bluuebunny/crossref_metadata_2025_split huggingface dataset:
DARTs: A DNA‐based in vitro polypeptide display technology
Authors: Figueiredo Paul , Roberts Radclyffe L. , Nester Eugene W. 
Published: August 2004

AbstractDisplay technologies link proteins with the genes that encode them, providing a means of selecting proteins with desired properties through the process of directed evolution. Here, we describe DNA/protein attachment and recovery tools (DARTs), a novel polypeptide display technology that utilizes the Agrobacterium tumefaciens protein VirD2 to generate DNA‐protein hybrid molecules. The resulting DNA‐protein hybrids are small, robust, and are not expected to be subject to the synthesis and selection biases associated with viral‐ and cell‐based display systems. We demonstrated that these DNA‐protein hybrids could be used to display a variety of peptides that bind to appropriate antibodies for immunodetection and immunopurification. Further, the DNA components of the hybrid molecules can hybridize to complementary DNA molecules in solution or on a solid substrate. Because full‐length VirD2 self‐associated, we constructed a truncation that did not self‐associate but still exhibited DNA linking activity and efficiently displayed peptides. Finally, we purified DNA‐protein hybrids using their displayed peptide epitopes and amplified their DNA components by polymerase chain reaction. We suggest that the DART polypeptide display system will be valuable for performing directed evolution and generating protein arrays.
Synthesis of chiral helical poly[p‐(oligopinanylsiloxanyl)phenylacetylene]s and enantioselective permeability of their membranes
Authors: Aoki Toshiki , Fukuda Tomoyuki , Shinohara Ken‐ichi , Kaneko Takashi , Teraguchi Masahiro , Yagi Masayuki 
Published: August 2004

AbstractTo develop better polymeric materials for optical‐resolution membranes, we synthesized nine chiral phenylacetylenes containing pinanyl groups. We used them to investigate the effects of chemical structures, including the number and position of the chiral groups in the monomers, on the induction of chirality in the main chain during polymerization and on the degree of enantioselectivity in the permeation of the polymeric membranes. The monomers included six new chiral p‐(oligomethylpinanylsiloxanyl)phenylacetylenes. The homopolymerizations of these nine monomers with a Rh complex produced high‐molecular‐weight polymers (molecular weight = 105–106). Of the five polymers with a chiral pinanyl group at the 1‐position of each oligosiloxanyl group, all except for two polymers showed high molar ellipticity in the main‐chain region in the circular dichroism spectra. This finding indicated that these polymers had a chiral helical main chain. The membranes fabricated from all the polymers synthesized in this study were high‐quality, except for two polymers. All these membranes showed enantioselective permeabilities for two amino acids and an alcohol. The membranes from the polymers with a chiral helical backbone, a high content of pinanyl groups, no oligodimethylsiloxane moieties, or a combination of these showed good enantioselectivities (= 1.7–640) in permeation. We propose that the sense of the main‐chain helicity determined the selectivity. © 2004 Wiley Periodicals, Inc. J Polym Sci Part A: Polym Chem 42: 4502–4517, 2004
Complexation of phthalate oxygens in poly(ethylene phthalate) with silver ions and its effect on the formation of silver nanoparticles
Authors: Kang Sang Wook , Kim Jong Hak , Ko Dongkyun , Kim Chang Kon , Won Jongok , Char Kookheon , Kang Yong Soo 
Published: August 2004

AbstractThe interaction of a phthalate group in poly(ethylene phthalate) (PEP) with silver ion has been elaborated in detail to understand the reduction behavior of silver ions to silver nanoparticles. Previously, the polymer electrolytes consisting of silver ions dissolved in PEP have shown highly stable separation performance for propylene/propane mixtures primarily due to the retardation of the reduction reaction of silver ions to silver nanoparticles, which is possible by means of the chelating bonds between phthalate groups and silver ions. Thus, in this study, the interaction was systematically investigated by both the theoretical ab initio calculation and the experimental Fourier transform infrared spectroscopy and X‐ray photoelectron spectroscopy. The results show that the interaction of silver ion with phthalate group in PEP is approximately two times stronger than that with other functional groups such as amide, ketone, and ester in various polymers, in which the latter ones show the rapid reduction reaction and consequently lose their olefin carrier activity with time. Therefore, it is concluded that the reduction reaction of silver ions to silver nanoparticles is retarded remarkably in PEP/silver salts systems primarily because of the strong interaction between the phthalate group in PEP and silver ion, and consequently the formation of silver nanoparticles would be effectively prohibited, as confirmed by transmission electron microscopy and ultraviolet–visible spectroscopy. © 2004 Wiley Periodicals, Inc. J Polym Sci Part B: Polym Phys 42: 3344–3350, 2004
Elastic excitations in polycarbonate membranes
Authors: Tommaseo G. , Lescanne M. , Steffen W. , Fytas G. , Stamm M. 
Published: August 2004

AbstractBrillouin light scattering was used to probe acoustic waves propagating with both longitudinal and transverse polarizations in the surface and the bulk of self‐supported particle track‐etched polycarbonate membranes with 15‐ and 80‐nm nanopores. The recorded scattering line shape at gigahertz frequencies reveals changes in the surface waves of the membranes which are more pronounced for the 80‐nm nanopores despite the low porosity (0.7 and 0.05%). Because the measured elastic constants (1.2 and 6.2 GPa) were found to compare very well with the values for thick polycarbonate film, modifications of the elasto‐optical coefficients and/or the transparency might be the reason for the different scattering line shapes. © 2004 Wiley Periodicals, Inc. J Polym Sci Part B: Polym Phys 42: 3311–3317, 2004
Fracture behavior of triglyceride‐based adhesives
Authors: Lorenz Christian D. , Stevens Mark J. , Wool Richard P. 
Published: August 2004

AbstractThe use of natural plant oils in the production of adhesives has been the focus of much research because natural oils are a renewable resource which have environmental and economic advantages over the petroleum‐derived chemicals used in traditional adhesives. The network formation and the stress–strain behavior of these plant oil–based adhesives is studied using a combination of simulation techniques. An off‐lattice Monte Carlo simulation has been developed to model the formation of these networks via the free‐radical copolymerization of the triglycerides present in natural oils. Networks of systems representing the triglycerides found in soybean oil, linseed oil, and olive oil are generated, as are networks made from other “theoretical” natural oils. The structure of the networks is characterized by percolation analysis. The stress–strain behavior of these networks is studied using large‐scale molecular dynamics simulations. Tensile strains are applied to the networks and it is observed that with increasingnthe failure stress increases but the failure strain decreases. Also, for systems with low values ofn, large voids form while the system is strained and then the system fails cohesively. However, for largen, no significant voiding is observed and the system fails close to the interface. The simulation results are shown to be consistent with the vector percolation theoretical prediction for how the failure stress relates ton. © 2004 Wiley Periodicals, Inc. J Polym Sci Part B: Polym Phys 42: 3333–3343, 2004
Type IIA on a compact Calabi‐Yau and D = 11 supergravity uplift of its orientifold
Authors: Misra A. 
Published: August 2004

AbstractUsing the prescription of [1] for defining period integrals in the Landau‐Ginsburg theory for compact Calabi‐Yau's, we obtain the Picard‐Fuchs equation and the Meijer basis of solutions for the compact Calabi‐Yau CY3(3,243) expressed as a degree‐24 Fermat hypersurface after resolution of the orbifold singularities. This is similar in spirit to the method of obtaining Meijer basis of solutions in [2] for the case wherein one is away from the orbifold singularities, and one is considering the large‐base limit of the Calabi‐Yau. The importance of the method lies in the ease with which one can consider the large and small complex structure limits, as well as the ability to get the “ln”‐terms in the periods without having to parametrically differentiate infinite series. We consider in detail the evaluation of the monodromy matrix in the large and small complex structure limits. We also consider the action of the freely acting antiholomorphic involution of [2,3] on D = 11 supergravity compactified on CY3(3,243) × S1 [4] and obtain the Kähler potential for the same in the limit of large volume of the Calabi‐Yau. As a by‐product, we also give a conjecture for the action of the orientation‐reversing antiholomorphic involution on the periods, given its action on the cohomology, using a canonical (co)homology basis. Finally, we also consider showing a null superpotential on the orientifold of type IIA on CY3(3,243), having taken care of the orbifold singularities, thereby completing the argument initiated in [2].
Abelian and non‐abelian D‐brane effective actions
Authors: Koerber P. 
Published: August 2004

AbstractIn this Ph.D. thesis, accepted at the Vrije Universiteit Brussel, we review and elaborate on a method to find the D‐brane effective action, based on BPS equations. Firstly, both for the Yang‐Mills action and the Born‐Infeld action it is shown that these configurations are indeed BPS, i.e. solutions to these equations saturate a Bogomolny bound and leave some supersymmetry unbroken. Next, we use the BPS equations as a tool to construct the D‐brane effective action and require that (a deformation of) these equations should still imply the equations of motion in more general cases. In the abelian case we managed to calculate all order in α′ four‐derivative corrections to the effective action and the BPS equations while in the non‐abelian case we obtained the effective action up to order α′4. Furthermore, we discuss a check based on the spectrum of strings stretching between intersecting branes. Finally, this Ph.D. thesis also discusses the construction of a boundary superspace which would be the first step to use the method of Weyl invariance in N = 2 superspace in order to again construct the D‐brane effective action. A more detailed summary of each section can be found in the introduction.
Remote homolog detection using local sequence–structure correlations
Authors: Hou Yuna , Hsu Wynne , Lee Mong Li , Bystroff Christopher 
Published: August 2004

AbstractRemote homology detection refers to the detection of structural homology in proteins when there is little or no sequence similarity. In this article, we present a remote homolog detection method called SVM‐HMMSTR that overcomes the reliance on detectable sequence similarity by transforming the sequences into strings of hidden Markov states that represent local folding motif patterns. These state strings are transformed into fixed‐dimension feature vectors for input to a support vector machine. Two sets of features are defined: an order‐independent feature set that captures the amino acid and local structure composition; and an order‐dependent feature set that captures the sequential ordering of the local structures. Tests using the Structural Classification of Proteins (SCOP) 1.53 data set show that the SVM‐HMMSTR gives a significant improvement over several current methods. Proteins 2004. © 2004 Wiley‐Liss, Inc.
A robust method to detect structural and functional remote homologues
Authors: Shachar Ori , Linial Michal 
Published: August 2004

AbstractWith currently available sequence data, it is feasible to conduct extensive comparisons among large sets of protein sequences. It is still a much more challenging task to partition the protein space into structurally and functionally related families solely based on sequence comparisons. The ProtoNet system automatically generates a treelike classification of the whole protein space. It stands to reason that this classification reflects evolutionary relationships, both close and remote. In this article, we examine this hypothesis. We present a semiautomatic procedure that singles out certain inner nodes in the ProtoNet tree that should ideally correspond to structurally and functionally defined protein families. We compare the performance of this method against several expert systems. Some of the competing methods incorporate additional extraneous information on protein structure or on enzymatic activities. The ProtoNet‐based method performs at least as well as any of the methods with which it was compared. This article illustrates the ProtoNet‐based method on several evolutionarily diverse families. Using this new method, an evolutionary divergence scheme can be proposed for a large number of structural and functional related superfamilies. Proteins 2004. © 2004 Wiley‐Liss, Inc.
Analysis of protein homology by assessing the (dis)similarity in protein loop regions
Authors: Panchenko Anna R. , Madej Thomas 
Published: August 2004

AbstractTwo proteins are considered to have a similar fold if sufficiently many of their secondary structure elements are positioned similarly in space and are connected in the same order. Such a common structural scaffold may arise due to either divergent or convergent evolution. The intervening unaligned regions (“loops”) between the superimposable helices and strands can exhibit a wide range of similarity and may offer clues to the structural evolution of folds. One might argue that more closely related proteins differ less in their nonconserved loop regions than distantly related proteins and, at the same time, the degree of variability in the loop regions in structurally similar but unrelated proteins is higher than in homologs. Here we introduce a new measure for structural (dis)similarity in loop regions that is based on the concept of the Hausdorff metric. This measure is used to gauge protein relatedness and is tested on a benchmark of homologous and analogous protein structures. It has been shown that the new measure can distinguish homologous from analogous proteins with the same or higher accuracy than the conventional measures that are based on comparing proteins in structurally aligned regions. We argue that this result can be attributed to the higher sensitivity of the Hausdorff (dis)similarity measure in detecting particularly evident dissimilarities in structures and draw some conclusions about evolutionary relatedness of proteins in the most populated protein folds. Proteins 2004. © 2004 Wiley‐Liss, Inc.
Conformations of variably linked chimeric proteins evaluated by synchrotron X‐ray small‐angle scattering
Authors: Arai Ryoichi , Wriggers Willy , Nishikawa Yukihiro , Nagamune Teruyuki , Fujisawa Tetsuro 
Published: August 2004

AbstractWe constructed chimeric proteins that consist of two green fluorescent protein variants, EBFP and EGFP, connected by flexible linkers, (GGGGS)n (n = 3∼4), and helical linkers, (EAAAK)n (n = 2∼5). The conformations of the chimeric proteins with the various linkers were evaluated using small‐angle X‐ray scattering (SAXS). The SAXS experiments showed that introducing the short helical linkers (n = 2∼3) causes multimerization, while the longer linkers (n = 4∼5) solvate monomeric chimeric proteins. With the moderate‐length linkers (n = 4), the observed radius of gyration (Rg) and maximum dimension (Dmax) were 38.8 Å and 120 Å with the flexible linker, and 40.2 Å and 130 Å with the helical linker, respectively. The chimeric protein with the helical linker assumed a more elongated conformation as compared to that with the flexible linker. When the length of the helical linker increased (n = 5), Rg and Dmax increased to 43.2 Å and 140 Å, respectively. These results suggest that the longer helix effectively separates the two domains of the chimeric protein. Considering the connectivity of the backbone peptide of the protein, the helical linker seems to connect the two domains diagonally. Surprisingly, the chimeric proteins with the flexible linker exhibited an elongated conformation, rather than the most compact side‐by‐side conformation expected from the fluorescence resonance energy transfer (FRET) analysis. Furthermore, the SAXS analyses suggest that destabilization of the short helical linker causes multimerization of the chimeric proteins. Information about the global conformation of the chimeric protein is thus be necessary for optimization of the linker design. Proteins 2004. © 2004 Wiley‐Liss, Inc.
Activity of spinosad on stored‐tobacco insects and persistence on cured tobacco strips
Authors: Blanc Michel P , Panighini Cécile , Gadani Ferruccio , Rossi Luca 
Published: August 2004

AbstractEvery year raw tobacco and manufactured tobacco products are lost to two major storage pests, the cigarette beetle, Lasioderma serricorne (F) and the tobacco moth, Ephestia elutella (Hübner). Post‐harvest management of both insects is achieved through sanitation, insect monitoring and fumigation with phosphine. However, insect resistance to phosphine and control failures have been reported, and fumigants are under constant regulatory pressure. Here we report the evaluation of spinosad, a bioinsecticide derived from the fermentation of the soil micro‐organism Saccharopolyspora spinosa Mertz & Yao. Spinosad was first registered in 1997 and is now widely used as a field pest control agent on many crops, including tobacco. The insecticidal activity of the fermentation product (technical spinosad, TS) was measured by diet incorporation assays against L serricorne and E elutella larvae. Mortality levels were determined on newly hatched larvae and over the whole insect life cycle. For both species, no emergence of adult insects was observed in cured tobacco sprayed with 50 mg TS kg−1 and inoculated with eggs or newly hatched larvae. These results indicated that spinosad has potential for the control of both species in stored tobacco, since 100% control of both pests could be achieved at 50 mg TS kg−1, and with almost full control (90–95%) at 10 mg kg−1. We also monitored the stability of the product on cured tobacco. The original concentration of the main active component of TS, spinosyn A, did not change significantly over 18 months, indicating no loss of spinosad during a typical leaf storage period of time. Bioassays against larvae confirmed that the bioinsecticidal activity of spinosad was retained. Copyright © 2004 Society of Chemical Industry
Bermudagrass (Cynodon spp) dose–response relationships with clethodim, glufosinate and glyphosate
Authors: Webster Theodore M , Hanna Wayne W , Mullinix Benjamin G 
Published: August 2004

AbstractGreenhouse studies were conducted to evaluate the sensitivity of three commercial cultivars, eight experimental cultivars and common bermudagrass to clethodim, glufosinate and glyphosate. Each herbicide was applied at eight doses. Data were regressed on herbicide dose using a log‐logistic curve (R2 = 0.56–0.95 for clethodim, R2 = 0.60–0.94 for glufosinate, and R2 = 0.70–0.96 for glyphosate). The herbicide rate that elicited a 50% plant response (I50) in the bermudagrass cultivars ranged from 0.04 to 0.19 kg ha−1 clethodim, 0.19 to 1.33 kg ha−1 glufosinate and 0.34 to 1.14 kg ha−1 glyphosate. Relative to other cultivars, common bermudagrass was intermediate in its response to clethodim and among the most tolerant cultivars to glufosinate and glyphosate. TifSport was relatively tolerant to clethodim and glufosinate compared with other cultivars, but relatively sensitive to glyphosate. One cultivar, 94‐437, was consistently among the most sensitive cultivars to each of the herbicides. While there were differential herbicide tolerances among the tested bermudagrass cultivars, there did not appear to be any naturally occurring herbicide resistance that could be commercially utilized. However, research indicated that breeding efforts should target herbicide resistance that is at least four times the registered use rate. Also, TifSport and Tifway have been identified as suitable representatives of triploid hybrid bermudagrass cultivars to be used to evaluate the success of turfgrass renovation programs. Copyright © 2004 Society of Chemical Industry
Activity of gut proteinases from Cry1Ab‐selected colonies of the European corn borer, Ostrinia nubilalis (Lepidoptera: Crambidae)
Authors: Siqueira Herbert A A , Nickerson Kenneth W , Moellenbeck Daniel , Siegfried Blair D 
Published: August 2004

AbstractSusceptibility to the Cry1Ab protoxin and toxin from Bacillus thuringiensis (Berliner) and activity of gut proteinases were assessed in both susceptible and Cry1Ab‐selected colonies of European corn borer, Ostrinia nubilalis (Hübner). Resistance in two different selected colonies was at least 6‐ and 15‐fold for the Cry1Ab protoxin and 108‐ and 484‐fold for the Cry1Ab toxin. Activities of trypsin‐like, chymotrypsin‐like and elastase‐like proteinases were variable among the colonies tested and not indicative of a major contribution to Cry1Ab resistance. Activation of the 130‐kDa Cry1Ab protoxin occurred rapidly in all colonies, with no apparent differences among colonies. In addition, there were no apparent changes in activated Cry1Ab processing, indicating that proteolytic degradation was not associated with resistance. These results suggest that mechanisms other than proteolytic activation of protoxin and toxin degradation, such as target site modification may be involved in the resistance to B thuringiensis Cry1Ab in these O nubilalis colonies. Copyright © 2004 Society of Chemical Industry
State arbitrariness of the noninteracting fermion model in quantal density functional theory
Authors: Sahni Viraht , Slamet Marlina 
Published: August 2004

AbstractIn quantal density functional theory (Q‐DFT), any nondegenerate or degenerate ground or excited state of a system of electrons may be mapped to one of noninteracting fermions such that the equivalent density, energy, and ionization potential are obtained. As these model fermions are noninteracting, their effective potential energy, a local (multiplicative) operator, is the same for a particular state of the model system. The state of the noninteracting fermions, however, is arbitrary in that they could be in a ground or excited state. Hence, within Q‐DFT, there exist, in principle, an infinite number of local effective potential energy functions that can generate the same density as that of the interacting electrons. In this article, we demonstrate this state arbitrariness by mapping a (nondegenerate) ground state of the Hookean atom to two different noninteracting fermion systems: one in a singlet ground state (1s2) and the other in a singlet first excited state (1s2s). In each case, the density and energy determined are equivalent to that of the Hookean atom in the ground state, with the highest occupied eigenvalues of the model system being the negative of the ionization potential. The contrast with the mapping within traditional Kohn–Sham and generalized adiabatic connection Kohn–Sham density functional theories is also made. © 2004 Wiley Periodicals, Inc. Int J Quantum Chem, 2004