Morphological and phylogenetic analyses reveal a new species of Anthracophyllum (Omphalotaceae, Agaricales) in Zhejiang Province, China.

During the investigations of macrofungi resources in Zhejiang Province, China, an interesting wood rot fungus was collected. Based on morphological and molecular phylogenetic studies, it is described as a new species, Anthracophyllum sinense. A.

Discovery of -Acyl Amino Acids and Novel Related -, -Acyl Lipids by Integrating Molecular Networking and an Extended In Silico Spectral Library.

Research on novel bioactive lipids has garnered increasing interest. Although lipids can be identified by searching mass spectral libraries, the discovery of novel lipids remains challenging as the query spectra of such lipids are not included in libraries. In this study, we propose a strategy to discover novel carboxylic acid-containing acyl lipids by integrating molecular networking with an extended spectral library.

Improving Accuracy in Mass Spectrometry-Based Mass Determination of Intact Heterogeneous Protein Utilizing the Universal Benefits of Charge Reduction and Alternative Gas-Phase Reactions.

In mass analysis of proteins, mass spectrometry directly measures the mass to charge ratios of ionized proteins and promises higher accuracy than that of indirect approaches measuring other physicochemical properties, provided that the charge states of detected ions are determined. Accurate mass determination of heterogeneously glycosylated proteins is often hindered by unreliable charge determination due to the insufficient resolution of signals from different charge states and inconsistency among mass profiles of ions in individual charge states. Limited charge reduction of a subpopulation of proteoforms using electron transfer/capture reactions (ETnoD/ETnoD) solves this problem by narrowing the mass distribution of examined proteoforms and preserving the mass profile of the precursor charge state in the reduced charge states.

Evaluation of the reliability of MS1-based approach to profile naturally occurring peptides with clinical relevance in urine samples.

Rationale: The profiling of natural urinary peptides is a valuable indicator of kidney condition. While front-end separation limits the speed of peptidomic profiling, MS1-based results suffer from limited peptide coverage and specificity. Clinical studies on chronic kidney disease require an effective strategy to balance the trade-off between identification depth and throughput.

A post processing strategy to score and rank the annotation confidence of saponins in natural products by integrating MS spectral similarity and fragment interpretation.

Tandem mass spectrometry-spectra-based annotation in natural products challenges a lot because of ambiguous structural characterization. It still lacks an efficiency method to score and rank the annotation confidence. Herein, we develop a novel approach to rank the annotation confidences of saponins.

Quantitative analysis and mathematic modeling of the global outbreak of COVID-19.

The coronavirus pandemic is the biggest in the past 100 years, affected over 200 countries and killed over 300 thousand people. To better understand the epidemics in different areas, the progress percentage was generated in this study by dividing everyday total confirmed case number by the up-to-date total case number, so data obtained from different countries and territories can be put together and compared directly regardless of the large difference in the magnitude of numbers. The global outbreak data were analyzed and categorized into 4 groups based on different epidemic curve stages.

Genomic insight into the origins and evolution of symbiosis genes in Phaseolus vulgaris microsymbionts.

Background: Phaseolus vulgaris (common bean) microsymbionts belonging to the bacterial genera Rhizobium, Bradyrhizobium, and Ensifer (Sinorhizobium) have been isolated across the globe. Individual symbiosis genes (e.g.

Exploring the evolutionary dynamics of Rhizobium plasmids through bipartite network analysis.

The genus Rhizobium usually has a multipartite genome architecture with a chromosome and several plasmids, making these bacteria a perfect candidate for plasmid biology studies. As there are no universally shared genes among typical plasmids, network analyses can complement traditional phylogenetics in a broad-scale study of plasmid evolution. Here, we present an exhaustive analysis of 216 plasmids from 49 complete genomes of Rhizobium by constructing a bipartite network that consists of two classes of nodes, the plasmids and homologous protein families that connect them.

Rhizobium chutanense sp. nov., isolated from root nodules of Phaseolus vulgaris in China.

Two Gram-stain-negative, rod-shaped bacterial strains (C5 and C16), isolated from root nodules of Phaseolus vulgaris L. in Jiangxi Province, PR China, were characterized by using a polyphasic taxonomical approach. The phylogenetic analysis of the 16S rRNA gene and three concatenated housekeeping genes (recA-glnII-atpD) revealed that C5 and C16 were members of the genus Rhizobium, yet were distinct from known species.

Quantitative analysis of microcystin variants by capillary electrophoresis mass spectrometry with dynamic pH barrage junction focusing.

Dynamic pH junction is an online focusing method in CE based on the electrophoretic mobility difference of analytes in the sample matrix and the background electrolyte. An advantage of this method over the conventional CE is that the sensitivity can be significantly improved. By injecting a long sample plug in the capillary and focusing the analytes at the pH boundary between the background electrolyte and sample matrix, the LOD can be improved by 10-100 folds.

Mass spectrometry and affinity capillary electrophoresis for characterization of host-guest interactions.

Affinity capillary electrophoresis (ACE) in a free solution must be used to confirm the molecular interaction observed in electrospray ionization mass spectrometry (ESI-MS) for affinity binding analysis in the drug discovery process. In this article, the affinity of ibuprofen with three cyclodextrin species of different cavity sizes is investigated by both ESI-MS and ACE methods. Because the binding interactions are measured in different environments using ESI-MS (gas phase) and ACE (liquid phase), the experimental results show significant differences.

Optimization of dynamic pH barrage junction focusing for weakly alkaline or zwitterionic analytes in capillary electrophoresis.

Dynamic pH junction focusing prior to electrophoretic separation has been widely used for online pre-concentration of biologically important analytes, which are mostly weakly alkaline/acidic or zwitterionic species such as neurotransmitters, peptides, and proteins. A pH junction is formed when background electrolytes with different pH values are injected sequentially into the separation column of a capillary electrophoresis (CE) system. Unlike the traditional dynamic pH junction configuration with analyte molecules located in a different chemical environment to the separation background electrolyte (BGE), the pH barrage junction has a separate high pH (or low pH) region containing no analyte.

High Resolution Capillary Isoelectric Focusing Mass Spectrometry Analysis of Peptides, Proteins, And Monoclonal Antibodies with a Flow-through Microvial Interface.

Capillary isoelectric focusing directly coupled to high resolution mass spectrometry (cIEF-MS) provides information on amphoteric molecules, including isoelectric point and accurate mass, which enables structural interrogation of biopolymer pI variants. The coupling of cIEF with MS was facilitated by a flow-through microvial interface, made by stainless steel with high chemical resistance and mechanical robustness. Two on-column electrolyte configurations of cIEF-MS were demonstrated using peptide and protein pI markers.

Liquid Chromatography Coupled with Linear Ion Trap Hybrid OrbitrapMass Spectrometry for Determination of Alkaloids in .

The characterization of alkaloids is challenging because of the diversity of structures and the complicated fragmentation of collision induced structural dissociation in mass spectrometry. In this study, we analyzed the alkaloids in () by high resolution mass spectrometry. Chromatographic separation was achieved on a Phenomenex Kinetex C18 (2.

A Novel Strategy for Detecting Recent Horizontal Gene Transfer and Its Application to Strains.

Recent horizontal gene transfer (HGT) is crucial for enabling microbes to rapidly adapt to their novel environments without relying upon rare beneficial mutations that arise spontaneously. For several years now, computational approaches have been developed to detect HGT, but they typically lack the sensitivity and ability to detect recent HGT events. Here we introduce a novel strategy, named .

Electrochemical detection of microcystin-LR based on its deleterious effect on DNA.

This work reveals the deleterious effect of microcystin-LR (MC-LR) on the conformation of DNA and develops an electrochemical biosensor for detection of MC-LR. The biosensor is prepared by physically immobilizing calf thymus DNA (ctDNA) on gold electrode. In the presence of MC-LR, the conformation change of immobilized ctDNA decreases the electron transfer impedance, thus enhances the amperometric response.

How can native mass spectrometry contribute to characterization of biomacromolecular higher-order structure and interactions?

Native mass spectrometry (MS) is an emerging approach for characterizing biomacromolecular structure and interactions under physiologically relevant conditions. In native MS measurement, intact macromolecules or macromolecular complexes are directly ionized from a non-denaturing solvent, and key noncovalent interactions that hold the complexes together can be preserved for MS analysis in the gas phase. This technique provides unique multi-level structural information such as conformational changes, stoichiometry, topology and dynamics, complementing conventional biophysical techniques.

Genomic insight into the taxonomy of Rhizobium genospecies that nodulate Phaseolus vulgaris.

Due to the wide cultivation of bean (Phaseolus vulgaris L.), rhizobia associated with this plant have been isolated from many different geographical regions. In order to investigate the species diversity of bean rhizobia, comparative genome sequence analysis was performed in the present study for 69 Rhizobium strains mainly isolated from root nodules of bean and clover (Trifolium spp.

Deducing disulfide patterns of cysteine-rich proteins using signature fragments produced by top-down mass spectrometry.

Direct mapping of protein disulfide patterns using top-down mass spectrometry (MS) is often hampered by inadequate fragmentation at the disulfide-enclosing region, and insufficient structural information provided by the fragments. Here we used electron-transfer/high energy collision dissociation (EThcD) to improve the fragmentation efficiency, and developed strategies that minimize the false positive identification of fragments and deconvolute the signals representing specific modifications made to the disulfide-cleavage-induced fragments. We observed clear correlations between unique modification (attachment or removal of H or SH) patterns and the number of disulfide bonds that enclose the corresponding region.

Varying congruence among spatial patterns of vascular plants and vertebrates based on habitat groups.

Proxies are adopted to represent biodiversity patterns due to inadequate information for all taxa. Despite the wide use of proxies, their efficacy remains unclear. Previous analyses focused on overall species richness for fewer groups, affecting the generality and depth of inference.

Structure of a Holliday junction complex reveals mechanisms governing a highly regulated DNA transaction.

The molecular machinery responsible for DNA expression, recombination, and compaction has been difficult to visualize as functionally complete entities due to their combinatorial and structural complexity. We report here the structure of the intact functional assembly responsible for regulating and executing a site-specific DNA recombination reaction. The assembly is a 240-bp Holliday junction (HJ) bound specifically by 11 protein subunits.

[DNA barcoding research and its application on medicinal plants of Bletilla H. G. Reichenbach].

To identify adulterants from medicinal plants of Bletilla H. G. Reichenbach, the suitable candidate DNA barcoding of Bletilla was evaluated.

Mapping the λ Integrase bridges in the nucleoprotein Holliday junction intermediates of viral integrative and excisive recombination.

The site-specific recombinase encoded by bacteriophage λ [λ Integrase (Int)] is responsible for integrating and excising the viral chromosome into and out of the chromosome of its Escherichia coli host. In contrast to the other well-studied and highly exploited tyrosine recombinase family members, such as Cre and Flp, Int carries out a reaction that is highly directional, tightly regulated, and depends on an ensemble of accessory DNA bending proteins acting on 240 bp of DNA encoding 16 protein binding sites. This additional complexity enables two pathways, integrative and excisive recombination, whose opposite, and effectively irreversible, directions are dictated by different physiological and environmental signals.