Capturing Wheat Phenotypes at the Genome Level

Recent technological advances in next-generation sequencing (NGS) technologies have dramatically reduced the cost of DNA sequencing, allowing species with large and complex genomes to be sequenced. Although bread wheat (Triticum aestivum L.) is one of the world's most important food crops, efficient exploitation of molecular marker-assisted breeding approaches has lagged behind that achieved in other crop species, due to its large polyploid genome. However, an international public-private effort spanning 9 years reported over 65% draft genome of bread wheat in 2014, and finally, after more than a decade culminated in the release of a gold-standard, fully annotated reference wheat-genome assembly in 2018. Shortly thereafter, in 2020, the genome of assemblies of additional 15 global wheat accessions was released. As a result, wheat has now entered into the pan-genomic era, where basic resources can be efficiently exploited. Wheat genotyping with a few hundred markers has been replaced by genotyping arrays, capable of characterizing hundreds of wheat lines, using thousands of markers, providing fast, relatively inexpensive, and reliable data for exploitation in wheat breeding. These advances have opened up new opportunities for marker-assisted selection (MAS) and genomic selection (GS) in wheat. Herein, we review the advances and perspectives in wheat genetics and genomics, with a focus on key traits, including grain yield, yield-related traits, end-use quality, and resistance to biotic and abiotic stresses. We also focus on reported candidate genes cloned and linked to traits of interest. Furthermore, we report on the improvement in the aforementioned quantitative traits, through the use of (i) clustered regularly interspaced short-palindromic repeats/CRISPR-associated protein 9 (CRISPR/Cas9)-mediated gene-editing and (ii) positional cloning methods, and of genomic selection. Finally, we examine the utilization of genomics for the next-generation wheat breeding, providing a practical example of using in silico bioinformatics tools that are based on the wheat reference-genome sequence.

Phenological optimization of late reproductive phase for raising wheat yield potential in irrigated mega-environments

Increasing grain number through fine-tuning duration of the late reproductive phase (LRP; terminal spikelet to anthesis) without altering anthesis time has been proposed as a genetic strategy to increase yield potential (YP) of wheat. Here we conducted a modelling analysis to evaluate the potential of fine-tuning LRP in raising YP in irrigated mega-environments. Using the known optimal anthesis and sowing date of current elite benchmark genotypes, we applied a gene-based phenology model for long-term simulations of phenological stages and yield-related variables of all potential germplasm with the same duration to anthesis as the benchmark genotypes. These diverse genotypes had the same duration to anthesis but varying LRP duration. Lengthening LRP increased YP and harvest index by increasing grain number to some extent and an excessively long LRP reduced YP due to reduced time for canopy construction for high biomass production of pre-anthesis phase. The current elite genotypes could have their LRP extended for higher YP in most sites. Genotypes with a ratio of the duration of LRP to pre-anthesis phase of about 0.42 ensured high yields (≥95% of YP) with their optimal sowing and anthesis dates. Optimization of intermediate growth stages could be further evaluated in breeding programmes to improve YP.

Genomic variants affecting homoeologous gene expression dosage contribute to agronomic trait variation in allopolyploid wheat

Allopolyploidy greatly expands the range of possible regulatory interactions among functionally redundant homoeologous genes. However, connection between the emerging regulatory complexity and expression and phenotypic diversity in polyploid crops remains elusive. Here, we use diverse wheat accessions to map expression quantitative trait loci (eQTL) and evaluate their effects on the population-scale variation in homoeolog expression dosage. The relative contribution of cis- and trans-eQTL to homoeolog expression variation is strongly affected by both selection and demographic events. Though trans-acting effects play major role in expression regulation, the expression dosage of homoeologs is largely influenced by cis-acting variants, which appear to be subjected to selection. The frequency and expression of homoeologous gene alleles showing strong expression dosage bias are predictive of variation in yield-related traits, and have likely been impacted by breeding for increased productivity. Our study highlights the importance of genomic variants affecting homoeolog expression dosage in shaping agronomic phenotypes and points at their potential utility for improving yield in polyploid crops.

Progress and Prospects of Developing Climate Resilient Wheat in South Asia Using Modern Pre-Breeding Methods

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Developing climate-resilient wheat is a priority for South Asia since the effect of climate change will be pronounced on the major crops that are staple to the region. South Asia must produce >400 million metric tons (MMT) of wheat by 2050 to meet the demand. However, the current average yield <3 t/ha is not sufficient to meet the requirement. In this review, we are addressing how pre-breeding methods in wheat can address the gap in grain yield as well as reduce the bottleneck of genetic diversity. Physiological pre-breeding which incorporates screening of diverse germplasm from gene banks for physiological and agronomic traits, the strategic crossing of complementary traits, high throughput phenotyping, molecular markers-based generation advancement, genomic prediction, and validation of high-value heat and drought tolerant lines to South Asia can help to alleviate the drastic effect of climate change on wheat production. There are several gene banks, if utilized well, can play a major role in breeding for climate-resilient wheat. CIMMYT’s wheat physiological pre-breeding has delivered several hundred lines via the Stress Adapted Trait Yield Nursery (SATYN) to the NARS in many South Asian countries; India, Pakistan, Nepal, Bangladesh, Afghanistan, and Iran. Some of these improved germplasms have resulted in varieties for farmer's field. We conclude the review by pointing out the importance of collaborative interdisciplinary translational research to alleviate the effects of climate change on wheat production in South Asia.

Using a gene-based phenology model to identify optimal flowering periods of spring wheat in irrigated mega-environments

To maximize the grain yield of spring wheat, flowering needs to coincide with the optimal flowering period (OFP) by minimizing frost and heat stress on reproductive development. This global study conducted a comprehensive modelling analysis of genotype, environment, and management to identify the OFPs for sites in irrigated mega-environments of spring wheat where the crop matures during a period of increasing temperatures. We used a gene-based phenology model to conduct long-term simulation analysis with parameterized genotypes to identify OFPs and optimal sowing dates for sites in irrigated mega-environments, considering the impacts of frost and heat stress on yield. The validation results showed that the gene-based model accurately predicted wheat heading dates across global wheat environments. The long-term simulations indicated that frost and heat stress significantly advanced or delayed OFPs and shrank the durations of OFPs in irrigated mega-environments when compared with OFPs where the model excluded frost and heat stress impacts. The simulation results (incorporating frost and heat penalties on yield) also showed that earlier flowering generally resulted in higher yields, and early sowing dates and/or early flowering genotypes were suggested to achieve early flowering. These results provided an interpretation of the regulation of wheat flowering to the OFP by the selection of sowing date and cultivar to achieve higher yields in irrigated mega-environments.

Harnessing translational research in wheat for climate resilience

Despite being the world's most widely grown crop, research investments in wheat (Triticum aestivum and Triticum durum) fall behind those in other staple crops. Current yield gains will not meet 2050 needs, and climate stresses compound this challenge. However, there is good evidence that heat and drought resilience can be boosted through translating promising ideas into novel breeding technologies using powerful new tools in genetics and remote sensing, for example. Such technologies can also be applied to identify climate resilience traits from among the vast and largely untapped reserve of wheat genetic resources in collections worldwide. This review describes multi-pronged research opportunities at the focus of the Heat and Drought Wheat Improvement Consortium (coordinated by CIMMYT), which together create a pipeline to boost heat and drought resilience, specifically: improving crop design targets using big data approaches; developing phenomic tools for field-based screening and research; applying genomic technologies to elucidate the bases of climate resilience traits; and applying these outputs in developing next-generation breeding methods. The global impact of these outputs will be validated through the International Wheat Improvement Network, a global germplasm development and testing system that contributes key productivity traits to approximately half of the global wheat-growing area.

An integrated framework reinstating the environmental dimension for GWAS and genomic selection in crops

Identifying mechanisms and pathways involved in gene-environment interplay and phenotypic plasticity is a long-standing challenge. It is highly desirable to establish an integrated framework with an environmental dimension for complex trait dissection and prediction. A critical step is to identify an environmental index that is both biologically relevant and estimable for new environments. With extensive field-observed complex traits, environmental profiles, and genome-wide single nucleotide polymorphisms for three major crops (maize, wheat, and oat), we demonstrated that identifying such an environmental index (i.e., a combination of environmental parameter and growth window) enables genome-wide association studies and genomic selection of complex traits to be conducted with an explicit environmental dimension. Interestingly, genes identified for two reaction-norm parameters (i.e., intercept and slope) derived from flowering time values along the environmental index were less colocalized for a diverse maize panel than for wheat and oat breeding panels, agreeing with the different diversity levels and genetic constitutions of the panels. In addition, we showcased the usefulness of this framework for systematically forecasting the performance of diverse germplasm panels in new environments. This general framework and the companion CERIS-JGRA analytical package should facilitate biologically informed dissection of complex traits, enhanced performance prediction in breeding for future climates, and coordinated efforts to enrich our understanding of mechanisms underlying phenotypic variation.

Genetic Dissection of Adult Plant Resistance to Sharp Eyespot Using an Updated Genetic Map of Niavt14 × Xuzhou25 Winter Wheat Recombinant Inbred Line Population

Wheat sharp eyespot, a disease mainly caused by soilborne fungus Rhizoctonia cerealis, is a threat to world wheat production. Wheat's genetic resistance to sharp eyespot is a potential approach to reducing the application of fungicides and farming practice inputs. To identify the genetic basis of sharp eyespot resistance in Niavt14, a recombinant inbred line population comprising 215 F₈ lines from Niavt14 × Xuzhou25, was developed. An earlier linkage map (148 simple sequence repeat markers) was updated with 5,792 polymorphic Affymetrix Axiom 55K single-nucleotide polymorphisms to a new map of 5,684.2 centimorgans with 1,406 nonredundant markers. The new linkage map covered all 21 chromosomes of common wheat and showed a good collinearity with the IWGSC RefSeq v1.0 genome. We conducted quantitative trait locus (QTL) mapping for sharp eyespot resistance using the adult plant response data from the field of five consecutive growing seasons and one greenhouse test. Two stable QTL on chromosomes 2B and 7D that were identified in the previous study were confirmed, and three novel, stable QTL, explaining 4.0 to 17.5% phenotypic variation, were mapped on 1D, 6D, and 7A, which were independent of QTL for phenology and plant height. The QTL on 1D, 2B, 6D, and 7A showed low frequencies in 384 landraces (0 to 10%) and 269 elite cultivars (5 to 23%) from the southern winter wheat region and the Yellow and Huai River Valley facultative wheat region in China, respectively. These identified QTL could be used in wheat breeding programs for improving sharp eyespot resistance through marker-assisted selection.

Breeder friendly phenotyping

The word phenotyping can nowadays invoke visions of a drone or phenocart moving swiftly across research plots collecting high-resolution data sets on a wide array of traits. This has been made possible by recent advances in sensor technology and data processing. Nonetheless, more comprehensive often destructive phenotyping still has much to offer in breeding as well as research. This review considers the 'breeder friendliness' of phenotyping within three main domains: (i) the 'minimum data set', where being 'handy' or accessible and easy to collect and use is paramount, visual assessment often being preferred; (ii) the high throughput phenotyping (HTP), relatively new for most breeders, and requiring significantly greater investment with technical hurdles for implementation and a steeper learning curve than the minimum data set; (iii) detailed characterization or 'precision' phenotyping, typically customized for a set of traits associated with a target environment and requiring significant time and resources. While having been the subject of debate in the past, extra investment for phenotyping is becoming more accepted to capitalize on recent developments in crop genomics and prediction models, that can be built from the high-throughput and detailed precision phenotypes. This review considers different contexts for phenotyping, including breeding, exploration of genetic resources, parent building and translational research to deliver other new breeding resources, and how the different categories of phenotyping listed above apply to each. Some of the same tools and rules of thumb apply equally well to phenotyping for genetic analysis of complex traits and gene discovery.

Efficacy of influenza vaccine (Fluvax) in cancer patients on treatment: a prospective single arm, open-label study

PURPOSE

Influenza virus infection has significant morbidity and mortality in patients with medical co-morbidities who are also immunosuppressed. The efficacy of the seasonal influenza vaccine has not been well studied in patients receiving chemotherapy. We assessed the efficacy of seasonal influenza vaccine in patients with non-haematological malignancy on active treatment (chemotherapy and targeted therapy).

METHODS

A prospective single arm, open label study with 53 patients with non-haematological cancers recruited during the 2011 and 2012 influenza seasons. Participants had one dose of 2011/2012 trivalent vaccine containing strains A/California/7/2009(H1N1), A/Perth/16/2009 (H3N2) and B/Brisbane/60/2008 (Fluvax) prior to or in-between treatment cycles. Haemagglutination inhibition antibody (HIA) titres in serum were measured at baseline 3, 6 and 24 weeks. Primary endpoint: seroconversion rate (SCR) at 3 weeks. Secondary endpoints: late SCR at 6 weeks. rate of sustained sero-protection titres (SPR) at 24 weeks. Seroconversion was defined as postvaccination ≥ 4-fold increase in HIA titre and sero-protection defined as a HIA ≥ 1:40.

RESULTS

The SCR at 3 weeks were 35%, 30% and 22.5% to the H1N1, H3N2 and B/Bris strains, respectively. There were no new cases of late SC at 6 weeks or 24 weeks. The SPR at 3 weeks were 72.5%, 65% and 40%, respectively, to H1N1, H3N2 and B/Bris. The SPR at 24 weeks to H1N1, H3N2 and B/Bris were 40%, 52.5% and 17.5%, respectively.

CONCLUSIONS

Patients on various solid tumour treatments achieve sero-protection rate congruent with the general population. The sero-protection HIA titres were not sustained at 24 weeks postvaccination.

Effect of pericardial effusion on outcomes in children admitted with systemic lupus erythematosus: a multicenter retrospective cohort study from the United States

OBJECTIVE

We sought to describe characteristics of children admitted with pericardial effusion (PCE) and systemic lupus erythematosus (SLE) and determine the association between PCE and outcomes of interest.

METHODS

We performed a retrospective cohort study of the Pediatric Health Information System (PHIS). Patients were included if they were admitted to a PHIS participating hospital from 2004 to 2015 with a diagnosis of SLE and age ≤18 years. Children with congenital heart disease or who had undergone heart surgery were excluded. PCE was the primary predictor variable; multivariable analysis was used to evaluate the effect of PCE on the following outcomes: mortality, length of stay (LOS), and readmission within 30 days.

RESULTS

There were 5679 admissions, of which 705 (12.4%) had PCE. Median age at admission was 15 years (interquartile range: 13-17). There were no significant differences for age or sex between patients admitted either with or without PCE. A significantly higher percentage of children in the PCE group were black compared with those without PCE (43% vs. 31%, p < 0.001). In multivariable analysis, the odds of a black patient having PCE were 1.7 higher than non-black patients ( p < 0.001). In-hospital mortality was 2.5 times higher in children with PCE compared with those without PCE ( p = 0.027). Those with PCE also had 1.5 greater odds of readmission within 30 days ( p < 0.001). PCE was not associated with increased LOS (0.99, p = 0.753).

CONCLUSION

PCE is common in admissions of children with SLE. There are disproportionately more black patients with SLE affected by PCE than non-black. PCE is associated with significantly higher mortality and rates of readmission.

Successful delayed-interval delivery in the presence of clinical chorioamnionitis in the leading twin: A report of two cases

We present two cases of diamniotic, dichorionic twin pregnancies in which after the loss of the first foetus in the setting of clinical chorioamnionitis, both pregnancies were successfully managed by delayed-interval delivery. A fourstage protocol including aspects of management in this specific setting is proposed. We consider the importance of a selection process when managing conservatively, measures to promote latency and decisions regarding delivery of the foetuses. Whilst we report successful case studies of conservative management with delayed-interval delivery, we support a cautious approach and understand that in the setting of clinical chorioamnionitis of the remaining foetus, delivery is necessary.

Genomic-enabled Prediction Accuracies Increased by Modeling Genotype × Environment Interaction in Durum Wheat

Genomic prediction studies incorporating genotype × environment (G×E) interaction effects are limited in durum wheat. We tested the genomic-enabled prediction accuracy (PA) of Genomic Best Linear Unbiased Predictor (GBLUP) models-six non-G × E and three G × E models-on three basic cross-validation (CV) schemes- in predicting incomplete field trials (CV2), new lines (CV1), and lines in untested environments (CV0)- in a durum wheat panel grown under yield potential, drought stress, and heat stress conditions. For CV0, three scenarios were considered: (i) leave-one environment out (CV0-Env); (ii) leave one site out (CV0-Site); and (iii) leave 1 yr out (CV0-Year). The reaction norm models with G × E effects showed higher PA than the non-G × E models. Among the CV schemes, CV2 and CV0-Env had higher PA (0.58 each) than the CV1 scheme (0.35). When the average of all the models and CV schemes were considered, among the eight traits- grain yield, thousand grain weight, grain number, days to anthesis, days to maturity, plant height, and normalized difference vegetation index at vegetative (NDVIvg) and grain filling (NDVIllg)-, plant height had the highest PA (0.68) and moderate values were observed for grain yield (0.34). The results indicated that genomic selection models incorporating G × E interaction show great promise for forward prediction and application in durum wheat breeding to increase genetic gains.

Genetic analysis of multi-environmental spring wheat trials identifies genomic regions for locus-specific trade-offs for grain weight and grain number

GWAS on multi-environment data identified genomic regions associated with trade-offs for grain weight and grain number. Grain yield (GY) can be dissected into its components thousand grain weight (TGW) and grain number (GN), but little has been achieved in assessing the trade-off between them in spring wheat. In the present study, the Wheat Association Mapping Initiative (WAMI) panel of 287 elite spring bread wheat lines was phenotyped for GY, GN, and TGW in ten environments across different wheat growing regions in Mexico, South Asia, and North Africa. The panel genotyped with the 90 K Illumina Infinitum SNP array resulted in 26,814 SNPs for genome-wide association study (GWAS). Statistical analysis of the multi-environmental data for GY, GN, and TGW observed repeatability estimates of 0.76, 0.62, and 0.95, respectively. GWAS on BLUPs of combined environment analysis identified 38 loci associated with the traits. Among them four loci-6A (85 cM), 5A (98 cM), 3B (99 cM), and 2B (96 cM)-were associated with multiple traits. The study identified two loci that showed positive association between GY and TGW, with allelic substitution effects of 4% (GY) and 1.7% (TGW) for 6A locus and 0.2% (GY) and 7.2% (TGW) for 2B locus. The locus in chromosome 6A (79-85 cM) harbored a gene TaGW2-6A. We also identified that a combination of markers associated with GY, TGW, and GN together explained higher variation for GY (32%), than the markers associated with GY alone (27%). The marker-trait associations from the present study can be used for marker-assisted selection (MAS) and to discover the underlying genes for these traits in spring wheat.

Correction to: Genetic analysis of multi-environmental spring wheat trials identifies genomic regions for locus-specific trade-offs for grain weight and grain number

Unfortunately, the Fig. 1 of this original article was incorrectly published. The corrected Fig. 1 is given below.

Abstract P3-05-07: Improving CAR T cell function by reversing the immunosuppressive tumor environment of breast cancer

Adoptive transfer of T cells redirected to tumor-associated antigens (TAAs) by expression of chimeric antigen receptors (CARs) can produce tumor responses, even in patients with resistant malignancies. To target breast cancer, we generated T cells expressing a CAR directed to the TAA mucin-1 (MUC1). T cells expressing this CAR (86±1.9%, n=5) specifically killed MUC1-expressing cells (MDA-MB-468 – 45.9±7.3%, MCF-7 – 36.8±3.6) but not MUC1(-) 293T cells (3.7±1.6% specific lysis, 20:1 E:T, n=3). Although these CAR T cells had potent anti-tumor activity against breast cancer cells, when exposed to the Th2-polarizing cytokine IL4 [which is upregulated in tumor samples (Oncomine, p&lt;0.05)] we observed a dramatic reduction in their cytolytic potential [IL2 - 45.9±7.3% vs IL4 - 11.3±3.7% specific lysis, 20:1 E:T ratio, n=4]. Thus, to protect our CAR.MUC1 T cells from the negative influences of IL4, we generated an inverted cytokine receptor (ICR) in which the IL4 receptor exodomain was fused to the IL7 receptor endodomain (4/7 ICR). Transgenic expression of this molecule in CAR.MUC1 T cells (55±4.8% double positive cells, n=5), restored the cytolytic function of CAR T cells (30.9±8.1% specific lysis, 20:1 E:T, n=3). Next, to determine the long term effects of this modification we co-cultured transgenic T cells with MUC1+ tumor cells and measured tumor and T cells numbers. In the presence of IL4, only double positive (CAR.MUC1-4/7) T cells expanded and eliminated the tumors in vitro and in vivo. However, upon tumor elimination, transgenic T cells rapidly contracted, demonstrating the antigen- and cytokine-dependence of the product. In conclusion, CAR.MUC1-4/7 T cells can effectively target breast cancer cells and retain their cytotoxic function even in the IL4-rich tumor microenvironment.

Citation Format: Bajgain P, Tawinwung S, Watanabe N, Sukumaran S, Anurathapan U, Heslop HE, Rooney CM, Brenner M, Leen AM, Vera JF. Improving CAR T cell function by reversing the immunosuppressive tumor environment of breast cancer [abstract]. In: Proceedings of the 2017 San Antonio Breast Cancer Symposium; 2017 Dec 5-9; San Antonio, TX. Philadelphia (PA): AACR; Cancer Res 2018;78(4 Suppl):Abstract nr P3-05-07.

Genome-Wide Association Analyses Identify QTL Hotspots for Yield and Component Traits in Durum Wheat Grown under Yield Potential, Drought, and Heat Stress Environments

Understanding the genetic bases of economically important traits is fundamentally important in enhancing genetic gains in durum wheat. In this study, a durum panel of 208 lines (comprised of elite materials and exotics from the International Maize and Wheat Improvement Center gene bank) were subjected to genome wide association study (GWAS) using 6,211 DArTseq single nucleotide polymorphisms (SNPs). The panel was phenotyped under yield potential (YP), drought stress (DT), and heat stress (HT) conditions for 2 years. Mean yield of the panel was reduced by 72% (to 1.64 t/ha) under HT and by 60% (to 2.33 t/ha) under DT, compared to YP (5.79 t/ha). Whereas, the mean yield of the panel under HT was 30% less than under DT. GWAS identified the largest number of significant marker-trait associations on chromosomes 2A and 2B with p-values 10-06 to 10-03 and the markers from the whole study explained 7-25% variation in the traits. Common markers were identified for stress tolerance indices: stress susceptibility index, stress tolerance, and stress tolerance index estimated for the traits under DT (82 cM on 2B) and HT (68 and 83 cM on 3B; 25 cM on 7A). GWAS of irrigated (YP and HT combined), stressed (DT and HT combined), combined analysis of three environments (YP + DT + HT), and its comparison with trait per se and stress indices identified QTL hotspots on chromosomes 2A (54-70 cM) and 2B (75-82 cM). This study enhances our knowledge about the molecular markers associated with grain yield and its components under different stress conditions. It identifies several marker-trait associations for further exploration and validation for marker-assisted breeding.

Correction to: Strategic crossing of biomass and harvest index-source and sink-achieves genetic gains in wheat

[This corrects the article DOI: 10.1007/s10681-017-2040-z.].

Correction to: Strategic crossing of biomass and harvest index-source and sink-achieves genetic gains in wheat

[This corrects the article DOI: 10.1007/s10681-017-2040-z.].

Impact of obstructive sleep apnea on neurological recovery after ischemic stroke: A prospective study

OBJECTIVES

The presence of obstructive sleep apnea (OSA) has been found to adversely affect the neurological recovery after acute ischemic stroke (AIS) in previous observational studies. However, in most of these studies, diagnosis of OSA was based on oximetry data alone, raising concern in the accuracy of diagnosis as well as estimation of severity. Purpose of our study was to determine the prevalence and severity of OSA (based on polysomnography and American Association of Sleep Medicine [AASM] criteria) in patients with AIS and to compare the post-stroke neurological and functional outcome, in those with and without OSA.

MATERIALS AND METHODS

A prospective single-centre study was conducted over a period of eighteen months from January 2013. The demographic and clinical data were collected, and the etiology of stroke was classified according to TOAST classification. Subsequently, all selected patients (N=99) underwent premorbid sleep status assessment by Epworth Sleepiness Scale followed by polysomnography using Resmed ApneaLink polysomnograph. Data were analyzed to find out the prevalence and severity of OSA as well as its impact on neurological recovery as assessed by National Institutes of Health Stroke Scale (NIHSS) and modified Rankin scale (mRS) at different time points, starting from admission.

RESULTS

There was a high prevalence of OSA (~60%) with a quarter of them having severe OSA. The OSA group had a significantly higher mean NIHSS score at discharge (P=.002) and significantly higher mRS score (irrespective of severity of OSA) at all points of evaluation.

CONCLUSION

Ischemic stroke patients with OSA tend to have poor neurological and functional recovery, across all segments of stroke and OSA severity.

Phenotypic and genome-wide association analysis of spike ethylene in diverse wheat genotypes under heat stress

The gaseous phytohormone ethylene plays an important role in spike development in wheat (Triticum aestivum). However, the genotypic variation and the genomic regions governing spike ethylene (SET) production in wheat under long-term heat stress remain unexplored. We investigated genotypic variation in the production of SET and its relationship with spike dry weight (SDW) in 130 diverse wheat elite lines and landraces under heat-stressed field conditions. We employed an Illumina iSelect 90K single nucleotide polymorphism (SNP) genotyping array to identify the genetic loci for SET and SDW through a genome-wide association study (GWAS) in a subset of the Wheat Association Mapping Initiative (WAMI) panel. The SET and SDW exhibited appreciable genotypic variation among wheat genotypes at the anthesis stage. There was a strong negative correlation between SET and SDW. The GWAS uncovered five and 32 significant SNPs for SET, and 22 and 142 significant SNPs for SDW, in glasshouse and field conditions, respectively. Some of these SNPs closely localized to the SNPs for plant height, suggesting close associations between plant height and spike-related traits. The phenotypic and genetic elucidation of SET and its relationship with SDW supports future efforts toward gene discovery and breeding wheat cultivars with reduced ethylene effects on yield under heat stress.

Genomic Prediction with Pedigree and Genotype × Environment Interaction in Spring Wheat Grown in South and West Asia, North Africa, and Mexico

Developing genomic selection (GS) models is an important step in applying GS to accelerate the rate of genetic gain in grain yield in plant breeding. In this study, seven genomic prediction models under two cross-validation (CV) scenarios were tested on 287 advanced elite spring wheat lines phenotyped for grain yield (GY), thousand-grain weight (GW), grain number (GN), and thermal time for flowering (TTF) in 18 international environments (year-location combinations) in major wheat-producing countries in 2010 and 2011. Prediction models with genomic and pedigree information included main effects and interaction with environments. Two random CV schemes were applied to predict a subset of lines that were not observed in any of the 18 environments (CV1), and a subset of lines that were not observed in a set of the environments, but were observed in other environments (CV2). Genomic prediction models, including genotype × environment (G×E) interaction, had the highest average prediction ability under the CV1 scenario for GY (0.31), GN (0.32), GW (0.45), and TTF (0.27). For CV2, the average prediction ability of the model including the interaction terms was generally high for GY (0.38), GN (0.43), GW (0.63), and TTF (0.53). Wheat lines in site-year combinations in Mexico and India had relatively high prediction ability for GY and GW. Results indicated that prediction ability of lines not observed in certain environments could be relatively high for genomic selection when predicting G×E interaction in multi-environment trials.

Pregnancy screening prior to chemotherapy administration

A retrospective case notes review was performed to determine compliance with screening for undetected pregnancy prior to commencement of chemotherapy at Flinders Medical Centre. All female patients aged 18-55 who commenced chemotherapy between January and December 2014 were included. During the first 12 months, for women identified as having childbearing potential, pre-chemotherapy pregnancy screening was performed only in 40% of patients under 40 years and in 20.5% of the entire age range.

Delayed onset of benign pleural effusion following concurrent chemoradiotherapy for inoperable non-small-cell lung cancer

Chronic benign pleural effusion (BPE) is a rare complication of concurrent chemoradiotherapy (CRT) for inoperable stage IIIA non-small-cell lung cancer (NSCLC). This report presents three cases of BPE, the workup to differentiate this benign condition from recurrence of cancer and recommends a pleural biopsy as part of the diagnostic process. These inflammatory exudates often remain indolent, and may not require drainage or surgical intervention. In the absence of clinical, radiological and pathological evidence of recurrent disease, we recommend clinicians manage these patients expectantly, using regular clinical assessment and imaging.

Genetic characterization of the wheat association mapping initiative (WAMI) panel for dissection of complex traits in spring wheat

The wheat association mapping initiative is appropriate for gene discovery without the confounding effects of phenology and plant height. The wheat association mapping initiative (WAMI) population is a set of 287 diverse advanced wheat lines with a narrow range of variation for days to heading (DH) and plant height (PH). This study aimed to characterize the WAMI and showed that this diverse panel has a favorable genetic background in which stress adaptive traits and their alleles contributing to final yield can be identified with reduced confounding major gene effects through genome-wide association studies (GWAS). Using single nucleotide polymorphism (SNP) markers, we observed lower gene diversity on the D genome, compared with the other genomes. Population structure was primarily related to the distribution of the 1B.1R rye translocation. The narrow range of variation for DH and PH in the WAMI population still entailed segregation for a few markers associated with the former traits, while Rht genes were associated with grain yield (GY). Genotype by environment (G × E) interaction for GY was primarily explained by Rht-B1, Vrn-A1 and markers on chromosomes 2D and 3A when running GWAS with genotype scores from the G × E biplot. The use of PC scores from the G × E biplot seems a promising tool to determine genes and markers associated with complex interactions across environments. The WAMI panel lends itself to GWAS for complex trait dissection by avoiding the confounding effects of DH and PH which were reduced to a minimum (using Rht-B1 and Vrn-A1 scores as covariables), with significant associations with GY on chromosomes 2D, 3A and 3B.

Genome-wide association study for grain yield and related traits in an elite spring wheat population grown in temperate irrigated environments

Through genome-wide association study, loci for grain yield and yield components were identified in chromosomes 5A and 6A in spring wheat (Triticum aestivum). Genome-wide association study (GWAS) was conducted for grain yield (YLD) and yield components on a wheat association mapping initiative (WAMI) population of 287 elite, spring wheat lines grown under temperate irrigated high-yield potential condition in Ciudad Obregón, Mexico, during four crop cycles (from 2009-2010 to 2012-2013). The population was genotyped with high-density Illumina iSelect 90K single nucleotide polymorphisms (SNPs) assay. An analysis of traits across subpopulations indicated that lines with 1B/1R translocation had higher YLD, grain weight, and taller plants than lines without the translocation. GWAS using 18,704 SNPs identified 31 loci that explained 5-14 % of the variation in individual traits. We identified SNPs in chromosome 5A and 6A that were significantly associated with yield and yield components. Four loci were detected for YLD in chromosomes 3B, 5A, 5B, and 6A and the locus in 5A explained 5 % of the variation for grain number/m(2). The locus for YLD in chromosome 6A also explained 6 % of the variation in grain weight. Loci significantly associated with maturity were identified in chromosomes 2B, 3B, 4B, 4D, and 6A and for plant height in 1A and 6A. Loci were also detected for canopy temperature at grain filling (2D, 4D, 6A), chlorophyll index at grain filling (3B and 6A), biomass (3D and 6A) and harvest index (1D, 1B, and 3B) that explained 5-10 % variation. These markers will be further validated.

Screening, diagnosis and management of gestational diabetes mellitus: A national survey

BACKGROUND AND METHODS

We conducted a National survey between February and June 2012 to evaluate the practices concerning screening, diagnosis and management of Gestational Diabetes (GDM) in England.

RESULTS

A total of 102/126 (80%) maternity units responded. The National Institute of Health and Clinical Excellence (NICE) recommended screening criteria were used by 83% of units. All the units performed 2 h 75 g oral glucose tolerance test (OGTT) between 24 and 28 weeks. There was a wide variation in the diagnostic blood glucose values used by different units. About 86% of units used a 2 h blood glucose value of ≥7.8 mmol/l and 45% of units used fasting value ≥6.1 mmol/l to diagnose GDM. Only 26% of units advised self-monitoring of blood glucose pre meal and 1 h post-meal, whereas 64% of units advised monitoring 2 h after the meal. Metformin was started when women did not respond to dietary measures in 101 units (99%). Regular growth scans every four weeks from 28 weeks onwards were performed by 99 units (97%). Women on metformin with no complications were offered induction of labour at 38 completed weeks in 97 units (95%). 84 maternity units (82.3%) offered OGTT six weeks postnatally.

CONCLUSION

Our survey has shown consistency in screening using the NICE criteria, use of 2 h 75 g OGTT at 24-28 weeks, in providing dietary support, use of metformin and ultrasound for fetal growth. But there is wide variation in the criteria used to diagnose GDM, self-monitoring of blood glucose, induction of labour and six weeks postnatal testing.

Phytochemical constituents and antibacterial efficacy of the flowers of Peltophorum pterocarpum (DC.) Baker ex Heyne

OBJECTIVE

To investigate the preliminary phytochemistry and antibacterial activity of the flower extract of Peltophorum pterocarpum .

METHODS

Phytochemical analysis was done by using the standard methods given by Harbone. The methanolic flower extract were tested against Escherichia coli, Klebsiella pneumonia, Pseudomonas aeruginosa, Staphylococcus aureus, Bacillus cereus, Salmonella typhi, Serratia marsecens, Acinetobacter baumannii, Enterobacter sp., Proteus mirabilis, Enterococcus faecalis and Streptococcus pyogenes by the agar disc diffusion method.

RESULTS

Preliminary phytochemical screening of flower extract showed the presence of phenolic compounds, flavonoids, saponins, steroids, tannins, xanthoproteins, carboxylic acids, coumarins and carbohydrates. The flower extract of Peltophorum pterocarpum showed significant activity against four gram positive (Staphylococcus aureus, Bacillus cereus, Enterococcus faecalis and Streptococcus pyogenes) and three gram negative bacteria (Proteus mirabilis, Acinetobacter baumannii and Serratia marsecens), out of 12 pathogenic bacteria studied.

CONCLUSIONS

The findings of the present study confirm the presence of significant antibacterial activity against human pathogens in the flowers of Peltophorum pterocarpum.

Population structure and marker-trait association analysis of the US peanut (Arachis hypogaea L.) mini-core collection

Peanut (Arachis hypogaea L.) is one of the most important oilseed and nutritional crops in the world. To efficiently utilize the germplasm collection, a peanut mini-core containing 112 accessions was established in the United States. To determine the population structure and its impact on marker-trait association, this mini-core collection was assessed by genotyping 94 accessions with 81 SSR markers and two functional SNP markers from fatty acid desaturase 2 (FAD2). Seed quality traits (including oil content, fatty acid composition, flavonoids, and resveratrol) were obtained through nuclear magnetic resonance (NMR), gas chromatography (GC), and high-performance liquid chromatography (HPLC) analysis. Genetic diversity and population structure analysis identified four major subpopulations that are related to four botanical varieties. Model comparison with different levels of population structure and kinship control was conducted for each trait and association analyses with the selected models verified that the functional SNP from the FAD2A gene is significantly associated with oleic acid (C18:1), linoleic acid (C18:2), and oleic-to-linoleic (O/L) ratio across this diverse collection. Even though the allele distribution of FAD2A was structured among the four subpopulations, the effect of FAD2A gene remained significant after controlling population structure and had a likelihood-ratio-based R ( 2 ) (R ( LR ) ( 2 ) ) value of 0.05 (oleic acid), 0.09 (linoleic acid), and 0.07 (O/L ratio) because the FAD2A alleles were not completely fixed within subpopulations. Our genetic analysis demonstrated that this peanut mini-core panel is suitable for association mapping. Phenotypic characterization for seed quality traits and association testing of the functional SNP from FAD2A gene provided information for further breeding and genetic research.

Capecitabine and irinotecan (XELIRI) in first-line treatment of metastatic colorectal cancer (mCRC): A systematic review of controlled clinical trials

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Background: Irinotecan and 5-Fluorouracil based combination is an effective regimen for mCRC. Capecitabine, an oral fluoropyrimidine, is a convenient alternative to intravenous 5- Fluorouracil. This study aims to systematically review all published and unpublished controlled phase II and III trials of XELIRI combination, used in first line treatment of mCRC, reported from 2000–2008, to describe its efficacy and safety. Methods: A literature search of MEDLINE, EMBASE, CINAHL and proceedings from ASCO, ESMO and WGIC was conducted. The primary end point was response rate (RR), secondary endpoints include: time to progression (TTP), overall survival (OS) and toxicity. Results: Thirty non-randomised phase II trials (n = 1380) along with 6 randomised phase II and 3 phase III trials, were included (pooled n = 1478). The daily dose of capecitabine ranged from 1,800 mg/m2 to 2,500 mg/m2 for 7 to 14 days per cycle and the dose of irinotecan varied from 180mg/m2 to 350 mg/m2, over a 3 week period per cycle. Amongst the non-randomised studies, the median patient age was 61 years (53–72).The median RR was 46.75% (25–78%). The median reported TTP was 7.9 months (mo) (5- 9.9 mo) and the median OS was 15.6 months (7–24.8 mo). Grade 3–4 toxicity incidence was: diarrhoea (21.5%), neutropenia (12%), vomiting (12.5%), fatigue (6%) and Hand-foot syndrome (6%). The pooled incidence of febrile neutropenia was 2.5%. Amongst the randomised trials, the comparator regimens were XELOX or FOLFIRI. Median age was 65 years (61–74). RR for XELIRI was 39% (34–56%) compared to 47% (27–61.8%) for the non XELIRI comparator arms. Median reported TTP was 8.2 mo (5.7–12.5 mo) for the XELIRI arms and 9.2 mo for the comparator arms. Conclusions: XELIRI is an effective and feasible regime in the first line management of mCRC. However the optimal role of this combination remains to be established.

No significant financial relationships to disclose.

Structure-function correlation of outer membrane protein porin from Paracoccus denitrificans

Porins from outer membrane of Gram-negative bacteria have a highly stable structure. Our previous studies on porin from Paracoccus denitrificans showed that the outer membrane protein porin is extremely stable toward heat, pH, and chemical denaturants. The major question we have addressed in this paper is whether the high stability of porin is a consequence of the beta-barrel structure and whether it is required for its function. To explain this we have analyzed two cases: first, we used porin wild-type and mutants and compared their structure and function; second, we compared the activity of porin preheated to different temperatures. Structural changes were monitored by infrared spectroscopy. We observed that the structural stability of porin is not equivalent to functional activity as minor alteration in the structure can result in drastic differences in the activity of porins.

Safety of newer generation anti-epileptic drugs in non-accidental overdose: an Irish population study

Seven new anti-epileptic drugs (AEDs) have become available in Ireland over the last 10 years; data from animal models and clinical trials suggest that they have a superior safety profile to older AEDs. A specific relationship between epilepsy and psychiatric co-morbidity has long been recognised, including the relationship between epilepsy and suicide. AEDs are common agents taken in intentional drug overdoses. We undertook a study to review the frequency and outcome of non-accidental overdose with seven new AEDS in an Irish population from 1996 to 2000.

METHOD

All reported cases of drug overdoses with AEDs from 1996 to 2000 were reviewed. Data was provided by the National Poisons Information Centre, Beaumont Hospital and the Central Statistics Office. Medical records from Beaumont Hospital were reviewed in specific cases of serious drug toxicities. An extensive review of published literature reviewing the safety profile of these AEDs was performed and medical literature retrieved from the databases of the pharmaceutical industry was similarly reviewed.

RESULTS

Of the 164 reported cases of newer AEDs, there were no fatalities among the cases followed up.

CONCLUSION

The absence of mortalities and serious consequences from deliberate self-poisoning with the newer agents is supportive evidence for the superior safety profile of the newer AEDs.