Assay for the quantification of small-sized fragmented genomic DNA

This paper presents a simple assay for the direct quantification of small-sized (up to 1000 bp) fragmented DNA based on the differential separation between large- and small-sized DNA by polyethylene glycol precipitation. The assay can be applied to as low as 1 microg ml(-1) DNA and has a very low DNA detection limit (0.01 microg ml(-1) fragmented DNA), which can be further lowered at least 10-fold with anion exchange chromatography. The assay quantifies for the first time a more direct indicator of the extent of DNA damage than the usually assessed DNA nicks and base modifications, since small-sized fragmented DNA represents an unrepairable DNA damage of necrotic and apoptotic events that are related to normal and abnormal biological conditions.     

Identification of essential residues within Lit, a cell death peptidase of Escherichia coli K-12

Bacteriophage exclusion is a suicide response to viral infection. In strains of Escherichia coli K-12 infected with T4 phage this process is mediated by the host-encoded Lit peptidase. Lit is activated by a unique sequence in the major head protein of the T4 phage (the Gol sequence) which then cleaves site-specifically the host translation factor EF-Tu, ultimately leading to cell death. Lit has very low sequence identity with other peptidases, with only a putative metallopeptidase motif, H(160)EXXH, giving an indication of its catalytic activity. The aim of the present study was to ascertain if Lit is a metallopeptidase, identify residues essential for Lit activity, and probe the involvement of the Gol sequence in the activation of enzymatic activity. Lit activity was inhibited by the zinc chelator 1,10-phenanthroline, consistent with the suggestion that it is a metallopeptidase. Preliminary covalent modification experiments found that Lit was susceptible to inactivation by diethyl pyrocarbonate, with about three histidines reversibly modified, one of which was found to be essential for proteolytic activity. Subsequently, 13 mutants of the Lit enzyme were constructed that included all 10 histidines as well as other residues within the metallopeptidase motif. This demonstrated that the residues within the HEXXH motif are required for Lit activity and further defined the essential catalytic core as H(160)EXXHX(67)H, with additional residues such as His169 being important but not essential for activity. Kinetic analysis of Lit activation by a synthetic Gol peptide highlighted that elevated concentrations of the peptide (>10-fold above activation K(M)) are inhibitory to Lit, with this effect also seen in partially active Lit mutants. The susceptibility of Lit to inhibition by its own activating peptide suggests that the Gol sequence may be able to bind nonproductively to the enzyme at high concentration. We discuss these data in the context of the currently understood models for Gol-mediated activation of the Lit peptidase and its mechanism of action.     

Monitoring of ozone pollution and the physiological activity of <Emphasis Type="Italic">Pinus halepensis</Emphasis> (Mill.) by electron paramagnetic resonance and other parameters

An investigation of selected Aleppo pines in the forests of Mt Hymettus and Mt Parnis near Athens (Greece) was undertaken at three different sites in the period 1999–2003, because a considerable proportion of pine trees showed visible signs of chlorotic mottle. This condition is characteristic of high and prolonged levels of ozone exposure. Needles from Aleppo pine trees (Pinus halepensis Mill.) were analyzed for their manganese content in combination with Electron Paramagnetic Resonance (EPR) spectra of Mn²⁺, involved in photosystem II. Manganese is considered as an important bioindicator for the vitality of trees. Also, we investigated the EPR spectrum of the needles in the region of g=2.0045 for healthy and diseased trees. The antioxidant capacity of the needles extract was measured from trees by the DPPH method. Finally, seasonal changes in chlorophyll concentration in the needles were measured to evaluate the effects of ozone. Measurements of ozone concentrations at the three sites showed that there were elevated levels during the summer months. Our experimental results suggest that the concentration of manganese in the needles was lower in the area with higher ozone concentrations, supported by EPR measurements. Higher ozone concentrations also affected the antioxidant potential of the needles and their chlorophyll content during summer months. Our findings also confirmed the resilience of Aleppo pines under stressful conditions and recovery in winter months. Despite the experimental problems, EPR spectra of Mn²⁺ in combination with other methods can be used as a sensitive bioindicator for ozone pollution, and is the result of oxidative stress affecting the growth cycle of the pine trees and their photosynthetic mechanisms.     

TMRPres2D: high quality visual representation of transmembrane protein models

The 'TransMembrane protein Re-Presentation in 2-Dimensions' (TMRPres2D) tool, automates the creation of uniform, two-dimensional, high analysis graphical images/models of alpha-helical or beta-barrel transmembrane proteins. Protein sequence data and structural information may be acquired from public protein knowledge bases, emanate from prediction algorithms, or even be defined by the user. Several important biological and physical sequence attributes can be embedded in the graphical representation.     

Kinetics of methyl t-butyl ether cometabolism at low concentrations by pure cultures of butane-degrading bacteria

Butane-oxidizing Arthrobacter (ATCC 27778) bacteria were shown to degrade low concentrations of methyl t-butyl ether (MTBE; range, 100 to 800 microg/liter) with an apparent half-saturation concentration (K(s)) of 2.14 mg/liter and a maximum substrate utilization rate (k(c)) of 0.43 mg/mg of total suspended solids per day. Arthrobacter bacteria demonstrated MTBE degradation activity when grown on butane but not when grown on glucose, butanol, or tryptose phosphate broth. The presence of butane, tert-butyl alcohol, or acetylene had a negative impact on the MTBE degradation rate. Neither Methylosinus trichosporium OB3b nor Streptomyces griseus was able to cometabolize MTBE.     

Isolation of high-affinity ligand-binding proteins by periplasmic expression with cytometric screening (PECS)

Periplasmic expression with cytometric screening (PECS) is a powerful and rapid "display-less" technology for isolating ligand-binding proteins from diverse libraries. Escherichia coli expressing a library of proteins secreted into the periplasmic space are incubated with a fluorescent conjugate of the target ligand. Under the proper conditions, ligands as large as about 10 kDa can equilibrate within the periplasmic space without compromising the cell's integrity or viability. The bacterial cell envelope effectively serves as a dialysis bag to selectively retain receptor-fluorescent probe complexes but not free ligand. Cells displaying increased fluorescence are then isolated by flow cytometry. We demonstrate that scFv antibodies with both very high and low affinity to digoxigenin can be isolated from libraries screened by PECS using a benchtop flow cytometer. We also show that preexisting libraries constructed for display on filamentous bacteriophage can be screened by PECS without the need for subcloning. In fact, PECS was found to select for proteins that could be missed by conventional phage panning and screening methods.     

A hollow-fiber membrane bioreactor for the removal of trichloroethylene from the vapor phase

A hollow-fiber membrane bioreactor was used to separate trichloroethylene (TCE) from a gaseous waste stream with subsequent cometabolic biodegradation by a pure culture of Methylosinus trichosporium OB3b PP358. The two-stage bioreactor system was successfully operated for 20 days. PP358 was grown in a continuous-flow chemostat and circulated through the fiber lumen of a hollow-fiber membrane module (HFMM), while TCE contaminated air (141 to 191 microg/L) was pumped through the HFMM shell. Between 54% -84% TCE transfer and 92%-96% TCE cometabolism were obtained in the HFMM reactor loop. Short shell-residence times, 1.6 to 5.0 minutes, demonstrated quick throughput of TCE contaminated air. Best-fit computer modeling of the biological experiments estimated mass transfer coefficients between 2.0 x 10(-3) cm/min and 5.6 x 10(-3) cm/min. The average pseudo-first-order biodegradation rate constant for the biological experiments was 0.46 L/mg TSS/d. These results demonstrate that the hollow-fiber membrane bioreactor represents an attractive technology for the bioremediation of gaseous waste streams.     

Sandhoff disease in Cyprus: population screening by biochemical and DNA analysis indicates a high frequency of carriers in the Maronite community

In the last 15 years, four patients with the infantile form of Sandhoff disease were diagnosed in four different families in Cyprus (population 703,000, birth rate 1.7%). Three of these cases came from the Christian Maronite community (less than 1% of the population) and one from the Greek community (84% of the population). This relatively large number of patients prompted us to initiate an epidemiological study in order to establish the frequency of the mutant allele in Cyprus. Carrier detection was initially based on the measurement of beta-hexosaminidase A and B in both leucocytes and serum. Using the enzyme test, 35 carriers were identified among 244 random Maronite samples and 15 among 28 Maronites with a family history of Sandhoff disease, but only one carrier was found out of 115 random samples from the Greek community. In parallel to the biochemical screening, DNA studies were undertaken in one of the three Maronite patients and in a Greek carrier related to the Greek patient. These studies resulted in the identification of two novel mutations, a deletion of A at nt76 and a G to C transversion at position 5 of the 5'-splice site of intron 8, which have been published. We subsequently screened the carriers detected in the biochemical study for these two mutations using PCR-based tests. Of 50 Maronite carriers examined, 42 were found to have the nt76 deletion. Eight Maronite samples, designated carriers from the biochemical results, were negative for both mutations. It is possible that these individuals were incorrectly classified as carriers since their enzyme values are equivocal, although the presence of another mutation has not been excluded. Two Greek Cypriot carriers and two obligate Lebanese carriers were negative for both mutations. We conclude that there is a high frequency of Sandhoff disease carriers in the Maronite community of Cyprus, approximately 1 in 7, and that a single mutation predominates in this population.     

Decidual spiral artery remodeling during early post-implantation period in mice: investigation of associations with decidual uNK cells and invasive trophoblast

Circumferential remodeling of spiral arteries (SAs) during pregnancy is crucial for regulating maternal blood flow into the placenta and clinically important. However its mechanism is still ill defined in humans and mice. In mice, several important aspects of decidual SA remodeling (SAR) remain unexplored and were addressed here using morphometrics by examining SAs within the mesometrial half of the decidua basalis between embryonic day 6.5 (E6.5) and midgestation (E10.5). The data presented here provide evidence that supports the following novel conclusions about SAR: (a) SAs (defined by their muscular walls) appear between E6.5 and E7.5, undergo 'outward hypertrophic' SAR (SA lumen widening with muscular wall thickening) during the E7.5-E8.5 and E9.5-E10.5 periods, and 'outward hypotrophic' SAR (SA lumen widening with muscular wall thinning) during the E8.5-E9.5 interval. (b) 'Outward hypotrophic' SAR is associated with decreases in the overall number, but not density, of SA media nuclei, suggesting loss of SA muscular wall cells. Proximity of placenta-derived invasive trophoblast to SAs appears not be involved in SAR, as these cells were undetectable in the mesometrial region of decidua basalis throughout the E6.5-E10.5 period. Although the maternally derived lymphocytes of the decidual uterine natural killer (uNK) cell type are required for decidual SAR, the timing of this, the uNK cell parameter involved and the type of SAR they influence have not been adequately explored. Evidence is presented here that not all decidual SAR during this period is uNK cell-dependent. Rather, the data suggest that uNKs only influence 'outward hypotrophic' SAR during the E8.5-E9.5 period. Evidence is presented that the uNK cell parameter involved is the attainment of a certain maturation state (based on uNK cell size) by SA wall uNKs of the Dolichos biflorus agglutinin (DBA) lectin-positive uNK cell subset. This work also suggests that the previously shown loss of contractile mural cell character from the SA wall does not depend on either uNKs or trophoblast proximity. The novel implications of the present data for early mouse pregnancy are discussed.