An integrative pan-cancer analysis of the molecular characteristics of dietary restriction in tumour microenvironment.

BACKGROUND: Dietary restriction (DR), a general term for dieting, has been demonstrated as an effective intervention in reducing the occurrence of cancers. Molecular activities associated with DR are crucial in mediating its anti-cancer effects, yet a comprehensive exploration of the landscape of these activities at the pan-cancer level is still lacking. METHODS: We proposed a computational approach for quantifying DR-related molecular activities and delineating the landscape of these activities across 33 cancer types and 30 normal tissues within 27,320 samples. We thoroughly examined the associations between DR-related molecular activities and various factors, including the tumour microenvironment, immunological phenotypes, genomic features, and clinical prognosis. Meanwhile, we identified two DR genes that show potential as prognostic predictors in hepatocellular carcinoma and verified them by immunohistochemical assays in 90 patients. FINDINGS: We found that DR-related molecular activities showed a close association with tumour immunity and hold potential for predicting immunotherapy responses in various cancers. Importantly, a higher level of DR-related molecular activities is associated with improved overall survival and cancer-specific survival. FZD1 and G6PD are two DR genes that serve as biomarkers for predicting the prognosis of patients with hepatocellular carcinoma. INTERPRETATION: This study presents a robust link between DR-related molecular activities and tumour immunity across multiple cancer types. Our research could open the path for further investigation of DR-related molecular processes in cancer treatment. FUNDING: National Natural Science Foundation of China (Grant No. 82000628) and the Guangdong-Hong Kong-Macao University Joint Laboratory of Interventional Medicine Foundation of Guangdong Province (Grant No. 2023LSYS001).

Metagenomic analysis reveals gut plasmids as diagnosis markers for colorectal cancer.

Background: Colorectal cancer (CRC) is linked to distinct gut microbiome patterns. The efficacy of gut bacteria as diagnostic biomarkers for CRC has been confirmed. Despite the potential to influence microbiome physiology and evolution, the set of plasmids in the gut microbiome remains understudied. Methods: We investigated the essential features of gut plasmid using metagenomic data of 1,242 samples from eight distinct geographic cohorts. We identified 198 plasmid-related sequences that differed in abundance between CRC patients and controls and screened 21 markers for the CRC diagnosis model. We utilize these plasmid markers combined with bacteria to construct a random forest classifier model to diagnose CRC. Results: The plasmid markers were able to distinguish between the CRC patients and controls [mean area under the receiver operating characteristic curve (AUC = 0.70)] and maintained accuracy in two independent cohorts. In comparison to the bacteria-only model, the performance of the composite panel created by combining plasmid and bacteria features was significantly improved in all training cohorts (mean AUCcomposite = 0.804 and mean AUCbacteria = 0.787) and maintained high accuracy in all independent cohorts (mean AUCcomposite = 0.839 and mean AUCbacteria = 0.821). In comparison to controls, we found that the bacteria-plasmid correlation strength was weaker in CRC patients. Additionally, the KEGG orthology (KO) genes in plasmids that are independent of bacteria or plasmids significantly correlated with CRC. Conclusion: We identified plasmid features associated with CRC and showed how plasmid and bacterial markers could be combined to further enhance CRC diagnosis accuracy.

Synergy between autotrophic denitrification and Anammox driven by FeS in a fluidized bed bioreactor for advanced nitrogen removal.

On the basis of the metabolic synergy between autotrophic denitrification (AuDen) and anaerobic ammonium oxidation (Anammox), the feasibility of a novel ferrous sulfide (FeS)-driven AuDen and Anammox coupled system (FS-DADAS) was investigated. The nitrogen removal performance of FS-DADAS was investigated in a lab-scale fluidized bed bioreactor fed with synthetic wastewater containing NH4+-N and NO3--N. The results of long-term operation (120 days) demonstrated the promising performance of the system with 100% NO3--N removal and NH4+-N concentrations lower than 8.11 mg L-1 in the effluent at a nitrogen loading rate of 0.20 g-N·(L·d)-1. Sufficient NO2--N was provided by the AuDen for Anammox where a high removal rate of total nitrogen (TN) was achieved. The contribution of Anammox to TN removal was at >80%. The reactor could maintain a stable pH with less SO42- production owing to the fact that Fe(II) and S acted as electron donors. FeS gradually transformed into a sheet-like secondary mineral, FeOOH. AuDen (Thiobacillus) and Anammox bacteria (Candidatus Kuenenia) were successfully retained in the bioreactor, with relative abundance values of 18.82%-23.64% and 3.52%-8.67%, respectively. FS-DADAS is a promising technology for the complete removal of TN from wastewaters with low C/N ratios at low energy consumption.

DeepHPV: a deep learning model to predict human papillomavirus integration sites.

Human papillomavirus (HPV) integrating into human genome is the main cause of cervical carcinogenesis. HPV integration selection preference shows strong dependence on local genomic environment. Due to this theory, it is possible to predict HPV integration sites. However, a published bioinformatic tool is not available to date. Thus, we developed an attention-based deep learning model DeepHPV to predict HPV integration sites by learning environment features automatically. In total, 3608 known HPV integration sites were applied to train the model, and 584 reviewed HPV integration sites were used as the testing dataset. DeepHPV showed an area under the receiver-operating characteristic (AUROC) of 0.6336 and an area under the precision recall (AUPR) of 0.5670. Adding RepeatMasker and TCGA Pan Cancer peaks improved the model performance to 0.8464 and 0.8501 in AUROC and 0.7985 and 0.8106 in AUPR, respectively. Next, we tested these trained models on independent database VISDB and found the model adding TCGA Pan Cancer performed better (AUROC: 0.7175, AUPR: 0.6284) than the model adding RepeatMasker peaks (AUROC: 0.6102, AUPR: 0.5577). Moreover, we introduced attention mechanism in DeepHPV and enriched the transcription factor binding sites including BHLHA15, CHR, COUP-TFII, DMRTA2, E2A, HIC1, INR, NPAS, Nr5a2, RARa, SCL, Snail1, Sox10, Sox3, Sox4, Sox6, STAT6, Tbet, Tbx5, TEAD, Tgif2, ZNF189, ZNF416 near attention intensive sites. Together, DeepHPV is a robust and explainable deep learning model, providing new insights into HPV integration preference and mechanism. Availability: DeepHPV is available as an open-source software and can be downloaded from https://github.com/JiuxingLiang/DeepHPV.git, Contact: huzheng1998@163.com, liangjiuxing@m.scnu.edu.cn, lizheyzy@163.com.

Effects of alkali, autoclaving, and Fe+ autoclaving pretreatment on anaerobic digestion performance of coking sludge from the perspective of sludge extracts and methane production.

Pretreatment of activated sludge is an important step in increasing the reaction speed during anaerobic digestion by accelerating the hydrolysis process. It is necessary not only to analyze the changes in the general properties of the sludge before and after pretreatment but also to further analyze and evaluate the sludge structure and extracellular polymeric substances (EPS). In this study, the changes in coking sludge extracts after pretreatments with alkali, autoclaving, and Fe+ autoclaving were analyzed and compared using EPS heat extraction method. Moreover, the methane production potential of the pretreated coking sludge was investigated via biochemical methane potential (BMP) test. The results showed that after alkali, autoclaving, and Fe+ autoclaving, the concentration of protein and polysaccharide in the bound sludge extract accounted for approximately 40% and 28%, 62% and 51%, and 66% and 83% of the total protein and polysaccharide extracted from the sludge, respectively. In the experiment without pretreatment, there is no phenomenon of gas production from coking sludge. According to the BMP test results, Fe+ autoclaving pretreatment showed the highest methane production of 257 mL/gVSS. This study revealed that the analysis of sludge extracts was necessary in assessing the effects of anaerobic digestion pretreatment and methanogenic potential. Moreover, coking sludge showed higher methanogenic potential after Fe+ autoclaving pretreatment.

Selection of optimum biological treatment for coking wastewater using analytic hierarchy process.

The design of biological treatment process for the coking wastewater (CW) is complicated since wastewater treatment demand is gradually increasing lacking the systematic strategy in efficiency evaluation and advisable selection. Therefore, this study develops a holistic approach by means of the analytic hierarchy process (AHP) that uses numerical representation to rank the preferences of each participating alternatives for evaluation of the advanced biological technologies in CW treatment. Based on survey results, six types reactor combinations were selected as the alternatives, which were further classified as two group according to COD load. The AHP methodology consists of weighting and ranking procedures considering technical, economic, environmental and administration factors defined as criteria layers. Eighteen indicators were chosen as sub-criteria layers. Inclusively beneficial and sustainable biological processes were assessed and ranked along the AHP implementation. The results placed technical indicators to the top position among the criteria layers in the weighting descending order 'technical indicators > economic indicators > environmental indicators > administrative indicators', whereas the weight of indicators in sub-criteria layers fitted in the range of 0.005 to 0.151. The inclusive priority calculation integrating all weight indices of criteria and sub-criteria layers resulted in the anaerobic-anoxic-oxic (A/A/O) combination rising in the hierarchy of the low load group, whereas the oxic-hydrolytic-oxic (O/H/O) process was prioritized in the high load group. The accuracy and objectivity of AHP application was also supported by sensitivity and variability analyses that examines a range for the weights' values and corresponding to alternative scenarios.

The correlations among wastewater internal energy, energy consumption and energy recovery/production potentials in wastewater treatment plant: An assessment of the energy balance.

Given the economic and environmental importance of energy use in wastewater treatment plants (WWTPs), the need to assess the energy balance of WWTPs has become a growing concern. Previous studies have suggested that energy balance or even net energy production may be achieved in WWTPs under specific conditions. However, information regarding the energy consumption and the energy recovery/production potential in WWTPs as a function of the influent characteristics is still very limited. In this paper, by exploring the correlations among wastewater internal energy, energy consumption and energy recovery in WWTPs, a novel net energy consumption (NEC) model was developed for predicting the energy self-sufficiency level of WWTPs. From our results, exponential regression showed a high accuracy in predicting the annual energy consumption, the annual excess sludge production and the bioreactor footprints in WWTPs. Wastewater with more internal energy which is determined by influent chemical oxygen demand (COD) concentration and flow rate, not only leads to higher energy consumption in WWTPs, but also results in an increase in the excess sludge production, bioreactor footprints and wastewater volume. This means that the WWTPs could achieve energy saving or even net energy production by incorporating sludge incineration, photovoltaic (PV) generation and thermal energy recovery. By combing regression analysis with theoretical formula, the annual net energy demand of WWTPs reached -0.187-0.466 kWh·m-3 in the range of wastewater condition studied (the influent COD concentration range of 60-800 mg·L-1 and the flow rate range of 1296-100,000 m3·d-1). The NEC model reveals that the net zero energy consumption may be achieved by integrating the better understandings of wastewater internal energy, energy conversion methods and environmental media energy, which is of value to policy makers for the planning of new WWTPs and provides theoretical support for the selection of available energy recovery methods.

Simultaneous decarburization, nitrification and denitrification (SDCND) in coking wastewater treatment using an integrated fluidized-bed reactor.

There are two problems in biological treatment of coking wastewater (CWW): incapability of pre-anaerobic treatment to eliminate the toxicity in wastewater, and the lack of carbon source for subsequent denitrification in pre-aerobic treatment. To achieve simultaneous decarburization, nitrification and denitrification (SDCND) in CWW treatment, biological carrier materials was used to build an integrated fluidized-bed reactor (Reactor B, RB). A conventional fluidized-bed reactor (Reactor A, RA) was used as a control reactor under the same condition. The results showed that RB was more advantageous since its removal efficiencies of COD and TN were 90% and 87%, respectively, which were significantly higher than these in RA (82% and 45%), at a hydraulic retention time (HRT) of 60 h. Microelectrode measurement indicated that oxygen transfer was limited inside the carrier where the formation of a dissolved oxygen (DO) concentration gradient was observed. Microbial community analysis showed that the aerobic and anoxic microenvironments in RB promoted the co-existence of a wider variety of bacteria, thus achieving SDCND. These results indicated the integrated fluidized-bed reactor exhibited promising feasibility for simultaneous carbon and nitrogen removal in CWW treatment under the same aeration driven conditions. The SDCND process realized by fluidized-bed reactor provided a reference for the treatment of toxic industrial wastewater with high carbon to nitrogen ratio.

Influence of macromolecules on aggregation kinetics of diesel soot nanoparticles in aquatic environments.

Soot nanoparticles (SNPs) produced from incomplete combustion have strong impacts on aquatic environments as they eventually reach surface water, where their environmental fate and transport are largely controlled by aggregation. This study investigated the aggregation kinetics of SNPs in the presence of macromolecules including fulvic acid (FA), humic acid (HA), alginate polysaccharide, and bovine serum albumin (BSA, protein) under various environmentally relevant solution conditions. Our results showed that increasing salt concentrations induced SNP aggregation by suppressing electrostatic repulsion and that CaCl2 exhibited stronger effect than NaCl in charge neutralization, which is in agreement with the Derjaguin-Landau-Verwey-Overbeek (DLVO) theory. The aggregation rates of SNPs were variously reduced by macromolecules, and such stabilization effect was the greatest by BSA, followed by HA, alginate, and FA. Steric repulsion resulting from macromolecules adsorbed on SNP surfaces was mainly responsible for enhancing SNP stability. Such steric repulsion appeared to be affected by macromolecular structure, as BSA having a more compact globular structure on SNP surfaces imparted long-range steric repulsive forces and retarded the SNP aggregation rate by 10-100 times. In addition, alginate was shown to enhance SNP aggregation by ∼10 times at high CaCl2 concentrations due to alginate gel formation via calcium bridging. The results may bear strong significance for the fate and transport of SNPs in both natural and controlled environmental systems.

Residual chemical oxygen demand (COD) fractionation in bio-treated coking wastewater integrating solution property characterization.

The refractory nature of residual COD in bio-treated coking wastewater (BTCW) creates barriers for its further treatment and reclamation. It is necessary to fractionate the residual COD in BTCW associated with characterization of solution properties. In this paper, a stepwise process composed of membrane filtration, coagulation, adsorption and ozonation was proposed to fractionate residual COD in the BTCW, in which the COD was stepwise reduced to near zero. In addition, the correlation between COD and water quality indexes as well as solution properties were discussed together with a safety assessment of the water quality. Results showed that the residual COD fractionation percentage contributed by suspended solids, colloids, dissolved organics and reductive inorganic substances in the BTCW was 43.7%, 22.1%, 26.2% and 4.9%, respectively. By stepwise fractionating of these substances, the residual COD was reduced from 168.8 to 5.2 mg L-1, and the UV254 value decreased from 1.90 to 0.15 cm-1. In addition, the particle size of the dominant substances contributing to the residual COD was smaller than 450 nm. Among these substances, the hydrophobic fraction accounted for 78.66% (in the term of TOC). Three-dimensional excitation-emission matrix (3D-EEM) analysis showed that hydrophobic neutral substances (HON) were the main fluorescence constituent in the BTCW, which was highly removable by adsorption. The residual COD after adsorption was mainly composed of reductive inorganic substances. Apart from pursuit of high COD removal rates, more emphasis should be given to the removal of toxic COD. Correlations were observed between the residual COD and water quality indicators as well as solution properties, providing a guideline for optimized removal of residual COD in the BTCW. In summary, these results gave a referential information about the nature of residual COD in the BTCW for the selection of advanced treatment technologies and the management of water quality safety.

A biosurfactant-producing Pseudomonas aeruginosa S5 isolated from coking wastewater and its application for bioremediation of polycyclic aromatic hydrocarbons.

Although polycyclic aromatic hydrocarbons (PAHs) are considered as toxic and refractory pollutants, their biodegradation can be facilitated by biosurfactants. However, few studies have been performed to understand the potential isolation and application of biosurfactant-producing microorganism for promoting the in-situ removal of PAHs from wastewaters. In this work, a biosurfactant-producing strain S5 isolated from coking wastewater was identified as Pseudomonas aeruginosa. The biosurfactant produced by strain S5 was determined as glycolipid with a critical micelle concentration (CMC) of 96.5 mg/L, and reduced the surface tension from 72.2 to 29.6 mN/m. Addition indigenous P. aeruginosa S5 to coking wastewater effectively promoted the biodegradation of high weight molecular (HWM) PAHs (reduction from 9141.02 to 5117.16 µg/L in 15 days) in sludge phase. The results showed that the removal of PAHs in the sludge was enhanced by inoculating indigenous biosurfactant-producing microorganism in coking wastewater serving as an in-site remediation technology.

Fabrication of terminal amino hyperbranched polymer modified graphene oxide and its prominent adsorption performance towards Cr(VI).

In order to increase the density and quantity of functional groups on adsorbent, three terminal amino hyperbranched polymer modified graphene oxide adsorbents including GO-HBP-NH2-DETA, GO-HBP-NH2-TETA and GO-HBP-NH2-TEPA with N-containing functional group density of 7.21 wt%, 10.20 wt% and 12.43 wt%, respectively, were prepared and used for the adsorption and reduction of toxic hexavalent chromium Cr(VI) to less toxic Cr(III). The morphology and structure of obtained adsorbents were characterized by FT-IR, SEM, XRD, Raman, BET, XPS and zeta potential. The density of receptor sites (Nm) of the three adsorbents calculated from statistical physics model with one energy site were found to be 456.62, 604.54 and 636.03, respectively. Adsorption experiments demonstrated that the high adsorption capacities of the three adsorbents obtained from Langmuir isotherm model towards Cr(VI) were 245.01, 257.26 and 300.88 mg/g, respectively, suggesting that GO-HBP-NH2-TEPA had better adsorption ability. The density functional theory calculation (DFT) indicated that GO-HBP-NH2-TEPA was more likely to adsorb HCrO4- rather than Cr2O72- at lower pH conditions. A possible adsorption mechanism was also proposed where electrostatic interaction between Cr(VI) (HCrO4- or Cr2O72-) and the N functional group (+) on GO-HBP-NH2-TEPA dominated the adsorption of Cr(VI) and reduction mechanism dominated the reduction of Cr(VI)-Cr(III).

[Behavior and Degradation of Polycyclic Aromatic Hydrocarbons (PAHs) in Coking Wastewater of A/O2 and A/O/H/O Processes].

Polycyclic aromatic hydrocarbons (PAHs) are typical organic pollutants found in coking wastewater, and their behavior and reduction can be affected by different treatment processes. Based on these considerations, this study investigated the behaviors of PAHs in coking wastewater under A/O2 and A/O/H/O treatment processes, respectively. In order to evaluate variations in PAH removal under two different treatment processes, samples were taken from different treatment units for quantification of PAHs using gas chromatography-mass spectrometry. Results showed that PAHs were barely degraded in anaerobic tanks of either treatment process and accumulated much higher concentrations than in aerobic and hydrolytic tanks. While low molecular weight PAHs (LMW PAHs) in aqueous phase from anaerobic tanks were degraded effectively in aerobic tanks, high molecular weight PAHs (HMW PAHs) mostly accumulated in the sludge phase; these potentially pose a higher environmental risk and therefore need to be treated separately. Moreover, the A/O/H/O process showed higher degradation of PAHs bioavailability and higher removal effectiveness for PAHs with four or more benzene rings than the A/O2 process; this is attributed to the hydrolytic tank's ability to promote hydrolysis of macromolecular organic compounds and therefore improve biodegradability of PAHs. Comprehensive results from the study indicated that the A/O/H/O process is more advantageous for degradation of PAHs than the A/O2 process.

[Characteristic of Benzo[a]pyrene Anaerobic Degradation by Phenol Co-substrate and Microbial Communities from Two Types of Sludge].

Benzo[a]pyrene (BaP) is a typical representative of PAHs in coking wastewater and priority-controlled pollutants in the coking industry; its response characteristics with microorganisms and the methods to promote its degradation are worth studying. On the other hand, because the inoculated sludge for the adjustment and operation of newly-constructed coking wastewater treatment plants comes from municipal sludge or other coking plants, currently, the study of the microbial properties of different sludges', sludge availability, and the conditions that influence these properties are lacking. On account of the above perspectives, an experiment to study and compare the durability of municipal sludge and coking sludge, and their ability to degrade BaP was carried out. An anaerobic reactor was selected for the experiment and anaerobic-activated sludges were collected from a coking wastewater processing unit and a municipal wastewater plant. Then, 10 mg·L-1 of BaP alone and BaP with phenol as a co-metabolic carbon source was added to the coking and municipal sludge samples, respectively, for comparison experiments to study the microbial degradation of BaP and its dynamics. Moreover, high-throughput sequencing technology was also used to analyze the changes in the microbial community structure before and after the degradation experiment. The results showed that:① Both sludges were capable of degrading BaP, but municipal sludge showed a higher degradation efficiency than coking sludge; ② Adding phenol as co-substrate promoted the biodegradation of BaP in both sludges. When BaP was the sole carbon source, the half-life of BaP in the two sludges was 155.41 d and 116.3 d respectively. After the addition of phenol, the half-life was reduced to 81.25 d and 38.44 d, respectively; ③ According to the analysis of the microbial community structure, the community composition in both sludges changed markedly. Moreover, the microbial community in the municipal sludge showed a more evident change than that of the coking sludge. In the coking sludge, the dominant bacteria community changed a little after acclimation, most of the observed bacteria were previously reported common PAH-degrading strains. In contrast, the dominant bacteria community in the municipal sludge varied greatly after acclimation, and the most abundant bacteria were not common PAH-degrading strains. In addition, some frequently reported PAHs-degrading bacteria such as Bacillus sp., Pseudomonas, Achromobacter, and Sphingomonas sp., were identified in both the sludges and were present in high abundance. The results indicated that municipal sludge utilized BaP more actively than coking sludge; this phenomenon can be explained by the fact that municipal sludge contained a higher diversity of microbes that were involved in the degradation of BaP. Furthermore, the presence of phenol promoted the degradation of PAHs like BaP. Therefore, we proposed that the PAHs in coking sludge discharge might be reduced by the addition phenol and municipal wastewater.

Quantification of the relationship between multiple metal(loid) distribution and integrated effect of internal-external factors in riverbed sediments across Xijiang River basin, South China.

Understanding the integrated effect of external factors (e.g., human activities) and internal factors (e.g., hydrodynamics, sediment properties) on metal(loid) distributions is necessary for relevant decision-makers to develop river basin management strategies. In attempts to understand the possible causes of the distribution of nine target metal(loid)s in riverbed sediments across Xijiang River basin in China, we grouped and portrayed the multiple metal(loid) distributions by calculating metal(loid)'s normalised-and-weighted average concentrations, and then canonical correlation analysis combined with a series of statistical operations, collectively called optimized CCA analysis, was applied to quantify the strength of relationship between multiple metal(loid) distribution and integrated effect of internal-external factors. Results showed that the target metal(loid)s can be divided into three groups according to their distribution patterns: Group A (including Zn, As, Cd, Sb and Pb), Group B (including Cr, Ni and Cu) and Group C (including Tl). Among them, metal(loid)s in Group A was significantly enriched in comparison with the reference values of Chinese sediments, and the wide-ranging accumulation of Cd and Sb in the whole study area needs paying great attention to. For those metals in natural states (e.g., metals in Group B), the affinity of sediment (e.g., Fe and Mn oxides) is responsible for their distributions. By contrast, when metal(loid)s (e.g., metal(loid)s in Group A and Group C) had obvious anthropogenic sources, the interferences of anthropogenic inputs (e.g., non-ferrous metal enterprises' waste-discharging activities) and the specific sedimentary characteristics (e.g. karst topography and low-energy hydrodynamic depositional conditions) in study area can weaken the correlation between the binding affinity of sediment and the contents of metal(loid)s. The optimized CCA analysis can be an alternative and advantageous statistical operation for determining the main types of causes of multiple metal(loid) distribution in the case of observations with relatively low case-per-variable ratios.