Vaginal homeostasis features of Vulvovaginal Candidiasis through vaginal metabolic profiling.

Vulvovaginal candidiasis (VVC) is an inflammatory disease primarily infected by Candida albicans. The condition has good short-term treatment effects, high recurrence, and seriously affects the quality of life of women. Metabolomics has been applied to research a variety of inflammatory diseases. In the present study, the vaginal metabolic profiles of VVC patients and healthy populations (Cnotrol (CTL)) were explored by a non-targeted metabolomics approach. In total, 211 differential metabolites were identified, with the VVC group having 128 over-expressed and 83 under-expressed metabolites compared with healthy individuals. Functional analysis showed that these metabolites were mainly involved in amino acid metabolism and lipid metabolism. In addition, network software analysis indicated that the differential metabolites were associated with mitogen-activated protein kinase (MAPK) signaling and NF-κB signaling. Further molecular docking suggested that linoleic acid can bind to the acyl-CoA synthetase 1 (ACSL1) protein, which has been shown to be associated with multiple inflammatory diseases and is an upstream regulator of the MAPK and NF-κB signaling pathways that mediate inflammation. Therefore, our preliminary analysis results suggest that VVC has a unique metabolic profile. Linoleic acid, a significantly elevated unsaturated fatty acid in the VVC group, may promote VVC development through the ACSL1/MAPK and ACSL1/NF-κB signaling pathways. This study's findings contribute to further exploring the mechanism of VVC infection and providing new perspectives for the treatment of Candida albicans vaginal infection.

Candida albicans is the main pathogen that causes VVC. Through non-targeted metabolomics, this study shows that VVC caused by C. albicans has unique vaginal metabolic characteristics, the changed metabolites might provide useful diagnostic and therapeutic methods for VVC.

Fish complement C4 gene evolution and gene/protein regulatory network analyses and simulated stereo conformation of C4-MASP-2 protein complex.

Complement C4 is a central protein by acting as pivotal molecule in the activation of the complement system. More than a decade ago, C4 gene duplication had been found in several species including fish, revealing the evolutionary origin of C4 gene. However, the evolutionary pattern and systematic function of C4 are still limited. In this study, C4 D and H types in different species groups were completely diverged. The codon usage of C4 H type in higher vertebrates were much closer to their own genome environment, in contrast to lower vertebrates, suggesting that the evolution may provide the dynamic for homogeneous codon usage between specific gene and genome. Multiple C4 sequence alignment showed that the sequences were conserved among different species. However, sequence similarity was obviously different between species C4 D and H type. Negative selection pressure was found on C4 gene evolution and it may be one of the possible reasons for the sequence broad similarity and conservation among interspecies. Proteins from C4 protein-protein interaction (PPI) network were enriched in more hematopoiesis, infections, diseases and immune-related pathways in human than zebrafish. The result suggested that the functional complexities of C4 isotypes are distinct in species from different evolutionary positions. The simulated C4 protein structures between human and grass carp shared structural similarity and the stereo structures of grass carp C4-MASP-2 protein complexes were further simulated according to a study of human. These results suggested that the interaction between C4 and MASP-2 proteins may also exist in grass carp. Our results can provide an insight for the evolutionary process of C4 and better understanding to the potential mechanism of interaction between C4 and MASP-2 in fish species.

Structural characteristics and gelling properties of citrus pectins after chemical and enzymatic modifications: Conformation plays a vital role in Ca2+-induced gelation.

Due to the excellent health benefits of rhamnogalacturonan I (RG-I)-enriched pectin, there has been increasing research interest in its gelling properties. To elucidate its structure-gelation relationship, chemical modifications were used to obtain RG-I-enriched pectin (P11). Then, enzymatic modification was performed to obtain debranched pectins GP11 and AP11, respectively. The effects of RG-I side chains on structural characteristics (especially spatial conformation) and gelling properties were investigated. Among the low-methoxylated pectins (LMPs), AP11, with a loose conformation (Dmax 52 nm) showed the poorest gelling, followed by GP11. In addition to primary structure, spatial conformation (Dmax and Rg) also showed strong correlations (r2 > 0.8) with gelation. We speculate that compact conformation may shorten distance between pectin chains and reduces steric hindrance, contributing to formation of strong gel network. This is particularly important in LMPs with abundant side chains. The results provide novel insights into relationship between spatial conformation and gelling properties of RG-I-enriched pectin.

Sequence and structure analyses of lytic polysaccharide monooxygenases mined from metagenomic DNA of humus samples around white-rot fungi in Cuc Phuong tropical forest, Vietnam.

Background: White-rot fungi and bacteria communities are unique ecosystems with different types of symbiotic interactions occurring during wood decomposition, such as cooperation, mutualism, nutritional competition, and antagonism. The role of chitin-active lytic polysaccharide monooxygenases (LPMOs) in these symbiotic interactions is the subject of this study. Method: In this study, bioinformatics tools were used to analyze the sequence and structure of putative LPMOs mined by hidden Markov model (HMM) profiles from the bacterial metagenomic DNA database of collected humus samples around white-rot fungi in Cuc Phuong primary forest, Vietnam. Two genes encoding putative LPMOs were expressed in E. coli and purified for enzyme activity assay. Result: Thirty-one full-length proteins annotated as putative LPMOs according to HMM profiles were confirmed by amino acid sequence comparison. The comparison results showed that although the amino acid sequences of the proteins were very different, they shared nine conserved amino acids, including two histidine and one phenylalanine that characterize the H1-Hx-Yz motif of the active site of bacterial LPMOs. Structural analysis of these proteins revealed that they are multidomain proteins with different functions. Prediction of the catalytic domain 3-D structure of these putative LPMOs using Alphafold2 showed that their spatial structures were very similar in shape, although their protein sequences were very different. The results of testing the activity of proteins GL0247266 and GL0183513 show that they are chitin-active LPMOs. Prediction of the 3-D structures of these two LPMOs using Alphafold2 showed that GL0247266 had five functional domains, while GL0183513 had four functional domains, two of which that were similar to the GbpA_2 and GbpA_3 domains of protein GbpA of Vibrio cholerae bacteria. The GbpA_2 - GbpA_3 complex was also detected in 11 other proteins. Based on the structural characteristics of functional domains, it is possible to hypothesize the role of chitin-active GbpA-like LPMOs in the relationship between fungal and bacterial communities coexisting on decomposing trees in primary forests.

Mechanism of Targeted Regulation of Ovalbumin Epitopes by Pulsed Electric Field-Assisted Alcalase Treatment.

Egg is one of the eight major food allergens, and ovalbumin (OVA) is the most abundant allergenic protein in eggs. In this study, the effects of pulsed electric field (PEF)-assisted Alcalase hydrolysis on the spatial conformation and potential allergenicity of OVA were studied, and the mechanism of its inhibiting allergic reactions effect was revealed. PEF-assisted Alcalase hydrolysis increased the degree of hydrolysis, surface hydrophobicity, and free sulfhydryl group content. Moreover, the reduction in the α-helix content, fluorescence intensity, and disulfide bond content suggested that PEF promoted the OVA hydrolysis by Alcalase. Additionally, enzyme-linked immunosorbent assay data indicated that PEF-assisted Alcalase hydrolysis hindered OVA binding to immunoglobulins E and G1. Finally, based on bioinformatics combined with mass spectrometry, PEF-assisted Alcalase reduced OVA-induced allergic reactions by destroying epitopes in OVA. Overall, PEF technology further destroyed the epitopes of allergens by targeting the binding sites of substrates and enzymes to improve the affinity of enzymes and substrates, reducing allergic reactions.

Pulsed Electric Field-Assisted Alcalase Treatment Reduces the Allergenicity and Eliminates the Antigenic Epitopes of Ovomucoid.

Physically assisted chemical modifications can effectively reduce the allergenicity of ovomucoid (OVM). However, only a few studies have used pulsed electric field (PEF)-assisted alcalase hydrolysis to reduce the allergenicity of OVM. Herein, we investigated the effect of PEF-assisted alcalase treatment on the spatial conformation, allergenicity, and antigenic epitopes of OVM based on multispectroscopic analyses, bioinformatics, and mass spectrometry. The results showed that PEF-assisted alcalase treatment promoted the hydrolysis of OVM; moreover, the α-helix content and surface hydrophobicity of OVM significantly decreased, which disordered its spatial conformation and weakened its intermolecular interactions. Additionally, enzyme-linked immunosorbent assay (ELISA) results showed that the PEF-assisted alcalase treatment significantly reduced the binding levels of IgE and IgG1, which were 47.66 and 36.41%, respectively. Finally, eight epitopes of OVM were obtained by immunoinformatic tools. Nano-high performance liquid chromatography coupled to tandem mass spectrometry (nano-HPLC MS/MS) results showed that the hydrolysate of OVM and alcalase (HOVM) had nine more peptide-containing epitopes than the hydrolysate of PEF-treated OVM and PEF-treated alcalase (HOVM-PP'), indicating that PEF could promote the elimination of linear epitopes in OVM, thereby reducing OVM allergenicity.

Managing Interfacial Defects and Carriers by Synergistic Modulation of Functional Groups and Spatial Conformation for High-Performance Perovskite Photovoltaics Based on Vacuum Flash Method.

Interfacial nonradiative recombination loss is a huge barrier to advance the photovoltaic performance. Here, one effective interfacial defect and carrier dynamics management strategy by synergistic modulation of functional groups and spatial conformation of ammonium salt molecules is proposed. The surface treatment with 3-ammonium propionic acid iodide (3-APAI) does not form 2D perovskite passivation layer while the propylammonium ions and 5-aminopentanoic acid hydroiodide post-treatment lead to the formation of 2D perovskite passivation layers. Due to appropriate alkyl chain length, theoretical and experimental results manifest that COOH and NH3 + groups in 3-APAI molecules can form coordination bonding with undercoordinated Pb2+ and ionic bonding and hydrogen bonding with octahedron PbI6 4- , respectively, which makes both groups be simultaneously firmly anchored on the surface of perovskite films. This will strengthen defect passivation effect and improve interfacial carrier transport and transfer. The synergistic effect of functional groups and spatial conformation confers 3-APAI better defect passivation effect than 2D perovskite layers. The 3-APAI-modified device based on vacuum flash technology achieves an alluring peak efficiency of 24.72% (certified 23.68%), which is among highly efficient devices fabricated without antisolvents. Furthermore, the encapsulated 3-APAI-modified device degrades by less than 4% after 1400 h of continuous one sun illumination.

Tracking the driving forces for the unfolding and folding of kidney bean protein isolates: Revealing mechanisms of dynamic changes in structure and function.

Tracking the dynamic changes in the structure of kidney bean protein isolate (KPI) during extreme pH-shifting can reveal the different mechanisms that drive the unfolding and refolding of the protein from a conformational perspective and elucidate the relationship between its structure and function. The secondary and tertiary structures of KPI were analyzed using multispectral techniques. The results showed that acidic-shifting affected the hydrophobic interactions of KPI molecules, whereas alkaline-shifting affected hydrogen bonding and electrostatic interactions of the molecules. Therefore, alkaline-shifting was more likely to affect KPI conformation. SEM revealed that pH-shifting transformed the sheet structure of KPI into spheres and rods; moreover, it improved the surface hydrophobicity, thermal stability, emulsification, foaming, and antioxidant properties of KPI. In summary, each pH-shifting stage disrupts a different intermolecular force, resulting in protein conformational diversity, while structural changes further affect function. Therefore, pH-shifting treatment broadens the applications scope of KPI in the food industry.

Evaluation of the structure-activity relationship between allergenicity and spatial conformation of ovalbumin treated by pulsed electric field.

The aim of the present study was to investigate the effect of pulsed electric field (PEF) treatment on ovalbumin (OVA) induced allergens and reveal potential allergy regulatory mechanisms. At 10 kV/cm, OVA-induced allergic symptoms were significantly reduced, and the capacity of OVA to bind with specific IgG1 and IgE was reduced by 10.32% and 3.61%, respectively. Furthermore, the degranulation of RBL-2H3 cells and allergen activity were also reduced by 4.63% and 22.15%, respectively. Interestingly, the α-helix content was reduced by 5.81% and the fluorescence intensity was increased by 6.90% with PEF treatment. At 10 kV/cm, water contact angle and surface hydrophobicity increased by 8.40% and 0.18%, respectively, indicating that PEF treatment increased the exposure of hydrophobic amino acid residues. PEF treatment alters the hydrogen bonding and hydrophobic interactions in the protein, which masks the binding sites of sensitized epitopes, and consequently reduces allergies.

Membrane occupation and recognition nexus (MORN) motif controls protein localization and function.

The membrane occupation and recognition nexus (MORN) motif was first defined in 2000, when it was identified in the junctophilin protein family. Dozens of studies have been published ever since, mainly focusing on the function of a given MORN motif-containing protein in parasites, plants or animal cells. Proteins with MORN motifs are not only expressed in most animal and plant cell types, but also significantly differ in their intracellular localization, suggesting that the MORN motifs may fulfill multiple physiological functions. Recent studies have found that MORN motif-containing proteins junctophilin-1/2 and MORN3 play a role in cardiac hypertrophy, skeletal muscle fiber stability and cancer. Hence, MORN motif-containing proteins may be exploited to develop improved treatments for various pathological conditions, such as cardiovascular diseases. Here, we review current research on MORN motif-containing proteins in different organisms and provide both ideas and approaches for follow-up exploration of their functions and applications.

The evolutionary analysis of complement component C5 and the gene co-expression network and putative interaction between C5a and C5a anaphylatoxin receptor (C5AR/CD88) in human and two Cyprinid fish.

The complement system is a complex network of soluble and membrane-associated serum proteins that regulate immune response. Activation of the complement C5 generates C5a and C5b which generate chemoattractive effect on myeloid cells and initiate the membrane attack complex (MAC) assembly. However, the study of evolutionary process and systematic function of C5 are still limited. In this study, we performed an evolutionary analysis of C5. Phylogeny analysis indicated that C5 sequences underwent complete divergence in fish and non-fish vertebrate. It was found that codon usage bias improved and provided evolution evidence of C5 in species. Notably, the codon usage bias of grass carp was evolutionarily closer to the zebrafish genome compared with humans and stickleback. This suggested that the zebrafish cell line may provide an alternative environment for heterologous protein expression of grass carp. Sequence comparison showed a higher similarity between human and mouse, grass carp, and zebrafish. Moreover, selective pressure analysis revealed that the C5 genes in fish and non-fish vertebrates exhibited different evolutionary patterns. To study the function of C5, gene co-expression networks of human and zebrafish were built which revealed the complexity of C5 function networks in different species. The protein structure simulation of C5 indicated that grass carp and zebrafish are more similar than to human, however, differences between species in C5a proteins are extremely smaller. Spatial conformations of C5a-C5AR (CD88) protein complex were constructed, which showed that possible interaction may exist between C5a and CD88 proteins. Furthermore, the protein docking sites/residues were measured and calculated according to the minimum distance for all atoms from C5a and CD88 proteins. In summary, this study provides insights into the evolutionary history, function and potential regulatory mechanism of C5 in fish immune responses.

[Advances in three-dimensional genomics].

Three-dimensional (3D) genomics is an emerging discipline that studies the 3D spatial structure and function of genomes, focusing on the 3D spatial conformation of genome sequences in the nucleus and its biological effects on biological processes such as DNA replication, DNA recombination and gene expression regulation. The invention of chromosome conformation capture (3C) technology speeds up the research on 3D genomics and its related fields. Furthermore, the development of 3C-based technologies, such as the genome-wide chromosome conformation capture (Hi-C) and chromatin interaction analysis using paired-end tag sequencing (ChIA-PET), help scientists get insight into the 3D genomes of various species. Aims of 3D genomics are to reveal the spatial genome organization, chromosomal interaction patterns, mechanisms underlying the transcriptional regulation and formation of biological traits of microorganism, plant, animal. Additionally, the identification of key genes and signaling pathways associated with biological processes and disease via chromosome 3C technology boosts the rapid development of agricultural science, life science and medical science. This paper reviews the research progress of 3D genomics, mainly in the concept of 3D genomics, the development of chromosome 3C technologies and their applications in agricultural science, life science and medical science, specifically in the field of tumor.

A Mixture of Functional Complex Extracts from Lycium barbarum and Grape Seed Enhances Immunity Synergistically In Vitro and In Vivo.

A mixture of multiple ingredients is often more effective than the individual ingredients. The functions of Lycium barbarum polysaccharide (LBP) glycoconjugate and grape seed procyanidins (GSP) are widely known. Here, we investigated the synergistic immune-enhancing activity of LBP and GSP. Atomic force microscopy results suggested that the mixture of LBP and GSP exhibited circular structure unlike LBP alone, and the addition of polyphenols may change the spatial conformation of the sugar chain. The changes in the structure were related to the synergistic effect of the two functional agents on immune recovery. In vitro, the proliferation rate of splenocytes was higher in LBP + GSP group (64.16%), rather than the sum of LBP group (13.01%) and GSP group (43.61%) individually used. This synergistical proliferation of splenocytes may be correlated to the increasing intracellular free calcium levels. Furthermore, the mixture significantly enhanced the immunity in vivo, as evident from the recovery of peripheral white blood cell counts in LBP + GSP group (18.535 × 109 /L) to normal group levels (18.115 × 109 /L) and higher B cell proliferation than normal group (P < 0.05). These results highlight the immune-enhancing activity of the combination of LBP and GSP associated with the structural changes, which may facilitate the development of functional foods with fewer resources but enhanced activities. PRACTICAL APPLICATION: The synergistic effects of LBP and GSP on immunomodulatory were better than the sum of the effects of the individual agents both in vitro and in vivo. Our results may provide a research-based support for the development of related functional products and an insight into the production of food resources with a fewer but more effective functional agents for better results.

Preparation and Antioxidant Activities In Vitro of a Designed Antioxidant Peptide from Pinctada fucata by Recombinant Escherichia coli.

An antioxidant peptide derived from Pinctada fucata meat using an Alcalase2.4L enzymatic hydrolysis method (named AOP) and identified by LC-TOF-MS has promising clinical potential for generating cosmetic products that protect skin from sunshine. To date, there have been few published studies investigating the structure-activity relationship in these peptides. To prepare antioxidant peptides better and improve their stability, the design and expression of an antioxidant peptide from Pinctada fucata (named DSAOP) was studied. The peptide contains a common precursor of an expression vector containing an α-helix tandemly linked according to the BamHI restriction sites. The DNA fragments encoding DSAOP were synthesized and subcloned into the expression vector pET-30a (+), and the peptide was expressed mostly as soluble protein in recombinant Escherichia coli. Meanwhile, the DPPH radical scavenging activity, superoxide radical scavenging activity, and hydroxyl radical scavenging activity of DSAOP IC50 values were 0.136 ± 0.006, 0.625 ± 0.025, and 0.306 ± 0.015 mg/ml, respectively, with 2-fold higher DPPH radical scavenging activity compared with chemosynthesized AOP (p < 0.05), as well as higher superoxide radical scavenging activity compared with natural AOP (p < 0.05). This preparation method was at the international advanced level. Furthermore, pilot-scale production results showed that DSAOP was expressed successfully in fermenter cultures, which indicated that the design strategy and expression methods would be useful for obtaining substantial amounts of stable peptides at low costs. These results showed that DSAOP produced with recombinant Escherichia coli could be useful in cosmetic skin care products, health foods, and pharmaceuticals.

Relationship between primary structure or spatial conformation and functional activity of antioxidant peptides from Pinctada fucata.

Antioxidant peptides from Pinctada fucata are ubiquitous in nature and can be utilized as ingredients in cosmetics or functional foods to positively regulate oxidative species in the human body against oxidation. Here, mutated peptides and a homologous series of peptides were designed and prepared, based on the original peptide sequence of an antioxidant peptide from Pinctada fucata meat (PFMAP), to better understand the structural relationships, including primary structure, spatial conformation and activity. The results showed that the antioxidant activity factors in order of importance were spatial conformation, amino acid sequence, amino acid position, amino acid composition, peptide chain length and degree of side-chain amino acid glycosylation. Moreover, this protocol had incomparable advantages in purity, speed and cost of preparing polypeptides, relative to enzymatic hydrolysis or chemosynthesis methods. This study also supplies test data information and a theoretical basis for the higher-value application of polypeptides from marine sources.

Fine mapping of a linear epitope on EDIII of Japanese encephalitis virus using a novel neutralizing monoclonal antibody.

The domain III (EDIII) of the envelope protein of Japanese encephalitis virus (JEV) is proposed to play an essential role in JEV replication and infection; it is involved in binding to host receptors and contains specific epitopes that elicit neutralizing antibodies. However, most previous studies have not provided detailed molecular information about the functional epitopes on JEV EDIII protein. In this study, we described a monoclonal antibody (mAb 2B4) we produced and characterized by IFA, PRNT, ELISA and Western blot analyses. The results showed that mAb 2B4 was specific to JEV EDIII protein and possessed high neutralization activity against JEV in vitro. Furthermore, we found that the motif, (394)HHWH(397), was the minimal unit of the linear epitope recognized by mAb 2B4 through screening a phage-displayed random 12-mer peptide library. Using sequence alignment analysis it was found that this motif was highly conserved among JEV strains and was present in West Nile Virus (WNV). Indeed, ELISA data showed that this epitope could be recognized by both JEV-positive swine serum and WNV-positive swine serum. Notably, this linear epitope was highly hydrophilic and was located within the terminal end of a ß-pleated sheet of EDIII. An analysis of the spatial conformation supported the possibility of inducing specific antibodies to this epitope. Taken together, we identified (394)HHWH(397) as an EDIII-specific linear epitope recognized by mAb 2B4, which would be beneficial for studying the pathogenic mechanism of JEV; and mAb 2B4 was also a potential diagnostic and therapeutic reagent.

Modeling and analysis of Schistosoma Argonaute protein molecular spatial conformation.

OBJECTIVE: To analyze the amino acid sequence composition, secondary structure, the spatial conformation of its domain and other characteristics of Argonaute protein. METHODS: Bioinformatics tools and the internet server were used. Firstly, the amino acid sequence composition features of the Argonaute protein were analyzed, and the phylogenetic tree was constructed. Secondly, Argonaute protein's distribution of secondary structure and its physicochemical properties were predicted. Lastly, the protein functional expression form of the domain group was established through the Phyre-based analysis on the spatial conformation of Argonaute protein domains. RESULTS: 593 amino acids were encoded by Argonaute protein, the phylogenetic tree was constructed, and Argonaute protein's distribution of secondary structure and its physicochemical properties were obtained through analysis. In addition, the functional expression form which comprised the N-terminal PAZ domain and C-terminal Piwi domain for the Argonaute protein was obtained with Phyre. CONCLUSIONS: The information relationship between the structure and function of the Argonaute protein can be initially established with bioinformatics tools and the internet server, and this provides the theoretical basis for further clarifying the function of Schistosoma Argonaute protein.