Searching for new bacterial species that break down polyaromatic hydrocarbons in coastal and oceanic waters

Polyaromatic hydrocarbons (PAHs) are recognized as priority pollutants that can negatively impact the environment and human health. These chemicals enter the environment from both natural and anthropogenic sources where they can persist and cause detrimental effects to biological systems. Like with most other environmental pollutants, the most important mechanism by which PAHs are removed occurs through the activities of certain types of bacteria (i.e. the PAH degraders). In recent years we have dramatically increased our knowledge on the types of bacteria playing key roles in the removal of PAHs in the marine environment. However, there remains a lack of complete understanding regarding the full breadth of species and their ecological functioning in PAH removal from contaminated waters. This paper discusses efforts to identify new species of marine bacteria that degrade PAHs using a DNA-based targeted approach called stable-isotope probing (DNA-SIP). In addition to providing greater insight on the identity and functioning of the marine microbial world, this information is anticipated to enhance our design of more efficient ways in cleaning up marine hydrocarbon pollution.     

Eph receptor function is modulated by heterooligomerization of A and B type Eph receptors

Eph receptors interact with ephrin ligands on adjacent cells to facilitate tissue patterning during normal and oncogenic development, in which unscheduled expression and somatic mutations contribute to tumor progression. EphA and B subtypes preferentially bind A- and B-type ephrins, respectively, resulting in receptor complexes that propagate via homotypic Eph-Eph interactions. We now show that EphA and B receptors cocluster, such that specific ligation of one receptor promotes recruitment and cross-activation of the other. Remarkably, coexpression of a kinase-inactive mutant EphA3 with wild-type EphB2 can cause either cross-activation or cross-inhibition, depending on relative expression. Our findings indicate that cellular responses to ephrin contact are determined by the EphA/EphB receptor profile on a given cell rather than the individual Eph subclass. Importantly, they imply that in tumor cells coexpressing different Ephs, functional mutations in one subtype may cause phenotypes that are a result of altered signaling from heterotypic rather from homotypic Eph clusters.     

Kinetic characterization of P-type membrane ATPase from Streptococcus mutans

The proton translocating membrane ATPase of oral streptococci has been implicated in cytoplasmatic pH regulation, acidurance and cariogenicity. Studies have confirmed that Streptococcus mutans is the most frequently detected species in dental caries. A P-type ATPase that can act together with F₁F_o-ATPase in S. mutans membrane has been recently described. The main objective of this work is to characterize the kinetic of ATP hydrolysis of this P-type ATPase. The optimum pH for ATP hydrolysis is around 6.0. The dependence of P-type ATPase activity on ATP concentration reveals high (K_0.5=0.27 mM) and low (K_0.5=3.31 mM) affinity sites for ATP, exhibiting positive cooperativity and a specific activity of about 74 U/mg. Equimolar concentrations of ATP and magnesium ions display a behavior similar to that described for ATP concentration in Mg²⁺ saturating condition (high affinity site, K_0.5=0.10 mM, and low affinity site, K_0.5=2.12 mM), exhibiting positive cooperativity and a specific activity of about 68 U/mg. Sodium, potassium, ammonium, calcium and magnesium ions stimulate the enzyme, showing a single saturation curve, all exhibiting positive cooperativities, whereas inhibition of ATPase activity is observed for zinc ions and EDTA. The kinetic characteristics reveal that this ATPase belongs to type IIIA, like the ones found in yeast and plants.     

The specificity of the influenza B virus hemagglutinin receptor binding pocket: what does it bind to?

The influenza surface glycoprotein hemagglutinin (HA) binds to sialylglycoproteins and sialylglycolipids on the surface of host cells. These sialyl‐glycans, usually linked to galactose in either α2,6 or α2,3 configurations, are the receptors for the viral HA, the binding to which promotes viral attachment, membrane fusion, and internalization of the virus. This review examines all of the available receptor binding data on the influenza B HA and provides a structure recognition perspective for the receptor binding preferences of influenza B virus HA regional and egg‐adapted variants. Overall, the review serves as an up‐to‐date compendium of the literature binding data, and the presented discussions assist the reader in reaching a consensus understanding of the receptor specificity determinants for the influenza B HA. Copyright © 2013 John Wiley & Sons, Ltd.     

Revised nomenclature for transposable genetic elements

Transposable DNA elements occur naturally in the genomes of nearly all species of prokaryotes. A proposal for a uniform transposable element nomenclature was published prominently in the 1970s but is not, at present, available online even in abstract form, and many of the newly discovered elements have been named without reference to it. We propose here an updated version of the original nomenclature system for all of the various types of prokaryotic, autonomous, transposable elements excluding insertion sequences, for which a nomenclature system already exists. The use of this inclusive and sequential Tn numbering system for transposable elements, as described here, recognizes the ease of interspecies spread of individual elements, and allows for the naming of mosaic elements containing segments from two or more previously described types of transposons or plasmids. It will guard against any future need to rename elements following changes in bacterial nomenclature which occurs constantly with our increased understanding of bacterial phylogenies and taxonomic groupings. It also takes into account the increasing importance of metagenomic sequencing projects and the continued identification of new mobile elements from unknown hosts.     

Measuring physical traits of primates remotely: the use of parallel lasers

Physical traits, such as body size, and processes like growth can be used as indices of primate health and can add to our understanding of life history and behavior. Accurately measuring physical traits in the wild can be challenging because capture is difficult, disrupts animals, and may cause injury. To measure physical traits of arboreal primates remotely, we adapted a parallel laser technique that has been used with terrestrial and marine mammals. Two parallel lasers separated by a known distance (4 cm) and mounted onto a digital camera are projected onto an animal. When a photograph is taken, the laser projections on the target provide a scale bar. We validated the technique for measuring the physical traits of identifiable red colobus monkeys (Procolobus rufomitratus) in Kibale National Park, Uganda. First, we photographed the tails of monkeys with laser projections and compared these with measurements previously obtained when the animals were captured. Second, we manually measured the distance between two markers placed on tree branches at similar heights to those used by monkeys, and compared them with the measurements obtained through digital photographs of the markers with parallel laser projections. The mean tail length of the monkeys via manual measurements was 63.3+/-4.4 cm, and via remote measurements was 63.0+/-4.1 cm. The mean distance between the markers on tree branches via manual measurements was 13.8+/-3.59 cm, and via remote measurements was 13.9+/-3.58 cm. The mean error using parallel lasers was 1.7% in both cases. Although the needed precision will depend on the question asked, our results suggest that sufficiently precise measurements of physical traits or substrates of arboreal primates can be obtained remotely using parallel lasers.     

Methylation of the DFNA5 increases risk of lymph node metastasis in human breast cancer

The pathogenesis of breast cancer involves multiple genetic and epigenetic events. In this study, we report an epigenetic alteration of DFNA5 in human breast cancer. DFNA5 gene was silenced in breast cancer cell lines that were methylated in the DFNA5 promoter, and restored by treatment with the demethylating agent, 5-aza-dC, and gene knock-down of DFNA5 increased cellular invasiveness in vitro. The mRNA expression of DFNA5 in breast cancer tissues was down-regulated as compared to normal tissues. Moreover, the DFNA5 promoter was found to be methylated in primary tumor tissues with high frequency (53%, 18/34). Quantitative methylation-specific PCR of DFNA5 clearly discriminated primary breast cancer tissues from normal breast tissues (15.3%, 2/13). Moreover, methylation status of DFNA5 was correlated with lymph node metastasis in breast cancer patients. Our data implicate DFNA5 promoter methylation as a novel molecular biomarker in human breast cancer.     

Role of a putative polysaccharide locus in Bordetella biofilm development

Bordetellae are gram-negative bacteria that colonize the respiratory tracts of animals and humans. We and others have recently shown that these bacteria are capable of living as sessile communities known as biofilms on a number of abiotic surfaces. During the biofilm mode of existence, bacteria produce one or more extracellular polymeric substances that function, in part, to hold the cells together and to a surface. There is little information on either the constituents of the biofilm matrix or the genetic basis of biofilm development by Bordetella spp. By utilizing immunoblot assays and by enzymatic hydrolysis using dispersin B (DspB), a glycosyl hydrolase that specifically cleaves the polysaccharide poly-beta-1,6-N-acetyl-D-glucosamine (poly-beta-1,6-GlcNAc), we provide evidence for the production of poly-beta-1,6-GlcNAc by various Bordetella species (Bordetella bronchiseptica, B. pertussis, and B. parapertussis) and its role in their biofilm development. We have investigated the role of a Bordetella locus, here designated bpsABCD, in biofilm formation. The bps (Bordetella polysaccharide) locus is homologous to several bacterial loci that are required for the production of poly-beta-1,6-GlcNAc and have been implicated in bacterial biofilm formation. By utilizing multiple microscopic techniques to analyze biofilm formation under both static and hydrodynamic conditions, we demonstrate that the bps locus, although not essential at the initial stages of biofilm formation, contributes to the stability and the maintenance of the complex architecture of Bordetella biofilms.