Search

Abstract T cells are one of the main cell types shaping the immune microenvironment in chronic obstructive pulmonary disease (COPD). They persist andplay cytotoxic roles. The purpose of this study aimed to explore the potential related-genes of T cells in lung tissue of COPD. Chip data GSE38974 and single_celldata GSE196638 were downloaded from the GEO database. Difference analyses and WGCNA of GSE38974 were performed to identify DEGs and the modules most associated with the COPD phenotype. Various cell subsets were obtained by GSE196638, and DEGs of T cells were further identified. GO, GSEA and KEGG enrichment analyses were conducted to explore the biological functions and regulatory signaling pathways of the DEGs and DEGs of T cells. The intersection of the DEGs, module genes and DEGs of T cells was assessed to acquire related-genes of T cells. The mRNA and protein expression levels of related-genes ofT cells were verified in lung tissue of mouse with emphysema model. Based on GSE38974 difference analysis, 3811 DEGs were obtained. The results of WGCNA showed that the red module had the highest correlation coefficient with the COPD phenotype. GSE196638 analysis identified 124 DEGs of T cells. The GO, GSEAand KEGG enrichment analyses mainly identified genes involved in I-kappaB kinase/NF-kappaB signaling, receptor signaling pathway via STAT, regulationof CD4-positive cells, regulation of T-helper cell differentiation, chemokine signaling pathway, Toll-likereceptor signaling pathway, CD8-positive cells, alpha–beta T cell differentiation, MAPK signaling pathway and Th17 cell differentiation. The DEGs, genes of the red module and DEGs of T cells were overlapped to acquire FOXO1 and DDX17. The results of RT-qPCR and Western Blot indicate that the mRNA and protein expression levels of FOXO1 and DDX17 in lung tissue of emphysema mice were significantly higher compared with those in air-exposed mice. FOXO1 as well as DDX17 may be related-genesof T cells in lung tissue of patient with COPD, and their participation in the biological processes of different signaling pathways may inspire further COPD research.

Abstract Background Mammary Pathogenic Escherichia coli (MPEC) is an important pathogen that can escape the attack of the host immune system through biofilm formation and proliferate in the mammary gland continuously, resulting in mastitis in cows and causing enormous economic losses. As an effector of AI-2 quorum sensing, LsrR extensively affects the expression levels of hundreds of genes related to multiple biological processes in model E. coli strain. However, the regulatory role of LsrR in MPEC and whether it is involved in pathogenesis has been seldom reported. Results In this study, the function of LsrR in strain MPEC5, obtained from a milk sample in dairy cows with mastitis, was investigated by performing high-throughput sequencing (RNA-seq) assays. The results revealed that LsrR down-regulated the transcript levels of fimAICDFGH (encoding Type 1 pili), which have been reported to be associated with biofilm formation process. Biofilm assays confirmed that deletion of lsrR resulted in a significant increase in biofilm formation in vitro. In addition, electrophoretic mobility shift assay (EMSA) provided evidence that LsrR protein could directly bind to the promoter regions of fimAICDFGH in a dose-dependent manner. Conclusions These results indicate that LsrR protein inhibits the biofilm formation ability of MPEC5 by directly binding to the fimAICDFGH promoter region. This study presents a novel clue for further exploration of the prevention and treatment of MPEC.

Abstract Objective To evaluate the predictive value of PD-1 expression in T lymphocytes for rehospitalization due to acute exacerbations of COPD (AECOPD) in discharged patients. Methods 115 participants hospitalized with COPD (average age 71.8 ± 6.0 years) were recruited at Fujian Provincial Hospital. PD1+T lymphocytes proportions (PD1+T%), baseline demographics and clinical data were recorded at hospital discharge. AECOPD re-admission were collected at 1-year follow-up. Kaplan-Meier analysis compared the time to AECOPD readmissions among groups stratified by PD1+T%. Multivariable Cox proportional hazards regression and stratified analysis determined the correlation between PD1+T%, potential confounders, and AECOPD re-admission. ROC and DCA evaluated PD1+T% in enhancing the clinical predictive values of Cox models, BODE and CODEX. Results 68 participants (59.1%) were AECOPD readmitted, those with AECOPD readmission exhibited significantly elevated baseline PD-1+CD4+T/CD4+T% and PD-1+CD8 + T/CD8 + T% compared to non-readmitted counterparts. PD1+ T lymphocyte levels statistically correlated with BODE and CODEX indices. Kaplan-Meier analysis demonstrated that those in Higher PD1+ T lymphocyte proportions had reduced time to AECOPD readmission (logRank p

Abstract Purpose The aim of this study is to construct a combined model that integrates radiomics, clinical risk factors and machine learning algorithms to predict para-laryngeal lymph node metastasis in esophageal squamous cell carcinoma. Methods A retrospective study included 361 patients with esophageal squamous cell carcinoma from 2 centers. Radiomics features were extracted from the computed tomography scans. Logistic regression, k nearest neighbor, multilayer perceptron, light Gradient Boosting Machine, support vector machine, random forest algorithms were used to construct radiomics models. The receiver operating characteristic curve and The Hosmer–Lemeshow test were employed to select the better-performing model. Clinical risk factors were identified through univariate logistic regression analysis and multivariate logistic regression analysis and utilized to develop a clinical model. A combined model was then created by merging radiomics and clinical risk factors. The performance of the models was evaluated using ROC curve analysis, and the clinical value of the models was assessed using decision curve analysis. Results A total of 1024 radiomics features were extracted. Among the radiomics models, the KNN model demonstrated the optimal diagnostic capabilities and accuracy, with an area under the curve (AUC) of 0.84 in the training cohort and 0.62 in the internal test cohort. Furthermore, the combined model exhibited an AUC of 0.97 in the training cohort and 0.86 in the internal test cohort. Conclusion A clinical-radiomics integrated nomogram can predict occult para-laryngeal lymph node metastasis in esophageal squamous cell carcinoma and provide guidance for personalized treatment.

The effect and underlying mechanism of tetrabromobisphenol A (TBBPA), a plastic additive, on biofilm formation of methicillin-resistant Staphylococcus aureus (MRSA USA300) remain unknown. This study first investigated the impact of different concentrations of TBBPA on the growth and biofilm formation of USA300. The results indicated that a low concentration (0.5 mg/L) of TBBPA promoted the growth and biofilm formation of USA300, whereas high concentrations (5 mg/L and 10 mg/L) of TBBPA had inhibitory effects. Further exploration revealed that the low concentration of TBBPA enhance biofilm formation by promoting the synthesis of extracellular proteins, release of extracellular DNA (eDNA), and production of staphyloxanthin. RTqPCR analysis demonstrated that the low concentration of TBBPA upregulated genes associated with extracellular protein synthesis (sarA, fnbA, fnbB, aur) and eDNA formation (atlA) and increased the expression of genes involved in staphyloxanthin biosynthesis (crtM), suggesting a potential mechanism for enhanced resistance of USA300 to adverse conditions. These findings shed light on how low concentrations of TBBPA facilitate biofilm formation in USA300 and highlight the indirect impact of plastic additives on pathogenic bacteria in terms of human health. In the future, in-depth studies about effects of plastic additives on pathogenicity of pathogenic bacteria should be conducted. Capsule: The protein and eDNA contents in biofilms of methicillin-resistant Staphylococcus aureus are increased by low concentrations of TBBPA.

Abstract Background Schizochytrium limacinum holds significant value utilized in the industrial-scale synthesis of natural DHA. Nitrogen-limited treatment can effectively increase the content of fatty acids and DHA, but there is currently no research on chromatin accessibility during the process of transcript regulation. The objective of this research was to delve into the workings of fatty acid production in S. limacinum by examining the accessibility of promoters and profiling gene expressions. Results Results showed that differentially accessible chromatin regions (DARs)-associated genes were enriched in fatty acid metabolism, signal transduction mechanisms, and energy production. By identifying and annotating DARs-associated motifs, the study obtained 54 target transcription factor classes, including BPC, RAMOSA1, SPI1, MYC, and MYB families. Transcriptomics results revealed that several differentially expressed genes (DEGs), including SlFAD2, SlALDH, SlCAS1, SlNSDHL, and SlDGKI, are directly related to the biosynthesis of fatty acids, meanwhile, SlRPS6KA, SlCAMK1, SlMYB3R1, and SlMYB3R5 serve as transcription factors that could potentially influence the regulation of fatty acid production. In the integration analysis of DARs and ATAC-seq, 13 genes were identified, which were shared by both DEGs and DARs-associated genes, including SlCAKM, SlRP2, SlSHOC2, SlTN, SlSGK2, SlHMP, SlOGT, SlclpB, and SlDNAAF3. Conclusions SlCAKM may act as a negative regulator of fatty acid and DHA synthesis, while SlSGK2 may act as a positive regulator, which requires further study in the future. These insights enhance our comprehension of the processes underlying fatty acid and DHA production in S. limacinum. They also supply a foundational theoretical framework and practical assistance for the development of strains rich in fatty acids and DHA.

Abstract Photoexcitation of the electron-donor-acceptor complexes have been an effective approach to achieve radicals by triggering electron transfer. However, the catalytic version of electron-donor-acceptor complex photoactivation is quite underdeveloped comparing to the well-established utilization of electronically biased partners. In this work, we utilize 4-nitrophthalonitrile as an electron acceptor to facilitate the efficient π-stacking with electron-rich aromatics to form electron-donor-acceptor complex. The characterization and energy profiles on the cocrystal of 4-nitrophthalonitrile and 1,3,5-trimethoxybenzene disclose that the electron transfer is highly favorable under the light irradiation. This electron acceptor catalyst can be efficiently applied in the benzylic C−H bond photoactivation by developing the Giese reaction of alkylanisoles and the oxidation of the benzyl alcohols. A broad scope of electron-rich aromatics can be tolerated and a mechanism is also proposed. Moreover, the corresponding π-anion interaction of 4-nitrophthalonitrile with potassium formate can further facilitate the hydrocarboxylation of alkenes efficiently.

ABSTRACT: Avian pathogenic Escherichia coli (APEC) is one of the common extraintestinal infectious disease pathogens in chickens, geese, and other birds, inducing serious impediments to the development of the poultry industry. Hence, investigating how bacteria regulate themselves amidst different challenging conditions is immense essential in prevention and treatment for bacterial pathogen infections. The ArcA regulatory factor has been reported to regulate oxygen availability in strains, but its role in regulation of antibiotics resistance in APEC is unclear. This study delved into understanding how ArcA regulates antibiotic resistance in APEC. An E. coli APEC40 arcA knockout strain was constructed, and the regulatory mechanism of arcA on APEC antibiotic susceptibility was identified by drug sensitivity test, colony counting assay, real-time quantitative PCR, β-galactosidase assays and electrophoretic mobility shift assay (EMSA). The results showed that ArcA directly binds to the promoter region of the outer membrane protein OmpC/OmpW and regulates bacterial susceptibility to kanamycin and penicillin G. At the same time, the double knockout of ompW and ompW/arcA resulted in an increase in resistance to kanamycin compared to the deletion of the arcA gene. This outcome provided experimental proof suggesting that the outer membrane protein OmpW could serve as a crucial pathway for the ingress of kanamycin into cells. These results confirmed the important regulatory role of ArcA transcription factors under APEC antibiotic stress.

Dunaliella salina is by far the most salt-tolerant organism and contains many active substances, including β-carotene, glycerol, proteins, and vitamins, using in the production of dried biomass or cell extracts for the biofuels, pharmaceutical formulations, food additives, and fine chemicals, especially β-carotene. We report a high-quality genome sequence of D. Salina FACHB435, which has a 472 Mb genome size, with a contig N50 of 458 Kb. A total of 30,752 protein-coding genes were predicted. The annotation results evaluated by BUSCO was shown that completeness was 91.0% and replication was 53.1%. The fragments were 6.3% and the deletions were 2.6%. Phylogenomic and comparative genomic analyses revealed that A. thaliana diverged from Volvocales about 448 million years ago, then Volvocales C. eustigma, D. salina, and other species diverged about 250 million years ago. High light could promote the accumulation of β-carotene in D. salina at a 13 d stage of culture. The enrichment of DEGs in KEGG, it notes that the predicted up-regulated genes of carotenoid metabolic pathway include DsCrtB, DsPDS, DsZ-ISO, DsZDS, DsCRTISO, DsLUT5, DsCrtL-B, and DsCCD8, while the predicted down-regulated genes include DsCrtF, and DsLUT1. The four genes that were both up-regulated and down-regulated were DsZEP, DsCrtR-b, DsCruA/P and DsCrtZ 4. The research results can provide scientific basis for the industrialization practice of D. salina.

The reservoirs in the seventh member of the Triassic Yanchang Formation (Chang 7 Member) in the Qingcheng Oilfield of the Ordos Basin are characterized by thin sandbody, tight rocks, high heterogeneity, low formation pressure coefficient, and complex geomorphology. Through the efforts in the stages of exploration, appraisal, pilot testing and development, a series of key technologies have been formed, including “sweet spot” optimization, differentiated three-dimensional well deployment, fast drilling and completion of large-scale horizontal well cluster, intensively-staged volume fracturing in long horizontal well, and optimization of rational production system. Furthermore, a production organization mode represented by factory-like operations on loess platform has been implemented. Application of these technologies has enabled to significantly improve the single-well production of the Qingcheng Oilfield, reduce the investment cost, and realize a large-scale and beneficial development at a full cost below $55 per barrel. In 2022, the annual production of Chang 7 shale oil in the Ordos Basin reached 221×104 t, accounting for 70% of the annual shale oil production of China. The practice of development technologies in the Qingcheng Oilfield provides valuable references for efficient development of continental shale oil.

To further enhance the industrial utilization value of Haematococcus lacustris, the plasma mutagenesis of Haematococcus lacustris was carried out by an atmospheric and room temperature plasma (ARTP) mutagenesis equipment. The optimum input power and mutagenesis time for plasma mutagenesis were determined with lethal rate of algal cells as the index. After mutagenesis, high-yield astaxanthin mutant algae strains were obtained through primary screening of solid plate culture and secondary screening of liquid culture. Then, the culture conditions of high yield algal plants at vegetative growth stage were optimized by single-factor and orthogonal experiment with algae cell density as the index, and the suitable high light conditions for astaxanthin accumulation during astaxanthin induction stage were selected. The genetic stability of the high yielding mutant algae strains was observed after multiple subcultures under the optimized culture conditions. The results showed that the optimum conditions for plasma mutagenesis of Haematococcus lacustris were 240 W for 150 s or 400 W for 120 s. 11 Mutant alga strains with fast growth and high astaxanthin yield were obtained through primary screening and rescreening, wherein the strain HP3 grew fastest and had the highest astaxanthin yield. After culture, its cell density and astaxanthin yield were increased by 25.5% and 61.6% respectively compared with the original strain. After two-stage optimization, the cell density and astaxanthin yield of HP3 increased by 14.3% and 19.3% respectively, reaching 7.2×105 cell/mL and 31.264 mg/L. HP3 showed good growth and stable heredity. Its cell density and astaxanthin yield were similar to those of primary culture. The results have practical significance for the breeding of industrial algal strains producing astaxanthin from Haematococcus lacustris.

Abstract Introduction Venous thromboembolism(VTE) is a leading cause of death in patients with lung cancer. Furthermore, hospitalization of patients with advanced lung cancer for VTE treatment represents a major economic burden on the national public health resources. Therefore, we performed this prospective study to identify clinical biomarkers for the early identification of VTE in lung cancer patients. Methods This prospective study enrolled 158 patients with confirmed lung cancer, including 27 who were diagnosed with VTE within six months of the follow-up after lung cancer diagnosis. Multivariate logistic regression analysis was used to evaluate the diagnostic performancese of all the relevant clinical features and laboratory indicators in identifying lung cancer patients with a higher risk of VTE. A novel risk prediction model was constructed consisting of five clinical variables with the best diagnostic performances and was validated using the receiver operation characteristic(ROC) curves. The diagnostic performances of the new risk prediction model was also compared with the Khorana risk score (KRS) and the Padua risk score (PRS). Results The VTE group of lung cancer patients (n = 27) showed significantly higher serum levels of fibrin degradation products (FDP), D-dimer, thrombomodulin (TM), thrombin-antithrombin-complex (TAT), α2-plasmin inhibitor-plasmin Complex (PIC), and tissue plasminogen activator-plasminogen activator inhibitor complex (t-PAIC) compared to those in the non-VTE group (n = 131). ROC curve analyses showed that the diagnostic efficacy of the new VTE risk prediction model with TM ≥ 9.75 TU/ml, TAT ≥ 2.25ng/ml, t-PAIC ≥ 7.35ng/ml, history of VTE, and ECOG PS score ≥ 2 was superior than the KRS and the PRS in the early identification of lung cancer patients with a higher risk of VTE. Conclusions The new risk prediction model showed significantly high diagnostic efficacy in the early identification of lung cancer patients with a high risk of VTE. The diagnostic efficacy of the new risk prediction model was higher than the KRS and the PRS in this cohort of lung cancer patients.

The limited ductility of Refractory High Entropy Alloy (RHEA) at room temperature hinders its widespread application. However, optimizing their properties through traditional “trial and error” methods is a challenging due to the intricate composition of High Entropy Alloys (HEAs). First principles calculation is an efficient and cost-effective method for predicting material properties. Three modeling methods for high entropy alloys are the most commonly used, namely Supercell (SC), Special quasi-random structure (SQS) and Virtual crystal approximation (VCA). To improve the plasticity of NbMoTaTiV at room temperature, the effects of Ti and Ta contents on the mechanical properties were studied. First principles calculations have been employed to predict the phase structure, elastic properties and electronic structure by three common modeling methods and validated against experimental data. The result revealed that MoNbTaTiV and MoNbTa0.5Ti1.5V RHEAs have BCC structure and increasing Ti and decreasing Ta contributed to enhanced toughness of the alloy. Notably, the three methods demonstrated good accuracy in predicting the effects of Ti and Ta content on the performance of NbMoTaTiV. The VCA method was particularly well-suited for predicting elastic properties, offering a balance between computational accuracy and efficiency. SQS and SC considered the complex atomic occupation in HEAs, making them more suitable for studying the electronic structure.

Bio-degradation of poly(butylene adipate-co-terephthalate) is an attractive tactic but requires an effective hydrolytic enzyme. Here, the authors demonstrate that cutinases are highly potent PBAT-decomposing enzymes and their mechanism is proposed based on substrate-binding mode.

The fault detection and diagnosis of a ship’s electric propulsion system is of great significance to the reliability and safety of large modern ships. The traditional fault diagnosis method based on mathematical models and expert knowledge is limited by the difficulty of establishing an accurate model of the complex system, and it is easy to cause false alarms. Data-driven methods, such as deep learning, can automatically learn from the mass of data, extract and analyze fault characteristics, and create a more objective distinction system state. A deep learning fault diagnosis model based on ResNet feature extraction capability and bidirectional long-term memory network timing processing capability is proposed to realize fault diagnosis of high resistance connections in ship electric propulsion systems. The results show that the res-convolutional BiLSTM deep neural network (Res-CBDNN) can fully integrate the advantages of the two networks, efficiently process fault current data, and achieve high-performance fault diagnosis. The accuracy of Res-CBDNN can be kept above 85% in a noisy environment, and it can effectively monitor the high resistance connection fault of ship electric propulsion systems.

The evaluation of shale reservoir quality is of great significance for the exploration and development of shale oil. To more effectively study the distribution characteristics of shale reservoir quality, thin-section observation, scanning electron microscopy and pressure-controlled porosimetry were used to obtain the pore structure characteristics of shale in Chang 7, including pore types, pore size distribution, etc. In addition, the fractal dimensions of the shale samples were calculated based on pressure-controlled porosimetry data. The results show that residual interparticle pores, dissolution pores and clay-dominated pores were the main pore types. The overall pore size was mainly distributed between 3 nm and 50 μm. The pore system was divided into four types using fractal features, and the shale reservoir was divided into four types based on the proportion of different types of pore system. In different types of reservoirs, the production capacity of exploration wells varies significantly, as does the production capacity of horizontal wells. The classification of shale reservoirs using mercury intrusion fractal analysis proved to be suited for the efficient development of Chang 7 shale oil reservoirs.

Breath is one of the most important physiological features of human life. In particular, it is significant to monitor the physical characteristics of breath, such as breath frequency and tidal volume. Breath sensors play an important role in the field of human health monitoring. However, an electronic breath sensor is not stable or even safe when the patient is in a Magnetic Resonance Imaging (MRI) system or during any oncology treatment that requires radiation and other high electric/magnetic fields. Fiber-optic-based sensors have attracted a considerable amount of attention from researchers since they are immune to electromagnetic interference. Here, we propose and demonstrate a fiber-optic-based relative-humidity (RH)-sensing strategy by depositing Ti3C2Tx nanosheets onto an etched single-mode fiber (ESMF). The humidity sensor function is realized by modulating the transmitted light in the ESMF using the excellent hydrophilic properties of Ti3C2Tx. Experiments show that the coated Ti3C2Tx nanosheets can effectively modulate the transmitted light in the ESMF in the relative humidity range of 30~80% RH. The sensor’s fast response time of 0.176 s and recovery time of 0.521 s allow it to be suitable for real-time human breath monitoring. The effective recognition of different breath rhythms, including fast, normal, deep, and strong breathing patterns, has been realized. This work demonstrates an all-optical Ti3C2Tx-based sensing platform that combines Ti3C2Tx with an optical fiber for humidity sensing for the first time, which has great promise for breath monitoring and presents novel options for gas-monitoring applications in the biomedical and chemical fields.

Isochrysis galbana is considered an ideal bait for functional foods and nutraceuticals of humans because of its high fucoxanthin (Fx) content. However, multi-omics analysis of the regulatory networks for Fx biosynthesis in I. galbana has not been reported. In this study, we report a high-quality genome assembly of I. galbana LG007, which has a genome size of 92.73 Mb, with a contig N50 of 6.99 Mb and 14,900 protein-coding genes. Phylogenetic analysis confirmed the monophyly of Haptophyta, with I. galbana sister to Emiliania huxleyi and Chrysochromulina tobinii. Evolutionary analysis revealed an estimated divergence time between I. galbana and E. huxleyi of ∼ 133 million years ago. Gene family analysis indicated that lipid metabolism-related genes exhibited significant expansion, including IgPLMT, IgOAR1, and IgDEGS1. Metabolome analysis showed that the content of carotenoids in I. galbana cultured under green light for 7 days was higher than that under white light, and β-carotene was the main carotenoid, accounting for 79.09% of the total carotenoids. Comprehensive multi-omics analysis revealed that the content of β-carotene, antheraxanthin, zeaxanthin, and Fx was increased by green light induction, which was significantly correlated with the expression of IgMYB98, IgZDS, IgPDS, IgLHCX2, IgZEP, IgLCYb, and IgNSY. These findings contribute to the understanding of Fx biosynthesis and its regulation, providing a valuable reference for food and pharmaceutical applications.

Abstract Osteoarthritis, characterized by articular cartilage degradation, is the leading cause of chronic disability in older adults. Studies have indicated that circular RNAs are crucial regulators of chondrocyte development and are involved in the progression of osteoarthritis. In this study, we investigated the function and mechanism of a circular RNA and its potential for osteoarthritis therapy. The expression levels of circCREBBP, screened by circular RNA sequencing during chondrogenic differentiation in adipose tissue-derived stem cells, and TGFβ2 were significantly increased in the cartilage of patients with osteoarthritis and IL-1β-induced chondrocytes. circCREBBP knockdown increased anabolism in the extracellular matrix and inhibited chondrocyte degeneration, whereas circCREBBP overexpression led to the opposite effects. Luciferase reporter assays, rescue experiments, RNA immunoprecipitation, and RNA pulldown assays confirmed that circCREBBP upregulated TGFβ2 expression by sponging miR-1208, resulting in significantly enhanced phosphorylation of Smad1/5 in chondrocytes. Moreover, intra-articular injection of adeno-associated virus-sh-circCrebbp alleviated osteoarthritis in a mouse model of destabilization of the medial meniscus. Our findings reveal a critical role for circCREBBP in the progression of osteoarthritis and provide a potential target for osteoarthritis therapy.

The intestine is a site of immune cell priming at birth. Therefore, spatial transcriptomes were performed to define how the transcriptomic landscape was spatially organized in the posterior intestine of Sebastes schlegelii following Edwardsiella piscicida infection. In the healthy condition, we identified a previously unappreciated molecular regionalization of the posterior intestine. Following bacterial infection, most immune-related genes were identified in mucosa layer. Moreover, investigation of immune-related genes and genes in immune-related KEGG pathways based on spatial transcriptomes shed light on which sections of these genes are in the posterior intestine. Meanwhile, the high expression of genes related to regeneration also indicated that the posterior intestine was responding to the invasion of pathogens by constantly proliferating new cells. In addition, the increasing microbiota communities indicated that these bacteria maintained posterior intestine integrity and shaped the mucosal immune system. Taken together, spatial transcriptomes and microbiota compositions have significant implications for understanding the immune mechanism that responds to E. piscicida infection in the posterior intestine of S. schlegelii, which also provides a theoretical basis for the spatial distribution of immune genes and changes in bacterial flora in other teleosts in the process of resisting pathogens.

IntroductionIn this study, the change detection paradigm was used to study the working memory of patterned movements and the relationship of this type of memory with the visuospatial sketchpad in three experiments.MethodsExperiment 1 measured participants’ working memory capacity for patterned movements and explored the influence of stimulus type with indicators such as response time and accuracy rate. Experiments 2 and 3 explored the relationship between patterned movements and the visual and spatial subsystems, respectively.ResultsThe results of Experiment 1 indicated that individuals can store 3–4 patterned movements in working memory; however, a change in stimulus format or an increase in memory load may decrease the speed and efficiency of working memory processing. The results of Experiment 2 showed that working memory and visual working memory are independent when processing patterned movements. The results of Experiment 3 showed that the working memory of patterned movements was affected by spatial working memory.DiscussionChanges in stimulus type and memory load exerted different effects on the working memory capacity of participants. These results provide behavioral evidence that the storage of patterned movement information is independent of the visual subsystem but requires the spatial subsystem of the visuospatial sketchpad.

BackgroundApproximately 94% of sensory information acquired by humans originates from the visual and auditory channels. Such information can be temporarily stored and processed in working memory, but this system has limited capacity. Working memory plays an important role in higher cognitive functions and is controlled by central executive function. Therefore, elucidating the influence of the central executive function on information processing in working memory, such as in audiovisual integration, is of great scientific and practical importance.PurposeThis study used a paradigm that combined N-back and Go/NoGo tasks, using simple Arabic numerals as stimuli, to investigate the effects of cognitive load (modulated by varying the magnitude of N) and audiovisual integration on the central executive function of working memory as well as their interaction.MethodsSixty college students aged 17–21 years were enrolled and performed both unimodal and bimodal tasks to evaluate the central executive function of working memory. The order of the three cognitive tasks was pseudorandomized, and a Latin square design was used to account for order effects. Finally, working memory performance, i.e., reaction time and accuracy, was compared between unimodal and bimodal tasks with repeated-measures analysis of variance (ANOVA).ResultsAs cognitive load increased, the presence of auditory stimuli interfered with visual working memory by a moderate to large extent; similarly, as cognitive load increased, the presence of visual stimuli interfered with auditory working memory by a moderate to large effect size.ConclusionOur study supports the theory of competing resources, i.e., that visual and auditory information interfere with each other and that the magnitude of this interference is primarily related to cognitive load.

Abstract The regenerative capacity of skeletal muscle is dependent on satellite cells. The circadian clock regulates the maintenance and function of satellite cells. Cryptochrome 2 (CRY2) is a critical component of the circadian clock, and its role in skeletal muscle regeneration remains controversial. Using the skeletal muscle lineage and satellite cell‐specific CRY2 knockout mice (CRY2scko), we show that the deletion of CRY2 enhances muscle regeneration. Single myofiber analysis revealed that deletion of CRY2 stimulates the proliferation of myoblasts. The differentiation potential of myoblasts was enhanced by the loss of CRY2 evidenced by increased expression of myosin heavy chain (MyHC) and myotube formation in CRY2−/− cells versus CRY2+/+ cells. Immunostaining revealed that the number of mononucleated paired box protein 7 (PAX7+) cells associated with myotubes formed by CRY2−/− cells was increased compared with CRY2+/+ cells, suggesting that more reserve cells were produced in the absence of CRY2. Loss of CRY2 leads to the activation of the ERK1/2 signaling pathway and ETS1, which binds to the promoter of PAX7 to induce its transcription. CRY2 deficient myoblasts survived better in ischemic muscle. Therefore, CRY2 is essential in regulating skeletal muscle repair.

Isochrysis galbana, as a potential accumulator of fucoxanthin, has become a valuable material to develop functional foods for humans. Our previous research revealed that green light effectively promotes the accumulation of fucoxanthin in I. galbana, but there is little research on chromatin accessibility in the process of transcriptional regulation. This study was conducted to reveal the mechanism of fucoxanthin biosynthesis in I. galbana under green light by analyzing promoter accessibility and gene expression profiles. Differentially accessible chromatin regions (DARs)-associated genes were enriched in carotenoid biosynthesis and photosynthesis-antenna protein formation, including IgLHCA1, IgLHCA4, IgPDS, IgZ-ISO, IglcyB, IgZEP, and IgVDE. The motifs for the MYB family were also identified as candidates controlling metabolic regulation responses to green light culture of I. galbana, including IgMYB1, IgMYB2, IgMYB33, IgMYB42, IgMYB98, IgMYB118, and IgMYB119. The results of differential expression analysis and WGCNA showed that several genes or transcription factors (TFs) related to carotenoid metabolism and photosynthesis exhibited a higher expression level and were significantly upregulated in A-G5d compared with A-0d and A-W5d, including IgMYB98, IgLHCA1, IgLHCX2, IgLHCB4, and IgLHCB5. This suggests that upregulation of these genes by green light may be the key factor leading to fucoxanthin accumulation by regulating the photosynthesis-antenna protein pathway. An integrated analysis of ATAC-seq and RNA-seq showed that 3 (IgphoA, IgPKN1, IgOTC) of 34 DARs-associated genes displayed obvious changes in their chromatin regions in ATAC-seq data, suggesting that these genes specific for green light may play a key role in fucoxanthin biosynthesis in I. galbana through a complex regulatory network of multiple metabolic pathways interacting with each other. These findings will facilitate in-depth understanding the molecular regulation mechanisms of fucoxanthin in I. galbana and its role in response to green light regulation, providing technical support for the construction of high fucoxanthin content strains.

Interstitial lung disease (ILD) is a group of diffuse parenchymal infiltrating diseases of different etiologies. The neutrophil-to-lymphocyte ratio (NLR) can reflect ILD's existence, progression, and prognosis and is currently regarded as a promising biological marker. This meta-analysis assessed elevated NLR levels in ILD for their predictive value. From inception to July 27, 2022, the Scopus, Cochrane Library, Web of Science, Embase, and PubMed databases were checked thoroughly. We used the weighted mean difference (WMD) and 95% confidence interval (CI) to compare blood NLR values between groups. We examined the relationship between poor prognoses and elevated NLR concentrations in ILD patients using odds ratios (ORs) and 95% CI. After initially including 443 studies, 24 were ultimately analyzed. Fifteen studies(ILD:n = 2,912, Non-ILD: n = 2,868) revealed that the NLR values in the ILD group were relatively high (WMD = 0.61, 95% CI 0.43-0.79, p = 0.001). Eight articles (with poor prognoses: n = 407, without poor prognoses: n = 340) indicated that ILD patients with poor prognoses had higher NLR values (WMD = 1.33, 95% CI 0.32-2.33, p = 0.01). This distinction was especially noticeable in patients with the connective tissue disease (CTD)associated with ILD subgroup (WMD = 3.53, 95% CI 1.54-5.51, p = 0.0005). The pooled OR for increased NLR levels forecasting poor prognoses of ILD was 1.09 (95% CI 1.03-1.15, p = 0.0008). Increasing blood NLR values have clinical significance and application value for detecting ILD and predicting its poor prognosis, especially in CTD patients.

Background Advancements in research have confirmed that gut microbiota can influence health through the microbiota–gut–brain axis. Meditation, as an inner mental exercise, can positively impact the regulation of an individual’s physical and mental health. However, few studies have comprehensively investigated faecal microbiota following long-term (several years) deep meditation. Therefore, we propose that long-term meditation may regulate gut microbiota homeostasis and, in turn, affect physical and mental health.Aims To investigate the effects of long-term deep meditation on the gut microbiome structure.Methods To examine the intestinal flora, 16S rRNA gene sequencing was performed on faecal samples of 56 Tibetan Buddhist monks and neighbouring residents. Based on the sequencing data, linear discriminant analysis effect size (LEfSe) was employed to identify differential intestinal microbial communities between the two groups. Phylogenetic Investigation of Communities by Reconstruction of Unobserved States (PICRUSt) analysis was used to predict the function of faecal microbiota. In addition, we evaluated biochemical indices in the plasma.Results The α-diversity indices of the meditation and control groups differed significantly. At the genus level, Prevotella and Bacteroides were significantly enriched in the meditation group. According to the LEfSe analysis, two beneficial bacterial genera (Megamonas and Faecalibacterium) were significantly enriched in the meditation group. Functional predictive analysis further showed that several pathways—including glycan biosynthesis, metabolism and lipopolysaccharide biosynthesis—were significantly enriched in the meditation group. Moreover, plasma levels of clinical risk factors were significantly decreased in the meditation group, including total cholesterol and apolipoprotein B.Conclusions Long-term traditional Tibetan Buddhist meditation may positively impact physical and mental health. We confirmed that the gut microbiota composition differed between the monks and control subjects. The microbiota enriched in monks was associated with a reduced risk of anxiety, depression and cardiovascular disease and could enhance immune function. Overall, these results suggest that meditation plays a positive role in psychosomatic conditions and well-being.

Parrots have undergone substantial karyotype evolution compared to most other birds. Here, Huang et al. analyze chromosome-level genome assemblies for four parrot species and elucidate the complex evolutionary history of parrot chromosomes.

Staphylococcus aureus (S. aureus), as the main pathogen in milk and dairy products, usually causes intoxication with vomiting and various kinds of inflammation after entering the human body. CodY, an important transcriptional regulator in S. aureus, plays an important role in regulating metabolism, growth, and virulence. However, little is known about the role of CodY on environmental stress tolerance. In this research, we revealed the role of CodY in environmental stress tolerance in foodborne S. aureus RMSA24. codY mutation significantly reduced the tolerance of S. aureus to desiccation and oxidative, salt, and high-temperature stresses. However, S. aureus was more tolerant to low temperature stress due to mutation of codY. We found that the expressions of two important heat shock proteins—GroEL and DanJ—were significantly down-regulated in the mutant codY. This suggests that CodY may indirectly regulate the high- and low-temperature tolerance of S. aureus by regulating the expressions of groEL and danJ. This study reveals a new mechanism of environmental stress tolerance in S. aureus and provides new insights into controlling the contamination and harm caused by S. aureus in the food industry.

The increasing morbidity and mortality of life-threatening Pneumocystis pneumonia (PCP) in immunocompromised people poses a global concern, prompting the World Health Organization to list it as one of the 19 priority invasive fungal diseases, calling for increased research and public health action. In response to this initiative, we provide this review on the epidemiology of PCP in non-HIV patients with various immunodeficient conditions, including the use of immunosuppressive agents, cancer therapies, solid organ and stem cell transplantation, autoimmune and inflammatory diseases, inherited or primary immunodeficiencies, and COVID-19. Special attention is given to the molecular epidemiology of PCP outbreaks in solid organ transplant recipients; the risk of PCP associated with the increasing use of immunodepleting monoclonal antibodies and a wide range of genetic defects causing primary immunodeficiency; the trend of concurrent infection of PCP in COVID-19; the prevalence of colonization; and the rising evidence supporting de novo infection rather than reactivation of latent infection in the pathogenesis of PCP. Additionally, we provide a concise discussion of the varying effects of different immunodeficient conditions on distinct components of the immune system. The objective of this review is to increase awareness and knowledge of PCP in non-HIV patients, thereby improving the early identification and treatment of patients susceptible to PCP.

Abstract Mammary pathogenic Escherichia coli (MPEC) is an important causative agent of mastitis in dairy cows that results in reduced milk quality and production, and is responsible for severe economic losses in the dairy industry worldwide. Oxidative stress, as an imbalance between reactive oxygen species (ROS) and antioxidants, is a stress factor that is common in most bacterial habitats. The presence of ROS can damage cellular sites, including iron-sulfur clusters, cysteine and methionine protein residues, and DNA, and may cause bacterial cell death. Previous studies have reported that Autoinducer 2 (AI-2) can regulate E. coli antibiotic resistance and pathogenicity by mediating the intracellular receptor protein LsrR. This study explored the regulatory mechanism of LsrR on the H2O2 stress response in MPEC, showing that the transcript levels of lsrR significantly decreased under H2O2 stress conditions. The survival cell count of lsrR mutant XW10/pSTV28 was increased about 3080-fold when compared with that of the wild-type WT/pSTV28 in the presence of H2O2 and overexpression of lsrR (XW10/pUClsrR) resulted in a decrease in bacterial survival rates under these conditions. The β-galactosidase reporter assays showed that mutation of lsrR led to a remarkable increase in expression of the promoters of ahpCF, katG and oxyR, while lsrR-overexpressing significantly reduced the expression of ahpCF and katG. The electrophoretic mobility shift assays confirmed that LsrR could directly bind to the promoter regions of ahpCF and katG. These results revealed the important role played by LsrR in the oxidative stress response of MPEC.

Exposure to nicotine is the first cause of entirely preventable death killing, which is commonly initiated in adolescence. Previous studies revealed the changes of electroencephalography (EEG) and inhibition control in smokers. However, little is known about the specific link between alpha coherence during the resting state and inhibition control ability in young smokers. The present study aimed to investigate inter-hemispherical and frontal-parietal alpha coherence changes and assessed the relationships between alpha coherence and inhibition control in young smokers. We collected resting-state EEG data from 23 young smokers and 24 healthy controls. Inhibition control ability was assessed by a Go/NoGo task. Compared to healthy controls, young smokers exhibited increased inter-hemispherical and frontal-parietal alpha coherence. Furthermore, young smokers committed more NoGo errors in the Go/NogGo task. It is noteworthy that alpha coherence at the frontal electrode sites was positively correlated with NoGo errors in healthy controls, whereas inverse correlations were observed in young smokers. Our findings suggested that alterations of alpha coherence may provide support to the earlier nicotine-dependence-related research findings, which may help us to understand the neuropathology of inhibitory control in young smokers.

Polygonatum cyrtonema is a medicinal and edible herb rich in polysaccharides, steroidal saponins, and flavonoids that has been widely used as a food, vegetable, and medicine over the years. Although previous studies have preliminarily explored the metabolic and transcriptional regulatory mechanisms of the main secondary metabolites in P. cyrtonema, the complex mechanism of microRNA (miRNA)-mediated posttranscriptional regulation remains unclear. Metabolome analysis showed that iso-ophiopogonanone B, (25S)-pratioside D1, disporopsin, and isodiosgenin-Glc-Glc, which are associated with intermediates in the flavonoids and saponins pathways, were significantly upregulated in the stem and leaf compared with the rhizome, and most saccharides, including arabinose, cellobiose, maltotetraose, and panose, showed the opposite trend, suggesting that they may contribute to the formation and accumulation of the main active ingredients in P. cyrtonema. We found that 4-hydroxymandelonitrile have a relatively good inhibitory effect on α-glucosidase, indicating that it may play a role in hypoglycemic functions. Transcriptome and weighted gene coexpression network analysis (WGCNA) were combined to reveal several candidate genes involved in the accumulation of polysaccharides, saponins, and flavonoids, including PcSQLE, PcCYP71A1, PcSUS, PcFK, and PcMYB102. Integrated analyses of miRNAs and messengerRNAs (mRNAs) showed that novel_miR14, novel_miR49, novel_miR75, and aof_miR164 were negatively correlated with alpha-linolenic acid metabolism and the mitogen activated protein kinase (MAPK) signaling pathway, including PcAOS, PcSPLA2, PcFRK1, and PcDELLA, indicating that these miRNAs may coordinately regulate the biosynthesis of other secondary metabolites in P. cyrtonema. These findings will facilitate in-depth research on the functions of these miRNAs and mRNAs related to the main active substances for pathological and biological regulation, which will be beneficial to provide theoretical guidance for the molecular breeding of P. cyrtonema.

Sugar beet (Beta vulgaris L.) is an important sugar-producing and energy crop worldwide. The sugar beet pure line IMA1 independently bred by Chinese scientists is a standard diploid parent material that is widely used in hybrid-breeding programs. In this study, a high-quality, chromosome-level genome assembly for IMA1was conducted, and 99.1% of genome sequences were assigned to nine chromosomes. A total of 35,003 protein-coding genes were annotated, with 91.56% functionally annotated by public databases. Compared with previously released sugar beet assemblies, the new genome was larger with at least 1.6 times larger N50 size, thereby substantially improving the completeness and continuity of the sugar beet genome. A Genome-Wide Association Studies analysis identified 10 disease-resistance genes associated with three important beet diseases and five genes associated with sugar yield per hectare, which could be key targets to improve sugar productivity. Nine highly expressed genes associated with pollen fertility of sugar beet were also identified. The results of this study provide valuable information to identify and dissect functional genes affecting sugar beet agronomic traits, which can increase sugar beet production and help screen for excellent sugar beet breeding materials. In addition, information is provided that can precisely incorporate biotechnology tools into breeding efforts.

The development of nicotine addiction was associated with the abnormalities of intrinsic functional networks during the resting state in young adult smokers. As a whole-brain imaging approach, EEG microstate analysis treated multichannel EEG recordings as a series of quasi-steady microscopic states which were related to the resting-state networks (RSNs) found by fMRI. The aim of this study was to examine whether the resting-state EEG microstate analysis may provide novel insights into the abnormal temporal properties of intrinsic brain activities in young smokers. We used 64-channel resting-state EEG datasets to investigate alterations in microstate characteristics between twenty-five young smokers and 25 age- and gender-matched non-smoking controls. Four classic EEG microstates (microstate A, B, C, and D) were obtained, and the four temporal parameters of each microstate were extracted, i.e., duration, occurrence, coverage, and transition probabilities. Compared with non-smoking controls, young smokers showed decreased occurrence of microstate C and increased duration of microstate D. Furthermore, both the duration and coverage of microstate D were significantly negatively correlated with Fagerstrom Test of Nicotine Dependence (FTND) in young smoker group. The complex changes in the microstate time-domain parameters might correspond to the abnormalities of RSNs in analyses of FC measured with fMRI in the previous studies and indicate the altered specific brain functions in young smokers. Microstate D could be potentially represented as a selective biomarker for predicting the dependence degree of adolescent smokers on cigarettes. These results suggested that EEG microstate analysis might detect the deviant functions of large-scale cortical activities in young smokers and provide a new perspective for the study of brain networks of adolescent smokers.

Objective: To establish a rapid, cost-effective, accurate, and acceptable osteoporosis (OP) screening model for the Chinese male population (age ≥ 40 years) based on data mining technology. Materials and methods: This was a 3-year retrospective cohort study, which belonged to the sub-cohort of the Chinese Reaction Study. The research period was from March 2011 to December 2014. A total of 1834 subjects who did not hav e OP at the baseline and completed a 3-year follow-up were included in this study. All subjects underwent quantitative ultrasound examinations for calcaneus at the baseline and follow-ups that lasted for 3 years. We utilized the least absolute shrinkage and selection operator (LASSO) regression model to select feature variables. The chara cteristic variables selected in the LASSO regression were analyzed by multivariable logistic regression (MLR) to construct the predictive model. This predictive model was displayed through a nomogram. We used the receiver operating characteristic (ROC) curve, C-index, calibration curve, and clinical decision curve analysis (DCA) to evaluate model performance and the bootstrapping validation to internally validate the model. Results: The predictive factors included in the prediction model were age, neck circumference, waist-to-height ratio, BMI, triglyceride, impaired fasting glucose, dyslipidemia, osteopenia, smoking history, and strenuous exercise. The area under the ROC (AUC) curve of the risk nomogram was 0.882 (95% CI, 0.8 58–0.907), exhibiting good predictive ability and performance. The C-index for the risk nomogram was 0.882 in the prediction model, which presented good refinement. In add ition, the nomogram calibration curve indicated that the prediction model was consistent. The DCA showed that when the threshold probability was between 1 and 100%, the nomogram had a good clinical application value. More importantly, the internal ly verified C-index of the nomogram was still very high, at 0.870. Conclusions: This novel nomogram can effectively predict the 3-year inciden ce risk of OP in the male population. It also helps clinicians to identify group s at high risk of OP early and formulate personalized intervention measures.

Summary: Skeletal muscle regeneration relies on satellite cells that can proliferate, differentiate, and form new myofibers upon injury. Emerging evidence suggests that misregulation of satellite cell fate and function influences the severity of Duchenne muscular dystrophy (DMD). The transcription factor Pax7 determines the myogenic identity and maintenance of the pool of satellite cells. The circadian clock regulates satellite cell proliferation and self-renewal. Here, we show that the CLOCK-interacting protein Circadian (CIPC) a negative-feedback regulator of the circadian clock, is up-regulated during myoblast differentiation. Specific deletion of Cipc in satellite cells alleviates myopathy, improves muscle function, and reduces fibrosis in mdx mice. Cipc deficiency leads to activation of the ERK1/2 and JNK1/2 signaling pathways, which activates the transcription factor SP1 to trigger the transcription of Pax7 and MyoD. Therefore, CIPC is a negative regulator of satellite cell function, and loss of Cipc in satellite cells promotes muscle regeneration.

Summary: Background: There have been mixed reports on the beneficial effects of meditation in cardiovascular disease (CVD), which is widely considered the leading cause of death worldwide. Methods: To clarify the role of meditation in modulating the heart-brain axis, we implemented an extreme phenotype strategy, i.e., Tibetan monks (BMI > 30) who practised 19.20 ± 7.82 years of meditation on average and their strictly matched non-meditative Tibetan controls. Hypothesis-free advanced proteomics strategies (Data Independent Acquisition and Targeted Parallel Reaction Monitoring) were jointly applied to systematically investigate and target the plasma proteome underlying meditation. Total cholesterol, low-density lipoprotein cholesterol (LDL-C), apolipoprotein B (Apo B) and lipoprotein (a) [Lp(a)] as the potential cardiovascular risk factors were evaluated. Heart rate variability (HRV) was assessed by electrocardiogram. Findings: Obesity, hypertension, and reduced HRV is offset by long-term meditation. Notably, meditative monks have blood pressure and HRV comparable to their matched Tibetan controls. Meditative monks have a protective plasma proteome, related to decreased atherosclerosis, enhanced glycolysis, and oxygen release, that confers resilience to the development of CVD. In addition, clinical risk factors in plasma were significantly decreased in monks compared with controls, including total cholesterol, LDL-C, Apo B, and Lp(a). Interpretation: To our knowledge, this work is the first well-controlled proteomics investigation of long-term meditation, which opens up a window for individuals characterized by a sedentary lifestyle to improve their cardiovascular health with an accessible method practised for more than two millennia. Funding: See the Acknowledgements section.

Avian pathogenic Escherichia coli (APEC) is one of the common extraintestinal infectious disease pathogens in chickens, geese, and other birds. It can cause a variety of infections, and even the death of poultry, causing enormous economic losses. However, the misuse and abuse of antibiotics in the poultry industry have led to the development of drug resistance in the gut microbes, posing a challenge for the treatment of APEC infections. It has been reported that the CpxRA two-component system has an effect on bacterial drug resistance, but the specific regulatory mechanism remains unclear. In this study, the regulatory mechanism of CpxRA on APEC biofilm formation and EmrKY efflux pump was investigated. The cpxRA knockout strain of E. coli APEC40 was constructed, and the molecular regulatory mechanism of CpxR on biofilms and efflux pump-coding genes were identified by biofilm formation assays, drug susceptibility test, real-time reverse transcription quantitative PCR, and electrophoretic mobility shift assay (EMSA). The results indicated that CpxR can directly bind to the promoter region of emrKY and negatively regulate the sensitivity of bacteria to ofloxacin and erythromycin. These results confirm the important regulatory role of the CpxRA two-component system under antibiotic stress in APEC.

Avian pathogenic Escherichia coli (APEC) causes a variety of bacterial infectious diseases known as avian colibacillosis leading to significant economic losses in the poultry industry worldwide and restricting the development of the poultry industry. The development of efflux pumps is one important bacterial antibiotic resistance mechanism. Efflux pumps are capable of extruding a wide range of antibiotics out of the cytoplasm of some bacterial species, including β-lactams, polymyxins, tetracyclines, fluoroquinolones, aminoglycosides, novobiocin, nalidixic acid, and fosfomycin. In the present study, we constructed the mcbR mutant and the mcbR-overexpressing strain of E. coli strain APECX40 and performed antimicrobial susceptibility testing, antibacterial activity assays, real-time reverse transcription PCR, and electrophoretic mobility shift assays (EMSA) to investigate the molecular regulatory mechanism of McbR on the genes encoding efflux pumps. Our results showed that McbR positively regulates cell susceptibility to 12 antibiotics, including clindamycin, lincomycin, cefotaxime, cefalexin, doxycycline, tetracycline, gentamicin, kanamycin, norfloxacin, ofloxacin, erythromycin, and rifampicin by activating the transcription of acrAB, acrD, emrD, and mdtD (P

Cyclocarya paliurus, a well-known nutrient and beverage plant, is under development for use in functional health care products best and natural and organic foods. We hypothesis that the composition and metabolic accumulation of hypoglycemic nutrient metabolites exhibit significant differences depending on harvest time. Therefore, it is of great significance to establish the best harvest time for C. paliurus leaves for the further development of healthy teas and other products. However, the detail compositions and molecular mechanisms of nutrients biosynthesis in C. paliurus leaves during different harvest stages remain largely unclear. Metabolome analysis showed that a suitable leaf-harvesting strategy for C. paliurus could be in September or October each year due to the high content of hypoglycemic nutrient metabolites. We found that two of the seven differentially accumulated phenolic acid metabolites have a relatively good inhibitory effect on α-amylase, indicating that they may play a role in the hypoglycemic function. Combined analysis of coexpression, ceRNA network, and weighted gene correlation network analysis (WGCNA) showed that several genes or transcription factors (TFs) in three modules correlated highly with hypoglycemic nutrient metabolites, including CpPMM, CpMan, CpFK, CpSUS, CpbglX, Cp4CL, CpHCT, and CpWRKY1. These findings help in the understanding of the molecular mechanisms and regulatory networks of the hypoglycemic nutrient metabolites in C. paliurus leaves which are dependent on harvest time and provide theoretical guidance in the development of functional health care products and foods from C. paliurus.

Avian pathogenic Escherichia coli (APEC) is a specific group of extraintestinal pathogenic E. coli that causes a variety of extraintestinal diseases in chickens, ducks, pigeons, turkeys, and other avian species. These diseases lead to significant economic losses in the poultry industry worldwide. However, owing to excessive use of antibiotics in the treatment of infectious diseases, bacteria have developed antibiotic resistance. The development of multidrug efflux pumps is one important bacterial antibiotic resistance mechanism. A multidrug efflux pump, MdtH, which belongs to the major facilitator superfamily of transporters, confers resistance to quinolone antibiotics such as norfloxacin and enoxacin. LsrR regulates hundreds of genes that participate in myriad biological processes, including mobility, biofilm formation, and antibiotic susceptibility. However, whether LsrR regulates mdtH transcription and then affects bacterial resistance to various antibiotics in APEC has not been reported. In the present study, the lsrR mutant was constructed from its parent strain APECX40 (WT), and high-throughput sequencing was performed to analyze the transcriptional profile of the WT and mutant XY10 strains. The results showed that lsrR gene deletion upregulated the mdtH transcript level. Furthermore, we also constructed the lsrR- and mdtH-overexpressing strains and performed antimicrobial susceptibility testing, antibacterial activity assays, real-time reverse transcription PCR, and electrophoretic mobility shift assays to investigate the molecular regulatory mechanism of LsrR on the MdtH multidrug efflux pump. The lsrR mutation and the mdtH-overexpressing strain decreased cell susceptibility to norfloxacin, ofloxacin, ciprofloxacin, and tetracycline by upregulating mdtH transcript levels. In addition, the lsrR-overexpressing strain increased cell susceptibility to norfloxacin, ofloxacin, ciprofloxacin, and tetracycline by downregulating mdtH transcript levels. Electrophoretic mobility shift assays indicated that LsrR directly binds to the mdtH promoter. Therefore, this study is the first to demonstrate that LsrR inhibits mdtH transcription by directly binding to its promoter region. This action subsequently increases susceptibility to the aforementioned four antibiotics in APECX40.

Abstract Background In this study, renewable tea waste hydrolysate was used as a sole carbon source for carotenoids and lipid production. A novel Rhodosporidium toruloides mutant strain, RM18, was isolated through atmospheric and room-temperature plasma mutagenesis and continuous domestication in tea waste hydrolysate from R. toruloides ACCC20341. Results RM18 produced a larger biomass and more carotenoids and α-linolenic acid compared with the control strain cultured in tea waste hydrolysate. The highest yields of torularhodin (481.92 μg/g DCW) and torulene (501 μg/g DCW) from RM18 cultured in tea waste hydrolysate were 12.86- and 1.5-fold higher, respectively, than that of the control strain. In addition, α-linolenic acid production from RM18 in TWH accounted for 5.5% of total lipids, which was 1.58 times more than that of the control strain. Transcriptomic profiling indicated that enhanced central metabolism and terpene biosynthesis led to improved carotenoids production, whereas aromatic amino acid synthesis and DNA damage checkpoint and sensing were probably relevant to tea waste hydrolysate tolerance. Conclusion Tea waste is suitable for the hydrolysis of microbial cell culture mediums. The R. toruloides mutant RM18 showed considerable carotenoids and lipid production cultured in tea waste hydrolysate, which makes it viable for industrial applications.

Abstract Background Pneumocystis jirovecii (P. jirovecii) is an opportunistic fungal pathogen and the role of its colonization in pulmonary diseases has become a popular focus in recent years. The aim of this study was to develop a modified loop-mediated isothermal amplification (LAMP) assay for detection of Pneumocystis jirovecii (P. jirovecii) DNA amongst non-HIV patients with various pulmonary diseases and use it to examine the prevalence and assess the association of P. jirovecii colonization with clinical characteristics of these diseases. Methods We modified the previously reported LAMP assay for P. jirovecii by adding real-time detection. This method was used to detect P. jirovecii colonization in pulmonary samples collected from 403 non-HIV patients with various pulmonary diseases enrolled from 5 hospitals in China. We determined the prevalence of P. jirovecii colonization in 7 types of pulmonary diseases and assessed the association of P. jirovecii colonization with clinical characteristics of these diseases. Results The modified LAMP assay showed no cross-reactivity with other common pulmonary microbes and was 1000 times more sensitive than that of conventional PCR. Using the modified LAMP assay, we detected P. jirovecii colonization in 281 (69.7%) of the 403 patients enrolled. P. jirovecii colonization was more common in interstitial lung diseases than in chronic obstructive pulmonary disease (COPD) (84.6% vs 64.5%, P

Background The pET expression system based on T7 promoter which is induced by isopropyl-β-D-1-thiogalactopyranoside (IPTG) is by far the most commonly used system for production of heterogeneous proteins in Escherichia coli. However, this system was limited by obvious drawbacks including the host toxicity and metabolic burden imposed by the presence of IPTG. Methods In this study, we incorporated the autoinducer-2 (AI-2) quorum sensing system to realize autoinduction of the pET expression system. The autoinduction expression vector pXWZ1 was constructed by inserting the lsr promoter regions into the pET28a(+) vector. The expression efficiency of the reporter genes gfpuv and lacZ by the pXWZ1 and pET28a(+) vectors were compared. Results The results showed that the expression levels of the both report genes in the cells transformed with pXWZ1 without any addition of exogenous inducer were higher than that transformed with pET28a(+) vectors by the induction of IPTG. Conclusion This new auto-induction system will exclude the limitations of the IPTG induction including toxic to host and increasing formation of inclusion body and will become a more economical and convenient tool for recombinant protein expression.

Long non-coding RNAs (lncRNAs) play pivotal roles in mesenchymal stem cell differentiation. However, the mechanisms by which non-coding RNA (ncRNA) networks regulate osteogenic differentiation remain unclear. Therefore, our aim was to identify RNA-associated gene and transcript expression profiles during osteogenesis in bone marrow mesenchymal stem cells (BMSCs). Using transcriptome sequencing for differentially expressed ncRNAs and mRNAs between days 0 and 21 of osteogenic differentiation of BMSCs, we found that the microRNA (miRNA) miR-503-5p was significantly downregulated. However, the putative miR-503-5p target, sorbin and SH3 domain containing 1 (SORBS1), was significantly upregulated in osteogenesis. Moreover, through lncRNA-miRNA-mRNA interaction analyses and loss- and gain-of-function experiments, we discovered that the lncRNAs LOC100126784 and POM121L9P were abundant in the cytoplasm and enhanced BMSC osteogenesis by promoting SORBS1 expression. In contrast, miR-503-5p reversed this effect. Ago2 RNA-binding protein immunoprecipitation and dual-luciferase reporter assays further validated the direct binding of miR-503-5p to LOC100126784 and POM121L9P. Furthermore, SORBS1 knockdown suppressed early osteogenic differentiation in BMSCs, and co-transfection with SORBS1 small interfering RNAs counteracted the BMSCs’ osteogenic capacity promoted by LOC100126784- and POM121L9P-overexpressing lentivirus plasmids. Thus, the present study demonstrated that the lncRNAs LOC100126784 and POM121L9P facilitate the osteogenic differentiation of BMSCs via the miR-503-5p/SORBS1 axis, providing potential therapeutic targets for treating osteoporosis and bone defects.

The brain is susceptible to perturbations of redox balance, affecting neurogenesis and increasing the risks of psychiatric disorders. Thioredoxin-interacting protein (TXNIP) is an endogenous inhibitor of the thioredoxin antioxidant system. Its deletion or inhibition suggests protection for a brain with ischemic stroke or Alzheimer’s disease. Combined with conditional knockout mice and schizophrenia samples, we aimed to investigate the function of TXNIP in healthy brain and psychiatric disorders, which are under-studied. We found TXNIP was remarkedly expressed in the prefrontal cortex (PFC) during healthy mice’s prenatal and early postnatal periods, whereas it rapidly decreased throughout adulthood. During early life, TXNIP was primarily distributed in inhibitory and excitatory neurons. Contrary to the protective effect, the embryonic deletion of TXNIP in GABAergic (gamma-aminobutyric acid-ergic) neurons enhanced oxidative stress in PV+ interneurons of aging mice. The deleterious impact was brain region-specific. We also investigated the relationship between TXNIP and schizophrenia. TXNIP was significantly increased in the PFC of schizophrenia-like mice after MK801 administration, followed by oxidative stress. First episode and drug naïve schizophrenia patients with a higher level of plasma TXNIP displayed severer psychiatric symptoms than patients with a low level. We indicated a bidirectional function of TXNIP in the brain, whose high expression in the early stage is protective for development but might be harmful in a later period, associated with mental disorders.

Chitooligosaccharide is a kind of functional food, which is the degradation product of chitosan (COS) catalyzed by the endo-chitosanase (COSE) enzyme. A COSE with a molecular weight of 34 kDa was purified and characterized from a newly isolated Mitsuaria sp. C4 (C4), and a 38.46% recovery rate and 4.79-fold purification were achieved. The purified C4 COSE exhibited optimum activity at 40°C and pH 7.2 and was significantly inhibited in the presence of Cu2+ and Fe3+. The Km and Vmin of the COSE toward COS were 2.449 g/L and 0.042 g/min/L, respectively. The highest COSE activity reached 8.344 U/ml after optimizing, which represented a 1.34-fold of increase. Additionally, chitooligosaccharide obtained by COSE hydrolysis of COS was verified by using thin-layer chromatography and high-performance liquid chromatography analysis. Whole-genome sequencing demonstrated that the C4 strain contains 211 carbohydrate enzymes, our purified COSE belonging to GHs-46 involved in carbohydrate degradation. Phylogenetic analysis showed that the novel COSE obtained from the C4 strain was clustered into the degree of polymerization = two to three groups, which can perform catalysis in a similar manner to produce (GlcN)2 and (GlcN)3. This work indicates that the C4 strain could be a good resource for enhancing carbohydrate degradation and might represent a useful tool for chitooligosaccharide production in the functional food industry.