Magnetostatics of Room Temperature Compensated Co/Gd/Co/Gd-based Synthetic Ferrimagnets

Flexibility for interface engineering, and access to all-optical switching of the magnetization, make synthetic ferrimagnets an interesting candidate for advanced opto-spintronic devices. Moreover, due to their layered structure and disordered interfaces they also bear promise for the emerging field of graded magnetic materials. The fastest and most efficient spin-orbit torque driven manipulation of the magnetic order in this material system generally takes place at compensation. Here, we present a systematic experimental and modeling study of the conditions for magnetization compensation and perpendicular magnetic anisotropy in the synthetic ferrimagnetic Co/Gd/Co/Gd system. A model based on partial intermixing at the Co/Gd interfaces of this system has been developed which explains the experiments well, and provides a new tool to understand its magnetic characteristics. More specifically, this work provides new insight in the decay of the Co proximity-induced magnetization in the Gd, and the role the capping layer plays in the Gd magnetization

SNP markers retrieval for a non-model species: a practical approach

<p>Abstract</p> <p>Background</p> <p>SNP (Single Nucleotide Polymorphism) markers are rapidly becoming the markers of choice for applications in breeding because of next generation sequencing technology developments. For SNP development by NGS technologies, correct assembly of the huge amounts of sequence data generated is essential. Little is known about assembler's performance, especially when dealing with highly heterogeneous species that show a high genome complexity and what the possible consequences are of differences in assemblies on SNP retrieval. This study tested two assemblers (CAP3 and CLC) on 454 data from four lily genotypes and compared results with respect to SNP retrieval.</p> <p>Results</p> <p>CAP3 assembly resulted in higher numbers of contigs, lower numbers of reads per contig, and shorter average read lengths compared to CLC. Blast comparisons showed that CAP3 contigs were highly redundant. Contrastingly, CLC in rare cases combined paralogs in one contig. Redundant and chimeric contigs may lead to erroneous SNPs. Filtering for redundancy can be done by blasting selected SNP markers to the contigs and discarding all the SNP markers that show more than one blast hit. Results on chimeric contigs showed that only four out of 2,421 SNP markers were selected from chimeric contigs.</p> <p>Conclusion</p> <p>In practice, CLC performs better in assembling highly heterogeneous genome sequences compared to CAP3, and consequently SNP retrieval is more efficient. Additionally a simple flow scheme is suggested for SNP marker retrieval that can be valid for all non-model species.</p

Consistent errors in first strand cDNA due to random hexamer mispriming

Abstract Priming of random hexamers in cDNA synthesis is known to show sequence bias, but in addition it has been suggested recently that mismatches in random hexamer priming could be a cause of mismatches between the original RNA fragment and observed sequence reads. To explore random hexamer mispriming as a potential source of these errors, we analyzed two independently generated RNA-seq datasets of synthetic ERCC spikes for which the reference is known. First strand cDNA synthesized by random hexamer priming on RNA showed consistent position and nucleotide-specific mismatch errors in the first seven nucleotides. The mismatch errors found in both datasets are consistent in distribution and thermodynamically stable mismatches are more common. This strongly indicates that RNA-DNA mispriming of specific random hexamers causes these errors. Due to their consistency and specificity, mispriming errors can have profound implications for downstream applications if not dealt with properly

Comparable Renal Function at 6 Months with Tacrolimus Combined with Fixed-Dose Sirolimus or MMF: Results of a Randomized Multicenter Trial in Renal Transplantation

In a multicenter trial, renal transplant recipients were randomized to tacrolimus with fixed-dose sirolimus (Tac/SRL, N = 318) or tacrolimus with MMF (Tac/MMF, N = 316). Targeted tacrolimus trough levels were lower in the Tac/SRL group after day 14. The primary endpoint was renal function at 6 months using creatinine clearance (Cockcroft-Gault) and was comparable at 66.4 mL/min (SE 1.4) with Tac/SRL and at 65.2mL/min (SE 1.3) with Tac/MMF (completers). Biopsy-confirmed acute rejection was 15.1% (Tac/SRL) and 12.3% (Tac/MMF). In both groups, graft survival was 93% and patient survival was 99.0%. Premature withdrawal due to an adverse event was twice as high in the Tac/SRL group, 15.1% versus 6.3%. Hypercholesterolemia incidence was higher with Tac/SRL (P < .05) while CMV, leukopenia, and diarrhea incidences were higher with Tac/MMF (P < .05). The incidence of any antidiabetic treatment for >30 consecutive days in previously nondiabetic patients was 17.8%, Tac/SRL, and 24.8%, Tac/MMF. Evaluation at 6 months showed comparable renal function using tacrolimus/sirolimus and tacrolimus/MMF regimens

Professional learning needs in using video calls identified through workshops

BACKGROUND: Most people want to die at home but only half do. Supporting patients in rural locations is challenging. Video calls such as Skype, might help but are not routinely used; we should consider learning needs to increase uptake and ensure effective use. We aimed to identify learning needs of healthcare professionals (HCPs) in using video calls to support patients (and their carers) to die at home. METHODS: Face-to-face workshops were held in five Southwest England locations. Participants discussed advantages, disadvantages, scenarios for use, and the learning needs of video call users. Ideas were documented on flipcharts and discussions audio-recorded. The 116 participants included nurses, allied HCPs, doctors and previously bereaved volunteers. Lists of advantages, disadvantages, scenarios and learning needs were compiled and circulated to participants. In a subsequent online workshop, 21 participants ranked seven groups of learning needs in priority order. RESULTS: Most participants thought video calls could be used to advantage in many end-of-life scenarios, especially in rural areas. Seven themes, covering 59 learning needs for HCPs, were identified (in priority order): (i) confidence and technical ability in using video calls; (ii) being aware of how video calls fit into clinical practice; (iii) managing video calls; (iv) communication skills on ‘camera’; (v) understanding how patients and families may be affected by video call use; (vi) presenting video calls as an option to patients and families to assess their readiness; (vii) normal professional skills that become essential for effective video calls. CONCLUSIONS: Although almost ubiquitous, video call software is not routinely and effectively used in British clinical practice. Supporting patients and families at end-of-life is one example where it could be used to advantage, but clinicians need to plan and practise before using it in real situations. Learning needs were identified that could be developed into learning modules and/or courses. ELECTRONIC SUPPLEMENTARY MATERIAL: The online version of this article (doi:10.1186/s12909-016-0657-6) contains supplementary material, which is available to authorized users

Transgenerational Effects of Stress Exposure on Offspring Phenotypes in Apomictic Dandelion

Heritable epigenetic modulation of gene expression is a candidate mechanism to explain parental environmental effects on offspring phenotypes, but current evidence for environment-induced epigenetic changes that persist in offspring generations is scarce. In apomictic dandelions, exposure to various stresses was previously shown to heritably alter DNA methylation patterns. In this study we explore whether these induced changes are accompanied by heritable effects on offspring phenotypes. We observed effects of parental jasmonic acid treatment on offspring specific leaf area and on offspring interaction with a generalist herbivore; and of parental nutrient stress on offspring root-shoot biomass ratio, tissue P-content and leaf morphology. Some of the effects appeared to enhance offspring ability to cope with the same stresses that their parents experienced. Effects differed between apomictic genotypes and were not always consistently observed between different experiments, especially in the case of parental nutrient stress. While this context-dependency of the effects remains to be further clarified, the total set of results provides evidence for the existence of transgenerational effects in apomictic dandelions. Zebularine treatment affected the within-generation response to nutrient stress, pointing at a role of DNA methylation in phenotypic plasticity to nutrient environments. This study shows that stress exposure in apomictic dandelions can cause transgenerational phenotypic effects, in addition to previously demonstrated transgenerational DNA methylation effects

Measuring stress-induced DNA methylation in apomictic Dandelions

The success or continuous existence of species requires continuous adaptation to changes in the environment to survive and contribute offspring to the next generation. Selection acts on the phenotype, which is in turn determined by the complex interplay of genetic, epigenetic and environmental variation. (Natural) selection leads to ‘survival of the fittest’ or best-adapted individuals to their local environment, ultimately determining which individuals contribute offspring to the next generation. Understanding the mechanisms by which epigenetic and genetic variation can arise and get passed on through generations determines our understanding of inheritance and evolution. Hitherto, the mechanistic understanding of genetics has shaped the scientific view of inheritance and evolution, leading to the gene-centered paradigm of Neo-Darwinism. However, recent studies indicate that besides genetic (DNA sequence) variation, epigenetic variation can also be transmitted between generations. Further studies on the properties and transgenerational dynamics of epigenetic variation are needed to enhance our understanding of heritability and evolution. Epigenetic variation has distinct properties and different transgenerational dynamics compared to genetic variation. Epigenetic variation helps to regulate gene expression and determines the different cell types and function in eukaryotes. The main function of DNA methylation, an important part of the epigenetic code, is to prevent the spread of selfish genetic elements in the genome and to establish the different cellular profiles observed in multicellular organisms. One differentiating feature of epigenetic variation compared to genetic variation is that (specific) epigenetic variation can arise under the influence of stress. This can enable a trans-generational stress-response of organisms which can have a positive influence on the phenotype and (natural) selection on either the (enhanced level of) transgenerational phenotypic plasticity or the epigenetic variation itself, potentially influencing natural selection and ultimately evolution. Where genetic variation can be characterized as hard-inheritance, the inheritance of epigenetic variation is often referred to as ‘soft-inheritance’ due to the lower transgenerational stability and resetting that occurs in the intergenerational transfer of epigenetic variation. Epigenetic variation is also often dependent on, or a downstream consequence, of genetic variation, suggesting that it is (in part) determined by genetic variation. Mechanistic studies in model species have contributed greatly to the understanding of the molecular mechanisms that control the dynamics of different epigenetic marks present in multicellular organisms. In plants, studies in the model plant Arabidopsis thaliana have resulted in deciphering the most important molecular mechanisms and actors, giving an ever-increasing insight into the dynamics of epigenetic regulation of cells and organisms. A key feature of model systems is the ability to ‘switch’ off certain genes or molecular pathways, for instance via the experimental use of mutants, enabling the study of their role in the heritability of epigenetic marks. DNA methylation is a well-studied epigenetic mark, which has shown high stability even in transgenerational experiments. From the perspective of studying epigenetic variation, plants are particularly interesting for several reasons, most importantly: 1) The separation between soma and germline, the Weismann barrier, is less strict in plants compared to other eukaryotes, as in higher plants germline cells are formed during floral development from somatic cells (which can occur throughout the life of the plant), whereas in most eukaryotes germline cell development is restricted to a defined point (early) in the organismal development. 2) The sessile nature of plants makes an adaptive plastic response to changing environments an important feature, a plant cannot just walk away when the going gets tough. 3) The transgenerational stability of DNA methylation is higher in plants compared to other eukaryotes such as mammals, in which epigenetic information is erased during germline reprogramming. These factors combined suggest that the potential importance of epigenetic variation in plants might be high. In this thesis, I focus on studying DNA methylation in apomictic Dandelions, applying Next Generation Sequencing (NGS) approaches to the study of this non-model plant species. Apomictic dandelions produce seeds that are genetically identical to the ‘mother’ plant, which makes it easier to study the influence of epigenetic variation without confounding effects of genetic variation. Working with Next Generation Sequencing data is still relatively new and therefore not always optimized for specific types of analysis. I discovered a distinct error pattern in RNAseq data that indicated an artificial source of variation that could be traced back to the way the RNAseq libraries were constructed. The first publication of this thesis contains a technical analysis of such artefacts present in RNAseq data, suggesting that these errors are related to random hexamer mispriming during library construction (Chapter 2). The main goal of my work is to better understand the role of epigenetic variation in adaptation and plasticity of plants. This role remains poorly understood. This is in part due to the lack of high-resolution techniques that allow for the detailed study of epigenetic marks such as DNA methylation in non-model organisms. Existing techniques for measuring DNA methylation such as methylation sensitive AFLPs offer only information on DNA methylation variation in an anonymous and limited fashion. The plummeting costs of sequencing techniques have enabled large-scale genotyping efforts (focusing on genetic variation only) for a wide variety of non-model organisms. Here, I extended this popular genotyping by sequencing technique, to allow for sequencing-based epigenotyping or epiGBS (chapter 3), which allows for measuring DNA methylation and genetic variation in hundreds of samples simultaneously. I have extensively validated the approach, providing evidence that with the right design, the accuracy of the DNA methylation measurements with epiGBS are as high as those with the gold standard Whole Genome Bisulfite Sequencing. An important aim of my PhD research was to investigate the stability of (stress induced) DNA methylation variation in apomictic dandelions and the potential of phenotypic variation underpinned by DNA methylation variation to be subjected to selection. I therefore studied the transgenerational stability of both stress induced and natural DNA methylation variation in different genotypes of apomictic dandelions in a six-generation experiment, comparing DNA methylation patterns between generations and tracking changes in them (chapter 4) using epiGBS. I found clear but limited evidence for environmental induction of heritable DNA methylation changes after application of Jasmonic Acid. Furthermore, I found a significant negative relation between the similarity of DNA methylation patterns and intergenerational distance, indicating epigenetic divergence over generations. I conclude that DNA methylation in both CG and CHG (where H can be any nucleotide except for G) sequence context are heritable and that environmental perturbation can result in heritable DNA methylation changes which are however not widespread. A prerequisite for epigenetic variation to contribute to adaptation is that epigenetic variants that affect the phenotype are heritable. To test whether an epigenetics-based selection response is possible, at least over the time course of a few generations, I selected early flowering for two subsequent generations in three genotypes of apomictic dandelions. This selection effort included lines that received a stress pre-treatment with either Jasmonic Acid or 5-azacytidine, to determine if stress-induced DNA methylation variation would increase the capacity to respond to selection. The selection experiment on flowering time (chapter 5) resulted in a shift in flowering time for all treatments in a young apomict, suggesting that natural and heritable epigenetic variation can underpin quantitative traits such as flowering time. I also found evidence for treatment induced (epi)genetic variation leading to a stronger selection response in one out of 3 genotypes. This suggests that stress- induced heritable epigenetic variation can lead to a selection response. Further study is however required to rule out genetic variants and to study the long-term stability of the variation selected upon. Finally, in the General Discussion I summarize the findings, putting them in context with recently published studies. I reflect on the state of the field of ecological epigenetics and in what sense the epiGBS technique that I developed and other emerging techniques can contribute to a better understanding of the role of epigenetic variation in ecology and evolution. I reflect on the place of epiGBS compared to other techniques. I point out that with the growing evidence of the inadequacy and misinterpretation of MS-AFLP results a systematic review of such results by replicating the studies employing sequencing based techniques such as epiGBS instead of MS-AFLP is in order.</p