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.     

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.     

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.     

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.     

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.     

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.     

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).     

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.     

Peroxidase,acid phosphatase,RNase and DNase activity and isoform patterns during <Emphasis Type=Italic>in vitro</Emphasis> rooting of <Emphasis Type=Italic>Petunia</Emphasis> × <Emphasis Type=Italic>hybrida</Emphasis> microshoots

Specific activities and isoform patterns of peroxidases, acid phosphatases, DNases and RNases were studied in relation to in vitro rooting of Petunia × hybrida microshoots in the presence of 4 μM indole-3-butyric acid (IBA). Specific activities of the above enzymes increased in the course of rooting. Rhizogenesis could be related with an increased specific activity of peroxidases during the initiation phase, in parallel with increased lignin content. Twelve peroxidases, six anionic (A1–A6) and six cationic (C1–C6), seven acid phosphatases (ACP1–ACP7), seven RNases (R1–R7) and four DNases (D1–D4) isoforms were detected following native PAGE. Variation in the number of the above isoforms and their quantity was observed during different stages of rooting. Particularly, A2, A3, C3, C4, C5, ACP2, R1, R2, R3, and D4 isoforms appeared after the induction phase and could be related to emergence of root primordia. Additionally, R3 and D4 could be associated with cell division and differentiation, since these are only expressed in rooted microshoots. Moreover, the higher number of roots in IBA-treated microshoots could be related to the higher expression of RNase and DNase isoforms during initiation and expression phases.     

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.     

Genetic engineering of <Emphasis Type=Italic>Enterobacter asburiae</Emphasis> strain JDR-1 for efficient <Emphasis Type=SmallCaps>d</Emphasis>(−) lactic acid production from hemicellulose hydrolysate

In the dilute acid pretreatment of lignocellulose, xylose substituted with α-1,2-methylglucuronate is released as methylglucuronoxylose (MeGAX), which cannot be fermented by biocatalysts currently used to produce biofuels and chemicals. Enterobacter asburiae JDR-1, isolated from colonized wood, efficiently fermented both MeGAX and xylose in acid hydrolysates of sweetgum xylan. Deletion of pflB and als genes in this bacterium modified the native mixed acid fermentation pathways to one for homolactate production. The resulting strain, Enterobacter asburiae L1, completely utilized both xylose and MeGAX in a dilute acid hydrolysate of sweetgum xylan and produced lactate approximating 100% of the theoretical maximum yield. Enterobacter asburiae JDR-1 offers a platform to develop efficient biocatalysts for production of fuels and chemicals from hemicellulose hydrolysates of hardwood and agricultural residues.     

Isozymes of <Emphasis Type=Italic>α</Emphasis>-amylases from newly isolated <Emphasis Type=Italic>Bacillus thuringiensis</Emphasis> CKB19: Production from immobilized cells

The aim of this study was to produce two isozymes of α-amylase by immobilization of a newly isolated soil bacterium. The bacterium was identified as Bacillus thuringiensis CKB19 on the basis of its 16S rRNA profile. Enzyme production by free cells increased linearly with cell growth up to 34 h in starch containing enriched liquid media. The active bacterial cells were immobilized in Caalginate beads, and operational stability of the entrapped cell was optimized for amylase production. Enzyme production was optimal at an alginate concentration of 2 g% (w/v), calcium chloride concentration of 1 M, and with 300 beads (each bead contained 2 × 10⁷ cells)/250 mL flask. Amylase production by the immobilized cells was about 3 times higher than free cell fermentation after 34 h of incubation. It was observed that the immobilized bacterium secreted two different amylases (Am-I and Am-II) into the culture fluid. The molecular masses of Am-I and Am-II were 59.6 and 44.7 kd, respectively, and showed optimum activity at pH 5.0 and 9.0. Both amylases showed optimum activity at 40°C and were stable at the same temperature, with losses of only 10 and 20% (for Am I and Am II, respectively) of their original activities after 24 h of incubation. Further, both amylases were salt tolerant (up to 4 M NaCl) and hydrolyzed raw starchy foods into glucose. All these characteristics make this enzyme mixture suitable for use as a digestive aid and for the improvement of digestibility of animal feed ingredients.     

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.     

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.     

The domain structure of <Emphasis Type=Italic>Entamoeba</Emphasis> α-actinin2

Entamoeba histolytica, a major agent of human amoebiasis, expresses two distinct forms of α-actinin, a ubiquitous actin-binding protein that is present in most eukaryotic organisms. In contrast to all metazoan α-actinins, in both isoforms the intervening rod domain that connects the N-terminal actin-binding domain with the C-terminal EF-hands is much shorter. It is suggested that these α-actinins may be involved in amoeboid motility and phagocytosis, so we cloned and characterised each domain of one of these α-actinins to better understand their functional role. The results clearly showed that the domains have properties very similar to those of conventional α-actinins.     

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.