Post-transcriptional regulation in root development

Overcoming resistance to belief revision and correction of misinformation beliefs: psychophysiological and behavioral effects of a counterfactual mindset

In a series of experiments involving beliefs and misinformation beliefs, we find that individuals who are prompted with a counterfactual mindset are significantly more likely to change their existing beliefs when presented with evidence that contradicts their beliefs. While research finds that beliefs that are considered part of one's identity are highly resistant to change in the face of evidence that challenges these beliefs, four experiments provide evidence that counterfactual generation causes individuals to adjust beliefs and correct misinformation beliefs in response to contradicting evidence. Indeed, we find that a counterfactual mindset was effective in promoting incorporation of accurate facts and causing individuals to revise misinformation beliefs about COVID vaccination safety for a large sample of individuals who have rejected COVID vaccinations. Finally, the results of the psychophysiological experiment reveal that counterfactual generation alters decision makers' search strategies, increases their cognitive arousal in response to evidence that challenges their beliefs, and increases their desire to seek out disconfirming evidence. Overall, the four experiments indicate that counterfactual generation can effectively activate mindsets that increase individuals' willingness to evaluate evidence that contradicts their beliefs and adjust their beliefs in response to evidence.

Identification and function of miRNA-mRNA interaction pairs during lateral root development of hemi-parasitic Santalum album L. seedlings

Sandalwood (Santalum album L.) is a hemi-parasitic tree species famous for its santalol and santalene, which are extracted from its heartwood and roots. The ability to understand root functionality within its branched root system would benefit the regulation of sandalwood growth and enhance the commercial value of sandalwood. Phenotypic and anatomical evidence in this study indicated that seed germination stage 4 (SG4) seemed pivotal for lateral root (LR) morphogenesis. Small RNA (sRNA) high-throughput sequencing of root tissues at three sub-stages of SG4 (lateral root primordia initiation (LRPI), lateral root primordia development (LRPD), and lateral root primordia emergence (LRPE)) was performed to identify microRNAs (miRNAs) associated with LR development. A total of 135 miRNAs, including 70 differentially expressed miRNAs (DEMs), were screened. Ten DEMs were selected to investigate transcript abundance in different organs or developmental stages. Among 100 negative DEM-mRNA interaction pairs, four targets (Sa-miR166m_2, 408d, 858a, and novel_Sa-miR8) were selected for studying cleavage sites by 5' RLM-RACE validation. The expression mode of the four miRNA-mRNA pairs was investigated after indole-3-acetic acid (IAA) treatment. IAA enhanced the abundance of homeobox-leucine-zipper protein 32 (HOX32), laccase 12 (LAC12), myeloblastosis86 (MYB86), and pectin methylesterase inhibitor6 (PMEI6) target transcripts by reducing the expression of Sa-miR166m_2, 408d, 858a, and novel_Sa-miR8 in the first 10 min. A schematic model of miRNA-regulated LR development is proposed for this hemi-parasitic species. This novel genetic information for improving sandalwood root growth and development may allow for the cultivation of fast-growing and high-yielding plantations.

Transcriptome-guided annotation and functional classification of long non-coding RNAs in Arabidopsis thaliana

Long non-coding RNAs (lncRNAs) are a prominent class of eukaryotic regulatory genes. Despite the numerous available transcriptomic datasets, the annotation of plant lncRNAs remains based on dated annotations that have been historically carried over. We present a substantially improved annotation of Arabidopsis thaliana lncRNAs, generated by integrating 224 transcriptomes in multiple tissues, conditions, and developmental stages. We annotate 6764 lncRNA genes, including 3772 that are novel. We characterize their tissue expression patterns and find 1425 lncRNAs are co-expressed with coding genes, with enriched functional categories such as chloroplast organization, photosynthesis, RNA regulation, transcription, and root development. This improved transcription-guided annotation constitutes a valuable resource for studying lncRNAs and the biological processes they may regulate.

Analysis of Whole Transcriptome RNA-seq Data Reveals Many Alternative Splicing Events in Soybean Roots under Drought Stress Conditions

Alternative splicing (AS) is a common post-transcriptional regulatory mechanism that modulates gene expression to increase proteome diversity. Increasing evidence indicates that AS plays an important role in regulating plant stress responses. However, the mechanism by which AS coordinates with transcriptional regulation to regulate drought responses in soybean remains poorly understood. In this study, we performed a genome-wide analysis of AS events in soybean (Glycine max) roots grown under various drought conditions using the high-throughput RNA-sequencing method, identifying 385, 989, 1429, and 465 AS events that were significantly differentially spliced under very mild drought stress, mild drought stress, severe drought stress, and recovery after severe drought conditions, respectively. Among them, alternative 3' splice sites and skipped exons were the major types of AS. Overall, 2120 genes that experienced significant AS regulation were identified from these drought-treated root samples. Gene Ontology term analysis indicated that the AS regulation of binding activity has vital roles in the drought response of soybean root. Notably, the genes encoding splicing regulatory factors in the spliceosome pathway and mRNA surveillance pathway were enriched according to the Kyoto Encyclopedia of Genes and Genomes pathway enrichment analysis. Splicing regulatory factor-related genes in soybean root also responded to drought stress and were alternatively spliced under drought conditions. Taken together, our data suggest that drought-responsive AS acts as a direct or indirect mode to regulate drought response of soybean roots. With further in-depth research of the function and mechanism of AS in the process of abiotic stress, these results will provide a new strategy for enhancing stress tolerance of plants.

Genome-wide analysis of long non-coding RNAs responsive to multiple nutrient stresses in Arabidopsis thaliana

Nutrient stress is the most important environmental stress that limits plant growth and development. Although recent evidence highlights the vital functions of long non-coding RNAs (lncRNA) in response to single nutrient stress in some model plants, a comprehensive investigation of the effect of lncRNAs in response to nutrient stress has not been performed in Arabidopsis thaliana. Here, we presented the identification and characterization of lncRNAs under seven nutrient stress conditions. The expression pattern analysis revealed that aberrant expression of lncRNAs is a stress-specific manner under nutrient stress conditions and that lncRNAs are more sensitive to nutrient stress than protein-coding genes (PCGs). Moreover, competing endogenous RNA (ceRNA) network and lncRNA-mRNA co-expression network (CEN) were constructed to explore the potential function of these lncRNAs under nutrient stress conditions. We further combined different expressed lncRNAs with ceRNA network and CEN to select key lncRNAs in response to nutrient stress. Together, our study provides important information for further insights into the role of lncRNAs in response to stress in plants.

Gestures convey different physiological responses when performed toward and away from the body

We assessed the sympathetic and parasympathetic activation associated to the observation of Pantomime (i.e. the mime of the use of a tool) and Intransitive gestures (i.e. expressive) performed toward (e.g. a comb and “thinking”) and away from the body (e.g. key and “come here”) in a group of healthy participants while both pupil dilation (N = 31) and heart rate variability (N = 33; HF-HRV) were recorded. Large pupil dilation was observed in both Pantomime and Intransitive gestures toward the body; whereas an increase of the vagal suppression was observed in Intransitive gestures away from the body but not in those toward the body. Our results suggest that the space where people act when performing a gesture has an impact on the physiological responses of the observer in relation to the type of social communicative information that the gesture direction conveys, from a more intimate (toward the body) to a more interactive one (away from the body).

Using task effort and pupil size to track covert shifts of visual attention independently of a pupillary light reflex

We tested the link between pupil size and the task effort involved in covert shifts of visual attention. The goal of this study was to establish pupil size as a marker of attentional shifting in the absence of luminance manipulations. In three experiments, participants evaluated two stimuli that were presented peripherally, appearing equidistant from and on opposite sides of eye fixation. The angle between eye fixation and the peripherally presented target stimuli varied from 12.5° to 42.5°. The evaluation of more distant stimuli led to poorer performance than did the evaluation of more proximal stimuli throughout our study, confirming that the former required more effort than the latter. In addition, in Experiment 1 we found that pupil size increased with increasing angle and that this effect could not be reduced to the operation of low-level visual processes in the task. In Experiment 2 the pupil dilated more strongly overall when participants evaluated the target stimuli, which required shifts of attention, than when they merely reported on the target's presence versus absence. Both conditions yielded larger pupils for more distant than for more proximal stimuli, however. In Experiment 3, we manipulated task difficulty more directly, by changing the contrast at which the target stimuli were presented. We replicated the results from Experiment 1 only with the high-contrast stimuli. With stimuli of low contrast, ceiling effects in pupil size were observed. Our data show that the link between task effort and pupil size can be used to track the degree to which an observer covertly shifts attention to or detects stimuli in peripheral vision.

ARF5/MONOPTEROS directly regulates miR390 expression in the Arabidopsis thaliana primary root meristem

The root meristem is organized around a quiescent center (QC) surrounded by stem cells that generate all cell types of the root. In the transit-amplifying compartment, progeny of stem cells further divides prior to differentiation. Auxin controls the size of this transit-amplifying compartment via auxin response factors (ARFs) that interact with auxin response elements (AuxREs) in the promoter of their targets. The microRNA miR390 regulates abundance of ARF2, ARF3, and ARF4 by triggering the production of trans-acting (ta)-siRNA from the TAS3 precursor. This miR390/TAS3/ARF regulatory module confers sensitivity and robustness to auxin responses in diverse developmental contexts and organisms. Here, we show that miR390 is expressed in the transit-amplifying compartment of the root meristem where it modulates response to exogenous auxin. We show that a single AuxRE located in miR390 promoter is necessary for miR390 expression in this compartment and identify that ARF5/MONOPTEROS (MP) binds miR390 promoter via the AuxRE. We show that interfering with ARF5/MP-dependent auxin signaling attenuates miR390 expression in the transit-amplifying compartment of the root meristem. Our results show that ARF5/MP regulates directly the expression of miR390 in the root meristem. We propose that ARF5, miR390, and the ta-siRNAs-regulated ARFs modulate the response of the transit-amplifying region of the meristem to exogenous auxin.

Pupil response hazard rates predict perceived gaze durations

We investigated the mechanisms for evaluating perceived gaze-shift duration. Timing relies on the accumulation of endogenous physiological signals. Here we focused on arousal, measured through pupil dilation, as a candidate timing signal. Participants timed gaze-shifts performed by face stimuli in a Standard/Probe comparison task. Pupil responses were binned according to “Longer/Shorter” judgements in trials where Standard and Probe were identical. This ensured that pupil responses reflected endogenous arousal fluctuations opposed to differences in stimulus content. We found that pupil hazard rates predicted the classification of sub-second intervals (steeper dilation = “Longer” classifications). This shows that the accumulation of endogenous arousal signals informs gaze-shift timing judgements. We also found that participants relied exclusively on the 2^nd stimulus to perform the classification, providing insights into timing strategies under conditions of maximum uncertainty. We observed no dissociation in pupil responses when timing equivalent neutral spatial displacements, indicating that a stimulus-dependent timer exploits arousal to time gaze-shifts.

MicroRNA858 Is a Potential Regulator of Phenylpropanoid Pathway and Plant Development

MicroRNAs (miRNAs) are endogenous, noncoding small RNAs that function as critical regulators of gene expression. In plants, miRNAs have shown their potential as regulators of growth, development, signal transduction, and stress tolerance. Although the miRNA-mediated regulation of several processes is known, the involvement of miRNAs in regulating secondary plant product biosynthesis is poorly understood. In this study, we functionally characterized Arabidopsis (Arabidopsis thaliana) miR858a, which putatively targets R2R3-MYB transcription factors involved in flavonoid biosynthesis. Overexpression of miR858a in Arabidopsis led to the down-regulation of several MYB transcription factors regulating flavonoid biosynthesis. In contrast to the robust growth and early flowering of miR858OX plants, reduction of plant growth and delayed flowering were observed in Arabidopsis transgenic lines expressing an artificial miRNA target mimic (MIM858). Genome-wide expression analysis using transgenic lines suggested that miR858a targets a number of regulatory factors that modulate the expression of downstream genes involved in plant development and hormonal and stress responses. Furthermore, higher expression of MYBs in MIM858 lines leads to redirection of the metabolic flux towards the synthesis of flavonoids at the cost of lignin synthesis. Altogether, our study has established the potential role of light-regulated miR858a in flavonoid biosynthesis and plant growth and development.