Complete mitochondrial genome of Melia azedarach L., reveals two conformations generated by the repeat sequence mediated recombination.

Melia azedarach is a species of enormous value of pharmaceutical industries. Although the chloroplast genome of M. azedarach has been explored, the information of mitochondrial genome (Mt genome) remains surprisingly limited. In this study, we used a hybrid assembly strategy of BGI short-reads and Nanopore long-reads to assemble the Mt genome of M. azedarach. The Mt genome of M. azedarach is characterized by two circular chromosomes with 350,142 bp and 290,387 bp in length, respectively, which encodes 35 protein-coding genes (PCGs), 23 tRNA genes, and 3 rRNA genes. A pair of direct repeats (R1 and R2) were associated with genome recombination, resulting in two conformations based on the Sanger sequencing and Oxford Nanopore sequencing. Comparative analysis identified 19 homologous fragments between Mt and chloroplast genome, with the longest fragment of 12,142 bp. The phylogenetic analysis based on PCGs were consist with the latest classification of the Angiosperm Phylogeny Group. Notably, a total of 356 potential RNA editing sites were predicted based on 35 PCGs, and the editing events lead to the formation of the stop codon in the rps10 gene and the start codons in the nad4L and atp9 genes, which were verified by PCR amplification and Sanger sequencing. Taken together, the exploration of M. azedarach gap-free Mt genome provides a new insight into the evolution research and complex mitogenome architecture.

Identification and Pathogenicity of Pestalotioid Species on Alpinia oxyphylla in Hainan Province, China.

Alpinia oxyphylla is a traditional Chinese medicinal plant with a medicinal history of more than 1700 years. Ring leaf blight (RLB) disease, caused by pestalotioid species, is an important disease of A. oxyphylla, seriously affecting the yield and quality of its fruits. The causal agent of RLB disease has not been systematically identified or characterized yet. In this study, thirty-six pestalotioid strains were isolated from the leaves and stems of A. oxyphylla that was collected from six cities of Hainan province, China. Based on the multi-locus phylogeny (ITS, tef-1α and tub2) and morphological characteristic analyses, seventeen species belonging to three genera (Neopestalotiopsis, Pestalotiopsis and Pseudopestalotiopsis) were identified, and six new species (N. baotingensis, N. oblatespora, N. olivaceous, N. oxyphylla, N. wuzhishanensis and N. yongxunensis) were described. Pathogenicity tests revealed that strains of Neopestalotiopsis species caused more severe ring leaf blight on A. oxyphylla than strains of Pestalotiopsis and Pseudopestalotiopsis under wounded inoculation conditions.

Complete mitochondrial genome of Angelica dahurica and its implications on evolutionary analysis of complex mitochondrial genome architecture in Apiaceae.

Angelica dahurica is a kind of Chinese traditional herbs with economic and ornament value, widely distributed in China. Despite its significance, there have been limited comprehensive investigations on the genome of A. dahurica, particularly regarding mitochondrial genomes. To investigate the conversion between mitochondrial genome and chloroplast genome, a complete and circular mitochondrial genome was assembled using Oxford Nanopore Technologies (ONT) long reads. The mitochondrial genome of A. dahurica had a length of 228,315 base pairs (bp) with 45.06% GC content. The mitochondrial genome encodes 56 genes, including 34 protein-coding genes, 19 tRNA genes and 3 rRNA genes. Moreover, we discovered that 9 homologous large fragments between chloroplast genome and mitochondrial genome based on sequence similarity. This is the first report for A. dahurica mitochondrial genome, which could provide an insight for communication between plastid genome, and also give a reference genome for medicinal plants within the Angelica family.

Elucidating phylogenetic relationships within the genus Curcuma through the comprehensive analysis of the chloroplast genome of Curcuma viridiflora Roxb. 1810 (Zingiberaceae).

Curcuma viridiflora Roxb., a plant species of significant pharmaceutical interest, has been the subject of limited chloroplast genomic research. In this study, we present the sequencing and assembly of the C. viridiflora chloroplast genome, which is characterized by a circular chromosome spanning 162,212 base pairs and a GC content of 36.20%. The genome encodes 87 protein-coding genes (PCGs), 38 transfer RNA (tRNA) genes, and eight ribosomal RNA (rRNA) genes. A phylogenetic analysis was conducted, incorporating eight related species, and based on the complete chloroplast genome and protein-coding DNA sequences of six related taxa within the genus. Outgroup species Zingiber zerumbet and Zingiber officinale were also included in the analysis. The results indicate a close relationship between C. viridiflora and Curcuma phaeocaulis, Curcuma sichuanensis, and Curcuma yunnanensis. This study provides the first chloroplast genome of C. viridiflora, thereby contributing a valuable genomic resource for future research on medicinal plants within the Curcuma genus.

The complete mitochondrial genome of Aglaia odorata, insights into its genomic structure and RNA editing sites.

Aglaia odorata, native to Guangdong, Guangxi, and Hainan provinces in China, has long been utilized as an herbal remedy in ancient China. In this study, we assembled and annotated the complete mitochondrial genome (mitogenome) of A. odorata, which spans a total length of 537,321 bp. Conformation of the A. odorata recombination was verified through PCR experiments and Sanger sequencing. We identified and annotated 35 protein-coding genes (PCGs), 22 tRNA genes, and 3 rRNA genes within the mitogenome. Analysis of repeated elements revealed the presence of 192 SSRs, 29 pairs of tandem repeats, and 333 pairs of dispersed repeats in the A. odorata mitogenome. Additionally, we analyzed codon usage and mitochondrial plastid DNAs (MTPTs). Twelve MTPTs between the plastome and mitogenome of A. odorata were identified, with a combined length of 2,501 bp, accounting for 0.47% of the mitogenome. Furthermore, 359 high-confidence C to U RNA editing sites were predicted on PCGs, and four selected RNA editing sites were specially examined to verify the creation of start and/or stop codons. Extensive genomic rearrangement was observed between A. odorata and related mitogenomes. Phylogenetic analysis based on mitochondrial PCGs were conducted to elucidate the evolutionary relationships between A. odorata and other angiosperms.

Cavitation-induced particle engulfment via enhancing particle-interface interaction in solidification.

Particle engulfment plays a vital role in the application of particulate reinforced metal matrix composites fabricated by ingot metallurgy. During solidification, particles are nevertheless pushed by an advancing front. As a model system, TiB2p/Al composites were used to investigate the particle engulfment facilitated by acoustic cavitation. The implosion of bubbles drives the particles plunging towards the solid/liquid interface, which increases the engulfment probability. The secondary dendrite arms are refined from 271.2 µm to 98.0 µm as a result of the forced movements of TiB2 particles. Owing to the particle engulfment and dendrite refinement, the composite with ultrasound vibration treatment shows a more rapid work-hardening rate and higher strength.

Novel anionic surfactant-modified chlorhexidine and its potent antimicrobial properties.

Chlorhexidine dodecyl sulfate (CHX-DS) was synthesized and characterized via single-crystal X-ray diffraction (SC-XRD), 1H nuclear magnetic resonance (NMR) spectroscopy, 1H nuclear Overhauser effect spectroscopy (NOESY), and attenuated total reflectance Fourier-transform infrared spectroscopy (ATR-FTIR). The solid-state structure, comprising a 1 : 2 stoichiometric ratio of chlorhexidine cations [C22H30Cl2N10]2+ to dodecyl sulfate anions [C12H25SO4]-, is the first report of chlorhexidine isolated with a surfactant. CHX-DS exhibits broad-spectrum antibacterial activity and demonstrates superior efficacy for reducing bacteria-generated volatile sulfur compounds (VSCs) as compared to chlorhexidine gluconate (CHG). The minimum inhibitory concentrations (MICs) of CHX-DS were 7.5, 2.5, 2.5, and 10 µM for S. enterica, E. coli, S. aureus, and S. mutans, respectively. Furthermore, MIC assays for E. coli and S. mutans demonstrate that CHX-DS and CHX exhibit a statistically significant efficacy enhancement in 2.5 µM treatment as compared to CHG. CHX-DS was incorporated into SBA-15, a mesoporous silica nanoparticle (MSN) framework, and its release was qualitatively measured via UV-vis in aqueous media, which suggests its potential as an advanced functional material for drug delivery applications.

MethMarkerDB: a comprehensive cancer DNA methylation biomarker database.

DNA methylation plays a crucial role in tumorigenesis and tumor progression, sparking substantial interest in the clinical applications of cancer DNA methylation biomarkers. Cancer-related whole-genome bisulfite sequencing (WGBS) data offers a promising approach to precisely identify these biomarkers with differentially methylated regions (DMRs). However, currently there is no dedicated resource for cancer DNA methylation biomarkers with WGBS data. Here, we developed a comprehensive cancer DNA methylation biomarker database (MethMarkerDB, https://methmarkerdb.hzau.edu.cn/), which integrated 658 WGBS datasets, incorporating 724 curated DNA methylation biomarker genes from 1425 PubMed published articles. Based on WGBS data, we documented 5.4 million DMRs from 13 common types of cancer as candidate DNA methylation biomarkers. We provided search and annotation functions for these DMRs with different resources, such as enhancers and SNPs, and developed diagnostic and prognostic models for further biomarker evaluation. With the database, we not only identified known DNA methylation biomarkers, but also identified 781 hypermethylated and 5245 hypomethylated pan-cancer DMRs, corresponding to 693 and 2172 genes, respectively. These novel potential pan-cancer DNA methylation biomarkers hold significant clinical translational value. We hope that MethMarkerDB will help identify novel cancer DNA methylation biomarkers and propel the clinical application of these biomarkers.

Structural characterization of tin in toothpaste by dynamic nuclear polarization enhanced 119Sn solid-state NMR spectroscopy.

Stannous fluoride (SnF2) is an effective fluoride source and antimicrobial agent that is widely used in commercial toothpaste formulations. The antimicrobial activity of SnF2 is partly attributed to the presence of Sn(II) ions. However, it is challenging to directly determine the Sn speciation and oxidation state within commercially available toothpaste products due to the low weight loading of SnF2 (0.454 wt% SnF2, 0.34 wt% Sn) and the amorphous, semi-solid nature of the toothpaste. Here, we show that dynamic nuclear polarization (DNP) enables 119Sn solid-state NMR experiments that can probe the Sn speciation within commercially available toothpaste. Solid-state NMR experiments on SnF2 and SnF4 show that 19F isotropic chemical shift and 119Sn chemical shift anisotropy (CSA) are highly sensitive to the Sn oxidation state. DNP-enhanced 119Sn magic-angle turning (MAT) 2D NMR spectra of toothpastes resolve Sn(II) and Sn(IV) by their 119Sn chemical shift tensor parameters. Fits of DNP-enhanced 1D 1H → 119Sn solid-state NMR spectra allow the populations of Sn(II) and Sn(IV) within the toothpastes to be estimated. This analysis reveals that three of the four commercially available toothpastes contained at least 80% Sn(II), whereas one of the toothpaste contained a significantly higher amount of Sn(IV).

Profiles of Cytokinins Metabolic Genes and Endogenous Cytokinins Dynamics during Shoot Multiplication In Vitro of Phalaenopsis.

Shoot multiplication induced by exogenous cytokinins (CKs) has been commonly used in Phalaenopsis micropropagation for commercial production. Despite this, mechanisms of CKs action on shoot multiplication remain unclear in Phalaenopsis. In this study, we first identified key CKs metabolic genes, including six isopentenyltransferase (PaIPTs), six cytokinin riboside 5' monophosphate phosphoribohydrolase (PaLOGs), and six cytokinin dehydrogenase (PaCKXs), from the Phalaenopsis genome. Then, we investigated expression profiles of these CKs metabolic genes and endogenous CKs dynamics in shoot proliferation by thidiazuron (TDZ) treatments (an artificial plant growth regulator with strong cytokinin-like activity). Our data showed that these CKs metabolic genes have organ-specific expression patterns. The shoot proliferation in vitro was effectively promoted with increased TDZ concentrations. Following TDZ treatments, the highly expressed CKs metabolic genes in micropropagated shoots were PaIPT1, PaLOG2, and PaCKX4. By 30 days of culture, TDZ treatments significantly induced CK-ribosides levels in micropropagated shoots, such as tZR and iPR (2000-fold and 200-fold, respectively) as compared to the controls, whereas cZR showed only a 10-fold increase. Overexpression of PaIPT1 and PaLOG2 by agroinfiltration assays resulted in increased CK-ribosides levels in tobacco leaves, while overexpression of PaCKX4 resulted in decreased CK-ribosides levels. These findings suggest de novo biosynthesis of CKs induced by TDZ, primarily in elevation of tZR and iPR levels. Our results provide a better understanding of CKs metabolism in Phalaenopsis micropropagation.

The integrity of synthetic magnesium silicate in charged compounds.

Magnesium silicate is an inorganic compound used as an ingredient in product formulations for many different purposes. Since its compatibility with other components is critical for product quality and stability, it is essential to characterize the integrity of magnesium silicate in different solutions used for formulations. In this paper, we have determined the magnitude of dissociation of synthetic magnesium silicate in solution with positively charged, neutral, and negatively charged compounds using Scanning Electron Microscopy (SEM), Energy Dispersive X-ray Spectroscopy (EDS), and Liquid Chromatography-High Resolution Mass Spectrometry (LC-HRMS). The EDS results were verified through Monte Carlo simulations of electron-sample interactions. The compounds chosen for this study were positively charged cetylpyridinium chloride (CPC), neutral lauryl glucoside, and negatively charged sodium cocoyl glutamate and sodium cocoyl glycinate since these are common compounds used in personal care and oral care formulations. Negatively charged compounds significantly impacted magnesium silicate dissociation, resulting in physio-chemical separation between magnesium and silicate ions. In contrast, the positively charged compound had a minor effect on dissociation due to ion competition, and the neutral compound did not have such an impact on magnesium silicate dissociation. Further, when the magnesium ions are dissociated from the synthetic magnesium silicate, the morphology is changed accordingly, and the structural integrity of the synthetic magnesium silicate is damaged. The results provide scientific confidence and guidance for product development using synthetic magnesium silicate.

Genome Sequence Analysis of the Fungal Pathogen Fusarium graminearum Using Oxford Nanopore Technology.

Fusarium graminearum is a plant pathogen of global importance which causes not only significant yield loss but also crop spoilage due to mycotoxins that render grain unsafe for human or livestock consumption. Although the full genome of several F. graminearum isolates from different parts of the world have been sequenced, there are no similar studies of isolates originating from China. The current study sought to address this by sequencing the F. graminearum isolate FG-12, which was isolated from the roots of maize seedlings exhibiting typical symptoms of blight growing in the Gansu province, China, using Oxford Nanopore Technology (ONT). The FG-12 isolate was found to have a 35.9 Mb genome comprised of five scaffolds corresponding to the four chromosomes and mitochondrial DNA of the F. graminearum type strain, PH-1. The genome was found to contain an approximately 2.23% repetitive sequence and encode 12,470 predicted genes. Additional bioinformatic analysis identified 437 genes that were predicted to be secreted effectors, one of which was confirmed to trigger a hypersensitive responses (HR) in the leaves of Nicotiana benthamiana during transient expression experiments utilizing agro-infiltration. The F. graminearum FG-12 genome sequence and annotation data produced in the current study provide an extremely useful resource for both intra- and inter-species comparative analyses as well as for gene functional studies, and could greatly advance our understanding of this important plant pathogen.

Evaluation of multiple hydrophilic interaction chromatography columns and surrogate matrix for arginine quantification in saliva by high-resolution mass spectrometry.

Arginine, a pivotal ingredient in many biochemical synthetic pathways, can be used as a biomarker for many oral care clinical applications. It is still a challenge to develop a sensitive and reliable chromatographic method to quantify arginine as a biomarker in saliva, with or without arginine product pretreatment. The current method solved two critical issues for arginine quantitation in human saliva. The first issue was how to optimize arginine peak shape. A hydrophilic interaction chromatography method based on the column selection, pH and pKa relationship, mobile phase ionic strength, organic solvent consideration, and temperature effects was developed. An optimized chromatographic condition for arginine quantitation in the saliva matrix was obtained. The second issue was how to build confidence in the use of a simple surrogate matrix methodology to replace the more complex traditional standard addition methodology. The surrogate matrix methodology we developed is applicable to the measurement of arginine as a potential non-invasive biomarker in human saliva. The method detection and quantification limit reached 2 and 6 ng/mL. The tailing factor was within the 0.9-1.1 range even though arginine had three pKa values at 2.18, 9.09, and 13.2.

Understanding Methyl Salicylate Hydrolysis in the Presence of Amino Acids.

Methyl salicylate, the major flavor component in wintergreen oil, is commonly used as food additives. It was found that amino acids can unexpectedly expedite methyl salicylate hydrolysis in an alkaline environment, while the detailed mechanism of this reaction merits investigation. Herein, the role of amino acid, more specifically, glycine, in methyl salicylate hydrolysis in aqueous solution was explored. 1H NMR spectroscopy, combined with density functional theory calculations, was employed to investigate the methyl salicylate hydrolysis in the presence and absence of glycine at pH 9. The addition of glycine was found to accelerate the hydrolysis by an order of magnitude at pH 9, compared to that at pH 7. The end hydrolyzed product was confirmed to be salicylic acid, suggesting that glycine does not directly form an amide bond with methyl salicylate via aminolysis. Importantly, our results indicate that the ortho-hydroxyl substituent in methyl salicylate is essential for its hydrolysis due to an intramolecular hydrogen bond, and the carboxyl group of glycine is crucial to methyl salicylate hydrolysis. This study gains a new understanding of methyl salicylate hydrolysis that will be helpful in finding ways of stabilizing wintergreen oil as a flavorant in consumer food products that also contain amino acids.

HRMS Detector for the New HILIC CBD Method Development in Hemp Seed Oil.

The cannabis analysis has gained new importance worldwide due to the rapid expansion of the hemp global market. Many reverse phase high performance liquid chromatography (HPLC) methods have been developed to analyze cannabidiol (CBD) and its analogues due to the nice fit with their log P values at around 6. However, when CBD was blended with hemp seed oil in consumer, cosmetic, and food industries, the high content of triacylglycerides (TAGs) from hemp seed oil were retained and accumulated inside C18 columns with the common mobile phases and caused a column pressure increase and ghost peaks after continuous sample injections. Coupled with the chemical profile from high resolution mass spectrometry (HRMS) detection, a novel hydrophilic interaction liquid chromatography (HILIC) CBD quantitation method was developed, specifically for CBD blended hemp seed oil materials, which can overcome the matrix buildup in reverse phase columns. The zwitterionic (ZIC)-cHILIC column containing a dense water layer on the stationary phase surface provided a stable partitioning separation mechanism to separate the CBD from TAGs in hemp seed oil. This water layer favors the sustaining NH4F buffer ions, which can maximize the salting-out action and help reduce the adsorptive interaction between TAGs and stationary phase sulfobetaine materials. The high percentage of acetonitrile (99%) contributed to method sensitivity and reduced instrument maintenance time. The method was developed and validated for the first time. It has been successfully applied to quantify CBD content in hemp seed oil samples, thus demonstrating it to be a useful tool for both quality control and safety assurance in CBD hemp seed oil raw materials and related products.

High-precision measurement of pH in the full toothpaste using NMR chemical shift.

The pH of toothpaste is a critical factor for product stability and customer acceptance. However, no reliable and consistent method is currently available to precisely quantify pH in toothpaste as it is. In this study, a new method to directly determine pH value in the full toothpaste contained sodium bicarbonate (NaHCO3) was developed. Briefly, we utilized the 13C NMR chemical shift of a small molecule that has been formulated in the toothpaste as a sensitive probe to consistently respond to the pH value of the full toothpaste. The ideal pH probe molecule has the following characteristics: (1) its NMR chemical shift is sensitive to pH within a certain range, and (2) the chemical shift only responses to pH value, not to other factors, such as molecular interaction. NaHCO3 is a common ingredient in many toothpaste products used as a mild abrasive and an effective pH adjustment compound. Its chemical shift is very sensitive to pH; therefore, it was used as a candidate molecule to test this concept. This technique was demonstrated on select toothpaste formula contained arginine and sodium bicarbonate with different abrasive bases. The result shows that the pH value of full toothpaste is significantly higher than the pH of the toothpaste slurry. Arginine is a key active ingredient in these toothpastes, and it does not interfere with the chemical shift of sodium bicarbonate. The traditional method to determine the pH of toothpaste using pH electrode in toothpaste slurry typically has a larger measuring error, ranging from 0.1 to 0.3. This new method greatly reduced the measuring error, providing a consistent way to reliably determine pH in the full toothpaste, and enabling the stability test of toothpaste with smaller variations. This newly developed method can be further extended to other low-water gel or paste products at a different pH range by using different probe molecules.

Synthesis, Characterization, and Antimicrobial Investigation of a Novel Chlorhexidine Cyclamate Complex.

The synthesis, crystal structure, and antimicrobial efficacy are reported for a novel material comprising a 1:2 ratio of chlorhexidine (CHX) to N-cyclohexylsulfamate (i.e., artificial sweetener known as cyclamate). The chemical structure is unambiguously identified by incorporating a combination of single-crystal X-ray diffraction (SC-XRD), electrospray ionization mass spectrometry (ESI-MS), 1H nuclear magnetic resonance (NMR) spectroscopy, correlation spectroscopy (COSY), and attenuated total reflection Fourier-transform infrared spectroscopy (ATR-FTIR). The new material: 1) is amongst only several reported structures identified to date incorporating the vital chlorhexidine antimicrobial drug; 2) exhibits broad spectrum antimicrobial activity at concentrations less than 15 µg/mL; and 3) provides a unique delivery method for the essential active pharmaceutical ingredient (API). Furthermore, substitution of inactive gluconate with bioactive cyclamate counterion potentially provides the additional benefit of improving the taste profile of chlorhexidine.

Lactic acid quantitation in hand dishwashing liquid using an HILIC-UV methodology.

Different hydrophilic interaction chromatography (HILIC) columns were screened for lactic acid separation in hand dishwashing liquid products and the influence of mobile phase strength, buffer concentration and column temperature on the retention of lactic acid on a Zorbax NH(2) column was investigated. An isocratic HILIC method for the quantitation of lactic acid in hand dishwashing liquid products was developed. The mobile phase consists of 70% methanol and 30% 20 mM sodium phosphate buffer (v/v) at pH 2.5. The HILIC stationary phase is Zorbax NH(2), 250x4.6 with a 5 microm particle size. Detection was carried out using a variable wavelength UV-VIS detector at 226 nm. The linear range and percent recovery for lactic acid in the products were 44.68-1206.39 microg/mL and 100.3%, respectively. This paper provides an optimized HILIC methodology for the analysis of an acidic polar analyte (lactic acid) on a basic stationary phase. The proposed method can be used for the routine analysis of lactic acid.

Impact of column temperature and mobile phase components on selectivity of hydrophilic interaction chromatography (HILIC).

The retention mechanism and chromatographic behavior for different polar analytes under hydrophilic interaction chromatography (HILIC) conditions have been studied by application of different mobile phases and stationary phases to various analytes at different temperatures. In addition to the commonly accepted mechanism of analyte liquid-liquid partitioning between mobile phase and water-enriched solvent layer which is partially immobilized onto the surface of the stationary phase, hydrogen-bonding, hydrophobic interaction, and ion-exchange interactions may also be involved. The predominant retention mechanism in HILIC separation is not always easily predictable. It can depend not only on the characteristics of the analytes but also on the selection of mobile and stationary phase compositions. The objective of this review is to evaluate the potential application of column temperature and mobile phase composition toward improving HILIC selectivity. The functional groups from analyte structures, stationary phase materials and organic mobile phase solvents will be highlighted.

Separation of amino acids, peptides and corresponding Amadori compounds on a silica column at elevated temperature.

Maillard reaction of glucose with amino acids and peptides has become a very important experimental model in the food flavor and pharmaceutical industries for better understanding the mechanism of food flavor generation and drug stability. Because of the amino acid and sugar functional groups present in their structures, most of the reaction components formed during the initial stages of Maillard reaction as well as the substrates are relatively polar. These compounds are poorly retained on a conventional reversed phase column. While polar stationary phases like HILIC column do provide better retention for these polar components, method selectivity could still be a challenge due to the structural similarity between these analytes. In this report, parameters such as pH, mobile phase composition and temperature were investigated using different brands of bare silica columns in order to separate glycine (G), diglycine (DG), triglycine (TG), and the corresponding Amadori compounds of glucose-glycine (GG), glucose-diglycine (GDG) and glucose-triglycine (GTG). An excellent separation for glycine, glycine peptides and their Amadori compounds was obtained on a bare silica column at an elevated temperature.