Addressing Inter-Gene Heterogeneity in Maximum Likelihood Phylogenomic Analysis: Yeasts Revisited

Phylogenomic approaches to the resolution of inter-species relationships have become well established in recent years. Often these involve concatenation of many orthologous genes found in the respective genomes followed by analysis using standard phylogenetic models. Genome-scale data promise increased resolution by minimising sampling error, yet are associated with well-known but often inappropriately addressed caveats arising through data heterogeneity and model violation. These can lead to the reconstruction of highly-supported but incorrect topologies. With the aim of obtaining a species tree for 18 species within the ascomycetous yeasts, we have investigated the use of appropriate evolutionary models to address inter-gene heterogeneities and the scalability and validity of supermatrix analysis as the phylogenetic problem becomes more difficult and the number of genes analysed approaches truly phylogenomic dimensions. We have extended a widely-known early phylogenomic study of yeasts by adding additional species to increase diversity and augmenting the number of genes under analysis. We have investigated sophisticated maximum likelihood analyses, considering not only a concatenated version of the data but also partitioned models where each gene constitutes a partition and parameters are free to vary between the different partitions (thereby accounting for variation in the evolutionary processes at different loci). We find considerable increases in likelihood using these complex models, arguing for the need for appropriate models when analyzing phylogenomic data. Using these methods, we were able to reconstruct a well-supported tree for 18 ascomycetous yeasts spanning about 250 million years of evolution

Chromatin and epigenetics: current biophysical views

Recent advances in high-throughput sequencing experiments and their theoretical descriptions have determined fast dynamics of the "chromatin and epigenetics" field, with new concepts appearing at high rate. This field includes but is not limited to the study of DNA-protein-RNA interactions, chromatin packing properties at different scales, regulation of gene expression and protein trafficking in the cell nucleus, binding site search in the crowded chromatin environment and modulation of physical interactions by covalent chemical modifications of the binding partners. The current special issue does not pretend for the full coverage of the field, but it rather aims to capture its development and provide a snapshot of the most recent concepts and approaches. Eighteen open-access articles comprising this issue provide a delicate balance between current theoretical and experimental biophysical approaches to uncover chromatin structure and understand epigenetic regulation, allowing free flow of new ideas and preliminary results

Orthostatic hypotension: clinical review and case study

Transient loss of consciousness (TLOC) accounts for 3% of all attendance in emergency departments within the UK. More than 90% of TLOC presentations are due to epileptic seizures, psychogenic seizures or syncope. However, in England and Wales in 2002, it was estimated that 92000 patients were incorrectly diagnosed with epilepsy, at an additional annual cost to the NHS of up to £189 million. This article will reflect on the case study of a 54-year-old female patient who presented with a possible TLOC, and had a background of long-term depression. Differential diagnoses will be discussed, but the article will focus on orthostatic hypotension. Being diagnosed with this condition is independently associated with an increased risk of all-cause mortality. Causes of orthostatic hypotension and the pathophysiology behind the condition will be discussed, highlighting the importance of obtaining an accurate clinical history. This is extremely pertinent if a patient collapses in an NHS setting and this is witnessed by nurses because they can contribute to the history of the type of collapse, to aid diagnosis and correct treatment. In addition, nurses have a valuable role to play in highlighting polypharmacy to doctors, and non-medical prescribers, as a contributing factor to orthostatic hypotension is polypharmacy. It is therefore important to accurately distinguish TLOC aetiology, not only to provide appropriate management, but to also identify patients at risk of morbidity/mortality related to underlying disease.N/

Schadstoffreduktion durch Magerverbrennung mit Vorverdampfung und Vorvermischung Abschlussbericht

In this final report, a combustion chamber with low emission of harmful substances according to the concept of lean burn with pre-evaporation and pre-mixing of liquid fuels is introduced. Results from medium pressure experiments up to 6 bar and high pressure tests up to 20 bar, and from an investigation of the two phase flow in the pre-mixing section are given and discussed. The NOx achieved emissions of around 35 ppm, at a working pressure of 20 bar and a combustion chamber entry temperature of 788K, are very low (reduction compared to a low - NOx diffusion combustion chamber by about 85 %/). The low NOx emissions are made possible by quick evaporation (degree of evaporation about 100 %/ after a distance of 150 mm) and an homogeneous mixture of the fuel of the pre-mixing section, without wetting of the pre-evaporator wallIn dem vorliegenden Abschlussbericht wird eine schadstoffarme Brennkammer nach dem Konzept der Magerverbrennung mit Vorverdampfung und Vorvermischung von fluessigen Brennstoffen vorgestellt. Es werden Ergebnisse aus Mitteldruckversuchen bis 6 bar und Hochdruckversuchen bis 20 bar aus einer Untersuchung der Zwei-Phasen-Stroemung in der Vormischstrecke dargestellt und diskutiert. Die erzielten NO_x-Emissionen liegen mit 35 ppm, bei einem Betriebsdruck von 20 bar und einer Brennkammer-Eintrittstemperatur von 788 K, sehr niedrig (Reduktion gegenueber einer Low-NO_x Diffusionsbrennkammer um ca. 85%). Ermoeglicht werden die niedrigen NO_x-Emissionen durch eine schnelle Verdampfung (ca. 100% Verdampfungsgrad nach 150 mm Lauflaenge) und eine homogene Mischung des Brennstoffs in der Vormischstrecke, ohne Benetzung der Vorverdampferwand. (orig./AKF)Available from TIB Hannover: RR 4026(97-0011)+a / FIZ - Fachinformationszzentrum Karlsruhe / TIB - Technische InformationsbibliothekSIGLEDEGerman

Evaluation and establishment of reference intervals using the i-STAT1 blood chemistry analyzer in turkeys

ABSTRACT: In veterinary medicine, point-of-care testing techniques have become popular, since they provide immediate results and only small amounts of blood are needed. The handheld i-STAT1 blood analyzer is used by poultry researchers and veterinarians; however, no studies have evaluated the accuracy of this analyzer determined reference intervals in turkey blood. The objectives of this study were to 1) investigate the effect of storage time on turkey blood analytes, 2) compare the results obtained by the i-STAT1 analyzer to those obtained by the GEM Premier 3000, a conventional laboratory analyzer, and 3) establish reference intervals for blood gases and chemistry analytes in growing turkeys using the i-Stat. For the first and second objectives, we used the CG8+ i-STAT1 cartridges to test blood from 30 healthy turkeys in triplicate and once with the conventional analyzer. To establish the reference intervals, we tested a total 330 blood samples from healthy turkeys from 6 independent flocks during a 3-yr period. Blood samples were then divided into brooder (<1 wk) and growing (1–12 wk of age). Friedman's test demonstrated significant time-dependent changes in blood gas analytes, but not for electrolytes. Bland-Altman analysis revealed that there was agreement between the i-STAT1 and the GEM Premier 300 for most of the analytes. However, Passing-Bablok regression analysis identified constant and proportional biases in the measurement of multiple analytes. Tukey's test revealed significant differences in the whole blood analytes between the means of brooding and growing birds. The data presented in the present study provide a basis for measuring and interpreting blood analytes in the brooding and growing stages of the turkey lifecycle, offering a new approach to health monitoring in growing turkeys