Why is the genome variable? Insights from Drosophila.

The analysis of variation in DNA restriction maps and DNA sequence in natural populations of Drosophila melanogaster and related species has revealed a remarkable richness of diversity. This review describes some of the results of population genetic studies of this variation that are beginning to reveal how interactions between natural selection, genetic drift, mutation rate, recombination rate and population size have contributed to the observed patterns.     

Why fuse the mandibular symphysis? A comparative analysis

Fused symphyses, which evolved independently in several mammalian taxa, including anthropoids, are stiffer and stronger than unfused symphyses. This paper tests the hypothesis that orientations of tooth movements during occlusion are the primary basis for variations in symphyseal fusion. Mammals whose teeth have primarily dorsally oriented occlusal trajectories and/or rotate their mandibles during occlusion will not benefit from symphyseal fusion because it prevents independent mandibular movements and because unfused symphyses transfer dorsally oriented forces with equal efficiency; mammals with predominantly transverse power strokes are predicted to benefit from symphyseal fusion or greatly restricted mediolateral movement at the symphysis in order to increase force transfer efficiency across the symphysis in the transverse plane. These hypotheses are tested with comparative data on symphyseal and occlusal morphology in several mammals, and with kinematic and EMG analyses of mastication in opossums (Didelphis virginiana) and goats (Capra hircus) that are compared with published data on chewing in primates. Among mammals, symphyseal fusion or a morphology that greatly restricts movement correlates significantly with occlusal orientation: species with more transversely oriented occlusal planes tend to have fused symphyses. The ratio of working- to balancing-side adductor muscle force in goats and opossums is close to 1:1, as in macaques, but goats and opossums have mandibles that rotate independently during occlusion, and have predominantly vertically oriented tooth movements during the power stroke. Symphyseal fusion is therefore most likely an adaptation for increasing the efficiency of transfer of transversely oriented occlusal forces in mammals whose mandibles do not rotate independently during the power stroke.     

Why the move to microfluidics for protein analysis?

There has been a recent trend towards the miniaturization of analytical tools, but what are the advantages of microfluidic devices and when is their use appropriate? Recent advances in the field of micro-analytical systems can be classified according to instrument performance (which refers here to the desired property of the analytical tool of interest) and two important features specifically related to miniaturisation, namely reduction of the sample volume and the time-to-result. Here we discuss the contribution of these different parameters and aim to highlight the factors of choice in the development and use of microfluidic devices dedicated to protein analysis.     

Our social genome?

Apocalyptic views on the natural order, chimeras and genetic engineering should not detract from the fact that medical research, similar to the promotion of health, is a public good. Genomics crosses all species, thereby requiring a global approach that respects human rights and public health priorities. Public trust and public participation in research demand clear stewardship as well as transparent and accountable oversight. Characterizing fundamental genomic data as a public resource might counterbalance the current overemphasis on individual rights but this will not be simple. It is only through an attachment to justice and solidarity that the dignity and well-being of persons, both as humans and as citizens, can truly be fostered.     

Proteome, transcriptome and genome: top down or bottom up analysis?

Biological systems are comprised of protein components found at a wide variety of abundances from millions of molecules of a single species per cell to less than one copy per cell. Because of this wide range of concentrations, measurement or a full accounting of each system is presently unavailable. Conventional separation and analytical methods (two-dimensional gel electrophoresis and mass spectrometry) allow identification and quantitation of many of the most abundant gene products (top down methods); and the majority of gene products, which are found at low abundance, can be neither identified nor measured in complex mixtures at present. The gene products that are found at low levels can be characterized and their properties analyzed by preparing ordered gene libraries of limited complexity from mRNA. When such preparations are expressed in cell free systems and analyzed by two-dimensional gel electrophoresis, the features of the gene products are available for analysis. This 'bottom up' approach allows identification of gene product properties so that analytical procedures can be devised and applied to complex mixtures.     

Whose genome is next?

A report from the 14th Genome Sequencing and Analysis Conference, Boston, USA, 2-5 October 2002.     

What is a genome?

The field of genomics is expanding rapidly, yet the meanings of the word ‘genome’ have yet to be conceptualized in explicit, coherent and useful frameworks. We develop and apply an evolutionary conceptualization of the genome, which represents a logical extension of the evolutionary definition of a gene developed by George C. Williams. An evolutionary genome thus represents a set of genetic material, in a lineage, that due to common interests tends to favour the same or similar phenotypes. This conceptualization provides novel perspectives on genome functions, boundaries and evolution, which should help to guide theoretical and empirical genomics research.     

Why weight?

Whether phylogenetic data should be differentially or equally weighted is currently debated. Further, if differential weighting is to be explored, there is no consensus among investigators as to which weighting scheme is most appropriate. Mitochondrial genome data offer a powerful tool in assessment of differential weighting schemes because taxa can be selected from which a highly corroborated phylogeny is available (so that accuracy can be assessed), and it can be assumed that different data partitions share the same history (so that gene-sorting issues are not so problematic). Using mitochondrial data from 17 mammalian genomes, we evaluated the most commonly used weighting schemes, such as successive weighting, transversion weighting, codon-based weighting, and amino acid coding, and compared them to more complex weighting schemes including a 6-parameter weighting, pseudoreplicate reweighting, and tri-level weighting. We found that the most commonly used weighting schemes perform the worst with these data. Some of the more complex schemes perform well, however, none of them is consistently superior. These results support ones biases; if one has a predilection to avoid differential weighting, these data support equally weighted parsimony and maximum likelihood. Others might be encouraged by these results to try weighting as a form of data exploration.