A Genome-wide Approach to Identify the Genes Involved in Biofilm Formation in E. coli

Biofilm forming cells are distinctive from the well-investigatedplanktonic cells and exhibit a different type of gene expression.Several new Escherichia coli genes related to biofilm formationhave recently been identified through genomic approaches suchas DNA microarray analysis. However, many others involved inthis process might have escaped detection due to poor expression,regulatory mechanism, or genetic backgrounds. Here, we screeneda collection of single-gene deletion mutants of E. coli named‘Keio collection’ to identify genes required forbiofilm formation. Of the 3985 mutants of non-essential genesin the collection thus examined, 110 showed a reduction in biofilmformation nine of which have not been well characterized yet.Systematic and quantitative analysis revealed the involvementof genes of various functions and reinforced the importancein biofilm formation of the genes for cell surface structuresand cell membrane. Characterization of the nine mutants of function-unknowngenes indicated that some of them, such as yfgA that geneticallyinteracts with a periplasmic chaperone gene surA together withyciB and yciM, might be required for the integrity of outermembrane.     

Temporal dynamics and spatial variability in the enhancement of canopy leaf area under elevated atmospheric CO2

Increased canopy leaf area (L) may lead to higher forest productivity and alter processes such as species dynamics and ecosystem mass and energy fluxes. Few CO₂ enrichment studies have been conducted in closed canopy forests and none have shown a sustained enhancement of L. We reconstructed 8 years (1996–2003) of L at Duke's Free Air CO₂ Enrichment experiment to determine the effects of elevated atmospheric CO₂ concentration ([CO₂]) on L before and after canopy closure in a pine forest with a hardwood component, focusing on interactions with temporal variation in water availability and spatial variation in nitrogen (N) supply. The dynamics of L were reconstructed using data on leaf litterfall mass and specific leaf area for hardwoods, and needle litterfall mass and specific leaf area combined with needle elongation rates, and fascicle and shoot counts for pines. The dynamics of pine L production and senescence were unaffected by elevated [CO₂], although L senescence for hardwoods was slowed. Elevated [CO₂] enhanced pine L and the total canopy L (combined pine and hardwood species; P<0.050); on average, enhancement following canopy closure was ～16% and 14% respectively. However, variation in pine L and its response to elevated [CO₂] was not random. Each year pine L under ambient and elevated [CO₂] was spatially correlated to the variability in site nitrogen availability (e.g. r²=0.94 and 0.87 in 2001, when L was highest before declining due to droughts and storms), with the [CO₂]‐induced enhancement increasing with N (P=0.061). Incorporating data on N beyond the range of native fertility, achieved through N fertilization, indicated that pine L had reached the site maximum under elevated [CO₂] where native N was highest. Thus closed canopy pine forests may be able to increase leaf area under elevated [CO₂] in moderate fertility sites, but are unable to respond to [CO₂] in both infertile sites (insufficient resources) and sites having high levels of fertility (maximum utilization of resources). The total canopy L, representing the combined L of pine and hardwood species, was constant across the N gradient under both ambient and elevated [CO₂], generating a constant enhancement of canopy L. Thus, in mixed species stands, L of canopy hardwoods which developed on lower fertility sites (～3 g N inputs m^?2 yr^?1) may be sufficiently enhanced under elevated [CO₂] to compensate for the lack of response in pine L, and generate an appreciable response of total canopy L (～14%).     

Effect of insertional mutations in the pueA and pueB genes encoding two polyurethanases in Pseudomonas chlororaphis contained within a gene cluster

AIMS: To better understand the role of PueA and PueB from Pseudomonas chlororaphis in polyurethane degradation, the present study was conducted to create insertional mutants in their respective genes. METHODS AND RESULTS: Growth kinetic studies showed that the pueA knockout mutant had a greater effect than the pueB knockout mutant. The pueA mutant had an 80% decrease in cell density from that of the wild type, while the pueB mutant had an 18% decrease in cell density. Polyurethane utilization followed Michaelis-Menten kinetics. The pueA and pueB mutants exhibited a 17% and 10% decrease respectively in growth rate using polyurethane when compared with the wild type. CONCLUSIONS: In this present study, pueA and pueB, are shown to be part of an ABC transporter gene cluster that consists of seven open reading frames. Mutational analysis results suggest that PueA may play a more major role in polyurethane degradation than PueB based on cell density and growth rates. SIGNIFICANCE AND IMPACT OF THE STUDY: The results from this study provide a starting point for the eventual enhancement and bioremediation of polyurethane waste. Understanding the role of polyurethane-degrading enzymes is useful for the creation of strains for this purpose.     

Pinnately ramified ensiform leaves in the genus Marathrum, (Podostemaceae-Podostemoideae)

The paper deals with the complex leaves of three species of the aquatic genus Marathrum (M. minutiflorum, M. rubrum and M. schiedeanum). It is shown that they represent pinnately ramified ensiform leaves. The dissection of the leaves contributes to surface enlargement and thus to improvement of their hydrophylls function. The ensiform structure is confirmed by the transverse position of the sheathing lower leaf zone and the subsequent intercalary elongational growth proceeding in the median plane towards the abaxial side of the leaf (upper leaf zone). The petiole continues into the rachis-like central axis of the blade from which pinnate-like segments diverge at the adaxial and abaxial edge of the ensiform blade. The segments give rise to tufts of clavate enations that end in long filaments. The filigree pinnately segmented ensiform leaves of Marathrum are interpreted as a further development of the fan-shaped and irregularly lobate ensiform leaves occurring in Mourera and Apinagia. Pinnately ramified ensiform leaves obviously evolved in convergence to the common type of pinnate leaves found in angiosperms.     

Morphogenesis of Pistillate Flowers of Cercidiphyllum japonicum(Cercidiphyllaceae)

Floral morphogenesis and the development of Cercidiphyllum japonicum Sieb.et Zucc.were observed by scanning electronmicroscopy(SEM).The results showed that the pistillate inflorescences were congested spikes with the flowers arrangedopposite.Great differences between the so-called"bract"and the vegetative leaf were observed both in morphogenesis andmorphology.In morphogenesis,the"bract"primordium is crescent-shaped,truncated at the apex and not conduplicate,has no stipule primordium at the base but does have some inconspicuous teeth in the margin that are not glandular.Theleaf primordium is triangular,cycloidal at the apex,conduplicate,has two stipule primordia at the base,has one gland-toothat the apex occurring at first and some gland-teeth in the margin that occur later.In morphology,the"bract"is also differentto the vegetative leaf in some characteristics that were also illustrated in the present paper.Based on the hypothesis thatthe bract is more similar to the vegetative leaf than the tepal,we considered that the so-called"bract"of C.japonicum mightbe the tepal of the pistillate flower in morphological nature.Therefore,each pistillate flower contains a tepal and a carpel.We did not find any trace of other floral organs in the morphogenesis of the pistillate flower.Therefore we consideredthat the unicarpellate status of extant Cercidiphyllum might be to highly reduce and advance characteristics that make theextant Cercidiphyllum isolated from both fossil Cercidiphyllum-like plants and its extant affinities.     

Molecular domain organization of BldD, an essential transcriptional regulator for developmental process of Streptomyces coelicolor A3(2)

A homodimeric protein, BldD is a key regulator for developmental process of Streptomyces coelicolor and the bldD mutant exhibits severely pleiotropic defects in the antibiotic production and morphological differentiation of the bacterium. In the present work, we approached domain organization of BldD, to structurally and functionally characterize the protein as a DNA-binding protein. We first observed a proteolytic cleavage of BldD by the cytoplasmic extracts of S. coelicolor, which was highly dependent on the developmental stage of the bacterium. The resulting fragment of BldD was identified by mass spectrometry as the N-terminal domain resistant to the proteolysis. Recombinant proteins corresponding to the intact BldD, the N-terminal domain (residues 1-79) and the rest part (C-terminal domain; residues 80-167) were used for comparative analyses by several spectroscopic, thermodynamic, and biochemical experiments, respectively. The results of circular dichroism and nuclear magnetic resonance spectroscopies certified each of the two determined domains could be regarded as an individual folding unit possessing an independent thermodynamic cooperativity. Structural interaction between the two domains was little observed in the DNA-free and DNA-bound states. Strikingly, it was revealed by gel permeation chromatography, chemical crosslink, gel mobility shift, and NMR-monitored DNA-binding experiments, that only the N-terminal domain is responsible for the dimerization as well as DNA-binding of BldD. Detailed inspection of the present results suggests that BldD function in a unique and complicated mode to totally regulate the diverse developmental stages of S. coelicolor.     

梭梭(Haloxylon ammodendron)生理与个体用水策略对降水改变的响应

随着全球变化的加剧,降水改变正导致荒漠生态系统中植物用水策略的适应性变化;对降水变化响应的种间差异性影响着荒漠植物群落组成。研究将生理生态与个体形态尺度相结合,调查中亚荒漠关键种梭梭Haloxylon ammodendron对降水变化导致的自然生境中水分条件改变的响应与适应。实验于2005年生长期开展,在古尔班通古特沙漠南缘原始盐生旱生荒漠中设置3个降水梯度（自然、双倍和无降水）;观测并比较不同降水条件下光合作用、蒸腾作用、叶水势、水分利用效率、地上生物量累积和根系分布的变化。结果表明,梭梭主要利用降水形成的浅层土壤水维持生存;有效的形态调节和较强的气孔控制是其维持光合能力以及适应降水变化的主要机制;降水增多对其产生正效应,预示着梭梭可能在未来种间竞争和群落演替中占有优势。     

Gas exchange and antioxidative compounds in young beech trees under free-air ozone exposure and comparisons to adult trees

Three-year-old beech (Fagus sylvatica) seedlings growing in containers were placed into the sun and shade crown of a mature beech stand exposed to ambient (1 x O(3)) and double ambient (2 x O(3)) ozone concentrations at a free-air exposure system ("Kranzberg Forst", Germany). Pigments, alpha-tocopherol, glutathione, ascorbate, and gas exchange were measured in leaves during 2003 (a drought year) and 2004 (an average year). Sun-exposed seedlings showed higher contents of antioxidants, xanthophylls, and beta-carotene and lower contents of chlorophyll, alpha-carotene, and neoxanthin than shade-exposed seedlings. In 2003 sun-exposed seedlings showed higher contents of carotenoids and total glutathione and lower net photosynthesis rates (A(max)) compared to 2004. O(3) exposure generally affected the content of chlorophyll, the xanthophyll cycle, and the intercellular CO(2) concentration (c(i)). Seedlings differed from the adjacent adult trees in most biochemical and physiological parameters investigated: Sun exposed seedlings showed higher contents of alpha-tocopherol and xanthophylls and lower contents of ascorbate, chlorophyll, neoxanthin, and alpha-carotene compared to adult trees. Shade exposed seedlings had lower contents of xanthophylls, alpha-carotene, and alpha-tocopherol than shade leaves of old-growth trees. In 2003, seedlings had higher A(max), stomatal conductance (g(s)), and c(i) under 2 x O(3) than adult trees. The results showed that shade acclimated beech seedlings are more sensitive to O(3), possibly due to a lower antioxidative capacity per O(3) uptake. We conclude that beech seedlings are uncertain surrogates for adult beech trees.     

Non-structural carbohydrates and nitrogen dynamics in mediterranean sub-shrubs: an analysis of the functional role of overwintering leaves

Previous studies have led to contrasting results about the role of overwintering leaves as storage sites, which is related to leaf longevity and life-form. The aim of this study was to evaluate the functional role of the leaves of four species of Mediterranean sub-shrubs, with different leaf phenology, as sources of nitrogen (N) and non-structural carbohydrates (NSC) for shoot growth. The seasonal dynamics of the concentrations and pools of N and NSC were assessed monthly in the leaves and woody organs of each species. Overwintering and spring leaves served as N and NSC sources for shoot growth in the evergreen species analyzed, providing up to 73 % and 324 % of the N demand for spring and autumn growth, respectively. Excess autumn N was stored in woody structures which contributed to the N and NSC requirements of spring growth. In the winter deciduous species, woody organs were the main N source for spring growth, while current photosynthesis from immature brachyblasts seemed to be the main carbon (C) source. Due to their short lifespan, overwintering and spring leaves did not show several translocation processes throughout their life time, their contribution to new growth being made during senescence. The successive exchange of leaf cohorts displayed by Mediterranean sub-shrubs might serve as a mechanism to recycle N and C between consecutive cohorts as plants perform the pheno-morphological changes needed to adapt their morphology to the seasonality of their environment.