Proteome-wide evidence for enhanced positive Darwinian selection within intrinsically disordered regions in proteins

Background  

Understanding the adaptive changes that alter the function of proteins during evolution is an important question for biology and medicine. The increasing number of completely sequenced genomes from closely related organisms, as well as individuals within species, facilitates systematic detection of recent selection events by means of comparative genomics.     

Persistence of Dispersal-limited Species in Structured Dynamic Landscapes

Dynamic landscape models have generally assumed random distributions of habitat although real landscapes show spatial organization at many scales. To explore the role of spatial structure in determining the frequency of dispersal-limited forest species, we used a cellular landscape model divided into two zones. Zones were distributed in a random, clustered, or regular spatial pattern. Within each zone habitat cells were randomly destroyed and regenerated, and habitat density and turnover rate were systematically varied. A hypothetical habitat-limited species dispersed between adjacent habitat cells. All trials showed a reduced species frequency relative to a static landscape. Reduction was greater at low habitat density (P = 0.30) than at high density (0.90) suggesting the importance of habitat connectivity in controlling species frequency. The greatest reduction occurred when habitat was concentrated in a small, regularly distributed zone at low habitat density reflecting the enforced isolation of individual habitat cells. Very little reduction was observed when habitat cells were packed into a small clustered zone, a situation promoting connectivity between cells. Moderate–severe frequency reduction occurred when habitat turnover was concentrated in a clustered zone at high habitat density, but little was observed when turnover was widely distributed in a regular or random pattern. These results can be interpreted in terms of a source-sink function in which spatial pattern controlled the degree of contact between landscape zones and determined opportunities for dispersal between habitat cells. We conclude that clustering of forest habitat has the potential to maintain herb species frequency in sparsely forested landscapes. Conversely, clustering of forest disturbance in heavily forested regions, or regular distribution of forest stands (as often occurs in agricultural regions) creates areas which are difficult to colonize, and should be avoided.     

Changes in plant chemical defenses and nutritional quality as a function of ontogeny in <Emphasis Type="Italic">Plantago lanceolata</Emphasis> (Plantaginaceae)

Numerous empirical studies have examined ontogenetic trajectories in plant defenses but only a few have explored the potential mechanisms underlying those patterns. Furthermore, most documented ontogenetic trajectories in plant defenses have generally concentrated on aboveground tissues; thus, our knowledge regarding whole plant trends in plant defenses throughout development or potential allocation constraints between growth and defenses is limited. Here, we document changes in plant biomass, nutritional quality and chemical defenses for below- and aboveground tissues across seven age classes of Plantago lanceolata (Plantaginaceae) to evaluate: (1) partial and whole plant ontogenetic trajectories in constitutive chemical defenses and nutritional quality, and (2) the role of resource allocation constraints, namely root:shoot (R:S) ratios, in explaining whole plant investment in chemical defenses over time. Overall investment in iridoid glycosides (IGs) significantly increased, while water and nitrogen concentrations in shoot tissues decreased with plant age. Significant variation in IG content between shoot and root tissues across development was observed: allocation of IGs into root tissues linearly increased from younger to older plants, while non-linear shifts in allocation of IGs during ontogeny were observed for shoot tissues. Finally, R:S ratios only weakly explained overall allocation of resources into defenses, with young stages showing a positive relationship, while older stages showed a negative relationship between R:S ratios and IG concentrations. Ontogenetic trajectories in plant quality and defenses within and among plant tissues can strongly influence insect herbivores’ performance and/or predation risk; thus, they are likely to play a significant role in mediating species interactions.     

The basic property of biomembranes

In order to explain the experimentally obtained results with biomembranes it has been assumed, that the diameter of all vesicles, defined by a lipid bilayer, form a perfect crystal. Later on it appeared that biomembranes are liquid crystals. Nevertheless already with biomembranes as crystals it was possible to calculate the diameters of all existing vesicles. As shown in the present paper, the results with liquid crystals were identical to those with a perfect crystal-model. Here I demonstrate that the geometric progression of the diameters of vesicles of biomembranes is based on the entropy of the lipids and it is shown that the diameters of biomembranes fit four geometric series. The surface areas of these series of biomembranes can be approximated by the two geometric series published previously. The experiments and the theoretical studies on which this work is based have been carried out at the Netherlands Cancer Institute, Amsterdam, The Netherlands.     

Prevalence of the 281 (Gly→Glu) mutation in hepatoerythropoietic porphyria and porphyria cutanea tarda

Summary The prevalence of the 281 (GlyGlu) mutation in hepatoerythropoietic porphyria (HEP) was investigated by the use of hybridization with a synthetic oligonucleotide probe. The mutation was found in HEP-affected members of two unrelated families from Spain, but was absent in two other patients from Italy and Portugal who also had HEP. Moreover, this mutation was not detected in 13 unrelated cases of familial (type II) porphyria cutanea tarda.     

A Neuro-Comparative Study between Single/Successive Thorium Dose Intoxication and Alginate Treatment

The adult male albino rats were grouped into five groups (control group and four variably treated groups with thorium (Th) in single or successive with or without alginate treatment). The IP administration of thorium nitrate (13.6 mg/kg b.wt.) induced a regional distribution and accumulation ordered as cerebellum > cerebral cortex > brain stem > hippocampus > hypothalamus > striatum. Also, it induces a significant increase in Na⁺, Ca²⁺, and Fe³⁺ ion content and malondialdehyde (MDA) level while K⁺ ions and glutathione (GSH) level were significantly decreased. On the other hand, the daily oral administration of 5% alginate showed a significant decreasing in the accumulation of thorium in the different brain areas and mitigated its hazardous effects. By the alginate treatment, Na⁺, Ca²⁺, Fe³⁺, and level of MDA were declined while K⁺ ions and GSH level showed a significant increase. The improvement of the investigated parameters was attributed to the specific chelating, regeneration, and antioxidant properties of the alginate. So, alginate administration could ameliorate the hazardous effects of thorium nitrate.     

Biodecolourization of azo and triphenylmethane dyes by <Emphasis Type="Italic">Dichomitus squalens</Emphasis> and <Emphasis Type="Italic">Phlebia</Emphasis> spp

Nine white-rot fungal strains were screened for biodecolourization of brilliant green, cresol red, crystal violet, congo red and orange II. Dichomitus squalens, Phlebia fascicularia and P. floridensis decolourized all of the dyes on solid agar medium and possessed better decolourization ability than Phanerochaete chrysosporium when tested in nitrogen-limited broth medium. Journal of Industrial Microbiology & Biotechnology (2002) 28, 201–203 DOI: 10.1038/sj/jim/7000222 Received 12 July 2001/ Accepted in revised form 22 October 2001     

Contribution of SELP and PSGL-1 genotypes and haplotypes to the presence of coronary heart disease in Tunisians

P-selectin (SELP) and its counter-receptor, P-selectin glycoprotein ligand-1 (PSGL-1), play key role in the transient attachment of leukocytes to endothelial cells predisposing to coronary heart disease (CHD). In the current report, 293 angiographically proven CHD patients and 327 age, gender, and race-matched controls were included. Our aim was to evaluate the contribution to CHD of the following SNPs: C-2123G, G-1969A and T715P in SELP, Met62Ile and the VNTR variants in PSGL-1 gene in a North African population from Tunisia. While there were no significant differences in the distribution of SELP or PSGL-1 alleles or genotypes between patients and controls, a trend for a significant association of the C-2123G genotypes distribution with incident CHD was observed (P = 0.06). Assuming an additive model of transmission, the risk was 74% higher among subjects carrying the GG genotypes in comparison to those carrying the CC genotype (OR = 1.74 [1.01–2.98], P = 0.04) and 80% higher in the recessive model (OR = 1.80 [1.08–3.01], P = 0.02). Haplotype analysis did not identify any specific SELP or PSGL-1 haplotypes to be associated with CHD. The present study demonstrated no evidence of association between individual SELP or PSGL-1 SNPs or haplotypes with incident CHD. However, this study replicates absence of association of the mostly studied SNP, T715P, previously reported in individuals with African origin.     

Inversions of chromosome arms 4AL and 2BS in wheat invert the patterns of chiasma distribution

In many species, including wheat, crossing over is distal, and the proximal regions of chromosome arms contribute little to genetic maps. This was thought to be a consequence of terminal initiation of synapsis favoring distal crossing over. However, in an inverted rye chromosome arm, the pattern of metaphase I chiasmata was also inverted, suggesting that crossover frequencies were specific to chromosome segments. Here, wheat chromosome arms 2BS and 4AL, with essentially entire arms inverted in reverse tandem duplications (rtd), were studied in the MI of meiosis. Inversion–duplication placed the recombining segments in the middle of the arms. While the overall pairing frequencies of the inverted–duplicated arms were considerably reduced relative to normal arms, chiasmata, if present, were always located in the same regions as in structurally normal arms, and relative chiasma frequencies remained the same. The frequencies of fragment or fragment + bridge configurations in AI and AII indicated that of the two tandemly arranged copies of segments in rtds, the more distal inverted segments were more likely to cross over than the segments in their original orientations. These observations show that also in wheat, relative crossover frequencies along chromosome arms are predetermined and independent of the segment location. The segments normally not licensed to cross over do not do so even when placed in seemingly most favorable positions for it.