A Monte Carlo model of DNA double-strand break clustering and rejoining kinetics for the analysis of pulsed-field gel electrophoresis data

In studies of radiation-induced DNA fragmentation and repair, analytical models may provide rapid and easy-to-use methods to test simple hypotheses regarding the breakage and rejoining mechanisms involved. The random breakage model, according to which lesions are distributed uniformly and independently of each other along the DNA, has been the model most used to describe spatial distribution of radiation-induced DNA damage. Recently several mechanistic approaches have been proposed that model clustered damage to DNA. In general, such approaches focus on the study of initial radiation-induced DNA damage and repair, without considering the effects of additional (unwanted and unavoidable) fragmentation that may take place during the experimental procedures. While most approaches, including measurement of total DNA mass below a specified value, allow for the occurrence of background experimental damage by means of simple subtractive procedures, a more detailed analysis of DNA fragmentation necessitates a more accurate treatment. We have developed a new, relatively simple model of DNA breakage and the resulting rejoining kinetics of broken fragments. Initial radiation-induced DNA damage is simulated using a clustered breakage approach, with three free parameters: the number of independently located clusters, each containing several DNA double-strand breaks (DSBs), the average number of DSBs within a cluster (multiplicity of the cluster), and the maximum allowed radius within which DSBs belonging to the same cluster are distributed. Random breakage is simulated as a special case of the DSB clustering procedure. When the model is applied to the analysis of DNA fragmentation as measured with pulsed-field gel electrophoresis (PFGE), the hypothesis that DSBs in proximity rejoin at a different rate from that of sparse isolated breaks can be tested, since the kinetics of rejoining of fragments of varying size may be followed by means of computer simulations. The problem of how to account for background damage from experimental handling is also carefully considered. We have shown that the conventional procedure of subtracting the background damage from the experimental data may lead to erroneous conclusions during the analysis of both initial fragmentation and DSB rejoining. Despite its relative simplicity, the method presented allows both the quantitative and qualitative description of radiation-induced DNA fragmentation and subsequent rejoining of double-stranded DNA fragments. (C) 2004 by Radiation Research Society.

Evidence for complexity at the nanometer scale of radiation-induced DNA DSBs as a determinant of rejoining kinetics

The rejoining kinetics of double-stranded DNA fragments, along with measurements of residual damage after postirradiation incubation, are often used as indicators of the biological relevance of the damage induced by ionizing radiation of different qualities. Although it is widely accepted that high-LET radiation-induced double-strand breaks (DSBs) tend to rejoin with kinetics slower than low-LET radiation-induced DSBs, possibly due to the complexity of the DSB itself, the nature of a slowly rejoining DSB-containing DNA lesion remains unknown. Using an approach that combines pulsed-field gel electrophoresis (PFGE) of fragmented DNA from human skin fibroblasts and a recently developed Monte Carlo simulation of radiation-induced DNA breakage and rejoining kinetics, we have tested the role of DSB-containing DNA lesions in the 8-kbp-5.7-Mbp fragment size range in determining the DSB rejoining kinetics. It is found that with low-LET X rays or high LET alpha particles, DSB rejoining kinetics data obtained with PFGE can be computer-simulated assuming that DSB rejoining kinetics does not depend on spacing of breaks along the chromosomes. After analysis of DNA fragmentation profiles, the rejoining kinetics of X-ray-induced DSBs could be fitted by two components: a fast component with a half-life of 0.9 +/- 0.5 h and a slow component with a half-life of 16 +/- 9 h. For a particles, a fast component with a half-life of 0.7 +/- 0.4 h and a slow component with a half-life of 12 5 h along with a residual fraction of unrepaired breaks accounting for 8% of the initial damage were observed. In summary, it is shown that genomic proximity of breaks along a chromosome does not determine the rejoining kinetics, so the slowly rejoining breaks induced with higher frequencies after exposure to high-LET radiation (0.37 +/- 0.12) relative to low-LET radiation (0.22 +/- 0.07) can be explained on the basis of lesion complexity at the nanometer scale, known as locally multiply damaged sites. (c) 2005 by Radiation Research Society.

Deficiencies of folate and vitamin B-6 exert distinct effects on homocysteine, serine, and methionine kinetics

Folate and vitamin B-6 act in generating methyl groups for homocysteine remethylation, but the kinetic effects of folate or vitamin B-6 deficiency are not known. We used an intravenous primed, constant infusion of stable isotope-labeled serine, methionine, and leucine to investigate one-carbon metabolism in healthy control (n = 5), folate-deficient (n = 4), and vitamin B-6-deficient (n = 5) human subjects. The plasma homocysteine concentration in folate-deficient subjects [15.9 +/-2.1 (SD) mu mol/l] was approximately two times that of control (7.4 +/-1.7 mmol/l) and vitamin B-6-deficient (7.7 +/-2.1 mmol/l) subjects. The rate of methionine synthesis by homocysteine remethylation was depressed (P = 0.027) in folate deficiency but not in vitamin B-6 deficiency. For all subjects, the homocysteine remethylation rate was not significantly associated with plasma homocysteine concentration (r = -0.44, P = 0.12). The fractional synthesis rate of homocysteine from methionine was positively correlated with plasma homocysteine concentration (r = 0.60, P = 0.031), and a model incorporating both homocysteine remethylation and synthesis rates closely predicted plasma homocysteine levels (r = 0.85, P = 0.0015). Rates of homocysteine remethylation and serine synthesis were inversely correlated (r = -0.89, P < 0.001). These studies demonstrate distinctly different metabolic consequences of vitamin B-6 and folate deficiencies.

Size-fitting of Intravaginal Rings for Macaques and in vitro Release Kinetics of Zinc Finger Inhibitors

Background: Small molecule inhibitors of the zinc finger domain (ZFI) in the nucleocapsid protein (NCp7) of HIV-1 are potent inhibitors of HIV and SIV
replication and may have utility as topical products to prevent infection. Furthermore, intravaginal rings (IVRs) were developed as coitally-independent,
sustained release devices which could be used for administration of HIV microbicides. The aims of these studies were to demonstrate that IVRs sized for
macaques are practical and compatible with the current generation of thioester-based NCp7 inhibitors.

Methods: Non-medicated silicone elastomer vaginal rings of various sizes thought to be applicable for macaques were prepared and tested for vaginal fit in Pigtailed and Chinese Rhesus macaques. Macaques were monitored for 8 weeks for mucosal disruption by colposcopy and proinflammatory cytokine markers in cervical vaginal lavages (CVL) using Luminex bead-based technology. Three different ZFIs (compounds 52, 89 and 122, each derived from an N-substituted S-acyl-2-mercaptobenzamide thioester scaffold) were loaded at 50 mg into an optimal matrix-type ring design. In vitro continuous release studies were then conducted over 28 days and analyzed by HPLC. Rate of release was determined by linear regression analysis.

Results: Qualitative evaluation at the time of ring insertion suggested that the 25 mm ring provided optimal fit in both macaque species. All rings remained in
place during the study period (2 to 4 weeks), and the animals did not attempt to remove the rings. No tissue irritation was observed, and no signs of physical
discomfort were noted. Also, no significant induction of cervicovaginal proinflammatory markers was observed during the 8-week period during and following ring insertion. One Pigtailed macaque showed elevated IL-8 levels in the CVL during the period when the ring was in place; however, these levels were comparable to those observed in two control macaques. In vitro release of the ZFIs peaked at day 1 and then continually declined to near steady-state rates between 20-30 mcg/day. The percent release after 14 days was 2.9, 2.0 and 0.9 for ZFI 89, 52 and 122, respectively.

Conclusions: IVRs of 25mm diameter, determined to be the optimal size for macaques, were well tolerated and did not induce inflammation. Release of all ZFI compounds followed t 0.5 kinetics. These findings suggest that efficacy testing in primate models is warranted to fully evaluate the potential to prevent
transmission.

Kinetics of semicarbazide and nitrofurazone in chicken eggs and egg powders

The accumulation, depletion and partitioning of semicarbazide (SEM) and its parent compound nitrofurazone (NFZ) in eggs were studied using hens fed NFZ at therapeutic and sub-therapeutic levels. Dietary NFZ correlated strongly with NFZ and total SEM in eggs, while 28% of observed SEM was present in the form of parent NFZ. Depletion half-life in eggs was 2.4 days for SEM and 1.1 days for NFZ. NFZ accumulated preferentially in yolk (57-63%) as opposed to albumen, while 71-80% of SEM was found in yolk. In whole egg, 29% of SEM was present as tissue-bound residues compared with 80% in breast muscle. Whilst NFZ and SEM were partly degraded by pasteurization and spray drying, sufficient NFZ remained to suggest it might be detectable in egg powders when SEM is observed at low µg kg -1 concentrations. NFZ was detectable in whole eggs during ingestion of only 0.1% of the therapeutic NFZ dose, making detection of intact NFZ in eggs a feasible means to prove conclusively the administration of this banned compound.

Reproductive biomass in Holcus lanatus clones that differ in their phosphate uptake kinetics and mycorrhizal colonization

In normal populations of the common grass Holcus lanatus there is a polymorphism for arsenate resistance, manifested as suppressed phosphate uptake (SPU), and controlled by a major gene with dominant expression. A natural population of SPU plants had greater arbuscular-mycorrhizal colonization than wild type, nonSPU plants. It was hypothesized that, in order to survive alongside plants with a normal rate of phosphate (P) uptake, SPU plants would be more dependent on mycorrhizal associations. We performed an experiment using plants with SPU phenotypes from both arsenate mine spoils and uncontaminated soils, as well as plants with a nonSPU phenotype. They were grown with and without a mycorrhizal inoculum and added N, which altered plant P requirements. We showed that grasses with SPU phenotypes accumulated more shoot P than nonSPU plants, the opposite of the expected result. SPY plants also produced considerably more flower panicles, and had greater shoot and root biomass. The persistence of SPU phenotypes in normal populations is not necessarily related to mycorrhizal colonization as there were no differences in percentage AM colonization between the phenotypes. Being mycorrhizal reduced flower biomass production, as mycorrhizal SPU plants had lower shoot P concentrations and produced fewer flower panicles than non-mycorrhizal, nonSPU plants. We now hypothesize that the SPU phenotype is brought about by a genotype that results in increased accumulation of P in shoots, and that suppression of the rate of uptake is a consequence of this high shoot P concentration, operating by means of a homeostatic feedback mechanism. We also postulate that increased flower production is linked to a high shoot P concentration. SPU plants thus allocate more resources into seed production, leading to a higher frequency of SPU genes. Increased reproductive allocation reduces vegetative allocation and may affect competitive ability and hence survival, explaining the maintenance of the polymorphism. As mycorrhizal SPU plants behave more like nonSPU plants, AM colonization itself could play a major part in the maintenance of the SPU polymorphism.

Mechanisms of arsenic hyperaccumulation in Pteris vittata. Uptake kinetics, interactions with phosphate, and arsenic speciation

The mechanisms of arsenic (As) hyperaccumulation in Pteris vittata, the first identified As hyperaccumulator, are unknown. We investigated the interactions of arsenate and phosphate on the uptake and distribution of As and phosphorus (P), and As speciation in P. vittata. In an 18-d hydroponic experiment with varying concentrations of arsenate and phosphate, P. vittata accumulated As in the fronds up to 27,000 mg As kg(-1) dry weight, and the frond As to root As concentration ratio varied between 1.3 and 6.7. Increasing phosphate supply decreased As uptake markedly, with the effect being greater on root As concentration than on shoot As concentration. Increasing arsenate supply decreased the P concentration in the roots, but not in the fronds. Presence of phosphate in the uptake solution decreased arsenate influx markedly, whereas P starvation for 8 d increased the maximum net influx by 2.5-fold. The rate of arsenite uptake was 10% of that for arsenate in the absence of phosphate. Neither P starvation nor the presence of phosphate affected arsenite uptake. Within 8 h, 50% to 78% of the As taken up was distributed to the fronds, with a higher translocation efficiency for arsenite than for arsenate. In fronds, 49% to 94% of the As was extracted with a phosphate buffer (pH 5.6). Speciation analysis using high-performance liquid chromatography-inductively coupled plasma mass spectroscopy showed that >85% of the extracted As was in the form of arsenite, and the remaining mostly as arsenate. We conclude that arsenate is taken up by P. vittata via the phosphate transporters, reduced to arsenite, and sequestered in the fronds primarily as As(III).

Uptake kinetics of arsenic species in rice plants

Arsenic (As) finds its way into soils used for rice (Oryza sativa) cultivation through polluted irrigation water, and through historic contamination with As-based pesticides. As is known to be present as a number of chemical species in such soils, so we wished to investigate how these species were accumulated by rice. As species found in soil solution from a greenhouse experiment where rice was irrigated with arsenate contaminated water were arsenite, arsenate, dimethylarsinic acid, and monomethylarsonic acid. The short-term uptake kinetics for these four As species were determined in 7-d-old excised rice roots. High-affinity uptake (0-0.0532 mM) for arsenite and arsenate with eight rice varieties, covering two growing seasons, rice var. Boro (dry season) and rice var. Aman (wet season), showed that uptake of both arsenite and arsenate by Boro varieties was less than that of Aman varieties. Arsenite uptake was active, and was taken up at approximately the same rate as arsenate. Greater uptake of arsenite, compared with arsenate, was found at higher substrate concentration (low-affinity uptake system). Competitive inhibition of uptake with phosphate showed that arsenite and arsenate were taken up by different uptake systems because arsenate uptake was strongly suppressed in the presence of phosphate, whereas arsenite transport was not affected by phosphate. At a slow rate, there was a hyperbolic uptake of monomethylarsonic acid, and limited uptake of dimethylarsinic acid.

Methane to higher hydrocarbons via halogenation

Activation of methane with a halogen followed by the metathesis of methyl halide is a novel route from methane to higher hydrocarbons or oxygenates. Thermodynamic analysis revealed that bromine is the most suitable halogen for this goal. Analysis of the published data on the reaction kinetics in a CSTR enabled us to judge on the effects of temperature, reactor residence time and the feed concentrations of bromine and methane to the conversion of methane and the selectivity towards mono or dibromomethane. The analysis indicated that high dibromomethane selectivity is attainable (over 90%) accompanied by high methane conversions. The metathesis of dibromomethane can provide an alternative route to the conversion of methane (natural gas) economically with smaller installations than the current syn-gas route. (c) 2005 Elsevier B.V. All rights reserved.

Numbered-up gas-liquid micro/milli channels reactor with modular flow distributor

Gas-liquid processing in microreactors remains mostly restricted to the laboratory scale due to the complexity and expenditure needed for an adequate numbering-up with a uniform flow distribution. Here, the numbering-up is presented for multi-phase (gas-liquid) flow in microreactor suitable for a production capacity of kg/h. Based on the barrier channels concept, the barrier-based micro/milli reactor (BMMR) is designed and fabricated to deliver flow non-uniformity of less than 10%. The BMMR consists of eight parallel channels all operated in the Taylor flow regime and with a liquid flow rate up to 150. mL/min. The quality of the flow distribution is reported by studying two aspects. The first aspect is the influence of different viscosities, surface tensions and flow rates. The second aspect is the influence of modularity by testing three different reaction channels type: (1) square channels fabricated in a stainless steel plate, (2) square channels fabricated in a glass plate, and (3) circular channels (capillaries) made of stainless steel. Additionally, the BMMR is compared to that of a single channel regard the slug and bubble lengths and bubble generation frequency. The results pave the ground for bringing multi-phase flow in microreactor one step closer for large scale production via numbering-up. © 2012 Elsevier B.V.

Transient distributions of composition and temperature in a gas-solid packed bed reactor by near-infrared tomography

Near-infrared diffuse tomography was used in order to observe dynamic behaviour of flowing gases by measuring the 3D distributions of composition and temperature in a weakly scattering packed bed reactor, subject to wall effects and non-isothermal conditions. The technique was applied to the vapour phase hydrogen isotopic exchange reaction in a hydrophobic packing of low aspect ratio made of platinum on styrene divinyl benzene sulphonate copolymer resin. The results of tomography revealed uneven temperature and composition maps of water and deuterated water vapours in the core-packed bed and in the vicinity of the wall owing to flow maldistribution. The dynamic lag between the near-wall water vapour and deuterated water vapour compositions were observed suggesting that the convective transfer which was significant near the wall at the start, owing to high porosity, was also effective at large conversions. (C) 2012 Elsevier B.V. All rights reserved.