Plutonium(IV) Reduction by the Metal-Reducing Bacteria Geobacter metallireducens GS15 and Shewanella oneidensis MR1

The bacterial reduction of actinides has been suggested as a possible remedial strategy for actinide-contaminated environments, and the bacterial reduction of Pu(VI/V) has the potential to produce highly insoluble Pu(IV) solid phases. However, the behavior of plutonium with regard to bacterial reduction is more complex than for other actinides because it is possible for Pu(IV) to be further reduced to Pu(III), which is relatively more soluble than Pu(IV). This work investigates the ability of the metal-reducing bacteria Geobacter metallireducens GS15 and Shewanella oneidensis MR1 to enzymatically reduce freshly precipitated amorphous Pu(IV) (OH)₄ [Pu(IV)(OH)_4(am)] and soluble Pu(IV)(EDTA). In cell suspensions without added complexing ligands, minor Pu(III) production was observed in cultures containing S. oneidensis, but little or no Pu(III) production was observed in cultures containing G. metallireducens. In the presence of EDTA, most of the Pu(IV)(OH)_4(am) present was reduced to Pu(III) and remained soluble in cell suspensions of both S. oneidensis and G. metallireducens. When soluble Pu(IV)(EDTA) was provided as the terminal electron acceptor, cell suspensions of both S. oneidensis and G. metallireducens rapidly reduced Pu(IV)(EDTA) to Pu(III)(EDTA) with nearly complete reduction within 20 to 40 min, depending on the initial concentration. Neither bacterium was able to use Pu(IV) (in any of the forms used) as a terminal electron acceptor to support growth. These results have significant implications for the potential remediation of plutonium and suggest that strongly reducing environments where complexing ligands are present may produce soluble forms of reduced Pu species.     

Predicting Secchi disk depth from average beam attenuation in a deep,ultra-clear lake

We addressed potential sources of error in estimating the water clarity of mountain lakes by investigating the use of beam transmissometer measurements to estimate Secchi disk depth. The optical properties Secchi disk depth (SD) and beam transmissometer attenuation (BA) were measured in Crater Lake (Crater Lake National Park, Oregon, USA) at a designated sampling station near the maximum depth of the lake. A standard 20 cm black and white disk was used to measure SD. The transmissometer light source had a nearly monochromatic wavelength of 660 nm and a path length of 25 cm. We created a SD prediction model by regression of the inverse SD of 13 measurements recorded on days when environmental conditions were acceptable for disk deployment with BA averaged over the same depth range as the measured SD. The relationship between inverse SD and averaged BA was significant and the average 95% confidence interval for predicted SD relative to the measured SD was ±1.6 m (range = −4.6 to 5.5 m) or ±5.0%. Eleven additional sample dates tested the accuracy of the predictive model. The average 95% confidence interval for these sample dates was ±0.7 m (range = −3.5 to 3.8 m) or ±2.2%. The 1996–2000 time-series means for measured and predicted SD varied by 0.1 m, and the medians varied by 0.5 m. The time-series mean annual measured and predicted SD’s also varied little, with intra-annual differences between measured and predicted mean annual SD ranging from −2.1 to 0.1 m. The results demonstrated that this prediction model reliably estimated Secchi disk depths and can be used to significantly expand optical observations in an environment where the conditions for standardized SD deployments are limited.     

Seasonal nutrient and plankton dynamics in a physical-biological model of Crater Lake

A coupled 1D physical-biological model of Crater Lake is presented. The model simulates the seasonal evolution of two functional phytoplankton groups, total chlorophyll, and zooplankton in good quantitative agreement with observations from a 10-year monitoring study. During the stratified period in summer and early fall the model displays a marked vertical structure: the phytoplankton biomass of the functional group 1, which represents diatoms and dinoflagellates, has its highest concentration in the upper 40 m; the phytoplankton biomass of group 2, which represents chlorophyta, chrysophyta, cryptomonads and cyanobacteria, has its highest concentrations between 50 and 80 m, and phytoplankton chlorophyll has its maximum at 120 m depth. A similar vertical structure is a reoccurring feature in the available data. In the model the key process allowing a vertical separation between biomass and chlorophyll is photoacclimation. Vertical light attenuation (i.e., water clarity) and the physiological ability of phytoplankton to increase their cellular chlorophyll-to-biomass ratio are ultimately determining the location of the chlorophyll maximum. The location of the particle maxima on the other hand is determined by the balance between growth and losses and occurs where growth and losses equal. The vertical particle flux simulated by our model agrees well with flux measurements from a sediment trap. This motivated us to revisit a previously published study by Dymond et al. (1996). Dymond et al. used a box model to estimate the vertical particle flux and found a discrepancy by a factor 2.5–10 between their model-derived flux and measured fluxes from a sediment trap. Their box model neglected the exchange flux of dissolved and suspended organic matter, which, as our model and available data suggests is significant for the vertical exchange of nitrogen. Adjustment of Dymond et al.’s assumptions to account for dissolved and suspended nitrogen yields a flux estimate that is consistent with sediment trap measurements and our model.     

Germ-line DNA copy number variation frequencies in a large North American population

Genomic copy number variation (CNV) is a recently identified form of global genetic variation in the human genome. The Affymetrix GeneChip 100 and 500 K SNP genotyping platforms were used to perform a large-scale population-based study of CNV frequency. We constructed a genomic map of 578 CNV regions, covering approximately 220 Mb (7.3%) of the human genome, identifying 183 previously unknown intervals. Copy number changes were observed to occur infrequently (<1%) in the majority (>93%) of these genomic regions, but encompass hundreds of genes and disease loci. This North American population-based map will be a useful resource for future genetic studies. Electronic supplementary material The online version of this article (doi:) contains supplementary material, which is available to authorized users.     

Correlation of carboxylic acid pKa to protein binding and antibacterial activity of a novel class of bacterial translation inhibitors

Previously we reported the discovery and initial optimization of a novel anthranilic acid derived class of antibacterial agents which suffered from extensive protein binding. This report describes efforts directed toward understanding the relationship of the acidity of the carboxylic acid with the extent of protein binding. The pK(a) of the acid was modified via the synthesis of a number of anthranilic acid analogs which vary the aromatic ring substituent at the 4-position. The pK(a) and HSA binding constants have been determined for each of the analogs. Our results indicate a correlation between pK(a) and HSA K(d). The physical properties and antibacterial activities will be discussed as well as how these results help address the protein binding issue with this series of compounds.     

Novel benzodifuran analogs as potent 5-HT2A receptor agonists with ocular hypotensive activity

A series of 8-substituted benzodifuran analogs was prepared and evaluated for 5-HT(2A) receptor binding and activation. Several compounds containing ether and ester functionality were found to be potent agonists. Topical ocular administration of 5, 18, and 25 effectively reduced intra-ocular pressure in the hypertensive cynomolgus monkey eye in the range of 25-37%.     

A whole-genome RNAi Screen for C. elegans miRNA pathway genes

BACKGROUND: miRNAs are an abundant class of small, endogenous regulatory RNAs. Although it is now appreciated that miRNAs are involved in a broad range of biological processes, relatively little is known about the actual mechanism by which miRNAs downregulate target gene expression. An exploration of which protein cofactors are necessary for a miRNA to downregulate a target gene should reveal more fully the molecular mechanisms by which miRNAs are processed, trafficked, and regulate their target genes. RESULTS: A weak allele of the C. elegans miRNA gene let-7 was used as a sensitized genetic background for a whole-genome RNAi screen to detect miRNA pathway genes, and 213 candidate miRNA pathway genes were identified. About 2/3 of the 61 candidates with the strongest phenotype were validated through genetic tests examining the dependence of the let-7 phenotype on target genes known to function in the let-7 pathway. Biochemical tests for let-7 miRNA production place the function of nearly all of these new miRNA pathway genes downstream of let-7 expression and processing. By monitoring the downregulation of the protein product of the lin-14 mRNA, which is the target of the lin-4 miRNA, we have identified 19 general miRNA pathway genes. CONCLUSIONS: The 213 candidate miRNA pathway genes identified could act at steps that produce and traffic miRNAs or in downstream steps that detect miRNA::mRNA duplexes to regulate mRNA translation. The 19 validated general miRNA pathway genes are good candidates for genes that may define protein cofactors for sorting or targeting miRNA::mRNA duplexes, or for recognizing the miRNA base-paired to the target mRNA to downregulate translation.     

Synthesis and biodistribution of new radiolabeled high-affinity choline transporter inhibitors [11C]hemicholinium-3 and [18F]hemicholinium-3

The high-affinity choline transporter (CHT1) system is an attractive target for the development of positron emission tomography (PET) biomarkers to probe brain, cardiac, and cancer diseases. An efficient and convenient synthesis of new radiolabeled CHT1 inhibitors [(11)C]hemicholinium-3 and [(18)F]hemicholinium-3 by solid-phase extraction (SPE) technique using a cation-exchange CM Sep-Pak cartridge has been well developed. The preliminary evaluation of both tracers through biodistribution studies in 9L-glioma rats has been performed, and the uptakes in the heart and tumor were observed, while very low brain uptake was seen.     

The structural topology of wild-type phospholamban in oriented lipid bilayers using 15N solid-state NMR spectroscopy

For the first time, 15N solid-state NMR experiments were conducted on wild-type phospholamban (WT-PLB) embedded inside mechanically oriented phospholipid bilayers to investigate the topology of its cytoplasmic and transmembrane domains. 15N solid-state NMR spectra of site-specific 15N-labeled WT-PLB indicate that the transmembrane domain has a tilt angle of 13 degrees+/-6 degrees with respect to the POPC (1-palmitoyl-2-oleoyl-sn-glycero-phosphocholine) bilayer normal and that the cytoplasmic domain of WT-PLB lies on the surface of the phospholipid bilayers. Comparable results were obtained from site-specific 15N-labeled WT-PLB embedded inside DOPC/DOPE (1,2-dioleoyl-sn-glycero-3-phosphocholine/1,2-dioleoyl-sn-glycero-3-phosphoethanolamine) mechanically oriented phospholipids' bilayers. The new NMR data support a pinwheel geometry of WT-PLB, but disagree with a bellflower structure in micelles, and indicate that the orientation of the cytoplasmic domain of the WT-PLB is similar to that reported for the monomeric AFA-PLB mutant.     

Mating trials validate the use of DNA barcoding to reveal cryptic speciation of a marine bryozoan taxon

Despite increasing threats to the marine environment, only a fraction of the biodiversity of the oceans has been described, owing in part to the widespread occurrence of cryptic species. DNA-based barcoding through screening of an orthologous reference gene has been proposed as a powerful tool to uncover biological diversity in the face of dwindling taxonomic expertise and the limitations of traditional species identification. Although DNA barcoding should be particularly useful in the sea, given the prevalence of marine cryptic species, the link between taxa identified through DNA barcodes and reproductively isolated taxa (biological species) has rarely been explicitly tested. Here, we use an integrated framework comparing breeding compatibility, morphology and mitochondrial (cytochrome c oxidase 1) and nuclear (elongation factor-1-alpha) DNA sequence variation among globally distributed samples of the cosmopolitan marine bryozoan Celleporella hyalina (L.). Our results reveal that C. hyalina comprises numerous deep, mostly allopatric, genetic lineages that are reproductively isolated, yet share very similar morphology, indicating rampant cryptic speciation. The close correspondence between genetic lineages and reproductively isolated taxa in the context of minimal morphological change suggests that DNA barcoding will play a leading role in uncovering the hidden biodiversity of the oceans and that the sole use of morphologically based taxonomy would grossly underestimate the number of marine species.