Lateral genomics

More than 20 complete prokaryotic genome sequences are now publicly available, each by itself an unparalleled resource for understanding organismal biology. Collectively, these data are even more powerful: they could force a dramatic reworking of the framework in which we understand biological evolution. It is possible that a single universal phylogenetic tree is not the best way to depict relationships between all living and extinct species. Instead a web- or net-like pattern, reflecting the importance of horizontal or lateral gene transfer between lineages of organisms, might provide a more appropriate visual metaphor. Here, I ask whether this way of thinking is really justified, and explore its implications.     

Lateral genomics

More than 20 complete prokaryotic genome sequences are now publicly available, each by itself an unparalleled resource for understanding organismal biology. Collectively, these data are even more powerful: they could force a dramatic reworking of the framework in which we understand biological evolution. It is possible that a single universal phylogenetic tree is not the best way to depict relationships between all living and extinct species. Instead a web- or net-like pattern, reflecting the importance of horizontal or lateral gene transfer between lineages of organisms, might provide a more appropriate visual metaphor. Here, I ask whether this way of thinking is really justified, and explore its implications.     

Detection of unrelated proteins in sequences multiple alignments by using predicted secondary structures

MOTIVATION: Multiple sequence alignments are essential tools for establishing the homology relations between proteins. Essential amino acids for the function and/or the structure are generally conserved, thus providing key arguments to help in protein characterization. However for distant proteins, it is more difficult to establish, in a reliable way, the homology relations that may exist between them. In this article, we show that secondary structure prediction is a valuable way to validate protein families at low identity rate. RESULTS: We show that the analysis of the secondary structures compatibility is a reliable way to discard non-related proteins in low identity multiple alignment. AVAILABILITY: This validation is possible through our NPS@ server (http://npsa-pbil.ibcp.fr)     

Protein folding: a problem with multiple solutions

There is continued interest in predicting the structure of proteins either at the simplest level of identifying their fold class or persevering all the way to an atomic resolution structure. Protein folding methods have become very sophisticated and many successes have been recorded with claims to have solved the native structure of the protein. But for any given protein, there may be more than one solution. Many proteins can exist in one of the other two (or more) different forms and some populate multiple metastable states. Here, the two-state case is considered and the key structural changes that take place when the protein switches from one state to the other are identified. Analysis of these results show that hydrogen bonding patterns and hydrophobic contacts vary considerably between different conformers. Contrary to what has often been assumed previously, these two types of interaction operate essentially independently of one another. Core packing is critical for proper protein structure and function and it is shown that there are considerable changes in internal cavity volumes in many cases. The way in which these switches are made is fold dependent. Considerations such as these need to be taken into account in protein structure prediction.     

Transport of beads by several kinesin motors

The movements of beads pulled by several kinesin-1 (conventional kinesin) motors are studied both theoretically and experimentally. While the velocity is approximately independent of the number of motors pulling the beads, the walking distance or run-length is strongly increased when more motors are involved. Run-length distributions are measured for a wide range of motor concentrations and matched to theoretically calculated distributions using only two global fit parameters. In this way, the maximal number of motors pulling the beads is estimated to vary between two and seven motors for total kinesin concentrations between 0.1 and 2.5 μg/ml or between 0.27 and 6.7 nM. In the same concentration regime, the average number of pulling motors is found to lie between 1.1 and 3.2 motors.     

The Use of Two‐Way Linear Mixed Models in Multitreatment Meta‐Analysis

Summary Meta‐analysis summarizes the results of a series of trials. When more than two treatments are included in the trials and when the set of treatments tested differs between trials, the combination of results across trials requires some care. Several methods have been proposed for this purpose, which feature under different labels, such as network meta‐analysis or mixed treatment comparisons. Two types of linear mixed model can be used for meta‐analysis. The one expresses the expected outcome of treatments as a contrast to a baseline treatment. The other uses a classical two‐way linear predictor with main effects for treatment and trial. In this article, we compare both types of model and explore under which conditions they give equivalent results. We illustrate practical advantages of the two‐way model using two published datasets. In particular, it is shown that between‐trial heterogeneity as well as inconsistency between different types of trial is straightforward to account for.     

A flexible approach to the calculation of resonance energy transfer efficiency between multiple donors and acceptors in complex geometries

Resonance energy transfer provides a practical way to measure distances in the range of 10-100 A between sites in biological molecules. Although the relationship between the efficiency of energy transfer and the distance between sites is well described for a single pair of fluorophores, the situation is more difficult when more than two fluorophores are present. Using a Monte Carlo calculation scheme, we demonstrate how resonance energy transfer can be used to measure distances between fluorophores in complex geometries. We demonstrate the versatility of the approach by calculating the efficiency of energy transfer for individual fluorophores randomly distributed in two and three dimensions, for linked pairs of donors and acceptors and pentameric structures of five linked fluorophores. This approach can be used to relate the efficiency of energy transfer to the distances between fluorophores, R0, molecular concentrations, laser power, and donor/acceptor ratios in ensembles of molecules or when many fluorophores are attached to a single molecule such as in multimeric proteins.     

A Method for Investigating Age-related Differences in the Functional Connectivity of Cognitive Control Networks Associated with Dimensional Change Card Sort Performance

The ability to adjust behavior to sudden changes in the environment develops gradually in childhood and adolescence. For example, in the Dimensional Change Card Sort task, participants switch from sorting cards one way, such as shape, to sorting them a different way, such as color. Adjusting behavior in this way exacts a small performance cost, or switch cost, such that responses are typically slower and more error-prone on switch trials in which the sorting rule changes as compared to repeat trials in which the sorting rule remains the same. The ability to flexibly adjust behavior is often said to develop gradually, in part because behavioral costs such as switch costs typically decrease with increasing age. Why aspects of higher-order cognition, such as behavioral flexibility, develop so gradually remains an open question. One hypothesis is that these changes occur in association with functional changes in broad-scale cognitive control networks. On this view, complex mental operations, such as switching, involve rapid interactions between several distributed brain regions, including those that update and maintain task rules, re-orient attention, and select behaviors. With development, functional connections between these regions strengthen, leading to faster and more efficient switching operations. The current video describes a method of testing this hypothesis through the collection and multivariate analysis of fMRI data from participants of different ages.     

Electron competition process in respiratory chain: Regulatory mechanisms and physiological functions

In mitochondria isolated from the yeast Saccharomyces cerevisiae, under non-phosphorylating conditions, we have previously shown that there is a right of way for electrons coming from the external NADH dehydrogenase, Nde1p. In this work, we show that the electron competition process is identical under more physiological conditions i.e. oxidative phosphorylation. Such a competition generates a priority for cytosolic NADH reoxidation. Furthermore, this electron competition process is associated with an energy wastage (the “active leak”) that allows an increase in redox equivalent oxidation when the redox pressure increases. When this redox pressure is decreased, i.e. under phosphorylating conditions, most of this energy wastage is alleviated. By studying mutant strains affected either in respiratory chain supramolecular organization or in electron competition activity, we show that the respiratory chain supramolecular organization is not responsible for the electron competition processes. Moreover, we show two distinct relationships between the respiratory rate and the quinone redox state that seem to indicate two quinone pools that are involved in the electron right of way. Indeed, the more reduced pool would be associated to the electron right of way for the external dehydrogenases whereas the less reduced pool would be associated to the electron right of way for the internal dehydrogenases.     

On Sample Size of the Kruskal–Wallis Test with Application to a Mouse Peritoneal Cavity Study

Summary As the nonparametric generalization of the one‐way analysis of variance model, the Kruskal–Wallis test applies when the goal is to test the difference between multiple samples and the underlying population distributions are nonnormal or unknown. Although the Kruskal–Wallis test has been widely used for data analysis, power and sample size methods for this test have been investigated to a much lesser extent. This article proposes new power and sample size calculation methods for the Kruskal–Wallis test based on the pilot study in either a completely nonparametric model or a semiparametric location model. No assumption is made on the shape of the underlying population distributions. Simulation results show that, in terms of sample size calculation for the Kruskal–Wallis test, the proposed methods are more reliable and preferable to some more traditional methods. A mouse peritoneal cavity study is used to demonstrate the application of the methods.     

Testing a simple stochastic model for the dynamics of waterfowl aggregations

We consider a simple stochastic model for the dynamics of mixed-species waterfowl aggregations and describe two methods for assessing the fit of this model to field data. The model does not incorporate species-specific behavior. It assumes that all birds act independently and incorrectly predicts an exponential distribution for inter-event times. We reject this model, show that 29% of the birds move in groups of two or more birds, and demonstrate that the distribution of inter-event times between the movements of groups of birds is exponential. We find no difference in movement rates or group sizes between seasons, and no difference between groups arriving into or departing from the observed aggregations. An analysis of group composition suggests that species at low abundance behave differently than species at high abundance: birds with few conspecifics are more likely to move in mixed-species groups than birds with many conspecifics. We suggest that simple stochastic models provide a useful way to explore the dynamics of animal behavior.     

Theoretical dynamics of competitors under predation

Summary Continuous population models of two prey species and a predator were explored by isocline analysis. When predator satiation and substitution between prey (with or without switching) are introduced in the models, many qualitatively different kinds of dynamic behaviour become possible. These depend in a complex but predictable way on competitive relations between prey and on predator feeding behaviour and efficiency. Under constant predation many cases of threshold responses between two or more alternate stable states are possibly; the numerical response of the predator population reduces some of the possibilities.Apparently contradictory community phenomena previously proposed, e.g. prey coexistence versus exclusion by addition of predator, exclusion versus stabilization by addition of alternate prey, are all possible as special cases. A prey which is relatively tolerant to predation can act as a keystone species, on which the existence of other prey species in the community depends, in either a positive or a negative sense. In certain conditions predator-induced obligatory mutualism between two prey species is theoretically possible.To Michael Evenari, pioneer, teacher and friend     

Evaluating options in LCA: The emergence of conflicting paradigms for impact assessment and evaluation

LCA aims to help direct decisions in an environmentally sustainable direction. It indicates the environmental effects of choices and evaluates these against this background. Approaches to evaluation in LCA differ substantially, related to the way of modelling environmental effects and to the way these effects are combined into an overall judgement on alternative options. Several approaches are now operational, which are linked to different paradigms in decision making. It is shown that the choice of paradigm is quite decisive on the outcome of the analysis. Also within similar paradigms, different methods now operational may lead to different outcomes. These latter differences may be alleviated more easily than those related to paradigmatic choices, as they are partly a matter of refinement, and they partly result from legitimate differences in subjective priorities. The more basic paradigmatic differences can hardly be bridged. The practical relevancy of the subject is proven by applying different operational methods to one case, showing widely differing outcomes. The paradigm behind evaluating environmental effects is either values based, directly or through policy decisions, or economics based, as individual preferences measured in the monetary terms of willingness-to-pay. Accordingly, the different methods are “policy-oriented” or “monetary”. It may be doubted if the differences between these can be overcome in standardisation.     

C-banding as a simple tool to discriminate between micronuclei induced by clastogens and aneugens

If mouse bone marrow preparations are treated with a classical C-banding procedure, it may be possible to distinguish between micronuclei with or without centromeres. This allows discrimination between micronuclei originating from chromosome breakage and those originating from chromosome loss. Thus, using C-banding, the micronucleus test can be used not only for the detection of clastogens but also aneugens. In this way, more exhaustive methods such as immunological staining using antikinetochore antibodies may not be necessary.     

Successional diversity and forest ecosystem function

Forest inventory data was used to examine the relationship between successional diversity and forest ecosytem function. The inventory data show that stands composed of early successional species are more productive than stands composed of late successional species, whereas stands composed of late successsional species have lower turnover than stands composed of early successional species. Taken alone, these results would suggest that forests should be managed in a way that favors the most productive early successional species or longest-lived late successional species, depending on whether the goal is to maximize productivity or maximize carbon storage. However, the inventory data also show that stands with low successional diversity fix and store less carbon than stands with high successional diversity. This result suggests that forests should be managed in such a way as to retain species diversity while also favoring species that maximize the ecosystem function of interest.     

C-Banding as a Simple Tool to Discriminate Between Micronuclei Induced by Clastogens and Aneugens

If mouse bone marrow preparations are treated with a classical C-banding procedure, it may be possible to distinguish between micronuclei with or without centromeres. This allows discrimination between micronuclei originating from chromosome breakage and those originating from chromosome loss. Thus, using C-banding, the micronucleus test can be used not only for the detection of clastogens but also aneugens. In this way, more exhaustive methods such as immunological staining using antikinetochore antibodies may not be necessary.     

Risks of transmissible diseases in relation to embryo transfer

Realizing the potential of Embryo transfer (ET) for rapid, cheap and widespread dissemination of genetic material, the risk of transmission disease through the embryos must be considered. The aim of this paper is to evaluate theses risks at each step of production, storage and transfer. The pathogen agent may potentially originate from the donor male (semen) or the donor female (oocytes, embryos) and finally from the environmental conditions. As the differences between in vivo and in vitro derived embryos have been well described, evaluation of the potential risks should be assessed separately for in vivo and in vitro produced embryos. Even if this paper insist on the diseases or diseases agents that are more questionable, it clearly appears that ET remains the more safety way to transfer gene, provided prevention measures are properly handled (use of donor that are specific pathogen free, washing of embryos, additional treatment...) and furthermore it can be easily seen as the best way to prevent some disease transmissions (TSEs, leukosis, foot-and-mouth disease...).     

A new mechanism for neuronal gain control (or how the gain in brains has mainly been explained)

One of the more prosaic but necessary features of almost any information processing system is gain control. All such systems must have some way to adjust the relationship between input, which can vary dramatically depending on changes in the environment, and output, which is almost always required to remain within a limited range of amplitudes. While the volume control on a radio or the brightness control on a computer monitor are not the most exciting or highly touted features, imagine such devices without these forms of gain control. Many an engineer can attest to the large effort required to design automatic gain controls in telephones, cameras, and radio transmitters.     

Why People Don't Die 'Naturally' any More: Changing Relations Between 'The Individual' and 'The State' in Post-Socialist Bulgaria

This article explores the theme of death as a means of illuminating the changing relationship between 'the individual' and 'the state' in the context of post-socialist Bulgaria. Previous research carried out on rituals and socialist society indicates a close connection between state ideology and the socially constructed 'natural' order – an order partly reproduced through engagement in state-sponsored life-cycle rituals, such as funerals. By focusing on the way in which funerals are presently carried out, and more specifically on the way in which villagers talk about death, I suggest that new discourse reveals important changes: a reordering of the relationship between 'the individual' and the socially constructed 'natural' order. The state is no longer such a strong mediating force in this relationship. Post-socialist reform, therefore, involves more than 'just' political and economic change; it represents a more general breakdown in the total set of relations that constituted the socialist world.