Of circles, forks and humanity: Topological organisation and replication of mammalian mitochondrial DNA

The organisation of mammalian mitochondrial DNA (mtDNA) is more complex than usually assumed. Despite often being depicted as a simple circle, the topology of mtDNA can vary from supercoiled monomeric circles over catenanes and oligomers to complex multimeric networks. Replication of mtDNA is also not clear cut. Two different mechanisms of replication have been found in cultured cells and in most tissues: a strand-asynchronous mode involving temporary RNA coverage of one strand, and a strand-coupled mode rather resembling conventional nuclear DNA replication. In addition, a recombination-initiated replication mechanism is likely to be associated with the multimeric mtDNA networks found in human heart. Although an insight into the general principles and key factors of mtDNA organisation and maintenance has been gained over the last few years, there are many open questions regarding replication initiation, termination and physiological factors determining mtDNA organisation and replication mode. However, common themes in mtDNA maintenance across eukaryotic kingdoms can provide valuable lessons for future work.     

Diagnosis of fragile X syndrome by direct mutation analysis

A total of 27 fragile X pedigrees consisting of over 100 nuclear families were analyzed by Southern blotting methods and probes StB12.3 and StB12.3xx to detect the expansion of the (CGG) _n repeat within the FMR-1 gene and the abnormal methylation pattern of the adjacent DNA region responsible for the fragile X syndrome. Clinical expression was found to be associated with the presence of a full mutation ( > 500 bp, associated with abnormal methylation) in all the males and 50% of the females studied, whereas individuals carrying a premutation ( = 100–700 bp) were normal. A preferential size increase in the enlarged (CGG) _n repeat was detected in successive generations, the instability being stronger when transmitted from a female than from a male. No expansion of the premutation to the full mutation occurred in the paternal transmissions, and the size increase was significantly smaller than in the maternal transmissions. This could partly explain the stability of the premutation through several generations in families with transmitting males. In the maternal transmissions, the risk of expansion of a premutation to a full mutation appeared to depend on its size. The critical maternal premutation size leading invariably to the full mutation was between = 175–200 bp. This is important for genetic counseling and also explains the commonly observed clustering of affected individuals in fragile X families.     

High-rate ferric sulfate generation by a Leptospirillum ferriphilum-dominated biofilm and the role of jarosite in biomass retention in a fluidized-bed reactor

The aims of this work were to develop a high-rate fluidized-bed bioprocess for ferric sulfate production, to characterize biomass retention, and to determine the phylogeny of the enrichment culture. After 7 months of continuous enrichment and air aeration at 37 degrees C, the iron oxidation rate of 8.2 g Fe(2+) L(-1)h(-1) (4.5.10(-12) g Fe(2+) cell(-1) h(-1)) was obtained at a hydraulic retention time (HRT) of 0.6 h. However, oxygen supply became the rate-limiting factor. With gas mixture (99.5% O(2)/0.5% CO(2) (vol/vol)) aeration and HRT of 0.2 h, the iron oxidation rate was 26.4 g Fe(2+) L(-1)h(-1) (1.0.10(-11) g Fe(2+) cell(-1) h(-1)). Leptospirillum sp. was predominant in the mesophilic fluidized-bed reactor (FBR) enrichment culture as determined by fluorescent in situ hybridization, while Acidithiobacillus ferrooxidans was not detected. Denaturing gradient gel electrophoresis (DGGE) of the amplified partial 16S rDNA showed only three bands, indicating a simple microbial community. DGGE fragment excision and sequencing showed that the populations were related to L. ferriphilum (100% similarity in sequence) and possibly to the genus Ferroplasma (96% similarity to F. acidiphilum). Jarosite precipitates accumulated on the top of the activated carbon biomass carrier material, increasing the rate of iron oxidation. The activated carbon carrier material, jarosite precipitates, and reactor liquid contained 59% (or 3.71.10(9) cells g(-1)), 31% (or 3.12.10(10) cells g(-1)) and 10% (or 1.24.10(8) cells mL(-1)) of the total FBR microbes, respectively, demonstrating that the jarosite precipitates played an important role in the FBR biomass retention.     

How well can blood pressure be controlled? Progress report on the Systolic Hypertension in Europe Follow-Up Study (Syst-Eur 2)

Background

The randomised, double-blind, placebo-controlled Systolic Hypertension in Europe trial (Syst-Eur 1) proved that blood pressure (BP) lowering therapy starting with nitrendipine reduces the risk of cardiovascular complications in elderly patients with isolated systolic hypertension. In an attempt to confirm the safety of long-term antihypertensive therapy based on a dihydropyridine, the Syst-Eur patients remained in open follow-up after the end of Syst-Eur 1. This paper presents the second progress report of this follow-up study (Syst-Eur 2). It describes BP control and adherence to study medications.

Methods

After the end of Syst-Eur 1 all patients, treated either actively or with placebo, were invited either to continue or to start antihypertensive treatment with the same drugs as previously used in the active treatment arm. In order to reach the target BP (sitting SBP <150 mmHg), the first line agent, nitrendipine, could be associated with enalapril and/or hydrochlorothiazide.

Results

Of the 3787 eligible patients, 3516 (93%) entered Syst-Eur 2. At the last available visit, 72% of the patients were taking nitrendipine. SBP/DBP at entry in Syst-Eur 2 averaged 160/83 mmHg in the former placebo group and 151/80 mmHg in the former active-treatment group. At the last follow-up visit SBP/DBP in the patients previously randomised to placebo or active treatment had decreased by 16/5 mmHg and 7/5 mmHg, respectively. The target BP was reached by 74% of the patients.

Conclusion

Substantial reductions in systolic BP may be achieved in older patients with isolated systolic hypertension with a treatment strategy starting with the dihydropyridine calcium-channel blocker, nitrendipine, with the possible addition of enalapril and/or hydrochlorothiazide.     

Functional prediction of unidentified lipids using supervised classifiers

Mass spectrometry (MS)-based metabolomics studies often require handling of both identified and unidentified metabolite data. In order to avoid bias in data interpretation, it would be of advantage for the data analysis to include all available data. A practical challenge in exploratory metabolomics analysis is therefore how to interpret the changes related to unidentified peaks. In this paper, we address the challenge by predicting the class membership of unknown peaks by applying and comparing multiple supervised classifiers to selected lipidomics datasets. The employed classifiers include k-nearest neighbours (k-NN), support vector machines (SVM), partial least squares and discriminant analysis (PLS-DA) and Naive Bayes methods which are known to be effective and efficient in predicting the labels for unseen data. Here, the class label predictions are sought for unidentified lipid profiles coming from high throughput global screening in Ultra Performance Liquid Chromatography Mass Spectrometry (UPLC^TM/MS) experimental setup. Our investigation reveals that k-NN and SVM classifiers outperform both PLS-DA and Naive Bayes classifiers. Naive Bayes classifier perform poorly among all models and this observation seems logical as lipids are highly co-regulated and do not respect Naive Bayes assumptions of features being conditionally independent given the class. Common label predictions from k-NN and SVM can serve as a good starting point to explore full data and thereby facilitating exploratory studies where label information is critical for the data interpretation.     

Cholesterol as a Risk Factor for Subarachnoid Hemorrhage: A Systematic Review

BackgroundThe role played by total cholesterol (TC) in risk for subarachnoid hemorrhage (SAH) is unclear because studies report both high and low TC each as a risk factor. We performed a systematic review to clarify associations between lipid profile and SAH.MethodsOur literature search comprised Pubmed, Scopus, and Cochrane Library databases with no language, publication year, or study type limitations. The Preferred Reporting Items for Systematic reviews and Meta-analyses (PRISMA) checklist guided our reporting. Data forms adapted from the Critical Appraisal Skills Program (CASP), and Cochrane Collaboration guidelines provided a platform for risk-of-bias evaluation. We used a random effects model to calculate pooled estimates and assessed heterogeneity with I²-statistics.ResultsOf the final 21 studies reviewed, 12 were prospective and 9 retrospective. All studies assessed TC, four assessed HDL, and none LDL in risk for SAH. Heterogeneity among all, retrospective, and Asian studies was high (I² = 79.5%, I² = 89.0%, and I² = 84.3%) and considerable in prospective (I² = 46.0%). We therefore focused on qualitative analysis and found that only two studies had a low risk of bias. According to these studies high TC increases risk for SAH in men, whereas the role of HDL remained unclear.ConclusionThe low-risk-of-bias studies suggest that elevated TC levels elevate risk for SAH in men. Due to the high prevalence of hypercholesterolemia, population attributable risk (PAR) of hypercholesterolemia may exceed the PARs of smoking and hypertension in men. Apart from diabetes and obesity, the risk-factor profile of SAH seems to resemble that of other cerebrovascular diseases, at least in men.     

Cyclic Alternating Pattern Is Associated with Cerebral Hemodynamic Variation: A Near-Infrared Spectroscopy Study of Sleep in Healthy Humans

The cyclic alternating pattern (CAP), that is, cyclic variation of brain activity within non-REM sleep stages, is related to sleep instability and preservation, as well as consolidation of learning. Unlike the well-known electrical activity of CAP, its cerebral hemodynamic counterpart has not been assessed in healthy subjects so far. We recorded scalp and cortical hemodynamics with near-infrared spectroscopy on the forehead and systemic hemodynamics (heart rate and amplitude of the photoplethysmograph) with a finger pulse oximeter during 23 nights in 11 subjects. Electrical CAP activity was recorded with a polysomnogram. CAP was related to changes in scalp, cortical, and systemic hemodynamic signals that resembled the ones seen in arousal. Due to their repetitive nature, CAP sequences manifested as low- and very-low-frequency oscillations in the hemodynamic signals. The subtype A3+B showed the strongest hemodynamic changes. A transient hypoxia occurred during CAP cycles, suggesting that an increased CAP rate, especially with the subtype A3+B, which may result from diseases or fragmented sleep, might have an adverse effect on the cerebral vasculature.     

Genetic structure of freshwater Atlantic salmon (<Emphasis Type="Italic">Salmo salar</Emphasis> L.) populations from the lakes Onega and Ladoga of northwest Russia and implications for conservation

Freshwater Atlantic salmon (Salmo salar L.) populations are a living example of adaptation to the changing conditions caused by glacial cycles. The uniqueness of these populations is emphasized by almost complete resistance to the dangerous parasite Gyrodactylus salaris. In Europe, freshwater salmon populations occur primarily in north-western Russia in the republic of Karelia. These systems include Lakes Ladoga and Onega, the two largest lakes in Europe, each of which harbours a number of freshwater salmon spawning rivers. We used microsatellite markers to study the genetic structure and temporal stability of 11 freshwater salmon populations in Russian Karelia. Populations clustered according their region of origin. Although temporal variation in allele frequencies was observed in the majority of temporal comparisons, various lines of evidence demonstrated that this influence was relatively minor compared to spatial variation that explained eight times more of the variability than temporal variation. Temporal stability tended to occur in populations from rivers with a higher linear lake coefficient. The high level of genetic structuring observed in both lake systems and the apparent low level of migration between populations suggests that treating each river as a separate management unit is recommended. In addition, as the number of populations is large, the best strategy for such fine scale management would be to ensure that the level of natural reproduction in each river is sufficient to sustain the population. A prioritization strategy for population conservation based on estimating the relative roles of different evolutionary forces shaping the gene pools highlighted a number of populations where further monitoring is warranted and also identified populations which could be prioritized for conservation as living gene banks in the event that conservation resources are limited. This prioritization agreed well with the occurrence of temporal (in)stability.     

Stroke research in GenomEUtwin.

Stroke is one of the leading causes of severe disability and death in the world. In the present article we outline possibilities and limitations for future stroke research within the GenomEUtwin. The combined sample of twins born before 1958 from Denmark, Finland, and Sweden, and available for follow-up into the second millennium for non-fatal and fatal stroke events through national inpatient and death registers exceeds 70,000 twin pairs. This sample size will enable the study of genetic influences on stroke and major stroke subtypes. Large samples of twins in GenomEUtwin have been followed up repeatedly through interviews and questionnaires concerning a variety of exposures and potential risk factors for stroke. We briefly outline how this information can be combined with the health register information for epidemiologic and genetic epidemiologic studies of stroke. We also present the number of twin pairs concordant and discordant for stroke in Denmark, Finland and Sweden, and time lags between events for twins concordant for stroke. This information illustrates that the number of affected sib pairs for linkage studies is relatively limited, but the sample sizes are promising for association studies.