Type Of Linkage Research Articles

N-Aldehyde-Modified Phosphatidylethanolamines generated by lipid peroxidation are robust substrates of N-Acyl Phosphatidylethanolamine Phospholipase D.

N-acyl phosphatidylethanolamine-hydrolyzing phospholipase D (NAPE-PLD) hydrolyzes phosphatidylethanolamines (PE) where the headgroup nitrogen has been enzymatically modified with acyl chains of four carbons or longer (N-acyl-PEs or NAPEs). The nitrogen headgroup of PE can also be non-enzymatically modified by reactive lipid aldehydes, thus forming N-aldehyde modified-PEs (NALPEs). Some NALPEs such as N-carboxyacyl-PEs are linked to PE via amide bonds similar to NAPEs, but others are linked by imine, pyrrole, or lactam moieties. Whether NAPE-PLD can hydrolyze NALPEs was unknown. We therefore characterized the major NALPE species formed during lipid peroxidation of arachidonic acid and linoleic acid and generated various NALPEs for characterization of their sensitivity to NAPE-PLD hydrolysis by reacting synthesized aldehydes with PE. We found that NAPE-PLD could act on NALPEs of various lengths and linkage types including those derived from PE modified by malondialdehyde (N-MDA-PE), butane dialdehyde (N-BDA-PE), 4-hydroxynonenal (N-HNE-PE), 4-oxo-nonenal (N-ONE-PE), 9-keto-12-oxo-dodecenoic acid (N-KODA-PE), and 15-E2-isolevuglandin (N-IsoLG-PE). To assess the relative preference of NAPE-PLD for various NALPEs versus its canonical NAPE substrates, we generated a substrate mixture containing roughly equimolar concentrations of the seven NALPEs as well as two NAPEs (N-palmitoyl-PE and N-linoleoyl-PE) and measured their rate of hydrolysis. Several NALPE species, including the N-HNE-PE pyrrole species, were hydrolyzed at a similar rate as N-linoleoyl-PE and many of the other NALPEs showed intermediate rates of hydrolysis. These results significantly expand the substrate repertoire of NAPE-PLD and suggest that it may play an important role in clearing products of lipid peroxidation in addition to its established role in the biosynthesis of N-acyl-ethanolamines.

Development of a digital Net-Map tool to analyse multi-stakeholder networks in risk analysis of emerging food safety issues

The circular economy brings sustainability benefits but also causes potential food safety issues as recycling can introduce new contaminants to food contact materials. These circular food safety issues cause changes in the risk analysis network. So far, social network analysis studies relevant to food safety investigated specific parts of the risk analysis network (such as risk assessment) and its formal stakeholders such as Food Safety Authorities. However, the risk analysis network also consists informal stakeholders, each with their own knowledge and views. A comprehensive analysis of risk analysis networks addressing circularity-related food safety issues from a multi-stakeholder perspective is yet lacking. This study aimed to explore the complex risk analysis network for paper recycling in Belgium. An adjusted and digitalised network mapping methodology, Net-Mapping, was developed to identify the stakeholders, to assess their goals and influence, to determine the different linkages types between them, and to elicit constraints. Forty-one identified stakeholders from science, policy, and society were interconnected through four linkage types (‘legally required information sharing’, ‘voluntary information sharing’, ‘data generation request’, and ‘public communication’). Results show federal policy stakeholders are central in all networks, whereas science and society stakeholders gain influence in the informal networks. Barriers hindering collaboration in the networks are a lack of data and challenges in information exchange. The Net-Mapping insights can assist scientists in gathering risk assessment data, guide policymakers in targeting interventions, and raise stakeholder awareness of collaborations. Future research could compare risk analysis networks across countries for the same food safety issue, or examine the risk analysis networks for different food safety issues in the same country.

A cross-sectional study of data linkage and artificial intelligence practices across European countries

Abstract Background The availability of different data sources is increasing with the possibility to link them with each other. However, linked administrative data can be complex to use and may require advanced expertise and skills in statistical analysis. The main objectives of this study were to describe the use of data linkage and artificial intelligence (AI) in routine public health activities and the constraints to linking different data sources. Methods A cross-sectional survey was performed across European countries to explore the current practices applied by national institutes of public health, health information and statistics for innovative use of data sources (i.e., the use of data linkage and/or AI). Results In Europe, the use of data linkage and AI at national institutes of public health, health information and statistics varies. The use data linkage in routine by applying a deterministic method or a combination of two types of linkages (i.e., deterministic & probabilistic) for public health surveillance and research purposes is common in majority of European countries. The use of AI to estimate health indicators is not frequent among these institutes. The complex data regulation laws, lack of human resources, skills and problems with data governance, were reported by European countries as main constraints to routine data linkage for public health surveillance and research. Conclusions Our study showed that the majority of European countries have integrated data linkage in their routine public health activities but only a few use AI. A sustainable national health information system allowing to link different data sources are essential to contribute to public health research. Moreover, it supports evidence-informed health policy making processes with an overview of various aspects affecting population health and may contribute to European pandemic preparedness.

Modeling conformational changes in alginic acid oligomers induced by external forces

In this study, the mechanism and nature of mechanical force-induced conformational transitions of alginate oligomers with different ratios of β-d-mannuronic acid (M unit) and α-l-guluronic acid (G unit) units were investigated. The influence of the type of glycosidic linkage in either homo- or heterooligomers on the nature of conformational transitions was also considered. For this purpose, two different theoretical methods were used: quantum mechanics (QM) at the DFT level with the EGO (Enforced Geometry Optimization) approach previously tested also for other saccharide systems, and molecular dynamics (MD) simulations within hybrid interaction potentials, which take into account both the ab initio (QM) level of theory and classical molecular mechanics (MM) force fields. This allowed to characterize in detail the structural and energetic properties of the conformational transition occurring upon the influence of external, mechanical forces (e.g. ring conformations at the path of ring-inversion process as well as the energies corresponding to initial, final and intermediate states). The results indicate qualitatively various responses against the applied force, depending on the G:M ratio, which have their source in differing topologies of glycosidic linkage in either G or M units. This is of potential relevance for determining the content of naturally heterogeneous alginate chains by the AFM experimental studies. The effects of explicit solvent and non-zero temperature are not of primarily importance in the context of determined stretching properties.

Guidelines for Identifying the Structure of Heavy Phenolics in Lignin Depolymerization by using High-Resolution Tandem Mass Spectrometry.

The efficient conversion of lignin contributes to reducing human reliance on fossil energy. As a complicated biopolymer, studies on the mechanism of lignin depolymerization is limited by inadequate structural identification of high molecular weight (MW) products like heavy phenolics. Up to now, no individual method can generate both MW and structural information in operando conditions. As a promising approach, tandem mass spectrometry (MS/MS) techniques can provide structural information via the dissociation of target ions. In this study, MS/MS technique was performed both in offline and in-situ mode during lignin depolymerization. The fundamental guidelines based on MS/MS dissociation principles for typical inter-unit linkages like β-O-4, 5-5, β-β, β-5, and β-1 were well established. Based on that, major phenolic dimers are successfully identified, including chemical formula and types of inter-unit linkages. More significantly, real-time monitoring of structural evolution was achieved by applying in-situ MS/MS analysis during lignin depolymerization. The results show the different evolution pathways of isomers with same chemical formula, confirming that structural changes during lignin depolymerization are common and obvious. Overall, this study develops an advanced strategy for the full-view analysis of lignin depolymerization, achieving the static analysis of composition and structure, both monitoring the dynamic evolution of structures.

Extraction, Structural Characterization, and Physicochemical and Biological Properties of Water-Soluble Polysaccharides from Adlay Bran.

Adlay bran, often discarded or used as animal feed, holds untapped potential. This study explores the beneficial properties of water-soluble polysaccharides (ABPs), extracted using a hot water method, with the aim of transforming what is commonly regarded as waste into a valuable resource. The response surface methodology (RSM) was employed to fine-tune the extraction parameters, establishing conditions at 80.0 °C, 2.5 h, and a water-to-material ratio of 31.6 mL/g. Structural studies showed that ABPs consist of different monosaccharides, including rhamnose, arabinose, glucosamine, glucose, galactose, xylose, mannose, and glucuronic acid, with respective molar ratios of 2.12%, 2.40%, 0.52%, 77.12%, 7.94%, 3.51%, 2.55%, and 3.82%. The primary component of these polysaccharides has a molecular weight averaging 12.88 kDa. The polysaccharides feature eight distinct linkage types: →3,4)-Rhap-(1→ at 5.52%, →4)-Glcp-(1→ at 25.64%, Glcp-(1→ at 9.70%, →3,4)-Glcp-(1→ at 19.11%, →4)-Xylp-(1→ at 7.05%, →3)-Glcp-(1→ at 13.23%, →3,4)-Galp-(1→ at 9.26%), and →4,6)-Gclp-(1→ at 12.49%. The semi-crystalline properties of ABPs and their shear-thinning characteristics were validated by X-ray diffraction and rheology tests. In vitro assays highlighted the strong antioxidant activities of ABPs, as evidenced by DPPH and ABTS hydroxyl radical scavenging tests, along with significant metal chelating and reducing powers. Additionally, ABPs showed significant inhibition of α-glucosidase and α-amylase, making them attractive as versatile additives or as agents with antioxidant and blood-sugar-lowering properties in both the food and pharmaceutical sectors. These findings support the utilization of adlay bran for higher-value applications, harnessing its bioactive components for health-related benefits.

Chemical Diversification of Enzymatically Assembled Polyubiquitin Chains to Decipher the Ubiquitin Codes Programmed on the Branch Structure.

The multimerization of ubiquitins at different positions of lysine residues to form heterotypic polyubiquitin chains is a post-translational modification that is essential for the precise regulation of protein functions and degradative fates in living cells. The understanding of structure-activity relationships underlying their diverse properties has been seriously impeded by difficulties in the preparation of a series of folded heterotypic chains appropriately functionalized with different chemical tags for the systematic evaluation of their multifaceted functions. Here, we report a chemical diversification of enzymatically assembled polyubiquitin chains that enables the facile preparation of folded heterotypic chains with different functionalities. By introducing an acyl hydrazide at the C terminus of the proximal ubiquitin, polyubiquitin chains were readily diversified from the same starting materials with a variety of molecules, ranging from small molecules to biopolymers, under nondenaturing conditions. This chemical diversification allowed the systematic study of the functional differences of K63/K48 heterotypic chains based on the position of the branch point during enzymatic deubiquitination and proteasomal proteolysis, thus demonstrating critical roles of the branch position in both the positive and negative control of ubiquitin-mediated reactions. The chemical diversification of the heterotypic chains provides a robust chemical platform to reframe the understanding of how the ubiquitin codes are regulated from the viewpoint of the branch structure for the precise control of cell functions, which has not been deciphered solely on the basis of the linkage types.

Explanatory frameworks in complex change and resilience system modelling

Abstract Heterogenous flows across system boundaries continue to pose significant problems for efficient resource allocation especially with respect to long term strategic planning and immediate problems about allocation to address particular resource shortages. The approach taken here to modelling such flows is an engineering change prediction one. This enables margin modelling by producing system models in dependency matrices with different linkage types. Change prediction approaches from engineering design can analyse where these bottlenecks in integrated systems would be so that resources can be deployed flexibility to avoid them and address them when they occur. Current state of the art of margin research can be furthered by identifying margins on multiple levels of system composition. It can usefully be complemented by a category theory based approach which allows representation of variable and constant properties of models under changing conditions, and the identification of flows within models. Category theory is useful for formalising such explanatory frameworks as it can both structure systems and permit analysis of their applications in a complementary way.

Chemo- and regioselective controlled synthesis and thermal analysis characterization of trifluoromethyl polypyrazoles

This study details the chemo- and regioselective synthesis and spectroscopic and thermal analysis characterization of trifluoromethyl bipyrazoles and polypyrazoles by stepwise N-alkylation of pyrazoles using (E)-4-(amino)-5-bromo-1,1,1-trifluoro-but-3-en-2-ones (5-bromo enaminones), followed by cyclocondensation of the enaminone moiety with hydrazines. A mechanism for the cyclocondensation reaction was proposed. Sixteen new methylene-bridged bipyrazoles and polypyrazole chains with up to five pyrazole units were achieved at very good yields. All the compounds were characterized by 1H and 13C NMR, and the 1,3-regiochemistry was evidenced by single-crystal X-ray diffraction. The polypyrazoles’ thermal behavior was elucidated by thermogravimetric analysis and differential scanning calorimetry. It is suggested that at approximately 300°C the polypyrazoles thermally decompose independent of the number of repeating units. The second and third heating/cooling cycles of the differential scanning calorimetry indicate that the majority of the polypyrazoles are amorphous materials, with glass transition values that can be tuned by the number of repeating units in the polymeric chain and the type of linkage between the pyrazole rings.

Polysaccharides from Seedless Chestnut Rose (Rosa sterilis) Fruits: Insights into Innovative Drying Technologies and Their Structural Characteristics, Antioxidant, Antiglycation, and α-Glucosidase Inhibitory Activities.

The selection of an optimal drying method is essential for extending the shelf life and enhancing the quality of Rosa sterilis fruits. This study investigated the effects of both innovative (microwave vacuum drying and infrared drying) and traditional (freeze-drying and hot air drying) techniques on the structural characteristics and bioactivities of polysaccharides from R. sterilis fruits (RSPs). Four different RSPs were obtained from fruits dried using these methods. Results demonstrated that the structural characteristics and bioactivities of RSPs varied significantly with the drying method. Notable differences were observed in extraction yield, total sugar, uronic acid content, monosaccharide molar ratios, molecular weight distribution, particle size, thermal stability, and microstructures of RSPs. Despite these variations, the types of constituent monosaccharides and major glycosidic linkages remained consistent across all methods. Notably, RSPs obtained via microwave vacuum drying (RSPs-MVD) showed a higher uronic acid content and lower molecular weight, and exhibited stronger in vitro antioxidant, α-glucosidase inhibitory, and antiglycation activities. These findings suggest that microwave vacuum drying is an effective pre-drying technique for extracting RSPs, making them suitable as bioactive ingredients in functional foods and pharmaceuticals for managing diabetes mellitus and its complications.

Abstract Mo063: Hacking the ubiquitin code to distinctively modulate ion channel functional expression

Ubiquitin is a powerful modulator of ion channel fate, yet the mechanistic basis and scope of its regulation has remained elusive due to the complexity of the ubiquitin code and an inability to achieve substrate-specific control of the ubiquitome. To circumvent this and to specifically interrogate the role of distinct ubiquitin linkages on the cardiac repolarizing I Ks channel KCNQ1 (Q1), we developed a toolkit of engineered deubiquitinases (enDUBs) featuring a GFP/YFP-targeted nanobody fused to catalytic domains of DUBs with preferences for hydrolyzing distinctive polyubiquitin linkage types: OTUD1 - K63; OTUD4 - K48; Cezanne - K11; TRABID - K27/K33; and USP21 - non-specific. Co-expressing each of the enDUBs with YFP-tagged Q1 channels in HEK293 cells led to decreased channel ubiquitination but produced quantitative and qualitative differences in Q1 expression. NanoCezanne and nanoTRABID significantly increased Q1 surface density and ionic currents, whereas nanoOTUD1 and nanoUSP21 yielded more moderate effects. In sharp contrast, nanoOTUD4 downregulated Q1 surface density and currents. The impact on steady-state Q1 surface density was achieved by divergent trafficking mechanisms – nanoTRABID and nanoCezanne increased channel forward trafficking to the surface, while nanoOTUD4 reduced channel forward trafficking. The E3 ligases NEDD4L and ITCH both eliminate Q1 functional expression but with different polyubiquitin signatures as assessed by mass spectrometry. The enDUBs nanoOTUD1, nanoCezanne and nanoUSP21 protected Q1 from NEDD4L; whereas nanoTRABID, nanoOTUD1, nanoCezanne and nanoUSP21 shielded Q1 from ITCH. In adult guinea ventricular cardiomyocytes, the enDUBs displayed context-specific regulatory effects, where nanoOTUD1, nanoCezanne and nanoUSP21 significantly enhanced Q1 surface expression and stability, with nanoTRABID having more moderate effects, while nanoOTUD4 sharply decreased Q1 trafficking to the sarcolemma. Finally, linkage-specific enDUBs demonstrated varying capabilities to rescue distinct trafficking-deficient mutant Q1 channels that cause long QT syndrome and predispose to sudden cardiac death. The results reveal a rich multi-faceted role for linkage-specific ubiquitination in regulating ion channel trafficking with implications to develop targeted therapies for trafficking-deficit ion channelopathies.

Highly sensitive two-dimensional profiling of N-linked glycans by hydrophilic interaction liquid chromatography and dual stacking capillary gel electrophoresis

BackgroundN-Glycosylation is one of the most important post-translational modifications in proteins. As the N-glycan profiles in biological samples are diverse and change according to the pathological condition, various profiling methods have been developed, such as liquid chromatography (LC), capillary electrophoresis (CE), and mass spectrometry. However, conventional analytical methods have limitations in sensitivity and/or resolution, hindering the discovery of minor but specific N-glycans that are important both in the basic glycobiology research and in the medical application as biomarkers. Therefore, a highly sensitive and high-resolution N-glycan profiling method is required. ResultsIn this study, we developed a novel two-dimensional (2D) separation system, which couples hydrophilic interaction liquid chromatography (HILIC) with capillary gel electrophoresis (CGE) via large-volume dual preconcentration by isotachophoresis and stacking (LDIS). Owing to the efficient preconcentration efficiency of LDIS, limit of detection reached 12 pM (60 amol, S/N = 3) with good calibration curve linearity (R2 > 0.999) in the 2D analysis of maltoheptaose. Finally, 2D profiling of N-glycans obtained from standard glycoproteins and cell lysates were demonstrated. High-resolution 2D profiles were successfully obtained by data alignment using triple internal standards. N-glycans were well distributed on the HILIC/CGE 2D plane based on the glycan size, number of sialic acids, linkage type, and so on. As a result, specific minor glycans were successfully identified in HepG2 and HeLa cell lysates. Significance and noveltyIn conclusion, the HILIC/CGE 2D analysis method showed sufficient sensitivity and resolution for identifying minor but specific N-glycans from complicated cellular samples, indicating the potential as a next-generation N-glycomics tool. Our novel approach for coupling LC and CE can also dramatically improve the sensitivity in other separation modes, which can be a new standard of 2D bioanalysis applicable not only to glycans, but also to other diverse biomolecules such as metabolites, proteins, and nucleic acids.

The Conformation of Glycosidic Linkages According to Various Force Fields: Monte Carlo Modeling of Polysaccharides Based on Extrapolation of Short-Chain Properties.

The conformational features of the glycosidic linkage are the most important variable to consider when studying di-, oligo-, and polysaccharide molecules using molecular dynamics (MD) simulations. The accuracy of the theoretical model describing this degree of freedom influences the quality of the results obtained from MD calculations based on this model. This article focuses on the following two issues related to the conformation of the glycosidic linkage. First, we describe the results of a comparative analysis of the predictions of three carbohydrate-dedicated classical force fields for MD simulations, namely, CHARMM, GLYCAM, and GROMOS, in the context of different parameters of structural and energetic nature related to the conformation of selected types of glycosidic linkages, α(1 → 4), β(1 → 3), and β(1 → 4), connecting glucopyranose units. This analysis revealed several differences, mainly concerning the energy levels of the secondary and tertiary conformers and the linkage flexibility within the dominant exo-syn conformation for α(1 → 4) and β(1 → 3) linkages. Some aspects of the comparative analysis also included the newly developed, carbohydrate-dedicated Martini 3 coarse-grained force field. Second, to overcome the time-scale problem associated with sampling slow degrees of freedom in polysaccharide chains during MD simulations, we developed a coarse-grained (CG) model based on the data from MD simulations and designed for Monte Carlo modeling. This model (CG MC) is based on information from simulations of short saccharide chains, effectively sampled in atomistic MD simulations, and is capable of extrapolating local conformational properties to the case of polysaccharides of arbitrary length. The CG MC model has the potential to estimate the conformations of very long polysaccharide chains, taking into account the influence of secondary and tertiary conformations of glycosidic linkages. With respect to the comparative analysis of force fields, the application of CG MC modeling showed that relatively small differences in the predictions of individual force fields with respect to a single glycosidic linkage accumulate when considering their effect on the structure of longer chains, leading to drastically different predictions with respect to parameters describing the polymer conformation, such as the persistence length.

Structural characterization and prebiotic potential of polysaccharides from Polygonatum sibiricum

Polygonatum sibiricum has been widely used due to its excellent biological activities. We prepared a novel polysaccharide from P. sibiricum (PSP) in this study. According a monosaccharide composition analysis, PSP was mainly composed of fructose and glucose with a molar percentage of 93.81:5.12. The main linkage types were identified as α-D-Glcp-1→ and →2-β-D-Fruf-1→. The molecular weight of PSP showed no significant change after simulated salivary and gastrointestinal digestion. However, PSP could be broken down by intestinal bacteria. Our findings revealed that PSP administration increased the abundance of probiotics such as Bifidobacterium. Furthermore, the results showed that gut microbes could utilize PSP to produce short-chain fatty acids including acetic acid, propionic acid, and butyric acid. Also, the PSP fermentation broth displayed an excellent scavenging effect on free radicals, including 2,2-diphenyl-1-picrylhydrazyl radical, superoxide radical, and hydroxyl radical. In summary, this study will help to promote the application of PSP as prebiotics in functional food and the medical industry.

Viral Hepatitis and HIV Screening in Seasonal Mountain Workers: Feasibility and Results of a First French Experiment

Introduction: The Mobile Hepatitis Team (MHT) was set up in 2013, with main objective was to increase outreach screening care treatment access and cure of our target population. Target population was drugs users, prisoners, homeless, precarious people, migrants, and psychiatric patients. Seasonal workers working in mid-mountain ski resorts in the Eastern Pyrenees constitute a population at risk of viral hepatitis and HIV. This young population presents sexual risk behaviors and consumption of addictive products without regular access to care because of their mobility, moving from one workplace to another according to the seasons. They do not have a regular general practitioner, do not perform screening tests and there is no access to care other than the mandatory occupational medicine visit at the beginning of the season. In previous actions on the health aera of the high cantons of the department of Pyrénées-Orientales. We met with invested partners who referred us to this specific population of seasonal workers and their lack of access to screening and care, except for the occupational medicine hiring visit, organized before the beginning of the winter season, late November in early December. Objective: To detect viral hepatitis and HIV in a population at viral risk and far from care and offer them immediate treatment of the type of linkage to care “TEST TO CURE”. Methodology: 2-weeks HCV HBV and HIV finger sticks by trained nurses and orientation to the hepatology or the infectious units. Results: only 28 HCV finger sticks were completed. We also met 4 patients with known HCV serology. Three patients received DAA treatment and one patient spontaneous cured with negative RNA. One new patient had RNA C positive on balance sheet without social rights. We oriented him towards sour social worker to treat him later. Two patients had 2 real time HCV viral load not detected (including one post treatment follow-up) and one RNA negative without antiviral treatment, in case of HCV spontaneous clearance. For HBV, 16 finger sticks were completed, all negative. We did not meet as many seasonal workers as originally planned. This is why we conducted a second session over 2 days only targeted on these temporary accommodations. We realized 26 HCV and HIV finger sticks. One patient was HIV positive. HIV serology was unknow until our screening session. Nobody was HCV positive but 62% of screened people were drugs users or former drugs users. Discussion: our study was a success even the low number of people screened in the first 2-week session. The second 2-day session was more efficient. It was the first experience of hepatitis and HIV screening in this population of seasonal mountain workers. Conclusion: despite all limits, hepatitis and HIV screening among seasonal mountain workers was an innovative and efficient action. This action could be easily replicated in all populations of seasonal workers, whether in the mountains or by the sea.

Isolation and characterization of a hepatoprotective polysaccharide from Lonicera caerulea L. var. edulis Turcz. ex Herd. fruit against APAP-induced acute liver injury mice

The structure and bioactivities of a novel polysaccharide from Lonicera caerulea L. var. edulis Turcz. ex Herd. fruit (THP-3) were investigated. The crude polysaccharides of Turcz. ex Herd. (THP) were extracted by hot water extraction. After purification, the chemical structure of polysaccharides was identified. Then, a mouse model of acute drug-induced liver injury was constructed using 4-acetamidophenol (APAP) and pretreated with THP. The number-average molecular weight of THP-3 was 48.89 kDa and the mass average molar mass was 97.87 kDa. THP-3 was mainly composed of arabinose (42.54 %), glucose (27.62 %), galacturonic acid and galactose (29.84 %). The main linkage types of THP-3 were 1-linked Araf, 1,4-linked Glcp, and 1,3,6-linked Galp. In addition, after THP treatment, serum Alanine aminotransferase (ALT), Aspartate aminotransferase (AST) and γ-glutamyl transpeptidase (γGT) in AILI mice were successfully down-regulated. The results showed that THP could prevent the characteristic morphological changes of hepatic lobular injury and lipid depletion caused by APAP, reduced the level of oxidative damage in mice, increased the expression of APAP-induced hypolipidemia and related inflammatory indicators, and improved the detoxification function of liver. In general, the newly extracted THP polysaccharide has a good liver protection effect and is an ideal natural medicine for the treatment of liver diseases.

K48- and K63-linked ubiquitin chain interactome reveals branch- and length-specific ubiquitin interactors.

The ubiquitin (Ub) code denotes the complex Ub architectures, including Ub chains of different lengths, linkage types, and linkage combinations, which enable ubiquitination to control a wide range of protein fates. Although many linkage-specific interactors have been described, how interactors are able to decode more complex architectures is not fully understood. We conducted a Ub interactor screen, in humans and yeast, using Ub chains of varying lengths, as well as homotypic and heterotypic branched chains of the two most abundant linkage types-lysine 48-linked (K48) and lysine 63-linked (K63) Ub. We identified some of the first K48/K63-linked branch-specific Ub interactors, including histone ADP-ribosyltransferase PARP10/ARTD10, E3 ligase UBR4, and huntingtin-interacting protein HIP1. Furthermore, we revealed the importance of chain length by identifying interactors with a preference for Ub3 over Ub2 chains, including Ub-directed endoprotease DDI2, autophagy receptor CCDC50, and p97 adaptor FAF1. Crucially, we compared datasets collected using two common deubiquitinase inhibitors-chloroacetamide and N-ethylmaleimide. This revealed inhibitor-dependent interactors, highlighting the importance of inhibitor consideration during pulldown studies. This dataset is a key resource for understanding how the Ub code is read.

Revisiting gas-chromatography/mass-spectrometry molar response factors for quantitative analysis (FID or TIC) of glycosidic linkages in polysaccharides produced by oral bacterial biofilms

Methylation analysis was performed on methylated alditol acetate standards and Streptococcus mutans extracellular polymeric substances (EPS) produced from wild-type and Gtf knockout strains (∆GtfB, ∆GtfB, and ∆GtfD). The methylated alditol acetate standards were representative of glycosidic linkages found in S. mutans EPS and were used to calibrate the GC–MS system for an FID detector and MS (TIC) and produce molar response factor, a necessary step in quantitative analysis. FID response factors were consistent with literature values (Sweet et al., 1975) and found to be the superior option for quantitative results, although the TIC response factors now give researchers without access to an FID detector a needed option for molar response factor correction. The GC–MS analysis is then used to deliver the ratio of the linkage types within a biofilm.

Octupolar Cyclotriphosphazene-Cored Self-Standing Covalent Organic Framework Membranes as Nonlinear Optical Materials: Impact of Linkage Types and Material Forms.

Conjugated and processable self-standing vinylene-linked covalent organic framework membranes (COFMs) are highly demanding for photonics and optoelectronics. In this work, we have fabricated the first cyclotriphosphazene (CTP) cored vinylene-linked self-standing COFM (CTP-PDAN). For comparison purposes, we have successfully fabricated the imine-linked congener (CTP-PDA). Leveraging the inherent nonlinear optical (NLO) response of the CTP core, both membranes were directly mounted to evaluate NLO parameters using the open-aperture (OA) Z-scan technique. Direct measurement of NLO responses on membranes is advantageous and free from solvent and scattering effects, making it a more practical approach compared to the conventional dispersion mode. The OA Z-scan transmission yields a reverse saturable absorption signature exhibiting a higher NLO absorption coefficient (β) of 58.37 cm/GW for CTP-PDAN, compared to that of the imine-linked CTP-PDA COFM (β = 8.5 cm/GW). These results can be correlated to the efficient conjugation through the vinylene linkage in CTP-PDAN compared to the imine linked congener.

Variation pattern in the macromolecular (cellulose, hemicelluloses, lignin) composition of cell walls in Pinus tabulaeformis tree trunks at different ages as revealed using multiple techniques

The plant cell wall is a complex, heterogeneous structure primarily composed of cellulose, hemicelluloses, and lignin. Exploring the variations in these three macromolecules over time is crucial for understanding wood formation to enhance chemical processing and utilization. Here, we comprehensively analyzed the chemical composition of cell walls in the trunks of Pinus tabulaeformis using multiple techniques. In situ analysis showed that macromolecules accumulated gradually in the cell wall as the plant aged, and the distribution pattern of lignin was opposite that of polysaccharides, and both showed heterogenous distribution patterns. In addition, gel permeation chromatography (GPC) results revealed that the molecular weights of hemicelluloses decreased while that of lignin increased with age. Two-dimensional heteronuclear single quantum coherence nuclear magnetic resonance (2D-HSQC NMR) analysis indicated that hemicelluloses mainly comprised galactoglucomannan and arabinoglucuronoxylan, and the lignin types were mainly comprised guaiacyl (G) and p-hydroxyphenyl (H) units with three main linkage types: β-O-4, β-β, and β-5. Furthermore, the C-O bond (β-O-4) signals of lignin decreased while the C-C bonds (β-β and β-5) signals increased over time. Taken together, these findings shed light on wood formation in P. tabulaeformis and lay the foundation for enhancing the processing and use of wood and timber products.