Windowed Decoding of Protograph-based LDPC Convolutional Codes over Erasure Channels

We consider a windowed decoding scheme for LDPC convolutional codes that is based on the belief-propagation (BP) algorithm. We discuss the advantages of this decoding scheme and identify certain characteristics of LDPC convolutional code ensembles that exhibit good performance with the windowed decoder. We will consider the performance of these ensembles and codes over erasure channels with and without memory. We show that the structure of LDPC convolutional code ensembles is suitable to obtain performance close to the theoretical limits over the memoryless erasure channel, both for the BP decoder and windowed decoding. However, the same structure imposes limitations on the performance over erasure channels with memory.Comment: 18 pages, 9 figures, accepted for publication in the IEEE Transactions on Information Theor

Origin, duplication and reshuffling of plasmid genes: Insights from Burkholderia vietnamiensis G4 genome.

Using a computational pipeline based on similarity networks reconstruction we analysed the 1133 genes of the Burkholderia vietnamiensis ( Bv) G4 five plasmids, showing that gene and operon duplication played an important role in shaping the plasmid architecture. Several single/multiple duplications occurring at intra- and/or interplasmids level involving 253 paralogous genes (stand-alone, clustered or operons) were detected. An extensive gene/operon exchange between plasmids and chromosomes was also disclosed. The larger the plasmid, the higher the number and size of paralogous fragments. Many paralogs encoded mobile genetic elements and duplicated very recently, suggesting that the rearrangement of the Bv plastic genome is ongoing. Concerning the "molecular habitat" and the "taxonomical status" (the Preferential Organismal Sharing) of Bv plasmid genes, most of them have been exchanged with other plasmids of bacteria belonging (or phylogenetically very close) to Burkholderia, suggesting that taxonomical proximity of bacterial strains is a crucial issue in plasmid-mediated gene exchange. © 2014 Elsevier Inc

Exploring the evolutionary dynamics of plasmids: the Acinetobacter pan-plasmidome

Background: Prokaryotic plasmids have a dual importance in the microbial world: first they have a great impact on the metabolic functions of the host cell, providing additional traits that can be accumulated in the cell without altering the gene content of the bacterial chromosome. Additionally and/or alternatively, from a genome perspective, plasmids can provide a basis for genomic rearrangements via homologous recombination and so they can facilitate the loss or acquisition of genes during these events, which eventually may lead to horizontal gene transfer (HGT). Given their importance for conferring adaptive traits to the host organisms, the interest in plasmid sequencing is growing and now many complete plasmid sequences are available online. Results: By using the newly developed Blast2Network bioinformatic tool, a comparative analysis was performed on the plasmid and chromosome sequence data available for bacteria belonging to the genus Acinetobacter, an ubiquitous and clinically important group of gamma-proteobacteria. Data obtained showed that, although most of the plasmids lack mobilization and transfer functions, they have probably a long history of rearrangements with other plasmids and with chromosomes. Indeed, traces of transfers between different species can be disclosed. Conclusions: We show that, by combining plasmid and chromosome similarity, identity based, network analysis, an evolutionary scenario can be described even for highly mobile genetic elements that lack extensively shared genes. In particular we found that transposases and selective pressure for mercury resistance seem to have played a pivotal role in plasmid evolution in Acinetobacter genomes sequenced so far

Exploring the HME and HAE1 efflux systems in the genus Burkholderia

<p>Abstract</p> <p>Background</p> <p>The genus <it>Burkholderia </it>includes a variety of species with opportunistic human pathogenic strains, whose increasing global resistance to antibiotics has become a public health problem. In this context a major role could be played by multidrug efflux pumps belonging to Resistance Nodulation Cell-Division (RND) family, which allow bacterial cells to extrude a wide range of different substrates, including antibiotics. This study aims to i) identify <it>rnd </it>genes in the 21 available completely sequenced <it>Burkholderia </it>genomes, ii) analyze their phylogenetic distribution, iii) define the putative function(s) that RND proteins perform within the <it>Burkholderia </it>genus and iv) try tracing the evolutionary history of some of these genes in <it>Burkholderia</it>.</p> <p>Results</p> <p>BLAST analysis of the 21 <it>Burkholderia </it>sequenced genomes, using experimentally characterized <it>ceoB </it>sequence (one of the RND family counterpart in the genus <it>Burkholderia</it>) as probe, allowed the assembly of a dataset comprising 254 putative RND proteins. An extensive phylogenetic analysis revealed the occurrence of several independent events of gene loss and duplication across the different lineages of the genus <it>Burkholderia</it>, leading to notable differences in the number of paralogs between different genomes. A putative substrate [antibiotics (HAE1 proteins)/heavy-metal (HME proteins)] was also assigned to the majority of these proteins. No correlation was found between the ecological niche and the lifestyle of <it>Burkholderia </it>strains and the number/type of efflux pumps they possessed, while a relation can be found with genome size and taxonomy. Remarkably, we observed that only HAE1 proteins are mainly responsible for the different number of proteins observed in strains of the same species. Data concerning both the distribution and the phylogenetic analysis of the HAE1 and HME in the <it>Burkholderia </it>genus allowed depicting a likely evolutionary model accounting for the evolution and spreading of HME and HAE1 systems in the <it>Burkholderia </it>genus.</p> <p>Conclusion</p> <p>A complete knowledge of the presence and distribution of RND proteins in <it>Burkholderia </it>species was obtained and an evolutionary model was depicted. Data presented in this work may serve as a basis for future experimental tests, focused especially on HAE1 proteins, aimed at the identification of novel targets in antimicrobial therapy against <it>Burkholderia </it>species.</p

An Acidic Loop and Cognate Phosphorylation Sites Define a Molecular Switch That Modulates Ubiquitin Charging Activity in Cdc34-Like Enzymes

E2 ubiquitin-conjugating enzymes are crucial mediators of protein ubiquitination, which strongly influence the ultimate fate of the target substrates. Recently, it has been shown that the activity of several enzymes of the ubiquitination pathway is finely tuned by phosphorylation, an ubiquitous mechanism for cellular regulation, which modulates protein conformation. In this contribution, we provide the first rationale, at the molecular level, of the regulatory mechanism mediated by casein kinase 2 (CK2) phosphorylation of E2 Cdc34-like enzymes. In particular, we identify two co-evolving signature elements in one of the larger families of E2 enzymes: an acidic insertion in β4α2 loop in the proximity of the catalytic cysteine and two conserved key serine residues within the catalytic domain, which are phosphorylated by CK2. Our investigations, using yeast Cdc34 as a model, through 2.5 µs molecular dynamics simulations and biochemical assays, define these two elements as an important phosphorylation-controlled switch that modulates opening and closing of the catalytic cleft. The mechanism relies on electrostatic repulsions between a conserved serine phosphorylated by CK2 and the acidic residues of the β4α2 loop, promoting E2 ubiquitin charging activity. Our investigation identifies a new and unexpected pivotal role for the acidic loop, providing the first evidence that this loop is crucial not only for downstream events related to ubiquitin chain assembly, but is also mandatory for the modulation of an upstream crucial step of the ubiquitin pathway: the ubiquitin charging in the E2 catalytic cleft

LTE Adaptation for Mobile Broadband Satellite Networks

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