HBO1 catalyzes lysine lactylation and mediates histone H3K9la to regulate gene transcription.

Lysine lactylation (Kla) links metabolism and gene regulation and plays a key role in multiple biological processes. However, the regulatory mechanism and functional consequence of Kla remain to be explored. Here, we report that HBO1 functions as a lysine lactyltransferase to regulate transcription. We show that HBO1 catalyzes the addition of Kla in vitro and intracellularly, and E508 is a key site for the lactyltransferase activity of HBO1. Quantitative proteomic analysis further reveals 95 endogenous Kla sites targeted by HBO1, with the majority located on histones. Using site-specific antibodies, we find that HBO1 may preferentially catalyze histone H3K9la and scaffold proteins including JADE1 and BRPF2 can promote the enzymatic activity for histone Kla. Notably, CUT&Tag assays demonstrate that HBO1 is required for histone H3K9la on transcription start sites (TSSs). Besides, the regulated Kla can promote key signaling pathways and tumorigenesis, which is further supported by evaluating the malignant behaviors of HBO1- knockout (KO) tumor cells, as well as the level of histone H3K9la in clinical tissues. Our study reveals HBO1 serves as a lactyltransferase to mediate a histone Kla-dependent gene transcription.

Magnaporthe oryzae effector MoSPAB1 directly activates rice Bsr-d1 expression to facilitate pathogenesis.

Fungal pathogens typically use secreted effector proteins to suppress host immune activators to facilitate invasion. However, there is rarely evidence supporting the idea that fungal secretory proteins contribute to pathogenesis by transactivating host genes that suppress defense. We previously found that pathogen Magnaporthe oryzae induces rice Bsr-d1 to facilitate infection and hypothesized that a fungal effector mediates this induction. Here, we report that MoSPAB1 secreted by M. oryzae directly binds to the Bsr-d1 promoter to induce its expression, facilitating pathogenesis. Amino acids 103-123 of MoSPAB1 are required for its binding to the Bsr-d1 promoter. Both MoSPAB1 and rice MYBS1 compete for binding to the Bsr-d1 promoter to regulate Bsr-d1 expression. Furthermore, MoSPAB1 homologues are highly conserved among fungi. In particular, Colletotrichum fructicola CfSPAB1 and Colletotrichum sublineola CsSPAB1 activate kiwifruit AcBsr-d1 and sorghum SbBsr-d1 respectively, to facilitate pathogenesis. Taken together, our findings reveal a conserved module that may be widely utilized by fungi to enhance pathogenesis.

Optimization of membrane filtration and cleaning strategy in a high solid thermophilic AnMBR treating food waste.

Anaerobic membrane bioreactor is advantageous over traditional processes for food waste treatment, i.e. short retention time, high loading rate, and particulate clean permeate. However, establishing a sustainable membrane filtration is a long-standing challenge because of its high viscosity and solids concentration characteristics. Therefore, this study investigated the changes in the membrane permeability before and after the cleaning during a 130-day thermophilic anaerobic experiment. Results show that the AnMBR system could maintain high stability even under a short HRT of 10 days and OLR of 9.0 kg-COD/(m3·d) with low volatile fatty acid of 50 mg/L. The membrane filtration deteriorates with the concurrence of a sharp increase of viscosity when the volatile solids reached 23 g/L. A critical flux was achieved at 5.5 L/(m2·h) under optimized operation conditions, membrane filtration/relaxing ratio with less than 4:1 at a hydraulic retention time of 15 d. Membrane fouling can be removed by soaking the membrane in NaClO (1 g/L, 15 h) and citric acid (2 g/L, 2 h). Conclusively, this work provides insight to establish the operation strategy for a thermophilic AnMBR treating food waste.

Chemically and biologically driven carbon transformation flow in MSW leachate treated by a high-solids anaerobic membrane bioreactor system.

Carbon transformation is important for an anaerobic process but is often overlooked when using an anaerobic membrane bioreactor (AnMBR). Material flow in an AnMBR treating calcium-rich MSW leachate was thus quantitatively investigated to illustrate how chemical and biological factors affect carbon transformation. The results show that a remarkable amount of carbon in the leachate was degraded, with 50.1% of it should be converted into CH4 and 37.7% of it into CO2. However, a much smaller value of 40.6% and 14.2% were experimentally obtained. Chemical analysis indicated that the precipitation of calcium carbonate captured 1.23 g/day of carbon. At the same time, about 23.2 g/L HCO3- and 16.6 mg/L CH4 (both as carbon) were dissolved in the liquid. Those features facilitated the high CH4 (74%) content in biogas. A carbon transformation model was therefore established and showed carbon flow into the gas, liquid, and solid phases, respectively. Carbon existed in biogas, permeate, and discharged sludge was also obtained.

Temperature changes of renal calyx during high-power flexible ureteroscopic Moses holmium laser lithotripsy: a case analysis study.

PURPOSE: The risk of thermal damage increases with the introduction of high-power lasers during holmium laser lithotripsy. This study aimed to quantitatively evaluate the temperature change of renal calyx in the human body and the 3D printed model during high-power flexible ureteroscopic holmium laser lithotripsy and map out the temperature curve. METHODS: The temperature was continuously measured by a medical temperature sensor secured to a flexible ureteroscope. Between December 2021 and December 2022, willing patients with kidney stones undergoing flexible ureteroscopic holmium laser lithotripsy were enrolled. High frequency and high-power settings (24 W, 80 Hz/0.3 J and 32 W, 80 Hz/0.4 J) were performed for each patient with room temperature (25 °C) irrigation. In the 3D printed model, we studied more holmium laser settings (24 W, 80 Hz/0.3 J, 32 W, 80 Hz/0.4 J and 40 W, 80 Hz/0.4 J) with warmed (37 °C) and room temperature (25 °C) irrigation. RESULTS: Twenty-two patients were enrolled in our study. With 30 ml/min or 60 ml/min irrigation, the local temperature of the renal calyx did not reach 43 °C in any patient under 25 °C irrigation after 60 s laser activation. There were similar temperature changes in the 3D printed model with the human body under the irrigation of 25 °C. Under the irrigation of 37 °C, the temperature rise slowed down, but the temperature in the renal calyces was close to or even exceeded the 43 °C at the setting of 32 W, 30 ml/min and 40 W, 30 ml/min after continuing laser activation. CONCLUSION: In the irrigation of 60 ml/min, the temperature in the renal calyces can still be maintained within a safe range after continuous activation of a holmium laser up to 40 W. However, continuous activation of 32 W or higher power holmium laser in the renal calyces for more than 60 s in the limited irrigation of 30 ml/min can cause excessive local temperature, in such situation room temperature perfusion at 25 ℃ may be a relatively safer option.

Visualization of Traditional Chinese Medicine Formulas: Development and Usability Study.

BACKGROUND: Traditional Chinese medicine (TCM) formulas are combinations of Chinese herbal medicines. Knowledge of classic medicine formulas is the basis of TCM diagnosis and treatment and is the core of TCM inheritance. The large number and flexibility of medicine formulas make memorization difficult, and understanding their composition rules is even more difficult. The multifaceted and multidimensional properties of herbal medicines are important for understanding the formula; however, these are usually separated from the formula information. Furthermore, these data are presented as text and cannot be analyzed jointly and interactively. OBJECTIVE: We aimed to devise a visualization method for TCM formulas that shows the composition of medicine formulas and the multidimensional properties of herbal medicines involved and supports the comparison of medicine formulas. METHODS: A TCM formula visualization method with multiple linked views is proposed and implemented as a web-based tool after close collaboration between visualization and TCM experts. The composition of medicine formulas is visualized in a formula view with a similarity-based layout supporting the comparison of compositing herbs; a shared herb view complements the formula view by showing all overlaps of pair-wise formulas; and a dimensionality-reduction plot of herbs enables the visualization of multidimensional herb properties. The usefulness of the tool was evaluated through a usability study with TCM experts. RESULTS: Our method was applied to 2 typical categories of medicine formulas, namely tonic formulas and heat-clearing formulas, which contain 20 and 26 formulas composed of 58 and 73 herbal medicines, respectively. Each herbal medicine has a 23-dimensional characterizing attribute. In the usability study, TCM experts explored the 2 data sets with our web-based tool and quickly gained insight into formulas and herbs of interest, as well as the overall features of the formula groups that are difficult to identify with the traditional text-based method. Moreover, feedback from the experts indicated the usefulness of the proposed method. CONCLUSIONS: Our TCM formula visualization method is able to visualize and compare complex medicine formulas and the multidimensional attributes of herbal medicines using a web-based tool. TCM experts gained insights into 2 typical medicine formula categories using our method. Overall, the new method is a promising first step toward new TCM formula education and analysis methodologies.

Exosomal circKDM4A Induces CUL4B to Promote Prostate Cancer Cell Malignancy in a miR-338-3p-Dependent Manner.

Circular RNA lysine demethylase 4A (circKDM4A) is also named circ_0012098 and its abnormal expression has been confirmed in serum exosomes of prostate cancer (PC) patients. However, whether PC progression involves the exosomal circ_0012098 remains unknown. RNA expression of circKDM4A, microRNA-338-3p (miR-338-3p) and cullin 4B (CUL4B) was detected by quantitative real-time polymerase chain reaction. Protein expression was checked by Western blot. The positive expression rate of nuclear proliferation marker (ki-67) was analyzed by immunohistochemistry assay. Dual-luciferase reporter assay and RNA immunoprecipitation assay were used to identify the interaction between miR-338-3p and circKDM4A or CUL4B. Mouse model assay was performed to determine the effect of exosomal circKDM4A on tumorigenesis in vivo. CircKDM4A expression was significantly upregulated in the serum exosomes from PC patients compared with the exosomes from healthy volunteers. Exosomes treatment promoted the proliferation, migration and invasion of PC cells but inhibited apoptosis; however, these effects were attenuated after circKDM4A knockdown. Meanwhile, circKDM4A depletion restored exosome-increased circKDM4A expression. Additionally, circKDM4A acted as a miR-338-3p sponge, and miR-338-3p bound to CUL4B in PC cells. CircKDM4A regulated the effect of exosome-induced PC cell malignancy by interacting with miR-338-3p and CUL4B. Moreover, circKDM4A silencing relieved exosome-induced tumor growth in vivo. Exosomal circKDM4A promoted PC malignant progression by the miR-338-3p/CUL4B axis, providing a therapeutic target for PC.

A Novel Strategy Based on Permanent Protein Modifications Induced by Formaldehyde for Food Safety Analysis.

The illegal additions of chemicals in food products are serious incidents threatening current public safety. To date, ideal methods to determine permanent traces of prohibited chemicals in foods are still lacking. For example, formaldehyde (FA) can be added illegally as a food preservative. However, most current methods that are dependent on the direct detection of FA are not able to determine if FA has ever been added once food products are rinsed completely. Herein, we present a novel approach relying upon protein modifications induced by FA (PMIF) to examine FA in foods. We reveal the entire catalog of PMIFs in food products by combining mass spectrometry analysis with unrestrictive identification of protein modifications. Consequently, four obvious PMIFs were identified and confirmed as markers to discriminate the addition of FA in foods. Our study demonstrates that the approach based on PMIFs enables detecting the imprinted trace of FA even if the food products have been washed thoroughly. Our work presents a novel strategy for analysis of chemical additives, offering broad potential applications in protein analysis and food safety.

Organizing Enzymes on Self-Assembled Protein Cages for Cascade Reactions.

Cells use self-assembled biomaterials such as lipid membranes or proteinaceous shells to coordinate thousands of reactions that simultaneously take place within crowded spaces. However, mimicking such spatial organization for synthetic applications in engineered systems remains a challenge, resulting in inferior catalytic efficiency. In this work, we show that protein cages as an ideal scaffold to organize enzymes to enhance cascade reactions both in vitro and in living cells. We demonstrate that not only enzyme-enzyme distance but also the improved Km value contribute to the enhanced reaction rate of cascade reactions. Three sequential enzymes for lycopene biosynthesis have been co-localized on the exterior of the engineered protein cages in Escherichia coli, leading to an 8.5-fold increase of lycopene production by streamlining metabolic flux towards its biosynthesis. This versatile system offers a powerful tool to achieve enzyme spatial organization for broad applications in biocatalysis.

Mitigating membrane fouling in a high solid food waste thermophilic anaerobic membrane bioreactor by incorporating fixed bed bio-carriers.

Hybrid anaerobic membrane bioreactor (Hy-AnMBR) was developed by incorporating polyurethane sponge carriers to mitigate membrane fouling. The results showed that the membrane fouling was well controlled in Hy-AnMBR from the aspects of sludge property and membrane filtration performance. The solid concentration, including TS and MLSS in the Hy-AnMBR was reduced after introducing the fixed bed carrier, which was 13% and 20% lower than the control AnMBR (Con-AnMBR), and this resulted in improved filtration performance. The scanning electron microscope (SEM) photograph showed that membrane pores could still be observed on the Hy-AnMBR surface, indicating that the cake layer fouling of the Hy-AnMBR was less than the Con-AnMBR. The increase of the EPS and SMP promoted the acceleration of the membrane fouling rate. Analysis through confocal laser scanning microscopy (CLSM) and membrane cleaning revealed that adding sponge carriers mitigated 3.3%-9% pore-blocking, and the total membrane resistance in the Hy-AnMBR was reduced by 52% compared to the Con-AnMBR. Chemical cleaning was essential for pollutant removal, and membrane permeability recovery was more than 97%.

Predicting membrane fouling in a high solid AnMBR treating OFMSW leachate through a genetic algorithm and the optimization of a BP neural network model.

Anaerobic membrane bioreactors are a promising technology in the treatment of high-strength wastewater; however, unpredictable membrane fouling largely limits their scale-up application. This study, therefore, adopted a backpropagation neural network model to predict the membrane filtration performance in a submerged system, which treats leachate from the organic fraction of municipal solid waste. Duration time, water yield flow, influent COD, pH, bulk sludge concentration, and the ratio of ΔTMP to filtration time were selected as input variables to simulate membrane permeability. The membrane pressure slightly increased by 1.1 kPa within 62 days of operation. The results showed that the AnMBR membrane filtration performance was acceptable when treating OFMSW leachate under a flux of 6 L/(m2·h). The model results indicated that the sludge concentration largely determined the membrane fouling with a contribution of 33.8%. Given the local minimization problem in the BP neural network process, a genetic algorithm was introduced to optimize the simulation process, and the relative error of the results was reduced from 5.57% to 3.57%. Conclusively, the artificial neural network could be a useful tool for the prediction of an AnMBR that is so far under development.

Enhancing the performance of thermophilic anaerobic digestion of food waste by introducing a hybrid anaerobic membrane bioreactor.

The thermophilic anaerobic digestion of food waste was a long-term challenge for maintaining process stability. A hybrid submerged anaerobic membrane bioreactor (AnMBR), integrating 27%(v/v) polyurethane sponge as fixed carriers were therefore investigated at (50 ± 2) °C. The organics removal efficiencies, COD mass balance, and membrane filtration performance were investigated in a 75-days continuously operated experiment. The results showed that methane production reached 0.31 L/(kg·COD) under an organic loading rate of 7.3 kg·COD/(m3·d). The low concentration of total volatile fatty acids of 247 ~ 274 mg/L and a high proportion of Methanosarcina (>97%) represented the high stability of the thermophilic process. Approximately 21% of biomass grew on the carriers in the hybrid AnMBR and induced a much lower suspended solids concentration and viscosity of bulk sludge. Noticeable lower trans-membrane pressure was consequently observed. The affecting factors identified by PCA analysis proved the advantages of the hybrid AnMBR for alleviating membrane fouling formation.

The materials flow and membrane filtration performance in treating the organic fraction of municipal solid waste leachate by a high solid type of submerged anaerobic membrane bioreactor.

The anaerobic digestion of leachate from organic fraction of municipal solid waste (OFMSW) is a long-standing challenge. A submerged anaerobic membrane bioreactor (AnMBR) embedding three flat sheet membrane was therefore continuously operated for 63 days to investigate the materials flow and membrane performance. The results obtained show that approximately 90% COD was removed and 86% was converted into methane under an OLR of 5.6 kgCOD/m3·d corresponding to a HRT of 10 days. Under the high solid condition (34.5-61.1 g/L total solids in AnMBR) and flux of 5 and 6 LMH, the membranes was operated practically at constant trans-membrane pressure (TMP). When the membrane was operated at a high flux of 7 LMH the TMP rapid increase occurred in 22 h resulting in a non-recoverable permeability. A sustainable flux was thus identified. This study demonstrated the feasibility of AnMBR treating OFMSW leachate under high solid condition with high flux.