Morphologic and Taxonomic Analysis of the Weedy and Cultivated Amaranthus hybridus Species Complex

The hybridus species complex of the genus Amaranthus is a group of weedy and cultivated plants from the New World that are considered difficult to identify. Classification schemes have varied between a single species approach, Amaranthus hybridus s.l., and a five species approach that recognizes the widespread weedy A. hybridus s.s., the South American endemic A. quitensis, and the three cultivated taxa (A. hypochondriacus, A. cruentus, and A. caudatus) as distinct species. The goals of this study were to analyze patterns of floral variation within the species complex and to determine distinguishing morphological features of the species. Twenty-one pistillate and twelve staminate floral characters from 41 specimens representing all five species were analyzed morphologically. Results indicate that morphological characters split the hybridus complex into two larger groups; that the widespread weedy A. hybridus divides into two morphologically distinct groups, each associated with different cultivated taxa; and that staminate morphological variation may be more taxonomically informative than previously assumed

Investigation of the T helper cell response against Epstein-Barr virus

The Epstein-Barr virus (EBV) is associated with a number of human malignancies. Following primary infection, the virus persists lifelong in the infected host by latently infecting B cells and occasional cycles of reactivation, virus production and re-infection. Adoptively transferred EBV-specific T cells, generated by repeated stimulation with autologous lymphoblastoid cell lines (LCL) in vitro, are able to cure post-transplant lymphoproliferative disease (PTLD). However, the generation of these vaccines is labor and cost intensive precluding their general availability for all patients at risk. Novel insights into the mechanisms of protective antiviral immunity is expected to provide a better understanding of the pathogenesis of EBV-associated diseases and to facilitate the development of novel and generally available immunotherapeutic options. The aim of this work was to assess specificity and breadth of the EBV-specific T helper cell response, using two different experimental strategies. To define specificity, LCL-stimulated CD4+ T cell lines were established from 23 EBV-negative and -positive donors. The T cell lines generated from EBV-negative donors responded poorly against LCL and failed to show EBV-specificity. By contrast, all T cell lines established from healthy virus carriers were EBV-specific. Half of the lines from acutely EBV-infected patients with infectious mononucleosis (IM) were also EBV-specific, while the other half recognized EBV-positive and EBV-negative target cells. Unexpectedly, the EBV-specific T cell lines did not recognize latent antigens of EBV expressed in all LCL. Instead, these lines were specific for lytic cycle antigens predominantly derived from virion proteins. Several of the T cell lines recognized BNRF1, a viral tegument protein. Most T cell lines, however, recognized different virion antigens, suggesting that the family of virion proteins forms the immunodominant targets of the EBV-specific T helper cell response. Studies on the breadth of the EBV-specific T helper response demonstrated that all healthy virus carriers maintain CD4+ T cell memory to lytic cycle antigens. T cells specific for virion antigens recognized EBV-positive cells directly and, surprisingly, a much higher percentage of target cells than those expressing lytic cycle proteins. Antigen was efficiently transferred to bystander B cells by receptor-mediated uptake of released virions, resulting in recognition of target cells incubated with less than one virion per cell. T cell recognition did not require productive infection and occurred early after virus entry before latency was established. By secreting perforin and granzyme B upon antigen recognition, virion-specific T helper cells inhibited proliferation of LCLs and suppressed the outgrowth of LCLs following infection of primary B cells with EBV. These results established a novel role for virion-specific T helper cells in the control of EBV infection, and identify virion proteins as important immune targets. The findings have implications for the treatment of diseases associated with EBV and potentially other coated viruses infecting MHC class II-positive cells

Amaranth: An Ancient and High-Quality Wholesome Crop

Amaranth was a staple of the Aztec diet and is described as a “superfood” in part because of its high protein content and well-balanced amino acid profile. In terms of nutrient content, amaranth surpasses many staple crops such as rice, corn, and wheat. Additionally, lysine content is twice as much than in rice and thrice as much than in corn. Along with desirable agronomic traits, this crop has been hugely applauded for its gluten-free nature. Not only can it benefit vegan and gluten allergy personals, but it also has the potential to supply high-quality proteins and at the same time provides antimicrobial activities in the packaged food items. Despite all of these properties, this crop is still not in the mainstream cultivation practices in North America and in many parts of the world. As the planet is expecting massive increase in human population and global climate change, we firmly believe that this widely distributed, ancient, protein-rich pseudo-cereal has a potential to augment our food system. In this book chapter, we aim to report the nutritional properties of grain amaranth

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

Late presentation of congenital diaphragmatic hernia: A diagnostic dilemma

Congenital diaphragmatic hernias are commonly symptomatic within 24 hours after birth, but late presentation is not uncommon. Late presentation of congenital diaphragmatic hernia poses diagnostic difficulties as clinical picture are vague, and more commonly presented with non-specific gastrointestinal and respiratory symptoms. Due to the vague and non-specific clinical presentation, clinician faces a diagnostic dilemma resulting in delay in diagnosis and many a times an inappropriate management. This article reports 2 cases of late-presenting congenital diaphragmatic hernia (over the period of 6 months from September 2014 to February 2015) in National Institute of Disease of Chest and Hospital (NIDCH). In first case, she was diagnosed as right-sided tubercular pleural effusion and was treated with CAT-1 anti-tubercular therapy for 6 months without any clinical improvement. Later CT scan of chest was done and diagnosed as a case of congenital diaphragmatic hernia. The second case was diagnosed as a left-sided hydropneumothorax and treated with left tube thoracostomy. During removal of the intercostal chest tube, some fatty tissue was pulled out of the thoracostomy site. In NIDCH, she was diagnosed as a case of diaphragmatic hernia by barium follow-through. Both cases were diagnosed as Bochdalek hernia during the repair of the hernia defect via thoracotomy

Immunodominance of Lytic Cycle Antigens in Epstein-Barr Virus-Specific CD4+ T Cell Preparations for Therapy

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. 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. 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

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 &lt; 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 &lt; 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

Gene expression signatures of mutualism and pathogenesis in flax roots

IntroductionFusarium 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.MethodsIn 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.ResultsWe 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.DiscussionThis 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

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

<p>Abstract</p> <p>Background</p> <p>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.</p> <p>Results</p> <p>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 <it>in silico </it>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.</p> <p>Conclusions</p> <p>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.</p