I/NI-calls for the exclusion of non-informative genes: a highly effective filtering tool for microarray data

MOTIVATION: DNA microarray technology typically generates many measurements of which only a relatively small subset is informative for the interpretation of the experiment. To avoid false positive results, it is therefore critical to select the informative genes from the large noisy data before the actual analysis. Most currently available filtering techniques are supervised and therefore suffer from a potential risk of overfitting. The unsupervised filtering techniques, on the other hand, are either not very efficient or too stringent as they may mix up signal with noise. We propose to use the multiple probes measuring the same target mRNA as repeated measures to quantify the signal-to-noise ratio of that specific probe set. A Bayesian factor analysis with specifically chosen prior settings, which models this probe level information, is providing an objective feature filtering technique, named informative/non-informative calls (I/NI calls). RESULTS: Based on 30 real-life data sets (including various human, rat, mice and Arabidopsis studies) and a spiked-in data set, it is shown that I/NI calls is highly effective, with exclusion rates ranging from 70% to 99%. Consequently, it offers a critical solution to the curse of high-dimensionality in the analysis of microarray data. AVAILABILITY: This filtering approach is publicly available as a function implemented in the R package FARMS (www.bioinf.jku.at/software/farms/farms.html).     

Increased heat requirement for leaf flushing in temperate woody species over 1980–2012: effects of chilling,precipitation and insolation

Recent studies have revealed large unexplained variation in heat requirement‐based phenology models, resulting in large uncertainty when predicting ecosystem carbon and water balance responses to climate variability. Improving our understanding of the heat requirement for spring phenology is thus urgently needed. In this study, we estimated the species‐specific heat requirement for leaf flushing of 13 temperate woody species using long‐term phenological observations from Europe and North America. The species were defined as early and late flushing species according to the mean date of leaf flushing across all sites. Partial correlation analyses were applied to determine the temporal correlations between heat requirement and chilling accumulation, precipitation and insolation sum during dormancy. We found that the heat requirement for leaf flushing increased by almost 50% over the study period 1980–2012, with an average of 30 heat units per decade. This temporal increase in heat requirement was observed in all species, but was much larger for late than for early flushing species. Consistent with previous studies, we found that the heat requirement negatively correlates with chilling accumulation. Interestingly, after removing the variation induced by chilling accumulation, a predominantly positive partial correlation exists between heat requirement and precipitation sum, and a predominantly negative correlation between heat requirement and insolation sum. This suggests that besides the well‐known effect of chilling, the heat requirement for leaf flushing is also influenced by precipitation and insolation sum during dormancy. However, we hypothesize that the observed precipitation and insolation effects might be artefacts attributable to the inappropriate use of air temperature in the heat requirement quantification. Rather than air temperature, meristem temperature is probably the prominent driver of the leaf flushing process, but these data are not available. Further experimental research is thus needed to verify whether insolation and precipitation sums directly affect the heat requirement for leaf flushing.     

Identification of a common risk haplotype for canine idiopathic epilepsy in the ADAM23 gene

Background

Idiopathic epilepsy is a common neurological disease in human and domestic dogs but relatively few risk genes have been identified to date. The seizure characteristics, including focal and generalised seizures, are similar between the two species, with gene discovery facilitated by the reduced genetic heterogeneity of purebred dogs. We have recently identified a risk locus for idiopathic epilepsy in the Belgian Shepherd breed on a 4.4 megabase region on CFA37.

Results

We have expanded a previous study replicating the association with a combined analysis of 157 cases and 179 controls in three additional breeds: Schipperke, Finnish Spitz and Beagle (p_c = 2.9e–07, p_GWAS = 1.74E-02). A targeted resequencing of the 4.4 megabase region in twelve Belgian Shepherd cases and twelve controls with opposite haplotypes identified 37 case-specific variants within the ADAM23 gene. Twenty-seven variants were validated in 285 cases and 355 controls from four breeds, resulting in a strong replication of the ADAM23 locus (p_raw = 2.76e–15) and the identification of a common 28 kb-risk haplotype in all four breeds. Risk haplotype was present in frequencies of 0.49–0.7 in the breeds, suggesting that ADAM23 is a low penetrance risk gene for canine epilepsy.

Conclusions

These results implicate ADAM23 in common canine idiopathic epilepsy, although the causative variant remains yet to be identified. ADAM23 plays a role in synaptic transmission and interacts with known epilepsy genes, LGI1 and LGI2, and should be considered as a candidate gene for human epilepsies.

Electronic supplementary material

The online version of this article (doi:10.1186/s12864-015-1651-9) contains supplementary material, which is available to authorized users.     

Inducing autoflocculation in the diatom <Emphasis Type="Italic">Phaeodactylum tricornutum</Emphasis> through CO<Subscript>2</Subscript> regulation

The effect of pH on flocculation was studied using the diatom Phaeodactylum tricornutum and the green algae Scenedesmus cf. obliquus as surrogate species. There was a distinct, species-specific threshold of pH where flocculation started. P. tricornutum started to flocculate at pH 10.5 and S. cf. obliquus at pH 11.3. Above this threshold, settling rates up to 360 cm h⁻¹ were observed for P. tricornutum and the concentrating factor was up to 60-fold. The combined effect of pH, turbulence, and cell density on flocculation of P. tricornutum was additionally studied in a factorial 5³-design experiment. pH was the most important factor affecting flocculation, but at the pH threshold (pH 10.5), the concentrating factor was increased by increasing cell density and turbulence. Algae increases the pH during photosynthesis, and the P. tricornutum and S. cf. obliquus cultures increased the pH to a maximum of 10.8 and 9.5, respectively, after discontinuing the CO₂ supply. For P. tricornutum, this was above the flocculation threshold, and rapid settling of this species due to increased pH was observed in a matter of hours after the CO₂ supply was turned off. This could be used as a simple, low-cost, initial dewatering step for this species.     

Tree seasonality in a warming climate

Climate warming has increased researchers' interest in plant phenology and its modelling. Although the main focus is on projections of accelerated springtime phenological events, also a further extension of the growing season by delayed growth cessation is often projected. However, ecophysiological studies indicate that, for boreal and temperate trees, such generalisations are precluded owing to differential climatic conditions and inter- and intraspecific genetic differences. The annual cycle of these trees is an integrated system, where one phase affects subsequent phases, resulting in delayed impacts, which are only partially addressed in current ecophysiological models. Here, we outline an updated integrated conceptual model of the annual cycle by identifying ecophysiological phenomena that are particularly significant under climate warming.     

Restoration of managed pine fens: effect on hydrology and vegetation

Question: How does restoration affect the hydrology and the understorey vegetation of managed pine fens? Location: Oligotrophic pine fens in Natura 2000 areas in Kainuu, eastern Finland. Methods: Eleven managed pine fens and eight pristine reference pine fens were chosen for the study in 2005. The managed fens, which had been drained for forestry during the 1970s and 1980s, were restored in 2007. The water table was monitored in all fens over four growing seasons during 2006 to 2009, and vegetation was surveyed from permanent sample plots in 2006 and 2009. Results: Before restoration in 2006, the water table was at a significantly lower level in the managed fens compared with the pristine fens. Immediately after restoration, the water table rose to the same level as in the pristine fens, and this change was permanent. Forest drainage had had little impact on the understorey vegetation of the managed fens in the three decades before restoration, with species typical of pristine fens still dominating the sites. Forest dwarf shrubs and feather mosses had started to increase in cover, but mire dwarf shrubs and Sphagnum mosses still dominated the managed fens. Only the typical hollow species Sphagnum majus, Sphagnum balticum and Scheuzeria palustris were missing from the managed fens. Two years after restoration, the changes in species composition were also marginal, with increased cover of mire dwarf shrubs and sedges being the only significant change. Conclusions: The success of restoration of oligotrophic pine fens seems likely, given that changes in hydrological functioning occurred rapidly, and since little change has occurred in the vegetation composition after draining. Speeding up the regeneration process in these peatland types by restoration may, therefore, be recommended, especially if the drainage effect extends to nearby pristine mires and influences their biodiversity.     

Serum lipidomics meets cardiac magnetic resonance imaging: profiling of subjects at risk of dilated cardiomyopathy

Dilated cardiomyopathy (DCM), characterized by left ventricular dilatation and systolic dysfunction, constitutes a significant cause for heart failure, sudden cardiac death or need for heart transplantation. Lamin A/C gene (LMNA) on chromosome 1p12 is the most significant disease gene causing DCM and has been reported to cause 7-9% of DCM leading to cardiac transplantation. We have previously performed cardiac magnetic resonance imaging (MRI) to LMNA carriers to describe the early phenotype. Clinically, early recognition of subjects at risk of developing DCM would be important but is often difficult. Thus we have earlier used the MRI findings of these LMNA carriers for creating a model by which LMNA carriers could be identified from the controls at an asymptomatic stage. Some LMNA mutations may cause lipodystrophy. To characterize possible effects of LMNA mutations on lipid profile, we set out to apply global serum lipidomics using Ultra Performance Liquid Chromatography coupled to mass spectrometry in the same LMNA carriers, DCM patients without LMNA mutation and controls. All DCM patients, with or without LMNA mutation, differed from controls in regard to distinct serum lipidomic profile dominated by diminished odd-chain triglycerides and lipid ratios related to desaturation. Furthermore, we introduce a novel approach to identify associations between the molecular lipids from serum and the MR images from the LMNA carriers. The association analysis using dependency network and regression approaches also helped us to obtain novel insights into how the affected lipids might relate to cardiac shape and volume changes. Our study provides a framework for linking serum derived molecular markers not only with clinical endpoints, but also with the more subtle intermediate phenotypes, as derived from medical imaging, of potential pathophysiological relevance.     

Riedel's thyroiditis in a patient with multiple sclerosis

Our patient developed Riedel's thyroiditis soon after having an exacerbation of multiple sclerosis (MS). MS has been associated with other autoimmune diseases, including thyroiditis, and both Hashimoto's thyroiditis and subacute thyroiditis have been described in connection with MS. Yet, we are not aware of any other patient reported to have concomitant MS and Riedel's thyroiditis. The association between MS and Riedel's thyroiditis remains obscure but may reflect an autoimmune disorder common to both diseases.