VISTRAJ: exploring protein conformational space

VISTRAJ is an application which allows 3D visualization, manipulation and editing of protein conformational space using probabilistic maps of this space called 'trajectory distributions'. Trajectory distributions serve as input to FOLDTRAJ which samples protein structures based on the represented conformational space. VISTRAJ also allows FOLDTRAJ to be used as a tool for homology model creation, and structures may be generated containing post-translationally modified amino acids. AVAILABILITY: Binaries are freely available for non-profit use as part of the FOLDTRAJ package at ftp://ftp.mshri.on.ca/pub/TraDES/foldtraj/.     

Transverse masticatory movements, occlusal orientation, and symphyseal fusion in selenodont artiodactyls

Based on extensive experimental work on primates, two masticatory loading regimes have emerged as the likely determinants of mandibular symphyseal fusion-dorsoventral shear and lateral transverse bending (wishboning) (Ravosa and Hylander, 1994; Hylander et al., 1998, 2000). Recently, however, it has been argued that, rather than functioning to strengthen the symphysis during mastication, fusion serves to stiffen the symphyseal joint so as to facilitate increased transverse jaw movements during occlusion (Lieberman and Crompton, 2000). As part of this transverse stiffness model, it has been suggested that taxa with fused symphyses should also exhibit more horizontally oriented occlusal wear facets. Using a series of univariate and bivariate analyses, we test predictions of these three models in a sample of 44 species of selenodont artiodactyls. Consistent with the wishboning and transverse stiffness models, taxa with fused symphyses (camelids) have more horizontally oriented M(2) and M(2) occlusal wear facets, anteroposteriorly (AP) elongate symphyses, and relatively wider corpora. Contrary to the dorsoventral shear model, camelids do not have relatively deeper corpora (due to greater parasagittal bending). While taxa with ossified symphyses have relatively larger symphysis cross-sectional areas, this appears to be the byproduct of an increase in AP symphysis length due to greater lateral transverse bending of the mandible. Theoretical consideration of the biomechanics of mastication further suggests that strength, not stiffness, is the critical factor in determining symphyseal ossification. Thus, like anthropoid primates, fusion in selenodont artiodactyls appears to function in resisting increased wishboning stresses arising from an emphasis on transverse occlusal/mandibular movements and loads.     

Delineation of a contiguous gene syndrome with multiple exostoses, enlarged parietal foramina, craniofacial dysostosis, and mental retardation, caused by deletions in the short arm of chromosome 11.

A contiguous gene syndrome due to deletions of the proximal short arm of chromosome 11 is described in eight patients belonging to four families. The main clinical features are multiple exostoses, enlarged parietal foramina, craniofacial dysostosis, and mental retardation. The patients have cytogenetic and/or molecular deletions of chromosome 11p11-p13. These deletions are located between the centromere and D11S914 in a region of approximately 20cM. The present study confirms the presence of a multiple exostoses gene on chromosome 11p. Furthermore, it suggests that the gene for isolated foramina parietalie permagna and genes associated with craniofacial dysostosis and mental retardation reside in the same chromosomal region.     

Effect of soil cadmium application and pH on growth and cadmium accumulation in roots, leaves and fruit of strawberry plants (Fragaria × ananassa Duch.)

Three strawberry (Fragaria × ananassa Duch.) cultivars Rainier, Totem and Selva were grown under greenhouse conditions in a Parkhill sandy loam soil with a background DTPA-extractable Cd concentration of 0.18 mg kg^-1 and a pH of 5.1. Experimental treatments included combinations of 4 Cd applications (0, 15, 30 and 60 mg Cd kg^-1 soil) applied as CdSO₄ and 2 soil pH values 5.1 and 6.8. Both the application of Cd and pH of the soil significantly affected plant growth, yield and Cd accumulation in plant tissue anf fruit. Although roots accumulated the highest concentrations of Cd of all plant parts investigated, increased soil Cd application reduced leaf weight more than root weight. In general, yield of strawberries was decreased by an increase in amount of soil-applied Cd, however the yield response varied among cultivars. At 60 mg Cd kg^-1 soil, yield of Rainier cultivar was reduced to 17.6% of control plants. Over 90% of total Cd taken up by plants grown in Cd-treated soil accumulated in roots, regardless of the Cd level in the soil. Root Cd concentrations ranged from 2.6 mg kg^-1 (control plants) to 505.7 mg kg^-1 (Totem plants grown in soil at highest Cd and a soil pH 5.1) and were directly related to soil Cd concentrations. Cd translocation from roots to leaves and fruit was very limited, resulting in a maximum Cd concentration in root leaf tissue of 10.2 mg kg^-1. Accumulation of Cd in fruit was found to correlate well with leaf Cd, although even at the highest amount of applied Cd, fruit Cd concentration did not exceed 700 g kg^-1 of fresh weight.Contribution no. 951     

Terbium luminescence in synthetic peptide loops from calcium-binding proteins with different energy donors

Fourteen 14-mer peptides corresponding to a consensus sequence of metal-binding loops from proteins of the calmodulin family were synthesized. The effect of varying both the position in the binding loop, and the type of aromatic side chains as energy donors for enhancement of terbium luminescence, was studied. It was concluded that tryptophan in loop position 7 gave optimal luminescence enhancement, and that the additional inclusion of a tyrosine in the loop at positions 2 or 4 could further boost emission from the bound terbium. In all further cases energy transfer from aromatic residues at positions other than 7 was markedly less efficient. These results suggest that the peptides assume a configuration which allows a hexadentate ligand structure around the bound terbium ion. This is consistent with a Dexter-type electron exchange model of energy transfer.     

Activation of pyruvate dehydrogenase by electrical stimulation, and low-Na+ perfusion of guinea-pig heart

(1) Electrical stimulation (2 Hz) of guinea-pig hearts, perfused with medium containing 11 mM D-glucose plus 0.1 mM octanoate as substrate, resulted in an increase in the percentage of pyruvate dehydrogenase in the active form (PDHa) from 16 to 68%. (2) Rapid isolation of mitochondria by a technique designed to minimize net loss or gain of Ca2+ revealed an increase in mitochondrial Ca2+ content of the stimulated hearts, as measured with 45Ca (2.74 +/- 0.27 versus 1.37 +/- 0.11 nmol/mg protein; stimulated versus rested). (3) Perfusion of rested hearts with a medium containing a reduced Na+ concentration (20 mM, with the remainder replaced with Li+) also gave increased values of PDHa content (30.9% versus 16% for the normal, physiological medium). This procedure is known to raise cytosol Ca2+ concentrations and would be expected to give mitochondrial Ca2+ loading. (4) These results are consistent with a role of mitochondrial Ca2+ in activating pyruvate dehydrogenase in the intact heart.     

Self-disclosure with Dogs: Dog Owners’ and Non-dog Owners’ Willingness to Disclose Emotional Topics

Many owners talk to their pets about a wide range of issues, but there is very little research that has considered the content of this, or its impact on owner wellbeing. Verbal disclosure brings a range of potential health benefits, yet a number of factors may prevent individuals from confiding in their partners or friends (confidants). As such, in some circumstances, dogs may provide a more favorable alternative focus for disclosure. In a survey, we assessed dog owners’ (n = 286) and non-dog owners’ (n = 64) self-reported willingness to talk to their dog (dog owners only), their partner and their confidant. We used the Emotional Self Disclosure Scale (ESDS) for non-dog owners, and an adapted version of this for dog owners: Emotional Self Disclosure Scale–Dog Owners (ESDS-DO). Both dog owners and non-dog owners demonstrated a greater willingness to disclose to their partner than a confidant. For dog owners, their dog appeared to play a similar role as their partner, with greater willingness to talk to their dog about depression, jealousy, anxiety, calmness, apathy, and fear-related emotions, compared with a confidant. When talking about jealousy and apathy, dog owners reported greater willingness to talk to their dog than their partner or a confidant, but between-group comparisons (dog owner vs non-dog owner) revealed that dog owners and non-dog owners did not significantly differ in their willingness to talk to their partner or confidant, suggesting human relationships were not negatively affected by confiding to the dog. Participant age and length of relationship with their partner did not affect disclosure patterns for dog owners or non-dog owners. Males and females showed different willingness to disclose to confidants, but not to dogs. The results have implications for considering the value of dogs for human psychological health.     

A mammalian lysosomal membrane protein confers multidrug resistance upon expression in Saccharomyces cerevisiae

Mouse transporter protein (MTP) is a highly conserved polytopic membrane protein present in mammalian lysosomes and endosomes. The role of MTP in regulating the in vivo subcellular distribution of numerous structurally distinct small molecules has been examined in this study by its expression in a drug-sensitive strain of the yeast Saccharomyces cerevisiae. Surprisingly, the expression of MTP in membranes of an intracellular compartment resulted in a cellular resistance or hypersensitivity to a range of drugs that included nucleoside and nucleobase analogs, antibiotics, anthracyclines, ionophores, and steroid hormones. The intracellular bioavailability of steroid hormones was altered by MTP, as determined using an in vivo glucocorticoid receptor-driven reporter assay in yeast, suggesting that the MTP-regulated drug sensitivity arose due to a change in the subcellular compartmentalization of steroid hormones and other drugs. MTP-regulated drug sensitivity in yeast was blocked to varying degrees by compounds that inhibit lysosomal function, interfere with intracellular cholesterol transport, or modulate the multidrug resistance phenotype of mammalian cells. These results indicate that MTP is involved in the subcellular compartmentalization of diverse hydrophobic small molecules and contributes to the inherent drug sensitivity or resistance of the mammalian cell.     

Computational Analysis and Experimental Validation of Gene Predictions in Toxoplasma gondii

Background

Toxoplasma gondii is an obligate intracellular protozoan that infects 20 to 90% of the population. It can cause both acute and chronic infections, many of which are asymptomatic, and, in immunocompromized hosts, can cause fatal infection due to reactivation from an asymptomatic chronic infection. An essential step towards understanding molecular mechanisms controlling transitions between the various life stages and identifying candidate drug targets is to accurately characterize the T. gondii proteome.

Methodology/Principal Findings

We have explored the proteome of T. gondii tachyzoites with high throughput proteomics experiments and by comparison to publicly available cDNA sequence data. Mass spectrometry analysis validated 2,477 gene coding regions with 6,438 possible alternative gene predictions; approximately one third of the T. gondii proteome. The proteomics survey identified 609 proteins that are unique to Toxoplasma as compared to any known species including other Apicomplexan. Computational analysis identified 787 cases of possible gene duplication events and located at least 6,089 gene coding regions. Commonly used gene prediction algorithms produce very disparate sets of protein sequences, with pairwise overlaps ranging from 1.4% to 12%. Through this experimental and computational exercise we benchmarked gene prediction methods and observed false negative rates of 31 to 43%.

Conclusions/Significance

This study not only provides the largest proteomics exploration of the T. gondii proteome, but illustrates how high throughput proteomics experiments can elucidate correct gene structures in genomes.