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.     

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.     

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.     

Airborne <Emphasis Type=Italic>Aspergillus</Emphasis> and <Emphasis Type=Italic>Penicillium</Emphasis> in the atmosphere of Szczecin, (Poland) (2004–2009)

The investigation into airborne fungal spore concentrations was conducted in Szczecin (Poland) between 2004 and 2009. The objective of the studies was to determine a seasonal variation in concentrations of amerospores on the basis of meteorological parameters. The presence of spores in Szczecin was recorded using a volumetric method. Fungal spores were present in the air in high numbers in late summer and early autumn. The highest concentrations were noted in September, October and November. The peak period was recorded in August, September, October and November. The highest annual number of spores occurred in 2005 and 2007 and the lowest in 2006. High values of daily concentration of amerospores occurred during the afternoon and late at night. In 2005 and 2007 the late-night maximum was overdue about 1 or 2 h. For daily values of dew point temperature and relative humidity, the coefficients were positive, significant for p = 0.001 and ranged from 0.342 to 0.258. The average wind speed was positively correlated for p = 0.01 and the coefficient was 0.291. The similar relations were noted for hourly values of spore concentrations for p = 0.05, p = 0.01 and p = 0.001. For these spore types, the dew point temperature and relative humidity appeared to be the most influential factor.     

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.     

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.     

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.     

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.     

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).     

Microcosm studies on the degradation of <Emphasis Type=Italic>o,p</Emphasis>′- and <Emphasis Type=Italic>p,p</Emphasis>′-DDT,DDE, and DDD in a muck soil

The muck soils of the north shore of Lake Apopka, near Orlando, Florida, USA are high in organic matter, inorganic nutrients, and water content. Ideally suited for agriculture, these soils have been exposed to a wide variety of agrochemicals. Some of the more recalcitrant organochlorine pesticides, such as DDT and its degradation products DDD and DDE, have persisted in the soil for over 30 years. Using the extracellular enzymes from wood rot fungi, it was demonstrated that it is possible to substantially reduce the amount of the o,p′ and p,p′ isomers of DDT, DDD, and DDE in this soil by more than 60% in 3 weeks. A fungal species with 99% DNA homology to Nectria mariannaeae was isolated from this muck soil and identified by nucleotide sequencing. When grown under nitrogen-limited conditions, this Nectria sp. has been shown to be comparable to Phanerochaete chrysosporium (ATCC 24725) in producing extracellular factors (or agents) that are capable of degrading these recalcitrant chlorinated chemicals.     

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.     

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.).     

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.     

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.     

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.