Comparison of the accuracies of several phylogenetic methods using protein and DNA sequences

A biologically realistic method was used to simulate evolutionary trees. The method uses a real DNA coding sequence as the starting point, simulates mutation according to the mutational spectrum of Escherichia coli-including base substitutions, insertions, and deletions-and separates the processes of mutation and selection. Trees of 8, 16, 32, and 64 taxa were simulated with average branch lengths of 50, 100, 150, 200, and 250 changes per branch. The resulting sequences were aligned with ClustalX, and trees were estimated by Neighbor Joining, Parsimony, Maximum Likelihood, and Bayesian methods from both DNA sequences and the corresponding protein sequences. The estimated trees were compared with the true trees, and both topological and branch length accuracies were scored. Over the variety of conditions tested, Bayesian trees estimated from DNA sequences that had been aligned according to the alignment of the corresponding protein sequences were the most accurate, followed by Maximum Likelihood trees estimated from DNA sequences and Parsimony trees estimated from protein sequences.     

Calculations of NMR dipolar coupling strengths in model peptides

Ab initio MP2 and density functional quantum chemistry calculations are used to explore geometries and vibrational properties of N-methylacetamide and of the alanine dipeptide with backbone angles characteristic of helix and sheet regions in proteins. The results are used to explore one-bond direct dipolar couplings for the N–H, C–H, C–N, and C–C bonds, as well as for the two-bond C–H interaction. Vibrational averaging affects these dipolar couplings, and these effects can be expressed as effective bond lengths that are 0.5–3% larger than the true bond lengths; bending and torsion vibrations have a bigger influence on the effective coupling than do stretching vibrations. Because of zero-point motion, these effects are important even at low temperature. Hydrogen bonding interactions at the amide group also increase the N-H effective bond length. Although vibrational contributions to effective bond lengths are small, they can have a significant influence on the extraction of order parameters from relaxation data, and a knowledge of relative bond lengths is needed when several types of dipolar couplings are to be simultaneously used for refinement. The present computational results are compared to both solid- and liquid-state NMR experiments. The analysis suggests that secondary structural elements in many proteins may be more rigid than is commonly thought.     

Correct folding of the beta-barrel of the human membrane protein VDAC requires a lipid bilayer

Spontaneous membrane insertion and folding of beta-barrel membrane proteins from an unfolded state into lipid bilayers has been shown previously only for few outer membrane proteins of Gram-negative bacteria. Here we investigated membrane insertion and folding of a human membrane protein, the isoform 1 of the voltage-dependent anion-selective channel (hVDAC1) of mitochondrial outer membranes. Two classes of transmembrane proteins with either alpha-helical or beta-barrel membrane domains are known from the solved high-resolution structures. VDAC forms a transmembrane beta-barrel with an additional N-terminal alpha-helix. We demonstrate that similar to bacterial OmpA, urea-unfolded hVDAC1 spontaneously inserts and folds into lipid bilayers upon denaturant dilution in the absence of folding assistants or energy sources like ATP. Recordings of the voltage-dependence of the single channel conductance confirmed folding of hVDAC1 to its active form. hVDAC1 developed first beta-sheet secondary structure in aqueous solution, while the alpha-helical structure was formed in the presence of lipid or detergent. In stark contrast to bacterial beta-barrel membrane proteins, hVDAC1 formed different structures in detergent micelles and phospholipid bilayers, with higher content of beta-sheet and lower content of alpha-helix when inserted and folded into lipid bilayers. Experiments with mixtures of lipid and detergent indicated that the content of beta-sheet secondary structure in hVDAC1 decreased at increased detergent content. Unlike bacterial beta-barrel membrane proteins, hVDAC1 was not stable even in mild detergents such as LDAO or dodecylmaltoside. Spontaneous folding of outer membrane proteins into lipid bilayers indicates that in cells, the main purpose of membrane-inserted or associated assembly factors may be to select and target beta-barrel membrane proteins towards the outer membrane instead of actively assembling them under consumption of energy as described for the translocons of cytoplasmic membranes.     

Longer tongues and swifter handling: why do more bumble bees (Bombus spp.) than honey bees (Apis mellifera) forage on lavender (Lavandula spp.)?

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The validity of different methods in the backcalculation of the lengths of roach—a comparison between scales and cleithra

The backcalculated lengths of roach Rutilus rutilus obtained with three different proportional methods [body proportional (BPH) and scale proportional hypotheses (SPH), Fraser—Lee] were compared. In the BPH and SPH methods both scales and cleithra were used, while the Fraser—Lee method was used with scales only. The validity of the results was evaluated by comparing the results with observed lengths within one cohort. Both body—scale and body-cleithrum relationships were best described by a power function ( r ²= 0·83). The backcalculated lengths of roach at age 1 varied from 51 mm (SPH, scales and cleithra) to 72 mm (Fraser—Lee), a 30% difference. In within-cohort comparisons, the difference compared with observed lengths was smallest in BPH (<4% with few exceptions). The linear Fraser—Lee method overestimated (up to 5%) the lengths at young ages and underestimated the lengths at older ages (3–5%). In SPH the difference with observed length was 12% at highest. The length estimates by SPH were more affected by the age—structure of the sample than the estimates by BPH, which suggested that Lee's phenomenon was present. This was tested by backcalculating the lengths at the age of 2 years for roach, separately from different age-groups. The backcalculated lengths declined with the increasing age of fish used in the calculations. The phenomenon was strongest in SPH and weakest in Fraser—Lee. The results suggested that in the backcalculation of the lengths of roach, BPH method gives the most reliable results. Considering the other methods, Fraser—Lee should be used rather than SPH.     

Synthesis and properties of methyl 9,12,15-octadecatrienoate geometric isomers

The eight geometrically isomeric methyl 9,12,15-octadecatrienoates were prepared by using the Wittig reaction to couple cis- or trans-3-hexyenyltriphenylphosphonium bromide and methyl 12-oxo-cis- or trans-9-dodecenoate. Pairs of geometric triene isomers formed were separated by partial silver resin chromatography. Physical constants including melting points, percent trans by infrared, equivalent chain lengths (ECL), and ¹³C nuclear magnetic resonance (NMR) chemcial shifts are tabulated for the individual isomers.     

Plant cells express telomerase activity upon transfer to callus culture, without extensively changing telomere lengths

Changes in telomere lengths and telomerase activity in tobacco cells were studied during dedifferentiation and differentiation; leaf tissues were used to initiate callus cultures, which were then induced to regenerate plants. While no significant changes in the range of telomere lengths were observed in response to dedifferentiation and differentiation, there was a conspicuous increase in telomerase activity in calli compared to the source leaves, where the activity was hardly detectable. In leaves of regenerated plants, the telomerase activity fell to almost the same level as in the original plant, showing on the average 0.04% of the level in callus. The process was then repeated using the regenerants as the source material. In the second round of dedifferentiation and differentiation, telomerase activity showed a similar increase in calli derived from regenerated plants and a drop in plants regenerated from these calli. Telomere lengths remained unchanged both in calli and in leaves of regenerants. The conservation of telomere lengths over repeated rounds of dedifferentiation and differentiation, which are associated with dramatic changes in cell division rate and corresponding variation in telomerase activity may reflect the function of a regulatory mechanism in plant cells which controls telomerase action to compensate for replicative loss of telomeric DNA. Received: 31 July 1998 / Accepted: 21 September 1998     

The comparative evolution of lizard claw and toe morphology and clinging performance

In this study, I utilize the expected functional relationships between claw and toe morphology and clinging performance as a basis for examining evolutionary trends across 85 lizard taxa from 13 families. After controlling for body size and phylogeny, multivariate comparisons indicate that several aspects of claw and toe morphology are correlated with clinging performance. Specifically, evolutionary increases in claw curvature, toe width and adhesive lamella number are correlated with increases in clinging performance on smooth substrates. Furthermore, evolutionary increases in claw height and decreases in toe length are correlated with increases in clinging performance on rough substrates. Sensitivity analyses revealed that changes in both branch lengths and procedural order of correction for body size and phylogeny do not generally have an effect on phylogenetic comparisons. These results demonstrate that the evolution of claw and toe morphology is correlated with the evolution of clinging performance across a wide range lizard taxa.     

Neuroprotective effects of purslane herb aquenous extracts against D-galactose induced neurotoxicity

In order to evaluate mechanisms of natural plant purslane herb aquenous extracts (PHAS) for neuroprotective, we assessed neuroprotective effects of PHAS at doses of 2.5, 5 and 10 mg/(kg day) on SD mice injected daily with D-gal (50 mg/(kg day)) by behavioral tests. PHAS-fed mice showed higher activity upon induction by new environmental stimuli, lower anxiety and higher novelty-seeking behavior in the open field tasks, and significantly improved learning and memory ability in step-through compared with D-gal-treated mice. We further examined the mechanisms involved in neuroprotective effects of PHAS on mouse brain. PHAS significantly increased superoxide dismutase (SOD) activity and decreased the malondialdehyde (MDA) level. Meanwhile, PHAS also could up-regulate telomere lengths and telomerase activity in PHAS-fed groups. Furthermore, we examined the expression of p21(waf1) and p53 mRNA and protein in mouse brain by western blot analysis and real-time RT-PCR. We found that p21(waf1)was down-regulated by PHAS without changing the expression of p53. The results of this study suggested that the PHAS might be a primary target of p21(waf1)and the neuroprotective effect of PHAS might be carried out through a p21(waf1)-dependent and p53-independent pathway.     

Accounting for molecular stochasticity in systematic revisions: Species limits and phylogeny of Paroaria

Different frameworks have been proposed for using molecular data in systematic revisions, but there is ongoing debate on their applicability, merits and shortcomings. In this paper we examine the fit between morphological and molecular data in the systematic revision of Paroaria, a group of conspicuous songbirds endemic to South America. We delimited species based on examination of >600 specimens, and developed distance-gap, and distance- and character-based coalescent simulations to test species limits with molecular data. The morphological and molecular data collected were then analyzed using parsimony, maximum likelihood, and Bayesian phylogenetics. The simulations were better at evaluating the new species limits than using genetic distances. Species diversity within Paroaria had been underestimated by 60%, and the revised genus comprises eight species. Phylogenetic analyses consistently recovered a congruent topology for the most recently derived species in the genus, but the most basal divergences were not resolved with these data. The systematic and phylogenetic hypotheses developed here are relevant to both setting conservation priorities and understanding the biogeography of South America.