GPI-anchored Gas1 protein regulates cytosolic proteostasis in budding yeast

The decline in protein homeostasis (proteostasis) is a hallmark of cellular aging and aging-related diseases. Maintaining a balanced proteostasis requires a complex network of molecular machineries that govern protein synthesis, folding, localization, and degradation. Under proteotoxic stress, misfolded proteins that accumulate in cytosol can be imported into mitochondria for degradation through the "mitochondrial as guardian in cytosol" (MAGIC) pathway. Here, we report an unexpected role of Gas1, a cell wall-bound glycosylphosphatidylinositol (GPI)-anchored β-1,3-glucanosyltransferase in the budding yeast, in differentially regulating MAGIC and ubiquitin-proteasome system (UPS). Deletion of GAS1 inhibits MAGIC but elevates protein ubiquitination and UPS-mediated protein degradation. Interestingly, we found that the Gas1 protein exhibits mitochondrial localization attributed to its C-terminal GPI anchor signal. But this mitochondria-associated GPI anchor signal is not required for mitochondrial import and degradation of misfolded proteins through MAGIC. By contrast, catalytic inactivation of Gas1 via the gas1-E161Q mutation inhibits MAGIC but not its mitochondrial localization. These data suggest that the glucanosyltransferase activity of Gas1 is important for regulating cytosolic proteostasis.

New-onset atrial fibrillation in critically ill adult patients-an SSAI clinical practice guideline

BACKGROUND

Acute or new-onset atrial fibrillation (NOAF) is the most common cardiac arrhythmia in critically ill adult patients, and observational data suggests that NOAF is associated to adverse outcomes.

METHODS

We prepared this guideline according to the Grading of Recommendations Assessment, Development and Evaluation methodology. We posed the following clinical questions: (1) what is the better first-line pharmacological agent for the treatment of NOAF in critically ill adult patients?, (2) should we use direct current (DC) cardioversion in critically ill adult patients with NOAF and hemodynamic instability caused by atrial fibrillation?, (3) should we use anticoagulant therapy in critically ill adult patients with NOAF?, and (4) should critically ill adult patients with NOAF receive follow-up after discharge from hospital? We assessed patient-important outcomes, including mortality, thromboembolic events, and adverse events. Patients and relatives were part of the guideline panel.

RESULTS

The quantity and quality of evidence on the management of NOAF in critically ill adults was very limited, and we did not identify any relevant direct or indirect evidence from randomized clinical trials for the prespecified PICO questions. We were able to propose one weak recommendation against routine use of therapeutic dose anticoagulant therapy, and one best practice statement for routine follow-up by a cardiologist after hospital discharge. We were not able to propose any recommendations on the better first-line pharmacological agent or whether to use DC cardioversion in critically ill patients with hemodynamic instability induced by NOAF. An electronic version of this guideline in layered and interactive format is available in MAGIC: https://app.magicapp.org/#/guideline/7197.

CONCLUSIONS

The body of evidence on the management of NOAF in critically ill adults is very limited and not informed by direct evidence from randomized clinical trials. Practice variation appears considerable.

Assessment of the MAGIC recommendations in context of evolving evidence based on the use of PICC in ICU

The goal of the 2015 Michigan Appropriateness Guide for Intravenous Catheters (MAGIC) was to define indications and appropriate practices for peripherally inserted central catheters (PICC) use; however, MAGIC recommendations virtually reduced the use of PICC in hospital settings, including critical care. The aim of this review is to present an assessment of the MAGIC guidelines, considering contemporary evidence to date. The validity of the MAGIC recommendations and their applicability to current practice are called into question given important concerns with the methodology for their development (e.g. high volume of clinical scenarios for evaluation) and the supporting evidence used. There is a considerable amount of contemporary evidence not considered in MAGIC that reports on evolving practices, techniques, and technologies targeted to reduce complications associated with central venous access devices (CVADs). Recent evidence dictates that CVADs are necessary in the intensive care unit (ICU), and that PICCs are a safe, reliable, and appropriate type of central lines, which cannot be replaced in several ICU situations. In light of evolving evidence and practice, as well as the methodological concerns identified, the MAGIC guidelines should be revisited. It is also recommended to create a clinical assessment tool that identifies potential uses of specific CVADs, based on patient needs. The choice of the CVAD should be based on unique clinical considerations and current scientific evidence, not on fears informed by antiquated data.

Which mouse multiparental population is right for your study? The Collaborative Cross inbred strains, their F1 hybrids, or the Diversity Outbred population

Multiparental populations (MPPs) encompass greater genetic diversity than traditional experimental crosses of two inbred strains, enabling broader surveys of genetic variation underlying complex traits. Two such mouse MPPs are the Collaborative Cross (CC) inbred panel and the Diversity Outbred (DO) population, which are descended from the same eight inbred strains. Additionally, the F1 intercrosses of CC strains (CC-RIX) have been used and enable study designs with replicate outbred mice. Genetic analyses commonly used by researchers to investigate complex traits in these populations include characterizing how heritable a trait is, i.e. its heritability, and mapping its underlying genetic loci, i.e. its quantitative trait loci (QTLs). Here we evaluate the relative merits of these populations for these tasks through simulation, as well as provide recommendations for performing the quantitative genetic analyses. We find that sample populations that include replicate animals, as possible with the CC and CC-RIX, provide more efficient and precise estimates of heritability. We report QTL mapping power curves for the CC, CC-RIX, and DO across a range of QTL effect sizes and polygenic backgrounds for samples of 174 and 500 mice. The utility of replicate animals in the CC and CC-RIX for mapping QTLs rapidly decreased as traits became more polygenic. Only large sample populations of 500 DO mice were well-powered to detect smaller effect loci (7.5-10%) for highly complex traits (80% polygenic background). All results were generated with our R package musppr, which we developed to simulate data from these MPPs and evaluate genetic analyses from user-provided genotypes.

hirsutum and a subsequent MAGIC population

Introgression of superior fiber traits from Pima cotton (Gossypium barbadense, GB) into high yield Upland cotton (G. hirsutum) has been a breeding objective for many years in a few breeding programs in the world. However, progress has been very slow due to introgression barriers resulting from whole genome hybridization between the two species. To minimize such barriers, chromosome substitution lines (CS-B) from Pima cotton 3-79 in an Upland cotton cultivar TM-1 were developed. A multiparent advanced generation inter-cross (MAGIC) population consisting of 180 recombinant inbred lines (RILs) was subsequently made using the 18 CS-B lines and three Upland cotton cultivars as parents. In this research, we sequenced the whole genomes of the 21 parents and 180 RILs to examine the G. barbadense introgression. Of the 18 CS-B lines, 11 contained the target GB chromosome or chromosome segment, two contained more than two GB chromosomes, and five did not have the expected introgression. Residual introgression in non-target chromosomes was prevalent in all CS-B lines. A clear structure existed in the MAGIC population and the 180 RILs were distributed into three groups, i.e., high, moderate, and low GB introgression. Large blocks of GB chromosome introgression were still present in some RILs after five cycles of random-mating, an indication of recombination suppression or other unknown reasons present in the population. Identity by descent analysis revealed that the MAGIC RILs contained less introgression than expected. This research presents an insight on understanding the complex problems of introgression between cotton species.

Genome wide association study of MAGIC population reveals a novel QTL for salinity and sodicity tolerance in rice

The present study was conducted to identify the novel QTLs controlling salinity and sodicity tolerance using indica MAGIC rice population. Phenotyping was carried out in salinity (EC ~ 10 dS/m) and sodicity (pH ~ 9.8) at the seedling stage. Among 391 lines, 43 and 98 lines were found tolerant and moderately tolerant to salinity. For sodicity condition, 2 and 45 lines were showed tolerance and moderately tolerance at seedling stage. MAGIC population was genotyped with the help of genotyping by sequencing (GBS) and filtered 27041SNPs were used for genome wide marker trait association studies. With respect to salinity tolerance, 25 SNPs were distributed on chromosomes 1, 5, 11 and 12, whereas 18 SNPs were mapped on chromosomes 6, 4 and 11 with LOD value of > 3.25 to sodicity tolerance in rice. The candidate gene analysis detected twelve causal genes including SKC1 gene at Saltol region for salinity and six associated genes for sodic stress tolerance. The significant haplotypes responsible for core histone protein coding gene (LOC_Os12g25120) and three uncharacterized protein coding genes (LOC_Os01g20710, LOC_Os01g20870 and LOC_Os12g22020) were identified under saline stress. Likewise, five significant haplotypes coding for ribose 5-phosphate isomerise (LOC_Os04g24140), aspartyl protease (LOC_Os06g15760), aluminum-activated malate transporter (LOC_Os06g15779), OsFBX421-Fbox domain containing protein (LOC_Os11g32940) and one uncharacterized protein (LOC_Os11g32930) were detected for sodic stress tolerance. The identified novel SNPs could be the potential candidates for functional characterization. These candidate genes aid to further understanding of genetic mechanism on salinity and sodicity stress tolerance in rice. The tolerant line could be used in future breeding programme to enhance the salinity and sodicity tolerance in rice.

SUPPLEMENTARY INFORMATION

The online version contains supplementary material available at 10.1007/s12298-022-01174-8.

Modeling allelic diversity of multiparent mapping populations affects detection of quantitative trait loci

The search for quantitative trait loci that explain complex traits such as yield and drought tolerance has been ongoing in all crops. Methods such as biparental quantitative trait loci mapping and genome-wide association studies each have their own advantages and limitations. Multiparent advanced generation intercross populations contain more recombination events and genetic diversity than biparental mapping populations and are better able to estimate effect sizes of rare alleles than association mapping populations. Here, we discuss the results of using a multiparent advanced generation intercross population of doubled haploid maize lines created from 16 diverse founders to perform quantitative trait loci mapping. We compare 3 models that assume bi-allelic, founder, and ancestral haplotype allelic states for quantitative trait loci. The 3 methods have differing power to detect quantitative trait loci for a variety of agronomic traits. Although the founder approach finds the most quantitative trait loci, all methods are able to find unique quantitative trait loci, suggesting that each model has advantages for traits with different genetic architectures. A closer look at a well-characterized flowering time quantitative trait loci, qDTA8, which contains vgt1, highlights the strengths and weaknesses of each method and suggests a potential epistatic interaction. Overall, our results reinforce the importance of considering different approaches to analyzing genotypic datasets, and shows the limitations of binary SNP data for identifying multiallelic quantitative trait loci.

Identification of single nucleotide polymorphisms (SNPs) for maize cell wall hydroxycinnamates using a multi-parent advanced generation intercross (MAGIC) population

Higher hydroxycinnamate content makes maize tissues more recalcitrant to damage by insects, less digestible by ruminants, and less suitable for biofuel production. In a Genome Wide Association Analysis (GWAS) study carried out in a maize MAGIC population, we identified 24 SNPs associated with esterified cell wall-bound hydroxycinnamates, that represented 15 Quantitative Traic Loci (QTL). We identified new genomic regions associated to cell wall bound hydroxycinnamates in maize stover that could have an impact on their content across different genetic backgrounds. The high resolution QTL described in this study could be valuable for addressing positional mapping of genes involved in hydroxycinnamate biosynthesis and could uncover genes implicated in the esterification of hydroxycinnamic acids to the arabinoxylan chains that are poorly understood. However, we found that genetic correlation coefficients between hydroxycinnamate content and economical important traits such as saccharification efficiency, animal digestibility andi pest resistance were low to moderate, so modify specific hydroxycinnamates to indirectly improve cultivar performance will be unsuitable.

Burden of hospitalizations and outpatient visits associated with moderate and severe acute graft-versus-host disease in Finland and Sweden: a real-world data study

PURPOSE

The aim of this study was to describe patient characteristics and quantify hospital stays and outpatient visits (H&OV) following diagnosis with moderate-to-severe acute graft-versus-host disease (aGVHD) in Finland and Sweden.

METHODS

A retrospective chart audit collected data from patient medical records of 3 specialized centers performing allogeneic hematopoietic stem cell transplantation (HSCT; Finland, n = 2; Sweden, n = 1). Eligible patients received allogeneic HSCT (January 1, 2016-June 30, 2017) from any donor source, were diagnosed with grade II-IV aGVHD (MAGIC or modified Glucksberg criteria) at any time from transplantation to 12 months before data collection, and were ≥ 18 years old at diagnosis. Criteria for comparing patients graded with modified Glucksberg and MAGIC severity scales were defined.

RESULTS

Fifty-five patients (Finland, n = 45; Sweden, n = 10) were included. Myeloablative conditioning was the most common conditioning regimen (81.8%); immunosuppression regimens were based on combinations of methotrexate (96.4%), in vivo T-cell depletion (80.0%), cyclosporine (63.6%), mycophenolate (40.0%), and tacrolimus (34.5%). Sixteen patients (29.1%) developed grade III/IV aGVHD; skin was the most common organ involved (80.0%). Most patients required ≥ 1 hospital stay (89.1%; median of 2 hospitalizations per patient); 7 patients (14.3%) required admission to an intensive care unit. Median hospitalization duration from HSCT to discharge was 26 days. Most patients also required outpatient or emergency department visits (90.9%). Subgroup analyses showed longer hospital stays for patients receiving multiple treatment lines; no clear differences in H&OV were observed between prophylactic regimens.

CONCLUSION

Based on this retrospective study, moderate-to-severe aGVHD is associated with considerable healthcare resource utilization in Finland and Sweden, particularly in patients who received multiple lines of therapy.

Genomics of maize resistance to kernel contamination with fumonisins using a multiparental advanced generation InterCross maize population (MAGIC)

Maize kernel is exposed to several fungal species, most notably Fusarium verticillioides, which can contaminate maize kernels with fumonisins. In an effort to increase genetic gains and avoid the laborious tasks of conventional breeding, the use of marker-assisted selection or genomic selection programs was proposed. To this end, in the present study a Genome Wide Association Study (GWAS) was performed on 339 RILs of a Multiparental Advanced Generation InterCross (MAGIC) population that had previously been used to locate Quantitative Trait Locus (QTL) for resistance to Fusarium Ear Rot (FER). Six QTLs for fumonisin content were detected in the bins 3.08, 4.07, 4.10, 7.03-7.04, 9.04-9.05 and 10.04-10.5. Five of the six QTLs collocate in regions where QTLs for FER were also found. However, the genetic variation for fumonisin content in kernel is conditioned by many other QTLs of small effect that could show QTL x environment interaction effects. Although a genomic selection approach to directly reduce fumonisin content in the kernel could be suitable, improving resistance to fumonisin content by genomic selection for FER would be more advisable.

Midaortic syndrome and renovascular hypertension

Midaortic syndrome (MAS) is a rare condition characterized by stenosis of the abdominal aorta with or without the involvement of branch vessels. The majority of cases are thought to be idiopathic though MAS has been associated with a number of conditions including granulomatous vasculitis, neurofibromatosis-1 (NF-1), Alagille Syndrome, fibromuscular dysplasia (FMD), and Williams syndrome. Patients typically present with hypertension due to decreased renal perfusion. Less common presentations include renal insufficiency, heart failure, claudication, stroke, and abdominal pain. Imaging modalities help establish the diagnosis of MAS including duplex ultrasound, computed tomography angiography (CTA), magnetic resonance angiography (MRA), and angiography. Initial therapy focuses on medical management with antihypertensives prior to intervention. Invasive interventions are indicated when there is evidence of end organ damage or dysfunction such as decreased renal function, poorly growing kidneys, cerebrovascular accident, left ventricular hypertrophy or frank cardiac failure. Endovascular interventions may assist in diagnosis and may treat some lesions although reintervention rates are high. Most patients require some type of surgical intervention, and a variety of surgical options are available based on anatomic findings. Renal revascularization may be accomplished by renal artery bypass, autotransplantation, or renal artery reconstruction. Aortic lesions may be repaired using patch angioplasty or aortoaortic bypass. Mesenteric arteries do not typically require reconstruction as they are rarely symptomatic. More novel options include the use of tissue expanders to lengthen the aorta to allow for primary aortic reconstruction (TESLA) or the use of the meandering mesenteric artery as an autologous aortic bypass graft (MAGIC).

Precision Mapping of a Maize MAGIC Population Identified a Candidate Gene for the Senescence-Associated Physiological Traits

Senescence is an important trait in maize (Zea mais L.), a key crop that provides nutrition values and a renewable source of bioenergy worldwide. Genome-wide association studies (GWAS) can be used to identify causative genetic variants that influence the major physiological measures of senescence, which is used by plants as a defense mechanism against abiotic and biotic stresses affecting its performance. We measured four physiological and two agronomic traits that affect senescence. Six hundred seventy-two recombinant inbred lines (RILs) were evaluated in two consecutive years. Thirty-six candidate genes were identified by genome-wide association study (GWAS), and 11 of them were supported by additional evidence for involvement in senescence-related processes including proteolysis, sugar transport, and sink activity. We identified a candidate gene, Zm00001d043586, significantly associated with chlorophyll, and independently studied its transcription expression in an independent panel. Our results showed that Zm00001d043586 affects chlorophyl rate degradation, a key determinant of senescence, at late plant development stages. These results contribute to better understand the genetic relationship of the important trait senescence with physiology related parameters in maize and provide new putative molecular markers that can be used in marker assisted selection for line development.

Genomic Prediction of Grain Yield in a Barley MAGIC Population Modeling Genotype per Environment Interaction

Multi-parent Advanced Generation Inter-crosses (MAGIC) lines have mosaic genomes that are generated shuffling the genetic material of the founder parents following pre-defined crossing schemes. In cereal crops, these experimental populations have been extensively used to investigate the genetic bases of several traits and dissect the genetic bases of epistasis. In plants, genomic prediction models are usually fitted using either diverse panels of mostly unrelated accessions or individuals of biparental families and several empirical analyses have been conducted to evaluate the predictive ability of models fitted to these populations using different traits. In this paper, we constructed, genotyped and evaluated a barley MAGIC population of 352 individuals developed with a diverse set of eight founder parents showing contrasting phenotypes for grain yield. We combined phenotypic and genotypic information of this MAGIC population to fit several genomic prediction models which were cross-validated to conduct empirical analyses aimed at examining the predictive ability of these models varying the sizes of training populations. Moreover, several methods to optimize the composition of the training population were also applied to this MAGIC population and cross-validated to estimate the resulting predictive ability. Finally, extensive phenotypic data generated in field trials organized across an ample range of water regimes and climatic conditions in the Mediterranean were used to fit and cross-validate multi-environment genomic prediction models including G×E interaction, using both genomic best linear unbiased prediction and reproducing kernel Hilbert space along with a non-linear Gaussian Kernel. Overall, our empirical analyses showed that genomic prediction models trained with a limited number of MAGIC lines can be used to predict grain yield with values of predictive ability that vary from 0.25 to 0.60 and that beyond QTL mapping and analysis of epistatic effects, MAGIC population might be used to successfully fit genomic prediction models. We concluded that for grain yield, the single-environment genomic prediction models examined in this study are equivalent in terms of predictive ability while, in general, multi-environment models that explicitly split marker effects in main and environmental-specific effects outperform simpler multi-environment models.

Genetic control of iron bioavailability is independent from iron concentration in a diverse winter wheat mapping population

BACKGROUND

Anemia is thought to affect up to 1.6 billion people worldwide. One of the major contributors to low iron (Fe) absorption is a higher proportion of cereals compared to meats and pulse crops in people's diets. This has now become a problem in both the developed and developing world, as a result of both modern food choice and food availability. Bread wheat accounts for 20 % of the calories consumed by humans and is an important source of protein, vitamins and minerals meaning it could be a major vehicle for bringing more bioavailable Fe into the diet.

RESULTS

To investigate whether breeding for higher concentrations of Fe in wheat grains could help increase Fe absorption, a multiparent advanced generation intercross (MAGIC) population, encompassing more than 80 % of UK wheat polymorphism, was grown over two seasons in the UK. The population was phenotyped for both Fe concentration and Fe bioavailability using an established Caco-2 cell bioassay. It was found that increasing Fe concentrations in the grains was not correlated with higher Fe bioavailability and that the underlying genetic regions controlling grain Fe concentrations do not co-localise with increased Fe absorption. Furthermore, we show that phytate concentrations do not correlate with Fe bioavailability in our wheat population and thus phytate-binding is insufficient to explain the lack of correlation between Fe bioavailability and Fe concentrations in the wheat grain. Finally, we observed no (Fe bioavailability) or low (Fe concentration) correlation between years for these traits, confirming that both are under strong environmental influence.

CONCLUSIONS

This suggests that breeders will have to select not only for Fe concentrations directly in grains, but also increased bioavailability. However the use of numerous controls and replicated trials limits the practicality of adoption of screening by Caco-2 cells by many breeders.

Limited haplotype diversity underlies polygenic trait architecture across 70 years of wheat breeding

Background

Selection has dramatically shaped genetic and phenotypic variation in bread wheat. We can assess the genomic basis of historical phenotypic changes, and the potential for future improvement, using experimental populations that attempt to undo selection through the randomizing effects of recombination.

Results

We bred the NIAB Diverse MAGIC multi-parent population comprising over 500 recombinant inbred lines, descended from sixteen historical UK bread wheat varieties released between 1935 and 2004. We sequence the founders’ genes and promoters by capture, and the MAGIC population by low-coverage whole-genome sequencing. We impute 1.1 M high-quality SNPs that are over 99% concordant with array genotypes. Imputation accuracy only marginally improves when including the founders’ genomes as a haplotype reference panel. Despite capturing 73% of global wheat genetic polymorphism, 83% of genes cluster into no more than three haplotypes. We phenotype 47 agronomic traits over 2 years and map 136 genome-wide significant associations, concentrated at 42 genetic loci with large and often pleiotropic effects. Around half of these overlap known quantitative trait loci. Most traits exhibit extensive polygenicity, as revealed by multi-locus shrinkage modelling.

Conclusions

Our results are consistent with a gene pool of low haplotypic diversity, containing few novel loci of large effect. Most past, and projected future, phenotypic changes arising from existing variation involve fine-scale shuffling of a few haplotypes to recombine dozens of polygenic alleles of small effect. Moreover, extensive pleiotropy means selection on one trait will have unintended consequences, exemplified by the negative trade-off between yield and protein content, unless selection and recombination can break unfavorable trait-trait associations.

Supplementary Information

The online version contains supplementary material available at 10.1186/s13059-021-02354-7.

Bi2O2Se-Based Memristor-Aided Logic

The implementation of two-dimensional materials into memristor architectures has recently been a new research focus by taking advantage of their atomic thickness, unique lattice, and physical and electronic properties. Among the van der Waals family, Bi₂O₂Se is an emerging ternary two-dimensional layered material with ambient stability, suitable band structure, and high conductivity that exhibits high potential for use in electronic applications. In this work, we propose and experimentally demonstrate a Bi₂O₂Se-based memristor-aided logic. By carefully tuning the electric field polarity of Bi₂O₂Se through a Pd contact, a reconfigurable NAND gate with zero static power consumption is realized. To provide more knowledge on NAND operation, a kinetic Monte Carlo simulation is carried out. Because the NAND gate is a universal logic gate, cascading additional NAND gates can exhibit versatile logic functions. Therefore, the proposed Bi₂O₂Se-based MAGIC can be a promising building block for developing next-generation in-memory logic computers with multiple functions.

Haplotype analysis from unmanned aerial vehicle imagery of rice MAGIC population for the trait dissection of biomass and plant architecture

Unmanned aerial vehicles (UAVs) are popular tools for high-throughput phenotyping of crops in the field. However, their use for evaluation of individual lines is limited in crop breeding because research on what the UAV image data represent is still developing. Here, we investigated the connection between shoot biomass of rice plants and the vegetation fraction (VF) estimated from high-resolution orthomosaic images taken by a UAV 10 m above a field during the vegetative stage. Haplotype-based genome-wide association studies of multi-parental advanced generation inter-cross (MAGIC) lines revealed four quantitative trait loci (QTLs) for VF. VF was correlated with shoot biomass, but the haplotype effect on VF was better correlated with that on shoot biomass at these QTLs. Further genetic characterization revealed the relationships between these QTLs and plant spreading habit, final shoot biomass and panicle weight. Thus, genetic analysis using high-throughput phenotyping data derived from low-altitude, high-resolution UAV images during early stages of rice growing in the field provides insights into plant growth, architecture, final biomass, and yield.

MAGIC: a Proposed Model Based on Common Factors

The author offers an initial formulation of what an approach integrating common factors and the processes of change would look like. The dodo-verdict has been extant in the psychology literature for almost 100 years, and it is time to acknowledge the veracity of the dodo-bird verdict as we move toward therapeutic approaches focusing on factors the empirical approaches have in common. Although we now have hundreds of different theoretical models, no one model appears to be superior to any other. However, certain presenting conditions may be more suited to certain interventions. The MAGIC approach introduced here incorporates client motivation, the therapeutic alliance, goal-setting, implementation, and commitment. This gives us a basic structure of commonalities around which we will be able to build comprehensive psychotherapeutic strategies drawing on intervention techniques from many different models. After a brief consideration of historical factors, I will present one idea for an integrated approach followed by a discussion of some assumptive processes which are at work in the therapeutic cadre as well as a consideration of cultural diversities.

oryzae

Effective and durable disease resistance for bacterial blight (BB) of rice is a continuous challenge due to the evolution and adaptation of the pathogen, Xanthomonas oryzae pv. oryzae (Xoo), on cultivated rice varieties. Fundamental to this pathogens' virulence is transcription activator-like (TAL) effectors that activate transcription of host genes and contribute differently to pathogen virulence, fitness or both. Host plant resistance is predicted to be more durable if directed at strategic virulence factors that impact both pathogen virulence and fitness. We characterized Tal7b, a minor-effect virulence factor that contributes incrementally to pathogen virulence in rice, is a fitness factor to the pathogen and is widely present in geographically diverse strains of Xoo. To identify sources of resistance to this conserved effector, we used a highly virulent strain carrying a plasmid borne copy of Tal7b to screen an indica multi-parent advanced generation inter-cross (MAGIC) population. Of 18 QTL revealed by genome-wide association studies and interval mapping analysis, six were specific to Tal7b (qBB-tal7b). Overall, 150 predicted Tal7b gene targets overlapped with qBB-tal7b QTL. Of these, 21 showed polymorphisms in the predicted effector binding element (EBE) site and 23 lost the EBE sequence altogether. Inoculation and bioinformatics studies suggest that the Tal7b target in one of the Tal7b-specific QTL, qBB-tal7b-8, is a disease susceptibility gene and that the resistance mechanism for this locus may be through loss of susceptibility. Our work demonstrates that minor-effect virulence factors significantly contribute to disease and provide a potential new approach to identify effective disease resistance.

Surgical management of pediatric renovascular hypertension and midaortic syndrome at a single-center multidisciplinary program

OBJECTIVE

To evaluate the outcomes of various surgical approaches in the treatment of renovascular hypertension and midaortic syndrome (MAS) in children.

METHODS

We performed a retrospective medical record review of patients who had undergone surgery for renovascular hypertension from 2010 to 2018 at our center under the care of a multidisciplinary team. The operative interventions included mesenteric artery growth improves circulation (MAGIC), tissue expander-stimulated lengthening of arteries (TESLA), aortic bypass using polytetrafluorethylene, renal artery reimplantation, and autotransplantation. The MAGIC procedure uses the meandering mesenteric artery as a free conduit for aortic bypass. The TESLA procedure is based on lengthening the normal distal aorta and iliac arteries by gradual filling of a retroaortic tissue expander for several weeks, followed by resection of the stenotic aorta and subsequent primary reconstruction.

RESULTS

A total of 39 patients were identified, 10 with isolated renal artery stenosis, 26 with MAS, and 3 with systemic inflammatory vasculitis. The median age at presentation and surgery was 6.4 years (range, 0-16.3 years) and 9.3 years (range, 0-9.2 years), respectively. The MAS-associated syndromes included neurofibromatosis type 1 (15.4%) and Williams syndrome (5.1%), although most cases were idiopathic. At surgery, 33.3% had had stage 1 hypertension (HTN), 53.8% stage 2 HTN, and 12.8% normal blood pressure with a median of three antihypertensive medications. Follow-up of 37 patients at a median of 2.5 years demonstrated normal blood pressure in 86.1%, stage 1 HTN in 8.3%, and stage 2 HTN in 5.6%, with a median of one antihypertensive medication for the entire cohort.

CONCLUSIONS

The patterns of vascular involvement leading to renovascular hypertension in children are variable and complex, requiring thoughtful multidisciplinary planning and surgical decision-making. The MAGIC and TESLA procedures provide feasible approaches for aortic bypass and reconstruction using autologous tissues and will result in normalization of blood pressure in 85% of children 2.5 years after surgery.

Inferring the Allelic Series at QTL in Multiparental Populations

Multiparental populations (MPPs) are experimental populations in which the genome of every individual is a mosaic of known founder haplotypes. These populations are useful for detecting quantitative trait loci (QTL) because tests of association can leverage inferred founder haplotype descent. It is difficult, however, to determine how haplotypes at a locus group into distinct functional alleles, termed the allelic series. The allelic series is important because it provides information about the number of causal variants at a QTL and their combined effects. In this study, we introduce a fully Bayesian model selection framework for inferring the allelic series. This framework accounts for sources of uncertainty found in typical MPPs, including the number and composition of functional alleles. Our prior distribution for the allelic series is based on the Chinese restaurant process, a relative of the Dirichlet process, and we leverage its connection to the coalescent to introduce additional prior information about haplotype relatedness via a phylogenetic tree. We evaluate our approach via simulation and apply it to QTL from two MPPs: the Collaborative Cross (CC) and the Drosophila Synthetic Population Resource (DSPR). We find that, although posterior inference of the exact allelic series is often uncertain, we are able to distinguish biallelic QTL from more complex multiallelic cases. Additionally, our allele-based approach improves haplotype effect estimation when the true number of functional alleles is small. Our method, Tree-Based Inference of Multiallelism via Bayesian Regression (TIMBR), provides new insight into the genetic architecture of QTL in MPPs.

Assessing diversity in canopy architecture, photosynthesis, and water-use efficiency in a cowpea magic population

Optimizing crops to improve light absorption and CO2 assimilation throughout the canopy is a proposed strategy to increase yield and meet the needs of a growing population by 2050. Globally, the greatest population increase is expected to occur in Sub-Saharan Africa where large yield gaps currently persist; therefore, it is crucial to develop high-yielding crops adapted to this region. In this study, we screened 50 cowpea (Vigna unguiculata (L.) Walp) genotypes from the multi-parent advanced generation inter-cross (MAGIC) population for canopy architectural traits, canopy photosynthesis, and water-use efficiency using a canopy gas exchange chamber in order to improve our understanding of the relationships among those traits. Canopy architecture contributed to 38.6% of the variance observed in canopy photosynthesis. The results suggest that the light environment within the canopy was a limiting factor for canopy CO2 assimilation. Traits favoring greater exposure of leaf area to light such as the width of the canopy relative to the total leaf area were associated with greater canopy photosynthesis, especially in canopies with high biomass. Canopy water-use efficiency was highly determined by canopy photosynthetic activity and therefore canopy architecture, which indicates that optimizing the canopy will also contribute to improving canopy water-use efficiency. We discuss different breeding strategies for future programs aimed at the improvement of cowpea yield for the Sub-Saharan African region. We show that breeding for high biomass will not optimize canopy CO2 assimilation and suggest that selection should include multiple canopy traits to improve light penetration.

GWAS reveals consistent QTL for drought and salt tolerance in a MAGIC population of 550 lines derived from intermating of 11 Upland cotton (Gossypium hirsutum) parents

Cotton is grown in arid and semi-arid regions where abiotic stresses such as drought and salt are prevalent. There is a lack of studies that simultaneously address the genetic and genomic basis of tolerance to drought and salt stress. In this study, a multi-parent advanced generation inter-cross (MAGIC) population of 550 recombinant inbred lines (RILs) together with their 11 Upland cotton parents with a total of 473,516 polymorphic SNP markers was used to identify quantitative trait loci (QTL) for drought tolerance (DT) and salt tolerance (ST) at the seedling stage based on two replicated greenhouse tests. Transgressive segregation occurred in the MAGIC-RILs, indicating that tolerant and sensitive alleles recombined for tolerance to the abiotic stress during the intermating process for the population development. A total of 20 QTL were detected for DT including 13 and 7 QTL based on plant height (PH) and dry shoot weight (DSW), respectively; and 23 QTL were detected for ST including 12 and 11 QTL for PH and DSW, respectively. There were several chromosomes with QTL clusters for abiotic stress tolerance including four QTL on chromosome A13 and three QTL on A01 for DT, and four QTL on D08 and three QTL on A11 for ST. Nine QTL (21% of the 43 QTL) detected were in common between DT and ST, indicating a common genetic basis for DT and ST. The narrow chromosomal regions for most of the QTL detected in this study allowed identification of 53 candidate genes associated with responses to salt and drought stress and abiotic stimulus. The QTL identified for both DT and ST have significantly augmented the repertoire of QTL for abiotic stress tolerance that can be used for marker-assisted selection to develop cultivars with resilience to drought and/or salt and further genomic studies towards the identification of drought and salt tolerance genes in cotton.

Multiple Genome Wide Association Mapping Models Identify Quantitative Trait Nucleotides for Brown Planthopper (Nilaparvata lugens) Resistance in MAGIC Indica Population of Rice

Brown planthopper (BPH), one of the most important pests of the rice (Oryza sativa) crop, becomes catastrophic under severe infestations and causes up to 60% yield loss. The highly disastrous BPH biotype in the Indian sub-continent is Biotype 4, which also known as the South Asian Biotype. Though many resistance genes were mapped until now, the utility of the resistance genes in the breeding programs is limited due to the breakdown of resistance and emergence of new biotypes. Hence, to identify the resistance genes for this economically important pest, we have used a multi-parent advanced generation intercross (MAGIC) panel consisting of 391 lines developed from eight indica founder parents. The panel was phenotyped at the controlled conditions for two consecutive years. A set of 27,041 cured polymorphic single nucleotide polymorphism (SNPs) and across-year phenotypic data were used for the identification of marker–trait associations. Genome-wide association analysis was performed to find out consistent associations by employing four single and two multi-locus models. Sixty-one SNPs were consistently detected by all six models. A set of 190 significant marker-associations identified by fixed and random model circulating probability unification (FarmCPU) were considered for searching resistance candidate genes. The highest number of annotated genes were found in chromosome 6 followed by 5 and 1. Ninety-two annotated genes identified across chromosomes of which 13 genes are associated BPH resistance including NB-ARC (nucleotide binding in APAF-1, R gene products, and CED-4) domain-containing protein, NHL repeat-containing protein, LRR containing protein, and WRKY70. The significant SNPs and resistant lines identified from our study could be used for an accelerated breeding program to develop new BPH resistant cultivars.

Effects of the MAGIC Guidelines on PICC Placement Volume: Advanced Practice Provider and Physician Trends Among Medicare Beneficiaries From 2010 to 2018

BACKGROUND. The Michigan Appropriateness Guide for Intravenous Catheters (MAGIC) was published in 2015, recommending more restricted indications for peripherally inserted central catheter (PICC) placement, particularly for those placed by physicians. Changes in PICC placement volume since the publication of MAGIC is largely unknown. OBJECTIVE. The purpose of this article was to study the trends in volume and reimbursement for PICC placement by physicians and advanced practice providers (APPs) for Medicare enrollees from 2010 to 2018 with specific attention to the changes in volume after the publication of MAGIC in 2015. METHODS. Claims from the Medicare Part B Physician/Supplier Procedure Summary Master File for the years 2010-2018 were extracted using the Current Procedural Terminology code for PICC placement. Total volume and payment amounts (for the professional component) were analyzed. Trendline slopes for volume per 100,000 Medicare beneficiaries before and after the 2015 publication of MAGIC were compared. RESULTS. Volume for PICC placement by physicians and APPs steadily declined from 243,837 in 2010 to 130,361 in 2018 (46.5%). The PICC placement volume decreased sharply after the 2015 publication of the MAGIC guidelines. The slope of the trendline for all providers from 2010 to 2015 was -3.4 compared with -7.3 from 2015 to 2018. The change in slope was more pronounced for radiologists (-3.1 to -5.6) than for APPs (0.0 to -1.1). Professional payment per procedure for radiologists decreased from $78.04 in 2010 to $70.17 in 2018, and reimbursement for APPs proportionally decreased from $65.76 to $60.66 during this time. The relative share of PICC placement by radiologists declined from 77.0% in 2010 to 70.6% in 2018, with a corresponding increase in relative share by APPs from 13.5% to 18.4%. The percentage placed in outpatient procedures increased from 15.1% to 18.2%. CONCLUSION. The volume of PICC placements has steadily decreased since 2010, with a sharper decline between 2015 and 2016 corresponding with the publication of the MAGIC evidence-based guidelines. The role of APPs in PICC placement has increased over this time period. CLINICAL IMPACT. The findings of this study suggest that evidence-based guidelines impact clinical practice on a national level.

Strong Recommendations Are Inappropriate in Person-Centred Care: The Case of Anti-Platelet Therapy

A 'Rapid Recommendation' has been produced by the GRADE group, in collaboration with MAGIC and BMJ, in response to an RCT showing Dual Anti-Platelet Therapy (DAPT) is superior to Aspirin alone for patients who had suffered acute high risk transient ischaemic attack or minor ischaemic stroke. The interactive MAGIC decision aid that accompanies each Rapid Recommendation is the main route to their clinical implementation. It can facilitate preference-sensitive person-centred care, but only if a Multi-Criteria Decision Analysis-based decision support tool is added. A demonstration version of such an add-on to the MAGIC aid, divested of recommendations, is available online. Exploring the results of different preference inputs into the tool raises questions about the strong recommendation for DAPT.

Determinants of QTL Mapping Power in the Realized Collaborative Cross

The Collaborative Cross (CC) is a mouse genetic reference population whose range of applications includes quantitative trait loci (QTL) mapping. The design of a CC QTL mapping study involves multiple decisions, including which and how many strains to use, and how many replicates per strain to phenotype, all viewed within the context of hypothesized QTL architecture. Until now, these decisions have been informed largely by early power analyses that were based on simulated, hypothetical CC genomes. Now that more than 50 CC strains are available and more than 70 CC genomes have been observed, it is possible to characterize power based on realized CC genomes. We report power analyses from extensive simulations and examine several key considerations: 1) the number of strains and biological replicates, 2) the QTL effect size, 3) the presence of population structure, and 4) the distribution of functionally distinct alleles among the founder strains at the QTL. We also provide general power estimates to aide in the design of future experiments. All analyses were conducted with our R package, SPARCC (Simulated Power Analysis in the Realized Collaborative Cross), developed for performing either large scale power analyses or those tailored to particular CC experiments.

Genetic Dissection of Resistance to the Three Fungal Plant Pathogens Blumeria graminis, Zymoseptoria tritici, and Pyrenophora tritici-repentis Using a Multiparental Winter Wheat Population

Bread wheat (Triticum aestivum L.) is one of the world’s most important crop species. The development of new varieties resistant to multiple pathogens is an ongoing task in wheat breeding, especially in times of increasing demand for sustainable agricultural practices. Despite this, little is known about the relations between various fungal disease resistances at the genetic level, and the possible consequences for wheat breeding strategies. As a first step to fill this gap, we analyzed the genetic relations of resistance to the three fungal diseases – powdery mildew (PM), septoria tritici blotch (STB), and tan spot (TS) – using a winter wheat multiparent advanced generation intercross population. Six, seven, and nine QTL for resistance to PM, STB, and TS, respectively, were genetically mapped. Additionally, 15 QTL were identified for the three agro-morphological traits plant height, ear emergence time, and leaf angle distribution. Our results suggest that resistance to STB and TS on chromosome 2B is conferred by the same genetic region. Furthermore, we identified two genetic regions on chromosome 1AS and 7AL, which are associated with all three diseases, but not always in a synchronal manner. Based on our results, we conclude that parallel marker-assisted breeding for resistance to the fungal diseases PM, STB, and TS appears feasible. Knowledge of the genetic co-localization of alleles with contrasting effects for different diseases, such as on chromosome 7AL, allows the trade-offs of selection of these regions to be better understood, and ultimately determined at the genic level.

R/qtl2: Software for Mapping Quantitative Trait Loci with High-Dimensional Data and Multiparent Populations

R/qtl2 is an interactive software environment for mapping quantitative trait loci (QTL) in experimental populations. The R/qtl2 software expands the scope of the widely-used R/qtl software package to include multiparental populations, better handles modern high-dimensional data....

R/qtl2 is an interactive software environment for mapping quantitative trait loci (QTL) in experimental populations. The R/qtl2 software expands the scope of the widely used R/qtl software package to include multiparent populations derived from more than two founder strains, such as the Collaborative Cross and Diversity Outbred mice, heterogeneous stocks, and MAGIC plant populations. R/qtl2 is designed to handle modern high-density genotyping data and high-dimensional molecular phenotypes, including gene expression and proteomics. R/qtl2 includes the ability to perform genome scans using a linear mixed model to account for population structure, and also includes features to impute SNPs based on founder strain genomes and to carry out association mapping. The R/qtl2 software provides all of the basic features needed for QTL mapping, including graphical displays and summary reports, and it can be extended through the creation of add-on packages. R/qtl2, which is free and open source software written in the R and C++ programming languages, comes with a test framework.

From Rapid Recommendation to Online Preference-Sensitive Decision Support: The Case of Severe Aortic Stenosis

The launch of ‘Rapid Recommendations’ by the Grading of Recommendations Assessment, Development and Evaluation (GRADE) group, in collaboration with Making GRADE the Irresistible Choice (MAGIC) and the British Medical Journal (BMJ), is a very interesting recent development in e-healthcare. Designed to respond quickly to developments that have created new decision situations, their first project resulted from the arrival of minimally invasive Transcatheter Aortic Valve Implantation (TAVI) as an alternative to Surgical Aortic Valve Replacement (SAVR), for patients with symptomatic severe aortic stenosis. The interactive MAGIC decision aid that accompanies a Rapid Recommendation and is the main route to its clinical implementation, represents a major advance in e-health, for a cardiovascular decision in this case. However, it needs to go further in order to facilitate fully person-centred care, where the weighted preferences of the individual person are elicited at the point of decision, and transparently integrated with the best (most personalised) estimates of option performances, to produce personalised, preference-sensitive option evaluations. This can be achieved by inputting the collated GRADE evidence on the criteria relevant in the TAVI/SAVR choice into a Multi-Criteria Decision Analysis-based decision support tool, generating a personalised, preference-sensitive opinion. A demonstration version of this add-on to the MAGIC aid, divested of recommendations, is available online as proof of method.

Genome-Wide Association Mapping in a Rice MAGIC Plus Population Detects QTLs and Genes Useful for Biofortification

The development of rice genotypes with micronutrient-dense grains and disease resistance is one of the major priorities in rice improvement programs. We conducted Genome-wide association studies (GWAS) using a Multi-parent Advanced Generation Inter-Cross (MAGIC) Plus population to identify QTLs and SNP markers that could potentially be integrated in biofortification and disease resistance breeding. We evaluated 144 MAGIC Plus lines for agronomic and biofortification traits over two locations for two seasons, while disease resistance was screened for one season in the screen house. X-ray fluorescence technology was used to measure grain Fe and Zn concentrations. Genotyping was carried out by genotype by sequencing and a total of 14,242 SNP markers were used in the association analysis. We used Mixed linear model (MLM) with kinship and detected 57 significant genomic regions with a -log10 (P-value) ≥ 3.0. The PH 1.1 and Zn 7.1 were consistently identified in all the four environments, ten QTLs qDF 3.1, qDF 6.2 qDF 9.1 qPH 5.1 qGL 3.1, qGW 3.1, qGW 11.1, and qZn 6.2 were detected in two environments, while two major loci qBLB 11.1 and qBLB 5.1 were identified for Bacterial Leaf Blight (BLB) resistance. The associated SNP markers were found to co-locate with known major genes and QTLs such as OsMADS50 for days to flowering, osGA20ox2 for plant height, and GS3 for grain length. Similarly, Xa4 and xa5 genes were identified for BLB resistance and Pi5(t), Pi28(t), and Pi30(t) genes were identified for Blast resistance. A number of metal homeostasis genes OsMTP6, OsNAS3, OsMT2D, OsVIT1, and OsNRAMP7 were co-located with QTLs for Fe and Zn. The marker-trait relationships from Bayesian network analysis showed consistency with the results of GWAS. A number of promising candidate genes reported in our study can be further validated. We identified several QTLs/genes pyramided lines with high grain Zn and acceptable yield potential, which are a good resource for further evaluation to release as varieties as well as for use in breeding programs.

Functional Mapping of Quantitative Trait Loci (QTLs) Associated With Plant Performance in a Wheat MAGIC Mapping Population

In crop genetic studies, the mapping of longitudinal data describing the spatio-temporal nature of agronomic traits can elucidate the factors influencing their formation and development. Here, we combine the mapping power and precision of a MAGIC wheat population with robust computational methods to track the spatio- temporal dynamics of traits associated with wheat performance. NIAB MAGIC lines were phenotyped throughout their lifecycle under smart house conditions. Growth models were fitted to the data describing growth trajectories of plant area, height, water use and senescence and fitted parameters were mapped as quantitative traits. Trait data from single time points were also mapped to determine when and how markers became and ceased to be significant. Assessment of temporal dynamics allowed the identification of marker-trait associations and tracking of trait development against the genetic contribution of key markers. We establish a data-driven approach for understanding complex agronomic traits and accelerate research in plant breeding.

The paradox of proteasome granules

Profound knowledge is available for the structure, function and regulation of proteasomes, the key proteases for ubiquitin-dependent protein degradation in dividing cells. Far less understood are proteasome structure and function in quiescence, the resting phase of our body's cells, as in yeast cells grown to stationary phase. In quiescent yeast proteasomes exit the nucleus and accumulate in cytoplasmic protein droplets, called proteasome storage granules (PSG). PSG-like structures also exist in non-dividing mammalian cells suggesting that the mechanism underlying PSG organization is conserved from yeast to human. The PSG has physiological significance as it protects yeast cells against stress and confers fitness during aging. The molecular architecture of PSG remains an enigma, since PSG freely move as spherical units without being surrounded by membranes through the cytoplasm. They rapidly resolve with the resumption of cell proliferation and proteasomes reenter the nucleus. Our systems biology and biochemical data revealed that PSG are mainly composed of proteasomes and free ubiquitin. Often intrinsically disordered proteins undergo liquid phase separations, allowing soluble proteins to condense into protein droplets in an aqueous solution. The question is which proteins and factors nucleate PSG formation, since proteasomes composed of folded subunits are able to degrade intrinsically disordered proteins.

Maximizing the potential of multi-parental crop populations

Most agriculturally significant crop traits are quantitatively inherited which limits the ease and efficiency of trait dissection. Multi-parent populations overcome the limitations of traditional trait mapping and offer new potential to accurately define the genetic basis of complex crop traits. The increasing popularity and use of nested association mapping (NAM) and multi-parent advanced generation intercross (MAGIC) populations raises questions about the optimal design and allocation of resources in their creation. In this paper we review strategies for the creation of multi-parent populations and describe two complementary in silico studies addressing the design and construction of NAM and MAGIC populations. The first simulates the selection of diverse founder parents and the second the influence of multi-parent crossing schemes (and number of founders) on haplotype creation and diversity. We present and apply two open software resources to simulate alternate strategies for the development of multi-parent populations.

Determining Phenological Patterns Associated with the Onset of Senescence in a Wheat MAGIC Mapping Population

The appropriate timing of developmental transitions is critical for adapting many crops to their local climatic conditions. Therefore, understanding the genetic basis of different aspects of phenology could be useful in highlighting mechanisms underpinning adaptation, with implications in breeding for climate change. For bread wheat (Triticum aestivum), the transition from vegetative to reproductive growth, the start and rate of leaf senescence and the relative timing of different stages of flowering and grain filling all contribute to plant performance. In this study we screened under Smart house conditions a large, multi-founder "NIAB elite MAGIC" wheat population, to evaluate the genetic elements that influence the timing of developmental stages in European elite varieties. This panel of recombinant inbred lines was derived from eight parents that are or recently have been grown commercially in the UK and Northern Europe. We undertook a detailed temporal phenotypic analysis under Smart house conditions of the population and its parents, to try to identify known or novel Quantitative Trait Loci associated with variation in the timing of key phenological stages in senescence. This analysis resulted in the detection of QTL interactions with novel traits such the time between "half of ear emergence above flag leaf ligule" and the onset of senescence at the flag leaf as well as traits associated with plant morphology such as stem height. In addition, strong correlations between several traits and the onset of senescence of the flag leaf were identified. This work establishes the value of systematically phenotyping genetically unstructured populations to reveal the genetic architecture underlying morphological variation in commercial wheat.

Allele mining and enhanced genetic recombination for rice breeding

Traditional rice varieties harbour a large store of genetic diversity with potential to accelerate rice improvement. For a long time, this diversity maintained in the International Rice Genebank has not been fully used because of a lack of genome information. The publication of the first reference genome of Nipponbare by the International Rice Genome Sequencing Project (IRGSP) marked the beginning of a systematic exploration and use of rice diversity for genetic research and breeding. Since then, the Nipponbare genome has served as the reference for the assembly of many additional genomes. The recently completed 3000 Rice Genomes Project together with the public database (SNP-Seek) provides a new genomic and data resource that enables the identification of useful accessions for breeding. Using disease resistance traits as case studies, we demonstrated the power of allele mining in the 3,000 genomes for extracting accessions from the GeneBank for targeted phenotyping. Although potentially useful landraces can now be identified, their use in breeding is often hindered by unfavourable linkages. Efficient breeding designs are much needed to transfer the useful diversity to breeding. Multi-parent Advanced Generation InterCross (MAGIC) is a breeding design to produce highly recombined populations. The MAGIC approach can be used to generate pre-breeding populations with increased genotypic diversity and reduced linkage drag. Allele mining combined with a multi-parent breeding design can help convert useful diversity into breeding-ready genetic resources.

Sensitivity analyses of MAGIC modelled predictions of future impacts of whole-tree harvest on soil calcium supply and stream acid neutralizing capacity

Forest biofuel is a main provider of energy in Sweden and the market is expected to grow even further in the future. Removal of logging residues via harvest can lead to short-term acidification but the long-term effects are largely unknown. The objectives of this study were to 1) model the long-term effect of whole-tree harvest (WTH) on soil and stream water acidity and 2) perform sensitivity analyses by varying the amounts of logging residues, calcium (Ca(2+)) concentrations in tree biomass and site productivity in nine alternate scenarios. Data from three Swedish forested catchments and the Model of Acidification of Groundwater in Catchments (MAGIC) were used to simulate changes in forest soil exchangeable Ca(2+) pools and stream water acid neutralizing capacity (ANC) at Gammtratten, Kindla and Aneboda. Large depletions in soil Ca(2+) supply and a reversal of the positive trend in stream ANC were predicted for all three sites after WTH. However, the magnitude of impact on stream ANC varied depending on site and the concentration of mobile strong acid anions. Contrary to common beliefs, the largest decrease in modelled ANC was observed at the well-buffered site Gammtratten. The effects at Kindla and Aneboda were much more limited and not large enough to offset the general recovery from acidification. Varying the tree biomass Ca(2+) concentrations exerted the largest impact on modelled outcome. Site productivity was the second most important variable whereas changing biomass amounts left on site only marginally affected the results. The outcome from the sensitivity analyses pointed in the same direction of change as in the base scenario, except for Kindla where soil Ca(2+) pools were predicted to be replenished under a given set of input data. The reliability of modelled outcome would increase by using site-specific Ca(2+) concentrations in tree biomass and field determined identification of site productivity.

Indirect detection of dark matter with γ rays

The details of what constitutes the majority of the mass that makes up dark matter in the Universe remains one of the prime puzzles of cosmology and particle physics today-80 y after the first observational indications. Today, it is widely accepted that dark matter exists and that it is very likely composed of elementary particles, which are weakly interacting and massive [weakly interacting massive particles (WIMPs)]. As important as dark matter is in our understanding of cosmology, the detection of these particles has thus far been elusive. Their primary properties such as mass and interaction cross sections are still unknown. Indirect detection searches for the products of WIMP annihilation or decay. This is generally done through observations of γ-ray photons or cosmic rays. Instruments such as the Fermi large-area telescope, high-energy stereoscopic system, major atmospheric gamma-ray imaging Cherenkov, and very energetic radiation imaging telescope array, combined with the future Cherenkov telescope array, will provide important complementarity to other search techniques. Given the expected sensitivities of all search techniques, we are at a stage where the WIMP scenario is facing stringent tests, and it can be expected that WIMPs will be either be detected or the scenario will be so severely constrained that it will have to be rethought. In this sense, we are on the threshold of discovery. In this article, I will give a general overview of the current status and future expectations for indirect searches of dark matter (WIMP) particles.

Efficient imputation of missing markers in low-coverage genotyping-by-sequencing data from multiparental crosses

We consider genomic imputation for low-coverage genotyping-by-sequencing data with high levels of missing data. We compensate for this loss of information by utilizing family relationships in multiparental experimental crosses. This nearly quadruples the number of usable markers when applied to a large rice Multiparent Advanced Generation InterCross (MAGIC) study.