Analysis of the bread wheat genome using whole-genome shotgun sequencing

Bread wheat (Triticum aestivum) is a globally important crop, accounting for 20 per cent of the calories consumed by humans. Major efforts are underway worldwide to increase wheat production by extending genetic diversity and analysing key traits, and genomic resources can accelerate progress. But so far the very large size and polyploid complexity of the bread wheat genome have been substantial barriers to genome analysis. Here we report the sequencing of its large, 17-gigabase-pair, hexaploid genome using 454 pyrosequencing, and comparison of this with the sequences of diploid ancestral and progenitor genomes. We identified between 94,000 and 96,000 genes, and assigned two-thirds to the three component genomes (A, B and D) of hexaploid wheat. High-resolution synteny maps identified many small disruptions to conserved gene order. We show that the hexaploid genome is highly dynamic, with significant loss of gene family members on polyploidization and domestication, and an abundance of gene fragments. Several classes of genes involved in energy harvesting, metabolism and growth are among expanded gene families that could be associated with crop productivity. Our analyses, coupled with the identification of extensive genetic variation, provide a resource for accelerating gene discovery and improving this major crop.

An improved assembly and annotation of the allohexaploid wheat genome identifies complete families of agronomic genes and provides genomic evidence for chromosomal translocations

Advances in genome sequencing and assembly technologies are generating many high-quality genome sequences, but assemblies of large, repeat-rich polyploid genomes, such as that of bread wheat, remain fragmented and incomplete. We have generated a new wheat whole-genome shotgun sequence assembly using a combination of optimized data types and an assembly algorithm designed to deal with large and complex genomes. The new assembly represents >78% of the genome with a scaffold N50 of 88.8 kb that has a high fidelity to the input data. Our new annotation combines strand-specific Illumina RNA-seq and Pacific Biosciences (PacBio) full-length cDNAs to identify 104,091 high-confidence protein-coding genes and 10,156 noncoding RNA genes. We confirmed three known and identified one novel genome rearrangements. Our approach enables the rapid and scalable assembly of wheat genomes, the identification of structural variants, and the definition of complete gene models, all powerful resources for trait analysis and breeding of this key global crop.

Effects of childhood trauma on psychological functioning in adults sexually abused as children

Standardized symptom measures were used to determine the effect of childhood trauma experiences on adults sexually victimized as children. One hundred eighty-eight sexually abused individuals were tested for mean scores for depression, self-esteem, general levels of trauma symptoms, sexual dysfunction, posttraumatic stress disorder symptoms, and dissociation. Childhood traumatic experiences (parents fighting, physical abuse by father or by mother, other childhood traumas) of a nonsexual nature correlated with increased symptom levels and accounted for significant changes in percentage of variance ranging from 5.2% (general trauma symptoms) to 12.3% (posttraumatic stress disorder). Even after controlling for nonsexual-abuse trauma, sexual trauma in childhood continued to contribute significantly to increased adult symptom levels. Variables tested included number of perpetrators; incest; age of first abuse; whether force, bribes, or threats were used by the perpetrator; and penetration. The use of force was the single most significant individual sexual abuse variable. Sexual abuse as a whole contributed significantly to all the symptom measures with the most change in variance noted for dissociation (20.5%). Gender contributed significant differences only for sexual dysfunction when men scored significantly worse.

Ubiquitylation activates a peptidase that promotes cleavage and destabilization of its activating E3 ligases and diverse growth regulatory proteins to limit cell proliferation in Arabidopsis

The characteristic shapes and sizes of organs are established by cell proliferation patterns and final cell sizes, but the underlying molecular mechanisms coordinating these are poorly understood. Here we characterize a ubiquitin-activated peptidase called DA1 that limits the duration of cell proliferation during organ growth in Arabidopsis thaliana The peptidase is activated by two RING E3 ligases, Big Brother (BB) and DA2, which are subsequently cleaved by the activated peptidase and destabilized. In the case of BB, cleavage leads to destabilization by the RING E3 ligase PROTEOLYSIS 1 (PRT1) of the N-end rule pathway. DA1 peptidase activity also cleaves the deubiquitylase UBP15, which promotes cell proliferation, and the transcription factors TEOSINTE BRANCED 1/CYCLOIDEA/PCF 15 (TCP15) and TCP22, which promote cell proliferation and repress endoreduplication. We propose that DA1 peptidase activity regulates the duration of cell proliferation and the transition to endoreduplication and differentiation during organ formation in plants by coordinating the destabilization of regulatory proteins.

Transcript-specific, single-nucleotide polymorphism discovery and linkage analysis in hexaploid bread wheat (Triticum aestivum L.)

Food security is a global concern and substantial yield increases in cereal crops are required to feed the growing world population. Wheat is one of the three most important crops for human and livestock feed. However, the complexity of the genome coupled with a decline in genetic diversity within modern elite cultivars has hindered the application of marker-assisted selection (MAS) in breeding programmes. A crucial step in the successful application of MAS in breeding programmes is the development of cheap and easy to use molecular markers, such as single-nucleotide polymorphisms. To mine selected elite wheat germplasm for intervarietal single-nucleotide polymorphisms, we have used expressed sequence tags derived from public sequencing programmes and next-generation sequencing of normalized wheat complementary DNA libraries, in combination with a novel sequence alignment and assembly approach. Here, we describe the development and validation of a panel of 1114 single-nucleotide polymorphisms in hexaploid bread wheat using competitive allele-specific polymerase chain reaction genotyping technology. We report the genotyping results of these markers on 23 wheat varieties, selected to represent a broad cross-section of wheat germplasm including a number of elite UK varieties. Finally, we show that, using relatively simple technology, it is possible to rapidly generate a linkage map containing several hundred single-nucleotide polymorphism markers in the doubled haploid mapping population of Avalon × Cadenza.

Volumetric object modeling for surgical simulation

Surgical simulation has many applications in medical education, surgical training, surgical planning and intra-operative assistance. However, extending current surface-based computer graphics methods to model phenomena such as the deformation, cutting, tearing or repairing of soft tissues poses significant challenges for real-time interactions. This paper discusses the use of volumetric methods for modeling complex anatomy and tissue interactions. New techniques are introduced that use volumetric methods for modeling soft-tissue deformation and tissue cutting at interactive rates. An initial prototype for simulating arthroscopic knee surgery is described which uses volumetric models of the knee derived from 3-D magnetic resonance imaging, visual feedback via real-time volume and polygon rendering, and haptic feedback provided by a force-feedback device.

Brugada syndrome masquerading as febrile seizures

Fever can precipitate ventricular tachycardia in adults with Brugada syndrome, but such a link has not been reported in children. A 21-month-old white girl presented repeatedly with decreased conscious level and seizures during fever. During a typical episode, rapid ventricular tachycardia was documented. The resting 12-lead electrocardiogram revealed a Brugada electrocardiogram signature. Resting electrocardiograms of the asymptomatic brother and mother were normal, but fever in the mother and pharmacologic stress with ajmaline in the brother revealed Brugada electrocardiogram features. Genetic testing revealed an SCN5A mutation in the affected family members.

Quick rating of depressed mood in patients with anxiety disorders

BACKGROUND

Regular assessment of mood is often important for treatment but traditional measures can be time-consuming. A quick'litmus test' is needed.

AIMS

To test the reliability and validity of a single-item scale for mood.

METHOD

Mood was measured repeatedly in 812 patients (258 in-patients, 554 out-patient) being treated in an anxiety disorders unit. Patients had self- and clinician ratings of a single-item depression scale and also rated the 21-item Beck Depression Inventory (BDI-21). Their single-item scores were compared with BDI-21 scores and with outcome measures.

RESULTS

The single-item depression scores correlated 0.71 to 0.78 with the BDI-21 scores. Clinically useful cut-off points were identified. Depression scores at discharge, but not pre-treatment, correlated significantly with improvement in the main problem.

CONCLUSIONS

The quick single-item depression scale, whether rated by patient or by clinician, is a reasonable rough guide to mood in anxiety disorders and saves time for the patient and the clinician compared to longer measures.

An integrated physical, genetic and cytogenetic map of Brachypodium distachyon, a model system for grass research

The pooid subfamily of grasses includes some of the most important crop, forage and turf species, such as wheat, barley and Lolium. Developing genomic resources, such as whole-genome physical maps, for analysing the large and complex genomes of these crops and for facilitating biological research in grasses is an important goal in plant biology. We describe a bacterial artificial chromosome (BAC)-based physical map of the wild pooid grass Brachypodium distachyon and integrate this with whole genome shotgun sequence (WGS) assemblies using BAC end sequences (BES). The resulting physical map contains 26 contigs spanning the 272 Mb genome. BES from the physical map were also used to integrate a genetic map. This provides an independent vaildation and confirmation of the published WGS assembly. Mapped BACs were used in Fluorescence In Situ Hybridisation (FISH) experiments to align the integrated physical map and sequence assemblies to chromosomes with high resolution. The physical, genetic and cytogenetic maps, integrated with whole genome shotgun sequence assemblies, enhance the accuracy and durability of this important genome sequence and will directly facilitate gene isolation.

Agrobacterium-mediated transformation of the temperate grass Brachypodium distachyon (genotype Bd21) for T-DNA insertional mutagenesis

Brachypodium distachyon is a promising model system for the structural and functional genomics of temperate grasses because of its physical, genetic and genome attributes. The sequencing of the inbred line Bd21 (http://www.brachypodium.org) started in 2007. However, a transformation method remains to be developed for the community standard line Bd21. In this article, a facile, efficient and rapid transformation system for Bd21 is described using Agrobacterium-mediated transformation of compact embryogenic calli (CEC) derived from immature embryos. Key features of this system include: (i) the use of the green fluorescent protein (GFP) associated with hygromycin selection for rapid identification of transgenic calli and plants; (ii) the desiccation of CEC after inoculation with Agrobacterium; (iii) the utilization of Bd21 plants regenerated from tissue culture as a source of immature embryos; (iv) the control of the duration of the selection process; and (v) the supplementation of culture media with CuSO4 prior to and during the regeneration of transgenic plants. Approximately 17% of CEC produced transgenic plants, enabling the generation of hundreds of T-DNA insertion lines per experiment. GFP expression was observed in primary transformed Bd21 plants (T0) and their progeny (T1). The Mendelian inheritance of the transgenes was confirmed. An adaptor-anchor strategy was developed for efficient retrieval of flanking sequence tags (FSTs) of T-DNA inserts, and the resulting sequences are available in public databases. The production of T-DNA insertion lines and the retrieval of associated FSTs reported here for the reference inbred line Bd21 will facilitate large-scale functional genomics research in this model system.

An SSR-based genetic linkage map of the model grass Brachypodium distachyon

The grass species Brachypodium distachyon (hereafter, Brachypodium) has been adopted as a model system for grasses. Here, we describe the development of a genetic linkage map of Brachypodium. The genetic linkage map was developed with an F2 population from a cross between the diploid Brachypodium lines Bd3-1 and Bd21. The map was populated with polymorphic simple sequence repeat (SSR) markers from Brachypodium expressed sequence tag (EST) and bacterial artificial chromosome (BAC) end sequences and conserved orthologous sequence (COS) markers from other grass species. The map is 1386 cM in length and consists of 139 marker loci distributed across 20 linkage groups. Five of the linkage groups exceed 100 cM in length, with the largest being 231 cM long. Assessment of colinearity between the Brachypodium linkage map and the rice genome sequence revealed significant regions of macrosynteny between the two genomes, as well as rearrangements similar to those reported in other grass comparative structural genomics studies. The Brachypodium genetic linkage map described here will serve as a new tool to pursue a range of molecular genetic analyses and other applications in this new model plant system.

Variation in Expression of the HECT E3 Ligase UPL3 Modulates LEC2 Levels, Seed Size, and Crop Yields in Brassica napus

Identifying genetic variation that increases crop yields is a primary objective in plant breeding. We used association analyses of oilseed rape/canola (Brassica napus) accessions to identify genetic variation that influences seed size, lipid content, and final crop yield. Variation in the promoter region of the HECT E3 ligase gene BnaUPL3 C03 made a major contribution to variation in seed weight per pod, with accessions exhibiting high seed weight per pod having lower levels of BnaUPL3 C03 expression. We defined a mechanism in which UPL3 mediated the proteasomal degradation of LEC2, a master transcriptional regulator of seed maturation. Accessions with reduced UPL3 expression had increased LEC2 protein levels, larger seeds, and prolonged expression of lipid biosynthetic genes during seed maturation. Natural variation in BnaUPL3 C03 expression appears not to have been exploited in current B napus breeding lines and could therefore be used as a new approach to maximize future yields in this important oil crop.

Ring trial of 2nd generation RT-QuIC diagnostic tests for sporadic CJD

Objective

Real‐time quaking‐induced conversion (RT‐QuIC) assays detect prion‐seeding activity in a variety of human biospecimens, including cerebrospinal fluid and olfactory mucosa swabs. The assay has shown high diagnostic accuracy in patients with prion disorders. Recently, advances in these tests have led to markedly improved diagnostic sensitivity and reduced assay times. Accordingly, an algorithm has been proposed that entails the use of RT‐QuIC analysis of both sample types to diagnose sporadic Creutzfeldt‐Jakob disease with nearly 100% accuracy. Here we present a multi‐center evaluation (ring trial) of the reproducibility of these improved “second generation” RT‐QuIC assays as applied to these diagnostic specimens.

Methods

Cerebrospinal fluid samples were analyzed from subjects with sporadic Creutzfeldt‐Jakob (n = 55) or other neurological diseases (n = 45) at multiple clinical centers. Olfactory mucosa brushings collected by multiple otolaryngologists were obtained from nine sporadic Creutzfeldt‐Jakob disease cases and 19 controls. These sample sets were initially tested blindly by RT‐QuIC by a coordinating laboratory, recoded, and then sent to five additional testing laboratories for blinded ring trial testing.

Results

Unblinding of the results by a third party indicated 98‐100% concordance between the results obtained by the testing of these cerebrospinal fluid and nasal brushings at the six laboratories.

Interpretation

This second‐generation RT‐QuIC assay is highly transferrable, reproducible, and therefore robust for the diagnosis of sporadic Creutzfeldt‐Jakob disease in clinical practice.

Randomised controlled trial of the use of a modified postal reminder card on the uptake of measles vaccination

OBJECTIVE

To determine whether rewording postal reminder cards according to the "health belief model", a theory about preventive health behaviour, would help to improve measles vaccination rates.

DESIGN

A randomised controlled trial, with blind assessment of outcome status. Parents of children due for their first measles vaccination were randomised to one of two groups, one receiving the health belief model reminder card, the other receiving the usual, neutrally worded card. The proportion of children subsequently vaccinated in each group over a five week period was ascertained from clinical (provider based) records.

SETTING

A local government operated public vaccination clinic.

PARTICIPANTS

Parents of 259 children due for measles vaccination.

MAIN RESULTS

The proportion of children vaccinated in the health belief model card group was 79% compared with 67% of those sent the usual card (95% CI, 2% to 23%), a modest but important improvement.

CONCLUSION

This study illustrates how the effectiveness of a minimal and widely practised intervention to promote vaccination compliance can be improved with negligible additional effort.

Early outcomes of coronary artery bypass with and without cardiopulmonary bypass in octogenarians

BACKGROUND

Off-pump coronary artery bypass (OPCAB) surgery has been successfully used in diverse patient populations and has been postulated to be safer than conventional coronary artery bypass (CCAB) surgery in some high-risk patients, including the elderly.

OBJECTIVE

To compare the safety of OPCAB surgery versus CCAB surgery in the octogenarian population of two large southwestern Ontario cardiac surgical units.

RESULTS

Two hundred thirty-six consecutive octogenarians underwent primary isolated coronary artery bypass surgery from November 2000 to March 2005. Patients undergoing OPCAB surgery tended to have higher Parsonnet scores, while patients undergoing CCAB surgery had a greater number of emergent operations. The Canadian Cardiovascular Network predicted that mortality risk was similar in both groups. In-hospital mortality was similar between groups, as was postoperative myocardial infarction and new onset of renal dysfunction. However, in the OPCAB group, there was a decreased incidence of postoperative neurological dysfunction (2.3% in the OPCAB group versus 10.5% in the CCAB group, P=0.01), in particular cerebrovascular accidents (1.5% in the OPCAB group versus 7.6% in the CCAB group, P=0.05), and a decreased incidence of prolonged intubation (5.3% in the OPCAB group versus 13.3% in the CCAB group, P=0.04). Multivariable analysis found that cardiopulmonary bypass had no significant impact on mortality or length of stay.

CONCLUSIONS

In octogenarian patients, OPCAB surgery is as safe as CCAB surgery in terms of mortality and major morbidity. Furthermore, a significant reduction in neurological dysfunction and prolonged intubation was seen in the OPCAB group compared with the CCAB group.

The parasympathetic nervous system and glucocorticoid-mediated hyperinsulinaemia in the genetically obese (fa/fa) Zucker rat

Lean (Fa/-) and genetically obese (fa/fa) Zucker rats were adrenalectomized at 18 days of age (3 days before weaning) before the onset of hyperinsulinaemia. At 40-41 days of age, basal and glucose-stimulated insulin concentrations did not differ significantly between lean and obese rats. Plasma insulin and glucose concentrations were higher in both phenotypes 24 h after administration of corticosterone (2.0 mg at 12-h intervals). Corticosterone-treated obese rats had higher basal and glucose-stimulated insulin levels than similarly treated lean animals, although plasma glucose concentrations did not differ between phenotypes. The basal plasma insulin concentration of obese rats treated with corticosterone for 24 h was reduced 15, 30 and 45 min after injection of atropine (0.3 mg) without any significant change in the plasma glucose level. Injection of atropine (0.3 mg) 20 min before a glucose load prevented the greater increment in plasma insulin concentration of corticosterone-treated obese rats compared with similarly treated lean animals. Atropine administration (0.3 mg) to intact obese rats at 40 days of age reduced, but did not abolish, their hyperinsulinaemia compared with intact lean animals. It is concluded that (1) pre-weaning adrenalectomy prevents the development of hyperinsulinaemia in genetically obese rats, (2) corticosterone replacement for only 24 h restores the hyperinsulinaemia of obese rats, (3) the differential effects of corticosterone on insulin secretion by lean and obese rats are mediated by the parasympathetic nervous system and (4) the parasympathetic nervous system contributes to, but is not the only cause of, hyperinsulinaemia in intact obese rats.

Reduced chromatin accessibility underlies gene expression differences in homologous chromosome arms of diploid Aegilops tauschii and hexaploid wheat

Background

Polyploidy is centrally important in the evolution and domestication of plants because it leads to major genomic changes, such as altered patterns of gene expression, which are thought to underlie the emergence of new traits. Despite the common occurrence of these globally altered patterns of gene expression in polyploids, the mechanisms involved are not well understood.

Results

Using a precisely defined framework of highly conserved syntenic genes on hexaploid wheat chromosome 3DL and its progenitor 3 L chromosome arm of diploid Aegilops tauschii, we show that 70% of these gene pairs exhibited proportionately reduced gene expression, in which expression in the hexaploid context of the 3DL genes was ∼40% of the levels observed in diploid Ae tauschii. Several genes showed elevated expression during the later stages of grain development in wheat compared with Ae tauschii. Gene sequence and methylation differences probably accounted for only a few cases of differences in gene expression. In contrast, chromosome-wide patterns of reduced chromatin accessibility of genes in the hexaploid chromosome arm compared with its diploid progenitor were correlated with both reduced gene expression and the imposition of new patterns of gene expression.

Conclusions

Our pilot-scale analyses show that chromatin compaction may orchestrate reduced gene expression levels in the hexaploid chromosome arm of wheat compared to its diploid progenitor chromosome arm.

Soil legacy data rescue via GlobalSoilMap and other international and national initiatives

Legacy soil data have been produced over 70 years in nearly all countries of the world. Unfortunately, data, information and knowledge are still currently fragmented and at risk of getting lost if they remain in a paper format. To process this legacy data into consistent, spatially explicit and continuous global soil information, data are being rescued and compiled into databases. Thousands of soil survey reports and maps have been scanned and made available online. The soil profile data reported by these data sources have been captured and compiled into databases. The total number of soil profiles rescued in the selected countries is about 800,000. Currently, data for 117, 000 profiles are compiled and harmonized according to GlobalSoilMap specifications in a world level database (WoSIS). The results presented at the country level are likely to be an underestimate. The majority of soil data is still not rescued and this effort should be pursued. The data have been used to produce soil property maps. We discuss the pro and cons of top-down and bottom-up approaches to produce such maps and we stress their complementarity. We give examples of success stories. The first global soil property maps using rescued data were produced by a top-down approach and were released at a limited resolution of 1km in 2014, followed by an update at a resolution of 250m in 2017. By the end of 2020, we aim to deliver the first worldwide product that fully meets the GlobalSoilMap specifications.

Embolization of iliac artery aneurysms following abdominal aortic aneurysm repair with a bifurcated graft

Six iliac artery aneurysms in four patients were percutaneously embolized. All patients had previous abdominal aortic aneurysm repair using a bifurcation graft with distal anastomoses to external iliac arteries. The iliac aneurysms involved the oversewn common iliac arteries in all patients. Embolizations were performed via an ipsilateral common femoral arterial approach, with metal coil occlusion of aneurysm inflow and outflow. All aneurysms were successfully thrombosed. Follow-up colour flow Doppler examinations showed continued aneurysm thrombosis in all patients. One patient developed post procedure buttock claudication, which improved over time; there was no other procedure related morbidity. In conclusion, we describe a technique for percutaneous embolization of iliac aneurysms following abdominal aortic aneurysm repair with a bifurcated graft. We have demonstrated the safety and efficacy of this approach.

Independent assessment and improvement of wheat genome sequence assemblies using Fosill jumping libraries

Background

The accurate sequencing and assembly of very large, often polyploid, genomes remains a challenging task, limiting long-range sequence information and phased sequence variation for applications such as plant breeding. The 15-Gb hexaploid bread wheat (Triticum aestivum) genome has been particularly challenging to sequence, and several different approaches have recently generated long-range assemblies. Mapping and understanding the types of assembly errors are important for optimising future sequencing and assembly approaches and for comparative genomics.

Results

Here we use a Fosill 38-kb jumping library to assess medium and longer–range order of different publicly available wheat genome assemblies. Modifications to the Fosill protocol generated longer Illumina sequences and enabled comprehensive genome coverage. Analyses of two independent Bacterial Artificial Chromosome (BAC)-based chromosome-scale assemblies, two independent Illumina whole genome shotgun assemblies, and a hybrid Single Molecule Real Time (SMRT-PacBio) and short read (Illumina) assembly were carried out. We revealed a surprising scale and variety of discrepancies using Fosill mate-pair mapping and validated several of each class. In addition, Fosill mate-pairs were used to scaffold a whole genome Illumina assembly, leading to a 3-fold increase in N50 values.

Conclusions

Our analyses, using an independent means to validate different wheat genome assemblies, show that whole genome shotgun assemblies based solely on Illumina sequences are significantly more accurate by all measures compared to BAC-based chromosome-scale assemblies and hybrid SMRT-Illumina approaches. Although current whole genome assemblies are reasonably accurate and useful, additional improvements will be needed to generate complete assemblies of wheat genomes using open-source, computationally efficient, and cost-effective methods.

Increased protein synthesis response to insulin in fibroblasts treated with the diacylglycerol kinase inhibitor R59022

Insulin stimulated protein synthesis in quiescent 3T3 fibroblasts. This effect of the hormone was greater in the presence of the diacylglycerol kinase inhibitor R59022 (10(-5) M) over a range of insulin concentrations from 1 microU to 1 mU/ml; R59022 increased the sensitivity of cells to insulin. The amount of radioactive diacylglycerol recovered from cells prelabelled with [3H]glycerol was increased transiently in response to insulin; the response was larger and prolonged in cells given the kinase inhibitor. The results (i) support the hypothesis that diacylglycerol production is part of the signal pathway by which insulin stimulates protein synthesis and (ii) suggest that inhibition of diacylglycerol breakdown leads to increased sensitivity to the hormone.