Transcriptome analysis of grain development in hexaploid wheat

Background: Hexaploid wheat is one of the most important cereal crops for human nutrition. Molecular understanding of the biology of the developing grain will assist the improvement of yield and quality traits for different environments. High quality transcriptomics is a powerful method to increase this understanding. Results: The transcriptome of developing caryopses from hexaploid wheat ( Triticum aestivum, cv. Hereward) was determined using Affymetrix wheat GeneChip (R) oligonucleotide arrays which have probes for 55,052 transcripts. Of these, 14,550 showed significant differential regulation in the period between 6 and 42 days after anthesis ( daa). Large changes in transcript abundance were observed which were categorised into distinct phases of differentiation ( 6 - 10 daa), grain fill ( 12 - 21 daa) and desiccation/maturation ( 28 - 42 daa) and were associated with specific tissues and processes. A similar experiment on developing caryopses grown with dry and/or hot environmental treatments was also analysed, using the profiles established in the first experiment to show that most environmental treatment effects on transcription were due to acceleration of development, but that a few transcripts were specifically affected. Transcript abundance profiles in both experiments for nine selected known and putative wheat transcription factors were independently confirmed by real time RT-PCR. These expression profiles confirm or extend our knowledge of the roles of the known transcription factors and suggest roles for the unknown ones. Conclusion: This transcriptome data will provide a valuable resource for molecular studies on wheat grain. It has been demonstrated how it can be used to distinguish general developmental shifts from specific effects of treatments on gene expression and to diagnose the probable tissue specificity and role of transcription factors

Cross-Sample Validation Provides Enhanced Proteome Coverage in Rat Vocal Fold Mucosa

The vocal fold mucosa is a biomechanically unique tissue comprised of a densely cellular epithelium, superficial to an extracellular matrix (ECM)-rich lamina propria. Such ECM-rich tissues are challenging to analyze using proteomic assays, primarily due to extensive crosslinking and glycosylation of the majority of high Mr ECM proteins. In this study, we implemented an LC-MS/MS-based strategy to characterize the rat vocal fold mucosa proteome. Our sample preparation protocol successfully solubilized both proteins and certain high Mr glycoconjugates and resulted in the identification of hundreds of mucosal proteins. A straightforward approach to the treatment of protein identifications attributed to single peptide hits allowed the retention of potentially important low abundance identifications (validated by a cross-sample match and de novo interpretation of relevant spectra) while still eliminating potentially spurious identifications (global single peptide hits with no cross-sample match). The resulting vocal fold mucosa proteome was characterized by a wide range of cellular and extracellular proteins spanning 12 functional categories

To bite or not to bite! A questionnaire-based survey assessing why some people are bitten more than others by midges

BACKGROUND: The Scottish biting midge, Culicoides impunctatus, responsible for more than 90% of biting attacks on human beings in Scotland, is known to demonstrate a preference for certain human hosts over others. METHODS: In this study we used a questionnaire-based survey to assess the association between people's perception of how badly they get bitten by midges and their demographic, lifestyle and health related characteristics. RESULTS: Most people (85.8%) reported being bitten sometimes, often or always with only 14.2% reporting never being bitten by midges when in Scotland. There was no association between level of bites received and age, smoking, diet, exercise, medication, eating strongly flavoured foods or alcohol consumption. However, there was a strong association between the probability of being bitten and increasing height (in men) and BMI (in women). A large proportion of participants (33.8%) reported experiencing a bad/severe reaction to midge bites while 53.1% reported a minor reaction and 13.1% no reaction at all. Also, women tend to react more than men to midge bites. Additionally, the results indicated that the susceptibility to being bitten by midges is hereditary. CONCLUSIONS: This study suggests that midges prefer to bite men that are tall and women that have a large BMI, and that the tendency for a child to be bitten or not could be inherited from their parent. The study is questionnaire-based; therefore, the interpretation of the results may be limited by the subjectivity of the answers given by the respondents. Although the results are relevant only to the Scottish biting midge, the approach used here could be useful for investigating human-insect interactions for other insects, particularly those which transmit pathogens that cause disease

Safety, immunogenicity, and reactogenicity of BNT162b2 and mRNA-1273 COVID-19 vaccines given as fourth-dose boosters following two doses of ChAdOx1 nCoV-19 or BNT162b2 and a third dose of BNT162b2 (COV-BOOST): a multicentre, blinded, phase 2, randomised trial

Background Some high-income countries have deployed fourth doses of COVID-19 vaccines, but the clinical need, effectiveness, timing, and dose of a fourth dose remain uncertain. We aimed to investigate the safety, reactogenicity, and immunogenicity of fourth-dose boosters against COVID-19.Methods The COV-BOOST trial is a multicentre, blinded, phase 2, randomised controlled trial of seven COVID-19 vaccines given as third-dose boosters at 18 sites in the UK. This sub-study enrolled participants who had received BNT162b2 (Pfizer-BioNTech) as their third dose in COV-BOOST and randomly assigned them (1:1) to receive a fourth dose of either BNT162b2 (30 µg in 0·30 mL; full dose) or mRNA-1273 (Moderna; 50 µg in 0·25 mL; half dose) via intramuscular injection into the upper arm. The computer-generated randomisation list was created by the study statisticians with random block sizes of two or four. Participants and all study staff not delivering the vaccines were masked to treatment allocation. The coprimary outcomes were safety and reactogenicity, and immunogenicity (antispike protein IgG titres by ELISA and cellular immune response by ELISpot). We compared immunogenicity at 28 days after the third dose versus 14 days after the fourth dose and at day 0 versus day 14 relative to the fourth dose. Safety and reactogenicity were assessed in the per-protocol population, which comprised all participants who received a fourth-dose booster regardless of their SARS-CoV-2 serostatus. Immunogenicity was primarily analysed in a modified intention-to-treat population comprising seronegative participants who had received a fourth-dose booster and had available endpoint data. This trial is registered with ISRCTN, 73765130, and is ongoing.Findings Between Jan 11 and Jan 25, 2022, 166 participants were screened, randomly assigned, and received either full-dose BNT162b2 (n=83) or half-dose mRNA-1273 (n=83) as a fourth dose. The median age of these participants was 70·1 years (IQR 51·6–77·5) and 86 (52%) of 166 participants were female and 80 (48%) were male. The median interval between the third and fourth doses was 208·5 days (IQR 203·3–214·8). Pain was the most common local solicited adverse event and fatigue was the most common systemic solicited adverse event after BNT162b2 or mRNA-1273 booster doses. None of three serious adverse events reported after a fourth dose with BNT162b2 were related to the study vaccine. In the BNT162b2 group, geometric mean anti-spike protein IgG concentration at day 28 after the third dose was 23 325 ELISA laboratory units (ELU)/mL (95% CI 20 030–27 162), which increased to 37 460 ELU/mL (31 996–43 857) at day 14 after the fourth dose, representing a significant fold change (geometric mean 1·59, 95% CI 1·41–1·78). There was a significant increase in geometric mean anti-spike protein IgG concentration from 28 days after the third dose (25 317 ELU/mL, 95% CI 20 996–30 528) to 14 days after a fourth dose of mRNA-1273 (54 936 ELU/mL, 46 826–64 452), with a geometric mean fold change of 2·19 (1·90–2·52). The fold changes in anti-spike protein IgG titres from before (day 0) to after (day 14) the fourth dose were 12·19 (95% CI 10·37–14·32) and 15·90 (12·92–19·58) in the BNT162b2 and mRNA-1273 groups, respectively. T-cell responses were also boosted after the fourth dose (eg, the fold changes for the wild-type variant from before to after the fourth dose were 7·32 [95% CI 3·24–16·54] in the BNT162b2 group and 6·22 [3·90–9·92] in the mRNA-1273 group).Interpretation Fourth-dose COVID-19 mRNA booster vaccines are well tolerated and boost cellular and humoral immunity. Peak responses after the fourth dose were similar to, and possibly better than, peak responses after the third dose

A variance shift model for detection of outliers in the linear mixed model

A variance shift outlier model (VSOM), previously used for detecting outliers in the linear model, is extended to the variance components model. This VSOM accommodates outliers as observations with inflated variance, with the status of the ith observation as an outlier indicated by the size of the associated shift in the variance. Likelihood ratio and score test statistics are assessed as objective measures for determining whether the ith observation has inflated variance and is therefore an outlier. It is shown that standard asymptotic distributions do not apply to these tests for a VSOM, and a modified distribution is proposed. A parametric bootstrap procedure is proposed to account for multiple testing. The VSOM framework is extended to account for outliers in random effects and is shown to have an advantage over case-deletion approaches. A simulation study is presented to verify the performance of the proposed tests. Challenges associated with computation and extensions of the VSOM to the general linear mixed model with correlated errors are discussed.Likelihood ratio test Linear mixed model Multiple testing Outlier detection REML Score test Variance shift outlier model

The analysis of longitudinal data using mixed model L-splines.

L-splines are a large family of smoothing splines defined in terms of a linear differential operator. This article develops L-splines within the context of linear mixed models and uses the resulting mixed model L-spline to analyze longitudinal data from a grassland experiment. In the spirit of time-series analysis, a periodic mixed model L-spline is developed, which partitions data into a smooth periodic component plus smooth long-term trend

The Analysis of Designed Experiments and Longitudinal Data by Using Smoothing Splines

In designed experiments and in particular longitudinal studies, the aim may be to assess the effect of a quantitative variable such as time on treatment effects. Modelling treatment effects can be complex in the presence of other sources of variation. Three examples are presented to illustrate an approach to analysis in such cases. The first example is a longitudinal experiment on the growth of cows under a factorial treatment structure where serial correlation and variance heterogeneity complicate the analysis. The second example involves the calibration of optical density and the concentration of a protein DNase in the presence of sampling variation and variance heterogeneity. The final example is a multienvironment agricultural field experiment in which a yield-seeding rate relationship is required for several varieties of lupins. Spatial variation within environments, heterogeneity between environments and variation between varieties all need to be incorporated in the analysis. In this paper, the cubic smoothing spline is used in conjunction with fixed and random effects, random coefficients and variance modelling to provide simultaneous modelling of trends and covariance structure. The key result that allows coherent and flexible empirical model building in complex situations is the linear mixed model representation of the cubic smoothing spline. An extension is proposed in which trend is partitioned into smooth and nonsmooth components. Estimation and inference, the analysis of the three examples and a discussion of extensions and unresolved issues are also presented

A COMPARISON OF MIXED MODEL SPLINES FOR CURVE FITTING

Three types of polynomial mixed model splines have been proposed: smoothing splines, P-splines and penalized splines using a truncated power function basis. The close connections between these models are demonstrated, showing that the default cubic form of the splines differs only in the penalty used. A general definition of the mixed model spline is given that includes general constraints and can be used to produce natural or periodic splines. The impact of different penalties is demonstrated by evaluation across a set of functions with specific features, and shows that the best penalty in terms of mean squared error of prediction depends on both the form of the underlying function and the signal:noise ratio

Three-point appraisal of genetic linkage maps

This paper develops a simple diagnostic for the investigation of uncertainty within genetic linkage maps using a Bayesian procedure. The method requires only the genotyping data and the proposed genetic map, and calculates the posterior probability for the possible orders of any set of three markers, accounting for the presence of genotyping error (mistyping) and for missing genotype data. The method uses a Bayesian approach to give insight into conflicts between the order in the proposed map and the genotype scores. The method can also be used to assess the accuracy of a genetic map at different genomic scales and to assess alternative potential marker orders. Simulation and two case studies were used to illustrate the method. In the first case study, the diagnostic revealed conflicts in map ordering for short inter-marker distances that were resolved at a distance of 8–12 cM, except for a set of markers at the end of the linkage group. In the second case study, the ordering did not resolve as distances increase, which could be attributed to regions of the map where many individuals were untyped