Deep integration of metabolome and transcriptome characterizes alkaloid metabolism in Houttuynia cordata.

Alkaloids are the main medicinal components in Houttuynia cordata. In this study, two accessions 6# and 7# of H. cordata underwent thorough metabolomic analyses to identify and quantify alkaloid phytometabolites. It turned out that the alkaloid types were largely similar between 6# and 7#, and the identified 81 alkaloids could be divided into nine structural classes. However, the content of alkaloids in the two accessions was quite different. According to transcriptome data, a total of 114 differentially expressed genes related to alkaloid metabolism were screened. The alkaloid synthesis pathway of the two varieties was mainly different in the isoquinoline alkaloid biosynthesis and indole alkaloid biosynthesis; four genes A22110063c_transcript_59323, A22110063c_transcript_60118, A22110063c_transcript_51672 and A22110063c_transcript_48784 were highly expressed in 7#, which could be key candidate genes of alkaloid metabolism and warrant further analysis. These results provide a reference for the medicinal application of H. cordata and breeding alkaloid rich varieties.

Differential performance of RoseTTAFold in antibody modeling.

Antibodies are essential to life, and knowing their structures can facilitate the understanding of antibody-antigen recognition mechanisms. Precise antibody structure prediction has been a core challenge for a prolonged period, especially the accuracy of H3 loop prediction. Despite recent progress, existing methods cannot achieve atomic accuracy, especially when the homologous structures required for these methods are not available. Recently, RoseTTAFold, a deep learning-based algorithm, has shown remarkable breakthroughs in predicting the 3D structures of proteins. To assess the antibody modeling ability of RoseTTAFold, we first retrieved the sequences of 30 antibodies as the test set and used RoseTTAFold to model their 3D structures. We then compared the models constructed by RoseTTAFold with those of SWISS-MODEL in a different way, in which we stratified Global Model Quality Estimate (GMQE) into three different ranges. The results indicated that RoseTTAFold could achieve results similar to SWISS-MODEL in modeling most CDR loops, especially the templates with a GMQE score under 0.8. In addition, we also compared the structures modeled by RoseTTAFold, SWISS-MODEL and ABodyBuilder. In brief, RoseTTAFold could accurately predict 3D structures of antibodies, but its accuracy was not as good as the other two methods. However, RoseTTAFold exhibited better accuracy for modeling H3 loop than ABodyBuilder and was comparable to SWISS-MODEL. Finally, we discussed the limitations and potential improvements of the current RoseTTAFold, which may help to further the accuracy of RoseTTAFold's antibody modeling.

Effects of ultrasound-assisted intermittent tumbling on the quality of cooked ham through modifying muscle structure and protein extraction.

BACKGROUND: Tumbling treatment is widely used in the production of cooked ham. However, traditional intermittent tumbling (IT) treatment is time-consuming. To enhance the tumbling efficiency, high-intensity ultrasound was used to assist IT treatment (UIT). RESULTS: UIT treatment reduced the tumbling time and significantly improved the water holding capacity, tenderness, sliceability and texture of cooked ham compared to IT treatment. Furthermore, more violent destruction of meat tissue was exhibited in the UIT treatment. This change facilitated extraction of more salt-soluble protein, which in turn welded meat pieces tightly and improved the quality of the cooked ham. CONCLUSION: UIT treatment could accelerate the tumbling process and enhance the quality of cooked ham. These results may provide guidance on effective strategies for a high-quality meat production process. © 2023 Society of Chemical Industry.

IsAb: a computational protocol for antibody design.

The design of therapeutic antibodies has attracted a large amount of attention over the years. Antibodies are widely used to treat many diseases due to their high efficiency and low risk of adverse events. However, the experimental methods of antibody design are time-consuming and expensive. Although computational antibody design techniques have had significant advances in the past years, there are still some challenges that need to be solved, such as the flexibility of antigen structure, the lack of antibody structural data and the absence of standard antibody design protocol. In the present work, we elaborated on an in silico antibody design protocol for users to easily perform computer-aided antibody design. First, the Rosetta web server will be applied to generate the 3D structure of query antibodies if there is no structural information available. Then, two-step docking will be used to identify the binding pose of an antibody-antigen complex when the binding information is unknown. ClusPro is the first method to be used to conduct the global docking, and SnugDock is applied for the local docking. Sequentially, based on the predicted binding poses, in silico alanine scanning will be used to predict the potential hotspots (or key residues). Finally, computational affinity maturation protocol will be used to modify the structure of antibodies to theoretically increase their affinity and stability, which will be further validated by the bioassays in the future. As a proof of concept, we redesigned antibody D44.1 and compared it with previously reported data in order to validate IsAb protocol. To further illustrate our proposed protocol, we used cemiplimab antibody, a PD-1 checkpoint inhibitor, as an example to showcase a step-by-step tutorial.

Bi-functional biochar-g-C3N4-MgO composites for simultaneously minimizing pollution：Photocatalytic degradation of pesticide and phosphorus recovery as slow-release fertilizer.

Significant progress has been made in the development of phosphorus recovery adsorbents and photocatalysts for degradation of pesticides. However, the bifunctional materials for phosphorus recovery and photocatalytic degradation of pesticides have not been designed, and the mechanism of the interaction between photocatalysis and P adsorption remains unexplored. Herein, we develop biochar-g-C3N4-MgO composites (BC-g-C3N4-MgO) with bi-function application to minimize water toxicity and eutrophication. The results show phosphorus adsorption capacity of the BC-g-C3N4-MgO composite reaches 111.0 mg·g-1, and its degradation ratio of dinotefuran reaches 80.1% within 260 min. The mechanism studies show that MgO can play variety roles in BC-g-C3N4-MgO composite, in which can improve the adsorption capacity of phosphorus, enhance the utilization efficiency of visible light and the separation efficiency of photoinduced electron-hole pairs. The biochar existed in BC-g-C3N4-MgO serves as charge transporter with a good conductivity, which promotes the fluent transfer of photo-generated charge carriers. The ESR indicates that both •O2- and •OH generated from BC-g-C3N4-MgO are responsible for dinotefuran degradation. Finally, pot experiments reveal that P laden BC-g-C3N4-MgO promotes the growth of pepper seedlings with high P utilization efficiency of 49.27%.

In Silico Prediction and Validation of CB2 Allosteric Binding Sites to Aid the Design of Allosteric Modulators.

Although the 3D structures of active and inactive cannabinoid receptors type 2 (CB2) are available, neither the X-ray crystal nor the cryo-EM structure of CB2-orthosteric ligand-modulator has been resolved, prohibiting the drug discovery and development of CB2 allosteric modulators (AMs). In the present work, we mainly focused on investigating the potential allosteric binding site(s) of CB2. We applied different algorithms or tools to predict the potential allosteric binding sites of CB2 with the existing agonists. Seven potential allosteric sites can be observed for either CB2-CP55940 or CB2-WIN 55,212-2 complex, among which sites B, C, G and K are supported by the reported 3D structures of Class A GPCRs coupled with AMs. Applying our novel algorithm toolset-MCCS, we docked three known AMs of CB2 including Ec2la (C-2), trans-ß-caryophyllene (TBC) and cannabidiol (CBD) to each site for further comparisons and quantified the potential binding residues in each allosteric binding site. Sequentially, we selected the most promising binding pose of C-2 in five allosteric sites to conduct the molecular dynamics (MD) simulations. Based on the results of docking studies and MD simulations, we suggest that site H is the most promising allosteric binding site. We plan to conduct bio-assay validations in the future.

Increasing the length of poly-pyrimidine bulges broadens RNA conformational ensembles with minimal impact on stacking energetics.

Helical elements separated by bulges frequently undergo transitions between unstacked and coaxially stacked conformations during the folding and function of noncoding RNAs. Here, we examine the dynamic properties of poly-pyrimidine bulges of varying length (n = 1-4, 7) across a range of Mg2+ concentrations using HIV-1 TAR RNA as a model system and solution NMR spectroscopy. In the absence of Mg2+, helices linked by bulges with n ≥ 3 residues adopt predominantly unstacked conformations (stacked population <15%), whereas one-bulge and two-bulge motifs adopt predominantly stacked conformations (stacked population >74%). In the presence of 3 mM Mg2+, the helices predominantly coaxially stack (stacked population >84%), regardless of bulge length, and the midpoint for the Mg2+-dependent stacking transition is within threefold regardless of bulge length. In the absence of Mg2+, the difference between free energy of interhelical coaxial stacking across the bulge variants is estimated to be ∼2.9 kcal/mol, based on an NMR chemical shift mapping with stacking being more energetically disfavored for the longer bulges. This difference decreases to ∼0.4 kcal/mol in the presence of Mg2+ NMR RDCs and resonance intensity data show increased dynamics in the stacked state with increasing bulge length in the presence of Mg2+ We propose that Mg2+ helps to neutralize the growing electrostatic repulsion in the stacked state with increasing bulge length thereby increasing the number of coaxial conformations that are sampled. Energetically compensated interhelical stacking dynamics may help to maximize the conformational adaptability of RNA and allow a wide range of conformations to be optimally stabilized by proteins and ligands.

[Endocytosis pathway and intracellular distribution of heparosan].

In this study, the endocytosis pathway of heparosan and its intracellular distribution were investigated in MCF-7 tumor cells and COS7 normal cells. The endocytosis inhibition and cellular probe location experiments showed that MCF-7 tumor cells took heparosan more efficiently and selectively than COS7 cells. The cellular uptake of heparosan was energy-dependent in both MCF-7 tumor cells and COS7 normal cells. Moreover, the major endocytosis pathway of heparosan into MCF-7 tumor cells was caveolin-mediated endocytosis and macropinocytosis. The internalized heparosan was mainly located in lysosomes of the cells.

Advancements in Dermatological Applications of Curcumin: Clinical Efficacy and Mechanistic Insights in the Management of Skin Disorders.

Curcumin, derived from Curcuma longa (turmeric), exhibits significant potential in dermatology, addressing conditions like atopic dermatitis, psoriasis, chronic wounds, skin cancer, and infections through its anti-inflammatory, antioxidant, anticancer, and antimicrobial properties. This review synthesizes evidence on curcumin's mechanisms, including modulation of immune responses and promotion of wound healing, showcasing its efficacy in reducing inflammation, cytokine levels, and enhancing skin barrier functions. Studies highlight curcumin's ability to selectively target tumor cells, suggesting a multifaceted approach to cancer therapy with minimal side effects. Despite promising therapeutic benefits, challenges remain in bioavailability, potency, and targeted delivery, underscoring the need for further research to optimize dosages, delivery methods, and assess long-term safety. The integration of curcumin into dermatological practice requires a balanced consideration of evidence-based efficacy and safety. Curcumin's comprehensive utility in dermatology, coupled with the necessity for advanced scientific exploration, emphasizes the importance of combining traditional knowledge with contemporary research to improve patient care in dermatology. This approach could significantly enhance outcomes for individuals with skin-related conditions, marking curcumin as a versatile and promising agent in the field.

An unsupervised water quality anomaly detection method based on a combination of time-frequency analysis and clustering.

Anomalies in water quality, which frequently arise due to pollution, constitute a substantial menace to human health. The preservation of public welfare critically entails the timely recognition of abnormal water quality. Conventional techniques for detecting water quality anomalies face obstacles such as the necessity of expert knowledge, limited accuracy in detection, and delays in identification. In this paper, we proposed an original unsupervised technique for identifying water quality anomalies combined with time-frequency analysis and clustering (TCAD). We chose time-frequency analysis because it effectively evaluates water quality changes, generating distinct multi-band signals that reflect different aspects of water quality dynamics. We also proposed a clustering technique which can identify water quality markers and amalgamate data from multi-band signals for accurate anomaly detection. We seek to clarify the reasoning behind our methodology by portraying how time-frequency analysis and clustering address the deficiencies of conventional methods. Our experiments evaluated various indicators of water quality, and the effectiveness of our proposed approach was supported by comparative analyses with commonly used models for detecting anomalies in water quality.

Soluble signal inhibitory receptor on leukocytes-1 reflects disease activity and assists diagnosis of patients with rheumatoid arthritis.

BACKGROUND: SIRL-1, an immunosuppressive receptor encoded by the VSTM1 gene, has recently been linked to rheumatoid arthritis (RA) due to its association with activated polymorphonuclear neutrophils (PMNs). Considering that the activated PMNs play a crucial role in the pathogenesis of rheumatoid arthritis (RA), we aimed to measure the levels of soluble SIRL-1, investigating whether they add value to RA in the clinical diagnosis. METHODS: Utilizing an enzyme-linked immunosorbent assay, the concentration of sSIRL-1 was measured in serum samples from cohort 1 diagnosed with RA (n = 96), gout (n = 54), osteoarthritis (n = 47), healthy controls (n = 86) and synovial fluid samples from OA (n = 8) and RA (n = 8) patients, respectively. Additionally, an external validation in cohort 2 (n = 156) comprising various inflammatory diseases was employed. RESULTS: The study revealed a distinctive upregulation of sSIRL-1 in the serum of RA compared to HC and other arthralgia diseases (p < 0.0001), which also displayed a significant elevation in synovial fluid from RA compared to OA (p < 0.05). Notably, sSIRL-1 levels exhibited a significant decrease in patients who achieved disease remission (p < 0.05). Furthermore, the diagnostic accuracy of RA was enhanced when sSIRL-1 was combined with anti-CCP and RF, yielding an impressive AUC value of 0.950. CONCLUSION: The expression pattern of sSIRL-1 in RA, coupled with its correlation with disease activity, underscores its potential clinical utility for both diagnosis and disease monitoring in RA patients. This study offers valuable insights into the evolving diagnostic landscape of RA.

Anti-Inflammatory Peptide-Conjugated Silk Fibroin/Cryogel Hybrid Dual Fiber Scaffold with Hierarchical Structure Promotes Healing of Chronic Wounds.

Chronic wounds resulting from diabetes, pressure, radiation therapy, and other factors continue to pose significant challenges in wound healing. To address this, this study introduces a novel hybrid fibroin fibrous scaffold (FFS) comprising randomly arranged fibroin fibers and vertically aligned cryogel fibers (CFs). The fibroin scaffold is efficiently degummed at room temperature and simultaneously formed a porous structure. The aligned CFs are produced via directional freeze-drying, achieved by controlling solution concentration and freezing polymerization temperature. The incorporation of aligned CFs into the expanded fibroin fiber scaffold leads to enhanced cell infiltration both in vitro and in vivo, further elevating the hybrid scaffold's tissue compatibility. The anti-inflammatory peptide 1 (AP-1) is also conjugated to the hybrid fibrous scaffold, effectively transforming the inflammatory status of chronic wounds from pro-inflammatory to pro-reparative. Consequently, the FFS-AP1+CF group demonstrates superior granulation tissue formation, angiogenesis, collagen deposition, and re-epithelialization during the proliferative phase compared to the commercial product PELNAC. Moreover, the FFS-AP1+CF group displays epidermis thickness, number of regenerated hair follicles, and collagen density closer to normal skin tissue. These findings highlight the potential of random fibroin fibers/aligned CFs hybrid fibrous scaffold as a promising approach for skin tissue filling and tissue regeneration.

Orthogonally woven 3D nanofiber scaffolds promote rapid soft tissue regeneration by enhancing bidirectional cell migration.

Repairing large-area soft tissue defects caused by traumas is a major surgical challenge. Developing multifunctional scaffolds with suitable scalability and favorable cellular response is crucial for soft tissue regeneration. In this study, we developed an orthogonally woven three-dimensional (3D) nanofiber scaffold combining electrospinning, weaving, and modified gas-foaming technology. The developed orthogonally woven 3D nanofiber scaffold had a modular design and controlled fiber alignment. In vitro, the orthogonally woven 3D nanofiber scaffold exhibited adjustable mechanical properties, good cell compatibility, and easy drug loading. In vivo, for one thing, the implantation of an orthogonally woven 3D nanofiber scaffold in a full abdominal wall defect model demonstrated that extensive granulation tissue formation with enough mechanical strength could promote recovery of abdominal wall defects while reducing intestinal adhesion. Another result of diabetic wound repair experiments suggested that orthogonally woven 3D nanofiber scaffolds had a higher wound healing ratio, granulation tissue formation, collagen deposition, and re-epithelialization. Taken together, this novel orthogonally woven 3D nanofiber scaffold may provide a promising and effective approach for optimal soft tissue regeneration.

Additively Manufactured Flexible Liquid Metal-Coated Self-Powered Magnetoelectric Sensors with High Design Freedom.

Although additive manufacturing enables controllable structural design and customized performance for magnetoelectric sensors, their design and fabrication still require careful matching of the size and modulus between the magnetic and conductive components. Achieving magnetoelectric integration remains challenging, and the rigid coils limit the flexibility of the sensors. To overcome these obstacles, this study proposes a composite process combining selective laser sintering (SLS) and 3D transfer printing for fabricating flexible liquid metal-coated magnetoelectric sensors. The liquid metal forms a conformal conductive network on the SLS-printed magnetic lattice structure. Deformation of the structure alters the magnetic flux passing through it, thereby generating voltage. A reverse model segmentation and summation method is established to calculate the theoretical magnetic flux. The impact of the volume fraction, unit size, and height of the sensors on the voltage is studied, and optimization of these factors yields a maximum voltage of 45.6 µV. The sensor has excellent sensing performance with a sensitivity of 10.9 kPa-1 and a minimum detection pressure of 0.1 kPa. The voltage can be generated through various external forces. This work presents a significant advancement in fabricating liquid metal-based magnetoelectric sensors by improving their structural flexibility, magnetoelectric integration, and design freedom.

TCAF1 promotes TRPV2-mediated Ca2+ release in response to cytosolic DNA to protect stressed replication forks.

The protection of the replication fork structure under stress conditions is essential for genome maintenance and cancer prevention. A key signaling pathway for fork protection involves TRPV2-mediated Ca2+ release from the ER, which is triggered after the generation of cytosolic DNA and the activation of cGAS/STING. This results in CaMKK2/AMPK activation and subsequent Exo1 phosphorylation, which prevent aberrant fork processing, thereby ensuring genome stability. However, it remains poorly understood how the TRPV2 channel is activated by the presence of cytosolic DNA. Here, through a genome-wide CRISPR-based screen, we identify TRPM8 channel-associated factor 1 (TCAF1) as a key factor promoting TRPV2-mediated Ca2+ release under replication stress or other conditions that activate cGAS/STING. Mechanistically, TCAF1 assists Ca2+ release by facilitating the dissociation of STING from TRPV2, thereby relieving TRPV2 repression. Consistent with this function, TCAF1 is required for fork protection, chromosomal stability, and cell survival after replication stress.

SARS-CoV-2 brainstem encephalitis in human inherited DBR1 deficiency.

Inherited deficiency of the RNA lariat-debranching enzyme 1 (DBR1) is a rare etiology of brainstem viral encephalitis. The cellular basis of disease and the range of viral predisposition are unclear. We report inherited DBR1 deficiency in a 14-year-old boy who suffered from isolated SARS-CoV-2 brainstem encephalitis. The patient is homozygous for a previously reported hypomorphic and pathogenic DBR1 variant (I120T). Consistently, DBR1 I120T/I120T fibroblasts from affected individuals from this and another unrelated kindred have similarly low levels of DBR1 protein and high levels of RNA lariats. DBR1 I120T/I120T human pluripotent stem cell (hPSC)-derived hindbrain neurons are highly susceptible to SARS-CoV-2 infection. Exogenous WT DBR1 expression in DBR1 I120T/I120T fibroblasts and hindbrain neurons rescued the RNA lariat accumulation phenotype. Moreover, expression of exogenous RNA lariats, mimicking DBR1 deficiency, increased the susceptibility of WT hindbrain neurons to SARS-CoV-2 infection. Inborn errors of DBR1 impair hindbrain neuron-intrinsic antiviral immunity, predisposing to viral infections of the brainstem, including that by SARS-CoV-2.

Large Language Models for Healthcare Data Augmentation: An Example on Patient-Trial Matching.

The process of matching patients with suitable clinical trials is essential for advancing medical research and providing optimal care. However, current approaches face challenges such as data standardization, ethical considerations, and a lack of interoperability between Electronic Health Records (EHRs) and clinical trial criteria. In this paper, we explore the potential of large language models (LLMs) to address these challenges by leveraging their advanced natural language generation capabilities to improve compatibility between EHRs and clinical trial descriptions. We propose an innovative privacy-aware data augmentation approach for LLM-based patient-trial matching (LLM-PTM), which balances the benefits of LLMs while ensuring the security and confidentiality of sensitive patient data. Our experiments demonstrate a 7.32% average improvement in performance using the proposed LLM-PTM method, and the generalizability to new data is improved by 12.12%. Additionally, we present case studies to further illustrate the effectiveness of our approach and provide a deeper understanding of its underlying principles.

Does air pollution exposure affect semen quality? Evidence from a systematic review and meta-analysis of 93,996 Chinese men.

Background: Air pollution may impair male fertility, but it remains controversial whether air pollution affects semen quality until now. Objectives: We undertake a meta-analysis to explore potential impacts of six pollutants exposure during the entire window (0-90 days prior to ejaculation) and critical windows (0-9, 10-14, and 70-90 days prior to ejaculation) on semen quality. Methods: Seven databases were retrieved for original studies on the effects of six pollutants exposure for 90 days prior to ejaculation on semen quality. The search process does not limit the language and search date. We only included original studies that reported regression coefficients (ß) with 95% confidence intervals (CIs). The ß and 95% CIs were pooled using the DerSimonian-Laird random effect models. Results: PM2.5 exposure was related with decreased total sperm number (10-14 lag days) and total motility (10-14, 70-90, and 0-90 lag days). PM10 exposure was related with reduced total sperm number (70-90 and 0-90 lag days) and total motility (0-90 lag days). NO2 exposure was related with reduced total sperm number (70-90 and 0-90 lag days). SO2 exposure was related with declined total motility (0-9, 10-14, 0-90 lag days) and total sperm number (0-90 lag days). Conclusion: Air pollution affects semen quality making it necessary to limit exposure to air pollution for Chinese men. When implementing protective measures, it is necessary to consider the key period of sperm development.

Weakly acidic microenvironment of the wound bed boosting the efficacy of acidic fibroblast growth factor to promote skin regeneration.

The pH value within the wound microenvironment influences indirectly and directly all biochemical reactions taking place in the process of skin wound healing. Currently, it is generally believed that a low pH value, such as it is found on normal skin, is favorable for wound regeneration, while some investigations have shown that in fact alkaline microenvironments are required for some healing processes. The role of growth factors in promoting wound healing requires a specific microenvironment. In wound microenvironments of different pH, growth factors with different isoelectric points may have different effects. To explore whether the application of FGF with different isoelectric points in wounds with different pH values interferes with the healing process to different degrees, GelMA hydrogels with different pH values were prepared to maintain the wounds microenvironment with the same pH values, in which aFGF and bFGF were loaded as well. The results show that GelMA hydrogels of different pH values maintained the same pH of the wound microenvironment sustainably on the 4th day. Moreover, aFGF and bFGF promoted skin wound healing to varying degrees in different pH wound microenvironments. In particular, aFGF significantly promoted wound re-epithelialization in a weak acidic microenvironment, while bFGF promoted collagen synthesis and deposition in the early stage of weak acid wounds. In addition, aFGF plays a superior role in inhibiting inflammation in weak acidic wounds.

Does exposure to air pollution during different time windows affect pregnancy outcomes of in vitro fertilization treatment? A systematic review and meta-analysis.

Few researches have examined the impact of air pollution exposure during various time windows on clinical outcomes in women receiving in vitro fertilization (IVF) therapy, and the findings of studies have been conflicting. We investigated the effects of six air pollutants exposure during different time windows (period 1, 85 days before egg retrieval to the beginning of gonadotropin; period 2, the beginning of gonadotropin to egg collection; period 3, egg collection to embryo transfer; period 4, embryo transfer to serum hCG measurement; period 5, serum hCG measurement to transvaginal ultrasonography; period 6, 85 days before egg retrieval to hCG measurement; period 7, 85 days before egg retrieval to transvaginal ultrasonography) on clinical outcomes of IVF therapy. A total of seven databases were searched. NO2 (period 6), SO2 (period 2, 3, and 7), CO (period 1, 2 and 7) exposure were linked to lower likelihoods of clinical pregnancy. PM2.5 (period 1), PM10 (period 1), SO2 (period 1, 2, 3, 4, and 6), NO2 (period 1) were linked to lower likelihoods of biochemical pregnancy. PM2.5 (period 1), SO2 (period 2 and 4) and CO (period 2) were linked to reduced probabilities of live birth. Our results implied that period 1 might be the most sensitive exposure window. Air pollution exposure is linked to reduced probabilities of clinical pregnancy, biochemical pregnancy, and live birth. Therefore, preventive measures to limit air pollution exposure should be started at least three months in advance of IVF therapy to improve pregnancy outcomes.