Testing for common structures in a panel of threshold models

We consider the problem of examining the extent of (partial) similarity in the dynamics of a panel of independent threshold autoregressive processes. We develop some tests for common structure via Wald's approach and by checking whether the parameter estimates of the unconstrained threshold models satisfy the constraints defining the common structure. One test concerns the equality of independent ratios of normal means, which is shown to have nonstandard asymptotic null distribution. These tests are illustrated with a modern panel of Canadian lynx data; our analysis suggests that the lynx data over Canada share similar dynamics in the decrease phase, but they appear to be different in the increase phase.     

Variation in scale shape among alternative sympatric phenotypes of Arctic charr Salvelinus alpinus from two lakes in Scotland

Landmark‐based geometric morphometric analysis was used to detect differences in scale shape between ecologically distinct phenotypes of Arctic charr Salvelinus alpinus coexisting in the same lake. Relative warp analysis and standard multivariate analyses of the partial warps, obtained after a Procrustes superimposition, showed that scale landmarks were efficient in discriminating among two closely related alternative phenotypes within each of the two lakes. In Loch Tay, S. alpinus exhibited a bimodal body size‐frequency distribution among sexually mature fish, whereas in Loch Awe, S. alpinus are unimodal in body size but segregated into two distinct spawning phenotypes. In both lakes, alternative phenotypes showed significant differences in foraging ecology, habitat use and life history. It is probable that differences in scale shape reflect differences in ecology of these forms.     

Immunochemical studies of Shigella flexneri 2a and 6, and Shigella dysenteriae type 1 O-specific polysaccharide-core fragments and their protein conjugates as vaccine candidates

There is no licensed vaccine for the prevention of shigellosis. Our approach to the development of a Shigella vaccines is based on inducing serum IgG antibodies to the O-specific polysaccharide (O-SP) domain of their lipopolysaccharides (LPS). We have shown that low molecular mass O-SP-core (O-SPC) fragments isolated from Shigella sonnei LPS conjugated to proteins induced significantly higher antibody levels in mice than the full length O-SP conjugates. This finding is now extended to the O-SPC of Shigella flexneri 2a and 6, and Shigella dysenteriae type 1. The structures of O-SPC, containing core plus 1-4 O-SP repeat units (RUs), were analyzed by NMR and mass spectroscopy. The first RUs attached to the cores of S. flexneri 2a and 6 LPS were different from the following RUs in their O-acetylation and/or glucosylation. Conjugates of core plus more than 1 RU were necessary to induce LPS antibodies in mice. The resulting antibody levels were comparable to those induced by the full length O-SP conjugates. In S. dysenteriae type 1, the first RU was identical to the following RUs, with the exception that the GlcNAc was bound to the core in the β-configuration, while in all other RUs the GlcNAc was present in the α-configuration. In spite of this difference, conjugates of S. dysenteriae type 1 core with 1, 2, or 3 RUs induced LPS antibodies in mice with levels statistically higher than those of the full size O-SP conjugates. O-SPC conjugates are easy to prepare, characterize, and standardize, and their clinical evaluation is planned.     

Triplet state spectra and dynamics of geometric isomers of carotenoids

The observation of preferential binding of cis-carotenoids in purple bacterial photosynthetic reaction centers versus trans-isomers in antenna pigment protein complexes has led to the hypothesis that the natural selection of stereoisomers has physiological significance. In order to test this hypothesis, we have undertaken a systematic series of investigations comparing the optical spectroscopic properties and excited state dynamics of cis and trans isomers of carotenoids. The present work compares the triplet state spectra, lifetimes, and energy transfer rates of all-trans-spheroidene and 13,14-locked-cis-spheroidene, the latter of which is incapable of isomerizing to the all-trans configuration, and therefore provides a unique opportunity to examine the triplet state properties of a structurally stable cis molecule. The data reveal only small differences in spectra, decay dynamics, and transfer times and suggest there is little intrinsic advantage in either triplet energy transfer or triplet state decay arising from the inherently different isomeric forms of cis compared to trans carotenoids.     

The paradoxical effects of nutrient ratios and supply rates on an outbreaking insect herbivore, the Australian plague locust

1. The Australian plague locust, Chortoicetes terminifera, develops following rainfall in an environment dominated by two host plants, the annual Dactyloctenium radulans and the perennial Astrebla lappacea. This simple system provides an ideal opportunity to explore the relationship between plant quality, individual herbivore performance and population responses. 2. We compared the two grasses chemically and structurally, and the behavioural, physiological and developmental responses of locust nymphs to these diets. 3. The grasses appeared to be of similar nutritional quality in terms of their chemical composition, although they differed in their physical properties. Early instar nymphs performed equally well on both grasses. However, older nymphs consuming D. radulans developed faster, survived better and attained a higher body weight compared with those consuming A. lappacea. 4. The differences in performance by the older nymphs related to the rate and ratio of supply of carbohydrate and protein from the two grasses, with less carbohydrate being assimilated from A. lappacea than D. radulans per unit of protein assimilated. Experiments showed that these differences arose as a direct result of the physical barrier to nutrient extraction provided by cell walls and indirectly through the amount of water contained within each cell. Paradoxically, nitrogen did not limit performance in the traditional sense through shortage,but rather its relative excess in A. lappacea appeared to impede intake and assimilation of adequate carbohydrate. 5. As a consequence, we predict that the length of time D. radulans remains available following rainfall will influence plaguing dynamics, although not for the reasons previously thought. 6. The results highlight the need to consider nutrient balance and actual rates of supply (rather than simply measuring the chemical composition of the plant) when attempting to understand herbivore nutritional ecology.     

Dental arch asymmetry in an isolated Adriatic community

Developmental stability reflects the ability of a genotype to develop in the same way under varying environmental conditions. Deviations from developmental stability, arising from disruptive effects of environmental and genetic stresses, can be measured in terms of fluctuating asymmetry, a particularly sensitive indicator of the ability to cope with these stresses during ontogeny. In an inbred Adriatic island population, we expected dental arch fluctuating asymmetry 1) to be higher than in an outbred sample from the same island, and 2) within this population, to increase with the level of inbreeding. Due to environmental stress, we also expected to find higher fluctuating asymmetry in the outbred island population than in an urban reference group from the same country. The material consisted of 506 dental casts of 253 children from 1) the island of Hvar, and 2) Zagreb, Croatia. Three-dimensional coordinates of 26 landmarks spanning the arches were digitized. The analysis partitioned the asymmetry of arch forms into components for directional and fluctuating bilateral asymmetry, using the appropriate Procrustes method (geometric morphometrics). The results corroborated the hypotheses. Fluctuating asymmetry was found to be higher on the island than in Zagreb in all groups and in both jaws, and increased significantly with endogamy level in the lower jaw. There was no significant directional asymmetry in the Zagreb sample and likewise none in the upper jaws of the outbred island group, but significant directional asymmetry in both jaws of the inbred population and also in the lower jaws of the outbred island group. These results suggest an environmental as well as a genetic influence on dental arch asymmetry. Although the lower jaws expressed these two stresses almost additively, the upper jaws appeared to be better buffered. The role of directional asymmetry as a potential indicator of craniofacial developmental instability clearly merits further attention.     

The QTN program and the alleles that matter for evolution: all that's gold does not glitter

The search for the alleles that matter, the quantitative trait nucleotides (QTNs) that underlie heritable variation within populations and divergence among them, is a popular pursuit. But what is the question to which QTNs are the answer? Although their pursuit is often invoked as a means of addressing the molecular basis of phenotypic evolution or of estimating the roles of evolutionary forces, the QTNs that are accessible to experimentalists, QTNs of relatively large effect, may be uninformative about these issues if large‐effect variants are unrepresentative of the alleles that matter. Although 20th century evolutionary biology generally viewed large‐effect variants as atypical, the field has recently undergone a quiet realignment toward a view of readily discoverable large‐effect alleles as the primary molecular substrates for evolution. I argue that neither theory nor data justify this realignment. Models and experimental findings covering broad swaths of evolutionary phenomena suggest that evolution often acts via large numbers of small‐effect polygenes, individually undetectable. Moreover, these small‐effect variants are different in kind, at the molecular level, from the large‐effect alleles accessible to experimentalists. Although discoverable QTNs address some fundamental evolutionary questions, they are essentially misleading about many others.