| shifting the genomic gold standard for the prokaryotic species definition. | dna-dna hybridization (ddh) has been used for nearly 50 years as the gold standard for prokaryotic species circumscriptions at the genomic level. it has been the only taxonomic method that offered a numerical and relatively stable species boundary, and its use has had a paramount influence on how the current classification has been constructed. however, now, in the era of genomics, ddh appears to be an outdated method for classification that needs to be substituted. the average nucleotide identi ... | 2009 | 19855009 |
| a comparison of protein extraction methods suitable for gel-based proteomic studies of aphid proteins. | protein extraction methods can vary widely in reproducibility and in representation of the total proteome, yet there are limited data comparing protein isolation methods. the methodical comparison of protein isolation methods is the first critical step for proteomic studies. to address this, we compared three methods for isolation, purification, and solubilization of insect proteins. the aphid schizaphis graminum, an agricultural pest, was the source of insect tissue. proteins were extracted usi ... | 2009 | 19721822 |
| cation/proton antiporter complements of bacteria: why so large and diverse? | most bacterial genomes have five to nine distinct genes predicted to encode transporters that exchange cytoplasmic na(+) and/or k(+) for h(+) from outside the cell, i.e. monovalent cation/proton antiporters. by contrast, pathogens that live primarily inside host cells usually possess zero to one such antiporter while other stress-exposed bacteria exhibit even higher numbers. the monovalent cation/proton antiporters encoded by these diverse genes fall into at least eight different transporter pro ... | 2009 | 19682259 |
| origin of an alternative genetic code in the extremely small and gc-rich genome of a bacterial symbiont. | the genetic code relates nucleotide sequence to amino acid sequence and is shared across all organisms, with the rare exceptions of lineages in which one or a few codons have acquired novel assignments. recoding of uga from stop to tryptophan has evolved independently in certain reduced bacterial genomes, including those of the mycoplasmas and some mitochondria. small genomes typically exhibit low guanine plus cytosine (gc) content, and this bias in base composition has been proposed to drive ug ... | 2009 | 19609354 |
| abstracts of the 2008 issol meeting. august 24-29, 2008. florence, italy. | | 2009 | 19468860 |
| lateral gene transfer between prokaryotes and multicellular eukaryotes: ongoing and significant? | the expansion of genome sequencing projects has produced accumulating evidence for lateral transfer of genes between prokaryotic and eukaryotic genomes. however, it remains controversial whether these genes are of functional importance in their recipient host. nikoh and nakabachi, in a recent paper in bmc biology, take a first step and show that two genes of bacterial origin are highly expressed in the pea aphid acyrthosiphon pisum. active gene expression of transferred genes is supported by thr ... | 2009 | 19416510 |
| prediction of protein binding regions in disordered proteins. | many disordered proteins function via binding to a structured partner and undergo a disorder-to-order transition. the coupled folding and binding can confer several functional advantages such as the precise control of binding specificity without increased affinity. additionally, the inherent flexibility allows the binding site to adopt various conformations and to bind to multiple partners. these features explain the prevalence of such binding elements in signaling and regulatory processes. in t ... | 2009 | 19412530 |
| computational biology methods and their application to the comparative genomics of endocellular symbiotic bacteria of insects. | comparative genomics has become a real tantalizing challenge in the postgenomic era. this fact has been mostly magnified by the plethora of new genomes becoming available in a daily bases. the overwhelming list of new genomes to compare has pushed the field of bioinformatics and computational biology forward toward the design and development of methods capable of identifying patterns in a sea of swamping data noise. despite many advances made in such endeavor, the ever-lasting annoying exception ... | 2009 | 19495914 |
| functional classification of genome-scale metabolic networks. | we propose two strategies to characterize organisms with respect to their metabolic capabilities. the first, investigative, strategy describes metabolic networks in terms of their capability to utilize different carbon sources, resulting in the concept of carbon utilization spectra. in the second, predictive, approach minimal nutrient combinations are predicted from the structure of the metabolic networks, resulting in a characteristic nutrient profile. both strategies allow for a quantification ... | 2009 | 19300528 |
| genome-enabled research on the ecology of plant-insect interactions. | | 2010 | 20921167 |
| evolutionary lability of a complex life cycle in the aphid genus brachycaudus. | most aphid species complete their life cycle on the same set of host-plant species, but some (heteroecious species) alternate between different hosts, migrating from primary (woody) to secondary (herbaceous) host plants. the evolutionary processes behind the evolution of this complex life cycle have often been debated. one widely accepted scenario is that heteroecy evolved from monoecy on woody host plants. several shifts towards monoecy on herbaceous plants have subsequently occurred and result ... | 2010 | 20920188 |
| fraggenescan: predicting genes in short and error-prone reads. | the advances of next-generation sequencing technology have facilitated metagenomics research that attempts to determine directly the whole collection of genetic material within an environmental sample (i.e. the metagenome). identification of genes directly from short reads has become an important yet challenging problem in annotating metagenomes, since the assembly of metagenomes is often not available. gene predictors developed for whole genomes (e.g. glimmer) and recently developed for metagen ... | 2010 | 20805240 |
| psrna: a computing engine for the comparative identification of putative small rna locations within intergenic regions. | small rnas (srnas) are non-coding transcripts exerting their functions in the cells directly. identification of srnas is a difficult task due to the lack of clear sequence and structural biases. most srnas are identified within genus specific intergenic regions in related genomes. however, several of these regions remain un-annotated due to lack of sequence homology and/or potent statistical identification tools. a computational engine has been built to search within the intergenic regions to id ... | 2010 | 20691398 |
| evolution of the mutation rate. | understanding the mechanisms of evolution requires information on the rate of appearance of new mutations and their effects at the molecular and phenotypic levels. although procuring such data has been technically challenging, high-throughput genome sequencing is rapidly expanding knowledge in this area. with information on spontaneous mutations now available in a variety of organisms, general patterns have emerged for the scaling of mutation rate with genome size and for the likely mechanisms t ... | 2010 | 20594608 |
| correlations between bacterial ecology and mobile dna. | several factors can affect the density of mobile dna in bacterial genomes including rates of exposure to novel gene pools, recombination, and reductive evolution. these traits are difficult to measure across a broad range of bacterial species, but the ecological niches occupied by an organism provide some indication of the relative magnitude of these forces. here, by analyzing 384 bacterial genomes assigned to three ecological categories (obligate intracellular, facultative intracellular, and ex ... | 2010 | 20577742 |
| correlations between bacterial ecology and mobile dna. | several factors can affect the density of mobile dna in bacterial genomes including rates of exposure to novel gene pools, recombination, and reductive evolution. these traits are difficult to measure across a broad range of bacterial species, but the ecological niches occupied by an organism provide some indication of the relative magnitude of these forces. here, by analyzing 384 bacterial genomes assigned to three ecological categories (obligate intracellular, facultative intracellular, and ex ... | 2010 | 20577742 |
| challenges in experimental data integration within genome-scale metabolic models. | a report of the meeting "challenges in experimental data integration within genome-scale metabolic models", institut henri poincaré, paris, october 10-11 2009, organized by the cnrs-mpg joint program in systems biology. | 2010 | 20412574 |
| a complex journey: transmission of microbial symbionts. | the perpetuation of symbioses through host generations relies on symbiont transmission. horizontally transmitted symbionts are taken up from the environment anew by each host generation, and vertically transmitted symbionts are most often transferred through the female germ line. mixed modes also exist. in this review we describe the journey of symbionts from the initial contact to their final residence. we provide an overview of the molecular mechanisms that mediate symbiont attraction and accu ... | 2010 | 20157340 |
| reconstructing genome trees of prokaryotes using overlapping genes. | overlapping genes (ogs) are defined as adjacent genes whose coding sequences overlap partially or entirely. in fact, they are ubiquitous in microbial genomes and more conserved between species than non-overlapping genes. based on this property, we have previously implemented a web server, named ogtree, that allows the user to reconstruct genome trees of some prokaryotes according to their pairwise og distances. by analogy to the analyses of gene content and gene order, the og distance between tw ... | 2010 | 20181237 |
| immunity and other defenses in pea aphids, acyrthosiphon pisum. | recent genomic analyses of arthropod defense mechanisms suggest conservation of key elements underlying responses to pathogens, parasites and stresses. at the center of pathogen-induced immune responses are signaling pathways triggered by the recognition of fungal, bacterial and viral signatures. these pathways result in the production of response molecules, such as antimicrobial peptides and lysozymes, which degrade or destroy invaders. using the recently sequenced genome of the pea aphid (acyr ... | 2010 | 20178569 |
| assembly of outer membrane β-barrel proteins: the bam complex. | the major class of integral proteins found in the outer membrane (om) of e. coli and salmonella adopt a β-barrel conformation (omps). omps are synthesized in the cytoplasm with a typical signal sequence at the amino terminus, which directs them to the secretion machinery (secyeg) located in the inner membrane for translocation to the periplasm. chaperones such as sura, or degp and skp, escort these proteins across the aqueous periplasm protecting them from aggregation. the chaperones then delive ... | 2011 | 26442509 |
| bacterial communities of two parthenogenetic aphid species cocolonizing two host plants across the hawaiian islands. | aphids (hemiptera: aphididae) have been the focus of several studies with respect to their interactions with inherited symbionts, but bacterial communities of most aphid species are still poorly characterized. in this research, we used bar-coded pyrosequencing to characterize bacterial communities in aphids. specifically, we examined the diversity of bacteria in two obligately parthenogenetic aphid species (the melon aphid, aphis gossypii, and the cardamom aphid, pentalonia caladii) cocolonizing ... | 2011 | 21965398 |
| molecular musings in microbial ecology and evolution. | a few major discoveries have influenced how ecologists and evolutionists study microbes. here, in the format of an interview, we answer questions that directly relate to how these discoveries are perceived in these two branches of microbiology, and how they have impacted on both scientific thinking and methodology.the first question is "what has been the influence of the 'universal tree of life' based on molecular markers?" for evolutionists, the tree was a tool to understand the past of known ( ... | 2011 | 22074255 |
| ecological and temporal constraints in the evolution of bacterial genomes. | studies on the experimental evolution of microorganisms, on their in vivo evolution (mainly in the case of bacteria producing chronic infections), as well as the availability of multiple full genomic sequences, are placing bacteria in the playground of evolutionary studies. in the present article we review the differential contribution to the evolution of bacterial genomes that processes such as gene modification, gene acquisition and gene loss may have when bacteria colonize different habitats ... | 2011 | 24710293 |
| differential responses of the coral host and their algal symbiont to thermal stress. | the success of any symbiosis under stress conditions is dependent upon the responses of both partners to that stress. the coral symbiosis is particularly susceptible to small increases of temperature above the long term summer maxima, which leads to the phenomenon known as coral bleaching, where the intracellular dinoflagellate symbionts are expelled. here we for the first time used quantitative pcr to simultaneously examine the gene expression response of orthologs of the coral acropora aspera ... | 2011 | 22039532 |
| from rna-seq to large-scale genotyping - genomics resources for rye (secale cereale l.). | the improvement of agricultural crops with regard to yield, resistance and environmental adaptation is a perpetual challenge for both breeding and research. exploration of the genetic potential and implementation of genome-based breeding strategies for efficient rye (secale cereale l.) cultivar improvement have been hampered by the lack of genome sequence information. to overcome this limitation we sequenced the transcriptomes of five winter rye inbred lines using roche/454 gs flx technology. | 2011 | 21951788 |
| effect of host genotype on symbiont titer in the aphid-buchnera symbiosis. | obligate nutritional symbioses require balance between the energetic needs of the host and the symbiont. the resident symbiont population size within a host may have major impacts on host fitness, as both host and symbiont consume and supply metabolites in a shared metabolite pool. given the massive genome degradation that is a hallmark of bacterial endosymbionts of insects, it is unclear at what level these populations are regulated, and how regulation varies among hosts within natural populati ... | 2011 | 26467737 |
| novel male-biased expression in paralogs of the aphid slimfast nutrient amino acid transporter expansion. | a major goal of molecular evolutionary biology is to understand the fate and consequences of duplicated genes. in this context, aphids are intriguing because the newly sequenced pea aphid genome harbors an extraordinary number of lineage-specific gene duplications relative to other insect genomes. though many of their duplicated genes may be involved in their complex life cycle, duplications in nutrient amino acid transporters appear to be associated rather with their essential amino acid poor d ... | 2011 | 21917168 |
| bacteriocyte-associated gammaproteobacterial symbionts of the adelges nordmannianae/piceae complex (hemiptera: adelgidae). | adelgids (insecta: hemiptera: adelgidae) are known as severe pests of various conifers in north america, canada, europe and asia. here, we present the first molecular identification of bacteriocyte-associated symbionts in these plant sap-sucking insects. three geographically distant populations of members of the adelges nordmannianae/piceae complex, identified based on coi and ef1alpha gene sequences, were investigated. electron and light microscopy revealed two morphologically different endosym ... | 2011 | 21833037 |
| bacteriocyte-associated gammaproteobacterial symbionts of the adelges nordmannianae/piceae complex (hemiptera: adelgidae). | adelgids (insecta: hemiptera: adelgidae) are known as severe pests of various conifers in north america, canada, europe and asia. here, we present the first molecular identification of bacteriocyte-associated symbionts in these plant sap-sucking insects. three geographically distant populations of members of the adelges nordmannianae/piceae complex, identified based on coi and ef1alpha gene sequences, were investigated. electron and light microscopy revealed two morphologically different endosym ... | 2011 | 21833037 |
| evolution of symbiotic organs and endosymbionts in lygaeid stinkbugs. | we investigated seed bugs of the genus nysius (insecta: hemiptera: lygaeidae) for their symbiotic bacteria. from all the samples representing 4 species, 18 populations and 281 individuals, specific bacterial 16s rrna gene sequences were consistently identified, which formed a distinct clade in the gammaproteobacteria. in situ hybridization showed that the bacterium was endocellularly localized in a pair of large bacteriomes that were amorphous in shape, deep red in color, and in association with ... | 2011 | 21814289 |
| evolution of symbiotic organs and endosymbionts in lygaeid stinkbugs. | we investigated seed bugs of the genus nysius (insecta: hemiptera: lygaeidae) for their symbiotic bacteria. from all the samples representing 4 species, 18 populations and 281 individuals, specific bacterial 16s rrna gene sequences were consistently identified, which formed a distinct clade in the gammaproteobacteria. in situ hybridization showed that the bacterium was endocellularly localized in a pair of large bacteriomes that were amorphous in shape, deep red in color, and in association with ... | 2011 | 21814289 |
| quantification of codon selection for comparative bacterial genomics. | statistics measuring codon selection seek to compare genes by their sensitivity to selection for translational efficiency, but existing statistics lack a model for testing the significance of differences between genes. here, we introduce a new statistic for measuring codon selection, the adaptive codon enrichment (ace). | 2011 | 21787402 |
| linking hydrothermal geochemistry to organismal physiology: physiological versatility in riftia pachyptila from sedimented and basalt-hosted vents. | much of what is known regarding riftia pachyptila physiology is based on the wealth of studies of tubeworms living at diffuse flows along the fast-spreading, basalt-hosted east pacific rise (epr). these studies have collectively suggested that riftia pachyptila and its chemoautotrophic symbionts are physiologically specialized, highly productive associations relying on hydrogen sulfide and oxygen to generate energy for carbon fixation, and the symbiont's nitrate reduction to ammonia for energy a ... | 2011 | 21779334 |
| metaorganisms as the new frontier. | because it appears that almost all organisms are part of an interdependent metaorganism, an understanding of the underlying host-microbe species associations, and of evolution and molecular underpinnings, has become the new frontier in zoology. the availability of novel high-throughput sequencing methods, together with the conceptual understanding that advances mostly originate at the intersection of traditional disciplinary boundaries, enable biologists to dissect the mechanisms that control th ... | 2011 | 21737250 |
| a pilot study of bacterial genes with disrupted orfs reveals a surprising profusion of protein sequence recoding mediated by ribosomal frameshifting and transcriptional realignment. | bacterial genome annotations contain a number of coding sequences (cdss) that, in spite of reading frame disruptions, encode a single continuous polypeptide. such disruptions have different origins: sequencing errors, frameshift, or stop codon mutations, as well as instances of utilization of nontriplet decoding. we have extracted over 1,000 cdss with annotated disruptions and found that about 75% of them can be clustered into 64 groups based on sequence similarity. analysis of the clusters reve ... | 2011 | 21673094 |
| aphids alter host-plant nitrogen isotope fractionation. | plant sap-feeding insects and blood-feeding parasites are frequently depleted in (15)n relative to their diet. unfortunately, most fluid-feeder/host nitrogen stable-isotope studies simply report stable-isotope signatures, but few attempt to elucidate the mechanism of isotopic trophic depletion. here we address this deficit by investigating the nitrogen stable-isotope dynamics of a fluid-feeding herbivore-host plant system: the green peach aphid, myzus persicae, feeding on multiple brassicaceous ... | 2011 | 21646532 |
| analysis of intact protein isoforms by mass spectrometry. | the diverse proteome of an organism arises from such events as single nucleotide substitutions at the dna level, different rna processing, and dynamic enzymatic post-translational modifications. this minireview focuses on the measurement of intact proteins to describe the diversity found in proteomes. the field of biological mass spectrometry has steadily advanced, enabling improvements in the characterization of single proteins to proteins derived from cells or tissues. in this minireview, we d ... | 2011 | 21632550 |
| direct image-based correlative microscopy technique for coupling identification and structural investigation of bacterial symbionts associated with metazoans. | coupling prokaryote identification with ultrastructural investigation of bacterial communities has proven difficult in environmental samples. prokaryotes can be identified by using specific probes and fluorescence in situ hybridization (fish), but resolution achieved by light microscopes does not allow ultrastructural investigation. in the case of symbioses involving bacteria associated with metazoan tissues, fish-based studies often indicate the co-occurrence of several bacterial types within a ... | 2011 | 21515722 |
| evolutionary mechanisms of microbial genomes. | | 2011 | 21716727 |
| a biophysical protein folding model accounts for most mutational fitness effects in viruses. | fitness effects of mutations fall on a continuum ranging from lethal to deleterious to beneficial. the distribution of fitness effects (dfe) among random mutations is an essential component of every evolutionary model and a mathematical portrait of robustness. recent experiments on five viral species all revealed a characteristic bimodal-shaped dfe featuring peaks at neutrality and lethality. however, the phenotypic causes underlying observed fitness effects are still unknown and presumably, are ... | 2011 | 21610162 |
| bacterial symbionts in insects or the story of communities affecting communities. | bacterial symbionts are widespread in insects and other animals. most of them are predominantly vertically transmitted, along with their hosts' genes, and thus extend the heritable genetic variation present in one species. these passengers have a variety of repercussions on the host's phenotypes: besides the cost imposed on the host for maintaining the symbiont population, they can provide fitness advantages to the host or manipulate the host's reproduction. we argue that insect symbioses are id ... | 2011 | 21444313 |
| cycads: an annotation database system to ease the development and update of biocyc databases. | in recent years, genomes from an increasing number of organisms have been sequenced, but their annotation remains a time-consuming process. the biocyc databases offer a framework for the integrated analysis of metabolic networks. the pathway tool software suite allows the automated construction of a database starting from an annotated genome, but it requires prior integration of all annotations into a specific summary file or into a genbank file. to allow the easy creation and update of a biocyc ... | 2011 | 21474551 |
| a novel abundance-based algorithm for binning metagenomic sequences using l-tuples. | metagenomics is the study of microbial communities sampled directly from their natural environment, without prior culturing. among the computational tools recently developed for metagenomic sequence analysis, binning tools attempt to classify the sequences in a metagenomic dataset into different bins (i.e., species), based on various dna composition patterns (e.g., the tetramer frequencies) of various genomes. composition-based binning methods, however, cannot be used to classify very short frag ... | 2011 | 21385052 |
| horizontal gene transfer between bacteria and animals. | horizontal gene transfer is increasingly described between bacteria and animals. such transfers that are vertically inherited have the potential to influence the evolution of animals. one classic example is the transfer of dna from mitochondria and chloroplasts to the nucleus after the acquisition of these organelles by eukaryotes. even today, many of the described instances of bacteria-to-animal transfer occur as part of intimate relationships such as those of endosymbionts and their invertebra ... | 2011 | 21334091 |
| loss of genetic redundancy in reductive genome evolution. | biological systems evolved to be functionally robust in uncertain environments, but also highly adaptable. such robustness is partly achieved by genetic redundancy, where the failure of a specific component through mutation or environmental challenge can be compensated by duplicate components capable of performing, to a limited extent, the same function. highly variable environments require very robust systems. conversely, predictable environments should not place a high selective value on robus ... | 2011 | 21379323 |
| n-gram analysis of 970 microbial organisms reveals presence of biological language models. | it has been suggested previously that genome and proteome sequences show characteristics typical of natural-language texts such as "signature-style" word usage indicative of authors or topics, and that the algorithms originally developed for natural language processing may therefore be applied to genome sequences to draw biologically relevant conclusions. following this approach of 'biological language modeling', statistical n-gram analysis has been applied for comparative analysis of whole prot ... | 2011 | 21219653 |
| selection-driven extinction dynamics for group ii introns in enterobacteriales. | transposable elements (tes) are one of the major driving forces of genome evolution, raising the question of the long-term dynamics underlying their evolutionary success. some tes were proposed to evolve under a pattern of periodic extinctions-recolonizations, in which elements recurrently invade and quickly proliferate within their host genomes, then start to disappear until total extinction. depending on the model, te extinction is assumed to be driven by purifying selection against colonized ... | 2012 | 23251705 |
| translation in giant viruses: a unique mixture of bacterial and eukaryotic termination schemes. | mimivirus and megavirus are the best characterized representatives of an expanding new family of giant viruses infecting acanthamoeba. their most distinctive features, megabase-sized genomes carried in particles of size comparable to that of small bacteria, fill the gap between the viral and cellular worlds. these giant viruses are also uniquely equipped with genes coding for central components of the translation apparatus. the presence of those genes, thought to be hallmarks of cellular organis ... | 2012 | 23271980 |
| hamap in 2013, new developments in the protein family classification and annotation system. | hamap (high-quality automated and manual annotation of proteins-available at http://hamap.expasy.org/) is a system for the classification and annotation of protein sequences. it consists of a collection of manually curated family profiles for protein classification, and associated annotation rules that specify annotations that apply to family members. hamap was originally developed to support the manual curation of uniprotkb/swiss-prot records describing microbial proteins. here we describe new ... | 2012 | 23193261 |
| hamap in 2013, new developments in the protein family classification and annotation system. | hamap (high-quality automated and manual annotation of proteins-available at http://hamap.expasy.org/) is a system for the classification and annotation of protein sequences. it consists of a collection of manually curated family profiles for protein classification, and associated annotation rules that specify annotations that apply to family members. hamap was originally developed to support the manual curation of uniprotkb/swiss-prot records describing microbial proteins. here we describe new ... | 2012 | 23193261 |
| rather than by direct acquisition via lateral gene transfer, ghf5 cellulases were passed on from early pratylenchidae to root-knot and cyst nematodes. | plant parasitic nematodes are unusual metazoans as they are equipped with genes that allow for symbiont-independent degradation of plant cell walls. among the cell wall-degrading enzymes, glycoside hydrolase family 5 (ghf5) cellulases are relatively well characterized, especially for high impact parasites such as root-knot and cyst nematodes. interestingly, ancestors of extant nematodes most likely acquired these ghf5 cellulases from a prokaryote donor by one or multiple lateral gene transfer ev ... | 2012 | 23171084 |
| bioinformatic approaches for functional annotation and pathway inference in metagenomics data. | metagenomic approaches are increasingly recognized as a baseline for understanding the ecology and evolution of microbial ecosystems. the development of methods for pathway inference from metagenomics data is of paramount importance to link a phenotype to a cascade of events stemming from a series of connected sets of genes or proteins. biochemical and regulatory pathways have until recently been thought and modelled within one cell type, one organism, one species. this vision is being dramatica ... | 2012 | 23175748 |
| expression of small rna in aphis gossypii and its potential role in the resistance interaction with melon. | the regulatory role of small rnas (srnas) in various biological processes is an active area of investigation; however, there has been limited information available on the role of srnas in plant-insect interactions. this study was designed to identify srnas in cotton-melon aphid (aphis gossypii) during the vat-mediated resistance interaction with melon (cucumis melo). | 2012 | 23173035 |
| a novel human-infection-derived bacterium provides insights into the evolutionary origins of mutualistic insect-bacterial symbioses. | despite extensive study, little is known about the origins of the mutualistic bacterial endosymbionts that inhabit approximately 10% of the world's insects. in this study, we characterized a novel opportunistic human pathogen, designated "strain hs," and found that it is a close relative of the insect endosymbiont sodalis glossinidius. our results indicate that ancestral relatives of strain hs have served as progenitors for the independent descent of sodalis-allied endosymbionts found in several ... | 2012 | 23166503 |
| knowing your friends: invertebrate innate immunity fosters beneficial bacterial symbioses. | the innate immune system is present in all animals and is a crucial first line of defence against pathogens. however, animals also harbour large numbers of beneficial microorganisms that can be housed in the digestive tract, in specialized organs or on tissue surfaces. although invertebrates lack conventional antibody-based immunity, they are capable of eliminating pathogens and, perhaps more importantly, discriminating them from other microorganisms. this review examines the interactions betwee ... | 2012 | 23147708 |
| water stress and aphid feeding differentially influence metabolite composition in arabidopsis thaliana (l.). | little is known about how drought stress influences plant secondary metabolite accumulation and how this affects plant defense against different aphids. we therefore cultivated arabidopsis thaliana (l.) plants under well-watered, drought, and water-logged conditions. two aphid species were selected for this study: the generalist myzus persicae (sulzer) and the crucifer specialist brevicoryne brassicae (l.). metabolite concentrations in the phloem sap, which influence aphid growth, changed partic ... | 2012 | 23144921 |
| long chain n-acyl homoserine lactone production by enterobacter sp. isolated from human tongue surfaces. | we report the isolation of n-acyl homoserine lactone-producing enterobacter sp. isolate t1-1 from the posterior dorsal surfaces of the tongue of a healthy individual. spent supernatants extract from enterobacter sp. isolate t1-1 activated the biosensor agrobacterium tumefaciens ntl4(pzlr4), suggesting production of long chain ahls by these isolates. high resolution mass spectrometry analysis of these extracts confirmed that enterobacter sp. isolate t1-1 produced a long chain n-acyl homoserine la ... | 2012 | 23202161 |
| comparative genomics of serratia spp.: two paths towards endosymbiotic life. | symbiosis is a widespread phenomenon in nature, in which insects show a great number of these associations. buchnera aphidicola, the obligate endosymbiont of aphids, coexists in some species with another intracellular bacterium, serratia symbiotica. of particular interest is the case of the cedar aphid cinara cedri, where b. aphidicola bcc and s. symbiotica scc need each other to fulfil their symbiotic role with the insect. moreover, various features seem to indicate that s. symbiotica scc is cl ... | 2012 | 23077583 |
| factors behind junk dna in bacteria. | although bacterial genomes have been traditionally viewed as being very compact, with relatively low amounts of repetitive and non-coding dna, this view has dramatically changed in recent years. the increase of available complete bacterial genomes has revealed that many species present abundant repetitive dna (i.e., insertion sequences, prophages or paralogous genes) and that many of these sequences are not functional but can have evolutionary consequences as concerns the adaptation to specializ ... | 2012 | 24705080 |
| whole genome sequencing of mutation accumulation lines reveals a low mutation rate in the social amoeba dictyostelium discoideum. | spontaneous mutations play a central role in evolution. despite their importance, mutation rates are some of the most elusive parameters to measure in evolutionary biology. the combination of mutation accumulation (ma) experiments and whole-genome sequencing now makes it possible to estimate mutation rates by directly observing new mutations at the molecular level across the whole genome. we performed an ma experiment with the social amoeba dictyostelium discoideum and sequenced the genomes of t ... | 2012 | 23056439 |
| drift-barrier hypothesis and mutation-rate evolution. | mutation dictates the tempo and mode of evolution, and like all traits, the mutation rate is subject to evolutionary modification. here, we report refined estimates of the mutation rate for a prokaryote with an exceptionally small genome and for a unicellular eukaryote with a large genome. combined with prior results, these estimates provide the basis for a potentially unifying explanation for the wide range in mutation rates that exists among organisms. natural selection appears to reduce the m ... | 2012 | 23077252 |
| multiscale modeling of metabolism and macromolecular synthesis in e. coli and its application to the evolution of codon usage. | biological systems are inherently hierarchal and multiscale in time and space. a major challenge of systems biology is to describe biological systems as a computational model, which can be used to derive novel hypothesis and drive experiments leading to new knowledge. the constraint-based reconstruction and analysis approach has been successfully applied to metabolism and to the macromolecular synthesis machinery assembly. here, we present the first integrated stoichiometric multiscale model of ... | 2012 | 23029152 |
| pyrosequencing-based analysis of the microbiome associated with the horn fly, haematobia irritans. | the horn fly, haematobia irritans, is one of the most economically important pests of cattle. insecticides have been a major element of horn fly management programs. growing concerns with insecticide resistance, insecticide residues on farm products, and non-availability of new generation insecticides, are serious issues for the livestock industry. alternative horn fly control methods offer the promise to decrease the use of insecticides and reduce the amount of insecticide residues on livestock ... | 2012 | 23028533 |
| deep sequencing of the transcriptomes of soybean aphid and associated endosymbionts. | the soybean aphid has significantly impacted soybean production in the u.s. transcriptomic analyses were conducted for further insight into leads for potential novel management strategies. | 2012 | 22984624 |
| ibdsite: a galaxy-interacting, integrative database for supporting inflammatory bowel disease high throughput data analysis. | inflammatory bowel diseases (ibd) refer to a group of inflammatory conditions concerning colon and small intestine, which cause socially uncomfortable symptoms and often are associated with an increased risk of colon cancer. ibd are complex disorders, which rely on genetic susceptibility, environmental factors, deregulation of the immune system, and host relationship with commensal microbiota. the complexity of these pathologies makes difficult to clearly understand the mechanisms of their onset ... | 2012 | 23095257 |
| identification and biochemical evidence of a medium-chain-length polyhydroxyalkanoate depolymerase in the bdellovibrio bacteriovorus predatory hydrolytic arsenal. | the obligate predator bdellovibrio bacteriovorus hd100 shows a large set of proteases and other hydrolases as part of its hydrolytic arsenal needed for its predatory life cycle. we present genetic and biochemical evidence that open reading frame (orf) bd3709 of b. bacteriovorus hd100 encodes a novel medium-chain-length polyhydroxyalkanoate (mcl-pha) depolymerase (phaz(bd)). the primary structure of phaz(bd) suggests that this enzyme belongs to the α/β-hydrolase fold family and has a typical seri ... | 2012 | 22706067 |
| exploration of the core metabolism of symbiotic bacteria. | a large number of genome-scale metabolic networks is now available for many organisms, mostly bacteria. previous works on minimal gene sets, when analysing host-dependent bacteria, found small common sets of metabolic genes. when such analyses are restricted to bacteria with similar lifestyles, larger portions of metabolism are expected to be shared and their composition is worth investigating. here we report a comparative analysis of the small molecule metabolism of symbiotic bacteria, explorin ... | 2012 | 22938206 |
| multipartite control of the dna translocase, mfd. | atp-dependent nucleic acid helicases and translocases play essential roles in many aspects of dna and rna biology. in order to ensure that these proteins act only in specific contexts, their activity is often regulated by intramolecular contacts and interaction with partner proteins. we have studied the bacterial mfd protein, which is an atp-dependent dna translocase that relocates or displaces transcription ecs in a variety of cellular contexts. when bound to rnap, mfd exhibits robust atpase an ... | 2012 | 22904071 |
| arsenophonus groel interacts with clcuv and is localized in midgut and salivary gland of whitefly b. tabaci. | cotton leaf curl virus (clcuv) (gemininiviridae: begomovirus) is the causative agent of leaf curl disease in cotton plants (gossypium hirsutum). clcuv is exclusively transmitted by the whitefly species b. tabaci (gennadius) (hemiptera: alerodidae). b. tabaci contains several biotypes which harbor dissimilar bacterial endo-symbiotic community. it is reported that these bacterial endosymbionts produce a 63 kda chaperon groel protein which binds to geminivirus particles and protects them from rapid ... | 2012 | 22900008 |
| making the most of "omics" for symbiosis research. | omics, including genomics, proteomics, and metabolomics, enable us to explain symbioses in terms of the underlying molecules and their interactions. the central task is to transform molecular catalogs of genes, metabolites, etc., into a dynamic understanding of symbiosis function. we review four exemplars of omics studies that achieve this goal, through defined biological questions relating to metabolic integration and regulation of animal-microbial symbioses, the genetic autonomy of bacterial s ... | 2012 | 22983030 |
| the cellular immune response of the pea aphid to foreign intrusion and symbiotic challenge. | recent studies suggest that the pea aphid (acyrthosiphon pisum) has low immune defenses. however, its immune components are largely undescribed, and notably, extensive characterization of circulating cells has been missing. here, we report characterization of five cell categories in hemolymph of adults of the ll01 pea aphid clone, devoid of secondary symbionts (ss): prohemocytes, plasmatocytes, granulocytes, spherulocytes and wax cells. circulating lipid-filed wax cells are rare; they otherwise ... | 2012 | 22848726 |
| endosymbiont tolerance and control within insect hosts. | bacterial endosymbioses are very common in insects and can range from obligate to facultative as well as from mutualistic to pathogenic associations. several recent studies provide new insight into how endosymbionts manage to establish chronic infections of their hosts without being eliminated by the host immune system. endosymbiont tolerance may be achieved either by specific bacterial adaptations or by host measurements shielding bacteria from innate defense mechanisms. nevertheless, insect ho ... | 2012 | 26466544 |
| altered trna characteristics and 3' maturation in bacterial symbionts with reduced genomes. | translational efficiency is controlled by trnas and other genome-encoded mechanisms. in organelles, translational processes are dramatically altered because of genome shrinkage and horizontal acquisition of gene products. the influence of genome reduction on translation in endosymbionts is largely unknown. here, we investigate whether divergent lineages of buchnera aphidicola, the reduced-genome bacterial endosymbiont of aphids, possess altered translational features compared with their free-liv ... | 2012 | 22689638 |
| the gastric caeca of pentatomids as a house for actinomycetes. | microbes are extensively associated with insects, playing key roles in insect defense, nutrition and reproduction. most of the associations reported involve proteobacteria. despite the fact that actinobacteria associated with insects were shown to produce antibiotic barriers against pathogens to the hosts or to their food and nutrients, there are few studies focusing on their association with insects. thus, we surveyed the actinobacteria diversity on a specific region of the midgut of seven spec ... | 2012 | 22682021 |
| metatranscriptomic analysis of small rnas present in soybean deep sequencing libraries. | a large number of small rnas unrelated to the soybean genome were identified after deep sequencing of soybean small rna libraries. a metatranscriptomic analysis was carried out to identify the origin of these sequences. comparative analyses of small interference rnas (sirnas) present in samples collected in open areas corresponding to soybean field plantations and samples from soybean cultivated in greenhouses under a controlled environment were made. different pathogenic, symbiotic and free-liv ... | 2012 | 22802714 |
| arabidopsis thaliana-aphid interaction. | aphids are important pests of plants that use their stylets to tap into the sieve elements to consume phloem sap. besides the removal of photosynthates, aphid infestation also alters source-sink patterns. most aphids also vector viral diseases. in this chapter, we will summarize on recent significant findings in plant-aphid interaction, and how studies involving arabidopsis thaliana and myzus persicae (sülzer), more commonly known as the green peach aphid (gpa), are beginning to provide importan ... | 2012 | 22666177 |
| dispensabilities of carbonic anhydrase in proteobacteria. | carbonic anhydrase (ca) (e.c. 4.2.1.1) is a ubiquitous enzyme catalysing interconversion between co(2) and bicarbonate. the irregular distribution of the phylogenetically distinct classes of ca in procaryotic genome suggests its complex evolutionary history in procaryotes. genetic evidence regarding the dispensability of ca under high-co(2) air in some model organisms indicates that ca-deficient microorganisms can persist in the natural environment by choosing high-co(2) niches. in this study, w ... | 2012 | 22675650 |
| repeated, selection-driven genome reduction of accessory genes in experimental populations. | genome reduction has been observed in many bacterial lineages that have adapted to specialized environments. the extreme genome degradation seen for obligate pathogens and symbionts appears to be dominated by genetic drift. in contrast, for free-living organisms with reduced genomes, the dominant force is proposed to be direct selection for smaller, streamlined genomes. most variation in gene content for these free-living species is of "accessory" genes, which are commonly gained as large chromo ... | 2012 | 22589730 |
| shared ancestry of symbionts? sagrinae and donaciinae (coleoptera, chrysomelidae) harbor similar bacteria. | when symbioses between insects and bacteria are discussed, the origin of a given association is regularly of interest. we examined the evolution of the symbiosis between reed beetles (coleoptera, chrysomelidae, donaciinae) and intracellular symbionts belonging to the enterobacteriaceae. we analyzed the partial sequence of the 16s rrna to assess the phylogenetic relationships with bacteria we found in other beetle groups (cerambycidae, anobiidae, other chrysomelidae). we discuss the ecology of ea ... | 2012 | 26466539 |
| cellular mechanism for selective vertical transmission of an obligate insect symbiont at the bacteriocyte-embryo interface. | many insects are associated with obligate symbiotic bacteria, which are localized in specialized cells called bacteriocytes, vertically transmitted through host generations via ovarial passage, and essential for growth and reproduction of their hosts. although vertical transmission is pivotal for maintenance of such intimate host-symbiont associations, molecular and cellular mechanisms underlying the process are largely unknown. here we report a cellular mechanism for vertical transmission of th ... | 2012 | 22517738 |
| the central role of the host cell in symbiotic nitrogen metabolism. | symbiotic nitrogen recycling enables animals to thrive on nitrogen-poor diets and environments. it traditionally refers to the utilization of animal waste nitrogen by symbiotic micro-organisms to synthesize essential amino acids (eaas), which are translocated back to the animal host. we applied metabolic modelling and complementary metabolite profiling to investigate nitrogen recycling in the symbiosis between the pea aphid and the intracellular bacterium buchnera, which synthesizes eaas. the re ... | 2012 | 22513857 |
| microbial symbionts: a resource for the management of insect-related problems. | microorganisms establish with their animal hosts close interactions. they are involved in many aspects of the host life, physiology and evolution, including nutrition, reproduction, immune homeostasis, defence and speciation. thus, the manipulation and the exploitation the microbiota could result in important practical applications for the development of strategies for the management of insect-related problems. this approach, defined as 'microbial resource management' (mrm), has been applied suc ... | 2012 | 22103294 |
| describing the structural robustness landscape of bacterial small rnas. | the potential role of rna molecules as gene expression regulators has led to a new perspective on the intracellular control and genome organization. because secondary structures are crucial for their regulatory role, we sought to investigate their robustness to mutations and environmental changes. | 2012 | 22500888 |
| diversity of symbiotic organs and bacterial endosymbionts of lygaeoid bugs of the families blissidae and lygaeidae (hemiptera: heteroptera: lygaeoidea). | here we present comparative data on the localization and identity of intracellular symbionts among the superfamily lygaeoidea (insecta: hemiptera: heteroptera: pentatomomorpha). five different lygaeoid species from the families blissidae and lygaeidae (sensu stricto; including the subfamilies lygaeinae and orsillinae) were analyzed. fluorescence in situ hybridization (fish) revealed that all the bugs studied possess paired bacteriomes that are differently shaped in the abdomen and harbor specifi ... | 2012 | 22307293 |
| large variations in bacterial ribosomal rna genes. | ribosomal rna (rrna) genes, essential to all forms of life, have been viewed as highly conserved and evolutionarily stable, partly because very little is known about their natural variations. here, we explored large-scale variations of rrna genes through bioinformatic analyses of available complete bacterial genomic sequences with an emphasis on formation mechanisms and biological significance. interestingly, we found bacterial genomes in which no 16s rrna genes harbor the conserved core of the ... | 2012 | 22446745 |
| parasitoids as vectors of facultative bacterial endosymbionts in aphids. | heritable bacterial endosymbionts play an important role in aphid ecology. sequence-based evidence suggests that facultative symbionts such as hamiltonella defensa or regiella insecticola also undergo horizontal transmission. other than through male-to-female transfer during the sexual generation in autumn, the routes by which this occurs remain largely unknown. here, we tested if parasitoids or ectoparasitic mites can act as vectors for horizontal transfer of facultative symbionts. using symbio ... | 2012 | 22417790 |
| constraining the metabolic genotype-phenotype relationship using a phylogeny of in silico methods. | reconstructed microbial metabolic networks facilitate a mechanistic description of the genotype-phenotype relationship through the deployment of constraint-based reconstruction and analysis (cobra) methods. as reconstructed networks leverage genomic data for insight and phenotype prediction, the development of cobra methods has accelerated following the advent of whole-genome sequencing. here, we describe a phylogeny of cobra methods that has rapidly evolved from the few early methods, such as f ... | 2012 | 22367118 |
| parasitic wasp responses to symbiont-based defense in aphids. | recent findings indicate that several insect lineages receive protection against particular natural enemies through infection with heritable symbionts, but little is yet known about whether enemies are able to discriminate and respond to symbiont-based defense. the pea aphid, acyrthosiphon pisum, receives protection against the parasitic wasp, aphidius ervi, when infected with the bacterial symbiont hamiltonella defensa and its associated bacteriophage apse (acyrthosiphon pisum secondary endosym ... | 2012 | 22364271 |
| factors affecting population dynamics of maternally transmitted endosymbionts in bemisia tabaci. | while every individual of bemisia tabaci (hemiptera: aleyrodidae) harbors the primary symbiont (p-symbiont) portiera, the infection frequencies of the six secondary symbionts (s-symbionts) including hamiltonella, arsenophonus, cardinium, wolbachia, rickettsia and fritschea vary greatly among different populations. to characterize the factors influencing the infection dynamics of the six s-symbionts in b. tabaci, gene-specific pcr were conducted to screen for the presence of the p-symbiont portie ... | 2012 | 22383972 |
| gemsim: general, error-model based simulator of next-generation sequencing data. | gemsim, or general error-model based simulator, is a next-generation sequencing simulator capable of generating single or paired-end reads for any sequencing technology compatible with the generic formats sam and fastq (including illumina and roche/454). gemsim creates and uses empirically derived, sequence-context based error models to realistically emulate individual sequencing runs and/or technologies. empirical fragment length and quality score distributions are also used. reads may be drawn ... | 2012 | 22336055 |
| insight into the transmission biology and species-specific functional capabilities of tsetse (diptera: glossinidae) obligate symbiont wigglesworthia. | ancient endosymbionts have been associated with extreme genome structural stability with little differentiation in gene inventory between sister species. tsetse flies (diptera: glossinidae) harbor an obligate endosymbiont, wigglesworthia, which has coevolved with the glossina radiation. we report on the ~720-kb wigglesworthia genome and its associated plasmid from glossina morsitans morsitans and compare them to those of the symbiont from glossina brevipalpis. while there was overall high synten ... | 2012 | 22334516 |
| dickeya dadantii, a plant pathogenic bacterium producing cyt-like entomotoxins, causes septicemia in the pea aphid acyrthosiphon pisum. | dickeya dadantii (syn. erwinia chrysanthemi) is a plant pathogenic bacteria that harbours a cluster of four horizontally-transferred, insect-specific toxin genes. it was recently shown to be capable of causing an acute infection in the pea aphid acyrthosiphon pisum (insecta: hemiptera). the infection route of the pathogen, and the role and in vivo expression pattern of these toxins, remain unknown. using bacterial numeration and immunolocalization, we investigated the kinetics and the pattern of ... | 2012 | 22292023 |
| metabolic networks of sodalis glossinidius: a systems biology approach to reductive evolution. | genome reduction is a common evolutionary process affecting bacterial lineages that establish symbiotic or pathogenic associations with eukaryotic hosts. such associations yield highly reduced genomes with greatly streamlined metabolic abilities shaped by the type of ecological association with the host. sodalis glossinidius, the secondary endosymbiont of tsetse flies, represents one of the few complete genomes available of a bacterium at the initial stages of this process. in the present study, ... | 2012 | 22292008 |
| aphid amino acid transporter regulates glutamine supply to intracellular bacterial symbionts. | endosymbiotic associations have played a major role in evolution. however, the molecular basis for the biochemical interdependence of these associations remains poorly understood. the aphid-buchnera endosymbiosis provides a powerful system to elucidate how these symbioses are regulated. in aphids, the supply of essential amino acids depends on an ancient nutritional symbiotic association with the gamma-proteobacterium buchnera aphidicola. buchnera cells are densely packed in specialized aphid ba ... | 2013 | 24367072 |
| aphid amino acid transporter regulates glutamine supply to intracellular bacterial symbionts. | endosymbiotic associations have played a major role in evolution. however, the molecular basis for the biochemical interdependence of these associations remains poorly understood. the aphid-buchnera endosymbiosis provides a powerful system to elucidate how these symbioses are regulated. in aphids, the supply of essential amino acids depends on an ancient nutritional symbiotic association with the gamma-proteobacterium buchnera aphidicola. buchnera cells are densely packed in specialized aphid ba ... | 2013 | 24367072 |
| testing the reproducibility of multiple displacement amplification on genomes of clonal endosymbiont populations. | the multiple displacement amplification method has revolutionized genomic studies of uncultured bacteria, where the extraction of pure dna in sufficient quantity for next-generation sequencing is challenging. however, the method is problematic in that it amplifies the target dna unevenly, induces the formation of chimeric reads and also amplifies contaminating dna. here, we have tested the reproducibility of the multiple displacement amplification method using serial dilutions of extracted genom ... | 2013 | 24312412 |
| development of reference transcriptomes for the major field insect pests of cowpea: a toolbox for insect pest management approaches in west africa. | cowpea is a widely cultivated and major nutritional source of protein for many people that live in west africa. annual yields and longevity of grain storage is greatly reduced by feeding damage caused by a complex of insect pests that include the pod sucking bugs, anoplocnemis curvipes fabricius (hemiptera: coreidae) and clavigralla tomentosicollis stål (hemiptera: coreidae); as well as phloem-feeding cowpea aphids, aphis craccivora koch (hemiptera: aphididae) and flower thrips, megalurothrips s ... | 2013 | 24278221 |
| natural selection for operons depends on genome size. | in prokaryotes, genome size is associated with metabolic versatility, regulatory complexity, effective population size, and horizontal transfer rates. we therefore analyzed the covariation of genome size and operon conservation to assess the evolutionary models of operon formation and maintenance. in agreement with previous results, intraoperonic pairs of essential and of highly expressed genes are more conserved. interestingly, intraoperonic pairs of genes are also more conserved when they enco ... | 2013 | 24201372 |
| what symbionts teach us about modularity. | the main goal of synthetic biology (sb) is to apply engineering principles to biotechnology in order to make life easier to engineer. these engineering principles include modularity: decoupling of complex systems into smaller, orthogonal sub-systems that can be used in a range of different applications. the successful use of modules in engineering is expected to be reproduced in synthetic biological systems. but the difficulties experienced up to date with sb approaches question the short-term f ... | 2013 | 25023877 |