bluuebunny/crossref_metadata_2025 huggingface dataset:
Copolycondensation of various compositions of isophthalic acid and terephthalic acid with hydroquinones or bisphenols by tosyl chloride/dimethylformamide/pyridine
Authors: Higashi Fukuji , Takakura Tomohiro , Sumi Yasuyuki
Published: April 2004

The polycondensation of isophthalic acid (IPA)/terephthalic acid (TPA) with aromatic diols by tosyl chloride/dimethylformamide/pyridine in solution was examined through changes in the IPA/TPA compositions, the kinds of dihydroxyl components, the periods of their addition, and the reaction temperatures. The reaction proceeded favorably at IPA/TPA ratios of 70/30 to 50/50, similarly to an earlier report on the interfacial reaction. The effects of the compositions were significant in the reactions with monosubstituted hydroquinones. The results were examined from distributions of the resulting oligomers prepared at a reaction extent of 0.7, determined by gel permeation chromatography. The reaction producing better results exhibited distributions closer to the theoretical ones. The period of addition also favorably affected the distributions as well as the results of the polycondensation. These results were attributed to the change in the reaction method, in which the diols reacted with the aggregates that formed from the activated IPA and TPA. The change was likely caused by the degree of association of IPA and TPA in the aggregates, on the basis of melting points and IR spectra of mixtures of dimethyl esters of IPA and TPA prepared by the quenching of the aggregates with methanol. © 2004 Wiley Periodicals, Inc. J Polym Sci Part A: Polym Chem 42: 2321–2328, 2004
Novel conducting polymer poly[bis(phenylamino)disulfide]: Synthesis, characterization, and properties
Authors: Su Yu‐Zhi , Niu Yong‐Ping , Xiao Yi‐Zhi , Xiao Min , Liang Zhao‐Xi , Gong Ke‐Cheng
Published: April 2004

A bis(phenylamino)disulfide was prepared through the reaction of S2Cl2 with aniline, and its configuration was confirmed with elemental analysis, Fourier transform infrared (FTIR), Fourier transform Raman (FT‐Raman), and 1H NMR spectroscopy. A novel conducting polymer, poly[bis(phenylamino)disulfide] (PPAD), was synthesized from bis(phenylamino)disulfide by both chemical and electrochemical polymerization. The structure of this polymer, in which the side‐chain disulfide bonds were linked to the nitrogen atoms of the main‐chain polyaniline, was characterized with FTIR, FT‐Raman, gel permeation chromatography, electron spectroscopy, and X‐ray photoelectron spectroscopy. A four‐probe measurement revealed that the electrical conductivity of PPAD was 1.8 × 10−2 to 2.1 × 10−3 S cm−1, depending on the doping agents and the pH of the medium for either chemical synthesis or electrochemical synthesis. The conductivity, molecular weight, and spectroscopic properties of the polymer, in comparison with those of polyaniline, showed decreases in the polaron delocalization, structural order, and doping level of the main chain because of the steric hindrance of side‐chain SS bonds. The cyclic voltammograms of the polymer and the monomer showed that the redox reactions (doping/undoping processes) of the main chain (π‐conjugated system) occurred in almost the same potential range of −0.3 to 0.3 V versus an Ag/AgCl (saturated KCl) electrode as that of thiol (thiolate anion)/disulfide of the side chain in PPAD; the bond cleavage (reduction) and formation (oxidation) reactions of the disulfide bond in the polymer became easier and more reversible than those of the monomer. These results suggested that this conducting organodisulfide polymer might be a candidate material for energy‐storage devices such as lithium secondary batteries, proton‐exchange batteries, and electrochemical capacitors. © 2004 Wiley Periodicals, Inc. J Polym Sci Part A: Polym Chem 42: 2329–2339, 2004
A general clustering approach with application to the Miyazawa–Jernigan potentials for amino acids
Authors: Esteve J.G. , Falceto F.
Published: April 2004

In this article, we address the problem of classification of amino acids. Starting from the Miyazawa–Jernigan matrix obtained from the relative positions of amino acids in the crystal structure of globular proteins, we develop a fully unsupervised method of classification for the amino acids. The method is based in the subdominant ultrametric associated to the distance induced by the Miyazawa–Jernigan matrix and the maximum likelihood principle to determine the cluster structure. We obtain a classification consistent with the five groups used in the literature, although with some peculiarities. We also show the stability of our results against changes of the method used to classify the amino acids. Proteins 2004. © 2004 Wiley‐Liss, Inc.
Molecular dynamics simulations of structural changes during procaspase 3 activation
Authors: Piana Stefano , Rothlisberger Ursula
Published: April 2004

Molecular dynamics (MD) simulations of the structural rearrangements on the pathway leading to procaspase 3 activation are presented. A retrostructural approach is used to build procaspase 3 from mature caspase 3. The peptide bond that is cleaved during enzyme maturation is gradually reformed during the MD simulation and the most relevant structural changes that occur as a consequence are analyzed. The main structural features that characterize this procaspase 3 model are compared with the available X‐ray structure of procaspase 7 as the only zymogen structure that has been crystallised so far. The MD simulations indicate that in the free caspase 3, the flexible selectivity loop is already preorganized to accomodate the substrate. Such a preorganization is not present in either monomeric caspase 3 or in the procaspase 3 dimer, indicating that the structure of the selectivity loop is highly sensitive to perturbations. Proteins 2004;55:000–000. © 2004 Wiley‐Liss, Inc.
Theoretical study of the ligand–CYP2B4 complexes: Effect of structure on binding free energies and heme spin state
Authors: Harris Danni L. , Park Jin‐Young , Gruenke Larry , Waskell Lucy
Published: April 2004

The molecular origins of temperature‐dependent ligand‐binding affinities and ligand‐induced heme spin state conversion have been investigated using free energy analysis and DFT calculations for substrates and inhibitors of cytochrome P450 2B4 (CYP2B4), employing models of CYP2B4 based on CYP2C5(3LVdH)/CYP2C9 crystal structures, and the results compared with experiment. DFT calculations indicate that large heme–ligand interactions (ca. −15 kcal/mol) are required for inducing a high to low spin heme transition, which is correlated with large molecular electrostatic potentials (∼−45 kcal/mol) at the ligand heteroatom. While type II ligands often contain oxygen and nitrogen heteroatoms that ligate heme iron, DFT results indicate that BP and MF heme complexes, with weak substrate–heme interactions (ca. −2 kcal/mol), and modest MEPS minima (>−35 kcal/mol) are high spin. In contrast, heme complexes of the CYP2B4 inhibitor, 4PI, the product of benzphetamine metabolism, DMBP, and water are low spin, have substantial heme–ligand interaction energies (<−15 kcal/mol) and deep MEPS minima (<−45 kcal/mol) near their heteroatoms. MMPBSA analysis of MD trajectories were made to estimate binding free energies of these ligands at the heme binding site of CYP2B4. In order to initially assess the realism of this approach, the binding free energy of 4PI inhibitor was computed and found to be a reasonable agreement with experiment: −7.7 kcal/mol [−7.2 kcal/mol (experiment)]. BP was determined to be a good substrate [−6.3 kcal/mol (with heme–ligand water), −7.3 kcal/mol (without ligand water)/−5.8 kcal/mol (experiment)], whereas the binding of MF was negligible, with only marginal binding binding free energy of −1.7 kcal/mol with 2‐MF bound [−3.8 kcal/mol (experiment)], both with and without retained heme–ligand water. Analysis of the free energy components reveal that hydrophobic/nonpolar contributions account for approximately 90% of the total binding free energy of these substrates and are the source of their differential and temperature‐dependent CYP2B4 binding. The results indicate the underlying origins of the experimentally observed differential binding affinities of BP and MF, and indicate the plausibility of the use of models derived from moderate sequence identity templates in conjunction with approximate free energy methods in the estimation of ligand‐P450 binding affinities. Proteins 2004. © 2004 Wiley‐Liss, Inc.
Direct measure of functional importance visualized atom‐by‐atom for photoactive yellow protein: Application to photoisomerization reaction
Authors: Yamada Atsushi , Ishikura Takakazu , Yamato Takahisa
Published: April 2004

Photoreceptor proteins serve as efficient nano‐machines for the photoenergy conversion and the photosignal transduction of living organisms. For instance, the photoactive yellow protein derived from a halophilic bacterium has the p‐coumaric acid chromophore, which undergoes an ultrafast photoisomerization reaction after light illumination. To understand the structure‐function relationship at the atomic level, we used a computational method to find functionally important atoms for the photoisomerization reaction of the photoactive yellow protein. In the present study, a “direct” measure of the functional significance was quantitatively evaluated for each atom by calculating the partial atomic driving force for the photoisomerization reaction. As a result, we revealed the reaction mechanism in which the specific role of each functionally important atom has been well characterized in a systematic manner. In addition, we observed that this mechanism is strongly conserved during the thermal fluctuation of the photoactive yellow protein. We compared the experimental data of fluorescence decay constant of several different mutants and the present analysis. As a result, we found that the reaction rate constant is decreased when a large positive driving force is missing. Proteins 2004. © 2004 Wiley‐Liss, Inc.
Irreversible formation of intermediate BSA oligomers requires and induces conformational changes
Authors: Vaiana S.M. , Emanuele A. , Palma‐Vittorelli M.B. , Palma M.U.
Published: April 2004

Understanding the relation between protein conformational changes and aggregation, and the physical mechanisms leading to such processes, is of primary importance, due to its direct relation to a vast class of severe pathologies. Growing evidence also suggests that oligomeric intermediates, which may occur early in the aggregation pathway, can be themselves pathogenic. The possible cytotoxicity of oligomers of non‐disease‐associated proteins adds generality to such suggestion and to the interest of studies of oligomer formation. Here we study the early stages of aggregation of Bovine Serum Albumin (BSA), a non pathogenic protein which has proved to be a useful model system. Dynamic light scattering and circular dichroism measurements in kinetic experiments following step‐wise temperature rises, show that the “intermediate” form, which initiates large‐scale aggregation, is the result of structural and conformational changes and concurrent formation of oligomers, of average size in the range of 100–200 Å. Two distinct thresholds are observed. Beyond the first one oligomerization starts and causes partial irreversibility of conformational changes. Beyond the second threshold, additional secondary structural changes occurring in proteins being recruited progress on the same time scale of oligomerization. The concurrent behavior causes a mutual stabilization of oligomerization, and of structural and conformational changes, evidenced by a progressive increase of their irreversibility. This process interaction appears to be pivotal in producing irreversible oligomers. Proteins 2004;9999:000–000. © 2004 Wiley‐Liss, Inc.
Solution structure of hypothetical nudix hydrolase DR0079 from extremely radiation‐resistant Deinococcus radiodurans bacterium
Authors: Buchko Garry W. , Ni Shuisong , Holbrook Stephen R. , Kennedy Michael A.
Published: April 2004

Using nuclear magnetic resonance (NMR) based methods, including residual dipolar coupling restraints, we have determined the solution structure of the hypothetical Deinococcus radiodurans Nudix protein DR0079 (171 residues, MW = 19.3 kDa). The protein contains eight β‐strands and three α‐helices organized into three subdomains: an N‐terminal β‐sheet (1–34), a central Nudix core (35–140), and a C‐terminal helix‐turn‐helix (141–171). The Nudix core and the C‐terminal helix‐turn‐helix form the fundamental fold common to the Nudix family, a large mixed β‐sheet sandwiched between α‐helices. The residues that compose the signature Nudix sequence, GX5EX7REUXEEXGU (where U = I, L, or V and X = any amino acid), are contained in a turn‐helix‐turn motif on the face of the mixed β‐sheet. Chemical shift mapping experiments suggest that DR0079 binds Mg2+. Experiments designed to determine the biological function of the protein indicate that it is not a type I isopentenyl‐diphosphate δ‐isomerase and that it does not bind α,β‐methyleneadenosine 5′‐triphosphate (AMPCPP) or guanosine 5′‐[β,γ‐imido]triphosphate (GMPPNP). In this article, the structure of DR0079 is compared to other known Nudix protein structures, a potential substrate‐binding surface is proposed, and its possible biological function is discussed. Proteins 2004;55:000–000. © 2004 Wiley‐Liss, Inc.
Modeling effects of mutations in coiled‐coil structures: Case study using epidermolysis bullosa simplex mutations in segment 1a of k5/k14 intermediate filaments
Authors: Smith Thomasin A. , Steinert Peter M. , Parry David A.D.
Published: April 2004

The sequence of a protein chain determines both its conformation and its function in vivo. An attempt is made to gain an understanding of the classes of deformations that can arise in an important structural motif, the α‐helical coiled coil, as a consequence of mutations occurring in its underlying heptad substructure. In order to do so we consider the model structure of segment 1A in intermediate filaments and then investigate the structures arising from each of the 22 mutations observed in cytokeratin K5/K14 molecules that lead to variants of epidermolysis bullosa simplex. These are refined separately using a molecular dynamics protocol. The mutations often result in a significant distortion of the backbone over a turn or so of the α helix in either the chain itself or its constituent partner, leading to the likelihood of impaired chain aggregation and hence molecular assembly. One mutant (K14‐L143P; 1A‐28) gave rise to structural distortion along almost the entire length of segment 1A. The remaining structures showed less deformation, and normal‐looking intermediate filaments are likely in vivo. In addition, an identical mutation in the same position in each of the chains in the heterodimer did not necessarily give equivalent structural distortions. Although proline mutations frequently lead to the most severe structural deformations, a non‐proline substitution (K14‐R125S; 1A‐10) gave rise to the largest local structural disruption that was observed. Unexpectedly, mutations in positions a and d were not always of the greatest structural significance, although three in position a were shown by AGADIR to result in a significant increase in α‐helix stability. Proteins 2004. © 2004 Wiley‐Liss, Inc.
Importance of hydrophobic cluster formation through long‐range contacts in the folding transition state of two‐state proteins
Authors: Selvaraj S. , Gromiha M. Michael
Published: April 2004

Understanding the folding pathways of proteins is a challenging task. The Φ value approach provides a detailed understanding of transition‐state structures of folded proteins. In this work, we have computed the hydrophobicity associated with each residue in the folded state of 16 two‐state proteins and compared the Φ values of each mutant residue. We found that most of the residues with high Φ value coincide with local maximum in surrounding hydrophobicity, or have nearby residues that show such maximum in hydrophobicity, indicating the importance of hydrophobic interactions in the transition state. We have tested our approach to different structural classes of proteins, such as α‐helical, SH3 domains of all‐β proteins, β‐sandwich, and α/β proteins, and we observed a good agreement with experimental results. Further, we have proposed a hydrophobic contact network pattern to relate the Φ values with long‐range contacts, which will be helpful to understand the transition‐state structures of folded proteins. The present approach could be used to identify potential hydrophobic clusters that may form through long‐range contacts during the transition state. Proteins 2004;55:000–000. © 2004 Wiley‐Liss, Inc.
Pex5p binding affinities for canonical and noncanonical PTS1 peptides
Authors: Maynard Ernest L. , Gatto Gregory J. , Berg Jeremy M.
Published: April 2004

The majority of proteins targeted to the peroxisomal lumen contain a C‐terminal peroxisomal targeting signal‐1 (PTS1) that is bound by the peroxin Pex5p. The PTS1 is generally regarded as a C‐terminal tripeptide that adheres to the consensus (S/A/C)(K/R/H)(L/M). Previously, we studied the binding affinity of peptides of the form YQX(‐3)X(‐2)X(‐1) to the peptide‐binding domain of human Pex5p (referred to as Pex5p‐C). Optimal affinity was found for YQSKL, which bound with an affinity of 200 ± 40 nM. To extend this work, we investigated the properties of a peptide containing the last 9 residues of acyl‐CoA oxidase (RHYLKPLQSKL) and discovered that it binds to Pex5p‐C with a dissociation constant of 1.4 ± 0.4 nM, 180 times tighter than YQSKL. Further analysis revealed that the enhanced affinity is primarily due to the presence of leucine in the (‐5) position. In addition, a peptide corresponding to the luciferase C‐terminus (YKGGKSKL) was found to bind Pex5p‐C about 20 times tighter than YQSKL. The majority of this effect results from having lysine in position (‐4). Catalase contains a noncanonical PTS1 (‐AREKANL). The affinity of YQANL was found to be 3600 ± 400 nM. This relatively weak binding is consistent with previous unsuccessful attempts to direct chloramphenicol acetyltransferase to the peroxisome by fusing ‐ANL to its C‐terminus (‐GGA‐ANL). The peptides YKANL, YEKANL, YREKANL, and YAREKANL all bound Pex5p‐C with higher affinities than did YQANL, but the affinities are still lower than peptides that correspond to functional targeting signals in other contexts. Because both catalase and Pex5p are tetramers (as opposed to the monomeric Pex5p‐C and the peptides used in our studies), multidentate effects on binding affinity between Pex5p and other oligomeric proteins should be considered. Our study provides direct thermodynamic data revealing that peptide binding to Pex5p‐C binding is favored by lysine in the (‐4) position and leucine in the (‐5) position. Our results suggest that peptides or proteins with optimized residues in the (‐4) and/or (‐5) positions can bind to Pex5p with affinities that are at least two orders of magnitude greater than that of YQSKL, and that this stabilization can compensates for otherwise weakly binding PTS1s. Proteins 2004. © 2004 Wiley‐Liss, Inc.
Solution structure of BmKK2, a new potassium channel blocker from the venom of chinese scorpion Buthus martensi Karsch
Authors: Zhang Naixia , Li Minghua , Chen Xiang , Wang Yuefeng , Wu Gong , Hu Guoyuan , Wu Houming
Published: April 2004

A natural K+ channel blocker, BmKK2 (a member of scorpion toxin subfamily α‐KTx 14), which is composed of 31 amino acid residues and purified from the venom of the Chinese scorpion Buthus martensi Karsch, was characterized using whole‐cell patch‐clamp recording in rat hippocampal neurons. The three dimensional structure of BmKK2 was determined with two‐dimensional NMR spectroscopy and molecular modelling techniques. In solution this toxin adopted a common α/β‐motif, but showed distinct local conformation in the loop between α‐helix and β‐sheet in comparison with typical short‐chain scorpion toxins (e.g., CTX and NTX). Also, the α helix is shorter and the β‐sheet element is smaller (each strand consisted only two residues). The unusual structural feature of BmKK2 was attributed to the shorter loop between the α‐helix and β‐sheet and the presence of two consecutive Pro residues at position 21 and 22 in the loop. Moreover, two models of BmKK2/hKv1.3 channel and BmKK2/rSK2 channel complexes were simulated with docking calculations. The results demonstrated the existence of a α‐mode binding between the toxin and the channels. The model of BmKK2/rSK2 channel complex exhibited favorable contacts both in electrostatic and hydrophobic, including a network of five hydrogen bonds and bigger interface containing seven pairs of inter‐residue interactions. In contrast, the model of BmKK2/hKv1.3 channel complex, containing only three pairs of inter‐residue interactions, exhibited poor contacts and smaller interface. The results well explained its lower activity towards Kv channel, and predicted that it may prefer a type of SK channel with a narrower entryway as its specific receptor. Proteins 2004. © 2004 Wiley‐Liss, Inc.
A 4.2 kDa synthetic peptide as a potential probe to evaluate the antibacterial activity of coumarin drugs
Authors: Scatigno Andreza C. , Garrido Saulo S. , Marchetto Reinaldo
Published: April 2004

The coumarin antibiotics are potent inhibitors of DNA replication whose target is the enzyme DNA gyrase, an ATP‐dependent bacterial type II topoisomerase. The coumarin drugs inhibit gyrase action by competitive binding to the ATP‐binding site of DNA gyrase B protein. The production of new biologically active products has stimulated additional studies on coumarin–gyrase interactions. In this regard, a 4.2 kDa peptide mimic of DNA gyrase B protein from Escherichia coli has been designed and synthesized. The peptide sequence includes the natural fragment 131–146 (coumarin resistance‐determining region) and a segment containing the gyrase–DNA interaction region (positions 753–770). The peptide mimic binds to novobiocin (Ka = 1.4 ± 0.3 × 105 M−1), plasmid (Ka = 1.6 ± 0.5 × 106 M−1) and ATP (Ka = 1.9 ± 0.4 × 103 M−1), results previously found with the intact B protein. On the other hand, the binding to novobiocin was reduced when a mutation of Arg‐136 to Leu‐136 was introduced, a change previously found in the DNA gyrase B protein from several coumarin‐resistant clinical isolates of Escherichia coli. In contrast, the binding to plasmid and to ATP was not altered. These results suggest that synthetic peptides designed in a similar way to that described here could be used as mimics of DNA gyrase in studies which seek a better understanding of the ATP, as well as coumarin, binding to the gyrase and also the mechanism of action of this class of antibacterial drugs. Copyright © 2004 European Peptide Society and John Wiley & Sons, Ltd.
[D‐Ala2]‐deltorphin I peptoid and retropeptoid analogues: synthesis, biological activity and conformational investigations
Authors: Biondi Laura , Giannini Elisa , Filira Fernando , Gobbo Marina , Negri Lucia , Rocchi Raniero
Published: April 2004

The synthesis is described of a [D‐Ala2]‐deltorphin I peptoid analogue in which all amino acid residues have been substituted by the corresponding N‐alkylglycine residues. The [D‐Ala2]‐deltorphin I retropeptoid was also prepared as well as [Ala1,D‐Ala2]‐deltorphin 1 and the corresponding peptoid. Structural investigations by FT‐IR and fluorescence measurements were carried out on the synthetic analogues and on some [D‐Ala2]‐deltorphin 1 peptide–peptoid hybrids previously prepared. According to the fluorescence measurements the distance between the aromatic residues in the deltorphin I peptoid and retropeptoid is similar to that suggested for the δ‐ and µ‐opioids, respectively. Measurements of CD in the presence of β‐cyclodextrin, and some preliminary pharmacological experiments were also performed. No dichroic bands are present in the spectrum of the [Ntyr1,D‐Ala2]‐deltorphin I, but an increasing dichroic effect appears in the spectra of both the deltorphin I peptoid and retropeptoid. Activity tests on isolated organ preparations showed that the modifications made produced a dramatic decrease in the agonistic activity of the synthetic derivatives. Copyright © 2004 European Peptide Society and John Wiley & Sons, Ltd.
Development of a liquid extraction method and comparison with dynamic thermal stripping–thermal desorption (DTS–TD) method: sorption of D‐limonene by flexible packaging films
Authors: Caner Cengiz
Published: March 2004

The sorption of D‐limonene into polymeric structures in contact with food simulant liquids (ethanol and acetic acid solutions) was determined using two methods, liquid extraction (LE) and dynamic thermal stripping–thermal desorption (DTS–TD). The polymeric films studied were PP (polypropylene), PE/nylon/EVOH/PE (polyethylene/nylon/ethylene vinyl alcohol/polyethylene) and metPET/VA EVA/LLDPE (metallized polyethylene terephthalate/ethylenevinyl acetate/linear low density polyethylene). Our assessment showed that both LE and DTS–TD techniques are valuable procedures. LE was evaluated as an alternative method with the advantage of being a simplified process. It was possible to measure the amount of D‐limonene in the polymers using both methods. Correlation between methods was >82% and for the single layer polymers >92%. The respective sorption values obtained by the two methods were also found to be in good agreement. LE is simple and rapid to perform and, in general, gives slightly lower results compared to DTS–TS sorption tests conducted with adequate food simulants. The results indicate that the liquid extraction method is an excellent technique for the determination of sorbate concentration in polymeric structures. Copyright © 2004 John Wiley & Sons, Ltd.
Operating Characteristic Curves for the Exponential Bayes‐Truncated Test
Authors: Wang Fu‐Kwun , Keats J. Bert
Published: April 2004

Operating characteristic (OC) curves are often useful in determining how large a sample is required to detect a specified difference for a particular consumer and producer risk. In this paper, OC curves with Bayes stopping rules for the exponential distribution are developed. Example curves are provided for the sequential and batch testing situations. The power of the test is greater under batch testing. A table illustrates the performance of the plans for stopping at each opportunity in a sample of size 20. Some examples are used to demonstrate the application of the proposed methodology. Copyright © 2004 John Wiley & Sons, Ltd.
Libra: a computational economy‐based job scheduling system for clusters
Authors: Sherwani Jahanzeb , Ali Nosheen , Lotia Nausheen , Hayat Zahra , Buyya Rajkumar
Published: April 2004

Clusters of computers have emerged as mainstream parallel and distributed platforms for high‐performance, high‐throughput and high‐availability computing. To enable effective resource management on clusters, numerous cluster management systems and schedulers have been designed. However, their focus has essentially been on maximizing CPU performance, but not on improving the value of utility delivered to the user and quality of services. This paper presents a new computational economy driven scheduling system called Libra, which has been designed to support allocation of resources based on the users' quality of service requirements. It is intended to work as an add‐on to the existing queuing and resource management system. The first version has been implemented as a plugin scheduler to the Portable Batch System. The scheduler offers market‐based economy driven service for managing batch jobs on clusters by scheduling CPU time according to user‐perceived value (utility), determined by their budget and deadline rather than system performance considerations. The Libra scheduler has been simulated using the GridSim toolkit to carry out a detailed performance analysis. Results show that the deadline and budget based proportional resource allocation strategy improves the utility of the system and user satisfaction as compared with system‐centric scheduling strategies. Copyright © 2004 John Wiley & Sons, Ltd.
Common subgraph isomorphism detection by backtracking search
Authors: Krissinel Evgeny B. , Henrick Kim
Published: April 2004

Graph theory offers a convenient and highly attractive approach to various tasks of pattern recognition. Provided there is a graph representation of the object in question (e.g. a chemical structure or protein fold), the recognition procedure is reduced to the problem of common subgraph isomorphism (CSI). Complexity of this problem shows combinatorial dependence on the size of input graphs, which in many practical cases makes the approach computationally intractable. Among the optimal algorithms for CSI, the leading place in practice belongs to algorithms based on maximal clique detection in the association graph. Backtracking algorithms for CSI, first developed two decades ago, are rarely used. We propose an improved backtracking algorithm for CSI, which differs from its predecessors by better search strategy and is therefore more efficient. We found that the new algorithm outperforms the traditional maximal clique approach by orders of magnitude in computational time. Copyright © 2004 John Wiley & Sons, Ltd.
Developmental regulation of connexins 26, 32, 36, and 43 in trigeminal neurons
Authors: Honma Shiho , De Shampa , Li Daniel , Shuler Charles F. , Turman Jack E.
Published: April 2004

The transition from sucking to chewing during postnatal development is accompanied by changes in masticatory muscle activity patterns. We previously demonstrated that changes in numerous parameters of chemical synapses among neurons, and intrinsic membrane properties of neurons, comprising brainstem oral‐motor circuits are coincident with changes in masticatory muscle activity patterns. Considering recent findings that implicate a role for gap junctions in early locomotor and respiratory behaviors, our present study focuses on the developmental regulation of connexin proteins in trigeminal neurons as a first step in understanding a role for gap junctions in developing oral‐motor circuits used for ingestive behaviors. We conducted immunohistochemistry studies to examine connexin (Cx) 26, 32, 36, and 43 expression in trigeminal motor and mesencephalic trigeminal nuclei during postnatal development at the light and electron microscopic levels. Postnatal days (P) 1, 6, 14, 21, and adult mice were used. Cx32, 36, and 43 expression was developmentally regulated in the trigeminal motor nucleus, while Cx26 expression remained high throughout postnatal development. In the mesencephalic trigeminal nucleus, Cx26, 32, and 43 expression was intense throughout development, with only Cx36 showing a developmental regulation. Ultrastructural examination of neonatal trigeminal motoneurons and mesencephalic trigeminal neurons revealed connexin expression in cell membranes, cytoplasm, and cell nuclei (Cx43, Cx32). Our results show that connexin proteins are differentially regulated between trigeminal motoneurons and mesencephalic trigeminal neurons during development, and suggest a possible role for gap junctions in the development of trigeminal neurons and the function and maturation of oral‐motor circuits. Synapse 52:258–271, 2004. © 2004 Wiley‐Liss, Inc.
Ultrastructural interactions between terminals expressing the norepinephrine transporter and dopamine neurons in the rat and monkey ventral tegmental area
Authors: Liprando Lindsay A. , Miner Leeann H. , Blakely Randy D. , Lewis David A. , Sesack Susan R.
Published: April 2004

The norepinephrine (NE) system is implicated in the etiology and treatment of depression and drugs blocking the NE transporter (NET) are effective antidepressants. It is possible that dopamine (DA) also plays a role in depression and the action of antidepressant drugs, although the mechanisms whereby NE and DA interact have not been fully elaborated. We examined whether NE neurons might alter DA transmission via synaptic projections to cells in the ventral tegmental area (VTA) by using electron microscopic dual labeling immunocytochemistry in the rat and monkey. NET was used as a marker for NE axons, whereas the catecholamine synthetic enzyme, tyrosine hydroxylase (TH), served as a label for DA neurons. We observed three types of spatial relationships between these profiles that were similar in type but varied in frequency between rodent and primate. The most common arrangement involved nonsynaptic appositions between NET‐immunoreactive (‐ir) axons and TH‐ir dendrites. Such relationships may facilitate extrasynaptic actions of NE on DA cell activity. The other commonly observed arrangement involved adjacent profiles that were otherwise separated by glia. These relationships may represent regions where NE is prevented from reaching DA cells. In only a few cases were synapses observed between NET‐ir axons and TH‐ir dendrites. This finding suggests that NE can synaptically regulate DA neurons, although functional interactions are more likely to involve extrasynaptic mechanisms. Finally, in the VTA of both species the majority of NET‐ir axons exhibited no detectable TH immunoreactivity. The latter finding agrees with observations in cortical regions and represents the first report of its type in a subcortical structure. Synapse 52:233–244, 2004. © 2004 Wiley‐Liss, Inc.
Comparison of unreamed nailing and external fixation of tibial diastases—mechanical conditions during healing and biological outcome
Authors: Klein P. , Opitz M. , Schell H. , Taylor W. R. , Heller M. O. , Kassi J.‐P. , Kandziora F. , Duda G. N.
Published: April 2004

Locked intramedullary nailing and external fixation are alternatives for the stabilization of tibial shaft fractures. The goal of this study was to determine to what extent the mechanical conditions at the fracture site influence the healing process after unreamed tibial nailing compared to external fixation. A standardized tibial diastasis was stabilized with either a locked unreamed tibial nail or a monolateral fixator in a sheep model. Interfragmentary movements and ground reaction parameters were monitored in vivo throughout the healing period. After sacrifice, the tibiae were examined mechanically and histologically. Bending angles and axial torsion at the fracture site were larger in the nail group within the first five weeks post‐operatively. Unlike the fixator group, the operated limb in the nail group did not return to full weight bearing during the treatment period. Mechanical and histomorphometrical observations showed significantly inferior bone healing in the nail group compared to the fixator group. In this study, unreamed nailing of a tibial diastasis did not provide rotational stability of the osteosynthesis and resulted in a significant delay in bone healing. © 2004 Orthopaedic Research Society. Published by Elsevier Ltd. All rights reserved.
The origin of the sodium‐dependent NADH oxidation by the respiratory chain of Klebsiella pneumoniae
Authors: Bertsova Yulia V , Bogachev Alexander V
Published: April 2004

Properties of Klebsiella pneumoniae respiratory chain enzymes catalyzing NADH oxidation have been studied. Using constructed K. pneumoniae mutant strains, it was shown that three enzymes belonging to different families of NADH:quinone oxidoreductases operate in this bacterium. The NDH‐2‐type enzyme is not coupled with energy conservation, the NDH‐1‐type enzyme is a primary proton pump, and the NQR‐type enzyme is homologous to the sodium‐motive NADH dehydrogenase of Vibrio and is shown to be a primary Na+ pump. It is concluded that the NQR‐type enzyme, not the NDH‐1‐type enzyme, catalyzes sodium‐dependent NADH oxidation in K. pneumoniae.
Enhancement of growth and cellulose accumulation by overexpression of xyloglucanase in poplar
Authors: Park Yong Woo , Baba Kei'ichi , Furuta Yuzo , Iida Ikuho , Sameshima Kazuhiko , Arai Motoh , Hayashi Takahisa
Published: April 2004

Because the loosening of xyloglucan in the cell wall promotes plant growth (Takeda et al. (2002) Proc. Natl. Acad. Sci. USA 99, 9055–9060; Park et al. (2003) Plant J. 33, 1099–1106), we expressed Aspergillus xyloglucanase constitutively in Populus alba. The expression increased the length of stem even in the presence of sucrose. Increased stem growth was accompanied by a decrease in Young's elastic modulus in the growth zone but an increased elasticity in mature tissue. The increased internode length corresponded to an increase in cellulose content as well as specific gravity, showing that the removal of xyloglucan might cause an increase in cellulose density in the secondary xylem.
P66ShcA interacts with MAPKAP kinase 2 and regulates its activity
Authors: Yannoni Yvonne M. , Gaestel Matthias , Lin Lih-Ling
Published: April 2004

Three mitogen activated protein kinase‐activated protein kinase 2 (MAPKAP kinase 2, MK2) interacting proteins were identified using a yeast two‐hybrid approach. ShcA, a signaling phospho‐protein, human polyhomeotic 2 (HPH2), a transcriptional regulator, and highly similar to smoothelin (HSTS), which is related to the cytoskeletal associated protein smoothelin, interact specifically with MK2. The interaction of MK2 with the 66 kDa isoform of ShcA, p66ShcA, and HPH2 was confirmed using co‐immunoprecipitation. MK2 is activated with p66ShcA co‐expression and p66ShcA is an in vitro substrate for MK2, further demonstrating their association and suggesting a biological role for p66Shc in MK2 activation.
Sp1 is involved in the transcriptional activation of p16INK4 by p21Waf1 in HeLa cells
Authors: Xue Lixiang , Wu Junfeng , Zheng Wenjie , Wang Peichang , Li Jun , Zhang Zongyu , Tong Tanjun
Published: April 2004

Both p16INK4 and p21Waf1 are very important negative regulators of the cell cycle. In this study we examined the effects of p21Waf1 on the transcription of p16INK4. We determined that p21Waf1 can activate the transcription of p16INK4, and that this effect is GC‐box dependent. We also found that the transcription factor Sp1 plays a key role in this event. Upregulation of Sp1 contributes to the transcriptional activation and protein level of p16INK4 mediated by p21Waf1, and is a potential point of cooperation between the p16/pRb and p14 (ARF)/p53 tumor suppressor pathways.
An antibody library for stabilizing and crystallizing membrane proteins – selecting binders to the citrate carrier CitS
Authors: Röthlisberger Daniela , Pos Klaas Martinus , Plückthun Andreas
Published: April 2004

Co‐crystallization of membrane proteins with antibody fragments may emerge as a general tool to facilitate crystal growth and improve crystal quality. The bound antibody fragment enlarges the hydrophilic part of the mostly hydrophobic membrane protein, thereby increasing the interaction area for possible protein–protein contacts in the crystal. Additionally, it may restrain flexible parts or lock the membrane protein in a defined conformational state. For successful co‐crystallization trials, the antibody fragments must be stable in detergents during the extended period of crystal growth and must be easily produced in amounts necessary for crystallography. Therefore, we constructed a library of antibody Fab fragments from a framework subset of the HuCAL GOLD® library (Morphosys, Munich, Germany). By combining the most stable and well expressed frameworks, VH3 and Vκ3, with the further stabilizing constant domains, a Fab library with the desired properties was obtained in a standard phage display format. As a proof of principle, we selected binders with phage display against the detergent‐solubilized citrate transporter CitS of Klebsiella pneumoniae. We describe efficient methods for the immobilization of the membrane protein during selection, for ELISA screening, and for BIAcore evaluation. We demonstrate that the selected Fab fragments form stable complexes with native CitS and recognize conformational epitopes with affinities in the low nanomolar range.
Evolution of photosystem I – from symmetry through pseudosymmetry to asymmetry
Authors: Ben-Shem Adam , Frolow Felix , Nelson Nathan
Published: April 2004

The evolution of photosystem (PS) I was probably initiated by the formation of a homodimeric reaction center similar to the one currently present in green bacteria. Gene duplication has generated a heterodimeric reaction center that subsequently evolved to the PSI present in cyanobacteria, algae and plant chloroplasts. During the evolution of PSI several attempts to maximize the efficiency of light harvesting took place in the various organisms. In the Chlorobiaceae, chlorosomes and FMO were added to the homodimeric reaction center. In cyanobacteria phycobilisomes and CP43′ evolved to cope with the light limitations and stress conditions. The plant PSI utilizes a modular arrangement of membrane light‐harvesting proteins (LHCI). We obtained structural information from the two ends of the evolutionary spectrum. Novel features in the structure of Chlorobium tepidum FMO are reported in this communication. Our structure of plant PSI reveals that the addition of subunit G provided the template for LHCI binding, and the addition of subunit H prevented the possibility of trimer formation and provided a binding site for LHCII and the onset of energy spillover from PSII to PSI.
Colonization and tropical deforestation in the Sierra Santa Marta, Southern Mexico
Authors: DURAND LETICIA , LAZOS ELENA
Published: April 2004

Understanding patterns of tropical deforestation is a crucial issue for Mexico, a country that has lost more than 95% of its original rainforest cover. This paper examines the causes of accelerated deforestation in the Sierra Santa Marta, Veracruz, Mexico, by looking at settlement history and the evolution of productive schemes in the villages of Venustiano Carranza and Magallanes. Both settlements were founded in the 1960s, after the government donated land to landless peasants. Conversion of forests into pastures, after several agricultural enterprises failed, resulted in more than 80% of the original tropical rainforests being removed in both communities between 1960 and 1998. The process of deforestation in the villages differed from models proposed for the Amazon and Central America, in which deforestation responded to capital-intensive efforts to open up the tropical frontier. In the villages, transformation of forests into pastures was, from the beginning, a smallholder phenomenon. Misguided policies and institutional malfunctions appeared to direct households toward deforestation. Nevertheless, environmental deterioration could not only be explained by external causes. Inside the communities, demographic pressure over land, the modification of traditional land tenure systems and the cultural adoption of cattle as a way to overcome poverty were significant factors in the relationship between colonization and forest clearance. Deforestation at Venustiano Carranza and Magallanes cannot be considered an ecologically destructive practice performed by peasants. In fact, the process reflects not only a lack of environmental awareness in national development policies, but also the intricate interaction of ecological, cultural, social and economical variables.
Ecological footprint of the Chinese population, environment and development
Authors: DONGJING CHEN , GUODONG CHENG , ZHONGMIN XU , ZHIQIANG ZHANG
Published: April 2004

The ecological footprint (EF) can be used to investigate relationships between population, environment and development. In China, the per caput EF is estimated to have increased by 83% between 1981 (0.82 ha caput-1) and 2000 (1.49 ha caput-1), to about 1.31 times China's area (including its oceanic territory), while the ecological deficit increased from 0.066 ha caput-1 in 1981 to 0.735 ha caput-1 in 2000. Over this period, the proportions of six sub-footprint types have changed considerably: the percentages of arable, fossil energy and forest land decreased from 44.8%, 41.5% and 4.1% to 27.1%, 40.1% and 3.0%, respectively; while sea, pasture and built-up land percentages increased from 3.8%, 4.4% and 1.3% to 15.2%, 12.4% and 2.2%, respectively. The production coefficients of gross domestic product (GDP) to the EF of China increased from 584 RMB ha-1 in 1981, to 1522 RMB ha-1 in 2000, reflecting an increasing efficiency in resource use. The EF correlates positively with disposable income and expenditure, which can be described by income and expenditure elasticity. Some measures are suggested to decrease the Chinese ecological deficit on the road to sustainability.
Local plant species depletion in a tropical dry deciduous forest of northern India
Authors: SAGAR R. , SINGH J.S.
Published: April 2004

The dry tropical ecosystems are among the world's most threatened, and the dry deciduous forest of northern India is being progressively converted to scrub, savannah and grasslands through industrialization, agriculture, fuelwood collection, lopping of trees for fodder and severe grazing/browsing. This habitat destruction threatens the survival of many species. This study examined the demographic instability of tree species in 3-ha permanent plots: at five sites differing in the degree of disturbance. Based on the proportion of seedlings of a species in its total population (seedling + sapling + adults), about 52% of the total 65 species exhibited local demographic instability, and at one or more sites a single individual represented 10 species. The increase in the proportion of declining species with increase in disturbance intensity indicated that local anthropogenic pressure is responsible for the depletion. Apart from stronger protection measures, it is necessary to encourage fuelwood plantations, develop village pastures and reduce livestock numbers.
Market profiles and trade in medicinal plants in the Lowveld, South Africa
Authors: BOTHA J. , WITKOWSKI E.T.F. , SHACKLETON C. M.
Published: April 2004

Rising demand for medicinal plants has led to increased pressure on wild plant populations. This, combined with shrinking habitats, means that many species in South Africa are now facing local extinction. In 1997, a study was initiated to determine the extent of trade in medicinal plants in the South African Lowveld (the low lying plains to the east of the Drakensberg escarpment), and to investigate socio-economic factors influencing trade and resource management. Trade was not as extensive in the Lowveld as in major urban markets such as Durban or the Witwatersrand (Johannesburg and surrounding towns), either in terms of the quantity, number or range of species sold, or the numbers of people relying on the trade for an income. In markets assessed in Mpumalanga Province, 176 species were identified (71% of the vernacular names encountered in the market place), representing 69 plant families. In Limpopo, 70 different species were identified (84% of the vernacular names encountered in the market place), representing 40 families. Imports were significant in Mpumalanga (33% of the plants on offer), mainly from Mozambique. A detrended correspondence analysis showed substantial differences between species traded in Mpumalanga and those sold in Limpopo. There was little variation in the species stocked by vendors in Mpumalanga, regardless of the season, the attributes of the seller, or whether business was carried out in urban or rural areas. In contrast, there was considerable variation in the stock inventories of the Limpopo traders. Despite the lower levels of local trade, increased harvesting pressure is being experienced regionally, to meet demand in metropolitan centres such as the Witwatersrand. This study showed considerable local variation and complexities in the harvesting and marketing of medicinal plants, with both a national and an international dimension. This dual spatial scale presents both opportunities and challenges in the management of these plants, which need to be addressed simultaneously, particularly with respect to research requirements and development of predictive models and capacity. Cooperation in conservation strategies and policies is required at regional, national and international levels, while ensuring that management initiatives take into account local market conditions and the socio-economic realities facing both consumers and those who depend on the trade for their livelihoods.