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.     

<Emphasis Type=Italic>Pseudomonas aeruginosa</Emphasis> β-lactamase induction requires two permeases,AmpG and AmpP

Background  

In Enterobacteriaceae, β-lactam antibiotic resistance involves murein recycling intermediates. Murein recycling is a complex process with discrete steps taking place in the periplasm and the cytoplasm. The AmpG permease is critical to this process as it transports N-acetylglucosamine anhydrous N-acetylmuramyl peptides across the inner membrane. In Pseudomonadaceae, this intrinsic mechanism remains to be elucidated. Since the mechanism involves two cellular compartments, the characterization of transporters is crucial to establish the link.     

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).     

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.     

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.     

An <Emphasis Type=Italic>R</Emphasis><Subscript>0</Subscript> theory for source–sink dynamics with application to <Emphasis Type=Italic>Dreissena</Emphasis> competition

Source–sink dynamics may be ubiquitous in ecology. We developed a theory for source–sink dynamics using spatial extensions of the net reproductive value, R ₀, which has been used elsewhere to define fitness, disease eradication, population growth, and invasion risk. R ₀ decomposes into biologically meaningful components—lifetime reproductive output, survival, and dispersal—that are widely adaptable and easily interpreted. The theory provides a general quantitative means for relating fundamental niche, biotic interactions, dispersal, and species distributions. We applied the methods to Dreissena and found a resolution to a paradox in invasion biology—competitive coexistence between quagga (Dreissena bugensis) and zebra (D. polymorpha) mussels among lakes despite extensive niche overlap within lakes. Source–sink dynamics within lakes between deepwater and shallow habitats, which favor quagga and zebra mussels, respectively, yield a metacommunity distribution where quagga mussels dominate large lakes and zebra mussels dominate small lakes. The source–sink framework may also be useful in spatial competition theory, habitat conservation, marine protected areas, and ecological responses to climate change.     

<Emphasis Type=Italic>Pseudomonas seleniipraecipitatus</Emphasis> sp. nov.: A Selenite Reducing γ-<Emphasis Type=Italic>Proteobacteria</Emphasis> Isolated from Soil

Microbial fuel cells (MFCs) are a technology that provides electrical energy from the microbial oxidation of organic compounds. Most MFCs use oxygen as the oxidant in the cathode chamber. This study examined the formation in culture of an unidentified bacterial oxidant and investigated the performance of this oxidant in a two-chambered MFC with a proton exchange membrane and an uncoated carbon cathode. DNA, FAME profile and characterization studies identified the microorganism that produced the oxidant as Burkholderia cenocepacia. The oxidant was produced by log phase cells, oxidized the dye 2,2′-azino-bis(3-ethylbenzthiazoline-6-sulphonic acid) (ABTS), had a mass below 1 kD, was heat stable (121°C) and was soluble in ethanol. In a MFC with a 1000 Ω load and ABTS as a mediator, the oxidizer increased cell voltage 11 times higher than atmospheric oxygen and 2.9 times higher than that observed with ferricyanide in the cathode chamber. No increase in cell voltage was observed when no mediator was present. Organisms that produce and release oxidizers into the media may prove useful as bio-cathodes by improving the electrical output of MFCs.     

Identification of a <Emphasis Type=Italic>Rice stripe necrosis virus</Emphasis> resistance locus and yield component QTLs using <Emphasis Type=Italic>Oryza sativa</Emphasis> × <Emphasis Type=Italic>O. glaberrima</Emphasis> introgression lines

Background  

Developing new population types based on interspecific introgressions has been suggested by several authors to facilitate the discovery of novel allelic sources for traits of agronomic importance. Chromosome segment substitution lines from interspecific crosses represent a powerful and useful genetic resource for QTL detection and breeding programs.     

High-level expression,purification and characterization of a recombinant medium-temperature <Emphasis Type=Italic>α</Emphasis>-amylase from <Emphasis Type=Italic>Bacillus subtilis</Emphasis>

Alpha-amylases are important industrial enzymes with a wide range of applications. Although medium-temperature alpha amylase (AmyE) has some practical advantages, its low yield has limited its applications. When an amyE gene from Bacillus subtilis BF768 was cloned into vector pWB980 and over-expressed in B. subtilis WB600, high activities (723 U ml⁻¹) of secreted AmyE were produced. Recombinant AmyE was purified to a specific activity of 36 U mg⁻¹ having optimal activity at pH 6.0 and 60°C.     

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.     

Water relations advantages for invasive <Emphasis Type=Italic>Rubus</Emphasis> <Emphasis Type=Italic>armeniacus</Emphasis> over two native ruderal congeners

Despite species in the Rubus fruticosus complex (wild blackberry) being among the most invasive plants globally in regions with large annual fluctuations in water availability, little is known about their water relations. We compared water relations of a prominent member of the complex, R. armeniacus (Himalayan blackberry), with species native to the Pacific Northwest of North America (PNW), R. spectabilis (salmonberry) and R. parviflorus (thimbleberry). In eight stands of each species located near Portland, Oregon, USA, we measured mid-day hydraulic resistance (R _plant), and daily time series of stomatal conductance (g _s), leaf water potential (Ψ_lf), and environmental conditions at four time periods spanning the 2007 growing season. Although all species maintained Ψ_lf above −0.5 MPa in spring, R. armeniacus maintained less negative Ψ_lf (≥−1.0 MPa) than the natives in summer, a factor attributable to advantages in both its root and shoot systems. R _plant of R. armeniacus was ≤0.1 MPa mmol⁻¹ m² s for the duration of the study, and approximately 25–50% of R _plant for the native species in summer. R. armeniacus had higher g _s compared to the native species throughout the spring and summer, with approximately twice their rates in summer. Our R _plant and g _s results show that R. armeniacus has access to more water during PNW summers than congeneric natives, allowing it to maintain high water-use, and potentially helping it achieve higher growth and reproductive rates. Water relations may therefore be a critical component of the competitive and invasive success of R. armeniacus and other R. fruticosus species worldwide.     

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.