Superhelicity of nucleosomal DNA changes its double-helical repeat

Winding DNA in a superhelix can be considered a process consisting of two smooth deformations: bending and twisting. The extra twist angle introduced by winding DNA into the nucleosomal superhelix is calculated by means of the Crick formula to be −0.5° per base pair (bp). This is equivalent to a change of −0.15±0.015 bp in the DNA double-helical repeat. Free DNA in solution is known to have a helical repeat of 10.55±0.1 bp. On the other hand, a weighted average of various estimates of the DNA repeat in the nucleosome is 10.38±0.02. The difference happens to be perfectly accounted for by the superhelicity of the nucleosomal DNA. This implies that the latter is essentially nonconstrained.     

Preoperative Anti-Class III β-Tubulin Antibodies As Relevant Clinical Biomarkers in Ovarian Cancer

Class III β-tubulin (TUBB3) overexpression in ovarian cancer (OC) associates with poor prognosis. We investigated whether TUBB3 overexpression elicited anti-TUBB3 antibody production in OC patients and whether these antibodies may have diagnostic and prognostic impact. The presence of serum anti-TUBB3 antibodies was investigated in 49 untreated OC patients and 44 healthy individuals by an in-house developed ELISA that used recombinant TUBB3 as the antigen. Receiver operating characteristic (ROC) curves were generated to assess the diagnostic accuracy of the assay. Anti-TUBB3 antibodies discriminated OC patients and healthy individuals with excellent sensitivity and specificity (91.8% and 90.9%, respectively). In multivariate analysis, anti-TUBB3 antibody level emerged as an independent prognostic factor for progression free and overall survival. The ELISA was then optimized using a biotin-labeled TUBB3 C-terminal peptide_424-450 instead of recombinant TUBB3 as the antigen and streptavidin-coated plates. The diagnostic role of the anti-TUBB3 antibodies was studied in an independent series of 99 OC patients and 80 gynecological benign disease patients. ROC-curve analysis showed a valuable diagnostic potential for serum anti-TUBB3 antibodies to identify OC patients with higher sensitivity and specificity (95.3% and 97.6%, respectively). Overall, our results provide evidence that preoperative anti-TUBB3 antibody level is a promising diagnostic and prognostic biomarker for the management of OC patients.     

Raman spectroscopy and order in biological systems

The Raman spectra in the low 5–200 cm⁻¹ frequency region of metabolically activeE. coli cells have been analyzed to determine whether they are indicators of a possible in vivo underlying order by applying standard concepts derived from the Raman spectroscopy of crystalline systems with varying degrees of order. The analysis suggests that in-vivo space-time ordered structures involving amino acids associated with DNA exist since the low frequency lines of metabolically active cells can be assigned to lines seen in the spectra of crystals of given amino acids known to associated with DNA early in the lifetime of a cell.     

Implications of reiterative DNA—Metal ion complexes in the induction and development of neoplastic cells

Experimental data on the content in metal ions of DNA preparations from various neoplastic and healthy tissues are summarized: metal ions are preferentially bound to reiterative DNA sequences, where they may induce conformational variations and thus modify the binding of effector molecules such as repressors and polymerases. A model is described where essential and toxic metals are successively loaded on ligand acceptor groups of increasing affinity and thus may reach the final active sites: enzymes and reiterative DNA sequences (equated at least partially to regulative DNA sequences). The effects of some molecules, including peptides, antibiotics, growth factors, hormones, and antineoplastic substances, on DNA conformation could be explained in part by their chelating ability. The neoplastic state may be induced by a modification of metal ion transfer chains: quantitatively by a continuous derepression of genes coding for metal ligands, genes that are only temporarily derepressed during development in normal cells, and qualitatively by modifications of the nucleotidic sequence of structural genes leading to an increase of the chelating ability of the coded metal ligand.     

Ancient DNA analysis of human neolithic remains found in northeastern Siberia

We successfully extracted DNA from a bone sample of a Neolithic skeleton (dated 3,600 +/- 60 years BP) excavated in northeastern Yakutia (east Siberia). Ancient DNA was analyzed by autosomal STRs (short tandem repeats) and by sequencing of the hypervariable region I (HV1) of the mitochondrial DNA (mtDNA) control region. The STR profile, the mitochondrial haplotype, and the haplogroup determined were compared with those of modern Eurasian and Native American populations. The results showed the affinity of this ancient skeleton with both east Siberian/Asian and Native American populations.     

COPD and disease-specific health status in a working population

Background

It has been debated whether treatment should be started early in subjects with mild to moderate COPD. An impaired health status score was associated with a higher probability of being diagnosed with COPD as compared with undiagnosed COPD.

Purpose

To investigate the health status in a healthy working population, to determine reference scores for healthy non-smoking subjects, and to investigate the relationship between their health status and airflow limitation.

Methods

A total of 1333 healthy industrial workers aged ≥40 years performed spirometry and completed the St. George’s Respiratory Questionnaire (SGRQ) and the COPD Assessment Test (CAT).

Results

The prevalence of COPD defined by the fixed ratio of the forced expiratory volume in one second (FEV₁)/forced vital capacity (FVC) was 10.9%, and the prevalence defined by the Lower Limit of Normal was 5.0%. All SGRQ and CAT scores were skewed to the milder end. In 512 non-smoking subjects with normal spirometry, the mean SGRQ score was 5.7, and the mean CAT score was 5.8. In 145 people with COPD defined by the fixed ratio, the mean SGRQ score was 7.9, with a zero score in 6.9% of the subjects. Using the CAT, the mean score was 7.3, with 7.6% of the scores being zero. The scores in patients identified using the Lower Limit of Normal approach were: SGRQ 8.4 (13.4% had a score of zero) and CAT 7.4 (13.4% had a score of zero). Although the 95th percentiles of the Total, Symptoms, Activity, and Impact scores of the SGRQ and CAT sores were 13.8, 34.0, 23.4, 7.2 and 13.6 in the 512 healthy non-smoking subjects, respectively, they were also distributed under their upper limits in over 80% of the COPD subjects.

Conclusion

The COPD-specific health status scores in a working population were good, even in those with spirometrically diagnosed COPD. All scores were widely distributed in both healthy non-smoking subjects and in subjects with COPD, and the score distribution overlapped remarkably between these two groups. This suggests that symptom-based methods are not suitable screening tools in a healthy general population.     

Early life social and ecological determinants of global DNA methylation in wild spotted hyenas

Environmental factors early in life can have lasting influence on the development and phenotypes of animals, but the underlying molecular modifications remain poorly understood. We examined cross‐sectional associations among early life socioecological factors and global DNA methylation in 293 wild spotted hyenas (Crocuta crocuta) in the Masai Mara National Reserve, Kenya, grouped according to three age classes (cub, subadult and adult). Explanatory variables of interest included annual maternal rank based on outcomes of dyadic agonistic interactions, litter size, wild ungulate prey density and anthropogenic disturbance in the year each hyena was born based on counts of illegal livestock in the Reserve. The dependent variable of interest was global DNA methylation, assessed via the LUminometric Methylation Assay, which provides a percentage methylation value calculated at CCGG sites across the genome. Among cubs, we observed approximately 2.75% higher CCGG methylation in offspring born to high‐ than low‐ranking mothers. Among cubs and subadults, higher anthropogenic disturbance corresponded with greater %CCGG methylation. In both cubs and adults, we found an inverse association between prey density measured before a hyena was 3 months old and %CCGG methylation. Our results suggest that maternal rank, anthropogenic disturbance and prey availability early in life are associated with later life global DNA methylation. Future studies are required to understand the extent to which these DNA methylation patterns relate to adult phenotypes and fitness outcomes.     

On the inverse problem in flow cytometry recovering DNA distribution from FMF data

The problem of recovering DNA distribution from cytofluorometric experimental data was investigated. Theoretical analysis led to a convenient formulation of the problem and to uniqueness results for its solution. A minimization algorithm has been implemented to get the optimal estimate of G₁, S, G₂, and M phase percentages. This algorithm was tested in some experimental cases.     

Analysis of cellular DNA distributions

In the fluorescent-flow cytophotometric measurement of cellular DNA content the DNA distributions usually have two peaks. The second peak, which corresponds to the 4C DNA content of G2 and M cells, is often positioned at lower values of DNA content than twice that of the 2C DNA peak which contains G1 cells. Computerized numerical analyses were performed on artificial DNA distributions in which the proportion of S-phase cells was varied. It was demonstrated that the contribution of late S-phase cells to the 4C DNA peak in the histogram shifts the second peak to a position below twice the 2C DNA value. Also, increasing the coefficient of variation of the DNA measurement shifts the second peak position to lower values. A group of 33 DNA distribution histograms was found to have an average G2/G1 peak position ratio of 1.90, in keeping with typical values obtained from the numerical analysis of the artificial populations.     

DNA diversity in the studies of genetic distance among isolated human populations in bosnia

Different degrees of isolation found in various part of Bosnia and Herzegovina may be induced by various factors. Bjelasnica-Treskavica region, located around 40 kilometers southwest from Sarajevo — capital of Bosnia and Herzegovina, is highly specific in that way. We chose three isolated communities: Dejcici, Bobovica and Lukomir for the study of genetic structure of isolated human populations. Based on general data three relative degrees of isolation/openness among the villages have been presumed as follows: first (lower-Dejcici), second (middle — Bobovica) and third (higher — Lukomir) 15 short tandem repeat (STR) loci and hypervariable region of mtDNA were chosen as a markers for study of population structure. Microsatellite allele frequencies, and mtDNA molecular diversity of Heterozigosity and coefficient of gene differentiation across all observed STR loci were estimated. Also, gene and nucleotide diversity of observed mtDNA regions were obtained. Genetic distance between three populations was calculated using method of Reynolds et al. (1983). For analysis of interpopulation relationship based on polymorphism of HV I and HV II region, estimation of pairwise differences was used. results of this research showed consistence with initial hypothesis on divergence based on socio-cultural factors.     

Chromatographic patterns of urinary ethynyl estrogen metabolites in various populations

Radioactive mestranol (ME) and/or ethynylestradiol (EE) were administered to women in Nigeria, Sri Lanka, and the USA, and the types and patterns of radioactive urinary conjugates examined by Sephadex LH-20 chromatography. There are no differences in the total excretion of urinary radioactivity over 3 days. Consistent geographic differences appear to be present in the proportion of 3-, 17-, and 3,17-glucuronides. If confirmed on larger population samples, these observations may indicate significant geographic differences in the hepatic metabolism of ethynyl estrogens.High performance liquid chromatographic patterns of the urinary aglycone metabolites of ME and EE were examined in a number of women. The separation was accomplished on a Chromegaprep Diol column with a gradient of isopropanol in heptane. Ethynyl estrogen metabolism shows considerable individual variation. EE is usually the principal compound excreted following ME or EE administration. Unmetabolized ME is present in the ME profiles. The profiles of EE and ME are similar, with EE demonstrating a more complex pattern. Oxidative metabolism occurs chiefly at positions 2, 6, and 16 and is fairly extensive in the USA subjects. The Sri Lankan women generally show less of the oxidative products and the Nigerian group display a notable lack of oxidative metabolism. There is no difference in the metabolic patterns of long-term oral contraceptive users vs. non-users. Using silver sulfoethylcellulose column chromatography, from 14.1 to 34.7% of the excreted radiolabeled aglycones are non-ethynyl (i.e., either D-homo or de-ethynylated estrogens).     

Analysis of DNA distributions from flow cytometry

A recently proposed automatic procedure for analyzing DNA distribution from flow cytometric data is extensively tested against simulated data. After a discussion of the procedure itself and of the simulation program, the results obtained are reported. They are evidence of the reliability of the procedure in extracting the proper underlying DNA distribution from sets of data obtained under various simulated instances. The different sources of error are then analyzed, along with their quantitative effects on the fit of the fluorescence histogram.     

Metabolic requirements for deactivation of insulin-stimulated glucose transport in isolated rat adipocytes

We have studied the rate of deactivation of the insulin-stimulated glucose transport system following the removal of insulin. Under all conditions, dissociation of insulin from its receptor proceeded much more rapidly than deactivation of the glucose transport system, indicating that deactivation was not simply a passive process reflecting a decline in receptor occupancy. The results demonstrate that deactivation of the glucose transport system is dependent upon ongoing cellular metabolism, and that this process occurs in a normal manner when a variety of substrates (glucose, fructose, or pyruvate) are available to the cells. When no substrate was present, then transport remained at or near the fully stimulated level. In an attempt to localize which metabolic sequence is involved in mediating glucose transport deactivation, studies were performed in the presence of a variety of substrates, inhibitors, and combinations of the two. NaF and citrate had marked effects to inhibit the normal rate of deactivation in the presence of glucose, whereas DNP had no effect on the rate of deactivation in the presence of added glucose. Pyruvate is a substrate which enters the glycolytic pathway distal to the site of action of NaF or citrate in the glycolytic pathway, and in the presence of pyruvate, the inhibiting effects of NaF and citrate on the rate of deactivation were abolished. These results demonstrate that deactivation of the insulin-stimulated glucose transport system is an active process dependent upon some aspect of cellular glucose metabolism. It is likely that the important metabolic step is distal to the point at which pyruvate enters the glycolytic pathway and possibly proximal to the step at which DNP inhibits mitochondrial oxidative phosphorylation.     

Rivers influence the population genetic structure of bonobos (Pan paniscus)

Bonobos are large, highly mobile primates living in the relatively undisturbed, contiguous forest south of the Congo River. Accordingly, gene flow among populations is assumed to be extensive, but may be impeded by large, impassable rivers. We examined mitochondrial DNA control region sequence variation in individuals from five distinct localities separated by rivers in order to estimate relative levels of genetic diversity and assess the extent and pattern of population genetic structure in the bonobo. Diversity estimates for the bonobo exceed those for humans, but are less than those found for the chimpanzee. All regions sampled are significantly differentiated from one another, according to genetic distances estimated as pairwise FSTs, with the greatest differentiation existing between region East and each of the two Northern populations (N and NE) and the least differentiation between regions Central and South. The distribution of nucleotide diversity shows a clear signal of population structure, with some 30% of the variance occurring among geographical regions. However, a geographical patterning of the population structure is not obvious. Namely, mitochondrial haplotypes were shared among all regions excepting the most eastern locality and the phylogenetic analysis revealed a tree in which haplotypes were intermixed with little regard to geographical origin, with the notable exception of the close relationships among the haplotypes found in the east. Nonetheless, genetic distances correlated with geographical distances when the intervening distances were measured around rivers presenting effective current-day barriers, but not when straight-line distances were used, suggesting that rivers are indeed a hindrance to gene flow in this species.     

Eye color prediction using single nucleotide polymorphisms in Saudi population

BackgroundDNA prediction of eye color represent one application of the externally visible characteristics (EVC), which attained growing interest in the field of DNA forensic phenotyping. This is mainly due to its ability to narrow the pool of suspects without the need to compare any retrieved DNA material from the crime scene to a reference DNA. Several methods and multiplex genetic panel were proposed with variable prediction accuracy between different populations. However, such panel was not previously tested in the Saudi population, nor any populations of the Middle East and North Africa origin.MethodA panel of eleven single nucleotide polymorphisms (SNPs) was tested for their association with three eye colors (brown, hazel, and intermediate) in 80 volunteer Saudi individuals. SNPs and haplotype association test with eye colors were performed to identify the top significant SNPs with the three eye colors. Also, multinomial logistic regression was used to construct the prediction model using a training set of 60 subjects, and a validation set of 20 subjects. The goodness of fit parameter of the model to correctly predicts each eye color as compared to the other was performed.ResultsEye color was significantly associated with rs12913832, rs7170852, and rs916977 that are located within HERC2. SNP rs12913832 was the top significant SNP (p-value = 1.78E?15) that accounted for the association in this region, as the other SNPs were not significant after adjusting for rs12913832. A prediction model containing five SNPs showed high prediction accuracy with Area Under the receiver operating characteristic Curves (AUC) equals to 0.95 and 0.83 for brown and intermediate eye colors, respectively. However, the model’s performance was very low for predicting the hazel eye color with AUC equals 0.75.DiscussionDespite the small sample size of our study, we reported very significant SNP associations with eye color. Our model to predict eye colors based on DNA material showed high accuracy for brown and intermediate eye colors. The eye color prediction-model underperformed for the hazel eye colors, suggesting that larger sample size, as well as more comprehensive set of SNPs, could improve the model-prediction accuracy.     

Genetic characterization of antibiotic-resistant Staphylococcus aureus from milk in the North-West Province,South Africa

Food borne diseases are a major public health concern worldwide. Staphylococcus aureus is one of the potential food borne pathogens which causes nosocomial and community acquired infections. In the present study, 74 representative strains of S. aureus isolated and characterized in previous study from different milk samples were subjected to random amplified polymorphic DNA (RAPD) polymerase chain reaction (PCR) and enterobacterial repetitive intergenic consensus (ERIC)-PCR to generate fingerprints to determine the genetic relationships of the isolated strains. A total of 20 RAPD patterns were generated and the number of amplified fragments obtained ranged from 0 to 8 with molecular weight ranging from 250 to 2000 bp. A dendrogram based on fingerprinting pattern grouped isolates into twelve major clusters (I–XII). In the case of ERIC-PCR 9 banding patterns were obtained with amplicons ranging from 1 to 8 and band sizes ranging from 250 to 2000 bp. A total of four major clusters (I–IV) were observed in the dendrogram based on ERIC fingerprints. The discrete banding patterns obtained both from ERIC-PCR and RAPD-PCR showed remarkably the genetic diversity of S. aureus. The findings of this study indicate that raw, bulk and pasteurized milk in the North-West Province was contaminated with toxigenic and multi-drug resistant S. aureus strains. This emphasizes the need to implement appropriate control measures to reduce contamination as well as the spread of virulent S. aureus strains to reduce the burden of disease in humans.