Detection of lateral gene transfer among microbial genomes

An increasingly comprehensive assessment is being developed of the extent and potential significance of lateral gene transfer among microbial genomes. Genomic sequences can be identified as being of putatively lateral origin by their unexpected phyletic distribution, atypical sequence composition, differential presence or absence in closely related genomes, or incongruent phylogenetic trees. These complementary approaches sometimes yield inconsistent results. Not only more data but also quantitative models and simulations are needed urgently.

On surrogate methods for detecting lateral gene transfer

Surrogate methods for detecting lateral gene transfer are those that do not require inference of phylogenetic trees. Herein I apply four such methods to identify open reading frames (ORFs) in the genome of Escherichia coli K12 that may have arisen by lateral gene transfer. Only two of these methods detect the same ORFs more frequently than expected by chance, whereas several intersections contain many fewer ORFs than expected. Each of the four methods detects a different non-random set of ORFs. The methods may detect lateral ORFs of different relative ages; testing this hypothesis will require rigorous inference of trees. (C) 2001 Federation of European Microbiological Societies. Published by Elsevier Science BN. All rights reserved.

Knowledge and markets

An economy is a coordinated system of distributed knowledge. Economic evolution occurs as knowledge grows and the structure of the system changes. This paper is about the role of markets in this process. Traditionally, the theory of markets has not been a central feature of evolutionary economics. This seems to be due to the orthodox view of markets as information-processing mechanisms for finding equilibria. But in economic evolution markets are actually knowledge-structuring mechanisms. What then is the relation between knowledge, information, markets and mechanisms? I argue that an evolutionary theory of markets, in the manner of Loasby (1999), requires a clear formulation of these relations. I suggest that a conception of knowledge and markets in terms of a graphical theory of complex systems furnishes precisely this.

The future role of government in knowledge-based economies

In this article, we draw together aspects of contemporary theories of knowledge (particularly organisational knowledge) and complexity theory to demonstrate how appropriate conceptual rigor enables both the role of government and the directions of policy development in knowledge-based economies to be identified. Specifically we ask, what is the role of government in helping shape the knowledge society of the future? We argue that knowledge policy regimes must go beyond the modes of policy analysis currently used in innovation, information and technology policy because they are based in an industrial rather than post-industrial analytical framework. We also argue that if we are to develop knowledge-based economies, more encompassing images of the future than currently obtain in policy discourse are required. We therefore seek to stimulate and provoke an array of lines of thought about government and policy for such economies. Our objective is to focus on ideas more than argument and persuasion.

Intramolecular electronic energy transfer in bichromophoric macrocyclic complexes

Efficient intramolecular electronic energy transfer (EET) has been demonstrated for three novel bichromophoric compounds utilizing a macrocyclic spacer as the bridge between the electronic energy donor and acceptor fragments. As their free base forms, emission from the electronically excited donor is absent and the acceptor emission is reductively quenched via photoinduced oxidation of proximate amine lone pairs. As their Zn(II) complexes, excitation of the donor results in sensitization of the electronic acceptor emission.

Wolbachia density and virulence attenuation after transfer into a novel host

The factors that control replication rate of the intracellular bacterium Wolbachia pipientis in its insect hosts are unknown and difficult to explore, given the complex interaction of symbiont and host genotypes. Using a strain of Wolbachia that is known to over-replicate and shorten the lifespan of its Drosophila melanogaster host, we have tracked the evolution of replication control in both somatic and reproductive tissues in a novel host/Wolbachia association. After transinfection (the transfer of a Wolbachia strain into a different species) of the over-replicating Wolbachia popcorn strain from D. metanogaster to Drosophila simulans, we demonstrated that initial high densities in the ovaries were in excess of what was required for perfect maternal transmission, and were likely causing reductions in reproductive fitness. Both densities and fitness costs associated with ovary infection rapidly declined in the generations after transinfection. The early death effect in D. simulans attenuated only slightly and was comparable to that induced in D. metanogaster. This study reveals a strong host involvement in Wolbachia replication rates, the independence of density control responses in different tissues, and the strength of natural selection acting on reproductive fitness.

Pro re nata medication for psychoses: the knowledge and beliefs of doctors and nurses

Objective: To examine the knowledge and beliefs of doctors and nurses in inpatient psychiatric units about pro re nata (PRN) (as needed) medications for psychotic disorders. Methods: Medical (n = 44) and nursing (n = 80) staff in two metropolitan public hospital units completed a structured questionnaire about their use of PRN psychotropic medications on one occasion during the four months from March-June 1999. Results: Nurses selected more indications for PRN antipsychotics than doctors (3.49 vs 2.72, p < 0.05), whereas doctors selected more indications for PRN benzodiazepines (3.77 vs 3.19, p < 0.05). The groups did not differ in the number of selected indications for using anticholinergics. For agitation, the majority of nurses viewed both benzodiazepines (56%) and antipsychotics (86%) as effective, with 60% preferring an antipsychotic. For the acute control of psychotic symptoms, 99% of nurses believed antipsychotics were effective and 58% benzodiazepines, with 87% preferring an antipsychotic. A large majority of doctors viewed both PRN benzodiazepines, 94% ,and antipsychotics, 81%, as effective for agitation, and 55% preferred to use a benzodiazepine. For psychotic symptoms, 80% believed PRN antipsychotics were effective, but only 32% viewed benzodiazepines as effective, and 64% preferred to use an antipsychotic. Nursing staff identified more non-pharmacological techniques for managing both agitation and psychotic symptoms and reported using these more often than doctors. Junior staff, both nursing and medical, had less knowledge of non-pharmacological alternatives to PRN medication than senior staff. Conclusions: Disparities existed between doctors and nurses views on the indications for PRN medication in the acute management of psychoses, thus it is important for doctors to specify indications when writing PRN prescriptions. Despite evidence for the safety and effectiveness of benzodiazepines, there was widespread reluctance to use them as PRN medication in acute psychoses. Beliefs of some staff about PRN medications were at odds with the known properties of these medicines. Educational interventions for both nurses and doctors are required to achieve best practice in PRN medication.

The politics of reintegrating Australian Aboriginal and American Indian indigenous knowledge into resource management: The dynamics of resource appropriation and cultural revival

As the United States and Australia struggle with contemporary crises over competing uses of rapidly depleting natural resources, there are striking parallels between American Indian and Australian Aboriginal communities demanding a place at the management table and offering culturally based understandings of and solutions for the ecosystems at risk. These efforts to integrate indigenous knowledge into mainstream natural resource management are part of larger legal and political debates over land tenure, the locus of control, indigenous self-governance, and holistic ecosystems management.

The trematodes of groupers (Serranidae : Epinephelinae) knowledge, nature and evolution

Groupers (Epinephelinae) are prominent marine fishes distributed in the warmer waters of the world. Review of the literature suggests that trematodes are known from only 62 of the 159 species and only 9 of 15 genera; nearly 90% of host-parasite combinations have been reported only once or twice. All 20 families and all but 7 of 76 genera of trematodes found in epinephelines also occur in non-epihephelines. Only 12 genera of trematodes are reported from both the Atlantic-Eastern Pacific and the Indo-West Pacific. Few (perhaps no) species are credibly cosmopolitan but some have wide distributions across the Indo-West Pacific. The hierarchical 'relatedness' of epinephelines as suggested by how they share trematode taxa (families, genera, species) shows little congruence with what is known of their phylogeny. The major determinant of relatedness appears to be geographical proximity. Together these attributes suggest that host-parasite coevolution has contributed little to the evolution of trematode communities of epinephelines. Instead, they appear to have arisen through localized episodes of host-switching, presumably both into and out of the epinephelines. The Epinephelinae may well be typical of most groups of marine fishes both in the extent to which their trematode parasites are known and in that, apparently, co-evolution has contributed little to the evolution of their communities of trematodes.

Children's body knowledge: Understanding 'life' as a biological goal

Two studies assessed the development of children's understanding of life as a biological goal of body functioning. In Study 1, 4-to-10-year-old children were given an interview consisting of a series of structured questions about the location and function of various body organs. Their responses were coded both for factual correctness and for appeals to the goal of maintaining life. The results showed a gradual increase in children's factual knowledge across this age range but an abrupt increase in appeals to life between the ages of 4 and 6. Analyses of the 4-year-olds' responses suggested that appeals to life were associated with increased knowledge of organ function, but not of organ location. Study 2 was designed to replicate the pattern found in Study I. A continuous sample of 4-to 5-year-old children was administered an abbreviated version of the interview from Study 1. Children's understanding of life as a biological goal was again found to be predictive of their knowledge of organ function, but not of organ location. These results indicate a reorganization in children's understanding of the body between the ages of 4 and 6, which coincides with children's discovery of 'life' as a biological goal for bodily function.