The quorum sensing SinI/R system contributes to cadmium immobilization in Ensifer adhaerens NER9 in the cadmium-contaminated solution

In this study, the cadmium (Cd)-tolerant Ensifer adhaerens strain NER9 with quorum sensing (QS) systems (responsible for N-acyl homoserine lactone (AHL) production) was characterized for QS system-mediated Cd immobilization and the underlying mechanisms involved. Whole-genome sequence analysis revealed that strain NER9 contains the QS SinI/R and TraI/R systems. Strains NER9 and the NER9∆sinI/R, NER9∆traI/R, and NER9∆sinI/R-traI/R mutants were constructed and compared for QS SinI/R and TraI/R system-mediated Cd immobilization in the solution and the mechanisms involved. After 24 h of incubation, strain NER9 significantly decreased the Cd concentration in the Cd-contaminated solution compared with the NER9∆sinI/R, NER9∆traI/R, and NER9∆sinI/R-traI/R mutants. The NER9∆sinI/R mutant had a greater impact on Cd immobilization and a lower impact on the activities of AHLs than did the NER9∆traI/R mutant. The NER9∆sinI/R mutant had significantly greater Cd concentrations and lower cell wall- and exopolysaccharide (EPS)-adsorbed Cd contents than did strain NER9. Furthermore, the NER9∆sinI/R mutant presented a decrease in the number of functional groups interacting with Cd, compared with strain NER9. These results suggested that the SinI/R system in strain NER9 contributed to Cd immobilization by mediating cell wall- and EPS-adsorption in Cd-containing solution.

Transdermal administration of farnesol-ethosomes enhances the treatment of cutaneous candidiasis induced by Candida albicans in mice

Cutaneous candidiasis, caused by Candida albicans, is a severe and frustrating condition, and finding effective treatments can be challenging. Therefore, the development of farnesol-loaded nanoparticles is an exciting breakthrough. Ethosomes are a novel transdermal drug delivery carrier that incorporates a certain concentration (10-45%) of alcohols into lipid vesicles, resulting in improved permeability and encapsulation rates compared to conventional liposomes. Farnesol is a quorum-sensing molecule involved in morphogenesis regulation in C. albicans, and these ethosomes offer a promising new approach to treating this common fungal infection. This study develops the formulation of farnesol-loaded ethosomes (farnesol-ethosomes) and assesses applications in treating cutaneous candidiasis induced by C. albicans in vitro and in vivo. Farnesol-ethosomes were successfully developed by ethanol injection method. Therapeutic properties of farnesol-ethosomes, such as particle size, zeta potential, and morphology, were well characterized. According to the results, farnesol-ethosomes demonstrated an increased inhibition effect on cells' growth and biofilm formation in C. albicans. In Animal infection models, treating farnesol-ethosomes by transdermal administration effectively relieved symptoms caused by cutaneous candidiasis and reduced fungal burdens in quantity. We also observed that ethosomes significantly enhanced drug delivery efficacy in vitro and in vivo. These results indicate that farnesol-ethosomes can provide future promising roles in curing cutaneous candidiasis.

IMPORTANCE

Cutaneous candidiasis attributed to Candida infection is a prevalent condition that impacts individuals of all age groups. As a type of microbial community, biofilms confer benefits to host infections and mitigate the clinical effects of antifungal treatments. In C. albicans, the yeast-to-hypha transition and biofilm formation are effectively suppressed by farnesol through its modulation of multiple signaling pathway. However, the characteristics of farnesol such as hydrophobicity, volatility, degradability, and instability in various conditions can impose limitations on its effectiveness. Nanotechnology holds the potential to enhance the efficiency and utilization of this molecule. Treatment of farnesol-ethosomes by transdermal administration demonstrated a very remarkable therapeutic effect against C. albicans in infection model of cutaneous candidiasis in mice. Many patients suffering fungal skin infection will benefit from this study.

Development of an Evaluation System for the Prophylactic Use of Antimicrobial Drugs in the Perioperative Period of Class I Surgical Incisions in Neurosurgery

BACKGROUND

This study aimed to establish a precise preoperative high-risk factor scoring system and algorithm for antibiotic prophylaxis decision-making, provide guidance for the judicious use of AMP, refine interventions, and ensure the appropriate application of AMP for class I incisions in neurosurgery.

METHODS

According to PRISMA guidelines, literature searches, study selection, methodology development, and quality appraisal were performed. The quality of evidence across the study population was assessed using the Newcastle-Ottawa Scale. A two-round Delphi expert consultation method involved 15 experts from leading tertiary hospitals in China. Establishing an algorithm of SOPs for perioperative antimicrobial prophylaxis in Class I neurosurgical incisions.

RESULTS

Thirteen studies, encompassing 11,936 patients undergoing clean neurosurgical procedures, were included. 791 patients experienced SSI, resulting in an average incidence of 6.62%. Identified risk factors significantly associated with an increased incidence of postoperative SSI (P < 0.05) included emergency surgery, preoperative hospitalization ≥7 days, intraoperative blood loss ≥300 mL, operation time ≥4 hours, diabetes mellitus, cerebrospinal fluid leakage, and repeat surgery. Sensitivity analysis demonstrated robust results for emergency surgery, intraoperative blood loss ≥300 mL, operation time ≥4 hours, cerebrospinal fluid leakage, and repeat surgery. Established a risk assessment system for Class I neurosurgical incisions by the Delphi method. Additionally, we have formulated an algorithm of SOPs for perioperative antimicrobial prophylaxis in Class I neurosurgical incisions.

CONCLUSIONS

The established index for AMP utilization and SOPs in the preoperative period of class I neurosurgical incisions proves valuable, contributing to improved patient outcomes in neurosurgical procedures.

Comparative Genome Analysis of Two Streptococcus suis Serotype 8 Strains Identifies Two New Virulence-Associated Genes

Streptococcus suis is an important zoonotic pathogen that can cause meningitis and septicemia in swine and humans. Among numerous pathogenic serotypes, S. suis serotype 8 has distinctive characteristics such as a high detection rate and causing multi-host infection. There is no complete genome of serotype 8 strains so far. In this study, the complete genome of two S. suis serotype 8 strains, virulent strain 2018WUSS151 and non-virulent strain WUSS030, were sequenced. Comparative genomic analysis showed that the homology of the two genomes reaches 99.68%, and the main difference is the distinctive prophages. There are 83 genes unique to virulent strain 2018WUSS151, including three putative virulence-associated genes (PVGs). Two PVGs, padR and marR, are passenger genes in ISSsu2 family transposons that are able to form circular DNA intermediates during transposition, indicating the possibility of horizontal transmission among S. suis strains. The deletion mutant of PVGs marR or atpase attenuated the virulence of serotype 2 virulent SC070731 in a mouse infection model, confirming their role in S. suis virulence. These findings contribute to clarifying the genomic characterization of S. suis serotype 8 and S. suis pathogenesis.

DNA hypomethylation mediates immune response in pan-cancer

Abnormal DNA methylation is a fundamental characterization of epigenetics in cancer. Here we demonstrate that aberrant DNA methylating can modulate the tumour immune microenvironment in 16 cancer types. Differential DNA methylation in promoter region can regulate the transcriptomic pattern of immune-related genes and DNA hypomethylation mainly participated in the processes of immunity, carcinogenesis and immune infiltration. Moreover, many cancer types shared immune-related functions, like activation of innate immune response, interferon gamma response and NOD-like receptor signalling pathway. DNA methylation can further help identify molecular subtypes of kidney renal clear cell carcinoma. These subtypes are characterized by DNA methylation pattern, major histocompatibility complex, cytolytic activity and cytotoxic t lymphocyte and tumour mutation burden, and subtype with hypomethylation pattern shows unstable immune status. Then, we investigate the DNA methylation pattern of exhaustion-related marker genes and further demonstrate the role of hypomethylation in tumour immune microenvironment. In summary, our findings support the use of hypomethylation as a biomarker to understand the mechanism of tumour immune environment.

Preparation and performance testing of corn starch/pullulan/gallic acid multicomponent composite films for active food packaging

The present study investigated the mechanical characteristics, hydrophobicity, antioxidant and antibacterial properties, FTIR, SEM and XRD of films fabricated with corn starch and pullulan (CS/PUL) by adding different concentrations of Gallic acid (GA) (0%, 0.5%, 1.0%, 1.5% w/v). The mechanical strength and opacity of CS/PUL films were enhanced by the addition of 1.0% GA. The water vapor permeability (WVP) of CS/PUL films was significantly lower in films with GA compared to those without (P < 0.05). The addition of GA, especially at concentrations of 1.0% and 1.5%, resulted in considerably better free radical scavenging activities on DPPH than films without GA (P < 0.05). Interestingly, the highest water contact angle (WCA) value was observed in films with 0.5% GA, indicating stronger hydrophobicity. Furthermore, the antibacterial capabilities of the films, particularly against E. coli and P. aeruginosa, improved with an increase in GA concentration. The results of FTIR, SEM and XRD analyses showed that GA was well distributed in the CS/PUL matrix.

Effect of high-fructose consumption in pregnancy on the bone growth of offspring rats

Growing evidence suggests that bone health is programmed in early life. Maternal diet may influence the skeletal development of offspring. We aimed to determine the possible effects of high-fructose intake during pregnancy on different aspects of long bone morphology in the offspring of rats and to initially explore the possible mechanisms. Pregnant Sprague-Dawley rats were randomly divided into four groups and intragastrically administered the same dose of distilled water (CON, n = 12), 20 g/kg/day glucose (GLU, n = 12), 10 g/kg/day fructose (LFRU, n = 12), or 20 g/kg/day fructose (HFRU, n = 12) for 21 days during gestation. Computed tomography was used to analyze the cortical and cancellous bones of the distal femur of the offspring rats, and circulating bone metabolic biomarkers were measured using enzyme immunoassay. The results showed that high-fructose intake during pregnancy could decrease body weight, impair glucose metabolism, and increase serum leptin and uric acid in offspring. The offspring in the HFRU group had higher levels of the N-terminal propeptide of type I procollagen (PINP) and the C-telopeptide of type I collagen (CTX). The bone mean density (BMD), the total cross-sectional area inside the periosteal envelope (Tt.Ar), cortical bone area (Ct.Ar), medullary (or marrow) area (Ma.Ar), and trabecular mean density of the offspring in the HFRU group were lower than those in the CON group. Tartrate-resistant acid phosphatase (Trap) staining showed that high-fructose intake during pregnancy could increase the number of osteoclasts and increase the absorption area. Our results suggested that excessive fructose intake during pregnancy could inhibit skeletal development in offspring. Thus, attention to fructose intake during pregnancy is important for bone development in offspring.

From Xiaoke to diabetes mellitus: a review of the research progress in traditional Chinese medicine for diabetes mellitus treatment

Diabetes mellitus (DM) is a chronic metabolic disorder characterized by hyperglycemia resulting from insulin secretion defects or insulin resistance. The global incidence of DM has been gradually increasing due to improvements in living standards and changes in dietary habits, making it a major non-communicable disease that poses a significant threat to human health and life. The pathogenesis of DM remains incompletely understood till now, and current pharmacotherapeutic interventions are largely inadequate, resulting in relapses and severe adverse reactions. Although DM is not explicitly mentioned in traditional Chinese medicine (TCM) theory and clinical practice, it is often classified as "Xiaoke" due to similarities in etiology, pathogenesis, and symptoms. With its overall regulation, multiple targets, and personalized medication approach, TCM treatment can effectively alleviate the clinical manifestations of DM and prevent or treat its complications. Furthermore, TCM exhibits desirable therapeutic effects with minimal side effects and a favorable safety profile. This paper provides a comprehensive comparison and contrast of Xiaoke and DM by examining the involvement of TCM in their etiology, pathogenesis, treatment guidelines, and other relevant aspects based on classical literature and research reports. The current TCM experimental research on the treatment of DM by lowering blood glucose levels also be generalized. This innovative focus not only illuminates the role of TCM in DM treatment, but also underscores the potential of TCM in DM management.

The FilZ Protein Contains a Single PilZ Domain and Facilitates the Swarming Motility of Pseudoalteromonas sp. SM9913

Swarming regulation is complicated in flagellated bacteria, especially those possessing dual flagellar systems. It remains unclear whether and how the movement of the constitutive polar flagellum is regulated during swarming motility of these bacteria. Here, we report the downregulation of polar flagellar motility by the c-di-GMP effector FilZ in the marine sedimentary bacterium Pseudoalteromonas sp. SM9913. Strain SM9913 possesses two flagellar systems, and filZ is located in the lateral flagellar gene cluster. The function of FilZ is negatively controlled by intracellular c-di-GMP. Swarming in strain SM9913 consists of three periods. Deletion and overexpression of filZ revealed that, during the period when strain SM9913 expands quickly, FilZ facilitates swarming. In vitro pull-down and bacterial two-hybrid assays suggested that, in the absence of c-di-GMP, FilZ interacts with the CheW homolog A2230, which may be involved in the chemotactic signal transduction pathway to the polar flagellar motor protein FliM_p, to interfere with polar flagellar motility. When bound to c-di-GMP, FilZ loses its ability to interact with A2230. Bioinformatic investigation indicated that filZ-like genes are present in many bacteria with dual flagellar systems. Our findings demonstrate a novel mode of regulation of bacterial swarming motility.

Two superconducting states with broken time-reversal symmetry in FeSe1-xSx

Iron-chalcogenide superconductors FeSe1-xSx possess unique electronic properties such as nonmagnetic nematic order and its quantum critical point. The nature of superconductivity with such nematicity is important for understanding the mechanism of unconventional superconductivity. A recent theory suggested the possible emergence of a fundamentally new class of superconductivity with the so-called Bogoliubov Fermi surfaces (BFSs) in this system. However, such an ultranodal pair state requires broken time-reversal symmetry (TRS) in the superconducting state, which has not been observed experimentally. Here, we report muon spin relaxation (μSR) measurements in FeSe1-xSx superconductors for 0 ≤ x ≤ 0.22 covering both orthorhombic (nematic) and tetragonal phases. We find that the zero-field muon relaxation rate is enhanced below the superconducting transition temperature Tc for all compositions, indicating that the superconducting state breaks TRS both in the nematic and tetragonal phases. Moreover, the transverse-field μSR measurements reveal that the superfluid density shows an unexpected and substantial reduction in the tetragonal phase (x > 0.17). This implies that a significant fraction of electrons remain unpaired in the zero-temperature limit, which cannot be explained by the known unconventional superconducting states with point or line nodes. The TRS breaking and the suppressed superfluid density in the tetragonal phase, together with the reported enhanced zero-energy excitations, are consistent with the ultranodal pair state with BFSs. The present results reveal two different superconducting states with broken TRS separated by the nematic critical point in FeSe1-xSx, which calls for the theory of microscopic origins that account for the relation between nematicity and superconductivity.

Prioritizing exhausted T cell marker genes highlights immune subtypes in pan-cancer

Exhausted T (TEX) cells are main immunotherapy targets in cancer, but it lacks a general identification method to characterize TEX cell in disease. To assess the characterization of TEX cell, we extract signature of TEX cell from large cancer and chronic infection cohorts. Based on single-cell transcriptomes, a systematic T cell exhaustion prediction (TEXP) model is designed to define TEX cell in cancer and chronic infection. We then prioritize 42 marker genes, including HAVCR2, PDCD1, TOX, TIGIT and LAG3, which are associated with T cell exhaustion. TEXP could identify high TEX and low TEX subtypes in pan-cancer of TCGA. The high TEX subtypes are characterized by high immune score, immune cell infiltration, high expression of TEX marker genes and poor prognosis. In summary, TEXP and marker genes provide a resource for understanding the function of TEX cell, with implications for immune prediction and immunotherapy in chronic infection and cancer.

[Effects of Rehmanniae Radix and Rehmanniae Radix Praeparata on proteomics and autophagy in mice with type 2 diabetes mellitus induced by high-fat diet coupled with streptozotocin]

To compare the pancreatic proteomics and autophagy between Rehmanniae Radix-and Rehmanniae Radix Praeparata-treated mice with type 2 diabetes mellitus(T2DM). The T2DM mouse model was established by high-fat diet coupled with streptozotocin(STZ, intraperitoneal injection, 100 mg·kg~(-1), once a day for three consecutive days). The mice were then randomly assigned into a control group, low-(5 g·kg~(-1)) and high-dose(15 g·kg~(-1)) Rehmanniae Radix groups, low-(150 mg·kg~(-1)) and high-dose(300 mg·kg~(-1)) catalpol groups, low-(5 g·kg~(-1)) and high-dose(15 g·kg~(-1)) Rehmanniae Radix Praeparata groups, low-(150 mg·kg~(-1)) and high-dose(300 mg·kg~(-1)) 5-hydroxymethyl furfuraldehyde(5-HMF) groups, and a metformin(250 mg·kg~(-1)) group. In addition, a normal group was also set and each group included 8 mice. The pancreas was collected after four weeks of administration and proteomics tools were employed to study the effects of Rehmanniae Radix and Rehmanniae Radix Praeparata on protein expression in the pancreas of T2DM mice. The expression levels of proteins involved in autophagy, inflammation, and oxidative stress response in the pancreatic tissues of T2DM mice were determined by western blotting, immunohistochemical assay, and transmission electron microscopy. The results showed that the differential proteins between the model group and Rehmanniae Radix/Rehmanniae Radix Prae-parata group were enriched in 7 KEGG pathways, such as autophagy-animal, which indicated that the 7 pathways may be associated with T2DM. Compared with the control group, drug administration significantly up-regulated the expression levels of beclin1 and phosphorylated mammalian target of rapamycin(p-mTOR)/mTOR and down-regulated those of the inflammation indicators, Toll-like receptor-4(TLR4) and Nod-like receptor protein 3(NLRP3), in the pancreas of T2DM mice, and Rehmanniae Radix showed better performance. In addition, the expression levels of inducible nitric oxide synthase(iNOS), nuclear factor erythroid 2-related factor 2(Nrf2), and heine oxygenase-1(HO-1) in the pancreas of T2DM mice were down-regulated after drug administration, and Rehmanniae Radix Praeparata demonstrated better performance. The results indicate that both Rehmanniae Radix and Rehmanniae Radix Praeparata can alleviate the inflammatory symptoms, reduce oxidative stress response, and increase the autophagy level in the pancreas of T2DM mice, while they exert the effect on different autophagy pathways.

Serum 25-hydroxyvitamin D levels and the risk of non-alcoholic fatty liver: A two-sample Mendelian randomization study

BACKGROUND

Accumulated studies have shown that low expression of 25-hydroxyvitamin D [25(OH)D] was significantly associated with the risk of non-alcoholic fatty liver disease (NAFLD). However, the exact causality is still unknown. The aim of this study was to investigate whether levels of 25(OH)D are associated with risk of NAFLD, using a two-sample Mendelian randomization (MR).

METHODS

Data from a recent large vitamin D genome-wide association study (GWAS) on 417,580 Europeans were utilized, and the largest published histology-based NAFLD GWAS study (1,483 cases and 17,781 healthy controls) for genetic variants predicted to cause NAFLD were searched. All genetic datasets for the MR analyses were obtained using publicly available summary statistics based on individuals of European ancestry from the MR-Base and NHGRI-EBI GWAS Catalog database. Inverse-variance weighted (IVW) MR approach was used to estimate causal effects in the main analysis, complemented by 4 additional methods to control for pleiotropy. Sensitivity analyses were conducted to verify whether heterogeneity and pleiotropy can bias the MR results.

RESULTS

The MR analysis did not provide strong evidence for the causal association of circulating 25(OH)D with NAFLD by IVW method (OR = 0.746, 95%CI 0.517-1.078; P = 0.119). The results were consistent using four other MR methods. Sensitivity analysis using all different analytical approaches yielded similar results. There was no evidence for pleiotropy (MR-Egger intercept: -0.0003758, P = 0.970). The replication process also showed consistent results using IVW method (P = 0.710).

CONCLUSION

This study indicates that serum 25(OH)D levels did not possess an obvious effect on the risk of NAFLD. The associations in previous studies may be due to residual confounding or reverse causation.

In situ visualization of Braun's lipoprotein on E. coli sacculi

Braun's lipoprotein (Lpp) plays a major role in stabilizing the integrity of the cell envelope in Escherichia coli, as it provides a covalent cross-link between the outer membrane and the peptidoglycan layer. An important challenge in elucidating the physiological role of Lpp lies in attaining a detailed understanding of its distribution on the peptidoglycan layer. Here, using atomic force microscopy, we visualized Lpp directly on peptidoglycan sacculi. Lpp is homogeneously distributed over the outer surface of the sacculus at a high density. However, it is absent at the constriction site during cell division, revealing its role in the cell division process with Pal, another cell envelope-associated protein. Collectively, we have established a framework to elucidate the distribution of Lpp and other peptidoglycan-bound proteins via a direct imaging modality.

Mechanistic Insight Into the Production of Collagen Oligopeptides by the S8 Family Protease A4095

Collagen oligopeptides have wide applications in foods, pharmaceuticals, cosmetics, and others due to their high bioactivities and bioavailability. The S8 family is the second-largest family of serine proteases. Several collagenolytic proteases from this family have been reported to have good potential in the preparation of collagen oligopeptides, however, the underlying mechanism remains unknown. A4095 was the most abundant S8 protease secreted by the protease-producing bacterium Anoxybacillus caldiproteolyticus 1A02591. Here, we characterized A4095 as an S8 collagenolytic protease and illustrated its structural basis to produce collagen oligopeptides. Protease A4095 preferentially hydrolyzed the Y-Gly peptide bonds in denatured bovine bone collagen, leading to high production (62.48% <1000 Da) of collagen oligopeptides. Structural and mutational analyses indicated that A4095 has a unique S1' substrate-binding pocket to preferentially bind Gly, which is the structural determinant for the high production of collagen oligopeptides. This study provides mechanistic insight into the advantage of the S8 collagenolytic proteases in preparing collagen oligopeptides.

Differential metabolites in cirrhotic patients with hepatitis B and muscle mass loss

Background

Sarcopenia leads to complications (infections, hepatic encephalopathy and ascites) and poor overall survival in patients with cirrhosis, in which the phenotypic presentation is loss of muscle mass. This study aimed to reveal the metabolic profile and identify potential biomarkers in cirrhotic patients with hepatitis B virus and muscle mass loss.

Method

Twenty decompensated cirrhotic patients with HBV and muscle mass loss were designated Group S; 20 decompensated cirrhotic patients with HBV and normal muscle mass were designated Group NS; and 20 healthy people were designated Group H. Muscle mass loss was defined as the skeletal muscle mass index less than 46.96 cm²/m² for males and less than 32.46 cm²/m² for females. Gas chromatography-mass spectrometry was used to explore the distinct metabolites and pathways in the three groups.

Results

Thirty-seven metabolic products and 25 associated metabolic pathways were significantly different in the Group S patients from Group NS patients. Strong predictive value of 11 metabolites (inosine-5'-monophosphate, phosphoglycolic acid, D-fructose-6-phosphate, N-acetylglutamate, pyrophosphate, trehalose-6-phosphate, fumaric acid, citrulline, creatinine, (r)-3-hydroxybutyric acid, and 2-ketobutyric acid) were selected as potential biomarkers in Group S patients compared with Group NS patients. Two pathways may be associated with loss of muscle mass in patients with liver cirrhosis: amino acid metabolism and central carbon metabolism in cancer.

Conclusion

Seventy differential metabolites were identified in patients who have liver cirrhosis and loss of muscle mass compared with patients who have cirrhosis and normal muscle mass. Certain biomarkers might distinguish between muscle mass loss and normal muscle mass in HBV-related cirrhosis patients.

Shikimic acid biosynthesis in microorganisms: Current status and future direction

Shikimic acid (SA), a hydroaromatic natural product, is used as a chiral precursor for organic synthesis of oseltamivir (Tamiflu®, an antiviral drug). The process of microbial production of SA has recently undergone vigorous development. Particularly, the sustainable construction of recombinant Corynebacterium glutamicum (141.2 g/L) and Escherichia coli (87 g/L) laid a solid foundation for the microbial fermentation production of SA. However, its industrial application is restricted by limitations such as the lack of fermentation tests for industrial-scale and the requirement of growth-limiting factors, antibiotics, and inducers. Therefore, the development of SA biosensors and dynamic molecular switches, as well as genetic modification strategies and optimization of the fermentation process based on omics technology could improve the performance of SA-producing strains. In this review, recent advances in the development of SA-producing strains, including genetic modification strategies, metabolic pathway construction, and biosensor-assisted evolution, are discussed and critically reviewed. Finally, future challenges and perspectives for further reinforcing the development of robust SA-producing strains are predicted, providing theoretical guidance for the industrial production of SA.

First demonstration of a fiber optic bolometer on a tokamak plasma (invited)

A fiber optic bolometer (FOB) was demonstrated observing a fusion plasma for the first time at the DIII-D tokamak. A FOB uses a fiber optics-based interferometric technique that is designed to have a high sensitivity to temperature changes [75 mK/(W/m²) responsivity in high vacuum with 0.38 mK noise level] with a negligible susceptibility to electromagnetic interference (EMI) that can be problematic for resistive bolometers in a tokamak environment. A single-channel test apparatus was installed on DIII-D consisting of a measurement FOB and shielded reference FOB. The single-channel FOB showed a negligible increase in the noise level during typical plasma operations (0.39 mK) compared to the benchtop results (0.38 mK), confirming an insignificant EMI impact to the FOB. Comparisons to DIII-D resistive bolometers showed good agreement with the single-channel FOB, indicating that the FOB is comparable to a resistive bolometer when the impulse calibration is applied. The noise-equivalent power density of the calibrated FOB during a plasma operation was 0.55 W/m² with an average sampling time of 20 ms. The major potential effect of ionizing radiation on the FOB would be the radiation-induced attenuation, which can be efficiently compensated for by adjusting the probing light power.

ImmCluster: an ensemble resource for immunology cell type clustering and annotations in normal and cancerous tissues

Single-cell transcriptome has enabled the transcriptional profiling of thousands of immune cells in complex tissues and cancers. However, subtle transcriptomic differences in immune cell subpopulations and the high dimensionality of transcriptomic data make the clustering and annotation of immune cells challenging. Herein, we introduce ImmCluster (http://bio-bigdata.hrbmu.edu.cn/ImmCluster) for immunology cell type clustering and annotation. We manually curated 346 well-known marker genes from 1163 studies. ImmCluster integrates over 420 000 immune cells from nine healthy tissues and over 648 000 cells from different tumour samples of 17 cancer types to generate stable marker-gene sets and develop context-specific immunology references. In addition, ImmCluster provides cell clustering using seven reference-based and four marker gene-based computational methods, and the ensemble method was developed to provide consistent cell clustering than individual methods. Five major analytic modules were provided for interactively exploring the annotations of immune cells, including clustering and annotating immune cell clusters, gene expression of markers, functional assignment in cancer hallmarks, cell states and immune pathways, cell-cell communications and the corresponding ligand-receptor interactions, as well as online tools. ImmCluster generates diverse plots and tables, enabling users to identify significant associations in immune cell clusters simultaneously. ImmCluster is a valuable resource for analysing cellular heterogeneity in cancer microenvironments.

A pathway for chitin oxidation in marine bacteria

Oxidative degradation of chitin, initiated by lytic polysaccharide monooxygenases (LPMOs), contributes to microbial bioconversion of crystalline chitin, the second most abundant biopolymer in nature. However, our knowledge of oxidative chitin utilization pathways, beyond LPMOs, is very limited. Here, we describe a complete pathway for oxidative chitin degradation and its regulation in a marine bacterium, Pseudoalteromonas prydzensis. The pathway starts with LPMO-mediated extracellular breakdown of chitin into C1-oxidized chitooligosaccharides, which carry a terminal 2-(acetylamino)-2-deoxy-D-gluconic acid (GlcNAc1A). Transmembrane transport of oxidized chitooligosaccharides is followed by their hydrolysis in the periplasm, releasing GlcNAc1A, which is catabolized in the cytoplasm. This pathway differs from the known hydrolytic chitin utilization pathway in enzymes, transporters and regulators. In particular, GlcNAc1A is converted to 2-keto-3-deoxygluconate 6-phosphate, acetate and NH₃ via a series of reactions resembling the degradation of D-amino acids rather than other monosaccharides. Furthermore, genomic and metagenomic analyses suggest that the chitin oxidative utilization pathway may be prevalent in marine Gammaproteobacteria.

Skeletal muscle index and muscle attenuation with liver cirrhosis as survival prognosticators by sex

BACKGROUND AND OBJECTIVES

It has been proven that skeletal muscle index (SMI) and muscle attenuation (MA) are correlated with outcomes in liver cirrhosis. However, whether there are sex differences in these factors re-mains unknown. We aimed to analyze the predictive ability of SMI and MA for the prognosis of cirrhotic patients of different sexes and promote computed tomography (CT) use in body composition assessment.

METHODS AND STUDY DESIGN

CT images taken at the 3rd lumbar vertebra from 223 patients were quantified for body composi-tion. A Cox regression model was used to assess associations between mortality and body composition. Time-dependent receiver operating characteristic curves were calculated to evaluate the predictive ability of SMI and MA for the 1-, 3- and 5- year mortality of cirrhotic patients.

RESULTS

The majority of patients with liver cirrhosis were male (64.6%), and there was a weak linear correlation between SMI and MA in males (r=0.33, p<0.001). In the sex stratified multivariate Cox regression analysis, SMI in males (HR=0.95; 95% CI, 0.91-0.98; p=0.002) and MA in females (HR=0.91; 95% CI, 0.87-0.96; p<0.001) were independently associated with mortality. The areas under the curve (AUCs) of SMI (AUC=0.718) and MA (AUC=0.705) were similar in the 5-year mortality predic-tion of males, while in females, MA (AUC=0.797) had a stronger predictive ability than SMI (AUC=0.541).

CONCLUSIONS

SMI in males and MA in females are independent prognostic factors for liver cirrhosis. For females, MA may be a more sensitive indicator of mortality prediction than SMI, while in males, they are equivalent.

Novel pathway and acetate-facilitated complete atenolol degradation by Hydrogenophaga sp. YM1 isolated from activated sludge

Atenolol is a widely prescribed beta-blocker that has been detected in wastewater at concentrations up to 300 μg/L. The parent compound and its transformation products pose risks to aquatic organisms. Efficient atenolol degrading microorganism has yet to be identified, and its biodegradation pathway is unknown. In this study, Hydrogenophaga sp. YM1 isolated from activated sludge can degrade atenolol efficiently (286.1 ± 4.0 μg/g dry wt/h in actual wastewater), where atenolol acid, and four newly detected products (4-hydroxyphenylacetic acid, 3-(isopropylamino)-1,2-propanediol, 3-amino-1,2-propanediol and 4-(1-amino-2-hydroxy-3-propoxy) benzeneacetic acid) were the main intermediates. Key genes involved in atenolol degradation were proposed based on RNA-seq and validated by RT-qPCR. The ether bond cleavage of atenolol acid was the rate-limiting step likely catalyzed by the α-ketoglutarate dependent 2,4-dichlorophenoxyacetate dioxygenase. The further degradation of 4-hydroxyphenylacetic acid followed the homoprotocatechuate degradation pathway, enabling complete conversion to CO₂. Acetate addition (39-156 mg COD/L) under aerobic condition enhanced atenolol degradation by 29-37% and decreased the accumulation of atenolol acid, likely because acetate oxidation provided α-ketoglutarate and additional reducing power. Activated sludge core microorganisms have limited atenolol mineralization potentials. Enriching Hydrogenophaga-like populations and/or providing such as acetate can drive more complete conversion of atenolol in natural and engineered biosystems.

d-Alanine Metabolism via d-Ala Aminotransferase by a Marine Gammaproteobacterium, Pseudoalteromonas sp. Strain CF6-2

As the most abundant d-amino acid (DAA) in the ocean, d-alanine (d-Ala) is a key component of peptidoglycan in the bacterial cell wall. However, the underlying mechanisms of bacterial metabolization of d-Ala through the microbial food web remain largely unknown. In this study, the metabolism of d-Ala by marine bacterium Pseudoalteromonas sp. strain CF6-2 was investigated. Based on genomic, transcriptional, and biochemical analyses combined with gene knockout, d-Ala aminotransferase was found to be indispensable for the catabolism of d-Ala in strain CF6-2. Investigation on other marine bacteria also showed that d-Ala aminotransferase gene is a reliable indicator for their ability to utilize d-Ala. Bioinformatic investigation revealed that d-Ala aminotransferase sequences are prevalent in genomes of marine bacteria and metagenomes, especially in seawater samples, and Gammaproteobacteria represents the predominant group containing d-Ala aminotransferase. Thus, Gammaproteobacteria is likely the dominant group to utilize d-Ala via d-Ala aminotransferase to drive the recycling and mineralization of d-Ala in the ocean. IMPORTANCE As the most abundant d-amino acid in the ocean, d-Ala is a component of the marine DON (dissolved organic nitrogen) pool. However, the underlying mechanism of bacterial metabolization of d-Ala to drive the recycling and mineralization of d-Ala in the ocean is still largely unknown. The results in this study showed that d-Ala aminotransferase is specific and indispensable for d-Ala catabolism in marine bacteria and that marine bacteria containing d-Ala aminotransferase genes are predominantly Gammaproteobacteria widely distributed in global oceans. This study reveals marine d-Ala-utilizing bacteria and the mechanism of their metabolization of d-Ala. The results shed light on the mechanisms of recycling and mineralization of d-Ala driven by bacteria in the ocean, which are helpful in understanding oceanic microbial-mediated nitrogen cycle.

Corrigendum: Case report: Cryptogenic giant brain abscess caused by Providencia rettgeri mimicking stroke and tumor in a patient with impaired immunity

[This corrects the article DOI: 10.3389/fneur.2022.1007435.].

Case report: Cryptogenic giant brain abscess caused by Providencia rettgeri mimicking stroke and tumor in a patient with impaired immunity

The highly lethal cryptogenic brain abscess can be easily misdiagnosed. However, cryptogenic brain abscess caused by Providencia rettgeri is rarely reported. We present the case of a cryptogenic Providencia rettgeri brain abscess and analyze the clinical manifestations, imaging findings, treatment, and outcome to improve the level of awareness, aid in accurate diagnosis, and highlight effective clinical management. A 39-year-old man was admitted to the hospital after experiencing acute speech and consciousness disorder for 1 day. The patient had a medical history of nephrotic syndrome and membranous nephropathy requiring immunosuppressant therapy. Magnetic resonance imaging revealed giant, space-occupying lesions involving the brain stem, basal ganglia, and temporal-parietal lobes without typical ring enhancement, mimicking a tumor. Initial antibiotic treatment was ineffective. Afterward, pathogen detection in cerebrospinal fluid using metagenomic next-generation sequencing revealed Providencia rettgeri. Intravenous maximum-dose ampicillin was administered for 5 weeks, and the patient's symptoms resolved. Cryptogenic Providencia rettgeri brain abscess typically occurs in patients with impaired immunity. Our patient exhibited a sudden onset with non-typical neuroimaging findings, requiring differentiation of the lesion from stroke and brain tumor. Metagenomic next-generation sequencing was important in identifying the pathogen. Rapid diagnosis and appropriate use of antibiotics were key to obtaining a favorable outcome.

Production of l-glutamate family amino acids in Corynebacterium glutamicum: Physiological mechanism, genetic modulation, and prospects

l-glutamate family amino acids (GFAAs), consisting of l-glutamate, l-arginine, l-citrulline, l-ornithine, l-proline, l-hydroxyproline, γ-aminobutyric acid, and 5-aminolevulinic acid, are widely applied in the food, pharmaceutical, cosmetic, and animal feed industries, accounting for billions of dollars of market activity. These GFAAs have many functions, including being protein constituents, maintaining the urea cycle, and providing precursors for the biosynthesis of pharmaceuticals. Currently, the production of GFAAs mainly depends on microbial fermentation using Corynebacterium glutamicum (including its related subspecies Corynebacterium crenatum), which is substantially engineered through multistep metabolic engineering strategies. This review systematically summarizes recent advances in the metabolic pathways, regulatory mechanisms, and metabolic engineering strategies for GFAA accumulation in C. glutamicum and C. crenatum, which provides insights into the recent progress in l-glutamate-derived chemical production.

Berberine exerts neuroprotective activities against cerebral ischemia/reperfusion injury through up-regulating PPAR-γ to suppress NF-κB-mediated pyroptosis

OBJECTIVE

Berberine (BBR) is an anti-inflammatory alkaloid compound extracted from herbs. The purpose of this study is to probe the possible effect and the mechanism of BBR against cerebral ischemia/reperfusion (I/R) injury.

METHODS

In vitro oxygen and glucose deprivation (OGD) model was established on neurons from rat hippocampus, which was then subjected to BBR, IVA337 (PPAR-γ agonist), or GW9662 (PPAR-γ antagonist) treatment, to identify their effects on neuronal pyroptosis. MTT assay was utilized to determine cell survival rates, TUNEL staining for observation of β-tubulin and MAP2 expressions, qRT-PCR for detection of mRNA expression of PPAR-γ, Western blot for assessment of protein expressions of PPAR-γ and pyroptosis-related proteins (AIM2, NLPR3, ASC, cleaved-Caspase-1, GSDMD, and GSDMD-N), and ELISA for examination of IL-18 and IL-1β expressions.

RESULTS

OGD modeling induced neuron pyroptosis, as evidenced by increased expression levels of pyroptosis-related proteins as well as IL-1β and IL-18, and elevated cell apoptosis rate. In addition, OGD exposure led to PPAR-γ up-regulation and NF-κB activation. Overexpression of PPAR-γ ameliorated cell pyroptosis, while knockdown of PPAR-γ intensified neuron pyroptosis that could be reversed by BBR. Furthermore, either BBR could block the activation of NF-κB signaling pathway through PPAR-γ.

CONCLUSION

BBR protects rats from cerebral I/R injury by up-regulating PPAR-γ to restrain NF-κB-mediated pyroptosis.

Hyper-Cross-Linked Polymer-Decorated Surfaces with Ultrahigh Efficiency for Oil/Water Emulsion Separation and Recovery

A novel superhydrophobic/superoleophilic surface has been developed by direct surface condensation of dichloroxylene that results in a controlled coating of hyper-cross-linked polymers. Specifically, the coating was successfully applied to a melamine formaldehyde sponge and optimized by fine-tuning the reaction variables. The resulting hierarchical porous sorbents stabilized by polydimethylsiloxane exhibited an increased surface area, good physiochemical stability, high selectivity, and adsorption capacities for a variety of oils and solvents. The composite can separate oil in water emulsions with ultrahigh separation efficiency >99% over 10 cycles in liter-scale experiments, wherein the highest separation efficiency was as low as 2 ppm even with a short period of filtration, suggesting strong potential for oil/water separation and recovery.

Cometabolism of 17α-ethynylestradiol by nitrifying bacteria depends on reducing power availability and leads to elevated nitric oxide formation

17α-ethynylestradiol (EE2) is a priority emerging contaminant (EC) in diverse environments that can be cometabolized by ammonia oxidizing bacteria (AOB). However, its transformation kinetics and the underlying molecular mechanism are unclear. In this study, kinetic parameters, including maximum specific EE2 transformation rate, EE2 half-saturation coefficient, and EE2transformation capacity of AOBwere obtained by using the model AOB strain, Nitrosomonas europaea 19718. The relationship between EE2 cometabolism and ammonia oxidation was divided into three phases according to reducing power availability, namely "activation", "coupling", and "saturation". Specifically, there was a universal lag of EE2 transformation after ammonia oxidation was initiated, suggesting that sufficient reducing power (approximately 0.95 ± 0.06 mol NADH/L) was required to activate EE2 cometabolism. Interestingly, nitric oxide emission increased by 12 ± 2% during EE2 cometabolism, along with significantly upregulated nirK cluster genes. The findings are of importance to understanding the cometabolic behavior and mechanism of EE2 in natural and engineered environments. Maintaining relatively high and stable reducing power supply from ammonia oxidation can potentially improve the cometabolic removal of EE2 and other ECs during wastewater nitrification processes.

Delayed pneumocephalus induced by repeated percutaneous aspiration after spinal surgery: A case report and literature review

RATIONALE

Severe tension pneumocephalus can lead to drowsiness, coma, and even brain hernia and death. The occurrence of delayed pneumocephalus after spinal surgery is rarely reported and often ignored. Herein, we report a case of delayed pneumocephalus after repeated percutaneous aspiration following spinal surgery.

PATIENT CONCERNS

A 55-year-old man was admitted in October 2020 because of aggravation in bilateral lower limb weakness and dysuria for seven days. He was diagnosed with liver cancer a year ago, and he underwent several operations because of tumor recurrence. The patient underwent thoracic vertebrae tumor excision on this admission, and no cerebrospinal fluid leakage was discovered during surgery. After the third drainage by percutaneous aspiration, the patient complained of severe headache and vomiting on postoperative day 16.

DIAGNOSIS

Emergency brain computed tomography revealed massive pneumocephalus.

INTERVENTIONS

Thereafter, suction drainage was discontinued, and he was placed on bed rest and administered intravenous mannitol.

OUTCOMES

Repeated computed tomography showed complete resolution of the pneumocephalus after five days.

LESSONS

Wound exudates and cystic fluid after spinal surgery should be differentiated from cerebrospinal fluid leakage. Reckless percutaneous aspirations can form pneumocephalus in patients with an occult dural injury, and pneumocephalus can occur up to 16 days after surgery. Early diagnosis of pneumocephalus is crucial to avoid severe consequences.

A novel ATP dependent dimethylsulfoniopropionate lyase in bacteria that releases dimethyl sulfide and acryloyl-CoA

Dimethylsulfoniopropionate (DMSP) is an abundant and ubiquitous organosulfur molecule in marine environments with important roles in global sulfur and nutrient cycling. Diverse DMSP lyases in some algae, bacteria, and fungi cleave DMSP to yield gaseous dimethyl sulfide (DMS), an infochemical with important roles in atmospheric chemistry. Here, we identified a novel ATP-dependent DMSP lyase, DddX. DddX belongs to the acyl-CoA synthetase superfamily and is distinct from the eight other known DMSP lyases. DddX catalyses the conversion of DMSP to DMS via a two-step reaction: the ligation of DMSP with CoA to form the intermediate DMSP-CoA, which is then cleaved to DMS and acryloyl-CoA. The novel catalytic mechanism was elucidated by structural and biochemical analyses. DddX is found in several Alphaproteobacteria, Gammaproteobacteria, and Firmicutes, suggesting that this new DMSP lyase may play an overlooked role in DMSP/DMS cycles.

The global sulfur cycle is a collection of geological and biological processes that circulate sulfur-containing compounds through the oceans, rocks and atmosphere. Sulfur itself is essential for life and important for plant growth, hence its widespread use in fertilizers.

Marine organisms such as bacteria, algae and phytoplankton produce one particular sulfur compound, called dimethylsulfoniopropionate, or DMSP, in massive amounts. DMSP made in the oceans gets readily converted into a gas called dimethyl sulfide (DMS), which is the largest natural source of sulfur entering the atmosphere. In the air, DMS is converted to sulfate and other by-products that can act as cloud condensation nuclei, which, as the name suggests, are involved in cloud formation. In this way, DMS can influence weather and climate, so it is often referred to as ‘climate-active’ gas.

At least eight enzymes are known to cleave DMSP into DMS gas with a few by-products. These enzymes are found in algae, bacteria and fungi, and are referred to as lyases, for the way they breakdown their target compounds (DMSP, in this case). Recently, researchers have identified some bacteria that produce DMS from DMSP without using known DMSP lyases. This suggests there are other, unidentified enzymes that act on DMSP in nature, and likely contribute to global sulfur cycling.

Li, Wang et al. set out to uncover new enzymes responsible for converting the DMSP that marine bacteria produce into gaseous DMS. One new enzyme called DddX was identified and found to belong to a superfamily of enzymes quite separate to other known DMSP lyases. Li, Wang et al. also showed how DddX drives the conversion of DMSP to DMS in a two-step reaction, and that the enzyme is found across several classes of bacteria. Further experiments to characterise the protein structure of DddX also revealed the molecular mechanism for its catalytic action.

This study offers important insights into how marine bacteria generate the climatically important gas DMS from DMSP, leading to a better understanding of the global sulfur cycle. It gives microbial ecologists a more comprehensive perspective of these environmental processes, and provides biochemists with data on a family of enzymes not previously known to act on sulfur-containing compounds.

Highly efficient biosynthesis of l-ornithine from mannitol by using recombinant Corynebacterium glutamicum

Mannitol is a promising six-carbon sugar alcohol that is widely found in macroalgae. The potential of mannitol as a renewable raw material is of interest due to the advantages of ocean farms. Herein, the biobased production of l-ornithine from mannitol was resoundingly demonstrated for the first time in engineered Corynebacterium glutamicum S9114 through the deletion of the mannitol repressor MtlR. By modulating the expression of mtlD and reinforcing the fructose metabolic pathway, we generated the strain MTL13 that produced 54.56 g/L of l-ornithine with a yield of 0.47 g/g on mannitol. These results illustrate the robust conversion from mannitol to l-ornithine using engineered Corynebacterium glutamicum, providing a reference for the biobased production of additional chemicals from mannitol.

A disease progression prediction model and nervous system symptoms in coronavirus disease 2019 patients

This study aimed to investigate factors affecting coronavirus disease 2019 (COVID-19) progression, also to explore the clinical features and prognosis of nervous system symptom (NSS) involved COVID-19 patients. 417 COVID-19 patients were analyzed in this retrospective study, and they were clinically classified as severe patients and non-severe patients. According to NSS involved status, COVID-19 patients were further divided into NSS patients and non-NSS patients. Elderly cases, males, common comorbidities, NSS, respiratory/cardiovascular/gastrointestinal symptoms, bilateral lesion, multifocal lesion, bacterial infection, bacterial&fungal infection were more common in severe patients compared to non-severe patients. Meanwhile, severe COVID-19 patients showed increased baseline APTT, TT, D-dimer, CRP, ESR, CK-MB, creatine kinase, AST, ALT, creatinine, but decreased baseline platelet level, lymphocyte, albumin, GFR compared to non-severe patients. Notably, the continuous differences of lymphocyte, D-dimer, CRP, AST, ALT, albumin, GFR between severe patients and non-severe patients during treatment were observed. Age, NSS, bacterial & fungal infection, CRP and creatinine were further identified as independent risk factors for severe COVID-19, which could predict severe COVID-19 with area under curve of 0.861. Furthermore, severe patients presented with worse prognosis. Regrading NSS patients, they were related to older age, surgery history, diabetes comorbidities, respiratory/cardiovascular/gastrointestinal symptoms, bilateral lesion, multifocal lesion, bacterial infection, bacterial&fungal infection and more dysregulated laboratory indexes compared to non-NSS patients. Besides, NSS patients were correlated with poor prognosis to some extent. More intensive attention should be paid to COVID-19 patients with severe-disease risk factors and those with NSS involvement, in case of rapid deterioration.

l-arginine production in Corynebacterium glutamicum: manipulation and optimization of the metabolic process

As an important semi-essential amino acid, l-arginine is extensively used in the food and pharmaceutical fields. At present, l-arginine production depends on cost-effective, green, and sustainable microbial fermentation by using a renewable carbon source. To enhance its fermentative production, various metabolic engineering strategies have been employed, which provide valid paths for reducing the cost of l-arginine production. This review summarizes recent advances in molecular biology strategies for the optimization of l-arginine-producing strains, including manipulating the principal metabolic pathway, modulating the carbon metabolic pathway, improving the intracellular biosynthesis of cofactors and energy usage, manipulating the assimilation of ammonia, improving the transportation and membrane permeability, and performing biosensor-assisted high throughput screening, providing useful insight into the current state of l-arginine production.

β-blockers in the environment: Distribution, transformation, and ecotoxicity

β-blockers are a class of medications widely used to treat cardiovascular disorders, including abnormal heart rhythms, high blood pressure, and angina pectoris. The prevalence of β-blockers has generated a widespread concern on their potential chronic toxicity on aquatic organisms, highlighting the necessity of comprehensive studies on their environmental distribution, fate, and toxicity. This review summarizes the up-to-date knowledge on the source, global distribution, analytical methods, transformation, and toxicity of β-blockers. Twelve β-blockers have been detected in various environmental matrices, displaying significant temporal and spatial variations. β-blockers can be reduced by 0-99% at wastewater treatment plants, where secondary processes contribute to the majority of removal. Advanced oxidation processes, e.g., photocatalysis and combined UV/persulfate can transform β-blockers more rapidly and completely than conventional wastewater treatment processes, but the transformation products could be more toxic than the parent compounds. Propranolol, especially its (S)-enantiomer, exhibits the highest toxicity among all β-blockers. Future research towards improved detection methods, more efficient and cost-effective removal techniques, and more accurate toxicity assessment is needed to prioritize β-blockers for environmental monitoring and control worldwide.

Glomerular endothelial derived vesicles mediate podocyte dysfunction: A potential role for miRNA

MicroRNAs (miRNA) are shown to be involved in the progression of several types of kidney diseases. Podocytes maintain the integrity of the glomerular basement membrane. Extracellular vesicles (EV) are important in cell-to-cell communication as they can transfer cellular content between cells, including miRNA. However, little is known about how extracellular signals from the glomerular microenvironment regulate podocyte activity. Using a non-contact transwell system, communication between glomerular endothelial cells (GEnC) and podocytes was characterised in-vitro. Identification of transferred EV-miRNAs from GEnC to podocytes was performed using fluorescence cell tracking and miRNA mimetics. To represent kidney disease, podocyte molecular profiling and functions were analysed after EV treatments derived from steady state or activated GEnC. Our data shows activation of GEnC alters EV-miRNA loading, but activation was not found to alter EV secretion. EV delivery of miRNA to recipient podocytes altered cellular miRNA abundance and effector functions in podocytes, including decreased secretion of VEGF and increased mitochondrial stress which lead to altered cellular metabolism and cytoskeletal rearrangement. Finally, results support our hypothesis that miRNA-200c-3p is transfered by EVs from GEnC to podocytes in response to activation, ultimately leading to podocyte dysfunction.

The effect of acetylation on the protein stability of BmApoLp-III in the silkworm, Bombyx mori

Acetylation is an important, reversible posttranslational modification to a protein. In a previous study, we found that there were a large number of acetylated sites in various nutrient storage proteins of the silkworm haemolymph. In this study, we confirmed that acetylation can affect the stability of nutrient storage protein Bombyx mori apolipophorin-III (BmApoLp-III). First, the expression of BmApoLp-III could be upregulated when BmN cells were treated with the deacetylase inhibitor panobinostat (LBH589); similarly, the expression was downregulated when the cells were treated with the acetylase inhibitor C646. Furthermore, the increase in acetylation by LBH589 could inhibit the degradation and improve the accumulation of BmApoLp-III in BmN cells treated with cycloheximide and MG132 respectively. Moreover, we found that an increase in acetylation could decrease the ubiquitination of BmApoLp-III and vice versa; therefore, we predicted that acetylation could improve the stability of BmApoLp-III by competing for ubiquitination and inhibiting the protein degradation pathway mediated by ubiquitin. Additionally, BmApoLp-III had an antiapoptosis function that increased after LBH589 treatment, which might have been due to the improved protein stability after acetylation. These results have laid the foundation for further study on the mechanism of acetylation in regulating the storage and utilization of silkworm nutrition.

Diversity of D-Amino Acid Utilizing Bacteria From Kongsfjorden, Arctic and the Metabolic Pathways for Seven D-Amino Acids

D-amino acids (DAAs) are an important component of the refractory dissolved organic matter pool in the ocean. Microbes play a vital role in promoting the recycling of DAAs in the ocean. However, the diversity of marine DAA-utilizing bacteria and how they metabolize DAAs are seldom studied. Here, by enrichment culture with DAAs as the sole nitrogen source, bacteria of 12 families from three phyla were recovered from surface seawater and sediment from Kongsfjorden, Arctic, and seven DAA-utilizing bacterial strains were isolated. These strains have different DAA-utilizing abilities. Of the seven DAAs used, Halomonas titanicae SM1922 and Pseudoalteromonas neustonica SM1927 were able to utilize seven and five of them, respectively, while the other strains were able to utilize only one or two. Based on genomic, transcriptional and biochemical analyses, the key genes involved in DAA metabolism in each strain were identified and the metabolic pathways for the seven DAAs in these marine bacteria were identified. Conversion of DAAs into α-keto acids is generally the main pathway in marine DAA-utilizing bacteria, which is performed by several key enzymes, including DAA oxidoreductases/dehydrogenases, D-serine ammonia-lyases, D-serine ammonia-lyase DSD1s and DAA transaminases. In addition, conversion of DAAs into LAAs is another pathway, which is performed by amino acid racemases. Among the identified key enzymes, D-serine ammonia-lyase DSD1 and Asp racemase are first found to be employed by bacteria for DAA utilization. These results shed light on marine DAA-utilizing bacteria and the involved DAA metabolism pathways, offering a better understanding of the DAA recycling in the ocean.

Cisplatin-mediated down-regulation of miR-145 contributes to up-regulation of PD-L1 via the c-Myc transcription factor in cisplatin-resistant ovarian carcinoma cells

Immune tolerance is one of the leading causes of chemotherapy resistance in carcinoma cases. Studies have shown that programmed cell death ligand-1 (PD-L1), an inhibitory molecule expressed by cancer cells, plays a significant role in immune tolerance through the induction of T cell dysfunction. The results of our RNA sequencing in previous studies revealed that microRNA-145 (miR-145), which is known to be down-regulated by cisplatin in cisplatin-resistant ovarian cancer cells, also represses gene PD-L1 expression. However, the mechanism by which miR-145 contributes to regulate PD-L1 expression in cisplatin resistance of ovarian cancer is yet to be fully understood. Here, we show that cisplatin-mediated miR-145 down-regulation increased PD-L1 expression via targeting the c-Myc transcription factor, thereby inducing T cell apoptosis in vitro. We also report that expression of miR-145 is negatively correlated with PD-L1 expression in human ovarian cancer tissues, malignant grades and the recurrent risks of ovarian cancer after chemotherapy. In summary, our findings suggest that the miR-145/c-Myc/PD-L1 axis contributes to cisplatin resistance in ovarian cancer and support that miR-145 might act as an adjuvant therapeutic target in chemotherapy of ovarian cancer.

Tripeptides From Casein Are Signal Molecules to Induce the Expression of the Extracellular Protease MCP-01 Gene in Marine Bacterium Pseudoalteromonas sp. SM9913

Microbial extracellular proteases play crucial roles in marine protein degradation and nitrogen recycling. Although a large number of marine bacteria are found to produce extracellular proteases, it is still unknown how marine bacteria respond to environmental proteins to activate the expression of genes encoding extracellular proteases. The inducing signal molecule for marine bacterial extracellular proteases has never been identified. In this study, we identified tripeptides as the inducing signal molecules for the extracellular protease MCP-01 of the deep-sea bacterium Pseudoalteromonas sp. SM9913. We found that casein, but not casamino acids, can induce the gene expression and synthesis of MCP-01, suggesting that peptides rather than amino acids derived from casein induce the gene expression and synthesis of MCP-01 in SM9913. Then, casein was hydrolyzed by SM9913 extracellular proteases, and the peptides with inducing effect were isolated and characterized. Finally, four tripeptides, SPP, RYP, RQF and FRQ, were shown to have significant inducing effect on the expression of MCP-01 gene, indicating that they are likely the inducing signal molecules for the expression of protease MCP-01 gene in SM9913. This study sheds light on the induction mechanism for the gene expression and biosynthesis of marine microbial extracellular proteases, which is helpful in better understanding the adaptation of bacteria to deep-sea sedimental environment.

Downregulation of H19 decreases the radioresistance in esophageal squamous cell carcinoma cells

Background: Radiotherapy is one of the most common treatments for esophageal squamous cell carcinoma (ESCC). Radioresistance is a major obstacle that limits the efficacy of radiotherapy. H19 has been considered as a factor affecting radioresistance, whereas the specific mechanism of H19 in ESCC radioresistance remains to be further elucidated.

Purpose: The objective of this study was to identify the relationship between H19 and radioresistance. The findings are expected to provide new insights into the treatment of radioresistant ESCC.

Methods: The expression levels of H19 in ESCC was analyzed using the online database starBase. The Oncomine database was used to further verify the association between H19 expression and patient age, gender, and tumor stage. The overall survival rates of ESCC patients were analyzed using the KM plotter database. Clonogenic survival was conducted to identify the value of survival fraction. The optical density values were obtained via MTS assays. Cells migration and stemness were observed through Transwell and sphere formation assays. The expression levels of H19, miR-22-3p and WNT1 were analyzed using qPCR.

Results: In our study, we firstly screened the H19 according to the online database starBase, and then the Oncomine database and KM plotter database showed that H19 expression was significantly upregulated in the ESCC tissues and associated with poor prognosis. Secondly, an ESCC radioresistant cell line, KYSE150R was established. Clonogenic survival showed that radiation decreased the value of survival fraction. MTS assays suggested that optical density values in KYSE150R cells were significantly higher than that in KYSE150 cells. Transwell and sphere formation assays showed radiation enhanced cell migration and stemness in ESCC cells. In addition, qPCR showed that H19 was upregulated in KYSE150R cells, and survival fraction assays showed that knockdown of H19 decreased the survival fraction values. MTS assays, migration and invasion assays suggested that H19 inhibited cells proliferation, migration and stemness in radioresistant KYSE150 cells. Moreover, qPCR assay showed that miR-22-3p expression levels was downregulated, but WNT1 was upregulated in KYSE150R cells as well as protein levels. Luciferase activity assay further showed that miR-22-3p inhibits the WNT1 expression.

Conclusion: Our results demonstrate that H19 knockdown downregulates the WNT1 via upregulating miR-22-3p expression, which leads to the inhibition of cells proliferation, migration and stemness in the radioresistant ESCC cells.

Theoretical study of substituent effects on electride characteristics and the nonlinear optical properties of Li@calix[4]pyrrole

A relationship between the electride characteristics and the NLO properties is found: the more delocalization the excess electron of the electride experiences, the larger the β₀ value is.

Obstructive sleep apnea exaggerates cognitive dysfunction in stroke patients

BACKGROUND

Obstructive sleep apnea (OSA) is very common in stroke survivors. It potentially worsens the cognitive dysfunction and inhibits their functional recovery. However, whether OSA independently damages the cognitive function in stroke patients is unclear. A simple method for evaluating OSA-induced cognitive impairment is also missing.

METHODS

Forty-four stroke patients six weeks after onset and 24 non-stroke patients with snoring were recruited for the polysomnographic study of OSA and sleep architecture. Their cognitive status was evaluated with a validated Chinese version of Cambridge Prospective Memory Test. The relationship between memory deficits and respiratory, sleeping, and dementia-related clinical variables were analyzed with correlation and multiple linear regression tests.

RESULTS

OSA significantly and independently damaged time- and event-based prospective memory in stroke patients, although it had less power than the stroke itself. The impairment of prospective memory was correlated with increased apnea-hypopnea index, decreased minimal and mean levels of peripheral oxygen saturation, and disrupted sleeping continuity (reduced sleep efficiency and increased microarousal index). The further regression analysis identified minimal levels of peripheral oxygen saturation and sleep efficiency to be the two most important predictors for the decreased time-based prospective memory in stroke patients.

CONCLUSIONS

OSA independently contributes to the cognitive dysfunction in stroke patients, potentially through OSA-caused hypoxemia and sleeping discontinuity. The prospective memory test is a simple but sensitive method to detect OSA-induced cognitive impairment in stroke patients. Proper therapies of OSA might improve the cognitive function and increase the life quality of stroke patients.

Structural mechanism for bacterial oxidation of oceanic trimethylamine into trimethylamine N-oxide

Trimethylamine (TMA) and trimethylamine N-oxide (TMAO) are widespread in the ocean and are important nitrogen source for bacteria. TMA monooxygenase (Tmm), a bacterial flavin-containing monooxygenase (FMO), is found widespread in marine bacteria and is responsible for converting TMA to TMAO. However, the molecular mechanism of TMA oxygenation by Tmm has not been explained. Here, we determined the crystal structures of two reaction intermediates of a marine bacterial Tmm (RnTmm) and elucidated the catalytic mechanism of TMA oxidation by RnTmm. The catalytic process of Tmm consists of a reductive half-reaction and an oxidative half-reaction. In the reductive half-reaction, FAD is reduced and a C4a-hydroperoxyflavin intermediate forms. In the oxidative half-reaction, this intermediate attracts TMA through electronic interactions. After TMA binding, NADP⁺ bends and interacts with D317, shutting off the entrance to create a protected micro-environment for catalysis and exposing C4a-hydroperoxyflavin to TMA for oxidation. Sequence analysis suggests that the proposed catalytic mechanism is common for bacterial Tmms. These findings reveal the catalytic process of TMA oxidation by marine bacterial Tmm and first show that NADP⁺ undergoes a conformational change in the oxidative half-reaction of FMOs.

Identification of Four Kinds of 2',3'-cNMPs in Escherichia coli and a Method for Their Preparation

Four kinds of 2',3'-cNMPs have been identified in animals and plants, and their physiological roles are also suggested. However, in prokaryotes, while 2',3'-cCMP and 2',3'-cUMP are reported, 2',3'-cGMP or 2',3'-cAMP have never been identified from bacteria or archaea. In addition, there has been no biological method to prepare these cyclic nucleotides. During the study of a novel gene LfliZ from deep-sea bacterium Pseudoalteromonas sp. SM9913, we found that the recombinant LfliZ oligomers contained endogenous substrates, which were then identified to be 2',3'-cCMP, 2',3'-cUMP, 2',3'-cGMP, and 2',3'-cAMP, showing the first evidence for the biological existence of four kinds of 2',3'-cNMPs in prokaryotes. In addition, we further developed a biological method to simultaneously prepare four kinds of 2',3'-cNMPs from Escherichia coli through expressing LfliZ.