Miracle-dz/UniFAR-FTUs huggingface dataset:
Ethylene-Inducible AP2/ERF Transcription Factor Involved in the Capsaicinoid Biosynthesis in Capsicum

Ethylene is very important in the process of plant development and regulates the biosynthesis of many secondary metabolites. In these regulatory mechanisms, transcription factors (TFs) that mediate ethylene signals play a very important role. Capsaicinoids (CAPs) are only synthesized and accumulated in Capsicum species, causing their fruit to have a special pungent taste, which can protect against attack from herbivores and pathogens. In this study, we identified the TF CcERF2, which is induced by ethylene, and demonstrated its regulatory effect on CAPs biosynthesis. Transcriptome sequencing analysis revealed that the expression patterns of CcERF2 and multiple genes associated with CAPs biosynthesis were basically the same. The spatiotemporal expression results showed CcERF2 was preferentially expressed in the placenta of the spicy fruit. Ethylene can induce the expression of CcERF2 and CAPs biosynthesis genes (CBGs). CcERF2 gene silencing and 1-methylcyclopropene (1-MCP) and pyrazinamide (PZA) treatments caused a decrease in expression of CBGs and a sharp decrease in content of CAPs. The results indicated that CcERF2 was indeed involved in the regulation of structural genes of the CAPs biosynthetic pathway.
Projected 21st-Century Glacial Lake Evolution in High Mountain Asia

In High Mountain Asia (HMA), rising temperatures and retreating glaciers are leading to the formation of new glacial lakes and the expansion of existing ones. The sudden release of water from such lakes can lead to devastating glacial lake outburst floods (GLOF) threatening people and infrastructure for many kilometers downstream. Therefore, information on future glacial lakes, e.g., their location, area and volume as well as the timing of their development, is vital for sustainable development of settlements and infrastructures. In this study, we present comprehensive estimates for future glacial lake development in HMA with unprecedented temporal resolution. We rely on an ensemble of fifteen global climate models using the newest CMIP6 data and employ a set of four Shared Socioeconomic Pathway (SSP) scenarios. With the Open Global Glacier Model (OGGM), we use a modeling framework that explicitly simulates glacier dynamics in order to model glacier change until 2100 and estimate the formation period for each of the 2,700 largest future glacial lakes (>0.1 km2) in HMA. We estimate the glacial lake area in the entire region to grow by 474 ± 121 km2 for SSP126 and 833 ± 148 km2 for SSP585. Following recent estimates of currently existing glacial lakes (>0.1 km2), this would constitute an increase in lake area of ∼120–∼210% in 2100 compared to 2018. The lake volume is expected to increase by 22.8 ± 6.7 km3 for SSP126 and 39.7 ± 7.7 km3 for SSP585. This range includes a drastic tenfold increase in lake volume, from estimated 3.9 km3 in 2018 to 43.6 ± 7.7 km3 in 2100. However, there is a considerable spread between total and relative increase in glacial lake area and volume for different sub-regions of High Mountain Asia. As both, lake area and lake volume, could to lead to an increase in GLOF risk, the results emphasize the urgent need for more localized, in-depth studies at especially vulnerable locations in order to enable local communities to adapt to emerging challenges, to implement risk minimization measures, and to improve sustainable development in High Mountain Asia.
Comprehensive Transcriptome Analysis of Stem-Differentiating Xylem Upon Compression Stress in Cunninghamia Lanceolata

Compression wood (CW) in gymnosperm brings great difficulties to wood industry using wood as raw materials since CW presents special wood structure and have different physical and chemical properties from those of normal wood (NW). Chinese fir (Cunninghamia lanceolata) is widely distributed in China. However, global transcriptome profiling of coding and long non-coding RNA in response to compression stress has not been reported in the gymnosperm species. In this study, we revealed that CW in Chinese fir exhibited distinct morphology and cytology properties compared with those of NW, including high lignin content, thick and round tracheid cells. Furthermore, we combined both PacBio long-read SMRT sequencing (Iso-Seq) and Illumina short-read RNA-Seq to reveal the transcriptome in stem-differentiating xylem (SDX) under different time points (2, 26, and 74 h) upon compression stress in NW, CW, and OW (opposite wood), respectively. Iso-Seq was successfully assembled into 41,253 de-novo full-length transcriptome reference (average length 2,245 bp). Moreover, there were striking differences in expression upon compression stress, which were involved 13 and 7 key enzyme genes in the lignin and cellulose synthesis, respectively. Especially, we revealed 11 secondary growth-related transcription factors show differential expression under compression stress, which was further validated by qRT-PCR. Finally, the correlation between 6,533 differentially expressed coding genes and 372 differentially expressed long non-coding RNAs (lncRNAs) indicates that these lncRNAs may affect cell wall biogenesis and xyloglucan metabolism. In conclusion, our results provided comprehensive cytology properties and full-length transcriptome profiling of wood species upon compression stress. Especially we explored candidate genes, including both coding and long non-coding genes, and provided a theoretical basis for further research on the formation mechanism of CW in gymnosperm Chinese fir.
Healthy Serum-Derived Exosomes Improve Neurological Outcomes and Protect Blood–Brain Barrier by Inhibiting Endothelial Cell Apoptosis and Reversing Autophagy-Mediated Tight Junction Protein Reduction in Rat Stroke Model

Blood–brain barrier (BBB) dysfunction causing edema and hemorrhagic transformation is one of the pathophysiological characteristics of stroke. Protection of BBB integrity has shown great potential in improving stroke outcome. Here, we assessed the efficacy of exosomes extracted from healthy rat serum in protection against ischemic stroke in vivo and in vitro. Exosomes were isolated by gradient centrifugation and ultracentrifugation and exosomes were characterized by transmission electron microscopy (TEM) and nanoparticle tracking video microscope. Exosomes were applied to middle cerebral artery occlusion (MCAO) rats or brain microvascular endothelial cell line (bEnd.3) subjected to oxygen-glucose deprivation (OGD) injury. Serum-derived exosomes were injected intravenously into adult male rats 2 h after transient MCAO. Infarct volume and gross cognitive function were assessed 24 h after reperfusion. Poststroke rats treated with serum-derived exosomes exhibited significantly reduced infarct volumes and enhanced neurological function. Apoptosis was assessed via terminal deoxynucleotidyl transferase (TdT)-mediated dUTP nick-end labeling (TUNEL) staining and the expression of B-cell lymphoma-2 (Bcl-2), Bax, and cleaved caspase-3 24 h after injury. Our data showed that serum exosomes treatment strikingly decreased TUNEL+ cells in the striatum, enhanced the ratio of Bcl-2 to Bax, and inhibited cleaved caspase-3 production in MCAO rats and OGD/reoxygenation insulted bEnd.3 cells. Under the consistent treatment, the expression of microtubule-associated protein 1 light chain 3B-II (LC3B-II), LC3B-I, and Sequestosome-1 (SQSTM1)/p62 was detected by Western blotting. Autolysosomes were observed via TEM. We found that serum exosomes reversed the ratio of LC3B-II to LC3B-I, prevented SQSTM1/p62 degradation, autolysosome formation, and autophagic flux. Together, these results indicated that exosomes isolated from healthy serum provided neuroprotection against experimental stroke partially via inhibition of endothelial cell apoptosis and autophagy-mediated BBB breakdown. Intravenous serum-derived exosome treatment may, therefore, provide a novel clinical therapeutic strategy for ischemic stroke.
More than Meets the Eye: The Aryl Hydrocarbon Receptor is an Environmental Sensor, Physiological Regulator and a Therapeutic Target in Ocular Disease

The aryl hydrocarbon receptor (AHR) is a ligand activated transcription factor originally identified as an environmental sensor of xenobiotic chemicals. However, studies have revealed that the AHR regulates crucial aspects of cell growth and metabolism, development and the immune system. The importance of the AHR and AHR signaling in eye development, toxicology and disease is now being uncovered. The AHR is expressed in many ocular tissues including the retina, choroid, cornea and the orbit. A significant role for the AHR in age-related macular degeneration (AMD), autoimmune uveitis, and other ocular diseases has been identified. Ligands for the AHR are structurally diverse organic molecules from exogenous and endogenous sources. Natural AHR ligands include metabolites of tryptophan and byproducts of the microbiome. Xenobiotic AHR ligands include persistent environmental pollutants such as dioxins, benzo (a) pyrene [B (a) P] and polychlorinated biphenyls (PCBs). Pharmaceutical agents including the proton pump inhibitors, esomeprazole and lansoprazole, and the immunosuppressive drug, leflunomide, activate the AHR. In this review, we highlight the role of the AHR in the eye and discuss how AHR signaling is involved in responding to endogenous and environmental stimuli. We also present the emerging concept that the AHR is a promising therapeutic target for eye disease.
The Impact of Consumer Purchase Behavior Changes on the Business Model Design of Consumer Services Companies Over the Course of COVID-19

The COVID-19 pandemic has had a profound psychological and behavioral impact on people around the world. Consumer purchase behaviors have thus changed greatly, and consumer services companies need to adjust their business models to adapt to this change. From the perspective of consumer psychology, this paper explores the impact of consumer purchase behavior changes over the course of the pandemic on the business model design of consumer services companies using a representative survey of 1,742 individuals. Our results show that changes in consumer purchase behavior have a significant impact on the design of consumer services firms’ business models. Specifically, changes in consumers’ purchase object, motive, and timeframe are more likely to spark a novelty-centered business model design, whereas changes in purchase method tend to inspire an efficiency-centered one. Our findings provide a theoretical reference for consumer services companies in designing business models when faced with unexpected crises.
A Comparative Study of Systems Pharmacology and Gene Chip Technology for Predicting Targets of a Traditional Chinese Medicine Formula in Primary Liver Cancer Treatment

Background: The systems pharmacology approach is a target prediction model for traditional Chinese medicine and has been used increasingly in recent years. However, the accuracy of this model to other prediction models is yet to be established. Objective : To compare the systems pharmacology modelwithexperimental gene chip technology by using these models to predict targets of a traditional Chinese medicine formulain the treatment of primary liver cancer. Methods: Systems pharmacology and gene chip target predictions were performed for the traditional Chinese medicine formula ZhenzhuXiaojiTang (ZZXJT). A third square alignment was performed with molecular docking. Results: Identification of systems pharmacology accounted for 17% of targets, whilegene chip-predicted outcomes accounted for 19%. Molecular docking showed that the top ten targets (excludingcommon targets) of the system pharmacology model had better binding free energies than the gene chip model using twocommon targets as a benchmark. For both models, the core drugs predictions were more consistent than the core small molecules predictions. Conclusion:In this study, the identified targets of systems pharmacology weredissimilar to those identified by gene chip technology; whereas the core drug and small molecule predictions were similar.
Arabidopsis Tetraspanins Facilitate Virus Infection via Membrane-Recognition GCCK/RP Motif and Cysteine Residues

Tetraspanins (TETs) function as key molecular scaffolds for surface signal recognition and transduction via the assembly of tetraspanin-enriched microdomains. TETs’ function in mammalian has been intensively investigated for the organization of multimolecular membrane complexes, regulation of cell migration and cellular adhesion, whereas plant TET studies lag far behind. Animal and plant TETs share similar topologies, despite the hallmark of “CCG” in the large extracellular loop of animal TETs, plant TETs contain a plant specific GCCK/RP motif and more conserved cysteine residues. Here, we showed that the GCCK/RP motif is responsible for TET protein association with the plasma membrane. Moreover, the conserved cysteine residues located within or neighboring the GCCK/RP motif are both crucial for TET anchoring to membrane. During virus infection, the intact TET3 protein enhanced but GCCK/RP motif or cysteine residues-deficient TET3 variants abolished the cell-to-cell movement capability of virus. This study provides cellular evidence that the GCCK/RP motif and the conserved cysteine residues are the primary determinants for the distribution and function of TET proteins in Arabidopsis.
The Phlorizin-Degrading Bacillus licheniformis XNRB-3 Mediates Soil Microorganisms to Alleviate Apple Replant Disease

In this study, an endophytic phlorizin-degrading Bacillus licheniformis XNRB-3 was isolated from the root tissue of healthy apple trees, and its control effect on apple replant disease (ARD) and how it alleviates the pathogen pressure via changes in soil microbiomes were studied. The addition of strain XNRB-3 in Fusarium infested soils significantly reduced the number of pathogens in the soil, thus resulting in a lower disease incidence, and the relative control effect on Fusarium oxysporum reached the highest of 66.11%. The fermentation broth can also protect the roots of the plants from Fusarium oxysporum, Fusarium moniliforme, Fusarium proliferatum, and Fusarium solani infection. These antagonistic effects were further validated using an in vitro assay in which the pathogen control was related to growth and spore germination inhibition via directly secreted antimicrobial substances and indirectly affecting the growth of pathogens. The secreted antimicrobial substances were identified using gas chromatography-mass spectrometry (GC-MS) technology. Among them, alpha-bisabolol and 2,4-di-tert-butylphenol had significant inhibitory effects on many planted pathogenic fungi. Butanedioic acid, monomethyl ester, and dibutyl phthalate promoted root development of Arabidopsis plants. Strain XNRB-3 has multifarious plant growth promoting traits and antagonistic potential. In pot and field experiments, the addition of strain XNRB-3 significantly promoted the growth of plants, and the activity of enzymes related to disease resistance [superoxide dismutase (SOD), peroxidase (POD), and catalase (CAT)] was also significantly enhanced. It also reduced the abundance of four species of Fusarium and the content of phenolic acids in the rhizosphere soil, improved soil microbial community structure and nutritional conditions, and increased soil microbial diversity and activity, as well as the soil enzyme activity. The above results indicated that B. licheniformis XNRB-3 could be developed into a promising biocontrol and plant-growth-promoting agent.
MAP3K1 Variant Causes Hyperactivation of Wnt4/β-Catenin/FOXL2 Signaling Contributing to 46,XY Disorders/Differences of Sex Development

Background: 46,XY disorders/differences of sex development (46,XY DSD) are congenital conditions that result from abnormal gonadal development (gonadal dysgenesis) or abnormalities in androgen synthesis or action. During early embryonic development, several genes are involved in regulating the initiation and maintenance of testicular or ovarian-specific pathways. Recent reports have shown that MAP3K1 genes mediate the development of the 46,XY DSD, which present as complete or partial gonadal dysgenesis. Previous functional studies have demonstrated that some MAP3K1 variants result in the gain of protein function. However, data on possible mechanisms of MAP3K1 genes in modulating protein functions remain scant. Methods: This study identified a Han Chinese family with the 46,XY DSD. To assess the history and clinical manifestations for the 46,XY DSD patients, the physical, operational, ultra-sonographical, pathological, and other examinations were performed for family members. Variant analysis was conducted using both trio whole-exome sequencing (trio WES) and Sanger sequencing. On the other hand, we generated transiently transfected testicular teratoma cells (NT2/D1) and ovary-derived granular cells (KGN), with mutant or wild-type MAP3K1 gene. We then performed functional assays such as determination of steady-state levels of gender related factors, protein interaction and luciferase assay system. Results: Two affected siblings were diagnosed with 46,XY DSD. Our analysis showed a missense c.556A > G/p.R186G variant in the MAP3K1 gene. Functional assays demonstrated that the MAP3K1R186G variant was associated with significantly decreased affinity to ubiquitin (Ub; 43–49%) and increased affinity to RhoA, which was 3.19 ± 0.18 fold, compared to MAP3K1. The MAP3K1R186G led to hyperphosphorylation of p38 and GSK3β, and promoted hyperactivation of the Wnt4/β-catenin signaling. In addition, there was increased recruitment of β-catenin into the nucleus, which enhanced the expression of pro-ovarian transcription factor FOXL2 gene, thus contributing to the 46,XY DSD. Conclusion: Our study identified a missense MAP3K1 variant associated with 46,XY DSD. We demonstrated that MAP3K1R186G variant enhances binding to the RhoA and improves its own stability, resulting in the activation of the Wnt4/β-catenin/FOXL2 pathway. Taken together, these findings provide novel insights into the molecular mechanisms of 46,XY DSD and promotes better clinical evaluation.
Stem Trait Spectra Underpin Multiple Functions of Temperate Tree Species

A central paradigm in comparative ecology is that species sort out along a slow-fast resource economy spectrum of plant strategies, but this has been rarely tested for a comprehensive set of stem traits and compartments. We tested how stem traits vary across wood and bark of temperate tree species, whether a slow-fast strategy spectrum exists, and what traits make up this plant strategy spectrum. For 14 temperate tree species, 20 anatomical, chemical, and morphological traits belonging to six key stem functions were measured for three stem compartments (inner wood, outer wood, and bark). The trait variation was explained by major taxa (38%), stem compartments (24%), and species within major taxa (19%). A continuous plant strategy gradient was found across and within taxa, running from hydraulic safe gymnosperms to conductive angiosperms. Both groups showed a second strategy gradient related to chemical defense. Gymnosperms strongly converged in their trait strategies because of their uniform tracheids. Angiosperms strongly diverged because of their different vessel arrangement and tissue types. The bark had higher concentrations of nutrients and phenolics whereas the wood had stronger physical defense. The gymnosperms have a conservative strategy associated with strong hydraulic safety and physical defense, and a narrow, specialized range of trait values, which allow them to grow well in drier and unproductive habitats. The angiosperm species show a wider trait variation in all stem compartments, which makes them successful in marginal- and in mesic, productive habitats. The associations between multiple wood and bark traits collectively define a slow-fast stem strategy spectrum as is seen also for each stem compartment.
Wearable System to Guide Crosswalk Navigation for People With Visual Impairment

Independent travelling is a significant challenge for visually impaired people in urban settings. Traditional and widely used aids such as guide dogs and long canes provide basic guidance and obstacle avoidance but are not sufficient for complex situations such as street crossing. We propose a new wearable system that can safely guide a user with visual impairment at a signalized crosswalk. Safe street crossing is an important element of fully independent travelling for people who are blind or visually impaired (BVI), but street crossing is challenging for BVI because it involves several steps reliant on vision, including scene understanding, localization, object detection, path planning, and path following. Street crossing also requires timely completion. Prior solutions for guiding BVI in crosswalks have focused on either detection of crosswalks or classifying crosswalks signs. In this paper, we demonstrate a system that performs all the functions necessary to safely guide BVI at a signalized crosswalk. Our system utilizes prior maps, similar to how autonomous vehicles are guided. The hardware components are lightweight such that they can be wearable and mobile, and all are commercially available. The system operates in real-time. Computer vision algorithms (Orbslam2) localize the user in the map and orient them to the crosswalk. The state of the crosswalk signal (don’t walk or walk) is detected (using a convolutional neural network), the user is notified (via verbal instructions) when it is safe to cross, and the user is guided (via verbal instructions) along a path towards a destination on the prior map. The system continually updates user position relative to the path and corrects the user’s trajectory with simple verbal commands. We demonstrate the system functionality in three BVI participants. With brief training, all three were able to use the system to successfully navigate a crosswalk in a safe manner.
Dual RNA Sequencing Reveals the Genome-Wide Expression Profiles During the Compatible and Incompatible Interactions Between Solanum tuberosum and Phytophthora infestans

Late blight, caused by Phytophthora infestans (P. infestans), is a devastating plant disease. P. infestans genome encodes hundreds of effectors, complicating the interaction between the pathogen and its host and making it difficult to understand the interaction mechanisms. In this study, the late blight-resistant potato cultivar Ziyun No.1 and the susceptible potato cultivar Favorita were infected with P. infestans isolate SCPZ16-3-1 to investigate the global expression profiles during the compatible and incompatible interactions using dual RNA sequencing (RNA-seq). Most of the expressed Arg-X-Leu-Arg (RXLR) effector genes were suppressed during the first 24 h of infection, but upregulated after 24 h. Moreover, P. infestans induced more specifically expressed genes (SEGs), including RXLR effectors and cell wall-degrading enzymes (CWDEs)-encoding genes, in the compatible interaction. The resistant potato activated a set of biotic stimulus responses and phenylpropanoid biosynthesis SEGs, including kirola-like protein, nucleotide-binding site-leucine-rich repeat (NBS-LRR), disease resistance, and kinase genes. Conversely, the susceptible potato cultivar upregulated more kinase, pathogenesis-related genes than the resistant cultivar. This study is the first study to characterize the compatible and incompatible interactions between P. infestans and different potato cultivars and provides the genome-wide expression profiles for RXLR effector, CWDEs, NBS-LRR protein, and kinase-encoding genes.