Construction and characterization of an absolute deletion mutant of Escherichia coli ribonuclease II

Abstract The degradation of mRNA plays a central role in the control of protein synthesis. In Escherichia coli , the rnb gene encodes ribonuclease II (RNase II), one of the two main exonucleases involved in mRNA decay. We have constructed strain CMA201, in which the rnb promoter region and the gene were deleted from the chromosome and replaced by a tet^tr cassette. This is the first rnb absolute deletion mutant that shows the complete absence of rnb -specific mRNA. This strain has growth characteristics similar to the wild-type, even though it has no RNase II activity, and it should be useful in studies of mRNA metabolism.     

Molecular architecture of the ribosome‐bound Hepatitis C Virus internal ribosomal entry site RNA

Internal ribosomal entry sites (IRESs) are structured cis‐acting RNAs that drive an alternative, cap‐independent translation initiation pathway. They are used by many viruses to hijack the translational machinery of the host cell. IRESs facilitate translation initiation by recruiting and actively manipulating the eukaryotic ribosome using only a subset of canonical initiation factor and IRES transacting factors. Here we present cryo‐EM reconstructions of the ribosome 80S‐ and 40S‐bound Hepatitis C Virus (HCV) IRES. The presence of four subpopulations for the 80S•HCV IRES complex reveals dynamic conformational modes of the complex. At a global resolution of 3.9 Å for the most stable complex, a derived atomic model reveals a complex fold of the IRES RNA and molecular details of its interaction with the ribosome. The comparison of obtained structures explains how a modular architecture facilitates mRNA loading and tRNA binding to the P‐site. This information provides the structural foundation for understanding the mechanism of HCV IRES RNA‐driven translation initiation.     

Effects of crude oil on survival,morphology, and anatomy of two aquatic macrophytes from the Amazon floodplains

Aquatic herbaceous macrophytes grow in profusion in the Amazon fertile varzea floodplains. A large number of species occur but only a few are particularly abundant, supporting food chains, contributing substantially to carbon and nutrient cycles. Their growth and role in the ecosystem depend, among other, on its life cycles and habits, floating or semi-aquatic. Although in the last decades, petroliferous activity intensified in the Central Amazon region and so did oil spills, the effect of petroleum on the native aquatic plants is unknown. The present study was designed to test experimentally the survival and morpho-anatomical modifications of the free floating water hyacinth Eichhornia crassipes and the semi-aquatic grass Echinochloa polystachya to 10 different concentrations of crude oil. Higher concentrations of crude oil caused the mortality in both species; however, lethal dose (LD₅₀) values showed that E. polystachya was more sensitive than E. crassipes. Despite the higher tolerance of E. crassipes, the inhibition of root and leaf growth as well as anatomical modifications in leaves were registered in higher concentrations. Additionally, the oil caused a reduction in leaf numbers in both species. Although mortality of the floating species was lower, it may increases over time, since important alterations in morphology and anatomy occurred. These results show that oil spills in the Amazon varzea can cause severe alterations in the aquatic flora and in the floodplain dynamics.     

Electrochemical sensing of the behaviour of oligonucleotide lipoplexes at charged interfaces

Complexes between short oligodeoxynucleotides (ODN) with a variable dG(x)dC(y) base composition and liposomes composed of the cationic lipid DOTAP (ODN lipoplexes) were studied by differential pulse voltammetry at a glassy carbon electrode. Since lipoplexes are spontaneously formed by electrostatic interactions, the objective of the voltammetric study was to investigate their behaviour at the electrode surface/solution interface. It was verified that the peak current in the voltammograms for ODN lipoplexes was due to guanosine oxidation and that it was influenced both by the applied adsorption potential and the lipoplex (+/-) charge ratio used. It was found that for low ODN lipoplexes (+/-) charge ratios the peak current obtained was enhanced when compared to that registered with free ODN for the same concentration. This allowed a higher sensitivity in the determination of ODN by differential pulse voltammetry and a limit of detection of 5.5 ng/mL was achieved. A model that explains the organisation of ODN lipoplexes at the electrode surface/solution interface is proposed. The electrochemical results presented account for a better physicochemical characterisation of lipoplexes at charged interfaces, which can be important for the understanding and development of gene therapy vectors based on ODN lipoplexes.     

Very high productivity of the C4 aquatic grass Echinochloa polystachya in the Amazon floodplain confirmed by net ecosystem CO2 flux measurements

Fluxes of CO₂ and H₂O vapour from dense stands of the C4 emergent macrophyte grass Echinochloa polystachya were measured by eddy covariance in both the low water (LW) and high water (HW, flooded) phases of the annual Amazon river cycle at Manaus, Brazil. Typical clear-sky midday CO₂ uptake rates by the vegetation stand (including detritus, sediment or water surface) were 30 and 35 µmol CO₂ (ground) m^-2 s^-1 in the LW and HW periods, respectively. A rectangular hyperbola model fitted the responses of "instantaneous" (20- or 30-min average) net CO₂ exchange rates to incident photosynthetic photon flux densities (PFD) well. Stand evaporation rates were linearly related to PFD. The major difference in CO₂ uptake rates between the two periods was the larger respiration flux during LW due to the CO₂ efflux from sediment, roots and litter. Integrated 20- or 30-min fluxes were used to derive relationships between daily CO₂ and H₂O vapour fluxes and incident radiation. The daily CO₂ fluxes were almost linearly related to incident radiation, but there was evidence of saturation at the highest daily radiation totals. Annual productivity estimated from the daily model in 1996-1997 agreed closely with that previously estimated for 1985-1986 from a leaf-scale photosynthetic model, but were some 15% less than those derived at that time from biomass harvests. Both CO₂ uptake and water use efficiency were comparable with those found in fertilised maize fields in warm temperate conditions.     

Treatment with apolipoprotein A-1 mimetic peptide reduces lupus-like manifestations in a murine lupus model of accelerated atherosclerosis

Introduction

The purpose of this study was to evaluate the effects of L-4F, an apolipoprotein A-1 mimetic peptide, alone or with pravastatin, in apoE^-/-Fas^-/-C57BL/6 mice that spontaneously develop immunoglobulin G (IgG) autoantibodies, glomerulonephritis, osteopenia, and atherosclerotic lesions on a normal chow diet.

Methods

Female mice, starting at eight to nine weeks of age, were treated for 27 weeks with 1) pravastatin, 2) L-4F, 3) L-4F plus pravastatin, or 4) vehicle control, followed by disease phenotype assessment.

Results

In preliminary studies, dysfunctional, proinflammatory high-density lipoproteins (piHDL) were decreased six hours after a single L-4F, but not scrambled L-4F, injection in eight- to nine-week old mice. After 35 weeks, L-4F-treated mice, in the absence/presence of pravastatin, had significantly smaller lymph nodes and glomerular tufts (P_{L, LP} < 0.05), lower serum levels of IgG antibodies to double stranded DNA (dsDNA) (P_L < 0.05) and oxidized phospholipids (oxPLs) (P_{L, LP} < 0.005), and elevated total and vertebral bone mineral density (P_{L, LP} < 0.01) compared to vehicle controls. Although all treatment groups presented larger aortic root lesions compared to vehicle controls, enlarged atheromas in combination treatment mice had significantly less infiltrated CD68⁺ macrophages (P_LP < 0.01), significantly increased mean α-actin stained area (P_LP < 0.05), and significantly lower levels of circulating markers for atherosclerosis progression, CCL19 (P_{L, LP} < 0.0005) and VCAM-1 (P_L < 0.0002).

Conclusions

L-4F treatment, alone or with pravastatin, significantly reduced IgG anti-dsDNA and IgG anti-oxPLs, proteinuria, glomerulonephritis, and osteopenia in a murine lupus model of accelerated atherosclerosis. Despite enlarged aortic lesions, increased smooth muscle content, decreased macrophage infiltration, and decreased pro-atherogenic chemokines in L-4F plus pravastatin treated mice suggest protective mechanisms not only on lupus-like disease, but also on potential plaque remodeling in a murine model of systemic lupus erythematosus (SLE) and accelerated atherosclerosis.     

A classification of major natural habitats of Amazonian white-water river floodplains (várzeas)

Most countries sharing the Amazon basin have signed the Ramsar Convention on Wetlands of International Importance but still lack complete wetland inventories, classification systems, and management plans. Amazonian wetlands vary considerably with respect to hydrology, water and soil fertility, vegetation cover, diversity in plant and animal species and primary and secondary productivity. Here, we propose a classification system of major natural habitats of Amazonian white-water river floodplains (várzeas) based on hydrological, water and soil chemistry and biological parameters. The Amazonian várzea is one of the largest Amazonian wetlands. It is exceptionally rich in plant and animal species and plays important roles in landscape history, evolution, hydrology and biogeochemical cycles of the Amazon basin. Most of Amazonia??s rural population lives in or along the várzea, emphasizing the economic importance of its natural resources. Our classification indicates five major systems, which are subdivided into 10 main habitats and up to 40 functional (vegetation) units of which the most important mesohabitats are described. We understand this classification as a dynamic system, as it is open to the inclusion of future research attempts and habitats without affecting the entire classification system. Our classification may be used for scientific purposes, such as comparative studies on biomass, productivity, biogeochemical cycles and biodiversity. Also, because the classification builds on habitat types and/or vegetation and functional units already distinguished by the local population it may be especially useful in guiding intelligent use of várzea habitat for specific management activities, such as agriculture, animal husbandry, forestry, fisheries, and conservation.     

Tree species composition and diversity gradients in white-water forests across the Amazon Basin

Aim Attention has increasingly been focused on the floristic variation within forests of the Amazon Basin. Variations in species composition and diversity are poorly understood, especially in Amazonian floodplain forests. We investigated tree species composition, richness and α diversity in the Amazonian white‐water (várzea) forest, looking particularly at: (1) the flood‐level gradient, (2) the successional stage (stand age), and (3) the geographical location of the forests. Location Eastern Amazonia, central Amazonia, equatorial western Amazonia and the southern part of western Amazonia. Methods The data originate from 16 permanent várzea forest plots in the central and western Brazilian Amazon and in the northern Bolivian Amazon. In addition, revised species lists of 28 várzea forest inventories from across the Amazon Basin were used. Most important families and species were determined using importance values. Floristic similarity between plots was calculated to detect similarity variations between forest types and over geographical distances. To check for spatial diversity gradients, α diversity (Fisher) of the plots was correlated with stand age, longitudinal and latitudinal plot location, and flood‐level gradient. Results More than 900 flood‐tolerant tree species were recorded, which indicates that Amazonian várzea forests are the most species‐rich floodplain forests worldwide. The most important plant families recorded also dominate most Neotropical upland forests, and c. 31% of the tree species listed also occur in the uplands. Species distribution and diversity varied: (1) on the flood‐level gradient, with a distinct separation between low‐várzea forests and high‐várzea forests, (2) in relation to natural forest succession, with species‐poor forests in early stages of succession and species‐rich forests in later stages, and (3) as a function of geographical distance between sites, indicating an increasing α diversity from eastern to western Amazonia, and simultaneously from the southern part of western Amazonia to equatorial western Amazonia. Main conclusions The east‐to‐west gradient of increasing species diversity in várzea forests reflects the diversity patterns also described for Amazonian terra firme. Despite the fine‐scale geomorphological heterogeneity of the floodplains, and despite high disturbance of the different forest types by sedimentation and erosion, várzea forests are dominated by a high proportion of generalistic, widely distributed tree species. In contrast to high‐várzea forests, where floristic dissimilarity increases significantly with increasing distance between the sites, low‐várzea forests can exhibit high floristic similarity over large geographical distances. The high várzea may be an important transitional zone for lateral immigration of terra firme species to the floodplains, thus contributing to comparatively high species richness. However, long‐distance dispersal of many low‐várzea trees contributes to comparatively low species richness in highly flooded low várzea.     

Voltammetric determination of gamma radiation-induced DNA damage

Homopolydeoxyribonucleotides, poly[dGuo], poly[dAdo], poly[dThd], and poly[dCyd], and calf thymus single-stranded DNA (ssDNA) and double-stranded DNA (dsDNA) aqueous solutions previously exposed to gamma radiation doses between 2 and 35 Gy, were studied by differential pulse voltammetry using a glassy carbon electrode. The interpretation of the voltammetric data was also supported by the electrophoretic migration profile obtained for the same ssDNA and dsDNA gamma-irradiated samples by nondenaturing agarose gel electrophoresis. The generation of 8-oxo-7,8-dihydroguanine, 2,8-dihydroxyadenine, 5-formyluracil, base-free sites, and single- and double-stranded breaks in the gamma-irradiated DNA samples was detected voltammetrically, with the amount depending on the irradiation time. It was found that the current peaks obtained for 8-oxoguanine increase linearly with the radiation dose applied to the nucleic acid sample, and values between 8 and 446 8-oxo-7,8-dihydroguanine (8-oxoGua) per 10(6) guanines per Gy were obtained according to the nucleic acid sample. The results showed that voltammetry can be used for monitoring and simultaneously characterizing different kinds of DNA damage caused by gamma radiation exposure.