Sperm competition in tropical versus temperate zone birds

Sperm competition represents an important component of post-copulatory sexual selection. It has been argued that the level of sperm competition declines in birds towards the equator. However, to date, sperm competition estimates have been available mainly for avian species inhabiting the northern temperate zone. Here we apply a novel approach, using the coefficient of between-male variation (CV_bm) in sperm size as an index for sperm competition risk, in a comparative analysis of 31 Afrotropical and 99 northern temperate zone passerine species. We found no difference in sperm competition risk between the two groups, nor any relationship with migration distance. However, a multivariate model indicated that sperm competition risk was highest in species with a combination of low body mass and few eggs per clutch. The effect of clutch size was most pronounced in tropical species, which indicates that sperm competition risk in tropical and temperate species is differently associated with particular life-history traits. Although tropical species had lower sperm competition risk than temperate zone species for overlapping clutch sizes, the idea of a generally reduced risk of sperm competition in tropical birds was not supported by our analysis.     

What,if anything,is a social niche?

The term “social niche” is rapidly increasing in usage, particularly in the context of “social niche construction.” But what (if anything) is a social niche? Here, we survey papers that have used the term to uncover commonalities and discrepancies in its definition. We aim to alert researchers to the need for more consistency in how the term is used in the literature, and we provide a working definition of “social niche:” the set of social environments in which the focal individual has non-zero inclusive fitness. We consider the extent to which a social niche is analogous to an ecological niche, discuss whether a population-level social niche can be meaningfully identified, and describe conceptual insights about the properties of social niches, focusing on social niche construction. We highlight questions about social niches that demand more theoretical and empirical attention.     

Effects of artificial defoliation of pines on the structure and physiology of the soil fungal community of a mixed pine-spruce forest

Loss of photosynthetic area can affect soil microbial communities by altering the availability of fixed carbon. We used denaturing gradient gel electrophoresis (DGGE) and Biolog filamentous-fungus plates to determine the effects of artificial defoliation of pines in a mixed pine-spruce forest on the composition of the fungal community in a forest soil. As measured by DGGE, two fungal species were affected significantly by the defoliation of pines (P < 0.001); the frequency of members of the ectomycorrhizal fungus genus Cenococcum decreased significantly, while the frequency of organisms of an unidentified soil fungus increased. The decrease in the amount of Cenococcum organisms may have occurred because of the formation of extensive hyphal networks by species of this genus, which require more of the carbon fixed by their host, or because this fungus is dependent upon quantitative differences in spruce root exudates. The defoliation of pines did not affect the overall composition of the soil fungal community or fungal-species richness (number of species per core). Biolog filamentous-fungus plate assays indicated a significant increase (P < 0.001) in the number of carbon substrates utilized by the soil fungi and the rate at which these substrates were used, which could indicate an increase in fungal-species richness. Thus, either small changes in the soil fungal community give rise to significant increases in physiological capabilities or PCR bias limits the reliability of the DGGE results. These data indicate that combined genetic and physiological assessments of the soil fungal community are needed to accurately assess the effect of disturbance on indigenous microbial systems.     

Ionic-strength-dependent effects in protein folding: analysis of rate equilibrium free-energy relationships and their interpretation

The traditional approach to studying protein folding involves applying a perturbation, usually denaturant or mutation, and determining the effect upon the free energy of folding, DeltaG0, and the activation free energy, DeltaG(not equal). Data collected as a function of the perturbation can be used to construct rate equilibrium free-energy relationships, which report on the development of interactions in the transition state for folding. We examine the use of the ionic-strength-dependent rate equilibrium free-energy relationship in protein folding using the N-terminal domain of L9, a small alpha-beta protein, as a model system. Folding is two-state for the range of ionic strength examined, 0.045-1.52 M. The plot of DeltaG(not equal) versus DeltaG0 is linear (r2= 0.918), with a slope equal to 0.45. The relatively low value of the slope indicates that the ionic-strength-dependent interactions are modestly developed in the transition state. The slope is, however, greater than that of a plot of DeltaG(not equal) versus DeltaG0 constructed by varying pH, thus demonstrating directly that ionic-strength-dependent studies probe more than simple electrostatic interactions. Potential transition movement was probed by analysis of the denaturant, ionic strength cross-interaction parameters. The values are small but nonzero and positive, suggesting a small shift of the transition state toward the native state as the protein is destabilized, i.e., Hammond behavior. The complications that arise in the interpretation of ionic-strength-dependent rate equilibrium free-energy relationships are discussed, and it is concluded that the ionic-strength-dependent studies do not provide a reliable indicator of the role of electrostatic interactions. Complications include incomplete screening of electrostatic interactions, specific ion binding, Hofmeister effects, and the potential presence of electrostatic interactions in the denatured state ensemble.     

Differential effects of serine side chain interactions in amyloid formation by islet amyloid polypeptide

Islet amyloid polypeptide (IAPP), a 37 residue polypeptide, is the main protein component of islet amyloid deposits produced in the pancreas in Type 2 diabetes. Human IAPP contains five serine residues at positions 19, 20, 28, 29, and 34. Models of the IAPP amyloid fibril indicate a structure composed of two closely aligned columns of IAPP monomers with each monomer contributing to two intermolecular β‐strands. Ser 19 and Ser 20 are in the partially ordered β‐turn region, which links the two strands, whereas Ser 28, Ser 29, and Ser 34 are in the core region of the amyloid fibril. Ser 29 is involved in contacts between the two columns of monomers and is the part of the steric zipper interface. We undertook a study of individual serine substitutions with the hydrophobic isostere 2‐aminobutyric acid (2‐Abu) to examine the site‐specific role of serine side chains in IAPP amyloid formation. All five variants formed amyloid. The Ser 19 to 2‐Abu mutant accelerates amyloid formation by a factor of 3 to 4, while the Ser 29 to 2‐Abu mutation modestly slows the rate of amyloid formation. 2‐Abu replacements at the other sites had even smaller effects. The data demonstrate that the cross‐column interactions made by residue 29 are not essential for amyloid formation and also show that cross‐strand networks of hydrogen‐bonded Ser side chains, so called Ser‐ladders, are not required for IAPP amyloid formation. The effect of the Ser 19 to 2‐Abu mutant suggests that residues in this region are important for amyloid formation by IAPP.     

Conformational analysis of peptide fragments derived from the peripheral subunit-binding domain from the pyruvate dehydrogenase multienzyme complex of Bacillus stearothermophilus: evidence for nonrandom structure in the unfolded state

There is currently a great deal of interest in the early events in protein folding. Two issues that have generated particular interest are the nature of the unfolded state under native conditions and the role of local interactions in folding. Here, we report the results of a study of a set of peptides derived from a small two-helix protein, the peripheral subunit-binding domain of the pyruvate dehydrogenase multienzyme complex. Five peptides of overlapping sequence were prepared, including sequences corresponding to each of the helices and to the region connecting them. The peptides were characterized by CD and, where possible, nmr. A peptide corresponding to the second helix is between 12 and 17% helical at neutral pH. CD also indicates a lower percentage of helical structure in the peptide corresponding to the first alpha-helix, although the values of the alpha-proton chemical shifts suggest some preference for nonrandom structure. Peptides corresponding to the interhelical loop, which in the full domain contains two overlapping beta-turns and a 5-residue 3(10)-helix, are less structured. There is no significant change in the helicity of any of these peptides with pH. To test for fragment complementation, CD spectra of the two peptides derived from each helix and the long connecting peptide were compared to the spectra of each possible pair, as well as to a mixture containing all three. No increase in structure was observed. We complement our peptide studies by characterizing a point mutant, D34V, which disrupts a critical hydrogen bonding network. This mutant is unable to fold and provides a useful model of the denatured state. The mutant is between 9 and 16% helical as judged by CD. The modest amount of helical structure formed in some of the peptide fragments and in the point mutant suggests that the denatured state of the peripheral subunit binding domain is not completely unstructured. This may contribute to the very rapid folding observed for the intact protein.     

Analysis of amylin cleavage products provides new insights into the amyloidogenic region of human amylin

Human chorionic gonadotropin (hCG), is a placental hormone which exerts its major effect by stimulating progesterone production, crucially sustaining the early weeks of pregnancy. Detection of hCG with specific monoclonal antibodies (mAbs) has become the chosen means for pregnancy diagnosis. We have used antibody Fv fragments derived from two high-affinity mAbs, one against the alpha and the other against the beta-hCG subunit to enable the crystallisation of intact or desialylated hCG. Crystals of a ternary complex composed of Fv anti-alpha/hCG/Fv anti-beta were found to diffract to 3.5 A resolution, and the structure was solved by molecular replacement. In the crystal, the two Fvs keep hCG as in a molecular cage, providing good protein-protein contacts and leaving enough space for the saccharides to be accommodated in the cell solvent. The two Fvs were found not to interact directly through their complementary-determining regions with the hCG saccharides, but only with the protein. The hCG structure in the ternary complex was very close to that of the HF partially deglycosylated hormone, thus indicating that neither the saccharides nor the Fvs had any substantial influence on hormone structure.     

Effects of breeding density, synchrony, and experience on extrapair paternity in tree swallows

Breeding density, synchrony, and experience are expected toinfluence the frequency of extrapair paternity in birds. UsingDNA fingerprinting, we examined the effect of these factorson tree swallows nesting at relatively high (grids of nest-boxes)and low (solitary boxes at least 100 m from the nearest neighbor)densities and in relatively synchronous (Alberta) and asynchronous(Ontario) populations in Canada. The mean percentage of extrapairoffspring per nest did not differ significantly between birdsnesting in grids (43%, n = 22 families) and solitary boxes (57%,n = 12 families). Similarly, there was no significant differencein the mean percentage of extrapair offspring per nest betweenrelatively synchronous (60%, n = 12 Alberta families) and asynchronous(41%, n = 22 Ontario families) populations. We also found noconsistent pattern between extrapair paternity and breedingexperience among seven males and seven females examined overtwo to three breeding seasons. Female tree swallows can influencethe fertilization success of extrapair males by active selectionand rejection of copulation partners. We suggest that this abilitylimits the predicted effect of various ecological factors onthe frequency of extrapair paternity