A Chemostat Model for Evolution by Persistence: Clade Selection and its Explanatory Autonomy

This is the author accepted manuscript. The final version is available from Cambridge University Press via the DOI in this recordMany contemporary biologists and philosophers of biology admit that selection occurs at any level of the biological hierarchy at which entities showing heritable variation in fitness are found, while insisting that fitness at any level entails differential reproduction, not differential persistence. Those who allow that persistence can be selected doubt that selection on non-reproducing entities can be reiterated, to produce “complex adaptations”. We present here a verbal model of sub-clones evolving in a simple idealized chemostat that calls into question these suppositions and is usefully explanatory when taken as an analogy to selection for persistence of clades.Gordon and Betty Moore FoundationNew Frontiers in Research Fun

Algorithms for Visualizing Phylogenetic Networks

We study the problem of visualizing phylogenetic networks, which are extensions of the Tree of Life in biology. We use a space filling visualization method, called DAGmaps, in order to obtain clear visualizations using limited space. In this paper, we restrict our attention to galled trees and galled networks and present linear time algorithms for visualizing them as DAGmaps.Comment: Appears in the Proceedings of the 24th International Symposium on Graph Drawing and Network Visualization (GD 2016

Considering Intra-individual Genetic Heterogeneity to Understand Biodiversity

In this chapter, I am concerned with the concept of Intra-individual Genetic Hetereogeneity (IGH) and its potential influence on biodiversity estimates. Definitions of biological individuality are often indirectly dependent on genetic sampling -and vice versa. Genetic sampling typically focuses on a particular locus or set of loci, found in the the mitochondrial, chloroplast or nuclear genome. If ecological function or evolutionary individuality can be defined on the level of multiple divergent genomes, as I shall argue is the case in IGH, our current genetic sampling strategies and analytic approaches may miss out on relevant biodiversity. Now that more and more examples of IGH are available, it is becoming possible to investigate the positive and negative effects of IGH on the functioning and evolution of multicellular individuals more systematically. I consider some examples and argue that studying diversity through the lens of IGH facilitates thinking not in terms of units, but in terms of interactions between biological entities. This, in turn, enables a fresh take on the ecological and evolutionary significance of biological diversity

Differences in lateral gene transfer in hypersaline versus thermal environments

<p>Abstract</p> <p>Background</p> <p>The role of lateral gene transfer (LGT) in the evolution of microorganisms is only beginning to be understood. While most LGT events occur between closely related individuals, inter-phylum and inter-domain LGT events are not uncommon. These distant transfer events offer potentially greater fitness advantages and it is for this reason that these "long distance" LGT events may have significantly impacted the evolution of microbes. One mechanism driving distant LGT events is microbial transformation. Theoretically, transformative events can occur between any two species provided that the DNA of one enters the habitat of the other. Two categories of microorganisms that are well-known for LGT are the thermophiles and halophiles.</p> <p>Results</p> <p>We identified potential inter-class LGT events into both a thermophilic class of Archaea (Thermoprotei) and a halophilic class of Archaea (Halobacteria). We then categorized these LGT genes as originating in thermophiles and halophiles respectively. While more than 68% of transfer events into Thermoprotei taxa originated in other thermophiles, less than 11% of transfer events into Halobacteria taxa originated in other halophiles.</p> <p>Conclusions</p> <p>Our results suggest that there is a fundamental difference between LGT in thermophiles and halophiles. We theorize that the difference lies in the different natures of the environments. While DNA degrades rapidly in thermal environments due to temperature-driven denaturization, hypersaline environments are adept at preserving DNA. Furthermore, most hypersaline environments, as topographical minima, are natural collectors of cellular debris. Thus halophiles would in theory be exposed to a greater diversity and quantity of extracellular DNA than thermophiles.</p

Lateral Gene Transfer (LGT) between Archaea and Escherichia coli is a contributor to the emergence of novel infectious disease

BACKGROUND: Lateral gene transfer is the major mechanism for acquisition of new virulence genes in pathogens. Recent whole genome analyses have suggested massive gene transfer between widely divergent organisms. PRESENTATION OF THE HYPOTHESIS: Archeal-like genes acting as virulence genes are present in several pathogens and genomes contain a number of archaeal-like genes of unknown function. Archaea, by virtue of their very different evolutionary history and different environment, provide a pool of potential virulence genes to bacterial pathogens. TESTING THE HYPOTHESIS: We can test this hypothesis by 1)identifying genes likely to have been transferred (directly or indirectly) to E. coli O157:H7 from archaea; 2)investigating the distribution of similar genes in pathogens and non-pathogens and 3)performing rigorous phylogenetic analyses on putative transfers. IMPLICATIONS OF THE HYPOTHESIS: Although this hypothesis focuses on archaea and E. coli, it will serve as a model having broad applicability to a number of pathogenic systems. Since no archaea are known vertebrate pathogens, archaeal-like transferred genes that are associated with virulence in bacteria represent a clear model for the emergence of virulence genes

Co-assortment in integron-associated gene cassette assemblages in environmental DNA samples

<p>Abstract</p> <p>Background</p> <p>It has been shown that integron-associated gene cassettes exist largely in tandem arrays of variable size, ranging from antibiotic resistance arrays of three to five cassettes up to arrays of more than 100 cassettes associated with the vibrios. Further, the ecology of the integron/gene cassette system has been investigated by showing that very many different cassettes are present in even small environmental samples. In this study, we seek to extend the ecological perspective on the integron/gene cassette system by investigating the way in which this diverse cassette metagenome is apportioned amongst prokaryote lineages in a natural environment.</p> <p>Results</p> <p>We used a combination of PCR-based techniques applied to environmental DNA samples and ecological analytical techniques to establish co-assortment within cassette populations, then establishing the relationship between this co-assortment and genomic structures. We then assessed the distribution of gene cassettes within the environment and found that the majority of gene cassettes existed in large co-assorting groups.</p> <p>Conclusions</p> <p>Our results suggested that the gene cassette diversity of a relatively pristine sampling environment was structured into co-assorting groups, predominantly containing large numbers of cassettes per group. These co-assorting groups consisted of different gene cassettes in stoichiometric relationship. Conservatively, we then attributed co-assorting cassettes to the gene cassette complements of single prokaryote lineages and by implication, to large integron-associated arrays. The prevalence of large arrays in the environment raises new questions about the assembly, maintenance and utility of large cassette arrays in prokaryote populations.</p

Gene cassette transcription in a large integron-associated array

<p>Abstract</p> <p>Background</p> <p>The integron/gene cassette system is a diverse and effective adaptive resource for prokaryotes. Short cassette arrays, with less than 10 cassettes adjacent to an integron, provide this resource through the expression of cassette-associated genes by an integron-borne promoter. However, the advantage provided by large arrays containing hundreds of cassettes is less obvious. In this work, using the 116-cassette array of <it>Vibrio </it>sp. DAT722 as a model, we investigated the theory that the majority of genes contained within large cassette arrays are widely expressed by intra-array promoters in addition to the integron-borne promoter.</p> <p>Results</p> <p>We demonstrated that the majority of the cassette-associated genes in the subject array were expressed. We further showed that cassette expression was conditional and that the conditionality varied across the array. We finally showed that this expression was mediated by a diversity of cassette-borne promoters within the array capable of responding to environmental stressors.</p> <p>Conclusions</p> <p>Widespread expression within large gene cassette arrays could provide an adaptive advantage to the host in proportion to the size of the array. Our findings explained the existence and maintenance of large cassette arrays within many prokaryotes. Further, we suggested that repeated rearrangement of cassettes containing genes and/or promoters within large arrays could result in the assembly of operon-like groups of co-expressed cassettes within an array. These findings add to our understanding of the adaptive repertoire of the integron/gene cassette system in prokaryotes and consequently, the evolutionary impact of this system.</p

Структура вірусних діарей у дітей на Сумщині

Гострі кишкові інфекції (ГКІ) стійко посідають одне з провідних місць серед усіх інфекційних захворювань, характеризуються широкою поширеністю, високою частотою розвитку тяжких форм і ускладнень. Прогрес у галузі лабораторних методів діагностики дозволив істотно розширити уявлення про етіологічні чинники хвороби: у країнах, що розвиваються, домінують діарейні інфекції бактерійної етіології, а в економічно розвинених країнах - вірусної. При цитуванні документа, використовуйте посилання http://essuir.sumdu.edu.ua/handle/123456789/3228

The allometry of the smallest: superlinear scaling of microbial metabolic rates in the Atlantic Ocean

Prokaryotic planktonic organisms are small in size but largely relevant in marine biogeochemical cycles. Due to their reduced size range (0.2 to 1 mu m in diameter), the effects of cell size on their metabolism have been hardly considered and are usually not examined in field studies. Here, we show the results of size-fractionated experiments of marine microbial respiration rate along a latitudinal transect in the Atlantic Ocean. The scaling exponents obtained from the power relationship between respiration rate and size were significantly higher than one. This superlinearity was ubiquitous across the latitudinal transect but its value was not universal revealing a strong albeit heterogeneous effect of cell size on microbial metabolism. Our results suggest that the latitudinal differences observed are the combined result of changes in cell size and composition between functional groups within prokaryotes. Communities where the largest size fraction was dominated by prokaryotic cyanobacteria, especially Prochlorococcus, have lower allometric exponents. We hypothesize that these larger, more complex prokaryotes fall close to the evolutionary transition between prokaryotes and protists, in a range where surface area starts to constrain metabolism and, hence, are expected to follow a scaling closer to linearity.Versión del editor8,951