Fluctuation-enhanced sensing

We present a short survey on fluctuation-enhanced gas sensing. We compare some of its main characteristics with those of classical sensing. We address the problem of linear response, information channel capacity, missed alarms and false alarms.Comment: Keynote Talk at SPIE's 4th international symposium on Fluctuations and Noise, Conference Noise and Fluctuations in Circuits, Devices and Materials, Florence, Italy, May 20-24, 200

Horizontal gene transfer to a defensive symbiont with a reduced genome in a multipartite beetle microbiome

Symbiotic mutualisms of bacteria and animals are ubiquitous in nature, running a continuum from facultative to obligate from the perspectives of both partners. The loss of functions required for living independently but not within a host gives rise to reduced genomes in many symbionts. Although the phenomenon of genome reduction can be explained by existing evolutionary models, the initiation of the process is not well understood. Here, we describe the microbiome associated with the eggs of the beetle Lagria villosa, consisting of multiple bacterial symbionts related to Burkholderia gladioli, including a reduced-genome symbiont thought to be the exclusive producer of the defensive compound lagriamide. We show that the putative lagriamide-producing symbiont is the only member of the microbiome undergoing genome reduction and that it has already lost the majority of its primary metabolism and DNA repair pathways. The key step preceding genome reduction in the symbiont was likely the horizontal acquisition of the putative lagriamide lga biosynthetic gene cluster. Unexpectedly, we uncovered evidence of additional horizontal transfers to the symbiont's genome while genome reduction was occurring and despite a current lack of genes needed for homologous recombination. These gene gains may have given the genome-reduced symbiont a selective advantage in the microbiome, especially given the maintenance of the large lga gene cluster despite ongoing genome reduction. IMPORTANCE Associations between microorganisms and an animal, plant, or fungal host can result in increased dependence over time. This process is due partly to the bacterium not needing to produce nutrients that the host provides, leading to loss of genes that it would need to live independently and to a consequent reduction in genome size. It is often thought that genome reduction is aided by genetic isolation-bacteria that live in monocultures in special host organs, or inside host cells, have less access to other bacterial species from which they can obtain genes. Here, we describe exposure of a genome-reduced beetle symbiont to a community of related bacteria with nonreduced genomes. We show that the symbiont has acquired genes from other bacteria despite going through genome reduction, suggesting that isolation has not yet played a major role in this case of genome reduction, with horizontal gene gains still offering a potential route for adaptation

Improving Gene-finding in Chlamydomonas reinhardtii:GreenGenie2

<p>Abstract</p> <p>Background</p> <p>The availability of whole-genome sequences allows for the identification of the entire set of protein coding genes as well as their regulatory regions. This can be accomplished using multiple complementary methods that include ESTs, homology searches and <it>ab initio </it>gene predictions. Previously, the Genie gene-finding algorithm was trained on a small set of <it>Chlamydomonas </it>genes and shown to improve the accuracy of gene prediction in this species compared to other available programs. To improve <it>ab initio </it>gene finding in <it>Chlamydomonas</it>, we assemble a new training set consisting of over 2,300 cDNAs by assembling over 167,000 <it>Chlamydomonas </it>EST entries in GenBank using the EST assembly tool PASA.</p> <p>Results</p> <p>The prediction accuracy of our cDNA-trained gene-finder, GreenGenie2, attains 83% sensitivity and 83% specificity for exons on short-sequence predictions. We predict about 12,000 genes in the version <it>v3 Chlamydomonas </it>genome assembly, most of which (78%) are either identical to or significantly overlap the published catalog of <it>Chlamydomonas </it>genes <abbrgrp><abbr bid="B1">1</abbr></abbrgrp>. 22% of the published catalog is absent from the GreenGenie2 predictions; there is also a fraction (23%) of GreenGenie2 predictions that are absent from the published gene catalog. Randomly chosen gene models were tested by RT-PCR and most support the GreenGenie2 predictions.</p> <p>Conclusion</p> <p>These data suggest that training with EST assemblies is highly effective and that GreenGenie2 is a valuable, complementary tool for predicting genes in <it>Chlamydomonas reinhardtii</it>.</p