Crystalline bacterial cell surface layers

Crystalline arrays of proteinaceous subunits forming surface layers (S-layers) are one of the most commonly observed prokaryotic cell envelope structures. They are ubiquitous amongst Gram-positive and Gram-negative archaeobacteria and eubacteria and, if present, account for the major protein species produced by the cells. S-layers can provide organisms with a selection advantage by providing various functions including protective coats, molecular sieves, ion traps and structures involved in cell surface interactions. S-layers were identified as contributing to virulence when present as a structural component of pathogens. In Gram-negative archaeobacteria they are involved in determining cell shape and cell division. The crystalline arrays reveal a broad-application potential in biotechnology, vaccine development and molecular nanotechnology.     

Fast optimal genome tiling with applications to microarray design and homology search.

In this paper, we consider several variations of the following basic tiling problem: given a sequence of real numbers with two size-bound parameters, we want to find a set of tiles of maximum total weight such that each tiles satisfies the size bounds. A solution to this problem is important to a number of computational biology applications such as selecting genomic DNA fragments for PCR-based amplicon microarrays and performing homology searches with long sequence queries. Our goal is to design efficient algorithms with linear or near-linear time and space in the normal range of parameter values for these problems. For this purpose, we first discuss the solution to a basic online interval maximum problem via a sliding-window approach and show how to use this solution in a nontrivial manner for many of the tiling problems introduced. We also discuss NP-hardness results and approximation algorithms for generalizing our basic tiling problem to higher dimensions. Finally, computational results from applying our tiling algorithms to genomic sequences of five model eukaryotes are reported.     

Culture and Rights: Anthropological Perspectives.

Culture and Rights: Anthropological Perspectives. Jane K. Cowan. Marie-Bénédicte Dembour. and Richard A. Wilson. eds. Cambridge: Cambridge University Press, 2001. 258 pp.     

Maintaining genetic code through adaptations of tRNA synthetases to taxonomic domains

The universal genetic code is determined by the aminoacylation of tRNAs. In spite of the universality of the code, there are barriers to aminoacylation across taxonomic domains. These barriers are thought to correlate with the co-segregation of sequences of synthetases and tRNAs into distinct taxonomic domains. By contrast, we show here examples of eukaryote-like synthetases that are found in certain prokaryotes. The associated tRNAs have retained their prokaryote-like character in each instance. Thus, co-segregation of domain-specific synthetases and tRNAs does not always occur. Instead, synthetases make adaptations of tRNA-protein contacts to cross taxonomic domains.     

Genetic variability in the European minnow,Phoxinus phoxinus (L.)

An electrophoretic study of genetic variation at 11 loci was performedfor a population of European minnows, Phoxinus phoxinus (L.). Ten loci, EST-1 ^*, EST-2 ^* EST-3 ^*,GPD-1 ^*,GPD-2 ^*,GPI-1 ^*,GPI-2 ^*,MPI ^*,6PGD ^* and PGM ^* were polymorphic. IDH ^*wasmonomorphic. The mean number of heterozygotic loci over all 176 fish was 3.05 ± 0.104(SE). Observed mean heterozygosity was 0.28±0.058(SE) and expected mean heterozygosity was 0.27±0.054(SE). EST-2 ^*, EST-3 ^* andPGM ^* were not in Hardy-Weinberg equilibrium. Length,condition, parasite numbers or male breeding characters, i.e. red colorationand tubercles, were not influenced by single enzyme loci.     

Effects of asexual reproduction on the neighborhood area of cyclical parthenogens

The habitat occupied by a subpopulation and withinwhich there is random mating is known as itsneighborhood area. Neighborhood area is dependenton dispersal rates and organisms with low rates ofdispersal are expected to have small neighborhoodareas. In the absence of evolutionary forces,neighborhood areas under sexual reproduction will beconstant in size as long as dispersal patterns do notchange. This scenario differs when reproduction is bycyclical parthenogenesis since recombination anddispersal may occur in different generations. Ingeneral, dispersal distances increase with the numberof parthenogenetic generations. We show that cyclicalparthenogenesis increases neighborhood area which,concomitantly, decreases the potential for geneticsubdivision. It is noteworthy, however, that theincrease in neighborhood area is a decreasing functionof the number of parthenogenetic generations.This mechanism may have important implications for thepopulation structure of planktonic rotifers living ina horizontally undifferentiated habitat. In suchhabitats organisms are effectively unrestricted intheir lateral movements. Because rotifers typicallyhave low dispersal rates spatial geneticdiscontinuities may develop that divide the populationinto genetically distinct subpopulations. Counteringthis tendency is the increased neighborhood areaproduced by dispersal during the parthenogeneticphase. Thus cyclical parthenogenesis in organismslike rotifers may have important and previouslyunreported effects on the population's geneticstructure.