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Search Results: 1 - 10 of 133151 matches for " Helen V. Lubarsky "
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Impairment of the Bacterial Biofilm Stability by Triclosan
Helen V. Lubarsky, Sabine U. Gerbersdorf, Cédric Hubas, Sebastian Behrens, Francesco Ricciardi, David M. Paterson
PLOS ONE , 2012, DOI: 10.1371/journal.pone.0031183
Abstract: The accumulation of the widely-used antibacterial and antifungal compound triclosan (TCS) in freshwaters raises concerns about the impact of this harmful chemical on the biofilms that are the dominant life style of microorganisms in aquatic systems. However, investigations to-date rarely go beyond effects at the cellular, physiological or morphological level. The present paper focuses on bacterial biofilms addressing the possible chemical impairment of their functionality, while also examining their substratum stabilization potential as one example of an important ecosystem service. The development of a bacterial assemblage of natural composition – isolated from sediments of the Eden Estuary (Scotland, UK) – on non-cohesive glass beads (<63 μm) and exposed to a range of triclosan concentrations (control, 2 – 100 μg L?1) was monitored over time by Magnetic Particle Induction (MagPI). In parallel, bacterial cell numbers, division rate, community composition (DGGE) and EPS (extracellular polymeric substances: carbohydrates and proteins) secretion were determined. While the triclosan exposure did not prevent bacterial settlement, biofilm development was increasingly inhibited by increasing TCS levels. The surface binding capacity (MagPI) of the assemblages was positively correlated to the microbial secreted EPS matrix. The EPS concentrations and composition (quantity and quality) were closely linked to bacterial growth, which was affected by enhanced TCS exposure. Furthermore, TCS induced significant changes in bacterial community composition as well as a significant decrease in bacterial diversity. The impairment of the stabilization potential of bacterial biofilm under even low, environmentally relevant TCS levels is of concern since the resistance of sediments to erosive forces has large implications for the dynamics of sediments and associated pollutant dispersal. In addition, the surface adhesive capacity of the biofilm acts as a sensitive measure of ecosystem effects.
The Stabilisation Potential of Individual and Mixed Assemblages of Natural Bacteria and Microalgae
Helen V. Lubarsky,Cédric Hubas,Melanie Chocholek,Fredrik Larson,Werner Manz,David M. Paterson,Sabine U. Gerbersdorf
PLOS ONE , 2012, DOI: 10.1371/journal.pone.0013794
Abstract: It is recognized that microorganisms inhabiting natural sediments significantly mediate the erosive response of the bed (“ecosystem engineers”) through the secretion of naturally adhesive organic material (EPS: extracellular polymeric substances). However, little is known about the individual engineering capability of the main biofilm components (heterotrophic bacteria and autotrophic microalgae) in terms of their individual contribution to the EPS pool and their relative functional contribution to substratum stabilisation. This paper investigates the engineering effects on a non-cohesive test bed as the surface was colonised by natural benthic assemblages (prokaryotic, eukaryotic and mixed cultures) of bacteria and microalgae. MagPI (Magnetic Particle Induction) and CSM (Cohesive Strength Meter) respectively determined the adhesive capacity and the cohesive strength of the culture surface. Stabilisation was significantly higher for the bacterial assemblages (up to a factor of 2) than for axenic microalgal assemblages. The EPS concentration and the EPS composition (carbohydrates and proteins) were both important in determining stabilisation. The peak of engineering effect was significantly greater in the mixed assemblage as compared to the bacterial (x 1.2) and axenic diatom (x 1.7) cultures. The possibility of synergistic effects between the bacterial and algal cultures in terms of stability was examined and rejected although the concentration of EPS did show a synergistic elevation in mixed culture. The rapid development and overall stabilisation potential of the various assemblages was impressive (x 7.5 and ×9.5, for MagPI and CSM, respectively, as compared to controls). We confirmed the important role of heterotrophic bacteria in “biostabilisation” and highlighted the interactions between autotrophic and heterotrophic biofilm consortia. This information contributes to the conceptual understanding of the microbial sediment engineering that represents an important ecosystem function and service in aquatic habitats.
The sea urchin joins the genome era
Barry Lubarsky
Genome Biology , 2000, DOI: 10.1186/gb-2000-1-6-reports0081
Abstract: The cornerstone of the sea urchin project was the construction of a contiguous set of bacterial artificial chromosomes (BACs) spanning the entire genome. To create a genomic scaffold, BAC clones were aligned using overlapping end sequences and additional sequence-tagged sites, then checked by comparing restriction enzyme digests. Analysis of the end sequences allowed the authors to estimate that the sea urchin genome contains about 27,000 genes, consistent with the urchin's genome being about one quarter the size of a human's. In addition to the BAC map, cDNA libraries were generated from several developmental stages and from particular organs. Each library was arrayed onto filters that are now available for hybridization screening. The genome project also includes a cDNA database that will expand as data from analyzed cDNAs become available.Further information about the Sea urchin genome project is available.The good news is that a complete BAC map of the genome makes the sea urchin ready for whole-genome sequencing. Unfortunately, it is not clear if such an effort will be undertaken any time soon. As the sea urchin genome is large - about a quarter the size of the three billion bases of the human genome - determining its entire sequence would require a significant effort. So far, only widely used model organisms such as the nematode Caenorhabditis elegans and the fruit fly Drosophila melanogaster have received so much attention. The latest focus is on the human genome, with the mouse likely to be next. Where the sea urchin fits into these sequencing schemes is uncertain. Despite a few particular advantages as a model research organism, the urchin is now rarely used as such, and its popularity is unlikely to increase in the near future.One major feature of interest, however, is the sea urchin's phylogeny, as echinoderms are more closely related to chordates, and thus to the vertebrates, than are other invertebrate groups. Although only very distantly related, we an
Probing the worm germline
Barry Lubarsky
Genome Biology , 2000, DOI: 10.1186/gb-2000-1-5-reports0073
Abstract: The authors constructed DNA microarrays containing almost 12,000 genes (63% of all those predicted to be present in the C. elegans genome). By hybridizing labeled RNA from a mutant in which all germ cells are absent to these arrays, and comparing the profiles obtained to similar hybridizations of wild-type RNA, they could determine which genes had significantly enriched transcript levels in the germline. Likewise, they compared RNA expression levels between two other mutants, one that produces only sperm and one that produces only oocytes (the worm is usually a hermaphrodite). In all, almost 12% (1,416) of the genes on the microarray were enriched in the germline. Among these were 650 genes enriched in sperm, 258 enriched in oocytes, and 508 genes expressed at similar levels in both mutant lines, suggesting that they are general factors required in the germ line. These experiments were repeated over a time span encompassing the last three larval stages and the adult animal. Sperm-enriched transcripts are present mostly in the final larval stage, whereas most oocyte and general germline genes are activated in the adult.The complete dataset from these microarray experiments can be found at the Kim lab website on the appropriate page - A global profile of germline gene expression in C. elegans.The sperm-enriched gene set included a large number of cytoplasmic protein kinases and phosphatases, reflecting the fact that most of sperm development involves post-translational events Enzymes required for fatty acid metabolism, to provide energy for mobility were also well-represented in the sperm-enriched gene set. The oocyte set included a large number of genes involved in DNA replication, early cell division, and embryonic patterning. Genes involved generally in the germline included those required for stem-cell maintenance, RNA metabolism, and RNA processing.Transcripts of almost all genes previously known to be involved in the worm germline were enriched in the germline a
Geometric spaces with no points
Robert Lubarsky
Journal of Logic and Analysis , 2010, DOI: 10.4115/jla.v2i0.64
Addendum and Erratum to “Geometric spaces with no points”
Robert Lubarsky
Journal of Logic and Analysis , 2010, DOI: 10.4115/jla.v2i0.80
CZF and Second Order Arithmetic
Robert Lubarsky
Mathematics , 2015,
Abstract: CZF + Separation is shown to be equiconsistent with second-order arithmetic, using realizability.
Independence Results around Constructive ZF
Robert Lubarsky
Mathematics , 2015,
Abstract: Using Kripke models, it is shown that CZF does not prove Power Set, and that CZF with Subset Collection substituted by Exponentiation does not prove Subset Collection.
IKP and Friends
Robert Lubarsky
Mathematics , 2015,
Abstract: The basics of Intuitionistic Kripke-Platek set theory are developed, and some independence results among related classically equivalent theories are shown using Kripke models.
Geometric Spaces with No Points
Robert Lubarsky
Mathematics , 2015, DOI: 10.4115/jla2010.2.6
Abstract: Some models of set theory are given which contain sets that have some of the important characteristics of being geometric, or spatial, yet do not have any points, in various ways. What's geometrical is that there are functions to these spaces defined on the ambient spaces which act much like distance functions, and they carry normable Riesz spaces which act like the Riesz spaces of real-valued functions. The first example has a family of sets, each one of which cannot be empty, but not in a uniform manner, so that it is false that all of them are inhabited. In the second, we define one fixed set which does not have any points, while retaining all of these geometrical properties.
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