wsp Gene sequences from the Wolbachia of filarial nematodes

Wolbachia endosymbiotic bacteria are widespread in arthropods and are also present in filarial nematodes. Almost all filarial species so far examined have been found to harbor these endosymbionts. The sequences of only three genes have been published for nematode Wolbachia (i.e., the genes coding for the proteins FtsZ and catalase and for 16S rRNA). Here we present the sequences of the genes coding for the Wolbachia surface protein (WSP) from the endosymbionts of eight species of filaria. Complete gene sequences were obtained from the endosymbionts of two different species, Dirofilaria immitis and Brugia malayi. These sequences allowed us to design general primers for amplification of the wsp gene from the Wolbachia of all filarial species examined. For these species, partial WSP sequences (about 600 base pairs) were obtained with these primers. Phylogenetic analysis groups these nematode wsp sequences into a coherent cluster. Within the nematode cluster, wsp-based Wolbachia phylogeny matches a previous phylogeny obtained with ftsZ gene sequences, with a good consistency of the phylogeny of hosts (nematodes) and symbionts (Wolbachia). In addition, different individuals of the same host species (Dirofilaria immitis and Wuchereria bancrofti) show identical wsp gene sequences.

A two-phase strategy for detecting recombination in nucleotide sequences

Genetic recombination can produce heterogeneous phylogenetic histories within a set of homologous genes. Delineating recombination events is important in the study of molecular evolution, as inference of such events provides a clearer picture of the phylogenetic relationships among different gene sequences or genomes. Nevertheless, detecting recombination events can be a daunting task, as the performance of different recombination-detecting approaches can vary, depending on evolutionary events that take place after recombination. We previously evaluated the effects of post-recombination events on the prediction accuracy of recombination-detecting approaches using simulated nucleotide sequence data. The main conclusion, supported by other studies, is that one should not depend on a single method when searching for recombination events. In this paper, we introduce a two-phase strategy, applying three statistical measures to detect the occurrence of recombination events, and a Bayesian phylogenetic approach to delineate breakpoints of such events in nucleotide sequences. We evaluate the performance of these approaches using simulated data, and demonstrate the applicability of this strategy to empirical data. The two-phase strategy proves to be time-efficient when applied to large datasets, and yields high-confidence results.

Bellerophon: a program to detect chimeric sequences in multiple sequence alignments

Bellerophon is a program for detecting chimeric sequences in multiple sequence datasets by an adaption of partial treeing analysis. Bellerophon was specifically developed to detect 16S rRNA gene chimeras in PCR-clone libraries of environmental samples but can be applied to other nucleotide sequence alignments.

PCR bias toward the wild-type k-ras and p53 sequences: Implications for PCR detection of mutations and cancer diagnosis

PCR-based cancer diagnosis requires detection of rare mutations in k-ras, p53 or other genes. The assumption has been that mutant and wild-type sequences amplify with near equal efficiency, so that they are eventually present in proportions representative of the starting material. Work factor IX suggests that this assumption is invalid for one case of near-sequence identity To test the generality of this phenomenon and its relevance to cancer diagnosis, primers distant from point mutations in p53 and k-ras were used to amplify, wild-type and mutant sequences from these genes. A substantial bias against PCR amplification of mutants was observed for two regions of the p53 gene and one region of k-ras. For kras and p53, bias was observed when the wild-type and mutant sequences were amplified separately or when mixed in equal proportions before PCR. Bias was present with proofreading and non-proofreading polymerases. Mutant and wild-type segments of the factor V cystic fibrosis transmembrane conductance regulator and prothrombin genes were amplified and did not exhibit PCR bias. Therefore, the assumption of equal PCR efficiency for point mutant and wild-type sequences is invalid in several systems. Quantitative or diagnostic PCR will require validation for each locus, and enrichment strategies may be needed to optimize detection of mutants.

Comparison of calcaneal ultrasound and DXA in young women

Purpose: The purpose of the study was to assess quantitative ultrasound (QUS) parameters in collegiate female gymnasts, a population whose training incorporates high-impact loading, which is particularly osteogenic, and to determine the discriminative capacity of this relatively new radiation-free technique compared with bone densitometry in a young healthy population. Methods: We studied 19 collegiate gymnasts and 23 healthy controls undergoing regular weight-bearing activity, matched for age (gymnasts 19.2 +/- 1.2, controls 19.9 +/- 1.6 yr) and body weight (gymnasts 56.7 +/- 3.7, controls 57.7 +/- 7.8 kg). QUS parameters of the calcaneus (broadband ultrasound attenuation (BUA), bone velocity (BV), and speed of sound (SOS)) were measured by a Walker Sonix UBA 575+. Bone mineral density (BMD; g.cm(-2)) of the lumbar spine, hip (Femoral neck, trochanter. Ward's triangle) and whole body was assessed by dual energy x-ray absorptiometry (DXA, Hologic QDR 1000/W). Data analysis included unpaired two-tailed Student's t-tests, analysis of variance, Pearson product-moment, and Spearman rank-order correlations. Results: Regional and whole body BMD of gymnasts was greater than controls (P < 0.001), with the difference being 7-28%. Average QUS parameters of the right and left calcaneus were also higher (P < 0.001) in the gymnasts. BUA, BV, and SOS were significantly (P < 0.001) correlated to each bone site with r = 0.54-0.79. Analysis of receiver operating characteristic (ROC) curves indicated no significant difference in sensitivity and specificity for QUS and DXA measures. Conclusions: These results indicate that QUS parameters of the calcaneus are higher in young women gymnasts compared to individuals who undergo regular weight-bearing activity and that QUS parameters are able to discriminate between these two groups in a similar manner as does regional and whole body BMD.

Structural basis of recognition of monopartite and bipartite nuclear localization sequences by mammalian importin-alpha

Importin-alpha is the nuclear import receptor that recognizes cargo proteins which contain classical monopartite and bipartite nuclear localization sequences (NLSs), and facilitates their transport into the nucleus. To determine the structural basis of the recognition of the two classes of NLSs by mammalian importin-alpha, we co-crystallized an N-terminally truncated mouse receptor protein with peptides corresponding to the monopartite NLS from the simian virus 40 (SV40) large T-antigen, and the bipartite NLS from nucleoplasmin. We show that the monopartite SV40 large T-antigen NLS binds to two binding sites on the receptor, similar to what was observed in yeast importin-alpha. The nucleoplasmin NLS-importin-alpha complex shows, for the first time, the mode of binding of bipartite NLSs to the receptor. The two basic clusters in the NLS occupy the two binding sites used by the monopartite NLS, while the sequence linking the two basic clusters is poorly ordered, consistent with its tolerance to mutations. The structures explain the structural basis for binding of diverse NLSs to the sole receptor protein. (C) 2000 Academic Press.

Analysis of Mouse Keratin 6a Regulatory Sequences in Transgenic Mice Reveals Constitutive, Tissue-Specific Expression by a Keratin 6a Minigene

The analysis of keratin 6 expression is complicated by the presence of multiple isoforms that are expressed constitutively in a number of internal stratified epithelia, in palmoplantar epidermis, and in the companion cell layer of the hair follicle. In addition, keratin 6 expression is inducible in interfollicular epidermis and the outer root sheath of the follicle, in response to wounding stimuli, phorbol esters, or retinoic acid. In order to establish the critical regions involved in the regulation of keratin 6a (the dominant isoform in mice), we generated transgenic mice with two different-sized mouse keratin 6a constructs containing either 1.3 kb or 0.12 kb of 5' flanking sequence linked to the lacZ reporter gene. Both constructs also contained the first intron and the 3' flanking sequence of mouse keratin 6a. Ectopic expression of either transgene was not observed. Double-label immunofluorescence analyses demonstrated expression of the reporter gene in keratin 6 expressing tissues, including the hair follicle, tongue, footpad, and nail bed, showing that both transgenes retained keratinocyte-specific expression. Quantitative analysis of beta -galactosidase activity verified that both the 1.3 and 0.12 kb keratin 6a promoter constructs produced similar levels of the reporter. Notably, both constructs were constitutively expressed in the outer root sheath and interfollicular epidermis in the absence of any activating stimulus, suggesting that they lack the regulatory elements that normally silence transcription in these cells. This study has revealed that a keratin 6a minigene contains critical cis elements that mediate tissue-specific expression and that the elements regulating keratin 6 induction lie distal to the 1.3 kb promoter region.

Initial results of ultrasound screening for aneurysm of the abdominal aorta in Western Australia: relevance for endoluminal treatment of aneurysm disease

Background. Increased life expectancy in men during the last thirty years is largely due to the decrease in mortality from cardiovascular disease in the age group 29-69 yr. This change has resulted in a change in the disease profile of the population with conditions such as aneurysm of the abdominal aorta (AAA) becoming more prevalent. The advent of endoluminal treatment for AAA has encouraged prophylactic intervention and fuelled the argument to screen for the disease. The feasibility of inserting an endoluminal graft is dependent on the morphology and growth characteristics of the aneurysm. This study used data from a randomized controlled trial of ultrasound screening for AAA in men aged 65-83 yr in Western Australia for the purpose of determining the norms of the living anatomy in the pressurized infrarenal aorta. Aims. To examine (1) the diameters of the infra-renal aorta in aneurysmal and non-aneurysmal cases, (2) the implications for treatment modalities, with particular reference to endoluminal grafting, which is most dependent on normal and aneurysmal morphology, and (3) any evidence to support the notion that northern Europeans are predisposed to aneurysmal disease. Methods. Using ultrasound, a randomized control trial was established in Western Australia to assess the value of a screening program in males aged 65-83 yr, The infra-renal aorta was defined as aneurysmal if the maximum diameter was 30 mm or more. Aortic diameter was modelled both as a continuous tin mm) and as a binary outcome variable, for those men who had an infra-renal diameter of 30 mm or more. ANOVA and linear regression were used for modelling aortic diameter as a continuum, while chi-square analysis and logistic regression were used in comparing men with and without the diagnosis of AAA. Findings. By December 1998, of 19.583 men had been invited to undergo ultrasound screening for AAA, 12.203 accepted the invitation (corrected response fraction 70.8%). The prevalence of AAA increased with age from 4.8% at 65 yr to 10.8% at 80 yr (chi (2) = 77.9, df = 3, P<0.001). The median (IQR) diameter for the non-aneurysmal group was 21.4 mm (3.3 mm) and there was an increase (<chi>(2) = 76.0, df = 1, P<0.001) in the diameter of the infra-renal aorta with age. Since 27 mm is the 95th centile for the non-aneurysmal infra-renal aorta, a diameter of 30 mm or more is justified as defining an aneurysm. The risk of AAA was higher in men of Australian (OR = 1.0) and northern European origin (OR = 1.0, 95%CL: 0.9. 1.2) compared with those of Mediterranean origin (OR = 0.5, 99%CL: 0.4, 0.7). Conclusion. Although screening has not yet been shown to reduce mortality from AAA. these population-based data assist the understanding of aneurysmal disease and the further development and use of endoluminal grafts for this condition. (C) 2001 Published by Elsevier Science Ltd on behalf of The International Society for Cardiovascular Surgery.

Ultrasound evaluation of polymer gel dosimeters

A new method for the evaluation of radiotherapy 3D polymer gel dosimeters has been developed using ultrasound to assess the significant structural changes that occur following irradiation of the dosimeters. The ultrasonic parameters of acoustic speed of propagation, attenuation and transmitted signal intensity were measured as a function of absorbed radiation dose. The dose sensitivities for each parameter were determined as 1.8 x 10(-4) s m(-1) Gy(-1), 3.9 dB m(-1) Gy(-1) and 3.2 V-1 Gy(-1) respectively. All parameters displayed a strong variation with absorbed dose that continued beyond absorbed doses of 15 Gy. The ultrasonic measurements demonstrated a significantly larger dynamic range in dose response curves than that achieved with previously published magnetic resonance imaging (MRI) dose response data. It is concluded that ultrasound shows great potential as a technique for the evaluation of polymer gel dosimeters.

Chimeric 16S rDNA sequences of diverse origin are accumulating in the public databases

A significant number of chimeric 16S rDNA sequences of diverse origin were identified in the public databases by partial treeing analysis. This suggests that chimeric sequences, representing phylogenetically novel non-existent organisms, are routinely being overlooked in molecular phylogenetic surveys despite a general awareness of PCR-generated artefacts amongst researchers.

Intra- and interspecific divergence in the nuclear sequences of the clock gene period in species of the Drosophila buzzatii cluster

We have measured nucleotide variation in the CLOCK/CYCLE heterodimer inhibition domain (CCID) of the clock X-linked gene period in seven species belonging to the Drosophila buzzatii cluster, namely D. buzzatii, Drosophila koepferae, Drosophila antonietae, Drosophila serido, Drosophila gouveai, Drosophila seriema and Drosophila borborema. We detected that the purifying selection is the main force driving the sequence evolution in period, in agreement with the important role of CCID in clock machinery. Our survey revealed that period provides valuable phylogenetic information that allowed to resolve phylogenetic relationships among D. gouveai, D. borborema and D. seriema, which composed a polytomic clade in preliminary studies. The analysis of patterns of intraspecific variation revealed two different lineages of period in D. koepferae, probably reflecting introgressive hybridization from D. buzzatii, in concordance with previous molecular data.

Ultrasound imaging in rehabilitation: Just a fad?

Real-time ultrasound imaging provides an unrivalled opportunity to observe muscle morphology and contraction. This has obvious potential for clinical practice and the tool is beginning to be adopted into physical therapy. The implementation of ultrasound imaging has become particularly widespread for assessment of size and activation of deep trunk muscles, such as the transversus abdominis and lumbar multifidus, and for assessment of the pelvic floor muscles. The obvious benefit for these areas is that ultrasound permits observation of muscles that are difficult to assess through noninvasive means. This realization of the clinical potential of ultrasound imaging has been paralleled by an explosion of clinical and physiological research. However, despite the enthusiasm for utilization of ultrasound imaging, a question that is critical to address is whether ultrasound can actually improve rehabilitation.

The systematic use of intraoperative vascular Doppler ultrasound during microsurgical subinguinal varicocelectomy improves precise identification and preservation of testicular blood supply

Objective: To evaluate the impact of systematic use of intraoperative Doppler ultrasound during microsurgical subinguinal varicocele repair. Design: Prospective clinical study. Setting: Andrology laboratory and male infertility section of the urology department of a tertiary care hospital. Patient(s): Two hundred and thirteen men with clinical varicocele. Intervention(s): Subinguinal microsurgical varicocele ligation using an intraoperative vascular Doppler flow detector. Main Outcome Measure(s): Number of veins ligated, lymphatic spared, arteries identified or accidentally ligated. Result(s): A statistically significant greater number of arteries were identified and preserved when intraoperative vascular Doppler was used. In addition, the average number of internal spermatic veins ligated was statistically significantly greater in the same group. Accidental artery ligation occurred in two cases (1.1%) in which the Doppler was not applied. There was no statistically significant difference in number of lymphatics spared between groups. Conclusion(s): Our findings showed that concomitant use of intraoperative vascular Doppler during microsurgical varicocelectomy allows more arterial branches to be preserved, and more internal spermatic veins are likely to be ligated. This device should be considered an attractive tool to improve surgical outcomes and safety. (Fertil Steril (R) 2010; 93: 2396-9. (C)2010 by American Society for Reproductive Medicine.)