OXCT1 functions as a succinyltransferase, contributing to hepatocellular carcinoma via succinylating LACTB.

Metabolic reprogramming is an important feature of cancers that has been closely linked to post-translational protein modification (PTM). Lysine succinylation is a recently identified PTM involved in regulating protein functions, whereas its regulatory mechanism and possible roles in tumor progression remain unclear. Here, we show that OXCT1, an enzyme catalyzing ketone body oxidation, functions as a lysine succinyltransferase to contribute to tumor progression. Mechanistically, we find that OXCT1 functions as a succinyltransferase, with residue G424 essential for this activity. We also identified serine beta-lactamase-like protein (LACTB) as a main target of OXCT1-mediated succinylation. Extensive succinylation of LACTB K284 inhibits its proteolytic activity, resulting in increased mitochondrial membrane potential and respiration, ultimately leading to hepatocellular carcinoma (HCC) progression. In summary, this study establishes lysine succinyltransferase function of OXCT1 and highlights a link between HCC prognosis and LACTB K284 succinylation, suggesting a potentially valuable biomarker and therapeutic target for further development.

Indian Ocean salinity build-up primes deglacial ocean circulation recovery.

The Indian Ocean provides a source of salt for North Atlantic deep-water convection sites, via the Agulhas Leakage, and may thus drive changes in the ocean's overturning circulation1-3. However, little is known about the salt content variability of Indian Ocean and Agulhas Leakage waters during past glacial cycles and how this may influence circulation. Here we show that the glacial Indian Ocean surface salt budget was notably different from the modern, responding dynamically to changes in sea level. Indian Ocean surface salinity increased during glacial intensification, peaking in glacial maxima. We find that this is due to rapid land exposure in the Indonesian archipelago induced by glacial sea-level lowering, and we suggest a mechanistic link via reduced input of relatively fresh Indonesian Throughflow waters into the Indian Ocean. Using climate model results, we show that the release of this glacial Indian Ocean salinity via the Agulhas Leakage during deglaciation can directly impact the Atlantic Meridional Overturning Circulation and global climate.

Non-canonical phosphoglycerate dehydrogenase activity promotes liver cancer growth via mitochondrial translation and respiratory metabolism.

Phosphoglycerate dehydrogenase (PHGDH) is a key serine biosynthesis enzyme whose aberrant expression promotes various types of tumors. Recently, PHGDH has been found to have some non-canonical functions beyond serine biosynthesis, but its specific mechanisms in tumorigenesis remain unclear. Here, we show that PHGDH localizes to the inner mitochondrial membrane and promotes the translation of mitochondrial DNA (mtDNA)-encoded proteins in liver cancer cells. Mechanistically, we demonstrate that mitochondrial PHGDH directly interacts with adenine nucleotide translocase 2 (ANT2) and then recruits mitochondrial elongation factor G2 (mtEFG2) to promote mitochondrial ribosome recycling efficiency, thereby promoting mtDNA-encoded protein expression and subsequent mitochondrial respiration. Moreover, we show that treatment with a mitochondrial translation inhibitor or depletion of mtEFG2 diminishes PHGDH-mediated tumor growth. Collectively, our findings uncover a previously unappreciated function of PHGDH in tumorigenesis acting via promotion of mitochondrial translation and bioenergetics.

Publisher Correction: Cleavable comonomers enable degradable, recyclable thermoset plastics.

An amendment to this paper has been published and can be accessed via a link at the top of the paper.

Cleavable comonomers enable degradable, recyclable thermoset plastics.

Thermosets-polymeric materials that adopt a permanent shape upon curing-have a key role in the modern plastics and rubber industries, comprising about 20 per cent of polymeric materials manufactured today, with a worldwide annual production of about 65 million tons1,2. The high density of crosslinks that gives thermosets their useful properties (for example, chemical and thermal resistance and tensile strength) comes at the expense of degradability and recyclability. Here, using the industrial thermoset polydicyclopentadiene as a model system, we show that when a small number of cleavable bonds are selectively installed within the strands of thermosets using a comonomer additive in otherwise traditional curing workflows, the resulting materials can display the same mechanical properties as the native material, but they can undergo triggered, mild degradation to yield soluble, recyclable products of controlled size and functionality. By contrast, installation of cleavable crosslinks, even at much higher loadings, does not produce degradable materials. These findings reveal that optimization of the cleavable bond location can be used as a design principle to achieve controlled thermoset degradation. Moreover, we introduce a class of recyclable thermosets poised for rapid deployment.

Methods for constructing and evaluating consensus genomic interval sets.

The amount of genomic region data continues to increase. Integrating across diverse genomic region sets requires consensus regions, which enable comparing regions across experiments, but also by necessity lose precision in region definitions. We require methods to assess this loss of precision and build optimal consensus region sets. Here, we introduce the concept of flexible intervals and propose three novel methods for building consensus region sets, or universes: a coverage cutoff method, a likelihood method, and a Hidden Markov Model. We then propose three novel measures for evaluating how well a proposed universe fits a collection of region sets: a base-level overlap score, a region boundary distance score, and a likelihood score. We apply our methods and evaluation approaches to several collections of region sets and show how these methods can be used to evaluate fit of universes and build optimal universes. We describe scenarios where the common approach of merging regions to create consensus leads to undesirable outcomes and provide principled alternatives that provide interoperability of interval data while minimizing loss of resolution.

Dux activates metabolism-lactylation-MET network during early iPSC reprogramming with Brg1 as the histone lactylation reader.

The process of induced pluripotent stem cells (iPSCs) reprogramming involves several crucial events, including the mesenchymal-epithelial transition (MET), activation of pluripotent genes, metabolic reprogramming, and epigenetic rewiring. Although these events intricately interact and influence each other, the specific element that regulates the reprogramming network remains unclear. Dux, a factor known to promote totipotency during the transition from embryonic stem cells (ESC) to 2C-like ESC (2CLC), has not been extensively studied in the context of iPSC reprogramming. In this study, we demonstrate that the modification of H3K18la induced by Dux overexpression controls the metabolism-H3K18la-MET network, enhancing the efficiency of iPSC reprogramming through a metabolic switch and the recruitment of p300 via its C-terminal domain. Furthermore, our proteomic analysis of H3K18la immunoprecipitation experiment uncovers the specific recruitment of Brg1 during reprogramming, with both H3K18la and Brg1 being enriched on the promoters of genes associated with pluripotency and epithelial junction. In summary, our study has demonstrated the significant role of Dux-induced H3K18la in the early reprogramming process, highlighting its function as a potent trigger. Additionally, our research has revealed, for the first time, the binding of Brg1 to H3K18la, indicating its role as a reader of histone lactylation.

Lactate modulates zygotic genome activation through H3K18 lactylation rather than H3K27 acetylation.

In spite of its essential role in culture media, the precise influence of lactate on early mouse embryonic development remains elusive. Previous studies have implicated lactate accumulation in medium affecting histone acetylation. Recent research has underscored lactate-derived histone lactylation as a novel epigenetic modification in diverse cellular processes and diseases. Our investigation demonstrated that the absence of sodium lactate in the medium resulted in a pronounced 2-cell arrest at the late G2 phase in embryos. RNA-seq analysis revealed that the absence of sodium lactate significantly impaired the maternal-to-zygotic transition (MZT), particularly in zygotic gene activation (ZGA). Investigations were conducted employing Cut&Tag assays targeting the well-studied histone acetylation and lactylation sites, H3K18la and H3K27ac, respectively. The findings revealed a noticeable reduction in H3K18la modification under lactate deficiency, and this alteration showed a significant correlation with changes in gene expression. In contrast, H3K27ac exhibited minimal correlation. These results suggest that lactate may preferentially influence early embryonic development through H3K18la rather than H3K27ac modifications.

Survival benefits of human papillomavirus 16 infection in patients with esophageal squamous cell carcinoma undergoing chemoradiotherapy: A retrospective cohort study.

The role of human papillomavirus 16 (HPV 16) in esophageal squamous cell carcinoma (ESCC) remains uncertain. Therefore, this study aimed to investigate the prevalence of HPV 16 in patients with ESCC and its impact on theirprognosis. HPV 16 was detected using FISH, and TP53 status was evaluated via immunohistochemistry. The factors influencing prognosis were ananalyzed using the Log-rank test and Cox regression analyses. Among 178 patients with ESCC, 105 and 73 patients were categorized into concurrent chemoradiotherapy (CCRT) and postoperative chemoradiotherapy (POCRT) cohorts, respectively. Among 178 patients, 87 (48.87%) tested positive for HPV 16. Log-rank tests revealed that the overall survival (OS) of patients with ESCC who were HPV 16-positive was longer than that of those who were HPV 16-negative (median OS: 57 months vs. 27 months, p < 0.01**). HPV 16 infection and TP53 mutation status were identified as independent events. The OS of patients with mutant TP53 who were HPV 16-positive was longer than that of those who were HPV 16-negative in both CCRT and POCRT cohorts (p = 0.002** for CCRT cohorts and p = 0.0023** for POCRT cohorts). Conversely, HPV 16 infection had no effect on OS in the wild-type TP53 subgroup (p = 0.13 and 0.052 for CCRT and POCRT cohorts, respectively). As a conclusion, the positive rate of HPV 16 in ESCC in this study was 48.87% (87/178). Among the patients with ESCC who had TP53 mutation, those who were HPV 16-positive exhibited a better prognosis than those who were HPV 16-negative.

Identification of kynurenine and quinolinic acid as promising serum biomarkers for drug-induced interstitial lung diseases.

BACKGROUND: Drug-induced interstitial lung disease (DILD) is a lung injury caused by various types of drugs and is a serious problem in both clinical practice and drug development. Clinical management of the condition would be improved if there were DILD-specific biomarkers available; this study aimed to meet that need. METHODS: Biomarker candidates were identified by non-targeted metabolomics focusing on hydrophilic molecules, and further validated by targeted approaches using the serum of acute DILD patients, DILD recovery patients, DILD-tolerant patients, patients with other related lung diseases, and healthy controls. RESULTS: Serum levels of kynurenine and quinolinic acid (and kynurenine/tryptophan ratio) were elevated significantly and specifically in acute DILD patients. The diagnostic potentials of these biomarkers were superior to those of conventional lung injury biomarkers, Krebs von den Lungen-6 and surfactant protein-D, in discriminating between acute DILD patients and patients with other lung diseases, including idiopathic interstitial pneumonia and lung diseases associated with connective tissue diseases. In addition to identifying and evaluating the biomarkers, our data showed that kynurenine/tryptophan ratios (an indicator of kynurenine pathway activation) were positively correlated with serum C-reactive protein concentrations in patients with DILD, suggesting the potential association between the generation of these biomarkers and inflammation. Our in vitro experiments demonstrated that macrophage differentiation and inflammatory stimulations typified by interferon gamma could activate the kynurenine pathway, resulting in enhanced kynurenine levels in the extracellular space in macrophage-like cell lines or lung endothelial cells. Extracellular quinolinic acid levels were elevated only in macrophage-like cells but not endothelial cells owing to the lower expression levels of metabolic enzymes converting kynurenine to quinolinic acid. These findings provide clues about the molecular mechanisms behind their specific elevation in the serum of acute DILD patients. CONCLUSIONS: The serum concentrations of kynurenine and quinolinic acid as well as kynurenine/tryptophan ratios are promising and specific biomarkers for detecting and monitoring DILD and its recovery, which could facilitate accurate decisions for appropriate clinical management of patients with DILD.

Continuous Synthesis of a Macrocyclic Sulfite of Polyethylene Glycol by Cascaded Continuous Stirred Tank Reactors (CSTRs).

Many macrocyclic compounds are attractive drug-like molecules or intermediates due to their special properties. However, the bulk synthesis of such compounds are hindered by the necessity of using diluted solutions, in order to prevent intermolecular reactions that yields oligomer impurities, thereby resulting in a low production efficiency. Such challenge can be adequately addressed by using continuous reactors, allowing improved efficiency with smaller space footprints. In this work, we proposed a novel continuous process for the synthesis of a macrocyclic sulfite of tetraethylene glycol (PEG4-MCSi), which is a precursor to a very useful building block, PEG4-macrocyclic sulfate (PEG4-MCS). The basic reaction parameters, including stoichiometry and temperature, were first confirmed with small batch reactions, and the effectiveness of coiled reactors and continuous stirred tank reactors (CSTRs) were compared. Cascaded CSTRs were proven to be suitable, and the reaction parameters were subject to further optimization to give a robust continuous process. The process was then tested with 4 parallel runs for up to 64 h. Finally, the merits and demerits of batch and continuous reactions were also compared, demonstrating the suitability of latter in the bulk production of macrocyclic PEG-MCSi compounds.

Continuous Synthesis of a Macrocyclic Sulfite of Polyethylene Glycol by Cascaded Continuous Stirred Tank Reactors (CSTRs).

Invited for the cover of this issue is the group of Long Pan and co-workers at Asymchem Life Sciences (Tianjin) Co. Ltd. The image depicts a novel continuous process for the synthesis of a macrocyclic poly(ethylene glycol) (PEG) sulfite, the precursor to PEG macrocyclic sulfate, a useful building block in PEG chemistry. Read the full text of the article at 10.1002/chem.202304319.

Experimental and Theoretical Studies on Long Alkyl Chain-Bearing Dibenzotriazole Ionic Liquids as Eco-friendly Corrosion Inhibitors in Aqueous Hydrochloride Acid.

Three long alkyl chain-bearing dibenzotriazole ionic liquids (BTA-R-BTA, R = 8, 12, and 16) were synthesized with high yield (>98%) through a simple and eco-friendly process. Their anticorrosion performance for Q235 carbon steel in 6 M hydrochloride acid was comprehensively evaluated by weight loss tests, electrochemical methods (potentiodynamic polarization and electrochemical impedance spectroscopy), and surface analysis techniques. As the length of the alkyl chain increased, the maximum corrosion inhibition efficiency enhanced from 55.02% (for BTA-8-BTA at 1.2 mM) to 97.10% (for BTA-12-BTA at 0.3 mM) and 98.84% (for BTA-16-BTA at 0.3 mM). Density functional theory calculation indicated that the alkyl chain length had little influence on the inhibitors' electronic structures, while molecular dynamics simulations revealed that the thickness, surface coverage, and compactness of adsorption films formed at the metal-electrolyte interface increased with the elongated alkyl chain. Corrosion inhibition efficiency is strongly correlated with the structures of the adsorption film.

Spin Crossover in [Fe(qsal-5-Brq)2]+ Complexes with a Quinoline-Substituted Qsal Ligand.

Using a quinoline substituted Qsal ligand, Hqsal-5-Brq (Hqsal-5-Brq = N-(5-bromo-8-quinolyl)salicylaldimine), four FeIII complexes, [Fe(qsal-5-Brq)2]A·CH3OH (Y = NO3- (1NO3), BF4- (2BF4), PF6- (3PF6), OTf- (4OTf), were prepared and characterized. Structure analysis revealed that complex 2BF4 contained two species (2BF4(P1̅) and 2BF4(C2/c)). In these compounds except 3PF6, the [Fe(qsal-5-Brq)2]+ cations form 1D chains through π-π interactions and other weak interactions. Adjacent chains are connected to form the 2D "Chain Layer" structures and 3D structures through various supramolecular interactions. For 3PF6, a "Dimer Chain" structure is formed from the loosely connected dimers. Magnetic studies revealed that compounds 1NO3 and 2BF4(P1̅) displayed abrupt hysteretic SCO with the transition temperature T1/2↓ = 235 K, T1/2↑ = 240 K for 1NO3 and T1/2↓ = 230 K, T1/2↑ = 235 K for 2BF4(P1̅), while compounds 3PF6 and 4OTf are in the HS state. Desolvation of the complexes significantly modifies their SCO properties: the desolvated 1NO3 and 2BF4 show a gradual SCO, desolvated 3PF6 undergoes a two-step SCO, and desolvated 4OTf exhibits a hysteretic transition. Overall, this work reported the FeIII-SCO complexes of the quinoline-substituted Hqsal ligand and highlighted the potential of these ligands for the development of interesting FeIII-SCO materials.

A dry polymer nanocomposite transcutaneous electrode for functional electrical stimulation.

BACKGROUND: Functional electrical stimulation (FES) can be used in rehabilitation to aid or improve function in people with paralysis. In clinical settings, it is common practice to use transcutaneous electrodes to apply the electrical stimulation, since they are non-invasive, and can be easily applied and repositioned as necessary. However, the current electrode options available for transcutaneous FES are limited and can have practical disadvantages, such as the need for a wet interface with the skin for better comfort and performance. Hence, we were motivated to develop a dry stimulation electrode which could perform equivalently or better than existing commercially available options. METHODS: We manufactured a thin-film dry polymer nanocomposite electrode, characterized it, and tested its performance for stimulation purposes with thirteen healthy individuals. We compared its functionality in terms of stimulation-induced muscle torque and comfort level against two other types of transcutaneous electrodes: self-adhesive hydrogel and carbon rubber. Each electrode type was also tested using three different stimulators and different intensity levels of stimulation. RESULTS: We found the proposed dry polymer nanocomposite electrode to be functional for stimulation, as there was no statistically significant difference between its performance to the other standard electrodes. Namely, the proposed dry electrode had comparable muscle torque generated and comfort level as the self-adhesive hydrogel and carbon rubber electrodes. From all combinations of electrode type and stimulators tested, the dry polymer nanocomposite electrode with the MyndSearch stimulator had the most comfortable average rating. CONCLUSIONS: The dry polymer nanocomposite electrode is a durable and flexible alternative to existing self-adhesive hydrogel and carbon rubber electrodes, which can be used without the addition of a wet interfacing agent (i.e., water or gel) to perform as well as the current electrodes used for stimulation purposes.

Feature Extraction Methods for Underwater Acoustic Target Recognition of Divers.

The extraction of typical features of underwater target signals and excellent recognition algorithms are the keys to achieving underwater acoustic target recognition of divers. This paper proposes a feature extraction method for diver signals: frequency-domain multi-sub-band energy (FMSE), aiming to achieve accurate recognition of diver underwater acoustic targets by passive sonar. The impact of the presence or absence of targets, different numbers of targets, different signal-to-noise ratios, and different detection distances on this method was studied based on experimental data under different conditions, such as water pools and lakes. It was found that the FMSE method has the best robustness and performance compared with two other signal feature extraction methods: mel frequency cepstral coefficient filtering and gammatone frequency cepstral coefficient filtering. Combined with the commonly used recognition algorithm of support vector machines, the FMSE method can achieve a comprehensive recognition accuracy of over 94% for frogman underwater acoustic targets. This indicates that the FMSE method is suitable for underwater acoustic recognition of diver targets.

Regiodivergent Hydrosilylation of Polar Enynes to Synthesize Site-Specific Silyl-Substituted Dienes.

Herein, we present catalyst-regulated switchable site-selective hydrosilylation of enynes, which are suitable for a wide range of alkyl and aryl substituted polar enynes and exhibit excellent functional group compatibility. Under the optimized conditions, silyl groups can be precisely installed at various positions of 1,3-dienes. While α- and γ-silylation products were obtained under platinum-catalytic systems, ß-silylation products were delivered with [Cp*RuCl]4 as catalyst. This process lead to the formation of 1,3-dienoates with diverse substitutions, which would pose challenges with other methodologies.

In Situ Probing of the Intrinsic Adhesion Strength of Single Anaerobic Microbial Cells.

Probing the single-cell mechanobiology in situ is imperative for microbial processes in the medical, industrial, and agricultural realms, but it remains a challenge. Herein, we present a single-cell force microscopy method that can be used to measure microbial adhesion strength under anaerobic conditions in situ. This method integrates atomic force microscopy with an anaerobic liquid cell and inverted fluorescence microscopy. We obtained the nanomechanical measurements of the single anaerobic bacterium Ethanoligenens harbinense YUAN-3 and the methanogenic archaeon Methanosarcina acetivorans C2A and their nanoscale adhesion forces in the presence of sulfoxaflor, a successor of neonicotinoid pesticides. This study presents a new tool for in situ single-cell force measurements of various anoxic and anaerobic species and provides new perspectives for evaluating the potential environmental risk of neonicotinoid applications in ecosystems.

Development and test of highly accurate endpoint free energy methods. 2: Prediction of logarithm of n-octanol-water partition coefficient (logP) for druglike molecules using MM-PBSA method.

The logarithm of n-octanol-water partition coefficient (logP) is frequently used as an indicator of lipophilicity in drug discovery, which has substantial impacts on the absorption, distribution, metabolism, excretion, and toxicity of a drug candidate. Considering that the experimental measurement of the property is costly and time-consuming, it is of great importance to develop reliable prediction models for logP. In this study, we developed a transfer free energy-based logP prediction model-FElogP. FElogP is based on the simple principle that logP is determined by the free energy change of transferring a molecule from water to n-octanol. The underlying physical method to calculate transfer free energy is the molecular mechanics-Poisson Boltzmann surface area (MM-PBSA), thus this method is named as free energy-based logP (FElogP). The superiority of FElogP model was validated by a large set of 707 structurally diverse molecules in the ZINC database for which the measurement was of high quality. Encouragingly, FElogP outperformed several commonly-used QSPR or machine learning-based logP models, as well as some continuum solvation model-based methods. The root-mean-square error (RMSE) and Pearson correlation coefficient (R) between the predicted and measured values are 0.91 log units and 0.71, respectively, while the runner-up, the logP model implemented in OpenBabel had an RMSE of 1.13 log units and R of 0.67. Given the fact that FElogP was not parameterized against experimental logP directly, its excellent performance is likely to be expanded to arbitrary organic molecules covered by the general AMBER force fields.

Development and test of highly accurate endpoint free energy methods. 1: Evaluation of ABCG2 charge model on solvation free energy prediction and optimization of atom radii suitable for more accurate solvation free energy prediction by the PBSA method.

Accurate estimation of solvation free energy (SFE) lays the foundation for accurate prediction of binding free energy. The Poisson-Boltzmann (PB) or generalized Born (GB) combined with surface area (SA) continuum solvation method (PBSA and GBSA) have been widely used in SFE calculations because they can achieve good balance between accuracy and efficiency. However, the accuracy of these methods can be affected by several factors such as the charge models, polar and nonpolar SFE calculation methods and the atom radii used in the calculation. In this work, the performance of the ABCG2 (AM1-BCC-GAFF2) charge model as well as other two charge models, that is, RESP (Restrained Electrostatic Potential) and AM1-BCC (Austin Model 1-bond charge corrections), on the SFE prediction of 544 small molecules in water by PBSA/GBSA was evaluated. In order to improve the performance of the PBSA prediction based on the ABCG2 charge, we further explored the influence of atom radii on the prediction accuracy and yielded a set of atom radius parameters for more accurate SFE prediction using PBSA based on the ABCG2/GAFF2 by reproducing the thermodynamic integration (TI) calculation results. The PB radius parameters of carbon, oxygen, sulfur, phosphorus, chloride, bromide and iodine, were adjusted. New atom types, on, oi, hn1, hn2, hn3, were introduced to further improve the fitting performance. Then, we tuned the parameters in the nonpolar SFE model using the experimental SFE data and the PB calculation results. By adopting the new radius parameters and new nonpolar SFE model, the root mean square error (RMSE) of the SFE calculation for the 544 molecules decreased from 2.38 to 1.05 kcal/mol. Finally, the new radius parameters were applied in the prediction of protein-ligand binding free energies using the MM-PBSA method. For the eight systems tested, we could observe higher correlation between the experiment data and calculation results and smaller prediction errors for the absolute binding free energies, demonstrating that our new radius parameters can improve the free energy calculation using the MM-PBSA method.