The molecular weight (MW) of an enzyme is a critical parameter in enzyme-constrained models (ecModels). It is determined by two factors: the presence of subunits and the abundance of each subunit. Although the number of subunits (NS) can potentially be obtained from UniProt, this information is not readily available for most proteins. In this study, we addressed this gap by extracting and curating subunit information from the UniProt database to establish a robust benchmark dataset. Subsequently, we propose a novel model named DeepSub, which leverages the protein language model and Bi-directional Gated Recurrent Unit (GRU), to predict NS in homo-oligomers solely based on protein sequences. DeepSub demonstrates remarkable accuracy, achieving an accuracy rate as high as 0.967, surpassing the performance of QUEEN. To validate the effectiveness of DeepSub, we performed predictions for protein homo-oligomers that have been reported in the literature but are not documented in the UniProt database. Examples include homoserine dehydrogenase from Corynebacterium glutamicum, Matrilin-4 from Mus musculus and Homo sapiens, and the Multimerins protein family from M. musculus and H. sapiens. The predicted results align closely with the reported findings in the literature, underscoring the reliability and utility of DeepSub.
Databases, Protein , Deep Learning , Protein Subunits , Protein Subunits/chemistry , Protein Subunits/metabolism , Animals , Humans , Protein Multimerization , Mice , Computational Biology/methods
To enhance the import of heme for the production of active hemoproteins in Escherichia coli C41 (DE3) lacking the special heme import system, heme receptor ChuA from E. coli Nissle 1917 was modified through molecular docking and the other components (ChuTUV) for heme import was overexpressed, while heme import was tested through growth assay and heme sensor HS1 detection. A ChuA mutant G360K was selected, which could import 3.91 nM heme, compared with 2.92 nM of the wild-type ChuA. In addition, it presented that the expression of heme transporters ChuTUV was not necessary for heme import. Based on the modification of ChuA (G360K), the titer of human hemoglobin and the peroxidase activity of leghemoglobin reached 1.19 µg g-1 DCW and 24.16 103 U g-1 DCW, compared with 1.09 µg g-1 DCW and 21.56 103 U g-1 DCW of the wild-type ChuA, respectively. Heme import can be improved through the modification of heme receptor and the engineered strain with improved heme import has a potential to efficiently produce high-active hemoproteins.
The huge volume expansion/contraction of silicon (Si) during the lithium (Li) insertion/extraction process, which can lead to cracking and pulverization, poses a substantial impediment to its practical implementation in lithium-ion batteries (LIBs). The development of low-strain Si-based composite materials is imperative to address the challenges associated with Si anodes. In this study, we have engineered a TiSi2 interface on the surface of Si particles via a high-temperature calcination process, followed by the introduction of an outermost carbon (C) shell, leading to the construction of a low-strain and highly stable Si@TiSi2@NC composite. The robust TiSi2 interface not only enhances electrical and ionic transport but also, more critically, significantly mitigates particle cracking by restraining the stress/strain induced by volumetric variations, thus alleviating pulverization during the lithiation/delithiation process. As a result, the as-fabricated Si@TiSi2@NC electrode exhibits a high initial reversible capacity (2172.7 mAh g-1 at 0.2 A g-1), superior rate performance (1198.4 mAh g-1 at 2.0 A g-1), and excellent long-term cycling stability (847.0 mAh g-1 after 1000 cycles at 2.0 A g-1). Upon pairing with LiNi0.6Co0.2Mn0.2O2 (NCM622), the assembled Si@TiSi2@NC||NCM622 pouch-type full cell exhibits exceptional cycling stability, retaining 90.1% of its capacity after 160 cycles at 0.5 C.
Two-dimensional van der Waals heterostructures (2D-vdWHs) based on transition metal dichalcogenides (TMDs) provide unparalleled control over electronic properties. However, the interlayer coupling is challenged by the interfacial misalignment and defects, which hinders a comprehensive understanding of the intertwined electronic orders, especially superconductivity and charge density wave (CDW). Here, by using pressure to regulate the interlayer coupling of non-centrosymmetric 6R-TaS2 vdWHs, we observe an unprecedented phase diagram in TMDs. This phase diagram encompasses successive suppression of the original CDW states from alternating H-layer and T-layer configurations, the emergence and disappearance of a new CDW-like state, and a double superconducting dome induced by different interlayer coupling effects. These results not only illuminate the crucial role of interlayer coupling in shaping the complex phase diagram of TMD systems but also pave a new avenue for the creation of a novel family of bulk heterostructures with customized 2D properties.
SRSF1 governs splicing of over 1500 mRNA transcripts. SRSF1 contains two RNA-recognition motifs (RRMs) and a C-terminal Arg/Ser-rich region (RS). It has been thought that SRSF1 RRMs exclusively recognize single-stranded exonic splicing enhancers, while RS lacks RNA-binding specificity. With our success in solving the insolubility problem of SRSF1, we can explore the unknown RNA-binding landscape of SRSF1. We find that SRSF1 RS prefers purine over pyrimidine. Moreover, SRSF1 binds to the G-quadruplex (GQ) from the ARPC2 mRNA, with both RRMs and RS being crucial. Our binding assays show that the traditional RNA-binding sites on the RRM tandem and the Arg in RS are responsible for GQ binding. Interestingly, our FRET and circular dichroism data reveal that SRSF1 unfolds the ARPC2 GQ, with RS leading unfolding and RRMs aiding. Our saturation transfer difference NMR results discover that Arg residues in SRSF1 RS interact with the guanine base but not other nucleobases, underscoring the uniqueness of the Arg/guanine interaction. Our luciferase assays confirm that SRSF1 can alleviate the inhibitory effect of GQ on gene expression in the cell. Given the prevalence of RNA GQ and SR proteins, our findings unveil unexplored SR protein functions with broad implications in RNA splicing and translation.
G-Quadruplexes , Protein Binding , Serine-Arginine Splicing Factors , Serine-Arginine Splicing Factors/metabolism , Serine-Arginine Splicing Factors/genetics , Serine-Arginine Splicing Factors/chemistry , Humans , Binding Sites , RNA Splicing , RNA Recognition Motif/genetics , RNA, Messenger/metabolism , RNA, Messenger/genetics , RNA, Messenger/chemistry , RNA/metabolism , RNA/genetics , RNA/chemistry
The mitochondrial calcium uniporter (MCU) occupies a noteworthy position in the regulation of mitochondrial calcium uptake. This study investigated the effects of MCU modulator-mediated mitochondrial calcium on mitochondrial dysfunction, oxidative stress, endogenous enzyme activities, and tenderness during postmortem aging. Spermine, as an activator of MCU, resulted in an increase in mitochondrial calcium levels, not only disrupting mitochondrial morphology but also triggering mitochondrial oxidative stress and downregulation of antioxidant factors. Additionally, the spermine group underwent later activation of calpain and earlier activation of caspases, as well as the myofibril fragmentation index was initially lower and then higher compared with control group, indicating that endogenous enzymes played an indispensable role in different aging periods. Interestingly, the results of the Ru360 (an inhibitor of MCU) group were opposite to those aforementioned findings. Our data provide a novel perspective on the regulatory mechanism of mitochondrial calcium homeostasis mediated by MCU on tenderness.
Chitosan stands out as the only known polysaccharide of its kind, second only to cellulose. As the second-largest biopolymer globally, chitosan and its derivatives are extensively used in diverse areas such as metal anti-corrosion prevention, food production, and medical fields. Its benefits include environmental friendliness, non-toxicity, cost-effectiveness, and biodegradability. Notably, the use of chitosan and its derivatives has gained substantial attention and has been extensively researched in the fields of metal anti-corrosion prevention and antibacterial applications. By means of chemical modification or synergistic action, the inherent limitations of chitosan can be substantially improved, thereby enhancing its biological and physicochemical properties to meet a wider range of applications and more demanding application requirements. This article offers a comprehensive review of chitosan and its modified composite materials, focusing on the enhancement of their anticorrosion and antibacterial properties, as well as the mechanisms by which they serve as anticorrosion and antibacterial agents. Additionally, it summarizes the synthesis routes of various modification methods of chitosan and their applications in different fields, aiming to contribute to the interdisciplinary development and potential applications of chitosan in various areas.
Corporate energy transition is crucial for long-term sustainable development. The widely discussed Artificial Intelligence (AI), as a disruptive technological innovation, is highly potential for enhancing environment performance. However, the specific impact of AI on the process of corporate energy transition and its underlying mechanisms have not been fully explored. This study focuses on A-share listed corporates in Shanghai and Shenzhen stock markets in China spanning from 2011 to 2021. Based on corporate annual report information and information from over 200,000 patent application texts, we innovatively construct indicators for corporate energy transition and AI technology application. Furthermore, we empirically investigate the impact of AI technology on corporate energy transition and its potential mechanisms through combining information asymmetry theory and institutional theory. The empirical results indicate that: 1) AI can drive corporate energy transition and the promoting effect of AI collaborative innovation on corporate energy transition should not be ignored. 2) AI can help corporates achieve energy transition through pathways such as mitigating information asymmetry, reducing financing constraints, adjusting sustainable development concepts and practices. 3) The driving effect of AI on corporate energy transition varies depending on the characteristics of different types of corporates, industries, and regions. This study provides strategic guidance and decision support for business managers and policymakers, assisting both corporates and governments in better utilizing AI technology during the social energy transition process to achieve a dual optimization of environmental and economic goals.
Artificial Intelligence , Organizations , China , Government , Commerce
BACKGROUND: Psoriasis is a chronic immune-mediated skin condition. Although biologic treatments are effective in controlling psoriasis, some patients do not respond or lose response to these therapies. Thus, new strategies for psoriasis treatment are still urgently needed. Double-negative T cells (DNT) play a significant immunoregulatory role in autoimmune diseases. In this study, we aimed to evaluate the protective effect of DNT in psoriasis and explore the underlying mechanism. METHODS: We conducted a single adoptive transfer of DNT into an imiquimod (IMQ)-induced psoriasis mouse model through tail vein injection. The skin inflammation and IL-17A producing γδ T cells were evaluated. RESULTS: DNT administration significantly reduced the inflammatory response in mouse skin, characterized by decreased skin folds, scales, and red patches. After DNT treatment, the secretion of IL-17A by RORc+ γδlow T cells in the skin was selectively suppressed, resulting in an amelioration of skin inflammation. Transcriptomic data suggested heightened expression of NKG2D ligands in γδlow T cells within the mouse model of psoriasis induced by IMQ. When blocking the NKG2D ligand and NKG2D (expressed by DNT) interaction, the cytotoxic efficacy of DNT against RORc+IL17A+ γδlow T cells was attenuated. Using Ccr5-/- DNT for treatment yielded evidence that DNT migrates into inflamed skin tissue and fails to protect IMQ-induced skin lesions. CONCLUSIONS: DNT could migrate to inflamed skin tissue through CCR5, selectively inhibit IL-17-producing γδlow T cells and finally ameliorate mouse psoriasis. Our study provides feasibility for using immune cell therapy for the prevention and treatment of psoriasis in the clinic.
Interleukin-17 , Psoriasis , Humans , Mice , Animals , Interleukin-17/metabolism , NK Cell Lectin-Like Receptor Subfamily K/metabolism , Psoriasis/therapy , Skin/pathology , Imiquimod/adverse effects , Imiquimod/metabolism , Inflammation/pathology , T-Lymphocytes/metabolism , Disease Models, Animal
From higher computational efficiency to enabling the discovery of novel and complex structures, deep learning has emerged as a powerful framework for the design and optimization of nanophotonic circuits and components. However, both data-driven and exploration-based machine learning strategies have limitations in their effectiveness for nanophotonic inverse design. Supervised machine learning approaches require large quantities of training data to produce high-performance models and have difficulty generalizing beyond training data given the complexity of the design space. Unsupervised and reinforcement learning-based approaches on the other hand can have very lengthy training or optimization times associated with them. Here we demonstrate a hybrid supervised learning and reinforcement learning approach to the inverse design of nanophotonic structures and show this approach can reduce training data dependence, improve the generalizability of model predictions, and significantly shorten exploratory training times. The presented strategy thus addresses several contemporary deep learning-based challenges, while opening the door for new design methodologies that leverage multiple classes of machine learning algorithms to produce more effective and practical solutions for photonic design.
Background: Asthma, characterized by recurrent wheezing, breathlessness, chest tightness, and coughing, is a major health concern among children and adolescents worldwide, currently affecting more than 5 million children. The increasing prevalence of obesity and overweight among the pediatric population has made the issue of childhood respiratory health more complex. Compared with children of healthy weight, the risk of asthma is higher in overweight and obese children. Zinc, a nutrient that regulates the oxidant-antioxidant balance, has been studied for its potential protective effects against asthma in adults and children. However, the results are controversial, with some studies reporting a beneficial effect and others showing no effect. Therefore, our objective was to assess the correlation between zinc intake from diet and asthma occurrence among children and adolescents who are overweight or obese. Methods: The National Health and Nutrition Examination Survey (NHANES) (2011-2020) provided data on individuals aged ≤20 who were overweight or obese, had asthma, and consumed zinc in their diet. The association between dietary zinc and asthma was evaluated using a variety of statistical methods, including multivariate logistic regression, restricted cubic spline analysis, and subgroup analysis. Results: A total of 4597 pediatrics and adolescents were enrolled, with 20.9% (963/4597) suffering from asthma. After adjusting for all covariates in the multivariate logistic regression, compared with the lowest zinc intake group Q1(≤5.68 mg/day), the adjusted OR values for zinc intake and asthma in Q2 (5.69-8.36 mg/day), Q3 (8.37-11.95 mg/day), and Q4 (≥11.96 mg/day) were 0.78 (95% CI: 0.62-0.98, p = 0.03), 0.76 (95% CI: 0.6â¼0.98, p = 0.032), 0.71 (95% CI: 0.53â¼0.95, p = 0.022), respectively. Stratified analysis showed no interactive role for dietary zinc intake and asthma in overweight or obese children and adolescents. Conclusions: Dietary zinc intake is inversely associated with asthma in overweight or obese children and adolescents.
Docosahexaenoic acid (DHA) is an essential component for brain development during fetal and early postnatal life. Hyperbilirubinemia is characterized by abnormally high levels of bilirubin in the bloodstream, frequently leading to jaundice in newborns. In severe instances, this condition can progress to neurological damage or kernicterus, a form of brain damage. Initial cell-based experiments conducted by our research team revealed that DHA significantly enhances the survival rate of nerve cells treated with bilirubin and diminishes the oxidative stress indicated by reduced peroxide activity caused by unconjugated bilirubin (UCB). Further investigations through animal studies demonstrated that DHA effectively mitigates bilirubin-induced brain injury in neonatal rats. However, the potential of DHA to decrease the incidence of bilirubin-induced brain damage in clinical settings has not been previously explored or reported. Infants with neonatal hyperbilirubinemia (n = 30 per group) participated in a double-blind, randomized, placebo-controlled parallel study. They received either 100 mg/d DHA or placebo syrup immediately when they were diagnosed. The study found that the bilirubin level at 48 hours of treatment, serum neuron-specific enolase (NSE) levels, mean phototherapy duration, and abnormal rate of cranial magnetic resonance imaging (MRI) were lower in the DHA group than those in the control group (P < .05). These results suggested that DHA is effective as an adjuvant treatment for hyperbilirubinemia in children. It can reduce the incidence of neonatal hyperbilirubinemia brain injury and plays a certain protective role. Clinical study on protective effect of DHA on neonatal bilirubin injury is registered at Chinese Clinical Trial Registry as ChiCTR2300070250.
The Ser/Arg-rich splicing factors (SR proteins) constitute a crucial protein family in alternative splicing, comprising twelve members characterized by unique repetitive Arg-Ser dipeptide sequences (RS) and one to two RNA-recognition motifs (RRM). The RS regions of SR proteins undergo variable phosphorylation, resulting in unphosphorylated, partially phosphorylated, or hyper-phosphorylated states based on functional requirements. Despite the identification of the SR protein family over 30 years ago, the purification of native SR proteins in soluble form at large quantities has presented challenges due to their low solubility. This protocol delineates a method for acquiring soluble, full-length, unphosphorylated, hypo- and hyper-phosphorylated SRSF1, a prototypical SR family member. Notably, this protocol facilitates the purification of SRSF1 in ample quantities suitable for NMR, as well as various biophysical and biochemical studies. The methodologies and principles outlined herein are expected to extend beyond SRSF1 protein production and can be adapted for purifying other SR protein family members or SR-related proteins, such as snRNP70 and U2AF-35. Given the involvement of these proteins in numerous essential biological processes, this protocol will prove beneficial to researchers in related fields. © 2024 The Authors. Current Protocols published by Wiley Periodicals LLC. Basic Protocol 1: Purification of SRSF1 from E. coli Support Protocol: Purification of ULP1 Basic Protocol 2: Purification of hypo-phosphorylated SRSF1 from E. coli Basic Protocol 3: Purification of hyper-phosphorylated SRSF1 from E. coli.
Escherichia coli , Proteins , Escherichia coli/genetics , Phosphorylation , Alternative Splicing
The Yangtze River fishery resources have declined strongly over the past few decades. One suspected reason for the decline in fishery productivity, including silver carp (Hypophthalmichthys molitrix), has been linked to organophosphate esters (OPEs) contaminant exposure. In this study, the adverse effect of OPEs on lipid metabolism in silver carp captured from the Yangtze River was examined, and our results indicated that muscle concentrations of the OPEs were positively associated with serum cholesterol and total lipid levels. In vivo laboratory results revealed that exposure to environmental concentrations of OPEs significantly increased the concentrations of triglyceride, cholesterol, and total lipid levels. Lipidome analysis further confirmed the lipid metabolism dysfunction induced by OPEs, and glycerophospholipids and sphingolipids were the most affected lipids. Hepatic transcriptomic analysis found that OPEs caused significant alterations in the transcription of genes involved in lipid metabolism. Pathways associated with lipid homeostasis, including the peroxisome proliferator-activated receptor (PPAR) signal pathway, cholesterol metabolism, fatty acid biosynthesis, and steroid biosynthesis, were significantly changed. Furthermore, the affinities of OPEs were different, but the 11 OPEs tested could bind with PPARγ, suggesting that OPEs could disrupt lipid metabolism by interacting with PPARγ. Overall, this study highlighted the harmful effects of OPEs on wild fish and provided mechanistic insights into OPE-induced metabolic disorders.
Carps , Flame Retardants , Metabolic Diseases , Animals , Rivers , PPAR gamma , Esters/analysis , Organophosphates/toxicity , Organophosphates/analysis , Cholesterol/analysis , Lipids , Flame Retardants/analysis , China , Environmental Monitoring/methods
Black goji berry (Lycium ruthenicum Murray) contains a rich source of health-promoting anthocyanins which are used in herbal medicine and nutraceutical foods in China. A natural variant producing white berries allowed us to identify two key genes involved in the regulation of anthocyanin biosynthesis in goji berries: one encoding a MYB transcription factor (LrAN2-like) and one encoding a basic helix-loop-helix (bHLH) transcription factor (LrAN1b). We previously found that LrAN1b expression was lost in the white berry variant, but the molecular basis for this phenotype was unknown. Here, we identified the molecular mechanism for loss of anthocyanins in white goji berries. In white goji, the LrAN1b promoter region has a 229-bp deletion that removes 3 MYB-binding elements and 1 bHLH-binding element, which are key to its expression. Complementation of the white goji berry LrAN1b allele with the LrAN1b promoter restored pigmentation. Virus-induced gene silencing of LrAN1b in black goji berry reduced fruit anthocyanin biosynthesis. Molecular analyses showed that LrAN2-like and another bHLH transcription factor LrJAF13 can activate LrAN1b by binding directly to the MYB-recognizing element (MRE) and bHLH-recognizing element (BRE) of its promoter-deletion region. LrAN1b expression is enhanced by the interaction of LrAN2-like with LrJAF13 and the WD40 protein LrAN11. LrAN2-like and LrAN11 interact with either LrJAF13 or LrAN1b to form two MYB-bHLH-WD40 (MBW) complexes, which hierarchically regulate anthocyanin biosynthesis in black goji berry. This study on a natural variant builds a comprehensive anthocyanin regulatory network that may be manipulated to tailor goji berry traits.
The fat in coconut milk contributes to unique flavour, while increasing fat content affects stability of the coconut milk. In this study, coconut water and fat were separated, recombined, and homogenized to obtain coconut milk with different fat contents (0-20 %). Emulsifying properties, stability, and digestibility of coconut milk with different fat contents were comprehensively evaluated. The results showed that as the fat content increased from 0 to 20 %, the droplet size increased from 2.18 to 4.70 µm and the viscosity showed an increasing trend. During storage and freeze-thaw, coconut milk with 5 % and 10 % fat content showed excellent stability. In addition, coconut milk with 10 % fat content had superior fat digestibility, which was related to high affinity of pancrelipase. In short, this study revealed that fat content below 10 % can withstand environmental factors such as storage, lipid oxidation, and freeze-thaw, which can be accurately developed as coconut milk products.
Cocos , Milk , Animals , Viscosity
The instability and high electron-hole recombination have limited the application of black phosphorus (BP) as an excellent photocatalyst. To address these challenges, poly dimethyl diallyl ammonium chloride (PDDA), poly (allylamine hydrochloride) (PAH), and polyethyleneimine (PEI) are introduced to the functionalization of BP (F-BP), which can not only enhance its stability, but also boost the carrier transfer. Furthermore, a high-performance heterojunction photocatalyst is fabricated using F-BP and titania nanosheets (TNs) via a layer-by-layer self-assembly approach. The experimental outcomes unequivocally indicate that F-BP exhibits fast charge migration compared to BP. The density functional theory (DFT), in situ Kelvin-probe force microscopy (KPFM) and other advanced characterization techniques collectively unfold that PDDA modified BP can notably boost separation and propagation of charges, along with an enhanced carrier abundance. In summary, this novel strategy of using polyelectrolytes to enhance the electron transfer and the stability of BP permits immense potential in building next-generation BP-based high efficiency photocatalysts.
The theory-led prediction of LaBeH8, which has a high superconducting critical temperature (Tc) above liquid nitrogen under a pressure level below 1 Mbar, has been experimentally confirmed. YBeH8, which has a structural configuration similar to that of LaBeH8, has also been predicted to be a high-temperature superconductor at high pressure. In this study, we focus on the structural phase transition and superconductivity of YBeH8 under pressure by using first-principles calculations. Except for the known face-centered cubic phase of Fm3Ìm, we found a monoclinic phase with P1Ì symmetry. Moreover, the P1Ì phase transforms to the Fm3Ìm phase at â¼200 GPa with zero-point energy corrections. Interestingly, the P1Ì phase undergoes a complex electronic phase transition from semiconductor to metal and then to superconducting states with a low Tc of 40 K at 200 GPa. The Fm3Ìm phase exhibits a high Tc of 201 K at 200 GPa, and its Tc does not change significantly with pressure. When we combine the method using two coupling constants, λopt and λac, with first-principles calculations, λopt is mainly supplied by the Be-H alloy backbone, which accounts for about 85% of total λ and makes the greatest contribution to the high Tc. These insights not only contribute to a deeper understanding of the superconducting behavior of this ternary hydride but may also guide the experimental synthesis of hydrogen-rich compounds.
Breast cancer stem cells (BCSCs) are responsible for breast cancer metastasis, recurrence and treatment resistance, all of which make BCSCs potential drivers of breast cancer aggression. Ginsenoside Rg3, a traditional Chinese herbal medicine, was reported to have multiple antitumor functions. Here, we revealed a novel effect of Rg3 on BCSCs. Rg3 inhibits breast cancer cell viability in a dose- and time-dependent manner. Importantly, Rg3 suppressed mammosphere formation, reduced the expression of stemness-related transcription factors, including c-Myc, Oct4, Sox2 and Lin28, and diminished ALDH(+) populations. Moreover, tumor-bearing mice treated with Rg3 exhibited robust delay of tumor growth and a decrease in tumor-initiating frequency. In addition, we found that Rg3 suppressed breast cancer stem-like properties mainly through inhibiting MYC expression. Mechanistically, Rg3 accelerated the degradation of MYC mRNA by enhancing the expression of the let-7 family, which was demonstrated to bind to the MYC 3' untranslated region (UTR). In conclusion, our findings reveal the remarkable suppressive effect of Rg3 on BCSCs, suggesting that Rg3 is a promising therapeutic treatment for breast cancer.
