The role of the Pin1-cis P-tau axis in the development and treatment of vascular contribution to cognitive impairment and dementia and preeclampsia.

Tauopathies are neurodegenerative diseases characterized by deposits of abnormal Tau protein in the brain. Conventional tauopathies are often defined by a limited number of Tau epitopes, notably neurofibrillary tangles, but emerging evidence suggests structural heterogeneity among tauopathies. The prolyl isomerase Pin1 isomerizes cis P-tau to inhibit the development of oligomers, tangles and neurodegeneration in multiple neurodegenerative diseases such as Alzheimer's disease, traumatic brain injury, vascular contribution to cognitive impairment and dementia (VCID) and preeclampsia (PE). Thus, cis P-tau has emerged as an early etiological driver, blood marker and therapeutic target for multiple neurodegenerative diseases, with clinical trials ongoing. The discovery of cis P-tau and other tau pathologies in VCID and PE calls attention for simplistic classification of tauopathy in neurodegenerative diseases. These recent advances have revealed the exciting novel role of the Pin1-cis P-tau axis in the development and treatment of vascular contribution to cognitive impairment and dementia and preeclampsia.

Higher-order epistasis within Pol II trigger loop haplotypes.

RNA polymerase II (Pol II) has a highly conserved domain, the trigger loop (TL), that controls transcription fidelity and speed. We previously probed pairwise genetic interactions between residues within and surrounding the TL and identified widespread incompatibility between TLs of different species when placed in the Saccharomyces cerevisiae Pol II context, indicating epistasis between the TL and its surrounding context. We sought to understand the nature of this incompatibility and probe higher order epistasis internal to the TL. We have employed deep mutational scanning with selected natural TL variants ("haplotypes"), and all possible intermediate substitution combinations between them and the yeast Pol II TL. We identified both positive and negative higher-order residue interactions within example TL haplotypes. Intricate higher-order epistasis formed by TL residues was sometimes only apparent from analysis of intermediate genotypes, emphasizing complexity of epistatic interactions. Furthermore, we distinguished TL substitutions with distinct classes of epistatic patterns, suggesting specific TL residues that potentially influence TL evolution. Our examples of complex residue interactions suggest possible pathways for epistasis to facilitate Pol II evolution.

Metal-Free Oxidative Dearomatization-Alkoxylation/Acyloxylation of Indoles: Synthesis of 2-Monosubstituted Indolin-3-ones.

A metal-free route for the preparation of 2-monosubstituted indolin-3-ones, including 2-alkoxyindolin-3-ones and 2-acyloxyindolin-3-ones from commercially available indoles, has been developed employing (bis(trifluoroacetoxy)iodo)benzene (PIFA) as an oxidant. The present protocol features mild reaction conditions, good tolerance with diverse functional groups, and a wide substrate scope, affording the desired products in good yields. This transformation is easy to scale up, and the desired products can be further modified. Most importantly, this method is suitable for the late-stage modification of bioactive molecules. Mechanism studies show that this transformation involves metal-free radical dearomatization and oxygenation. Furthermore, this method also provides a practical and efficient way to prepare indolin-3-ones from commercially available reagents in one step.

Widespread epistasis shapes RNA Polymerase II active site function and evolution.

Multi-subunit RNA Polymerases (msRNAPs) are responsible for transcription in all kingdoms of life. At the heart of these msRNAPs is an ultra-conserved active site domain, the trigger loop (TL), coordinating transcription speed and fidelity by critical conformational changes impacting multiple steps in substrate selection, catalysis, and translocation. Previous studies have observed several different types of genetic interactions between eukaryotic RNA polymerase II (Pol II) TL residues, suggesting that the TL's function is shaped by functional interactions of residues within and around the TL. The extent of these interaction networks and how they control msRNAP function and evolution remain to be determined. Here we have dissected the Pol II TL interaction landscape by deep mutational scanning in Saccharomyces cerevisiae Pol II. Through analysis of over 15000 alleles, representing all single mutants, a rationally designed subset of double mutants, and evolutionarily observed TL haplotypes, we identify interaction networks controlling TL function. Substituting residues creates allele-specific networks and propagates epistatic effects across the Pol II active site. Furthermore, the interaction landscape further distinguishes alleles with similar growth phenotypes, suggesting increased resolution over the previously reported single mutant phenotypic landscape. Finally, co-evolutionary analyses reveal groups of co-evolving residues across Pol II converge onto the active site, where evolutionary constraints interface with pervasive epistasis. Our studies provide a powerful system to understand the plasticity of RNA polymerase mechanism and evolution, and provide the first example of pervasive epistatic landscape in a highly conserved and constrained domain within an essential enzyme.

Characterization of RNA polymerase II trigger loop mutations using molecular dynamics simulations and machine learning.

Catalysis and fidelity of multisubunit RNA polymerases rely on a highly conserved active site domain called the trigger loop (TL), which achieves roles in transcription through conformational changes and interaction with NTP substrates. The mutations of TL residues cause distinct effects on catalysis including hypo- and hyperactivity and altered fidelity. We applied molecular dynamics simulation (MD) and machine learning (ML) techniques to characterize TL mutations in the Saccharomyces cerevisiae RNA Polymerase II (Pol II) system. We did so to determine relationships between individual mutations and phenotypes and to associate phenotypes with MD simulated structural alterations. Using fitness values of mutants under various stress conditions, we modeled phenotypes along a spectrum of continual values. We found that ML could predict the phenotypes with 0.68 R2 correlation from amino acid sequences alone. It was more difficult to incorporate MD data to improve predictions from machine learning, presumably because MD data is too noisy and possibly incomplete to directly infer functional phenotypes. However, a variational auto-encoder model based on the MD data allowed the clustering of mutants with different phenotypes based on structural details. Overall, we found that a subset of loss-of-function (LOF) and lethal mutations tended to increase distances of TL residues to the NTP substrate, while another subset of LOF and lethal substitutions tended to confer an increase in distances between TL and bridge helix (BH). In contrast, some of the gain-of-function (GOF) mutants appear to cause disruption of hydrophobic contacts among TL and nearby helices.

Regioselective peri-C-H selenylation of aromatic compounds with weakly coordinating ketone groups.

A novel and versatile method for peri-C-H selenylation of aromatic compounds bearing ketone groups, including chromones, xanthones, acridinones, quinolinones and naphthoquinones with diselenides under Ru(II) catalysis is presented. Various chromones and diselenides are applicable for this transformation, affording 5-selenyl chromones in a highly regioselective manner in good to excellent yields. This transformation is easy to scale up and the desired products can be further modified. Most importantly, this transformation allows the late-stage selenylation of bioactive compounds. Mechanistic studies show that radicals may be involved in this novel transformation.

Prediction of tannin profile in grape (Vitis vinifera L.) skins during berry maturation using a rapid mechanical puncture approach.

Tannin structure and composition are variable during grape maturation, and crucially determine perceived astringency, body structure and aging capacity of red wines. This study investigated the evolution of condensed tannins (CTs) in grape skins as maturation progressed and the feasibility of using a rapid mechanical puncture approach for assessing the CTs profile. The results showed that the mean degree of polymerization (mDP), molecular mass (MM), and proportions of (-)-epigallocatechin in extension subunits (EGC_ext) and (-)-epicatechin-3-O-gallate in terminal subunits (ECG_term) of skins increased during grape maturation, while CTs content and the proportion of (-)-epicatechin-3-O-gallate in extension subunits decreased. The predictive models built by random forest for CTs content based on skin weight, mDP, MM_subunit, EGC_ext, and ECG_term obtained good results with high squared correlation coefficients of prediction and calibration (R2_P > 0.85 and R2_C ≈ 0.95). In addition, the classifications of CTs characteristics obtained from ripe and unripe samples were observed in different principal component spaces. This study indicated that the mechanical properties were useful for predicting skin CTs profile, estimating tannin maturity stages, and providing information for optimal harvesting and winemaking protocols.

Bioactive triple peptide inhibits inflammasome activation to alleviate Salmonella-induced intestinal inflammation in mice via modulation of host defense and bacterial virulence.

Over the past years, Salmonella typhimurium has been considered an important pathogen that causes intestinal diseases and spells enormous economic shock to animal husbandry all over the world. Pyroptosis and inflammasome are involved in intestinal S. typhimurium infections. This study aims to explore the protective effects and potential mechanisms of a bioactive triple peptide (BTP) on S. typhimurium-induced intestinal infection. In this report, BTP exhibited anti-inflammatory and antibacterial activities in vivo (S. typhimurium-infected C57BL/6 mice) and in vitro (S. typhimurium-challenged THP-1 cells). We found that BTP significantly alleviated intestinal injuries and inflammation in S. typhimurium-infected mice. Besides, organ hypertrophy and bacteria translocation were improved effectively after BTP treatment. In macrophages, inflammasome activation caused by S. typhimurium infection was inhibited by BTP treatment. Of note, BTP significantly inhibited the adhesion and invasion of S. typhimurium to THP-1 cells. Moreover, the gene expressions of fljB and fliC were suppressed by BTP. All in all, our results suggest that BTP has the potential for alleviating S. typhimurium-induced inflammation.

Noninvasive examination of the cardiac properties of insect embryos enabled by optical coherence tomography.

Understanding the cardiac properties of insect embryos at different development stages is important, however, few works have been conducted probably due to the lack of effective tools. Using locust embryos as an example, here we show, for the first time, that optical coherence tomography (OCT) is capable of obtaining detailed information of embryos' heart activities and irregularities, such as the heart rate, cardiac cycle, diastolic and systolic diameters, hemolymph pumping rate and ejection fraction at different stages of embryonic development and at different temperatures. We develop algorithms and mathematical methods for extracting and analyzing cardiac behavior information of locust embryos. We discover that locust embryos experienced suspended development (quiescence) caused by cold storage have a heart rate 20% more than that of embryos without experiencing quiescence and that the hemolymph pumping rate of the two types of embryos behaves differently as the embryos grow. In addition, using OCT as an accurate cardiac activity examination tool, we show that the heart rates of locust embryos are effectively reduced due to nitric oxide synthase gene silencing by RNA interference, indicating potential application of using locust embryos as a good model organism to study cardiovascular diseases, including the congenital heart disease and arrhythmia. Finally, the capabilities offered by OCT in the studies of locust embryonic development may also prove helpful to promote locust reproduction for nutritions or restrain locust reproduction for pest control.

Deficit irrigation and leaf removal modulate anthocyanin and proanthocyanidin repartitioning of Cabernet Sauvignon (Vitis vinifera L.) grape and resulting wine profile.

BACKGROUND: In monsoonal climates, grape anthocyanin and proanthocyanidin (PA) accumulations are unsatisfactory for producing optimal wine. Agronomical practices are often considered to be effective means for regulating fruit components. However, there is a lack of quantitative information on the effects of deficit irrigation (DI), basal leaf removal (LR) or their combination of deficit irrigation and leaf removal (DILR) on the characteristics of anthocyanin and PA compositions and their implications on the resulting wine quality. In this study, the dynamics of grape anthocyanin and PA accumulation were investigated in DI, LR and DILR during grape ripening, and the resulting wine profile was assessed. RESULTS: The contents of reducing sugar and total anthocyanins in Cabernet Sauvignon berries were significantly increased by DI, LR and DILR, while titratable acidity, total flavan-3-ols and tannins levels were generally decreased. Notably, the levels of 3'5'-substituted anthocyanins, such as malvidin and its derivatives significantly increased, and 3'-substituted anthocyanins decreased in both grape and wine under DI and DILR strategies. Skin PAs were sensitive to water deficits, whereas they were insensitive to LR. In resulting wine, PAs content and the proportion of 3'-hydroxylated PAs, such as (+)-catechin, (-)-epicatechin and (-)-epicatechin-3-O-gallate units were significantly decreased under DI and DILR, while molecular mass and the proportion of 3'5'-hydroxylated units of PAs were increased in response to DILR. CONCLUSION: The DILR was the most favorable for the repartitioning of anthocyanin and PA metabolites, and promoted the accumulation of tri-substituted forms contributing a higher color intensity, mouthfeel persistence, structure, and astringency of wine. This information provides an important strategy for modulating the anthocyanin and PA compositions by agricultural practices and achieving the desired quality of grapes and wines in monsoonal climates. © 2021 Society of Chemical Industry.

Ruthenium(II)-Catalyzed Direct C7-Selective Amidation of Indoles with Dioxazolones at Room Temperature.

A protocol for the preparation of 7-amido indoles via regioselective C-H bond functionalization has been first accomplished under Ru(II) catalysis. Indole derivatives and 4-aryl/heteroaryl/benzyl/alkyl dioxzaolines containing various substituents were applicable for this transformation, readily providing the amidated indoles in moderate to good yields. This novel process has many advantages, including good compatibility with diverse functional groups, broad substrate scopes, and mild reaction conditions. Deuteration studies and control experiments have been performed to understand the mechanism of this transformation.

1-Aminocyclopropane-1-Carboxylate Deaminase-Producing Plant Growth-Promoting Rhizobacteria Improve Drought Stress Tolerance in Grapevine (Vitis vinifera L.).

Plant growth-promoting rhizobacteria (PGPRs) that produce 1-aminocyclopropane-1-carboxylate (ACC) deaminase are capable of reducing limits to plant growth due to water-deficient conditions. Here, seven PGPR strains that can produce ACC deaminase were successfully obtained from the rhizosphere soil of grapevine (Vitis vinifera L.) in arid regions of China. The strains belonged to three different genera: Pseudomonas, Enterobacter, and Achromobacter, according to their 16S rDNA sequencing analysis. A drought tolerance experiment revealed two PGPR strains (DR3 and DR6) with exceptionally high phosphate solubilization, nitrogen fixation, indoleacetic acid (IAA), and exopolysaccharides secretion potential. Both strains were selected for use in a pot experiment to evaluate their growth-promoting effects on grapevines under drought conditions. Each of these two PGPRs and their mixed inoculation into grapevines were expected to alleviate the comprehensive growth inhibition of grapevines caused by drought stress. The mixed inoculation was hypothesized to elicit the best growth-promoting effects. Inoculation with the PGPRs not only enhanced the root-adhering soil/root tissue ratios and soil aggregate stability, but it also increased the nitrogen and phosphorus levels in the soil and plant leaves. Further, inoculation with PGPRs significantly altered the plant height, biomass of shoot and root organs, relative water contents, and net photosynthetic rate of leaves, enabling grapevines to better cope with drought. Moreover, the contents of IAA, abscisic acid, and malondialdehyde in these grapevines under drought stress were significantly changed by PGPRs. They indirectly affected biochemical and physiological properties of grapevines to alleviate their drought stress. Taken together, these results demonstrate that the DR3 and DR6 PGPRs might be useful for effectively weakening the growth inhibition caused by drought in grapevines. The strains might also be applied as effective bioinoculants to maintain the quality of wine grapes.

Dynamic changes in anthocyanin biosynthesis regulation of Cabernet Sauvignon (Vitis vinifera L.) grown during the rainy season under rain-shelter cultivation.

The grapevine (Vitis vinifera L.) berry coloring mechanism in response to seasonal rain during grape ripening remains poorly understood. Therefore, anthocyanin biosynthesis regulation, dynamic changes in anthocyanin accumulation, biosynthetic enzyme activities, and related gene expression patterns were investigated in Cabernet Sauvignon grown under rain-shelter cultivation and open-field cultivation. Results showed that anthocyanin biosynthesis was strongly repressed during the rainy season. Environmental fluctuation from seasonal rain provoked metabolic responses in grapes, and there was a significantly greater accumulation of most of the anthocyanins, mainly the compositions of non-acylated and non-methylated, under rain-shelter cultivation; these findings indicate that rain-shelter cultivation may help improve tolerance to seasonal rain-induced stresses. Obvious resilience was observed in anthocyanins of open-field-cultivated grapes at harvest. Hierarchical cluster analysis indicated strong correlations between anthocyanin contents, CHI and DFR activities, and VvMYB5b transcriptional level. These findings provide novel insight into the crucial factors that directly modulate anthocyanin biosynthesis and consequently control grape coloration.

Genome sequence and genetic transformation of a widely distributed and cultivated poplar.

Populus alba is widely distributed and cultivated in Europe and Asia. This species has been used for diverse studies. In this study, we assembled a de novo genome sequence of P. alba var. pyramidalis (= P. bolleana) and confirmed its high transformation efficiency and short transformation time by experiments. Through a process of hybrid genome assembly, a total of 464 M of the genome was assembled. Annotation analyses predicted 37 901 protein-coding genes. This genome is highly collinear to that of P. trichocarpa, with most genes having orthologs in the two species. We found a marked expansion of gene families related to histone and the hormone auxin but loss of disease resistance genes in P. alba if compared with the closely related P. trichocarpa. The genome sequence presented here represents a valuable resource for further molecular functional analyses of this species as a new tree model, poplar breeding practices and comparative genomic analyses across different poplars.

Coexpression of PalbHLH1 and PalMYB90 Genes From Populus alba Enhances Pathogen Resistance in Poplar by Increasing the Flavonoid Content.

Secondary metabolites of the flavonoid pathway participate in plant defense, and bHLH and MYB transcription factors regulate the synthesis of these metabolites. Here, we define the regulatory mechanisms in response to pathogens. Two transcription factors from Populus alba var. pyramidalis, PalbHLH1 and PalMYB90, were overexpressed together in poplar, and transcriptome analysis revealed differences in response to pathogen infection. The transgenic plants showed elevated levels of several key flavonoid pathway components: total phenols, proanthocyanidins (PAs), and anthocyanins and intermediates quercetin and kaempferol. Furthermore, PalbHLH1 and PalMYB90 overexpression in poplar enhanced antioxidase activities and H2O2 release and also increased resistance to Botrytis cinerea and Dothiorella gregaria infection. Gene expression profile analysis showed most genes involved in the flavonoid biosynthesis pathway or antioxidant response to be upregulated in MYB90/bHLH1-OE poplar, but significant differential expression occurred in response to pathogen infection. Specifically, expression of PalF3H (flavanone 3-hydroxylase), PalDFR (dihydroflavonol 4-seductase), PalANS (anthocyanin synthase), and PalANR (anthocyanin reductase), which function in initial, middle, and final steps of anthocyanin and PA biosynthesis, respectively, was significantly upregulated in D. gregaria-infected MYB90/bHLH1-OE poplar. Our results highlight that PalbHLH1 and PalMYB90 function as transcriptional activators of flavonoid pathway secondary-metabolite synthesis genes, with differential mechanisms in response to bacterial or fungal infection.

Influence of natural variation in berry size on the volatile profiles of Vitis vinifera L. cv. Merlot and Cabernet Gernischt grapes.

This study was conducted during the 2014 and 2015 vintages on Vitis vinifera L. cv. Merlot and Cabernet Gernischt to investigate whether natural variation in berry size could affect grape aromatic compounds. Grape berries were separated into three size categories based on their diameter: small, middle and large. The results showed that berry size exerted a significant influence on the volatile profiles of both winegrape varieties. Hierarchical clustering analysis demonstrated that the volatile profiles of middle berries were different from those of large and small berries. Middle berries had the greatest abundance of aroma compounds, followed by small and large berries. Especially, C6/C9 compounds, norisoprenoids, terpenoids showed markedly different concentrations among differently sized Merlot berries and C6/C9 compounds, terpenoids among differently sized Cabernet Gernischt berries. Middle berries of both grape varieties may possess the greatest intensity of fresh-green, fruity and floral aromas due to the high odour activity values (OAVs) of decanal, hexanal, (E)-2-hexenal, (E)-ß-damascenone and ß-ionone in middle sizes of Merlot berries and the high OAVs of (E)-2-hexenal and (E)-ß-damascenone in middle sizes of Cabernet Gernischt berries. This knowledge could be important for winemakers to conduct targeted berry sorting, thereby improving the aromatic quality of grapes.

Foliar applications of iron promote flavonoids accumulation in grape berry of Vitis vinifera cv. Merlot grown in the iron deficiency soil.

Flavonoids are important compounds for grape and wine quality. Foliar fertilization with iron compounds has been reported to have a substantial impact on grape composition in the grapevines growing in calcareous soil. However, much less is known about its real impact on flavonoid composition. In the present study, Ferric ethylenediamine di (O-hydroxyphenylacetic) acid (Fe-EDDHA) was foliar applied to Merlot (Vitis vinifera L.) grapevines growing in calcareous soil over two consecutive vintages in order to study its effect on grape flavonoid composition. Fe-EDDHA foliar supply tended to increase grape sugar, anthocyanin and flavonol content, decrease acid content and enhance the juice pH when compared to the control. Principal component analysis showed that the vintage also had influence on grape quality. The results suggested that Fe-EDDHA foliar application had an enhancement effect on grape secondary metabolism, and the effect increased the nutritional value of the consequent grapes and wines.

Genome-Wide Survey Reveals Transcriptional Differences Underlying the Contrasting Trichome Phenotypes of Two Sister Desert Poplars.

Trichomes, which are widely used as an important diagnostic characteristic in plant species delimitation, play important roles in plant defense and adaptation to adverse environments. In this study, we used two sister poplar species, Populus pruinosa and Populus euphratica-which have, respectively, dense and sparse trichomes-to examine the genetic differences associated with these contrasting phenotypes. The results showed that 42 and 45 genes could be identified as candidate genes related to trichomes in P. pruinosa and P. euphratica, respectively; most of these genes possessed high degrees of diversification in their coding sequences, but they were similar in intron/exon structure in the two species. We also found that most of the candidate trichome genes were expressed at higher levels in P. pruinosa, which has dense trichomes, than in P. euphratica, where there are few trichomes. Based on analyses of transcriptional profiles, a total of 195 genes, including many transcription factors, were found to show distinct differences in expression. The results of gene function annotation suggested that the genes identified as having contrasting levels of expression level are mainly associated with trichome elongation, ATPase activity, and hormone transduction. Changes in the expression of these and other related genes with high sequence diversification may have contributed to the contrast in the pattern of trichome phenotypes between the two species.

Genome-wide Identification of WRKY Genes in the Desert Poplar Populus euphratica and Adaptive Evolution of the Genes in Response to Salt Stress.

WRKY transcription factors play important roles in plant development and responses to various stresses in plants. However, little is known about the evolution of the WRKY genes in the desert poplar species Populus euphratica, which is highly tolerant of salt stress. In this study, we identified 107 PeWRKY genes from the P. euphratica genome and examined their evolutionary relationships with the WRKY genes of the salt-sensitive congener Populus trichocarpa. Ten PeWRKY genes are specific to P. euphratica, and five of these showed altered expression under salt stress. Furthermore, we found that two pairs of orthologs between the two species showed evidence of positive evolution, with dN/dS ratios>1 (nonsynonymous/synonymous substitutions), and both of them altered their expression in response to salinity stress. These findings suggested that both the development of new genes and positive evolution in some orthologs of the WRKY gene family may have played an important role in the acquisition of high salt tolerance by P. euphratica.