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

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

Burden of disease scenarios for 204 countries and territories, 2022–2050: a forecasting analysis for the Global Burden of Disease Study 2021

Background: Future trends in disease burden and drivers of health are of great interest to policy makers and the public at large. This information can be used for policy and long-term health investment, planning, and prioritisation. We have expanded and improved upon previous forecasts produced as part of the Global Burden of Diseases, Injuries, and Risk Factors Study (GBD) and provide a reference forecast (the most likely future), and alternative scenarios assessing disease burden trajectories if selected sets of risk factors were eliminated from current levels by 2050. Methods: Using forecasts of major drivers of health such as the Socio-demographic Index (SDI; a composite measure of lag-distributed income per capita, mean years of education, and total fertility under 25 years of age) and the full set of risk factor exposures captured by GBD, we provide cause-specific forecasts of mortality, years of life lost (YLLs), years lived with disability (YLDs), and disability-adjusted life-years (DALYs) by age and sex from 2022 to 2050 for 204 countries and territories, 21 GBD regions, seven super-regions, and the world. All analyses were done at the cause-specific level so that only risk factors deemed causal by the GBD comparative risk assessment influenced future trajectories of mortality for each disease. Cause-specific mortality was modelled using mixed-effects models with SDI and time as the main covariates, and the combined impact of causal risk factors as an offset in the model. At the all-cause mortality level, we captured unexplained variation by modelling residuals with an autoregressive integrated moving average model with drift attenuation. These all-cause forecasts constrained the cause-specific forecasts at successively deeper levels of the GBD cause hierarchy using cascading mortality models, thus ensuring a robust estimate of cause-specific mortality. For non-fatal measures (eg, low back pain), incidence and prevalence were forecasted from mixed-effects models with SDI as the main covariate, and YLDs were computed from the resulting prevalence forecasts and average disability weights from GBD. Alternative future scenarios were constructed by replacing appropriate reference trajectories for risk factors with hypothetical trajectories of gradual elimination of risk factor exposure from current levels to 2050. The scenarios were constructed from various sets of risk factors: environmental risks (Safer Environment scenario), risks associated with communicable, maternal, neonatal, and nutritional diseases (CMNNs; Improved Childhood Nutrition and Vaccination scenario), risks associated with major non-communicable diseases (NCDs; Improved Behavioural and Metabolic Risks scenario), and the combined effects of these three scenarios. Using the Shared Socioeconomic Pathways climate scenarios SSP2-4.5 as reference and SSP1-1.9 as an optimistic alternative in the Safer Environment scenario, we accounted for climate change impact on health by using the most recent Intergovernmental Panel on Climate Change temperature forecasts and published trajectories of ambient air pollution for the same two scenarios. Life expectancy and healthy life expectancy were computed using standard methods. The forecasting framework includes computing the age-sex-specific future population for each location and separately for each scenario. 95% uncertainty intervals (UIs) for each individual future estimate were derived from the 2·5th and 97·5th percentiles of distributions generated from propagating 500 draws through the multistage computational pipeline. Findings: In the reference scenario forecast, global and super-regional life expectancy increased from 2022 to 2050, but improvement was at a slower pace than in the three decades preceding the COVID-19 pandemic (beginning in 2020). Gains in future life expectancy were forecasted to be greatest in super-regions with comparatively low life expectancies (such as sub-Saharan Africa) compared with super-regions with higher life expectancies (such as the high-income super-region), leading to a trend towards convergence in life expectancy across locations between now and 2050. At the super-region level, forecasted healthy life expectancy patterns were similar to those of life expectancies. Forecasts for the reference scenario found that health will improve in the coming decades, with all-cause age-standardised DALY rates decreasing in every GBD super-region. The total DALY burden measured in counts, however, will increase in every super-region, largely a function of population ageing and growth. We also forecasted that both DALY counts and age-standardised DALY rates will continue to shift from CMNNs to NCDs, with the most pronounced shifts occurring in sub-Saharan Africa (60·1% [95% UI 56·8–63·1] of DALYs were from CMNNs in 2022 compared with 35·8% [31·0–45·0] in 2050) and south Asia (31·7% [29·2–34·1] to 15·5% [13·7–17·5]). This shift is reflected in the leading global causes of DALYs, with the top four causes in 2050 being ischaemic heart disease, stroke, diabetes, and chronic obstructive pulmonary disease, compared with 2022, with ischaemic heart disease, neonatal disorders, stroke, and lower respiratory infections at the top. The global proportion of DALYs due to YLDs likewise increased from 33·8% (27·4–40·3) to 41·1% (33·9–48·1) from 2022 to 2050, demonstrating an important shift in overall disease burden towards morbidity and away from premature death. The largest shift of this kind was forecasted for sub-Saharan Africa, from 20·1% (15·6–25·3) of DALYs due to YLDs in 2022 to 35·6% (26·5–43·0) in 2050. In the assessment of alternative future scenarios, the combined effects of the scenarios (Safer Environment, Improved Childhood Nutrition and Vaccination, and Improved Behavioural and Metabolic Risks scenarios) demonstrated an important decrease in the global burden of DALYs in 2050 of 15·4% (13·5–17·5) compared with the reference scenario, with decreases across super-regions ranging from 10·4% (9·7–11·3) in the high-income super-region to 23·9% (20·7–27·3) in north Africa and the Middle East. The Safer Environment scenario had its largest decrease in sub-Saharan Africa (5·2% [3·5–6·8]), the Improved Behavioural and Metabolic Risks scenario in north Africa and the Middle East (23·2% [20·2–26·5]), and the Improved Nutrition and Vaccination scenario in sub-Saharan Africa (2·0% [–0·6 to 3·6]). Interpretation: Globally, life expectancy and age-standardised disease burden were forecasted to improve between 2022 and 2050, with the majority of the burden continuing to shift from CMNNs to NCDs. That said, continued progress on reducing the CMNN disease burden will be dependent on maintaining investment in and policy emphasis on CMNN disease prevention and treatment. Mostly due to growth and ageing of populations, the number of deaths and DALYs due to all causes combined will generally increase. By constructing alternative future scenarios wherein certain risk exposures are eliminated by 2050, we have shown that opportunities exist to substantially improve health outcomes in the future through concerted efforts to prevent exposure to well established risk factors and to expand access to key health interventions

Convalescent plasma in patients admitted to hospital with COVID-19 (RECOVERY): a randomised controlled, open-label, platform trial

SummaryBackground Azithromycin has been proposed as a treatment for COVID-19 on the basis of its immunomodulatoryactions. We aimed to evaluate the safety and efficacy of azithromycin in patients admitted to hospital with COVID-19.Methods In this randomised, controlled, open-label, adaptive platform trial (Randomised Evaluation of COVID-19Therapy [RECOVERY]), several possible treatments were compared with usual care in patients admitted to hospitalwith COVID-19 in the UK. The trial is underway at 176 hospitals in the UK. Eligible and consenting patients wererandomly allocated to either usual standard of care alone or usual standard of care plus azithromycin 500 mg once perday by mouth or intravenously for 10 days or until discharge (or allocation to one of the other RECOVERY treatmentgroups). Patients were assigned via web-based simple (unstratified) randomisation with allocation concealment andwere twice as likely to be randomly assigned to usual care than to any of the active treatment groups. Participants andlocal study staff were not masked to the allocated treatment, but all others involved in the trial were masked to theoutcome data during the trial. The primary outcome was 28-day all-cause mortality, assessed in the intention-to-treatpopulation. The trial is registered with ISRCTN, 50189673, and ClinicalTrials.gov, NCT04381936.Findings Between April 7 and Nov 27, 2020, of 16 442 patients enrolled in the RECOVERY trial, 9433 (57%) wereeligible and 7763 were included in the assessment of azithromycin. The mean age of these study participants was65·3 years (SD 15·7) and approximately a third were women (2944 [38%] of 7763). 2582 patients were randomlyallocated to receive azithromycin and 5181 patients were randomly allocated to usual care alone. Overall,561 (22%) patients allocated to azithromycin and 1162 (22%) patients allocated to usual care died within 28 days(rate ratio 0·97, 95% CI 0·87–1·07; p=0·50). No significant difference was seen in duration of hospital stay (median10 days [IQR 5 to >28] vs 11 days [5 to >28]) or the proportion of patients discharged from hospital alive within 28 days(rate ratio 1·04, 95% CI 0·98–1·10; p=0·19). Among those not on invasive mechanical ventilation at baseline, nosignificant difference was seen in the proportion meeting the composite endpoint of invasive mechanical ventilationor death (risk ratio 0·95, 95% CI 0·87–1·03; p=0·24).Interpretation In patients admitted to hospital with COVID-19, azithromycin did not improve survival or otherprespecified clinical outcomes. Azithromycin use in patients admitted to hospital with COVID-19 should be restrictedto patients in whom there is a clear antimicrobial indication

Development of genetic resources and functional analysis of betalains in Amaranthus species

Amaranth is an ancient crop in which interest is being renewed, due to its adaptability, stress tolerance, and nutritional value. The grain amaranths (Amaranthus caudatus L., A. cruentus L., A. hypochondriacus L.) are grown primarily for their seeds, which are protein-rich pseudocereals. Some species of amaranths are also major noxious weeds (e.g A. palmeri). Many members of the amaranth family (Amaranthaceae) produce red (betacyanin) or yellow (betaxanthin) betalain pigments, which are chemically distinct from the anthocyanins responsible for red pigmentation. My objective was to develop resources that will aid in further research and improvement of grain amaranths, and to use these resources to investigate the ecological significance of betalains. I produced the first major catalog of amaranth genes by assembling transcriptomes from eight tissues of A. hypochondriacus cv. Plainsman, the major commercial cultivar. These tissues included seeds and embryos at three stages of development. Reverse genetics techniques are useful to induce a loss-of-function and therefore infer gene function. I succeeded in establishing the first reverse genetics protocol for amaranths, using virus-induced gene silencing (VIGS). I used VIGS to target putative betalain biosynthetic genes AtriCYP76AD1 and AtriPPO1 in an intensely red-pigmented amaranth species, A. tricolor. VIGS of AtriPPO1 resulted in severe necrosis. VIGS of AtriCYP76AD1 resulted in a nearly complete loss of detectable red pigment in some tissues. Protection from UV-induced damage is one of the roles that has been proposed for betalains. To test this hypothesis, I compared UV responses in a red-pigmented A. tricolor variety with green tissues in VIGS treated plants of the same variety, and with a green variety of A. tricolor. Following UV exposure, the red and green tissues showed similar responses in photosynthetic activity, oxidative damage, and in the production of markers of UV-B stress. However, the red tissues uniquely showed an increase in photosynthetic pigments under UV-B treatment, whereas the photosynthetic pigments decreased in green tissues. Thus, although our experiment did not provide any evidence that betacyanins are UV-B or ROS-protective, the presence of betacyanin was correlated with a differential response of photosynthetic pigments, perhaps due to filtering of specific visible wavelengths.Arts and Sciences, Irving K. Barber School of (Okanagan)Biology, Department of (Okanagan)Graduat