A Single Molecule Investigation of I-Motif: Stability, Folding Kinetics, and Potential as an In-situ pH Sensor

We present a collection of single molecule work on the i-motif structure formed by the human telomeric sequence. Even though it was largely ignored in earlier years of its discovery due to its modest stability and requirement for physiologically low pH levels (pH<6.5), the i-motif has been attracting more attention recently as both a physiologically relevant structure and as a potent pH sensor. In this manuscript, we establish single molecule F&oumlrster resonance energy transfer (smFRET) as a tool to study the i-motif over a broad pH and ionic conditions. We demonstrate pH and salt dependence of i-motif formation under steady state conditions and illustrate the kinetics of i-motif folding in real time at the single molecule level. We also show the prominence of intermediate folding states and reversible folding/unfolding transitions. We present an example of using the i-motif as an in-situ pH sensor and use this sensor establish the time scale for the pH drop in a commonly used oxygen scavenging system.

The Modulatory Influence of Plant-Derived Compounds on Human Keratinocyte Function

The plant kingdom is a rich source of secondary metabolites with numerous properties, including the potential to modify keratinocyte biology. Keratinocytes are important epithelial cells that play a protective role against various chemical, physical and biological stimuli, and participate in reactive oxygen scavenging and inflammation and wound healing processes. The epidermal cell response may be modulated by phytochemicals via changes in signal transduction pathways. Plant extracts and single secondary compounds can possess a high antioxidant capacity and may suppress reactive oxygen species release, inhibit pro-apoptotic proteins and apoptosis and activate antioxidant enzymes in keratinocytes. Moreover, selected plant extracts and single compounds also exhibit anti-inflammatory properties and exposure may result in limited production of adhesion molecules, pro-inflammatory cytokines and chemokines in keratinocytes. In addition, plant extracts and single compounds may promote keratinocyte motility and proliferation via the regulation of growth factor production and enhance wound healing. While such plant compounds may modulate keratinocyte functions, further in vitro and in vivo studies are needed on their mechanisms of action, and more specific toxicity and clinical studies are needed to ensure their effectiveness and safety for use on human skin.

Stabilization of the ferroelectric phase in Hf-based oxides by oxygen scavenging

We propose an oxygen scavenging technique based on thermodynamic considerations of metal and oxygen systems to stabilize the ferroelectric phase and enhance the ferroelectricity in Hf-based oxides. By using an oxygen scavenging metal to control the oxygen vacancy concentration in Hf-based oxides, the effect of this oxygen scavenging technique in ferroelectric Hf-based oxides was systematically investigated. It was revealed that controlling the oxygen vacancies during the crystallization process is of vital importance to stabilizing the ferroelectric properties. This oxygen scavenging technique is an effective method of improving the performance of Hf-based ferroelectric materials without employing any dopant in HfO2.

Changes in Ultrastructure and Oxidation Resistance of Peel of Pear Cultivars during Shelf Life

Postharvest period is a process of natural maturation and senescence. The peel structure and antioxidant capacity of pears are the most important factors that affect its postharvest quality. However, the changes in pear peel properties are still unclear during shelf life. In this study, transmission electron microscopy (TEM) and scanning electron microscopy (SEM) were used to investigate the ultrastructural characteristics of pear peel during shelf life, and to determine the changes in peel antioxidants, active oxygen scavenging enzymes, and antioxidant capacity. The results showed that after a 30-day shelf life, the peel cuticles of all tested varieties had varying degrees of color loss and withering, and the integrity of the cells of peel was also damaged, but the surface layer cells of Xuehuali (XH), Huangguan (HG), and Yali (YL) were smoother than Wonhwang (WH) and Housui (HS), and the integrity of the peel cells was also better. In this experiment, there were significant differences in the contents of total polyphenol and total flavonoids among different varieties, and also significant differences in the variation range and variation trends in the activities of peroxidase and catalase (p < 0.05). The total antioxidant capacity of YL pear peel was the highest (68.76 Ug−1), while that of WH pear peel was the lowest (26.37 Ug−1). In conclusion, YL and XH, the representative varieties of White Pear, have better skin structure stability and antioxidant capacity than Sand Pear varieties HS and WH. The overall results provide a theoretical basis for further structure and function investigation of pear peel.

Prediction and Chemical Interpretation of Singlet-Oxygen-Scavenging Activity of Small Molecule Compounds by Using Machine Learning

A chemically explainable machine learning model was constructed with a small dataset to quantitatively predict the singlet-oxygen-scavenging ability. In this model, ensemble learning based on decision trees resulted in high accuracy. For explanatory variables, molecular descriptors by computational chemistry and Morgan fingerprints were used for achieving high accuracy and simple prediction. The singlet-oxygen-scavenging mechanism was explained by the feature importance obtained from machine learning outputs. The results are consistent with conventional chemical knowledge. The use of machine learning and reduction in the number of measurements for screening high-antioxidant-capacity compounds can considerably improve prediction accuracy and efficiency.

Antioxidant gene expression analysis and evaluation of total phenol content and oxygen-scavenging system in tea accessions under normal and drought stress conditions

Background Abiotic and biotic stresses induce oxidative processes in plant cells that this process starts with the production of ROSs which cause damage to the proteins. Therefore, plants have increased their antioxidant activity to defend against this oxidative stress to be able to handle stress better. In this research, 14 different tea accessions in a randomized complete block design with two replications were evaluated in two normal and drought stress conditions, and their antioxidant activity was measured by DPPH-free radicals’ assay and gene expression analysis. Results The results of gene expression analysis showed that the 100 and 399 accessions and Bazri cultivar had high values for most of the antioxidant enzymes, ascorbate peroxidase, superoxide dismutase, catalase, and peroxidase under drought stress conditions while the 278 and 276 accessions had the lowest amount of antioxidant enzymes in the same situation. Results showed that the IC50 of the BHT combination was 90.12 μg/ ml. Also, The IC50 of accessions ranged from 218 to 261 μg/ml and 201–264 μg/ml at normal and drought stress conditions, respectively. The 100 and 399 accessions showed the lowest IC50 under normal and drought stress conditions, while 278 and 276 accessions had the highest value for IC50. The antioxidant activity of tea accession extracts under normal conditions was ranged from 25 to 69% for accessions 278 and 100, respectively. While, the antioxidant activities of extracts under drought stress condition was 12 to 83% for accessions 276 and 100, respectively. So, according to the results, 100 and 399 accessions exhibited the least IC50 and more antioxidant activity under drought stress conditions and were identified as stress-tolerant accessions. However, 278 and 276 accessions did not show much antioxidant activity and were recognized as sensitive accessions under drought stress conditions. Conclusions These results demonstrate that total phenol content, antioxidant activity, and the oxygen-scavenging system can be used as a descriptor for identifying drought-tolerant accessions.

Microscopic and transcriptomic analyses of Dalbergoid legume peanut reveal a divergent evolution leading to Nod Factor dependent epidermal crack-entry and terminal bacteroid differentiation.

Root nodule symbiosis (RNS) is the pillar behind sustainable agriculture and plays a pivotal role in the environmental nitrogen cycle. Most of the genetic, molecular, and cell-biological knowledge on RNS come from model legumes that exhibit a root-hair mode of bacterial infection in contrast to the Dalbergoid legumes exhibiting crack-entry of rhizobia. As a step towards understanding this important group of legumes, we have combined microscopic analysis and temporal transcriptome to obtain a dynamic view of plant gene expression during Arachis hypogaea (peanut) nodule development. We generated a comprehensive transcriptome data by mapping the reads to A. hypogaea, and two diploid progenitor genomes. Additionally, we performed BLAST searches to identify nodule-induced yet-to-be annotated peanut genes. Comparison between peanut, Medicago truncatula, Lotus japonicus, and Glycine max showed upregulation of 61 peanut orthologs among 111 tested known RNS-related genes, indicating conservation in mechanisms of nodule development among members of the Papilionoid family. Unlike model legumes, recruitment of class 1 phytoglobin derived symbiotic hemoglobin (SymH) in peanut indicates diversification of oxygen scavenging mechanisms in the Papilionoid family. Finally, absence of cysteine-rich motif-1 containing-NCRs, but the recruitment of defensin like NCRs suggest a diverse molecular mechanism of terminal bacteroid differentiation. In summary, our work describes genetic conservation and diversification in legume-rhizobial symbiosis in the Papilionoid family, as well as among members of the Dalbergoid legumes.