Structural and sequence analysis of the RPO30 gene of sheeppox and goatpox viruses from India

Sheeppox and goatpox are transboundary viral diseases of sheep and goats that cause significant economic losses to small and marginal farmers worldwide, including India. Members of the genus Capripoxvirus (CaPV), namely Sheeppox virus (SPPV), Goatpox virus (GTPV), and Lumpy skin disease virus (LSDV), are antigenically similar, and species differentiation can only be accomplished using molecular approaches. The present study aimed to understand the molecular epidemiology and host specificity of SPPV and GTPV circulating in India through sequencing and structural analysis of the RNA polymerase subunit-30 kDa (RPO30) gene. A total of 29 field isolates from sheep (n = 19) and goats (n = 10) belonging to different geographical regions of India during the period: Year 2015 to 2023, were analyzed based on the sequence and structure of the full-length RPO30 gene/protein. Phylogenetically, all the CaPV isolates were separated into three major clusters: SPPV, GTPV, and LSDV. Multiple sequence alignment revealed a highly conserved RPO30 gene, with a stretch of 21 nucleotide deletion in all SPPV isolates. Additionally, the RPO30 gene of the Indian SPPV and GTPV isolates possessed several species-specific conserved signature residues/motifs that could act as genotyping markers. Secondary structure analysis of the RPO30 protein showed four α-helices, two loops, and three turns, similar to that of the E4L protein of vaccinia virus (VACV). All the isolates in the present study exhibited host preferences across different states of India. Therefore, in order to protect vulnerable small ruminants from poxviral infections, it is recommended to take into consideration a homologous vaccination strategy.

Evaluation of the impact of two C5 genetic variants on C5-eculizumab complex stability at the molecular level

Complement C5 is the target of the monoclonal antibody eculizumab, used in complement dysregulating disorders, like the rare disease Paroxysmal Nocturnal Hemoglobinuria (PNH). PNH is an acquired hematopoietic stem cell condition characterized by aberrant destruction of erythrocytes, chronic hemolytic anemia, and thromboembolism propensity. C5 is a protein component of the complement system which is part of the immune system of the body and plays a prominent role in the destruction of red blood cells, misidentifying them as a threat. This work describes the application of molecular dynamics simulations to the study of the underlying interactions between complement C5 and eculizumab. This study also reveals the importance of single nucleotide polymorphisms on C5 protein concerning the effective inhibition of the mAB, involving the mechanistic events taking place at the interface spots of the complex. The predicted conformational change in the C5 Arg885/His/Cys mutation has implications on the protein's interaction with eculizumab, compromising their compatibility. The acquired insights into the conformational changes, dynamics, flexibility, and interactions shed light on the knowledge of the function of this biomolecule providing answers about the poor response to the treatment in PNH patient carriers of the mutations. By investigating the intricate dynamics, significant connections between C5 and eculizumab can be uncovered. Such insights may aid in the creation of novel compounds or lead to the enhancement of eculizumab's efficacy.Communicated by Ramaswamy H. Sarma.

Amino acid pattern reveals multi-functionality of ORF3 protein from HEV

The smallest open reading frame (ORF) encoded protein ORF3 of hepatitis E virus (HEV), recently, has been demonstrated to perform multiple functions besides accessory roles. ORF3 could act as a target for vaccine against HEV infections. The IDR (intrinsically disordered region); IDP (ID protein)/IDPR (ID protein region), plays critical role in various regulatory functions of viruses. The dark proteome of HEV-ORF3 protein including its structure and function was systematically examined by computer predictors to explicate its role in viral pathogenesis and drug resistance beyond its functions as accessory viral protein. Amino acid distribution showed ORF3 enrichment with disorder-promoting residues (Ala, Pro, Ser, Gly) while deficiency in order-promoting residues (Asn, Ile, Phe, Tyr and Trp). Initial investigation revealed ORF3 as IDP (entirely disordered protein) or IDPR (proteins consisting of IDRs with structured globular domains). Structural examination revealed preponderance of disordered regions interpreting ORF3 as moderately/highly disordered protein. Further disorder predictors categorized ORF3 as highly disordered protein/IDP. Identified sites and associated-crucial molecular functions revealed ORF3 involvement in diverse biological processes, substantiating them as targets of regulation. As ORF3 functions are yet to completely explored, thus, data on its disorderness could help in elucidating its disorder related functions.

Expression and Purification of Cp3GT: Structural Analysis and Modeling of a Key Plant Flavonol-3-O Glucosyltransferase from Citrus paradisi

Glycosyltransferases (GTs) are pivotal enzymes in the biosynthesis of various biological molecules. This study focuses on the scale-up, expression, and purification of a plant flavonol-specific 3-O glucosyltransferase (Cp3GT), a key enzyme from Citrus paradisi, for structural analysis and modeling. The challenges associated with recombinant protein production in Pichia pastoris, such as proteolytic degradation, were addressed through the optimization of culture conditions and purification processes. The purification strategy employed affinity, anion exchange, and size exclusion chromatography, leading to greater than 95% homogeneity for Cp3GT. In silico modeling, using D-I-TASSER and COFACTOR integrated with the AlphaFold2 pipeline, provided insights into the structural dynamics of Cp3GT and its ligand binding sites, offering predictions for enzyme-substrate interactions. These models were compared to experimentally derived structures, enhancing understanding of the enzyme's functional mechanisms. The findings present a comprehensive approach to produce a highly purified Cp3GT which is suitable for crystallographic studies and to shed light on the structural basis of flavonol specificity in plant GTs. The significant implications of these results for synthetic biology and enzyme engineering in pharmaceutical applications are also considered.

Advances in Mass Spectrometry of Gangliosides Expressed in Brain Cancers

Gangliosides are highly abundant in the human brain where they are involved in major biological events. In brain cancers, alterations of ganglioside pattern occur, some of which being correlated with neoplastic transformation, while others with tumor proliferation. Of all techniques, mass spectrometry (MS) has proven to be one of the most effective in gangliosidomics, due to its ability to characterize heterogeneous mixtures and discover species with biomarker value. This review highlights the most significant achievements of MS in the analysis of gangliosides in human brain cancers. The first part presents the latest state of MS development in the discovery of ganglioside markers in primary brain tumors, with a particular emphasis on the ion mobility separation (IMS) MS and its contribution to the elucidation of the gangliosidome associated with aggressive tumors. The second part is focused on MS of gangliosides in brain metastases, highlighting the ability of matrix-assisted laser desorption/ionization (MALDI)-MS, microfluidics-MS and tandem MS to decipher and structurally characterize species involved in the metastatic process. In the end, several conclusions and perspectives are presented, among which the need for development of reliable software and a user-friendly structural database as a search platform in brain tumor diagnostics.

Unveiling Novel ERCC1-XPF Complex Inhibitors: Bridging the Gap from In Silico Exploration to Experimental Design

Modifications in DNA repair pathways are recognized as prognostic markers and potential therapeutic targets in various cancers, including non-small cell lung cancer (NSCLC). Overexpression of ERCC1 correlates with poorer prognosis and response to platinum-based chemotherapy. As a result, there is a pressing need to discover new inhibitors of the ERCC1-XPF complex that can potentiate the efficacy of cisplatin in NSCLC. In this study, we developed a structure-based virtual screening strategy targeting the inhibition of ERCC1 and XPF interaction. Analysis of crystal structures and a library of small molecules known to act against the complex highlighted the pivotal role of Phe293 (ERCC1) in maintaining complex stability. This residue was chosen as the primary binding site for virtual screening. Using an optimized docking protocol, we screened compounds from various databases, ultimately identifying more than one hundred potential inhibitors. Their capability to amplify cisplatin-induced cytotoxicity was assessed in NSCLC H1299 cells, which exhibited the highest ERCC1 expression of all the cell lines tested. Of these, 22 compounds emerged as promising enhancers of cisplatin efficacy. Our results underscore the value of pinpointing crucial molecular characteristics in the pursuit of novel modulators of the ERCC1-XPF interaction, which could be combined with cisplatin to treat NSCLC more effectively.

An in vitro experimental pipeline to characterize the epitope of a SARS-CoV-2 neutralizing antibody

IMPORTANCE

The COVID-19 pandemic remains a significant public health concern for the global population; the development and characterization of therapeutics, especially ones that are broadly effective, will continue to be essential as severe acute respiratory syndrome-coronavirus-2 (SARS-CoV-2) variants emerge. Neutralizing monoclonal antibodies remain an effective therapeutic strategy to prevent virus infection and spread so long as they recognize and interact with circulating variants. The epitope and binding specificity of a neutralizing anti-SARS-CoV-2 Spike receptor-binding domain antibody clone against many SARS-CoV-2 variants of concern were characterized by generating antibody-resistant virions coupled with cryo-EM structural analysis and VSV-spike neutralization studies. This workflow can serve to predict the efficacy of antibody therapeutics against emerging variants and inform the design of therapeutics and vaccines.

Hepatoprotective effects of peach gum polysaccharides against alcoholic liver injury: moderation of oxidative stress and promotion of lipid metabolism

Natural polysaccharides extracted from plants have received increasing attention due to their rich bioactivity. In our study, peach gum polysaccharides (PGPs) were extracted by water extraction-alcohol precipitation method. PGPs are typical pyranose polysaccharides with a mean molecular weight of 3.68 × 106 g/mol. The antioxidant activity and hepatoprotective capacity of PGPs were studied. In vitro, assays showed that PGPs scavenged DPPH, OH, and O2- in a dose-dependent manner. PGPs exhibited antioxidative properties against alcohol-induced HL7702 cells, as evidenced by the normalization of MDA, SOD, ROS, and GSH levels. To further elucidate the hepatoprotective mechanism of PGPs, we carried out in vivo experiments in male mice. PGPs exerted hepatoprotective effects in alcohol liver disease (ALD) mice by exerting antioxidant effects, decreasing the inflammatory response and modulating lipid metabolism. In addition, metabolomic analysis indicated that PGPs mainly regulate D-glutamine and D-glutamate metabolism, alanine, aspartate and glutamate metabolism, and arginine biosynthesis to promote hepatic metabolism and maintain body functions. Overall, this study revealed that the hepatoprotective mechanism of PGPs against ALD might be associated with the regulation of oxidative stress and lipid metabolism.

Preparation, Structural Analysis, and Intestinal Probiotic Properties of a Novel Oligosaccharide from Enzymatic Degradation of Huangshui Polysaccharide

Huangshui polysaccharide (HSP) has attracted more and more interest due to its potential health benefits. Despite being an excellent source for the preparation of oligosaccharides, there are currently no relevant research reports on HSP. In the present study, a novel oligosaccharide (HSO) with a molecular weight of 1791 Da and a degree of polymerization of 11 was prepared through enzymatic degradation of crude HSP (cHSP). Methylation and NMR analyses revealed that the main chain of HSO was (1 → 4)-α-d-glucose with two O-6-linked branched chains. Morphological observations indicated that HSO exhibited smooth surface with lamellar and filamentary structure, and the glycan size ranged from 0.03 to 0.20 μm. Notably, HSO significantly promoted the proliferation of Bifidobacterium, Bacteroides, and Phascolarctobacterium, thereby making positive alterations in intestinal microbiota composition. Moreover, HSO markedly increased the content of short-chain fatty acids during in vitro fermentation. Metabolomics analysis illustrated the important metabolic pathways primarily involving glucose metabolism, amino acid metabolism, and fatty acid metabolism.

A computational study on structural and functional consequences of nsSNPs in human dopa decarboxylase

The Dopa Decarboxylase (DDC) gene plays an important role in the synthesis of biogenic amines such as dopamine, serotonin, and histamine. Non-synonymous single nucleotide polymorphisms (nsSNPs) in the DDC gene have been linked with various neurodegenerative disorders. In this study, a comprehensive in silico analysis of nsSNPs in the DDC gene was conducted to assess their potential functional consequences and associations with disease outcomes. Using publicly available databases, a complete list of nsSNPs in the DDC gene was obtained. 29 computational tools and algorithms were used to characterise the effects of these nsSNPs on protein structure, function, and stability. In addition, the population-based association studies were performed to investigate possible associations between specific nsSNPs and arthritis. Our research identified four novel DDC gene nsSNPs that have a major impact on the structure and function of proteins. Through molecular dynamics simulations (MDS), we observed changes in the stability of the DDC protein induced by specific nsSNPs. Furthermore, population-based association studies have revealed potential associations between certain DDC nsSNPs and various neurological disorders, including Parkinson's disease and dementia. The in silico approach used in this study offers insightful information about the functional effects of nsSNPs in the DDC gene. These discoveries provide insight into the cellular processes that underlie cognitive disorders. Furthermore, the detection of disease-associated nsSNPs in the DDC gene may facilitate the development of tailored and targeted therapy approaches.Communicated by Ramaswamy H. Sarma.

Tailoring the Structural and Optical Properties of Cerium Oxide Nanoparticles Prepared by an Ecofriendly Green Route Using Plant Extracts

The present study explores an environmentally friendly green approach to obtain cerium oxide nanoparticles via a biomediated route using Mellisa officinalis and Hypericum perforatum plant extracts as reducing agents. The as-prepared nanoparticles were studied for their structural and morphological characteristics using XRD diffractometry, scanning electron microscopy, Raman, fluorescence and electronic absorption spectra, and X-ray photoelectron spectroscopy (XPS). The XRD pattern has shown the centered fluorite crystal structure of cerium oxide nanoparticles with average crystallite size below 10 nm. These observations were in agreement with the STEM data. The cubic fluorite structure of the cerium oxide nanoparticles was confirmed by the vibrational mode around 462 cm-1 due to the Ce-08 unit. The optical band gap was estimated from UV-Vis reflectance spectra, which was found to decrease from 3.24 eV to 2.98 eV. A higher specific area was determined for the sample using M. officinalis aqueous extract. The EDX data indicated that only cerium and oxygen are present in the green synthesized nanoparticles.

Computational identification of key residues regulating fluorescence emission in a red/green cyanobacteriochrome

Cyanobacteriochromes (CBCRs) are linear tetrapyrrole bilin-binding photoreceptors of cyanobacteria that exhibit high spectral diversity, gaining attention in optogenetics and bioimaging applications. Several engineering studies on CBCRs were attempted, especially for designing near-infrared (NIR) fluorescent proteins with longer fluorescence wavelengths. However, despite continuous efforts, a key component regulating fluorescence emission property in CBCRs is still poorly understood. As a model system, we focused on red/green CBCR Slr1393g3, from the unicellular cyanobacterium Synechocystis sp. PCC 6803 to engineer Pr to get far-red light-emitting property. Energy profiling and pairwise structural comparison of Slr1393g3 variants effectively reveal the mutations that are critical to the fluorescence changes. H497 seems to play a key role in stabilizing the chromophore environment, especially the α3 helix, while H495, T499, and Q502 are potential key residues determining fluorescence emission peak wavelength. We also found that mutations of α2 and α4 helical regions are closely related to the chromophore binding stability and likely affect fluorescence properties. Taken together, our computational analysis suggests that the fluorescence of Slr1393g3 is mainly controlled by the stabilization of the chromophore binding pocket. The predicted key residues potentially regulating the fluorescence emission property of a red/green CBCR will be advantageous for designing improved NIR fluorescent protein when combined with in vitro molecular evolution approaches.

Structural and Thermal Characterization of Milled Wood Lignin from Bamboo (Phyllostachys pubescens) Grown in Korea

The structural and thermal characterization of milled wood lignin (MWL) prepared from bamboo (Phyllostachys pubescens) grown in Korea was investigated, and the results were compared with bamboo MWLs from other studies. The C9 formula of the bamboo MWL was C9H7.76O3.23N0.02 (OCH3)1.41. The Mw and Mn of MWL were 13,000 and 4400 Da, respectively, which resulted in a polydispersity index (PDI) of 3.0. The PDI of the prepared MWL was higher than other bamboo MWLs (1.3-2.2), suggesting a broader molecular weight distribution. The structural features of MWL were elucidated using FT-IR spectroscopy and NMR techniques (1H, 13C, HSQC, 31P NMR), which indicate that MWL is of the HGS-type lignin. The major lignin linkages (β-O-4, β-β, β-5) were not different from other bamboo MWLs. The syringyl/guaiacyl ratio, determined from 1H NMR, was calculated as 0.89. 31P NMR revealed variations in hydroxyl content, with a higher aliphatic hydroxyl content in MWL compared to other bamboo MWLs. Thermal properties were investigated through TGA, DSC, and pyrolysis-GC/MS spectrometry (Py-GC/MS). The DTGmax of MWL under inert conditions was 287 °C, and the Tg of MWL was 159 °C. Py-GC/MS at 675 °C revealed a syringyl, guaiacyl, p-hydroxyphenyl composition of 17:37:47.

Morphologies of Comb-like Polyacrylic Acid/Polyacrylate Copolymers as Functions of the Degree of Derivatization with n-C22H45 Side Chains

Polymers with crystallizable side chains have numerous applications, and their properties depend on their crystal morphologies and phase separation. Structural analysis on a wide spatial scale plays an important role in controlling the thermal properties and higher-order structures of these polymers. In this study, we elucidated the melting and crystallization processes of copolymers with varying crystallizable side-chain fractions over a wide spatial range. Differential scanning calorimetry revealed that the enthalpies of melting and crystallization increased linearly with increasing crystallizable side-chain fraction. The results of wide-angle X-ray scattering indicated that the crystal lattice was hexagonal. Conversely, spherulite-like higher-order architectures with linear structures and radial spreading were observed in the highly crystallizable components, but no micrometer-scale structures were observed in the less crystallizable components. In situ small-angle X-ray scattering was used to elucidate the phase separation and mixing processes. Lamellar crystallites were observed at crystallizable side-chain fractions of >55 wt.%, whereas small crystallites were observed at fractions of <45 wt.%. At temperatures above the order-disorder transition temperature, density fluctuations caused by correlation holes were observed. These properties have a strong effect on the crystallizable side-chain fraction.

Mass Spectrometric Identification of Metabolites after Magnetic-Pulse Treatment of Infected Pyrus communis L. Microplants

The major goal of this study is to create a venue for further work on the effect of pulsed magnetic fields on plant metabolism. It deals with metabolite synthesis in the aforementioned conditions in microplants of Pyrus communis L. So far, there have been glimpses into the governing factors of plant biochemistry in vivo, and low-frequency pulsed magnestatic fields have been shown to induce additional electric currents in plant tissues, thus perturbing the value of cell membrane potential and causing the biosynthesis of new metabolites. In this study, sixty-seven metabolites synthesized in microplants within 3-72 h after treatment were identified and annotated. In total, thirty-one metabolites were produced. Magnetic-pulse treatment caused an 8.75-fold increase in the concentration of chlorogenic acid (RT = 8.33 ± 0.0197 min) in tissues and the perturbation of phenolic composition. Aucubin, which has antiviral and antistress biological activity, was identified as well. This study sheds light on the effect of magnetic fields on the biochemistry of low-molecular-weight metabolites of pear plants in vitro, thus providing in-depth metabolite analysis under optimized synthetic conditions. This study utilized high-resolution gas chromatography-mass spectrometry, metabolomics methods, stochastic dynamics mass spectrometry, quantum chemistry, and chemometrics, respectively. Stochastic dynamics uses the relationships between measurands and molecular structures of silylated carbohydrates, showing virtually identical mass spectra and comparable chemometrics parameters.

Molecular Cloning, In Silico Analysis, and Characterization of a Novel Cellulose Microfibril Swelling Gene Isolated from Bacillus sp. Strain AY8

A novel cellulose microfibril swelling (Cms) gene of Bacillus sp. AY8 was successfully cloned and sequenced using a set of primers designed based on the conserved region of the gene from the genomic database. The molecular cloning of the Cms gene revealed that the gene consisted of 679 bp sequences encoding 225 amino acids. Further in silico analysis unveiled that the Cms gene contained the NlpC/P60 conserved region that exhibited a homology of 98% with the NlpC/P60 family proteins found in both the strains, Burkholderialata sp. and Burkholderia vietnamiensis. The recombinant Cms enzyme had a significant impact on the reduction of crystallinity indices (CrI) of various substrates including a 3%, a 3.97%, a 4.66%, and a substantial 14.07% for filter paper, defatted cotton fiber, avicel, and alpha cellulose, respectively. Additionally, notable changes in the spectral features were observed among the substrates treated with recombinant Cms enzymes compared to the untreated control. Specifically, there was a decrease in band intensities within the spectral regions of 3000-3450 cm-1, 2900 cm-1, 1429 cm-1, and 1371 cm-1 for the treated filter paper, cotton fiber, avicel, and alpha cellulose, respectively. Furthermore, the recombinant Cms enzyme exhibited a maximum cellulose swelling activity at a pH of 7.0 along with a temperature of 40 °C. The molecular docking data revealed that ligand molecules, such as cellobiose, dextrin, maltose 1-phosphate, and feruloyated xyloglucan, effectively bonded to the active site of the Cms enzyme. The molecular dynamics simulations of the Cms enzyme displayed stable interactions with cellobiose and dextrin molecules up to 100 ns. It is noteworthy to mention that the conserved region of the Cms enzyme did not match with those of the bioadditives like expansins and swollenin proteins. This study is the initial report of a bacterial cellulose microfibril swellase enzyme, which could potentially serve as an additive to enhance biofuel production by releasing fermentable sugars from cellulose.

Molecular diversity and evolution of far-red light-acclimated photosystem I

The need to acclimate to different environmental conditions is central to the evolution of cyanobacteria. Far-red light (FRL) photoacclimation, or FaRLiP, is an acclimation mechanism that enables certain cyanobacteria to use FRL to drive photosynthesis. During this process, a well-defined gene cluster is upregulated, resulting in changes to the photosystems that allow them to absorb FRL to perform photochemistry. Because FaRLiP is widespread, and because it exemplifies cyanobacterial adaptation mechanisms in nature, it is of interest to understand its molecular evolution. Here, we performed a phylogenetic analysis of the photosystem I subunits encoded in the FaRLiP gene cluster and analyzed the available structural data to predict ancestral characteristics of FRL-absorbing photosystem I. The analysis suggests that FRL-specific photosystem I subunits arose relatively late during the evolution of cyanobacteria when compared with some of the FRL-specific subunits of photosystem II, and that the order Nodosilineales, which include strains like Halomicronema hongdechloris and Synechococcus sp. PCC 7335, could have obtained FaRLiP via horizontal gene transfer. We show that the ancestral form of FRL-absorbing photosystem I contained three chlorophyll f-binding sites in the PsaB2 subunit, and a rotated chlorophyll a molecule in the A0B site of the electron transfer chain. Along with our previous study of photosystem II expressed during FaRLiP, these studies describe the molecular evolution of the photosystem complexes encoded by the FaRLiP gene cluster.

Synthesis and Structural Characterization of Novel Dimers of Dipyridothiazine as Promising Antiproliferative Agents

Many new isomeric dipyridothiazine dimers have been presented as molecules with anticancer potential. These compounds were obtained in efficient syntheses of 1,6-, 1,8-, 2,7- and 3,6-diazaphenothiazines with selected alkylaromatic linkers. The structures of these compounds has been proven with two-dimensional spectroscopic techniques (COSY, NOESY, HSQC and HMBC) and high-resolution mass spectrometry (HRMS). In silico analyses of probable molecular targets were performed using the Way2Drug server. All new dimers were tested for anticancer activity against breast cancer line MCF7 and colon cancer line SW480. Cytotoxicity was assessed on normal L6 muscle cells. The tested dimers had high anticancer potential expressed as IC50 and the selectivity index SI. The most active derivative, 4c, showed an IC50 activity of less than 1 µM and an SI selectivity index higher than 100. Moreover, the compounds were characterized by low toxicity towards normal cells, simultaneously indicating a high cytostatic potential.

Identification of sequence determinants for the ABHD14 enzymes

Over the course of evolution, enzymes have developed remarkable functional diversity in catalyzing important chemical reactions across various organisms, and understanding how new enzyme functions might have evolved remains an important question in modern enzymology. To systematically annotate functions, based on their protein sequences and available biochemical studies, enzymes with similar catalytic mechanisms have been clustered together into an enzyme superfamily. Typically, enzymes within a superfamily have similar overall three-dimensional structures, conserved catalytic residues, but large variations in substrate recognition sites and residues to accommodate the diverse biochemical reactions that are catalyzed within the superfamily. The serine hydrolases are an excellent example of such an enzyme superfamily. Based on known enzymatic activities and protein sequences, they are split almost equally into the serine proteases and metabolic serine hydrolases. Within the metabolic serine hydrolases, there are two outlying members, ABHD14A and ABHD14B, that have high sequence similarity, but their biological functions remained cryptic till recently. While ABHD14A still lacks any functional annotation to date, we recently showed that ABHD14B functions as a lysine deacetylase in mammals. Given their high sequence similarity, automated databases often wrongly assign ABHD14A and ABHD14B as the same enzyme, and therefore, annotating functions to them in various organisms has been problematic. In this article, we present a bioinformatics study coupled with biochemical experiments, which identifies key sequence determinants for both ABHD14A and ABHD14B, and enable better classification for them. In addition, we map these enzymes on an evolutionary timescale and provide a much-wanted resource for studying these interesting enzymes in different organisms.

Zn-Based Metal-Organic Frameworks Using Triptycene Hexacarboxylate Ligands: Synthesis, Structure, and Gas-Sorption Properties

A series of metal-organic frameworks (MOFs) based on zinc ions and two triptycene ligands of different size have been synthesized under solvothermal conditions. Structural analyses revealed that they are isostructural 3D-network MOFs. The high porosity and thermal stability of these MOFs can be attributed to the highly rigid triptycene-based ligands. Their BET specific surface areas depend on the size of the triptycene ligands. In contrast to these surface-area data, the H2 and CO2 adsorption of these MOFs is larger for MOFs with small pores. Consequently, we introduced functional groups to the bridge-head position of the triptycene ligands and investigated their effect on the gas-sorption properties. The results unveiled the role of the functional groups in the specific CO2 binding via an induced interaction between adsorbates and the functional groups. Excellent H2 and CO2 properties in these MOFs were achieved in the absence of open metal sites.

longum XZ01

Bifidobacterium longum subsp. longum XZ01 (BLSL1) is a new strain (isolated from the intestines of healthy people and deposited with the preservation number GDMCC 61618). An exopolysaccharide, S-EPS-1, was successfully isolated from the strain and then systematically investigated for the first time. Some structural features of S-EPS-1 were analyzed by chemical component, HPLC, ultraviolet, infrared, and nuclear magnetic resonance spectrum analyses. These analyses revealed that S-EPS-1 is a neutral heteropolysaccharide with an α-configuration. It contains mainly mannose and glucose, as well as small amounts of rhamnose and galactose. The molecular weight of S-EPS-1 was calculated to be 638 kDa. Several immunoregulatory activity assays indicated that S-EPS-1 could increase proliferation, phagocytosis, and NO production in vitro. In addition, S-EPS-1 could upregulate the expression of cytokines at the mRNA level through TLR4-mediated activation of the NF-κB signaling pathway in RAW 264.7 cells. Finally, S-EPS-1 was demonstrated to exhibit antioxidant activity by ABTS+• scavenging, DPPH• scavenging, and ferric-ion reducing power assays. Furthermore, S-EPS-1 can protect cells from oxidative stress and shows no cytotoxicity. These beneficial effects can be partly attributed to its antioxidant ability. Thus, the antioxidant S-EPS-1 may be applied as a functional food in the future.

Molecular dynamics studies of the solubility behavior of carbon dioxide (CO2 ), difluoromethane (R-32), 1-chloro-3,3,3-trifluoropropene (R-1233zd(E)) and 2,3,3,3-tetrafluoro-1-propene (R-1234yf) in pentaerythritol tetra(2-ethylhexanoate) (PEB8), pentaerythritol tetrabutyrate (PEC4) and pentaerythritol tetraoctanoate (PEC8)

To reduce the climate impact of thermal engines such as heat pumps or refrigeration machines, refrigerants with a low global warming potential need to be paired with fitting lubricants. As the contamination of those liquid components influences the efficiency and lifetime of these machines, knowledge about their solubility behavior is of great interest. Molecular simulations offer mighty tools to investigate these solubilities while giving structural insight into the systems. Here the solubility behavior of CO2 , R-32, R-1233zd(E), and R-1234yf in PEB8, PEC4, and PEC8 is compared through the solvation free energy ∆GSolv obtained by molecular dynamics simulations. To derive ∆GSolv at low computational cost, an iterative method is used to find an optimal number and distribution of intermediate states. The resulting distributions are investigated with regard to different parameters of the employed softcore-potential. ∆GSolv values for the different refrigerant-lubricant pairings at different temperatures are provided, followed by a structural analysis.

Reduced Cortical Complexity in Children with Developmental Delay in Saudi Arabia

INTRODUCTION

Developmental delay (DD) is a neurodevelopmental disorder characterized by delays in multiple domains. The investigation of brain structure in DD has been enhanced by advanced neuroimaging techniques that can identify regional surface deformities. Neuroimaging studies have identified structural brain abnormalities in individuals with DD, but research specific to the Saudi Arabian population is limited. In this study, we examine the neuroanatomical abnormalities in the cortical and subcortical regions of Saudi Arabian children with DD.

METHOD

A T1-weighted, 1-mm-thick MRI was used to acquire structural brain images of 29 children with DD and age-matched healthy controls.

RESULTS

Analysis of the MRI data revealed significant differences in several cortical and subcortical structures of gray matter (GM) and white matter (WM) in several brain regions of the DD group. Specifically, significant deformities were observed in the caudate nucleus, globus pallidus, frontal gyrus, pars opercularis, pars orbitalis, cingulate gyrus, and subcallosal gyrus. These findings suggest disrupted neurodevelopment in these regions, which may contribute to the cognitive, motor, and behavioral impairments commonly observed in individuals with DD.

CONCLUSIONS

The present study provides valuable insights into the neuroanatomical differences in Saudi Arabian children with DD. Our results provide evidence for cortical and subcortical abnormalities in DD. Deformities in the observed regions may contribute to cognitive impairment, emotional dysregulation, mood disorders, and language deficits commonly observed in DD. The structural analysis may enable the identification of neuroanatomical biomarkers to facilitate the early diagnosis or progression of DD. These results suggest that lower cortical complexity in DD children due to alterations in networks may play a critical role in early brain development.

Preparation of Bioactive Polyamide Fibres Modified with Acetanilide and Copper Sulphate

This paper presents a simple method of obtaining polyamide 6 fibres modified with acetanilide and copper ions. During the spinning of the fibres with the additives applied, a partial reduction of CuSO4 to Cu2+ and Cu+ ions occurs, which is observed as a change in the blue colour of the prepared polyamide granulate to the grey-brown colour of the formed fibres. CuMPs obtained as a result of the salt reduction should give the obtained fibres bioactive properties. Three types of microorganisms were selected to assess the microbiological activity of the obtained fibres, i.e., Gram-positive Staphylococcus aureus and Gram-negative Pseudomonas aeruginosa and Escherichia coli. The fibres have antibacterial activity against Gram-positive and Gram-negative bacteria. The largest inhibition zones were obtained for the Gram-positive bacteria Staphylococcus aureus, ranging from 1.5 to 4.5 mm, depending on the concentration of CuMPs. The morphology of the fibres' surfaces was examined by means of scanning electron microscopy (SEM) and optical microscopy (OM). The changes in the polymer structure chemistry are studied by Fourier transform infrared spectroscopy (FTIR), Raman spectroscopy, X-ray structure studies (WAXS and SAXS) and an energy-dispersive spectroscopy (EDS) analysis. The newly obtained bioactive polyamide fibres can be used in many areas, including medicine, clothing and environmental protection for the production of filters.

L protein characterization and in silico screening of putative broad range target molecules for pathogenic mammarenaviruses from South America

The genus Mammarenavirus belonging to the family Arenaviridae encompasses pathogenic viral species capable of triggering severe diseases in humans, causing concern for the health system due to the high fatality rate associated with them. Currently, there is a dearth of specific therapies against pathogens of the genus. Natural products isolated from plants have impacted the development of drugs against several diseases. The Núcleo de Bioensaios, Biossíntese e Ecofisiologia de Produtos Naturais (NuBBE) database offers several natural compounds with antimicrobial activities that can be used in the development of new antiviral drugs. In this context, here we modeled the arenavirus L protein, multifunctional machinery essential for the viral replicative cycle, making this enzyme a potential candidate for targeting the development of antivirals against genus pathogens. Using the modeled L protein, a virtual screening was performed, which suggested eleven molecules from the NuBBE database that binds to the active site of the L protein, which was promising in the in silico predictions of absorption and toxicity analysis. The NuBBE 1642 molecule proved to be the best candidate for four of the five species evaluated, acting as a possible broad-spectrum molecule. Additionally, our results showed that the L protein is highly conserved among species of the genus, as well as presenting close phylogenetic relationships between many of the species studied, strengthening its candidacy as a therapeutic target. The data presented here demonstrate that some NuBBE molecules are potential ligands for the L protein of arenaviruses, which may help to contain possible outbreaks.Communicated by Ramaswamy H. Sarma.

Determining Magnitudes of Forces at Known Locations through a Strain Gauge Force Transducer

A novel strain gauge force transducer was developed to minimize the number of strain gauges needed to determine the magnitudes of loads when the locations are known. This innovative methodology requires only one strain gauge for each force magnitude desired, reducing the complexity and cost associated with traditional approaches. The theory was verified with laboratory experiments. Seven uniaxial strain gauges were attached to the underside of a simply supported, slender, aluminum beam. One or more loads were applied either directly atop strain gauges or in known positions between strain gauges. Experiments were conducted on several different single and double-load configurations to evaluate the extent of the new methodology which yielded average errors under 5% for the cases where loads were direct atop strain gauges and 6.6% for the cases where the loads were between strain gauges. These findings indicate the potential of this novel strain gauge force transducer to revolutionize load measurement in scenarios where load locations are predetermined.

Relationship between Structure and Performance of Atomic-Scale Electrocatalysts for Water Splitting

Atomic-scale electrocatalysts greatly improve the performance and efficiency of water splitting but require special adjustments of the supporting structures for anchoring and dispersing metal single atoms. Here, the structural evolution of atomic-scale electrocatalysts for water splitting is reviewed based on different synthetic methods and structural properties that create different environments for electrocatalytic activity. The rate-determining step or intermediate state for hydrogen or oxygen evolution reactions is energetically stabilized by the coordination environment to the single-atom active site from the supporting material. In large-scale practical use, maximizing the loading amount of metal single atoms increases the efficiency of the electrocatalyst and reduces the economic cost. Dual-atom electrocatalysts with two different single-atom active sites react with an increased number of water molecules and reduce the adsorption energy of water derived from the difference in electronegativity between the two metal atoms. In particular, single-atom dimers induce asymmetric active sites that promote the degradation of H2 O to H2 or O2 evolution. Consequently, the structural properties of atomic-scale electrocatalysts clarify the atomic interrelation between the catalytic active sites and the supporting material to achieve maximum efficiency.

Enzyme-assisted extraction, characterization, and in vitro antioxidant activity of polysaccharides from Potentilla anserina L

Introduction

Potentilla anserina (Potentilla anserina L.), also known as ginseng fruit, is a plant that can be used as both medicine and food. Potentilla anserina L. has high medical value in Chinese medicine, such as strengthening the spleen and stomach, replenishing qi and blood, and astringing hemostasis.

Methods

In this study, polysaccharides of Potentilla anserina L. were extracted from the root using an enzyme-assisted extraction method. According to the principle of Box-Behnken design, response surface methodology was designed to optimize the extraction conditions. Fourier transform infrared spectroscopy and scanning electron microscopy were used to investigate the structure and appearance of Potentilla anserina L. polysaccharides. The monosaccharide composition of Potentilla anserina L. polysaccharides was determined using high-performance liquid chromatography. The antioxidant activities were also studied.

Results

Under the optimal extraction conditions (the ratio of solid to liquid, 1:15; ratio of cellulase to pectinase, 1:2; extraction pH, 8.0; enzyme reaction temperature, 60°C), the extraction yield of Potentilla anserina L. polysaccharides was 19.80 ± 0.01%, equal to the model prediction value 19.84%. The data of Fourier transform infrared spectrum, scanning electron microscopy, and high-performance liquid chromatography showed that the Potentilla anserina L. polysaccharide was a kind of α-pyran polysaccharide, mainly consisting of galactose, glucose, rhamnose, and arabinose. The antioxidant results showed that Potentilla anserina L. polysaccharides had a strong hydroxyl radical scavenging ability (IC₅₀ = 0.367 mg/mL), superoxide anion scavenging ability (IC₅₀ = 45.017 mg/mL), and a certain degree of total reducing ability.

Discussion

Enzyme-assisted extraction is an efficient method to extract Potentilla anserina L. polysaccharides. The Potentilla anserina L. polysaccharides could have potential use in functional foods as a natural antioxidant.

PDE4 Inhibitors: Profiling Hits through the Multitude of Structural Classes

Cyclic nucleotide phosphodiesterases 4 (PDE4) are a family of enzymes which specifically promote the hydrolysis and degradation of cAMP. The inhibition of PDE4 enzymes has been widely investigated as a possible alternative strategy for the treatment of a variety of respiratory diseases, including chronic obstructive pulmonary disease and asthma, as well as psoriasis and other autoimmune disorders. In this context, the identification of new molecules as PDE4 inhibitors continues to be an active field of investigation within drug discovery. This review summarizes the medicinal chemistry journey in the design and development of effective PDE4 inhibitors, analyzed through chemical classes and taking into consideration structural aspects and binding properties, as well as inhibitory efficacy, PDE4 selectivity and the potential as therapeutic agents.

A structural analysis of physician agency and pharmaceutical demand

This paper examines the significance of physician agency in medical providers' prescription choices. Physician agency is considered as medical providers' responses to the price and markup percentage of prescription drugs. Their preferences are allowed to be heterogeneous using a random coefficient logit model. Using a sample of anti-diabetic prescriptions with metformin from a population-based database in Taiwan, empirical results reveal that physician owners, privately-owned medical providers, small medical providers and the medical providers facing less competition are more likely to prescribe drugs with higher profit margins. The aggregate pharmaceutical demand is also found to increase with the markup, which is allowed to be endogenous in the estimation. Price elasticity estimates suggest medical providers are quite responsive to pharmaceutical price changes in Taiwan. Counterfactual analysis reveals the potential impact of physician agency is economically significant. Removing markups and lowering pharmaceutical prices are found to be more welfare enhancing than restricting physicians' dispensing services.

Comprehensive bioinformatics analysis of structural and functional consequences of deleterious missense mutations in the human QDPR gene

Quinonoid dihydropteridine reductase (QDPR) is an enzyme that regulates tetrahydrobiopterin (BH4), a cofactor for enzymes involved in neurotransmitter synthesis and blood pressure regulation. Reduced QDPR activity can cause dihydrobiopterin (BH2) accumulation and BH4 depletion, leading to impaired neurotransmitter synthesis, oxidative stress, and increased risk of Parkinson's disease. A total of 10,236 SNPs were identified in the QDPR gene, with 217 being missense SNPs. Over 18 different sequence-based and structure-based tools were employed to assess the protein's biological activity, with several computational tools identifying deleterious SNPs. Additionally, the article provides detailed information about the QDPR gene and protein structure and conservation analysis. The results showed that 10 mutations were harmful and linked to brain and central nervous system disorders, and were predicted to be oncogenic by Dr. Cancer and CScape. Following conservation analysis, the HOPE server was used to analyse the effect of six selected mutations (L14P, V15G, G23S, V54G, M107K, G151S) on the protein structure. Overall, the study provides insights into the biological and functional impact of nsSNPs on QDPR activity and the potential induced pathogenicity and oncogenicity. In the future, research can be conducted to systematically evaluate QDPR gene variation through clinical studies, investigate mutation prevalence across different geographical regions, and validate computational results with conclusive experiments.Communicated by Ramaswamy H. Sarma.

Structural characterization and antioxidant activity of pectic polysaccharides from Veronica peregrina L

Background

Pectins are a class of acidic polysaccharides with complex structures. Different pectin molecules are composed of different domains, which have an important impact on their biological activity.

Objective

This study aimed to determine the structural features and the antioxidant activities of the pectic polysaccharides isolated from Veronica peregrina L.

Methods

The polysaccharide was isolated from Veronica peregrina L by water extraction and fractionated by ion exchange chromatography and gel permeation chromatography. The structure features of the pectic polysaccharides were determined by Fourier transforminfrared spectroscopy (FT-IR) and Nuclear magnetic resonance (NMR). The antioxidant activities was evaluated by the DPPH, OH and ABTS radical scavenging ability.

Results

WVPP-A2b and WVPP-A3b, with molecular weights of 48.7 × 10⁴ and 77.6 × 10⁴  kDa, respectively, contained homogalacturonan (HG), rhamnogalacturonan I (RG-I), and rhamnogalacturonan II (RG-II) domains with a mass ratio of 2.08:2.64:1.00 and 3.87:4.65:1:00, respectively. The RG-I domain contained an arabinogalactan II backbone and arabinans consisting of t-Araf, (1→5)-α-Araf, and (1→3,5)-α-Araf. WVPP-A3b also contained short chains consisting of the [t-Araf-(1→5)-α-Araf-(1→] structural unit. WVPP-A3b showed stronger ability to scavenge DPPH, hydroxyl, and ABTS radicals, which was potentially associated with its high content of galacturonic acid and presence of the HG domain.

Conclusion

The results provide information for enhancing knowledge of the structureactivity relationship of pectic polysaccharides from V. peregrina and their potential application in the healthcare food field.

Structural Analysis and Identity Confirmation of Anthocyanins in Brassica oleracea Extracts by Direct Injection Ion Mobility-Mass Spectrometry

Anthocyanins are a subclass of plant-derived flavonoids that demonstrate immense structural heterogeneity which is challenging to capture in complex extracts by traditional liquid chromatography-mass spectrometry (MS)-based approaches. Here, we investigate direct injection ion mobility-MS as a rapid analytical tool to characterize anthocyanin structural features in red cabbage (Brassica oleracea) extracts. Within a 1.5 min sample run time, we observe localization of structurally similar anthocyanins and their isobars into discrete drift time regions based upon their degree of chemical modifications. Furthermore, drift time-aligned fragmentation enables simultaneous collection of MS, MS/MS, and collisional cross-section data for individual anthocyanin species down to a low picomole scale to generate structural identifiers for rapid identity confirmation. We finally identify anthocyanins in three other Brassica oleracea extracts based on red cabbage anthocyanin identifiers to demonstrate our high-throughput approach. Direct injection ion mobility-MS therefore provides wholistic structural information on structurally similar, and even isobaric, anthocyanins in complex plant extracts, which can inform the nutritional value of a plant and bolster drug discovery pipelines.

Molecular characterization and re-interpretation of HNF1A variants identified in Indian MODY subjects towards precision medicine

Background

HNF1A is an essential component of the transcription factor network that controls pancreatic β-cell differentiation, maintenance, and glucose stimulated insulin secretion (GSIS). A continuum of protein malfunction is caused by variations in the HNF1A gene, from severe loss-of-function (LOF) variants that cause the highly penetrant Maturity Onset Diabetes of the Young (MODY) to milder LOF variants that are far less penetrant but impart a population-wide risk of type 2 diabetes that is up to five times higher. Before classifying and reporting the discovered variations as relevant in clinical diagnosis, a critical review is required. Functional investigations offer substantial support for classifying a variant as pathogenic, or otherwise as advised by the American College of Medical Genetics and Genomics (ACMG) and the Association for Molecular Pathology (AMP) ACMG/AMP criteria for variant interpretation.

Objective

To determine the molecular basis for the variations in the HNF1A gene found in patients with monogenic diabetes in India.

Methods

We performed functional protein analyses such as transactivation, protein expression, DNA binding, nuclear localization, and glucose stimulated insulin secretion (GSIS) assay, along with structural prediction analysis for 14 HNF1A variants found in 20 patients with monogenic diabetes.

Results

Of the 14 variants, 4 (28.6%) were interpreted as pathogenic, 6 (42.8%) as likely pathogenic, 3 (21.4%) as variants of uncertain significance, and 1 (7.14%) as benign. Patients harboring the pathogenic/likely pathogenic variants were able to successfully switch from insulin to sulfonylureas (SU) making these variants clinically actionable.

Conclusion

Our findings are the first to show the need of using additive scores during molecular characterization for accurate pathogenicity evaluations of HNF1A variants in precision medicine.

Genome-wide characterization of plant CTP:phosphocholine cytidylyltransferases through evolutionary, biochemical and structural analyses

Phosphatidylcholine has essential functions in many eukaryotic cells, and its de novo biosynthesis is rate-limited by cytidine triphosphate:phosphocholine cytidylyltransferase (CCT). Although the biological and biochemical functions of CCT have been reported in mammals and several plants, this key enzyme has yet to be examined at a genome-wide level. As such, certain fundamental questions remain unanswered, including the evolutionary history, genetic and functional relationships, and structural variations among CCTs in the green lineage. In the current study, in-depth phylogenetic analysis, as well as the conservation and diversification in CCT gene structure and motif patterns, indicated that CCTs exist broadly in chlorophytes, bryophytes, lycophytes, monilophytes, gymnosperms, early-diverging angiosperms, monocots, and eudicots, and form eight relatively conserved clades. To further explore the potential function of selection pressure, we conducted extensive selection pressure analysis with a representative CCT gene, CCT1 from the model plant Arabidopsis thaliana (AthCCT1), and identified two positive selection sites, L59 and Q156. Site-directed mutagenesis and in vitro enzyme assays demonstrated that these positively selected sites were indeed important for the activity and substrate affinity of AthCCT1, and subsequent 3D structure analyses explained the potential biochemical mechanism. Taken together, our results unraveled the evolution and diversity of CCTs in the green lineage, as well as their association with the enzyme's biochemical and structural properties, and expanded our understanding of this important enzyme at the genome-wide level.

Research Progress on Extraction, Isolation, Structural Analysis and Biological Activity of Polysaccharides from Panax Genus

The panax genus is a widely used medicinal plant with good biological activity. As one of the main active components of the Panax genus, polysaccharides have various pharmacological effects. This review summarizes the latest research reports on ginseng, American ginseng, and Panax notoginseng polysaccharides and compares the differences in extraction, isolation and purification, structural characteristics, and biological activities. The current research mainly focuses on ginseng polysaccharides, and the process of extraction, isolation, and structure analysis of each polysaccharide is roughly the same. Modern pharmacological studies have shown that these polysaccharides have antioxidants, antitumor, immunomodulatory, antidiabetic, intestinal protection, skin repair, and other biological activities. This review provides new insights into the differences between the three kinds of ginseng polysaccharides which will help to further study the medicinal value of ginseng in traditional Chinese medicine.

Structural Analysis and Characterization of 4-F-α-PVP Analog 4-F-3-Methyl-α- PVP Hydrochloride

OBJECTIVES

To identify 1-(4-fluorophenyl)-2-(1-pyrrolidinyl) pentan-1-one (4-F-α-PVP) analog 1-(4-fluoro-3-methyl phenyl)-2-(1-pyrrolidinyl) pentan-1-one (4-F-3-Methyl-α-PVP) hydrochloride without reference substance.

METHODS

The direct-injection electron ionization-mass spectrometry (EI-MS), GC-MS, electrospray ionization-high resolution mass spectrometry (ESI-HRMS), ultra-high performance liquid chromatography-high resolution tandem mass spectrometry (UPLC-HRMS/MS), nuclear magnetic resonance (NMR), ion chromatography and Fourier transform infrared spectroscopy (FTIR) were integrated utilized to achieve the structural analysis and characterization of the unknown compound in the sample, and the cleavage mechanism of the fragment ions was deduced by EI-MS and UPLC-HRMS/MS.

RESULTS

By analyzing the direct-injection EI-MS, GC-MS, ESI-HRMS and UPLC-HRMS/MS of the compound in the samples, it was concluded that the unknown compound was a structural analog of 4-F-α-PVP, possibly with one more methyl group in the benzene ring. According to the analysis results of ¹H-NMR and ¹³C-NMR, it was further proved that the methyl group is located at the 3-position of the benzene ring. Since the actual number of hydrogen in ¹H-NMR analysis was one more than 4-F-3-Methyl-α-PVP neutral molecule, it was inferred that the compound existed in the form of salt. Ion chromatography analysis results showed that the compound contained chlorine anion (content 11.14%-11.16%), with the structural analysis of main functional group information by FTIR, the unknown compound was finally determined to be 4-F-3-Methyl-α-PVP hydrochloride.

CONCLUSIONS

A comprehensive method using EI-MS, GC-MS, ESI-HRMS, UPLC-HRMS/MS, NMR, ion chromatography and FTIR to identify 4-F-3-Methyl-α-PVP hydrochloride in samples is established, which will be helpful for the forensic science laboratory to identify this compound or other analog compounds.

Phytoceramides from the Marine Sponge Monanchora clathrata: Structural Analysis and Cytoprotective Effects

In our research on sphingolipids from marine invertebrates, a mixture of phytoceramides was isolated from the sponge Monanchora clathrata (Western Australia). Total ceramide, ceramide molecular species (obtained by RP-HPLC, high-performance liquid chromatography on reversed-phase column) and their sphingoid/fatty acid components were analyzed by NMR (nuclear magnetic resonance) spectroscopy and mass spectrometry. Sixteen new (1b, 3a, 3c, 3d, 3f, 3g, 5c, 5d, 5f, 5g, 6b-g) and twelve known (2b, 2e, 2f, 3b, 3e, 4a-c, 4e, 4f, 5b, 5e) compounds were shown to contain phytosphingosine-type backbones i-t17:0 (1), n-t17:0 (2), i-t18:0 (3), n-t18:0 (4), i-t19:0 (5), or ai-t19:0 (6), N-acylated with saturated (2R)-2-hydroxy C21 (a), C22 (b), C23 (c), i-C23 (d), C24 (e), C25 (f), or C26 (g) acids. The used combination of the instrumental and chemical methods permitted the more detailed investigation of the sponge ceramides than previously reported. It was found that the cytotoxic effect of crambescidin 359 (alkaloid from M. clathrata) and cisplatin decreased after pre-incubation of MDA-MB-231 and HL-60 cells with the investigated phytoceramides. In an in vitro paraquat model of Parkinson's disease, the phytoceramides decreased the neurodegenerative effect and ROS (reactive oxygen species) formation induced by paraquat in neuroblastoma cells. In general, the preliminary treatment (for 24 or 48 h) of the cells with the phytoceramides of M. clathrata was necessary for their cytoprotective functions, otherwise the additive damaging effect of these sphingolipids and cytotoxic compounds (crambescidin 359, cisplatin or paraquat) was observed.

Impact of Ti and Zn Dual-Substitution in P2 Type Na2/3 Ni1/3 Mn2/3 O2 on Ni-Mn and Na-Vacancy Ordering and Electrochemical Properties

High-entropy layered oxide materials containing various metals that exhibit smooth voltage curves and excellent electrochemical performances have attracted attention in the development of positive electrode materials for sodium-ion batteries. However, a smooth voltage curve can be obtained by suppression of the Na⁺ -vacancy ordering, and therefore, transition metal slabs do not need to be more multi-element than necessary. Here, the Na⁺ -vacancy ordering is found to be disturbed by dual substitution of Ti^IV for Mn^IV and Zn^II for Ni^II in P2-Na_2/3 [Ni_1/3 Mn_2/3 ]O₂ . Dual-substituted Na_2/3 [Ni_1/4 Mn_1/2 Ti_1/6 Zn_1/12 ]O₂ demonstrates almost non-step voltage curves with a reversible capacity of 114 mAh g^-1 and less structural changes with a high crystalline structure maintained during charging and discharging. Synchrotron X-ray, neutron, and electron diffraction measurements reveal that dual-substitution with Ti^IV and Zn^II uniquely promotes in-plane Ni^II -Mn^IV ordering, which is quite different from the disordered mixing in conventional multiple metal substitution.

Computational Procedure for Analysis of Crystallites in Polycrystalline Solids of Quasilinear Molecules

In the current work, a comprehensive procedure for structural analysis of quasilinear organic molecules arranged in a polycrystalline sample generated by molecular dynamics is developed. A linear alkane, hexadecane, is used as a test case because of its interesting behavior upon cooling. Instead of a direct transition from isotropic liquid to the solid crystalline phase, this compound forms first a short-lived intermediate state known as a "rotator phase". The rotator phase and the crystalline one are distinguished by a set of structural parameters. We propose a robust methodology to evaluate the type of ordered phase obtained after a liquid-to-solid phase transition in a polycrystalline assembly. The analysis starts with the identification and separation of the individual crystallites. Then, the eigenplane of each of them is fit and the tilt angle of the molecules relative to it is computed. The average area per molecule and the distance to the nearest neighbors are estimated by a 2D Voronoi tessellation. The orientation of the molecules with respect to each other is quantified by visualization of the second molecular principal axis. The suggested procedure may be applied to different quasilinear organic compounds in the solid state and to various data compiled in a trajectory.

Glycomics by ion mobility tandem mass spectrometry of chondroitin sulfate disaccharide domain in biglycan

Biglycan (BGN), a small leucine-rich repeat proteoglycan, is involved in a variety of pathological processes including malignant transformation, for which the upregulation of BGN was found related to cancer cell invasiveness. Because the functions of BGN are mediated by its chondroitin/dermatan sulfate (CS/DS) chains through the sulfates, the determination of CS/DS structure and sulfation pattern is of major importance. In this study, we have implemented an advanced glycomics method based on ion mobility separation (IMS) mass spectrometry (MS) and tandem MS (MS/MS) to characterize the CS disaccharide domains in BGN. The high separation efficiency and sensitivity of this technique allowed the discrimination of five distinct CS disaccharide motifs, of which four irregulated in their sulfation pattern. For the first time, trisulfated unsaturated and bisulfated saturated disaccharides were found in BGN, the latter species documenting the non-reducing end of the chains. The structural investigation by IMS MS/MS disclosed that in one or both of the CS/DS chains, the non-reducing end is 3-O-sulfated GlcA in a rather rare bisulfated motif having the structure 3-O-sulfated GlcA-4-O-sulfated GalNAc. Considering the role played by BGN in cancer cell spreading, the influence on this process of the newly identified sequences will be investigated in the future.

Properties and Microstructure Evaluation in NiAl-xWC (x = 0 - 90 wt.%) Intermetallic-Based Composites Prepared by Mechanical Alloying

In this work, NiAl-xWC (x = 0 - 90 wt.% WC) intermetallic-based composites were successfully synthesized by mechanical alloying (MA) and a hot-pressing approach. As initial powders, a mixture of nickel, aluminum and tungsten carbide was used. The phase changes in analyzed systems after mechanical alloying and hot pressing were evaluated by an X-ray diffraction method. Scanning electron microscopy and hardness test examination were used for evaluating microstructure and properties for all fabricated systems from the initial powder to the final sinter stage. The basic sinter properties were evaluated to estimate their relative densities. Synthesized and fabricated NiAl-xWC composites showed an interesting relationship between the structure of the constituting phases, analyzed by planimetric and structural methods and sintering temperature. The analyzed relationship proves that the structural order reconstructed by sintering strongly depends on the initial formulation and its decomposition after MA processing. The results confirm that it is possible to obtain an intermetallic NiAl phase after 10 h of MA. For processed powder mixtures, the results showed that increased WC content intensifies fragmentation and structural disintegration. The final structure of the sinters fabricated in lower (800 °C) and higher temperature regimes (1100 °C), consisted of recrystallized NiAl and WC phases. The macro hardness of sinters obtained at 1100 °C increased from 409 HV (NiAl) to 1800 HV (NiAl + 90% WC). Obtained results reveal a new applicable perspective in the field of intermetallic-based composites and remain highly anticipated for possible application in severe-wear or high-temperature conditions.

Ganglioside analysis in body fluids by liquid-phase separation techniques hyphenated to mass spectrometry

The expression of gangliosides in central nervous system is a few times higher than in the extraneural tissue, a characteristic highlighting their major role at this level. Although in very low amounts, gangliosides are ubiquitously distributed in body fluids too, where, depending on many factors, including pathological states, their composition fluctuates, thus having diagnostic value. Ganglioside investigation in biological fluids, which, except for cerebrospinal fluid (CSF), may be sampled noninvasively, was for years impeded by the limited sensitivity of the analytical instrumentation available in glycomics. However, because the last decade has witnessed significant developments in biological mass spectrometry (MS) and the hyphenated separation techniques, marked by a major increase in sensitivity, reproducibility, and data reliability, ganglioside research started to be focused on biofluid analysis by separation techniques coupled to MS. In this context, our review presents the achievements in this emerging field of gangliosidomics, with a particular emphasis on modern liquid chromatography (LC), thin-layer chromatography, hydrophilic interaction LC, and ion mobility separation coupled to high-performance MS, as well as the results generated by these systems and allied experimental procedures in profiling and structural analysis of gangliosides in healthy or diseased body fluids, such as CSF, plasma/serum, and milk.

Distinct in vitro and in vivo neutralization profiles of monoclonal antibodies elicited by the receptor binding domain of the ancestral SARS-CoV-2

Broadly neutralizing antibodies against severe acute respiratory syndrome coronavirus 2 (SARS-CoV-2) variants are sought to curb coronavirus disease 2019 (COVID-19) infections. Here we produced and characterized a set of mouse monoclonal antibodies (mAbs) specific for the ancestral SARS-CoV-2 receptor binding domain (RBD). Two of them, 17A7 and 17B10, were highly potent in microneutralization assay with 50% inhibitory concentration (IC50 ) ≤135 ng/mL against infectious SARS-CoV-2 variants, including G614, Alpha, Beta, Gamma, Delta, Epsilon, Zeta, Kappa, Lambda, B.1.1.298, B.1.222, B.1.5, and R.1. Both mAbs (especially 17A7) also exhibited strong in vivo efficacy in protecting K18-hACE2 transgenic mice from the lethal infection with G614, Alpha, Beta, Gamma, and Delta viruses. Structural analysis indicated that 17A7 and 17B10 target the tip of the receptor binding motif in the RBD-up conformation. A third RBD-reactive mAb (3A6) although escaped by Beta and Gamma, was highly effective in cross-neutralizing Delta and Omicron BA.1 variants in vitro and in vivo. In competition experiments, antibodies targeting epitopes similar to these 3 mAbs were rarely enriched in human COVID-19 convalescent sera or postvaccination sera. These results are helpful to inform new antibody/vaccine design and these mAbs can be useful tools for characterizing SARS-CoV-2 variants and elicited antibody responses.

In Vitro Neurotrophic Properties and Structural Characterization of a New Polysaccharide LTC-1 from Pyrola corbieri Levl (Luticao)

Pyrola corbieri Levl has been used to strengthen bones and nourish the kidney (the kidney governs the bone and is beneficial to the brain) by the local Miao people in China. However, the functional components and neurotrophic activity have not been reported. A new acidic homogeneous heteropolysaccharide named LTC-1 was obtained and characterized by periodate oxidation, Smith degradation, partial acid hydrolysis, GC-MS spectrometry, methylation analysis, and Fourier transform infrared spectroscopy, and its molecular weight was 3239 Da. The content of mannuronic acid (Man A) in LTC-1 was 46%, and the neutral sugar was composed of L-rhamnose (L-Rha), L-arabinose (L-Ara), D-xylose (D-Xyl), D-mannose (D-Man), D-glucose (D-Glc) and D-galactose (D-Gal) with a molar ratio of 1.00:3.63:0.86:1.30:6.97:1.30. The main chain of LTC-1 was composed of Glc, Gal, Man, Man A and the branched chain Ara, Glc, Gal. The terminal residues were composed of Glc and Gal. The main chain and branched chains were linked by (1→5)-linked-Ara, (1→3)-linked-Glc, (1→4)-linked-Glc, (1→6)-linked-Glc, (1→3)-linked-Gal, (1→6)-linked-Gal, (1→3, 6)-linked-Man and ManA. Meanwhile, neurotrophic activity was evaluated through PC12 and primary hippocampal neuronal cell models. LTC-1 exhibited neurotrophic activity in a concentration-dependent manner, which significantly induced the differentiation of PC12 cells, promoted the neurite outgrowth of PC12 cells, enhanced the formation of the web architecture of dendrites, and increased the density of dendritic spines in hippocampal neurons and the expression of PSD-95. These results displayed significant neurotrophic factor-like activity of LTC-1, which suggests that LTC-1 is a potential treatment option for neurodegenerative diseases.

GO-Enabled Bacterial Cellulose Membranes by Multistep, In Situ Loading: Effect of Bacterial Strain and Loading Pattern on Nanocomposite Properties

This paper presents the results of research on the preparation and properties of GO/BC nanocomposite from bacterial cellulose (BC) modified with graphene oxide (GO) using the in situ method. Two bacterial strains were used for the biosynthesis of the BC: Komagataeibacter intermedius LMG 18909 and Komagataeibacter sucrofermentans LMG 18788. A simple biosynthesis method was developed, where GO water dispersion was added to reinforced acetic acid-ethanol (RAE) medium at concentrations of 10 ppm, 25 ppm, and 50 ppm at 24 h and 48 h intervals. As a result, a GO/BC nanocomposite membrane was obtained, characterized by tensile strength greater by 150% as compared with the pure BC (̴ 50 MPa) and lower volume resistivity of ~4 ∙ 10⁹ Ω × cm. Moreover, GO addition increases membrane thickness up to ~10% and affects higher mass production, especially with low GO concentration. All of this may indicate the possibility of using GO/BC membranes in fuel cell applications.

"You gotta give them hope": A structural psychobiography of Harvey Milk (1930-1978)

OBJECTIVE

In this psychobiographical study, we examined the life and times of social change agent Harvey Milk, one of the first openly gay public officials in the United States. Milk is remembered as a gay hero who fought for the rights of marginalized people, often by invoking the importance of hope. Milk was assassinated less than 1 year after his election.

METHOD

We adopt a structural psychobiographical approach, foregrounding social, cultural, political, and historical forces that intersect with personal factors to explain Milk's ascension to the status of social change agent.

RESULTS

This psychobiography tells the story of a man not destined to become a social change agent but who became one anyway because of shifting tides in the political climate of San Francisco in the 1970s, because of a series of catalytic events that started him down this path, because of a history of persecution as a gay Jew, and because of his enduring need for a stage upon which he could express his generative concern.

CONCLUSIONS

Our analysis raises questions about the story that "belongs" to the agent of social change, and the story that "belongs" to the rest of us, as we remember him.

Biallelic Variants in TULP1 Are Associated with Heterogeneous Phenotypes of Retinal Dystrophy

Biallelic pathogenic variants in TULP1 are mostly associated with severe rod-driven inherited retinal degeneration. In this study, we analyzed clinical heterogeneity in 17 patients and characterized the underlying biallelic variants in TULP1. All patients underwent thorough ophthalmological examinations. Minigene assays and structural analyses were performed to assess the consequences of splice variants and missense variants. Three patients were diagnosed with Leber congenital amaurosis, nine with early onset retinitis pigmentosa, two with retinitis pigmentosa with an onset in adulthood, one with cone dystrophy, and two with cone-rod dystrophy. Seventeen different alleles were identified, namely eight missense variants, six nonsense variants, one in-frame deletion variant, and two splice site variants. For the latter two, minigene assays revealed aberrant transcripts containing frameshifts and premature termination codons. Structural analysis and molecular modeling suggested different degrees of structural destabilization for the missense variants. In conclusion, we report the largest cohort of patients with TULP1-associated IRD published to date. Most of the patients exhibited rod-driven disease, yet a fraction of the patients exhibited cone-driven disease. Our data support the hypothesis that TULP1 variants do not fold properly and thus trigger unfolded protein response, resulting in photoreceptor death.

Light-Transmitting Lithium Aluminosilicate Glass-Ceramics with Excellent Mechanical Properties Based on Cluster Model Design

In this study, for the first time, a cluster-plus-glue-atom model was used to optimize the composition of lithium aluminosilicate glass-ceramics. Basic glass in glass-ceramics was considered to be a 16-unit combination of three-valence {M₂O₃} and one-valence {Li₂O} units. By adjusting the ratio of {M₂O₃} and {Li₂O}, the composition of basic glass could be optimized. After optimization, the average cation valence of the base glass was increased to 2.875. After heat treatment of the optimized base glass, it is found that the crystal size, proportion, and crystallinity changed obviously compared with that before optimization. The main crystalline phases of all the lithium aluminosilicate glass-ceramics prepared in this work were Li₂Si₂O₅ and LiAlSi₄O_10. All optimized glass-ceramics had an obvious improvement in the crystallinity, with one of the largest having a crystallinity of over 90%. Furthermore, its bending strength was 159 MPa, the microhardness was 967 Hv, and the visible light transmission rate exceeded 90%. Compared with the widely used touch panel cover glass, the optical properties were close, and the mechanical properties were greatly improved. Due to its excellent performance, it could be used in microelectronics, aerospace, deep-sea exploration, and other fields.