Validation of microarray-based resequencing of 93 worldwide mitochondrial genomes

The human mitochondrial genome consists of a multicopy, circular dsDNA molecule of 16,569 base pairs. It encodes for 13 proteins, two ribosomal genes, and 22 tRNAs that are essential in the generation of cellular ATP by oxidative phosphorylation in eukaryotic cells. Germline mutations in mitochondrial DNA (mtDNA) are an important cause of maternally inherited diseases, while somatic mtDNA mutations may play important roles in aging and cancer. mtDNA polymorphisms are also widely used in population and forensic genetics. Therefore, methods that allow the rapid, inexpensive and accurate sequencing of mtDNA are of great interest. One such method is the Affymetrix GeneChip Human Mitochondrial Resequencing Array 2.0 (MitoChip v.2.0) (Santa Clara, CA). A direct comparison of 93 worldwide mitochondrial genomes sequenced by both the MitoChip and dideoxy terminator sequencing revealed an average call rate of 99.48% and an accuracy of > or =99.98% for the MitoChip. The good performance was achieved by using in-house software for the automated analysis of additional probes on the array that cover the most common haplotypes in the hypervariable regions (HVR). Failure to call a base was associated mostly with the presence of either a run of > or =4 C bases or a sequence variant within 12 bases up- or downstream of that base. A major drawback of the MitoChip is its inability to detect insertions/deletions and its low sensitivity and specificity in the detection of heteroplasmy. However, the vast majority of haplogroup defining polymorphism in the mtDNA phylogeny could be called unambiguously and more rapidly than with conventional sequencing.     

Health Professionals’ Attitudes Towards Using a Web 2.0 Portal for Child and Adolescent Diabetes Care: Qualitative Study

Background

The Internet, created and maintained in part by third-party apomediation, has become a dynamic resource for living with a chronic disease. Modern management of type 1 diabetes requires continuous support and problem-based learning, but few pediatric clinics offer Web 2.0 resources to patients as part of routine diabetes care.

Objectives

To explore pediatric practitioners’ attitudes towards the introduction of a local Web portal for providing young type 1 diabetes patients with interactive pedagogic devices, social networking tools, and locally produced self-care and treatment information. Opportunities and barriers related to the introduction of such systems into clinical practice were sought.

Methods

Twenty clinicians (seven doctors, nine nurses, two dieticians, and two social welfare officers) from two pediatric diabetes teams participated in the user-centered design of a local Web 2.0 portal. After completion of the design, individual semi-structured interviews were performed and data were analyzed using phenomenological methods.

Results

The practitioners reported a range of positive attitudes towards the introduction of a local Web 2.0 portal to their clinical practice. Most interviewees were satisfied with how the portal turned out, and a sense of community emerged during the design process and development of the portal’s contents. A complementary role was suggested for the portal within the context of health practice culture, where patients and their parents would be able to learn about the disease before, between, and after scheduled contacts with their health care team. Although some professionals expected that email communication with patients and online patient information would save time during routine care, others emphasized the importance of also maintaining face-to-face communication. Online peer-to-peer communication was regarded as a valuable function; however, most clinicians did not expect that the portal would be used extensively for social networking amongst their patients. There were no major differences in attitudes between different professions or clinics, but some differences appeared in relation to work tasks.

Conclusions

Experienced clinical practitioners working in diabetes teams exhibited positive attitudes towards a Web 2.0 portal tailored for young patients with type 1 diabetes and their parents. The portal included provision of third-party information, as well as practical and social means of support. The practitioners’ early and active participation provides a possible explanation for these positive attitudes. The findings encourage close collaboration with all user groups when implementing Web 2.0 systems for the care of young patients with chronic diseases, particularly type 1 diabetes. The study also highlights the need for efforts to educate clinical practitioners in the use of Web publishing, social networking, and other Web 2.0 resources. Investigations of attitudes towards implementing similar systems in the care of adults with chronic diseases are warranted.     

Persistence of Helicobacter pylori infection in patients with peptic ulcer perforation

OBJECTIVE: In patients with perforated peptic ulcer (PPU) the convergence between the high eradication rate of Helicobacter pylori infection and low rates of ulcer relapse after treatment has been associated with reinfection by non-virulent strains. The objective of this study was to evaluate the persistence of infection by virulent H. pylori strains and ulcer recurrence in 33 patients with PPU one year after surgery and antimicrobial treatment. MATERIAL AND METHODS: The histological evaluation and molecular detection of H. pylori cagA and ureA genes, vacA allelic types and the polymerase chain reaction-restriction fragment length polymorphism (PCR-RFLP) analyses of the glmM gene products from antral mucosa specimens were performed initially, 2-5 months and 1 year after therapy. RESULTS: The density of H. pylori colonization was temporarily decreased (p<0.05) 2-5 months after therapy. After one year, complete eradication was achieved in only 7 patients (23%) at histological examination and recurrent ulcers were found in 3/33 (9%) patients. The vacA s1a allelic type of cagA-positive strains persisted in 19/33 (58%) PPU patients with identical PCR-RFLP fingerprints in 8/9 (89%) of the patients. CONCLUSIONS: In PPU patients with a low eradication rate of H. pylori infection after surgical and antimicrobial treatment, the frequent recrudescence of the infection is mostly caused by the persisting virulent strains of the cagA and vacA s1a subtypes. In the 1-year follow-up period the recurrent ulceration can be postponed just by the lowered colonization density of H. pylori after eradicative therapy.     

The emergence of Y-chromosome haplogroup J1e among Arabic-speaking populations

Haplogroup J1 is a prevalent Y-chromosome lineage within the Near East. We report the frequency and YSTR diversity data for its major sub-clade (J1e). The overall expansion time estimated from 453 chromosomes is 10 000 years. Moreover, the previously described J1 (DYS388=13) chromosomes, frequently found in the Caucasus and eastern Anatolian populations, were ancestral to J1e and displayed an expansion time of 9000 years. For J1e, the Zagros/Taurus mountain region displays the highest haplotype diversity, although the J1e frequency increases toward the peripheral Arabian Peninsula. The southerly pattern of decreasing expansion time estimates is consistent with the serial drift and founder effect processes. The first such migration is predicted to have occurred at the onset of the Neolithic, and accordingly J1e parallels the establishment of rain-fed agriculture and semi-nomadic herders throughout the Fertile Crescent. Subsequently, J1e lineages might have been involved in episodes of the expansion of pastoralists into arid habitats coinciding with the spread of Arabic and other Semitic-speaking populations.     

Prevalence and correlates of insufficient calcium intake in a Swedish population

OBJECTIVE: To examine associations between calcium intake in the diet, lifestyle factors, and forearm bone mineral density (BMD) in order to identify population subgroups for targeting by screening programs. METHODS: A questionnaire was sent to a random sample of 15% of the inhabitants aged 20-79 years from 2 Swedish municipalities, and the subsample from one of the municipalities was invited to measurement of BMD. The survey response rate was 74% (n = 1,112/1,510) and participation in BMD measurements was 68% (n = 448/659). RESULTS: Only a tendency ( p = .085) toward direct association between calcium intake and forearm BMD was found, and the best multiple regression model was retained to explain BMD excluded calcium intake. Low calcium intake was, instead, in complementary analyses, found to be correlated with the factors old age, female sex, and urban residence in the best multiple regression model. CONCLUSIONS: Population subgroups whose calcium intake is in a range that justifies preventive action could be identified. Screening programs staffed by public health nurses can thereby be informed regarding the subgroups of the population that are at the highest risk of insufficient calcium intake.     

Relationship Between Markers of Body Fat and Calcaneal Bone Stiffness Differs Between Preschool and Primary School Children: Results from the IDEFICS Baseline Survey

The aim of this study was to investigate the relationship between markers of body fat and bone status assessed as calcaneal bone stiffness in a large sample of European healthy pre- and primary school children. Participants were 7,447 children from the IDEFICS study (spread over eight different European countries), age 6.1?±?1.8?years (range 2.1-9.9), 50.5?% boys. Anthropometric measurements (weight, height, bioelectrical impedance, waist and hip circumference, and tricipital and subscapular skinfold thickness) as well as quantitative ultrasonographic measurements to determine calcaneal stiffness index (SI) were performed. Partial correlation analysis, linear regression analysis, and ANCOVA were stratified by sex and age group: preschool boys (n?=?1,699) and girls (n?=?1,599) and primary school boys (n?=?2,062) and girls (n?=?2,087). In the overall study population, the average calcaneal SI was equal to 80.2?±?14.0, ranging 42.4-153. The results showed that preschool children with higher body fat had lower calcaneal SI (significant correlation coefficients between -0.05 and -0.20), while primary school children with higher body fat had higher calcaneal SI (significant correlation coefficients between 0.05 and 0.13). After adjusting for fat-free mass, both preschool and primary school children showed an inverse relationship between body fat and calcaneal stiffness. To conclude, body fat is negatively associated with calcaneal bone stiffness in children after adjustment for fat-free mass. Fat-free mass may confound the association in primary school children but not in preschool children. Muscle mass may therefore be an important determinant of bone stiffness.     

What is going on when the general practitioner doesn't grasp the situation?

Forty-six consultations with 12 GPs in four primary health centres were videotaped. Afterwards the GPs commented on the tapes. Fourteen consultations, in which it was obvious that the GP felt uncertain and did not grasp the situation, were especially studied. One important contributing factor was that the GP often did not fully understand the patient's reason for the consultation. A general outcome was that the GP usually did not allow himself to use his feelings of uncertainty as useful information about the situation.     

Role of dopamine receptors in the dual effect of naloxone on quinpirole-induced yawning in morphine pretreated rats

Summary The present study was undertaken to determine the state of sensitivity of dopamine D2/133 receptors involved in the mediation of yawning behaviour at various times following acute morphine administration to rats. Morphine (3.0 mg/kg, s.c.) induced a biphasic effect on locomotor activity: an initial inhibitory phase lasting for about 30 min was after about an hour followed by a phase of locomotor activation lasting for about 60 min. Dopamine D2/D3 receptor agonist quinpirole (0.01–0.1 mg/kg, s.c.) induced yawning behaviour in rats. Morphine given at 15 or 60 min before (inhibitory phase) inhibited the yawning response to quinpirole (0.1 mg/kg) but not when given at 90 or 120 min before (stimulatory phase). Naloxone (1.0 mg/kg) given 10 min before quinpirole restored yawning inhibited by morphine pretreatment during the inhibitory phase (15–60 min after morphine). However, during the morphine-induced stimulatory phase naloxone strongly inhibited the yawning response to quinpirole. D 1 receptor antagonist SCH 23390 [R-(+)-8-chloro-2,3,4,5-tetrahydro-3-methyl-5-phenyl-1H-3-benzazepin-7-ol hemimaleate] at 0.01 mg/ kg did not affect quinpirole-induced yawning or its inhibition by morphine. However, in rats which received morphine 90 min prior to testing yawning, SCH 23390 enhanced quinpirole-induced yawning behaviour as compared with morphine- or saline-pretreated animals. The data obtained in the present study indicate that morphine pretreatment initially induces a lack of responsiveness of the D2/D3 receptors mediating yawning behaviour and subsequently increases their sensitivity. However, the behavioural expression of hypersensitivity of these receptors seems to be attenuated by the concomitant activation of D1 receptors after morphine pretreatment, and thus the enhanced response to quinpirole is first seen after blockade of D1 receptors. Correspondence to L. Ahtee at the above address     

Diagnosis and treatment of acute myocardial infarction in tertiary and secondary care hospitals in Estonia

AIM: To compare validity of AMI diagnosis and treatment of AMI patients between tertiary and secondary care hospitals in Estonia. METHODS: Two tertiary and seven secondary care hospitals responsible for the treatment of most AMI patients in Estonia were included in the analysis. A random sample of 520 patients admitted to these hospitals with AMI in 2001 was taken from the Estonian Health Insurance Fund database. Medical records were reviewed by trained experts using a standardized data collection form. RESULTS: Forty cases were excluded due to selection errors by the Health Insurance Fund. Of the remaining cases, a diagnosis of AMI was confirmed in 93.3% of cases in tertiary care hospitals and in 83.5% of cases in secondary care hospitals (p < 0.001). A total of 210 cases from tertiary and 213 cases from secondary care hospitals with confirmed AMI diagnoses were included in subsequent analysis. Utilization of beta-blockers, aspirin, and reperfusion therapy was similar in both types of hospitals. In tertiary care hospitals, ACE inhibitors and statins were more frequently used during hospital stay and recommended at discharge compared with secondary care hospitals. In-hospital mortality was similar in both types of hospitals both before and after adjustment. CONCLUSIONS: Tertiary care physicians adhered more strictly to the current definition and guidelines for the management of AMI than did secondary care physicians. However, there is still a need for further improvement in both hospital settings according to international guidelines.