Borys Wróbel

16S rDNA Pyrosequencing Analysis of Bacterial Community in Heavy Metals Polluted Soils

Soil contamination with heavy metals is a widespread problem, especially prominent on grounds lying in the vicinity of mines, smelters, and other industrial facilities. Many such areas are located in Southern Poland; they are polluted mainly with Pb, Zn, Cd, or Cu, and locally also with Cr. As for now, little is known about most bacterial species thriving in such soils and even less about a core bacterial community—a set of taxa common to polluted soils. Therefore, we wanted to answer the question if such a set could be found in samples differing physicochemically and phytosociologically. To answer the question, we analyzed bacterial communities in three soil samples contaminated with Pb and Zn and two contaminated with Cr and lower levels of Pb and Zn. The communities were assessed with 16S rRNA gene fragments pyrosequencing. It was found that the samples differed significantly and Zn decreased both diversity and species richness at species and family levels, while plant species richness did not correlate with bacterial diversity. In spite of the differences between the samples, they shared many operational taxonomic units (OTUs) and it was possible to delineate the core microbiome of our sample set. The core set of OTUs comprised members of such taxa as Sphingomonas, Candidatus Solibacter, or Flexibacter showing that particular genera might be shared among sites ~40xa0km distant.

Co-evolution of morphology and control of soft-bodied multicellular animats

We present a platform that allows for co-evolution of development and motion control of soft-bodied, multicellular animats in a 2-dimensional fluid-like environment. Artificial gene regulatory networks (GRNs) with real-valued expression levels control cell division and differentiation in multicellular embryos. Embryos develop in a simulated physics environment and are converted into animat structures by connecting neighboring cells with elastic springs. The springs connecting outer cells form the external envelope which is subject to fluid drag. Both the developmental program and motion control are encoded indirectly in a single linear genome, which consists of regulatory regions and regions that code for regulatory products (some of which act as morphogens). We applied a genetic algorithm to co-evolve morphology and control using a fitness measure whose value depends on distance traveled during the evaluation phase. We obtained various emergent morphologies and types of locomotion, some of them showing the use of appendages.

Influence of the Escherichia coli oxyR gene function on λ prophage maintenance

In Escherichia coli hosts, hydrogen peroxide is one of the factors that may cause induction of λ prophage. Here, we demonstrate that H2O2-mediated λ prophage induction is significantly enhanced in the oxyR mutant host. The mRNA levels for cI gene expression were increased in a λ lysogen in the presence of H2O2. On the other hand, stimulation of the pM promoter by cI857 overproduced from a multicopy plasmid was decreased in the ΔoxyR mutant in the presence of H2O2 but not under normal growth conditions. The purified OxyR protein did bind specifically to the pM promoter region. This binding impaired efficiency of interaction of the cI protein with the OR3 site, while stimulating such a binding to OR2 and OR1 sites, in the regulatory region of the pM promoter. We propose that changes in cI gene expression, perhaps in combination with moderately induced SOS response, may be responsible for enhanced λ prophage induction by hydrogen peroxide in the oxyR mutant. Therefore, OxyR seems to be a factor stimulating λ prophage maintenance under conditions of oxidative stress. This proposal is discussed in the light of efficiency of induction of lambdoid prophages bearing genes coding for Shiga toxins.

A Model of Evolution of Development Based on Germline Penetration of New “No-Junk” DNA

There is a mounting body of evidence that somatic transposition may be involved in normal development of multicellular organisms and in pathology, especially cancer. Epigenetic Tracking (ET) is an abstract model of multicellular development, able to generate complex 3-dimensional structures. Its aim is not to model the development of a particular organism nor to merely summarise mainstream knowledge on genetic regulation of development. Rather, the goal of ET is to provide a theoretical framework to test new postulated genetic mechanisms, not fully established yet in mainstream biology. The first proposal is that development is orchestrated through a subset of cells which we call driver cells. In these cells, the cellular state determines a specific pattern of gene activation which leads to the occurrence of developmental events. The second proposal is that evolution of development is affected by somatic transposition events. We postulate that when the genome of a driver cell does not specify what developmental event should be undertaken when the cell is in a particular cellular state, somatic transposition events can reshape the genome, build new regulatory regions, and lead to a new pattern of gene activation in the cell. Our third hypothesis, not supported yet by direct evidence, but consistent with some experimental observations, is that these new “no-junk” sequences—regulatory regions created by transposable elements at new positions in the genome—can exit the cell and enter the germline, to be incorporated in the genome of the progeny. We call this mechanism germline penetration. This process allows heritable incorporation of novel developmental events in the developmental trajectory. In this paper we will present the model and link these three postulated mechanisms to biological observations.

Diversity of tailed phages in Baltic Sea sediment: large number of siphoviruses with extremely long tails

We present the first attempt at quantitative analysis of morphological diversity of tailed viruses obtained from marine sediments without ultracentrifugation or enrichment on specific host strains. Sandy mud samples were collected in the Gulf of Gdańsk in the spring, autumn and winter. VLPs were analyzed by transmission electron microscopy. The distribution of three groups of tailed phages was similar in all seasons (Siphoviridae: 52% on average; Myoviridae: 42%; Podoviridae: 6%). 19% of siphoviruses had prolate heads. Interestingly, 11% of siphoviral particles had tails longer than 300xa0nm, and 6% longer than 600xa0nm.

Embryogenesis, morphogens and cancer stem cells: Putting the puzzle together

This paper describes a model which puts together three key elements of cancer theory: the analogies between embryogenesis and carcinogenesis, the role played in both processes by morphogens and related pathways, and the recently emerged paradigm of cancer stem cells. The model is called Epigenetic Tracking. Originally conceived as a model of embryonic development, it was later extended to interpret other aspects of biology, such as the presence of junk DNA, the phenomenon of ageing and the process of cancer formation. In this work we deepen our vision of carcinogenesis, and propose a novel hypothesis on the role of morphogen-processing pathways. According to the hypothesis, the interplay of these pathways leads in stem cells to the production of new transcription factors, which act as drivers of cellular differentiation. The disruption of these pathways, caused by mutations in specific genes, would represent the first and most distinctive event in the carcinogenic process. Our hypothesis allows us to make testable predictions on patterns of gene mutations involved in carcinogenesis. Our hypothesis also suggests that cancer stem cells can stay dormant until they are activated in a process that resembles activation of stem cells during tissue repair or at a specific time during development.

Morphogen-based self-generation of evolving artificial multicellular structures with millions of cells

Epigenetic Tracking is a model of Artificial Embryology whose central feature is separation of cells into normal cells and driver cells. Drivers are much fewer in number than normal cells and orchestrate developmental events. This separation allows for generation of structures with much more complexity and much higher number of cells (in the order of millions) than in other Artificial Embryology models. We introduce in this paper a new mechanism for the generation of driver cells, based on diffusing morphogens. We show that this change preserves the evolvability of very large complex structures, provided that the density of the drivers is sufficiently high. We than draw the outline of the future work that will build on this mechanism towards evolution of structures robust to damage and developmental noise in our system.

The application of microarray technology to the identification of Tc1-like element sequences in fish genomes

Abstract The phylogenetic relationships between Tc1 transposable elements have previously been reported for the genomes of some fish species. However, research in this field has been hindered by the low number of fish genome sequences available in databases. The application of a DNA microarray as a universal tool for Tc1 transposon sequence analysis in fish genomes is described here. A prototype oligonucleotide microarray was constructed and used to compare samples of genomic DNA isolated from selected fish species. These results, combined with earlier reported molecular analysis of Tc1 showed the usefulness of DNA microarray in the screening of transposon sequences.

Evolving spiking neural networks for temporal pattern recognition in the presence of noise

Nervous systems of biological organisms use temporal patterns of spikes to encode sensory input, but the mechanisms that underlie the recognition of such patterns are unclear. In the present work, we explore how networks of spiking neurons can be evolved to recognize temporal input patterns without being able to adjust signal conduction delays. We evolve the networks with GReaNs, an artificial life platform that encodes the topology of the network (and the weights of connections) in a fashion inspired by the encoding of gene regulatory networks in biological genomes. The number of computational nodes or connections is not limited in GReaNs, but here we limit the size of the networks to analyze the functioning of the networks and the effect of network size on the evolvability of robustness to noise. Our results show that even very small networks of spiking neurons can perform temporal pattern recognition in the presence of input noise.

Evolution and development of complex computational systems using the paradigm of metabolic computing in Epigenetic Tracking.

Epigenetic Tracking (ET) is an Artificial Embryology system which allows for the evolution and development of large complex structures built from artificial cells. In terms of the number of cells, the complexity of the bodies generated with ET is comparable with the complexity of biological organisms. We have previously used ET to simulate the growth of multicellular bodies with arbitrary 3-dimensional shapes which perform computation using the paradigm of metabolic computing. In this paper we investigate the memory capacity of such computational structures and analyse the trade-off between shape and computation. We now plan to build on these foundations to create a biologically-inspired model in which the encoding of the phenotype is efficient (in terms of the compactness of the genome) and evolvable in tasks involving non-trivial computation, robust to damage and capable of self-maintenance and self-repair.