Exogenous application of the apocarotenoid retinaldehyde negatively regulates auxin-mediated root growth.

Root development is essential for plant survival. The lack of carotenoid biosynthesis in the phytoene desaturase 3 (pds3) mutant results in short primary roots (PR) and reduced lateral root (LR) formation. In this study, we showed that short-term inhibition of PDS by fluridone suppresses PR growth in WT, but to a lesser extent in auxin mutants of Arabidopsis (Arabidopsis thaliana). Such an inhibition of PDS activity increased endogenous indole-3-acetic acid (IAA) levels, promoted auxin signaling, and partially complemented the PR growth of an auxin deficient mutant, the YUCCA 3 5 7 8 9 quadruple mutant (yucQ). The exogenous application of retinaldehyde (retinal), an apocarotenoid derived from ß-carotene, complemented the fluridone-induced suppression of root growth, as well as the short roots of the pds3 mutant. Retinal also partially complemented the auxin-induced suppression of root growth. These results suggest that retinal may play a role in regulating root growth by modulating endogenous auxin levels.

Lactylome Analysis Unveils Lactylation-Dependent Mechanisms of Stemness Remodeling in the Liver Cancer Stem Cells.

Lactate plays a critical role as an energy substrate, metabolite, and signaling molecule in hepatocellular carcinoma (HCC). Intracellular lactate-derived protein lysine lactylation (Kla) is identified as a contributor to the progression of HCC. Liver cancer stem cells (LCSCs) are believed to be the root cause of phenotypic and functional heterogeneity in HCC. However, the impact of Kla on the biological processes of LCSCs remains poorly understood. Here enhanced glycolytic metabolism, lactate accumulation, and elevated levels of lactylation are observed in LCSCs compared to HCC cells. H3K56la was found to be closely associated with tumourigenesis and stemness of LCSCs. Notably, a comprehensive examination of the lactylome and proteome of LCSCs and HCC cells identified the ALDOA K230/322 lactylation, which plays a critical role in promoting the stemness of LCSCs. Furthermore, this study demonstrated the tight binding between aldolase A (ALDOA) and dead box deconjugate enzyme 17 (DDX17), which is attenuated by ALDOA lactylation, ultimately enhancing the regulatory function of DDX17 in maintaining the stemness of LCSCs. This investigation highlights the significance of Kla in modulating the stemness of LCSCs and its impact on the progression of HCC. Targeting lactylation in LCSCs may offer a promising therapeutic approach for treating HCC.

Non-targeted metabolomics and explainable artificial intelligence: Effects of processing and color on coniferyl aldehyde levels in Eucommiae cortex.

Eucommia ulmoides, a plant native to China, is valued for its medicinal properties and has applications in food, health products, and traditional Chinese medicine. Processed Eucommiae Cortex (EC) has historically been a highly valued medicine. Ancient doctors had ample experience processing EC, especially with ginger juice, as documented in traditional Chinese medical texts. The combination of EC and ginger juice helps release and transform the active ingredients, strengthening the medicine's effectiveness and improving its taste and shelf life. However, the lack of quality control standards for Ginger-Eucommiae Cortex (G-EC), processed from EC and ginger, presents challenges for its industrial and clinical use. This study optimized G-EC processing using the CRITIC and Box-Behnken methods. Metabolomics showed 517 chemical changes between raw and processed G-EC, particularly an increase in coniferyl aldehyde (CFA). Explainable artificial intelligence techniques revealed the feasibility of using color to CFA content, providing insights into quality indicators.

Binding uric acid: a pure chemical solution for the treatment of hyperuricemia.

Hyperuricemia, characterized by elevated uric acid levels and subsequent crystal deposition, contributing to conditions such as gout, cardiovascular events, and kidney injury, poses a significant health threat, particularly in developed countries. Current drug options for treatment are limited, with safety concerns, leading to suboptimal therapeutic outcomes in symptomatic hyperuricemia patients and a lack of pharmaceutical interventions for asymptomatic cases. Distinguishing from the previous drug design strategies, we directly target uric acid, the pathological molecule of hyperuricemia, resulting in a pyrimidine derivative capable of increasing the solubility and excretion of uric acid by forming a complex with it. Its prodrug showed an anti-hyperuricemia activity comparable to benzbromarone and a favorable safety profile in vivo. Our finding provides a strategy purely based on organic chemistry to address the largely unmet therapeutic needs on novel anti-hyperuricemia drugs.

Lumican promotes calcific aortic valve disease through H3 histone lactylation.

BACKGROUND AND AIMS: Valve interstitial cells (VICs) undergo a transition to intermediate state cells before ultimately transforming into the osteogenic cell population, which is a pivotal cellular process in calcific aortic valve disease (CAVD). Herein, this study successfully delineated the stages of VIC osteogenic transformation and elucidated a novel key regulatory role of lumican (LUM) in this process. METHODS: Single-cell RNA-sequencing (scRNA-seq) from nine human aortic valves was used to characterize the pathological switch process and identify key regulatory factors. The in vitro, ex vivo, in vivo, and double knockout mice were constructed to further unravel the calcification-promoting effect of LUM. Moreover, the multi-omic approaches were employed to analyse the molecular mechanism of LUM in CAVD. RESULTS: ScRNA-seq successfully delineated the process of VIC pathological transformation and highlighted the significance of LUM as a novel molecule in this process. The pro-calcification role of LUM is confirmed on the in vitro, ex vivo, in vivo level, and ApoE-/-//LUM-/- double knockout mice. The LUM induces osteogenesis in VICs via activation of inflammatory pathways and augmentation of cellular glycolysis, resulting in the accumulation of lactate. Subsequent investigation has unveiled a novel LUM driving histone modification, lactylation, which plays a role in facilitating valve calcification. More importantly, this study has identified two specific sites of histone lactylation, namely, H3K14la and H3K9la, which have been found to facilitate the process of calcification. The confirmation of these modification sites' association with the expression of calcific genes Runx2 and BMP2 has been achieved through ChIP-PCR analysis. CONCLUSIONS: The study presents novel findings, being the first to establish the involvement of lumican in mediating H3 histone lactylation, thus facilitating the development of aortic valve calcification. Consequently, lumican would be a promising therapeutic target for intervention in the treatment of CAVD.

Molecular characterization and clinical relevance of metabolic signature subtypes in gastric cancer.

Metabolic reprogramming dictates tumor molecular attributes and therapeutic potentials. However, the comprehensive metabolic characteristics in gastric cancer (GC) remain obscure. Here, metabolic signature-based clustering analysis identifies three subtypes with distinct molecular and clinical features: MSC1 showed better prognosis and upregulation of the tricarboxylic acid (TCA) cycle and lipid metabolism, combined with frequent TP53 and RHOA mutation; MSC2 had moderate prognosis and elevated nucleotide and amino acid metabolism, enriched by intestinal histology and mismatch repair deficient (dMMR); and MSC3 exhibited poor prognosis and enhanced glycan and energy metabolism, accompanied by diffuse histology and frequent CDH1 mutation. The Shandong Provincial Hospital (SDPH) in-house dataset with matched transcriptomic, metabolomic, and spatial-metabolomic analysis also validated these findings. Further, we constructed the metabolic subtype-related prognosis gene (MSPG) scoring model to quantify the activity of individual tumors and found a positive correlation with cuproptosis signaling. In conclusion, comprehensive recognition of the metabolite signature can enhance the understanding of diversity and heterogeneity in GC.

Photoinduced Charge Injection from Shallow Point Defects in Diamond into Water.

Thanks to its low or negative surface electron affinity and chemical inertness, diamond is attracting broad attention as a source material of solvated electrons produced by optical excitation of the solid-liquid interface. Unfortunately, its wide bandgap typically imposes the use of wavelengths in the ultraviolet range, hence complicating practical applications. Here, we probe the photocurrent response of water surrounded by single-crystal diamond surfaces engineered to host shallow nitrogen-vacancy (NV) centers. We observe clear signatures of diamond-induced photocurrent generation throughout the visible range and for wavelengths reaching up to 594 nm. Experiments as a function of laser power suggest that NV centers and other coexisting defects─likely in the form of surface traps─contribute to carrier injection, though we find that NVs dominate the system response in the limit of high illumination intensities. Given our growing understanding of near-surface NV centers and adjacent point defects, these results open new perspectives in the application of diamond-liquid interfaces to photocarrier-initiated chemical and spin processes in fluids.

Highly oriented BN-based TIMs with high through-plane thermal conductivity and low compression modulus.

In the pursuit of effective thermal management for electronic devices, it is crucial to develop insulation thermal interface materials (TIMs) that exhibit exceptional through-plane thermal conductivity, low thermal resistance, and minimal compression modulus. Boron nitride (BN), given its outstanding thermal conduction and insulation properties, has garnered significant attention as a potential material for this purpose. However, previously reported BN-based composites have consistently demonstrated through-plane thermal conductivity below 10 W m-1 K-1 and high compression modulus, whilst also presenting challenges in terms of mass production. In this study, low molecular weight polydimethylsiloxane (PDMS) and large-size BN were utilized as the foundational materials. Utilizing a rolling-curing integrated apparatus, we successfully accomplished the continuous preparation of large-sized, high-adhesion BN films. Subsequent implementation of stacking, cold pressing, and vertical cutting techniques enabled the attainment of a remarkable BN-based TIM, characterized by an unprecedented through-plane thermal conductivity of up to 12.11 W m-1 K-1, remarkably low compression modulus (55 kPa), and total effective thermal resistance (0.16 °C in2 W-1, 50 Psi). During the TIMs performance evaluation, our TIMs demonstrated superior heat dissipation capabilities compared with commercial TIMs. At a heating power density of 40 W cm-2, the steady-state temperature of the ceramic heating element was found to be 7 °C lower than that of the commercial TIMs. This pioneering feat not only contributes valuable technical insights for the development of high-performance insulating TIMs but also establishes a solid foundation for widespread implementation in thermal management applications across a range of electronic devices.

Comprehensive characterization of the differences in metabolites, lipids, and volatile flavor compounds between Ningxiang and Berkshire pigs using multi-omics techniques.

This study was conducted to comprehensively characterize, metabolites, lipids, and volatile flavor compounds of NingXiang (NX) pigs, Berkshire (BKS) pigs, and their crossbred (Berkshire × Ningxiang, BN) pigs using multi-omics technique. The results showed that NX had high intramuscular fat (IMF) content and meat redness. The metabolite and lipid compositions were varied greatly among three pig breeds. The NX pigs exhibited distinctive sweet, fruity, and floral aroma while BN pigs have inherited this flavor profile. 2-pentylfuran, pentanal, 2-(E)-octenal, and acetic acid were the key volatile flavor compounds (VOC) of NX and BKS pork. The VOCs were influenced by the composition and content of metabolites and lipids. The NX pigs have excellent meat quality traits, unique flavor profiles, and high degree of genetic stability regarding flavor. The study deepens our understanding of the flavor of Chinese indigenous pigs, providing theoretical basis to understand the meat flavor regulation under different feeding conditions.

Linking Interfacial Structure and Electrochemical Behaviors of Batteries by High-Resolution Electrocapillarity.

The electrode-electrolyte interface governs the kinetics and reversibility of all electrochemical processes. While theoretical models can calculate and simulate the structure and associated properties of this intriguing component, their validation by direct experimental measurement has been a long-standing challenge. Electrocapillarity is a classical technique that derives the interfacial structure through potential-dependent surface tensions, but its limited resolution has confined its application to ideal systems such as extremely diluted aqueous electrolytes. In this work, we revive this technique with unprecedented time resolution, which allows fast and precise extraction of intrinsic interfacial structure and properties for a wide spectrum of electrolytes, be it ideal or nonideal, aqueous or nonaqueous, dilute or superconcentrated. For the very first time, this new electrocapillarity enables the measurements of a set of interfacial quantities, such as ion concentration distribution and potential drop across Helmholtz planes. Applying it on Zn-battery electrolytes, we discovered that Cl- specific adsorption at the inner-Helmholtz plane results in unexpected Zn2+ aggregation at the outer-Helmholtz plane, and identified such a unique interfacial structure as the fundamental driving force for fast Zn deposition/stripping kinetics and crystallographic texturing. The renaissance of electrocapillarity brings a new tool to the understanding and design of new electrolytes for future battery systems.

Functional network reorganization after endovascular thrombectomy in patients with anterior circulation stroke.

BACKGROUND: Endovascular thrombectomy has been confirmed to be an effective therapy for acute ischemic stroke (AIS). However, how functional brain networks reorganize after restoration of blood supply in AIS patients, and whether the degree of reperfusion associates with functional network changes remains unclear. METHODS: Resting-state fMRI data were collected from 43 AIS patients with anterior circulation occlusion after thrombectomy and 37 healthy controls (HCs). Both static and dynamic functional connectivity (FC) within four advanced functional networks including dorsal attention network (DAN), ventral attention network (VAN), executive control network (ECN) and default mode network (DMN), were calculated and compared between post-thrombectomy patients and HCs, and between two subgroups of post-thrombectomy patients with different reperfusion conditions. RESULTS: As compared to HCs, patients showed significant differences in static FC of four functional networks, and in dynamic FC of DAN, ECN and DMN. Furthermore, patients with better reperfusion conditions exhibited increased static FC with precuneus, and altered dynamic FC within precuneus. Moreover, these alterations were associated with clinical assessments of stroke severity and functional recovery in post-thrombectomy patients. CONCLUSIONS: Collectively, these findings may provide the potential imaging markers for assessment of thrombectomy efficacy and help establish the specific rehabilitation treatments for post-thrombectomy patients.

Applicability of wheat brewer's spent grain in steamed bread-making based on physicochemical and visual profiles assessment of doughs and breads.

Brewer's spent grain (BSG), one of the main byproducts of brewing, has been widely used in the food industry due to its high nutritional components of dietary fiber, proteins, polysaccharides, and polyphenols. This study investigated the influence of wheat brewer's spent grain (WBSG) on the physicochemical properties of dough and steamed bread-making performance. The incorporation of WBSG in wheat flour significantly increased water absorption, development time, and degree of softening while decreasing the stability time of blending dough. Excessive WBSG up to 20% restricted the dough formation. WBSG contributed to the remarkable increase of pasting viscosities, pasting temperature, and immobilized water proportion in doughs. For all doughs, storage moduli (G') were higher than viscous moduli (G″). WBSG addition resulted in higher moduli values and the formation of highly networked gluten structure, finally leading to the lower specific volume, spread ratio, and elasticity of bread. Lightness (L*) of bread decreased with increasing WBSG while redness (a*) and total color difference (ΔE) augmented. Low WBSG addition (≤5%) could endow steamed bread with the appearance of a chocolate-like color and pleasant malt flavor, which is acceptable for most consumers. Nevertheless, the improvement of nutritional and functional characteristics of steamed bread incorporated with WBSG should be more focused in the future.

Guiding post-pancreaticoduodenectomy interventions for pancreatic cancer patients utilizing decision tree models.

Background: Pancreatic ductal adenocarcinoma (PDAC) is frequently diagnosed in advanced stages, necessitating pancreaticoduodenectomy (PD) as a primary therapeutic approach. However, PD surgery can engender intricate complications. Thus, understanding the factors influencing postoperative complications documented in electronic medical records and their impact on survival rates is crucial for improving overall patient outcomes. Methods: A total of 749 patients were divided into two groups: 598 (79.84%) chose the RPD (Robotic pancreaticoduodenectomy) procedure and 151 (20.16%) chose the LPD (Laparoscopic pancreaticoduodenectomy) procedure. We used correlation analysis, survival analysis, and decision tree models to find the similarities and differences about postoperative complications and prognostic survival. Results: Pancreatic cancer, known for its aggressiveness, often requires pancreaticoduodenectomy as an effective treatment. In predictive models, both BMI and surgery duration weigh heavily. Lower BMI correlates with longer survival, while patients with heart disease and diabetes have lower survival rates. Complications like delayed gastric emptying, pancreatic fistula, and infection are closely linked post-surgery, prompting conjectures about their causal mechanisms. Interestingly, we found no significant correlation between nasogastric tube removal timing and delayed gastric emptying, suggesting its prompt removal post-decompression. Conclusion: This study aimed to explore predictive factors for postoperative complications and survival in PD patients. Effective predictive models enable early identification of high-risk individuals, allowing timely interventions. Higher BMI, heart disease, or diabetes significantly reduce survival rates in pancreatic cancer patients post-PD. Additionally, there's no significant correlation between DGE incidence and postoperative extubation time, necessitating further investigation into its interaction with pancreatic fistula and infection.

Aromaticity Tuning of Heavy-Atom-Free Photosensitizers for Singlet Fission-Enhanced Immunogenic Photodynamic Oncotherapy.

The quantum yield of reactive oxygen species is of central importance for the development of organic photosensitizers and photodynamic therapy (PDT). A common molecular design approach for optimizing organic photosensitizers involves the incorporation of heavy atoms into their backbones. However, this raises concerns regarding heightened dark cytotoxicity and a shortened triplet-state lifetime. Herein, we demonstrate a heavy-atom-free (HAF) photosensitizer design strategy founded on the singlet fission (SF) mechanism for cancer PDT. Through the "single-atom surgery" approach to deleting oxygen atoms in pyrazino[2,3-g]quinoxaline skeleton photosensitizers, photosensitizers PhPQ and TriPhPQ are produced with Huckel's aromaticity and Baird's aromaticity in the ground state and triplet state, respectively, enabling the generation of two triplet excitons through SF. The SF process endows photosensitizer PhPQ with an ultrahigh triplet-state quantum yield (186%) and an outstanding 1O2 quantum yield (177%). Notably, HAF photosensitizers PhPQ and TriPhPQ enhanced PDT efficacy and potentiated αPD-L1 immune check blockade therapy in vivo, which show their promise for translational oncology treatment.

Stratifying TAD boundaries pinpoints focal genomic regions of regulation, damage, and repair.

Advances in chromatin mapping have exposed the complex chromatin hierarchical organization in mammals, including topologically associating domains (TADs) and their substructures, yet the functional implications of this hierarchy in gene regulation and disease progression are not fully elucidated. Our study delves into the phenomenon of shared TAD boundaries, which are pivotal in maintaining the hierarchical chromatin structure and regulating gene activity. By integrating high-resolution Hi-C data, chromatin accessibility, and DNA double-strand breaks (DSBs) data from various cell lines, we systematically explore the complex regulatory landscape at high-level TAD boundaries. Our findings indicate that these boundaries are not only key architectural elements but also vibrant hubs, enriched with functionally crucial genes and complex transcription factor binding site-clustered regions. Moreover, they exhibit a pronounced enrichment of DSBs, suggesting a nuanced interplay between transcriptional regulation and genomic stability. Our research provides novel insights into the intricate relationship between the 3D genome structure, gene regulation, and DNA repair mechanisms, highlighting the role of shared TAD boundaries in maintaining genomic integrity and resilience against perturbations. The implications of our findings extend to understanding the complexities of genomic diseases and open new avenues for therapeutic interventions targeting the structural and functional integrity of TAD boundaries.

Metabolic engineering for compartmentalized biosynthesis of the valuable compounds in Saccharomyces cerevisiae.

Saccharomyces cerevisiae is commonly used as a microbial cell factory to produce high-value compounds or bulk chemicals due to its genetic operability and suitable intracellular physiological environment. The current biosynthesis pathway for targeted products is primarily rewired in the cytosolic compartment. However, the related precursors, enzymes, and cofactors are frequently distributed in various subcellular compartments, which may limit targeted compounds biosynthesis. To overcome above mentioned limitations, the biosynthesis pathways are localized in different subcellular organelles for product biosynthesis. Subcellular compartmentalization in the production of targeted compounds offers several advantages, mainly relieving competition for precursors from side pathways, improving biosynthesis efficiency in confined spaces, and alleviating the cytotoxicity of certain hydrophobic products. In recent years, subcellular compartmentalization in targeted compound biosynthesis has received extensive attention and has met satisfactory expectations. In this review, we summarize the recent advances in the compartmentalized biosynthesis of the valuable compounds in S. cerevisiae, including terpenoids, sterols, alkaloids, organic acids, and fatty alcohols, etc. Additionally, we describe the characteristics and suitability of different organelles for specific compounds, based on the optimization of pathway reconstruction, cofactor supplementation, and the synthesis of key precursors (metabolites). Finally, we discuss the current challenges and strategies in the field of compartmentalized biosynthesis through subcellular engineering, which will facilitate the production of the complex valuable compounds and offer potential solutions to improve product specificity and productivity in industrial processes.

Challenges and Advancements in the Electrochemical Utilization of Ammonia Using Solid Oxide Fuel Cells.

Solid oxide fuel cells utilized with NH3 (NH3-SOFCs) have great potential to be environmentally friendly devices with high efficiency and energy density. The advancement of this technology is hindered by the sluggish kinetics of chemical or electrochemical processes occurring on anodes/catalysts. Extensive efforts have been devoted to developing efficient and durable anode/catalysts in recent decades. Although modifications to the structure, composition, and morphology of anodes or catalysts are effective, the mechanistic understandings of performance improvements or degradations remain incompletely understood. This review informatively commences by summarizing existing reports on the progress of NH3-SOFCs. It subsequently outlines the influence of factors on the performance of NH3-SOFCs. The degradation mechanisms of the cells/systems are also reviewed. Lastly, the persistent challenges in designing highly efficient electrodes/catalysts for low-temperature NH3-SOFCs, and future perspectives derived from SOFCs are discussed. Notably, durability, thermal cycling stability, and power density are identified as crucial indicators for enhancing low-temperature (550 °C or below) NH3-SOFCs. This review aims to offer an updated overview of how catalysts/electrodes affect electrochemical activity and durability, offering critical insights for improving performance and mechanistic understanding, as well as establishing the scientific foundation for the design of electrodes for NH3-SOFCs.

CanCellVar: A database for single-cell variants map in human cancer.

Numerous variants, including both single-nucleotide variants (SNVs) in DNA and A>G RNA edits in mRNA as essential drivers of cellular proliferation and tumorigenesis, are commonly associated with cancer progression and growth. Thus, mining and summarizing single-cell variants will provide a refined and higher-resolution view of cancer and further contribute to precision medicine. Here, we established a database, CanCellVar, which aims to provide and visualize the comprehensive atlas of single-cell variants in tumor microenvironment. The current CanCellVar identified ∼3 million variants (∼1.4 million SNVs and ∼1.4 million A>G RNA edits) involved in 2,754,531 cells of 5 major cell types across 37 cancer types. CanCellVar provides the basic annotation information as well as cellular and molecular function properties of variants. In addition, the clinical relevance of variants can be obtained including tumor grade, treatment, metastasis, and others. Several flexible tools were also developed to aid retrieval and to analyze cell-cell interactions, gene expression, cell-development trajectories, regulation, and molecular structure affected by variants. Collectively, CanCellVar will serve as a valuable resource for investigating the functions and characteristics of single-cell variations and their roles in human tumor evolution and treatment.

Clinical features and molecular landscape of cuproptosis signature-related molecular subtype in gastric cancer.

Recent studies have highlighted the biological significance of cuproptosis in disease occurrence and development. However, it remains unclear whether cuproptosis signaling also has potential impacts on tumor initiation and prognosis of gastric cancer (GC). In this study, 16 cuproptosis-related genes (CRGs) transcriptional profiles were harnessed to perform the regularized latent variable model-based clustering in GC. A cuproptosis signature risk scoring (CSRS) scheme, based on a weighted sum of principle components of the CRGs, was used to evaluate the prognosis and risk of individual tumors of GC. Four distinct cuproptosis signature-based clusters, characterized by differential expression patterns of CRGs, were identified among 1136 GC samples across three independent databases. The four clusters were also associated with different clinical outcomes and tumor immune contexture. Based on the CSRS, GC patients can be divided into CSRS-High and CSRS-Low subtypes. We found that DBT, MTF1, and ATP7A were significantly elevated in the CSRS-High subtype, while SLC31A1, GCSH, LIAS, DLAT, FDX1, DLD, and PDHA1 were increased in the CSRS-Low subtype. Patients with CSRS-Low score were characterized by prolonged survival time. Further analysis indicated that CSRS-Low score also correlated with greater tumor mutation burden (TMB) and higher mutation rates of significantly mutated genes (SMG) in GC. In addition, the CSRS-High subtype harbored more significantly amplified focal regions related to tumorigenesis (3q27.1, 12p12.1, 11q13.3, etc.) than the CSRS-Low tumors. Drug sensitivity analyses revealed the potential compounds for the treatment of gastric cancer with CSRS-High score, which were experimentally validated using GC cells. This study highlights that cuproptosis signature-based subtyping is significantly associated with different clinical features and molecular landscape of GC. Quantitative evaluation of the CSRS of individual tumors will strengthen our understanding of the occurrence and development of cuproptosis and the treatment progress of GC.