Physicochemical, Structural, and Functional Properties of Fructans from Single-Clove Garlic and Multiclove Garlic: A Comparison

This study aimed to compare the structural features and functional properties of polysaccharides from single-clove garlic (SGPs) and multiclove garlic (MGPs) and to establish their structure-function relationships. Both SGPs and MGPs were identified as fructans consisting mainly of →1)-β-d-Fruf (2→ and →6)-β-d-Fruf (2→ residues but differed in average molecular weights (6.76 and 5.40 kDa, respectively). They shared similar thermodynamic properties, X-ray diffraction patterns, and high gastrointestinal digestive stability. These two purified fructans could dose-dependently scavenge free radicals, reduce oxidized metals, and effectively alleviate metronidazole-induced oxidative stress and CuSO4-induced inflammation in zebrafish via inhibiting the overexpression of inflammation-related proteins and cytokines. SGPs showed lower free radical scavenging activity in vitro than MGPs but higher antioxidant and anti-inflammatory activities in vivo. Taken together, the molecular weight was the main structural difference between the two garlic fructans of different varieties, which is a potential reason for their differences in biological activities.

Predicting TCR sequences for unseen antigen epitopes using structural and sequence features

T-cell receptor (TCR) recognition of antigens is fundamental to the adaptive immune response. With the expansion of experimental techniques, a substantial database of matched TCR-antigen pairs has emerged, presenting opportunities for computational prediction models. However, accurately forecasting the binding affinities of unseen antigen-TCR pairs remains a major challenge. Here, we present convolutional-self-attention TCR (CATCR), a novel framework tailored to enhance the prediction of epitope and TCR interactions. Our approach utilizes convolutional neural networks to extract peptide features from residue contact matrices, as generated by OpenFold, and a transformer to encode segment-based coded sequences. We introduce CATCR-D, a discriminator that can assess binding by analyzing the structural and sequence features of epitopes and CDR3-β regions. Additionally, the framework comprises CATCR-G, a generative module designed for CDR3-β sequences, which applies the pretrained encoder to deduce epitope characteristics and a transformer decoder for predicting matching CDR3-β sequences. CATCR-D achieved an AUROC of 0.89 on previously unseen epitope-TCR pairs and outperformed four benchmark models by a margin of 17.4%. CATCR-G has demonstrated high precision, recall and F1 scores, surpassing 95% in bidirectional encoder representations from transformers score assessments. Our results indicate that CATCR is an effective tool for predicting unseen epitope-TCR interactions. Incorporating structural insights enhances our understanding of the general rules governing TCR-epitope recognition significantly. The ability to predict TCRs for novel epitopes using structural and sequence information is promising, and broadening the repository of experimental TCR-epitope data could further improve the precision of epitope-TCR binding predictions.

Introduction of a human- and keyboard-friendly N-glycan nomenclature

In the beginning was the word. But there were no words for N-glycans, at least, no simple words. Next to chemical formulas, the IUPAC code can be regarded as the best, most reliable and yet immediately comprehensible annotation of oligosaccharide structures of any type from any source. When it comes to N-glycans, the venerable IUPAC code has, however, been widely supplanted by highly simplified terms for N-glycans that count the number of antennae or certain components such as galactoses, sialic acids and fucoses and give only limited room for exact structure description. The highly illustrative - and fortunately now standardized - cartoon depictions gained much ground during the last years. By their very nature, cartoons can neither be written nor spoken. The underlying machine codes (e.g., GlycoCT, WURCS) are definitely not intended for direct use in human communication. So, one might feel the need for a simple, yet intelligible and precise system for alphanumeric descriptions of the hundreds and thousands of N-glycan structures. Here, we present a system that describes N-glycans by defining their terminal elements. To minimize redundancy and length of terms, the common elements of N-glycans are taken as granted. The preset reading order facilitates definition of positional isomers. The combination with elements of the condensed IUPAC code allows to describe even rather complex structural elements. Thus, this "proglycan" coding could be the missing link between drawn structures and software-oriented representations of N-glycan structures. On top, it may greatly facilitate keyboard-based mining for glycan substructures in glycan repositories.

Isolation, structure characterization and in vitro immune-enhancing activity of a glucan from the peels of stem lettuce (Lactuca sativa)

BACKGROUND

Stem lettuce is a medicinal and edible plant. The peels, accounting for 300-400 g kg-1 raw stem lettuce and containing polysaccharides 200 g kg-1 , are discarded as industrial waste, causing environment pollution and resource waste.

RESULTS

A polysaccharide named PPSL10-2 was obtained from the peels of stem lettuce after hot water extraction, and gradation with cascade ultrafiltration and purification using DEAE-Sepharose cellulose. The purity and molecular weight of PPSL10-2 is 96.10% and 2.2 × 104  Da respectively, as detected by high-performance gel permeation chromatography. PPSL10-2 was found to be an α-(1→4)-d-glucan that branched at O-6 with a terminal 1-linked α-d-Glcp as side chain, and devoid of helix conformation, which was characterized by monosaccharide composition analysis, Fourier-transform infrared spectroscopy, Congo red test, scanning electron microscopy, methylation analysis and NMR spectroscopy. Furthermore, PPSL10-2 exhibited potent immune-enhancing effect by improving proliferation and phagocytosis, promoting the secretion of nitric oxide and cytokines, as well as the expression of related genes in RAW264.7 macrophages.

CONCLUSION

The findings of the present study suggest that peels as an agricultural by-product of stem lettuce are good sources of polysaccharides, which could be developed as immunopotentiator for improving human health. © 2023 Society of Chemical Industry.

In silico study to recognize novel angiotensin-converting-enzyme-I inhibitors by 2D-QSAR and constraint-based molecular simulations

Cardiovascular diseases (CVD) such as heart failure, stroke, and hypertension affect 64.3 million people worldwide and are responsible for 30% of all deaths. Primary inhibition of the angiotensin-converting enzyme (ACE) is significant in the management of CVD. In the present study, the genetic algorithm-multiple linear regressions (GA-MLR) method is used to generate highly predictive and statistically significant (R2 = 0.70-0.75, Q2LOO=0.67-0.73, Q2LMO=0.66-0.72, CCCex=0.70-0.78) quantitative structure-activity relationships (QSAR) models conferring to OECD requirements using a dataset of 255 structurally diverse and experimentally validated ACE inhibitors. The models contain simply illustratable Padel, Estate, and PyDescriptors that correlate structural scaffold requisite for ACE inhibition. Also, constraint-based molecular docking reveals an interaction profile between ligands and enzymes which is then correlated with the essential structural features associated with the QSAR models. The QSAR-based virtual screening was utilized to find novel lead molecules from a designed database of 102 thiadiazole derivatives. The Applicability domain (AD), Molecular Docking, Molecular dynamics, and ADMET analysis suggest two compound D24 and D40 are inflexibly linked to the protein binding site and follows drug-likeness properties.Communicated by Ramaswamy H. Sarma.

Bacterial cytochrome P450s: a bioinformatics odyssey of substrate discovery

Bacterial P450 cytochromes (BacCYPs) are versatile heme-containing proteins responsible for oxidation reactions on a wide range of substrates, contributing to the production of valuable natural products with limitless biotechnological potential. While the sequencing of microbial genomes has provided a wealth of BacCYP sequences, functional characterization lags behind, hindering our understanding of their roles. This study employs a comprehensive approach to predict BacCYP substrate specificity, bridging the gap between sequence and function. We employed an integrated approach combining sequence and functional data analysis, genomic context exploration, 3D structural modeling with molecular docking, and phylogenetic clustering. The research begins with an in-depth analysis of BacCYP sequence diversity and structural characteristics, revealing conserved motifs and recurrent residues in the active site. Phylogenetic analysis identifies distinct groups within the BacCYP family based on sequence similarity. However, our study reveals that sequence alone does not consistently predict substrate specificity, necessitating additional perspectives. The study delves into the genetic context of BacCYPs, utilizing neighboring gene information to infer potential substrates, a method proven very effective in many cases. Molecular docking is employed to assess BacCYP-substrate interactions, confirming potential substrates and providing insights into selectivity. Finally, a comprehensive strategy is proposed for predicting BacCYP substrates, involving all the evaluated approaches. The effectiveness of this strategy is demonstrated with two case studies, highlighting its potential for substrate discovery.

Herbicide Safeners: From Molecular Structure Design to Safener Activity

Herbicide safeners, highly effective antidotes, find widespread application in fields for alleviating the phytotoxicity of herbicides to crops. Designing new herbicide safeners remains a notable issue in pesticide research. This review focuses on discussing and summarizing the structure-activity relationships, molecular structures, physicochemical properties, and molecular docking of herbicide safeners in order to explore how different structures affect the safener activities of target compounds. It also provides insights into the application prospects of computer-aided drug design for designing and synthesizing new safeners in the future.

Structural Characterization and Anticoagulant Activities of a Keratan Sulfate-like Polysaccharide from the Sea Cucumber Holothuria fuscopunctata

A sulfated polysaccharide (AG) was extracted and isolated from the sea cucumber H. fuscopunctata, consisting of GlcNAc, GalNAc, Gal, Fuc and lacking any uronic acid residues. Importantly, several chemical depolymerization methods were used to elucidate the structure of the AG through a bottom-up strategy. A highly sulfated galactose (oAG-1) and two disaccharides labeled with 2,5-anhydro-D-mannose (oAG-2, oAG-3) were obtained from the deaminative depolymerized product along with the structures of the disaccharide derivatives (oAG-4~oAG-6) identified from the free radical depolymerized product, suggesting that the repeating building blocks in a natural AG should comprise the disaccharide β-D-GalS-1,4-D-GlcNAc6S. The possible disaccharide side chains (bAG-1) were obtained with mild acid hydrolysis. Thus, a natural AG may consist of a keratan sulfate-like (KS-like) glycosaminoglycan with diverse modifications, including the sulfation types of the Gal residue and the possible disaccharide branches α-D-GalNAc4S6S-1,2-α/β-L-Fuc3S linked to the KS-like chain. Additionally, the anticoagulant activities of the AG and its depolymerized products (dAG1-9) were evaluated in vitro using normal human plasma. The AG could prolong activated partial thromboplastin time (APTT) in a dose-dependent manner, and the activity potency was positively related to the chain length. The AG and dAG1-dAG3 could prolong thrombin time (TT), while they had little effect on prothrombin time (PT). The results indicate that the AG could inhibit the intrinsic and common coagulation pathways.

An updated dataset and a structure-based prediction model for protein-RNA binding affinity

Understanding the process of protein-RNA interaction is essential for structural biology. The thermodynamic process is an important part to uncover the protein-RNA interaction mechanism. The regulatory networks between protein and RNA in organisms are dominated by the binding or dissociation in the cells. Therefore, determining the binding affinity for protein-RNA complexes can help us to understand the regulation mechanism of protein-RNA interaction. Since it is time-consuming and labor-intensive to determine the binding affinity for protein-RNA complexes by experimental methods, it is necessary and urgent to develop computational methods to predict that. To develop a binding affinity prediction model, first we update the dataset of protein-RNA binding affinity benchmark (PRBAB), which includes 145 complexes now. Second, we extract the structural features based on complex structure, and then we analyze and select the representative structural features to train the regression model. Third, we random select the subset from the PRBAB2.0 to fit the protein-RNA binding affinity determined by experiment. In the end, we tested our model on the nonredundant PDBbind dataset, and the results showed that Pearson correlation coefficient r = .57 and RMSE = 2.51 kcal/mol. The Pearson correlation coefficient achieves 0.7 while removing 5 complex structures with modified residues/nucleotides and metal ions. While testing on ProNAB, the results showed that 71.60% of the prediction achieves Pearson correlation coefficient r = .61 and RMSE = 1.56 kcal/mol with experiment values.

Bioactive polysaccharides from Momordica charantia as functional ingredients: a review of their extraction, bioactivities, structural-activity relationships, and application prospects

Momordica charantia L. is a well-known medicine and food homology plant with high pharmaceutical and nutritional values. Polysaccharides are carbohydrate polymers connected by glycosidic bonds, one of the key functional ingredients of M. charantia. Recently, M. charantia polysaccharides (MCPs) have attracted much attention from industries and researchers due to their anti-oxidant, anti-tumor, anti-diabetes, anti-bacteria, immunomodulatory, neuroprotection, and organ protection activities. However, the development and utilization of MCPs-based functional foods and medicines were hindered by the lack of a deeper understanding of the structure-activity relationship (SAR), structural modification, applications, and safety of MCPs. Herein, we provide an overview of the extraction, purification, structural characterization, bioactivities, and mechanisms of MCPs. Besides, SAR, toxicities, application, and influences of the modification associated with bioactivities are spotlighted, and the potential development and future study direction are scrutinized. This review provides knowledge and research underpinnings for the further research and application of MCPs as therapeutic agents and functional food additives.

Bioactive polysaccharides from lotus as potent food supplements: a review of their preparation, structures, biological features and application prospects

Lotus is a famous plant of the food and medicine continuum for millennia, which possesses unique nutritional and medicinal values. Polysaccharides are the main bioactive component of lotus and have been widely used as health nutritional supplements and therapeutic agents. However, the industrial production and application of lotus polysaccharides (LPs) are hindered by the lack of a deeper understanding of the structure-activity relationship (SAR), structural modification, applications, and safety of LPs. This review comprehensively comments on the extraction and purification methods and structural characteristics of LPs. The SARs, bioactivities, and mechanisms involved are further evaluated. The potential application and safety issues of LPs are discussed. This review provides valuable updated information and inspires deeper insights for the large scale development and application of LPs.

Catalytic Decomposition of H2O2 in the Aqueous Dispersions of the Potassium Polytitanates Produced in Different Conditions of Molten Salt Synthesis

It is shown that the potassium polytitanate powder (PPT) synthesized at 500 °C via the treatment of powdered TiO₂ (rutile) in molten mixtures of KOH and KNO₃ is a cheap and effective catalyst of H₂O₂ chemical decomposition in aqueous solutions. At the same time, the PPT catalytic activity strongly depends on the [TiO₂]:[KOH]:[KNO₃] weight ratio in the mixture used for the synthesis, increasing with [KNO₃] in the order of PPT (30:30:40) < PPT (30:50:20) < PPT (30:70:0). The obtained results are explained by increased [Ti³⁺] in the PPT structure (XPS data), which is grown in this order from 0 to 4.0 and 21.9 at.%, respectively, due to the reduced oxidation activity of the melt used for PPT synthesis. The mechanism of the autocatalytic process taking place in the PPT-H₂O₂-H₂O system is analyzed. Taking into account the data of FT-IR spectroscopy, it is assumed that the increased catalytic activity of the investigated materials is related to the increased surface concentration of the Ti⁴⁺-O(H)-Ti⁴⁺ groups, formed from the Ti³⁺-O(H₃O⁺)-Ti⁴⁺ clusters and further transformed into Ti-O-O-H catalytic centers. Some possible applications of the PPT-H₂O₂-H₂O catalytic system, including the oxidation processes of green chemistry and photo-catalysis, are discussed.

Investigating gaming structural features associated with gaming disorder and proposing a revised taxonomical model: A scoping review

Background and aims

Gaming disorder (GD) is a mental health concern that has been heavily contested by experts. This scoping review synthesizes the literature to identify the structural features of video game design that can contribute to GD. Furthermore, a taxonomy of the structural features implicated with GD is proposed, revised from earlier work.

Methods

Seven databases, in addition to Google Scholar, were searched. Peer-reviewed studies were included if they assessed a link between gaming structural characteristics and GD or a proxy. The final pool included 105 articles.

Results

Avatar creation and customizability, multiplayer characteristics, and reward and punishment features were highly represented in the literature. There was no evidence for three categories in the original taxonomy: support network features, sexual content, and explicit language. Furthermore, structural feature sub-categories emerged that were absent from the previous taxonomy, such as general socialization features, type of virtual world, and in-game currency. Manipulation and control features and presentation features were less represented than social features, narrative and identity features, and reward and punishment features. The reviewers propose two broad classes of addictive gaming structural features: 'features enhancing in-game immersion and realism' and 'gambling-like features'.

Discussion and conclusions

Numerous studies found a relationship between social, narrative and identity, and reward and punishment structural characteristics with GD. Two broad classes of gaming structural features were associated with addiction. The first, 'features enhancing in-game immersion and realism,' including social gameplay, avatar creation, storytelling, and graphics/sound. The second, 'gambling-like features,' included different mechanisms of rewards-and-punishment.

Structure-Selectivity Relationship Prediction of Tau Imaging Tracers Using Machine Learning-Assisted QSAR Models and Interaction Fingerprint Map

Protein aggregates composed of tau fibrils are major pathologic findings in different tauopathies. An ideal agent for imaging tau fibrils must be highly selective. The molecular basis for the binding of current available compounds to tau aggregates is not well understood. Herein, we provide insights into previously studied positron emission tomography tracers using various computational methods, including machine learning-based quantitative structure-activity relationship (QSAR) classification, docking, and molecular dynamics (MD) simulations to investigate the structural basis of selective tau aggregate binding for potential compounds. The QSAR classification model based on the Random Forest algorithm with an accuracy of 96.6% for the selective and 97.6% for the nonselective class of compounds revealed essential selective moieties. The combination of molecular docking, MD simulations, and molecular mechanics Poisson-Boltzmann surface area (MM/PBSA) binding free-energy calculation showed superior binding energy of ligand 63 toward tau and PHF6, a key hexapeptide in tau aggregation, as the most selective compound in the data set. Dissecting the binding properties of ligand 63 and ligand 8 (the least selective compound) within tau and Aβ structures confirmed that these two compounds favor different binding sites of tau; however, the preferential binding site in Aβ was similar for both with lower binding energies calculated for ligand 8. Results revealed that the number of N-heterocycles, the position of nitrogen atoms, and the presence of tertiary amine are important components of selective binding moieties, and they should be maintained in molecules for selective binding to tau aggregates. The predicted structure-selectivity relationship will facilitate the rational design and further development of selective tau imaging agents.

The Advancement in Membrane Bioreactor (MBR) Technology toward Sustainable Industrial Wastewater Management

The advancement in water treatment technology has revolutionized the progress of membrane bioreactor (MBR) technology in the modern era. The large space requirement, low efficiency, and high cost of the traditional activated sludge process have given the necessary space for the MBR system to come into action. The conventional activated sludge (CAS) process and tertiary filtration can be replaced by immersed and side-stream MBR. This article outlines the historical advancement of the MBR process in the treatment of industrial and municipal wastewaters. The structural features and design parameters of MBR, e.g., membrane surface properties, permeate flux, retention time, pH, alkalinity, temperature, cleaning frequency, etc., highly influence the efficiency of the MBR process. The submerged MBR can handle lower permeate flux (requires less power), whereas the side-stream MBR can handle higher permeate flux (requires more power). However, MBR has some operational issues with conventional water treatment technologies. The quality of sludge, equipment requirements, and fouling are major drawbacks of the MBR process. This review paper also deals with the approach to address these constraints. However, given the energy limitations, climatic changes, and resource depletion, conventional wastewater treatment systems face significant obstacles. When compared with CAS, MBR has better permeate quality, simpler operational management, and a reduced footprint requirement. Thus, for sustainable water treatment, MBR can be an efficient tool.

A Sojourn on Liposomal Delivery System: Recent Advances and Future Prospects

Liposomes are unique novel drug delivery carriers that favor the effective transportation of pharmaceuticals. These vesicles acquire one or more phospholipid bilayer membranes, and an inner aqueous core can carry both aqueous and lipid drugs. While hydrophilic molecules can be confined in the aqueous core, hydrophobic molecules are injected into the bilayer membrane. Liposomes have many benefits as a drug delivery method, including biocompatibility, the capacity to carry large drug payloads, and a variety of physicochemical and biological parameters that can be altered to influence their biological characteristics. In addition, being a size of 10-100 nm range can have numerous additional benefits, including enhanced pharmacokinetics, clever escape from the reticuloendothelial system, greater in vivo stability, longer and site-specific administration, and increased internalization in tumor tissue (enhanced permeability and retention impact). The current review focuses on the structural composition of liposomes, formulation technologies, and suitable case studies for optimizing biopharmaceutical performance. Moreover, clinical trials and marketed formulations of liposomes have been also stated in the prior art.

Thermo-L-Asparaginases: From the Role in the Viability of Thermophiles and Hyperthermophiles at High Temperatures to a Molecular Understanding of Their Thermoactivity and Thermostability

L-asparaginase (L-ASNase) is a vital enzyme with a broad range of applications in medicine, food industry, and diagnostics. Among various organisms expressing L-ASNases, thermophiles and hyperthermophiles produce enzymes with superior performances-stable and heat resistant thermo-ASNases. This review is an attempt to take a broader view on the thermo-ASNases. Here we discuss the position of thermo-ASNases in the large family of L-ASNases, their role in the heat-tolerance cellular system of thermophiles and hyperthermophiles, and molecular aspects of their thermoactivity and thermostability. Different types of thermo-ASNases exhibit specific L-asparaginase activity and additional secondary activities. All products of these enzymatic reactions are associated with diverse metabolic pathways and are important for mitigating heat stress. Thermo-ASNases are quite distinct from typical mesophilic L-ASNases based on structural properties, kinetic and activity profiles. Here we attempt to summarize the current understanding of the molecular mechanisms of thermo-ASNases' thermoactivity and thermostability, from amino acid composition to structural-functional relationships. Research of these enzymes has fundamental and biotechnological significance. Thermo-ASNases and their improved variants, cloned and expressed in mesophilic hosts, can form a large pool of enzymes with valuable characteristics for biotechnological application.

Bacterial Communities of Lamiacea L. Medicinal Plants: Structural Features and Rhizosphere Effect

Bacterial communities associated with medicinal plants are an essential part of ecosystems. The rhizosphere effect is rather important in the cultivation process. The purpose of the study was to analyze the rhizosphere effect of oregano (Origanum vulgare L.), peppermint (Mentha piperita L.), thyme (Thymus vulgaris L.), creeping thyme (Thymus serpillum L.) and sage (Salvia officinalis L.). To estimate the quantity of 16S bacteria ribosomal genes, qPCR assays were used. To compare bacterial communities' structure of medicinal plants rhizosphere with bulk soil high-throughput sequencing of the 16S rRNA targeting variable regions V3-V4 of bacteria was carried out. The highest bacterial abundance was associated with T. vulgaris L., M. piperita L. and S. officinalis L., and the lowest was associated with the O. vulgare L. rhizosphere. Phylum Actinobacteriota was predominant in all rhizosphere samples. The maximum bacterial α-diversity was found in S. officinalis L. rhizosphere. According to bacterial β-diversity calculated by the Bray-Curtis metric, T. vulgaris L. root zone significantly differed from bulk soil. The rhizosphere effect was positive to the Myxococcota, Bacteroidota, Verrucomicrobiota, Proteobacteria and Gemmatimonadota.

Advances in health-promoting effects of natural polysaccharides: Regulation on Nrf2 antioxidant pathway

Natural polysaccharides (NPs) possess numerous health-promoting effects, such as liver protection, kidney protection, lung protection, neuroprotection, cardioprotection, gastrointestinal protection, anti-oxidation, anti-diabetic, and anti-aging. Nuclear factor erythroid 2-related factor 2 (Nrf2) antioxidant pathway is an important endogenous antioxidant pathway, which plays crucial roles in maintaining human health as its protection against oxidative stress. Accumulating evidence suggested that Nrf2 antioxidant pathway might be one of key regulatory targets for the health-promoting effects of NPs. However, the information concerning regulation of NPs on Nrf2 antioxidant pathway is scattered, and NPs show different regulatory behaviors in their different health-promoting processes. Therefore, in this article, structural features of NPs having regulation on Nrf2 antioxidant pathway are overviewed. Moreover, regulatory effects of NPs on this pathway for health-promoting effects are summarized. Furthermore, structure-activity relationship of NPs for health-promoting effects by regulating the pathway is preliminarily discussed. Otherwise, the prospects on future work for regulation of NPs on this pathway are proposed. This review is beneficial to well-understanding of underlying mechanisms for health-promoting effects of NPs from the view angle of Nrf2 antioxidant pathway, and provides a theoretical basis for the development and utilization of NPs in promoting human health.

A Review of Structural Features, Biological Functions and Biotransformation Studies in Adipose Tissues and an Assessment of Progress and Implications

Roles for adipose tissues in energy metabolism, health maintenance and disease onset have been established. Evidence indicates that white, brown and beige fats are quite different in terms of their cellular origin and biological characteristics. These differences are significant in targeting adipocytes to study the pathogenesis and prevention strategies of related diseases. The biotransformations of white, brown and beige fat cells constitute an intriguing topic worthy of further study, and the molecular mechanisms underlying the biotransformations of white, brown and beige fat cells remain to be elucidated. Hence, we herein collected evidence from studies on adipose tissue or adipocytes, and we extracted the structural features, biologic functions, and biotransformations of adipose tissue/adipocytes. The present review aimed to summarize the latest research progress and propose novel research directions with respect to adipose tissue and adipocytes. We posit that this work will provide new insights and opportunities in the effective treatment strategies for obesity, diabetes and other lipid-related diseases. It will also contribute to our knowledge of the basic biologic underpinnings of adipocyte biology.

Structural Features of Eu3+ and Tb3+-Bipyridinedicarboxamide Complexes

Photoluminescent lanthanide complexes of Eu³⁺ and Tb³⁺ as central atoms and N⁶,N⁶'-diisopropyl-[2,2'-bipyridine]-6,6'-dicarboxamide as ligand were synthesized. The structure of these complexes was established by single-crystal X-ray diffraction, mass spectrometry, ¹H and ¹³C nuclear magnetic resonance, ultraviolet-visible, infrared spectroscopy, and thermogravimetry. Bipyridinic ligands provide formation of coordinatively saturated complexes of lanthanide ions and strong photoluminescence (PL). The Eu³⁺- and Tb³⁺-complexes exhibit PL emission in the red and green regions observed at a 340 nm excitation. The quantum yield for the complexes was revealed to be 36.5 and 12.6% for Tb³⁺- and Eu³⁺-complexes, respectively. These lanthanide compounds could be employed as photoluminescent solid-state compounds and as emitting fillers in polymer (for example, polyethylene glycol) photoluminescent materials.

Structural, antioxidant, and immunomodulatory activities of an acidic exopolysaccharide from Lactiplantibacillus plantarum DMDL 9010

This study investigated the structural, antioxidant, and immunomodulatory activities of acidic exopolysaccharide (EPS-LP2) isolated from Lactiplantibacillus plantarum DMDL 9010. EPS-LP2 is composed of fucose (Fuc), arabinose (Ara), galactose (Gal), glucose (Glc), mannose (Man), and D-fructose (Fru) with a molar ratio of 0.13: 0.69: 8.32: 27.57: 62.07: 0.58: 0.46, respectively. Structural analysis of EPS-LP2 exhibited a smooth irregular lamellar surface, rod-like structure with swollen ends and slippery surfaces, and good thermal stability. Based on the methylation and NMR analysis, sugar residues including t-Manp, t-Glcp, 2-Manp, 6-Galp, 6-Glcp, and 4-Glcp were found to exist in EPS-LP2. In the 50∼400 μg/ml range, EPS-LP2 showed negligible neurotoxicity to RAW264.7 cells. Moreover, EPS-LP2 could protect RAW264.7 cells from oxidative injury by lowering the generation of reactive oxygen species (ROS), malondialdehyde (MDA), and the secretion of lactate dehydrogenase (LDH). In contrast, an increase in superoxide dismutase (SOD), catalase (CAT), glutathione peroxidase (GSH-Px), and the concentrations of glutathione (GSH) were observed. Immunoreactivity assays showed that EPS-LP2 could suppress the expression of NO, tumor necrosis factor-α (TNF-α), and interleukin 6 (IL-6) and inhibit the activation of the mitogen-activated protein kinase (MAPK)/nuclear factor-κB-gene binding (NF-κB) cell pathway. Conclusively, EPS-LP2 could be a potential natural antioxidant and immunomodulatory agent in functional foods and medicines.

Different Structures of Arabinoxylan Hydrolysates Alleviated Caco-2 Cell Barrier Damage by Regulating the TLRs/MyD88/NF-κB Pathway

Arabinoxylan (AX) has been associated with alleviating intestinal barrier damage, and different structures of AX give rise to different effects on the intestinal barrier. This study investigated the main structural characteristics of AX, whose functional properties are attributed to alleviating intestinal barrier damage, and clarified their underlying mechanisms. An in vitro Caco-2 cell model was established to investigate the intestinal barrier effects of AX with various degrees of substitution (Ds) and molecular weight (Mw), with an added MyD88 inhibitor to verify the signaling pathways. Arabinoxylan treated with endo-1,4-β-xylanase (AXX) with higher Ds and Mw showed stronger physiological activity, which might be correlated with the uronic acid and bound ferulic acid contents in AXX. Moreover, AXX alleviated the intestinal barrier damage by upregulating the transepithelial electrical resistance (TER) and alleviating the decrease of claudin-1 (p < 0.05). AXX regulated the expression of inflammatory factors IL-2, TNF-α, IL-6 and IL-10 (p < 0.05). In addition, AXX reduced the intestinal barrier damage induced via inhibiting the TLRs/MyD88/NF-κB pathway and activating the TLRs/PKC pathway. Thus, AX with higher Ds and Mw might be better in alleviating intestinal barrier damage, and MyD88 might be the key point of AXX to identify these signaling pathways.

Collagen Fiber-Based Advanced Separation Materials: Recent Developments and Future Perspectives

Separation plays a critical role in a broad range of industrial applications. Developing advanced separation materials is of great significance for the future development of separation technology. Collagen fibers (CFs), the typical structural proteins, exhibit unique structural hierarchy, amphiphilic wettability, and versatile chemical reactivity. These distinctive properties provide infinite possibilities for the rational design of advanced separation materials. During the past 2 decades, many progressive achievements in the development of CFs-derived advanced separation materials have been witnessed already. Herein, the CFs-based separation materials are focused on and the recent progresses in this topic are reviewed. CFs widely existing in animal skins display unique hierarchically fibrous structure, amphiphilicity-enabled surface wetting behaviors, multi-functionality guaranteed covalent/non-covalent reaction versatility. These outstanding merits of CFs bring great opportunities for realizing rational design of a variety of advanced separation materials that were capable of achieving high-performance separations to diverse specific targets, including oily pollutants, natural products, metal ions, anionic contaminants and proteins, etc. Besides, the important issues for the further development of CFs-based advanced separation materials are also discussed.

Sulfated Galactofucans: An Outstanding Class of Fucoidans with Promising Bioactivities

Fucoidans encompass versatile and heterogeneous sulfated biopolysaccharides of marine origin, specifically brown algae and marine invertebrates. Their chemistry and bioactivities have been extensively investigated in the last few decades. The reported studies revealed diverse chemical skeletons in which l-fucose is the main sugar monomer. However, other sugars, i.e., galactose, mannose, etc., have been identified to be interspersed, forming several heteropolymers, including galactofucans/fucogalactans (G-fucoidans). Particularly, sulfated galactofucans are associated with rich chemistry contributing to more promising bioactivities than fucans and other marine polysaccharides. The previous reports in the last 20 years showed that G-fucoidans derived from Undaria pinnatifida were the most studied; 21 bioactivities were investigated, especially antitumor and antiviral activities, and unique biomedical applications compared to other marine polysaccharides were demonstrated. Hence, the current article specifically reviews the biogenic sources, chemistry, and outstanding bioactivities of G-fucoidans providing the opportunity to discover novel drug candidates.

Effects of different combinations of probiotics on rheology, microstructure, and moisture distribution of soy materials-based yogurt

The effects of different probiotics on the texture, rheological properties, microstructure, and water distribution of yogurt fermented with soy powder, soy isolate protein powder, soy umbilical powder, and soy whey as the main raw materials were studied. The soy materials-based yogurt fermented by Danisco mixed probiotic reached the end of fermentation after 4 h, which significantly shortened the fermentation time compared with other probiotic combinations. The fermentation with Danisco mixed probiotic and Kefir mixed probiotic respectively resulted in good texture and a denser and more homogeneous microstructure, which was consistent with the sensory evaluation results. Both fermentations had a high water holding capacity of 90.92% and 78.30%, respectively, in agreement with the results of moisture distribution tests. However, the elastic and viscous behaviors were weaker at certain shear frequency. This study achieved a high value-added utilization of soy whey and the development of a new soy materials-based yogurt that met the consumption needs of people with lactose intolerance and high cholesterol. PRACTICAL APPLICATION: In this study, high value-added utilization of soy whey was realized, which solved the problems of resource waste and environmental pollution. Meanwhile, the research and development of soy materials-based yogurt provided another nutritional and healthy consumption demand for lactose intolerant people.

Introducing a Chemically Intuitive Core-Substituent Fingerprint Designed to Explore Structural Requirements for Effective Similarity Searching and Machine Learning

Fingerprint (FP) representations of chemical structure continue to be one of the most widely used types of molecular descriptors in chemoinformatics and computational medicinal chemistry. One often distinguishes between two- and three-dimensional (2D and 3D) FPs depending on whether they are derived from molecular graphs or conformations, respectively. Primary application areas for FPs include similarity searching and compound classification via machine learning, especially for hit identification. For these applications, 2D FPs are particularly popular, given their robustness and for the most part comparable (or better) performance to 3D FPs. While a variety of FP prototypes has been designed and evaluated during earlier times of chemoinformatics research, new developments have been rare over the past decade. At least in part, this has been due to the situation that topological (atom environment) FPs derived from molecular graphs have evolved as a gold standard in the field. We were interested in exploring the question of whether the amount of structural information captured by state-of-the-art 2D FPs is indeed required for effective similarity searching and compound classification or whether accounting for fewer structural features might be sufficient. Therefore, pursuing a "structural minimalist" approach, we designed and implemented a new 2D FP based upon ring and substituent fragments obtained by systematically decomposing large numbers of compounds from medicinal chemistry. The resulting FP termed core-substituent FP (CSFP) captures much smaller numbers of structural features than state-of-the-art 2D FPs. However, CSFP achieves high performance in similarity searching and machine learning, demonstrating that less structural information is required for establishing molecular similarity relationships than is often believed. Given its high performance and chemical tangibility, CSFP is also relevant for practical applications in medicinal chemistry.

Phylogenetic signal and rate of evolutionary change in language structures

Within linguistics, there is an ongoing debate about whether some language structures remain stable over time, which structures these are and whether they can be used to uncover the relationships between languages. However, there is no consensus on the definition of the term 'stability'. I define 'stability' as a high phylogenetic signal and a low rate of change. I use metric D to measure the phylogenetic signal and Hidden Markov Model to calculate the evolutionary rate for 171 structural features coded for 12 Japonic, 2 Koreanic, 14 Mongolic, 11 Tungusic and 21 Turkic languages. To more deeply investigate the differences in evolutionary dynamics of structural features across areas of grammar, I divide the features into 4 language domains, 13 functional categories and 9 parts of speech. My results suggest that there is a correlation between the phylogenetic signal and evolutionary rate and that, overall, two-thirds of the features have a high phylogenetic signal and over a half of the features evolve at a slow rate. Specifically, argument marking (flagging and indexing), derivation and valency appear to be the most stable functional categories, pronouns and nouns the most stable parts of speech, and phonological and morphological levels the most stable language domains.

New pectic polysaccharides from Codonopsis pilosula and Codonopsis tangshen: structural characterization and cellular antioxidant activities

BACKGROUND

Codonopsis pilosula and Codonopsis tangshen are plants widely used in traditional Chinese medicine. Two pectic polysaccharides from the roots of C. pilosula and C. tangshen named as CPP-1 and CTP-1 were obtained by boiling water extraction and column chromatography.

RESULTS

The core structures of both CPP-1 and CTP-1 comprise the long homogalacturonan region (HG) as the backbone and the rhamnogalacturonan I (RG-I) region as the side chains. CPP-1 has methyl esterified galacturonic acid units and a slightly lower molecular weight than CTP-1. Biological testing suggested that CPP-1 and CTP-1 can protect IPEC-J2 cells against the H₂ O₂ -induced oxidative stress by up-regulating nuclear factor-erythroid 2-related factor 2 and related genes in IPEC-J2 cells. The different antioxidative activities of polysaccharides from different source of C. pilosula may be result of differences in their structures.

CONCLUSION

All of the results indicated that pectic polysaccharides CPP-1 and CTP-1 from different species of C. pilosula roots could be used as a potential natural antioxidant source. These findings will be valuable for further studies and new applications of pectin-containing health products. © 2021 Society of Chemical Industry.

Characterization of promoters in archaeal genomes based on DNA structural parameters

The transcription machinery of archaea can be roughly classified as a simplified version of eukaryotic organisms. The basal transcription factor machinery binds to the TATA box found around 28 nucleotides upstream of the transcription start site; however, some transcription units lack a clear TATA box and still have TBP/TFB binding over them. This apparent absence of conserved sequences could be a consequence of sequence divergence associated with the upstream region, operon, and gene organization. Furthermore, earlier studies have found that a structural analysis gains more information compared with a simple sequence inspection. In this work, we evaluated and coded 3630 archaeal promoter sequences of three organisms, Haloferax volcanii, Thermococcus kodakarensis, and Sulfolobus solfataricus into DNA duplex stability, enthalpy, curvature, and bendability parameters. We also split our dataset into conserved TATA and degenerated TATA promoters to identify differences among these two classes of promoters. The structural analysis reveals variations in archaeal promoter architecture, that is, a distinctive signal is observed in the TFB, TBP, and TFE binding sites independently of these being TATA-conserved or TATA-degenerated. In addition, the promoter encountering method was validated with upstream regions of 13 other archaea, suggesting that there might be promoter sequences among them. Therefore, we suggest a novel method for locating promoters within the genome of archaea based on DNA energetic/structural features.

Influence of Tire Rubber Particles Addition in Different Branching Degrees Polyethylene Matrix Composites on Physical and Structural Behavior

Waste from pneumatic wheels is one of the major environmental problems, and the scientific community is looking for methods to recycle this type of waste. In this paper, ground tire rubber particles (GTR) from disused tires have been mixed with samples of low-density polyethylene (LDPE) and high-density polyethylene (HDPE), and morphological tests have been performed using scanning electron microscopy (SEM), as well as the dynamic electric analysis (DEA) dielectric characterization technique using impedance spectroscopy. From this experience, how GTR reinforcement influences polyethylene and what influence GTR particles have on the branched polyethylene has been detected. For pure LDPE samples, a Debye-type dielectric behavior is observed with an imperfect semicircle, which depends on the temperature, as it shows differences for the samples at 30 °C and 120 °C, unlike the HDPE samples, which do not show such a trend. The behavior in samples with Debye behavior is like an almost perfect dipole and is due to the crystalline behavior of polyethylene at high temperature and without any reinforcement. These have been obtained evidence that for branched PE (LPDE) the Maxwell Wagner Sillars (MWS) effect is highly remarkable and that this happens due to the intrachain polarization effect combined with MWS. This means that the permittivity and conductivity at LDPE/50%GTR are high than LDPE/70%GTR. However, it does not always occur that way with HDPE composites in which HDPE/70%GTR has the highest values of permittivity and conductivity, due to the presence of conductive fraction (Carbon Black-30%) in the GTR particles and their dielectric behavior.

Comparisons of Isolation Methods, Structural Features, and Bioactivities of the Polysaccharides from Three Common Panax Species: A Review of Recent Progress

Panax spp. (Araliaceae family) are widely used medicinal plants and they mainly include Panax ginseng C.A. Meyer, Panax quinquefolium L. (American ginseng), and Panax notoginseng (notoginseng). Polysaccharides are the main active ingredients in these plants and have demonstrated diverse pharmacological functions, but comparisons of isolation methods, structural features, and bioactivities of these polysaccharides have not yet been reported. This review summarizes recent advances associated with 112 polysaccharides from ginseng, 25 polysaccharides from American ginseng, and 36 polysaccharides from notoginseng and it compares the differences in extraction, purification, structural features, and bioactivities. Most studies focus on ginseng polysaccharides and comparisons are typically made with the polysaccharides from American ginseng and notoginseng. For the extraction, purification, and structural analysis, the processes are similar for the polysaccharides from the three Panax species. Previous studies determined that 55 polysaccharides from ginseng, 18 polysaccharides from American ginseng, and 9 polysaccharides from notoginseng exhibited anti-tumor activity, immunoregulatory effects, anti-oxidant activity, and other pharmacological functions, which are mediated by multiple signaling pathways, including mitogen-activated protein kinase, nuclear factor kappa B, or redox balance pathways. This review can provide new insights into the similarities and differences among the polysaccharides from the three Panax species, which can facilitate and guide further studies to explore the medicinal properties of the Araliaceae family used in traditional Chinese medicine.

Predicting mutant outcome by combining deep mutational scanning and machine learning

Deep mutational scanning provides unprecedented wealth of quantitative data regarding the functional outcome of mutations in proteins. A single experiment may measure properties (eg, structural stability) of numerous protein variants. Leveraging the experimental data to gain insights about unexplored regions of the mutational landscape is a major computational challenge. Such insights may facilitate further experimental work and accelerate the development of novel protein variants with beneficial therapeutic or industrially relevant properties. Here we present a novel, machine learning approach for the prediction of functional mutation outcome in the context of deep mutational screens. Using sequence (one-hot) features of variants with known properties, as well as structural features derived from models thereof, we train predictive statistical models to estimate the unknown properties of other variants. The utility of the new computational scheme is demonstrated using five sets of mutational scanning data, denoted "targets": (a) protease specificity of APPI (amyloid precursor protein inhibitor) variants; (b-d) three stability related properties of IGBPG (immunoglobulin G-binding β1 domain of streptococcal protein G) variants; and (e) fluorescence of GFP (green fluorescent protein) variants. Performance is measured by the overall correlation of the predicted and observed properties, and enrichment-the ability to predict the most potent variants and presumably guide further experiments. Despite the diversity of the targets the statistical models can generalize variant examples thereof and predict the properties of test variants with both single and multiple mutations.

Local crystalline order features in disordered packings of monodisperse spheres

A new tetrahedral structure model was developed for disordered sphere packings, including not only regular tetrahedron (T), but also quartoctahedron (Q) and bcc simplex (B), the tetrahedral building blocks in fcc, hcp and bcc crystal structures, respectively. Both geometric frustrated configurations and local configurations associated with crystalline order in disordered packings can be comprehensively characterized. It is found that with increasing packing fraction, the population of T, Q, and B increases. Moreover, the crystal-type local configurations formed by face-adjacent T, Q and B increases as packing fraction increases, which is more prevalent than the geometric frustrated ones formed by face-adjacent T. In addition, as packing fraction increases, the local density of irregular simplexes is found to increase more quickly than regular ones, playing more important roles in the density increase in disordered packings. These structure features are found to be intrinsic in the jammed random sphere packings with different friction coefficients, which is independent of interparticle friction and only determined by the packing fraction. Our findings provide new understanding for the structural nature of disordered packings and the underlying structural basis of the random close packing.

Uncovering the Effect of pS202/pT205/pS208 Triple Phosphorylations on the Conformational Features of the Key Fragment G192-T212 of Tau Protein

Microtubule-associated protein tau is abnormally phosphorylated and forms the aggregates of paired helical filaments in Alzheimer's disease (AD) and other tauopathies. So far, the relationship and mechanism between the abnormal phosphorylation of tau and fibril formation is still unclear. Therefore, studying the effect of phosphorylation on the structure of tau protein is helpful to elucidate the pathogenic mechanism of tauopathies. It has been shown that pS202/pT205/pS208 triple phosphorylations located in the proline-rich region can promote tau aggregation. In this work, the effect of triple phosphorylations on tau structure was investigated by molecular dynamics simulations combined with multiple analytical methods of trajectories. The results showed that the conformational diversity of G192-T212 fragments decreased after phosphorylation compared with that of the wild-type. Moreover, the dynamic network and hydrogen bond analyses showed that the addition of pS208 phosphorylation can destroy the key hydrogen bonds and the network structure formed centered on pT205 at the C-terminal of the pS202/pT205 double phosphorylated peptide and then destroy the turn structure formed in the region of G207-R211. The destruction of this turn structure is considered to be the main reason for the aggregation of pS202/pT205/pS208 triple phosphorylations. For the pS202/pT205/pS208 triple phosphorylated system, the G207-R211 region is a coil structure, which is more extended and prone to aggregation. In a word, our results reveal the mechanism that pS202/pT205/pS208 triple phosphorylations promote tau aggregation at the atomic level, which can provide useful theoretical guidance for the rational design of effective therapeutic drugs against AD and other tauopathies.

PupStruct: Prediction of Pupylated Lysine Residues Using Structural Properties of Amino Acids

Post-translational modification (PTM) is a critical biological reaction which adds to the diversification of the proteome. With numerous known modifications being studied, pupylation has gained focus in the scientific community due to its significant role in regulating biological processes. The traditional experimental practice to detect pupylation sites proved to be expensive and requires a lot of time and resources. Thus, there have been many computational predictors developed to challenge this issue. However, performance is still limited. In this study, we propose another computational method, named PupStruct, which uses the structural information of amino acids with a radial basis kernel function Support Vector Machine (SVM) to predict pupylated lysine residues. We compared PupStruct with three state-of-the-art predictors from the literature where PupStruct has validated a significant improvement in performance over them with statistical metrics such as sensitivity (0.9234), specificity (0.9359), accuracy (0.9296), precision (0.9349), and Mathew’s correlation coefficient (0.8616) on a benchmark dataset.

Crosslinked Recombinant-Ara h 1 Catalyzed by Microbial Transglutaminase: Preparation, Structural Characterization and Allergic Assessment

As the one of the major allergens in peanut, the allergenicity of Ara h 1 is influenced by its intrinsic structure, which can be modified by different processing. However, molecular information in this modification has not been clarified to date. Here, we detected the influence of microbial transglutaminase (MTG) catalyzed cross-linking on the recombinant peanut protein Ara h 1 (rAra h 1). Electrophoresis and spectroscopic methods were used to analysis the structural changes. The immunoreactivity alterations were characterized by enzyme linked immunosorbent assay (ELISA), immunoblotting and degranulation test. Structural features of cross-linked rAra h 1 varied at different reaction stages. Hydrogen bonds and disulfide bonds were the main molecular forces in polymers induced by heating and reducing. In MTG-catalyzed cross-linking, ε-(γ-glutamyl) lysine isopeptide bonds were formed, thus inducing a relatively stable structure in polymers. MTG catalyzed cross-linking could modestly but significantly reduce the immunoreactivity of rAra h 1. Decreased content of conserved secondary structures led to a loss of protection of linear epitopes. Besides, the reduced surface hydrophobic index and increased steric hindrance of rAra h 1 made it more difficult to bind with antibodies, thus hindering the subsequent allergic reaction.

The role of NAC transcription factor in plant cold response

The NAC transcription factor (TF) is one of the largest families of TFs in plants and plays an important role in plant growth, development, and response to environmental stress. The structural and functional characteristics of NAC TFs have been uncovered in the past years, including sequence binding features of the DNA-binding domain located in the N-terminus and dynamic interplay between the domain located at the C-terminus and other proteins. Studies on NAC TF are increasing in number; these studies distinctly contribute to our understanding of the regulatory networks of NAC-mediated complex signaling and transcriptional reprogramming. Previous studies have indicated that NAC TFs are key regulators of the plant stress response. However, these studies have been for six years so far and mainly focused on drought and salt stress. There are relatively few reports about NAC TFs in plant cold signal pathway and no related reviews have been published. In this review article, we summarize the structural features of NAC TFs, the target genes, upstream regulators and interaction proteins of stress-responsive NAC TFs, and the roles NAC TFs play in plant cold stress signal pathway.

Animal, Herb, and Microbial Toxins for Structural and Pharmacological Study of Acid-Sensing Ion Channels

Acid-sensing ion channels (ASICs) are of the most sensitive molecular sensors of extracellular pH change in mammals. Six isoforms of these channels are widely represented in membranes of neuronal and non-neuronal cells, where these molecules are involved in different important regulatory functions, such as synaptic plasticity, learning, memory, and nociception, as well as in various pathological states. Structural and functional studies of both wild-type and mutant ASICs are essential for human care and medicine for the efficient treatment of socially significant diseases and ensure a comfortable standard of life. Ligands of ASICs serve as indispensable tools for these studies. Such bioactive compounds can be synthesized artificially. However, to date, the search for such molecules has been most effective amongst natural sources, such as animal venoms or plants and microbial extracts. In this review, we provide a detailed and comprehensive structural and functional description of natural compounds acting on ASICs, as well as the latest information on structural aspects of their interaction with the channels. Many of the examples provided in the review demonstrate the undoubted fundamental and practical successes of using natural toxins. Without toxins, it would not be possible to obtain data on the mechanisms of ASICs' functioning, provide detailed study of their pharmacological properties, or assess the contribution of the channels to development of different pathologies. The selectivity to different isoforms and variety in the channel modulation mode allow for the appraisal of prospective candidates for the development of new drugs.

Effect of Cellulose Nanocrystals Nanofiller on the Structure and Sorption Properties of Carboxymethyl Cellulose-Glycerol-Cellulose Nanocrystals Nanocomposite Systems

Biobased materials present a great interest due to their properties and biodegradability. Cellulose nanocrystals (CNC) nanofiller, in various amounts, was incorporated into a carboxymethyl cellulose (CMC)–glycerol (G) matrix in order to obtain nanocomposite systems with improved properties. The effect of the nanofiller on the structural features was investigated by Fourier transform infrared (FT-IR) spectroscopy, principal component analysis (PCA), two-dimensional correlation spectroscopy (2D-COS), and X-ray diffraction, while the sorption properties were evaluated by water vapor isotherms using the gravimetric method coupled with infrared spectroscopy. We observed the presence of the interactions taking place between the CMC-G and CNC involving the hydroxyl and carboxylate groups, which decreased the number of water sorption sites. Following this, the moisture content in the nanocomposite films decreased with the increase in the amount of CNC. Moreover, the bands associated to water molecules presented different wavenumber values separated for CMC-G and CNC components.

EGFR exon 20 insertion mutations in non-small cell lung cancer

Mutations in the epidermal growth factor receptor (EGFR) gene are the most common targetable genomic drivers of non-small cell lung cancer (NSCLC). 90% of the EGFR mutations comprise of EGFR exon 19 deletion and exon 21 L858R mutation, while EGFR exon 20 insertion (EGFR Ex20Ins) is the third most common type of EGFR mutation. Currently, studies on EGFR Ex20Ins are relatively scarce and limited. The frequency of EGFR Ex20Ins mutations in NSCLC was 1–10%. Patients harboring EGFR Ex20Ins exhibited similar clinical characteristics except for poorer prognosis as compared to patients with sensitizing mutations in EGFR. Conventional TKIs have poor efficacy in a majority of EGFR Ex20Ins subtypes. Chemotherapy remains the preferred treatment for advanced NSCLC patients harboring EGFR Ex20Ins. However, some novel inhibitors are considered as putative candidates. This review focuses on the structural and biochemical features, clinical characteristics, treatments, and prognosis of EGFR Ex20Ins in NSCLC.

Structural Features of Three Hetero-Galacturonans from Passiflora foetida Fruits and Their in Vitro Immunomodulatory Effects

Passiflora foetida is a horticultural plant and vital traditional Chinese herbal medicine. In our previous study, the characterization and immuno-enhancing effect of fruits polysaccharide 1 (PFP1), a water-eluted hetero-mannan from wild Passiflora foetida fruits, were investigated. Herein, another three salt-eluted novel polysaccharides, namely PFP2, PFP3, and PFP4, were obtained and structurally characterized. The results showed that PFP2, PFP3, and PFP4 were three structurally similar hetero-galacturonans with different molecular weights of 6.11 × 104, 4.37 × 104, and 3.48 × 105 g/mol, respectively. All three of these hetero-galacturonans are mainly composed of galacturonic acid, galactose, arabinose (75.69%, 80.39%, and 74.30%, respectively), and other monosaccharides including mannose, fucose, glucose, ribose, xylose, and glucuronic acid (24.31%, 19.61, and 25.70%, respectively), although differences in their backbone structure exist. Additionally, immunomodulatory assay indicated that the three hetero-galacturonans possess the ability to promote the production of nitric oxide (NO), tumor necrosis factor-α (TNF-α), and interleukin-6 (IL-6) in RAW264.7 macrophages in a concentration-dependent manner (p < 0.05). Especially, PFP3 displayed a stronger enhancing effect than PFP2 and PFP4 at the minimum effective concentration. Therefore, the results suggested that the obtained three salt-eluted hetero-galacturonans, especially PFP3, could be utilized as immunomodulatory effectivity ingredients in nutritional/pharmaceutical industries.

Structural Features and Photoelectric Properties of Si-Doped GaAs under Gamma Irradiation

GaAs has been demonstrated to be a promising material for manufacturing semiconductor light-emitting devices and integrated circuits. It has been widely used in the field of aerospace, due to its high electron mobility and wide band gap. In this study, the structural and photoelectric characteristics of Si-doped GaAs under different gamma irradiation doses (0, 0.1, 1 and 10 KGy) are investigated. Surface morphology studies show roughen of the surface with irradiation. Appearance of transverse-optical (TO) phonon mode and blueshift of TO peak reflect the presence of internal strain with irradiation. The average strain has been measured to be 0.009 by Raman spectroscopy, indicating that the irradiated zone still has a good crystallinity even at a dose of 10 KGy. Photoluminescence intensity is increased by about 60% under 10 KGy gamma irradiation due to the strain suppression of nonradiative recombination centers. Furthermore, the current of Si-doped GaAs is reduced at 3V bias with the increasing gamma dose. This study demonstrates that the Si-doped GaAs has good radiation resistance under gamma irradiation, and appropriate level of gamma irradiation can be used to enhance the luminescence property of Si-doped GaAs.

Microstructure and Mechanical/Hydrophilic Features of Agar-Based Films Incorporated with Konjac Glucomannan

Different characterization methods spanning length scales from molecular to micron scale were applied to inspect the microstructures and mechanical/hydrophilic features of agar/konjac glucomannan (KGM) films prepared under different drying temperatures (40 and 60 °C). Note that the lower preparation temperature (40 °C) could increase the strength and elongation of agar/KGM films at high KGM levels (18:82 wt/wt KGM-agar, or higher). This was related to the variations in the film multi-scale structures with the increment of KGM content: the reduced crystallinity, the increased perfection of nanoscale orders at some KGM amounts, and the negligibly-changed morphology and molecular chemical structure under 40 °C preparation temperature. These structural changes initially decreased the film tensile strength, and subsequently increased the film strength and elongation with increasing KGM content. Moreover, under the higher drying temperature (60 °C), the increased KGM content could concurrently reduce the strength and elongation for the films, associated with probable phase separations on nano and smaller scales. In addition, the increased KGM amount tended to make the film more hydrophilic, whereas the changes in the film structures did not dominantly affect the changing trend of hydrophilicity.

Structure, Antioxidant, and Hypoglycemic Activities of Arabinoxylans Extracted by Multiple Methods from Triticale

Different methods of isolating arabinoxylans (AXs) from triticale were performed to investigate the extraction methods’ effects on the physiological functions of the AXs. Structural, antioxidant, and hypoglycemic activities were determined. The molecular weights (MWs) of enzyme- or water-extracted AXs were lower than those of alkali-extracted AXs. Opposite trends were shown by the arabinose–xylose ratio. Enzyme-extracted AXs exhibited higher glucose adsorption capacity and hydroxyl radical-scavenging efficiency than alkali-extracted AXs. The α-amylase inhibition ability, DPPH radical-scavenging capacity, and metal-chelating activity of alkali-extracted AXs were higher than those of enzyme-extracted AXs. Water-extracted AXs had the highest glucose dialysis retardation index. In conclusion, extraction methods can influence the physiological function of AXs through their structural features. AXs with higher MWs and esterified ferulic acid (FA) levels had higher antioxidant ability, whereas AXs with higher solubility and free FA level exhibited higher hypoglycemic activity.

Food flavonoid ligand structure/estrogen receptor-α affinity relationships - toxicity or food functionality?

In silico molecular modelling is used to study interactions between flavonoid phytoestrogens and estrogen receptor (ER)α. Twenty flavonoids from foods were studied; e.g., genistein from soy, naringenin from grapefruit, phloretin from pears, chrysin from oyster mushrooms. These potential ligands' molecular attributes and their spatial arrangements that favour binding to the ligand binding cleft (LBC) of ERα are identified, and Docking Scores calculated. The Docking Score order is the same as the estrogenicity order for 8 of the flavonoids studied in detail. The number and position of flavonoid ring hydroxyls influence the Docking Scores which might relate to ERα's bio-activity. Hydrophobic interactions between ligands and ERα are also important; the number of rotatable CC bonds in ligands likely affects the magnitude of hydrophobic interactions and ligand fit. Our findings suggest that flavonoids with diverse structural features could have different binding energies and binding affinities with ERα, which might confer different functionalities and toxicities.

Influence of Land Use on the Structural Feature of Sedimentary Humic Acids in Rivers in Northwest Hokkaido, Japan

Colloidal organic matter is an important factor in our understanding of the transport of trace metals by rivers to coastal areas and the characteristics of organic matter in the sediment, including the effect of humic substances on the transport of such metals. The structural features of humic acids (HAs) derived from surface sediments collected from the mouths of four rivers in northwest Hokkaido, Japan, were evaluated from the perspective of land use in their basins. The sediments in two rivers (referred to as NS and SK) were lacking in HAs, but the sediments of the others (referred to as SM and PO) contained relatively high levels of HAs. UV-vis spectroscopic characteristics suggested that the HAs in SM and PO contained components derived from humified materials. The PO and SM basins contain rice paddy fields, and TMAH-py-GC/MS analysis showed that the pyrograms of paddy soil HA had a similar character to those of PO-HA and SM-HA samples. Thus, the differences of the structural features can be attributed to the land use in river basins. The findings indicate that the properties of organic river sediments are heavily influenced by the type of land use in the river basins.

Characteristics of the Water- and Alkali-Soluble Hemicelluloses Fractionated by Sequential Acidification and Graded-Ethanol from Sweet Maize Stems

Sweet maize stems were treated with hot water and potassium hydroxide to fractionate hemicellulosic polymers. The results showed that the water-soluble hemicelluloses were mainly composed of glucose (27.83%), xylose (27.32%), and galactose (16.81%). In comparison, alkali-soluble hemicelluloses fractionated by acidification and a graded ethanol solution (10%, 20%, 35%, 50%, 65%, and 80%) were mainly composed of xylose (69.73 to 88.62%) and arabinose (5.41 to 16.20%). More highly branched hemicelluloses tended to be precipitated in a higher concentration of ethanol solution, as revealed by the decreasing xylose to arabinose ratio from 16.43 to 4.21. Structural characterizations indicated that alkali-soluble hemicelluloses fractionated from sweet maize stems were mainly arabinoxylans. The results provided fundamental information on hemicelluloses composition and structure and their potential utilization in the fields of biofuels, biochemicals, and biomaterials.

Temperature dependent dynamics in highly homologous adenylate kinases

To correlate the structural features of enzymes to temperature adaptation, we studied psychrophile, mesophile, and thermophile adenylate kinases as model enzymes using bioinformatics and computational tools. Phylogenetic analysis revealed that mesophile and thermophile variants are clustered in one stem of phylogenetic tree and are close to contemporary time, while psychrophile enzyme is more close to their common ancestor. This finding is in good agreement with the process of environmental changes from ice age toward current warm conditions on the earth. We also performed Molecular Dynamics simulation at corresponding temperatures of all enzyme variants including 308, 318, and 328 K. It was found that mesophile enzyme has no distinct deviation of Root Mean Square Deviation (RMSD) and Radius of Gyration (Rg) values from equilibrium states at operating temperature of thermophile enzyme as well as its own optimum temperature. However, psychrophile enzyme undergoes more fluctuations with higher amplitude of change; particularly at 328 K. It was also found that initial increasing of RMSD and Rg for Psychrophile enzyme at all temperatures is occurred gradually; while, the increment of this structural parameters for thermophile enzyme at 328 K is occurred in a highly cooperative and switching manner demonstrating snap structural change of thermophile enzyme in its own temperature. By analysis of Root Mean Square Fluctuation values at different temperatures, we identified two flexible fragments in adenylate kinases so that different dynamic behavior of these regions in mesophile enzyme against operating temperatures of psychrophile and thermophile variants is critical in compensation of flexibility challenges at respective temperatures.

iProtGly-SS: Identifying protein glycation sites using sequence and structure based features

Glycation is chemical reaction by which sugar molecule bonds with a protein without the help of enzymes. This is often cause to many diseases and therefore the knowledge about glycation is very important. In this paper, we present iProtGly-SS, a protein lysine glycation site identification method based on features extracted from sequence and secondary structural information. In the experiments, we found the best feature groups combination: Amino Acid Composition, Secondary Structure Motifs, and Polarity. We used support vector machine classifier to train our model and used an optimal set of features using a group based forward feature selection technique. On standard benchmark datasets, our method is able to significantly outperform existing methods for glycation prediction. A web server for iProtGly-SS is implemented and publicly available to use: http://brl.uiu.ac.bd/iprotgly-ss/.