Locating transposable element polymorphisms in bacterial genomes.

Although whole-genome sequencing is greatly extending our knowledge of the genetic capacity of those bacterial species, it is only directly informative for the particular strain sequenced. Many bacterial species exhibit more or less genetic polymorphism within their populations and characterising this variety is an extremely important way of elucidating the biology of these species. Often genomic polymorphisms are associated with multicopy elements, particularly transposable elements. We describe a novel method that efficiently characterises the sequences of such polymorphisms. We have optimised heminested inverse PCR (hINVPCR) to assess the diversity of insertional polymorphisms of a transposable element (IS6110) in clinical isolates of Mycobacterium tuberculosis. To increase the yield of information, genomic DNA was digested with different endonucleases (Bsp1286I, HaeII or PvuI), and primers based on both the 5' and 3' ends of IS6110 were used to amplify and determine the genomic sequence upstream (or downstream) of the transposable element. We found that both the choice of restriction enzyme and the use of primers at both ends of the transposable element significantly increased the diversity of the insertion sites identified. Band stabbing was incorporated into the method as an alternative to cloning in order to screen large number of isolates at a sequence level in a rapid and labour-efficient fashion. We describe some of the purposes to which such data can be put.

Monitoring cerebral hemodynamics with transcranial Doppler ultrasound during cognitive and exercise testing in adults following unilateral stroke.

An observational study was performed as a preliminary investigation into the use of transcranial Doppler ultrasound (TCD) for recording cerebral hemodynamic changes during multiple tasks. TCD is a method of measuring cerebral blood flow (CBF) using ultrasound transducers in contact with the surface of the head. Using the maximum flow envelope of the Doppler spectrum returning from the middle cerebral artery (MCA), standard clinical flow indices can be calculated and displayed in real time providing information concerning perturbations in CBF and their potential cause. These indices as well as flow velocity measurements have been recognized as useful in measuring changes in responses to various stimulus that can be used to indicate cardiovascular health. For this study, the pulsatility index (PI) and resistivity index (RI) were chosen since they indicate composite changes indicative of vasoconstriction and vasodilatation which are normal hemodynamic responses under appropriate conditions. A total of eleven participants were recruited to take part in this study. Nine of these individuals had no known disability (Controls); two had experienced unilateral cerebrovascular accidents (Strokes) in the ipsilateral MCA distribution. Maximum velocity envelopes of the spectral Doppler data were recorded using a fixation device designed to stabilize two ultrasound probes (2 MHz) to sample the bilateral MCAs CBF. These measures were performed separately while the subject performed four activities: 1) rest, 2) cognitive challenge, 3) cardiovascular exercise, and 4) simultaneous exercise and cognitive challenge. Cardiovascular parameters were calculated from the data by extracting maximum (Vs) and minimum flow velocities (Vd), PI, RI, and time signatures for each cardiac cycle. The data for all participants shows significant changes in cardiovascular parameters between states of rest and exercise, as well as slight trends across time. Although the data are preliminary, they show the capability of using Doppler spectral examination of the bilateral MCAs in individuals with physical limitation performing cardiovascular exercise. The novelty of examining a population using dynamic exercise who before could not perform such exercise offers the opportunity to study the impact of exercise on global cerebral recovery in unilateral stroke with significant physical impairment.

Molecular epidemiology of disease due to Mycobacterium bovis in humans in the United Kingdom.

Mycobacterium bovis is the causative agent of bovine tuberculosis, with a wide host range. Fifty human M. bovis isolates were typed using spoligotyping and variable number tandem repeats (VNTR). Fifteen of these spoligotypes have not yet been recorded in cattle. The predominant spoligotype in humans and cattle was subdivided by VNTR.