What can biological barcoding do for marine biology?

The idea of using nucleotide sequences as barcodes for species identification has stirred up debates in the community of taxonomists and systematists. We argue that barcodes are potentially extremely useful tools for taxonomy for several reasons. Barcodes may, for example, help to identify cryptic and polymorphic species and give means to associate life history stages of unknown identity. Barcode systems would thus be particularly helpful in cases when morphology is ambiguous or uninformative and would provide tools for higher taxonomic resolution of disparate life forms. Comparative analysis of short DNA sequences may also represent heuristic access cards to a deeper understanding of evolutionary relationships between organisms. However, barcodes are the “essence” of species identities no more than taxonomic holotypes are “the species”. It makes no sense to think that morphology and other biological information about organisms can be made obsolete by barcode systems. The biological significance of matching or diverging nucleotide sequences will still have to be the subject of taxonomic decisions that must be open for scrutiny. It is imperative, therefore, that barcodes are associated with specimen vouchers.     

What to do, or how to do it?

In this issue of Neuron, Ajemian et al. present a computational model of the activity of neurons in primary motor cortex (M1) during isometric movements in different postures. By modeling the output of M1 neurons in terms of their influence on muscles, they find each M1 neuron maps its output into a particular pattern of muscle actions.     

What to do with HLA-DO?

Antigenic peptide binding to MHC class II molecules in the endocytic pathway occurs via a multifactorial process that requires the support of a specialized lysosomal chaperone called HLA-DM. DM shows both in primary amino acid sequence and quaternary structure a high homology to both MHC class I and class II molecules. Like the peptide presenting class II molecules, DM is expressed in all professional antigen presenting cells. DM catalyzes the dissociation of peptides that do not bind stably to the class II peptide-binding groove, thereby leading to the preferential presentation of stably binding antigenic peptides. The recently discovered HLA-DO molecule is mainly expressed in B cells and associates with DM, thereby markedly affecting DM function. Like DM, the genes encoding the HLA-DO heterodimer lie within the MHC class II region and exhibit strong homology to classical class II molecules. This review evaluates the unique effects of DO on DM-mediated antigen presentation by MHC class II molecules and discusses the possible physiological relevance for the B cell-specific expression of DO and its function.     

What would constitute success for UK biotechnology in 2005?

This paper presents the rationale and results of a scenario exercise concerning possible future developments in UK biotechnology. The final output of this exercise is a 'consensus' vision of what success might look like for the UK in biotechnology in 2005. The 'success scenario' was developed during a two-day workshop through structured discussions in a group of people active in biotechnology in industry, research agencies, consultancies or academe.     

What should and what can biotechnology contribute to chemical bulk production?

Abstract: In terms of the chemical industry most biotech products have a fine chemical or even speciality character. Nevertheless there is at least one striking example of a fermentation-derived bulk chemical, bio-ethanol, which provides an excellent case study of the economic and technological prerequisites which biotechnology has to attain as a supplier to the chemical marketplace. The competitive position of existing and new products produced from renewable resources through biotechnological conversion methods will depend on its market acceptance - overall environmental compatibility and cost performance. In order to provide significant contributions to chemical bulk production beyond 2000, biotechnologists and chemical engineers are requested to search for new products, new processes to existing products and new technologies to overcome present cost constraints in fermentation, bioconversion and downstream processing.     

What do mice select for in seeds?

Summary Knowledge of the basis upon which granivores select seeds is crucial to the understanding of granivory. In this study the preferences of three rodent granivores among seeds of 11 plants from the semi-arid Karoo of South Africa were estimated, and related to the physical and chemical attributes of the seeds. Seed weights and calorific, moisture, protein, polyphenol, ash, lipid and silica contents were estimated and cell contents, soluble ash and soluble carbohydrate contents were derived from these values. These attributes were determined for both the intact seeds and the portion of the seed that is ingested by the mice. The efficiency with which mice ingested the seeds (in terms of time and mass) was recorded. All three mouse species ranked the seeds similarly, and the two species for which handling efficiency was measured did not differ in this regard. Preference hierachies were highly correlated with the rate of energy intake, as predicted by optimal foraging theory. There was no correlation between rodent preferences and the gross energy content of the seeds, emphasising the importance of measuring relevant parameters. The energy yield of the seeds calculated here, in conjunction with rodent population energy requirements and dietary data, may be used to estimate potential granivore impact on the seed production of the plant community.     

What can myosin VI do in cells?

The recently solved structure of the myosin VI motor demonstrates that the unique insert at the end of the motor is responsible for the reversal of the normal myosin directionality. A second class-specific insert near the nucleotide-binding pocket contributes to myosin VI's unique kinetic tuning, allowing it to function either as an actin-based transporter or as an anchoring protein. Recent biochemical and biophysical studies have shown that the native molecule can form dimers upon clustering, and cell biological studies have demonstrated that it clearly does play both transport and anchoring roles in cells. These mechanistic insights allow us to speculate on how unusual aspects of myosin VI structure and function allow it to fill unique niches in cells.     

What do family physicians see in practice?

Health care problems dealt with in their practices were recorded by seven family physicians over a period of 1 year (two others recorded for 3 months), each diagnosis being coded according to the Canuck Disease Classification Index. Problems were classified into four types: physical, psychosocial, diseases of choice (or lifestyle) and diseases of social impact. More than 85% of the 23 108 problems recorded were physical in origin and had physical manifestations. More time was spent on routine checkups and treatment of respiratory disease than on any other activity. Venereal disease and alcoholism were infrequent problems. The family physician is in a favourable position to act as health educator and counsellor and must be throughly trained in the physical aspects of disease.     

What do we need to know about speciation?

Speciation has been a major focus of evolutionary biology research in recent years, with many important advances. However, some of the traditional organising principles of the subject area no longer provide a satisfactory framework, such as the classification of speciation mechanisms by geographical context into allopatric, parapatric and sympatry classes. Therefore, we have asked where speciation research should be directed in the coming years. Here, we present a distillation of questions about the mechanisms of speciation, the genetic basis of speciation and the relationship between speciation and diversity. Our list of topics is not exhaustive; rather we aim to promote discussion on research priorities and on the common themes that underlie disparate speciation processes.     

How fast do marine invertebrates burrow?

The burrowing of bivalves, arthropods, and echinoderms collected from tidal flats and shallow subtidal sediments of the Ogeechee estuary, Georgia, U.S.A was analyzed using time-elapse, X-ray analysis of thin-walled aquaria. The rate of sediment intrusion was determined for each animal. Burrowing rates ranged between 0.01 and 0.15 cm³/h for suspension-feeding animals. Deposit-feeding animals moved between 1 and 10 cm³ of sand per hour, approximately 10 to 100 times more sediment than the suspension feeders moved over similar times.Neoichnological experiments show that ten filter-feeding individuals could take as long as 115 yr to churn a 1 m² plot of sediment, by indexing the measured burrowing rates to realistic animal population densities. Ten such mobile deposit feeders as irregular echinoderms could bioturbate the same sediment in just 42 days. Under the maximum population densities modeled, the animals could bioturbate the sediment plot in 61 min. Given the reported results, qualitative interpretation of the rock record is possible: highly burrowed examples of the Skolithos Ichnofacies reflect high population densities and at least seasonal time spans. Highly burrowed examples of the Cruziana Ichnofacies may represent moderate population densities and short time spans.     

What do Eulerian and Hamiltonian cycles have to do with genome assembly?

Many students are taught about genome assembly using the dichotomy between the complexity of finding Eulerian and Hamiltonian cycles (easy versus hard, respectively). This dichotomy is sometimes used to motivate the use of de Bruijn graphs in practice. In this paper, we explain that while de Bruijn graphs have indeed been very useful, the reason has nothing to do with the complexity of the Hamiltonian and Eulerian cycle problems. We give 2 arguments. The first is that a genome reconstruction is never unique and hence an algorithm for finding Eulerian or Hamiltonian cycles is not part of any assembly algorithm used in practice. The second is that even if an arbitrary genome reconstruction was desired, one could do so in linear time in both the Eulerian and Hamiltonian paradigms.     

What does mental health have to do with well-being?

Positive mental health involves not the absence of mental disorder but rather the presence of certain mental goods. Institutions, practitioners, and theorists often identify positive mental health with well-being. There are strong reasons, however, to keep the concepts of well-being and positive mental health separate. Someone with high positive mental health can have low well-being, someone with high well-being can have low positive mental health, and well-being and positive mental health sometimes conflict. But, while positive mental health and well-being are not identical, there is an informative conceptual connection between them. Positive mental health usually contributes instrumentally to the living of a good human life, where a good human life includes (but is not limited to) well-being.