A bulk water-dependent desolvation energy model for analyzing the effects of secondary solutes on biological equilibria

A new phenomenological model for interpreting the effects of solutes on biological equilibria is presented. The model attributes changes in equilibria to differences in the desolvation energy of the reacting species that, in turn, reflect changes in the free energy of the bulk water upon addition of secondary solutes. The desolvation approach differs notably from that of other solute models by treating the free energy of bulk water as a variable and by not ascribing the observed shifts in reaction equilibria to accumulation or depletion of solutes next to the surfaces of the reacting species. On the contrary, the partitioning of solutes is viewed as a manifestation of the different subpopulations of water that arise in response to the surface boundary conditions. A thermodynamic framework consistent with the proposed model is used to derive a relationship for a specific reaction, an aqueous solubility equilibrium, in two or more solutions. The resulting equation reconciles some potential issues with the transfer free energy model of Tanford. Application of the desolvation energy model to the analysis of a two-state protein folding equilibrium is discussed and contrasted to the application of two other solute models developed by Timasheff and by Parsegian. Future tabulation of solvation energies and bulk water energies may allow biophysical chemists to confirm the mechanism by which secondary solutes influence binding and conformational equilibria and may provide a common ground on which experimentalists and theoreticians can compare and evaluate their results.     

Inhibitors of HIV-1 attachment. Part 11: The discovery and structure–activity relationships associated with 4,6-diazaindole cores

A series of HIV-1 attachment inhibitors containing a 4,6-diazaindole core were examined in an effort to identify a compound which improved upon the potency and oral exposure of BMS-488043 (2). BMS-488043 (2) is a 6-azaindole-based HIV-1 attachment inhibitor which established proof-of-concept for this mechanism in human clinical studies but required high doses and concomitant administration of a high fat meal to achieve efficacious exposures. Based on previous studies in indole and azaindole scaffolds, SAR investigation was concentrated around the key 7-position in the 4,6-diazaindole series and led to the discovery of molecules with 5- to 20-fold increases in potency and three- to seven-fold increases in exposure over 2 in a rat PK studies.     

Evolution of oil-producing trichomes in Sisyrinchium (Iridaceae): insights from the first comprehensive phylogenetic analysis of the genus

Background and Aims

Sisyrinchium (Iridaceae: Iridoideae: Sisyrinchieae) is one of the largest, most widespread and most taxonomically complex genera in Iridaceae, with all species except one native to the American continent. Phylogenetic relationships within the genus were investigated and the evolution of oil-producing structures related to specialized oil-bee pollination examined.

Methods

Phylogenetic analyses based on eight molecular markers obtained from 101 Sisyrinchium accessions representing 85 species were conducted in the first extensive phylogenetic analysis of the genus. Total evidence analyses confirmed the monophyly of the genus and retrieved nine major clades weakly connected to the subdivisions previously recognized. The resulting phylogenetic hypothesis was used to reconstruct biogeographical patterns, and to trace the evolutionary origin of glandular trichomes present in the flowers of several species.

Key Results and Conclusions

Glandular trichomes evolved three times independently in the genus. In two cases, these glandular trichomes are oil-secreting, suggesting that the corresponding flowers might be pollinated by oil-bees. Biogeographical patterns indicate expansions from Central America and the northern Andes to the subandean ranges between Chile and Argentina and to the extended area of the Paraná river basin. The distribution of oil-flower species across the phylogenetic trees suggests that oil-producing trichomes may have played a key role in the diversification of the genus, a hypothesis that requires future testing.     

Rod vision is controlled by dopamine-dependent sensitization of rod bipolar cells by GABA

Dark and light adaptation of retinal neurons allow our vision to operate over an enormous light intensity range. Here we report a mechanism that controls the light sensitivity and operational range of rod-driven bipolar cells that mediate dim-light vision. Our data indicate that the light responses of these cells are enhanced by sustained chloride currents via GABA(C) receptor channels. This sensitizing GABAergic input is controlled by dopamine D1 receptors, with horizontal cells serving as a plausible source of GABA release. Our findings expand the role of dopamine in vision from its well-established function of suppressing rod-driven signals in bright light to enhancing the same signals under dim illumination. They further reveal a role for GABA in sensitizing the circuitry for dim-light vision, thereby complementing GABA's traditional role in providing dynamic feedforward and feedback inhibition in the retina.     

Spontaneous neoplasia in the baboon (Papio spp.)

BACKGROUND: There are several comprehensive reviews of spontaneous neoplasia in non-human primates that compile individual cases or small numbers of cases, but do not provide statistical analysis of tumor incidence, demographics, or epidemiology. METHODS: This paper reports all spontaneous neoplasms (n = 363) diagnosed over a 15-year period in a baboon colony with an average annual colony population of 4000. RESULTS: A total of 363 spontaneous neoplasms were diagnosed in 313 baboons: 77 cases were males (25%) and 236 were females (75%); ages ranged from 1 month to 33 years (mean 16.5, median 17). CONCLUSIONS: The organ systems affected in descending order of number of neoplasms were hematopoietic organs (n = 101, 28%), urogenital tract (n = 78, 21%), integument (n = 43, 12%), alimentary tract (n = 43, 12%), endocrine organs (n = 40, 11%), nervous system (n = 33, 9%), musculoskeletal system (n = 5, 1%), and respiratory system (n = 4, 1%). Malignant cases numbered 171 (47%); 192 (53%) cases were benign.     

Individual‐based modelling of resource competition to predict density‐dependent population dynamics: a case study with white storks

Density regulation influences population dynamics through its effects on demographic rates and consequently constitutes a key mechanism explaining the response of organisms to environmental changes. Yet, it is difficult to establish the exact form of density dependence from empirical data. Here, we developed an individual‐based model to explore how resource limitation and behavioural processes determine the spatial structure of white stork Ciconia ciconia populations and regulate reproductive rates. We found that the form of density dependence differed considerably between landscapes with the same overall resource availability and between home range selection strategies, highlighting the importance of fine‐scale resource distribution in interaction with behaviour. In accordance with theories of density dependence, breeding output generally decreased with density but this effect was highly variable and strongly affected by optimal foraging strategy, resource detection probability and colonial behaviour. Moreover, our results uncovered an overlooked consequence of density dependence by showing that high early nestling mortality in storks, assumed to be the outcome of harsh weather, may actually result from density dependent effects on food provision. Our findings emphasize that accounting for interactive effects of individual behaviour and local environmental factors is crucial for understanding density‐dependent processes within spatially structured populations. Enhanced understanding of the ways animal populations are regulated in general, and how habitat conditions and behaviour may dictate spatial population structure and demographic rates is critically needed for predicting the dynamics of populations, communities and ecosystems under changing environmental conditions.     

Impact of Ralstonia eutropha's Poly(3-Hydroxybutyrate) (PHB) Depolymerases and Phasins on PHB Storage in Recombinant Escherichia coli

The model organism for polyhydroxybutyrate (PHB) biosynthesis, Ralstonia eutropha H16, possesses multiple isoenzymes of granules coating phasins as well as of PHB depolymerases, which degrade accumulated PHB under conditions of carbon limitation. In this study, recombinant Escherichia coli BL21(DE3) strains were used to study the impact of selected PHB depolymerases of R. eutropha H16 on the growth behavior and on the amount of accumulated PHB in the absence or presence of phasins. For this purpose, 20 recombinant E. coli BL21(DE3) strains were constructed, which harbored a plasmid carrying the phaCAB operon from R. eutropha H16 to ensure PHB synthesis and a second plasmid carrying different combinations of the genes encoding a phasin and a PHB depolymerase from R. eutropha H16. It is shown in this study that the growth behavior of the respective recombinant E. coli strains was barely affected by the overexpression of the phasin and PHB depolymerase genes. However, the impact on the PHB contents was significantly greater. The strains expressing the genes of the PHB depolymerases PhaZ1, PhaZ2, PhaZ3, and PhaZ7 showed 35% to 94% lower PHB contents after 30 h of cultivation than the control strain. The strain harboring phaZ7 reached by far the lowest content of accumulated PHB (only 2.0% [wt/wt] PHB of cell dry weight). Furthermore, coexpression of phasins in addition to the PHB depolymerases influenced the amount of PHB stored in cells of the respective strains. It was shown that the phasins PhaP1, PhaP2, and PhaP4 are not substitutable without an impact on the amount of stored PHB. In particular, the phasins PhaP2 and PhaP4 seemed to limit the degradation of PHB by the PHB depolymerases PhaZ2, PhaZ3, and PhaZ7, whereas almost no influence of the different phasins was observed if phaZ1 was coexpressed. This study represents an extensive analysis of the impact of PHB depolymerases and phasins on PHB accumulation and provides a deeper insight into the complex interplay of these enzymes.     

Latex Clearing Protein—an Oxygenase Cleaving Poly(cis-1,4-Isoprene) Rubber at the cis Double Bonds

Gordonia polyisoprenivorans strain VH2, a potent rubber-degrading actinomycete, harbors two latex clearing proteins (Lcps), which are known to be essential for the microbial degradation of rubber. However, biochemical information on the exact role of this protein in the degradation of polyisoprene was lacking. In this study, the gene encoding Lcp1_VH2 was heterologously expressed in strains of Escherichia coli, the corresponding protein was purified, and its role in rubber degradation was examined by measurement of oxygen consumption as well as by chromatographic and spectroscopic methods. It turned out that active Lcp1_VH2 is a monomer and is responsible for the oxidative cleavage of poly(cis-1,4-isoprene) in synthetic as well as in natural rubber by the addition of oxygen (O₂) to the cis double bonds. The resulting oligomers possess repetitive isoprene units with aldehyde (CHO-CH₂—) and ketone (—CH₂-CO-CH₃) functional groups at the termini. Two fractions with average isoprene contents of 18 and 10, respectively, were isolated, thus indicating an endocleavage mechanism. The activity of Lcp1_VH2 was determined by applying a polarographic assay. Alkenes, acyclic terpenes, or other rubber-like polymers, such as poly(cis-1,4-butadiene) or poly(trans-1,4-isoprene), are not oxidatively cleaved by Lcp1_VH2. The pH and temperature optima of the enzyme are at pH 7 and 30°C, respectively. Furthermore, it was demonstrated that active Lcp1_VH2 is a Cu(II)-containing oxygenase that exhibits a conserved domain of unknown function which cannot be detected in any other hitherto-characterized enzyme. The results presented here indicate that this domain might represent a new protein family of oxygenases.     

Investigation of the effects of head irradiation with gamma rays and protons on startle and pre-pulse inhibition behavior in mice

With the increased international emphasis on manned space exploration, there is a growing need to understand the impact of the spaceflight environment on health and behavior. One particularly important aspect of this environment is low-dose radiation. In the present studies, we first characterized the γ- and proton-irradiation dose effect on acoustic startle and pre-pulse inhibition behaviors in mice exposed to 0-5 Gy brain-localized irradiation, and assessed these effects 2 days later. Subsequently, we used 2 Gy to assess the time course of γ- and proton-radiation effects on startle reactivity 0-8 days after exposure. Exposures targeted the brain to minimize the impact of peripheral inflammation-induced sickness behavior. The effects of radiation on startle were subtle and acute. Radiation reduced the startle response at 2 and 5 Gy. Following a 2-Gy exposure, the response reached a minimum at the 2-day point. Proton and γ-ray exposures did not differ in their impact on startle. We found there were no effects of radiation on pre-pulse inhibition of the startle response.