Unzipping Kinetics of Double-Stranded DNA in a Nanopore

We studied the unzipping kinetics of single molecules of double-stranded DNA by pulling one of their two strands through a narrow protein pore. PCR analysis yielded the first direct proof of DNA unzipping in such a system. The time to unzip each molecule was inferred from the ionic current signature of DNA traversal. The distribution of times to unzip under various experimental conditions fit a simple kinetic model. Using this model, we estimated the enthalpy barriers to unzipping and the effective charge of a nucleotide in the pore, which was considerably smaller than previously assumed.Comment: 10 pages, 5 figures, Accepted: Physics Review Letter

Cell cycle genes and ovarian cancer susceptibility: a tagSNP analysis

BACKGROUND: Dysregulation of the cell cycle is a hallmark of many cancers including ovarian cancer, a leading cause of gynaecologic cancer mortality worldwide.METHODS: We examined single nucleotide polymorphisms (SNPs) (n = 288) from 39 cell cycle regulation genes, including cyclins, cyclin-dependent kinases (CDKs) and CDK inhibitors, in a two-stage study. White, non-Hispanic cases (n = 829) and ovarian cancer-free controls (n = 941) were genotyped using an Illumina assay.RESULTS: Eleven variants in nine genes (ABL1, CCNB2, CDKN1A, CCND3, E2F2, CDK2, E2F3, CDC2, and CDK7) were associated with risk of ovarian cancer in at least one genetic model. Seven SNPs were then assessed in four additional studies with 1689 cases and 3398 controls. Association between risk of ovarian cancer and ABL1 rs2855192 found in the original population [odds ratio, ORBB vs AA 2.81 (1.29-6.09), P = 0.01] was also observed in a replication population, and the association remained suggestive in the combined analysis [ORBB vs AA 1.59 (1.08-2.34), P = 0.02]. No other SNP associations remained suggestive in the replication populations.CONCLUSION: ABL1 has been implicated in multiple processes including cell division, cell adhesion and cellular stress response. These results suggest that characterization of the function of genetic variation in this gene in other ovarian cancer populations is warranted. British Journal of Cancer (2009) 101, 1461-1468. doi: 10.1038/sj.bjc.6605284 www.bjcancer.com Published online 8 September 2009 (C) 2009 Cancer Research U

Effective interaction between helical bio-molecules

The effective interaction between two parallel strands of helical bio-molecules, such as deoxyribose nucleic acids (DNA), is calculated using computer simulations of the "primitive" model of electrolytes. In particular we study a simple model for B-DNA incorporating explicitly its charge pattern as a double-helix structure. The effective force and the effective torque exerted onto the molecules depend on the central distance and on the relative orientation. The contributions of nonlinear screening by monovalent counterions to these forces and torques are analyzed and calculated for different salt concentrations. As a result, we find that the sign of the force depends sensitively on the relative orientation. For intermolecular distances smaller than $6\AA$ it can be both attractive and repulsive. Furthermore we report a nonmonotonic behaviour of the effective force for increasing salt concentration. Both features cannot be described within linear screening theories. For large distances, on the other hand, the results agree with linear screening theories provided the charge of the bio-molecules is suitably renormalized.Comment: 18 pages, 18 figures included in text, 100 bibliog

Association between Common Germline Genetic Variation in 94 Candidate Genes or Regions and Risks of Invasive Epithelial Ovarian Cancer

Background: Recent studies have identified several single nucleotide polymorphisms (SNPs) in the population that are associated with variations in the risks of many different diseases including cancers such as breast, prostate and colorectal. For ovarian cancer, the known highly penetrant susceptibility genes (BRCA1 and BRCA2) are probably responsible for only 40% of the excess familial ovarian cancer risks, suggesting that other susceptibility genes of lower penetrance exist.Methods: We have taken a candidate approach to identifying moderate risk susceptibility alleles for ovarian cancer. To date, we have genotyped 340 SNPs from 94 candidate genes or regions, in up to 1,491 invasive epithelial ovarian cancer cases and 3,145 unaffected controls from three different population based studies from the UK, Denmark and USA.Results: After adjusting for population stratification by genomic control, 18 SNPs (5.3%) were significant at the 5% level, and 5 SNPs (1.5%) were significant at the 1% level. The most significant association was for the SNP rs2107425, located on chromosome 11p15.5, which has previously been identified as a susceptibility allele for breast cancer from a genome wide association study (P-trend = 0.0012). When SNPs/genes were stratified into 7 different pathways or groups of validation SNPs, the breast cancer associated SNPs were the only group of SNPs that were significantly associated with ovarian cancer risk (P-heterogeneity = 0.0003; P-trend = 0.0028; adjusted (for population stratification) P-trend = 0.006). We did not find statistically significant associations when the combined data for all SNPs were analysed using an admixture maximum likelihood (AML) experiment- wise test for association (P-heterogeneity = 0.051; P-trend = 0.068).Conclusion: These data suggest that a proportion of the SNPs we evaluated were associated with ovarian cancer risk, but that the effect sizes were too small to detect associations with individual SNPs

Can narratives of white identity reduce opposition to immigration and support for Hard Brexit? A survey experiment

Britain’s vote to leave the European Union highlights the importance of white majority opposition to immigration. This article presents the results of a survey experiment examining whether priming an open form of ethno-nationalism based on immigrant assimilation reduces hostility to immigration and support for right-wing populism in Britain. Results show that drawing attention to the idea that assimilation leaves the ethnic majority unchanged significantly reduces hostility to immigration and support for Hard Brexit in the UK. Treatment effects are strongest among UKIP, Brexit and white working-class voters. This is arguably the first example of an experimental treatment leading to more liberal immigration policy preferences

Biophysical and electrochemical studies of protein-nucleic acid interactions

This review is devoted to biophysical and electrochemical methods used for studying protein-nucleic acid (NA) interactions. The importance of NA structure and protein-NA recognition for essential cellular processes, such as replication or transcription, is discussed to provide background for description of a range of biophysical chemistry methods that are applied to study a wide scope of protein-DNA and protein-RNA complexes. These techniques employ different detection principles with specific advantages and limitations and are often combined as mutually complementary approaches to provide a complete description of the interactions. Electrochemical methods have proven to be of great utility in such studies because they provide sensitive measurements and can be combined with other approaches that facilitate the protein-NA interactions. Recent applications of electrochemical methods in studies of protein-NA interactions are discussed in detail

CSF biochemical correlates of mixed affective states

To evaluate the question of whether “mixed” bipolar disorder is a distinct entity, we compared selected cerebrospinal fluid (CSF) biochemical parameters from patients with bipolar disorder, mixed, to those with mania and major depression. Fourteen patients in each category (DSM-III) were studied with regard to CSF HVA, 5HIAA, sodium, potassium, calcium, and magnesium levels under carefully controlled conditions. CSF HVA, 5HIAA, and sodium were found to be significantly higher in manics than in major depressives. Discriminant analysis of the biochemical variables of the mixed affective group identified two biochemically distinct and clinically different subgroups of seven patients each, one resembling the manic group and the other the major depressive group. These findings suggest that mixed affective states do not exist as a separate entity, but are compsed of two subgroups obtained from the manic and major depressive categories.Peer Reviewedhttp://deepblue.lib.umich.edu/bitstream/2027.42/66203/1/j.1600-0447.1988.tb06339.x.pd

Comparison of acute and chronic lithium treatment on 3 H-norepinephrine uptake by rat brain slices

The effects of lithium chloride, given IP in high (2.5–15 mEq/kg) and low (1.25 mEq/kg) doses twice daily, upon 3 H-norepinephrine uptake and retention were examined with slices from four regions of the rat brain, namely brain stem, hypothalamus, parietal cortex, and caudate nucleus. Control uptake was significantly higher in slices from the caudate nucleus and lower in brain stem slices than in slices from hypothalamus or parietal cortex. With the higher doses, uptake increased significantly in all regions after 2 days of treatment and returned to normal by 7 days. With the lowest dose, uptake was increased after 7 days but normal at 14 days. Only in caudate slices was there a second elevation of 3 H-norepinephrine uptake after 21 days of treatment, which returned to normal by 42 days. No other effects were observed during 70 days of treatment with lithium. The correlation between changes in 3 H-norepinephrine uptake and plasma lithium levels was studied.Peer Reviewedhttp://deepblue.lib.umich.edu/bitstream/2027.42/46411/1/213_2004_Article_BF00427599.pd