Scrapie transmission in Britain: a recipe for a mathematical model

Responses to an anonymous postal survey concerning scrapie are analysed. Risk factors associated with farms that have had scrapie are identified as size, geographical region, lambing practices and holding of certain breeds. Further analysis of farms that have scrapie only in bought-in animals reveals that such farms tend to breed a smaller proportion of their replacement animals than farms without scrapie. Farms that have had scrapie in home-bred animals have attributes associated with breeding many animals: large numbers of rams bought, few ewes bought, and many animals that are home-bred. The demography of British sheep farms as described by size, breeds, purchasing behaviour, age structure and proportion of animals that are home-bred is summarized. British farms with scrapie reveal certain special features: they have more sheep that are found dead, more elderly ewes and more cases of scab.     

Butterflyfish social behaviour,with special reference to the incidence of territoriality: a review

Synopsis Butterflyfishes (Chaetodontidae) are among the best studied of coral reef fishes. Feeding ecology and some aspects of behaviour have been firmly established. However, spacing behaviour remains controversial. Two major studies made in the 1970s concluded that the majority of species were not territorial. We suggest that these and other studies which have concluded that territories are not held have generally suffered from short observation periods, and have not mapped the ranges occupied by individuals. Further, low frequencies of agonistic behaviour have been interpreted as evidence of non-territoriality. By contrast, studies which have proven territoriality have had long observation periods and have mapped ranges. These have shown that territories are usually maintained with very little overt aggression. Spacing behaviour and feeding behaviour are clearly linked, with territoriality common among benthic-feeding species, especially obligate corallivores. Species with broad dietary flexibility tend to have flexible social systems, while plankton feeders are usually gregarious. The widespread occurrence of monogamy in butterflyfishes appears linked to territoriality, the majority of territorial species identified to date occurring predominantly as pairs. Data currently available suggest that this is because pair defence of the territory is more efficient than by individuals. However, several alternative hypotheses for the evolution of monogamy based on spawning constraints and predation risk cannot yet be ruled out.     

Novel chemistry of invasive exotic plants

Of the many exotic plants that have become naturalized in North America, only a small proportion are pests capable of invading and dominating intact natural communities. In the present study, we tested the hypothesis that the most invasive plants are phytochemically unique in their new habitats. A comparison of exotic plant species that are highly invasive in North America with exotics that are widespread, but non-invasive revealed that the invasive plants were more likely to have potent secondary compounds that have not been reported from North American native plants. On average, the compounds found in the invasive plants were reported from fewer species, fewer genera and fewer families than those from non-invasive plants. Many of the unique phytochemicals from invasive plants have been reported to have multiple activities, including antiherbivore, antifungal, antimicrobial and allelopathic (phytotoxic) effects, which may provide the plants with several advantages in their new environments.     

Human endogenous retroviruses

Several studies have revealed the presence in human DNA of thousands of endogenous retrovirus genomes, or HERVs. Many HERVs are related to extant retroviruses that infect other vertebrates and some have been present in the germ line of primates for millions of years. Although the HERVs that have been isolated are defective and thus do not encode infectious retroviruses, there may be HERVs that are capable of infection. In addition, because HERVs are so ancient in the human lineage, evolution of the human genome may have included the acquisition of some HERV genes for strictly cellular functions.     

Staphylococci in colonization and disease: prospective targets for drugs and vaccines

Pathogenic staphylococci are now regarded in the scientific community as antibiotic resistant 'superbugs' because they have an amazing capacity to acquire resistance traits. Surprisingly, antibiotic development has decelerated. Promising targets for drug development are enzymes involved in the biosynthesis of cell envelope structures such as peptidoglycan, teichoic acids, membrane lipids, or cell wall associated adhesins. Compounds that inactivate or neutralize the most aggressive toxins such as the superantigens and the pore forming toxins have also been considered. In the past decade, global regulatory systems have been studied that contribute to virulence and might be candidates for target development. Targets that are particularly promising include all enzymatic reactions that are unique to bacteria and that are involved in central metabolism, such as methionine-tRNA(fMet) formyltransferase or the peptide deformylase, which have been successfully used for designing new inhibitors. There are also several known antibiotics that have roused new interest especially if they are active against multi-resistant staphylococci. Various cell wall components are promising candidates for active and passive immunization strategies such as capsule, slime, teichoic acids or cell wall bound adhesins. Several new targets for drugs or vaccines will arise from the functional analysis of the staphylococcal genomes that contain many hitherto unknown targets.     

Flagella in prokaryotes and lower eukaryotes.

During the past year, significant advances have been made in the understanding of both prokaryotic and eukaryotic flagella. About 50 genes are dedicated to the assembly and operation of bacterial flagella. Recent discoveries have advanced our understanding of how these genes are regulated and how their products assemble into a functional, rotating organelle. The dynein arms of eukaryotic flagella are now also better understood. Several genes that are found in the mechanochemical macroassemblies have been cloned, and other loci have been identified, suggesting that there is even greater complexity than first expected.     

Defining selection criteria to improve yield under drought

The many selection criteria that have been proposed to increase drought resistance of our crops have had little, if any, impact on improving crop yields in dry environments. There are several likely reasons for this lack of success. Some of these are: (i) criteria proposed have been related more to survival mechanisms under drought than to productivity, (ii) criteria are inappropriate to the target environment, and (iii) criteria are temporal and are therefore likely to have minimal impact on growth and yield over the entire lifecycle. Another important reason is that breeders have not been convinced the proposed criteria will be successful as they are too difficult to measure. On the other hand, empirical breeding programmes to improve yield under drought have been successful. Surprisingly, some of the greatest successes have been achieved by breeding in environments where water is non-limiting. This paper reviews breeding approaches to improve yield under drought. It focuses on critical factors that must be considered to identify likely plant attributes that can be targeted. These factors, their link with yield, the nature of the target environment, the level of organisation where the trait is expressed are discussed. Three quite different examples are given to emphasize the above considerations and which show substantial promise in targeting traits to improve yield under drought. They are drought at flowering, improving transpiration efficiency and improving early leaf area development.     

Functional restraints on the patterns of amino acid substitutions: application to sequence-structure homology recognition

Amino acid residues that are involved in functional interactions in proteins have strong evolutionary pressure to remain unchanged and consequently their substitution patterns are different from those that are noninteracting. To characterize and quantify the differences between amino acid substitution patterns due to structural restraints and those under functional restraints, we have made a comparative analysis of families of homologous proteins. Residues classified as having the same amino acid type, secondary structure, accessibility, and side-chain hydrogen bonds are shown to be better conserved if they are close to the active site. We have focused on enzyme families for this analysis since they have functional sites that are easily defined by their catalytic residues. We have derived new sets of environment-specific substitution tables, which we term function-dependent environment-specific substitution tables, where amino acid residues are classified according to their distance from the functional sites. The residues that are within a distance of 9 A from the active site have distinct amino acid substitution patterns when compared to the other sites. The function-dependent environment-specific substitution tables have been tested using the sequence-structure homology recognition program FUGUE and the results compared with the recognition performance obtained using the standard environment-specific substitution tables. Significant improvements are obtained in both recognition performance and alignment accuracy using the function-dependent environment-specific substitution tables (P-value = 0.02, according to the Wilcoxon signed rank test for alignment accuracy). The alignments near the active site are greatly improved with pronounced improvements at lower percentage identities (less than 30%).     

Construction and Characterization of Virus-Like Particles: A Review

Over the last three decades, virus-like particles (VLPs) have evolved to become a widely accepted technology, especially in the field of vaccinology. In fact, some VLP-based vaccines are currently used as commercial medical products, and other VLP-based products are at different stages of clinical study. Several remarkable advantages have been achieved in the development of VLPs as gene therapy tools and new nanomaterials. The analysis of published data reveals that at least 110 VLPs have been constructed from viruses belonging to 35 different families. This review therefore discusses the main principles in the cloning of viral structural genes, the relevant host systems and the purification procedures that have been developed. In addition, the methods that are used to characterize the structural integrity, stability, and components, including the encapsidated nucleic acids, of newly synthesized VLPs are analyzed. Moreover, some of the modifications that are required to construct VLP-based carriers of viral origin with defined properties are discussed, and examples are provided.     

Rainforest frogs of the Australian Wet Tropics: guild classification and the ecological similarity of declining species.

Rainforest frogs are classified into nine ecological guilds based on features of reproduction, habitat use, temporal activity, microhabitat and body size. The largest ecological differences are between the microhylid frogs and the rest of the frog species. Within the non-microhylids, there are two primary groups consisting of (i) regionally endemic rainforest specialists, and (ii) a more ecologically diverse group of species that are less specialized in their habitat requirements. Most of the regionally endemic rainforest specialists, which includes species in three ecological guilds, have declined or gone missing in recent years. Multivariate analyses of the ecological characteristics of these species show that it is not a single characteristic that isolates those species that have declined from those which have not. The guilds that have undergone significant population declines in the Wet Tropics are all characterized by the combination of low fecundity, a high degree of habitat specialization and reproduction in flowing streams. These results have important implications for the determination of the causal factors in the unexplained global decline of many amphibian species.     

Normal structure and expression of Zfy genes in XY female mice mutant in Tdy.

Zfy-1 and Zfy-2 are candidate genes for Tdy, the testis-determining gene in mice. We have analysed these genes in a line of XY female mice that have been shown to be mutated in Tdy. We have used Southern blot analysis to show that the Zfy genes have not undergone any major structural alterations, and have also demonstrated that both genes are transcribed normally from the mutant Y chromosome (Y) in both adult XYY testis and XY female embryonic gonads. The fact that these genes show a normal structure and expression pattern in mice with a Y chromosome known to carry a mutation in Tdy and that mutant embryos develop into females despite Zfy-1 expression, strongly supports other recent evidence that Zfy genes are not directly involved in primary testis determination.     

Macro effects of microRNAs in plants

MicroRNAs (miRNAs) are 20- to 22-nucleotide fragments that regulate expression of mRNAs that have complementary sequences. They are numerous and widespread among eukaryotes, being conserved throughout evolution. The few miRNAs that have been fully characterized were found in Caenorhabditis elegans and are required for development. Recently, a study of miRNAs isolated from Arabidopsis showed that here also developmental genes are putative regulatory targets. A role for miRNAs have in plant development is supported by the developmental phenotypes of mutations in the genes required for miRNA processing.     

Models of the regulation of ribonucleotide reductase and their evaluation in intact mammalian cells

Enzymological studies have shown that ribonucleotide reductase is allosterically inhibited or stimulated by endproduct deoxyribonucleoside triphosphates, and various investigators have put forward schematized models of the regulation of this enzyme; the various models have in practice been considered to be equivalent or at least very similar. Here each of eleven published models is critically examined, and it is shown that there are important differences among them that have not previously been appreciated. In addition, studies using intact mammalian cells have generally been taken as being consistent with the enzymological data, but this point has not received much systematic attention. The available data are examined critically, and the implications of multiple, partially different models are considered.     

Do Embryos Have Interests? Why Embryos Are Identical to Future Persons but Not Harmed by Death

Are embryos deserving of moral consideration in our actions? A standard view suggests that embryos are considerable only if they have interests. One argument for embryonic interests contends that embryos are harmed by death because they are deprived of valuable future lives as adult persons. Some have challenged this argument on the grounds that embryos aren’t identical to adults: either due to the potential for embryos to twin or because we do not exist until the fetus develops consciousness. These arguments fail to show that embryos do not have future adult lives. There is a better reason to think that embryos cannot have interests; namely, because they are not capable of having desires. Others have held this view but have not sufficiently justified it. The justification lies in the fact that the capacity for desires is necessary to make sense of the normativity of interests.     

Are species names proper names?

The nature of species names has been a source of controversy, and has played a role in developing ideas about the status of species, such as the species‐as‐individuals hypothesis. Some argue that species names are Millian proper names: names that have no meaning. Others have countered that species names are Millian general names that have stipulative definitions. Here I argue that species names belong to neither category. In particular, unlike Millian proper names, species names have unique referents and are connotative. Further, species names are names of intension that, unlike Millian general names, refer to specific collective entities. Because species names have unique properties not associated with Millian general or proper names, but recognizing the similarity to proper names in most respects, I propose that they be categorized as extra‐proper names.
     

Peptides and neurotransmission in the central nervous system

Radioimmunoassays of brain extracts have shown that several peptides occur in high concentrations in the CNS. The releasing-factor peptides TRF, LRF, somatostatin, CRF and GRF have the highest concentration in the hypothalamic extracts. High levels of somatostatin, CCK octapeptide, neuropeptide Y (NPY) and vasoactive intestinal peptide (VIP) are found in cortical extracts. Substance P, CCK, NPY, and enkephalins are present in high concentrations in basal ganglia and mesolimbic areas. Pharmacological doses of these peptides result in several behavioural and vegetative effects. Immunocytochemical studies show that the CNS peptides are localised in neurones and in synaptic vesicles. In vitro studies with brain tissues show that peptides are capable of modifying the ongoing classical neurotransmission. In depressive patients several neuropeptides (CCK, CRF and NPY) have been shown to have low CSF levels. Patients dying of senile dementia have low cortical levels of somatostatin, CRF and substance P. In schizophrenic patients CCK peptides have shown to improve some symptoms. At present the therapeutic potentials of peptides are poorly known. More studies are required to understand their role in neurotransmission and related pathological states.     

Novel class of glutathione transferases from cyanobacteria exhibit high catalytic activities towards naturally occurring isothiocyanates

In the present paper, we report a novel class of GSTs (glutathione transferases), called the Chi class, originating from cyanobacteria and with properties not observed previously in prokaryotic enzymes. GSTs constitute a widespread multifunctional group of proteins, of which mammalian enzymes are the best characterized. Although GSTs have their origin in prokaryotes, few bacterial representatives have been characterized in detail, and the catalytic activities and substrate specificities observed have generally been very modest. The few well-studied bacterial GSTs have largely unknown physiological functions. Genome databases reveal that cyanobacteria have an extensive arsenal of glutathione-associated proteins. We have studied two cyanobacterial GSTs which are the first examples of bacterial enzymes that are as catalytically efficient as the best mammalian enzymes. GSTs from the thermophile Thermosynechococcus elongatus BP-1 and from Synechococcus elongatus PCC 6301 were found to catalyse the conjugation of naturally occurring plant-derived isothiocyanates to glutathione at high rates. The cyanobacterial GSTs studied are smaller than previously described members of this enzyme family, but display many of the typical structural features that are characteristics of GSTs. They are also active towards several classical substrates, but at the same moderate rates that have been observed for other GSTs derived from prokaryotes. The cloning, expression and characterization of two cyanobacterial GSTs are described. The possible significance of the observed catalytic properties is discussed in the context of physiological relevance and GST evolution.