133 research outputs found

    Closed form representations for the compactly supported radial basis functions of Buhmann, Wendland and Wu

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    The original compactly supported radial basis functions of Wendland and Wu have a polynomial form and are constructed using a two-step dimension walk strategy. Focussing on the Wendland functions, Schaback proposed a one-step dimension walk which is shown to recover the original Wendland functions at every second step but also introduces new examples, the so-called missing Wendland functions at the intermediate steps. In a recent paper by Huang et at., the analogue of Schaback's work is presented for the Wu functions and so deliver the so-called missing Wu functions. The original and missing Wendland functions belong to a much wider class proposed by Buhmann. The classical Buhmann functions, which are related to thin-plate spline radial basis functions, also belong to this much wider class. The theme uniting the classical Buhmann functions and the missing Wendland/Wu functions is that they are non-polynomial and closed form expressions are not known for all of them. In this paper we revisit these functions and show how closed form representations can be given using direct techniques. The results for the classical Buhmann and Wu functions are new and the resulting expressions for the missing Wendland functions improve on those given iby the first author and so their implementation should be more straightforward

    Interactions between diatoms and bacteria in laboratory biofilm model communities

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    Sunlit zones of benthic shallow water habitats belong to the most diverse and productive ecosystems on earth. Here, almost all submerged surfaces are covered by photoautotrophic biofilms that form the basis of benthic food-webs. These biofilms consist of microbial communities that are comprised of photoautotrophic microorganisms, such as diatoms, green algae or cyanobacteria, which via photosynthesis provide the energy for associated heterotrophic microorganisms, mostly bacteria. In this close association the bacteria significantly influence the diatoms in terms of growth, aggregation and secretion of extracellular polymeric substances.At the beginning of this project no suitable cultivation-, and growth assessment method for defined communities of adherent microalgae was available. Therefore, a sterile incubation chamber for the growth of bacteria-free biofilms, and defined diatom/bacteria co-cultures was developed. This illuminated continuous-flow system is equipped with light sensors and allows for the computer-based monitoring of phototrophic biofilms and for example the investigation of the influence of bacteria on growth and biofilm formation of marine and freshwater diatom strains.For laboratory studies the diatom strain Planothidium frequentissimum and associated bacteria were isolated from photoautotrophic biofilms sampled from Lake Constance, Germany. Like most diatoms this strain suffers irreversible cell shrinkage upon prolonged maintenance under laboratory conditions by serial transfers that leads to cell death, when no sexual cycle is induced. Particularly freshwater diatoms are regarded as recalcitrant towards cryopreservation, probably due to lower osmotolerance when compared with marine strains. Therefore, alternative strategies are required for the long-term maintenance of this strain as a laboratory model organism. Conventional cryopreservation approaches have previously proven unsuccessful with no or low regrowth for freshwater diatoms. However, we found that viability levels of P. frequentissimum were enhanced from 0.3 ± 0.4 % to 80 ± 3 % when thawed cells were allowed to recover for two days in the dark before being exposed to light. Omission of this recovery step resulted in obvious cell damage with photo-bleaching of pigments with subsequent deterioration of cellular architecture.To study diatom/bacteria interactions on the molecular level, we have established a model community, in which the marine alphaproteobacterium Roseovarius sp. strain 217 influences the biofilm formation of Phaeodactylum tricornutum, inducing a morphotypic transition fromplanktonic fusiform cells towards benthic, oval cells. To investigate the organismal interactions, we have analyzed the extracellular proteome of P. tricornutum in presence and absence of the bacterial strain. We found an extracellular phosphatase to be downregulated in the presence of bacteria together with newly identified mucin-like protein domains that appear to be typical for extracellular diatom proteins. However, unlike in mucins, the proline-, serine-, threonine-rich domains in these proteins were also found in combination with protease-, glucosidase and leucine-rich repeat (LRR-) domains. Bioinformatic functional predictions indicate that indeed several of these diatom-specific proteins may be involved in algal defense, intercellular signaling, and aggregation.publishe

    An integrated model system to gain mechanistic insights into biofilm formation and antimicrobial resistance development in <i>Pseudomonas aeruginosa</i> MPAO1

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    Pseudomonas aeruginosa MPAO1 is the parental strain of the widely utilized transposon mutant collection for this important clinical pathogen. Here, we validate a model system to identify genes involved in biofilm growth and antibiotic resistance.Our model employs a genomics-driven workflow to assemble the complete MPAO1 genome, identify unique and conserved genes by comparative genomics with the PAO1 reference strain and missed genes by proteogenomics. Among over 200 unique MPAO1 genes, we identified six general essential genes that were overlooked when mapping public Tn-seq datasets against PAO1, including an antitoxin. Genomic data were integrated with phenotypic data from an experimental workflow using a user-friendly, soft lithography-based microfluidic flow chamber for biofilm growth. Experiments conducted across three laboratories delivered reproducible data on P. aeruginosa biofilms and validated both known and novel genes involved in biofilm growth and antibiotic resistance identified in screens of the mutant collection. Differential protein expression data from planktonic cells versus biofilm confirmed upregulation of candidates known to affect biofilm formation, of structural and secreted proteins of type six secretion systems, and provided proteogenomic evidence for some missed MPAO1 genes. This integrated, broadly applicable model promises to improve the mechanistic understanding of biofilm formation, antimicrobial tolerance and resistance evolution

    Photoautotrophic-heterotrophic biofilm communities : a laboratory incubator designed for growing axenic diatoms and bacteria in defined mixed-species biofilms

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    Biofilm communities in the euphotic zone of aquatic habitats comprise photoautotrophic microorganisms, such as diatoms, green algae and cyanobacteria, which produce the organic carbon that fuels the life of a heterotrophic contingent of microorganisms, mostly bacteria. Such photoautotrophic–heterotrophic mixed-species biofilms have received little attention in biofilm research due to a lack of suitable pure-culture laboratory model systems. However, they offer important insight into microbial population dynamics and community interactions during a biofilm-developmental process that shapes highly structured, extremely well-adapted microbial landscapes. Here, we report on the development of a sterile incubation chamber for growing and monitoring axenic phototrophic biofilms, i.e. a sterilizable, illuminated, continuous-flow system for a routine work with pure cultures. The system has been designed to simulate the growth conditions in the shallow, littoral zone of aquatic habitats (horizontal surface, submerged in water, illuminated, aerated). Additional features of the concept include automated photometrical monitoring of biofilm density (as biofilm turbidity), analysis via confocal microscopy, direct harvesting of cells, and options to control illumination, flow velocity, and composition of culture fluid. The application of the system was demonstrated in growth experiments using axenic diatom biofilms, or axenic diatom biofilms co-cultivated with different bacterial strains isolated from epilithic biofilms of an oligotrophic freshwater lake.publishe

    The role of Plasmodium falciparum var genes in malaria in pregnancy

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    Sequestration of Plasmodium falciparum-infected erythrocytes in the placenta is responsible for many of the harmful effects of malaria during pregnancy. Sequestration occurs as a result of parasite adhesion molecules expressed on the surface of infected erythrocytes binding to host receptors in the placenta such as chondroitin sulphate A (CSA). Identification of the parasite ligand(s) responsible for placental adhesion could lead to the development of a vaccine to induce antibodies to prevent placental sequestration. Such a vaccine would reduce the maternal anaemia and infant deaths that are associated with malaria in pregnancy. Current research indicates that the parasite ligands mediating placental adhesion may be members of the P. falciparum variant surface antigen family PfEMP1, encoded by var genes. Two relatively well-conserved subfamilies of var genes have been implicated in placental adhesion, however, their role remains controversial. This review examines the evidence for and against the involvement of var genes in placental adhesion, and considers whether the most appropriate vaccine candidates have yet been identified
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