Sharing out control in distributed processes

AbstractIn this paper, we discuss the problem of distributed control of discrete processes. Given n sites from which only partial information is available about a process, we describe how to share out controllable events in order that the process meets a given global specification. As with many problems involving partial observation, the solution relies on inefficient algorithms. The second part of the paper treats the question of identifying problems that can be solved efficiently

A minor alternative transcript of the fumarylacetoacetate hydrolase gene produces a protein despite being likely subjected to nonsense-mediated mRNA decay

BACKGROUND: Coupling of alternative splicing with nonsense-mediated mRNA decay (NMD) may regulate gene expression. We report here the identification of a nonsense alternative transcript of the fumarylacetoacetate hydrolase (fah) gene, which produces a protein despite the fact that it is subject to NMD. RESULTS: During the characterization of the effects of the W262X nonsense mutation on FAH mRNA metabolism, two alternative transcripts (del100 and del231) of the fah gene were identified. Del100 lacks exon 8 and as a consequence, the reading frame is shifted and a premature termination codon appears at the 3'end of exon 10. Exons 8 and 9 are skipped in del231, without any disruption of the reading frame. Specific amplification of these transcripts demonstrate that they are produced through minor alternative splicing pathways, and that they are not caused by the W262X mutation per se. As shown with an antiserum raised against the C-terminal part of the putative DEL100 protein, the del100 transcript produces a protein, expressed at different levels in various human tissues. Interestingly, the del100 transcript seems to be subjected to nonsense-mediated mRNA decay, as its level was stabilized following a cycloheximide treatment. CONCLUSIONS: The del100 and del231 transcripts arise due to minor alternative splicing pathways and del100 is likely subjected to nonsense-mediated mRNA decay. However the remaining amount of transcript seems sufficient to produce a protein in different human tissues. This suggests that NMD has a broader role than simply eliminating aberrant transcripts and when coupled to alternative splicing, may act to modulate gene expression, by allowing the production of low amounts of protein

The evolution of the tape measure protein: units, duplications and losses

<p>Abstract</p> <p>Background</p> <p>A large family of viruses that infect bacteria, called <it>phages</it>, is characterized by long tails used to inject DNA into their victims' cells. The <it>tape measure protein</it> got its name because the length of the corresponding gene is proportional to the length of the phage's tail: a fact shown by actually copying or splicing out parts of DNA in exemplar species. A natural question is whether there exist <it>units</it> for these tape measures, and if different tape measures have different units and lengths. Such units would allow us to retrace the evolution of tape measure proteins using their duplication/loss history. The vast number of sequenced phages genomes allows us to attack this problem with a comparative genomics approach.</p> <p>Results</p> <p>Here we describe a subset of phages whose tape measure proteins contain variable numbers of an 11 amino acids sequence repeat, aligned with sequence similarity, structural properties, and simple arithmetics. This subset provides a unique opportunity for the combinatorial study of phage evolution, without the added uncertainties of multiple alignments, which are trivial in this case, or of protein functions, that are well established. We give a heuristic that reconstructs the duplication history of these sequences, using divergent strains to discriminate between mutations that occurred before and after speciation, or lineage divergence. The heuristic is based on an efficient algorithm that gives an exhaustive enumeration of all possible parsimonious reconstructions of the duplication/speciation history of a single nucleotide. Finally, we present a method that allows, when possible, to discriminate between duplication and loss events.</p> <p>Conclusions</p> <p>Establishing the evolutionary history of viruses is difficult, in part due to extensive recombinations and gene transfers, and high mutation rates that often erase detectable similarity between homologous genes. In this paper, we introduce new tools to address this problem.</p

The strategic role of IT as an antecedent to the IT sophistication and IT performance of manufacturing SMEs

The business value of IT (information technology) applications for SMEs (small- and medium-sized enterprises) is dependent upon how such applications “fit” with the strategic orientation of these firms. Based on the strategic alignment of IT, this study uses a systemic approach to test the contribution of three predictors of IT performance in an organization: the strategic role of IT as well as the sophistication of the management and the use of IT. A multivariate mediation perspective is used to conceptualize alignment. The results of an empirical investigation of 44 manufacturing SMEs establish an important mediating effect of IT management and IT usage sophistication between the strategic role of IT and IT performance

An algorithmic view of gene teams

International audienc

Computing commons interval of K permutations, with applications to modular decomposition of graphs

International audienceWe introduce a new way to compute common intervals of K permutations based on a very simple and general notion of generators of common intervals. This formalism leads to simple and efficient algorithms to compute the set of all common intervals of K permutations, that can contain a quadratic number of intervals, as well as a linear space basis of this set of common intervals. Finally, we show how our results on permutations can be used for computing the modular decomposition of graphs in linear time

A Holocene landscape dynamic multiproxy reconstruction: How do interactions between fire and insect outbreaks shape an ecosystem over long time scales?

At a multi-millennial scale, various disturbances shape boreal forest stand mosaics and the distribution of species. Despite the importance of such disturbances, there is a lack of studies focused on the long-term dynamics of spruce budworm (Choristoneura fumiferana (Clem.)) (SBW) outbreaks and the interaction of insect outbreaks and fire. Here, we combine macrocharcoal and plant macrofossils with a new proxy-lepidopteran scalesto describe the Holocene ecology around a boreal lake. Lepidopteran scales turned out to be a more robust proxy of insect outbreaks than the traditional proxies such as cephalic head capsules and feces. We identified 87 significant peaks in scale abundance over the last 10 000 years. These results indicate that SBW outbreaks were more frequent over the Holocene than suggested by previous studies. Charcoal accumulation rates match the established fire history in eastern Canada: A more fire-prone early and late Holocene and reduced fire frequency during the mid-Holocene. Although on occasion, both fire and insect outbreaks were coeval, our results show a generally inverse relationship between fire frequency and insect outbreaks over the Holocene

Divide and Conquer: Enriching Environmental Sequencing Data

In environmental sequencing projects, a mix of DNA from a whole microbial community is fragmented and sequenced, with one of the possible goals being to reconstruct partial or complete genomes of members of the community. In communities with high diversity of species, a significant proportion of the sequences do not overlap any other fragment in the sample. This problem will arise not only in situations with a relatively even distribution of many species, but also when the community in a particular environment is routinely dominated by the same few species. In the former case, no genomes may be assembled at all, while in the latter case a few dominant species in an environment will always be sequenced at high coverage to the detriment of coverage of the greater number of sparse species.Here we show that, with the same global sequencing effort, separating the species into two or more sub-communities prior to sequencing can yield a much higher proportion of sequences that can be assembled. We first use the Lander-Waterman model to show that, if the expected percentage of singleton sequences is higher than 25%, then, under the uniform distribution hypothesis, splitting the community is always a wise choice. We then construct simulated microbial communities to show that the results hold for highly non-uniform distributions. We also show that, for the distributions considered in the experiments, it is possible to estimate quite accurately the relative diversity of the two sub-communities.Given the fact that several methods exist to split microbial communities based on physical properties such as size, density, surface biochemistry, or optical properties, we strongly suggest that groups involved in environmental sequencing, and expecting high diversity, consider splitting their communities in order to maximize the information content of their sequencing effort

Surveying the endomicrobiome and ectomicrobiome of bark beetles: The case of Dendroctonus simplex.

International audienceMany bark beetles belonging to the Dendroctonus genus carry bacterial and fungal microbiota, forming a symbiotic complex that helps the insect to colonize the subcortical environment of the host tree. However, the biodiversity of those bacteria at the surface of the cuticle or inside the body parts of bark beetles is not well established. The aim of this study was to characterize the bacterial microbiome associated with the eastern larch beetle, Dendroctonus simplex, using bacterial 16S rRNA gene pyrosequencing. The ecto- and endomicrobiome and the subcortical galleries were investigated. Several bacterial genera were identified, among which Pseudomonas, Serratia and Yersinia are associated with the surface of the beetle cuticle, and genera belonging to Enterobacteriaceae and Gammaproteobacteria with the interior of the insect body. The index of dissimilarity indicates that the bacterial microbiome associated with each environment constitutes exclusive groups. These results suggest the presence of distinct bacterial microbiota on the surface of the cuticle and the interior of D. simplex body. Additionally, the bacterial diversity identified in the galleries is substantially different from the ectomicrobiome, which could indicate a selection by the insect. This study reports for the first time the identification of the eastern larch beetle microbiome