Cdk5 is required for the neuroprotective effect of transforming growth factor-ß1 against cerebral ischemia-reperfusion.

Transforming Growth Factor ß1 (TGF-ß1), a well-known neuroprotective and neurotrophic factor in the central nervous system, is also involved in the repair process responses after ischemia-reperfusion injury. Herein, we found that TGF-ß1 enhanced Cdk5 expression while decreased Tunel-positive cells compared with the ischemia group, and roscovitine(Cdk5 inhibitor) treatment could blunt these effects. In vitro study, TGF-ß1 facilitated Cdk5/p35 complex, the proliferation, neurite growth and differentiation of PC12 cells, effects of which could be blunted by roscovitine and Cdk5 silencing. Moreover, ERK1/2 inhibitor SCH772984 abrogated the effects of TGF- ß1 on Cdk5 and Bax levels. Taken together, we conclude that Cdk5 contributes to the neuroprotective function of TGF- ß1 via ERK1/2 signaling.

Shewanella gelidii sp. nov., isolated from the red algae Gelidium amansii, and emended description of Shewanella waksmanii.

A novel Gram-stain-negative, straight or slightly curved rod-shaped, non-spore-forming, facultatively anaerobic bacterium with a single polar flagellum, designated RZB5-4T, was isolated from a sample of the red algae Gelidium amansii collected from the coastal region of Rizhao, PR China (119.625° E 35.517° N). The organism grew optimally between 24 and 28 °C, at pH 7.0 and in the presence of 2-3 % (w/v) NaCl. The strain required seawater or artificial seawater for growth, and NaCl alone did not support growth. Strain RZB5-4T contained C16 : 1ω7c and/or C16 : 1ω6c, C16 : 0 and iso-C15 : 0 as the dominant fatty acids. The respiratory quinones detected in strain RZB5-4T were ubiquinone 7, ubiquinone 8, menaquinone 7 and methylmenaquinone 7. The polar lipids of strain RZB5-4T comprised phosphatidylethanolamine, phosphatidylglycerol, phosphatidylmonomethylethanolamine, one unidentified glycolipid, one unidentified phospholipid and one unknown lipid. The DNA G+C content of strain RZB5-4T was 47 mol %. Phylogenetic analysis based on 16S rRNA and gyrase B (gyrB) gene sequences showed that strain RZB5-4T belonged to the genus Shewanella, clustering with Shewanella waksmanii ATCC BAA-643T. Strain RZB5-4T exhibited the highest 16S rRNA gene sequence similarity value (96.6 %) and the highest gyrB gene sequence similarity value (80.7 %), respectively, to S. waksmanii ATCC BAA-643T. On the basis of polyphasic analyses, strain RZB5-4T represents a novel species of the genus Shewanella, for which the name Shewanella gelidii sp. nov. is proposed. The type strain is RZB5-4T (=JCM 30804T=KCTC 42663T=MCCC 1K00697T).

Methylocystis dominates methane oxidation in glacier foreland soil at elevated temperature.

Methane-oxidizing bacteria (methanotrophs) play an important role in mitigating methane emissions in various ecological environments, including cold regions. However, the response of methanotrophs in these cold environments to extreme temperatures above the in-situ temperature has not been thoroughly explored. Therefore, this study collected soil samples from Longxiazailongba (LXZ) and Qiangyong (QY) glacier forelands and incubated them with 13CH4 at 35°C under different soil water conditions. The active methanotroph populations were identified using DNA stable isotope probing (DNA-SIP) and high throughput sequencing techniques. The results showed that the methane oxidation potential in LXZ and QY glacier foreland soils was significantly enhanced at an unusually high temperature of 35°C during microcosm incubations, where abundant substrate (methane and oxygen) was provided. Moreover, the influence of soil water conditions on this potential was observed. Interestingly, Methylocystis, a type II and mesophilic methanotroph, was detected in the unincubated in-situ soil samples and became the active and dominant methanotroph in methane oxidation at 35°C. This suggests that Methylocystis can survive at low temperatures for a prolonged period and thrive under suitable growth conditions. Furthermore, the presence of mesophilic methanotrophs in cold habitats could have potential implications for reducing greenhouse gas emissions in warming glacial environments.

Lipid-based nanoparticles to address the limitations of GBM therapy by overcoming the blood-brain barrier, targeting glioblastoma stem cells, and counteracting the immunosuppressive tumor microenvironment.

Glioblastoma multiforme (GBM) is the most common primary malignant brain tumor, characterized by high heterogeneity, strong invasiveness, poor prognosis, and a low survival rate. A broad range of nanoparticles have been recently developed as drug delivery systems for GBM therapy owing to their inherent size effect and ability to cross the blood-brain barrier (BBB). Lipid-based nanoparticles (LBNPs), such as liposomes, solid lipid NPs (SLNs), and nano-structured lipid carriers (NLCs), have emerged as the most promising drug delivery system for the treatment of GBM because of their unique size, surface modification possibilities, and proven bio-safety. In this review, the main challenges of the current clinical treatment of GBM and the strategies on how novel LBNPs overcome them were explored. The application and progress of LBNP-based drug delivery systems in GBM chemotherapy, immunotherapy, and gene therapy in recent years were systematically reviewed, and the prospect of LBNPs for GBM treatment was discussed.

Methylomonadaceae was the active and dominant methanotroph in Tibet lake sediments.

Methane (CH4), an important greenhouse gas, significantly impacts the local and global climate. Our study focused on the composition and activity of methanotrophs residing in the lakes on the Tibetan Plateau, a hotspot for climate change research. Based on the field survey, the family Methylomonadaceae had a much higher relative abundance in freshwater lakes than in brackish and saline lakes, accounting for ~92% of total aerobic methanotrophs. Using the microcosm sediment incubation with 13CH4 followed by high throughput sequencing and metagenomic analysis, we further demonstrated that the family Methylomonadaceae was actively oxidizing CH4. Moreover, various methylotrophs, such as the genera Methylotenera and Methylophilus, were detected in the 13C-labeled DNAs, which suggested their participation in CH4-carbon sequential assimilation. The presence of CH4 metabolism, such as the tetrahydromethanopterin and the ribulose monophosphate pathways, was identified in the metagenome-assembled genomes of the family Methylomonadaceae. Furthermore, they had the potential to adapt to oxygen-deficient conditions and utilize multiple electron acceptors, such as metal oxides (Fe3+), nitrate, and nitrite, for survival in the Tibet lakes. Our findings highlighted the predominance of Methylomonadaceae and the associated microbes as active CH4 consumers, potentially regulating the CH4 emissions in the Tibet freshwater lakes. These insights contributed to understanding the plateau carbon cycle and emphasized the significance of methanotrophs in mitigating climate change.

Distinct responses of soil methanotrophy in hummocks and hollows to simulated glacier meltwater and temperature rise in Tibetan glacier foreland.

Glacier foreland soils are known to be essential methane (CH4) consumers. However, global warming and increased glacier meltwater have turned some foreland meadows into swamp meadows. The potential impact of this change on the function of foreland soils in methane consumption remains unclear. Therefore, we collected Tibetan glacier foreland soils in the non-melting season from typical microtopography in swamp meadows (hummock and hollow). Three soil moisture conditions (moist, saturated, and submerged) were set by adding glacier runoff water. Soil samples were then incubated in the laboratory for two weeks at 10 °C and 20 °C. About 5 % of 13CH4/12CH4 was added to the incubation bottles, and daily methane concentrations were measured. DNA stable isotope probing (DNA-SIP) and high-throughput sequencing were combined to target the active methanotroph populations. The results showed that type Ia methanotrophs, including Crenothrix, Methylobacter, and an unclassified Methylomonadaceae cluster, actively oxidized methane at 10 °C and 20 °C. There were distinct responses of methanotrophs to soil moisture rises in hummock and hollow soils, resulting in different methane oxidation potentials. In both hummock and hollow soils, the methane oxidation potential was positively correlated with temperature. Furthermore, saturated hummock soils exhibited the highest methane oxidation potential and methanotroph populations, while submerged hollow soils had the lowest. This suggests that the in-situ hummock soils, generally saturated with water, are more essential than in-situ hollows, typically submerged in water, for alleviating the global warming potential of swamp meadows in the Tibetan glacier foreland during the growing season.

Vertical variations in microbial diversity, composition, and interactions in freshwater lake sediments on the Tibetan plateau.

Microbial communities in freshwater lake sediments exhibit a distinct depth-dependent variability. Further exploration is required to understand their biodiversity pattern and microbial interactions in vertical sediments. In this study, sediment cores from two freshwater lakes, Mugecuo (MGC) and Cuopu (CP), on the Tibetan plateau were sampled and subsequently sliced into layers at a depth of every centimeter or half a centimeter. Amplicon sequencing was used to analyze the composition, diversity, and interaction of microbial communities. Results showed that sediment samples of both lakes could be clustered into two groups at a sediment depth of about 20 cm, with obvious shifts in microbial community compositions. In lake MGC, the richness component dominated ß-diversity and increased with depth, indicating that the microbial communities in the deep layer of MGC was selected from the surface layer. Conversely, the replacement component dominated ß-diversity in CP, implying a high turnover rate in the surface layer and inactive seed banks with a high variety in the deep layer. A co-occurrence network analysis showed that negative microbial interactions were prevalent in the surface layers with high nutrient concentrations, while positive microbial interactions were more common in the deep layers with low nutrient concentrations, suggesting that microbial interactions are influenced by nutrient conditions in the vertical sediments. Additionally, the results highlight the significant contributions of abundant and rare taxa to microbial interactions and vertical fluctuations of ß-diversity, respectively. Overall, this work deepens our understanding of patterns of microbial interactions and vertical fluctuation in ß-diversity in lake sediment columns, particularly in freshwater lake sediments from the Tibetan plateau.

The lncRNA NEAT1/miRNA-766-5p/E2F3 Regulatory Axis Promotes Prostate Cancer Progression.

BACKGROUND: Prostate cancer (PCa) is one of the most common malignancies in men. Increasing evidence has demonstrated that dysregulation of long noncoding RNAs (lncRNAs) is closely related to carcinogenesis and cancer progression. lncRNA NEAT1 has recently been identified as a carcinogenic regulator of multiple cancers; however, the role of NEAT1 on PCa is still poorly understood. METHODS: Kaplan-Meier was conducted to determine the overall survival rate in PCa patients with aberrant NEAT1 levels. qRT-PCR analysis was performed to detect expressions of NEAT1 and miR-766-5p in tissues and cells. In addition, CCK-8, colony formation, flow cytometry analysis, wound healing, and transwell assay were conducted to determine cell proliferation, cell arrest, apoptosis, migration, and invasion. The western blot assay was utilized to determine E2F3 and cell growth-related proteins. The relationship between NEAT1 and miR-766-5p or miR-766-5p and E2F3 was verified by correlation analysis and dual-luciferase reporter assay. RESULTS: Here, we find that NEAT1 is overexpressed in PCa tissues and cell lines. Besides, silencing of NEAT1 inhibits cell proliferation, invasion, and migration and promotes cell apoptosis and cell cycle arrest. Further mechanistic studies find that NEAT1 sponges miR-766-5p, and miRNA-766-5p is negatively correlated with the expression of NEAT1. In addition, the functional experiment shows that upregulation of miRNA-766-5p inhibits PCa proliferation, migration, and invasion. Furthermore, E2F transcription factor 3 (E2F3) is testified to be the downstream target gene of miRNA-766-5p. Finally, the rescue experiment revealed that miRNA-766-5p inhibition largely restores NEAT1 downregulation-mediated function on PCa progression, while E2F3 knockdown partly removes the effects of miRNA-766-5p inhibitor. CONCLUSIONS: In conclusion, NEAT1 facilitates PCa progression by targeting the miRNA-766-5p/E2F3 axis.

Properties of sediment dissolved organic matter respond to eutrophication and interact with bacterial communities in a plateau lake.

Sediment dissolved organic matter (DOM) in inland waters is commonly affected by environmental changes. However, knowledge about how sediment DOM responds to eutrophication and the associations between sediment DOM and bacterial communities requires further investigation. We selected a sediment core from Dianchi Lake (China) that was dated from 1864 to 2019 by the activity of radionuclides (210Pb and 137Cs). δ13CDOC changes fit well with the historical record that heavy eutrophic status in Dianchi Lake were observed since 1980s. Large amounts of dissolved organic carbon (DOC), chromophoric (CDOM) and fluorescent (FDOM) DOM accumulated at the top of the sediments during the eutrophication period (1982-present). The additional algae sources with a higher degradation rate altered the composition, aromaticity and humification of DOM. After long-term mineralization, the remaining DOM became more and more recalcitrant and kept a relatively stable level at older sediments. A co-occurrence network analysis revealed that Proteobacteria, Chloroflexi, Acidobacteriota, Bacteroidota and Desulfobacterota were the most abundant species at the phylum level and clustered into three primary modules. Different microbes shared unique preferences for niches, causing a heterogeneous bacterial distribution at different depths. We conducted Spearman's correlation and redundancy analysis (RDA) to explore potential interactions between bacterial community and sediment DOM. The richness and diversity of bacterial communities were positively related to DOM content, suggesting abundant DOM can produce more available resources for bacteria. RDA results showed some specific species might modify DOM composition and structure. This study suggests that sediment DOM properties were regulated by source transformation during eutrophication, and emphasizes the importance of microbial role on sediment biogeochemical process.

Immobilization of laccase by 3D bioprinting and its application in the biodegradation of phenolic compounds.

Due to the increasing quantities of phenolic compounds present in wastewater, the use of enzymatic degradation with the laccase has attracted much attention as a green option for their removal. In this work, we developed a novel immobilization technology using 3D bioprinting for laccase immobilization. The hydrogel mechanism properties were optimized by experimenting with different component ratios of sodium alginate (SA), acrylamide (AM), and hydroxyapatite (HA). The improved mechanism properties were validated by morphology pictures and rheology characteristics. The optimal AM:HA:SA ratio was determined to be 4:1.2:1. We then employed an extrusion-based bioprinting technique to prepare the immobilized laccase. The substrate conversion was increased with the addition of HA, which improved the permeability of the matrix, and proved to be suitable for immobilization. The resulting immobilized laccase was used for the biodegradation of p-chlorophenol. The effects of the initial substrate concentration, pH, and temperature were evaluated. The immobilized laccase exhibited good storage stability and reusability, retaining over 80% of its initial activity after 72 h of storage, and was able to be reused for seven batches. These results highlight that the immobilized laccase prepared by 3D bioprinting has great potential for use in the biodegradation of phenolic compounds.

LncRNA FOXD3-AS1 Mediates AKT Pathway to Promote Growth and Invasion in Hepatocellular Carcinoma Through Regulating RICTOR.

Background: Hepatocellular carcinoma (HCC) has high morbidity and mortality, but current therapeutic methods cannot effectively improve patient's prognosis. FOXD3-AS1, a new identified long noncoding RNA, is dysregulated in several cancers and functions as a carcinogenic or tumor-suppressor factor. However, the function of FOXD3-AS1 in HCC has not been reported. Materials and Methods: Quantitative real time-polymerase chain reaction was applied to evaluate the expression of FOXD3-AS1 in HCC tissues and cell lines. miRDB and TargetScan websites were utilized to predict the interaction network of FOXD3-AS1 as a competing endogenous RNA. The interaction was confirmed by luciferase reporter assay and RNA binding protein immunoprecipitation (RIP) assay. The effect of FOXD3-AS1 on HCC cells (Huh6) were measured by cell counting kit (CCK)-8, BrdU cell proliferation assay, Transwell invasion assay, and wound healing assay. Results: FOXD3-AS1 was overexpressed in HCC, and HCC patients with the high level of FOXD3-AS1 had a poor prognosis. In addition, FOXD3-AS1 knockdown considerably inhibited the proliferation, migration, and invasion of Huh6 cells. Besides, FOXD3-AS1 functioned as a sponge of miR-335, and RICTOR was a direct target gene of miR-335. Furthermore, FOXD3-AS1 could enhance the level of RICTOR through sponging miR-335. Moreover, the knockdown of FOXD3-AS1 could competitively bind with miR-335 to suppress RICTOR expression, thereby inhibiting the growth of Huh6 cells through the deactivation of AKT signaling pathway. Conclusions: FOXD3-AS1 is crucial for the tumorigenesis and progression of HCC. The interaction among FOXD3-AS1, miR-335, and RICTOR provides a novel insight for understanding the molecular mechanism of HCC, and FOXD3-AS1, miR-335, and RICTOR can be regarded as the potential targets for HCC treatment.

Exploration of a N-terminal disulfide bridge to improve the thermostability of a GH11 xylanase from Aspergillus niger.

To improve the thermostability of xylanase XynZF-2 from Aspergillus niger XZ-3S, a disulfide bridge was introduced in the N-terminal domains by site-directed mutagenesis (V1C and E27C). Simultaneously, the active sites of XynZF-2 were predicted by bioinformatics software and verified by site-directed mutagenesis (E103D and E194D). The mutated active sites xynED- and the mutated disulfide bridge xynDC-encoding genes were constructed and expressed in Escherichia coli BL21 (DE3). Compared to the native xylanase, it was found that the residual activity of the mutated XynED was 0.17%. The optimum temperature of the variant XynDC was increased to 45°C from 40°C of XynZF-2. After treatment at 40°C for 60 min, the variant XynDC retained 66.77% of their original activity, while the XynZF-2 retained about 44.36% residual activity. t1/2(45°C) of the variant XynDC also increased from 7 min to 14 min. The results of the mutated xylanases indicated that the active center of XynZF-2 mainly consisted of two catalytic residues (Glu103 and Glu194), and the introduction of a disulfide bridge in the N-terminal domains can improve the thermostability of XynZF-2.

Metabolic adaption of ethanol-tolerant Clostridium thermocellum.

Clostridium thermocellum is a major candidate for bioethanol production via consolidated bioprocessing. However, the low ethanol tolerance of the organism dramatically impedes its usage in industry. To explore the mechanism of ethanol tolerance in this microorganism, systematic metabolomics was adopted to analyse the metabolic phenotypes of a C. thermocellum wild-type (WT) strain and an ethanol-tolerant strain cultivated without (ET0) or with (ET3) 3% (v/v) exogenous ethanol. Metabolomics analysis elucidated that the levels of numerous metabolites in different pathways were changed for the metabolic adaption of ethanol-tolerant C. thermocellum. The most interesting phenomenon was that cellodextrin was significantly more accumulated in the ethanol-tolerant strain compared with the WT strain, although cellobiose was completely consumed in both the ethanol-tolerant and wild-type strains. These results suggest that the cellodextrin synthesis was active, which might be a potential mechanism for stress resistance. Moreover, the overflow of many intermediate metabolites, which indicates the metabolic imbalance, in the ET0 cultivation was more significant than in the WT and ET3 cultivations. This indicates that the metabolic balance of the ethanol-tolerant strain was adapted better to the condition of ethanol stress. This study provides additional insight into the mechanism of ethanol tolerance and is valuable for further metabolic engineering aimed at higher bioethanol production.

Simultaneous determination of amino acids and carbohydrates in culture media of Clostridium thermocellum by valve-switching ion chromatography.

An improved method for the simultaneous determination of 20 amino acids and 7 carbohydrates using one-valve switching after injection, ion chromatography, and integrated pulsed amperometric detection is proposed. The resolution of the amino acids and carbohydrates in the cation trap column was investigated. In addition, parameters including flow liquid type, flow rate, concentration, and valve-switch timing were optimized. The method is time-saving, effective, and accurate for the simultaneous separation of amino acids and carbohydrates, with a mean correlation coefficient of >0.99 and repeatability of 0.5-4.6% for eight replicates. The method was successfully applied in the analysis of amino acids and carbohydrates in aseptic media and in extracellular culture media of three phenotypes of Clostridium thermocellum.