An amplification-free CRISPR-Cas12a assay for titer determination and composition analysis of the rAAV genome.

The viral genome titer is a crucial indicator for the clinical dosing, manufacturing, and analytical testing of recombinant adeno-associated virus (rAAV) gene therapy products. Although quantitative PCR and digital PCR are the common methods used for quantifying the rAAV genome titer, they are limited by inadequate accuracy and robustness. The clustered regularly interspaced short palindromic repeat (CRISPR)-Cas12a biosensor is being increasingly used in virus detection; however, there is currently no report on its application in the titer determination of gene therapy products. In the present study, an amplification-free CRISPR-Cas12a assay was developed, optimized, and applied for rAAV genome titer determination. The assay demonstrated high precision and accuracy within the detection range of 4 × 109 and 1011 vg/mL. No significant difference was observed between the Cas12a and qPCR assay results (p < 0.05, t test). Moreover, Cas12a exhibited similar activity on both single-stranded and double-stranded DNA substrates. Based on this characteristic, the titers of positive-sense and negative-sense strands were determined separately, which revealed a significant difference between their titers for an in-house reference AAV5-IN. This study presents the inaugural report of a Cas12a assay developed for the titer determination and composition analysis of the rAAV genome.

Prognostic model incorporating immune checkpoint genes to predict the immunotherapy efficacy for lung adenocarcinoma: a cohort study integrating machine learning algorithms.

This study aimed to develop and validate a nomogram based on immune checkpoint genes (ICGs) for predicting prognosis and immune checkpoint blockade (ICB) efficacy in lung adenocarcinoma (LUAD) patients. A total of 385 LUAD patients from the TCGA database and 269 LUAD patients in the combined dataset (GSE41272 + GSE50081) were divided into training and validation cohorts, respectively. Three different machine learning algorithms including random forest (RF), least absolute shrinkage and selection operator (LASSO) logistic regression analysis, and support vector machine (SVM) were employed to select the predictive markers from 82 ICGs to construct the prognostic nomogram. The X-tile software was used to stratify patients into high- and low-risk subgroups based on the nomogram-derived risk scores. Differences in functional enrichment and immune infiltration between the two subgroups were assessed using gene set variation analysis (GSVA) and various algorithms. Additionally, three lung cancer cohorts receiving ICB therapy were utilized to evaluate the ability of the model to predict ICB efficacy in the real world. Five ICGs were identified as predictive markers across all three machine learning algorithms, leading to the construction of a nomogram with strong potential for prognosis prediction in both the training and validation cohorts (all AUC values close to 0.800). The patients were divided into high- (risk score ≥ 185.0) and low-risk subgroups (risk score < 185.0). Compared to the high-risk subgroup, the low-risk subgroup exhibited enrichment in immune activation pathways and increased infiltration of activated immune cells, such as CD8 + T cells and M1 macrophages (P < 0.05). Furthermore, the low-risk subgroup had a greater likelihood of benefiting from ICB therapy and longer progression-free survival (PFS) than did the high-risk subgroup (P < 0.05) in the two cohorts receiving ICB therapy. A nomogram based on ICGs was constructed and validated to aid in predicting prognosis and ICB treatment efficacy in LUAD patients.

Predictive Model to Identify the Long Time Survivor in Patients with Glioblastoma: A Cohort Study Integrating Machine Learning Algorithms.

We aimed to develop and validate a predictive model for identifying long-term survivors (LTS) among glioblastoma (GB) patients, defined as those with an overall survival (OS) of more than 3 years. A total of 293 GB patients from CGGA and 169 from TCGA database were assigned to training and validation cohort, respectively. The differences in expression of immune checkpoint genes (ICGs) and immune infiltration landscape were compared between LTS and short time survivor (STS) (OS<1.5 years). The differentially expressed genes (DEGs) and weighted gene co-expression network analysis (WGCNA) were used to identify the genes differentially expressed between LTS and STS. Three different machine learning algorithms were employed to select the predictive genes from the overlapping region of DEGs and WGCNA to construct the nomogram. The comparison between LTS and STS revealed that STS exhibited an immune-resistant status, with higher expression of ICGs (P<0.05) and greater infiltration of immune suppression cells compared to LTS (P<0.05). Four genes, namely, OSMR, FMOD, CXCL14, and TIMP1, were identified and incorporated into the nomogram, which possessed good potential in predicting LTS probability among GB patients both in the training (C-index, 0.791; 0.772-0.817) and validation cohort (C-index, 0.770; 0.751-0.806). STS was found to be more likely to exhibit an immune-cold phenotype. The identified predictive genes were used to construct the nomogram with potential to identify LTS among GB patients.

Preoperative glucose-to-lymphocyte ratio predicts survival in cancer.

Background: Systemic inflammation and glucose metabolism have been closely related to the survival of cancer patients. Therefore, we aimed to evaluate whether preoperative glucose-to-lymphocyte ratio (GLR) can be used to predict the survival of cancer patients. Methods: We retrospectively examined 2172 cancer patients who underwent surgery from January 1, 2014, to December 31, 2016. There were 240 patients with non-small cell lung cancer (NSCLC), 378 patients with colorectal cancer (CRC), 221 patients with breast cancer (BC), 335 patients with gastric cancer (GC), 270 patients with liver cancer, 233 patients with esophageal cancer (EC), 295 patients with renal cancer, and 200 patients with melanoma. The formula for preoperative GLR calculation was as follows: GLR=glucose/lymphocyte count. The overall survival (OS) was estimated using the Kaplan-Meier method. The predictive factors for OS were determined using multivariate analysis. Results: The Kaplan-Meier analysis showed that the median survival time in the high-GLR group was much shorter than that of those in the low-GLR group for different cancers. Cox multivariate regression analysis reveals that preoperative GLR was an independent factor for predicting overall survival in different tumor types. Conclusion: Elevated preoperative GLR was remarkably associated with a poorer prognosis in patients with NSCLC, CRC, breast cancer, gastric cancer, kidney cancer, liver cancer, esophageal cancer, and melanoma. Preoperative GLR promises to be an essential predictor of survival for cancer patients.

Dynamics of Benthic Nitrate Reduction Pathways and Associated Microbial Communities Responding to the Development of Seasonal Deoxygenation in a Coastal Mariculture Zone.

Intensive mariculture activities result in eutrophication and enhance coastal deoxygenation. Deoxygenation profoundly influences nitrate reduction processes and further the fate of nitrogen (N) in coastal systems. Herein, 15N isotope labeling, real-time PCR, and high-throughput sequencing techniques were jointly used to investigate the participation and seasonal dynamics of sediment nitrate reduction pathways and the succession of functional microbial communities during the development of seasonal deoxygenation in a coastal aquaculture zone. Denitrification dominated benthic nitrate reduction (46.26-80.91%). Both denitrification and dissimilatory nitrate reduction to ammonium were significantly enhanced by summer deoxygenation (dissolved oxygen levels fell to 2.94 ± 0.28 mg L-1), while anammox remained unchanged. The abundance of the nitrous oxide reductase gene nosZ increased during deoxygenation. The community of the nosZ gene was sensitive to deoxygenation, with Azospirillum and Ruegeria accounting for the majority. Pelobacter was overwhelming in the nrfA gene (encoding dissimilatory nitrite reductase) community, which was less affected by deoxygenation. The variations of benthic nitrate reduction processes were driven by bottom water oxygen combined with temperature, chlorophyll a, and microbial gene abundances and community compositions. Our results implicated that seasonal oxygen-deficient zones could be substantial N sinks of coastal ecosystems and important for N balance. Effective management measures need to be developed to avoid further exacerbation of coastal deoxygenation and maintain the sustainable development of mariculture.

Abundance and characteristics of microplastics in the Wanquan River estuary, Hainan Island.

As the nexus where rivers and oceans meet, estuaries are vulnerable to microplastic (MP) pollution derived from rivers. However, few studies have focused on the pollution status of MPs in small estuarine areas. Here, the abundance and characteristics of MPs in surface water and sediment samples from a small estuary, the Wanquan River estuary, were studied. The average abundance of MPs was 6573 ± 2659 n/m3 in surface water and 1065 ± 696 n/kg dw in sediment samples from the Wanquan River estuary. Most of the MPs in water samples and sediments were red (92.9 % and 88.1 %) fragments (87.4 % and 95.5 %) with sizes <1.0 mm (90.8 % and 92.4 %) made up of antifouling paint particles (APPs) (83.5 % and 89.8 %), respectively. A significant positive correlation (p < 0.01) was found between the concentration of Cu2+ and the abundance of APPs in sediment samples from the Wanquan River estuary. The APPs in the sediments can act as a continuous source of toxic chemicals (e.g., Cu2+) to marine environments. The results of this study expand our knowledge about MP pollution in small estuaries, and the ecological risk of APPs in the Wanquan River estuary to aquatic organisms should not be ignored.

Antimicrobial Biosynthetic Potential and Phylogenetic Analysis of Culturable Bacteria Associated with the Sponge Ophlitaspongia sp. from the Yellow Sea, China.

Sponge-derived bacteria are considered to be a promising source of novel drugs, owing to their abundant secondary metabolites that have diverse biological activities. In this study, we explored the antimicrobial biosynthetic potential and phylogenetics of culturable bacteria associated with the sponge Ophlitaspongia sp. from the Yellow Sea, China. Using culture-dependent methods, we obtained 151 bacterial strains, which were then analysed for their antimicrobial activities against seven indicator strains. The results indicate that 94 (62.3%) of the 151 isolated strains exhibited antimicrobial activities and inhibited at least one of the indicator strains. Fifty-two strains were selected for further phylogenetic analysis using 16S rRNA gene sequencing, as well as for the presence of polyketide synthase (PKS) and non-ribosomal peptide synthetase (NRPS) genes. These 52 strains belonged to 20 genera from 18 families in 4 phyla, including Actinobacteria, Bacteroidetes, Firmicutes, and Proteobacteria. Five strains with PKS genes and ten strains with NRPS genes were detected. Among them, two strains contained both PKS and NRPS genes. Notoacmeibacter sp. strain HMA008 (class Alphaproteobacteria) exhibited potent antimicrobial activity; thus, whole genome sequencing methods were used to analyse its secondary metabolite biosynthetic gene clusters. The genome of HMA008 contained 12 biosynthetic gene clusters that potentially encode secondary metabolites belonging to compound classes such as non-ribosomal peptides, prodigiosin, terpene, ß-lactones, and siderophore, among others. This study indicates that the sponge Ophlitaspongia sp. harbours diverse bacterial strains with antimicrobial properties and may serve as a potential source of bioactive compounds.

Clinical performance evaluation of O-Ring Halcyon Linac: A real-world study.

BACKGROUND: Radiation therapy, especially the development of linear accelerators, plays a key role in cancer management. The fast-rotating coplanar O-ring Halcyon Linac has demonstrated many advantages. The previous literature has mainly focused on the machine parameters and plan quality of Halcyon, with a lack of relevant research on its clinical application. AIM: To evaluate the clinical performance of the O-ring Halcyon treatment system in a real-world application setting. METHODS: Data from sixty-one patients who were treated with the Halcyon system throughout the entire radiotherapy process in Peking Union Medical College Hospital between August 2019 and September 2020 were retrospectively reviewed. We evaluated the target tumour response to radiotherapy and irradiation toxicity from 1 to 3 mo after treatment. Dosimetric verification of Halcyon plans was performed using a quality assurance procedure, including portal dosimetry, ArcCHECK and point dose measurements for verification of the system delivery accuracy. RESULTS: Of the 61 patients in the five groups, 16, 12, 7 and 26 patients had complete response, partial response, progressive disease and stable disease, respectively. No increase in the irradiated target tumour volume was observed when separately evaluating the local response. Regarding irradiation toxicity, no radiation-induced deaths were observed. Thirty-eight percent (23/61 patients) had no radiation toxicity after radiotherapy, 56% (34/61 patients) experienced radiation toxicity that resolved after treatment, and 6% (4/61 patients) had irreversible adverse reactions. The average gamma passing rates with a 2% dose difference and 2-mm distance to agreement for IMRT/VMAT/SRT plans were ArcCHECK at 96.4% and portal dosimetry at 96.7%, respectively. All of the validated clinical plans were within 3% for point dose measurements, and Halcyon's ArcCHECK demonstrated a high pass rate of 99.1% ± 1.1% for clinical gamma passing criteria of 3%/3 mm. CONCLUSION: The O-ring Halcyon Linac could achieve a better therapeutic effect on the target volume by providing accurate treatment delivery plans with tolerable irradiation toxicity.

Association between c-type lectin-like receptor 2 and microsatellite instability in colorectal cancer: a cross-sectional study.

BACKGROUND: As a transmembrane protein, C-type lectin-like receptor 2 (CLEC-2) is mainly expressed on platelets and released into plasma after platelet activation. Activated platelets participate in the regulation of innate immune cells. Patients with different microsatellite statuses have distinct immune profiles. This study aimed to investigate the association of plasma CLEC-2 levels with microsatellite status among colorectal cancer (CRC) patients. METHODS: A cross-sectional analysis of 430 CRC patients from Harbin Medical University Cancer Hospital was conducted. CLEC-2 levels were measured with fasting venous blood samples drawn from each participant before any treatment. The microsatellite status was evaluated with DNA obtained from fresh frozen tumor tissue samples. The other clinical data were collected and recorded based on the medical system records. RESULTS: CLEC-2 levels were significantly higher among patients with high microsatellite instability phenotype than the stable microsatellite group, adjusting for other confounding variables. CONCLUSIONS: The increased CLEC-2 is associated with the high microsatellite instability subtype of CRC.

[Applicability of mixed effect model in the prediction of forest fire]. / 混合效应模型在林火发生预测中的适用性.

Fire is an important influencing factor in forest ecosystems. Establishing an accurate forest fire forecasting model is important for forest fire management. We used different meteorological factors as predictors to construct a forest fire prediction model in Fujian Province, based on Logistic regression and generalized linear mixed effect model. We compared the fitness and prediction accuracy of the two models, judged the applicability of the mixed effect model in forest fire forecasting. The results showed that the AUC and accuracy values of the Logistic base model were 0.664 and 60.4%, respectively. Models considering random effects gave better fitting and validating statistics. Among them, the two-level mixed model containing both area and altitude difference effects performed best, with increases of 0.057 and 6.0% for the AUC and accuracy values, respectively. By applying the model to predict the probability of forest fires in Fujian Province, we found that the middle-incidence and high-incidence areas of forest fires distributed in northwest and south Fujian, whereas the low-incidence areas of forest fires distributed in southwest and east Fujian, which was consistent with the observed data. The data fitting and forest fire prediction of the mixed effects model was better than those of the Logistic basic model. Therefore, it could be used as an important tool for forest fire prediction and management.

Preoperative PDW levels predict pulmonary metastasis in patients with hepatocellular carcinoma.

BACKGROUND: In hepatocellular carcinoma (HCC), pulmonary metastasis (PM) after hepatectomy is associated with poor clinical outcomes. The crucial phases of tumour cell proliferation, angiogenesis, and metastasis all entail platelet activation. In HCC, platelet distribution width (PDW) suggests platelet size changes and predicts a worse prognosis. The aim of this study was to assess the association between PDW and PMs in HCC patients receiving hepatectomy. MATERIAL/METHODS: From January 2013 to December 2015, a cohort of patients who underwent hepatectomy for HCC at the Harbin Medical University Cancer Hospital in China were retrospectively evaluated. The relationship between PDW levels and clinical and demographic parameters was examined. To investigate the relationships between predicted factors and PM, a competing risk model was used. From January 2016 to December 2018, a validation cohort of 109 patients from the First Affiliated Hospital of Harbin Medical University was studied independently. RESULTS: In the primary cohort, 19 out of 214 patients had postoperative PMs. In HCC patients with PM, PDW levels were lower than in those without PM. There was a significant difference in the cumulative incidence of 2-year PM between the high-PDW and low-PDW groups after controlling for competing risk events (death prior to the development of PM) (p < 0.001). In addition, PDW was also found to be an independent predictor for PM in a multivariable competing risk analysis. The results were externally validated in another cohort. CONCLUSIONS: In HCC, preoperative PDW is significantly associated with PM. PDW could be a biomarker for post-operative PM in HCC patients.

Culturable Microorganisms Associated with Sea Cucumbers and Microbial Natural Products.

Sea cucumbers are a class of marine invertebrates and a source of food and drug. Numerous microorganisms are associated with sea cucumbers. Seventy-eight genera of bacteria belonging to 47 families in four phyla, and 29 genera of fungi belonging to 24 families in the phylum Ascomycota have been cultured from sea cucumbers. Sea-cucumber-associated microorganisms produce diverse secondary metabolites with various biological activities, including cytotoxic, antimicrobial, enzyme-inhibiting, and antiangiogenic activities. In this review, we present the current list of the 145 natural products from microorganisms associated with sea cucumbers, which include primarily polyketides, as well as alkaloids and terpenoids. These results indicate the potential of the microorganisms associated with sea cucumbers as sources of bioactive natural products.

Structures of the glucocorticoid-bound adhesion receptor GPR97-Go complex.

Adhesion G-protein-coupled receptors (GPCRs) are a major family of GPCRs, but limited knowledge of their ligand regulation or structure is available1-3. Here we report that glucocorticoid stress hormones activate adhesion G-protein-coupled receptor G3 (ADGRG3; also known as GPR97)4-6, a prototypical adhesion GPCR. The cryo-electron microscopy structures of GPR97-Go complexes bound to the anti-inflammatory drug beclomethasone or the steroid hormone cortisol revealed that glucocorticoids bind to a pocket within the transmembrane domain. The steroidal core of glucocorticoids is packed against the 'toggle switch' residue W6.53, which senses the binding of a ligand and induces activation of the receptor. Active GPR97 uses a quaternary core and HLY motif to fasten the seven-transmembrane bundle and to mediate G protein coupling. The cytoplasmic side of GPR97 has an open cavity, where all three intracellular loops interact with the Go protein, contributing to the high basal activity of GRP97. Palmitoylation at the cytosolic tail of the Go protein was found to be essential for efficient engagement with GPR97 but is not observed in other solved GPCR complex structures. Our work provides a structural basis for ligand binding to the seven-transmembrane domain of an adhesion GPCR and subsequent G protein coupling.

Metformin protects high glucose­cultured cardiomyocytes from oxidative stress by promoting NDUFA13 expression and mitochondrial biogenesis via the AMPK signaling pathway.

Tissue damage in diabetes is at least partly due to elevated reactive oxygen species production by the mitochondrial respiratory chain during hyperglycemia. Sustained hyperglycemia results in mitochondrial dysfunction and the abnormal expression of mitochondrial genes, such as NADH: Ubiquinone oxidoreductase subunit A13 (NDUFA13). Metformin, an AMP­activated protein kinase (AMPK) activator, protects cardiomyocytes from oxidative stress by improving mitochondrial function; however, the exact underlying mechanisms are not completely understood. The aim of the present study was to investigated the molecular changes and related regulatory mechanisms in the response of H9C2 cardiomyocytes to metformin under high glucose conditions. H9C2 cells were subjected to CCK­8 assay to assess cell viability. Reactive oxygen species generation was measured with DCFH­DA assay. Western blotting was used to analyze the expression levels of NDUFA13, AMPK, p­AMPK and GAPDH. Reverse transcription­quantitative PCR was used to evaluate the expression levels of mitochondrial genes and transcription factors. It was observed that metformin protected H9C2 cardiomyocytes by suppressing high glucose (HG)­induced elevated oxidative stress. In addition, metformin stimulated mitochondrial biogenesis, as indicated by increased expression levels of mitochondrial genes (NDUFA1, NDUFA2, NDUFA13 and manganese superoxide dismutase) and mitochondrial biogenesis­related transcription factors [peroxisome proliferator­activated receptor­gamma coactivator­1α, nuclear respiratory factor (NRF)­1, and NRF­2] in the metformin + HG group compared with the HG group. Moreover, metformin promoted mitochondrial NDUFA13 protein expression via the AMPK signaling pathway, which was abolished by pretreatment with the AMPK inhibitor, Compound C. The results suggested that metformin protected cardiomyocytes against HG­induced oxidative stress via a mechanism involving AMPK, NDUFA13 and mitochondrial biogenesis.

Phylogenetic Analysis and Screening of Antimicrobial and Antiproliferative Activities of Culturable Bacteria Associated with the Ascidian Styela clava from the Yellow Sea, China.

Over 1,000 compounds, including ecteinascidin-743 and didemnin B, have been isolated from ascidians, with most having bioactive properties such as antimicrobial, antitumor, and enzyme-inhibiting activities. In recent years, direct and indirect evidence has shown that some bioactive compounds isolated from ascidians are not produced by ascidians themselves but by their symbiotic microorganisms. Isolated culturable bacteria associated with ascidians and investigating their potential bioactivity are an important approach for discovering novel compounds. In this study, a total of 269 bacteria were isolated from the ascidian Styela clava collected from the coast of Weihai in the north of the Yellow Sea, China. Phylogenetic relationships among 183 isolates were determined using their 16S rRNA gene sequences. Isolates were tested for antimicrobial activity against seven indicator strains, and an antiproliferative activity assay was performed to test for inhibition of human hepatocellular carcinoma Bel 7402 and human cervical carcinoma HeLa cell proliferation. Our results showed that the isolates belonged to 26 genera from 18 families in four phyla (Firmicutes, Actinobacteria, Proteobacteria, and Bacteroidetes). Bacillus and Streptomyces were the most dominant genera; 146 strains had potent antimicrobial activities and inhibited at least one of the indicator strains. Crude extracts from 29 strains showed antiproliferative activity against Bel 7402 cells with IC50 values below 500 µg·mL-1, and 53 strains showed antiproliferative activity against HeLa cells, with IC50 values less than 500 µg·mL-1. Our results suggest that culturable bacteria associated with the ascidian Styela clava may be a promising source of novel bioactive compounds.

Marinilabilia rubra sp. nov., isolated from a marine solar saltern.

A novel cherry-red-pigmented, Gram-stain-negative, gliding, facultatively anaerobic and rod-shaped bacterium, designated strain WTE16T, was isolated from a sediment sample taken from a marine solar saltern of Wendeng, China (36° 59' 56.49'' N 122° 1' 38.84'' E). The novel isolate was able to grow at 20-40 °C (optimum 33 °C), at pH 6.0-9.0 (optimum pH 7.0) and with 1.0-12.0 % (w/v) NaCl (optimum 3.0-5.0 %). Phylogenetic analysis based on 16S rRNA gene sequences indicated that the most closely related validly published species is Marinilabilia salmonicolor JCM 21150T (96.0 % similarity). Average nucleotide identity, average amino acid identity, percentage of conserved proteins and digital DNA-DNA hybridization values between strain WTE16T and Marinilabilia salmonicolor JCM 21150T were 73.8 %, 73.5 %, 63.4 % and 19.5-24.2 %, respectively. The genomic DNA G+C content of strain WTE16T was 40.8 mol%. Chemotaxonomic analysis showed that the sole respiratory quinone was menaquinone 7 (MK-7), and the major fatty acids included iso-C15 : 0 and anteiso-C15 : 0. The polar lipid profile of strain WTE16T included phosphatidylethanolamine, three unidentified phospholipids and three unidentified lipids. On the basis of its phylogenetic, phenotypic, chemotaxonomic, genotypic and genomic characteristics, strain WTE16T is suggested to represent a novel species of the genus Marinilabilia, for which the name Marinilabilia rubra sp. nov. is proposed. The type strain is WTE16T (=KCTC 62599T=MCCC 1H00311T).

Theoretical and experimental research on self-assembly system of molecularly imprinted polymers formed via chloramphenicol and methacrylic acid.

Chloramphenicol was chosen as the imprinting molecule and the methacrylic acid was chosen as the functional monomer to prepare molecularly imprinted polymers. Ethylene glycol dimethacrylate, pentaerythritol triacrylate, and trimethylolpropane trimethylacrylate were used as the cross-linking agents, respectively. The interaction processes between chloramphenicol and methacrylic acid were simulated by using the ωB97XD/6-31G (d,p) method. The self-assembled configuration, bonding sites, binding number, binding energy, and interaction principle of stable complex formed by chloramphenicol and methacrylic acid with different molar ratios have been studied. The selectivity of the most stable complex formed from chloramphenicol and methacrylic acid was discussed with the thiamphenicol and florfenicol as the analogues of chloramphenicol. The results showed that chloramphenicol and methacrylic acid were interacted through the hydrogen bonds. When the molar ratio was 1:10 and pentaerythritol triacrylate as the cross-linking agent, the ordered complex formed by chloramphenicol and methacrylic acid has the largest amount of hydrogen bonds and the lowest binding energy. Scatchard analysis showed that the maximum apparent adsorption capacity was 173.3 mg/g (0.536 mol/g), and the selection factor of florfenicol was the largest. This study provides a reliable theoretical and experimental basis for the design, preparation, and characterization of chloramphenicol molecularly imprinted polymers.

Biological and Chemical Diversity of Ascidian-Associated Microorganisms.

Ascidians are a class of sessile filter-feeding invertebrates, that provide unique and fertile niches harboring various microorganisms, such as bacteria, actinobacteria, cyanobacteria and fungi. Over 1000 natural products, including alkaloids, cyclic peptides, and polyketides, have been isolated from them, which display diverse properties, such as antibacterial, antifungal, antitumor, and anti-inflammatory activities. Strikingly, direct evidence has confirmed that ~8% of natural products from ascidians are actually produced by symbiotic microorganisms. In this review, we present 150 natural products from microorganisms associated with ascidians that have been reported up to 2017.

Mammillary body regulates state-dependent fear by alternating cortical oscillations.

State-dependent memory describes a phenomenon that memory will be efficiently retrieved only when the brain state during retrieval matches the state during encoding. While a variety of psychoactive drugs, such as ethanol, cocaine, morphine and NMDA receptor antagonists, are able to induce state-dependent memory, the biological hallmark of brain state and neural mechanism of its regulation are still unknown. In this study, we found that MK-801 enhanced delta oscillations in awake mice, representing a drug-induced brain state, in which fear memory could only be successfully retrieved when the same drug condition was presented. We identified a key nucleus, mammillary body (MB), which regulates the specific brain state associated with MK-801. Chemogenetic silencing of MB neurons enhanced cortical delta oscillations and generated state-dependent memory. Moreover, optogenetic reconstitution of delta oscillations alone facilitated retrieval of fear memory encoded under MK-801. Our results indicated that delta oscillations in awake animals defined a specific brain state, in which memory formed is inaccessible under the normal condition, shining light on the neural mechanism underlying the fluctuation of memory retrieval and the role of MB in memory encoding and recall.

Integrated bioinformatic analysis unveils significant genes and pathways in the pathogenesis of supratentorial primitive neuroectodermal tumor.

PURPOSE: This study aimed to explore significant genes and pathways involved in the pathogenesis of supratentorial primitive neuroectodermal tumor (sPNET). MATERIALS AND METHODS: Gene expression profile of GSE14295 was downloaded from publicly available Gene Expression Omnibus (GEO) database. Differentially expressed genes (DEGs) were screened out in primary sPNET samples compared with normal fetal and adult brain reference samples (sPNET vs fetal brain and sPNET vs adult brain). Pathway enrichment analysis of these DEGs was conducted, followed by protein-protein interaction (PPI) network construction and significant module selection. Additionally, transcription factors (TFs) regulating the common DEGs in the two comparison groups were identified, and the regulatory network was constructed. RESULTS: In total, 526 DEGs (99 up- and 427 downregulated) in sPNET vs fetal brain and 815 DEGs (200 up- and 615 downregulated) in sPNET vs adult brain were identified. DEGs in sPNET vs fetal brain and sPNET vs adult brain were associated with calcium signaling pathway, cell cycle, and p53 signaling pathway. CDK1, CDC20, BUB1B, and BUB1 were hub nodes in the PPI networks of DEGs in sPNET vs fetal brain and sPNET vs adult brain. Significant modules were extracted from the PPI networks. In addition, 64 upregulated and 200 downregulated overlapping DEGs were identified in both sPNET vs fetal brain and sPNET vs adult brain. The genes involved in the regulatory network upon overlapping DEGs and the TFs were correlated with calcium signaling pathway. CONCLUSION: Calcium signaling pathway and several genes (CDK1, CDC20, BUB1B, and BUB1) may play important roles in the pathogenesis of sPNET.