The constancy of gene conservation across divergent bacterial orders

<p>Abstract</p> <p>Background</p> <p>Orthologous genes are frequently presumed to perform similar functions. However, outside of model organisms, this is rarely tested. One means of inferring changes in function is if there are changes in the level of gene conservation and selective constraint. Here we compare levels of gene conservation across three bacterial groups to test for changes in gene functionality.</p> <p>Findings</p> <p>The level of gene conservation for different orthologous genes is highly correlated across clades, even for highly divergent groups of bacteria. These correlations do not arise from broad differences in gene functionality (e.g. informational genes vs. metabolic genes), but instead seem to result from very specific differences in gene function. Furthermore, these functional differences appear to be maintained over very long periods of time.</p> <p>Conclusion</p> <p>These results suggest that even over broad time scales, most bacterial genes are under a nearly constant level of purifying selection, and that bacterial evolution is thus dominated by selective and functional stasis.</p

The Effect of Straight-Line and Accelerated Depreciation Rules on Risky Investment Decisions - An Experimental Study

The aim of this study is to analyze how depreciation rules influence the decision behavior of investors. For this purpose, we conduct a laboratory experiment in which participants decide on the composition of an asset portfolio in different choice situations. Using an experimental setting with different payment periods, we show that accelerated compared to straight-line depreciation can increase the willingness to invest as hypothesized by theory. However, this expected behavior is only observed in a more complex environment (with a subsidy) and not in a less complex environment (without a subsidy)

DNA Sequences Shaped by Selection for Stability

The sequence of a stretch of nucleotides affects its propensity for errors during replication and expression. Are proteins encoded by stable or unstable nucleotide sequences? If selection for variability is prevalent, one could expect an excess of unstable sequences. Alternatively, if selection against targets for errors were substantial, an excess of stable sequences would be expected. We screened the genome sequences of different organisms for an important determinant of stability, the presence of mononucleotide repeats. We find that codons are used to encode proteins in a way that avoids the emergence of mononucleotide repeats, and we can attribute this bias to selection rather than a neutral process. This indicates that selection for stability, rather than for the generation of variation, substantially influences how information is encoded in the genome

Microbial life cycles link global modularity in regulation to mosaic evolution

Microbes are exposed to changing environments, to which they can respond by adopting various lifestyles such as swimming, colony formation or dormancy. These lifestyles are often studied in isolation, thereby giving a fragmented view of the life cycle as a whole. Here, we study lifestyles in the context of this whole. We first use machine learning to reconstruct the expression changes underlying life cycle progression in the bacterium Bacillus subtilis, based on hundreds of previously acquired expression profiles. This yields a timeline that reveals the modular organization of the life cycle. By analysing over 380 Bacillales genomes, we then show that life cycle modularity gives rise to mosaic evolution in which life stages such as motility and sporulation are conserved and lost as discrete units. We postulate that this mosaic conservation pattern results from habitat changes that make these life stages obsolete or detrimental. Indeed, when evolving eight distinct Bacillales strains and species under laboratory conditions that favour colony growth, we observe rapid and parallel losses of the sporulation life stage across species, induced by mutations that affect the same global regulator. We conclude that a life cycle perspective is pivotal to understanding the causes and consequences of modularity in both regulation and evolution

Bacterial growth properties at low optical densities

A method for accurate quantification of growth rate and yield of bacterial populations at low densities was developed with a modified version of a stepwise linear model for fitting growth curves based on optical density measurements, and adapted to measurements at low optical densities in 96-well microtiter plates. The method can be used for rapid and precise estimates of growth rate and yield, based on optical density measurements of large numbers of cultures of Escherichia coli. E. coli B lines were serially propagated at low glucose concentration during a long-term evolution experiment. Growth rate and yield of populations sampled from each of 12 lines that evolved for 20,000 generations under these conditions and two ancestral clones was measured. Populations were grown at three different glucose concentrations. Consistent with earlier findings, statistical analysis showed that both exponential growth rate and yield per unit of glucose differed significantly between the three glucose concentrations tested. Significant adaptation of the evolved populations to the nutrient conditions in which they evolved for 20,000 generations was observe

Comparing charge transfer tuning effects by chemical substitution and uniaxial pressure in the organic charge transfer complex tetramethoxypyrene-tetracyanoquinodimethane

In the search for novel organic charge transfer salts with variable charge transfer degree we study the effects of two modifications to the recently synthesized donor-acceptor Tetramethoxypyrene (TMP)-Tetracyanoquinodimethane (TCNQ). One is of chemical nature by substituting the acceptor TCNQ molecules by F4TCNQ molecules. The second consists in simulating the application of uniaxial pressure along the stacking axis of the system. In order to test the chemical substitution, we have grown single crystals of TMP-F4TCNQ and analyzed its electronic structure via electronic transport measurements, ab initio density functional theory (DFT) calculations and UV/VIS/IR absorption spectroscopy. This system shows an almost ideal geometrical overlap of nearly planar molecules alternately stacked (mixed stack) and this arrangement is echoed by a semiconductor-like transport behavior with an increased conductivity along the stacking direction. This is in contrast to TMP-TCNQ which shows a less pronounced anisotropy and a smaller conductivity response. Our bandstructure calculations confirm the one-dimensional behavior of TMP-F4TCNQ with pro- nounced dispersion only along the stacking axis. Infrared measurements illustrating the CN vibration frequency shift in F4TCNQ suggest however no improvement on the degree of charge transfer in TMP-F4TCNQ with respect to TMP-TCNQ. In both complexes about 0.1 is transferred from TMP to the acceptor. Concerning the pressure effect, our DFT calculations on designed TMP-TCNQ and TMP-F4TCNQ structures under different pressure conditions show that application of uniaxial pressure along the stacking axis of TMP-TCNQ may be the route to follow in order to obtain a much more pronounced charge transfer

Review on Neutrino Telescopes

I will discuss the motivations for Neutrino Astronomy and its prospects given the current experimental scenario, which is the main focus of this paper. I will also go through the first results of the IceCube detector deep in the ice and of the ANTARES undersea telescope underlying complementary aspects, common and different challenges. It is an exciting time for this science since the first completed undersea detector is successfully taking data and the first cubic kilometer detector is going to be shortly more than half-way from its completion in Antarctica.Comment: Proceeding of CRIS2008 Conference, Salina, Sept. 2008, 9 pages, 8 figure

Language-independent look-ahead for checking multi-perspective declarative process models

Declarative process modelling languages focus on describing a process by restrictions over the behaviour, which must be satisfied throughout the whole process execution. Hence, they are well suited for modelling knowledge-intensive processes with many decision points. However, such models can be hard to read and understand, which affect the modelling and maintenance of the process models tremendously as well as their execution. When executing such declarative (multi-perspective) process models, it may happen that the execution of activities or the change of data values may result in the non-executability of crucial activities. Hence, it would be beneficial to know all consequences of decisions to give recommendations to the process participants. A look-ahead attempts to predict the effects of executing an activity towards possible consequences within an a priori defined time window. The prediction is based on the current state of the process execution, the intended next event and the underlying process model. While execution engines for single-perspective imperative process models already implement such functionality, execution approaches, for multi-perspective declarative process models that involve constraints on data and resources, are less mature. In this paper, we introduce a simulation-based look-ahead approach for multi-perspective declarative process models. This approach transforms the problem of a context-aware process simulation into a SAT problem, by translating a declarative multi-perspective process model and the current state of a process execution into a specification of the logic language Alloy. Via a SAT solver, process trajectories are generated that either satisfy or violate this specification. The simulated process trajectories are used to derive consequences and effects of certain decisions at any time of process execution. We evaluate our approach by means of three examples and give some advice for further optimizations

The SPO1-related bacteriophages

A large and diverse group of bacteriophages has been termed ‘SPO1-like viruses'. To date, molecular data and genome sequences are available for Bacillus phage SPO1 and eight related phages infecting members of other bacterial genera. Many additional bacteriophages have been described as SPO1-related, but very few data are available for most of them. We present an overview of putative ‘SPO1-like viruses' and shall discuss the available data in view of the recently proposed expansion of this group of bacteriophages to the tentative subfamily Spounavirinae. Characteristics of SPO1-related phages include (a) the host organisms are Firmicutes; (b) members are strictly virulent myoviruses; (c) all phages feature common morphological properties; (d) the phage genome consists of a terminally redundant, non-permuted dsDNA molecule of 127-157kb in size; and (e) phages share considerable amino acid homology. The number of phages isolated consistent with these parameters is large, suggesting a ubiquitous nature of this group of viruse