An optimized procedure for the design and evaluation of Ecotilling assays

<p>Abstract</p> <p>Background</p> <p>Single nucleotide polymorphisms (SNPs) are the most common form of genetic variability in the human genome and play a prominent role in the heritability of phenotypes. Especially rare alleles with frequencies less than 5% may exhibit a particularly strong influence on the development of complex diseases. The detection of rare alleles by standard DNA sequencing is time-consuming and cost-intensive. Here we discuss an alternative approach for a high throughput detection of rare mutations in large population samples using Ecotilling embedded in a collection of bioinformatic analysis tools. Ecotilling originally was introduced as TILLING for the screening for rare chemically induced mutations in plants and later adopted for human samples, showing an outstanding suitability for the detection of rare alleles in humans. An actual problem in the use of Ecotilling for large mutation screening projects in humans without bioinformatic support is represented by the lack of solutions to quickly yet comprehensively evaluate each newly found variation and place it into the correct genomic context.</p> <p>Results</p> <p>We present an optimized strategy for the design, evaluation and interpretation of Ecotilling results by integrating several mostly freely available bioinformatic tools. A major focus of our investigations was the evaluation and meaningful economical combination of these software tools for the inference of different possible regulatory functions for each newly detected mutation.</p> <p>Conclusion</p> <p>Our streamlined procedure significantly facilitates the experimental design and evaluation of Ecotilling assays and strongly improves the decision process on prioritizing the newly found SNPs for further downstream analysis.</p

eCOMPAGT – efficient Combination and Management of Phenotypes and Genotypes for Genetic Epidemiology

<p>Abstract</p> <p>Background</p> <p>High-throughput genotyping and phenotyping projects of large epidemiological study populations require sophisticated laboratory information management systems. Most epidemiological studies include subject-related personal information, which needs to be handled with care by following data privacy protection guidelines. In addition, genotyping core facilities handling cooperative projects require a straightforward solution to monitor the status and financial resources of the different projects.</p> <p>Description</p> <p>We developed a database system for an efficient combination and management of phenotypes and genotypes (eCOMPAGT) deriving from genetic epidemiological studies. eCOMPAGT securely stores and manages genotype and phenotype data and enables different user modes with different rights. Special attention was drawn on the import of data deriving from TaqMan and SNPlex genotyping assays. However, the database solution is adjustable to other genotyping systems by programming additional interfaces. Further important features are the scalability of the database and an export interface to statistical software.</p> <p>Conclusion</p> <p>eCOMPAGT can store, administer and connect phenotype data with all kinds of genotype data and is available as a downloadable version at <url>http://dbis-informatik.uibk.ac.at/ecompagt</url>.</p

Differences in biocompatibility of microneedles from cyclic olefin polymers with human endothelial and epithelial skin cells

Microneedles are promising devices for transdermal delivery and diagnostic applications, due to their minimally invasive and painless nature of application. However, so far, applications are limited to small scale research projects. Material selection and production for larger projects remain a challenge. In vitro testing using human cell culture could bridge the gap between cost effective screening of suitable materials and concerns for safety and ethics. In this study, materials were tested for effects on viability and morphology of human endothelial cells and keratinocytes. In addition, materials were assessed for their potential to influence cellular differentiation and barrier formation. Elution-based testing of inflammatory markers revealed no negative effects in all applied tests, whereas the assessment of differentiation markers on cells in direct contact with the material showed differences and allowed the selection of candidate materials for future medical device applications. This study illustrates that elution-based biocompatibility testing can paint an incomplete picture. Advanced staining techniques and cell types specific for the application of the medical device improve material selection to reduce and replace animal testing at an early stage in the development process. © 2018 The Authors. journal Of Biomedical Materials Research Part A Published By Wiley Periodicals, Inc. J Biomed Mater Res Part A: 107A: 505–512, 2019

Piezoelectric inkjet coating of injection moulded, reservoir-tipped microneedle arrays for transdermal delivery

Coated microneedles have significant potential for use in transdermal delivery applications. In this paper, we describe the fabrication of microneedle master templates using microstereolithography techniques and subsequently use a commercial injection moulding process to replicate these microneedles in biocompatible cyclic olefin polymer (COP) materials. Notably, the 475 μm-tall needle designs feature a shallow pit or reservoir at the tip, thereby providing both a target and holder for incoming droplets that are deposited using a piezoelectric inkjet printer. Using this design, no tilting or rotation of the needle array is required during the filling process. In the preliminary tests reported here, the reservoir is filled with a FITC-labelled dye that acts as a model drug, and ex vivo skin tests are used to verify skin penetration, the transfer of this model drug to the skin and to measure the reliability of the needles themselves. To our knowledge, this is the first time that such an inkjet-filled, reservoir-tipped microneedle has been demonstrated

Genetic evidence for a role of adiponutrin in the metabolism of apolipoprotein B-containing lipoproteins

Adiponutrin (PNPLA3) is a predominantly liver-expressed transmembrane protein with phospholipase activity that is regulated by fasting and feeding. Recent genome-wide association studies identified PNPLA3 to be associated with hepatic fat content and liver function, thus pointing to a possible involvement in the hepatic lipoprotein metabolism. The aim of this study was to examine the association between two common variants in the adiponutrin gene and parameters of lipoprotein metabolism in 23 274 participants from eight independent West-Eurasian study populations including six population-based studies [Bruneck (n = 800), KORA S3/F3 (n = 1644), KORA S4/F4 (n = 1814), CoLaus (n = 5435), SHIP (n = 4012), Rotterdam (n = 5967)], the SAPHIR Study as a healthy working population (n = 1738) and the Utah Obesity Case-Control Study including a group of 1037 severely obese individuals (average BMI 46 kg/m2) and 827 controls from the same geographical region of Utah. We observed a strong additive association of a common non-synonymous variant within adiponutrin (rs738409) with age-, gender-, and alanine-aminotransferase-adjusted lipoprotein concentrations: each copy of the minor allele decreased levels of total cholesterol on average by 2.43 mg/dl (P = 8.87 × 10−7), non-HDL cholesterol levels by 2.35 mg/dl (P = 2.27 × 10−6) and LDL cholesterol levels by 1.48 mg/dl (P = 7.99 × 10−4). These associations remained significant after correction for multiple testing. We did not observe clear evidence for associations with HDL cholesterol or triglyceride concentrations. In conclusion, our study suggests that adiponutrin is involved in the metabolism of apoB-containing lipoprotein

Candidate Gene Sequencing of SLC11A2 and TMPRSS6 in a Family with Severe Anaemia: Common SNPs, Rare Haplotypes, No Causative Mutation

Contains fulltext : 110476.pdf (publisher's version ) (Open Access)BACKGROUND: Iron-refractory iron deficiency anaemia (IRIDA) is a rare disorder which was linked to mutations in two genes (SLC11A2 and TMPRSS6). Common polymorphisms within these genes were associated with serum iron levels. We identified a family of Serbian origin with asymptomatic non-consanguineous parents with three of four children presenting with IRIDA not responding to oral but to intravenous iron supplementation. After excluding all known causes responsible for iron deficiency anaemia we searched for mutations in SLC11A2 and TMPRSS6 that could explain the severe anaemia in these children. METHODOLOGY/RESULTS: We sequenced the exons and exon-intron boundaries of SLC11A2 and TMPRSS6 in all six family members. Thereby, we found seven known and fairly common SNPs, but no new mutation. We then genotyped these seven SNPs in the population-based SAPHIR study (n = 1,726) and performed genetic association analysis on iron and ferritin levels. Only two SNPs, which were top-hits from recent GWAS on iron and ferritin, exhibited an effect on iron and ferritin levels in SAPHIR. Six SAPHIR participants carrying the same TMPRSS6 genotypes and haplotype-pairs as one anaemic son showed lower ferritin and iron levels than the average. One individual exhibiting the joint SLC11A2/TMPRSS6 profile of the anaemic son had iron and ferritin levels lying below the 5(th) percentile of the population's iron and ferritin level distribution. We then checked the genotype constellations in the Nijmegen Biomedical Study (n = 1,832), but the profile of the anaemic son did not occur in this population. CONCLUSIONS: We cannot exclude a gene-gene interaction between SLC11A2 and TMPRSS6, but we can also not confirm it. As in this case candidate gene sequencing did not reveal causative rare mutations, the samples will be subjected to whole exome sequencing

Fuel Cell Modeling and Simulations

Fundamental and phenomenological models for cells, stacks, and complete systems of PEFC and SOFC are reviewed and their predictive power is assessed by comparing model simulations against experiments. Computationally efficient models suited for engineering design include the (1+1) dimensionality approach, which decouples the membrane in-plane and through-plane processes, and the volume-averaged-method (VAM) that considers only the lumped effect of pre-selected system components. The former model was shown to capture the measured lateral current density inhomogeneities in a PEFC and the latter was used for the optimization of commercial SOFC systems. State Space Modeling (SSM) was used to identify the main reaction pathways in SOFC and, in conjunction with the implementation of geometrically well- defined electrodes, has opened a new direction for the understanding of electrochemical reactions. Furthermore, SSM has advanced the understanding of the COpoisoning- induced anode impedance in PEFC. Detailed numerical models such as the Lattice Boltzmann (LB) method for transport in porous media and the full 3-D Computational Fluid Dynamics (CFD) Navier-Stokes simulations are addressed. These models contain all components of the relevant physics and they can improve the understanding of the related phenomena, a necessary condition for the development of both appropriate simplified models as well as reliable technologies. Within the LB framework, a technique for the characterization and computer- reconstruction of the porous electrode structure was developed using advanced pattern recognition algorithms. In CFD modeling, 3-D simulations were used to investigate SOFC with internal methane steam reforming and have exemplified the significance of porous and novel fractal channel distributors for the fuel and oxidant delivery, as well as for the cooling of PEFC. As importantly, the novel concept has been put forth of functionally designed, fractal-shaped fuel cells, showing promise of significant performance improvements over the conventional rectangular shaped units. Thermo-economic modeling for the optimization of PEFC is finally addressed

Nanostructured Ceramics: Ionic Transport and Electrochemical Activity

Ceramics with nm-sized dimensions are widely used in various applications such as batteries, fuel cells or sensors. Their oftentimes superior electrochemical properties as well as their capabilities to easily conduct ions are, however, not completely understood. Depending on the method chosen to prepare the materials, nanostructured ceramics may be equipped with a large area fraction of interfacial regions that exhibit structural disorder. Elucidating the relationship between microscopic disorder and ion dynamics as well as electrochemical performance is necessary to develop new functionalized materials. Here, we highlight some of the very recent studies on ion transport and electrochemical properties of nanostructured ceramics. Emphasis is put on TiO2 in the form of nanorods, nanotubes or being present as mesoporous material. Further examples deal with nanocrystalline peroxides such as Li2O2 or nanostructured oxides (Li2TiO3, LiAlO2, LiTaO3, Li2CO3 and Li2B4O7). These materials served as model systems to explore the influence of ball-milling on overall ionic transport

Limitations of Fe^(2+) and Mn^(2+) site occupancy in tourmaline: Evidence from Fe^(2+)- and Mn^(2+)-rich tourmaline

Fe^(2+)- and Mn^(2+)-rich tourmalines were used to test whether Fe^(2+) and Mn^(2+) substitute on the Z site of tourmaline to a detectable degree. Fe-rich tourmaline from a pegmatite from Lower Austria was characterized by crystal-structure refinement, chemical analyses, and Mössbauer and optical spectroscopy. The sample has large amounts of Fe^(2+) (~2.3 apfu), and substantial amounts of Fe^(3+) (~1.0 apfu). On basis of the collected data, the structural refinement and the spectroscopic data, an initial formula was determined by assigning the entire amount of Fe^(3+) (no delocalized electrons) and Ti^(4+) to the Z site and the amount of Fe^(2+) and Fe^(3+) from delocalized electrons to the Y-Z ED doublet (delocalized electrons between Y-Z and Y-Y): X(Na_(0.9)Ca_(0.1)) ^Y(Fe^(2+)_(2.0)Al_(0.4)Mn^(2+)_(0.3)Fe^(3+)_(0.2)) ^Z(Al_(4.8)Fe^(3+)_(0.8)Fe^(2+)_(0.2)Ti^(4+)_(0.1)) ^T(Si_(5.9)Al_(0.1))O_(18) (BO_3)_3^V(OH)_3 ^W[O_(0.5)F_(0.3)(OH)_(0.2)] with α = 16.039(1) and c = 7.254(1) Å. This formula is consistent with lack of Fe^(2+) at the Z site, apart from that occupancy connected with delocalization of a hopping electron. The formula was further modified by considering two ED doublets to yield: ^X(Na_(0.9)Ca_(0.1)) ^Y(Fe^(2+)_(1.8)Al_(0.5)Mn^(2+)_(0.3)Fe^(3+)_(0.3)) ^Z(Al_(4.8)Fe^(3+)_(0.7)Fe^(2+)_(0.4)Ti^(4+)_(0.1)) ^T(Si_(5.9_Al_(0.1))O_(18) (BO_3)_3 ^V(OH)_3 ^W[O_(0.5)F_(0.3)(OH)_(0.2)]. This formula requires some Fe^(2+) (~0.3 apfu) at the Z site, apart from that connected with delocalization of a hopping electron. Optical spectra were recorded from this sample as well as from two other Fe^(2+)-rich tourmalines to determine if there is any evidence for Fe^(2+) at Y and Z sites. If Fe^(2+) were to occupy two different 6-coordinated sites in significant amounts and if these polyhedra have different geometries or metal-oxygen distances, bands from each site should be observed. However, even in high-quality spectra we see no evidence for such a doubling of the bands. We conclude that there is no ultimate proof for Fe^(2+) at the Z site, apart from that occupancy connected with delocalization of hopping electrons involving Fe cations at the Y and Z sites. A very Mn-rich tourmaline from a pegmatite on Elba Island, Italy, was characterized by crystal-structure determination, chemical analyses, and optical spectroscopy. The optimized structural formula is ^X(Na_(0.6)□_(0.4)) ^Y(Mn^(2+)_(1.3)Al_(1.2)Li_(0.5)) ^ZAl_6 ^TSi_6O_(18) (BO_3)_3 ^V(OH)_3 ^W[F_(0.5)O_(0.5)], with α = 15.951(2) and c = 7.138(1) Å. Within a 3σ error there is no evidence for Mn occupancy at the Z site by refinement of Al ↔ Mn, and, thus, no final proof for Mn^(2+) at the Z site, either. Oxidation of these tourmalines at 700–750 °C and 1 bar for 10–72 h converted Fe^(2+) to Fe^(3+) and Mn^(2+) to Mn^(3+) with concomitant exchange with Al of the Z site. The refined ^ZFe content in the Fe-rich tourmaline increased by ~40% relative to its initial occupancy. The refined YFe content was smaller and the distance was significantly reduced relative to the unoxidized sample. A similar effect was observed for the oxidized Mn^(2+)-rich tourmaline. Simultaneously, H and F were expelled from both samples as indicated by structural refinements, and H expulsion was indicated by infrared spectroscopy. The final species after oxidizing the Fe^(2+)-rich tourmaline is buergerite. Its color had changed from blackish to brown-red. After oxidizing the Mn^(2+)-rich tourmaline, the previously dark yellow sample was very dark brown-red, as expected for the oxidation of Mn^(2+) to Mn^(3+). The unit-cell parameter α decreased during oxidation whereas the c parameter showed a slight increase

Genetic variants in novel pathways influence blood pressure and cardiovascular disease risk.

Blood pressure is a heritable trait influenced by several biological pathways and responsive to environmental stimuli. Over one billion people worldwide have hypertension (≥140 mm Hg systolic blood pressure or  ≥90 mm Hg diastolic blood pressure). Even small increments in blood pressure are associated with an increased risk of cardiovascular events. This genome-wide association study of systolic and diastolic blood pressure, which used a multi-stage design in 200,000 individuals of European descent, identified sixteen novel loci: six of these loci contain genes previously known or suspected to regulate blood pressure (GUCY1A3-GUCY1B3, NPR3-C5orf23, ADM, FURIN-FES, GOSR2, GNAS-EDN3); the other ten provide new clues to blood pressure physiology. A genetic risk score based on 29 genome-wide significant variants was associated with hypertension, left ventricular wall thickness, stroke and coronary artery disease, but not kidney disease or kidney function. We also observed associations with blood pressure in East Asian, South Asian and African ancestry individuals. Our findings provide new insights into the genetics and biology of blood pressure, and suggest potential novel therapeutic pathways for cardiovascular disease prevention