Sea urchin bioerosion on coral reefs: place in the carbonate budget and relevant variables

Two aspects of erosion by sea urchins (Echinoidea) in coral reef habitats are: the direct passage of reef framework material through the gut and the indirect effects through the weakening of the reef structure. Urchin bioerosion can equal or exceed reef carbonate production. The impact of urchins on reefs depends on three variables: species type, test size and population density. Large differences in bioerosion by urchins of the same test size occur between different species. Size differences between species in a sea urchin community, as well as size differences within a species along a reef, can be significant. Bioerosion per urchin increases enormously with size. Changes in population density, through time and space, result in significant changes in bioerosion. It is demonstrated how the interaction of these variables determines in-situ sea urchin bioerosion.     

Extracting the dynamics of behavior in sensory decision-making experiments

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Pichia acaciae Killer System: Genetic Analysis of Toxin Immunity

The gene responsible for self-protection in the Pichia acaciae killer plasmid system was identified by heterologous expression in Saccharomyces cerevisiae. Resistance profiling and conditional toxin/immunity coexpression analysis revealed dose-independent protection by pPac1-2 ORF4 and intracellular interference with toxin function, suggesting toxin reinternalization in immune killer cells.     

Calcium accumulation in plasmodia of Physarum polycephalum

The total concentration of calcium in the endoplasm of plasmodia of was measured using a calcein fluorescence-quenching technique. The calcium concentration of the endoplasm increases with the time of cultivation on different substrates under culture conditions frequently used for routine experiments. Calcium accumulation within endo- and ectoplasm as well as in microplasmodia is most pronounced when plasmodia are starved and illuminated. Starvation and illumination lead to calcium concentrations frequently exceeding 200 mM in the case of macroplasmodia and 20 mM in the case of microplasmodia.     

Comparative Genomic Analysis of Pathogenic Factors of Pectobacterium Species Isolated in South Korea Using Whole-Genome Sequencing

In this study, we conducted whole-genome sequencing with six species of Pectobacterium composed of seven strains, JR1.1, {"type":"entrez-nucleotide","attrs":{"text":"BP201601.1","term_id":"52051741","term_text":"BP201601.1"}}BP201601.1, JK2.1, HNP201719, MYP201603, PZ1, and HC, for the analysis of pathogenic factors associated with the genome of Pectobacterium. The genome sizes ranged from 4,724,337 bp to 5,208,618 bp, with the GC content ranging from 50.4% to 52.3%. The average nucleotide identity was 98% among the two Pectobacterium species and ranged from 88% to 96% among the remaining six species. A similar distribution was observed in the carbohydrate-active enzymes (CAZymes) class and extracellular plant cell wall degrading enzymes (PCWDEs). HC showed the highest number of enzymes in CAZymes and the lowest number in the extracellular PCWDEs. Six strains showed four subsets, and HC demonstrated three subsets, except hasDEF, in type I secretion system, while the type II secretion system of the seven strains was conserved. Components of human pathogens, such as Salmonella pathogenicity island 1 type type III secretion system (T3SS) and effectors, were identified in PZ1; T3SSa was not identified in HC. Two putative effectors, including hrpK, were identified in seven strains along with dspEF. We also identified 13 structural genes, six regulator genes, and five accessory genes in the type VI secretion system (T6SS) gene cluster of six Pectobacterium species, along with the loss of T6SS in PZ1. HC had two subsets, and JK2.1 had three subsets of T6SS. With the GxSxG motif, the phospholipase A gene did locate among tssID and duf4123 genes in the T6SSa cluster of all strains. Important domains were identified in the vgrG/paar islands, including duf4123, duf2235, vrr-nuc, and duf3396.     

Cell surface constituents of sarcoma 180 ascites tumor cells

The cell surface protein components of Sarcoma 180 ascites tumor cells have been investigated by a combination of plasma membrane isolation techniques and lactoperoxidase iodination. For plasma membrane isolation cells were homogenized in the presence or absence of Zn²⁺ and fractionated by sucrose density gradient centrifugation or a two-phase partition to give large membrane fragments or membrane envelopes. Membrane purification was monitored by phase contrast microscopy and chemical and enzyme marker assays. The membrane preparations were analyzed by acrylamide gel electrophoresis in sodium dodecylsulfate. Each preparation showed a common protein pattern of about 15 bands ranging in molecular weights from 33 000 to >300000. Two carbohydrate-containing bands were also present in all preparations. Membranes prepared with Zn²⁺ were much less fragmented and showed much greater amounts of three high molecular weight components than those prepared in the absence of Zn²⁺. This might suggest a role for these components in membrane stabilization.The tumor cells were also subjected to iodination with lactoperoxidase, followed by membrane isolation and acrylamide gel electrophoresis in sodium dodecylsulfate in order to identify polypeptides accessible to the cell surface. The major radioactive band coincided with the major carbohydrate-containing band, presumably a surface glycoprotein. A second carbohydrate-containing band showed variable labeling behavior between different cell preparations. This material had a high molecular weight, as indicated by both acrylamide gel electrophoresis and gel permeation chromatography in dodecylsulfate. Several other components are labeled to a lesser extent in the intact cell.     

Inhibition of oleic acid incorporation into a non-lipid fraction by chloroacetamide herbicides

Oleic acid is incorporated into an insoluble fraction left over after lipid extraction in Scenedesmus acutus. This incorporation is extremely sensitive to the chloroacetamide herbicide, metazachlor (I₅₀= ca 20 nM). Therefore, factors influencing the incorporation of radioactivity from oleic acid into this non-lipid fraction were investigated. S. acutus cells were cultivated under various conditions with or without inhibitors and [¹⁴C]-oleic acid was supplied to the algae; the lipids were extracted and the radioactivity incorporated in the remaining fraction monitored. The inhibition seemed specific for chloroacetamides and related classes since it was also observed with alachlor, dimethenamid and mefenacet (an oxyacetamide). In contrast, it could not be found with diuron, oryzalin, nor could it be observed with a non-herbicidal metazachlor derivative or iodoacetamide. Incorporation of oleic acid into that fraction required meta-bolically active cells and was stimulated by light. Other fatty acids (16:0, 18:2, and 18:3) were also incorporated into the non-lipid fraction but their incorporation was not inhibited by metazachlor. Among other components, the fraction contains proteins. However, a possible specific effect of chloroacetamides on the binding of oleic acid to proteins or on the in vitro activity of lipid transfer proteins could not be detected. Not much is known yet about mechanism and chemistry of oleic acid incorporation but this finding opens a new path for investigations towards the primary target of these herbicides.     

Genetic manipulation of Kluyveromyces lactis linear DNA plasmids: gene targeting and plasmid shuffles

Genetic manipulation of yeast linear DNA plasmids, particularly of k1 and k2 from the non-conventional dairy yeast Kluyveromyces lactis, has been advanced by the recent establishment of DNA transformation-mediated one-step gene disruption and allele replacement techniques. These methods provide the basis for a strategy for the functional analysis of plasmid genes and DNA elements. By use of double selection regimens, these single-gene procedures have been extended to effect disruption of individual genes on plasmid k2 and transplacement of a functional copy onto plasmid k1, resulting in the production of yeast strains with an altered plasmid composition. This cytoplasmic gene shuffle system facilitates the introduction of specifically modified alleles into k1 or k2 in order to study the function, expression (from UCS promoters) and regulation of cytoplasmic linear plasmid genes. Additionally, identification, characterization and localization of plasmid gene products of interest are made possible by shuffling GFP-, epitope- or affinity purification-tagged alleles between k2 and k1. The gene shuffle approach can also be used for vector development and heterologous protein expression in order to exploit the biotechnical potential of the K. lactis k1/k2 system in yeast cell factory research.