Potential Anti-Gouty Arthritis of Citronella Essential Oil and Nutmeg Essential Oil through Reducing Oxidative Stress and Inhibiting PI3K/Akt/mTOR Activation-Induced NLRP3 Activity.

Citronella and Nutmeg are two common spices used for seasoning and medicinal purposes, both of which have significant economic value. This study aimed to investigate whether Citronella essential oil and Nutmeg essential oil (NEO) can ameliorate monosodium urate (MSU)-induced gouty arthritis in rats and the potential mechanisms. The results showed that CEO and NEO reduced swelling and redness at joint sites, inhibited neutrophil infiltration, and limited proinflammatory mediator secretion in mice with MSU-induced gouty arthritis. Based on the results of network pharmacology, molecular docking, and western blotting, CEO and NEO may exert anti-gouty arthritis effects by reducing the expression of reactive oxygen species and oxidative stress and downregulating the phosphorylation of the PI3K/AKT/mTOR signaling pathway, thereby inhibiting the production of the NLRP3 inflammasome and inhibiting the production of inflammatory cytokines. Therefore, these two essential oils show potential for use as adjuvant treatments for gouty arthritis in specific aromatherapy products or food seasonings.

Study on the formation and anti-biofilm properties of cinnamon essential oil inclusion complexes by the structure of modified ß-cyclodextrins.

Essential oils (EOs), which are plant-oriented anti-biofilm agents, are extensively encapsulated by cyclodextrins to overcome their aqueous solubility and chemical instability, and achieve slow release during long-term storage. However, the biological activities of EOs decreased after initial encapsulation in CDs. In this study, modified-ß-cyclodextrins (ß-CDs) were screened as wall materials to maintained the initial anti-biofilm effect of pure CEO. The inhibitory and bactericidal activities of CEO encapsulated in five types of ß-CDs with different substituents (primary hydroxyl, maltosyl, hydroxypropyl, methyl, and carboxymethyl) against Staphylococcus aureus biofilm were evaluated. Crystal violet assay and 3D-View observations suggested that CEO and its inclusion complexes (CEO-ICs) inhibited Staphylococcus aureus biofilm formation through the inhibition of colonising spreading, exopolysaccharide synthesis, and cell surface properties. Molecular docking revealed the causes of the decrease in the anti-biofilm effect after encapsulation, and quantitative structure-activity relationship assays provided MIC and MBIC prediction equation for modified-ß-cyclodextrins inclusion complexes. Maltosyl-ß-CD was screened as the best wall material to retained the anti-biofilm activities as pure cinnamon essential oil in initial stage, and its inclusion complexes can effectively inhibited biofilm formation in milk. This study provides a theoretical guidance for the selection ß-CDs to encapsulate CEO as plant-oriented anti-biofilm agents to inhibit bacterial biofilm formation.

Cancer SIGVAR: A semiautomated interpretation tool for germline variants of hereditary cancer-related genes.

Cancer is one of the most important health issues globally and the accuracy of interpretation of cancer-related variants is critical for the clinical management of hereditary cancer. ClinGen Sequence Variant Interpretation Working Groups have developed many adaptations of American College of Medical Genetics and Genomics and the Association of Molecular Pathologists guidelines to improve the consistency of interpretation. We combined the most recent adaptations to expand the number of the criteria from 28 to 48 and developed a tool called Cancer SIGVAR to help genetic counselors interpret the clinical significance of cancer germline variants. Our tool can accept VCF files as input and realize fully automated interpretation based on 21 criteria and semiautomated interpretation based on 48 criteria. We validated the performance of our tool with the ClinVar and CLINVITAE benchmark databases, achieving an average consistency for pathogenic and benign assessment up to 93.71% and 79.38%, respectively. We compared Cancer SIGVAR with two similar tools, InterVar and PathoMAN, and analyzed the main differences in criteria and implementation. Furthermore, we selected 911 variants from another two in-house benchmark databases, and semiautomated interpretation reached an average classification consistency of 98.35%. Our findings highlight the need to optimize automated interpretation tools based on constantly updated guidelines. Cancer SIGVAR is publicly available at http://cancersigvar.bgi.com/.

Temporal persistence of residual fetal cell-free DNA from a deceased cotwin after selective fetal reduction in dichorionic diamniotic twin pregnancies.

OBJECTIVES: To determine the temporal persistence of the residual cell-free DNA (cfDNA) of the deceased cotwin in maternal circulation after selective fetal reduction and evaluate its long persistence in noninvasive prenatal testing (NIPT). METHODS: Dichorionic diamniotic twins (N = 5) undergoing selective fetal reduction because of a trisomy were recruited. After informed consent, maternal blood was collected immediately before reduction and periodically after reduction until birth. The plasma cfDNA of each sample was sequenced and analyzed for fetal aneuploidy and fetal fractions. RESULTS: In all pregnancies, the fetal fraction of the cfDNA of the deceased fetus increased to peak at 7-9 weeks after fetal reduction, and subsequently decreased gradually to almost undetectable during the late third trimester. The NIPT T-scores persistently reflected the detection of fetal trisomy up to 16 (median 9.5) weeks after fetal reduction. CONCLUSIONS: Residual cfDNA from the deceased cotwin after selective reduction at 14-17 gestational weeks led to the persistent generation of false-positive NIPT results for up to 16 weeks postdemise. Thus, providing NIPT for pregnancies with a cotwin demise in early second trimester is prone to misleading results and not recommended.

Prevalence of hereditary breast and ovarian cancer (HBOC) predisposition gene mutations among 882 HBOC high-risk Chinese individuals.

Identification of deleterious variants in hereditary breast and ovarian cancer (HBOC) susceptibility genes allows for increased clinical surveillance and early detection, and could predict the response to poly (ADP-ribose) polymerase (PARP) inhibitor in patients with advanced ovarian carcinomas. To determine the prevalence and clinical prediction factors for HBOC syndrome, 882 selected individuals underwent multigene panel testing for HBOC risk assessment during the period from January 2015 to March 2018. Overall, 176 deleterious mutations were observed in 19.50% (n = 172) of individuals. Twenty-six of 176 mutations could not be retrieved in related public databases and were considered to be novel. Among patients with ovarian cancer, 115 deleterious mutations were identified in 429 patients (48.6%) with significant enrichment for a family history of breast or ovarian cancer syndrome (P < .05). In the breast cancer subgroup, 31 deleterious mutations were identified in 261 patients. Besides BRCA1 (8; 25.8%) and BRCA2 (11; 35.5%), the most frequently occurring genes, an additional 12 deleterious mutations (38.7%) were found in seven other susceptibility genes. Higher mutation incidence (57.9%) was observed in subjects with histories of breast and ovarian cancer. Our results highlighted the genetic heterogeneity of HBOC and the efficiency of a multigene panel in carrying out risk assessment.

Comparative study of a liposome and emulsion system with cinnamon essential oil on the quality and proteolysis of refrigerated minced pork.

Essential oils have been recognized for their strong antibacterial property, making them an innovative approach for preserving meat. However, their chemical instability and direct impact on meat proteins limit their application. To overcome these limitations, various loading systems have been explored. This study aimed to compare the effect of cinnamon essential oil (CEO) loaded in a liposome and emulsion system on the proteolysis of minced pork and to evaluate the advantages of each delivery system in preventing microorganism-induced quality deterioration of meat. Minced pork treated with CEO-liposomes exhibited lower pH, total volatile basic nitrogen (TVB-N), and total viable count (TVC) values than CEO-emulsions and provided better protection against microorganisms. SDS-polyacrylamide gel electrophoresis (PAGE) analysis confirmed that CEO-liposome was more effective in protecting proteins from degradation. Moreover, CEO-liposome produced lower amount of bitter amino acids and harmful biogenic amines. Antibacterial mechanisms indicated that CEO-liposome exhibited a stronger inhibitory effect against major spoilage bacteria in meat products by increasing cell membrane permeability. The membrane damage was further supported by an increase in conductivity and the leakage of nucleic acids. Compared to the CEO-emulsion system, CEO-liposome emerged as an effective preservative for minced pork. These results provided important theoretical support for using a bioactive compound delivery system to prevent microorganism-induced quality deterioration in meat.

Enhanced in vitro bioavailability of resveratrol-loaded emulsion stabilized by ß-lactoglobulin-catechin with excellent antioxidant activity.

The study aimed to fabricate ß-Lactoglobulin-catechin (ß-La-Ca) conjugates as a natural designed antioxidant emulsifier to improve the physicochemical stability of resveratrol emulsion delivery system. Fourier transform infrared (FT-IR) and fluorescence spectroscopy analysis confirmed the formation of conjugates using free radical grafting. The antioxidant ability of emulsion was evaluated by DPPH scavenging activities and ORAC experiments. The emulsion stabilized by ß-La-Ca conjugates exhibited strong antioxidant activity with ORAC value of 2541.39 ± 29.58 µmol TE/g, which was significantly higher than that by ß-Lactoglobulin alone with 387.96 ± 23.45 µmol TE/g or their mixture with 948.23 ± 32.77 µmol TE/g. During the whole simulated gastrointestinal digestion, emulsion stabilized by ß-La-Ca conjugates exhibited excellent oxidative stability that the lipid was mainly digested in the small intestine. This behavior attributed to the greater stability of resveratrol to chemical transformation leading to a higher overall bioavailability in vivo. These results suggested that the ß-La-Ca conjugates could be used to fabricate the emulsion-based delivery system to improve the oxidative stability and bioavailability of chemically labile hydrophobic bioactive compounds.

Trans-cinnamaldehyde fumigation inhibits Escherichia coli by affecting the mechanism of intracellular biological macromolecules.

This study aimed to determine the antibacterial mechanism of cinnamaldehyde fumigation in Escherichia coli (E. coli). Through vapour fumigation, cinnamaldehyde was confirmed to exhibit effective antibacterial activity against E. coli. The minimum inhibitory concentration (MIC) and minimum bacterial concentration (MBC) were 0.25 µL/mL and 0.5 µL/mL, respectively. Based on transmission electron microscopy, the wrinkled bacterial cells observed after fumigation could be related to the leakage of intracellular substances. Laser tweezers Raman spectroscopy revealed changes in the main chain of proteins, the hydrogen bond system and spatial structure, and single- and double-stranded DNA breaks. In addition, breakage of the fatty acyl chain backbone was found to affect the vertical order degree of the lipid bilayer and cell membrane fluidity, thereby inhibiting the growth of E. coli. Overall, our findings indicate that cinnamaldehyde fumigation inhibits E. coli growth by inducing changes in intracellular biological macromolecules.

A short-read multiplex sequencing method for reliable, cost-effective and high-throughput genotyping in large-scale studies.

Accurate genotyping is important for genetic testing. Sanger sequencing-based typing is the gold standard for genotyping, but it has been underused, due to its high cost and low throughput. In contrast, short-read sequencing provides inexpensive and high-throughput sequencing, holding great promise for reaching the goal of cost-effective and high-throughput genotyping. However, the short-read length and the paucity of appropriate genotyping methods, pose a major challenge. Here, we present RCHSBT-reliable, cost-effective and high-throughput sequence based typing pipeline-which takes short sequence reads as input, but uses a unique variant calling, haploid sequence assembling algorithm, can accurately genotype with greater effective length per amplicon than even Sanger sequencing reads. The RCHSBT method was tested for the human MHC loci HLA-A, HLA-B, HLA-C, HLA-DQB1, and HLA-DRB1, upon 96 samples using Illumina PE 150 reads. Amplicons as long as 950 bp were readily genotyped, achieving 100% typing concordance between RCHSBT-called genotypes and genotypes previously called by Sanger sequence. Genotyping throughput was increased over 10 times, and cost was reduced over five times, for RCHSBT as compared with Sanger sequence genotyping. We thus demonstrate RCHSBT to be a genotyping method comparable to Sanger sequencing-based typing in quality, while being more cost-effective, and higher throughput.

Characterization of 27 novel HLA class II alleles from China marrow donor program.

Twenty-seven novel human leukocyte antigen (HLA) class II alleles in Chinese Marrow Donors are described: 10 HLA-DRB1 alleles and 17 HLA-DQB1 alleles.

Enhanced mechanical and functional properties of chitosan/polyvinyl alcohol/hydroxypropyl methylcellulose/alizarin composite film by incorporating cinnamon essential oil and tea polyphenols.

In this study, cinnamon essential oil and tea polyphenols were added to chitosan/ polyvinyl alcohol/ hydroxypropyl methylcellulose/ alizarin composite films to enhance their mechanical and functional properties. Their addition to the composite films enhanced their antibacterial and antioxidant properties and significantly improved its elongation at break (p < 0.05). Cinnamon essential oil reduced the water vapor permeability, water content, and water solubility of composite films and improved their transparency. The composite films with additive exhibited excellent UV-barrier ability and pH responsivity. Fourier Transform infrared spectroscopy and X-Ray Diffraction analyses confirmed hydrogen bond formation between the polymer molecules and additives. The results of Scanning Electron Microscope-Focused Ion Beam revealed improved surface and cross-section morphology of the films, leading to the generation of a cross-linked structure. Thermogravimetric and differential scanning calorimetry analysis indicated enhanced thermal stability of the composite films upon cinnamon essential oil addition. Analysis of storage quality indicators (TBARS value, TVC, and TVB-N) revealed that the composite films could prolong the freshness of surimi. The incorporation of cinnamon essential oil and tea polyphenols into the composite films has demonstrated significant potential as an effective and natural alternative for active food packaging.

Preparation and antibacterial and antioxidant ability of ß-cyclodextrin complexes of vaporized Illicium verum essential oil.

Compared with traditional liquid-liquid embedding method and solid-liquid embedding method of inclusion complexes of ß-cyclodextrin (ß-CD) inclusion of essential oil to form stable properties, the gas-liquid embedding method was applied to encapsulate vaporized illicium verum essential oil (IvEO), with ß-CD as wall materials so that core and wall materials molecules are in active state during complexing process. At optimal conditions with a mass ratio of 1:10, temperature of 80°C, time of 1 h, the ß-CD-IvEO inclusion complexes (ß-CD-IvEO-ICs) had an encapsulation efficiency (EE) of 84.55 ± 2.31%. Fourier transform infrared spectroscopy (FTIR) revealed the encapsulation of IvEO into inclusion complexes, differential scanning calorimetry (DSC) and thermogravimetric analysis (TGA) demonstrated the enhanced thermal stability of IvEO after embedding. Furthermore, the reducing power and 2-phenyl-4,4,5,5-tetramethylimidazoline-1-oxyl-3-oxide (PTIO)-scavenging capacity displayed certain capacity of antioxidation in a short time but stronger antioxidative activities as reaction time was extended. The diameter of growth zone (DGZ) indicated stronger antibacterial activity of ß-CD-IvEO-ICs against Escherichia coli, Bacillus subtilis, Staphylococcus epidermidis, and Staphylococcus aureus. Moreover, the ß-CD-IvEO-ICs could induce the bacteria producing more reactive oxygen species (ROS) than IvEO, resulting in bacterial death.

Encapsulation Efficiency and Functional Stability of Cinnamon Essential Oil in Modified ß-cyclodextrins: In Vitro and In Silico Evidence.

Essential oils (EOs) have good natural antioxidant and antimicrobial properties; however, their volatility, intense aroma, poor aqueous solubility, and chemical instability limit their applications in the food industry. The encapsulation of EOs in ß-cyclodextrins (ß-CDs) is a widely accepted strategy for enhancing EO applications. The complexation of cinnamon essential oil (CEO) with five types of ß-CDs, containing different substituent groups (ß-CD with primary hydroxyl, Mal-ß-CD with maltosyl, CM-ß-CD with carboxymethyl, HP-ß-CD with hydroxypropyl, and DM-ß-CD with methyl), inclusion process behaviors, volatile components, and antioxidant and antibacterial activities of the solid complexes were studied. The CEOs complexed with Mal-ß-CD, CM-ß-CD, and ß-CD were less soluble than those complexed with DM-ß-CD and HP-ß-CD. Molecular docking confirmed the insertion of the cinnamaldehyde benzene ring into various ß-CD cavities via hydrophobic interactions and hydrogen bonds. GC-MS analysis revealed that HP-ß-CD had the greatest adaptability to cinnamaldehyde. The CEO encapsulated in ß-, Mal-ß-, and CM-ß-CD showed lower solubility but better control-release characteristics than those encapsulated in DM- and HP-ß-CD, thereby increasing their antioxidant and antibacterial activities. This study demonstrated that ß-, Mal-ß-, and CM-ß-CD were suitable alternatives for the encapsulation of CEO to preserve its antioxidant and antibacterial activities for long-time use.

Study of antimicrobial activity and mechanism of vapor-phase cinnamaldehyde for killing Escherichia coli based on fumigation method.

The vapor-phase antibacterial activity of essential oils makes them suitable for applications in air disinfection and other fields. At present, vapor-phase antibacterial activity of plant-based essential oils has rarely been reported. Herein, we report a new approach to investigate the antimicrobial activity and mechanism of vapor-phase cinnamaldehyde using Escherichia coli (E. coli) and three other pathogenic bacteria (Pseudomonas aeruginosa, Salmonella, Staphylococcus aureus) as model bacteria. Plate fumigation and agar block transfer techniques were used to determine the antimicrobial activities of vapor-phase cinnamaldehyde fumigation on the four types of bacteria, and the mechanism of action was determined by electrical conductivity (EC), OD260nm measurement, transmission electron microscopy (TEM), Fourier transform infrared spectroscopy (FTIR), and fluorescence spectroscopy. Cinnamaldehyde had good vapor-phase antibacterial activity against the four types of bacteria. The TEM, EC, and OD260nm measurements showed that after fumigation with cinnamaldehyde, the ultrastructures of the cells were damaged, and plasmolysis, cell collapse, and leakage of intracellular substances were observed. The FTIR and fluorescence spectroscopy analyses showed that the secondary and tertiary structures of bacterial membrane proteins were altered. These findings indicate that the cell membrane is an important target for plant-based essential oils to exert their vapor-phase antimicrobial effects. The results showed that plant-based essential oils can be developed as volatile broad-spectrum disinfection products and vapor-phase antiseptics.

Physical and oxidative stability of chicken oil-in-water emulsion stabilized by chicken protein hydrolysates.

The emulsifying and antioxidant properties of chicken protein hydrolysates for the physical and oxidative stabilization of chicken oil-in-water emulsion were investigated. The chicken protein pepsin hydrolysates obtained at reaction temperature of 33℃, 1.8% enzyme addition, liquid-solid ratio of 5:1, and reaction time of 4h, showed the DPPH radical scavenging rate of 92.12% and emulsion stability index of 0.07. The hydrolysate exerted significantly improved antioxidant activity and emulsion ability compared to the native chicken protein. The amino acid composition analysis indicated that the contents of hydrophobic amino acids including tyrosine, phenylalanine, and tryptophan were increased after hydrolysis, which contributed to the higher hydrophobicity and antioxidant activity of chicken hydrolysates. The results suggested that the chicken protein hydrolysates could be used as an alternative protein emulsifier for the production of oxidatively stable chicken oil-in-water emulsion.

FF-QuantSC: accurate quantification of fetal fraction by a neural network model.

BACKGROUND: Noninvasive prenatal testing (NIPT) is one of the most commonly employed clinical measures for screening of fetal aneuploidy. Fetal Fraction (ff) has been demonstrated to be one of the key factors affecting the performance of NIPT. Accurate quantification of ff plays vital role in NIPT. METHODS: In this study, we present a new approach, the accurate Quantification of Fetal Fraction with Shallow-Coverage sequencing of maternal plasma DNA (FF-QuantSC), for the estimation of ff in NIPT. The method employs neural network model and utilizes differential genomic patterns between fetal and maternal genomes to quantify ff. RESULTS: Our results show that the predicted ff by FF-QuantSC exhibit high correlation with the Y chromosome-based method on male pregnancies, and achieves the highest accuracy compared with other ff estimation approaches. We also demonstrate that the model generates statistically similar results on both male and female pregnancies. CONCLUSION: FF-QuantSC achieves high accuracy in ff quantification. The method is suitable for application in both male and female pregnancies. Since the method does not require additional information upon NIPT routines, it can be easily incorporated into current NIPT settings without causing extra costs. We believe that FF-QuantSC shall provide valuable additions to NIPT.

Mechanisms of vapor-phase antibacterial action of essential oil from Cinnamomum camphora var. linaloofera Fujita against Escherichia coli.

The purpose of this study was to investigate antibacterial activity of essential oil from Cinnamomum camphora var. linaloofera Fujita (EOL) at vapor phase and its mechanism of bactericidal action against Escherichia coli. Results showed that the vapor-phase EOL had significant antibacterial activity with a minimum inhibitory concentration (MIC) and minimum bactericidal concentration (MBC) of 200 µl/L. Further analyses showed that treatment of E. coli with vapor-phase EOL resulted in partial degradation of cell membrane, increased membrane permeability, leakage of cytoplasm materials, and prominent distortion and shrinkage of bacterial cells. FTIR showed that EOL altered bacterial protein secondary and tertiary structures. GC/MS analysis showed that the components of vapor-phase EOL included linalool (69.94%), camphor (10.90%), nerolidol (10.92%), and safrole (8.24%), of which linalool had bactericidal activity. Quantum chemical analysis suggested that the antibacterial reactive center of linalool was oxygen atom (O10) which transferred electrons during antibacterial action by the donation of electrons.

IMPre: An Accurate and Efficient Software for Prediction of T- and B-Cell Receptor Germline Genes and Alleles from Rearranged Repertoire Data.

Large-scale study of the properties of T-cell receptor (TCR) and B-cell receptor (BCR) repertoires through next-generation sequencing is providing excellent insights into the understanding of adaptive immune responses. Variable(Diversity)Joining [V(D)J] germline genes and alleles must be characterized in detail to facilitate repertoire analyses. However, most species do not have well-characterized TCR/BCR germline genes because of their high homology. Also, more germline alleles are required for humans and other species, which limits the capacity for studying immune repertoires. Herein, we developed "Immune Germline Prediction" (IMPre), a tool for predicting germline V/J genes and alleles using deep-sequencing data derived from TCR/BCR repertoires. We developed a new algorithm, "Seed_Clust," for clustering, produced a multiway tree for assembly and optimized the sequence according to the characteristics of rearrangement. We trained IMPre on human samples of T-cell receptor beta (TRB) and immunoglobulin heavy chain and then tested it on additional human samples. Accuracy of 97.7, 100, 92.9, and 100% was obtained for TRBV, TRBJ, IGHV, and IGHJ, respectively. Analyses of subsampling performance for these samples showed IMPre to be robust using different data quantities. Subsequently, IMPre was tested on samples from rhesus monkeys and human long sequences: the highly accurate results demonstrated IMPre to be stable with animal and multiple data types. With rapid accumulation of high-throughput sequence data for TCR and BCR repertoires, IMPre can be applied broadly for obtaining novel genes and a large number of novel alleles. IMPre is available at https://github.com/zhangwei2015/IMPre.

A reliable, high-resolution and high-throughput genotyping method for HLA-DRB1.

Human leukocyte antigen (HLA) DNA typing is an essential part to identify a donor who may be a good match for the patients who need haematopoietic stem cells from bone marrow. Thus, fetching quickly high-resolution genotype is very important at present. However, current HLA DNA typing methods especially for HLA-DRB1 generally yielded ambiguous typing results because of high degree of heterozygosity on exome region and primer pairs design limitations, which generally amplified only exon2 of HLA-DRB1 and the position of its primer pairs is on exome region. To solve this problem, we developed a reliable, high-resolution and high-throughput (RHH) sequence based typing approach for HLA-DRB1 through massively parallel paired-end sequencing. Several primer pairs were designed to amplify three exon regions, which are part of exon1, the whole region of exon2 and exon3 of HLA-DRB1, to genotyping for HLA-DRB1 by synthesis. 94 samples were included to analyze and the highly successful genotyping ratio (98.94%) and no ambiguous genotyping result demonstrated the accurate performance of our method for HLA-DRB1 genotyping.

[Effects of phytohormones on growth and DHA production by Thraustochytrium roseum].

In this paper, effects of phytohormones on growth and DHA production by Thraustochytrium roseum MF2 were studied. Results showed that phytohormones had significant affect on growth and DHA production by T. roseum MF2. GA could promote the synthesis of DHA, and BA could accelerate the growth of T. roseum MF2, so the combination of GA and BA could increase DHA yield. The maximum DHA yield of 982mg/L was observed with 2mg/L GA and 3mg/L BA in medium.