Ultrasound to Decontaminate Organics in Dredged Sediments

Sediments contaminated with organics compounds due to past disposal practices threaten the environment and require remediation. This study was an attempt to develop a technology to decontaminate organics in dredged sediments using ultrasound coupled with vacuum pressure. A set of laboratory scale experiments were carried out using simulated dredged sediments from New York/New Jersey harbor, category III sediments that failed to meet USEPA requirements for toxicity or bioaccumulation, and required secure disposal. Acoustic cavitation due to ultrasound energy coupled with vacuum pressure was used to facilitate the removal of p-terphenyl (the selected organic contaminant) from the sediments. Two coupled processes were used to separate and to treat both coarse (Process 1) and fine (Process 2) fractions of sediments. Selected variables for evaluation of Process 1 were ultrasound power, solvent to sediment ratio, vacuum pressure, and sonication time. Process 2 was evaluated without and with surfactants. Process 2 without surfactant had three variables: power, solvent to sediment ratio, and sonication time, while Process 2 with surfactant had four variable contributing to its performance: power, solvent to sediment ratio, surfactant concentration, and sonication time. Laboratory-scale experiments were carried out with various combinations of these parameters according to the factorial design. Experimental test results showed that Process 1 had 99% contaminant removal efficiency at 60% power (900 Watts), 15:1 solvent to sediment ratio, 15?psi vacuum pressure, and 9?min of sonication time. Similarly, Process 2 without the surfactant had 55% contaminant removal efficiency at 80% power (1200 Watts), 50:1 solvent to sediment ratio, and 90?min of sonication time. Modification of Process 2 with the addition of a surfactant produced 89% contaminant removal efficiency at 80% power (1200 Watts), 50:1 solvent to sediment ratio, 0.1% surfactant concentration, and 60?min of sonication time. The study showed that the proposed treatment technique is effective for treating dredged sediments.     

Identification and characterization of a divalent metal ion-dependent cleavage site in the hammerhead ribozyme.

We describe a new RNA cleavage motif, found in the hammerhead ribozyme. Cleavage occurs between nucleotides G8 and A9, yielding a free 5'-hydroxyl group and a 2',3'-cyclic phosphate. This cleavage is dependent upon divalent metal ions and is the first evidence for a metalloribozyme known to show preference for Zn(2+). Cleavage is also observed in the presence of Ni(2+), Co(2+), Mn(2+), Cd(2+), and Pb(2+), while negligible cleavage was detected in the presence of the alkaline-earth metal ions Mg(2+), Ca(2+), Sr(2+), and Ba(2+). A linear relationship between the logarithm of the rate and pH was observed for the Zn(2+)-dependent cleavage, which is indicative of proton loss in the cleavage mechanism, either prior to or in the rate-determining step. We postulate that a zinc hydroxide complex, bound to the known A9/G10.1 metal ion binding site, abstracts the proton from the 2'-hydroxyl group of G8, which attacks the A9 phosphate and initiates cleavage. This hypothesis is supported by a previously reported crystal structure [Murray, J. B., Terwey, D. P., Maloney, L., Karpeisky, A., Usman, N., Beigelman, L., and Scott, W. G. (1998) Cell 92, 665-673], which shows the conformation required for RNA cleavage and proximity of the 2'-hydroxyl group to the metal ion complex.     

4-amino-1H-benzo[g]quinazoline-2-one: a fluorescent analog of cytosine to probe protonation sites in triplex forming oligonucleotides

We developed a new fluorescent analog of cytosine, the 4-amino-1H-benzo[g]quinazoline-2-one, which constitute a probe sensitive to pH. The 2′-O-Me ribonucleoside derivative of this heterocycle was synthesized and exhibited a fluorescence emission centered at 456 nm, characterized by four major excitation maxima (250, 300, 320 and 370 nm) and a fluorescence quantum yield of Φ = 0.62 at pH 7.1. The fluorescence emission maximum shifted from 456 to 492 nm when pH was decreased from 7.1 to 2.1. The pK_a (4) was close to that of cytosine (4.17). When introduced in triplex forming oligonucleotides this new nucleoside can be used to reveal the protonation state of triplets in triple-stranded structures. Complex formation was detected by a significant quenching of fluorescence emission (~88%) and the N-3 protonation of the quinazoline ring by a shift of the emission maximum from 485 to 465 nm. Using this probe we unambiguously showed that triplex formation of the pyrimidine motif does not require the protonation of all 4-amino-2-one pyrimidine rings.     

Genetic consequences of anthropogenic disturbances and population fragmentation in <Emphasis Type="Italic">Acacia senegal</Emphasis>

Acacia senegal is endemic to dry forest and woodland ecosystems of Sub-Saharan Africa and provides both ecological and socio-economic benefits. However, these ecosystems are threatened by escalating human disturbances and fragmentation. To investigate the human impacts on genetic diversity and structure of A. senegal, we studied genetic variability and differentiation of 330 individual trees from 11 natural A. senegal populations, grouped into lightly and heavily disturbed, using 12 polymorphic nuclear microsatellite markers. Gene diversity (H _E ) ranged from H _E = 0.570 to H _E = 0.632. Significant differences (P < 0.05) between the levels of disturbances are reported for mean gene diversity, number of alleles and allelic richness with lightly disturbed populations showing higher values. Overall, the indirect estimates of average outcrossing rates ranged from 0.794 (Kiserian) to 0.999 (Kampi ya Moto) with a mean of 0.997 suggesting a predominantly outcrossing species. There was no significant relationship (P > 0.05) detected between genetic and geographic distances, showing lack of isolation by distance. Analysis of population structure using unweighted pair group method with arithmetic mean and Bayesian model suggests presence of three gene pools as most probable, although most individuals showed mixed ancestry. The diversity and genetic structure reported in this study revealed negative impacts of human disturbance on A. senegal within this ecosystem. We recommend in-situ conservation strategies to safeguard the woodland ecosystem from further deforestation.     

Quantitative and localized element analysis in cross-sections of spruce [Picea abies (L.) Karst.] needles with different degrees of damage

Summary Proton-induced X-ray microanalysis (micro-PIXE) permits the simultaneous determination of the content and the distribution of elements with atomic numbers higher than Z = 13 in biological samples. This method was used to investigate element content and localization in cross-sections of 6-month-old spruce needles. It was possible to detect the elements silicon, phosphorus, sulphur, chlorine, potassium, calcium, manganese, iron and zinc in semithin (10 m) sections of the needles. The localization of the cationic elements like potassium, calcium and manganese was determined in the one-dimensional line scan mode and in the two-dimensional raster scan mode. To demonstrate the usefulness of this method for forest decline research, element content and localization were compared in needles from two trees, which differed in their degree of damage. We were able to detect differences in the amount of cations and in their distribution inside the needles.     

Chromatin structure of Schizosaccharomyces pombe. A nucleosome repeat length that is shorter than the chromatosomal DNA length.

We have used new methods for chromatin isolation, together with conventional methods for measuring the nucleosome repeat length, to determine the repeat length of Schizosaccharomyces pombe chromatin. We obtain a result of 156(+/- 2) bp. Equivalent results are obtained using a psoralen crosslinking method for measuring the repeat length in viable spheroplasts. That result, together with other control experiments, rules out many possible artifacts. The measured value of 156(+/- 2) bp is smaller than the length of DNA found in the chromatosome. Thus, the chromatosome cannot be the fundamental unit of chromatin structure in all eukaryotes. The crossed linker model of chromatin higher order structure is incompatible with a nucleosome repeat length of 156 bp, and thus cannot apply to all eukaryotes. The solenoid model of higher order structure is compatible with this repeat length only if the solenoid is right-handed. We note two other properties of this chromatin. (1) Early in digestion, the DNA length of mononucleosomes from S. pombe and Aspergillus nidulans exceeds the nucleosome repeat length. (2) Many methods for isolating chromatin from S. pombe yield an apparent nucleosome repeat length of less than or equal to 140 bp; this result is found to be an artifactual consequence of nucleosome sliding.