Molecular analysis of three Aeromonas hydrophila AH-3 (serotype O34) lipopolysaccharide core biosynthesis gene clusters

By the isolation of three different Aeromonas hydrophila strain AH-3 (serotype O34) mutants with an altered lipopolysaccharide (LPS) migration in gels, three genomic regions encompassing LPS core biosynthesis genes were identified and characterized. When possible, mutants were constructed using each gene from the three regions, containing seven, four, and two genes (regions 1 to 3, respectively). The mutant LPS core structures were elucidated by using mass spectrometry, methylation analysis, and comparison with the full core structure of an O-antigen-lacking AH-3 mutant previously established by us. Combining the gene sequence and complementation test data with the structural data and phenotypic characterization of the mutant LPSs enabled a presumptive assignment of all LPS core biosynthesis gene functions in A. hydrophila AH-3. The three regions and the genes contained are in complete agreement with the recently sequenced genome of A. hydrophila ATCC 7966. The functions of the A. hydrophila genes waaC in region 3 and waaF in region 2 were completely established, allowing the genome annotations of the two heptosyl transferase products not previously assigned. Having the functions of all genes involved with the LPS core biosynthesis and most corresponding single-gene mutants now allows experimental work on the role of the LPS core in the virulence of A. hydrophila.     

Habitat choice in rotifera communities of three shallow lakes: impact of macrophyte substratum and season

The distribution of rotifer communities between emergent (Typha angustifolia) and submerged (Chara tomentosa) vegetation and a comparatively open water zone were compared during the spring, summer and autumn seasons at three macrophyte-dominated lakes. This survey identified 107 rotifera species of which 58% of the taxonomical structure was common for the three examined lakes. Stoneworts with a more complicated spatial and morphological structure (having a much longer stem length than the narrow leaf cattail), supported higher rotifer densities. The stem length appeared to be the best predictor of all the macrophyte parameters and pH and chlorophyll a for the chemical variables, for explaining the variation of rotifer densities using the stepwise multiple forward regressions. The distribution of pelagic species did not differ between particular sites, which may have reflected the behavioural requirements of those rotifers. Some of them remained in the open water zone while others seeking an anti-predator refuge, gathered within macrophyte stands during the daytime. Moreover, there were nine Chara-associated species recorded and only one Typha-associated species was noted. The similarity of rotifer communities was most strongly influenced by particular habitat and season. Guest editors: S. S. S. Sarma, R. D. Gulati, R. L. Wallace, S. Nandini, H. J. Dumont & R. Rico-Martínez Advances in Rotifer Research     

Trisomy 17 in a baboon (Papio hamadryas) with polydactyly, patent foramen ovale and pyelectasis

Trisomy 13 in humans is the third most common autosomal abnormality at birth, after trisomy 21 and trisomy 18. It has a reported incidence of between 1:5,000 and 1:30,000 live births. It is associated with multiple abnormalities, many of which shorten lifespan. We describe here the first reported case of a baboon (Papio hamadryas) with trisomy of chromosome 17, which is homologous to human chromosome 13. The trisomic infant was born to a consanguineous pair of baboons and had morphological characteristics similar to those observed in human trisomy 13, including bilateral polydactyly in the upper limbs, a patent foramen ovale, and pyelectasis. Molecular DNA analysis using human chromosome 13 markers was consistent with the affected infant inheriting two copies of chromosome 17 derived from the same parental chromosome. This trisomy was, therefore, due to either an error in meiosis II or the result of postzygotic nondisjunction. The parental origin, however, could not be determined.     

Development of Vacuoles and Vacuolar H+-ATPase Activity under Extremely High CO2 Conditions in Chiorococcum littorale Cells

Abstract: The number and cross-sectional area of vacuoles in Chlorococcum littorale cells visualized with a differential interfer ence fluorescence microscope increased after their transfer from air to 40% CO₂. An immunological observation indicated that the level of subunit B of vacuolar H*ATPase also increased under 40% CO₂ conditions. The activity of nitrate-sensitive ATP-ase associated with the vacuolar membrane was 2–fold higher in 40% CO₂-_-grown cells than in air-grown cells. The effects of inhi bitors on the ATPase activity confirmed that these activities were derived from vacuolar-type H-ATPase. These results sug gest that vacuole development associated with that of vacuolar H⁺-ATPase occurred during the acclimatization of C. littorale cells to extremely high CO₂ conditions.     

Antimicrobial polymers: mechanism of action,factors of activity,and applications

Complex epidemiological situation, nosocomial infections, microbial contamination, and infection risks in hospital and dental equipment have led to an ever-growing need for prevention of microbial infection in these various areas. Macromolecular systems, due to their properties, allow one to efficiently use them in various fields, including the creation of polymers with the antimicrobial activity. In the past decade, the intensive development of a large class of antimicrobial macromolecular systems, polymers, and copolymers, either quaternized or functionalized with bioactive groups, has been continued, and they have been successfully used as biocides. Various permanent microbicidal surfaces with non-leaching polymer antimicrobial coatings have been designed. Along with these trends, new moderately hydrophobic polymer structures have been synthesized and studied, which contain protonated primary or secondary/tertiary amine groups that exhibited rather high antimicrobial activity, often unlike their quaternary analogues. This mini-review briefly highlights and summarizes the results of studies during the past decade and especially in recent years, which concern the mechanism of action of different antimicrobial polymers and non-leaching microbicidal surfaces, and factors influencing their activity and toxicity, as well as major applications of antimicrobial polymers.     

Use of simulated data sets to evaluate the fidelity of metagenomic processing methods

Metagenomics is a rapidly emerging field of research for studying microbial communities. To evaluate methods presently used to process metagenomic sequences, we constructed three simulated data sets of varying complexity by combining sequencing reads randomly selected from 113 isolate genomes. These data sets were designed to model real metagenomes in terms of complexity and phylogenetic composition. We assembled sampled reads using three commonly used genome assemblers (Phrap, Arachne and JAZZ), and predicted genes using two popular gene-finding pipelines (fgenesb and CRITICA/GLIMMER). The phylogenetic origins of the assembled contigs were predicted using one sequence similarity-based (blast hit distribution) and two sequence composition-based (PhyloPythia, oligonucleotide frequencies) binning methods. We explored the effects of the simulated community structure and method combinations on the fidelity of each processing step by comparison to the corresponding isolate genomes. The simulated data sets are available online to facilitate standardized benchmarking of tools for metagenomic analysis.     

Changes in cytokine production and morphology of murine lymphoma NK/Ly cells in course of tumor development

The main goal of this study was to evaluate if specific cytokine expression in the NK/Ly lymphoma cells might be involved in development of intoxication in the tumor-bearing animals. RT-PCR analysis was used to study an expression of mRNA coding for IL-1α, IL-6, TNF-α, TNF-β and VEGF. ELISA was used to evaluate IL-6 and IFN-γ concentration in the ascitic fluid. Cytomorphological investigation of tumor cells was done after standard Romanovsky-Giemsa staining, and chromatin staining was performed with hematoxyline and neutral red. Lactate dehydrogenase and acid phosphatase release from tumor cells was estimated. It was revealed that the level of mRNA coding for VEGF and IL-6 was significant in the lymphoma cells. The level of VEGF mRNA was initially high and did not change during tumor progression, while the level of expression of IL6 mRNA was low at the initial stages of tumor growth and markedly increased (up to 5-fold) at the terminal stages. The obtained data on IL-6 mRNA expression were confirmed by ELISA, which showed more than 6-fold increase (from 90 to 570 pg/ml) in the IL-6 concentration in the ascitic fluid at late stages of NK/Ly tumor development. On the contrary to IL-6, concentration of IFN-γ in the ascitic fluid was very high at early stages of tumor development (1,000 pg/ml) and it markedly decreased (up to 30-fold, 30 pg/ml) at the terminal stages of tumor development. The high levels of IL-6 mRNA in tumor cells and IL-6 content in extracellular medium correlated with cell deterioration, as revealed by cytomorphologic study and the release of intracellular enzymes into extracellular medium. We suggest that an enhanced production and release of IL-6 by lymphoma cells can cause intoxication and exhaustion of the organism observed at terminal stages of tumor growth.     

Effect of bedaquiline on the functions of rat liver mitochondria

The paper considers the effects of bedaquiline (BDQ), an antituberculous preparation of the new generation, on rat liver mitochondria. It was shown that 50?μM BDQ inhibited mitochondrial respiration measured with substrates of complexes I and II (glutamate/malate and succinate/rotenone systems respectively) in the states V₃ and V_DNP. At the same time, at concentrations below 50?μM, BDQ slightly stimulated respiration with substrates of complex I in the state V₂. BDQ was also found to suppress, in a dose-dependent manner, the activity of complex II and the total activity of complexes II?+?III of the mitochondrial transport chain. It was discovered that at concentrations up to 10?μM, BDQ inhibited H₂O₂ production in mitochondria. BDQ (10–50?μM) suppressed the opening of Ca²⁺-dependent CsA-sensitive mitochondrial permeability transition pore. The latter was revealed experimentally as the inhibition of Ca²⁺/P_i-dependent swelling of mitochondria, suppression of cytochrome c release, and an increase in the Ca²⁺ capacity of the organelles. BDQ also decreased the rate of mitochondrial energy-dependent K⁺ transport, which was evaluated by the energy-dependent swelling of mitochondria in a K⁺ buffer and DNP-induced K⁺ efflux from the organelles. The possible mechanisms of BDQ effect of rat liver mitochondria are discussed.     

Complete genome sequence of Hirschia baltica type strain (IFAM 1418(T))

The family Hyphomonadaceae within the Alphaproteobacteria is largely comprised of bacteria isolated from marine environments with striking morphologies and an unusual mode of cell growth. Here, we report the complete genome sequence Hirschia baltica, which is only the second a member of the Hyphomonadaceae with a published genome sequence. H. baltica is of special interest because it has a dimorphic life cycle and is a stalked, budding bacterium. The 3,455,622 bp long chromosome and 84,492 bp plasmid with a total of 3,222 protein-coding and 44 RNA genes were sequenced as part of the DOE Joint Genome Institute Program CSP 2008.