Integrated Analysis of Metabolomics, Flavoromics, and Transcriptomics for Evaluating New Varieties of Amomum villosum Lour.

Amomum villosum Lour. (A. villosum) is the original plant of the medicinal and culinary spice Amomi Fructus (Sharen) and is an important economic crop in the Lingnan region of China. During the cultivation and production of A. villosum, prolonged reliance on single asexual reproduction has exacerbated the degradation of its varieties, leading to inconsistent yields and quality. Building upon earlier cultivar selection efforts, this study provides a comprehensive evaluation of two newly bred A. villosum varieties (A11 and A12) from perspectives including plant traits, product characteristics, active ingredients, and multi-omics analysis. It was found that A12 plants display enhanced robustness, more aromatic fruits, higher yields, and elevated levels of bornyl acetate, A11 shows the advantage of a high camphor content, and the different metabolites and differentially expressed genes of the two varieties were significantly enriched in multiple metabolic pathways. Additionally, A12 contained more terpenoids and substances with aromatic odors such as sweet, fruity, floral, and green. Furthermore, a key gene (Wv_032842) regulating the acetylation of bornyl was discovered, and its significantly higher expression, in A12. In conclusion, this study has a guiding significance for the evaluation of germplasm resources and the breeding of excellent varieties of A. villosum.

The accumulation of polysaccharides in Dendrobium officinale is closely related to rhizosphere bacteria.

Dendrobium officinale Kimura et Migo has long been utilized in traditional Chinese medicine and other Asian cultures for its medicinal properties. One of the key bioactive compounds found in D. officinale is D. officinale polysaccharides (DOPs). Recent studies have indicated that the rhizosphere microbiome can influence the accumulation of bioactive compounds in medicinal plants. Our findings revealed that the bacterial phylum Bacteroidetes played a significant role in shaping the ecological stability of the rhizosphere bacteria associated with D. officinale. Additionally, Pandoraea may have the potential to enhance the production of polysaccharides in D. officinale. Overall, this research contributes to our understanding of the intricate relationship between the rhizosphere microbiome and the accumulation of bioactive compounds in D. officinale. It highlights the potential of specific bacterial taxa, such as Pandoraea, in promoting the production of polysaccharides, thus further establishing the medicinal value of this plant. Our results provide insights for further development of specific fertilizers for medicinal plants.

YELLOW, SERRATED LEAF is essential for cotyledon vein patterning in Arabidopsis.

Venation develops complex patterns within the leaves of angiosperms, and the mechanism of leaf vein patterning remains poorly understood. Here, we report a spontaneous mutant that exhibits yellow serrated leaves and defective cotyledon vein patterning. We mapped and cloned the relevant gene YELLOW, SERRATED LEAF (YSL), a previously unreported gene in plants. YSL interacts with VH1-interacting kinase (VIK), a protein that functions in cotyledon venation development. VIK is a vascular-specific adaptor protein kinase that interacts with another vascular developmental protein, VASCULAR HIGHWAY1 (VH1)/BRASSINOSTEROID INSENSITIVE 1-LIKE 2 (BRL2), which is a receptor-like kinase of the BRASSINOSTEROID INSENSITIVE 1 (BRI1) family. Mutation of YSL affects the auxin response and the expression of auxin-related genes in Arabidopsis (Arabidopsis thaliana). Our results reveal that YSL affects cotyledon vein patterning by interacting with VIK in Arabidopsis.

[Retracted] Long non­coding RNA Igf2as controls hepatocellular carcinoma progression through the ERK/MAPK signaling pathway.

[This retracts the article DOI: 10.3892/ol.2017.6492.].

Corrigendum: A novel approach for sports injury risk prediction: based on time-series image encoding and deep learning.

[This corrects the article DOI: 10.3389/fphys.2023.1174525.].

Resistance behavior of Sb7Se3 thin films based on flexible mica substrate.

In this paper, we explored the resistivity behavior of Sb7Se3 thin films on flexible mica. The films maintained their resistance characteristics through various thicknesses and bending cycles. With increasing bends, resistivity and phase transition temperature of both amorphous and crystalline states rose, while the resistance drift coefficient gradually increased. Raman and near infrared experiments confirmed the internal structural changes and bandgap enhancement after bending. Transmission electron microscopy showed enhanced crystallization and uniform element distribution after annealing. Atomic force microscopy observed cracks, explaining the property changes. Additionally, we developed a flexible Sb7Se3 thin-film resistive device with swift reversibility (∼10 ns) regardless of bending, opening new avenues for flexible information storage.

Dual beam optical coherence tomography angiography for decoupling axial velocity gradient.

Axial velocity gradient (AVG) in the optical coherence tomography angiography (OCTA) signal affects measurement accuracy when the flow is not perpendicular to the scanning beam. We developed a dual beam OCTA method to decouple the contribution of AVG from the decorrelation signal. Decoupling is first verified by phantom experiments which reduces measurement uncertainty from 1.5 to 0.7% (standard deviation). We also tested the method in human skin in vivo and the results indicate that the contribution of AVG to decorrelation signal is reduced.

SPIN1 facilitates chemoresistance and HR repair by promoting Tip60 binding to H3K9me3.

The tandem Tudor-like domain-containing protein Spindlin1 (SPIN1) is a transcriptional coactivator with critical functions in embryonic development and emerging roles in cancer. However, the involvement of SPIN1 in DNA damage repair has remained unclear. Our study shows that SPIN1 is recruited to DNA lesions through its N-terminal disordered region that binds to Poly-ADP-ribose (PAR), and facilitates homologous recombination (HR)-mediated DNA damage repair. SPIN1 promotes H3K9me3 accumulation at DNA damage sites and enhances the interaction between H3K9me3 and Tip60, thereby promoting the activation of ATM and HR repair. We also show that SPIN1 increases chemoresistance. These findings reveal a novel role for SPIN1 in the activation of H3K9me3-dependent DNA repair pathways, and suggest that SPIN1 may contribute to cancer chemoresistance by modulating the efficiency of double-strand break (DSB) repair.

A stepwise prediction and interpretation of gestational diabetes mellitus: Foster the practical application of machine learning in clinical decision.

Background: Machine learning has shown to be an effective method for early prediction and intervention of Gestational diabetes mellitus (GDM), which greatly decreases GDM incidence, reduces maternal and infant complications and improves the prognosis. However, there is still much room for improvement in data quality, feature dimension, and accuracy. The contributions and mechanism explanations of clinical data at different pregnancy stages to the prediction accuracy are still lacking. More importantly, current models still face notable obstacles in practical applications due to the complex and diverse input features and difficulties in redeployment. As a result, a simple, practical but accurate enough model is urgently needed. Design and methods: In this study, 2309 samples from two public hospitals in Shenzhen, China were collected for analysis. Different algorithms were systematically compared to build a robust and stepwise prediction system (level A to C) based on advanced machine learning, and models under different levels were interpreted. Results: XGBoost reported the best performance with ACC of 0.922, 0.859 and 0.850, AUC of 0.974, 0.924 and 0.913 for the selected level A to C models in the test set, respectively. Tree-based feature importance and SHAP method successfully identified the commonly recognized risk factors, while indicated new inconsistent impact trends for GDM in different stages of pregnancy. Conclusion: A stepwise prediction system was successfully established. A practical tool that enables a quick prediction of GDM was released at https://github.com/ifyoungnet/MedGDM.This study is expected to provide a more detailed profiling of GDM risk and lay the foundation for the application of the model in practice.

Mitochondrial calcium uniporter complex: Unveiling the interplay between its regulators and calcium homeostasis.

The mitochondrial calcium uniporter complex (MCUc), serving as the specific channel for calcium influx into the mitochondrial matrix, is integral to calcium homeostasis and cellular integrity. Given its importance, ongoing research spans various disease models to understand the properties of the MCUc in pathophysiological contexts, but reported a different conclusion. Therefore, this review delves into the profound connection between MCUc-mediated calcium transients and cellular signaling pathways, mitochondrial dynamics, metabolism, and cell death. Additionally, we shed light on the recent advancements concerning the structural intricacies and auxiliary components of the MCUc in both resting and activated states. Furthermore, emphasis is placed on novel extrinsic and intrinsic regulators of the MCUc and their therapeutic implications across a spectrum of diseases. Meanwhile, we employed molecular docking simulations and identified candidate traditional Chinese medicine components with potential binding sites to the MCUc, potentially offering insights for further research on MCUc modulation.

Quality of life and survival analyses of breast cancer cases treated with integrated traditional Chinese and Western medicine.

BACKGROUND: Breast cancer (BC) is the second leading cause of tumor-related mortality after lung cancer. Chemotherapy resistance remains a major challenge to progress in BC treatment, warranting further exploration of feasible and effective alternative therapies. AIM: To analyzed the quality of life (QoL) and survival of patients with BC treated with integrated traditional Chinese and Western medicine (TCM-WM). METHODS: This study included 226 patients with BC admitted to the First Affiliated Hospital of Guangxi University of Traditional Chinese Medicine between February 2018 and February 2023, including 100 who received conventional Western medicine treatment (control group) and 126 who received TCM-WM treatment (research group). The total effective rate, side effects (alopecia, nausea and vomiting, hepatorenal toxicity, and myelosuppression), QoL assessed using the European Organization for Research and Treatment of Cancer Core Quality of Life Questionnaire (EORTC QLQ-C30), 1-year overall survival (OS), recurrence and metastasis rates, and serum inflammatory factors [interleukin (IL)-6, IL-10, and tumor necrosis factor alpha] were comparatively analyzed. RESULTS: The research group showed statistically better overall efficacy, EORTC QoL-C30 scores, and 1-year OS than the control group, with markedly lower side effects and 1-year recurrence and metastasis rates. Moreover, the posttreatment levels of serum inflammatory in the research group were significantly lower than the baseline and those in the control group. CONCLUSION: Overall, TCM-WM demonstrated significantly improved therapeutic efficacy while ensuring drug safety in BC, which not only improved patients' QoL and prolonged survival, but also significantly inhibited the inflammatory response.

Programmable "triple attack" cancer therapy through in situ activation of disulfiram toxification combined with phototherapeutics.

Effectively and completely eliminating residual tumor cells is the key to reducing the risk of tumor metastasis and recurrence. Designing an "ideal" nanoplatform for programmable cancer therapy has great prospects for completely eliminating residual tumor cells. Herein, an intelligent nanoplatform of disulfiram (DSF)-loaded CuS-tannic acid nanohexahedrons (denoted as "DSF-CuS@TA") with thermal- and pH-sensitive degradation, as well as near-infrared (NIR-II) phototherapeutics properties, was constructed. And then, it was employed for in situ DSF toxification activation programmable "triple attack" cancer therapy. After accumulating in the tumor, DSF-CuS@TA first releases the loaded Cu(DTC)2, and simultaneously degrades and releases Cu2+ and DSF under mildly acidic stimulation to trigger instant intratumoral Cu(DTC)2 chelation, thereby achieving the "first strike." Next, under irradiation by a NIR-II laser, light energy is converted into heat to generate NIR-II photothermal therapy, thereby achieving the second strike. Subsequently, under thermal stimulation, DSF-CuS@TA degrades further, triggering the chelation of Cu(DTC)2 for a second time to reach the third strike. As expected, in vitro and in vivo studies showed that the synergistic integration of DSF-based programmed chemotherapy and NIR-II phototherapeutics could achieve effective tumor removal. Therefore, we propose a novel type of programmed therapy against cancer by designing a nanoplatform via "nontoxicity-to-toxicity" chemical chelation transformation.

The SIRT2-AMPK axis regulates autophagy induced by acute liver failure.

This study explores the role of SIRT2 in regulating autophagy and its interaction with AMPK in the context of acute liver failure (ALF). This study investigated the effects of SIRT2 and AMPK on autophagy in ALF mice and TAA-induced AML12 cells. The results revealed that the liver tissue in ALF model group had a lot of inflammatory cell infiltration and hepatocytes necrosis, which were reduced by SIRT2 inhibitor AGK2. In comparison to normal group, the level of SIRT2, P62, MDA, TOS in TAA group were significantly increased, which were decreased in AGK2 treatment. Compared with normal group, the expression of P-PRKAA1, Becilin1 and LC3B-II was decreased in TAA group. However, AGK2 enhanced the expression of P-PRKAA1, Becilin1 and LC3B-II in model group. Overexpression of SIRT2 in AML12 cell resulted in decreased P-PRKAA1, Becilin1 and LC3B-II level, enhanced the level of SIRT2, P62, MDA, TOS. Overexpression of PRKAA1 in AML12 cell resulted in decreased SIRT2, TOS and MDA level and triggered more autophagy. In conclusion, the data suggested the link between AMPK and SIRT2, and reveals the important role of AMPK and SIRT2 in autophagy on acute liver failure.

Nonlinear compliance of NompC gating spring and its implication in mechanotransduction.

Cytoskeleton-tethered mechanosensitive channels (MSCs) utilize compliant proteins or protein domains called gating springs to convert mechanical stimuli into electric signals, enabling sound and touch sensation and proprioception. The mechanical properties of these gating springs, however, remain elusive. Here, we explored the mechanical properties of the homotetrameric NompC complex containing long ankyrin-repeat domains (ARDs). We developed a toehold-mediated strand displacement approach to tether single membrane proteins, allowing us to exert force on them and precisely measure their absolute extension using optical tweezers. Our findings revealed that each ARD has a low stiffness of ~0.7 pN/nm and begins to unfold stepwise at ~7 pN, leading to nonlinear compliance. Our calculations indicate that this nonlinear compliance may help regulate NompC's sensitivity, dynamic range, and kinetics to detect mechanical stimuli. Overall, our research highlights the importance of a compliant and unfolding-refolding gating spring in facilitating a graded response of MSC ion transduction across a wide spectrum of mechanical stimuli.

The impact of extreme precipitation on water use efficiency along vertical vegetation belts in Hengduan Mountain during 2001 and 2020.

In the context of climate change, extreme precipitation events are continuously increasing and impact the water­carbon coupling of ecosystems. The vertical vegetation zonation, as a characteristic of mountain ecosystems, reflects the differences in vegetation response to climate change at different elevations. In this study, we used the water use efficiency (WUE) as an indicator to evaluate the water­carbon relationship. By using MODIS data, we analyzed the spatiotemporal patterns of gross primary productivity (GPP), evapotranspiration (ET), and WUE from 2001 to 2020, as well as the responses of WUE to extreme wetness factor Number of precipitation days (R0.1), extreme dryness factor Consecutive dry days (CDD), and meteorological factors under the vertical vegetation zonation. Our results showed that annual GPP and ET displayed a significant increasing trend between 2001 and 2020, whereas WUE showed a weak decreasing trend. Spatially, GPP and WUE decreased with increasing elevation. Analyzing the WUE of mountainous ecosystems as a unified whole may not precisely capture the reactions of vegetation to severe rainfall occurrences. In fact, across different vegetation belts in mountainous areas, there exists a negative correlation between WUE and R0.1, and a positive correlation with CDD. In terms of meteorological factors, the temporal variation of GPP was primarily associated with vapor pressure deficit (VPD) and temperature (Ta), while those of ET was mainly related to soil water content (SWC). WUE was affected by a combination of meteorological factors and had a certain degree of variation between different altitude intervals. These findings contribute to a better understanding and prediction of the relationship between extreme rainfall climate and water­carbon coupling in mountainous areas.

Epidemiology and distribution of 207 rare diseases in China: A systematic literature review.

Epidemiological data on rare diseases in China are currently limited. The objective of this study was to provide a comprehensive understanding of the prevalence and incidence of rare diseases by systematically analyzing the available epidemiological data. We conducted a comprehensive search of English and Chinese databases, the Incidence and Prevalence Database, the Chinese Rare Disease Guideline, and the Taiwan Health Promotion Administration from 2010 to 2023. We identified the top diseases and regions based on epidemiological data and present the maximum, minimum, and median prevalence and incidence values in tables and forest plots. 1,264 prevalence and incidence data were retrieved from 277 studies, guidelines and official websites, covering 110 rare diseases (53.1%) and 32 regions (94.1%). In terms of geographical regions, incidence or prevalence data were available for 32 regions (94.1%), excluding Tibet Hui Autonomous Region and Macao Special Administrative Region. In terms of rate, 60 and 77 out of 207 diseases (29.0% and 37.2%) had available incidence and prevalence data, respectively. Eight diseases had an incidence rate equal to or greater than that of 1,000 patients per million. The present study provides a comprehensive epidemiological analysis and valuable insights into the prevalence and incidence of rare diseases in China. Our findings underscore the pressing need for sustained drug research and medical support for individuals and families impacted by rare diseases.

Deacetylated MDH1 and IDH1 aggravates PANoptosis in acute liver failure through endoplasmic reticulum stress signaling.

Acute liver failure (ALF) is a disease with a high mortality rate and poor prognosis, whose pathogenesis is not fully understood. PANoptosis is a recently proposed mode of cell death characterized by pyroptosis, apoptosis, and necroptosis, but it cannot be explained by any of them alone. This study aims to explore the role of PANoptosis in ALF and the impact and mechanism of deacetylated malate dehydrogenase 1 (MDH1) and isocitrate dehydrogenase 1 (IDH1) on PANoptosis. Our results found that, compared with the control group, the cell viability in the lipopolysaccharide (LPS)/D-galactosamine (D-Gal) group decreased, lactate dehydrogenase (LDH) release increased, cell death increased, and the levels of PANoptosis-related molecules RIPK1, GSDMD, caspase-3, MLKL, IL-18, IL-1ß increased, indicating that PANoptosis increased during ALF. Deacetylated MDH1 at K118 and IDH1 at K93 increased the expression of PANoptosis-related molecules RIPK1, GSDMD, caspase-3, MLKL, IL-18, and IL-1ß in vivo and in vitro. The deacetylation weakened the inhibitory effect of histone deacetylase (HDAC) inhibitor ACY1215 on PANoptosis-related molecules, suggesting that deacetylated MDH1 at K118 and IDH1 at K93 aggravated PANoptosis during ALF. Deacetylated MDH1 at K118 and IDH1 at K93 also promoted the expression of endoplasmic reticulum stress-related molecules BIP, ATF6, XBP1, and CHOP in vivo and in vitro. The use of endoplasmic reticulum stress inhibitor 4-PBA weakened the promotion effect of deacetylated MDH1 K118 and IDH1 K93 on PANoptosis. The results suggested that deacetylated MDH1 at K118 and IDH1 at K93 may aggravate PANoptosis in ALF through endoplasmic reticulum stress signaling. In conclusion, deacetylated MDH1 and IDH1 may aggravate PANoptosis in ALF, and the mechanism may act through endoplasmic reticulum stress signaling.

Comparative Transcriptome Analysis Revealed Candidate Gene Modules Involved in Salt Stress Response in Sweet Basil and Overexpression of ObWRKY16 and ObPAL2 Enhanced Salt Tolerance of Transgenic Arabidopsis.

Sweet basil (Ocimum basilicum L.) is an important aromatic plant with high edibility and economic value, widely distributed in many regions of the tropics including the south of China. In recent years, environmental problems, especially soil salinization, have seriously restricted the planting and spread of sweet basil. However, the molecular mechanism of the salt stress response in sweet basil is still largely unknown. In this study, seed germination, seedling growth, and chlorophyll synthesis in sweet basil were inhibited under salt stress conditions. Through comparative transcriptome analysis, the gene modules involved in the metabolic processes, oxidative response, phytohormone signaling, cytoskeleton, and photosynthesis were screened out. In addition, the landscape of transcription factors during salt treatment in sweet basil was displayed as well. Moreover, the overexpression of the WRKY transcription factor-encoding gene, ObWRKY16, and the phenylalanine ammonia-lyase-encoding gene, ObPAL2, enhanced the seed germination, seedling growth, and survival rate, respectively, of transgenic Arabidopsis, suggesting that they might be important candidates for the creation of salt-tolerant sweet basil cultivars. Our data enrich the study on salt responses in sweet basil and provide essential gene resources for genetic improvements in sweet basil in the future.