Root foraging theory put to the test

Roots have a tremendous plasticity that has long fascinated plant scientists. Root proliferation into enriched soil patches is commonly considered as a way for plants to acquire patchily distributed soil resources. In a recent synthetic study involving the responses of over 100 species, Kembel and Cahill concluded that long-standing generalizations explaining variation in root proliferation should be reconsidered.     

Declarative versus episodic: two theories put to the test

The question of whether the hippocampus plays a selective role in episodic memory or a more general role in both episodic and semantic memory (together termed declarative memory) is an unresolved and much-debated topic in the current literature. In two back-to-back articles in this issue of Neuron, Squire and his colleagues describe findings from a group of six patients with damage thought to be limited to the hippocampus. The reported findings provide new evidence toward resolving this much-debated controversy.     

Metabolite secretion in microorganisms: the theory of metabolic overflow put to the test

Introduction

Microbial cells secrete many metabolites during growth, including important intermediates of the central carbon metabolism. This has not been taken into account by researchers when modeling microbial metabolism for metabolic engineering and systems biology studies.

Materials and Methods

The uptake of metabolites by microorganisms is well studied, but our knowledge of how and why they secrete different intracellular compounds is poor. The secretion of metabolites by microbial cells has traditionally been regarded as a consequence of intracellular metabolic overflow.

Conclusions

Here, we provide evidence based on time-series metabolomics data that microbial cells eliminate some metabolites in response to environmental cues, independent of metabolic overflow. Moreover, we review the different mechanisms of metabolite secretion and explore how this knowledge can benefit metabolic modeling and engineering.

     

A new rig for standardized craniofacial photography put to the test

This article describes and tests a photography rig that has been built at the University of Melbourne, Australia, specifically for the purpose of taking rapid and highly standardized craniofacial photographs, in simultaneous views of front and profile. The rig uses a novel projected light range-finding system that has been designed for easy and accurate positioning of subjects, in the natural head position, at precise distances from the frontal camera. Results of experiments examining the intraobserver error of multiple photographs taken on the rig indicate that high-quality, repeatable photographs can be taken after a reasonably large amount of time has lapsed between photography sessions (e.g., 30 days). This study also indicates that some variability remains between photographs even when highly standardized protocols are followed. Consequently, it is expected that the variation between photographs with limited standardization is much larger and more likely to cause significant errors in any comparisons.     

Chromatin modification: How to put a HAT on the histones

Specific patterns of acetylation of the core histones are associated with specific structures and functions of chromatin. A basis for the specificity of acetylation is now apparent in the recent crystal structures of two acetyltransferases.     

From aquatic science to ecosystem health: a philosophical perspective

The development of an ecosystem (social, economic, environmental) approach to water management is traced from its origins in the Great Lakes of North America. The focus on health and integrity of ecosystems is an outgrowth of the Lamarckian concept of The Biosphere as a global system of matter, life, and mind. The driving forces behind the development of an ecosystem approach have been negative feedback from excessive demotechnic growth and faith that we can maintain a healthy relationship with Mother Earth.     

Using phylogeographic analyses of gene trees to test species status and processes

A gene tree is an evolutionary reconstruction of the genealogical history of the genetic variation found in a sample of homologous genes or DNA regions that have experienced little or no recombination. Gene trees have the potential of straddling the interface between intra- and interspecific evolution. It is precisely at this interface that the process of speciation occurs, and gene trees can therefore be used as a powerful tool to probe this interface. One application is to infer species status. The cohesion species is defined as an evolutionary lineage or set of lineages with genetic exchangeability and/or ecological interchangeability. This species concept can be phrased in terms of null hypotheses that can be tested rigorously and objectively by using gene trees. First, an overlay of geography upon the gene tree is used to test the null hypothesis that the sample is from a single evolutionary lineage. This phase of testing can indicate that the sampled organisms are indeed from a single lineage and therefore a single cohesion species. In other cases, this null hypothesis is not rejected due to a lack of power or inadequate sampling. Alternatively, this null hypothesis can be rejected because two or more lineages are in the sample. The test can identify lineages even when hybridization and lineage sorting occur. Only when this null hypothesis is rejected is there the potential for more than one cohesion species. Although all cohesion species are evolutionary lineages, not all evolutionary lineages are cohesion species. Therefore, if the first null hypothesis is rejected, a second null hypothesis is tested that all lineages are genetically exchangeable and/or ecologically interchangeable. This second test is accomplished by direct contrasts of previously identified lineages or by overlaying reproductive and/or ecological data upon the gene tree and testing for significant transitions that are concordant with the previously identified lineages. Only when this second null hypothesis is rejected is a lineage elevated to the status of cohesion species. By using gene trees in this manner, species can be identified with objective, a priori criteria with an inference procedure that automatically yields much insight into the process of speciation. When one or more of the null hypotheses cannot be rejected, this procedure also provides specific guidance for future work that will be needed to judge species status.     

A molecular test of cyanobacterial phylogeny: inferences from constraint analyses

Parsimony and neighbor-joining analyses of 16S rDNA nucleotide sequences of 68 species and strains of cyanobacteria and prochlorophytes supported a monophyletic Nostocales, a monophyletic Stigonematales, three independent lineages of prochlorophytes within the cyanobacteria, and a paraphyletic Chroococcales (p<0.0001) and Oscillatoriales (p = 0.0147). Within the Oscillatoriales, the genus Oscillatoria formed an unnatural taxon (p<0.0001) and needs major revisions. Using constraint analysis, the genus Microcystis was found to be monophyletic and the paraphyletic positions of Microcystis elabens and M. holsatica are probably due to long-branch attraction. Further, a separation of Chroococcales based on varying levels of polyunsaturated fatty acids is more consistent with nucleotide-based phylogenies than with existing morphological groupings. It is proposed that Chroococcales be redefined to exclude the genus Microcystis, and that a new order be erected for Microcystis. Finally, it is more parsimonious to assume a common cyanobacterial/prochlorophyte ancestor, than to evoke de novo synthesis of chlb in each prochlorophyte lineage plus in the lineage leading to green chloroplasts. This common ancestor is proposed to have contained both chlorophyll a and b plus phycobilins. Subsequent multiple losses of chlb in cyanobacteria and the loss of chla and phycobilins in prochlorophytes, led to the currently observed pigment distribution. It is therefore, recommended that Prochlorales be reclassified as cyanobacteria.     

Sociobiology and philosophical ethics: Narrowing the gap

Though there are good reasons for thinking that sociobiology is capable of contributing to the solution of one of the central problems of philosophical ethics, the problem of other-benefitting behaviour, philosophers have not welcomed the new discipline with open arms. This has been so for three reasons: it is said that sociobiology studies behaviour, and not its proximal causes, that sociobiology tells us about the evolutionary history of behaviour and not about its justification, and that sociobiology prescribes morally unacceptable ways of acting. I argue that the first of the objections is simply mistaken, and that when we realize this, the second loses some of its force. I also argue in favour of atwo-factor model of motivation with reason and the emotions engaged in a dialogue with each other concerning the morally relevant features of a given situation. This two-factor model helps us overcome the third objection above, namely to the morally unacceptable dictates of sociobiology, and also to weaken claims that sociobiology is committed to a lack of freedom of the will in human action. Broadly speaking, my argument suggest that the ethical framework most suited to accommodating sociobiological insights into human motivation is an Aristotelian structure.     

Hashimoto's Thyroiditis: From Genes to the Disease

Hashimoto's thyroiditis (HT) is the most prevalent autoimmune thyroid disorder. Intrathyroidal lymphocytic infiltration is followed by a gradual destruction of the thyroid gland which may lead to subclinical or overt hypothyroidism. Biochemical markers of the disease are thyroid peroxidase and/or thyroglobulin autoantibodies in the serum which are present with a higher prevalence in females than in males and increase with age. Although exact mechanisms of aetiology and pathogenesis of the disorder are not completely understood, a strong genetic susceptibility to the disease has been confirmed predominantly by family and twin studies. Several genes were shown to be associated with the disease occurrence, progression, and severity. Genes for human leukocyte antigen, cytotoxic T lymphocyte antigen-4, protein tyrosine phosphatase nonreceptor-type 22, thyroglobulin, vitamin D receptor, and cytokines are considered to be of utmost importance. Amongst endogenous factors for the disease development, the attention is focused predominantly on female sex, pregnancy with postpartum period and fetal microchimerism. Environmental factors influencing HT development are iodine intake, drugs, infections and different chemicals. Disturbed self-tolerance accompanied by the increased antigen presentation is a prerequisite for the HT occurrence, whereas proper interaction of thyroid cells, antigen presenting cells, and T cells are necessary for the initiation of thyroid autoimmunity. Secreted cytokines lead predominantly to T-helper type 1 (Th1) response as well as to Th 17 response which has only recently been implicated. Final outcome of HT is thyroid destruction which is mostly a consequence of the apoptotic processes combined with T-cell mediated cytotoxicity.     

Outlier analyses to test for local adaptation to breeding grounds in a migratory arctic seabird

Investigating the extent (or the existence) of local adaptation is crucial to understanding how populations adapt. When experiments or fitness measurements are difficult or impossible to perform in natural populations, genomic techniques allow us to investigate local adaptation through the comparison of allele frequencies and outlier loci along environmental clines. The thick‐billed murre (Uria lomvia) is a highly philopatric colonial arctic seabird that occupies a significant environmental gradient, shows marked phenotypic differences among colonies, and has large effective population sizes. To test whether thick‐billed murres from five colonies along the eastern Canadian Arctic coast show genomic signatures of local adaptation to their breeding grounds, we analyzed geographic variation in genome‐wide markers mapped to a newly assembled thick‐billed murre reference genome. We used outlier analyses to detect loci putatively under selection, and clustering analyses to investigate patterns of differentiation based on 2220 genomewide single nucleotide polymorphisms (SNPs) and 137 outlier SNPs. We found no evidence of population structure among colonies using all loci but found population structure based on outliers only, where birds from the two northernmost colonies (Minarets and Prince Leopold) grouped with birds from the southernmost colony (Gannet), and birds from Coats and Akpatok were distinct from all other colonies. Although results from our analyses did not support local adaptation along the latitudinal cline of breeding colonies, outlier loci grouped birds from different colonies according to their non‐breeding distributions, suggesting that outliers may be informative about adaptation and/or demographic connectivity associated with their migration patterns or nonbreeding grounds.