Do we still need supertrees?

The up-dated species level phylogeny for the carnivores using a supertree approach provides new insights into the evolutionary origin and relationships of carnivores. While the gain in biological knowledge is substantial, the supertree approach is not undisputed. I discuss the principles of supertree methods and the competitor supermatrix approaches. I argue that both methods are important to infer phylogenetic relationships.     

Do we need an intravenous fluoroquinolone?

Intravenous ciprofloxacin, the first parenteral fluoroquinolone available in this country, represents another class of antimicrobial agents from which physicians must choose when treating nosocomial infections. Fluoroquinolones are bactericidal antimicrobial agents that act by inhibiting DNA gyrase. They are active in vitro against most gram-negative bacteria and methicillin-susceptible staphylococci. Activity against anaerobic bacteria and streptococci is poor. The rapid development of bacterial resistance in centers with high quinolone usage is of great concern. Resistance develops most commonly in Pseudomonas aeruginosa and staphylococci. Resistance emerges most often when quinolones are used to treat chronic infections or in patients with poorly drained abscesses, necrotic tissue, or indwelling catheters. Clinical trials have shown ciprofloxacin to be as effective as ceftazidime in the treatment of infections caused by gram-negative bacteria. Although the overall frequency of side effects to fluoroquinolones is low, seizures and allergic reactions have been attributed to their use. Ciprofloxacin inhibits the metabolism of theophylline, and morbidity and death have been reported in patients taking the two drugs concomitantly. Parenteral fluoroquinolones should be reserved for the treatment of gram-negative bacterial infections in patients in whom standard agents cannot be used.     

Do we need new autoantibodies in lupus?

Systemic lupus erythematosus (SLE) is a clinically and serologically complex disease that demonstrates clinical, epidemiological and genetic differences among racial and ethnic groups. Some autoantibodies are useful for diagnosis of the illness. Others are clinically important because of associations with a particular manifestation of SLE. Antibodies to RNA helicase A (anti-RHA) comprise a newly described class of SLE autoantibodies. These antibodies have so far been found only in SLE patients and differ substantially in prevalence and nature between Mexican and white American SLE patients. Study of anti-RHA may provide insights into the origin of population differences in SLE.     

Do we really need the “detriment” for radiation protection?

The purpose of the ICRP detriment concept is to enable a quantitative comparison of stochastic radiation damage for the various organs. For this purpose, the organ-specific nominal risk coefficients are weighted with a function that is intended to express the amount of damage or, respectively, the severity of a disease. This function incorporates a variety of variables that do not depend on radiation parameters, but on characteristics of the disease itself. The question is raised as to whether the rather subtle way of defining the amount of damage is necessary for radiation protection purposes and whether a much simpler relationship can serve for this purpose as well or even better.

     

Do we need many genes for phylogenetic inference?

Fifty-six nuclear protein coding genes from Taxonomically Broad EST Database and other databases were selected for phylogenomic-based examination of alternative phylogenetic hypotheses concerning intergroup relationship between multicellular animals (Metazoa) and other representatives of Opisthokonta. The results of this work support sister group relationship between Metazoa and Choanoflagellata. Both of these groups form the taxon Holozoa along with the monophyletic Ichthyosporea or Mesomycetozoea (a group that includes Amoebidium parasiticum, Sphaeroforma arctica, and Capsaspora owczarzaki). These phylogenetic hypotheses receive high statistical support both when utilizing whole alignment and when only 5000 randomly selected alignment positions are used. The presented results suggest subdivision of Fungi into Eumycota and lower fungi, Chytridiomycota. The latter form a monophyletic group that comprises Chytridiales+Spizellomycetales+Blastocladiales (Batrachochytrium, Spizellomyces, Allomyces, Blastocladiella), contrary to the earlier reports based on the analysis of 18S rRNA and a limited set of protein coding genes. The phylogenetic distribution of genes coding for a ubiquitin-fused ribosomal protein S30 implies at least three independent cases of gene fusion: in the ancestors of Holozoa, in heterotrophic Heterokonta (Oomycetes and Blastocystis) and in the ancestors of Cryptophyta and Glaucophyta. Ubiquitin-like sequences fused with ribosomal protein S30 outside of Holozoa are not FUBI orthologs. Two independent events of FUBI replacement by the ubiquitin sequence were detected in the lineage of C. owczarzaki and in the monophyletic group of nematode worms Tylenchomorpha+Cephalobidae. Bursaphelenchus xylophilus (Aphelenchoidoidea) retains a state typical of the rest of the Metazoa. The data emphasize the fact that the reliability of phylogenetic reconstructions depends on the number of analyzed genes to a lesser extent than on our ability to recognize reconstruction artifacts.     

Have we overstated the tropical biodiversity crisis?

Tropical forests are the most biologically diverse and ecologically complex of terrestrial ecosystems, and are disappearing at alarming rates. It has long been suggested that rapid forest loss and degradation in the tropics, if unabated, could ultimately precipitate a wave of species extinctions, perhaps comparable to mass extinction events in the geological history of the Earth. However, a vigorous debate has erupted following a study by Wright and Muller-Landau that challenges the notion of large-scale tropical extinctions, at least over the next century. Here, I summarize this controversy and describe how the debate is stimulating a serious examination of the causes and biological consequences of future tropical deforestation.     

Source-sink partitioning. Do we need Münch?

The simulation of phloem translocation by the Münch theory commonly uses resistances from sources to sinks: the resistances are therefore regarded as important in partitioning. Although resistance is generally a set constant, it is in fact strongly affected by viscosity, and thus the concentration of the transported solute. In this paper, the model of partitioning proposed by Minchin et al. was first corrected for variations in viscosity. The model was further modified, with the source considered as an activity of solute production rather than as a compartment concentration. When so defined, the source cannot differ from the sum of sink activities, largely outdating the source- or sink-limitation concepts. The corrected model confined the effect of resistances on the partitioning to low source activities. In the example of wheat grain filling analysed, such activities would be so low that they would correspond only to pathological conditions. In that case, the use of resistances in modelling is therefore just a mathematical burden, not even easily quantifiable since they are related to anatomical traits that are difficult to access. Leaving out resistances, it becomes easy to calculate the sink activities directly from the source activities, using an intuitive, accessible parametrization. The conditions for such a simplification are discussed.     

Do we need new rhizosphere models for rock-dominated landscapes?

Background

In this issue, Estrada-Medina and coworkers described the diversity of materials in the rhizosphere of the Yucatán karst, México, and quantified the distribution of roots across karst features.

Scope

This commentary explores the implications of their work for below-ground competition and the dynamics of plant-available water on seasonal to inter-annual timescales. Though details differ, seasonal dynamics of water use were consistent with a two-layer model, characterized by water uptake from shallow soil and rock layers during the wet season and deeper soil pockets and rock layers during the dry season. Soil pockets were more densely rooted than rock and experienced large fluctuations in soil moisture, suggesting intense below-ground competition. Total water storage capacity in the rhizosphere was far greater than actual storage in the year of the study. This raises the question whether some storage components in the karst rhizosphere fluctuate on time scales exceeding 1 year.

Conclusions

Despite the significant global extent of karst and their larger than proportional contribution to global biodiversity, vegetation models have ignored their unique rhizosphere structure. Differences in water storage could affect the responses of karst ecosystems and communities to climate change.     

Do we need a ‘theory’ of development?

Edited by Alessandro Minelli and Thomas Pradeu, Towards a Theory of Development gathers essays by biologists and philosophers, which display a diversity of theoretical perspectives. The discussions not only cover the state of art, but broaden our vision of what development includes and provide pointers for future research. Interestingly, all contributors agree that explanations should not just be gene-centered, and virtually none use design and other engineering metaphors to articulate principles of cellular and organismal organization. I comment in particular on the issue of how to construe the notion of a ‘theory’ and whether developmental biology has or should aspire to have theories, which four of the contributions discuss in detail while taking opposing positions. Beyond construing a theory in terms of its empirical content (established knowledge about biological phenomena), my aim is to shift the focus toward the role that theories have for guiding future scientific theorizing and practice. Such a conception of ‘theory’ is particularly important in the context of development, because arriving at a theoretical framework that provides guidance for the discipline of developmental biology as a whole is more plausible than a unified representation of development across all taxa.