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1.
Nature ; 588(7837): 277-283, 2020 12.
Article in English | MEDLINE | ID: mdl-33239791

ABSTRACT

Advances in genomics have expedited the improvement of several agriculturally important crops but similar efforts in wheat (Triticum spp.) have been more challenging. This is largely owing to the size and complexity of the wheat genome1, and the lack of genome-assembly data for multiple wheat lines2,3. Here we generated ten chromosome pseudomolecule and five scaffold assemblies of hexaploid wheat to explore the genomic diversity among wheat lines from global breeding programs. Comparative analysis revealed extensive structural rearrangements, introgressions from wild relatives and differences in gene content resulting from complex breeding histories aimed at improving adaptation to diverse environments, grain yield and quality, and resistance to stresses4,5. We provide examples outlining the utility of these genomes, including a detailed multi-genome-derived nucleotide-binding leucine-rich repeat protein repertoire involved in disease resistance and the characterization of Sm16, a gene associated with insect resistance. These genome assemblies will provide a basis for functional gene discovery and breeding to deliver the next generation of modern wheat cultivars.


Subject(s)
Genetic Variation , Genome, Plant/genetics , Genomics , Internationality , Plant Breeding/methods , Triticum/genetics , Acclimatization/genetics , Animals , Centromere/genetics , Centromere/metabolism , Chromosome Mapping , Cloning, Molecular , DNA Copy Number Variations/genetics , DNA Transposable Elements/genetics , Edible Grain/genetics , Edible Grain/growth & development , Genes, Plant/genetics , Genetic Introgression , Haplotypes , Insecta/pathogenicity , NLR Proteins/genetics , Plant Diseases/genetics , Plant Proteins/genetics , Polymorphism, Single Nucleotide/genetics , Polyploidy , Triticum/classification , Triticum/growth & development
2.
Genes Dev ; 31(2): 197-208, 2017 01 15.
Article in English | MEDLINE | ID: mdl-28167503

ABSTRACT

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.


Subject(s)
Arabidopsis Proteins/metabolism , Arabidopsis/enzymology , Arabidopsis/growth & development , LIM Domain Proteins/metabolism , Ubiquitin-Protein Ligases/metabolism , Ubiquitination , Arabidopsis/genetics , Arabidopsis Proteins/genetics , Cell Proliferation , Enzyme Activation , LIM Domain Proteins/genetics , Protein Stability
3.
Int J Mol Sci ; 24(7)2023 Mar 23.
Article in English | MEDLINE | ID: mdl-37047069

ABSTRACT

Cerebrospinal fluid-based real-time quaking-induced conversion (CSF RT-QuIC) is currently the most prominent method for early detection of sporadic Creutzfeldt-Jakob disease (sCJD), the most common prion disease. CSF RT-QuIC delivers high sensitivity (>90%) and specificity (100%), which has been demonstrated by large ring-trial studies testing probable and definitive sCJD cohorts. Following the inclusion of CSF RT-QuIC in the revised European CJD Surveillance Network diagnostic criteria for sCJD, it has become a standard diagnostic procedure in many prion disease reference or surveillance centers around the world. In this study, we present the implementation of the second-generation CSF RT-QuIC (commonly known as Improved QuIC or IQ) at the Danish Reference Center for Prion Diseases (DRCPD). The method's sensitivity and specificity were evaluated and validated by analyzing 63 CSF samples. These 63 samples were also analyzed at the National CJD Research and Surveillance Unit (NCJDRSU), based at the University of Edinburgh, UK; analysis was carried out using the first generation or previous CSF RT-QuIC method (PQ). The sensitivity and specificity of PQ during tests at the NCJDRSU were 92% and 100%, respectively. Using these 63 CSF samples, the agreement between the two RT-QuIC generations at DRCPD and NCJDRSU prion laboratories was 100%.


Subject(s)
Creutzfeldt-Jakob Syndrome , Prion Diseases , Prions , Humans , Creutzfeldt-Jakob Syndrome/diagnosis , Prion Diseases/diagnosis , Sensitivity and Specificity , Denmark
4.
Plant Cell ; 31(10): 2370-2385, 2019 10.
Article in English | MEDLINE | ID: mdl-31439805

ABSTRACT

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.


Subject(s)
Brassica napus/metabolism , Crops, Agricultural/metabolism , Plant Proteins/metabolism , Seeds/metabolism , Transcription Factors/metabolism , Ubiquitin-Protein Ligases/metabolism , Arabidopsis Proteins/genetics , Arabidopsis Proteins/metabolism , Brassica napus/enzymology , Brassica napus/genetics , Crops, Agricultural/chemistry , Crops, Agricultural/growth & development , Gene Expression Regulation, Plant/genetics , Homeodomain Proteins/metabolism , Ligases/genetics , Ligases/metabolism , Lipid Metabolism/genetics , Lipid Metabolism/physiology , Mutation , Phenotype , Plant Mucilage/biosynthesis , Polymorphism, Single Nucleotide , Promoter Regions, Genetic , Proteasome Endopeptidase Complex/genetics , Proteasome Endopeptidase Complex/metabolism , Rapeseed Oil/metabolism , Seeds/chemistry , Seeds/genetics , Seeds/growth & development , Transcription Factors/genetics , Transcriptome/genetics , Ubiquitin-Protein Ligases/genetics
5.
Eur J Neurol ; 29(8): 2431-2438, 2022 08.
Article in English | MEDLINE | ID: mdl-35524506

ABSTRACT

BACKGROUND AND PURPOSE: Cerebrospinal fluid (CSF) real-time quaking-induced conversion (RT-QuIC) has a high degree of sensitivity and specificity for the diagnosis of sporadic Creutzfeldt-Jakob disease (sCJD) and this has led to its being included in revised European CJD Surveillance Network diagnostic criteria for sCJD. As CSF RT-QuIC becomes more widely established, it is crucial that the analytical performance of individual laboratories is consistent. The aim of this ring-trial was to ascertain the degree of concordance between European countries undertaking CSF RT-QuIC. METHODS: Ten identical CSF samples, seven from probable or neuropathologically confirmed sCJD and three from non-CJD cases, were sent to 13 laboratories from 11 countries for RT-QuIC analysis. A range of instrumentation and different recombinant prion protein substrates were used. Each laboratory analysed the CSF samples blinded to the diagnosis and reported the results as positive or negative. RESULTS: All 13 laboratories correctly identified five of the seven sCJD cases and the remaining two sCJD cases were identified by 92% of laboratories. Of the two sCJD cases that were not identified by all laboratories, one had a disease duration >26 months with a negative 14-3-3, whilst the remaining case had a 4-month disease duration and a positive 14-3-3. A single false positive CSF RT-QuIC result was observed in this study. CONCLUSIONS: This study shows that CSF RT-QuIC demonstrates an excellent concordance between centres, even when using a variety of instrumentation, recombinant prion protein substrates and CSF volumes. The adoption of CSF RT-QuIC by all CJD surveillance centres is recommended.


Subject(s)
Creutzfeldt-Jakob Syndrome , Prions , Creutzfeldt-Jakob Syndrome/cerebrospinal fluid , Creutzfeldt-Jakob Syndrome/diagnosis , Humans , Prion Proteins , Prions/cerebrospinal fluid , Recombinant Proteins , Sensitivity and Specificity
6.
Genome Res ; 27(5): 885-896, 2017 05.
Article in English | MEDLINE | ID: mdl-28420692

ABSTRACT

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.


Subject(s)
Contig Mapping/methods , Genome, Plant , Molecular Sequence Annotation/methods , Plant Proteins/genetics , Translocation, Genetic , Triticum/genetics , Algorithms , Contig Mapping/standards , Molecular Sequence Annotation/standards , Polymorphism, Genetic , Polyploidy
7.
BMC Plant Biol ; 20(1): 482, 2020 Oct 22.
Article in English | MEDLINE | ID: mdl-33092536

ABSTRACT

BACKGROUND: The same species of plant can exhibit very diverse sizes and shapes of organs that are genetically determined. Characterising genetic variation underlying this morphological diversity is an important objective in evolutionary studies and it also helps identify the functions of genes influencing plant growth and development. Extensive screens of mutagenised Arabidopsis populations have identified multiple genes and mechanisms affecting organ size and shape, but relatively few studies have exploited the rich diversity of natural populations to identify genes involved in growth control. RESULTS: We screened a relatively well characterised collection of Arabidopsis thaliana accessions for variation in petal size. Association analyses identified sequence and gene expression variation on chromosome 4 that made a substantial contribution to differences in petal area. Variation in the expression of a previously uncharacterised gene At4g16850 (named as KSK) had a substantial role on variation in organ size by influencing cell size. Over-expression of KSK led to larger petals with larger cells and promoted the formation of stamenoid features. The expression of auxin-responsive genes known to limit cell growth was reduced in response to KSK over-expression. ANT expression was also reduced in KSK over-expression lines, consistent with altered floral identities. Auxin responses were reduced in KSK over-expressing cells, consistent with changes in auxin-responsive gene expression. KSK may therefore influence auxin responses during petal development. CONCLUSIONS: Understanding how genetic variation influences plant growth is important for both evolutionary and mechanistic studies. We used natural populations of Arabidopsis thaliana to identify sequence variation in a promoter region of Arabidopsis accessions that mediated differences in the expression of a previously uncharacterised membrane protein. This variation contributed to altered auxin responses and cell size during petal growth.


Subject(s)
Arabidopsis Proteins/metabolism , Arabidopsis/growth & development , Flowers/growth & development , Indoleacetic Acids/metabolism , Membrane Proteins/metabolism , Plant Growth Regulators/metabolism , Arabidopsis/metabolism , Flowers/metabolism , Gene Expression Regulation, Plant , Genes, Plant/genetics
8.
Nature ; 491(7426): 705-10, 2012 Nov 29.
Article in English | MEDLINE | ID: mdl-23192148

ABSTRACT

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.


Subject(s)
Bread , Genome, Plant/genetics , Triticum/genetics , Brachypodium/genetics , Chromosomes, Plant/genetics , Crops, Agricultural/genetics , DNA, Complementary/genetics , DNA, Plant/genetics , Evolution, Molecular , Genes, Plant/genetics , Genomics , Multigene Family/genetics , Oryza/genetics , Polymorphism, Single Nucleotide/genetics , Polyploidy , Pseudogenes/genetics , Sequence Alignment , Sequence Analysis, DNA , Triticum/classification , Zea mays/genetics
9.
J Cardiothorac Vasc Anesth ; 31(4): 1174-1182, 2017 Aug.
Article in English | MEDLINE | ID: mdl-28159523

ABSTRACT

OBJECTIVE: Peripheral nerve injury (PNI) is a common and potentially devastating complication in cardiac surgery. Somatosensory evoked potential (SSEP) monitoring is one of the modalities for PNI; however, its application is limited by complicated logistics. This study aimed to assess the feasibility of using a novel, automated SSEP device (EPAD; SafeOp Surgical, Hunt Valley, MD) for detection of intraoperative PNI during cardiac surgery. DESIGN: Prospective, observational study. SETTING: Single university hospital. PARTICIPANTS: Cardiac surgical patients. INTERVENTIONS: After Ethics Board approval and written consent, study participants were monitored using the EPAD automated SSEP device during cardiac surgery. All patients with prolonged and abnormal SSEP changes were evaluated postoperatively, and if they were symptomatic, they were referred for further nerve conduction and electromyographic assessment. MEASUREMENTS AND MAIN RESULTS: Of the 43 patients who consented to study inclusion, 33 were monitored successfully. With increasing clinical experience the authors encountered minimal technical issues, and satisfactory signals were obtained in most patients. Abnormal SSEP signal changes, which were encountered in 5 (15.2%) patients, were interpreted as impending PNI; 3 patients experienced prolonged signal changes (>1 h), and 2 (6.1%) of these developed symptomatic peripheral neuropathy that was confirmed with nerve conduction studies. CONCLUSIONS: The EPAD automated SSEP device is a viable option for detecting PNI during cardiac surgery. A high incidence of intraoperative peripheral nerve compromise and a 6.1% incidence of postoperative peripheral neuropathy were observed. This study reports the clinical feasibility of using the EPAD automated SSEP device; additional studies are required to evaluate the diagnostic test accuracy and the outcome benefit of routine SSEP monitoring in cardiac surgical patients.


Subject(s)
Cardiac Surgical Procedures/adverse effects , Evoked Potentials, Somatosensory/physiology , Intraoperative Neurophysiological Monitoring/methods , Peripheral Nerve Injuries/diagnosis , Peripheral Nerve Injuries/physiopathology , Aged , Feasibility Studies , Female , Humans , Intraoperative Neurophysiological Monitoring/instrumentation , Male , Middle Aged , Peripheral Nerve Injuries/etiology , Prospective Studies
10.
BMC Plant Biol ; 15: 215, 2015 Sep 05.
Article in English | MEDLINE | ID: mdl-26341899

ABSTRACT

BACKGROUND: Plant cell walls are dynamic structures involved in all aspects of plant growth, environmental interactions and defense responses, and are the most abundant renewable source of carbon-containing polymers on the planet. To balance rigidity and extensibility, the composition and integrity of cell wall components need to be tightly regulated, for example during cell elongation. RESULTS: We show that mutations in the MED25/PFT1 and MED8 subunits of the Mediator transcription complex suppressed the sugar-hypersensitive hypocotyl elongation phenotype of the hsr8-1 mutant, which has cell wall defects due to arabinose deficiency that do not permit normal cell elongation. This suppression occurred independently of light and jasmonic acid (JA) signaling. Gene expression analyses revealed that the expression of genes induced in hsr8-1 that encode enzymes and proteins that are involved in cell expansion and cell wall strengthening is reduced in the pft1-2 mutant line, and the expression of genes encoding transcription factors involved in reducing hypocotyl cell elongation, genes encoding cell wall associated enzymes and proteins is up-regulated in pft1-2. PFT1 was also required for the expression of several glucose-induced genes, including those encoding cell wall components and enzymes, regulatory and enzymatic components of anthocyanin biosynthesis, and flavonoid and glucosinolate biosynthetic pathways. CONCLUSIONS: These results establish that MED25 and MED8 subunits of the Mediator transcriptional complex are required for the transcriptional regulation of genes involved in cell elongation and cell wall composition in response to defective cell walls and in sugar- responsive gene expression.


Subject(s)
Arabidopsis Proteins/genetics , Arabidopsis/genetics , Arabinose/metabolism , Gene Expression Regulation, Plant , Glucose/metabolism , Mediator Complex/genetics , Nuclear Proteins/genetics , Arabidopsis/metabolism , Arabidopsis Proteins/metabolism , Cell Wall/enzymology , Cell Wall/metabolism , DNA-Binding Proteins , Hypocotyl/genetics , Mediator Complex/metabolism , Nuclear Proteins/metabolism
11.
Cell Host Microbe ; 31(6): 949-961.e5, 2023 06 14.
Article in English | MEDLINE | ID: mdl-37167970

ABSTRACT

White blister rust, caused by the oomycete Albugo candida, is a widespread disease of Brassica crops. The Brassica relative Arabidopsis thaliana uses the paired immune receptor complex CSA1-CHS3/DAR4 to resist Albugo infection. The CHS3/DAR4 sensor NLR, which functions together with its partner, the helper NLR CSA1, carries an integrated domain (ID) with homology to DA1 peptidases. Using domain swaps with several DA1 homologs, we show that the LIM-peptidase domain of the family member CHS3/DAR4 functions as an integrated decoy for the family member DAR3, which interacts with and inhibits the peptidase activities of the three closely related peptidases DA1, DAR1, and DAR2. Albugo infection rapidly lowers DAR3 levels and activates DA1 peptidase activity, thereby promoting endoreduplication of host tissues to support pathogen growth. We propose that the paired immune receptor CSA1-CHS3/DAR4 detects the actions of a putative Albugo effector that reduces DAR3 levels, resulting in defense activation.


Subject(s)
Arabidopsis Proteins , Arabidopsis , Arabidopsis Proteins/metabolism , Peptide Hydrolases , Protein Domains , Crops, Agricultural , Plant Diseases
12.
Plant Biotechnol J ; 9(9): 1086-99, 2011 Dec.
Article in English | MEDLINE | ID: mdl-21627760

ABSTRACT

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.


Subject(s)
Genetic Linkage , Polymorphism, Single Nucleotide , Polyploidy , Triticum/genetics , Alleles , Biomarkers/analysis , Chromosome Mapping , Databases, Genetic , Expressed Sequence Tags , Gene Library , Genotype , Polymerase Chain Reaction/methods , Sequence Alignment
13.
Genome ; 53(1): 1-13, 2010 Jan.
Article in English | MEDLINE | ID: mdl-20130744

ABSTRACT

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.


Subject(s)
Chromosome Mapping/methods , Microsatellite Repeats/genetics , Models, Theoretical , Poaceae/genetics , Base Sequence , Chromosomes, Plant , Cluster Analysis , Genes, Plant , Models, Biological , Sequence Alignment , Sequence Analysis, DNA
14.
CMAJ ; 187(3): 208, 2015 Feb 17.
Article in English | MEDLINE | ID: mdl-25691798
15.
Gigascience ; 9(6)2020 06 01.
Article in English | MEDLINE | ID: mdl-32562491

ABSTRACT

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.


Subject(s)
Aegilops/genetics , Chromatin Assembly and Disassembly , Chromatin/genetics , Chromosomes, Plant , Gene Expression Regulation, Plant , Ploidies , Triticum/genetics , Chromatin/metabolism , Computational Biology/methods , DNA Methylation , Evolution, Molecular , Genome, Plant , Genomics/methods , Pseudogenes
16.
Ann Clin Transl Neurol ; 7(11): 2262-2271, 2020 11.
Article in English | MEDLINE | ID: mdl-33185334

ABSTRACT

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.


Subject(s)
Biological Assay/standards , Creutzfeldt-Jakob Syndrome/cerebrospinal fluid , Creutzfeldt-Jakob Syndrome/diagnosis , Diagnostic Techniques, Neurological/standards , Olfactory Mucosa/metabolism , Prions/cerebrospinal fluid , Adult , Aged , Aged, 80 and over , Female , Humans , Male , Middle Aged , Reproducibility of Results
17.
Can J Surg ; 52(2): 125-8, 2009 Apr.
Article in English | MEDLINE | ID: mdl-19399207

ABSTRACT

BACKGROUND: Gastrointestinal (GI) complications following coronary artery bypass grafting (CABG), although infrequent, are associated with significant morbidity and mortality. It has been suggested that systemic inflammatory response plays an important role in these complications. Cardiopulmonary bypass (CPB) is well known to cause increased systemic inflammation, and therefore it has been proposed that performing CABG using an off-pump technique could substantially minimize the risk of GI complications. Prolonged CPB duration has been shown to be an independent predictor of GI complications; however, the effect of avoiding CPB altogether through off-pump procedures has not been thoroughly examined. We sought to compare the incidence of GI complications in patients undergoing on-pump and off-pump CABG. METHODS: We analyzed prospectively entered data on 2451 patients who underwent isolated CABG between January 2000 and October 2004. We compared GI complication rates in 5 predetermined areas (GI bleed, ileus, pancreatitis, ischemic bowel and cholecystitis) among patients who had on-pump CABG with those of patients who had off-pump CABG. We also compared in-hospital mortality due to these complications between the 2 groups. RESULTS: We compared data for a total of 2010 patients in the on-pump group and 441 in the off-pump group. In the on-pump group, 30 (1.49%) patients experienced GI complications compared with 4 (0.91%) in the off-pump group (p = 0.34). Gastrointestinal bleed was the most common complication in the off-pump group. Eight patients in the on-pump group experienced ischemic bowels compared with no patients in the off-pump group. Six patients (0.3%) in the on-pump group died from GI complications, whereas no patients in the off-pump group died from such complications (p = 0.25). CONCLUSION: We found no significant difference in the total number of GI complications between the off-pump and on-pump groups; however, trends could be seen in the types of GI complications that occurred in the 2 groups. Owing to the relatively infrequent occurrence of GI complications, a larger scale study would be beneficial to determine whether the differences observed would be significant.


Subject(s)
Cardiopulmonary Bypass/adverse effects , Coronary Artery Bypass, Off-Pump/adverse effects , Coronary Artery Bypass/adverse effects , Female , Gastrointestinal Hemorrhage/epidemiology , Gastrointestinal Hemorrhage/etiology , Humans , Ileus/epidemiology , Ileus/etiology , Intestines/blood supply , Ischemia/epidemiology , Ischemia/etiology , Male , Prospective Studies
18.
Plant Biotechnol J ; 6(3): 236-45, 2008 Apr.
Article in English | MEDLINE | ID: mdl-18004984

ABSTRACT

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.


Subject(s)
DNA, Bacterial/genetics , Mutagenesis, Insertional/methods , Poaceae/genetics , Rhizobium/genetics , Transformation, Genetic/genetics , Cell Cycle Proteins , Gene Expression Regulation, Plant , Genotype , Poaceae/classification , Poaceae/microbiology , Polymorphism, Genetic , Rhizobium/physiology , Terminal Repeat Sequences/genetics
19.
Gigascience ; 7(5)2018 05 01.
Article in English | MEDLINE | ID: mdl-29762659

ABSTRACT

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.


Subject(s)
Gene Library , Genome, Plant , Sequence Analysis, DNA/methods , Triticum/genetics , Chromosomes, Artificial, Bacterial/genetics , Chromosomes, Plant/genetics , Contig Mapping
20.
J Neuropathol Exp Neurol ; 77(8): 673-684, 2018 08 01.
Article in English | MEDLINE | ID: mdl-29889261

ABSTRACT

This is the first report of presumed sporadic Creutzfeldt-Jakob disease (sCJD) and Gerstmann-Sträussler-Scheinker disease (GSS) with the prion protein gene c.305C>T mutation (p.P102L) occurring in one family. The father and son were affected with GSS and the mother had a rapidly progressive form of CJD. Diagnosis of genetic, variant, and iatrogenic CJD was ruled out based on the mother's clinical history, genetic tests, and biochemical investigations, all of which supported the diagnosis of sCJD. However, given the low incidence of sCJD and GSS, their co-occurrence in one family is extraordinary and challenging. Thus, a hypothesis for the transmission of infectious prion proteins (PrPSc) via microchimerism was proposed and investigated. DNA from 15 different brain regions and plasma samples of the CJD patient was subjected to PCR and shallow sequencing for detection of a male sex-determining chromosome Y (chr. Y). However, no trace of chr. Y was found. A long CJD incubation period or presumed small concentrations of chr. Y may explain the obtained results. Further studies of CJD and GSS animal models with controlled genetic and proteomic features are needed to determine whether maternal CJD triggered via microchimerism by a GSS fetus might present a new PrPSc transmission route.


Subject(s)
Chimerism , Creutzfeldt-Jakob Syndrome/genetics , Creutzfeldt-Jakob Syndrome/transmission , Gerstmann-Straussler-Scheinker Disease/genetics , Gerstmann-Straussler-Scheinker Disease/transmission , Prion Proteins/genetics , Aged , Creutzfeldt-Jakob Syndrome/pathology , Female , Gerstmann-Straussler-Scheinker Disease/pathology , Humans , Male , Middle Aged , Pedigree , Spouses
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