Conformational analysis of methyl 6-O-[(R)- and (S)-1-carboxyethyl]-α-D-galactopyranoside by MM and Langevin dynamics simulations

The conformational space of methyl 6-O-[(R)- and (S)- 1-carboxyethyl]-α-D-galactopyranoside has been investigated. A grid search employing energy minimization at each grid point over the three major degrees of freedom, namely φ, ψ and ω, identified low energy regions. The R-isomer shows five low energy conformers within ca. 1 kcal mol−1 of the global energy minimum. The S-isomer has two conformers within a few tenths of a kcal mol−1 of the global energy minimum. Langevin dynamics simulations have been have been performed at 300 K for 30 ns of each isomer. The φ dihedral angle has as its major conformer (g−1) for the R-isomer whereas it is the (g+) conformer for the S-isomer. For the ψ dihedral angle the (t) conformer has the highest population for both isomers. The dihedral angle ω has the (g+) conformer most highly populated, both for the R- and S-isomer. The above five and two conformational states for the R- and S-isomers, respectively, make up 90% in each case of the populated states during the Langevin dynamics (LD) simulations. Rate constants for the ω dihedral angle have been calculated based on a number correlation function. Three bond homo- and heteronuclear, i.e. proton and carbon-13, coupling constants have been calculated from the dynamics trajectories for comparison to experimental values. The heteronuclear coupling constant H2′,C6 has been measured for the S-isomer and found to be 3.3 Hz. The J value calculated from the LD simulations, namely 2.6 Hz, is in fair agreement with experiment. A comparison to the X-ray structure of the R-isomer shows that the conformation of the crystalline compound occupies the low energy region most highly populated as a single R-conformer (30%) during the LD simulations. This revised version was published online in August 2006 with corrections to the Cover Date.     

Auxin-Cytokinin Interactions in Wild-Type and Transgenic Tobacco

Cytokinins and auxins are important regulators of plant growthand development, but there is incomplete and conflicting evidencethat auxins affect cytokinin metabolism and vice versa. We haveinvestigated these interactions in Nicotiana tabacum L. by separatein planta manipulation of levels of the hormones followed byanalysis of the induced changes in the metabolism of the otherhormone. Cytokinin-overproducing plants (expressing the Agrobacte-riumtumefaciens ipt gene) had lower than wild-type levels of freeIAA, and reduced rates of IAA synthesis and turnover, but therewere no differences in the profiles of metabolites they producedfrom fed IAA. Similarly, auxin-overproducing plants (expressingthe A.tumefaciens iaaM and iaaH genes), had lower levels ofthe major cytokinins than wild-type plants and lower cytokininoxidase activity, but there were no differences in the profilesof metabolites they produced from fed cytokinins. The data demonstratethat cytokinin or auxin overproduction decreases the contentof the other hormone, apparently by decreasing its rate of synthesisand/or transport, rather than by increasing rates of turnoveror conjugation. Implications for the importance of cytokinin: auxin ratios in plant development are considered. (Received September 24, 1996; Accepted December 4, 1996)     

DNA break repair: refined rules of an already complicated game.

Of the many types of DNA-damage repair, this review concentrates on the aspects of DNA single- and double-strand break repair. Originally considered to represent separate routes based on distinct enzymatic machineries, it has recently been shown that these pathways converge and are interlinked at a number of points. Poly(ADP-ribose) polymerase-1 (PARP-1) is a central player in this complicated game. We present new data and our view on the mechanisms by which PARP-1 is guided to its respective interaction partners to coordinate or participate in repair or apoptosis.     

Studies on solution NMR structure of brazzein——Secondary structure and molecular scaffold

Brazzein is a sweet-tasting protein isolated from the fruit of West African plantPentadiplandra brazzeana Baillon. It is the smallest and the most water-soluble sweet protein discovered so far and is highly thermostable. The proton NMR study of brazzein at 600 MHz (pH 3.5, 300 K) is presented. The complete sequence specific assignments of the individual backbone and sidechain proton resonances were achieved using through-bond and through-space connectivities obtained from standard two-dimensional NMR techniques. The secondary structure of brazzein contains one alpha-helix (residues 21-29), one short 3(10)-helix (residues 14-17), two strands of antiparallel beta-sheet (residues 34-39, 44-50) and probably a third strand (residues 5-7) near the N-terminus. A comparative analysis found that brazzein shares a so-called 'cysteine-stabilized alpha-beta' (CSalphabeta) motif with scorpion neurotoxins, insect defensins and plant gamma - thionins. The significance of this multi-function motif, the possible active sites and the structural basis of themostability were discussed.     

Interactive Multimedia for Promoting Physical Activity (IMPACT) in Children

Objective: To develop and examine the efficacy of a computer‐based interactive multimedia curriculum for promoting physical activity in fourth grade children. Research Methods and Procedures: The participants were 209 fourth grade children (mean age of 9.5 ± 0.4 years) from four schools. Two schools received an 8‐week multimedia intervention delivered by interactive CD‐ROM, supplemented by four classroom and four homework assignments. Two control schools received educational CD‐ROMS not related to health outcomes. Measures conducted before and after intervention included height, weight, percentage body fat (bioimpedance analysis), physical activity (5‐day accelerometry), and psychosocial aspects of physical activity by questionnaire. All outcomes were examined using general linear models. Results: There was a significant treatment effect for obesity reduction in girls but not in boys. There were no significant treatment effects on total physical activity by accelerometry (total counts per minute), but there was an overall treatment effect on reducing percent of time in moderate‐intensity activity (16.5% to 15% of the time) and significant sex‐by‐ treatment interactions for light‐intensity activities (reduction in boys from 78% to 75% of the time and an increase in girls from 78% to 81% of the time). There were marginal/significant treatment effects for improvements in behavioral outcomes, including self‐efficacy (p = 0.06), social norms (p = 0.07), and outcome expectancies (p = 0.049). Discussion: The interactive multimedia curriculum favored an improvement in obesity indices in girls and was associated with subtle changes in physical activity in girls and general improvement in psychosocial outcomes related to physical activity.     

Influence of drug-to-lipid ratio on drug release properties and liposome integrity in liposomal doxorubicin formulations

Recent studies have shown that the release properties of vincristine encapsulated in large unilamellar vesicles (LUV) can be regulated by varying the drug-to-lipid (D/L) ratio. In this work it is shown that the drug-to-lipid ratio technique for regulating drug release also applies to doxorubicin encapsulated in LUV. In particular it is shown that the half-times (T(1/2)) for doxorubicin release from distearoylphosphatidylcholine (DSPC)/cholesterol LUV in vitro can be increased more than six-fold by increasing the D/L ratio from 0.05 (wt/wt) to 0.39 (wt/wt). This behavior is consistent with the behavior expected for drugs that precipitate following accumulation into liposomes. It is shown that the release properties of ciprofloxacin--a drug that does not precipitate following accumulation into LUV--are not affected by the D/L ratio. It is also shown that the crystalline intravesicular doxorubicin precipitates observed as the D/L ratio is raised from 0.05 to 0.46 adopt increasingly unusual morphologies. Linear crystals are observed at lower D/L values, however triangular and rectangular variations are observed as the D/L ratio is increased, and induce considerable distortion in vesicle morphology. It is noted that trapping efficiency following uptake of external doxorubicin into LUV is reduced from nearly 100% at a D/L ratio of 0.05 (wt/wt) to less than 70% at an (initial) D/L ratio of 0.8 (wt/wt). It is suggested that this arises, at least in part, from membrane-disrupting effects of internal drug crystals as they increase in size.     

Using linear algebra for protein structural comparison and classification

In this article, we describe a novel methodology to extract semantic characteristics from protein structures using linear algebra in order to compose structural signature vectors which may be used efficiently to compare and classify protein structures into fold families. These signatures are built from the pattern of hydrophobic intrachain interactions using Singular Value Decomposition (SVD) and Latent Semantic Indexing (LSI) techniques. Considering proteins as documents and contacts as terms, we have built a retrieval system which is able to find conserved contacts in samples of myoglobin fold family and to retrieve these proteins among proteins of varied folds with precision of up to 80%. The classifier is a web tool available at our laboratory website. Users can search for similar chains from a specific PDB, view and compare their contact maps and browse their structures using a JMol plug-in.     

Brief communication: Minimally invasive bone sampling method for DNA analysis

Obtaining a bone sample for DNA analysis has traditionally been a destructive practice, which has resulted in reluctance on behalf of curators for skeletal collections to allow invasive testing. A novel minimally invasive bone sampling method for DNA analysis is presented here. This method uses a conventional hand drill wherein the bone sample is extracted from the intercondylar fossa of the femur; it does not interfere with any known anthropometric landmarks and only leaves a small hole on the surface of the bone. The temperature of the drill is documented and it was established due to the minor increase in temperature, that this should not affect the molecular integrity of the sample. This method is easily replicated and is suitable for both human and other animal skeletal material and can be applied to rare specimens with little risk. Am J Phys Anthropol, 2009. © 2009 Wiley‐Liss, Inc.     

The history and composition of the Raymond A. Dart Collection of Human Skeletons at the University of the Witwatersrand,Johannesburg, South Africa

The Raymond A. Dart Collection of Human Skeletons (Dart Collection) is housed in the School of Anatomical Sciences at the University of the Witwatersrand, Johannesburg, South Africa, and comprises one of the largest documented cadaver‐derived human skeletal assemblages in the world. This collection originated in the early 1920s as a result of the efforts of Raymond Dart and continues to grow. The skeletons included represent varied indigenous and immigrant populations from southern Africa, Europe and Asia. This contribution documents the history of the collection and provides an updated inventory and demographic assessment of this valuable research collection. According to a recent inventory the Dart Collection currently comprises 2,605 skeletons representing individuals from regional SA African (76%), White (15%), Coloured (4%) and Indian (0.3%) populations. A large proportion of the skeletons (71%) represent males. The recorded ages at death range from the first year to over 100 years of age, but the majority of individuals died between the ages of 20 and 70. The Dart Collection has been affected by collection procedures based on availability. All of the cadavers collected before 1958, and large proportions subsequently, were derived from unclaimed bodies in regional South African hospitals. Some details of documentation (age at death, population group) are estimates and some aspects of the collection demographics (sex ratios) do not closely reflect any living South African population. Our inventory and analysis of the Dart Collection is aimed to assist researchers planning research on the materials from this collection. Am J Phys Anthropol, 2009. © 2009 Wiley‐Liss, Inc.