Structure and electronic properties of ion pairs accompanying cyclic morpholinium cation and alkylphosphite anion based ionic liquids

NASA Astrophysics Data System (ADS)

Verma, Prakash L.; Singh, Priti; Gejji, Shridhar P.

2017-07-01

Molecular insights for the formation of ion pairs accompanying the cyclic ammonium cation based room temperature ionic liquids (RTILs) composed of alkyl substituted N-methylmorpholinium (RMMor) and alkylphosphite [(Rsbnd O)2PHdbnd O] (Rdbnd ethyl, butyl, hexyl, octyl) anion have been derived from the M06-2x level of theory. Electronic structures, binding energies, and spectral characteristics of the ion pairs underlying these RTILs have been characterized. The ion pair formation is largely governed by Csbnd H⋯O and other intermolecular interactions. Calculated binding energies increase with the increasing alkyl chain on either cation or alkylphosphite anion. The cation-anion binding reveals signature in the frequency down-(red) shift of the characteristic anionic Pdbnd O stretching whereas the Psbnd H stretching exhibits a shift in the opposite direction in vibrational spectra which has further been rationalized through molecular electron density topography. Correlations of measured electrochemical stability with the separation of frontier orbital energies and binding energies in the ion pairs have further been established.

Control of box C/D snoRNP assembly by N6-methylation of adenine.

PubMed

Huang, Lin; Ashraf, Saira; Wang, Jia; Lilley, David Mj

2017-09-01

N 6 -methyladenine is the most widespread mRNA modification. A subset of human box C/D snoRNA species have target GAC sequences that lead to formation of N 6 -methyladenine at a key trans Hoogsteen-sugar A·G base pair, of which half are methylated in vivo The GAC target is conserved only in those that are methylated. Methylation prevents binding of the 15.5-kDa protein and the induced folding of the RNA Thus, the assembly of the box C/D snoRNP could in principle be regulated by RNA methylation at its critical first stage. Crystallography reveals that N 6 -methylation of adenine prevents the formation of trans Hoogsteen-sugar A·G base pairs, explaining why the box C/D RNA cannot adopt its kinked conformation. More generally, our data indicate that sheared A·G base pairs (but not Watson-Crick base pairs) are more susceptible to disruption by N 6 mA methylation and are therefore possible regulatory sites. The human signal recognition particle RNA and many related Alu retrotransposon RNA species are also methylated at N6 of an adenine that forms a sheared base pair with guanine and mediates a key tertiary interaction. © 2017 The Authors. Published under the terms of the CC BY 4.0 license.

Triple Helix Formation in a Topologically Controlled DNA Nanosystem.

PubMed

Yamagata, Yutaro; Emura, Tomoko; Hidaka, Kumi; Sugiyama, Hiroshi; Endo, Masayuki

2016-04-11

In the present study, we demonstrate single-molecule imaging of triple helix formation in DNA nanostructures. The binding of the single-molecule third strand to double-stranded DNA in a DNA origami frame was examined using two different types of triplet base pairs. The target DNA strand and the third strand were incorporated into the DNA frame, and the binding of the third strand was controlled by the formation of Watson-Crick base pairing. Triple helix formation was monitored by observing the structural changes in the incorporated DNA strands. It was also examined using a photocaged third strand wherein the binding of the third strand was directly observed using high-speed atomic force microscopy during photoirradiation. We found that the binding of the third strand could be controlled by regulating duplex formation and the uncaging of the photocaged strands in the designed nanospace. © 2016 WILEY-VCH Verlag GmbH & Co. KGaA, Weinheim.

Sequence Effect on the Formation of DNA Minidumbbells.

PubMed

Liu, Yuan; Lam, Sik Lok

2017-11-16

The DNA minidumbbell (MDB) is a recently identified non-B structure. The reported MDBs contain two TTTA, CCTG, or CTTG type II loops. At present, the knowledge and understanding of the sequence criteria for MDB formation are still limited. In this study, we performed a systematic high-resolution nuclear magnetic resonance (NMR) and native gel study to investigate the effect of sequence variations in tandem repeats on the formation of MDBs. Our NMR results reveal the importance of hydrogen bonds, base-base stacking, and hydrophobic interactions from each of the participating residues. We conclude that in the MDBs formed by tandem repeats, C-G loop-closing base pairs are more stabilizing than T-A loop-closing base pairs, and thymine residues in both the second and third loop positions are more stabilizing than cytosine residues. The results from this study enrich our knowledge on the sequence criteria for the formation of MDBs, paving a path for better exploring their potential roles in biological systems and DNA nanotechnology.

A single Watson-Crick G x C base pair in water: aqueous hydrogen bonds in hydrophobic cavities.

PubMed

Sawada, Tomohisa; Fujita, Makoto

2010-05-26

Hydrogen bond (H-bond) formation in water has been a challenging task because water molecules are constant competitors. In biological systems, however, stable H-bonds are formed by shielding the H-bonding sites from the competing water molecules within hydrophobic pockets. Inspired by the nature's elaborated way, we found that even mononucleotides (G and C) can form the minimal G x C Watson-Crick pair in water by simply providing a synthetic cavity that efficiently shields the Watson-Crick H-bonding sites. The minimal Watson-Crick structure in water was elucidated by NMR study and firmly characterized by crystallographic analysis. The crystal structure also displays that, within the cavity, coencapsulated anions and solvents efficiently mediate the minimal G x C Watson-Crick pair formation. Furthermore, the competition experiments with the other nucleobases clearly revealed the evident selectivity for the G x C base pairing in water. These results show the fact that a H-bonded nucleobase pair was effectively induced and stabilized in the local environment of an artificial hydrophobic cavity.

Thermodynamics and kinetics of Na+/K+-formate ion pairs association in polarizable water: A molecular dynamics study

NASA Astrophysics Data System (ADS)

Nguyen, Phuong T. M.; Nguyen, Van T.; Annapureddy, Harsha V. R.; Dang, Liem X.; Do, D. D.

2012-12-01

To enhance our understanding of ion specific activity in biological systems, the potential of mean force approach was utilized to study solvent effects on the interactions between two alkali cations (Na+ and K+) with a formate anion in water. A very complex free energy landscape was observed, much more so than alkali-halide ion pairs. Furthermore, a stronger binding between the Na+-formate pair was found in comparison to the K+-formate pair in water, which is in agreement with experimental and theoretical studies [1-4]. The kinetics of ion-pair inter-conversions was studied using the transition rate theory, along with a number of theoretical approaches such as the Kramers and Grote-Hynes theories. These kinetic results were used to predict solvent effects on dynamical features of ion-pair association, in which we have found that the dynamics of K+-formate pairs is faster than Na+-formate pairs.

Problem-Based Learning in a General Psychology Course.

ERIC Educational Resources Information Center

Willis, Sandra A.

2002-01-01

Describes the adoption of problem-based learning (PBL) techniques in a general psychology course. States that the instructor used a combination of techniques, including think-pair-share, lecture/discussion, and PBL. Notes means and standard deviations for graded components of PBL format versus lecture/discussion format. (Contains 18 references.)…

Concealed d -wave pairs in the s ± condensate of iron-based superconductors

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

Ong, Tzen; Coleman, Piers; Schmalian, Jörg

A central question in iron-based superconductivity is the mechanism by which the paired electrons minimize their strong mutual Coulomb repulsion. In most unconventional superconductors, Coulomb repulsion is minimized through the formation of higher angular momentum Cooper pairs, with Fermi surface nodes in the pair wavefunction. The apparent absence of such nodes in the iron-based superconductors has led to a belief they form an s-wave (s ±) singlet state, which changes sign between the electron and hole pockets. However, the multiorbital nature of these systems opens an alternative possibility. In this paper, we propose a new class of s ± statemore » containing a condensate of d-wave Cooper pairs, concealed by their entanglement with the iron orbitals. By combining the d-wave (L=2) motion of the pairs with the internal angular momenta I =2 of the iron orbitals to make a singlet (J =L+I =0), an s ± superconductor with a nontrivial topology is formed. This scenario allows us to understand the development of octet nodes in potassium-doped Ba 1$-$xK XFe 2As 2 as a reconfiguration of the orbital and internal angular momentum into a high spin (J =L+I =4) state; the reverse transition under pressure into a fully gapped state can then be interpreted as a return to the low-spin singlet. Finally, the formation of orbitally entangled pairs is predicted to give rise to a shift in the orbital content at the Fermi surface, which can be tested via laser-based angle-resolved photoemission spectroscopy.« less

Concealed d -wave pairs in the s ± condensate of iron-based superconductors

DOE PAGES

Ong, Tzen; Coleman, Piers; Schmalian, Jörg

2016-05-02

A central question in iron-based superconductivity is the mechanism by which the paired electrons minimize their strong mutual Coulomb repulsion. In most unconventional superconductors, Coulomb repulsion is minimized through the formation of higher angular momentum Cooper pairs, with Fermi surface nodes in the pair wavefunction. The apparent absence of such nodes in the iron-based superconductors has led to a belief they form an s-wave (s ±) singlet state, which changes sign between the electron and hole pockets. However, the multiorbital nature of these systems opens an alternative possibility. In this paper, we propose a new class of s ± statemore » containing a condensate of d-wave Cooper pairs, concealed by their entanglement with the iron orbitals. By combining the d-wave (L=2) motion of the pairs with the internal angular momenta I =2 of the iron orbitals to make a singlet (J =L+I =0), an s ± superconductor with a nontrivial topology is formed. This scenario allows us to understand the development of octet nodes in potassium-doped Ba 1$-$xK XFe 2As 2 as a reconfiguration of the orbital and internal angular momentum into a high spin (J =L+I =4) state; the reverse transition under pressure into a fully gapped state can then be interpreted as a return to the low-spin singlet. Finally, the formation of orbitally entangled pairs is predicted to give rise to a shift in the orbital content at the Fermi surface, which can be tested via laser-based angle-resolved photoemission spectroscopy.« less

Concealed d-wave pairs in the s± condensate of iron-based superconductors.

PubMed

Ong, Tzen; Coleman, Piers; Schmalian, Jörg

2016-05-17

A central question in iron-based superconductivity is the mechanism by which the paired electrons minimize their strong mutual Coulomb repulsion. In most unconventional superconductors, Coulomb repulsion is minimized through the formation of higher angular momentum Cooper pairs, with Fermi surface nodes in the pair wavefunction. The apparent absence of such nodes in the iron-based superconductors has led to a belief they form an s-wave ([Formula: see text]) singlet state, which changes sign between the electron and hole pockets. However, the multiorbital nature of these systems opens an alternative possibility. Here, we propose a new class of [Formula: see text] state containing a condensate of d-wave Cooper pairs, concealed by their entanglement with the iron orbitals. By combining the d-wave ([Formula: see text]) motion of the pairs with the internal angular momenta [Formula: see text] of the iron orbitals to make a singlet ([Formula: see text]), an [Formula: see text] superconductor with a nontrivial topology is formed. This scenario allows us to understand the development of octet nodes in potassium-doped Ba1-x KXFe2As2 as a reconfiguration of the orbital and internal angular momentum into a high spin ([Formula: see text]) state; the reverse transition under pressure into a fully gapped state can then be interpreted as a return to the low-spin singlet. The formation of orbitally entangled pairs is predicted to give rise to a shift in the orbital content at the Fermi surface, which can be tested via laser-based angle-resolved photoemission spectroscopy.

Dual door entry to exciplex emission in a chimeric DNA duplex containing non-nucleoside-nucleoside pair.

PubMed

Bag, Subhendu Sekhar; Talukdar, Sangita; Kundu, Rajen; Saito, Isao; Jana, Subhashis

2014-01-25

Dual door entry to exciplex formation was established in a chimeric DNA duplex wherein a fluorescent non-nucleosidic base surrogate () is paired against a fluorescent nucleosidic base surrogate (). Packing of the nucleobases via intercalative stacking interactions led to an exciplex emission either via FRET from the donor or direct excitation of the FRET acceptor .

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

Vyas, Rajan; Reed, Andrew J.; Tokarsky, E. John

One common oxidative DNA lesion, 8-oxo-7,8-dihydro-2'-deoxyguanine (8-oxoG), is highly mutagenic in vivo due to its anti-conformation forming a Watson–Crick base pair with correct deoxycytidine 5'-triphosphate (dCTP) and its syn-conformation forming a Hoogsteen base pair with incorrect deoxyadenosine 5'-triphosphate (dATP). Here in this article, we utilized time-resolved X-ray crystallography to follow 8-oxoG bypass by human DNA polymerase β (hPolβ). In the 12 solved structures, both Watson–Crick (anti-8-oxoG:anti-dCTP) and Hoogsteen (syn-8-oxoG:anti-dATP) base pairing were clearly visible and were maintained throughout the chemical reaction. Additionally, a third Mg 2+ appeared during the process of phosphodiester bond formation and was located between the reactingmore » α- and β-phosphates of the dNTP, suggesting its role in stabilizing reaction intermediates. After phosphodiester bond formation, hPolβ reopened its conformation, pyrophosphate was released, and the newly incorporated primer 3'-terminal nucleotide stacked, rather than base paired, with 8-oxoG. These structures provide the first real-time pictures, to our knowledge, of how a polymerase correctly and incorrectly bypasses a DNA lesion.« less

Quantum anharmonic oscillator plus delta-function potential: a molecular view of pairing formation and breaking in the coordinate space

NASA Astrophysics Data System (ADS)

Sumaryada, Tony; Maha Putra, Bima; Pramudito, Sidikrubadi

2017-05-01

We propose an alternative way to describe the pairing formation and breaking via a quantum anharmonic oscillator with a delta-function potential model. Unlike BCS theory, which describes the pairing formation in the momentum space, this model works in the coordinate space and is able to give a molecular view of pairing formation and breaking in the coordinate space. By exploring the dynamical interplay between the intrinsic factor (dissociation energy) and external factor (pairing strength) of this system additional information was gained, including the critical pairing strength and critical scattering length, which might relate to the BCS-BEC crossover phenomena and halo state formation. Although only the energetic aspect of pairing is described by this model, its simplicity and pedagogical steps might help undergraduate students to understand the pairing problem in a simple way.

pKa shifting in double-stranded RNA is highly dependent upon nearest neighbors and bulge positioning.

PubMed

Wilcox, Jennifer L; Bevilacqua, Philip C

2013-10-22

Shifting of pKa's in RNA is important for many biological processes; however, the driving forces responsible for shifting are not well understood. Herein, we determine how structural environments surrounding protonated bases affect pKa shifting in double-stranded RNA (dsRNA). Using (31)P NMR, we determined the pKa of the adenine in an A(+)·C base pair in various sequence and structural environments. We found a significant dependence of pKa on the base pairing strength of nearest neighbors and the location of a nearby bulge. Increasing nearest neighbor base pairing strength shifted the pKa of the adenine in an A(+)·C base pair higher by an additional 1.6 pKa units, from 6.5 to 8.1, which is well above neutrality. The addition of a bulge two base pairs away from a protonated A(+)·C base pair shifted the pKa by only ~0.5 units less than a perfectly base paired hairpin; however, positioning the bulge just one base pair away from the A(+)·C base pair prohibited formation of the protonated base pair as well as several flanking base pairs. Comparison of data collected at 25 °C and 100 mM KCl to biological temperature and Mg(2+) concentration revealed only slight pKa changes, suggesting that similar sequence contexts in biological systems have the potential to be protonated at biological pH. We present a general model to aid in the determination of the roles protonated bases may play in various dsRNA-mediated processes including ADAR editing, miRNA processing, programmed ribosomal frameshifting, and general acid-base catalysis in ribozymes.

Birds choose long-term partners years before breeding

USGS Publications Warehouse

Teitelbaum, Claire S.; Converse, Sarah J.; Mueller, Thomas

2017-01-01

Pair bonds can provide social benefits to long-term monogamous species alongside their benefits for reproduction. However, little is known about when these bonds form, in particular how long they are present before breeding. Previous studies of pair formation in long-term monogamous birds have been rather data-limited, but for many migratory birds they report pair formation on the wintering grounds. We provide the first systematic investigation of prebreeding association patterns of long-term monogamous pairs by examining entire life histories based on tracking data of migratory whooping cranes, Grus americana. We found that a substantial portion (62%) of breeding pairs started associating at least 12 months before first breeding, with 16 of 58 breeding pairs beginning to associate over 2 years before first breeding. For most pairs, these associations with future breeding partners also became unique and distinguishable from association patterns with nonpartner individuals 12 months before first breeding. In addition, 60% of pair associations began before at least one partner had reached nominal sexual maturity. Most pairs began associating in the late spring upon arrival at the summer grounds, while associations beginning at other times of the year were rare. Patterns in the associations of pairs prior to breeding can point to the potential benefits of prebreeding relationships, for instance providing support in competitive interactions or increasing partner familiarity.

Understanding the kinetic mechanism of RNA single base pair formation

PubMed Central

Xu, Xiaojun; Yu, Tao; Chen, Shi-Jie

2016-01-01

RNA functions are intrinsically tied to folding kinetics. The most elementary step in RNA folding is the closing and opening of a base pair. Understanding this elementary rate process is the basis for RNA folding kinetics studies. Previous studies mostly focused on the unfolding of base pairs. Here, based on a hybrid approach, we investigate the folding process at level of single base pairing/stacking. The study, which integrates molecular dynamics simulation, kinetic Monte Carlo simulation, and master equation methods, uncovers two alternative dominant pathways: Starting from the unfolded state, the nucleotide backbone first folds to the native conformation, followed by subsequent adjustment of the base conformation. During the base conformational rearrangement, the backbone either retains the native conformation or switches to nonnative conformations in order to lower the kinetic barrier for base rearrangement. The method enables quantification of kinetic partitioning among the different pathways. Moreover, the simulation reveals several intriguing ion binding/dissociation signatures for the conformational changes. Our approach may be useful for developing a base pair opening/closing rate model. PMID:26699466

Silver(I)-Mediated Base Pairs in DNA Sequences Containing 7-Deazaguanine/Cytosine: towards DNA with Entirely Metallated Watson-Crick Base Pairs.

PubMed

Méndez-Arriaga, José M; Maldonado, Carmen R; Dobado, José A; Galindo, Miguel A

2018-03-26

DNA sequences comprising noncanonical 7-deazaguanine ( 7C G) and canonical cytosine (C) are capable of forming Watson-Crick base pairs via hydrogen bonds as well as silver(I)-mediated base pairs by coordination to central silver(I) ions. Duplexes I and II containing 7C G and C have been synthesized and characterized. The incorporation of silver(I) ions into these duplexes has been studied by means of temperature-dependent UV spectroscopy, circular dichroism, and DFT calculations. The results suggest the formation of DNA molecules comprising contiguous metallated 7C G-Ag I -C Watson-Crick base pairs that preserve the original B-type conformation. Furthermore, additional studies performed on duplex III indicated that, in the presence of Ag I ions, 7C G-C and 7C A-T Watson-Crick base pairs ( 7C A, 7-deazadenine; T, thymine) can be converted to metallated 7C G-Ag I -C and 7C A-Ag I -T base pairs inside the same DNA molecule whilst maintaining its initial double helix conformation. These findings are very important for the development of customized silver-DNA nanostructures based on a Watson-Crick complementarity pattern. © 2018 Wiley-VCH Verlag GmbH & Co. KGaA, Weinheim.

Viewing Human DNA Polymerase β Faithfully and Unfaithfully Bypass an Oxidative Lesion by Time-Dependent Crystallography

DOE PAGES

Vyas, Rajan; Reed, Andrew J.; Tokarsky, E. John; ...

2015-03-31

One common oxidative DNA lesion, 8-oxo-7,8-dihydro-2'-deoxyguanine (8-oxoG), is highly mutagenic in vivo due to its anti-conformation forming a Watson–Crick base pair with correct deoxycytidine 5'-triphosphate (dCTP) and its syn-conformation forming a Hoogsteen base pair with incorrect deoxyadenosine 5'-triphosphate (dATP). Here in this article, we utilized time-resolved X-ray crystallography to follow 8-oxoG bypass by human DNA polymerase β (hPolβ). In the 12 solved structures, both Watson–Crick (anti-8-oxoG:anti-dCTP) and Hoogsteen (syn-8-oxoG:anti-dATP) base pairing were clearly visible and were maintained throughout the chemical reaction. Additionally, a third Mg 2+ appeared during the process of phosphodiester bond formation and was located between the reactingmore » α- and β-phosphates of the dNTP, suggesting its role in stabilizing reaction intermediates. After phosphodiester bond formation, hPolβ reopened its conformation, pyrophosphate was released, and the newly incorporated primer 3'-terminal nucleotide stacked, rather than base paired, with 8-oxoG. These structures provide the first real-time pictures, to our knowledge, of how a polymerase correctly and incorrectly bypasses a DNA lesion.« less

Viewing Human DNA Polymerase β Faithfully and Unfaithfully Bypass an Oxidative Lesion by Time-Dependent Crystallography

PubMed Central

Vyas, Rajan; Reed, Andrew J.; Tokarsky, E. John; Suo, Zucai

2015-01-01

One common oxidative DNA lesion, 8-oxo-7,8-dihydro-2′-deoxyguanine (8-oxoG), is highly mutagenic in vivo due to its anti-conformation forming a Watson–Crick base pair with correct deoxycytidine 5′-triphosphate (dCTP) and its syn-conformation forming a Hoogsteen base pair with incorrect deoxyadenosine 5′-triphosphate (dATP). Here, we utilized time-resolved X-ray crystallography to follow 8-oxoG bypass by human DNA polymerase β (hPolβ). In the 12 solved structures, both Watson–Crick (anti-8-oxoG:anti-dCTP) and Hoogsteen (syn-8-oxoG:anti-dATP) base pairing were clearly visible and were maintained throughout the chemical reaction. Additionally, a third Mg2+ appeared during the process of phosphodiester bond formation and was located between the reacting α- and β-phosphates of the dNTP, suggesting its role in stabilizing reaction intermediates. After phosphodiester bond formation, hPolβ reopened its conformation, pyrophosphate was released, and the newly incorporated primer 3′-terminal nucleotide stacked, rather than base paired, with 8-oxoG. These structures provide the first real-time pictures, to our knowledge, of how a polymerase correctly and incorrectly bypasses a DNA lesion. PMID:25825995

Maintenance of Dimer Conformation by the Dengue Virus Core Protein α4-α4′ Helix Pair Is Critical for Nucleocapsid Formation and Virus Production

PubMed Central

Teoh, Pak-Guan; Huang, Zhi-Shun; Pong, Wen-Li; Chen, Po-Chiang

2014-01-01

ABSTRACT The virion of dengue virus (DENV) is composed of a viral envelope covering a nucleocapsid formed by a complex of viral genomic RNA and core protein (CP). DENV CP forms a dimer via the internal α2 and α4 helices of each monomer. Pairing of α2-α2′ creates a continuous hydrophobic surface, while the α4-α4′ helix pair joins the homodimer via side-chain interactions of the inner-edge residues. However, the importance of dimer conformation and the α4 helix of DENV CP in relation to its function are poorly understood. Loss of association between CP and lipid droplets (LDs) due to mutation suggests that the CP hydrophobic surface was not exposed, offering a possible explanation for the absence of dimers. Further assays suggest the connection between CP folding and protein stability. Attenuation of full-length RNA-derived virus production is associated with CP mutation, since no significant defects were detected in virus translation and replication. The in vitro characterization assays further highlighted that the α4-α4′ helix pair conformation is critical in preserving the overall α-helical content, thermostability, and dimer formation ability of CP, features correlated with the efficiency of nucleocapsid formation. Addition of Tween 20 improves in vitro nucleocapsid-like particle formation, suggesting the role of the LD in nucleocapsid formation in vivo. This study provides the first direct link between the α4-α4′ helix pair interaction and the CP dimer conformation that is the basis of CP function, particularly in nucleocapsid formation during virion production. IMPORTANCE Structure-based mutagenesis study of the dengue virus core protein (CP) reveals that the α4-α4′ helix pair is the key to maintaining its dimer conformation, which is the basis of CP function in nucleocapsid formation and virus production. Attenuation of full-length RNA-derived virus production is associated with CP mutation, since no significant defects in virus translation and replication were detected. In vitro inefficiency and size of nucleocapsid-like particle (NLP) formation offer a possible explanation for in vivo virus production inefficiency upon CP mutation. Further, the transition of NLP morphology from an incomplete state to an intact particle shown by α4-α4′ helix pair mutants in the presence of a nonionic detergent suggests the regulatory role of the intracellular lipid droplet (LD) in CP-LD interaction and in promoting nucleocapsid formation. This study provides the first direct link between the α4-α4′ helix pair interaction and CP dimer conformation that is the fundamental requirement of CP function, particularly in nucleocapsid formation during virion production. PMID:24807709

Thermodynamics and Kinetics of Na+/K+-Formate Ion Pairs Association in Polarizable Water: A Molecular Dynamics Study

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

Nguyen, Phuong T.; Nguyen, Van T.; Annapureddy, Harsha V.

2012-12-03

To elevate our understanding of ion specific activity in biological systems, the potential of mean force approach was utilized to study solvent effects on interactions between two alkali cations (Na+ and K+) with a formate anion in water. A very complex free energy landscape was observed, much more so than alkali-halide ion pairs. Furthermore, stronger binding between the Na+-formate pair was found in comparison to the K+-formate pair in water, a finding that agrees with experimental and theoretical studies of these systems. The kinetics of ion-pair interconversions were studied using transition rate theory, along with a variety of theoretical approachesmore » such as the Kramers and Grote Hynes theories. These rate results were used to predict solvent effects on dynamical features of contact ion-pair association, in which faster dynamics were found for K+-formate pairs than for Na+-formate pairs. This work was supported by the U.S. Department of Energy (DOE), Office of Basic Energy Sciences (BES), Division of Chemical Sciences, Geosciences and Biosciences. Pacific Northwest National Laboratory is a multiprogram national laboratory operated for DOE by Battelle.« less

DNA base dimers are stabilized by hydrogen-bonding interactions including non-Watson-Crick pairing near graphite surfaces.

PubMed

Shankar, Akshaya; Jagota, Anand; Mittal, Jeetain

2012-10-11

Single- and double-stranded DNA are increasingly being paired with surfaces and nanoparticles for numerous applications, such as sensing, imaging, and drug delivery. Unlike the majority of DNA structures in bulk that are stabilized by canonical Watson-Crick pairing between Ade-Thy and Gua-Cyt, those adsorbed on surfaces are often stabilized by noncanonical base pairing, quartet formation, and base-surface stacking. Not much is known about these kinds of interactions. To build an understanding of the role of non-Watson-Crick pairing on DNA behavior near surfaces, one requires basic information on DNA base pair stacking and hydrogen-bonding interactions. All-atom molecular simulations of DNA bases in two cases--in bulk water and strongly adsorbed on a graphite surface--are conducted to study the relative strengths of stacking and hydrogen bond interactions for each of the 10 possible combinations of base pairs. The key information obtained from these simulations is the free energy as a function of distance between two bases in a pair. We find that stacking interactions exert the dominant influence on the stability of DNA base pairs in bulk water as expected. The strength of stability for these stacking interactions is found to decrease in the order Gua-Gua > Ade-Gua > Ade-Ade > Gua-Thy > Gua-Cyt > Ade-Thy > Ade-Cyt > Thy-Thy > Cyt-Thy > Cyt-Cyt. On the other hand, mutual interactions of surface-adsorbed base pairs are stabilized mostly by hydrogen-bonding interactions in the order Gua-Cyt > Ade-Gua > Ade-Thy > Ade-Ade > Cyt-Thy > Gua-Gua > Cyt-Cyt > Ade-Cyt > Thy-Thy > Gua-Thy. Interestingly, several non-Watson-Crick base pairings, which are commonly ignored, have similar stabilization free energies due to interbase hydrogen bonding as Watson-Crick pairs. This clearly highlights the importance of non-Watson-Crick base pairing in the development of secondary structures of oligonucleotides near surfaces.

The formation of catalytically competent enzyme-substrate complex is not a bottleneck in lesion excision by human alkyladenine DNA glycosylase.

PubMed

Kuznetsov, N A; Kiryutin, A S; Kuznetsova, A A; Panov, M S; Barsukova, M O; Yurkovskaya, A V; Fedorova, O S

2017-04-01

Human alkyladenine DNA glycosylase (AAG) protects DNA from alkylated and deaminated purine lesions. AAG flips out the damaged nucleotide from the double helix of DNA and catalyzes the hydrolysis of the N-glycosidic bond to release the damaged base. To understand better, how the step of nucleotide eversion influences the overall catalytic process, we performed a pre-steady-state kinetic analysis of AAG interaction with specific DNA-substrates, 13-base pair duplexes containing in the 7th position 1-N6-ethenoadenine (εA), hypoxanthine (Hx), and the stable product analogue tetrahydrofuran (F). The combination of the fluorescence of tryptophan, 2-aminopurine, and 1-N6-ethenoadenine was used to record conformational changes of the enzyme and DNA during the processes of DNA lesion recognition, damaged base eversion, excision of the N-glycosidic bond, and product release. The thermal stability of the duplexes characterized by the temperature of melting, T m , and the rates of spontaneous opening of individual nucleotide base pairs were determined by NMR spectroscopy. The data show that the relative thermal stability of duplexes containing a particular base pair in position 7, (T m (F/T) < T m (εA/T) < T m (Hx/T) < T m (A/T)) correlates with the rate of reversible spontaneous opening of the base pair. However, in contrast to that, the catalytic lesion excision rate is two orders of magnitude higher for Hx-containing substrates than for substrates containing εA, proving that catalytic activity is not correlated with the stability of the damaged base pair. Our study reveals that the formation of the catalytically competent enzyme-substrate complex is not the bottleneck controlling the catalytic activity of AAG.

Comprehensive thermodynamic analysis of 3′ double-nucleotide overhangs neighboring Watson–Crick terminal base pairs

PubMed Central

O'Toole, Amanda S.; Miller, Stacy; Haines, Nathan; Zink, M. Coleen; Serra, Martin J.

2006-01-01

Thermodynamic parameters are reported for duplex formation of 48 self-complementary RNA duplexes containing Watson–Crick terminal base pairs (GC, AU and UA) with all 16 possible 3′ double-nucleotide overhangs; mimicking the structures of short interfering RNAs (siRNA) and microRNAs (miRNA). Based on nearest-neighbor analysis, the addition of a second dangling nucleotide to a single 3′ dangling nucleotide increases stability of duplex formation up to 0.8 kcal/mol in a sequence dependent manner. Results from this study in conjunction with data from a previous study [A. S. O'Toole, S. Miller and M. J. Serra (2005) RNA, 11, 512.] allows for the development of a refined nearest-neighbor model to predict the influence of 3′ double-nucleotide overhangs on the stability of duplex formation. The model improves the prediction of free energy and melting temperature when tested against five oligomers with various core duplex sequences. Phylogenetic analysis of naturally occurring miRNAs was performed to support our results. Selection of the effector miR strand of the mature miRNA duplex appears to be dependent upon the identity of the 3′ double-nucleotide overhang. Thermodynamic parameters for 3′ single terminal overhangs adjacent to a UA pair are also presented. PMID:16820533

Structural features of the DNA hairpin d(ATCCTA-GTTA-TAGGAT): formation of a G-A base pair in the loop.

PubMed Central

van Dongen, M J; Mooren, M M; Willems, E F; van der Marel, G A; van Boom, J H; Wijmenga, S S; Hilbers, C W

1997-01-01

The three-dimensional structure of the hairpin formed by d(ATCCTA-GTTA-TAGGAT) has been determined by means of two-dimensional NMR studies, distance geometry and molecular dynamics calculations. The first and the last residues of the tetraloop of this hairpin form a sheared G-A base pair on top of the six Watson-Crick base pairs in the stem. The glycosidic torsion angles of the guanine and adenine residues in the G-A base pair reside in the anti and high- anti domain ( approximately -60 degrees ) respectively. Several dihedral angles in the loop adopt non-standard values to accommodate this base pair. The first and second residue in the loop are stacked in a more or less normal helical fashion; the fourth loop residue also stacks upon the stem, while the third residue is directed away from the loop region. The loop structure can be classified as a so-called type-I loop, in which the bases at the 5'-end of the loop stack in a continuous fashion. In this situation, loop stability is unlikely to depend heavily on the nature of the unpaired bases in the loop. Moreover, the present study indicates that the influence of the polarity of a closing A.T pair is much less significant than that of a closing C.G base pair. PMID:9092659

Thermodynamics of triple helix formation: spectrophotometric studies on the d(A)10.2d(T)10 and d(C+3T4C+3).d(G3A4G3).d(C3T4C3) triple helices.

PubMed Central

Pilch, D S; Brousseau, R; Shafer, R H

1990-01-01

We have stabilized the d(A)10.2d(T)10 and d(C+LT4C+3).d(G3A4G3).d(C3T4C3) triple helices with either NaCl or MgCl2 at pH 5.5. UV mixing curves demonstrate a 1:2 stoichiometry of purine to pyrimidine strands under the appropriate conditions of pH and ionic strength. Circular dichroic titrations suggest a possible sequence-independent spectral signature for triplex formation. Thermal denaturation profiles indicate the initial loss of the third strand followed by dissociation of the underlying duplex with increasing temperature. Depending on the base sequence and ionic conditions, the binding affinity of the third strand for the duplex at 25 degrees C is two to five orders of magnitude lower than that of the two strands forming the duplex. Thermodynamic parameters for triplex formation were determined for both sequences in the presence of 50 mM MgCl2 and/or 2.0 M NaCl. Hoogsteen base pairs are 0.22-0.64 kcal/mole less stable than Watson-Crick base pairs, depending on ionic conditions and base composition. C+.G and T.A Hoogsteen base pairs appear to have similar stability in the presence of Mg2+ ions at low pH. PMID:2216768

tRNA1Ser(G34) with the anticodon GGA can recognize not only UCC and UCU codons but also UCA and UCG codons.

PubMed

Yamada, Yuko; Matsugi, Jitsuhiro; Ishikura, Hisayuki

2003-04-15

The tRNA1Ser (anticodon VGA, V=uridin-5-oxyacetic acid) is essential for translation of the UCA codon in Escherichia coli. Here, we studied the translational abilities of serine tRNA derivatives, which have different bases from wild type at the first positions of their anticodons, using synthetic mRNAs containing the UCN (N=A, G, C, or U) codon. The tRNA1Ser(G34) having the anticodon GGA was able to read not only UCC and UCU codons but also UCA and UCG codons. This means that the formation of G-A or G-G pair allowed at the wobble position and these base pairs are noncanonical. The translational efficiency of the tRNA1Ser(G34) for UCA or UCG codon depends on the 2'-O-methylation of the C32 (Cm). The 2'-O-methylation of C32 may give rise to the space necessary for G-A or G-G base pair formation between the first position of anticodon and the third position of codon.

Evidence That Intergenic Spacer Repeats of Drosophila Melanogaster Rrna Genes Function as X-Y Pairing Sites in Male Meiosis, and a General Model for Achiasmatic Pairing

PubMed Central

McKee, B. D.; Habera, L.; Vrana, J. A.

1992-01-01

In Drosophila melanogaster males, X-Y meiotic chromosome pairing is mediated by the nucleolus organizers (NOs) which are located in the X heterochromatin (Xh) and near the Y centromere. Deficiencies for Xh disrupt X-Y meiotic pairing and cause high frequencies of X-Y nondisjunction. Insertion of cloned rRNA genes on an Xh(-) chromosome partially restores normal X-Y pairing and disjunction. To map the sequences within an inserted, X-linked rRNA gene responsible for stimulating X-Y pairing, partial deletions were generated by P element-mediated destabilization of the insert. Complete deletions of the rRNA transcription unit did not interfere with the ability to stimulate X-Y pairing as long as most of the intergenic spacer (IGS) remained. Within groups of deletions that lacked the entire transcription unit and differed only in length of residual IGS material, pairing ability was proportional to the dose of 240-bp intergenic spacer repeats. Deletions of the complete rRNA transcription unit or of the 28S sequences alone blocked nucleolus formation, as determined by binding of an antinucleolar antibody, yet did not interfere with pairing ability, suggesting that X-Y pairing may not be mechanistically related to nucleolus formation. A model for achiasmatic pairing in Drosophila males based upon the combined action of topoisomerase I and a strand transferase is proposed. PMID:1330825

Loss of G-A base pairs is insufficient for achieving a large opening of U4 snRNA K-turn motif.

PubMed

Cojocaru, Vlad; Klement, Reinhard; Jovin, Thomas M

2005-01-01

Upon binding to the 15.5K protein, two tandem-sheared G-A base pairs are formed in the internal loop of the kink-turn motif of U4 snRNA (Kt-U4). We have reported that the folding of Kt-U4 is assisted by protein binding. Unstable interactions that contribute to a large opening of the free RNA ('k-e motion') were identified using locally enhanced sampling molecular dynamics simulations, results that agree with experiments. A detailed analysis of the simulations reveals that the k-e motion in Kt-U4 is triggered both by loss of G-A base pairs in the internal loop and backbone flexibility in the stems. Essential dynamics show that the loss of G-A base pairs is correlated along the first mode but anti-correlated along the third mode with the k-e motion. Moreover, when enhanced sampling was confined to the internal loop, the RNA adopted an alternative conformation characterized by a sharper kink, opening of G-A base pairs and modified stacking interactions. Thus, loss of G-A base pairs is insufficient for achieving a large opening of the free RNA. These findings, supported by previously published RNA structure probing experiments, suggest that G-A base pair formation occurs upon protein binding, thereby stabilizing a selective orientation of the stems.

MSP-HTPrimer: a high-throughput primer design tool to improve assay design for DNA methylation analysis in epigenetics.

PubMed

Pandey, Ram Vinay; Pulverer, Walter; Kallmeyer, Rainer; Beikircher, Gabriel; Pabinger, Stephan; Kriegner, Albert; Weinhäusel, Andreas

2016-01-01

Bisulfite (BS) conversion-based and methylation-sensitive restriction enzyme (MSRE)-based PCR methods have been the most commonly used techniques for locus-specific DNA methylation analysis. However, both methods have advantages and limitations. Thus, an integrated approach would be extremely useful to quantify the DNA methylation status successfully with great sensitivity and specificity. Designing specific and optimized primers for target regions is the most critical and challenging step in obtaining the adequate DNA methylation results using PCR-based methods. Currently, no integrated, optimized, and high-throughput methylation-specific primer design software methods are available for both BS- and MSRE-based methods. Therefore an integrated, powerful, and easy-to-use methylation-specific primer design pipeline with great accuracy and success rate will be very useful. We have developed a new web-based pipeline, called MSP-HTPrimer, to design primers pairs for MSP, BSP, pyrosequencing, COBRA, and MSRE assays on both genomic strands. First, our pipeline converts all target sequences into bisulfite-treated templates for both forward and reverse strand and designs all possible primer pairs, followed by filtering for single nucleotide polymorphisms (SNPs) and known repeat regions. Next, each primer pairs are annotated with the upstream and downstream RefSeq genes, CpG island, and cut sites (for COBRA and MSRE). Finally, MSP-HTPrimer selects specific primers from both strands based on custom and user-defined hierarchical selection criteria. MSP-HTPrimer produces a primer pair summary output table in TXT and HTML format for display and UCSC custom tracks for resulting primer pairs in GTF format. MSP-HTPrimer is an integrated, web-based, and high-throughput pipeline and has no limitation on the number and size of target sequences and designs MSP, BSP, pyrosequencing, COBRA, and MSRE assays. It is the only pipeline, which automatically designs primers on both genomic strands to increase the success rate. It is a standalone web-based pipeline, which is fully configured within a virtual machine and thus can be readily used without any configuration. We have experimentally validated primer pairs designed by our pipeline and shown a very high success rate of primer pairs: out of 66 BSP primer pairs, 63 were successfully validated without any further optimization step and using the same qPCR conditions. The MSP-HTPrimer pipeline is freely available from http://sourceforge.net/p/msp-htprimer.

Aggregation and folding phase transitions of RNA molecules

NASA Astrophysics Data System (ADS)

Bundschuh, Ralf

2007-03-01

RNA is a biomolecule that is involved in nearly all aspects of cellular functions. In order to perform many of these functions, RNA molecules have to fold into specific secondary structures. This folding is driven by the tendency of the bases to form Watson-Crick base pairs. Beyond the biological importance of RNA, the relatively simple rules for structure formation of RNA make it a very interesting system from the statistical physics point of view. We will present examples of phase transitions in RNA secondary structure formation that are amenable to analytical descriptions. A special focus will be on aggregation between several RNA molecules which is important for some regulatory circuits based on RNA structure, triplet repeat diseases like Huntington's, and as a model for prion diseases. We show that depending on the relative strength of the intramolecular and the intermolecular base pairing, RNA molecules undergo a transition into an aggregated phase and quantitatively characterize this transition.

Modified Extraction-Free Ion-Pair Methods for the Determination of Flunarizine Dihydrochloride in Bulk Drug, Tablets, and Human Urine

NASA Astrophysics Data System (ADS)

Prashanth, K. N.; Basavaiah, K.

2018-01-01

Two simple and sensitive extraction-free spectrophotometric methods are described for the determination of flunarizine dihydrochloride. The methods are based on the ion-pair complex formation between the nitrogenous compound flunarizine (FNZ), converted from flunarizine dihydrochloride (FNH), and the acidic dye phenol red (PR), in which experimental variables were circumvented. The first method (method A) is based on the formation of a yellow-colored ion-pair complex (1:1 drug:dye) between FNZ and PR in chloroform, which is measured at 415 nm. In the second method (method B), the formed drug-dye ion-pair complex is treated with ethanolic potassium hydroxide in an ethanolic medium, and the resulting base form of the dye is measured at 580 nm. The stoichiometry of the formed ion-pair complex between the drug and dye (1:1) is determined by Job's continuous variations method, and the stability constant of the complex is also calculated. These methods quantify FNZ over the concentration ranges 5.0-70.0 in method A and 0.5-7.0 μg/mL in method B. The calculated molar absorptivities are 6.17 × 103 and 5.5 × 104 L/mol·cm-1 for method A and method B, respectively, with corresponding Sandell sensitivity values of 0.0655 and 0.0074 μg/cm2. The methods are applied to the determination of FNZ in pure drug and human urine.

Premicellar and micelle formation behavior of dye surfactant ion pairs in aqueous solutions: deprotonation of dye in ion pair micelles.

PubMed

Gohain, Biren; Dutta, Robin K

2008-07-15

The premicellar and micelle formation behavior of dye surfactant ion pairs in aqueous solutions monitored by surface tension and spectroscopic measurements has been described. The measurements have been made for three anionic sulfonephthalein dyes and cationic surfactants of different chain lengths, head groups, and counterions. The observations have been attributed to the formation of closely packed dye surfactant ion pairs which is similar to nonionic surfactants in very dilute concentrations of the surfactant. These ion pairs dominate in the monolayer at the air-water interface of the aqueous dye surfactant solutions below the CMC of the pure surfactant. It has been shown that the dye in the ion pair deprotonates on micelle formation by the ion pair surfactants at near CMC but submicellar surfactant concentrations. The results of an equilibrium study at varying pH agree with the model of deprotonated 1:1 dye-surfactant ion pair formation in the near CMC submicellar solutions. At concentrations above the CMC of the cationic surfactant the dye is solubilized in normal micelles and the monolayer at the air-water interface consists of the cationic surfactant alone even in the presence of the dyes.

Sex-specific rejection in mate-guarding pair formation in the intertidal copepod, Tigriopus californicus

PubMed Central

Burton, Ronald S.

2017-01-01

Securing a potential mate is one of the most important processes in sexual reproduction of animals. Intertidal copepods of the genus Tigriopus show mate-guarding behavior where a male captures a female and continues to clasp her for up to two weeks prior to copulation. Although these copepods form a mate-guarding pair between a male and a female with high accuracy, interactions between the sexes in pair formation have not been well described and the mechanism allowing successful male-female pair formation is not yet understood. In this study, we performed experiments with Tigriopus californicus to analyze the behavior of both a capturer (male) and a captured individual (female or male) in formation of a guarding pair. While capturer males were attracted by both females and males, capture of virgin males was terminated in a significantly shorter time than that of virgin females. However, when presented freshly killed females or males, regardless of the sex of the body, capturer males continued to clasp the body for a comparable time as in an attempt on a living female. Our results suggest that a sex-specific rejection signal actively sent by captured males prevents male-male pair formation. Experiments also suggest that mated females reject an attempt of pair formation. To our knowledge, this is the first study to suggest involvement of active rejection by a captured individual in facilitation of reproductively successful male-female guarding pair formation in the genus Tigriopus. PMID:28832683

A directional nucleation-zipping mechanism for triple helix formation

PubMed Central

Alberti, Patrizia; Arimondo, Paola B.; Mergny, Jean-Louis; Garestier, Thérèse; Hélène, Claude; Sun, Jian-Sheng

2002-01-01

A detailed kinetic study of triple helix formation was performed by surface plasmon resonance. Three systems were investigated involving 15mer pyrimidine oligonucleotides as third strands. Rate constants and activation energies were validated by comparison with thermodynamic values calculated from UV-melting analysis. Replacement of a T·A base pair by a C·G pair at either the 5′ or the 3′ end of the target sequence allowed us to assess mismatch effects and to delineate the mechanism of triple helix formation. Our data show that the association rate constant is governed by the sequence of base triplets on the 5′ side of the triplex (referred to as the 5′ side of the target oligopurine strand) and provides evidence that the reaction pathway for triple helix formation in the pyrimidine motif proceeds from the 5′ end to the 3′ end of the triplex according to the nucleation-zipping model. It seems that this is a general feature for all triple helices formation, probably due to the right-handedness of the DNA double helix that provides a stronger base stacking at the 5′ than at the 3′ duplex–triplex junction. Understanding the mechanism of triple helix formation is not only of fundamental interest, but may also help in designing better triple helix-forming oligonucleotides for gene targeting and control of gene expression. PMID:12490709

The energetic basis of the DNA double helix: a combined microcalorimetric approach

PubMed Central

Vaitiekunas, Paulius; Crane-Robinson, Colyn; Privalov, Peter L.

2015-01-01

Microcalorimetric studies of DNA duplexes and their component single strands showed that association enthalpies of unfolded complementary strands into completely folded duplexes increase linearly with temperature and do not depend on salt concentration, i.e. duplex formation results in a constant heat capacity decrement, identical for CG and AT pairs. Although duplex thermostability increases with CG content, the enthalpic and entropic contributions of an AT pair to duplex formation exceed that of a CG pair when compared at the same temperature. The reduced contribution of AT pairs to duplex stabilization comes not from their lower enthalpy, as previously supposed, but from their larger entropy contribution. This larger enthalpy and particularly the greater entropy results from water fixed by the AT pair in the minor groove. As the increased entropy of an AT pair exceeds that of melting ice, the water molecule fixed by this pair must affect those of its neighbors. Water in the minor groove is, thus, orchestrated by the arrangement of AT groups, i.e. is context dependent. In contrast, water hydrating exposed nonpolar surfaces of bases is responsible for the heat capacity increment on dissociation and, therefore, for the temperature dependence of all thermodynamic characteristics of the double helix. PMID:26304541

Modeling DNA bubble formation at the atomic scale

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

Beleva, V; Rasmussen, K. O.; Garcia, A. E.

We describe the fluctuations of double stranded DNA molecules using a minimalist Go model over a wide range of temperatures. Minimalist models allow us to describe, at the atomic level, the opening and formation of bubbles in DNA double helices. This model includes all the geometrical constraints in helix melting imposed by the 3D structure of the molecule. The DNA forms melted bubbles within double helices. These bubbles form and break as a function of time. The equilibrium average number of broken base pairs shows a sharp change as a function of T. We observe a temperature profile of sequencemore » dependent bubble formation similar to those measured by Zeng et al. Long nuclei acid molecules melt partially through the formations of bubbles. It is known that CG rich sequences melt at higher temperatures than AT rich sequences. The melting temperature, however, is not solely determined by the CG content, but by the sequence through base stacking and solvent interactions. Recently, models that incorporate the sequence and nonlinear dynamics of DNA double strands have shown that DNA exhibits a very rich dynamics. Recent extensions of the Bishop-Peyrard model show that fluctuations in the DNA structure lead to opening in localized regions, and that these regions in the DNA are associated with transcription initiation sites. 1D and 2D models of DNA may contain enough information about stacking and base pairing interactions, but lack the coupling between twisting, bending and base pair opening imposed by the double helical structure of DNA that all atom models easily describe. However, the complexity of the energy function used in all atom simulations (including solvent, ions, etc) does not allow for the description of DNA folding/unfolding events that occur in the microsecond time scale.« less

Ultraviolet Absorption Induces Hydrogen-Atom Transfer in G⋅C Watson-Crick DNA Base Pairs in Solution.

PubMed

Röttger, Katharina; Marroux, Hugo J B; Grubb, Michael P; Coulter, Philip M; Böhnke, Hendrik; Henderson, Alexander S; Galan, M Carmen; Temps, Friedrich; Orr-Ewing, Andrew J; Roberts, Gareth M

2015-12-01

Ultrafast deactivation pathways bestow photostability on nucleobases and hence preserve the structural integrity of DNA following absorption of ultraviolet (UV) radiation. One controversial recovery mechanism proposed to account for this photostability involves electron-driven proton transfer (EDPT) in Watson-Crick base pairs. The first direct observation is reported of the EDPT process after UV excitation of individual guanine-cytosine (G⋅C) Watson-Crick base pairs by ultrafast time-resolved UV/visible and mid-infrared spectroscopy. The formation of an intermediate biradical species (G[-H]⋅C[+H]) with a lifetime of 2.9 ps was tracked. The majority of these biradicals return to the original G⋅C Watson-Crick pairs, but up to 10% of the initially excited molecules instead form a stable photoproduct G*⋅C* that has undergone double hydrogen-atom transfer. The observation of these sequential EDPT mechanisms across intermolecular hydrogen bonds confirms an important and long debated pathway for the deactivation of photoexcited base pairs, with possible implications for the UV photochemistry of DNA. © 2015 WILEY-VCH Verlag GmbH & Co. KGaA, Weinheim.

Galaxy pairs in the SDSS - XIII. The connection between enhanced star formation and molecular gas properties in galaxy mergers

NASA Astrophysics Data System (ADS)

Violino, Giulio; Ellison, Sara L.; Sargent, Mark; Coppin, Kristen E. K.; Scudder, Jillian M.; Mendel, Trevor J.; Saintonge, Amelie

2018-05-01

We investigate the connection between star formation and molecular gas properties in galaxy mergers at low redshift (z ≤ 0.06). The study we present is based on IRAM 30-m CO(1-0) observations of 11 galaxies with a close companion selected from the Sloan Digital Sky Survey (SDSS). The pairs have mass ratios ≤4, projected separations rp ≤ 30 kpc and velocity separations ΔV ≤ 300 km s-1, and have been selected to exhibit enhanced specific star formation rates (sSFRs). We calculate molecular gas (H2) masses, assigning to each galaxy a physically motivated conversion factor αCO, and we derive molecular gas fractions and depletion times. We compare these quantities with those of isolated galaxies from the extended CO Legacy Data base for the GALEX Arecibo SDSS Survey sample (xCOLDGASS; Saintonge et al.) with gas quantities computed in an identical way. Ours is the first study which directly compares the gas properties of galaxy pairs and those of a control sample of normal galaxies with rigorous control procedures and for which SFR and H2 masses have been estimated using the same method. We find that the galaxy pairs have shorter depletion times and an average molecular gas fraction enhancement of 0.4 dex compared to the mass matched control sample drawn from xCOLDGASS. However, the gas masses (and fractions) in galaxy pairs and their depletion times are consistent with those of non-mergers whose SFRs are similarly elevated. We conclude that both external interactions and internal processes may lead to molecular gas enhancement and decreased depletion times.

Defect engineering of the oxygen-vacancy clusters formation in electron irradiated silicon by isovalent doping: An infrared perspective

NASA Astrophysics Data System (ADS)

Londos, C. A.; Sgourou, E. N.; Chroneos, A.

2012-12-01

Infrared spectroscopy was used to study the production and evolution of oxygen-vacancy (VOn for n = 1, 2, 3 and VmO for m = 1, 2, 3) clusters, in electron-irradiated Czochralski silicon (Cz-Si) samples, doped with isovalent dopants. It was determined that the production of the VO pair is enhanced in Ge-doped Si but is suppressed in Sn and Pb-doped Si. The phenomenon is discussed in terms of the competition between isovalent dopants and oxygen atoms in capturing vacancies in the course of irradiation. In the case of Ge, only transient GeV pairs form, leading finally to an increase of the VO production. Conversely, for Sn and Pb the corresponding pairs with vacancies are stable, having an opposite impact on the formation of VO pairs. Regarding V2O and V3O clusters, our measurements indicate that Ge doping enhances their formation, although Sn and Pb dopants suppress it. Similar arguments as those for the VO pair could be put forward, based on the effect of isovalent impurities on the availability of vacancies. Additionally, it was found that the conversion ratio of VO to VO2 decreases as the covalent radius of the isovalent dopant increases. These results are discussed in terms of the local strains introduced by the isovalent dopants in the Si lattice. These local strains affect the balance of the intrinsic defects created as a result of irradiation, as well as the balance between the two main reactions (VO + Oi → VO2 and VO + SiI → Oi) participating in the VO annealing, leading finally to a decrease of the VO2 production. The larger the covalent radius of the isovalent dopant (rGe < rSn < rPb), the larger the introduced strains in the lattice and then the less the VO2 formation in accordance with our experimental results. Interestingly, an opposite trend was observed for the conversion ratio of VO2 to VO3. The phenomenon is attributed to the enhanced diffusivity of oxygen impurity as a result of the presence of isovalent dopants, leading to an enhanced formation of the VO3 cluster. The results indicate that isovalent doping of Si is an effective way to control the formation of the deleterious oxygen-vacancy clustering that can affect Si-based devices.

Twin hydroxymethyluracil-A base pair steps define the binding site for the DNA-binding protein TF1.

PubMed

Grove, A; Figueiredo, M L; Galeone, A; Mayol, L; Geiduschek, E P

1997-05-16

The DNA-bending protein TF1 is the Bacillus subtilis bacteriophage SPO1-encoded homolog of the bacterial HU proteins and the Escherichia coli integration host factor. We recently proposed that TF1, which binds with high affinity (Kd was approximately 3 nM) to preferred sites within the hydroxymethyluracil (hmU)-containing phage genome, identifies its binding sites based on sequence-dependent DNA flexibility. Here, we show that two hmU-A base pair steps coinciding with two previously proposed sites of DNA distortion are critical for complex formation. The affinity of TF1 is reduced 10-fold when both of these hmU-A base pair steps are replaced with A-hmU, G-C, or C-G steps; only modest changes in affinity result when substitutions are made at other base pairs of the TF1 binding site. Replacement of all hmU residues with thymine decreases the affinity of TF1 greatly; remarkably, the high affinity is restored when the two hmU-A base pair steps corresponding to previously suggested sites of distortion are reintroduced into otherwise T-containing DNA. T-DNA constructs with 3-base bulges spaced apart by 9 base pairs of duplex also generate nM affinity of TF1. We suggest that twin hmU-A base pair steps located at the proposed sites of distortion are key to target site selection by TF1 and that recognition is based largely, if not entirely, on sequence-dependent DNA flexibility.

Galaxy bachelors, couples, spouses: Star formation in interacting galaxies

NASA Astrophysics Data System (ADS)

Sun, Jing; Barger, Kathleen; Richstein, Hannah; SDSS-IV/MaNGA

2017-01-01

We investigate the star formation activity in three galaxy systems in different stages of interaction to determine how the environment of galaxies affects their star forming ability and potential. These systems include an isolated galaxy, a pair of interacting galaxies, and a pair of merging galaxies. All of the target galaxies in these systems have similar stellar masses and similar radii and are at similar redshifts. We trace the star formation activity over the past 1-2 Gyr using spatially and kinematically resolved H-alpha emission, H-alpha equivalent width, and 4000-Angstrom break maps. This work is based on data from the fourth-generation Sloan Digital Sky Survey (SDSS-IV)/Mapping Nearby Galaxies at Apache Point Observatory (MaNGA), and is part of the Project No.0285 in SDSS-IV.

Free energy landscape and transition pathways from Watson–Crick to Hoogsteen base pairing in free duplex DNA

PubMed Central

Yang, Changwon; Kim, Eunae; Pak, Youngshang

2015-01-01

Houghton (HG) base pairing plays a central role in the DNA binding of proteins and small ligands. Probing detailed transition mechanism from Watson–Crick (WC) to HG base pair (bp) formation in duplex DNAs is of fundamental importance in terms of revealing intrinsic functions of double helical DNAs beyond their sequence determined functions. We investigated a free energy landscape of a free B-DNA with an adenosine–thymine (A–T) rich sequence to probe its conformational transition pathways from WC to HG base pairing. The free energy landscape was computed with a state-of-art two-dimensional umbrella molecular dynamics simulation at the all-atom level. The present simulation showed that in an isolated duplex DNA, the spontaneous transition from WC to HG bp takes place via multiple pathways. Notably, base flipping into the major and minor grooves was found to play an important role in forming these multiple transition pathways. This finding suggests that naked B-DNA under normal conditions has an inherent ability to form HG bps via spontaneous base opening events. PMID:26250116

The cyc1-11 mutation in yeast reverts by recombination with a nonallelic gene: composite genes determining the iso-cytochromes c.

PubMed Central

Ernst, J F; Stewart, J W; Sherman, F

1981-01-01

DNA sequence analysis of a cloned fragment directly established that the cyc1-11 mutation of iso-1-cytochrome c in the yeast Saccharomyces cerevisiae is a two-base-pair substitution that changes the CCA proline codon at amino acid position 76 to a UAA nonsense codon. Analysis of 11 revertant proteins and one cloned revertant gene showed that reversion of the cyc1-11 mutation can occur in three ways: a single base-pair substitution, which produces a serine replacement at position 76; recombination with the nonallelic CYC7 gene of iso-2-cytochrome c, which causes replacement of a segment in the cyc1-11 gene by the corresponding segment of the CYC7 gene; and either a two-base-pair substitution or recombination with the CYC7 gene, which causes the formation of the normal iso-1-cytochrome c sequence. These results demonstrate the occurrence of low frequencies of recombination between nonallelic genes having extensive but not complete homology. The formation of composite genes that share sequences from nonallelic genes may be an evolutionary mechanism for producing protein diversities and for maintaining identical sequences at different loci. Images PMID:6273865

Formative Assessment and the Intuitive Incorporation of Research-Based Instruction Techniques

ERIC Educational Resources Information Center

Kuiper, Paula; VanOeffelen, Rachel; Veldkamp, Simon; Bokma, Isaac; Breems, Luke; Fynewever, Herb

2015-01-01

Using Max Weber's theory of ideal types, the authors classify the formative assessment techniques used by 12 college instructors. Their data reveal two pairs of opposing preferences: (1) highly preplanned vs. highly emergent and (2) focused on individual students vs. focused on the class as a whole. Using interview data, they illustrate how each…

Hydroxylamine and methoxyamine mutagenesis: displacement of the tautomeric equilibrium of the promutagen N6-methoxyadenosine by complementary base pairing.

PubMed

Stolarski, R; Kierdaszuk, B; Hagberg, C E; Shugar, D

1984-06-19

The imino-amino tautomeric equilibrium of the promutagenic adenosine analogue N6-methoxy-2',3',5'-tri-O-methyladenosine [OMe6A(Me)3], in solvents of various polarities, has been studied with the aid of 1H and 13C NMR spectroscopy. The high energy barrier (free enthalpy delta G = 80 +/- 5 kJ X mol-1) between the two tautomeric species renders possible direct observation of the independent sets of all 1H and 13C signals from each of them. The equilibrium ranges from 10% imino in CCl4 to 90% in aqueous medium. Thermodynamic parameters, including energy barriers and lifetimes, were calculated from the temperature dependence of the equilibrium. Essentially similar results prevail for the promutagenic N6-hydroxy analogue. The conformations of the sugar moieties, and of the base about the glycosidic bond, for both tautomers are similar to those for adenosine. The conformation of the exocyclic N6-OCH3 group, which determines the ability of each species to form planar associates (hydrogen-bonded base pairs), has also been evaluated. Formation of autoassociates of OMe6A(Me)3 and of heteroassociates with the potentially complementary 2',3',5'-tri-O-methyluridine and -cytidine, in chloroform solution, was also investigated. The amino form base pairs with uridine and the imino form with cytidine. Formation of a complementary base pair by a given tautomeric species was accompanied by an increase of up to 10% in the population of this species and a concomitant decrease in population of the other species.(ABSTRACT TRUNCATED AT 250 WORDS)

HI properties and star formation history of a fly-by pair of blue compact dwarf galaxies

NASA Astrophysics Data System (ADS)

Kim, Jinhyub; Chung, Aeree; Wong, O. Ivy; Lee, Bumhyun; Sung, Eon-Chang; Staveley-Smith, Lister

2017-09-01

A fly-by interaction has been suggested to be one of the major explanations for enhanced star formation in blue compact dwarf (BCD) galaxies, yet no direct evidence for this scenario has been found to date. In the Hi Parkes all-sky survey (HIPASS), ESO 435-IG 020 and ESO 435-G 016, a BCD pair were found in a common, extended gas envelope of atomic hydrogen, providing an ideal case to test the hypothesis that the starburst in BCDs can be indeed triggered by a fly-by interaction. Using high-resolution data from the Australia Telescope Compact Array (ATCA), we investigated Hi properties and the spectral energy distribution (SED) of the BCD pair to study their interaction and star formation histories. The high-resolution Hi data of both BCDs reveal a number of peculiarities, which are suggestive of tidal perturbation. Meanwhile, 40% of the HIPASS flux is not accounted for in the ATCA observations with no Hi gas bridge found between the two BCDs. Intriguingly, in the residual of the HIPASS and the ATCA data, 10% of the missing flux appears to be located between the two BCDs. While the SED-based age of the most dominant young stellar population is old enough to have originated from the interaction with any neighbors (including the other of the two BCDs), the most recent star formation activity traced by strong Hα emission in ESO 435-IG 020 and the shear motion of gas in ESO 435-G 016, suggest a more recent or current tidal interaction. Based on these and the residual emission between the HIPASS and the ATCA data, we propose an interaction between the two BCDs as the origin of their recently enhanced star formation activity. The shear motion on the gas disk, potentially with re-accretion of the stripped gas, could be responsible for the active star formation in this BCD pair. The reduced datacube (FITS file) is only available at the CDS via anonymous ftp to http://cdsarc.u-strasbg.fr (http://130.79.128.5) or via http://cdsarc.u-strasbg.fr/viz-bin/qcat?J/A+A/605/A54

Formation of a parallel-stranded DNA homoduplex by d(GGA) repeat oligonucleotides.

PubMed Central

Suda, T; Mishima, Y; Asakura, H; Kominami, R

1995-01-01

The GGA9-H molecules consisting of a double helical stretch followed by a single-stranded 3'-terminal overhang of nine GGA sequence repeats exhibited a gel mobility-shifted band in a concentration-dependent manner, suggestive of the intermolecular complex formation. The position of the shifted band in a gel was almost identical to that of the Y-shaped dimer marker of the same molecular weight that had the two double-helices at one side. This suggests that GGA9-H dimerizes in a parallel orientation without the formation of four-stranded hairpin structure. Since the GGA9-H homoduplex was stably formed at pH 4, 7 and 9, the formation does not require protonation or deprotonation of the N1 position of adenines. Neither does it require the N7 group of guanines responsible for Hoogsteen base pairing from the methylation interference and modification studies. Modification of the N7 group of guanines with dimethyl sulfate (DMS) did not inhibit the association and also the N7 group in the homoduplex was not protected from DMS. On the other hand, the GAA9-H having the G to A base substitution did not show such an association with either GGA9-H or GAA9-H. These results suggest that the homoduplex formation may be due to G.G base pairing through non-Hoogsteen hydrogen bonds. Images PMID:7479009

Controlled Interactions between Two Dimensional Layered Inorganic Nanosheets and Polymers

DTIC Science & Technology

2016-06-15

transition metal and non- pair electrons of amine allows us to develop scalable, stable and uniform composite films with numerous combinations of TMD...modification of TMDs sheets with amine-terminated polymers is introduced and the strong Lewis acid-base interaction between transition metal and non- pair ...can be readily entangled with other chains of the matrix polymer, thereby ensuring homogeneous PNC formation. The solvent medium offers an extra

HERSCHEL OBSERVATIONS OF MAJOR MERGER PAIRS AT z = 0: DUST MASS AND STAR FORMATION

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

Cao, Chen; Xu, Cong Kevin; Lu, Nanyao

We present Herschel PACS and SPIRE far-infrared (FIR) and submillimeter imaging observations for a large K-band selected sample of 88 close major-merger pairs of galaxies (H-KPAIRs) in 6 photometric bands (70, 100, 160, 250, 350, and 500 μm). Among 132 spiral galaxies in the 44 spiral–spiral (S+S) pairs and 44 spiral–elliptical (S+E) pairs, 113 are detected in at least 1 Herschel band. The star formation rate (SFR) and dust mass (M{sub dust}) are derived from the IR SED fitting. The mass of total gas (M{sub gas}) is estimated by assuming a constant dust-to-gas mass ratio of 0.01. Star-forming spiral galaxiesmore » (SFGs) in S+S pairs show significant enhancements in both specific star formation rate (sSFR) and star formation efficiency (SFE), while having nearly the same gas mass compared to control galaxies. On the other hand, for SFGs in S+E pairs, there is no significant sSFR enhancement and the mean SFE enhancement is significantly lower than that of SFGs in S+S pairs. This suggests an important role for the disk–disk collision in the interaction-induced star formation. The M{sub gas} of SFGs in S+E pairs is marginally lower than that of their counterparts in both S+S pairs and the control sample. Paired galaxies with and without interaction signs do not differ significantly in their mean sSFR and SFE. As found in previous works, this much larger sample confirms that the primary and secondary spirals in S+S pairs follow a Holmberg effect correlation on sSFR.« less

Ion pair reinforced semi-interpenetrating polymer network for direct methanol fuel cell applications.

PubMed

Fang, Chunliu; Julius, David; Tay, Siok Wei; Hong, Liang; Lee, Jim Yang

2012-06-07

This paper describes the synthesis of ion-pair-reinforced semi-interpenetrating polymer networks (SIPNs) as proton exchange membranes (PEMs) for the direct methanol fuel cells (DMFCs). Specifically, sulfonated poly(2,6-dimethyl-1,4-phenylene oxide) (SPPO), a linear polymer proton source, was immobilized in a brominated PPO (BPPO) network covalently cross-linked by ethylenediamine (EDA). The immobilization of SPPO in the SIPN network was accomplished not only by the usual means of mechanical interlocking but also by ion pair formation between the sulfonic acid groups of SPPO and the amine moieties formed during the cross-linking reaction of BPPO with EDA. Through the ion pair interactions, the immobilization of SPPO polymer in the BPPO network was made more effective, resulting in a greater uniformity of sulfonic acid cluster distribution in the membrane. The hydrophilic amine-containing cross-links also compensated for some of the decrease in proton conductivity caused by ion pair formation. The SIPN membranes prepared as such showed good proton conductivity, low methanol permeability, good mechanical properties, and dimensional stability. Consequently, the PPO based SIPN membranes were able to deliver a higher maximum power density than Nafion, demonstrating the potential of the SIPN structure for PEM designs.

Distance-dependent duplex DNA destabilization proximal to G-quadruplex/i-motif sequences

PubMed Central

König, Sebastian L. B.; Huppert, Julian L.; Sigel, Roland K. O.; Evans, Amanda C.

2013-01-01

G-quadruplexes and i-motifs are complementary examples of non-canonical nucleic acid substructure conformations. G-quadruplex thermodynamic stability has been extensively studied for a variety of base sequences, but the degree of duplex destabilization that adjacent quadruplex structure formation can cause has yet to be fully addressed. Stable in vivo formation of these alternative nucleic acid structures is likely to be highly dependent on whether sufficient spacing exists between neighbouring duplex- and quadruplex-/i-motif-forming regions to accommodate quadruplexes or i-motifs without disrupting duplex stability. Prediction of putative G-quadruplex-forming regions is likely to be assisted by further understanding of what distance (number of base pairs) is required for duplexes to remain stable as quadruplexes or i-motifs form. Using oligonucleotide constructs derived from precedented G-quadruplexes and i-motif-forming bcl-2 P1 promoter region, initial biophysical stability studies indicate that the formation of G-quadruplex and i-motif conformations do destabilize proximal duplex regions. The undermining effect that quadruplex formation can have on duplex stability is mitigated with increased distance from the duplex region: a spacing of five base pairs or more is sufficient to maintain duplex stability proximal to predicted quadruplex/i-motif-forming regions. PMID:23771141

6-Oxocytidine a novel protonated C-base analogue for stable triple helix formation.

PubMed Central

Berressem, R; Engels, J W

1995-01-01

2'-O-Methyl-3'-O-phosphoramidite building blocks of 6-oxocytidine 6 and its 5-methyl derivative 7, respectively, were synthesized and incorporated via phosphoramidite chemistry in 15 mer oligodeoxynucleotides [d(T72T7), S2; d(T73T7), S3] to obtain potential Py.Pu.Py triplex forming homopyrimidine strands. UV thermal denaturation studies and CD spectroscopy of 1:1 mixtures of these oligomers and a 21 mer target duplex [d(C3A7GA7C3)-d(G3T7CT7G3), D1] with a complementary purine tract showed a nearly pH-independent (6.0-8.0) triple helix formation with melting temperatures of 21-19 degrees C and 18.5-17.5 degrees C, respectively (buffer system: 50 mM sodium cacodylate, 100 mM NaCl, 20 mM MgCl2). In contrast, with the corresponding 15mer deoxy-C-containing oligonucleotide [d(T(7)1T7), S1] triplex formation was observed only below pH 6.6. Specificity for the recognition of Watson-Crick GC-base pairs was observed by pairing the modified C-bases of the 15mers with all other possible Watson-Crick-base compositions in the target duplex [d(C3A7XA7C3)-d(G3T7YT7G3), X = A,C,T; Y = T,G,A, D2-4]. Additionally, the Watson-Crick-pairing of the modified oligomers S2 and S3 was studied. PMID:7567457

6-Oxocytidine a novel protonated C-base analogue for stable triple helix formation.

PubMed

Berressem, R; Engels, J W

1995-09-11

2'-O-Methyl-3'-O-phosphoramidite building blocks of 6-oxocytidine 6 and its 5-methyl derivative 7, respectively, were synthesized and incorporated via phosphoramidite chemistry in 15 mer oligodeoxynucleotides [d(T72T7), S2; d(T73T7), S3] to obtain potential Py.Pu.Py triplex forming homopyrimidine strands. UV thermal denaturation studies and CD spectroscopy of 1:1 mixtures of these oligomers and a 21 mer target duplex [d(C3A7GA7C3)-d(G3T7CT7G3), D1] with a complementary purine tract showed a nearly pH-independent (6.0-8.0) triple helix formation with melting temperatures of 21-19 degrees C and 18.5-17.5 degrees C, respectively (buffer system: 50 mM sodium cacodylate, 100 mM NaCl, 20 mM MgCl2). In contrast, with the corresponding 15mer deoxy-C-containing oligonucleotide [d(T(7)1T7), S1] triplex formation was observed only below pH 6.6. Specificity for the recognition of Watson-Crick GC-base pairs was observed by pairing the modified C-bases of the 15mers with all other possible Watson-Crick-base compositions in the target duplex [d(C3A7XA7C3)-d(G3T7YT7G3), X = A,C,T; Y = T,G,A, D2-4]. Additionally, the Watson-Crick-pairing of the modified oligomers S2 and S3 was studied.

Carbonic acid ionization and the stability of sodium bicarbonate and carbonate ion pairs to 200 °C - A potentiometric and spectrophotometric study

NASA Astrophysics Data System (ADS)

Stefánsson, Andri; Bénézeth, Pascale; Schott, Jacques

2013-11-01

Carbonic acid ionization and sodium bicarbonate and carbonate ion pair formation constants have been experimentally determined in dilute hydrothermal solutions to 200 °C. Two experimental approaches were applied, potentiometric acid-base titrations at 10-60 °C and spectrophotometric pH measurements using the pH indicators, 2-napthol and 4-nitrophenol, at 25-200 °C. At a given temperature, the first and second ionization constants of carbonic acid (K1, K2) and the ion pair formation constants for NaHCO(aq)(K) and NaCO3-(aq)(K) were simultaneously fitted to the data. Results of this study compare well with previously determined values of K1 and K2. The NaHCO(aq) and NaCO3-(aq) ion pair formation constants vary between 25 and 200 °C having values of logK=-0.18 to 0.58 and logK=1.01 to 2.21, respectively. These ion pairs are weak at low-temperatures but become increasingly important with increasing temperature under neutral to alkaline conditions in moderately dilute to concentrated NaCl solutions, with NaCO3-(aq) predominating over CO32-(aq) in ⩾0.1 M NaCl solution at temperatures above 100 °C. The results demonstrate that NaCl cannot be considered as an inert (non-complexing) electrolyte in aqueous carbon dioxide containing solutions at elevated temperatures.

Interacting star clusters in the Large Magellanic Cloud. Overmerging problem solved by cluster group formation

NASA Astrophysics Data System (ADS)

Leon, Stéphane; Bergond, Gilles; Vallenari, Antonella

1999-04-01

We present the tidal tail distributions of a sample of candidate binary clusters located in the bar of the Large Magellanic Cloud (LMC). One isolated cluster, SL 268, is presented in order to study the effect of the LMC tidal field. All the candidate binary clusters show tidal tails, confirming that the pairs are formed by physically linked objects. The stellar mass in the tails covers a large range, from 1.8x 10(3) to 3x 10(4) \\msun. We derive a total mass estimate for SL 268 and SL 356. At large radii, the projected density profiles of SL 268 and SL 356 fall off as r(-gamma ) , with gamma = 2.27 and gamma =3.44, respectively. Out of 4 pairs or multiple systems, 2 are older than the theoretical survival time of binary clusters (going from a few 10(6) years to 10(8) years). A pair shows too large age difference between the components to be consistent with classical theoretical models of binary cluster formation (Fujimoto & Kumai \\cite{fujimoto97}). We refer to this as the ``overmerging'' problem. A different scenario is proposed: the formation proceeds in large molecular complexes giving birth to groups of clusters over a few 10(7) years. In these groups the expected cluster encounter rate is larger, and tidal capture has higher probability. Cluster pairs are not born together through the splitting of the parent cloud, but formed later by tidal capture. For 3 pairs, we tentatively identify the star cluster group (SCG) memberships. The SCG formation, through the recent cluster starburst triggered by the LMC-SMC encounter, in contrast with the quiescent open cluster formation in the Milky Way can be an explanation to the paucity of binary clusters observed in our Galaxy. Based on observations collected at the European Southern Observatory, La Silla, Chile}

Self-organization of quantum-dot pairs by high-temperature droplet epitaxy

PubMed Central

Holmes, Kyland; Mazur, Yuriy I; Ramsey, Kimberly A; Salamo, Gregory J

2006-01-01

The spontaneously formation of epitaxial GaAs quantum-dot pairs was demonstrated on an AlGaAs surface using Ga droplets as a Ga nano-source. The dot pair formation was attributed to the anisotropy of surface diffusion during high-temperature droplet epitaxy.

Fine-scale genetic structure and social organization in female white-tailed deer.

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

Comer, Christopher E.; Kilgo, John C.; D'Angelo, Gino J.

Abstract: Social behavior of white-tailed deer (Odocoileus virginianus) can have important management implications. The formation of matrilineal social groups among female deer has been documented and management strategies have been proposed based on this well-developed social structure. Using radiocollared (n = 17) and hunter or vehicle-killed (n = 21) does, we examined spatial and genetic structure in white-tailed deer on a 7,000-ha portion of the Savannah River Site in the upper Coastal Plain of South Carolina, USA. We used 14 microsatellite DNA loci to calculate pairwise relatedness among individual deer and to assign doe pairs to putative relationship categories. Linearmore » distance and genetic relatedness were weakly correlated (r = –0.08, P = 0.058). Relationship categories differed in mean spatial distance, but only 60% of first-degree-related doe pairs (full sibling or mother–offspring pairs) and 38% of second-degree-related doe pairs (half sibling, grandmother–granddaughter pairs) were members of the same social group based on spatial association. Heavy hunting pressure in this population has created a young age structure among does, where the average age is <2.5 years, and <4% of does are >4.5 years old. This—combined with potentially elevated dispersal among young does—could limit the formation of persistent, cohesive social groups. Our results question the universal applicability of recently proposed models of spatial and genetic structuring in white-tailed deer, particularly in areas with differing harvest histories.« less

Detection of protonated non-Watson-Crick base pairs using electrospray ionization mass spectrometry.

PubMed

Ishida, Riyoko; Iwahashi, Hideo

2018-03-01

Many studies have shown that protonated nucleic acid base pairs are involved in a wide variety of nucleic acid structures. However, little information is available on relative stability of hemiprotonated self- and non-self-dimers at monomer level. We used electrospray ionization mass spectrometry (ESI-MS) to evaluate the relative stability under various concentrations of hydrogen ion. These enable conjecture of the formation of protonated non-Watson-Crick base pairs based on DNA and RNA base sequence. In the present study, we observed that ESI-MS peaks corresponded to respective self-dimers for all examined nucleosides except for adenosine. Peak heights depended on the concentration of hydrogen ion. The ESI-MS peak heights of the hemiprotonated cytidine dimers and the hemiprotonated thymidine dimer sharply increased with increased concentration of hydrogen ion, suggesting direct participation of hydrogen ion in dimer formations. In ESI-MS measurements of the solutions containing adenosine, cytidine, thymidine and guanosine, we observed protonated cytidine-guanosine dimer (CH+-G) and protonated cytidine-thymidine dimer (CH+-T) in addition to hemiprotonated cytidine-cytidine dimer (CH+-C) with following relative peak height, (CH+-C) > (CH+-G) ≈ (CH+-T) > (CH+-A). Additionally, in the ESI-MS measurements of solutions containing adenosine, thymidine and guanosine, we observed a considerable amount of protonated adenosine-guanosine (AH+-G) and protonated adenosine-thymidine (AH+-T).

Action of Penetrating Radiation on Radio Parts,

DTIC Science & Technology

1984-05-24

the formation of the pair of particles the electron - positron . This process is called the effect of the formation of electron- positron pairs. Pair...formation can occur during the absorption 7-quantum with the energy, greater than total rest energy of electron and positron (more than the doubled...rest energy of electron, equal to 2mc 2=!.02 MeV). Positron (unstable elementary DOC - 83167601 PAGE 9 particle) in turn interacts with the electron of

Modified nucleotides reveal the indirect role of the central base pairs in stabilizing the lac repressor-operator complex.

PubMed Central

Zhang, X; Gottlieb, P A

1995-01-01

Guanine residues in the lac operator were replaced by 2-aminopurine or purine analogues, pairing the modified nucleotides with C. The observed equilibrium dissociation constants for lac repressor binding to substituted operators were measured in 10 mM Tris, 150 mM KCl, 0.1 mM EDTA, 0.1 mM DTE, pH 7.6 at 25 degrees C. These measurements revealed five positions that destabilized the complex when substituted with either analogue. Two positions, which are related by a 2-fold symmetry, are in the major groove of the operator thought to directly interact with the protein. Three sites were in the central region of the operator. A purine analogue at a sixth site perturbed the local DNA structure and destabilized the complex. Alkylation interference experiments of the 2-aminopurine substituted operators demonstrated that, of the five affected, two substitutions displayed altered phosphate interference patterns at the phosphate adjacent to the substituted base. For these operators, complex formation was measured in different concentrations of KCl to assess the contribution of counterion release to the bimolecular process. The results indicated that both complexes were similar to wild-type, although minor changes were observed. The Kobs of the complex was then measured when 2-aminopurine or purine analogues were paired with uracil nucleotide, a base pair that serves to stabilize the DNA. The introduction of the new base pairs revealed two effects on the bimolecular interaction. For those operator sites that are thought to perturb the interaction directly, the affinity of the complex was weakened to levels observed for the singly-substituted operators. In contrast, the nucleotides of 2-aminopurine paired with uracil positioned in the central region of the operator served to enhance the stability of the complex. The purine-uracil base pair substitution on the other hand had a significant destabilizing effect on the interaction. We propose that the central base pairs modulate binding of the complex by altering the intrinsic properties of the DNA. Two specific attributes are required to achieve the lowest free energy of interaction. The DNA must have two interstrand hydrogen bonds to stabilize the duplex and it must have properties associated with directional bending or unwinding. This analysis does not rule out contributions by direct interactions between the protein and the central region of the operator but underscores how indirect effects play a major role in complex formation in this system. Images PMID:7784203

Binding of DNA hairpins to an assembler-strand as part of a primordial translation device

NASA Astrophysics Data System (ADS)

Baumann, Ulrich

1987-09-01

A crucial event in the process leading to the origin of life is the emergence of a simple translation device. To approach experimental realization of this device the binding ability of short DNA hairpins to complementary oligonucleotides fixed on a solid support was investigated. The binding is achieved by base pairing between the loop nucleotides of the hairpins containing different numbers of adenosine residues and oligothymidylates covalently linked to cellulose. The loop has to consist of at least five nucleotides to achieve binding. The exact number of established base pairs was determined in two ways. First, the elution temperatures of hairpins and those of oligoadenylates which had the length of the loop were compared. Secondly, the architecture of the loop was analyzed by means of the single-strand-specific nuclease from mung bean acting as structural probe. Onlyn-2 of n loop nucleotides of a hairpin are able to form base pairs. Therefore, a strong evidence for the formation of a triplet of base pairs between primeval tRNA and mRNA sufficient to stabilize the complex enzyme-free is given.

Evaluation of Contextual Variability in Prediction of Reinforcer Effectiveness

ERIC Educational Resources Information Center

Pino, Olimpia; Dazzi, Carla

2005-01-01

Previous research has shown that stimulus preference assessments based on caregiver-opinion did not coincide with results of a more systematic method of assessing reinforcing value unless stimuli that were assessed to represent preferences were also preferred on paired stimulus presentation format, and that the relative preference based on the…

Entropy Beacon: A Hairpin-Free DNA Amplification Strategy for Efficient Detection of Nucleic Acids

PubMed Central

2015-01-01

Here, we propose an efficient strategy for enzyme- and hairpin-free nucleic acid detection called an entropy beacon (abbreviated as Ebeacon). Different from previously reported DNA hybridization/displacement-based strategies, Ebeacon is driven forward by increases in the entropy of the system, instead of free energy released from new base-pair formation. Ebeacon shows high sensitivity, with a detection limit of 5 pM target DNA in buffer and 50 pM in cellular homogenate. Ebeacon also benefits from the hairpin-free amplification strategy and zero-background, excellent thermostability from 20 °C to 50 °C, as well as good resistance to complex environments. In particular, based on the huge difference between the breathing rate of a single base pair and two adjacent base pairs, Ebeacon also shows high selectivity toward base mutations, such as substitution, insertion, and deletion and, therefore, is an efficient nucleic acid detection method, comparable to most reported enzyme-free strategies. PMID:26505212

Free energy landscape and transition pathways from Watson-Crick to Hoogsteen base pairing in free duplex DNA.

PubMed

Yang, Changwon; Kim, Eunae; Pak, Youngshang

2015-09-18

Houghton (HG) base pairing plays a central role in the DNA binding of proteins and small ligands. Probing detailed transition mechanism from Watson-Crick (WC) to HG base pair (bp) formation in duplex DNAs is of fundamental importance in terms of revealing intrinsic functions of double helical DNAs beyond their sequence determined functions. We investigated a free energy landscape of a free B-DNA with an adenosine-thymine (A-T) rich sequence to probe its conformational transition pathways from WC to HG base pairing. The free energy landscape was computed with a state-of-art two-dimensional umbrella molecular dynamics simulation at the all-atom level. The present simulation showed that in an isolated duplex DNA, the spontaneous transition from WC to HG bp takes place via multiple pathways. Notably, base flipping into the major and minor grooves was found to play an important role in forming these multiple transition pathways. This finding suggests that naked B-DNA under normal conditions has an inherent ability to form HG bps via spontaneous base opening events. © The Author(s) 2015. Published by Oxford University Press on behalf of Nucleic Acids Research.

Think Pair Share with Formative Assessment for Junior High School Student

NASA Astrophysics Data System (ADS)

Pradana, O. R. Y.; Sujadi, I.; Pramudya, I.

2017-09-01

Geometry is a science related to abstract thinking ability so that not many students are able to understand this material well. In this case, the learning model plays a crucial role in improving student achievement. This means that a less precise learning model will cause difficulties for students. Therefore, this study provides a quantitative explanation of the Think Pair Share learning model combined with the formative assessment. This study aims to test the Think Pair Share with the formative assessment on junior high school students. This research uses a quantitative approach of Pretest-Posttest in control group and experiment group. ANOVA test and Scheffe test used to analyse the effectiveness this learning. Findings in this study are student achievement on the material geometry with Think Pair Share using formative assessment has increased significantly. This happens probably because this learning makes students become more active during learning. Hope in the future, Think Pair Share with formative assessment be a useful learning for teachers and this learning applied by the teacher around the world especially on the material geometry.

Precision Formation Keeping at L2 Using the Autonomous Formation Flying Sensor

NASA Technical Reports Server (NTRS)

McLoughlin, Terence H.; Campbell, Mark

2004-01-01

Recent advances in formation keeping for large numbers of spacecraft using the Autonomous Formation Flying are presented. This sensor, currently under development at JPL, has been identified as a key component in future formation flying spacecraft missions. The sensor provides accurate range and bearing measurements between pairs of spacecraft using GPS technology. Previous theoretical work by the authors has focused on developing a decentralized scheduling algorithm to control the tasking of such a sensor between the relative range and bearing measurements to each node in the formation. The resulting algorithm has been modified to include switching constraints in the sensor. This paper also presents a testbed for real time validation of a sixteen-node formation based on the Stellar Imager mission. Key aspects of the simulation include minimum fuel maneuvers based on free-body dynamics and a three body propagator for simulating the formation at L2.

Hydrolysis of N3-methyl-2'-deoxycytidine: model compound for reactivity of protonated cytosine residues in DNA.

PubMed

Sowers, L C; Sedwick, W D; Shaw, B R

1989-11-01

Protonation of cytosine residues at physiological pH may occur in DNA as a consequence of both alkylation and aberrant base-pair formation. When cytosine derivatives are protonated, they undergo hydrolysis reactions at elevated rates and can either deaminate to form the corresponding uracil derivatives or depyrimidinate generating abasic sites. The kinetic parameters for reaction of protonated cytosine are derived by studying the hydrolysis of N3-methyl-2'-deoxycytidine (m3dC), a cytosine analogue which is predominantly protonated at physiological pH. Both deamination and depyrimidimation reaction rates are shown to be linearly dependent upon the fraction of protonated molecules. We present here thermodynamic parameters which allow determination of hydrolysis rates of m3dC as functions of pH and temperature. Protonation of cytosine residues in DNA, as induced by aberrant base-pair formation or base modification, may accelerate the rate of both deamination and depyrimidation up to several thousand-fold under physiological conditions.

On the role of covarying functions in stimulus class formation and transfer of function.

PubMed Central

Markham, Rebecca G; Markham, Michael R

2002-01-01

This experiment investigated whether directly trained covarying functions are necessary for stimulus class formation and transfer of function in humans. Initial class training was designed to establish two respondent-based stimulus classes by pairing two visual stimuli with shock and two other visual stimuli with no shock. Next, two operant discrimination functions were trained to one stimulus of each putative class. The no-shock group received the same training and testing in all phases, except no stimuli were ever paired with shock. The data indicated that skin conductance response conditioning did not occur for the shock groups or for the no-shock group. Tests showed transfer of the established discriminative functions, however, only for the shock groups, indicating the formation of two stimulus classes only for those participants who received respondent class training. The results suggest that transfer of function does not depend on first covarying the stimulus class functions. PMID:12507017

Enol tautomers of Watson-Crick base pair models are metastable because of nuclear quantum effects.

PubMed

Pérez, Alejandro; Tuckerman, Mark E; Hjalmarson, Harold P; von Lilienfeld, O Anatole

2010-08-25

Intermolecular enol tautomers of Watson-Crick base pairs could emerge spontaneously via interbase double proton transfer. It has been hypothesized that their formation could be facilitated by thermal fluctuations and proton tunneling, and possibly be relevant to DNA damage. Theoretical and computational studies, assuming classical nuclei, have confirmed the dynamic stability of these rare tautomers. However, by accounting for nuclear quantum effects explicitly through Car-Parrinello path integral molecular dynamics calculations, we find the tautomeric enol form to be dynamically metastable, with lifetimes too insignificant to be implicated in DNA damage.

The Effects of Varying Group Size on the Reading Recovery Approach to Preventive Early Intervention

ERIC Educational Resources Information Center

Iversen, Sandra; Tunmer, William E.; Chapman, James W.

2005-01-01

The purpose of this study was to determine whether an early intervention program based on the Reading Recovery (RR) format could be developed for pairs of struggling readers that would allow them to make accelerated progress similar to that experienced in the 1-to-1 RR tutorial. A preliminary pilot study showed that the RR lesson format could be…

Nitrogen vacancy, self-interstitial diffusion, and Frenkel-pair formation/dissociation in B 1 TiN studied by ab initio and classical molecular dynamics with optimized potentials

NASA Astrophysics Data System (ADS)

Sangiovanni, D. G.; Alling, B.; Steneteg, P.; Hultman, L.; Abrikosov, I. A.

2015-02-01

We use ab initio and classical molecular dynamics (AIMD and CMD) based on the modified embedded-atom method (MEAM) potential to simulate diffusion of N vacancy and N self-interstitial point defects in B 1 TiN. TiN MEAM parameters are optimized to obtain CMD nitrogen point-defect jump rates in agreement with AIMD predictions, as well as an excellent description of Ti Nx(˜0.7

Spectrophotometric determination of trazodone, amineptine and amitriptyline hydrochlorides through ion-pair formation with molybdenum and thiocyanate

NASA Astrophysics Data System (ADS)

Mohamed, Gehad G.; Nour El-Dien, F. A.; Khalil, S. M.; Mohamed, Nehad A.

2006-12-01

Extraction spectrophotometric method has been developed for the determination of tricyclic drugs such as trazodone (TZH), amineptine (APH) and amitriptyline (ATPH) hydrochlorides in pure form and in the dosage forms coming from different Egyptian markets. The method based on the formation of ion-pairs between these drugs under investigation and inorganic complex of Mo(V)-thiocyanate followed by its extraction with methylene chloride. The optimum conditions for the ion-pairs formation are established. The method permits the determination of TZH, APH and ATPH over the concentration range of 2-28, 2-32 and 1-30 μg ml -1, respectively. The Sandell sensitivity ( S) is found to be 0.105, 0.138 and 0.118 g cm -2 for TZH, APH and ATPH, respectively. The SD is found to be 0.16-0.377, 0.12-0.259 and 0.091-0.286 and the R.S.D. are 0.14-0.55, 0.12-0.399 and 0.095-0.485 for TZH, APH and ATPH, respectively. The method is applicable for the assay of the investigated drugs in different dosage forms and the results are in good agreement with those obtained by the official method.

Precursor Mediated Synthesis of Nanostructured Silicas: From Precursor-Surfactant Ion Pairs to Structured Materials.

PubMed

Hesemann, Peter; Nguyen, Thy Phung; Hankari, Samir El

2014-04-11

The synthesis of nanostructured anionic-surfactant-templated mesoporous silica (AMS) recently appeared as a new strategy for the formation of nanostructured silica based materials. This method is based on the use of anionic surfactants together with a co-structure-directing agent (CSDA), mostly a silylated ammonium precursor. The presence of this CSDA is necessary in order to create ionic interactions between template and silica forming phases and to ensure sufficient affinity between the two phases. This synthetic strategy was for the first time applied in view of the synthesis of surface functionalized silica bearing ammonium groups and was then extended on the formation of materials functionalized with anionic carboxylate and bifunctional amine-carboxylate groups. In the field of silica hybrid materials, the "anionic templating" strategy has recently been applied for the synthesis of silica hybrid materials from cationic precursors. Starting from di- or oligosilylated imidazolium and ammonium precursors, only template directed hydrolysis-polycondensation reactions involving complementary anionic surfactants allowed accessing structured ionosilica hybrid materials. The mechanistic particularity of this approach resides in the formation of precursor-surfactant ion pairs in the hydrolysis-polycondensation mixture. This review gives a systematic overview over the various types of materials accessed from this cooperative ionic templating approach and highlights the high potential of this original strategy for the formation of nanostructured silica based materials which appears as a complementary strategy to conventional soft templating approaches.

Equivalence Class Formation in a Trace Stimulus Pairing Two-Response Format: Effects of Response Labels and Prior Programmed Transitivity Induction

ERIC Educational Resources Information Center

Fields, Lanny; Doran, Erica; Marroquin, Michael

2009-01-01

Three experiments identified factors that did and did not enhance the formation of two-node four-member equivalence classes when training and testing were conducted with trials presented in a trace stimulus pairing two-response (SP2R) format. All trials contained two separately presented stimuli. Half of the trials, called within-class trials,…

Quantitative assessment of pair formation behavior in captive whooping cranes (Grus americana)

USGS Publications Warehouse

Nelson, J.T.; Small, C.R.; Ellis, D.H.

1995-01-01

Instantaneous scan sampling for mean distance and synchronous action patterns and all-occurrence sampling for unison call, dance, strut, and hoover-up behaviors were conducted for five potential whooping crane pairs at Patuxent Environmental Science Center, Laurel. Maryland. Dance, strut, and hoover-up differed among pairs, as did total frequency of social behaviors. It was unclear whether or not total frequency of social behaviors during pair formation can be used as an index for potential breeding success. The relative importance of different action patterns should be used as indices of pair compatibility in captive whooping cranes.

Technological applications arising from the interactions of DNA bases with metal ions.

PubMed

Park, Ki Soo; Park, Hyun Gyu

2014-08-01

An intense interest has grown in the unique interactions of nucleic acids with metal ions, which lead to the formation of metal-base pairs and the generation of fluorescent nanomaterials. In this review, different types of metal-base pairs, especially those formed from naturally occurring nucleosides, are described with emphasis also being given to recent advances made in employing these complexes to govern enzymatic reactions. The review also contains a comprehensive description of DNA-templated inorganic nanomaterials such as silver nanoclusters which possess excellent fluorescence properties. Finally, a summary is given about how these materials have led to recent advances in the field of nanobiotechnology. Copyright © 2013 Elsevier Ltd. All rights reserved.

Planning a School-Based Mentoring Program. Lessons Learned. Volume 1, Issue 4

ERIC Educational Resources Information Center

Garringer, Michael

2010-01-01

School-based mentoring (SBM) has exploded in popularity in recent years: Today approximately one fourth of the youth mentoring programs in the country use a school-based format (Herrera, Grossman, Kauh, Feldman, & McMaken, 2007). In SBM, a K-12 student is paired with an adult from the community or an older (usually high school) student in a…

Ni2+-binding RNA motifs with an asymmetric purine-rich internal loop and a G-A base pair.

PubMed Central

Hofmann, H P; Limmer, S; Hornung, V; Sprinzl, M

1997-01-01

RNA molecules with high affinity for immobilized Ni2+ were isolated from an RNA pool with 50 randomized positions by in vitro selection-amplification. The selected RNAs preferentially bind Ni2+ and Co2+ over other cations from first series transition metals. Conserved structure motifs, comprising about 15 nt, were identified that are likely to represent the Ni2+ binding sites. Two conserved motifs contain an asymmetric purine-rich internal loop and probably a mismatch G-A base pair. The structure of one of these motifs was studied with proton NMR spectroscopy and formation of the G-A pair at the junction of helix and internal loop was demonstrated. Using Ni2+ as a paramagnetic probe, a divalent metal ion binding site near this G-A base pair was identified. Ni2+ ions bound to this motif exert a specific stabilization effect. We propose that small asymmetric purine-rich loops that contain a G-A interaction may represent a divalent metal ion binding site in RNA. PMID:9409620

Structure of an anti-HIV-1 hammerhead ribozyme complex with a 17-mer DNA substrate analog of HIV-1 gag RNA and a mechanism for the cleavage reaction: 750 MHz NMR and computer experiments

NASA Technical Reports Server (NTRS)

Ojha, R. P.; Dhingra, M. M.; Sarma, M. H.; Myer, Y. P.; Setlik, R. F.; Shibata, M.; Kazim, A. L.; Ornstein, R. L.; Rein, R.; Turner, C. J.;

PDF Lecture Materials for Online and ``Flipped'' Format Astronomy Courses

NASA Astrophysics Data System (ADS)

Kary, D. M.; Eisberg, J.

2013-04-01

Online astronomy courses typically rely on students reading the textbook and/or a set of text-based lecture notes to replace the “lecture” material. However, many of our students report that this is much less engaging than in-person lectures, especially given the amount of interactive work such as “think-pair-share” problems done in many astronomy classes. Students have similarly criticized direct lecture-capture. To address this, we have developed a set of PowerPoint-style presentations with embedded lecture audio combined with prompts for student interaction including think-pair-share questions. These are formatted PDF packages that can be used on a range of different computers using free software. The presentations are first developed using Microsoft PowerPoint software. Audio recordings of scripted lectures are then synchronized with the presentations and the entire package is converted to PDF using Adobe Presenter. This approach combines the ease of editing that PowerPoint provides along with the platform-independence of PDF. It's easy to add, remove, or edit individual slides as needed, and PowerPoint supports internal links so that think-pair-share questions can be inserted with links to feedback based on the answers selected. Modern PDF files support animated visuals with synchronized audio and they can be read using widely available free software. Using these files students in an online course can get many of the benefits of seeing and hearing the course material presented in an in-person lecture format. Students needing extra help in traditional lecture classes can use these presentations to help review the materials covered in lecture. Finally, the presentations can be used in a “flipped” format in which students work through the presentations outside of class time while spending the “lecture” time on in-class interaction.

Structure and decomposition of the silver formate Ag(HCO{sub 2})

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

Puzan, Anna N., E-mail: anna_puzan@mail.ru; Baumer, Vyacheslav N.; Mateychenko, Pavel V.

Crystal structure of the silver formate Ag(HCO{sub 2}) has been determined (orthorhombic, sp.gr. Pccn, a=7.1199(5), b=10.3737(4), c=6.4701(3)Å, V=477.88(4) Å{sup 3}, Z=8). The structure contains isolated formate ions and the pairs Ag{sub 2}{sup 2+} which form the layers in (001) planes (the shortest Ag–Ag distances is 2.919 in the pair and 3.421 and 3.716 Å between the nearest Ag atoms of adjacent pairs). Silver formate is unstable compound which decompose spontaneously vs time. Decomposition was studied using Rietveld analysis of the powder diffraction patterns. It was concluded that the diffusion of Ag atoms leads to the formation of plate-like metal particlesmore » as nuclei in the (100) planes which settle parallel to (001) planes of the silver formate matrix. - Highlights: • Silver formate Ag(HCO{sub 2}) was synthesized and characterized. • Layered packing of Ag-Ag pairs in the structure was found. • Decomposition of Ag(HCO{sub 2}) and formation of metal phase were studied. • Rietveld-refined micro-structural characteristics during decomposition reveal the space relationship between the matrix structure and forming Ag phase REPLACE with: Space relationship between the matrix structure and forming Ag phase.« less

AB INITIO PULSAR MAGNETOSPHERE: THREE-DIMENSIONAL PARTICLE-IN-CELL SIMULATIONS OF OBLIQUE PULSARS

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

Philippov, Alexander A.; Spitkovsky, Anatoly; Cerutti, Benoit, E-mail: sashaph@princeton.edu

2015-03-01

We present “first-principles” relativistic particle-in-cell simulations of the oblique pulsar magnetosphere with pair formation. The magnetosphere starts to form with particles extracted from the surface of the neutron star. These particles are accelerated by surface electric fields and emit photons capable of producing electron–positron pairs. We inject secondary pairs at the locations of primary energetic particles whose energy exceeds the threshold for pair formation. We find solutions that are close to the ideal force-free magnetosphere with the Y-point and current sheet. Solutions with obliquities ≤40° do not show pair production in the open field line region because the local currentmore » density along the magnetic field is below the Goldreich–Julian value. The bulk outflow in these solutions is charge-separated, and pair formation happens in the current sheet and return current layer only. Solutions with higher inclinations show pair production in the open field line region, with high multiplicity of the bulk flow and the size of the pair-producing region increasing with inclination. We observe the spin-down of the star to be comparable to MHD model predictions. The magnetic dissipation in the current sheet ranges between 20% for the aligned rotator and 3% for the orthogonal rotator. Our results suggest that for low obliquity neutron stars with suppressed pair formation at the light cylinder, the presence of phenomena related to pair activity in the bulk of the polar region, e.g., radio emission, may crucially depend on the physics beyond our simplified model, such as the effects of curved spacetime or multipolar surface fields.« less

The SCOPE mission

NASA Astrophysics Data System (ADS)

Fujimoto, Masaki

In order to open the new horizon of research in the Plasma Universe, SCOPE will perform simultaneous multi-scale observations that enables data-based study on the key space plasma processes from the cross-scale coupling point of view. The key processes to be studied are magnetic reconnection under various boundary conditions, shocks in space plasma, collisionless plasma mixing at the boundaries, and physics of current sheets embedded in complex magnetic geometries. The orbit is equatorial, 10x25 Re, such that in-situ observations of the above key processes are possible. The SCOPE mission is made up of a pair of mother-daughter spacecraft and a three spacecraft formation. The spacecraft pair will zoom-in to the microphysics while the spacecraft formation will observe macro-scale dynamics surrouding the key region to be studied by the mother-daughter pair. The mother spacecraft is equipped with a full suite of particle detector including ultra-high sampling cycle electron detector. The daughter spacecraft remains near ( 10km) the mother spacecraft and the spacecraft-pair will focus on wave-particle interaction utilizing inter-spacecraft communication. The inter-spacecraft distance of the for-mation varies from below 100km to above 3000km so that surrounding dynamics at various scales (electron, ion and MHD) can be studied. While the core part of the mission is planned to be a CSA-JAXA (Canada-Japan) collaboration, further international collaborations to en-hance the science return of the mission are welcome.

Development of an ion-pair to improve the colon permeability of a low permeability drug: Atenolol.

PubMed

Lozoya-Agullo, Isabel; González-Álvarez, Isabel; González-Álvarez, Marta; Merino-Sanjuán, Matilde; Bermejo, Marival

2016-10-10

To ensure the optimal performance of oral controlled release formulations, drug colon permeability is one of the critical parameters. Consequently developing this kind of formulations for low permeability molecules requires strategies to increase their ability to cross the colonic membrane. The objective of this work is to show if an ion-pair formation can improve the colon permeability of atenolol as a low permeability drug model. Two counter ions have been tested: brilliant blue and bromophenol blue. The Distribution coefficients at pH7.00 (DpH7) of atenolol, atenolol + brilliant blue and atenolol + bromophenol blue were experimentally determined in n-octanol. Moreover, the colonic permeability was determined in rat colon using in situ closed loop perfusion method based in Doluisio's Technique. To check the potential effects of the counter ions on the membrane integrity, a histological assessment of colonic tissue was done. The results of the partitioning studies were inconclusive about ion-pair formation; nevertheless colon permeability was significantly increased by both counter ions (from 0.232±0.021cm/s to 0.508±0.038cm/s in the presence of brilliant blue and to 0.405±0.044cm/s in the presence of bromophenol blue). Neither damage on the membrane was observed on the histological studies, nor any change on paracellular permeability suggesting that the permeability enhancement could be attributed to the ion-pair formation. Copyright © 2016 Elsevier B.V. All rights reserved.

Facile Modulation of FLP Properties: A Phosphinylvinyl Grignard Reagent and Ga/P- and In/P2 -Based Frustrated Lewis Pairs.

PubMed

Backs, Jana; Lange, Merten; Possart, Josephine; Wollschläger, Agnes; Mück-Lichtenfeld, Christian; Uhl, Werner

2017-03-06

An Al/P-based frustrated Lewis pair (FLP) reacted with PhMgCl by an unexpected transmetalation and formation of a phosphinylvinyl Grignard reagent. This compound is well suited for the transfer of the basic FLP component to other Lewis acidic metal atoms and allowed the generation of a Ga/P and an In/P 2 FLP. The Ga FLP showed a behavior different to that of the corresponding Al FLP, the In FLP allowed the chelating coordination of an Au atom by Au-Cl bond activation. © 2017 Wiley-VCH Verlag GmbH & Co. KGaA, Weinheim.

Preparation and analysis of multilayer composites based on polyelectrolyte complexes

NASA Astrophysics Data System (ADS)

Petrova, V. A.; Orekhov, A. S.; Chernyakov, D. D.; Baklagina, Yu. G.; Romanov, D. P.; Kononova, S. V.; Volod'ko, A. V.; Ermak, I. M.; Klechkovskaya, V. V.; Skorik, Yu. A.

2016-11-01

A method for preparing multilayer film composites based on chitosan has been developed by the example of polymer pairs: chitosan-hyaluronic acid, chitosan-alginic acid, and chitosan-carrageenan. The structure of the composite films is characterized by X-ray diffractometry and scanning electron microscopy. It is shown that the deposition of a solution of hyaluronic acid, alginic acid, or carrageenan on a chitosan gel film leads to the formation of a polyelectrolyte complex layer at the interface, which is accompanied by the ordering of chitosan chains in the surface region; the microstructure of this layer depends on the nature of contacting polymer pairs.

A Bridging Water Anchors the Tethered 5-(3-Aminopropyl)-2′-deoxyuridine Amine in the DNA Major Groove Proximate to the N+2 C·G Base Pair: Implications for Formation of Interstrand 5′-GNC-3′ Cross-Links by Nitrogen Mustards‡

PubMed Central

Wang, Feng; Li, Feng; Ganguly, Manjori; Marky, Luis A.; Gold, Barry; Egli, Martin; Stone, Michael P.

2009-01-01

Site-specific insertion of 5-(3-aminopropyl)-2′-deoxyuridine (Z3dU) and 7-deaza-dG into the Dickerson-Drew dodecamers 5′-d(C1G2C3G4A5A6T7T8C9Z10C11G12)-3′ · 5′-d(C13G14C15G16A17A18T19T20-C21Z22C23G24)-3′ (named DDDZ10) and 5′-d(C1G2C3G4A5A6T7X8C9Z10C11G12)-3′ · 5′-d(C13G14C15G16A17A18-T19X20C21Z22C23G24)-3′ (named DDD2+Z10)(X = Z3dU; Z = 7-deaza-dG) suggests a mechanism underlying the formation of interstrand N+2 DNA cross-links by nitrogen mustards, e.g., melphalan and mechlorethamine. Analysis of the DDD2+Z10 duplex reveals that the tethered cations at base pairs A5 · X20 and X8 · A17 extend within the major groove in the 3′-direction, toward conserved Mg2+ binding sites located adjacent to N+2 base pairs C3 · Z22 and Z10 · C15. Bridging waters located between the tethered amines and either Z10 or Z22 O6 stabilize the tethered cations and allow interactions with the N + 2 base pairs without DNA bending. Incorporation of 7-deaza-dG into the DDD2+Z10 duplex weakens but does not eliminate electrostatic interactions between tethered amines and Z10 O6 and Z22 O6. The results suggest a mechanism by which tethered N7-dG aziridinium ions, the active species involved in formation of interstrand 5′-GNC-3′ cross-links by nitrogen mustards, modify the electrostatics of the major groove and position the aziridinium ions proximate to the major groove edge of the N+2 C · G base pair, facilitating interstrand cross-linking. PMID:18549246

Effect of post-implantation annealing on Al-N isoelectronic trap formation in silicon: Al-N pair formation and defect recovery mechanisms

NASA Astrophysics Data System (ADS)

Mori, Takahiro; Morita, Yukinori; Matsukawa, Takashi

2018-05-01

The effect of post-implantation annealing (PIA) on Al-N isoelectronic trap (IET) formation in silicon has been experimentally investigated to discuss the Al-N IET formation and implantation-induced defect recovery mechanisms. We performed a photoluminescence study, which indicated that self-interstitial clusters and accompanying vacancies are generated in the ion implantation process. It is supposed that Al and N atoms move to the vacancy sites and form stable Al-N pairs in the PIA process. Furthermore, the PIA process recovers self-interstitial clusters while transforming their atomic configuration. The critical temperature for the formation/dissociation of Al-N pairs was found to be 450 °C, with which we describe the process integration for devices utilizing Al-N IET technology.

Ion pair particles at the air–water interface

NASA Astrophysics Data System (ADS)

Kumar, Manoj; Francisco, Joseph S.

2017-11-01

Although the role of methanesulfonic acid (HMSA) in particle formation in the gas phase has been extensively studied, the details of the HMSA-induced ion pair particle formation at the air–water interface are yet to be examined. In this work, we have performed Born–Oppenheimer molecular dynamics simulations and density functional theory calculations to investigate the ion pair particle formation from HMSA and (R1)(R2)NH (for NH3, R1 = R2 = H; for CH3NH2, R1 = H and R2 = CH3; and for CH3NH2, R1 = R2 = CH3) at the air–water interface. The results show that, at the air–water interface, HMSA deprotonates within a few picoseconds and results in the formation of methanesulfonate ion (MSA‑)ṡṡH3O+ ion pair. However, this ion pair decomposes immediately, explaining why HMSA and water alone are not sufficient for forming stable particles in atmosphere. Interestingly, the particle formation from the gas-phase hydrogen-bonded complexes of HMSA with (R1)(R2)NH on the water droplet is observed with a few femtoseconds, suggesting a mechanism for the gas to particle conversion in aqueous environments. The reaction involves a direct proton transfer between HMSA and (R1)(R2)NH, and the resulting MSA‑ṡṡ(R1)(R2)NH2+ complex is bound by one to four interfacial water molecules. The mechanistic insights gained from this study may serve as useful leads for understanding about the ion pair particle formation from other precursors in forested and polluted urban environments.

Potentiometric and spectrophotometric study of the stability of magnesium carbonate and bicarbonate ion pairs to 150 °C and aqueous inorganic carbon speciation and magnesite solubility

NASA Astrophysics Data System (ADS)

Stefánsson, Andri; Bénézeth, Pascale; Schott, Jacques

2014-08-01

The formation constants of magnesium bicarbonate and carbonate ion pairs have been experimentally determined in dilute hydrothermal solutions to 150 °C. Two experimental approaches were applied, potentiometric acid-base titrations at 10-60 °C and spectrophotometric pH measurements using two pH indicators, 2-naphthol and 4-nitrophenol, at 25 and 80-150 °C. At a given temperature, the first and second ionization constants of carbonic acid (K1, K2) and the ion pair formation constants for MgHCO3+(aq) (KMgHCO3+) and MgCO3(aq) (KMgCO3) were simultaneously fitted to the data. Results of this study compare well with previously determined values of K1 and K2. The formation constants of MgHCO3+(aq) and MgCO3(aq) ion pairs increased significantly with increasing temperature, with values of logKMgHCO3+ = 1.14 and 1.75 and of logKMgCO3 = 2.86 and 3.48 at 10 °C and 100 °C, respectively. These ion pairs are important aqueous species under neutral to alkaline conditions in moderately dilute to concentrated Mg-containing solutions, with MgCO3(aq) predominating over CO32-(aq) in solutions at pH >8. The predominance of magnesium carbonate over carbonate is dependent on the concentration of dissolved magnesium and the ratio of magnesium over carbonate. With increasing temperature and at alkaline pH, brucite solubility further reduced the magnesium concentration to levels below 1 mmol kg-1, thus limiting availability of Mg2+(aq) for magnesite precipitation.

On the binding of indeno[1,2-c]isoquinolines in the DNA-topoisomerase I cleavage complex.

PubMed

Xiao, Xiangshu; Antony, Smitha; Pommier, Yves; Cushman, Mark

2005-05-05

An ab initio quantum mechanics calculation is reported which predicts the orientation of indenoisoquinoline 4 in the ternary cleavage complex formed from DNA and topoisomerase I (top1). The results of this calculation are consistent with the hypothetical structures previously proposed for the indenoisoquinoline-DNA-top1 ternary complexes based on molecular modeling, the crystal structure of a recently reported ternary complex, and the biological results obtained with a pair of diaminoalkyl-substituted indenoisoquinoline enantiomers. The results of these studies indicate that the pi-pi stacking interactions between the indenoisoquinolines and the neighboring DNA base pairs play a major role in determining binding orientation. The calculation of the electrostatic potential surface maps of the indenoisoquinolines and the adjacent DNA base pairs shows electrostatic complementarity in the observed binding orientation, leading to the conclusion that electrostatic attraction between the intercalators and the base pairs in the cleavage complex plays a major stabilizing role. On the other hand, the calculation of LUMO and HOMO energies of indenoisoquinoline 13b and neighboring DNA base pairs in conjunction with NBO analysis indicates that charge transfer complex formation plays a relatively minor role in stabilizing the ternary complexes derived from indenoisoquinolines, DNA, and top1. The results of these studies are important in understanding the existing structure-activity relationships for the indenoisoquinolines as top1 inhibitors and as anticancer agents, and they will be important in the future design of indenoisoquinoline-based top1 inhibitors.

Formation of rings from segments of HeLa-cell nuclear deoxyribonucleic acid

PubMed Central

Hardman, Norman

1974-01-01

Duplex segments of HeLa-cell nuclear DNA were generated by cleavage with DNA restriction endonuclease from Haemophilus influenzae. About 20–25% of the DNA segments produced, when partly degraded with exonuclease III and annealed, were found to form rings visible in the electron microscope. A further 5% of the DNA segments formed structures that were branched in configuration. Similar structures were generated from HeLa-cell DNA, without prior treatment with restriction endonuclease, when the complementary polynucleotide chains were exposed by exonuclease III action at single-chain nicks. After exposure of an average single-chain length of 1400 nucleotides per terminus at nicks in HeLa-cell DNA by exonuclease III, followed by annealing, the physical length of ring closures was estimated and found to be 0.02–0.1μm, or 50–300 base pairs. An almost identical distribution of lengths was recorded for the regions of complementary base sequence responsible for branch formation. It is proposed that most of the rings and branches are formed from classes of reiterated base sequence with an average length of 180 base pairs arranged intermittenly in HeLa-cell DNA. From the rate of formation of branched structures when HeLa-cell DNA segments were heat-denatured and annealed, it is estimated that the reiterated sequences are in families containing approximately 2400–24000 copies. ImagesPLATE 2PLATE 1 PMID:4462738

Asteroid Systems: Binaries, Triples, and Pairs

NASA Astrophysics Data System (ADS)

Margot, J.-L.; Pravec, P.; Taylor, P.; Carry, B.; Jacobson, S.

In the past decade, the number of known binary near-Earth asteroids has more than quadrupled and the number of known large main-belt asteroids with satellites has doubled. Half a dozen triple asteroids have been discovered, and the previously unrecognized populations of asteroid pairs and small main-belt binaries have been identified. The current observational evidence confirms that small (≲20 km) binaries form by rotational fission and establishes that the Yarkovsky-O'Keefe-Radzievskii-Paddack (YORP) effect powers the spin-up process. A unifying paradigm based on rotational fission and post-fission dynamics can explain the formation of small binaries, triples, and pairs. Large (>~20 km) binaries with small satellites are most likely created during large collisions.

Unconventional Cooper pairing results in a pseudogap-like phase in s-wave superconductors

NASA Astrophysics Data System (ADS)

Springer, Daniel; Cheong, Siew Ann

2015-10-01

The impact of disorder on the superconducting (SC) pairing mechanism is the centre of much debate. Some evidence suggests a loss of phase coherence of pairs while others point towards the formation of a competing phase. In our work we show that the two perspectives may be different sides of the same coin. Using an extension of the perturbative renormalization group approach we compare the impact of different disorder-induced interactions on a SC ground state. We find that in the strongly disordered regime an interaction between paired fermions and their respective disordered environment replaces conventional Cooper pairing. For these unconventional Cooper pairs the phase coherence condition, required for the formation of a SC condensate, is not satisfied.

Roles of the amino group of purine bases in the thermodynamic stability of DNA base pairing.

PubMed

Nakano, Shu-ichi; Sugimoto, Naoki

2014-08-05

The energetic aspects of hydrogen-bonded base-pair interactions are important for the design of functional nucleotide analogs and for practical applications of oligonucleotides. The present study investigated the contribution of the 2-amino group of DNA purine bases to the thermodynamic stability of oligonucleotide duplexes under different salt and solvent conditions, using 2'-deoxyriboinosine (I) and 2'-deoxyribo-2,6-diaminopurine (D) as non-canonical nucleotides. The stability of DNA duplexes was changed by substitution of a single base pair in the following order: G • C > D • T ≈ I • C > A • T > G • T > I • T. The apparent stabilization energy due to the presence of the 2-amino group of G and D varied depending on the salt concentration, and decreased in the water-ethanol mixed solvent. The effects of salt concentration on the thermodynamics of DNA duplexes were found to be partially sequence-dependent, and the 2-amino group of the purine bases might have an influence on the binding of ions to DNA through the formation of a stable base-paired structure. Our results also showed that physiological salt conditions were energetically favorable for complementary base recognition, and conversely, low salt concentration media and ethanol-containing solvents were effective for low stringency oligonucleotide hybridization, in the context of conditions employed in this study.

Precursor Mediated Synthesis of Nanostructured Silicas: From Precursor-Surfactant Ion Pairs to Structured Materials

PubMed Central

Hesemann, Peter; Nguyen, Thy Phung; Hankari, Samir El

2014-01-01

The synthesis of nanostructured anionic-surfactant-templated mesoporous silica (AMS) recently appeared as a new strategy for the formation of nanostructured silica based materials. This method is based on the use of anionic surfactants together with a co-structure-directing agent (CSDA), mostly a silylated ammonium precursor. The presence of this CSDA is necessary in order to create ionic interactions between template and silica forming phases and to ensure sufficient affinity between the two phases. This synthetic strategy was for the first time applied in view of the synthesis of surface functionalized silica bearing ammonium groups and was then extended on the formation of materials functionalized with anionic carboxylate and bifunctional amine-carboxylate groups. In the field of silica hybrid materials, the “anionic templating” strategy has recently been applied for the synthesis of silica hybrid materials from cationic precursors. Starting from di- or oligosilylated imidazolium and ammonium precursors, only template directed hydrolysis-polycondensation reactions involving complementary anionic surfactants allowed accessing structured ionosilica hybrid materials. The mechanistic particularity of this approach resides in the formation of precursor-surfactant ion pairs in the hydrolysis-polycondensation mixture. This review gives a systematic overview over the various types of materials accessed from this cooperative ionic templating approach and highlights the high potential of this original strategy for the formation of nanostructured silica based materials which appears as a complementary strategy to conventional soft templating approaches. PMID:28788602

Critical Period of Memory Enhancement during Taste Avoidance Conditioning in Lymnaea stagnalis

PubMed Central

Sunada, Hiroshi; Lukowiak, Ken; Sakakibara, Manabu

2013-01-01

The present study investigated the optimal training procedure leading to long-lasting taste avoidance behavior in Lymnaea. A training procedure comprising 5 repeated pairings of a conditional stimulus (CS, sucrose), with an unconditional stimulus (US, a tactile stimulation to the animal’s head), over a 4-day period resulted in an enhanced memory formation than 10 CS-US repeated pairings over a 2-day period or 20 CS-US repeated pairings on a single day. Backward conditioning (US-CS) pairings did not result in conditioning. Thus, this taste avoidance conditioning was CS-US pairing specific. Food avoidance behavior was not observed following training, however, if snails were immediately subjected to a cold-block (4°C for 10 min). It was critical that the cold-block be applied within 10 min to block long-term memory (LTM) formation. Further, exposure to the cold-block 180 min after training also blocked both STM and LTM formation. The effects of the cold-block on subsequent learning and memory formation were also examined. We found no long lasting effects of the cold-block on subsequent memory formation. If protein kinase C was activated before the conditioning paradigm, snails could still acquire STM despite exposure to the cold-block. PMID:24098373

Adapting an in-person patient-caregiver communication intervention to a tailored web-based format.

PubMed

Zulman, Donna M; Schafenacker, Ann; Barr, Kathryn L C; Moore, Ian T; Fisher, Jake; McCurdy, Kathryn; Derry, Holly A; Saunders, Edward W; An, Lawrence C; Northouse, Laurel

2012-03-01

Interventions that target cancer patients and their caregivers have been shown to improve patient-caregiver communication, support, and emotional well-being. To adapt an in-person communication intervention for cancer patients and caregivers to a web-based format, and to examine the usability and acceptability of the web-based program among representative users. A tailored, interactive web-based communication program for cancer patients and their family caregivers was developed based on an existing in-person, nurse-delivered intervention. The development process involved: (1) building a multidisciplinary team of content and web design experts, (2) combining key components of the in-person intervention with the unique tailoring and interactive features of a web-based platform, and (3) conducting focus groups and usability testing to obtain feedback from representative program users at multiple time points. Four focus groups with 2-3 patient-caregiver pairs per group (n = 22 total participants) and two iterations of usability testing with four patient-caregiver pairs per session (n = 16 total participants) were conducted. Response to the program's structure, design, and content was favorable, even among users who were older or had limited computer and Internet experience. The program received high ratings for ease of use and overall usability (mean System Usability Score of 89.5 out of 100). Many elements of a nurse-delivered patient-caregiver intervention can be successfully adapted to a web-based format. A multidisciplinary design team and an iterative evaluation process with representative users were instrumental in the development of a usable and well-received web-based program. Copyright © 2011 John Wiley & Sons, Ltd.

Brief Report: Adapting an In-Person Patient-Caregiver Communication Intervention to a Tailored Web-Based Format

PubMed Central

Zulman, Donna M.; Schafenacker, Ann; Barr, Kathryn L.C.; Moore, Ian T.; Fisher, Jake; McCurdy, Kathryn; Derry, Holly A.; Saunders, Edward W.; An, Lawrence C.; Northouse, Laurel

2011-01-01

Background Interventions that target cancer patients and their caregivers have been shown to improve communication, support, and emotional well-being. Objective To adapt an in-person communication intervention for cancer patients and caregivers to a web-based format, and to examine the usability and acceptability of the web-based program among representative users. Methods A tailored, interactive web-based communication program for cancer patients and their family caregivers was developed based on an existing in-person, nurse-delivered intervention. The development process involved: 1) building a multidisciplinary team of content and web design experts, 2) combining key components of the in-person intervention with the unique tailoring and interactive features of a web-based platform, and 3) conducting focus groups and usability testing to obtain feedback from representative program users at multiple time points. Results Four focus groups with 2 to 3 patient-caregiver pairs per group (n = 22 total participants) and two iterations of usability testing with 4 patient-caregiver pairs per session (n = 16 total participants) were conducted. Response to the program's structure, design, and content was favorable, even among users who were older or had limited computer and internet experience. The program received high ratings for ease of use and overall usability (mean System Usability Score of 89.5 out of 100). Conclusions Many elements of a nurse-delivered patient-caregiver intervention can be successfully adapted to a web-based format. A multidisciplinary design team and an iterative evaluation process with representative users were instrumental in the development of a usable and well-received web-based program. PMID:21830255

Cumulative approaches to track formation under swift heavy ion (SHI) irradiation: Phenomenological correlation with formation energies of Frenkel pairs

NASA Astrophysics Data System (ADS)

Crespillo, M. L.; Agulló-López, F.; Zucchiatti, A.

2017-03-01

An extensive survey for the formation energies of Frenkel pairs, as representative candidates for radiation-induced point defects, is presented and discussed in relation to the cumulative mechanisms (CM) of track formation in dielectric materials under swift heavy ion (SHI) irradiation. These mechanisms rely on the generation and accumulation of point defects during irradiation followed by collapse of the lattice once a threshold defect concentration is reached. The physical basis of those approaches has been discussed by Fecht as a defect-assisted transition to an amorphous phase. Although a first quantitative analysis of the CM model was previously performed for LiNbO3 crystals, we have, here, adopted a broader phenomenological approach. It explores the correlation between track formation thresholds and the energies for Frenkel pair formation for a broad range of materials. It is concluded that the threshold stopping powers can be roughly scaled with the energies required to generate a critical Frenkel pair concentration in the order of a few percent of the total atomic content. Finally, a comparison with the predictions of the thermal spike model is discussed within the analytical Szenes approximation.

Dancing to CHANGA: a self-consistent prediction for close SMBH pair formation time-scales following galaxy mergers

NASA Astrophysics Data System (ADS)

Tremmel, M.; Governato, F.; Volonteri, M.; Quinn, T. R.; Pontzen, A.

2018-04-01

We present the first self-consistent prediction for the distribution of formation time-scales for close supermassive black hole (SMBH) pairs following galaxy mergers. Using ROMULUS25, the first large-scale cosmological simulation to accurately track the orbital evolution of SMBHs within their host galaxies down to sub-kpc scales, we predict an average formation rate density of close SMBH pairs of 0.013 cMpc-3 Gyr-1. We find that it is relatively rare for galaxy mergers to result in the formation of close SMBH pairs with sub-kpc separation and those that do form are often the result of Gyr of orbital evolution following the galaxy merger. The likelihood and time-scale to form a close SMBH pair depends strongly on the mass ratio of the merging galaxies, as well as the presence of dense stellar cores. Low stellar mass ratio mergers with galaxies that lack a dense stellar core are more likely to become tidally disrupted and deposit their SMBH at large radii without any stellar core to aid in their orbital decay, resulting in a population of long-lived `wandering' SMBHs. Conversely, SMBHs in galaxies that remain embedded within a stellar core form close pairs in much shorter time-scales on average. This time-scale is a crucial, though often ignored or very simplified, ingredient to models predicting SMBH mergers rates and the connection between SMBH and star formation activity.

Intermolecular interactions of trifluorohalomethanes with Lewis bases in the gas phase: an ab initio study.

PubMed

Wang, Yi-Siang; Yin, Chih-Chien; Chao, Sheng D

2014-10-07

We perform an ab initio computational study of molecular complexes with the general formula CF3X-B that involve one trifluorohalomethane CF3X (X = Cl or Br) and one of a series of Lewis bases B in the gas phase. The Lewis bases are so chosen that they provide a range of electron-donating abilities for comparison. Based on the characteristics of their electron pairs, we consider the Lewis bases with a single n-pair (NH3 and PH3), two n-pairs (H2O and H2S), two n-pairs with an unsaturated bond (H2CO and H2CS), and a single π-pair (C2H4) and two π-pairs (C2H2). The aim is to systematically investigate the influence of the electron pair characteristics and the central atom substitution effects on the geometries and energetics of the formed complexes. The counterpoise-corrected supermolecule MP2 and coupled-cluster single double with perturbative triple [CCSD(T)] levels of theory have been employed, together with a series of basis sets up to aug-cc-pVTZ. The angular and radial configurations, the binding energies, and the electrostatic potentials of the stable complexes have been compared and discussed as the Lewis base varies. For those complexes where halogen bonding plays a significant role, the calculated geometries and energetics are consistent with the σ-hole model. Upon formation of stable complexes, the C-X bond lengths shorten, while the C-X vibrational frequencies increase, thus rendering blueshifting halogen bonds. The central atom substitution usually enlarges the intermolecular bond distances while it reduces the net charge transfers, thus weakening the bond strengths. The analysis based on the σ-hole model is grossly reliable but requires suitable modifications incorporating the central atom substitution effects, in particular, when interaction components other than electrostatic contributions are involved.

Formation and behavior of counter-rotating vortex rings

NASA Astrophysics Data System (ADS)

Sadri, V.; Krueger, P. S.

2017-08-01

Concentric, counter-rotating vortex ring formation by transient jet ejection between concentric cylinders was studied numerically to determine the effects of cylinder gap ratio, Δ R/R, and jet stroke length-to-gap ratio, L/Δ R, on the evolution of the vorticity and the trajectories of the resulting axisymmetric vortex pair. The flow was simulated at a jet Reynolds number of 1000 (based on Δ R and the jet velocity), L/Δ R in the range 1-20, and Δ R/R in the range 0.05-0.25. Five characteristic flow evolution patterns were observed and classified based on L/Δ R and Δ R/R. The results showed that the relative position, relative strength, and radii of the vortex rings during and soon after formation played a prominent role in the evolution of the trajectories of their vorticity centroids at the later time. The conditions on relative strength of the vortices necessary for them to travel together as a pair following formation were studied, and factors affecting differences in vortex circulation following formation were investigated. In addition to the characteristics of the primary vortices, the stopping vortices had a strong influence on the initial vortex configuration and effected the long-time flow evolution at low L/Δ R and small Δ R/R. For long L/Δ R and small Δ R/R, shedding of vorticity was sometimes observed and this shedding was related to the Kelvin-Benjamin variational principle of maximal energy for steadily translating vortex rings.

How a low-fidelity DNA polymerase chooses non-Watson-Crick from Watson-Crick incorporation.

PubMed

Wu, Wen-Jin; Su, Mei-I; Wu, Jian-Li; Kumar, Sandeep; Lim, Liang-Hin; Wang, Chun-Wei Eric; Nelissen, Frank H T; Chen, Ming-Chuan Chad; Doreleijers, Jurgen F; Wijmenga, Sybren S; Tsai, Ming-Daw

2014-04-02

A dogma for DNA polymerase catalysis is that the enzyme binds DNA first, followed by MgdNTP. This mechanism contributes to the selection of correct dNTP by Watson-Crick base pairing, but it cannot explain how low-fidelity DNA polymerases overcome Watson-Crick base pairing to catalyze non-Watson-Crick dNTP incorporation. DNA polymerase X from the deadly African swine fever virus (Pol X) is a half-sized repair polymerase that catalyzes efficient dG:dGTP incorporation in addition to correct repair. Here we report the use of solution structures of Pol X in the free, binary (Pol X:MgdGTP), and ternary (Pol X:DNA:MgdGTP with dG:dGTP non-Watson-Crick pairing) forms, along with functional analyses, to show that Pol X uses multiple unprecedented strategies to achieve the mutagenic dG:dGTP incorporation. Unlike high fidelity polymerases, Pol X can prebind purine MgdNTP tightly and undergo a specific conformational change in the absence of DNA. The prebound MgdGTP assumes an unusual syn conformation stabilized by partial ring stacking with His115. Upon binding of a gapped DNA, also with a unique mechanism involving primarily helix αE, the prebound syn-dGTP forms a Hoogsteen base pair with the template anti-dG. Interestingly, while Pol X prebinds MgdCTP weakly, the correct dG:dCTP ternary complex is readily formed in the presence of DNA. H115A mutation disrupted MgdGTP binding and dG:dGTP ternary complex formation but not dG:dCTP ternary complex formation. The results demonstrate the first solution structural view of DNA polymerase catalysis, a unique DNA binding mode, and a novel mechanism for non-Watson-Crick incorporation by a low-fidelity DNA polymerase.

Role of 6-Mercaptopurine in the potential therapeutic targets DNA base pairs and G-quadruplex DNA: insights from quantum chemical and molecular dynamics simulations.

PubMed

Radhika, R; Shankar, R; Vijayakumar, S; Kolandaivel, P

2018-05-01

The theoretical studies on DNA with the anticancer drug 6-Mercaptopurine (6-MP) are investigated using theoretical methods to shed light on drug designing. Among the DNA base pairs considered, 6-MP is stacked with GC with the highest interaction energy of -46.19 kcal/mol. Structural parameters revealed that structure of the DNA base pairs is deviated from the planarity of the equilibrium position due to the formation of hydrogen bonds and stacking interactions with 6-MP. These deviations are verified through the systematic comparison between X-H bond contraction and elongation and the associated blue shift and red shift values by both NBO analysis and vibrational analysis. Bent's rule is verified for the C-H bond contraction in the 6-MP interacted base pairs. The AIM results disclose that the higher values of electron density (ρ) and Laplacian of electron density (∇ 2 ρ) indicate the increased overlap between the orbitals that represent the strong interaction and positive values of the total electron density show the closed-shell interaction. The relative sensitivity of the chemical shift values for the DNA base pairs with 6-MP is investigated to confirm the hydrogen bond strength. Molecular dynamics simulation studies of G-quadruplex DNA d(TGGGGT) 4 with 6-MP revealed that the incorporation of 6-MP appears to cause local distortions and destabilize the G-quadruplex DNA.

Damage mechanism of hydroxyl radicals toward adenine—thymine base pair

NASA Astrophysics Data System (ADS)

Tan, Rong-Ri; Wang, Dong-Qi; Zhang, Feng-Shou

2014-02-01

The adenine—thymine base pair was studied in the presence of hydroxyl radicals in order to probe the hydrogen bond effect. The results show that the hydrogen bonds have little effect on the hydroxylation and dehydrogenation happened at the sites, which are not involved in a hydrogen bond, while at the sites involved in hydrogen bond formation in the base pair, the reaction becomes more difficult, both in view of the free energy barrier and the exothermicity. With a 6-311++G(d,p) level of description, both B3LYP and MP2 methods confirm that the C8 site of isolated adenine has the highest possibility to form covalent bond with the hydroxyl radicals, though with different energetics: B3LYP predicts a barrierless pathway, while MP2 finds a transition state with an energy of 106.1 kJ/mol. For the dehydrogenation reactions, B3LYP method predicts that the free energy barrier increases in the order of HN9 < HN61 < HN62 < H2 < H8.

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

Petrova, V. A.; Orekhov, A. S.; Chernyakov, D. D.

A method for preparing multilayer film composites based on chitosan has been developed by the example of polymer pairs: chitosan–hyaluronic acid, chitosan–alginic acid, and chitosan–carrageenan. The structure of the composite films is characterized by X-ray diffractometry and scanning electron microscopy. It is shown that the deposition of a solution of hyaluronic acid, alginic acid, or carrageenan on a chitosan gel film leads to the formation of a polyelectrolyte complex layer at the interface, which is accompanied by the ordering of chitosan chains in the surface region; the microstructure of this layer depends on the nature of contacting polymer pairs.

Developing a patient-centered outcome measure for complementary and alternative medicine therapies II: Refining content validity through cognitive interviews

PubMed Central

2011-01-01

Background Available measures of patient-reported outcomes for complementary and alternative medicine (CAM) inadequately capture the range of patient-reported treatment effects. The Self-Assessment of Change questionnaire was developed to measure multi-dimensional shifts in well-being for CAM users. With content derived from patient narratives, items were subsequently focused through interviews on a new cohort of participants. Here we present the development of the final version in which the content and format is refined through cognitive interviews. Methods We conducted cognitive interviews across five iterations of questionnaire refinement with a culturally diverse sample of 28 CAM users. In each iteration, participant critiques were used to revise the questionnaire, which was then re-tested in subsequent rounds of cognitive interviews. Following all five iterations, transcripts of cognitive interviews were systematically coded and analyzed to examine participants' understanding of the format and content of the final questionnaire. Based on this data, we established summary descriptions and selected exemplar quotations for each word pair on the final questionnaire. Results The final version of the Self-Assessment of Change questionnaire (SAC) includes 16 word pairs, nine of which remained unchanged from the original draft. Participants consistently said that these stable word pairs represented opposite ends of the same domain of experience and the meanings of these terms were stable across the participant pool. Five pairs underwent revision and two word pairs were added. Four word pairs were eliminated for redundancy or because participants did not agree on the meaning of the terms. Cognitive interviews indicate that participants understood the format of the questionnaire and considered each word pair to represent opposite poles of a shared domain of experience. Conclusions We have placed lay language and direct experience at the center of questionnaire revision and refinement. In so doing, we provide an innovative model for the development of truly patient-centered outcome measures. Although this instrument was designed and tested in a CAM-specific population, it may be useful in assessing multi-dimensional shifts in well-being across a broader patient population. PMID:22206409

Patterns of pair formation and mating in an ectoparasitic caligid copepod Lepeophtheirus salmonis (Krøyer 1837): implications for its sensory and mating biology

PubMed Central

Hull, M. Q.

1998-01-01

Non-invasive observations of single cohort and manipulated populations of the sealouse on laboratory-maintained salmon established the sequence of reproductive events and mating. Protandry occurs with adult male emergence synchronized with pre-adult II female emergence, the stage at which most pair formation and pre-copular guarding takes place. Male competence for pair formation and mating was achieved within 24 h of the final moult and pairing occurred according to the preference hierarchy, virgin adult females greater than pre-adult II females much greater than pre-adult I females. This hierarchy broke down when the adult male to unmated female ratio increased rapidly. Males mated successfully not only with newly moulted adult females, but also with older virgin females in which enlargement of the genital complex and premature extrusion of egg strings had occurred. Multiple mating by adult males was demonstrated and may be widespread. Significant inter-host transfer was also demonstrated. Adult males were more mobile than adult females and showed significantly more inter-host transfer. Ablation of the distal tip of the antennules significantly reduced the success of host-finding, pair formation and males' mating.

Ag(I)-mediated homo and hetero pairs of guanosine and cytidine: monitoring by circular dichroism spectroscopy.

PubMed

Goncharova, Iryna

2014-01-24

Ag(I)-containing compounds are attractive as antibacterial and antifungal agents. The renewed interest in the application of silver(I) compounds has led to the need for detailed knowledge of the mechanism of their action. One of the possible ways is the coordination of Ag(I) to G-C pairs of DNA, where Ag(+) ions form Ag(I)-mediated base pairs and inhibit the transcription. Herein, a systematic chiroptical study on silver(I)-mediated homo and mixed pairs of the C-G complementary-base derivatives cytidine(C) and 5'-guanosine monophosphate(G) in water is presented. Ag(I)-mediated homo and hetero pairs of G and C and their self-assembled species were studied under two pH levels (7.0 and 10.0) by vibrational (VCD) and electronic circular dichroism(ECD). VCD was used for the first time in this field and showed itself to be a powerful method for obtaining specific structural information in solution. Based on results of the VCD experiments, the different geometries of the homo pairs were proposed under pH 7.0 and 10.0. ECD was used as a diagnostic tool to characterize the studied systems and as a contact point between the previously defined structures of the metal or proton mediated pairs of nucleobases and the systems studied here. On the basis of the obtained data, the formation of the self-assembled species of cytidine with a structure similar to the i-motif structure in DNA was proposed at pH 10.0. Copyright © 2013 Elsevier B.V. All rights reserved.

Ag(I)-mediated homo and hetero pairs of guanosine and cytidine: Monitoring by circular dichroism spectroscopy

NASA Astrophysics Data System (ADS)

Goncharova, Iryna

2014-01-01

Ag(I)-containing compounds are attractive as antibacterial and antifungal agents. The renewed interest in the application of silver(I) compounds has led to the need for detailed knowledge of the mechanism of their action. One of the possible ways is the coordination of Ag(I) to G-C pairs of DNA, where Ag+ ions form Ag(I)-mediated base pairs and inhibit the transcription. Herein, a systematic chiroptical study on silver(I)-mediated homo and mixed pairs of the C-G complementary-base derivatives cytidine(C) and 5‧-guanosine monophosphate(G) in water is presented. Ag(I)-mediated homo and hetero pairs of G and C and their self-assembled species were studied under two pH levels (7.0 and 10.0) by vibrational (VCD) and electronic circular dichroism(ECD). VCD was used for the first time in this field and showed itself to be a powerful method for obtaining specific structural information in solution. Based on results of the VCD experiments, the different geometries of the homo pairs were proposed under pH 7.0 and 10.0. ECD was used as a diagnostic tool to characterize the studied systems and as a contact point between the previously defined structures of the metal or proton mediated pairs of nucleobases and the systems studied here. On the basis of the obtained data, the formation of the self-assembled species of cytidine with a structure similar to the i-motif structure in DNA was proposed at pH 10.0.

Raman spectroscopic studies on single supersaturated droplets of sodium and magnesium acetate.

PubMed

Wang, Liang-Yu; Zhang, Yun-Hong; Zhao, Li-Jun

2005-02-03

Raman spectroscopy was used to study structural changes, in particular, the formation of contact-ion pairs in supersaturated aqueous NaCH(3)COO and Mg(CH(3)COO)(2) droplets at ambient temperatures. The single droplets levitated in an electrodynamic balance (EDB), lost water, and became supersaturated when the relative humidity (RH) decreased. For NaCH(3)COO droplet the water-to-solute molar ratio (WSR) was 3.87 without solidification when water molecules were not enough to fill in the first hydration layer of Na(+), in favor of the formation of contact-ion pairs. However, the symmetric stretching vibration band (nu(3) mode) of free -COO(-) constantly appeared at 1416 cm(-1), and no spectroscopic information related to monodentate, bidentate, or bridge bidentate contact-ion pairs was observed due to the weak interactions between the Na(+) and acetate ion. On the other hand, the band of methyl deformation blue shifted from 1352 to 1370 cm(-1) (at RH = 34.2%, WSR = 2.43), corresponding to the solidification process of a novel metastable phase in the highly supersaturated solutions. With further decreasing RH, a small amount of supersaturated solution still existed and was proposed to be hermetically covered by the metastable phase of the particle. In contrast, the interaction between Mg(2+) and acetate ion is much stronger. When WSR decreased from 21.67 to 2.58 for the Mg(CH(3)COO)(2) droplet, the band of C-C-symmetric stretching (nu(4) mode) had a blue shift from 936 to 947 cm(-1). The intensity of the two new shoulders (approximately 1456 and approximately 1443 cm(-1)) of the nu(3) band of free -COO(-) at 1420 cm(-1) increased with the decrease of WSR. These changes were attributed to the formation of contact-ion pairs with bidentate structures. In particular, the small frequency difference between the shoulder at approximately 1443 cm(-1) and the nu(3) band of the free -COO(-) group (approximately 1420 cm(-1)) was proposed to be related to the formation of a chain structure based on the contact-ion pairs of bridge bidentate. The continuous formation of various contact-ion pairs started at higher WSR value (WSR = 15.5) greatly reduced the hygroscopic properties of Mg(CH(3)COO)(2) droplet, so that the WSR of Mg(CH(3)COO)(2) droplets was even lower than that of NaCH(3)COO in the RH range of 40-60%.

Structural basis of DNA folding and recognition in an AMP-DNA aptamer complex: distinct architectures but common recognition motifs for DNA and RNA aptamers complexed to AMP.

PubMed

Lin, C H; Patel, D J

1997-11-01

Structural studies by nuclear magnetic resonance (NMR) of RNA and DNA aptamer complexes identified through in vitro selection and amplification have provided a wealth of information on RNA and DNA tertiary structure and molecular recognition in solution. The RNA and DNA aptamers that target ATP (and AMP) with micromolar affinity exhibit distinct binding site sequences and secondary structures. We report below on the tertiary structure of the AMP-DNA aptamer complex in solution and compare it with the previously reported tertiary structure of the AMP-RNA aptamer complex in solution. The solution structure of the AMP-DNA aptamer complex shows, surprisingly, that two AMP molecules are intercalated at adjacent sites within a rectangular widened minor groove. Complex formation involves adaptive binding where the asymmetric internal bubble of the free DNA aptamer zippers up through formation of a continuous six-base mismatch segment which includes a pair of adjacent three-base platforms. The AMP molecules pair through their Watson-Crick edges with the minor groove edges of guanine residues. These recognition G.A mismatches are flanked by sheared G.A and reversed Hoogsteen G.G mismatch pairs. The AMP-DNA aptamer and AMP-RNA aptamer complexes have distinct tertiary structures and binding stoichiometries. Nevertheless, both complexes have similar structural features and recognition alignments in their binding pockets. Specifically, AMP targets both DNA and RNA aptamers by intercalating between purine bases and through identical G.A mismatch formation. The recognition G.A mismatch stacks with a reversed Hoogsteen G.G mismatch in one direction and with an adenine base in the other direction in both complexes. It is striking that DNA and RNA aptamers selected independently from libraries of 10(14) molecules in each case utilize identical mismatch alignments for molecular recognition with micromolar affinity within binding-site pockets containing common structural elements.

Structure, stability and behaviour of nucleic acids in ionic liquids

PubMed Central

Tateishi-Karimata, Hisae; Sugimoto, Naoki

2014-01-01

Nucleic acids have become a powerful tool in nanotechnology because of their conformational polymorphism. However, lack of a medium in which nucleic acid structures exhibit long-term stability has been a bottleneck. Ionic liquids (ILs) are potential solvents in the nanotechnology field. Hydrated ILs, such as choline dihydrogen phosphate (choline dhp) and deep eutectic solvent (DES) prepared from choline chloride and urea, are ‘green’ solvents that ensure long-term stability of biomolecules. An understanding of the behaviour of nucleic acids in hydrated ILs is necessary for developing DNA materials. We here review current knowledge about the structures and stabilities of nucleic acids in choline dhp and DES. Interestingly, in choline dhp, A–T base pairs are more stable than G–C base pairs, the reverse of the situation in buffered NaCl solution. Moreover, DNA triplex formation is markedly stabilized in hydrated ILs compared with aqueous solution. In choline dhp, the stability of Hoogsteen base pairs is comparable to that of Watson–Crick base pairs. Moreover, the parallel form of the G-quadruplex is stabilized in DES compared with aqueous solution. The behaviours of various DNA molecules in ILs detailed here should be useful for designing oligonucleotides for the development of nanomaterials and nanodevices. PMID:25013178

Blind prediction of noncanonical RNA structure at atomic accuracy.

PubMed

Watkins, Andrew M; Geniesse, Caleb; Kladwang, Wipapat; Zakrevsky, Paul; Jaeger, Luc; Das, Rhiju

2018-05-01

Prediction of RNA structure from nucleotide sequence remains an unsolved grand challenge of biochemistry and requires distinct concepts from protein structure prediction. Despite extensive algorithmic development in recent years, modeling of noncanonical base pairs of new RNA structural motifs has not been achieved in blind challenges. We report a stepwise Monte Carlo (SWM) method with a unique add-and-delete move set that enables predictions of noncanonical base pairs of complex RNA structures. A benchmark of 82 diverse motifs establishes the method's general ability to recover noncanonical pairs ab initio, including multistrand motifs that have been refractory to prior approaches. In a blind challenge, SWM models predicted nucleotide-resolution chemical mapping and compensatory mutagenesis experiments for three in vitro selected tetraloop/receptors with previously unsolved structures (C7.2, C7.10, and R1). As a final test, SWM blindly and correctly predicted all noncanonical pairs of a Zika virus double pseudoknot during a recent community-wide RNA-Puzzle. Stepwise structure formation, as encoded in the SWM method, enables modeling of noncanonical RNA structure in a variety of previously intractable problems.

Affected twins in the familial intracranial aneurysm study.

PubMed

Mackey, Jason; Brown, Robert D; Sauerbeck, Laura; Hornung, Richard; Moomaw, Charles J; Koller, Daniel L; Foroud, Tatiana; Deka, Ranjan; Woo, Daniel; Kleindorfer, Dawn; Flaherty, Matthew L; Meissner, Irene; Anderson, Craig; Rouleau, Guy; Connolly, E Sander; Huston, John; Broderick, Joseph P

2015-01-01

Very few cases of intracranial aneurysms (IAs) in twins have been reported. Previous work has suggested that vulnerability to IA formation is heritable. Twin studies provide an opportunity to evaluate the impact of genetics on IA characteristics, including IA location. We therefore sought to examine IA location concordance, multiplicity, and rupture status within affected twin-pairs. The Familial Intracranial Aneurysm study was a multicenter study whose goal was to identify genetic and other risk factors for formation and rupture of IAs. The study required at least three affected family members or an affected sibling pair for inclusion. Subjects with fusiform aneurysms, an IA associated with an AVM, or a family history of conditions known to predispose to IA formation, such as polycystic kidney disease, Ehlers-Danlos syndrome, Marfan syndrome, fibromuscular dysplasia, or moyamoya syndrome were excluded. Twin-pairs were identified by birth date and were classified as monozygotic (MZ) or dizygotic (DZ) through DNA marker genotypes. In addition to zygosity, we evaluated twin-pairs by smoking status, major arterial territory of IAs, and rupture status. Location concordance was defined as the presence of an IA in the same arterial distribution (ICA, MCA, ACA, and vertebrobasilar), irrespective of laterality, in both members of a twin-pair. The Fisher exact test was used for comparisons between MZ and DZ twin-pairs. A total of 16 affected twin-pairs were identified. Location concordance was observed in 8 of 11 MZ twin-pairs but in only 1 of 5 DZ twin-pairs (p = 0.08). Three MZ subjects had unknown IA locations and comprised the three instances of MZ discordance. Six of the 11 MZ twin-pairs and none of the 5 DZ twin-pairs had IAs in the ICA distribution (p = 0.03). Multiple IAs were observed in 11 of 22 MZ and 5 of 10 DZ twin-pairs. Thirteen (13) of the 32 subjects had an IA rupture, including 10 of 22 MZ twins. We found that arterial location concordance was greater in MZ than DZ twins, which suggests a genetic influence upon aneurysm location. The 16 twin-pairs in the present study are nearly the total of affected twin-pairs that have been reported in the literature to date. Further studies are needed to determine the impact of genetics in the formation and rupture of IAs. © 2015 S. Karger AG, Basel.

Pair-instability supernovae of fast rotating stars

NASA Astrophysics Data System (ADS)

Chen, Ke-Jung

2015-01-01

We present 2D simulations of pair-instability supernovae considering rapid rotation during their explosion phases. Recent studies of the Population III (Pop III) star formation suggested that these stars could be born with a mass scale about 100 M⊙ and with a strong rotation. Based on stellar evolution models, these massive Pop III stars might have died as highly energetic pair-instability supernovae. We perform 2D calculations to investigate the impact of rotation on pair-instability supernovae. Our results suggest that rotation leads to an aspherical explosion due to an anisotropic collapse. If the first stars have a 50% of keplerian rotational rate of the oxygen core before their pair-instability explosions, the overall 56Ni production can be significantly reduced by about two orders of magnitude. An extreme case of 100% keplerian rotational rate shows an interesting feature of fluid instabilities along the equatorial plane caused by non-synchronized and non-isotropic ignitions of explosions, so that the shocks run into the in-falling gas and generate the Richtmyer-Meshkov instability.

Pulsar Polar Cap Heating and Surface Thermal X-ray Emission. 1; Curvature Radiation Pair Fronts

NASA Technical Reports Server (NTRS)

Harding, Alice K.; Muslimov, Alexander G.; White, Nicholas E. (Technical Monitor)

2002-01-01

We investigate the effect of pulsar polar cap (PC) heating produced by positrons returning from the upper pair formation front. Our calculations are based on a self-consistent treatment of the pair dynamics and the effect of electric field screening by the returning positrons. We calculate the resultant X-ray luminosities and discuss the dependence of the PC heating efficiencies on pulsar parameters, such as characteristic spin-down age, spin period, and surface magnetic field strength. In this study we concentrate on the regime where the pairs are produced in a magnetic field by curvature photons emitted by accelerating electrons. Our theoretical results are not in conflict with the available observational x-ray data and suggest that the effect of PC heating should significantly contribute to the thermal x-ray fluxes from middle-aged and old pulsars. The implications for current and future x-ray observations of pulsars are briefly outlined.

Interaction of a parabolic-shaped pulse pair in a passively mode-locked Yb-doped fiber laser

NASA Astrophysics Data System (ADS)

Wang, Da-Shuai; Wu, Ge; Gao, Bo; Tian, Xiao-Jian

2013-01-01

We numerically investigate the formation and interaction of a parabolic-shaped pulse pair in a passively mode-locked Yb-doped fiber laser. Based on a lumped model, the parabolic-shaped pulse pair is obtained by controlling the inter-cavity average dispersion and gain saturation energy, Moreover, pulse repulsive and attractive motion are also achieved with different pulse separations. Simulation results show that the phase shift plays an important role in pulse interaction, and the interaction is determined by the inter-cavity average dispersion and gain saturation energy, i.e., the strength of the interaction is proportional to the gain saturation energy, a stronger gain saturation energy will result in a higher interaction intensity. On the contrary, the increase of the inter-cavity dispersion will counterbalance some interaction force. The results also show that the interaction of a parabolic-shaped pulse pair has a larger interaction distance compared to conventional solitons.

Lewis pair polymerization by classical and frustrated Lewis pairs: acid, base and monomer scope and polymerization mechanism.

PubMed

Zhang, Yuetao; Miyake, Garret M; John, Mallory G; Falivene, Laura; Caporaso, Lucia; Cavallo, Luigi; Chen, Eugene Y-X

2012-08-14

Classical and frustrated Lewis pairs (LPs) of the strong Lewis acid (LA) Al(C(6)F(5))(3) with several Lewis base (LB) classes have been found to exhibit exceptional activity in the Lewis pair polymerization (LPP) of conjugated polar alkenes such as methyl methacrylate (MMA) as well as renewable α-methylene-γ-butyrolactone (MBL) and γ-methyl-α-methylene-γ-butyrolactone (γ-MMBL), leading to high molecular weight polymers, often with narrow molecular weight distributions. This study has investigated a large number of LPs, consisting of 11 LAs as well as 10 achiral and 4 chiral LBs, for LPP of 12 monomers of several different types. Although some more common LAs can also be utilized for LPP, Al(C(6)F(5))(3)-based LPs are far more active and effective than other LA-based LPs. On the other hand, several classes of LBs, when paired with Al(C(6)F(5))(3), can render highly active and effective LPP of MMA and γ-MMBL; such LBs include phosphines (e.g., P(t)Bu(3)), chiral chelating diphosphines, N-heterocyclic carbenes (NHCs), and phosphazene superbases (e.g., P(4)-(t)Bu). The P(4)-(t)Bu/Al(C(6)F(5))(3) pair exhibits the highest activity of the LP series, with a remarkably high turn-over frequency of 9.6 × 10(4) h(-1) (0.125 mol% catalyst, 100% MMA conversion in 30 s, M(n) = 2.12 × 10(5) g mol(-1), PDI = 1.34). The polymers produced by LPs at RT are typically atactic (P(γ)MMBL with ∼47% mr) or syndio-rich (PMMA with ∼70-75% rr), but highly syndiotactic PMMA with rr ∼91% can be produced by chiral or achiral LPs at -78 °C. Mechanistic studies have identified and structurally characterized zwitterionic phosphonium and imidazolium enolaluminates as the active species of the current LPP system, which are formed by the reaction of the monomer·Al(C(6)F(5))(3) adduct with P(t)Bu(3) and NHC bases, respectively. Kinetic studies have revealed that the MMA polymerization by the (t)Bu(3)P/Al(C(6)F(5))(3) pair is zero-order in monomer concentration after an initial induction period, and the polymerization is significantly catalyzed by the LA, thus pointing to a bimetallic, activated monomer propagation mechanism. Computational study on the active species formation as well as the chain initiation and propagation events involved in the LPP of MMA with some of the most representative LPs has added our understanding of fundamental steps of LPP. The main difference between NHC and PR(3) bases is in the energetics of zwitterion formation, with the NHC-based zwitterions being remarkably more stable than the PR(3)-based zwitterions. Comparison of the monometallic and bimetallic mechanisms for MMA addition shows a clear preference for the bimetallic mechanism.

Unfolding and Targeting Thermodynamics of a DNA Intramolecular Complex with Joined Triplex-Duplex Domains.

PubMed

Johnson, Sarah E; Reiling-Steffensmeier, Calliste; Lee, Hui-Ting; Marky, Luis A

2018-01-25

Our laboratory is interested in developing methods that can be used for the control of gene expression. In this work, we are investigating the reaction of an intramolecular complex containing a triplex-duplex junction with partially complementary strands. We used a combination of isothermal titration calorimetry (ITC), differential scanning calorimetry (DSC), and spectroscopy techniques to determine standard thermodynamic profiles for these targeting reactions. Specifically, we have designed single strands to target one loop (CTTTC) or two loops (CTTTC and GCAA) of this complex. Both reactions yielded exothermic enthalpies of -66.3 and -82.8 kcal/mol by ITC, in excellent agreement with the reaction enthalpies of -72.7 and -88.7 kcal/mol, respectively, obtained from DSC Hess cycles. The favorable heat contributions result from the formation of base-pair stacks involving mainly the unpaired bases of the loops. This shows that each complementary strand is able to invade and disrupt the secondary structure. The simultaneous targeting of two loops yielded a more favorable reaction free energy, by approximately -8 kcal/mol, which corresponds to the formation of roughly four base-pair stacks involving the unpaired bases of the 5'-GCAA loop. The main conclusion is that the targeting of loops with a large number of unpaired bases results in a more favorable reaction free energy.

A Bridging Water Anchors the Tethered 5-(3-Aminopropyl)-2′-deoxyuridine Amine in the DNA Major Groove Proximate to the N+2 C·G Base Pair: Implications for Formation of Interstrand 5′-GNC-3′ Cross-Links by Nitrogen Mustards

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

Wang, Feng; Li, Feng; Ganguly, Manjori

2008-11-14

Site-specific insertion of t-(3-aminopropyl)-2'-deoxyuridine (Z3dU) and 7-deaza-dG into the Dickerson-Drew dodecamers 5'-d(C{sup 1}G{sup 2}C{sup 3}G{sup 4}A{sup 5}A{sup 6}T{sup 7}T{sup 8}C{sup 9}{und Z}{sup 10}C{sup 11}G{sup 12})-3'{center_dot}5'-d (C{sup 13}G{sup 14}C{sup 15}G{sup 16}A{sup 17}A{sup 18}T{sup 19}T{sup 20}C{sup 21}{und Z}{sup 22}C{sup 23}G{sup 24})-3' (named DDD{sup Z10}) and 5'-d(C{sup 1}G{sup 2}C{sup 3}G{sup 4}A{sup 5}A{sup 6}T{sup 7}{und X}{sup 20}C{sup 21}{und Z}{sup 22}C{sup 23}G{sup 24})-3' (named DDD{sup 2+Z10}) (X = 73dU; Z = 7-deaza-dG) suggests a mechanism underlying the formation of interstrand N+2 DNA cross-links by nitrogen mustards, e.g., melphalan and mechlorethamine. Analysis of the DDD{sup 2+Z10} duplex reveals that the tethered cations at base pairs A{supmore » 5}{center_dot}X{sup 20} and X{sup 8}{center_dot}A{sup 17} extend within the major groove in the 3'-direction, toward conserved Mg{sup 2+} binding sites located adjacent to N+2 base pairs C{sup 3}{center_dot}Z{sup 22} and Z{sup 10}{center_dot}C{sup 15}. Bridging waters located between the tethered amines and either Z{sup 10} or Z{sup 22} O{sup 6} stabilize the tethered cations and allow interactions with the N + 2 base pairs without DNA bending. Incorporation of 7-deaza-dG into the DDD{sup 2+Z10} duplex weakens but does not eliminate electrostatic interactions between tethered amines and Z{sup 10} O{sup 6} and Z{sup 22} O{sup 6}. The results suggest a mechanism by which tethered N7-dG aziridinium ions, the active species involved in formation of interstrand 5'-GNC-3' cross-links by nitrogen mustards, modify the electrostatics of the major groove and position the aziridinium ions proximate to the major groove edge of the N+2 C{center_dot}G base pair, facilitating interstrand cross-linking.« less

Energetic basis for selective recognition of T*G mismatched base pairs in DNA by imidazole-rich polyamides.

PubMed

Lacy, Eilyn R; Nguyen, Binh; Le, Minh; Cox, Kari K; OHare, Caroline; Hartley, John A; Lee, Moses; Wilson, W David

2004-01-01

To complement available structure and binding results and to develop a detailed understanding of the basis for selective molecular recognition of T.G mismatches in DNA by imidazole containing polyamides, a full thermodynamic profile for formation of the T.G-polyamide complex has been determined. The amide-linked heterocycles f-ImImIm and f-PyImIm (where f is formamido group, Im is imidazole and Py is pyrrole) were studied by using biosensor-surface plasmon resonance (SPR) and isothermal titration calorimetry (ITC) with a T.G mismatch containing DNA hairpin duplex and a similar DNA with only Watson-Crick base pairs. Large negative binding enthalpies for all of the polyamide-DNA complexes indicate that the interactions are enthalpically driven. SPR results show slower complex formation and stronger binding of f-ImImIm to the T.G than to the match site. The thermodynamic analysis indicates that the enhanced binding to the T.G site is the result of better entropic contributions. Negative heat capacity changes for the complex are correlated with calculated solvent accessible surface area changes and indicate hydrophobic contributions to complex formation. DNase I footprinting analysis in a long DNA sequence provided supporting evidence that f-ImImIm binds selectively to T.G mismatch sites.

Energetic basis for selective recognition of T·G mismatched base pairs in DNA by imidazole-rich polyamides

PubMed Central

Lacy, Eilyn R.; Nguyen, Binh; Le, Minh; Cox, Kari K.; O'Hare, Caroline; Hartley, John A.; Lee, Moses; Wilson, W. David

2004-01-01

To complement available structure and binding results and to develop a detailed understanding of the basis for selective molecular recognition of T·G mismatches in DNA by imidazole containing polyamides, a full thermodynamic profile for formation of the T·G–polyamide complex has been determined. The amide-linked heterocycles f-ImImIm and f-PyImIm (where f is formamido group, Im is imidazole and Py is pyrrole) were studied by using biosensor-surface plasmon resonance (SPR) and isothermal titration calorimetry (ITC) with a T·G mismatch containing DNA hairpin duplex and a similar DNA with only Watson–Crick base pairs. Large negative binding enthalpies for all of the polyamide–DNA complexes indicate that the interactions are enthalpically driven. SPR results show slower complex formation and stronger binding of f-ImImIm to the T·G than to the match site. The thermodynamic analysis indicates that the enhanced binding to the T·G site is the result of better entropic contributions. Negative heat capacity changes for the complex are correlated with calculated solvent accessible surface area changes and indicate hydrophobic contributions to complex formation. DNase I footprinting analysis in a long DNA sequence provided supporting evidence that f-ImImIm binds selectively to T·G mismatch sites. PMID:15064359

Intermolecular interactions of trifluorohalomethanes with Lewis bases in the gas phase: An ab initio study

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

Wang, Yi-Siang; Yin, Chih-Chien; Chao, Sheng D., E-mail: sdchao@spring.iam.ntu.edu.tw

2014-10-07

We perform an ab initio computational study of molecular complexes with the general formula CF{sub 3}X—B that involve one trifluorohalomethane CF{sub 3}X (X = Cl or Br) and one of a series of Lewis bases B in the gas phase. The Lewis bases are so chosen that they provide a range of electron-donating abilities for comparison. Based on the characteristics of their electron pairs, we consider the Lewis bases with a single n-pair (NH{sub 3} and PH{sub 3}), two n-pairs (H{sub 2}O and H{sub 2}S), two n-pairs with an unsaturated bond (H{sub 2}CO and H{sub 2}CS), and a single π-pairmore » (C{sub 2}H{sub 4}) and two π-pairs (C{sub 2}H{sub 2}). The aim is to systematically investigate the influence of the electron pair characteristics and the central atom substitution effects on the geometries and energetics of the formed complexes. The counterpoise-corrected supermolecule MP2 and coupled-cluster single double with perturbative triple [CCSD(T)] levels of theory have been employed, together with a series of basis sets up to aug-cc-pVTZ. The angular and radial configurations, the binding energies, and the electrostatic potentials of the stable complexes have been compared and discussed as the Lewis base varies. For those complexes where halogen bonding plays a significant role, the calculated geometries and energetics are consistent with the σ-hole model. Upon formation of stable complexes, the C–X bond lengths shorten, while the C–X vibrational frequencies increase, thus rendering blueshifting halogen bonds. The central atom substitution usually enlarges the intermolecular bond distances while it reduces the net charge transfers, thus weakening the bond strengths. The analysis based on the σ-hole model is grossly reliable but requires suitable modifications incorporating the central atom substitution effects, in particular, when interaction components other than electrostatic contributions are involved.« less

Intrinsic flexibility of B-DNA: the experimental TRX scale.

PubMed

Heddi, Brahim; Oguey, Christophe; Lavelle, Christophe; Foloppe, Nicolas; Hartmann, Brigitte

2010-01-01

B-DNA flexibility, crucial for DNA-protein recognition, is sequence dependent. Free DNA in solution would in principle be the best reference state to uncover the relation between base sequences and their intrinsic flexibility; however, this has long been hampered by a lack of suitable experimental data. We investigated this relationship by compiling and analyzing a large dataset of NMR (31)P chemical shifts in solution. These measurements reflect the BI <--> BII equilibrium in DNA, intimately correlated to helicoidal descriptors of the curvature, winding and groove dimensions. Comparing the ten complementary DNA dinucleotide steps indicates that some steps are much more flexible than others. This malleability is primarily controlled at the dinucleotide level, modulated by the tetranucleotide environment. Our analyses provide an experimental scale called TRX that quantifies the intrinsic flexibility of the ten dinucleotide steps in terms of Twist, Roll, and X-disp (base pair displacement). Applying the TRX scale to DNA sequences optimized for nucleosome formation reveals a 10 base-pair periodic alternation of stiff and flexible regions. Thus, DNA flexibility captured by the TRX scale is relevant to nucleosome formation, suggesting that this scale may be of general interest to better understand protein-DNA recognition.

Origin of the U(1) field mass in superconductors

NASA Astrophysics Data System (ADS)

Koizumi, Hiroyasu

2017-05-01

Recently, a new theory for superconductivity has been put forward, in which the persistent current generation is attributed to the emergent singularities of the electronic wave function that are created by the spin-twisting itinerant circular motion of electrons. The persistent current generated by this mechanism behaves in every respect like supercurrent in superconductors, yielding the flux quantum h/2e and the Josephson frequency 2eV/h, where h is Planck’s constant, -e is the electron charge, and V is the voltage across the Josephson junction. The mass generation of the U(1) gauge field (or the Meissner effect) in the new theory is due to the emergence of topological objects, ‘instantons’ generated by the single-valued requirement of the wave function in the presence of the emergent singularities. The current standard theory of superconductivity is based on the BCS theory, and explains the emergence of superconductivity as due to the global U(1) gauge symmetry breaking realized by the Cooper pair formation. The U(1) field mass generation is believed to be due to this global U(1) gauge symmetry breaking. However, the feasibility of this mechanism has been questioned since no known interaction can prepare the global U(1) symmetry broken state from the normal state. We argue here that the U(1) mass generation in the BCS superconductor can be attributed to the one by the instanton mentioned above if the Rashba spin-orbit interaction is added. Then, the occurrence of persistent current generation becomes due to the instanton formation, and the role of the Cooper pair formation is to stabilize the instanton by providing an energy gap for perturbative excitations. Upon forming the Cooper pair, the instanton is stabilized and persistent current generation becomes possible. Thus, the superconducting transition temperature coincides with the Cooper pair formation temperature.

Tracking the coherent generation of polaron pairs in conjugated polymers

NASA Astrophysics Data System (ADS)

de Sio, Antonietta; Troiani, Filippo; Maiuri, Margherita; Réhault, Julien; Sommer, Ephraim; Lim, James; Huelga, Susana F.; Plenio, Martin B.; Rozzi, Carlo Andrea; Cerullo, Giulio; Molinari, Elisa; Lienau, Christoph

2016-12-01

The optical excitation of organic semiconductors not only generates charge-neutral electron-hole pairs (excitons), but also charge-separated polaron pairs with high yield. The microscopic mechanisms underlying this charge separation have been debated for many years. Here we use ultrafast two-dimensional electronic spectroscopy to study the dynamics of polaron pair formation in a prototypical polymer thin film on a sub-20-fs time scale. We observe multi-period peak oscillations persisting for up to about 1 ps as distinct signatures of vibronic quantum coherence at room temperature. The measured two-dimensional spectra show pronounced peak splittings revealing that the elementary optical excitations of this polymer are hybridized exciton-polaron-pairs, strongly coupled to a dominant underdamped vibrational mode. Coherent vibronic coupling induces ultrafast polaron pair formation, accelerates the charge separation dynamics and makes it insensitive to disorder. These findings open up new perspectives for tailoring light-to-current conversion in organic materials.

Intermolecular interactions and aggregation of fac-tris(2-phenylpyridinato-C2,N)iridium(III) in nonpolar solvents.

PubMed

Takayasu, Satoshi; Suzuki, Takayoshi; Shinozaki, Kazuteru

2013-08-15

The intermolecular interaction and aggregation of the neutral complex fac-tris(2-phenylpyridinato-C(2),N)iridium(III) (fac-Ir(ppy)3) in solution was investigated. Intermolecular interactions were found to effectively decrease the luminescence lifetime via self-quenching with increasing fac-Ir(ppy)3 concentrations. A Stern-Volmer plot for quenching in acetonitrile was linear, due to bimolecular self-quenching, but curved in toluene as the result of excimer formation. (1)H NMR spectra demonstrated a monomer-aggregate equilibrium which resulted in spectral shifts depending on solvent polarity. X-ray crystallography provided structural information concerning the aggregate, which is based on a tetramer consisting of two Δ-fac-Ir(ppy)3-Λ-fac-Ir(ppy)3 pairs. Offset π-π stacking of ppy ligands and electrostatic dipole-dipole interactions between complex molecules play an important role in the formation of these molecular pairs.

Evolution of specific 3'-5'-linkages in RNA in pre-biotic soup: a new hypothesis.

PubMed

Kumar, Vaijayanti A

2016-11-02

This article reviews the different possibilities towards progression of the formation of DNA/RNA in the chemical world, before life, in enzyme-free conditions. The advent of deoxyribo- and ribopentose-sugars, nucleosides, nucleotides and oligonucleotides in the prebiotic soup is briefly discussed. Further, the formation of early single stranded oligomers, base-pairing possibilities and information transfer based on the stability parameters of the derived duplexes is reviewed. Each theory has its own merits and demerits which we have elaborated upon. Lastly, using clues from this literature, a possible explanation for the specific 3'-5'-linkages in RNA is proposed.

Distinct dissociation kinetics between ion pairs: Solvent-coordinate free-energy landscape analysis.

PubMed

Yonetani, Yoshiteru

2015-07-28

Different ion pairs exhibit different dissociation kinetics; however, while the nature of this process is vital for understanding various molecular systems, the underlying mechanism remains unclear. In this study, to examine the origin of different kinetic rate constants for this process, molecular dynamics simulations were conducted for LiCl, NaCl, KCl, and CsCl in water. The results showed substantial differences in dissociation rate constant, following the trend kLiCl < kNaCl < kKCl < kCsCl. Analysis of the free-energy landscape with a solvent reaction coordinate and subsequent rate component analysis showed that the differences in these rate constants arose predominantly from the variation in solvent-state distribution between the ion pairs. The formation of a water-bridging configuration, in which the water molecule binds to an anion and a cation simultaneously, was identified as a key step in this process: water-bridge formation lowers the related dissociation free-energy barrier, thereby increasing the probability of ion-pair dissociation. Consequently, a higher probability of water-bridge formation leads to a higher ion-pair dissociation rate.

[Network of plastic neurons capable of forming conditioned reflexes ("membrane" model of learning)].

PubMed

Litvinov, E G; Frolov, A A

1978-01-01

Simple net neuronal model was suggested which was able to form the conditioning due to changes of the neuron excitability. The model was based on the following main concepts: (a) the conditioning formation should result in reduction of the firing threshold in the same neurons where the conditioning and reinforcement stimuli were converged, (b) neuron threshold may have only two possible states: initial and final ones, these were identical for all cells, the threshold may be changed only once from the initial value to the final one, (c) isomorphous relation may be introduced between some pair of arbitrary stimuli and some subset of the net neurons; any two pairs differing at least in one stimulus have unlike subsets of the convergent neurons. Stochastically organized neuronal net was used for analysis of the model. Considerable information capacity of the net gives the opportunity to consider that the conditioning formation is possible on the basis of the nervous cells. The efficienty of the model turn out to be comparable with the well known models where the conditioning formation was due to the modification of the synapses.

Reversed-phase ion-pair liquid chromatography method for purification of duplex DNA with single base pair resolution

PubMed Central

Wysoczynski, Christina L.; Roemer, Sarah C.; Dostal, Vishantie; Barkley, Robert M.; Churchill, Mair E. A.; Malarkey, Christopher S.

2013-01-01

Obtaining quantities of highly pure duplex DNA is a bottleneck in the biophysical analysis of protein–DNA complexes. In traditional DNA purification methods, the individual cognate DNA strands are purified separately before annealing to form DNA duplexes. This approach works well for palindromic sequences, in which top and bottom strands are identical and duplex formation is typically complete. However, in cases where the DNA is non-palindromic, excess of single-stranded DNA must be removed through additional purification steps to prevent it from interfering in further experiments. Here we describe and apply a novel reversed-phase ion-pair liquid chromatography purification method for double-stranded DNA ranging in lengths from 17 to 51 bp. Both palindromic and non-palindromic DNA can be readily purified. This method has the unique ability to separate blunt double-stranded DNA from pre-attenuated (n-1, n-2, etc) synthesis products, and from DNA duplexes with single base pair overhangs. Additionally, palindromic DNA sequences with only minor differences in the central spacer sequence of the DNA can be separated, and the purified DNA is suitable for co-crystallization of protein–DNA complexes. Thus, double-stranded ion-pair liquid chromatography is a useful approach for duplex DNA purification for many applications. PMID:24013567

Communication: Towards catalytic nitric oxide reduction via oligomerization on boron doped graphene

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

Cantatore, Valentina, E-mail: valcan@chalmers.se; Panas, Itai

We use density functional theory to describe a novel way for metal free catalytic reduction of nitric oxide NO utilizing boron doped graphene. The present study is based on the observation that boron doped graphene and O—N=N—O{sup −} act as Lewis acid-base pair allowing the graphene surface to act as a catalyst. The process implies electron assisted N=N bond formation prior to N—O dissociation. Two N{sub 2} + O{sub 2} product channels, one of which favoring N{sub 2}O formation, are envisaged as outcome of the catalytic process. Besides, we show also that the N{sub 2} + O{sub 2} formation pathwaysmore » are contrasted by a side reaction that brings to N{sub 3}O{sub 3}{sup −} formation and decomposition into N{sub 2}O + NO{sub 2}{sup −}.« less

Tectonic implications of the Indian Run Formation; a newly recognized sedimentary melange in the northern Virginia Piedmont

USGS Publications Warehouse

Drake, Avery Ala

1985-01-01

Sedimentary melange in the northeastern part of Fairfax County, Virginia, contains both mesoscopic and mappable fragments of Accotink Schist, Lake Barcroft Metasandstone, metagabbro, and ultramafic rocks as well as smaller fragments of other rock types. This melange was originally mapped as the Sykesville Formation, a major precursory sedimentary melange in northern Virginia and Maryland. The fragments of Accotink Schist and Lake Barcroft Metasandstone within the Sykesville were considered to be rip-ups of these units over which the Sykesville slid when finally emplaced. More recent study has shown that fragments of Accotink and Lake Barcroft are restricted to a certain area of sedimentary melange originally defined as Sykesville, and this part of the melange is now considered to be a separate mappable unit, here named the Indian Run Formation. The Indian Run underlies the sequence Accotink Schist and Lake Barcroft Metasandstone which is here formally named the Annandale Group. The Indian Run is intruded by the Occoquan Granite of Cambrian age, so it is of Cambrian or Late Proterozoic age. The Sykesville Formation (restricted) is a much more extensive unit than the Indian Run Formation and is characterized by its contained olistoliths of the Peters Creek Schist, the unit that tectonically overlies it. The Sykesville and Peters Creek constitute a precursory melange-allochthon pair which is here termed a 'tectonic motif.' The Indian Run-Annandale pair then forms a tectonically lower motif, and the overlying pair, the Yorkshire Formation-Piney Branch Complex, forms a tectonically higher motif. The Chopawamsic Formation and underlying sedimentary melange in the area south of Fairfax County may form a tectonic motif beneath the Indian Run-Annandale tectonic motif. Thus, three and perhaps four repetitions of precursory melange-allochthon pairs occur in northern Virginia. Other percursory melanges and motifs may occur in the Maryland Piedmont to the north. The tectonic setting of the motif formation and assemblage is uncertain at this time. A model involving the obduction of several separate sheets onto the ancestral North American continental margin is appealing in that it involves the closing and destruction of a marginal basin, a relatively simple concept. This model fails, however, to supply a source for the sediment necessary to form the precursory melanges. A trench-slope origin would supply the vast amount of needed sediment by accretion. The precursory melangeallochthon motifs would then be stacked near the base of the trench slope. This model is appealing and requires a rather complicated assemblage of continental, arc, and oceanic fragments, such as those that occur on many modern continental margins.

Benzophenone as a photoprobe of polymer films

NASA Astrophysics Data System (ADS)

Levin, Peter P.; Efremkin, Alexei F.; Khudyakov, Igor V.

2017-09-01

The review article is devoted to kinetics of fast reactions following photoexcitation of benzophenone in polymer films. We observed three processes by ns laser flash photolysis in elastomers: (i) decay of a triple state of benzophenone with hydrogen abstraction from polymer matrix, (ii) formation and decay of geminate radical pairs, (iii) cross-termination of the formed radicals in the polymer bulk. Application of external magnetic field (MF) of B = 0.2 T essentially affects recombination of geminate (G-) and a bimolecular recombination of free radicals, which escaped polymer cage (F-pairs). Theoretical calculation of MF effects on G- and F-pairs is in agreement with corresponding experimental data. Elongation of elastomer leads to an unexpected observation: recombination in the bulk becomes slower. An explanation of this phenomenon based on elastomer free volume Vf approach was suggested.

Asymmetrical bonding in cold spraying of dissimilar materials

NASA Astrophysics Data System (ADS)

Nikbakht, R.; Seyedein, S. H.; Kheirandish, S.; Assadi, H.; Jodoin, B.

2018-06-01

Characteristics of particle bonding, especially for dissimilar materials, remains a key question in cold spray deposition. There are limited reports in direct correlation to particle/substrate bonding and peripheral shear zones. Cold spraying experiments and numerical simulations are conducted to characterise and analyse the correlation between bonding and peripheral shear zones for asymmetric particle/substrate pairs of intermetallic-forming elements of nickel and titanium. The correlation between metallic bonding and highly strained areas is explored in view of the growth of the intermetallic phase at the particle/substrate interface during subsequent heat treatments. Characterisation of the as-sprayed samples reveal that for the Ni(particle)/Ti(substrate) pair, plastic deformation of the particle is dominating over substrate deformation. However, for the Ti(particle)/Ni(substrate) pair, it is observed that the substrate and particle deform to similar extents. Characterisation of the samples after a brief heat treatment at 700 °C indicate that intermetallic formation, and hence metallurgical bonding of the pairs is more likely to occur at the particle peripheries where the interface areas are highly strained, and rarely achieved at the particle base. Results also reveal that bonding extends from peripheries toward the central part of the interfaces with increasing the impact velocity. The kinetics of interfacial intermetallic formation at peripheral areas and its correlation to particle bonding is discussed in view of deformation-enhanced interdiffusion.

[Biological and neural bases of partner preferences in rodents: models to understand human pair bonds].

PubMed

Coria-Avila, G A; Hernández-Aguilar, M E; Toledo-Cárdenas, R; García-Hernández, L I; Manzo, J; Pacheco, P; Miquel, M; Pfaus, J G

To analyse the biological and neural bases of partner preference formation in rodents as models to understand human pair bonding. Rodents are social individuals, capable of forming short- or long-lasting partner preferences that develop slowly by stimuli like cohabitation, or rapidly by stimuli like sex and stress. Dopamine, corticosteroids, oxytocin, vasopressin, and opioids form the neurochemical substrate for pair bonding in areas like the nucleus accumbens, the prefrontal cortex, the piriform cortex, the medial preoptic area, the ventral tegmental area and the medial amygdala, among others. Additional areas may participate depending on the nature of the conditioned stimuli by which and individual recognizes a preferred partner. Animal models help us understand that the capacity of an individual to display long-lasting and selective preferences depends on neural bases, selected throughout evolution. The challenge in neuroscience is to use this knowledge to create new solutions for mental problems associated with the incapacity of an individual to display a social bond, keep one, or cope with the disruption of a consolidated one.

A Multifaceted Approach to Investigating Pre-Task Planning Effects on Paired Oral Test Performance

ERIC Educational Resources Information Center

Nitta, Ryo; Nakatsuhara, Fumiyo

2014-01-01

Despite the growing popularity of paired format speaking assessments, the effects of pre-task planning time on performance in these formats are not yet well understood. For example, some studies have revealed the benefits of planning but others have not. Using a multifaceted approach including analysis of the process of speaking performance, the…

Soliton-dark pulse pair formation in birefringent cavity fiber lasers through cross phase coupling.

PubMed

Shao, Guodong; Song, Yufeng; Zhao, Luming; Shen, Deyuan; Tang, Dingyuan

2015-10-05

We report on the experimental observation of soliton-dark pulse pair formation in a birefringent cavity fiber laser. Temporal cavity solitons are formed in one polarization mode of the cavity. It is observed that associated with each of the cavity solitons a dark pulse is induced on the CW background of the orthogonal polarization mode. We show that the dark pulse formation is a result of the incoherent cross polarization coupling between the soliton and the CW beam and has a mechanism similar to that of the polarization domain formation observed in the fiber lasers.

Influence of C-5 substituted cytosine and related nucleoside analogs on the formation of benzo[a]pyrene diol epoxide-dG adducts at CG base pairs of DNA.

PubMed

Guza, Rebecca; Kotandeniya, Delshanee; Murphy, Kristopher; Dissanayake, Thakshila; Lin, Chen; Giambasu, George Madalin; Lad, Rahul R; Wojciechowski, Filip; Amin, Shantu; Sturla, Shana J; Hudson, Robert H E; York, Darrin M; Jankowiak, Ryszard; Jones, Roger; Tretyakova, Natalia Y

2011-05-01

Endogenous 5-methylcytosine ((Me)C) residues are found at all CG dinucleotides of the p53 tumor suppressor gene, including the mutational 'hotspots' for smoking induced lung cancer. (Me)C enhances the reactivity of its base paired guanine towards carcinogenic diolepoxide metabolites of polycyclic aromatic hydrocarbons (PAH) present in cigarette smoke. In the present study, the structural basis for these effects was investigated using a series of unnatural nucleoside analogs and a representative PAH diolepoxide, benzo[a]pyrene diolepoxide (BPDE). Synthetic DNA duplexes derived from a frequently mutated region of the p53 gene (5'-CCCGGCACCC GC[(15)N(3),(13)C(1)-G]TCCGCG-3', + strand) were prepared containing [(15)N(3), (13)C(1)]-guanine opposite unsubstituted cytosine, (Me)C, abasic site, or unnatural nucleobase analogs. Following BPDE treatment and hydrolysis of the modified DNA to 2'-deoxynucleosides, N(2)-BPDE-dG adducts formed at the [(15)N(3), (13)C(1)]-labeled guanine and elsewhere in the sequence were quantified by mass spectrometry. We found that C-5 alkylcytosines and related structural analogs specifically enhance the reactivity of the base paired guanine towards BPDE and modify the diastereomeric composition of N(2)-BPDE-dG adducts. Fluorescence and molecular docking studies revealed that 5-alkylcytosines and unnatural nucleobase analogs with extended aromatic systems facilitate the formation of intercalative BPDE-DNA complexes, placing BPDE in a favorable orientation for nucleophilic attack by the N(2) position of guanine. © The Author(s) 2011. Published by Oxford University Press.

Influence of C-5 substituted cytosine and related nucleoside analogs on the formation of benzo[a]pyrene diol epoxide-dG adducts at CG base pairs of DNA

PubMed Central

Guza, Rebecca; Kotandeniya, Delshanee; Murphy, Kristopher; Dissanayake, Thakshila; Lin, Chen; Giambasu, George Madalin; Lad, Rahul R.; Wojciechowski, Filip; Amin, Shantu; Sturla, Shana J.; Hudson, Robert H.E.; York, Darrin M.; Jankowiak, Ryszard; Jones, Roger; Tretyakova, Natalia Y.

2011-01-01

Endogenous 5-methylcytosine (MeC) residues are found at all CG dinucleotides of the p53 tumor suppressor gene, including the mutational ‘hotspots’ for smoking induced lung cancer. MeC enhances the reactivity of its base paired guanine towards carcinogenic diolepoxide metabolites of polycyclic aromatic hydrocarbons (PAH) present in cigarette smoke. In the present study, the structural basis for these effects was investigated using a series of unnatural nucleoside analogs and a representative PAH diolepoxide, benzo[a]pyrene diolepoxide (BPDE). Synthetic DNA duplexes derived from a frequently mutated region of the p53 gene (5′-CCCGGCACCC GC[15N3,13C1-G]TCCGCG-3′, + strand) were prepared containing [15N3, 13C1]-guanine opposite unsubstituted cytosine, MeC, abasic site, or unnatural nucleobase analogs. Following BPDE treatment and hydrolysis of the modified DNA to 2′-deoxynucleosides, N2-BPDE-dG adducts formed at the [15N3, 13C1]-labeled guanine and elsewhere in the sequence were quantified by mass spectrometry. We found that C-5 alkylcytosines and related structural analogs specifically enhance the reactivity of the base paired guanine towards BPDE and modify the diastereomeric composition of N2-BPDE-dG adducts. Fluorescence and molecular docking studies revealed that 5-alkylcytosines and unnatural nucleobase analogs with extended aromatic systems facilitate the formation of intercalative BPDE–DNA complexes, placing BPDE in a favorable orientation for nucleophilic attack by the N2 position of guanine. PMID:21245046

Statistical analysis of dimer formation in supersaturated metal vapor based on molecular dynamics simulation

NASA Astrophysics Data System (ADS)

Korenchenko, Anna E.; Vorontsov, Alexander G.; Gelchinski, Boris R.; Sannikov, Grigorii P.

2018-04-01

We discuss the problem of dimer formation during the homogeneous nucleation of atomic metal vapor in an inert gas environment. We simulated nucleation with molecular dynamics and carried out the statistical analysis of double- and triple-atomic collisions as the two ways of long-lived diatomic complex formation. Close pair of atoms with lifetime greater than the mean time interval between atom-atom collisions is called a long-lived diatomic complex. We found that double- and triple-atomic collisions gave approximately the same probabilities of long-lived diatomic complex formation, but internal energy of the resulted state was essentially lower in the second case. Some diatomic complexes formed in three-particle collisions are stable enough to be a critical nucleus.

A high-throughput assay for the comprehensive profiling of DNA ligase fidelity

PubMed Central

Lohman, Gregory J. S.; Bauer, Robert J.; Nichols, Nicole M.; Mazzola, Laurie; Bybee, Joanna; Rivizzigno, Danielle; Cantin, Elizabeth; Evans, Thomas C.

2016-01-01

DNA ligases have broad application in molecular biology, from traditional cloning methods to modern synthetic biology and molecular diagnostics protocols. Ligation-based detection of polynucleotide sequences can be achieved by the ligation of probe oligonucleotides when annealed to a complementary target sequence. In order to achieve a high sensitivity and low background, the ligase must efficiently join correctly base-paired substrates, while discriminating against the ligation of substrates containing even one mismatched base pair. In the current study, we report the use of capillary electrophoresis to rapidly generate mismatch fidelity profiles that interrogate all 256 possible base-pair combinations at a ligation junction in a single experiment. Rapid screening of ligase fidelity in a 96-well plate format has allowed the study of ligase fidelity in unprecedented depth. As an example of this new method, herein we report the ligation fidelity of Thermus thermophilus DNA ligase at a range of temperatures, buffer pH and monovalent cation strength. This screen allows the selection of reaction conditions that maximize fidelity without sacrificing activity, while generating a profile of specific mismatches that ligate detectably under each set of conditions. PMID:26365241

A high-throughput assay for the comprehensive profiling of DNA ligase fidelity.

PubMed

Lohman, Gregory J S; Bauer, Robert J; Nichols, Nicole M; Mazzola, Laurie; Bybee, Joanna; Rivizzigno, Danielle; Cantin, Elizabeth; Evans, Thomas C

2016-01-29

DNA ligases have broad application in molecular biology, from traditional cloning methods to modern synthetic biology and molecular diagnostics protocols. Ligation-based detection of polynucleotide sequences can be achieved by the ligation of probe oligonucleotides when annealed to a complementary target sequence. In order to achieve a high sensitivity and low background, the ligase must efficiently join correctly base-paired substrates, while discriminating against the ligation of substrates containing even one mismatched base pair. In the current study, we report the use of capillary electrophoresis to rapidly generate mismatch fidelity profiles that interrogate all 256 possible base-pair combinations at a ligation junction in a single experiment. Rapid screening of ligase fidelity in a 96-well plate format has allowed the study of ligase fidelity in unprecedented depth. As an example of this new method, herein we report the ligation fidelity of Thermus thermophilus DNA ligase at a range of temperatures, buffer pH and monovalent cation strength. This screen allows the selection of reaction conditions that maximize fidelity without sacrificing activity, while generating a profile of specific mismatches that ligate detectably under each set of conditions. © The Author(s) 2015. Published by Oxford University Press on behalf of Nucleic Acids Research.

Contact pair dynamics during folding of two small proteins: Chicken villin head piece and the Alzheimer protein β-amyloid

NASA Astrophysics Data System (ADS)

Mukherjee, Arnab; Bagchi, Biman

2004-01-01

The folding of an extended protein to its unique native state requires establishment of specific, predetermined, often distant, contacts between amino acid residue pairs. The dynamics of contact pair formation between various hydrophobic residues during folding of two different small proteins, the chicken villin head piece (HP-36) and the Alzheimer protein β-amyloid (βA-40), are investigated by Brownian dynamics (BD) simulations. These two proteins represent two very different classes—HP-36 being globular while βA-40 is nonglobular, stringlike. Hydropathy scale and nonlocal helix propensity of amino acids are used to model the complex interaction potential among the various amino acid residues. The minimalistic model we use here employs a connected backbone chain of atoms of equal size while an amino acid is attached to each backbone atom as an additional atom of differing sizes and interaction parameters, determined by the characteristics of each amino acid. Even for such simple models, we find that the low-energy structures obtained by BD simulations of both the model proteins mimic the native state of the real protein rather well, with a best root-mean-square deviation of 4.5 Å for HP-36. For βA-40 (where a single well-defined structure is not available), the simulated structures resemble the reported ensemble rather well, with the well-known β-bend correctly reproduced. We introduce and calculate a contact pair distance time correlation function, CPij(t), to quantify the dynamical evolution of the pair contact formation between the amino acid residue pairs i and j. The contact pair time correlation function exhibits multistage dynamics, including a two stage fast collapse, followed by a slow (microsecond long) late stage dynamics for several specific pairs. The slow late stage dynamics is in accordance with the findings of Sali et al. [A. Sali, E. Shakhnovich, and M. Karplus, Nature 369, 248 (1994)]. Analysis of the individual trajectories shows that the slow decay is due to the attempt of the protein to form energetically more favorable pair contacts to replace the less favorable ones. This late stage contact formation is a highly cooperative process, involving participation of several pairs and thus entropically unfavorable and expected to face a large free energy barrier. This is because any new pair contact formation among hydrophobic pairs will require breaking of several contacts, before the favorable ones can be formed. This aspect of protein folding dynamics is similar to relaxation in glassy liquids, where also α relaxation requires highly cooperative process of hopping. The present analysis suggests that waiting time for the necessary pair contact formation may obey the Poissonian distribution. We also study the dynamics of Förster energy transfer during folding between two tagged amino acid pairs. This dynamics can be studied by fluorescence resonance energy transfer (FRET). It is found that suitably placed donor-acceptor pairs can capture the slow dynamics during folding. The dynamics probed by FRET is predicted to be nonexponential.

A fully synthetic human Fab antibody library based on fixed VH/VL framework pairings with favorable biophysical properties

PubMed Central

Tiller, Thomas; Schuster, Ingrid; Deppe, Dorothée; Siegers, Katja; Strohner, Ralf; Herrmann, Tanja; Berenguer, Marion; Poujol, Dominique; Stehle, Jennifer; Stark, Yvonne; Heßling, Martin; Daubert, Daniela; Felderer, Karin; Kaden, Stefan; Kölln, Johanna; Enzelberger, Markus; Urlinger, Stefanie

2013-01-01

This report describes the design, generation and testing of Ylanthia, a fully synthetic human Fab antibody library with 1.3E+11 clones. Ylanthia comprises 36 fixed immunoglobulin (Ig) variable heavy (VH)/variable light (VL) chain pairs, which cover a broad range of canonical complementarity-determining region (CDR) structures. The variable Ig heavy and Ig light (VH/VL) chain pairs were selected for biophysical characteristics favorable to manufacturing and development. The selection process included multiple parameters, e.g., assessment of protein expression yield, thermal stability and aggregation propensity in fragment antigen binding (Fab) and IgG1 formats, and relative Fab display rate on phage. The framework regions are fixed and the diversified CDRs were designed based on a systematic analysis of a large set of rearranged human antibody sequences. Care was taken to minimize the occurrence of potential posttranslational modification sites within the CDRs. Phage selection was performed against various antigens and unique antibodies with excellent biophysical properties were isolated. Our results confirm that quality can be built into an antibody library by prudent selection of unmodified, fully human VH/VL pairs as scaffolds. PMID:23571156

Ion-pair partition of quarternary ammonium drugs: the influence of counter ions of different lipophilicity, size, and flexibility.

PubMed

Takács-Novák, K; Szász, G

1999-10-01

The ion-pair partition of quaternary ammonium (QA) pharmacons with organic counter ions of different lipophilicity, size, shape and flexibility was studied to elucidate relationships between ion-pair formation and chemical structure. The apparent partition coefficient (P') of 4 QAs was measured in octanol/pH 7.4 phosphate buffer system by the shake-flask method as a function of molar excess of ten counter ions (Y), namely: mesylate (MES), acetate (AC), pyruvate (PYRU), nicotinate (NIC), hydrogenfumarate (HFUM), hydrogenmaleate (HMAL), p-toluenesulfonate (PTS), caproate (CPR), deoxycholate (DOC) and prostaglandin E1 anion (PGE1). Based on 118 of highly precise logP' values (SD< 0.05), the intrinsic lipophilicity (without external counter ions) and the ion-pair partition of QAs (with different counter ions) were characterized. Linear correlation was found between the logP' of ion-pairs and the size of the counter ions described by the solvent accessible surface area (SASA). The lipophilicity increasing effect of the counter ions were quantified and the following order was established: DOC approximate to PGE1 > CPR approximate to PTS > NIC approximate to HMAL > PYRU approximate to AC approximate to MES approximate to HFUM. Analyzing the lipophilicity/molar ratio (QA:Y) profile, the differences in the ion-pair formation were shown and attributed to the differences in the flexibility/rigidity and size both of QA and Y. Since the largest (in average, 300 X) lipophilicity enhancement was found by the influence of DOC and PGE1 and considerable (on average 40 X) increase was observed by CPR and PTS, it was concluded that bile acids and prostaglandin anions may play a significant role in the ion-pair transport of quaternary ammonium drugs and caproic acid and p-toluenesulfonic acid may be useful salt forming agents to improve the pharmacokinetics of hydrophilic drugs.

“Thought experiments” as dry-runs for “tough experiments”: novel approaches to the hydration behavior of oxyanions

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

Chialvo, Ariel A.; Vlcek, Lukas

We explore the deconvolution of correlations for the interpretation of the microstructural behavior of aqueous electrolytes according to the neutron diffraction with isotopic substitution (NDIS) approach toward the experimental determination of ion coordination numbers of systems involving oxyanions, in particular, sulfate anions. We discuss the alluded interplay in the title of this presentation, emphasized the expectations, and highlight the significance of tackling the challenging NDIS experiments. Specifically, we focus on the potential occurrence of Nmore » $$2+\\atop{i}$$ ...SO$$2-\\atop{4}$$ pair formation, identify its signature, suggest novel ways either for the direct probe of the contact ion pair (CIP) strength and the subsequent correction of its effects on the measured coordination numbers, or for the determination of anion coordination numbers free of CIP contributions through the implementation of null-cation environments. For that purpose we perform simulations of NiSO 4 aqueous solutions at ambient conditions to generate the distribution functions required in the analysis (a) to identify the individual partial contributions to the total neutron-weighted distribution function, (b) to isolate and assess the contribution of N$$2+\\atop{i}$$ ...SO$$2-\\atop{4}$$ pair formation, (c) to test the accuracy of the neutron diffraction with isotope substitution based coordination calculations and X-ray diffraction based assumptions, and (d) to describe the water coordination around both the sulfur and oxygen sites of the sulfate anion. In conclusion, we finally discuss the strength of this interplay on the basis of the inherent molecular simulation ability to provide all pair correlation functions that fully characterize the system microstructure and allows us to “reconstruct” the eventual NDIS output, i.e., to take an atomistic “peek” (e.g., see Figure 1) at the local environment around the isotopically-labeled species before any experiment is ever attempted, and ultimately, to test the accuracy of the “measured” NDIS-based coordination numbers against the actual values by the “direct” counting.« less

“Thought experiments” as dry-runs for “tough experiments”: novel approaches to the hydration behavior of oxyanions

DOE PAGES

Chialvo, Ariel A.; Vlcek, Lukas

2016-01-21

We explore the deconvolution of correlations for the interpretation of the microstructural behavior of aqueous electrolytes according to the neutron diffraction with isotopic substitution (NDIS) approach toward the experimental determination of ion coordination numbers of systems involving oxyanions, in particular, sulfate anions. We discuss the alluded interplay in the title of this presentation, emphasized the expectations, and highlight the significance of tackling the challenging NDIS experiments. Specifically, we focus on the potential occurrence of Nmore » $$2+\\atop{i}$$ ...SO$$2-\\atop{4}$$ pair formation, identify its signature, suggest novel ways either for the direct probe of the contact ion pair (CIP) strength and the subsequent correction of its effects on the measured coordination numbers, or for the determination of anion coordination numbers free of CIP contributions through the implementation of null-cation environments. For that purpose we perform simulations of NiSO 4 aqueous solutions at ambient conditions to generate the distribution functions required in the analysis (a) to identify the individual partial contributions to the total neutron-weighted distribution function, (b) to isolate and assess the contribution of N$$2+\\atop{i}$$ ...SO$$2-\\atop{4}$$ pair formation, (c) to test the accuracy of the neutron diffraction with isotope substitution based coordination calculations and X-ray diffraction based assumptions, and (d) to describe the water coordination around both the sulfur and oxygen sites of the sulfate anion. In conclusion, we finally discuss the strength of this interplay on the basis of the inherent molecular simulation ability to provide all pair correlation functions that fully characterize the system microstructure and allows us to “reconstruct” the eventual NDIS output, i.e., to take an atomistic “peek” (e.g., see Figure 1) at the local environment around the isotopically-labeled species before any experiment is ever attempted, and ultimately, to test the accuracy of the “measured” NDIS-based coordination numbers against the actual values by the “direct” counting.« less

Energetics of defects formation and oxygen migration in pyrochlore compounds from first principles calculations

NASA Astrophysics Data System (ADS)

Li, Yan; Kowalski, Piotr M.

2018-07-01

In order to get better understanding of the selective order-disorder transition in pyrochlore compounds, using ab initio methods we calculated the formation energies of coupled cation anti-site and anion Frenkel pair defects and the energy barriers for the oxygen migration for number of families of A2B2 O7 pyrochlore-type compounds. While these parameters have been previously computed with force field-based methods, the ab initio results provide more reliable values that can be confidently used in subsequent analysis. We found a fairly good correlation between the formation energies of the coupled defects and the stability field of pyrochlores. In line with previous studies, the compounds that crystallize in defect fluorite structure are found to have smaller values of coupled defect formation energies than those crystallizing in the pyrochlore phase, although the correlation is not that sharp as in the case of isolated anion Frenkel pair defect. The investigation of the energy barriers for the oxygen migration shows that it is not a good, sole indicator of the tendency of the order-disorder phase transition in pyrochlores. However, we found that the oxygen migration barrier is reduced in the presence of the cation antisite defect. This points at disordering-induced enhancement of oxygen diffusion in pyrochlore compounds.

Pharmacological evidence that both cognitive memory and habit formation contribute to within-session learning of concurrent visual discriminations

PubMed Central

Turchi, Janita; Devan, Bryan; Yin, Pingbo; Sigrist, Emmalynn; Mishkin, Mortimer

2010-01-01

The monkey's ability to learn a set of visual discriminations presented concurrently just once a day on successive days (24-hr ITI task) is based on habit formation, which is known to rely on a visuo-striatal circuit and to be independent of visuo-rhinal circuits that support one-trial memory. Consistent with this dissociation, we recently reported that performance on the 24-hr ITI task is impaired by a striatal-function blocking agent, the dopaminergic antagonist haloperidol, and not by a rhinal-function blocking agent, the muscarinic cholinergic antagonist scopolamine. In the present study, monkeys were trained on a short-ITI form of concurrent visual discrimination learning, one in which a set of stimulus pairs is repeated not only across daily sessions but also several times within each session (in this case, at about 4-min ITIs). Asymptotic discrimination learning rates in the non-drug condition were reduced by half, from ~11 trials/pair on the 24-hr ITI task to ~5 trials/pair on the 4-min ITI task, and this faster learning was impaired by systemic injections of either haloperidol or scopolamine. The results suggest that in the version of concurrent discrimination learning used here, the short ITIs within a session recruit both visuo-rhinal and visuo-striatal circuits, and that the final performance level is driven by both cognitive memory and habit formation working in concert. PMID:20144631

Pharmacological evidence that both cognitive memory and habit formation contribute to within-session learning of concurrent visual discriminations.

PubMed

Turchi, Janita; Devan, Bryan; Yin, Pingbo; Sigrist, Emmalynn; Mishkin, Mortimer

2010-07-01

The monkey's ability to learn a set of visual discriminations presented concurrently just once a day on successive days (24-h ITI task) is based on habit formation, which is known to rely on a visuo-striatal circuit and to be independent of visuo-rhinal circuits that support one-trial memory. Consistent with this dissociation, we recently reported that performance on the 24-h ITI task is impaired by a striatal-function blocking agent, the dopaminergic antagonist haloperidol, and not by a rhinal-function blocking agent, the muscarinic cholinergic antagonist scopolamine. In the present study, monkeys were trained on a short-ITI form of concurrent visual discrimination learning, one in which a set of stimulus pairs is repeated not only across daily sessions but also several times within each session (in this case, at about 4-min ITIs). Asymptotic discrimination learning rates in the non-drug condition were reduced by half, from approximately 11 trials/pair on the 24-h ITI task to approximately 5 trials/pair on the 4-min ITI task, and this faster learning was impaired by systemic injections of either haloperidol or scopolamine. The results suggest that in the version of concurrent discrimination learning used here, the short ITIs within a session recruit both visuo-rhinal and visuo-striatal circuits, and that the final performance level is driven by both cognitive memory and habit formation working in concert.

Star formation history: Modeling of visual binaries

NASA Astrophysics Data System (ADS)

Gebrehiwot, Y. M.; Tessema, S. B.; Malkov, O. Yu.; Kovaleva, D. A.; Sytov, A. Yu.; Tutukov, A. V.

2018-05-01

Most stars form in binary or multiple systems. Their evolution is defined by masses of components, orbital separation and eccentricity. In order to understand star formation and evolutionary processes, it is vital to find distributions of physical parameters of binaries. We have carried out Monte Carlo simulations in which we simulate different pairing scenarios: random pairing, primary-constrained pairing, split-core pairing, and total and primary pairing in order to get distributions of binaries over physical parameters at birth. Next, for comparison with observations, we account for stellar evolution and selection effects. Brightness, radius, temperature, and other parameters of components are assigned or calculated according to approximate relations for stars in different evolutionary stages (main-sequence stars, red giants, white dwarfs, relativistic objects). Evolutionary stage is defined as a function of system age and component masses. We compare our results with the observed IMF, binarity rate, and binary mass-ratio distributions for field visual binaries to find initial distributions and pairing scenarios that produce observed distributions.

Tailoring entanglement through domain engineering in a lithium niobate waveguide

PubMed Central

Ming, Yang; Tan, Ai-Hong; Wu, Zi-Jian; Chen, Zhao-Xian; Xu, Fei; Lu, Yan-Qing

2014-01-01

We propose to integrate the electro-optic (EO) tuning function into on-chip domain engineered lithium niobate (LN) waveguide. Due to the versatility of LN, both the spontaneously parametric down conversion (SPDC) and EO interaction could be realized simultaneously. Photon pairs are generated through SPDC, and the formation of entangled state is modulated by EO processes. An EO tunable polarization-entangled photon state is proposed. Orthogonally-polarized and parallel-polarized entanglements of photon pairs are instantly switchable by tuning the applied field. The characteristics of the source are theoretically investigated showing adjustable bandwidths and high entanglement degrees. Moreover, other kinds of reconfigurable entanglement are also achievable based on suitable domain-design. We believe tailoring entanglement based on domain engineering is a very promising solution for next generation function-integrated quantum circuits. PMID:24770555

Pair-correlations in swimmer suspensions

NASA Astrophysics Data System (ADS)

Nambiar, Sankalp; Subramanian, Ganesh

2017-11-01

Suspensions of rear-actuated swimming microorganisms, such as E.coli, exhibit several interesting phenomena including spontaneous pattern formation above a critical concentration, novel rheological properties, shear-induced concentration banding etc. Explanations based on mean-field theory are only qualitative, since interactions between swimmers are important for typical experimental concentrations. We analytically characterize the hydrodynamic pair-interactions in a quiescent suspension of slender straight swimmers. The pair-correlation, calculated at leading order by integrating the swimmer velocity disturbances along straight trajectories, decays as 1/r2 for r >> L (L being the swimmer size). This allows us to characterize both polar and nematic correlations in an interacting swimmer suspension. In the absence of correlations, the velocity covariance asymptotes from a constant for r << L to a far-field decay of O(1/r2) for r >> L, the latter being characteristic of a suspension of non-interacting point force-dipoles. On including correlations, the slow decay of the pair-orientation correlation leads to an additional contribution to the velocity covariance that diverges logarithmically with system size.

Alignment of RNA molecules: Binding energy and statistical properties of random sequences

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

Valba, O. V., E-mail: valbaolga@gmail.com; Nechaev, S. K., E-mail: sergei.nechaev@gmail.com; Tamm, M. V., E-mail: thumm.m@gmail.com

2012-02-15

A new statistical approach to the problem of pairwise alignment of RNA sequences is proposed. The problem is analyzed for a pair of interacting polymers forming an RNA-like hierarchical cloverleaf structures. An alignment is characterized by the numbers of matches, mismatches, and gaps. A weight function is assigned to each alignment; this function is interpreted as a free energy taking into account both direct monomer-monomer interactions and a combinatorial contribution due to formation of various cloverleaf secondary structures. The binding free energy is determined for a pair of RNA molecules. Statistical properties are discussed, including fluctuations of the binding energymore » between a pair of RNA molecules and loop length distribution in a complex. Based on an analysis of the free energy per nucleotide pair complexes of random RNAs as a function of the number of nucleotide types c, a hypothesis is put forward about the exclusivity of the alphabet c = 4 used by nature.« less

Raman spectroscopy of DNA-metal complexes. I. Interactions and conformational effects of the divalent cations: Mg, Ca, Sr, Ba, Mn, Co, Ni, Cu, Pd, and Cd.

PubMed

Duguid, J; Bloomfield, V A; Benevides, J; Thomas, G J

1993-11-01

Interactions of divalent metal cations (Mg2+, Ca2+, Ba2+, Sr2+, Mn2+, Co2+, Ni2+, Cu2+, Pd2+, and Cd2+) with DNA have been investigated by laser Raman spectroscopy. Both genomic calf-thymus DNA (> 23 kilobase pairs) and mononucleosomal fragments (160 base pairs) were employed as targets of metal interaction in solutions containing 5 weight-% DNA and metal:phosphate molar ratios of 0.6:1. Raman difference spectra reveal that transition metal cations (Mn2+, Co2+, Ni2+, Cu2+, Pd2+, and Cd2+) induce the greatest structural changes in B-DNA. The Raman (vibrational) band differences are extensive and indicate partial disordering of the B-form backbone, reduction in base stacking, reduction in base pairing, and specific metal interaction with acceptor sites on the purine (N7) and pyrimidine (N3) rings. Many of the observed spectral changes parallel those accompanying thermal denaturation of B-DNA and suggest that the metals link the bases of denatured DNA. While exocyclic carbonyls of dT, dG, and dC may stabilize metal ligation, correlation plots show that perturbations of the carbonyls are mainly a consequence of metal-induced denaturation of the double helix. Transition metal interactions with the DNA phosphates are weak in comparison to interactions with the bases, except in the case of Cu2+, which strongly perturbs both base and phosphate group vibrations. On the other hand, the Raman signature of B-DNA is largely unperturbed by Mg2+, Ca2+, Sr2+, and Ba2+, suggesting much weaker interactions of the alkaline earth metals with both base and phosphate sites. A notable exception is a moderate perturbation by alkaline earths of purine N7 sites in 160-base pair DNA, with Ca2+ causing the greatest effect. Correlation plots demonstrate a strong interrelationship between perturbations of Raman bands assigned to ring vibrations of the bases and those of bands assigned to exocyclic carbonyls and backbone phosphodiester groups. However, strong correlations do not occur between the Raman phosphodioxy band (centered near 1092 cm-1) and other Raman bands, suggesting that the former is not highly sensitive to the structural changes induced by divalent metal cations. The structural perturbations induced by divalent cations are much greater for > 23-kilobase pair DNA than for 160-base pair DNA, as evidenced by both the Raman difference spectra and the tendency toward the formation of insoluble aggregates. In the presence of transition metals, aggregation of high-molecular-weight DNA is evident at temperatures as low as 11 degrees C. A relationship between DNA melting and aggregation is proposed in which initial metal binding at major groove sites locally destabilizes the B-DNA double helix, causing displacement of the bases away from one another and exposing additional metal binding sites. Metal cation linkage of two displaced bases would allow separate DNA strands to crosslink. Aggregation is proposed to result from the formation of an extended network of these crosslinks.

Analysis of Structural Flexibility of Damaged DNA Using Thiol-Tethered Oligonucleotide Duplexes

PubMed Central

Fujita, Masashi; Watanabe, Shun; Yoshizawa, Mariko; Yamamoto, Junpei; Iwai, Shigenori

2015-01-01

Bent structures are formed in DNA by the binding of small molecules or proteins. We developed a chemical method to detect bent DNA structures. Oligonucleotide duplexes in which two mercaptoalkyl groups were attached to the positions facing each other across the major groove were prepared. When the duplex contained the cisplatin adduct, which was proved to induce static helix bending, interstrand disulfide bond formation under an oxygen atmosphere was detected by HPLC analyses, but not in the non-adducted duplex, when the two thiol-tethered nucleosides were separated by six base pairs. When the insert was five and seven base pairs, the disulfide bond was formed and was not formed, respectively, regardless of the cisplatin adduct formation. The same reaction was observed in the duplexes containing an abasic site analog and the (6–4) photoproduct. Compared with the cisplatin case, the disulfide bond formation was slower in these duplexes, but the reaction rate was nearly independent of the linker length. These results indicate that dynamic structural changes of the abasic site- and (6–4) photoproduct-containing duplexes could be detected by our method. It is strongly suggested that the UV-damaged DNA-binding protein, which specifically binds these duplexes and functions at the first step of global-genome nucleotide excision repair, recognizes the easily bendable nature of damaged DNA. PMID:25679955

Solvent-coordinate free-energy landscape view of water-mediated ion-pair dissociation

NASA Astrophysics Data System (ADS)

Yonetani, Yoshiteru

2017-12-01

Water-mediated ion-pair dissociation is studied by molecular dynamics simulations of NaCl in water. Multidimensional free-energy analysis clarifies the relation between two essential solvent coordinates: the water coordination number and water-bridge formation. These two are related in a complex way. Both are necessary to describe ion-pair dissociation. The mechanism constructed with both solvent variables clearly shows the individual roles. The water coordination number is critical for starting ion-pair dissociation. Water-bridge formation is also important because it increases the likelihood of ion-pair dissociation by reducing the dissociation free-energy barrier. Additional Ca-Cl and NH4-Cl calculations show that these conclusions are unaffected by changes in the ion charge and shape. The present results will contribute to future explorations of many other molecular events such as surface water exchange and protein-ligand dissociation because the same mechanism is involved in such events.

Evaluation of a computer-based approach to teaching acid/base physiology.

PubMed

Rawson, Richard E; Quinlan, Kathleen M

2002-12-01

Because acid/base physiology is a difficult subject for most medical and veterinary students, the first author designed a software program, Acid/Base Primer, that would help students with this topic. The Acid/Base Primer was designed and evaluated within a conceptual framework of basic educational principles. Seventy-five first-year veterinary students (of 81; 93% response rate) participated in this study. Students took both a pre- and posttest of content understanding. After completing the Acid/Base Primer in pairs, each student filled out a survey evaluating the features of the program and describing his/her use and experience of it. Four pairs of students participated in interviews that elaborated on the surveys. Scores improved from 53 +/- 2% on the pretest to 74 +/- 1% on an immediate posttest. On surveys and in interviews, students reported that the program helped them construct their own understanding of acid/base physiology and prompted discussions in pairs of students when individual understandings differed. The case-based format provided anchors and a high degree of relevance. Repetition of concepts helped students develop a more complex network of understanding. Questions in the program served to scaffold the learning process by providing direction, accentuating the relevant features of the cases, and provoking discussion. Guidelines for software development were generated on the basis of the findings and relevant educational literature.

Structure and conversion kinetics of a bi-stable DNA i-motif: broken symmetry in the [d(5mCCTCC)]4 tetramer.

PubMed

Nonin, S; Leroy, J L

1996-08-23

At slightly acidic pH, protonation of C-rich oligomers results in the formation of a four-stranded structure composed of two parallel duplexes in a head to tail orientation with their hemi-protonated C.C+ pairs intercalated in a so-called i-motif. In all cases reported previously the duplexes are identical. The tetramer formed by the d(5mCCTCC) oligomer is different. The structure is computed on the basis of 55 inter-residue distances derived from NOESY cross-peaks measured at short mixing times. It consists of two intercalated non-equivalent symmetrical duplexes. The base stacking order is C5* C1 C4* C2 (T3*) T3 C2* C4 C1* C5, but the thymidine bases (T3*) of one duplex are looped out and lie in the wide grooves of the tetramer. The thymidine bases T3 stack as a symmetrical T.T pair between the sequentially adjacent C2.C2+ pair and the C2*.C2*+ pair of the other duplex. Numerous exchange cross-peaks provide evidence for duplex interconversion. The interconversion rate is 1.4 s-1 at 0 degree C and the activation energy is 94 kJ/mol. The opening of the T3.T3 pair, the closing of the T3*.T3 pair, and the opening of the C2*.C2*+ pair occur simultaneously with the duplex interconversion. This suggests that the concerted opening and closing of the thymidine bases drive the duplex interconversion. Opening of the C4.C4+ and C4*.C4*+ pairs, and dissociation of the tetramer are not part of the interconversion since they occur at much slower rates. Duplex interconversion within the [d(5mCCTCC)]4 tetramer provides the first structural and kinetics characterization of broken symmetry in a biopolymer. The tetramer formed by d(5mCCUCC) adopts a similar structure, but the rate of duplex interconversion is faster: 40 s-1 at 0 degree C. At 32 degrees C, interconversion is fast on the NMR time scale.

Extractive Spectrophotometric Methods for the Determination of Zolmitriptan in Bulk Drug and Pharmaceutical Formulation Using Bromocresol Green

NASA Astrophysics Data System (ADS)

Prashanth, K. N.; Swamy, N.; Basavaiah, K.

2013-11-01

Considering the basic property of zolmitriptan (ZMT) to generate ion-pairs with sulfonephthalein dyes two methods have been developed for its assay in bulk drug and dosage form. The first method (method A) is based on the formation of a colored ion-pair complex (1:1 drug:dye) of ZMT with bromocresol green (BCG) at pH 4.20 ± 0.01 and extraction of the complex into chloroform followed by measurement of the yellow ion-pair complex at 435 nm. In the second method (method B), the drug-dye ion-pair complex was treated with ethanolic potassium hydroxide in ethanolic medium and the resulting base form of the dye was measured at 630 nm. Beer's law was obeyed in the concentration range of 0.8-18.0 and 0.08-1.4 μg/ml for method A and B, respectively, and the corresponding molar absorptivity values were 1.50ṡ104 and 1.52ṡ105 l/(molṡcm). The Sandell sensitivity values were 0.0191 and 0.0019 μg/cm2 for method A and method B, respectively. The stoichiometry of the ion-pair complex formed between the drug and dye (1:1) was determined by Job's continuous variation method and the stability constant of the complex was also calculated. The proposed method was successfully extended to dosage form (tablets).

Mapping Structurally Defined Guanine Oxidation Products along DNA Duplexes: Influence of Local Sequence Context and Endogenous Cytosine Methylation

PubMed Central

2015-01-01

DNA oxidation by reactive oxygen species is nonrandom, potentially leading to accumulation of nucleobase damage and mutations at specific sites within the genome. We now present the first quantitative data for sequence-dependent formation of structurally defined oxidative nucleobase adducts along p53 gene-derived DNA duplexes using a novel isotope labeling-based approach. Our results reveal that local nucleobase sequence context differentially alters the yields of 2,2,4-triamino-2H-oxal-5-one (Z) and 8-oxo-7,8-dihydro-2′-deoxyguanosine (OG) in double stranded DNA. While both lesions are overproduced within endogenously methylated MeCG dinucleotides and at 5′ Gs in runs of several guanines, the formation of Z (but not OG) is strongly preferred at solvent-exposed guanine nucleobases at duplex ends. Targeted oxidation of MeCG sequences may be caused by a lowered ionization potential of guanine bases paired with MeC and the preferential intercalation of riboflavin photosensitizer adjacent to MeC:G base pairs. Importantly, some of the most frequently oxidized positions coincide with the known p53 lung cancer mutational “hotspots” at codons 245 (GGC), 248 (CGG), and 158 (CGC) respectively, supporting a possible role of oxidative degradation of DNA in the initiation of lung cancer. PMID:24571128

T box transcription antitermination riboswitch: Influence of nucleotide sequence and orientation on tRNA binding by the antiterminator element

PubMed Central

Fauzi, Hamid; Agyeman, Akwasi; Hines, Jennifer V.

2008-01-01

Many bacteria utilize riboswitch transcription regulation to monitor and appropriately respond to cellular levels of important metabolites or effector molecules. The T box transcription antitermination riboswitch responds to cognate uncharged tRNA by specifically stabilizing an antiterminator element in the 5′-untranslated mRNA leader region and precluding formation of a thermodynamically more stable terminator element. Stabilization occurs when the tRNA acceptor end base pairs with the first four nucleotides in the seven nucleotide bulge of the highly conserved antiterminator element. The significance of the conservation of the antiterminator bulge nucleotides that do not base pair with the tRNA is unknown, but they are required for optimal function. In vitro selection was used to determine if the isolated antiterminator bulge context alone dictates the mode in which the tRNA acceptor end binds the bulge nucleotides. No sequence conservation beyond complementarity was observed and the location was not constrained to the first four bases of the bulge. The results indicate that formation of a structure that recognizes the tRNA acceptor end in isolation is not the determinant driving force for the high phylogenetic sequence conservation observed within the antiterminator bulge. Additional factors or T box leader features more likely influenced the phylogenetic sequence conservation. PMID:19152843

Interaction of Cu(+) with cytosine and formation of i-motif-like C-M(+)-C complexes: alkali versus coinage metals.

PubMed

Gao, Juehan; Berden, Giel; Rodgers, M T; Oomens, Jos

2016-03-14

The Watson-Crick structure of DNA is among the most well-known molecular structures of our time. However, alternative base-pairing motifs are also known to occur, often depending on base sequence, pH, or the presence of cations. Pairing of cytosine (C) bases induced by the sharing of a single proton (C-H(+)-C) may give rise to the so-called i-motif, which occurs primarily in expanded trinucleotide repeats and the telomeric region of DNA, particularly at low pH. At physiological pH, silver cations were recently found to stabilize C dimers in a C-Ag(+)-C structure analogous to the hemiprotonated C-dimer. Here we use infrared ion spectroscopy in combination with density functional theory calculations at the B3LYP/6-311G+(2df,2p) level to show that copper in the 1+ oxidation state induces an analogous formation of C-Cu(+)-C structures. In contrast to protons and these transition metal ions, alkali metal ions induce a different dimer structure, where each ligand coordinates the alkali metal ion in a bidentate fashion in which the N3 and O2 atoms of both cytosine ligands coordinate to the metal ion, sacrificing hydrogen-bonding interactions between the ligands for improved chelation of the metal cation.

Central region component1, a novel synaptonemal complex component, is essential for meiotic recombination initiation in rice.

PubMed

Miao, Chunbo; Tang, Ding; Zhang, Honggen; Wang, Mo; Li, Yafei; Tang, Shuzhu; Yu, Hengxiu; Gu, Minghong; Cheng, Zhukuan

2013-08-01

In meiosis, homologous recombination entails programmed DNA double-strand break (DSB) formation and synaptonemal complex (SC) assembly coupled with the DSB repair. Although SCs display extensive structural conservation among species, their components identified are poorly conserved at the sequence level. Here, we identified a novel SC component, designated central region component1 (CRC1), in rice (Oryza sativa). CRC1 colocalizes with ZEP1, the rice SC transverse filament protein, to the central region of SCs in a mutually dependent fashion. Consistent with this colocalization, CRC1 interacts with ZEP1 in yeast two-hybrid assays. CRC1 is orthologous to Saccharomyces cerevisiae pachytene checkpoint2 (Pch2) and Mus musculus THYROID receptor-interacting protein13 (TRIP13) and may be a conserved SC component. Additionally, we provide evidence that CRC1 is essential for meiotic DSB formation. CRC1 interacts with homologous pairing aberration in rice meiosis1 (PAIR1) in vitro, suggesting that these proteins act as a complex to promote DSB formation. PAIR2, the rice ortholog of budding yeast homolog pairing1, is required for homologous chromosome pairing. We found that CRC1 is also essential for the recruitment of PAIR2 onto meiotic chromosomes. The roles of CRC1 identified here have not been reported for Pch2 or TRIP13.

CENTRAL REGION COMPONENT1, a Novel Synaptonemal Complex Component, Is Essential for Meiotic Recombination Initiation in Rice[C][W

PubMed Central

Miao, Chunbo; Tang, Ding; Zhang, Honggen; Wang, Mo; Li, Yafei; Tang, Shuzhu; Yu, Hengxiu; Gu, Minghong; Cheng, Zhukuan

2013-01-01

In meiosis, homologous recombination entails programmed DNA double-strand break (DSB) formation and synaptonemal complex (SC) assembly coupled with the DSB repair. Although SCs display extensive structural conservation among species, their components identified are poorly conserved at the sequence level. Here, we identified a novel SC component, designated CENTRAL REGION COMPONENT1 (CRC1), in rice (Oryza sativa). CRC1 colocalizes with ZEP1, the rice SC transverse filament protein, to the central region of SCs in a mutually dependent fashion. Consistent with this colocalization, CRC1 interacts with ZEP1 in yeast two-hybrid assays. CRC1 is orthologous to Saccharomyces cerevisiae pachytene checkpoint2 (Pch2) and Mus musculus THYROID RECEPTOR-INTERACTING PROTEIN13 (TRIP13) and may be a conserved SC component. Additionally, we provide evidence that CRC1 is essential for meiotic DSB formation. CRC1 interacts with HOMOLOGOUS PAIRING ABERRATION IN RICE MEIOSIS1 (PAIR1) in vitro, suggesting that these proteins act as a complex to promote DSB formation. PAIR2, the rice ortholog of budding yeast homolog pairing1, is required for homologous chromosome pairing. We found that CRC1 is also essential for the recruitment of PAIR2 onto meiotic chromosomes. The roles of CRC1 identified here have not been reported for Pch2 or TRIP13. PMID:23943860

Time-Resolved Magnetic Field Effects Distinguish Loose Ion Pairs from Exciplexes

PubMed Central

2013-01-01

We describe the experimental investigation of time-resolved magnetic field effects in exciplex-forming organic donor–acceptor systems. In these systems, the photoexcited acceptor state is predominantly deactivated by bimolecular electron transfer reactions (yielding radical ion pairs) or by direct exciplex formation. The delayed fluorescence emitted by the exciplex is magnetosensitive if the reaction pathway involves loose radical ion pair states. This magnetic field effect results from the coherent interconversion between the electronic singlet and triplet radical ion pair states as described by the radical pair mechanism. By monitoring the changes in the exciplex luminescence intensity when applying external magnetic fields, details of the reaction mechanism can be elucidated. In this work we present results obtained with the fluorophore-quencher pair 9,10-dimethylanthracene/N,N-dimethylaniline (DMA) in solvents of systematically varied permittivity. A simple theoretical model is introduced that allows discriminating the initial state of quenching, viz., the loose ion pair and the exciplex, based on the time-resolved magnetic field effect. The approach is validated by applying it to the isotopologous fluorophore-quencher pairs pyrene/DMA and pyrene-d10/DMA. We detect that both the exciplex and the radical ion pair are formed during the initial quenching stage. Upon increasing the solvent polarity, the relative importance of the distant electron transfer quenching increases. However, even in comparably polar media, the exciplex pathway remains remarkably significant. We discuss our results in relation to recent findings on the involvement of exciplexes in photoinduced electron transfer reactions. PMID:24041160

Item Response Modeling of Paired Comparison and Ranking Data

ERIC Educational Resources Information Center

Maydeu-Olivares, Alberto; Brown, Anna

2010-01-01

The comparative format used in ranking and paired comparisons tasks can significantly reduce the impact of uniform response biases typically associated with rating scales. Thurstone's (1927, 1931) model provides a powerful framework for modeling comparative data such as paired comparisons and rankings. Although Thurstonian models are generally…

Star formation rates in isolated galaxies selected from the Two-Micron All-Sky Survey

NASA Astrophysics Data System (ADS)

Melnyk, O.; Karachentseva, V.; Karachentsev, I.

2015-08-01

We have considered the star formation properties of 1616 isolated galaxies from the 2MASS XSC (Extended Source Catalog) selected sample (2MIG) with the far-ultraviolet GALEX magnitudes. This sample was then compared with corresponding properties of isolated galaxies from the Local Orphan Galaxies (LOG) catalogue and paired galaxies. We found that different selection algorithms define different populations of isolated galaxies. The population of the LOG catalogue, selected from non-clustered galaxies in the Local Supercluster volume, mostly consists of low-mass spiral and late-type galaxies. The specific star formation rate (SSFR) upper limit in isolated and paired galaxies does not exceed the value of ˜dex(-9.4). This is probably common for galaxies of differing activity and environment (at least at z < 0.06). The fractions of quenched galaxies are nearly twice as high in the paired galaxy sample as in the 2MIG isolated galaxy sample. From the behaviour of (S)SFR versus M* relations we deduced that the characteristic value influencing evolutionary processes is the galaxy mass. However, the environmental influence is notable: paired massive galaxies with logM* > 11.5 have higher (S)SFR than isolated galaxies. Our results suggest that the environment helps to trigger the star formation in the highest mass galaxies. We found that the fraction of AGN in the paired sample is only a little higher than in our isolated galaxy sample. We assume that AGN phenomenon is probably defined by secular galaxy evolution.

Determination of redox potentials for the Watson-Crick base pairs, DNA nucleosides, and relevant nucleoside analogues.

PubMed

Crespo-Hernandez, Carlos E; Close, David M; Gorb, Leonid; Leszczynski, Jerzy

2007-05-17

Redox potentials for the DNA nucleobases and nucleosides, various relevant nucleoside analogues, Watson-Crick base pairs, and seven organic dyes are presented based on DFT/B3LYP/6-31++G(d,p) and B3YLP/6-311+G(2df,p)//B3LYP/6-31+G* levels of calculations. The values are determined from an experimentally calibrated set of equations that correlate the vertical ionization (electron affinity) energy of 20 organic molecules with their experimental reversible oxidation (reduction) potential. Our results are in good agreement with those estimated experimentally for the DNA nucleosides in acetonitrile solutions (Seidel et al. J. Phys. Chem. 1996, 100, 5541). We have found that nucleosides with anti conformation exhibit lower oxidation potentials than the corresponding syn conformers. The lowering in the oxidation potential is due to the formation of an intramolecular hydrogen bonding interaction between the 5'-OH group of the sugar and the N3 of the purine bases or C2=O of the pyrimidine bases in the syn conformation. Pairing of adenine or guanine with its complementary pyrimidine base decreases its oxidation potential by 0.15 or 0.28 V, respectively. The calculated energy difference between the oxidation potential for the G.C base pair and that of the guanine base is in good agreement with the experimental value estimated recently (0.34 V: Caruso, T.; et al. J. Am. Chem. Soc. 2005, 127, 15040). The complete and consistent set of reversible redox values determined in this work for the DNA constituents is expected to be of considerable value to those studying charge and electronic energy transfer in DNA.

Microkinetic modeling of H 2SO 4 formation on Pt based diesel oxidation catalysts

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

Sharma, Hom N.; Sun, Yunwei; Glascoe, Elizabeth A.

The presence of water vapor and sulfur oxides in diesel engine exhaust leads to the formation of sulfuric acid (H 2SO 4), which severely impacts the performance of Pt/Pd based emissions aftertreatment catalysts. In this study, a microkinetic model is developed to investigate the reaction pathways of H 2SO 4 formation on Pt based diesel oxidation catalysts (DOCs). The microkinetic model consists of 14 elementary step reactions (7 reversible pairs) and yields prediction in excellent agreement with data obtained from experiments at practically relevant sulfur oxides environment in engine exhaust. The model simulation utilizing a steady-state plug flow reactor demonstratesmore » that it matches experimental data in both kinetically and thermodynamically controlled regions. Results clearly show the negative impact of SO 3 on the SO 2 oxidation light-off temperature, consistent with experimental observations. A reaction pathway analysis shows that the primary pathway of sulfuric acid formation on Pt surface involves SO 2* oxidation to form SO 3* with the subsequent interaction of SO 3* with H 2O* to form H 2SO 4*.« less

Microkinetic modeling of H 2SO 4 formation on Pt based diesel oxidation catalysts

DOE PAGES

Sharma, Hom N.; Sun, Yunwei; Glascoe, Elizabeth A.

2017-08-10

The presence of water vapor and sulfur oxides in diesel engine exhaust leads to the formation of sulfuric acid (H 2SO 4), which severely impacts the performance of Pt/Pd based emissions aftertreatment catalysts. In this study, a microkinetic model is developed to investigate the reaction pathways of H 2SO 4 formation on Pt based diesel oxidation catalysts (DOCs). The microkinetic model consists of 14 elementary step reactions (7 reversible pairs) and yields prediction in excellent agreement with data obtained from experiments at practically relevant sulfur oxides environment in engine exhaust. The model simulation utilizing a steady-state plug flow reactor demonstratesmore » that it matches experimental data in both kinetically and thermodynamically controlled regions. Results clearly show the negative impact of SO 3 on the SO 2 oxidation light-off temperature, consistent with experimental observations. A reaction pathway analysis shows that the primary pathway of sulfuric acid formation on Pt surface involves SO 2* oxidation to form SO 3* with the subsequent interaction of SO 3* with H 2O* to form H 2SO 4*.« less

In vitro evidence for the formation of reactive intermediates of resveratrol in human liver microsomes.

PubMed

Steenwyk, R C; Tan, B

2010-01-01

Resveratrol (3,4',5-trihydroxystilbene) is a naturally occurring polyphenolic compound found in a variety of foods and over-the-counter health products. It has gained wide public use due to its potential health properties, and is available over-the-counter at health product stores. Although the safety profile of resveratrol has been minimally investigated in humans, resveratrol has been associated with observations of toxicity in vitro, and has been identified as a mechanism-based inhibitor of cytochrome P450 3A4. In addition, resveratrol has been rationally hypothesized to form reactive quinone methide metabolites, despite experimental evidence supporting this assumption. This work evaluates the potential for resveratrol to form glutathione-trapped reactive intermediates in human liver microsomes utilizing liquid chromatography and electrospray tandem mass spectrometry, and has resulted in the identification of several in vitro products including two hydroxylated metabolites (piceatannol and metabolite 2), and two pairs of regioisomeric glutathione adducts. The parallel metabolism of resveratrol to piceatannol and metabolite 2 (a putative quinone methide) are demonstrated to result in the formation of two putative quinone methide intermediates resulting in divergent mechanisms for formation of each pair of regioisomeric glutathione adducts.

Exact calculation of loop formation probability identifies folding motifs in RNA secondary structures

PubMed Central

Sloma, Michael F.; Mathews, David H.

2016-01-01

RNA secondary structure prediction is widely used to analyze RNA sequences. In an RNA partition function calculation, free energy nearest neighbor parameters are used in a dynamic programming algorithm to estimate statistical properties of the secondary structure ensemble. Previously, partition functions have largely been used to estimate the probability that a given pair of nucleotides form a base pair, the conditional stacking probability, the accessibility to binding of a continuous stretch of nucleotides, or a representative sample of RNA structures. Here it is demonstrated that an RNA partition function can also be used to calculate the exact probability of formation of hairpin loops, internal loops, bulge loops, or multibranch loops at a given position. This calculation can also be used to estimate the probability of formation of specific helices. Benchmarking on a set of RNA sequences with known secondary structures indicated that loops that were calculated to be more probable were more likely to be present in the known structure than less probable loops. Furthermore, highly probable loops are more likely to be in the known structure than the set of loops predicted in the lowest free energy structures. PMID:27852924

Dewar Lesion Formation in Single- and Double-Stranded DNA is Quenched by Neighboring Bases.

PubMed

Bucher, Dominik B; Pilles, Bert M; Carell, Thomas; Zinth, Wolfgang

2015-07-16

UV-induced Dewar lesion formation is investigated in single- and double-stranded oligonucleotides with ultrafast vibrational spectroscopy. The quantum yield for the conversion of the (6-4) lesion to the Dewar isomer in DNA strands is reduced by a factor of 4 in comparison to model dinucleotides. Time resolved spectroscopy reveals a fast process in the excited state with spectral characteristics of bases which are adjacent to the excited (6-4) lesion. These kinetic components have large amplitudes and indicate that an additional quenching channel acts in the stranded DNA systems and reduces the Dewar formation yield. Presumably relaxation evolves via a charge transfer to the neighboring guanine and the paired cytosine participates in a double-stranded oligomer. Changes in the decay of the relaxed excited electronic state of the (6-4) chromophore point to modifications in the excited state energy landscape which may lead to an additional reduction of the Dewar formation yield.

UV-vis, IR and 1H NMR spectroscopic studies and characterization of ionic-pair crystal violet-oxytetracycline

NASA Astrophysics Data System (ADS)

Orellana, Sandra; Soto, César; Toral, M. Inés

2010-01-01

The present study shows the formation and characterization of the ionic-pair between the antibiotic oxytetracycline and the dye crystal violet in ammonia solution pH 9.0 ± 0.2 extracted into chloroform. The characterization was demonstrated using UV-vis spectrophotometry, 1H NMR, measurement of relaxation times T1 and IR spectroscopy, using a comparison between the signals of individual pure compounds with the signals with the mixture CV-OTC in different alkaline media. The formation of ionic-pair was also corroborated by new signals and chemical shifts. (2D) NMR spectroscopy experiments show that the interaction is electrostatic.

Single-Molecule Mechanical (Un)folding of RNA Hairpins: Effects of Single A-U to A∙C Pair Substitutions and Single Proton Binding and Implications for mRNA Structure-Induced -1 Ribosomal Frameshifting.

PubMed

Yang, Lixia; Zhong, Zhensheng; Tong, Cailing; Jia, Huan; Liu, Yiran; Chen, Gang

2018-06-08

A wobble A∙C pair can be protonated at near physiological pH to form a more stable wobble A+∙C pair. Here, we constructed an RNA hairpin (rHP) and three mutants with one A-U base pair substituted with an A∙C mismatch on the top (near the loop, U22C), middle (U25C) and bottom (U29C) positions of the stem, respectively. Our results on single-molecule mechanical (un)folding using optical tweezers reveal the destabilization effect of A-U to A∙C pair substitution, and protonation-dependent enhancement of mechanical stability facilitated through an increased folding rate, or decreased unfolding rate, or both. Our data show that protonation may occur rapidly upon the formation of apparent mechanical folding transition state. Furthermore, we measured the bulk -1 ribosomal frameshifting efficiencies of the hairpins by a cell-free translation assay. For the mRNA hairpins studied, -1 frameshifting efficiency correlates with mechanical unfolding force at equilibrium and folding rate at around 15 pN. U29C has a frameshifting efficiency similar to that of rHP (~2%). Accordingly, the bottom 2-4 base pairs of U29C may not form under a stretching force at pH 7.3, which is consistent with the fact that the bottom base pairs of the hairpins may be disrupted by ribosome at the slippery site. U22C and U25C have a similar frameshifting efficiency (~1%), indicating that both unfolding and folding rates of an mRNA hairpin in a crowded environment may affect frameshifting. Our data indicate that mechanical (un)folding of RNA hairpins may mimic how mRNAs unfold and fold in the presence of translating ribosomes.

Extension of helix II of an HIV-1-directed hammerhead ribozyme with long antisense flanks does not alter kinetic parameters in vitro but causes loss of the inhibitory potential in living cells.

PubMed Central

Homann, M; Tabler, M; Tzortzakaki, S; Sczakiel, G

1994-01-01

When designed to cleave a target RNA in trans, the hammerhead ribozyme contains two antisense flanks which form helix I and helix III by pairing with the complementary target RNA. The sequences forming helix II are contained on the ribozyme strand and represent a major structural component of the hammerhead structure. In the case of an inhibitory 429 nucleotides long trans-ribozyme (2as-Rz12) which was directed against the 5'-leader/gag region of the human immunodeficiency virus type 1 (HIV-1), helix II was not pre-formed in the single-stranded molecule. Thus, major structural changes are necessary before cleavage can occur. To study whether pre-formation of helix II in the non-paired 2as-Rz12 RNA could influence the observed cleavage rate in vitro and its inhibitory activity on HIV-1 replication, we extended the 4 base pair helix II of 2as-Rz12 to 6, 10, 21, and 22 base pairs respectively. Limited RNase cleavage reactions performed in vitro at 37 degrees C and at physiological ion strength indicated that a helix II of the hammerhead domain was pre-formed when its length was at least six base pairs. This modification neither affected the association rate with target RNA nor the cleavage rate in vitro. In contrast to this, extension of helix II led to a significantly decreased inhibition of HIV-1 replication in human cells. Together with the finding of others that shortening of helix II to less than two base pairs reduces the catalytic activity in vitro, this observation indicates that the length of helix II in the naturally occurring RNAs with a hammerhead domain is already close or identical to the optimal length for catalytic activity in vitro and in vivo. Images PMID:7524030

Ion Pair Formation between Tertiary Aliphatic Amines and Perchlorate in the Biphasic Water/Dichloromethane System.

PubMed

Badocco, Denis; Di Marco, Valerio; Venzo, Alfonso; Frasconi, Marco; Frezzato, Diego; Pastore, Paolo

2017-10-12

The ability of aliphatic amines (AAs), namely, tripropylamine (TPrA), trisobutylamine (TisoBuA), and tributylamine (TBuA), to form ion pairs with perchlorate anion (ClO 4 - ) in biphasic aqueous/dichloromethane (CH 2 Cl 2 ) mixtures containing ClO 4 - 0.1 M has been demonstrated by GC with flame ionization (FID) and mass detectors (MS) and by NMR measurements. The extraction efficiency of the AAs to the organic phase was modeled by equations that were used to fit the experimental GC data, allowing us to determine values for K P (partition constant of the free AA), K IP (formation constant of the ion pair), and K P IP (partition constant of the ion pair) for TPrA, TisoBuA, and TBuA at 25 °C. Ion pairs were shown to form in CH 2 Cl 2 also when ClO 4 - is replaced by other inorganic anions, like NO 3 - , ClO 3 - , Cl - , H 2 PO 4 - , and IO 3 - . No ion pairs formed when CH 2 Cl 2 was replaced by n-hexane, suggesting that aliphatic amine ion pairs can form in polar organic solvents but not in nonpolar ones.

Design and evaluation of a Dean vortex-based micromixer.

PubMed

Howell, Peter B; Mott, David R; Golden, Joel P; Ligler, Frances S

2004-12-01

A mixer, based on the Dean vortex, is fabricated and tested in an on-chip format. When fluid is directed around a curve under pressure driven flow, the high velocity streams in the center of the channel experience a greater centripetal force and so are deflected outward. This creates a pair of counter-rotating vortices moving fluid toward the inner wall at the top and bottom of the channel and toward the outer wall in the center. For the geometries studied, the vortices were first seen at Reynolds numbers between 1 and 10 and became stronger as the flow velocity is increased. Vortex formation was monitored in channels with depth/width ratios of 0.5, 1.0, and 2.0. The lowest aspect ratio strongly suppressed vortex formation. Increasing the aspect ratio above 1 appeared to provide improved mixing. This design has the advantages of easy fabrication and low surface area.

Analysis of a variety of inorganic and organic additives in food products by ion-pairing liquid chromatography coupled to high-resolution mass spectrometry.

PubMed

Kaufmann, Anton; Widmer, Mirjam; Maden, Kathryn; Butcher, Patrick; Walker, Stephan

2018-03-05

A reversed-phase ion-pairing chromatographic method was developed for the detection and quantification of inorganic and organic anionic food additives. A single-stage high-resolution mass spectrometer (orbitrap ion trap, Orbitrap) was used to detect the accurate masses of the unfragmented analyte ions. The developed ion-pairing chromatography method was based on a dibutylamine/hexafluoro-2-propanol buffer. Dibutylamine can be charged to serve as a chromatographic ion-pairing agent. This ensures sufficient retention of inorganic and organic anions. Yet, unlike quaternary amines, it can be de-charged in the electrospray to prevent the formation of neutral analyte ion-pairing agent adducts. This process is significantly facilitated by the added hexafluoro-2-propanol. This approach permits the sensitive detection and quantification of additives like nitrate and mono-, di-, and triphosphate as well as citric acid, a number of artificial sweeteners like cyclamate and aspartame, flavor enhancers like glutamate, and preservatives like sorbic acid. This is a major advantage, since the currently used analytical methods as utilized in food safety laboratories are only capable in monitoring a few compounds or a particular category of food additives. Graphical abstract Deptotonation of ion pair agent in the electrospray interface.

An unusual mode of DNA duplex association: Watson-Crick interaction of all-purine deoxyribonucleic acids.

PubMed

Battersby, Thomas R; Albalos, Maria; Friesenhahn, Michel J

2007-05-01

Nucleic acid duplexes associating through purine-purine base pairing have been constructed and characterized in a remarkable demonstration of nucleic acids with mixed sequence and a natural backbone in an alternative duplex structure. The antiparallel deoxyribose all-purine duplexes associate specifically through Watson-Crick pairing, violating the nucleobase size-complementarity pairing convention found in Nature. Sequence-specific recognition displayed by these structures makes the duplexes suitable, in principle, for information storage and replication fundamental to molecular evolution in all living organisms. All-purine duplexes can be formed through association of purines found in natural ribonucleosides. Key to the formation of these duplexes is the N(3)-H tautomer of isoguanine, preferred in the duplex, but not in aqueous solution. The duplexes have relevance to evolution of the modern genetic code and can be used for molecular recognition of natural nucleic acids.

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

Kondo, Takeshi; Palczewski, Ari; Hamaya, Yoichiro

We use angle-resolved photoemission spectroscopy and a new quantitative approach based on the partial density of states to study properties of seemingly disconnected portions of the Fermi surface (FS) that are present in the pseudogap state of cuprates called Fermi arcs. We find that the normal state FS collapses very abruptly into Fermi arcs at the pseudogap temperature (T*). Surprisingly, the length of the Fermi arcs remains constant over an extended temperature range between (T*) and T pair, consistent with the presence of an ordered state below T*. These arcs collapse again at the temperature below which pair formation occursmore » (T pair) either to a point or a very short arc, whose length is limited by our experimental resolution. The tips of the arcs span between points defining a set of wave vectors in momentum space, which are the fingerprints of the ordered state that causes the pseudogap.« less

Intracistronic complementation in the simian virus 40 A gene.

PubMed Central

Tornow, J; Cole, C N

1983-01-01

A set of eight simian virus 40 mutants was constructed with lesions in the A gene, which encodes the large tumor (T) antigen. These mutants have small deletions (3-20 base pairs) at either 0.497, 0.288, or 0.243 map units. Mutants having both in-phase and frameshift mutations at each site were isolated. Neither plaque formation nor replication of the mutant DNAs could be detected after transfection of monkey kidney cells. Another nonviable mutant, dlA2459, had a 14-base-pair deletion at 0.193 map unit and was positive for viral DNA replication. Each of the eight mutants were tested for ability to form plaques after cotransfection with dlA2459 DNA. The four mutants that had in-phase deletions were able to complement dlA2459. The other four, which had frameshift deletions, did not. No plaques were formed after cotransfection of cells with any other pair of group A mutants. This suggests that the defect in dlA2459 defines a distinct functional domain of simian virus 40 T antigen. Images PMID:6312452

Dark-bright soliton pairs in nonlocal nonlinear media.

PubMed

Lin, Yuan Yao; Lee, Ray-Kuang

2007-07-09

We study the formation of dark-bright vector soliton pairs in nonlocal Kerr-type nonlinear medium. We show, by analytical analysis and direct numerical calculation, that in addition to stabilize of vector soliton pairs nonlocal nonlinearity also helps to reduce the threshold power for forming a guided bright soliton. With help of the nonlocality, it is expected that the observation of dark-bright vector soliton pairs in experiments becomes more workable.

Mitomycin C-induced pairing of heterochromatin reflects initiation of DNA repair and chromatid exchange formation.

PubMed

Abdel-Halim, H I; Natarajan, A T; Mullenders, L H F; Boei, J J W A

2005-04-15

Chromatid interchanges induced by the DNA cross-linking agent mitomycin C (MMC) are over-represented in human chromosomes containing large heterochromatic regions. We found that nearly all exchange breakpoints of chromosome 9 are located within the paracentromeric heterochromatin and over 70% of exchanges involving chromosome 9 are between its homologues. We provide evidence that the required pairing of chromosome 9 heterochromatic regions occurs in G(0)/G(1) and S-phase cells as a result of an active cellular process initiated upon MMC treatment. By contrast, no pairing was observed for a euchromatic paracentromeric region of the equal-sized chromosome 8. The MMC-induced pairing of chromosome 9 heterochromatin is observed in a subset of cells; its percentage closely mimics the frequency of homologous interchanges found at metaphase. Moreover, the absence of pairing in cells derived from XPF patients correlates with an altered spectrum of MMC-induced exchanges. Together, the data suggest that the heterochromatin-specific pairing following MMC treatment reflects the initiation of DNA cross-link repair and the formation of exchanges.

Interaction of model aryl- and alkyl-boronic acids and 1,2-diols in aqueous solution.

PubMed

Marinaro, William A; Prankerd, Richard; Kinnari, Kaisa; Stella, Valentino J

2015-04-01

The goal of this work was to quantitate ester formation between alkyl and aryl boronic acids and vicinal-diols or 1,2-diols in aqueous solution. As used here, 1,2-diols includes polyols with one or more 1,2-diol pairs. Multiple techniques were used including apparent pKa shifts of the boronic acids using UV spectrophotometry (for aryl acids) and titration (for aryl and alkyl acids). Isothermal microcalorimetry was also used, with all reactions being enthalpically favored. For all the acids and 1,2-diols and the conditions studied, evidence only supported 1:1 ester formation. All the esters formed were found to be significantly more acidic, as Lewis acids, by 3-3.5 pKa units than the corresponding nonesterified boronic acid. The equilibrium constants for ester formation increased with increasing number of 1,2-diol pairs but stereochemistry may also play a role as sorbitol with five possible 1,2-diol pairs and five isomers (taking into account the stereochemistry of the alcohol groups) was twice as efficient at ester formation compared with mannitol, also with five possible 1,2-diol pairs but only three isomers. Alkyl boronic acids formed esters to a greater extent than aryl acids. Although some quantitative differences were seen between the various techniques used, rank ordering of the structure/reactivity was consistent. Formulation implications of ester formation between boronic acids and 1,2-diols are discussed. © 2015 Wiley Periodicals, Inc. and the American Pharmacists Association.

Ion-pair cloud-point extraction: a new method for the determination of water-soluble vitamins in plasma and urine.

PubMed

Heydari, Rouhollah; Elyasi, Najmeh S

2014-10-01

A novel, simple, and effective ion-pair cloud-point extraction coupled with a gradient high-performance liquid chromatography method was developed for determination of thiamine (vitamin B1 ), niacinamide (vitamin B3 ), pyridoxine (vitamin B6 ), and riboflavin (vitamin B2 ) in plasma and urine samples. The extraction and separation of vitamins were achieved based on an ion-pair formation approach between these ionizable analytes and 1-heptanesulfonic acid sodium salt as an ion-pairing agent. Influential variables on the ion-pair cloud-point extraction efficiency, such as the ion-pairing agent concentration, ionic strength, pH, volume of Triton X-100, extraction temperature, and incubation time have been fully evaluated and optimized. Water-soluble vitamins were successfully extracted by 1-heptanesulfonic acid sodium salt (0.2% w/v) as ion-pairing agent with Triton X-100 (4% w/v) as surfactant phase at 50°C for 10 min. The calibration curves showed good linearity (r(2) > 0.9916) and precision in the concentration ranges of 1-50 μg/mL for thiamine and niacinamide, 5-100 μg/mL for pyridoxine, and 0.5-20 μg/mL for riboflavin. The recoveries were in the range of 78.0-88.0% with relative standard deviations ranging from 6.2 to 8.2%. © 2014 WILEY-VCH Verlag GmbH & Co. KGaA, Weinheim.

Milestones and Millennials: A Perfect Pairing-Competency-Based Medical Education and the Learning Preferences of Generation Y.

PubMed

Desy, Janeve R; Reed, Darcy A; Wolanskyj, Alexandra P

2017-02-01

Millennials are quickly becoming the most prevalent generation of medical learners. These individuals have a unique outlook on education and have different preferences and expectations than their predecessors. As evidenced by its implementation by the Accreditation Council for Graduate Medical Education in the United States and the Royal College of Physicians and Surgeons in Canada, competency based medical education is rapidly gaining international acceptance. Characteristics of competency based medical education can be perfectly paired with Millennial educational needs in several dimensions including educational expectations, the educational process, attention to emotional quotient and professionalism, assessment, feedback, and intended outcomes. We propose that with its attention to transparency, personalized learning, and frequent formative assessment, competency based medical education is an ideal fit for the Millennial generation as it realigns education and assessment with the needs of these 21st century learners. Copyright © 2016 Mayo Foundation for Medical Education and Research. Published by Elsevier Inc. All rights reserved.

Massive dominance of Epsilonproteobacteria in formation waters from a Canadian oil sands reservoir containing severely biodegraded oil

PubMed Central

Hubert, Casey R J; Oldenburg, Thomas B P; Fustic, Milovan; Gray, Neil D; Larter, Stephen R; Penn, Kevin; Rowan, Arlene K; Seshadri, Rekha; Sherry, Angela; Swainsbury, Richard; Voordouw, Gerrit; Voordouw, Johanna K; Head, Ian M

2012-01-01

Summary The subsurface microbiology of an Athabasca oil sands reservoir in western Canada containing severely biodegraded oil was investigated by combining 16S rRNA gene- and polar lipid-based analyses of reservoir formation water with geochemical analyses of the crude oil and formation water. Biomass was filtered from formation water, DNA was extracted using two different methods, and 16S rRNA gene fragments were amplified with several different primer pairs prior to cloning and sequencing or community fingerprinting by denaturing gradient gel electrophoresis (DGGE). Similar results were obtained irrespective of the DNA extraction method or primers used. Archaeal libraries were dominated by Methanomicrobiales (410 of 414 total sequences formed a dominant phylotype affiliated with a Methanoregula sp.), consistent with the proposed dominant role of CO2-reducing methanogens in crude oil biodegradation. In two bacterial 16S rRNA clone libraries generated with different primer pairs, > 99% and 100% of the sequences were affiliated with Epsilonproteobacteria (n = 382 and 72 total clones respectively). This massive dominance of Epsilonproteobacteria sequences was again obtained in a third library (99% of sequences; n = 96 clones) using a third universal bacterial primer pair (inosine-341f and 1492r). Sequencing of bands from DGGE profiles and intact polar lipid analyses were in accordance with the bacterial clone library results. Epsilonproteobacterial OTUs were affiliated with Sulfuricurvum, Arcobacter and Sulfurospirillum spp. detected in other oil field habitats. The dominant organism revealed by the bacterial libraries (87% of all sequences) is a close relative of Sulfuricurvum kujiense – an organism capable of oxidizing reduced sulfur compounds in crude oil. Geochemical analysis of organic extracts from bitumen at different reservoir depths down to the oil water transition zone of these oil sands indicated active biodegradation of dibenzothiophenes, and stable sulfur isotope ratios for elemental sulfur and sulfate in formation waters were indicative of anaerobic oxidation of sulfur compounds. Microbial desulfurization of crude oil may be an important metabolism for Epsilonproteobacteria indigenous to oil reservoirs with elevated sulfur content and may explain their prevalence in formation waters from highly biodegraded petroleum systems. PMID:21824242

Structural studies on choline-carboxylate bio-ionic liquids by x-ray scattering and molecular dynamics.

PubMed

Tanzi, Luana; Ramondo, Fabio; Caminiti, Ruggero; Campetella, Marco; Di Luca, Andrea; Gontrani, Lorenzo

2015-09-21

We report a X-ray diffraction and molecular dynamics study on three choline-based bio-ionic liquids, choline formate, [Ch] [For], choline propanoate, [Ch][Pro], and choline butanoate, [Ch][But]. For the first time, this class of ionic liquids has been investigated by X-ray diffraction. Experimental and theoretical structure factors have been compared for each term of the series. Local structural organization has been obtained from ab initio calculations through static models of isolated ion pairs and dynamic simulations of small portions of liquids through twelve, ten, and nine ion pairs for [Ch][For], [Ch][Pro], and [Ch][But], respectively. All the theoretical models indicate that cations and anions are connected by strong hydrogen bonding and form stable ion pairs in the liquid that are reminiscent of the static ab initio ion pairs. Different structural aspects may affect the radial distribution function, like the local structure of ion pairs and the conformation of choline. When small portions of liquids have been simulated by dynamic quantum chemical methods, some key structural features of the X-ray radial distribution function were well reproduced whereas the classical force fields here applied did not entirely reproduce all the observed structural features.

Structural studies on choline-carboxylate bio-ionic liquids by x-ray scattering and molecular dynamics

NASA Astrophysics Data System (ADS)

Tanzi, Luana; Ramondo, Fabio; Caminiti, Ruggero; Campetella, Marco; Di Luca, Andrea; Gontrani, Lorenzo

2015-09-01

We report a X-ray diffraction and molecular dynamics study on three choline-based bio-ionic liquids, choline formate, [Ch] [For], choline propanoate, [Ch][Pro], and choline butanoate, [Ch][But]. For the first time, this class of ionic liquids has been investigated by X-ray diffraction. Experimental and theoretical structure factors have been compared for each term of the series. Local structural organization has been obtained from ab initio calculations through static models of isolated ion pairs and dynamic simulations of small portions of liquids through twelve, ten, and nine ion pairs for [Ch][For], [Ch][Pro], and [Ch][But], respectively. All the theoretical models indicate that cations and anions are connected by strong hydrogen bonding and form stable ion pairs in the liquid that are reminiscent of the static ab initio ion pairs. Different structural aspects may affect the radial distribution function, like the local structure of ion pairs and the conformation of choline. When small portions of liquids have been simulated by dynamic quantum chemical methods, some key structural features of the X-ray radial distribution function were well reproduced whereas the classical force fields here applied did not entirely reproduce all the observed structural features.

Substituent-Modulated Assembly Formation: An Approach to Enhancing the Photostability of Photoelectric-Sensitive Chalcogenide-Based Ion-Pair Hybrids.

PubMed

Lin, Jian; Fu, Zhixing; Zhang, Jiaxu; Zhu, Yujia; Hu, Dandan; Li, Dongsheng; Wu, Tao

2017-03-20

A series of electronically active viologen dications (RV) with tunable substituent groups were utilized to hybridize with [Ge 4 S 10 ] 4- (T2 cluster) to form the hybrids of T2@RV. These hybrids exhibited variable supermolecular assembly formation, tunable optical absorption properties, and different photoelectric response under the influence of different RV dications. Raman testing and time-dependent photocurrent response indicated that the photosensitivity and photostability of T2@RV could be integrated while choosing suitable RV dications. Current research provides a general method to build a tunable hybrid system based on crystalline metal chalcogenide compounds through the replacement of photoinactive cationic organic templates with photoactive ones with different substituent groups.

The importance of formative assessment in science and engineering ethics education: some evidence and practical advice.

PubMed

Keefer, Matthew W; Wilson, Sara E; Dankowicz, Harry; Loui, Michael C

2014-03-01

Recent research in ethics education shows a potentially problematic variation in content, curricular materials, and instruction. While ethics instruction is now widespread, studies have identified significant variation in both the goals and methods of ethics education, leaving researchers to conclude that many approaches may be inappropriately paired with goals that are unachievable. This paper speaks to these concerns by demonstrating the importance of aligning classroom-based assessments to clear ethical learning objectives in order to help students and instructors track their progress toward meeting those objectives. Two studies at two different universities demonstrate the usefulness of classroom-based, formative assessments for improving the quality of students' case responses in computational modeling and research ethics.

Modulation of p-Cyanophenylalanine Fluorescence by Amino Acid Side-chains and Rational Design of Fluorescence Probes of α-Helix Formation

PubMed Central

Taskent-Sezgin, Humeyra; Marek, Peter; Thomas, Rosanne; Goldberg, Daniel; Chung, Juah; Carrico, Isaac; Raleigh, Daniel P.

2011-01-01

p-Cyanophenylalanine is an extremely useful fluorescence probe of protein structure which can be recombinantly and chemically incorporated into proteins. The probe has been used to study protein folding, protein-membrane interactions, protein-peptide interactions and amyloid formation, however the factors that control its fluorescence are not fully understood. Hydrogen bonding to the cyano group is known to play a major role in modulating the fluorescence quantum yield, but the role of potential side-chain quenchers has not yet been elucidated. A systematic study on the effects of different side-chains on p-cyanophenylalanine fluorescence is reported. Tyr is found to have the largest effect followed by deprotonated His, Met, Cys, protonated His, Asn, Arg, and protonated Lys. Deprotonated amino groups are much more effective fluorescence quenchers than protonated amino groups. Free neutral imidazole and hydroxide ion are also effective quenchers of p-cyanophenylalanine fluorescence with Stern-Volmer constants of 39.8 M−1 and 22.1 M−1, respectively. The quenching of p-cyanophenylalanine fluorescence by specific side-chains is exploited to develop specific, high sensitivity, fluorescence probes of helix formation. The approach is demonstrated with Ala based peptides that contain a p-cyanophenylalanine-His or a p-cyanophenylalanine-Tyr pair located at positions i and i+4. The p-cyanophenylalanine-His pair is most useful when the His side-chain is deprotonated and is, thus, complimentary to Trp-His pair which is most sensitive when the His side-chain is protonated. PMID:20565125

Matrix isolation technique for the study of some factors affecting the partitioning of trace elements. [using vibrational spectroscopy

NASA Technical Reports Server (NTRS)

Grzybowski, J. M.; Allen, R. O.

1974-01-01

The factors that affect the preferred positions of cations in ionic solid solutions were investigated utilizing vibrational spectroscopy. Solid solutions of the sulfate and chromate ions codoped with La(+3) and Ca(+2) in a KBr host lattice were examined as a function of the polyvalent cation concentration. The cation-anion pairing process was found to be random for Ca(+2), whereas the formation of La(+3)-SO4(-2) ion pairs with a C2 sub v bonding geometry is highly preferential to any type of La(+3)-CrO4(-2) ion pair formation. The relative populations of ion pair site configurations are discussed in terms of an energy-entropy competition model which can be applied to the partition of trace elements during magmatic processes.

Analyses of interactions among pair-rule genes and the gap gene Krüppel in Bombyx segmentation.

PubMed

Nakao, Hajime

2015-09-01

In the short-germ insect Tribolium, a pair-rule gene circuit consisting of the Tribolium homologs of even-skipped, runt, and odd-skipped (Tc-eve, Tc-run and Tc-odd, respectively) has been implicated in segment formation. To examine the application of the model to other taxa, I studied the expression and function of pair-rule genes in Bombyx mori, together with a Bombyx homolog of Krüppel (Bm-Kr), a known gap gene. Knockdown embryos of Bombyx homologs of eve, run and odd (Bm-eve, Bm-run and Bm-odd) exhibited asegmental phenotypes similar to those of Tribolium knockdowns. However, pair-rule gene interactions were similar to those of both Tribolium and Drosophila, which, different from Tribolium, shows a hierarchical segmentation mode. Additionally, the Bm-odd expression pattern shares characteristics with those of Drosophila pair-rule genes that receive upstream regulatory input. On the other hand, Bm-Kr knockdowns exhibited a large posterior segment deletion as observed in short-germ insects. However, a detailed analysis of these embryos indicated that Bm-Kr modulates expression of pair-rule genes like in Drosophila, although the mechanisms appear to be different. This suggested hierarchical interactions between Bm-Kr and pair-rule genes. Based on these results, I concluded that the pair-rule gene circuit model that describes Tribolium development is not applicable to Bombyx. Copyright © 2015 Elsevier Inc. All rights reserved.

Associative-memory representations emerge as shared spatial patterns of theta activity spanning the primate temporal cortex

PubMed Central

Nakahara, Kiyoshi; Adachi, Ken; Kawasaki, Keisuke; Matsuo, Takeshi; Sawahata, Hirohito; Majima, Kei; Takeda, Masaki; Sugiyama, Sayaka; Nakata, Ryota; Iijima, Atsuhiko; Tanigawa, Hisashi; Suzuki, Takafumi; Kamitani, Yukiyasu; Hasegawa, Isao

2016-01-01

Highly localized neuronal spikes in primate temporal cortex can encode associative memory; however, whether memory formation involves area-wide reorganization of ensemble activity, which often accompanies rhythmicity, or just local microcircuit-level plasticity, remains elusive. Using high-density electrocorticography, we capture local-field potentials spanning the monkey temporal lobes, and show that the visual pair-association (PA) memory is encoded in spatial patterns of theta activity in areas TE, 36, and, partially, in the parahippocampal cortex, but not in the entorhinal cortex. The theta patterns elicited by learned paired associates are distinct between pairs, but similar within pairs. This pattern similarity, emerging through novel PA learning, allows a machine-learning decoder trained on theta patterns elicited by a particular visual item to correctly predict the identity of those elicited by its paired associate. Our results suggest that the formation and sharing of widespread cortical theta patterns via learning-induced reorganization are involved in the mechanisms of associative memory representation. PMID:27282247

A high-throughput platform for population reformatting and mammalian expression of phage display libraries to enable functional screening as full-length IgG.

PubMed

Xiao, Xiaodong; Douthwaite, Julie A; Chen, Yan; Kemp, Ben; Kidd, Sara; Percival-Alwyn, Jennifer; Smith, Alison; Goode, Kate; Swerdlow, Bonnie; Lowe, David; Wu, Herren; Dall'Acqua, William F; Chowdhury, Partha S

Phage display antibody libraries are a rich resource for discovery of potential therapeutic antibodies. Single-chain variable fragment (scFv) libraries are the most common format due to the efficient display of scFv by phage particles and the ease by which soluble scFv antibodies can be expressed for high-throughput screening. Typically, a cascade of screening and triaging activities are performed, beginning with the assessment of large numbers of E. coli-expressed scFv, and progressing through additional assays with individual reformatting of the most promising scFv to full-length IgG. However, use of high-throughput screening of scFv for the discovery of full-length IgG is not ideal because of the differences between these molecules. Furthermore, the reformatting step represents a bottle neck in the process because each antibody has to be handled individually to preserve the unique VH and VL pairing. These problems could be resolved if populations of scFv could be reformatted to full-length IgG before screening without disrupting the variable region pairing. Here, we describe a novel strategy that allows the reformatting of diverse populations of scFv from phage selections to full-length IgG in a batch format. The reformatting process maintains the diversity and variable region pairing with high fidelity, and the resulted IgG pool enables high-throughput expression of IgG in mammalian cells and cell-based functional screening. The improved process led to the discovery of potent candidates that are comparable or better than those obtained by traditional methods. This strategy should also be readily applicable to Fab-based phage libraries. Our approach, Screening in Product Format (SiPF), represents a substantial improvement in the field of antibody discovery using phage display.

Energetics, Ion and Water Binding of the Unfolding of AA/UU Base Pair Stacks and UAU/UAU Base Triplet Stacks in RNA.

PubMed

Carr, Carolyn E; Khutsishvili, Irine; Marky, Luis A

2018-06-22

Triplex formation occurs via interaction of a third strand with the major groove of double stranded nucleic acid, through Hoogsteen hydrogen bonding. In this work, we use a combination of temperature-dependent UV spectroscopy and differential scanning calorimetry to determine complete thermodynamic profiles for the unfolding of poly(rA)•poly(rU) (Duplex) and poly(rA)•2poly(rU) (Triplex). Our thermodynamic results are in good agreement with the much earlier work of Krakauer and Sturtevant using only UV melting techniques. The folding of these two helices yielded an uptake of ions, ΔnNa+ = 0.15 mol Na+/mol base-pair (Duplex) and 0.30 mol Na+/mole base-triplet (Triplex), which are consistent with their polymer behavior and the higher charge density parameter of triple helices. The osmotic stress technique yielded a release of structural water, ΔnW = 2 mol H2O/mol base-pair (Duplex unfolding into single strands) and an uptake of structural water, ΔnW = 2 mol H2O/mole base-pair (Triplex unfolding into Duplex and a single strand). However, an overall release of electrostricted waters is obtained for the unfolding of both complexes from pressure perturbation calorimetric experiments. In total, the ΔV values obtained for the unfolding of Triplex into Duplex and a single strand correspond to an immobilization of two structural waters and a release of three electrostricted waters. The ΔV values obtained for the unfolding of Duplex into two single strands correspond to the release of two structural waters and the immobilization of four electrostricted water molecules.

Students' satisfaction to hybrid problem-based learning format for basic life support/advanced cardiac life support teaching.

PubMed

Chilkoti, Geetanjali; Mohta, Medha; Wadhwa, Rachna; Saxena, Ashok Kumar; Sharma, Chhavi Sarabpreet; Shankar, Neelima

2016-11-01

Students are exposed to basic life support (BLS) and advanced cardiac life support (ACLS) training in the first semester in some medical colleges. The aim of this study was to compare students' satisfaction between lecture-based traditional method and hybrid problem-based learning (PBL) in BLS/ACLS teaching to undergraduate medical students. We conducted a questionnaire-based, cross-sectional survey among 118 1 st -year medical students from a university medical college in the city of New Delhi, India. We aimed to assess the students' satisfaction between lecture-based and hybrid-PBL method in BLS/ACLS teaching. Likert 5-point scale was used to assess students' satisfaction levels between the two teaching methods. Data were collected and scores regarding the students' satisfaction levels between these two teaching methods were analysed using a two-sided paired t -test. Most students preferred hybrid-PBL format over traditional lecture-based method in the following four aspects; learning and understanding, interest and motivation, training of personal abilities and being confident and satisfied with the teaching method ( P < 0.05). Implementation of hybrid-PBL format along with the lecture-based method in BLS/ACLS teaching provided high satisfaction among undergraduate medical students.

Stabilised DNA secondary structures with increasing transcription localise hypermutable bases for somatic hypermutation in IGHV3-23.

PubMed

Duvvuri, Bhargavi; Duvvuri, Venkata R; Wu, Jianhong; Wu, Gillian E

2012-07-01

Somatic hypermutation (SHM) mediated by activation-induced cytidine deaminase (AID) is a transcription-coupled mechanism most responsible for generating high affinity antibodies. An issue remaining enigmatic in SHM is how AID is preferentially targeted during transcription to hypermutable bases in its substrates (WRC motifs) on both DNA strands. AID targets only single stranded DNA. By modelling the dynamical behaviour of IGHV3-23 DNA, a commonly used human variable gene segment, we observed that hypermutable bases on the non-transcribed strand are paired whereas those on transcribed strand are mostly unpaired. Hypermutable bases (both paired and unpaired) are made accessible to AID in stabilised secondary structures formed with increasing transcription levels. This observation provides a rationale for the hypermutable bases on both the strands of DNA being targeted to a similar extent despite having differences in unpairedness. We propose that increasing transcription and RNAP II stalling resulting in the formation and stabilisation of stem-loop structures with AID hotspots in negatively supercoiled region can localise the hypermutable bases of both strands of DNA, to AID-mediated SHM.

Search and Characterization of Optical Ceramics and Crystals for Diode-pumped Laser Oscillations

DTIC Science & Technology

2013-04-01

results in a lower oscillation efficiency due to a strong loss of excitation energy during fast nonradiative interactions in Nd-Nd pairs than...associated nonradiative losses due to the formation of unquenched Nd-La pairs. To ensure that Nd-La pairs predominate in a SrF2-LaF3 solid solution, a

Stereoselective virtual screening of the ZINC database using atom pair 3D-fingerprints.

PubMed

Awale, Mahendra; Jin, Xian; Reymond, Jean-Louis

2015-01-01

Tools to explore large compound databases in search for analogs of query molecules provide a strategically important support in drug discovery to help identify available analogs of any given reference or hit compound by ligand based virtual screening (LBVS). We recently showed that large databases can be formatted for very fast searching with various 2D-fingerprints using the city-block distance as similarity measure, in particular a 2D-atom pair fingerprint (APfp) and the related category extended atom pair fingerprint (Xfp) which efficiently encode molecular shape and pharmacophores, but do not perceive stereochemistry. Here we investigated related 3D-atom pair fingerprints to enable rapid stereoselective searches in the ZINC database (23.2 million 3D structures). Molecular fingerprints counting atom pairs at increasing through-space distance intervals were designed using either all atoms (16-bit 3DAPfp) or different atom categories (80-bit 3DXfp). These 3D-fingerprints retrieved molecular shape and pharmacophore analogs (defined by OpenEye ROCS scoring functions) of 110,000 compounds from the Cambridge Structural Database with equal or better accuracy than the 2D-fingerprints APfp and Xfp, and showed comparable performance in recovering actives from decoys in the DUD database. LBVS by 3DXfp or 3DAPfp similarity was stereoselective and gave very different analogs when starting from different diastereomers of the same chiral drug. Results were also different from LBVS with the parent 2D-fingerprints Xfp or APfp. 3D- and 2D-fingerprints also gave very different results in LBVS of folded molecules where through-space distances between atom pairs are much shorter than topological distances. 3DAPfp and 3DXfp are suitable for stereoselective searches for shape and pharmacophore analogs of query molecules in large databases. Web-browsers for searching ZINC by 3DAPfp and 3DXfp similarity are accessible at www.gdb.unibe.ch and should provide useful assistance to drug discovery projects. Graphical abstractAtom pair fingerprints based on through-space distances (3DAPfp) provide better shape encoding than atom pair fingerprints based on topological distances (APfp) as measured by the recovery of ROCS shape analogs by fp similarity.

Ab initio calculation of atomic interactions on Al(110): implications for epitaxial growth

NASA Astrophysics Data System (ADS)

Fichthorn, Kristen; Tiwary, Yogesh

2007-03-01

Using first-principles calculations based on density-functional theory, we resolved atomic interactions between adsorbed Al atoms on Al(110). Relevant pair and trio interactions were quantified. We find that pair interactions extend to the third in-channel and second cross-channel neighbor on the anisotropic (110) surface. Beyond these distances, pair interactions are negligible. The nearest-neighbor interaction in the in-channel direction is attractive, but nearest-neighbor cross-channel interaction is repulsive. While nearest-neighbor, cross-channel repulsion does not support the experimental observation of 3D hut formation in Al/Al(110) homoepitaxial growth [1], we find that trio interactions can be significant and attractive and they support cross-channel bonding. The pair and trio interactions have direct and indirect components. We have quantified the electronic and elastic components of the indirect, substrate-mediated interactions. We also probe the influence of these interactions on the energy barriers for adatom hopping. [1] F. Buatier de Mongeot, W. Zhu, A. Molle, R. Buzio, C. Boragno, U. Valbusa, E. Wang, and Z. Zhang, Phys. Rev. Lett. 91, 016102 (2003).

Nonlinear structure formation in ion-temperature-gradient driven drift waves in pair-ion plasma with nonthermal electron distribution

NASA Astrophysics Data System (ADS)

Razzaq, Javaria; Haque, Q.; Khan, Majid; Bhatti, Adnan Mehmood; Kamran, M.; Mirza, Arshad M.

2018-02-01

Nonlinear structure formation in ion-temperature-gradient (ITG) driven waves is investigated in pair-ion plasma comprising ions and nonthermal electrons (kappa, Cairns). By using the transport equations of the Braginskii model, a new set of nonlinear equations are derived. A linear dispersion relation is obtained and discussed analytically as well as numerically. It is shown that the nonthermal population of electrons affects both the linear and nonlinear characteristics of the ITG mode in pair-ion plasma. This work will be useful in tokamaks and stellarators where non-Maxwellian population of electrons may exist due to resonant frequency heating, electron cyclotron heating, runaway electrons, etc.

Influence of Glu/Arg, Asp/Arg, and Glu/Lys Salt Bridges on α-Helical Stability and Folding Kinetics.

PubMed

Meuzelaar, Heleen; Vreede, Jocelyne; Woutersen, Sander

2016-06-07

Using a combination of ultraviolet circular dichroism, temperature-jump transient-infrared spectroscopy, and molecular dynamics simulations, we investigate the effect of salt bridges between different types of charged amino-acid residue pairs on α-helix folding. We determine the stability and the folding and unfolding rates of 12 alanine-based α-helical peptides, each of which has a nearly identical composition containing three pairs of positively and negatively charged residues (either Glu(-)/Arg(+), Asp(-)/Arg(+), or Glu(-)/Lys(+)). Within each set of peptides, the distance and order of the oppositely charged residues in the peptide sequence differ, such that they have different capabilities of forming salt bridges. Our results indicate that stabilizing salt bridges (in which the interacting residues are spaced and ordered such that they favor helix formation) speed up α-helix formation by up to 50% and slow down the unfolding of the α-helix, whereas salt bridges with an unfavorable geometry have the opposite effect. Comparing the peptides with different types of charge pairs, we observe that salt bridges between side chains of Glu(-) and Arg(+) are most favorable for the speed of folding, probably because of the larger conformational space of the salt-bridging Glu(-)/Arg(+) rotamer pairs compared to Asp(-)/Arg(+) and Glu(-)/Lys(+). We speculate that the observed impact of salt bridges on the folding kinetics might explain why some proteins contain salt bridges that do not stabilize the final, folded conformation. Copyright © 2016 Biophysical Society. Published by Elsevier Inc. All rights reserved.

Dependence of Ion Transport on the Electronegativity of the Constituting Atoms in Ionic Crystals.

PubMed

Zhang, Qian; Kaghazchi, Payam

2017-04-19

Ion transport in electrode and electrolyte materials is a key process in Li-based batteries. In this work, we study the mechanism and activation energy of ion transport (Ea ) in rock-salt Li-based LiX (X=Cl, Br, and I) materials. It is found that Ea at low external voltages, where Li-X Schottky pairs are the most favorable defect types, is about 0.42 times the Gibbs energy of formation of LiX compound (ΔGf ). The value of 0.42 is the slope of the electronegativity of anions of binary Li-based materials as a function of ΔGf . At high voltages, where the Fermi level is located very close to the valence band maximum (VBM), electrons can be excited from the VB to Li vacancy-induced states close to the Fermi level. Under this condition, the formation of Li vacancies that are compensated by holes is energetically more favorable than that of Li-X Schottky pairs, and therefore, the activation energies are lower in the former case. The wide range of reported experimental values of activation energies lies between calculated values at low and high voltage regimes. This work motivates further studies on the relation between the activation energy for ionic conductivity in solid materials and the intrinsic ground-state properties of their free atoms. © 2017 Wiley-VCH Verlag GmbH & Co. KGaA, Weinheim.

Enhanced pair plasma generation in the relativistic transparency regime

NASA Astrophysics Data System (ADS)

Liu, W. Y.; Luo, W.; Yuan, T.; Yu, J. Y.; Chen, M.; Sheng, Z. M.

2017-10-01

Electron-positron ( e - e + ) pair plasma generation in the relativistic transparency regime in a thin foil with a fixed thickness irradiated by two counter-propagating laser pulses is investigated through multi-dimensional particle-in-cell simulations. It is shown that target transparency can significantly enhance the pair generation due to the formation of a stable standing wave. An optimum foil density of 200-280 n c (with nc being the critical plasma density of the incident laser at the wavelength of 1 μm) is found for enhanced e - e + pair generation for laser intensity around 10 PW. With such foil density, laser energy transformed to pair plasma formation is approximately four times higher than that with a foil density of 710 nc, while the laser energy transformed to γ-photons remains almost the same. Dense e - e + plasma with a density as high as 10 22 cm - 3 ( ≃ 10 n c ) can be produced accordingly. Comparison of pair plasma generation between cases with fundamental and double frequency driver lasers further demonstrates such an enhancement effect. It shows that when the duration of the laser pulse is relatively short, the double frequency driver can generate more pair plasmas due to the earlier excitation of relativistic transparency.

What triggers starbursts in dwarf galaxies?

NASA Astrophysics Data System (ADS)

Johnson, Kelsey

While the processes regulating star formation and the interstellar medium in massive interacting galaxies have been studied extensively, the extent to which these processes occur in the shallower gravitational potential wells of lower mass dwarf galaxies is relatively unconstrained. While dwarf galaxies are known to undergo starbursts (Heckman et al. 1998; Johnson et al. 2000), the origins of these bursts remain unclear, and interactions and mergers with other dwarfs have not been ruled out (Lelli et al. 2012; Koleva et al. 2014). These gas-rich dwarf galaxies in the nearby universe are expected to offer glimpses of star formation modes at high redshift with their low metal content and large amounts of fuel for forming stars. Given that dwarf-dwarf mergers dominate the merger rate at any given redshift (i.e. De Lucia et al. 2006; Fakhouri et al. 2010), this lack of observational constraints leaves a significant mode of galaxy evolution in the universe mostly unexplored. While a few individual dwarf mergers/pairs have been observed (e.g., Henize 2-10: Reines et al. 2012; NGC4490: Clemens et al. 1998; NGC3448: Noreau & Kronberg 1986; IIZw40: Lequeux et al. 1980), a systematic study of the star formation histories of interacting dwarfs as a population has never been done. We propose to obtain and further process near- and far-ultraviolet (NUV/FUV), nearinfrared (NIR), and mid-infrared (MIR) imaging for a sample of 58 dwarf galaxy pairs (116 dwarfs) and 348 unpaired dwarfs (analogs matched in stellar mass, redshift, and local density enhancement) using the NASA archives for the Galaxy Evolution Explorer (GALEX; Martin et al. 2003), the Two Micron All Sky Survey (2MASS; Skrutskie et al. 2006), and the Wide-Field Infrared Survey Explorer (WISE; Wright et al. 2010) missions. We aim to characterize the impact interactions have on fueling star formation in the nearby universe for a complete sample of dwarf galaxy pairs caught in a variety of interaction stages from the TiNy Titans Survey. The archival UV observations will first allow us to determine the presence of stellar bridges and tidal tails and whether dwarf-dwarf interactions alone can trigger significant levels of star formation and/or remove stars from their host galaxies. We will then use the UV and IR photometry to place age constraints on the stellar populations and to determine stellar mass surface densities, ages, and host galaxy stellar mass as a function of pair separation and dwarf-dwarf mass ratio. We will distinguish tidally triggered star formation from star formation derived from stochastic processes by taking advantage of the wealth of observations available in all three archives for "normal" non-interacting dwarfs that we have carefully selected to be analogs to our paired dwarfs (matched in stellar mass, redshift, and environment) and by comparing the stellar populations of those dwarfs with the interacting dwarfs in our sample. Ultimately, we can combine the UV and IR imaging from this proposal with ground-based optical photometry from our current, ongoing program to model the star formation histories of these dwarfs as part of a larger, multi-wavelength effort to understand the role low-mass mergers play in galaxy evolution. This study will thus characterize evidence for the hierarchical evolution of dwarf galaxies as well as the extent of pre-processing (i.e., dwarf-dwarf interactions occurring before the accretion by a massive host) that occurs.

Synthesis and monitored selection of nucleotide surrogates for binding T:A base pairs in homopurine-homopyrimidine DNA triple helices.

PubMed

Mokhir, A A; Connors, W H; Richert, C

2001-09-01

A total of 16 oligodeoxyribonucleotides of general sequence 5'-TCTTCTZTCTTTCT-3', where Z denotes an N-acyl-N-(2-hydroxyethyl)glycine residue, were prepared via solid phase synthesis. The ability of these oligonucleotides to form triplexes with the duplex 5'-AGAAGATAGAAAGA-HEG-TCTTTCTATCTTCT-3', where HEG is a hexaethylene glycol linker, was tested. In these triplexes, an 'interrupting' T:A base pair faces the Z residue in the third strand. Among the acyl moieties of Z tested, an anthraquinone carboxylic acid residue linked via a glycinyl group gave the most stable triplex, whose UV melting point was 8.4 degrees C higher than that of the triplex with 5'-TCTTCTGTCTTTCT-3' as the third strand. The results from exploratory nuclease selection experiments suggest that a combinatorial search for strands capable of recognizing mixed sequences by triple helix formation is feasible.

Immunoglobulin domain interface exchange as a platform technology for the generation of Fc heterodimers and bispecific antibodies.

PubMed

Skegro, Darko; Stutz, Cian; Ollier, Romain; Svensson, Emelie; Wassmann, Paul; Bourquin, Florence; Monney, Thierry; Gn, Sunitha; Blein, Stanislas

2017-06-09

Bispecific antibodies (bsAbs) are of significant importance to the development of novel antibody-based therapies, and heavy chain (Hc) heterodimers represent a major class of bispecific drug candidates. Current technologies for the generation of Hc heterodimers are suboptimal and often suffer from contamination by homodimers posing purification challenges. Here, we introduce a new technology based on biomimicry wherein the protein-protein interfaces of two different immunoglobulin (Ig) constant domain pairs are exchanged in part or fully to design new heterodimeric domains. The method can be applied across Igs to design Fc heterodimers and bsAbs. We investigated interfaces from human IgA CH3, IgD CH3, IgG1 CH3, IgM CH4, T-cell receptor (TCR) α/β, and TCR γ/δ constant domain pairs, and we found that they successfully drive human IgG1 CH3 or IgM CH4 heterodimerization to levels similar to or above those of reference methods. A comprehensive interface exchange between the TCR α/β constant domain pair and the IgG1 CH3 homodimer was evidenced by X-ray crystallography and used to engineer examples of bsAbs for cancer therapy. Parental antibody pairs were rapidly reformatted into scalable bsAbs that were free of homodimer traces by combining interface exchange, asymmetric Protein A binding, and the scFv × Fab format. In summary, we successfully built several new CH3- or CH4-based heterodimers that may prove useful for designing new bsAb-based therapeutics, and we anticipate that our approach could be broadly implemented across the Ig constant domain family. To our knowledge, CH4-based heterodimers have not been previously reported. © 2017 by The American Society for Biochemistry and Molecular Biology, Inc.

Prediction of terrestrial gamma dose rate based on geological formations and soil types in the Johor State, Malaysia.

PubMed

Saleh, Muneer Aziz; Ramli, Ahmad Termizi; bin Hamzah, Khaidzir; Alajerami, Yasser; Moharib, Mohammed; Saeed, Ismael

2015-10-01

This study aims to predict and estimate unmeasured terrestrial gamma dose rate (TGDR) using statistical analysis methods to derive a model from the actual measurement based on geological formation and soil type. The measurements of TGDR were conducted in the state of Johor with a total of 3873 measured points which covered all geological formations, soil types and districts. The measurements were taken 1 m above the soil surface using NaI [Ti] detector. The measured gamma dose rates ranged from 9 nGy h(-1) to 1237 nGy h(-1) with a mean value of 151 nGy h(-1). The data have been normalized to fit a normal distribution. Tests of significance were conducted among all geological formations and soil types, using the unbalanced one way ANOVA. The results indicated strong significant differences due to the different geological formations and soil types present in Johor State. Pearson Correlation was used to measure the relations between gamma dose rate based on geological formation and soil type (D(G,S)) with the gamma dose rate based on geological formation (D(G)) or soil type (D(s)). A very good correlation was found between D(G,S) and D(G) or D(G,S) and D(s). A total of 118 pairs of geological formations and soil types were used to derive the statistical contribution of geological formations and soil types to gamma dose rates. The contribution of the gamma dose rate from geological formation and soil type were found to be 0.594 and 0.399, respectively. The null hypotheses were accepted for 83% of examined data, therefore, the model could be used to predict gamma dose rates based on geological formation and soil type information. Copyright © 2015 Elsevier Ltd. All rights reserved.

The impact of motivation on race-based impression formation.

PubMed

Li, Tianyi; Cardenas-Iniguez, Carlos; Correll, Joshua; Cloutier, Jasmin

2016-01-01

Affective biases toward racial out-group members, characterized by White perceivers' negative evaluations of Black individuals, prevail in U.S. culture. Such affective associations have been found to guide race-based impression formation. Accordingly, individuals may strive to resolve inconsistencies when perceiving targets violating their expectations. The current study focuses on the impact of evaluative incongruence on the activity of the dorsomedial prefrontal cortex (dmPFC) - a brain region previously shown to support impression formation. When asking participants to form impressions of positively and negatively evaluated Black and White individuals, we found preferential dmPFC activity in response to individuals paired with information that violates race-based affective associations. Importantly, individual differences in internal motivation to respond without prejudice (IMS) were found to shape the extent to which dmPFC activity indexes the interactive effects of race and affective associations during impression formation. Specifically, preferential dmPFC activity in response to evaluatively incongruent targets (i.e., Black-positive & White-negative) was present among participants with lower, but not those with higher, levels of IMS. Implications and future directions are discussed in the context of dmPFC involvement in social cognition. Copyright © 2015 Elsevier Inc. All rights reserved.

The coupling between stability and ion pair formation in magnesium electrolytes from first-principles quantum mechanics and classical molecular dynamics

DOE PAGES

Rajput, Nav Nidhi; Qu, Xiaohuui; Sa, Niya; ...

2015-02-10

Here in this work we uncover a novel effect between concentration dependent ion pair formation and anion stability at reducing potentials, e.g., at the metal anode. Through comprehensive calculations using both first-principles as well as well-benchmarked classical molecular dynamics over a matrix of electrolytes, covering solvents and salt anions with a broad range in chemistry, we elucidate systematic correlations between molecular level interactions and composite electrolyte properties, such as electrochemical stability, solvation structure, and dynamics. We find that Mg electrolytes are highly prone to ion pair formation, even at modest concentrations, for a wide range of solvents with different dielectricmore » constants, which have implications for dynamics as well as charge transfer. Specifically, we observe that, at Mg metal potentials, the ion pair undergoes partial reduction at the Mg cation center (Mg 2+ -> Mg +), which competes with the charge transfer mechanism and can activate the anion to render it susceptible to decomposition. Specifically, TFSI exhibits a significant bond weakening while paired with the transient, partially reduced Mg +. In contrast, BH 4 $-$ and BF 4 $-$ are shown to be chemically stable in a reduced ion pair configuration. Furthermore, we observe that higher order glymes as well as DMSO improve the solubility of Mg salts, but only the longer glyme chains reduce the dynamics of the ions in solution. This information provides critical design metrics for future electrolytes as it elucidates a close connection between bulk solvation and cathodic stability as well as the dynamics of the salt.« less

Exact calculation of loop formation probability identifies folding motifs in RNA secondary structures.

PubMed

Sloma, Michael F; Mathews, David H

2016-12-01

RNA secondary structure prediction is widely used to analyze RNA sequences. In an RNA partition function calculation, free energy nearest neighbor parameters are used in a dynamic programming algorithm to estimate statistical properties of the secondary structure ensemble. Previously, partition functions have largely been used to estimate the probability that a given pair of nucleotides form a base pair, the conditional stacking probability, the accessibility to binding of a continuous stretch of nucleotides, or a representative sample of RNA structures. Here it is demonstrated that an RNA partition function can also be used to calculate the exact probability of formation of hairpin loops, internal loops, bulge loops, or multibranch loops at a given position. This calculation can also be used to estimate the probability of formation of specific helices. Benchmarking on a set of RNA sequences with known secondary structures indicated that loops that were calculated to be more probable were more likely to be present in the known structure than less probable loops. Furthermore, highly probable loops are more likely to be in the known structure than the set of loops predicted in the lowest free energy structures. © 2016 Sloma and Mathews; Published by Cold Spring Harbor Laboratory Press for the RNA Society.

Electronic and optical properties of Cu2XSnS4 (X = Be, Mg, Ca, Mn, Fe, and Ni) and the impact of native defect pairs

NASA Astrophysics Data System (ADS)

Chen, Rongzhen; Persson, Clas

2017-05-01

Reducing or controlling cation disorder in Cu2ZnSnS4 is a major challenge, mainly due to low formation energies of the anti-site pair ( CuZn - + ZnCu +) and the compensated Cu vacancy ( VCu - + ZnCu +). We study the electronic and optical properties of Cu2XSnS4 (CXTS, with X = Be, Mg, Ca, Mn, Fe, and Ni) and the impact of defect pairs, by employing the first-principles method within the density functional theory. The calculations indicate that these compounds can be grown in either the kesterite or stannite tetragonal phase, except Cu2CaSnS4 which seems to be unstable also in its trigonal phase. In the tetragonal phase, all six compounds have rather similar electronic band structures, suitable band-gap energies Eg for photovoltaic applications, as well as good absorption coefficients α(ω). However, the formation of the defect pairs ( C u X + X Cu) and ( V Cu + X Cu) is an issue for these compounds, especially considering the anti-site pair which has formation energy in the order of ˜0.3 eV. The ( C u X + X Cu) pair narrows the energy gap by typically ΔEg ≈ 0.1-0.3 eV, but for Cu2NiSnS4, the complex yields localized in-gap states. Due to the low formation energy of ( C u X + X Cu), we conclude that it is difficult to avoid disordering from the high concentration of anti-site pairs. The defect concentration in Cu2BeSnS4 is however expected to be significantly lower (as much as ˜104 times at typical device operating temperature) compared to the other compounds, which is partly explained by larger relaxation effects in Cu2BeSnS4 as the two anti-site atoms have different sizes. The disadvantage is that the stronger relaxation has a stronger impact on the band-gap narrowing. Therefore, instead of trying to reduce the anti-site pairs, we suggest that one shall try to compensate ( C u X + X Cu) with ( V Cu + X Cu) or other defects in order to stabilize the gap energy.

Sequence specificity, statistical potentials, and three-dimensional structure prediction with self-correcting distance geometry calculations of beta-sheet formation in proteins.

PubMed Central

Zhu, H.; Braun, W.

1999-01-01

A statistical analysis of a representative data set of 169 known protein structures was used to analyze the specificity of residue interactions between spatial neighboring strands in beta-sheets. Pairwise potentials were derived from the frequency of residue pairs in nearest contact, second nearest and third nearest contacts across neighboring beta-strands compared to the expected frequency of residue pairs in a random model. A pseudo-energy function based on these statistical pairwise potentials recognized native beta-sheets among possible alternative pairings. The native pairing was found within the three lowest energies in 73% of the cases in the training data set and in 63% of beta-sheets in a test data set of 67 proteins, which were not part of the training set. The energy function was also used to detect tripeptides, which occur frequently in beta-sheets of native proteins. The majority of native partners of tripeptides were distributed in a low energy range. Self-correcting distance geometry (SECODG) calculations using distance constraints sets derived from possible low energy pairing of beta-strands uniquely identified the native pairing of the beta-sheet in pancreatic trypsin inhibitor (BPTI). These results will be useful for predicting the structure of proteins from their amino acid sequence as well as for the design of proteins containing beta-sheets. PMID:10048326

Structure and stability of hexa-aqua V(III) cations in vanadium redox flow battery electrolytes.

PubMed

Vijayakumar, M; Li, Liyu; Nie, Zimin; Yang, Zhenguo; Hu, JianZhi

2012-08-07

The vanadium(III) cation structure in mixed acid based electrolyte solution from vanadium redox flow batteries is studied by (17)O and (35/37)Cl nuclear magnetic resonance (NMR) spectroscopy, electronic spectroscopy and density functional theory (DFT) based computational modelling. Both computational and experimental results reveal that the V(III) species can complex with counter anions (sulfate/chlorine) depending on the composition of its solvation sphere. By analyzing the powder precipitate it was found that the formation of sulfate complexed V(III) species is the crucial process in the precipitation reaction. The precipitation occurs through nucleation of neutral species formed through deprotonation and ion-pair formation process. However, the powder precipitate shows a multiphase nature which warrants multiple reaction pathways for precipitation reaction.

Quantum memory receiver for superadditive communication using binary coherent states

NASA Astrophysics Data System (ADS)

Klimek, Aleksandra; Jachura, Michał; Wasilewski, Wojciech; Banaszek, Konrad

2016-11-01

We propose a simple architecture based on multimode quantum memories for collective readout of classical information keyed using a pair coherent states, exemplified by the well-known binary phase shift keying format. Such a configuration enables demonstration of the superadditivity effect in classical communication over quantum channels, where the transmission rate becomes enhanced through joint detection applied to multiple channel uses. The proposed scheme relies on the recently introduced idea to prepare Hadamard sequences of input symbols that are mapped by a linear optical transformation onto the pulse position modulation format [Guha, S. Phys. Rev. Lett. 2011, 106, 240502]. We analyze two versions of readout based on direct detection and an optional Dolinar receiver which implements the minimum-error measurement for individual detection of a binary coherent state alphabet.

Quantum memory receiver for superadditive communication using binary coherent states.

PubMed

Klimek, Aleksandra; Jachura, Michał; Wasilewski, Wojciech; Banaszek, Konrad

2016-11-12

We propose a simple architecture based on multimode quantum memories for collective readout of classical information keyed using a pair coherent states, exemplified by the well-known binary phase shift keying format. Such a configuration enables demonstration of the superadditivity effect in classical communication over quantum channels, where the transmission rate becomes enhanced through joint detection applied to multiple channel uses. The proposed scheme relies on the recently introduced idea to prepare Hadamard sequences of input symbols that are mapped by a linear optical transformation onto the pulse position modulation format [Guha, S. Phys. Rev. Lett. 2011 , 106 , 240502]. We analyze two versions of readout based on direct detection and an optional Dolinar receiver which implements the minimum-error measurement for individual detection of a binary coherent state alphabet.

Assortative Mating: Encounter-Network Topology and the Evolution of Attractiveness

PubMed Central

Dipple, S.; Jia, T.; Caraco, T.; Korniss, G.; Szymanski, B. K.

2017-01-01

We model a social-encounter network where linked nodes match for reproduction in a manner depending probabilistically on each node’s attractiveness. The developed model reveals that increasing either the network’s mean degree or the “choosiness” exercised during pair formation increases the strength of positive assortative mating. That is, we note that attractiveness is correlated among mated nodes. Their total number also increases with mean degree and selectivity during pair formation. By iterating over the model’s mapping of parents onto offspring across generations, we study the evolution of attractiveness. Selection mediated by exclusion from reproduction increases mean attractiveness, but is rapidly balanced by skew in the offspring distribution of highly attractive mated pairs. PMID:28345625

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

Otto, C., Thomas, G.A.; Peticolas, W.L.; Rippe, K.

Raman spectra of the parallel-stranded duplex formed from the deoxyoligonucleotides 5{prime}-d-((A){sub 10}TAATTTTAAATATTT)-3{prime} (D1) and 5{prime}-d((T){sub 10}ATTAAAATTTATAAA)-3{prime} (D2) in H{sub 2}O and D{sub 2}O have been acquired. The spectra of the parallel-stranded DNA are then compared to the spectra of the antiparallel double helix formed from the deoxyoligonucleotides D1 and 5{prime}-d(AAATATTTAAAATTA-(T){sub 10})-3{prime} (D3). The Raman spectra of the antiparallel-stranded (aps) duplex are reminiscent of the spectra of poly(d(A)){center dot}poly(d(T)) and a B-form structure similar to that adopted by the homopolymer duplex is assigned to the antiparallel double helix. The spectra of the parallel-stranded (ps) and antiparallel-stranded duplexes differ significantly due tomore » changes in helical organization, i.e., base pairing, base stacking, and backbone conformation. Large changes observed in the carbonyl stretching region implicate the involvement of the C(2) carbonyl of thymine in base pairing. The interaction of adenine with the C(2) carbonyl of thymine is consistent with formation of reverse Watson-Crick base pairing in parallel-stranded DNA. Phosphate-furanose vibrations similar to those observed for B-form DNA of heterogeneous sequence and high A,T content are observed at 843 and 1,092 cm{sup {minus}1} in the spectra of the parallel-stranded duplex.« less

An Integrated Vision-Based System for Spacecraft Attitude and Topology Determination for Formation Flight Missions

NASA Technical Reports Server (NTRS)

Rogers, Aaron; Anderson, Kalle; Mracek, Anna; Zenick, Ray

2004-01-01

With the space industry's increasing focus upon multi-spacecraft formation flight missions, the ability to precisely determine system topology and the orientation of member spacecraft relative to both inertial space and each other is becoming a critical design requirement. Topology determination in satellite systems has traditionally made use of GPS or ground uplink position data for low Earth orbits, or, alternatively, inter-satellite ranging between all formation pairs. While these techniques work, they are not ideal for extension to interplanetary missions or to large fleets of decentralized, mixed-function spacecraft. The Vision-Based Attitude and Formation Determination System (VBAFDS) represents a novel solution to both the navigation and topology determination problems with an integrated approach that combines a miniature star tracker with a suite of robust processing algorithms. By combining a single range measurement with vision data to resolve complete system topology, the VBAFDS design represents a simple, resource-efficient solution that is not constrained to certain Earth orbits or formation geometries. In this paper, analysis and design of the VBAFDS integrated guidance, navigation and control (GN&C) technology will be discussed, including hardware requirements, algorithm development, and simulation results in the context of potential mission applications.

Structural studies on choline-carboxylate bio-ionic liquids by x-ray scattering and molecular dynamics

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

Tanzi, Luana; Ramondo, Fabio, E-mail: fabio.ramondo@univaq.it; Caminiti, Ruggero

2015-09-21

We report a X-ray diffraction and molecular dynamics study on three choline-based bio-ionic liquids, choline formate, [Ch] [For], choline propanoate, [Ch][Pro], and choline butanoate, [Ch][But]. For the first time, this class of ionic liquids has been investigated by X-ray diffraction. Experimental and theoretical structure factors have been compared for each term of the series. Local structural organization has been obtained from ab initio calculations through static models of isolated ion pairs and dynamic simulations of small portions of liquids through twelve, ten, and nine ion pairs for [Ch][For], [Ch][Pro], and [Ch][But], respectively. All the theoretical models indicate that cations andmore » anions are connected by strong hydrogen bonding and form stable ion pairs in the liquid that are reminiscent of the static ab initio ion pairs. Different structural aspects may affect the radial distribution function, like the local structure of ion pairs and the conformation of choline. When small portions of liquids have been simulated by dynamic quantum chemical methods, some key structural features of the X-ray radial distribution function were well reproduced whereas the classical force fields here applied did not entirely reproduce all the observed structural features.« less

Completion of biosynthetic pathways for bacteriochlorophyll g in Heliobacterium modesticaldum: The C8-ethylidene group formation.

PubMed

Tsukatani, Yusuke; Yamamoto, Haruki; Mizoguchi, Tadashi; Fujita, Yuichi; Tamiaki, Hitoshi

2013-10-01

Heliobacteria have the simplest photosynthetic apparatus, i.e., a type-I reaction center lacking a peripheral light-harvesting complex. Bacteriochlorophyll (BChl) g molecules are bound to the reaction center complex and work both as special-pair and antenna pigments. The C8-ethylidene group formation for BChl g is the last missing link in biosynthetic pathways for bacterial special-pair pigments, which include BChls a and b as well. Here, we report that chlorophyllide a oxidoreductase (COR) of Heliobacterium modesticaldum catalyzes the C8-ethylidene formation from 8-vinyl-chlorophyllide a, producing bacteriochlorophyllide g, the direct precursor for BChl g without the farnesyl tail. The finding led to plausible biosynthetic pathways for 8(1)-hydroxy-chlorophyll a, a primary electron acceptor from the special pair in heliobacterial reaction centers. Proposed catalytic mechanisms on hydrogenation reaction of the ethylidene synthase-type CORs are also discussed. Copyright © 2013 Elsevier B.V. All rights reserved.

In trans paired nicking triggers seamless genome editing without double-stranded DNA cutting.

PubMed

Chen, Xiaoyu; Janssen, Josephine M; Liu, Jin; Maggio, Ignazio; 't Jong, Anke E J; Mikkers, Harald M M; Gonçalves, Manuel A F V

2017-09-22

Precise genome editing involves homologous recombination between donor DNA and chromosomal sequences subjected to double-stranded DNA breaks made by programmable nucleases. Ideally, genome editing should be efficient, specific, and accurate. However, besides constituting potential translocation-initiating lesions, double-stranded DNA breaks (targeted or otherwise) are mostly repaired through unpredictable and mutagenic non-homologous recombination processes. Here, we report that the coordinated formation of paired single-stranded DNA breaks, or nicks, at donor plasmids and chromosomal target sites by RNA-guided nucleases based on CRISPR-Cas9 components, triggers seamless homology-directed gene targeting of large genetic payloads in human cells, including pluripotent stem cells. Importantly, in addition to significantly reducing the mutagenicity of the genome modification procedure, this in trans paired nicking strategy achieves multiplexed, single-step, gene targeting, and yields higher frequencies of accurately edited cells when compared to the standard double-stranded DNA break-dependent approach.CRISPR-Cas9-based gene editing involves double-strand breaks at target sequences, which are often repaired by mutagenic non-homologous end-joining. Here the authors use Cas9 nickases to generate coordinated single-strand breaks in donor and target DNA for precise homology-directed gene editing.

biobambam: tools for read pair collation based algorithms on BAM files

PubMed Central

2014-01-01

Background Sequence alignment data is often ordered by coordinate (id of the reference sequence plus position on the sequence where the fragment was mapped) when stored in BAM files, as this simplifies the extraction of variants between the mapped data and the reference or of variants within the mapped data. In this order paired reads are usually separated in the file, which complicates some other applications like duplicate marking or conversion to the FastQ format which require to access the full information of the pairs. Results In this paper we introduce biobambam, a set of tools based on the efficient collation of alignments in BAM files by read name. The employed collation algorithm avoids time and space consuming sorting of alignments by read name where this is possible without using more than a specified amount of main memory. Using this algorithm tasks like duplicate marking in BAM files and conversion of BAM files to the FastQ format can be performed very efficiently with limited resources. We also make the collation algorithm available in the form of an API for other projects. This API is part of the libmaus package. Conclusions In comparison with previous approaches to problems involving the collation of alignments by read name like the BAM to FastQ or duplication marking utilities our approach can often perform an equivalent task more efficiently in terms of the required main memory and run-time. Our BAM to FastQ conversion is faster than all widely known alternatives including Picard and bamUtil. Our duplicate marking is about as fast as the closest competitor bamUtil for small data sets and faster than all known alternatives on large and complex data sets.

An investigation on the physicochemical properties of the nanostructured [(4-X)PMAT][N(CN)2] ion pairs as energetic and tunable aryl alkyl amino tetrazolium based ionic liquids

NASA Astrophysics Data System (ADS)

Khalili, Behzad; Rimaz, Mehdi

2017-06-01

In this study the different class of tunable and high nitrogen content ionic liquids termed TAMATILs (Tunable Aryl Methyl Amino Tetrazolium based Ionic Liquids) were designed. The physicochemical properties of the nanostructured TAMATILs composed of para substituted phenyl methyl amino tetrazolium cations [(4-X)PMAT]+ (X = H, Me, OCH3, OH, NH2, NO2, F, CN, CHO, CF3, COMe and CO2Me) and dicyanimide anion [N(CN)2]- were fully investigated using M06-2X functional in conjunction with the 6-311++G(2d,2p) basis set. For all of the studied nanostructured ILs the structural parameters, interaction energy, cation's enthalpy of formation, natural charges, charge transfer values and topological properties were calculated and discussed. The substituent effect on the interaction energy and physicochemical properties also is taking into account. The results showed that the strength of interaction has a linear correlation with electron content of the phenyl ring in a way the substituents with electron withdrawing effects lead to make more stable ion pairs with higher interaction energies. Some of the main physical properties of ILs such as surface tension, melting point, critical-point temperature, electrochemical stability and conductivity are discussed and estimated for studying ion pairs using quantum chemical computationally obtained thermochemical data. Finally the enthalpy and Gibbs free energy of formation for twelve nanostructured individual cations with the general formula of [(4-X)PMAT]+ (X = 4-H, 4-Me, 4-OMe, 4-OH, 4-NH2, 4-NO2, 4-F, 4-CN, 4-CHO, 4-CF3, 4-COMe and 4-CO2Me) are calculated.

Catalytic Activity of a Binary Informational Macromolecule

NASA Technical Reports Server (NTRS)

Reader, John S.; Joyce, Gerald F.

2003-01-01

RNA molecules are thought to have played a prominent role in the early history of life on Earth based on their ability both to encode genetic information and to exhibit catalytic function. The modern genetic alphabet relies on two sets of complementary base pairs to store genetic information. However, due to the chemical instability of cytosine, which readily deaminates to uracil, a primitive genetic system composed of the bases A, U, G and C may have been difficult to establish. It has been suggested that the first genetic material instead contained only a single base-pairing unie'. Here we show that binary informational macromolecules, containing only two different nucleotide subunits, can act as catalysts. In vitro evolution was used to obtain ligase ribozymes composed of only 2,6-diaminopurine and uracil nucleotides, which catalyze the template-directed joining of two RNA molecules, one bearing a 5'-triphosphate and the other a 3'-hydroxyl. The active conformation of the fastest isolated ribozyme had a catalytic rate that was about 36,000-fold faster than the uncatalyzed rate of reaction. This ribozyme is specific for the formation of biologically relevant 3',5'-phosphodiester linkages.

The Weak Lensing Masses of Filaments between Luminous Red Galaxies

NASA Astrophysics Data System (ADS)

Epps, Seth D.; Hudson, Michael J.

2017-07-01

In the standard model of non-linear structure formation, a cosmic web of dark-matter-dominated filaments connects dark matter haloes. In this paper, we stack the weak lensing signal of an ensemble of filaments between groups and clusters of galaxies. Specifically, we detect the weak lensing signal, using CFHTLenS galaxy ellipticities, from stacked filaments between Sloan Digital Sky Survey (SDSS)-III/Baryon Oscillation Spectroscopic Survey luminous red galaxies (LRGs). As a control, we compare the physical LRG pairs with projected LRG pairs that are more widely separated in redshift space. We detect the excess filament mass density in the projected pairs at the 5σ level, finding a mass of (1.6 ± 0.3) × 1013 M⊙ for a stacked filament region 7.1 h-1 Mpc long and 2.5 h-1 Mpc wide. This filament signal is compared with a model based on the three-point galaxy-galaxy-convergence correlation function, as developed in Clampitt et al., yielding reasonable agreement.

Biochemical behavior of N-oxidized cytosine and adenine bases in DNA polymerase-mediated primer extension reactions

PubMed Central

Tsunoda, Hirosuke; Kudo, Tomomi; Masaki, Yoshiaki; Ohkubo, Akihiro; Seio, Kohji; Sekine, Mitsuo

2011-01-01

To clarify the biochemical behavior of 2′-deoxyribonucleoside 5′-triphosphates and oligodeoxyribonucleotides (ODNs) containing cytosine N-oxide (Co) and adenine N-oxide (Ao), we examined their base recognition ability in DNA duplex formation using melting temperature (Tm) experiments and their substrate specificity in DNA polymerase-mediated replication. As the result, it was found that the Tm values of modified DNA–DNA duplexes incorporating 2′-deoxyribonucleoside N-oxide derivatives significantly decreased compared with those of the unmodified duplexes. However, single insertion reactions by DNA polymerases of Klenow fragment (KF) (exo−) and Vent (exo−) suggested that Co and Ao selectively recognized G and T, respectively. Meanwhile, the kinetic study showed that the incorporation efficiencies of the modified bases were lower than those of natural bases. Ab initio calculations suggest that these modified bases can form the stable base pairs with the original complementary bases. These results indicate that the modified bases usually recognize the original bases as partners for base pairing, except for misrecognition of dATP by the action of KF (exo−) toward Ao on the template, and the primers could be extended on the template DNA. When they misrecognized wrong bases, the chain could not be elongated so that the modified base served as the chain terminator. PMID:21300642

Biochemical behavior of N-oxidized cytosine and adenine bases in DNA polymerase-mediated primer extension reactions.

PubMed

Tsunoda, Hirosuke; Kudo, Tomomi; Masaki, Yoshiaki; Ohkubo, Akihiro; Seio, Kohji; Sekine, Mitsuo

2011-04-01

To clarify the biochemical behavior of 2'-deoxyribonucleoside 5'-triphosphates and oligodeoxyribonucleotides (ODNs) containing cytosine N-oxide (C(o)) and adenine N-oxide (A(o)), we examined their base recognition ability in DNA duplex formation using melting temperature (T(m)) experiments and their substrate specificity in DNA polymerase-mediated replication. As the result, it was found that the T(m) values of modified DNA-DNA duplexes incorporating 2'-deoxyribonucleoside N-oxide derivatives significantly decreased compared with those of the unmodified duplexes. However, single insertion reactions by DNA polymerases of Klenow fragment (KF) (exo(-)) and Vent (exo(-)) suggested that C(o) and A(o) selectively recognized G and T, respectively. Meanwhile, the kinetic study showed that the incorporation efficiencies of the modified bases were lower than those of natural bases. Ab initio calculations suggest that these modified bases can form the stable base pairs with the original complementary bases. These results indicate that the modified bases usually recognize the original bases as partners for base pairing, except for misrecognition of dATP by the action of KF (exo(-)) toward A(o) on the template, and the primers could be extended on the template DNA. When they misrecognized wrong bases, the chain could not be elongated so that the modified base served as the chain terminator.

Protein Phosphatase 4 Promotes Chromosome Pairing and Synapsis, and Contributes to Maintaining Crossover Competence with Increasing Age

PubMed Central

Sato-Carlton, Aya; Li, Xuan; Crawley, Oliver; Testori, Sarah; Martinez-Perez, Enrique; Sugimoto, Asako; Carlton, Peter M.

2014-01-01

Prior to the meiotic divisions, dynamic chromosome reorganizations including pairing, synapsis, and recombination of maternal and paternal chromosome pairs must occur in a highly regulated fashion during meiotic prophase. How chromosomes identify each other's homology and exclusively pair and synapse with their homologous partners, while rejecting illegitimate synapsis with non-homologous chromosomes, remains obscure. In addition, how the levels of recombination initiation and crossover formation are regulated so that sufficient, but not deleterious, levels of DNA breaks are made and processed into crossovers is not understood well. We show that in Caenorhabditis elegans, the highly conserved Serine/Threonine protein phosphatase PP4 homolog, PPH-4.1, is required independently to carry out four separate functions involving meiotic chromosome dynamics: (1) synapsis-independent chromosome pairing, (2) restriction of synapsis to homologous chromosomes, (3) programmed DNA double-strand break initiation, and (4) crossover formation. Using quantitative imaging of mutant strains, including super-resolution (3D-SIM) microscopy of chromosomes and the synaptonemal complex, we show that independently-arising defects in each of these processes in the absence of PPH-4.1 activity ultimately lead to meiotic nondisjunction and embryonic lethality. Interestingly, we find that defects in double-strand break initiation and crossover formation, but not pairing or synapsis, become even more severe in the germlines of older mutant animals, indicating an increased dependence on PPH-4.1 with increasing maternal age. Our results demonstrate that PPH-4.1 plays multiple, independent roles in meiotic prophase chromosome dynamics and maintaining meiotic competence in aging germlines. PP4's high degree of conservation suggests it may be a universal regulator of meiotic prophase chromosome dynamics. PMID:25340746

Comparing models of star formation simulating observed interacting galaxies

NASA Astrophysics Data System (ADS)

Quiroga, L. F.; Muñoz-Cuartas, J. C.; Rodrigues, I.

2017-07-01

In this work, we make a comparison between different models of star formation to reproduce observed interacting galaxies. We use observational data to model the evolution of a pair of galaxies undergoing a minor merger. Minor mergers represent situations weakly deviated from the equilibrium configuration but significant changes in star fomation (SF) efficiency can take place, then, minor mergers provide an unique scene to study SF in galaxies in a realistic but yet simple way. Reproducing observed systems also give us the opportunity to compare the results of the simulations with observations, which at the end can be used as probes to characterize the models of SF implemented in the comparison. In this work we compare two different star formation recipes implemented in Gadget3 and GIZMO codes. Both codes share the same numerical background, and differences arise mainly in the star formation recipe they use. We use observations from Pico dos Días and GEMINI telescopes and show how we use observational data of the interacting pair in AM2229-735 to characterize the interacting pair. Later we use this information to simulate the evolution of the system to finally reproduce the observations: Mass distribution, morphology and main features of the merger-induced star formation burst. We show that both methods manage to reproduce roughly the star formation activity. We show, through a careful study, that resolution plays a major role in the reproducibility of the system. In that sense, star formation recipe implemented in GIZMO code has shown a more robust performance. Acknowledgements: This work is supported by Colciencias, Doctorado Nacional - 617 program.

Paired and interacting galaxies: Conference summary

NASA Technical Reports Server (NTRS)

Norman, Colin A.

1990-01-01

The author gives a summary of the conference proceedings. The conference began with the presentation of the basic data sets on pairs, groups, and interacting galaxies with the latter being further discussed with respect to both global properties and properties of the galactic nuclei. Then followed the theory, modelling and interpretation using analytic techniques, simulations and general modelling for spirals and ellipticals, starbursts and active galactic nuclei. Before the conference the author wrote down the three questions concerning pairs, groups and interacting galaxies that he hoped would be answered at the meeting: (1) How do they form, including the role of initial conditions, the importance of subclustering, the evolution of groups to compact groups, and the fate of compact groups; (2) How do they evolve, including issues such as relevant timescales, the role of halos and the problem of overmerging, the triggering and enhancement of star formation and activity in the galactic nuclei, and the relative importance of dwarf versus giant encounters; and (3) Are they important, including the frequency of pairs and interactions, whether merging and interactions are very important aspects of the life of a normal galaxy at formation, during its evolution, in forming bars, shells, rings, bulges, etc., and in the formation and evolution of active galaxies? Where possible he focuses on these three central issues in the summary.

Real-time observation of formation and relaxation dynamics of NH4 in (CH3OH)m(NH3)n clusters.

PubMed

Yamada, Yuji; Nishino, Yoko; Fujihara, Akimasa; Ishikawa, Haruki; Fuke, Kiyokazu

2009-03-26

The formation and relaxation dynamics of NH4(CH3OH)m(NH3)n clusters produced by photolysis of ammonia-methanol mixed clusters has been observed by a time-resolved pump-probe method with femtosecond pulse lasers. From the detailed analysis of the time evolutions of the protonated cluster ions, NH4(+)(CH3OH)m(NH3)n, the kinetic model has been constructed, which consists of sequential three-step reaction: ultrafast hydrogen-atom transfer producing the radical pair (NH4-NH2)*, the relaxation process of radical-pair clusters, and dissociation of the solvated NH4 clusters. The initial hydrogen transfer hardly occurs between ammonia and methanol, implying the unfavorable formation of radical pair, (CH3OH2-NH2)*. The remarkable dependence of the time constants in each step on the number and composition of solvents has been explained by the following factors: hydrogen delocalization within the clusters, the internal conversion of the excited-state radical pair, and the stabilization of NH4 by solvation. The dependence of the time profiles on the probe wavelength is attributed to the different ionization efficiency of the NH4(CH3OH)m(NH3)n clusters.

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

Tripathi, S.; Zhang, D.; Paukstelis, P. J.

DNA has proved to be an excellent material for nanoscale construction because complementary DNA duplexes are programmable and structurally predictable. However, in the absence of Watson–Crick pairings, DNA can be structurally more diverse. Here, we describe the crystal structures of d(ACTCGGATGAT) and the brominated derivative, d(AC BrUCGGA BrUGAT). These oligonucleotides form parallel-stranded duplexes with a crystallographically equivalent strand, resulting in the first examples of DNA crystal structures that contains four different symmetric homo base pairs. Two of the parallel-stranded duplexes are coaxially stacked in opposite directions and locked together to form a tetraplex through intercalation of the 5'-most A–A basemore » pairs between adjacent G–G pairs in the partner duplex. The intercalation region is a new type of DNA tertiary structural motif with similarities to the i-motif. 1H– 1H nuclear magnetic resonance and native gel electrophoresis confirmed the formation of a parallel-stranded duplex in solution. Finally, we modified specific nucleotide positions and added d(GAY) motifs to oligonucleotides and were readily able to obtain similar crystals. This suggests that this parallel-stranded DNA structure may be useful in the rational design of DNA crystals and nanostructures.« less

An intercalation-locked parallel-stranded DNA tetraplex

DOE PAGES

Tripathi, S.; Zhang, D.; Paukstelis, P. J.

2015-01-27

DNA has proved to be an excellent material for nanoscale construction because complementary DNA duplexes are programmable and structurally predictable. However, in the absence of Watson–Crick pairings, DNA can be structurally more diverse. Here, we describe the crystal structures of d(ACTCGGATGAT) and the brominated derivative, d(AC BrUCGGA BrUGAT). These oligonucleotides form parallel-stranded duplexes with a crystallographically equivalent strand, resulting in the first examples of DNA crystal structures that contains four different symmetric homo base pairs. Two of the parallel-stranded duplexes are coaxially stacked in opposite directions and locked together to form a tetraplex through intercalation of the 5'-most A–A basemore » pairs between adjacent G–G pairs in the partner duplex. The intercalation region is a new type of DNA tertiary structural motif with similarities to the i-motif. 1H– 1H nuclear magnetic resonance and native gel electrophoresis confirmed the formation of a parallel-stranded duplex in solution. Finally, we modified specific nucleotide positions and added d(GAY) motifs to oligonucleotides and were readily able to obtain similar crystals. This suggests that this parallel-stranded DNA structure may be useful in the rational design of DNA crystals and nanostructures.« less

A small RNA activates CFA synthase by isoform-specific mRNA stabilization

PubMed Central

Fröhlich, Kathrin Sophie; Papenfort, Kai; Fekete, Agnes; Vogel, Jörg

2013-01-01

Small RNAs use a diversity of well-characterized mechanisms to repress mRNAs, but how they activate gene expression at the mRNA level remains not well understood. The predominant activation mechanism of Hfq-associated small RNAs has been translational control whereby base pairing with the target prevents the formation of an intrinsic inhibitory structure in the mRNA and promotes translation initiation. Here, we report a translation-independent mechanism whereby the small RNA RydC selectively activates the longer of two isoforms of cfa mRNA (encoding cyclopropane fatty acid synthase) in Salmonella enterica. Target activation is achieved through seed pairing of the pseudoknot-exposed, conserved 5′ end of RydC to an upstream region of the cfa mRNA. The seed pairing stabilizes the messenger, likely by interfering directly with RNase E-mediated decay in the 5′ untranslated region. Intriguingly, this mechanism is generic such that the activation is equally achieved by seed pairing of unrelated small RNAs, suggesting that this mechanism may be utilized in the design of RNA-controlled synthetic circuits. Physiologically, RydC is the first small RNA known to regulate membrane stability. PMID:24141880

A small RNA activates CFA synthase by isoform-specific mRNA stabilization.

PubMed

Fröhlich, Kathrin Sophie; Papenfort, Kai; Fekete, Agnes; Vogel, Jörg

2013-11-13

Small RNAs use a diversity of well-characterized mechanisms to repress mRNAs, but how they activate gene expression at the mRNA level remains not well understood. The predominant activation mechanism of Hfq-associated small RNAs has been translational control whereby base pairing with the target prevents the formation of an intrinsic inhibitory structure in the mRNA and promotes translation initiation. Here, we report a translation-independent mechanism whereby the small RNA RydC selectively activates the longer of two isoforms of cfa mRNA (encoding cyclopropane fatty acid synthase) in Salmonella enterica. Target activation is achieved through seed pairing of the pseudoknot-exposed, conserved 5' end of RydC to an upstream region of the cfa mRNA. The seed pairing stabilizes the messenger, likely by interfering directly with RNase E-mediated decay in the 5' untranslated region. Intriguingly, this mechanism is generic such that the activation is equally achieved by seed pairing of unrelated small RNAs, suggesting that this mechanism may be utilized in the design of RNA-controlled synthetic circuits. Physiologically, RydC is the first small RNA known to regulate membrane stability.

Increasing positive ion number densities below the peak of ion-electron pair production in Titan's ionosphere

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

Vigren, E.; Galand, M.; Shebanits, O.

2014-05-01

We combine derived ion-electron pair formation rates with Cassini Radio Plasma Wave Science Langmuir Probe measurements of electron and positive ion number densities in Titan's sunlit ionosphere. We show that positive ion number densities in Titan's sunlit ionosphere can increase toward significantly lower altitudes than the peak of ion-electron pair formation despite that the effective ion-electron recombination coefficient increases. This is explained by the increased mixing ratios of negative ions, which are formed by electron attachment to neutrals. While such a process acts as a sink for free electrons, the positive ions become longer-lived as the rate coefficients for ion-anionmore » neutralization reactions are smaller than those for ion-electron dissociative recombination reactions.« less

Extraction of organic acids by ion-pair formation with tri-n-octylamine. Part 7. Comparison of methods for extraction of synthetic dyes from yogurt.

PubMed

Puttemans, M L; de Voogt, M; Dryon, L; Massart, D

1985-01-01

Synthetic dyes were extracted from yogurt by different methods, but all methods had in common a liberation of dyes from the food followed by ion-pair formation with tri-n-octylamine. Extraction with pH 5.5 phosphate buffer gave high recoveries for 5 of the 7 dyes investigated and was relatively fast. Precipitation of proteins followed by polyamide adsorption and desorption gave high yields for all the dyes but was tedious and long.

Tuning the electronic structure of graphene through alkali metal and halogen atom intercalation

NASA Astrophysics Data System (ADS)

Ahmad, Sohail; Miró, Pere; Audiffred, Martha; Heine, Thomas

2018-04-01

The deposition, intercalation and co-intercalation of heavy alkali metals and light halogens atoms in graphene mono- and bilayers have been studied using first principles density-functional calculations. Both the deposition and the intercalation of alkali metals gives rise to n-type doping due to the formation of M+-C- pairs. The co-intercalation of a 1:1 ratio of alkali metals and halogens derives into the formation of ionic pairs among the intercalated species, unaltering the electronic structure of the layered material.

Ionic liquid-induced aggregate formation and their applications.

PubMed

Dutta, Rupam; Kundu, Sangita; Sarkar, Nilmoni

2018-06-01

In the last two decades, researchers have extensively studied highly stable and ordered supramolecular assembly formation using oppositely charged surfactants. Thereafter, surface-active ionic liquids (SAILs), a special class of room temperature ionic liquids (RTILs), replace the surfactants to form various supramolecular aggregates. Therefore, in the last decade, the building blocks of the supramolecular aggregates (micelle, mixed micelle, and vesicular assemblies) have changed from oppositely charged surfactant/surfactant pair to surfactant/SAIL and SAIL/SAIL pair. It is also found that various biomolecules can also interact with SAILs to construct biologically important supramolecular assemblies. The very latest addition to this combination of ion pairs is the dye molecules having a long hydrophobic chain part along with a hydrophilic ionic head group. Thus, dye/surfactant or dye/SAIL pair also produces different assemblies through electrostatic, hydrophobic, and π-π stacking interactions. Vesicles are one of the important self-assemblies which mimic cellular membranes, and thus have biological application as a drug carrier. Moreover, vesicles can act as a suitable microreactor for nanoparticle synthesis.

Fractional statistics and quantum scaling properties of the integrable Penson-Kolb-Hubbard chain

NASA Astrophysics Data System (ADS)

Vitoriano, Carlindo; Coutinho-Filho, M. D.

2010-09-01

We investigate the ground-state and low-temperature properties of the integrable version of the Penson-Kolb-Hubbard chain. The model obeys fractional statistical properties, which give rise to fractional elementary excitations and manifest differently in the four regions of the phase diagram U/t versus n , where U is the Coulomb coupling, t is the correlated hopping amplitude, and n is the particle density. In fact, we can find local pair formation, fractionalization of the average occupation number per orbital k , or U - and n -dependent average electric charge per orbital k . We also study the scaling behavior near the U -driven quantum phase transitions and characterize their universality classes. Finally, it is shown that in the regime of parameters where local pair formation is energetically more favorable, the ground state exhibits power-law superconductivity; we also stress that above half filling the pair-hopping term stabilizes local Cooper pairs in the repulsive- U regime for U

Effects of Concentration on Like-Charge Pairing of Guanidinium Ions and on the Structure of Water: An All-Atom Molecular Dynamics Simulation Study.

PubMed

Bandyopadhyay, Dibyendu; Bhanja, K; Mohan, Sadhana; Ghosh, Swapan K; Choudhury, Niharendu

2015-08-27

Like-charge ion-pair formation in an aqueous solution of guanidinium chloride (GdmCl) has two important facets. On one hand, it describes the role of the arginine (ARG) side chain in aggregation and dimer formation in proteins, and on the other hand, it lends support for the direct mechanism of protein denaturation by GdmCl. We employ all-atom molecular dynamics simulations to investigate the effect of GdmCl concentration on the like-charge ion-pair formation of guanidinium ions (Gdm(+)). From analyses of the radial distribution function (RDF) between the carbon atoms of two guanidinium moieties, the existence of both contact pairs and solvent-separated pairs has been observed. Although the peak height corresponding to the contact-pair state decreases, the number of Gdm(+) ions in the contact-pair state actually increases with increasing GdmCl concentration. We have also investigated the effect of the concentration of Gdm(+) on the structure of water. The effect of GdmCl concentration on the radial and tetrahedral structures of water is found to be negligibly small; however, GdmCl concentration has a considerable effect on the hydrogen-bonding structure of water. It is demonstrated that the presence of chloride ions, not Gdm(+), in the first solvation shell of water causes the distortion in the hydrogen-bonding network of water. In order to establish that Gdm(+) not only stacks against another Gdm(+) but also directly attacks the ARG residue of a protein or peptide, simulation of an ARG-rich peptide in 6 M aqueous solution of GdmCl has been performed. The analyses of RDFs and orientation distributions reveal that the Gdm(+) moiety of the GdmCl attacks the same moiety in the ARG side chain with a parallel stacking orientation.

Gaia Assorted Mass Binaries Long Excluded from SLoWPoKES (GAMBLES): Identifying Ultra-wide Binary Pairs with Components of Diverse Mass

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

Oelkers, Ryan J.; Stassun, Keivan G.; Dhital, Saurav, E-mail: ryan.j.oelkers@vanderbilt.edu

The formation and evolution of binary star systems are some of the remaining key questions in modern astronomy. Wide binary pairs (separations >10{sup 3} au) are particularly intriguing because their low binding energies make it difficult for the stars to stay gravitationally bound over extended timescales, and thus to probe the dynamics of binary formation and dissolution. Our previous SLoWPoKES catalogs, I and II, provided the largest and most complete sample of wide-binary pairs of low masses. Here we present an extension of these catalogs to a broad range of stellar masses: the Gaia Assorted Mass Binaries Long Excluded frommore » SloWPoKES (GAMBLES), comprising 8660 statistically significant wide pairs that we make available in a living online database. Within this catalog we identify a subset of 543 long-lived (dissipation timescale >1.5 Gyr) candidate binary pairs, of assorted mass, with typical separations between 10{sup 3} and 10{sup 5.5} au (0.002–1.5 pc), using the published distances and proper motions from the Tycho -Gaia Astrometric Solution and Sloan Digital Sky Survey photometry. Each pair has at most a false positive probability of 0.05; the total expectation is 2.44 false binaries in our sample. Among these, we find 22 systems with 3 components, 1 system with 4 components, and 15 pairs consisting of at least 1 possible red giant. We find the largest long-lived binary separation to be nearly 3.2 pc; even so, >76% of GAMBLES long-lived binaries have large binding energies and dissipation lifetimes longer than 1.5 Gyr. Finally, we find that the distribution of binary separations is clearly bimodal, corroborating the findings from SloWPoKES and suggesting multiple pathways for the formation and dissipation of the widest binaries in the Galaxy.« less

Gaia Assorted Mass Binaries Long Excluded from SLoWPoKES (GAMBLES): Identifying Ultra-wide Binary Pairs with Components of Diverse Mass

NASA Astrophysics Data System (ADS)

Oelkers, Ryan J.; Stassun, Keivan G.; Dhital, Saurav

2017-06-01

The formation and evolution of binary star systems are some of the remaining key questions in modern astronomy. Wide binary pairs (separations >103 au) are particularly intriguing because their low binding energies make it difficult for the stars to stay gravitationally bound over extended timescales, and thus to probe the dynamics of binary formation and dissolution. Our previous SLoWPoKES catalogs, I and II, provided the largest and most complete sample of wide-binary pairs of low masses. Here we present an extension of these catalogs to a broad range of stellar masses: the Gaia Assorted Mass Binaries Long Excluded from SloWPoKES (GAMBLES), comprising 8660 statistically significant wide pairs that we make available in a living online database. Within this catalog we identify a subset of 543 long-lived (dissipation timescale >1.5 Gyr) candidate binary pairs, of assorted mass, with typical separations between 103 and 105.5 au (0.002-1.5 pc), using the published distances and proper motions from the Tycho-Gaia Astrometric Solution and Sloan Digital Sky Survey photometry. Each pair has at most a false positive probability of 0.05; the total expectation is 2.44 false binaries in our sample. Among these, we find 22 systems with 3 components, 1 system with 4 components, and 15 pairs consisting of at least 1 possible red giant. We find the largest long-lived binary separation to be nearly 3.2 pc even so, >76% of GAMBLES long-lived binaries have large binding energies and dissipation lifetimes longer than 1.5 Gyr. Finally, we find that the distribution of binary separations is clearly bimodal, corroborating the findings from SloWPoKES and suggesting multiple pathways for the formation and dissipation of the widest binaries in the Galaxy.

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.

IVisTMSA: Interactive Visual Tools for Multiple Sequence Alignments.

PubMed

Pervez, Muhammad Tariq; Babar, Masroor Ellahi; Nadeem, Asif; Aslam, Naeem; Naveed, Nasir; Ahmad, Sarfraz; Muhammad, Shah; Qadri, Salman; Shahid, Muhammad; Hussain, Tanveer; Javed, Maryam

2015-01-01

IVisTMSA is a software package of seven graphical tools for multiple sequence alignments. MSApad is an editing and analysis tool. It can load 409% more data than Jalview, STRAP, CINEMA, and Base-by-Base. MSA comparator allows the user to visualize consistent and inconsistent regions of reference and test alignments of more than 21-MB size in less than 12 seconds. MSA comparator is 5,200% efficient and more than 40% efficient as compared to BALiBASE c program and FastSP, respectively. MSA reconstruction tool provides graphical user interfaces for four popular aligners and allows the user to load several sequence files at a time. FASTA generator converts seven formats of alignments of unlimited size into FASTA format in a few seconds. MSA ID calculator calculates identity matrix of more than 11,000 sequences with a sequence length of 2,696 base pairs in less than 100 seconds. Tree and Distance Matrix calculation tools generate phylogenetic tree and distance matrix, respectively, using neighbor joining% identity and BLOSUM 62 matrix.

Entanglement in a quantum neural network based on quantum dots

NASA Astrophysics Data System (ADS)

Altaisky, M. V.; Zolnikova, N. N.; Kaputkina, N. E.; Krylov, V. A.; Lozovik, Yu E.; Dattani, N. S.

2017-05-01

We studied the quantum correlations between the nodes in a quantum neural network built of an array of quantum dots with dipole-dipole interaction. By means of the quasiadiabatic path integral simulation of the density matrix evolution in a presence of the common phonon bath we have shown the coherence in such system can survive up to the liquid nitrogen temperature of 77 K and above. The quantum correlations between quantum dots are studied by means of calculation of the entanglement of formation in a pair of quantum dots with the typical dot size of a few nanometers and interdot distance of the same order. We have shown that the proposed quantum neural network can keep the mixture of entangled states of QD pairs up to the above mentioned high temperatures.

Dark-bright quadratic solitons with a focusing effective Kerr nonlinearity

NASA Astrophysics Data System (ADS)

Chen, Manna; Ping, Xiaorou; Liang, Guo; Guo, Qi; Lu, Daquan; Hu, Wei

2018-01-01

Dark solitons are traditionally considered to exist in defocusing Kerr nonlinearity media. We investigate dark quadratic solitons with a focusing effective Kerr nonlinearity and a sine-oscillatory nonlocal response. A nonlinear refractive index with a focusing sine-oscillatory response leads to a defocusing effect with a strong degree of nonlocality, which causes the formation of dark solitons. By analyzing the modulational instability, we determine the parameter domain for dark quadratic solitons with a stable background and numerically obtain dark-bright soliton solutions in the form of pairs, which avoid radiative phenomena. Based on a numerical simulation, we find that all dark-bright soliton pairs are unstable after a relatively long propagation distance, and their stabilities are affected by the soliton interval and the degree of nonlocality.

Collisional Lifetimes of Elementary Excitations in Two-Dimensional Systems in the Field of a Strong Electromagnetic Wave

NASA Astrophysics Data System (ADS)

Kovalev, V. M.

2018-04-01

A two-dimensional system with two nonequivalent valleys in the field of a strong circularly polarized electromagnetic wave is considered. It is assumed that the optical selection rules for a given polarization of light allow band-to-band transitions only in valleys of one, optically active, type (two-dimensional layer based on transition metal dichalcogenides, gapped graphene, etc.). This leads to the formation of photon-coupled electron-hole pairs, or an "optical insulator" state. It is assumed that the valleys of the second type (optically inactive) are populated with an equilibrium electron gas. The relaxation of elementary excitations in this hybrid system consisting of an electron gas and a gas of electron-hole pairs caused by the Coulomb interaction between the particles is investigated.

Evaluation of antioxidant activity and electronic structure of aspirin and paracetamol

NASA Astrophysics Data System (ADS)

Motozaki, W.; Nagatani, Y.; Kimura, Y.; Endo, K.; Takemura, T.; Kurmaev, E. Z.; Moewes, A.

2011-01-01

We present a study of electronic structure, chemical bonding, and antioxidant activity of phenolic antioxidants (aspirin and paracetamol). X-ray photoelectron and emission spectra of the antioxidants have been simulated by deMon density functional theory (DFT) calculations of the molecules. The chemical bonding of aspirin is characterized by the formation of oxygen 'lone-pair' π-orbitals which can neutralize free radicals and thus be related to antioxidant properties of the drug. In the case of paracetamol the additional nitrogen 'lone pair' is formed which can explain toxicity of the drug. We propose an evaluation method of antioxidant activity based on the relationship between experimental half-wave oxidation potential ( Ep/2 ) and calculated ionization potentials ( IP) by the DFT calculations, and can conclude that paracetamol has the higher antioxidant activity than aspirin.

Self-Organization of Vocabularies under Different Interaction Orders.

PubMed

Vera, Javier

2017-01-01

Traditionally, the formation of vocabularies has been studied by agent-based models (primarily, the naming game) in which random pairs of agents negotiate word-meaning associations at each discrete time step. This article proposes a first approximation to a novel question: To what extent is the negotiation of word-meaning associations influenced by the order in which agents interact? Automata networks provide the adequate mathematical framework to explore this question. Computer simulations suggest that on two-dimensional lattices the typical features of the formation of word-meaning associations are recovered under random schemes that update small fractions of the population at the same time; by contrast, if larger subsets of the population are updated, a periodic behavior may appear.

Format Comparison of the Old and New Esquire: A Survey of Graduate Communication Students.

ERIC Educational Resources Information Center

Misisco, Peter

A survey of 194 graduate students compared the old and new formats of "Esquire" magazine, combining two issues of each format in a sequence of four viewing pairs (to negate possible bias effects of content). The subjects indicated their preferences and reasons for preferences for old and new logos, typefaces, tables of content formats,…

Formation of massive clouds and dwarf galaxies during tidal encounters

NASA Technical Reports Server (NTRS)

Kaufman, Michele; Elmegreen, Bruce G.; Thomasson, Magnus; Elmegreen, Debra M.

1993-01-01

Gerola et al. (1983) propose that isolated dwarf galaxies can form during galaxy interactions. As evidence of this process, Mirabel et al. (1991) find 10(exp 9) solar mass clouds and star formation complexes at the outer ends of the tidal arms in the Antennae and Superantennae galaxies. We describe observations of HI clouds with mass greater than 10(exp 8) solar mass in the interacting galaxy pair IC 2163/NGC 2207. This pair is important because we believe it represents an early stage in the formation of giant clouds during an encounter. We use a gravitational instability model to explain why the observed clouds are so massive and discuss a two-dimensional N-body simulation of an encounter that produces giant clouds.

Cooper Pairs in Insulators?!

ScienceCinema

James Valles

2017-12-09

Nearly 50 years elapsed between the discovery of superconductivity and the emergence of the microscopic theory describing this zero resistance state. The explanation required a novel phase of matter in which conduction electrons joined in weakly bound pairs and condensed with other pairs into a single quantum state. Surprisingly, this Cooper pair formation has also been invoked to account for recently uncovered high-resistance or insulating phases of matter. To address this possibility, we have used nanotechnology to create an insulating system that we can probe directly for Cooper pairs. I will present the evidence that Cooper pairs exist and dominate the electrical transport in these insulators and I will discuss how these findings provide new insight into superconductor to insulator quantum phase transitions. 

Exciplex formation in bimolecular photoinduced electron-transfer investigated by ultrafast time-resolved infrared spectroscopy.

PubMed

Koch, Marius; Letrun, Romain; Vauthey, Eric

2014-03-12

The dynamics of bimolecular photoinduced electron-transfer reactions has been investigated with three donor/acceptor (D/A) pairs in tetrahydrofuran (THF) and acetonitrile (ACN) using a combination of ultrafast spectroscopic techniques, including time-resolved infrared absorption. For the D/A pairs with the highest driving force of electron transfer, all transient spectroscopic features can be unambiguously assigned to the excited reactant and the ionic products. For the pair with the lowest driving force, three additional transient infrared bands, more intense in THF than in ACN, with a time dependence that differs from those of the other bands are observed. From their frequency and solvent dependence, these bands can be assigned to an exciplex. Moreover, polarization-resolved measurements point to a relatively well-defined mutual orientation of the constituents and to a slower reorientational time compared to those of the individual reactants. Thanks to the minimal overlap of the infrared signature of all transient species in THF, a detailed reaction scheme including the relevant kinetic and thermodynamic parameters could be deduced for this pair. This analysis reveals that the formation and recombination of the ion pair occur almost exclusively via the exciplex.

A simple method to design non-collision relative orbits for close spacecraft formation flying

NASA Astrophysics Data System (ADS)

Jiang, Wei; Li, JunFeng; Jiang, FangHua; Bernelli-Zazzera, Franco

2018-05-01

A set of linearized relative motion equations of spacecraft flying on unperturbed elliptical orbits are specialized for particular cases, where the leader orbit is circular or equatorial. Based on these extended equations, we are able to analyze the relative motion regulation between a pair of spacecraft flying on arbitrary unperturbed orbits with the same semi-major axis in close formation. Given the initial orbital elements of the leader, this paper presents a simple way to design initial relative orbital elements of close spacecraft with the same semi-major axis, thus preventing collision under non-perturbed conditions. Considering the mean influence of J 2 perturbation, namely secular J 2 perturbation, we derive the mean derivatives of orbital element differences, and then expand them to first order. Thus the first order expansion of orbital element differences can be added to the relative motion equations for further analysis. For a pair of spacecraft that will never collide under non-perturbed situations, we present a simple method to determine whether a collision will occur when J 2 perturbation is considered. Examples are given to prove the validity of the extended relative motion equations and to illustrate how the methods presented can be used. The simple method for designing initial relative orbital elements proposed here could be helpful to the preliminary design of the relative orbital elements between spacecraft in a close formation, when collision avoidance is necessary.

Identification of Ion-Pair Structures in Solution by Vibrational Stark Effects.

PubMed

Hack, John; Grills, David C; Miller, John R; Mani, Tomoyasu

2016-02-18

Ion pairing is a fundamental consideration in many areas of chemistry and has implications in a wide range of sciences and technologies that include batteries and organic photovoltaics. Ions in solution are known to inhabit multiple possible states, including free ions (FI), contact ion pairs (CIP), and solvent-separated ion pairs (SSIP). However, in solutions of organic radicals and nonmetal electrolytes, it is often difficult to distinguish between these states. In the first part of this work, we report evidence for the formation of SSIPs in low-polarity solvents and distinct measurements of CIP, SSIP, and FI, by using the ν(C≡N) infrared (IR) band of a nitrile-substituted fluorene radical anion. Use of time-resolved IR detection following pulse radiolysis allowed us to unambiguously assign the peak of the FI. In the presence of nonmetal electrolytes, two distinct red-shifted peaks were observed and assigned to the CIP and SSIP. The assignments are interpreted in the framework of the vibrational Stark effect (VSE) and are supported by (1) the solvent dependence of ion-pair populations, (2) the observation of a cryptand-separated sodium ion pair that mimics the formation of SSIPs, and (3) electronic structure calculations. In the second part of this work, we show that a blue-shift of the ν(C≡N) IR band due to the VSE can be induced in a nitrile-substituted fluorene radical anion by covalently tethering it to a metal-chelating ligand that forms an intramolecular ion pair upon reduction and complexation with sodium ion. This adds support to the conclusion that the shift in IR absorptions by ion pairing originates from the VSE. These results combined show that we can identify ion-pair structures by using the VSE, including the existence of SSIPs in a low-polarity solvent.

A Survey of Aspartate Phenylalanine and Glutamate Phenylalanine Interactions in the Protein Data Bank: Searching for Anion Pairs

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

Philip, Vivek M; Harris, Jason B; Adams, Rachel M

Protein structures are stabilized using noncovalent interactions. In addition to the traditional noncovalent interactions, newer types of interactions are thought to be present in proteins. One such interaction, an anion pair, in which the positively charged edge of an aromatic ring interacts with an anion, forming a favorable anion quadrupole interaction, has been previously proposed [Jackson, M. R., et al. (2007) J. Phys. Chem. B111, 8242 8249]. To study the role of anion interactions in stabilizing protein structure, we analyzed pairwise interactions between phenylalanine (Phe) and the anionic amino acids, aspartate (Asp) and glutamate (Glu). Particular emphasis was focused onmore » identification of Phe Asp or Glu pairs separated by less than 7 in the high-resolution, nonredundant Protein Data Bank. Simplifying Phe to benzene and Asp or Glu to formate molecules facilitated in silico analysis of the pairs. Kitaura Morokuma energy calculations were performed on roughly 19000 benzene formate pairs and the resulting energies analyzed as a function of distance and angle. Edgewise interactions typically produced strongly stabilizing interaction energies (2 to 7.3 kcal/mol), while interactions involving the ring face resulted in weakly stabilizing to repulsive interaction energies. The strongest, most stabilizing interactions were identified as preferentially occurring in buried residues. Anion pairs are found throughout protein structures, in helices as well as strands. Numerous pairs also had nearby cation interactions as well as potential stacking. While more than 1000 structures did not contain an anion pair, the 3134 remaining structures contained approximately 2.6 anion pairs per protein, suggesting it is a reasonably common motif that could contribute to the overall structural stability of a protein.« less

A Survey of Aspartate-Phenylalanine and Glutamate-Phenylalanine Interactions in the Protein Data Bank: Searching for Anion-pi Pairs

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

Philip, Vivek M; Harris, Jason B; Adams, Rachel M

Protein structures are stabilized using noncovalent interactions. In addition to the traditional noncovalent interactions, newer types of interactions are thought to be present in proteins. One such interaction, an anion-{pi} pair, in which the positively charged edge of an aromatic ring interacts with an anion, forming a favorable anion-quadrupole interaction, has been previously proposed [Jackson, M. R., et al. (2007) J. Phys. Chem. B111, 8242-8249]. To study the role of anion-{pi} interactions in stabilizing protein structure, we analyzed pairwise interactions between phenylalanine (Phe) and the anionic amino acids, aspartate (Asp) and glutamate (Glu). Particular emphasis was focused on identification ofmore » Phe-Asp or -Glu pairs separated by less than 7 {angstrom} in the high-resolution, nonredundant Protein Data Bank. Simplifying Phe to benzene and Asp or Glu to formate molecules facilitated in silico analysis of the pairs. Kitaura-Morokuma energy calculations were performed on roughly 19000 benzene-formate pairs and the resulting energies analyzed as a function of distance and angle. Edgewise interactions typically produced strongly stabilizing interaction energies (-2 to -7.3 kcal/mol), while interactions involving the ring face resulted in weakly stabilizing to repulsive interaction energies. The strongest, most stabilizing interactions were identified as preferentially occurring in buried residues. Anion-{pi} pairs are found throughout protein structures, in helices as well as {beta} strands. Numerous pairs also had nearby cation-{pi} interactions as well as potential {pi}-{pi} stacking. While more than 1000 structures did not contain an anion-{pi} pair, the 3134 remaining structures contained approximately 2.6 anion-{pi} pairs per protein, suggesting it is a reasonably common motif that could contribute to the overall structural stability of a protein.« less

A survey of aspartate-phenylalanine and glutamate-phenylalanine interactions in the protein data bank: searching for anion-π pairs.

PubMed

Philip, Vivek; Harris, Jason; Adams, Rachel; Nguyen, Don; Spiers, Jeremy; Baudry, Jerome; Howell, Elizabeth E; Hinde, Robert J

2011-04-12

Protein structures are stabilized using noncovalent interactions. In addition to the traditional noncovalent interactions, newer types of interactions are thought to be present in proteins. One such interaction, an anion-π pair, in which the positively charged edge of an aromatic ring interacts with an anion, forming a favorable anion-quadrupole interaction, has been previously proposed [Jackson, M. R., et al. (2007) J. Phys. Chem. B111, 8242-8249]. To study the role of anion-π interactions in stabilizing protein structure, we analyzed pairwise interactions between phenylalanine (Phe) and the anionic amino acids, aspartate (Asp) and glutamate (Glu). Particular emphasis was focused on identification of Phe-Asp or -Glu pairs separated by less than 7 Å in the high-resolution, nonredundant Protein Data Bank. Simplifying Phe to benzene and Asp or Glu to formate molecules facilitated in silico analysis of the pairs. Kitaura-Morokuma energy calculations were performed on roughly 19000 benzene-formate pairs and the resulting energies analyzed as a function of distance and angle. Edgewise interactions typically produced strongly stabilizing interaction energies (-2 to -7.3 kcal/mol), while interactions involving the ring face resulted in weakly stabilizing to repulsive interaction energies. The strongest, most stabilizing interactions were identified as preferentially occurring in buried residues. Anion-π pairs are found throughout protein structures, in helices as well as β strands. Numerous pairs also had nearby cation-π interactions as well as potential π-π stacking. While more than 1000 structures did not contain an anion-π pair, the 3134 remaining structures contained approximately 2.6 anion-π pairs per protein, suggesting it is a reasonably common motif that could contribute to the overall structural stability of a protein.

Transfer of a weakly bound electron in collisions of Rydberg atoms with neutral particles. II. Ion-pair formation and resonant quenching of the Rb(nl) and Ne(nl) States by Ca, Sr, and Ba atoms

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

Narits, A. A.; Mironchuk, E. S.; Lebedev, V. S., E-mail: vlebedev@sci.lebedev.ru

2013-10-15

Electron-transfer processes are studied in thermal collisions of Rydberg atoms with alkaline-earth Ca(4s{sup 2}), Sr(5s{sup 2}), and Ba(6s{sup 2}) atoms capable of forming negative ions with a weakly bound outermost p-electron. We consider the ion-pair formation and resonant quenching of highly excited atomic states caused by transitions between Rydberg covalent and ionic terms of a quasi-molecule produced in collisions of particles. The contributions of these reaction channels to the total depopulation cross section of Rydberg states of Rb(nl) and Ne(nl) atoms as functions of the principal quantum number n are compared for selectively excited nl-levels with l Much-Less-Than n andmore » for states with large orbital quantum numbers l = n - 1, n - 2. It is shown that the contribution from resonant quenching dominates at small values of n, and the ion-pair formation process begins to dominate with increasing n. The values and positions of the maxima of cross sections for both processes strongly depend on the electron affinity of an alkaline-earth atom and on the orbital angular momentum l of a highly excited atom. It is shown that in the case of Rydberg atoms in states with large l {approx} n - 1, the rate constants of ion-pair formation and collisional quenching are considerably lower than those for nl-levels with l Much-Less-Than n.« less

pH-Modulated Watson-Crick duplex-quadruplex equilibria of guanine-rich and cytosine-rich DNA sequences 140 base pairs upstream of the c-kit transcription initiation site.

PubMed

Bucek, Pavel; Jaumot, Joaquim; Aviñó, Anna; Eritja, Ramon; Gargallo, Raimundo

2009-11-23

Guanine-rich regions of DNA are sequences capable of forming G-quadruplex structures. The formation of a G-quadruplex structure in a region 140 base pairs (bp) upstream of the c-kit transcription initiation site was recently proposed (Fernando et al., Biochemistry, 2006, 45, 7854). In the present study, the acid-base equilibria and the thermally induced unfolding of the structures formed by a guanine-rich region and by its complementary cytosine-rich strand in c-kit were studied by means of circular dichroism and molecular absorption spectroscopies. In addition, competition between the Watson-Crick duplex and the isolated structures was studied as a function of pH value and temperature. Multivariate data analysis methods based on both hard and soft modeling were used to allow accurate quantification of the various acid-base species present in the mixtures. Results showed that the G-quadruplex and i-motif coexist with the Watson-Crick duplex over the pH range from 3.0 to 6.5, approximately, under the experimental conditions tested in this study. At pH 7.0, the duplex is practically the only species present.

Structural requirements for protein-catalyzed annealing of U4 and U6 RNAs during di-snRNP assembly

PubMed Central

Didychuk, Allison L.; Montemayor, Eric J.; Brow, David A.; Butcher, Samuel E.

2016-01-01

Base-pairing of U4 and U6 snRNAs during di-snRNP assembly requires large-scale remodeling of RNA structure that is chaperoned by the U6 snRNP protein Prp24. We investigated the mechanism of U4/U6 annealing in vitro using an assay that enables visualization of ribonucleoprotein complexes and faithfully recapitulates known in vivo determinants for the process. We find that annealing, but not U6 RNA binding, is highly dependent on the electropositive character of a 20 Å-wide groove on the surface of Prp24. During annealing, we observe the formation of a stable ternary complex between U4 and U6 RNAs and Prp24, indicating that displacement of Prp24 in vivo requires additional factors. Mutations that stabilize the U6 ‘telestem’ helix increase annealing rates by up to 15-fold, suggesting that telestem formation is rate-limiting for U4/U6 pairing. The Lsm2–8 complex, which binds adjacent to the telestem at the 3′ end of U6, provides a comparable rate enhancement. Collectively, these data identify domains of the U6 snRNP that are critical for one of the first steps in assembly of the megaDalton U4/U6.U5 tri-snRNP complex, and lead to a dynamic model for U4/U6 pairing that involves a striking degree of evolved cooperativity between protein and RNA. PMID:26673715

Entropy Transfer between Residue Pairs and Allostery in Proteins: Quantifying Allosteric Communication in Ubiquitin.

PubMed

Hacisuleyman, Aysima; Erman, Burak

2017-01-01

It has recently been proposed by Gunasakaran et al. that allostery may be an intrinsic property of all proteins. Here, we develop a computational method that can determine and quantify allosteric activity in any given protein. Based on Schreiber's transfer entropy formulation, our approach leads to an information transfer landscape for the protein that shows the presence of entropy sinks and sources and explains how pairs of residues communicate with each other using entropy transfer. The model can identify the residues that drive the fluctuations of others. We apply the model to Ubiquitin, whose allosteric activity has not been emphasized until recently, and show that there are indeed systematic pathways of entropy and information transfer between residues that correlate well with the activities of the protein. We use 600 nanosecond molecular dynamics trajectories for Ubiquitin and its complex with human polymerase iota and evaluate entropy transfer between all pairs of residues of Ubiquitin and quantify the binding susceptibility changes upon complex formation. We explain the complex formation propensities of Ubiquitin in terms of entropy transfer. Important residues taking part in allosteric communication in Ubiquitin predicted by our approach are in agreement with results of NMR relaxation dispersion experiments. Finally, we show that time delayed correlation of fluctuations of two interacting residues possesses an intrinsic causality that tells which residue controls the interaction and which one is controlled. Our work shows that time delayed correlations, entropy transfer and causality are the required new concepts for explaining allosteric communication in proteins.

Molecular Hydrogen Formation from Proximal Glycol Pairs on TiO2(110)

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

Chen, Long; Li, Zhenjun; Smith, R. Scott

2014-04-16

Understanding hydrogen formation on TiO2 surfaces is of great importance as it could provide fundamental insight into water splitting for hydrogen production using solar energy. In this work, hydrogen formation from glycols having different numbers of methyl end-groups have been studied using temperature pro-grammed desorption on reduced, hydroxylated, and oxidized TiO2(110) surfaces. The results from OD-labeled glycols demon-strate that gas-phase molecular hydrogen originates exclusively from glycol hydroxyl groups. The yield is controlled by a combi-nation of glycol coverage, steric hindrance, TiO2(110) order and the amount of subsurface charge. Combined, these results show that proximal pairs of hydroxyl aligned glycol moleculesmore » and subsurface charge are required to maximize the yield of this redox reaction. These findings highlight the importance of geometric and electronic effects in hydrogen formation from adsorbates on TiO2(110).« less

Determining resistivity of a formation adjacent to a borehole having casing using multiple electrodes and with resistances being defined between the electrodes

DOEpatents

Vail, III, William B.

1996-01-01

Methods of operation of different types of multiple electrode apparatus vertically disposed in a cased well to measure information related to the resistivity of adjacent geological formations from inside the cased well. The multiple electrode apparatus have a minimum of three spaced apart voltage measurement electrodes that electrically engage the interior of the cased well. Measurement information is obtained related to current which is caused to flow from the cased well into the adjacent geological formation. First compensation information is obtained related to a first casing resistance between a first pair of the spaced apart voltage measurement electrodes. Second compensation information is obtained related to a second casing resistance between a second pair of the spaced apart voltage measurement electrodes. The measurement information, and first and second compensation information are used to determine a magnitude related to the adjacent formation resistivity.

Determining resistivity of a formation adjacent to a borehole having casing using multiple electrodes and with resistances being defined between the electrodes

DOEpatents

Vail, W.B. III

1996-10-29

Methods of operation are disclosed for different types of multiple electrode apparatus vertically disposed in a cased well to measure information related to the resistivity of adjacent geological formations from inside the cased well. The multiple electrode apparatus have a minimum of three spaced-apart voltage measurement electrodes that electrically engage the interior of the cased well. Measurement information is obtained related to current which is caused to flow from the cased well into the adjacent geological formation. First compensation information is obtained related to a first casing resistance between a first pair of the spaced-apart voltage measurement electrodes. Second compensation information is obtained related to a second casing resistance between a second pair of the spaced-apart voltage measurement electrodes. The measurement information, and first and second compensation information are used to determine a magnitude related to the adjacent formation resistivity. 13 figs.

Drastic stability change of X-X mismatch in d(CXG) trinucleotide repeat disorders under molecular crowding condition.

PubMed

Teng, Ye; Pramanik, Smritimoy; Tateishi-Karimata, Hisae; Ohyama, Tatsuya; Sugimoto, Naoki

2018-02-05

The trinucleotide repeat d(CXG) (X = A, C, G or T) is the most common sequence causing repeat expansion disorders. The formation of non-canonical structures, such as hairpin structures with X-X mismatches, has been proposed to affect gene expression and regulation, which are important in pathological studies of these devastating neurological diseases. However, little information is available regarding the thermodynamics of the repeat sequence under crowded cellular conditions where many non-canonical structures such as G-quadruplexes are highly stabilized, while duplexes are destabilised. In this study, we investigated the different stabilities of X-X mismatches in the context of internal d(CXG) self-complementary sequences in an environment with a high concentration of cosolutes to mimic the crowding conditions in cells. The stabilities of full-matched duplexes and duplexes with A-A, G-G, and T-T mismatched base pairs under molecular crowding conditions were notably decreased compared to under dilute conditions. However, the stability of the DNA duplex with a C-C mismatch base pair was only slightly destabilised. Investigating different stabilities of X-X mismatches in d(CXG) sequences is important for improving our understanding of the formation and transition of multiple non-canonical structures in trinucleotide repeat diseases, and may provide insights for pathological studies and drug development. Copyright © 2018 Elsevier Inc. All rights reserved.

Generation of strip-format fibrin-based engineered heart tissue (EHT).

PubMed

Schaaf, Sebastian; Eder, Alexandra; Vollert, Ingra; Stöhr, Andrea; Hansen, Arne; Eschenhagen, Thomas

2014-01-01

This protocol describes a method for casting fibrin-based engineered heart tissue (EHT) in standard 24-well culture dishes. In principle, a hydrogel tissue engineering method requires cardiomyocytes, a liquid matrix that forms a gel, a casting mold, and a device that keeps the developing tissue in place. This protocol refers to neonatal rat heart cells as the cell source; the matrix of choice is fibrin, and the tissues are generated in rectangular agarose-casting molds (12 × 3 × 3 mm) prepared in standard 24-well cell culture dishes, in which a pair of flexible silicone posts is suspended from above. A master mix of freshly isolated cells, medium, fibrinogen, and thrombin is pipetted into the casting mold and, over a period of 2 h, polymerizes and forms a fibrin cell block around two silicone posts. Silicone racks holding four pairs of silicone posts each are used to transfer the fresh fibrin cell blocks into new 24-well dishes with culture medium. Without further handling, the cells start to remodel the fibrin gel, form contacts with each other, elongate, and condense the gel to approximately ¼ of the initial volume. Spontaneous and rhythmic contractions start after 1 week. EHTs are viable and relatively stable for several weeks in this format and can be subjected to repeated measurements of contractile function and final morphological and molecular analyses.

Structural and thermodynamic analysis of modified nucleosides in self-assembled DNA cross-tiles.

PubMed

Hakker, Lauren; Marchi, Alexandria N; Harris, Kimberly A; LaBean, Thomas H; Agris, Paul F

2014-01-01

DNA Holliday junctions are important natural strand-exchange structures that form during homologous recombination. Immobile four-arm junctions, analogs to Holliday junctions, have been designed to self-assemble into cross-tile structures by maximizing Watson-Crick base pairing and fixed crossover points. The cross-tiles, self-assembled from base pair recognition between designed single-stranded DNAs, form higher order lattice structures through cohesion of self-associating sticky ends. These cross-tiles have 16 unpaired nucleosides in the central loop at the junction of the four duplex stems. The importance of the centralized unpaired nucleosides to the structure's thermodynamic stability and self-assembly is unknown. Cross-tile DNA nanostructures were designed and constructed from nine single-stranded DNAs with four shell strands, four arms, and a central loop containing 16 unpaired bases. The 16 unpaired bases were either 2'-deoxyribothymidines, 2'-O-methylribouridines, or abasic 1',2'-dideoxyribonucleosides. Thermodynamic profiles and structural base-stacking contributions were assessed using UV absorption spectroscopy during thermal denaturation and circular dichroism spectroscopy, respectively, and the resulting structures were observed by atomic force microscopy. There were surprisingly significant changes in the thermodynamic and structural properties of lattice formation as a result of altering only the 16 unpaired, centralized nucleosides. The 16 unpaired 2'-O-methyluridines were stabilizing and produced uniform tubular structures. In contrast, the abasic nucleosides were destabilizing producing a mixture of structures. These results strongly indicate the importance of a small number of centrally located unpaired nucleosides within the structures. Since minor modifications lead to palpable changes in lattice formation, DNA cross-tiles present an easily manipulated structure convenient for applications in biomedical and biosensing devices.

Conjugate fracture pairs in the Molina Member of the Wasatch Formation, Piceance basin, Colorado: Implications for fracture origins and hydrocarbon production/exploration

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

Lorenz, J.C.

1997-05-01

The sandstones of the Molina Member of the Wasatch Formation in the Piceance basin of northwestern Colorado contain a suite of fractures that have a conjugate-pair geometry. The fractures are vertical and intersect at an acute angle of between 20 and 40 degrees. Although direct evidence of shear is rare, the fracture surfaces commonly display small steps. The fracture geometries suggest that the maximum compressive stress during fracturing was in the plane of the acute angle of the conjugate fractures: the steps are interpreted as broken-face manifestations of very low angle en echelon fractures, formed within exceptionally narrow zones ofmore » incipient shear. In contrast to the highly anisotropic permeability enhancement created by subparallel vertical extension fractures in the underlying Mesaverde Formation, the conjugate pairs in the Molina sandstones should create a well connected and relatively isotropic mesh of fracture conductivity. Increases in stress magnitudes and anisotropy during production drawdown of reservoir pressures should cause shear offsets along the fractures, initially enhancing permeability.« less

QM and QM/MM Studies on Excited-State Relaxation Mechanisms of Unnatural Bases in Vacuo and Base Pairs in DNA.

PubMed

Wang, Qian; Xie, Xiao-Ying; Han, Juan; Cui, Ganglong

2017-11-22

Semisynthetic alphabet can potentially increase the genetic information stored in DNA through the formation of unusual base pairs such as d5SICS:dNaM. However, recent experiments show that near-visible-light irradiation on the d5SICS and dNaM chromophores could lead to genetic mutations and damages. Until now, their photophysical mechanisms remain elusive. Herein, we have employed MS-CASPT2//CASSCF and QM(MS-CASPT2//CASSCF)/MM methods to explore the spectroscopic properties and excited-state relaxation mechanisms of d5SICS, dNaM, and d5SICS:dNaM in DNA. We have found that (1) the S 2 state of d5SICS, the S 1 state of dNaM, and the S 2 state of d5SICS:dNaM are initially populated upon near-visible-light irradiation and (2) for d5SICS and d5SICS:dNaM, there are several parallel relaxation pathways to populate the lowest triplet state, but for dNaM, a main relaxation pathway is uncovered. Moreover, we have found that the excited-state relaxation mechanism of d5SICS:dNaM in DNA is similar to that of the isolated d5SICS chromophore. These mechanistic insights contribute to the understanding of photophysics and photochemistry of unusual base pairs and to the design of better semisynthetic genetic alphabet.

Defective pairing and synaptonemal complex formation in a Sordaria mutant (spo44) with a translocated segment of the nucleolar organizer.

PubMed

Zickler, D; de Lares, L; Moreau, P J; Leblon, G

1985-01-01

The recessive meiotic mutant spo44 of Sordaria macrospora, with 90% ascospore abortion, exhibits striking effects on recombination (67% decrease), irregular segregation of the almost unpaired homologues, and a decrease in chiasma frequency in the few cases where bivalents are formed. Three-dimensional reconstructions of ten prophase nuclei indicate that pairing, as judged by the absence of fully formed synaptonemal complexes (SC), is not achieved although lateral elements (LE) assemble. The pairing failure is attributable to defects in the alignment of homologous chromosomes. The leptotene alignment seen in the wild type before SC formation was not observed in the spo44 nuclei. Dense material, considered to be precursor of SC central elements, was found scattered among the LE in two nuclei. The behaviour of spo44 substantiates the hypothesis that chromosome matching and SC formation are separable events. - The total length of the LE in the mutant is the same as in the wild type, but due to variable numbers and length of the individual LE, homologues cannot be lined up. Light microscopic observations indicate that the irregular length and number of LE is due to extensive chromosome breakage. The wild-type function corresponding to spo44 is required for both LE integrity and chromosome matching. Reconstructions of heterozygous nuclei reveal the presence of a supernumerary nucleolar organizer in one arm of chromosome 7. It is suggested that rDNA has been inserted into a gene whose function is involved in pairing or into a controlling sequence that interacts with the pairing process.

Fired Cartridge Case Identification Using Optical Images and the Congruent Matching Cells (CMC) Method

PubMed Central

Tong, Mingsi; Song, John; Chu, Wei; Thompson, Robert M

2014-01-01

The Congruent Matching Cells (CMC) method for ballistics identification was invented at the National Institute of Standards and Technology (NIST). The CMC method is based on the correlation of pairs of small correlation cells instead of the correlation of entire images. Four identification parameters – TCCF, Tθ, Tx and Ty are proposed for identifying correlated cell pairs originating from the same firearm. The correlation conclusion (matching or non-matching) is determined by whether the number of CMC is ≥ 6. This method has been previously validated using a set of 780 pair-wise 3D topography images. However, most ballistic images stored in current local and national databases are in an optical intensity (grayscale) format. As a result, the reliability of applying the CMC method on optical intensity images is an important issue. In this paper, optical intensity images of breech face impressions captured on the same set of 40 cartridge cases are correlated and analyzed for the validation test of CMC method using optical images. This includes correlations of 63 pairs of matching images and 717 pairs of non-matching images under top ring lighting. Tests of the method do not produce any false identification (false positive) or false exclusion (false negative) results, which support the CMC method and the proposed identification criterion, C = 6, for firearm breech face identifications using optical intensity images. PMID:26601045

Fired Cartridge Case Identification Using Optical Images and the Congruent Matching Cells (CMC) Method.

PubMed

Tong, Mingsi; Song, John; Chu, Wei; Thompson, Robert M

2014-01-01

The Congruent Matching Cells (CMC) method for ballistics identification was invented at the National Institute of Standards and Technology (NIST). The CMC method is based on the correlation of pairs of small correlation cells instead of the correlation of entire images. Four identification parameters - T CCF, T θ, T x and T y are proposed for identifying correlated cell pairs originating from the same firearm. The correlation conclusion (matching or non-matching) is determined by whether the number of CMC is ≥ 6. This method has been previously validated using a set of 780 pair-wise 3D topography images. However, most ballistic images stored in current local and national databases are in an optical intensity (grayscale) format. As a result, the reliability of applying the CMC method on optical intensity images is an important issue. In this paper, optical intensity images of breech face impressions captured on the same set of 40 cartridge cases are correlated and analyzed for the validation test of CMC method using optical images. This includes correlations of 63 pairs of matching images and 717 pairs of non-matching images under top ring lighting. Tests of the method do not produce any false identification (false positive) or false exclusion (false negative) results, which support the CMC method and the proposed identification criterion, C = 6, for firearm breech face identifications using optical intensity images.

Positron Annihilation Ratio Spectroscopy (PsARS) Applied to Positronium Formation Studies

DTIC Science & Technology

2010-03-01

POSITRON ANNIHILATION RATIO SPECTROSCOPY (PsARS) APPLIED TO POSITRONIUM FORMATION STUDIES THESIS...AFIT/GNE/ENP/10-M07 POSITRON ANNIHILATION RATIO SPECTROSCOPY (PsARS) APPLIED TO POSITRONIUM FORMATION STUDIES ...lifetime studies in local electric field experiments. High local electric fields can polarize a positron -electron pair, which may result in an extended

Possibility of Cooper-pair formation controlled by multi-terminal spin injection

NASA Astrophysics Data System (ADS)

Ohnishi, K.; Sakamoto, M.; Ishitaki, M.; Kimura, T.

2018-03-01

A multi-terminal lateral spin valve consisting of three ferromagnetic nanopillars on a Cu/Nb bilayer has been fabricated. We investigated the influence of the spin injection on the superconducting properties at the Cu/Nb interface. The non-local spin valve signal exhibits a clear spin insulation signature due to the superconducting gap of the Nb. The magnitude of the spin signal is found to show the probe configuration dependence. From the careful analysis of the bias current dependence, we found the suppression of the superconductivity due to the exchange interaction between the Cooper pair and accumulated spin plays an important role in the multi-terminal spin injections. We also discuss about the possibility of the Cooper-pair formation due to the spin injection from the two injectors with the anti-parallel alignment.

Report on Pairing-based Cryptography.

PubMed

Moody, Dustin; Peralta, Rene; Perlner, Ray; Regenscheid, Andrew; Roginsky, Allen; Chen, Lily

2015-01-01

This report summarizes study results on pairing-based cryptography. The main purpose of the study is to form NIST's position on standardizing and recommending pairing-based cryptography schemes currently published in research literature and standardized in other standard bodies. The report reviews the mathematical background of pairings. This includes topics such as pairing-friendly elliptic curves and how to compute various pairings. It includes a brief introduction to existing identity-based encryption (IBE) schemes and other cryptographic schemes using pairing technology. The report provides a complete study of the current status of standard activities on pairing-based cryptographic schemes. It explores different application scenarios for pairing-based cryptography schemes. As an important aspect of adopting pairing-based schemes, the report also considers the challenges inherent in validation testing of cryptographic algorithms and modules. Based on the study, the report suggests an approach for including pairing-based cryptography schemes in the NIST cryptographic toolkit. The report also outlines several questions that will require further study if this approach is followed.

Report on Pairing-based Cryptography

PubMed Central

Moody, Dustin; Peralta, Rene; Perlner, Ray; Regenscheid, Andrew; Roginsky, Allen; Chen, Lily

2015-01-01

This report summarizes study results on pairing-based cryptography. The main purpose of the study is to form NIST’s position on standardizing and recommending pairing-based cryptography schemes currently published in research literature and standardized in other standard bodies. The report reviews the mathematical background of pairings. This includes topics such as pairing-friendly elliptic curves and how to compute various pairings. It includes a brief introduction to existing identity-based encryption (IBE) schemes and other cryptographic schemes using pairing technology. The report provides a complete study of the current status of standard activities on pairing-based cryptographic schemes. It explores different application scenarios for pairing-based cryptography schemes. As an important aspect of adopting pairing-based schemes, the report also considers the challenges inherent in validation testing of cryptographic algorithms and modules. Based on the study, the report suggests an approach for including pairing-based cryptography schemes in the NIST cryptographic toolkit. The report also outlines several questions that will require further study if this approach is followed. PMID:26958435

Identification of DSB-1, a Protein Required for Initiation of Meiotic Recombination in Caenorhabditis elegans, Illuminates a Crossover Assurance Checkpoint

PubMed Central

Stamper, Ericca L.; Rodenbusch, Stacia E.; Rosu, Simona; Ahringer, Julie; Villeneuve, Anne M.; Dernburg, Abby F.

2013-01-01

Meiotic recombination, an essential aspect of sexual reproduction, is initiated by programmed DNA double-strand breaks (DSBs). DSBs are catalyzed by the widely-conserved Spo11 enzyme; however, the activity of Spo11 is regulated by additional factors that are poorly conserved through evolution. To expand our understanding of meiotic regulation, we have characterized a novel gene, dsb-1, that is specifically required for meiotic DSB formation in the nematode Caenorhabditis elegans. DSB-1 localizes to chromosomes during early meiotic prophase, coincident with the timing of DSB formation. DSB-1 also promotes normal protein levels and chromosome localization of DSB-2, a paralogous protein that plays a related role in initiating recombination. Mutations that disrupt crossover formation result in prolonged DSB-1 association with chromosomes, suggesting that nuclei may remain in a DSB-permissive state. Extended DSB-1 localization is seen even in mutants with defects in early recombination steps, including spo-11, suggesting that the absence of crossover precursors triggers the extension. Strikingly, failure to form a crossover precursor on a single chromosome pair is sufficient to extend the localization of DSB-1 on all chromosomes in the same nucleus. Based on these observations we propose a model for crossover assurance that acts through DSB-1 to maintain a DSB-permissive state until all chromosome pairs acquire crossover precursors. This work identifies a novel component of the DSB machinery in C. elegans, and sheds light on an important pathway that regulates DSB formation for crossover assurance. PMID:23990794

Search extension transforms Wiki into a relational system: a case for flavonoid metabolite database.

PubMed

Arita, Masanori; Suwa, Kazuhiro

2008-09-17

In computer science, database systems are based on the relational model founded by Edgar Codd in 1970. On the other hand, in the area of biology the word 'database' often refers to loosely formatted, very large text files. Although such bio-databases may describe conflicts or ambiguities (e.g. a protein pair do and do not interact, or unknown parameters) in a positive sense, the flexibility of the data format sacrifices a systematic query mechanism equivalent to the widely used SQL. To overcome this disadvantage, we propose embeddable string-search commands on a Wiki-based system and designed a half-formatted database. As proof of principle, a database of flavonoid with 6902 molecular structures from over 1687 plant species was implemented on MediaWiki, the background system of Wikipedia. Registered users can describe any information in an arbitrary format. Structured part is subject to text-string searches to realize relational operations. The system was written in PHP language as the extension of MediaWiki. All modifications are open-source and publicly available. This scheme benefits from both the free-formatted Wiki style and the concise and structured relational-database style. MediaWiki supports multi-user environments for document management, and the cost for database maintenance is alleviated.

Search extension transforms Wiki into a relational system: A case for flavonoid metabolite database

PubMed Central

Arita, Masanori; Suwa, Kazuhiro

2008-01-01

Background In computer science, database systems are based on the relational model founded by Edgar Codd in 1970. On the other hand, in the area of biology the word 'database' often refers to loosely formatted, very large text files. Although such bio-databases may describe conflicts or ambiguities (e.g. a protein pair do and do not interact, or unknown parameters) in a positive sense, the flexibility of the data format sacrifices a systematic query mechanism equivalent to the widely used SQL. Results To overcome this disadvantage, we propose embeddable string-search commands on a Wiki-based system and designed a half-formatted database. As proof of principle, a database of flavonoid with 6902 molecular structures from over 1687 plant species was implemented on MediaWiki, the background system of Wikipedia. Registered users can describe any information in an arbitrary format. Structured part is subject to text-string searches to realize relational operations. The system was written in PHP language as the extension of MediaWiki. All modifications are open-source and publicly available. Conclusion This scheme benefits from both the free-formatted Wiki style and the concise and structured relational-database style. MediaWiki supports multi-user environments for document management, and the cost for database maintenance is alleviated. PMID:18822113

Comparison of Heavy-Duty Scuffing Behavior between Chromium-Based Ceramic Composite and Nickel-Chromium-Molybdenum-Coated Ring Sliding against Cast Iron Liner under Starvation

PubMed Central

Shen, Yan; Yu, Baihong; Lv, Yutao; Li, Bin

2017-01-01

A running-in and starved lubrication experiment is designed to investigate the heavy-duty scuffing behavior of piston ring coatings against cast iron (Fe) cylinder liner using the piston ring reciprocating liner test rig. The scuffing resistance of the piston ring with the chromium-based ceramic composite coating (CKS), and that with the thermally sprayed nickel-chromium-molybdenum coating (NCM) is compared at different nominal pressures (40~100 MPa) and temperatures (180~250 °C). With the failure time as a criterion, the rank order is as follows: NCM/Fe > CKS/Fe. Before the scoring occurs at the interface of the piston ring and cylinder liner (PRCL), the cast iron liner enters into a “polish wear” stage, and iron-based adhesive materials begin to form on the piston ring surface. With the macroscopic adhesion formation, the plastic shearing cycle causes surface damages mainly due to abrasive effects for the CKS/Fe pairs and adhesive effects for the NCM/Fe pairs. PMID:29036911

The mechanism of the emergence of distinct overstretched DNA states

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

Zhu, You-Liang; Sun, Zhao-Yan, E-mail: zysun@ciac.ac.cn; Lu, Zhong-Yuan

Although multiple overstretched DNA states were identified in experiments, the mechanism of the emergence of distinct states is still unclear. Molecular dynamics simulation is an ideal tool to clarify the mechanism, but the force loading rates in stretching achieved by conventional all-atom DNA models are much faster, which essentially affect overstretching states. We employed a modified coarse-grained DNA model with an unprecedented low loading rate in simulations to study the overstretching transitions of end-opened double-stranded DNA. We observed two-strand peeling off for DNA with low stability and the S-DNA with high stability under tension. By introducing a melting-forbidden model whichmore » prevents base-pair breaking, we still observed the overstretching transition induced by the formation of S-DNA due to the change of dihedral angle. Hence, we confirmed that the competition between the two strain-softening manners, i.e., base-pair breaking and dihedral angle variation, results in the emergence of distinct overstretched DNA states.« less

Anion dependent ion pairing in concentrated ytterbium halide solutions

NASA Astrophysics Data System (ADS)

Klinkhammer, Christina; Böhm, Fabian; Sharma, Vinay; Schwaab, Gerhard; Seitz, Michael; Havenith, Martina

2018-06-01

We have studied ion pairing of ytterbium halide solutions. THz spectra (30-400 cm-1) of aqueous YbCl3 and YbBr3 solutions reveal fundamental differences in the hydration structures of YbCl3 and YbBr3 at high salt concentrations: While for YbBr3 no indications for a changing local hydration environment of the ions were experimentally observed within the measured concentration range, the spectra of YbCl3 pointed towards formation of weak contact ion pairs. The proposed anion specificity for ion pairing was confirmed by supplementary Raman measurements.

Initiation and strain compatibility of connected extension twins in AZ31 magnesium alloy at high temperature

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

Liu, Xiao, E-mail: liuxiao0105@163.com

2016-12-15

Uniaxial compression tests were carried out at 350 °C and a strain rate of 0.3 s{sup −1} on as-extruded AZ31 magnesium alloy samples. At a true strain of − 0.1, extension twin pairs in a grain and twin chains across adjacent grains were detected. The orientation of selected twins and their host grains were determined by electron backscattered diffraction (EBSD) techniques. The Schmid factors (SFs), accommodation strains and geometric compatibility factors (m{sup ′}) were calculated. Analysis of the data indicated that the formation of twin pair and twin chain was related to the SF and m{sup ′}. Regarding to twinmore » chain across adjacent grains, accommodation strain was also involved. The selection of twin variants in twin chain was generally determined by m{sup ′}. When the twins required the operation of pyramidal slip or twinning in adjacent grain, the corresponding connected twins with a relative high m{sup ′} were selected in this adjacent grain. - Highlights: •The formation of paired twins is studied during high temperature deformation. •The initiation of twinning in twin pair and twin chain obeys the Schmid law. •The twin variants' selection in twin chain is related to the geometric compatibility factor. •The accommodation strain plays an important role on the formation of twin chain.« less

Repairing the sickle cell mutation. I. Specific covalent binding of a photoreactive third strand to the mutated base pair.

PubMed

Broitman, S; Amosova, O; Dolinnaya, N G; Fresco, J R

1999-07-30

A DNA third strand with a 3'-psoralen substituent was designed to form a triplex with the sequence downstream of the T.A mutant base pair of the human sickle cell beta-globin gene. Triplex-mediated psoralen modification of the mutant T residue was sought as an approach to gene repair. The 24-nucleotide purine-rich target sequence switches from one strand to the other and has four pyrimidine interruptions. Therefore, a third strand sequence favorable to two triplex motifs was used, one parallel and the other antiparallel to it. To cope with the pyrimidine interruptions, which weaken third strand binding, 5-methylcytosine and 5-propynyluracil were used in the third strand. Further, a six residue "hook" complementary to an overhang of a linear duplex target was added to the 5'-end of the third strand via a T(4) linker. In binding to the overhang by Watson-Crick pairing, the hook facilitates triplex formation. This third strand also binds specifically to the target within a supercoiled plasmid. The psoralen moiety at the 3'-end of the third strand forms photoadducts to the targeted T with high efficiency. Such monoadducts are known to preferentially trigger reversion of the mutation by DNA repair enzymes.

Role of a polymorphism in a Hox/Pax-responsive enhancer in the evolution of the vertebrate spine

USGS Publications Warehouse

Guerreiro, Isabel; Nunes, Andreia; Woltering, Joost M.; Casaca, Ana; Nóvoa, Ana; Vinagre, Tânia; Hunter, Margaret E.; Duboule, Denis; Mallo, Moisés

2013-01-01

Patterning of the vertebrate skeleton requires the coordinated activity of Hox genes. In particular, Hox10 proteins are essential to set the transition from thoracic to lumbar vertebrae because of their rib-repressing activity. In snakes, however, the thoracic region extends well into Hox10-expressing areas of the embryo, suggesting that these proteins are unable to block rib formation. Here, we show that this is not a result of the loss of rib-repressing properties by the snake proteins, but rather to a single base pair change in a Hox/Paired box (Pax)-responsive enhancer, which prevents the binding of Hox proteins. This polymorphism is also found in Paenungulata, such as elephants and manatees, which have extended rib cages. In vivo, this modified enhancer failed to respond to Hox10 activity, supporting its role in the extension of rib cages. In contrast, the enhancer could still interact with Hoxb6 and Pax3 to promote rib formation. These results suggest that a polymorphism in the Hox/Pax-responsive enhancer may have played a role in the evolution of the vertebrate spine by differently modulating its response to rib-suppressing and rib-promoting Hox proteins.

WebGIVI: a web-based gene enrichment analysis and visualization tool.

PubMed

Sun, Liang; Zhu, Yongnan; Mahmood, A S M Ashique; Tudor, Catalina O; Ren, Jia; Vijay-Shanker, K; Chen, Jian; Schmidt, Carl J

2017-05-04

A major challenge of high throughput transcriptome studies is presenting the data to researchers in an interpretable format. In many cases, the outputs of such studies are gene lists which are then examined for enriched biological concepts. One approach to help the researcher interpret large gene datasets is to associate genes and informative terms (iTerm) that are obtained from the biomedical literature using the eGIFT text-mining system. However, examining large lists of iTerm and gene pairs is a daunting task. We have developed WebGIVI, an interactive web-based visualization tool ( http://raven.anr.udel.edu/webgivi/ ) to explore gene:iTerm pairs. WebGIVI was built via Cytoscape and Data Driven Document JavaScript libraries and can be used to relate genes to iTerms and then visualize gene and iTerm pairs. WebGIVI can accept a gene list that is used to retrieve the gene symbols and corresponding iTerm list. This list can be submitted to visualize the gene iTerm pairs using two distinct methods: a Concept Map or a Cytoscape Network Map. In addition, WebGIVI also supports uploading and visualization of any two-column tab separated data. WebGIVI provides an interactive and integrated network graph of gene and iTerms that allows filtering, sorting, and grouping, which can aid biologists in developing hypothesis based on the input gene lists. In addition, WebGIVI can visualize hundreds of nodes and generate a high-resolution image that is important for most of research publications. The source code can be freely downloaded at https://github.com/sunliang3361/WebGIVI . The WebGIVI tutorial is available at http://raven.anr.udel.edu/webgivi/tutorial.php .

Effects of secular evolution on the star formation history of galaxies

NASA Astrophysics Data System (ADS)

Lorenzo, M. Fernández; Sulentic, J.; Verdes-Montenegro, L.; Argudo-Fernández, M.; Ruiz, J. E.; Sabater, J.; Sánchez-Expósito, S.

2015-03-01

We report the study performed as part of the AMIGA (Analysis of the interstellar Medium of Isolated GAlaxies; http://www.amiga.iaa.es) project, focused on the SDSS (g-r) colors of the sample. Assuming that color is an indicator of star formation history, this work better records the signature of passive star formation via pure secular evolution. Median values for each morphological type in AMIGA were compared with equivalent measures for galaxies in denser environments. We found a tendency for AMIGA spiral galaxies to be redder than galaxies in close pairs, but no clear difference when we compare with galaxies in other (e.g. group) environments. The (g-r) color of isolated galaxies presents a Gaussian distribution, as indicative of pure secular evolution, and a smaller median absolute deviation (almost half) compared to both wide and close pairs. This redder color and lower color dispersion of AMIGA spirals compared with close pairs is likely due to a more passive star formation in very isolated galaxies. In Fig. 1, we represent the size versus stellar mass for early and late-type galaxies of our sample, compared with the local relations of Shen et al. (2003). The late-type isolated galaxies are ~1.2 times larger or have less stellar mass than local spirals in other environments. The latter would be in agreement with the passive star formation found in the previous part. We acknowledge Grant AYA2011-30491-C02-01, P08-FQM-4205 and TIC-114.

Nucleic acid duplexes incorporating a dissociable covalent base pair

NASA Technical Reports Server (NTRS)

Gao, K.; Orgel, L. E.; Bada, J. L. (Principal Investigator)

1999-01-01

We have used molecular modeling techniques to design a dissociable covalently bonded base pair that can replace a Watson-Crick base pair in a nucleic acid with minimal distortion of the structure of the double helix. We introduced this base pair into a potential precursor of a nucleic acid double helix by chemical synthesis and have demonstrated efficient nonenzymatic template-directed ligation of the free hydroxyl groups of the base pair with appropriate short oligonucleotides. The nonenzymatic ligation reactions, which are characteristic of base paired nucleic acid structures, are abolished when the covalent base pair is reduced and becomes noncoplanar. This suggests that the covalent base pair linking the two strands in the duplex is compatible with a minimally distorted nucleic acid double-helical structure.

The Connection Between Sediment Supply and Paired Strath Terrace Formation at Arroyo Seco, CA, USA.

NASA Astrophysics Data System (ADS)

Finnegan, N. J.

2015-12-01

Although wide, longitudinally traceable, paired strath terraces in river canyons are frequently argued to reflect periods of higher sediment supply, there is no consensus on how changes in sediment supply translate into dramatic changes in valley morphology. Here, quantitative analysis of LiDAR data is combined with field observations in Arroyo Seco, in the Santa Lucia Range of Central California, to develop a conceptual model for paired bedrock terrace formation and its connection to sediment supply. The most recently formed bedrock terrace in Arroyo Seco grades onto a prominent alluvial fan surface, suggesting that planation of straths in Arroyo Seco occurs as downstream alluvial fans aggrade. This aggradation apparently buffers Arroyo Seco's bedrock channel from base level fall on the Reliz Canyon Fault, which separates the bedrock and alluvial sections of the river. Notably, despite the fact that bedrock terraces grade smoothly onto alluvial fan surfaces, the deep aggradation of sediment downstream is not seen upstream in bedrock channel sections. Gravel on straths is typically only 0.5-1 m thick. Instead, excess gravel appears to be accommodated by the lateral planation of the wide strath itself. LiDAR evidence suggests that strath planation is associated with braiding, which is often triggered by increases in sediment supply. Given the high lateral mobility of braided streams and the extremely fractured (and hence easily detached) mudstone valley walls along Arroyo Seco, braiding provides a simple connection between sediment supply and lateral planation in Arroyo Seco. In Arroyo Seco, fan incision (under decreased sediment supply) should exhume a bedrock step whose height represents the accumulated fault slip during fan aggradation. The upstream propagation of this exhumed step as a knickpoint provides a simple mechanism to connect drops in sediment supply to rapid vertical incision, valley narrowing and strath terrace formation. Long profile data for Arroyo Seco shows clear evidence that the last two generations of strath terraces terminate upstream at knickpoints. OSL dating (Taylor and Sweetkind, 2014) constrains the formation of the two most recent strath terraces to the last ~ 35 kyr, implying at least two reductions in sediment supply relative to capacity during this interval.

Using Paired Comparisons to Assess Maslow's Hierarchy of Needs.

ERIC Educational Resources Information Center

Strong, Lisa L.; Fiebert, Martin S.

Past studies which have examined need levels have identified individuals as functioning at specific need levels without an adequate assessment of the intensity of each need or a clear comparison with other need levels. To address these issues, a self-report inventory using a modified paired comparison format was developed to assess need potencies…

Identity in Activity: Examining Teacher Professional Identity Formation in the Paired-Placement of Student Teachers

ERIC Educational Resources Information Center

Dang, Thi Kim Anh

2013-01-01

This paper examines the evolution of the professional identities of student teachers (STs) in a paired-placement teaching practicum in Vietnam. The study draws on activity theory, its notion of contradiction, and Vygotsky's concepts of ZPD and "perezhivanie", to identify the factors driving the intricate learning process. Opportunities…

How to make stripes: deciphering the transition from non-periodic to periodic patterns in Drosophila segmentation

PubMed Central

Schroeder, Mark D.; Greer, Christina; Gaul, Ulrike

2011-01-01

The generation of metameric body plans is a key process in development. In Drosophila segmentation, periodicity is established rapidly through the complex transcriptional regulation of the pair-rule genes. The ‘primary’ pair-rule genes generate their 7-stripe expression through stripe-specific cis-regulatory elements controlled by the preceding non-periodic maternal and gap gene patterns, whereas ‘secondary’ pair-rule genes are thought to rely on 7-stripe elements that read off the already periodic primary pair-rule patterns. Using a combination of computational and experimental approaches, we have conducted a comprehensive systems-level examination of the regulatory architecture underlying pair-rule stripe formation. We find that runt (run), fushi tarazu (ftz) and odd skipped (odd) establish most of their pattern through stripe-specific elements, arguing for a reclassification of ftz and odd as primary pair-rule genes. In the case of run, we observe long-range cis-regulation across multiple intervening genes. The 7-stripe elements of run, ftz and odd are active concurrently with the stripe-specific elements, indicating that maternal/gap-mediated control and pair-rule gene cross-regulation are closely integrated. Stripe-specific elements fall into three distinct classes based on their principal repressive gap factor input; stripe positions along the gap gradients correlate with the strength of predicted input. The prevalence of cis-elements that generate two stripes and their genomic organization suggest that single-stripe elements arose by splitting and subfunctionalization of ancestral dual-stripe elements. Overall, our study provides a greatly improved understanding of how periodic patterns are established in the Drosophila embryo. PMID:21693522

A semi-empirical model for the formation and depletion of the high burnup structure in UO 2

DOE PAGES

Pizzocri, D.; Cappia, F.; Luzzi, L.; ...

2017-01-31

In the rim zone of UO 2 nuclear fuel pellets, the combination of high burnup and low temperature drives a microstructural change, leading to the formation of the high burnup structure (HBS). In this work, we propose a semi-empirical model to describe the formation of the HBS, which embraces the polygonisation/recrystallization process and the depletion of intra-granular fission gas, describing them as inherently related. To this end, we per-formed grain-size measurements on samples at radial positions in which the restructuring was incomplete. Moreover, based on these new experimental data, we assume an exponential reduction of the average grain size withmore » local effective burnup, paired with a simultaneous depletion of intra-granular fission gas driven by diffusion. The comparison with currently used models indicates the applicability of the herein developed model within integral fuel performance codes.« less

Residue frequencies and pairing preferences at protein-protein interfaces.

PubMed

Glaser, F; Steinberg, D M; Vakser, I A; Ben-Tal, N

2001-05-01

We used a nonredundant set of 621 protein-protein interfaces of known high-resolution structure to derive residue composition and residue-residue contact preferences. The residue composition at the interfaces, in entire proteins and in whole genomes correlates well, indicating the statistical strength of the data set. Differences between amino acid distributions were observed for interfaces with buried surface area of less than 1,000 A(2) versus interfaces with area of more than 5,000 A(2). Hydrophobic residues were abundant in large interfaces while polar residues were more abundant in small interfaces. The largest residue-residue preferences at the interface were recorded for interactions between pairs of large hydrophobic residues, such as Trp and Leu, and the smallest preferences for pairs of small residues, such as Gly and Ala. On average, contacts between pairs of hydrophobic and polar residues were unfavorable, and the charged residues tended to pair subject to charge complementarity, in agreement with previous reports. A bootstrap procedure, lacking from previous studies, was used for error estimation. It showed that the statistical errors in the set of pairing preferences are generally small; the average standard error is approximately 0.2, i.e., about 8% of the average value of the pairwise index (2.9). However, for a few pairs (e.g., Ser-Ser and Glu-Asp) the standard error is larger in magnitude than the pairing index, which makes it impossible to tell whether contact formation is favorable or unfavorable. The results are interpreted using physicochemical factors and their implications for the energetics of complex formation and for protein docking are discussed. Proteins 2001;43:89-102. Copyright 2001 Wiley-Liss, Inc.

Theoretical study on the sound absorption of electrolytic solutions. I. Theoretical formulation.

PubMed

Yamaguchi, T; Matsuoka, T; Koda, S

2007-04-14

A theory is formulated that describes the sound absorption of electrolytic solutions due to the relative motion of ions, including the formation of ion pairs. The theory is based on the Kubo-Green formula for the bulk viscosity. The time correlation function of the pressure is projected onto the bilinear product of the density modes of ions. The time development of the product of density modes is described by the diffusive limit of the generalized Langevin equation, and approximate expressions for the three- and four-body correlation functions required are given with the hypernetted-chain integral equation theory. Calculations on the aqueous solutions of model electrolytes are performed. It is demonstrated that the theory describes both the activated barrier crossing between contact and solvent-separated ion pairs and the Coulombic correlation between ions.

Theoretical study on the sound absorption of electrolytic solutions. I. Theoretical formulation

NASA Astrophysics Data System (ADS)

Yamaguchi, T.; Matsuoka, T.; Koda, S.

2007-04-01

A theory is formulated that describes the sound absorption of electrolytic solutions due to the relative motion of ions, including the formation of ion pairs. The theory is based on the Kubo-Green formula for the bulk viscosity. The time correlation function of the pressure is projected onto the bilinear product of the density modes of ions. The time development of the product of density modes is described by the diffusive limit of the generalized Langevin equation, and approximate expressions for the three- and four-body correlation functions required are given with the hypernetted-chain integral equation theory. Calculations on the aqueous solutions of model electrolytes are performed. It is demonstrated that the theory describes both the activated barrier crossing between contact and solvent-separated ion pairs and the Coulombic correlation between ions.

A molecular model for illegitimate recombination in Bacillus subtilis.

PubMed

Temeyer, K B; Hopkins, K M; Chapman, L F

1991-01-01

The recombinant DNA junctions at which pUB110 and Bacillus subtilis chromosomal DNA were joined to form the plasmid pKBT1 were cloned and sequenced. From the sequencing data we conclude that the pUB110 sequence is intact in the pair of cloned pKBT1 fragments and pTL12 sequences are not present. A molecular model for the formation of pKBT1 based on structural motifs characteristic of the joint sites is presented.

Enzymatically Regulated Peptide Pairing and Catalysis for the Bioanalysis of Extracellular Prometastatic Activities of Functionally Linked Enzymes

NASA Astrophysics Data System (ADS)

Li, Hao; Huang, Yue; Yu, Yue; Li, Tianqi; Li, Genxi; Anzai, Jun-Ichi

2016-05-01

Diseases such as cancer arise from systematical reconfiguration of interactions of exceedingly large numbers of proteins in cell signaling. The study of such complicated molecular mechanisms requires multiplexed detection of the inter-connected activities of several proteins in a disease-associated context. However, the existing methods are generally not well-equipped for this kind of application. Here a method for analyzing functionally linked protein activities is developed based on enzyme controlled pairing between complementary peptide helix strands, which simultaneously enables elaborate regulation of catalytic activity of the paired peptides. This method has been used to detect three different types of protein modification enzymes that participate in the modification of extracellular matrix and the formation of invasion front in tumour. In detecting breast cancer tissue samples using this method, up-regulated activity can be observed for two of the assessed enzymes, while the third enzyme is found to have a subtle fluctuation of activity. These results may point to the application of this method in evaluating prometastatic activities of proteins in tumour.

Natal and breeding philopatry in a black brant, Branta bernicla nigricans, metapopulation

USGS Publications Warehouse

Lindberg, Mark S.; Sedinger, James S.; Derksen, Dirk V.; Rockwell, Robert F.

1998-01-01

We estimated natal and breeding philopatry and dispersal probabilities for a metapopulation of Black Brant (Branta bernicla nigricans) based on observations of marked birds at six breeding colonies in Alaska, 1986–1994. Both adult females and males exhibited high (>0.90) probability of philopatry to breeding colonies. Probability of natal philopatry was significantly higher for females than males. Natal dispersal of males was recorded between every pair of colonies, whereas natal dispersal of females was observed between only half of the colony pairs. We suggest that female-biased philopatry was the result of timing of pair formation and characteristics of the mating system of brant, rather than factors related to inbreeding avoidance or optimal discrepancy. Probability of natal philopatry of females increased with age but declined with year of banding. Age-related increase in natal philopatry was positively related to higher breeding probability of older females. Declines in natal philopatry with year of banding corresponded negatively to a period of increasing population density; therefore, local population density may influence the probability of nonbreeding and gene flow among colonies.

Comparison of Accuracy and Speed of Information Identification by Nonpathologists in Synoptic Reports With Different Formats.

PubMed

Renshaw, Andrew A; Gould, Edwin W

2017-03-01

- The College of American Pathologists requires synoptic reports for specific types of pathology reports. - To compare the accuracy and speed of information retrieval in synoptic reports of different formats. - We assessed the performance of 28 nonpathologists from 4 different types of users (cancer registrars, MDs, medical non-MDs, and nonmedical) at identifying specific information in various formatted synoptic reports, using a computerized quiz that measured both accuracy and speed. - There was no significant difference in the accuracy of data identification for any user group or in any format. While there were significant differences in raw time between users, these were eliminated when normalized times were used. Compared with the standard format of a required data element (RDE) and response on 1 line, both a list of responses without an RDE (21%, P < .001) and a paired response with more concise text (33%, P < .001) were significantly faster. In contrast, both the 2-line format (RDE header on one line, response indented on the second line) (12%, P < .001) and a report with the RDE response pairs in a random order were significantly slower (16%, P < .001). - There are significant differences in ease of use by nonpathologists between different synoptic report formats. Such information may be useful in deciding between different format options.

Tree Islands of the Florida Everglades - A Disappearing Resource

USGS Publications Warehouse

,

2003-01-01

Until recently, the timing and cause of tree island formation have been poorly understood, with estimates of initial tree-island development as early as thousands of years ago to as recently as the last few decades. To increase our knowledge about the origins of these features, sediment cores were collected on and around tree islands. These cores were dated using radioisotopic techniques, including carbon-14 dating, which provides reliable dates from ~40,000 to ~300 years ago, and lead-210 dating, which provides age models for the last century. These age models were paired with vegetational reconstruction based on pollen analysis from cores to identify the timing of tree-island formation and assess past tree-island response to hydrologic changes in the 20th century.

Carrier-induced transient defect mechanism for non-radiative recombination in InGaN light-emitting devices

DOE PAGES

Bang, Junhyeok; Sun, Y. Y.; Song, Jung -Hoon; ...

2016-04-14

Non-radiative recombination (NRR) of excited carriers poses a serious challenge to optoelectronic device efficiency. Understanding the mechanism is thus crucial to defect physics and technological applications. Here, by using first-principles calculations, we propose a new NRR mechanism, where excited carriers recombine via a Frenkel-pair (FP) defect formation. While in the ground state the FP is high in energy and is unlikely to form, in the electronic excited states its formation is enabled by a strong electron-phonon coupling of the excited carriers. As a result, this NRR mechanism is expected to be general for wide-gap semiconductors, rather than being limited tomore » InGaN-based light emitting devices.« less

Starbursts triggered by central overpressure in interacting galaxies

NASA Technical Reports Server (NTRS)

Jog, Chanda J.; Das, Mousumi

1993-01-01

A triggering mechanism for the origin of enhanced, massive-star formation in the central regions of interacting spiral galaxy pairs is proposed. Our mechanism is based on the detailed evolution of a realistic interstellar medium in a galaxy following an encounter. As a disk giant molecular cloud (GMC) tumbles into the central region following a galaxy encounter, it undergoes a radiative shock compression via the pre-existing high pressure of the central intercloud medium. The shocked outer shell of a GMC becomes gravitationally unstable and begins to fragment thus resulting in a burst of star formation, when the growth time for the gravitational instabilities in the shell becomes smaller than the crossing time of the shock. The resulting values of typical infrared luminosity agree with observations.

The nearest neighbor and next nearest neighbor effects on the thermodynamic and kinetic properties of RNA base pair

NASA Astrophysics Data System (ADS)

Wang, Yujie; Wang, Zhen; Wang, Yanli; Liu, Taigang; Zhang, Wenbing

2018-01-01

The thermodynamic and kinetic parameters of an RNA base pair with different nearest and next nearest neighbors were obtained through long-time molecular dynamics simulation of the opening-closing switch process of the base pair near its melting temperature. The results indicate that thermodynamic parameters of GC base pair are dependent on the nearest neighbor base pair, and the next nearest neighbor base pair has little effect, which validated the nearest-neighbor model. The closing and opening rates of the GC base pair also showed nearest neighbor dependences. At certain temperature, the closing and opening rates of the GC pair with nearest neighbor AU is larger than that with the nearest neighbor GC, and the next nearest neighbor plays little role. The free energy landscape of the GC base pair with the nearest neighbor GC is rougher than that with nearest neighbor AU.

Evolution in slow motion

NASA Image and Video Library

2015-09-14

It is known today that merging galaxies play a large role in the evolution of galaxies and the formation of elliptical galaxies in particular. However there are only a few merging systems close enough to be observed in depth. The pair of interacting galaxies picture seen here — known as NGC 3921 — is one of these systems. NGC 3921 — found in the constellation of Ursa Major (The Great Bear) — is an interacting pair of disc galaxies in the late stages of its merger. Observations show that both of the galaxies involved were about the same mass and collided about 700 million years ago. You can see clearly in this image the disturbed morphology, tails and loops characteristic of a post-merger. The clash of galaxies caused a rush of star formation and previous Hubble observations showed over 1000 bright, young star clusters bursting to life at the heart of the galaxy pair.

QED cascade saturation in extreme high fields.

PubMed

Luo, Wen; Liu, Wei-Yuan; Yuan, Tao; Chen, Min; Yu, Ji-Ye; Li, Fei-Yu; Del Sorbo, D; Ridgers, C P; Sheng, Zheng-Ming

2018-05-30

Upcoming ultrahigh power lasers at 10 PW level will make it possible to experimentally explore electron-positron (e - e + ) pair cascades and subsequent relativistic e - e + jets formation, which are supposed to occur in extreme astrophysical environments, such as black holes, pulsars, quasars and gamma-ray bursts. In the latter case it is a long-standing question as to how the relativistic jets are formed and what their temperatures and compositions are. Here we report simulation results of pair cascades in two counter-propagating QED-strong laser fields. A scaling of QED cascade growth with laser intensity is found, showing clear cascade saturation above threshold intensity of ~10 24 W/cm 2 . QED cascade saturation leads to pair plasma cooling and longitudinal compression along the laser axis, resulting in the subsequent formation of relativistic dense e - e + jets along transverse directions. Such laser-driven QED cascade saturation may open up the opportunity to study energetic astrophysical phenomena in laboratory.

Exact solution of CKP equation and formation and interaction of two solitons in pair-ion-electron plasma

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

Batool, Nazia; Jahangir, R.; National Center of Physics

In the present investigation, cylindrical Kadomstev-Petviashvili (CKP) equation is derived in pair-ion-electron plasmas to study the propagation and interaction of two solitons. Using a novel gauge transformation, two soliton solutions of CKP equation are found analytically by using Hirota's method and to the best of our knowledge have been used in plasma physics for the first time. Interestingly, it is observed that unlike the planar Kadomstev-Petviashvili (KP) equation, the CKP equation admits horseshoe-like solitary structures. Another non-trivial feature of CKP solitary solution is that the interaction parameter gets modified by the plasma parameters contrary to the one obtained for Korteweg–demore » Vries equation. The importance of the present investigation to understand the formation and interaction of solitons in laboratory produced pair plasmas is also highlighted.« less

Formation of vacancy-impurity complexes in heavily Zn-doped InP

NASA Astrophysics Data System (ADS)

Slotte, J.; Saarinen, K.; Salmi, A.; Simula, S.; Aavikko, R.; Hautojärvi, P.

2003-03-01

Positron annihilation spectroscopy has been applied to observe the spontaneous formation of vacancy-type defects by annealing of heavily Zn-doped InP at 500 700 K. The defect is identified as the VP-Zn pair by detecting the annihilation of positrons with core electrons. We conclude that the defect is formed through a diffusion process; a phosphorus vacancy migrates until trapped by a Zn impurity and forms a negatively charged VP-Zn pair. The kinetics of the diffusion process is investigated by measuring the average positron lifetime as a function of annealing time and by fitting a diffusion model to the experimental results. We deduce a migration energy of 1.8±0.2 eV for the phosphorus vacancy. Our results explain both the presence of native VP-Zn pairs in Zn-doped InP and their disappearance in post-growth annealings.

MAJOR-MERGER GALAXY PAIRS IN THE COSMOS FIELD-MASS-DEPENDENT MERGER RATE EVOLUTION SINCE z = 1

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

Xu, C. Kevin; Zhao, Yinghe; Gao, Y.

2012-03-10

We present results of a statistical study of the cosmic evolution of the mass-dependent major-merger rate since z = 1. A stellar mass limited sample of close major-merger pairs (the CPAIR sample) was selected from the archive of the COSMOS survey. Pair fractions at different redshifts derived using the CPAIR sample and a local K-band-selected pair sample show no significant variations with stellar mass. The pair fraction exhibits moderately strong cosmic evolution, with the best-fitting function of f{sub pair} = 10{sup -1.88({+-}0.03)}(1 + z){sup 2.2({+-}0.2)}. The best-fitting function for the merger rate is R{sub mg} (Gyr{sup -1}) = 0.053 Multiplication-Signmore » (M{sub star}/10{sup 10.7} M{sub Sun} ){sup 0.3}(1 + z){sup 2.2}/(1 + z/8). This rate implies that galaxies of M{sub star} {approx} 10{sup 10}-10{sup 11.5} M{sub Sun} have undergone {approx}0.5-1.5 major mergers since z = 1. Our results show that, for massive galaxies (M{sub star} {>=} 10{sup 10.5} M{sub Sun }) at z {<=} 1, major mergers involving star-forming galaxies (i.e., wet and mixed mergers) can account for the formation of both ellipticals and red quiescent galaxies (RQGs). On the other hand, major mergers cannot be responsible for the formation of most low mass ellipticals and RQGs of M{sub star} {approx}< 10{sup 10.3} M{sub Sun }. Our quantitative estimates indicate that major mergers have significant impact on the stellar mass assembly of the most massive galaxies (M{sub star} {>=} 10{sup 11.3} M{sub Sun }), but for less massive galaxies the stellar mass assembly is dominated by the star formation. Comparison with the mass-dependent (ultra)luminous infrared galaxies ((U)LIRG) rates suggests that the frequency of major-merger events is comparable to or higher than that of (U)LIRGs.« less

Pairing phase diagram of three holes in the generalized Hubbard model

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

Navarro, O.; Espinosa, J.E.

Investigations of high-{Tc} superconductors suggest that the electronic correlation may play a significant role in the formation of pairs. Although the main interest is on the physic of two-dimensional highly correlated electron systems, the one-dimensional models related to high temperature superconductivity are very popular due to the conjecture that properties of the 1D and 2D variants of certain models have common aspects. Within the models for correlated electron systems, that attempt to capture the essential physics of high-temperature superconductors and parent compounds, the Hubbard model is one of the simplest. Here, the pairing problem of a three electrons system hasmore » been studied by using a real-space method and the generalized Hubbard Hamiltonian. This method includes the correlated hopping interactions as an extension of the previously proposed mapping method, and is based on mapping the correlated many body problem onto an equivalent site- and bond-impurity tight-binding one in a higher dimensional space, where the problem was solved in a non-perturbative way. In a linear chain, the authors analyzed the pairing phase diagram of three correlated holes for different values of the Hamiltonian parameters. For some value of the hopping parameters they obtain an analytical solution for all kind of interactions.« less

Electron attraction mediated by Coulomb repulsion.

PubMed

Hamo, A; Benyamini, A; Shapir, I; Khivrich, I; Waissman, J; Kaasbjerg, K; Oreg, Y; von Oppen, F; Ilani, S

2016-07-21

One of the defining properties of electrons is their mutual Coulomb repulsion. However, in solids this basic property may change; for example, in superconductors, the coupling of electrons to lattice vibrations makes the electrons attract one another, leading to the formation of bound pairs. Fifty years ago it was proposed that electrons can be made attractive even when all of the degrees of freedom in the solid are electronic, by exploiting their repulsion from other electrons. This attraction mechanism, termed 'excitonic', promised to achieve stronger and more exotic superconductivity. Yet, despite an extensive search, experimental evidence for excitonic attraction has yet to be found. Here we demonstrate this attraction by constructing, from the bottom up, the fundamental building block of the excitonic mechanism. Our experiments are based on quantum devices made from pristine carbon nanotubes, combined with cryogenic precision manipulation. Using this platform, we demonstrate that two electrons can be made to attract each other using an independent electronic system as the 'glue' that mediates attraction. Owing to its tunability, our system offers insights into the underlying physics, such as the dependence of the emergent attraction on the underlying repulsion, and the origin of the pairing energy. We also demonstrate transport signatures of excitonic pairing. This experimental demonstration of excitonic pairing paves the way for the design of exotic states of matter.

Electron attraction mediated by Coulomb repulsion

NASA Astrophysics Data System (ADS)

Hamo, A.; Benyamini, A.; Shapir, I.; Khivrich, I.; Waissman, J.; Kaasbjerg, K.; Oreg, Y.; von Oppen, F.; Ilani, S.

2016-07-01

One of the defining properties of electrons is their mutual Coulomb repulsion. However, in solids this basic property may change; for example, in superconductors, the coupling of electrons to lattice vibrations makes the electrons attract one another, leading to the formation of bound pairs. Fifty years ago it was proposed that electrons can be made attractive even when all of the degrees of freedom in the solid are electronic, by exploiting their repulsion from other electrons. This attraction mechanism, termed ‘excitonic’, promised to achieve stronger and more exotic superconductivity. Yet, despite an extensive search, experimental evidence for excitonic attraction has yet to be found. Here we demonstrate this attraction by constructing, from the bottom up, the fundamental building block of the excitonic mechanism. Our experiments are based on quantum devices made from pristine carbon nanotubes, combined with cryogenic precision manipulation. Using this platform, we demonstrate that two electrons can be made to attract each other using an independent electronic system as the ‘glue’ that mediates attraction. Owing to its tunability, our system offers insights into the underlying physics, such as the dependence of the emergent attraction on the underlying repulsion, and the origin of the pairing energy. We also demonstrate transport signatures of excitonic pairing. This experimental demonstration of excitonic pairing paves the way for the design of exotic states of matter.

N vacancy, self-interstitial diffusion, and Frenkel-pair formation/dissociation in TiN studied by ab-initio and classical molecular dynamics

NASA Astrophysics Data System (ADS)

Sangiovanni, Davide G.; Alling, Björn; Hultman, Lars; Abrikosov, Igor A.

2015-03-01

We use ab-initio and classical molecular dynamics (AIMD, CMD) to simulate diffusion of N vacancy and N self-interstitial point-defects in B1 TiN. The physical properties of TiN, important material system for thin film and coatings applications, are largely dictated by concentration and mobility of point defects. We determine N dilute-point-defect diffusion pathways, activation energies, attempt frequencies, and diffusion coefficients as a function of temperature. In addition, MD simulations reveal an unanticipated atomistic process, which controls the spontaneous formation of N-self-interstitial/N-vacancy pairs (Frenkel pairs) in defect-free TiN. This entails that a N lattice atom leaves its bulk position and bonds to a neighboring N lattice atom. In most cases, Frenkel-pair NI and NV recombine within a fraction of ns; 50% of these processes result in the exchange of two nitrogen lattice atoms. Occasionally, however, Frenkel-pair N-interstitial atoms permanently escape from the anion vacancy site, thus producing unpaired NI and NV point defects. The Knut and Alice Wallenberg foundation (Isotope Project, 2011.0094), the Swedish Research Council (VR) Linköping Linnaeus Initiative LiLi-NFM (Grant 2008-6572), and the Swedish Government Strategic Research (Grant MatLiU 2009-00971).

[Structural and Dipole Structure Peculiarities of Hoogsteen Base Pairs Formed in Complementary Nucleobases according to ab initio Quantum Mechanics Studies].

PubMed

Petrenko, Y M

2015-01-01

Ab initio quantum mechanics studies for the detection of structure and dipole structure peculiarities of Hoogsteen base pairs relative to Watson-Crick base pairs, were performed during our work. These base pairs are formed as a result of complementary interactions. It was revealed, that adenine-thymine Hoogsteen base pair and adenine-thymine Watson-Crick base pairs can be formed depending on initial configuration. Cytosine-guanine Hoogsteen pairs are formed only when cytosine was originally protonated. Both types of Hoogsteen pairs have noticeable difference in the bond distances and angles. These differences appeared in purine as well as in pyrimidine parts of the pairs. Hoogsteen pairs have mostly shorter hydrogen bond lengths and significantly larger angles of hydrogen bonds and larger angles between the hydrogen bonds than Watson-Crick base pairs. Notable differences are also observed with respect to charge distribution and dipole moment. Quantitative data on these differences are shown in our work. It is also reported that the values of local parameters (according to Cambridge classification of the parameters which determine DNA properties) in Hoogsteen base pairs, are greatly different from Watson-Crick ones.

Nucleic acid duplexes incorporating a dissociable covalent base pair

PubMed Central

Gao, Kui; Orgel, Leslie E.

1999-01-01

We have used molecular modeling techniques to design a dissociable covalently bonded base pair that can replace a Watson-Crick base pair in a nucleic acid with minimal distortion of the structure of the double helix. We introduced this base pair into a potential precursor of a nucleic acid double helix by chemical synthesis and have demonstrated efficient nonenzymatic template-directed ligation of the free hydroxyl groups of the base pair with appropriate short oligonucleotides. The nonenzymatic ligation reactions, which are characteristic of base paired nucleic acid structures, are abolished when the covalent base pair is reduced and becomes noncoplanar. This suggests that the covalent base pair linking the two strands in the duplex is compatible with a minimally distorted nucleic acid double-helical structure. PMID:10611299

Influence of nucleotide modifications at the C2’ position on the Hoogsteen base-paired parallel-stranded duplex of poly(A) RNA

PubMed Central

Copp, William; Denisov, Alexey Y.; Xie, Jingwei; Noronha, Anne M.; Liczner, Christopher; Safaee, Nozhat

2017-01-01

Abstract Polyadenylate (poly(A)) has the ability to form a parallel duplex with Hoogsteen adenine:adenine base pairs at low pH or in the presence of ammonium ions. In order to evaluate the potential of this structural motif for nucleic acid-based nanodevices, we characterized the effects on duplex stability of substitutions of the ribose sugar with 2′-deoxyribose, 2′-O-methyl-ribose, 2′-deoxy-2′-fluoro-ribose, arabinose and 2′-deoxy-2′-fluoro-arabinose. Deoxyribose substitutions destabilized the poly(A) duplex both at low pH and in the presence of ammonium ions: no duplex formation could be detected with poly(A) DNA oligomers. Other sugar C2’ modifications gave a variety of effects. Arabinose and 2′-deoxy-2′-fluoro-arabinose nucleotides strongly destabilized poly(A) duplex formation. In contrast, 2′-O-methyl and 2′-deoxy-2′-fluoro-ribo modifications were stabilizing either at pH 4 or in the presence of ammonium ions. The differential effect suggests they could be used to design molecules selectively responsive to pH or ammonium ions. To understand the destabilization by deoxyribose, we determined the structures of poly(A) duplexes with a single DNA residue by nuclear magnetic resonance spectroscopy and X-ray crystallography. The structures revealed minor structural perturbations suggesting that the combination of sugar pucker propensity, hydrogen bonding, pKa shifts and changes in hydration determine duplex stability. PMID:28973475

Influence of nucleotide modifications at the C2' position on the Hoogsteen base-paired parallel-stranded duplex of poly(A) RNA.

PubMed

Copp, William; Denisov, Alexey Y; Xie, Jingwei; Noronha, Anne M; Liczner, Christopher; Safaee, Nozhat; Wilds, Christopher J; Gehring, Kalle

2017-09-29

Polyadenylate (poly(A)) has the ability to form a parallel duplex with Hoogsteen adenine:adenine base pairs at low pH or in the presence of ammonium ions. In order to evaluate the potential of this structural motif for nucleic acid-based nanodevices, we characterized the effects on duplex stability of substitutions of the ribose sugar with 2'-deoxyribose, 2'-O-methyl-ribose, 2'-deoxy-2'-fluoro-ribose, arabinose and 2'-deoxy-2'-fluoro-arabinose. Deoxyribose substitutions destabilized the poly(A) duplex both at low pH and in the presence of ammonium ions: no duplex formation could be detected with poly(A) DNA oligomers. Other sugar C2' modifications gave a variety of effects. Arabinose and 2'-deoxy-2'-fluoro-arabinose nucleotides strongly destabilized poly(A) duplex formation. In contrast, 2'-O-methyl and 2'-deoxy-2'-fluoro-ribo modifications were stabilizing either at pH 4 or in the presence of ammonium ions. The differential effect suggests they could be used to design molecules selectively responsive to pH or ammonium ions. To understand the destabilization by deoxyribose, we determined the structures of poly(A) duplexes with a single DNA residue by nuclear magnetic resonance spectroscopy and X-ray crystallography. The structures revealed minor structural perturbations suggesting that the combination of sugar pucker propensity, hydrogen bonding, pKa shifts and changes in hydration determine duplex stability. © The Author(s) 2017. Published by Oxford University Press on behalf of Nucleic Acids Research.

Pair bond formation leads to a sustained increase in global cerebral glucose metabolism in monogamous male titi monkeys (Callicebus cupreus).

PubMed

Maninger, Nicole; Hinde, Katie; Mendoza, Sally P; Mason, William A; Larke, Rebecca H; Ragen, Benjamin J; Jarcho, Michael R; Cherry, Simon R; Rowland, Douglas J; Ferrer, Emilio; Bales, Karen L

2017-04-21

Social bonds, especially attachment relationships, are crucial to our health and happiness. However, what we know about the neural substrates of these bonds is almost exclusively limited to rodent models and correlational experiments in humans. Here, we used socially monogamous non-human primates, titi monkeys (Callicebus cupreus) to experimentally examine changes in regional and global cerebral glucose metabolism (GCGM) during the formation and maintenance of pair bonds. Baseline positron emission tomography (PET) scans were taken of thirteen unpaired male titi monkeys. Seven males were then experimentally paired with females, scanned and compared, after one week, to six age-matched control males. Five of the six control males were then also paired and scanned after one week. Scans were repeated on all males after four months of pairing. PET scans were coregistered with structural magnetic resonance imaging (MRI), and region of interest (ROI) analysis was carried out. A primary finding was that paired males showed a significant increase in [ 18 F]-fluorodeoxyglucose (FDG) uptake in whole brain following one week of pairing, which is maintained out to four months. Dopaminergic, "motivational" areas and those involved in social behavior showed the greatest change in glucose uptake. In contrast, control areas changed only marginally more than GCGM. These findings confirm the large effects of social bonds on GCGM. They also suggest that more studies should examine how social manipulations affect whole-brain FDG uptake, as opposed to assuming that it does not change across condition. Copyright © 2017 IBRO. Published by Elsevier Ltd. All rights reserved.

The differential effects of emotional salience on direct associative and relational memory during a nap.

PubMed

Alger, Sara E; Payne, Jessica D

2016-12-01

Relational memories are formed from shared components between directly learned memory associations, flexibly linking learned information to better inform future judgments. Sleep has been found to facilitate both direct associative and relational memories. However, the impact of incorporating emotionally salient information into learned material and the interaction of emotional salience and sleep in facilitating both types of memory is unknown. Participants encoded two sets of picture pairs, with either emotionally negative or neutral objects paired with neutral faces. The same objects were present in both sets, paired with two different faces across the sets. Baseline memory for these directly paired associates was tested immediately after encoding, followed by either a 90-min nap opportunity or wakefulness. Five hours after learning, a surprise test assessed relational memory, the indirect association between two faces paired with the same object during encoding, followed by a retest of direct associative memory. Overall, negative information was remembered better than neutral for directly learned pairs. A nap facilitated both preservation of direct associative memories and formation of relational memories, compared to remaining awake. Interestingly, however, this sleep benefit was observed specifically for neutral directly paired associates, while both neutral and negative relational associations benefitted from a nap. Finally, REM sleep played opposing roles in neutral direct and relational associative memory formation, with more REM sleep leading to forgetting of direct associations but promoting relational associations, suggesting that, while not benefitting memory consolidation for directly learned details, REM sleep may foster the memory reorganization needed for relational memory.

Pair bond Formation Leads to a Sustained Increase in Global Cerebral Glucose Metabolism in Monogamous Male Titi Monkeys (Callicebus cupreus)

PubMed Central

Maninger, Nicole; Hinde, Katie; Mendoza, Sally P.; Mason, William A.; Larke, Rebecca H.; Ragen, Benjamin J; Jarcho, Michael R.; Cherry, Simon R.; Rowland, Douglas J.; Ferrer, Emilio; Bales, Karen L.

2017-01-01

Social bonds, especially attachment relationships, are crucial to our health and happiness. However, what we know about the neural substrates of these bonds is almost exclusively limited to rodent models and correlational experiments in humans. Here, we used socially monogamous non-human primates, titi monkeys (Callicebus cupreus) to experimentally examine changes in regional and global cerebral glucose metabolism during the formation and maintenance of pair bonds. Baseline positron emission tomography (PET) scans were taken of thirteen unpaired male titi monkeys. Seven males were then experimentally paired with females, scanned and compared, after one week, to six age-matched control males. Five of the six control males were then also paired and scanned after one week. Scans were repeated on all males after four months of pairing. PET scans were coregistered with structural magnetic resonance imaging (MRI), and region of interest (ROI) analysis was carried out. A primary finding was that paired males showed a significant increase in FDG uptake in whole brain following one week of pairing, which is maintained out to four months. Dopaminergic, “motivational” areas and those involved in social behavior showed the greatest change in glucose uptake. In contrast, control areas changed only marginally more than GCGM. These findings confirm the large effects of social bonds on global cerebral glucose metabolism. They also suggest that more studies should examine how social manipulations affect whole brain FDG uptake, as opposed to assuming that it does not change across condition. PMID:28242440

Neural mechanisms of mother-infant bonding and pair bonding: Similarities, differences, and broader implications.

PubMed

Numan, Michael; Young, Larry J

2016-01-01

This article is part of a Special Issue "Parental Care". Mother-infant bonding is a characteristic of virtually all mammals. The maternal neural system may have provided the scaffold upon which other types of social bonds in mammals have been built. For example, most mammals exhibit a polygamous mating system, but monogamy and pair bonding between mating partners occur in ~5% of mammalian species. In mammals, it is plausible that the neural mechanisms that promote mother-infant bonding have been modified by natural selection to establish the capacity to develop a selective bond with a mate during the evolution of monogamous mating strategies. Here we compare the details of the neural mechanisms that promote mother-infant bonding in rats and other mammals with those that underpin pair bond formation in the monogamous prairie vole. Although details remain to be resolved, remarkable similarities and a few differences between the mechanisms underlying these two types of bond formation are revealed. For example, amygdala and nucleus accumbens-ventral pallidum (NA-VP) circuits are involved in both types of bond formation, and dopamine and oxytocin actions within NA appear to promote the synaptic plasticity that allows either infant or mating partner stimuli to persistently activate NA-VP attraction circuits, leading to an enduring social attraction and bonding. Further, although the medial preoptic area is essential for maternal behavior, its role in pair bonding remains to be determined. Our review concludes by examining the broader implications of this comparative analysis, and evidence is provided that the maternal care system may have also provided the basic neural foundation for other types of strong social relationships, beyond pair bonding, in mammals, including humans. Copyright © 2015 Elsevier Inc. All rights reserved.

Neural mechanisms of mother-infant bonding and pair bonding: Similarities, differences, and broader implications

PubMed Central

Numan, Michael; Young, Larry J.

2015-01-01

Mother-infant bonding is a characteristic of virtually all mammals. The maternal neural system may have provided the scaffold upon which other types of social bonds in mammals have been built. For example, most mammals exhibit a polygamous mating system, but monogamy and pair bonding between mating partners occurs in ∼5% of mammalian species. In mammals, it is plausible that the neural mechanisms that promote mother-infant bonding have been modified by natural selection to establish the capacity to develop a selective bond with a mate during the evolution of monogamous mating strategies. Here we compare the details of the neural mechanisms that promote mother-infant bonding in rats and other mammals with those that underpin pair bond formation in the monogamous prairie vole. Although details remain to be resolved, remarkable similarities and a few differences between the mechanisms underlying these two types of bond formation are revealed. For example, amygdala and nucleus accumbens-ventral pallidum (NA-VP) circuits are involved in both types of bond formation, and dopamine and oxytocin action within NA appears to promote the synaptic plasticity that allows either infant or mating partner stimuli to persistently activate NA-VP attraction circuits, leading to an enduring social attraction and bonding. Further, although the medial preoptic area is essential for maternal behavior, its role in pair bonding remains to be determined. Our review concludes by examining the broader implications of this comparative analysis, and evidence is provided that the maternal care system may have also provided the basic neural foundation for other types of strong social relationships, beyond pair bonding, in mammals, including humans. PMID:26062432

Molecular recognition of DNA base pairs by the formamido/pyrrole and formamido/imidazole pairings in stacked polyamides.

PubMed

Buchmueller, Karen L; Staples, Andrew M; Uthe, Peter B; Howard, Cameron M; Pacheco, Kimberly A O; Cox, Kari K; Henry, James A; Bailey, Suzanna L; Horick, Sarah M; Nguyen, Binh; Wilson, W David; Lee, Moses

2005-01-01

Polyamides containing an N-terminal formamido (f) group bind to the minor groove of DNA as staggered, antiparallel dimers in a sequence-specific manner. The formamido group increases the affinity and binding site size, and it promotes the molecules to stack in a staggered fashion thereby pairing itself with either a pyrrole (Py) or an imidazole (Im). There has not been a systematic study on the DNA recognition properties of the f/Py and f/Im terminal pairings. These pairings were analyzed here in the context of f-ImPyPy, f-ImPyIm, f-PyPyPy and f-PyPyIm, which contain the central pairing modes, -ImPy- and -PyPy-. The specificity of these triamides towards symmetrical recognition sites allowed for the f/Py and f/Im terminal pairings to be directly compared by SPR, CD and DeltaT (M) experiments. The f/Py pairing, when placed next to the -ImPy- or -PyPy- central pairings, prefers A/T and T/A base pairs to G/C base pairs, suggesting that f/Py has similar DNA recognition specificity to Py/Py. With -ImPy- central pairings, f/Im prefers C/G base pairs (>10 times) to the other Watson-Crick base pairs; therefore, f/Im behaves like the Py/Im pair. However, the f/Im pairing is not selective for the C/G base pair when placed next to the -PyPy- central pairings.

Colistin-Resistant Acinetobacter baumannii Clinical Strains with Deficient Biofilm Formation

PubMed Central

Dafopoulou, Konstantina; Xavier, Basil Britto; Hotterbeekx, An; Janssens, Lore; Lammens, Christine; Dé, Emmanuelle; Goossens, Herman; Tsakris, Athanasios; Malhotra-Kumar, Surbhi

2015-01-01

In two pairs of clinical colistin-susceptible/colistin-resistant (Csts/Cstr) Acinetobacter baumannii strains, the Cstr strains showed significantly decreased biofilm formation in static and dynamic assays (P < 0.001) and lower relative fitness (P < 0.05) compared with those of the Csts counterparts. The whole-genome sequencing comparison of strain pairs identified a mutation converting a stop codon to lysine (*241K) in LpsB (involved in lipopolysaccharide [LPS] synthesis) in one Cstr strain and a frameshift mutation in CarO and the loss of a 47,969-bp element containing multiple genes associated with biofilm production in the other. PMID:26666921

Defect pair formation in fluorine and nitrogen codoped TiO2

NASA Astrophysics Data System (ADS)

Kordatos, A.; Kelaidis, N.; Chroneos, A.

2018-04-01

Titanium oxide is extensively investigated because of its high chemical stability and its photocatalytic properties; nevertheless, the large band gap limits its activity to a small portion of the solar spectrum. Nitrogen and fluorine codoping is an efficient defect engineering strategy to increase the photocatalytic activity of titanium oxide. In the present study, we apply density functional theory to investigate the interaction of nitrogen with fluorine and the formation of defect pairs. We show that in fluorine and nitrogen codoped titanium oxide, the FiNi, FONi, and FiNTi defects can form. Their impact on the electronic structure of titanium oxide is discussed.

Scattering of a vortex pair by a single quantum vortex in a Bose–Einstein condensate

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

Smirnov, L. A., E-mail: smirnov-lev@allp.sci-nnov.ru; Smirnov, A. I., E-mail: smirnov@appl.sci-nnov.ru; Mironov, V. A.

We analyze the scattering of vortex pairs (the particular case of 2D dark solitons) by a single quantum vortex in a Bose–Einstein condensate with repulsive interaction between atoms. For this purpose, an asymptotic theory describing the dynamics of such 2D soliton-like formations in an arbitrary smoothly nonuniform flow of a ultracold Bose gas is developed. Disregarding the radiation loss associated with acoustic wave emission, we demonstrate that vortex–antivortex pairs can be put in correspondence with quasiparticles, and their behavior can be described by canonical Hamilton equations. For these equations, we determine the integrals of motion that can be used tomore » classify various regimes of scattering of vortex pairs by a single quantum vortex. Theoretical constructions are confirmed by numerical calculations performed directly in terms of the Gross–Pitaevskii equation. We propose a method for estimating the radiation loss in a collision of a soliton-like formation with a phase singularity. It is shown by direct numerical simulation that under certain conditions, the interaction of vortex pairs with a core of a single quantum vortex is accompanied by quite intense acoustic wave emission; as a result, the conditions for applicability of the asymptotic theory developed here are violated. In particular, it is visually demonstrated by a specific example how radiation losses lead to a transformation of a vortex–antivortex pair into a vortex-free 2D dark soliton (i.e., to the annihilation of phase singularities).« less

Zinc Vacancy Formation and its Effect on the Conductivity of ZnO

NASA Astrophysics Data System (ADS)

Khan, Enamul; Weber, Marc; Langford, Steve; Dickinson, Tom

2010-03-01

Exposing single crystal ZnO to 193-nm ArF excimer laser radiation can produce metallic zinc nanoparticles along the surface. The particle production mechanism appears to involve interstitial-vacancy pair formation in the near-surface bulk. Conductivity measurements made with one probe inside the laser spot and the other outside show evidence for rectifying behavior. Positron annihilation spectroscopy confirms the presence of Zn vacancies. We suggest that Zn vacancies are a possible source of p-type behavior in irradiated ZnO. Quadrupole mass spectroscopy shows that both oxygen and zinc are emitted during irradiation. Electron-hole pair production has previously been invoked to account for particle desorption from ZnO during UV illumination. Our results suggest that preexisting and laser-generated defects play a critical role in particle desorption and Zn vacancy formation.

Unique Thermal Stability of Unnatural Hydrophobic Ds Bases in Double-Stranded DNAs.

PubMed

Kimoto, Michiko; Hirao, Ichiro

2017-10-20

Genetic alphabet expansion technology, the introduction of unnatural bases or base pairs into replicable DNA, has rapidly advanced as a new synthetic biology area. A hydrophobic unnatural base pair between 7-(2-thienyl)imidazo[4,5-b]pyridine (Ds) and 2-nitro-4-propynylpyrrole (Px) exhibited high fidelity as a third base pair in PCR. SELEX methods using the Ds-Px pair enabled high-affinity DNA aptamer generation, and introducing a few Ds bases into DNA aptamers extremely augmented their affinities and selectivities to target proteins. Here, to further scrutinize the functions of this highly hydrophobic Ds base, the thermal stabilities of double-stranded DNAs (dsDNA) containing a noncognate Ds-Ds or G-Ds pair were examined. The thermal stability of the Ds-Ds self-pair was as high as that of the natural G-C pair, and apart from the generally higher stability of the G-C pair than that of the A-T pair, most of the 5'-pyrimidine-Ds-purine-3' sequences, such as CDsA and TDsA, exhibited higher stability than the 5'-purine-Ds-pyrimidine-3' sequences, such as GDsC and ADsC, in dsDNAs. This trait enabled the GC-content-independent control of the thermal stability of the designed dsDNA fragments. The melting temperatures of dsDNA fragments containing the Ds-Ds pair can be predicted from the nearest-neighbor parameters including the Ds base. In addition, the noncognate G-Ds pair can efficiently distinguish its neighboring cognate natural base pairs from noncognate pairs. We demonstrated that real-time PCR using primers containing Ds accurately detected a single-nucleotide mismatch in target DNAs. These unique properties of the Ds base that affect the stabilities of the neighboring base pairs could impart new functions to DNA molecules and technologies.

Entropy Transfer between Residue Pairs and Allostery in Proteins: Quantifying Allosteric Communication in Ubiquitin

PubMed Central

2017-01-01

It has recently been proposed by Gunasakaran et al. that allostery may be an intrinsic property of all proteins. Here, we develop a computational method that can determine and quantify allosteric activity in any given protein. Based on Schreiber's transfer entropy formulation, our approach leads to an information transfer landscape for the protein that shows the presence of entropy sinks and sources and explains how pairs of residues communicate with each other using entropy transfer. The model can identify the residues that drive the fluctuations of others. We apply the model to Ubiquitin, whose allosteric activity has not been emphasized until recently, and show that there are indeed systematic pathways of entropy and information transfer between residues that correlate well with the activities of the protein. We use 600 nanosecond molecular dynamics trajectories for Ubiquitin and its complex with human polymerase iota and evaluate entropy transfer between all pairs of residues of Ubiquitin and quantify the binding susceptibility changes upon complex formation. We explain the complex formation propensities of Ubiquitin in terms of entropy transfer. Important residues taking part in allosteric communication in Ubiquitin predicted by our approach are in agreement with results of NMR relaxation dispersion experiments. Finally, we show that time delayed correlation of fluctuations of two interacting residues possesses an intrinsic causality that tells which residue controls the interaction and which one is controlled. Our work shows that time delayed correlations, entropy transfer and causality are the required new concepts for explaining allosteric communication in proteins. PMID:28095404

Mechanism-based inhibition of C5-cytosine DNA methyltransferases by 2-H pyrimidinone.

PubMed

Hurd, P J; Whitmarsh, A J; Baldwin, G S; Kelly, S M; Waltho, J P; Price, N C; Connolly, B A; Hornby, D P

1999-02-19

DNA duplexes in which the target cytosine base is replaced by 2-H pyrimidinone have previously been shown to bind with a significantly greater affinity to C5-cytosine DNA methyltransferases than unmodified DNA. Here, it is shown that 2-H pyrimidinone, when incorporated into DNA duplexes containing the recognition sites for M.HgaI-2 and M.MspI, elicits the formation of inhibitory covalent nucleoprotein complexes. We have found that although covalent complexes are formed between 2-H pyrimidinone-modified DNA and both M.HgaI-2 and M.MspI, the kinetics of complex formation are quite distinct in each case. Moreover, the formation of a covalent complex is still observed between 2-H pyrimidinone DNA and M.MspI in which the active-site cysteine residue is replaced by serine or threonine. Covalent complex formation between M.MspI and 2-H pyrimidinone occurs as a direct result of nucleophilic attack by the residue at the catalytic position, which is enhanced by the absence of the 4-amino function in the base. The substitution of the catalytic cysteine residue by tyrosine or chemical modification of the wild-type enzyme with N-ethylmaleimide, abolishes covalent interaction. Nevertheless the 2-H pyrimidinone-substituted duplex still binds to M.MspI with a greater affinity than a standard cognate duplex, since the 2-H pyrimidinone base is mis-paired with guanine. Copyright 1999 Academic Press.

Hierarchical Star Formation in Turbulent Media: Evidence from Young Star Clusters

NASA Astrophysics Data System (ADS)

Grasha, K.; Elmegreen, B. G.; Calzetti, D.; Adamo, A.; Aloisi, A.; Bright, S. N.; Cook, D. O.; Dale, D. A.; Fumagalli, M.; Gallagher, J. S., III; Gouliermis, D. A.; Grebel, E. K.; Kahre, L.; Kim, H.; Krumholz, M. R.; Lee, J. C.; Messa, M.; Ryon, J. E.; Ubeda, L.

2017-06-01

We present an analysis of the positions and ages of young star clusters in eight local galaxies to investigate the connection between the age difference and separation of cluster pairs. We find that star clusters do not form uniformly but instead are distributed so that the age difference increases with the cluster pair separation to the 0.25-0.6 power, and that the maximum size over which star formation is physically correlated ranges from ˜200 pc to ˜1 kpc. The observed trends between age difference and separation suggest that cluster formation is hierarchical both in space and time: clusters that are close to each other are more similar in age than clusters born further apart. The temporal correlations between stellar aggregates have slopes that are consistent with predictions of turbulence acting as the primary driver of star formation. The velocity associated with the maximum size is proportional to the galaxy’s shear, suggesting that the galactic environment influences the maximum size of the star-forming structures.

Infrared Colors of Dwarf-Dwarf Galaxy Interactions

NASA Astrophysics Data System (ADS)

Liss, Sandra; Stierwalt, Sabrina; Johnson, Kelsey; Patton, Dave; Kallivayalil, Nitya

2015-10-01

We request Spitzer Warm Mission IRAC Channel 1 & 2 imaging for a sample of 60 isolated dwarf galaxy pairs as a key component of a larger, multi-wavelength effort to understand the role low-mass mergers play in galaxy evolution. A systematic study of dwarf-dwarf mergers has never been done, and we wish to characterize the impact such interactions have on fueling star formation in the nearby universe. The Spitzer imaging proposed here will allow us to determine the extent to which the 3.6 and 4.5 mum bands are dominated by stellar light and investigate a) the extent to which interacting pairs show IR excess and b) whether the excess is related to the pair separation. Second, we will use this IR photometry to constrain the processes contributing to the observed color excess and scatter in each system. We will take advantage of the wealth of observations available in the Spitzer Heritage Archive for 'normal' non-interacting dwarfs by comparing the stellar populations of those dwarfs with the likely interacting dwarfs in our sample. Ultimately, we can combine the Spitzer imaging proposed here with our current, ongoing efforts to obtain groundbased optical photometry to model the star formation histories of these dwarfs and to help constrain the timescales and impact dwarf-dwarf mergers have on fueling star formation. The sensitivity and resolution offered by Spitzer are necessary to determine the dust properties of these interacting systems, and how these properties vary as a function of pair separation, mass ratio, and gas fraction.

Identification of ion-pair structures in solution by vibrational stark effects

DOE PAGES

Hack, John; Mani, Tomoyasu; Grills, David C.; ...

2016-01-25

Here, ion pairing is a fundamental consideration in many areas of chemistry and has implications in a wide range of sciences and technologies that include batteries and organic photovoltaics. Ions in solution are known to inhabit multiple possible states, including free ions (FI), contact ion pairs (CIP), and solvent-separated ion pairs (SSIP). However, in solutions of organic radicals and nonmetal electrolytes, it is often difficult to distinguish between these states. In the first part of this work, we report evidence for the formation of SSIPs in low-polarity solvents and distinct measurements of CIP, SSIP, and FI, by using the ν(C≡N)more » infrared (IR) band of a nitrile-substituted fluorene radical anion. Use of time-resolved IR detection following pulse radiolysis allowed us to unambiguously assign the peak of the FI. In the presence of nonmetal electrolytes, two distinct red-shifted peaks were observed and assigned to the CIP and SSIP. The assignments are interpreted in the framework of the vibrational Stark effect (VSE) and are supported by (1) the solvent dependence of ion-pair populations, (2) the observation of a cryptand-separated sodium ion pair that mimics the formation of SSIPs, and (3) electronic structure calculations. In the second part of this work, we show that a blue-shift of the ν(C≡N) IR band due to the VSE can be induced in a nitrile-substituted fluorene radical anion by covalently tethering it to a metal-chelating ligand that forms an intramolecular ion pair upon reduction and complexation with sodium ion. This adds support to the conclusion that the shift in IR absorptions by ion pairing originates from the VSE. These results combined show that we can identify ion-pair structures by using the VSE, including the existence of SSIPs in a low-polarity solvent.« less

Identification of ion-pair structures in solution by vibrational stark effects

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

Hack, John; Mani, Tomoyasu; Grills, David C.

Here, ion pairing is a fundamental consideration in many areas of chemistry and has implications in a wide range of sciences and technologies that include batteries and organic photovoltaics. Ions in solution are known to inhabit multiple possible states, including free ions (FI), contact ion pairs (CIP), and solvent-separated ion pairs (SSIP). However, in solutions of organic radicals and nonmetal electrolytes, it is often difficult to distinguish between these states. In the first part of this work, we report evidence for the formation of SSIPs in low-polarity solvents and distinct measurements of CIP, SSIP, and FI, by using the ν(C≡N)more » infrared (IR) band of a nitrile-substituted fluorene radical anion. Use of time-resolved IR detection following pulse radiolysis allowed us to unambiguously assign the peak of the FI. In the presence of nonmetal electrolytes, two distinct red-shifted peaks were observed and assigned to the CIP and SSIP. The assignments are interpreted in the framework of the vibrational Stark effect (VSE) and are supported by (1) the solvent dependence of ion-pair populations, (2) the observation of a cryptand-separated sodium ion pair that mimics the formation of SSIPs, and (3) electronic structure calculations. In the second part of this work, we show that a blue-shift of the ν(C≡N) IR band due to the VSE can be induced in a nitrile-substituted fluorene radical anion by covalently tethering it to a metal-chelating ligand that forms an intramolecular ion pair upon reduction and complexation with sodium ion. This adds support to the conclusion that the shift in IR absorptions by ion pairing originates from the VSE. These results combined show that we can identify ion-pair structures by using the VSE, including the existence of SSIPs in a low-polarity solvent.« less

Predicting links based on knowledge dissemination in complex network

NASA Astrophysics Data System (ADS)

Zhou, Wen; Jia, Yifan

2017-04-01

Link prediction is the task of mining the missing links in networks or predicting the next vertex pair to be connected by a link. A lot of link prediction methods were inspired by evolutionary processes of networks. In this paper, a new mechanism for the formation of complex networks called knowledge dissemination (KD) is proposed with the assumption of knowledge disseminating through the paths of a network. Accordingly, a new link prediction method-knowledge dissemination based link prediction (KDLP)-is proposed to test KD. KDLP characterizes vertex similarity based on knowledge quantity (KQ) which measures the importance of a vertex through H-index. Extensive numerical simulations on six real-world networks demonstrate that KDLP is a strong link prediction method which performs at a higher prediction accuracy than four well-known similarity measures including common neighbors, local path index, average commute time and matrix forest index. Furthermore, based on the common conclusion that an excellent link prediction method reveals a good evolving mechanism, the experiment results suggest that KD is a considerable network evolving mechanism for the formation of complex networks.

Cloning of hydrogenase genes and fine structure analysis of an operon essential for H/sub 2/ metabolism in Escherichia coli

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

Sankar, P.; Lee, J.H.; Shanmugam, K.T.

1985-04-01

Escherichia coli has two unlinked genes that code for hydrogenase synthesis and activity. The DNA fragments containing the two genes (hydA and hydB) were cloned into a plasmid vector, pBR322. The plasmids containing the hyd genes (pSE-290 and pSE-111 carrying the hydA and hydB genes, respectively) were used to genetically map a total of 51 mutant strains with defects in hydrogenase activity. A total of 37 mutants carried a mutation in the hydB gene, whereas the remaining 14 hyd were hydA. This complementation analysis also established the presence of two new genes, so far unidentified, one coding for formate dehydrogenase-2more » (fdv) and another producing an electron transport protein (fhl) coupling formate dehydrogenase-2 to hydrogenase. Three of the four genes, hydB, fhl, and fdv, may constitute a single operon, and all three genes are carried by a 5.6-kilobase-pair chromosomal DNA insert in plasmid pSE-128. Plasmids carrying a part of this 5.6-kilobase-pair DNA (pSE-130) or fragments derived from this DNA in different orientations (pSE-126 and pSE-129) inhibited the production of active formate hydrogenlyase. This inhibition occurred even in a prototrophic E. coli, strain K-10, but only during an early induction period. These results, based on complementation analysis with cloned DNA fragments, show that both hydA and hydB genes are essential for the production of active hydrogenase. For the expression of active formate hydrogenlyase, two other gene products, fhl and fdv are also needed. All four genes map between 58 and 59 min in the E. coli chromosome.« less

Metabolic parameters linked by phenotype microarray to acid resistance profiles of poultry-associated Salmonella enterica.

PubMed

Guard, Jean; Rothrock, Michael J; Shah, Devendra H; Jones, Deana R; Gast, Richard K; Sanchez-Ingunza, Roxana; Madsen, Melissa; El-Attrache, John; Lungu, Bwalya

Phenotype microarrays were analyzed for 51 datasets derived from Salmonella enterica. The top 4 serotypes associated with poultry products and one associated with turkey, respectively Typhimurium, Enteritidis, Heidelberg, Infantis and Senftenberg, were represented. Datasets were partitioned initially into two clusters based on ranking by values at pH 4.5 (PM10 A03). Negative control wells were used to establish 90 respiratory units as the point differentiating acid resistance from sensitive strains. Thus, 24 isolates that appeared most acid-resistant were compared initially to 27 that appeared most acid-sensitive (24 × 27 format). Paired cluster analysis was also done and it included the 7 most acid-resistant and -sensitive datasets (7 × 7 format). Statistical analyses of ranked data were then calculated in order of standard deviation, probability value by the Student's t-test and a measure of the magnitude of difference called effect size. Data were reported as significant if, by order of filtering, the following parameters were calculated: i) a standard deviation of 24 respiratory units or greater from all datasets for each chemical, ii) a probability value of less than or equal to 0.03 between clusters and iii) an effect size of at least 0.50 or greater between clusters. Results suggest that between 7.89% and 23.16% of 950 chemicals differentiated acid-resistant isolates from sensitive ones, depending on the format applied. Differences were more evident at the extremes of phenotype using the subset of data in the paired 7 × 7 format. Results thus provide a strategy for selecting compounds for additional research, which may impede the emergence of acid-resistant Salmonella enterica in food. Published by Elsevier Masson SAS.

Sequence specificity of mutagen-nucleic acid complexes in solution: intercalation and mutagen-base pair overlap geometries for proflavine binding to dC-dC-dG-dG and dG-dG-dC-dC self-complementary duplexes.

PubMed

Patel, D J; Canuel, L L

1977-07-01

The complex formed between the mutagen proflavine and the dC-dC-dG-dG and dG-dG-dC-dC self-complementary tetranucleotide duplexes has been monitored by proton high resolution nuclear magnetic resonance spectroscopy in 0.1 M phosphate solution at high nucleotide/drug ratios. The large upfield shifts (0.5 to 0.85 ppm) observed at all the proflavine ring nonexchangeable protons on complex formation are consistent with intercalation of the mutagen between base pairs of the tetranucleotide duplex. We have proposed an approximate overlap geometry between the proflavine ring and nearest neighbor base pairs at the intercalation site from a comparison between experimental shifts and those calculated for various stacking orientations. We have compared the binding of actinomycin D, propidium diiodide, and proflavine to self-complementary tetranucleotide sequences dC-dC-dG-dG and dG-dG-dC-dC by UV absorbance changes in the drug bands between 400 and 500 nm. Actinomycin D exhibits a pronounced specificity for sequences with dG-dC sites (dG-dG-dC-dC), while propidium diiodide and proflavine exhibit a specificity for sequences with dC-dG sites (dC-dC-dG-dG). Actinomycin D binds more strongly than propidium diiodide and proflavine to dC-dG-dC-dG (contains dC-dG and dG-dC binding sites), indicative of the additional stabilization from hydrogen bonding and hydrophobic interactions between the pentapeptide lactone rings of actinomycin D and the base pair edges and sugar-phosphate backbone of the tetranucleotide duplex.

Sequence specificity of mutagen-nucleic acid complexes in solution: Intercalation and mutagen-base pair overlap geometries for proflavine binding to dC-dC-dG-dG and dG-dG-dC-dC self-complementary duplexes

PubMed Central

Patel, Dinshaw J.; Canuel, Lita L.

1977-01-01

The complex formed between the mutagen proflavine and the dC-dC-dG-dG and dG-dG-dC-dC self-complementary tetranucleotide duplexes has been monitored by proton high resolution nuclear magnetic resonance spectroscopy in 0.1 M phosphate solution at high nucleotide/drug ratios. The large upfield shifts (0.5 to 0.85 ppm) observed at all the proflavine ring nonexchangeable protons on complex formation are consistent with intercalation of the mutagen between base pairs of the tetranucleotide duplex. We have proposed an approximate overlap geometry between the proflavine ring and nearest neighbor base pairs at the intercalation site from a comparison between experimental shifts and those calculated for various stacking orientations. We have compared the binding of actinomycin D, propidium diiodide, and proflavine to self-complementary tetranucleotide sequences dC-dC-dG-dG and dG-dG-dC-dC by UV absorbance changes in the drug bands between 400 and 500 nm. Actinomycin D exhibits a pronounced specificity for sequences with dG-dC sites (dG-dG-dC-dC), while propidium diiodide and proflavine exhibit a specificity for sequences with dC-dG sites (dC-dC-dG-dG). Actinomycin D binds more strongly than propidium diiodide and proflavine to dC-dG-dC-dG (contains dC-dG and dG-dC binding sites), indicative of the additional stabilization from hydrogen bonding and hydrophobic interactions between the pentapeptide lactone rings of actinomycin D and the base pair edges and sugar-phosphate backbone of the tetranucleotide duplex. PMID:268613

Molecular recognition of DNA base pairs by the formamido/pyrrole and formamido/imidazole pairings in stacked polyamides

PubMed Central

Buchmueller, Karen L.; Staples, Andrew M.; Uthe, Peter B.; Howard, Cameron M.; Pacheco, Kimberly A. O.; Cox, Kari K.; Henry, James A.; Bailey, Suzanna L.; Horick, Sarah M.; Nguyen, Binh; Wilson, W. David; Lee, Moses

2005-01-01

Polyamides containing an N-terminal formamido (f) group bind to the minor groove of DNA as staggered, antiparallel dimers in a sequence-specific manner. The formamido group increases the affinity and binding site size, and it promotes the molecules to stack in a staggered fashion thereby pairing itself with either a pyrrole (Py) or an imidazole (Im). There has not been a systematic study on the DNA recognition properties of the f/Py and f/Im terminal pairings. These pairings were analyzed here in the context of f-ImPyPy, f-ImPyIm, f-PyPyPy and f-PyPyIm, which contain the central pairing modes, –ImPy– and –PyPy–. The specificity of these triamides towards symmetrical recognition sites allowed for the f/Py and f/Im terminal pairings to be directly compared by SPR, CD and ΔTM experiments. The f/Py pairing, when placed next to the –ImPy– or –PyPy– central pairings, prefers A/T and T/A base pairs to G/C base pairs, suggesting that f/Py has similar DNA recognition specificity to Py/Py. With –ImPy– central pairings, f/Im prefers C/G base pairs (>10 times) to the other Watson–Crick base pairs; therefore, f/Im behaves like the Py/Im pair. However, the f/Im pairing is not selective for the C/G base pair when placed next to the –PyPy– central pairings. PMID:15703305

Prebiotic chemistry and nucleic acid replication

NASA Technical Reports Server (NTRS)

Orgel, L. E.; Lohrmann, R.

1974-01-01

Recent work is reviewed on some reactions that could have occurred on the primitive earth and that could have played a part in the evolution of a self-replicating system. The transition from the primitive atmosphere to the simplest replicating molecules is considered in four stages: (1) the formation of a 'prebiotic soup' of organic precursors, including the purine and pyrimidine bases and the pentose sugars; (2) the condensation of these precursors and inorganic phosphate to form monomeric nucleotides and activated nucleotide derivatives; (3) the polymerization of nucleotide derivatives to oligonucleotides; and (4) the complementary replication of oligonucleotides in a template-directed process that depends on Watson-Crick base pairing.

Base-Pairing Energies of Protonated Nucleoside Base Pairs of dCyd and m5dCyd: Implications for the Stability of DNA i-Motif Conformations

NASA Astrophysics Data System (ADS)

Yang, Bo; Rodgers, M. T.

2015-08-01

Hypermethylation of cytosine in expanded (CCG)n•(CGG)n trinucleotide repeats results in Fragile X syndrome, the most common cause of inherited mental retardation. The (CCG)n•(CGG)n repeats adopt i-motif conformations that are preferentially stabilized by base-pairing interactions of protonated base pairs of cytosine. Here we investigate the effects of 5-methylation and the sugar moiety on the base-pairing energies (BPEs) of protonated cytosine base pairs by examining protonated nucleoside base pairs of 2'-deoxycytidine (dCyd) and 5-methyl-2'-deoxycytidine (m5dCyd) using threshold collision-induced dissociation techniques. 5-Methylation of a single or both cytosine residues leads to very small change in the BPE. However, the accumulated effect may be dramatic in diseased state trinucleotide repeats where many methylated base pairs may be present. The BPEs of the protonated nucleoside base pairs examined here significantly exceed those of Watson-Crick dGuo•dCyd and neutral dCyd•dCyd base pairs, such that these base-pairing interactions provide the major forces responsible for stabilization of DNA i-motif conformations. Compared with isolated protonated nucleobase pairs of cytosine and 1-methylcytosine, the 2'-deoxyribose sugar produces an effect similar to the 1-methyl substituent, and leads to a slight decrease in the BPE. These results suggest that the base-pairing interactions may be slightly weaker in nucleic acids, but that the extended backbone is likely to exert a relatively small effect on the total BPE. The proton affinity (PA) of m5dCyd is also determined by competitive analysis of the primary dissociation pathways that occur in parallel for the protonated (m5dCyd)H+(dCyd) nucleoside base pair and the absolute PA of dCyd previously reported.

The Effects of Dominance on Leadership and Energetic Gain: A Dynamic Game between Pairs of Social Foragers

PubMed Central

Rands, Sean A.

2011-01-01

Although social behaviour can bring many benefits to an individual, there are also costs that may be incurred whenever the members of a social group interact. The formation of dominance hierarchies could offer a means of reducing some of the costs of social interaction, but individuals within the hierarchy may end up paying differing costs dependent upon their position within the hierarchy. These differing interaction costs may therefore influence the behaviour of the group, as subordinate individuals may experience very different benefits and costs to dominants when the group is conducting a given behaviour. Here, a state-dependent dynamic game is described which considers a pair of social foragers where there is a set dominance relationship within the pair. The model considers the case where the subordinate member of the pair pays an interference cost when it and the dominant individual conduct specific pairs of behaviours together. The model demonstrates that if the subordinate individual pays these energetic costs when it interacts with the dominant individual, this has effects upon the behaviour of both subordinate and the dominant individuals. Including interaction costs increases the amount of foraging behaviour both individuals conduct, with the behaviour of the pair being driven by the subordinate individual. The subordinate will tend to be the lighter individual for longer periods of time when interaction costs are imposed. This supports earlier suggestions that lighter individuals should act as the decision-maker within the pair, giving leadership-like behaviours that are based upon energetic state. Pre-existing properties of individuals such as their dominance will be less important for determining which individual makes the decisions for the pair. This suggests that, even with strict behavioural hierarchies, identifying which individual is the dominant one is not sufficient for identifying which one is the leader. PMID:22028645

Metal-mediated DNA base pairing: alternatives to hydrogen-bonded Watson-Crick base pairs.

PubMed

Takezawa, Yusuke; Shionoya, Mitsuhiko

2012-12-18

With its capacity to store and transfer the genetic information within a sequence of monomers, DNA forms its central role in chemical evolution through replication and amplification. This elegant behavior is largely based on highly specific molecular recognition between nucleobases through the specific hydrogen bonds in the Watson-Crick base pairing system. While the native base pairs have been amazingly sophisticated through the long history of evolution, synthetic chemists have devoted considerable efforts to create alternative base pairing systems in recent decades. Most of these new systems were designed based on the shape complementarity of the pairs or the rearrangement of hydrogen-bonding patterns. We wondered whether metal coordination could serve as an alternative driving force for DNA base pairing and why hydrogen bonding was selected on Earth in the course of molecular evolution. Therefore, we envisioned an alternative design strategy: we replaced hydrogen bonding with another important scheme in biological systems, metal-coordination bonding. In this Account, we provide an overview of the chemistry of metal-mediated base pairing including basic concepts, molecular design, characteristic structures and properties, and possible applications of DNA-based molecular systems. We describe several examples of artificial metal-mediated base pairs, such as Cu(2+)-mediated hydroxypyridone base pair, H-Cu(2+)-H (where H denotes a hydroxypyridone-bearing nucleoside), developed by us and other researchers. To design the metallo-base pairs we carefully chose appropriate combinations of ligand-bearing nucleosides and metal ions. As expected from their stronger bonding through metal coordination, DNA duplexes possessing metallo-base pairs exhibited higher thermal stability than natural hydrogen-bonded DNAs. Furthermore, we could also use metal-mediated base pairs to construct or induce other high-order structures. These features could lead to metal-responsive functional DNA molecules such as artificial DNAzymes and DNA machines. In addition, the metallo-base pairing system is a powerful tool for the construction of homogeneous and heterogeneous metal arrays, which can lead to DNA-based nanomaterials such as electronic wires and magnetic devices. Recently researchers have investigated these systems as enzyme replacements, which may offer an additional contribution to chemical biology and synthetic biology through the expansion of the genetic alphabet.

DNA Hairpins Containing the Cytidine Analog Pyrrolo-dC: Structural, Thermodynamic, and Spectroscopic Studies

PubMed Central

Zhang, Xu; Wadkins, Randy M.

2009-01-01

Structures formed by single-strand DNA have become increasingly interesting because of their roles in a number of biological processes, particularly transcription and its regulation. Of particular importance is the fact that antitumor drugs such as Actinomycin D can selectively bind DNA hairpins over fully paired, double-strand DNA. A new fluorescent base analog, pyrrolo-deoxycytidine (PdC), can now be routinely incorporated into single-strand DNA. The fluorescence of PdC is particularly useful for studying the formation of single-strand DNA in regions of double-strand DNA. The fluorescence is quenched when PdC is paired with a complementary guanine residue, and thus is greatly enhanced upon formation of single-strand DNA. Hence, any process that results in melting or opening of DNA strands produces an increase in the fluorescence intensity of this base analog. In this study we measured the structural effects of incorporating PdC into DNA hairpins, and the effect of this incorporation on the binding of the hairpins by a fluorescent analog of the drug Actinomycin D. Two hairpin DNAs were used: one with PdC in the stem (basepaired) and one with PdC in the loop (unpaired). The thermal stability, 7-aminoactinomycin D binding, and three-dimensional structures of PdC incorporated into these DNA hairpins were all quite similar as compared to the hairpins containing an unmodified dC residue. Fluorescence lifetime measurements indicate that two lifetimes are present in PdC, and that the increase in fluorescence of the unpaired PdC residue compared to the basepaired PdC is due to an increase in the contribution of the longer lifetime to the average fluorescence lifetime. Our data indicate that PdC can be used effectively to differentiate paired and unpaired bases in DNA hairpin secondary structures, and should be similarly applicable for related structures such as cruciforms and quadruplexes. Further, our data indicate that PdC can act as a fluorescence resonance energy transfer donor for the fluorescent drug 7-aminoactinomycin D. PMID:19254547

DNA hairpins containing the cytidine analog pyrrolo-dC: structural, thermodynamic, and spectroscopic studies.

PubMed

Zhang, Xu; Wadkins, Randy M

2009-03-04

Structures formed by single-strand DNA have become increasingly interesting because of their roles in a number of biological processes, particularly transcription and its regulation. Of particular importance is the fact that antitumor drugs such as Actinomycin D can selectively bind DNA hairpins over fully paired, double-strand DNA. A new fluorescent base analog, pyrrolo-deoxycytidine (PdC), can now be routinely incorporated into single-strand DNA. The fluorescence of PdC is particularly useful for studying the formation of single-strand DNA in regions of double-strand DNA. The fluorescence is quenched when PdC is paired with a complementary guanine residue, and thus is greatly enhanced upon formation of single-strand DNA. Hence, any process that results in melting or opening of DNA strands produces an increase in the fluorescence intensity of this base analog. In this study we measured the structural effects of incorporating PdC into DNA hairpins, and the effect of this incorporation on the binding of the hairpins by a fluorescent analog of the drug Actinomycin D. Two hairpin DNAs were used: one with PdC in the stem (basepaired) and one with PdC in the loop (unpaired). The thermal stability, 7-aminoactinomycin D binding, and three-dimensional structures of PdC incorporated into these DNA hairpins were all quite similar as compared to the hairpins containing an unmodified dC residue. Fluorescence lifetime measurements indicate that two lifetimes are present in PdC, and that the increase in fluorescence of the unpaired PdC residue compared to the basepaired PdC is due to an increase in the contribution of the longer lifetime to the average fluorescence lifetime. Our data indicate that PdC can be used effectively to differentiate paired and unpaired bases in DNA hairpin secondary structures, and should be similarly applicable for related structures such as cruciforms and quadruplexes. Further, our data indicate that PdC can act as a fluorescence resonance energy transfer donor for the fluorescent drug 7-aminoactinomycin D.

The N-terminal cysteine pair of yeast sulfhydryl oxidase Erv1p is essential for in vivo activity and interacts with the primary redox centre.

PubMed

Hofhaus, Götz; Lee, Jeung-Eun; Tews, Ivo; Rosenberg, Beate; Lisowsky, Thomas

2003-04-01

Yeast Erv1p is a ubiquitous FAD-dependent sulfhydryl oxidase, located in the intermembrane space of mitochondria. The dimeric enzyme is essential for survival of the cell. Besides the redox-active CXXC motif close to the FAD, Erv1p harbours two additional cysteine pairs. Site-directed mutagenesis has identified all three cysteine pairs as essential for normal function. The C-terminal cysteine pair is of structural importance as it contributes to the correct arrangement of the FAD-binding fold. Variations in dimer formation and unique colour changes of mutant proteins argue in favour of an interaction between the N-terminal cysteine pair with the redox centre of the partner monomer.

Electrostatic shocks and solitons in pair-ion plasmas in a two-dimensional geometry

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

Masood, W.; Mahmood, S.; Imtiaz, N.

2009-12-15

Nonlinear electrostatic waves are studied in unmagnetized, dissipative pair-ion plasmas in the presence of weak transverse perturbations. The dissipation in the system is taken into account by incorporating the kinematic viscosity of both positive and negative ions in plasmas. The Kadomtsev-Petviashvili-Burger equation is derived using the small amplitude expansion method. The Kadomtsev-Petviashvili equation for pair-ion plasmas is also presented by ignoring the dissipative effects. Both compressive and rarefactive shocks and solitary waves are found to exist in pair-ion plasmas. The dependence of compression and rarefaction on the temperature ratios between the ion species is numerically shown. The present study maymore » have relevance to the understanding of the formation of electrostatic shocks and solitons in laboratory produced pair-ion plasmas.« less

Base pairing and base mis-pairing in nucleic acids

NASA Technical Reports Server (NTRS)

Wang, A. H. J.; Rich, A.

1986-01-01

In recent years we have learned that DNA is conformationally active. It can exist in a number of different stable conformations including both right-handed and left-handed forms. Using single crystal X-ray diffraction analysis we are able to discover not only additional conformations of the nucleic acids but also different types of hydrogen bonded base-base interactions. Although Watson-Crick base pairings are the predominant type of interaction in double helical DNA, they are not the only types. Recently, we have been able to examine mismatching of guanine-thymine base pairs in left-handed Z-DNA at atomic resolution (1A). A minimum amount of distortion of the sugar phosphate backbone is found in the G x T pairing in which the bases are held together by two hydrogen bonds in the wobble pairing interaction. Because of the high resolution of the analysis we can visualize water molecules which fill in to accommodate the other hydrogen bonding positions in the bases which are not used in the base-base interactions. Studies on other DNA oligomers have revealed that other types of non-Watson-Crick hydrogen bonding interactions can occur. In the structure of a DNA octamer with the sequence d(GCGTACGC) complexed to an antibiotic triostin A, it was found that the two central AT base pairs are held together by Hoogsteen rather than Watson-Crick base pairs. Similarly, the G x C base pairs at the ends are also Hoogsteen rather than Watson-Crick pairing. Hoogsteen base pairs make a modified helix which is distinct from the Watson-Crick double helix.

Differences between the events preceding spina bifida and anencephaly.

PubMed

James, W H

1981-02-01

It is usually held that there is a time continuum in the formation of monoxygotic (MZ) twins which is indexed by their placentation, running from dichorionic to monochorionic diamniotic to monochorionic monoamniotic and conjoined pairs. There is good evidence that this continuum is characterised by a continuum of predisposition to anencephaly, slightly raised in dichorionic pairs but very high in some sorts of conjoined pairs. Although MZ twins, especially monoamniotic and conjoined pairs, are peculiarly liable to anencephaly, they are not particularly susceptible to spina bifida. Among twin pairs concordant for anencephaly or spina bifida, there are strikingly few concordant in the sense of one twin having anencephaly and the other spina bifida, in contrast with the numbers of pairs concordant for the same malformation. The prevalence of anencephaly in double monsters varies with the type of monster, being high in diprosopus. These findings may be explained by the timing of embryonic events.

Differences between the events preceding spina bifida and anencephaly.

PubMed Central

James, W H

1981-01-01

It is usually held that there is a time continuum in the formation of monoxygotic (MZ) twins which is indexed by their placentation, running from dichorionic to monochorionic diamniotic to monochorionic monoamniotic and conjoined pairs. There is good evidence that this continuum is characterised by a continuum of predisposition to anencephaly, slightly raised in dichorionic pairs but very high in some sorts of conjoined pairs. Although MZ twins, especially monoamniotic and conjoined pairs, are peculiarly liable to anencephaly, they are not particularly susceptible to spina bifida. Among twin pairs concordant for anencephaly or spina bifida, there are strikingly few concordant in the sense of one twin having anencephaly and the other spina bifida, in contrast with the numbers of pairs concordant for the same malformation. The prevalence of anencephaly in double monsters varies with the type of monster, being high in diprosopus. These findings may be explained by the timing of embryonic events. PMID:7019447

Pair Formation of Hard Core Bosons in Flat Band Systems

NASA Astrophysics Data System (ADS)

Mielke, Andreas

2018-05-01

Hard core bosons in a large class of one or two dimensional flat band systems have an upper critical density, below which the ground states can be described completely. At the critical density, the ground states are Wigner crystals. If one adds a particle to the system at the critical density, the ground state and the low lying multi particle states of the system can be described as a Wigner crystal with an additional pair of particles. The energy band for the pair is separated from the rest of the multi-particle spectrum. The proofs use a Gerschgorin type of argument for block diagonally dominant matrices. In certain one-dimensional or tree-like structures one can show that the pair is localised, for example in the chequerboard chain. For this one-dimensional system with periodic boundary condition the energy band for the pair is flat, the pair is localised.

[The study of complex-formation of DNA with the antimicrobial drug decamethoxine].

PubMed

Sorokin, V A; Blagoĭ, Iu P; Valeev, V A; Gladchenko, G O; Sukhodub, L F; Volianskiĭ, Iu L

1990-01-01

The interaction of effective antibacterial drug decametoxyn with natural DNA was studied by UV-spectroscopy. Decametoxyn shows a specificity to nucleotides: it decreases the cooperativity of melting and the thermal stability of DNA parts enriched by AT pairs. The characteristics of the helix-coil transition on the DNA parts enriched by GC-pairs are invariable. Interaction with AT-pairs results in their partial or complete melting at room temperature, followed by intermolecule aggregation. Interacting with phosphates decametoxyn manifests itself not as a dication but as two single-charged ions.

Signal Study of the Pair Production of Z’ Bosons Decaying to Dark Matter and Boosted Jets at CMS

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

Silverio, Diana Leon; Jayatilaka, Bo; Cremonesi, Matteo

2017-01-01

This study aims to develop a search for Dark Matter (DM) in a signature of missing transverse energy and jets in the CMS detector at the Large Hadron Collider at CERN. We study the generation of a simplified model for the pair production of spin-1 Z’ bosons, with one of them decaying into a pair of DM particles. The signal events are generated via MadGraph, in the LHE (Les Houches Event) file format, and their kinematics are studied.

Hidden in Plain Sight: Subtle Effects of the 8-Oxoguanine Lesion on the Structure, Dynamics, and Thermodynamics of a 15-Base-Pair Oligodeoxynucleotide Duplex†

PubMed Central

Crenshaw, Charisse M.; Wade, Jacqueline E.; Arthanari, Haribabu; Frueh, Dominique; Lane, Benjamin F.; Núñez, Megan E.

2011-01-01

The base lesion 8-oxoguanine is formed readily by oxidation of DNA, potentially leading to G→T transversion mutations. Despite the apparent similarity of 8-oxoguanine-cytosine base pairs to normal guanine-cytosine base pairs, cellular base excision repair systems effectively recognize the lesion base. Here we apply several techniques to examine a single 8-oxoguanine lesion at the center of a nonpalindromic 15-mer duplex oligonucleotide in an effort to determine what, if anything, distinguishes an 8-oxoguanine-cytosine base pair from a normal base pair. The lesion duplex is globally almost indistinguishable from the unmodified parent duplex using CD spectroscopy and UV melting thermodynamics. The DNA mismatch-detecting photocleavage agent Rh(bpy)2chrysi3+ cleaves only weakly and nonspecifically, revealing that the 8oxoG-C pair is locally stable at the level of the individual base pairs. NMR spectra are also consistent with a well-conserved B-form duplex structure. In the 2D NOESY spectra, base-sugar and imino-imino crosspeaks are strikingly similar between parent and lesion duplexes. Changes in chemical shift due to the 8oxoG lesion are localized to its complementary cytosine and to the 2–3 base pairs immediately flanking the lesion on the lesion strand. Residues further removed from the lesion are shown to be unperturbed by its presence. Notably, imino exchange experiments indicate that the 8-oxoguanine-cytosine pair is strong and stable, with an apparent equilibrium constant for opening equal to that of other internal guanine-cytosine base pairs, on the order of 10−6. This collection of experiments shows that the 8-oxoguanine-cytosine base pair is incredibly stable and similar to the native pair. PMID:21902242

Vectoring of parallel synthetic jets

NASA Astrophysics Data System (ADS)

Berk, Tim; Ganapathisubramani, Bharathram; Gomit, Guillaume

2015-11-01

A pair of parallel synthetic jets can be vectored by applying a phase difference between the two driving signals. The resulting jet can be merged or bifurcated and either vectored towards the actuator leading in phase or the actuator lagging in phase. In the present study, the influence of phase difference and Strouhal number on the vectoring behaviour is examined experimentally. Phase-locked vorticity fields, measured using Particle Image Velocimetry (PIV), are used to track vortex pairs. The physical mechanisms that explain the diversity in vectoring behaviour are observed based on the vortex trajectories. For a fixed phase difference, the vectoring behaviour is shown to be primarily influenced by pinch-off time of vortex rings generated by the synthetic jets. Beyond a certain formation number, the pinch-off timescale becomes invariant. In this region, the vectoring behaviour is determined by the distance between subsequent vortex rings. We acknowledge the financial support from the European Research Council (ERC grant agreement no. 277472).

Reproductive pair correlations and the clustering of organisms.

PubMed

Young, W R; Roberts, A J; Stuhne, G

2001-07-19

Clustering of organisms can be a consequence of social behaviour, or of the response of individuals to chemical and physical cues. Environmental variability can also cause clustering: for example, marine turbulence transports plankton and produces chlorophyll concentration patterns in the upper ocean. Even in a homogeneous environment, nonlinear interactions between species can result in spontaneous pattern formation. Here we show that a population of independent, random-walking organisms ('brownian bugs'), reproducing by binary division and dying at constant rates, spontaneously aggregates. Using an individual-based model, we show that clusters form out of spatially homogeneous initial conditions without environmental variability, predator-prey interactions, kinesis or taxis. The clustering mechanism is reproductively driven-birth must always be adjacent to a living organism. This clustering can overwhelm diffusion and create non-poissonian correlations between pairs (parent and offspring) or organisms, leading to the emergence of patterns.

Recombination, Pairing, and Synapsis of Homologs during Meiosis

PubMed Central

Zickler, Denise; Kleckner, Nancy

2015-01-01

Recombination is a prominent feature of meiosis in which it plays an important role in increasing genetic diversity during inheritance. Additionally, in most organisms, recombination also plays mechanical roles in chromosomal processes, most notably to mediate pairing of homologous chromosomes during prophase and, ultimately, to ensure regular segregation of homologous chromosomes when they separate at the first meiotic division. Recombinational interactions are also subject to important spatial patterning at both early and late stages. Recombination-mediated processes occur in physical and functional linkage with meiotic axial chromosome structure, with interplay in both directions, before, during, and after formation and dissolution of the synaptonemal complex (SC), a highly conserved meiosis-specific structure that links homolog axes along their lengths. These diverse processes also are integrated with recombination-independent interactions between homologous chromosomes, nonhomology-based chromosome couplings/clusterings, and diverse types of chromosome movement. This review provides an overview of these diverse processes and their interrelationships. PMID:25986558

Multipartite entanglement indicators based on monogamy relations of n-qubit symmetric states

PubMed Central

Liu, Feng; Gao, Fei; Qin, Su-Juan; Xie, Shu-Cui; Wen, Qiao-Yan

2016-01-01

Constructed from Bai-Xu-Wang-class monogamy relations, multipartite entanglement indicators can detect the entanglement not stored in pairs of the focus particle and the other subset of particles. We investigate the k-partite entanglement indicators related to the αth power of entanglement of formation (αEoF) for k ≤ n, αϵ and n-qubit symmetric states. We then show that (1) The indicator based on αEoF is a monotonically increasing function of k. (2) When n is large enough, the indicator based on αEoF is a monotonically decreasing function of α, and then the n-partite indicator based on works best. However, the indicator based on 2 EoF works better when n is small enough. PMID:26842264

Multipartite entanglement indicators based on monogamy relations of n-qubit symmetric states.

PubMed

Liu, Feng; Gao, Fei; Qin, Su-Juan; Xie, Shu-Cui; Wen, Qiao-Yan

2016-02-04

Constructed from Bai-Xu-Wang-class monogamy relations, multipartite entanglement indicators can detect the entanglement not stored in pairs of the focus particle and the other subset of particles. We investigate the k-partite entanglement indicators related to the αth power of entanglement of formation (αEoF) for k ≤ n, αϵ and n-qubit symmetric states. We then show that (1) The indicator based on αEoF is a monotonically increasing function of k. (2) When n is large enough, the indicator based on αEoF is a monotonically decreasing function of α, and then the n-partite indicator based on works best. However, the indicator based on 2 EoF works better when n is small enough.

Multipartite entanglement indicators based on monogamy relations of n-qubit symmetric states

NASA Astrophysics Data System (ADS)

Liu, Feng; Gao, Fei; Qin, Su-Juan; Xie, Shu-Cui; Wen, Qiao-Yan

2016-02-01

Constructed from Bai-Xu-Wang-class monogamy relations, multipartite entanglement indicators can detect the entanglement not stored in pairs of the focus particle and the other subset of particles. We investigate the k-partite entanglement indicators related to the αth power of entanglement of formation (αEoF) for k ≤ n, αɛ and n-qubit symmetric states. We then show that (1) The indicator based on αEoF is a monotonically increasing function of k. (2) When n is large enough, the indicator based on αEoF is a monotonically decreasing function of α, and then the n-partite indicator based on works best. However, the indicator based on 2 EoF works better when n is small enough.

On microscopic structure of the QCD vacuum

NASA Astrophysics Data System (ADS)

Pak, D. G.; Lee, Bum-Hoon; Kim, Youngman; Tsukioka, Takuya; Zhang, P. M.

2018-05-01

We propose a new class of regular stationary axially symmetric solutions in a pure QCD which correspond to monopole-antimonopole pairs at macroscopic scale. The solutions represent vacuum field configurations which are locally stable against quantum gluon fluctuations in any small space-time vicinity. This implies that the monopole-antimonopole pair can serve as a structural element in microscopic description of QCD vacuum formation.

Orotidine-Containing RNA: Implications for the Hierarchical Selection (Systems Chemistry Emergence) of RNA.

PubMed

Kim, Eun-Kyong; Martin, Vincent; Krishnamurthy, Ramanarayanan

2017-09-12

The prebiotic synthesis of canonical nucleobases from HCN is a cornerstone for the RNA world hypothesis. However, their role in the primordial pathways to RNA is still debated. The very same process starting from HCN also gives rise to orotic acid, which (via orotidine) plays a crucial role in extant biology in the de novo synthesis of uridine and cytidine, the informational base-pairs in RNA. However, orotidine itself is absent in RNA. Given the prebiotic and biological relevance of orotic acid vis-à-vis uracil, we investigated orotidine-containing RNA oligonucleotides and show that they have severely compromised base-pairing properties. While not unexpected, these results suggest that the emergence of extant RNA cannot just be a consequence of the plausible prebiotic formation of its chemical constituents/building blocks. In combination with other investigations on alternative prebiotic nucleobases, sugars, and linkers, these findings imply that the selection of the components of extant RNA occurred at a higher hierarchical level of an oligomer/polymer based on its functional properties-pointing to a systems chemistry emergence of RNA from a library of precursors. © 2017 Wiley-VCH Verlag GmbH & Co. KGaA, Weinheim.

Insights into DNA-mediated interparticle interactions from a coarse-grained model

NASA Astrophysics Data System (ADS)

Ding, Yajun; Mittal, Jeetain

2014-11-01

DNA-functionalized particles have great potential for the design of complex self-assembled materials. The major hurdle in realizing crystal structures from DNA-functionalized particles is expected to be kinetic barriers that trap the system in metastable amorphous states. Therefore, it is vital to explore the molecular details of particle assembly processes in order to understand the underlying mechanisms. Molecular simulations based on coarse-grained models can provide a convenient route to explore these details. Most of the currently available coarse-grained models of DNA-functionalized particles ignore key chemical and structural details of DNA behavior. These models therefore are limited in scope for studying experimental phenomena. In this paper, we present a new coarse-grained model of DNA-functionalized particles which incorporates some of the desired features of DNA behavior. The coarse-grained DNA model used here provides explicit DNA representation (at the nucleotide level) and complementary interactions between Watson-Crick base pairs, which lead to the formation of single-stranded hairpin and double-stranded DNA. Aggregation between multiple complementary strands is also prevented in our model. We study interactions between two DNA-functionalized particles as a function of DNA grafting density, lengths of the hybridizing and non-hybridizing parts of DNA, and temperature. The calculated free energies as a function of pair distance between particles qualitatively resemble experimental measurements of DNA-mediated pair interactions.

Structural landscape of base pairs containing post-transcriptional modifications in RNA

PubMed Central

Seelam, Preethi P.; Sharma, Purshotam

2017-01-01

Base pairs involving post-transcriptionally modified nucleobases are believed to play important roles in a wide variety of functional RNAs. Here we present our attempts toward understanding the structural and functional role of naturally occurring modified base pairs using a combination of X-ray crystal structure database analysis, sequence analysis, and advanced quantum chemical methods. Our bioinformatics analysis reveals that despite their presence in all major secondary structural elements, modified base pairs are most prevalent in tRNA crystal structures and most commonly involve guanine or uridine modifications. Further, analysis of tRNA sequences reveals additional examples of modified base pairs at structurally conserved tRNA regions and highlights the conservation patterns of these base pairs in three domains of life. Comparison of structures and binding energies of modified base pairs with their unmodified counterparts, using quantum chemical methods, allowed us to classify the base modifications in terms of the nature of their electronic structure effects on base-pairing. Analysis of specific structural contexts of modified base pairs in RNA crystal structures revealed several interesting scenarios, including those at the tRNA:rRNA interface, antibiotic-binding sites on the ribosome, and the three-way junctions within tRNA. These scenarios, when analyzed in the context of available experimental data, allowed us to correlate the occurrence and strength of modified base pairs with their specific functional roles. Overall, our study highlights the structural importance of modified base pairs in RNA and points toward the need for greater appreciation of the role of modified bases and their interactions, in the context of many biological processes involving RNA. PMID:28341704

Stability of non-Watson-Crick G-A/A-G base pair in synthetic DNA and RNA oligonucleotides.

PubMed

Ito, Yuko; Sone, Yumiko; Mizutani, Takaharu

2004-03-01

A non-Watson-Crick G-A/A-G base pair is found in SECIS (selenocysteine-insertion sequence) element in the 3'-untranslated region of Se-protein mRNAs and in the functional site of the hammerhead ribozyme. We studied the stability of G-A/A-G base pair (bold) in 17mer GT(U)GACGGAAACCGGAAC synthetic DNA and RNA oligonucleotides by thermal melting experiments and gel electrophoresis. The measured Tm value of DNA oligonucleotide having G-A/A-G pair showed an intermediate value (58 degrees C) between that of Watson-Crick G-C/C-G base pair (75 degrees C) and that of G-G/A-A of non-base-pair (40 degrees C). Similar thermal melting patterns were obtained with RNA oligonucleotides. This result indicates that the secondary structure of oligonucleotide having G-A/A-G base pair is looser than that of the G-C type Watson-Crick base pair. In the comparison between RNA and DNA having G-A/A-G base pair, the Tm value of the RNA oligonucleotide was 11 degrees C lower than that of DNA, indicating that DNA has a more rigid structure than RNA. The stained pattern of oligonucleotide on polyacrylamide gel clarified that the mobility of the DNA oligonucleotide G-A/A-G base pair changed according to the urea concentration from the rigid state (near the mobility of G-C/C-G oligonucleotide) in the absence of urea to the random state (near the mobility of G-G/A-A oligonucleotide) in 7 M urea. However, the RNA oligonucleotide with G-A/A-G pair moved at an intermediate mobility between that of oligonucleotide with G-C/C-G and of the oligonucleotide with G-G/A-A, and the mobility pattern did not depend on urea concentration. Thus, DNA and RNA oligonucleotides with the G-A/A-G base pair showed a pattern indicating an intermediate structure between the rigid Watson-Crick base pair and the random structure of non-base pair. RNA with G-A/A-G base pair has the intermediate structure not influenced by urea concentration. Finally, this study indicated that the intermediate rigidity imparted by Non-Watson-Crick base pair in SECIS element plays an important role in the selenocysteine expression by UGA codon.

Introducing a model of pairing based on base pair specific interactions between identical DNA sequences

NASA Astrophysics Data System (ADS)

(O' Lee, Dominic J.

2018-02-01

At present, there have been suggested two types of physical mechanism that may facilitate preferential pairing between DNA molecules, with identical or similar base pair texts, without separation of base pairs. One mechanism solely relies on base pair specific patterns of helix distortion being the same on the two molecules, discussed extensively in the past. The other mechanism proposes that there are preferential interactions between base pairs of the same composition. We introduce a model, built on this second mechanism, where both thermal stretching and twisting fluctuations are included, as well as the base pair specific helix distortions. Firstly, we consider an approximation for weak pairing interactions, or short molecules. This yields a dependence of the energy on the square root of the molecular length, which could explain recent experimental data. However, analysis suggests that this approximation is no longer valid at large DNA lengths. In a second approximation, for long molecules, we define two adaptation lengths for twisting and stretching, over which the pairing interaction can limit the accumulation of helix disorder. When the pairing interaction is sufficiently strong, both adaptation lengths are finite; however, as we reduce pairing strength, the stretching adaptation length remains finite but the torsional one becomes infinite. This second state persists to arbitrarily weak values of the pairing strength; suggesting that, if the molecules are long enough, the pairing energy scales as length. To probe differences between the two pairing mechanisms, we also construct a model of similar form. However, now, pairing between identical sequences solely relies on the intrinsic helix distortion patterns. Between the two models, we see interesting qualitative differences. We discuss our findings, and suggest new work to distinguish between the two mechanisms.

Synthesis and characterization of bifunctional surfaces with tunable functional group pairs

NASA Astrophysics Data System (ADS)

Galloway, John M.; Kung, Mayfair; Kung, Harold H.

2016-06-01

Grafting of pairs of functional groups onto a silica surface was demonstrated by tethering both terminals of an organochlorosilane precursor molecule, Cl2(CH3)Si(CH2)4(CO)(OSi(i-Pr)2)(CH2)2Si(CH3)Cl2, that possess a cleavable silyl ester bond, onto a silica surface. Hydrolytic cleavage of the silyl ester bond of the grafted molecule resulted in the generation of organized pairs of carboxylic acid and organosilanol groups. This organosilanol moiety was easily transformed into other functional groups through condensation reactions to form, together with the neighboring acid group, pairs such as carboxylic acid/secondary amine, carboxylic acid/pyridine, and carboxylic acid/phosphine. In the case of carboxylic acid/amine pairing, there was evidence of the formation of amide. A sample grafted with amine-carboxylic acid pairs was three times more active (per free amine) than a sample without such pairs for the nitroaldol condensation of 4-nitrobenzaldehyde and nitromethane.

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

Devadoss, C.; Fessenden, R.W.

The transient that is produced in the quenching of triplet benzophenone by 1,4-diazabicyclo(2.2.2)octane (DABCO) has been examined by use of nano- and picosecond laser photolysis. The initial step in all solvents, both polar and nonpolar, is electron transfer to form a triplet contact ion pair. In nonpolar solvents, the ion pair remains in this form until it decays. For polar solvents, the spectra change somewhat over the first 100 ps showing that the solvation changes and the ion pair becomes solvent separated. The lifetime of the ion pair varies greatly with the solvent. In saturated hydrocarbons it is about 80more » ps. Nonpolar solvents with either {pi} electrons or a lone pair of electrons stabilize the ion pair on the nanosecond to microsecond time scale. A small amount of alcohol in benzene also stabilizes the ion pair by hydrogen bonding. A shift in the peak position with time toward the blue accompanies the formation of hydrogen bonds in this case.« less

Interaction of Aircraft Wakes From Laterally Spaced Aircraft

NASA Technical Reports Server (NTRS)

Proctor, Fred H.

2009-01-01

Large Eddy Simulations are used to examine wake interactions from aircraft on closely spaced parallel paths. Two sets of experiments are conducted, with the first set examining wake interactions out of ground effect (OGE) and the second set for in ground effect (IGE). The initial wake field for each aircraft represents a rolled-up wake vortex pair generated by a B-747. Parametric sets include wake interactions from aircraft pairs with lateral separations of 400, 500, 600, and 750 ft. The simulation of a wake from a single aircraft is used as baseline. The study shows that wake vortices from either a pair or a formation of B-747 s that fly with very close lateral spacing, last longer than those from an isolated B-747. For OGE, the inner vortices between the pair of aircraft, ascend, link and quickly dissipate, leaving the outer vortices to decay and descend slowly. For the IGE scenario, the inner vortices ascend and last longer, while the outer vortices decay from ground interaction at a rate similar to that expected from an isolated aircraft. Both OGE and IGE scenarios produce longer-lasting wakes for aircraft with separations less than 600 ft. The results are significant because concepts to increase airport capacity have been proposed that assume either aircraft formations and/or aircraft pairs landing on very closely spaced runways.

Classical calculation of the equilibrium constants for true bound dimers using complete potential energy surface.

PubMed

Buryak, Ilya; Vigasin, Andrey A

2015-12-21

The present paper aims at deriving classical expressions which permit calculation of the equilibrium constant for weakly interacting molecular pairs using a complete multidimensional potential energy surface. The latter is often available nowadays as a result of the more and more sophisticated and accurate ab initio calculations. The water dimer formation is considered as an example. It is shown that even in case of a rather strongly bound dimer the suggested expression permits obtaining quite reliable estimate for the equilibrium constant. The reliability of our obtained water dimer equilibrium constant is briefly discussed by comparison with the available data based on experimental observations, quantum calculations, and the use of RRHO approximation, provided the latter is restricted to formation of true bound states only.

A theoretical study of the omega-phase transformation in metals

NASA Astrophysics Data System (ADS)

Sanati, Mahdi

I have studied the formation of o-phase from electronic and mesoscopic (domain wall) points of view. To study the formation of domain walls, I have extended the Landau model of Cook for the o-phase transition by including a spatial gradient (Ginzburg) term of the scalar order parameter. In general, the Landau free energy is an asymmetric double-well potential. From the variational derivative of the total free energy I obtained a static equilibrium condition. By solving this equation for different physical parameters and boundary conditions, I obtained different quasi-one-dimensional soliton-like solutions. These solutions correspond to three different types of domain walls between the o-phase and the beta-matrix. These results are used to model the formation of the o-phase in bcc Ti. Canonical band model and first principles calculations confirmed the instability of the bcc-phase of group III and IV transition metals with respect to the o-phase transformation. I showed that the d-electron density is the controlling parameter for this type of the transformation. Also the possibility of formation of the o-phase for rare earth metals is discussed. First-principles full-potential linear muffin-tin orbital method (FPLMTO) calculations are performed for o-type displacement of the atoms to study the formation of the o-phase in TiAl and Ti 3Al2Nb alloys. The results of my calculations showed an instability in ordered B2 TiAl structure with respect to the o-phase when one third of the Al atoms are replaced by Nb atoms. These phenomena are explained, first by symmetry arguments; then a pair potential model is used to illustrate this instability based on interactions between different pair of atoms derived from the electronic structure. In addition, importance of the atomic arrangements on the structural stability of the Ti3Al2 Nb system is discussed.

How Does Student Performance on Formative Assessments Relate to Learning Assessed by Exams?

ERIC Educational Resources Information Center

Smith, Gary

2007-01-01

A retrospective analysis examines the relationships between formative assessments and exam grades in two undergraduate geoscience courses. Pair and group-work grades correlate weakly with individual exam grades. Exam performance correlates to individual, weekly online assessments. Student attendance and use of assessment feedback are also…

CryoEM structure of the spliceosome immediately after branching

PubMed Central

Galej, Wojciech P.; Wilkinson, Max E.; Fica, Sebastian M.; Oubridge, Chris; Newman, Andrew J.; Nagai, Kiyoshi

2016-01-01

Pre-mRNA splicing proceeds by two consecutive trans-esterification reactions via a lariat-intron intermediate. We present the 3.8Å cryoEM structure of the spliceosome immediately after lariat formation. The 5’-splice site is cleaved but remains close to the catalytic Mg2+ site in the U2/U6 snRNA triplex, and the 5’-phosphate of the intron nucleotide G(+1) is linked to the branch adenosine 2’OH. The 5’-exon is held between the Prp8 N-terminal and Linker domains, and base-pairs with U5 snRNA loop 1. Non-Watson-Crick interactions between the branch helix and 5’-splice site dock the branch adenosine into the active site, while intron nucleotides +3 to +6 base-pair with the U6 snRNA ACAGAGA sequence. Isy1 and the step one factors Yju2 and Cwc25 stabilise docking of the branch helix. The intron downstream of the branch site emerges between the Prp8 RT and Linker domains and extends towards Prp16 helicase, suggesting a plausible mechanism of remodelling before exon ligation. PMID:27459055

U14 small nucleolar RNA makes multiple contacts with the pre-ribosomal RNA.

PubMed

Morrissey, J P; Tollervey, D

1997-06-01

The small nucleolar RNA (snoRNA) U14 has two regions of extended primary sequence complementarity to the 18S rRNA. The 3' region (domain B) shows the consensus structure for the methylation guide class of snoRNAs, whereas base-pairing between the 5' region (domain A) and the 18S rRNA sequence is required for the formation of functional ribosomes. Between domains A and B lies another essential region (domain Y). Here we report that yeast U14 can be cross-linked in vivo to the pre-rRNA; cross-linking is detected exclusively with the 35S primary transcript. Many nucleotides in U14 that lie outside of domains A and B are cross-linked to the pre-rRNA; in particular the essential domain Y region is cross-linked at several sites. U14 is, therefore, in far more extensive contact with the pre-rRNA than predicted from simple base-pairing models. Moreover, U14 can be cross-linked to other small RNA species. The functional interactions made by U14 during ribosome synthesis are likely to be very complex.

Concepts relating magnetic interactions, intertwined electronic orders, and strongly correlated superconductivity

PubMed Central

Davis, J. C. Séamus; Lee, Dung-Hai

2013-01-01

Unconventional superconductivity (SC) is said to occur when Cooper pair formation is dominated by repulsive electron–electron interactions, so that the symmetry of the pair wave function is other than an isotropic s-wave. The strong, on-site, repulsive electron–electron interactions that are the proximate cause of such SC are more typically drivers of commensurate magnetism. Indeed, it is the suppression of commensurate antiferromagnetism (AF) that usually allows this type of unconventional superconductivity to emerge. Importantly, however, intervening between these AF and SC phases, intertwined electronic ordered phases (IP) of an unexpected nature are frequently discovered. For this reason, it has been extremely difficult to distinguish the microscopic essence of the correlated superconductivity from the often spectacular phenomenology of the IPs. Here we introduce a model conceptual framework within which to understand the relationship between AF electron–electron interactions, IPs, and correlated SC. We demonstrate its effectiveness in simultaneously explaining the consequences of AF interactions for the copper-based, iron-based, and heavy-fermion superconductors, as well as for their quite distinct IPs. PMID:24114268

Rhesus macaques form preferences for brand logos through sex and social status based advertising

PubMed Central

Watson, Karli K.; Fitzsimons, Gavan J.; Platt, Michael L.

2018-01-01

Like humans, monkeys value information about sex and status, inviting the hypothesis that our susceptibility to these factors in advertising arises from shared, ancestral biological mechanisms that prioritize social information. To test this idea, we asked whether rhesus macaques (Macaca mulatta) show choice behavior that is similar to humans in response to sex and social status in advertising. Our results show that monkeys form preferences for brand logos repeatedly paired with images of macaque genitals and high status monkeys. Moreover, monkeys sustain preferences for these brand logos even though choosing them provided no tangible rewards, a finding that cannot be explained by a decision mechanism operating solely on material outcomes. Together, our results endorse the hypothesis that the power of sex and status in advertising emerges from the spontaneous engagement of shared, ancestral neural circuits that prioritize information useful for navigating the social environment. Finally, our results show that simple associative conditioning is sufficient to explain the formation of preferences for brand logos paired with sexual or status-based images. PMID:29462189

Rhesus macaques form preferences for brand logos through sex and social status based advertising.

PubMed

Acikalin, M Yavuz; Watson, Karli K; Fitzsimons, Gavan J; Platt, Michael L

2018-01-01

Like humans, monkeys value information about sex and status, inviting the hypothesis that our susceptibility to these factors in advertising arises from shared, ancestral biological mechanisms that prioritize social information. To test this idea, we asked whether rhesus macaques (Macaca mulatta) show choice behavior that is similar to humans in response to sex and social status in advertising. Our results show that monkeys form preferences for brand logos repeatedly paired with images of macaque genitals and high status monkeys. Moreover, monkeys sustain preferences for these brand logos even though choosing them provided no tangible rewards, a finding that cannot be explained by a decision mechanism operating solely on material outcomes. Together, our results endorse the hypothesis that the power of sex and status in advertising emerges from the spontaneous engagement of shared, ancestral neural circuits that prioritize information useful for navigating the social environment. Finally, our results show that simple associative conditioning is sufficient to explain the formation of preferences for brand logos paired with sexual or status-based images.

Lax Integrability and the Peakon Problem for the Modified Camassa-Holm Equation

NASA Astrophysics Data System (ADS)

Chang, Xiangke; Szmigielski, Jacek

2018-02-01

Peakons are special weak solutions of a class of nonlinear partial differential equations modelling non-linear phenomena such as the breakdown of regularity and the onset of shocks. We show that the natural concept of weak solutions in the case of the modified Camassa-Holm equation studied in this paper is dictated by the distributional compatibility of its Lax pair and, as a result, it differs from the one proposed and used in the literature based on the concept of weak solutions used for equations of the Burgers type. Subsequently, we give a complete construction of peakon solutions satisfying the modified Camassa-Holm equation in the sense of distributions; our approach is based on solving certain inverse boundary value problem, the solution of which hinges on a combination of classical techniques of analysis involving Stieltjes' continued fractions and multi-point Padé approximations. We propose sufficient conditions needed to ensure the global existence of peakon solutions and analyze the large time asymptotic behaviour whose special features include a formation of pairs of peakons that share asymptotic speeds, as well as Toda-like sorting property.

Long-lived charge carrier generation in ordered films of a covalent perylenediimide–diketopyrrolopyrrole–perylenediimide molecule

DOE PAGES

Hartnett, Patrick E.; Dyar, Scott M.; Margulies, Eric A.; ...

2015-07-31

The photophysics of a covalently linked perylenediimide–diketopyrrolopyrrole–perylenediimide acceptor–donor–acceptor molecule (PDI–DPP–PDI, 1) were investigated and found to be markedly different in solution versus in unannealed and solvent annealed films. Photoexcitation of 1 in toluene results in quantitative charge separation in τ = 3.1 ± 0.2 ps, with charge recombination in τ = 340 ± 10 ps, while in unannealed/disordered films of 1, charge separation occurs in τ < 250 fs, while charge recombination displays a multiexponential decay in ~6 ns. The absence of long-lived, charge separation in the disordered film suggests that few free charge carriers are generated. In contrast, uponmore » CH₂Cl₂ vapor annealing films of 1, grazing-incidence X-ray scattering shows that the molecules form a more ordered structure. Photoexcitation of the ordered films results in initial formation of a spin-correlated radical ion pair (electron–hole pair) as indicated by magnetic field effects on the formation of free charge carriers which live for ~4 μs. This result has significant implications for the design of organic solar cells based on covalent donor–acceptor systems and shows that long-lived, charge-separated states can be achieved by controlling intramolecular charge separation dynamics in well-ordered systems.« less

Database of non-canonical base pairs found in known RNA structures

NASA Technical Reports Server (NTRS)

Nagaswamy, U.; Voss, N.; Zhang, Z.; Fox, G. E.

2000-01-01

Atomic resolution RNA structures are being published at an increasing rate. It is common to find a modest number of non-canonical base pairs in these structures in addition to the usual Watson-Crick pairs. This database summarizes the occurrence of these rare base pairs in accordance with standard nomenclature. The database, http://prion.bchs.uh.edu/, contains information such as sequence context, sugar pucker conformation, anti / syn base conformations, chemical shift, p K (a)values, melting temperature and free energy. Of the 29 anticipated pairs with two or more hydrogen bonds, 20 have been encountered to date. In addition, four unexpected pairs with two hydrogen bonds have been reported bringing the total to 24. Single hydrogen bond versions of five of the expected geometries have been encountered among the single hydrogen bond interactions. In addition, 18 different types of base triplets have been encountered, each of which involves three to six hydrogen bonds. The vast majority of the rare base pairs are antiparallel with the bases in the anti configuration relative to the ribose. The most common are the GU wobble, the Sheared GA pair, the Reverse Hoogsteen pair and the GA imino pair.

Highly Conductive Thin Uniform Gold-Coated DNA Nanowires.

PubMed

Stern, Avigail; Eidelshtein, Gennady; Zhuravel, Roman; Livshits, Gideon I; Rotem, Dvir; Kotlyar, Alexander; Porath, Danny

2018-06-01

Over the past decades, DNA, the carrier of genetic information, has been used by researchers as a structural template material. Watson-Crick base pairing enables the formation of complex 2D and 3D structures from DNA through self-assembly. Various methods have been developed to functionalize these structures for numerous utilities. Metallization of DNA has attracted much attention as a means of forming conductive nanostructures. Nevertheless, most of the metallized DNA wires reported so far suffer from irregularity and lack of end-to-end electrical connectivity. An effective technique for formation of thin gold-coated DNA wires that overcomes these drawbacks is developed and presented here. A conductive atomic force microscopy setup, which is suitable for measuring tens to thousands of nanometer long molecules and wires, is used to characterize these DNA-based nanowires. The wires reported here are the narrowest gold-coated DNA wires that display long-range conductivity. The measurements presented show that the conductivity is limited by defects, and that thicker gold coating reduces the number of defects and increases the conductive length. This preparation method enables the formation of molecular wires with dimensions and uniformity that are much more suitable for DNA-based molecular electronics. © 2018 WILEY-VCH Verlag GmbH & Co. KGaA, Weinheim.

High-resolution biophysical analysis of the dynamics of nucleosome formation

PubMed Central

Hatakeyama, Akiko; Hartmann, Brigitte; Travers, Andrew; Nogues, Claude; Buckle, Malcolm

2016-01-01

We describe a biophysical approach that enables changes in the structure of DNA to be followed during nucleosome formation in in vitro reconstitution with either the canonical “Widom” sequence or a judiciously mutated sequence. The rapid non-perturbing photochemical analysis presented here provides ‘snapshots’ of the DNA configuration at any given moment in time during nucleosome formation under a very broad range of reaction conditions. Changes in DNA photochemical reactivity upon protein binding are interpreted as being mainly induced by alterations in individual base pair roll angles. The results strengthen the importance of the role of an initial (H3/H4)2 histone tetramer-DNA interaction and highlight the modulation of this early event by the DNA sequence. (H3/H4)2 binding precedes and dictates subsequent H2A/H2B-DNA interactions, which are less affected by the DNA sequence, leading to the final octameric nucleosome. Overall, our results provide a novel, exciting way to investigate those biophysical properties of DNA that constitute a crucial component in nucleosome formation and stabilization. PMID:27263658

Using Sphinx to Improve Onion Routing Circuit Construction

NASA Astrophysics Data System (ADS)

Kate, Aniket; Goldberg, Ian

This paper presents compact message formats for onion routing circuit construction using the Sphinx methodology developed for mixes. We significantly compress the circuit construction messages for three onion routing protocols that have emerged as enhancements to the Tor anonymizing network; namely, Tor with predistributed Diffie-Hellman values, pairing-based onion routing, and certificateless onion routing. Our new circuit constructions are also secure in the universal composability framework, a property that was missing from the original constructions. Further, we compare the performance of our schemes with their older counterparts as well as with each other.

Preferential Nucleosome Assembly at DNA Triplet Repeats from the Myotonic Dystrophy Gene

NASA Astrophysics Data System (ADS)

Wang, Yuh-Hwa; Amirhaeri, Sorour; Kang, Seongman; Wells, Robert D.; Griffith, Jack D.

1994-07-01

The expansion of CTG repeats in DNA occurs in or near genes involved in several human diseases, including myotonic dystrophy and Huntington's disease. Nucleosomes, the basic structural element of chromosomes, consist of 146 base pairs of DNA coiled about an octamer of histone proteins and mediate general transcriptional repression. Electron microscopy was used to examine in vitro the nucleosome assembly of DNA containing repeating CTG triplets. The efficiency of nucleosome formation increased with expanded triplet blocks, suggesting that such blocks may repress transcription through the creation of stable nucleosomes.

RECALL: A Management Information Retrieval System for the Wang 2200

DTIC Science & Technology

1976-11-01

B-5. APPENDIX B TABLE B-l. VARIABLE DEFINITIONS Name Meaning Data base format R$(l-60) Page of blocks R1 Present block index within page RO...Present page index in memory R2 Number of blocks allowed in memory (60) R3 Last-used character index in present block R1* Number of sectors per page...5) Rl(l- 5) General CO BS(1- 15) L0 LS15 C csd- 12) Cl$(l -12) FOR cond i t ion Number of range pairs Starting record index Ending

PNA containing isocytidine nucleobase: synthesis and recognition of double helical RNA

PubMed Central

Zengeya, Thomas; Li, Ming; Rozners, Eriks

2011-01-01

Peptide nucleic acid (PNA1) containing a 5-methylisocytidine (iC) nucleobase has been synthesized. Triple helix formation between PNA1 and RNA hairpins having variable base pairs interacting with iC was studied using isothermal titration calorimetry. The iC nucleobase recognized the proposed target, C-G inversion in polypurine tract of RNA, with slightly higher affinity than the natural nucleobases, though the sequence selectivity of recognition was low. Compared to non-modified PNA, PNA1 had lower affinity for its RNA target. PMID:21333533

Base pair probability estimates improve the prediction accuracy of RNA non-canonical base pairs

PubMed Central

2017-01-01

Prediction of RNA tertiary structure from sequence is an important problem, but generating accurate structure models for even short sequences remains difficult. Predictions of RNA tertiary structure tend to be least accurate in loop regions, where non-canonical pairs are important for determining the details of structure. Non-canonical pairs can be predicted using a knowledge-based model of structure that scores nucleotide cyclic motifs, or NCMs. In this work, a partition function algorithm is introduced that allows the estimation of base pairing probabilities for both canonical and non-canonical interactions. Pairs that are predicted to be probable are more likely to be found in the true structure than pairs of lower probability. Pair probability estimates can be further improved by predicting the structure conserved across multiple homologous sequences using the TurboFold algorithm. These pairing probabilities, used in concert with prior knowledge of the canonical secondary structure, allow accurate inference of non-canonical pairs, an important step towards accurate prediction of the full tertiary structure. Software to predict non-canonical base pairs and pairing probabilities is now provided as part of the RNAstructure software package. PMID:29107980

QM/MM studies on the excited-state relaxation mechanism of a semisynthetic dTPT3 base.

PubMed

Guo, Wei-Wei; Zhang, Teng-Shuo; Fang, Wei-Hai; Cui, Ganglong

2018-02-14

Semisynthetic alphabets can potentially increase the genetic information stored in DNA through the formation of unusual base pairs. Recent experiments have shown that near-visible-light irradiation of the dTPT3 chromophore could lead to the formation of a reactive triplet state and of singlet oxygen in high quantum yields. However, the detailed excited-state relaxation paths that populate the lowest triplet state are unclear. Herein, we have for the first time employed the QM(MS-CASPT2//CASSCF)/MM method to explore the spectroscopic properties and excited-state relaxation mechanism of the aqueous dTPT3 chromophore. On the basis of the results, we have found that (1) the S 2 ( 1 ππ*) state of dTPT3 is the initially populated excited singlet state upon near-visible light irradiation; and (2) there are two efficient relaxation pathways to populate the lowest triplet state, i.e. T 1 ( 3 ππ*). In the first one, the S 2 ( 1 ππ*) system first decays to the S 1 ( 1 nπ*) state near the S 2 /S 1 conical intersection, which is followed by an efficient S 1 → T 1 intersystem crossing process at the S 1 /T 1 crossing point; in the second one, an efficient S 2 → T 2 intersystem crossing takes place first, and then, the T 2 ( 3 nπ*) system hops to the T 1 ( 3 ππ*) state through an internal conversion process at the T 2 /T 1 conical intersection. Moreover, an S 2 /S 1 /T 2 intersection region is found to play a vital role in the excited-state relaxation. These new mechanistic insights help in understanding the photophysics and photochemistry of unusual base pairs.

B-DNA Structure and Stability as Function of Nucleic Acid Composition: Dispersion-Corrected DFT Study of Dinucleoside Monophosphate Single and Double Strands

PubMed Central

Barone, Giampaolo; Fonseca Guerra, Célia; Bickelhaupt, F Matthias

2013-01-01

We have computationally investigated the structure and stability of all 16 combinations of two out of the four natural DNA bases A, T, G and C in a di-2′-deoxyribonucleoside-monophosphate model DNA strand as well as in 10 double-strand model complexes thereof, using dispersion-corrected density functional theory (DFT-D). Optimized geometries with B-DNA conformation were obtained through the inclusion of implicit water solvent and, in the DNA models, of sodium counterions, to neutralize the negative charge of the phosphate groups. The results obtained allowed us to compare the relative stability of isomeric single and double strands. Moreover, the energy of the Watson–Crick pairing of complementary single strands to form double-helical structures was calculated. The latter furnished the following increasing stability trend of the double-helix formation energy: d(TpA)2

Spin-imbalanced pairing and Fermi surface deformation in flat bands

NASA Astrophysics Data System (ADS)

Huhtinen, Kukka-Emilia; Tylutki, Marek; Kumar, Pramod; Vanhala, Tuomas I.; Peotta, Sebastiano; Törmä, Päivi

2018-06-01

We study the attractive Hubbard model with spin imbalance on two lattices featuring a flat band: the Lieb and kagome lattices. We present mean-field phase diagrams featuring exotic superfluid phases, similar to the Fulde-Ferrell-Larkin-Ovchinnikov (FFLO) state, whose stability is confirmed by dynamical mean-field theory. The nature of the pairing is found to be richer than just the Fermi surface shift responsible for the usual FFLO state. The presence of a flat band allows for changes in the particle momentum distributions at null energy cost. This facilitates formation of nontrivial superfluid phases via multiband Cooper pair formation: the momentum distribution of the spin component in the flat band deforms to mimic the Fermi surface of the other spin component residing in a dispersive band. The Fermi surface of the unpaired particles that are typical for gapless superfluids becomes deformed as well. The results highlight the profound effect of flat dispersions on Fermi surface instabilities, and provide a potential route for observing spin-imbalanced superfluidity and superconductivity.

Tunable hybridization of Majorana bound states at the quantum spin Hall edge

NASA Astrophysics Data System (ADS)

Keidel, Felix; Burset, Pablo; Trauzettel, Björn

2018-02-01

Confinement at the helical edge of a topological insulator is possible in the presence of proximity-induced magnetic (F) or superconducting (S) order. The interplay of both phenomena leads to the formation of localized Majorana bound states (MBS) or likewise (under certain resonance conditions) the formation of ordinary Andreev bound states (ABS). We investigate the properties of bound states in junctions composed of alternating regions of F or S barriers. Interestingly, the direction of magnetization in F regions and the relative superconducting phase between S regions can be exploited to hybridize MBS or ABS at will. We show that the local properties of MBS translate into a particular nonlocal superconducting pairing amplitude. Remarkably, the symmetry of the pairing amplitude contains information about the nature of the bound state that it stems from. Hence this symmetry can in principle be used to distinguish MBS from ABS, owing to the strong connection between local density of states and nonlocal pairing in our setup.

Thermodynamic insights into 2-thiouridine-enhanced RNA hybridization

PubMed Central

Larsen, Aaron T.; Fahrenbach, Albert C.; Sheng, Jia; Pian, Julia; Szostak, Jack W.

2015-01-01

Nucleobase modifications dramatically alter nucleic acid structure and thermodynamics. 2-thiouridine (s2U) is a modified nucleobase found in tRNAs and known to stabilize U:A base pairs and destabilize U:G wobble pairs. The recently reported crystal structures of s2U-containing RNA duplexes do not entirely explain the mechanisms responsible for the stabilizing effect of s2U or whether this effect is entropic or enthalpic in origin. We present here thermodynamic evaluations of duplex formation using ITC and UV thermal denaturation with RNA duplexes containing internal s2U:A and s2U:U pairs and their native counterparts. These results indicate that s2U stabilizes both duplexes. The stabilizing effect is entropic in origin and likely results from the s2U-induced preorganization of the single-stranded RNA prior to hybridization. The same preorganizing effect is likely responsible for structurally resolving the s2U:U pair-containing duplex into a single conformation with a well-defined H-bond geometry. We also evaluate the effect of s2U on single strand conformation using UV- and CD-monitored thermal denaturation and on nucleoside conformation using 1H NMR spectroscopy, MD and umbrella sampling. These results provide insights into the effects that nucleobase modification has on RNA structure and thermodynamics and inform efforts toward improving both ribozyme-catalyzed and nonenzymatic RNA copying. PMID:26240387

Persistent Ion Pairing in Aqueous Hydrochloric Acid

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

Baer, Marcel D.; Fulton, John L.; Balasubramanian, Mahalingam

2014-07-03

For strong acids, like hydrochloric acid, the complete dissociation into an excess proton and conjugated base as well as the formation of independent solvated charged fragments is assumed. The existence of a chloride-Hyronium (Cl-H3O+) contact ion pairs even in moderate concentration hydrochloric acid (2.5 m) demonstrates that the counter ions do not behave merely as spectators. Through the use of modern extended X-ray absorption fine structure (EXAFS) measurements in conjunction with state-of-the-art density functional theory (DFT) simulations, we are able to obtain an unprecedented view into the molecular structure of medium to high concentrated electrolytes. Here we report that themore » Cl-H3O+ contact ion pair structure persists throughout the entire concentration range studied and that these structures differ significantly from moieties studied in micro-solvated hydrochloric acid clusters. Characterizing distinct populations of these ion pairs gives rise to a novel molecular level description of how to think about the activity of the proton that impacts our picture of the pH scale. Funding for CJM, GKS, and JLF was provided by DOE Office of Science, Office of Basic Energy Science, Division of Chemical Sciences, Geosciences, and Biosciences. Funding for MDB was provided throught the Laboratory Directed Research and Development program at Pacific Northwest National Laboratory. MB was funded through Argonne National Laboratory.« less

Formation of Polychlorinated Biphenyls on Secondary Copper Production Fly Ash: Mechanistic Aspects and Correlation to Other Persistent Organic Pollutants

NASA Astrophysics Data System (ADS)

Jiang, Xiaoxu; Liu, Guorui; Wang, Mei; Zheng, Minghui

2015-09-01

Emission of unintentionally formed polychlorinated biphenyls (PCBs) from industrial thermal processes is a global issue. Because the production and use of technical PCB mixtures has been banned, industrial thermal processes have become increasingly important sources of PCBs. Among these processes, secondary copper smelting is an important PCB source in China. In the present study, the potential for fly ash-mediated formation of PCBs in the secondary copper industry, and the mechanisms involved, were studied in laboratory thermochemical experiments. The total PCB concentrations were 37-70 times higher than the initial concentrations. Thermochemical reactions on the fly ash amplified the potential toxic equivalents of PCBs. The formation of PCBs over time and the effect of temperature were investigated. Based on analyses of PCB homologue profiles with different reaction conditions, a chlorination mechanism was proposed for forming PCBs in addition to a de novo synthesis mechanism. The chlorination pathway was supported by close correlations between each pair of adjacent homologue groups. Formation of PCBs and multiple persistent organic pollutants, including polychlorinated dibenzo-p-dioxins, polychlorinated dibenzofurans and polychlorinated naphthalenes, occurred during the tests, indicating that these compounds may share similar formation mechanisms.

Photo-Responsive Soft Ionic Crystals: Ion-Pairing Assemblies of Azobenzene Carboxylates.

PubMed

Yamakado, Ryohei; Hara, Mitsuo; Nagano, Shusaku; Seki, Takahiro; Maeda, Hiromitsu

2017-07-12

This report delineates the design and synthesis of negatively charged azobenzene derivatives that form photo-responsive ion-pairing assemblies. The azobenzene carboxylates possessing aliphatic chains were prepared as photo-responsive anions that promote the formation of ion-pairing dimension-controlled assemblies, including mesophases, when used in conjunction with a tetrabutylammonium (TBA) cation. The photo-responsive properties of the ion pairs and the precursory carboxylic acids in the bulk state were examined by polarized optical microscopy (POM) and X-ray diffraction (XRD), demonstrating that liquid crystal (LC)-liquid and crystal-liquid phase transitions occurred, depending on the number and lengths of the aliphatic chains of each assembly. An ion pair exhibited photo-induced crystal-crystal phase transitions upon switching between two irradiation wavelengths (365/436 nm). © 2017 Wiley-VCH Verlag GmbH & Co. KGaA, Weinheim.

Emission line galaxy pairs up to z=1.5 from the WISP survey

NASA Astrophysics Data System (ADS)

Teplitz, Harry I.; Dai, Yu Sophia; Malkan, Matthew Arnold; Scarlata, Claudia; Colbert, James W.; Atek, Hakim; Bagley, Micaela B.; Baronchelli, Ivano; Bedregal, Alejandro; Beck, Melanie; Bunker, Andrew; Dominguez, Alberto; Hathi, Nimish P.; Henry, Alaina L.; Mehta, Vihang; Pahl, Anthony; Rafelski, Marc; Ross, Nathaniel; Rutkowski, Michael J.; Siana, Brian D.; WISPs Team

2016-01-01

We present a sample of spectroscopically identified emission line galaxy pairs up to z=1.5 from WISPs (WFC3 Infrared Spectroscopic Parallel survey) using high resolution direct and grism images from HST. We searched ~150 fields with a covered area of ~600 arcmin^2, and a comoving volume of > 400 Gpc^3 at z=1-2, and found ~80 very close physical pairs (projected separation Dp < 50 h^{-1}kpc, relative velocity d_v < 500 kms^{-1}), and ~100 close physical pairs (50 < Dp < 100 h^{-1}kpc, d_v < 1000 kms^{-1}) of emission line galaxies, including two dozen triplets and quadruples. In this poster we present the multi-wavelength data, star formation rate (SFR), mass ratio, and study the merger rate evolution with this special galaxy pair sample.

Theoretical Studies of the Glycosidation of 2-O-Substituted 5-Fluorouracil: N-Regioselective Synthesis with the Phase-Transfer-Catalysis Method.

PubMed

Wang, Yi-Gui; Barnes, Ericka C

2017-11-22

The observed N-regioselective glycosidation of 2-O-substituted 5-fluorouracil (5-FU) via the phase-transfer-catalysis (PTC) method was investigated computationally. The Gibbs free energy reaction barrier of the N-reaction between the 5-FU anion and 1-bromo-1-deoxy-2,3,4,6-tetra-O-acetyl-α-d-glucopyranose was computed at the MP2/6-311++G(2d,p)//B3LYP/6-31+G* level. The calculated transition states were, in general, quite "loose", with the ambident reaction sites at the N3- or O4-positions on 5-FU located approximately 2.0 Å from the anomeric carbon. With the S N 2 mechanism, the formation of β-glycosides was explained by the characteristics of transition states, and the N-regioselectivity was explained by three considerations: (1) the conformations of initial complexes and the structural requirement of the reactions; (2) the formation of an ionic pair between nBu 4 N + and 2-O-substituted 5-FU anions; and (3) the thermodynamic conversion of O-glycosides to N-glycosides. The reactions between the oxocarbenium ion and the 2-O-substituted 5-FU anions (the fast step of S N 1 mechanism) were also examined at the same level of theory. Because there were no "promoters" to extract Br in the PTC method, the S N 1 mechanism might have an unfavorably high barrier to produce oxocarbenium ion. However, both the formation of β-glycosides and the experimentally observed N-regioselectivity could also be explained by the S N 1 mechanism: The former was explained by the neighboring group participation, and the latter was explained by the formation of ionic pairs between nBu 4 N + and 2-O-substituted 5-FU anions. The formation of ionic pairs possibly changed the diffusion-controlled mechanism into an activation-controlled mechanism. Two factors were demonstrated by Marcus theory to play an important role for the experimentally observed N-resioselectivity in the PTC method: (1) the thermodynamic stability of N-products over O-products; (2) the formation of ionic pair between nBu 4 N + and 2-O-substituted 5-FU anions.

Lithium formate for EPR dosimetry: radiation-induced radical trapping at low temperatures.

PubMed

Krivokapić, André; Aalbergsjø, Siv G; De Cooman, Hendrik; Hole, Eli Olaug; Nelson, William H; Sagstuen, Einar

2014-05-01

Radiation-induced primary radicals in lithium formate. A material used in EPR dosimetry have been studied using electron paramagnetic resonance (EPR), electron nuclear double resonance (ENDOR) and ENDOR-Induced EPR (EIE) techniques. In this study, single crystals were X irradiated at 6-8 K and radical formation at these and higher temperatures were investigated. Periodic density functional theory calculations were used to assist in assigning the radical structures. Mainly two radicals are present at 6 K, the well-known CO2(•-) radical and a protonated electron-gain product. Hyperfine coupling tensors for proton and lithium interactions were obtained for these two radicals and show that the latter radical exists in four conformations with various degrees of bending at the radical center. Pairs of CO2(•-) radicals were also observed and the tensor for the electron-electron dipolar coupling was determined for the strongest coupled pair, which exhibited the largest spectral intensity. Upon warming, both the radical pairs and the reduction product decay, the latter apparently by a transient species. Above 200 K the EPR spectrum was mainly due to the CO2(•-) (mono) radicals, which were previously characterized as the dominant species present at room temperature and which account for the dosimetric EPR signal.

Mouse HFM1/Mer3 Is Required for Crossover Formation and Complete Synapsis of Homologous Chromosomes during Meiosis

PubMed Central

Guiraldelli, Michel F.; Eyster, Craig; Wilkerson, Joseph L.; Dresser, Michael E.; Pezza, Roberto J.

2013-01-01

Faithful chromosome segregation during meiosis requires that homologous chromosomes associate and recombine. Chiasmata, the cytological manifestation of recombination, provide the physical link that holds the homologs together as a pair, facilitating their orientation on the spindle at meiosis I. Formation of most crossover (CO) events requires the assistance of a group of proteins collectively known as ZMM. HFM1/Mer3 is in this group of proteins and is required for normal progression of homologous recombination and proper synapsis between homologous chromosomes in a number of model organisms. Our work is the first study in mammals showing the in vivo function of mouse HFM1. Cytological observations suggest that initial steps of recombination are largely normal in a majority of Hfm1−/− spermatocytes. Intermediate and late stages of recombination appear aberrant, as chromosomal localization of MSH4 is altered and formation of MLH1foci is drastically reduced. In agreement, chiasma formation is reduced, and cells arrest with subsequent apoptosis at diakinesis. Our results indicate that deletion of Hfm1 leads to the elimination of a major fraction but not all COs. Formation of chromosome axial elements and homologous pairing is apparently normal, and Hfm1−/− spermatocytes progress to the end of prophase I without apparent developmental delay or apoptosis. However, synapsis is altered with components of the central region of the synaptonemal complex frequently failing to extend the full length of the chromosome axes. We propose that initial steps of recombination are sufficient to support homology recognition, pairing, and initial chromosome synapsis and that HFM1 is required to form normal numbers of COs and to complete synapsis. PMID:23555294

Central oxytocin receptors mediate mating-induced partner preferences and enhance correlated activation across forebrain nuclei in male prairie voles.

PubMed

Johnson, Zachary V; Walum, Hasse; Jamal, Yaseen A; Xiao, Yao; Keebaugh, Alaine C; Inoue, Kiyoshi; Young, Larry J

2016-03-01

Oxytocin (OT) is a deeply conserved nonapeptide that acts both peripherally and centrally to modulate reproductive physiology and sociosexual behavior across divergent taxa, including humans. In vertebrates, the distribution of the oxytocin receptor (OTR) in the brain is variable within and across species, and OTR signaling is critical for a variety of species-typical social and reproductive behaviors, including affiliative and pair bonding behaviors in multiple socially monogamous lineages of fishes, birds, and mammals. Early work in prairie voles suggested that the endogenous OT system modulates mating-induced partner preference formation in females but not males; however, there is significant evidence that central OTRs may modulate pair bonding behavior in both sexes. In addition, it remains unclear how transient windows of central OTR signaling during sociosexual interaction modulate neural activity to produce enduring shifts in sociobehavioral phenotypes, including the formation of selective social bonds. Here we re-examine the role of the central OT system in partner preference formation in male prairie voles using a selective OTR antagonist delivered intracranially. We then use the same antagonist to examine how central OTRs modulate behavior and immediate early gene (Fos) expression, a metric of neuronal activation, in males during brief sociosexual interaction with a female. Our results suggest that, as in females, OTR signaling is critical for partner preference formation in males and enhances correlated activation across sensory and reward processing brain areas during sociosexual interaction. These results are consistent with the hypothesis that central OTR signaling facilitates social bond formation by coordinating activity across a pair bonding neural network. Copyright © 2015 Elsevier Inc. All rights reserved.

Observing Galaxy Mergers in Simulations

NASA Astrophysics Data System (ADS)

Snyder, Gregory

2018-01-01

I will describe results on mergers and morphology of distant galaxies. By mock-observing 3D cosmological simulations, we aim to contrast theory with data, design better diagnostics of physical processes, and examine unexpected signatures of galaxy formation. Recently, we conducted mock surveys of the Illustris Simulations to learn how mergers would appear in deep HST and JWST surveys. With this approach, we reconciled merger rates estimated using observed close galaxy pairs with intrinsic merger rates predicted by theory. This implies that the merger-pair observability time is probably shorter in the early universe, and therefore that major mergers are more common than implied by the simplest arguments. Further, we show that disturbance-based diagnostics of late-stage mergers can be improved significantly by combining multi-dimensional image information with simulated merger identifications to train automated classifiers. We then apply these classifiers to real measurements from the CANDELS fields, recovering a merger fraction increasing with redshift in broad agreement with pair fractions and simulations, and with statistical errors smaller by a factor of two than classical morphology estimators. This emphasizes the importance of using robust training sets, including cosmological simulations and multidimensional data, for interpreting observed processes in galaxy evolution.

Accurate SHAPE-directed RNA secondary structure modeling, including pseudoknots.

PubMed

Hajdin, Christine E; Bellaousov, Stanislav; Huggins, Wayne; Leonard, Christopher W; Mathews, David H; Weeks, Kevin M

2013-04-02

A pseudoknot forms in an RNA when nucleotides in a loop pair with a region outside the helices that close the loop. Pseudoknots occur relatively rarely in RNA but are highly overrepresented in functionally critical motifs in large catalytic RNAs, in riboswitches, and in regulatory elements of viruses. Pseudoknots are usually excluded from RNA structure prediction algorithms. When included, these pairings are difficult to model accurately, especially in large RNAs, because allowing this structure dramatically increases the number of possible incorrect folds and because it is difficult to search the fold space for an optimal structure. We have developed a concise secondary structure modeling approach that combines SHAPE (selective 2'-hydroxyl acylation analyzed by primer extension) experimental chemical probing information and a simple, but robust, energy model for the entropic cost of single pseudoknot formation. Structures are predicted with iterative refinement, using a dynamic programming algorithm. This melded experimental and thermodynamic energy function predicted the secondary structures and the pseudoknots for a set of 21 challenging RNAs of known structure ranging in size from 34 to 530 nt. On average, 93% of known base pairs were predicted, and all pseudoknots in well-folded RNAs were identified.

Suppression of Boride Formation in Transient Liquid Phase Bonding of Pairings of Parent Superalloy Materials with Different Compositions and Grain Structures and Resulting Mechanical Properties

NASA Astrophysics Data System (ADS)

Steuer, Susanne; Singer, Robert F.

2014-07-01

Two Ni-based superalloys, columnar grained Alloy 247 and single-crystal PWA1483, are joined by transient liquid phase bonding using an amorphous brazing foil containing boron as a melting point depressant. At lower brazing temperatures, two different morphologies of borides develop in both base materials: plate-like and globular ones. Their ratio to each other is temperature dependent. With very high brazing temperatures, the deleterious boride formation in Alloy 247 can be totally avoided, probably because the three-phase-field moves to higher alloying element contents. For the superalloy PWA1483, the formation of borides cannot be completely avoided at high brazing temperatures as incipient melting occurs. During subsequent solidification of these areas, Chinese-script-like borides precipitate. The mechanical properties (tensile tests at room and elevated temperatures and short-term creep rupture tests at elevated temperatures) for brazed samples without boride precipitation are very promising. Tensile strengths and creep times to 1 pct strain are comparable, respectively, higher than the ones of the weaker parent material for all tested temperatures and creep conditions (from 90 to 100 pct rsp. 175 to 250 pct).

Electronic structure of strongly reduced (1 ‾ 1 1) surface of monoclinic HfO2

NASA Astrophysics Data System (ADS)

Cheng, YingXing; Zhu, Linggang; Ying, Yile; Zhou, Jian; Sun, Zhimei

2018-07-01

Material surface is playing an increasingly important role in electronic devices as their size down to nanoscale. Here, by first-principles calculations we studied the surface oxygen-vacancies (Vos) induced electronic-structure variation of HfO2 , in order to explore its potential applications in surface-controlled electronic devices. Firstly, it is found that single Vo tends to segregate onto the surface and attracts each other as they form pairs, making the formation of vacancies-contained functional surface possible. Then extensive Vo-chains whose formation/rupture can represent the high/low conductivity state are constructed. The electronic states induced by the Vos remain localized in the band-gap region for most of the Vo-chains studied here. A transition to a metallic conductance is found in metastable Vo-chain with formation energy increased by 0.25 eV per Vo. Moreover, we highlight the significance of the Hubbard U correction for density functional theory when studying the electronic-structure based conductance in the oxides. By comprehensive calculations, we find a conductivity-stability dilemma of the Vo-chains, providing guideline for understanding and designing the electronic devices based on HfO2 surface.

Certainty rating in pre-and post-tests of study modules in an online clinical pharmacy course - A pilot study to evaluate teaching and learning.

PubMed

Luetsch, Karen; Burrows, Judith

2016-10-14

Graduate and post-graduate education for health professionals is increasingly delivered in an e-learning environment, where automated, continuous formative testing with integrated feedback can guide students' self-assessment and learning. Asking students to rate the certainty they assign to the correctness of their answers to test questions can potentially provide deeper insights into the success of teaching, with test results informing course designers whether learning outcomes have been achieved. It may also have implications for decision making in clinical practice. A study of pre-and post-tests for five study modules was designed to evaluate the teaching and learning within a pharmacotherapeutic course in an online postgraduate clinical pharmacy program. Certainty based marking of multiple choice questions (MCQ) was adapted for formative pre- and post-study module testing by asking students to rate their certainty of correctness of MCQ answers. Paired t-tests and a coding scheme were used to analyse changes in answers and certainty between pre-and post-tests. A survey evaluated students' experience with the novel formative testing design. Twenty-nine pharmacists enrolled in the postgraduate program participated in the study. Overall 1315 matched pairs of MCQ answers and certainty ratings between pre- and post-module tests were available for evaluation. Most students identified correct answers in post-tests and increased their certainty compared to pre-tests. Evaluation of certainty ratings in addition to correctness of answers identified MCQs and topic areas for revision to course designers. A survey of students showed that assigning certainty ratings to their answers assisted in structuring and focusing their learning throughout online study modules, facilitating identification of areas of uncertainty and gaps in their clinical knowledge. Adding certainty ratings to MCQ answers seems to engage students with formative testing and feedback and focus their learning in a web-based postgraduate pharmacy course. It also offers deeper insight into the successful delivery of online course content, identifying areas for improvement of teaching and content delivery as well as test question design.

Star Formation in Dwarf-Dwarf Mergers: Fueling Hierarchical Assembly

NASA Astrophysics Data System (ADS)

Stierwalt, Sabrina; Johnson, K. E.; Kallivayalil, N.; Patton, D. R.; Putman, M. E.; Besla, G.; Geha, M. C.

2014-01-01

We present early results from the first systematic study a sample of isolated interacting dwarf pairs and the mechanisms governing their star formation. Low mass dwarf galaxies are ubiquitous in the local universe, yet the efficiency of gas removal and the enhancement of star formation in dwarfs via pre-processing (i.e. dwarf-dwarf interactions occurring before the accretion by a massive host) are currently unconstrained. Studies of Local Group dwarfs credit stochastic internal processes for their complicated star formation histories, but a few intriguing examples suggest interactions among dwarfs may produce enhanced star formation. We combine archival UV imaging from GALEX with deep optical broad- and narrow-band (Halpha) imaging taken with the pre- One Degree Imager (pODI) on the WIYN 3.5-m telescope and with the 2.3-m Bok telescope at Steward Observatory to confirm the presence of stellar bridges and tidal tails and to determine whether dwarf-dwarf interactions alone can trigger significant levels of star formation. We investigate star formation rates and global galaxy colors as a function of dwarf pair separation (i.e. the dwarf merger sequence) and dwarf-dwarf mass ratio. This project is a precursor to an ongoing effort to obtain high spatial resolution HI imaging to assess the importance of sequential triggering caused by dwarf-dwarf interactions and the subsequent affect on the more massive hosts that later accrete the low mass systems.

Mismatch and G-Stack Modulated Probe Signals on SNP Microarrays

PubMed Central

Binder, Hans; Fasold, Mario; Glomb, Torsten

2009-01-01

Background Single nucleotide polymorphism (SNP) arrays are important tools widely used for genotyping and copy number estimation. This technology utilizes the specific affinity of fragmented DNA for binding to surface-attached oligonucleotide DNA probes. We analyze the variability of the probe signals of Affymetrix GeneChip SNP arrays as a function of the probe sequence to identify relevant sequence motifs which potentially cause systematic biases of genotyping and copy number estimates. Methodology/Principal Findings The probe design of GeneChip SNP arrays enables us to disentangle different sources of intensity modulations such as the number of mismatches per duplex, matched and mismatched base pairings including nearest and next-nearest neighbors and their position along the probe sequence. The effect of probe sequence was estimated in terms of triple-motifs with central matches and mismatches which include all 256 combinations of possible base pairings. The probe/target interactions on the chip can be decomposed into nearest neighbor contributions which correlate well with free energy terms of DNA/DNA-interactions in solution. The effect of mismatches is about twice as large as that of canonical pairings. Runs of guanines (G) and the particular type of mismatched pairings formed in cross-allelic probe/target duplexes constitute sources of systematic biases of the probe signals with consequences for genotyping and copy number estimates. The poly-G effect seems to be related to the crowded arrangement of probes which facilitates complex formation of neighboring probes with at minimum three adjacent G's in their sequence. Conclusions The applied method of “triple-averaging” represents a model-free approach to estimate the mean intensity contributions of different sequence motifs which can be applied in calibration algorithms to correct signal values for sequence effects. Rules for appropriate sequence corrections are suggested. PMID:19924253

Interactions in ion pairs of protic ionic liquids: Comparison with aprotic ionic liquids

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

Tsuzuki, Seiji, E-mail: s.tsuzuki@aist.go.jp; Shinoda, Wataru; Miran, Md. Shah

2013-11-07

The stabilization energies for the formation (E{sub form}) of 11 ion pairs of protic and aprotic ionic liquids were studied by MP2/6-311G{sup **} level ab initio calculations to elucidate the difference between the interactions of ions in protic ionic liquids and those in aprotic ionic liquids. The interactions in the ion pairs of protic ionic liquids (diethylmethylammonium [dema] and dimethylpropylammonium [dmpa] based ionic liquids) are stronger than those of aprotic ionic liquids (ethyltrimethylammonium [etma] based ionic liquids). The E{sub form} for the [dema][CF{sub 3}SO{sub 3}] and [dmpa][CF{sub 3}SO{sub 3}] complexes (−95.6 and −96.4 kcal/mol, respectively) are significantly larger (more negative)more » than that for the [etma][CF{sub 3}SO{sub 3}] complex (−81.0 kcal/mol). The same trend was observed for the calculations of ion pairs of the three cations with the Cl{sup −}, BF{sub 4}{sup −}, TFSA{sup −} anions. The anion has contact with the N–H bond of the dema{sup +} or dmpa{sup +} cations in the most stable geometries of the dema{sup +} and dmpa{sup +} complexes. The optimized geometries, in which the anions locate on the counter side of the cations, are 11.0–18.0 kcal/mol less stable, which shows that the interactions in the ions pairs of protic ionic liquids have strong directionality. The E{sub form} for the less stable geometries for the dema{sup +} and dmpa{sup +} complexes are close to those for the most stable etma{sup +} complexes. The electrostatic interaction, which is the major source of the attraction in the ion pairs, is responsible for the directionality of the interactions and determining the magnitude of the interaction energy. Molecular dynamic simulations of the [dema][TFSA] and [dmpa][TFSA] ionic liquids show that the N–H bonds of the cations have contact with the negatively charged (oxygen and nitrogen) atoms of TFSA{sup −} anion, while the strong directionality of the interactions was not suggested from the simulation of the [etma][CF{sub 3}SO{sub 3}] ionic liquid.« less

Triplex-forming oligonucleotides: a third strand for DNA nanotechnology

PubMed Central

2018-01-01

Abstract DNA self-assembly has proved to be a useful bottom-up strategy for the construction of user-defined nanoscale objects, lattices and devices. The design of these structures has largely relied on exploiting simple base pairing rules and the formation of double-helical domains as secondary structural elements. However, other helical forms involving specific non-canonical base-base interactions have introduced a novel paradigm into the process of engineering with DNA. The most notable of these is a three-stranded complex generated by the binding of a third strand within the duplex major groove, generating a triple-helical (‘triplex’) structure. The sequence, structural and assembly requirements that differentiate triplexes from their duplex counterparts has allowed the design of nanostructures for both dynamic and/or structural purposes, as well as a means to target non-nucleic acid components to precise locations within a nanostructure scaffold. Here, we review the properties of triplexes that have proved useful in the engineering of DNA nanostructures, with an emphasis on applications that hitherto have not been possible by duplex formation alone. PMID:29228337

Structural insights into the histone H1-nucleosome complex

PubMed Central

Zhou, Bing-Rui; Feng, Hanqiao; Kato, Hidenori; Dai, Liang; Yang, Yuedong; Zhou, Yaoqi; Bai, Yawen

2013-01-01

Linker H1 histones facilitate formation of higher-order chromatin structures and play important roles in various cell functions. Despite several decades of effort, the structural basis of how H1 interacts with the nucleosome remains elusive. Here, we investigated Drosophila H1 in complex with the nucleosome, using solution nuclear magnetic resonance spectroscopy and other biophysical methods. We found that the globular domain of H1 bridges the nucleosome core and one 10-base pair linker DNA asymmetrically, with its α3 helix facing the nucleosomal DNA near the dyad axis. Two short regions in the C-terminal tail of H1 and the C-terminal tail of one of the two H2A histones are also involved in the formation of the H1–nucleosome complex. Our results lead to a residue-specific structural model for the globular domain of the Drosophila H1 in complex with the nucleosome, which is different from all previous experiment-based models and has implications for chromatin dynamics in vivo. PMID:24218562

PWC - PAIRWISE COMPARISON SOFTWARE: SOFTWARE PROGRAM FOR PAIRWISE COMPARISON TASK FOR PSYCHOMETRIC SCALING AND COGNITIVE RESEARCH

NASA Technical Reports Server (NTRS)

Ricks, W. R.

1994-01-01

PWC is used for pair-wise comparisons in both psychometric scaling techniques and cognitive research. The cognitive tasks and processes of a human operator of automated systems are now prominent considerations when defining system requirements. Recent developments in cognitive research have emphasized the potential utility of psychometric scaling techniques, such as multidimensional scaling, for representing human knowledge and cognitive processing structures. Such techniques involve collecting measurements of stimulus-relatedness from human observers. When data are analyzed using this scaling approach, an n-dimensional representation of the stimuli is produced. This resulting representation is said to describe the subject's cognitive or perceptual view of the stimuli. PWC applies one of the many techniques commonly used to acquire the data necessary for these types of analyses: pair-wise comparisons. PWC administers the task, collects the data from the test subject, and formats the data for analysis. It therefore addresses many of the limitations of the traditional "pen-and-paper" methods. By automating the data collection process, subjects are prevented from going back to check previous responses, the possibility of erroneous data transfer is eliminated, and the burden of the administration and taking of the test is eased. By using randomization, PWC ensures that subjects see the stimuli pairs presented in random order, and that each subject sees pairs in a different random order. PWC is written in Turbo Pascal v6.0 for IBM PC compatible computers running MS-DOS. The program has also been successfully compiled with Turbo Pascal v7.0. A sample executable is provided. PWC requires 30K of RAM for execution. The standard distribution medium for this program is a 5.25 inch 360K MS-DOS format diskette. Two electronic versions of the documentation are included on the diskette: one in ASCII format and one in MS Word for Windows format. PWC was developed in 1993.

Efficient formation of heterokaryotic sclerotia in the filamentous fungus Aspergillus oryzae.

PubMed

Wada, Ryuta; Jin, Feng Jie; Koyama, Yasuji; Maruyama, Jun-ichi; Kitamoto, Katsuhiko

2014-01-01

Heterokaryon formation by hyphal fusion occurs during a sexual/parasexual cycle in filamentous fungi, and therefore, it is biotechnologically important for crossbreeding. In the industrial filamentous fungus Aspergillus oryzae, a parasexual cycle has been reported, and it was recently suggested that sexual reproduction should be possible. However, as A. oryzae enters into hyphal fusion with a much lower frequency than Neurospora crassa, the process of heterokaryon formation has not been extensively characterized in A. oryzae. Here, we developed a detection system for heterokaryon formation by expressing red or green fluorescent proteins in nuclei and conferring uridine/uracil or adenine auxotrophy to MAT1-1 and MAT1-2 strains of A. oryzae. The heterokaryon formation of A. oryzae was investigated in paired culture using the genetically modified strains. No sclerotial formation was observed in the hyphal contact regions of the two strains with the same auxotrophy, whereas numerous sclerotia were formed between the strains with different auxotrophies. In most of the formed sclerotia, the uridine/uracil and adenine auxotrophies were complemented, and both red and green fluorescence were detected, indicating that heterokaryotic fusants were formed by hyphal fusion before or during sclerotial formation. Moreover, overexpressing the sclR gene, which encodes a transcription factor promoting sclerotial formation, increased the number of heterokaryotic sclerotia formed between the two auxotrophic strains. Notably, these effects in sclerotial formation of heterokaryotic fusants were observed independently of the mating type pairing combinations. Taken together, these findings demonstrated that paring of different auxotrophs and sclR overexpression promote the formation of heterokaryotic sclerotia in A. oryzae.

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

Sun, Junming; Baylon, Rebecca A.; Liu, Changjun

The effects of surface acidity on the cascade ethanol-to-isobutene conversion were studied using ZnxZryOz catalysts. The ethanol-to-isobutene reaction was found to be limited by the secondary reaction of the key intermediate, acetone, namely the acetone-to-isobutene reaction. Although the catalysts with coexisting Brønsted acidity could catalyze the rate-limiting acetone-to-isobutene reaction, the presence of Brønsted acidity is also detrimental. First, secondary isobutene isomerization is favored, producing a mixture of butene isomers. Second, undesired polymerization and coke formation prevail, leading to rapid catalyst deactivation. Most importantly, both steady-state and kinetic reaction studies as well as FTIR analysis of adsorbed acetone-d6 and D2O unambiguouslymore » showed that a highly active and selective nature of balanced Lewis acid-base pairs was masked by the coexisting Brønsted acidity in the aldolization and self-deoxygenation of acetone to isobutene. As a result, ZnxZryOz catalysts with only Lewis acid-base pairs were discovered, on which nearly a theoretical selectivity to isobutene (~88.9%) was successfully achieved, which has never been reported before. Moreover, the absence of Brønsted acidity in such ZnxZryOz catalysts also eliminates the side isobutene isomerization and undesired polymerization/coke reactions, resulting in the production of high purity isobutene with significantly improved catalyst stability (< 2% activity loss after 200 h time-on-stream). This work not only demonstrates a balanced Lewis acid-base pair for the highly active and selective cascade ethanol-to-isobutene reaction, but also sheds light on the rational design of selective and robust acid-base catalyst for C-C coupling via aldolization reaction.« less

Structure-based approach to the prediction of disulfide bonds in proteins.

PubMed

Salam, Noeris K; Adzhigirey, Matvey; Sherman, Woody; Pearlman, David A

2014-10-01

Protein engineering remains an area of growing importance in pharmaceutical and biotechnology research. Stabilization of a folded protein conformation is a frequent goal in projects that deal with affinity optimization, enzyme design, protein construct design, and reducing the size of functional proteins. Indeed, it can be desirable to assess and improve protein stability in order to avoid liabilities such as aggregation, degradation, and immunogenic response that may arise during development. One way to stabilize a protein is through the introduction of disulfide bonds. Here, we describe a method to predict pairs of protein residues that can be mutated to form a disulfide bond. We combine a physics-based approach that incorporates implicit solvent molecular mechanics with a knowledge-based approach. We first assign relative weights to the terms that comprise our scoring function using a genetic algorithm applied to a set of 75 wild-type structures that each contains a disulfide bond. The method is then tested on a separate set of 13 engineered proteins comprising 15 artificial stabilizing disulfides introduced via site-directed mutagenesis. We find that the native disulfide in the wild-type proteins is scored well, on average (within the top 6% of the reasonable pairs of residues that could form a disulfide bond) while 6 out of the 15 artificial stabilizing disulfides scored within the top 13% of ranked predictions. Overall, this suggests that the physics-based approach presented here can be useful for triaging possible pairs of mutations for disulfide bond formation to improve protein stability. © The Author 2014. Published by Oxford University Press. All rights reserved. For Permissions, please e-mail: journals.permissions@oup.com.

Correlation of RNA secondary structure statistics with thermodynamic stability and applications to folding.

PubMed

Wu, Johnny C; Gardner, David P; Ozer, Stuart; Gutell, Robin R; Ren, Pengyu

2009-08-28

The accurate prediction of the secondary and tertiary structure of an RNA with different folding algorithms is dependent on several factors, including the energy functions. However, an RNA higher-order structure cannot be predicted accurately from its sequence based on a limited set of energy parameters. The inter- and intramolecular forces between this RNA and other small molecules and macromolecules, in addition to other factors in the cell such as pH, ionic strength, and temperature, influence the complex dynamics associated with transition of a single stranded RNA to its secondary and tertiary structure. Since all of the factors that affect the formation of an RNAs 3D structure cannot be determined experimentally, statistically derived potential energy has been used in the prediction of protein structure. In the current work, we evaluate the statistical free energy of various secondary structure motifs, including base-pair stacks, hairpin loops, and internal loops, using their statistical frequency obtained from the comparative analysis of more than 50,000 RNA sequences stored in the RNA Comparative Analysis Database (rCAD) at the Comparative RNA Web (CRW) Site. Statistical energy was computed from the structural statistics for several datasets. While the statistical energy for a base-pair stack correlates with experimentally derived free energy values, suggesting a Boltzmann-like distribution, variation is observed between different molecules and their location on the phylogenetic tree of life. Our statistical energy values calculated for several structural elements were utilized in the Mfold RNA-folding algorithm. The combined statistical energy values for base-pair stacks, hairpins and internal loop flanks result in a significant improvement in the accuracy of secondary structure prediction; the hairpin flanks contribute the most.

The effect of gas physics on the halo mass function

NASA Astrophysics Data System (ADS)

Stanek, R.; Rudd, D.; Evrard, A. E.

2009-03-01

Cosmological tests based on cluster counts require accurate calibration of the space density of massive haloes, but most calibrations to date have ignored complex gas physics associated with halo baryons. We explore the sensitivity of the halo mass function to baryon physics using two pairs of gas-dynamic simulations that are likely to bracket the true behaviour. Each pair consists of a baseline model involving only gravity and shock heating, and a refined physics model aimed at reproducing the observed scaling of the hot, intracluster gas phase. One pair consists of billion-particle resimulations of the original 500h-1Mpc Millennium Simulation of Springel et al., run with the smoothed particle hydrodynamics (SPH) code GADGET-2 and using a refined physics treatment approximated by pre-heating (PH) at high redshift. The other pair are high-resolution simulations from the adaptive-mesh refinement code ART, for which the refined treatment includes cooling, star formation and supernova feedback (CSF). We find that, although the mass functions of the gravity-only (GO) treatments are consistent with the recent calibration of Tinker et al. (2008), both pairs of simulations with refined baryon physics show significant deviations. Relative to the GO case, the masses of ~1014h-1Msolar haloes in the PH and CSF treatments are shifted by the averages of -15 +/- 1 and +16 +/- 2 per cent, respectively. These mass shifts cause ~30 per cent deviations in number density relative to the Tinker function, significantly larger than the 5 per cent statistical uncertainty of that calibration.

Highly Dynamic Anion-Quadrupole Networks in Proteins.

PubMed

Kapoor, Karan; Duff, Michael R; Upadhyay, Amit; Bucci, Joel C; Saxton, Arnold M; Hinde, Robert J; Howell, Elizabeth E; Baudry, Jerome

2016-11-01

The dynamics of anion-quadrupole (or anion-π) interactions formed between negatively charged (Asp/Glu) and aromatic (Phe) side chains are for the first time computationally characterized in RmlC (Protein Data Bank entry 1EP0 ), a homodimeric epimerase. Empirical force field-based molecular dynamics simulations predict anion-quadrupole pairs and triplets (anion-anion-π and anion-π-π) are formed by the protein during the simulated trajectory, which suggests that the anion-quadrupole interactions may provide a significant contribution to the overall stability of the protein, with an average of -1.6 kcal/mol per pair. Some anion-π interactions are predicted to form during the trajectory, extending the number of anion-quadrupole interactions beyond those predicted from crystal structure analysis. At the same time, some anion-π pairs observed in the crystal structure exhibit marginal stability. Overall, most anion-π interactions alternate between an "on" state, with significantly stabilizing energies, and an "off" state, with marginal or null stabilizing energies. The way proteins possibly compensate for transient loss of anion-quadrupole interactions is characterized in the RmlC aspartate 84-phenylalanine 112 anion-quadrupole pair observed in the crystal structure. A double-mutant cycle analysis of the thermal stability suggests a possible loss of anion-π interactions compensated by variations of hydration of the residues and formation of compensating electrostatic interactions. These results suggest that near-planar anion-quadrupole pairs can exist, sometimes transiently, which may play a role in maintaining the structural stability and function of the protein, in an otherwise very dynamic interplay of a nonbonded interaction network as well as solvent effects.

Transcript Profiling of Individual Twin Blastomeres Derived by Splitting Two-Cell Stage Murine Embryos1

PubMed Central

Roberts, R. Michael; Katayama, Mika; Magnuson, Scott R.; Falduto, Michael T.; Torres, Karen E.O.

2010-01-01

In invertebrates and amphibians, informational macromolecules in egg cytoplasm are organized to provide direction to the formation of embryonic lineages, but it is unclear whether vestiges of such prepatterning exist in mammals. Here we examined whether twin blastomeres from 2-cell stage mouse embryos differ in mRNA content. mRNA from 26 blastomeres derived from 13 embryos approximately mid-way through their second cell cycle was subjected to amplification. Twenty amplified samples were hybridized to arrays. Of those samples that hybridized successfully, 12 samples in six pairs were used in the final analysis. Probes displaying normalized values >0.25 (n = 4573) were examined for consistent bias in expression within blastomere pairs. Although transcript content varied between both individual embryos and twin blastomeres, no consistent asymmetries were observed for the majority of genes, with only 178 genes displaying a >1.4-fold difference in expression across all six pairs. Although class discovery clustering showed that blastomere pairs separated into two distinct groups in terms of their differentially expressed genes, when the data were tested for significance of asymmetrical expression, only 39 genes with >1.4-fold change ratios in six of six blastomere pairs passed the two-sample t-test (P < 0.05). Transcripts encoding proteins implicated in RNA processing and cytoskeletal organization were among the most abundant, differentially distributed mRNA, suggesting that a stochastically based lack of synchrony in cell cycle progression between the two cells might explain at least some and possibly all of the asymmetries in transcript composition. PMID:21076082

The Human SepSecS-tRNASec Complex Reveals the Mechanism of Selenocysteine Formation

PubMed Central

Palioura, Sotiria; Sherrer, R. Lynn; Steitz, Thomas A.; Söll, Dieter; Simonović, Miljan

2010-01-01

Selenocysteine is the only genetically encoded amino acid in humans whose biosynthesis occurs on its cognate transfer RNA (tRNA). O-Phosphoseryl-tRNA:selenocysteinyl-tRNA synthase (SepSecS) catalyzes the final step of selenocysteine formation by a poorly understood tRNA-dependent mechanism. The crystal structure of human tRNASec in complex with SepSecS, phosphoserine, and thiophosphate, together with in vivo and in vitro enzyme assays, supports a pyridoxal phosphate–dependent mechanism of Sec-tRNASec formation. Two tRNASec molecules, with a fold distinct from other canonical tRNAs, bind to each SepSecS tetramer through their 13–base pair acceptor-TΨC arm (where Ψ indicates pseudouridine). The tRNA binding is likely to induce a conformational change in the enzyme’s active site that allows a phosphoserine covalently attached to tRNASec, but not free phosphoserine, to be oriented properly for the reaction to occur. PMID:19608919

Hierarchical Star Formation in Turbulent Media: Evidence from Young Star Clusters

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

Grasha, K.; Calzetti, D.; Elmegreen, B. G.

We present an analysis of the positions and ages of young star clusters in eight local galaxies to investigate the connection between the age difference and separation of cluster pairs. We find that star clusters do not form uniformly but instead are distributed so that the age difference increases with the cluster pair separation to the 0.25–0.6 power, and that the maximum size over which star formation is physically correlated ranges from ∼200 pc to ∼1 kpc. The observed trends between age difference and separation suggest that cluster formation is hierarchical both in space and time: clusters that are closemore » to each other are more similar in age than clusters born further apart. The temporal correlations between stellar aggregates have slopes that are consistent with predictions of turbulence acting as the primary driver of star formation. The velocity associated with the maximum size is proportional to the galaxy’s shear, suggesting that the galactic environment influences the maximum size of the star-forming structures.« less

Formation of In Vitro Mixed-Species Biofilms by Lactobacillus pentosus and Yeasts Isolated from Spanish-Style Green Table Olive Fermentations.

PubMed

León-Romero, Ángela; Domínguez-Manzano, Jesús; Garrido-Fernández, Antonio; Arroyo-López, Francisco Noé; Jiménez-Díaz, Rufino

2016-01-15

The present work details the in vitro interactions between Lactobacillus pentosus and yeast strains isolated from table olive processing to form mixed biofilms. Among the different pairs assayed, the strongest biofilms were obtained from L. pentosus and Candida boidinii strain cocultures. However, biofilm formation was inhibited in the presence of d-(+)-mannose. In addition, biofilm formation by C. boidinii monoculture was stimulated in the absence of cell-cell contact with L. pentosus. Scanning electron microscopy revealed that a sort of "sticky" material formed by the yeasts contributed to substrate adherence. Hence, the data obtained in this work suggest that yeast-lactobacilli biofilms may be favored by the presence of a specific mate of yeast and L. pentosus, and that more than one mechanism might be implicated in the biofilm formation. This knowledge will help in the design of appropriate mixed starter cultures of L. pentosus-yeast species pairs that are able to improve the quality and safety of Spanish-style green table olive processing. Copyright © 2016, American Society for Microbiology. All Rights Reserved.

Temperature Dependence of Quasiparticle Spectral Weight and Coherence in High Tc Superconductors

NASA Astrophysics Data System (ADS)

He, Yang; Zhang, Jessie; Hoffman, Jennifer; Hoffman Lab Team

2014-03-01

Superconductivity arises from the Cooper pairing of quasiparticles on the Fermi surface. Understanding the formation of Cooper pairs is an essential step towards unveiling the mechanism of high Tc superconductivity. We compare scanning tunneling microscope investigations of the temperature dependence of quasiparticle spectral weight and quasiparticle interference in several families of high Tc materials. We calculate the coherent spectral weight related to superconductivity, despite the coexistence of competing orders. The relation between pairing temperature and coherent spectral weight is discussed. We acknowledge support by the New York Community Trust-George Merck Fund.

Pair Interaction of Dislocations in Two-Dimensional Crystals

NASA Astrophysics Data System (ADS)

Eisenmann, C.; Gasser, U.; Keim, P.; Maret, G.; von Grünberg, H. H.

2005-10-01

The pair interaction between crystal dislocations is systematically explored by analyzing particle trajectories of two-dimensional colloidal crystals measured by video microscopy. The resulting pair energies are compared to Monte Carlo data and to predictions derived from the standard Hamiltonian of the elastic theory of dislocations. Good agreement is found with respect to the distance and temperature dependence of the interaction potential, but not regarding the angle dependence where discrete lattice effects become important. Our results on the whole confirm that the dislocation Hamiltonian allows a quantitative understanding of the formation and interaction energies of dislocations in two-dimensional crystals.

Solvation and Ion Pair Association in Aqueous Metal Sulfates: Interpretation of NDIS raw data by isobaric-isothermal molecular dynamics simulation.

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

Chialvo, Ariel A; Simonson, J Michael

2010-01-01

We analyzed the solvation behavior of aqueous lithium, nickel, and ytterbium sulfates at ambient conditions in terms of the relevant radial distributions functions and the corresponding first-order difference of the sulfur-site neutronweighted distribution functions generated by isothermal-isobaric molecular dynamics simulation. We determined of the partial contributions to the neutronweighted distribution functions, to identify the main peaks, and the effect of the contact ion-pair configuration on the resulting H ! S coordination number. Finally, we assessed the extent of the ion-pair formation according to Poirier- DeLap formalism and highlighted the significant increase of the ion-pair association exhibited by these salts withmore » cation charge.« less

Systematics of ground state multiplets of atomic nuclei in the delta-interaction approach

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

Imasheva, L. T.; Ishkhanov, B. S.; Stepanov, M. E., E-mail: stepanov@depni.sinp.msu.ru

2015-12-15

Pairing forces between nucleons in an atomic nucleus strongly influence its structure. One of the manifestations of pair interaction is the ground state multiplet (GSM) formation in the spectrum of low-lying excited states of even–even nuclei. The value of GSM splitting is determined by the value of pair interaction of nucleons; for each isotope, it can be estimated on the basis of experimental nuclear masses. The quality of this estimate is characterized by the degree of reproduction of GSM levels in the nucleus. The GSM systematics in even–even nuclei with a pair of identical nucleons in addition to the filledmore » nuclear core is considered on the basis of delta interaction.« less

Pnicogen bonds between X═PH3 (X = O, S, NH, CH2) and phosphorus and nitrogen bases.

PubMed

Alkorta, Ibon; Sánchez-Sanz, Goar; Elguero, José; Del Bene, Janet E

2014-02-27

Ab initio MP2/aug'-cc-pVTZ calculations have been carried out to investigate the pnicogen bonded complexes formed between the acids O═PH3, S═PH3, HN═PH3, and H2C═PH3 and the bases NH3, NCH, N2, PH3, and PCH. All nitrogen and phosphorus bases form complexes in which the bases are lone pair electron donors. The binding energies of complexes involving the stronger bases NH3, NCH, and PH3 differentiate among the acids, but the binding energies of complexes with the weaker bases do not. These complexes are stabilized by charge transfer from the lone pair orbital of N or P to the σ*P═A orbital of X═PH3, where A is the atom of X directly bonded to P. PCH also forms complexes with the X═PH3 acids as a π electron donor to the σ*P═A orbital. The binding energies and the charge-transfer energies of the π complexes are greater than those of the complexes in which PCH is a lone pair donor. Whether the positive charge on P increases, decreases, or remains the same upon complex formation, the chemical shieldings of (31)P decrease in the complexes relative to the corresponding monomers. (1p)J(P-N) and (1p)J(P-P) values correlate best with the corresponding P-N and P-P distances as a function of the nature of the base. (1)J(P-A) values do not correlate with P-A distances. Rather, the absolute values of (1)J(P-O), (1)J(P-S), and (1)J(P-N) decrease upon complexation. Decreasing (1)J(P-A) values correlate linearly with increasing complex binding energies. In contrast, (1)J(P-C) values increase upon complexation and correlate linearly with increasing binding energies.

Complexity in Acid–Base Titrations: Multimer Formation Between Phosphoric Acids and Imines

PubMed Central

Malm, Christian; Kim, Heejae; Wagner, Manfred

2017-01-01

Abstract Solutions of Brønsted acids with bases in aprotic solvents are not only common model systems to study the fundamentals of proton transfer pathways but are also highly relevant to Brønsted acid catalysis. Despite their importance the light nature of the proton makes characterization of acid–base aggregates challenging. Here, we track such acid–base interactions over a broad range of relative compositions between diphenyl phosphoric acid and the base quinaldine in dichloromethane, by using a combination of dielectric relaxation and NMR spectroscopy. In contrast to what one would expect for an acid–base titration, we find strong deviations from quantitative proton transfer from the acid to the base. Even for an excess of the base, multimers consisting of one base and at least two acid molecules are formed, in addition to the occurrence of proton transfer from the acid to the base and simultaneous formation of ion pairs. For equimolar mixtures such multimers constitute about one third of all intermolecular aggregates. Quantitative analysis of our results shows that the acid‐base association constant is only around six times larger than that for the acid binding to an acid‐base dimer, that is, to an already protonated base. Our findings have implications for the interpretation of previous studies of reactive intermediates in organocatalysis and provide a rationale for previously observed nonlinear effects in phosphoric acid catalysis. PMID:28597513

Rotational-translational fourier imaging system

NASA Technical Reports Server (NTRS)

Campbell, Jonathan W. (Inventor)

2004-01-01

This invention has the ability to create Fourier-based images with only two grid pairs. The two grid pairs are manipulated in a manner that allows (1) a first grid pair to provide multiple real components of the Fourier-based image and (2) a second grid pair to provide multiple imaginary components of the Fourier-based image. The novelty of this invention resides in the use of only two grid pairs to provide the same imaging information that has been traditionally collected with multiple grid pairs.

Thermodynamic stability of Hoogsteen and Watson-Crick base pairs in the presence of histone H3-mimicking peptide.

PubMed

Pramanik, Smritimoy; Nakamura, Kaori; Usui, Kenji; Nakano, Shu-ichi; Saxena, Sarika; Matsui, Jun; Miyoshi, Daisuke; Sugimoto, Naoki

2011-03-14

We found that Hoogsteen base pairs were stabilized by molecular crowding and a histone H3-mimicking peptide, which was not observed for Watson-Crick base pairs. Our findings demonstrate that the type of DNA base pair is critical for the interaction between DNA and histones.

Cisplatin enhances the formation of DNA single- and double-strand breaks by hydrated electrons and hydroxyl radicals.

PubMed

Rezaee, Mohammad; Sanche, Léon; Hunting, Darel J

2013-03-01

The synergistic interaction of cisplatin with ionizing radiation is the clinical rationale for the treatment of several cancers including head and neck, cervical and lung cancer. The underlying molecular mechanism of the synergy has not yet been identified, although both DNA damage and repair processes are likely involved. Here, we investigate the indirect effect of γ rays on strand break formation in a supercoiled plasmid DNA (pGEM-3Zf-) covalently modified by cisplatin. The yields of single- and double-strand breaks were determined by irradiation of DNA and cisplatin/DNA samples with (60)Co γ rays under four different scavenging conditions to examine the involvement of hydrated electrons and hydroxyl radicals in inducing the DNA damage. At 5 mM tris in an N2 atmosphere, the presence of an average of two cisplatins per plasmid increased the yields of single- and double-strand breaks by factors of 1.9 and 2.2, respectively, relative to the irradiated unmodified DNA samples. Given that each plasmid of 3,200 base pairs contained an average of two cisplatins, this represents an increase in radiosensitivity of 3,200-fold on a per base pair basis. When hydrated electrons were scavenged by saturating the samples with N2O, these enhancement factors decreased to 1.5 and 1.2, respectively, for single- and double-strand breaks. When hydroxyl radicals were scavenged using 200 mM tris, the respective enhancement factors were 1.2 and 1.6 for single- and double-strand breaks, respectively. Furthermore, no enhancement in DNA damage by cisplatin was observed after scavenging both hydroxyl radicals and hydrated electrons. These findings show that hydrated electrons can induce both single- and double-strand breaks in the platinated DNA, but not in unmodified DNA. In addition, cisplatin modification is clearly an extremely efficient means of increasing the formation of both single- and double-strand breaks by the hydrated electrons and hydroxyl radicals created by ionizing radiation.

Revisiting The First Galaxies: The effects of Population III stars on their host galaxies

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

Muratov, Alexander L.; Gnedin, Oleg Y.; Gnedin, Nickolay Y.

2013-07-12

We revisit the formation and evolution of the first galaxies using new hydrodynamic cosmological simulations with the adaptive refinement tree code. Our simulations feature a recently developed model for H 2 formation and dissociation, and a star formation recipe that is based on molecular rather than atomic gas. Here, we develop and implement a recipe for the formation of metal-free Population III (Pop III) stars in galaxy-scale simulations that resolve primordial clouds with sufficiently high density. We base our recipe on the results of prior zoom-in simulations that resolved the protostellar collapse in pre-galactic objects. We find the epoch duringmore » which Pop III stars dominated the energy and metal budget of the first galaxies to be short-lived. Galaxies that host Pop III stars do not retain dynamical signatures of their thermal and radiative feedback for more than 10 8 years after the lives of the stars end in pair-instability supernovae, even when we consider the maximum reasonable efficiency of the feedback. Though metals ejected by the supernovae can travel well beyond the virial radius of the host galaxy, they typically begin to fall back quickly, and do not enrich a large fraction of the intergalactic medium. Galaxies with a total mass in excess of 3 × 10 6 M ⊙ re-accrete most of their baryons and transition to metal-enriched Pop II star formation.« less

REVISITING THE FIRST GALAXIES: THE EFFECTS OF POPULATION III STARS ON THEIR HOST GALAXIES

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

Muratov, Alexander L.; Gnedin, Oleg Y.; Zemp, Marcel

2013-08-01

We revisit the formation and evolution of the first galaxies using new hydrodynamic cosmological simulations with the adaptive refinement tree code. Our simulations feature a recently developed model for H{sub 2} formation and dissociation, and a star formation recipe that is based on molecular rather than atomic gas. Here, we develop and implement a recipe for the formation of metal-free Population III (Pop III) stars in galaxy-scale simulations that resolve primordial clouds with sufficiently high density. We base our recipe on the results of prior zoom-in simulations that resolved the protostellar collapse in pre-galactic objects. We find the epoch duringmore » which Pop III stars dominated the energy and metal budget of the first galaxies to be short-lived. Galaxies that host Pop III stars do not retain dynamical signatures of their thermal and radiative feedback for more than 10{sup 8} years after the lives of the stars end in pair-instability supernovae, even when we consider the maximum reasonable efficiency of the feedback. Though metals ejected by the supernovae can travel well beyond the virial radius of the host galaxy, they typically begin to fall back quickly, and do not enrich a large fraction of the intergalactic medium. Galaxies with a total mass in excess of 3 Multiplication-Sign 10{sup 6} M{sub Sun} re-accrete most of their baryons and transition to metal-enriched Pop II star formation.« less

Efficient Implementation of the Pairing on Mobilephones Using BREW

NASA Astrophysics Data System (ADS)

Yoshitomi, Motoi; Takagi, Tsuyoshi; Kiyomoto, Shinsaku; Tanaka, Toshiaki

Pairing based cryptosystems can accomplish novel security applications such as ID-based cryptosystems, which have not been constructed efficiently without the pairing. The processing speed of the pairing based cryptosystems is relatively slow compared with the other conventional public key cryptosystems. However, several efficient algorithms for computing the pairing have been proposed, namely Duursma-Lee algorithm and its variant ηT pairing. In this paper, we present an efficient implementation of the pairing over some mobilephones. Moreover, we compare the processing speed of the pairing with that of the other standard public key cryptosystems, i. e. RSA cryptosystem and elliptic curve cryptosystem. Indeed the processing speed of our implementation in ARM9 processors on BREW achieves under 100 milliseconds using the supersingular curve over F397. In addition, the pairing is more efficient than the other public key cryptosystems, and the pairing can be achieved enough also on BREW mobilephones. It has become efficient enough to implement security applications, such as short signature, ID-based cryptosystems or broadcast encryption, using the pairing on BREW mobilephones.

Formation and Repair of Mismatches Containing Ribonucleotides and Oxidized Bases at Repeated DNA Sequences*

PubMed Central

Cilli, Piera; Minoprio, Anna; Bossa, Cecilia; Bignami, Margherita; Mazzei, Filomena

2015-01-01

The cellular pool of ribonucleotide triphosphates (rNTPs) is higher than that of deoxyribonucleotide triphosphates. To ensure genome stability, DNA polymerases must discriminate against rNTPs and incorporated ribonucleotides must be removed by ribonucleotide excision repair (RER). We investigated DNA polymerase β (POL β) capacity to incorporate ribonucleotides into trinucleotide repeated DNA sequences and the efficiency of base excision repair (BER) and RER enzymes (OGG1, MUTYH, and RNase H2) when presented with an incorrect sugar and an oxidized base. POL β incorporated rAMP and rCMP opposite 7,8-dihydro-8-oxoguanine (8-oxodG) and extended both mispairs. In addition, POL β was able to insert and elongate an oxidized rGMP when paired with dA. We show that RNase H2 always preserves the capacity to remove a single ribonucleotide when paired to an oxidized base or to incise an oxidized ribonucleotide in a DNA duplex. In contrast, BER activity is affected by the presence of a ribonucleotide opposite an 8-oxodG. In particular, MUTYH activity on 8-oxodG:rA mispairs is fully inhibited, although its binding capacity is retained. This results in the reduction of RNase H2 incision capability of this substrate. Thus complex mispairs formed by an oxidized base and a ribonucleotide can compromise BER and RER in repeated sequences. PMID:26338705

Very strong Rydberg atom scattering in K(12p)-CH3NO2 collisions: Role of transient ion pair formation

NASA Astrophysics Data System (ADS)

Kelley, M.; Buathong, S.; Dunning, F. B.

2017-05-01

Collisions between K(12p) Rydberg atoms and CH3NO2 target molecules are studied. Whereas CH3NO2 can form long-lived valence-bound CH3NO2-ions, the data provide no evidence for production of long-lived K+⋯ CH3NO2 - ion pair states. Rather, the data show that collisions result in unusually strong Rydberg atom scattering. This behavior is attributed to ion-ion scattering resulting from formation of transient ion pair states through transitions between the covalent K(12p) + CH3NO2 and ionic K+ + (dipole bound) CH3NO2-terms in the quasimolecule formed during collisions. The ion-pair states are destroyed through rapid dissociation of the CH3NO2 - ions induced by the field of the K+ core ion, the detached electron remaining bound to the K+ ion in a Rydberg state. Analysis of the experimental data shows that ion pair lifetimes ≳10 ps are sufficient to account for the present observations. The present results are consistent with recent theoretical predictions that Rydberg collisions with CH3NO2 will result in strong collisional quenching. The work highlights a new mechanism for Rydberg atom scattering that could be important for collisions with other polar targets. For purposes of comparison, results obtained following K(12p)-SF6 collisions are also included.

Interesting features of nonlinear shock equations in dissipative pair-ion-electron plasmas

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

Masood, W.; National Centre for Physics; Rizvi, H.

2011-09-15

Two dimensional nonlinear electrostatic waves are studied in unmagnetized, dissipative pair-ion-electron plasmas in the presence of weak transverse perturbation. The dissipation in the system is taken into account by incorporating the kinematic viscosity of both positive and negative ions. In the linear case, a biquadratic dispersion relation is obtained, which yields the fast and slow modes in a pair-ion-electron plasma. It is shown that the limiting cases of electron-ion and pair-ion can be retrieved from the general biquadratic dispersion relation, and the differences in the characters of the waves propagating in both the cases are also highlighted. Using the smallmore » amplitude approximation method, the nonlinear Kadomtsev Petviashvili Burgers as well as Burgers-Kadomtsev Petviashvili equations are derived and their applicability for pair-ion-electron plasma is explained in detail. The present study may have relevance to understand the formation of two dimensional electrostatic shocks in laboratory produced pair-ion-electron plasmas.« less

A newly developed highly selective Zn2+-AcO- ion-pair sensor through partner preference: equal efficiency under solitary and colonial situation.

PubMed

Karar, Monaj; Paul, Suvendu; Biswas, Bhaskar; Majumdar, Tapas; Mallick, Arabinda

2018-05-10

Unusual self-sorting of an ion-pair under highly crowded conditions driven by a synthesized intelligent molecule 2-((E)-(3-((E)-2-hydroxy-3-methoxybenzylideneamino)-2-hydroxypropyl imino)methyl)-6-methoxyphenol, hereafter HBP, is described. When a mixture of various metal salts was allowed to react with HBP, only a specific ion-pair ZnII/AcO- in the solution simultaneously reacted, resulting in high-fidelity ion-pair recognition of HBP. This phenomenon was evidenced by significant changes in the absorption spectra and huge enhancement in emission intensity of HBP. The property that one molecule preferring one particular cation-anion pair over others is a rare but interesting phenomenon. Thus, the potential to interact selectively with the targeted ion-pair resulting in the formation of a specific complex recognized HBP as a new class of molecule that might find future applications in real time and on-site monitoring and separation of new molecules.

Multiscale synchrony behaviors of paired financial time series by 3D multi-continuum percolation

NASA Astrophysics Data System (ADS)

Wang, M.; Wang, J.; Wang, B. T.

2018-02-01

Multiscale synchrony behaviors and nonlinear dynamics of paired financial time series are investigated, in an attempt to study the cross correlation relationships between two stock markets. A random stock price model is developed by a new system called three-dimensional (3D) multi-continuum percolation system, which is utilized to imitate the formation mechanism of price dynamics and explain the nonlinear behaviors found in financial time series. We assume that the price fluctuations are caused by the spread of investment information. The cluster of 3D multi-continuum percolation represents the cluster of investors who share the same investment attitude. In this paper, we focus on the paired return series, the paired volatility series, and the paired intrinsic mode functions which are decomposed by empirical mode decomposition. A new cross recurrence quantification analysis is put forward, combining with multiscale cross-sample entropy, to investigate the multiscale synchrony of these paired series from the proposed model. The corresponding research is also carried out for two China stock markets as comparison.

Highly efficient exciplex formation via radical ion pair recombination in X-irradiated alkane solutions for luminophores with short fluorescence lifetimes.

PubMed

Melnikov, Anatoly R; Kalneus, Evgeny V; Korolev, Valeri V; Dranov, Igor G; Kruppa, Alexander I; Stass, Dmitri V

2014-08-01

X-irradiation of alkane solutions of N,N-dimethylaniline with various organic luminophores produces characteristic emission bands ascribed to the corresponding exciplexes. In contrast to optical generation, which requires diffusion-controlled quenching of excited states, an additional channel of exciplex formation via irreversible recombination of radical ion pairs is operative here, which produces exciplexes in solution with high efficiency even for p-terphenyl and diphenylacetylene having fluorescence decay times of 0.95 ns and 8 ps, respectively. The exciplex emission band is sensitive to an external magnetic field and exerts a very large observed magnetic field effect of up to 20%, the maximum possible value under the conditions of the described experiment.

Matrix-isolation and comparative far-IR investigation of free linear [Cl3]- and a series of alkali trichlorides.

PubMed

Redeker, F A; Beckers, H; Riedel, S

2017-11-30

Here we discuss the reaction products of laser ablated alkali chlorides and elemental chlorine. Salt ablation using this technique combined with matrix-isolation spectroscopy allows for the formation and characterization of novel anionic species. The laser ablation of solid MCl with M = Cs, Rb, and K in the presence of Cl 2 produced free [Cl 3 ] - ions which were isolated in solid noble-gas matrices. For M = Cs, Rb, K, and Na, the ion pairs M + [Cl 3 ] - are the main reaction products. Trends in the formation and bonding of these trichloride anions will be discussed. In contrast to the trifluoride analogues, the isolated ion pairs M + [Cl 3 ] - feature a systematic distortion due to metal coordination.

"I Didn't Know of a Better Way to Prepare to Teach": A Case Study of Paired Student Teaching Abroad

ERIC Educational Resources Information Center

Cross, Stephanie Behm; Dunn, Alyssa Hadley

2016-01-01

It has been a year since Sarah and Brian traveled to Malmo, Sweden, as part of a fellowship through their U.S. teacher preparation program. Their experience was unique and life changing, not only because it occurred in another country but because they completed their student teaching in a paired format. They planned and implemented all of their…

Molecular Correlates of Separate Components of Training That Contribute to Long-Term Memory Formation after Learning That Food Is Inedible in "Aplysia"

ERIC Educational Resources Information Center

Briskin-Luchinsky, Valeria; Levy, Roi; Halfon, Maayan; Susswein, Abraham J.

2018-01-01

Training "Aplysia" with inedible food for a period that is too brief to produce long-term memory becomes effective in producing memory when training is paired with a nitric oxide (NO) donor. Lip stimulation for the same period of time paired with an NO donor is ineffective. Using qPCR, we examined molecular correlates of brief training…

Femtosecond-picosecond laser photolysis studies on the dynamics of excited charge-transfer complexes: Aromatic hydrocarbon-acid anhydride, -tetracyanoethylene, and -tetracyanoquinodimethane systems in acetonitrile solutions

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

Asahi, Tsuyoshi; Mataga, Noboru

1991-03-07

Formation processes of contact ion pairs (CIP) from the excited Franck-Condon (FC) state of charge-transfer (CT) complexes of aromatic hydrocarbons with acid anhydride as well as cyano compound acceptors in acetonitrile solution and charge recombination (CR) rates (k{sub CR}{sup CIP}) of produced CIP states have been investigated by femtosecond and picosecond laser phototlysis and time-resolved absorption spectral measurements covering a wide range of free energy gap-{Delta}G{degree}{sub ip} between the ion pair and the ground state. It has been confirmed that the CIP formation becomes faster and k{sub CR}{sup CIP} of the produced CIP increases with increase of the strengths ofmore » the electron donor (D) and acceptor (A) in the complex, i.e., with decrease of the {minus}{Delta}G{degree}{sub ip} value. This peculiar energy gap dependence of k{sub CR}{sup CIP}, quite different from the bell-shaped one observed in the case of the solvent-separated ion pairs (SSIP) or loose ion pairs (LIP) formed by encounter between fluorescer and quencher in the fluoresence quenching reaction, has been interpreted by assuming the change of electronic and geometrical structures of CIP depending on the strengths of D and A.« less

Improving associative memory in older adults with unitization.

PubMed

Ahmad, Fahad N; Fernandes, Myra; Hockley, William E

2015-01-01

We examined if unitization inherent preexperimentally could reduce the associative deficit in older adults. In Experiment 1, younger and older adults studied compound word (CW; e.g., store keeper) and noncompound word (NCW; e.g., needle birth) pairs. We found a reduction in the age-related associative deficit such that older but not younger adults showed a discrimination advantage for CW relative to NCW pairs on a yes-no associative recognition test. These results suggest that CW compared to NCW word pairs provide schematic support that older adults can use to improve their memory. In Experiment 2, reducing study time in younger adults decreased associative recognition performance, but did not produce a discrimination advantage for CW pairs. In Experiment 3, both older and younger adults showed a discrimination advantage for CW pairs on a two-alternative forced-choice recognition test, which encourages greater use of familiarity. These results suggest that test format influenced young adults' use of familiarity during associative recognition of unitized pairs, and that older adults rely more on familiarity than recollection for associative recognition. Unitization of preexperimental associations, as in CW pairs, can alleviate age-related associative deficits.

Time lapse microscopy of temperature control during self-assembly of 3D DNA crystals

NASA Astrophysics Data System (ADS)

Conn, Fiona W.; Jong, Michael Alexander; Tan, Andre; Tseng, Robert; Park, Eunice; Ohayon, Yoel P.; Sha, Ruojie; Mao, Chengde; Seeman, Nadrian C.

2017-10-01

DNA nanostructures are created by exploiting the high fidelity base-pairing interactions of double-stranded branched DNA molecules. These structures present a convenient medium for the self-assembly of macroscopic 3D crystals. In some self-assemblies in this system, crystals can be formed by lowering the temperature, and they can be dissolved by raising it. The ability to monitor the formation and melting of these crystals yields information that can be used to monitor crystal formation and growth. Here, we describe the development of an inexpensive tool that enables direct observation of the crystal growth process as a function of both time and temperature. Using the hanging-drop crystallization of the well-characterized 2-turn DNA tensegrity triangle motif for our model system, its response to temperature has been characterized visually.

An ensemble of SVM classifiers based on gene pairs.

PubMed

Tong, Muchenxuan; Liu, Kun-Hong; Xu, Chungui; Ju, Wenbin

2013-07-01

In this paper, a genetic algorithm (GA) based ensemble support vector machine (SVM) classifier built on gene pairs (GA-ESP) is proposed. The SVMs (base classifiers of the ensemble system) are trained on different informative gene pairs. These gene pairs are selected by the top scoring pair (TSP) criterion. Each of these pairs projects the original microarray expression onto a 2-D space. Extensive permutation of gene pairs may reveal more useful information and potentially lead to an ensemble classifier with satisfactory accuracy and interpretability. GA is further applied to select an optimized combination of base classifiers. The effectiveness of the GA-ESP classifier is evaluated on both binary-class and multi-class datasets. Copyright © 2013 Elsevier Ltd. All rights reserved.

Observation of self-excited acoustic vortices in defect-mediated dust acoustic wave turbulence.

PubMed

Tsai, Ya-Yi; I, Lin

2014-07-01

Using the self-excited dust acoustic wave as a platform, we demonstrate experimental observation of self-excited fluctuating acoustic vortex pairs with ± 1 topological charges through spontaneous waveform undulation in defect-mediated turbulence for three-dimensional traveling nonlinear longitudinal waves. The acoustic vortex pair has helical waveforms with opposite chirality around the low-density hole filament pair in xyt space (the xy plane is the plane normal to the wave propagation direction). It is generated through ruptures of sequential crest surfaces and reconnections with their trailing ruptured crest surfaces. The initial rupture is originated from the amplitude reduction induced by the formation of the kinked wave crest strip with strong stretching through the undulation instability. Increasing rupture causes the separation of the acoustic vortex pair after generation. A similar reverse process is followed for the acoustic vortex annihilating with the opposite-charged acoustic vortex from the same or another pair generation.

Strong Neutron Pairing in core+4 n Nuclei

NASA Astrophysics Data System (ADS)

Revel, A.; Marqués, F. M.; Sorlin, O.; Aumann, T.; Caesar, C.; Holl, M.; Panin, V.; Vandebrouck, M.; Wamers, F.; Alvarez-Pol, H.; Atar, L.; Avdeichikov, V.; Beceiro-Novo, S.; Bemmerer, D.; Benlliure, J.; Bertulani, C. A.; Boillos, J. M.; Boretzky, K.; Borge, M. J. G.; Caamaño, M.; Casarejos, E.; Catford, W. N.; Cederkäll, J.; Chartier, M.; Chulkov, L.; Cortina-Gil, D.; Cravo, E.; Crespo, R.; Datta Pramanik, U.; Díaz Fernández, P.; Dillmann, I.; Elekes, Z.; Enders, J.; Ershova, O.; Estradé, A.; Farinon, F.; Fraile, L. M.; Freer, M.; Galaviz, D.; Geissel, H.; Gernhäuser, R.; Golubev, P.; Göbel, K.; Hagdahl, J.; Heftrich, T.; Heil, M.; Heine, M.; Heinz, A.; Henriques, A.; Ignatov, A.; Johansson, H. T.; Jonson, B.; Kahlbow, J.; Kalantar-Nayestanaki, N.; Kanungo, R.; Kelic-Heil, A.; Knyazev, A.; Kröll, T.; Kurz, N.; Labiche, M.; Langer, C.; Le Bleis, T.; Lemmon, R.; Lindberg, S.; Machado, J.; Marganiec, J.; Movsesyan, A.; Nacher, E.; Najafi, M.; Nilsson, T.; Nociforo, C.; Paschalis, S.; Perea, A.; Petri, M.; Pietri, S.; Plag, R.; Reifarth, R.; Ribeiro, G.; Rigollet, C.; Röder, M.; Rossi, D.; Savran, D.; Scheit, H.; Simon, H.; Syndikus, I.; Taylor, J. T.; Tengblad, O.; Thies, R.; Togano, Y.; Velho, P.; Volkov, V.; Wagner, A.; Weick, H.; Wheldon, C.; Wilson, G.; Winfield, J. S.; Woods, P.; Yakorev, D.; Zhukov, M.; Zilges, A.; Zuber, K.; R³B Collaboration

2018-04-01

The emission of neutron pairs from the neutron-rich N =12 isotones 18C and 20O has been studied by high-energy nucleon knockout from 19N and 21O secondary beams, populating unbound states of the two isotones up to 15 MeV above their two-neutron emission thresholds. The analysis of triple fragment-n -n correlations shows that the decay 19N (-1 p ) 18C* → 16C +n +n is clearly dominated by direct pair emission. The two-neutron correlation strength, the largest ever observed, suggests the predominance of a 14C core surrounded by four valence neutrons arranged in strongly correlated pairs. On the other hand, a significant competition of a sequential branch is found in the decay 21O (-1 n )20O*→18O +n +n , attributed to its formation through the knockout of a deeply bound neutron that breaks the 16O core and reduces the number of pairs.

Chlorine-Incorporation-Induced Formation of the Layered Phase for Antimony-Based Lead-Free Perovskite Solar Cells.

PubMed

Jiang, Fangyuan; Yang, Dongwen; Jiang, Youyu; Liu, Tiefeng; Zhao, Xingang; Ming, Yue; Luo, Bangwu; Qin, Fei; Fan, Jiacheng; Han, Hongwei; Zhang, Lijun; Zhou, Yinhua

2018-01-24

The environmental toxicity of Pb in organic-inorganic hybrid perovskite solar cells remains an issue, which has triggered intense research on seeking alternative Pb-free perovskites for solar applications. Halide perovskites based on group-VA cations of Bi 3+ and Sb 3+ with the same lone-pair ns 2 state as Pb 2+ are promising candidates. Herein, through a joint experimental and theoretical study, we demonstrate that Cl-incorporated methylammonium Sb halide perovskites (CH 3 NH 3 ) 3 Sb 2 Cl X I 9-X show promise as efficient solar absorbers for Pb-free perovskite solar cells. Inclusion of methylammonium chloride into the precursor solutions suppresses the formation of the undesired zero-dimensional dimer phase and leads to the successful synthesis of high-quality perovskite films composed of the two-dimensional layered phase favored for photovoltaics. Solar cells based on the as-obtained (CH 3 NH 3 ) 3 Sb 2 Cl X I 9-X films reach a record-high power conversion efficiency over 2%. This finding offers a new perspective for the development of nontoxic and low-cost Sb-based perovskite solar cells.

ITS all right mama: investigating the formation of chimeric sequences in the ITS2 region by DNA metabarcoding analyses of fungal mock communities of different complexities.

PubMed

Bjørnsgaard Aas, Anders; Davey, Marie Louise; Kauserud, Håvard

2017-07-01

The formation of chimeric sequences can create significant methodological bias in PCR-based DNA metabarcoding analyses. During mixed-template amplification of barcoding regions, chimera formation is frequent and well documented. However, profiling of fungal communities typically uses the more variable rDNA region ITS. Due to a larger research community, tools for chimera detection have been developed mainly for the 16S/18S markers. However, these tools are widely applied to the ITS region without verification of their performance. We examined the rate of chimera formation during amplification and 454 sequencing of the ITS2 region from fungal mock communities of different complexities. We evaluated the chimera detecting ability of two common chimera-checking algorithms: perseus and uchime. Large proportions of the chimeras reported were false positives. No false negatives were found in the data set. Verified chimeras accounted for only 0.2% of the total ITS2 reads, which is considerably less than what is typically reported in 16S and 18S metabarcoding analyses. Verified chimeric 'parent sequences' had significantly higher per cent identity to one another than to random members of the mock communities. Community complexity increased the rate of chimera formation. GC content was higher around the verified chimeric break points, potentially facilitating chimera formation through base pair mismatching in the neighbouring regions of high similarity in the chimeric region. We conclude that the hypervariable nature of the ITS region seems to buffer the rate of chimera formation in comparison with other, less variable barcoding regions, due to shorter regions of high sequence similarity. © 2016 John Wiley & Sons Ltd.

Envisaging quantum transport phenomenon in a muddled base pair of DNA

NASA Astrophysics Data System (ADS)

Vohra, Rajan; Sawhney, Ravinder Singh

2018-05-01

The effect of muddled base pair on electron transfer through a deoxyribonucleic acid (DNA) molecule connected to the gold electrodes has been elucidated using tight binding model. The effect of hydrogen and nitrogen bonds on the resistance of the base pair has been minutely observed. Using the semiempirical extended Huckel approach within NEGF regime, we have determined the current and conductance vs. bias voltage for disordered base pairs of DNA made of thymine (T) and adenine (A). The asymmetrical behaviour amid five times depreciation in the current characteristics has been observed for deviated Au-AT base pair-Au devices. An interesting revelation is that the conductance of the intrinsic AT base pair configuration attains dramatically high values with the symmetrical zig-zag pattern of current, which clearly indicates the transformation of the bond length within the strands of base pair when compared with other samples. A thorough investigation of the transmission coefficients T( E) and HOMO-LUMO gap reveals the misalignment of the strands in base pairs of DNA. The observed results present an insight to extend this work to build biosensing devices to predict the abnormality with the DNA.

Higher order structural effects stabilizing the reverse Watson–Crick Guanine-Cytosine base pair in functional RNAs

PubMed Central

Chawla, Mohit; Abdel-Azeim, Safwat; Oliva, Romina; Cavallo, Luigi

2014-01-01

The G:C reverse Watson–Crick (W:W trans) base pair, also known as Levitt base pair in the context of tRNAs, is a structurally and functionally important base pair that contributes to tertiary interactions joining distant domains in functional RNA molecules and also participates in metabolite binding in riboswitches. We previously indicated that the isolated G:C W:W trans base pair is a rather unstable geometry, and that dicationic metal binding to the Guanine base or posttranscriptional modification of the Guanine can increase its stability. Herein, we extend our survey and report on other H-bonding interactions that can increase the stability of this base pair. To this aim, we performed a bioinformatics search of the PDB to locate all the occurencies of G:C trans base pairs. Interestingly, 66% of the G:C trans base pairs in the PDB are engaged in additional H-bonding interactions with other bases, the RNA backbone or structured water molecules. High level quantum mechanical calculations on a data set of representative crystal structures were performed to shed light on the structural stability and energetics of the various crystallographic motifs. This analysis was extended to the binding of the preQ1 metabolite to a preQ1-II riboswitch. PMID:24121683

Conformational analysis and design of cross-strand disulfides in antiparallel β-sheets.

PubMed

Indu, S; Kochat, V; Thakurela, S; Ramakrishnan, C; Varadarajan, Raghavan

2011-01-01

Cross-strand disulfides bridge two cysteines in a registered pair of antiparallel β-strands. A nonredundant data set comprising 5025 polypeptides containing 2311 disulfides was used to study cross-strand disulfides. Seventy-six cross-strand disulfides were found of which 75 and 1 occurred at non-hydrogen-bonded (NHB) and hydrogen-bonded (HB) registered pairs, respectively. Conformational analysis and modeling studies demonstrated that disulfide formation at HB pairs necessarily requires an extremely rare and positive χ¹ value for at least one of the cysteine residues. Disulfides at HB positions also have more unfavorable steric repulsion with the main chain. Thirteen pairs of disulfides were introduced in NHB and HB pairs in four model proteins: leucine binding protein (LBP), leucine, isoleucine, valine binding protein (LIVBP), maltose binding protein (MBP), and Top7. All mutants LIVBP T247C V331C showed disulfide formation either on purification, or on treatment with oxidants. Protein stability in both oxidized and reduced states of all mutants was measured. Relative to wild type, LBP and MBP mutants were destabilized with respect to chemical denaturation, although the sole exposed NHB LBP mutant showed an increase of 3.1°C in T(m). All Top7 mutants were characterized for stability through guanidinium thiocyanate chemical denaturation. Both exposed and two of the three buried NHB mutants were appreciably stabilized. All four HB Top7 mutants were destabilized (ΔΔG⁰ = -3.3 to -6.7 kcal/mol). The data demonstrate that introduction of cross-strand disulfides at exposed NHB pairs is a robust method of improving protein stability. All four exposed Top7 disulfide mutants showed mild redox activity. © 2010 Wiley-Liss, Inc.

Bifacial Base-Pairing Behaviors of 5-Hydroxyuracil DNA Bases through Hydrogen Bonding and Metal Coordination.

PubMed

Takezawa, Yusuke; Nishiyama, Kotaro; Mashima, Tsukasa; Katahira, Masato; Shionoya, Mitsuhiko

2015-10-12

A novel bifacial ligand-bearing nucleobase, 5-hydroxyuracil (U(OH) ), which forms both a hydrogen-bonded base pair (U(OH) -A) and a metal-mediated base pair (U(OH) -M-U(OH) ) has been developed. The U(OH) -M-U(OH) base pairs were quantitatively formed in the presence of lanthanide ions such as Gd(III) when U(OH) -U(OH) pairs were consecutively incorporated into DNA duplexes. This result established metal-assisted duplex stabilization as well as DNA-templated assembly of lanthanide ions. Notably, a duplex possessing U(OH) -A base pairs was destabilized by addition of Gd(III) ions. This observation suggests that the hybridization behaviors of the U(OH) -containing DNA strands are altered by metal complexation. Thus, the U(OH) nucleobase with a bifacial base-pairing property holds great promise as a component for metal-responsive DNA materials. © 2015 WILEY-VCH Verlag GmbH & Co. KGaA, Weinheim.

Molecular switching behavior in isosteric DNA base pairs.

PubMed

Jissy, A K; Konar, Sukanya; Datta, Ayan

2013-04-15

The structures and proton-coupled behavior of adenine-thymine (A-T) and a modified base pair containing a thymine isostere, adenine-difluorotoluene (A-F), are studied in different solvents by dispersion-corrected density functional theory. The stability of the canonical Watson-Crick base pair and the mismatched pair in various solvents with low and high dielectric constants is analyzed. It is demonstrated that A-F base pairing is favored in solvents with low dielectric constant. The stabilization and conformational changes induced by protonation are also analyzed for the natural as well as the mismatched base pair. DNA sequences capable of changing their sequence conformation on protonation are used in the construction of pH-based molecular switches. An acidic medium has a profound influence in stabilizing the isostere base pair. Such a large gain in stability on protonation leads to an interesting pH-controlled molecular switch, which can be incorporated in a natural DNA tract. Copyright © 2013 WILEY-VCH Verlag GmbH & Co. KGaA, Weinheim.

1,8-Naphthyridine-2,7-diamine: a potential universal reader of Watson-Crick base pairs for DNA sequencing by electron tunneling.

PubMed

Liang, Feng; Lindsay, Stuart; Zhang, Peiming

2012-11-21

With the aid of Density Functional Theory (DFT), we designed 1,8-naphthyridine-2,7-diamine as a recognition molecule to read DNA base pairs for genomic sequencing by electron tunneling. NMR studies show that it can form stable triplets with both A : T and G : C base pairs through hydrogen bonding. Our results suggest that the naphthyridine molecule should be able to function as a universal base pair reader in a tunneling gap, generating distinguishable signatures under electrical bias for each of DNA base pairs.

1,8-Naphthyridine-2,7-diamine: A Potential Universal Reader of the Watson-Crick Base Pairs for DNA Sequencing by Electron Tunneling

PubMed Central

Liang, Feng; Lindsay, Stuart; Zhang, Peiming

2013-01-01

With the aid of Density Functional Theory (DFT), we designed 1,8-naphthyridine-2,7-diamine as a recognition molecule to read the DNA base pairs for genomic sequencing by electron tunneling. NMR studies show that it can form stable triplets with both A:T and G:C base pairs through hydrogen bonding. Our results suggest that the naphthyridine molecule should be able to function as a universal base pair reader in a tunneling gap, generating distinguishable signatures under electrical bias for each of DNA base pairs. PMID:23038027

Cognitive Association Formation in Episodic Memory: Evidence from Event-Related Potentials

ERIC Educational Resources Information Center

Kim, Alice S. N.; Vallesi, Antonino; Picton, Terence W.; Tulving, Endel

2009-01-01

The present study focused on the processes underlying cognitive association formation by investigating subsequent memory effects. Event-related potentials were recorded as participants studied pairs of words, presented one word at a time, for later recall. The findings showed that a frontal-positive late wave (LW), which occurred 1-1.6 s after the…

New insights on multiplicity and clustering in Taurus.

NASA Astrophysics Data System (ADS)

Joncour, Isabelle; Duchene, Gaspard; Moraux, Estelle; Mundy, Lee

2018-01-01

Multiplicity and clustering of young stars are critical clues to constraint star formation process. The Taurus molecular complex is the archetype of a quiescent star forming region that may retain primeval signature of star formation.Using statistical and clustering tools such as nearest neighbor statistics, correlation functions and the density-Based Spatial Clustering of Applications with Noise (DBSCAN) algorithm, this work reveals new spatial substructures in Taurus.We have identified unexpected ultra wide pairs (UWPs) candidates of high order multiplicity in Taurus in the 5-60 kAU separation range (Joncour et al 2017), beyond the separation assessed for wide pairs (Kraus & Hillenbrand 2009).Our work reveals 20 local stellar substructures, the Nested Elementary Structures (NESTs). These NESTs contain nearly half the stars of Taurus and 75% of the Class 0/I objects probing that they are the preferred sites of star formation (Joncour et al, sub.). The NESTs size ranges from few kAU up to 80 kAU making a length scale bridge between wide pairs and loose group (few hundreds kAU, Kirk & Myers, 2011). The NESTs mass ranges from 0.5-10 solar mass. The balance between Class I, II and III in NESTs suggests that they may be ordered as an evolutionary temporal scheme, some of them got infertile, while other shelter stars in infancy.The UWPs and the NESTs may be pristine imprints of their spatial configuration at birth. The UWPs population may result from a cascade fragmentation scenario of the natal molecular core. They could be the older counterparts, to the 0.5 Myr prestellar cores/Class 0 multiple objects observed at radio/millimeter wavelengths (Tobin et al 2010, 2016) and the precursors of the large number of UWPs (10–100 kAU) recently identified in older moving groups (Floriano-Alonso et al, 2015 ; Elliot et al 2016). The NESTs may result from the gravitational collapse of a gas clump that fragments to give a tight collection of stars within few millions years.This project has been partly supported by the StarFormMapper project funded by the European Union's Horizon 2020 Research and Innovation Action (RIA) program under grant agreement number 687528.

High resolution 2D numerical models from rift to break-up: Crustal hyper-extension, Margin asymmetry, Sequential faulting

NASA Astrophysics Data System (ADS)

Brune, Sascha; Heine, Christian; Pérez-Gussinyé, Marta; Sobolev, Stephan

2013-04-01

Numerical modelling is a powerful tool to integrate a multitude of geological and geophysical data while addressing fundamental questions of passive margin formation such as the occurrence of crustal hyper-extension, (a-)symmetries between conjugate margin pairs, and the sometimes significant structural differences between adjacent margin segments. This study utilises knowledge gathered from two key examples of non-magmatic, asymmetric, conjugate margin pairs, i.e. Iberia-New Foundland and Southern Africa-Brazil, where many published seismic lines provide solid knowledge on individual margin geometry. While both margins involve crustal hyper-extension, it is much more pronounced in the South Atlantic. We investigate the evolution of these two margin pairs by carefully constraining our models with detailed plate kinematic history, laboratory-based rheology, and melt fraction evaluation of mantle upwelling. Our experiments are consistent with observed fault patterns, crustal thickness, and basin stratigraphy. We conduct 2D thermomechanical rift models using the finite element code SLIM3D that operates with nonlinear stress- and temperature-dependent elasto-visco-plastic rheology, with parameters provided by laboratory experiments on major crustal and upper mantle rocks. In our models we also calculate the melt fraction within the upwelling asthenosphere, which allows us to control whether the model indeed corresponds to the non-magmatic margin type or not. Our modelling highlights two processes as fundamental for the formation of hyper-extension and margin asymmetry at non-magmatic margins: (1) Strain hardening in the rift center due to cooling of upwelling mantle material (2) The formation of a weak crustal domain adjacent to the rift center caused by localized viscous strain softening and heat transfer from the mantle. Simultaneous activity of both processes promotes lateral rift migration in a continuous way that generates a wide layer of hyper-extended crust on one side of the rift basin. This mechanism implies that syn-rift deformation at the distal margin postdates faulting at the proximal margin by several million years. The succession of events holds intriguing implications not only for peak heat flow migration but also for processes like serpentinization and magmatic underplating.

Quantifying stickiness: thermodynamic characterization of intramolecular domain interactions to guide the design of förster resonance energy transfer sensors.

PubMed

Lindenburg, Laurens H; Malisauskas, Mantas; Sips, Tari; van Oppen, Lisanne; Wijnands, Sjors P W; van de Graaf, Stan F J; Merkx, Maarten

2014-10-14

The introduction of weak, hydrophobic interactions between fluorescent protein domains (FPs) can substantially increase the dynamic range (DR) of Förster resonance energy transfer (FRET)-based sensor systems. Here we report a comprehensive thermodynamic characterization of the stability of a range of self-associating FRET pairs. A new method is introduced that allows direct quantification of the stability of weak FP interactions by monitoring intramolecular complex formation as a function of urea concentration. The commonly used S208F mutation stabilized intramolecular FP complex formation by 2.0 kCal/mol when studied in an enhanced cyan FP (ECFP)-linker-enhanced yellow FP (EYFP) fusion protein, whereas a significantly weaker interaction was observed for the homologous Cerulean/Citrine FRET pair (ΔG0(o-c) = 0.62 kCal/mol). The latter effect could be attributed to two mutations in Cerulean (Y145A and H148D) that destabilize complex formation with Citrine. Systematic analysis of the contribution of residues 125 and 127 at the dimerization interface in mOrange.linker.mCherry fusion proteins yielded a toolbox of new mOrange-mCherry combinations that allowed tuning of their intramolecular interaction from very weak (ΔG0(o-c) = .0.39 kCal/mol) to relatively stable (ΔG0(o-c) = 2.2 kCal/mol). The effects of these mutations were also studied by monitoring homodimerization of mCherry variants using fluorescence anisotropy. These mutations affected intramolecular and intermolecular domain interactions similarly, although FP interactions were found to be stronger in the latter. The knowledge thus obtained allowed successful construction of a red-shifted variant of the bile acid FRET sensor BAS-1 by replacement of the self-associating Cerulean-Citrine pair by mOrange.mCherry variants with a similar intramolecular affinity. Our findings thus allow a better understanding of the subtle but important role of intramolecular domain interactions in current FRET sensors and help guide the construction of new sensors using modular design strategies.

Observing interactions between DNA bases using ion dip spectroscopy.

NASA Astrophysics Data System (ADS)

Vries Mattanjah, De

2002-03-01

We investigate biomolecular building blocks and their clusters with each other and with water on a single molecular level. The motivation is the need to distinguish between intrinsic molecular properties and those that result from the biological environment. This is achieved by a combination of laser desorption and jet cooling, applied to aromatic amino acids, small peptides containing those, purine bases and nucleosides. This approach is coupled with a number of gas phase laser spectroscopic techniques. We will present results for DNA bases guanine, adenine, cytosine, and their derivatives, for which we obtained tautomer selected vibronic spectra. Capitalizing on these results we use these bases as chromophores to study interactions in single base pairs, obtained by formation of clusters of laser desorbed bases in a supersonic beam. For analysis we employ both UV/UV and IR/UV ion-dip spectroscopy, the results of which we compare with ab initio calculations.

The extension of a DNA double helix by an additional Watson-Crick base pair on the same backbone.

PubMed

Kumar, Pawan; Sharma, Pawan K; Madsen, Charlotte S; Petersen, Michael; Nielsen, Poul

2013-06-17

Additional base pair: The DNA duplex can be extended with an additional Watson-Crick base pair on the same backbone by the use of double-headed nucleotides. These also work as compressed dinucleotides and form two base pairs with cognate nucleobases on the opposite strand. Copyright © 2013 WILEY-VCH Verlag GmbH & Co. KGaA, Weinheim.

Pairs of Asteroids Probably of a Common Origin

NASA Astrophysics Data System (ADS)

Vokrouhlický, David; Nesvorný, David

2008-07-01

We report the first observational evidence for pairs of main-belt asteroids with bodies in each pair having nearly identical orbits. The existence of ~60 pairs identified here cannot be reconciled with random fluctuations of the asteroid orbit density and rather suggests a common origin of the paired objects. We propose that the identified pairs formed by (i) collisional disruptions of km-sized and larger parent asteroids, (ii) Yarkovsky-O'Keefe-Radzievski-Paddack (YORP)-induced spin-up and rotational fission of fast-rotating objects, and/or (iii) splitting of unstable asteroid binaries. In case (i), the pairs would be parts of compact collisional families with many km- and sub-km-size members that should be found by future asteroid surveys. Our dynamical analysis suggests that most identified pairs formed within the past lsim1 Myr, in several cases even much more recently. For example, paired asteroids (6070) Rheinland and (54827) 2001 NQ8 probably separated from their common ancestor only 16.5-19 kyr ago. Given their putatively very recent formation, the identified objects are prime candidates for astronomical observations. The title paraphrases that of Hirayama's 1918 paper "Groups of asteroids probably of a common origin," where the first evidence was given for groups of asteroid fragments produced by disruptive collisions.

Key-value store with internal key-value storage interface

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

Bent, John M.; Faibish, Sorin; Ting, Dennis P. J.

A key-value store is provided having one or more key-value storage interfaces. A key-value store on at least one compute node comprises a memory for storing a plurality of key-value pairs; and an abstract storage interface comprising a software interface module that communicates with at least one persistent storage device providing a key-value interface for persistent storage of one or more of the plurality of key-value pairs, wherein the software interface module provides the one or more key-value pairs to the at least one persistent storage device in a key-value format. The abstract storage interface optionally processes one or moremore » batch operations on the plurality of key-value pairs. A distributed embodiment for a partitioned key-value store is also provided.« less

VizieR Online Data Catalog: Dust properties of major-merger galaxy pairs (Domingue+, 2016)

NASA Astrophysics Data System (ADS)

Domingue, D. L.; Cao, C.; Xu, C. K.; Jarrett, T. H.; Ronca, J.; Hill, E.; Jacques, A.

2018-04-01

We present an analysis of dust properties of a sample of close major-merger galaxy pairs selected by Ks magnitude and redshift. The pairs represent the two populations of spiral-spiral (S+S) and mixed morphology spiral-elliptical (S+E). The Code Investigating GALaxy Emission (CIGALE) software is used to fit dust models to the Two Micron All Sky Survey, Wide-Field Infrared Survey Explorer, and Herschel flux density measurements, and to derive the parameters describing the polycyclic aromatic hydrocarbons contribution, interstellar radiation field, and photodissociation regions. Model fits verify our previous Spitzer Space Telescope analysis that S+S and S+E pairs do not have the same level of enhancement of star formation and differ in dust composition. (1 data file).

Pair-Starved Pulsar Magnetospheres

NASA Technical Reports Server (NTRS)

Muslimov, Alex G.; Harding, Alice K.

2009-01-01

We propose a simple analytic model for the innermost (within the light cylinder of canonical radius, approx. c/Omega) structure of open-magnetic-field lines of a rotating neutron star (NS) with relativistic outflow of charged particles (electrons/positrons) and arbitrary angle between the NS spin and magnetic axes. We present the self-consistent solution of Maxwell's equations for the magnetic field and electric current in the pair-starved regime where the density of electron-positron plasma generated above the pulsar polar cap is not sufficient to completely screen the accelerating electric field and thus establish thee E . B = 0 condition above the pair-formation front up to the very high altitudes within the light cylinder. The proposed mode1 may provide a theoretical framework for developing the refined model of the global pair-starved pulsar magnetosphere.

Biomechanical comparison of single-row arthroscopic rotator cuff repair technique versus transosseous repair technique.

PubMed

Tocci, Stephen L; Tashjian, Robert Z; Leventhal, Evan; Spenciner, David B; Green, Andrew; Fleming, Braden C

2008-01-01

This study determined the effect of tear size on gap formation of single-row simple-suture arthroscopic rotator cuff repair (ARCR) vs transosseous Mason-Allen suture open RCR (ORCR) in 13 pairs of human cadaveric shoulders. A massive tear was created in 6 pairs and a large tear in 7. Repairs were cyclically tested in low-load and high-load conditions, with no significant difference in gap formation. Under low-load, gapping was greater in massive tears. Under high-load, there was a trend toward increased gap with ARCR for large tears. All repairs of massive tears failed in high-load. Gapping was greater posteriorly in massive tears for both techniques. Gap formation of a modeled RCR depends upon the tear size. ARCR of larger tears may have higher failure rates than ORCR, and the posterior aspect appears to be the site of maximum gapping. Specific attention should be directed toward maximizing initial fixation of larger rotator cuff tears, especially at the posterior aspect.