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Periodontitis is an oral chronic inflammatory disease. Inhibiting tissue destruction and promoting tissue regeneration are important means for the treatment of periodontitis. Metformin not only has hypoglycemic effect but also has anti-inflammatory effect. Metformin has been shown to inhibit oxidative stress and activate autophagy through AMPK/mTOR pathway. High mobility group box 1 (HMGB1) has been implicated in the pathogenesis of many inflammatory diseases including periodontitis, it can participate in the induction of oxidative stress. HMGB1 is an autophagy regulator under oxidative stress, which can activate mTOR pathway. However, it is not clear whether metformin is related to HMGB1 and its mechanism in the process of periodontitis. Cell viability and expression of inflammatory cytokines were clarified by Cell Counting Kit-8, real-time PCR and enzyme-linked immunosorbent assay. Western blot and immunofluorescence were conducted to determine HMGB1 intracellular localization and expression of autophagy-associated proteins in vitro. Experimental periodontitis mice model was induced by administering a ligature. Immunohistochemistry was performed to detect the expression and localization of HMGB1 in vivo. The results of CCK-8, real-time PCR, enzyme-linked immunosorbent assay, Western blot and immunofluorescence showed lipopolysaccharide (LPS) treatment inhibited cell viability, and increased HMGB1 expression at a dose-independent manner. Metformin can reduce the effect of LPS. It also improves autophagy pathway inhibited by LPS and down-regulates mTOR expression. In addition, metformin attenuated alveolar bone resorption induced by ligation. This study provides new evidence for that metformin is a potential drug for the treatment of periodontitis and HMGB1 may be a potential target for periodontal intervention.

The efficacious delivery of antimicrobial drugs to intractable oral biofilms remains a challenge due to inadequate biofilm penetration and lack of pathogen targeting. Herein, we have developed a microenvironment-activated poly(ethylene glycol) (PEG)-sheddable nanoplatform to mediate targeted delivery of drugs into oral biofilms for the efficient prevention of dental caries. The PEGylated nanoplatform with enhanced biofilm penetration is capable of deshielding the PEG layer under slightly acidic conditions in a PEG chain length-dependent manner to re-expose the bacteria-targeting ligands, thereby facilitating targeted codelivery of ciprofloxacin (CIP) and IR780 to the bacteria after accumulation within biofilms. The nanoplatform tends to induce bacterial agglomeration and suffers from degradation in the acidic oral biofilm microenvironment, triggering rapid drug release on demand around bacterial cells. The self-modulating nanoplatform under near-infrared (NIR) irradiation accordingly displays greatly augmented potency in oral biofilm penetration and disruption compared with drugs alone. Topical oral treatment with nanoplatforms involving synergetic pharmacological and photothermal/photodynamic trinary therapy results in robust biofilm dispersion and efficacious suppression of severe tooth decay in rats. This versatile nanoplatform can promote local accumulation and specific drug transport into biofilms and represents a new paradigm for targeted drug delivery for the management of oral biofilm-associated infections.

Common scab (CS) caused by Streptomyces spp. is a significant soilborne potato disease that results in tremendous economic losses globally. Identification of CS-associated species of the genus Streptomyces can enhance understanding of the genetic variation of these bacterial species and is necessary for the control of this epidemic disease. The present study isolated Streptomyces strain 6-2-1(1) from scabby potatoes in Keshan County, Heilongjiang Province, China. PCR analysis confirmed that the strain harbored the characteristic Streptomyces pathogenicity island (PAI) genes (txtA, txtAB, nec1, and tomA). Pathogenicity assays proved that the strain caused typical scab lesions on potato tuber surfaces and necrosis on radish seedlings and potato slices. Subsequently, the strain was systemically characterized at morphological, physiological, biochemical, and phylogenetic levels. Phylogenetic analysis based on 16S rRNA gene sequences revealed that strain 6-2-1(1) shared 99.86% sequence similarity with Streptomyces rhizophilus JR-41T, isolated initially from bamboo in rhizospheric soil in Korea. PCR amplification followed by Sanger sequencing of the 16S rRNA gene of 164 scabby potato samples collected in Heilongjiang Province from 2019 to 2020 demonstrated that approximately 2% of the tested samples were infected with S. rhizophilus. Taken together, these results demonstrate that S. rhizophilus is capable of causing potato CS disease and may pose a potential challenge to potato production in Heilongjiang Province of China.

Abstract: Staphylococcus aureus (S. aureus), a prominent, highly contagious nosocomial and com-munity-acquired bacterial pathogen, can cause a broad spectrum of diseases. Antibiotic-resistant S. aureus strains, which pose potential causes of morbidity and mortality, have continuously emerged in recent years, calling for novel anti-S. aureus agents. 1,2,3-Triazole and 1,2,4-triazole, the bioisostere of amides, esters, and carboxylic acids, are potent inhibitors of DNA gyrase, topoisomerase IV, efflux pumps, filamentous temperature-sensitive protein Z, and penicillin-binding protein. In particular, 1,2,3-triazole- and 1,2,4-triazole-containing hybrids have the potential to exert dual or multiple anti-bacterial mechanisms of action. Moreover, 1,2,3-triazole-cephalosporin hybrid cefatrizine, 1,2,3-triazole-oxazolidinone hybrid radezolid, and 1,2,4-triazolo[1,5-a]pyrimidine hybrid essramycin, have already been used in clinical practice to treat bacterial infections. Hence, 1,2,3-triazole- and 1,2,4-triazole-containing hybrids possess promising broad-spectrum antibacterial activity against diverse clinically significant organisms, including drug-resistant forms. This review is an update on the latest development of 1,2,3-triazole- and 1,2,4-triazole-containing hybrids with anti-S. aureus activity, cov-ering articles published between January 2020 and July 2021.

High fluence low-level laser (HF-LLL), a mitochondria-targeted tumour phototherapy, results in oxidative damage and apoptosis of tumour cells, as well as damage to normal tissue. To circumvent this, the therapeutic effect of low fluence LLL (LFL), a non-invasive and drug-free therapeutic strategy, was identified for tumours and the underlying molecular mechanisms were investigated. We observed that LFL enhanced antigen-specific immune response of macrophages and dendritic cells by upregulating MHC class II, which was induced by mitochondrial reactive oxygen species (ROS)-activated signalling, suppressing tumour growth in both CD11c-DTR and C57BL/6 mice. Mechanistically, LFL upregulated MHC class II in an MHC class II transactivator (CIITA)-dependent manner. LFL-activated protein kinase C (PKC) promoted the nuclear translocation of CIITA, as inhibition of PKC attenuated the DNA-binding efficiency of CIITA to MHC class II promoter. CIITA mRNA and protein expression also improved after LFL treatment, characterised by direct binding of Src and STAT1, and subsequent activation of STAT1. Notably, scavenging of ROS downregulated LFL-induced Src and PKC activation and antagonised the effects of LFL treatment. Thus, LFL treatment altered the adaptive immune response via the mitochondrial ROS-activated signalling pathway to control the progress of neoplastic disease.

Background Gut microbiota dysbiosis and sarcopenia commonly occur in the elderly. Although the concept of the gut–muscle axis has been raised, the casual relationship is still unclear. This systematic review analyses the current evidence of gut microbiota effects on muscle/sarcopenia. Methods A systematic review was performed in PubMed, Embase, Web of Science, and The Cochrane Library databases using the keywords (microbiota* OR microbiome*) AND (sarcopen* OR muscle). Studies reporting the alterations of gut microbiota and muscle/physical performance were analysed. Results A total of 26 pre‐clinical and 10 clinical studies were included. For animal studies, three revealed age‐related changes and relationships between gut microbiota and muscle. Three studies focused on muscle characteristics of germ‐free mice. Seventy‐five per cent of eight faecal microbiota transplantation studies showed that the recipient mice successfully replicated the muscle phenotype of donors. There were positive effects on muscle from seven probiotics, two prebiotics, and short‐chain fatty acids (SCFAs). Ten studies investigated on other dietary supplements, antibiotics, exercise, and food withdrawal that affected both muscle and gut microbiota. Twelve studies explored the potential mechanisms of the gut–muscle axis. For clinical studies, 6 studies recruited 676 elderly people (72.8 ± 5.6 years, 57.8% female), while 4 studies focused on 244 young adults (29.7 ± 7.8 years, 55.4% female). The associations of gut microbiota and muscle had been shown in four observational studies. Probiotics, prebiotics, synbiotics, fermented milk, caloric restriction, and exercise in six studies displayed inconsistent effects on muscle mass, function, and gut microbiota. Conclusions Altering the gut microbiota through bacteria depletion, faecal transplantation, and various supplements was shown to directly affect muscle phenotypes. Probiotics, prebiotics, SCFAs, and bacterial products are potential novel therapies to enhance muscle mass and physical performance. Lactobacillus and Bifidobacterium strains restored age‐related muscle loss. Potential mechanisms of microbiome modulating muscle mainly include protein, energy, lipid, and glucose metabolism, inflammation level, neuromuscular junction, and mitochondrial function. The role of the gut microbiota in the development of muscle loss during aging is a crucial area that requires further studies for translation to patients.

Introduction The risk of venous thromboembolism (VTE) varies among tumour types, and different cancer type-specific risks for VTE prediction remain undefined. We aimed to establish a prediction model for non-small lung cancer (NSCLC)-associated VTE. Materials and methods We analysed data from a prospective cohort of patients with newly diagnosed NSCLC. We then developed a VTE risk prediction model using data of patients who were recruited from 2013 to 2017 (n = 602, development cohort) and validated this model using date of patients recruited from 2018 to 2019 (n = 412, validation cohort). The cumulative 6 months VTE incidence observed in both cohorts was calculated. Results The parameters in this new model included Eastern Cooperative Oncology Group (ECOG) performance status ≥2 (1 point), EGFR mutation (−1 point), neutrophil count ≥7.5 × 109/L (2 points), hemoglobin Conclusions The new VTE risk prediction model incorporated patient characteristics, laboratory values, and oncogenic status, and was able to stratify patients at high risk of VTE in newly diagnosed NSCLC within 6 months of diagnosis.

Non-coding RNAs are a class of RNAs, including circRNA and miRNA, that cannot be translated into proteins, but play an important role in the regulation of the expression of protein-coding genes. More and more evidences showed that circRNA can regulate the expression of miRNA target genes by adsorbing miRNA and form the circRNA-miRNA-mRNA regulatory network. The inactivated Aeromonas salmonicida vaccine is a commercial vaccine for many teleost. Understanding the role of circRNA and miRNA in the early stage of vaccine injection will provide a new insight for the study of the early immune response process in teleost. In this study, the expression profiles of circRNA, miRNA and mRNA were analyzed by high-throughput sequencing at 6 h, 12 h, 24 h and 96 h after injection of inactivated Aeromonas salmonicida vaccine and normal turbot spleen. Compared with the control group, 111, 141 and 453 differentially expressed circRNAs, miRNAs and mRNAs were identified in the four vaccination groups, respectively. The targeting relationships of differentially expressed miRNA to circRNA and mRNA were predicted by using miRanda software, and the results showed that a variety of differentially expressed immune-related genes were targeted. A total of 53 differentially expressed circRNA-miRNA-mRNA regulatory networks were constructed according to circRNA-miRNA pairs and miRNA-mRNA pairs. Among them, cell adhesion molecule 3 and immunoglobulin superfamily member 21 were regulated by the same miRNA (novel_880) and circRNA (novel_circ_0000311/novel_circ_0005326). These suggest that these circRNA-miRNA-mRNA regulatory networks may be a multi-molecule regulatory network, and its regulatory mechanism needs to be further studied.

The HIV-1 epidemic was mainly driven by men who have sex with men (MSM) recently in Beijing, China, with high genetic diversity. Novel recombinant strains were frequently reported at 3.4%-9.9%. It is imperative to interpret the recombinant modes and the putative transmission sources by near full-length genome (NFLG). Four individuals from the MSM population were identified as novel recombinant strains during surveillance of pretreatment drug resistance. NFLG sequences were harvested by near end-point dilution and nested PCR with two overlapping half fragments. Phylogenetic inference was performed with subtyping reference sequences and major parental strain sequences, to explore the patterns of genetic recombinant and potential sources of parent strains. The breakpoints were determined using SimPlot 3.5 to draw genome mosaic map, and the potential parental strains were confirmed by Mega 6.0 using segmental neighbor-joining trees. BL19487-00 and BL1948-00 sequences were obtained from epidemiologically linked individuals and shared similar breakpoints (HXB2 nt 4,497 ± 8 to 4,722) with substitution of subtype B

Accurate identification of species from timber is an essential step to help control illegal logging and forest loss. However, current approaches to timber identification based on morphological and anatomical characteristics have limited species resolution. DNA barcoding is a proven tool for plant species identification, but there is a need to build reliable reference data across broad taxonomic and spatial scales. Here, we construct a species barcoding library consisting of 1550 taxonomically diverse timber species from 656 genera and 124 families, representing a comprehensive genetic reference data set for Chinese timber species and international commercial traded timber species, using four barcodes (rbcL, matK, trnH-psbA, and ITS2). The ITS2 fragment was found to be the most efficient locus for Chinese timber species identification among the four barcodes tested, both at the species and genus level, despite its low recovery rate. Nevertheless, the barcode combination matK+trnH-psbA+ITS2 was required as a complementary barcode to distinguish closely related species in complex data sets involving internationally traded timber species. Comparative analyses of family-level discrimination and species/genus ratios indicated that the inclusion of closely related species is an important factor affecting the resolution ability of barcodes for timber species verification. Our study indicates that although nuclear ITS2 is the most efficient single barcode for timber species authentication in China, complementary combinations like matK+trnH-psbA+ITS2 are required to provide broader discrimination power. These newly-generated sequences enrich the existing publicly available databases, especially for tropical and subtropical evergreen timber trees and this current timber species barcode reference library can serve as an important genetic resource for forestry monitoring, illegal logging prosecution and biodiversity projects.

The grass carp is one of the most important herbivore consumers in aquatic ecosystems and plays key roles in controlling macrophyte abundance. To assess the trophic role of grass carp and their potential grazing pressure on macrophytes in their native range, we quantified their relative abundance (RA), diet composition and trophic niches in two major tributaries and the central delta of the Pearl River using a fish capture survey, high-throughput analysis of the 18S rDNA sequences of their gut contents, and stable isotope analysis. The grass carp RA variation among the sampling regions was explained most by river discharge range. The RA was the highest in the West River with high discharge range, and the lowest in the central delta with low discharge range. The grass carp fed primarily on Streptophyta (relative read abundance: 0.40 ± 0.33) and facultatively on Arthropoda, Rotifera, Ascomycota, and Chlorophyta. The Streptophyta proportion increased from the tributaries to the central delta. Such variation contributed most to the dietary difference among regions. Grass carp belonged to the second trophic level. The position and size of isotopic niche of grass carp differed among regions, and their niche breadth decreased from the tributaries to the central delta, as indicated by the corrected standard ellipse areas (SEAs) and the Bayesian SEAs. The regional differences in hydrological regime and grass carp RA probably affected the macrophyte distribution. The availability of macrophytes likely further contributed to the regional difference in the Streptophyta proportion in grass carp diet.

Purpose. Using network pharmacology and in vivo experiments, we investigated the antidrug-induced liver injury components and functional processes of Sedum sarmentosum Bunge (SSBE). Methods. The effective components, primary active ingredients, and possible target in the therapy of DILI were predicted using network pharmacology and bioinformatics. APAP was inducing the DILI model. In vivo testing of the pharmacodynamic foundation of SSBE in the treatment of DILI was performed. Results. The TCMSP database evaluated five main active components and 299 related targets. In addition, 707 differential genes for DILI were obtained from the DisGeNET database, DigSee database, and OMIM database. 61 related targets were mapped to predict the targets of SSBE acting on DILI. The protein-protein interaction (PPI) core network contained 59 proteins, including IL-β, MARK14, SSP1, and MMP9. These genes are closely related to the Nrf2/ARE signaling pathway, and they may play a key role in the hepatoprotective effect of SSBE. Verification experiment results showed that, in the DILI mouse model, SSBE promoted inflammation diminution and regulation of Nrf2-ARE cascade. SSBE protected normal hepatocyte growth and inhibited apoptosis of normal liver cells induced by APAP. SSBE inhibited the expression of Nrf2 and ARE proteins in the liver tissue of the DILI mouse model in vivo. Conclusion. By modulating the Nrf2 signaling pathway, the active components in SSBE may protect against drug-induced liver damage.

Aims Tert-butylhydroquinone (tBHQ) has been identified as an inhibitor of oxidative stress-induced injury and apoptosis in human neural stem cells. However, the role of tBHQ in osteoarthritis (OA) is unclear. This study was carried out to investigate the role of tBHQ in OA. Methods OA animal model was induced by destabilization of the medial meniscus (DMM). Different concentrations of tBHQ (25 and 50 mg/kg) were intraperitoneally injected in ten-week-old female mice. Chondrocytes were isolated from articular cartilage of mice and treated with 5 ng/ml lipopolysaccharide (LPS) or 10 ng/ml interleukin 1 beta (IL-1β) for 24 hours, and then treated with different concentrations of tBHQ (10, 20, and 40 μM) for 12 hours. The expression levels of malondialdehyde (MDA) and superoxide dismutase (SOD) in blood were measured. The expression levels of interleukin 6 (IL-6), IL-1β, and tumour necrosis factor alpha (TNF-α) leptin in plasma were measured using enzyme-linked immunoabsorbent assay (ELISA) kits. The expression of nuclear factor kappa-light-chain-enhancer of activated B cells (NF-κB) and mitogen-activated protein kinase (MAPK) signalling pathway proteins, and macrophage repolarization-related markers, were detected by western blot. Results Tert-butylhydroquinone significantly attenuated cartilage destruction in DMM-induced mice in vivo. It demonstrated clear evidence of inhibiting IL-1β-induced chondrocyte apoptosis, inflammation, and differentiation defect in vitro. Meanwhile, tBHQ inhibited LPS-induced activation of NF-κB and MAPK signalling pathways, and also inhibited LPS-induced reactive oxygen species production and macrophages repolarization in vitro. Conclusion Taken together, tBHQ might be a potential therapeutic strategy for protecting against OA development. Cite this article: Bone Joint Res 2021;10(11):704–713.

Expounding the heterogeneity for ovarian cancer (OC) with the cognition in developmental biology might be helpful to search for robust prognostic markers and effective treatments. In the present study, we employed single-cell RNA-seq with ovarian cancers, normal ovary, and embryo tissue to explore their heterogeneity. Then the differentiation process of clusters was explored; the pivotal cluster and markers were identified. Furthermore, the consensus clustering algorithm was used to explore the different clinical phenotypes in OC. At last, a prognostic model was construct and used to assess the prognosis for OCs. As a result, eight diverse clusters were identified, and the similarity existed in some clusters between embryo and tumours based on their gene expression. Meaningfully, a subtype of malignant epithelial cluster, PEG10+ EME, was associated with poor survival and was an intermediate stage of embryo to tumour. PEG10 was a CSC marker and might influence CSC self-renewal and promote cisplatin resistance via NOTCH pathway. Utilising specific gene profiles of PEG10+ EME based on public data sets, four phenotypes with different survival and clinical response to anti-PD-1/PD-L1 immunotherapy were identified. These insights allowed for the investigation of single-cell transcriptome of OCs and embryo, which advanced our current understanding of OC pathogenesis and resulted in promising therapeutic strategies.

Introduction Piperlongumine (PL) is a bioactive alkaloid and medicinal compound of piperamide isolated from the long pepper (Piper longum Linn). It has demonstrated bactericidal action against Mycobacterium tuberculosis (MTB), the cause of pulmonary tuberculosis; nevertheless, immunomodulatory activity had not been identified for it in MTB-triggered granulomatous inflammation. This study investigated if piperlongumine could inhibit such inflammation. Material and Methods Mycobacterium tuberculosis strain H37Rv was subjected to a broth microdilution assay. Piperlongumine at 5, 15, and 25 μg/mL, 0.2% dimethyl sulphoxide as control or 4 μM of dexamethasone were tested in vitro on MH-S murine alveolar macrophages. BALB/c mice were orally administered PL at 50, 100 and 150 mg/kg b.w. after trehalose-6,6-dimycolate (TDM) stimulation. Chemokine and cytokine concentrations were determined in lung supernatants. Flow cytometry and Western blot analysis were performed to determine phosphorylated spleen tyrosine kinase (Syk), c-Jun N-terminal kinase (JNK) and extracellular signal-regulated kinase (ERK) pathways. Results Piperlongumine inhibited inflammatory mediators and adherence of lymphocyte function-associated antigen 1 to MH-S cells following TDM activation. It also improved macrophage clearance of MTB. In TDM-stimulated MH-S cells, PL significantly influenced the macrophage inducible Ca2+-dependent lectin receptor (Mincle)-Syk-ERK signalling pathway. Oral dosing of PL effectively suppressed the development of pulmonary granulomas and inflammatory reactions in the TDM-elicited mouse granuloma model. Conclusion PL as an inhibitor of MTB-triggered granulomatous inflammation may be an effective complementary treatment for mycobacterial infection.

An investigation of changes in lake diatom assemblages and diversity with water depth can help determine whether the biodiversity of a single sediment core is representative of that of the entire lake, as well as can improve our understanding of the relationship between diatom assemblages and water depth. In this study, Huguang Maar Lake in Southern China was investigated in order to explore the spatial patterns of diatom diversity and diatom assemblages of 95 surface sediment samples from different locations and depth zones within the lake. The results show an essentially constant diatom diversity, dominated by planktonic diatoms, in the open deep water zone (OD), and consistent diatom diversity in the northern gently-sloping shallow water zone (NS). However, there is a much higher diatom diversity in different microhabitats in the southern and western shallow water zone (SWS), where the bathymetry is much steeper. This difference may reflect the influence of the bathymetry on the occurrence of sediment slumping. In the steeply-sloping SWS zone, frequently influenced by wave action and sediment slumping, diatom diversity is less representative of that of the entire lake, possibly due to the presence of diatoms from different sources and of different depositional ages. The results indicate that for relatively strongly mixed lakes with a simple morphometry, water depth has little influence on diatom diversity; however, the possible influence of local lake basin topography should be considered when reconstructing past diatom diversity changes from sediment cores.

Rationale: Brain arteriovenous malformations (bAVMs) are abnormal entanglement of blood vessels in brain, with direct connections from arteries to veins, lacking functional capillary bed. Although several somatic mutations were reported, the molecular mechanism and genetic disposition of bAVM remain poorly understood. Objective: We aim to identify transcriptional anomalies and critical functional pathways in bAVM lesions and explore their association with key de novo germline and somatic variants in bAVM patients. Methods and Results: We established a comprehensive bAVM dataset from 269 patients, by performing single-cell sequencing of 17 bAVM lesions, whole-exome sequencing of germline DNA from 60 case-unaffected-parental trios, and genomic/transcriptomic sequencing of 231 bAVM lesions. We found abnormal expression of endothelial and mesenchymal markers in bAVM at both bulk and single-cell level, which was validated by flow cytometric analysis and immunofluorescence staining, suggesting an involvement of endothelial-to-mesenchymal transition (EndMT) process in AVM (arteriovenous-malformation). Using data from the 60 trios, we identified nonsynonymous de novo germline mutations affecting 46 genes, including EXPH5 (detected in 2 independent cases), and vessel-related genes, such as EPAS1 and ENG . Interestingly, knockdown of epas1 in zebrafish embryo showed AVM-like phenotype exclusively in brain. Subsequent computational and experimental analyses demonstrated that expression of genes affected by de novo germline mutations was enriched in vascular cell types and was involved in EndMT-relevant behaviors including cell migration, angiogenesis, and cell marker transition. Moreover, we detected somatic KRAS mutations in 129 of 179 (72%) cases and showed that KRAS mutations were associated with bleeding as the first symptom ( P =0.0072). Following experimental studies demonstrated that KRAS mutations independently regulated EndMT features, consolidating the involvement of EndMT in this disease. Lastly, we showed that lovastatin reversed EndMT features in vitro and ex vivo. Conclusions: Our results suggest the convergent role of de novo germline mutations and somatic mutations in regulating EndMT in bAVM and provided a potential therapeutic option.

In this study, we aim to identify the clinical significance of basonuclin 1 ( BNC1) expression in ovarian carcinoma (OV) and to explore its latent mechanisms. Via integrating in-house tissue microarrays, gene chips, and RNA-sequencing data, we explored the expression and clinical value of BNC1 in OV. Immunohistochemical staining was utilized to confirm the protein expression status of BNC1. A combined SMD of –2.339 (95% CI: –3.649 to –1.028, P < 0.001) identified that BNC1 was downregulated based on 1346 samples, and the sROC (AUC = 0.93) showed a favorable discriminatory ability of BNC1 in OV patients. We used univariate and multivariate Cox regulation to evaluate the prognostic role of BNC1 for OV patients, and a combined hazard ratio of 0.717 (95% CI: 0.445–0.989, P < 0.001) revealed that BNC1 was a protective factor for OV. Furthermore, the fraction of infiltrating naive B cells, memory B cells, and other immune cells showed statistical differences between the high- and low- BNC1 expression groups through cell-type identification by estimating relative subsets of RNA transcripts (CIBERSORT) algorithm. Enrichment analysis showed that BNC1 may have a relationship with immune-related items in OV. By predicting the potential regulatory transcription factors (TFs) of BNC1, friend leukemia virus integration 1 ( FLI1) may be a potential upstream TF of BNC1. Corporately, a decreasing trend of BNC1 may serve as a tumor suppressor and prognostic biomarker in OV patients. Moreover, BNC1 may take part in immune-related pathways and influence the fraction of tumor-infiltrating immune cells.

Sponge iron (SFe) is a zero-valent iron (Fe0) composite with a high-purity and porous structure. In this study, SFe was coupled with microorganisms that were gradually domesticated to form a Fe0/iron-oxidizing bacteria system (Fe0-FeOB system). The enhancement effect of the Fe0-FeOB system on refractory organics was verified, the mechanism of its strengthening action was investigated, and the relationship and influencing factors between the Fe0 and microorganisms were revealed. The average removal rates of the Fe0-FeOB system were 8.98%, 5.69%, and 40.67% higher than those of the SBR system for AF, AN, and NB wastewater treatment, respectively. With the addition of SFe, the microbial community structure was gradually enhanced with a large number of FeOB were detected. Moreover, the bacteria with strong iron corrosion and Fe(II) oxidation abilities plays a critical role in improving the Fenton-like effect. Interestingly, the variation trend of ⋅OH was fairly consistent with that of Fe(II). Thus, the main drivers of the Fenton-like effect are biological corrosion and metabolism. Consequently, microbial degradation and Fenton-like effect contributed to the degradation performance of the Fe0-FeOB system. Among them, the microbial degradation accounted for 96.09%, of which the biogenic Fenton effect accounted for 8.9%, and the microbial metabolic activity accounted for 87.19%. However, the augmentation of the Fe0-FeOB system was strongly dependent on SFe for the strengthening effect of microorganisms disappeared after leaving the SFe 35 days.

Kin recognition has been used to explain plant interactions among siblings. However, the phenotypic-based measurements have drawn various results, and the mechanism of plant kin recognition remains unclear. Here, we tested plant kin recognition based on plant nitrogen (N) use efficiency induced by the rhizosphere effect, plant growth performance and fitness. Glycine max (L.) Merr. was planted pairwise either with siblings or with non-siblings (strangers). Several characteristics, including plant height, specific leaf area (SLA), plant biomass, fitness, chlorophyll content, and plant N use efficiency (NUE) were measured. The root exudation rates of carbon (C) and N, soil microbial biomass C (MBC) and N, and the abundance of functional genes, as well as soil archaeal, bacterial, and fungal abundance, were quantified. Significant increases in plant height, seed and shoot biomass, chlorophyll content, and NUE were observed in G. max plants living with siblings compared to strangers, suggesting that plant kin recognition results in superior growth and fitness. The root exudation rate of C was significantly higher in individuals living with siblings than with strangers. The input of C from root exudates further induced the rhizosphere effect, enhancing the soil MBC and increasing the abundance of soil archaea and soil ammonia-oxidizing archaea (AOAs). Plants living with siblings increased NUE for enriched available N in soil, and increased aboveground growth and fitness compared to those living with strangers for G. max. The rhizosphere effect on soil microbes and N turnover triggered by the root exudates depend on the neighbor's identity and could be a potential underground feedback mechanism for plant kin recognition.

Background Bashbay sheep (Bbs) has a certain degree of resistance to Mycoplasma ovipneumoniae (Mo), however, Argali hybrid sheep (Ahs) is susceptible to Mo. To understand the molecular mechanisms underlying the difference of the susceptibility for Mo infection, RNA-sequencing technology was used to compare the transcriptomic response of the lung tissue of Mo-infected Bbs and Ahs. Results Six Bbs and six Ahs were divided into experimental group and control group respectively, all of them were experimentally infected with Mo by intratracheal injection. For collecting lung tissue samples, three Bbs and three Ahs were sacrificed on day 4 post-infection, and the others were sacrificed on day 14 post-infection. Total RNA extracted from lung tissue were used for transcriptome analyses based on high-throughput sequencing technique and bioinformatics. The results showed that 212 (146 up-regulated, 66 down-regulated) DEGs were found when comparing transcriptomic data of Bbs and Ahs at 4th dpi, besides, 311 (158 up-regulated, 153 down-regulated) DEGs were found at 14th dpi. After GO analysis, three main GO items protein glycosylation, immune response and positive regulation of gene expression were found related to Mo infection. In addition, there were 20 DEGs enriched in these above items, such as SPLUC1 (BPIFA1), P2X7R, DQA, HO-1 and SP-A (SFTPA-1). Conclusions These selected 20 DEGs associated with Mo infection laid the foundation for further study on the underlying molecular mechanism involved in high level of resistance to Mo expressed by Bbs, meanwhile, provided deeper understandings about the development of pathogenicity and host-pathogen interactions.

BACKGROUND Dietary nucleotides (NTs) have been reported to affect hepatic function and composition. However, the effects on hepatic lipid deposition are less studied. OBJECTIVES We aimed to identify the regulatory role of dietary NTs in hepatic lipid deposition of zebrafish and elucidate the underlying mechanisms. METHODS Zebrafish (60 ± 1.69 mg; 1 mo old) were fed control diet (16.2% energy as fat) or diet supplemented with 0.1% NTs or 0.02% AMP in feeding experiments 1 and 2. Experiment 3 was conducted with zebrafish larvae. In experiment 4, 1-mo-old zebrafish were fed a high-fat diet (HFD, 38.2% energy as fat) or an HFD supplemented with 0.1% NTs or 0.02% AMP. Hepatic lipid deposition was evaluated by triglyceride (TG) content and staining. Phosphorylation of AMP-activated protein kinase (AMPK) and acetyl-CoA carboxylase (ACC) was assayed by immunoblotting. Zebrafish liver (ZFL) cells were treated with exogenous adenosine. Small interfering RNA was used to knock down AMPK or nucleoside transporter SLC28a1 in ZFL cells. Vivo-morpholino was used to knock down AMPK in zebrafish larvae. RESULTS Dietary 0.1% NTs or 0.02% AMP reduced hepatic TGs by 62% and 32%, respectively, compared with control (P

Genetically encoded fluorescent proteins have been used for metal ion detections by combining fluorescent proteins with metal-binding proteins or peptides. However, their applications are largely restricted to a limited number of metal ions, such as Ca(2+) and Zn(2+), due to the lack of available metal-binding proteins or peptides that can be fused to fluorescent proteins and the difficulty in transforming the binding of metal ions into a change of fluorescent signal. To overcome these limitations, we report herein the use of Mg(2+)-specific 10-23 or Zn(2+)-specific 8-17 RNA-cleaving DNAzymes to regulate the expression of fluorescent proteins as a new class of ratiometric fluorescent sensors for metal ions. Specifically, we demonstrate the use of DNAzymes to suppress the expression of Clover2, a variant of the green fluorescent protein, by cleaving the mRNA of Clover2, while the expression of Ruby2, a mutant of the red fluorescent protein, is not affected. The Mg(2+) or Zn(2+) in Hela cells can be detected using both fluorescent confocal imaging and flow cytometry. Since a wide variety of metal-specific DNAzymes, such as for Mg(2+), Na(+), Cu(2+), Zn(2+), Pb(2+), Hg(2+), Ag(+), and UO(2)(2+), can be obtained through in vitro selection, and the resulting DNAzymes often share a similar secondary structure and reaction mechanism, the method described in this work can likely be applied to imaging many other metal ions and thus significantly expand beyond the range of the current genetically-encoded fluorescent proteins, allowing this class of sensors to be even more powerful in providing deeper understanding of the roles of metal ions in biology.

The BMPRIB gene is one of the main genes that can be used as a molecular genetic marker for the early selection of highly productive ewes. It is well-documented that the p.Q249R (g.746A > G) is the first mutation in the kinase domain of the BMPR1B gene that is highly related to increased ovulation rate and litter size. It is likely that the presence of the p.Q249R mutation in the sheep population is one of the factors contributing to the outstanding productivity of the sheep. Moreover, in recent years, researchers have been explored other polymorphisms in the BMPR1B gene with respect to reproductive traits in sheep. Therefore, we carried out the current study to evaluate the association between polymorphisms in this gene and sheep litter size from all appropriate studies. As a result, among 41 polymorphisms in the ovine BMPRIB gene, eight variants, including p.Q249R (g.746A > G), g.29362047T > C, g.29427689G > A, BMPR1B-2 (ss:1960972599), g.29382337G > A, g.29382340G > A, rs1092293287 (10 bp insertion/deletion) and g.29380965A > G were found to be associated with litter size in sheep. This systematic analysis presents the most current data evidence for BMPRIB polymorphisms, highlighting the need for further large-scale studies to determine more important variants.

Evidence is mounting that PM2.5 exposure could lead to learning disability, memory deficits, and cognitive impairment; however, the underlying mechanisms are still not well demonstrated yet. Long non-coding RNAs (LncRNAs) play a crucial role in many human diseases. Although the relationship of Alzheimer's disease (AD) and lncRNAs have been discovered, the role of lncRNA in AD-like phenotype induced by PM2.5 needs further exploration. In this study, we profiled the expression of messenger RNAs (mRNAs) and lncRNAs in hippocampus after confirming the AD-like changes in mice. Compared with the control group, a total of 478 mRNAs and 151 lncRNAs were dysregulated after PM2.5 exposure. ECM-receptor interaction, focal adhesion, complement and coagulation cascades, and AGE-RAGE signaling pathway were found dysregulated through lncRNA-co-expressed genes analysis based on the Gene Ontology (GO) and Kyoto Encyclopedia of Genes and Genomes (KEGG). Meanwhile, the genes related to microglia were significantly altered, such as CX3CR1, CD163, lncRNA Gm44750, and lncRNA Gm43509. Above evidences suggested that microglia-related lncRNAs dysregulation probably plays a crucial role in PM2.5exposure-associated learning and memory deficits.

Using a novel three-dimensional (3D) approach, we tracked histological changes to elucidate the earliest stages of renal clear cell neoplasia in normal kidney tissue of patients with von Hippel-Lindau (VHL) disease. Tissue blocks of interest were procured, serially sectioned, and 3D reconstruction of the entirety of pathologic events was performed. The results reveal an abundance of foci with aberrant clear cell proliferation that initially develop along the tubular lining, but have the potential to aggregate within individual tubules. This stage is followed by the extension of clear cell aggregates beyond the tubular basement membrane, which allows for the recruitment of angiogenesis derived from interstitial vasculature. The results suggest that the most frequent pathologic event in VHL kidneys is the presence of isolated or aggregated clear cells within the tubular epithelium, potentially developing further into a protracted process of neoplasia. The abundance of independent pathologic events in VHL kidneys confirms developmental mechanisms to precede tumor initiation. To our knowledge, this is the first report demonstrating that tracking of histologic changes in the 3rd dimension enables the confirmation of the sequence of events from the earliest pathologic change in the VHL kidney to the neoplastic stage. This approach is not only useful for visualization and quantification of pathologic changes but also for targeted sampling allowing selective analysis of the earliest stages of clear cell carcinogenesis.

Recently, it was reported that ubiquilin 4 (UBQLN4) alteration was associated with genomic instability in some cancers. However, whether UBQLN4 is a valuable biomarker for the prognosis of immunotherapy in pan-cancer was not identified. We evaluated the biologic and oncologic significance of UBQLN4 in pan-cancer at multiomics level, such as expression, mutation, copy number variation (CNV), methylation, and N6-methyladenosine (m6A) methylation. These omics data were obtained from several public databases, including Oncomine, The Cancer Genome Atlas (TCGA), Gene Expression Omnibus (GEO), the Genotype-Tissue Expression (GTEx), the Human Protein Atlas (HPA), Gene Set Cancer Analysis (GSCA), m6A-Atlas, CancerSEA, and RNAactDrug. We found that UBQLN4 mRNA and protein were overexpressed in most cancer types, and the expression, mutation, CNV, and methylation of UBQLN4 were associated with the prognosis of some cancers. Mechanistically, UBQLN4 was involved in angiogenesis, DNA damage, apoptosis, and the pathway of PI3K/AKT and TSC/mTOR. Moreover, UBQLN4 mRNA was significantly correlated with immune checkpoints, tumor mutational burden (TMB), microsatellite instability (MSI), and mismatch repair (MMR). And, the correlation among UBQLN4 mRNA, CNV, and methylation and immune microenvironment was also identified. Furthermore, UBQLN4 was associated with the sensitivity of chemotherapy and targeted drugs at multiomics level. In conclusion, UBQLN4 was a promising prognostic biomarker of immune-related therapy in pan-cancer.

Background Myeloid sarcoma (MS) is a tumor secondary to myeloid leukemia that consists of immature granulocytes with or without mature granulocytes and is a rare extramedullary manifestation of acute myeloid leukemia (AML). Case presentation We report a case of a 34-year-old woman diagnosed with AML-M4 who achieved remission after chemotherapy and received allogeneic stem cell transplantation (allo-SCT) for consolidation. Her past medical history showed that she received bilateral breast implants 7 years ago. This patient underwent ultrasound examination of the breast and multiple bilateral breast nodules were revealed that were not considered by clinicians to be concerning. Several months later, the patient’s bilateral nodules rapidly progressed to large palpable masses. Ultrasound-guided biopsy revealed diffuse infiltration of undifferentiated tumor cells and immunohistochemistry (IHC) indicated that the tumor was positive for myeloperoxidase (MPO), cluster of differentiation (CD) 34, CD43, CD68, CD117, and Ki67. The pathological diagnosis was extramedullary recurrence of AML as MS of breast. After the diagnosis, the patient received systemic chemotherapy and drugs containing cytarabine, azacitidine, and methotrexate. However, 1 year after achieving partial remission, the patient died from intracranial invasion of leukemia, brain herniation, and respiratory failure. Conclusion It is necessary for the specialist to have a high suspicion index by careful inquiry of the patient’s medical history if a patient presents at the breast clinic with a breast tumor as the chief complaint. Combining information from the patient’s medical history with a tumor biopsy is critical for obtaining the correct diagnosis of the disease.

Biting midges of the genus Culicoides (order Diptera, family Ceratopogonidae) are potential biological vectors for the transmission of certain arboviruses among humans, livestock, and wild animals. This study collected a total of 405 Culicoides individuals from seven animal farms located in five counties in the border areas of Yunnan Province, China, and examined the Culicoides species composition and the major arboviruses carried by the Culicoides species. The collected Culicoides were classified into seven species with variable abundances: Culicoides arakawae (5.43%, 22/405), Culicoides homotomus (1.23%, 5/405), Culicoides obsoletus (19.75%, 80/405), Culicoides orientalis (17.28%, 70/405), Culicoides oxystoma (29.38%, 119/405), Culicoides peregrinus (5.68%, 23/405), and Culicoides nipponensis (21.23%, 86/405). Among the seven species, C. oxystoma and C. nipponensis were distributed in all the five counties with abundances of 13.33–44.87% and 10.00–46.83%, respectively, suggesting that these were the dominant species of Culicoides widespread on animal farms in the border areas. PCR was used to detect major arboviruses in the collected Culicoides specimens, including bluetongue virus (BTV), Japanese encephalitis virus, Dengue virus, Zika virus, African swine fever virus, and African horse sickness virus. Among the tested viruses, only BTV serotype 1 was tested positive in C. oxystoma specimens collected from a buffalo farm. Culicoides oxystoma was the dominant species on animal farms in the sampled areas, but it has not previously been documented as positive for BTV in China. The current results thus suggest that C. oxystoma could be an important vector for BTV transmission in these border areas, which, however, needs to be confirmed by further comprehensive experiments. Overall, the present study provides the first profile of Culicoides species on animal farms in the China, Vietnam, and Myanmar border areas, establishes the prevalence of arboviruses carried by these Culicoides species, and suggests the vector potential of C. oxystoma species for the transmission of BTV.

Somatic mutations accumulated in normal tissues are associated with aging and disease. Here, we performed a comprehensive genomic analysis of 1,737 morphologically normal tissue biopsies (~ 600 cells each), mostly from the epithelia, of nine organs from five donors. We found that somatic mutation accumulations and clonal expansions are widespread, although with variable extent, in morphologically normal human tissues. Somatic copy number alterations were rarely detected, except for tissues from esophagus and cardia. Endogenous mutational processes like SBS1 and SBS5 are ubiquitous among normal tissues though exhibiting different relative activities. Exogenous mutational processes like SBS22 were found in different tissues from the same donor. We reconstructed the spatial somatic clonal architecture with sub-millimeter resolution. In epithelial tissues from esophagus and cardia, macroscopic somatic clones expanded to several millimeters were frequently seen, whereas in tissues from colon, rectum, and duodenum somatic clones were microscopic in size and evolved independently. Our study depicted a body map of somatic mutations and clonal expansions from the same individuals, and it revealed that the degree of somatic clonal expansion and enrichment of driver mutations are highly organ specific.

Introduction Septic cardiomyopathy is a common complication of sepsis with high morbidity and mortality, but lacks specific therapy. This study aimed to reveal the role of circTLK1 and its potential mechanisms in septic cardiomyopathy. Materials and Methods The in vitro and in vivo models of septic cardiomyopathy were established. Cell viability and apoptosis were detected by CCK8, TUNEL and flow cytometry, respectively. LDH, CK, SOD, MDA, ATP, 8‐OHdG, NAD+/NADH ratio, ROS level, mitochondrial membrane potential and cytochrome C distribution were evaluated using commercial kits. qRT‐PCR and western blotting were performed to detect RNA and protein levels. Mitochondrial DNA (mtDNA) copy number and transcription were assessed by quantitative PCR. Dual‐luciferase assay, RNA immunoprecipitation and co‐immunoprecipitation were performed to verify the interaction between circTLK1/PARP1 and miR‐17‐5p. Results CircTLK1, PARP1 and HMGB1 were up‐regulated in the in vitro and in vivo models of septic cardiomyopathy. CircTLK1 inhibition restrained LPS‐induced up‐regulation of PARP1 and HMGB1. Moreover, circTLK1 knockdown repressed sepsis‐induced mtDNA oxidative damage, mitochondrial dysfunction and consequent cardiomyocyte apoptosis by inhibiting PARP1/HMGB1 axis in vitro and in vivo. In addition, circTLK1 enhanced PARP1 expression via sponging miR‐17‐5p. Inhibition of miR‐17‐5p abolished the protective effects of circTLK1 silencing on oxidative mtDNA damage and cardiomyocyte apoptosis. Conclusion CircTLK1 sponged miR‐17‐5p to aggravate mtDNA oxidative damage, mitochondrial dysfunction and cardiomyocyte apoptosis via activating PARP1/HMGB1 axis during sepsis, indicating that circTLK1 may be a putative therapeutic target for septic cardiomyopathy.

Chronic infections caused by Pseudomonas aeruginosa pose severe threats to human health. Traditional antibiotic therapy has lost its total supremacy in this battle. Here, nanoplatforms activated by the clinical microenvironment are developed to treat P. aeruginosa infection on the basis of dynamic borate ester bonds. In this design, the nanoplatforms expose targeted groups for bacterial capture after activation by an acidic infection microenvironment, resulting in directional transport delivery of the payload to bacteria. Subsequently, the production of hyperpyrexia and reactive oxygen species enhances antibacterial efficacy without systemic toxicity. Such a formulation with a diameter less than 200 nm can eliminate biofilm up to 75%, downregulate the level of cytokines, and finally promote lung repair. Collectively, the biomimetic design with phototherapy killing capability has the potential to be an alternative strategy against chronic infections caused by P. aeruginosa.

Zika virus (ZIKV) infection during pregnancy can cause microcephaly in newborns, yet the underlying mechanisms remain largely unexplored. Here, we reveal extensive and large-scale metabolic reprogramming events in ZIKV-infected mouse brains by performing a multi-omics study comprising transcriptomics, proteomics, phosphoproteomics and metabolomics approaches. Our proteomics and metabolomics analyses uncover dramatic alteration of nicotinamide adenine dinucleotide (NAD+)-related metabolic pathways, including oxidative phosphorylation, TCA cycle and tryptophan metabolism. Phosphoproteomics analysis indicates that MAPK and cyclic GMP-protein kinase G signaling may be associated with ZIKV-induced microcephaly. Notably, we demonstrate the utility of our rich multi-omics datasets with follow-up in vivo experiments, which confirm that boosting NAD+ by NAD+ or nicotinamide riboside supplementation alleviates cell death and increases cortex thickness in ZIKV-infected mouse brains. Nicotinamide riboside supplementation increases the brain and body weight as well as improves the survival in ZIKV-infected mice. Our study provides a comprehensive resource of biological data to support future investigations of ZIKV-induced microcephaly and demonstrates that metabolic alterations can be potentially exploited for developing therapeutic strategies.

Abnormal migration of subventricular zone (SVZ)-derived neural progenitor cells (SDNPs) is involved in the pathological and epileptic processes of focal cortical dysplasias (FCDs), but the underlying mechanisms are not clear. Recent studies indicated that high mobility group box 1 (HMGB1)/receptor for advanced glycation end products (RAGE) are widely expressed in epileptic specimens of FCDs, which suggests that the HMGB1-RAGE pathway is involved in the pathological and/or epileptic processes of FCDs. The present study used Nestin-GFPtg/+ transgenic mice, and we established a model of freezing lesion (FL), as described in our previous report. A "migrating stream" composed of GFP-Nestin+ SDNPs was derived from the SVZ region and migrated to the cortical FL area. We found that translocated HMGB1 and RAGE were expressed in cortical lesion in a clustered distribution pattern, which was especially obvious in the early stage of FL compared to the sham group. Notably, the number of GFP-Nestin+ SDNPs within the "migrating stream" was significantly decreased when the HMGB1-RAGE pathway was blocked by a RAGE antagonist or deletion of the RAGE gene. The absence of RAGE also decreased the activity of pentylenetetrazol-induced cortical epileptiform discharge. In summary, this study provided experimental evidence that the levels of extranuclear HMGB1 and its receptor RAGE were increased in cortical lesion in the early stage of the FL model. Activation of the HMGB1-RAGE pathway may contribute to the abnormal migration of SDNPs and the hyperexcitability of cortical lesion in the FL model.

SARS-CoV-2, as the causation of severe epidemic of COVID-19, is one kind of positive single-stranded RNA virus with high transmissibility. However, whether or not SARS-CoV-2 can integrate into host genome needs thorough investigation. Here, we performed both RNA sequencing (RNA-seq) and whole genome sequencing on SARS-CoV-2 infected human and monkey cells, and investigated the presence of host-virus chimeric events. Through RNA-seq, we did detect the chimeric host-virus reads in the infected cells. But further analysis using mixed libraries of infected cells and uninfected zebrafish embryos demonstrated that these reads are falsely generated during library construction. In support, whole genome sequencing also didn’t identify the existence of chimeric reads in their corresponding regions. Therefore, the evidence for SARS-CoV-2’s integration into host genome is lacking. One-Sentence Summary SARS-CoV-2 does not integrate into host genome through whole genome sequencing.

MYC rearrangement is a relatively rare genetic abnormality in follicular lymphoma (FL). In this study, we evaluated the relative frequency of MYC rearrangement in 522 cases of FL and studied their clinicopathologic, cytogenetic, and molecular characteristics. Fluorescence in situ hybridization studies for MYC (break-apart probe), MYC/IGH, IGH/BCL2, and BCL6 rearrangements were performed on tissue microarrays. Immunohistochemical stains for CD10, BCL2, BCL6, and MYC were performed and scored on MYC-rearranged cases. On 4 FL cases, a custom targeted panel of 356 genes was used for mutation analysis. Ten cases (1.9%) were positive for MYC rearrangement. Histologically, 6 of 10 cases were grade 1-2, and 4 cases were grade 3A. By immunohistochemistry, 9 of 9 tested cases were CD10+, all cases were BCL6+, and 9/10 cases were BCL2+. MYC protein staining was low in all cases tested. IGH/BCL2 rearrangement was detected in 5 of 9 cases, whereas BCL6 rearrangement was detected in 3 of 7 tested cases and 4 of 10 cases showed MYC/IGH rearrangement. The most commonly detected mutations in the MYC-positive cases included HLA-B, TNFRSF14, and KMT2D. MYC and/or B2M abnormalities were detected in 2 cases. In conclusion, MYC rearrangement is uncommon in FL and these cases do not appear to have specific histologic characteristics. Molecular analysis showed abnormalities in genes associated with transformation, namely MYC and B2M. Larger studies are needed to evaluate if MYC-rearrangement in FL has prognostic significance.

BACKGROUND: Studies over the past decade have shown that long non-coding RNAs (lncRNAs) play an essential role in the tumorigenesis and progression of kidney renal clear cell carcinoma (KIRC). Meanwhile, autophagy has been demonstrated to regulate KIRC pathogenesis and targeting therapy resistance. However, the prognostic value of autophagy-related lncRNAs in KIRC patients has not been reported before. METHODS: In this study, we obtained transcriptome data of 611 KIRC cases from the TCGA database and 258 autophagy-related mRNAs from the HADb database to identify autophagy-related lncRNAs by co-expression network. A prognostic model was then established basing on these autophagy-related lncRNAs, dividing patients into high-risk and low-risk groups. Survival analysis, clinical variables dependent receiver operating characteristic (ROC) analyses, univariate/multivariate Cox analyses, and clinical correlation analysis were performed based on risk signature with R language. Gene set enrichment analysis (GSEA) was then performed to investigate the potential mechanism of the risk signature promoting KIRC progression with GSEA software. CIBERSORT algorithm was performed to assess the impact of these lncRNAs on the infiltration of immune cells. RESULTS: A total of 17 lncRNAs were screened out and all these lncRNAs were found significantly related to KIRC patients’ overall survival in subsequent survival analyses. Besides, the overall survival time in the high-risk group was much poorer than in the low-risk group. The ROC analysis revealed that the prognostic value of risk signature was better than age, gender, grade, and N stage. Univariate/multivariate analyses suggested that the risk signature was an independent predictive factor for KIRC patients. Immune and autophagy related pathways were dramatically enriched in high-risk and low-risk groups, respectively, and lncRNAs related immune cells were identified by CIBERSORT. CONCLUSIONS: In summary, our identified 17 autophagy-related lncRNAs had prognostic value for KIRC patients which may function in immunomodulation.

The present study aimed to construct and evaluate a novel experiment-based hypoxia signature to help evaluations of GBM patient status. First, the 426 proteins, which were previously found to be differentially expressed between normal and hypoxia groups in glioblastoma cells with statistical significance, were converted into the corresponding genes, among which 212 genes were found annotated in TCGA. Second, after evaluated by single-variable Cox analysis, 19 different expressed genes (DEGs) with prognostic value were identified. Based on λ value by LASSO, a gene-based survival risk score model, named RiskScore, was built by 7 genes with LASSO coefficient, which were FKBP2, GLO1, IGFBP5, NSUN5, RBMX, TAGLN2 and UBE2V2. Kaplan–Meier (K–M) survival curve analysis and the area under the curve (AUC) were plotted to further estimate the efficacy of this risk score model. Furthermore, the survival curve analysis was also plotted based on the subtypes of age, IDH, radiotherapy and chemotherapy. Meanwhile, immune infiltration, GSVA, GSEA and chemo drug sensitivity of this risk score model were evaluated. Third, the 7 genes expression were evaluated by AUC, overall survival (OS) and IDH subtype in datasets, importantly, also experimentally verified in GBM cell lines exposed to hypoxic or normal oxygen condition, which showed significant higher expression in hypoxia than in normal group. Last, combing the hypoxia RiskScore with clinical and molecular features, a prognostic composite nomogram was generated, showing the good sensitivity and specificity by AUC and OS. Meanwhile, univariate analysis and multivariate analysis were used for performed to identify variables in nomogram that were significant in independently predicting duration of survival. It is a first time that we successfully established and validated an independent prognostic risk model based on hypoxia microenvironment from glioblastoma cells and public database. The 7 key genes may provide potential directions for future biochemical and pharmaco-therapeutic research.

The regulation mechanism of the hybrid yellow catfish "Huangyou-1" was assessed under conditions of hypoxia and reoxygenation by examination of oxygen sensors and by monitoring respiratory metabolism, oxidative stress, and apoptosis. The expressions of genes related to oxygen sensors (HIF-1α, HIF-2α, VHL, HIF-1β, PHD2, and FIH-1) were upregulated in the brain and liver during hypoxia, and recovered compared with control upon reoxygenation. The expressions of genes related to glycolysis (HK1, PGK1, PGAM2, PFK, and LDH) were increased during hypoxia and then recovered compared with control upon reoxygenation. The mRNA levels of CS did not change during hypoxia in the brain and liver, but increased during reoxygenation. The mRNA levels of SDH decreased significantly only in the liver during hypoxia, but later increased compared with control upon reoxygenation in both tissues. Under hypoxic conditions, the expressions of genes related to oxidative stress (SOD1, SOD2, GSH-Px, and CAT) and the activity of antioxidant enzymes (SOD, CAT, and GSH-Px) and MDA were upregulated compared with control. The expressions of genes related to apoptosis (Apaf-1, Bax, Caspase 3, Caspase 9, and p53) were higher than those in control during hypoxic exposure, while the expressions of Bcl-2 and Cyt C were decreased. The findings of the transcriptional analyses will provide insights into the molecular mechanisms of hybrid yellow catfish "Huangyou-1" under conditions of hypoxia and reoxygenation. Overall, these findings showed that oxygen sensors of "Huangyou-1" are potentially useful biomarkers of environmental hypoxic exposure. Together with genes related to respiratory metabolism, oxidative stress and apoptosis occupy a quite high position in enhancing hypoxia tolerance. Our findings provided new insights into the molecular regulatory mechanism of hypoxia in "Huangyou-1."

Hypoxia, a common characteristic of bacterial infections, is known to be closely associated with the emergence of multidrug-resistant bacteria, which hastens the need to develop advanced microbicides and antibacterial techniques. Photodynamic therapy is a promising strategy to reduce bacterial antibiotic resistance and employs photosensitizers, excitation light sources, and sufficient oxygen to generate toxic reactive oxygen species (ROS). The inherent limitation of PDT is that the generation of ROS is restricted by the hypoxic microenvironment in infection sites. Here, an oxygen self-supplying nanotherapeutic is developed to enhance antibacterial activity against multidrug-resistant bacteria on the basis of fluorinated boron dipyrromethene (BODIPY)-based glycomimetics. The nanotherapeutic not only could capture the bacteria efficiently but also was able to act as an oxygen carrier to relieve the hypoxic microenvironment of bacterial infections, thus achieving enhanced PDT efficacy. In a Pseudomonas aeruginosa infection of a rat cornea, typical administration of the nanotherapeutic decreased the infiltrate and showed a faster healing capacity in comparison with BODIPY-based glycomimetics. Self-supplying oxygen nanotherapeutics that relieve the hypoxic microenvironment and interfere with bacterial colonization have been shown to be a promising candidate for the management of drug-resistant microbial keratitis.

Bioconversion of food waste oil (FWO) into biodegradable plastic is a promising method for converting waste into high-value products. In this study, a strain (Pseudomonas sp. H3) was isolated for polyhydroxyalkanoate (PHA) synthesis from FWO. After 72 h of cultivation with 20 g/L of FWO, the high cell dry weight (CDW) of 3.6 g/L, PHA yield of 2.4 g/L, and PHA content of 65 wt% were obtained under the optimal temperature (25 °C) and inoculum amount (6% (v/v)). Fed-batch fermentation was conducted in a 5 L bioreactor with a maximum CDW of 16 g/L, PHA content of 54 wt%, and PHA productivity of 0.23 g/(L·h) after 36 h. The PHA had a molecular weight of 54 782 Da and a low polydispersity index of 1.41 with glass transition, melting, and degradation temperatures of −20 °C, 34 °C, and 210 °C, respectively. To further utilize the wastewater after PHA production, anaerobic digestion was employed for CH4 production, and the CH4 yield was 284 mL/g volatile solids. Microbial community analysis showed that the abundance of acetate-oxidizing bacteria and Methanobacterium significantly increased during anaerobic digestion. This study describes a new strain for the economical synthesis of biodegradable plastics and presents a novel framework for fully utilizing FWO with the production of PHA and CH4.

Determining the temporal community composition of fish eggs in particular regions and understanding the reproductive times of regional fish taxa are key aspects of the management and regulation of regional fish stocks. However, it is extremely difficult to accurately identify fish eggs due to the absence of diagnostic morphological characters. We sampled fish eggs in the lower Hongshuihe River (an upper mainstem of the Pearl River) between May and September 2020. We then used DNA barcoding to determine the species composition of the egg pool and to predict the spawning periods of the identified species. A total of 641 eggs and 17 larvae were chosen for molecular identification; 397 eggs and 17 larvae yielded high‐quality barcoding sequences. The high failure rate (~38%) was most likely due to long‐term storage in low concentrations of ethanol prior to molecular analysis. We successfully classified 392 eggs into 10 species and 13 larvae into four species using public databases. Most of the species identified in the egg pool were small and/or benthic, and migratory species were rare. This may partially reflect the adverse effects of hydropower cascade development in this river section. We also found that spawning periods tended to be species‐specific. Our study provides a reference for the conservation and management of regional fishery stocks., We sampled fish eggs in the lower Hongshuihe River (an upper mainstem of the Pearl River) between May and September 2020. We then used DNA barcoding to determine the species composition of the egg pool and to predict the spawning periods of the identified species.

Background Jujube is a typical fruit tree species from China. ‘Muzao’, a cracking-susceptible cultivar, and ‘Linhuang No. 1’, a cracking-resistant cultivar, were selected in a previous study as contrasting research materials. Whole-genome resequencing and transcriptomic analysis of ‘Linhuang No. 1’ and ‘Muzao’ allowed the identification of differentially expressed genes with different gene structures between the two cultivars and could be helpful in explaining the differences and similarities between the two cultivars. Results Resequencing identified 664,129 polymorphic variable sites between ‘Linhuang No. 1’ and ‘Muzao’. To determine the genetic relationship among ‘Linhuang No. 1’, ‘Muzao’ and the jujube genome reference cultivar ‘Dongzao’, the characteristic polymorphic variable sites were analysed by principal component analysis. The genetic relationship between ‘Linhuang No. 1’ and ‘Muzao’ was closer than that of either variety and ‘Dongzao’. Nineteen differentially expressed genes were identified by combining transcriptomic analysis with resequencing analysis. LOC107427052 (encoding a nitrite reductase) was identified by Kyoto Encyclopedia of Genes and Genomes (KEGG) enrichment analysis for further study. The identified insertion was not in the domain region of the LOC107427052 gene coding sequence (CDS) region and was verified by the finding that the insertion did not affect translation of the protein. The LOC107427052 gene expression levels, nitrite reductase activities and nitrite contents of ‘Muzao’ were significantly higher than the corresponding values of ‘Linhuang No. 1’ at the young fruit stage. There was no significant difference in the quantity of the product of nitrite reductase, namely, ammonia, between the two cultivars. Conclusions The present study was the first to explore the differences between different jujube cultivars (‘Linhuang No. 1’ and ‘Muzao’) by combining genome resequencing and transcriptomics. LOC107427052 (encoding a nitrite reductase) was characterized by KEGG enrichment analysis. The insertion in the CDS region of the LOC107427052 gene provides a new direction for the study of nitrogen metabolism in jujube. Our study has laid a foundation for the comparative analysis of nitrite metabolism between the jujube cultivars ‘Linhuang No. 1’ and ‘Muzao’.

Species delimitation is one of the most fundamental processes in biology. Biodiversity undertakings, for instance, require explicit species concepts and criteria for species delimitation in order to be relevant and translatable. However, a perfect species concept does not exist for Fungi. Here, we review the species concepts commonly used in Basidiomycota, the second largest phylum of Fungi that contains some of the best known species of mushrooms, rusts, smuts, and jelly fungi. In general, best practice is to delimitate species, publish new taxa, and conduct taxonomic revisions based on as many independent lines of evidence as possible, that is, by applying a so-called unifying (or integrative) conceptual framework. However, the types of data used vary considerably from group to group. For this reason we discuss the different classes of Basidiomycota, and for each provide: (i) a general introduction with difficulties faced in species recognition, (ii) species concepts and methods for species delimitation, and (iii) community recommendations and conclusions.