Unraveling Immune Heterogeneity across Pan-Cancer and Deep Insights in Lung Adenocarcinoma based on Alternative Splicing.

Alternative splicing (AS) participates in tumor development and tumor microenvironment formation. However, the landscape of immune infiltrating AS events (IIASE) in pan-cancer and mechanisms of AS in lung adenocarcinoma (LUAD) have not been comprehensively characterized. We systematically profiled the IIASE landscape of pan-cancer using data from The Cancer Genome Atlas (TCGA), analyzing both commonalities and specific characteristics among different cancer types. We found that AS events tend to occur specifically in one cancer type rather than in multiple cancer types. AS events were used to classify 512 LUAD samples into two subtypes by unsupervised clustering: aberrant splicing subtype (ABS) and immune infiltrating subtype (IIS). The two subtypes showed significant differences in clinicopathology, prognosis, transcriptomics, genomics and immune microenvironment. We constructed a classification signature comprising 10 genes involved in 14 AS events using Logistic regression. The robustness of the signature was validated in three independent datasets using survival analysis. To explore AS mechanisms in LUAD, we constructed subtype-specific co-expression networks using Pearson correlation analysis. AS event of AKT3 regulated by splicing factor ENOX1 was associated with poor prognosis in LUAD. Overall, we outline AS events associated with immune infiltration in pan-cancer and this study provides insights into AS mechanisms in LUAD patient classification.

Harnessing genetic interactions for prediction of immune checkpoint inhibitors response signature in cancer cells.

Genetic interactions (GIs) refer to two altered genes having a combined effect that is not seen individually. They play a crucial role in influencing drug efficacy. We utilized CGIdb 2.0 (http://www.medsysbio.org/CGIdb2/), an updated database of comprehensively published GIs information, encompassing synthetic lethality (SL), synthetic viability (SV), and chemical-genetic interactions. CGIdb 2.0 elucidates GIs relationships between or within protein complex models by integrating protein-protein physical interactions. Additionally, we introduced GENIUS (GENetic Interactions mediated drUg Signature) to leverage GIs for identifying the response signature of immune checkpoint inhibitors (ICIs). GENIUS identified high MAP4K4 expression as a resistant signature and high HERC4 expression as a sensitive signature for ICIs treatment. Melanoma patients with high expression of MAP4K4 were associated with decreased efficacy and poorer survival following ICIs treatment. Conversely, overexpression of HERC4 in melanoma patients correlated with a positive response to ICIs. Notably, HERC4 enhances sensitivity to immunotherapy by facilitating antigen presentation. Analyses of immune cell infiltration and single-cell data revealed that B cells expressing MAP4K4 may contribute to resistance to ICIs in melanoma. Overall, CGIdb 2.0, provides integrated GIs data, thus serving as a crucial tool for exploring drug effects.

Unravelling the resilience of magnetite assisted granules to starvation and oxytetracycline stress.

Starvation and antibiotics pollution are two frequent perturbations during breeding wastewater treatment process. Supplying magnetite into anaerobic system has been proved efficient to accelerate microbial aggregates and alleviate the adverse effect caused by process disturbance. Nevertheless, whether these magnetite-based granules are still superior over normal granules after a long-term starvation period remains unknown, the responsiveness of these granules to antibiotics stress is also ambiguous. In current study, we investigated the resilience of magnetite-based anaerobic granular sludge (AnGS) to starvation and oxytetracycline (OTC) stress, by unravelling the variations of reactor performance, sludge properties, ARGs dissemination and microbial community. Compared with the AnGS formed without magnetite, the magnetite assisted AnGS appeared more robust defense to starvation and OTC stress. With magnetite supplement, the average methane yield after starvation recovery, 50 mg/L and 200 mg/L OTC stress was enhanced by 48.95%, 115.87% and 488.41%, respectively, accompanied with less VFAs accumulation, improved tetracycline removal rate (76.3-86.6% vs. 51.0-53.5%) and higher ARGs reduction. Meanwhile, magnetite supplement effectively ameliorated the potential sludge breakage by triggering more large granules formation. Trichococcus was considered an important impetus in maintaining the stability of magnetite-based AnGS process. By inducing more syntrophic methanogenesis partnerships, especially for hydrogenotrophic methanogenesis, magnetite ensured the improved reactor performance and stronger resilience at stress conditions.

Effect of magnetite on anaerobic digestion treating saline wastewater: Methane production, biomass aggregation and microbial community dynamics.

In this study, the effect of magnetite amendment on anaerobic digestion was investigated at three increasing salinity levels (0.5%, 1% and 2% NaCl). The amendment of magnetite enhanced the methane yield by 36.3%, 33.3% and 16.5% at low salinity (0.5% NaCl) and high salinity (1% and 2% NaCl), respectively. Meanwhile, a larger proportion of granules was obtained in the magnetite amended reactor (48.05% vs 33.16% at the end of operation). Microbial analysis suggested magnetite could induce more methanogenesis partnerships between hydrogenotrophic methanogens and syntrophic bacteria. Methanosaeta and Methanocorpusculum were the alternating dominant methanogens at low salinity and high salinity. While Streptococcus and Mesotoga were two prevalent bacteria that showed totally different transition tendency in two reactors. Additionally, the supplement of magnetite could relieve the suppression of methanogenesis-related gene expression caused by salinity, thus facilitated the higher methane production.

Generation mechanisms of active free radicals during ciprofloxacin degradation in the ultrasonic/K2S2O8 system.

Ciprofloxacin (CIP) removal efficiency in aqueous solutions in the ultrasonic (US), K2S2O8, and US/K2S2O8 systems was investigated. The free radical generation and action ratio were studied based on variations of K2S2O8 concentration, ultrasonic power, pH, and the addition of isopropanol (ISP) or tert-butyl alcohol (TBA) in the US/K2S2O8 system. The results showed that under conditions of 20 mg·L-1 CIP concentration, 20 mmol·L-1 K2S2O8 concentration, an ultrasonic power of 360 W and pH = 7, CIP removal efficiency in the US/K2S2O8 system was 92.20% after 180 min. The reaction in the US/K2S2O8 system was explicitly divided into two stages: free radical generation and pollutants degradation. The ultrasonic and chain reaction facilitated enhanced generation of SO4-• and HO•. The presence of K2S2O8 can promote HO• generation and K2S2O8 concentration also exerted a significant effect on SO4-• generation, however, high concentrations were not beneficial to the reaction. Quenching reactions occurred under high concentrations of HO• and SO4-•. During the initial stage of the reaction, HO• played a more prominent role than SO4-•, however, the role of SO4-• gradually increased as the reaction proceeded and eventually surpassed HO•.

Insight into the performance and microbial community profiles of magnetite-amended anaerobic digestion: Varying promotion effects at increased loads.

In current study, the enhancement effect of magnetite on anaerobic digestion was evaluated at increased organic loading rate (OLR) from 1.6 to 25.6 kg COD·m-3·d-1. The supplement of magnetite enhanced the methane yield by 7-483% accompanied with faster VFAs conversion. Microbial analysis suggested the varied enhancing effect achieved at different OLRs was attributed to different syntrophic interactions triggered by magnetite. More specially, an electroactive syntropy was established between Trichococcus with Methanobacterium at OLR lower than 6.4 kg COD·m-3·d-1, while with the OLR increase, more acid fermentative bacteria (Propionimicrobium, Syner-01) were enriched and further enhanced methanogenesis in a syntrophic way with Methanosaeta. Overall, the incorporation of magnetite was a promising approach to achieve efficient anaerobic digestion, OLR was also critical factor affecting the methanogenesis and should be carefully regulated in future application.

Short- and medium-chain chlorinated paraffins in the Henan section of the Yellow River: Occurrences, fates, and fluxes.

Short- and medium-chain chlorinated paraffins (SCCPs and MCCPs) were measured in sediment and suspended particulate matter (SPM) from the middle and lower reaches of the Yellow River in the three seasons to elucidate their environmental behavior. The mean concentrations of ∑SCCPs and ∑MCCPs were 262 and 97.1 ng g-1 dw (dry weight) in sediment and 17,055 and 2573 ng g-1 dw in SPM, respectively, and higher SCCP levels did not clearly reflect a shift to more MCCPs in this section of the Yellow River. The predominant homologue groups were C10-CP and C11-CP for SCCPs and C14-CP for MCCPs. The CPs possibly mainly derived from the use of CP commercial mixtures, mainly included CP-42 and CP-52. The spatial distributions and principal component analysis indicated that industrial inputs, dams, and topography played important roles in influencing the environmental behavior of CPs in both sediment and SPM. In addition, decreasing fluxes of CPs were observed in SPM from Tongguan to Aishan stations, particularly in reservoirs, which implies that CPs may have accumulated in the Henan section of the Yellow River.

Modeling techniques and fluorescence imaging investigation of the interactions of an anthraquinone derivative with HSA and ctDNA.

A new anthraquinone derivative (AORha) was synthesized. Its interactions with human serum albumin (HSA) and calf thymus DNA (ctDNA) were investigated by fluorescence spectroscopy, UV-visible absorption spectroscopy and molecular modeling. Cell viability assay and cell imaging experiment were performed using cervical cancer cells (HepG2 cells). The fluorescence results revealed that the quenching mechanism was static quenching. At different temperatures (290, 300, 310 K), the binding constants (K) and the number of binding sites (n) were determined, respectively. The positive ΔH and ΔS values showed that the binding of AORha with HSA was hydrophobic force, which was identical with the molecular docking result. Studying the fluorescence spectra, UV spectra and molecular modeling also verified that the binding mode of AORha and ctDNA might be intercalative. When HepG2 cells were treated with AORha, the fluorescence became brighter and turned green, which could be used for bioimaging.

Three-dimensional excitation-emission matrix fluorescence spectroscopy and fractions of dissolved organic matter change in landfill leachate by biological treatment.

The water quality improvement of landfill leachate after sequencing batch reactor (SBR) activated sludge process were evaluated by chemical oxygen demand (COD), dissolved organic matter (DOM) fractions, and three-dimensional excitation-emission matrix (EEM), from which the new understanding was obtained. The results indicated that less than 14% COD was removed by SBR. The EEM of leachate and SBR effluent showed that HPO-A and TPI-A were appeared in the peak C, while the HPI, HPO-N, and TPI-N could not be found due to dilution. Although humic acid appeared in peak C, not all the organic materials in peak C are humic acid. And because landfill leachate is a kind of complicated wastewater, therefore, only EEM cannot efficiently reflect the water quality.

[Influence of Biological Activated Carbon on Simultaneous Nitrification and Denitrification in Inflow with Different C/N Ratios].

Influence of biological activated carbon (BAC) on simultaneous nitrification and denitrification (SND) in inflow with different C/N ratios was investigated with continuous operation of BAC reactor and SBR. Methanol was added as carbon source and the inflow C/N ratio was set to 3, 5, 8 and 10 to run for about 120 cycles, under conditions of indoor temperature (15-27℃), initial DO 2-3mg·L-1. The TN removal efficiency and stability of two reactors were compared. The results showed that, BAC reactor had a higher TN removal efficiency than SBR at different C/N ratios. TN removal rate of BAC reactor was 44.88%, 58.07% and 66.64%, when the C/N ratio was 3, 5 and 8 respectively. After increasing the C/N ratio to 10, the BAC reactor could maintain TN removal rate of 63.65%, but the SBR showed sludge bulking. BAC provided various DO environments for microorganisms in a vessel, which was beneficial to SND. BAC could reduce the influence of excessive carbon source on the nitrification system, enlarge the application range and improve the stability of reactor at different C/N ratios, and increase the nitrogen removal capacity of organic matter. BAC provided condition for efficient nitrogen removal.

[Extraction of Heavy Metals from Sludge Using Biodegradable Chelating Agent N,N-bis(carboxymethyl) Glutamic Acid Tetrasodium].

N, N-bis (carboxymethyl) glutamic acid tetrasodium (GLDA), a novel biodegradable and green chelating agent, has excellent metal chelating ability. Batch experiment was conducted to study the extraction process of Cd, Ni, Cu and Zn in industrial sludge using GLDA. The effects of contact time, pH of the system, content of chelating agent were investigated, and the forms of heavy metals in sludge pre- and post-extraction using the modified BCR sequential extraction procedure were studied. The results showed that GLDA was effective for cadmium extraction in sludge. Several heavy metals could be effectively extracted under the condition of pH 4 and molar ratio of chelating agent to total heavy metal 3:1. Residual fraction took the largest fraction in Zn, which caused the low extraction efficiency of this metal. Chelating properties were related not only to contact time, pH, chelating agent's concentration, and stability constant but also to species distribution of metals.

Effective removal of heavy metals from industrial sludge with the aid of a biodegradable chelating ligand GLDA.

Tetrasodium of N,N-bis(carboxymethyl) glutamic acid (GLDA), a novel readily biodegradable chelating ligand, was employed for the first time to remove heavy metals from industrial sludge generated from a local battery company. The extraction of cadmium, nickel, copper, and zinc from battery sludge with the presence of GLDA was studied under different experimental conditions such as contact times, pH values, as well as GLDA concentrations. Species distribution of metals in the sludge sample before and after extraction with GLDA was also analyzed. Current investigation showed that (i) GLDA was effective for Cd extraction from sludge samples under various conditions. (ii) About 89% cadmium, 82% nickel and 84% copper content could be effectively extracted at the molar ratio of GLDA:M(II)=3:1 and at pH=4, whereas the removal efficiency of zinc was quite low throughout the experiment. (iii) A variety of parameters, such as contact time, pH values, the concentration of chelating agent, stability constant, as well as species distribution of metals could affect the chelating properties of GLDA.

Removal of heavy metal species from industrial sludge with the aid of biodegradable iminodisuccinic acid as the chelating ligand.

High level of heavy metals in industrial sludge was the obstacle of sludge disposal and resource recycling. In this study, iminodisuccinic acid (IDS), a biodegradable chelating ligand, was used to remove heavy metals from industrial sludge generated from battery industry. The extraction of cadmium, copper, nickel, and zinc from battery sludge with aqueous solution of IDS was studied under various conditions. It was found that removal efficiency greatly depends on pH, chelating agent's concentration, as well as species distribution of metals. The results showed that mildly acidic and neutral systems were not beneficial to remove cadmium. About 68 % of cadmium in the sample was extracted at the molar ratio of IDS to heavy metals 7:1 without pH adjustment (pH 11.5). Copper of 91.3 % and nickel of 90.7 % could be removed by IDS (molar ratio, IDS: metals = 1:1) with 1.2 % phosphoric acid effectively. Removal efficiency of zinc was very low throughout the experiment. Based on the experimental results, IDS could be a potentially useful chelant for heavy metal removal from battery industry sludge.

[Influence of biological activated carbon dosage on landfill leachate treatment].

Effects of biological activated carbon (BAC) dosage on COD removal in landfill leachate treatment were compared. The COD removal efficiency of reactors with 0, 100 and 300 g activated carbon dosage per litre activated sludge was 12.9%, 19.6% and 27.7%, respectively. The results indicated that BAC improved the refractory organic matter removal efficiency and there was a positive correlation between COD removal efficiency and BAC dosage. The output of carbon dioxide after 8h of aeration in reactors was 109, 193 and 306 mg corresponding to the activated carbon dosages mentioned above, which indicated the amount of biodegradation and BAC dosage also had a positive correlation. The combination of adsorption and bioregeneration of BAC resulted in the positive correlation betweem organic matter removal efficiency and BAC dosage, and bioregeneration was the root cause for the microbial decomposition of refractory organics.

Interaction of one anthraquinone derivative with ctDNA analyzed by spectroscopic and modeling methods.

The interaction of one anthraquinone derivative (AOMan) with calf thymus deoxyribonucleic acid (ctDNA) was systematically investigated at physiological pH 7.4 by fluorescence spectroscopy and molecular modeling. Binding constants of ctDNA with AOMan were calculated at different temperatures. Thermodynamic parameters, enthalpy and entropy changes were calculated according to Van't Hoff equation, which indicated that the reaction was spontaneous and predominantly enthalpically driven. The increasing viscosity of ctDNA indicated that AOMan could intercalate into the base pairs of ctDNA. This conclusion was also demonstrated by the results obtained from KI quenching, denatured DNA studies and fluorescence polarization experiment. Furthermore, the molecular modeling results showed that anthraquinone ring tended to slide into the G-C rich region of ctDNA through the hydrogen bond, which are consistent with the results from experimental methods. Studying the binding interaction of target anthraquinones with DNA is one of the key steps in their DNA-changing action and the design of new drugs.

Layer-by-layer construction of graphene-based microbial fuel cell for improved power generation and methyl orange removal.

Development of highly efficient anode is critical for enhancing the power output of microbial fuel cells (MFCs). The aim of this work is to investigate whether modification of carbon paper (CP) anode with graphene (GR) via layer-by-layer assembly technique is an effective approach to promote the electricity generation and methyl orange removal in MFCs. Using cyclic voltammetry and electrochemical impedance spectroscopy, the GR/CP electrode exhibited better electrochemical behavior. Scanning electron microscopy results revealed that the surface roughness of GR/CP increased, which was favorable for more bacteria to attach to the anode surface. The MFCs equipped with GR/CP anode achieved a stable maximum power density of 368 mW m(-2) under 1,000 Ω external resistance and a start time for the initial maximum voltage of 180 h, which were, respectively, 51 % higher and 31 % shorter than the corresponding values of the MFCs with blank anode. The anode and cathode polarization curves revealed negligible difference in cathode potentials but obviously difference in anode potentials, indicating that the GR-modified anode other than the cathode was responsible for the performance improvement of MFC. Meanwhile, compared with MFCs with blank anode, 11 % higher decolorization efficiency and 16 % higher the chemical oxygen demand removal rate were achieved in MFC with GR-modified anode during electricity generation. This study might provide an effective way to modify the anode for enhanced electricity generation and efficient removal of azo dye in MFCs.

Investigations on the interactions of diclofenac sodium with HSA and ctDNA using molecular modeling and multispectroscopic methods.

A tentative study on interaction of diclofenac sodium (DF-Na) with human serum albumin (HSA) and calf thymus DNA (ctDNA) was conducted by using multi-spectroscopic and molecular modeling techniques under simulative physiological conditions. The results of spectroscopic measurements suggested that the quenching mechanisms were static quenching. Three-dimensional fluorescence spectroscopy clearly demonstrated the occurrence of conformational changes of HSA with addition of DF-Na. In addition, competitive studies with ethidium bromide (EB) have shown that DF-Na can bind to ctDNA relatively strong via groove binding. Based on the values of thermodynamic parameters and the results of molecular modeling, it was confirmed that hydrophobic forces and hydrogen bond were the mainly binding forces in DF-Na-HSA and DF-Na-DNA systems. The binding distance between DF-Na and HSA was also determined using the theory of the Förster energy transference.

[Determination of the proteins in serum albumins by synchronous fluorescence technique with 3-(2-cyanoethyl) cytosine as a probe].

Under simulative biological conditions and upon the interactions between 3-(2-cyanoethyl) cytosine (CECT) and human serum albumin (HSA) or bovine serum albumin (BSA), the authors studied the characteristics of synchronous fluorescence spectra of CECT-protein system with CECT as a molecular spectral probe. The spectral characteristics and intensity of synchronous fluorescence were related to the value of deltalambda, reaction medium, reaction temperature and so on. On the basis of these, the new method for the determination of proteins in serum albumin was developed with CECT as a molecular spectral probe. Under the optimum experimental conditions, the synchronous fluorescence intensities of CECT-HSA and CECT-BSA systems were in good proportion to the concentrations of HSA and BSA in the ranges of 0-441.4 and 0-351.0 microg x mL(-1), respectively. The detection limits were 0.023 and 0.035 microg x mL(-1), respectively. Relative standard deviations located between 12% and 3.3%, and the addition standard recovery was 97.2%-100.4% for all elements. The results suggested that the method features easy of implementation, rapidity, high sensitivity, broad linear range, and better RSD and recovery etc., and was employed directly to determine the total proteins in serum albumin samples with satisfactory results.

Investigation of interaction between human serum albumin and N6-(2-hydroxyethyl)-adenosine by fluorescence spectroscopy and molecular modelling.

The interaction between human serum albumin (HSA) and N(6)-(2-hydroxyethyl)-adenosine (HEA) was investigated using fluorescence spectroscopy in combination with UV absorption spectroscopy for the first time. The results of spectroscopic measurements suggested that the hydrophobic interaction was the predominant intermolecular force stabilizing the complex, which was in good agreement with the results of molecular modelling study. The enthalpy change (DeltaH) and the entropy change (DeltaS) were calculated, according to the Van't Hoff equation, to be -24.05 kJ/mol and 30.23 J/mol/K, respectively. The effects of common ions on the binding constant of the HEA-HSA complex at room temperature were also investigated.

Binding of human serum albumin to N-(p-ethoxy-phenyl)-N'-(1-naphthyl)thiourea and synchronous fluorescence determination of human serum albumin.

The binding of N-(p-ethoxy-phenyl)-N'-(1-naphthyl)thiourea (EPNT) to human serum albumin (HSA) was investigated under simulative physiological conditions by fluorescence spectra in combination with UV absorption spectroscopy and a molecular modeling method. A strong fluorescence quenching reaction of EPNT to HSA was observed, and the quenching mechanism was suggested to be static quenching according to the Stern-Volmer equation. The binding constants (K) at different temperatures as well as thermodynamic parameters, enthalpy change (DeltaH) and entropy change (DeltaS), were calculated according to relevant fluorescent data and the vant' Hoff equation. This indicated that a hydrophobic interaction was a predominant intermolecular force for stabilizing the complex, which is in agreement with the results of molecule modeling study. The effects of energy transfer and other ions on the binding constant were considered. In addition, synchronous fluorescence technology was successfully applied to the determination of HSA added into the EPNT solution.