Genetic contributions to preterm birth: implications from epidemiological and genetic association studies

Infants born before term (<37 weeks) have an increased risk of neonatal mortality as well as other health problems. The increasing rate of preterm birth in recent decades, despite improvements in health care, creates an impetus to better understand and prevent this disorder. Preterm birth likely depends on a number of interacting factors, including genetic, epigenetic, and environmental risk factors. Genetic studies may identify markers, which more accurately predict preterm birth than currently known risk factors, or novel proteins and/or pathways involved in the disorder. This review summarizes epidemiological and genetic studies to date, emphasizing the complexity of genetic influences on birth timing. While several candidate genes have been reportedly associated with the disorder, inconsistency across studies has been problematic. More systematic and unbiased genetic approaches are needed for future studies to examine the genetic etiology of human birth timing thoroughly.     

Genetic contributions to preterm birth: Implications from epidemiological and genetic association studies

Infants born before term (<37 weeks) have an increased risk of neonatal mortality as well as other health problems. The increasing rate of preterm birth in recent decades, despite improvements in health care, creates an impetus to better understand and prevent this disorder. Preterm birth likely depends on a number of interacting factors, including genetic, epigenetic, and environmental risk factors. Genetic studies may identify markers, which more accurately predict preterm birth than currently known risk factors, or novel proteins and/or pathways involved in the disorder. This review summarizes epidemiological and genetic studies to date, emphasizing the complexity of genetic influences on birth timing. While several candidate genes have been reportedly associated with the disorder, inconsistency across studies has been problematic. More systematic and unbiased genetic approaches are needed for future studies to examine the genetic etiology of human birth timing thoroughly.     

DNA pooling as a tool for large-scale association studies in complex traits

Pooled genotyping is a powerful and efficient tool for high throughput association analysis, both case-control and family-based. The use of pooling designs can significantly reduce the consumable and labour costs of a study. At the same time, since it is also extremely efficient with DNA resources, pooling can be an extremely effective method for conserving DNA. Here, we consider the main points in study design, and illustrate the application of pooling using psychiatric phenotypes as an example.     

Quantitative profiling of folate and one-carbon metabolism in large-scale epidemiological studies by mass spectrometry.

BACKGROUND: Derangements of one-carbon metabolism have been related to the development of chronic diseases. Metabolic profiling as part of epidemiological studies in this area should include intermediates involved in the transfer of one-carbon units, cofactors for the relevant enzymes and markers of inflammation, kidney function and smoking. METHODS: We established five platforms that measured 6-16 analytes each. Platforms A (gas chromatography-mass spectrometry; GC-MS) and B (gas chromatography-tandem mass spectrometry; GC-MS/MS) involved methylchloroformate derivatization of primary amines, thiols and carboxylic acids. Platform C determined basic compounds by liquid chromatography-tandem mass spectrometry (LC-MS/MS), using an ether-linked phenyl reversed-phase column. Platforms D and E (LC-MS/MS) exploited the efficient ionization and high sensitivity obtained for a wide range of analytes, using a mobile phase containing a high concentration of acetic acid. The chromatographic run times ranged from 3 to 8 min. RESULTS: The analyte concentrations ranged from 0.2 nmol/L to 400 micromol/L. Platforms A and B both measured methylmalonic acid, total homocysteine and related amino acids. Platform B also included sarcosine, cystathionine, tryptophan and kynurenine. Platform C was optimized for the measurement of choline and betaine, but also included arginine, asymmetric and symmetric dimethylarginine and creatinine. A diversity of low abundance compounds mainly occurring in the nanomolar range were measured on platform D. These were vitamin B(2) and B(6) species, neopterin, cotinine and tryptophan metabolites. Platform E measured folates and folate catabolites. CONCLUSIONS: Approximately 40 analytes related to one-carbon metabolism were determined in less than 1 mL of plasma/serum using five complementary analytical platforms. As a method control, several metabolites were measured on two or more platforms. Logistics and data handling were carried out by specially designed software. This strategy allows profiling of one-carbon metabolism in large-scale epidemiological studies.     

Pneumocystis jirovecii multilocus genotyping in pooled DNA samples: a new approach for clinical and epidemiological studies

Specific single-nucleotide polymorphisms (SNPs) are recognized as important DNA sequence variations influencing the pathogenesis of Pneumocystis jirovecii and the clinical outcome of Pneumocystis pneumonia, which is a major worldwide cause of illness among immunocompromised patients. Genotyping platforms for pooled DNA samples are promising methodologies for genetic characterization of infectious organisms. We have developed a new typing strategy for P. jirovecii, which consisted of DNA pools prepared according to clinical data (HIV diagnosis, microscopic and molecular detection of P. jirovecii, parasite burden, clinical diagnosis and follow-up of infection) from individual samples using quantitative real-time PCR followed by multiplex-PCR/single base extension (MPCR/SBE). The frequencies of multiple P. jirovecii SNPs (DHFR312, mt85, SOD215 and SOD110) encoded at three distinct loci, the dihydrofolate reductase (DHFR), the mitochondrial large-subunit rRNA (mtLSU rRNA) and the superoxide dismutase (SOD) loci, were estimated in seven DNA pooled samples, representing a total of 100 individual samples. The studied SNPs were confirmed to be associated with distinct clinical parameters of infection such as parasite burden and follow-up. The MPCR/SBE-DNA pooling methodology, described in the present study, was demonstrated to be a useful high-throughput procedure for large-scale P. jirovecii SNPs screening and a powerful tool for evaluation of clinically relevant SNPs potentially related to parasite burden, clinical diagnosis and follow-up of P. jirovecii infection. In further studies, the candidate SNPs mt85, SOD215 and SOD110 may be used as molecular markers in association with MPCR/SBE-DNA pooling to generate useful information for understanding the patterns and causes of Pneumocystis pneumonia.     

Stability of soluble adhesion molecules, selectins, and C-reactive protein at various temperatures: implications for epidemiological and large-scale clinical studies

BACKGROUND: We assessed the impact of sample storage conditions on soluble vascular cell adhesion molecules (sVCAM), soluble intracellular adhesion molecules (sICAM-1), soluble (s)E-selectin, C-reactive protein (CRP), and sP-selectin. METHODS: Markers were measured by ELISA in venous blood from 10 healthy volunteers on aliquots stored as plasma or whole blood at 4, 21, or 30 degrees C for 1-5 days and after 1-5 freeze-thaw cycles. We compared results on these samples to results for samples processed immediately and stored at -80 degrees C. Statistical models assessed time-related effects and effects of postprocessing conditions. RESULTS: Using an upper limit of 10% variation from baseline with P >0.05, we found that stability duration in plasma was 5 days for sVCAM-1 and sICAM-1 and at least 2 days for sE-selectin at 4, 21, and 30 degrees C and 5 days for CRP at 4 and 21 degrees C and 1 day at 30 degrees C. Stability duration in whole blood was 5 days for sVCAM-1 and sICAM-1 and at least 2 days for sE-selectin at 4, 21, and 30 degrees C and 5 days for CRP at 4 and 21 degrees C and 2 days at 30 degrees C. sP-selectin was not stable in plasma or whole blood. sICAM-1, sVCAM-1, CRP, and sE-selectin were stable after 5 freeze-thaw cycles. CONCLUSIONS: sVCAM-1, sICAM-1, and CRP are stable in plasma or whole blood at 4 and 21 degrees C for at least 3 days and sE-selectin for 2 days. sP-selectin is not stable and therefore requires immediate assay.     

Mass casualty management of a large-scale bioterrorist event: an epidemiological approach that shapes triage decisions

The threat of a BT event has catalyzed serious reflection on the troublesome issues that come with event management and triage. Such reflection has had the effect of multiplying the efforts to find solutions to what could become a catastrophic public health disaster. Management options are becoming more robust, as are reliable detection devices and rapid access to stockpiled antibiotics and vaccines. There is much to be done, however, especially in the organizing, warehousing, and granting/exercising authority for resource allocations. The introduction of these new options should encourage one to believe that, in time, evolving standards of care will make it possible to rethink the currently unthinkable consequences. Unfortunately the cost of such preparedness is high and out of reach of most governments. Most of the developing world has neither the will nor the means to plan for BT events and remains overwhelmed with basic public health concerns (i.e., water, food, sanitation, shelter) that must take priority. Therefore, developed countries will be expected to respond using international exogenous resources to mitigate the effects of such a disaster. As a result, the state capacity of the effected government will be severely compromised. If triage and management of casualties is further compromised, terrorists will have met their goals. One could argue that health sciences will continue for decades to play catch up with the advanced technology driving potential bioagent weaponry. If one lesson was learned from the review of the former Soviet Union's biological weapons program, it is that the unthinkable remains an option to terrorists who have comparable expertise. It is crucial to develop realistic strategies for a BT event. Triage planning (the process of establishing criteria for health care prioritization) permits society to see cases in the context of diverse moral perspectives, limited resources, and compelling health care demands. This includes a competent and compassionate management and triage system and an in-depth and accurate health information system that appropriately addresses every level of threat or consequence. In a PICE stage I to III BT event resources will be compromised. Triage and management will be one process requiring multiple levels of cooperation, coordination, and decision-making. An immediate challenge to existing emergency medical services systems (EMSS) is the recognition that locally there will be a shift of emphasis and decision-making from prehospital first responders to community public health authorities. The author suggests that a working relationship, in most areas, between EMSS and the public health system is lacking. As priorities shift in a BT event to hospitals and public health care systems, they need to: 1. Improve their capabilities and capacities in surveillance, discovery, and in the consequences of different triage and management decisions and interventions in a BT environment, starting at the local level. 2. Develop triage and management systems (with clear lines of authority) based on public health and epidemiologic requirements, capability, and capacity (triage teams, categories, tags, rapid response, established operational priorities, resource-driven responsible management process), and link local level surveillance systems with those at the national or regional level. 3. Use a triage and management system that reflects the population (cohort) at risk, such as the epidemiologic based SEIRV triage framework. 4. Develop an organizational capacity that uses lateral decision-making skills, pre-hospital outpatient centers for triage-specific treatments, health information systems, and resource-driven hospital level pre-designated protocols appropriate for a surge of unprecedented proportions. Such standards of care, it is recommended, should be set at the local to federal levels and spelled out in existing incident-management system protocols.     

Use of a collaborative database for epidemiological analyses and professional practice evaluation

Rationale In nephrology, the NEOERICA project assessed the feasibility of the diagnosis scheme based on a general practice database. This approach opened a new area where routinely collected data could be used for purposes other than patient management, such as epidemiological analysis and professional practice evaluation. In Lyon, the TIRCEL network is made up of a coordination team and an online database. In 2008, a total of 468 professionals participated and 983 patients were in the database corresponding to 4114 consultations and 9250 biological assessments. Objective To investigate the impact of a quality control process on the data from operational databases. Methods We set up a quality control process and we described the impact of this process on data. We also specifically investigated the role of measurement scales in error frequency and we studied the impact of data quality on variables which could be used for professional practice evaluation. Results Quality control allowed us to detect as inconsistent data 7.5% of tested data. This rate is linked to the parameters and varied from less than 1% (weight, diastolic blood pressure and urinary sodium) to more than 30% (serum iron and ferritin). Quality control led mainly to the validation of the identified data for 80.4%, a direct correction was realized for 12.9%, 5.6% by the lab and only 1.2% were set to missing. Average proteinuria was modified with the quality control process (2.09 g per 24 hours vs. 0.82 g per 24 hours); however, the median remained stable (0.21 g per 24 hours). Conclusion Specialty databases such as TIRCEL could not be used for epidemiological research or for the extraction of indicators for professional practice evaluation without strict quality control or the set‐up of data‐entering limits and alarms.     

Saliva as a viable alternative source of human genomic DNA in genetic epidemiology

BACKGROUND: Saliva is a potentially useful but untapped source of genomic DNA for genetic epidemiological studies. However, current commercial methods are mainly concerned with DNA extraction and do not address important issues concerning saliva preservation and storage. As such, we evaluated how various saliva storage conditions affected DNA yield and quality obtained using a new commercially available method that proposes to integrate these aspects in a single kit. METHODS: The conditions involved the extraction of the DNA immediately after saliva collection (condition 1) or when stored at air-conditioned room temperature (20 degrees C) for 1 month (condition 2) and 6 months (condition 3) as well as at -80 degrees C for 6 months (condition 4). The effect of incorporating an additional incubation of saliva samples at 30 degrees C for 2 weeks was also examined. RESULTS: Overall average DNA yield from 2 ml of saliva was 35.5 microg (8.5-85.2 microg). DNA yield was unaffected by incubation of saliva at 30 degrees C but DNA yield under condition 3 was significantly higher compared to conditions 1 and 2. OD260/280 values were acceptable and comparable across all conditions. Differences in storage conditions did not impact DNA quality in real time PCR experiments and genotyping fidelity remained undiminished. CONCLUSION: Saliva is a viable alternative source of human genomic DNA for genetic epidemiological studies and that this new commercial method and possibly other related techniques can be effective means towards this end.     

Evaluation of acute stress-induced regional myocardial ischemia: Comparison of regional contractile and metabolic indices to easily accessible global left ventricular indices

In clinical studies stress-induced myocardial ischemia in patients with coronary artery disease is used to evaluate the severity of this disease. The discussion on the importance of some parameters measured during this intervention is controversial, other parameters are difficult to obtain. On the basis of an experimental model of stress-induced myocardial ischemia, we tried to find an index that reflects best this cardiac state. We therefore compared in eight anesthetized open-chest dogs control conditions with three other hemodynamic states with increasing imbalance between myocardial oxygen demand and oxygen supply: severe stenosis on circumflex coronary artery, 60 s cardiac sympathetic nerve stimulation (CSNS) with a severe stenosis on circumflex coronary artery, and 60 s complete occlusion of circumflex coronary artery. Using a one-way analysis of variance, we found two significantly changed parameters during the stress-induced ischemia: Regional lactate extraction was turned to production (32 +/- 4 vs. -4 +/- 1%) and the ratio of dP/dtmin to dP/dtmax was decreased (1.13 +/- 0.05 vs. 0.67 +/- 0.05; control vs. CSNS with a severe stenosis on circumflex coronary artery). We conclude that the ratio of dP/dtmin to dP/dtmax is an easily accessible, sensitive, and dynamic index for characterization of an stress-induced myocardial ischemia.     

Carcinoma of the cervix and oral contraceptives: epidemiological studies

The relationship between squamous carcinoma of the cervix and oral contraceptive use has been examined in a substantial number of epidemiological studies. On balance there is reasonably convincing evidence that prolonged oral contraceptive use slightly increases the risk of the disease, but some doubt remains as to whether or not confounding factors have been controlled adequately in the studies reporting positive findings. The data are too few at present for any reasoned comment to be made about the possible relationship between oral contraceptives and adenocarcinoma of the cervix.     

Headaches and stress in schoolchildren: an epidemiological study

Headache parameters, personality variables and stress factors were assessed in a sample of about 2,300 school pupils between 10 and 17 years of age in Amsterdam. More than 15% of the subjects reported headaches occurring weekly. Fear of failure and school problems, but not achievement motivation, had significant positive correlations with headache complaints after correction for differences in sex and age. Menarche and social class had little bearing in relation to the headache variables. From all reported causes of headache, stress was mentioned most frequently in both elementary and secondary schools.     

LuckyProfiler: an ImageJ plug-in capable of quantifying FWHM resolution easily and effectively for super-resolution images

Quantifying the resolution of a super-resolution image is vital for biologists trying to apply super-resolution microscopy in various research fields. Among the reported image resolution estimation methods, the one that calculates the full width at half maximum (FWHM) of line profile, called FWHM resolution, continues the traditional resolution criteria and has been popularly used by many researchers. However, quantifying the FWHM resolution of a super-resolution image is a time-consuming, labor-intensive, and error-prone process because this method typically involves a manual and careful selection of one or several of the smallest structures. In this paper, we investigate the influencing factors in FWHM resolution quantification systematically and present an ImageJ plug-in called LuckyProfiler for biologists so that they can have an easy and effective way of quantifying the FWHM resolution of super-resolution images.