A dynamic programming approach for finding common patterns in RNAs.

We developed a dynamic programming approach of computing common sequence structure patterns among two RNAs given their primary sequences and their secondary structures. Common patterns between two RNAs are defined to share the same local sequential and structural properties. The locality is based on the connections of nucleotides given by their phosphodiester and hydrogen bonds. The idea of interpreting secondary structures as chains of structure elements leads us to develop an efficient dynamic programming approach in time O(nm) and space O(nm), where n and m are the lengths of the RNAs. The biological motivation is given by detecting common, local regions of RNAs, although they do not necessarily share global sequential and structural properties. This might happen if RNAs fold into different structures but share a lot of local, stable regions. Here, we illustrate our algorithm on Hepatitis C virus internal ribosome entry sites. Our method is useful for detecting and describing local motifs as well. An implementation in C++ is available and can be obtained by contacting one of the authors.     

Artbildung bei der CopepodengattungLimnocalanus durch akkumulative Fernwirkung einer Milieuver?nderung

Ohne Zusammenfassung     

Homogeneous assay for real-time and simultaneous detection of thymidine kinase 1 and deoxycytidine kinase activities

Measurement of thymidine kinase-1 (TK1) and deoxycytidine kinase (dCK) activity may be useful in cancer disease management. Therefore, a one-step homogeneous assay for real-time determination of TK1 and dCK was developed by combining enzyme complementation with fluorescent signal generation using primer extension and a quenched probe oligodeoxyribonucleotide system at 37 °C. Complementation, for producing dCTP and TTP from nucleoside substrates, was carried out by dTMP kinase and/or UMP/CMP kinase and nucleoside diphosphate kinase. dNTP was continuously incorporated into a fixed oligodeoxyribonucleotide primer, template, and probe system, and the fluorescent signal was generated by using the combined actions of primer extension and 5′ exonuclease activity of Thermophilus aquaticus (Taq) DNA polymerase for specific relief of fluorescent quenching. Fluorescence was captured at 1-min intervals using a real-time polymerase chain reaction (PCR) instrument. A horizontal threshold line, crossing all sample relative fluorescent units (RFU) values at the level of the RFU of the blank sample at the end of the assay (i.e., 90 min), was drawn, obtaining RFU measurement data in minutes for each sample. Duplex proof of principle was demonstrated by the independent determination of different amounts of dCK and TK1 in combination. R² values of 0.90 were demonstrated with Prolifigen TK-REA U/L reference values obtained from pathological canine and human serum samples.     

The Intestinal Eukaryotic Virome in Healthy and Diarrhoeic Neonatal Piglets

Neonatal porcine diarrhoea of uncertain aetiology has been reported from a number of European countries. The aim of the present study was to use viral metagenomics to examine a potential viral involvement in this diarrhoea and to describe the intestinal virome with focus on eukaryotic viruses. Samples from the distal jejunum of 50 diarrhoeic and 19 healthy piglets from 10 affected herds were analysed. The viral fraction of the samples was isolated and nucleic acids (RNA and DNA fractions) were subjected to sequence independent amplification. Samples from diarrhoeic piglets from the same herds were pooled whereas samples from healthy piglets were analysed individually. In total, 29 clinical samples, plus two negative controls and one positive control consisting of a mock metagenome were sequenced using the Ion Torrent platform. The resulting sequence data was subjected to taxonomic classification using Kraken, Diamond and HMMER. In the healthy specimens, eight different mammalian virus families were detected (Adenoviridae, Anelloviridae, Astroviridae, Caliciviridae, Circoviridae, Parvoviridae, Picornaviridae, and Reoviridae) compared to four in the pooled diarrhoeic samples (Anelloviridae, Circoviridae, Picornaviridae, and Reoviridae). It was not possible to associate a particular virus family with the investigated diarrhoea. In conclusion, this study does not support the hypothesis that the investigated diarrhoea was caused by known mammalian viruses. The results do, however, indicate that known mammalian viruses were present in the intestine as early as 24–48 hours after birth, indicating immediate infection post-partum or possibly transplacental infection.     

A rolling-gliding wear simulator for the investigation of tribological material pairings for application in total knee arthroplasty

Background  

Material wear testing is an important technique in the development and evaluation of materials for use in implant for total knee arthroplasty. Since a knee joint induces a complex rolling-gliding movement, standardised material wear testing devices such as Pin-on-Disc or Ring-on-Disc testers are suitable to only a limited extent because they generate pure gliding motion only.     

Influence of temperature changes on migraine occurrence in Germany

Many factors trigger migraine attacks. Weather is often reported to be one of the most common migraine triggers. However, there is little scientific evidence about the underlying mechanisms and causes. In our pilot study, we used smartphone apps and a web form to collect around 4,700 migraine messages in Germany between June 2011 and February 2012. Taking interdiurnal temperature changes as an indicator for changes in the prevailing meteorological conditions, our analyses were focused on the relationship between temperature changes and the frequency of occurrence of migraine attacks. Linear trends were fitted to the total number of migraine messages with respect to temperature changes. Statistical and systematic errors were estimated. Both increases and decreases in temperature lead to a significant increase in the number of migraine messages. A temperature increase (decrease) of 5 °C resulted in an increase of 19?±?7 % (24?±?8 %) in the number of migraine messages.     

Getting into shape: How do rod-like bacteria control their geometry?

Rod-like bacteria maintain their cylindrical shapes with remarkable precision during growth. However, they are also capable to adapt their shapes to external forces and constraints, for example by growing into narrow or curved confinements. Despite being one of the simplest morphologies, we are still far from a full understanding of how shape is robustly regulated, and how bacteria obtain their near-perfect cylindrical shapes with excellent precision. However, recent experimental and theoretical findings suggest that cell-wall geometry and mechanical stress play important roles in regulating cell shape in rod-like bacteria. We review our current understanding of the cell wall architecture and the growth dynamics, and discuss possible candidates for regulatory cues of shape regulation in the absence or presence of external constraints. Finally, we suggest further future experimental and theoretical directions which may help to shed light on this fundamental problem.     

Does Gender Matter? Female Representation on Corporate Boards and Firm Financial Performance - A Meta-Analysis

In recent years, there has been an ongoing, worldwide debate about the representation of females in companies. Our study aimed to meta-analytically investigate the controversial relationship between female representation on corporate boards and firm financial performance. Following a systematic literature search, data from 20 studies on 3097 companies published in peer-reviewed academic journals were included in the meta-analysis. On average, the boards consisted of eight members and female participation was low (mean 14%) in all studies. Half of the 20 studies were based on data from developing countries and 62% from higher income countries. According to the random-effects model, the overall mean weighted correlation between percentage of females on corporate boards and firm performance was small and non-significant (r = .01, 95% confidence interval: -.04, .07). Similar small effect sizes were observed when comparing studies based on developing vs. developed countries and higher vs. lower income countries. The mean board size was not related to the effect sizes in studies. These results indicate that the mere representation of females on corporate boards is not related to firm financial performance if other factors are not considered. We conclude our study with a discussion of its implications and limitations.