CLIX: a search algorithm for finding novel ligands capable of binding proteins of known three-dimensional structure.

A computer algorithm, CLIX, capable of searching a crystallographic data-base of small molecules for candidates which have both steric and chemical likelihood of binding a protein of known three-dimensional structure is presented. The algorithm is a significant advance over previous strategies which consider solely steric or chemical requirements for binding. The algorithm is shown to be capable of predicting the correct binding geometry of sialic acid to a mutant influenza-virus hemagglutinin and of proposing a number of potential new ligands to this protein.     

Cellulose-microfibril-orienting mechanisms in plant cells walls

A brief review is given of the changing views over the years, as knowledge of wall structure has developed, concerning the mechanism whereby cellulose chains may be oriented. This leads to an examination of current concepts, particularly those concerning microtubules. It is shown that none of the mechanisms suggested whereby microtubules might cause orientation of cellulose microfibrils is consistent with the known range of molecular architectures found in plant cell walls. It is further concluded that any mechanism which necessitates an indissoluble link between the plasmalemma and the cellulose-synthesising complex at the tip of a microfibril is unacceptable. A new proposal is presented in which it is speculated that both microtubules and microfibrils are oriented by a mechanism separate from both. It is shown that if two vectors are contemplated, one parallel to cell length and one at right angles, and a sensor exists on the plasmalemma surface which responds to changes in the vectors, then all known wall structures may be explained. The possible nature of the vectors and the sensor are considered.     

Host plant growth characteristics as determinants of abundance and phenology in jumping plant-lice on downy willow

1. Salix lapponum host plants at an upper altitudinal site differed significantly in size, structural density, phenology, growth performance, and spatial isolation from those growing at a lower site. 2. Plant differences were paralleled by significant differences in psyllid population density and phenology parameters, with psyllid population density, percentage of catkins occupied, and phenological development relatively lower or retarded at the upper site. Population densities at the upper site, nevertheless, remained high. 3. Plant measurements were good predictors of insect density, often explaining up to 73% of the variance in abundance among plants at a given site. 4. Sets of four plant characters identified by best subsets regression were better predictors of psyllid density and development than single factors, although differences were often not great and the combinations of characters selected by multiple regression sometimes differed from the best single predictors. 5. Best single predictors of psyllid density on catkins were measurements of plant size, particularly height, length, and basal stem diameter. Shoot density and catkin phenology were occasionally important but plant isolation and prior growth performance were less important. 6. By contrast with density, age structure of the psyllid population was predicted best from plant phenological measurements, notably catkin phenology.     

Microgeographic genetic structure and intraspecific parasitism in the ant Leptothorax nylanderi

1. Genetic colony structure of the small central European ant Leptothorax nylanderi is affected strongly by ecological constraints such as nest site availability and intraspecific social parasitism. 2. Although L. nylanderi is generally monogynous and monandrous, more than a quarter of all nests collected in a dense population near Würzburg, Germany, contained several matrilines. As shown by microsatellite analysis, the average nest‐mate relatedness in these nests was 0.20. Genetically heterogeneous nests arise from nest take‐over by alien colonies or founding queens, a result of severe competition for nest sites. 3. In summer, more than one‐third of all colonies inhabited several nest sites at a time. Polydomy appears to be rather limited, with two or three nests belonging to a single polydomous colony. 4. Queens appear to dominate male production; only a small fraction (8%) of males was definitively not progeny of the queen present but might have been worker progeny or offspring of another queen. 5. Strong evidence for heterozygote deficiency was found and a total of nine diploid males was discovered in two colonies. These findings suggest deviation from random mating through small, localised nuptial flights.     

Latitudinal variation in population structure of wintering Pacific Black Brant

ABSTRACT.   Latitudinal variation in population structure during the winter has been reported in many migratory birds, but has been documented in few species of waterfowl. Variation in environmental and social conditions at wintering sites can potentially influence the population dynamics of differential migrants. We examined latitudinal variation in sex and age classes of wintering Pacific Black Brant ( Branta bernicla nigricans ). Brant are distributed along a wide latitudinal gradient from Alaska to Mexico during the winter. Accordingly, migration distances for brant using different wintering locations are highly variable and winter settlement patterns are likely associated with a spatially variable food resource. We used resightings of brant banded in southwestern Alaska to examine sex and age ratios of birds wintering at Boundary Bay in British Columbia, and at San Quintin Bay, Ojo de Liebre Lagoon, and San Ignacio Lagoon in Baja California from 1998 to 2000. Sex ratios were similar among wintering locations for adults and were consistent with the mating strategy of geese. The distribution of juveniles varied among wintering areas, with greater proportions of juveniles observed at northern (San Quintin Bay and Ojo de Liebre Lagoon) than at southern (San Ignacio Lagoon) locations in Baja California. We suggest that age-related variation in the winter distribution of Pacific Black Brant is mediated by variation in productivity among individuals at different wintering locations and by social interactions among wintering family groups.     

Fine structural recognition specificities of IgE antibodies distinguishing amoxicilloyl and amoxicillanyl determinants in allergic subjects.

IgE antibodies in the sera of subjects allergic to beta-lactam antibiotics detect a spectrum of specificities ranging from side-chain groups to an entire penicillin or cephalosporin molecule. In addition to such structural heterogeneity of allergenic determinants, IgE antibodies in the sera of different allergic subjects show heterogeneous recognition responses. Detailed immunochemical studies were carried out on the sera of penicillin-allergic subjects that showed selective and unexpected reactions with the frequently prescribed penicillin, amoxicillin. Antibodies from one subject reacted only with the amoxicilloyl determinant while IgE from another subject showed multiple reactivity with penicilloyl and penicillanyl determinants of different penicillins but not with the amoxicilloyl determinant. Quantitative hapten inhibition studies revealed that the combining sites of the former antibodies were complementary to amoxicillin in a form that permits binding to the hydroxyaminobenzyl side-chain and the thiazolidine ring carboxyl. These conditions are satisfied with the drug in the '-oyl' but not in the '-anyl' form which involves linkage through the 2-carboxyl of the thiazolidine ring. With the second serum, adsorption studies showed that the wide-ranging reactivity of IgE was due to a single population of antibodies that detected a common specificity on the different penicillins. Combining site studies revealed clear recognition of the benzyl portion of the side-chain of benzylpenicilloyl, benzylpenicillanyl, ampicilloyl, ampicillanyl and amoxicillanyl determinants when free antibody access to the side-chain was possible but little or no recognition of the ring hydroxyl of amoxicillin. Such uninhibited access may not occur, however, when amoxicillin is conjugated in the '-oyl' form since opening the beta-lactam ring allows increased flexibility and rotation of the molecule and the possibility of close association of the hydroxyaminobenzyl side-chain of amoxicillin with the linked peptide carrier. In such close steric association, H-bonding involving the ring hydroxyl and amino acids of the carrier may prevent antibody access to the side-chain region of the amoxicilloyl determinant.     

Methods for detecting non-randomness in species co-occurrences: a contribution

Summary Comparison of co-occurrences between species on a group of islands with those expected from a randombased null model could provide evidence on community structure. However, it is difficult to decide on the appropriate null model. Gilpin and Diamond proposed a model and a test for departure from it, but this test is shown to indicate significant structure even when applied to a matrix of random numbers. An alternative method is suggested, using the distribution of Gilpin and Diamond's deviation as test statistic, but determining the expected distribution by Monto Carlo simulation, and using many such simulations as a randomisation test of significance. The null model used accepts the observed totals of occurrences for islands and species; it therefore offers a somewhat conservative test. Applied to the Vanuatu bird data that Gilpin and Diamond used, significant departure from a null model is seen, but with an excess of extreme negative associations, the opposite result from that given by Gilpin and Diamond's method. It is not possible to tell whether the negative associations are due to autecology, biogeography, or to interactions between species.     

Effects of clonal variation of the host plant,interspecific competition,and climate on the population size of a folivorous thrips

Summary The effects of clonal variation, interspecific competition, and climate upon the population size of Apterothrips secticornis was assessed by a series of observations and experimental manipulations. Three clones of the host plant, Erigeron glaucus, consistently supported different numbers of thrips during monthly censuses. When rosettes of the three clones were transplanted to a common garden, relative numbers of thrips on the clones remained the same as those observed where the clones grew in situ. The presence or absence of other hervivores had no effect on thrips numbers in the common garden. Plume moth caterpillars and thrips were observed to co-occur less often than expected in the field but this was caused by differences in habitat selection by these two species rather than being the result of interspecific competition. Populations of thrips were affected by climate, but analyses suggest that the host clone was a more important factor.