Zinc and cadmium contamination in an Avicennia schaueriana mangrove environment: Mass balance and tissue distribution.

The leachate pond of a Zn processing plant in Rio de Janeiro, Brazil, released Zn and Cd into a mangrove during three decades. Soil, root, stems, leaves and phloem bark samples of Avicenna schaueriana from the mangrove were collected and analyzed. Zn and Cd levels were measured by atomic absorption and were much more concentrated in soil at 76 kg/ha and 424 kg/ha respectively than in the trees (272.

Tremella saccharicola f.a., sp. nov., a novel tremellaceous yeast species isolated from tropical regions.

Ten strains representing a single anamorphic novel yeast species were isolated from the external surface (DMKU-SP23 and DMKU-SP40) and tissue (DMKU-SE89, DMKU-SE99, DMKU-SE100 and DMKU-SE147) of sugarcane leaves in Thailand, and phylloplane (IMUFRJR 52034) and rhizoplane (IMUFRJ 52036 and 52037) of sugarcane and associated soil (IMUFRJ 52035) in Brazil. These strains showed zero to two nucleotide substitutions in the sequences of the D1/D2 region of the LSU rRNA gene and zero to three nucleotide substitutions in the internal transcribed spacer (ITS) region. Tremella globispora was the most closely related species, but with 1.

Force field development phase II: Relaxation of physics-based criteria… or inclusion of more rigorous physics into the representation of molecular energetics.

In the previous paper, we reviewed the origins of energy based calculations, and the early science of FF development. The initial efforts spanning the period from roughly the early 1970s to the mid to late 1990s saw the development of methodologies and philosophies of the derivation of FFs. The use of Cartesian coordinates, derivation of the H-bond potential, different functional forms including diagonal quadratic expressions, coupled valence FFs, functional form of combination rules, and out of plane angles, were all investigated in this period.

Biomolecular force fields: where have we been, where are we now, where do we need to go and how do we get there?

In this perspective, we review the theory and methodology of the derivation of force fields (FFs), and their validity, for molecular simulations, from their inception in the second half of the twentieth century to the improved representations at the end of the century. We examine the representations of the physics embodied in various force fields, their accuracy and deficiencies. The early days in the 1950s and 60s saw FFs first introduced to analyze vibrational spectra.

Diversity of Quaternary Structures Regulates Nuclear Receptor Activities.

Nuclear receptors (NRs) form homo- and/or heterodimers as central scaffolds of multiprotein complexes, which activate or repress gene transcription to regulate development, homeostasis, and metabolism. Recent studies on NR quaternary structure reveal novel mechanisms of receptor dimerization, the existence of tetrameric chromatin-bound NRs, and previously unanticipated protein-protein/protein-DNA interactions.

Occultifur plantarum f.a., sp. nov., a novel cystobasidiomycetous yeast species.

Nine strains representing a single anamorphic novel yeast species in dispersed tropical and subtropical habitats were isolated from sugarcane leaf tissue (DMKU-SE24, DMKU-SE45T, DMKU-SE129 and DMKU-SE134) and corn leaf tissue (DMKU-CE36) in Thailand, phylloplane and rhizoplane of sugarcane in Brazil (IMUFRJ 52018 and IMUFRJ 52019), bromeliad leaf tissue in Brazil (IMUFRJ 51954) and plant leaf in Japan (IPM31-24). These strains showed identical or only 1 nt substitution in the sequences of the D1/D2 region of the LSU rRNA gene and 0-5 nt substitutions in the internal transcribed spacer (ITS) region. Phylogenetic analysis based on the combined sequences of the ITS and the D1/D2 regions showed that the eight of these strains represented a single species in the genus Occultifur that was distinct from related species.

Quantum Derivative Fitting and Biomolecular Force Fields: Functional Form, Coupling Terms, Charge Flux, Nonbond Anharmonicity, and Individual Dihedral Potentials.

Computer simulations are increasingly prevalent, complementing experimental studies in all fields of biophysics, chemistry, and materials. Their utility, however, is critically dependent on the validity of the underlying force fields employed. In this Perspective we review the ability of quantum mechanics, and in particular analytical ab initio derivatives, to inform on the nature of intra- and intermolecular interactions.

Chemical Structure Similarity Search for Ligand-based Virtual Screening: Methods and Computational Resources.

For many years the assumption that "Chemical compounds with similar structures may have similar activities" has been a foundation for lead identification. The similarity can be computed based upon topological, steric, electronic, and/or physical properties. The chemical structure similarity search differs from the chemical substructure search in that the former requires assessment of the properties of each compound and thus no filter can be applied for skipping structures before they are assessed to accelerate the computation.

Occultifur tropicalis f.a., sp. nov., a novel cystobasidiomycetous yeast species isolated from tropical regions.

Five strains representing a single novel anamorphic yeast species were isolated from sugar cane. Two strains were from tissue (DMKU-SE38, DMKU-SE59(T)) and two from the external surface (DMKU-SP385, DMKU-SP403) of leaves collected in Thailand and the fifth (IMUFRJ 52020) from the rhizoplane of sugar cane in an organically cultivated field in Brazil. On the basis of sequence analysis of the D1/D2 region of the large subunit (LSU) rRNA gene and the internal transcribed spacer (ITS) region, they were classified as representing a single species of the genus Occultifur.

Allosteric mechanisms of nuclear receptors: insights from computational simulations.

The traditional structural view of allostery defines this key regulatory mechanism as the ability of one conformational event (allosteric site) to initiate another in a separate location (active site). In recent years computational simulations conducted to understand how this phenomenon occurs in nuclear receptors (NRs) has gained significant traction. These results have yield insights into allosteric changes and communication mechanisms that underpin ligand binding, coactivator binding site formation, post-translational modifications, and oncogenic mutations.

Constructing the foundations for compassionate care: how service-learning affects nursing students' attitudes towards the poor.

When nurses possess negative attitudes toward people with low socio-economic status it can negatively influence patient care. This study examines whether providing care in a service-learning environment positively affects nursing students' world views and empathy toward the poor. Using a pre-post design, the Attitudes about Poverty and Poor People Scale and the Just World Scale were administered to both a control group and nursing students engaged in a clinical rotation at a low-income housing facility or homeless shelter in spring and fall 2010.

Discovery of new selective human aldose reductase inhibitors through virtual screening multiple binding pocket conformations.

Aldose reductase reduces glucose to sorbitol. It plays a key role in many of the complications arising from diabetes. Thus, aldose reductase inhibitors (ARI) have been identified as promising therapeutic agents for treating such complications of diabetes, as neuropathy, nephropathy, retinopathy, and cataracts.

Wickerhamiella slavikovae sp. nov. and Wickerhamiella goesii sp. nov., two yeast species isolated from natural substrates.

Two novel yeast species were isolated during three independent studies of yeasts associated with natural substrates in Brazil and Taiwan. Analysis of the sequences of the D1/D2 domains of the large subunit rRNA gene showed that these novel species belong to the Wickerhamiella clade. The first was isolated from freshwater and a leaf of sugar cane (Saccharum officinarum) in Brazil and from leaves of Wedelia biflora in Taiwan.

Optimizing lactose hydrolysis by computer-guided modification of the catalytic site of a wild-type enzyme.

Lactose intolerance is a serious global health problem. A lactose hydrolysis enzyme, thermostable β-galactosidase, BgaB (from Geobacillus stearothermophilus) has attracted the attention of industrial biologists because of its potential application in processing lactose-containing products. However, this enzyme experiences galactose product inhibition.

On the value of homology models for virtual screening: discovering hCXCR3 antagonists by pharmacophore-based and structure-based approaches.

Human chemokine receptor CXCR3 (hCXCR3) antagonists have potential therapeutic applications as antivirus, antitumor, and anti-inflammatory agents. A novel virtual screening protocol, which combines pharmacophore-based and structure-based approaches, was proposed. A three-dimensional QSAR pharmacophore model and a structure-based docking model were built to virtually screen for hCXCR3 antagonists.

Generation of receptor structural ensembles for virtual screening using binding site shape analysis and clustering.

Accounting for protein flexibility is an essential yet challenging component of structure-based virtual screening. Whereas an ideal approach would account for full protein and ligand flexibility during the virtual screening process, this is currently intractable using available computational resources. An alternative is ensemble docking, where calculations are performed on a set of individual rigid receptor conformations and the results combined.

Exploring protein flexibility: incorporating structural ensembles from crystal structures and simulation into virtual screening protocols.

The capacity of proteins to adapt their structure in response to various perturbations including covalent modifications, and interactions with ligands and other proteins plays a key role in biological processes. Here, we explore the ability of molecular dynamics (MD), replica exchange molecular dynamics (REMD), and a library of structures of crystal-ligand complexes, to sample the protein conformational landscape and especially the accessible ligand binding site geometry. The extent of conformational space sampled is measured by the diversity of the shapes of the ligand binding sites.

Kluyveromyces aestuarii, a potential environmental quality indicator yeast for mangroves in the State of Rio de Janeiro, Brazil.

Kluyveromyces aestuarii was found in sediments from 7 of 8 mangroves in Rio de Janeiro; and absent only at one site with heavy plastic bag pollution. Its presence suggests influence in other habitats from a mangrove and its absence in a mangrove suggests some non- fecal pollution or other habitat alteration.

Candida middelhoveniana sp. nov., a new yeast species found on the rhizoplane of organically cultivated sugarcane.

A novel yeast species within the Metschnikowiaceae is described based on a strain from the sugarcane (Saccharum sp.) rhizoplane of an organically managed farm in Rio de Janeiro, Brazil. The D1/D2 domain of the large subunit ribosomal RNA gene sequence analysis showed that the closest related species were Candida tsuchiyae with 86.

Kazachstania bromeliacearum sp. nov., a yeast species from water tanks of bromeliads.

Cultures of a novel nutritionally specialized, fermentative yeast species were isolated from 34 water tanks of five bromeliad species, two mangrove sediment samples and one swamp water sample in Rio de Janeiro, Brazil. Sequence analysis of the D1/D2 domains of the large subunit of the rRNA gene showed that the novel species belongs to the genus Kazachstania. The novel species differs from Kazachstania martiniae by 11 substitutions and 2 gaps in the sequence of the domains D1/D2 of the LSU rRNA gene.

Mechanism of androgen receptor antagonism by bicalutamide in the treatment of prostate cancer.

The androgen receptor (AR) plays a key role in regulating gene expression in a variety of tissues, including the prostate. In that role, it is one of the primary targets in the development of new chemotherapeutics for treatment of prostate cancer and the target of the most widely prescribed current drug, bicalutamide (Bcu), for this disease. In view of its importance, and the absence of a crystal structure for any antagonist--AR complex, we have conducted a series of molecular dynamics-based simulations of the AR--Bcu complex and quantum mechanical (QM) calculations of Bcu, to elucidate the structural basis for antagonism of this key target.

Killer yeasts inhibit the growth of the phytopathogen Moniliophthora perniciosa, the causal agent of Witches' Broom disease.

Fruit and soil yeasts isolated from the Amazon, Atlantic Rainforests and an organic farm were screened for killer activity against yeasts. Killer yeasts were then tested against the phytopathogen Moniliophthora perniciosa (syn. Crinipellis perniciosa) and a Dipodascus capitatus strain and a Candida sp strain inhibited its growth.

Psychosocial correlates of dietary intake among overweight and obese men.

Objectives: To investigate the relationship between theoretically based psychosocial constructs and dietary components among overweight men.

Methods: Participants were 441 men (BMI M = 34.2).

Pseudomonas fluorescens dynamics in the soil surface to subsurface transect.

Microbial displacement in the soil is an important process for bioremediation and dispersal of wastewater pathogens. We evaluated cell movement in surface and subsurface red-yellow podzolic soil driven by advection and microbial motility and also survival of a microbial population at high pressure as is prevalent in deep soil layers. Pseudomonas fluorescens Br 12, resistant to rifampycin and kanamycin, was used as a model organism traceable in non-sterile soil.

Construct validity of physical activity and sedentary behaviors staging measures for adolescents.

Purpose: To evaluate the construct validity of physical activity (PA) and sedentary behaviors (SB) staging measures for adolescents that incorporate the current national recommendations.

Method: The Progressive Aerobic Cardiovascular Endurance Run, Actigraph accelerometer, and self-reported hours of TV viewing served as criterion measures. Participants were 878 adolescents (M age = 12.