bluuebunny/crossref_metadata_2025 huggingface dataset:
Cross‐talk between the epidermal growth factor‐like repeats/fibronectin 6–8 repeats domains of Tenascin‐R and microglia modulates neural stem/progenitor cell proliferation and differentiation
Authors: Liao Hong , Huang Wenhui , Niu Rui , Sun Lixin , Zhang Luyong
Published: September 2007

Mounting evidence has demonstrated that the microenvironment of stem/progenitor cells plays an important role in their proliferation and commitment to their fate. However, it remains unclear how all elements, such as astrocytes, microglia, extracellular matrix molecules, soluble factors, and their cross‐talk interactions in the microenvironments, affect neural stem/progenitor cell fate. This work explored the influences of cross‐talk between Tenascin‐R (TN‐R) and microglia on neural stem/progenitor cell proliferation and differentiation. Our results show that microglia triggered by TN‐R distinct domains EGF‐like repeats (EGFL) and fibronectin 6–8 repeats (FN6–8) significantly enhanced the proliferation of neural stem/progenitor cells and also obviously induced the differentiation into neurons but not oligodendrocytes. Neurite processes of neurons generated from neural progenitor cells were promoted by both EGFL and FN6–8 domains‐activated microglia. Microglia triggered by EGFL and FN6–8 secreted brain‐derived neurotrophic factor (BDNF) and transforming growth factor‐β (TGF‐β); interestingly, FN6–8 could activate microglia to secrete nerve growth factor in addition to BDNF and TGF‐β, but EGFL domain could not. All these data implied that the cross‐talk between TN‐R distinct domains EGFL/FN6–8 and microglia promoted neural stem/progenitor cell proliferation and induced their differentiation into neurons. © 2007 Wiley‐Liss, Inc.
Effects of antipsychotic medication on muscarinic M1 receptor mRNA expression in the rat brain
Authors: Han Mei , Newell Kelly , Zavitsanou Katerina , Deng Chao , Huang Xu‐Feng
Published: September 2007

Alterations in muscarinic M1 receptor protein and mRNA expression have been revealed in post‐mortem brains of schizophrenia patients. Most patients had been treated with antipsychotics, so medication effects cannot be excluded as a possible explanation for these results. With in situ hybridization, this study investigated M1 receptor mRNA expression in rats treated with the typical antipsychotic haloperidol (0.3 mg/kg/day) and the atypical antipsychotics olanzapine (1.5 mg/kg/day) and aripiprazole (2.25 mg/kg/day) for 1 or 12 weeks. Compared with the control group, haloperidol significantly increased (∼13–21%, P < 0.05) M1 mRNA expression in the CA1, CA2, and CA3 regions of the hippocampus after both 1 and 12 weeks of treatment, and it also increased (∼17%, P < 0.01) M1 mRNA expression in the substantia nigra compacta after 1 week of treatment. Olanzapine significantly increased (14–22%, P < 0.05) M1 mRNA expression in the hippocampus (CA1, CA2, and CA3) and substantia nigra compacta after 12 weeks of treatment, but not after 1 week. Aripiprazole significantly increased (17%, P < 0.01) M1 mRNA expression in the hippocampus (CA1) after both 1 and 12 week treatments and increased (12%, P < 0.05) M1 mRNA expression in the nucleus accumbens after 1 week of treatment. Despite their different affinities for muscarinic M1 receptors, all three antipsychotic medications induced a similar trend of change in M1 mRNA expression in selected brain regions. These data suggest that the decreased M1 receptor protein and mRNA expression observed in schizophrenia patients is unlikely to be a consequence of drug treatments and implicates muscarinic M1 receptors in the pharmacotherapy of the disease. © 2007 Wiley‐Liss, Inc.
High‐frequency precipitation changes in southeastern Africa due to anthropogenic forcing
Authors: Rocha Alfredo , Melo‐Gonçalves Paulo , Marques Carlos , Ferreira Juan , Castanheira José M.
Published: September 2007

This study evaluates differences in the precipitation regime over southeastern Africa simulated by two global climate models under present (1961–1990) and future (2071–2100) conditions as a result of greenhouse gases anthropogenic forcing. In particular, the characteristics of precipitation episodes with duration of some days are compared in both simulations. Precipitation in the models is previously compared to precipitation data obtained from the ERA‐40 reanalyses and the Climate Prediction Centre (CPC), Climate Prediction Merged Analysis of Precipitation (CMAP). A precipitation episode is defined here as a period with a minimum number of consecutive days with daily precipitation above a threshold amount.

We consider a great range of episodes according to the preset threshold number of days (1–15 days) and daily precipitation amount (1–15 mm/day). For both climates, the number of episodes, their average duration and intensity are compared. The analysis is performed for both models. The results clearly show a tendency for a decrease in the number of episodes, in most of the region and for most episode categories, due to anthropogenic climate change. The duration of the episodes is reduced in the future climate for weak episode categories. For mild to intense episodes their duration is expected to increase over a small part of the region. The intensity of all episode categories is increased practically over the whole region. The spatial structure of these changes and its distribution according to the episode category are documented in this study. Copyright © 2007 Royal Meteorological Society
Characterization of the Inhibition of Enveloped Virus Infectivity by the Cationic Acrylate Polymer Eudragit E100
Authors: Alasino Roxana V. , Bianco Ismael D. , Vitali María S. , Zarzur Jorge A. , Beltramo Dante M.
Published: September 2007

The antiviral effects of the cationic acrylate polymer E100 on a panel of lipid‐enveloped viruses and the interactions involved are studied. The treatment of several common viruses with E100 induced a dose‐dependent inhibition of the infectivity of viruses below the detection limit of the assays employed. Similarly, the treatment of human sera infected with HIV or HCV reduced virus RNA plasma levels to undetectable values. This implies that Eudragit E100 can interact with enveloped viruses, even in the presence of proteins, through a mechanism that is not reversed by titration of the positively charged groups of the polymer, opening the possibility to remove viral particles with the polymer as it is eliminated.

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Design and Synthesis of Cellulose Derivatives with Antioxidant Activity
Authors: Trombino Sonia , Cassano Roberta , Bloise Ermelinda , Muzzalupo Rita , Leta Sonia , Puoci Francesco , Picci Nevio
Published: September 2007

In this study we report the synthesis and characterisation of cellulose ferulate, lipoate and α‐tocopherulate, and their ability to inhibit lipid peroxidation in rat‐liver microsomal membranes, induced in vitro by two different sources of free radicals: tert‐butyl hydroperoxide and 2,2′‐azobis‐(2‐amidinopropane). We also compared the antioxidant efficiency of the ferulate derivatives obtained through two different synthetic runs, and of a tocopherulate derivative prepared from 6‐carboxycellulose. This study showed that the designed systems, preserving the antioxidant activity of the free substrates, are more effective in protecting from tert‐butyl hydroperoxide than from 2,2′‐azobis‐(2‐amidinopropane). Moreover, the cellulose ferulate with the higher degree of substitution acted as the best antioxidant.

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New Polyester‐Based Terpyridine Macroligands and their Blue Iron(II) Complexes
Authors: Winter Andreas , Schubert Ulrich S.
Published: September 2007

A library of hydroxy‐ and amino‐functionalized Kröhnke‐type terpyridines have been used to synthesize new terpyridine end‐functionalized poly(ε‐caprolactone)s and poly(L‐lactide)s, via Sn(II)‐catalyzed ring‐opening polymerization. It has also been possible to prepare a set of metallo‐supramolecular AA homopolymers by complexation with Fe(II) metal ions. All of these complexes have been fully characterized. Stable metallo‐polymers with an intense blue color have been obtained from the quaternized macroligands. This color property might be of great interest for the design of functional supramolecular materials, with respect to color tuning and optical applications.

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RAFT Synthesis and Solution Properties of pH‐Responsive Styrenic‐Based AB Diblock Copolymers of 4‐Vinylbenzyltrimethylphosphonium Chloride with N,N‐Dimethylbenzylvinylamine
Authors: Lowe Andrew B. , Wang Ran , Tiriveedhi Venkataswarup , Butko Peter , McCormick Charles L.
Published: September 2007

The RAFT synthesis and solution properties of AB block copolymers of 4‐vinylbenzyltrimethylphosphonium chloride (TMP) and N,N‐dimethylbenzylvinylamine (DMBVA) is described. The pH‐dependent self‐assembly properties of the AB diblock copolymers were examined using of 1H NMR, DLS, and fluorescence spectroscopy. The size of the polymeric aggregates depends on the block copolymer composition/molecular mass. The self assembly is completely reversible, as predicted from the tunable hydrophilicity/hydrophobicity of the DMBVA residues. The AB diblock copolymers can be effectively locked in the self‐assembled state using a straightforward core crosslinking reaction between the tertiary amine residues of DMBVA and difunctional 1,4‐bis(bromomethyl)benzene.

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(Photo)crosslinkable Smectic LC Main‐Chain Polymers
Authors: Beyer Patrick , Braun Lydia , Zentel Rudolf
Published: September 2007

This paper presents the synthetic route to SmA LC main‐chain polymers, that can be (photo)crosslinked without solvent in the bulk phase. They are based on soluble polymalonates, in which higher ordered phases can be suppressed by copolymerization with a laterally brominated biphenyl. Two routes were developed to incorporate the crosslinkable groups into the polyester backbone. The first consists in the incorporation of phenols into the polyester. These phenols are not reactive enough to participate in the transesterification reaction used to build up the polymer, but they can be esterified afterwards with acrylates. Thermally or photochemically created radicals then start the crosslinking. The second route is based on the incorporation of benzophenone as side group. It allows a photochemical crosslinking. Crosslinked fibers (monodomains) show the potential of the smectic LC main‐chain elastomers as actuators.

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Robust Organic/Inorganic Hybrid Porous Thin Films via Breath‐Figure Method and Gelation Process
Authors: Zhang Ke , Zhang Liwei , Chen Yongming
Published: September 2007

A novel organic/inorganic hybrid honeycomb patterned porous thin film was prepared using the breath‐figure method combined with a sol‐gel process. An in situ formed gelable block copolymer, formed by mixing poly(styrene‐alt‐maleic anhydride)‐block‐polystyrene (P(St‐a‐MAn)‐b‐PS) and 3‐aminopropyltrimethoxysilane (APS), was used as the structure directing agent. The porous film produced was dipped into an acid aqueous solution to induce a sol‐gel process in the wall of film. As a result of gelation, the structure of this film transformed into a crosslinked silica oxide hybridized with PS, and this film resisted those organic solvents which were once good solvents for the copolymer precursor.

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A Hermite reproducing kernel approximation for thin‐plate analysis with sub‐domain stabilized conforming integration
Authors: Wang Dongdong , Chen Jiun‐Shyan
Published: September 2007

A Hermite reproducing kernel (RK) approximation and a sub‐domain stabilized conforming integration (SSCI) are proposed for solving thin‐plate problems in which second‐order differentiation is involved in the weak form. Although the standard RK approximation can be constructed with an arbitrary order of continuity, the proposed approximation based on both deflection and rotation variables is shown to be more effective in solving plate problems. By imposing the Kirchhoff mode reproducing conditions on deflectional and rotational degrees of freedom simultaneously, it is demonstrated that the minimum normalized support size (coverage) of kernel functions can be significantly reduced. With this proposed approximation, the Galerkin meshfree framework for thin plates is then formulated and the integration constraint for bending exactness is also derived. Subsequently, an SSCI method is developed to achieve the exact pure bending solution as well as to maintain spatial stability. Numerical examples demonstrate that the proposed formulation offers superior convergence rates, accuracy and efficiency, compared with those based on higher‐order Gauss quadrature rule. Copyright © 2007 John Wiley & Sons, Ltd.
Prenatally diagnosed fetal lung lesions with associated conotruncal heart defects: Is there a genetic association?
Authors: Hüsler Margaret R. , Wilson R. Douglas , Rychik Jack , Bebbington Michael W. , Johnson Mark P. , Mann Stephanie E. , Hedrick Holly L. , Adzick Scott
Published: September 2007

Congenital lung malformation can easily be diagnosed by prenatal ultrasound. Associated extrapulmonary malformations such as heart defects and chromosomal aberrations are rare.

Objective

The objective of this study was to describe the natural history, outcome and other associated malformations in fetuses with lung lesions and an associated heart defect.

Methods

Retrospective analysis of 4 cases of prenatally diagnosed fetal CCAMs and hybrid lesions with an associated heart defect and review of 8 cases in the literature.

Results

At a single referral center 1.9% of the fetuses with Congenital cystic adenomatoid malformation (CCAM) were diagnosed with an associated heart defect. Seven of the total 12 cases (58%) reviewed had a conotruncal heart abnormality. Chromosomal abnormalities were found in 5 (42%) of the cases.

Conclusion

This retrospective review shows that karyotyping in fetal lung lesions with an associated heart defect or isolated large lung lesions is indicated. It also suggests that there is a subpopulation of fetuses with CCAMs who have conotruncal heart defects. This finding may suggest a common genetic background. Copyright © 2007 John Wiley & Sons, Ltd.
Comparison of potential solar electricity output from fixed‐inclined and two‐axis tracking photovoltaic modules in Europe
Authors: Huld Thomas , Šúri Marcel , Dunlop Ewan D.
Published: September 2007

We present an approach to determine the potential energy gains of flat plate non‐concentrating photovoltaic systems for the case of two‐axis tracking and two inclination angles with fixed orientation (assuming biannual adjustment) compared to the configuration of single fixed optimum angle. The calculation is based on the Photovoltaic Geographic Information System (PVGIS), which integrates modelling tools with the pan‐European solar radiation database. The results indicate that in the case of a PV system with two seasonal inclination angles, the maximum yearly gains, compared to the single fixed optimum angle, do not exceed 60–70 kWh per kWp in the Mediterranean region, while in the Baltic and North Sea regions this configuration gives less than 20 kWh extra. For the case of two‐axis tracking, the relative energy gain compared to single fixed optimum angle is highest in the Northern latitudes but the absolute gain is much higher in the South. Typical yearly gains in Portugal and the Mediterranean region are in the range of 400–600 kWh per kWp. The smallest absolute increase is found in the Northwest and Central Europe including the British Isles, where it is lower than 250 kWh per kWp. For crystalline silicon we also investigate the effects of temperature and shallow‐angle reflectivity on the comparison between fixed and tracking systems. While both effects reduce the overall energy output, the temperature degradation is stronger for tracking systems while the reflectivity reduces output more for fixed systems. The combined effect is almost equal for fixed and two‐axis tracking systems. Copyright © 2007 John Wiley & Sons, Ltd.
Silicon nitride coating and crucible—effects of using upgraded materials in the casting of multicrystalline silicon ingots
Authors: Olsen E. , Øvrelid E. J.
Published: September 2007

A method for removal of metallic contaminants from commercial Si3N4‐powders has been developed. The method is based on acid leaching and shows promising results. Analyses show that the content of both intermetallic compunds as Fe, Ti and Al as well as O are significantly reduced. Clean, synthetic fused silica crucibles have been used along with normal sintered ones based on natural quartz. The crucibles were coated with normal, commercial silicon nitride powder and with purified Si3N4in a cleanest possible environment. The crucibles were then used as vessels for directional solidification of multicrystalline silicon in a pilot scale furnace. The average lifetime of minority charge carriers in the cast silicon was determined by quasi steady state photoconductance (QSSPC) from the bottom to the top of the ingots. These varied in a systematic way, so that the materials cast in the pure environment had significantly higher values than the materials cast with conventional coating‐ and crucible materials. The maximum values for the lifetimes in the individual ingots varied from 7 to 135 µs. Copyright © 2007 John Wiley & Sons, Ltd.
Analyses of intricate kinetics of the serum proteome during and after colon surgery by protein expression time series
Authors: Roelofsen Han , Alvarez‐Llamas Gloria , Dijkstra Martijn , Breitling Rainer , Havenga Klaas , Bijzet Johan , Zandbergen Wouter , de Vries Marcel P. , Ploeg Rutger J. , Vonk Roel J.
Published: September 2007

Monitoring changes in serum protein expression in response to acute events such as trauma, infection or drug intervention may reveal key proteins of great value in predicting recovery or treatment response. Concerted actions of many proteins are expected. Proteins sharing similar expression changes may function in the same physiological process. As a model we analyzed expression changes in serum of colon cancer patients, before, during, and after laparoscopic colon resection. Eight samples were taken from each of four patients before, during, and up to 5 days after surgery. Total serum and a low molecular weight fraction were analyzed by SELDI‐TOF‐MS. In total 146 masses were detected. A principal components analysis (PCA) illustrates the temporal variation in the postsurgery proteome. Time series for each mass could be clustered into four distinct groups based on similarity in expression pattern. Two masses of 11.4 and 11.6 kDa, part of a slow response cluster, were identified as forms of the acute phase protein serum amyloid A (SAA). Fourteen more proteins belong to this cluster and may also function in acute phase response. We present an approach to analyze temporal variation in the proteome. This approach may be useful to evaluate surgical, nutritional, and pharmacological interventions.
Global proteomic profiling of native outer membrane vesicles derived from Escherichia coli
Authors: Lee Eun‐Young , Bang Joo Young , Park Gun Wook , Choi Dong‐Sic , Kang Ji Seoun , Kim Hyun‐Jung , Park Kyong‐Su , Lee Jeong‐Ok , Kim Yoon‐Keun , Kwon Kyung‐Hoon , Kim Kwang‐Pyo , Gho Yong Song
Published: September 2007

Gram‐negative bacteria constitutively secrete native outer membrane vesicles (OMVs) into the extracellular milieu. Although recent progress in this area has revealed that OMVs are essential for bacterial survival and pathogenesis, the mechanism of vesicle formation and the biological roles of OMVs have not been clearly defined. Using a proteomics approach, we identified 141 protein components of Escherichia coli‐derived native OMVs with high confidence; two separate analyses yielded identifications of 104 and 117 proteins, respectively, with 80 proteins overlapping between the two trials. In the group of identified proteins, the outer membrane proteins were highly enriched, whereas inner membrane proteins were lacking, suggesting that a specific sorting mechanism for vesicular proteins exists. We also identified proteins involved in vesicle formation, the removal of toxic compounds and attacking phage, and the elimination of competing organisms, as well as those involved in facilitating the transfer of genetic material and protein to other bacteria, targeting host cells, and modulating host immune responses. This study provides a global view of native bacterial OMVs. This information will help us not only to elucidate the biogenesis and functions of OMV from nonpathogenic and pathogenic bacteria but also to develop vaccines and antibiotics effective against pathogenic strains.
Effect of pendent oxyethylene moieties on the properties of aromatic polyisophthalamides
Authors: Ferreiro Juan J. , de la Campa José G. , Lozano Angel E. , de Abajo Javier , Preston Jack
Published: September 2007

Twelve novel polyisophthalamides containing short sequences of oxyethylene as pendent substituents were synthesized by the reaction of three aromatic diamine monomers and four novel diacid monomers containing pendent oxyethylene units. Two of the diacid monomers were derived from 5‐hydroxyisophthalic acid and the other two diacid monomers were derived from 5‐aminoisophthalic acid. The polymers were prepared in high yield and high molecular weight by the phosphorylation method of polycondensation. All of the polymers were soluble in organic aprotic solvents at room temperature and gave creasable films by casting from solution. The mechanical properties of the films were reasonably good, with tensile strengths in the range of 70–100 MPa and moduli around 2.5 GPa. However, the presence of the oxyethylene side sequences greatly diminished the thermal resistance and the glass transition temperatures of the present polymers compared with wholly aromatic polyisophthalamides. A study was also made on the effect of the chemical composition on water uptake. © 2007 Wiley Periodicals, Inc. J Polym Sci Part A: Polym Chem 45:4671–4683, 2007
Lattice simulations of cotranslational folding of single domain proteins
Authors: Wang Peiyu , Klimov Dmitri K.
Published: September 2007

We use lattice protein models and Monte Carlo simulations to study cotranslational folding of small single domain proteins. We show that the assembly of native structure begins during late extrusion stages, but final formation of native state occurs during de novo folding, when all residues are extruded. There are three main results in our study. First, for the sequences displaying two‐state refolding mechanism de novo cotranslational folding pathway differs from that sampled in in vitro refolding. The change in folding pathways is due to partial assembly of native interactions during extrusion that results in different starting conditions for in vitro refolding and for de novo cotranslational folding. For small single domain proteins cotranslational folding is slower than in vitro refolding, but is generally fast enough to be completed before the release from a ribosome. Second, we found that until final stages of biosynthesis cotranslational folding is essentially equilibrium. This observation is explained by low stability of structured states for partially extruded chains. Finally, our data suggest that the proteins, which refold in vitro slowly via intermediates, complete their de novo folding after the release from a ribosome. Comparison of our lattice cotranslational simulations with recent experimental and computational studies is discussed. Proteins 2008. © 2007 Wiley‐Liss, Inc.
New insight into long‐range nonadditivity within protein double‐mutant cycles
Authors: Istomin Andrei Y. , Gromiha M. Michael , Vorov Oleg K. , Jacobs Donald J. , Livesay Dennis R.
Published: September 2007

Additivity principles in chemistry, biochemistry, and biophysics have been used extensively for decades. Nevertheless, it is well known that additivity frequently breaks down in complex biomacromolecules. Nonadditivity within protein double mutant free energy cycles of spatially close residue pairs is a generally well‐understood phenomenon, whereas a robust description of nonadditivity extending over large distances remains to be developed. Here, we test the hypothesis that the mutational effects tend to be nonadditive if two structurally well‐separated mutated residues belong to the same rigid cluster within the wild type protein, and additive if they are located within different clusters. We find the hypothesis to be statistically significant with P‐values that range from 10−5 to 10−6. To the best of our knowledge, this result represents the first demonstration of a statistically significant preponderance for nonadditivity over long distances. These findings provide new insight into the origins of long‐range nonadditivity in double mutant cycles, which complements the conventional wisdom that nonadditivity arises in double mutations involving contacting residues. Consequently, these results should have far‐reaching implications for a proper understanding of protein stability, structure/function analyses, and protein design. Proteins 2008. © 2007 Wiley‐Liss, Inc.
Docking of protein molecular surfaces with evolutionary trace analysis
Authors: Kanamori Eiji , Murakami Yoichi , Tsuchiya Yuko , Standley Daron M. , Nakamura Haruki , Kinoshita Kengo
Published: September 2007

We have developed a new method to predict protein– protein complexes based on the shape complementarity of the molecular surfaces, along with sequence conservation obtained by evolutionary trace (ET) analysis. The docking is achieved by optimization of an object function that evaluates the degree of shape complementarity weighted by the conservation of the interacting residues. The optimization is carried out using a genetic algorithm in combination with Monte Carlo sampling. We applied this method to CAPRI targets and evaluated the performance systematically. Consequently, our method could achieve native‐like predictions in several cases. In addition, we have analyzed the feasibility of the ET method for docking simulations, and found that the conservation information was useful only in a limited category of proteins (signal related proteins and enzymes). Proteins 2007. © 2007 Wiley‐Liss, Inc.
Docking without docking: ISEARCH—prediction of interactions using known interfaces
Authors: Günther Stefan , May Patrick , Hoppe Andreas , Frömmel Cornelius , Preissner Robert
Published: September 2007

The increasing number of solved protein structures provides a solid number of interfaces, if protein–protein interactions, domain–domain contacts, and contacts between biological units are taken into account. An interface library gives us the opportunity to identify surface regions on a target molecule that are similar by local structure and residue composition. If both unbound components of a possible protein complex exhibit structural similarities to a known interface, the unbound structures can be superposed onto the known interfaces. The approach is accompanied by two mathematical problems. Protein surfaces have to be quickly screened by thousands of patches, and similarity has to be evaluated by a suitable scoring scheme. The used algorithm (NeedleHaystack) identifies similar patches within minutes. Structurally related sites are recognized even if only parts of the template patches are structurally related to the interface region. A successful prediction of the protein complex depends on a suitable template of the library. However, the performed tests indicate that interaction sites are identified even if the similarity is very low. The approach complements existing ab initio methods and provides valuable results on standard benchmark sets. Proteins 2007. © 2007 Wiley‐Liss, Inc.
The performance of ZDOCK and ZRANK in rounds 6–11 of CAPRI
Authors: Wiehe Kevin , Pierce Brian , Tong Wei Wei , Hwang Howook , Mintseris Julian , Weng Zhiping
Published: September 2007

We present an evaluation of our protein–protein docking approach using the ZDOCK and ZRANK algorithms, in combination with structural clustering and filtering, utilizing biological data in Rounds 6–11 of the CAPRI docking experiment. We achieved at least one prediction of acceptable accuracy for five of six targets submitted. In addition, two targets resulted in medium‐accuracy predictions. In the new scoring portion of the CAPRI exercise, we were able to attain at least one acceptable prediction for the three targets submitted and achieved three medium‐accuracy predictions for Target 26. Scoring was performed using ZRANK, a new algorithm for reranking initial‐stage docking predictions using a weighted energy function and no structural refinement. Here we outline a practical and successful docking strategy, given limited prior biological knowledge of the complex to be predicted. Proteins 2007. © 2007 Wiley‐Liss, Inc.
A holistic approach to protein docking
Authors: Qin Sanbo , Zhou Huan‐Xiang
Published: September 2007

Docking of unbound protein structures into a complex has gained significant progress in recent years, but nonetheless still poses a great challenge. We have pursued a holistic approach to docking which brings together effective methods at different stages. First, protein‐protein interaction sites are predicted or obtained from experimental studies in the literature. Interface prediction/experimental data are then used to guide the generation of docked poses or to rank docked poses generated from an unbiased search. Finally, selected models are refined by lengthy molecular dynamics (MD) simulations in explicit water. For CAPRI target T27, we used information on interaction sites as input to drive docking and as a filter to rank docked poses. Lead candidates were then clustered according to RMSD among them. From the clustering, 10 models were selected and subject to refinement by MD simulations. Our Model 7 is rated number one among all submissions according to L_rmsd. Six of our other submissions are rated acceptable. As scorer, eight of our submissions are rated acceptable. Proteins 2007. © 2007 Wiley‐Liss, Inc.
A theory for the spinup of tropical depressions
Authors: Raymond D. J. , Sessions S. L. , Fuchs Ž.
Published: September 2007

Recent advances in our understanding of the physics of precipitation over tropical oceans is married with vorticity dynamics to produce a simple theory for the development or non‐development of tropical depressions. This early phase of tropical cyclogenesis is perhaps the least understood part of the whole process. The theory predicts a finite amplitude threshold for intensification, with weaker disturbances decaying. Furthermore, only disturbances with radii larger than a critical value develop. Rough estimates of this critical radius place it near 1600 km, though better estimates of various parameters could change this value significantly. Copyright © 2007 Royal Meteorological Society
Role of nocturnal turbulence and advection in the formation of shallow cumulus over land
Authors: Vilà‐Guerau de Arellano Jordi
Published: September 2007

Shallow cumuli over land are normally studied from a diurnal perspective. However, the thermodynamic vertical profiles of the morning transition may play an important role in setting up favourable conditions for the formation of shallow cumuli. In turn, these profiles are highly dependent on the evolution of the nocturnal boundary characteristics and of their layer aloft.

By analysing thermodynamic profiles measured by radiosondes launched every three hours at four different stations, we are able to determine how horizontal advection and turbulent mixing modify the atmospheric stability and the differences in potential temperature and specific humidity at the interface between the atmospheric boundary layer and the layer above it. Two consecutive nights are studied. They show very similar boundary‐layer development; but variations in the layer aloft by a low‐level‐jet advection event during the second night, and intense turbulent mechanical mixing, lead to the development of two diurnal boundary layers with very different characteristics: the first one clear, the second cloudy.

To complete the observational study, we perform a sensitivity analysis using a mixed‐layer model to examine the role of the morning initial conditions in the formation of shallow cumuli over land. The complexity and subtlety of the observed situation—namely, the interaction of a strongly‐mixed nocturnal boundary layer and horizontal advection—make this case suitable for testing the capacity of mesoscale models to reproduce cloudy boundary layers that are largely dependent on conditions during the previous night. Copyright © 2007 Royal Meteorological Society
Prenatal ultrasound detection of talipes equinovarus in a non‐selected population of 49 314 deliveries in Norway
Authors: Offerdal K. , Jebens N. , Blaas H. G. K. , Eik‐Nes S. H.
Published: September 2007

Objectives

To evaluate prenatal ultrasound detection of talipes equinovarus (TEV) in a large non‐selected population and to study trends in detection rates over time, as well as the prevalence and outcome of isolated TEV and TEV with associated anomalies.

Methods

All cases of pre‐ or postnatally diagnosed TEV between 1987 and 2004 within a non‐selected population of 49 314 deliveries were investigated. The study period was divided into three 6‐year periods to shed light on changes in detection rates and other aspects of the anomaly over time.

Results

A total of 113 cases of TEV were registered during the 18‐year period, of which 49% had isolated TEV and 51% had associated anomalies. During the three 6‐year periods, there was a significant improvement (P = 0.006) in the overall detection of TEV from 43% to 67% and 77%, respectively. The detection rate for isolated TEV increased over time. Isolated bilateral TEV cases were detected more than twice as often as isolated unilateral TEV. The three largest groups of associated anomalies were syndromes/sequences (26%), chromosome aberrations (26%), and musculoskeletal disorders (24%). Pregnancies were terminated in 23% of the cases, all with severe additional anomalies. Treatment of TEV included surgery in 86% of the cases.

Conclusion

The overall detection rate of TEV improved significantly over time. Prenatal detection was higher when TEV was bilateral and when other associated anomalies were present. Parents should be informed that, in suspected isolated TEV, associated anomalies might remain undetected prenatally. Copyright © 2007 ISUOG. Published by John Wiley & Sons, Ltd.
Modeling the effect of fire on the demography ofDicerandra frutescensssp.frutescens(Lamiaceae), an endangered plant endemic to Florida scrub
Authors: Evans Margaret E. K. , Holsinger Kent E. , Menges Eric S.
Published: September 2007

Managing populations, either for conservation, harvesting, or control, requires a mechanistic or semi‐mechanistic understanding of population dynamics. Here, we investigate how time‐since‐fire affects demographic transitions in an endangered plant,Dicerandra frutescensssp.frutescens(Lamiaceae), which is specialized to gaps created by fire. We used a hierarchical Bayesian model to estimate transition probabilities (i.e., the elements of population projection matrices) as a function of time‐since‐fire and random effects, from 13 years of data on marked individuals in five populations. Using a standard Bayesian criterion to compare models, we find that death becomes increasingly probable and progression increasingly improbable with time‐since‐fire. The magnitude of some of the time‐since‐fire effects is substantial: death is 3–5 times more likely for flowering plants >6 years versus 3–6 years post‐fire, 3‐step progression is almost 7 times less likely, and large flowering plants are more than 6 times more likely to stop flowering. These insights inspire new hypotheses about the underlying cause of decline with time‐since‐fire, and how it can be managed. Our approach can be used by others who wish to model the effect of an exogenous factor on demography, while rigorously accounting for uncertainty and variability.
Kinetics of Palm Oil Methanolysis
Authors: Narváez P. C. , Rincón S. M. , Sánchez F. J.
Published: September 2007

A kinetics study of palm oil methanolysis was conducted at three different temperatures and three different concentrations of catalyst, sodium hydroxide, keeping constant the molar ratio of methanol to oil and the rotational speed of the impeller (6:1 and 400 rpm). The maximum conversion of palm oil and productivity to methyl esters were obtained at 60 °C and 1 wt% of NaOH based on palm oil, and they were 100 and 97.6%, respectively. The statistical analysis of conversions of palm oil and productivities to methyl esters as functions of temperature and concentration of catalyst, after 80 min of reaction, allowed them to fit second order polynomial equations, which adequately describe the experimental behavior. The experimental data appear to be a good fit into a second order kinetic model for the three stepwise reactions, and the reaction rate constants and the activation energies were determined. In this article we present the kinetic constant and activation energies for the experiments with 0.2% wt of NaOH. The effect of molar ratio on the concentration of products was investigated, while the temperature (55 °C), the concentration of catalyst (0.60 wt% of NaOH), and the rotational speed (400 rpm), were held constant. The results showed that the conversion and the productivity increased due to methanol excess, and were higher for the reactions with a molar ratio of 6:1.
Intramuscular administration of morphine reduces mustard oil‐induced craniofacial muscle pain behavior in lightly anesthetized rats
Authors: Han Seung R. , Lee Min K. , Lim Koang H. , Yang Gwi Y. , Jeon Hye J. , Ju Jin S. , Yoon Young W. , Kim Sung K. , Ahn Dong K.
Published: September 2007

The present study investigated the role of peripheral opioid receptors in mustard oil‐induced nociceptive behavior and inflammation in the masseter muscles of lightly anesthetized rats. Experiments were carried out on male Sprague–Dawley rats weighing between 300 and 400g. After initial anesthesia with sodium pentobarbital (40mg/kg, i.p.), one femoral vein was cannulated and connected to an infusion pump for the intravenous infusion of sodium pentobarbital. The rate of infusion was adjusted to provide a constant level of anesthesia. Mustard oil (MO, 30μl) was injected into the mid‐region of the left masseter muscle via a 30‐gauge needle. Intramuscularly‐administered morphine significantly reduced shaking behavior but not MO‐induced inflammation. Intramuscular pretreatment with naloxone, an opioid receptor antagonist, reversed antinociception produced by intramuscularly‐administered morphine, while intracisternal administration of naloxone did not affect the antinociception of peripheral morphine. Pretreatment withd‐Pen‐Cys‐Tyr‐d‐Trp‐Orn‐Thr‐Pen‐Thr‐NH2 (CTOP), a μ opioid receptor antagonist, but not naltrindole, a δ opioid receptor antagonist, nor norbinaltorphimine (nor‐BNI), a κ opioid receptor antagonist, reversed intramuscularly‐administered morphine‐induced antinociception. These results indicate that intramuscularly‐administered morphine produces antinociception in craniofacial muscle nociception and that this intramuscularly‐administered morphine‐induced antinociception is mediated by a peripheral μ opioid receptor. Our observations further support the clinical approach of administering opioids in the periphery for the treatment of craniofacial muscle nociception.
PrrC, a Sco homologue from Rhodobacter sphaeroides, possesses thiol‐disulfide oxidoreductase activity
Authors: Badrick Alison C. , Hamilton Amanda J. , Bernhardt Paul V. , Jones Christopher E. , Kappler Ulrike , Jennings Michael P. , McEwan Alastair G.
Published: September 2007

PrrC is a Sco homologue in Rhodobacter sphaeroides that is associated with PrrBA, a two‐component signal transduction system that induces photosynthesis gene expression in response to a decrease in oxygen tension. Although Sco proteins have been shown to bind copper the observation that they are structurally‐related to thioredoxins suggested that they might possess thiol‐disulfide oxidoreductase activity. Our results show that PrrC reduces Cu2+ to Cu+ and possesses disulfide reductase activity. These results indicate that some bacterial Sco proteins may have biochemical properties that are distinct from those of mitochondrial Sco proteins.
Gene expression profiling identifies Hes6 as a transcriptional target of ATOH1 in cochlear hair cells
Authors: Scheffer Deborah , Sage Cyrille , Corey David P. , Pingault Veronique
Published: September 2007

ATOH1 is a basic Helix‐Loop‐Helix transcription factor crucial for hair cell (HC) differentiation in the inner ear. In order to identify ATOH1 target genes, we performed a genome‐wide expression profiling analysis in cells expressing ATOH1 under the control of a tetracycline‐off system and found that HES6 expression is induced by ATOH1. We performed in situ hybridisation and showed that the rise and fall of Hes6 expression closely follow that of Atoh1 in cochlear HC. Moreover, electrophoretic mobility shift assays and luciferase assays show that ATOH1 activates HES6 transcription through binding to three clustered E boxes of its promoter.
Catalytic role of conserved HQGE motif in the CE6 carbohydrate esterase family
Authors: López-Cortés Nieves , Reyes-Duarte Dolores , Beloqui Ana , Polaina Julio , Ghazi Iraj , Golyshina Olga V. , Ballesteros Antonio , Golyshin Peter N. , Ferrer Manuel
Published: September 2007

An acetylxylan esterase (R.44), belonging to the carbohydrate esterase family 6 (CE6), retrieved from bovine rumen metagenome was analyzed. Molecular modelling and site‐directed mutagenesis indicated that the enzyme possesses a catalytic triad formed by Ser14, His231 and Glu152. The catalytic Ser and His have been identified in highly conserved sequences GQSX and DXXH in the CE6 family, respectively, and the active‐site glutamate was part of a highly conserved sequence HQGE. This motif is situated near to the so‐called Block III in the CE6 family and its role in catalysis has not been identified so far.
CpG/CpNpG motifs in the coding region are preferred sites for mutagenesis in the breast cancer susceptibility genes
Authors: Cheung Lydia W.T. , Lee Yiu Fai , Ng Tuen Wai , Ching Wai Ki , Khoo Ui Soon , Ng Michael K.P. , Wong Alice S.T.
Published: September 2007

The range of BRCA1/BRCA2 gene mutations is diverse and the mechanism accounting for this heterogeneity is obscure. To gain insight into the endogenous mutational mechanisms involved, we evaluated the association of specific sequences (i.e. CpG/CpNpG motifs, homonucleotides, short repeats) and mutations within the genes. We classified 1337 published mutations in BRCA1 (1765 BRCA2 mutations) for each specific sequence, and employed computer simulation combined with mathematical calculations to estimate the true underlying tendency of mutation occurrence. Interestingly, we found no mutational bias to homonucleotides and repeats in deletions/insertions and substitutions but striking bias to CpG/CpNpG in substitutions in both genes. This suggests that methylation‐dependent DNA alterations would be a major mechanism for mutagenesis.
Search for a dextransucrase minimal motif involved in dextran binding
Authors: Suwannarangsee Surisa , Moulis Claire , Potocki-Veronese Gabrielle , Monsan Pierre , Remaud-Simeon Magali , Chulalaksananukul Warawut
Published: September 2007

Fourteen truncated forms of Leuconostoc mesenteroides NRRL B512‐F dextransucrase, involving N‐, C‐ or N‐ plus C‐terminal domain truncations were tested for their ability to bind dextrans. The shortest fragment (14 kDa molecular weight) that still exhibited a strong interaction with dextran was localized between amino acids N1397 and A1527 of the C‐terminal domain (GBD‐7) and consists of six YG repeats. With a dissociation constant K
d of 2.8 × 10−9
M, this motif shows a very high affinity for isomaltohexaose and longer dextrans, supporting the proposed role of GBD in polymer formation. The potential application of GBD‐7 as an affinity tag onto cheap resins like Sephacryl® S300HR for rapid purification was evaluated and is discussed.
Sex mediates dopamine and adrenergic receptor expression in adult rats exposed prenatally to cocaine
Authors: Ferris Mark J. , Mactutus Charles F. , Silvers Janelle M. , Hasselrot Ulla , Beaudin Stephane A. , Strupp Barbara J. , Booze Rosemarie M.
Published: September 2007

The extent of catecholaminergic receptor and respective behavioral alterations associated with prenatal cocaine exposure varies according to exogenous factors such as the amount, frequency, and route of maternal exposure, as well as endogenous factors such as specific brain regions under consideration and sex of the species. The goal of the current study was to use autoradiography to delineate possible moderators of dopaminergic and adrenergic receptor expression in adult rat offspring exposed to cocaine in utero. The current study demonstrated sex‐dependent D1 receptor, α2, and noradrenergic transporter binding alterations in prelimbic, hippocampus, and anterior cingulate regions of adult rat brains exposed to cocaine during gestational days 8–21. Of further interest was the lack of alterations in the nucleus accumbens for nearly all receptors/transporters investigated, as well as the lack of alterations in D3 receptor binding in nearly all of the regions investigated (nucleus accumbens, prelimbic region, hippocampus, and cingulate gyrus).

Thus, the current investigation demonstrated persistent receptor and transporter alterations that extend well into adulthood as a result of cocaine exposure in utero. Furthermore, the demonstration that sex played a mediating role in prenatal cocaine‐induced, aberrant receptor/transporter expression is of primary importance for future studies that seek to control for sex in either design or analysis.
Genetic and pharmacologic manipulation of oxidative stress after neonatal hypoxia‐ischemia
Authors: Sheldon R. Ann , Christen Stephan , Ferriero Donna M.
Published: September 2007

Oxidative stress is a critical component of the injury response to hypoxia‐ischemia (HI) in the neonatal brain, and this response is unique and at times paradoxical to that seen in the mature brain. Previously, we showed that copper‐zinc superoxide‐dismutase (SOD1) over‐expression is not beneficial to the neonatal mouse brain with HI injury, unlike the adult brain with ischemic injury. However, glutathione peroxidase 1 (GPx1) over‐expression is protective to the neonatal mouse brain with HI injury. To further test the hypothesis that an adequate supply of GPx is critical to protection from HI injury, we crossed SOD1 over‐expressing mice (hSOD‐tg) with GPx1 over‐expressing mice (hGPx‐tg). Resulting litters contained wild‐type (wt), hGPx‐tg, hSOD‐tg and hybrid hGPx‐tg/hSOD‐tg pups, which were subjected to HI at P7. Confirming previous results, the hGPx‐tg mice had reduced injury compared to both Wt and hSOD‐tg littermates. Neonatal mice over‐expressing both GPx1 and SOD1 also had less injury compared to wt or hSOD‐tg alone. A result of oxidative stress after neonatal HI is a decrease in the concentration of reduced (i.e. antioxidant‐active) glutathione (GSH). In this study, we tested the effect of systemic administration of α‐lipoic acid on levels of GSH in the cortex after HI. Although GSH levels were restored by 24 h after HI, injury was not reduced compared to vehicle‐treated mice. We also tested two other pharmacological approaches to reducing oxidative stress in hSOD‐tg and wild‐type littermates. Both the specific inhibitor of neuronal nitric oxide synthase, 7‐nitroindazole (7NI), and the spin‐trapping agent alpha‐phenyl‐tert‐butyl‐nitrone (PBN) did not reduce HI injury, however. Taken together, these results imply that H2O2 is a critical component of neonatal HI injury, and GPx1 plays an important role in the defense against this H2O2 and is thereby neuroprotective.