Information‐theoretic analysis of the reference state in contact potentials used for protein structure prediction

Using information‐theoretic concepts, we examine the role of the reference state, a crucial component of empirical potential functions, in protein fold recognition. We derive an information‐based connection between the probability distribution functions of the reference state and those that characterize the decoy set used in threading. In examining commonly used contact reference states, we find that the quasi‐chemical approximation is informatically superior to other variant models designed to include characteristics of real protein chains, such as finite length and variable amino acid composition from protein to protein. We observe that in these variant models, the total divergence, the operative function that quantifies discrimination, decreases along with threading performance. We find that any amount of nativeness encoded in the reference state model does not significantly improve threading performance. A promising avenue for the development of better potentials is suggested by our information‐theoretic analysis of the action of contact potentials on individual protein sequences. Our results show that contact potentials perform better when the compositional properties of the data set used to derive the score function probabilities are similar to the properties of the sequence of interest. Results also suggest to use only sequences of similar composition in deriving contact potentials, to tailor the contact potential specifically for a test sequence. Proteins 2010. © 2009 Wiley‐Liss, Inc.     

A Preliminary Study of the Surface Properties of Earthworms and Their Relations to Non-Stain Behaviour

The surface properties of earthworms were studied using nitrogen adsorption/desorption isotherm and dynamic contact angle measurement with the aim to understand their non-stain behaviour. The results obtained by applying dynamic contact angle technique using water, glycerol, cooking oil and dimethylsilicone show that the surface properties of earthworms are a function of time. The critical surface energy, calculated using advancing angle, is as low as 11 × 10~(-3) J·m~(-2). However this hydrophobic behaviour at the initial contact moment changes progressively into hydrophilic as time goes by. This behaviour together with the creeping movement of corrugated surface is believed to be responsible for the non-stain behaviour of earthworms. The nitrogen adsorption isotherm of dried skin of earthworms at 77.3 K exhibits more or less Type V isotherm with surface area of 13 m~2·g~(-1) calculated using the α_s plot. The Type V isotherm is the indication of weak interaction between nitrogen and the worm surface.     

Using differential introgression in hybrid zones to identify genomic regions involved in speciation

Hybrids between species provide information about the evolutionary processes involved in divergence. In addition to creating hybrids in the laboratory, biologists can take advantage of natural hybrid zones to understand the factors that shape gene flow between divergent lineages. In the early stages of speciation, most regions of the genome continue to flow freely between populations. Alternatively, the subset of the genome that confers reproductive barriers between nascent species is expected to reject introgression. Now enabled by advances in genomics, this perspective is motivating detailed comparisons of gene flow across genomic regions in hybrid zones. Here, I review methods for measuring and interpreting introgression at multiple loci in hybrid zones, focusing on the problem of identifying loci that contribute to reproductive isolation. Emerging patterns from multi-locus studies of hybrid zones are highlighted, including remarkable variance in introgression across the genome. Although existing methods have been useful, there is scope for development of new analytical approaches that better connect differential patterns of gene flow in hybrid zones with current knowledge of speciation mechanisms. I outline future prospects for differential introgression studies on a genomic scale.     

The supramolecular assemblies of voltage-dependent anion channels in the native membrane

Voltage-dependent anion channels (VDACs) are major constituents of the outer mitochondrial membrane (OMM). These primary transporters of nucleotides, ions and metabolites mediate a substantial portion of the OMM molecular traffic. To study the native supramolecular organization of the VDAC, we have isolated, characterized and imaged OMMs from potato tubers. SDS-PAGE and mass spectrometry of OMMs revealed the presence of the VDAC isoforms POM34 and POM36, as well as the translocase of the OMM complex. Tubular two-dimensional crystals of the VDAC spontaneously formed after incubation of OMMs for two to three months at 4 degrees C. Transmission electron microscopy revealed an oblique lattice and unit cells housing six circular depressions arranged in a hexagon. Atomic force microscopy of freshly isolated OMMs demonstrated (i) the existence of monomers to tetramers, hexamers and higher oligomers of the VDAC and (ii) its spatial arrangement within the oligomers in the native membrane. We discuss the importance of the observed oligomerization for modulation of the VDAC function, for the binding of hexokinase and creatine kinase to the OMM and for mitochondria-mediated apoptosis.     

Analysis of a secondary contact between divergent lineages of brown trout Salmo trutta L. from Duero basin using microsatellites and mtDNA RFLPs

The analysis of 12 microsatellite loci in 16 native populations of Salmo trutta from Duero basin evidenced a strong genetic differentiation in accordance with the existence of two divergent Atlantic mtDNA lineages, Atlantic (AT) and Duero (DU). These lineages were observed spatially segregated mainly in the Lower-course and in the inner part of the basin. Unlike previous isozyme information, microsatellite data suggested a more downstream location of the sharpest genetic divergence in Duero basin and a more complex structure in the inward area. Putative hybrid populations evidenced higher Hardy–Weinberg and gametic disequilibria than pure ones (Pisuerga, Lower-course), not explained by mixture due to differential immigration pattern across the basin. Hybridization indexes suggested a bimodal pattern of hybridization and a higher weight of Pisuerga region in the genetic composition of hybrid samples in accordance with mtDNA data. The results suggested a limited introgression between AT and DU lineages. Taking into account the time of divergence between both lineages, selection and/or genetic incompatibility appeared necessary to explain the genetic structure observed and the ancient location of DU lineage restricted to this area.     

Effects of Joint Space Use and Group Membership on Contact Rates Among White-Tailed Deer

Abstract: Establishment and spread of infectious diseases are controlled by the frequency of contacts among hosts. Although managers can estimate transmission coefficients from the relationship between disease prevalence and age or time, they may wish to quantify or compare contact rates before a disease is established or while it is at very low prevalence. Our objectives were to quantify direct and indirect contacts rates among white-tailed deer (Odocoileus virginianus) and to compare these measures of contact rate with simpler measures of joint space use. We deployed Global Positioning System (GPS) collars on 23 deer near Carbondale, Illinois, USA, from 2002 to 2005. We used location data from the GPS collars to measure pairwise rates of direct and indirect contact, based on a range of proximity criteria and time lags, as well as volume of intersection (VI) of kernel utilization distributions. We analyzed contact rates at a given distance criterion and time lag using mixed-model logistic regression. Direct contact rates increased with increasing VI and were higher in autumn—spring than in summer. After accounting for VI, the estimated odds of direct contact during autumn—spring periods were 5.0–22.1-fold greater (depending on the proximity criterion) for pairs of deer in the same social group than for between-group pairs, but for direct contacts during summer the within:between-group odds ratio did not differ significantly from 1. Indirect contact rates also increased with VI, but the effects of both season and pair-type were much smaller than for direct contacts and differed little as the time lag increased from 1–30 days. These results indicate that simple measures of joint space use are insufficient indices of direct contact because group membership can substantially increase contacts at a given level of joint space use. With indirect transmission, however, group membership had a much smaller influence after accounting for VI. Relationships between contact rates and season, VI, and pair-type were generally robust to changes in the proximity criterion defining a contact, and patterns of indirect contacts were affected little by the choice of time lag from 1–30 days. The use of GPS collars provides a framework for testing hypotheses about the form of contact networks among large mammals and comparing potential direct and indirect contact rates across gradients of ecological factors, such as population density or landscape configuration.     

Rho-family small GTPases are involved in forskolin-induced cell-cell contact formation of renal glomerular podocytes in vitro

Intercellular adhesions between renal glomerular epithelial cells (also called podocytes) are necessary for the proper function of the glomerular filtration barrier. Although our knowledge of the molecular composition of podocyte cell-cell contact sites has greatly progressed, the underlying molecular mechanism regulating the formation of these cell-cell contacts remains largely unknown. We have used forskolin, an activator of adenylyl cyclase that elevates the level of intracellular cAMP, to investigate the effect of cAMP and three Rho-family small GTPases (RhoA, Cdc42, and Rac1) on the regulation of cell-cell contact formation in a murine podocyte cell line. Transmission electron microscopy and the immunostaining of cell adhesion molecules and actin-associated proteins have revealed a structural change at the site of cell-cell contact following forskolin treatment. The activity of the Rho-family small GTPases before and after forskolin treatment has been evaluated with a glutathione-S-transferase pull-down assay. Forskolin reinforces the integrity of cell-cell contacts, resulting in the closure of an intercellular adhesion zipper, accompanied by a redistribution of cell adhesion molecules and actin-associated proteins in a continuous linear pattern at cell-cell contacts. The Rho-family small GTPases Rac1 and Cdc42 are activated during closure of the adhesion zipper, whereas RhoA is suppressed. Thus, cAMP promotes the assembly of cell-cell contacts between podocytes via a mechanism that probably involves Rho-family small GTPases. This study was supported in part by a grant-in-aid for scientific research from the Japanese Ministry for Education, Culture, Sports, Science, and Technology (to N. K., no. 14570015). S-Y.G. is a recipient of a grant awarded by the Japanese government to graduate students from foreign countries.     

Population dynamics of diploid and hexaploid populations of a perennial herb

BACKGROUND AND AIMS: Despite the recent enormous increase in the number of studies on polyploid species, no studies to date have explored the population dynamics of these taxa. It is thus not known whether the commonly reported differences in single life-history traits between taxa of different ploidy levels result in differences in population dynamics. METHODS: This study explores differences in single life-history traits and in the complete life cycle between populations of different ploidy levels and compares these differences with differences observed between different habitat types and years. Diploid and hexaploid populations of a perennial herb, Aster amellus, are used as the study system. Transition matrix models were used to describe the dynamics of the populations, and population growth rates, elasticity values and life-table response experiments were used to compare the dynamics between populations and years. KEY RESULTS: The results indicate that between-year variation in population dynamics is much larger than variation between different ploidy levels and different habitat conditions. Significant differences exist, however, in the structure of the transition matrices, indicating that the dynamics of the different ploidy levels are different. Strong differences in probability of extinction of local populations were also found, with hexaploid populations having higher probability than diploid populations, indicating strong potential differences in persistence of these populations. CONCLUSIONS: This is the first study on complete population dynamics of plants of different ploidy levels. This knowledge will help to understand the ability of new ploidy levels to spread into new areas and persist there, and the interactions of different ploidy levels in secondary contact zones. This knowledge will also contribute to understanding of interactions of different ploidy levels with other plant species or other interacting organisms such as pollinators or herbivores.     

Effects of phthalate esters on dendritic cell subsets and interleukin-4 production in fluorescein isothiocyanate-induced contact hypersensitivity

Phthalate esters with short alkyl chains, such as di-ethyl (DEP), di-n-propyl (DPP), and di-butyl phthalate (DBP), have adjuvant effects on an FITC-induced contact hypersensitivity mouse model. The adjuvant effects of DPP and DBP are associated with enhanced trafficking of FITC-presenting CD11b(+) dendritic cells (DC). DEP has relatively weak activity as to FITC-positive cell migration. Here we demonstrated that DBP and DPP also increased the number of FITC-positive CD8alpha(+) DC in draining lymph nodes. We also found enhanced production of interleukin-4 in draining lymph nodes after FITC sensitization with DEP, DPP, or DBP, suggesting an additional adjuvant mechanism of phthalate esters.