bluuebunny/crossref_metadata_2025 huggingface dataset:
Molecular identification of a major quantitative trait locus,
qLTG3–1
, controlling low-temperature germinability in rice
Authors: Fujino Kenji , Sekiguchi Hiroshi , Matsuda Yasuyuki , Sugimoto Kazuhiko , Ono Kazuko , Yano Masahiro
Published: August 2008

Tolerance to abiotic stress is an important agronomic trait in crops and is controlled by many genes, which are called quantitative trait loci (QTLs). Identification of these QTLs will contribute not only to the understanding of plant biology but also for plant breeding, to achieve stable crop production around the world. Previously, we mapped three QTLs controlling low-temperature tolerance at the germination stage (called low-temperature germinability). To understand the molecular basis of one of these QTLs,
qLTG3–1
(quantitative trait locus for low-temperature germinability on chromosome 3), map-based cloning was performed, and this QTL was shown to be encoded by a protein of unknown function. The QTL
qLTG3–1
is strongly expressed in the embryo during seed germination. Before and during seed germination, specific localization of beta-glucuronidase staining in the tissues covering the embryo, which involved the epiblast covering the coleoptile and the aleurone layer of the seed coat, was observed. Expression of
qLTG3–1
was tightly associated with vacuolation of the tissues covering the embryo. This may cause tissue weakening, resulting in reduction of the mechanical resistance to the growth potential of the coleoptile. These phenomena are quite similar to the model system of seed germination presented by dicot plants, suggesting that this model may be conserved in both dicot and monocot plants.
Mutant dynein (Loa) triggers proprioceptive axon loss that extends survival only in the SOD1 ALS model with highest motor neuron death
Authors: Ilieva Hristelina S. , Yamanaka Koji , Malkmus Shelle , Kakinohana Osamu , Yaksh Tony , Marsala Martin , Cleveland Don W.
Published: August 2008

Dominant mutations in cytoplasmic dynein (Loa or Cra) have been reported to provoke selective, age-dependent killing of motor neurons, while paradoxically slowing degeneration and death of motor neurons in one mouse model of an inherited form of ALS. Examination of Loa animals reveals no degeneration of large caliber α-motor neurons beyond an age-dependent loss (initiating only after 18 months) that was comparable in Loa and wild-type littermates. Absence of Loa-mediated α-motor neuron loss contrasted with dramatic, sustained, mutant dynein-mediated postnatal loss of lumbar proprioceptive sensory axons, accompanied by decreased excitatory glutamatergic inputs to motor neurons. In mouse models of inherited ALS caused by mutations in superoxide dismutase (SOD1), mutant dynein modestly prolonged survival in the one mouse model with the most extensive motor neuron loss (SOD
G93A
) while showing marginal (SOD
G85R
) or no (SOD
G37R
) benefit in models with higher numbers of surviving motor neurons at end stage. These findings support a noncell autonomous, excitotoxic contribution from proprioceptive sensory neurons that modestly accelerates disease onset in inherited ALS.
Erythromycin derivatives inhibit HIV-1 replication in macrophages through modulation of MAPK activity to induce small isoforms of C/EBPβ
Authors: Komuro Iwao , Sunazuka Toshiaki , Akagawa Kiyoko S. , Yokota Yasuko , Iwamoto Aikichi , Ōmura Satoshi
Published: August 2008

Macrophages (MΦs) are a major source of HIV-1 especially in patients with tuberculosis. There are MΦs that are permissive and those that restrict HIV-1. Regulation of hematopoietic cell kinase (Hck) activity and selective expression of CCAAT enhancer binding protein β (C/EBPβ) isoforms greatly contribute to determine distinct susceptibility of MΦs to HIV-1. Resistance is attributable to reduced expression of Hck and augmented expression of an inhibitory small isoform of C/EBPβ. Derivatives of erythromycin A (EMA) EM201 and EM703 inhibit the replication of HIV-1 in tissue MΦs, at posttranscriptional and translational levels. We demonstrate that EM201 and EM703 convert tissue MΦs from HIV-1 susceptible to HIV-1 resistant through down-regulation of Hck and induction of small isoforms of C/EBPβ. These drugs inhibit p38MAPK activation which is expressed only in susceptible tissue MΦs. Activated CD4+T cells stimulate the viral replication in HIV-1 resistant MΦs through down-regulation of small isoforms of C/EBPβ via activation of ERK1/2. EM201 and EM703 can inhibit the MAPK activation and inhibit the burst of viral replication produced when CD4+T cells and MΦs interact. These EM derivatives may be highly beneficial for repression of residual HIV-1 in the lymphoreticular system of HIV-1-infected patients and offer great promise for the creation of new anti-HIV drugs for the future treatment of AIDS patients.
Polyubiquitination of proliferating cell nuclear antigen by HLTF and SHPRH prevents genomic instability from stalled replication forks
Authors: Motegi Akira , Liaw Hung-Jiun , Lee Kyoo-Young , Roest Henk P. , Maas Alex , Wu Xiaoli , Moinova Helen , Markowitz Sanford D. , Ding Hao , Hoeijmakers Jan H. J. , Myung Kyungjae
Published: August 2008

Chronic stalling of DNA replication forks caused by DNA damage can lead to genomic instability. Cells have evolved lesion bypass pathways such as postreplication repair (PRR) to resolve these arrested forks. In yeast, one branch of PRR involves proliferating cell nuclear antigen (PCNA) polyubiquitination mediated by the Rad5-Ubc13-Mms2 complex that allows bypass of DNA lesion by a template-switching mechanism. Previously, we identified human SHPRH as a functional homologue of yeast Rad5 and revealed the existence ofRAD5-like pathway in human cells. Here we report the identification of HLTF as a secondRAD5homologue in human cells. HLTF, like SHPRH, shares a unique domain architecture with Rad5 and promotes lysine 63-linked polyubiquitination of PCNA. Similar to yeast Rad5, HLTF is able to interact with UBC13 and PCNA, as well as SHPRH; and the reduction of eitherSHPRHorHLTFexpression enhances spontaneous mutagenesis. Moreover,Hltf-deficient mouse embryonic fibroblasts show elevated chromosome breaks and fusions after methyl methane sulfonate treatment. Our results suggest that HLTF and SHPRH are functional homologues of yeast Rad5 that cooperatively mediate PCNA polyubiquitination and maintain genomic stability.
Dissecting the roles of MuB in Mu transposition: ATP regulation of DNA binding is not essential for target delivery
Authors: Schweidenback Caterina T. H. , Baker Tania A.
Published: August 2008

Collaboration between MuA transposase and its activator protein, MuB, is essential for properly regulated transposition. MuB activates MuA catalytic activity, selects target DNA, and stimulates transposition into the selected target site. Selection of appropriate target DNA requires ATP hydrolysis by the MuB ATPase. By fusing MuB to a site-specific DNA-binding protein, the Arc repressor, we generated a MuB variant that could select target DNA independently of ATP. This Arc-MuB fusion protein allowed us to test whether ATP binding and hydrolysis by MuB are necessary for stimulation of transposition into selected DNA, a process termed target delivery. We find that with the fusion proteins, MuB-dependent target delivery occurs efficiently under conditions where ATP hydrolysis is prevented by mutation or use of ADP. In contrast, no delivery was detected in the absence of nucleotide. These data indicate that the ATP- and MuA-regulated DNA-binding activity of MuB is not essential for target delivery but that activation of MuA by MuB strictly requires nucleotide-bound MuB. Furthermore, we find that the fusion protein directs transposition to regions of the DNA within 40–750 bp of its own binding site. Taken together, these results suggest that target delivery by MuB occurs as a consequence of the ability of MuB to stimulate MuA while simultaneously tethering MuA to a selected target DNA. This tethered-activator model provides an attractive explanation for other examples of protein-stimulated control of target site selection.
Highly efficient differentiation of hESCs to functional hepatic endoderm requires ActivinA and Wnt3a signaling
Authors: Hay David C. , Fletcher Judy , Payne Catherine , Terrace John D. , Gallagher Ronald C. J. , Snoeys Jan , Black James R. , Wojtacha Davina , Samuel Kay , Hannoun Zara , Pryde Anne , Filippi Celine , Currie Ian S. , Forbes Stuart J. , Ross James A. , Newsome Philip N. , Iredale John P.
Published: August 2008

Human embryonic stem cells (hESCs) are a valuable source of pluripotential primary cells. To date, however, their homogeneous cellular differentiation to specific cell types
in vitro
has proven difficult. Wnt signaling has been shown to play important roles in coordinating development, and we demonstrate that Wnt3a is differentially expressed at critical stages of human liver development
in vivo
. The essential role of Wnt3a in hepatocyte differentiation from hESCs is paralleled by our
in vitro
model, demonstrating the importance of a physiologic approach to cellular differentiation. Our studies provide compelling evidence that Wnt3a signaling is important for coordinated hepatocellular function
in vitro
and
in vivo
. In addition, we demonstrate that Wnt3a facilitates clonal plating of hESCs exhibiting functional hepatic differentiation. These studies represent an important step toward the use of hESC-derived hepatocytes in high-throughput metabolic analysis of human liver function.
Dipolar interaction of pyridine with isomeric butanols
Authors: Palaniappan L. , Jaafar Mohamad Suhaimi , Jafri Mohamad Zubir Mat
Published: August 2008

The net interaction energy between pyridine and isomeric forms of butanol are found experimentally from the excess values of internal pressure and free volume using ultrasonic techniques. The significance of the interaction relation is given in terms of the polar van der Waals force contribution, which is primarily dependent on statistical mixing rules. The net interaction energy, which is calculated directly from the dipole moment values, and the polarizability values are related to the energy contributions resulting from the various polar and non-polar van der Waals forces active in the interaction process. These energy contributions, which make up the total interaction energy are calculated for the interaction of the isomeric butanols with pyridine. On the basis of the results obtained, the effects of chain length and functionality of the alcohol on the interaction mechanism is discussed.
DFT and 1H NMR molecular spectroscopic studies on biologically anti-oxidant active paramagnetic lanthanide(III)-chrysin complexes
Authors: Ansari Anees A.
Published: August 2008

The interaction of trivalent lanthanide chlorides and chrysin in methanol results in formation of the complexes [Ln(chrysin)3], where Ln = La, Pr, Nd, Sm, Gd, Tb and Ho. The complexes have been characterized by elemental analyses, molar conductance, IR, UV–Vis, TGA/DTA and NMR spectroscopic studies. They behave as non-electrolytes in DMF solution. The TGA data indicated that the complexes were anhydrous. The electronic spectra of the complexes were recorded in methanol DMF and DMSO solutions. 1H NMR spectra of lanthanum, praseodymium, neodymium, samarium and gadolinium complexes have been studied in DMSO-d6. 1H NMR spectra of paramagnetic and diamagnetic complexes exhibit down-field as well as up-field shifts of chrysin resonances that shows a change in geometry during the ligand coordination to the metal ion. A theoretical study of the chrysin molecule was conducted through DFT, ab initio, and AM1 methods and this determined the coordination environment of the metal ions.
Molecular structure, atomization energy, ionization energy, electron affinity and vibrational spectrum of SiX2 (X = F, Cl, Br, I) by theoretical methods
Authors: Kinoo Farheen Shenaz , Ramasami Ponnadurai
Published: August 2008

The molecular structure, atomization energy, ionization energy, electron affinity and vibrational spectra of silicon dihalides, SiX2 (X = F, Cl, Br, I), have been obtained using theoretical methods in the gas phase. The neutral dihalides, their cations and anions have been studied in C2v symmetry. The neutral species have been considered in both the 1A1 singlet and 3B1 triplet states whereas the cations (SiX2+) and anions (SiX2−) have been considered in the 2A1 and 2B1 states, respectively. The methods used are Møller-Plesset perturbation theory (MP2), density functional theory (DFT), Gaussian-2 (G2) and complete basis set methods (CBS-4 and CBS-Q). The functional used for the DFT method is B3LYP. The basis sets used are 6-311++G(d,p) for all atoms except that 6-311G(d,p) has been used for iodine atom only. The silicon dihalides, their cations and anions have been fully optimized using MP2 and DFT methods. Single point energy computations (G2, CBS-4M and CBS-Q) have been performed except for silicon diiodide. The results obtained are in good agreement with literature although they are method dependent.
Synthesis, X-ray crystal structure, spectroscopic characterization, and thermal chemistry of trans-diaqua-bis-(2-hydroxyiminopropionato-N,O) zinc(II), trans-{(H2O)2[H3CC(=NOH)COO)]2Zn} – A precursor for nano-crystalline zincite
Authors: Bagabas Abdulaziz A. , Apblett Allen W. , Shemsi Ahsan M. , Seddigi Zaki S.
Published: August 2008

Zinc(II) 2-oximinopropionate dihydrate [Zn(PAO)2(H2O)2] was precipitated by treatment of an aqueous solution of zinc sulfate with sodium pyruvate oxime, Na(PAO)·H2O. The product was characterized by infrared spectroscopy, solid-state carbon-13 nuclear magnetic resonance spectroscopy, X-ray diffraction (XRD), and thermal gravimetric and differential thermal analyses (TGA and DTA). A stepwise decomposition pathway was observed in the TGA trace of this complex. The product produced at each step was investigated by IR, XRD, solid-state, 13C NMR, and scanning and transmission electron microscopy (SEM and TEM). The crystallite size of the zincite was measured by XRD. Surface area of the zincite was also measured. Furthermore, the structure of the Zn(PAO)2(H2O)2 complex was established for the first time by X-ray single crystal diffraction of suitable crystals obtained in aqueous medium.
The Influence of a Micropolar Fluid on Peristaltic Transport in an Annulus: Application of the Clot Model
Authors: Mekheimer Kh. S. , Elmaboud Y. Abd
Published: August 2008

A serious pathological condition is encountered when some blood constituents deposited on the blood vessels get detached from the wall, join the blood stream again and form a clot. Study of the peristaltic transport of a micropolar fluid in an annular region is investigated under low Reynolds number and long wavelength approximations. We model a small artery as a tube having a sinusoidal wave travelling down its wall and a clot model inside it. Closed form solutions are obtained for the velocity and the microrotation components, as well as the stream function, and they contain new additional parameters, namely, δ, the height of the clot, N, the coupling number and m, the micropolar parameter. The pressure rise and friction force on the inner and the outer tubes have been discussed for various values of the physical parameters of interest.
The role of attention during retrieval in working-memory span: A dual-task study
Authors: Healey M. Karl , Miyake Akira
Published: August 2008

We tested the hypothesis that retrieving target words in operation span (OSpan) involves attention-demanding processes. Participants completed the standard OSpan task and a modified version in which all equations preceded all target words. Recall took place under either full attention or easy versus hard divided-attention conditions. Recall suffered under divided attention with the recall decrement being greater for the hard secondary task. Moreover, secondary-task performance was disrupted more by the standard OSpan task than by the modified version with the hard secondary task showing the larger decrement. Finally, the time taken to start recalling the first word was considerably longer for the standard version than for the modified version. These results are consistent with the proposal that successful OSpan task performance in part involves the attention-demanding retrieval of targets from long-term memory.
Surface but not volumetric part structure mediates three-dimensional shape representation: Evidence from part–whole priming
Authors: Leek E. Charles , Reppa Irene , Rodriguez Elly , Arguin Martin
Published: August 2008

The decomposition of three-dimensional (3-D) objects into shape primitives consisting of geometric volumes is a key proposal of some theories of object recognition. It implicitly assumes that recognition involves volumetric completion—the derivation of a three-dimensional structure that comprises inferred shape properties, such as surfaces, that are not directly visible due to self-occlusion. The goal of this study was to test this claim. In Experiment 1 participants memorized novel objects and then discriminated these from previously unseen objects. Targets were preceded by primes containing a subset of object surfaces that either matched those visible in the whole objects or that could only be inferred through volumetric completion. The results showed performance benefits through priming from visible surfaces but not from inferred surfaces. In Experiment 2, we found equivalent priming for part-primes containing two visible surfaces from the same volumetric part and for primes containing one surface from each of two volumes. These results challenge the view that 3-D object recognition is mediated by shape primitives comprising geometric volumes. Instead, the results support an alternative model that proposes that 3-D shapes are represented as a non-volumetric surface-based structural description.
Rtreemix: an R package for estimating evolutionary pathways and genetic progression scores
Authors: Bogojeska Jasmina , Alexa Adrian , Altmann André , Lengauer Thomas , Rahnenführer Jörg
Published: August 2008

Summary: In genetics, many evolutionary pathways can be modeled by the ordered accumulation of permanent changes. Mixture models of mutagenetic trees have been used to describe disease progression in cancer and in HIV. In cancer, progression is modeled by the accumulation of chromosomal gains and losses in tumor cells; in HIV, the accumulation of drug resistance-associated mutations in the viral genome is known to be associated with disease progression. From such evolutionary models, genetic progression scores can be derived that assign measures for the disease state to single patients. Rtreemix is an R package for estimating mixture models of evolutionary pathways from observed cross-sectional data and for estimating associated genetic progression scores. The package also provides extended functionality for estimating confidence intervals for estimated model parameters and for evaluating the stability of the estimated evolutionary mixture models.

Availability:  Rtreemix is an R package that is freely available from the Bioconductor project at http://www.bioconductor.org and runs on Linux and Windows.

Contact:  jasmina@mpi-inf.mpg.de
Eigen-R2 for dissecting variation in high-dimensional studies
Authors: Chen Lin S. , Storey John D.
Published: August 2008

Summary: We provide a new statistical algorithm and software package called ‘eigen-R2’ for dissecting the variation of a high-dimensional biological dataset with respect to other measured variables of interest. We apply eigen-R2 to two real-life examples and compare it with simply averaging R2 over many features.

Availability: An R-package eigenR2 is available at http://www.genomine.org/eigenr2/ and will be made publicly available via Bioconductor.

Contact:  jstorey@princeton.edu

Supplementary information:  Supplementary data are available at Bioinformatics online.
Empirical profile mixture models for phylogenetic reconstruction
Authors: Si Quang Le , Gascuel Olivier , Lartillot Nicolas
Published: August 2008

Motivation: Previous studies have shown that accounting for site-specific amino acid replacement patterns using mixtures of stationary probability profiles offers a promising approach for improving the robustness of phylogenetic reconstructions in the presence of saturation. However, such profile mixture models were introduced only in a Bayesian context, and are not yet available in a maximum likelihood (ML) framework. In addition, these mixture models only perform well on large alignments, from which they can reliably learn the shapes of profiles, and their associated weights.

Results: In this work, we introduce an expectation–maximization algorithm for estimating amino acid profile mixtures from alignment databases. We apply it, learning on the HSSP database, and observe that a set of 20 profiles is enough to provide a better statistical fit than currently available empirical matrices (WAG, JTT), in particular on saturated data.

Availability: We have implemented these models into two currently available Bayesian and ML phylogenetic reconstruction programs. The two implementations, PhyloBayes, and PhyML, are freely available on our web site (http://atgc.lirmm.fr/cat). They run under Linux and MaxOSX operating systems.

Contact:  nicolas.lartillot@lirmm.fr

Supplementary information:  Supplementary data are available at Bioinformatics online.
Novel pathway compendium analysis elucidates mechanism of pro-angiogenic synthetic small molecule
Authors: Wieghaus Kristen A. , Gianchandani Erwin P. , Paige Mikell A. , Brown Milton L. , Botchwey Edward A. , Papin Jason A.
Published: August 2008

Motivation: Computational techniques have been applied to experimental datasets to identify drug mode-of-action. A shortcoming of existing approaches is the requirement of large reference databases of compound expression profiles. Here, we developed a new pathway-based compendium analysis that couples multi-timepoint, controlled microarray data for a single compound with systems-based network analysis to elucidate drug mechanism more efficiently.

Results: We applied this approach to a transcriptional regulatory footprint of phthalimide neovascular factor 1 (PNF1)—a novel synthetic small molecule that exhibits significant in vitro endothelial potency—spanning 1–48 h post-supplementation in human micro-vascular endothelial cells (HMVEC) to comprehensively interrogate PNF1 effects. We concluded that PNF1 first induces tumor necrosis factor-alpha (TNF-α) signaling pathway function which in turn affects transforming growth factor-beta (TGF-β) signaling. These results are consistent with our previous observations of PNF1-directed TGF-β signaling at 24 h, including differential regulation of TGF-β-induced matrix metalloproteinase 14 (MMP14/MT1-MMP) which is implicated in angiogenesis. Ultimately, we illustrate how our pathway-based compendium analysis more efficiently generates hypotheses for compound mechanism than existing techniques.

Availability: The microarray data generated as part of this study are available in the Gene Expression Omnibus (http://www.ncbi.nlm.nih.gov/geo/).

Contact:  botchwey@virginia.edu; papin@virginia.edu

Supplementary information:  Supplementary data are available at Bioinformatics online.
Pathogen corruption and site-directed recombination at a plant disease resistance gene cluster
Authors: Nagy Ervin D. , Bennetzen Jeffrey L.
Published: August 2008

The Pc locus of sorghum (Sorghum bicolor) determines dominant sensitivity to a host-selective toxin produced by the fungal pathogen Periconia circinata. The Pc region was cloned by a map-based approach and found to contain three tandemly repeated genes with the structures of nucleotide binding site–leucine-rich repeat (NBS–LRR) disease resistance genes. Thirteen independent Pc-to-pc mutations were analyzed, and each was found to remove all or part of the central gene of the threesome. Hence, this central gene is Pc. Most Pc-to-pc mutations were associated with unequal recombination. Eight recombination events were localized to different sites in a 560-bp region within the ∼3.7-kb NBS–LRR genes. Because any unequal recombination located within the flanking NBS–LRR genes would have removed Pc, the clustering of cross-over events within a 560-bp segment indicates that a site-directed recombination process exists that specifically targets unequal events to generate LRR diversity in NBS–LRR loci.
The consolidation of object and context recognition memory involve different regions of the temporal lobe
Authors: Balderas Israela , Rodriguez-Ortiz Carlos J. , Salgado-Tonda Paloma , Chavez-Hurtado Julio , McGaugh James L. , Bermudez-Rattoni Federico
Published: August 2008

These experiments investigated the involvement of several temporal lobe regions in consolidation of recognition memory. Anisomycin, a protein synthesis inhibitor, was infused into the hippocampus, perirhinal cortex, insular cortex, or basolateral amygdala of rats immediately after the sample phase of object or object-in-context recognition memory training. Anisomycin infused into perirhinal or insular cortices blocked long-term (24 h), but not short-term (90 min) object recognition memory. Infusions into the hippocampus or amygdala did not impair object recognition memory. Anisomycin infused into the hippocampus blocked long-term, but not short-term object-in-context recognition memory, whereas infusions administered into the perirhinal cortex, insular cortex, or amygdala did not affect object-in-context recognition memory. These results clearly indicate that distinct regions of the temporal lobe are differentially involved in long-term object and object-in-context recognition memory. Whereas perirhinal and insular cortices are required for consolidation of familiar objects, the hippocampus is necessary for consolidation of contextual information of recognition memory. Altogether, these results suggest that temporal lobe structures are differentially involved in recognition memory consolidation.
Contributions of the medial temporal lobe to declarative memory retrieval: Manipulating the amount of contextual retrieval
Authors: Tendolkar Indira , Arnold Jennifer , Petersson Karl Magnus , Weis Susanne , Brockhaus-Dumke Anke , van Eijndhoven Philip , Buitelaar Jan , Fernández Guillén
Published: August 2008

We investigated how the hippocampus and its adjacent mediotemporal structures contribute to contextual and noncontextual declarative memory retrieval by manipulating the amount of contextual information across two levels of the same contextual dimension in a source memory task. A first analysis identified medial temporal lobe (MTL) substructures mediating either contextual or noncontextual retrieval. A linearly weighted analysis elucidated which MTL substructures show a gradually increasing neural activity, depending on the amount of contextual information retrieved. A hippocampal engagement was found during both levels of source memory but not during item memory retrieval. The anterior MTL including the perirhinal cortex was only engaged during item memory retrieval by an activity decrease. Only the posterior parahippocampal cortex showed an activation increasing with the amount of contextual information retrieved. If one assumes a roughly linear relationship between the blood-oxygenation level-dependent (BOLD) signal and the associated cognitive process, our results suggest that the posterior parahippocampal cortex is involved in contextual retrieval on the basis of memory strength while the hippocampus processes representations of item-context binding. The anterior MTL including perirhinal cortex seems to be particularly engaged in familiarity-based item recognition. If one assumes departure from linearity, however, our results can also be explained by one-dimensional modulation of memory strength.
MESPEUS: a database of the geometry of metal sites in proteins
Authors: Hsin K. , Sheng Y. , Harding M. M. , Taylor P. , Walkinshaw M. D.
Published: August 2008

A database with details of the geometry of metal sites in proteins has been set up. The data are derived from metalloprotein structures that are in the Protein Data Bank [PDB; Berman, Henrick, Nakamura & Markley (2006).Nucleic Acids Res.35, D301–D303] and have been determined at 2.5 Å resolution or better. The database contains all contacts within the crystal asymmetric unit considered to be chemical bonds to any of the metals Na, Mg, K, Ca, Mn, Fe, Co, Ni, Cu or Zn. The stored information includes PDB code, crystal data, resolution of structure determination, refinement program andRfactor, protein class (from PDB header), contact distances, atom names of metal and interacting atoms as they appear in the PDB, site occupancies,Bvalues, coordination numbers, information on coordination shapes, and metal–metal distances. This may be accessed by SQL queries, or by a user-friendly web interface which searches for contacts between specified types of atoms [for example Ca and carboxylate O of aspartate, Co and imidazole Nδ of histidine] or which delivers details of all the metal sites in a specified protein. The web interface allows graphical display of the metal site, on its own or within the whole protein molecule, and may be accessed at http://eduliss.bch.ed.ac.uk/MESPEUS/. Some applications are briefly described, including a study of the characteristics of Mg sites that bind adenosine triphosphate, the derivation of an average Mg—Ophosphatedistance and some problems that arise when average bond distances with high precision are required.
{2-[(2,5-Dimethylphenyl)iminomethyl]pyridine-κ2
N,N′}diiodidozinc(II)
Authors: Talei Bavil Olyai Mohamad Reza , Dehghanpour Saeed , Hoormehr Bita , Gholami Fahimeh , Khavasi Hamid Reza
Published: August 2008

In the molecule of the title compound, [ZnI2(C14H14N2)], the Zn atom is four-coordinated in a distorted tetrahedral geometry by two N atoms of the Schiff base ligand and by two I atoms. The benzene and pyridine rings are oriented at a dihedral angle of 70.75 (3)°. The five-membered ring has an envelope conformation. There is a weak π–π interaction between benzene rings, with a centroid-to-centroid distance of 3.975 (4) Å.
Ethylenediammonium bis(5-methyl-3-oxo-2-phenyl-2,3-dihydropyrazol-1-ide): a hydrogen-bond-supported supramolecular ionic assembly
Authors: Xu Ruibo , Xu Xingyou , Wang Daqi , Yang Xujie , Wang Xin
Published: August 2008

The title compound, C2H10N2
2+·2C10H9N2O−, is composed of deprotonated 5-methyl-2-phenyl-1H-pyrazol-3(2H)-one anions (PMP−) and protonated ethylenediamine cations (H2en2+). The ethylenediammonium ion is located on a crystallographic inversion center. The dihedral angle between the phenyl and pyrazole rings is 39.73 (8)°. The two components are connected through N—H...O and N—H...N hydrogen bonds, forming an infinite three-dimensional network.
cis-Bis(butylamine-κN)bis[sulfadiazine(1−)-κ2
N,N′]copper(II) pentahydrate
Authors: Paşaoğlu Hümeyra , Kaştaş Gökhan , Heren Zerrin , Büyükgüngör Orhan
Published: August 2008

In the title compound {systematic name: cis-bis[4-amino-N-(pyrimidin-2-yl)benzenesulfonamidato-κ2
N,N′]bis(butylamine-κN)copper(II) pentahydrate}, [Cu(C10H9N4O2S)2(C4H11N)2]·5H2O or [Cu(sdz)2(ba)2]·5H2O [ba is butylamine and sdz = sulfadiazine(1−)], the copper(II) cation is six-coordinated by four N atoms of two sulfadiazine ligands and two N atoms of butylamine ligands. The copper(II) ion and one of the water molecules lie on twofold rotation axes. One of the butyl groups is disordered over two sites, with occupancies of 0.395 (8) and 0.605 (8). The geometry around the S atom is distorted tetrahedral. The crystal structure involves intermolecular N—H...N and N—H...O hydrogen bonds. N—H...N hydrogen bonds between sdz ligands lead to a sheet structure parallel to the ab plane.
S-Benzylisothiouronium nitrate
Authors: Hemalatha P. , Veeravazhuthi V.
Published: August 2008

In the crystal structure of the title compound, C8H11N2S+·NO3
−, cations and anions are linked by intermolecular N—H...O hydrogen bonds, forming one-dimensional chains along [110].
(E)-3-(2,4-Dichlorophenyl)-1-(2-thienyl)prop-2-en-1-one
Authors: Fun Hoong-Kun , Patil P. S. , Dharmaprakash S. M. , Chantrapromma Suchada , Razak Ibrahim Abdul
Published: August 2008

In the title chalcone derivative, C13H8Cl2OS, the prop-2-en-1-one unit and the thiophene and 2,4-dichlorophenyl rings are each essentially planar. The interplanar angle between the thiophene and 2,4-dichlorophenyl rings is 19.87 (6)°. Weak intramolecular C—H...O and C—H...Cl interactions involving the prop-2-en-1-one unit generate an S(5)S(5) ring motif. In the crystal structure, molecules are linked into head-to-tail zigzag chains along the a axis and adjacent chains are cross-linked. These cross-linked chains are arranged into sheets parallel to the ab plane. The crystal structure is stabilized by weak C—H...O, C—H...Cl and C—H...π interactions. A π–π interaction was also observed with a centroid–centroid distance of 3.6845 (6) Å.
(E,E)-1,5-Di-2-thienylpenta-1,4-dien-3-one
Authors: Murugavel S. , Ganesh G. , SubbiahPandi A. , Murugan Ramalingam , SrimanNarayanan S.
Published: August 2008

In the title compound, C13H10OS2, the dihedral angle between the thiophene rings is 14.3 (1)°. The molecular structure is stabilized by C—H...π interactions between a thiophene H atom and an adjacent thiophene ring, and by intermolecular C—H...O hydrogen bonds.
(±)-trans-3-Oxo-1,2,3,4,4a,9,10,10a-octahydrophenanthrene-10a-carboxylic acid: catemeric hydrogen bonding in a δ-keto acid
Authors: Davison Mark , Lalancette Roger A. , Thompson Hugh W. , Miller Alan J.
Published: August 2008

The title compound, C15H16O3, aggregates as hydrogen-bonded catemers progressing from each carboxyl to the ketone of a screw-related neighbor [O...O = 2.6675 (14) Å and O—H...O = 170°]. Two parallel centrosymmetrically related single-strand hydrogen-bonding helices proceed through the cell in the b-axis direction. The packing includes three intermolecular C—H...O=C close contacts, involving both the ketone and the carboxyl group. The structure is isomorphous with that of the previously described Δ4 α,β-unsaturated ketone.
N,N′-Bis(3-methoxybenzylidene)ethane-1,2-diamine
Authors: Fun Hoong-Kun , Mirkhani Valiollah , Vartooni Akbar Rostami
Published: August 2008

The molecule of the title bidentate Schiff base ligand, C18H20N2O2, has twofold crystallographic rotation symmetry, giving one half-molecule per asymmetric unit. It adopts a twisted E configuration with respect to the azomethine C=N bond. The imino group is coplanar with the aromatic ring. The dihedral angle between the two benzene rings is 69.52 (5)°. The methoxy group is coplanar with the benzene ring, as indicated by the C—O—C—C torsion angle of −179.56 (8)°. In the unit cell, molecules are linked together by intermolecular C—H...O hydrogen bonds, forming chains along the a axis; these chains are further stacked down the b axis by both intermolecular C—H...O and C—H...π interactions.
Ethyl 2-allylsulfanyl-4-(4-methoxyphenyl)-6-methyl-1,4-dihydropyrimidine-5-carboxylate
Authors: Nizam Mohideen M. , Rasheeth A. , Huq C. A. M. A.
Published: August 2008

In the title compound, C18H22N2O3S, the pyrimidine ring is not planar. It adopts a half-chair conformation The crystal structure is characterized by classical N—H...O and C—H...O inter- and intramolecular hydrogen bonds, respectively. The title compound exhibits a wide spectrum of biological activities.
Redetermination of olivenite from an untwinned single-crystal
Authors: Li Chen , Yang Hexiong , Downs Robert T.
Published: August 2008

The crystal structure of olivenite, ideally Cu2(AsO4)(OH) [dicopper(II) arsenate(V) hydroxide], was redetermined from an untwinned and phosphate-containing natural sample, composition Cu2(As0.92P0.08O4), from Majuba Hill (Nevada, USA). Olivenite is structurally analogous with the important rock-forming mineral andalusite, Al2OSiO4. Its structure consists of chains of edge-sharing, distorted [CuO4(OH)2] octahedra extending parallel to [001]. These chains are cross-linked by isolated AsO4 tetrahedra through corner-sharing, forming channels in which dimers of edge-sharing [CuO4(OH)] trigonal bipyramids are located. The structure is stabilized by medium to weak O—H...O hydrogen bonds. In contrast to the previous refinements from powder and single crystal X-ray data, all non-H atoms were refined with anisotropic displacement parameters and the H atom was located.
Safflorite, (Co,Ni,Fe)As2, isomorphous with marcasite
Authors: Yang Hexiong , Downs Robert T. , Eichler Carla
Published: August 2008

Safflorite, a naturally occurring cobalt-nickel-iron diarsenide (Co,Ni,Fe)As2, possesses the marcasite-type structure, with cations (M = Co + Ni + Fe) at site symmetry 2/m and As anions at m. The MAs6 octahedra share two edges, forming chains parallel to c. The chemical formula for safflorite should be expressed as (Co,Ni,Fe)As2, rather than the end-member format CoAs2, as its structure stabilization requires the simultaneous interaction of the electronic states of Co, Ni, and Fe with As2
2− dianions.
cis-Bis[2-(diphenylphosphino)benzenethiolato-κ2
P,S]palladium(II)
Authors: Fierro-Arias Jaime , Morales-Morales David , Hernández-Ortega Simón
Published: August 2008

The title compound, [Pd(C18H14PS)2], was synthesized by the reaction of (Ph2PC6H4SH) with [PdCl2(NCC6H5)2] in a 2:1 molar ratio in the presence of a slight excess of NEt3 as base in dichloromethane. The compound crystallizes with the Pd(II) atom on a twofold rotation axis. The palladium center has a slightly distorted square-planar environment, with the two P—S chelating ligands adopting a cis configuration. The present structure is a pseudo-polymorph of [Pd(C18H14PS)2]·CH2Cl2.
Ethyl 2-(2-methyl-1H-benzimidazol-1-yl)acetate
Authors: Xu Guang-Hai , Wang Wei
Published: August 2008

A new benzimidazole compound, C12H14N2O2, has been synthesized by the reaction of 2-methyl-1H-benzimidazole and ethyl 2-bromoacetate. In the crystal structure, weak intermolecular C—H...N hydrogen bonds link the molecules into chains. π...π Contacts (centroid...centroid distance = 3.713 Å) are observed. A C—H...π interaction is also present. The N—C—C—O torsion angle is 178.4 (2)°.
Quinoxalin-2-yl o-tolyl ether
Authors: Hassan Nor Duha , Tajuddin Hairul Anuar , Abdullah Zanariah , Ng Seik Weng
Published: August 2008

The dihedral angle between the two aromatic ring systems in the title compound, C15H12N2O, is 85.9 (1)°; The angle at the O atom is widened to 118.2 (2)°. The quinoxalinyloxy part of the molecule lies on a mirror plane and the tolyl group is disordered over two positions about the mirror plane.
1-[5-(3,4-Dichlorophenyl)-3-(2-naphthyl)-4,5-dihydropyrazol-1-yl]ethanone
Authors: Lu Zhi-Ke , Li Shen , Feng Yan
Published: August 2008

In the title compound, C21H16Cl2N2O, the central pyrazoline ring makes dihedral angles of 90.1 (3) and 7.8 (3)°, with the pendant benzene ring and naphthalene ring system, respectively. In the crystal structure, weak C—H...O interactions lead to chains of molecules.
4-Methoxy-2-[(E)-(phenylimino)methyl]phenol
Authors: Uçan Selma , Öztürk Aslı , Sarıkavaklı Nursabah , Hökelek Tuncer
Published: August 2008

In the molecule of the title compound, C14H13NO2, the two aromatic rings are oriented at a dihedral angle of 0.78 (20)°; with the exception of two methyl H atoms the molecule is essentially planar. The intramolecular O—H...N hydrogen bond results in the formation of a non-planar, six-membered ring, which adopts a flattened-boat conformation. In the crystal structure, intermolecular C—H...O hydrogen bonds link the molecules to form parallel networks. There is a C—H...π contact between the methyl group and the benzene ring. A π–π contact between the benzene and phenyl rings [centroid–centroid distance = 4.681 (5) Å] is also observed.
N-(3-Chlorophenyl)benzenesulfonamide
Authors: Gowda B. Thimme , Foro Sabine , Babitha K. S. , Fuess Hartmut
Published: August 2008

In the crystal structure of the title compound, C12H10ClNO2S, the N—H bond is trans to one of the S=O bonds. The two aromatic rings form a dihedral angle of 65.4 (1)°, compared with a value of 49.1 (1)° in N-(2-chlorophenyl)-benzenesulfonamide. The molecules are connected by intermolecular N—H...O hydrogen bonds into chains running along the b axis.
Bis[3-allyl-1-(4-cyanobenzyl)-2-methylbenzimidazolium] di-μ-bromido-bis[bromidocuprate(I)]
Authors: Xu Guang-Hai , Wang Wei
Published: August 2008

The asymmetric unit of the title compound, (C19H18N3)2[Cu2Br4], contains one cation and one half-anion; there is a centre of symmetry mid-way between the two Cu atoms. In the cation, the nearly planar benzimidazole ring system is oriented at dihedral angles of 75.31 (3) and 21.39 (3)° with respect to the cyanobenzyl and allyl groups, respectively. The dihedral angle between cyanobenzyl and allyl groups is 87.94 (3)°. In the crystal structure, intermolecular C—H...Br hydrogen bonds link the molecules. There is a C—H...π contact between the cyanobenzyl ring and the anion; π—π contacts also exist between the benzimidazole ring systems as well as between the anion and the cyanobenzyl ring [centroid–centroid distances = 4.024 (1) and 4.617 (1) Å, respectively].
Morphology versus molecules: the phylogenetic relationships of Sepsidae (Diptera: Cyclorrhapha) based on morphology and DNA sequence data from ten genes
Authors: Feng‐Yi Su Kathy , Narayanan Kutty Sujatha , Meier Rudolf
Published: August 2008

The Sepsidae is, with approximately 300 described species, a relatively small family of cyclorrhaphan flies whose behaviour, morphology, and development have been extensively studied. However, currently the only available tree for Sepsidae is more than 10 years old and was based entirely on morphological characters. Here, we present the results of parsimony and Bayesian analyses based on 75 species, ten genes, and morphology. Parsimony and Bayesian analyses produce largely congruent and well‐supported topologies regardless of whether indels are coded as 5th character states, as missing values, or all sites with indels are removed. The tree confirms the monophyly of Sepsidae and identifies the Ropalomeridae as its sister group. With regard to higher‐level relationships, we identify widespread conflict between the morphological and the DNA sequence data. The proposed hypothesis based on both partitions largely reflects the signal in the molecular data. Particularly surprising is the rejection of two relationship hypotheses with strong morphological support, namely the sister group relationship between Orygma and the remaining Sepsidae and the monophyly of the Sepsis species group. Our partitioned Bremer support (PBS) analyses imply that indel coding has a stronger effect on the relative performance of individual gene partitions than the exclusion of alignment‐ambiguous sequences or the location of a gene on the mitochondrial or nuclear genome. However, these analyses also reveal unexpectedly strong fluctuations in PBS values given that indel treatment has only a minor effect on tree topology and jacknife support. These unexpected fluctuations highlight the need for a comparative study across multiple data sets that investigates the influence of conflict and indel treatment on PBS values.

© The Willi Hennig Society 2008.
The Technologisation of Childhood? Young Children and Technology in the Home
Authors: Plowman Lydia , McPake Joanna , Stephen Christine
Published: August 2008

We describe an 18‐month empirical investigation of three‐ and four‐year‐old children’s uses of technology at home, based on a survey of 346 families and 24 case studies. The findings are reported in the context of social commentators’ anxieties about the ways in which childhood is being transformed by technology. Although we report evidence of some parental disquiet about the role of technology in children’s lives, we illustrate some of the complexities in families’ attitudes to, and uses of, technology and conclude that it is not perceived by parents to be the threat to modern childhood that is claimed.
Visiting America: notes from an alcohol‐focused study tour made in 1961
Authors: Edwards Griffith
Published: August 2008

Aims  This paper has as its focus a study tour made by the author in 1961. Diary notes are used to capture a historical moment in the evolution of alcohol studies. The paper will argue for the continuing value today of such experiences in support of career development and the building of ‘the field’.

Data sources  Diary notes and personal recollection.

Findings  The United States was at the time more active than the United Kingdom in its response to alcohol problems. There was, however, a disjunction between the elite American research world and the world of action, which was not informed greatly by research. For the most part, treatment services and prevention strategies seemed driven by opinion rather than by evidence. But at the level of serious scientific endeavour there was opportunity to meet influential figures including Seldon Bacon, Morris Chafetz, Milton Gross, Ebbe Curtis Hoff, Harris Isbell, E. M. Jellinek, Mark Keller, Benjamin Kissen, Robert Strauss, Wolf Schmidt and Abraham Wikler, who generously made their time available.

Conclusions  These diary notes provide a snapshot of a field of endeavour at a critical stage of transition from uninformed assumptions towards establishment of a research base which can inform public action. The visit was of tangible value to the visitor in several different identified ways. Such an experience is inevitably time‐bound and personal, but there are general conclusions to be drawn as to the benefits which will be derived from early travel opportunities in a field such as alcohol studies, which is all too easily culture‐bound in its horizons and assumptions. Alcohol science needs to be more reflective on its history and the mechanisms that help to make it happen.
Association between wind speed and the occurrence of sickle cell acute painful episodes: results of a case‐crossover study
Authors: Nolan Vikki G. , Zhang Yuqing , Lash Timothy , Sebastiani Paola , Steinberg Martin H.
Published: August 2008

The role of the weather as a trigger of sickle cell acute painful episodes has long been debated. To more accurately describe the role of the weather as a trigger of painful events, we conducted a case‐crossover study of the association between local weather conditions and the occurrence of painful episodes. From the Cooperative Study of Sickle Cell Disease, we identified 813 patients with sickle cell anaemia who had 3570 acute painful episodes. We found an association between wind speed and the onset of pain, specifically wind speed during the 24‐h period preceding the onset of pain. Analysing wind speed as a categorical trait, showed a 13% increase (95% confidence interval: 3%, 24%) in odds of pain, when comparing the high wind speed to lower wind speed (P = 0·007). In addition, the association between wind speed and painful episodes was found to be stronger among men, particularly those in the warmer climate regions of the United States. These results are in agreement with another study that found an association between wind speed and hospital visits for pain in the United Kingdom, and lends support to physiological and clinical studies that have suggested that skin cooling is associated with sickle vasoocclusion and perhaps pain.