Barrierless reactions of C2 Criegee intermediates with H2SO4 and their implication to oligomers and new particle formation

The formation of oligomeric hydrogen peroxide triggered by Criegee intermediate maybe contributes significantly to the formation and growth of secondary organic aerosol (SOA). However, to date, the reactivity of C2 Criegee intermediates (CH3CHOO) in areas contaminated with acidic gas remains poorly understood. Herein, high-level quantum chemical calculations and Born-Oppenheimer molecular dynamics (BOMD) simulations are used to explore the reaction of CH3CHOO and H2SO4 both in the gas phase and at the air-water interface. In the gas phase, the addition reaction of CH3CHOO with H2SO4 to generate CH3HC(OOH)OSO3H (HPES) is near-barrierless, regardless of the presence of water molecules. BOMD simulations show that the reaction at the air-water interface is even faster than that in the gas phase. Further calculations reveal that the HPES has a tendency to aggregate with sulfuric acids, ammonias, and water molecules to form stable clusters, meanwhile the oligomerization reaction of CH3CHOO with HPES in the gas phase is both thermochemically and kinetically favored. Also, it is noted that the interfacial HPES- ion can attract H2SO4, NH3, (COOH)2 and HNO3 for particle formation from the gas phase to the water surface. Thus, the results of this work not only elucidate the high atmospheric reactivity of C2 Criegee intermediates in polluted regions, but also deepen our understanding of the formation process of atmospheric SOA induced by Criegee intermediates.

Study of two-dimensional information writing, reading and error correction at micro/nanoscale based on gold nanosphere arrays

Surface plasmon driven photocatalytic reactions have great potential for information encryption as well as information security. In this paper, explored the detection concentrations of dye molecule Rhodamine6G (R6G) on three substrates, where complete original Raman spectra signals were still obtained at a concentration of 10-8 M. Utilized photosensitive molecules to investigate the photocatalytic characteristics of 4-nitrobenzenethiol (4-NBT) on three substrates. Excitation light at a wavelength of 633 nm enables local photocatalytic for information signals writing, while 785 nm wavelength excitation light combined with two-dimensional Mapping technology is used for information signal reading. Read information signals are often prone to reading errors due to their own lack of resolution or strong interference from back bottom signals, so error correction processing of information signals is essential. Through comparative exploration, it is found that the ratio method can obtain high-precision and high-resolution information signals, and the interference of the background signals were well suppressed. Leveraging the advantages of Raman fingerprint spectra at the micro/nanoscale, it solves the challenge of incomplete information signals presentation at smaller scales. Additionally, through error correction processing of the information signals, high precision and high-resolution information signals are obtained.

Extending the emission peak tail of indole cyanine for deep-near-infrared bioimaging

We propose a novel strategy for tailoring the structure of fluorescent molecules to achieve emission at the tail end of the NIR-II window. The favorable spectroscopic properties and low cytotoxicity of YNs make them powerful tools for bioimaging. Notably, YN-4 exhibits a brightness 2.5 times greater than YN-3, 6 times that of IR-783, and 5 times that of ICG. This enhanced brightness enabled high-resolution imaging of mouse thoracic and abdominal cavities, tumor vasculature, and real-time monitoring of gastrointestinal motility using YN-4. Furthermore, covalent grafting of glucose onto the YN-Glu scaffold significantly improved tumor-targeting capability and facilitated tracking of glucose metabolism. This work aims to extend the application of fluorescent molecule imaging beyond the NIR-IIa window.

Molecular mechanisms behind BRACO19 and human telomeric G-quadruplex interaction

Human telomeres (HTs) can form DNA G-quadruplex (G4), an attractive target for anticancer and antiviral drugs. HT-G4s exhibit inherent structural polymorphism, posing challenges for understanding their specific recognition by ligands. Here, we aim to explore the impact of different topologies within a small segment of the HT (Tel22) on its interaction with BRACO19, a rationally designed G4 ligand with high quadruplex affinity, already employed in in-vivo treatments. Our multi-technique approach is based on the combined use of a set of contactless spectroscopic tools. Circular dichroism and UV resonance Raman spectroscopy probe ligand-induced conformational changes in the G4 sequence, while UV-visible absorption, coupled with steady-state fluorescence spectroscopy, provides further insights into the electronic features of the complex, exploiting the photoresponsive properties of BRACO19. Overall, we find that modifying the topology of the unbound Tel22 through cations (K+ or Na+), serves as a critical determinant for ligand interactions and binding modes, thus influencing the HT-G4's assembly capabilities. Furthermore, we show how fluorescence serves as a valuable probe for recognizing cation-driven multimeric structures, which may be present in living organisms, giving rise to pathological forms.

Emergent microenvironments of nucleoli

In higher eukaryotes, the nucleolus harbors at least three sub-phases that facilitate multiple functionalities including ribosome biogenesis. The three prominent coexisting sub-phases are the fibrillar center (FC), the dense fibrillar component (DFC), and the granular component (GC). Here, we review recent efforts in profiling sub-phase compositions that shed light on the types of physicochemical properties that emerge from compositional biases and territorial organization of specific types of macromolecules. We highlight roles played by molecular grammars which refers to protein sequence features including the substrate binding domains, the sequence features of intrinsically disordered regions, and the multivalence of these distinct types of domains / regions. We introduce the concept of a barcode of emergent physicochemical properties of nucleoli. Although our knowledge of the full barcode remains incomplete, we hope that the concept prompts investigations into undiscovered emergent properties and engenders an appreciation for how and why unique microenvironments control biochemical reactions.

o-Vanillin binds covalently to MAL/TIRAP Lys-210 but independently inhibits TLR2

Toll-like receptor (TLR) innate immunity signalling protects against pathogens, but excessive or prolonged signalling contributes to a range of inflammatory conditions. Structural information on the TLR cytoplasmic TIR (Toll/interleukin-1 receptor) domains and the downstream adaptor proteins can help us develop inhibitors targeting this pathway. The small molecule o-vanillin has previously been reported as an inhibitor of TLR2 signalling. To study its mechanism of action, we tested its binding to the TIR domain of the TLR adaptor MAL/TIRAP (MALTIR). We show that o-vanillin binds to MALTIR and inhibits its higher-order assembly in vitro. Using NMR approaches, we show that o-vanillin forms a covalent bond with lysine 210 of MAL. We confirm in mouse and human cells that o-vanillin inhibits TLR2 but not TLR4 signalling, independently of MAL, suggesting it may covalently modify TLR2 signalling complexes directly. Reactive aldehyde-containing small molecules such as o-vanillin may target multiple proteins in the cell.

AnoChem: Prediction of chemical structural abnormalities based on machine learning models

De novo drug design aims to rationally discover novel and potent compounds while reducing experimental costs during the drug development stage. Despite the numerous generative models that have been developed, few successful cases of drug design utilizing generative models have been reported. One of the most common challenges is designing compounds that are not synthesizable or realistic. Therefore, methods capable of accurately assessing the chemical structures proposed by generative models for drug design are needed. In this study, we present AnoChem, a computational framework based on deep learning designed to assess the likelihood of a generated molecule being real. AnoChem achieves an area under the receiver operating characteristic curve score of 0.900 for distinguishing between real and generated molecules. We utilized AnoChem to evaluate and compare the performances of several generative models, using other metrics, namely SAscore and Fréschet ChemNet distance (FCD). AnoChem demonstrates a strong correlation with these metrics, validating its effectiveness as a reliable tool for assessing generative models. The source code for AnoChem is available at https://github.com/CSB-L/AnoChem.

A systematic discussion and comparison of the construction methods of synthetic microbial community

Synthetic microbial community has widely concerned in the fields of agriculture, food and environment over the past few years. However, there is little consensus on the method to synthetic microbial community from construction to functional verification. Here, we review the concept, characteristics, history and applications of synthetic microbial community, summarizing several methods for synthetic microbial community construction, such as isolation culture, core microbiome mining, automated design, and gene editing. In addition, we also systematically summarized the design concepts, technological thresholds, and applicable scenarios of various construction methods, and highlighted their advantages and limitations. Ultimately, this review provides four efficient, detailed, easy-to-understand and -follow steps for synthetic microbial community construction, with major implications for agricultural practices, food production, and environmental governance.

TET1 displays catalytic and non-catalytic functions in the adult mouse cortex

TET1/2/3 dioxygenases iteratively demethylate 5-methylcytosine, beginning with the formation of 5-hydroxymethylcytosine (5hmC). The post-mitotic brain maintains higher levels of 5hmC than most peripheral tissues, and TET1 ablation studies have underscored the critical role of TET1 in brain physiology. However, deletion of Tet1 precludes the disentangling of the catalytic and non-catalytic functions of TET1. Here, we dissect these functions of TET1 by comparing adult cortex of Tet1 wildtype (Tet1 WT), a novel Tet1 catalytically dead mutant (Tet1 HxD), and Tet1 knockout (Tet1 KO) mice. Using DNA methylation array, we uncover that Tet1 HxD and KO mutations perturb the methylation status of distinct subsets of CpG sites. Gene ontology (GO) analysis on specific differential 5hmC regions indicates that TET1's catalytic activity is linked to neuronal-specific functions. RNA-Seq further shows that Tet1 mutations predominantly impact the genes that are associated with alternative splicing. Lastly, we performed High-performance Liquid Chromatography Mass-Spectrometry lipidomics on WT and mutant cortices and uncover accumulation of lysophospholipids lysophosphatidylethanolamine and lysophosphatidylcholine in Tet1 HxD cortex. In summary, we show that Tet1 HxD does not completely phenocopy Tet1 KO, providing evidence that TET1 modulates distinct cortical functions through its catalytic and non-catalytic roles.

Enhancing polyethylene degradation: a novel bioprocess approach using Acinetobacter nosocomialis pseudo-resting cells

Despite the discovery of several bacteria capable of interacting with polymers, the activity of the natural bacterial isolates is limited. Furthermore, there is a lack of knowledge regarding the development of bioprocesses for polyethylene (PE) degradation. Here, we report a bioprocess using pseudo-resting cells for efficient degradation of PE. The bacterial strain Acinetobacter nosocomialis was isolated from PE-containing landfills and characterized using low-density PE (LDPE) surface oxidation when incubated with LDPE. We optimized culture conditions to generate catalytic pseudo-resting cells of A. nosocomialis that are capable of degrading LDPE films in a bioreactor. After 28 days of bioreactor operation using pseudo-resting cells of A. nosocomialis, we observed the formation of holes on the PE film (39 holes per 217 cm2, a maximum diameter of 1440 μm). This study highlights the potential of bacteria as biocatalysts for the development of PE degradation processes. KEY POINTS: • New bioprocess has been proposed to degrade polyethylene (PE). • Process with pseudo-resting cells results in the formation of holes in PE film. • We demonstrated PE degradation using A. nosocomialis as a biocatalyst.

Chirality-driven strong thioredoxin reductase inhibition

Overexpression of thioredoxin reductase (TXNRD) plays crucial role in tumorigenesis. Therefore, designing TXNRD inhibitors is a promising strategy for targeted anticancer drug development. However, poor selectivity has always been a challenge, resulting in unavoidable toxicity in clinic. Herein we demonstrate a strategy to develop highly selective chiral metal complexes-based TXNRD inhibitors. By manipulating the conformation of two distinct weakly interacting groups, we optimize the compatibility between the drug and the electrophilic group within the active site of TXNRD to enhance their non-covalent interaction, thus effectively avoids the poor selectivity deriving from covalent drug interaction, on the basis of ensuring the strong inhibition. Detailed experimental and computational results demonstrate that the chiral isomeric drugs bind to the active site of TXNRD, and the interaction strength is well modulated by chirality. Especially, the meso-configuration, in which the two large sterically hindered active groups are positioned on opposite sides of the drug, exhibits the highest number of non-covalent interactions and most effective inhibition on TXNRD. Taken together, this work not only provides a novel approach for developing highly selective proteinase inhibitors, but also sheds light on possible underlying mechanisms for future application.

Development of a multi-targeted chemotherapeutic approach based on G-quadruplex stabilisation and carbonic anhydrase inhibition

A novel class of compounds designed to hit two anti-tumour targets, G-quadruplex structures and human carbonic anhydrases (hCAs) IX and XII is proposed. The induction/stabilisation of G-quadruplex structures by small molecules has emerged as an anticancer strategy, disrupting telomere maintenance and reducing oncogene expression. hCAs IX and XII are well-established anti-tumour targets, upregulated in many hypoxic tumours and contributing to metastasis. The ligands reported feature a berberine G-quadruplex stabiliser scaffold connected to a moiety inhibiting hCAs IX and XII. In vitro experiments showed that our compounds selectively stabilise G-quadruplex structures and inhibit hCAs IX and XII. The crystal structure of a telomeric G-quadruplex in complex with one of these ligands was obtained, shedding light on the ligand/target interaction mode. The most promising ligands showed significant cytotoxicity against CA IX-positive HeLa cancer cells in hypoxia, and the ability to stabilise G-quadruplexes within tumour cells.

Do selectivity filter carbonyls in K+ channels flip away from the pore? Two-dimensional infrared spectroscopy study

Molecular dynamics simulations revealed that the carbonyls of the Val residue in the conserved selectivity filter sequence TVGTG of potassium ion channels can flip away from the pore to form hydrogen bonds with the network of water molecules residing behind the selectivity filter. Such a configuration has been proposed to be relevant for C-type inactivation. Experimentally, X-ray crystallography of the KcsA channel admits the possibility that the Val carbonyls can flip, but it cannot decisively confirm the existence of such a configuration. In this study, we combined molecular dynamics simulations and line shape theory to design two-dimensional infrared spectroscopy experiments that can corroborate the existence of the selectivity filter configuration with flipped Val carbonyls. This ability to distinguish between flipped and unflipped carbonyls is based on the varying strength of the electric field inside and outside the pore, which is directly linked to carbonyl stretching frequencies that can be resolved using infrared spectroscopy.

Elucidation of critical chemical moieties of metallo-β-lactamase inhibitors and prioritisation of target metallo-β-lactamases

The urgent demand for effective countermeasures against metallo-β-lactamases (MBLs) necessitates development of novel metallo-β-lactamase inhibitors (MBLIs). This study is dedicated to identifying critical chemical moieties within previously developed MBLIs, and critical MBLs should serve as the target in MBLI evaluations. Using the Preferred Reporting Items for Systematic Reviews and Meta-Analyses (PRISMA), a systematic literature analysis was conducted, and the NCBI RefSeq genome database was exploited to access the abundance profile and taxonomic distribution of MBLs and their variant types. Through the implementation of two distinct systematic approaches, we elucidated critical chemical moieties of MBLIs, providing pivotal information for rational drug design. We also prioritised MBLs and their variant types, highlighting the imperative need for comprehensive testing to ensure the potency and efficacy of the newly developed MBLIs. This approach contributes valuable information to advance the field of antimicrobial drug discovery.

Biosynthesis of eriodictyol in citrus waster by endowing P450BM3 activity of naringenin hydroxylation

The flavonoid naringenin is abundantly present in pomelo peels, and the unprocessed naringenin in wastes is not friendly for the environment once discarded directly. Fortunately, the hydroxylated product of eriodictyol from naringenin exhibits remarkable antioxidant and anticancer properties. The P450s was suggested promising for the bioconversion of the flavonoids, but less naturally existed P450s show hydroxylation activity to C3' of the naringenin. By well analyzing the catalytic mechanism and the conformations of the naringenin in P450, we proposed that the intermediate Cmpd I ((porphyrin)Fe = O) is more reasonable as key conformation for the hydrolyzation, and the distance between C3'/C5' of naringenin to the O atom of CmpdI determines the hydroxylating activity for the naringenin. Thus, the "flying kite model" that gradually drags the C-H bond of the substrate to the O atom of CmpdI was put forward for rational design. With ab initio design, we successfully endowed the self-sufficient P450-BM3 hydroxylic activity to naringenin and obtained mutant M5-5, with kcat, Km, and kcat/Km values of 230.45 min-1, 310.48 µM, and 0.742 min-1 µM-1, respectively. Furthermore, the mutant M4186 was screened with kcat/Km of 4.28-fold highly improved than the reported M13. The M4186 also exhibited 62.57% yield of eriodictyol, more suitable for the industrial application. This study provided a theoretical guide for the rational design of P450s to the nonnative compounds. KEY POINTS: •The compound I is proposed as the starting point for the rational design of the P450BM3 •"Flying kite model" is proposed based on the distance between O of Cmpd I and C3'/C5' of naringenin •Mutant M15-5 with 1.6-fold of activity than M13 was obtained by ab initio modification.

Nuclear pore dysfunction and disease: a complex opportunity

The separation of genetic material from bulk cytoplasm has enabled the evolution of increasingly complex organisms, allowing for the development of sophisticated forms of life. However, this complexity has created new categories of dysfunction, including those related to the movement of material between cellular compartments. In eukaryotic cells, nucleocytoplasmic trafficking is a fundamental biological process, and cumulative disruptions to nuclear integrity and nucleocytoplasmic transport are detrimental to cell survival. This is particularly true in post-mitotic neurons, where nuclear pore injury and errors to nucleocytoplasmic trafficking are strongly associated with neurodegenerative disease. In this review, we summarize the current understanding of nuclear pore biology in physiological and pathological contexts and discuss potential therapeutic approaches for addressing nuclear pore injury and dysfunctional nucleocytoplasmic transport.

Multifunctional scaffolds for bone repair following age-related biological decline: Promising prospects for smart biomaterial-driven technologies

The repair of large bone defects due to trauma, disease, and infection can be exceptionally challenging in the elderly. Despite best clinical practice, bone regeneration within contemporary, surgically implanted synthetic scaffolds is often problematic, inconsistent, and insufficient where additional osteobiological support is required to restore bone. Emergent smart multifunctional biomaterials may drive important and dynamic cellular crosstalk that directly targets, signals, stimulates, and promotes an innate bone repair response following age-related biological decline and when in the presence of disease or infection. However, their role remains largely undetermined. By highlighting their mechanism/s and mode/s of action, this review spotlights smart technologies that favorably align in their conceivable ability to directly target and enhance bone repair and thus are highly promising for future discovery for use in the elderly. The four degrees of interactive scaffold smartness are presented, with a focus on bioactive, bioresponsive, and the yet-to-be-developed autonomous scaffold activity. Further, cell- and biomolecular-assisted approaches were excluded, allowing for contemporary examination of the capabilities, demands, vision, and future requisites of next-generation biomaterial-induced technologies only. Data strongly supports that smart scaffolds hold significant promise in the promotion of bone repair in patients with a reduced osteobiological response. Importantly, many techniques have yet to be tested in preclinical models of aging. Thus, greater clarity on their proficiency to counteract the many unresolved challenges within the scope of aging bone is highly warranted and is arguably the next frontier in the field. This review demonstrates that the use of multifunctional smart synthetic scaffolds with an engineered strategy to circumvent the biological insufficiencies associated with aging bone is a viable route for achieving next-generation therapeutic success in the elderly population.

Synergistic increase in coproporphyrin III biosynthesis by mitochondrial compartmentalization in engineered Saccharomyces cerevisiae

Coproporphyrin III (CP III), a natural porphyrin derivative, has extensive applications in the biomedical and material industries. S. cerevisiae has previously been engineered to highly accumulate the CP III precursor 5-aminolevulinic acid (ALA) through the C4 pathway. In this study, a combination of cytoplasmic metabolic engineering and mitochondrial compartmentalization was used to enhance CP III production in S. cerevisiae. By integrating pathway genes into the chromosome, the CP III titer gradually increased to 32.5 ± 0.5 mg/L in shake flask cultivation. Nevertheless, increasing the copy number of pathway genes did not consistently enhance CP III synthesis. Hence, the partial synthesis pathway was compartmentalized in mitochondria to evaluate its effectiveness in increasing CP III production. Subsequently, by superimposing the mitochondrial compartmentalization strategy on cytoplasmic metabolic engineered strains, the CP III titer was increased to 64.3 ± 1.9 mg/L. Furthermore, augmenting antioxidant pathway genes to reduce reactive oxygen species (ROS) levels effectively improved the growth of engineered strains, resulting in a further increase in the CP III titer to 82.9 ± 1.4 mg/L. Fed-batch fermentations in a 5 L bioreactor achieved a titer of 402.8 ± 9.3 mg/L for CP III. This study provides a new perspective on engineered yeast for the microbial production of porphyrins.

Discovery and biocatalytic characterization of opine dehydrogenases by metagenome mining

Enzymatic processes play an increasing role in synthetic organic chemistry which requires the access to a broad and diverse set of enzymes. Metagenome mining is a valuable and efficient way to discover novel enzymes with unique properties for biotechnological applications. Here, we report the discovery and biocatalytic characterization of six novel metagenomic opine dehydrogenases from a hot spring environment (mODHs) (EC 1.5.1.X). These enzymes catalyze the asymmetric reductive amination between an amino acid and a keto acid resulting in opines which have defined biochemical roles and represent promising building blocks for pharmaceutical applications. The newly identified enzymes exhibit unique substrate specificity and higher thermostability compared to known examples. The feature that they preferably utilize negatively charged polar amino acids is so far unprecedented for opine dehydrogenases. We have identified two spatially correlated positions in their active sites that govern this substrate specificity and demonstrated a switch of substrate preference by site-directed mutagenesis. While they still suffer from a relatively narrow substrate scope, their enhanced thermostability and the orthogonality of their substrate preference make them a valuable addition to the toolbox of enzymes for reductive aminations. Importantly, enzymatic reductive aminations with highly polar amines are very rare in the literature. Thus, the preparative-scale enzymatic production, purification, and characterization of three highly functionalized chiral secondary amines lend a special significance to our work in filling this gap. KEY POINTS: • Six new opine dehydrogenases have been discovered from a hot spring metagenome • The newly identified enzymes display a unique substrate scope • Substrate specificity is governed by two correlated active-site residues.

Molecular mechanisms underlying Tao-Hong-Si-Wu decoction treating hyperpigmentation based on network pharmacology, Mendelian randomization analysis, and experimental verification

CONTEXT

Hyperpigmentation, a common skin condition marked by excessive melanin production, currently has limited effective treatment options.

OBJECTIVE

This study explores the effects of Tao-Hong-Si-Wu decoction (THSWD) on hyperpigmentation and to elucidate the underlying mechanisms.

MATERIALS AND METHODS

We employed network pharmacology, Mendelian randomization, and molecular docking to identify THSWD's hub targets and mechanisms against hyperpigmentation. The Cell Counting Kit-8 (CCK-8) assay determined suitable THSWD treatment concentrations for PIG1 cells. These cells were exposed to graded concentrations of THSWD-containing serum (2.5%, 5%, 10%, 15%, 20%, 30%, 40%, and 50%) and treated with α-MSH (100 nM) to induce an in vitro hyperpigmentation model. Assessments included melanin content, tyrosinase activity, and Western blotting.

RESULTS

ALB, IL6, and MAPK3 emerged as primary targets, while quercetin, apigenin, and luteolin were the core active ingredients. The CCK-8 assay indicated that concentrations between 2.5% and 20% were suitable for PIG1 cells, with a 50% cytotoxicity concentration (CC50) of 32.14%. THSWD treatment significantly reduced melanin content and tyrosinase activity in α-MSH-induced PIG1 cells, along with downregulating MC1R and MITF expression. THSWD increased ALB and p-MAPK3/MAPK3 levels and decreased IL6 expression in the model cells.

DISCUSSION AND CONCLUSION

THSWD mitigates hyperpigmentation by targeting ALB, IL6, and MAPK3. This study paves the way for clinical applications of THSWD as a novel treatment for hyperpigmentation and offers new targeted therapeutic strategies.

Epigenetic landscape of 5-hydroxymethylcytosine and associations with gene expression in placenta

5-hydroxymethylcystosine (5hmC), is an intermediate product in the DNA demethylation pathway, but may act as a functional epigenetic modification. We have conducted the largest study of site-specific 5hmC in placenta to date using parallel bisulphite and oxidative bisulphite modification with array-based assessment. Incorporating parallel RNA-sequencing data allowed us to assess associations between 5hmC and gene expression, using expression quantitative trait hydroxymethylation (eQTHM) analysis. We identified ~ 47,000 loci with consistently elevated (systematic) 5hmC proportions. Systematic 5hmC was significantly depleted (p < 0.0001) at CpG islands (CGI), and enriched (p < 0.0001) in 'open sea' regions (CpG >4 kb from CGI). 5hmC was most and least abundant at CpGs in enhancers and active transcription start sites (TSS), respectively (p < 0.05). We identified 499 significant (empirical-p <0.05) eQTHMs within 1 MB of the assayed gene. At most (75.4%) eQTHMs, the proportion of 5hmC was positively correlated with transcript abundance. eQTHMs were significantly enriched among enhancer CpGs and depleted among CpGs in active TSS (p < 0.05 for both). Finally, we identified 107 differentially hydroxymethylated regions (DHMRs, p < 0.05) across 100 genes. Our study provides insight into placental distribution of 5hmC, and sheds light on the functional capacity of this epigenetic modification in placenta.

NanoConstruct: A web application builder of ellipsoidal nanoparticles for the investigation of their crystal growth, stability, and the calculation of atomistic descriptors

NanoConstruct is a state-of-the-art computational tool that enables a) the digital construction of ellipsoidal neutral energy minimized nanoparticles (NPs) in vacuum through its graphical user-friendly interface, and b) the calculation of NPs atomistic descriptors. It allows the user to select NP's shape and size by inserting its ellipsoidal axes and rotation angle while the NP material is selected by uploading its Crystallography Information File (CIF). To investigate the stability of materials not yet synthesised, NanoConstruct allows the substitution of the chemical elements of an already synthesized material with chemical elements that belong into the same group and neighbouring rows of the periodic table. The process is divided into three stages: 1) digital construction of the unit cell, 2) digital construction of NP using geometry rules and keeping its stoichiometry and 3) energy minimization of the geometrically constructed NP and calculation of its atomistic descriptors. In this study, NanoConstruct was applied for the investigation of the crystal growth of Zirconia (ZrO2) NPs when in the rutile form. The most stable configuration and the crystal growth route were identified, showing a preferential direction for the crystal growth of ZrO2 in its rutile form. NanoConstruct is freely available through the Enalos Cloud Platform (https://enaloscloud.novamechanics.com/riskgone/nanoconstruct/).

Identification of a human type XVII collagen fragment with high capacity for maintaining skin health

Collagen XVII (COL17) is a transmembrane protein that mediates skin homeostasis. Due to expression of full length collagen was hard to achieve in microorganisms, arising the needs for selection of collagen fragments with desired functions for microbial biosynthesis. Here, COL17 fragments (27-33 amino acids) were extracted and replicated 16 times for recombinant expression in Escherichia coli. Five variants were soluble expressed, with the highest yield of 223 mg/L. The fusion tag was removed for biochemical and biophysical characterization. Circular dichroism results suggested one variant (sample-1707) with a triple-helix structure at >37 °C. Sample-1707 can assemble into nanofiber (width, 5.6 nm) and form hydrogel at 3 mg/mL. Sample-1707 was shown to induce blood clotting and promote osteoblast differentiation. Furthermore, sample-1707 exhibited high capacity to induce mouse hair follicle stem cells differentiation and osteoblast migration, demonstrating a high capacity to induce skin cell regeneration and promote wound healing. A strong hydrogel was prepared from a chitosan and sample-1707 complex with a swelling rate of >30 % higher than simply using chitosan. Fed-batch fermentation of sample-1707 with a 5-L bioreactor obtained a yield of 600 mg/L. These results support the large-scale production of sample-1707 as a biomaterial for use in the skin care industry.

Sparsely PEGylated poly(beta-amino ester) polyplexes enhance antigen specific T-cell response of a bivalent SARS-CoV-2 DNA vaccine

DNA technology has emerged as a promising route to accelerated manufacture of sequence agnostic vaccines. For activity, DNA vaccines must be protected and delivered to the correct antigen presenting cells. However, the physicochemical properties of the vector must be carefully tuned to enhance interaction with immune cells and generate sufficient immune response for disease protection. In this study, we have engineered a range of polymer-based nanocarriers based on the poly(beta-amino ester) (PBAE) polycation platform to investigate the role that surface poly(ethylene glycol) (PEG) density has on pDNA encapsulation, formulation properties and gene transfectability both in vitro and in vivo. We achieved this by synthesising a non-PEGylated and PEGylated PBAE and produced formulations containing these PBAEs, and mixed polyplexes to tune surface PEG density. All polymers and co-formulations produced small polyplex nanoparticles with almost complete encapsulation of the cargo in all cases. Despite high gene transfection in HEK293T cells, only the fully PEGylated and mixed formulations displayed significantly higher expression of the reporter gene than the negative control in dendritic cells. Further in vivo studies with a bivalent SARS-CoV-2 pDNA vaccine revealed that only the mixed formulation led to strong antigen specific T-cell responses, however this did not translate into the presence of serum antibodies indicating the need for further studies into improving immunisation with polymer delivery systems.

Dual-template magnetic molecularly imprinted polymers for selective extraction and sensitive detection of aflatoxin B1 and benzo(α)pyrene in environmental water and edible oil

The coexistence of multiple contaminates in the environment and food is of growing concern due to their extremely hazard as a well-known class I carcinogen, like aflatoxin B1 (AFB1) and benzo(α)pyrene (BaP). AFB1 and BaP are susceptible to coexistence in environmental water and edible oil, posing a significant potential risk to environmental monitoring and food safety. The remaining challenges in detecting multiple contaminates include unsatisfied sensitivity, insufficient targets selectivity, and interferences in complex matrices. Here, we developed dual-template magnetic molecularly imprinted polymers (DMMIPs) for selective extraction of dual targets in complex matrices from the environment and food. The DMMIPs were fabricated by surface imprinting with vinyl-functionalized Fe3O4 as carrier, 5,7-dimethoxycoumarin and pyrene as dummy templates, and methacrylamide as functional monomer. The DMMIPs showed excellent adsorption ability (12.73-15.80 mg/g), imprinting factors (2.01-2.58), and reusability of three adsorption-desorption cycles for AFB1 and BaP. The adsorption mechanism including hydrogen bond, electrostatic interaction and van der Waals force was confirmed by physical characterization and DFT calculation. Applying DMMIPs in magnetic solid phase extraction (MSPE) followed by high-performance liquid chromatography (HPLC) analysis enabled detection limits of 0.134 μg/L for AFB1 and 0.107 μg/L for BaP. Recovery rates for water and edible oil samples were recorded as 86.2%-110.3% with RSDs of 4.1%-11.9%. This approach demonstrates potential for simultaneous identification and extraction of multiple contaminants in environmental and food.

Integrated analysis of ferroptosis and stemness based on single-cell and bulk RNA-sequencing data provide insights into the prognosis and treatment of esophageal carcinoma

BACKGROUND

Cancer stem cells (CSCs) play a significant role in the recurrence and drug resistance of esophageal carcinoma (ESCA). Ferroptosis is a promising anticancer therapeutic strategy that effectively targets CSCs exhibiting high tumorigenicity and treatment resistance. However, there is a lack of research on the combined role of ferroptosis-related genes (FRGs) and stemness signature in the prognosis of ESCA.

METHODS

The cellular compositions were characterized using single-cell RNA sequencing (scRNA-seq) data from 18 untreated ESCA samples. 50 ferroptosis-related stemness genes (FRSGs) were identified by integrating FRGs with stemness-related genes (SRGs), and then the cells were grouped by AUCell analysis. Next, functional enrichment, intercellular communication, and trajectory analyses were performed to characterize the different groups of cells. Subsequently, the stem-ferr-index was calculated using machine learning algorithms based on the expression profiles of the identified risk genes. Additionally, therapeutic drugs were predicted by analyzing the GDSC2 database. Finally, the expression and functional roles of the identified marker genes were validated through in vitro experiments.

RESULTS

The analysis of scRNA-seq data demonstrates the diversity and cellular heterogeneity of ESCA. Then, we identified 50 FRSGs and classified cells into high or low ferroptosis score stemness cells accordingly. Functional enrichment analysis conducted on the differentially up-regulated genes between these groups revealed predominant enrichment in pathways associated with intercellular communication and cell differentiation. Subsequently, we identified 9 risk genes and developed a prognostic signature, termed stem_ferr_index, based on these identified risk genes. We found that the stem-ferr-index was correlated with the clinical characteristics of patients, and patients with high stem-ferr-index had poor prognosis. Furthermore, we identified four drugs (Navitoclax, Foretinib, Axitinib, and Talazoparib) with potential efficacy targeting patients with a high stem_ferr_index. Additionally, we delineated two marker genes (STMN1 and SLC2A1). Particularly noteworthy, SLC2A1 exhibited elevated expression levels in ESCA tissues and cells. We provided evidence suggesting that SLC2A1 could influence the migration, invasion, and stemness of ESCA cells, and it was associated with sensitivity to Foretinib.

CONCLUSION

This study constructed a novel ferroptosis-related stemness signature, identified two marker genes for ESCA, and provided valuable insights for developing more effective therapeutic targets targeting ESCA CSCs in the future.

Discrimination of bottled mineral water from tap water using a Dip-Type colorimetric paper-based sensor array and chemometrics

Mineral water is a natural water that originated from an underground water table, a well, or a natural spring which is considered microbiologically intact. The revenue from the bottled mineral water industry will be USD 342.40 billion in 2023, and it is expected to grow at a compound annual growth rate (CAGR) of 5.24 %. Consequently, the discrimination of original bottled mineral water from tap water is an important issue that requires designing sensors for simple and portable identification of these two types of water. In this work, we have developed a Dip-Type colorimetric paper-based sensor array with three organic dyes (Bromothymol Blue, Bromophenol Blue, and Methyl Red) followed by chemometrics' pattern recognition methods (PCA and LDA) for discrimination of original bottled mineral waters from tap waters based on differences in ion variety and ion quantity. Forty brands of mineral water and twenty-six Tap water samples from different regions of Shiraz and other Iranian cities were analyzed by this sensor array. Moreover, these experiments were performed in two consecutive years to check the versatility of the sensor with seasonal changes in waters. This sensor array was able to discriminate these two water types from each other with an accuracy of > 95 % based on the analysis of 85 water samples.

A close-looped DNAzyme walker with an available catalytic domain for electrochemiluminescent detection of acetamiprid

Traditional DNA walkers face enormous challenges due to limited biostability and reaction kinetics. Herein, we designed a self-driven close-looped DNAzyme walker (cl-DW) with high structural biostability and catalytic activity that enabled rapid electrochemiluminescence (ECL) detection of pesticide residue acetamiprid. Specifically, cl-DW exhibited increasing ability to resist nuclease degradation with a 570-fold longer half-degradation time than that of the single-stranded DNAzyme walker (ss-DW) due to the protected DNA terminal. Furthermore, cl-DW achieved high catalytic activity with a 4.3-fold faster reaction kinetic than that of ss-DW due to the circularized nanostructure of an available catalytic domain. Consequently, we utilized cl-DW as a signal amplifier and tin-based sulfide (SnS2) nanoflowers as ECL emitters to construct an ECL aptasensor, which realized the sensitive detection of acetamiprid with a limit of detection of 0.85 nM. This work provides a reliable approach to exploring DNA walkers with high catalytic activity and better biostability for molecular monitoring.

Implications of liquid-liquid phase separation and ferroptosis in Alzheimer's disease

Neuronal cell demise represents a prevalent occurrence throughout the advancement of Alzheimer's disease (AD). However, the mechanism of triggering the death of neuronal cells remains unclear. Its potential mechanisms include aggregation of soluble amyloid-beta (Aβ) to form insoluble amyloid plaques, abnormal phosphorylation of tau protein and formation of intracellular neurofibrillary tangles (NFTs), neuroinflammation, ferroptosis, oxidative stress, liquid-liquid phase separation (LLPS) and metal ion disorders. Among them, ferroptosis is an iron-dependent lipid peroxidation-driven cell death and emerging evidences have demonstrated the involvement of ferroptosis in the pathological process of AD. The sensitivity to ferroptosis is tightly linked to numerous biological processes. Moreover, emerging evidences indicate that LLPS has great impacts on regulating human health and diseases, especially AD. Soluble Aβ can undergo LLPS to form liquid-like droplets, which can lead to the formation of insoluble amyloid plaques. Meanwhile, tau has a high propensity to condensate via the mechanism of LLPS, which can lead to the formation of NFTs. In this review, we summarize the most recent advancements pertaining to LLPS and ferroptosis in AD. Our primary focus is on expounding the influence of Aβ, tau protein, iron ions, and lipid oxidation on the intricate mechanisms underlying ferroptosis and LLPS within the domain of AD pathology. Additionally, we delve into the intricate cross-interactions that occur between LLPS and ferroptosis in the context of AD. Our findings are expected to serve as a theoretical and experimental foundation for clinical research and targeted therapy for AD.

Formation of persistent free radicals from epigallocatechin Gallate in tea processing and their implications on DNA damage and cell cytotoxicity

Tea is widely consumed in both beverages and food. Epigallocatechin gallate (EGCG) is the most crucial active ingredient in tea. Currently, knowledges on transformation processes of EGCG during tea processing are lacking. Understanding the chemical reactions of EGCG and its products during tea processing is important for assessing the safety of tea-containing food. Here, we revealed the formation of persistent free radicals (PFRs) from EGCG under the influence of heating and light irradiation, which was substantiated with evidence. These PFRs exhibited stability for >30 min in simulated gastric fluid. Furthermore, we observed potential effects of these PFRs on DNA damage and cell cytotoxicity in vitro. By combining electron paramagnetic resonance spectrometer with Fourier transform ion cyclotron resonance mass spectrometry, we elucidated the pathways involved in free radical formation. These findings are expected to contribute to a comprehensive understanding of free radical chemistry in tea-containing food.

Characterization of the volatile flavor profiles of black garlic using nanomaterial-based colorimetric sensor array, HS-SPME-GC/MS coupled with chemometrics strategies

This work investigated the feasibility of applying headspace solid phase microextraction-gas chromatography-mass spectrometry (HS-SPME-GC/MS) combining olfactory visualization for flavor characterization of black garlic. Volatile organic compounds (VOCs) analysis was performed to select important differential VOCs during black garlic processing. A multi-channels nanocomposite CSA assembled with two porous metal-organic frameworks was then developed to characterize flavor profiles changes during black garlic processing, and garlic samples during processing could be divided into five clusters, consistent with VOCs analysis. Artificial neural network (ANN) model outperformed other pattern recognition methods in discriminating processing stages. Furthermore, SVR model for odor sensory scores with the correlation coefficient for prediction set of 0.8919 exhibited a better performance than PLS model, indicating a preferable prediction ability for odor quality. This work demonstrated that the nanocomposite CSA combining appropriate chemometrics can offer an effective tool for objectively and rapidly characterizing flavor quality of black garlic or other food matrixes.

Self-assembled Abietic acid encapsulated nanoparticles to improve the stability of Proanthocyanin B2

Procyanidin B2 (Pac B2) has attracted much attention due to its strong antioxidant activity, but poor in vivo stability limits its wide application in food and medicine. In this paper, composite nanoparticles (NPs) were constructed using abietic acid (AA) as a carrier, which significantly enhanced Pac B2 stability. A spherical morphology and average diameter of 396.05 nm were observed in AA-Pac B2 NPs synthesized by solvent co-precipitation. Pac B2 encapsulation was 11.28 %, and thermal stability is improved. Infrared, Ultraviolet spectrum, and MD (molecular dynamics) spectroscopy revealed hydrogen bonding and hydrophobic interaction between AA and Pac B2. For up to 2 h at 37 °C, Pac B2 can be sustainably released in simulated gastric and intestinal fluids. In vitro, AA-Pac B2 NPs at the same concentration exhibited higher bioavailability and uptake efficiency than free Pac B2. The data demonstrate the potential of AA NPs for improving polyphenol thermal stability and bioavailability.

Distinct responses of urban and rural O3 pollution with secondary particle changes to anthropogenic emission reductions: Insights from a case study over North China

Ozone (O3) pollution with excessive near-surface O3 levels has been an important environmental issue in China, although the anthropogenic emission reductions (AER) have improved air quality since 2013. In this study, we investigated the sensitivities of atmospheric chemical environment with the urban and rural changes to the AER targeting a typical O3 pollution episode over North China in summer 2019, by conducting two WRF-Chem simulation experiments under two scenarios of anthropogenic emission inventories of years 2012 and 2019 with the meteorological conditions in the 2019 summertime O3 pollution episode for excluding the meteorological impacts on O3 pollution. The results show that the unbalanced AER aroused more serious O3 pollution in urban and rural areas. The intense NO reduction was responsible for the significant increments of urban O3, while the falling NO2 and NO synergistically devoted to the slight O3 variations in rural areas. Induced by the recent-year AER, the urban O3 production was governed by VOCs-limited and transition regime, whereas the NOx-limited regime dominated over rural areas in North China. Also, the AER reinforced the atmospheric oxidation capacity with the elevations of atmospheric oxidants O3 and ROx radicals, strengthening the chemical conversions to secondary inorganic particles. In both urban and rural areas, the sharp drop in SO2 caused a decrease in sulfate fraction, while the enhanced AOC accelerated the transformation to nitrate even when NOx was reduced. The AER induced nitrate to occupy the principal position in secondary PM2.5 in urban and rural areas. The AER promoted daytime and suppressed nighttime the nitrate production in urban areas, and more vigorous conversion of secondary aerosols were found in rural areas with much lower AOC increments. This study provides insights from a case study over North China in distinct responses of urban and rural O3 pollution with secondary particle changes to AER in urban and rural atmospheric environment changes, with implications for an effective abatement strategy on O3 pollution.

Insight into the photodynamic mechanism and protein binding of a nitrosyl iron-sulfur [Fe2S2(NO)4]2- cluster

Iron-sulfur cluster conversion and nitrosyl modification are involved in regulating their functions and play critical roles in signaling for biological systems. Hereby, the photo-induced dynamic process of (Me4N)2[Fe2S2(NO)4] was monitored using time-resolved electron paramagnetic resonance (EPR) spectra, MS spectra and cellular imaging methods. Photo-irradiation and the solvent affect the reaction rates and products. Spectroscopic and kinetic studies have shown that the process involves at least three intermediates: spin-trapped NO free radical species with a gav at 2.040, and two other iron nitrosyl species, dinitrosyl iron units (DNICs) and mononitrosyl iron units (MNICs) with gav values at 2.031 and 2.024, respectively. Moreover, the [Fe2S2(NO)4]2- cluster could bind with ferritin and decompose gradually, and a binding state of dinitrosyl iron coordinated with Cys102 of the recombinant human heavy chain ferritin (rHuHF) was finally formed. This study provides insight into the photodynamic mechanism of nitrosyl iron - sulfur clusters to improve the understanding of physiological activity.

A theoretical study of the photochemistry of 1,3-cyclopentadiene and its cyano derivatives bound to a water dimer: Assessing reactivity of ionized clusters and possible photoproducts

We theoretically investigate the photoionization scenarios of molecular complexes involving cyclopentadiene and cyanocyclopentadiene bound to water dimers. Using electronic structure calculations within density-functional theory (DFT) and time dependent DFT (TD-DFT), we explore the potential photochemical pathways following ionization, and determine the charge transfer excitations related to the possible subsequent reactions. Our findings suggest that the investigated photochemical pathways of the hydrated complexes take place in two well-defined ultraviolet regions: (i) 8.2-9.5 eV for the cyclic compounds and (ii) 11.2-11.4 eV for the bound water dimer. We quantify how H-bonding effects can influence the photoionization channels. Before forming possible photoproducts, we also examine the regiospecificity of OH addition to 1,3-cyclopentadiene and its cyano derivatives We analyze our results in light of photoionization studies of jet-cooled molecular complexes and possible implications in astrochemical environments.

Hydrostatic pressure effect on excited state properties of room temperature phosphorescence molecules: A QM/MM study

Stimulus-responsive organic room temperature phosphorescence (RTP) materials exhibit variations in their luminescent characteristics (lifetime and efficiency) upon exposure to external stimuli, including force, heat, light and acid-base conditions, the development of stimulus-responsive RTP molecules becomes imperative. However, the inner responsive mechanism is unclear, theoretical investigations to reveal the relationship among hydrostatic pressures, molecular structures and photophysical properties are highly desired. Herein, taking the Se-containing RTP molecule (SeAN) as a model, based on the dispersion corrected density functional theory (DFT-D), the combined quantum mechanics and molecular dynamics (QM/MM) method and thermal vibration correlation function (TVCF) theory, the influences of hydrostatic pressure on molecular structures, transition properties as well as lifetimes and efficiencies of RTP molecule are theoretically studied. Results show that extended lifetime and enhanced efficiency are observed at 2 Gpa compared with molecule at normal pressure, and this is related with the small reorganization energy and large oscillator strength. Moreover, due to the small energy gap (0.34 eV) and remarkable spin-orbit coupling (SOC) constant (8.56 cm-1) between first singlet excited state and triplet state, fast intersystem crossing (ISC) process is determined for molecule at 6 Gpa. Furthermore, the intermolecular interactions are visualized using independent gradient model based on Hirshfeld partition (IGMH) and the changes of molecular packing modes, SOC values, lifetimes and efficiencies with pressures are detected. These results reveal the relationship between molecular structures and RTP properties. Our work provides theoretical insights into the hydrostatic pressure response mechanism and could promote the development new efficient stimulus-responsive molecules.

Investigating the influence of molybdenum disulfide quantum dots coated with DSPE-PEG-TPP on molecular structures of liver lipids and proteins: An in vivo study

Molybdenum disulfide (MoS2) quantum dots (QDs) based therapeutic approaches hold great promise for biomedical applications, necessitating a thorough evaluation of their potential effects on biological systems. In this study, we systematically investigated the impact of MoS2 QDs coated with 1,2-distearoyl-sn-glycero-3-phosphoethanolamine-N-[amino(polyethyleneglycol)-2000](DPSE-PEG) linked with (3-carboxypropyl)triphenyl-phosphonium-bromide (TPP) on molecular structures of hepatic tissue lipids and proteins through a multifaceted analysis. The DSPE-PEG-TPP-MoS2 QDs were prepared and administered to the mice daily for 7 weeks. Liver tissues were subjected to a comprehensive examination using various techniques, including Fourier-transform infrared (FTIR) spectroscopy, UV-vis spectroscopy, and liver function tests. FTIR revealed subtle changes in the lipid composition of liver tissues, indicating potential modifications in the cell membrane structure. Also, the (CH stretching and amides I and II regions) analysis unveiled tiny alterations in lipid chain length and fluidity without changes in the protein structures, suggesting a minor influence of DSPE-PEG-TPP-MoS2 QDs on the liver's cellular membrane and no effect on the protein structures. Further scrutiny using UV-vis spectroscopy demonstrated that DSPE-PEG-TPP-MoS2 QDs had no discernible impact on the absorbance intensities of aromatic amino acids and the Soret band. This observation implies that the treatment with SPE-PEG-TPP-MoS2 QDs did not induce significant alterations in helical conformation or the microenvironment surrounding prosthetic groups in liver tissues. The liver function tests, including ALP, ALT, AST, and BIL levels, revealed no statistically significant changes in these key biomarkers despite minor fluctuations in their values, indicating a lack of significant liver dysfunction. This study provides a detailed understanding of the effects of DSPE-PEG-TPP-MoS2 QDs on hepatic lipids and proteins, offering valuable insights into the biocompatibility and limited impact on the molecular and functional aspects of the liver tissue. These findings could be essential for the application of MoS2 QDs-based therapies.

Atomically dispersed copper-zinc dual sites anchored on nitrogen-doped porous carbon toward peroxymonosulfate activation for degradation of various organic contaminants

Single-atom catalysts (SACs) have been widely studied in Fenton-like reactions, wherein their catalytic performance could be further enhanced by adjusting electronic structure and regulating coordination environment, although relevant research is rarely reported. This text elucidates fabrication of dual atom catalyst systems aimed at augmenting their catalytic efficiency. Herein, atomically dispersed copper-zinc (Cu-Zn) dual sites anchored on nitrogen (N)-doped porous carbon (NC), referred to as CuZn-NC, were synthesized using cage-encapsulated pyrolysis and host-guest strategies. The CuZn-NC catalyst exhibited high activity in activation of peroxymonosulfate (PMS) for degradation of organic pollutants. Based on synergistic effects of adjacent Cu and Zn atom pairs, CuZn-NC (PMS) system achieved 94.44 % bisphenol A (BPA) degradation in 24 min. The radical pathway predominated, and coexistence of non-radical species was demonstrated for BPA degradation in CuZn-NC/PMS system. More importantly, CuZn-NC/PMS system showed generality for degradation of various refractory contaminants. Our experiments indicate that CuZn-N sites on CuZn-NC act as active sites for bonding PMS molecules with optimal binding energy, while pyrrolic N sites are considered as adsorption sites for organic molecules. Overall, this research designs diatomic site catalysts (DACs), with promising implications for wastewater treatment.

Selective exposure of (111) crystal plane in Pd49Ag30Te4 by Tb doping to weaken Pd - C bond and promote electroreduction of CO2 to CO

Employing electric energy to convert carbon dioxide (CO2) into valuable small molecules is a potentially practical method in energy storage and greenhouse gas alleviation. A huge challenge for electrocatalytic CO2 reduction is to reduce overpotential to improve energy efficiency. Herein, we demonstrate that doping alloy Pd49Ag30Te4 (PAT) with rare-earth element Tb is beneficial for selective exposure of (111) crystal plane, which is a highly active crystal plane for producing carbon monoxide (CO). The as-prepared Tb2.9PAT exhibited high electrocatalytic performance with 95.7 % CO faradic efficiency at - 0.8 V (vs RHE), far exceeding that of PAT, and coupled with good durability. In situ spectral study and theoretical calculations disclose that the introduction of Tb regulates the d-band center of PAT alloy, weakens the Pd - C bonding ability, and promotes the desorption of *CO in the rate-determining step. This study provides a method for doping induced selective exposure of crystal face, which provides new idea for improving catalytic performance.

Preconcentration and detection of SARS-CoV-2 in wastewater: A comprehensive review

Severe acute respiratory syndrome coronaviruses 2 (SARS-CoV-2) causing coronavirus disease 2019 (COVID-19) affected the health of human beings and the global economy. The patients with SARS-CoV-2 infection had viral RNA or live infectious viruses in feces. Thus, the possible transmission of SARS-CoV-2 through wastewater received great attentions. Moreover, SARS-CoV-2 in wastewater can serve as an early indicator of the infection within communities. We summarized the preconcentration and detection technology of SARS-CoV-2 in wastewater aiming at the complex matrices of wastewater and low virus concentration and compared their performance characteristics. We described the emerging tests that would be possible to realize the rapid detection of SARS-CoV-2 in fields and encourage academics to advance their technologies beyond conception. We concluded with a brief discussion on the outlook for integrating preconcentration and the detection of SARS-CoV-2 with emerging technologies.

Unveiling the influence of hydrophobicity on inhibiting hydrogen dissociation for enhanced photocatalytic hydrogen evolution of covalent organic frameworks

Covalent organic frameworks (COFs) have gained considerable interest as candidate photocatalysts for hydrogen evolution. In this work, we synthesized β-keto-enamine-based COFs (TpPa-X, TpDB, and TpDTP) to explore the relations between structures and photocatalytic hydrogen evolution. COFs were divided into two groups: (1) TpPa-X with different substituents attached to the TpPa backbone and (2) COFs featuring diamine linkers of varied lengths (TpDB and TpDTP). Experiments and density functional theory (DFT) calculations show that moderate hydrophobicity is favorable for the photocatalytic hydrogen evolution process, and acceptable contact angles are anticipated to range from 65° to 80°. Naturally, there are comprehensive factors that affect photocatalytic reactions, and the regulation of different backbones and substituents can considerably affect the performance of COFs for photocatalytic hydrogen evolution in terms of electronic structure, specific surface area, surface wettability, carrier separation efficiency, and hydrogen dissociation energy. Results show that TpPa-Cl2 (TpPa-X, X  = Cl2) demonstrates the highest photocatalytic activity, approximately 14.51 mmol g-1h-1, with an apparent quantum efficiency of 4.62 % at 420 nm. This work provides guidance for designing efficient COF-based photocatalysts.

Rational design of diblock copolymer enables efficient cytosolic protein delivery

Polymer-mediated cytosolic protein delivery demonstrates a promising strategy for the development of protein therapeutics. Here, we propose a new designed diblock copolymer which realizes efficient cytosolic protein delivery both in vitro and in vivo. The polymer contains one protein-binding block composed of phenylboronic acid (PBA) and N-(3-dimethylaminopropyl) (DMAP) pendant units for protein binding and endosomal escape, respectively, followed by the response to ATP enriched in the cytosol which triggers the protein release. The other block is PEG designed to improve particle size control and circulation in vivo. By optimizing the block composition, sequence and length of the copolymer, the optimal one (BP20) was identified with the binding block containing 20 units of both PBA and DMAP, randomly distributed along the chain. When mixed with proteins, the BP20 forms stable nanoparticles and mediates efficient cytosolic delivery of a wide range of proteins including enzymes, toxic proteins and CRISPR/Cas9 ribonucleoproteins (RNP), to various cell lines. The PEG block, especially when further modified with folic acid (FA), enables tumor-targeted delivery of Saporin in vivo, which significantly suppresses the tumor growth. Our results shall inspire the design of novel polymeric vehicles with robust capability for cytosolic protein delivery, which holds great potential for both biological research and therapeutic applications.

Understanding the origins of reversible and hysteretic pathways of adsorption phase transitions in metal-organic frameworks

Phase behavior of nanoconfined fluids adsorbed in metal-organic frameworks is of paramount importance for the design of advanced materials for energy and gas storage, separations, electrochemical devices, sensors, and drug delivery, as well as for the pore structure characterization. Phase transformations in adsorbed fluids often involve long-lasting metastable states and hysteresis that has been well-documented in gas adsorption-desorption and nonwetting fluid intrusion-extrusion experiments. However, theoretical prediction of the observed nanophase behavior remains a challenging problem. The mesoscopic canonical, or mesocanonical, ensemble (MCE) is devised to study the nanophase behavior under conditions of controlled fluctuations to stabilize metastable and labile states. Here, we implement and apply the MCE Monte Carlo (MCEMC) simulation scheme to predict the origins of reversible and hysteric adsorption phase transitions in a series of practical MOF materials, including IRMOF-1, ZIF-412, UiO-66, Cu-BTC, IRMOF-74-V, VII, and IX. The MCEMC method, called the gauge cell method, allows to produce Van der Waals type isotherms with distinctive swings around the phase transition regions. The constructed isotherms determine the positions of phase equilibrium and spinodals, as well as the nucleation barriers separating metastable states. We demonstrate the unique capabilities of the MCEMC method in quantitative predictions of experimental observations compared with the conventional grand canonical and canonical ensemble simulations. The MCEMC method is implemented in the open-source RASPA and LAMMPS software packages and recommended for studies of adsorption behavior and pore structure characterization of MOFs and other nanoporous materials.

Construction of portable hydrogel kits with self-ratio optical bimodal detection and smartphone imaging for on-site nitrite screening

Accurate on-site detection of nitrite in complex matrices remains a significant challenge. Herin, we construct a self-ratio optical bimodal portable kit via co-assembling NaErF4:0.5%Tm@NaYF4@NaYbF4:0.5%Tm@NaYF4 (Er:Tm@Yb:Tm) and nitrogen-doped carbon platinum nanomaterials (Pt/CN) in sodium alginate (SA) hydrogel. Pt/CN nanomaterials are synthesized by high-temperature sintering using a zinc-based zeolite imidazolium framework as a sacrificial template. The Pt/CN nanozyme possesses excellent oxidase-like activity to produce the oxidation state 3,3',5,5'-tetramethylbenzidine (oxTMB). Nitrite mediates diazotization of oxTMB to trigger the change of absorption signals, accompanying the ratio fluorescence response of the Er:Tm@Yb:Tm. Crucially, Er:Tm@Yb:Tm and Pt/CN are embedded in SA hydrogel to fabricate a portable kit with efficient and sensitive performance. An image processing algorithm is used to analyze the nitrite-induced signal change of the portable hydrogel kit, resulting in detection limits of 0.63 μM. This method has great potential for point-of-care applications due to its reliability, long-term stability, accuracy, sensitivity, and portability.

Encapsulating fullerene into Ti-based metal-organic frameworks with anchored atomically dispersed Pt cocatalysts for efficient hydrogen evolution

Ti-based Metal-organic frameworks (Ti-MOF) have been extensively investigated for producing hydrogen via solar water splitting, while their intrinsic activities are still retarded by the poor performance of photocarriers separation and utilization. Herein, a donor-acceptor (D-A) supramolecular photocatalyst is successfully constructed via encapsulating fullerene (C60) into MIL-125-NH2 and meanwhile depositing individual Pt atoms as cocatalyst. The as-prepared C60@MIL-125-NH2-Pt exhibits remarkable activity in photocatalytic water splitting, with a H2 formation rate of 1180 μmol g-1 h-1, which is ∼ 12 times higher than that of the pristine MIL-125-NH2. Further investigations indicate that the host-guest interactions between C60 and MIL-125-NH2 strengthen the built-in electric field, which greatly facilitates the separation and migration of photogenerated charge carriers. In addition, the cocatalyst of individual Pt atoms not only further promotes the separation and transport of carriers but also enhances the contact between water and the catalyst. All of these factors directly contribute to the superior activity of C60@MIL-125-NH2-Pt. This work provides a new perspective for constructing D-A supramolecular photocatalysts for enhanced charge separation and making full use of photoelectrons to realize efficient hydrogen production.

Protective effects of a novel bicyclic γ-butyrolactone compound against H2O2 or corticosterone-induced neural cell apoptosis

Oxidative stress plays a pivotal role in various neurological disorders, encompassing both neurodegenerative diseases such as Alzheimer's and Parkinson's, and mood disorders like depression. The balance between the generation of reactive oxygen species (ROS) and the cell's antioxidant defenses, when disrupted, can lead to neuronal damage and neurologic dysfunction. In this study, we focused on the pathogenic role of oxidative stress in various neurologic disease models in vitro and investigated the neuroprotective capabilities of some novel bicyclic γ-butyrolactone compounds, with particular emphasis on the compound designated as 'bd'. Our investigation leveraged the HT22 and SH-SY5Y cells to model oxidative stress induced by H2O2 or corticosterone (CORT), common triggers of neuronal damage in neurodegenerative and mood disorders. We discovered that compound bd robustly reduced ROS production and suppressed neuronal apoptosis, suggesting its potential in treating a wider array of neurological conditions influenced by oxidative stress. In conclusion, our research underscores the importance of addressing oxidative stress in the context of diverse neurological disorders. The identification of compound bd as a neuroprotective agent with potential efficacy against ROS-induced apoptosis in neural cells opens new horizons for therapeutic development, offering hope for patients suffering from neurodegenerative diseases, depression, and other stress-related neurological conditions.

Dual-enhanced enzyme cascade hybrid hydrogel for the construction of optical biosensor

The biomimetic enzyme cascade system plays a key role in biosensing as a sophisticated signal transduction and amplification strategy. However, constructing a regulated enzyme cascade sensing system remains challenging due to the mismatch of multiple enzyme activities and poor stability. Herein, we design an efficient dual-enhanced enzyme cascade hybrid system (UFD-DEC) containing DNA-controlled nanozymes (Fe-cdDNA) and enzyme (urease) via combining the electrostatic contact effect with the hydrogel-directed confinement effect. Precise modulation of Fe-cdDNA nanozyme by DNA offers a means to control its catalytic efficiency. This regulated UFD-DEC system accelerates the reaction rate and provides remarkable stability compared with the free enzyme system. Benefiting from the plasticity properties of hydrogels, a "lab-in-a-tube" platform was constructed by encapsulating UFD-DEC in a microcentrifuge tube. Such a UFD-DEC-based hydrogel tube exhibits sufficient adaptability to profile urea when used in conjunction with a smartphone-assisted image processing algorithm, which on-site delivers urea information with a detection limit of 0.12 mmol L-1. This customizable and inexpensive miniaturized biosensor platform for monitoring urea may facilitate point-of-care testing applications.

Side-chain-engineered fluorescent dyes for 3D and long-term dynamic tracking of the plasma membrane in living cells

The plasma membrane involves in many important biological events such as cell fusion and programmed cell death, but most of current plasma membrane probes cannot meet the requirement of long-term specific anchoring to the plasma membrane. Herein, we propose a molecular side-chain engineering strategy to modulate the long-term imaging performance of fluorescent dyes to the plasma membrane by regulating the cell permeability and anchoring ability. A series of FMR dyes with different lengths of side chains were designed and synthesized, and their transmembrane behaviours and staining performance were evaluated in living HeLa cells. We found that short-chain and medium-chain FMR dyes have excellent cell permeability without the labeling ability to the plasma membrane while the long-chain FMR dyes specifically stain the plasma membrane and can be firmly anchored to the plasma membrane for a long period of time. These long-chain FMR dyes have high stain specificality to the plasma membrane, and C10-FMR can be anchored to the plasma membrane of living cells for 2 h, which enables it to continuously monitor dynamic changes of the plasma membrane. The three-dimensional precision imaging of various cells was achieved using C10-FMR, which provides an opportunity to obtain complete information on the three-dimensional spatial morphology of the plasma membrane. The PEG-induced cell fusion of chicken red blood cells and H2O2-induced apoptosis of HeLa cells were monitored by real-time tracking of dynamic changes of the plasma membrane during these processes, which provide solid examples to prove the usefulness of these fluorescent dyes as long-term imaging tools. This work validates the hypothesis that cell permeability of membrane dyes can be readily regulated by tuning the side chains, and provides the effective design strategy of fluorescent dyes for 3D and long-term dynamic tracking of the plasma membrane of diverse animal cells.

Collision cross-section measurements of small molecules via transient decay profiles observed in Orbitrap mass analyzers

Collision cross section (CCS) of organic compounds can be measured via Fourier transform-based mass spectrometry (MS) by modeling the decay rate of transient signals in the analyzer. Deriving CCS values of low-mass molecules (mass < 2000 Da and CCS < 500 Å2) with Orbitrap MS is challenging due to their high axial frequencies and small absolute variances in cross-sectional profiles. Here, we acquired mass spectra of progressively more complex low-mass analytes using commercial Orbitrap mass spectrometers. The transient signals were processed using Fast Fourier transform (FFT) and short-time Fourier transform (StFFT) to derive decay constants of multiple select ionic species from a single MS full-scan experiment. Decay constants were translated into CCS values using at least two internal standards in the same mass spectrum. Our results suggest target ionic species should have high S/N in order to derive CCS values with ≤0.5% uncertainty. Limitations in the precision of CCS measurements reflect local space charge effects that disturb ion motion in the analyzer. The derived CCS values of polymer like fragments of Ultramark 1621 and small molecules such as individual protonated amino acids can achieve average ±1% error with selection of internal standards across a wide mass range. Future studies need to optimize the strategy to select internal standards in order to improve the precision and accuracy of CCS measurements for small molecules via Orbitrap MS.

Preparation, design, identification and application of self-assembly peptides from seafood: A review

Hydrogels formed by self-assembling peptides with low toxicity and high biocompatibility have been widely used in food and biomedical fields. Seafood contains rich protein resources and is also one of the important sources of natural bioactive peptides. The self-assembled peptides in seafood have good functional activity and are very beneficial to human health. In this review, the sequence of seafood self-assembly peptide was introduced, and the preparation, screening, identification and characterization. The rule of self-assembled peptides was elucidated from amino acid sequence composition, amino acid properties (hydrophilic, hydrophobic and electric), secondary structure, interaction and peptide properties (hydrophilic and hydrophobic). It was introduced that the application of hydrogels formed by self-assembled peptides, which lays a theoretical foundation for the development of seafood self-assembled peptides in functional foods and the application of biological materials.