Ab initio studies on graphyne (GY) for the detection of rare bases in DNA.

Graphyne (GY) and functionalized GY have become cutting-edge research materials for the scientific community. In the present work, the adsorption of rare bases -cytosine (Cyt), 5-methylcytosine (5-meCyt), 5-hydroxymethylcytosine (5-hmCyt), 5-formoxylcytosine (5-fCyt), and 5-carboxylcytosine (5-caCyt) on pristine, B- and N-doped γ-GY was investigated by the first-principles density functional method; methods were designed to distinguish these rare bases by the translocation time and sensitivity. Initially, the stability of pristine, B- and N-doped γ-GY was ascertained by the cohesion energy, and the electronic properties were also analyzed by the energy gap and density of state (DOS). When adsorbing over pristine γ-GY, the translocation times of rare bases were 1.34 × 101, 4.71 × 101, 1.19 × 104, 3.77 × 10-1 and 1.93 × 101 s, respectively. The sensitivities were 2.19%, 0.88%, 0.22%, 2.41%, and 0.88%, respectively, which indicates that they were not clearly separated. By doping the impurity atom, the electronic properties can be fine-tuned to change their selectivity. When adsorbing on the B-doped γ-GY, these rare bases showed sensitivities of 24.69%, 27.20%, 43.32%, 29.97%, and 32.24%, respectively. The rare bases showed sensitivities of 10.15%, 9.02%, 17.29%, 0.38%, and 3.76%, respectively, when adsorbing over the N-doped γ-GY, which greatly increases selectivities for recognization. Thus, these results indicate that pristine and doped γ-GY, as the electrical sensing material, can be used to detect rare bases.

Roles of mitochondrial energy dissipation systems in plant development and acclimation to stress.

BACKGROUND: Plants are sessile organisms that have the ability to integrate external cues into metabolic and developmental signals. The cues initiate specific signal cascades that can enhance the tolerance of plants to stress, and these mechanisms are crucial to the survival and fitness of plants. The adaption of plants to stresses is a complex process that involves decoding stress inputs as energy-deficiency signals. The process functions through vast metabolic and/or transcriptional reprogramming to re-establish the cellular energy balance. Members of the mitochondrial energy dissipation pathway (MEDP), alternative oxidases (AOXs) and uncoupling proteins (UCPs), act as energy mediators and might play crucial roles in the adaption of plants to stresses. However, their roles in plant growth and development have been relatively less explored. SCOPE: This review summarizes current knowledge about the role of members of the MEDP in plant development as well as recent advances in identifying molecular components that regulate the expression of AOXs and UCPs. Highlighted in particular is a comparative analysis of the expression, regulation and stress responses between AOXs and UCPs when plants are exposed to stresses, and a possible signal cross-talk that orchestrates the MEDP, reactive oxygen species (ROS), calcium signalling and hormone signalling. CONCLUSIONS: The MEDP might act as a cellular energy/metabolic mediator that integrates ROS signalling, energy signalling and hormone signalling with plant development and stress accumulation. However, the regulation of MEDP members is complex and occurs at transcriptional, translational, post-translational and metabolic levels. How this regulation is linked to actual fluxes through the AOX/UCP in vivo remains elusive.

The roles of autophagy in development and stress responses in Arabidopsis thaliana.

Autophagy is a dynamic process that involves the recycling process of the degradation of intracellular materials. Over the past decade, our molecular and physiological understanding of plant autophagy has greatly been increased. Most essential autophagic machineries are conserved from yeast to plants. The roles that autophagy-related genes (ATGs) family play in the lifecycle of the Arabidopsis are proved to be similar to that in mammal. Autophagy is activated during certain stages of development, senescence or in response to starvation, or environmental stress in Arabidopsis. In the progression of autophagy, ATGs act as central signaling regulators and could develop sophisticated mechanisms to survive when plants are suffering unfavorable environments. It will facilitate further understanding of the molecular mechanisms of autophagy in plant. In this review, we will discuss recent advances in our understanding of autophagy in Arabidopsis, areas of controversy, and highlight potential future directions in autophagy research.

Corrigendum: Tetraploidy in Citrus wilsonii enhances drought tolerance via synergistic regulation of photosynthesis, phosphorylation, and hormonal changes.

[This corrects the article DOI: 10.3389/fpls.2022.875011.].

Tetraploidy in Citrus wilsonii Enhances Drought Tolerance via Synergistic Regulation of Photosynthesis, Phosphorylation, and Hormonal Changes.

Polyploidy varieties have been reported to exhibit higher stress tolerance relative to their diploid relatives, however, the underlying molecular and physiological mechanisms remain poorly understood. In this study, a batch of autotetraploid Citrus wilsonii were identified from a natural seedling population, and these tetraploid seedlings exhibited greater tolerance to drought stress than their diploids siblings. A global transcriptome analysis revealed that a large number of genes involved in photosynthesis response were enriched in tetraploids under drought stress, which was consistent with the changes in photosynthetic indices including Pn, gs, Tr, Ci, and chlorophyll contents. Compared with diploids, phosphorylation was also modified in the tetraploids after drought stress, as detected through tandem mass tag (TMT)-labeled proteomics. Additionally, tetraploids prioritized the regulation of plant hormone signal transduction at the transcriptional level after drought stress, which was also demonstrated by increased levels of IAA, ABA, and SA and reduced levels of GA3 and JA. Collectively, our results confirmed that the synergistic regulation of photosynthesis response, phosphorylation modification and plant hormone signaling resulted in drought tolerance of autotetraploid C. wilsonii germplasm.

Effect of Chitosan/Thyme Oil Coating and UV-C on the Softening and Ripening of Postharvest Blueberry Fruits.

This study investigated the possible mechanism of softening and senescence of blueberry after harvest using chitosan/thyme oil coating combined with UV-C (short wave ultraviolet irradiation) treatment. On the 56th day of storage, the CBP, cellulose, and hemicellulose contents in the chitosan/thyme oil coating +UV-C-treated group were 1.41, 1.65, and 1.20 times higher than those in the control group. Compared with the control group, the activities of polygalacturonase (PG), pectin methylesterase (PME), ß-glucosidase (ß-Gal), and cellulose (Cx) were significantly reduced (p < 0.05) after chitosan/thyme oil coating +UV-C, and their maximum values decreased by 5.41 µg/h g, 5.40 U/g, 12.41 U/g, and 3.85 µg/h g, respectively. Moreover, chitosan/thyme oil coating combined with UV-C treatment inhibited the gene expression of PG, PME, Cx, and ß-Gal and then regulated the decrease in PG, PME, Cx, and ß-Gal activities, inhibited the degradation of cell wall polysaccharides, and delayed the softening and senescence of postharvest blueberries. The results showed that chitosan/thyme oil coating, UV-C, and chitosan/thyme oil coating + UV-C could significantly inhibit postharvest softening of blueberry; chitosan/thyme oil coating +UV-C had the best effect.

Physiological and TMT-labeled proteomic analyses reveal important roles of sugar and secondary metabolism in Citrus junos under cold stress.

Citrus junos is a widely used citrus grafting rootstock in china because of its excellent tolerance to cold stress. However, the physiological and molecular mechanisms underlying this process remain unknown. In this study, physiological and tandem mass tag-based proteomic analyses were performed to elucidate the mechanism of the Citrus junos response to cold stress. Physiological data showed that severe cold stress decreased photosynthetic parameters and caused cell membrane damage and membrane lipid peroxidation in Citrus junos leaves compared to the control. A total of 6, 678 distinct proteins species were identified, and 413 proteins species were significantly differentially accumulated in the leaves of Citrus junos seedling after cold stress. Bioinformatics analysis revealed that the differentially abundance protein species mainly related to the starch and sucrose metabolism, secondary metabolites biosynthesis and phenylpropanoid biosynthesis in the leaves of Citrus junos seedling after cold stress. Further physiological assays showed that the contents of soluble starch, fructose, glucose and phenols were significantly increased in Citrus junos leaves after cold stress. Collectively, our data reveals that sugar and secondary metabolism could play important roles in Citrus junos in response to cold stress.

Anthocyanins Are Converted into Anthocyanidins and Phenolic Acids and Effectively Absorbed in the Jejunum and Ileum.

Anthocyanins have been known for their health benefits. However, the in vivo digestion and absorption of anthocyanins through the gastrointestinal tract have not been fully clarified, creating challenges for understanding why anthocyanins have high biological activities and purported low bioavailability in vivo. Twenty-seven male rats were intubated with a 500 mg/kg dose of cyanidin-3-glucoside (C3G). Samples from rats' stomach, duodenum, jejunum, ileum, colon, and serum were collected at 0.5, 1, 2, 3, 4, 5, 6, 12, and 24 h after intubation. Three rats without C3G were used as the control with samples collected at 0 h. C3G and its metabolites in each sample were analyzed using high-performance liquid chromatography-PDA-electrospray ionization-MS/MS. These in vivo studies' results unequivocally demonstrated that cyanidin and phenolic acids were the primary C3G metabolites absorbed, mainly in the jejunum and ileum, between 1 and 5 h post-ingestion. We speculate that C3G uses phloroglucinaldehyde and protocatechuic acid metabolic pathways in its metabolism in vivo.