CONAN: copy number variation analysis software for genome-wide association studies

Background  

Genome-wide association studies (GWAS) based on single nucleotide polymorphisms (SNPs) revolutionized our perception of the genetic regulation of complex traits and diseases. Copy number variations (CNVs) promise to shed additional light on the genetic basis of monogenic as well as complex diseases and phenotypes. Indeed, the number of detected associations between CNVs and certain phenotypes are constantly increasing. However, while several software packages support the determination of CNVs from SNP chip data, the downstream statistical inference of CNV-phenotype associations is still subject to complicated and inefficient in-house solutions, thus strongly limiting the performance of GWAS based on CNVs.     

Die wirkung subletaler bleikonzentrationen auf die chemorezeptoren zweier süßwasserfischarten

Sublethal concentrations of lead acetate damage the chemoreceptors of the common catfish and the tench. Histological examinations reveal erosion of the terminal buds.     

Blunt Traumatic Aortic Injury of Right Aortic Arch in a Patient with an Aberrant Left Subclavian Artery

Right-sided aortic arch (RAA) is a rare congenital developmental variant present in about 0.1 percent of the population. This anatomical anomaly is commonly associated with congenital heart disease and complications from compression of mediastinal structures. However, it is unknown if patients are at a higher risk of blunt thoracic aortic injury (BTAI). We report a case of a 20-year-old man admitted to the hospital after being hit by an automobile. Computed tomographic scan revealed an RAA with an aberrant left subclavian artery originating from a Kommerell’s diverticulum. A pseudo-aneurysm was also seen along the aortic arch. A diagnosis of blunt traumatic aortic injury was made. The patient was successfully treated with a 26mm Vascutek hybrid stentgraft using the frozen elephant trunk technique.A literature review of the pathophysiology of BTAI was performed to investigate if patients with right-sided aortic arch are at a higher risk of suffering from BTAI. Results from the review suggest that although theoretically there may be a higher risk of BTAI in RAA patients, the rarity of this condition has prevented large studies to be conducted. Previously reported cases of BTAI in RAA have highlighted the possibility that the aortic isthmus may be anatomically weak and therefore prone to injury. We have explored this possibility by reviewing current literature of the embryological origins of the aortic arch and descending aorta.     

Whole-Exome Sequencing in a South American Cohort Links ALDH1A3, FOXN1 and Retinoic Acid Regulation Pathways to Autism Spectrum Disorders

Autism spectrum disorders (ASDs) are a range of complex neurodevelopmental conditions principally characterized by dysfunctions linked to mental development. Previous studies have shown that there are more than 1000 genes likely involved in ASD, expressed mainly in brain and highly interconnected among them. We applied whole exome sequencing in Colombian—South American trios. Two missense novel SNVs were found in the same child: ALDH1A3 (RefSeq NM_000693: c.1514T>C (p.I505T)) and FOXN1 (RefSeq NM_003593: c.146C>T (p.S49L)). Gene expression studies reveal that Aldh1a3 and Foxn1 are expressed in ~E13.5 mouse embryonic brain, as well as in adult piriform cortex (PC; ~P30). Conserved Retinoic Acid Response Elements (RAREs) upstream of human ALDH1A3 and FOXN1 and in mouse Aldh1a3 and Foxn1 genes were revealed using bioinformatic approximation. Chromatin immunoprecipitation (ChIP) assay using Retinoid Acid Receptor B (Rarb) as the immunoprecipitation target suggests RA regulation of Aldh1a3 and Foxn1 in mice. Our results frame a possible link of RA regulation in brain to ASD etiology, and a feasible non-additive effect of two apparently unrelated variants in ALDH1A3 and FOXN1 recognizing that every result given by next generation sequencing should be cautiously analyzed, as it might be an incidental finding.     

Decomposition of specifically 14C-labelled phenols and dehydropolymers of coniferyl alcohol as models for lignin degradation by soft and white rot fungi

Several soft and white rot fungi were compared in their ability to degrade specifically ¹⁴C-labelled phenols and dehydropolymers of labelled coniferyl alcohol. Furthermore, plant material, which was expected to be specifically labelled in the lignin part was used in the degradation studies. The experiments showed that both groups of fungi were able to release CO₂ from methoxyl and carboxyl groups of phenol-carboxylic acids, to degrade side chains of cinnamic acids and cinnamyl alcohols and even to decompose aromatic structures. With the dehydropolymers and the plant material a CO₂ release from the methoxyl groups, the side chains and the aromatic carbons was observed. The time dependant course of the CO₂ release from these different groups showed in the beginning a higher CO₂ evolution from the side chain carbons than from the methoxyl groups, which were later on released to a higher extent. No laccase activity could be detected in the soft rot fungi and the peroxidase activity was lower than in the white rot fungi.     

Non-native and native organisms moving into high elevation and high latitude ecosystems in an era of climate change: new challenges for ecology and conservation

Cold environments at high elevation and high latitude are often viewed as resistant to biological invasions. However, climate warming, land use change and associated increased connectivity all increase the risk of biological invasions in these environments. Here we present a summary of the key discussions of the workshop ‘Biosecurity in Mountains and Northern Ecosystems: Current Status and Future Challenges’ (Flen, Sweden, 1–3 June 2015). The aims of the workshop were to (1) increase awareness about the growing importance of species expansion—both non-native and native—at high elevation and high latitude with climate change, (2) review existing knowledge about invasion risks in these areas, and (3) encourage more research on how species will move and interact in cold environments, the consequences for biodiversity, and animal and human health and wellbeing. The diversity of potential and actual invaders reported at the workshop and the likely interactions between them create major challenges for managers of cold environments. However, since these cold environments have experienced fewer invasions when compared with many warmer, more populated environments, prevention has a real chance of success, especially if it is coupled with prioritisation schemes for targeting invaders likely to have greatest impact. Communication and co-operation between cold environment regions will facilitate rapid response, and maximise the use of limited research and management resources.     

Theoretical and Numerical Approaches for Determining the Reflection and Transmission Coefficients of OPEFB-PCL Composites at X-Band Frequencies

Bio-composites of oil palm empty fruit bunch (OPEFB) fibres and polycaprolactones (PCL) with a thickness of 1 mm were prepared and characterized. The composites produced from these materials are low in density, inexpensive, environmentally friendly, and possess good dielectric characteristics. The magnitudes of the reflection and transmission coefficients of OPEFB fibre-reinforced PCL composites with different percentages of filler were measured using a rectangular waveguide in conjunction with a microwave vector network analyzer (VNA) in the X-band frequency range. In contrast to the effective medium theory, which states that polymer-based composites with a high dielectric constant can be obtained by doping a filler with a high dielectric constant into a host material with a low dielectric constant, this paper demonstrates that the use of a low filler percentage (12.2%OPEFB) and a high matrix percentage (87.8%PCL) provides excellent results for the dielectric constant and loss factor, whereas 63.8% filler material with 36.2% host material results in lower values for both the dielectric constant and loss factor. The open-ended probe technique (OEC), connected with the Agilent vector network analyzer (VNA), is used to determine the dielectric properties of the materials under investigation. The comparative approach indicates that the mean relative error of FEM is smaller than that of NRW in terms of the corresponding S₂₁ magnitude. The present calculation of the matrix/filler percentages endorses the exact amounts of substrate utilized in various physics applications.