky, Andrew; Tokmakoff, Andrei

Two-dimensional infrared (2D IR) spectroscopy has proven itself an indispensable tool for studying molecular dynamics and intermolecular interactions on ultrafast timescales. Using a novel source of broadband mid-IR pulses, we have collected 2D IR spectra of protein films at varying levels of hydration. With 2D IR, we can directly observe coupling between water's motions and the protein's. Protein films provide us with the ability to discriminate hydration waters from bulk water and thus give us access to studying water dynamics along the protein backbone, fluctuations in the protein structure, and the interplay between the molecular dynamics of the two. We present two representative protein films: poly-L-proline (PLP) and hen egg-white lysozyme (HEWL). Having no N-H groups, PLP allows us to look at water dynamics without interference from resonant energy transfer between the protein N-H stretch and the water O-H stretch. We conclude that at low hydration levels water-protein interactions dominate, and the water's dynamics are tied to those of the protein. In HEWL films, we take advantage of the robust secondary structure to partially deuterate the film, allowing us to spectrally distinguish the protein core from the exterior. From this, we show that resonant energy transfer to water provides an effective means of dissipating excess energy within the protein, while maintaining the structure. These methods are general and can easily be extended to studying specific protein-water interactions.

The Graphical Representation of the Digital Astronaut Physiology Backbone

NASA Technical Reports Server (NTRS)

Briers, Demarcus

2010-01-01

This report summarizes my internship project with the NASA Digital Astronaut Project to analyze the Digital Astronaut (DA) physiology backbone model. The Digital Astronaut Project (DAP) applies integrated physiology models to support space biomedical operations, and to assist NASA researchers in closing knowledge gaps related to human physiologic responses to space flight. The DA physiology backbone is a set of integrated physiological equations and functions that model the interacting systems of the human body. The current release of the model is HumMod (Human Model) version 1.5 and was developed over forty years at the University of Mississippi Medical Center (UMMC). The physiology equations and functions are scripted in an XML schema specifically designed for physiology modeling by Dr. Thomas G. Coleman at UMMC. Currently it is difficult to examine the physiology backbone without being knowledgeable of the XML schema. While investigating and documenting the tags and algorithms used in the XML schema, I proposed a standard methodology for a graphical representation. This standard methodology may be used to transcribe graphical representations from the DA physiology backbone. In turn, the graphical representations can allow examination of the physiological functions and equations without the need to be familiar with the computer programming languages or markup languages used by DA modeling software.

Peptoid Backbone Flexibilility Dictates Its Interaction with Water and Surfaces: A Molecular Dynamics Investigation

DOE Office of Scientific and Technical Information (OSTI.GOV)

Prakash, Arushi; Baer, Marcel D.; Mundy, Christopher J.

Peptoids are peptide-mimetic biopolymers that are easy-to-synthesize and adaptable for use in drugs, chemical scaffolds, and coatings. However, there is insufficient information about their structural preferences and interactions with the environment in various applications. We conducted a study to understand the fundamental differences between peptides and peptoids using molecular dynamics simulations with semi-empirical (PM6) and empirical (AMBER) potentials, in conjunction with metadynamics enhanced sampling. From studies of single molecules in water and on surfaces, we found that sarcosine (model peptoid) is much more flexible than alanine (model peptide) in different environments. However, the sarcosine and alanine interact similarly with amore » hydrophobic or a hydrophilic. Finally, this study highlights the conformational landscape of peptoids and the dominant interactions that drive peptoids towards these conformations. ACKNOWLEDGMENT: MD simulations and manuscript preparation were supported by the MS3 (Materials Synthesis and Simulation Across Scales) Initiative at Pacific Northwest National Laboratory (PNNL), a multi-program national laboratory operated by Battelle for the U.S. Department of Energy. CJM was supported by the U.S. Department of Energy, Office of Science, Office of Basic Energy Sciences Division of Chemical Sciences, Geosciences, and Biosciences. MDB was supported by the US Department of Energy, Office of Basic Energy Sciences, Biomolecular Materials Program at PNNL. Computing resources were generously allocated by University of Washington's IT department and PNNL's Institutional Computing program. The authors greatly acknowledge conversations with Dr. Kayla Sprenger, Josh Smith, and Dr. Yeneneh Yimer.« less

Slow dynamics of a protein backbone in molecular dynamics simulation revealed by time-structure based independent component analysis

NASA Astrophysics Data System (ADS)

Naritomi, Yusuke; Fuchigami, Sotaro

2013-12-01

We recently proposed the method of time-structure based independent component analysis (tICA) to examine the slow dynamics involved in conformational fluctuations of a protein as estimated by molecular dynamics (MD) simulation [Y. Naritomi and S. Fuchigami, J. Chem. Phys. 134, 065101 (2011)]. Our previous study focused on domain motions of the protein and examined its dynamics by using rigid-body domain analysis and tICA. However, the protein changes its conformation not only through domain motions but also by various types of motions involving its backbone and side chains. Some of these motions might occur on a slow time scale: we hypothesize that if so, we could effectively detect and characterize them using tICA. In the present study, we investigated slow dynamics of the protein backbone using MD simulation and tICA. The selected target protein was lysine-, arginine-, ornithine-binding protein (LAO), which comprises two domains and undergoes large domain motions. MD simulation of LAO in explicit water was performed for 1 μs, and the obtained trajectory of Cα atoms in the backbone was analyzed by tICA. This analysis successfully provided us with slow modes for LAO that represented either domain motions or local movements of the backbone. Further analysis elucidated the atomic details of the suggested local motions and confirmed that these motions truly occurred on the expected slow time scale.

Side-chain to backbone interactions dictate the conformational preferences of a cyclopentane arginine analogue

PubMed Central

Revilla-López, Guillem; Torras, Juan; Jiménez, Ana I.; Cativiela, Carlos; Nussinov, Ruth; Alemán, Carlos

2009-01-01

The intrinsic conformational preferences of the non-proteinogenic amino acids constructed by incorporating the arginine side chain in the β position of 1-aminocyclopentane-1-carboxylic acid (either in a cis or a trans orientation relative to the amino group) have been investigated using computational methods. These compounds may be considered as constrained analogues of arginine (denoted as c5Arg) in which the orientation of the side chain is fixed by the cyclopentane moiety. Specifically, the N-acetyl-N′-methylamide derivatives of cis and trans-c5Arg have been examined in the gas phase and in solution using B3LYP/6-311+G(d,p) calculations and Molecular Dynamics simulations. Results indicate that the conformational space available to these compounds is highly restricted, their conformational preferences being dictated by the ability of the guanidinium group in the side chain to establish hydrogen-bond interactions with the backbone. A comparison with the behavior previously described for the analogous phenylalanine derivatives is presented. PMID:19236034

Simulation of Ames Backbone Network

NASA Technical Reports Server (NTRS)

Shahnasser, Hamid

1998-01-01

The networking demands of Ames Research Center are dramatically increasing. More and more workstations are requested to run video and audio applications on the network. These applications require a much greater bandwidth than data applications. The existing ARCLAN 2000 network bandwidth is insufficient, due to the use of FDDI as its backbone, for accommodating video applications. Operating at a maximum of 100 Mbps, FDDI can handle only a few workstations running multimedia applications. The ideal solution is to replace the current ARCLAN 2000 FDDI backbone with an ATM backbone. ATM has the capability to handle the increasing traffic loads on the ARCLAN 2000 that results from these new applications. As it can be seen from Figure 1, ARCLAN 2000 have a total of 32 routers (5 being core routers) each connected to the FDDI backbone via a 100 Mbps link. This network serves 34 different locations by using 34 hubs that are connected to secondary routers. End users are connected to the secondary routers with 10 Mbps links.

Solid state nuclear magnetic resonance investigation of polymer backbone dynamics in poly(ethylene oxide) based lithium and sodium polyether-ester-sulfonate ionomers.

PubMed

Roach, David J; Dou, Shichen; Colby, Ralph H; Mueller, Karl T

2013-05-21

Polymer backbone dynamics of single ion conducting poly(ethylene oxide) (PEO)-based ionomer samples with low glass transition temperatures (T(g)) have been investigated using solid-state nuclear magnetic resonance. Experiments detecting (13)C with (1)H decoupling under magic angle spinning (MAS) conditions identified the different components of the polymer backbone (PEO spacer and isophthalate groups) and their relative mobilities for a suite of lithium- and sodium-containing ionomer samples with varying cation contents. Variable temperature (203-373 K) (1)H-(13)C cross-polarization MAS (CP-MAS) experiments also provided qualitative assessment of the differences in the motions of the polymer backbone components as a function of cation content and identity. Each of the main backbone components exhibit distinct motions, following the trends expected for motional characteristics based on earlier Quasi Elastic Neutron Scattering and (1)H spin-lattice relaxation rate measurements. Previous (1)H and (7)Li spin-lattice relaxation measurements focused on both the polymer backbone and cation motion on the nanosecond timescale. The studies presented here assess the slower timescale motion of the polymer backbone allowing for a more comprehensive understanding of the polymer dynamics. The temperature dependences of (13)C linewidths were used to both qualitatively and quantitatively examine the effects of cation content and identity on PEO spacer mobility. Variable contact time (1)H-(13)C CP-MAS experiments were used to further assess the motions of the polymer backbone on the microsecond timescale. The motion of the PEO spacer, reported via the rate of magnetization transfer from (1)H to (13)C nuclei, becomes similar for T≳1.1 T(g) in all ionic samples, indicating that at similar elevated reduced temperatures the motions of the polymer backbones on the microsecond timescale become insensitive to ion interactions. These results present an improved picture, beyond those of

Structural test of the parameterized-backbone method for protein design.

PubMed

Plecs, Joseph J; Harbury, Pehr B; Kim, Peter S; Alber, Tom

2004-09-03

Designing new protein folds requires a method for simultaneously optimizing the conformation of the backbone and the side-chains. One approach to this problem is the use of a parameterized backbone, which allows the systematic exploration of families of structures. We report the crystal structure of RH3, a right-handed, three-helix coiled coil that was designed using a parameterized backbone and detailed modeling of core packing. This crystal structure was determined using another rationally designed feature, a metal-binding site that permitted experimental phasing of the X-ray data. RH3 adopted the intended fold, which has not been observed previously in biological proteins. Unanticipated structural asymmetry in the trimer was a principal source of variation within the RH3 structure. The sequence of RH3 differs from that of a previously characterized right-handed tetramer, RH4, at only one position in each 11 amino acid sequence repeat. This close similarity indicates that the design method is sensitive to the core packing interactions that specify the protein structure. Comparison of the structures of RH3 and RH4 indicates that both steric overlap and cavity formation provide strong driving forces for oligomer specificity.

Cost-effectiveness analysis of dolutegravir plus backbone compared with raltegravir plus backbone, darunavir+ritonavir plus backbone and efavirenz/tenofovir/emtricitabine in treatment naïve and experienced HIV-positive patients.

PubMed

Restelli, Umberto; Rizzardini, Giuliano; Antinori, Andrea; Lazzarin, Adriano; Bonfanti, Marzia; Bonfanti, Paolo; Croce, Davide

2017-01-01

In January 2014, the European Medicines Agency issued a marketing authorization for dolutegravir (DTG), a second-generation integrase strand transfer inhibitor for HIV treatment. The study aimed at determining the incremental cost-effectiveness ratio (ICER) of the use of DTG+backbone compared with raltegravir (RAL)+backbone, darunavir (DRV)+ritonavir(r)+backbone and efavirenz/tenofovir/emtricitabine (EFV/TDF/FTC) in HIV-positive treatment-naïve patients and compared with RAL+backbone in treatment-experienced patients, from the Italian National Health Service's point of view. A published Monte Carlo Individual Simulation Model (ARAMIS-DTG model) was used to perform the analysis. Patients pass through mutually exclusive health states (defined in terms of diagnosis of HIV with or without opportunistic infections [OIs] and cardiovascular disease [CVD]) and successive lines of therapy. The model considers costs (2014) and quality of life per monthly cycle in a lifetime horizon. Costs and quality-adjusted life years (QALYs) are dependent on OI, CVD, AIDS events, adverse events and antiretroviral therapies. In treatment-naïve patients, DTG dominates RAL; compared with DRV/r, the ICER obtained is of 38,586 €/QALY (6,170 €/QALY in patients with high viral load) and over EFV/TDF/FTC, DTG generates an ICER of 33,664 €/QALY. In treatment-experienced patients, DTG compared to RAL leads to an ICER of 12,074 €/QALY. The use of DTG+backbone may be cost effective in treatment-naïve and treatment-experienced patients compared with RAL+backbone and in treatment-naïve patients compared with DRV/r+backbone and EFV/TDF/FTC considering a threshold of 40,000 €/QALY.

The Inherent Conformational Preferences of Glutamine-Containing Peptides: the Role for Side-Chain Backbone Hydrogen Bonds

NASA Astrophysics Data System (ADS)

Walsh, Patrick S.; McBurney, Carl; Gellman, Samuel H.; Zwier, Timothy S.

2015-06-01

Glutamine is widely known to be found in critical regions of peptides which readily fold into amyloid fibrils, the structures commonly associated with Alzheimer's disease and glutamine repeat diseases such as Huntington's disease. Building on previous single-conformation data on Gln-containing peptides containing an aromatic cap on the N-terminus (Z-Gln-OH and Z-Gln-NHMe), we present here single-conformation UV and IR spectra of Ac-Gln-NHBn and Ac-Ala-Gln-NHBn, with its C-terminal benzyl cap. These results point towards side-chain to backbone hydrogen bonds dominating the structures observed in the cold, isolated environment of a molecular beam. We have identified and assigned three main conformers for Ac-Gln-NHBn all involving primary side-chain to backbone interactions. Ac-Ala-Gln-NHBn extends the peptide chain by one amino acid, but affords an improvement in the conformational flexibility. Despite this increase in the flexibility, only a single conformation is observed in the gas-phase: a structure which makes use of both side-chain-to-backbone and backbone-to-backbone hydrogen bonds.

Cost-effectiveness analysis of dolutegravir plus backbone compared with raltegravir plus backbone, darunavir+ritonavir plus backbone and efavirenz/tenofovir/emtricitabine in treatment naïve and experienced HIV-positive patients

PubMed Central

Restelli, Umberto; Rizzardini, Giuliano; Antinori, Andrea; Lazzarin, Adriano; Bonfanti, Marzia; Bonfanti, Paolo; Croce, Davide

2017-01-01

Background In January 2014, the European Medicines Agency issued a marketing authorization for dolutegravir (DTG), a second-generation integrase strand transfer inhibitor for HIV treatment. The study aimed at determining the incremental cost-effectiveness ratio (ICER) of the use of DTG+backbone compared with raltegravir (RAL)+backbone, darunavir (DRV)+ritonavir(r)+backbone and efavirenz/tenofovir/emtricitabine (EFV/TDF/FTC) in HIV-positive treatment-naïve patients and compared with RAL+backbone in treatment-experienced patients, from the Italian National Health Service’s point of view. Materials and methods A published Monte Carlo Individual Simulation Model (ARAMIS-DTG model) was used to perform the analysis. Patients pass through mutually exclusive health states (defined in terms of diagnosis of HIV with or without opportunistic infections [OIs] and cardiovascular disease [CVD]) and successive lines of therapy. The model considers costs (2014) and quality of life per monthly cycle in a lifetime horizon. Costs and quality-adjusted life years (QALYs) are dependent on OI, CVD, AIDS events, adverse events and antiretroviral therapies. Results In treatment-naïve patients, DTG dominates RAL; compared with DRV/r, the ICER obtained is of 38,586 €/QALY (6,170 €/QALY in patients with high viral load) and over EFV/TDF/FTC, DTG generates an ICER of 33,664 €/QALY. In treatment-experienced patients, DTG compared to RAL leads to an ICER of 12,074 €/QALY. Conclusion The use of DTG+backbone may be cost effective in treatment-naïve and treatment-experienced patients compared with RAL+backbone and in treatment-naïve patients compared with DRV/r+backbone and EFV/TDF/FTC considering a threshold of 40,000 €/QALY. PMID:28721059

Cyclo-hexa-peptides at the water/cyclohexane interface: a molecular dynamics simulation.

PubMed

Cen, Min; Fan, Jian Fen; Liu, Dong Yan; Song, Xue Zeng; Liu, Jian; Zhou, Wei Qun; Xiao, He Ming

2013-02-01

Molecular dynamic (MD) simulations have been performed to study the behaviors of ten kinds of cyclo-hexa-peptides (CHPs) composed of amino acids with the diverse hydrophilic/hydrophobic side chains at the water/cyclohexane interface. All the CHPs take the "horse-saddle" conformations at the interface and the hydrophilicity/hydrophobicity of the side chains influences the backbones' structural deformations. The orientations and distributions of the CHPs at the interface and the differences of interaction energies (ΔΔE) between the CHPs and the two liquid phases have been determined. RDF analysis shows that the H-bonds were formed between the O(C) atoms of the CHPs' backbones and H(w) atoms of water molecules. N atoms of the CHPs' backbones formed the H-bonds or van der Waals interactions with the water solvent. It was found that there is a parallel relationship between ΔΔE and the lateral diffusion coefficients (D ( xy )) of the CHPs at the interface. The movements of water molecules close to the interface are confined to some extent, indicating that the dynamics of the CHPs and interfacial water molecules are strongly coupled.

Process-based network decomposition reveals backbone motif structure

PubMed Central

Wang, Guanyu; Du, Chenghang; Chen, Hao; Simha, Rahul; Rong, Yongwu; Xiao, Yi; Zeng, Chen

2010-01-01

A central challenge in systems biology today is to understand the network of interactions among biomolecules and, especially, the organizing principles underlying such networks. Recent analysis of known networks has identified small motifs that occur ubiquitously, suggesting that larger networks might be constructed in the manner of electronic circuits by assembling groups of these smaller modules. Using a unique process-based approach to analyzing such networks, we show for two cell-cycle networks that each of these networks contains a giant backbone motif spanning all the network nodes that provides the main functional response. The backbone is in fact the smallest network capable of providing the desired functionality. Furthermore, the remaining edges in the network form smaller motifs whose role is to confer stability properties rather than provide function. The process-based approach used in the above analysis has additional benefits: It is scalable, analytic (resulting in a single analyzable expression that describes the behavior), and computationally efficient (all possible minimal networks for a biological process can be identified and enumerated). PMID:20498084

High-resolution protein design with backbone freedom.

PubMed

Harbury, P B; Plecs, J J; Tidor, B; Alber, T; Kim, P S

1998-11-20

Recent advances in computational techniques have allowed the design of precise side-chain packing in proteins with predetermined, naturally occurring backbone structures. Because these methods do not model protein main-chain flexibility, they lack the breadth to explore novel backbone conformations. Here the de novo design of a family of alpha-helical bundle proteins with a right-handed superhelical twist is described. In the design, the overall protein fold was specified by hydrophobic-polar residue patterning, whereas the bundle oligomerization state, detailed main-chain conformation, and interior side-chain rotamers were engineered by computational enumerations of packing in alternate backbone structures. Main-chain flexibility was incorporated through an algebraic parameterization of the backbone. The designed peptides form alpha-helical dimers, trimers, and tetramers in accord with the design goals. The crystal structure of the tetramer matches the designed structure in atomic detail.

Optical burst switching based satellite backbone network

NASA Astrophysics Data System (ADS)

Li, Tingting; Guo, Hongxiang; Wang, Cen; Wu, Jian

2018-02-01

We propose a novel time slot based optical burst switching (OBS) architecture for GEO/LEO based satellite backbone network. This architecture can provide high speed data transmission rate and high switching capacity . Furthermore, we design the control plane of this optical satellite backbone network. The software defined network (SDN) and network slice (NS) technologies are introduced. Under the properly designed control mechanism, this backbone network is flexible to support various services with diverse transmission requirements. Additionally, the LEO access and handoff management in this network is also discussed.

Backbone amide 15N chemical shift tensors report on hydrogen bonding interactions in proteins: A magic angle spinning NMR study.

PubMed

Paramasivam, Sivakumar; Gronenborn, Angela M; Polenova, Tatyana

2018-08-01

Chemical shift tensors (CSTs) are an exquisite probe of local geometric and electronic structure. 15 N CST are very sensitive to hydrogen bonding, yet they have been reported for very few proteins to date. Here we present experimental results and statistical analysis of backbone amide 15 N CSTs for 100 residues of four proteins, two E. coli thioredoxin reassemblies (1-73-(U- 13 C, 15 N)/74-108-(U- 15 N) and 1-73-(U- 15 N)/74-108-(U- 13 C, 15 N)), dynein light chain 8 LC8, and CAP-Gly domain of the mammalian dynactin. The 15 N CSTs were measured by a symmetry-based CSA recoupling method, ROCSA. Our results show that the principal component δ 11 is very sensitive to the presence of hydrogen bonding interactions due to its unique orientation in the molecular frame. The downfield chemical shift change of backbone amide nitrogen nuclei with increasing hydrogen bond strength is manifested in the negative correlation of the principal components with hydrogen bond distance for both α-helical and β-sheet secondary structure elements. Our findings highlight the potential for the use of 15 N CSTs in protein structure refinement. Copyright © 2018 Elsevier Inc. All rights reserved.

Coupling Protein Side-Chain and Backbone Flexibility Improves the Re-design of Protein-Ligand Specificity.

PubMed

Ollikainen, Noah; de Jong, René M; Kortemme, Tanja

2015-01-01

Interactions between small molecules and proteins play critical roles in regulating and facilitating diverse biological functions, yet our ability to accurately re-engineer the specificity of these interactions using computational approaches has been limited. One main difficulty, in addition to inaccuracies in energy functions, is the exquisite sensitivity of protein-ligand interactions to subtle conformational changes, coupled with the computational problem of sampling the large conformational search space of degrees of freedom of ligands, amino acid side chains, and the protein backbone. Here, we describe two benchmarks for evaluating the accuracy of computational approaches for re-engineering protein-ligand interactions: (i) prediction of enzyme specificity altering mutations and (ii) prediction of sequence tolerance in ligand binding sites. After finding that current state-of-the-art "fixed backbone" design methods perform poorly on these tests, we develop a new "coupled moves" design method in the program Rosetta that couples changes to protein sequence with alterations in both protein side-chain and protein backbone conformations, and allows for changes in ligand rigid-body and torsion degrees of freedom. We show significantly increased accuracy in both predicting ligand specificity altering mutations and binding site sequences. These methodological improvements should be useful for many applications of protein-ligand design. The approach also provides insights into the role of subtle conformational adjustments that enable functional changes not only in engineering applications but also in natural protein evolution.

Computational protein design with backbone plasticity

PubMed Central

MacDonald, James T.; Freemont, Paul S.

2016-01-01

The computational algorithms used in the design of artificial proteins have become increasingly sophisticated in recent years, producing a series of remarkable successes. The most dramatic of these is the de novo design of artificial enzymes. The majority of these designs have reused naturally occurring protein structures as ‘scaffolds’ onto which novel functionality can be grafted without having to redesign the backbone structure. The incorporation of backbone flexibility into protein design is a much more computationally challenging problem due to the greatly increased search space, but promises to remove the limitations of reusing natural protein scaffolds. In this review, we outline the principles of computational protein design methods and discuss recent efforts to consider backbone plasticity in the design process. PMID:27911735

DETECTION OF EXTREMELY BROAD WATER EMISSION FROM THE MOLECULAR CLOUD INTERACTING SUPERNOVA REMNANT G349.7+0.2

DOE Office of Scientific and Technical Information (OSTI.GOV)

Rho, J.; Hewitt, J. W.; Boogert, A.

2015-10-10

We performed Herschel HIFI, PACS, and SPIRE observations toward the molecular cloud interacting supernova remnant G349.7+0.2. An extremely broad emission line was detected at 557 GHz from the ground state transition 1{sub 10}-1{sub 01} of ortho-water. This water line can be separated into three velocity components with widths of 144, 27, and 4 km s{sup −1}. The 144 km s{sup −1} component is the broadest water line detected to date in the literature. This extremely broad line width shows the importance of probing shock dynamics. PACS observations revealed three additional ortho-water lines, as well as numerous high-J carbon monoxide (CO)more » lines. No para-water lines were detected. The extremely broad water line is indicative of a high velocity shock, which is supported by the observed CO rotational diagram that was reproduced with a J-shock model with a density of 10{sup 4} cm{sup −3} and a shock velocity of 80 km s{sup −1}. Two far-infrared fine-structure lines, [O i] at 145 μm and [C ii] line at 157 μm, are also consistent with the high velocity J-shock model. The extremely broad water line could be simply from short-lived molecules that have not been destroyed in high velocity J-shocks; however, it may be from more complicated geometry such as high-velocity water bullets or a shell expanding in high velocity. We estimate the CO and H{sub 2}O densities, column densities, and temperatures by comparison with RADEX and detailed shock models.« less

Quantifying Interactions of Nucleobase Atoms with Model Compounds for the Peptide Backbone and Glutamine and Asparagine Side Chains in Water.

PubMed

Cheng, Xian; Shkel, Irina A; Molzahn, Cristen; Lambert, David; Karim, Rezwana; Record, M Thomas

2018-04-17

Alkylureas display hydrocarbon and amide groups, the primary functional groups of proteins. To obtain the thermodynamic information that is needed to analyze interactions of amides and proteins with nucleobases and nucleic acids, we quantify preferential interactions of alkylureas with nucleobases differing in the amount and composition of water-accessible surface area (ASA) by solubility assays. Using an established additive ASA-based analysis, we interpret these thermodynamic results to determine interactions of each alkylurea with five types of nucleobase unified atoms (carbonyl sp 2 O, amino sp 3 N, ring sp 2 N, methyl sp 3 C, and ring sp 2 C). All alkylureas interact favorably with nucleobase sp 2 C and sp 3 C atoms; these interactions become more favorable with an increasing level of alkylation of urea. Interactions with nucleobase sp 2 O are most favorable for urea, less favorable for methylurea and ethylurea, and unfavorable for dialkylated ureas. Contributions to overall alkylurea-nucleobase interactions from interactions with each nucleobase atom type are proportional to the ASA of that atom type with proportionality constant (interaction strength) α, as observed previously for urea. Trends in α-values for interactions of alkylureas with nucleobase atom types parallel those for corresponding amide compound atom types, offset because nucleobase α-values are more favorable. Comparisons between ethylated and methylated ureas show interactions of amide compound sp 3 C with nucleobase sp 2 C, sp 3 C, sp 2 N, and sp 3 N atoms are favorable while amide sp 3 C-nucleobase sp 2 O interactions are unfavorable. Strongly favorable interactions of urea with nucleobase sp 2 O but weakly favorable interactions with nucleobase sp 3 N indicate that amide sp 2 N-nucleobase sp 2 O and nucleobase sp 3 N-amide sp 2 O hydrogen bonding (NH···O═C) interactions are favorable while amide sp 2 N-nucleobase sp 3 N interactions are unfavorable. These favorable amide

Understanding traffic dynamics at a backbone POP

NASA Astrophysics Data System (ADS)

Taft, Nina; Bhattacharyya, Supratik; Jetcheva, Jorjeta; Diot, Christophe

2001-07-01

Spatial and temporal information about traffic dynamics is central to the design of effective traffic engineering practices for IP backbones. In this paper we study backbone traffic dynamics using data collected at a major POP on a tier-1 IP backbone. We develop a methodology that combines packet-level traces from access links in the POP and BGP routing information to build components of POP-to-POP traffic matrices. Our results show that there is wide disparity in the volume of traffic headed towards different egress POPs. At the same time, we find that current routing practices in the backbone tend to constrain traffic between ingress-egress POP pairs to a small number of paths. As a result, there is a wide variation in the utilization level of links in the backbone. Frequent capacity upgrades of the heavily used links are expensive; the need for such upgrades can be reduced by designing load balancing policies that will route more traffic over less utilized links. We identify traffic aggregates based on destination address prefixes and find that this set of criteria isolates a few aggregates that account for an overwhelmingly large portion of inter-POP traffic. We also demonstrate that these aggregates exhibit stability throughout the day on per-hour time scales, and thus they form a natural basis for splitting traffic over multiple paths in order to improve load balancing.

Large-scale measurement and modeling of backbone Internet traffic

NASA Astrophysics Data System (ADS)

Roughan, Matthew; Gottlieb, Joel

2002-07-01

There is a brewing controversy in the traffic modeling community concerning how to model backbone traffic. The fundamental work on self-similarity in data traffic appears to be contradicted by recent findings that suggest that backbone traffic is smooth. The traffic analysis work to date has focused on high-quality but limited-scope packet trace measurements; this limits its applicability to high-speed backbone traffic. This paper uses more than one year's worth of SNMP traffic data covering an entire Tier 1 ISP backbone to address the question of how backbone network traffic should be modeled. Although the limitations of SNMP measurements do not permit us to comment on the fine timescale behavior of the traffic, careful analysis of the data suggests that irrespective of the variation at fine timescales, we can construct a simple traffic model that captures key features of the observed traffic. Furthermore, the model's parameters are measurable using existing network infrastructure, making this model practical in a present-day operational network. In addition to its practicality, the model verifies basic statistical multiplexing results, and thus sheds deep insight into how smooth backbone traffic really is.

The determinants of bond angle variability in protein/peptide backbones: A comprehensive statistical/quantum mechanics analysis.

PubMed

Improta, Roberto; Vitagliano, Luigi; Esposito, Luciana

2015-11-01

The elucidation of the mutual influence between peptide bond geometry and local conformation has important implications for protein structure refinement, validation, and prediction. To gain insights into the structural determinants and the energetic contributions associated with protein/peptide backbone plasticity, we here report an extensive analysis of the variability of the peptide bond angles by combining statistical analyses of protein structures and quantum mechanics calculations on small model peptide systems. Our analyses demonstrate that all the backbone bond angles strongly depend on the peptide conformation and unveil the existence of regular trends as function of ψ and/or φ. The excellent agreement of the quantum mechanics calculations with the statistical surveys of protein structures validates the computational scheme here employed and demonstrates that the valence geometry of protein/peptide backbone is primarily dictated by local interactions. Notably, for the first time we show that the position of the H(α) hydrogen atom, which is an important parameter in NMR structural studies, is also dependent on the local conformation. Most of the trends observed may be satisfactorily explained by invoking steric repulsive interactions; in some specific cases the valence bond variability is also influenced by hydrogen-bond like interactions. Moreover, we can provide a reliable estimate of the energies involved in the interplay between geometry and conformations. © 2015 Wiley Periodicals, Inc.

An ``Alternating-Curvature'' Model for the Nanometer-scale Structure of the Nafion Ionomer, Based on Backbone Properties Detected by NMR

NASA Astrophysics Data System (ADS)

Schmidt-Rohr, Klaus; Chen, Q.

2006-03-01

The perfluorinated ionomer, Nafion, which consists of a (-CF2-)n backbone and charged side branches, is useful as a proton exchange membrane in H2/O2 fuel cells. A modified model of the nanometer-scale structure of hydrated Nafion will be presented. It features hydrated ionic clusters familiar from some previous models, but is based most prominently on pronounced backbone rigidity between branch points and limited orientational correlation of local chain axes. These features have been revealed by solid-state NMR measurements, which take advantage of fast rotations of the backbones around their local axes. The resulting alternating curvature of the backbones towards the hydrated clusters also better satisfies the requirement of dense space filling in solids. Simulations based on this ``alternating curvature'' model reproduce orientational correlation data from NMR, as well as scattering features such as the ionomer peak and the I(q) ˜ 1/q power law at small q values, which can be attributed to modulated cylinders resulting from the chain stiffness. The shortcomings of previous models, including Gierke's cluster model and more recent lamellar or bundle models, in matching all requirements imposed by the experimental data will be discussed.

A Novel Approach for Evaluation of Water Quality Trends in Gulf Coast Estuaries

EPA Science Inventory

Water quality data form the backbone of management programs aimed at protecting environmental resources. The increasing availability of long-term monitoring data for estuaries can improve detection of temporal and spatial changes in water quality. However, the relatively simple...

Predicting the tolerated sequences for proteins and protein interfaces using RosettaBackrub flexible backbone design.

PubMed

Smith, Colin A; Kortemme, Tanja

2011-01-01

Predicting the set of sequences that are tolerated by a protein or protein interface, while maintaining a desired function, is useful for characterizing protein interaction specificity and for computationally designing sequence libraries to engineer proteins with new functions. Here we provide a general method, a detailed set of protocols, and several benchmarks and analyses for estimating tolerated sequences using flexible backbone protein design implemented in the Rosetta molecular modeling software suite. The input to the method is at least one experimentally determined three-dimensional protein structure or high-quality model. The starting structure(s) are expanded or refined into a conformational ensemble using Monte Carlo simulations consisting of backrub backbone and side chain moves in Rosetta. The method then uses a combination of simulated annealing and genetic algorithm optimization methods to enrich for low-energy sequences for the individual members of the ensemble. To emphasize certain functional requirements (e.g. forming a binding interface), interactions between and within parts of the structure (e.g. domains) can be reweighted in the scoring function. Results from each backbone structure are merged together to create a single estimate for the tolerated sequence space. We provide an extensive description of the protocol and its parameters, all source code, example analysis scripts and three tests applying this method to finding sequences predicted to stabilize proteins or protein interfaces. The generality of this method makes many other applications possible, for example stabilizing interactions with small molecules, DNA, or RNA. Through the use of within-domain reweighting and/or multistate design, it may also be possible to use this method to find sequences that stabilize particular protein conformations or binding interactions over others.

Mechanism of interaction of the antileukemic drug cytosine arabinoside with aromatic peptides: role of sugar conformation and peptide backbone.

PubMed

Datta, G; Hosur, R V; Verma, N C; Khetrapal, C L; Gurnani, S

1989-01-01

Interaction of the antileukemic drugs, cytosine-arabinoside (Ara-C) and adenosine-arabinoside (Ara-A) and a structural analogue, cytidine, with aromatic dipeptides has been studied by fluorescence and NMR spectroscopy. Ara-C and cytidine bind tryptophanyl and histidyl dipeptides but not tyrosyl dipeptides, while Ara-A does not bind to any of them. Both studies indicate association involving stacking of aromatic moieties. NMR spectra also indicate a protonation of the histidine moiety by Ara-C. In case of cytidine, the chemical shifts observed on binding to His-Phe imply that the backbone protons of the dipeptide participate in the binding. The conformation of the sugar and the base seem to play a very important role in the binding phenomenon as three similar molecules, Ara-C, Ara-A and cytidine bind in totally different ways.

Effect of Backbone Design on Hybridization Thermodynamics of Oligo-nucleic Acids: A Coarse-Grained Molecular Dynamics Simulation Study

NASA Astrophysics Data System (ADS)

Ghobadi, Ahmadreza F.; Jayaraman, Arthi

DNA hybridization is the basis of various bio-nano technologies, such as DNA origami and assembly of DNA-functionalized nanoparticles. A hybridized double stranded (ds) DNA is formed when complementary nucleobases on hybridizing strands exhibit specific and directional hydrogen bonds through canonical Watson-Crick base-pairing interactions. In recent years, the need for cheaper alternatives and significant synthetic advances have driven design of DNA mimics with new backbone chemistries. However, a fundamental understanding of how these backbone modifications in the oligo-nucleic acids impact the hybridization and melting behavior of the duplex is still lacking. In this talk, we present our recent findings on impact of varying backbone chemistry on hybridization of oligo-nucleic acid duplexes. We use coarse-grained molecular dynamics simulations to isolate the effect of strand flexibility, electrostatic interactions and nucleobase spacing on the melting curves for duplexes with various strand sequences and concentrations. Since conjugation of oligo-nucleic acids with polymers serve as building blocks for thermo-responsive polymer networks and gels, we also present the effect of such conjugation on hybridization thermodynamics and polymer conformation.

Backbone resonance assignments of the PRYSPRY domain of TRIM25.

PubMed

Kong, Chen; Penumutchu, Srinivasa R; Hung, Kuo-Wei; Huang, Huiying; Lin, Tianwei; Yu, Chin

2015-10-01

TRIM25 is a member of the tripartite motif (TRIM) family and has been implicated in the regulation of innate immune signaling via the RIG-I (retinoic acid-inducible gene-I) pathway for antiviral defense. As the essential first step towards the structural and functional characterization of the TRIM25/RIG-I interaction, the backbone resonance of the PRYSPRY domain of TRIM25 is assigned here based on triple-resonance experiments using uniformly [(2)H, (13)C, (15)N]-labeled protein.

Induced helical backbone conformations of self-organizable dendronized polymers.

PubMed

Rudick, Jonathan G; Percec, Virgil

2008-12-01

Control of function through the primary structure of a molecule presents a significant challenge with valuable rewards for nanoscience. Dendritic building blocks encoded with information that defines their three-dimensional shape (e.g., flat-tapered or conical) and how they associate with each other are referred to as self-assembling dendrons. Self-organizable dendronized polymers possess a flat-tapered or conical self-assembling dendritic side chain on each repeat unit of a linear polymer backbone. When appended to a covalent polymer, the self-assembling dendrons direct a folding process (i.e., intramolecular self-assembly). Alternatively, intermolecular self-assembly of dendrons mediated by noncovalent interactions between apex groups can generate a supramolecular polymer backbone. Self-organization, as we refer to it, is the spontaneous formation of periodic and quasiperiodic arrays from supramolecular elements. Covalent and supramolecular polymers jacketed with self-assembling dendrons self-organize. The arrays are most often comprised of cylindrical or spherical objects. The shape of the object is determined by the primary structure of the dendronized polymer: the structure of the self-assembling dendron and the length of the polymer backbone. It is therefore possible to predictably generate building blocks for single-molecule nanotechnologies or arrays of supramolecules for bottom-up self-assembly. We exploit the self-organization of polymers jacketed with self-assembling dendrons to elucidate how primary structure determines the adopted conformation and fold (i.e., secondary and tertiary structure), how the supramolecules associate (i.e., quaternary structure), and their resulting functions. A combination of experimental techniques is employed to interrogate the primary, secondary, tertiary, and quaternary structure of the self-organizable dendronized polymers. We refer to the process by which we interpolate between the various levels of structural

On topological RNA interaction structures.

PubMed

Qin, Jing; Reidys, Christian M

2013-07-01

Recently a folding algorithm of topological RNA pseudoknot structures was presented in Reidys et al. (2011). This algorithm folds single-stranded γ-structures, that is, RNA structures composed by distinct motifs of bounded topological genus. In this article, we set the theoretical foundations for the folding of the two backbone analogues of γ structures: the RNA γ-interaction structures. These are RNA-RNA interaction structures that are constructed by a finite number of building blocks over two backbones having genus at most γ. Combinatorial properties of γ-interaction structures are of practical interest since they have direct implications for the folding of topological interaction structures. We compute the generating function of γ-interaction structures and show that it is algebraic, which implies that the numbers of interaction structures can be computed recursively. We obtain simple asymptotic formulas for 0- and 1-interaction structures. The simplest class of interaction structures are the 0-interaction structures, which represent the two backbone analogues of secondary structures.

The multiscale backbone of the human phenotype network based on biological pathways.

PubMed

Darabos, Christian; White, Marquitta J; Graham, Britney E; Leung, Derek N; Williams, Scott M; Moore, Jason H

2014-01-25

Networks are commonly used to represent and analyze large and complex systems of interacting elements. In systems biology, human disease networks show interactions between disorders sharing common genetic background. We built pathway-based human phenotype network (PHPN) of over 800 physical attributes, diseases, and behavioral traits; based on about 2,300 genes and 1,200 biological pathways. Using GWAS phenotype-to-genes associations, and pathway data from Reactome, we connect human traits based on the common patterns of human biological pathways, detecting more pleiotropic effects, and expanding previous studies from a gene-centric approach to that of shared cell-processes. The resulting network has a heavily right-skewed degree distribution, placing it in the scale-free region of the network topologies spectrum. We extract the multi-scale information backbone of the PHPN based on the local densities of the network and discarding weak connection. Using a standard community detection algorithm, we construct phenotype modules of similar traits without applying expert biological knowledge. These modules can be assimilated to the disease classes. However, we are able to classify phenotypes according to shared biology, and not arbitrary disease classes. We present examples of expected clinical connections identified by PHPN as proof of principle. We unveil a previously uncharacterized connection between phenotype modules and discuss potential mechanistic connections that are obvious only in retrospect. The PHPN shows tremendous potential to become a useful tool both in the unveiling of the diseases' common biology, and in the elaboration of diagnosis and treatments.

Interplay Between Hydrophobic Effect and Dipole Interactions in Peptide Aggregation

NASA Astrophysics Data System (ADS)

Ganesan, Sai; Matysiak, Silvina

In the past decade, the development of various coarse-grained models for proteins have provided key insights into the driving forces in folding and aggregation.We recently developed a low resolution Water Explicit Polarizable PROtein coarse-grained Model by adding oppositely charged dummy particles inside protein backbone beads.With this model,we were able to achieve significant α/ β secondary structure content,without any added bias.We now extend the model to study peptide aggregation at hydrophobic-hydrophilic interface using elastin-like octapeptides (GV)4 as a model system.A condensation-ordering mechanism of aggregation is observed in water.Our results suggest that backbone interpeptide dipolar interactions,not hydrophobicity,plays a more significant role in fibril-like peptide aggregation.We observe a cooperative effect in hydrogen bonding or dipolar interactions, with increase in aggregate size in water and interface.Based on this cooperative effect, we provide a potential explanation for the observed nucleus size in peptide aggregation pathways.Without dipolar particles,peptide aggregation is not observed at the hydrophilic-hydrophobic interface.Thus,the presence of dipoles,not hydrophobicity plays a key role in aggregation observed at hydrophobic interfaces.

The dominant interaction between peptide and urea is electrostatic in nature: a molecular dynamics simulation study.

PubMed

Tobi, Dror; Elber, Ron; Thirumalai, Devarajan

2003-03-01

The conformational equilibrium of a blocked valine peptide in water and aqueous urea solution is studied using molecular dynamics simulations. Pair correlation functions indicate enhanced concentration of urea near the peptide. Stronger hydrogen bonding of urea-peptide compared to water-peptide is observed with preference for helical conformation. The potential of mean force, computed using umbrella sampling, shows only small differences between urea and water solvation that are difficult to quantify. The changes in solvent structure around the peptide are explained by favorable electrostatic interactions (hydrogen bonds) of urea with the peptide backbone. There is no evidence for significant changes in hydrophobic interactions in the two conformations of the peptide in urea solution. Our simulations suggest that urea denatures proteins by preferentially forming hydrogen bonds to the peptide backbone, reducing the barrier for exposing protein residues to the solvent, and reaching the unfolded state. Copyright 2003 Wiley Periodicals, Inc. Biopolymers: 359-369, 2003

Multi-source micro-friction identification for a class of cable-driven robots with passive backbone

NASA Astrophysics Data System (ADS)

Tjahjowidodo, Tegoeh; Zhu, Ke; Dailey, Wayne; Burdet, Etienne; Campolo, Domenico

2016-12-01

This paper analyses the dynamics of cable-driven robots with a passive backbone and develops techniques for their dynamic identification, which are tested on the H-Man, a planar cabled differential transmission robot for haptic interaction. The mechanism is optimized for human-robot interaction by accounting for the cost-benefit-ratio of the system, specifically by eliminating the necessity of an external force sensor to reduce the overall cost. As a consequence, this requires an effective dynamic model for accurate force feedback applications which include friction behavior in the system. We first consider the significance of friction in both the actuator and backbone spaces. Subsequently, we study the required complexity of the stiction model for the application. Different models representing different levels of complexity are investigated, ranging from the conventional approach of Coulomb to an advanced model which includes hysteresis. The results demonstrate each model's ability to capture the dynamic behavior of the system. In general, it is concluded that there is a trade-off between model accuracy and the model cost.

Determination of backbone chain direction of PDA using FFM

NASA Astrophysics Data System (ADS)

Jo, Sadaharu; Okamoto, Kentaro; Takenaga, Mitsuru

2010-01-01

The effect of backbone chains on friction force was investigated on both Langmuir-Blodgett (LB) films of 10,12-heptacosadiynoic acid and the (0 1 0) surfaces of single crystals of 2,4-hexadiene-1,6-diol using friction force microscopy (FFM). It was observed that friction force decreased when the scanning direction was parallel to the [0 0 1] direction in both samples. Moreover, friction force decreased when the scanning direction was parallel to the crystallographic [1 0 2], [1 0 1], [1 0 0] and [1 0 1¯] directions in only the single crystals. For the LB films, the [0 0 1] direction corresponds to the backbone chain direction of 10,12-heptacosadiynoic acid. For the single crystals, both the [0 0 1] and [1 0 1] directions correspond to the backbone chain direction, and the [1 0 2], [1 0 0] and [1 0 1¯] directions correspond to the low-index crystallographic direction. In both the LB films and single crystals, the friction force was minimized when the directions of scanning and the backbone chain were parallel.

Backbone dynamics of the antifungal Psd1 pea defensin and its correlation with membrane interaction by NMR spectroscopy.

PubMed

de Medeiros, Luciano Neves; Angeli, Renata; Sarzedas, Carolina G; Barreto-Bergter, Eliana; Valente, Ana Paula; Kurtenbach, Eleonora; Almeida, Fabio C L

2010-02-01

Plant defensins are cysteine-rich cationic peptides, components of the innate immune system. The antifungal sensitivity of certain exemplars was correlated to the level of complex glycosphingolipids in the membrane of fungi strains. Psd1 is a 46 amino acid residue defensin isolated from pea seeds which exhibit antifungal activity. Its structure is characterized by the so-called cysteine-stabilized alpha/beta motif linked by three loops as determined by two-dimensional NMR. In the present work we explored the measurement of heteronuclear Nuclear Overhauser Effects, R1 and R2 (15)N relaxation ratios, and chemical shift to probe the backbone dynamics of Psd1 and its interaction with membrane mimetic systems with phosphatidylcholine (PC) or dodecylphosphocholine (DPC) with glucosylceramide (CMH) isolated from Fusarium solani. The calculated R2 values predicted a slow motion around the highly conserved among Gly12 residue and also in the region of the Turn3 His36-Trp38. The results showed that Psd1 interacts with vesicles of PC or PC:CMH in slightly different forms. The interaction was monitored by chemical shift perturbation and relaxation properties. Using this approach we could map the loops as the binding site of Psd1 with the membrane. The major binding epitope showed conformation exchange properties in the mus-ms timescale supporting the conformation selection as the binding mechanism. Moreover, the peptide corresponding to part of Loop1 (pepLoop1: Gly12 to Ser19) is also able to interact with DPC micelles acquiring a stable structure and in the presence of DPC:CMH the peptide changes to an extended conformation, exhibiting NOE mainly with the carbohydrate and ceramide parts of CMH. Copyright 2009 Elsevier B.V. All rights reserved.

Rational Design of Orthogonal Multipolar Interactions with Fluorine in Protein–Ligand Complexes

DOE PAGES

Pollock, Jonathan; Borkin, Dmitry; Lund, George; ...

2015-08-19

Multipolar interactions involving fluorine and the protein backbone have been frequently observed in protein–ligand complexes. Such fluorine–backbone interactions may substantially contribute to the high affinity of small molecule inhibitors. Here we found that introduction of trifluoromethyl groups into two different sites in the thienopyrimidine class of menin–MLL inhibitors considerably improved their inhibitory activity. In both cases, trifluoromethyl groups are engaged in short interactions with the backbone of menin. In order to understand the effect of fluorine, we synthesized a series of analogues by systematically changing the number of fluorine atoms, and we determined high-resolution crystal structures of the complexes withmore » menin. Here, we found that introduction of fluorine at favorable geometry for interactions with backbone carbonyls may improve the activity of menin–MLL inhibitors as much as 5- to 10-fold. In order to facilitate the design of multipolar fluorine–backbone interactions in protein–ligand complexes, we developed a computational algorithm named FMAP, which calculates fluorophilic sites in proximity to the protein backbone. We demonstrated that FMAP could be used to rationalize improvement in the activity of known protein inhibitors upon introduction of fluorine. Furthermore, FMAP may also represent a valuable tool for designing new fluorine substitutions and support ligand optimization in drug discovery projects. Analysis of the menin–MLL inhibitor complexes revealed that the backbone in secondary structures is particularly accessible to the interactions with fluorine. Lastly, considering that secondary structure elements are frequently exposed at protein interfaces, we postulate that multipolar fluorine–backbone interactions may represent a particularly attractive approach to improve inhibitors of protein–protein interactions.« less

Solution, solid phase and computational structures of apicidin and its backbone-reduced analogs.

PubMed

Kranz, Michael; Murray, Peter John; Taylor, Stephen; Upton, Richard J; Clegg, William; Elsegood, Mark R J

2006-06-01

The recently isolated broad-spectrum antiparasitic apicidin (1) is one of the few naturally occurring cyclic tetrapeptides (CTP). Depending on the solvent, the backbone of 1 exhibits two gamma-turns (in CH(2)Cl(2)) or a beta-turn (in DMSO), differing solely in the rotation of the plane of one of the amide bonds. In the X-ray crystal structure, the peptidic C==Os and NHs are on opposite sides of the backbone plane, giving rise to infinite stacks of cyclotetrapeptides connected by three intermolecular hydrogen bonds between the backbones. Conformational searches (Amber force field) on a truncated model system of 1 confirm all three backbone conformations to be low-energy states. The previously synthesized analogs of 1 containing a reduced amide bond exhibit the same backbone conformation as 1 in DMSO, which is confirmed further by the X-ray crystal structure of a model system of the desoxy analogs of 1. This similarity helps in explaining why the desoxy analogs retain some of the antiprotozoal activities of apicidin. The backbone-reduction approach designed to facilitate the cyclization step of the acyclic precursors of the CTPs seems to retain the conformational preferences of the parent peptide backbone.

Genotype by watering regime interaction in cultivated tomato: lessons from linkage mapping and gene expression.

PubMed

Albert, Elise; Gricourt, Justine; Bertin, Nadia; Bonnefoi, Julien; Pateyron, Stéphanie; Tamby, Jean-Philippe; Bitton, Frédérique; Causse, Mathilde

2016-02-01

In tomato, genotype by watering interaction resulted from genotype re-ranking more than scale changes. Interactive QTLs according to watering regime were detected. Differentially expressed genes were identified in some intervals. As a result of climate change, drought will increasingly limit crop production in the future. Studying genotype by watering regime interactions is necessary to improve plant adaptation to low water availability. In cultivated tomato (Solanum lycopersicum L.), extensively grown in dry areas, well-mastered water deficits can stimulate metabolite production, increasing plant defenses and concentration of compounds involved in fruit quality, at the same time. However, few tomato Quantitative Trait Loci (QTLs) and genes involved in response to drought are identified or only in wild species. In this study, we phenotyped a population of 119 recombinant inbred lines derived from a cross between a cherry tomato and a large fruit tomato, grown in greenhouse under two watering regimes, in two locations. A large genetic variability was measured for 19 plant and fruit traits, under the two watering treatments. Highly significant genotype by watering regime interactions were detected and resulted from re-ranking more than scale changes. The population was genotyped for 679 SNP markers to develop a genetic map. In total, 56 QTLs were identified among which 11 were interactive between watering regimes. These later mainly exhibited antagonist effects according to watering treatment. Variation in gene expression in leaves of parental accessions revealed 2259 differentially expressed genes, among which candidate genes presenting sequence polymorphisms were identified under two main interactive QTLs. Our results provide knowledge about the genetic control of genotype by watering regime interactions in cultivated tomato and the possible use of deficit irrigation to improve tomato quality.

ExScal Backbone Network Architecture

DTIC Science & Technology

2005-01-01

802.11 battery powered nodes was laid over the sensor network. We adopted the Stargate platform for the backbone tier to serve as the basis for...its head. XSS Hardware and Network: XSS stands for eXtreme Scaling Stargate . A stargate is a linux-based single board computer. It has a 400 MHz

TRX-LOGOS - a graphical tool to demonstrate DNA information content dependent upon backbone dynamics in addition to base sequence.

PubMed

Fortin, Connor H; Schulze, Katharina V; Babbitt, Gregory A

2015-01-01

It is now widely-accepted that DNA sequences defining DNA-protein interactions functionally depend upon local biophysical features of DNA backbone that are important in defining sites of binding interaction in the genome (e.g. DNA shape, charge and intrinsic dynamics). However, these physical features of DNA polymer are not directly apparent when analyzing and viewing Shannon information content calculated at single nucleobases in a traditional sequence logo plot. Thus, sequence logos plots are severely limited in that they convey no explicit information regarding the structural dynamics of DNA backbone, a feature often critical to binding specificity. We present TRX-LOGOS, an R software package and Perl wrapper code that interfaces the JASPAR database for computational regulatory genomics. TRX-LOGOS extends the traditional sequence logo plot to include Shannon information content calculated with regard to the dinucleotide-based BI-BII conformation shifts in phosphate linkages on the DNA backbone, thereby adding a visual measure of intrinsic DNA flexibility that can be critical for many DNA-protein interactions. TRX-LOGOS is available as an R graphics module offered at both SourceForge and as a download supplement at this journal. To demonstrate the general utility of TRX logo plots, we first calculated the information content for 416 Saccharomyces cerevisiae transcription factor binding sites functionally confirmed in the Yeastract database and matched to previously published yeast genomic alignments. We discovered that flanking regions contain significantly elevated information content at phosphate linkages than can be observed at nucleobases. We also examined broader transcription factor classifications defined by the JASPAR database, and discovered that many general signatures of transcription factor binding are locally more information rich at the level of DNA backbone dynamics than nucleobase sequence. We used TRX-logos in combination with MEGA 6.0 software

Modeling backbone flexibility to achieve sequence diversity: The design of novel alpha-helical ligands for Bcl-xL

PubMed Central

Fu, Xiaoran; Apgar, James R.; Keating, Amy E.

2007-01-01

Computational protein design can be used to select sequences that are compatible with a fixed-backbone template. This strategy has been used in numerous instances to engineer novel proteins. However, the fixed-backbone assumption severely restricts the sequence space that is accessible via design. For challenging problems, such as the design of functional proteins, this may not be acceptable. In this paper, we present a method for introducing backbone flexibility into protein design calculations and apply it to the design of diverse helical BH3 ligands that bind to the anti-apoptotic protein Bcl-xL, a member of the Bcl-2 protein family. We demonstrate how normal mode analysis can be used to sample different BH3 backbones, and show that this leads to a larger and more diverse set of low-energy solutions than can be achieved using a native high-resolution Bcl-xL complex crystal structure as a template. We tested several of the designed solutions experimentally and found that this approach worked well when normal mode calculations were used to deform a native BH3 helix structure, but less well when they were used to deform an idealized helix. A subsequent round of design and testing identified a likely source of the problem as inadequate sampling of the helix pitch. In all, we tested seventeen designed BH3 peptide sequences, including several point mutants. Of these, eight bound well to Bcl-xL and four others showed weak but detectable binding. The successful designs showed a diversity of sequences that would have been difficult or impossible to achieve using only a fixed backbone. Thus, introducing backbone flexibility via normal mode analysis effectively broadened the set of sequences identified by computational design, and provided insight into positions important for binding Bcl-xL. PMID:17597151

Underestimated Halogen Bonds Forming with Protein Backbone in Protein Data Bank.

PubMed

Zhang, Qian; Xu, Zhijian; Shi, Jiye; Zhu, Weiliang

2017-07-24

Halogen bonds (XBs) are attracting increasing attention in biological systems. Protein Data Bank (PDB) archives experimentally determined XBs in biological macromolecules. However, no software for structure refinement in X-ray crystallography takes into account XBs, which might result in the weakening or even vanishing of experimentally determined XBs in PDB. In our previous study, we showed that side-chain XBs forming with protein side chains are underestimated in PDB on the basis of the phenomenon that the proportion of side-chain XBs to overall XBs decreases as structural resolution becomes lower and lower. However, whether the dominant backbone XBs forming with protein backbone are overlooked is still a mystery. Here, with the help of the ratio (R F ) of the observed XBs' frequency of occurrence to their frequency expected at random, we demonstrated that backbone XBs are largely overlooked in PDB, too. Furthermore, three cases were discovered possessing backbone XBs in high resolution structures while losing the XBs in low resolution structures. In the last two cases, even at 1.80 Å resolution, the backbone XBs were lost, manifesting the urgent need to consider XBs in the refinement process during X-ray crystallography study.

LETTER TO THE EDITOR: Backbones of traffic jams

NASA Astrophysics Data System (ADS)

Shikhar Gupta, Himadri; Ramaswamy, Ramakrishna

1996-11-01

We study the jam phase of the deterministic traffic model in two dimensions. Within the jam phase, there is a phase transition, from a self-organized jam (formed by initial synchronization followed by jamming), to a random-jam structure. The backbone of the jam is defined and used to analyse self-organization in the jam. The fractal dimension and interparticle correlations on the backbone indicate a continous phase transition at density 0305-4470/29/21/003/img1 with critical exponent 0305-4470/29/21/003/img2, which are characterized through simulations.

Molecular interaction between lipoteichoic acids and Lactobacillus delbrueckii phages depends on D-alanyl and alpha-glucose substitution of poly(glycerophosphate) backbones.

PubMed

Räisänen, Liisa; Draing, Christian; Pfitzenmaier, Markus; Schubert, Karin; Jaakonsaari, Tiina; von Aulock, Sonja; Hartung, Thomas; Alatossava, Tapani

2007-06-01

Lipoteichoic acids (LTAs) have been shown to act as bacterial counterparts to the receptor binding proteins of LL-H, LL-H host range mutant LL-H-a21, and JCL1032. Here we have used LTAs purified by hydrophobic interaction chromatography from different phage-resistant and -sensitive strains of Lactobacillus delbrueckii subsp. lactis. Nuclear magnetic resonance analyses revealed variation in the degree of alpha-glucosyl and D-alanyl substitution of the 1,3-linked poly(glycerophosphate) LTAs between the phage-sensitive and phage-resistant strains. Inactivation of phages was less effective if there was a high level of D-alanine residues in the LTA backbones. Prior incubation of the LTAs with alpha-glucose-specific lectin inhibited the LL-H phage inactivation. The overall level of decoration or the specific spatial combination of alpha-glucosyl-substituted, D-alanyl-substituted, and nonsubstituted glycerol residues may also affect phage adsorption.

Cooperative UAV-Based Communications Backbone for Sensor Networks

DOE Office of Scientific and Technical Information (OSTI.GOV)

Roberts, R S

2001-10-07

The objective of this project is to investigate the use of unmanned air vehicles (UAVs) as mobile, adaptive communications backbones for ground-based sensor networks. In this type of network, the UAVs provide communication connectivity to sensors that cannot communicate with each other because of terrain, distance, or other geographical constraints. In these situations, UAVs provide a vertical communication path for the sensors, thereby mitigating geographic obstacles often imposed on networks. With the proper use of UAVs, connectivity to a widely disbursed sensor network in rugged terrain is readily achieved. Our investigation has focused on networks where multiple cooperating UAVs aremore » used to form a network backbone. The advantage of using multiple UAVs to form the network backbone is parallelization of sensor connectivity. Many widely spaced or isolated sensors can be connected to the network at once using this approach. In these networks, the UAVs logically partition the sensor network into sub-networks (subnets), with one UAV assigned per subnet. Partitioning the network into subnets allows the UAVs to service sensors in parallel thereby decreasing the sensor-to-network connectivity. A UAV services sensors in its subnet by flying a route (path) through the subnet, uplinking data collected by the sensors, and forwarding the data to a ground station. An additional advantage of using multiple UAVs in the network is that they provide redundancy in the communications backbone, so that the failure of a single UAV does not necessarily imply the loss of the network.« less

Nonribosomal biosynthesis of backbone-modified peptides

NASA Astrophysics Data System (ADS)

Niquille, David L.; Hansen, Douglas A.; Mori, Takahiro; Fercher, David; Kries, Hajo; Hilvert, Donald

2018-03-01

Biosynthetic modification of nonribosomal peptide backbones represents a potentially powerful strategy to modulate the structure and properties of an important class of therapeutics. Using a high-throughput assay for catalytic activity, we show here that an L-Phe-specific module of an archetypal nonribosomal peptide synthetase can be reprogrammed to accept and process the backbone-modified amino acid (S)-β-Phe with near-native specificity and efficiency. A co-crystal structure with a non-hydrolysable aminoacyl-AMP analogue reveals the origins of the 40,000-fold α/β-specificity switch, illuminating subtle but precise remodelling of the active site. When the engineered catalyst was paired with downstream module(s), (S)-β-Phe-containing peptides were produced at preparative scale in vitro (~1 mmol) and high titres in vivo (~100 mg l-1), highlighting the potential of biosynthetic pathway engineering for the construction of novel nonribosomal β-frameworks.

A Discontinuous Potential Model for Protein-Protein Interactions.

PubMed

Shao, Qing; Hall, Carol K

2016-01-01

Protein-protein interactions play an important role in many biologic and industrial processes. In this work, we develop a two-bead-per-residue model that enables us to account for protein-protein interactions in a multi-protein system using discontinuous molecular dynamics simulations. This model deploys discontinuous potentials to describe the non-bonded interactions and virtual bonds to keep proteins in their native state. The geometric and energetic parameters are derived from the potentials of mean force between sidechain-sidechain, sidechain-backbone, and backbone-backbone pairs. The energetic parameters are scaled with the aim of matching the second virial coefficient of lysozyme reported in experiment. We also investigate the performance of several bond-building strategies.

Chemical characteristics and antithrombotic effect of chondroitin sulfates from sturgeon skull and sturgeon backbone.

PubMed

Gui, Meng; Song, Juyi; Zhang, Lu; Wang, Shun; Wu, Ruiyun; Ma, Changwei; Li, Pinglan

2015-06-05

Chondroitin sulfates (CSs) were extracted from sturgeon skull and backbone, and their chemical composition, anticoagulant, anti-platelet and thrombolysis activities were evaluated. The average molecular weights of CS from sturgeon skull and backbone were 38.5kDa and 49.2kDa, respectively. Disaccharide analysis indicated that the sturgeon backbone CS was primarily composed of disaccharide monosulfated in position four of the GalNAc (37.8%) and disaccharide monosulfated in position six of the GalNAc (59.6%) while sturgeon skull CS was primarily composed of nonsulfated disaccharide (74.2%). Sturgeon backbone CS showed stronger antithrombotic effect than sturgeon skull CS. Sturgeon backbone CS could significantly prolong activated partial thromboplastin time (APTT) and thrombin time (TT), inhibited ADP-induced platelet aggregation and dissolved platelet plasma clots in vitro. The results suggested that sturgeon backbone CS can be explored as a functional food with antithrombotic function. Copyright © 2015 Elsevier Ltd. All rights reserved.

Water Detection Based on Sky Reflections

NASA Technical Reports Server (NTRS)

Rankin, Arturo L.; Matthies, Larry H.

2010-01-01

This software has been designed to detect water bodies that are out in the open on cross-country terrain at mid- to far-range (approximately 20 100 meters), using imagery acquired from a stereo pair of color cameras mounted on a terrestrial, unmanned ground vehicle (UGV). Non-traversable water bodies, such as large puddles, ponds, and lakes, are indirectly detected by detecting reflections of the sky below the horizon in color imagery. The appearance of water bodies in color imagery largely depends on the ratio of light reflected off the water surface to the light coming out of the water body. When a water body is far away, the angle of incidence is large, and the light reflected off the water surface dominates. We have exploited this behavior to detect water bodies out in the open at mid- to far-range. When a water body is detected at far range, a UGV s path planner can begin to look for alternate routes to the goal position sooner, rather than later. As a result, detecting water hazards at far range generally reduces the time required to reach a goal position during autonomous navigation. This software implements a new water detector based on sky reflections that geometrically locates the exact pixel in the sky that is reflecting on a candidate water pixel on the ground, and predicts if the ground pixel is water based on color similarity and local terrain features

Fighting detection using interaction energy force

NASA Astrophysics Data System (ADS)

Wateosot, Chonthisa; Suvonvorn, Nikom

2017-02-01

Fighting detection is an important issue in security aimed to prevent criminal or undesirable events in public places. Many researches on computer vision techniques have studied to detect the specific event in crowded scenes. In this paper we focus on fighting detection using social-based Interaction Energy Force (IEF). The method uses low level features without object extraction and tracking. The interaction force is modeled using the magnitude and direction of optical flows. A fighting factor is developed under this model to detect fighting events using thresholding method. An energy map of interaction force is also presented to identify the corresponding events. The evaluation is performed using NUSHGA and BEHAVE datasets. The results show the efficiency with high accuracy regardless of various conditions.

NMR detects molecular interactions of graphene with aromatic and aliphatic hydrocarbons in water

NASA Astrophysics Data System (ADS)

Bichenkova, Elena V.; Raju, Arun P. A.; Burusco, Kepa K.; Kinloch, Ian A.; Novoselov, Kostya S.; Clarke, David J.

2018-03-01

Polyaromatic carbon is widely held to be strongly diamagnetic and hydrophobic, with textbook van der Waals and ‘π-stacked’ binding of hydrocarbons, which disrupt their self-assembled supramolecular structures. The NMR of organic molecules sequestered by polyaromatic carbon is expected to be dominated by shielding from the orbital diamagnetism of π electrons. We report the first evidence of very different polar and magnetic behavior in water, wherein graphene remained well-dispersed after extensive dialysis and behaved as a 1H-NMR-silent ghost. Magnetic effects dominated the NMR of organic structures which interacted with graphene, with changes in spin-spin coupling, vast increase in relaxation, line broadening and decrease in NMR peak heights when bound to graphene. However, the interactions were weak, reversible and did not disrupt organic self-assemblies reliant on hydrophobic ‘π-stacking’, even when substantially sequestered on the surface of graphene by the high surface area available. Interacting assemblies of aromatic molecules retained their strongly-shielded NMR signals and remained within self-assembled structures, with slower rates of diffusion from association with graphene, but with no further shielding from graphene. Binding to graphene was selective for positively-charged organic assemblies, weaker for non-aromatic and negligible for strongly-negatively-charged molecules, presumably repelled by a negative zeta potential of graphene in water. Stronger binders, or considerable excess of weaker binders readily reversed physisorption, with no evidence of structural changes from chemisorption. The fundamental nature of these different electronic interactions between organic and polyaromatic carbon is considered with relevance to electronics, charge storage, sensor, medical, pharmaceutical and environmental research.

Detection of magnetic dipolar coupling of water molecules at the nanoscale using quantum magnetometry

NASA Astrophysics Data System (ADS)

Yang, Zhiping; Shi, Fazhan; Wang, Pengfei; Raatz, Nicole; Li, Rui; Qin, Xi; Meijer, Jan; Duan, Changkui; Ju, Chenyong; Kong, Xi; Du, Jiangfeng

2018-05-01

It is a crucial issue to study interactions among water molecules and hydrophobic interfacial water at the nanoscale. Here we succeed in measuring the nuclear magnetic resonance spectrum of a diamond-water interfacial ice with a detection volume of about 2.2 ×10-22 L. More importantly, the magnetic dipolar coupling between the two protons of a water molecule is resolved by measuring the signal contributed from about 7000 water molecules at the nanoscale. The resolved intramolecule magnetic dipolar interactions are about 15 and 33 kHz with spectral resolution of 5 kHz. This work provides a platform for hydrophobic interfacial water study under ambient conditions, with further applications in more general nanoscale structural analysis.

Water Detection Based on Object Reflections

NASA Technical Reports Server (NTRS)

Rankin, Arturo L.; Matthies, Larry H.

2012-01-01

Water bodies are challenging terrain hazards for terrestrial unmanned ground vehicles (UGVs) for several reasons. Traversing through deep water bodies could cause costly damage to the electronics of UGVs. Additionally, a UGV that is either broken down due to water damage or becomes stuck in a water body during an autonomous operation will require rescue, potentially drawing critical resources away from the primary operation and increasing the operation cost. Thus, robust water detection is a critical perception requirement for UGV autonomous navigation. One of the properties useful for detecting still water bodies is that their surface acts as a horizontal mirror at high incidence angles. Still water bodies in wide-open areas can be detected by geometrically locating the exact pixels in the sky that are reflecting on candidate water pixels on the ground, predicting if ground pixels are water based on color similarity to the sky and local terrain features. But in cluttered areas where reflections of objects in the background dominate the appearance of the surface of still water bodies, detection based on sky reflections is of marginal value. Specifically, this software attempts to solve the problem of detecting still water bodies on cross-country terrain in cluttered areas at low cost.

Water Detection Based on Color Variation

NASA Technical Reports Server (NTRS)

Rankin, Arturo L.

2012-01-01

This software has been designed to detect water bodies that are out in the open on cross-country terrain at close range (out to 30 meters), using imagery acquired from a stereo pair of color cameras mounted on a terrestrial, unmanned ground vehicle (UGV). This detector exploits the fact that the color variation across water bodies is generally larger and more uniform than that of other naturally occurring types of terrain, such as soil and vegetation. Non-traversable water bodies, such as large puddles, ponds, and lakes, are detected based on color variation, image intensity variance, image intensity gradient, size, and shape. At ranges beyond 20 meters, water bodies out in the open can be indirectly detected by detecting reflections of the sky below the horizon in color imagery. But at closer range, the color coming out of a water body dominates sky reflections, and the water cue from sky reflections is of marginal use. Since there may be times during UGV autonomous navigation when a water body does not come into a perception system s field of view until it is at close range, the ability to detect water bodies at close range is critical. Factors that influence the perceived color of a water body at close range are the amount and type of sediment in the water, the water s depth, and the angle of incidence to the water body. Developing a single model of the mixture ratio of light reflected off the water surface (to the camera) to light coming out of the water body (to the camera) for all water bodies would be fairly difficult. Instead, this software detects close water bodies based on local terrain features and the natural, uniform change in color that occurs across the surface from the leading edge to the trailing edge.

Molybdenum disulfide and water interaction parameters

NASA Astrophysics Data System (ADS)

Heiranian, Mohammad; Wu, Yanbin; Aluru, Narayana R.

2017-09-01

Understanding the interaction between water and molybdenum disulfide (MoS2) is of crucial importance to investigate the physics of various applications involving MoS2 and water interfaces. An accurate force field is required to describe water and MoS2 interactions. In this work, water-MoS2 force field parameters are derived using the high-accuracy random phase approximation (RPA) method and validated by comparing to experiments. The parameters obtained from the RPA method result in water-MoS2 interface properties (solid-liquid work of adhesion) in good comparison to the experimental measurements. An accurate description of MoS2-water interaction will facilitate the study of MoS2 in applications such as DNA sequencing, sea water desalination, and power generation.

NIR detection of honey adulteration reveals differences in water spectral pattern.

PubMed

Bázár, György; Romvári, Róbert; Szabó, András; Somogyi, Tamás; Éles, Viktória; Tsenkova, Roumiana

2016-03-01

High fructose corn syrup (HFCS) was mixed with four artisanal Robinia honeys at various ratios (0-40%) and near infrared (NIR) spectra were recorded with a fiber optic immersion probe. Levels of HFCS adulteration could be detected accurately using leave-one-honey-out cross-validation (RMSECV=1.48; R(2)CV=0.987), partial least squares regression and the 1300-1800nm spectral interval containing absorption bands related to both water and carbohydrates. Aquaphotomics-based evaluations showed that unifloral honeys contained more highly organized water than the industrial sugar syrup, supposedly because of the greater variety of molecules dissolved in the multi-component honeys. Adulteration with HFCS caused a gradual reduction of water molecular structures, especially water trimers, which facilitate interaction with other molecules. Quick, non-destructive NIR spectroscopy combined with aquaphotomics could be used to describe water molecular structures in honey and to detect a rather common form of adulteration. Copyright © 2015 Elsevier Ltd. All rights reserved.

Uganda's National Transmission Backbone Infrastructure Project: Technical Challenges and the Way Forward

NASA Astrophysics Data System (ADS)

Bulega, T.; Kyeyune, A.; Onek, P.; Sseguya, R.; Mbabazi, D.; Katwiremu, E.

2011-10-01

Several publications have identified technical challenges facing Uganda's National Transmission Backbone Infrastructure project. This research addresses the technical limitations of the National Transmission Backbone Infrastructure project, evaluates the goals of the project, and compares the results against the technical capability of the backbone. The findings of the study indicate a bandwidth deficit, which will be addressed by using dense wave division multiplexing repeaters, leasing bandwidth from private companies. Microwave links for redundancy, a Network Operation Center for operation and maintenance, and deployment of wireless interoperability for microwave access as a last-mile solution are also suggested.

Weak interactions between water and clathrate-forming gases at low pressures

DOE PAGES

Thürmer, Konrad; Yuan, Chunqing; Kimmel, Greg A.; ...

2015-07-17

Using scanning probe microscopy and temperature programed desorption we examined the interaction between water and two common clathrate-forming gases, methane and isobutane, at low temperature and low pressure. Water co-deposited with up to 10 –1 mbar methane or 10 –5 mbar isobutane at 140 K onto a Pt(111) substrate yielded pure crystalline ice, i.e., the exposure to up to ~ 10 7 gas molecules for each deposited water molecule did not have any detectable effect on the growing films. Exposing metastable, less than 2 molecular layers thick, water films to 10 –5 mbar methane does not alter their morphology, suggestingmore » that the presence of the Pt(111) surface is not a strong driver for hydrate formation. This weak water–gas interaction at low pressures is supported by our thermal desorption measurements from amorphous solid water and crystalline ice where 1 ML of methane desorbs near ~ 43 K and isobutane desorbs near ~ 100 K. As a result, similar desorption temperatures were observed for desorption from amorphous solid water.« less

Interplay between water uptake, ion interactions, and conductivity in an e-beam grafted poly(ethylene-co-tetrafluoroethylene) anion exchange membrane

DOE Office of Scientific and Technical Information (OSTI.GOV)

Pandey, Tara P.; Maes, Ashley M.; Sarode, Himanshu N.

We demonstrate that the true hydroxide conductivity in an e-beam grafted poly(ethylene-co-tetrafluoroethylene) [ETFE] anion exchange membrane (AEM) is as high as 132 mS cm -1 at 80 °C and 95% RH, comparable to a proton exchange membrane, but with very much less water present in the film. To understand this behaviour we studied ion transport of hydroxide, carbonate, bicarbonate and chloride, as well as water uptake and distribution. Water uptake of the AEM in water vapor is an order of magnitude lower than when submerged in liquid water. In addition 19F pulse field gradient spin echo NMR indicates that theremore » is little tortuosity in the ionic pathways through the film. A complete analysis of the IR spectrum of the AEM and the analyses of water absorption using FT-IR led to conclusion that the fluorinated backbone chains do not interact with water and that two types of water domains exist within the membrane. The reduction in conductivity was measured during exposure of the OH - form of the AEM to air at 95% RH and was seen to be much slower than the reaction of CO 2 with OH - as the amount of water in the film determines its ionic conductivity and at relative wet RHs its re-organization is slow.« less

Interplay between water uptake, ion interactions, and conductivity in an e-beam grafted poly(ethylene-co-tetrafluoroethylene) anion exchange membrane.

PubMed

Pandey, Tara P; Maes, Ashley M; Sarode, Himanshu N; Peters, Bethanne D; Lavina, Sandra; Vezzù, Keti; Yang, Yuan; Poynton, Simon D; Varcoe, John R; Seifert, Soenke; Liberatore, Matthew W; Di Noto, Vito; Herring, Andrew M

2015-02-14

We demonstrate that the true hydroxide conductivity in an e-beam grafted poly(ethylene-co-tetrafluoroethylene) [ETFE] anion exchange membrane (AEM) is as high as 132 mS cm(-1) at 80 °C and 95% RH, comparable to a proton exchange membrane, but with very much less water present in the film. To understand this behaviour we studied ion transport of hydroxide, carbonate, bicarbonate and chloride, as well as water uptake and distribution. Water uptake of the AEM in water vapor is an order of magnitude lower than when submerged in liquid water. In addition (19)F pulse field gradient spin echo NMR indicates that there is little tortuosity in the ionic pathways through the film. A complete analysis of the IR spectrum of the AEM and the analyses of water absorption using FT-IR led to conclusion that the fluorinated backbone chains do not interact with water and that two types of water domains exist within the membrane. The reduction in conductivity was measured during exposure of the OH(-) form of the AEM to air at 95% RH and was seen to be much slower than the reaction of CO2 with OH(-) as the amount of water in the film determines its ionic conductivity and at relative wet RHs its re-organization is slow.

Interplay between water uptake, ion interactions, and conductivity in an e-beam grafted poly(ethylene-co-tetrafluoroethylene) anion exchange membrane

DOE PAGES

Pandey, Tara P.; Maes, Ashley M.; Sarode, Himanshu N.; ...

2014-12-23

We demonstrate that the true hydroxide conductivity in an e-beam grafted poly(ethylene-co-tetrafluoroethylene) [ETFE] anion exchange membrane (AEM) is as high as 132 mS cm -1 at 80 °C and 95% RH, comparable to a proton exchange membrane, but with very much less water present in the film. To understand this behaviour we studied ion transport of hydroxide, carbonate, bicarbonate and chloride, as well as water uptake and distribution. Water uptake of the AEM in water vapor is an order of magnitude lower than when submerged in liquid water. In addition 19F pulse field gradient spin echo NMR indicates that theremore » is little tortuosity in the ionic pathways through the film. A complete analysis of the IR spectrum of the AEM and the analyses of water absorption using FT-IR led to conclusion that the fluorinated backbone chains do not interact with water and that two types of water domains exist within the membrane. The reduction in conductivity was measured during exposure of the OH - form of the AEM to air at 95% RH and was seen to be much slower than the reaction of CO 2 with OH - as the amount of water in the film determines its ionic conductivity and at relative wet RHs its re-organization is slow.« less

An exhaustive survey of regular peptide conformations using a new metric for backbone handedness (h)

PubMed Central

2017-01-01

The Ramachandran plot is important to structural biology as it describes a peptide backbone in the context of its dominant degrees of freedom—the backbone dihedral angles φ and ψ (Ramachandran, Ramakrishnan & Sasisekharan, 1963). Since its introduction, the Ramachandran plot has been a crucial tool to characterize protein backbone features. However, the conformation or twist of a backbone as a function of φ and ψ has not been completely described for both cis and trans backbones. Additionally, little intuitive understanding is available about a peptide’s conformation simply from knowing the φ and ψ values of a peptide (e.g., is the regular peptide defined by φ = ψ =  − 100°  left-handed or right-handed?). This report provides a new metric for backbone handedness (h) based on interpreting a peptide backbone as a helix with axial displacement d and angular displacement θ, both of which are derived from a peptide backbone’s internal coordinates, especially dihedral angles φ, ψ and ω. In particular, h equals sin(θ)d∕|d|, with range [−1, 1] and negative (or positive) values indicating left(or right)-handedness. The metric h is used to characterize the handedness of every region of the Ramachandran plot for both cis (ω = 0°) and trans (ω = 180°) backbones, which provides the first exhaustive survey of twist handedness in Ramachandran (φ, ψ) space. These maps fill in the ‘dead space’ within the Ramachandran plot, which are regions that are not commonly accessed by structured proteins, but which may be accessible to intrinsically disordered proteins, short peptide fragments, and protein mimics such as peptoids. Finally, building on the work of (Zacharias & Knapp, 2013), this report presents a new plot based on d and θ that serves as a universal and intuitive alternative to the Ramachandran plot. The universality arises from the fact that the co-inhabitants of such a plot include every possible peptide backbone including cis

River water quality analysis via headspace detection of volatile organic compounds

NASA Astrophysics Data System (ADS)

Tang, Johnny Jock Lee; Nishi, Phyllis Jacqueline; Chong, Gabriel Eng Wee; Wong, Martin Gideon; Chua, Hong Siang; Persaud, Krishna; Ng, Sing Muk

2017-03-01

Human civilization has intensified the interaction between the community and the environment. This increases the threat on the environm ent for being over exploited and contaminated with m anmade products and synthetic chemicals. Of all, clean water is one of the resources that can be easily contaminated since it is a universal solvent and of high mobility. This work reports the development and optimization of a water quality monitoring system based on metal oxide sensors. The system is intended to a ssist the detection of volatile organic compounds (VOCs) present in water sources online and onsite. The sampling mechanism was based on contactless mode, where headspace partial pressure of the VOCs formed above the water body in a close chamber was drawn for detection at the sensor platform. Pure toluene was used as standard to represent the broad spectrum of VOCs, and the sensor dynamic range was achieved from 1-1000 ppb. Several sensing parameters such as sampling time, headspace volume, and sensor recovery were s tudied and optimized. Besides direct detection of VOC contaminants in the water, the work has also been extended to detect VOCs produced by microbial communities and to c orrelate the size of the communities with the reading of V OCs recorded. This can serve to give b etter indication of water quality, not only on the conce ntration of VOCs c ontamination from chemicals, but also the content of microbes, which some can have severe effect on human health.

Daytime Water Detection Based on Sky Reflections

NASA Technical Reports Server (NTRS)

Rankin, Arturo; Matthies, Larry; Bellutta, Paolo

2011-01-01

A water body s surface can be modeled as a horizontal mirror. Water detection based on sky reflections and color variation are complementary. A reflection coefficient model suggests sky reflections dominate the color of water at ranges > 12 meters. Water detection based on sky reflections: (1) geometrically locates the pixel in the sky that is reflecting on a candidate water pixel on the ground (2) predicts if the ground pixel is water based on color similarity and local terrain features. Water detection has been integrated on XUVs.

No-Enclave Percolation Corresponds to Holes in the Cluster Backbone.

PubMed

Hu, Hao; Ziff, Robert M; Deng, Youjin

2016-10-28

The no-enclave percolation (NEP) model introduced recently by Sheinman et al. can be mapped to a problem of holes within a standard percolation backbone, and numerical measurements of such holes give the same size-distribution exponent τ=1.82(1) as found for the NEP model. An argument is given that τ=1+d_{B}/2≈1.822 for backbone holes, where d_{B} is the backbone dimension. On the other hand, a model of simple holes within a percolation cluster yields τ=1+d_{f}/2=187/96≈1.948, where d_{f} is the fractal dimension of the cluster, and this value is consistent with the experimental results of gel collapse of Sheinman et al., which give τ=1.91(6). This suggests that the gel clusters are of the universality class of percolation cluster holes. Both models give a discontinuous maximum hole size at p_{c}, signifying explosive percolation behavior.

Daytime Water Detection Based on Sky Reflections

NASA Technical Reports Server (NTRS)

Rankin, Arturo L.; Matthies, Larry H.; Bellutta, Paolo

2011-01-01

Robust water detection is a critical perception requirement for unmanned ground vehicle (UGV) autonomous navigation. This is particularly true in wide-open areas where water can collect in naturally occurring terrain depressions during periods of heavy precipitation and form large water bodies. One of the properties of water useful for detecting it is that its surface acts as a horizontal mirror at large incidence angles. Water bodies can be indirectly detected by detecting reflections of the sky below the horizon in color imagery. The Jet Propulsion Laboratory (JPL) has implemented a water detector based on sky reflections that geometrically locates the pixel in the sky that is reflecting on a candidate water pixel on the ground and predicts if the ground pixel is water based on color similarity and local terrain features. This software detects water bodies in wide-open areas on cross-country terrain at mid- to far-range using imagery acquired from a forward-looking stereo pair of color cameras mounted on a terrestrial UGV. In three test sequences approaching a pond under a clear, overcast, and cloudy sky, the true positive detection rate was 100% when the UGV was beyond 7 meters of the water's leading edge and the largest false positive detection rate was 0.58%. The sky reflection based water detector has been integrated on an experimental unmanned vehicle and field tested at Ft. Indiantown Gap, PA, USA.

Potential interactions among disease, pesticides, water quality and adjacent land cover in amphibian habitats in the United States.

PubMed

Battaglin, W A; Smalling, K L; Anderson, C; Calhoun, D; Chestnut, T; Muths, E

2016-10-01

To investigate interactions among disease, pesticides, water quality, and adjacent land cover, we collected samples of water, sediment, and frog tissue from 21 sites in 7 States in the United States (US) representing a variety of amphibian habitats. All samples were analyzed for >90 pesticides and pesticide degradates, and water and frogs were screened for the amphibian chytrid fungus Batrachochytrium dendrobatidis (Bd) using molecular methods. Pesticides and pesticide degradates were detected frequently in frog breeding habitats (water and sediment) as well as in frog tissue. Fungicides occurred more frequently in water, sediment, and tissue than was expected based upon their limited use relative to herbicides or insecticides. Pesticide occurrence in water or sediment was not a strong predictor of occurrence in tissue, but pesticide concentrations in tissue were correlated positively to agricultural and urban land, and negatively to forested land in 2-km buffers around the sites. Bd was detected in water at 45% of sites, and on 34% of swabbed frogs. Bd detections in water were not associated with differences in land use around sites, but sites with detections had colder water. Frogs that tested positive for Bd were associated with sites that had higher total fungicide concentrations in water and sediment, but lower insecticide concentrations in sediments relative to frogs that were Bd negative. Bd concentrations on frog swabs were positively correlated to dissolved organic carbon, and total nitrogen and phosphorus, and negatively correlated to pH and water temperature. Data were collected from a range of locations and amphibian habitats and represent some of the first field-collected information aimed at understanding the interactions between pesticides, land use, and amphibian disease. These interactions are of particular interest to conservation efforts as many amphibians live in altered habitats and may depend on wetlands embedded in these landscapes to survive

Potential interactions among disease, pesticides, water quality and adjacent land cover in amphibian habitats in the United States

USGS Publications Warehouse

Battaglin, William A.; Smalling, Kelly L.; Anderson, Chauncey; Calhoun, Daniel L.; Chestnut, Tara E.; Muths, Erin L.

2016-01-01

To investigate interactions among disease, pesticides, water quality, and adjacent land cover, we collected samples of water, sediment, and frog tissue from 21 sites in 7 States in the United States (US) representing a variety of amphibian habitats. All samples were analyzed for > 90 pesticides and pesticide degradates, and water and frogs were screened for the amphibian chytrid fungus Batrachochytrium dendrobatidis (Bd) using molecular methods. Pesticides and pesticide degradates were detected frequently in frog breeding habitats (water and sediment) as well as in frog tissue. Fungicides occurred more frequently in water, sediment, and tissue than was expected based upon their limited use relative to herbicides or insecticides. Pesticide occurrence in water or sediment was not a strong predictor of occurrence in tissue, but pesticide concentrations in tissue were correlated positively to agricultural and urban land, and negatively to forested land in 2-km buffers around the sites. Bd was detected in water at 45% of sites, and on 34% of swabbed frogs. Bd detections in water were not associated with differences in land use around sites, but sites with detections had colder water. Frogs that tested positive for Bd were associated with sites that had higher total fungicide concentrations in water and sediment, but lower insecticide concentrations in sediments relative to frogs that were Bd negative. Bd concentrations on frog swabs were positively correlated to dissolved organic carbon, and total nitrogen and phosphorus, and negatively correlated to pH and water temperature.Data were collected from a range of locations and amphibian habitats and represent some of the first field-collected information aimed at understanding the interactions between pesticides, land use, and amphibian disease. These interactions are of particular interest to conservation efforts as many amphibians live in altered habitats and may depend on wetlands embedded in these landscapes to

Comparative analysis of methods for detecting interacting loci

PubMed Central

2011-01-01

Background Interactions among genetic loci are believed to play an important role in disease risk. While many methods have been proposed for detecting such interactions, their relative performance remains largely unclear, mainly because different data sources, detection performance criteria, and experimental protocols were used in the papers introducing these methods and in subsequent studies. Moreover, there have been very few studies strictly focused on comparison of existing methods. Given the importance of detecting gene-gene and gene-environment interactions, a rigorous, comprehensive comparison of performance and limitations of available interaction detection methods is warranted. Results We report a comparison of eight representative methods, of which seven were specifically designed to detect interactions among single nucleotide polymorphisms (SNPs), with the last a popular main-effect testing method used as a baseline for performance evaluation. The selected methods, multifactor dimensionality reduction (MDR), full interaction model (FIM), information gain (IG), Bayesian epistasis association mapping (BEAM), SNP harvester (SH), maximum entropy conditional probability modeling (MECPM), logistic regression with an interaction term (LRIT), and logistic regression (LR) were compared on a large number of simulated data sets, each, consistent with complex disease models, embedding multiple sets of interacting SNPs, under different interaction models. The assessment criteria included several relevant detection power measures, family-wise type I error rate, and computational complexity. There are several important results from this study. First, while some SNPs in interactions with strong effects are successfully detected, most of the methods miss many interacting SNPs at an acceptable rate of false positives. In this study, the best-performing method was MECPM. Second, the statistical significance assessment criteria, used by some of the methods to control the

Comparative analysis of methods for detecting interacting loci.

PubMed

Chen, Li; Yu, Guoqiang; Langefeld, Carl D; Miller, David J; Guy, Richard T; Raghuram, Jayaram; Yuan, Xiguo; Herrington, David M; Wang, Yue

2011-07-05

Interactions among genetic loci are believed to play an important role in disease risk. While many methods have been proposed for detecting such interactions, their relative performance remains largely unclear, mainly because different data sources, detection performance criteria, and experimental protocols were used in the papers introducing these methods and in subsequent studies. Moreover, there have been very few studies strictly focused on comparison of existing methods. Given the importance of detecting gene-gene and gene-environment interactions, a rigorous, comprehensive comparison of performance and limitations of available interaction detection methods is warranted. We report a comparison of eight representative methods, of which seven were specifically designed to detect interactions among single nucleotide polymorphisms (SNPs), with the last a popular main-effect testing method used as a baseline for performance evaluation. The selected methods, multifactor dimensionality reduction (MDR), full interaction model (FIM), information gain (IG), Bayesian epistasis association mapping (BEAM), SNP harvester (SH), maximum entropy conditional probability modeling (MECPM), logistic regression with an interaction term (LRIT), and logistic regression (LR) were compared on a large number of simulated data sets, each, consistent with complex disease models, embedding multiple sets of interacting SNPs, under different interaction models. The assessment criteria included several relevant detection power measures, family-wise type I error rate, and computational complexity. There are several important results from this study. First, while some SNPs in interactions with strong effects are successfully detected, most of the methods miss many interacting SNPs at an acceptable rate of false positives. In this study, the best-performing method was MECPM. Second, the statistical significance assessment criteria, used by some of the methods to control the type I error rate

Cellulose nanofiber backboned Prussian blue nanoparticles as powerful adsorbents for the selective elimination of radioactive cesium.

PubMed

Vipin, Adavan Kiliyankil; Fugetsu, Bunshi; Sakata, Ichiro; Isogai, Akira; Endo, Morinobu; Li, Mingda; Dresselhaus, Mildred S

2016-11-15

On 11 March 2011, the day of the unforgettable disaster of the 9 magnitude Tohoku earthquake and quickly followed by the devastating Tsunami, a damageable amount of radionuclides had dispersed from the Fukushima Daiichi's damaged nuclear reactors. Decontamination of the dispersed radionuclides from seawater and soil, due to the huge amounts of coexisting ions with competitive functionalities, has been the topmost difficulty. Ferric hexacyanoferrate, also known as Prussian blue (PB), has been the most powerful material for selectively trapping the radioactive cesium ions; its high tendency to form stable colloids in water, however, has made PB to be impossible for the open-field radioactive cesium decontamination applications. A nano/nano combinatorial approach, as is described in this study, has provided an ultimate solution to this intrinsic colloid formation difficulty of PB. Cellulose nanofibers (CNF) were used to immobilize PB via the creation of CNF-backboned PB. The CNF-backboned PB (CNF/PB) was found to be highly tolerant to water and moreover, it gave a 139 mg/g capability and a million (10 6 ) order of magnitude distribution coefficient (K d ) for absorbing of the radioactive cesium ion. Field studies on soil and seawater decontaminations in Fukushima gave satisfactory results, demonstrating high capabilities of CNF/PB for practical applications.

Cellulose nanofiber backboned Prussian blue nanoparticles as powerful adsorbents for the selective elimination of radioactive cesium

PubMed Central

Vipin, Adavan Kiliyankil; Fugetsu, Bunshi; Sakata, Ichiro; Isogai, Akira; Endo, Morinobu; Li, Mingda; Dresselhaus, Mildred S.

2016-01-01

On 11 March 2011, the day of the unforgettable disaster of the 9 magnitude Tohoku earthquake and quickly followed by the devastating Tsunami, a damageable amount of radionuclides had dispersed from the Fukushima Daiichi’s damaged nuclear reactors. Decontamination of the dispersed radionuclides from seawater and soil, due to the huge amounts of coexisting ions with competitive functionalities, has been the topmost difficulty. Ferric hexacyanoferrate, also known as Prussian blue (PB), has been the most powerful material for selectively trapping the radioactive cesium ions; its high tendency to form stable colloids in water, however, has made PB to be impossible for the open-field radioactive cesium decontamination applications. A nano/nano combinatorial approach, as is described in this study, has provided an ultimate solution to this intrinsic colloid formation difficulty of PB. Cellulose nanofibers (CNF) were used to immobilize PB via the creation of CNF-backboned PB. The CNF-backboned PB (CNF/PB) was found to be highly tolerant to water and moreover, it gave a 139 mg/g capability and a million (106) order of magnitude distribution coefficient (Kd) for absorbing of the radioactive cesium ion. Field studies on soil and seawater decontaminations in Fukushima gave satisfactory results, demonstrating high capabilities of CNF/PB for practical applications. PMID:27845441

Modulation of intra- and inter-sheet interactions in short peptide self-assembly by acetonitrile in aqueous solution

NASA Astrophysics Data System (ADS)

Deng, Li; Zhao, Yurong; Zhou, Peng; Xu, Hai; Wang, Yanting

2016-12-01

Besides our previous experimental discovery (Zhao Y R, et al. 2015 Langmuir, 31, 12975) that acetonitrile (ACN) can tune the morphological features of nanostructures self-assembled by short peptides KIIIIK (KI4K) in aqueous solution, further experiments reported in this work demonstrate that ACN can also tune the mass of the self-assembled nanostructures. To understand the microscopic mechanism how ACN molecules interfere peptide self-assembly process, we conducted a series of molecular dynamics simulations on a monomer, a cross-β sheet structure, and a proto-fibril of KI4K in pure water, pure ACN, and ACN-water mixtures, respectively. The simulation results indicate that ACN enhances the intra-sheet interaction dominated by the hydrogen bonding (H-bonding) interactions between peptide backbones, but weakens the inter-sheet interaction dominated by the interactions between hydrophobic side chains. Through analyzing the correlations between different groups of solvent and peptides and the solvent behaviors around the proto-fibril, we have found that both the polar and nonpolar groups of ACN play significant roles in causing the opposite effects on intermolecular interactions among peptides. The weaker correlation of the polar group of ACN than water molecule with the peptide backbone enhances H-bonding interactions between peptides in the proto-fibril. The stronger correlation of the nonpolar group of ACN than water molecule with the peptide side chain leads to the accumulation of ACN molecules around the proto-fibril with their hydrophilic groups exposed to water, which in turn allows more water molecules close to the proto-fibril surface and weakens the inter-sheet interactions. The two opposite effects caused by ACN form a microscopic mechanism clearly explaining our experimental observations. Project supported by the National Basic Research Program of China (Grant No. 2013CB932804), the National Natural Science Foundation of China (Grant Nos. 91227115, 11421063

Non-enzymatic browning kinetics analysed through water-solids interactions and water mobility in dehydrated potato.

PubMed

Acevedo, Nuria C; Schebor, Carolina; Buera, Pilar

2008-06-01

Non-enzymatic browning (NEB) development was studied in dehydrated potato at 70°C. It was related to the macroscopic and molecular properties and to water-solid interactions over a wide range of water activities. Time resolved (1)H NMR, thermal transitions and water sorption isotherms were evaluated. Although non-enzymatic browning could be detected in the glassy state; colour development was higher in the supercooled state. The reaction rate increased up to a water content of 26g/100g of solids (aw=0.84) and then decreased at higher water contents, concomitantly with the increase of water proton mobility. The joint analyses of NEB kinetics, water sorption isotherm and proton relaxation behaviour made it evident that the point at which the reaction rate decreased, after a maximum value, could be related to the appearance of highly mobile water. The results obtained in this work indicate that the prediction of chemical reaction kinetics can be performed through the integrated analysis of water sorption, water and solids mobility and the physical state of the matrix. Copyright © 2007 Elsevier Ltd. All rights reserved.

Sulfation and cation effects on the conformational properties of the glycan backbone of chondroitin sulfate disaccharides.

PubMed

Faller, Christina E; Guvench, Olgun

2015-05-21

Chondroitin sulfate (CS) is one of several glycosaminoglycans that are major components of proteoglycans. A linear polymer consisting of repeats of the disaccharide -4GlcAβ1-3GalNAcβ1-, CS undergoes differential sulfation resulting in five unique sulfation patterns. Because of the dimer repeat, the CS glycosidic "backbone" has two distinct sets of conformational degrees of freedom defined by pairs of dihedral angles: (ϕ1, ψ1) about the β1-3 glycosidic linkage and (ϕ2, ψ2) about the β1-4 glycosidic linkage. Differential sulfation and the possibility of cation binding, combined with the conformational flexibility and biological diversity of CS, complicate experimental efforts to understand CS three-dimensional structures at atomic resolution. Therefore, all-atom explicit-solvent molecular dynamics simulations with Adaptive Biasing Force sampling of the CS backbone were applied to obtain high-resolution, high-precision free energies of CS disaccharides as a function of all possible backbone geometries. All 10 disaccharides (β1-3 vs β1-4 linkage × five different sulfation patterns) were studied; additionally, ion effects were investigated by considering each disaccharide in the presence of either neutralizing sodium or calcium cations. GlcAβ1-3GalNAc disaccharides have a single, broad, thermodynamically important free-energy minimum, whereas GalNAcβ1-4GlcA disaccharides have two such minima. Calcium cations but not sodium cations bind to the disaccharides, and binding is primarily to the GlcA -COO(-) moiety as opposed to sulfate groups. This binding alters the glycan backbone thermodynamics in instances where a calcium cation bound to -COO(-) can act to bridge and stabilize an interaction with an adjacent sulfate group, whereas, in the absence of this cation, the proximity of a sulfate group to -COO(-) results in two like charges being both desolvated and placed adjacent to each other and is found to be destabilizing. In addition to providing information

Detecting Darwinism from Molecules in the Enceladus Plumes, Jupiter's Moons, and Other Planetary Water Lagoons.

PubMed

Benner, Steven A

2017-09-01

To the astrobiologist, Enceladus offers easy access to a potential subsurface biosphere via the intermediacy of a plume of water emerging directly into space. A direct question follows: If we were to collect a sample of this plume, what in that sample, through its presence or its absence, would suggest the presence and/or absence of life in this exotic locale? This question is, of course, relevant for life detection in any aqueous lagoon that we might be able to sample. This manuscript reviews physical chemical constraints that must be met by a genetic polymer for it to support Darwinism, a process believed to be required for a chemical system to generate properties that we value in biology. We propose that the most important of these is a repeating backbone charge; a Darwinian genetic biopolymer must be a "polyelectrolyte." Relevant to mission design, such biopolymers are especially easy to recover and concentrate from aqueous mixtures for detection, simply by washing the aqueous mixtures across a polycharged support. Several device architectures are described to ensure that, once captured, the biopolymer meets two other requirements for Darwinism, homochirality and a small building block "alphabet." This approach is compared and contrasted with alternative biomolecule detection approaches that seek homochirality and constrained alphabets in non-encoded biopolymers. This discussion is set within a model for the history of the terran biosphere, identifying points in that natural history where these alternative approaches would have failed to detect terran life. Key Words: Enceladus-Life detection-Europa-Icy moon-Biosignatures-Polyelectrolyte theory of the gene. Astrobiology 17, 840-851.

Observation of CH⋅⋅⋅π Interactions between Methyl and Carbonyl Groups in Proteins.

PubMed

Perras, Frédéric A; Marion, Dominique; Boisbouvier, Jérôme; Bryce, David L; Plevin, Michael J

2017-06-19

Protein structure and function is dependent on myriad noncovalent interactions. Direct detection and characterization of these weak interactions in large biomolecules, such as proteins, is experimentally challenging. Herein, we report the first observation and measurement of long-range "through-space" scalar couplings between methyl and backbone carbonyl groups in proteins. These J couplings are indicative of the presence of noncovalent C-H⋅⋅⋅π hydrogen-bond-like interactions involving the amide π network. Experimentally detected scalar couplings were corroborated by a natural bond orbital analysis, which revealed the orbital nature of the interaction and the origins of the through-space J couplings. The experimental observation of this type of CH⋅⋅⋅π interaction adds a new dimension to the study of protein structure, function, and dynamics by NMR spectroscopy. © 2017 Wiley-VCH Verlag GmbH & Co. KGaA, Weinheim.

Photophysical investigations of squaraine and cyanine dyes and their interaction with bovine serum albumin

NASA Astrophysics Data System (ADS)

Saikiran, M.; Sato, D.; Pandey, S. S.; Kato, T.

2016-04-01

A model far-red sensitive symmetrical squaraine dye (SQ-3) and unsymmetrical near infra-red sensitive cyanine dye (UCD-1) bearing direct-COOH functionalized indole ring were synthesized, characterized and subjected to photophysical investigations including their interaction with bovine serum albumin (BSA) as a model protein in phosphate buffer solution (PBS). Both of the dyes exhibit strong interaction with BSA in phosphate buffer with high apparent binding constant. A judicious tuning of hydrophobic main backbone with reactive functionality for associative interaction with active site of BSA has been found to be necessary for BSA detection in PBS.

Methods in Enzymology: “Flexible backbone sampling methods to model and design protein alternative conformations”

PubMed Central

Ollikainen, Noah; Smith, Colin A.; Fraser, James S.; Kortemme, Tanja

2013-01-01

Sampling alternative conformations is key to understanding how proteins work and engineering them for new functions. However, accurately characterizing and modeling protein conformational ensembles remains experimentally and computationally challenging. These challenges must be met before protein conformational heterogeneity can be exploited in protein engineering and design. Here, as a stepping stone, we describe methods to detect alternative conformations in proteins and strategies to model these near-native conformational changes based on backrub-type Monte Carlo moves in Rosetta. We illustrate how Rosetta simulations that apply backrub moves improve modeling of point mutant side chain conformations, native side chain conformational heterogeneity, functional conformational changes, tolerated sequence space, protein interaction specificity, and amino acid co-variation across protein-protein interfaces. We include relevant Rosetta command lines and RosettaScripts to encourage the application of these types of simulations to other systems. Our work highlights that critical scoring and sampling improvements will be necessary to approximate conformational landscapes. Challenges for the future development of these methods include modeling conformational changes that propagate away from designed mutation sites and modulating backbone flexibility to predictively design functionally important conformational heterogeneity. PMID:23422426

Negative Differential Conductance in Polyporphyrin Oligomers with Nonlinear Backbones.

PubMed

Kuang, Guowen; Chen, Shi Zhang; Yan, Linghao; Chen, Ke Qiu; Shang, Xuesong; Liu, Pei Nian; Lin, Nian

2018-01-17

We study negative differential conductance (NDC) effects in polyporphyrin oligomers with nonlinear backbones. Using a low-temperature scanning tunneling microscope, we selectively controlled the charge transport path in single oligomer wires. We observed robust NDC when charge passed through a T-shape junction, bistable NDC when charge passed through a 90° kink and no NDC when charge passed through a 120° kink. Aided by density functional theory with nonequilibrium Green's functions simulations, we attributed this backbone-dependent NDC to bias-modulated hybridization of the electrode states with the resonant transport molecular orbital. We argue this mechanism is generic in molecular systems, which opens a new route of designing molecular NDC devices.

Geometry motivated alternative view on local protein backbone structures.

PubMed

Zacharias, Jan; Knapp, Ernst Walter

2013-11-01

We present an alternative to the classical Ramachandran plot (R-plot) to display local protein backbone structure. Instead of the (φ, ψ)-backbone angles relating to the chemical architecture of polypeptides generic helical parameters are used. These are the rotation or twist angle ϑ and the helical rise parameter d. Plots with these parameters provide a different view on the nature of local protein backbone structures. It allows to display the local structures in polar (d, ϑ)-coordinates, which is not possible for an R-plot, where structural regimes connected by periodicity appear disconnected. But there are other advantages, like a clear discrimination of the handedness of a local structure, a larger spread of the different local structure domains--the latter can yield a better separation of different local secondary structure motives--and many more. Compared to the R-plot we are not aware of any major disadvantage to classify local polypeptide structures with the (d, ϑ)-plot, except that it requires some elementary computations. To facilitate usage of the new (d, ϑ)-plot for protein structures we provide a web application (http://agknapp.chemie.fu-berlin.de/secsass), which shows the (d, ϑ)-plot side-by-side with the R-plot. © 2013 The Protein Society.

Detecting Protein-Glycolipid Interactions Using Glycomicelles and CaR-ESI-MS

NASA Astrophysics Data System (ADS)

Han, Ling; Kitova, Elena N.; Klassen, John S.

2016-11-01

This study reports on the use of the catch-and-release electrospray ionization mass spectrometry (CaR-ESI-MS) assay, combined with glycomicelles, as a method for detecting specific interactions between water-soluble proteins and glycolipids (GLs) in aqueous solution. The B subunit homopentamers of cholera toxin (CTB5) and Shiga toxin type 1 B (Stx1B5) and the gangliosides GM1, GM2, GM3, GD1a, GD1b, GT1b, and GD2 served as model systems for this study. The CTB5 exhibits broad specificity for gangliosides and binds to GM1, GM2, GM3, GD1a, GD1b, and GT1b; Stx1B5 does not recognize gangliosides. The CaR-ESI-MS assay was used to analyze solutions of CTB5 or Stx1B5 and individual gangliosides (GM1, GM2, GM3, GD1a, GD1b, GT1b, and GD2) or mixtures thereof. The high affinity interaction of CTB5 with GM1 was successfully detected. However, the apparent affinity, as determined from the mass spectra, is significantly lower than that of the corresponding pentasaccharide or when GM1 is presented in model membranes such as nanodiscs. Interactions between CTB5 and the low affinity gangliosides GD1a, GD1b, and GT1b, as well as GD2, which served as a negative control, were detected; no binding of CTB5 to GM2 or GM3 was observed. The CaR-ESI-MS results obtained for Stx1B5 reveal that nonspecific protein-ganglioside binding can occur during the ESI process, although the extent of binding varies between gangliosides. Consequently, interactions detected for CTB5 with GD1a, GD1b, and GT1b are likely nonspecific in origin. Taken together, these results reveal that the CaR-ESI-MS/glycomicelle approach for detecting protein-GL interactions is prone to false positives and false negatives and must be used with caution.

Electrochemical impedance study of the interaction of metal ions with unlabeled PNA.

PubMed

Gao, Lan; Li, Congjuan; Li, Xiaohong; Kraatz, Heinz-Bernhard

2010-09-14

The interactions of the metal ions Mg(2+), Zn(2+), Ni(2+), and Co(2+) with thin films of peptide nucleic acids (PNAs) were studied by electrochemical impedance spectroscopy (EIS), and the results show that Zn(2+), Ni(2+) and Co(2+) interacted favorably with the PNA film involving the backbone and the nucleobases with the exception of Mg(2+) for which the interaction with the backbone appears to be dominant.

Remote consultation and diagnosis in medical imaging using a global PACS backbone network

NASA Astrophysics Data System (ADS)

Martinez, Ralph; Sutaria, Bijal N.; Kim, Jinman; Nam, Jiseung

1993-10-01

A Global PACS is a national network which interconnects several PACS networks at medical and hospital complexes using a national backbone network. A Global PACS environment enables new and beneficial operations between radiologists and physicians, when they are located in different geographical locations. One operation allows the radiologist to view the same image folder at both Local and Remote sites so that a diagnosis can be performed. The paper describes the user interface, database management, and network communication software which has been developed in the Computer Engineering Research Laboratory and Radiology Research Laboratory. Specifically, a design for a file management system in a distributed environment is presented. In the remote consultation and diagnosis operation, a set of images is requested from the database archive system and sent to the Local and Remote workstation sites on the Global PACS network. Viewing the same images, the radiologists use pointing overlay commands, or frames to point out features on the images. Each workstation transfers these frames, to the other workstation, so that an interactive session for diagnosis takes place. In this phase, we use fixed frames and variable size frames, used to outline an object. The data pockets for these frames traverses the national backbone in real-time. We accomplish this feature by using TCP/IP protocol sockets for communications. The remote consultation and diagnosis operation has been tested in real-time between the University Medical Center and the Bowman Gray School of Medicine at Wake Forest University, over the Internet. In this paper, we show the feasibility of the operation in a Global PACS environment. Future improvements to the system will include real-time voice and interactive compressed video scenarios.

Nanomaterial-enabled Rapid Detection of Water Contaminants.

PubMed

Mao, Shun; Chang, Jingbo; Zhou, Guihua; Chen, Junhong

2015-10-28

Water contaminants, e.g., inorganic chemicals and microorganisms, are critical metrics for water quality monitoring and have significant impacts on human health and plants/organisms living in water. The scope and focus of this review is nanomaterial-based optical, electronic, and electrochemical sensors for rapid detection of water contaminants, e.g., heavy metals, anions, and bacteria. These contaminants are commonly found in different water systems. The importance of water quality monitoring and control demands significant advancement in the detection of contaminants in water because current sensing technologies for water contaminants have limitations. The advantages of nanomaterial-based sensing technologies are highlighted and recent progress on nanomaterial-based sensors for rapid water contaminant detection is discussed. An outlook for future research into this rapidly growing field is also provided. © 2015 WILEY-VCH Verlag GmbH & Co. KGaA, Weinheim.

An exhaustive survey of regular peptide conformations using a new metric for backbone handedness ( h )

DOE Office of Scientific and Technical Information (OSTI.GOV)

Mannige, Ranjan V.

The Ramachandran plot is important to structural biology as it describes a peptide backbone in the context of its dominant degrees of freedom—the backbone dihedral anglesφandψ(Ramachandran, Ramakrishnan & Sasisekharan, 1963). Since its introduction, the Ramachandran plot has been a crucial tool to characterize protein backbone features. However, the conformation or twist of a backbone as a function ofφandψhas not been completely described for bothcisandtransbackbones. Additionally, little intuitive understanding is available about a peptide’s conformation simply from knowing theφandψvalues of a peptide (e.g., is the regular peptide defined byφ = ψ =  - 100°  left-handed or right-handed?). This report provides a new metric for backbone handednessmore » (h) based on interpreting a peptide backbone as a helix with axial displacementdand angular displacementθ, both of which are derived from a peptide backbone’s internal coordinates, especially dihedral anglesφ,ψandω. In particular,hequals sin(θ)d/d|, with range [-1, 1] and negative (or positive) values indicating left(or right)-handedness. The metrichis used to characterize the handedness of every region of the Ramachandran plot for bothcis(ω = 0°) and trans (ω = 180°) backbones, which provides the first exhaustive survey of twist handedness in Ramachandran (φ,ψ) space. These maps fill in the ‘dead space’ within the Ramachandran plot, which are regions that are not commonly accessed by structured proteins, but which may be accessible to intrinsically disordered proteins, short peptide fragments, and protein mimics such as peptoids. Finally, building on the work of (Zacharias & Knapp, 2013), this report presents a new plot based ondandθthat serves as a universal and intuitive alternative to the Ramachandran plot. The universality arises from the fact that the co-inhabitants of such a plot include every possible peptide backbone includingcisandtransbackbones. The intuitiveness

An exhaustive survey of regular peptide conformations using a new metric for backbone handedness ( h )

DOE PAGES

Mannige, Ranjan V.

2017-05-16

The Ramachandran plot is important to structural biology as it describes a peptide backbone in the context of its dominant degrees of freedom—the backbone dihedral anglesφandψ(Ramachandran, Ramakrishnan & Sasisekharan, 1963). Since its introduction, the Ramachandran plot has been a crucial tool to characterize protein backbone features. However, the conformation or twist of a backbone as a function ofφandψhas not been completely described for bothcisandtransbackbones. Additionally, little intuitive understanding is available about a peptide’s conformation simply from knowing theφandψvalues of a peptide (e.g., is the regular peptide defined byφ = ψ =  - 100°  left-handed or right-handed?). This report provides a new metric for backbone handednessmore » (h) based on interpreting a peptide backbone as a helix with axial displacementdand angular displacementθ, both of which are derived from a peptide backbone’s internal coordinates, especially dihedral anglesφ,ψandω. In particular,hequals sin(θ)d/d|, with range [-1, 1] and negative (or positive) values indicating left(or right)-handedness. The metrichis used to characterize the handedness of every region of the Ramachandran plot for bothcis(ω = 0°) and trans (ω = 180°) backbones, which provides the first exhaustive survey of twist handedness in Ramachandran (φ,ψ) space. These maps fill in the ‘dead space’ within the Ramachandran plot, which are regions that are not commonly accessed by structured proteins, but which may be accessible to intrinsically disordered proteins, short peptide fragments, and protein mimics such as peptoids. Finally, building on the work of (Zacharias & Knapp, 2013), this report presents a new plot based ondandθthat serves as a universal and intuitive alternative to the Ramachandran plot. The universality arises from the fact that the co-inhabitants of such a plot include every possible peptide backbone includingcisandtransbackbones. The intuitiveness

Nature of the water/aromatic parallel alignment interactions.

PubMed

Mitoraj, Mariusz P; Janjić, Goran V; Medaković, Vesna B; Veljković, Dušan Ž; Michalak, Artur; Zarić, Snežana D; Milčić, Miloš K

2015-01-30

The water/aromatic parallel alignment interactions are interactions where the water molecule or one of its O-H bonds is parallel to the aromatic ring plane. The calculated energies of the interactions are significant, up to ΔE(CCSD)(T)(limit) = -2.45 kcal mol(-1) at large horizontal displacement, out of benzene ring and CH bond region. These interactions are stronger than CH···O water/benzene interactions, but weaker than OH···π interactions. To investigate the nature of water/aromatic parallel alignment interactions, energy decomposition methods, symmetry-adapted perturbation theory, and extended transition state-natural orbitals for chemical valence (NOCV), were used. The calculations have shown that, for the complexes at large horizontal displacements, major contribution to interaction energy comes from electrostatic interactions between monomers, and for the complexes at small horizontal displacements, dispersion interactions are dominant binding force. The NOCV-based analysis has shown that in structures with strong interaction energies charge transfer of the type π → σ*(O-H) between the monomers also exists. © 2014 Wiley Periodicals, Inc.

Bacteria in atmospheric waters: Detection, characteristics and implications

NASA Astrophysics Data System (ADS)

Hu, Wei; Niu, Hongya; Murata, Kotaro; Wu, Zhijun; Hu, Min; Kojima, Tomoko; Zhang, Daizhou

2018-04-01

In this review paper, we synthesize the current knowledges about bacteria in atmospheric waters, e.g., cloud, fog, rain, and snow, most of which were obtained very recently. First, we briefly describe the importance of bacteria in atmospheric waters, i.e., the essentiality of studying bacteria in atmospheric waters in understanding aerosol-cloud-precipitation-climate interactions in the Earth system. Next, approaches to collect atmospheric water samples for the detection of bacteria and methods to identify the bacteria are summarized and compared. Then the available data on the abundance, viability and community composition of bacteria in atmospheric waters are summarized. The average bacterial concentration in cloud water was usually on the order 104-105 cells mL-1, while that in precipitation on the order 103-104 cells mL-1. Most of the bacteria were viable or metabolically active. Their community composition was highly diverse and differed at various sites. Factors potentially influencing the bacteria, e.g., air pollution levels and sources, meteorological conditions, seasonal effect, and physicochemical properties of atmospheric waters, are described. After that, the implications of bacteria present in atmospheric waters, including their effect on nucleation in clouds, atmospheric chemistry, ecosystems and public health, are briefly discussed. Finally, based on the current knowledges on bacteria in atmospheric waters, which in fact remains largely unknown, we give perspectives that should be paid attention to in future studies.

Water system virus detection

NASA Technical Reports Server (NTRS)

Fraser, A. S.; Wells, A. F.; Tenoso, H. J.

1975-01-01

A monitoring system developed to test the capability of a water recovery system to reject the passage of viruses into the recovered water is described. A nonpathogenic marker virus, bacteriophage F2, is fed into the process stream before the recovery unit and the reclaimed water is assayed for its presence. Detection of the marker virus consists of two major components, concentration and isolation of the marker virus, and detection of the marker virus. The concentration system involves adsorption of virus to cellulose acetate filters in the presence of trivalent cations and low pH with subsequent desorption of the virus using volumes of high pH buffer. The detection of the virus is performed by a passive immune agglutination test utilizing specially prepared polystyrene particles. An engineering preliminary design was performed as a parallel effort to the laboratory development of the marker virus test system. Engineering schematics and drawings of a fully functional laboratory prototype capable of zero-G operation are presented. The instrument consists of reagent pump/metering system, reagent storage containers, a filter concentrator, an incubation/detector system, and an electronic readout and control system.

Impact of aggregation on scaling behavior of Internet backbone traffic

NASA Astrophysics Data System (ADS)

Zhang, Zhi-Li; Ribeiro, Vinay J.; Moon, Sue B.; Diot, Christophe

2002-07-01

We study the impact of aggregation on the scaling behavior of Internet backbone tra ffic, based on traces collected from OC3 and OC12 links in a tier-1 ISP. We make two striking observations regarding the sub-second small time scaling behaviors of Internet backbone traffic: 1) for a majority of these traces, the Hurst parameters at small time scales (1ms - 100ms) are fairly close to 0.5. Hence the traffic at these time scales are nearly uncorrelated; 2) the scaling behaviors at small time scales are link-dependent, and stay fairly invariant over changing utilization and time. To understand the scaling behavior of network traffic, we develop analytical models and employ them to demonstrate how traffic composition -- aggregation of traffic with different characteristics -- affects the small-time scalings of network traffic. The degree of aggregation and burst correlation structure are two major factors in traffic composition. Our trace-based data analysis confirms this. Furthermore, we discover that traffic composition on a backbone link stays fairly consistent over time and changing utilization, which we believe is the cause for the invariant small-time scalings we observe in the traces.

A new characterization of three-dimensional conductivity backbone above and below the percolation threshold

NASA Astrophysics Data System (ADS)

Skal, Asya S.

1996-08-01

A new definition of three-dimensional conductivity backbone, obtained from a distribution function of Joule heat and the Hall coefficient is introduced. The fractal dimension d fB = d - ( {g}/{v}) = 2.25 of conductivity backbone for both sides of the threshold is obtained from a critical exponent of the Hall coefficient g = 0.6. This allows one to construct, below the threshold, a new order parameter of metal-conductor transition—the two-component infinite conductivity back-bone and tested scaling relation, proposed by Alexander and Orbach [ J. Phys. Rev. Lett.43, 1982, L625] for both sides of a threshold.

Directional virtual backbone based data aggregation scheme for Wireless Visual Sensor Networks.

PubMed

Zhang, Jing; Liu, Shi-Jian; Tsai, Pei-Wei; Zou, Fu-Min; Ji, Xiao-Rong

2018-01-01

Data gathering is a fundamental task in Wireless Visual Sensor Networks (WVSNs). Features of directional antennas and the visual data make WVSNs more complex than the conventional Wireless Sensor Network (WSN). The virtual backbone is a technique, which is capable of constructing clusters. The version associating with the aggregation operation is also referred to as the virtual backbone tree. In most of the existing literature, the main focus is on the efficiency brought by the construction of clusters that the existing methods neglect local-balance problems in general. To fill up this gap, Directional Virtual Backbone based Data Aggregation Scheme (DVBDAS) for the WVSNs is proposed in this paper. In addition, a measurement called the energy consumption density is proposed for evaluating the adequacy of results in the cluster-based construction problems. Moreover, the directional virtual backbone construction scheme is proposed by considering the local-balanced factor. Furthermore, the associated network coding mechanism is utilized to construct DVBDAS. Finally, both the theoretical analysis of the proposed DVBDAS and the simulations are given for evaluating the performance. The experimental results prove that the proposed DVBDAS achieves higher performance in terms of both the energy preservation and the network lifetime extension than the existing methods.

Rapid detection of Naegleria fowleri in water distribution pipeline biofilms and drinking water samples.

PubMed

Puzon, Geoffrey J; Lancaster, James A; Wylie, Jason T; Plumb, Iason J

2009-09-01

Rapid detection of pathogenic Naegleria fowler in water distribution networks is critical for water utilities. Current detection methods rely on sampling drinking water followed by culturing and molecular identification of purified strains. This culture-based method takes an extended amount of time (days), detects both nonpathogenic and pathogenic species, and does not account for N. fowleri cells associated with pipe wall biofilms. In this study, a total DNA extraction technique coupled with a real-time PCR method using primers specific for N. fowleri was developed and validated. The method readily detected N. fowleri without preculturing with the lowest detection limit for N. fowleri cells spiked in biofilm being one cell (66% detection rate) and five cells (100% detection rate). For drinking water, the detection limit was five cells (66% detection rate) and 10 cells (100% detection rate). By comparison, culture-based methods were less sensitive for detection of cells spiked into both biofilm (66% detection for <10 cells) and drinking water (0% detection for <10 cells). In mixed cultures of N. fowleri and nonpathogenic Naegleria, the method identified N. fowleri in 100% of all replicates, whereastests with the current consensus primers detected N. fowleri in only 5% of all replicates. Application of the new method to drinking water and pipe wall biofilm samples obtained from a distribution network enabled the detection of N. fowleri in under 6 h, versus 3+ daysforthe culture based method. Further, comparison of the real-time PCR data from the field samples and the standard curves enabled an approximation of N. fowleri cells in the biofilm and drinking water. The use of such a method will further aid water utilities in detecting and managing the persistence of N. fowleri in water distribution networks.

Optical detection of glyphosate in water

NASA Astrophysics Data System (ADS)

de Góes, R. E.; Possetti, G. R. C.; Muller, M.; Fabris, J. L.

2017-04-01

This work shows preliminary results of the detection of Glyphosate in water by using optical fiber spectroscopy. A colloid with citrate-caped silver nanoparticles was employed as substrate for the measurements. A cross analysis between optical absorption and inelastic scattering evidenced a controlled aggregation of the sample constituents, leading to the possibility of quantitative detection of the analyte. The estimate limit of detection for Glyphosate in water for the proposed sensing scheme was about 1.7 mg/L.

Human-technology interaction for standoff IED detection

NASA Astrophysics Data System (ADS)

Zhang, Evan; Zou, Yiyang; Zachrich, Liping; Fulton, Jack

2011-03-01

IEDs kill our soldiers and innocent people every day. Lessons learned from Iraq and Afghanistan clearly indicated that IEDs cannot be detected/defeated by technology alone; human-technology interaction must be engaged. In most cases, eye is the best detector, brain is the best computer, and technologies are tools, they must be used by human being properly then can achieve full functionality. In this paper, a UV Raman/fluorescence, CCD and LWIR 3 sensor fusion system for standoff IED detection and a handheld fusion system for close range IED detection are developed and demonstrated. We must train solders using their eyes or CCD/LWIR cameras to do wide area search while on the move to find small suspected area first then use the spectrometer because the laser spot is too small, to scan a one-mile long and 2-meter wide road needs 185 days although our fusion system can detect the IED in 30m with 1s interrogating time. Even if the small suspected area (e.g., 0.5mx0.5m) is found, human eyes still cannot detect the IED, soldiers must use or interact with the technology - laser based spectrometer to scan the area then they are able to detect and identify the IED in 10 minutes not 185 days. Therefore, the human-technology interaction approach will be the best solution for IED detection.

Water's Interfacial Hydrogen Bonding Structure Reveals the Effective Strength of Surface-Water Interactions.

PubMed

Shin, Sucheol; Willard, Adam P

2018-06-05

We combine all-atom molecular dynamics simulations with a mean field model of interfacial hydrogen bonding to analyze the effect of surface-water interactions on the structural and energetic properties of the liquid water interface. We show that the molecular structure of water at a weakly interacting ( i.e., hydrophobic) surface is resistant to change unless the strength of surface-water interactions are above a certain threshold. We find that below this threshold water's interfacial structure is homogeneous and insensitive to the details of the disordered surface, however, above this threshold water's interfacial structure is heterogeneous. Despite this heterogeneity, we demonstrate that the equilibrium distribution of molecular orientations can be used to quantify the energetic component of the surface-water interactions that contribute specifically to modifying the interfacial hydrogen bonding network. We identify this specific energetic component as a new measure of hydrophilicity, which we refer to as the intrinsic hydropathy.

Detection of water bodies in Saline County, Kansas

NASA Technical Reports Server (NTRS)

Barr, B. G. (Principal Investigator)

1973-01-01

The author has identified the following significant results. A total of 2,272 water bodies were mapped in Saline County, Kansas in 1972 using ERTS-1 imagery. A topographic map of 1955 shows 1,056 water bodies in the county. The major increase took place in farm ponds. Preliminary comparison of image and maps indicates that water bodies larger than ten acres in area proved consistently detectable. Most water areas between four and ten acres are also detectable, although occasionally image context prevents detection. Water areas less than four acres in extent are sometimes detected, but the number varies greatly depending on image context and the individual interpretor.

Backbone conformation affects duplex initiation and duplex propagation in hybridisation of synthetic H-bonding oligomers.

PubMed

Iadevaia, Giulia; Núñez-Villanueva, Diego; Stross, Alexander E; Hunter, Christopher A

2018-06-06

Synthetic oligomers equipped with complementary H-bond donor and acceptor side chains form multiply H-bonded duplexes in organic solvents. Comparison of the duplex forming properties of four families of oligomers with different backbones shows that formation of an extended duplex with three or four inter-strand H-bonds is more challenging than formation of complexes that make only two H-bonds. The stabilities of 1 : 1 complexes formed between length complementary homo-oligomers equipped with either phosphine oxide or phenol recognition modules were measured in toluene. When the backbone is very flexible (pentane-1,5-diyl thioether), the stability increases uniformly by an order of magnitude for each additional base-pair added to the duplex: the effective molarities for formation of the first intramolecular H-bond (duplex initiation) and subsequent intramolecular H-bonds (duplex propagation) are similar. This flexible system is compared with three more rigid backbones that are isomeric combinations of an aromatic ring and methylene groups. One of the rigid systems behaves in exactly the same way as the flexible backbone, but the other two do not. For these systems, the effective molarity for formation of the first intramolecular H-bond is the same as that found for the other two backbones, but additional H-bonds are not formed between the longer oligomers. The effective molarities are too low for duplex propagation in these systems, because the oligomer backbones cannot adopt conformations compatible with formation of an extended duplex.

Impact of Backbone Tether Length and Structure on the Electrochemical Performance of Viologen Redox Active Polymers

DOE Office of Scientific and Technical Information (OSTI.GOV)

Burgess, Mark; Chénard, Etienne; Hernández-Burgos, Kenneth

The design of chemically stable and electrochemically reversible redox active polymers (RAPs) is of great interest for energy storage technologies. Particularly, RAPs are new players for flow batteries relying on a size-exclusion based mechanism of electrolyte separation, but few studies have provided detailed molecular understanding of redox polymers in solution. Here, we use a systematic molecular design approach to investigate the impact of linker and redox-pendant electronic interactions on the performance of viologen RAPs. We used scanning electrochemical microscopy, cyclic voltammetry, bulk electrolysis, temperature-dependent absorbance, and spectroelectrochemistry to study the redox properties, charge transfer kinetics, and self-exchange of electrons throughmore » redox active dimers and their equivalent polymers. Stark contrast was observed between the electrochemical properties of viologen dimers and their corresponding polymers. Electron self-exchange kinetics in redox active dimers that only differ by their tether length and rigidity influences their charge transfer properties. Predictions from the Marcus Hush theory were consistent with observations in redox active dimers, but they failed to fully capture the behavior of macromolecular systems. For example, polymer bound viologen pendants, if too close in proximity, do not retain chemical reversibility. In contrast to polymer films, small modifications to the backbone structure decisively impact the bulk electrolysis of polymer solutions. This first comprehensive study highlights the careful balance between electronic interactions and backbone rigidity required to design RAPs with superior electrochemical performance.« less

Optical detection of oil on water

NASA Technical Reports Server (NTRS)

Millard, J. P.; Arvesen, J. C.

1973-01-01

Three radiometric techniques utilizing sunlight reflected and backscattered from water bodies have potential application for remote sensing of oil spills. Oil on water can be detected by viewing perpendicular polarization component of reflected light or difference between polarization components. Best detection is performed in ultraviolet or far-red portions of spectrum and in azimuth directions toward or opposite sun.

Detecting Protein-Glycolipid Interactions Using Glycomicelles and CaR-ESI-MS.

PubMed

Han, Ling; Kitova, Elena N; Klassen, John S

2016-11-01

This study reports on the use of the catch-and-release electrospray ionization mass spectrometry (CaR-ESI-MS) assay, combined with glycomicelles, as a method for detecting specific interactions between water-soluble proteins and glycolipids (GLs) in aqueous solution. The B subunit homopentamers of cholera toxin (CTB 5 ) and Shiga toxin type 1 B (Stx1B 5 ) and the gangliosides GM1, GM2, GM3, GD1a, GD1b, GT1b, and GD2 served as model systems for this study. The CTB 5 exhibits broad specificity for gangliosides and binds to GM1, GM2, GM3, GD1a, GD1b, and GT1b; Stx1B 5 does not recognize gangliosides. The CaR-ESI-MS assay was used to analyze solutions of CTB 5 or Stx1B 5 and individual gangliosides (GM1, GM2, GM3, GD1a, GD1b, GT1b, and GD2) or mixtures thereof. The high affinity interaction of CTB 5 with GM1 was successfully detected. However, the apparent affinity, as determined from the mass spectra, is significantly lower than that of the corresponding pentasaccharide or when GM1 is presented in model membranes such as nanodiscs. Interactions between CTB 5 and the low affinity gangliosides GD1a, GD1b, and GT1b, as well as GD2, which served as a negative control, were detected; no binding of CTB 5 to GM2 or GM3 was observed. The CaR-ESI-MS results obtained for Stx1B 5 reveal that nonspecific protein-ganglioside binding can occur during the ESI process, although the extent of binding varies between gangliosides. Consequently, interactions detected for CTB 5 with GD1a, GD1b, and GT1b are likely nonspecific in origin. Taken together, these results reveal that the CaR-ESI-MS/glycomicelle approach for detecting protein-GL interactions is prone to false positives and false negatives and must be used with caution. Graphical Abstract .

Machine Learning for Detecting Gene-Gene Interactions

PubMed Central

McKinney, Brett A.; Reif, David M.; Ritchie, Marylyn D.; Moore, Jason H.

2011-01-01

Complex interactions among genes and environmental factors are known to play a role in common human disease aetiology. There is a growing body of evidence to suggest that complex interactions are ‘the norm’ and, rather than amounting to a small perturbation to classical Mendelian genetics, interactions may be the predominant effect. Traditional statistical methods are not well suited for detecting such interactions, especially when the data are high dimensional (many attributes or independent variables) or when interactions occur between more than two polymorphisms. In this review, we discuss machine-learning models and algorithms for identifying and characterising susceptibility genes in common, complex, multifactorial human diseases. We focus on the following machine-learning methods that have been used to detect gene-gene interactions: neural networks, cellular automata, random forests, and multifactor dimensionality reduction. We conclude with some ideas about how these methods and others can be integrated into a comprehensive and flexible framework for data mining and knowledge discovery in human genetics. PMID:16722772

General order parameter based correlation analysis of protein backbone motions between experimental NMR relaxation measurements and molecular dynamics simulations

DOE Office of Scientific and Technical Information (OSTI.GOV)

Liu, Qing; Shi, Chaowei; Yu, Lu

Internal backbone dynamic motions are essential for different protein functions and occur on a wide range of time scales, from femtoseconds to seconds. Molecular dynamic (MD) simulations and nuclear magnetic resonance (NMR) spin relaxation measurements are valuable tools to gain access to fast (nanosecond) internal motions. However, there exist few reports on correlation analysis between MD and NMR relaxation data. Here, backbone relaxation measurements of {sup 15}N-labeled SH3 (Src homology 3) domain proteins in aqueous buffer were used to generate general order parameters (S{sup 2}) using a model-free approach. Simultaneously, 80 ns MD simulations of SH3 domain proteins in amore » defined hydrated box at neutral pH were conducted and the general order parameters (S{sup 2}) were derived from the MD trajectory. Correlation analysis using the Gromos force field indicated that S{sup 2} values from NMR relaxation measurements and MD simulations were significantly different. MD simulations were performed on models with different charge states for three histidine residues, and with different water models, which were SPC (simple point charge) water model and SPC/E (extended simple point charge) water model. S{sup 2} parameters from MD simulations with charges for all three histidines and with the SPC/E water model correlated well with S{sup 2} calculated from the experimental NMR relaxation measurements, in a site-specific manner. - Highlights: • Correlation analysis between NMR relaxation measurements and MD simulations. • General order parameter (S{sup 2}) as common reference between the two methods. • Different protein dynamics with different Histidine charge states in neutral pH. • Different protein dynamics with different water models.« less

UV Absorption Spectroscopy in Water-Filled Antiresonant Hollow Core Fibers for Pharmaceutical Detection.

PubMed

Nissen, Mona; Doherty, Brenda; Hamperl, Jonas; Kobelke, Jens; Weber, Karina; Henkel, Thomas; Schmidt, Markus A

2018-02-06

Due to a worldwide increased use of pharmaceuticals and, in particular, antibiotics, a growing number of these substance residues now contaminate natural water resources and drinking supplies. This triggers a considerable demand for low-cost, high-sensitivity methods for monitoring water quality. Since many biological substances exhibit strong and characteristic absorption features at wavelengths shorter than 300 nm, UV spectroscopy presents a suitable approach for the quantitative identification of such water-contaminating species. However, current UV spectroscopic devices often show limited light-matter interaction lengths, demand sophisticated and bulky experimental infrastructure which is not compatible with microfluidics, and leave large fractions of the sample analyte unused. Here, we introduce the concept of UV spectroscopy in liquid-filled anti-resonant hollow core fibers, with large core diameters and lengths of approximately 1 m, as a means to overcome such limitations. This extended light-matter interaction length principally improves the concentration detection limit by two orders of magnitude while using almost the entire sample volume-that is three orders of magnitude smaller compared to cuvette based approaches. By integrating the fibers into an optofluidic chip environment and operating within the lowest experimentally feasible transmission band, concentrations of the application-relevant pharmaceutical substances, sulfamethoxazole (SMX) and sodium salicylate (SS), were detectable down to 0.1 µM (26 ppb) and 0.4 µM (64 ppb), respectively, with the potential to reach significantly lower detection limits for further device integration.

UV Absorption Spectroscopy in Water-Filled Antiresonant Hollow Core Fibers for Pharmaceutical Detection

PubMed Central

Nissen, Mona; Doherty, Brenda; Hamperl, Jonas; Kobelke, Jens; Weber, Karina; Henkel, Thomas; Schmidt, Markus A.

2018-01-01

Due to a worldwide increased use of pharmaceuticals and, in particular, antibiotics, a growing number of these substance residues now contaminate natural water resources and drinking supplies. This triggers a considerable demand for low-cost, high-sensitivity methods for monitoring water quality. Since many biological substances exhibit strong and characteristic absorption features at wavelengths shorter than 300 nm, UV spectroscopy presents a suitable approach for the quantitative identification of such water-contaminating species. However, current UV spectroscopic devices often show limited light-matter interaction lengths, demand sophisticated and bulky experimental infrastructure which is not compatible with microfluidics, and leave large fractions of the sample analyte unused. Here, we introduce the concept of UV spectroscopy in liquid-filled anti-resonant hollow core fibers, with large core diameters and lengths of approximately 1 m, as a means to overcome such limitations. This extended light-matter interaction length principally improves the concentration detection limit by two orders of magnitude while using almost the entire sample volume—that is three orders of magnitude smaller compared to cuvette based approaches. By integrating the fibers into an optofluidic chip environment and operating within the lowest experimentally feasible transmission band, concentrations of the application-relevant pharmaceutical substances, sulfamethoxazole (SMX) and sodium salicylate (SS), were detectable down to 0.1 µM (26 ppb) and 0.4 µM (64 ppb), respectively, with the potential to reach significantly lower detection limits for further device integration. PMID:29415468

What induces pocket openings on protein surface patches involved in protein-protein interactions?

PubMed

Eyrisch, Susanne; Helms, Volkhard

2009-02-01

We previously showed for the proteins BCL-X(L), IL-2, and MDM2 that transient pockets at their protein-protein binding interfaces can be identified by applying the PASS algorithm to molecular dynamics (MD) snapshots. We now investigated which aspects of the natural conformational dynamics of proteins induce the formation of such pockets. The pocket detection protocol was applied to three different conformational ensembles for the same proteins that were extracted from MD simulations of the inhibitor bound crystal conformation in water and the free crystal/NMR structure in water and in methanol. Additional MD simulations studied the impact of backbone mobility. The more efficient CONCOORD or normal mode analysis (NMA) techniques gave significantly smaller pockets than MD simulations, whereas tCONCOORD generated pockets comparable to those observed in MD simulations for two of the three systems. Our findings emphasize the influence of solvent polarity and backbone rearrangements on the formation of pockets on protein surfaces and should be helpful in future generation of transient pockets as putative ligand binding sites at protein-protein interfaces.

What induces pocket openings on protein surface patches involved in protein-protein interactions?

NASA Astrophysics Data System (ADS)

Eyrisch, Susanne; Helms, Volkhard

2009-02-01

We previously showed for the proteins BCL-XL, IL-2, and MDM2 that transient pockets at their protein-protein binding interfaces can be identified by applying the PASS algorithm to molecular dynamics (MD) snapshots. We now investigated which aspects of the natural conformational dynamics of proteins induce the formation of such pockets. The pocket detection protocol was applied to three different conformational ensembles for the same proteins that were extracted from MD simulations of the inhibitor bound crystal conformation in water and the free crystal/NMR structure in water and in methanol. Additional MD simulations studied the impact of backbone mobility. The more efficient CONCOORD or normal mode analysis (NMA) techniques gave significantly smaller pockets than MD simulations, whereas tCONCOORD generated pockets comparable to those observed in MD simulations for two of the three systems. Our findings emphasize the influence of solvent polarity and backbone rearrangements on the formation of pockets on protein surfaces and should be helpful in future generation of transient pockets as putative ligand binding sites at protein-protein interfaces.

Direct optical detection of protein-ligand interactions.

PubMed

Gesellchen, Frank; Zimmermann, Bastian; Herberg, Friedrich W

2005-01-01

Direct optical detection provides an excellent means to investigate interactions of molecules in biological systems. The dynamic equilibria inherent to these systems can be described in greater detail by recording the kinetics of a biomolecular interaction. Optical biosensors allow direct detection of interaction patterns without the need for labeling. An overview covering several commercially available biosensors is given, with a focus on instruments based on surface plasmon resonance (SPR) and reflectometric interference spectroscopy (RIFS). Potential assay formats and experimental design, appropriate controls, and calibration procedures, especially when handling low molecular weight substances, are discussed. The single steps of an interaction analysis combined with practical tips for evaluation, data processing, and interpretation of kinetic data are described in detail. In a practical example, a step-by-step procedure for the analysis of a low molecular weight compound interaction with serum protein, determined on a commercial SPR sensor, is presented.

Analysis of stationary availability factor of two-level backbone computer networks with arbitrary topology

NASA Astrophysics Data System (ADS)

Rahman, P. A.

2018-05-01

This scientific paper deals with the two-level backbone computer networks with arbitrary topology. A specialized method, offered by the author for calculation of the stationary availability factor of the two-level backbone computer networks, based on the Markov reliability models for the set of the independent repairable elements with the given failure and repair rates and the methods of the discrete mathematics, is also discussed. A specialized algorithm, offered by the author for analysis of the network connectivity, taking into account different kinds of the network equipment failures, is also observed. Finally, this paper presents an example of calculation of the stationary availability factor for the backbone computer network with the given topology.

End Functionalized Nonionic Water-Dispersible Conjugated Polymers.

PubMed

Zhan, Ruoyu; Liu, Bin

2017-09-01

2,7-Dibromofluorene monomers carrying two or four oligo(ethylene glycol) (OEG) side chains are synthesized. Heck coupling between the monomers and 1,4-divinylbenzene followed by end capping with [4-(4-bromophenoxy)butyl]carbamic acid tert-butyl ester leads to two nonionic water-dispersible poly(fluorene-alt-1,4-divinylenephenylene)s end-functionalized with amine groups after hydrolysis. In water, the polymer with a lower OEG density (P1) has poor water dispersibility with a quantum yield of 0.24, while the polymer with a higher OEG density (P2) possesses excellent water-dispersibility with a high quantum yield of 0.45. Both polymers show fluorescence enhancement and blue-shifted absorption and emission maxima in the presence of surfactant sodium dodecyl sulfate and dodecyltrimethylammonium bromide. The polymers are also resistant to ionic strength with minimal nonspecific interactions to bovine serum albumin. When biotin is incorporated into the end of the polymer backbones through N-hydroxysuccinimide/amine coupling reaction, the biotinylated polymers interact specifically with streptavidin on solid surface. © 2017 WILEY-VCH Verlag GmbH & Co. KGaA, Weinheim.

Detecting Darwinism from Molecules in the Enceladus Plumes, Jupiter's Moons, and Other Planetary Water Lagoons

PubMed Central

2017-01-01

Abstract To the astrobiologist, Enceladus offers easy access to a potential subsurface biosphere via the intermediacy of a plume of water emerging directly into space. A direct question follows: If we were to collect a sample of this plume, what in that sample, through its presence or its absence, would suggest the presence and/or absence of life in this exotic locale? This question is, of course, relevant for life detection in any aqueous lagoon that we might be able to sample. This manuscript reviews physical chemical constraints that must be met by a genetic polymer for it to support Darwinism, a process believed to be required for a chemical system to generate properties that we value in biology. We propose that the most important of these is a repeating backbone charge; a Darwinian genetic biopolymer must be a “polyelectrolyte.” Relevant to mission design, such biopolymers are especially easy to recover and concentrate from aqueous mixtures for detection, simply by washing the aqueous mixtures across a polycharged support. Several device architectures are described to ensure that, once captured, the biopolymer meets two other requirements for Darwinism, homochirality and a small building block “alphabet.” This approach is compared and contrasted with alternative biomolecule detection approaches that seek homochirality and constrained alphabets in non-encoded biopolymers. This discussion is set within a model for the history of the terran biosphere, identifying points in that natural history where these alternative approaches would have failed to detect terran life. Key Words: Enceladus—Life detection—Europa—Icy moon—Biosignatures—Polyelectrolyte theory of the gene. Astrobiology 17, 840–851. PMID:28665680

Biosensor for detection of dissolved chromium in potable water: A review.

PubMed

Biswas, Puja; Karn, Abhinav Kumar; Balasubramanian, P; Kale, Paresh G

2017-08-15

The unprecedented deterioration rate of the environmental quality due to rapid urbanization and industrialization causes a severe global health concern to both ecosystem and humanity. Heavy metals are ubiquitous in nature and being used extensively in industrial processes, the exposure to excessive levels could alter the biochemical cycles of living systems. Hence the environmental monitoring through rapid and specific detection of heavy metal contamination in potable water is of paramount importance. Various standard analytical techniques and sensors are used for the detection of heavy metals include spectroscopy and chromatographic methods along with electrochemical, optical waveguide and polymer based sensors. However, the mentioned techniques lack the point of care application as it demands huge capital cost as well as the attention of expert personnel for sample preparation and operation. Recent advancements in the synergetic interaction among biotechnology and microelectronics have advocated the biosensor technology for a wide array of applications due to its characteristic features of sensitivity and selectivity. This review paper has outlined the overview of chromium toxicity, conventional analytical techniques along with a particular emphasis on electrochemical based biosensors for chromium detection in potable water. This article emphasized porous silicon as a host material for enzyme immobilization and elaborated the working principle, mechanism, kinetics of an enzyme-based biosensor for chromium detection. The significant characteristics such as pore size, thickness, and porosity make the porous silicon suitable for enzyme entrapment. Further, several schemes on porous silicon-based immobilized enzyme biosensors for the detection of chromium in potable water are proposed. Copyright © 2017 Elsevier B.V. All rights reserved.

Toward Improved Description of DNA Backbone: Revisiting Epsilon and Zeta Torsion Force Field Parameters

PubMed Central

Zgarbová, Marie; Luque, F. Javier; Šponer, Jiří; Cheatham, Thomas E.; Otyepka, Michal; Jurečka, Petr

2013-01-01

We present a refinement of the backbone torsion parameters ε and ζ of the Cornell et al. AMBER force field for DNA simulations. The new parameters, denoted as εζOL1, were derived from quantum-mechanical calculations with inclusion of conformation-dependent solvation effects according to the recently reported methodology (J. Chem. Theory Comput. 2012, 7(9), 2886-2902). The performance of the refined parameters was analyzed by means of extended molecular dynamics (MD) simulations for several representative systems. The results showed that the εζOL1 refinement improves the backbone description of B-DNA double helices and G-DNA stem. In B-DNA simulations, we observed an average increase of the helical twist and narrowing of the major groove, thus achieving better agreement with X-ray and solution NMR data. The balance between populations of BI and BII backbone substates was shifted towards the BII state, in better agreement with ensemble-refined solution experimental results. Furthermore, the refined parameters decreased the backbone RMS deviations in B-DNA MD simulations. In the antiparallel guanine quadruplex (G-DNA) the εζOL1 modification improved the description of non-canonical α/γ backbone substates, which were shown to be coupled to the ε/ζ torsion potential. Thus, the refinement is suggested as a possible alternative to the current ε/ζ torsion potential, which may enable more accurate modeling of nucleic acids. However, long-term testing is recommended before its routine application in DNA simulations. PMID:24058302

The Dominant Folding Route Minimizes Backbone Distortion in SH3

PubMed Central

Lammert, Heiko; Noel, Jeffrey K.; Onuchic, José N.

2012-01-01

Energetic frustration in protein folding is minimized by evolution to create a smooth and robust energy landscape. As a result the geometry of the native structure provides key constraints that shape protein folding mechanisms. Chain connectivity in particular has been identified as an essential component for realistic behavior of protein folding models. We study the quantitative balance of energetic and geometrical influences on the folding of SH3 in a structure-based model with minimal energetic frustration. A decomposition of the two-dimensional free energy landscape for the folding reaction into relevant energy and entropy contributions reveals that the entropy of the chain is not responsible for the folding mechanism. Instead the preferred folding route through the transition state arises from a cooperative energetic effect. Off-pathway structures are penalized by excess distortion in local backbone configurations and contact pair distances. This energy cost is a new ingredient in the malleable balance of interactions that controls the choice of routes during protein folding. PMID:23166485

A framework to find the logic backbone of a biological network.

PubMed

Maheshwari, Parul; Albert, Réka

2017-12-06

Cellular behaviors are governed by interaction networks among biomolecules, for example gene regulatory and signal transduction networks. An often used dynamic modeling framework for these networks, Boolean modeling, can obtain their attractors (which correspond to cell types and behaviors) and their trajectories from an initial state (e.g. a resting state) to the attractors, for example in response to an external signal. The existing methods however do not elucidate the causal relationships between distant nodes in the network. In this work, we propose a simple logic framework, based on categorizing causal relationships as sufficient or necessary, as a complement to Boolean networks. We identify and explore the properties of complex subnetworks that are distillable into a single logic relationship. We also identify cyclic subnetworks that ensure the stabilization of the state of participating nodes regardless of the rest of the network. We identify the logic backbone of biomolecular networks, consisting of external signals, self-sustaining cyclic subnetworks (stable motifs), and output nodes. Furthermore, we use the logic framework to identify crucial nodes whose override can drive the system from one steady state to another. We apply these techniques to two biological networks: the epithelial-to-mesenchymal transition network corresponding to a developmental process exploited in tumor invasion, and the network of abscisic acid induced stomatal closure in plants. We find interesting subnetworks with logical implications in these networks. Using these subgraphs and motifs, we efficiently reduce both networks to succinct backbone structures. The logic representation identifies the causal relationships between distant nodes and subnetworks. This knowledge can form the basis of network control or used in the reverse engineering of networks.

Two-dimensional NMR spectroscopy reveals cation-triggered backbone degradation in polysulfone-based anion exchange membranes

PubMed Central

Arges, Christopher G.; Ramani, Vijay

2013-01-01

Anion exchange membranes (AEMs) find widespread applications as an electrolyte and/or electrode binder in fuel cells, electrodialysis stacks, flow and metal-air batteries, and electrolyzers. AEMs exhibit poor stability in alkaline media; their degradation is induced by the hydroxide ion, a potent nucleophile. We have used 2D NMR techniques to investigate polymer backbone stability (as opposed to cation stability) of the AEM in alkaline media. We report the mechanism behind a peculiar, often-observed phenomenon, wherein a demonstrably stable polysulfone backbone degrades rapidly in alkaline solutions upon derivatization with alkaline stable fixed cation groups. Using COSY and heteronuclear multiple quantum correlation spectroscopy (2D NMR), we unequivocally demonstrate that the added cation group triggers degradation of the polymer backbone in alkaline via quaternary carbon hydrolysis and ether hydrolysis, leading to rapid failure. This finding challenges the existing perception that having a stable cation moiety is sufficient to yield a stable AEM and emphasizes the importance of the often ignored issue of backbone stability. PMID:23335629

Phyllosilicate emission from protoplanetary disks: is the indirect detection of extrasolar water possible?

PubMed

Morris, Melissa A; Desch, Steven J

2009-12-01

Phyllosilicates are hydrous minerals formed by interaction between rock and liquid water, and are commonly found in meteorites that originate in the asteroid belt. Collisions between asteroids contribute to zodiacal dust, which therefore reasonably could include phyllosilicates. Collisions between planetesimals in protoplanetary disks may also produce dust that contains phyllosilicates. These minerals possess characteristic emission features in the mid-infrared and could be detectable in extrasolar protoplanetary disks. We have determined whether phyllosilicates in protoplanetary disks are detectable in the infrared, using instruments such as those on board the Spitzer Space Telescope and the Stratospheric Observatory for Infrared Astronomy (SOFIA). We calculated opacities for the phyllosilicates most common in meteorites and, using a two-layer radiative transfer model, computed the emission of radiation from a protoplanetary disk. We found that phyllosilicates present at the 3% level lead to observationally significant differences in disk spectra and should therefore be detectable with the use of infrared observations and spectral modeling. Detection of phyllosilicates in a protoplanetary disk would be diagnostic of liquid water in planetesimals in that disk and would demonstrate similarity to our own Solar System. We also discuss use of phyllosilicate emission to test the "water worlds" hypothesis, which proposes that liquid water in planetesimals should correlate with the inventory of short-lived radionuclides in planetary systems, especially (26)Al.

Integrating quantum key distribution with classical communications in backbone fiber network.

PubMed

Mao, Yingqiu; Wang, Bi-Xiao; Zhao, Chunxu; Wang, Guangquan; Wang, Ruichun; Wang, Honghai; Zhou, Fei; Nie, Jimin; Chen, Qing; Zhao, Yong; Zhang, Qiang; Zhang, Jun; Chen, Teng-Yun; Pan, Jian-Wei

2018-03-05

Quantum key distribution (QKD) provides information-theoretic security based on the laws of quantum mechanics. The desire to reduce costs and increase robustness in real-world applications has motivated the study of coexistence between QKD and intense classical data traffic in a single fiber. Previous works on coexistence in metropolitan areas have used wavelength-division multiplexing, however, coexistence in backbone fiber networks remains a great experimental challenge, as Tbps data of up to 20 dBm optical power is transferred, and much more noise is generated for QKD. Here we present for the first time, to the best of our knowledge, the integration of QKD with a commercial backbone network of 3.6 Tbps classical data at 21 dBm launch power over 66 km fiber. With 20 GHz pass-band filtering and large effective core area fibers, real-time secure key rates can reach 4.5 kbps and 5.1 kbps for co-propagation and counter-propagation at the maximum launch power, respectively. This demonstrates feasibility and represents an important step towards building a quantum network that coexists with the current backbone fiber infrastructure of classical communications.

Origin of higher affinity to RNA of the N-terminal RNA-binding domain than that of the C-terminal one of a mouse neural protein, musashi1, as revealed by comparison of their structures, modes of interaction, surface electrostatic potentials, and backbone dynamics.

PubMed

Miyanoiri, Youhei; Kobayashi, Hisanori; Imai, Takao; Watanabe, Michinao; Nagata, Takashi; Uesugi, Seiichi; Okano, Hideyuki; Katahira, Masato

2003-10-17

Musashi1 is an RNA-binding protein abundantly expressed in the developing mouse central nervous system. Its restricted expression in neural precursor cells suggests that it is involved in maintenance of the character of progenitor cells. Musashi1 contains two ribonucleoprotein-type RNA-binding domains (RBDs), RBD1 and RBD2, the affinity to RNA of RBD1 being much higher than that of RBD2. We previously reported the structure and mode of interaction with RNA of RBD2. Here, we have determined the structure and mode of interaction with RNA of RBD1. We have also analyzed the surface electrostatic potential and backbone dynamics of both RBDs. The two RBDs exhibit the same ribo-nucleoprotein-type fold and commonly make contact with RNA on the beta-sheet side. On the other hand, there is a remarkable difference in surface electrostatic potential, the beta-sheet of RBD1 being positively charged, which is favorable for binding negatively charged RNA, but that of RBD2 being almost neutral. There is also a difference in backbone dynamics, the central portion of the beta-sheet of RBD1 being flexible, but that of RBD2 not being flexible. The flexibility of RBD1 may be utilized in the recognition process to facilitate an induced fit. Thus, comparative studies have revealed the origin of the higher affinity of RBD1 than that of RBD2 and indicated that the affinity of an RBD to RNA is not governed by its fold alone but is also determined by its surface electrostatic potential and/or backbone dynamics. The biological role of RBD2 with lower affinity is also discussed.

Planetary-scale surface water detection from space

NASA Astrophysics Data System (ADS)

Donchyts, G.; Baart, F.; Winsemius, H.; Gorelick, N.

2017-12-01

Accurate, efficient and high-resolution methods of surface water detection are needed for a better water management. Datasets on surface water extent and dynamics are crucial for a better understanding of natural and human-made processes, and as an input data for hydrological and hydraulic models. In spite of considerable progress in the harmonization of freely available satellite data, producing accurate and efficient higher-level surface water data products remains very challenging. This presentation will provide an overview of existing methods for surface water extent and change detection from multitemporal and multi-sensor satellite imagery. An algorithm to detect surface water changes from multi-temporal satellite imagery will be demonstrated as well as its open-source implementation (http://aqua-monitor.deltares.nl). This algorithm was used to estimate global surface water changes at high spatial resolution. These changes include climate change, land reclamation, reservoir construction/decommissioning, erosion/accretion, and many other. This presentation will demonstrate how open satellite data and open platforms such as Google Earth Engine have helped with this research.

Sulfation and Cation Effects on the Conformational Properties of the Glycan Backbone of Chondroitin Sulfate Disaccharides

PubMed Central

Faller, Christina E.; Guvench, Olgun

2015-01-01

Chondroitin sulfate (CS) is one of several glycosaminoglycans that are major components of proteoglycans. A linear polymer consisting of repeats of the disaccharide -4GlcAβ1-3GalNAcβ1-, CS undergoes differential sulfation resulting in five unique sulfation patterns. Because of the dimer repeat, the CS glycosidic “backbone” has two distinct sets of conformational degrees of freedom defined by pairs of dihedral angles: (ϕ1, ψ1) about the β1-3 glycosidic linkage and (ϕ2, ψ2) about the β1-4 glycosidic linkage. Differential sulfation and the possibility of cation binding, combined with the conformational flexibility and biological diversity of CS, complicate experimental efforts to understand CS three-dimensional structures at atomic resolution. Therefore, all-atom explicit-solvent molecular dynamics simulations with Adaptive Biasing Force sampling of the CS backbone were applied to obtain high resolution, high precision free energies of CS disaccharides as a function of all possible backbone geometries. All ten disaccharides (β1-3 vs. β1-4 linkage x five different sulfation patterns) were studied; additionally, ion effects were investigated by considering each disaccharide in the presence of either neutralizing sodium or calcium cations. GlcAβ1-3GalNAc disaccharides have a single, broad, thermodynamically important free-energy minimum whereas GalNAcβ1-4GlcA disaccharides have two such minima. Calcium cations but not sodium cations bind to the disaccharides, and binding is primarily to the GlcA –COO− moiety as opposed to sulfate groups. This binding alters the glycan backbone thermodynamics in instances where a calcium cation bound to –COO− can act to bridge and stabilize an interaction with an adjacent sulfate group, whereas, in the absence of this cation, the proximity of a sulfate group to –COO− results in two like charges being both desolvated and placed adjacent to each other and is found to be destabilizing. In addition to providing

Subsurface And Surface Water Flow Interactions

EPA Science Inventory

In this chapter we present basic concepts and principles underlying the phenomena of groundwater and surface water interactions. Fundamental equations and analytical and numerical solutions describing stream-aquifer interactions are presented in hillslope and riparian aquifer en...

On the relationship between NMR-derived amide order parameters and protein backbone entropy changes

PubMed Central

Sharp, Kim A.; O’Brien, Evan; Kasinath, Vignesh; Wand, A. Joshua

2015-01-01

Molecular dynamics simulations are used to analyze the relationship between NMR-derived squared generalized order parameters of amide NH groups and backbone entropy. Amide order parameters (O2NH) are largely determined by the secondary structure and average values appear unrelated to the overall flexibility of the protein. However, analysis of the more flexible subset (O2NH < 0.8) shows that these report both on the local flexibility of the protein and on a different component of the conformational entropy than that reported by the side chain methyl axis order parameters, O2axis. A calibration curve for backbone entropy vs. O2NH is developed which accounts for both correlations between amide group motions of different residues, and correlations between backbone and side chain motions. This calibration curve can be used with experimental values of O2NH changes obtained by NMR relaxation measurements to extract backbone entropy changes, e.g. upon ligand binding. In conjunction with our previous calibration for side chain entropy derived from measured O2axis values this provides a prescription for determination of the total protein conformational entropy changes from NMR relaxation measurements. PMID:25739366

On the relationship between NMR-derived amide order parameters and protein backbone entropy changes.

PubMed

Sharp, Kim A; O'Brien, Evan; Kasinath, Vignesh; Wand, A Joshua

2015-05-01

Molecular dynamics simulations are used to analyze the relationship between NMR-derived squared generalized order parameters of amide NH groups and backbone entropy. Amide order parameters (O(2) NH ) are largely determined by the secondary structure and average values appear unrelated to the overall flexibility of the protein. However, analysis of the more flexible subset (O(2) NH  < 0.8) shows that these report both on the local flexibility of the protein and on a different component of the conformational entropy than that reported by the side chain methyl axis order parameters, O(2) axis . A calibration curve for backbone entropy vs. O(2) NH is developed, which accounts for both correlations between amide group motions of different residues, and correlations between backbone and side chain motions. This calibration curve can be used with experimental values of O(2) NH changes obtained by NMR relaxation measurements to extract backbone entropy changes, for example, upon ligand binding. In conjunction with our previous calibration for side chain entropy derived from measured O(2) axis values this provides a prescription for determination of the total protein conformational entropy changes from NMR relaxation measurements. © 2015 Wiley Periodicals, Inc.

Backbone assignment of the little finger domain of a Y-family DNA polymerase.

PubMed

Ma, Dejian; Fowler, Jason D; Suo, Zucai

2011-10-01

Sulfolobus solfataricus DNA polymerase IV (Dpo4), a prototype Y-family DNA polymerase, contains a unique little finger domain besides a catalytic core. Here, we report the chemical shift assignments for the backbone nitrogens, α and β carbons, and amide protons of the little finger domain of Dpo4. This work and our published backbone assignment for the catalytic core provide the basis for investigating the conformational dynamics of Dpo4 during catalysis using solution NMR spectroscopy.

Advanced Atmospheric Water Vapor DIAL Detection System

NASA Technical Reports Server (NTRS)

Refaat, Tamer F.; Elsayed-Ali, Hani E.; DeYoung, Russell J. (Technical Monitor)

2000-01-01

Measurement of atmospheric water vapor is very important for understanding the Earth's climate and water cycle. The remote sensing Differential Absorption Lidar (DIAL) technique is a powerful method to perform such measurement from aircraft and space. This thesis describes a new advanced detection system, which incorporates major improvements regarding sensitivity and size. These improvements include a low noise advanced avalanche photodiode detector, a custom analog circuit, a 14-bit digitizer, a microcontroller for on board averaging and finally a fast computer interface. This thesis describes the design and validation of this new water vapor DIAL detection system which was integrated onto a small Printed Circuit Board (PCB) with minimal weight and power consumption. Comparing its measurements to an existing DIAL system for aerosol and water vapor profiling validated the detection system.

Ion specific effects: decoupling ion-ion and ion-water interactions

PubMed Central

Song, Jinsuk; Kang, Tae Hui; Kim, Mahn Won; Han, Songi

2015-01-01

Ion-specific effects in aqueous solution, known as the Hofmeister effect is prevalent in diverse systems ranging from pure ionic to complex protein solutions. The objective of this paper is to explicitly demonstrate how complex ion-ion and ion-water interactions manifest themselves in the Hofmeister effects, based on a series of recent experimental observation. These effects are not considered in the classical description of ion effects, such as the Deryaguin-Landau-Verwey-Overbeek (DLVO) theory that, likely for that reason, fail to describe the origin of the phenomenological Hofmeister effect. However, given that models considering the basic forces of electrostatic and van der Waals interactions can offer rationalization for the core experimental observations, a universal interaction model stands a chance to be developed. In this perspective, we separately derive the contribution from ion-ion electrostatic interaction and ion-water interaction from second harmonic generation (SHG) data at the air-ion solution interface, which yields an estimate of ion-water interactions in solution. Hofmeister ion effects observed on biological solutes in solution should be similarly influenced by contributions from ion-ion and ion-water interactions, where the same ion-water interaction parameters derived from SHG data at the air-ion solution interface could be applicable. A key experimental data set available from solution systems to probe ion-water interaction is the modulation of water diffusion dynamics near ions in bulk ion solution, as well as near biological liposome surfaces. It is obtained from Overhauser dynamic nuclear polarization (ODNP), a nuclear magnetic resonance (NMR) relaxometry technique. The surface water diffusivity is influenced by the contribution from ion-water interactions, both from localized surface charges and adsorbed ions, although the relative contribution of the former is larger on liposome surfaces. In this perspective, ion-water interaction

Increased Diels-Alderase activity through backbone remodeling guided by Foldit players.

PubMed

Eiben, Christopher B; Siegel, Justin B; Bale, Jacob B; Cooper, Seth; Khatib, Firas; Shen, Betty W; Players, Foldit; Stoddard, Barry L; Popovic, Zoran; Baker, David

2012-01-22

Computational enzyme design holds promise for the production of renewable fuels, drugs and chemicals. De novo enzyme design has generated catalysts for several reactions, but with lower catalytic efficiencies than naturally occurring enzymes. Here we report the use of game-driven crowdsourcing to enhance the activity of a computationally designed enzyme through the functional remodeling of its structure. Players of the online game Foldit were challenged to remodel the backbone of a computationally designed bimolecular Diels-Alderase to enable additional interactions with substrates. Several iterations of design and characterization generated a 24-residue helix-turn-helix motif, including a 13-residue insertion, that increased enzyme activity >18-fold. X-ray crystallography showed that the large insertion adopts a helix-turn-helix structure positioned as in the Foldit model. These results demonstrate that human creativity can extend beyond the macroscopic challenges encountered in everyday life to molecular-scale design problems.

Elastic Backbone Defines a New Transition in the Percolation Model

NASA Astrophysics Data System (ADS)

Sampaio Filho, Cesar I. N.; Andrade, José S.; Herrmann, Hans J.; Moreira, André A.

2018-04-01

The elastic backbone is the set of all shortest paths. We found a new phase transition at peb above the classical percolation threshold at which the elastic backbone becomes dense. At this transition in 2D, its fractal dimension is 1.750 ±0.003 , and one obtains a novel set of critical exponents βeb=0.50 ±0.02 , γeb=1.97 ±0.05 , and νeb=2.00 ±0.02 , fulfilling consistent critical scaling laws. Interestingly, however, the hyperscaling relation is violated. Using Binder's cumulant, we determine, with high precision, the critical probabilities peb for the triangular and tilted square lattice for site and bond percolation. This transition describes a sudden rigidification as a function of density when stretching a damaged tissue.

Backbone conformational preferences of an intrinsically disordered protein in solution.

PubMed

Espinoza-Fonseca, L Michel; Ilizaliturri-Flores, Ian; Correa-Basurto, José

2012-06-01

We have performed a 4-μs molecular dynamics simulation to investigate the native conformational preferences of the intrinsically disordered kinase-inducible domain (KID) of the transcription factor CREB in solution. There is solid experimental evidence showing that KID does not possess a bound-like structure in solution; however, it has been proposed that coil-to-helix transitions upon binding to its binding partner (CBP) are template-driven. While these studies indicate that IDPs possess a bias towards the bound structure, they do not provide direct evidence on the time-dependent conformational preferences of IDPs in atomic detail. Our simulation captured intrinsic conformational characteristics of KID that are in good agreement with experimental data such as a very small percentage of helical structure in its segment α(B) and structural disorder in solution. We used dihedral principal component analysis dPCA to map the conformations of KID in the microsecond timescale. By using principal components as reaction coordinates, we further constructed dPCA-based free energy landscapes of KID. Analysis of the free energy landscapes showed that KID is best characterized as a conformational ensemble of rapidly interconverting conformations. Interestingly, we found that despite the conformational heterogeneity of the backbone and the absence of substantial secondary structure, KID does not randomly sample the conformational space in solution: analysis of the (Φ, Ψ) dihedral angles showed that several individual residues of KID possess a strong bias toward the helical region of the Ramachandran plot. We suggest that the intrinsic conformational preferences of KID provide a bias toward the folded state without having to populate bound-like conformations before binding. Furthermore, we argue that these conformational preferences do not represent actual structural constraints which drive binding through a single pathway, which allows for specific interactions with multiple

Structural insights into the backbone-circularized granulocyte colony-stimulating factor containing a short connector.

PubMed

Miyafusa, Takamitsu; Shibuya, Risa; Honda, Shinya

2018-06-02

Backbone circularization is a powerful approach for enhancing the structural stability of polypeptides. Herein, we present the crystal structure of the circularized variant of the granulocyte colony-stimulating factor (G-CSF) in which the terminal helical region was circularized using a short, two-amino acid connector. The structure revealed that the N- and C-termini were indeed connected by a peptide bond. The local structure of the C-terminal region transited from an α helix to 3 10 helix with a bend close to the N-terminal region, indicating that the structural change offset the insufficient length of the connector. This is the first-ever report of a crystal structure of the backbone of a circularized protein. It will facilitate the development of backbone circularization methodology. Copyright © 2018 Elsevier Inc. All rights reserved.

Macromolecular properties of cepacian in water and in dimethylsulfoxide.

PubMed

Herasimenka, Yury; Cescutti, Paola; Sampaio Noguera, Carlos E; Ruggiero, Josè R; Urbani, Ranieri; Impallomeni, Giuseppe; Zanetti, Flavio; Campidelli, Stéphane; Prato, Maurizio; Rizzo, Roberto

2008-01-14

Cepacian is the exopolysaccharide produced by the majority of the so far investigated clinical strains of the Burkholderia cepacia complex. This is a group of nine closely related bacterial species that might cause serious lung infections in cystic fibrosis patients, in some cases leading to death. In this paper the aggregation ability and the conformational properties of cepacian chain were investigated to understand its role in biofilm formation. Viscosity and atomic force microscopy studies in water and in mixed (dimethylsulfoxide/water) solvent indicated the formation of double stranded molecular structures in aqueous solutions. Inter-residue short distances along cepacian chain were investigated by NOE NMR, which showed that two side chains of cepacian were not conformationally free due to strong interactions with the polymer backbone. These interactions were attributed to hydrogen bonding and contributed to structure rigidity.

Orientation Preferences of Backbone Secondary Amide Functional Groups in Peptide Nucleic Acid Complexes: Quantum Chemical Calculations Reveal an Intrinsic Preference of Cationic D-Amino Acid-Based Chiral PNA Analogues for the P-form

PubMed Central

Topham, Christopher M.; Smith, Jeremy C.

2007-01-01

Geometric descriptions of nonideal interresidue hydrogen bonding and backbone-base water bridging in the minor groove are established in terms of polyamide backbone carbonyl group orientation from analyses of residue junction conformers in experimentally determined peptide nucleic acid (PNA) complexes. Two types of interresidue hydrogen bonding are identified in PNA conformers in heteroduplexes with nucleic acids that adopt A-like basepair stacking. Quantum chemical calculations on the binding of a water molecule to an O2 base atom in glycine-based PNA thymine dimers indicate that junctions modeled with P-form backbone conformations are lower in energy than a dimer comprising the predominant conformation observed in A-like helices. It is further shown in model systems that PNA analogs based on D-lysine are better able to preorganize in a conformation exclusive to P-form helices than is glycine-based PNA. An intrinsic preference for this conformation is also exhibited by positively charged chiral PNA dimers carrying 3-amino-D-alanine or 4-aza-D-leucine residue units that provide for additional rigidity by side-chain hydrogen bonding to the backbone carbonyl oxygen. Structural modifications stabilizing P-form helices may obviate the need for large heterocycles to target DNA pyrimidine bases via PNA·DNA-PNA triplex formation. Quantum chemical modeling methods are used to propose candidate PNA Hoogsteen strand designs. PMID:17071666

Modeling pH-Responsive Adsorption of Polyelectrolytes at Oil-Water Interfaces

NASA Astrophysics Data System (ADS)

Qin, Shiyi; Yong, Xin

We use dissipative particle dynamics (DPD) to discover the interfacial adsorption of pH-responsive polyelectrolytes in oil-water binary systems under different pH values. The electrostatic interactions between charged beads and the dielectric discontinuity across the interface are modeled by exploiting a modified Particle-Particle-Particle-Mesh (PPPM) method, which uses an iterative method to solve the Poisson equation on a uniform grid. We first model the adsorption behavior of a single linear polyelectrolyte from the aqueous phase. The Henderson-Hasselbalch equation describes the relation between pH and the degree of ionization of the modeled polyelectrolytes. Through changing the degree of ionization, we explore the influence of pH on the adsorption behavior and show that the electrostatic interactions significantly modulate the adsorption. Time evolutions of the position and conformation of the polyelectrolytes and the variation in the oil-water surface tension will be measured to characterize the adsorption behavior. Furthermore, we model the pH-dependent adsorption behavior of polyelectrolytes with more complicated structures, namely, branched polyelectrolytes with hydrophobic backbones and hydrophilic side chains. We also find that the addition of salts in the medium and the lengths of the backbone and ionized side chain affect the adsorption. This research supported by the American Chemical Society Petroleum Research Fund (Award 56884-DNI9).

Thermodynamic contribution of backbone conformational entropy in the binding between SH3 domain and proline-rich motif.

PubMed

Zeng, Danyun; Shen, Qingliang; Cho, Jae-Hyun

2017-02-26

Biological functions of intrinsically disordered proteins (IDPs), and proteins containing intrinsically disordered regions (IDRs) are often mediated by short linear motifs, like proline-rich motifs (PRMs). Upon binding to their target proteins, IDPs undergo a disorder-to-order transition which is accompanied by a large conformational entropy penalty. Hence, the molecular mechanisms underlying control of conformational entropy are critical for understanding the binding affinity and selectivity of IDPs-mediated protein-protein interactions (PPIs). Here, we investigated the backbone conformational entropy change accompanied by binding of the N-terminal SH3 domain (nSH3) of CrkII and PRM derived from guanine nucleotide exchange factor 1 (C3G). In particular, we focused on the estimation of conformational entropy change of disordered PRM upon binding to the nSH3 domain. Quantitative characterization of conformational dynamics of disordered peptides like PRMs is limited. Hence, we combined various methods, including NMR model-free analysis, δ2D, DynaMine, and structure-based calculation of entropy loss. This study demonstrates that the contribution of backbone conformational entropy change is significant in the PPIs mediated by IDPs/IDRs. Copyright © 2017 Elsevier Inc. All rights reserved.

Remote detection of magmatic water in Bullialdus crater on the Moon

USGS Publications Warehouse

Klima, Rachel L.; Cahill, John; Hagerty, Justin J.; Lawrence, David

2013-01-01

Once considered dry compared with Earth, laboratory analyses of igneous components of lunar samples have suggested that the Moon’s interior is not entirely anhydrous. Water and hydroxyl have also been detected from orbit on the lunar surface, but these have been attributed to nonindigenous sources, such as interactions with the solar wind. Magmatic lunar volatiles—evidence for water indigenous to the lunar interior—have not previously been detected remotely. Here we analyse spectroscopic data from the Moon Mineralogy Mapper (M3) and report that the central peak of Bullialdus Crater is significantly enhanced in hydroxyl relative to its surroundings. We suggest that the strong and localized hydroxyl absorption features are inconsistent with a surficial origin. Instead, they are consistent with hydroxyl bound to magmatic minerals that were excavated from depth by the impact that formed Bullialdus Crater. Furthermore, estimates of thorium concentration in the central peak using data from the Lunar Prospector orbiter indicate an enhancement in incompatible elements, in contrast to the compositions of water-bearing lunar samples. We suggest that the hydroxyl-bearing material was excavated from a magmatic source that is distinct from that of samples analysed thus far.

Polyolefin backbone substitution in binders for low temperature powder injection moulding feedstocks.

PubMed

Hausnerova, Berenika; Kuritka, Ivo; Bleyan, Davit

2014-02-27

This paper reports the substitution of polyolefin backbone binder components with low melting temperature carnauba wax for powder injection moulding applications. The effect of various binder compositions of Al₂O₃ feedstock on thermal degradation parameters is investigated by thermogravimetric analysis. Within the experimental framework 29 original feedstock compositions were prepared and the superiority of carnauba wax over the polyethylene binder backbone was demonstrated in compositions containing polyethylene glycol as the initial opening agent and governing the proper mechanism of the degradation process. Moreover, the replacement of synthetic polymer by the natural wax contributes to an increase of environmental sustainability of modern industrial technologies.

Increasing Sequence Diversity with Flexible Backbone Protein Design: The Complete Redesign of a Protein Hydrophobic Core

DOE Office of Scientific and Technical Information (OSTI.GOV)

Murphy, Grant S.; Mills, Jeffrey L.; Miley, Michael J.

2015-10-15

Protein design tests our understanding of protein stability and structure. Successful design methods should allow the exploration of sequence space not found in nature. However, when redesigning naturally occurring protein structures, most fixed backbone design algorithms return amino acid sequences that share strong sequence identity with wild-type sequences, especially in the protein core. This behavior places a restriction on functional space that can be explored and is not consistent with observations from nature, where sequences of low identity have similar structures. Here, we allow backbone flexibility during design to mutate every position in the core (38 residues) of a four-helixmore » bundle protein. Only small perturbations to the backbone, 12 {angstrom}, were needed to entirely mutate the core. The redesigned protein, DRNN, is exceptionally stable (melting point >140C). An NMR and X-ray crystal structure show that the side chains and backbone were accurately modeled (all-atom RMSD = 1.3 {angstrom}).« less

Structural basis for the enhanced stability of protein model compounds and peptide backbone unit in ammonium ionic liquids.

PubMed

Vasantha, T; Attri, Pankaj; Venkatesu, Pannuru; Devi, R S Rama

2012-10-04

Protein folding/unfolding is a fascinating study in the presence of cosolvents, which protect/disrupt the native structure of protein, respectively. The structure and stability of proteins and their functional groups may be modulated by the addition of cosolvents. Ionic liquids (ILs) are finding a vast array of applications as novel cosolvents for a wide variety of biochemical processes that include protein folding. Here, the systematic and quantitative apparent transfer free energies (ΔG'(tr)) of protein model compounds from water to ILs through solubility measurements as a function of IL concentration at 25 °C have been exploited to quantify and interpret biomolecular interactions between model compounds of glycine peptides (GPs) with ammonium based ILs. The investigated aqueous systems consist of zwitterionic glycine peptides: glycine (Gly), diglycine (Gly(2)), triglycine (Gly(3)), tetraglycine (Gly(4)), and cyclic glycylglycine (c(GG)) in the presence of six ILs such as diethylammonium acetate (DEAA), diethylammonium hydrogen sulfate (DEAS), triethylammonium acetate (TEAA), triethylammonium hydrogen sulfate (TEAS), triethylammonium dihydrogen phosphate (TEAP), and trimethylammonium acetate (TMAA). We have observed positive values of ΔG'(tr) for GPs from water to ILs, indicating that interactions between ILs and GPs are unfavorable, which leads to stabilization of the structure of model protein compounds. Moreover, our experimental data ΔG'(tr) is used to obtain transfer free energies (Δg'(tr)) of the peptide backbone unit (or glycyl unit) (-CH(2)C═ONH-), which is the most numerous group in globular proteins, from water to IL solutions. To obtain the mechanism events of the ILs' role in enhancing the stability of the model compounds, we have further obtained m-values for GPs from solubility limits. These results explicitly elucidate that all alkyl ammonium ILs act as stabilizers for model compounds through the exclusion of ILs from model compounds of

Daytime Water Detection Based on Color Variation

NASA Technical Reports Server (NTRS)

Rankin, Arturo L.; Matthies, Larry H.

2010-01-01

Robust water detection is a critical perception requirement for unmanned ground vehicle (UGV) autonomous navigation. This is particularly true in wide open areas where water can collect in naturally occurring terrain depressions during periods of heavy precipitation and form large water bodies (such as ponds). At far range, reflections of the sky provide a strong cue for water. But at close range, the color coming out of a water body dominates sky reflections and the water cue from sky reflections is of marginal use. We model this behavior by using water body intensity data from multiple frames of RGB imagery to estimate the total reflection coefficient contribution from surface reflections and the combination of all other factors. Then we describe an algorithm that uses one of the color cameras in a forward- looking, UGV-mounted stereo-vision perception system to detect water bodies in wide open areas. This detector exploits the knowledge that the change in saturation-to-brightness ratio across a water body from the leading to trailing edge is uniform and distinct from other terrain types. In test sequences approaching a pond under clear, overcast, and cloudy sky conditions, the true positive and false negative water detection rates were (95.76%, 96.71%, 98.77%) and (0.45%, 0.60%, 0.62%), respectively. This software has been integrated on an experimental unmanned vehicle and field tested at Ft. Indiantown Gap, PA.

Shifts in water availability mediate plant-pollinator interactions.

PubMed

Gallagher, M Kate; Campbell, Diane R

2017-07-01

Altered precipitation patterns associated with anthropogenic climate change are expected to have many effects on plants and insect pollinators, but it is unknown if effects on pollination are mediated by changes in water availability. We tested the hypothesis that impacts of climate on plant-pollinator interactions operate through changes in water availability, and specifically that such effects occur through alteration of floral attractants. We manipulated water availability in two naturally occurring Mertensia ciliata (Boraginaceae) populations using water addition, water reduction and control plots and measured effects on vegetative and floral traits, pollinator visitation and seed set. While most floral trait values, including corolla size and nectar, increased linearly with increasing water availability, in this bumblebee-pollinated species, pollinator visitation peaked at intermediate water levels. Visitation also peaked at an intermediate corolla length, while its relationship to corolla width varied across sites. Seed set, however, increased linearly with water. These results demonstrate the potential for changes in water availability to impact plant-pollinator interactions through pollinator responses to differences in floral attractants, and that the effects of water on pollinator visitation can be nonlinear. Plant responses to changes in resource availability may be an important mechanism by which climate change will affect species interactions. © 2017 The Authors. New Phytologist © 2017 New Phytologist Trust.

Anisotropy of the water-carbon interaction: molecular simulations of water in low-diameter carbon nanotubes.

PubMed

Pérez-Hernández, Guillermo; Schmidt, Burkhard

2013-04-14

Effective Lennard-Jones models for the water-carbon interaction are derived from existing high-level ab initio calculations of water adsorbed on graphene models. The resulting potential energy well (εCO + 2εCH ≈ 1 kJ mol(-1)) is deeper than most of the previously used values in the literature on water in carbon nanotubes (CNTs). Moreover, a substantial anisotropy of the water-carbon interaction (εCO ≈ 2εCH) is obtained, which is neglected in most of the literature. We systematically investigate the effect of this anisotropy on structure and dynamics of TIP5P water confined in narrow, single-walled CNTs by means of molecular dynamics simulations for T = 300 K. While for isotropic models water usually forms one-dimensional, ordered chains inside (6,6) CNTs, we find frequent chain ruptures in simulations with medium to strongly anisotropic potentials. Here, the water molecules tend to form denser clusters displaying a liquid-like behaviour, allowing for self-diffusion along the CNT axis, in contrast to all previous simulations employing spherical (εCH = 0) interaction models. For (7,7) CNTs we observe structures close to trigonal, helical ice nanotubes which exhibit a non-monotonous dependence on the anisotropy of the water-carbon interaction. Both for vanishing and for large values of εCH we find increased fluctuations leading to a more liquid-like behaviour, with enhanced axial diffusion. In contrast, structure and dynamics of water inside (8,8) CNTs are found to be almost independent of the anisotropy of the underlying potential, which is attributed to the higher stability of the non-helical fivefold water prisms. We predict this situation to also prevail for larger CNTs, as the influence of the water-water interaction dominates over that of the water-carbon interaction.

Optical fluorescence biosensor for plant water stress detection

NASA Astrophysics Data System (ADS)

Chong, Jenny P. C.; Liew, O. W.; Li, B. Q.; Asundi, A. K.

2007-05-01

Precision farming in arable agriculture and horticulture allows conservative use of resources that are applied according to plant needs. The growing concern for sustainability in crop production has accentuated the significance of our work to develop a rapid, sensitive and non-destructive spectroscopic method for real-time monitoring of plant water stress. Elucidation of crop water status before the onset of irreversible cellular damage is critical for effective water management to ensure maximum crop yield and profit margin. A two-component bio-sensing system comprising transgenic 'Indicator Plants' and a spectrometer-linked stereoscopic microscope was developed to detect early signs of water stress before the permanent wilting point is reached. The 'Indicator Plants' are transgenic Petunia hybrida genetically engineered with a drought-responsive promoter-linked enhanced green fluorescent protein marker gene (EGFP). No EGFP fluorescence was detected prior to induction of dehydration stress. Fluorescence emission intensity increased with dehydration period and was found mainly in the stems, leaf veins and leaf tips. While fluorescence emission above endogenous background was detectable after 2 hours of water stress treatment, the plants reached permanent wilting point after 6 hours, showing that our system was able to detect water stress prior to plant entry into the stage of irreversible damage. Future work will be geared towards overcoming biological and instrument-related difficulties encountered in our initial detection system.

A New Secondary Structure Assignment Algorithm Using Cα Backbone Fragments

PubMed Central

Cao, Chen; Wang, Guishen; Liu, An; Xu, Shutan; Wang, Lincong; Zou, Shuxue

2016-01-01

The assignment of secondary structure elements in proteins is a key step in the analysis of their structures and functions. We have developed an algorithm, SACF (secondary structure assignment based on Cα fragments), for secondary structure element (SSE) assignment based on the alignment of Cα backbone fragments with central poses derived by clustering known SSE fragments. The assignment algorithm consists of three steps: First, the outlier fragments on known SSEs are detected. Next, the remaining fragments are clustered to obtain the central fragments for each cluster. Finally, the central fragments are used as a template to make assignments. Following a large-scale comparison of 11 secondary structure assignment methods, SACF, KAKSI and PROSS are found to have similar agreement with DSSP, while PCASSO agrees with DSSP best. SACF and PCASSO show preference to reducing residues in N and C cap regions, whereas KAKSI, P-SEA and SEGNO tend to add residues to the terminals when DSSP assignment is taken as standard. Moreover, our algorithm is able to assign subtle helices (310-helix, π-helix and left-handed helix) and make uniform assignments, as well as to detect rare SSEs in β-sheets or long helices as outlier fragments from other programs. The structural uniformity should be useful for protein structure classification and prediction, while outlier fragments underlie the structure–function relationship. PMID:26978354

Water system virus detection

NASA Technical Reports Server (NTRS)

Fraser, A. S.; Wells, A. F.; Tenoso, H. J. (Inventor)

1978-01-01

The performance of a waste water reclamation system is monitored by introducing a non-pathogenic marker virus, bacteriophage F2, into the waste-water prior to treatment and, thereafter, testing the reclaimed water for the presence of the marker virus. A test sample is first concentrated by absorbing any marker virus onto a cellulose acetate filter in the presence of a trivalent cation at low pH and then flushing the filter with a limited quantity of a glycine buffer solution to desorb any marker virus present on the filter. Photo-optical detection of indirect passive immune agglutination by polystyrene beads indicates the performance of the water reclamation system in removing the marker virus. A closed system provides for concentrating any marker virus, initiating and monitoring the passive immune agglutination reaction, and then flushing the system to prepare for another sample.

Extended-gate organic field-effect transistor for the detection of histamine in water

NASA Astrophysics Data System (ADS)

Minamiki, Tsukuru; Minami, Tsuyoshi; Yokoyama, Daisuke; Fukuda, Kenjiro; Kumaki, Daisuke; Tokito, Shizuo

2015-04-01

As part of our ongoing research program to develop health care sensors based on organic field-effect transistor (OFET) devices, we have attempted to detect histamine using an extended-gate OFET. Histamine is found in spoiled or decayed fish, and causes foodborne illness known as scombroid food poisoning. The new OFET device possesses an extended gate functionalized by carboxyalkanethiol that can interact with histamine. As a result, we have succeeded in detecting histamine in water through a shift in OFET threshold voltage. This result indicates the potential utility of the designed OFET devices in food freshness sensing.

Organic materials able to detect analytes

NASA Technical Reports Server (NTRS)

Swager, Timothy M. (Inventor); Zhu, Zhengguo (Inventor); Bulovic, Vladimir (Inventor); Rose, Aimee (Inventor); Madigan, Conor Francis (Inventor)

2012-01-01

The present invention generally relates to polymers with lasing characteristics that allow the polymers to be useful in detecting analytes. In one aspect, the polymer, upon an interaction with an analyte, may exhibit a change in a lasing characteristic that can be determined in some fashion. For example, interaction of an analyte with the polymer may affect the ability of the polymer to reach an excited state that allows stimulated emission of photons to occur, which may be determined, thereby determining the analyte. In another aspect, the polymer, upon interaction with an analyte, may exhibit a change in stimulated emission that is at least 10 times greater with respect to a change in the spontaneous emission of the polymer upon interaction with the analyte. The polymer may be a conjugated polymer in some cases. In one set of embodiments, the polymer includes one or more hydrocarbon side chains, which may be parallel to the polymer backbone in some instances. In another set of embodiments, the polymer may include one or more pendant aromatic rings. In yet another set of embodiments, the polymer may be substantially encapsulated in a hydrocarbon. In still another set of embodiments, the polymer may be substantially resistant to photobleaching. In certain aspects, the polymer may be useful in the detection of explosive agents, such as 2,4,6-trinitrotoluene (TNT) and 2,4-dinitrotoluene (DNT).

Detection of Oil in Water Column: Sensor Design

DTIC Science & Technology

2013-02-01

rivers , and initiating dispersant application or oil recovery operations. Challenges in detecting oil within the water column include poor...facility and along transects in the Delaware River . However, all readings were at background, even when there was visible oil on the water surface...levels for extremely high CDOM rich rivers . Detection of Oil in Water Column: Sensor Design 14 UNCLAS//Public | CG-926 RDC | Fitzpatrick, et al

Detection of copper ions in drinking water using the competitive adsorption of proteins.

PubMed

Wang, Ran; Wang, Wei; Ren, Hao; Chae, Junseok

2014-07-15

Heavy metal ions, i.e., Cu(2+), are harmful to the environment and our health. In order to detect them, and circumvent or alleviate the weaknesses of existing detecting technologies, we contrive a unique Surface Plasmon Resonance (SPR) biosensor combined with competitive adsorption of proteins, termed the Vroman effect. This approach adopts native proteins (albumin) as bio-receptors that interact with Cu(2+) to be denatured. Denaturation disrupts the conformation of albumin so that it weakens its affinity to adsorb on the sensing surface. Through the competitive adsorption between the denatured albumins and the native ones, the displacement occurs adjacent to the sensing surface, and this process is real-time monitored by SPR, a surface-sensitive label-free biosensor. The affinities of native albumin is significantly higher than that of denatured albumin, demonstrated by measured KD of native and denatured albumin to gold surafce, 5.8±0.2×10(-5) M and 5.4±0.1×10(-4) M, respectively. Using our biosensor, Cu(2+) with concentration down to 0.1mg/L is detected in PBS, tap water, deionized water, and bottled water. The SPR biosensor is characterized for 5 different heavy metal ions, Cu(2+), Fe(3+), Mn(2+), Pb(2+), and Hg(2+), most common heavy metal ions found in tap water. At the maximum contaminant level (MCL) suggested by the United States Environmental Protection Agency (EPA), the SPR biosensor produces 13.5±0.4, 1.5±0.4, 0, 0, and 0 mDeg, respectively, suggesting the biosensor may be used to detect Cu(2+) in tap water samples. Copyright © 2014 Elsevier B.V. All rights reserved.

Evaluation of ATP measurements to detect microbial ingress by wastewater and surface water in drinking water.

PubMed

Vang, Óluva K; Corfitzen, Charlotte B; Smith, Christian; Albrechtsen, Hans-Jørgen

2014-11-01

Fast and reliable methods are required for monitoring of microbial drinking water quality in order to protect public health. Adenosine triphosphate (ATP) was investigated as a potential real-time parameter for detecting microbial ingress in drinking water contaminated with wastewater or surface water. To investigate the ability of the ATP assay in detecting different contamination types, the contaminant was diluted with non-chlorinated drinking water. Wastewater, diluted at 10(4) in drinking water, was detected with the ATP assay, as well as 10(2) to 10(3) times diluted surface water. To improve the performance of the ATP assay in detecting microbial ingress in drinking water, different approaches were investigated, i.e. quantifying microbial ATP or applying reagents of different sensitivities to reduce measurement variations; however, none of these approaches contributed significantly in this respect. Compared to traditional microbiological methods, the ATP assay could detect wastewater and surface water in drinking water to a higher degree than total direct counts (TDCs), while both heterotrophic plate counts (HPC 22 °C and HPC 37 °C) and Colilert-18 (Escherichia coli and coliforms) were more sensitive than the ATP measurements, though with much longer response times. Continuous sampling combined with ATP measurements displays definite monitoring potential for microbial drinking water quality, since microbial ingress in drinking water can be detected in real-time with ATP measurements. The ability of the ATP assay to detect microbial ingress is influenced by both the ATP load from the contaminant itself and the ATP concentration in the specific drinking water. Consequently, a low ATP concentration of the specific drinking water facilitates a better detection of a potential contamination of the water supply with the ATP assay. Copyright © 2014 Elsevier Ltd. All rights reserved.

Solubility of methane in water: the significance of the methane-water interaction potential.

PubMed

Konrad, Oliver; Lankau, Timm

2005-12-15

The influence of the methane-water interaction potential on the value of the Henry constant obtained from molecular dynamics simulations was investigated. The SPC, SPC/E, MSPC/E, and TIP3P potentials were used to describe water and the OPLS-UA and TraPPE potentials for methane. Nonbonding interactions between unlike atoms were calculated both with one of four mixing rules and with our new methane-water interaction potential. The Henry constants obtained from simulations using any of the mixing rules differed significantly from the experimental ones. Good agreement between simulation and experiment was achieved with the new potential over the whole temperature range.

Biomimetic MEMS sensor array for navigation and water detection

NASA Astrophysics Data System (ADS)

Futterknecht, Oliver; Macqueen, Mark O.; Karman, Salmah; Diah, S. Zaleha M.; Gebeshuber, Ille C.

2013-05-01

The focus of this study is biomimetic concept development for a MEMS sensor array for navigation and water detection. The MEMS sensor array is inspired by abstractions of the respective biological functions: polarized skylight-based navigation sensors in honeybees (Apis mellifera) and the ability of African elephants (Loxodonta africana) to detect water. The focus lies on how to navigate to and how to detect water sources in desert-like or remote areas. The goal is to develop a sensor that can provide both, navigation clues and help in detecting nearby water sources. We basically use the information provided by the natural polarization pattern produced by the sunbeams scattered within the atmosphere combined with the capability of the honeybee's compound eye to extrapolate the navigation information. The detection device uses light beam reactive MEMS, which are capable to detect the skylight polarization based on the Rayleigh sky model. For water detection we present various possible approaches to realize the sensor. In the first approach, polarization is used: moisture saturated areas near ground have a small but distinctively different effect on scattering and polarizing light than less moist ones. Modified skylight polarization sensors (Karman, Diah and Gebeshuber, 2012) are used to visualize this small change in scattering. The second approach is inspired by the ability of elephants to detect infrasound produced by underground water reservoirs, and shall be used to determine the location of underground rivers and visualize their exact routes.

Thermodynamics of water sorption in high performance glassy thermoplastic polymers

PubMed Central

Scherillo, Giuseppe; Petretta, Mauro; Galizia, Michele; La Manna, Pietro; Musto, Pellegrino; Mensitieri, Giuseppe

2014-01-01

Sorption thermodynamics of water in two glassy polymers, polyetherimide (PEI) and polyetheretherketone (PEEK), is investigated by coupling gravimetry and on line FTIR spectroscopy in order to gather information on the total amount of sorbed water as well as on the different species of water molecules absorbed within the polymers, addressing the issue of cross- and self-interactions occurring in the polymer/water systems. Water sorption isotherms have been determined at temperatures ranging from 30 to 70°C while FTIR spectroscopy has been performed only at 30°C. The experimental analysis provided information on the groups present on the polymer backbones involved in hydrogen bonding interactions with absorbed water molecules. Moreover, it also supplied qualitative indications about the different “populations” of water molecules present within the PEEK and a quantitative assessment of these “populations” in the case of PEI. The results of the experimental analysis have been interpreted using an equation of state theory based on a compressible lattice fluid model for the Gibbs energy of the polymer-water mixture, developed by extending to the case of out of equilibrium glassy polymers a previous model intended for equilibrium rubbery polymers. The model accounts for the non-equilibrium nature of glassy polymers as well as for mean field and for hydrogen bonding interactions, providing a satisfactory quantitative interpretation of the experimental data. PMID:24860802

NMR studies of the backbone flexibility and structure of human growth hormone: a comparison of high and low pH conformations.

PubMed

Kasimova, Marina R; Kristensen, Søren M; Howe, Peter W A; Christensen, Thorkild; Matthiesen, Finn; Petersen, Jørgen; Sørensen, Hans H; Led, Jens J

2002-05-03

(15)N NMR relaxation parameters and amide (1)H/(2)H-exchange rates have been used to characterize the structural flexibility of human growth hormone (rhGH) at neutral and acidic pH. Our results show that the rigidity of the molecule is strongly affected by the solution conditions. At pH 7.0 the backbone dynamics parameters of rhGH are uniform along the polypeptide chain and their values are similar to those of other folded proteins. In contrast, at pH 2.7 the overall backbone flexibility increases substantially compared to neutral pH and the average order parameter approaches the lower limit expected for a folded protein. However, a significant variation of the backbone dynamics through the molecule indicates that under acidic conditions the mobility of the residues becomes more dependent on their location within the secondary structure units. In particular, the order parameters of certain loop regions decrease dramatically and become comparable to those found in unfolded proteins. Furthermore, the HN-exchange rates at low pH reveal that the residues most protected from exchange are clustered at one end of the helical bundle, forming a stable nucleus. We suggest that this nucleus maintains the overall fold of the protein under destabilizing conditions. We therefore conclude that the acid state of rhGH consists of a structurally conserved, but dynamically more flexible helical core surrounded by an aura of highly mobile, unstructured loops. However, in spite of its prominent flexibility the acid state of rhGH cannot be considered a "molten globule" state because of its high stability. It appears from our work that under certain conditions, a protein can tolerate a considerable increase in flexibility of its backbone, along with an increased penetration of water into its core, while still maintaining a stable folded conformation.

3d interaction homology: The structurally known rotamers of tyrosine derive from a surprisingly limited set of information-rich hydropathic interaction environments described by maps.

PubMed

Ahmed, Mostafa H; Koparde, Vishal N; Safo, Martin K; Neel Scarsdale, J; Kellogg, Glen E

2015-06-01

Sidechain rotamer libraries are obtained through exhaustive statistical analysis of existing crystallographic structures of proteins and have been applied in multiple aspects of structural biology, for example, crystallography of relatively low-resolution structures, in homology model building and in biomolecular NMR. Little is known, however, about the driving forces that lead to the preference or suitability of one rotamer over another. Construction of 3D hydropathic interaction maps for nearly 30,000 tyrosines reveals the environment around each, in terms of hydrophobic (π-π stacking, etc.) and polar (hydrogen bonding, etc.) interactions. After partitioning the tyrosines into backbone-dependent (ϕ, ψ) bins, a map similarity metric based on the correlation coefficient was applied to each map-map pair to build matrices suitable for clustering with k-means. The first bin (-200° ≤ ϕ < -155°; -205° ≤ ψ < -160°), representing 631 tyrosines, reduced to 14 unique hydropathic environments, with most diversity arising from favorable hydrophobic interactions with many different residue partner types. Polar interactions for tyrosine include surprisingly ubiquitous hydrogen bonding with the phenolic OH and a handful of unique environments surrounding the tyrosine backbone. The memberships of all but one of the 14 environments are dominated (>50%) by a single χ(1)/χ(2) rotamer. The last environment has weak or no interactions with the tyrosine ring and its χ(1)/χ(2) rotamer is indeterminate, which is consistent with it being composed of mostly surface residues. Each tyrosine residue attempts to fulfill its hydropathic valence and thus, structural water molecules are seen in a variety of roles throughout protein structure. © 2015 Wiley Periodicals, Inc.

Hydrogen Bond Networks and Hydrophobic Effects in the Amyloid β30-35 Chain in Water: A Molecular Dynamics Study.

PubMed

Jong, KwangHyok; Grisanti, Luca; Hassanali, Ali

2017-07-24

We have studied the conformational landscape of the C-terminal fragment of the amyloid protein Aβ 30-35 in water using well-tempered metadynamics simulations and found that it resembles an intrinsically disordered protein. The conformational fluctuations of the protein are facilitated by a collective reorganization of both protein and water hydrogen bond networks, combined with electrostatic interactions between termini as well as hydrophobic interactions of the side chains. The stabilization of hydrophobic interactions in one of the conformers involves a collective collapse of the side chains along with a squeeze-out of water sandwiched between them. The charged N- and C-termini play a critical role in stabilizing different types of protein conformations, including those involving contact-ion salt bridges as well as solvent-mediated interactions of the termini and the amide backbone. We have examined this by probing the distribution of directed water wires forming the hydrogen bond network enveloping the polypeptide. Water wires and their fluctuations form an integral part of structural signature of the protein conformation.

Improved Force Fields for Peptide Nucleic Acids with Optimized Backbone Torsion Parameters.

PubMed

Jasiński, Maciej; Feig, Michael; Trylska, Joanna

2018-06-06

Peptide nucleic acids are promising nucleic acid analogs for antisense therapies as they can form stable duplex and triplex structures with DNA and RNA. Computational studies of PNA-containing duplexes and triplexes are an important component for guiding their design, yet existing force fields have not been well validated and parametrized with modern computational capabilities. We present updated CHARMM and Amber force fields for PNA that greatly improve the stability of simulated PNA-containing duplexes and triplexes in comparison with experimental structures and allow such systems to be studied on microsecond time scales. The force field modifications focus on reparametrized PNA backbone torsion angles to match high-level quantum mechanics reference energies for a model compound. The microsecond simulations of PNA-PNA, PNA-DNA, PNA-RNA, and PNA-DNA-PNA complexes also allowed a comprehensive analysis of hydration and ion interactions with such systems.

Recent experimental advances on hydrophobic interactions at solid/water and fluid/water interfaces.

PubMed

Zeng, Hongbo; Shi, Chen; Huang, Jun; Li, Lin; Liu, Guangyi; Zhong, Hong

2015-03-15

Hydrophobic effects play important roles in a wide range of natural phenomena and engineering processes such as coalescence of oil droplets in water, air flotation of mineral particles, and folding and assembly of proteins and biomembranes. In this work, the authors highlight recent experimental attempts to reveal the physical origin of hydrophobic effects by directly quantifying the hydrophobic interaction on both solid/water and fluid/water interfaces using state-of-art nanomechanical techniques such as surface forces apparatus and atomic force microscopy (AFM). For solid hydrophobic surfaces of different hydrophobicity, the range of hydrophobic interaction was reported to vary from ∼10 to >100 nm. With various characterization techniques, the very long-ranged attraction (>100 nm) has been demonstrated to be mainly attributed to nonhydrophobic interaction mechanisms such as pre-existing nanobubbles and molecular rearrangement. By ruling out these factors, intrinsic hydrophobic interaction was measured to follow an exponential law with decay length of 1-2 nm with effective range less than 20 nm. On the other hand, hydrophobic interaction measured at fluid interfaces using AFM droplet/bubble probe technique was found to decay with a much shorter length of ∼0.3 nm. This discrepancy of measured decay lengths is proposed to be attributed to inherent physical distinction between solid and fluid interfaces, which impacts the structure of interface-adjacent water molecules. Direct measurement of hydrophobic interaction on a broader range of interfaces and characterization of interfacial water molecular structure using spectroscopic techniques are anticipated to help unravel the origin of this rigidity-related mismatch of hydrophobic interaction and hold promise to uncover the physical nature of hydrophobic effects. With improved understanding of hydrophobic interaction, intrinsic interaction mechanisms of many biological and chemical pathways can be better

Detecting signals of drug-drug interactions in a spontaneous reports database.

PubMed

Thakrar, Bharat T; Grundschober, Sabine Borel; Doessegger, Lucette

2007-10-01

The spontaneous reports database is widely used for detecting signals of ADRs. We have extended the methodology to include the detection of signals of ADRs that are associated with drug-drug interactions (DDI). In particular, we have investigated two different statistical assumptions for detecting signals of DDI. Using the FDA's spontaneous reports database, we investigated two models, a multiplicative and an additive model, to detect signals of DDI. We applied the models to four known DDIs (methotrexate-diclofenac and bone marrow depression, simvastatin-ciclosporin and myopathy, ketoconazole-terfenadine and torsades de pointes, and cisapride-erythromycin and torsades de pointes) and to four drug-event combinations where there is currently no evidence of a DDI (fexofenadine-ketoconazole and torsades de pointes, methotrexade-rofecoxib and bone marrow depression, fluvastatin-ciclosporin and myopathy, and cisapride-azithromycine and torsade de pointes) and estimated the measure of interaction on the two scales. The additive model correctly identified all four known DDIs by giving a statistically significant (P < 0.05) positive measure of interaction. The multiplicative model identified the first two of the known DDIs as having a statistically significant or borderline significant (P < 0.1) positive measure of interaction term, gave a nonsignificant positive trend for the third interaction (P = 0.27), and a negative trend for the last interaction. Both models correctly identified the four known non interactions by estimating a negative measure of interaction. The spontaneous reports database is a valuable resource for detecting signals of DDIs. In particular, the additive model is more sensitive in detecting such signals. The multiplicative model may further help qualify the strength of the signal detected by the additive model.

Detecting signals of drug–drug interactions in a spontaneous reports database

PubMed Central

Thakrar, Bharat T; Grundschober, Sabine Borel; Doessegger, Lucette

2007-01-01

Aims The spontaneous reports database is widely used for detecting signals of ADRs. We have extended the methodology to include the detection of signals of ADRs that are associated with drug–drug interactions (DDI). In particular, we have investigated two different statistical assumptions for detecting signals of DDI. Methods Using the FDA's spontaneous reports database, we investigated two models, a multiplicative and an additive model, to detect signals of DDI. We applied the models to four known DDIs (methotrexate-diclofenac and bone marrow depression, simvastatin-ciclosporin and myopathy, ketoconazole-terfenadine and torsades de pointes, and cisapride-erythromycin and torsades de pointes) and to four drug-event combinations where there is currently no evidence of a DDI (fexofenadine-ketoconazole and torsades de pointes, methotrexade-rofecoxib and bone marrow depression, fluvastatin-ciclosporin and myopathy, and cisapride-azithromycine and torsade de pointes) and estimated the measure of interaction on the two scales. Results The additive model correctly identified all four known DDIs by giving a statistically significant (P< 0.05) positive measure of interaction. The multiplicative model identified the first two of the known DDIs as having a statistically significant or borderline significant (P< 0.1) positive measure of interaction term, gave a nonsignificant positive trend for the third interaction (P= 0.27), and a negative trend for the last interaction. Both models correctly identified the four known non interactions by estimating a negative measure of interaction. Conclusions The spontaneous reports database is a valuable resource for detecting signals of DDIs. In particular, the additive model is more sensitive in detecting such signals. The multiplicative model may further help qualify the strength of the signal detected by the additive model. PMID:17506784

Long-term forecasting of internet backbone traffic.

PubMed

Papagiannaki, Konstantina; Taft, Nina; Zhang, Zhi-Li; Diot, Christophe

2005-09-01

We introduce a methodology to predict when and where link additions/upgrades have to take place in an Internet protocol (IP) backbone network. Using simple network management protocol (SNMP) statistics, collected continuously since 1999, we compute aggregate demand between any two adjacent points of presence (PoPs) and look at its evolution at time scales larger than 1 h. We show that IP backbone traffic exhibits visible long term trends, strong periodicities, and variability at multiple time scales. Our methodology relies on the wavelet multiresolution analysis (MRA) and linear time series models. Using wavelet MRA, we smooth the collected measurements until we identify the overall long-term trend. The fluctuations around the obtained trend are further analyzed at multiple time scales. We show that the largest amount of variability in the original signal is due to its fluctuations at the 12-h time scale. We model inter-PoP aggregate demand as a multiple linear regression model, consisting of the two identified components. We show that this model accounts for 98% of the total energy in the original signal, while explaining 90% of its variance. Weekly approximations of those components can be accurately modeled with low-order autoregressive integrated moving average (ARIMA) models. We show that forecasting the long term trend and the fluctuations of the traffic at the 12-h time scale yields accurate estimates for at least 6 months in the future.

Effect of Backbone Chemistry on the Structure of Polyurea Films Deposited by Molecular Layer Deposition

DOE PAGES

Bergsman, David S.; Closser, Richard G.; Tassone, Christopher J.; ...

2017-01-01

An experimental investigation into the growth of polyurea films by molecular layer deposition was performed by examining trends in the growth rate, crystallinity, and orientation of chains as a function of backbone flexibility. Growth curves obtained for films containing backbones of aliphatic and phenyl groups indicate that an increase in backbone flexibility leads to a reduction in growth rate from 4 to 1 Å/cycle. Crystallinity measurements collected using grazing incidence X-ray diffraction and Fourier transform infrared spectroscopy suggest that some chains form paracrystalline, out-of-plane stacks of polymer segments with packing distances ranging from 4.4 to 3.7 Å depending on themore » monomer size. Diffraction intensity is largely a function of the homogeneity of the backbone. Near-edge X-ray absorption fine structure measurements for thin and thick samples show an average chain orientation of ~25° relative to the substrate across all samples, suggesting that changes in growth rate are not caused by differences in chain angle but instead may be caused by differences in the frequency of chain terminations. In conclusion, these results suggest a model of molecular layer deposition-based chain growth in which films consist of a mixture of upward growing chains and horizontally aligned layers of paracrystalline polymer segments.« less

Impact of lignin polymer backbone esters on ionic liquid pretreatment of poplar

DOE Office of Scientific and Technical Information (OSTI.GOV)

Kim, Kwang Ho; Dutta, Tanmoy; Ralph, John

Biomass pretreatment remains an essential step in lignocellulosic biofuel production, largely to facilitate the efficient removal of lignin and increase enzyme accessibility to the polysaccharides. In recent years, there have been significant efforts in planta to reduce lignin content or modify its composition to overcome the inherent recalcitrance that it imposes on lignocellulosic biomass during processing. Here, transgenic poplar lines in which monolignol ferulate conjugates were synthesized during cell wall development to introduce, during lignification, readily cleavable ester linkages into the lignin polymer backbone (i.e., "zip lignin"), along with wild-type (WT) controls, were pretreated with different ionic liquids (ILs). Themore » strategic introduction of ester bonds into the lignin backbone resulted in increased pretreatment efficiency and released more carbohydrates with lower energy input. After pretreatment with any of three different ILs, and after limited saccharification, the transgenic poplars, especially those with relatively higher amounts of incorporated monolignol ferulate conjugates, yielded up to 23% higher sugar levels compared to WT plants. Our findings clearly demonstrate that the introduction of ester linkages into the lignin polymer backbone decreases biomass recalcitrance in poplar has the potential to reduce the energy and/or amount of IL required for effective pretreatment, and could enable the development of an economically viable and sustainable biorefinery process.« less

Impact of lignin polymer backbone esters on ionic liquid pretreatment of poplar

DOE PAGES

Kim, Kwang Ho; Dutta, Tanmoy; Ralph, John; ...

2017-04-20

Biomass pretreatment remains an essential step in lignocellulosic biofuel production, largely to facilitate the efficient removal of lignin and increase enzyme accessibility to the polysaccharides. In recent years, there have been significant efforts in planta to reduce lignin content or modify its composition to overcome the inherent recalcitrance that it imposes on lignocellulosic biomass during processing. Here, transgenic poplar lines in which monolignol ferulate conjugates were synthesized during cell wall development to introduce, during lignification, readily cleavable ester linkages into the lignin polymer backbone (i.e., "zip lignin"), along with wild-type (WT) controls, were pretreated with different ionic liquids (ILs). Themore » strategic introduction of ester bonds into the lignin backbone resulted in increased pretreatment efficiency and released more carbohydrates with lower energy input. After pretreatment with any of three different ILs, and after limited saccharification, the transgenic poplars, especially those with relatively higher amounts of incorporated monolignol ferulate conjugates, yielded up to 23% higher sugar levels compared to WT plants. Our findings clearly demonstrate that the introduction of ester linkages into the lignin polymer backbone decreases biomass recalcitrance in poplar has the potential to reduce the energy and/or amount of IL required for effective pretreatment, and could enable the development of an economically viable and sustainable biorefinery process.« less

Smectic order and backbone anisotropy of a side-chain liquid crystalline polymer by Small-Angle Neutron Scattering

NASA Astrophysics Data System (ADS)

Noirez, L.; Pépy, G.; Keller, P.; Benguigui, L.

1991-07-01

We have simultaneously measured, for the first time, the extension of the polymer backbone of a side-chain liquid crystalline polymer and the intensity of the 001 Bragg reflection, which gives the smectic order parameter Psi as a function of temperature in the smectic phase. We have qualitatively demonstrated that the more the smectic phase is ordered, the more the polymer backbone is localized between the mesogenic layers. It is shown that the Landau theory allows us to relate the radius of gyration parallel to the magnetic field of the polymer backbone to the smectic order parameter. We also show that the Renz-Warner theory is suitable at low temperatures.

Systems and Methods for Automated Water Detection Using Visible Sensors

NASA Technical Reports Server (NTRS)

Rankin, Arturo L. (Inventor); Matthies, Larry H. (Inventor); Bellutta, Paolo (Inventor)

2016-01-01

Systems and methods are disclosed that include automated machine vision that can utilize images of scenes captured by a 3D imaging system configured to image light within the visible light spectrum to detect water. One embodiment includes autonomously detecting water bodies within a scene including capturing at least one 3D image of a scene using a sensor system configured to detect visible light and to measure distance from points within the scene to the sensor system, and detecting water within the scene using a processor configured to detect regions within each of the at least one 3D images that possess at least one characteristic indicative of the presence of water.

The Magmatic-hydromagmatic Transition During Explosive Eruptions: Highlights From Mwi (magma- Water Interaction ) Laboratory Experiments

NASA Astrophysics Data System (ADS)

Mincione, V.; Trigila, R.

The transition from a mere magmatic to a hydromagmatic regime has been frequently recognized for basaltic explosive eruptions. Indeed, due to great efficiency of MWI to transform the magma thermal energy in mechanical energy, the detection of this transition is particularly relevant for the evaluation of volcanic hazard. The study of this transition is being realized using the MAQUA pressure vessel built on purpose for MWI experiments. With this setup the distribution of the produced mechanical energy among magma fragmentation, system expansion and transport of fragmented material has been measured. By means of two different experimental procedures, the fragmentation is achieved either because of water exsolution (magmatic regime) and as the result of magma-water interaction (hydromagmatic regime). In both cases, acoustic microphones on input and output pressure tubings have been connected with our data aquisition system allowing the record of acoustic signals. During the magmatic fragmentation some acoustic waves were emitted, whereas after a few seconds following the water injection a shockwave was recorded. In the latter case, special particles are produced as the result of the magma-water interaction ("interactive particles" Zimanowski et al., JGR, 102, b1, 803-814, 1997). More experiments are in progress in order to better constrain the occurrence of the shock wave associated with the explosive MWI.

Animals without Backbones: The Invertebrate Story. Grade Level 5-9.

ERIC Educational Resources Information Center

Jerome, Brian; Fuqua, Paul

This guide, when used in tandem with the videotape "Animals Without Backbones," helps students learn about invertebrates. These materials promote hands-on discovery and learning. The guide is composed of six curriculum-based teaching units: (1) "Getting Started"; (2) "Porifera"; (3) "Cnidarians"; (4) "Worms"; (5) "Mollusks"; (6) "Arthropods"; and…

Extreme Water Deficit in Brazil Detected from Space

NASA Technical Reports Server (NTRS)

Vieira Getirana

2016-01-01

Extreme droughts have caused significant socioeconomic and environmental damage worldwide. In Brazil, ineffective energy development and water management policies have magnified the impacts of recent severe droughts, which include massive agricultural losses, water supply restrictions, and energy rationing. Spaceborne remote sensing data advance our understanding of the spatiotemporal variability of large-scale droughts and enhance the detection and monitoring of extreme water-related events. In this study, data derived from the Gravity Recovery and Climate Experiment (GRACE) mission are used to detect and quantify an extended major drought over eastern Brazil and provide estimates of impacted areas and region-specific water deficits. Two structural breakpoint detection methods were applied to time series of GRACE-based terrestrial water storage anomalies (TWSA), determining when two abrupt changes occurred. One, in particular, defines the beginning of the current drought. Using TWSA, a water loss rate of 26.1 cmyr21 over southeastern Brazil was detected from 2012 to 2015. Based on analysis of Global Land Data Assimilation System(GLDAS) outputs, the extreme drought is mostly related to lower-than-usual precipitation rates, resulting in high soil moisture depletion and lower-than-usual rates of evapotranspiration. A reduction of 2023 of precipitation over an extended period of 3 years is enough to raise serious water scarcity conditions in the country. Correlations between monthly time series of both grid-based TWSA and ground-based water storage measurements at 16 reservoirs located within southeastern Brazil varied from 0.42 to 0.82. Differences are mainly explained by reservoir sizes and proximity to the drought nucleus.

Energies and 2'-Hydroxyl Group Orientations of RNA Backbone Conformations. Benchmark CCSD(T)/CBS Database, Electronic Analysis, and Assessment of DFT Methods and MD Simulations.

PubMed

Mládek, Arnošt; Banáš, Pavel; Jurečka, Petr; Otyepka, Michal; Zgarbová, Marie; Šponer, Jiří

2014-01-14

Sugar-phosphate backbone is an electronically complex molecular segment imparting RNA molecules high flexibility and architectonic heterogeneity necessary for their biological functions. The structural variability of RNA molecules is amplified by the presence of the 2'-hydroxyl group, capable of forming multitude of intra- and intermolecular interactions. Bioinformatics studies based on X-ray structure database revealed that RNA backbone samples at least 46 substates known as rotameric families. The present study provides a comprehensive analysis of RNA backbone conformational preferences and 2'-hydroxyl group orientations. First, we create a benchmark database of estimated CCSD(T)/CBS relative energies of all rotameric families and test performance of dispersion-corrected DFT-D3 methods and molecular mechanics in vacuum and in continuum solvent. The performance of the DFT-D3 methods is in general quite satisfactory. The B-LYP-D3 method provides the best trade-off between accuracy and computational demands. B3-LYP-D3 slightly outperforms the new PW6B95-D3 and MPW1B95-D3 and is the second most accurate density functional of the study. The best agreement with CCSD(T)/CBS is provided by DSD-B-LYP-D3 double-hybrid functional, although its large-scale applications may be limited by high computational costs. Molecular mechanics does not reproduce the fine energy differences between the RNA backbone substates. We also demonstrate that the differences in the magnitude of the hyperconjugation effect do not correlate with the energy ranking of the backbone conformations. Further, we investigated the 2'-hydroxyl group orientation preferences. For all families, we conducted a QM and MM hydroxyl group rigid scan in gas phase and solvent. We then carried out set of explicit solvent MD simulations of folded RNAs and analyze 2'-hydroxyl group orientations of different backbone families in MD. The solvent energy profiles determined primarily by the sugar pucker match well with the

Solubility of polyethers in hydrocarbons at low temperatures. A model for potential genetic backbones on warm titans.

PubMed

McLendon, Christopher; Opalko, F Jeffrey; Illangkoon, Heshan I; Benner, Steven A

2015-03-01

Ethers are proposed here as the repeating backbone linking units in linear genetic biopolymers that might support Darwinian evolution in hydrocarbon oceans. Hydrocarbon oceans are found in our own solar system as methane mixtures on Titan. They may be found as mixtures of higher alkanes (propane, for example) on warmer hydrocarbon-rich planets in exosolar systems ("warm Titans"). We report studies on the solubility of several short polyethers in propane over its liquid range (from 85 to 231 K, or -188 °C to -42 °C). These show that polyethers are reasonably soluble in propane at temperatures down to ca. 200 K. However, their solubilities drop dramatically at still lower temperatures and become immeasurably low below 170 K, still well above the ∼ 95 K in Titan's oceans. Assuming that a liquid phase is essential for any living system, and genetic biopolymers must dissolve in that biosolvent to support Darwinism, these data suggest that we must look elsewhere to identify linear biopolymers that might support genetics in Titan's surface oceans. However, genetic molecules with polyether backbones may be suitable to support life in hydrocarbon oceans on warm Titans, where abundant organics and environments lacking corrosive water might make it easier for life to originate.

NBC detection in air and water

NASA Technical Reports Server (NTRS)

Hartley, Frank T.; Smith, Steven J.; McMurtry, Gary M.

2003-01-01

Participating in a Navy STTR project to develop a system capable of the 'real-time' detection and quanitification of nuclear, biological and chemical (NBC) warfare agents, and of related industrial chemicals including NBC agent synthesis by-products in water and in air immediately above the water's surface. This project uses JPL's Soft Ionization Membrane (SIM) technology which totally ionizes molecules without fragmentation (a process that can markedly improve the sensitivity and specificity of molecule compostition identification), and JPL's Rotating Field Mass Spectrometer (RFMS) technology which has large enough dynamic mass range to enable detection of nuclear materials as well as biological and chemical agents. This Navy project integrates these JPL Environmental Monitoring UnitS (REMUS) an autonomous underwater vehicle (AUV). It is anticipated that the REMUS AUV will be capable of 'real-time' detection and quantification of NBC warefare agents.

Experimental Tracking of Limit-Point Bifurcations and Backbone Curves Using Control-Based Continuation

NASA Astrophysics Data System (ADS)

Renson, Ludovic; Barton, David A. W.; Neild, Simon A.

Control-based continuation (CBC) is a means of applying numerical continuation directly to a physical experiment for bifurcation analysis without the use of a mathematical model. CBC enables the detection and tracking of bifurcations directly, without the need for a post-processing stage as is often the case for more traditional experimental approaches. In this paper, we use CBC to directly locate limit-point bifurcations of a periodically forced oscillator and track them as forcing parameters are varied. Backbone curves, which capture the overall frequency-amplitude dependence of the system’s forced response, are also traced out directly. The proposed method is demonstrated on a single-degree-of-freedom mechanical system with a nonlinear stiffness characteristic. Results are presented for two configurations of the nonlinearity — one where it exhibits a hardening stiffness characteristic and one where it exhibits softening-hardening.

Water-mediated protein-fluorophore interactions modulate the affinity of an ABC-ATPase/TNP-ADP complex.

PubMed

Oswald, Christine; Jenewein, Stefan; Smits, Sander H J; Holland, I Barry; Schmitt, Lutz

2008-04-01

TNP-modified nucleotides have been used extensively to study protein-nucleotide interactions. In the case of ABC-ATPases, application of these powerful tools has been greatly restricted due to the significantly higher affinity of the TNP-nucleotide for the corresponding ABC-ATPase in comparison to the non-modified nucleotides. To understand the molecular changes occurring upon binding of the TNP-nucleotide to an ABC-ATPase, we have determined the crystal structure of the TNP-ADP/HlyB-NBD complex at 1.6A resolution. Despite the higher affinity of TNP-ADP, no direct fluorophore-protein interactions were observed. Unexpectedly, only water-mediated interactions were detected between the TNP moiety and Tyr(477), that is engaged in pi-pi stacking with the adenine ring, as well as with two serine residues (Ser(504) and Ser(509)) of the Walker A motif. Interestingly, the side chains of these two serine residues adopt novel conformations that are not observed in the corresponding ADP structure. However, in the crystal structure of the S504A mutant, which binds TNP-ADP with similar affinity to the wild type enzyme, a novel TNP-water interaction compensates for the missing serine side chain. Since this water molecule is not present in the wild type enzyme, these results suggest that only water-mediated interactions provide a structural explanation for the increased affinity of TNP-nucleotides towards ABC-ATPases. However, our results also imply that in silico approaches such as docking or modeling cannot directly be applied to generate 'affinity-adopted' ADP- or ATP-analogs for ABC-ATPases.

Correlating the Effects of Antimicrobial Preservatives on Conformational Stability, Aggregation Propensity, and Backbone Flexibility of an IgG1 mAb.

PubMed

Arora, Jayant; Joshi, Sangeeta B; Middaugh, C Russell; Weis, David D; Volkin, David B

2017-06-01

Multidose formulations of biotherapeutics, which offer better dosage management and reduced production costs, require the addition of antimicrobial preservatives (APs). APs have been shown, however, to decrease protein stability in solution and cause protein aggregation. In this report, the effect of 4 APs, m-cresol, phenol, phenoxyethanol, and benzyl alcohol on conformational stability, aggregation propensity, and backbone flexibility of an IgG1 mAb, mAb-4, is investigated. Compared with no preservative control, each of the APs decreased the conformational stability of mAb-4 as measured by differential scanning calorimetry and extrinsic fluorescence spectroscopy. The addition of APs resulted in increased monomer loss and aggregate accumulation at 50°C over 28 days, as monitored by size-exclusion chromatography. The extent of conformational destabilization and protein aggregation of mAb-4 induced by APs followed their calculated octanol-water partition coefficients. Increases in backbone flexibility, as measured by hydrogen exchange, of a region located in the C H 2 domain of the mAb (heavy chain 237-254) in the presence of APs also correlated with hydrophobicity. Based on these results, the destabilizing effect of APs on mAb-4 correlates with the increased hydrophobicity of the APs and their ability to enhance the local backbone flexibility of an aggregation hot spot within the C H 2 domain of the mAb. Copyright © 2017 American Pharmacists Association®. Published by Elsevier Inc. All rights reserved.

Role of water mediated interactions in protein-protein recognition landscapes.

PubMed

Papoian, Garegin A; Ulander, Johan; Wolynes, Peter G

2003-07-30

The energy landscape picture of protein folding and binding is employed to optimize a number of pair potentials for direct and water-mediated interactions in protein complex interfaces. We find that water-mediated interactions greatly complement direct interactions in discriminating against various types of trap interactions that model those present in the cell. We highlight the context dependent nature of knowledge-based binding potentials, as contrasted with the situation for autonomous folding. By performing a Principal Component Analysis (PCA) of the corresponding interaction matrixes, we rationalize the strength of the recognition signal for each combination of the contact type and reference trap states using the differential in the idealized "canonical" amino acid compositions of native and trap layers. The comparison of direct and water-mediated contact potential matrixes emphasizes the importance of partial solvation in stabilizing charged groups in the protein interfaces. Specific water-mediated interresidue interactions are expected to influence significantly the kinetics as well as thermodynamics of protein association.

Colorimetric detection of copper in water using a Schiff base derivative

NASA Astrophysics Data System (ADS)

Peralta Domínguez, D.; Ramos-Ortiz, G.; Maldonado, J. L.; Rodriguez, M.; Meneses-Nava, M. A.; Barbosa-Garcia, O.; Santillan, R.; Farfán, N.

2013-09-01

Organic molecular sensors have the advantage of being used through an easy, fast, economical and reliable optical method for detecting toxic metal ions in our environment. In this work, we present a simple but highly specific organic ligand compound 5-Chloro-2-((E)-((E)-3-(4-(dimethylamino)phenyl)allylidene)amino)phenol (L1) that acts as a colorimetric sensor for ions in a mixture of acetonitrile/water (ratio 10:1, v:v). Binding interaction between L1 and various metal-ions has been established by ultraviolet-visible spectroscopic measurements that indicate favorable coordination of the ligand with selective metal ions, particularly, with copper. These results showed that the electronic transition band shape of L1 change after binding with copper in aqueous solution. L1 exhibited binding-induced color changes from yellow to pink one detected by the naked eye. This new sensor presented 2.5 × 10-6 M as limit detection, even under the presence of other metal ions.

Coupling between myosin head conformation and the thick filament backbone structure.

PubMed

Hu, Zhongjun; Taylor, Dianne W; Edwards, Robert J; Taylor, Kenneth A

2017-12-01

The recent high-resolution structure of the thick filament from Lethocerus asynchronous flight muscle shows aspects of thick filament structure never before revealed that may shed some light on how striated muscles function. The phenomenon of stretch activation underlies the function of asynchronous flight muscle. It is most highly developed in flight muscle, but is also observed in other striated muscles such as cardiac muscle. Although stretch activation is likely to be complex, involving more than a single structural aspect of striated muscle, the thick filament itself, would be a prime site for regulatory function because it must bear all of the tension produced by both its associated myosin motors and any externally applied force. Here we show the first structural evidence that the arrangement of myosin heads within the interacting heads motif is coupled to the structure of the thick filament backbone. We find that a change in helical angle of 0.16° disorders the blocked head preferentially within the Lethocerus interacting heads motif. This observation suggests a mechanism for how tension affects the dynamics of the myosin heads leading to a detailed hypothesis for stretch activation and shortening deactivation, in which the blocked head preferentially binds the thin filament followed by the free head when force production occurs. Copyright © 2017 Elsevier Inc. All rights reserved.

Self-assembly of diphenylalanine backbone homologues and their combination with functionalized carbon nanotubes.

PubMed

Dinesh, Bhimareddy; Squillaci, Marco A; Ménard-Moyon, Cécilia; Samorì, Paolo; Bianco, Alberto

2015-10-14

The integration of carbon nanotubes (CNTs) into organized nanostructures is of great interest for applications in materials science and biomedicine. In this work we studied the self-assembly of β and γ homologues of diphenylalanine peptides under different solvent and pH conditions. We aimed to investigate the role of peptide backbone in tuning the formation of different types of nanostructures alone or in combination with carbon nanotubes. In spite of having the same side chain, β and γ peptides formed distinctively different nanofibers, a clear indication of the role played by the backbone homologation on the self-assembly. The variation of the pH allowed to transform the nanofibers into spherical structures. Moreover, the co-assembly of β and γ peptides with carbon nanotubes covalently functionalized with the same peptide generated unique dendritic assemblies. This comparative study on self-assembly using diphenylalanine backbone homologues and of the co-assembly with CNT covalent conjugates is the first example exploring the capacity of β and γ peptides to adopt precise nanostructures, particularly in combination with carbon nanotubes. The dendritic organization obtained by mixing carbon nanotubes and peptides might find interesting applications in tissue engineering and neuronal interfacing.

Recent advances in understanding the interaction of groundwater and surface water

USGS Publications Warehouse

Winter, Thomas C.

1995-01-01

The most common image of the interaction of groundwater and surface water is that of the interaction of streams with a contiguous alluvial aquifer. This type of system has been the focus of study for more than 100 years, from the work of Boussinesq (1877) to the present, and stream-aquifer interaction continues to be the most common topic of papers discussing the interaction of groundwater and surface water. However, groundwater and surface water interact in a wide variety of landscapes from alpine to coastal. Within these landscapes, ground-water systems range in scale from local to regional, and the types of surface water include streams, lakes, wetlands, and oceans. Given the broad spectrum of the topic of groundwater and surface water interaction, an overview of studies of this topic could be organized according to surface water type, landscape type, scale of hydrologic systems, or field and analytical methods. All these factors are discussed, but this paper is organized according to landscape type because of the great increase in studies of the interaction of groundwater and surface water in landscapes other than riverine systems in the last 15 years. Furthermore, discussing studies by landscape type facilitates comparison of methods and results from different geologic and climatic settings. The general landscapes discussed are mountain terrane, riverine systems, coastal terrane, hummocky terrane, and karst terrane.

Bound Water at Protein-Protein Interfaces: Partners, Roles and Hydrophobic Bubbles as a Conserved Motif

PubMed Central

Ahmed, Mostafa H.; Spyrakis, Francesca; Cozzini, Pietro; Tripathi, Parijat K.; Mozzarelli, Andrea; Scarsdale, J. Neel; Safo, Martin A.; Kellogg, Glen E.

2011-01-01

Background There is a great interest in understanding and exploiting protein-protein associations as new routes for treating human disease. However, these associations are difficult to structurally characterize or model although the number of X-ray structures for protein-protein complexes is expanding. One feature of these complexes that has received little attention is the role of water molecules in the interfacial region. Methodology A data set of 4741 water molecules abstracted from 179 high-resolution (≤ 2.30 Å) X-ray crystal structures of protein-protein complexes was analyzed with a suite of modeling tools based on the HINT forcefield and hydrogen-bonding geometry. A metric termed Relevance was used to classify the general roles of the water molecules. Results The water molecules were found to be involved in: a) (bridging) interactions with both proteins (21%), b) favorable interactions with only one protein (53%), and c) no interactions with either protein (26%). This trend is shown to be independent of the crystallographic resolution. Interactions with residue backbones are consistent for all classes and account for 21.5% of all interactions. Interactions with polar residues are significantly more common for the first group and interactions with non-polar residues dominate the last group. Waters interacting with both proteins stabilize on average the proteins' interaction (−0.46 kcal mol−1), but the overall average contribution of a single water to the protein-protein interaction energy is unfavorable (+0.03 kcal mol−1). Analysis of the waters without favorable interactions with either protein suggests that this is a conserved phenomenon: 42% of these waters have SASA ≤ 10 Å2 and are thus largely buried, and 69% of these are within predominantly hydrophobic environments or “hydrophobic bubbles”. Such water molecules may have an important biological purpose in mediating protein-protein interactions. PMID:21961043

Selectivity differences of water-soluble vitamins separated on hydrophilic interaction stationary phases.

PubMed

Yang, Yuanzhong; Boysen, Reinhard I; Hearn, Milton T W

2013-06-01

In this study, the retention behavior and selectivity differences of water-soluble vitamins were evaluated with three types of polar stationary phases (i.e. an underivatized silica phase, an amide phase, and an amino phase) operated in the hydrophilic interaction chromatographic mode with ESI mass spectrometric detection. The effects of mobile phase composition, including buffer pH and concentration, on the retention and selectivity of the vitamins were investigated. In all stationary phases, the neutral or weakly charged vitamins exhibited very weak retention under each of the pH conditions, while the acidic and more basic vitamins showed diverse retention behaviors. With the underivatized silica phase, increasing the salt concentration of the mobile phase resulted in enhanced retention of the acidic vitamins, but decreased retention of the basic vitamins. These observations thus signify the involvement of secondary mechanisms, such as electrostatic interaction in the retention of these analytes. Under optimized conditions, a baseline separation of all vitamins was achieved with excellent peak efficiency. In addition, the effects of water content in the sample on retention and peak efficiency were examined, with sample stacking effects observed when the injected sample contained a high amount of water. © 2013 WILEY-VCH Verlag GmbH & Co. KGaA, Weinheim.

Salmonella rarely detected in Mississippi coastal waters and sediment.

PubMed

Carr, M R; Wang, S Y; McLean, T I; Flood, C J; Ellender, R D

2010-12-01

Standards for the rapid detection of individual pathogens from environmental samples have not been developed, but in their absence, the use of molecular-based detection methods coupled with traditional microbiology techniques allows for rapid and accurate pathogen detection from environmental waters and sediment. The aim of this research was to combine the use of enrichment with PCR for detection of Salmonella in Mississippi coastal waters and sediment and observe if that presence correlated with levels of enterococci and climatological variables. Salmonella were primarily found in samples that underwent nutrient enrichment and were present more frequently in freshwater than marine waters. Salmonella were detected infrequently in marine and freshwater sediments. There was a significant positive correlation between the presence of detectable Salmonella and the average enterococcal count. An inverse relationship, however, was observed between the frequency of detection and the levels of salinity, turbidity and sunlight exposure. Results from this study indicated the presence of Salmonella in Mississippi coastal waters, and sediments are very low with significant differences between freshwater and marine environments. Using pathogenic and novel nonpathogenic molecular markers, Salmonella do not appear to be a significant pathogenic genus along the Mississippi Coast. © 2010 The Authors. Journal of Applied Microbiology © 2010 The Society for Applied Microbiology.

13C multiplet nuclear magnetic resonance relaxation-derived ring puckering and backbone dynamics in proline-containing glycine-based peptides.

PubMed Central

Mikhailov, D; Daragan, V A; Mayo, K H

1995-01-01

13CH2-multiplet nuclear magnetic resonance relaxation studies on proline (P)-containing glycine (G)-based peptides, GP, PG, GPG, PGG, and GPGG, provided numerous dipolar auto- and cross-correlation times for various motional model analyses of backbone and proline-ring bond rotations. Molecular dynamics simulations and bond rotation energy profiles were calculated to assess which motions could contribute most to observed relaxation phenomena. Results indicate that proline restricts backbone psi 1, psi 2, and phi 2 motions by 50% relative to those found for a polyglycine control peptide. psi 1 rotations are more restricted in the trans-proline isomer state than in the cis form. A two-state jump model best approximates proline ring puckering which in water could occur either by the C gamma endo-exo or by the C2 interconversion mechanism. The temperature dependence (5 degrees to 75 degrees C) of C beta, and C gamma, and C delta angular changes is rather flat, suggesting a near zero enthalpic contribution to the ring puckering process. In lower dielectric solvents, dimethylsulfoxide and methanol, which may mimic the hydrophobic environment within a protein, the endo-exo mechanism is preferred. PMID:7787039

Hydrogen bond formation between the naturally modified nucleobase and phosphate backbone

PubMed Central

Sheng, Jia; Zhang, Wen; Hassan, Abdalla E. A.; Gan, Jianhua; Soares, Alexei S.; Geng, Song; Ren, Yi; Huang, Zhen

2012-01-01

Natural RNAs, especially tRNAs, are extensively modified to tailor structure and function diversities. Uracil is the most modified nucleobase among all natural nucleobases. Interestingly, >76% of uracil modifications are located on its 5-position. We have investigated the natural 5-methoxy (5-O-CH3) modification of uracil in the context of A-form oligonucleotide duplex. Our X-ray crystal structure indicates first a H-bond formation between the uracil 5-O-CH3 and its 5′-phosphate. This novel H-bond is not observed when the oxygen of 5-O-CH3 is replaced with a larger atom (selenium or sulfur). The 5-O-CH3 modification does not cause significant structure and stability alterations. Moreover, our computational study is consistent with the experimental observation. The investigation on the uracil 5-position demonstrates the importance of this RNA modification at the atomic level. Our finding suggests a general interaction between the nucleobase and backbone and reveals a plausible function of the tRNA 5-O-CH3 modification, which might potentially rigidify the local conformation and facilitates translation. PMID:22641848

Temperature dependence of fast carbonyl backbone dynamics in chicken villin headpiece subdomain

PubMed Central

Vugmeyster, Liliya; Ostrovsky, Dmitry

2012-01-01

Temperature-dependence of protein dynamics can provide information on details of the free energy landscape by probing the characteristics of the potential responsible for the fluctuations. We have investigated the temperature-dependence of picosecond to nanosecond backbone dynamics at carbonyl carbon sites in chicken villin headpiece subdomain protein using a combination of three NMR relaxation rates: 13C′ longitudinal rate, and two cross-correlated rates involving dipolar and chemical shift anisotropy (CSA) relaxation mechanisms, 13C′/13C′−13Cα CSA/dipolar and 13C′/13C′−15N CSA/dipolar. Order parameters have been extracted using the Lipari-Szabo model-free approach assuming a separation of the time scales of internal and molecular motions in the 2–16°C temperature range. There is a gradual deviation from this assumption from lower to higher temperatures, such that above 16°C the separation of the time scales is inconsistent with the experimental data and, thus, the Lipari-Szabo formalism can not be applied. While there are variations among the residues, on the average the order parameters indicate a markedly steeper temperature dependence at backbone carbonyl carbons compared to that probed at amide nitrogens in an earlier study. This strongly advocates for probing sites other than amide nitrogen for accurate characterization of the potential and other thermodynamics characteristics of protein backbone. PMID:21416162

[Detection of Cryptospordium spp. in environmental water samples by FTA-PCR].

PubMed

Zhang, Xiao-Ping; Zhu, Qian; He, Yan-Yan; Jiang, Li; Jiang, Shou-Fu

2011-02-01

To establish a FTA-polymeras chain reaction (FTA-PCR) method in detection of Cryptospordium spp. in different sources of water. The semi automated immunomagnetic separation (IMS) of Cryptospordium oocysts in environmental water samples was performed firstly, and then genomic DNA of Cryptospordium oocysts was extracted by FTA filters disk. Oligonucleotide primers were designed based on the DNA fragment of the 18 S rRNA gene from C. parvum. Plate DNA was amplified with primers in PCR. The control DNA samples from Toxoplasma gondii,Sarcocystis suihominis, Echinococcus granulosus, and Clonorchis sinensis were amplified simultaneously. All PCR products were detected by agar electrophoresis dyed with ethidium bromide. The 446 bp fragment of DNA was detected in all samples of C. parvum, C. andersoni, and C. baileyi, while it was not detected in control groups in laboratory. No positive samples were found from 10 samples collected from tape water in 5 districts of Shanghai City by FTA-PCR. Nine positive samples were detected totally from 70 different environmental water samples, there were 0 out of 15 samples from the source of tape water, 2 out of 25 from the Huangpu River, 5 out of 15 from rivers around the animal farmers, 1 out of 9 from output water of contaminating water treatment factory, 1 out of 6 from the out gate of living contaminating water. The 446 bp fragment was detected from all the amplified positive water samples. FTA-PCR is an efficient method for gene detection of Cryptospordium oocysts, which could be used in detection of environmental water samples. The contamination degree of Cryptospordium oocysts in the river water around animal farms is high.

Exploring backbone-cation alkyl spacers for multi-cation side chain anion exchange membranes

NASA Astrophysics Data System (ADS)

Zhu, Liang; Yu, Xuedi; Hickner, Michael A.

2018-01-01

In order to systematically study how the arrangement of cations on the side chain and length of alkyl spacers between cations impact the performance of multi-cation AEMs for alkaline fuel cells, a series of polyphenylene oxide (PPO)-based AEMs with different cationic side chains were synthesized. This work resulted in samples with two or three cations in a side chain pendant to the PPO backbone. More importantly, the length of the spacer between cations varied from 3 methylene (-CH2-) (C3) groups to 8 methylene (C8) groups. The highest conductivity, up to 99 mS/cm in liquid water at room temperature, was observed for the triple-cation side chain AEM with pentyl (C5) or hexyl (C6) spacers. The multi-cation AEMs were found to have decreased water uptake and ionic conductivity when the spacer chains between cations were lengthened from pentyl (C5) or hexyl (C6) to octyl (C8) linking groups. The triple-cation membranes with pentyl (C5) or hexyl (C6) groups between cations showed greatest stability after immersion in 1 M NaOH at 80 °C for 500 h.

DETECTION OF CRYPTOSPORIDIUM OOCYSTS IN WATER MATRICES

EPA Science Inventory

Since the advent and recognition of waterborne outbreaks of cryptosporidiosis great effort has been expended on development of methods for detecting Cryptosporidium oocysts in water. Oocysts recovery rates using a method originally developed for detecting Giardia cysts ranged fr...

Detection of Thermal Water Vapor Emission from W Hydrae

NASA Technical Reports Server (NTRS)

Neufeld, David A.; Chen, Wesley; Melnick, Gary J.; DeGraauw, Thijs; Feuchtgruber, Helmut; Harwitt, Martin

1997-01-01

We have detected four far-infrared emission lines of water vapor toward the evolved star W Hydrae, using the Short Wavelength Spectrometer (SWS) of the Infrared Space Observatory (ISO). This is the first detection of thermal water vapor emission from a circumstellar outflow.

Smart-Grid Backbone Network Real-Time Delay Reduction via Integer Programming.

PubMed

Pagadrai, Sasikanth; Yilmaz, Muhittin; Valluri, Pratyush

2016-08-01

This research investigates an optimal delay-based virtual topology design using integer linear programming (ILP), which is applied to the current backbone networks such as smart-grid real-time communication systems. A network traffic matrix is applied and the corresponding virtual topology problem is solved using the ILP formulations that include a network delay-dependent objective function and lightpath routing, wavelength assignment, wavelength continuity, flow routing, and traffic loss constraints. The proposed optimization approach provides an efficient deterministic integration of intelligent sensing and decision making, and network learning features for superior smart grid operations by adaptively responding the time-varying network traffic data as well as operational constraints to maintain optimal virtual topologies. A representative optical backbone network has been utilized to demonstrate the proposed optimization framework whose simulation results indicate that superior smart-grid network performance can be achieved using commercial networks and integer programming.

[Detection of oil spills on water by differential polarization FTIR spectrometry].

PubMed

Yuan, Yue-ming; Xiong, Wei; Fang, Yong-hua; Lan, Tian-ge; Li, Da-cheng

2010-08-01

Detection of oil spills on water, by traditional thermal remote sensing, is based on the radiance contrast between the large area of clean water and the polluted area of water. And the categories of oil spills can not be identified by analysing the thermal infrared image. In order to find out the extent of pollution and identify the oil contaminants, an approach to the passive detection of oil spills on water by differential polarization FTIR spectrometry is proposed. This approach can detect the contaminants by obtaining and analysing the subtracted spectrum of horizontal and vertical polarization intensity spectrum. In the present article, the radiance model of differential polarization FTIR spectrometry is analysed, and an experiment about detection of No. O diesel and SF96 film on water by this method is presented. The results of this experiment indicate that this method can detect the oil contaminants on water without radiance contrast with clean water, and it also can identify oil spills by analysing the spectral characteristic of differential polarization FTIR spectrum. So it well makes up for the shortage of traditional thermal remote sensing on detecting oil spills on water.

Detection of Cu2+ in Water Based on Histidine-Gold Labeled Multiwalled Carbon Nanotube Electrochemical Sensor

PubMed Central

Zhu, Rilong; Zhou, Gangqiang; Tang, Fengxia; Wang, Yeyao

2017-01-01

Based on the strong interaction between histidine and copper ions and the signal enhancement effect of gold-labeling carbon nanotubes, an electrochemical sensor is established and used to measure copper ions in river water. In this study the results show that the concentrations of copper ion have well linear relationship with the peak current in the range of 10−11–10−7 mol/L, and the limit of detection is 10−12 mol/L. When using this method to detect copper ions in the Xiangjiang River, the test results are consistent with the atomic absorption method. This study shows that the sensor is convenient to be used in daily monitoring of copper ions in river water. PMID:28408929

Water-Tree Modelling and Detection for Underground Cables

NASA Astrophysics Data System (ADS)

Chen, Qi

In recent years, aging infrastructure has become a major concern for the power industry. Since its inception in early 20th century, the electrical system has been the cornerstone of an industrial society. Stable and uninterrupted delivery of electrical power is now a base necessity for the modern world. As the times march-on, however, the electrical infrastructure ages and there is the inevitable need to renew and replace the existing system. Unfortunately, due to time and financial constraints, many electrical systems today are forced to operate beyond their original design and power utilities must find ways to prolong the lifespan of older equipment. Thus, the concept of preventative maintenance arises. Preventative maintenance allows old equipment to operate longer and at better efficiency, but in order to implement preventative maintenance, the operators must know minute details of the electrical system, especially some of the harder to assess issues such water-tree. Water-tree induced insulation degradation is a problem typically associated with older cable systems. It is a very high impedance phenomenon and it is difficult to detect using traditional methods such as Tan-Delta or Partial Discharge. The proposed dissertation studies water-tree development in underground cables, potential methods to detect water-tree location and water-tree severity estimation. The dissertation begins by developing mathematical models of water-tree using finite element analysis. The method focuses on surface-originated vented tree, the most prominent type of water-tree fault in the field. Using the standard operation parameters of North American electrical systems, the water-tree boundary conditions are defined. By applying finite element analysis technique, the complex water-tree structure is broken down to homogeneous components. The result is a generalized representation of water-tree capacitance at different stages of development. The result from the finite element analysis

NAA-modified DNA oligonucleotides with zwitterionic backbones: stereoselective synthesis of A-T phosphoramidite building blocks.

PubMed

Schmidtgall, Boris; Höbartner, Claudia; Ducho, Christian

2015-01-01

Modifications of the nucleic acid backbone are essential for the development of oligonucleotide-derived bioactive agents. The NAA-modification represents a novel artificial internucleotide linkage which enables the site-specific introduction of positive charges into the otherwise polyanionic backbone of DNA oligonucleotides. Following initial studies with the introduction of the NAA-linkage at T-T sites, it is now envisioned to prepare NAA-modified oligonucleotides bearing the modification at X-T motifs (X = A, C, G). We have therefore developed the efficient and stereoselective synthesis of NAA-linked 'dimeric' A-T phosphoramidite building blocks for automated DNA synthesis. Both the (S)- and the (R)-configured NAA-motifs were constructed with high diastereoselectivities to furnish two different phosphoramidite reagents, which were employed for the solid phase-supported automated synthesis of two NAA-modified DNA oligonucleotides. This represents a significant step to further establish the NAA-linkage as a useful addition to the existing 'toolbox' of backbone modifications for the design of bioactive oligonucleotide analogues.

Electron-impact total ionization cross sections of DNA sugar-phosphate backbone and an additivity principle

NASA Technical Reports Server (NTRS)

Huo, Winifred M.; Dateo, Christopher E.

2005-01-01

The improved binary-encounter dipole (iBED) model [W.M. Huo, Phys. Rev. A64, 042719-1 (2001)l is used to study the total ionization cross sections of the DNA sugar-phosphate backbone by electron impact. Calculations using neutral fragments found that the total ionization cross sections of C3' - and C5', -deoxyribose-phospate, two conformers of the sugar-phosphate backbone, are close to each other. Furthermore, the sum of the ionization cross sections of the separate deoxyribose and phosphate fragments is in close agreement with the C3' - and C5" -deoxyribose-phospate cross sections, differing by less than 10%. The result implies that certain properties of the-DNA, like the total singly ionization cross section, are localized properties and a building-up or additivity principle may apply. This allows us to obtain accurate properties of larger molecular systems built up from the results of smaller subsystem fragments. Calculations are underway using a negatively charged sugar-phosphate backbone with a metal counter-ion.

Detection of Social Interaction in Smart Spaces.

PubMed

Cook, Diane J; Crandall, Aaron; Singla, Geetika; Thomas, Brian

2010-02-01

The pervasive sensing technologies found in smart environments offer unprecedented opportunities for monitoring and assisting the individuals who live and work in these spaces. An aspect of daily life that is important for one's emotional and physical health is social interaction. In this paper we investigate the use of smart environment technologies to detect and analyze interactions in smart spaces. We introduce techniques for collect and analyzing sensor information in smart environments to help in interpreting resident behavior patterns and determining when multiple residents are interacting. The effectiveness of our techniques is evaluated using two physical smart environment testbeds.

Detection of Social Interaction in Smart Spaces

PubMed Central

Cook, Diane J.; Crandall, Aaron; Singla, Geetika; Thomas, Brian

2010-01-01

The pervasive sensing technologies found in smart environments offer unprecedented opportunities for monitoring and assisting the individuals who live and work in these spaces. An aspect of daily life that is important for one's emotional and physical health is social interaction. In this paper we investigate the use of smart environment technologies to detect and analyze interactions in smart spaces. We introduce techniques for collect and analyzing sensor information in smart environments to help in interpreting resident behavior patterns and determining when multiple residents are interacting. The effectiveness of our techniques is evaluated using two physical smart environment testbeds. PMID:20953347

Hexagonal boron nitride and water interaction parameters

DOE Office of Scientific and Technical Information (OSTI.GOV)

Wu, Yanbin; Aluru, Narayana R., E-mail: aluru@illinois.edu; Wagner, Lucas K.

2016-04-28

The study of hexagonal boron nitride (hBN) in microfluidic and nanofluidic applications at the atomic level requires accurate force field parameters to describe the water-hBN interaction. In this work, we begin with benchmark quality first principles quantum Monte Carlo calculations on the interaction energy between water and hBN, which are used to validate random phase approximation (RPA) calculations. We then proceed with RPA to derive force field parameters, which are used to simulate water contact angle on bulk hBN, attaining a value within the experimental uncertainties. This paper demonstrates that end-to-end multiscale modeling, starting at detailed many-body quantum mechanics andmore » ending with macroscopic properties, with the approximations controlled along the way, is feasible for these systems.« less

Reorientation Motion and Preferential Interactions of a Peptide in Denaturants and Osmolyte.

PubMed

Jas, Gouri S; Rentchler, Eric C; Słowicka, Agnieszka M; Hermansen, John R; Johnson, Carey K; Middaugh, C Russell; Kuczera, Krzysztof

2016-03-31

Fluorescence anisotropy decay measurements and all atom molecular dynamics simulations are used to characterize the orientational motion and preferential interaction of a peptide, N-acetyl-tryptophan-amide (NATA) containing two peptide bonds, in aqueous, urea, guanidinium chloride (GdmCl), and proline solution. Anisotropy decay measurements as a function of temperature and concentration showed moderate slowing of reorientations in urea and GdmCl and very strong slowing in proline solution, relative to water. These effects deviate significantly from simple proportionality of peptide tumbling time to solvent viscosity, leading to the investigation of microscopic preferential interaction behavior through molecular dynamics simulations. Examination of the interactions of denaturants and osmolyte with the peptide backbone uncovers the presence of strongest interaction with urea, intermediate with proline, and weakest with GdmCl. In contrast, the strongest preferential solvation of the peptide side chain is by the nonpolar part of the proline zwitterion, followed by urea, and GdmCl. Interestingly, the local density of urea around the side chain is higher, but the GdmCl distribution is more organized. Thus, the computed preferential solvation of the side chain by the denaturants and osmolyte can account for the trend in reorientation rates. Analysis of water structure and its dynamics uncovered underlying differences between urea, GdmCl, and proline. Urea exerted the smallest perturbation of water behavior. GdmCl had a larger effect on water, slowing kinetics and stabilizing interactions. Proline had the largest overall interactions, exhibiting a strong stabilizing effect on both water-water and water-peptide hydrogen bonds. The results for this elementary peptide system demonstrate significant differences in microscopic behavior of the examined solvent environments. For the commonly used denaturants, urea tends to form disorganized local aggregates around the peptide

Semiconducting polymers for gas detection

NASA Technical Reports Server (NTRS)

Byrd, N. R.; Sheratte, M. B.

1975-01-01

Conjugated polyenes, and polyesters containing phthalocyanine in their backbone, were synthesized. These polymers were characterized by chemical analysis, thermogravimetric analysis, spectral analysis, and X-ray diffraction studies for crystallinity, as well as for their film-forming capability and gas/polymer interactions. Most of the polymers were relatively insensitive to water vapor up to 50 percent relative humidity, but the polyester/phthalocyanine (iron) polymer was relatively insensitive up to 100 percent RH. On the other hand, poly(p-dimethylaminophenylacetylene) was too conductive at 100 percent RH. Of the gases tested, the only ones that gave any evidence of interacting with the polymers were SO2, NOx, HCN and NH3. Poly(imidazole)/thiophene responded to each of these gases at all relative humidities, while the other polymers gave varying response, depending upon the RH. Thus, since most of these gases were electron-accepting, the electron-donating character of poly(imidazole)/thiophene substantiates the concept of electronegativity being the operating principle for interaction effects. Of the six polymers prepared, poly(imidazole)/thiophene first showed a very good response to smoldering cotton, but it later became nonresponsive; presumably due to oxidation effects.

A discrete search algorithm for finding the structure of protein backbones and side chains.

PubMed

Sallaume, Silas; Martins, Simone de Lima; Ochi, Luiz Satoru; Da Silva, Warley Gramacho; Lavor, Carlile; Liberti, Leo

2013-01-01

Some information about protein structure can be obtained by using Nuclear Magnetic Resonance (NMR) techniques, but they provide only a sparse set of distances between atoms in a protein. The Molecular Distance Geometry Problem (MDGP) consists in determining the three-dimensional structure of a molecule using a set of known distances between some atoms. Recently, a Branch and Prune (BP) algorithm was proposed to calculate the backbone of a protein, based on a discrete formulation for the MDGP. We present an extension of the BP algorithm that can calculate not only the protein backbone, but the whole three-dimensional structure of proteins.

Interactions between soy protein from water-soluble soy extract and polysaccharides in solutions with polydextrose.

PubMed

Spada, Jordana C; Marczak, Ligia D F; Tessaro, Isabel C; Cardozo, Nilo S M

2015-12-10

This study focuses on the investigation of the interactions between polysaccharides (carrageenan and carboxymethylcellulose--CMC) and soy proteins from the water-soluble soy extract. The influence of pH (2-7) and protein-polysaccharide ratio (5:1-40:1) on the interaction between these polyelectrolytes was investigated in aqueous solutions with 10% of polydextrose and without polydextrose. The studied systems were analyzed in terms of pH-solubility profile of protein, ζ-potential, methylene blue-polysaccharide interactions, differential scanning calorimetry (DSC), Fourier transform infrared spectroscopy (FTIR), and confocal laser scanning microscopy. Although the mixtures of soy extract with both carrageenan and CMC showed dependency on the pH and protein-polysaccharide ratio, they did not present the same behavior. Both polysaccharides modified the pH-solubility profile of the soy protein, shifting the pH range in which the coacervate is formed to a lower pH region with the decrease of the soy extract-polysaccharide ratio. The samples also presented detectable differences regarding to ζ-potential, DSC, FTIR and microscopy analyses. The complex formation was also detected even in a pH range where both biopolymers were net-negatively charged. The changes promoted by the presence of polydextrose were mainly detected by blue-polysaccharide interactions measures and confocal microscopy. Copyright © 2015 Elsevier Ltd. All rights reserved.

Fishing in the Water: Effect of Sampled Water Volume on Environmental DNA-Based Detection of Macroinvertebrates.

PubMed

Mächler, Elvira; Deiner, Kristy; Spahn, Fabienne; Altermatt, Florian

2016-01-05

Accurate detection of organisms is crucial for the effective management of threatened and invasive species because false detections directly affect the implementation of management actions. The use of environmental DNA (eDNA) as a species detection tool is in a rapid development stage; however, concerns about accurate detections using eDNA have been raised. We evaluated the effect of sampled water volume (0.25 to 2 L) on the detection rate for three macroinvertebrate species. Additionally, we tested (depending on the sampled water volume) what amount of total extracted DNA should be screened to reduce uncertainty in detections. We found that all three species were detected in all volumes of water. Surprisingly, however, only one species had a positive relationship between an increased sample volume and an increase in the detection rate. We conclude that the optimal sample volume might depend on the species-habitat combination and should be tested for the system where management actions are warranted. Nevertheless, we minimally recommend sampling water volumes of 1 L and screening at least 14 μL of extracted eDNA for each sample to reduce uncertainty in detections when studying macroinvertebrates in rivers and using our molecular workflow.

Water quality responses to the interaction between surface water and groundwater along the Songhua River, NE China

NASA Astrophysics Data System (ADS)

Teng, Yanguo; Hu, Bin; Zheng, Jieqiong; Wang, Jinsheng; Zhai, Yuanzheng; Zhu, Chen

2018-03-01

Investigation of surface water and groundwater interaction (SW-GW interaction) provides basic information for regional water-resource protection, management, and development. In this survey of a 10-km-wide area along both sides of the Songhua River, northeast China, the hydrogeochemical responses to different SW-GW interactions were studied. Three types of SW-GW interactions were identified—"recharge", "discharge", and "flow-through"—according to the hydraulic connection between the surface water and groundwater. The single factor index, principal component analysis, and hierarchical cluster analysis of the hydrogeochemistry and pollutant data illuminated the hydrogeochemical response to the various SW-GW interactions. Clear SW-GW interactions along the Songhua River were revealed: (1) upstream in the study area, groundwater usually discharges into the surface water, (2) groundwater is recharged by surface water downstream, and (3) discharge and flow-through coexist in between. Statistical analysis indicated that the degree of hydrogeochemical response in different types of hydraulic connection varied, being clear in recharge and flow-through modes, and less obvious in discharge mode. During the interaction process, dilution, adsorption, redox reactions, nitrification, denitrification, and biodegradation contributed to the pollutant concentration and affected hydrogeochemical response in the hyporheic zone.

Water Stress Detection using Temperature, Emissivity, and Reflectance

NASA Astrophysics Data System (ADS)

Gerhards, Max; Rock, Gilles; Schlerf, Martin; Udelhoven, Thomas

2017-04-01

Water stress is one of the most critical abiotic stressors limiting crop development. The main imaging and non-imaging remote sensing based techniques for the detection of plant stress (water stress and other types of stress) are thermography, visible (VIS), near- and shortwave infrared (NIR/SWIR) reflectance, and fluorescence. Just very recently, in addition to broadband thermography, narrowband (hyperspectral) thermal imaging has become available, which even facilitates the retrieval of spectral emissivity as an additional measure of plant stress. It is, however, still unclear at what stage plant stress is detectable with the various techniques. During summer 2014 a water treatment experiment was run on 60 potato plants (Solanum tuberosum L. Cilena) with one half of the plants watered and the other half stressed. Crop response was measured using broadband and hyperspectral thermal cameras and a VNIR/SWIR spectrometer. Stomatal conductance was measured using a leaf porometer. Various measures and indices were computed and analysed for their sensitivity towards water stress (Crop Water Stress Index (CWSI), Moisture Stress Index (MSI), Photochemical Reflectance Index (PRI), and spectral emissivity, amongst others). The results show that water stress as measured through stomatal conductance started on day 2 after watering was stopped. The fastest reacting, i.e., starting on day 7, indices were temperature based measures (e.g., CWSI) and NIR/SWIR reflectance based indices related to plant water content (e.g., MSI). Spectral emissivity reacted equally fast. Contrarily, visual indices (e.g., PRI) either did not respond at all or responded in an inconsistent manner. This experiment shows that pre-visual water stress detection is feasible using indices depicting leaf temperature, leaf water content and spectral emissivity.

Constraining the Energetics of Explosive Lava-Water Interactions

NASA Astrophysics Data System (ADS)

Fitch, E. P.; Fagents, S. A.

2017-12-01

During volcanic eruptions, water, such as groundwater or melted ice or snow, may interact with magma within the conduit during eruption, generating explosions when the heat of the magma causes the water to rapidly turn to steam and expand, resulting in what we call a "phreatomagmatic" eruption. In 2010, the eruption of Eyjafjallajökull volcano in Iceland produced a plume of fine ash, through the interaction between magma and glacial melt water, which resulted in the closure of substantial airspace, ultimately costing a total of almost 5 billion dollars. Although an important area of study, it is difficult to quantify the effect of eternal water on eruption intensity when the gas inside of magma is also expanding and fragmenting the magma. In an attempt to understand the energetics of magma-water interactions, small-scale laboratory experiments have been performed. Explosion energy is found to depend mostly on kinetic energy, which is proportional to dispersal distance, and fragmentation energy, which is proportional to the mean grain size of the ejecta, and the mass percent of ash-sized grains. It is thought that in order to generate heat transfer rates sufficiently rapid to cause explosive detonation, the source melt must be finely fragmented, producing ash-sized grains. Those grains undergo brittle fragmentation due to rapid cooling and weak shock waves generated by the vaporization of superheated water. We take the novel approach of studying explosive interactions between lava and water to obtain additional explosion energy constraints. We identified and analyzed numerous beds of lava-water explosion ejecta of varying explosion energy, and we analyzed the ash-sized grains of these beds in detail. We verified that the mass of ash-sized grains increases with increasing explosion energy, and can form at the interface between lava and water. We found that brittle fragmentation occurs to a greater degree as grain size decreases and that the ash of highly

Theoretical and experimental studies of water interaction in acetate based ionic liquids.

PubMed

Shi, Wei; Damodaran, Krishnan; Nulwala, Hunaid B; Luebke, David R

2012-12-05

Water interactions in 1-ethyl-3-methylimidazolium acetate ([emim][CH(3)COO]) were studied utilizing classical and ab initio simulation methods. The self-diffusivities for water and the ionic liquid (IL) were studied experimentally using pulse field gradient NMR spectroscopy and correlated with computational results. Water forms hydrogen bonding networks with the ionic liquid, and depending on the concentration of water, there are profound effects on the self-diffusivities of the various species. Both simulation and experiments show that the self-diffusivities for species in the water-[emim][CH(3)COO] system exhibit minima at 40-50 mol% water. Water interaction with the [CH(3)COO](-) anion predominates over the water-water and water-cation interactions at most water concentrations. Simulations further indicate that decreasing water-[CH(3)COO](-) interaction will increase the IL and water self-diffusivities. Self-diffusivities in the water-IL systems are dependent upon the cation in a complex way. Water interactions with [P(4444)][CH(3)COO] are reduced compared to [emim][CH(3)COO]. The [P(4444)](+) cation is bulkier than the [emim](+) cation and has a smaller self-diffusivity, but when water was introduced to [P(4444)] [CH(3)COO], the water-[CH(3)COO](-) hydrogen bonding network in the [P(4444)][CH(3)COO] was much smaller than the one observed in [emim][CH(3)COO].

[Interactive patterns detection in family communication with adolescents].

PubMed

Gimeno Collado, Adelina; Anguera Argilaga, M Teresa; Berzosa Sanz, Amparo; Ramírez Ramírez, Luis

2006-11-01

Interactive patterns detection in family communication with adolescents. Nondistant communication is a relevant indicator for family functionality valuation. The goal of this study is to analyze this communication in order to identify specific kinds of leadership, interaction patterns and the relation between verbal and nonverbal elements in communication. The observational design exposed is an idiographic one, punctual and multidimensional, which uses field format as observation instrument. Participants were seven standardized families made up of both ancestors and an adolescent son or daughter. According to the family models analyzed, results show a predominantly democratic communication style in adults with recurrent support expressions. The sequential analysis incorporates only categories from the emitter point of view, and detects relevant sequences which show symmetric interaction between all three family members. Verbal and nonverbal channels provide complementary information. Depending on adolescents' gender different patterns in behaviour can be identified as well.

A Copper(II)-Paddlewheel Metal-Organic Framework with Exceptional Hydrolytic Stability and Selective Adsorption and Detection Ability of Aniline in Water.

PubMed

Chen, Ya; Wang, Bin; Wang, Xiaoqing; Xie, Lin-Hua; Li, Jinping; Xie, Yabo; Li, Jian-Rong

2017-08-16

Copper(II)-paddlewheel-based metal-organic frameworks (CP-MOFs) represent a unique subclass of MOFs with highly predictable porous structures, facile syntheses, and functional open metal sites. However, the lack of high hydrolytic stability is an obstacle for CP-MOFs in many practical applications. In this work, we report a new CP-MOF, [Cu 4 (tdhb)] (BUT-155), which is constructed from a judiciously designed carboxylate ligand with high coordination connectivity (octatopic), abundant hydrophobic substituents (six methyl groups), and substituent constrained geometry (tetrahedral backbone), tdhb 8- [H 8 tdhb = 3,3',5,5'-tetrakis(3,5-dicarboxyphenyl)-2,2',4,4',6,6'-hexamethylbiphenyl)]. BUT-155 shows high porosity with a Brunauer-Emmett-Teller surface area of 2070 m 2 /g. Quite interestingly, this CP-MOF retains its structural integrity after being treated in water for 10 days at room temperature or in boiling water for 24 h. To the best of our knowledge, BUT-155 represents the first CP-MOF that is demonstrated to retain its structural integrity in boiling water. The high hydrolytic stability of BUT-155 allowed us to carry out adsorption studies of water vapor and aqueous organic pollutants on it. Water-vapor adsorption reveals a sigmoidal isotherm and a high uptake (46.7 wt %), which is highly reversible and regenerable. In addition, because of the availability of soft-acid-type open Cu(II) sites, BUT-155 shows a high performance for selective adsorption of soft-base-type aniline over water or phenol, and a naked-eye detectable color change for the MOF sample accompanies this. The adsorption selectivity and high adsorption capacity of aniline in BUT-155 are also well-interpreted by single-crystal structures of the water- and aniline-included phases of BUT-155.

FIND: difFerential chromatin INteractions Detection using a spatial Poisson process

PubMed Central

Chen, Yang; Zhang, Michael Q.

2018-01-01

Polymer-based simulations and experimental studies indicate the existence of a spatial dependency between the adjacent DNA fibers involved in the formation of chromatin loops. However, the existing strategies for detecting differential chromatin interactions assume that the interacting segments are spatially independent from the other segments nearby. To resolve this issue, we developed a new computational method, FIND, which considers the local spatial dependency between interacting loci. FIND uses a spatial Poisson process to detect differential chromatin interactions that show a significant difference in their interaction frequency and the interaction frequency of their neighbors. Simulation and biological data analysis show that FIND outperforms the widely used count-based methods and has a better signal-to-noise ratio. PMID:29440282

Assignment by Negative-Ion Electrospray Tandem Mass Spectrometry of the Tetrasaccharide Backbones of Monosialylated Glycans Released from Bovine Brain Gangliosides

NASA Astrophysics Data System (ADS)

Chai, Wengang; Zhang, Yibing; Mauri, Laura; Ciampa, Maria G.; Mulloy, Barbara; Sonnino, Sandro; Feizi, Ten

2018-05-01

Gangliosides, as plasma membrane-associated sialylated glycolipids, are antigenic structures and they serve as ligands for adhesion proteins of pathogens, for toxins of bacteria, and for endogenous proteins of the host. The detectability by carbohydrate-binding proteins of glycan antigens and ligands on glycolipids can be influenced by the differing lipid moieties. To investigate glycan sequences of gangliosides as recognition structures, we have underway a program of work to develop a "gangliome" microarray consisting of isolated natural gangliosides and neoglycolipids (NGLs) derived from glycans released from them, and each linked to the same lipid molecule for arraying and comparative microarray binding analyses. Here, in the first phase of our studies, we describe a strategy for high-sensitivity assignment of the tetrasaccharide backbones and application to identification of eight of monosialylated glycans released from bovine brain gangliosides. This approach is based on negative-ion electrospray mass spectrometry with collision-induced dissociation (ESI-CID-MS/MS) of the desialylated glycans. Using this strategy, we have the data on backbone regions of four minor components among the monosialo-ganglioside-derived glycans; these are of the ganglio-, lacto-, and neolacto-series.

Direct observation of backbone planarization via side-chain alignment in single bulky-substituted polythiophenes

NASA Astrophysics Data System (ADS)

Raithel, Dominic; Simine, Lena; Pickel, Sebastian; Schötz, Konstantin; Panzer, Fabian; Baderschneider, Sebastian; Schiefer, Daniel; Lohwasser, Ruth; Köhler, Jürgen; Thelakkat, Mukundan; Sommer, Michael; Köhler, Anna; Rossky, Peter J.; Hildner, Richard

2018-03-01

The backbone conformation of conjugated polymers affects, to a large extent, their optical and electronic properties. The usually flexible substituents provide solubility and influence the packing behavior of conjugated polymers in films or in bad solvents. However, the role of the side chains in determining and potentially controlling the backbone conformation, and thus the optical and electronic properties on the single polymer level, is currently under debate. Here, we investigate directly the impact of the side chains by studying the bulky-substituted poly(3-(2,5-dioctylphenyl)thiophene) (PDOPT) and the common poly(3-hexylthiophene) (P3HT), both with a defined molecular weight and high regioregularity, using low-temperature single-chain photoluminescence (PL) spectroscopy and quantum-classical simulations. Surprisingly, the optical transition energy of PDOPT is significantly (˜2,000 cm‑1 or 0.25 eV) red-shifted relative to P3HT despite a higher static and dynamic disorder in the former. We ascribe this red shift to a side-chain induced backbone planarization in PDOPT, supported by temperature-dependent ensemble PL spectroscopy. Our atomistic simulations reveal that the bulkier 2,5-dioctylphenyl side chains of PDOPT adopt a clear secondary helical structural motif and thus protect conjugation, i.e., enforce backbone planarity, whereas, for P3HT, this is not the case. These different degrees of planarity in both thiophenes do not result in different conjugation lengths, which we found to be similar. It is rather the stronger electronic coupling between the repeating units in the more planar PDOPT which gives rise to the observed spectral red shift as well as to a reduced calculated electron‑hole polarization.

Trace Water as Prominent Factor to Induce Peptide Self-Assembly: Dynamic Evolution and Governing Interactions in Ionic Liquids.

PubMed

Wang, Juan; Yuan, Chengqian; Han, Yuchun; Wang, Yilin; Liu, Xiaomin; Zhang, Suojiang; Yan, Xuehai

2017-11-01

The interaction between water and biomolecules including peptides is of critical importance for forming high-level architectures and triggering life's functions. However, the bulk aqueous environment has limitations in detecting the kinetics and mechanisms of peptide self-assembly, especially relating to interactions of trace water. With ionic liquids (ILs) as a nonconventional medium, herein, it is discovered that trace amounts of water play a decisive role in triggering self-assembly of a biologically derived dipeptide. ILs provide a suitable nonaqueous environment, enabling us to mediate water content and follow the dynamic evolution of peptide self-assembly. The trace water is found to be involved in the assembly process of dipeptide, especially leading to the formation of stable noncovalent dipeptide oligomers in the early stage of nucleation, as evident by both experimental studies and theoretical simulations. The thermodynamics of the growth process is mainly governed by a synergistic effect of hydrophobic interaction and hydrogen bonds. Each step of assembly presents a different trend in thermodynamic energy. The dynamic evolution of assembly process can be efficiently mediated by changing trace water content. The decisive role of trace water in triggering and mediating self-assembly of biomolecules provides a new perspective in understanding supramolecular chemistry and molecular self-organization in biology. © 2017 WILEY-VCH Verlag GmbH & Co. KGaA, Weinheim.

Effect of oligonucleic acid (ONA) backbone features on assembly of ONA-star polymer conjugates: a coarse-grained molecular simulation study.

PubMed

Condon, Joshua E; Jayaraman, Arthi

2017-10-04

Understanding the impact of incorporating new physical and chemical features in oligomeric DNA mimics, termed generally as "oligonucleic acids" (ONAs), on their structure and thermodynamics will be beneficial in designing novel materials for a variety of applications. In this work, we conduct coarse-grained molecular simulations of ONA-star polymer conjugates with varying ONA backbone flexibility, ONA backbone charge, and number of arms in the star polymer at a constant ONA strand volume fraction to elucidate the effect of these design parameters on the thermodynamics and assembly of multi-arm ONA-star polymer conjugates. We quantify the thermo-reversible behavior of the ONA-star polymer conjugates by quantifying the hybridization of the ONA strands in the system as a function of temperature (i.e. melting curve). Additionally, we characterize the assembly of the ONA-star polymer conjugates by tracking cluster formation and percolation as a function of temperature, as well as cluster size distribution at temperatures near the assembly transition region. The key results are as follows. The melting temperature (T m ) of the ONA strands decreases upon going from a neutral to a charged ONA backbone and upon increasing flexibility of the ONA backbone. Similar behavior is seen for the assembly transition temperature (T a ) with varying ONA backbone charge and flexibility. While the number of arms in the ONA-star polymer conjugate has a negligible effect on the ONA T m in these systems, as the number of ONA-star polymer arms increase, the assembly temperature T a increases and local ordering in the assembled state improves. By understanding how factors like ONA backbone charge, backbone flexibility, and ONA-star polymer conjugate architecture impact the behavior of ONA-star polymer conjugate systems, we can better inform how the selection of ONA chemistry will influence resulting ONA-star polymer assembly.

Cophylogenetic signal is detectable in pollination interactions across ecological scales.

PubMed

Hutchinson, Matthew C; Cagua, Edgar Fernando; Stouffer, Daniel B

2017-10-01

That evolutionary history can influence the way that species interact is a basic tenet of evolutionary ecology. However, when the role of evolution in determining ecological interactions is investigated, focus typically centers on just one side of the interaction. A cophylogenetic signal, the congruence of evolutionary history across both sides of an ecological interaction, extends these previous explorations and provides a more complete picture of how evolutionary patterns influence the way species interact. To date, cophylogenetic signal has most typically been studied in interactions that occur between fine taxonomic clades that show high intimacy. In this study, we took an alternative approach and made an exhaustive assessment of cophylogeny in pollination interactions. To do so, we assessed the strength of cophylogenetic signal at four distinct scales of pollination interaction: (1) across plant-pollinator associations globally, (2) in local pollination communities, (3) within the modular structure of those communities, and (4) in individual modules. We did so using a globally distributed dataset comprised of 54 pollination networks, over 4000 species, and over 12,000 interactions. Within these data, we detected cophylogenetic signal at all four scales. Cophylogenetic signal was found at the level of plant-pollinator interactions on a global scale and in the majority of pollination communities. At the scale defined by the modular structure within those communities, however, we observed a much weaker cophylogenetic signal. Cophylogenetic signal was detectable in a significant proportion of individual modules and most typically when within-module phylogenetic diversity was low. In sum, the detection of cophylogenetic signal in pollination interactions across scales provides a new dimension to the story of how past evolution shapes extant pollinator-angiosperm interactions. © 2017 by the Ecological Society of America.

Detecting single DNA molecule interactions with optical microcavities (Presentation Recording)

NASA Astrophysics Data System (ADS)

Vollmer, Frank

2015-09-01

Detecting molecules and their interactions lies at the heart of all biosensor devices, which have important applications in health, environmental monitoring and biomedicine. Achieving biosensing capability at the single molecule level is, moreover, a particularly important goal since single molecule biosensors would not only operate at the ultimate detection limit by resolving individual molecular interactions, but they could also monitor biomolecular properties which are otherwise obscured in ensemble measurements. For example, a single molecule biosensor could resolve the fleeting interaction kinetics between a molecule and its receptor, with immediate applications in clinical diagnostics. We have now developed a label-free biosensing platform that is capable of monitoring single DNA molecules and their interaction kinetics[1], hence achieving an unprecedented sensitivity in the optical domain, Figure 1. We resolve the specific contacts between complementary oligonucleotides, thereby detecting DNA strands with less than 2.4 kDa molecular weight. Furthermore we can discern strands with single nucleotide mismatches by monitoring their interaction kinetics. Our device utilizes small glass microspheres as optical transducers[1,2, 3], which are capable of increasing the number of interactions between a light beam and analyte molecules. A prism is used to couple the light beam into the microsphere. Ourr biosensing approach resolves the specific interaction kinetics between single DNA fragments. The optical transducer is assembled in a simple three-step protocol, and consists of a gold nanorod attached to a glass microsphere, where the surface of the nanorod is further modified with oligonucleotide receptors. The interaction kinetics of an oligonucleotide receptor with DNA fragments in the surrounding aqueous solution is monitored at the single molecule level[1]. The light remains confined inside the sphere where it is guided by total internal reflections along a

Real-time detection of laser-GaAs interaction process

NASA Astrophysics Data System (ADS)

Jia, Zhichao; Li, Zewen; Lv, Xueming; Ni, Xiaowu

2017-05-01

A real-time method based on laser scattering technology was used to detect the interaction process of GaAs with a 1080 nm laser. The detector collected the scattered laser beam from the GaAs wafer. The main scattering sources were back surface at first, later turn into front surface and vapor, so scattering signal contained much information of the interaction process. The surface morphologies of GaAs with different irradiation times were observed using an optical microscope to confirm occurrence of various phenomena. The proposed method is shown to be effective for the real-time detection of GaAs. By choosing a proper wavelength, the scattering technology can be promoted in detection of thicker GaAs wafer or other materials.

Using Excel To Study The Relation Between Protein Dihedral Angle Omega And Backbone Length

NASA Astrophysics Data System (ADS)

Shew, Christopher; Evans, Samari; Tao, Xiuping

How to involve the uninitiated undergraduate students in computational biophysics research? We made use of Microsoft Excel to carry out calculations of bond lengths, bond angles and dihedral angles of proteins. Specifically, we studied protein backbone dihedral angle omega by examining how its distribution varies with the length of the backbone length. It turns out Excel is a respectable tool for this task. An ordinary current-day desktop or laptop can handle the calculations for midsized proteins in just seconds. Care has to be taken to enter the formulas for the spreadsheet column after column to minimize the computing load. Supported in part by NSF Grant #1238795.

Detection of Salmonella bacterium in drinking water using microring resonator.

PubMed

Bahadoran, Mahdi; Noorden, Ahmad Fakhrurrazi Ahmad; Mohajer, Faeze Sadat; Abd Mubin, Mohamad Helmi; Chaudhary, Kashif; Jalil, Muhammad Arif; Ali, Jalil; Yupapin, Preecha

2016-01-01

A new microring resonator system is proposed for the detection of the Salmonella bacterium in drinking water, which is made up of SiO2-TiO2 waveguide embedded inside thin film layer of the flagellin. The change in refractive index due to the binding of the Salmonella bacterium with flagellin layer causes a shift in the output signal wavelength and the variation in through and drop port's intensities, which leads to the detection of Salmonella bacterium in drinking water. The sensitivity of proposed sensor for detecting of Salmonella bacterium in water solution is 149 nm/RIU and the limit of detection is 7 × 10(-4)RIU.

An improved DNA force field for ssDNA interactions with gold nanoparticles

DOE Office of Scientific and Technical Information (OSTI.GOV)

Jiang, Xiankai; Huai, Ping; Fan, Chunhai

The widespread applications of single-stranded DNA (ssDNA) conjugated gold nanoparticles (AuNPs) have spurred an increasing interest in the interactions between ssDNA and AuNPs. Despite extensive studies using the most sophisticated experimental techniques, the detailed molecular mechanisms still remain largely unknown. Large scale molecular dynamics (MD) simulations can thus be used to supplement experiments by providing complementary information about ssDNA-AuNP interactions. However, up to now, all modern force fields for DNA were developed based on the properties of double-stranded DNA (dsDNA) molecules, which have hydrophilic outer backbones “protecting” hydrophobic inner nucleobases from water. Without the double-helix structure of dsDNA and thusmore » the “protection” by the outer backbone, the nucleobases of ssDNA are directly exposed to solvent, and their behavior in water is very different from that of dsDNA, especially at the interface with nanoparticles. In this work, we have improved the force field of ssDNA for use with nanoparticles, such as AuNPs, based on recent experimental results and quantum mechanics calculations. With the new improved force field, we demonstrated that a poly(A) sequence adsorbed on a AuNP surface is much more stable than a poly(T) sequence, which is consistent with recent experimental observations. On the contrary, the current standard force fields, including AMBER03, CHARMM27, and OPLSAA, all gave erroneous results as compared to experiments. The current improved force field is expected to have wide applications in the study of ssDNA with nanomaterials including AuNPs, which might help promote the development of ssDNA-based biosensors and other bionano-devices.« less

An improved DNA force field for ssDNA interactions with gold nanoparticles

NASA Astrophysics Data System (ADS)

Jiang, Xiankai; Gao, Jun; Huynh, Tien; Huai, Ping; Fan, Chunhai; Zhou, Ruhong; Song, Bo

2014-06-01

The widespread applications of single-stranded DNA (ssDNA) conjugated gold nanoparticles (AuNPs) have spurred an increasing interest in the interactions between ssDNA and AuNPs. Despite extensive studies using the most sophisticated experimental techniques, the detailed molecular mechanisms still remain largely unknown. Large scale molecular dynamics (MD) simulations can thus be used to supplement experiments by providing complementary information about ssDNA-AuNP interactions. However, up to now, all modern force fields for DNA were developed based on the properties of double-stranded DNA (dsDNA) molecules, which have hydrophilic outer backbones "protecting" hydrophobic inner nucleobases from water. Without the double-helix structure of dsDNA and thus the "protection" by the outer backbone, the nucleobases of ssDNA are directly exposed to solvent, and their behavior in water is very different from that of dsDNA, especially at the interface with nanoparticles. In this work, we have improved the force field of ssDNA for use with nanoparticles, such as AuNPs, based on recent experimental results and quantum mechanics calculations. With the new improved force field, we demonstrated that a poly(A) sequence adsorbed on a AuNP surface is much more stable than a poly(T) sequence, which is consistent with recent experimental observations. On the contrary, the current standard force fields, including AMBER03, CHARMM27, and OPLSAA, all gave erroneous results as compared to experiments. The current improved force field is expected to have wide applications in the study of ssDNA with nanomaterials including AuNPs, which might help promote the development of ssDNA-based biosensors and other bionano-devices.

An improved DNA force field for ssDNA interactions with gold nanoparticles.

PubMed

Jiang, Xiankai; Gao, Jun; Huynh, Tien; Huai, Ping; Fan, Chunhai; Zhou, Ruhong; Song, Bo

2014-06-21

The widespread applications of single-stranded DNA (ssDNA) conjugated gold nanoparticles (AuNPs) have spurred an increasing interest in the interactions between ssDNA and AuNPs. Despite extensive studies using the most sophisticated experimental techniques, the detailed molecular mechanisms still remain largely unknown. Large scale molecular dynamics (MD) simulations can thus be used to supplement experiments by providing complementary information about ssDNA-AuNP interactions. However, up to now, all modern force fields for DNA were developed based on the properties of double-stranded DNA (dsDNA) molecules, which have hydrophilic outer backbones "protecting" hydrophobic inner nucleobases from water. Without the double-helix structure of dsDNA and thus the "protection" by the outer backbone, the nucleobases of ssDNA are directly exposed to solvent, and their behavior in water is very different from that of dsDNA, especially at the interface with nanoparticles. In this work, we have improved the force field of ssDNA for use with nanoparticles, such as AuNPs, based on recent experimental results and quantum mechanics calculations. With the new improved force field, we demonstrated that a poly(A) sequence adsorbed on a AuNP surface is much more stable than a poly(T) sequence, which is consistent with recent experimental observations. On the contrary, the current standard force fields, including AMBER03, CHARMM27, and OPLSAA, all gave erroneous results as compared to experiments. The current improved force field is expected to have wide applications in the study of ssDNA with nanomaterials including AuNPs, which might help promote the development of ssDNA-based biosensors and other bionano-devices.

Direct measurements of the interactions between clathrate hydrate particles and water droplets.

PubMed

Liu, Chenwei; Li, Mingzhong; Zhang, Guodong; Koh, Carolyn A

2015-08-14

Clathrate hydrate particle agglomeration is often considered to be one of the key limiting factors in plug formation. The hydrate particle-water interaction can play a critical role in describing hydrate agglomeration, yet is severely underexplored. Therefore, this work investigates the interactions between water droplets and cyclopentane hydrate particles using a micromechanical force (MMF) apparatus. Specifically, the effect of contact time, temperature/subcooling, contact area, and the addition of Sorbitane monooleate (Span 80) surfactant on the water droplet-hydrate particle interaction behavior are studied. The measurements indicate that hydrate formation during the measurement would increase the water-hydrate interaction force significantly. The results also indicate that the contact time, subcooling and concentration of cyclopentane, which determine the hydrate formation rate and hydrate amount, will affect the hydrate-water interaction force. In addition, the interaction forces also increase with the water-hydrate contact area. The addition of Span 80 surfactant induces a change in the hydrate morphology and renders the interfaces stable versus unstable (leading to coalescence), and the contact force can affect the hydrate-water interaction behavior significantly. Compared with the hydrate-hydrate cohesion force (measured in cyclopentane), the hydrate-water adhesion force is an order of magnitude larger. These new measurements can help to provide new and critical insights into the hydrate agglomeration process and potential strategies to control this process.

75 FR 76742 - Detecting Oil Leaks From Vessels Into the Water

Federal Register 2010, 2011, 2012, 2013, 2014

2010-12-09

... to detect leaks from oil tanks into the water? (E) What is the threshold for detection, accuracy... than leak detection from oil cargo tanks into the water? (H) Are methods or equipment being applied for... DEPARTMENT OF HOMELAND SECURITY Coast Guard [Docket No. USCG-2010-1085] Detecting Oil Leaks From...

Modeling the interactions of phthalocyanines in water: from the Cu(II)-tetrasulphonate to the metal-free phthalocyanine.

PubMed

Martín, Elisa I; Martínez, Jose M; Sánchez Marcos, Enrique

2011-01-14

A quantum and statistical study on the effects of the ions Cu(2+) and SO(3)(-) in the solvent structure around the metal-free phthalocyanine (H(2)Pc) is presented. We developed an ab initio interaction potential for the system CuPc-H(2)O based on quantum chemical calculations and studied its transferability to the H(2)Pc-H(2)O and [CuPc(SO(3))(4)](4-)-H(2)O interactions. The use of the molecular dynamics technique allows the determination of energetic and structural properties of CuPc, H(2)Pc, and [CuPc(SO(3))(4)](4-) in water and the understanding of the keys for the different behaviors of the three phthalocyanine (Pc) derivatives in water. The inclusion of the Cu(2+) cation in the Pc structure reinforces the appearance of two axial water molecules and second-shell water molecules in the solvent structure, whereas the presence of SO(3)(-) anions implies a well defined hydration shell of about eight water molecules around them making the macrocycle soluble in water. Debye-Waller factors for axial water molecules have been obtained in order to examine the potential sensitivity of the extended x-ray absorption fine structure technique to detect the axial water molecules.

Effects of Ignoring Item Interaction on Item Parameter Estimation and Detection of Interacting Items

ERIC Educational Resources Information Center

Chen, Cheng-Te; Wang, Wen-Chung

2007-01-01

This study explores the effects of ignoring item interaction on item parameter estimation and the efficiency of using the local dependence index Q[subscript 3] and the SAS NLMIXED procedure to detect item interaction under the three-parameter logistic model and the generalized partial credit model. Through simulations, it was found that ignoring…

Neglected waterborne parasitic protozoa and their detection in water.

PubMed

Plutzer, Judit; Karanis, Panagiotis

2016-09-15

Outbreak incidents raise the question of whether the less frequent aetiological agents of outbreaks are really less frequent in water. Alternatively, waterborne transmission could be relevant, but the lack of attention and rapid, sensitive methods to recover and detect the exogenous stages in water may keep them under-recognized. High quality information on the prevalence and detection of less frequent waterborne protozoa, such as Cyclospora cayetanensis, Toxoplasma gondii, Isospora belli, Balantidium coli, Blastocystis hominis, Entamoeba histolytica and other free-living amoebae (FLA), are not available. This present paper discusses the detection tools applied for the water surveillance of the neglected waterborne protozoa mentioned above and provides future perspectives. Copyright © 2016 Elsevier Ltd. All rights reserved.

Detecting Dementia Through Interactive Computer Avatars

PubMed Central

Adachi, Hiroyoshi; Ukita, Norimichi; Ikeda, Manabu; Kazui, Hiroaki; Kudo, Takashi; Nakamura, Satoshi

2017-01-01

This paper proposes a new approach to automatically detect dementia. Even though some works have detected dementia from speech and language attributes, most have applied detection using picture descriptions, narratives, and cognitive tasks. In this paper, we propose a new computer avatar with spoken dialog functionalities that produces spoken queries based on the mini-mental state examination, the Wechsler memory scale-revised, and other related neuropsychological questions. We recorded the interactive data of spoken dialogues from 29 participants (14 dementia and 15 healthy controls) and extracted various audiovisual features. We tried to predict dementia using audiovisual features and two machine learning algorithms (support vector machines and logistic regression). Here, we show that the support vector machines outperformed logistic regression, and by using the extracted features they classified the participants into two groups with 0.93 detection performance, as measured by the areas under the receiver operating characteristic curve. We also newly identified some contributing features, e.g., gap before speaking, the variations of fundamental frequency, voice quality, and the ratio of smiling. We concluded that our system has the potential to detect dementia through spoken dialog systems and that the system can assist health care workers. In addition, these findings could help medical personnel detect signs of dementia. PMID:29018636

Interactions between groundwater and surface water: The state of the science

USGS Publications Warehouse

Sophocleous, M.

2002-01-01

The interactions between groundwater and surface water are complex. To understand these interactions in relation to climate, landform, geology, and biotic factors, a sound hydrogeoecological framework is needed. All these aspects are synthesized and exemplified in this overview. In addition, the mechanisms of interactions between groundwater and surface water (GW-SW) as they affect recharge-discharge processes are comprehensively outlined, and the ecological significance and the human impacts of such interactions are emphasized. Surface-water and groundwater ecosystems are viewed as linked components of a hydrologic continuum leading to related sustainability issues. This overview concludes with a discussion of research needs and challenges facting this evolving field. The biogeochemical processes within the upper few centimeters of sediments beneath nearly all surface-water bodies (hyporheic zone) have a profound effect on the chemistry of the water interchange, and here is where most of the recent research has been focusing. However, to advance conceptual and other modeling of GW-SW systems, a broader perspective of such interactions across and between surface-water bodies is needed, including multidimensional analyses, interface hydraulic characterization and spatial variability, site-to-region regionalization approaches, as well as cross-disciplinary collaborations.

The Interaction of Water with Solid Surfaces: Fundamental Aspects Revisited

DOE Office of Scientific and Technical Information (OSTI.GOV)

Henderson, Michael A.

2002-05-01

Water is perhaps the most important and most pervasive chemical on our planet. The influence of water permeates virtually all areas of biochemical, chemical and physical importance, and is especially evident in phenomena occurring at the interfaces of solid surfaces. Since 1987, when Thiel and Madey (TM) published their review titled "The Interaction of Water with Solid Surfaces: Fundamental Aspects" in Surface Science Reports, there has been considerable progress made in further understanding the fundamental interactions of water with solid surfaces. In the decade and a half, the increased capability of surface scientists to probe at the molecular-level has resultedmore » in more detailed information of the properties of water on progressively more complicated materials and under more stringent conditions. This progress in understanding the properties of water on solid surfaces is evident both in areas for which surface science methodology has traditionally been strong (catalysis and electronic materials) and also in new areas not traditionally studied by surface scientists, such as electrochemistry, photoconversion, mineralogy, adhesion, sensors, atmospheric chemistry, and tribology. Researchers in all these fields grapple with very basic questions regarding the interactions of water with solid surfaces, such as how is water adsorbed, what are the chemical and electrostatic forces that constitute the adsorbed layer, how is water thermally or non-thermally activated, and how do coadsorbates influence these properties of water. The attention paid to these and other fundamental questions in the past decade and a half has been immense. In this review, experimental studies published since the TM review are assimilated with those covered by TM to provide a current picture of the fundamental interactions of water with solid surfaces.« less

Modeling decadal timescale interactions between surface water and ground water in the central Everglades, Florida, USA

USGS Publications Warehouse

Harvey, J.W.; Newlin, J.T.; Krupa, S.L.

2006-01-01

Surface-water and ground-water flow are coupled in the central Everglades, although the remoteness of this system has hindered many previous attempts to quantify interactions between surface water and ground water. We modeled flow through a 43,000 ha basin in the central Everglades called Water Conservation Area 2A. The purpose of the model was to quantify recharge and discharge in the basin's vast interior areas. The presence and distribution of tritium in ground water was the principal constraint on the modeling, based on measurements in 25 research wells ranging in depth from 2 to 37 m. In addition to average characteristics of surface-water flow, the model parameters included depth of the layer of 'interactive' ground water that is actively exchanged with surface water, average residence time of interactive ground water, and the associated recharge and discharge fluxes across the wetland ground surface. Results indicated that only a relatively thin (8 m) layer of the 60 m deep surfical aquifer actively exchanges surface water and ground water on a decadal timescale. The calculated storage depth of interactive ground water was 3.1 m after adjustment for the porosity of peat and sandy limestone. Modeling of the tritium data yielded an average residence time of 90 years in interactive ground water, with associated recharge and discharge fluxes equal to 0.01 cm d -1. 3H/3He isotopic ratio measurements (which correct for effects of vertical mixing in the aquifer with deeper, tritium-dead water) were available from several wells, and these indicated an average residence time of 25 years, suggesting that residence time was overestimated using tritium measurements alone. Indeed, both residence time and storage depth would be expected to be overestimated due to vertical mixing. The estimate of recharge and discharge (0.01 cm d-1) that resulted from tritium modeling therefore is still considered reliable, because the ratio of residence time and storage depth (used to

Modeling decadal timescale interactions between surface water and ground water in the central Everglades, Florida, USA

NASA Astrophysics Data System (ADS)

Harvey, Judson W.; Newlin, Jessica T.; Krupa, Steven L.

2006-04-01

Surface-water and ground-water flow are coupled in the central Everglades, although the remoteness of this system has hindered many previous attempts to quantify interactions between surface water and ground water. We modeled flow through a 43,000 ha basin in the central Everglades called Water Conservation Area 2A. The purpose of the model was to quantify recharge and discharge in the basin's vast interior areas. The presence and distribution of tritium in ground water was the principal constraint on the modeling, based on measurements in 25 research wells ranging in depth from 2 to 37 m. In addition to average characteristics of surface-water flow, the model parameters included depth of the layer of 'interactive' ground water that is actively exchanged with surface water, average residence time of interactive ground water, and the associated recharge and discharge fluxes across the wetland ground surface. Results indicated that only a relatively thin (8 m) layer of the 60 m deep surfical aquifer actively exchanges surface water and ground water on a decadal timescale. The calculated storage depth of interactive ground water was 3.1 m after adjustment for the porosity of peat and sandy limestone. Modeling of the tritium data yielded an average residence time of 90 years in interactive ground water, with associated recharge and discharge fluxes equal to 0.01 cm d -1. 3H/ 3He isotopic ratio measurements (which correct for effects of vertical mixing in the aquifer with deeper, tritium-dead water) were available from several wells, and these indicated an average residence time of 25 years, suggesting that residence time was overestimated using tritium measurements alone. Indeed, both residence time and storage depth would be expected to be overestimated due to vertical mixing. The estimate of recharge and discharge (0.01 cm d -1) that resulted from tritium modeling therefore is still considered reliable, because the ratio of residence time and storage depth (used to

Interactions between biochar and mycorrhizal fungi in a water-stressed agricultural soil.

PubMed

Mickan, Bede S; Abbott, Lynette K; Stefanova, Katia; Solaiman, Zakaria M

2016-08-01

Biochar may alleviate plant water stress in association with arbuscular mycorrhizal (AM) fungi but research has not been conclusive. Therefore, a glasshouse experiment was conducted to understand how interactions between AM fungi and plants respond to biochar application under water-stressed conditions. A twin chamber pot system was used to determine whether a woody biochar increased root colonisation by a natural AM fungal population in a pasture soil ('field' chamber) and whether this was associated with increased growth of extraradical AM fungal hyphae detected by plants growing in an adjacent ('bait') chamber containing irradiated soil. The two chambers were separated by a mesh that excluded roots. Subterranean clover was grown with and without water stress and harvested after 35, 49 and 63 days from each chamber. When biochar was applied to the field chamber under water-stressed conditions, shoot mass increased in parallel with mycorrhizal colonisation, extraradical hyphal length and shoot phosphorus concentration. AM fungal colonisation of roots in the bait chamber indicated an increase in extraradical mycorrhizal hyphae in the field chamber. Biochar had little effect on AM fungi or plant growth under well-watered conditions. The biochar-induced increase in mycorrhizal colonisation was associated with increased growth of extraradical AM fungal hyphae in the pasture soil under water-stressed conditions.

Protein-lipid interactions at the air/water interface.

PubMed

Lad, Mitaben D; Birembaut, Fabrice; Frazier, Richard A; Green, Rebecca J

2005-10-07

Surface pressure measurements and external reflection FTIR spectroscopy have been used to probe protein-lipid interactions at the air/water interface. Spread monomolecular layers of stearic acid and phosphocholine were prepared and held at different compressed phase states prior to the introduction of protein to the buffered subphase. Contrasting interfacial behaviour of the proteins, albumin and lysozyme, was observed and revealed the role of both electrostatic and hydrophobic interactions in protein adsorption. The rate of adsorption of lysozyme to the air/water interface increased dramatically in the presence of stearic acid, due to strong electrostatic interactions between the negatively charged stearic acid head group and lysozyme, whose net charge at pH 7 is positive. Introduction of albumin to the subphase resulted in solubilisation of the stearic acid via the formation of an albumin-stearic acid complex and subsequent adsorption of albumin. This observation held for both human and bovine serum albumin. Protein adsorption to a PC layer held at low surface pressure revealed adsorption rates similar to adsorption to the bare air/water interface and suggested very little interaction between the protein and the lipid. For PC layers in their compressed phase state some adsorption of protein occurred after long adsorption times. Structural changes of both lysozyme and albumin were observed during adsorption, but these were dramatically reduced in the presence of a lipid layer compared to that of adsorption to the pure air/water interface.

Water Stress Impacts Tree-Atmosphere Interaction in the Amazon

NASA Astrophysics Data System (ADS)

van Emmerik, T. H. M.; Steele-Dunne, S. C.; Gentine, P.; Oliveira, R. S.; Van De Giesen, N.

2017-12-01

Land-atmosphere interactions depend on momentum exchange from the atmosphere to the canopy, which depends on the tree drag coefficient. It is known that the drag coefficient, and thus tree-atmosphere interaction, can vary strongly within a canopy. Yet, only few measurements are available to study the variation of tree-atmosphere interaction in time and space, and in response to vegetation water stress. Recent work [1] demonstrated how accelerometers can be used to study tree properties and responses. For this study, accelerometers were used to derive a measure of tree-atmosphere interaction for 19 individual trees of seven different species in the Brazilian Amazon. This study demonstrates that under field conditions, tree-atmosphere interaction can vary considerably in time and space. The five month measurement period included the transitioning from the wet to the dry season. We demonstrate that increased tree water deficit, measured with dendrometers, is related to observed changes in tree-atmosphere interaction, which is hypothesized to be caused by water stress induced changes in tree mass. References [1]. van Emmerik, T.; Steele-Dunne, S.; Hut, R.; Gentine, P.; Guerin, M.; Oliveira, R.S.; Wagner, J.; Selker, J.; van de Giesen, N. Measuring Tree Properties and Responses Using Low-Cost Accelerometers. Sensors 2017, 17, 1098.

Solid polymer battery electrolyte and reactive metal-water battery

DOEpatents

Harrup, Mason K.; Peterson, Eric S.; Stewart, Frederick F.

2000-01-01

In one implementation, a reactive metal-water battery includes an anode comprising a metal in atomic or alloy form selected from the group consisting of periodic table Group 1A metals, periodic table Group 2A metals and mixtures thereof. The battery includes a cathode comprising water. Such also includes a solid polymer electrolyte comprising a polyphosphazene comprising ligands bonded with a phosphazene polymer backbone. The ligands comprise an aromatic ring containing hydrophobic portion and a metal ion carrier portion. The metal ion carrier portion is bonded at one location with the polymer backbone and at another location with the aromatic ring containing hydrophobic portion. The invention also contemplates such solid polymer electrolytes use in reactive metal/water batteries, and in any other battery.

Daytime Water Detection by Fusing Multiple Cues for Autonomous Off-Road Navigation

NASA Technical Reports Server (NTRS)

Rankin, A. L.; Matthies, L. H.; Huertas, A.

2004-01-01

Detecting water hazards is a significant challenge to unmanned ground vehicle autonomous off-road navigation. This paper focuses on detecting the presence of water during the daytime using color cameras. A multi-cue approach is taken. Evidence of the presence of water is generated from color, texture, and the detection of reflections in stereo range data. A rule base for fusing water cues was developed by evaluating detection results from an extensive archive of data collection imagery containing water. This software has been implemented into a run-time passive perception subsystem and tested thus far under Linux on a Pentium based processor.

Universal scaling of potential energy functions describing intermolecular interactions. II. The halide-water and alkali metal-water interactions

DOE Office of Scientific and Technical Information (OSTI.GOV)

Werhahn, Jasper C.; Akase, Dai; Xantheas, Sotiris S.

2014-08-14

The scaled versions of the newly introduced [S. S. Xantheas and J. C. Werhahn, J. Chem. Phys.141, 064117 (2014)] generalized forms of some popular potential energy functions (PEFs) describing intermolecular interactions – Mie, Lennard-Jones, Morse, and Buckingham exponential-6 – have been used to fit the ab initio relaxed approach paths and fixed approach paths for the halide-water, X -(H 2O), X = F, Cl, Br, I, and alkali metal-water, M +(H 2O), M = Li, Na, K, Rb, Cs, interactions. The generalized forms of those PEFs have an additional parameter with respect to the original forms and produce fits tomore » the ab initio data that are between one and two orders of magnitude better in the χ 2 than the original PEFs. They were found to describe both the long-range, minimum and repulsive wall of the respective potential energy surfaces quite accurately. Overall the 4-parameter extended Morse (eM) and generalized Buckingham exponential-6 (gBe-6) potentials were found to best fit the ab initio data for these two classes of ion-water interactions. Finally, the fitted values of the parameter of the (eM) and (gBe-6) PEFs that control the repulsive wall of the potential correlate remarkably well with the ionic radii of the halide and alkali metal ions.« less

Generation of Marker- and/or Backbone-Free Transgenic Wheat Plants via Agrobacterium-Mediated Transformation.

PubMed

Wang, Gen-Ping; Yu, Xiu-Dao; Sun, Yong-Wei; Jones, Huw D; Xia, Lan-Qin

2016-01-01

Horizontal transfer of antibiotic resistance genes to animals and vertical transfer of herbicide resistance genes to the weedy relatives are perceived as major biosafety concerns in genetically modified (GM) crops. In this study, five novel vectors which used gusA and bar as a reporter gene and a selection marker gene, respectively, were constructed based on the pCLEAN dual binary vector system. Among these vectors, 1G7B and 5G7B carried two T-DNAs located on two respective plasmids with 5G7B possessing an additional virGwt gene. 5LBTG154 and 5TGTB154 carried two T-DNAs in the target plasmid with either one or double right borders, and 5BTG154 carried the selectable marker gene on the backbone outside of the T-DNA left border in the target plasmid. In addition, 5BTG154, 5LBTG154, and 5TGTB154 used pAL154 as a helper plasmid which contains Komari fragment to facilitate transformation. These five dual binary vector combinations were transformed into Agrobacterium strain AGL1 and used to transform durum wheat cv Stewart 63. Evaluation of the co-transformation efficiencies, the frequencies of marker-free transgenic plants, and integration of backbone sequences in the obtained transgenic lines indicated that two vectors (5G7B and 5TGTB154) were more efficient in generating marker-free transgenic wheat plants with no or minimal integration of backbone sequences in the wheat genome. The vector series developed in this study for generation of marker- and/or backbone-free transgenic wheat plants via Agrobacterium -mediated transformation will be useful to facilitate the creation of "clean" GM wheat containing only the foreign genes of agronomic importance.

Human interactions with ground-water

USGS Publications Warehouse

Zaporozec, A.

1983-01-01

Ground-Water could be considered as an immense reservoir, from which only a certain amount of water can be withdrawn without affecting the quantity and quality of water. This amount is determined by the characteristics of the environment in which ground-water occurs and by the interactions of ground-water with precipitation, surface water, and people. It should be recognized that quantity and quality of ground-water are intimately related and should be considered accordingly. Quantity refers to usable water and water is usable for any specific purpose only so long as its quality has not deteriorated beyond acceptable limits. Thus an overall quantitative and qualitative management of ground water is inevitable, and its should also involve the uses of ground-water reservoirs for purposes other than water supply. The main objective of ground-water management is to ensure that ground-water resources will be available in appropriate time and in appropriate quantity and quality to meet the most important demands of our society. Traditional, and obvious uses of ground-water are the extraction of water for water supplies (domestic, municipal, agricultural, and industrial) and the natural discharge feeding lakes and maintaining base flow of streams. Not so obvious are the uses of ground-water reservoirs, the very framework within which ground-water occurs and moves, and in which other fluids or materials can be stored. In the last two decades, ground-water reservoirs have been intensively considered for many other purposes than water supplies. Diversified and very often conflicting uses need to be evaluated and dealt with in the most efficient way in order to determine the importance of each possible use, and to assign priorities of these uses. With rising competition for the use of ground-water reservoirs, we will also need to increase the potential for effective planning of ground-water development and protection. Man's development and use of ground-water necessarily

Ultrasensitive molecular detection using thermal conductance of a hydrophobic gold-water interface.

PubMed

Green, Andrew J; Alaulamie, Arwa A; Baral, Susil; Richardson, Hugh H

2013-09-11

The thermal conductance from a hydrophobic gold aqueous interface is measured with increasing solute concentration. A small amount of aqueous solute molecules (1 solute molecule in 550 water molecules) dramatically increases the heat dissipation into the surrounding liquid. This result is consistent with a thermal conductance that is limited by an interface interaction where minority aqueous components significantly alter the surface properties and heat transport through the interface. The increase in heat dissipation can be used to make an extremely sensitive molecular detector that can be scaled to give single molecule detection without amplification or utilizing fluorescence labels.

Rapid detection of bacteria in drinking water and water contamination case studies

NASA Astrophysics Data System (ADS)

Deininger, Rolf A.; Lee, Jiyoung; Clark, Robert M.

2011-12-01

Water systems are inherently vulnerable to physical, chemical and biologic threats that might compromise a systems' ability to reliably deliver safe water. The ability of a water supply to provide water to its customers can be compromised by destroying or disrupting key physical elements of the water system. However, contamination is generally viewed as the most serious potential terrorist threat to water systems. Chemical or biologic agents could spread throughout a distribution system and result in sickness or death among the consumers and for some agents the presence of the contaminant might not be known until emergency rooms report an increase in patients with a particular set of symptoms. Even without serious health impacts, just the knowledge that a water system had been breached could seriously undermine consumer confidence in public water supplies. Therefore, the ability to rapidly detect contamination, especially microbiological contamination, is highly desirable. The authors summarize water contamination case studies and discuss a technique for identifying microbiological contamination based on ATP bioluminescence. This assay allows an estimation of bacterial populations within minutes and can be applied using a local platform. Previous ATP-based methods requires one hour, one liter of water, and has a sensitivity of 100000 cells for detection. The improved method discussed here is 100 times more sensitive, requires one-hundredth of the sample volume, and is over 10 times faster than standard method. This technique has a great deal of potential for application in situations in which a water system has been compromised.

FIND: difFerential chromatin INteractions Detection using a spatial Poisson process.

PubMed

Djekidel, Mohamed Nadhir; Chen, Yang; Zhang, Michael Q

2018-02-12

Polymer-based simulations and experimental studies indicate the existence of a spatial dependency between the adjacent DNA fibers involved in the formation of chromatin loops. However, the existing strategies for detecting differential chromatin interactions assume that the interacting segments are spatially independent from the other segments nearby. To resolve this issue, we developed a new computational method, FIND, which considers the local spatial dependency between interacting loci. FIND uses a spatial Poisson process to detect differential chromatin interactions that show a significant difference in their interaction frequency and the interaction frequency of their neighbors. Simulation and biological data analysis show that FIND outperforms the widely used count-based methods and has a better signal-to-noise ratio. © 2018 Djekidel et al.; Published by Cold Spring Harbor Laboratory Press.

Electrostatic interaction based approach to thrombin detection by surface-enhanced Raman spectroscopy.

PubMed

Hu, Juan; Zheng, Peng-Cheng; Jiang, Jian-Hui; Shen, Guo-Li; Yu, Ru-Qin; Liu, Guo-Kun

2009-01-01

We have developed an electrostatic interaction based biosensor for thrombin detection using surface-enhanced Raman spectroscopy (SERS). This method utilized the electrostatic interaction between capture (thrombin aptamer) and probe (crystal violet, CV) molecules. The specific interaction between thrombin and aptamer could weaken the electrostatic barrier effect from the negative charged aptamer SAMs to the diffusion process of the positively charged CV from the bulk solution to the Au nanoparticle surface. Therefore, the more the bound thrombin, the more the CV molecules near the Au nanoparticle surface and the stronger the observed Raman signal of CV, provided the Raman detections were set at the same time point for each case. This procedure presented a highly specific selectivity and a linear detection of thrombin in the range from 0.1 nM to 10 nM with a detection limit of about 20 pM and realized the thrombin detection in human blood serum solution directly. The electrostatic interaction based technique provides an easy and fast-responding optical platform for a "signal-on" detection of proteins, which might be applicable for the real time assay of proteins.

Evolution of functional nucleic acids in the presence of nonheritable backbone heterogeneity.

PubMed

Trevino, Simon G; Zhang, Na; Elenko, Mark P; Lupták, Andrej; Szostak, Jack W

2011-08-16

Multiple lines of evidence support the hypothesis that the early evolution of life was dominated by RNA, which can both transfer information from generation to generation through replication directed by base-pairing, and carry out biochemical activities by folding into functional structures. To understand how life emerged from prebiotic chemistry we must therefore explain the steps that led to the emergence of the RNA world, and in particular, the synthesis of RNA. The generation of pools of highly pure ribonucleotides on the early Earth seems unlikely, but the presence of alternative nucleotides would support the assembly of nucleic acid polymers containing nonheritable backbone heterogeneity. We suggest that homogeneous monomers might not have been necessary if populations of heterogeneous nucleic acid molecules could evolve reproducible function. For such evolution to be possible, function would have to be maintained despite the repeated scrambling of backbone chemistry from generation to generation. We have tested this possibility in a simplified model system, by using a T7 RNA polymerase variant capable of transcribing nucleic acids that contain an approximately 11 mixture of deoxy- and ribonucleotides. We readily isolated nucleotide-binding aptamers by utilizing an in vitro selection process that shuffles the order of deoxy- and ribonucleotides in each round. We describe two such RNA/DNA mosaic nucleic acid aptamers that specifically bind ATP and GTP, respectively. We conclude that nonheritable variations in nucleic acid backbone structure may not have posed an insurmountable barrier to the emergence of functionality in early nucleic acids.

Exposing hidden alternative backbone conformations in X-ray crystallography using qFit

DOE PAGES

Keedy, Daniel A.; Fraser, James S.; van den Bedem, Henry; ...

2015-10-27

Proteins must move between different conformations of their native ensemble to perform their functions. Crystal structures obtained from high-resolution X-ray diffraction data reflect this heterogeneity as a spatial and temporal conformational average. Although movement between natively populated alternative conformations can be critical for characterizing molecular mechanisms, it is challenging to identify these conformations within electron density maps. Alternative side chain conformations are generally well separated into distinct rotameric conformations, but alternative backbone conformations can overlap at several atomic positions. Our model building program qFit uses mixed integer quadratic programming (MIQP) to evaluate an extremely large number of combinations of sidechainmore » conformers and backbone fragments to locally explain the electron density. Here, we describe two major modeling enhancements to qFit: peptide flips and alternative glycine conformations. We find that peptide flips fall into four stereotypical clusters and are enriched in glycine residues at the n+1 position. The potential for insights uncovered by new peptide flips and glycine conformations is exemplified by HIV protease, where different inhibitors are associated with peptide flips in the “flap” regions adjacent to the inhibitor binding site. Our results paint a picture of peptide flips as conformational switches, often enabled by glycine flexibility, that result in dramatic local rearrangements. Our results furthermore demonstrate the power of large-scale computational analysis to provide new insights into conformational heterogeneity. Furthermore, improved modeling of backbone heterogeneity with high-resolution X-ray data will connect dynamics to the structure-function relationship and help drive new design strategies for inhibitors of biomedically important systems.« less

Water in Massive protostellar objects: first detection of THz water maser and water inner abundance.

NASA Astrophysics Data System (ADS)

Herpin, Fabrice

2014-10-01

The formation massive stars is still not well understood. Despite numerous water line observations with Herschel telescope, over a broad range of energies, in most of the observed sources the WISH-KP (Water In Star-forming regions with Herschel, Co-PI: F. Herpin) observations were not able to trace the emission from the hot core. Moreover, water maser model predict that several THz water maser should be detectable in these objects. We aim to detect for the first time the THz maser lines o-H2O 8(2,7)- 7(3,4) at 1296.41106 GHz and p-H2O 7(2,6)- 6(3,3) at 1440.78167 GHz as predicted by the model. We propose two sources for a northern flight as first priority and two other sources for a possible southern flight. This will 1) constrain the maser theory, 2) constrain the physical conditions and water abundance in the inner layers of the prostellar environnement. In addition, we will use the p-H2O 3(3,1)- 4(0,4) thermal line at 1893.68651 GHz (L2 channel) in order to probe the physical conditions and water abundance in the inner layers of the prostellar objects where HIFI-Herschel has partially failed.

Further optimization of a hybrid united-atom and coarse-grained force field for folding simulations: Improved backbone hydration and interactions between charged side chains

PubMed Central

Han, Wei; Schulten, Klaus

2012-01-01

PACE, a hybrid force field which couples united-atom protein models with coarse-grained (CG) solvent, has been further optimized, aiming to improve itse ciency for folding simulations. Backbone hydration parameters have been re-optimized based on hydration free energies of polyalanyl peptides through atomistic simulations. Also, atomistic partial charges from all-atom force fields were combined with PACE in order to provide a more realistic description of interactions between charged groups. Using replica exchange molecular dynamics (REMD), ab initio folding using the new PACE has been achieved for seven small proteins (16 – 23 residues) with different structural motifs. Experimental data about folded states, such as their stability at room temperature, melting point and NMR NOE constraints, were also well reproduced. Moreover, a systematic comparison of folding kinetics at room temperature has been made with experiments, through standard MD simulations, showing that the new PACE may speed up the actual folding kinetics 5-10 times. Together with the computational speedup benefited from coarse-graining, the force field provides opportunities to study folding mechanisms. In particular, we used the new PACE to fold a 73-residue protein, 3D, in multiple 10 – 30 μs simulations, to its native states (Cα RMSD ~ 0.34 nm). Our results suggest the potential applicability of the new PACE for the study of folding and dynamics of proteins. PMID:23204949

Goaf water detection using the grounded electrical source airborne transient electromagnetic system

NASA Astrophysics Data System (ADS)

Li, D.; Ji, Y.; Guan, S.; Wu, Y.; Wang, A.

2017-12-01

To detect the geoelectric characteristic of goaf water, the grounded electrical source airborne transient electromagnetic (GREATEM) system (developed by Jilin University, China) is applied to the goaf water detection since its advantages of considerable prospecting depth, lateral resolution and detection efficiency. For the test of GREATEM system in goaf water detection, an experimental survey was conducted at Qinshui coal mine (Shanxi province, China). After data acquisition, noise reduction and inversion, the resistivity profiles of survey area is presented. The results highly agree the investigation information provided by Shanxi Coal Geology Geophysical Surveying Exploration Institute (China), conforming that the GREATEM system is an effective technique for resistivity detection of goaf water.

Optimization of Protein Backbone Dihedral Angles by Means of Hamiltonian Reweighting

PubMed Central

2016-01-01

Molecular dynamics simulations depend critically on the accuracy of the underlying force fields in properly representing biomolecules. Hence, it is crucial to validate the force-field parameter sets in this respect. In the context of the GROMOS force field, this is usually achieved by comparing simulation data to experimental observables for small molecules. In this study, we develop new amino acid backbone dihedral angle potential energy parameters based on the widely used 54A7 parameter set by matching to experimental J values and secondary structure propensity scales. In order to find the most appropriate backbone parameters, close to 100 000 different combinations of parameters have been screened. However, since the sheer number of combinations considered prohibits actual molecular dynamics simulations for each of them, we instead predicted the values for every combination using Hamiltonian reweighting. While the original 54A7 parameter set fails to reproduce the experimental data, we are able to provide parameters that match significantly better. However, to ensure applicability in the context of larger peptides and full proteins, further studies have to be undertaken. PMID:27559757

Characterization of air contaminants formed by the interaction of lava and sea water.

PubMed

Kullman, G J; Jones, W G; Cornwell, R J; Parker, J E

1994-05-01

We made environmental measurements to characterize contaminants generated when basaltic lava from Hawaii's Kilauea volcano enters sea water. This interaction of lava with sea water produces large clouds of mist (LAZE). Island winds occasionally directed the LAZE toward the adjacent village of Kalapana and the Hawaii Volcanos National Park, creating health concerns. Environmental samples were taken to measure airborne concentrations of respirable dust, crystalline silica and other mineral compounds, fibers, trace metals, inorganic acids, and organic and inorganic gases. The LAZE contained quantifiable concentrations of hydrochloric acid (HCl) and hydrofluoric acid (HF); HCl was predominant. HCl and HF concentrations were highest in dense plumes of LAZE near the sea. The HCl concentration at this sampling location averaged 7.1 ppm; this exceeds the current occupational exposure ceiling of 5 ppm. HF was detected in nearly half the samples, but all concentrations were <1 ppm Sulfur dioxide was detected in one of four short-term indicator tube samples at approximately 1.5 ppm. Airborne particulates were composed largely of chloride salts (predominantly sodium chloride). Crystalline silica concentrations were below detectable limits, less than approximately 0.03 mg/m3 of air. Settled dust samples showed a predominance of glass flakes and glass fibers. Airborne fibers were detected at quantifiable levels in 1 of 11 samples. These fibers were composed largely of hydrated calcium sulfate. These findings suggest that individuals should avoid concentrated plumes of LAZE near its origin to prevent over exposure to inorganic acids, specifically HCl.

Evaluation of two methods for direct detection of Fusarium spp. in water.

PubMed

Graça, Mariana G; van der Heijden, Inneke M; Perdigão, Lauro; Taira, Cleison; Costa, Silvia F; Levin, Anna S

2016-04-01

Fusarium is a waterborne fungus that causes severe infections especially in patients with prolonged neutropenia. Traditionally, the detection of Fusarium in water is done by culturing which is difficult and time consuming. A faster method is necessary to prevent exposure of susceptible patients to contaminated water. The objective of this study was to develop a molecular technique for direct detection of Fusarium in water. A direct DNA extraction method from water was developed and coupled to a genus-specific PCR, to detect 3 species of Fusarium (verticillioides, oxysporum and solani). The detection limits were 10 cells/L and 1 cell/L for the molecular and culture methods, respectively. To our knowledge, this is the first method developed to detect Fusarium directly from water. Copyright © 2016 Elsevier B.V. All rights reserved.

Colorimetric detection of uranium in water

DOEpatents

DeVol, Timothy A [Clemson, SC; Hixon, Amy E [Piedmont, SC; DiPrete, David P [Evans, GA

2012-03-13

Disclosed are methods, materials and systems that can be used to determine qualitatively or quantitatively the level of uranium contamination in water samples. Beneficially, disclosed systems are relatively simple and cost-effective. For example, disclosed systems can be utilized by consumers having little or no training in chemical analysis techniques. Methods generally include a concentration step and a complexation step. Uranium concentration can be carried out according to an extraction chromatographic process and complexation can chemically bind uranium with a detectable substance such that the formed substance is visually detectable. Methods can detect uranium contamination down to levels even below the MCL as established by the EPA.

[Detection of protein-protein interactions by FRET and BRET methods].

PubMed

Matoulková, E; Vojtěšek, B

2014-01-01

Nowadays, in vivo protein-protein interaction studies have become preferable detecting meth-ods that enable to show or specify (already known) protein interactions and discover their inhibitors. They also facilitate detection of protein conformational changes and discovery or specification of signaling pathways in living cells. One group of in vivo methods enabling these findings is based on fluorescent resonance energy transfer (FRET) and its bio-luminescent modification (BRET). They are based on visualization of protein-protein interactions via light or enzymatic excitation of fluorescent or bio-luminescent proteins. These methods allow not only protein localization within the cell or its organelles (or small animals) but they also allow us to quantify fluorescent signals and to discover weak or strong interaction partners. In this review, we explain the principles of FRET and BRET, their applications in the characterization of protein-protein interactions and we describe several findings using these two methods that clarify molecular and cellular mechanisms and signals related to cancer biology.

Multiple Interactive Pollutants in Water Quality Trading

NASA Astrophysics Data System (ADS)

Sarang, Amin; Lence, Barbara J.; Shamsai, Abolfazl

2008-10-01

Efficient environmental management calls for the consideration of multiple pollutants, for which two main types of transferable discharge permit (TDP) program have been described: separate permits that manage each pollutant individually in separate markets, with each permit based on the quantity of the pollutant or its environmental effects, and weighted-sum permits that aggregate several pollutants as a single commodity to be traded in a single market. In this paper, we perform a mathematical analysis of TDP programs for multiple pollutants that jointly affect the environment (i.e., interactive pollutants) and demonstrate the practicality of this approach for cost-efficient maintenance of river water quality. For interactive pollutants, the relative weighting factors are functions of the water quality impacts, marginal damage function, and marginal treatment costs at optimality. We derive the optimal set of weighting factors required by this approach for important scenarios for multiple interactive pollutants and propose using an analytical elasticity of substitution function to estimate damage functions for these scenarios. We evaluate the applicability of this approach using a hypothetical example that considers two interactive pollutants. We compare the weighted-sum permit approach for interactive pollutants with individual permit systems and TDP programs for multiple additive pollutants. We conclude by discussing practical considerations and implementation issues that result from the application of weighted-sum permit programs.

The Application of Ligand-Mapping Molecular Dynamics Simulations to the Rational Design of Peptidic Modulators of Protein-Protein Interactions.

PubMed

Tan, Yaw Sing; Spring, David R; Abell, Chris; Verma, Chandra S

2015-07-14

A computational ligand-mapping approach to detect protein surface pockets that interact with hydrophobic moieties is presented. In this method, we incorporated benzene molecules into explicit solvent molecular dynamics simulations of various protein targets. The benzene molecules successfully identified the binding locations of hydrophobic hot-spot residues and all-hydrocarbon cross-links from known peptidic ligands. They also unveiled cryptic binding sites that are occluded by side chains and the protein backbone. Our results demonstrate that ligand-mapping molecular dynamics simulations hold immense promise to guide the rational design of peptidic modulators of protein-protein interactions, including that of stapled peptides, which show promise as an exciting new class of cell-penetrating therapeutic molecules.

Automated optimization of water-water interaction parameters for a coarse-grained model.

PubMed

Fogarty, Joseph C; Chiu, See-Wing; Kirby, Peter; Jakobsson, Eric; Pandit, Sagar A

2014-02-13

We have developed an automated parameter optimization software framework (ParOpt) that implements the Nelder-Mead simplex algorithm and applied it to a coarse-grained polarizable water model. The model employs a tabulated, modified Morse potential with decoupled short- and long-range interactions incorporating four water molecules per interaction site. Polarizability is introduced by the addition of a harmonic angle term defined among three charged points within each bead. The target function for parameter optimization was based on the experimental density, surface tension, electric field permittivity, and diffusion coefficient. The model was validated by comparison of statistical quantities with experimental observation. We found very good performance of the optimization procedure and good agreement of the model with experiment.

RNA Bricks—a database of RNA 3D motifs and their interactions

PubMed Central

Chojnowski, Grzegorz; Waleń, Tomasz; Bujnicki, Janusz M.

2014-01-01

The RNA Bricks database (http://iimcb.genesilico.pl/rnabricks), stores information about recurrent RNA 3D motifs and their interactions, found in experimentally determined RNA structures and in RNA–protein complexes. In contrast to other similar tools (RNA 3D Motif Atlas, RNA Frabase, Rloom) RNA motifs, i.e. ‘RNA bricks’ are presented in the molecular environment, in which they were determined, including RNA, protein, metal ions, water molecules and ligands. All nucleotide residues in RNA bricks are annotated with structural quality scores that describe real-space correlation coefficients with the electron density data (if available), backbone geometry and possible steric conflicts, which can be used to identify poorly modeled residues. The database is also equipped with an algorithm for 3D motif search and comparison. The algorithm compares spatial positions of backbone atoms of the user-provided query structure and of stored RNA motifs, without relying on sequence or secondary structure information. This enables the identification of local structural similarities among evolutionarily related and unrelated RNA molecules. Besides, the search utility enables searching ‘RNA bricks’ according to sequence similarity, and makes it possible to identify motifs with modified ribonucleotide residues at specific positions. PMID:24220091

Capturing non-local interactions by long short-term memory bidirectional recurrent neural networks for improving prediction of protein secondary structure, backbone angles, contact numbers and solvent accessibility.

PubMed

Heffernan, Rhys; Yang, Yuedong; Paliwal, Kuldip; Zhou, Yaoqi

2017-09-15

The accuracy of predicting protein local and global structural properties such as secondary structure and solvent accessible surface area has been stagnant for many years because of the challenge of accounting for non-local interactions between amino acid residues that are close in three-dimensional structural space but far from each other in their sequence positions. All existing machine-learning techniques relied on a sliding window of 10-20 amino acid residues to capture some 'short to intermediate' non-local interactions. Here, we employed Long Short-Term Memory (LSTM) Bidirectional Recurrent Neural Networks (BRNNs) which are capable of capturing long range interactions without using a window. We showed that the application of LSTM-BRNN to the prediction of protein structural properties makes the most significant improvement for residues with the most long-range contacts (|i-j| >19) over a previous window-based, deep-learning method SPIDER2. Capturing long-range interactions allows the accuracy of three-state secondary structure prediction to reach 84% and the correlation coefficient between predicted and actual solvent accessible surface areas to reach 0.80, plus a reduction of 5%, 10%, 5% and 10% in the mean absolute error for backbone ϕ , ψ , θ and τ angles, respectively, from SPIDER2. More significantly, 27% of 182724 40-residue models directly constructed from predicted C α atom-based θ and τ have similar structures to their corresponding native structures (6Å RMSD or less), which is 3% better than models built by ϕ and ψ angles. We expect the method to be useful for assisting protein structure and function prediction. The method is available as a SPIDER3 server and standalone package at http://sparks-lab.org . yaoqi.zhou@griffith.edu.au or yuedong.yang@griffith.edu.au. Supplementary data are available at Bioinformatics online. © The Author (2017). Published by Oxford University Press. All rights reserved. For Permissions, please email

Dynamic ion-ion and water-ion interactions in ion channels.

PubMed Central

Wu, J V

1992-01-01

The dynamic interactions among ions and water molecules in ion channels are treated based on an assumption that ions at binding sites can be knocked off by both transient entering ions and local water molecules. The theory, when applied to a single-site model K+ channel, provides solutions for super- and subsaturations, flux-ratio exponent (n') greater than 1, osmotic streaming current, activity-dependent reversal potentials, and anomalous mole-fraction behavior. The analysis predicts that: (a) the saturation may but, in general, does not follow the Michaelis-Menten relation; (b) streaming current results from imbalanced water-ion knock-off interactions; (c) n' greater than 1 even for single-site channels, but it is unlikely to exceed 1.4 unless the pore is occupied by one or more ion(s); (d) in the calculation involving two permeant ion species with similar radii, the heavier ions show higher affinity; the ion-ion knock-off dissociation from the site is more effective when two interacting ions are identical. Therefore, the "multi-ion behaviors" found in most ion channels are the consequences of dynamic ion-ion and water-ion interactions. The presence of these interactions does not require two or more binding sites in channels. PMID:1376158

Protein- protein interaction detection system using fluorescent protein microdomains

DOEpatents

Waldo, Geoffrey S.; Cabantous, Stephanie

2010-02-23

The invention provides a protein labeling and interaction detection system based on engineered fragments of fluorescent and chromophoric proteins that require fused interacting polypeptides to drive the association of the fragments, and further are soluble and stable, and do not change the solubility of polypeptides to which they are fused. In one embodiment, a test protein X is fused to a sixteen amino acid fragment of GFP (.beta.-strand 10, amino acids 198-214), engineered to not perturb fusion protein solubility. A second test protein Y is fused to a sixteen amino acid fragment of GFP (.beta.-strand 11, amino acids 215-230), engineered to not perturb fusion protein solubility. When X and Y interact, they bring the GFP strands into proximity, and are detected by complementation with a third GFP fragment consisting of GFP amino acids 1-198 (strands 1-9). When GFP strands 10 and 11 are held together by interaction of protein X and Y, they spontaneous association with GFP strands 1-9, resulting in structural complementation, folding, and concomitant GFP fluorescence.

A Classroom Simulation of Water-Rock Interaction for Upper-Level Geochemistry Courses.

ERIC Educational Resources Information Center

Cercone, Karen Rose

1988-01-01

Describes a simple hands-on model of water-rock interaction that can be constructed in the classroom using styrofoam bowls and foil-wrapped candies. This interactive simulation allows students to vary the factors which control water-rock interaction and to obtain immediate results. (Author/CW)

Special features of high-speed interaction of supercavitating solids in water

DOE Office of Scientific and Technical Information (OSTI.GOV)

Ishchenko, Aleksandr, E-mail: ichan@niipmm.tsu.ru; Afanas’eva, Svetlana, E-mail: s.a.afanasyeva@mail.ru; Burkin, Viktor, E-mail: v.v.burkin@mail.ru

Special features of material behavior of a supercavitating projectile are investigated at various initial velocities of entering water on the basis of the developed stress-strain state model with possibility of destruction of solids when moving in water and interacting with various underwater barriers with the use of consistent methodological approach of mechanics of continuous media. The calculation-experimental method was used to study the modes of motion of supercavitating projectiles at sub- and supersonic velocities in water medium after acceleration in the barrelled accelerator, as well as their interaction with barriers. Issues of stabilization of the supercavitating projectile on the initialmore » flight path in water were studied. Microphotographs of state of solids made of various materials, before and after interaction with water, at subsonic and supersonic velocities were presented. Supersonic velocity of the supercavitating projectile motion in water of 1590 m/s was recorded.« less

Special features of high-speed interaction of supercavitating solids in water

NASA Astrophysics Data System (ADS)

Ishchenko, Aleksandr; Akinshin, Ruslan; Afanas'eva, Svetlana; Borisenkov, Igor; Burkin, Viktor; Diachkovskii, Aleksei; Korolkov, Leonid; Moiseev, Dmitrii; Khabibullin, Marat

2016-01-01

Special features of material behavior of a supercavitating projectile are investigated at various initial velocities of entering water on the basis of the developed stress-strain state model with possibility of destruction of solids when moving in water and interacting with various underwater barriers with the use of consistent methodological approach of mechanics of continuous media. The calculation-experimental method was used to study the modes of motion of supercavitating projectiles at sub- and supersonic velocities in water medium after acceleration in the barrelled accelerator, as well as their interaction with barriers. Issues of stabilization of the supercavitating projectile on the initial flight path in water were studied. Microphotographs of state of solids made of various materials, before and after interaction with water, at subsonic and supersonic velocities were presented. Supersonic velocity of the supercavitating projectile motion in water of 1590 m/s was recorded.

Molecular dynamics approach to probe PKCβII-ligand interactions and influence of crystal water molecules on these interactions.

PubMed

Grewal, Baljinder K; Bhat, Jyotsna; Sobhia, Masilamani Elizabeth

2015-01-01

PKCβII is a potential target for therapeutic intervention against pandemic diabetic complications. Present study probes the molecular interactions of PKCβII with its clinically important ligands, viz. ruboxistaurin, enzastaurin and co-crystallized ligand, 2-methyl-1H-indol-3-yl-BIM-1. The essentials of PKCβII-ligand interaction, crystal water-induced alterations in these interactions and key interacting flexible residues are analyzed. Computational methodologies, viz. molecular docking and molecular simulation coupled with molecular mechanics-Poisson-Boltzmann surface area and generalized born surface area (MM-PB[GB]SA) are employed. The structural changes in the presence and absence of crystal water molecules in PKCβII ATP binding site residues, and its interaction with bound ligand, are identified. Difference in interaction of selective and nonselective ligand with ATP binding site residues of PKCβII is reported. The study showed that the nonbonding interactions contribute significantly in PKCβII-ligand binding and presence of crystal water molecules affects the interactions. The findings of present work may integrate the new aspects in the drug design process of PKCβII inhibitors.

Degenerate primer MOB typing of multiresistant clinical isolates of E. coli uncovers new plasmid backbones.

PubMed

Garcillán-Barcia, M Pilar; Ruiz del Castillo, Belén; Alvarado, Andrés; de la Cruz, Fernando; Martínez-Martínez, Luis

2015-01-01

Degenerate Primer MOB Typing is a PCR-based protocol for the classification of γ-proteobacterial transmissible plasmids in five phylogenetic relaxase MOB families. It was applied to a multiresistant E. coli collection, previously characterized by PCR-based replicon-typing, in order to compare both methods. Plasmids from 32 clinical isolates of multiresistant E. coli (19 extended spectrum beta-lactamase producers and 13 non producers) and their transconjugants were analyzed. A total of 95 relaxases were detected, at least one per isolate, underscoring the high potential of these strains for antibiotic-resistance transmission. MOBP12 and MOBF12 plasmids were the most abundant. Most MOB subfamilies detected were present in both subsets of the collection, indicating a shared mobilome among multiresistant E. coli. The plasmid profile obtained by both methods was compared, which provided useful data upon which decisions related to the implementation of detection methods in the clinic could be based. The phylogenetic depth at which replicon and MOB-typing classify plasmids is different. While replicon-typing aims at plasmid replication regions with non-degenerate primers, MOB-typing classifies plasmids into relaxase subfamilies using degenerate primers. As a result, MOB-typing provides a deeper phylogenetic depth than replicon-typing and new plasmid groups are uncovered. Significantly, MOB typing identified 17 plasmids and an integrative and conjugative element, which were not detected by replicon-typing. Four of these backbones were different from previously reported elements. Copyright © 2014 Elsevier Inc. All rights reserved.

Surface-Water and Ground-Water Interactions in the Central Everglades, Florida

USGS Publications Warehouse

Harvey, Judson W.; Newlin, Jessica T.; Krest, James M.; Choi, Jungyill; Nemeth, Eric A.; Krupa, Steven L.

2004-01-01

Recharge and discharge are hydrological processes that cause Everglades surface water to be exchanged for subsurface water in the peat soil and the underlying sand and limestone aquifer. These interactions are thought to be important to water budgets, water quality, and ecology in the Everglades. Nonetheless, relatively few studies of surface water and ground water interactions have been conducted in the Everglades, especially in its vast interior areas. This report is a product of a cooperative investigation conducted by the USGS and the South Florida Water Management District (SFWMD) aimed at developing and testing techniques that would provide reliable estimates of recharge and discharge in interior areas of WCA-2A (Water Conservation Area 2A) and several other sites in the central Everglades. The new techniques quantified flow from surface water to the subsurface (recharge) and the opposite (discharge) using (1) Darcy-flux calculations based on measured vertical gradients in hydraulic head and hydraulic conductivity of peat; (2) modeling transport through peat and decay of the naturally occurring isotopes 224Ra and 223Ra (with half-lives of 4 and 11 days, respectively); and (3) modeling transport and decay of naturally occurring and 'bomb-pulse' tritium (half-life of 12.4 years) in ground water. Advantages and disadvantages of each method for quantifying recharge and discharge were compared. In addition, spatial and temporal variability of recharge and discharge were evaluated and controlling factors identified. A final goal was to develop appropriately simplified (that is, time averaged) expressions of the results that will be useful in addressing a broad range of hydrological and ecological problems in the Everglades. Results were compared with existing information about water budgets from the South Florida Water Management Model (SFWMM), a principal tool used by the South Florida Water Management District to plan many of the hydrological aspects of the

Detecting vapour bubbles in simulations of metastable water

DOE Office of Scientific and Technical Information (OSTI.GOV)

González, Miguel A.; Abascal, Jose L. F.; Valeriani, Chantal, E-mail: christoph.dellago@univie.ac.at, E-mail: cvaleriani@quim.ucm.es

2014-11-14

The investigation of cavitation in metastable liquids with molecular simulations requires an appropriate definition of the volume of the vapour bubble forming within the metastable liquid phase. Commonly used approaches for bubble detection exhibit two significant flaws: first, when applied to water they often identify the voids within the hydrogen bond network as bubbles thus masking the signature of emerging bubbles and, second, they lack thermodynamic consistency. Here, we present two grid-based methods, the M-method and the V-method, to detect bubbles in metastable water specifically designed to address these shortcomings. The M-method incorporates information about neighbouring grid cells to distinguishmore » between liquid- and vapour-like cells, which allows for a very sensitive detection of small bubbles and high spatial resolution of the detected bubbles. The V-method is calibrated such that its estimates for the bubble volume correspond to the average change in system volume and are thus thermodynamically consistent. Both methods are computationally inexpensive such that they can be used in molecular dynamics and Monte Carlo simulations of cavitation. We illustrate them by computing the free energy barrier and the size of the critical bubble for cavitation in water at negative pressure.« less

Interactive-predictive detection of handwritten text blocks

NASA Astrophysics Data System (ADS)

Ramos Terrades, O.; Serrano, N.; Gordó, A.; Valveny, E.; Juan, A.

2010-01-01

A method for text block detection is introduced for old handwritten documents. The proposed method takes advantage of sequential book structure, taking into account layout information from pages previously transcribed. This glance at the past is used to predict the position of text blocks in the current page with the help of conventional layout analysis methods. The method is integrated into the GIDOC prototype: a first attempt to provide integrated support for interactive-predictive page layout analysis, text line detection and handwritten text transcription. Results are given in a transcription task on a 764-page Spanish manuscript from 1891.

Bio-nano interactions detected by nanochannel electrophoresis.

PubMed

Luan, Binquan

2016-08-01

Engineered nanoparticles have been widely used in industry and are present in many consumer products. However, their bio-safeties especially in a long term are largely unknown. Here, a nanochannel-electrophoresis-based method is proposed for detecting the potential bio-nano interactions that may further lead to damages to human health and/or biological environment. Through proof-of-concept molecular dynamics simulations, it was demonstrated that the transport of a protein-nanoparticle complex is very different from that of a protein along. By monitoring the change of ionic currents induced by a transported analyte as well as the transport velocities of the analyte, the complex (with bio-nano interaction) can be clearly distinguished from the protein alone (with no interaction with tested nanoparticles). © 2016 WILEY-VCH Verlag GmbH & Co. KGaA, Weinheim.

The Detection Method of Escherichia coli in Water Resources: A Review

NASA Astrophysics Data System (ADS)

Nurliyana, M. R.; Sahdan, M. Z.; Wibowo, K. M.; Muslihati, A.; Saim, H.; Ahmad, S. A.; Sari, Y.; Mansor, Z.

2018-04-01

This article reviews several approaches for Escherichia coli (E. coli) bacteria detection from conventional methods, emerging method and goes to biosensor-based techniques. Detection and enumeration of E. coli bacteria usually required long duration of time in obtaining the result since laboratory-based approach is normally used in its assessment. It requires 24 hours to 72 hours after sampling to process the culturing samples before results are available. Although faster technique for detecting E. coli in water such as Polymerase Chain Reaction (PCR) and Enzyme-Linked Immunosorbent Assay (ELISA) have been developed, it still required transporting the samples from water resources to the laboratory, high-cost, complicated equipment usage, complex procedures, as well as the requirement of skilled specialist to cope with the complexity which limit their wide spread practice in water quality detection. Recently, development of biosensor device that is easy to perform, portable, highly sensitive and selective becomes indispensable in detecting extremely lower consolidation of pathogenic E. coli bacteria in water samples.

Development of bacteria-based bioassays for arsenic detection in natural waters.

PubMed

Diesel, Elizabeth; Schreiber, Madeline; van der Meer, Jan Roelof

2009-06-01

Arsenic contamination of natural waters is a worldwide concern, as the drinking water supplies for large populations can have high concentrations of arsenic. Traditional techniques to detect arsenic in natural water samples can be costly and time-consuming; therefore, robust and inexpensive methods to detect arsenic in water are highly desirable. Additionally, methods for detecting arsenic in the field have been greatly sought after. This article focuses on the use of bacteria-based assays as an emerging method that is both robust and inexpensive for the detection of arsenic in groundwater both in the field and in the laboratory. The arsenic detection elements in bacteria-based bioassays are biosensor-reporter strains; genetically modified strains of, e.g., Escherichia coli, Bacillus subtilis, Staphylococcus aureus, and Rhodopseudomonas palustris. In response to the presence of arsenic, such bacteria produce a reporter protein, the amount or activity of which is measured in the bioassay. Some of these bacterial biosensor-reporters have been successfully utilized for comparative in-field analyses through the use of simple solution-based assays, but future methods may concentrate on miniaturization using fiberoptics or microfluidics platforms. Additionally, there are other potential emerging bioassays for the detection of arsenic in natural waters including nematodes and clams.

Lifshitz interaction can promote ice growth at water-silica interfaces

NASA Astrophysics Data System (ADS)

Boström, Mathias; Malyi, Oleksandr I.; Parashar, Prachi; Shajesh, K. V.; Thiyam, Priyadarshini; Milton, Kimball A.; Persson, Clas; Parsons, Drew F.; Brevik, Iver

2017-04-01

At air-water interfaces, the Lifshitz interaction by itself does not promote ice growth. On the contrary, we find that the Lifshitz force promotes the growth of an ice film, up to 1-8 nm thickness, near silica-water interfaces at the triple point of water. This is achieved in a system where the combined effect of the retardation and the zero frequency mode influences the short-range interactions at low temperatures, contrary to common understanding. Cancellation between the positive and negative contributions in the Lifshitz spectral function is reversed in silica with high porosity. Our results provide a model for how water freezes on glass and other surfaces.

Time-resolved energy transfer in DNA sequence detection using water-soluble conjugated polymers: the role of electrostatic and hydrophobic interactions.

PubMed

Xu, Qing-Hua; Gaylord, Brent S; Wang, Shu; Bazan, Guillermo C; Moses, Daniel; Heeger, Alan J

2004-08-10

We have investigated the energy transfer processes in DNA sequence detection by using cationic conjugated polymers and peptide nucleic acid (PNA) probes with ultrafast pump-dump-emission spectroscopy. Pump-dump-emission spectroscopy provides femtosecond temporal resolution and high sensitivity and avoids interference from the solvent response. The energy transfer from donor (the conjugated polymer) to acceptor (a fluorescent molecule attached to a PNA terminus) has been time resolved. The results indicate that both electrostatic and hydrophobic interactions contribute to the formation of cationic conjugated polymers/PNA-C/DNA complexes. The two interactions result in two different binding conformations. This picture is supported by the average donor-acceptor separations as estimated from time-resolved and steady-state measurements. Electrostatic interactions dominate at low concentrations and in mixed solvents.

Improving the accuracy of protein stability predictions with multistate design using a variety of backbone ensembles.

PubMed

Davey, James A; Chica, Roberto A

2014-05-01

Multistate computational protein design (MSD) with backbone ensembles approximating conformational flexibility can predict higher quality sequences than single-state design with a single fixed backbone. However, it is currently unclear what characteristics of backbone ensembles are required for the accurate prediction of protein sequence stability. In this study, we aimed to improve the accuracy of protein stability predictions made with MSD by using a variety of backbone ensembles to recapitulate the experimentally measured stability of 85 Streptococcal protein G domain β1 sequences. Ensembles tested here include an NMR ensemble as well as those generated by molecular dynamics (MD) simulations, by Backrub motions, and by PertMin, a new method that we developed involving the perturbation of atomic coordinates followed by energy minimization. MSD with the PertMin ensembles resulted in the most accurate predictions by providing the highest number of stable sequences in the top 25, and by correctly binning sequences as stable or unstable with the highest success rate (≈90%) and the lowest number of false positives. The performance of PertMin ensembles is due to the fact that their members closely resemble the input crystal structure and have low potential energy. Conversely, the NMR ensemble as well as those generated by MD simulations at 500 or 1000 K reduced prediction accuracy due to their low structural similarity to the crystal structure. The ensembles tested herein thus represent on- or off-target models of the native protein fold and could be used in future studies to design for desired properties other than stability. Copyright © 2013 Wiley Periodicals, Inc.

Farm water budgets for semiarid irrigated floodplains of northern New Mexico: characterizing the surface water-groundwater interactions

NASA Astrophysics Data System (ADS)

Gutierrez, K. Y.; Fernald, A.; Ochoa, C. G.; Guldan, S. J.

2013-12-01

KEY WORDS - Hydrology, Water budget, Deep percolation, Surface water-Groundwater interactions. With the recent projections for water scarcity, water balances have become an indispensable water management tool. In irrigated floodplains, deep percolation from irrigation can represent one of the main aquifer recharge sources. A better understanding of surface water and groundwater interactions in irrigated valleys is needed for properly assessing the water balances in these systems and estimating potential aquifer recharge. We conducted a study to quantify the parameters and calculate the water budgets in three flood irrigated hay fields with relatively low, intermediate and, high water availability in northern New Mexico. We monitored different hydrologic parameters including total amount of water applied, change in soil moisture, drainage below the effective root zone, and shallow water level fluctuations in response to irrigation. Evapotranspiration was calculated from weather station data collected in-situ using the Samani-Hargreaves. Previous studies in the region have estimated deep percolation as a residual parameter of the water balance equation. In this study, we used both, the water balance method and actual measurements of deep percolation using passive lysimeters. Preliminary analyses for the three fields show a relatively rapid movement of water through the upper 50 cm of the vadose zone and a quick response of the shallow aquifer under flood irrigation. Further results from this study will provide a better understanding of surface water-groundwater interactions in flood irrigated valleys in northern New Mexico.

Detecting protein-protein interactions using Renilla luciferase fusion proteins.

PubMed

Burbelo, Peter D; Kisailus, Adam E; Peck, Jeremy W

2002-11-01

We have developed a novel system designated the luciferase assay for protein detection (LAPD) to study protein-protein interactions. This method involves two protein fusions, a soluble reporter fusion and a fusion for immobilizing the target protein. The soluble reporter is an N-terminal Renilla luciferase fusion protein that exhibits high Renilla luciferase activity. Crude cleared lysates from transfected Cos1 cells that express the Renilla luciferase fusion protein can be used in binding assays with immobilized target proteins. Following incubation and washing, target-bound Renilla luciferase fusion proteins produce light from the coelenterazine substrate, indicating an interaction between the two proteins of interest. As proof of the principle, we reproduced known, transient protein-protein interactions between the Cdc42 GTPase and its effector proteins. GTPase Renilla fusion proteins produced in Cos1 cells were tested with immobilized recombinant GST-N-WASP and CEP5 effector proteins. Using this assay, we could detect specific interactions of Cdc42 with these effector proteins in approximately 50 min. The specificity of these interactions was demonstrated by showing that they were GTPase-specific and GTP-dependent and not seen with other unrelated target proteins. These results suggest that the LAPD method, which is both rapid and sensitive, may have research and practical applications.

Direct synthesis of hydrogen peroxide from plasma-water interactions

PubMed Central

Liu, Jiandi; He, Bangbang; Chen, Qiang; Li, Junshuai; Xiong, Qing; Yue, Guanghui; Zhang, Xianhui; Yang, Size; Liu, Hai; Liu, Qing Huo

2016-01-01

Hydrogen peroxide (H2O2) is usually considered to be an important reagent in green chemistry since water is the only by-product in H2O2 involved oxidation reactions. Early studies show that direct synthesis of H2O2 by plasma-water interactions is possible, while the factors affecting the H2O2 production in this method remain unclear. Herein, we present a study on the H2O2 synthesis by atmospheric pressure plasma-water interactions. The results indicate that the most important factors for the H2O2 production are the processes taking place at the plasma-water interface, including sputtering, electric field induced hydrated ion emission, and evaporation. The H2O2 production rate reaches ~1200 μmol/h when the liquid cathode is purified water or an aqueous solution of NaCl with an initial conductivity of 10500 μS cm−1. PMID:27917925

Interaction of SO2 with the Surface of a Water Nanodroplet.

PubMed

Zhong, Jie; Zhu, Chongqin; Li, Lei; Richmond, Geraldine L; Francisco, Joseph S; Zeng, Xiao Cheng

2017-11-29

We present a comprehensive computational study of interaction of a SO 2 with water molecules in the gas phase and with the surface of various sized water nanodroplets to investigate the solvation behavior of SO 2 in different atmospheric environments. Born-Oppenheimer molecular dynamics (BOMD) simulation shows that, in the gas phase and at a temperature of 300 K, the dominant interaction between SO 2 and H 2 O is (SO 2 ) S···O (H 2 O) , consistent with previous density-functional theory (DFT) computation at 0 K. However, at the surface of a water nanodroplet, BOMD simulation shows that the hydrogen-bonding interaction of (SO 2 ) O···H (H 2 O) becomes increasingly important with the increase of droplet size, reflecting a marked effect of the water surface on the SO 2 solvation. This conclusion is in good accordance with spectroscopy evidence obtained previously (J. Am. Chem. Soc. 2005, 127, 16806; J. Am. Chem. Soc. 2006, 128, 3256). The prevailing interaction (SO 2 ) O···H (H 2 O) on a large droplet is mainly due to favorable exposure of H atoms of H 2 O at the air-water interface. Indeed, the conversion of the dominant interaction in the gas phase (SO 2 ) S···O (H 2 O) to the dominant interaction on the water nanodroplet (SO 2 ) O···H (H 2 O) may incur effects on the SO 2 chemistry in atmospheric aerosols because the solvation of SO 2 at the water surface can affect the reactive sites and electrophilicity of SO 2 . Hence, the solvation of SO 2 on the aerosol surface may have new implications when studying SO 2 chemistry in the aerosol-containing troposphere.

Backbone degradable multiblock N-(2-hydroxypropyl)methacrylamide copolymer conjugates via reversible addition-fragmentation chain transfer polymerization and thiol-ene coupling reaction.

PubMed

Pan, Huaizhong; Yang, Jiyuan; Kopecková, Pavla; Kopecek, Jindrich

2011-01-10

Telechelic water-soluble HPMA copolymers and HPMA copolymer-doxorubicin (DOX) conjugates have been synthesized by RAFT polymerization mediated by a new bifunctional chain transfer agent (CTA) that contains an enzymatically degradable oligopeptide sequence. Postpolymerization aminolysis followed by chain extension with a bis-maleimide resulted in linear high molecular weight multiblock HPMA copolymer conjugates. These polymers are enzymatically degradable; in addition to releasing the drug (DOX), the degradation of the polymer backbone resulted in products with molecular weights similar to the starting material and below the renal threshold. The new multiblock HPMA copolymers hold potential as new carriers of anticancer drugs.

ADAPTIVE MONITORING TO ENHANCE WATER SENSOR CAPABILITIES FOR CHEMICAL AND BIOLOGICAL CONTAMINANT DETECTION IN DRINKING WATER SYSTEMS

EPA Science Inventory

Optoelectronic and other conventional water quality sensors offer a potential for real-time online detection of chemical and biological contaminants in a drinking water supply and distribution system. The nature of the application requires sensors of detection capabilities at lo...

Antimicrobial Activity of Chitosan Derivatives Containing N-Quaternized Moieties in Its Backbone: A Review

PubMed Central

Martins, Alessandro F.; Facchi, Suelen P.; Follmann, Heveline D. M.; Pereira, Antonio G. B.; Rubira, Adley F.; Muniz, Edvani C.

2014-01-01

Chitosan, which is derived from a deacetylation reaction of chitin, has attractive antimicrobial activity. However, chitosan applications as a biocide are only effective in acidic medium due to its low solubility in neutral and basic conditions. Also, the positive charges carried by the protonated amine groups of chitosan (in acidic conditions) that are the driving force for its solubilization are also associated with its antimicrobial activity. Therefore, chemical modifications of chitosan are required to enhance its solubility and broaden the spectrum of its applications, including as biocide. Quaternization on the nitrogen atom of chitosan is the most used route to render water-soluble chitosan-derivatives, especially at physiological pH conditions. Recent reports in the literature demonstrate that such chitosan-derivatives present excellent antimicrobial activity due to permanent positive charge on nitrogen atoms side-bonded to the polymer backbone. This review presents some relevant work regarding the use of quaternized chitosan-derivatives obtained by different synthetic paths in applications as antimicrobial agents. PMID:25402643

Radiometric Method for the Detection of Coliform Organisms in Water

PubMed Central

Bachrach, Uriel; Bachrach, Zelilah

1974-01-01

A new radiometric method for the detection of coliform bacteria in water has been described. The method is based on the release of 14CO2 from [14C]lactose by bacteria suspended in growth medium and incubated at 37 C. The evolved 14CO2 is trapped by hyamine hydroxide and counted in a liquid scintillation spectrometer. The method permits the detection of 1 to 10 organisms within 6 h of incubation. Coliform bacteria suspended in water for several days recover from starvation and may be quantitated by the proposed method. Bacteria from water samples may also be concentrated by filtration through membrane filters and detected by the radiometric assay. PMID:4605007

Low-cost label-free electrical detection of artificial DNA nanostructures using solution-processed oxide thin-film transistors.

PubMed

Kim, Si Joon; Jung, Joohye; Lee, Keun Woo; Yoon, Doo Hyun; Jung, Tae Soo; Dugasani, Sreekantha Reddy; Park, Sung Ha; Kim, Hyun Jae

2013-11-13

A high-sensitivity, label-free method for detecting deoxyribonucleic acid (DNA) using solution-processed oxide thin-film transistors (TFTs) was developed. Double-crossover (DX) DNA nanostructures with different concentrations of divalent Cu ion (Cu(2+)) were immobilized on an In-Ga-Zn-O (IGZO) back-channel surface, which changed the electrical performance of the IGZO TFTs. The detection mechanism of the IGZO TFT-based DNA biosensor is attributed to electron trapping and electrostatic interactions caused by negatively charged phosphate groups on the DNA backbone. Furthermore, Cu(2+) in DX DNA nanostructures generates a current path when a gate bias is applied. The direct effect on the electrical response implies that solution-processed IGZO TFTs could be used to realize low-cost and high-sensitivity DNA biosensors.

Explosion interaction with water in a tube

NASA Astrophysics Data System (ADS)

Homae, T.; Sugiyama, Y.; Wakabayashi, K.; Matsumura, T.; Nakayama, Y.

2017-02-01

As proposed and legislated in Japan, subsurface magazines have an explosive storage chamber, a horizontal passageway, and a vertical shaft for a vent. The authors found that a small amount of water on the floor of the storage chamber mitigated blast pressure remarkably. The mitigation mechanism has been examined more closely. To examine the effect of water, the present study assesses explosions in a transparent, square cross section, and a straight tube. A high-speed camera used to observe the tube interior. Blast pressure in and around the tube was also measured. Images obtained using the high-speed camera revealed that water inside the tube did not move after the explosion. Differences between cases of tubes without water and with water were unclear. Along with blast pressure measurements, these study results suggest that blast pressure mitigation by water occurs because of interaction between the explosion and the water near the explosion point.

Water Pollution Detection by Reflectance Measurements

NASA Technical Reports Server (NTRS)

Goolsby, A. D.

1971-01-01

Measurement of the intensity of light reflected from various planar liquid surfaces has been performed. The results of this brief study show that the presence of a film of foreign material floating on a reference substrate is easily detected by reflectance measurement if the two liquids possess significantly different refractive indices, for example, oil (n = 1.40) and water (n = 1.33). Additional study of various optical configurations, and the building and testing of a prototype monitoring device revealed that the method is sufficiently practical for application to continuous water quality monitoring.

Machine vision extracted plant movement for early detection of plant water stress.

PubMed

Kacira, M; Ling, P P; Short, T H

2002-01-01

A methodology was established for early, non-contact, and quantitative detection of plant water stress with machine vision extracted plant features. Top-projected canopy area (TPCA) of the plants was extracted from plant images using image-processing techniques. Water stress induced plant movement was decoupled from plant diurnal movement and plant growth using coefficient of relative variation of TPCA (CRV[TPCA)] and was found to be an effective marker for water stress detection. Threshold value of CRV(TPCA) as an indicator of water stress was determined by a parametric approach. The effectiveness of the sensing technique was evaluated against the timing of stress detection by an operator. Results of this study suggested that plant water stress detection using projected canopy area based features of the plants was feasible.

Molecular mechanical studies of DNA flexibility: Coupled backbone torsion angles and base-pair openings

PubMed Central

Keepers, Joe W.; Kollman, Peter A.; Weiner, Paul K.; James, Thomas L.

1982-01-01

Molecular mechanics studies have been carried out on “B-DNA-like” structures of [d(C-G-C-G-A-A-T-T-C-G-C-G)]2 and [d(A)]12·[d(T)]12. Each of the backbone torsion angles (ψ, φ, ω, ω′, φ′) has been “forced” to alternative values from the normal B-DNA values (g+, t, g-, g-, t conformations). Compensating torsion angle changes preserve most of the base stacking energy in the double helix. In a second part of the study, one purine N3-pyrimidine N1 distance at a time has been forced to a value of 6 Å in an attempt to simulate the base opening motions required to rationalize proton exchange data for DNA. When the 6-Å constraint is removed, many of the structures revert to the normal Watson-Crick hydrogen-bonded structure, but a number are trapped in structures ≈5 kcal/mol higher in energy than the starting B-DNA structure. The relative energy of these structures, some of which involve a non-Watson-Crick thymine C2(carbonyl)[unk]adenine 6NH2 hydrogen bond, are qualitatively consistent with the ΔH for a “base pair-open state” suggested by Mandal et al. of 4-6 kcal/mol [Mandal, C., Kallenbach, N. R. & Englander, S. W. (1979) J. Mol. Biol. 135, 391-411]. The picture of DNA flexibility emerging from this study depicts the backbone as undergoing rapid motion between local torsional minima on a nanosecond time scale. Backbone motion is mainly localized within a dinucleoside segment and generally not conformationally coupled along the chain or across the base pairs. Base motions are much smaller in magnitude than backbone motions. Base sliding allows imino N—H exchange, but it is localized, and only a small fraction of the N—H groups is exposed at any one time. Stacking and hydrogen bonding cause a rigid core of bases in the center of the molecule accounting for the hydrodynamic properties of DNA. PMID:6957879

Conjugated-Backbone Effect of Organic Small Molecules for n-Type Thermoelectric Materials with ZT over 0.2.

PubMed

Huang, Dazhen; Yao, Huiying; Cui, Yutao; Zou, Ye; Zhang, Fengjiao; Wang, Chao; Shen, Hongguang; Jin, Wenlong; Zhu, Jia; Diao, Ying; Xu, Wei; Di, Chong-An; Zhu, Daoben

2017-09-20

Conjugated backbones play a fundamental role in determining the electronic properties of organic semiconductors. On the basis of two solution-processable dihydropyrrolo[3,4-c]pyrrole-1,4-diylidenebis(thieno[3,2-b]thiophene) derivatives with aromatic and quinoid structures, we have carried out a systematic study of the relationship between the conjugated-backbone structure and the thermoelectric properties. In particular, a combination of UV-vis-NIR spectra, photoemission spectroscopy, and doping optimization are utilized to probe the interplay between energy levels, chemical doping, and thermoelectric performance. We found that a moderate change in the conjugated backbone leads to varied doping mechanisms and contributes to dramatic changes in the thermoelectric performance. Notably, the chemically doped A-DCV-DPPTT, a small molecule with aromatic structure, exhibits an electrical conductivity of 5.3 S cm -1 and a high power factor (PF 373 K ) up to 236 μW m -1 K -2 , which is 50 times higher than that of Q-DCM-DPPTT with a quinoid structure. More importantly, the low thermal conductivity enables A-DCV-DPPTT to possess a figure of merit (ZT) of 0.23 ± 0.03, which is the highest value reported to date for thermoelectric materials based on organic small molecules. These results demonstrate that the modulation of the conjugated backbone represents a powerful strategy for tuning the electronic structure and mobility of organic semiconductors toward a maximum thermoelectric performance.

Time-resolved energy transfer in DNA sequence detection using water-soluble conjugated polymers: The role of electrostatic and hydrophobic interactions

PubMed Central

Xu, Qing-Hua; Gaylord, Brent S.; Wang, Shu; Bazan, Guillermo C.; Moses, Daniel; Heeger, Alan J.

2004-01-01

We have investigated the energy transfer processes in DNA sequence detection by using cationic conjugated polymers and peptide nucleic acid (PNA) probes with ultrafast pump-dump-emission spectroscopy. Pump-dump-emission spectroscopy provides femtosecond temporal resolution and high sensitivity and avoids interference from the solvent response. The energy transfer from donor (the conjugated polymer) to acceptor (a fluorescent molecule attached to a PNA terminus) has been time resolved. The results indicate that both electrostatic and hydrophobic interactions contribute to the formation of cationic conjugated polymers/PNA-C/DNA complexes. The two interactions result in two different binding conformations. This picture is supported by the average donor–acceptor separations as estimated from time-resolved and steady-state measurements. Electrostatic interactions dominate at low concentrations and in mixed solvents. PMID:15282375

Protein backbone engineering as a strategy to advance foldamers toward the frontier of protein-like tertiary structure.

PubMed

Reinert, Zachary E; Horne, W Seth

2014-11-28

A variety of non-biological structural motifs have been incorporated into the backbone of natural protein sequences. In parallel work, diverse unnatural oligomers of de novo design (termed "foldamers") have been developed that fold in defined ways. In this Perspective article, we survey foundational studies on protein backbone engineering, with a focus on alterations made in the context of complex tertiary folds. We go on to summarize recent work illustrating the potential promise of these methods to provide a general framework for the construction of foldamer mimics of protein tertiary structures.

Low-cost field test kits for arsenic detection in water.

PubMed

Das, Joyati; Sarkar, Priyabrata; Panda, Jigisha; Pal, Priyabrata

2014-01-01

Arsenic, a common contaminant of groundwater, affects human health adversely. According to the World Health Organization (WHO), the maximum recommended contamination level of arsenic in drinking water is 10 μg/L. The purpose of this research was to develop user-friendly kits for detection of arsenic to measure at least up to 10 μg/L in drinking water, so that a preventive measure could be taken. Two different kits for detection of total arsenic in water are reported here. First, the arsenic in drinking water was converted to arsine gas by a strong reducing agent. The arsine produced was then detected by paper strips via generation of color due to reaction with either mercuric bromide (KIT-1) or silver nitrate (KIT-2). These were previously immobilized on the detector strip. The first one gave a yellow color and the second one grey. Both of these kits could detect arsenic contamination within a range of 10 μg/L-250 μg/L. The detection time for both the kits was only 7 min. The kits exhibited excellent performance compared to other kits available in the market with respect to detection time, ease of operation, cost and could be easily handled by a layman. The field trials with these kits gave very satisfactory results. A study on interference revealed that these kits could be used in the presence of 24 common ions present in the arsenic contaminated water. Though the kits were meant for qualitative assay, the results with unknown concentrations of real samples, when compared with atomic absorption spectrophotometer (AAS) were in good agreement as revealed by the t-test.

Electron spin-echo envelope modulation (ESEEM) reveals water and phosphate interactions with the KcsA potassium channel.

PubMed

Cieslak, John A; Focia, Pamela J; Gross, Adrian

2010-02-23

Electron spin-echo envelope modulation (ESEEM) spectroscopy is a well-established technique for the study of naturally occurring paramagnetic metal centers. The technique has been used to study copper complexes, hemes, enzyme mechanisms, micellar water content, and water permeation profiles in membranes, among other applications. In the present study, we combine ESEEM spectroscopy with site-directed spin labeling (SDSL) and X-ray crystallography in order to evaluate the technique's potential as a structural tool to describe the native environment of membrane proteins. Using the KcsA potassium channel as a model system, we demonstrate that deuterium ESEEM can detect water permeation along the lipid-exposed surface of the KcsA outer helix. We further demonstrate that (31)P ESEEM is able to identify channel residues that interact with the phosphate headgroup of the lipid bilayer. In combination with X-ray crystallography, the (31)P data may be used to define the phosphate interaction surface of the protein. The results presented here establish ESEEM as a highly informative technique for SDSL studies of membrane proteins.

Plant Water Stress Detection Using Radar: The Influence Of Water Stress On Leaf Dielectric Properties

NASA Astrophysics Data System (ADS)

van Emmerik, Tim; Steele-Dunne, Susan; Judge, Jasmeet; van de Giesen, Nick

2015-04-01

Recent research on an agricultural maize canopy has demonstrated that leaf water content can change considerably during the day and in response to water stress. Model simulations suggest that these changes have a significant impact on radar backscatter, particularly in times of water stress. Radar is already used for several vegetation and soil monitoring applications, and might be used for water stress detection in agricultural canopies. Radar observations of the land surface are sensitive because it results in two-way attenuation of the reflected signal from the soil surface, and vegetation contributes to total backscatter from the canopy itself. An important driver that determines the impact of vegetation on backscatter is the dielectric constant of the leaves, which is primarily a function of their moisture content. Understanding the effects of water stress on the dynamics of leaf dielectric properties might shed light on how radar can be used to detect vegetation water stress. Previous studies have investigated the dielectric properties of vegetation. However, this has mainly been done using destructive sampling or in-vivo measurements of tree trunks. Unfortunately, few in-vivo measurements of leaf dielectric properties exist. This study presents datasets of in-vivo dielectric measurements of maize leaves, taken during two field experiments. One experiment was done using was done during a period of water stress, the other during a period without. Field measurements revealed a different vertical profile in dielectric properties for the period with and without water stress. During a period of increased water stress, the diurnal dynamics of leaves at different heights responded differently to a decrease in bulk moisture content. This study provides insight in the effect of water stress on leaf dielectric properties and water content, and highlights the potential use of radar for water stress detection in agricultural canopies.

Land Use, Climate, and Water Resources-Global Stages of Interaction.

PubMed

Kaushal, Sujay S; Gold, Arthur J; Mayer, Paul M

2017-10-24

Land use and climate change can accelerate the depletion of freshwater resources that support humans and ecosystem services on a global scale. Here, we briefly review studies from around the world, and highlight those in this special issue. We identify stages that characterize increasing interaction between land use and climate change. During the first stage, hydrologic modifications and the built environment amplify overland flow via processes associated with runoff-dominated ecosystems (e.g., soil compaction, impervious surface cover, drainage, and channelization). During the second stage, changes in water storage impact the capacity of ecosystems to buffer extremes in water quantity and quality (e.g., either losses in snowpack, wetlands, and groundwater recharge or gains in water and nutrient storage behind dams in reservoirs). During the third stage, extremes in water quantity and quality contribute to losses in ecosystem services and water security (e.g., clean drinking water, flood mitigation, and habitat availability). During the final stage, management and restoration strategies attempt to regain lost ecosystem structure, function, and services but need to adapt to climate change. By anticipating the increasing interaction between land use and climate change, intervention points can be identified, and management strategies can be adjusted to improve outcomes for realistic expectations. Overall, global water security cannot be adequately restored without considering an increasing interaction between land use and climate change across progressive stages and our ever-increasing human domination of the water cycle from degradation to ecosystem restoration.

The interaction of caffeine with substituted cyclodextrins in water

NASA Astrophysics Data System (ADS)

Terekhova, I. V.; Kumeev, R. S.; Al'Per, G. A.

2007-07-01

The interaction of caffeine with hydroxypropyl-and methylcyclodextrins in water was studied by the calorimetry, spectroscopy, and solubility methods at 298.15 K. The interaction of caffeine with these cyclodextrins did not result in the formation of stable inclusion complexes and was mostly accompanied by predominantly endothermic effects of particle dehydration. The introduction of substituents and changes in the size of cyclodextrin molecular cavity did not influence the ability of cyclodextrins to form complexes with caffeine. The conclusion was drawn that substituted cyclodextrins could not be used for increasing the solubility of caffeine in water.

Phosphorylation effects on cis/trans isomerization and the backbone conformation of serine-proline motifs: accelerated molecular dynamics analysis.

PubMed

Hamelberg, Donald; Shen, Tongye; McCammon, J Andrew

2005-02-16

The presence of serine/threonine-proline motifs in proteins provides a conformational switching mechanism of the backbone through the cis/trans isomerization of the peptidyl-prolyl (omega) bond. The reversible phosphorylation of the serine/threonine modulates this switching in regulatory proteins to alter signaling and transcription. However, the mechanism is not well understood. This is partly because cis/trans isomerization is a very slow process and, hence, difficult to study. We have used our accelerated molecular dynamics method to study the cis/trans proline isomerization, preferred backbone conformation of a serine-proline motif, and the effects of phosphorylation of the serine residue. We demonstrate that, unlike normal molecular dynamics, the accelerated molecular dynamics allows for the system to escape very easily from the trans isomer to cis isomer, and vice versa. Moreover, for both the unphosphorylated and phosphorylated peptides, the statistical thermodynamic properties are recaptured, and the results are consistent with experimental values. Isomerization of the proline omega bond is shown to be asymmetric and strongly dependent on the psi backbone angle before and after phosphorylation. The rates of escape decrease after phosphorylation. Also, the alpha-helical backbone conformation is more favored after phosphorylation. This accelerated molecular dynamics approach provides a general approach for enhancing the conformational transitions of molecular systems without having prior knowledge of the location of the minima and barriers on the potential-energy landscape.

Noninvasive detection of nanoparticle clustering by water proton NMR

DOE Office of Scientific and Technical Information (OSTI.GOV)

Taraban, Marc B.; Truong, Huy C.; Ilavsky, Jan

It is shown that water proton NMR can detect uncontrolled clustering of inert nanoparticles (NPs) formulated as aqueous suspensions. The clustering of NPs causes the compartmentalization of water molecules, leading to accelerated proton spin de-coherence, and hence, much faster water transverse relaxation rates. The results suggest that water proton NMR can be used to noninvasively inspect NP products by commercial end users and researchers.

On the role of thermal backbone fluctuations in myoglobin ligand gate dynamics.

PubMed

Krokhotin, Andrey; Niemi, Antti J; Peng, Xubiao

2013-05-07

We construct an energy function that describes the crystallographic structure of sperm whale myoglobin backbone. As a model in our construction, we use the Protein Data Bank entry 1ABS that has been measured at liquid helium temperature. Consequently, the thermal B-factor fluctuations are very small, which is an advantage in our construction. The energy function that we utilize resembles that of the discrete nonlinear Schrödinger equation. Likewise, ours supports topological solitons as local minimum energy configurations. We describe the 1ABS backbone in terms of topological solitons with a precision that deviates from 1ABS by an average root-mean-square distance, which is less than the experimentally observed Debye-Waller B-factor fluctuation distance. We then subject the topological multi-soliton solution to extensive numerical heating and cooling experiments, over a very wide range of temperatures. We concentrate in particular to temperatures above 300 K and below the Θ-point unfolding temperature, which is around 348 K. We confirm that the behavior of the topological multi-soliton is fully consistent with Anfinsen's thermodynamic principle, up to very high temperatures. We observe that the structure responds to an increase of temperature consistently in a very similar manner. This enables us to characterize the onset of thermally induced conformational changes in terms of three distinct backbone ligand gates. One of the gates is made of the helix F and the helix E. The two other gates are chosen similarly, when open they provide a direct access route for a ligand to reach the heme. We find that out of the three gates we investigate, the one which is formed by helices B and G is the most sensitive to thermally induced conformational changes. Our approach provides a novel perspective to the important problem of ligand entry and exit.

On the role of thermal backbone fluctuations in myoglobin ligand gate dynamics

NASA Astrophysics Data System (ADS)

Krokhotin, Andrey; Niemi, Antti J.; Peng, Xubiao

2013-05-01

We construct an energy function that describes the crystallographic structure of sperm whale myoglobin backbone. As a model in our construction, we use the Protein Data Bank entry 1ABS that has been measured at liquid helium temperature. Consequently, the thermal B-factor fluctuations are very small, which is an advantage in our construction. The energy function that we utilize resembles that of the discrete nonlinear Schrödinger equation. Likewise, ours supports topological solitons as local minimum energy configurations. We describe the 1ABS backbone in terms of topological solitons with a precision that deviates from 1ABS by an average root-mean-square distance, which is less than the experimentally observed Debye-Waller B-factor fluctuation distance. We then subject the topological multi-soliton solution to extensive numerical heating and cooling experiments, over a very wide range of temperatures. We concentrate in particular to temperatures above 300 K and below the Θ-point unfolding temperature, which is around 348 K. We confirm that the behavior of the topological multi-soliton is fully consistent with Anfinsen's thermodynamic principle, up to very high temperatures. We observe that the structure responds to an increase of temperature consistently in a very similar manner. This enables us to characterize the onset of thermally induced conformational changes in terms of three distinct backbone ligand gates. One of the gates is made of the helix F and the helix E. The two other gates are chosen similarly, when open they provide a direct access route for a ligand to reach the heme. We find that out of the three gates we investigate, the one which is formed by helices B and G is the most sensitive to thermally induced conformational changes. Our approach provides a novel perspective to the important problem of ligand entry and exit.

Dynamic Ice-Water Interactions Form Europa's Chaos Terrains

NASA Astrophysics Data System (ADS)

Blankenship, D. D.; Schmidt, B. E.; Patterson, G. W.; Schenk, P.

2011-12-01

Unique to the surface of Europa, chaos terrain is diagnostic of the properties and dynamics of its icy shell. We present a new model that suggests large melt lenses form within the shell and that water-ice interactions above and within these lenses drive the production of chaos. This model is consistent with key observations of chaos, predicts observables for future missions, and indicates that the surface is likely still active today[1]. We apply lessons from ice-water interaction in the terrestrial cryosphere to hypothesize a dynamic lense-collapse model to for Europa's chaos terrain. Chaos terrain morphology, like that of Conamara chaos and Thera Macula, suggests a four-phase formation [1]: 1) Surface deflection occurs as ice melts over ascending thermal plumes, as regularly occurs on Earth as subglacial volcanoes activate. The same process can occur at Europa if thermal plumes cause pressure melt as they cross ice-impurity eutectics. 2) Resulting hydraulic gradients and driving forces produce a sealed, pressurized melt lense, akin to the hydraulic sealing of subglacial caldera lakes. On Europa, the water cannot escape the lense due to the horizontally continuous ice shell. 3) Extension of the brittle ice lid above the lense opens cracks, allowing for the ice to be hydrofractured by pressurized water. Fracture, brine injection and percolation within the ice and possible iceberg toppling produces ice-melange-like granular matrix material. 4) Refreezing of the melt lense and brine-filled pores and cracks within the matrix results in raised chaos. Brine soaking and injection concentrates the ice in brines and adds water volume to the shell. As this englacial water freezes, the now water-filled ice will expand, not unlike the process of forming pingos and other "expansion ice" phenomena on Earth. The refreezing can raise the surface and create the oft-observed matrix "domes" In this presentation, we describe how catastrophic ice-water interactions on Earth have

First-principles study of the effect of functional groups on polyaniline backbone

PubMed Central

Chen, X. P.; Jiang, J. K.; Liang, Q. H.; Yang, N.; Ye, H. Y.; Cai, M.; Shen, L.; Yang, D. G.; Ren, T. L.

2015-01-01

We present a first-principles density functional theory study focused on how the chemical and electronic properties of polyaniline are adjusted by introducing suitable substituents on a polymer backbone. Analyses of the obtained energy barriers, reaction energies and minimum energy paths indicate that the chemical reactivity of the polyaniline derivatives is significantly enhanced by protonic acid doping of the substituted materials. Further study of the density of states at the Fermi level, band gap, HOMO and LUMO shows that both the unprotonated and protonated states of these polyanilines are altered to different degrees depending on the functional group. We also note that changes in both the chemical and electronic properties are very sensitive to the polarity and size of the functional group. It is worth noting that these changes do not substantially alter the inherent chemical and electronic properties of polyaniline. Our results demonstrate that introducing different functional groups on a polymer backbone is an effective approach to obtain tailored conductive polymers with desirable properties while retaining their intrinsic properties, such as conductivity. PMID:26584671

Transferability of polarizable models for ion-water electrostatic interaction

NASA Astrophysics Data System (ADS)

Masia, Marco

2009-06-01

Studies of ion-water systems at condensed phase and at interfaces have pointed out that molecular and ionic polarization plays an important role for many phenomena ranging from hydrogen bond dynamics to water interfaces' structure. Classical and ab initio Molecular Dynamics simulations reveal that induced dipole moments at interfaces (e.g. air-water and water-protein) are usually high, hinting that polarizable models to be implemented in classical force fields should be very accurate in reproducing the electrostatic properties of the system. In this paper the electrostatic properties of three classical polarizable models for ion-water interaction are compared with ab initio results both at gas and condensed phase. For Li+- water and Cl--water dimers the reproducibility of total dipole moments obtained with high level quantum chemical calculations is studied; for the same ions in liquid water, Car-Parrinello Molecular Dynamics simulations are used to compute the time evolution of ionic and molecular dipole moments, which are compared with the classical models. The PD2-H2O model developed by the author and coworkers [Masia et al. J. Chem. Phys. 2004, 121, 7362] together with the gaussian intermolecular damping for ion-water interaction [Masia et al. J. Chem. Phys. 2005, 123, 164505] showed to be the fittest in reproducing the ab initio results from gas to condensed phase, allowing for force field transferability.

Probing the interactions between ionic liquids and water: experimental and quantum chemical approach.

PubMed

Khan, Imran; Kurnia, Kiki A; Mutelet, Fabrice; Pinho, Simão P; Coutinho, João A P

2014-02-20

For an adequate choice or design of ionic liquids, the knowledge of their interaction with other solutes and solvents is an essential feature for predicting the reactivity and selectivity of systems involving these compounds. In this work, the activity coefficient of water in several imidazolium-based ionic liquids with the common cation 1-butyl-3-methylimidazolium was measured at 298.2 K. To contribute to a deeper insight into the interaction between ionic liquids and water, COSMO-RS was used to predict the activity coefficient of water in the studied ionic liquids along with the excess enthalpies. The results showed good agreement between experimental and predicted activity coefficient of water in ionic liquids and that the interaction of water and ionic liquids was strongly influenced by the hydrogen bonding of the anion with water. Accordingly, the intensity of interaction of the anions with water can be ranked as the following: [CF3SO3](-) < [SCN](-) < [TFA](-) < Br(-) < [TOS](-) < Cl(-) < [CH3SO3](-) [DMP](-) < [Ac](-). In addition, fluorination and aromatization of anions are shown to reduce their interaction with water. The effect of temperature on the activity coefficient of water at infinite dilution was measured by inverse gas chromatography and predicted by COSMO-RS. Further analysis based on COSMO-RS provided information on the nature of hydrogen bonding between water and anion as well as the possibility of anion-water complex formation.

Structure and backbone dynamics of a microcrystalline metalloprotein by solid-state NMR.

PubMed

Knight, Michael J; Pell, Andrew J; Bertini, Ivano; Felli, Isabella C; Gonnelli, Leonardo; Pierattelli, Roberta; Herrmann, Torsten; Emsley, Lyndon; Pintacuda, Guido

2012-07-10

We introduce a new approach to improve structural and dynamical determination of large metalloproteins using solid-state nuclear magnetic resonance (NMR) with (1)H detection under ultrafast magic angle spinning (MAS). The approach is based on the rapid and sensitive acquisition of an extensive set of (15)N and (13)C nuclear relaxation rates. The system on which we demonstrate these methods is the enzyme Cu, Zn superoxide dismutase (SOD), which coordinates a Cu ion available either in Cu(+) (diamagnetic) or Cu(2+) (paramagnetic) form. Paramagnetic relaxation enhancements are obtained from the difference in rates measured in the two forms and are employed as structural constraints for the determination of the protein structure. When added to (1)H-(1)H distance restraints, they are shown to yield a twofold improvement of the precision of the structure. Site-specific order parameters and timescales of motion are obtained by a gaussian axial fluctuation (GAF) analysis of the relaxation rates of the diamagnetic molecule, and interpreted in relation to backbone structure and metal binding. Timescales for motion are found to be in the range of the overall correlation time in solution, where internal motions characterized here would not be observable.

Application of an interactive water simulation model in urban water management: a case study in Amsterdam.

PubMed

Leskens, J G; Brugnach, M; Hoekstra, A Y

2014-01-01

Water simulation models are available to support decision-makers in urban water management. To use current water simulation models, special expertise is required. Therefore, model information is prepared prior to work sessions, in which decision-makers weigh different solutions. However, this model information quickly becomes outdated when new suggestions for solutions arise and are therefore limited in use. We suggest that new model techniques, i.e. fast and flexible computation algorithms and realistic visualizations, allow this problem to be solved by using simulation models during work sessions. A new Interactive Water Simulation Model was applied for two case study areas in Amsterdam and was used in two workshops. In these workshops, the Interactive Water Simulation Model was positively received. It included non-specialist participants in the process of suggesting and selecting possible solutions and made them part of the accompanying discussions and negotiations. It also provided the opportunity to evaluate and enhance possible solutions more often within the time horizon of a decision-making process. Several preconditions proved to be important for successfully applying the Interactive Water Simulation Model, such as the willingness of the stakeholders to participate and the preparation of different general main solutions that can be used for further iterations during a work session.

Review: Groundwater management and groundwater/surface-water interaction in the context of South African water policy

NASA Astrophysics Data System (ADS)

Levy, Jonathan; Xu, Yongxin

2012-03-01

Groundwater/surface-water interaction is receiving increasing focus in Africa due to its importance to ecologic systems and sustainability. In South Africa's 1998 National Water Act (NWA), water-use licenses, including groundwater, are granted only after defining the Reserve, the amount of water needed to supply basic human needs and preserve some ecological integrity. Accurate quantification of groundwater contributions to ecosystems for successful implementation of the NWA proves challenging; many of South Africa's aquifers are in heterogeneous and anisotropic fractured-rock settings. This paper reviews the current conceptualizations and investigative approaches regarding groundwater/surface-water interactions in the context of South African policies. Some selected pitfall experiences are emphasized. The most common approach in South Africa is estimation of average annual fluxes at the scale of fourth-order catchments (˜500 km2) with baseflow separation techniques and then subtracting the groundwater discharge rate from the recharge rate. This approach might be a good start, but it ignores spatial and temporal variability, potentially missing local impacts associated with production-well placement. As South Africa's NWA has already been emulated in many countries including Zambia, Zimbabwe and Kenya, the successes and failures of the South African experience dealing with the groundwater/surface-water interaction will be analyzed to guide future policy directions.

Sea water - basalt interactions and genesis of the coastal thermal waters of Maharashtra, India

DOE Office of Scientific and Technical Information (OSTI.GOV)

Muthuraman, K.

1986-01-01

The thermal waters close to the western coastal belt of India (in Maharashtra State) generally discharge Na-Ca-Cl and Ca-Na-Cl types of waters through the basic lava flows of late Cretaceous-early Tertiary age. Experimental work to study the reactions between the dilute sea water and basalt conducted in static autoclaves at selected elevated temperatures, indicates the possibility of producing chloride waters with relatively high calcium, similar to these thermal waters. In view of the increase in Ca in the resultant solutions during sea water-basalt reactions at elevated temperatures, the base temperatures computed by Na-K-Ca geothermometry would be far lower than themore » actual temperatures of the system. At lower temperatures (around 100/sup 0/C) absorption by K by basalt is possible and, hence, alkali geothermometry also may not be reliable for such systems. Anhydrite saturation temperature seems to be a reliable geothermometer for such coastal thermal water systems involving a sea water component. The results of the computer processing of the chemistry of some of these thermal waters using ''WATEQ'' are discussed. Two of these waters are oversaturated with diopside, tremolite, calcite and aragonite, indicating a rather low temperature of origin. In two other cases, interaction with ultramafic rocks is indicated, as these waters are oversaturated with diopside, tremolite, talc, chrysotile, sepiolite and its precipitate. There is no clear evidence to show that the thermal waters of the west coast of India emerge directly from either marine evaporites or oil field waters. It is proposed that the majority of these thermal waters should have originated through interaction of an admixture of sea water and meteoric water with the local basalt flows at some elevated temperatures.« less

Cr(3+) Binding to DNA Backbone Phosphate and Bases: Slow Ligand Exchange Rates and Metal Hydrolysis.

PubMed

Zhou, Wenhu; Yu, Tianmeng; Vazin, Mahsa; Ding, Jinsong; Liu, Juewen

2016-08-15

The interaction between chromium ions and DNA is of great interest in inorganic chemistry, toxicology, and analytical chemistry. Most previous studies focused on in situ reduction of Cr(VI), producing Cr(3+) for DNA binding. Recently, Cr(3+) was reported to activate the Ce13d DNAzyme for RNA cleavage. Herein, the Ce13d is used to study two types of Cr(3+) and DNA interactions. First, Cr(3+) binds to the DNA phosphate backbone weakly through reversible electrostatic interactions, which is weakened by adding competing inorganic phosphate. However, Cr(3+) coordinates with DNA nucleobases forming stable cross-links that can survive denaturing gel electrophoresis condition. The binding of Cr(3+) to different nucleobases was further studied in terms of binding kinetics and affinity by exploiting carboxyfluorescein-labeled DNA homopolymers. Once binding takes place, the stable Cr(3+)/DNA complex cannot be dissociated by EDTA, attributable to the ultraslow ligand exchange rate of Cr(3+). The binding rate follows the order of G > C > T ≈ A. Finally, Cr(3+) gradually loses its DNA binding ability after being stored at neutral or high pH, attributable to hydrolysis. This hydrolysis can be reversed by lowering the pH. This work provides a deeper insight into the bioinorganic chemistry of Cr(3+) coordination with DNA, clarifies some inconsistency in the previous literature, and offers practically useful information for generating reproducible results.

Hyperspectral detection of a subsurface CO2 leak in the presence of water stressed vegetation.

PubMed

Bellante, Gabriel J; Powell, Scott L; Lawrence, Rick L; Repasky, Kevin S; Dougher, Tracy

2014-01-01

Remote sensing of vegetation stress has been posed as a possible large area monitoring tool for surface CO2 leakage from geologic carbon sequestration (GCS) sites since vegetation is adversely affected by elevated CO2 levels in soil. However, the extent to which remote sensing could be used for CO2 leak detection depends on the spectral separability of the plant stress signal caused by various factors, including elevated soil CO2 and water stress. This distinction is crucial to determining the seasonality and appropriateness of remote GCS site monitoring. A greenhouse experiment tested the degree to which plants stressed by elevated soil CO2 could be distinguished from plants that were water stressed. A randomized block design assigned Alfalfa plants (Medicago sativa) to one of four possible treatment groups: 1) a CO2 injection group; 2) a water stress group; 3) an interaction group that was subjected to both water stress and CO2 injection; or 4) a group that received adequate water and no CO2 injection. Single date classification trees were developed to identify individual spectral bands that were significant in distinguishing between CO2 and water stress agents, in addition to a random forest classifier that was used to further understand and validate predictive accuracies. Overall peak classification accuracy was 90% (Kappa of 0.87) for the classification tree analysis and 83% (Kappa of 0.77) for the random forest classifier, demonstrating that vegetation stressed from an underground CO2 leak could be accurately discerned from healthy vegetation and areas of co-occurring water stressed vegetation at certain times. Plants appear to hit a stress threshold, however, that would render detection of a CO2 leak unlikely during severe drought conditions. Our findings suggest that early detection of a CO2 leak with an aerial or ground-based hyperspectral imaging system is possible and could be an important GCS monitoring tool.

Hyperspectral Detection of a Subsurface CO2 Leak in the Presence of Water Stressed Vegetation

PubMed Central

Bellante, Gabriel J.; Powell, Scott L.; Lawrence, Rick L.; Repasky, Kevin S.; Dougher, Tracy

2014-01-01

Remote sensing of vegetation stress has been posed as a possible large area monitoring tool for surface CO2 leakage from geologic carbon sequestration (GCS) sites since vegetation is adversely affected by elevated CO2 levels in soil. However, the extent to which remote sensing could be used for CO2 leak detection depends on the spectral separability of the plant stress signal caused by various factors, including elevated soil CO2 and water stress. This distinction is crucial to determining the seasonality and appropriateness of remote GCS site monitoring. A greenhouse experiment tested the degree to which plants stressed by elevated soil CO2 could be distinguished from plants that were water stressed. A randomized block design assigned Alfalfa plants (Medicago sativa) to one of four possible treatment groups: 1) a CO2 injection group; 2) a water stress group; 3) an interaction group that was subjected to both water stress and CO2 injection; or 4) a group that received adequate water and no CO2 injection. Single date classification trees were developed to identify individual spectral bands that were significant in distinguishing between CO2 and water stress agents, in addition to a random forest classifier that was used to further understand and validate predictive accuracies. Overall peak classification accuracy was 90% (Kappa of 0.87) for the classification tree analysis and 83% (Kappa of 0.77) for the random forest classifier, demonstrating that vegetation stressed from an underground CO2 leak could be accurately discerned from healthy vegetation and areas of co-occurring water stressed vegetation at certain times. Plants appear to hit a stress threshold, however, that would render detection of a CO2 leak unlikely during severe drought conditions. Our findings suggest that early detection of a CO2 leak with an aerial or ground-based hyperspectral imaging system is possible and could be an important GCS monitoring tool. PMID:25330232

Evaluation of Polymerase Chain Reaction for Detecting Coliform Bacteria in Drinking Water Sources.

PubMed

Isfahani, Bahram Nasr; Fazeli, Hossein; Babaie, Zeinab; Poursina, Farkhondeh; Moghim, Sharareh; Rouzbahani, Meisam

2017-01-01

Coliform bacteria are used as indicator organisms for detecting fecal pollution in water. Traditional methods including microbial culture tests in lactose-containing media and enzyme-based tests for the detection of β-galactosidase; however, these methods are time-consuming and less specific. The aim of this study was to evaluate polymerase chain reaction (PCR) for detecting coliform. Totally, 100 of water samples from Isfahan drinking water source were collected. Coliform bacteria and Escherichia coli were detected in drinking water using LacZ and LamB genes in PCR method performed in comparison with biochemical tests for all samples. Using phenotyping, 80 coliform isolates were found. The results of the biochemical tests illustrated 78.7% coliform bacteria and 21.2% E. coli . PCR results for LacZ and LamB genes were 67.5% and 17.5%, respectively. The PCR method was shown to be an effective, sensitive, and rapid method for detecting coliform and E. coli in drinking water from the Isfahan drinking water sources.

Chemical synthesis of membrane proteins by the removable backbone modification method.

PubMed

Tang, Shan; Zuo, Chao; Huang, Dong-Liang; Cai, Xiao-Ying; Zhang, Long-Hua; Tian, Chang-Lin; Zheng, Ji-Shen; Liu, Lei

2017-12-01

Chemical synthesis can produce membrane proteins bearing specifically designed modifications (e.g., phosphorylation, isotope labeling) that are difficult to obtain through recombinant protein expression approaches. The resulting homogeneously modified synthetic membrane proteins are valuable tools for many advanced biochemical and biophysical studies. This protocol describes the chemical synthesis of membrane proteins by condensation of transmembrane peptide segments through native chemical ligation. To avoid common problems encountered due to the poor solubility of transmembrane peptides in almost any solvent, we describe an effective procedure for the chemical synthesis of membrane proteins through the removable-backbone modification (RBM) strategy. Two key steps of this protocol are: (i) installation of solubilizing Arg4-tagged RBM groups into the transmembrane peptides at any primary amino acid through Fmoc (9-fluorenylmethyloxycarbonyl) solid-phase peptide synthesis and (ii) native ligation of the full-length sequence, followed by removal of the RBM tags by TFA (trifluoroacetic acid) cocktails to afford the native protein. The installation of RBM groups is achieved by using 4-methoxy-5-nitrosalicyladehyde by reduction amination to incorporate an activated O-to-N acyl transfer auxiliary. The Arg4-tag-modified membrane-spanning peptide segments behave like water-soluble peptides to facilitate their purification, ligation and mass characterization.

Adenovirus, MS2 and PhiX174 interactions with drinking water biofilms developed on PVC, cement and cast iron.

PubMed

Helmi, K; Menard-Szczebara, F; Lénès, D; Jacob, P; Jossent, J; Barbot, C; Delabre, K; Arnal, C

2010-01-01

Biofilms colonizing pipe surfaces of drinking water distribution systems could provide habitat and shelter for pathogenic viruses present in the water phase. This study aims (i) to develop a method to detect viral particles present in a drinking water biofilm and (ii) to study viral interactions with drinking water biofilms. A pilot scale system was used to develop drinking water biofilms on 3 materials (7 cm(2) discs): PVC, cast iron and cement. Biofilms were inoculated with viral model including MS2, PhiX174 or adenovirus. Five techniques were tested to recover virus from biofilms. The most efficient uses beef extract and glycine at pH = 9. After sonication and centrifugation, the pH of the supernatant is neutralized prior to viral analysis. The calculated recovery rates varied from 29.3 to 74.6% depending on the virus (MS2 or PhiX174) and the material. Applying this protocol, the interactions of virus models (MS2 and adenovirus) with drinking water biofilms were compared. Our results show that adsorption of viruses to biofilms depends on their isoelectric points, the disc material and the hydrodynamic conditions. Applying hydrodynamic conditions similar to those existing in drinking water networks resulted in a viral adsorption corresponding to less than 1% of the initial viral load.

Life estimation and analysis of dielectric strength, hydrocarbon backbone and oxidation of high voltage multi stressed EPDM composites

NASA Astrophysics Data System (ADS)

Khattak, Abraiz; Amin, Muhammad; Iqbal, Muhammad; Abbas, Naveed

2018-02-01

Micro and nanocomposites of ethylene propylene diene monomer (EPDM) are recently studied for different characteristics. Study on life estimation and effects of multiple stresses on its dielectric strength and backbone scission and oxidation is also vital for endorsement of these composites for high voltage insulation and other outdoor applications. In order to achieve these goals, unfilled EPDM and its micro and nanocomposites are prepared at 23 phr micro silica and 6 phr nanosilica loadings respectively. Prepared samples are energized at 2.5 kV AC voltage and subjected for a long time to heat, ultraviolet radiation, acid rain, humidity and salt fog in accelerated manner in laboratory. Dielectric strength, leakage current and intensity of saturated backbone and carbonyl group are periodically measured. Loss in dielectric strength, increase in leakage current and backbone degradation and oxidation were observed in all samples. These effects were least in the case of EPDM nanocomposite. The nanocomposite sample also demonstrated longest shelf life.

Statistical models for detecting differential chromatin interactions mediated by a protein.

PubMed

Niu, Liang; Li, Guoliang; Lin, Shili

2014-01-01

Chromatin interactions mediated by a protein of interest are of great scientific interest. Recent studies show that protein-mediated chromatin interactions can have different intensities in different types of cells or in different developmental stages of a cell. Such differences can be associated with a disease or with the development of a cell. Thus, it is of great importance to detect protein-mediated chromatin interactions with different intensities in different cells. A recent molecular technique, Chromatin Interaction Analysis by Paired-End Tag Sequencing (ChIA-PET), which uses formaldehyde cross-linking and paired-end sequencing, is able to detect genome-wide chromatin interactions mediated by a protein of interest. Here we proposed two models (One-Step Model and Two-Step Model) for two sample ChIA-PET count data (one biological replicate in each sample) to identify differential chromatin interactions mediated by a protein of interest. Both models incorporate the data dependency and the extent to which a fragment pair is related to a pair of DNA loci of interest to make accurate identifications. The One-Step Model makes use of the data more efficiently but is more computationally intensive. An extensive simulation study showed that the models can detect those differentially interacted chromatins and there is a good agreement between each classification result and the truth. Application of the method to a two-sample ChIA-PET data set illustrates its utility. The two models are implemented as an R package MDM (available at http://www.stat.osu.edu/~statgen/SOFTWARE/MDM).

Statistical Models for Detecting Differential Chromatin Interactions Mediated by a Protein

PubMed Central

Niu, Liang; Li, Guoliang; Lin, Shili

2014-01-01

Chromatin interactions mediated by a protein of interest are of great scientific interest. Recent studies show that protein-mediated chromatin interactions can have different intensities in different types of cells or in different developmental stages of a cell. Such differences can be associated with a disease or with the development of a cell. Thus, it is of great importance to detect protein-mediated chromatin interactions with different intensities in different cells. A recent molecular technique, Chromatin Interaction Analysis by Paired-End Tag Sequencing (ChIA-PET), which uses formaldehyde cross-linking and paired-end sequencing, is able to detect genome-wide chromatin interactions mediated by a protein of interest. Here we proposed two models (One-Step Model and Two-Step Model) for two sample ChIA-PET count data (one biological replicate in each sample) to identify differential chromatin interactions mediated by a protein of interest. Both models incorporate the data dependency and the extent to which a fragment pair is related to a pair of DNA loci of interest to make accurate identifications. The One-Step Model makes use of the data more efficiently but is more computationally intensive. An extensive simulation study showed that the models can detect those differentially interacted chromatins and there is a good agreement between each classification result and the truth. Application of the method to a two-sample ChIA-PET data set illustrates its utility. The two models are implemented as an R package MDM (available at http://www.stat.osu.edu/~statgen/SOFTWARE/MDM). PMID:24835279

Centrifugal sedimentation immunoassays for multiplexed detection of enteric bacteria in ground water

PubMed Central

Litvinov, Julia; Moen, Scott T.; Koh, Chung-Yan; Singh, Anup K.

2016-01-01

Waterborne pathogens pose significant threat to the global population and early detection plays an important role both in making drinking water safe, as well as in diagnostics and treatment of water-borne diseases. We present an innovative centrifugal sedimentation immunoassay platform for detection of bacterial pathogens in water. Our approach is based on binding of pathogens to antibody-functionalized capture particles followed by sedimentation of the particles through a density-media in a microfluidic disk. Beads at the distal end of the disk are imaged to quantify the fluorescence and determine the bacterial concentration. Our platform is fast (20 min), can detect as few as ∼10 bacteria with minimal sample preparation, and can detect multiple pathogens simultaneously. The platform was used to detect a panel of enteric bacteria (Escherichia coli, Salmonella typhimurium, Shigella, Listeria, and Campylobacter) spiked in tap and ground water samples. PMID:26858815

High-cost, high-capacity backbone for global brain communication.

PubMed

van den Heuvel, Martijn P; Kahn, René S; Goñi, Joaquín; Sporns, Olaf

2012-07-10

Network studies of human brain structural connectivity have identified a specific set of brain regions that are both highly connected and highly central. Recent analyses have shown that these putative hub regions are mutually and densely interconnected, forming a "rich club" within the human brain. Here we show that the set of pathways linking rich club regions forms a central high-cost, high-capacity backbone for global brain communication. Diffusion tensor imaging (DTI) data of two sets of 40 healthy subjects were used to map structural brain networks. The contributions to network cost and communication capacity of global cortico-cortical connections were assessed through measures of their topology and spatial embedding. Rich club connections were found to be more costly than predicted by their density alone and accounted for 40% of the total communication cost. Furthermore, 69% of all minimally short paths between node pairs were found to travel through the rich club and a large proportion of these communication paths consisted of ordered sequences of edges ("path motifs") that first fed into, then traversed, and finally exited the rich club, while passing through nodes of increasing and then decreasing degree. The prevalence of short paths that follow such ordered degree sequences suggests that neural communication might take advantage of strategies for dynamic routing of information between brain regions, with an important role for a highly central rich club. Taken together, our results show that rich club connections make an important contribution to interregional signal traffic, forming a central high-cost, high-capacity backbone for global brain communication.

Landsat change detection can aid in water quality monitoring

NASA Technical Reports Server (NTRS)

Macdonald, H. C.; Steele, K. F.; Waite, W. P.; Shinn, M. R.

1977-01-01

Comparison between Landsat-1 and -2 imagery of Arkansas provided evidence of significant land use changes during the 1972-75 time period. Analysis of Arkansas historical water quality information has shown conclusively that whereas point source pollution generally can be detected by use of water quality data collected by state and federal agencies, sampling methodologies for nonpoint source contamination attributable to surface runoff are totally inadequate. The expensive undertaking of monitoring all nonpoint sources for numerous watersheds can be lessened by implementing Landsat change detection analyses.

Controlled conjugated backbone twisting for an increased open-circuit voltage while having a high short-circuit current in poly(hexylthiophene) derivatives.

PubMed

Ko, Sangwon; Hoke, Eric T; Pandey, Laxman; Hong, Sanghyun; Mondal, Rajib; Risko, Chad; Yi, Yuanping; Noriega, Rodrigo; McGehee, Michael D; Brédas, Jean-Luc; Salleo, Alberto; Bao, Zhenan

2012-03-21

Conjugated polymers with nearly planar backbones have been the most commonly investigated materials for organic-based electronic devices. More twisted polymer backbones have been shown to achieve larger open-circuit voltages in solar cells, though with decreased short-circuit current densities. We systematically impose twists within a family of poly(hexylthiophene)s and examine their influence on the performance of polymer:fullerene bulk heterojunction (BHJ) solar cells. A simple chemical modification concerning the number and placement of alkyl side chains along the conjugated backbone is used to control the degree of backbone twisting. Density functional theory calculations were carried out on a series of oligothiophene structures to provide insights on how the sterically induced twisting influences the geometric, electronic, and optical properties. Grazing incidence X-ray scattering measurements were performed to investigate how the thin-film packing structure was affected. The open-circuit voltage and charge-transfer state energy of the polymer:fullerene BHJ solar cells increased substantially with the degree of twist induced within the conjugated backbone--due to an increase in the polymer ionization potential--while the short-circuit current decreased as a result of a larger optical gap and lower hole mobility. A controlled, moderate degree of twist along the poly(3,4-dihexyl-2,2':5',2''-terthiophene) (PDHTT) conjugated backbone led to a 19% enhancement in the open-circuit voltage (0.735 V) vs poly(3-hexylthiophene)-based devices, while similar short-circuit current densities, fill factors, and hole-carrier mobilities were maintained. These factors resulted in a power conversion efficiency of 4.2% for a PDHTT:[6,6]-phenyl-C(71)-butyric acid methyl ester (PC(71)BM) blend solar cell without thermal annealing. This simple approach reveals a molecular design avenue to increase open-circuit voltage while retaining the short-circuit current.

Blue Thermally Activated Delayed Fluorescence Polymers with Nonconjugated Backbone and Through-Space Charge Transfer Effect.

PubMed

Shao, Shiyang; Hu, Jun; Wang, Xingdong; Wang, Lixiang; Jing, Xiabin; Wang, Fosong

2017-12-13

We demonstrate novel molecular design for thermally activated delayed fluorescence (TADF) polymers based on a nonconjugated polyethylene backbone with through-space charge transfer effect between pendant electron donor (D) and acceptor (A) units. Different from conventional conjugated D-A polymers with through-bond charge transfer effect, the nonconjugated architecture avoids direct conjugation between D and A units, enabling blue emission. Meanwhile, spatial π-π interaction between the physically separated D and A units results in both small singlet-triplet energy splitting (0.019 eV) and high photoluminescence quantum yield (up to 60% in film state). The resulting polymer with 5 mol % acceptor unit gives efficient blue electroluminescence with Commission Internationale de l'Eclairage coordinates of (0.176, 0.269), together with a high external quantum efficiency of 12.1% and low efficiency roll-off of 4.9% (at 1000 cd m -2 ), which represents the first example of blue TADF nonconjugated polymer.

Simulated effects of development on regional ground-water/surface-water interactions in the northern Coastal Plain of New Jersey

NASA Astrophysics Data System (ADS)

Pucci, Amleto A.; Pope, Daryll A.

1995-05-01

Stream flow in the Coastal Plain of New Jersey is primarily controlled by ground-water discharge. Ground-water flow in a 400 square mile area (1035 km 2) of the Potomac-Raritan-Magothy aquifer system (PRMA) in the northern Coastal Plain of New Jersey was simulated to examine development effects on water resources. Simulations showed that historical development caused significant capture of regional ground-water discharge to streams and wetlands. The Cretaceous PRMA primarily is composed of fine to coarse sand, clays and silts which form the Upper and Middle aquifers and their confining units. The aquifer outcrops are the principal areas of recharge and discharge for the regional flow system and have many traversing streams and surface-water bodies. A quasi-three-dimensional numerical model that incorporated ground-water/surface-water interactions and boundary flows from a larger regional model was used to represent the PRMA. To evaluate the influence of ground-water development on interactions in different areas, hydrogeologically similar and contiguous model stream cells were aggregated as 'stream zones'. The model representation of surface-water and ground-water interaction was limited in the areas of confining unit outcrops and because of this, simulated ground-water discharge could not be directly compared with base flow. Significant differences in simulated ground-water and surface-water interactions between the predevelopment and developed system, include; (1) redistribution of recharge and discharge areas; (2) reduced ground-water discharge to streams. In predevelopment, the primary discharge for the Upper and Middle aquifers is to low-lying streams and wetlands; in the developed system, the primary discharge is to ground-water withdrawals. Development reduces simulated ground-water discharge to streams in the Upper Aquifer from 61.4 to 10% of the Upper Aquifer hydrologic budget (28.9%, if impounded stream flow is included). Ground-water discharge to streams

Detection of Leaks in Water Distribution System using Non-Destructive Techniques

NASA Astrophysics Data System (ADS)

Aslam, H.; Kaur, M.; Sasi, S.; Mortula, Md M.; Yehia, S.; Ali, T.

2018-05-01

Water is scarce and needs to be conserved. A considerable amount of water which flows in the water distribution systems was found to be lost due to pipe leaks. Consequently, innovations in methods of pipe leakage detections for early recognition and repair of these leaks is vital to ensure minimum wastage of water in distribution systems. A major component of detection of pipe leaks is the ability to accurately locate the leak location in pipes through minimum invasion. Therefore, this paper studies the leak detection abilities of the three NDT’s: Ground Penetration Radar (GPR) and spectrometer and aims at determining whether these instruments are effective in identifying the leak. An experimental setup was constructed to simulate the underground conditions of water distribution systems. After analysing the experimental data, it was concluded that both the GPR and the spectrometer were effective in detecting leaks in the pipes. However, the results obtained from the spectrometer were not very differentiating in terms of observing the leaks in comparison to the results obtained from the GPR. In addition to this, it was concluded that both instruments could not be used if the water from the leaks had reached on the surface, resulting in surface ponding.

Measuring indigenous photosynthetic organisms to detect chemical warefare agents in water

DOEpatents

Greenbaum, Elias; Sanders, Charlene A.

2005-11-15

A method of testing water to detect the presence of a chemical or biological warfare agent is disclosed. The method is carried out by establishing control data by providing control water containing indigenous organisms but substantially free of a chemical and a biological warfare agent. Then measuring photosynthetic activity of the control water with a fluorometer to obtain control data to compare with test data to detect the presence of the chemical or agent. The test data is gathered by providing test water comprising the same indigenous organisms as contained in the control water. Further, the test water is suspected of containing the chemical or agent to be tested for. Photosynthetic activity is also measured by fluorescence induction in the test water using a fluorometer.

Detection of protein complex from protein-protein interaction network using Markov clustering

NASA Astrophysics Data System (ADS)

Ochieng, P. J.; Kusuma, W. A.; Haryanto, T.

2017-05-01

Detection of complexes, or groups of functionally related proteins, is an important challenge while analysing biological networks. However, existing algorithms to identify protein complexes are insufficient when applied to dense networks of experimentally derived interaction data. Therefore, we introduced a graph clustering method based on Markov clustering algorithm to identify protein complex within highly interconnected protein-protein interaction networks. Protein-protein interaction network was first constructed to develop geometrical network, the network was then partitioned using Markov clustering to detect protein complexes. The interest of the proposed method was illustrated by its application to Human Proteins associated to type II diabetes mellitus. Flow simulation of MCL algorithm was initially performed and topological properties of the resultant network were analysed for detection of the protein complex. The results indicated the proposed method successfully detect an overall of 34 complexes with 11 complexes consisting of overlapping modules and 20 non-overlapping modules. The major complex consisted of 102 proteins and 521 interactions with cluster modularity and density of 0.745 and 0.101 respectively. The comparison analysis revealed MCL out perform AP, MCODE and SCPS algorithms with high clustering coefficient (0.751) network density and modularity index (0.630). This demonstrated MCL was the most reliable and efficient graph clustering algorithm for detection of protein complexes from PPI networks.

An efficient randomized algorithm for contact-based NMR backbone resonance assignment.

PubMed

Kamisetty, Hetunandan; Bailey-Kellogg, Chris; Pandurangan, Gopal

2006-01-15

Backbone resonance assignment is a critical bottleneck in studies of protein structure, dynamics and interactions by nuclear magnetic resonance (NMR) spectroscopy. A minimalist approach to assignment, which we call 'contact-based', seeks to dramatically reduce experimental time and expense by replacing the standard suite of through-bond experiments with the through-space (nuclear Overhauser enhancement spectroscopy, NOESY) experiment. In the contact-based approach, spectral data are represented in a graph with vertices for putative residues (of unknown relation to the primary sequence) and edges for hypothesized NOESY interactions, such that observed spectral peaks could be explained if the residues were 'close enough'. Due to experimental ambiguity, several incorrect edges can be hypothesized for each spectral peak. An assignment is derived by identifying consistent patterns of edges (e.g. for alpha-helices and beta-sheets) within a graph and by mapping the vertices to the primary sequence. The key algorithmic challenge is to be able to uncover these patterns even when they are obscured by significant noise. This paper develops, analyzes and applies a novel algorithm for the identification of polytopes representing consistent patterns of edges in a corrupted NOESY graph. Our randomized algorithm aggregates simplices into polytopes and fixes inconsistencies with simple local modifications, called rotations, that maintain most of the structure already uncovered. In characterizing the effects of experimental noise, we employ an NMR-specific random graph model in proving that our algorithm gives optimal performance in expected polynomial time, even when the input graph is significantly corrupted. We confirm this analysis in simulation studies with graphs corrupted by up to 500% noise. Finally, we demonstrate the practical application of the algorithm on several experimental beta-sheet datasets. Our approach is able to eliminate a large majority of noise edges and to

Shallow Alluvial Aquifer Ground Water System and Surface Water/Ground Water Interaction, Boulder Creek, Boulder, Colorado

NASA Astrophysics Data System (ADS)

Babcock, K. P.; Ge, S.; Crifasi, R. R.

2006-12-01

Water chemistry in Boulder Creek, Colorado, shows significant variation as the Creek flows through the City of Boulder [Barber et al., 2006]. This variation is partially due to ground water inputs, which are not quantitatively understood. The purpose of this study is (1) to understand ground water movement in a shallow alluvial aquifer system and (2) to assess surface water/ground water interaction. The study area, encompassing an area of 1 mi2, is located at the Sawhill and Walden Ponds area in Boulder. This area was reclaimed by the City of Boulder and Boulder County after gravel mining operations ceased in the 1970's. Consequently, ground water has filled in the numerous gravel pits allowing riparian vegetation regrowth and replanting. An integrated approach is used to examine the shallow ground water and surface water of the study area through field measurements, water table mapping, graphical data analysis, and numerical modeling. Collected field data suggest that lateral heterogeneity exists throughout the unconsolidated sediment. Alluvial hydraulic conductivities range from 1 to 24 ft/day and flow rates range from 0.01 to 2 ft/day. Preliminary data analysis suggests that ground water movement parallels surface topography and does not noticeably vary with season. Recharge via infiltrating precipitation is dependent on evapotranspiration (ET) demands and is influenced by preferential flow paths. During the growing season when ET demand exceeds precipitation rates, there is little recharge; however recharge occurs during cooler months when ET demand is insignificant. Preliminary data suggest that the Boulder Creek is gaining ground water as it traverses the study area. Stream flow influences the water table for distances up to 400 feet. The influence of stream flow is reflected in the zones relatively low total dissolved solids concentration. A modeling study is being conducted to synthesize aquifer test data, ground water levels, and stream flow data. The

Water velocity influences prey detection and capture by drift-feeding juvenile coho salmon (Oncorhynchus kisutch) and steelhead (Oncorhynchus mykiss irideus)

Treesearch

John J. Piccolo; Nicholas F. Hughes; Mason D. Bryant

2008-01-01

We examined the effects of water velocity on prey detection and capture by drift-feeding juvenile coho salmon (Oncorhynchus kisutch) and steelhead (sea-run rainbow trout,Oncorhynchus mykiss irideus) in laboratory experiments. We used repeated-measures analysis of variance to test the effects of velocity, species, and the velocity x species interaction on prey capture...

Highly efficient bioinspired molecular Ru water oxidation catalysts with negatively charged backbone ligands.

PubMed

Duan, Lele; Wang, Lei; Li, Fusheng; Li, Fei; Sun, Licheng

2015-07-21

The oxygen evolving complex (OEC) of the natural photosynthesis system II (PSII) oxidizes water to produce oxygen and reducing equivalents (protons and electrons). The oxygen released from PSII provides the oxygen source of our atmosphere; the reducing equivalents are used to reduce carbon dioxide to organic products, which support almost all organisms on the Earth planet. The first photosynthetic organisms able to split water were proposed to be cyanobacteria-like ones appearing ca. 2.5 billion years ago. Since then, nature has chosen a sustainable way by using solar energy to develop itself. Inspired by nature, human beings started to mimic the functions of the natural photosynthesis system and proposed the concept of artificial photosynthesis (AP) with the view to creating energy-sustainable societies and reducing the impact on the Earth environments. Water oxidation is a highly energy demanding reaction and essential to produce reducing equivalents for fuel production, and thereby effective water oxidation catalysts (WOCs) are required to catalyze water oxidation and reduce the energy loss. X-ray crystallographic studies on PSII have revealed that the OEC consists of a Mn4CaO5 cluster surrounded by oxygen rich ligands, such as oxyl, oxo, and carboxylate ligands. These negatively charged, oxygen rich ligands strongly stabilize the high valent states of the Mn cluster and play vital roles in effective water oxidation catalysis with low overpotential. This Account describes our endeavors to design effective Ru WOCs with low overpotential, large turnover number, and high turnover frequency by introducing negatively charged ligands, such as carboxylate. Negatively charged ligands stabilized the high valent states of Ru catalysts, as evidenced by the low oxidation potentials. Meanwhile, the oxygen production rates of our Ru catalysts were improved dramatically as well. Thanks to the strong electron donation ability of carboxylate containing ligands, a seven

Violent Interaction Detection in Video Based on Deep Learning

NASA Astrophysics Data System (ADS)

Zhou, Peipei; Ding, Qinghai; Luo, Haibo; Hou, Xinglin

2017-06-01

Violent interaction detection is of vital importance in some video surveillance scenarios like railway stations, prisons or psychiatric centres. Existing vision-based methods are mainly based on hand-crafted features such as statistic features between motion regions, leading to a poor adaptability to another dataset. En lightened by the development of convolutional networks on common activity recognition, we construct a FightNet to represent the complicated visual violence interaction. In this paper, a new input modality, image acceleration field is proposed to better extract the motion attributes. Firstly, each video is framed as RGB images. Secondly, optical flow field is computed using the consecutive frames and acceleration field is obtained according to the optical flow field. Thirdly, the FightNet is trained with three kinds of input modalities, i.e., RGB images for spatial networks, optical flow images and acceleration images for temporal networks. By fusing results from different inputs, we conclude whether a video tells a violent event or not. To provide researchers a common ground for comparison, we have collected a violent interaction dataset (VID), containing 2314 videos with 1077 fight ones and 1237 no-fight ones. By comparison with other algorithms, experimental results demonstrate that the proposed model for violent interaction detection shows higher accuracy and better robustness.

Plant viruses in aqueous environment - survival, water mediated transmission and detection.

PubMed

Mehle, Nataša; Ravnikar, Maja

2012-10-15

The presence of plant viruses outside their plant host or insect vectors has not been studied intensively. This is due, in part, to the lack of effective detection methods that would enable their detection in difficult matrixes and in low titres, and support the search for unknown viruses. Recently, new and sensitive methods for detecting viruses have resulted in a deeper insight into plant virus movement through, and transmission between, plants. In this review, we have focused on plant viruses found in environmental waters and their detection. Infectious plant pathogenic viruses from at least 7 different genera have been found in aqueous environment. The majority of the plant pathogenic viruses so far recovered from environmental waters are very stable, they can infect plants via the roots without the aid of a vector and often have a wide host range. The release of such viruses from plants can lead to their dissemination in streams, lakes, and rivers, thereby ensuring the long-distance spread of viruses that otherwise, under natural conditions, would remain restricted to limited areas. The possible sources and survival of plant viruses in waters are therefore discussed. Due to the widespread use of hydroponic systems and intensive irrigation in horticulture, the review is focused on the possibility and importance of spreading viral infection by water, together with measures for preventing the spread of viruses. The development of new methods for detecting multiple plant viruses at the same time, like microarrays or new generation sequencing, will facilitate the monitoring of environmental waters and waters used for irrigation and in hydroponic systems. It is reasonable to expect that the list of plant viruses found in waters will thereby be expanded considerably. This will emphasize the need for further studies to determine the biological significance of water-mediated transport. Copyright © 2012 Elsevier Ltd. All rights reserved.

Designing heteropolymers to fold into unique structures via water-mediated interactions.

PubMed

Jamadagni, Sumanth N; Bosoy, Christian; Garde, Shekhar

2010-10-28

Hydrophobic homopolymers collapse into globular structures in water driven by hydrophobic interactions. Here we employ extensive molecular dynamics simulations to study the collapse of heteropolymers containing one or two pairs of oppositely charged monomers. We show that charging a pair of monomers can dramatically alter the most stable conformations from compact globular to more open hairpin-like. We systematically explore a subset of the sequence space of one- and two-charge-pair polymers, focusing on the locations of the charge pairs. Conformational stability is governed by a balance of hydrophobic interactions, hydration and interactions of charge groups, water-mediated charged-hydrophobic monomer repulsions, and other factors. As a result, placing charge pairs in the middle, away from the hairpin ends, leads to stable hairpin-like structures. Turning off the monomer-water attractions enhances hydrophobic interactions significantly leading to a collapse into compact globular structures even for two-charge-pair heteropolymers. In contrast, the addition of salt leads to open and extended structures, suggesting that solvation of charged monomer sites by salt ions dominates the salt-induced enhancement of hydrophobic interactions. We also test the ability of a predictive scheme based on the additivity of free energy of contact formation. The success of the scheme for symmetric two-charge-pair sequences and the failure for their flipped versions highlight the complexity of the heteropolymer conformation space and of the design problem. Collectively, our results underscore the ability of tuning water-mediated interactions to design stable nonglobular structures in water and present model heteropolymers for further studies in the extended thermodynamic space and in inhomogeneous environments.

Impact of interspecific interactions on the soil water uptake depth in a young temperate mixed species plantation

NASA Astrophysics Data System (ADS)

Grossiord, Charlotte; Gessler, Arthur; Granier, André; Berger, Sigrid; Bréchet, Claude; Hentschel, Rainer; Hommel, Robert; Scherer-Lorenzen, Michael; Bonal, Damien

2014-11-01

Interactions between tree species in forests can be beneficial to ecosystem functions and services related to the carbon and water cycles by improving for example transpiration and productivity. However, little is known on below- and above-ground processes leading to these positive effects. We tested whether stratification in soil water uptake depth occurred between four tree species in a 10-year-old temperate mixed species plantation during a dry summer. We selected dominant and co-dominant trees of European beech, Sessile oak, Douglas fir and Norway spruce in areas with varying species diversity, competition intensity, and where different plant functional types (broadleaf vs. conifer) were present. We applied a deuterium labelling approach that consisted of spraying labelled water to the soil surface to create a strong vertical gradient of the deuterium isotope composition in the soil water. The deuterium isotope composition of both the xylem sap and the soil water was measured before labelling, and then again three days after labelling, to estimate the soil water uptake depth using a simple modelling approach. We also sampled leaves and needles from selected trees to measure their carbon isotope composition (a proxy for water use efficiency) and total nitrogen content. At the end of the summer, we found differences in the soil water uptake depth between plant functional types but not within types: on average, coniferous species extracted water from deeper layers than did broadleaved species. Neither species diversity nor competition intensity had a detectable influence on soil water uptake depth, foliar water use efficiency or foliar nitrogen concentration in the species studied. However, when coexisting with an increasing proportion of conifers, beech extracted water from progressively deeper soil layers. We conclude that complementarity for water uptake could occur in this 10-year-old plantation because of inherent differences among functional groups (conifers

Backbone Brackets and Arginine Tweezers delineate Class I and Class II aminoacyl tRNA synthetases

PubMed Central

Haupt, V. Joachim; Schroeder, Michael; Labudde, Dirk

2018-01-01

The origin of the machinery that realizes protein biosynthesis in all organisms is still unclear. One key component of this machinery are aminoacyl tRNA synthetases (aaRS), which ligate tRNAs to amino acids while consuming ATP. Sequence analyses revealed that these enzymes can be divided into two complementary classes. Both classes differ significantly on a sequence and structural level, feature different reaction mechanisms, and occur in diverse oligomerization states. The one unifying aspect of both classes is their function of binding ATP. We identified Backbone Brackets and Arginine Tweezers as most compact ATP binding motifs characteristic for each Class. Geometric analysis shows a structural rearrangement of the Backbone Brackets upon ATP binding, indicating a general mechanism of all Class I structures. Regarding the origin of aaRS, the Rodin-Ohno hypothesis states that the peculiar nature of the two aaRS classes is the result of their primordial forms, called Protozymes, being encoded on opposite strands of the same gene. Backbone Brackets and Arginine Tweezers were traced back to the proposed Protozymes and their more efficient successors, the Urzymes. Both structural motifs can be observed as pairs of residues in contemporary structures and it seems that the time of their addition, indicated by their placement in the ancient aaRS, coincides with the evolutionary trace of Proto- and Urzymes. PMID:29659563

Characterization of air contaminants formed by the interaction of lava and sea water.

PubMed Central

Kullman, G J; Jones, W G; Cornwell, R J; Parker, J E

1994-01-01

We made environmental measurements to characterize contaminants generated when basaltic lava from Hawaii's Kilauea volcano enters sea water. This interaction of lava with sea water produces large clouds of mist (LAZE). Island winds occasionally directed the LAZE toward the adjacent village of Kalapana and the Hawaii Volcanos National Park, creating health concerns. Environmental samples were taken to measure airborne concentrations of respirable dust, crystalline silica and other mineral compounds, fibers, trace metals, inorganic acids, and organic and inorganic gases. The LAZE contained quantifiable concentrations of hydrochloric acid (HCl) and hydrofluoric acid (HF); HCl was predominant. HCl and HF concentrations were highest in dense plumes of LAZE near the sea. The HCl concentration at this sampling location averaged 7.1 ppm; this exceeds the current occupational exposure ceiling of 5 ppm. HF was detected in nearly half the samples, but all concentrations were <1 ppm Sulfur dioxide was detected in one of four short-term indicator tube samples at approximately 1.5 ppm. Airborne particulates were composed largely of chloride salts (predominantly sodium chloride). Crystalline silica concentrations were below detectable limits, less than approximately 0.03 mg/m3 of air. Settled dust samples showed a predominance of glass flakes and glass fibers. Airborne fibers were detected at quantifiable levels in 1 of 11 samples. These fibers were composed largely of hydrated calcium sulfate. These findings suggest that individuals should avoid concentrated plumes of LAZE near its origin to prevent over exposure to inorganic acids, specifically HCl. Images Figure 1. Figure 2. Figure 3. Figure 4. A Figure 4. B Figure 4. C Figure 4. D PMID:8593853

TANGLE: Two-Level Support Vector Regression Approach for Protein Backbone Torsion Angle Prediction from Primary Sequences

PubMed Central

Song, Jiangning; Tan, Hao; Wang, Mingjun; Webb, Geoffrey I.; Akutsu, Tatsuya

2012-01-01

Protein backbone torsion angles (Phi) and (Psi) involve two rotation angles rotating around the Cα-N bond (Phi) and the Cα-C bond (Psi). Due to the planarity of the linked rigid peptide bonds, these two angles can essentially determine the backbone geometry of proteins. Accordingly, the accurate prediction of protein backbone torsion angle from sequence information can assist the prediction of protein structures. In this study, we develop a new approach called TANGLE (Torsion ANGLE predictor) to predict the protein backbone torsion angles from amino acid sequences. TANGLE uses a two-level support vector regression approach to perform real-value torsion angle prediction using a variety of features derived from amino acid sequences, including the evolutionary profiles in the form of position-specific scoring matrices, predicted secondary structure, solvent accessibility and natively disordered region as well as other global sequence features. When evaluated based on a large benchmark dataset of 1,526 non-homologous proteins, the mean absolute errors (MAEs) of the Phi and Psi angle prediction are 27.8° and 44.6°, respectively, which are 1% and 3% respectively lower than that using one of the state-of-the-art prediction tools ANGLOR. Moreover, the prediction of TANGLE is significantly better than a random predictor that was built on the amino acid-specific basis, with the p-value<1.46e-147 and 7.97e-150, respectively by the Wilcoxon signed rank test. As a complementary approach to the current torsion angle prediction algorithms, TANGLE should prove useful in predicting protein structural properties and assisting protein fold recognition by applying the predicted torsion angles as useful restraints. TANGLE is freely accessible at http://sunflower.kuicr.kyoto-u.ac.jp/~sjn/TANGLE/. PMID:22319565

Characterization of a backbone cleavage product of BMS-196854 (Oncostatin M), a recombinant anti-inflammatory cytokine.

PubMed

Zhao, F; Stein, D J; Paborji, M; Cash, P W; Root, B J; Wei, Z; Knupp, C J

2001-01-01

BMS-196843 (Oncostatin M) is a therapeutic recombinant protein in development. Scale-up process changes led to unexpected instability of the bulk drug substance solution during storage. A product with an apparent higher MW than the parent protein was observed by the size-exclusion chromatography (SEC). This study was aimed to fully characterize the product and to identify a solution to stabilize the protein. SEC, SDS-PAGE, tryptic mapping, and N-terminal sequencing were performed to characterize the unknown product. The effect of pH, temperature, bulk concentration, and immobilized trypsin inhibitor on the degradation rate was studied to elucidate the mechanism and to identify stabilization strategies. Despite the apparent high MW indicated initially by SEC, the unknown was characterized to be a degradation product resulted from a backbone cleavage between residues Arg145-Gly146. The resulting fragments from the backbone cleavage were, however, still linked through an intramolecular disulfide bond. Thus, the final product had a more open structure with an increased hydrodynamic radius compared to the parent protein, which explains the initial SEC results. The site-specific backbone cleavage was suspected to be catalyzed by trypsin-like protease impurities in the bulk solution. The bulk drug substance solution was subsequently treated with immobilized soybean trypsin inhibitor, and the degradation rate was significantly reduced. Furthermore, increasing the solution pH from 5 to 8 led to an increase in the degradation rate, which was consistent with the expected pH dependency of trypsin activity. In addition, the effect of bulk concentration also supported the involvement of protease impurities rather than a spontaneous peptide bond hydrolysis reaction. Trace trypsin-like protease impurities led to an unusual site-specific backbone cleavage of BMS-196854. The proteolytic degradation can be minimized by treating the bulk solution with immobilized soybean trypsin

Airborne optical detection of oil on water.

NASA Technical Reports Server (NTRS)

Millard, J. P.; Arvesen, J. C.

1972-01-01

Airborne measurements were made over controlled oil-spill test sites to evaluate various techniques, utilizing reflected sunlight, for detecting oil on water. The results of these measurements show that (1) maximum contrast between oil and water is in the UV and red portions of the spectrum; (2) minimum contrast is in the blue-green; (3) differential polarization appears to be a very promising technique; (4) no characteristic absorption bands, which would permit one oil to be distinguished from another, were discovered in the spectral regions measured; (5) sky conditions greatly influence the contrast between oil and water; and (6) highest contrast was achieved under overcast sky conditions.

A stoichiometry driven universal spatial organization of backbones of folded proteins: are there Chargaff's rules for protein folding?

PubMed

Mittal, A; Jayaram, B; Shenoy, Sandhya; Bawa, Tejdeep Singh

2010-10-01

Protein folding is at least a six decade old problem, since the times of Pauling and Anfinsen. However, rules of protein folding remain elusive till date. In this work, rigorous analyses of several thousand crystal structures of folded proteins reveal a surprisingly simple unifying principle of backbone organization in protein folding. We find that protein folding is a direct consequence of a narrow band of stoichiometric occurrences of amino-acids in primary sequences, regardless of the size and the fold of a protein. We observe that "preferential interactions" between amino-acids do not drive protein folding, contrary to all prevalent views. We dedicate our discovery to the seminal contribution of Chargaff which was one of the major keys to elucidation of the stoichiometry-driven spatially organized double helical structure of DNA.

Solitary water wave interactions

NASA Astrophysics Data System (ADS)

Craig, W.; Guyenne, P.; Hammack, J.; Henderson, D.; Sulem, C.

2006-05-01

This article concerns the pairwise nonlinear interaction of solitary waves in the free surface of a body of water lying over a horizontal bottom. Unlike solitary waves in many completely integrable model systems, solitary waves for the full Euler equations do not collide elastically; after interactions, there is a nonzero residual wave that trails the post-collision solitary waves. In this report on new numerical and experimental studies of such solitary wave interactions, we verify that this is the case, both in head-on collisions (the counterpropagating case) and overtaking collisions (the copropagating case), quantifying the degree to which interactions are inelastic. In the situation in which two identical solitary waves undergo a head-on collision, we compare the asymptotic predictions of Su and Mirie [J. Fluid Mech. 98, 509 (1980)] and Byatt-Smith [J. Fluid Mech. 49, 625 (1971)], the wavetank experiments of Maxworthy [J. Fluid Mech. 76, 177 (1976)], and the numerical results of Cooker, Weidman, and Bale [J. Fluid Mech. 342, 141 (1997)] with independent numerical simulations, in which we quantify the phase change, the run-up, and the form of the residual wave and its Fourier signature in both small- and large-amplitude interactions. This updates the prior numerical observations of inelastic interactions in Fenton and Rienecker [J. Fluid Mech. 118, 411 (1982)]. In the case of two nonidentical solitary waves, our precision wavetank experiments are compared with numerical simulations, again observing the run-up, phase lag, and generation of a residual from the interaction. Considering overtaking solitary wave interactions, we compare our experimental observations, numerical simulations, and the asymptotic predictions of Zou and Su [Phys. Fluids 29, 2113 (1986)], and again we quantify the inelastic residual after collisions in the simulations. Geometrically, our numerical simulations of overtaking interactions fit into the three categories of Korteweg-deVries two

RosettaRemodel: A Generalized Framework for Flexible Backbone Protein Design

PubMed Central

Huang, Po-Ssu; Ban, Yih-En Andrew; Richter, Florian; Andre, Ingemar; Vernon, Robert; Schief, William R.; Baker, David

2011-01-01

We describe RosettaRemodel, a generalized framework for flexible protein design that provides a versatile and convenient interface to the Rosetta modeling suite. RosettaRemodel employs a unified interface, called a blueprint, which allows detailed control over many aspects of flexible backbone protein design calculations. RosettaRemodel allows the construction and elaboration of customized protocols for a wide range of design problems ranging from loop insertion and deletion, disulfide engineering, domain assembly, loop remodeling, motif grafting, symmetrical units, to de novo structure modeling. PMID:21909381

Evaluation of Polymerase Chain Reaction for Detecting Coliform Bacteria in Drinking Water Sources

PubMed Central

Isfahani, Bahram Nasr; Fazeli, Hossein; Babaie, Zeinab; Poursina, Farkhondeh; Moghim, Sharareh; Rouzbahani, Meisam

2017-01-01

Background: Coliform bacteria are used as indicator organisms for detecting fecal pollution in water. Traditional methods including microbial culture tests in lactose-containing media and enzyme-based tests for the detection of β-galactosidase; however, these methods are time-consuming and less specific. The aim of this study was to evaluate polymerase chain reaction (PCR) for detecting coliform. Materials and Methods: Totally, 100 of water samples from Isfahan drinking water source were collected. Coliform bacteria and Escherichia coli were detected in drinking water using LacZ and LamB genes in PCR method performed in comparison with biochemical tests for all samples. Results: Using phenotyping, 80 coliform isolates were found. The results of the biochemical tests illustrated 78.7% coliform bacteria and 21.2% E. coli. PCR results for LacZ and LamB genes were 67.5% and 17.5%, respectively. Conclusion: The PCR method was shown to be an effective, sensitive, and rapid method for detecting coliform and E. coli in drinking water from the Isfahan drinking water sources. PMID:29142893

Optimizing Noble Gas-Water Interactions via Monte Carlo Simulations.

PubMed

Warr, Oliver; Ballentine, Chris J; Mu, Junju; Masters, Andrew

2015-11-12

In this work we present optimized noble gas-water Lennard-Jones 6-12 pair potentials for each noble gas. Given the significantly different atomic nature of water and the noble gases, the standard Lorentz-Berthelot mixing rules produce inaccurate unlike molecular interactions between these two species. Consequently, we find simulated Henry's coefficients deviate significantly from their experimental counterparts for the investigated thermodynamic range (293-353 K at 1 and 10 atm), due to a poor unlike potential well term (εij). Where εij is too high or low, so too is the strength of the resultant noble gas-water interaction. This observed inadequacy in using the Lorentz-Berthelot mixing rules is countered in this work by scaling εij for helium, neon, argon, and krypton by factors of 0.91, 0.8, 1.1, and 1.05, respectively, to reach a much improved agreement with experimental Henry's coefficients. Due to the highly sensitive nature of the xenon εij term, coupled with the reasonable agreement of the initial values, no scaling factor is applied for this noble gas. These resulting optimized pair potentials also accurately predict partitioning within a CO2-H2O binary phase system as well as diffusion coefficients in ambient water. This further supports the quality of these interaction potentials. Consequently, they can now form a well-grounded basis for the future molecular modeling of multiphase geological systems.

Backbone-only restraints for fast determination of the protein fold: The role of paramagnetism-based restraints. Cytochrome b562 as an example

NASA Astrophysics Data System (ADS)

Banci, Lucia; Bertini, Ivano; Felli, Isabella C.; Sarrou, Josephine

2005-02-01

CH α residual dipolar couplings (Δ rdc's) were measured for the oxidized cytochrome b562 from Escherichia coli as a result of its partial self-orientation in high magnetic fields due to the anisotropy of the overall magnetic susceptibility tensor. Both the low spin iron (III) heme and the four-helix bundle fold contribute to the magnetic anisotropy tensor. CH α Δ rdc's, which span a larger range than the analogous NH values (already available in the literature) sample large space variations at variance with NH Δ rdc's, which are largely isooriented within α helices. The whole structure is now significantly refined with the chemical shift index and CH α Δ rdc's. The latter are particularly useful also in defining the molecular magnetic anisotropy parameters. It is shown here that the backbone folding can be conveniently and accurately determined using backbone restraints only, which include NOEs, hydrogen bonds, residual dipolar couplings, pseudocontact shifts, and chemical shift index. All these restraints are easily and quickly determined from the backbone assignment. The calculated backbone structure is comparable to that obtained by using also side chain restraint. Furthermore, the structure obtained with backbone only restraints is, in its whole, very similar to that obtained with the complete set of restraints. The paramagnetism based restraints are shown to be absolutely relevant, especially for Δ rdc's.

Detecting population–environmental interactions with mismatched time series data

PubMed Central

Ferguson, Jake M.; Reichert, Brian E.; Fletcher, Robert J.; Jager, Henriëtte I.

2017-01-01

Time series analysis is an essential method for decomposing the influences of density and exogenous factors such as weather and climate on population regulation. However, there has been little work focused on understanding how well commonly collected data can reconstruct the effects of environmental factors on population dynamics. We show that, analogous to similar scale issues in spatial data analysis, coarsely sampled temporal data can fail to detect covariate effects when interactions occur on timescales that are fast relative to the survey period. We propose a method for modeling mismatched time series data that couples high-resolution environmental data to low-resolution abundance data. We illustrate our approach with simulations and by applying it to Florida’s southern Snail kite population. Our simulation results show that our method can reliably detect linear environmental effects and that detecting nonlinear effects requires high-resolution covariate data even when the population turnover rate is slow. In the Snail kite analysis, our approach performed among the best in a suite of previously used environmental covariates explaining Snail kite dynamics and was able to detect a potential phenological shift in the environmental dependence of Snail kites. Our work provides a statistical framework for reliably detecting population–environment interactions from coarsely surveyed time series. An important implication of this work is that the low predictability of animal population growth by weather variables found in previous studies may be due, in part, to how these data are utilized as covariates. PMID:28759123

Tritium containing polymers having a polymer backbone substantially void of tritium

DOEpatents

Jensen, George A.; Nelson, David A.; Molton, Peter M.

1992-01-01

A radioluminescent light source comprises a solid mixture of a phosphorescent substance and a tritiated polymer. The solid mixture forms a solid mass having length, width, and thickness dimensions, and is capable of self-support. In one aspect of the invention, the phosphorescent substance comprises solid phosphor particles supported or surrounded within a solid matrix by a tritium containing polymer. The tritium containing polymer comprises a polymer backbone which is essentially void of tritium.

Bracing the Infantry’s Backbone for 21st Century Operations

DTIC Science & Technology

2010-04-27

TERMS Strategic Corporal, NCO Training and Education, Enlisted Retention. 16 . SECURITY CLASSIFICATION OF: 17. LIMITATION OF 18. NUMBER ABSTRACT OF...Demographics and Why We Must Change .......... 9 Building the Backbone One Vertebrae at a Time: Fixing NCO Training and Education .. 16 Don’t Let a Good Thing...scorn of nearly everything on earth. .... They were the Leathernecks, the Old Timers: collected from ship’s guards and shore stations all over the

Presence of Cryptosporidium parvum and Giardia lamblia in water samples from Southeast Asia: towards an integrated water detection system.

PubMed

Kumar, Thulasi; Abd Majid, Mohamad Azlan; Onichandran, Subashini; Jaturas, Narong; Andiappan, Hemah; Salibay, Cristina C; Tabo, Hazel A L; Tabo, Norbel; Dungca, Julieta Z; Tangpong, Jitbanjong; Phiriyasamith, Sucheep; Yuttayong, Boonyaorn; Polseela, Raxsina; Do, Binh Nhu; Sawangjaroen, Nongyao; Tan, Tian-Chye; Lim, Yvonne A L; Nissapatorn, Veeranoot

2016-01-13

Access to clean and safe drinking water that is free from pathogenic protozoan parasites, especially Cryptosporidium parvum and Giardia lamblia that cause gastrointestinal illness in humans, is still an issue in Southeast Asia (SEA). This study is the first attempt to detect the aforementioned protozoan parasites in water samples from countries in SEA, using real-time polymerase chain reaction (qPCR) assays. A total of 221 water samples of 10 l each were collected between April and October 2013 from Malaysia (53), Thailand (120), the Philippines (33), and Vietnam (15). A physicochemical analysis was conducted. The water samples were processed in accordance with the US Environmental Protection Agency's methods 1622/1623.1, microscopically observed and subsequently screened using qPCR assays. Cryptosporidium oocysts were detected in treated water samples from the Philippines (1/10), with a concentration of 0.06 ± 0.19 oocyst/L, and untreated water samples from Thailand (25/93), Malaysia (17/44), and the Philippines (11/23), with concentrations ranging from 0.13 ± 0.18 to 0.57 ± 1.41 oocyst/L. Giardia cysts were found in treated water samples from the Philippines (1/10), with a concentration of 0.02 ± 0.06 cyst/L, and in untreated water samples from Thailand (20/93), Vietnam (5/10), Malaysia (22/44), and the Philippines (16/23), with concentrations ranging from 0.12 ± 0.3 to 8.90 ± 19.65 cyst/L. The pathogens C. parvum and G. lamblia were detected using using qPCR assays by targeting the 138-bp fragment and the small subunit gene, respectively. C. parvum was detected in untreated water samples from the Philippines (1/23) and Malaysia (2/44), whilst, G. lamblia detected was detected in treated water samples from the Philippines (1/10) and in untreated water samples from Thailand (21/93), Malaysia (12/44), and the Philippines (17/23). Nitrate concentration was found to have a high positive correlation with (oo)cyst (0.993). The presence of

Effects of counterion size and backbone rigidity on the dynamics of ionic polymer melts and glasses

DOE Office of Scientific and Technical Information (OSTI.GOV)

Fu, Yao; Bocharova, Vera; Ma, Mengze

Backbone rigidity, counterion size and the static dielectric constant affect the glass transition temperature, segmental relaxation time and decoupling between counterion and segmental dynamics in significant manners.

Peptide backbone orientation and dynamics in spider dragline silk and two-photon excitation in nuclear magnetic and quadrupole resonance

NASA Astrophysics Data System (ADS)

Eles, Philip Thomas

2005-07-01

In the first part of the dissertation, spider dragline silk is studied by solid state NMR techniques. The dependence of NMR frequency on molecular orientation is exploited using the DECODER experiment to determine the orientation of the protein backbone within the silk fibre. Practical experimental considerations require that the silk fibres be wound about a cylindrical axis perpendicular to the external magnetic field, complicating the reconstruction of the underlying orientation distribution and necess-itating the development of numerical techniques for this purpose. A two-component model of silk incorporating static b-sheets and polyglycine II helices adequately fits the NMR data and suggests that the b-sheets are well aligned along the silk axis (20 FWHM) while the helices are poorly aligned (68 FWHM). The effects of fibre strain, draw rate and hydration on orientation are measured. Measurements of the time-scale for peptide backbone motion indicate that when wet, a strain-dependent frac-tion of the poorly aligned component becomes mobile. This suggests a mechanism for the supercontraction of silk involving latent entropic springs that undergo a local strain-dependent phase transition, driving supercontraction. In the second part of this dissertation a novel method is developed for exciting NMR and nuclear quadrupole resonance (NQR) by rf irradiation at multiple frequencies that sum to (or differ by) the resonance frequency. This is fundamentally different than traditional NMR experiments where irradiation is applied on-resonance. With excitation outside the detection bandwidth, two-photon excitation allows for detection of free induction signals during excitation, completely eliminating receiver dead-time. A theoretical approach to describing two-photon excitation is developed based on average Hamiltonian theory. An intuition for two-photon excitation is gained by analogy to the coherent absorption of multiple photons requiring conservation of total energy and

Enhancement of Thermodynamic Gas-Phase Acidity and Basicity of Water by Means of Secondary Interactions.

PubMed

Montero-Campillo, M Merced; Alkorta, Ibon; Elguero, Jose

2018-06-26

A series of A···water, B···water complexes (A = acid, B =base) are studied at the G4 level of theory to show that water acidity or basicity can be modulated by non-covalent interactions. Protic and non-protic acids interacting with water form hydrogen bonds or other kind of non-covalent interactions, respectively, that may dramatically change the acidity of water up to almost 360 kJ·mol-1 in terms of enthalpy. Similarly, hydrogen bonds responsible for the interaction between typical small nitrogen-containing Lewis bases and water can enhance the proton affinity of water by almost 300 kJ·mol-1. Our results reveal that these large enhancements are linearly related with the binding energy of the charged complexes, and are determined by the Lewis acid-base properties of the molecule involved in the interaction, allowing a quite precise modulation of the corresponding acid-base properties of water. © 2018 WILEY-VCH Verlag GmbH & Co. KGaA, Weinheim.

Vestibular-somatosensory interactions: effects of passive whole-body rotation on somatosensory detection.

PubMed

Ferrè, Elisa Raffaella; Kaliuzhna, Mariia; Herbelin, Bruno; Haggard, Patrick; Blanke, Olaf

2014-01-01

Vestibular signals are strongly integrated with information from several other sensory modalities. For example, vestibular stimulation was reported to improve tactile detection. However, this improvement could reflect either a multimodal interaction or an indirect interaction driven by vestibular effects on spatial attention and orienting. Here we investigate whether natural vestibular activation induced by passive whole-body rotation influences tactile detection. In particular, we assessed the ability to detect faint tactile stimuli to the fingertips of the left and right hand during spatially congruent or incongruent rotations. We found that passive whole-body rotations significantly enhanced sensitivity to faint shocks, without affecting response bias. Critically, this enhancement of somatosensory sensitivity did not depend on the spatial congruency between the direction of rotation and the hand stimulated. Thus, our results support a multimodal interaction, likely in brain areas receiving both vestibular and somatosensory signals.

Detecting Service Chains and Feature Interactions in Sensor-Driven Home Network Services

PubMed Central

Inada, Takuya; Igaki, Hiroshi; Ikegami, Kosuke; Matsumoto, Shinsuke; Nakamura, Masahide; Kusumoto, Shinji

2012-01-01

Sensor-driven services often cause chain reactions, since one service may generate an environmental impact that automatically triggers another service. We first propose a framework that can formalize and detect such service chains based on ECA (event, condition, action) rules. Although the service chain can be a major source of feature interactions, not all service chains lead to harmful interactions. Therefore, we then propose a method that identifies feature interactions within the service chains. Specifically, we characterize the degree of deviation of every service chain by evaluating the gap between expected and actual service states. An experimental evaluation demonstrates that the proposed method successfully detects 11 service chains and 6 feature interactions within 7 practical sensor-driven services. PMID:23012499

Predicting disease-related proteins based on clique backbone in protein-protein interaction network.

PubMed

Yang, Lei; Zhao, Xudong; Tang, Xianglong

2014-01-01

Network biology integrates different kinds of data, including physical or functional networks and disease gene sets, to interpret human disease. A clique (maximal complete subgraph) in a protein-protein interaction network is a topological module and possesses inherently biological significance. A disease-related clique possibly associates with complex diseases. Fully identifying disease components in a clique is conductive to uncovering disease mechanisms. This paper proposes an approach of predicting disease proteins based on cliques in a protein-protein interaction network. To tolerate false positive and negative interactions in protein networks, extending cliques and scoring predicted disease proteins with gene ontology terms are introduced to the clique-based method. Precisions of predicted disease proteins are verified by disease phenotypes and steadily keep to more than 95%. The predicted disease proteins associated with cliques can partly complement mapping between genotype and phenotype, and provide clues for understanding the pathogenesis of serious diseases.

Application of a laser Doppler vibrometer for air-water to subsurface signature detection

NASA Astrophysics Data System (ADS)

Land, Phillip; Roeder, James; Robinson, Dennis; Majumdar, Arun

2015-05-01

There is much interest in detecting a target and optical communications from an airborne platform to a platform submerged under water. Accurate detection and communications between underwater and aerial platforms would increase the capabilities of surface, subsurface, and air, manned and unmanned vehicles engaged in oversea and undersea activities. The technique introduced in this paper involves a Laser Doppler Vibrometer (LDV) for acousto-optic sensing for detecting acoustic information propagated towards the water surface from a submerged platform inside a 12 gallon water tank. The LDV probes and penetrates the water surface from an aerial platform to detect air-water surface interface vibrations caused by an amplifier to a speaker generating a signal generated from underneath the water surface (varied water depth from 1" to 8"), ranging between 50Hz to 5kHz. As a comparison tool, a hydrophone was used simultaneously inside the water tank for recording the acoustic signature of the signal generated between 50Hz to 5kHz. For a signal generated by a submerged platform, the LDV can detect the signal. The LDV detects the signal via surface perturbations caused by the impinging acoustic pressure field; proving a technique of transmitting/sending information/messages from a submerged platform acoustically to the surface of the water and optically receiving the information/message using the LDV, via the Doppler Effect, allowing the LDV to become a high sensitivity optical-acoustic device. The technique developed has much potential usage in commercial oceanography applications. The present work is focused on the reception of acoustic information from an object located underwater.

Neutron scattering studies of nano-scale wood-water interactions

Treesearch

Nayomi Z. Plaza Rodriguez

2017-01-01

Understanding and controlling water in wood is critical to both improving forest products moisture durability and developing new sustainable forest products-based technologies. While wood is known to be hygroscopic, there is still a lack of understanding of the nanoscale wood-water interactions necessary for increased moisture-durability and dimensional stability. My...

Modeling and Detecting Feature Interactions among Integrated Services of Home Network Systems

NASA Astrophysics Data System (ADS)

Igaki, Hiroshi; Nakamura, Masahide

This paper presents a framework for formalizing and detecting feature interactions (FIs) in the emerging smart home domain. We first establish a model of home network system (HNS), where every networked appliance (or the HNS environment) is characterized as an object consisting of properties and methods. Then, every HNS service is defined as a sequence of method invocations of the appliances. Within the model, we next formalize two kinds of FIs: (a) appliance interactions and (b) environment interactions. An appliance interaction occurs when two method invocations conflict on the same appliance, whereas an environment interaction arises when two method invocations conflict indirectly via the environment. Finally, we propose offline and online methods that detect FIs before service deployment and during execution, respectively. Through a case study with seven practical services, it is shown that the proposed framework is generic enough to capture feature interactions in HNS integrated services. We also discuss several FI resolution schemes within the proposed framework.

Panta Rhei-Everything flows: Global Hotspots of Human-Water Interactions

NASA Astrophysics Data System (ADS)

Di Baldassarre, G.; Srinivasan, V.; Tian, F.; Mohamed, Y.; Krueger, T.; Kreibich, H.; Liu, J.; Troy, T. J.; AghaKouchak, A.

2017-12-01

Panta Rhei-Everything Flows is the scientific decade (2013-2022) of the International Association of Hydrological Sciences (IAHS). This initiative aims to reach an improved interpretation of the processes governing the water cycle by focusing on their changing dynamics in connection with rapidly changing human systems (Montanari et al., 2013; McMillan et al., 2016). More than 400 water scientists have been involved in Panta Rhei so far, and several working groups have produced significant outcomes. In this presentation, we first summarize some key achievements of this initiative by showing how they have advanced our understanding of the way in which humans impact on, and respond to, hydrological change. Then, we suggest simple indicators to characterize interactions between water and human systems. These indicators aim to capture the relevance of human-water interactions and their potential to generate negative effects, such as water crises or unintended consequences. Finally, we show an application of these indicators to global hotspots, i.e. contrasting case studies from around the world. Our goal is to facilitate a community-wide effort in collecting and sharing essential data to map the role of human-water interactions across social and hydrological conditions. ReferencesMontanari et al. (2013) Panta Rhei—Everything Flows: Change in hydrology and society—The IAHS Scientific Decade 2013-2022, Hydrological Sciences Journal, 58(6), 1256-1275. McMillan et al. (2016) Panta Rhei 2013-2015: Global perspectives on hydrology, society and change. Hydrological sciences journal 61(7), 1174-1191.

Novel cell-based assay for detection of thyroid receptor beta-interacting environmental contaminants.

PubMed

Stavreva, Diana A; Varticovski, Lyuba; Levkova, Ludmila; George, Anuja A; Davis, Luke; Pegoraro, Gianluca; Blazer, Vicki; Iwanowicz, Luke; Hager, Gordon L

2016-08-10

Even though the presence of endocrine disrupting chemicals (EDCs) with thyroid hormone (TH)-like activities in the environment is a major health concern, the methods for their efficient detection and monitoring are still limited. Here we describe a novel cell assay, based on the translocation of a green fluorescent protein (GFP)-tagged chimeric molecule of glucocorticoid receptor (GR) and the thyroid receptor beta (TRβ) from the cytoplasm to the nucleus in the presence of TR ligands. Unlike the constitutively nuclear TRβ, this GFP-GR-TRβ chimera is cytoplasmic in the absence of hormone while translocating to the nucleus in a time- and concentration-dependent manner upon stimulation with triiodothyronine (T3) and thyroid hormone analogue, TRIAC, while the reverse triiodothyronine (3,3',5'-triiodothyronine, or rT3) was inactive. Moreover, GFP-GR-TRβ chimera does not show any cross-reactivity with the GR-activating hormones, thus providing a clean system for the screening of TR beta-interacting EDCs. Using this assay, we demonstrated that Bisphenol A (BPA) and 3,3',5,5'-Tetrabromobisphenol (TBBPA) induced GFP-GR-TRβ translocation at micro molar concentrations. We screened over 100 concentrated water samples from different geographic locations in the United States and detected a low, but reproducible contamination in 53% of the samples. This system provides a novel high-throughput approach for screening for endocrine disrupting chemicals (EDCs) interacting with TR beta. Published by Elsevier Ireland Ltd.

Novel cell-based assay for detection of thyroid receptor beta-interacting environmental contaminants

USGS Publications Warehouse

Stavreva, Diana A.; Varticovski, Lyuba; Levkova, Ludmila; George, Anuja A.; Davis, Luke; Pegoraro, Gianluca; Blazer, Vicki S.; Iwanowicz, Luke R.; Hager, Gordon L.

2016-01-01

Even though the presence of endocrine disrupting chemicals (EDCs) with thyroid hormone (TH)-like activities in the environment is a major health concern, the methods for their efficient detection and monitoring are still limited. Here we describe a novel cell assay, based on the translocation of a green fluorescent protein (GFP)—tagged chimeric molecule of glucocorticoid receptor (GR) and the thyroid receptor beta (TRβ) from the cytoplasm to the nucleus in the presence of TR ligands. Unlike the constitutively nuclear TRβ, this GFP-GR-TRβ chimera is cytoplasmic in the absence of hormone while translocating to the nucleus in a time- and concentration-dependent manner upon stimulation with triiodothyronine (T3) and thyroid hormone analogue, TRIAC, while the reverse triiodothyronine (3,3′,5′-triiodothyronine, or rT3) was inactive. Moreover, GFP-GR-TRβ chimera does not show any cross-reactivity with the GR-activating hormones, thus providing a clean system for the screening of TR beta-interacting EDCs. Using this assay, we demonstrated that Bisphenol A (BPA) and 3,3′,5,5′-Tetrabromobisphenol (TBBPA) induced GFP-GR-TRβ translocation at micro molar concentrations. We screened over 100 concentrated water samples from different geographic locations in the United States and detected a low, but reproducible contamination in 53% of the samples. This system provides a novel high-throughput approach for screening for endocrine disrupting chemicals (EDCs) interacting with TR beta.

Novel cell-based assay for detection of thyroid receptor beta-interacting environmental contaminants

PubMed Central

Stavreva, Diana A.; Varticovski, Lyuba; Levkova, Ludmila; George, Anuja A.; Davis, Luke; Pegoraro, Gianluca; Blazer, Vicki; Iwanowicz, Luke; Hager, Gordon L.

2016-01-01

Even though the presence of endocrine disrupting chemicals (EDCs) with thyroid hormone (TH)-like activities in the environment is a major health concern, the methods for their efficient detection and monitoring are still limited. Here we describe a novel cell assay, based on the translocation of a green fluorescent protein (GFP) - tagged chimeric molecule of glucocorticoid receptor (GR) and the thyroid receptor beta (TRβ) from the cytoplasm to the nucleus in the presence of TR ligands. Unlike the constitutively nuclear TRβ, this GFP-GR-TRβ chimera is cytoplasmic in the absence of hormone while translocating to the nucleus in a time- and concentration-dependent manner upon stimulation with triiodothyronine (T3) and thyroid hormone analogue, TRIAC, while the reverse triiodothyronine (3,3′,5′-triiodothyronine, or rT3) was inactive. Moreover, GFP-GR-TRβ chimera does not show any cross-reactivity with the GR-activating hormones, thus providing a clean system for the screening of TR beta -interacting EDCs. Using this assay, we demonstrated that Bisphenol A (BPA) and 3,3′,5,5′-Tetrabromobisphenol (TBBPA) induced GFP-GR-TRβ translocation at micro molar concentrations. We screened over 100 concentrated water samples from different geographic locations in the United States and detected a low, but reproducible contamination in 53 % of the samples. This system provides a novel high-throughput approach for screening for endocrine disrupting chemicals (EDCs) interacting with TR beta. PMID:27528272

Thermodynamic and Structural Properties of Methanol-Water Solutions Using Non-Additive Interaction Models

PubMed Central

Zhong, Yang; Warren, G. Lee; Patel, Sandeep

2014-01-01

We study bulk structural and thermodynamic properties of methanol-water solutions via molecular dynamics simulations using novel interaction potentials based on the charge equilibration (fluctuating charge) formalism to explicitly account for molecular polarization at the atomic level. The study uses the TIP4P-FQ potential for water-water interactions, and the CHARMM-based (Chemistry at HARvard Molecular Mechanics) fluctuating charge potential for methanol-methanol and methanol-water interactions. In terms of bulk solution properties, we discuss liquid densities, enthalpies of mixing, dielectric constants, self-diffusion constants, as well as structural properties related to local hydrogen bonding structure as manifested in radial distribution functions and cluster analysis. We further explore the electronic response of water and methanol in the differing local environments established by the interaction of each species predominantly with molecules of the other species. The current force field for the alcohol-water interaction performs reasonably well for most properties, with the greatest deviation from experiment observed for the excess mixing enthalpies, which are predicted to be too favorable. This is qualitatively consistent with the overestimation of the methanol-water gas-phase interaction energy for the lowest-energy conformer (methanol as proton donor). Hydration free energies for methanol in TIP4P-FQ water are predicted to be −5.6±0.2 kcal/mole, in respectable agreement with the experimental value of −5.1 kcal/mole. With respect to solution micro-structure, the present cluster analysis suggests that the micro-scale environment for concentrations where select thermodynamic quantities reach extremal values is described by a bi-percolating network structure. PMID:18074339

Directed-Backbone Dissociation Following Bond-Specific Carbon-Sulfur UVPD at 213 nm

NASA Astrophysics Data System (ADS)

Talbert, Lance E.; Julian, Ryan R.

2018-04-01

Ultraviolet photodissociation or UVPD is an increasingly popular option for tandem-mass spectrometry experiments. UVPD can be carried out at many wavelengths, and it is important to understand how the results will be impacted by this choice. Here, we explore the utility of 213 nm photons for initiating bond-selective fragmentation. It is found that bonds previously determined to be labile at 266 nm, including carbon-iodine and sulfur-sulfur bonds, can also be cleaved with high selectivity at 213 nm. In addition, many carbon-sulfur bonds that are not subject to direct dissociation at 266 nm can be selectively fragmented at 213 nm. This capability can be used to site-specifically create alaninyl radicals that direct backbone dissociation at the radical site, creating diagnostic d-ions. Furthermore, the additional carbon-sulfur bond fragmentation capability leads to signature triplets for fragmentation of disulfide bonds. Absorption of amide bonds can enhance dissociation of nearby labile carbon-sulfur bonds and can be used for stochastic backbone fragmentation typical of UVPD experiments at shorter wavelengths. Several potential applications of the bond-selective fragmentation chemistry observed at 213 nm are discussed. [Figure not available: see fulltext.

Photocatalysts Based on Cobalt-Chelating Conjugated Polymers for Hydrogen Evolution from Water

DOE Office of Scientific and Technical Information (OSTI.GOV)

Li, Lianwei; Hadt, Ryan G.; Yao, Shiyu

Developing photocatalytic systems for water splitting to generate oxygen and hydrogen is one of the biggest chemical challenges in solar energy utilization. In this work, we report the first example of heterogeneous photocatalysts for hydrogen evolution based on in-chain cobalt-chelating conjugated polymers. Four conjugated polymers chelated with earth abundant cobalt ions were synthesized and found to evolve hydrogen photocatalytically from water. These polymers are designed to combine functions of the conjugated backbone as light-harvesting antenna and electron transfer conduit with the in-chain bipyridyl chelated transition metal centers as catalytic active sites. In addition, these polymers are soluble in organic solvents,more » enabling effective interactions with the substrates as well as detailed characterization. We also found a polymer-dependent optimal cobalt chelating concentration at which the highest photocatalytic hydrogen production (PHP) activity can be achieved.« less

Oxygen K edge scattering from bulk comb diblock copolymer reveals extended, ordered backbones above lamellar order-disorder transition

DOE PAGES

Kortright, Jeffrey Barrett; Sun, Jing; Spencer, Ryan K.; ...

2016-12-14

The evolution of molecular morphology in bulk samples of comb diblock copolymer pNdc 12-b-pNte 21 across the lamellar order-disorder transition (ODT) is studied using resonant x-ray scattering at the oxygen K edge, with the goal of determining whether the molecules remain extended or collapse above the ODT. The distinct spectral resonances of carbonyl oxygen on the backbone and ether oxygen in the pNte side chains combine with their different site symmetry within the molecule to yield strong differences in bulk structural sensitivity at all temperatures. Comparison with simple models for the disordered phase clearly reveals that disordering at the ODTmore » corresponds to loss of positional order of molecules with extended backbones that retain orientational order, rather than backbone collapse into a locally isotropic disordered phase. This conclusion is facilitated directly by the distinct structural sensitivity at the two resonances. Lastly, we discuss the roles of depolarized scattering in enhancing this sensitivity, and background fluorescence in limiting dynamic range, in oxygen resonant scattering.« less

Role of monomer sequence and backbone chemistry in polypeptoid copolymers for marine antifouling coatings

NASA Astrophysics Data System (ADS)

Patterson, Anastasia; Wenning, Brandon; Rizis, Georgios; Calabrese, David; Finlay, John; Franco, Sofia; Clare, Anthony; Kramer, Edward; Ober, Christopher; Segalman, Rachel

The design rules elucidated in this work suggest that antifouling coatings bearing pendant peptoid side chains perform better overall in marine fouling tests than those with peptide side chains, with extremely low attachment of N. incerta and high removal of U. linza. This difference in performance is likely due to the lack of a hydrogen bond donor in the peptoid backbone. Furthermore, we show that the bulk polymer material of these hierarchical coatings (based on PEO or PDMS) plays a key role in determining both surface presentation and fouling release performance. We demonstrate these trends utilizing a modular coating based on a triblock copolymer consisting of polystyrene and a vinyl-containing midblock, to which sequence-defined pendant oligomers (peptides or peptoids with sequences of oligo-PEO and fluoroalkyl groups) are attached via thiol-ene ``click'' chemistry. Surface presentation was analyzed with X-ray photoelectron spectroscopy and captive bubble water contact angle, and antifouling performance was evaluated with attachment and removal bioassays of the marine macroalga U. linza and diatom N. incerta. NSF GRFP and ONR PECASE.

Water-mediated ion–ion interactions are enhanced at the water vapor–liquid interface

PubMed Central

Venkateshwaran, Vasudevan; Vembanur, Srivathsan; Garde, Shekhar

2014-01-01

There is overwhelming evidence that ions are present near the vapor–liquid interface of aqueous salt solutions. Charged groups can also be driven to interfaces by attaching them to hydrophobic moieties. Despite their importance in many self-assembly phenomena, how ion–ion interactions are affected by interfaces is not understood. We use molecular simulations to show that the effective forces between small ions change character dramatically near the water vapor–liquid interface. Specifically, the water-mediated attraction between oppositely charged ions is enhanced relative to that in bulk water. Further, the repulsion between like-charged ions is weaker than that expected from a continuum dielectric description and can even become attractive as the ions are drawn to the vapor side. We show that thermodynamics of ion association are governed by a delicate balance of ion hydration, interfacial tension, and restriction of capillary fluctuations at the interface, leading to nonintuitive phenomena, such as water-mediated like charge attraction. “Sticky” electrostatic interactions may have important consequences on biomolecular structure, assembly, and aggregation at soft liquid interfaces. We demonstrate this by studying an interfacially active model peptide that changes its structure from α-helical to a hairpin-turn–like one in response to charging of its ends. PMID:24889634

Water-mediated ion-ion interactions are enhanced at the water vapor-liquid interface.

PubMed

Venkateshwaran, Vasudevan; Vembanur, Srivathsan; Garde, Shekhar

2014-06-17

There is overwhelming evidence that ions are present near the vapor-liquid interface of aqueous salt solutions. Charged groups can also be driven to interfaces by attaching them to hydrophobic moieties. Despite their importance in many self-assembly phenomena, how ion-ion interactions are affected by interfaces is not understood. We use molecular simulations to show that the effective forces between small ions change character dramatically near the water vapor-liquid interface. Specifically, the water-mediated attraction between oppositely charged ions is enhanced relative to that in bulk water. Further, the repulsion between like-charged ions is weaker than that expected from a continuum dielectric description and can even become attractive as the ions are drawn to the vapor side. We show that thermodynamics of ion association are governed by a delicate balance of ion hydration, interfacial tension, and restriction of capillary fluctuations at the interface, leading to nonintuitive phenomena, such as water-mediated like charge attraction. "Sticky" electrostatic interactions may have important consequences on biomolecular structure, assembly, and aggregation at soft liquid interfaces. We demonstrate this by studying an interfacially active model peptide that changes its structure from α-helical to a hairpin-turn-like one in response to charging of its ends.

The backbone N-(4-azidobutyl) linker for the preparation of peptide chimera.

PubMed

Fernández-Llamazares, Ana I; García, Jesús; Adan, Jaume; Meunier, David; Mitjans, Francesc; Spengler, Jan; Albericio, Fernando

2013-09-06

A robust synthetic strategy for the introduction of the N-(4-azidobutyl) linker into peptides using standard SPPS techniques is described. Based on the example of Cilengitide it is shown that the N-(4-azidobutyl) group exerts similar conformational restraints as a backbone N-Me group and allows conjugation of a desired molecule either via click chemistry or-after azide reduction-via acylation or reductive alkylation.

Membrane Curvature Sensing by Amphipathic Helices Is Modulated by the Surrounding Protein Backbone.

PubMed

Doucet, Christine M; Esmery, Nina; de Saint-Jean, Maud; Antonny, Bruno

2015-01-01

Membrane curvature is involved in numerous biological pathways like vesicle trafficking, endocytosis or nuclear pore complex assembly. In addition to its topological role, membrane curvature is sensed by specific proteins, enabling the coordination of biological processes in space and time. Amongst membrane curvature sensors are the ALPS (Amphipathic Lipid Packing Sensors). ALPS motifs are short peptides with peculiar amphipathic properties. They are found in proteins targeted to distinct curved membranes, mostly in the early secretory pathway. For instance, the ALPS motif of the golgin GMAP210 binds trafficking vesicles, while the ALPS motif of Nup133 targets nuclear pores. It is not clear if, besides curvature sensitivity, ALPS motifs also provide target specificity, or if other domains in the surrounding protein backbone are involved. To elucidate this aspect, we studied the subcellular localization of ALPS motifs outside their natural protein context. The ALPS motifs of GMAP210 or Nup133 were grafted on artificial fluorescent probes. Importantly, ALPS motifs are held in different positions and these contrasting architectures were mimicked by the fluorescent probes. The resulting chimeras recapitulated the original proteins localization, indicating that ALPS motifs are sufficient to specifically localize proteins. Modulating the electrostatic or hydrophobic content of Nup133 ALPS motif modified its avidity for cellular membranes but did not change its organelle targeting properties. In contrast, the structure of the backbone surrounding the helix strongly influenced targeting. In particular, introducing an artificial coiled-coil between ALPS and the fluorescent protein increased membrane curvature sensitivity. This coiled-coil domain also provided membrane curvature sensitivity to the amphipathic helix of Sar1. The degree of curvature sensitivity within the coiled-coil context remains correlated to the natural curvature sensitivity of the helices. This suggests

Strong CH/O interactions between polycyclic aromatic hydrocarbons and water: Influence of aromatic system size.

PubMed

Veljković, Dušan Ž

2018-03-01

Energies of CH/O interactions between water molecule and polycyclic aromatic hydrocarbons with a different number of aromatic rings were calculated using ab initio calculations at MP2/cc-PVTZ level. Results show that an additional aromatic ring in structure of polycyclic aromatic hydrocarbons significantly strengthens CH/O interactions. Calculated interaction energies in optimized structures of the most stable tetracene/water complex is -2.27 kcal/mol, anthracene/water is -2.13 kcal/mol and naphthalene/water is -1.97 kcal/mol. These interactions are stronger than CH/O contacts in benzene/water complex (-1.44 kcal/mol) while CH/O contacts in tetracene/water complex are even stronger than CH/O contacts in pyridine/water complexes (-2.21 kcal/mol). Electrostatic potential maps for different polycyclic aromatic hydrocarbons were calculated and used to explain trends in the energies of interactions. Copyright © 2017 Elsevier Inc. All rights reserved.

Tritium containing polymers having a polymer backbone substantially void of tritium

DOEpatents

Jensen, G.A.; Nelson, D.A.; Molton, P.M.

1992-03-31

A radioluminescent light source comprises a solid mixture of a phosphorescent substance and a tritiated polymer. The solid mixture forms a solid mass having length, width, and thickness dimensions, and is capable of self-support. In one aspect of the invention, the phosphorescent substance comprises solid phosphor particles supported or surrounded within a solid matrix by a tritium containing polymer. The tritium containing polymer comprises a polymer backbone which is essentially void of tritium. 2 figs.

Small molecule-mediated duplex formation of nucleic acids with 'incompatible' backbones.

PubMed

Cafferty, Brian J; Musetti, Caterina; Kim, Keunsoo; Horowitz, Eric D; Krishnamurthy, Ramanarayanan; Hud, Nicholas V

2016-04-07

Proflavine, a known intercalator of DNA and RNA, promotes duplex formation by nucleic acids with natural and non-natural backbones that otherwise form duplexes with low thermal stability, and even some that show no sign of duplex formation in the absence of proflavine. These findings demonstrate the potential for intercalators to be used as cofactors for the assembly of rationally designed nucleic acid structures, and could provide fundamental insights regarding intercalation of natural nucleic acid duplexes.

Detection of Cyanotoxins During Potable Water Treatment

USDA-ARS?s Scientific Manuscript database

In 2007, the U.S. EPA listed three cyanobacterial toxins on the CCL3 containment priority list for potable drinking waters. This paper describes all methodologies used for detection of these toxins, and assesses each on a cost/benefit basis. Methodologies for microcystin, cylindrospermopsin, and a...

A new analytical approach to understanding nanoscale lead-iron interactions in drinking water distribution systems.