RecA protein-facilitated DNA strand breaks. A mechanism for bypassing DNA structural barriers during strand exchange

RecA protein promotes an unexpectedly efficient DNA strand exchange between circular single-stranded DNA and duplex DNAs containing short (50-400-base pair) heterologous sequences at the 5' (initiating) end. The major mechanism by which this topological barrier is bypassed involves DNA strand breakage. Breakage is both strand and position specific, occurring almost exclusively in the displaced (+) strand of the duplex within a 15-base pair region of the heterology/homology junction. Breakage also requires recA protein, ATP hydrolysis, and homologous sequences 3' to the heterology. Although the location of the breaks and the observed requirements clearly indicate a major role for recA protein in this phenomenon, the molecular mechanism is not yet clear. The breakage may reflect a DNA structure and/or some form of structural stress within the DNA during recA protein-mediated DNA pairing which either exposes the DNA at this precise position to the action of a contaminating nuclease or induces a direct mechanical break. We also find that when heterology is located at the 3' end of the linear duplex, strand exchange is halted (without DNA breakage) about 500 base pairs from the homology/heterology junction.     

Differential processing of human and rat E1 α precursors of the branched-chain α-keto acid dehydrogenase complex caused by an N-terminal proline in the rat sequence

The N-terminal sequences of the E1 α, E1β and E2 subunits of the human branched-chain α-keto acid dehydrogenase complex have been determined by microsequencing. The N-termini of human E1β and E2 subunits (Val and Gly, respectively) are indentical to those of the corresponding rat and bovine subunits. However, the N-terminus of the human E1 α subunit (Ser) is identical to bovine, but differs from the rat E1 α (Phe0 subunit. Comparison of the N-terminal sequences of human and rat E1 α subunits shows that the serine residue at the + 1 position in the human sequence is replaced by a proline residue in the rat sequence. The presence of the proline residue apparently causes a 5′-shift by one residue in the cleavage site by the mitochondrial processing peptidase in the rat sequence, when compared to the human sequence. The results provide evidence that the mitochondrial processing peptidase cannot cleave an X-pro bond, similar to trypsin, chymotrypsinand microsomal signal peptidases.     

Primary structure of three minor isoforms of amphioxus sarcoplasmic calcium-binding proteins.

Previously we reported the amino acid sequences of 4 well-defined sacroplasmic, high-affinity Ca(2+)-binding proteins in the protochordate amphioxus, Branchiostoma lanceolatum [1]. Here we report on the complete amino acid sequence determination of 3 additional minor isoforms. The seven isoforms differ from each other in 9 positions of a contiguous 17-residue-long segment (positions 20-36) and can be classified in a alpha (ASCP I, III and IV) and a beta lineage (ASCP II, V, VI and VII).     

Towards fully automated genotyping: use of an X linked recessive spastic paraplegia family to test alternative analysis methods

Advances in dinucleotide-based genetic maps open possibilities for large scale genotyping at high resolution. The current rate-limiting steps in use of these dense maps is data interpretation (allele definition), data entry, and statistical calculations. We have recently reported automated allele identification methods. Here we show that a 10-cM framework map of the human X chromosome can be analyzed on two lanes of an automated sequencer per individual (10–12 loci per lane). We use this map and analysis strategy to generate allele data for an X-linked recessive spastic paraplegia family with a known PLP mutation. We analyzed 198 genotypes in a single gel and used the data to test three methods of data analysis: manual meiotic breakpoint mapping, automated concordance analysis, and whole chromosome multipoint linkage analysis. All methods pinpointed the correct location of the gene. We propose that multipoint exclusion mapping may permit valid inflation of LOD scores using the equation max LOD — (next best LOD).     

Late cataractogenesis in rhesus monkeys irradiated with protons and radiogenic cataract in other species

Rhesus monkeys (Macaca mulatta) which were irradiated at ca. 2 years of age with acute doses (less than or equal to 5 Gy) of protons (32-2300 MeV) are exhibiting the late progressive phase of radiation cataractogenesis 20-24 years after exposure, the period during which we have been monitoring the sequelae of irradiation of the lens. The median life span of the primate is approximately 24 years. Analogous late ocular changes also occur in a similar period of the lifetimes of New Zealand White (NZW) rabbits (Oryctolagus cuniculus) exposed at 8-10 weeks of age to 460-MeV 56Fe ions. In this experiment, which has been in progress for ca. 6 years, we are following the development of radiation-induced lenticular opacification (cataractogenic profiles) throughout the life span. The median life span of the lagomorph is 5-7 years. Cataractogenic profiles for NZW rabbits irradiated with 20Ne and 40Ar ions and 60Co gamma photons were obtained previously. Reference is also made to measurements of the cataractogenic profiles of a short-lived rodent, the Fischer 344 rat (Rattus norvegicus) during the first year after exposure at 8-10 weeks of age to spread-Bragg-peak protons of 55 MeV nominal energy. The median life span of the rodent is reported to be 2-3 years.     

The sensitivity of rapid (partial) review of cervical smears

SHIELD P. W. AND COX N. C. (1998) Cytopathology 9, 84–92 The sensitivity of rapid (partial) review of cervical smears Rapid review involves a daily rapid (e.g. 30 s) review of all smears not normally double-screened. It has been suggested that the method may increase the sensitivity of cervical cytology by identifying abnormalities not reported on initial screening, true false negatives (TFN). Rapid screening is reported to have high sensitivity for cervical neoplasia when used as a preview tool. To be effective, however, in a review mode it must be able to detect TFN. Several studies have found that many TFN result from factors such as low numbers of abnormal cells or subtle expression of diagnostic criteria. Studies on the sensitivity of rapid screening for detecting TFN would therefore provide a more reliable estimate of its value as a review tool. The sensitivity of rapid re-screening was evaluated using a test set of 200 cases. Each of 15 screeners rapidly reviewed (30 s partial screen) the set over a 2-week period. The set consisted of 129 normal, 28 low-grade squamous lesions (CIN I), 37 high-grade lesions (CIN II, III and adenocarcinoma in situ (AIS)) and six invasive carcinomas. The abnormals included 20 TFN cases. The median sensitivity for abnormalities was 62%. Rapid review was more sensitive for CIN II and CIN III (67%) and invasive carcinoma (66.7%) than for CIN I (53%). Great variation was apparent in the sensitivity for individual screeners, with a range of 41–86% for all abnormalities. The sensitivity for TFN cases varied even more (10–75%, median 35%) and for most screeners was significantly (P < 0.05) lower than for cases which were detected on initial screen (53–90%, median 70.6%). Following this trial rapid review was used routinely for a period of 3 months. In this time 11 413 cases were rapidly reviewed. This led to the full review of 415 slides (3.5%) and the identification of 16 cases of undetected CIN (12 CIN I, three CIN II, one CIN III). Based on current estimates of our laboratory false-negative rate this represents between a quarter and half of the TFN cases of CIN that probably occurred in this period. In conclusion, rapid screening is likely to be significantly less sensitive when used in a review rather than a preview mode. In routine practice the method requires a daily commitment of screener time, but does provide a higher yield of TFN smears than does random review, and allows amendment of these results prior to reporting.     

Enrichment of fungi and degradation of styrene in biofilters

Summary Experiments were set up in order to enrich styrene-degrading fungi in biofilters under conditions representative for industrial off-gas treatment. From the support materials tested, polyurethane and perlite proved to be most suitable for enrichment of styrene-degrading fungi. The biofilter with perlite completely degraded styrene when amounts ranging between 290 and 675 mg/m in the influent gas were present. An elimination capacity of at least 70 g styrene per m3 filter bed per hour was calculated.