Lipidomic and transcriptomic analysis of the increase in eicosapentaenoic acid under cobalamin deficiency of Schizochytrium sp.

Schizochytrium sp. is a heterotrophic microorganism capable of accumulating polyunsaturated fatty acids and has achieved industrial production of docosahexaenoic acid (DHA). It also has the potential for eicosapentaenoic acid (EPA) production. In this study, it was found that the cell growth, lipid synthesis and fatty acid composition of Schizochytrium sp. were significantly affected by the level of cobalamin in the medium, especially with regard to the content of EPA in the fatty acids. The content of EPA in the fatty acids increased 17.91 times, reaching 12.00%, but cell growth and lipid synthesis were significantly inhibited under cobalamin deficiency. The response mechanism for this phenomenon was revealed through combined lipidomic and transcriptomic analysis. Although cell growth was inhibited under cobalamin deficiency, the genes encoding key enzymes in central carbon metabolism were still up-regulated to provide precursors (Acetyl-CoA) and reducing power (NADPH) for the synthesis and accumulation of fatty acids. Moreover, the main lipid subclasses observed during cobalamin deficiency were glycerolipids (including glycerophospholipids), with EPA primarily distributed in them. The genes involved in the biosynthesis of these lipid subclasses were significantly up-regulated, such as the key enzymes in the Kennedy pathway for the synthesis of triglycerides. Thus, this study provided insights into the specific response of Schizochytrium sp. to cobalamin deficiency and identified a subset of new genes that can be engineered for modification.

Comparative metabolic profiling of mycelia, fermentation broth, spore powder and fruiting bodies of Ophiocordyceps gracilis by LC-MS/MS.

INTRODUCTION: Ophiocordyceps gracilis, a type of edible and medicinal fungus, exhibits multiple health-promoting effects. Due to the scarcity of natural O. gracilis, artificial cultures have been developed as its substitutes. However, lacking comprehension of the metabolite composition of cultures limits its utilisation. OBJECTIVE: This research aimed to evaluate the nutritional and medicinal value of four cultures of O. gracilis by analysing their metabolite composition. In addition, metabolic pathways in mycelia and fruiting bodies were analysed to explore fruiting body formation mechanism at metabolic level. METHOD: The mycelia, fermentation broth, spore powder and fruiting bodies of O. gracilis were cultivated in this study. Their metabolite composition was compared using an untargeted metabolomics approach based on liquid chromatography-tandem mass spectrometry (LC-MS/MS). RESULTS: Principal component analysis (PCA) and orthogonal projections to latent structures discriminant analysis (OPLS-DA) showed that the four cultures have noticeable differences in metabolite composition. A total of 612 metabolites were identified, among which 159 metabolites showed significant differences, and these differential metabolites were classified into 13 categories. The metabolites in the fruiting bodies were the most abundant compared with other cultures. However, each culture had its own advantages and significantly accumulates some active metabolites respectively. Pearson's correlation analysed the mutual relationship among metabolites. In addition, seven metabolic pathways were closely related to fruiting body formation, such as "Biosynthesis of plant secondary metabolites", "amino acids metabolism", "tricarboxylic acid (TCA) cycle". CONCLUSION: This study offered a reference to mycelia, fermentation broth, spore powder and fruiting bodies of O. gracilis as health-promoting functional foods and medicine.

Development of a novel microplate for high-throughput screening and optimization of DHA producing strains based on CFD technology.

Microtiter plates are suitable for screening and process development of most microorganisms. They are currently the container of choice for high-throughput and small-scale microbial culture, but require optimization for specific work. In this research, a novel type of microtiter plate was developed using computational fluid dynamics (CFD) technology. The new plate provided high oxygen supply and optimal mixing effects for the fermentation culture of docosahexaenoic acid (DHA) producing strains, surpassing the conventional method of strain screening with shake flasks, which was insufficient. The shape of the microtiter plate was modified, and baffles were introduced to improve mass transfer and oxygen supply effects in the vibrating bioreactor. CFD technology was used to model the new plate's characteristics, establishing the superiority of hexagonal microtiter plates with six baffles. Parameters in the incubation process, such as vibration frequency and liquid load, were optimized, and the final result achieved an oxygen transfer coefficient (KL a) of 0.61 s-1 and a volume power input of 2364 w m-3 , which was four to five times better than the original 96-well plate. The culture results optimized by the model were also verified. Therefore, this new microtiter plate provides a powerful tool for future high-throughput screening of strains.

Integration of Physiological, Transcriptomic and Metabolomic Reveals Molecular Mechanism of Paraisaria dubia Response to Zn2+ Stress.

Utilizing mycoremediation is an important direction for managing heavy metal pollution. Zn2+ pollution has gradually become apparent, but there are few reports about its pollution remediation. Here, the Zn2+ remediation potential of Paraisaria dubia, an anamorph of the entomopathogenic fungus Ophiocordyceps gracilis, was explored. There was 60% Zn2+ removed by Paraisaria dubia mycelia from a Zn2+-contaminated medium. To reveal the Zn2+ tolerance mechanism of Paraisaria dubia, transcriptomic and metabolomic were executed. Results showed that Zn2+ caused a series of stress responses, such as energy metabolism inhibition, oxidative stress, antioxidant defense system disruption, autophagy obstruction, and DNA damage. Moreover, metabolomic analyses showed that the biosynthesis of some metabolites was affected against Zn2+ stress. In order to improve the tolerance to Zn2+ stress, the metabolic mechanism of metal ion transport, extracellular polysaccharides (EPS) synthesis, and microcycle conidiation were activated in P. dubia. Remarkably, the formation of microcycle conidiation may be triggered by reactive oxygen species (ROS) and mitogen-activated protein kinase (MAPK) signaling pathways. This study supplemented the gap of the Zn2+ resistance mechanism of Paraisaria dubia and provided a reference for the application of Paraisaria dubia in the bioremediation of heavy metals pollution.

Development of a green fermentation strategy with resource cycle for the docosahexaenoic acid production by Schizochytrium sp.

The fermentation production of docosahexaenoic acid (DHA) is an industrial process with huge consumption of freshwater resource and nutrient, such as carbon sources and nitrogen sources. In this study, seawater and fermentation wastewater were introduced into the fermentation production of DHA, which could solve the problem of fermentation industry competing with humans for freshwater. In addition, a green fermentation strategy with pH control using waste ammonia, NaOH and citric acid as well as FW recycling was proposed. It could provide a stable external environment for cell growth and lipid synthesis while alleviating the dependence on organic nitrogen sources of Schizochytrium sp. It was proved that this strategy has good industrialization potential for DHA production, and the biomass, lipid and DHA yield reached to 195.8 g/L, 74.4 g/L and 46.4 g/L in 50 L bioreactor, respectively. This study provides a green and economic bioprocess technology for DHA production by Schizochytrium sp.

Identification of novel cuproptosis-related lncRNA signatures to predict the prognosis and immune microenvironment of breast cancer patients.

Background: Cuproptosis is a new modality of cell death regulation that is currently considered as a new cancer treatment strategy. Nevertheless, the prognostic predictive value of cuproptosis-related lncRNAs in breast cancer (BC) remains unknown. Using cuproptosis-related lncRNAs, this study aims to predict the immune microenvironment and prognosis of BC patients. and develop new therapeutic strategies that target the disease. Methods: The Cancer Genome Atlas (TCGA) database provided the RNA-seq data along with the corresponding clinical and prognostic information. Univariate and multivariate Cox regression analyses were performed to acquire lncRNAs associated with cuproptosis to establish predictive features. The Kaplan-Meier method was used to calculate the overall survival rate (OS) in the high-risk and low-risk groups. High risk and low risk gene sets were enriched to explore functional discrepancies among risk teams. The mutation data were analyzed using the "MAFTools" r-package. The ties of predictive characteristics and immune status had been explored by single sample gene set enrichment analysis (ssGSEA). Last, the correlation between predictive features and treatment condition in patients with BC was analyzed. Based on prognostic risk models, we assessed associations between risk subgroups and immune scores and immune checkpoints. In addition, drug responses in at-risk populations were predicted. Results: We identified a set of 11 Cuproptosis-Related lncRNAs (GORAB-AS1, AC 079922.2, AL 589765.4, AC 005696.4, Cytor, ZNF 197-AS1, AC 002398.1, AL 451085.3, YTH DF 3-AS1, AC 008771.1, LINC 02446), based on which to construct the risk model. In comparison to the high-risk group, the low-risk patients lived longer (p < 0.001). Moreover, cuproptosis-related lncRNA profiles can independently predict prognosis in BC patients. The AUC values for receiver operating characteristics (ROC) of 1-, 3-, and 5-year risk were 0.849, 0.779, and 0.794, respectively. Patients in the high-risk group had lower OS than those in the low-risk group when they were divided into groups based on various clinicopathological variables. The tumor burden mutations (TMB) correlation analysis showed that high TMB had a worse prognosis than low-TMB, and gene mutations were found to be different in high and low TMB groups, such as PIK3CA (36% versus 32%), SYNE1 (4% versus 6%). Gene enrichment analysis indicated that the differential genes were significantly concentrated in immune-related pathways. The predictive traits were significantly correlated with the immune status of BC patients, according to ssGSEA results. Finally, high-risk patients showed high sensitivity in anti-CD276 immunotherapy and conventional chemotherapeutic drugs such as imatinib, lapatinib, and pazopanib. Conclusion: We successfully constructed of a cuproptosis-related lncRNA signature, which can independently predict the prognosis of BC patients and can be used to estimate OS and clinical treatment outcomes in BRCA patients. It will serve as a foundation for further research into the mechanism of cuproptosis-related lncRNAs in breast cancer, as well as for the development of new markers and therapeutic targets for the disease.

Comprehensive analysis of immune ferroptosis gene in renal clear cell carcinoma: prognosis and influence of tumor microenvironment.

OBJECTIVE: We conducted an in-depth study of the immune system and ferroptosis to identify prognostic biomarkers and therapeutic targets for renal clear cell carcinoma. METHODS: Immune ferroptosis-related differentially expressed genes (IFR-DEGs) were selected from The Cancer Genome Atlas (TCGA). A lasso-Cox risk scoring model was established; its prognostic value was determined using prognostic analysis and single multivariate Cox analysis. Model genes were subjected to subcellular fluorescence localization, mRNA and protein expression analyses, and single-cell RNA sequencing localization analysis. Risk score was analyzed using the immune score, immune infiltrating cell correlation, immune checkpoint, TIDE, and drug sensitivity. RESULTS: A total of 103 IFR-DEGs were identified; a risk model comprising ACADSB, CHAC1, LURAP1L, and PLA2G6 was established. The survival curve, single multivariate Cox regression, and receiver operating characteristic (ROC) curve analysis showed that the model had good predictive ability (p < 0.05). It was also validated using the validation set and total cohort. Subcellular fluorescence localization revealed that ACADSB, CHAC1, and PLA2G6 were distributed in the cytoplasm and LURAP1L in the nucleus. The mRNA and protein expression trends were consistent. Single-cell RNA sequencing mapping revealed that ACADSB was enriched in distal tubule cell clusters. In the Kidney renal clear cell carcinoma (KIRC) mutation correlation analysis, 1.56% of the patients were found to have genetic alterations; The Spearman correlation analysis of model gene mutations showed that ACADSB was positively correlated with LURAP1L, which may have a synergistic effect; it was negatively correlated with CHAC1 and PLA2G6, and CHAC1 was negatively correlated with LURAP1L, which may have an antagonistic effect. Model and immune correlation analyses found that high-risk patients had significantly higher levels of CD8+ T cells, regulatory T cells (Tregs), immune checkpoints, immune scores, and immune escape than those in low-risk patients. High-risk patients had a higher susceptibility to small-molecule drugs. CONCLUSION: A novel prognostic model of immune ferroptosis-related genes (ACADSB, CHAC1, LURAP1L, and PLA2G6), which plays an important role in immune infiltration, microenvironment, and immune escape, was constructed. It effectively predicts the survival of patients with KIRC.

Optimization and Scale-Up of Fermentation Processes Driven by Models.

In the era of sustainable development, the use of cell factories to produce various compounds by fermentation has attracted extensive attention; however, industrial fermentation requires not only efficient production strains, but also suitable extracellular conditions and medium components, as well as scaling-up. In this regard, the use of biological models has received much attention, and this review will provide guidance for the rapid selection of biological models. This paper first introduces two mechanistic modeling methods, kinetic modeling and constraint-based modeling (CBM), and generalizes their applications in practice. Next, we review data-driven modeling based on machine learning (ML), and highlight the application scope of different learning algorithms. The combined use of ML and CBM for constructing hybrid models is further discussed. At the end, we also discuss the recent strategies for predicting bioreactor scale-up and culture behavior through a combination of biological models and computational fluid dynamics (CFD) models.

Social capital and health-protective behavior intentions in an influenza pandemic.

Health-protective behaviors, such as receiving a vaccine, wearing a face mask, and washing hands frequently, can reduce the risk of contracting influenza. However, little is known about how social capital may influence health-protective behavior in the general population. This study examined whether each of the social capital dimensions (bonding, bridging, and linking) contributed to the intention to adopt any of the health-protective behaviors in an influenza pandemic. The data of this study were from the 2014 Taiwan Social Change Survey. A stratified, three-stage probability proportional-to-size sampling from across the nation, was conducted to select adults aged 20 years and older (N = 1,745). Bonding social capital was measured by the frequency of neighborly contact and support. Bridging social capital was measured based on association membership. Linking social capital was measured according to general government trust and trust in the government's capacity to counter an influenza pandemic. Binary logistic regressions were used to assess the multivariate associations between social capital and behavioral intention. The study results indicate that social capital may influence the response to influenza pandemic. Specifically, the intention to receive a vaccine and to wash hands more frequently were associated with the linking dimension and the bonding dimension of social capital, while the intention to wear a face mask was associated with all forms of social capital. The findings of this study suggest that government credibility and interpersonal networks may play a crucial role in health-protective behavior. This study provides new insights into how to improve the effectiveness of influenza prevention campaigns.

Reducing the fear of falling among community-dwelling elderly adults through cognitive-behavioural strategies and intense Tai Chi exercise: a randomized controlled trial.

AIM: To examine the effectiveness of cognitive-behavioural strategies with/without intense Tai Chi exercise in reducing fear of falling among community-dwelling elderly adults. Background. Fear of falling is a major health problem among community-dwelling older persons. The prevalence of this fear ranges from 29% to 77%, indicating the importance of developing effective strategies to reduce fear of falling among elderly adults. METHODS: Data were collected from January to December 2007. A randomized controlled trial with three groups (control, cognitive-behavioural and cognitive-behavioural with Tai Chi). Participants were assessed at baseline for demographic data, falls-related history, and fear of falling. Data on these variables plus falls, mobility, social support behaviour and satisfaction, and quality of life were also collected at 2 and 5 months after interventions. RESULTS: Participants in the three groups differed significantly in both measures of fear of falling (F = 20·89, P < 0·001; F = 6·09, P < 0·001) and mobility (F = 30·33, P < 0·001), social support behaviour and satisfaction (F = 3·32, P < 0·05 and F = 6·35, P < 0·001, respectively), and quality of life (F = 16·66, P< 0·001). In addition, participants who received the cognitive-behavioural intervention with Tai Chi had significantly lower fear of falling scores (P < 0·001) and higher mobility (P < 0·001), social support satisfaction (P < 0·01) and quality of life (P < 0·001) than the cognitive-behavioural alone and control groups at 5 months. The three groups did not differ significantly in falls. CONCLUSION: The results of this trial suggest that the cognitive-behavioural intervention with Tai Chi exercise helped community-dwelling elderly adults to enhance their mobility, to manage their fear of falling and to increase their quality of life.

[Effects of TNF alpha on the expression of SCAP and triglyceride contents in cultured steatotic hepatocytes].

OBJECTIVE: To explore the effects of TNF alpha on the expression of sterol regulatory element binding proteins cleavage activating protein (SCAP) and triglyceride contents in cells of a model of cultured steatotic hepatocytes. METHODS: A steatotic hepatocytes model was established by treating L-02 cell strain with oleic acid. The cells were treated with TNF alpha and/or TNF alpha antibody. The cells were divided into six groups: a control group (C), a model group (F), a control group with TNF alpha (C1), a control group with TNFalpha antibody (C2), a model group with TNFalpha(F1) and a model group with TNFalpha antibody (F2). The expression of SREBP-1c mRNA was measured with RT-PCR; the protein expression of SCAP was measured by Western blot; lipid droplets in the hepatocytes were observed with oil red O staining; the contents of triglyceride in hepatocytes were measured with an analytical kit. RESULTS: The mRNA expression of SCAP in the groups treated with TNF alpha were upregulated compared with those of the control group (C1 vs C increased 67%, F1 vs F increased 55%, F = 212.98), the protein expression of SCAP in the groups treated with TNF alpha was upregulated compared with those of the control group (C1 vs C increased 45%, F1 vs F increased 95%, F = 104.3), and triglyceride contents in hepatocytes of these groups were increased compared with those of the control group [C (2.02+/-0.67) mg/10(7) cells, F(7.79+/-1.35) mg/10(7) cells, F1(13.36+/-1.99) mg/10(7) cells, F = 82.94]. CONCLUSION: TNF alpha upregulates the expression of SCAP and promotes the synthesis of triglyceride; it probably participates in the process of developing steatosis of hepatocytes.