C-banding visualized by atomic force microscopy

C-banding is a method used for studying chromosome rearrangements near centromeres and for investigating polymorphisms. In human chromosomes, the C-bands are located at the centromere of all the chromosomes and the distal long arm of the Y chromosome. In this study, we aimed to detect the structural changes in chromosomes during the stages of C-banding by atomic force microscopy. We observed crater-like structures in the chromosomes after 2xSSC (saline sodium citrate) treatment and measured the relative difference between the heights of chromatid and centromere of the chromosomes. Results showed that the relative difference was 3 nm in chromosomes 1, 9, 16, and Y, whereas in the other chromosomes this value was 11.6 nm. After Giemsa staining, the relative difference increased by a factor of 16 in chromosomes 1, 9, 16, and Y. The other chromosomes showed no such increase, which is in accordance with our suggestion that nonhiston proteins associated with DNA in constitutive heterochromatin can make the constitutive heterochromatin resistant to C-banding.

The mechanism of G-banding detected by atomic force microscopy

The morphologic changes occurring in human chromosomes during G-banding by trypsin treatment on the same metaphase were followed with the aid of an atomic force microscope (AFM). It was found that trypsin treatment alone caused a pattern of collapse in the chromosomes that was clearly dependent on the duration of trypsinization. The progressive pattern of collapse first indicated the loss of internal differentiation between chromatids, then bands, and finally all internal structures, except for edges running around the chromosomes' perimeter. When stained with Giemsa, the collapsed chromosomes partly regained their original form, and transverse ridges appeared that correspond to G-positive band regions. However, the treatment of fixed chromosomes with trypsin for 42 s diminished the chromosomal edges, and the z-dimensions could not be measured even with the subsequent application of Giemsa.

Data on the PCR Turkish population based loci: LDLR, GYPA, HBGG, D7S8, and Gc

Allele and genotype frequencies for the five PCR-based loci were analyzed in 157 unrelated Turkish individuals. The five PCR-based loci included LDLR, GYPA, HBGG, D7S8, and Gc. The results of the chi-square and exact tests showed that the genotype distribution at the LDLR, GYPA, D7S8, and Gc loci did not significantly differ from the Hardy-Weinberg Expectation (HWE). However, the genotype distribution at the HBGG locus did not conform to HWE. Moreover, the genotype frequencies calculated in this study were compared with the published genotype frequencies of US African American and US Caucasian populations. The Turkish population was significantly different at the HBGG locus from the US Caucasian population. However, there were highly significant differences at the LDLR, HBGG, and Gc loci between the Turkish and African American populations.

Numerical chromosomal abnormalities detected by atomic force microscopy

The numerical abnormalities of human metaphase chromosomes, fixed according to standard procedures for optical microscopy but not treated for banding, were detected by atomic force microscopy (AFM). High-resolution AFM imaging of chromosomes in trisomy 13, 21, and Klinefelter syndrome can be compared directly with the traditional optical image. The unbanded metaphase chromosomes, including the extra ones in trisomic patients showed a structural pattern very similar to G-banding. Comparison of AFM images with light microscopic data allows the identification of specific chromosomes, and images of chromosomes showing numerical and structural abnormalities can then be analysed.

Interactions of DNA with fluorescent dyes: by scanning tunneling microscopy

Genomic DNA was obtained from peripheral blood samples of healthy volunteers and interacted with two fluorescent dyes (i.e. Hoechst 33,258 and ethidium bromide) in aqueous media. These media containing DNA-dye complexes deposited on the gold coated mica surfaces. Then, STM images were obtained in which the STM was operated in air at atmospheric pressure with a tip-to-substrate bias voltage of 250-1000 mV (sample positive) and the tunneling currents in the range of 10-20 pA by using etched tips of Pt/Ir, in constant current mode. Both dyes from molecular clusters on DNA. While, the Hoechst molecules were observed on the DNA chains at regular distances, the ethidium bromide molecular clusters did not.

Serum beta-carotene, vitamin E, vitamin C and malondialdehyde levels in several types of cancer

We measured the levels of serum carotenoids (beta-carotene), total tocopherol (vitamin E), ascorbic acid and malondialdehyde (MDA) in newly diagnosed cancer cases. Levels of the antioxidants and MDA in serum samples from 208 subjects with cancer affecting different sites (59 breast, 38 head and neck, 46 genitourinary, 12 lung, 20 gastrointestinal and 33 other sites) were compared with levels in 156 controls. Cases and controls were compared with respect to a number of potentially confounding factors: age, sex, smoking status, Quetelet index (kg/m2), diet and alcohol intake. Mean (+/- SD) levels of beta-carotene, vitamin E and vitamin C were significantly lower among the cases than the controls (49.35 +/- 36.55 micrograms/l, 0.60 +/- 0.14 mg/dl, 0.40 +/- 0.27 mg/dl and 75.31 +/- 28.59 mg/dl, 0.98 +/- 0.13 mg/dl, 0.88 +/- 0.47 mg/dl, respectively) (P < 0.05). On the other hand, mean levels of MDA were significantly higher among the cases than the controls (6.79 +/- 1.22 nmol/ml and 3.52 +/- 0.97 nmol/ml, respectively) (P < 0.05). The results obtained suggest that measurement of serum antioxidants and MDA levels may provide further useful information when evaluating cancer patients.

[Salmonella tester strain TA104 for the detection of mutagenic and carcinogenic chemicals in our environment]

We used the Salmonella mutagenicity test for detecting chemical carcinogens as mutagens in the Salmonella typhimurium tester strain TA104 . The mutagenicity of several compounds was assessed by induction of histidine revertants in the TA104 . In each experiment we routinely included positive mutagenesis controls using three different concentrations of known mutagens. The mutagenic chemicals such as sodium azide, hydrogen peroxide and hydroxylamine were found to be mutagenic to TA104 at very low concentration (10(-4) mg/ml). Their mutagenic activity decreased while their concentrations were increased. The effect of acridine orange, 2, 4, 6-trinitrobenzene sulphonic acid, 2- phenylnaphthalene and 20- methylcholanthrene were also found to be mutagenic to TA104 at the concentration of 10(-2) mg/ml. The mutagenicity of other materials such as hair dyes, meat- broth preparations+ and cigarette smoke condensates were also tested, and all of them were found to be mutagenic to TA104 . The highest mutagenic activities were observed at the concentration of 10 mg/ml for two different hair dyes and of 1 mg/ml for cigarette smoke condensates.