Hippo-signaling-controlled MHC class I antigen processing and presentation pathway potentiates antitumor immunity.

The major histocompatibility complex class I (MHC class I)-mediated tumor antigen processing and presentation (APP) pathway is essential for the recruitment and activation of cytotoxic CD8+ T lymphocytes (CD8+ CTLs). However, this pathway is frequently dysregulated in many cancers, thus leading to a failure of immunotherapy. Here, we report that activation of the tumor-intrinsic Hippo pathway positively correlates with the expression of MHC class I APP genes and the abundance of CD8+ CTLs in mouse tumors and patients. Blocking the Hippo pathway effector Yes-associated protein/transcriptional enhanced associate domain (YAP/TEAD) potently improves antitumor immunity. Mechanistically, the YAP/TEAD complex cooperates with the nucleosome remodeling and deacetylase complex to repress NLRC5 transcription. The upregulation of NLRC5 by YAP/TEAD depletion or pharmacological inhibition increases the expression of MHC class I APP genes and enhances CD8+ CTL-mediated killing of cancer cells. Collectively, our results suggest a crucial tumor-promoting function of YAP depending on NLRC5 to impair the MHC class I APP pathway and provide a rationale for inhibiting YAP activity in immunotherapy for cancer.

A Laboratory Experimental Study on Enhancing the Oil Recovery Mechanisms of Polymeric Surfactants.

In order to evaluate the physical and chemical properties of polymer surfactants and analyze their oil displacement mechanisms, three types of poly-surfactant used in the Daqing oil field were chosen to be researched, and the oil displacement effects were studied using poly-surfactants of different viscosity, dehydrating rate, and core permeability. The main purpose is to determine the reasonable range of different characteristic indexes of polymeric surfactant flooding. The oil displacement effect of 15 cores was analyzed, and the effects of viscosity, the dehydrating rate of emulsion, and permeability on EOR (Enhanced Oil Recovery) were analyzed. The oil displacement mechanisms of polymeric surfactants were researched using a photolithographic glass core. This paper explores the mechanism underlying production enhancement as an EOR target, while simultaneously conducting laboratory tests to assess the physical and chemical properties of polymeric surfactants. The poly-surfactant agents exhibit a notable increase in viscosity, with the optimal displacement effect observed at a core effective permeability exceeding 400 mD, resulting in a potential EOR of 15% or higher. Moreover, at a viscosity ranging between 40 and 70 mPa·s, the total EOR can reach 73%, with the peak efficiency occurring at a viscosity of 60 mPa·s. The water loss rate of the emulsion, ranging between 30% and 70%, achieves optimal performance at 50%. The poly-surfactants' higher viscosity extends the oil sweep area, enhancing recovery efficiency, and noticeably reducing residual oil compared to water flooding. During poly-surfactant flooding, a substantial amount of residual oil is extracted and transformed into droplets. The rapid emulsification of the polymeric surfactant solution with crude oil forms a stable emulsion, contributing to its significant oil recovery effect. This research provides valuable technical support for EOR in thin and low-quality reservoirs of onshore multi-layered sandstone reservoirs.

Effect of flow fluctuation on water pollution in drinking water distribution systems.

The detachment of biofilm caused by changes in hydraulic conditions is an essential reason for the pollution of water in the drinking water distribution system (DWDS). In this research, the effect of flow fluctuation on bulk water quality was studied. The turbidity, iron concentration, manganese concentration, the total number of bacteria, biodegradable dissolved organic carbon (BDOC), bacterial community structure, and pathogenic genes in bacteria of bulk water were analyzed. The results indicate that the detachment of biofilm caused by fluctuant flow and reverse flow (especially instant reverse flow) can lead to the pollution of water. Throughout the entire experimental period, the turbidity under fluctuant flow velocity is 4.92%∼49.44% higher than that under other flow velocities. BDOC concentration is 5.68%∼53.99% higher than that under low and high flow velocities. The flow fluctuation increases bacterial regrowth potential (BRP) and reduces the biological stability of the bulk water. Low flow velocity is more conducive to the expression of pathogenic functional genes. In the short term, the water quality under low flow velocity is the best. Nevertheless, in a long-term operation (about seven days later), the water quality under high flow velocity is better than that under other flow velocities. This research brings new knowledge about the fluctuant hydraulic conditions on the bulk water quality within the DWDS and provides data support for stable drinking water distribution.

Effects of flow velocity on biofilm composition and microbial molecular ecological network in reclaimed water distribution systems.

The existence of biofilm on the reclaimed water pipeline seriously affects the safety of water distribution. And the flow regimes in the pipeline play a crucial role in the growth of biofilms. In this study, the biofilm composition, surface topography and bacterial community were detected under eight levels of flow velocity in the range of 0.10-1.40 m s-1. The results showed that the dry weight, the concentration of extracellular protein and extracellular polysaccharide in the biofilm reached a dynamic stable period after 640 h. The biofilm composition and surface topography of biofilm were significantly different under the different flow regimes (laminar flow belongs to [0.10, 0.19] m s-1, and turbulent flow belongs to [0.29, 1.40] m s-1). As the flow velocity range increases, the concentration of each component in the biofilm and the parameters of biofilm surface topography increased and then decreased. The flow velocity could be a strong environmental stimulus resulting in the succession of bacterial community in biofilm. As the flow velocity increased from 0.10 m s-1 to 1.40 m s-1, at the phylum level, the average relative abundance of Firmicutes mainly showed a trend of first increasing and then decreasing with the highest abundance value of 71.57% at 0.49 m s-1. The flow velocity increased from 0.10 m s-1 to 0.49 m s-1, a significant increase in microbial diversity could be detected. The increase in flow velocity promoted the proliferation of microorganisms, and the interaction between different microbial components was enhanced. At 0.49 m s-1, the function of the biofilm is complex, and the ability to resist environmental stress is the strongest. This study can effectively improve the cognition depth of biofilms under the influence of flow velocity in the reclaimed water distribution systems, and provide an important theoretical support for the safe distribution of reclaimed water.

DNA base order parameter determination without influence of chemical exchange.

Nuclear magnetic resonance (NMR) spectroscopy is a versatile tool used to investigate the dynamic properties of biological macromolecules and their complexes. NMR relaxation data can provide order parameters S2, which represent the mobility of bond vectors reorienting within a molecular frame. Determination of S2 parameters typically involves the use of transverse NMR relaxation rates. However, the accuracy in S2 determination can be diminished by elevation of the transverse relaxation rates through conformational or chemical exchange involving protonation/deprotonation or non-Watson-Crick base-pair states of nucleic acids. Here, we propose an approach for determination of S2 parameters without the influence of exchange processes. This approach utilizes transverse and longitudinal 13C chemical shift anisotropy (CSA) - dipole-dipole (DD) cross-correlation rates instead of 13C transverse relaxation rates. Anisotropy in rotational diffusion is taken into consideration. An application of this approach to nucleotide base CH groups of a uniformly 13C/15N-labeled DNA duplex is demonstrated.

Diffusion NMR-based comparison of electrostatic influences of DNA on various monovalent cations.

Counterions are important constituents for the structure and function of nucleic acids. Using 7Li and 133Cs nuclear magnetic resonance (NMR) spectroscopy, we investigated how ionic radii affect the behavior of counterions around DNA through diffusion measurements of Li+ and Cs+ ions around a 15-bp DNA duplex. Together with our previous data on 23Na+ and 15NH4+ ions around the same DNA under the same conditions, we were able to compare the dynamics of four different monovalent ions around DNA. From the apparent diffusion coefficients at varied concentrations of DNA, we determined the diffusion coefficients of these cations inside and outside the ion atmosphere around DNA (Db and Df, respectively). We also analyzed ionic competition with K+ ions for the ion atmosphere and assessed the relative affinities of these cations for DNA. Interestingly, all cations (i.e., Li+, Na+, NH4+, and Cs+) analyzed by diffusion NMR spectroscopy exhibited nearly identical Db/Df ratios despite the differences in their ionic radii, relative affinities, and diffusion coefficients. These results, along with the theoretical relationship between diffusion and entropy, suggest that the entropy change due to the release of counterions from the ion atmosphere around DNA is also similar regardless of the monovalent ion types. These findings and the experimental diffusion data on the monovalent ions are useful for examination of computational models for electrostatic interactions or ion solvation.

Control strategies for biofilm control in reclaimed water distribution systems from the perspective of microbial antagonism and electrochemistry.

Biofilm formation in reclaimed water (RW) distribution systems presents significant technical challenges to RW utilization. Two main technologies to control biofilm formation, microbial antagonism (MA) and electrochemical oxidation (EO), are not yet widely used in drip irrigation systems (DIS) and their mechanisms of action need further clarification. In this study, we first showed that the MA and EO treatments reduced biofilm formation by about 62% and 68%, respectively, and extracellular polymeric substance (EPS) content by 14% and 49%, respectively, in biofilms compared with raw RW type 1 (R-RW1) in unused pipes, thus effectively improving the performance of DIS. When MA-RW and EO-RW were applied to already clogged systems, the degree of clogging alleviation varied depending on the severity of the original clogging. We recommend adding the antagonist, Bacillus subtilis, to RW at 25% clogging for the maximum effect and to slow the microbial adaptation process. Compared to MA, the recovery effect of EO was slower initially but lasted longer and had a significantly better alleviating effect on severely clogged pipelines. Illumina Mi-SEQ high-throughput sequencing data showed that both MA and EO resulted in a significant decrease in microbial diversity, dynamic changes in bacterial community structure, and disruption of network interaction and network modularity. Meanwhile, both treatments promoted the growth of specific microorganisms, enhanced the interaction between certain microbial components, and improved the efficiency of information, matter, and energy exchange within the modules. In summary, we verified the dredging effect of two strategies on DIS under different water conditions, revealed the differences in their mechanisms of action, and proposed their application scenarios. Our results will help improve the efficiency of RW in agricultural drip irrigation systems and effectively reduce maintenance costs.

Structure-activity relationship studies on O-alkylamino-tethered salicylamide derivatives with various amino acid linkers as potent anticancer agents.

In our continued SAR study efforts, a series of O-alkylamino-tethered salicylamide derivatives with various amino acid linkers has been designed, synthesized, and biologically evaluated as potent anticancer agents. Five selected compounds with different representative chemical structures were found to show broad anti-proliferative activities, effective against all tested ER-positive breast cancer (BC) and triple-negative breast cancer (TNBC) cell lines with low micromolar IC50 values. Among these compounds, compound 9a (JMX0293) maintained good potency against MDA-MB-231 cell line (IC50 = 3.38 ± 0.37 µM) while exhibiting very low toxicity against human non-tumorigenic breast epithelial cell line MCF-10A (IC50 > 60 µM). Further mechanistic studies showed that compound 9a could inhibit STAT3 phosphorylation and contribute to apoptosis in TNBC MDA-MB-231 cells. More importantly, compound 9a significantly suppressed MDA-MB-231 xenograft tumor growth in vivo without significant toxicity, indicating its great potential as a promising anticancer drug candidate for further clinical development.

Further lead optimization on Bax activators: Design, synthesis and pharmacological evaluation of 2-fluoro-fluorene derivatives for the treatment of breast cancer.

To further pursue potent Bax activators with better safety profiles for the treatment of breast cancer, structural optimization was conducted based on lead compound CYD-4-61 through several strategies, including scaffold hopping on the 2-nitro-fluorene ring, replacement of the nitro group with bioisosteres to avoid potential toxicity, and further optimization on the upper pyridine by exploring diverse alkylamine linkers as a tail or replacing the pyridine with bioisosteric heterocycles. F-containing compound 22d (GL0388) exhibited a good balance between the activity and toxicity, displaying submicromolar activities against a variety of cancer cell lines with 5.8-10.7-fold selectivity of decreased activity to MCF-10A human mammary epithelial cell line. Compound 22d dose-dependently blocked colony formation of breast cancer cells and prevented the migration and invasion of MDA-MB-231 cells. Mechanism of action studies indicate that 22d activated Bax, rendering its insertion into mitochondrial membrane, thereby leading to cytochrome c release from the mitochondria into the cytoplasm, subsequently inducing release of apoptotic biomarkers. Further in vivo efficacy studies of 22d in human breast cancer xenografts arisen from MDA-MB-231 cells demonstrated that this drug candidate significantly suppressed tumor growth, indicating the therapeutic promise of this class of compounds for the treatment of breast cancer as well as the potential for developing F-radiolabeled imaging ligands as anticancer chemical probes.

High performance exhaled breath biomarkers for diagnosis of lung cancer and potential biomarkers for classification of lung cancer.

Exhaled breath analysis has emerged as a promising non-invasive method for diagnosing lung cancer (LC), whereas reliable biomarkers are lacking. Herein, a standardized and systematic study was presented for LC diagnosis, classification and metabolism exploration. To improve the reliability of biomarkers, a validation group was included, and quality control for breath sampling and analysis, comprehensive pollutants analysis, and strict biomarker screening were performed. The performance of exhaled breath biomarkers was shown to be excellent in diagnosing LC even in early stages (stage I and II) with surpassing 0.930 area under the receiver operating characteristic (ROC) curve (AUC), 90% of sensitivity and 88% of specificity both in the discovery and validation analyses. Meanwhile, in these two groups, diagnosing subtypes of LC attained AUCs over 0.930 and reached 1.00 in the two subtypes of adenocarcinomas. It is demonstrated that the metabolism changes in LC are possibly related to lipid oxidation, gut microbial, cytochrome P450 and glutathione S-transferase, and glutathione pathways change in LC progression. Overall, the reliable biomarkers contribute to the clinical application of breath analysis in screening LC patients as well as those in early stages.

Synergetic effect of laser and micro-fabricated glow discharge plasma in a new ion source for ambient mass spectrometry.

A new ambient ionization technique named laser ablation micro-fabricated glow discharge plasma (LA-MFGDP) was developed for mass spectrometry in this study. This technique used low energy laser for sample ablation and ionized sample aerosol with MFGDP in sequence. The combination of laser ablation and MFGDP exhibited a synergetic effect that significantly improved the performance of MFGDP. Experimental results showed that MFGDP dominated the ionization process while laser played the role of desorption in LA-MFGDP. [M+H]+ and M+ proved that proton transfer reactions and charge transfer reactions were involved in the ionization process, respectively, indicating that the ionization character was the same as MFGDP. LA-MFGDP could analyze less volatile samples that were unable to be detected by MFGDP because laser significantly improved the ionization capability of MFGDP. Strong ion signals were obtained by LA-MFGDP with low sample consumption. The limits of detection (LODs) of LA-MFGDP was as low as three orders of magnitude than that of MFGDP, which demonstrated that LA-MFGDP possessed an outstanding advantage in detecting trace substances. LA-MFGDP was successfully applied to detect pharmaceutical tablets without any pretreatment. Benefited from the excellent performance, LA-MFGDP offers great potential in broadening the application of ambient mass spectrometry.

Tunable plasmon-induced transparency with a dielectric grating-coupled graphene structure for slowing terahertz waves.

We present a tunable plasmon-induced transparency (PIT) structure that is composed of dielectric grating and a graphene system to manipulate terahertz (THz) waves. The graphene system consists of a graphene sheet and a graphene ribbon layer, with a spacer between them. By exploiting the diffraction coupling of THz wave with dielectric grating, graphene plasmonic resonance is efficiently excited on both graphene sheet and graphene ribbons. This leads to the surface plasmon mode of the graphene sheet and the localized plasmon mode of the graphene ribbons. The coupling between the two-plasmon modes via near-field destructive interference generates a strong PIT effect with slowing the group velocity of THz waves. A group delay over 0.2 ps and group index beyond 170 can be achievable. The group slowing effect is dynamically tunable with varying the Fermi level of graphene. The work suggests a promising scheme for on-chip graphene slow-wave devices at the THz regime.

Accumulation mechanism of biofilm under different water shear forces along the networked pipelines in a drip irrigation system.

The behavior of clogging has a close relationship with the biofilm attached on inner surface of the pipeline in a drip irrigation system using reclaimed water. Therefore, inhibiting biofilm growth is the key to completely addressing the clogging problem. Water shear forces play a vital role in the formation, development and detachment of biofilm. In order to find out the accumulation mechanism of biofilm under different water shear forces, this paper considered 8 different shear forces with a range of [0, 0.7]Pa on the inner surface of pipelines in drip irrigation systems using three kinds of reclaimed water. The results indicate that dry weight (DW), phospholipid fatty acids (PLFAs) and extracellular polymeric substance (EPS) of biofilms show a S-type trend, the maximum contents were observed when τ was 0.2 Pa or 0. 35 Pa. Besides, the influence of water shear forces on biofilms is dual. The formation of biofilm is a dynamic stabilization process. When there is a relatively large shear force, it is favorable to the transport and renewal of microorganisms and nutrients. Meantime, the renewal speed of biofilms is also relatively fast. It is easy to form the biofilms with large surface and small thickness due to relatively high possibility of detachment. When the shear force is small, the transport speed of microorganisms and nutrients are limited, and the ability of microorganisms to secrete polysaccharides is reduced, which makes the nutrients needed for microbial growth insufficient and the adhesion between particles is also reduced, resulting in loose, unstable and an easily removed biofilm structure. After a comprehensive consideration of the dual influence, the critical controlling threshold of internal water shear force was obtained as [0, 0.20] ∪ [0.35, +∞] Pa. In addition, the growth model established in this paper can well describe the growth kinetics of attached biofilms, and provide theoretical reference for monitoring the occurrence of bio-clogging process in drip irrigation systems.

Variations in the microbial community of biofilms under different near-wall hydraulic shear stresses in agricultural irrigation systems.

The hydraulic characteristics along agricultural irrigation pipelines directly affect the local near-wall hydraulic shear stress and biofilm accumulation. However, the variations in the microbial community during the process remain unknown. Based on the Couette-Taylor reactor, a device was developed to accurately control the hydraulic shear stress. The results indicated that the near-wall hydraulic shear stresses showed quadratic correlations with microbial contents (represented by phospholipid fatty acids r > 0.77, p < 0.05), and the maximum values were obtained under the shear stresses of 0.20-0.35 Pa. For two types of treated wastewater, the mutual operational taxonomic units among different shear stress treatments showed good consistency (>185). Their corresponding response in the microbial community was represented by the quantitative correlations between the near-wall hydraulic shear stresses and the polymorphism indices (r > 0.82, p < 0.05). Among the microorganisms, Firmicutes at the phylum level were significantly affected by the shear stress and significantly influenced the biofilm accumulation process.

1H, 13C and 15N resonance assignments of translation initiation factor 3 from Pseudomonas aeruginosa.

Translation initiation factor 3 (IF3) is one of the three protein factors that bind to the small ribosomal subunit and it is required for the initiation of protein biosynthesis in bacteria. IF3 contains two independent domains, N- and C-terminal domains, which are connected by a lysine-rich interdomain linker. IF3 undergoes large-scale movements and conformational changes upon binding to the 30S subunit and also during the functional regulation of initiation. However, the precise dynamic interplay of the two domains and the molecular mechanism of IF3 is not well understood. A high-resolution 3D structure of a complete IF3 in bacteria has not been solved. Pseudomonas aeruginosa, a gram-negative opportunistic pathogen, is a primary cause of nosocomial infections in humans. Here we report the NMR chemical shift assignments of IF3 from P. aeruginosa as the first step toward NMR structure determination and interaction studies. Secondary structure analyses deduced from the NMR chemical shift data identified nine ß-strands and four α-helices arranged in the sequential order ß1-ß2-α1-ß3-ß4-α2-ß5-α3-ß6-α4-ß7-ß8-ß9.

Development of microwave plasma proton transfer reaction mass spectrometry (MWP-PTR-MS) for on-line monitoring of volatile organic compounds: Design, characterization and performance evaluation.

Proton transfer reaction mass spectrometry (PTR-MS) is a revolutionary on-line VOCs monitoring method. In this study, a new microwave plasma-based proton transfer reaction mass spectrometry (MWP-PTR-MS) is developed. The MWP consists of a surfatron type resonator and a cooperative ion extraction device to achieve high efficiency production of hydronium ions. Non-local thermodynamic equilibrium water plasma is generated in a quartz tube at 200 Pa with 2.45 GHz microwave. Characters of MWP, such as emission spectroscopy, input power, dirty ion suppressing and ion extraction, are explored systematically. With the same test platform, MWP has a 7-fold increment of hydronium ion production rate than glow discharge source. The counts rate of hydronium ion is 8 × 106 cps with abundance of NO+ and O2+ is less than 0.4% and 5% respectively. The performance of MWP-PTR-MS is validated by analysis of several chemicals and demonstration application is conducted. The instrument showed good linearity above 99% in the range of 4.5 × 10-11 to 4.5 × 10-9 mol/L. Benefited from the character of surface wave and 2.45 GHz microwave, MWP has high potential in improving the performance and reliability of current PTR-MS.

Graphene/liquid crystal hybrid tuning terahertz perfect absorber.

We present, by simulations, a metastructured graphene/liquid crystal hybrid tuning terahertz perfect absorber that consists of graphene disk resonator arrays above a metallic layer separated with liquid crystal substrate. The liquid crystal refractive index and the graphene Fermi level are utilized to implement double-tuning operation to push the spectra scanning limit of the terahertz absorber. Our simulations demonstrate high performance of a near-linear broad tuning region and near-unity absorbance with wide incident angle and polarization independence. The range of the resonant frequency scan is notably enlarged at a spectral ratio of as high as Δf/f=50% while ensuring absorbance beyond 90%. Such graphene/liquid crystal hybrid tuning scheme would be preferable to push the working-band limit of terahertz perfect absorbers.

Evoking picomolar binding in RNA by a single phosphorodithioate linkage.

RNA aptamers are synthetic oligonucleotide-based affinity molecules that utilize unique three-dimensional structures for their affinity and specificity to a target such as a protein. They hold the promise of numerous advantages over biologically produced antibodies; however, the binding affinity and specificity of RNA aptamers are often insufficient for successful implementation in diagnostic assays or as therapeutic agents. Strong binding affinity is important to improve the downstream applications. We report here the use of the phosphorodithioate (PS2) substitution on a single nucleotide of RNA aptamers to dramatically improve target binding affinity by ∼1000-fold (from nanomolar to picomolar). An X-ray co-crystal structure of the α-thrombin:PS2-aptamer complex reveals a localized induced-fit rearrangement of the PS2-containing nucleotide which leads to enhanced target interaction. High-level quantum mechanical calculations for model systems that mimic the PS2 moiety and phenylalanine demonstrate that an edge-on interaction between sulfur and the aromatic ring is quite favorable, and also confirm that the sulfur analogs are much more polarizable than the corresponding phosphates. This favorable interaction involving the sulfur atom is likely even more significant in the full aptamer-protein complexes than in the model systems.

ent-Kaurane-based regio- and stereoselective inverse electron demand hetero-Diels-Alder reactions: synthesis of dihydropyran-fused diterpenoids.

A mild and concise approach for the construction of a 3,4-dihydro-2H-pyran ring integrated into the A-ring of the natural product oridonin using an optimized inverse electron demand hetero-Diels-Alder (IED HDA) reaction is reported herein. A self-dimerization of the exocyclic enone installed in the A-ring through a homo-HDA reaction was identified to exclusively give a dimeric ent-kaurane diterpenoid with the spirochroman core. Moreover, efficient cross-HDA cycloadditions of this enone with various vinyl ethers or vinyl sulfides, instead of its own homo-HDA dimerization, were achieved in a regio- and stereoselective manner, thus providing access to novel dihydropyran-fused diterpenoids as potential anticancer agents to overcome chemoresistance.

Genetic regulation of vesiculogenesis and immunomodulation in Mycobacterium tuberculosis.

Mycobacterium tuberculosis (Mtb) restrains immune responses well enough to escape eradication but elicits enough immunopathology to ensure its transmission. Here we provide evidence that this host-pathogen relationship is regulated in part by a cytosolic, membrane-associated protein with a unique structural fold, encoded by the Mtb gene rv0431. The protein acts by regulating the quantity of Mtb-derived membrane vesicles bearing Toll-like receptor 2 ligands, including the lipoproteins LpqH and SodC. We propose that rv0431 be named "vesiculogenesis and immune response regulator."