Weighted gene Co-expression network analysis (WGCNA) reveals a set of hub genes related to chlorophyll metabolism process in chlorella (Chlorella vulgaris) response androstenedione

Multigenerational toxic effects in Daphnia pulex are induced by environmental concentrations of tire wear particle leachate

Microplastic pollution has emerged as the second most significant scientific issue in environmental science and ecology. Similarly, the biological effects of tire wear particles (TWPs) have garnered considerable research attention; however, studies on chronic TWP leachate toxicity at environmentally relevant concentrations remain sparse. Here, we investigated the effects of TWP leachate at environmentally relevant concentrations (0.3 mg/L and 3 mg/L) on multigenerational and transgenerational Daphnia pulex for 21 days/generation, spanning three generations (F0-F2). Growth and reproductive indices (body length, growth rate, time to first clutch, number of clutches, and total offspring/female) across generations were analyzed. Multigenerational exposure to TWP leachate did not cause D. pulex death, but impaired growth and development, prolonged sexual maturity time, and reduced reproductive capacity. The transgenerational exposure group (3 mg/L) also exhibited some sub-lethal effects, such as delayed reproduction, suggesting a transgenerational impact. Gene transcription analyses and weighted gene co-expression network analysis showed that the most impacted pathways were associated with lysosome function, apoptosis, and glutathione metabolism, indicating that TWP leachate exposure compromised immune defense mechanisms and disrupted APs, CTSB, GST, DUSP1, and ERN1 gene expression. These findings underscore multigenerational toxicity effects and TWP leachate transmission patterns on aquatic organisms at realistic environmental concentrations.

Overestimated role of inoculation bacteria-algae ratio in wastewater treatment

Microalgae-bacteria systems present a promising approach for CO2 reduction in wastewater treatment. The effect of inoculation bacteria-algae ratio on performance was investigated in this study. Different inoculation ratios (bacteria: algae 1:2, 1:1, 1:0.5, 1:0.25, 1:0.125, w/w) obtained comparable nutrients removal (p > 0.05). Over time, the bacteria-algae ratios converged into two groups (3:1 and 4:1), demonstrating self-adaption between bacteria and microalgae. Furthermore, principal component analysis (PCA) distinguished the performance of reactors into two groups, one group consisting of 1:2, 1:1, and 1:0.5 ratios and the other group consisting of 1:0.25 and 1:0.125 ratios, confirming their convergence in terms of nutrient removal and photosynthetic properties. The performance differed merely in sludge volume index (SVI) and nitrite accumulation, with 1:2 and 1:0.125 being the most prone to accumulate nitrite. This study implies that photobioreactor performance was not sensitive to inoculation ratio, whose role was overestimated, since microalgae and bacteria self-assemble to form niches. PRACTITIONER POINTS: Effect of inoculation bacteria-algae ratio on performance was overestimated Photosynthesis and nutrients removal were grouped at different inoculation ratios Different ratio showed similar nutrients removal efficiency Self-adaption made ratios of 1:2, 1:1, 1:0.5 converge into 3:1.

Identification and validation of the diagnostic biomarker MFAP5 for CAVD with type 2 diabetes by bioinformatics analysis

Introduction

Calcific aortic valve disease (CAVD) is increasingly prevalent among the aging population, and there is a notable lack of drug therapies. Consequently, identifying novel drug targets will be of utmost importance. Given that type 2 diabetes is an important risk factor for CAVD, we identified key genes associated with diabetes - related CAVD via various bioinformatics methods, which provide further potential molecular targets for CAVD with diabetes.

Methods

Three transcriptome datasets related to CAVD and two related to diabetes were retrieved from the Gene Expression Omnibus (GEO) database. To distinguish key genes, differential expression analysis with the "Limma" package and WGCNA was applied. Machine learning (ML) algorithms were employed to screen potential biomarkers. The receiver operating characteristic curve (ROC) and nomogram were then constructed. The CIBERSORT algorithm was utilized to investigate immune cell infiltration in CAVD. Lastly, the association between the hub genes and 22 types of infiltrating immune cells was evaluated.

Results

By intersecting the results of the "Limma" and WGCNA analyses, 727 and 190 CAVD - related genes identified from the GSE76717 and GSE153555 datasets were obtained. Then, through differential analysis and interaction, 619 genes shared by the two diabetes mellitus datasets were acquired. Next, we intersected the differential genes and module genes of CAVD with the differential genes of diabetes, and the obtained genes were used for subsequent analysis. ML algorithms and the PPI network yielded a total of 12 genes, 10 of which showed a higher diagnostic value. Immune cell infiltration analysis revealed that immune dysregulation was closely linked to CAVD progression. Experimentally, we have verified the gene expression differences of MFAP5, which has the potential to serve as a diagnostic biomarker for CAVD.

Conclusion

In this study, a multi-omics approach was used to identify 10 CAVD-related biomarkers (COL5A1, COL5A2, THBS2, MFAP5, BTG2, COL1A1, COL1A2, MXRA5, LUM, CD34) and to develop an exploratory risk model. Western blot (WB) and immunofluorescence experiments revealed that MFAP5 plays a crucial role in the progression of CAVD in the context of diabetes, offering new insights into the disease mechanism.

Dissection of genetic architecture for desirable traits in sugarcane by integrated transcriptomics and metabolomics

Sugarcane is an important sugar and energy crop. Breeding varieties with high yield and sugar, strong stress tolerance, as well as beneficial for mechanized harvesting are the goal of sugarcane breeder. In the present study, transcriptomics and metabolomics were conducted to explore the molecular basis for outstanding performance of five elite varieties GT42, GT44, LC05-136, YZ08-1609, and YZ05-51, along with the cross-parent CP72-1210 compared to ROC22. Transcriptomics revealed a total of 18,353 differentially expressed genes (DEGs) and several regulatory pathways, including carbon fixation, starch and sucrose metabolism, phenylpropanoids biosynthesis, flavonoid biosynthesis, cysteine and methionine metabolism, as well as zeatin biosynthesis. Expression patterns of genes involved in these pathways confirmed their role in determining the agronomic traits. Besides, metabolomics disclosed 175 differentially accumulated metabolites (DAMs), including specific metabolites of amino acids and secondary metabolites. Furthermore, conjoint analysis of transcriptomics and metabolomics highlighted the manipulation of 113 genes led to changed levels of 20 metabolites associated with carbon fixation, sucrose accumulation, phytohormone response and secondary metabolism. Finally, we depicted here a blueprint outlining the genetic basis underlying the desirable traits in sugarcane. This study will accelerate the dissection of the molecular basis for sugarcane traits and provide targets for molecular breeding.

Reduction of Oxygen Production by Algal Cells in the Presence of O-Chlorobenzylidene Malononitrile

Chemical compounds, such as the CS gas employed in military operations, have a number of characteristics that impact the ecosystem by upsetting its natural balance. In this work, the toxicity limit and microorganism's reaction to the oxidative stress induced by O-chlorobenzylidenemalonitrile, a chemical found in CS gas, were assessed in relation to the green algae Chlorella pyrenoidosa. A number of parameters, including the cell growth curve, the percent inhibition in yield, the dry cell weight, the percentage viability and productivity of algal biomass flocculation activity, and the change in oxygen production, were analyzed in order to comprehend the toxicological mechanisms of O-chlorobenzylidenemalonitrile on algal culture. Using fluorescence and Fourier transform infrared spectroscopy (FTIR), the content of chlorophyll pigments was determined. The values obtained for pH during the adaptation period of the C. pyrenoidosa culture were between 6.0 and 6.8, O2 had values between 6.5 and 7.0 mg/L, and the conductivity was 165-210 µS/cm. For the 20 µg/mL O-chlorobenzylidenemalonitrile concentration, the cell viability percentage was over 97.4%, and for the 150 µg/mL O-chlorobenzylidenemalonitrile concentration was 74%. The ECb50 value for C. pyrenoidosa was determined from the slope of the calibration curve; it was estimated by extrapolation to the value of 298.24 µg/mL. With the help of this study, basic information on the toxicity of O-chlorobenzylidenemalonitrile to aquatic creatures will be available, which will serve as a foundation for evaluating the possible effects on aquatic ecosystems. The management of the decontamination of the impacted areas could take the results into consideration.

Comprehensive Transcriptome and Proteome Analyses Reveal the Drought Responsive Gene Network in Potato Roots

The root system plays a decisive role in the growth and development of plants. The water requirement of a root system depends strongly on the plant species. Potatoes are an important food and vegetable crop grown worldwide, especially under irrigation in arid and semi-arid regions. However, the expected impact of global warming on potato yields calls for an investigation of genes related to root development and drought resistance signaling pathways in potatoes. In this study, we investigated the molecular mechanisms of different drought-tolerant potato root systems in response to drought stress under controlled water conditions, using potato as a model. We analyzed the transcriptome and proteome of the drought-sensitive potato cultivar Atlantic (Atl) and the drought-tolerant cultivar Qingshu 9 (Q9) under normal irrigation (CK) and weekly drought stress (D). The results showed that a total of 14,113 differentially expressed genes (DEGs) and 5596 differentially expressed proteins (DEPs) were identified in the cultivars. A heat map analysis of DEGs and DEPs showed that the same genes and proteins in Atl and Q9 exhibited different expression patterns under drought stress. Weighted gene correlation network analysis (WGCNA) showed that in Atl, Gene Ontology (GO) terms and Kyoto Encyclopedia of Genes and Genomes (KEGG)-enriched pathways were related to pyruvate metabolism and glycolysis, as well as cellular signaling and ion transmembrane transporter protein activity. However, GO terms and KEGG-enriched pathways related to phytohormone signaling and the tricarboxylic acid cycle were predominantly enriched in Q9. The present study provides a unique genetic resource to effectively explore the functional genes and uncover the molecular regulatory mechanism of the potato root system in response to drought stress.

Effects of abiotic stress on chlorophyll metabolism

Chlorophyll, an essential pigment in the photosynthetic machinery of plants, plays a pivotal role in the absorption of light energy and its subsequent transfer to reaction centers. Given that the global production of chlorophyll reaches billions of tons annually, a comprehensive understanding of its biosynthetic pathways and regulatory mechanisms is important. The metabolic pathways governing chlorophyll biosynthesis and catabolism are complex, encompassing a series of interconnected reactions mediated by a spectrum of enzymes. Environmental fluctuations, particularly abiotic stressors such as drought, extreme temperature variations, and excessive light exposure, can significantly perturb these processes. Such disruptions in chlorophyll metabolism have profound implications for plant growth and development. This review delves into the core aspects of chlorophyll metabolism, encompassing both biosynthetic and degradative pathways. It elucidates key genes and enzymes instrumental in these processes and underscores the impact of abiotic stress on chlorophyll metabolism. Furthermore, the review aims to deepen the understanding of the interplay between chlorophyll metabolic dynamics and stress responses, thereby shedding light on potential regulatory mechanisms.

Exploring the molecular mechanism of Chlorella vulgaris in response to androstenedione exposure based on genes continuously up-regulated in transcription analysis

Androstenedione (ADSD) is one of the widely detected androgens in diverse aquatic environments. However, there were few reports on the molecular mechanism of Chlorella vulgaris exposure to ADSD. In our previous research, we have investigated the genes associated with chlorophyll metabolism in Chlorella vulgaris response to ADSD. In this study, we focus on continuously up-regulated genes to explore the mechanism underlying Chlorella vulgaris resistance to ADSD toxicity. Chlorella vulgaris was exposed to ADSD with five concentration gradients. The continuously up-regulated genes were enriched by Series Test of Cluster (STC) analysis and verified by qRT-PCR. Microalgae Super Oxidase Dimutase (SOD) and Microalgae Malonic dialdehyde (MDA), two indicators of oxidative stress, were determined by ELISA after exposure to ADSD. The results showed that ADSD can stimulate the production of extracellular polymeric substances (EPS) and lead to enlargement in the cell body of Chlorella vulgaris. In addition, steroid biosynthesis and oxidoreductase activity processes were consistently up-regulated upon exposure to ADSD. In conclusion, our study highlighted the crucial role of phenotypic modification, hormone synthesis, and redox mechanisms in protecting Chlorella vulgaris cells from the harmful effects of ADSD contamination.

Identification and validation of hub genes and molecular classifications associated with chronic myeloid leukemia

Background

Chronic myeloid leukemia (CML) is a kind of malignant blood tumor, which is prone to drug resistance and relapse. This study aimed to identify novel diagnostic and therapeutic targets for CML.

Methods

Differentially expressed genes (DEGs) were obtained by differential analysis of the CML cohort in the GEO database. Weighted gene co-expression network analysis (WGCNA) was used to identify CML-related co-expressed genes. Least absolute shrinkage and selection operator (LASSO) regression analysis was used to screen hub genes and construct a risk score model based on hub genes. Consensus clustering algorithm was used for the identification of molecular subtypes. Clinical samples and in vitro experiments were used to verify the expression and biological function of hub genes.

Results

A total of 378 DEGs were identified by differential analysis. 369 CML-related genes were identified by WGCNA analysis, which were mainly enriched in metabolism-related signaling pathways. In addition, CML-related genes are mainly involved in immune regulation and anti-tumor immunity, suggesting that CML has some immunodeficiency. Immune infiltration analysis confirmed the reduced infiltration of immune killer cells such as CD8+ T cells in CML samples. 6 hub genes (LINC01268, NME8, DMXL2, CXXC5, SCD and FBN1) were identified by LASSO regression analysis. The receiver operating characteristic (ROC) curve confirmed the high diagnostic value of the hub genes in the analysis and validation cohorts, and the risk score model further improved the diagnostic accuracy. hub genes were also associated with cell proliferation, cycle, and metabolic pathway activity. Two molecular subtypes, Cluster A and Cluster B, were identified based on hub gene expression. Cluster B has a lower risk score, higher levels of CD8+ T cell and activated dendritic cell infiltration, and immune checkpoint expression, and is more sensitive to commonly used tyrosine kinase inhibitors. Finally, our clinical samples validated the expression and diagnostic efficacy of hub genes, and the knockdown of LINC01268 inhibited the proliferation of CML cells, and promoted apoptosis.

Conclusion

Through WGCNA analysis and LASSO regression analysis, our study provides a new target for CML diagnosis and treatment, and provides a basis for further CML research.

Developing industry-scale microfluidization for cell disruption, biomolecules release and bioaccessibility improvement of Chlorella pyrenoidosa

To facilitate biomolecules extraction and bioaccessibility of Chlorella pyrenoidosa, a novel industry-scale microfluidization (ISM) was used to disrupt cells effectively. Microscope images showed ISM damaged cell integrity, disorganized cell wall structure, pulverized cell membrane and promoted the release of intracellular components. The decrease of particle size and the increase of ζ-potential also confirmed the cell disruption. The cell breakage ratio of sample treated at 120 MPa was 98%. Compared with untreated samples, total soluble solid content and protein extraction rate of the sample treated at 120 MPa increased by 2 °Brix and 12%. Protein was degraded by ISM, the release of intracellular protein and the reduction of molecular weight increased protein digestibility by 20% in in vitro gastric phase. Lipid yield and chlorophyll b content were also increased by ISM. These results provided a new solution to cell disruption of microalgae and expanded the application field of ISM.

Integrated comparative transcriptome and weighted gene co-expression network analysis provide valuable insights into the response mechanisms of crayfish (Procambarus clarkii) to copper stress

One of the significant limitations of aquaculture worldwide is the prevalence of divalent copper (Cu). Crayfish (Procambarus clarkii) are economically important freshwater species adapted to a variety of environmental stimuli, including heavy metal stresses; however, large-scale transcriptomic data of the hepatopancreas of crayfish in response to Cu stress are still scarce. Here, integrated comparative transcriptome and weighted gene co-expression network analyses were initially applied to investigate gene expression profiles of the hepatopancreas of crayfish subjected to Cu stress for different periods. As a result, 4662 significant differentially expressed genes (DEGs) were identified following Cu stress. Bioinformatics analyses revealed that the "focal adhesion" pathway was one of the most significantly upregulated response pathways following Cu stress, and seven DEGs mapped to this pathway were identified as hub genes. Furthermore, the seven hub genes were examined by quantitative PCR, and each was found to have a substantial increase in transcript abundance, suggesting a critical role of the "focal adhesion" pathway in the response of crayfish to Cu stress. Our transcriptomic data can be a good resource for the functional transcriptomics of crayfish, and these results may provide valuable insights into the molecular response mechanisms underlying crayfish to Cu stress.

Transcriptomic analysis reveals up-regulated histone genes may play a key role in zebrafish embryo-larvae response to Bisphenol A (BPA) exposure

Bisphenol A (BPA) can induce complex regulatory mechanisms in many aquatic organisms, and it is difficult to find a suitable analytical method to efficiently enrich key genes responding to BPA exposure. In this study, zebrafish embryo transcriptomic data were obtained from two types of different BPA exposure methods. After BPA exposure, three differential gene enrichment methods were used jointly to identify up-regulated genes or pathways in zebrafish embryo larvae. The results showed that the systemic lupus erythematosus signaling pathway was significantly enriched in all BPA exposure groups. It was also noteworthy that most of the up-regulated genes in systemic lupus erythematosus signaling were histones. In conclusion, this study suggested that autoimmunity signaling was the most common important pathway in zebrafish embryo-larvae response to different BPA exposures, and histones may play a key role in response to low-concentration BPA.

Weighted Gene Co-Expression Network Analysis to Explore Hub Genes of Resveratrol Biosynthesis in Exocarp and Mesocarp of 'Summer Black' Grape

Resveratrol is a polyphenol compound beneficial to human health, and its main source is grapes. In the present study, the molecular regulation of resveratrol biosynthesis in developing grape berries was investigated using weighted gene co-expression network analysis (WGCNA). At the same time, the reason for the resveratrol content difference between grape exocarp (skin) and mesocarp (flesh) was explored. Hub genes (CHS, STS, F3'5'H, PAL, HCT) related to resveratrol biosynthesis were screened with Cytoscape software. The expression level of hub genes in the exocarp was significantly higher than that in the mesocarp, and the expressions of the hub genes and the content of resveratrol in exocarp peaked at the maturity stage. While the expression levels of PAL, CHS and STS in the mesocarp, reached the maximum at the maturity stage, and F3'5'H and HCT decreased. These hub genes likely play a key role in resveratrol biosynthesis. Kyoto Encyclopedia of Genes and Genomes (KEGG) pathway analysis further indicated that resveratrol biosynthesis was related to flavonoid biosynthesis, phenylalanine metabolism, phenylpropanoid biosynthesis, and stilbene biosynthesis pathways. This study has theoretical significance for exploring genes related to resveratrol biosynthesis in the exocarp and mesocarp of grapes, and provides a theoretical basis for the subsequent function and regulatory mechanism of hub genes.

Effects of methanol, sodium citrate, and chlorella powder on enhanced anaerobic treatment of coal pyrolysis wastewater

To better promote environment friendly development of the coal chemical industry, this study investigated effects of methanol, sodium citrate, and chlorella powder (a type of microalgae) as co-metabolic substances on enhanced anaerobic treatment of coal pyrolysis wastewater with anaerobic sludge. The anaerobic sludge was loaded into four 2 L anaerobic reactors for co-metabolism enhanced anaerobic experiments. Anaerobic reactor 1 (R1) as control group did not add a co-metabolic substance; anaerobic reactor 2 (R2) added methanol; anaerobic reactor 3 (R3) added sodium citrate; and anaerobic reactor 4 (R4) added chlorella powder. In the blank control group, the removal ratios of total phenol (TPh), quinoline, and indole were only 12.07%, 42.15%, and 50.47%, respectively, indicating that 50 mg/L quinoline, 50 mg/L indole, and 600 mg/L TPh produced strong toxicity inhibition function on the anaerobic microorganism in reactor. When the concentration of methanol, sodium citrate, and chlorella was 400 μg/L, the reactors with co-metabolic substances had better treatment effect on TPh. Among them, the strengthening effects of sodium citrate (TPh removal ratio: 44.87%) and chlorella (47.85%) were better than that of methanol (38.72%) and the control group (10.62%). Additionally, the reactors with co-metabolic substances had higher degradation ratios on quinoline, indole, and chemical oxygen demand (COD). The data of extracellular polymeric substances showed that with the co-metabolic substances, anaerobic microorganisms produced more humic acids by degrading phenols and nitrogen-containing heterocyclic compounds (NHCs). Compared with the control group, the reactors added with sodium citrate and chlorella had larger average particle size of sludge. Thus, sodium citrate and chlorella could improve sludge sedimentation performance by increasing the sludge particle size. The bacterial community structures of reactors were explored and the results showed that Aminicenantes genera incertae sedis, Levinea, Geobacter, Smithella, Brachymonas, and Longilinea were the main functional bacteria in reactor added with chlorella.