A search for H/ACA snoRNAs in yeast using MFE secondary structure prediction

MOTIVATION: Noncoding RNA genes produce functional RNA molecules rather than coding for proteins. One such family is the H/ACA snoRNAs. Unlike the related C/D snoRNAs these have resisted automated detection to date. RESULTS: We develop an algorithm to screen the yeast genome for novel H/ACA snoRNAs. To achieve this, we introduce some new methods for facilitating the search for noncoding RNAs in genomic sequences which are based on properties of predicted minimum free-energy (MFE) secondary structures. The algorithm has been implemented and can be generalized to enable screening of other eukaryote genomes. We find that use of primary sequence alone is insufficient for identifying novel H/ACA snoRNAs. Only the use of secondary structure filters reduces the number of candidates to a manageable size. From genomic context, we identify three strong H/ACA snoRNA candidates. These together with a further 47 candidates obtained by our analysis are being experimentally screened.     

A Probabilistic Model for Hydrokinetic Turbine Collision Risks: Exploring Impacts on Fish

A variety of hydrokinetic turbines are currently under development for power generation in rivers, tidal straits and ocean currents. Because some of these turbines are large, with rapidly moving rotor blades, the risk of collision with aquatic animals has been brought to attention. The behavior and fate of animals that approach such large hydrokinetic turbines have not yet been monitored at any detail. In this paper, we conduct a synthesis of the current knowledge and understanding of hydrokinetic turbine collision risks. The outcome is a generic fault tree based probabilistic model suitable for estimating population-level ecological risks. New video-based data on fish behavior in strong currents are provided and models describing fish avoidance behaviors are presented. The findings indicate low risk for small-sized fish. However, at large turbines (≥5 m), bigger fish seem to have high probability of collision, mostly because rotor detection and avoidance is difficult in low visibility. Risks can therefore be substantial for vulnerable populations of large-sized fish, which thrive in strong currents. The suggested collision risk model can be applied to different turbine designs and at a variety of locations as basis for case-specific risk assessments. The structure of the model facilitates successive model validation, refinement and application to other organism groups such as marine mammals.     

Endonuclease Specificity and Sequence Dependence of Type IIS Restriction Enzymes

Restriction enzymes that recognize specific sequences but cleave unknown sequence outside the recognition site are extensively utilized tools in molecular biology. Despite this, systematic functional categorization of cleavage performance has largely been lacking. We established a simple and automatable model system to assay cleavage distance variation (termed slippage) and the sequence dependence thereof. We coupled this to massively parallel sequencing in order to provide sensitive and accurate measurement. With this system 14 enzymes were assayed (AcuI, BbvI, BpmI, BpuEI, BseRI, BsgI, Eco57I, Eco57MI, EcoP15I, FauI, FokI, GsuI, MmeI and SmuI). We report significant variation of slippage ranging from 1–54%, variations in sequence context dependence, as well as variation between isoschizomers. We believe this largely overlooked property of enzymes with shifted cleavage would benefit from further large scale classification and engineering efforts seeking to improve performance. The gained insights of in-vitro performance may also aid the in-vivo understanding of these enzymes.     

Immunohistology on Formol-Sublimate Fixed and Paraplast Embedded Kidney Tissue with Comparison to Formalin Fixation and to Pre-Embedding Immunofluorescent Staining

Many alternative methods for immunopathological evaluation of kidney tissue are now available. Immunofluorescent or immunoperoxidase staining of kidney can be performed after formalin fixation and paraffin embedding. This is also possible after fixation with formol-sublimate (Stieve's fluid) using the immunoperoxidase technique or by immunofluorescence after removal of mercury. Reduction of strong nonspecific fluorescence caused by the mercury fixative parallels the elimination of mercury as verified by X-ray microanalysis of the sections. Using a mouse model with injection of graded dilutions of antiglomerular basement membrane antibodies, immunofluorescent staining after Stieve fixation and embedding in Paraplast was about 60% of that in cryostat sections. Immunofluorescent staining after mercury removal can be followed by silver staining for detailed morphologic study of the same 1 μm Paraplast sections. A case of antiglomerular basement membrane glomerulonephritis is illustrated in more detail to show the necessity of alternative methods, including the technique presented, pre-embedding immunofluorescent staining of Epon sections, and electron microscopy, to make a reliable diagnosis of this disease.     

The Semantic Representation of Event Information Depends on the Cue Modality: An Instance of Meaning-Based Retrieval

The semantic content, or the meaning, is the essence of autobiographical memories. In comparison to previous research, which has mainly focused on the phenomenological experience and the age distribution of retrieved events, the present study provides a novel view on the retrieval of event information by quantifying the information as semantic representations. We investigated the semantic representation of sensory cued autobiographical events and studied the modality hierarchy within the multimodal retrieval cues. The experiment comprised a cued recall task, where the participants were presented with visual, auditory, olfactory or multimodal retrieval cues and asked to recall autobiographical events. The results indicated that the three different unimodal retrieval cues generate significantly different semantic representations. Further, the auditory and the visual modalities contributed the most to the semantic representation of the multimodally retrieved events. Finally, the semantic representation of the multimodal condition could be described as a combination of the three unimodal conditions. In conclusion, these results suggest that the meaning of the retrieved event information depends on the modality of the retrieval cues.     

Efficient algorithms for quantitative trait loci mapping problems.

Rapid advances in molecular genetics push the need for efficient data analysis. Advanced algorithms are necessary for extracting all possible information from large experimental data sets. We present a general linear algebra framework for quantitative trait loci (QTL) mapping, using both linear regression and maximum likelihood estimation. The formulation simplifies future comparisons between and theoretical analyses of the methods. We show how the common structure of QTL analysis models can be used to improve the kernel algorithms, drastically reducing the computational effort while retaining the original analysis results. We have evaluated our new algorithms on data sets originating from two large F(2) populations of domestic animals. Using an updating approach, we show that 1-3 orders of magnitude reduction in computational demand can be achieved for matrix factorizations. For interval-mapping/composite-interval-mapping settings using a maximum likelihood model, we also show how to use the original EM algorithm instead of the ECM approximation, significantly improving the convergence and further reducing the computational time. The algorithmic improvements makes it feasible to perform analyses which have previously been deemed impractical or even impossible. For example, using the new algorithms, it is reasonable to perform permutation testing using exhaustive search on populations of 200 individuals using an epistatic two-QTL model.     

Assessing the Environmental Risks of Silver from Clothes in an Urban Area

The environmental risks from the use of silver-containing clothes (“silver clothes”) were assessed for an urban area. First, we evaluated whether the use of silver clothes may cause contamination of wastewater treatment sludge that exceeds certain risk thresholds. Second, we assessed the risk of silver exposure to earthworms from applying the sludge as fertilizer to agricultural land. The most critical parameter was the concentration of silver in silver clothes, for which estimates in the literature vary by more than five orders of magnitude. For concentrations at the high end of that parameter range, there is considerably increased concentration of silver in the sludge, and toxic effects on earthworms even at modest use rates of silver clothes suggest high risk. At the low end, no risks can be expected. The main recommendation from this study is that if silver is used in clothes, the silver concentration must be kept at the lower end of the range applied in this study if risks are to be avoided. This can be done either by design choices of companies, or by regulation. If the function of the applied silver is not maintained at these lower levels, the use of silver clothes should be minimized.     

Effects of parathyroid hormone on cyclic AMP-formation and cytoplasmic free Ca2+ in the osteosarcoma cell line UMR 106-01

The effects of parathyroid hormone (PTH) on cytoplasmic free CA²⁺ (Ca _i ²⁺ ) and cAMP-formation were investigated in the rat osteosarcoma cell line UMR 106-01.In fura-2 loaded adherent single cells bPTH 1-34 (10 nM–1M) induced a rapid transient increase in Ca _i ²⁺ in 11% of the studied cells. In fura-2 tracings from UMR 106-01 cells in suspension, bPTH 1-34 (0.1 M) induced a transient increase in Ca _i ²⁺ in 20% of the experiments. The transient increase in Ca _i ²⁺ seen in suspensions of cells was not abolished by addition of EGTA (2.5 mM) prior to challenge with PTH, suggesting that the increase in Ca _i ²⁺ was derived from intracellular stores.A marked rapid increase in cAMP-formation was observed in all experiments with cells in suspension, also in the experiments where PTH did not affect Ca _i ²⁺ .These data show that PTH causes a release of Ca²⁺ from intracellular stores in a small percentage of osteosarcoma UMR 106-01 cells, and that PTH is capable of inducing an increase in cAMP-formation without affecting Ca _i ²⁺ in osteoblasts.     

Science commentary: Why wine might be less harmful than beer and spirits

Objective: To analyse sick leave in women at risk of primary hyperparathyroidism before its diagnosis. Design: Case-control study nested within a screened cohort of postmenopausal women. Cases were women with hyperparathyroidism without prior knowledge of their disease and no traditional symptoms or complications. Controls were women from the screened population without hyperparathyroidism. Setting: Population based screening within a Swedish community. Subject: 48 case-control pairs of women aged 55-70 years. Main outcome measure: Sick leave during the 5 years before diagnosis. Results: Total duration of sickness benefits was longer in the cases than controls, and this discrepancy included sick leave on full time or half time and for periods of longer than a week. Cases had an increased risk of sick leave more than half of the investigated time compared with controls (odds ratio 12). Doctors’ certificates showed that the overrepresented sick leave in the cases related mainly to cardiovascular diseases. Conclusion: Asymptomatic mild primary hyperparathyroidism in postmenopausal women is accompanied by a previously unrecognised morbidity, which has consequences for clinical management of the disorder and its impact on the health economy.

Key messages

• Primary hyperparathyroidism mainly affects postmenopausal women, many of whom lack classic symptoms and complications of the disorder and are currently considered suitable for conservative follow up
• Postmenopausal women with asymptomatic primary hyperparathyroidism drew more sickness benefit than matched controls during the 5 years before the diagnosis
• Cardiovascular diseases were the main cause of sick leave
• The duration of sick leave was not correlated with age or serum calcium concentration
• Mild undiagnosed hyperparathyroidism in postmenopausal women is linked with previously unrecognised ill health of importance to the clinical and economic impact of the disorder

     

Increasing the efficiency of variance component quantitative trait loci analysis by using reduced-rank identity-by-descent matrices

Recent technological development in genetics has made large-scale marker genotyping fast and practicable, facilitating studies for detection of QTL in large general pedigrees. We developed a method that speeds up restricted maximum-likelihood (REML) algorithms for QTL analysis by simplifying the inversion of the variance-covariance matrix of the trait vector. The method was tested in an experimental chicken pedigree including 767 phenotyped individuals and 14 genotyped markers on chicken chromosome 1. The computation time in a chromosome scan covering 475 cM was reduced by 43% when the analysis was based on linkage only and by 72% when linkage disequilibrium information was included. The relative advantage of using our method increases with pedigree size, marker density, and linkage disequilibrium, indicating even greater improvements in the future.