Control of Epstein-Barr virus infection in vitro by T helper cells specific for virion glycoproteins

Epstein-Barr virus (EBV) establishes lifelong persistent infections in humans by latently infecting B cells, with occasional cycles of reactivation, virus production, and reinfection. Protective immunity against EBV is mediated by T cells, but the role of EBV-specific T helper (Th) cells is still poorly defined. Here, we study the Th response to the EBV lytic cycle proteins BLLF1 (gp350/220), BALF4 (gp110), and BZLF1 and show that glycoprotein-specific Th cells recognize EBV-positive cells directly; surprisingly, a much higher percentage of target cells than those expressing lytic cycle proteins were recognized. Antigen is efficiently transferred to bystander B cells by receptor-mediated uptake of released virions, resulting in recognition of target cells incubated with <1 virion/cell. T cell recognition does not require productive infection and occurs early after virus entry before latency is established. Glycoprotein-specific Th cells are cytolytic and inhibit proliferation of lymphoblastoid cell lines (LCL) and the outgrowth of LCL after infection of primary B cells with EBV. These results establish a novel role for glycoprotein-specific Th cells in the control of EBV infection and identify virion proteins as important immune targets. These findings have implications for the treatment of diseases associated with EBV and potentially other coated viruses infecting MHC class II–positive cells.

Immunodominance of lytic cycle antigens in Epstein-Barr virus-specific CD4+ T cell preparations for therapy

BACKGROUND

Epstein-Barr virus (EBV) is associated with a number of human malignancies. EBV-positive post-transplant lymphoproliferative disease in solid organ and hematopoietic stem cell transplant recipients has been successfully treated by the adoptive transfer of polyclonal EBV-specific T cell lines containing CD4+ and CD8+ T cell components. Although patients receiving T cell preparations with a higher CD4+ T cell proportion show better clinical responses, the specificity of the infused CD4+ component has remained completely unknown.

METHODOLOGY/PRINCIPAL FINDINGS

We generated LCL-stimulated T cell lines from 21 donors according to clinical protocols, and analyzed the antigen specificity of the CD4+ component in EBV-specific T cell preparations using a genetically engineered EBV mutant that is unable to enter the lytic cycle, and recombinantly expressed and purified EBV proteins. Surprisingly, CD4+ T cell lines from acutely and persistently EBV-infected donors consistently responded against EBV lytic cycle antigens and autoantigens, but barely against latent cycle antigens of EBV hitherto considered principal immunotherapeutic targets. Lytic cycle antigens were predominantly derived from structural proteins of the virus presented on MHC II via receptor-mediated uptake of released viral particles, but also included abundant infected cell proteins whose presentation involved intercellular protein transfer. Importantly, presentation of virion antigens was severely impaired by acyclovir treatment of stimulator cells, as currently performed in most clinical protocols.

CONCLUSIONS/SIGNIFICANCE

These results indicate that structural antigens of EBV are the immunodominant targets of CD4+ T cells in LCL-stimulated T cell preparations. These findings add to our understanding of the immune response against this human tumor-virus and have important implications for the improvement of immunotherapeutic strategies against EBV.

The Amaranth Genome: Genome, Transcriptome, and Physical Map Assembly

Amaranth ( L.) is an emerging pseudocereal native to the New World that has garnered increased attention in recent years because of its nutritional quality, in particular its seed protein and more specifically its high levels of the essential amino acid lysine. It belongs to the Amaranthaceae family, is an ancient paleopolyploid that shows disomic inheritance (2 = 32), and has an estimated genome size of 466 Mb. Here we present a high-quality draft genome sequence of the grain amaranth. The genome assembly consisted of 377 Mb in 3518 scaffolds with an N of 371 kb. Repetitive element analysis predicted that 48% of the genome is comprised of repeat sequences, of which -like elements were the most commonly classified retrotransposon. A de novo transcriptome consisting of 66,370 contigs was assembled from eight different amaranth tissue and abiotic stress libraries. Annotation of the genome identified 23,059 protein-coding genes. Seven grain amaranths (, , and ) and their putative progenitor () were resequenced. A single nucleotide polymorphism (SNP) phylogeny supported the classification of as the progenitor species of the grain amaranths. Lastly, we generated a de novo physical map for using the BioNano Genomics' Genome Mapping platform. The physical map spanned 340 Mb and a hybrid assembly using the BioNano physical maps nearly doubled the N of the assembly to 697 kb. Moreover, we analyzed synteny between amaranth and sugar beet ( L.) and estimated, using analysis, the age of the most recent polyploidization event in amaranth.

Model SNP development for complex genomes based on hexaploid oat using high-throughput 454 sequencing technology

Background

Genetic markers are pivotal to modern genomics research; however, discovery and genotyping of molecular markers in oat has been hindered by the size and complexity of the genome, and by a scarcity of sequence data. The purpose of this study was to generate oat expressed sequence tag (EST) information, develop a bioinformatics pipeline for SNP discovery, and establish a method for rapid, cost-effective, and straightforward genotyping of SNP markers in complex polyploid genomes such as oat.

Results

Based on cDNA libraries of four cultivated oat genotypes, approximately 127,000 contigs were assembled from approximately one million Roche 454 sequence reads. Contigs were filtered through a novel bioinformatics pipeline to eliminate ambiguous polymorphism caused by subgenome homology, and 96 in silico SNPs were selected from 9,448 candidate loci for validation using high-resolution melting (HRM) analysis. Of these, 52 (54%) were polymorphic between parents of the Ogle1040 × TAM O-301 (OT) mapping population, with 48 segregating as single Mendelian loci, and 44 being placed on the existing OT linkage map. Ogle and TAM amplicons from 12 primers were sequenced for SNP validation, revealing complex polymorphism in seven amplicons but general sequence conservation within SNP loci. Whole-amplicon interrogation with HRM revealed insertions, deletions, and heterozygotes in secondary oat germplasm pools, generating multiple alleles at some primer targets. To validate marker utility, 36 SNP assays were used to evaluate the genetic diversity of 34 diverse oat genotypes. Dendrogram clusters corresponded generally to known genome composition and genetic ancestry.

Conclusions

The high-throughput SNP discovery pipeline presented here is a rapid and effective method for identification of polymorphic SNP alleles in the oat genome. The current-generation HRM system is a simple and highly-informative platform for SNP genotyping. These techniques provide a model for SNP discovery and genotyping in other species with complex and poorly-characterized genomes.

Epstein-Barr virus nuclear antigen 1 evades direct immune recognition by CD4+ T helper cells

The Epstein-Barr virus (EBV) nuclear antigen 1 (EBNA1) is the only viral protein regularly expressed in EBV-associated malignancies. Immune recognition of EBNA1 by CD8+ T cells is prevented by an internal glycine-alanine repeat (GAr) which blocks proteasomal degradation. To test whether EBV-infected cells could be recognized by T helper cells, human CD4+ T cell clones specific for EBNA1 were isolated from latently EBV-infected individuals. These T cells, however, failed to recognize EBV-positive target cells. To investigate whether endogenous presentation of EBNA1 epitopes on MHC class II was prevented by the GAr domain, a mutant EBV strain with an EBNA1 lacking the GAr (EBNA1DeltaGA) was generated and used to establish an Epstein-Barr virus-immortalized lymphoblastoid B cell line (LCL). The EBNA1DeltaGA LCL were not recognized by the EBNA1-specific T cell clones either, indicating that the GAr domain does not mediate this effect. Immune recognition could be restored by overexpression of EBNA1, for which at least 60-fold higher levels of both EBNA1 or EBNA1DeltaGAr protein were required. These results demonstrate that EBNA1 evades direct recognition by CD4+ T helper cells, since its steady state level is below the threshold required for efficient presentation on MHC class II. These findings have important implications for the design of immunotherapeutic approaches to target EBV-positive malignancies.

Hepatitis E virus seroprevalence in three hyperendemic areas: Nepal, Bangladesh and southwest France

BACKGROUND

Hepatitis E causes a significant burden of disease in developing countries and has recently been increasingly recognized in developed countries. Comparing population anti-hepatitis E virus (HEV) seroprevalence across populations has been difficult.

OBJECTIVES

The aim of this study was to compare the anti-HEV IgG seroprevalence in both adults and children in three hyper-endemic areas (Nepal, Bangladesh and southwest France) using a sensitive, commercial anti-HEV IgG assay.

STUDY DESIGN

Serum or plasma from adults and children in Nepal (n=498), Bangladesh (n=1,009) and Southwest France (n=1031) were tested for anti-HEV IgG using the Wantai assay.

RESULTS

After age-standardization, anti-HEV IgG seroprevalence was 47.1%, 49.8% and 34.0% in Nepal, Bangladesh and southwest France, respectively. There was no difference in seroprevalence by gender in any of the countries. A paucity of infections in children 1-10 years-old was consistently observed (less than 15%) at all 3 locations.

CONCLUSIONS

Surprisingly similar high rates of anti-HEV antibodies were detected using a common, sensitive assay. Despite differences in the epidemiology and circulating genotype of HEV in Nepal, Bangladesh and southwest France, this study found more similarities in population seroprevalence than expected.

Medical Cannabis and Industrial Hemp Tissue Culture: Present Status and Future Potential

In recent years high-THC (psychoactive) and low-THC (industrial hemp) type cannabis (Cannabis sativa L.) have gained immense attention in medical, food, and a plethora of other consumer product markets. Among the planting materials used for cultivation, tissue culture clones provide various advantages such as economies of scale, production of disease-free and true-to-type plants for reducing the risk of GMP-EuGMP level medical cannabis production, as well as the development and application of various technologies for genetic improvement. Various tissue culture methods have the potential application with cannabis for research, breeding, and novel trait development, as well as commercial mass propagation. Although tissue culture techniques for plant regeneration and micropropagation have been reported for different cannabis genotypes and explant sources, there are significant variations in the response of cultures and the morphogenic pathway. Methods for many high-yielding elite strains are still rudimentary, and protocols are not established. With a recent focus on sequencing and genomics in cannabis, genetic transformation systems are applied to medical cannabis and hemp for functional gene annotation via traditional and transient transformation methods to create novel phenotypes by gene expression modulation and to validate gene function. This review presents the current status of research focusing on different aspects of tissue culture, including micropropagation, transformation, and the regeneration of medicinal cannabis and industrial hemp transformants. Potential future tissue culture research strategies helping elite cannabis breeding and propagation are also presented.

Standardized and highly efficient expansion of Epstein-Barr virus-specific CD4+ T cells by using virus-like particles

Epstein-Barr virus (EBV)-specific T-cell lines generated by repeated stimulation with EBV-immortalized lymphoblastoid B-cell lines (LCL) have been successfully used to treat EBV-associated posttransplant lymphoproliferative disease (PTLD) in hematopoietic stem cell transplant recipients. However, PTLD in solid-organ transplant recipients and other EBV-associated malignancies respond less efficiently to this adoptive T-cell therapy. LCL-stimulated T-cell preparations are polyclonal and contain CD4(+) and CD8(+) T cells, but the composition varies greatly between lines. Because T-cell lines with higher CD4(+) T-cell proportions show improved clinical efficacy, we assessed which factors might compromise the expansion of this T-cell population. Here we show that spontaneous virus production by LCL and, hence, the presentation of viral antigens varies intra- and interindividually and is further impaired by acyclovir treatment of LCL. Moreover, the stimulation of T cells with LCL grown in medium supplemented with fetal calf serum (FCS) caused the expansion of FCS-reactive CD4(+) T cells, whereas human serum from EBV-seropositive donors diminished viral antigen presentation. To overcome these limitations, we used peripheral blood mononuclear cells pulsed with nontransforming virus-like particles as antigen-presenting cells. This strategy facilitated the specific and rapid expansion of EBV-specific CD4(+) T cells and, thus, might contribute to the development of standardized protocols for the generation of T-cell lines with improved clinical efficacy.

Virus and autoantigen-specific CD4+ T cells are key effectors in a SCID mouse model of EBV-associated post-transplant lymphoproliferative disorders

Polyclonal Epstein-Barr virus (EBV)-infected B cell line (lymphoblastoid cell lines; LCL)-stimulated T-cell preparations have been successfully used to treat EBV-positive post-transplant lymphoproliferative disorders (PTLD) in transplant recipients, but function and specificity of the CD4+ component are still poorly defined. Here, we assessed the tumor-protective potential of different CD4+ T-cell specificities in a PTLD-SCID mouse model. Injection of different virus-specific CD4+ T-cell clones showed that single specificities were capable of prolonging mouse survival and that the degree of tumor protection directly correlated with recognition of target cells in vitro. Surprisingly, some CD4+ T-cell clones promoted tumor development, suggesting that besides antigen recognition, still elusive functional differences exist among virus-specific T cells. Of several EBV-specific CD4+ T-cell clones tested, those directed against virion antigens proved most tumor-protective. However, enriching these specificities in LCL-stimulated preparations conferred no additional survival benefit. Instead, CD4+ T cells specific for unknown, probably self-antigens were identified as principal antitumoral effectors in LCL-stimulated T-cell lines. These results indicate that virion and still unidentified cellular antigens are crucial targets of the CD4+ T-cell response in this preclinical PTLD-model and that enriching the corresponding T-cell specificities in therapeutic preparations may enhance their clinical efficacy. Moreover, the expression in several EBV-negative B-cell lymphoma cell lines implies that these putative autoantigen(s) might also qualify as targets for T-cell-based immunotherapy of virus-negative B cell malignancies.

Chenopodium polyploidy inferences from Salt Overly Sensitive 1 (SOS1) data

PREMISE OF THE STUDY

Single-copy nuclear loci can provide powerful insights into polyploid evolution. Chenopodium (Amaranthaceae) is a globally distributed genus composed of approximately 50-75 species. The genus includes several polyploid species, some of which are considered noxious agricultural weeds, and a few are domesticated crops. Very little research has addressed their evolutionary origin to date. We construct a phylogeny for Chenopodium based on two introns of the single-copy nuclear locus Salt Overly Sensitive 1 (SOS1) to clarify the relationships among the genomes of the allotetraploid and allohexaploid species, and to help identify their genome donors.

METHODS

Diploid species were sequenced directly, whereas homeologous sequences of polyploid genomes were first separated by plasmid-mediated cloning. Data were evaluated in maximum likelihood and Bayesian phylogenetic analyses.

KEY RESULTS

Homeologous sequences of polyploid species were found in four clades, which we designate as A-D. Two distinct polyploid lineages were identified: one composed of American tetraploid species with A and B class homeologs and a second composed of Eastern Hemisphere hexaploid species with B, C, and D class homeologs.

CONCLUSIONS

We infer that the two polyploid lineages arose independently and that each lineage may have originated only once. The American diploid, C. standleyanum, was identified as the closest living diploid relative of the A genome donor for American tetraploids, including domesticated C. quinoa, and is of potential importance for quinoa breeding. The east Asian diploid species, C. bryoniifolium, groups with American diploid species, which suggests a transoceanic dispersal.

Identification of major histocompatibility complex class II-restricted antigens and epitopes of the Epstein-Barr virus by a novel bacterial expression cloning approach

Epstein-Barr virus (EBV)-specific T cells have been successfully used to treat or prevent EBV-positive lymphoproliferative disease in hematopoietic stem cell transplant recipients, but the antigens recognized by the infused CD4+ T cells have remained unknown. Here, we describe a simple procedure that permits the identification of viral T-helper (TH)-cell antigens and epitopes. This direct antigen identification method is based on the random expression of viral polypeptides fused to chloramphenicol acetyltransferase (CAT) in bacteria, which are subsequently fed to major histocompatibility complex class II+ antigen-presenting cells and probed with antigen-specific T cells. The fusion of antigenic fragments to CAT offers several advantages. First, chloramphenicol treatment allows the selection of bacteria expressing antigen-CAT fusion proteins in frame, which greatly reduces the number of colonies to be screened. Second, antigenic fragments fused to CAT are expressed at high levels, even when derived from proteins that are toxic to bacteria. Third, the uniformly high expression level of antigen-CAT fusion proteins permits the establishment of large and representative pool sizes. Finally, antigen identification does not require knowledge of the restriction element and often leads directly to the identification of the T-cell epitope. Using this approach, the BALF4 and BNRF1 proteins were identified as targets of the EBV-specific T-helper-cell response, demonstrating that lytic cycle antigens are a relevant component of the EBV-specific TH-cell response.

A single nucleotide polymorphism assay sheds light on the extent and distribution of genetic diversity, population structure and functional basis of key traits in cultivated north American cannabis

BACKGROUND

The taxonomic classification of Cannabis genus has been delineated through three main types: sativa (tall and less branched plant with long and narrow leaves), indica (short and highly branched plant with broader leaves) and ruderalis (heirloom type with short stature, less branching and small thick leaves). While still under discussion, particularly whether the genus is polytypic or monotypic, this broad classification reflects putative geographical origins of each group and putative chemotype and pharmacologic effect.

METHODS

Here we describe a thorough investigation of cannabis accessions using a set of 23 highly informative and polymorphic SNP (Single Nucleotide Polymorphism) markers associated with important traits such as cannabinoid and terpenoid expression as well as fibre and resin production. The assay offers insight into cannabis population structure, phylogenetic relationship, population genetics and correlation to secondary metabolite concentrations. We demonstrate the utility of the assay for rapid, repeatable and cost-efficient genotyping of commercial and industrial cannabis accessions for use in product traceability, breeding programs, regulatory compliance and consumer education.

RESULTS

We identified 5 clusters in the sample set, including industrial hemp (K5) and resin hemp, which likely underwent a bottleneck to stabilize cannabidiolic acid (CBDA) accumulation (K2, Type II & III). Tetrahydrocannabinolic acid (THCA) resin (Type I) makes up the other three clusters with terpinolene (K4 - colloquial "sativa" or "Narrow Leaflet Drug" (NLD), myrcene/pinene (K1) and myrcene/limonene/linalool (K3 - colloquial "indica", "Broad Leaflet Drug" (BLD), which also putatively harbour an active version of the cannabichrometic acid Synthase gene (CBCAS).

CONCLUSION

The final chemical compositions of cannabis products have key traits related to their genetic identities. Our analyses in the context of the NCBI Cannabis sativa Annotation Release 100 allows for hypothesis testing with regards to secondary metabolite production. Genetic markers related to secondary metabolite production will be important in many sectors of the cannabis marketplace. For example, markers related to THC production will be important for adaptable and compliant large-scale seed production under the new US Domestic Hemp Production Program.

Epstein-Barr virus strain heterogeneity impairs human T-cell immunity

The Epstein-Barr virus (EBV) establishes lifelong infections in > 90% of the human population. Although contained as asymptomatic infection by the immune system in most individuals, EBV is associated with the pathogenesis of approximately 1.5% of all cancers in humans. Some of these EBV-associated tumors have been successfully treated by the infusion of virus-specific T-cell lines. Recent sequence analyses of a large number of viral isolates suggested that distinct EBV strains have evolved in different parts of the world. Here, we assessed the impact of such sequence variations on EBV-specific T-cell immunity. With the exceptions of EBNA2 and the EBNA3 family of proteins, an overall low protein sequence disparity of about 1% was noted between Asian viral isolates, including the newly characterized M81 strain, and the prototypic EBV type 1 and type 2 strains. However, when T-cell epitopes including their flanking regions were compared, a substantial proportion was found to be polymorphic in different EBV strains. Importantly, CD4+ and CD8+ T-cell clones specific for viral epitopes from one strain often showed diminished recognition of the corresponding epitopes in other strains. In addition, T-cell recognition of a conserved epitope was affected by amino acid exchanges within the epitope flanking region. Moreover, the CD8+ T-cell response against polymorphic epitopes varied between donors and often ignored antigen variants. These results demonstrate that viral strain heterogeneity may impair antiviral T-cell immunity and suggest that immunotherapeutic approaches against EBV should preferably target broad sets of conserved epitopes including their flanking regions.

A virus-induced gene-silencing system for functional genetics in a betalainic species, Amaranthus tricolor (Amaranthaceae)

PREMISE OF THE STUDY

Research in Amaranthaceae could be accelerated by developing methods for targeted gene silencing. Most amaranths, including Amaranthus tricolor, produce betalains. However, the physiological and ecological roles of these pigments are uncertain. We sought to establish a virus-induced gene-silencing (VIGS) method for amaranths, using silencing of betalain pigments as a proof-of-principle.

METHODS

We targeted AtriCYP76AD1, a putative cytochrome P450 component of the betalain biosynthetic pathway, using VIGS, and compared two different methods of introducing the VIGS construct into plants. We measured transcript abundance and concentrations of betalains and their l-DOPA precursor in VIGS-treated plants, and compared these to controls.

RESULTS

We observed that when AtriCYP76AD1 was targeted by VIGS in normally red plants, AtriCYP76AD1 and the related genes AtriCYP76AD6 and AtriCYP76AD5 had diminished transcript abundance. Furthermore, newly emergent petioles and leaves of VIGS-treated plants appeared green, betacyanin accumulation was strongly reduced, and l-DOPA accumulation was increased. No betaxanthin could be detected in this variety of A. tricolor, either before or after VIGS treatment.

DISCUSSION

These results help to establish the genetic basis of betalain synthesis in amaranths. Furthermore, this is the first report of VIGS in amaranths and demonstrates the potential of this technique for basic and applied research in these species.

A Proteome-Level Investigation Into Plasmodiophora brassicae Resistance in Brassica napus Canola

Clubroot of Brassicaceae, an economically important soil borne disease, is caused by Plasmodiophora brassicae Woronin, an obligate, biotrophic protist. This disease poses a serious threat to canola and related crops in Canada and around the globe causing significant losses. The pathogen is continuously evolving and new pathotypes are emerging, which necessitates the development of novel resistant canola cultivars to manage the disease. Proteins play a crucial role in many biological functions and the identification of differentially abundant proteins (DAP) using proteomics is a suitable approach to understand plant-pathogen interactions to assist in the development of gene specific markers for developing clubroot resistant (CR) cultivars. In this study, P. brassicae pathotype 3 (P3H) was used to challenge CR and clubroot susceptible (CS) canola lines. Root samples were collected at three distinct stages of pathogenesis, 7-, 14-, and 21-days post inoculation (DPI), protein samples were isolated, digested with trypsin and subjected to liquid chromatography with tandem mass spectrometry (LC-MS/MS) analysis. A total of 937 proteins demonstrated a significant (q-value < 0.05) change in abundance in at least in one of the time points when compared between control and inoculated CR-parent, CR-progeny, CS-parent, CS-progeny and 784 proteins were significantly (q < 0.05) changed in abundance in at least in one of the time points when compared between the inoculated- CR and CS root proteomes of parent and progeny across the three time points tested. Functional annotation of differentially abundant proteins (DAPs) revealed several proteins related to calcium dependent signaling pathways. In addition, proteins related to reactive oxygen species (ROS) biochemistry, dehydrins, lignin, thaumatin, and phytohormones were identified. Among the DAPs, 73 putative proteins orthologous to CR proteins and quantitative trait loci (QTL) associated with eight CR loci in different chromosomes including chromosomes A3 and A8 were identified. Proteins including BnaA02T0335400WE, BnaA03T0374600WE, BnaA03T0262200WE, and BnaA03T0464700WE are orthologous to identified CR loci with possible roles in mediating clubroot responses. In conclusion, these results have contributed to an improved understanding of the mechanisms involved in mediating response to P. brassicae in canola at the protein level.

Early-stage responses to Plasmodiophora brassicae at the transcriptome and metabolome levels in clubroot resistant and susceptible oilseed Brassica napus

Clubroot, a devastating soil-borne root disease, in Brassicaceae is caused by Plasmodiophora brassicae Woronin (P. brassicae W.), an obligate biotrophic protist. Plant growth and development, as well as seed yield of Brassica crops, are severely affected due to this disease. Several reports described the molecular responses of B. napus to P. brassicae; however, information on the early stages of pathogenesis is limited. In this study, we have used transcriptomics and metabolomics to characterize P. brassicae pathogenesis at 1-, 4-, and 7-days post-inoculation (DPI) in clubroot resistant (CR) and susceptible (CS) doubled-haploid (DH) canola lines. When we compared between inoculated and uninoculated groups, a total of 214 and 324 putative genes exhibited differential expression (q-value < 0.05) at one or more time-points in the CR and CS genotypes, respectively. When the inoculated CR and inoculated CS genotypes were compared, 4765 DEGs were differentially expressed (q-value < 0.05) at one or more time-points. Several metabolites related to organic acids (e.g., citrate, pyruvate), amino acids (e.g., proline, aspartate), sugars, and mannitol, were differentially accumulated in roots in response to pathogen infection when the CR and CS genotypes were compared. Several DEGs also corresponded to differentially accumulated metabolites, including pyrroline-5-carboxylate reductase (BnaC04g11450D), citrate synthase (BnaC02g39080D), and pyruvate kinase (BnaC04g23180D) as detected by transcriptome analysis. Our results suggest important roles for these genes in mediating resistance to clubroot disease. To our knowledge, this is the first report of an integrated transcriptome and metabolome analysis aimed at characterizing the molecular basis of resistance to clubroot in canola.

A single nucleotide polymorphism assay sheds light on the extent and distribution of genetic diversity, population structure and functional basis of key traits in cultivated north American cannabis

BACKGROUND

The taxonomic classification of Cannabis genus has been delineated through three main types: sativa (tall and less branched plant with long and narrow leaves), indica (short and highly branched plant with broader leaves) and ruderalis (heirloom type with short stature, less branching and small thick leaves). While still under discussion, particularly whether the genus is polytypic or monotypic, this broad classification reflects putative geographical origins of each group and putative chemotype and pharmacologic effect.

METHODS

Here we describe a thorough investigation of cannabis accessions using a set of 23 highly informative and polymorphic SNP (Single Nucleotide Polymorphism) markers associated with important traits such as cannabinoid and terpenoid expression as well as fibre and resin production. The assay offers insight into cannabis population structure, phylogenetic relationship, population genetics and correlation to secondary metabolite concentrations. We demonstrate the utility of the assay for rapid, repeatable and cost-efficient genotyping of commercial and industrial cannabis accessions for use in product traceability, breeding programs, regulatory compliance and consumer education.

RESULTS

We identified 5 clusters in the sample set, including industrial hemp (K5) and resin hemp, which likely underwent a bottleneck to stabilize cannabidiolic acid (CBDA) accumulation (K2, Type II & III). Tetrahydrocannabinolic acid (THCA) resin (Type I) makes up the other three clusters with terpinolene (K4 - colloquial "sativa" or "Narrow Leaflet Drug" (NLD), myrcene/pinene (K1) and myrcene/limonene/linalool (K3 - colloquial "indica", "Broad Leaflet Drug" (BLD), which also putatively harbour an active version of the cannabichrometic acid Synthase gene (CBCAS).

CONCLUSION

The final chemical compositions of cannabis products have key traits related to their genetic identities. Our analyses in the context of the NCBI Cannabis sativa Annotation Release 100 allows for hypothesis testing with regards to secondary metabolite production. Genetic markers related to secondary metabolite production will be important in many sectors of the cannabis marketplace. For example, markers related to THC production will be important for adaptable and compliant large-scale seed production under the new US Domestic Hemp Production Program.

Silicon ameliorates clubroot responses in canola (Brassica napus): A "multi-omics"-based investigation into possible mechanisms

Clubroot disease, caused by Plasmodiophora brassicae Woronin, results in severe yield losses in Brassica crops, including canola. Silicon (Si) mitigates several stresses and enhances plant resistance to phytopathogens. We investigated the effects of Si on clubroot disease symptoms in canola at two concentrations of Si, Si: soil in 1: 100 w/w (Si1.0) and Si: soil in 1:200 w/w (Si0.5) under greenhouse conditions. In addition, the effects of Si on P. brassicae-induced gene expression, endogenous levels of phytohormones and metabolites were studied using "omics" approaches. Si application reduced clubroot symptoms and improved plant growth parameters. Gene expression analysis revealed increased transcript-level responses in Si1.0 compared to Si0.5 plants at 7-, 14-, and 21-days post-inoculation (dpi). Pathogen-induced transcript-level changes were affected by Si treatment, with genes related to antioxidant activity (e.g., POD, CAT), phytohormone biosynthesis and signalling (e.g., PDF1.2, NPR1, JAZ, IPT, TAA), nitrogen metabolism (e.g., NRT, AAT), and secondary metabolism (e.g., PAL, BCAT4) exhibiting differential expression. Endogenous levels of phytohormones (e.g., auxin, cytokinin), a majority of the amino acids and secondary metabolites (e.g., glucosinolates) were increased at 7 dpi, followed by a decrease at 14- and 21-dpi due to Si-treatment. Stress hormones such as abscisic acid (ABA), salicylic acid (SA), and jasmonic acid (JA) also decreased at the later time points in Si0.5, and Si1.0 treated plants. Si appears to improve clubroot symptoms while enhancing plant growth and associated metabolic processes, including nitrogen metabolism and secondary metabolite biosynthesis.

Proteome- and metabolome-level changes during early stages of clubroot infection in Brassica napus canola

Clubroot is a destructive root disease of canola (Brassica napus L.) caused by Plasmodiophora brassicae Woronin. Despite extensive research into the molecular responses of B. napus to P. brassicae, there is limited information on proteome- and metabolome-level changes in response to the pathogen, especially during the initial stages of infection. In this study, we have investigated the proteome- and metabolome- level changes in the roots of clubroot-resistant (CR) and -susceptible (CS) doubled-haploid (DH) B. napus lines, in response to P. brassicae pathotype 3H at 1-, 4-, and 7-days post-inoculation (DPI). Root proteomes were analyzed using nanoflow liquid chromatography coupled with tandem mass spectrometry (nano LC-MS/MS). Comparisons of pathogen-inoculated and uninoculated root proteomes revealed 2515 and 1556 differentially abundant proteins at one or more time points (1-, 4-, and 7-DPI) in the CR and CS genotypes, respectively. Several proteins related to primary metabolites (e.g., amino acids, fatty acids, and lipids), secondary metabolites (e.g., glucosinolates), and cell wall reinforcement-related proteins [e.g., laccase, peroxidases, and plant invertase/pectin methylesterase inhibitors (PInv/PMEI)] were identified. Eleven nucleotides and nucleoside-related metabolites, and eight fatty acids and sphingolipid-related metabolites were identified in the metabolomics study. To our knowledge, this is the first report of root proteome-level changes and associated alterations in metabolites during the early stages of P. brassicae infection in B. napus.

Fast Tract Anesthesia Using Isoflurane and Propofol During Off-pump Coronary Artery Bypass Graft Surgery

This study aimed to evaluate myocardial protective effect of isoflurane and propofol as a fast tract anesthesia in off pump coronary artery bypass graft surgery by measuring postoperative cardiac enzyme Troponin-I, and liver enzyme. The study was conducted on 260 patients scheduled to undergo elective off pump coronary artery bypass graft surgery. Patients were randomly allocated to receive either isoflurane or propofol anesthesia and was aimed to extubated within 6 hours. Troponin-I levels were measured preoperatively, at arrival in postoperative intensive care unit, at 12, 24, 48, 72 hours and 4 weeks following surgery. Liver function was also assessed and compared between preoperative and postoperative values. There is no difference in Troponin-I levels between the two studies groups at observed pre and post-operative time intervals. Fast tract anesthesia using isoflurane and propofol provides same myocardial protection during and after OPCABG and overall outcome was excellent.

Pregnancy Outcome with Prosthetic Heart Valve in Bangladesh: A Retrospective Cohort Study

The aim of this retrospective cohort study was to evaluate the occurrence of the maternal and fetal outcome during pregnancy and immediately after delivery in women with prosthetic heart valve, especially with oral anticoagulants therapy that must be weighed against the risk of intracardiac thrombosis. This study was undertaken at Department of Cardiac surgery, Bangabandhu Sheikh Mujib Medical University, Dhaka, Bangladesh from January 2012 to December 2017. A total of 82 pregnancies with heart valve prosthesis were evaluated in two groups: Group I (n=58) includes pregnancy with mechanical heart valve, while Group II (n=24) includes pregnancy with bioprosthetic valve. The mean age of patients was 25.7±2.5 years and 24.9±5.5 years in Group I and Group II respectively. Approximately 70% pregnancies ended in healthy live births, however about 75% of study population developed maternal complications in Group I, which is significantly higher than Group II. First trimester spontaneous miscarriage was statistically significant between two groups (p value <0.005). Mean birth weight and mean APGAR score was found normal in both study group. Majority of the patients were found in good health status during and after pregnancy. Proper antenatal care and early risk stratification are the fundamental measures to improve the maternal and fetal outcome in a patient with prosthetic heart valve.

Impact of Socio-demographic Variables, Surgical Techniques and Risk Factors on the Outcome of Coronary Artery Bypass Graft Surgery among Bangladeshi Population

This study was intended to evaluate the pathological outcome of cardiopulmonary bypass whilst considering socio-demographic variables and surgical technique on early postoperative results following coronary artery bypass graft (CABG) surgery in patients at a tertiary level hospital in Bangladesh. This observational study evaluated a total of 880 patients with ischemic heart disease in Bangabandhu Sheikh Mujib Medical University, Bangladesh from 2011 to 2019 who were undergoing an isolated CABG surgery. In this current study, the population divided into two groups- Group A: Off-pump CABG (n=440) and Group B: On-pump CABG (n=440). The mean age of the patients was 55.25±5.0 years in off-pump and 50.75±5.2 years in the on-pump group. Risk factors, including smoking, hypertension, and hyperlipidemia, were predominant in both study groups. Total operative time was notably higher in the on-pump CABG group. However, grafting time was more in the off-pump CABG procedures. Postoperative neurological deficits were higher amongst the on-pump CABG population. The mean time of mechanical ventilation, intensive care unit (ICU) stay, total hospital stay, and mortality was notably higher in the on-pump CABG group. Moreover, the number of mortalities in on-pump CABG patients was primarily due to the low output syndrome, failure of weaning from cardiopulmonary bypass (CPB) and sudden cardiac arrest. Off-pump CABG is now more acceptable due to its potentiality to avoid CPB induced complications, aortic cannulation, and cross-clamping. Cardiac arrest in on-pump CABG induces global ischemia and reperfusion injury to the cardiac muscle. Besides, the Off-pump CABG provides a conspicuous survival advantage compared to the on-pump CABG, in association with a notable reduction in postoperative morbidity and mortality.

Gene expression signatures of mutualism and pathogenesis in flax roots

Introduction

Fusarium wilt, a devastating soil-borne fungal disease in flax (Linum usitatissimum), is caused by Fusarium oxysporum f. sp. lini, a hemibiotrophic plant pathogen that penetrates plant roots. There are several reports of the molecular response of L. usitatissimum to F. oxysporum f. sp. lini; however, comparisons of the effects of mutualistic and pathogenic fungi on plants are more limited.

Methods

In this study, we have integrated phenotyping and RNA-Seq approaches to examine the response of flax to F. oxysporum f.sp. lini and to a mutualistic arbuscular mycorrhizal fungus (AMF) Rhizoglomus irregulare. R. irregulare is a common soil fungus and also widely used as a commercial inoculant to improve plant growth. We measured flax growth parameters after plant inoculation with each or both fungi, in comparison with non-inoculated control. We performed transcriptome analysis of root tissues collected at 9 and 14 days post-inoculation.

Results

We identified several differentially expressed genes (DEGs) in response to pathogenic and mutualistic fungi. These included genes related to ethylene and salicylic acid biosynthesis, carbohydrate binding, oxidoreductases, and sugar transmembrane transporters. Genes related to calcium signaling, nutrient transport, lipid metabolism, cell wall, and polysaccharide-modifying were up-regulated by R. irregulare; however, the same genes were down-regulated by F. oxysporum f. sp. lini when treated independently. In the combined treatment, genes related to cell wall modifications, hormone regulation and nutrient uptake were up-regulated. These results suggest that inoculation with R. irregulare reduced gene expression related to F. oxysporum f. sp. lini infection, leading to a reduced response to the pathogen. In response to AMF, flax prioritized mutualism-related gene expression over defense, reversing the growth inhibition caused by F. oxysporum f. sp.lini in the combined treatment.

Discussion

This research provides insights into the protective effects of AMF, revealing the pre-symbiotic gene expression profile of flax in response to mutualism in comparison with pathogenicity. Potential target genes for crop improvement were identified, especially defense related genes.

A 15 Year's Experience with Minimally Invasive Mitral Valve Replacement in Bangladesh

This study was aimed to compare the long-term outcomes and survival rate among mitral valve replacement using thoracotomy and standard median sternotomy in a single surgeon's practice. Total 250 patients were evaluated; Group I (n=65) patients had anterolateral thoracotomy and Group II (n=185) had standard median sternotomy for valve replacement. Mean age was 25.1±5 years in Group I and 41.8±10.5 years in Group II. Female was predominant in Group I. Total operative time and bypass time was statistically significant in Group I (235.5±25.8 minutes; 84.2±12.75 minutes) in contrast to Group II (203.8±15.5 minutes; 71.5±10.5 minutes). Incision scar was not visible in females in Group I but full incision scar was visible in Group II. Post-operative ICU stay duration was significant high in Group II. Though, wound infection incidence was 0% in Group I; however, 9.73% patient had wound infection in Group II. Only 1.62% patient developed unstable sternum in Group II. Most of the patients from both study group were in regular follow up and 1-year mortality rate was 4.62% and 5.94% in Group I and Group II respectively. Mitral valve replacement through a right anterolateral thoracotomy is easy and safe to perform; while getting maximum benefits for the patients. Besides satisfactory cosmetic outcome especially in female, this approach provides better exposure to mitral apparatus even in patients with small left atrium, cost effectiveness, less duration of hospital stays and absence of the risk for unstable sternum.