Microbial degradation of petroleum hydrocarbons in a polluted tropical stream

Summary Crude oil degradation was observed in water samples from three sites along the course of a polluted stream in Lagos, Nigeria. Consistent increase and decrease in the total viable counts (TVCs) of indigenous organisms occurred in the test and control experiments, respectively. Enrichments of the water samples with crude oil resulted in the isolation of nine bacteria belonging to seven genera. A mixed culture was developed from the assemblage of the nine species. The defined microbial consortium utilized a wide range of pure HCs including cycloalkane and aromatic HCs. Utilization of crude oil and petroleum cuts, i.e., kerosene and diesel resulted in an increase in TVC (till day 10) concomitant with decreases in pH and residual oil concentration. Crude oil, diesel and kerosene were degraded by 88, 85 and 78%, respectively, in 14 days. Substrate uptake studies with axenic cultures showed that growth was not sustainable on either cyclohexane or aromatics while degradation of the petroleum fractions fell below 67% in spite of extended incubation period (20 day). From the GC analysis of recovered oil, while reductions in peaks of n-alkane fractions and in biomarkers namely n-C₁₇/pristane and n-C₁₈/phytane ratios were observed in culture fluids of pure strains, complete removal of all the HC components of kerosene, diesel and crude oil including the isoprenoids was obtained with the consortium within 14 days.     

A comparative location database (CompLDB): map integration within and between species

We have adapted the Location Database (LDB) map-integration strategy of Morton et al. [Ann Hum Genet 56:223–232] (1992) as above to create an integrated map for each of several species for which fully annotated genome sequences are not yet available (sheep, cattle, pig, wallaby), using all types of partial maps for that species, including cytogenetic, linkage, somatic-cell hybrid, and radiation hybrid maps. An integrated map provides not only predictions of the kilobase location of every locus, but also predicts locations (in cM) and cytogenetic band locations for every locus. In this way a comprehensive linkage map and a comprehensive cytogenetic map are created, including all loci, irrespective of whether they have ever been linkage mapped or physically mapped, respectively. High-resolution physical maps from annotated sequenced species have also been placed alongside the integrated maps. This has created a powerful tool for comparative genomics. The LDB map-integration strategy has been extended to make use of zoo-FISH comparative information. It has also been extended to enable the creation of a “virtual” map for each species not yet sequenced by using mapping data from fully sequenced species. All of the partial maps, together with the integrated map, for each species have been placed in a database called Comparative Location Database (CompLDB), which is available for querying, browsing, or download in tabular form at . Electronic supplementary material The online version of this article (doi:) contains supplementary material, which is available to authorized users.     

Phytoplankton and bacterial assemblages in ballast water of U.S. military ships as a function of port of origin, voyage time, and ocean exchange practices

We characterized the physical/chemical conditions and the algal and bacterial assemblages in ballast water from 62 ballast tanks aboard 28 ships operated by the U.S. Military Sealift Command and the Maritime Administration, sampled at 9 ports on the U.S. West Coast and 4 ports on the U.S. East Coast. The ballast tank waters had been held for 2–176 days, and 90% of the tanks had undergone ballast exchange with open ocean waters. Phytoplankton abundance was highly variable (grand mean for all tanks, 3.21 × 10⁴ viable cells m⁻³; median, 7.9 × 10³ cells m⁻³) and was unrelated to physical/chemical parameters, except for a positive relationship between centric diatom abundance and nitrate concentration. A total of 100 phytoplankton species were identified from the ballast tanks, including 23 potentially harmful taxa (e.g. Chaetoceros concavicornis, Dinophysis acuminata, Gambierdiscus toxicus, Heterosigma akashiwo, Karlodinium veneficum, Prorocentrum minimum, Pseudo-nitzschia multiseries). Assemblages were dominated by chain-forming diatoms and dinoflagellates, and viable organisms comprised about half of the total cells. Species richness was higher in ballast tanks with coastal water, and in tanks containing Atlantic or Pacific Ocean source waters rather than Indian Ocean water. Total and viable phytoplankton numbers decreased with age of water in the tanks. Diversity also generally decreased with water age, and tanks with ballast water age >33 days did not produce culturable phytoplankton. Abundance was significantly higher in tanks with recently added coastal water than in tanks without coastal sources, but highly variable in waters held less than 30 days. Bacterial abundance was significantly lower in ballast tanks with Atlantic than Pacific Ocean source water, but otherwise was surprisingly consistent among ballast tanks (overall mean across all tanks, 3.13 ± 1.27 × 10¹¹ cells m⁻³; median, 2.79 × 10¹¹ cells m⁻³) and was unrelated to vessel type, exchange status, age of water, environmental conditions measured, or phytoplankton abundance. At least one of four pathogenic eubacteria (Listeria monocytogenes, Escherichia coli, Mycobacterium spp., Pseudomonas aeruginosa) was detected in 48% of the ballast tanks, but toxigenic strains of Vibrio cholerae were not detected. For ships with tanks of similar ballasting history, the largest source of variation in phytoplankton and bacteria abundance was among ships; for ships with tanks of differing ballasting histories, and for all ships/tanks considered collectively, the largest source of variation was within ships. Significant differences in phytoplankton abundance, but not bacterial abundance, sometimes occurred between paired tanks with similar ballasting history; hence, for regulatory purposes phytoplankton abundance cannot be estimated from single tanks only. Most tanks (94%) had adequate records to determine the source locations and age of the ballast water and, as mentioned, 90% had had ballast exchange with open-ocean waters. Although additional data are needed from sediments that can accumulate at the bottom of ballast tanks, the data from this water-column study indicate that in general, U.S. Department of Defense (DoD) ships are well managed to minimize the risk for introduction of harmful microbiota. Nevertheless, abundances of viable phytoplankton with maximum dimension >50 μm exceeded proposed International Maritime Organization standards in 47% of the ballast tanks sampled. The data suggest that further treatment technologies and/or alternative management strategies will be necessary to enable DoD vessels to comply with proposed standards.     

Prescribed fires in Artemisia tridentata ssp. vaseyana steppe have minor and transient effects on vegetation cover and composition

Question: What is the impact of prescribed fires on the cover and composition of vegetation in Artemisia tridentata ssp. vaseyana steppe? Location: United States Department of Agriculture, Agricultural Research Service, United States Sheep Experiment Station, eastern Idaho (44°14′44′’ N, 112°12′47′’ W). Methods: Multiple prescribed fires were lit in 2002 and 2003 in an Artemisia tridentata ssp. vaseyana (mountain big sagebrush) steppe ecosystem that was relatively free of exotic plants. Measurements of cover components and plant species frequencies were taken pre‐ and for 2 to 3 years post‐fire. Results: Cover of forbs and grasses returned to pre‐fire levels after two years. Shrub cover declined from 36 to 6% in the first year post‐fire. Fire reduced the frequencies of three species, A. tridentata ssp. vaseyana, Festuca idahoensis, and Cordylanthus ramosus, of rangeland plants. Frequencies of four plant species, Hesperostipa comata, Polygonum douglasii, Chenopodium fremontii and Chenopodium leptophyllum increased, but only P. douglasii increased for more than a year. Conclusion: This study demonstrates that in an Artemisia tridentata ssp. vaseyana steppe ecosystem without significant non‐native species or anthropogenic disturbances vegetative cover and species composition of the herbaceous community are only minimally altered by fire. The herbaceous component returned to pre‐fire conditions within three years of a fire.     

Nodule Symbiosis of Invasive <Emphasis Type="Italic">Mimosa pigra</Emphasis> in Australia and in Ancestral Habitats: A Comparative Analysis

Ninety isolates of root nodule bacteria from an invasive Mimosa pigra population in Australia were characterized by PCR assays and by sequencing of ribosomal genes. All isolates belonged to the same bacterial genus (Burkholderia) that predominates on M. pigra in its native geographic range in tropical America. However, the Australian Burkholderia strains represented several divergent lineages, none of which had a close relationship to currently known Burkholderia strains in American M. pigra populations. Inoculation of M. pigra with Australian strains resulted in equal or higher plant growth and nodule nitrogenase activity (measured by acetylene reduction assays) relative to outcomes with bacteria from M. pigra’s native geographic region. The main difference in symbiotic phenotype for bacteria from the two regions involved responses to an alternate Mimosa host species: Central American strains failed to fix nitrogen in association with Mimosa pudica, while most Australian Burkholderia isolates tested had high nodule nitrogenase activity in association with both Mimosa species. Invasive M. pigra populations in Australia have therefore acquired a diverse assemblage of nodule bacteria that are effective nitrogen-fixing symbionts, despite having a broader host range and a distant genetic relationship to bacterial strains found in the plant’s ancestral region.     

RNA interference based gene therapy for neurological disease.

Neurodegenerative disorders represent a major class of disorders for which thus far any effective small molecule drug therapy has failed to emerge. RNA interference (RNAi), by which disease genes such as those identified for spino-cerebellar ataxia and Huntington's disease can be specifically silenced, has great potential in becoming a successful therapeutic strategy for these diseases. RNAi has shown therapeutic value in vitro and in animal disease models and clinical trials are currently on their way. However, there are problems, such as toxicity due to non-specific silencing, generation of immune responses and over-saturation of RNAi pathway components that must be overcome in order to establish RNAi as a safe and effective therapy. Current research on the endogenous roles of RNAi, through the action of microRNAs, has offered much knowledge to optimise the exploitation of RNAi.     

Measuring the Binding Stoichiometry of HIV-1 Gag to Very-Low-Density Oligonucleotide Surfaces Using Surface Plasmon Resonance Spectroscopy

The interaction of the HIV Gag polyprotein with nucleic acid is a critical step in the assembly of viral particles. The Gag polyprotein is composed of the matrix (MA), capsid (CA), and nucleocapsid (NC) domains. The NC domain is required for nucleic acid interactions, and the CA domain is required for Gag-Gag interactions. Previously, we have investigated the binding of the NC protein to d(TG)(n) oligonucleotides using surface plasmon resonance (SPR) spectroscopy. We found a single NC protein is able to bind to more than one immobilized oligonucleotide, provided that the oligonucleotides are close enough together. As NC is believed to be the nucleic acid binding domain of Gag, we might expect Gag to show the same complex behavior. We wished to analyze the stoichiometry of Gag binding to oligonucleotides without this complication due to tertiary complex formation. We have therefore analyzed Gag binding to extremely low oligonucleotide density on SPR chips. Such low densities of oligonucleotides are difficult to accurately quantitate. We have determined by Fourier transform ion cyclotron (FTICR) mass spectrometry that four molecules of NC bind to d(TG)(10) (a 20-base oligonucleotide). We developed a method of calibrating low-density surfaces using NC calibration injections. Knowing the maximal response and the stoichiometry of binding, we can precisely determine the amount of oligonucleotide immobilized at these very-low-density surfaces (<1 Response Unit). Using this approach, we have measured the binding of Gag to d(TG)(10). Gag binds to a 20-mer with a stoichiometry of greater than 4. This suggests that once Gag is bound to the immobilized oligonucleotide, additional Gag molecules can bind to this complex.     

Preliminary observations on the life history of the white-streaked grouper, <Emphasis Type="Italic">Epinephelus ongus</Emphasis>, from Okinawa,Japan

A preliminary analysis of 175 specimens of the white-streaked grouper, Epinephelus ongus (Serranidae), was undertaken to determine life history characteristics of the species. Sagittal otoliths, stomachs, and a subsample of gonads were removed to determine age at length, diet, and reproductive strategy. The von Bertalanffy growth equation was used to describe growth in this species and yielded the growth parameters L^∞ = 438.3, K = 0.04334, and t₀ = −8.752. Fish ranged in age from 1 to 20 years. Diet was consistent with other serranid species and included crabs, shrimps, octopi, and fishes. Based on a very limited number of specimens (n = 12), the larger size and older age of males compared to females suggests that E. ongus may be a protogynous hermaphrodite.     

<Emphasis Type="Italic">Burkholderia</Emphasis> Hep_Hag autotransporter (BuHA) proteins elicit a strong antibody response during experimental glanders but not human melioidosis

Background  

The bacterial biothreat agents Burkholderia mallei and Burkholderia pseudomallei are the cause of glanders and melioidosis, respectively. Genomic and epidemiological studies have shown that B. mallei is a recently emerged, host restricted clone of B. pseudomallei.