Can a reductionist be a pluralist?

Pluralism is often put forth as a counter-position to reductionism. In this essay, I argue that reductionism and pluralism are in fact consistent. I propose that there are several potential goals for reductions and that the proper form of a reduction should be considered in tandem with the goal that it aims to achieve. This insight provides a basis for clarifying what version(s) of reductionism are currently defended, for explicating the notion of a fundamental level of explanation, and for showing how one can be both a reductionist and a pluralist.     

When is a peroxisome not a peroxisome?

It is time to drop the glyoxysome name. Recent functional genomics analysis together with cell biology studies emphasize the unifying features of peroxisomes rather than their differences. Plant peroxisomes contain 300 or more proteins, the functions of which are dominated by activities related to fatty acid oxidation (>70 enzymes). By comparison, relatively few proteins are committed to metabolism of reactive oxygen species ( approximately 20) and to photorespiration ( approximately 10). Analysis of triglyceride metabolism in Arabidopsis seedlings now indicates that only two enzymes (isocitrate lyase and malate synthase) potentially distinguish glyoxysomes from other peroxisomes. Future research is best served by focusing on the common features of peroxisomes to establish how these dynamic organelles contribute to energy metabolism, development and responses to environmental challenges.     

Between a rock and a hard place?

Developing small-molecule inhibitors against protein-protein interaction targets is among the most difficult challenges in contemporary drug discovery. Recent developments in our understanding of this problem, and in the knowledge and tools available to address it, give cause for renewed hope, but substantial challenges remain.     

What genes make a tree a tree?

Woody growth is evolutionarily ancient, yet has been gained and lost multiple times in plant evolution and is readily enhanced or minimized in eudicot speciation. New molecular genetic and genomic studies in Populus and Arabidopsis that are defining the genes responsible for cambium function and woody growth suggest that the genes regulating woody growth are not unique to woody plants. Surprisingly, key genetic mechanisms originally characterized as regulating the meristematic cells of the shoot apical meristem are also expressed in the vascular cambium during woody growth. This has important implications for the development of Populus as a model species and illustrates why forest trees constitute a contrived group of plants that have more in common with herbaceous relatives than we foresters like to admit.     

When is a parasite species a species?

Regrettably, 140 years after the publication of Darwin's Origin of Species, we face the grotesque situation that we still do not know what is a species whose origin Darwin wanted to explain. A generally applicable species definition is not available. Is there a basic unit of biodiversity above the level of individuals? Do we try to define something that does not exist in reality? The strong potential for the evolution of genetic variability in parasites together with the importance of species diagnosis for applied fields of parasite research make biodiversity research a key role in parasitology. Frequent occurrence of sympatric speciation, clonal reproduction, selfing, sib mating or parthenogenesis imply exceptional conditions for the evolution of gene pool diversities in parasites.     

Horizontal transmission of a parasitic nematode from a non-native to a native woodwasp?

In eastern North America, the exotic invasive woodwasp, Sirex noctilio, attacks pines (Pinus spp.) and often shares larval habitat with the native woodwasp, Sirex nigricornis. The parasitic nematode, Deladenus siricidicola, has been used widely in the southern hemisphere as a biological control agent because it sterilizes female S. noctilio. This nematode was introduced accidentally to North America along with S. noctilio. Historical reports indicate nematode-woodwasp fidelity: the parasitic nematode, D. siricidicola, exclusively infects S. noctilio, and the native nematode, Deladenus proximus, exclusively infects S. nigricornis. From two sites in southern Ontario, separated by 225 km, we collected woodwasps from three Pinus sylvestris, and identified the nematode species present in the abdomens of infected wasps. Both wasp species co-occurred in all three trees. D. siricidicola was present in the haemocoel, but not inside the eggs, of infected S. noctilio and S. nigricornis. This evidence suggests horizontal transmission of D. siricidicola likely occurred from S. noctilio to S. nigricornis.     

What Makes a Protein Sequence a Prion?

Typical amyloid diseases such as Alzheimer''s and Parkinson''s were thought to exclusively result from de novo aggregation, but recently it was shown that amyloids formed in one cell can cross-seed aggregation in other cells, following a prion-like mechanism. Despite the large experimental effort devoted to understanding the phenomenon of prion transmissibility, it is still poorly understood how this property is encoded in the primary sequence. In many cases, prion structural conversion is driven by the presence of relatively large glutamine/asparagine (Q/N) enriched segments. Several studies suggest that it is the amino acid composition of these regions rather than their specific sequence that accounts for their priogenicity. However, our analysis indicates that it is instead the presence and potency of specific short amyloid-prone sequences that occur within intrinsically disordered Q/N-rich regions that determine their prion behaviour, modulated by the structural and compositional context. This provides a basis for the accurate identification and evaluation of prion candidate sequences in proteomes in the context of a unified framework for amyloid formation and prion propagation.     

Is there a pilot in a pseudopod?

The concept of pilot pseudopodia is reconsidered 30 years after its inauguration (Gerisch, G., Hülser, D., Malchow, D., Wick, U., 1975. Cell communication by periodic cyclic-AMP pulses. Phil. Trans. R. Soc. Lond. B 272, 181-192). The original hypothesis stated that protruding pseudopodia serve as dynamic sensory organelles that aid a cell in perceiving variations of chemoattractant concentration and, consequently, in navigation during chemotaxis. This influential idea is reevaluated in the light of recent findings about the mechanisms governing chemotactic cell motility, morphology and dynamics of pseudopodia, and about molecular constituents and regulators of pseudopod extension and retraction. It is proposed that stimulation by a chemoattractant modulates speed of pseudopod protrusion and thereby increases cell elongation. Elongation further enhances chemotactic sensitivity of the cell to shallow chemoattractant gradients, reinforces cell polarization, and finally leads to suppression of lateral pseudopodia and continuation of cell migration in the gradient direction.     

When is a herbivore not a herbivore?

Summary Young herbivores are not herbivores. With the apparent exception of some chewing insects they cannot survive and growth without eating animal or microbial protein. Further reinforcing how short available nitrogen is in plant food, adult herbivores must feed selectively and depend on intestinal microorganisms to obtain sufficient nitrogen for maintenance and breeding.