Seven-fluorochrome mouse M-FISH for high-resolution analysis of interchromosomal rearrangements

The mouse has evolved to be the primary mammalian genetic model organism. Important applications include the modeling of human cancer and cloning experiments. In both settings, a detailed analysis of the mouse genome is essential. Multicolor karyotyping technologies have emerged to be invaluable tools for the identification of mouse chromosomes and for the deciphering of complex rearrangements. With the increasing use of these multicolor technologies resolution limits are critical. However, the traditionally used probe sets, which employ 5 different fluorochromes, have significant limitations. Here, we introduce an improved labeling strategy. Using 7 fluorochromes we increased the sensitivity for the detection of small interchromosomal rearrangements (700 kb or less) to virtually 100%. Our approach should be important to unravel small interchromosomal rearrangements in mouse models for DNA repair defects and chromosomal instability. Copyright (C) 2003 S. Karger AG, Basel

Computer simulation of pulsed field gel runs allows the quantitation of radiation-induced double-strand breaks in yeast

A procedure for the quantification of double-strand breaks in yeast is presented that utilizes pulsed field gel electrophoresis (PFGE) and a comparison of the observed DNA mass distribution in the gel lanes with calculated distributions. Calculation of profiles is performed as follows. If double-strand breaks are produced by sparsely ionizing radiation, one can assume that they are distributed randomly in the genome, and the resulting DNA mass distribution in molecular length can be predicted by means of a random breakage model. The input data for the computation of molecular length profiles are the breakage frequency per unit length, , as adjustable parameter, and the molecular lengths of the intact chromosomes. The obtained DNA mass distributions in molecular length must then be transformed into distributions of DNA mass in migration distance. This requires a calibration of molecular length vs. migration distance that is specific for the gel lane in question. The computed profiles are then folded with a Lorentz distribution with adjusted spread parameter to account for and broadening. The DNA profiles are calculated for different breakage frequencies and for different values of , and the parameters resulting in the best fit of the calculated to the observed profile are determined

Social Factors of Dietary Risk Behavior in Older German Adults: Results of a Multivariable Analysis

With this analysis, we aimed to examine the associations between social factors and dietary risk behavior in older adults. Data were collected through a full-population postal survey of German adults aged 65 years or older (n = 1687, 33% response proportion, 52% female, mean age = 76 years). Using principal component analysis (PCA), a data-driven Dietary Risk Behavior Index (DRB) was computed. Dietary risk behavior was defined as consumption frequencies of vegetables/fruit, whole grains, and dairy products below national dietary recommendations. By performing a multiple linear regression, we analyzed associations between sociodemographic, socioeconomic, psychosocial, and behavioral factors and dietary risk behavior. Physical activity, female gender, socioeconomic status, social support, and age (in the male sample) were negatively associated with dietary risk behavior. Alcohol consumption and smoking were positively associated with dietary risk behavior. A group-specific analysis revealed a higher goodness-of-fit for the low socioeconomic status group, older adults aged 65–79 years, and women. A comprehensive understanding of the relationships between social factors and dietary risk behavior in older adults assists the group-specific targeting of dietary-related interventions. Demand-oriented dietary interventions should account for underlying social conditions to reduce inequity in dietary risk behavior among older adults. The results of this work may be transferable to municipalities in high-income European countries.Peer Reviewe

Application of Pulsed Field Gel Electrophoresis to Determine γ-ray-induced Double-strand Breaks in Yeast Chromosomal Molecules

The frequency of DNA double-strand breaks (dsb) was determined in yeast cells exposed to γ-rays under anoxic conditions. Genomic DNA of treated cells was separated by pulsed field gel electrophoresis, and two different approaches for the evaluation of the gels were employed: (1) The DNA mass distribution profile obtained by electrophoresis was compared to computed profiles, and the number of DSB per unit length was then derived in terms of a fitting procedure; (2) hybridization of selected chromosomes was performed, and a comparison of the hybridization signals in treated and untreated samples was then used to derive the frequency of dsb

Familial Aggregation of Urinary Tract and Bone Tumors: Searching for a Syndrome

Positive family anamnesis is an important risk factor for cancer, and therefore further investigations need to be done if familial aggregation of cancer is observed. Due to a rare combination of urinary tract and bone tumors occurring in the family presented herein we hypothesized a hereditary predisposition and thus, Li-Fraumeni syndrome was considered to be the most likely differential diagnosis. To confirm Li-Fraumeni syndrome, we set out to investigate this case by analyzing the tumor suppressor gene p53. However, taking into account all the diagnostic results obtained, Li-Fraumeni syndrome could not be confirmed, but there is still uncertainty regarding a definitive diagnosis

Germline mutations in the DNA damage response genes BRCA1, BRCA2, BARD1 and TP53 in patients with therapy related myeloid neoplasms

Therapy related myeloid neoplasms (t-MNs) are complex diseases originating from an interplay between exogenous toxicities and a susceptible organism. It has been hypothesised that in a subset of cases t-MNs develop in the context of hereditary cancer predisposition syndromes

Whole-genome plasma sequencing reveals focal amplifications as a driving force in metastatic prostate cancer

Genomic alterations in metastatic prostate cancer remain incompletely characterized. Here we analyse 493 prostate cancer cases from the TCGA database and perform whole-genome plasma sequencing on 95 plasma samples derived from 43 patients with metastatic prostate cancer. From these samples, we identify established driver aberrations in a cancer-related gene in nearly all cases (97.7%), including driver gene fusions (TMPRSS2:ERG), driver focal deletions (PTEN, RYBP and SHQ1) and driver amplifications (AR and MYC). In serial plasma analyses, we observe changes in focal amplifications in 40% of cases. The mean time interval between new amplifications was 26.4 weeks (range: 5–52 weeks), suggesting that they represent rapid adaptations to selection pressure. An increase in neuron-specific enolase is accompanied by clonal pattern changes in the tumour genome, most consistent with subclonal diversification of the tumour. Our findings suggest a high plasticity of prostate cancer genomes with newly occurring focal amplifications as a driving force in progression