Complex genetic architecture underlying the plasticity of maize agronomic traits

Phenotypic plasticity is the ability of a given genotype to produce multiple phenotypes in response to changing environmental conditions. Understanding the genetic basis of phenotypic plasticity and establishing a predictive model is highly relevant to future agriculture under a changing climate. Here we report findings on the genetic basis of phenotypic plasticity for 23 complex traits using a diverse maize population planted at five sites with distinct environmental conditions. We found that latitude -related environmental factors were the main drivers of across-site variation in flowering time traits but not in plant architecture or yield traits. For the 23 traits, we detected 109 quantitative trait loci (QTLs), 29 for mean values, 66 for plasticity, and 14 for both parameters, and 80% of the QTLs interacted with latitude. The effects of several QTLs changed in magnitude or sign, driving variation in phenotypic plasticity. We experimentally validated one plastic gene, ZmTPS14.1, whose effect was likely mediated by the compen-sation effect of ZmSPL6 from a downstream pathway. By integrating genetic diversity, environmental vari-ation, and their interaction into a joint model, we could provide site-specific predictions with increased accuracy by as much as 9.9%, 2.2%, and 2.6% for days to tassel, plant height, and ear weight, respectively. This study revealed a complex genetic architecture involving multiple alleles, pleiotropy, and genotype-by -environment interaction that underlies variation in the mean and plasticity of maize complex traits. It provides novel insights into the dynamic genetic architecture of agronomic traits in response to changing environments, paving a practical way toward precision agriculture

Molecular Dynamics Analysis Reveals Structural Insights into Mechanism of Nicotine N-Demethylation Catalyzed by Tobacco Cytochrome P450 Mono-Oxygenase

CYP82E4, a cytochrome P450 monooxygenase, has nicotine N-demethylase (NND) activity, which mediates the bioconversion of nicotine into nornicotine in senescing tobacco leaves. Nornicotine is a precursor of the carcinogen, tobacco-specific nitrosamine. CYP82E3 is an ortholog of CYP82E4 with 95% sequence identity, but it lacks NND activity. A recent site-directed mutagenesis study revealed that a single amino acid substitution, i.e., cysteine to tryptophan at the 330 position in the middle of protein, restores the NND activity of CYP82E3 entirely. However, the same amino acid change caused the loss of the NND activity of CYP82E4. To determine the mechanism of the functional turnover of the two molecules, four 3D structures, i.e., the two molecules and their corresponding cys–trp mutants were modeled. The resulting structures exhibited that the mutation site is far from the active site, which suggests that no direct interaction occurs between the two sites. Simulation studies in different biological scenarios revealed that the mutation introduces a conformation drift with the largest change at the F-G loop. The dynamics trajectories analysis using principal component analysis and covariance analysis suggests that the single amino acid change causes the opening and closing of the transfer channels of the substrates, products, and water by altering the motion of the F-G and B-C loops. The motion of helix I is also correlated with the motion of both the F-G loop and the B-C loop and; the single amino acid mutation resulted in the curvature of helix I. These results suggest that the single amino acid mutation outside the active site region may have indirectly mediated the flexibility of the F-G and B-C loops through helix I, causing a functional turnover of the P450 monooxygenase

The attention modulation on timing: an event-related potential study.

The present study examined the neural mechanisms of attention modulation on timing using ERP and sLORETA measurements in a dual-task paradigm. We parametrically varied the attention to the durations of a 1000-Hz pure tone and further localized the cortical regions that were sensitive to the attention modulation on timing. Results demonstrated that the attention modulation might happen at early stage, approximately 200 ms after stimulus presentation. The P2 component at frontal area served as an early neural correlate of attention effects on timing. More importantly, the contingent negative variation (CNV) appeared at fronto-central area was sensitive to the attention effect. In addition, the supplementary motor area (SMA) was assumed to be one of the key regions for selectively attending to and estimating time. These findings provide temporal and spatial correlates of attention-modulated time processing and potentially help to investigate the neural mechanisms of patients with time perception deficits

Exploring the roles of ZmARM gene family in maize development and abiotic stress response

Armadillo (ARM) was a gene family important to plants, with crucial roles in regulating plant growth, development, and stress responses. However, the properties and functions of ARM family members in maize had received limited attention. Therefore, this study employed bioinformatics methods to analyze the structure and evolution of ARM-repeat protein family members in maize. The maize (Zea mays L.) genome contains 56 ARM genes distributed over 10 chromosomes, and collinearity analysis indicated 12 pairs of linkage between them. Analysis of the physicochemical properties of ARM proteins showed that most of these proteins were acidic and hydrophilic. According to the number and evolutionary analysis of the ARM genes, the ARM genes in maize can be divided into eight subgroups, and the gene structure and conserved motifs showed similar compositions in each group. The findings shed light on the significant roles of 56 ZmARM domain genes in development and abiotic stress, particularly drought stress. RNA-Seq and qRT-PCR analysis revealed that drought stress exerts an influence on specific members of the ZmARM family, such as ZmARM4, ZmARM12, ZmARM34 and ZmARM36. The comprehensive profiling of these genes in the whole genome, combined with expression analysis, establishes a foundation for further exploration of plant gene function in the context of abiotic stress and reproductive development

Illustration of the experimental procedure.

<p>A, Practice phase I. B, Practice phase ii. C, the formal experiment. The ERP data were collected in response to the 1000-Hz tones with 1.5- and 2.5-s durations. D, the five attentional cues used in this study.</p

Distribution of ERP measurements in different attention conditions (data are collected at the electrode of FCz).

<p>A, the distribution of P2 amplitudes. The three horizontal lines in every box reflect the lower quartile (25%), median (50%), and upper quartile (75%) of the P2 amplitudes (refer to the legend of <a href="http://www.plosone.org/article/info:doi/10.1371/journal.pone.0066190#pone-0066190-g002" target="_blank">Figure 2</a> for more details). B, the distribution of CNV amplitudes. C, the average and 95% confidential interval (CI) of the ERPs in response to the 1.5-s tone. For the sake of brevity, only the ERPs in the T and the P conditions are displayed. D, the average and 95% CI of the ERPs in response to the 2.5-s tone.</p

sLORETA images of the standardized current density maximum in the T vs. the P attention conditions.

<p>A, the results at the time interval of P2 (180-220 ms). B, the results at the time interval of CNV (800-1600 ms). The color scale is equal in all the maps, of which the strongest activations are indexed in yellow.</p

Potential impact of B lineage mismatch on trivalent influenza vaccine effectiveness during the 2015–2016 influenza season among nursery school children in Suzhou, China

Background: We actively followed a cohort of nursery school children in Suzhou, China to assess the impact of vaccination with trivalent influenza vaccine on the prevention of influenza like illness (ILI). Methods: We enrolled children aged 36 to 72 months from 13 nursery schools in Suzhou starting two weeks after vaccination during October 2015-February 2016. Every school-day, teachers reported the names of students with ILI to study clinicians, who collected the student's nasopharyngeal swab or throat swab, either at a study clinic or the child's home. Swabs were sent to the Suzhou Center for Disease Control and Prevention's laboratory for influenza testing by RT-PCR. Results: In total, 3278 children were enrolled; 83 (3%) were lost to follow-up, while 3195 (vaccinated: 1492, unvaccinated: 1703) were followed for 24 weeks. During the study, 40 samples tested positive; 17 in the vaccinated (B Victoria: 12; A(H1N1)pdm09: 5) and 23 in the unvaccinated group (B Victoria: 10; B Yamagata: 2; A(H1N1)pdm09: 11). The VE estimates were: 16% overall (95%CI:-58%,56%), 48% (−47%,84%) for influenza A(H1N1)pdm09, 43% (−650%,98%) for influenza B Yamagata, and −37% (−227%,42%) for influenza B Victoria. Data were analyzed by vaccinated and unvaccinated groups based on enrollees' vaccination records. Conclusions: The VE for A(H1N1)pdm09 was moderate but not significant. Mismatching of B lineage may have compromised trivalent influenza vaccine effectiveness during the 2015–2016 influenza season among nursery school children in Suzhou, China. Additional larger studies are warranted to inform policy related to quadrivalent influenza vaccine licensure in China in the future

Grand-mean ERP waveforms and topographies of the P2 and CNV components.

<p>A, the P2 topography at 180-220 ms post-stimuli. B: the CNV topography at 800-1600 ms post-stimuli. C, the ERP waveforms (at FCz electrode site) in response to the 1.5-s tone. D, the ERP waveforms (at FCz electrode site) in response to the 2.5-s tone.</p