Nonlinear electrophoresis and focusing of macromolecules

Effects of nonlinear dependence drift velocity of (double-stranded) DNA vs. electric field strength were investigated. In comparatively weak fields, the molecular drift velocity is proportional to the external electric field, while in strong fields there is additional nonlinear component. This effect offers possibilities to manipulate the total drift velocity at will-the macromolecules of different size can be made to move in opposite directions in pulsed field gel electrophoresis.A new approach for focusing DNA molecules based on nonlinear electrophoresis and geometric trapping in electric fields is proposed. The focusing is carried out in an alternating nonuniform electric field, created by using a wedge gel with hyperbolic boundaries. It is shown that the fractions separated in such wedge retain their rectilinear shape.Gel electrophoresis experiments supported the possibility of a pronounced nonlinear focusing of DNA molecules. This nonlinear separation technique presents encouraging prospects for micromanipulating systems and also for preparative isolation of long DNA fragments and development of new separation methods for bacterial fingerprinting.     

<Emphasis Type="Italic">Scoredist</Emphasis>: A simple and robust protein sequence distance estimator

Background  

Distance-based methods are popular for reconstructing evolutionary trees thanks to their speed and generality. A number of methods exist for estimating distances from sequence alignments, which often involves some sort of correction for multiple substitutions. The problem is to accurately estimate the number of true substitutions given an observed alignment. So far, the most accurate protein distance estimators have looked for the optimal matrix in a series of transition probability matrices, e.g. the Dayhoff series. The evolutionary distance between two aligned sequences is here estimated as the evolutionary distance of the optimal matrix. The optimal matrix can be found either by an iterative search for the Maximum Likelihood matrix, or by integration to find the Expected Distance. As a consequence, these methods are more complex to implement and computationally heavier than correction-based methods. Another problem is that the result may vary substantially depending on the evolutionary model used for the matrices. An ideal distance estimator should produce consistent and accurate distances independent of the evolutionary model used.     

Improved profile HMM performance by assessment of critical algorithmic features in SAM and HMMER

Background  

Profile hidden Markov model (HMM) techniques are among the most powerful methods for protein homology detection. Yet, the critical features for successful modelling are not fully known. In the present work we approached this by using two of the most popular HMM packages: SAM and HMMER. The programs' abilities to build models and score sequences were compared on a SCOP/Pfam based test set. The comparison was done separately for local and global HMM scoring.     

Headaches in overweight children and adolescents referred to a tertiary-care center in Israel

Objective: To assess the association between obesity and primary headaches in children and adolescents. Methods and Procedures: In a prospective study, the short‐questionnaire version based on existing International Headache Society diagnostic criteria was administered. Two hundred and seventy‐three children and adolescents (61% females) aged 9–17 years were assessed. One hundred and sixteen (42.5%) subjects were of normal weight, 45 (16.5%) were at risk for overweight (BMI >85th and <95th percentile for age and gender) and 112 (41%) were overweight (BMI ≥95th percentile). The outcome measures were prevalence of headaches, type of headaches, association between headaches and elevated blood pressure in overweight subjects. Results: Headache was reported in 39 (14.3%) subjects, with a similar rate in females (14.5%) and males (14%). Among 39 subjects with headaches, 20 (17.9%) were overweight, 7 (15.6%) were at risk for overweight and 12 (10.3%) were normal‐weight children. Among females, 7.7% of normal‐weight group suffered from headaches, compared with 14.8% of the at risk for overweight group and 20.3% of the overweight group (P for trend 0.04). Among males, the occurrence of headaches was similar in all three weight groups (P = 0.96). The occurrence of headaches increased from 10.6% among children aged 9–11 years to 21.8% in the 15–18 years age group (P < 0.05). In multivariate analysis, a significant independent risk for headaches was present in overweight females (odds ratio (OR) = 3.93, 95% confidence interval (CI) 1.28–12.1) and in adolescents aged 15–18 years (OR = 2.62, 95% CI 1.07–6.45). Elevated blood pressure was not independently associated with headaches. Of the 15 children with migraine, 12 were either at risk for overweight or overweight. Discussion: Overweight females had an almost fourfold excess risk of headaches when compared with normal‐weight girls.