Dataset Information

Unidirectional versus bidirectional brushing: Simulating wind influence on Arabidopsis thaliana.

ABSTRACT: Plants acclimate to various types of mechanical stresses through thigmomorphogenesis and alterations in their mechanical properties. Although resemblance between wind- and touch-induced responses provides the foundation for studies where wind influence was mimicked by mechanical perturbations, factorial experiments revealed that it is not always straightforward to extrapolate results induced by one type of perturbation to the other. To investigate whether wind-induced changes in morphological and biomechanical traits can be reproduced, we subjected Arabidopsis thaliana to two vectorial brushing treatments. Both treatments significantly affected the length, mechanical properties and anatomical tissue composition of the primary inflorescence stem. While some of the morphological changes were found to be in line with those induced by wind, changes in the mechanical properties exhibited opposite trends irrespective of the brushing direction. Overall, a careful design of the brushing treatment gives the possibility to obtain a closer match to wind-induced changes, including a positive tropic response.

SUBMITTER: Zhdanov O

PROVIDER: S-EPMC10095948 | biostudies-literature | 2022

REPOSITORIES: biostudies-literature

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Publications

Unidirectional versus bidirectional brushing: Simulating wind influence on <i>Arabidopsis thaliana</i>.

Zhdanov Oleksandr O Blatt Michael R MR Zare-Behtash Hossein H Busse Angela A

Quantitative plant biology 20220411

Plants acclimate to various types of mechanical stresses through thigmomorphogenesis and alterations in their mechanical properties. Although resemblance between wind- and touch-induced responses provides the foundation for studies where wind influence was mimicked by mechanical perturbations, factorial experiments revealed that it is not always straightforward to extrapolate results induced by one type of perturbation to the other. To investigate whether wind-induced changes in morphological an ...[more]

PMID: 37077979

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Project description:BACKGROUND: A "bidirectional gene pair" is defined as two adjacent genes which are located on opposite strands of DNA with transcription start sites (TSSs) not more than 1000 base pairs apart and the intergenic region between two TSSs is commonly designated as a putative "bidirectional promoter". Individual examples of bidirectional gene pairs have been reported for years, as well as a few genome-wide analyses have been studied in mammalian and human genomes. However, no genome-wide analysis of bidirectional genes for plants has been done. Furthermore, the exact mechanism of this gene organization is still less understood. RESULTS: We conducted comprehensive analysis of bidirectional gene pairs through the whole Arabidopsis thaliana genome and identified 2471 bidirectional gene pairs. The analysis shows that bidirectional genes are often coexpressed and tend to be involved in the same biological function. Furthermore, bidirectional gene pairs associated with similar functions seem to have stronger expression correlation. We pay more attention to the regulatory analysis on the intergenic regions between bidirectional genes. Using a hierarchical stochastic language model (HSL) (which is developed by ourselves), we can identify intergenic regions enriched of regulatory elements which are essential for the initiation of transcription. Finally, we picked 27 functionally associated bidirectional gene pairs with their intergenic regions enriched of regulatory elements and hypothesized them to be regulated by bidirectional promoters, some of which have the same orthologs in ancient organisms. More than half of these bidirectional gene pairs are further supported by sharing similar functional categories as these of handful experimental verified bidirectional genes. CONCLUSION: Bidirectional gene pairs are concluded also prevalent in plant genome. Promoter analyses of the intergenic regions between bidirectional genes could be a new way to study the bidirectional gene structure, which may provide a important clue for further analysis. Such a method could be applied to other genomes.

Project description:Interpersonal communication includes verbal and nonverbal communication. Verbal communication comprises one-way (e.g., a speech or lecture) and interactive verbal communication (e.g., daily conversations or meetings), which we frequently encounter. Nonverbal communication has considerable influence on interpersonal communication, and body motion synchrony is known to be an important factor for successful communication and social interaction. However, most research on body motion synchrony has been elucidated by either the setting of one-way verbal transmission or the verbal interaction setting, and it remains unclear whether verbal directionality and interactivity affect body motion synchrony. One-way and two-way (interactive) verbal communication is implicated in designed or undesigned leader-follower relationships, and also in the complexity and diversity of interpersonal interactions, where two-way verbal communication is more complex and diverse than in the one-way condition. In this study, we tested head motion synchrony between the one-way verbal communication condition (in which the roles of the speaker and listener are fixed) and the two-way verbal communication condition (where the speaker and listener can freely engage in a conversation). Therefore, although no statistically significant difference in synchrony activity (relative frequency) was found, a statistically significant difference was observed in synchrony direction (temporal lead-lag structure as mimicry) and intensity. Specifically, the synchrony direction in two-way verbal communication was close to zero, but this in one-way verbal communication was synchronized with the listener's movement predominantly delayed. Furthermore, synchrony intensity, in terms of the degree of variation in the phase difference distribution, was significantly higher in the one-way verbal communication than in the two-way condition, with bigger time-shifts being observed in the latter. This result suggests that verbal interaction does not affect the overall frequency of head motion synchrony but does affect the temporal lead-lag structure and coherence.

Project description:BackgroundThe analysis of molecular variation within and between populations is crucial to establish strategies for conservation as well as to detect the footprint of spatially heterogeneous selection. The traditional estimator of genetic differentiation (F(ST)) has been shown to be misleading if genetic diversity is high. Alternative estimators of F(ST) have been proposed, but their robustness to variation in mutation rate is not clearly established. We first investigated the effect of mutation and migration rate using computer simulations and examined their joint influence on Q(ST), a measure of genetic differentiation for quantitative traits. We further used experimental data in natural populations of Arabidopsis thaliana to characterize the effect of mutation rate on various estimates of population differentiation. Since natural species exhibit various degrees of self-fertilisation, we also investigated the effect of mating system on the different estimators.ResultsIf mutation rate is high and migration rate low, classical measures of genetic differentiation are misleading. Only Phi(ST), an estimator that takes the mutational distances between alleles into account, is independent of mutation rate, for all migration rates. However, the performance of Phi(ST) depends on the underlying mutation model and departures from this model cause its performance to degrade. We further show that Q(ST) has the same bias. We provide evidence that, in A. thaliana, microsatellite variation correlates with mutation rate. We thereby demonstrate that our results on estimators of genetic differentiation have important implications, even for species that are well established models in population genetics and molecular biology.ConclusionsWe find that alternative measures of differentiation like F'(ST) and D are not suitable for estimating effective migration rate and should not be used in studies of local adaptation. Genetic differentiation should instead be measured using an estimator that takes mutation rate into account, such as Phi(ST). Furthermore, in systems where migration between populations is low, such as A. thaliana, Q(ST) < F(ST) cannot be taken as evidence for homogenising selection as has been traditionally thought.

Dataset Information

Unidirectional versus bidirectional brushing: Simulating wind influence on Arabidopsis thaliana.

Publications

Unidirectional versus bidirectional brushing: Simulating wind influence on <i>Arabidopsis thaliana</i>.

Similar Datasets

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