Responses of benthic community metabolism to abiotic factors in a mountain river in southern Poland

Seasonal and longitudinal metabolic trends in benthic communities were studied in the five orders of a natural mountain river (the Stradomka) in southern Poland. The method of oxygen change of rocky substrata in chambers was applied. Metabolic data were compared with abiotic (light regime, channel geomorphology and stream hydrology), and water chemical variables. A tendency of downstream increase in gross production and community respiration was observed between 1st and 4th stream orders. The highest values of GP (0.94 g C m^-2 24 h ^-1) and CR (1.12 g C m^-2 24 h ^-1) were observed in the middle Stradomka course (3–4 orders) in spring. A distinct negative NDM (heterotrophy) of the benthic community was measured in autumn and spring. During winter NDM was almost constant and oscillated around zero. The P/R ratio changed according to season and fluctuated between heterotrophy (P/R < 1) and autotrophy (P/R > 1). In general, heterotrophy prevailed in the study system (except 5th order). A marked shift in P/R between 4th and 5th stream orders confirms the prediction included in the RCC. Water temperature and PAR accounted for 56% in GP variability, whereas CR and NDM were not related to these variables. The combined variables (PAR and PO₄–P) attributed to 69% in GP variability. The set of chemical factors was less related to Stradomka metabolic data. These results suggest that metabolic processes in this mountain river remarkably depend on physical variables (solar radiation, altitude, water temperature and conductivity). Metabolic parameters were similar to other geographical mountain systems. This revised version was published online in July 2006 with corrections to the Cover Date.     

Assessing chimpanzee personality and subjective well‐being in Japan

We tested whether the cultural background of raters influenced ratings of chimpanzee personality. Our study involved comparing personality and subjective well‐being ratings of 146 chimpanzees in Japan that were housed in zoos, research institutes, and a retirement sanctuary to ratings of chimpanzees in US and Australian zoos. Personality ratings were made on a translated and expanded version of a questionnaire used to rate chimpanzees in the US and Australia. Subjective well‐being ratings were made on a translated version of a questionnaire used to rate chimpanzees in the US and Australia. The mean interrater reliabilities of the 43 original adjectives did not markedly differ between the present sample and the original sample of 100 zoo chimpanzees in the US. Interrater reliabilities of these samples were highly correlated, suggesting that their rank order was preserved. Comparison of the factor structures for the Japanese sample and for the original sample of chimpanzees in US zoos indicated that the overall structure was replicated and that the Dominance, Extraversion, Conscientiousness, and Agreeableness domains clearly generalized. Consistent with earlier studies, older chimpanzees had higher Dominance and lower Extraversion and Openness scores. Correlations between the six domain scores and subjective well‐being were comparable to those for chimpanzees housed in the US and Australia. These findings suggest that chimpanzee personality ratings are not affected by the culture of the raters. Am. J. Primatol. 71:283–292, 2009. © 2009 Wiley‐Liss, Inc.     

氮磷添加对红壤区城郊湿地松林凋落叶分解的影响

城市化易导致城市森林氮(N)沉降和磷(P)富集,进而对凋落物分解过程产生影响。以位于南昌市郊的湿地松(Pinuse lliottii Engelm.)林为研究对象,采用尼龙网袋分解法,模拟N沉降(10g N·m-2·a-1,[N])、P积累(2.5g P·m-2·a-1,[P])和N沉降+P积累(10N·m-2·a-1+2.5g P·m-2·a-1,[N+P])对凋落叶分解速率与C、N、P含量及其化学计量比动态变化的影响。结果表明:与对照(CK)相比,[N]、[P]和[N+P]均促进凋落叶的前期(0～180d)分解速率,抑制中期(180～360d)、后期(360～540d)的分解速率;至540d时分解速率表现为[N]、[P]和CK无差异,但均高于[N+P](P0.05)。[N]提高分解过程中凋落叶N浓度,N含量表现为分解前期积累、后期释放;[P]提高分解过程中凋落叶P浓度,P含量持续积累;[N+P]提高N和P浓度,分解前期N、P含量积累,后期释放;而不同处理的C含量均表现为释放。凋落物基质C/N/P比与分解速率的相关性随分解阶段而表现各异。综合来看,城市化导致的N沉降和P富集叠加效应具有抑制城市森林凋落物分解过程的潜在性。     

Calculation of pKas in RNA: on the structural origins and functional roles of protonated nucleotides

pK(a) calculations based on the Poisson-Boltzmann equation have been widely used to study proteins and, more recently, DNA. However, much less attention has been paid to the calculation of pK(a) shifts in RNA. There is accumulating evidence that protonated nucleotides can stabilize RNA structure and participate in enzyme catalysis within ribozymes. Here, we calculate the pK(a) shifts of nucleotides in RNA structures using numerical solutions to the Poisson-Boltzmann equation. We find that significant shifts are predicted for several nucleotides in two catalytic RNAs, the hairpin ribozyme and the hepatitis delta virus ribozyme, and that the shifts are likely to be related to their functions. We explore how different structural environments shift the pK(a)s of nucleotides from their solution values. RNA structures appear to use two basic strategies to shift pK(a)s: (a) the formation of compact structural motifs with structurally-conserved, electrostatic interactions; and (b) the arrangement of the phosphodiester backbone to focus negative electrostatic potential in specific regions.     

Maintenance of species boundaries in a Neotropical radiation of Begonia

A major goal of evolutionary biology is to determine the mechanisms generating biodiversity. In Begonia, one of the largest plant genera (1900+ species), it has been postulated that the high number of endemic species is a by‐product of low gene flow among populations, which predisposes the group to speciation. However, this model of divergence requires that reproductive barriers accumulate rapidly among diverging species that overlap in their geographic ranges, otherwise speciation will be opposed by homogenizing gene flow in zones of secondary contact. Here, we test the outcomes of secondary contact in Begonia by genotyping multiple sympatric sites with 12 nuclear and seven plastid loci. We show that three sites of secondary contact between B. heracleifolia and B. nelumbiifolia are highly structured, mostly containing parental genotypes, with few F1 hybrids. A sympatric site between B. heracleifolia and B. sericoneura contains a higher proportion of F1s, but little evidence of introgression. The lack of later‐generation hybrids contrasts with that documented in many other plant taxa, where introgression is extensive. Our results, in conjunction with previous genetic work, show that Begonia demonstrate properties making them exceptionally prone to speciation, at multiple stages along the divergence continuum. Not only are populations weakly connected by gene flow, promoting allopatric speciation, but species often show strong reproductive barriers in secondary contact. Whether similar mechanisms contribute to diversification in other large genera remains to be tested.     

Genetics of Obesity: What have we Learned?

Candidate gene and genome-wide association studies have led to the discovery of nine loci involved in Mendelian forms of obesity and 58 loci contributing to polygenic obesity. These loci explain a small fraction of the heritability for obesity and many genes remain to be discovered. However, efforts in obesity gene identification greatly modified our understanding of this disorder. In this review, we propose an overlook of major lessons learned from 15 years of research in the field of genetics and obesity. We comment on the existence of the genetic continuum between monogenic and polygenic forms of obesity that pinpoints the role of genes involved in the central regulation of food intake and genetic predisposition to obesity. We explain how the identification of novel obesity predisposing genes has clarified unsuspected biological pathways involved in the control of energy balance that have helped to understand past human history and to explore causality in epidemiology. We provide evidence that obesity predisposing genes interact with the environment and influence the response to treatment relevant to disease prediction.     

Action-at-a-distance interactions enhance protein binding affinity

The identification of protein mutations that enhance binding affinity may be achieved by computational or experimental means, or by a combination of the two. Sources of affinity enhancement may include improvements to the net balance of binding interactions of residues forming intermolecular contacts at the binding interface, such as packing and hydrogen-bonding interactions. Here we identify noncontacting residues that make substantial contributions to binding affinity and that also provide opportunities for mutations that increase binding affinity of the TEM1 beta-lactamase (TEM1) to the beta-lactamase inhibitor protein (BLIP). A region of BLIP not on the direct TEM1-binding surface was identified for which changes in net charge result in particularly large increases in computed binding affinity. Some mutations to the region have previously been characterized, and our results are in good correspondence with this results of that study. In addition, we propose novel mutations to BLIP that were computed to improve binding significantly without contacting TEM1 directly. This class of noncontacting electrostatic interactions could have general utility in the design and tuning of binding interactions.     

Comparison between Generalized-Born and Poisson–Boltzmann methods in physics-based scoring functions for protein structure prediction

Continuum solvent models such as Generalized-Born and Poisson–Boltzmann methods hold the promise to treat solvation effect efficiently and to enable rapid scoring of protein structures when they are combined with physics-based energy functions. Yet, direct comparison of these two approaches on large protein data set is lacking. Building on our previous work with a scoring function based on a Generalized-Born (GB) solvation model, and short molecular-dynamics simulations, we further extended the scoring function to compare with the MM-PBSA method to treat the solvent effect. We benchmarked this scoring function against seven publicly available decoy sets. We found that, somewhat surprisingly, the results of MM-PBSA approach are comparable to the previous GB-based scoring function. We also discussed the effect to the scoring function accuracy due to presence of large ligands and ions in some native structures of the decoy sets.     

The influence of a transmembrane pH gradient on protonation probabilities of bacteriorhodopsin: the structural basis of the back-pressure effect

Bacteriorhodopsin pumps protons across a membrane using the energy of light. The proton pumping is inhibited when the transmembrane proton gradient that the protein generates becomes larger than four pH units. This phenomenon is known as the back-pressure effect. Here, we investigate the structural basis of this effect by predicting the influence of a transmembrane pH gradient on the titration behavior of bacteriorhodopsin. For this purpose we introduce a method that accounts for a pH gradient in protonation probability calculations. The method considers that in a transmembrane protein, which is exposed to two different aqueous phases, each titratable residue is accessible for protons from one side of the membrane depending on its hydrogen-bond pattern. This method is applied to several ground-state structures of bacteriorhodopsin, which residues already present complicated titration behaviors in the absence of a proton gradient. Our calculations show that a pH gradient across the membrane influences in a non-trivial manner the protonation probabilities of six titratable residues which are known to participate in the proton transfer: D85, D96, D115, E194, E204, and the Schiff base. The residues connected to one side of the membrane are influenced by the pH on the other side because of their long-range electrostatic interactions within the protein. In particular, D115 senses the pH at the cytoplasmic side of the membrane and transmits this information to D85 and the Schiff base. We propose that the strong electrostatic interactions found between D85, D115, and the Schiff base as well as the interplay of their respective protonation states under the influence of a transmembrane pH gradient are responsible for the back-pressure effect on bacteriorhodopsin.