Small colony variants of <Emphasis Type=Italic>Staphylococcus aureus</Emphasis> — <Emphasis Type=Italic>review</Emphasis>

Bacterial variants of Staphylococcus aureus called small colony variants (SCVs) originate by mutations in metabolic genes, resulting in emergence of auxotrophic bacterial subpopulations. These variants are not particularly virulent but are able to persist viable inside host cells. SCVs show their characteristic auxotrophic growth deficiency and depressed α-cytotoxin activity. Environmental pressure such as antibiotics, select for isogenic SCV cells that are frequently found coexisting with their parent wild-type strains in a mixed bacterial culture. SCV strains often grow on blood agar as non-pigmented or pinpoint pigmented colonies and their key biochemical tests are often non-reactive. Their altered metabolism or auxotrophism can result in long generation time and thus SCV phenotype, more often than not SCV can be overgrown by their wild-type counterparts and other competitive respiratory flora. This could affect laboratory detection. Thus, molecular methods, such as 16S rRNA partial sequencing or amplification of species-specific DNA targets (e.g. coagulase, nuclease) directly from clinical material or isolated bacterial colonies, become the method of choice. Patients at risk of infection by S. aureus SCVs include cystic fibrosis patients (CF), patients with skin and foreign-body related infections and osteomyelitis, as they suffer from chronic staphylococcal infections and are subject to long-term antibiotic therapy. Molecular evidence of SCV development has not been found except for some random mutations of the thymidylate synthase gene (thyA) described in SCV S. aureus strains of CF patients. These variants are able to bypass the antibiotic effect of folic acid antagonists such as sulfonamides and trimethoprim. Resistance to gentamicin and aminoglycosides in the hemin or menadione auxotrophic SCVs was hypothesized as being due to decreased influx of the drugs into cells as a result of decreased ATP production and decreased electrochemical gradient on cell membranes.     

Revision of “<Emphasis Type=Italic>Septonema ochraceum</Emphasis>” revealed three new species of <Emphasis Type=Italic>Venturiaceae</Emphasis> and <Emphasis Type=Italic>Herpotrichiellaceae</Emphasis>

Survey of seven strains determined as Septonema ochraceum (Dothideomycetes, inc. sed.) isolated from pine litter or obtained from public collections revealed three new species, Fusicladium cordae, F. sicilianum (Venturiaceae), Cladophialophora matsushimae (Herpotrichiellaceae) and a cryptic species morphologically identical to Devriesia americana (Teratosphaeriaceae), but phylogenetically distinct. Morphological survey and phylogenetic analysis using nucleotide sequence data from the nuclear ribosomal subunit genes indicate a close relationship within three species colonising pine litter needles, F. cordae, F. pini and F. ramoconidii. F. sicilianum is most related to F. rhodense. C. matsushimae represents a species belonging to one of the lineages of the polyphyletic genus Cladophialophora. None of the strains observed can be classified morphologically as S. ochraceum, of which the type material does not exist.     

A computational study of the mechanism of the unimolecular elimination of <Emphasis Type=Italic>α</Emphasis>,<Emphasis Type=Italic>β</Emphasis>-unsaturated aldehydes in the gas phase

The mechanism for the decarbonylation of (E)-2-butenal and (E)-2-methyl-3-pheny-2-propenal was studied with different levels of ab initio and DFT methods. Reactants, products and transition structures were optimized for two kinds of reaction channel: a one-step reaction which involves a three-membered cyclic transition state, and a two-step reaction which involves an initial four-membered cyclic transition state. According to our calculations, these two possible mechanisms entail similar energetic costs, and there are only small differences depending on the reactant. The elimination of (E)-2-methyl-3-pheny-2-propenal yields different products depending on the channel followed. Only one of the three possible one-step mechanisms leads directly to (E)-β-methylstyrene (the main product according to experiment). This fact is reasonably well reproduced by our results, since the corresponding transition state gave rise to the lowest activation Gibbs free energy.     

Spatial patterns of genetic differentiation in <Emphasis Type=Italic>Brachionus</Emphasis> <Emphasis Type=Italic>calyciflorus</Emphasis> species complex collected from East China in summer

In this study, the mtDNA COI genes of 124 individuals in Brachionus calyciflorus complex were sequenced and analyzed. Overall, 84 mtDNA haplotypes were defined, and were split into three clades by the phylogenetic trees. The divergences of COI gene sequence among the three clades ranged from 11.4 to 22.5%, indicating the occurrence of three cryptic species (cryptic species 1, cryptic species 2, and cryptic species 3). Within cryptic species 3, a remarkable degree of differentiation (F _st = 0.0947) might be attributable to habitat fragmentation, restricted gene flow, and founder effect, most probably together with local adaptation. The more shared haplotypes were observed, and a non-significant correlation existed between geographic and genetic distance, suggesting that some ancestral haplotypes might be involved in a past range expansion, and as founders give a similar distribution pattern among geographic populations. The networks were also in agreement with the pattern of genetic differentiation in B. calyciflorus species complex revealed by molecular phylogeny. The nested clade analysis suggested a slight geographic structure in the network I, network II, and the highest nesting clade levels within the network III. Under the possible effect of the Younger Dryas Event, the three cryptic species might have survived in multiple relict refugia throughout the south of China. The co-occurrence of cryptic species 2 and 3 might be found in Guangzhou and Hainan due to the possible interference of the barrier and contiguous range expansion. After the Younger Dryas Event, cryptic species 3 with high colonization ability might have arrived and colonized whole habitats at first, and reduce effective gene flow among cryptic species, thus effectively increasing persistence of founder events. Cryptic species 2 might, respectively, have expanded their ranges into Wuhu and Nanjing regions only because of the probable barrier of the Yangtze River, its weak colonization abilities and the ‘priority effects’ of cryptic species 3. Cryptic species 1 distributed exclusively in Danzhou probably failed to expand its ranges into mainland China because of small population size, weaker dispersal capacity, and the barrier of the Qiongzhou Strait.     

Polygenic control for fermentation of β-fructosides in the yeast <Emphasis Type=Italic>Saccharomyces cerevisiae</Emphasis>: New genes <Emphasis Type=Italic>SUC9</Emphasis> and <Emphasis Type=Italic>SUC10</Emphasis>

Using molecular karyotyping and genetic hybridization analysis, two new polymeric β-fructosidase genes, SUC9 and SUC10, were identified in the yeast Saccharomyces cerevisiae, which are located on chromosome XIV and on the chromosome XVI/XIII doublet, respectively. The genes are responsible for fermentation of sucrose and raffinose. The SUC gene genotypes of strains VKM Y-1831 and DBVPG 1340 are SUC2 SUC9 and suc2 ⁰ SUC10, respectively. suc2 ⁰ is a silent sequence. The scientific and applied significance of SUC genes is discussed.     

A monograph of <Emphasis Type=Italic>Octoknema</Emphasis> (Octoknemaceae — Olacaceae <Emphasis Type=Italic>s.l.</Emphasis>)

A revision of Octoknema Pierre is provided, based on morphological data gathered from a study of herbarium specimens and observations in the field. Fourteen species of Octoknema are recognised including six new species: O. bakossiensis Gosline & Malécot, O. belingensis Gosline & Malécot, O. chailluensis Malécot & Gosline, O. kivuensis Gosline & Malécot, O. mokoko Gosline & Malécot and O. ogoouensis Malécot & Gosline. Data are given for four additional poorly known taxa (Octoknema species A, B, C and D).     

Change in compactness of inclusion bodies of recombinant β-galactosidase expressed in the <Emphasis Type=Italic>araBAD</Emphasis> promoter system of <Emphasis Type=Italic>Escherichia coli</Emphasis>

We investigated the relevance of the relationship between the compactness of β-galactosidase inclusion bodies (β-gal IBs) and their enhanced enzymatic activity with or without the addition of D-fucose (inducer analog) or methyl α-D-glucopyranoside (α-MG, catabolite repressor) after induction in the araBAD promoter system of Escherichia coli. Experiments conducted to evaluate the solubilization of β-gal IBs in guanidine hydrochloride as well as their trypsin degradation and temperature stability revealed that β-gal IBs expressed in response to the addition of D-fucose or α-MG had a looser structure. Additionally, β-gal IBs expressed when D-fucose or α-MG was added were more quickly solubilized in guanidine hydrochloride or degraded by trypsin-treatment than those produced when these compounds were not added. Moreover, the activity of β-gal IBs expressed when D-fucose or α-MG were added was less stable at various temperatures. Consequently, we deduced that the looser structure of β-gal IBs resulted in enhanced enzymatic activity of β-gal IBs upon addition of D-fucose or α-MG after induction.     

Effect of <Emphasis Type=Italic>Azotobacter chroococcum</Emphasis> on <Emphasis Type=Italic>in vitro</Emphasis> pineapple plants’ growth during acclimatization

Pineapple is one of the most important tropical fruits, but the availability of planting material is insufficient to agricultural demands. Therefore, several pineapple micropropagation protocols have been developed. However, acclimatization of in vitro plants continues to take a prolonged period. Biofertilizers have been found as safe alternatives to improve the agricultural performances of many crops. This study highlights some of the effects of the application of Azotobacter chroococcum (INIFAT5 strain) on in vitro pineapple plants during acclimatization. The bacteria were sprayed immediately after transplanting to the ex vitro environment; the plants were then sprayed every 4 wk. A control group of plants was established. Subsequently, after 5 mo, the evaluated variables included fresh and dry plant weight, plant height (cm), and root length (cm). The anatomy of middle-aged leaves and roots was also studied: transversal thickness and width of cuticle, epidermis, hypodermis, aquiferous parenchyma, and photosynthetic parenchyma. Thickness of root exoderm, external cortex, internal cortex, and stele were also evaluated. In general, the INIFAT5 strain improved the plant development. Results showed that the bacteria significantly provoked changes in the plant fresh weight, the thickness of the leaf abaxial and adaxial cuticles, and the root exoderm width. Contrastingly, A. chroococcum did not affect the thickness of the leaf photosynthetic parenchyma.     

Differences in the timing of cell death,differentiation and function among three different types of ray parenchyma cells in the hardwood <Emphasis Type=Italic>Populus sieboldii</Emphasis> × <Emphasis Type=Italic>P</Emphasis>. <Emphasis Type=Italic>grandidentata</Emphasis>

Differences in the timing of cell death, differentiation and function among three different types of ray parenchyma cells in the hardwood Populus sieboldii × P. grandidentata which form uniseriate and homocellular rays were examined and clarified. Ray parenchyma cells died within 5 years, and the disappearance of nuclei from ray parenchyma cells did not occur successively from the pith side, even within individual radial cell lines of a given ray. Cell death occurred earliest in contact cells, which were connected to adjacent vessel elements through pits, in the fourth annual ring from the cambium. Cell death occurred next in intermediate cells, which were located within the same cell lines as contact cells but were not adjacent to vessel elements, in the fourth annual ring from the cambium. Finally, isolation cells, which were located within the other cell lines of a given ray, died in the fifth annual ring from the cambium. Secondary wall thickenings in contact cells and intermediate cells were initiated before those in isolation cells in the current year’s xylem. Most starch grains were localized in intermediate cells, and there were more lipid droplets in contact cells and intermediate cells than in isolation cells. In addition, the largest quantities of protein were found in contact cells. Our results indicate that the position within a ray and neighboring short-lived vessel elements might affect the timing of cell death and differentiation and, thus, the function of long-lived ray parenchyma cells in Populus sieboldii × P. grandidentata.     

β<Subscript>2</Subscript> Adrenoreceptor-Mediated Noradrenergic Effect on GABA-ergic Transmission in the <Emphasis Type=Italic>CA1</Emphasis> Zone of the Rat Hippocampus <Emphasis Type=Italic>in vitro</Emphasis>

Using extracellular recording of evoked potentials, we examined the effect of an agonist of β₂ adrenoreceptors, metaproterenol (MPT), on GABA-ergic transmission in the CA1 zone of slices of the rat hippocampus. Isolated application of GABA evoked in these slices rapid reversible suppression of orthodromic population discharges recorded from the pyramidal layer of the above hippocampal zone after electrical stimulation of Schaffer collaterals in the radial layer. In most cases (13 of 19 preparations), combined application of GABA and MPT interfered with the development of the inhibitory GABA effect. In the case of the action of both of the above agents, the amplitude and duration of evoked responses decreased, but these changes were significantly weaker than those observed upon isolated GABA application. Our experiments showed that the noradrenergic system is capable of modulating GABA-ergic inhibition via β₂ adrenoreceptors and, in such a way, is probably involved in regulation of the inhibition level in the hippocampus. Noradrenaline-induced effects on inhibitory neuronal networks in the hippocampus, similarly to those exerted by several other cerebral neurotransmitter systems, underlie the involvement of the noradrenergic cerebral system in a few physiological processes (emotions, attention, and memory) and are related to some pathological states (Alzheimer’s disease, schizophrenia, epilepsy, etc.).     

Anatomical observation of polyphenol changes in epidermal cells during the development of <Emphasis Type=Italic>Quercus acutissima</Emphasis>–<Emphasis Type=Italic>Scleroderma verrucosum</Emphasis> ectomycorrhizae

Quercus acutissima seedlings were cultivated in growth pouches and inoculated with Scleroderma verrucosum in order to assess the changes in polyphenol contents in epidermal cells during ECM development. Semithin sections stained with metachromatic Toluidine Blue O (TBO) were compared among non-inoculated lateral roots, early mantled lateral roots, and mycorrhizal roots with a mature mantle. Hyphae adhered closely or were embedded in mucilage-like materials on the epidermis. Epidermal cells and root hairs of the non-inoculated second-order lateral roots developing from the taproot harbored polyphenolic compounds that were stained by TBO. At non-inoculated stage, the average numbers of epidermal cells stained entirely (PC2), stained partially (PC1) or remaining unstained (PC0) were 16.5 ± 0.7, 0 ± 0, and 0 ± 0, respectively. At the early mantled stage, the numbers were 6.5 ± 1.6, 5.2 ± 1.4, and 4.2 ± 1.0, and at the mycorrhizal stage, it was 0 ± 0, 0 ± 0, and 32.8 ± 1.3 for PC2, PC1, and PC0, respectively. Total phenolic content in the root tips at each developmental stage declined with ECM development. The early mantled stage involved a dynamic process of polyphenol localization. However, some epidermal cells and endodermal cells of the proximal zone accumulated polyphenols. Eventually, polyphenolic compounds, which were found abundantly in the epidermal cells and root hairs of the non-inoculated lateral roots of the host, disappeared at the mycorrhization process with the symbiont.     

Comparative genetics of yeasts: A novel β-fructosidase gene <Emphasis Type=Italic>SUC8</Emphasis> in <Emphasis Type=Italic>Saccharomyces cerevisiae</Emphasis>

Molecular and genetic analyses revealed that the distillers race XII, which is an ancestor of Saccharomyces cerevisiae Peterhof and Gatchina genetic lines, has three polymeric β-fructosidase genes: SUC2, SUC5, and SUC8. The latter gene located on the X chromosome was identitied in this work for the first time. The presence of the single SUC2 gene in yeasts used in the international project on sequencing of the S. cerevisiae genome is discussed.     

Pseudolysogeny of <Emphasis Type=Italic>Pseudomonas aeruginosa</Emphasis> bacteria infected with φKZ-like bacteriophages

In this work, a final piece of evidence proving that bacteria Pseudomonas aeruginosa are capable of transition to the pseudolysogenic state after infection with φKZ-like phages has been produced. It was shown that the decisive factor in this process is multiple infection of bacteria with bacteriophages belonging to this genus. In the course of this work, stable clinical isolates of bacteria liberating novel bacteriophages of this genus (Che2/2 and Che21/5) were detected and attributed to species φKZ and EL, respectively, according to their phenotypic characters and the results of DNA analysis. For three bacteriophages belonging to species EL (EL, RU, and Che21/5), mutants with disorders in the capability for pseudolysogenization were isolated. One of the mutants of phage EL possesses properties of virulent mutants of typical temperate phages (vir mutant). This mutant fails to form pseudolysogens and, moreover, provides the effect of dominance upon coinfection of bacteria with the wild-type phage EL, but however is unable to exhibit this effect upon joint infection of bacteria with wild-type phages of species φKZ and Lin68. It is assumed that the effect of pseudolysogeny may be connected with functioning of φKZ and EL genes that control the products similar to repressors of other phages. Because earlier wild-type φKZ-like phages were shown to be present in commercial phage-therapeutic preparations (which represents certain problems), it is expedient to use virulent mutants of phages belonging to this genus rather than phages of the wild type.     

Enhanced production and characterization of a β-glucosidase from <Emphasis Type=Italic>Bacillus halodurans</Emphasis> expressed in <Emphasis Type=Italic>Escherichia coli</Emphasis>

A putative β-glucosidase gene from the genome of Bacillus halodurans C-125 was expressed in E. coli under the regulation of T7lac promoter. On induction with isopropyl-β-D-1-thiogalactopyranoside, the enzyme expressed at ∼40% of the cell protein producing 238 mg/liter culture. With increase in culture cell density to A ₆₀₀ 12 in auto-inducing M9NG medium, β-glucosidase production increased 3-fold. Approximately 70% of the expressed enzyme was in a soluble form, while the rest was in an insoluble fraction of the cell lysate. The soluble and active form of the expressed enzyme was purified by ammonium sulfate precipitation followed by ion-exchange chromatography to a purity >98%. The mass of the enzyme as determined by MALDI-TOF mass spectrometry was 51,601 Da, which is nearly the same as the calculated value. Phylogenetic analysis of the β-glucosidase of B. halodurans was found to cluster with members of the genus Bacillus. Temperature and pH optima of the enzyme were found to be 45°C and 8.0, respectively, under the assay conditions. K _m and k _cat against p-nitrophenyl-β-D-glucopyranoside were 4 mM and 0.75 sec⁻¹, respectively. To our knowledge, this is the first report of high-level expression and characterization of a β-glucosidase from B. halodurans.