Characterization of some fish and shrimp spoiling bacteria

The classification of some important groups of bacteria involved in fish and shrimp spoilage was studied. Trimethylamine is produced byPseudomonas putrefaciens, a “non-defined” group resemblingPs. putrefaciens, Photobacterium spp. and someMoraxella-like bacteria. Hypoxanthine is produced by the same groups of bacteria except the last named and also by the “typical shrimp spoilers” (presumptiveAlteromonas). Strong off-odours are produced on fresh fish byPs. putrefaciens, dextroseoxidativePseudomonas spp. (Groups I and 11 according to Shewan, Hobbs and Hodgkiss, 1960), the above mentioned “non-defined” group and by only some of the “typical shrimp spoilers”, whereasMoraxella-like bacteria andPhotobacterium spp. failed to produce strong odours. Strong off-odours are produced on boiled shrimp by the “typical shrimp spoilers” (presumptiveAltermonas),Ps. putrefaciens, the dextrose-oxidativePseudomonas spp. and the “non-defined” group;Moraxella-like bacteria produced less offensive odours or none, nor didPhotobacterium.     

Skeletal growth, ultrastructure and composition of the azooxanthellate scleractinian coral Balanophyllia regia

The biomineralization process and skeletal growth dynamics of azooxanthellate corals are poorly known. Here, the growth rate of the shallow-water dendrophyllid scleractinian coral Balanophyllia regia was evaluated with calcein-labeling experiments that showed higher lateral than vertical extension. The structure, mineralogy and trace element composition of the skeleton were characterized at high spatial resolution. The epitheca and basal floor had the same ultrastructural organization as septa, indicating a common biological control over their formation. In all of these aragonitic skeletal structures, two main ultrastructural components were present: “centers of calcification” (COC) also called rapid accretion deposits (RAD) and “fibers” (thickening deposits, TD). Heterogeneity in the trace element composition, i.e., the Sr/Ca and Mg/Ca ratios, was correlated with the ultrastructural organization: magnesium was enriched by a factor three in the rapid accretion deposits compared with the thickening deposits. At the interface with the skeleton, the skeletogenic tissue (calicoblastic epithelium) was characterized by heterogeneity of cell types, with chromophile cells distributed in clusters regularly spaced between calicoblasts. Cytoplasmic extensions at the apical surface of the calicoblastic epithelium created a three-dimensional organization that could be related to the skeletal surface microarchitecture. Combined measurements of growth rate and skeletal ultrastructural increments suggest that azooxanthellate shallow-water corals produce well-defined daily growth steps.     

Life and death near a windy oasis

We propose a simple experiment to study delocalization and extinction in inhomogeneous biological systems. The nonlinear steady state for, say, a bacteria colony living on and near a patch of nutrient or favorable illumination (“oasis”) in the presence of a drift term (“wind”) is computed. The bacteria, described by a simple generalization of the Fisher equation, diffuse, divide A→A + A, die A→ 0, and annihilate A + A→ 0. At high wind velocities all bacteria are blown into an unfavorable region (“desert”), and the colony dies out. At low velocity a steady state concentration survives near the oasis. In between these two regimes there is a critical velocity at which bacteria first survive. If the “desert” supports a small nonzero population, this extinction transition is replaced by a delocalization transition with increasing velocity. Predictions for the behavior as a function of wind velocity are made for one and two dimensions. Received: 3 August 1998 / Revised version: 17 July 1999 / Published online: 4 July 2000     

“Bioshrouding”—a novel approach for securing reactive mineral tailings

A novel technique (“bioshrouding”) for safeguarding highly reactive sulfidic mineral tailings deposits is proposed. In this, freshly milled wastes are colonised with ferric iron-reducing heterotrophic acidophilic bacteria that form biofilms on reactive mineral surfaces, thereby preventing or minimising colonisation by iron sulfide-oxidising chemolithotrophs such as Acidithiobacillus ferrooxidans and Leptospirillum spp. Data from initial experiments showed that dissolution of pyrite could be reduced by between 57 and 75% by “bioshrouding” the mineral with three different species of heterotrophic acidophiles (Acidiphilium, Acidocella and Acidobacterium spp.), under conditions that were conducive to microbial oxidative dissolution of the iron sulfide.     

Prediction of biological functions of Shewanella-like protein phosphatases (Shelphs) across different domains of life

PPP protein phosphatases are an important enzyme family involved in a variety of aspects of cellular signalling and metabolism. PPPs are ubiquitous in eukaryotes, and are also present in many bacteria. Canonical eukaryotic PPP phosphotases are represented by five major subfamilies (PP1, PP2A, calcineurin, PP5 and PPEF/PP7). We previously reported that three “bacterial-like” PPP groups span the prokaryote–eukaryote boundary, including “Shewanella-like” phosphatases (Shelphs), which are in the focus of this study. Here we predict possible biological functions and functional partners of Shelphs by examining composition of bacterial operons and expression data for eukaryotes available in public databases. In Arabidopsis thaliana, the predicted possible roles include light-dependent regulation of chloroplast functions, signalling between the nucleus and the chloroplast, and defence responses. In Plasmodium falciparum, Shelphs are predicted to be associated with host cell invasion. One isoform has been located in the apical complex, essential for the interaction with the host cell. This makes P. falciparum Shelphs obvious potential candidates for therapeutic targets. Shelphs are also present in bacteria that constitute a considerable proportion of symbiotic microflora in humans. The predicted involvement of bacterial Shelphs in sensing and import of nutrients and extrusion of toxins may be relevant to the links between physiology of humans and our symbionts. Thus, despite the absence of Shelphs in animals, including humans, they may have a direct relationship to human health. Some predicted biological processes and potential functional partners of Shelphs are common between different bacterial and/or eukaryotic lineages, suggesting evolutionary conservation of some Shelph regulatory modules.     

Yeast assessment during alcoholic fermentation inoculated with a natural “pied de cuve” or a commercial yeast strain

The present study has been carried out in an organic winery established in 2003 in the Denomination of Origin “Sierras de Málaga” (Southern Spain) region during the 2007 vintage. The aim of this work was to ascertain the yeast microflora present in the winery and during the vinifications and to obtain a collection of autochthonous S. cerevisiae strains from this area. Yeast populations from three vats containing fermenting musts from different grape varieties were analysed. Two of them were inoculated with a natural “pied de cuve” while the third one was sown with a rehydrated commercial yeast strain. A total of 382 yeasts were isolated and identified, initially by restriction analysis of ribosomal DNA and further by sequencing of this region. Non-Saccharomyces yeasts were found in all three musts but they practically disappeared as the fermentations progressed. Analysis of mitochondrial DNA RFLP revealed 13 different restriction patterns of Saccharomyces cerevisiae strains, five of them similar to those of commercial strains used in the winery. Commercial strains were found even in vats inoculated with a “pied de cuve” generated by spontaneous fermentation of a must sample. The analysis of samples recovered from different winery surfaces and equipments demonstrated that non-Saccharomyces and both commercial and autochthonous Saccharomyces strains were part of the resident microflora in the winery. Biodiversity of autochthonous S. cerevisiae in fermentation vats was low but two of them were able to compete with the commercial ones and they were isolated even at the end of the fermentation.     

Microheological properties of different erythrocyte populations in persons with elevated arterial pressure and in physically active persons

Microrheological properties (aggregation and deformability) of erythrocytes separated by centrifugation at 30000×g density gradient into “young” and “old” (the upper and lower fractions, respectively) were studied. The erythrocytes were taken from physically active persons (PAP) and from those with elevated arterial pressure (EAP). A significant difference in microrheological properties of the “young” and “old” erythrocytes was found. The aggregation degree of “old” cells was nearly twice that of “young” cells. The deformability of the erythrocyte subpopulations was significantly different, though the difference was not so pronounced as in the case of aggregation. The aggregation of “young” and “old” erythrocytes in the PAP group was the least (28% lower than in the control). Note, that “old” erythrocytes in the PAP group had better microrheological properties than in the other groups. All erythrocyte populations in the EAP group were characterized by higher aggregation, decreased deformability, and decreased capacity for oxygen transport.     

Evaluation of the Behavior of Some Native Dogs in Vietnam to Determine Their Suitability as Detector Dogs

Biology Bulletin - In dogs of native breeds (“Hmong,” “Phu Quoc,” and “Zang Soi”), the features of behavior pre-adapted to interaction with humans and formed in...     

Regulation of immune response at intestinal and peripheral sites by probiotics

The gut associated lymphoid tissue (GALT) should protect intestinal mucosa against pathogens, but also avoid hypersensitivity reactions to food proteins, normal bacterial flora and other environmental macromolecules. The interaction between epithelial cells and microflora is fundamental to establish gut mucosal barrier and GALT development. The normal colonization of intestine by commensal bacteria is thus crucial for a correct development of mucosal immune system. Probiotic bacteria are normal inhabitants of microflora and may confer health benefits to the host. The modification of the intestinal microflora towards a healthier probiotics enriched microflora may generate beneficial mucosal immunomodulatory effects and may represent a new strategy to cure intestinal and allergic diseases. The health benefits may be specific for different probiotic strains. Ongoing research is providing new insights into the probiotic beneficial effects and related mechanisms. This review represents an update of immunomodulatory activity of different probiotics and of the more accredited mechanisms underlying such activities. Presented at the Second Probiotic Conference, Košice, 15–19 September 2004, Slovakia.     

Colicins—Exocellular lethal proteins ofEscherichia coli

Colicins are toxic exoproteins produced by bacteria of colicinogenic strains ofEscherichia coli and some related species ofEnterobacteriaceae, during the growth of their cultures. They inhibit sensitive bacteria of the same family. About 35%E. coli strains appearing in human intestinal tract are colicinogenic. Synthesis of colicins is coded by genes located on Col plasmids. Until now more than 34 types of colicins have been described, 21 of them in greater detail,viz. colicins A, B, D, E1–E9, Ia, Ib, J_S, K, M, N, U, 5, 10. In general, their interaction with sensitive bacteria includes three steps: (1) binding of the colicin molecule to a specific receptor in the bacterial outer membrane; (2) its translocation through the cell envelope; and (3) its lethal interaction with the specific molecular target in the cell. The classification of colicins is based on differences in the molecular events of these three steps. The original version of this review was published in Czech in the journal “Biologické listy”,62, 107–130 (1997).     

Culturable Fungi of Stored ‘Golden Delicious’ Apple Fruits: A One-Season Comparison Study of Organic and Integrated Production Systems in Switzerland

The effects of organic and integrated production systems on the culturable fungal microflora of stored apple fruits from five matched pairs of certified organic and integrated ‘Golden Delicious’ farms were studied at five representative production sites in Switzerland. Isolated fungi were identified morphologically. Colonization frequency (percentage of apples colonized), abundance (colony numbers), and diversity (taxon richness) were assessed for each orchard. The standard quality of the stored fruits was comparable for both organic and integrated apples and complied with national food hygiene standards. Yeasts (six taxa) and the yeast-like fungus Aureobasidium pullulans were the dominant epiphytes, filamentous fungi (21 taxa) the dominant endophytes. The most common fungi occurred at all sites and belonged to the “white” and “pink” yeasts, yeast-like A. pullulans, filamentous fungi Cladosporium spp., Alternaria spp., and sterile filamentous fungi. Canonical correspondence analysis of the total fungal community revealed a clear differentiation among production systems and sites. Compared to integrated apples, organic apples had significantly higher frequencies of filamentous fungi, abundance of total fungi, and taxon diversity. The effects of the production system on the fungal microflora are most likely due to the different plant protection strategies. The incidence of potential mycotoxin producers such as Penicillium and Alternaria species was not different between production systems. We suggest that higher fungal diversity may generally be associated with organic production and may increase the level of beneficial and antagonistically acting species known for their potential to suppress apple pathogens, which may be an advantage to organic apples, e.g., in respect to natural disease control.     

Organisms can essentially be classified according to two codon patterns

We recently classified 23 bacteria into two types based on their complete genomes; “S-type” as represented by Staphylococcus aureus and “E-type” as represented by Escherichia coli. Classification was characterized by concentrations of Arg, Ala or Lys in the amino acid composition calculated from the complete genome. Based on these previous classifications, not only prokaryotic but also eukaryotic genome structures were investigated by amino acid compositions and nucleotide contents. Organisms consisting of 112 bacteria, 15 archaea and 18 eukaryotes were classified into two major groups by cluster analysis using GC contents at the three codon positions calculated from complete genomes. The 145 organisms were classified into “AT-type” and “GC-type” represented by high A or T (low G or C) and high G or C (low A or T) contents, respectively, at every third codon position. Reciprocal changes between G or C and A or T contents at the third codon position occurred almost synchronously in every codon among the organisms. Correlations between amino acid concentrations (Ala, Ile and Lys) and the nucleotide contents at the codon position were obtained in both “AT-type” and “GC-type” organisms, but with different regression coefficients. In certain correlations of amino acid concentrations with GC contents, eukaryotes, archaea and bacteria showed different behaviors; thus these kingdoms evolved differently. All organisms are basically classifiable into two groups having characteristic codon patterns; organisms with low GC and high AT contents at the third codon position and their derivatives, and organisms with an inverse relationship.     

Cytotoxic and fluorescent assays for thymocyte subpopulations differing in surface thy-1 level

A number of analytical techniques for distinguishing and separating the “high θ” and “low θ” subpopulations of mouse thymocytes have been compared. A differential cytotoxic assay was compared to a quantitative immunofluorescent assay on individual cells using flow cytofluorometry and cell sorting. Conventional anti-Thy-1 antisera were compared with a monoclonal IgM anti-Thy-1. The monoclonal reagent greatly improved both types of assay, eliminated a number of artifacts and allowed either procedure to be used to give a clear distinction, based on Thy-1 level, between the two subpopulations. The distribution of Thy-1 on thymocytes is bimodal, rather than continuous. These separate “high θ” and “low θ” categories each includes a population of dividing cells.     

Characteristics of stress response in a mushroom-pathogenic bacterium,Pseudomonas tolaasii, during the interaction withPleurotus ostreatus and carbon/nitrogen starvation in vitro

A brown blotch bacterium,Pseudomonas tolaasii strain PT814, expresses a high degree of cross-protection against generalized stress imposed by physical/chemical treatment, H₂O₂, UV, high temperature, ethanol and NaCl during the interaction withPleurotus ostreatus. Stress resistance was also noted in the bacterium in vitro under limited carbon and nitrogen sources. In addition, changes in cell morphology from a “metabolically active” rod to an “energy-saving” spherical shape were detected during starvation and the interaction. All the changes under stress were reversible. A homologue ofrpoS (σ ^S), a regulator that controls such physiological status during starvation in other bacteria, was identified inP. tolaasii strain PT814. Data suggest that the bacterium is able to withstand a complex stress environment for its survival through changes in its metabolic pattern.     

<Emphasis Type="Italic">Escherichia coli,Pseudomonas aeruginosa</Emphasis>, and<Emphasis Type="Italic"> Staphylococcus aureus</Emphasis> Attachment Patterns on Glass Surfaces with Nanoscale Roughness

Attachment tendencies of Escherichia coli K12, Pseudomonas aeruginosa ATCC 9027, and Staphylococcus aureus CIP 68.5 onto glass surfaces of different degrees of nanometer-scale roughness have been studied. Contact-angle and surface-charge measurements, atomic force microscopy (AFM), scanning electron microscopy (SEM), and confocal laser scanning microscopy (CLSM) were employed to characterize substrata and bacterial surfaces. Modification of the glass surface resulted in nanometer-scale changes in the surface topography, whereas the physicochemical characteristics of the surfaces remained almost constant. AFM analysis indicated that the overall surface roughness parameters were reduced by 60–70%. SEM, CLSM, and AFM analysis clearly demonstrates that although E. coli, P. aeruginosa and S. aureus present significantly different patterns of attachment, all of the species exhibited a greater propensity for adhesion to the “nano-smooth” surface. The bacteria responded to the surface modification with a remarkable change in cellular metabolic activity, as shown by the characteristic cell morphologies, production of extracellular polymeric substances, and an increase in the number of bacterial cells undergoing attachment.     

Preparation,Optimization, and Characterization of SERS Sensor Substrates Based on Two-Dimensional Structures of Gold Colloid

Generally, the immobilization of two-dimensional nanoparticles in immersion procedures is time-consuming (over 24 h). In this paper, we report a very effective and simple method to fabricate two-dimensional gold nanoparticle patterns over large areas with high regularity for surface-enhanced Raman scattering (SERS). We achieved a highly sensitive SERS colloid surface by optimizing temperature and immersion time. The surfaces were characterized by X-ray photoelectron spectroscopy, UV–Vis, atomic force microscopy, and scanning electron microscopy. The SERS activity of surfaces was compared by using two techniques: “dip” and “dip and dry” in an aqueous solution of 10⁻⁶ M crystal violet. The influence of the morphology of the surface was investigated with both the dip and dip and dry techniques.     

An ethological analysis of types of agonistic interaction in a captive group of Java-monkeys (Macaca fascicularis)

The primate literature provides many indications not only that the nature of dyadic interactions is to a large extent determined by the relations of the interacting animals with others and between these others, but also of the existence of polyadic interactions in which more than two individuals are simultaneously involved. The objectives of the present study are to obtain a quantitative categorization of the agonistic interaction types of captive Java-monkeys and an analysis of their dynamics. After having described the agonistic behaviour patterns of Java-monkeys we shall discuss the categorization of agonistic interaction types (depending on the number of involvees: “dyads”, “triads” and “polyads”), the way in which these types can be further differentiated on the basis of the nature and the direction of the behaviours shown (e.g., different types of alliances), and the existence of so-called “sub-directed” behaviours (i.e., non-agonistic behaviours which are shown towards a dominant third animal more or less simultaneously with aggressive behaviour directed towards an opponent). The analysis indicates that agonistic behaviour is different both in its form and its regulation in interactions of different complexity. This research was supported in part by a government grant (i.e.: Beleidsruimte project: 16-21-06, “Brain and Behaviour”) to the first author. The investigation was supported by a grant from the Beleidsruimtemiddelen Hersenen en Gedrag to the first author.     

An evaluation of the outer membrane charge and softness of<Emphasis Type="Italic">Thiobacillus ferrooxidans</Emphasis> by the Ohshima's electrophoretic model of a “soft” particle

The surface charge of bacterial cells plays an important role in their interfacial physiology and adhesion to substrata mediated by the electrostatic double-layer interaction. The surface charge or potential of biological cells is generally calculated from the experimentally measurable electrophoretic velocity of these cells migrating in an external electric field, applying the well-known Smoluchowski equation which is valid for “hard” particles with a sharp interface. However, bacterial cells possessing a structured outer membrane of a finite thickness (dependent on the ionic strength and pH of the surrounding liquid medium) are expected to obey Ohshima's electrophoretic mobility equation derived recently for ‘soft” particles. The electrophoretic mobility ofThiobacillus ferrooxidans was measured here by the fully automated technique of electrophoretic light scattering, based on the proportionality between the mobility and the Doppler shift in the frequency of light scattered by electrophoresing cells. Agreement was obtained between the experimentally determined electrophoretic mobility expressed as a function of low ionic strength (60–6000 μmol/L) at different pH values and the best-fit theoretical predictions of the “soft” particle electrophoresis theory, which is better than in the case of applying the Smoluchowski formula. The best-fit surface-charge and softness parameters predict a rather rigid and low-charge outer membrane of the bacterium examined, as compared to the parameters obtained for other bacteria in media of high ionic strength.     

Bacterial aerobic degradation of benzene,toluene, ethylbenzene and xylene

Several aerobic metabolic pathways for the degradation of benzene, toluene, ethylbenzene and xylene (BTEX), which are provided by two enzymic systems (dioxygenases and monooxygenases), have been identified. The monooxygenase attacks methyl or ethyl substituents of the aromatic ring, which are subsequently transformed by several oxidations to corresponding substituted pyrocatechols or phenylglyoxal, respectively. Alternatively, one oxygen atom may be first incorporated into aromatic ring while the second atom of the oxygen molecule is used for oxidation of either aromatic ring or a methyl group to corresponding pyrocatechols or protocatechuic acid, respectively. The dioxygenase attacks aromatic ring with the formation of 2-hydroxy-substituted compounds. Intermediates of the “upper” pathway are then mineralized by eitherortho-ormeta-ring cleavage (“lower” pathway). BTEX are relatively water-soluble and there-fore they are often mineralized by indigenous microflora. Therefore, natural attenuation may be considered as a suitable way for the clean-up of BTEX contaminants from gasoline-contaminated soil and groundwater.     

Integrated Evaluation of Environmental Parameters Influencing <Emphasis Type="Italic">Vibrio</Emphasis> Occurrence in the Coastal Northern Adriatic Sea (Italy) Facing the Venetian Lagoon

In the marine environment, the persistence and abundance of Vibrio are related to a number of environmental parameters. The influence of the different environmental variables in determining the Vibrio occurrence could be different in the specific geographic areas around the world. Moreover, oceanographic parameters are generally interdependent and should not be considered separately when their influence on bacterial presence and concentration is tested. In this study, an integrated approach was used to identify key parameters determining the abundance of Vibrio spp in marine samples from the Venetian Lagoon in Italy, which is an important area for fish farming and tourism. Multivariate techniques have been adopted to analyze the dataset: using PCA, it was shown that a relatively high proportion of the total variance in this area was mainly due to two independent variables, namely salinity and temperature. Using cluster analysis, it was possible to categorize different groups with homogeneous features as regards space (“stations”) and time (“seasons”) distribution, as well as to quantify the values of environmental variables and the Vibrio abundances in each category. Furthermore, integrating key environmental factors and bacterial concentration values, it was possible to identify levels of salinity and sea surface temperature which were optimal for Vibrio concentration in water, plankton, and sediment samples. The identification of key environmental variables conditioning Vibrio occurrence should facilitate ocean monitoring, making it possible to predict unexpected variations in marine microflora which determine possible public health risks in coastal areas.