Mismatch repair of deaminated 5-methyl-cytosine

Deamination of 5-methyl-cytosine in double-stranded DNA produces a G-T mismatch. Heteroduplexes of bacteriophage lambda DNA containing a G-T mismatch at the site of a G-5-meC base-pair in one of the parental phages were constructed and used to transfect Escherichia coli cells. Genetic analysis of the progeny phages derived from such heteroduplexes suggests that, in E. coli, mismatches resulting from the deamination of 5-methyl-cytosine are repaired by a system requiring the E. coli dcm methylase and some, but not all, of the functions of the E. coli methyl-directed mismatch repair system. The repair appears to act only on the G-T mismatch and acts specifically to restore the cytosine methylation sequence.     

Free mutual mate preferences in house mice affect reproductive success and offspring performance

When social constraints on the expression of mate preferences are absent, variation in offspring viability is predicted to favour females and males that display mate preferences. Earlier studies showed that female and male house mice, Mus domesticus, tested individually and mated with preferred (P) partners had higher reproductive success and better progeny performance than individuals mated with nonpreferred (NP) partners. Here we tested the effects of mutual mate preferences on reproductive success, offspring viability and performance. We conducted mate preference tests and created four types of reproductive pairings. One involved females and males that preferred each other (P-P); the second type had females that preferred the male but the male did not prefer the female (P-NP); the third had females that did not prefer the male but the male did prefer the female (NP-P). The last set consisted of females and males that did not prefer each other (NP-NP). We measured components of fitness for breeders (reproductive success) and offspring viability (birth-to-weaning viability and weight variation) as well as measures of offspring performance. There were no statistical differences in reproductive success of breeders or offspring viability and quality (weight variation) among the four types of pairings. There were, however, consistent differences between P-P versus NP-NP matings. The number of pups weaned, time to first litter, birth-to-weaning viability, pup body weight at birth and weaning, and the growth rates for pups of both sexes were consistently greater for progeny from P-P matings than NP-NP matings. Significant differences occurred among the four mating types in dominance of sons during aggression trials, nest construction and predator avoidance. Progeny from P-P matings displayed behaviour associated with higher fitness more often than progeny from NP-NP matings. These data show that breeders produce more highly competent progeny, most likely to survive, when social constraints on the expression of mate preferences in both sexes are relaxed.Copyright 2003 The Association for the Study of Animal Behaviour. Published by Elsevier Science Ltd. All rights reserved.      

Competition between n-alkane-assimilating yeasts and bacteria during colonization of sandy soil microcosms

An n-alkane-assimilating strain of Candida tropicalis was selected in sandy soil inoculated with microorganisms from contaminated sites. Competition experiments with n-alkane utilizers from different strain collections confirmed that yeasts overgrow bacteria in sandy soil. Acidification of the soil is one of the colonization factors useful for the yeasts. It can be counteracted by addition of bentonite, a clay mineral with high ion exchange capacity, but not, however, by kaolin. Strains of different yeast species showed different levels of competitiveness. Strains of Arxula adeninivorans, Candida maltosa, and Yarrowia lipolytica overgrew strains of C. tropicalis, C. shehatae or Pichia stipitis. Two strains of C. maltosa and Y. lipolytica coexisted during several serial transfers under microcosm conditions. Received: 20 October 1999 / Received revision: 26 January 2000 / Accepted: 27 January 2000     

Identification and evaluation of novel synovial tissue biomarkers in rheumatoid arthritis by laser scanning cytometry

Introduction

Suitable biomarkers are essential for therapeutic strategies in personalized medicine in terms of diagnosis as well as of prognosis. With highly specific biomarkers, it is possible, for example, to identify patients with poor prognosis, which enables early intervention and intensive treatment. The aim of this study was to identify and validate biomarkers and possible combinations for a prospective use in immunoscintigraphy, which may improve diagnosis of rheumatoid arthritis (RA) patients with consideration of inflammatory activity in the affected joints. Therefore, we tested several monoclonal antibodies (mAbs) directed against cellular-surface molecules on cells likely to be involved in the pathogenesis of RA.

Methods

Synovial tissue from patients with long-standing RA (accompanied by synovitis with varying states of current activity) and patients with acute non-RA arthritis were stained for surface molecules on different cell types by using fluorochrome-labeled antibodies. Tissue analysis was done by laser scanning cytometry (LSC), and statistical evaluation, by discriminant analysis and ROC analysis.

Results

CD11b, HLA-DR, CD90, and CD64 revealed significant differences between tissues from patients with RA and acute non-RA arthritis. Especially with the expression of CD64, both patient cohorts could be discriminated with high sensitivity and specificity. RA classification was improved by simultaneously investigating the expression of two or three different surface proteins, such as HLA-DR, CD90, and CD29 in the tissue. The simultaneous analysis of CD64 together with CD304 or the combination of CD11b and CD38 was suitable for the identification of RA patients with high current activity in synovitis.

Conclusions

In this study, we showed that LSC is a novel reliable method in biomarker prevalidation in RA. Hence, identified mAbs in situ may allow their potential use in in vivo approaches. Moreover, we proved that biomarker-combination analysis resulted in better discrimination than did single-marker analysis. Combinations of these markers make a novel and reliable panel for the discrimination between RA and acute non-RA arthritis. In addition, further expedient combinations may be novel promising biomarker panels to identify current activity in synovitis in RA.     

Sensitive Troponins – Which Suits Better for Hemodialysis Patients? Associated Factors and Prediction of Mortality

Background

In hemodialysis patients, elevated plasma troponin concentrations are a common finding that has even increased with the advent of newly developed sensitive assays. However, the interpretation and relevance of this is still under debate.

Methods

In this cross-sectional study, we analyzed plasma concentrations of sensitive troponin I (TnI) and troponin T (TnT) in stable ambulatory hemodialysis patients (n = 239) and investigated their associations with clinical factors and mortality.

Results

In all of the enrolled patients, plasma TnI or TnT was detectable at a median concentration of 14 pg/ml (interquartile range: 7–29) using the Siemens TnI ultra assay and 49 pg/ml (31–74) using the Roche Elecsys high sensitive TnT assay. Markedly more patients exceeded the 99th percentile for TnT than for TnI (95% vs. 14%, p<0.0001). In a multivariate linear regression model, TnT was independently associated with age, gender, systolic dysfunction, time on dialysis, residual diuresis and systolic blood pressure, whereas TnI was independently associated with age, systolic dysfunction, pulse pressure, time on dialysis and duration of a HD session. During a follow-up period of nearly two years, TnT concentration above 38 pg/mL was associated with a 5-fold risk of death, whereas elevation of TnI had a gradual association to mortality.

Conclusion

In hemodialysis patients, elevations of plasma troponin concentrations are explained by cardiac function and dialysis-related parameters, which contribute to cardiac strain. Both are highly predictive of increased risk of death.     

A Mammalian Cell Based FACS-Panning Platform for the Selection of HIV-1 Envelopes for Vaccine Development

An increasing number of broadly neutralizing monoclonal antibodies (bnMAb) against the HIV-1 envelope (Env) protein has been discovered recently. Despite this progress, vaccination efforts with the aim to re-elicit bnMAbs that provide protective immunity have failed so far. Herein, we describe the development of a mammalian cell based FACS-panning method in which bnMAbs are used as tools to select surface-exposed envelope variants according to their binding affinity. For that purpose, an HIV-1 derived lentiviral vector was developed to infect HEK293T cells at low multiplicity of infection (MOI) in order to link Env phenotype and genotype. For proof of principle, a gp145 Env model-library was established in which the complete V3 domain was substituted by five strain specific V3 loop sequences with known binding affinities to nMAb 447-52D, respectively. Env genes were recovered from selected cells by PCR, subcloned into a lentiviral vector (i) to determine and quantify the enrichment nMAb binders and (ii) to generate a new batch of transduction competent particles. After 2 selection cycles the Env variant with highest affinity was enriched 20-fold and represented 80% of the remaining Env population. Exploiting the recently described bnMAbs, this procedure might prove useful in selecting Env proteins from large Env libraries with the potential to elicit bnMAbs when used as vaccine candidates.     

Respiratory Phenomics across Multiple Models of Protein Hyperacylation in Cardiac Mitochondria Reveals a Marginal Impact on Bioenergetics

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Seasonal and diurnal variations in ultraviolet-B and ultraviolet-A irradiances at and below the sea surface at Helgoland (North Sea) over a 6-year period

Ultraviolet (UV) radiation at four wavelengths (305, 320, 340 and 380 nm) and photosynthetically active radiation (PAR) were measured from May 1994 to October 1999 using Biospherical UV radiometers. A surface reference sensor located on the roof of the Marine Station at Helgoland recorded values every 5 min, and an equivalent profiling underwater sensor was used for measurements in the sea at approximately monthly intervals. The ratio of 305-nm radiation to PAR varied seasonally, with a 14-fold increase from winter to summer. A much weaker seasonal trend (ca. 1.5-fold) was apparent in the ratio of 320-nm radiation to PAR, but there was no seasonal trend in the ratios of 340- or 380-nm radiation to PAR. The year-to-year variations in 305-nm radiation were also much greater relative to PAR than for the other UV wavelengths, but there was no evidence of a change in the 305 nm:PAR ratio over the study period. The ratios of both 305- and 320-nm radiation to PAR increased from dawn to midday, but those of 340- and 380-nm radiation were almost constant through the day, except shortly before sunrise and after sunset when the proportions of 340- and 380-nm radiation increased. Underwater measurements of PAR and UV suggest that the 1% depth for 305-nm radiation was little more than 1 m, but this estimate is valid only for summer and autumn because, in other seasons, few reliable readings for 305-nm radiation could be obtained underwater, and no attenuation coefficient could be calculated. The 1% depths recorded for the other UV wavelengths in the middle 6 months of the year were 2.0 m for 320 nm, 2.6 m for 340 nm and 4.6 m for 380 nm, compared with 12 m for PAR, but the attenuation of all wavebands increased sharply in October and remained higher until March. An analysis of the influence of sun angle, total column ozone concentration, the proportion of skylight, and cloud cover on the ratio of UV wavelengths to PAR in surface irradiance demonstrated that solar angle has a greater influence than ozone concentration on the irradiance at 305 nm, and that the typical occurrence of ozone "holes" in spring may not result in higher UV-B irradiances than occur under higher ozone concentrations in summer. The implications of the data for attempts to model the biological effects of natural UV radiation on marine organisms are considered. Received in revised form: 3 July 2000 Electronic Publication