Inequality relations for NMR-based polymer homoblock analysis and extended application: Reanalysis of historical data on alginates, chitosans, homogalacturonans, and galactomannans.

There has been a long-standing bottleneck in the quantitative analysis of the frequencies of homoblock polyads beyond triads using 1H and 13C NMR for linear polysaccharides, primarily because monosaccharides within a long homoblock share similar chemical environments due to identical neighboring units, resulting in indistinct NMR peaks. In this study, through rigorous mathematical induction, inequality relations were established that enabled the calculation of frequency ranges of homoblock polyads from historically reported NMR-derived frequency values of diads and/or triads of alginates, chitosans, homogalacturonans, and galactomannans. The calculated homoblock frequency ranges were then applied to evaluate three chain growth statistical models, including the Bernoulli chain, first-order Markov chain, and second-order Markov chain, for predicting homoblock frequencies in these polysaccharides. Furthermore, based on the mathematically derived inequality relations, a novel 2D array was constructed, enabling the graphical visualization of homoblock features in polysaccharides. It was demonstrated, as a proof of concept, that the novel 2D array, along with a 1D code generated from it, could serve as an effective feature engineering tool for polymer classification using machine learning algorithms.

SACCHARIS v2: Streamlining Prediction of Carbohydrate-Active Enzyme Specificities Within Large Datasets.

Carbohydrates are chemically and structurally diverse, composed of a wide array of monosaccharides, stereochemical linkages, substituent groups, and intermolecular associations with other biological molecules. A large repertoire of carbohydrate-active enzymes (CAZymes) and enzymatic activities are required to form, dismantle, and metabolize these complex molecules. The software SACCHARIS (Sequence Analysis and Clustering of CarboHydrate Active enzymes for Rapid Informed prediction of Specificity) provides a rapid, easy-to-use pipeline for the prediction of potential CAZyme function in new datasets. We have updated SACCHARIS to (i) simplify its installation by re-writing in Python and packaging for Conda; (ii) enhance its usability through a new (optional) interactive GUI; and (iii) enable semi-automated annotation of phylogenetic tree output via a new R package or the commonly-used webserver iTOL. Significantly, SACCHARIS v2 has been developed with high-throughput omics in mind, with pipeline automation geared toward complex (meta)genome and (meta)transcriptome datasets to reveal the total CAZyme content ("CAZome") of an organism or community. Here, we outline the development and use of SACCHARIS v2 to discover and annotate CAZymes and provide insight into complex carbohydrate metabolisms in individual organisms and communities.

Two glycosyl transferase 2 genes from the gram-positive bacterium Clostridium ventriculi encode (1,3;1,4)-ß-D-glucan synthases.

The exopolysaccharides of the Gram-positive bacterium Romboutsia ilealis have recently been shown to include (1,3;1,4)-ß-D-glucans. In the present study, we examined another Clostridia bacterium Clostridium ventriculi that has long been considered to contain abundant amounts of cellulose in its exopolysaccharides. We treated alcohol insoluble residues of C. ventriculi that include the exopolysaccharides with the enzyme lichenase that specifically hydrolyses (1,3;1,4)-ß-D-glucans, and examined the oligosaccharides released. This showed the presence of (1,3;1,4)-ß-D-glucans, which may have previously been mistaken for cellulose. Through genomic analysis, we identified the two family 2 glycosyltransferase genes CvGT2-1 and CvGT2-2 as possible genes encoding (1,3;1,4)-ß-D-glucan synthases. Gain-of-function experiments in the yeast Saccharomyces cerevisiae demonstrated that both of these genes do indeed encode (1,3;1,4)-ß-D-glucan synthases.

Methylation-GC-MS/FID-Based Glycosidic Linkage Analysis of Unfractionated Polysaccharides in Red Seaweeds.

Glycosidic linkage analysis was conducted on the unfractionated polysaccharides in alcohol-insoluble residues (AIRs) prepared from six red seaweeds (Gracilariopsis sp., Prionitis sp., Mastocarpus papillatus, Callophyllis sp., Mazzaella splendens, and Palmaria palmata) using GC-MS/FID analysis of partially methylated alditol acetates (PMAAs). The cell walls of P. palmata primarily contained mixed-linkage xylans and small amounts of sulfated galactans and cellulose. In contrast, the unfractionated polysaccharides of the other five species were rich in galactans displaying diverse 3,6-anhydro-galactose and galactose linkages with varied sulfation patterns. Different levels of cellulose were also observed. This glycosidic linkage method offers advantages for cellulose analysis over traditional monosaccharide analysis that is known for underrepresenting glucose in crystalline cellulose. Relative linkage compositions calculated from GC-MS and GC-FID measurements showed that anhydro sugar linkages generated more responses in the latter detection method. This improved linkage workflow presents a useful tool for studying polysaccharide structural variations across red seaweed species. Furthermore, for the first time, relative linkage compositions from GC-MS and GC-FID measurements, along with normalized FID and total ion current (TIC) chromatograms without peak assignments, were analyzed using principal component analysis (PCA) as a proof-of-concept demonstration of the technique's potential to differentiate various red seaweed species.

Conversion of Phytochemicals by Lactobacilli: (Phospho)-ß-glucosidases Are Specific for Glucosylated Phytochemicals Rather than Disaccharides.

Food-fermenting lactobacilli convert glycosylated phytochemicals to glycosyl hydrolases and thereby alter their biological activity. This study aimed to investigate the microbial transformation of ß-glucosides of phytochemicals in comparison with utilization of cellobiose. Four homofermentative and four heterofermentative lactobacilli were selected to represent the metabolic diversity of Lactobacillaceae. The genomes of Lactobacillus crispatus, Companilactobacillus paralimentarius, Lacticaseibacillus paracasei, and Lactiplantibacillus plantarum encoded for 8 to 22 enzymes, predominantly phospho-ß-glucosidases, with predicted activity on ß-glucosides. Levilactobacillus hammesii and Furfurilactobacillus milii encoded for 3 ß-glucosidases, Furfurilactobacillus rossiae for one, and Fructilactobacillus sanfranciscensis for none. The hydrolysis of amygdalin, esculin, salicin, glucosides of quercetin and genistein, and ginsenosides demonstrated that several strains hydrolyzed ß-glucosides of phytochemicals but not cellobiose. Taken together, several of the carbohydrate-active enzymes of food-fermenting lactobacilli are specific for glycosides of phytochemicals.

Observation of Single-Top-Quark Production in Association with a Photon Using the ATLAS Detector.

This Letter reports the observation of single top quarks produced together with a photon, which directly probes the electroweak coupling of the top quark. The analysis uses 139 fb^{-1} of 13 TeV proton-proton collision data collected with the ATLAS detector at the Large Hadron Collider. Requiring a photon with transverse momentum larger than 20 GeV and within the detector acceptance, the fiducial cross section is measured to be 688±23(stat) _{-71}^{+75}(syst) fb, to be compared with the standard model prediction of 515_{-42}^{+36} fb at next-to-leading order in QCD.

Observation of the γγ→ττ Process in Pb+Pb Collisions and Constraints on the τ-Lepton Anomalous Magnetic Moment with the ATLAS Detector.

This Letter reports the observation of τ-lepton-pair production in ultraperipheral lead-lead collisions Pb+Pb→Pb(γγ→ττ)Pb and constraints on the τ-lepton anomalous magnetic moment a_{τ}. The dataset corresponds to an integrated luminosity of 1.44 nb^{-1} of LHC Pb+Pb collisions at sqrt[s_{NN}]=5.02 TeV recorded by the ATLAS experiment in 2018. Selected events contain one muon from a τ-lepton decay, an electron or charged-particle track(s) from the other τ-lepton decay, little additional central-detector activity, and no forward neutrons. The γγ→ττ process is observed in Pb+Pb collisions with a significance exceeding 5 standard deviations and a signal strength of µ_{ττ}=1.03_{-0.05}^{+0.06} assuming the standard model value for a_{τ}. To measure a_{τ}, a template fit to the muon transverse-momentum distribution from τ-lepton candidates is performed, using a dimuon (γγ→µµ) control sample to constrain systematic uncertainties. The observed 95% confidence-level interval for a_{τ} is -0.057

Strong Constraints on Jet Quenching in Centrality-Dependent p+Pb Collisions at 5.02 TeV from ATLAS.

Jet quenching is the process of color-charged partons losing energy via interactions with quark-gluon plasma droplets created in heavy-ion collisions. The collective expansion of such droplets is well described by viscous hydrodynamics. Similar evidence of collectivity is consistently observed in smaller collision systems, including pp and p+Pb collisions. In contrast, while jet quenching is observed in Pb+Pb collisions, no evidence has been found in these small systems to date, raising fundamental questions about the nature of the system created in these collisions. The ATLAS experiment at the Large Hadron Collider has measured the yield of charged hadrons correlated with reconstructed jets in 0.36 nb^{-1} of p+Pb and 3.6 pb^{-1} of pp collisions at 5.02 TeV. The yields of charged hadrons with p_{T}^{ch}>0.5 GeV near and opposite in azimuth to jets with p_{T}^{jet}>30 or 60 GeV, and the ratios of these yields between p+Pb and pp collisions, I_{pPb}, are reported. The collision centrality of p+Pb events is categorized by the energy deposited by forward neutrons from the struck nucleus. The I_{pPb} values are consistent with unity within a few percent for hadrons with p_{T}^{ch}>4 GeV at all centralities. These data provide new, strong constraints that preclude almost any parton energy loss in central p+Pb collisions.

Search for Heavy Neutral Leptons in Decays of W Bosons Using a Dilepton Displaced Vertex in sqrt[s]=13 TeV pp Collisions with the ATLAS Detector.

A search for a long-lived, heavy neutral lepton (N) in 139 fb^{-1} of sqrt[s]=13 TeV pp collision data collected by the ATLAS detector at the Large Hadron Collider is reported. The N is produced via W→Nµ or W→Ne and decays into two charged leptons and a neutrino, forming a displaced vertex. The N mass is used to discriminate between signal and background. No signal is observed, and limits are set on the squared mixing parameters of the N with the left-handed neutrino states for the N mass range 3 GeV

Test of CP Invariance in Higgs Boson Vector-Boson-Fusion Production Using the H→γγ Channel with the ATLAS Detector.

A test of CP invariance in Higgs boson production via vector-boson fusion has been performed in the H→γγ channel using 139 fb^{-1} of proton-proton collision data at sqrt[s]=13 TeV collected by the ATLAS detector at the LHC. The optimal observable method is used to probe the CP structure of interactions between the Higgs boson and electroweak gauge bosons, as described by an effective field theory. No sign of CP violation is observed in the data. Constraints are set on the parameters describing the strength of the CP-odd component in the coupling between the Higgs boson and the electroweak gauge bosons in two effective field theory bases: d[over ˜] in the HISZ basis and c_{HW[over ˜]} in the Warsaw basis. The results presented are the most stringent constraints on CP violation in the coupling between Higgs and weak bosons. The 95% C.L. constraint on d[over ˜] is derived for the first time and the 95% C.L. constraint on c_{HW[over ˜]} has been improved by a factor of 5 compared to the previous measurement.

Carbohydrate flow through agricultural ecosystems: Implications for synthesis and microbial conversion of carbohydrates.

Carbohydrates are chemically and structurally diverse biomolecules, serving numerous and varied roles in agricultural ecosystems. Crops and horticulture products are inherent sources of carbohydrates that are consumed by humans and non-human animals alike; however carbohydrates are also present in other agricultural materials, such as soil and compost, human and animal tissues, milk and dairy products, and honey. The biosynthesis, modification, and flow of carbohydrates within and between agricultural ecosystems is intimately related with microbial communities that colonize and thrive within these environments. Recent advances in -omics techniques have ushered in a new era for microbial ecology by illuminating the functional potential for carbohydrate metabolism encoded within microbial genomes, while agricultural glycomics is providing fresh perspective on carbohydrate-microbe interactions and how they influence the flow of functionalized carbon. Indeed, carbohydrates and carbohydrate-active enzymes are interventions with unrealized potential for improving carbon sequestration, soil fertility and stability, developing alternatives to antimicrobials, and circular production systems. In this manner, glycomics represents a new frontier for carbohydrate-based biotechnological solutions for agricultural systems facing escalating challenges, such as the changing climate.

Development of a spore-based mucosal vaccine against the bovine respiratory pathogen Mannheimia haemolytica.

Bovine respiratory disease (BRD) is a significant health issue in the North American feedlot industry, causing substantial financial losses due to morbidity and mortality. A lack of effective vaccines against BRD pathogens has resulted in antibiotics primarily being used for BRD prevention. The aim of this study was to develop a mucosal vaccine against the BRD pathogen, Mannheimia haemolytica, using Bacillus subtilis spores as an adjuvant. A chimeric protein (MhCP) containing a tandem repeat of neutralizing epitopes from M. haemolytica leukotoxin A (NLKT) and outer membrane protein PlpE was expressed to produce antigen for adsorption to B. subtilis spores. Adsorption was optimized by comparing varying amounts of antigen and spores, as well as different buffer pH and reaction temperatures. Using the optimal adsorption parameters, spore-bound antigen (Spore-MhCP) was prepared and administered to mice via two mucosal routes (intranasal and intragastric), while intramuscular administration of free MhCP and unvaccinated mice were used as positive and negative control treatments, respectively. Intramuscular administration of MhCP elicited the strongest serum IgG response. However, intranasal immunization of Spore-MhCP generated the best secretory IgA-specific response against both PlpE and NLKT in all samples evaluated (bronchoalveolar lavage, saliva, and feces). Since proliferation of M. haemolytica in the respiratory tract is a prerequisite to lung infection, this spore-based vaccine may offer protection in cattle by limiting colonization and subsequent infection, and Spore-MhCP warrants further evaluation in cattle as a mucosal vaccine against M. haemolytica.

The Gram-positive bacterium Romboutsia ilealis harbors a polysaccharide synthase that can produce (1,3;1,4)-ß-D-glucans.

(1,3;1,4)-ß-D-Glucans are widely distributed in the cell walls of grasses (family Poaceae) and closely related families, as well as some other vascular plants. Additionally, they have been found in other organisms, including fungi, lichens, brown algae, charophycean green algae, and the bacterium Sinorhizobium meliloti. Only three members of the Cellulose Synthase-Like (CSL) genes in the families CSLF, CSLH, and CSLJ are implicated in (1,3;1,4)-ß-D-glucan biosynthesis in grasses. Little is known about the enzymes responsible for synthesizing (1,3;1,4)-ß-D-glucans outside the grasses. In the present study, we report the presence of (1,3;1,4)-ß-D-glucans in the exopolysaccharides of the Gram-positive bacterium Romboutsia ilealis CRIBT. We also report that RiGT2 is the candidate gene of R. ilealis that encodes (1,3;1,4)-ß-D-glucan synthase. RiGT2 has conserved glycosyltransferase family 2 (GT2) motifs, including D, D, D, QXXRW, and a C-terminal PilZ domain that resembles the C-terminal domain of bacteria cellulose synthase, BcsA. Using a direct gain-of-function approach, we insert RiGT2 into Saccharomyces cerevisiae, and (1,3;1,4)-ß-D-glucans are produced with structures similar to those of the (1,3;1,4)-ß-D-glucans of the lichen Cetraria islandica. Phylogenetic analysis reveals that putative (1,3;1,4)-ß-D-glucan synthase candidate genes in several other bacterial species support the finding of (1,3;1,4)-ß-D-glucans in these species.

Multivalent Carbohydrate Nanocomposites for Tumor Microenvironment Remodeling to Enhance Antitumor Immunity.

Current cancer immunotherapeutic strategies mainly focus on remodeling the tumor microenvironment (TME) to make it favorable for antitumor immunity. Increasing attention has been paid to developing innovative immunomodulatory adjuvants that can restore weakened antitumor immunity by conferring immunogenicity to inflamed tumor tissues. Here, a galactan-enriched nanocomposite (Gal-NC) is developed from native carbohydrate structures through an optimized enzymatic transformation for effective, stable, and biosafe innate immunomodulation. Gal-NC is characterized as a carbohydrate nanoadjuvant with a macrophage-targeting feature. It is composed of repeating galactan glycopatterns derived from heteropolysaccharide structures of plant origin. The galactan repeats of Gal-NC function as multivalent pattern-recognition sites for Toll-like receptor 4 (TLR4). Functionally, Gal-NC-mediated TLR activation induces the repolarization of tumor-associated macrophages (TAMs) toward immunostimulatory/tumoricidal M1-like phenotypes. Gal-NC increases the intratumoral population of cytotoxic T cells, the main effector cells of antitumor immunity, via re-educated TAMs. These TME alterations synergistically enhance the T-cell-mediated antitumor response induced by αPD-1 administration, suggesting that Gal-NC has potential value as an adjuvant for immune checkpoint blockade combination therapies. Thus, the Gal-NC model established herein suggests a glycoengineering strategy to design a carbohydrate-based nanocomposite for advanced cancer immunotherapies.

Visualization of Carbohydrate Uptake Using Fluorescent Polysaccharides.

Fluorescently labeled polysaccharides enable the visualization of carbohydrate-bacterial interactions and the quantification of carbohydrate hydrolysis rates in cultures and complex communities. Here, we present the method of generating polysaccharides conjugated to the fluorescent molecule, fluoresceinamine. Further, we describe the protocol of incubating these probes in bacterial cultures and complex environmental microbial communities, visualizing bacterial-probe interactions using fluorescence microscopy, and quantifying these interactions using flow cytometry. Finally, we present a novel approach for the in situ metabolic phenotyping of bacterial cells using fluorescently activated cell sorting coupled with omics-based analysis.

Evaluation of Rumen Fermentation and Microbial Adaptation to Three Red Seaweeds Using the Rumen Simulation Technique.

Several red seaweeds have been shown to inhibit enteric CH4 production; however, the adaptation of fermentation parameters to their presence is not well understood. The objective of this study was to examine the effect of three red seaweeds (Asparargopsis taxiformis, Mazzaella japonica, and Palmaria mollis) on in vitro fermentation, CH4 production, and adaptation using the rumen simulation technique (RUSITEC). The experiment was conducted as a completely randomized design with four treatments, duplicated in two identical RUSITEC apparatus equipped with eight fermenter vessels each. The four treatments included the control and the three red seaweeds added to the control diet at 2% diet DM. The experimental period was divided into four phases including a baseline phase (d 0-7; no seaweed included), an adaptation phase (d 8-11; seaweed included in treatment vessels), an intermediate phase (d 12-16), and a stable phase (d 17-21). The degradability of organic matter (p = 0.04) and neutral detergent fibre (p = 0.05) was decreased by A. taxiformis during the adaptation phase, but returned to control levels in the stable phase. A. taxiformis supplementation resulted in a decrease (p < 0.001) in the molar proportions of acetate, propionate, and total volatile fatty acid (VFA) production, with an increase in the molar proportions of butyrate, caproate, and valerate; the other seaweeds had no effect (p > 0.05) on the molar proportions or production of individual VFA. A. taxiformis was the only seaweed to suppress CH4 production (p < 0.001), with the suppressive effect increasing (p < 0.001) across phases. Similarly, A. taxiformis increased (p < 0.001) the production of hydrogen (H2, %, mL/d) across the adaptation, intermediate, and stable phases, with the intermediate and stable phases having greater H2 production than the adaptation phase. In conclusion, M. japonica and P. mollis did not impact rumen fermentation or inhibit CH4 production within the RUSITEC. In contrast, we conclude that A. taxiformis is an effective CH4 inhibitor and its introduction to the ruminal environment requires a period of adaptation; however, the large magnitude of CH4 suppression by A. taxiformis inhibits VFA synthesis, which may restrict the production performance in vivo.

Comparative analysis of macroalgae supplementation on the rumen microbial community: Asparagopsis taxiformis inhibits major ruminal methanogenic, fibrolytic, and volatile fatty acid-producing microbes in vitro.

Seaweeds have received a great deal of attention recently for their potential as methane-suppressing feed additives in ruminants. To date, Asparagopsis taxiformis has proven a potent enteric methane inhibitor, but it is a priority to identify local seaweed varieties that hold similar properties. It is essential that any methane inhibitor does not compromise the function of the rumen microbiome. In this study, we conducted an in vitro experiment using the RUSITEC system to evaluate the impact of three red seaweeds, A. taxiformis, Palmaria mollis, and Mazzaella japonica, on rumen prokaryotic communities. 16S rRNA sequencing showed that A. taxiformis had a profound effect on the microbiome, particularly on methanogens. Weighted Unifrac distances showed significant separation of A. taxiformis samples from the control and other seaweeds (p < 0.05). Neither P. mollis nor M. japonica had a substantial effect on the microbiome (p > 0.05). A. taxiformis reduced the abundance of all major archaeal species (p < 0.05), leading to an almost total disappearance of the methanogens. Prominent fiber-degrading and volatile fatty acid (VFA)-producing bacteria including Fibrobacter and Ruminococcus were also inhibited by A. taxiformis (p < 0.05), as were other genera involved in propionate production. The relative abundance of several other bacteria including Prevotella, Bifidobacterium, Succinivibrio, Ruminobacter, and unclassified Lachnospiraceae were increased by A. taxiformis suggesting that the rumen microbiome adapted to an initial perturbation. Our study provides baseline knowledge of microbial dynamics in response to seaweed feeding over an extended period and suggests that feeding A. taxiformis to cattle to reduce methane may directly, or indirectly, inhibit important fiber-degrading and VFA-producing bacteria.

Glycogen-Degrading Activities of Catalytic Domains of α-Amylase and α-Amylase-Pullulanase Enzymes Conserved in Gardnerella spp. from the Vaginal Microbiome.

Gardnerella spp. are associated with bacterial vaginosis in which normally dominant lactobacilli are replaced with facultative and anaerobic bacteria, including Gardnerella spp. Co-occurrence of multiple species of Gardnerella is common in the vagina, and competition for nutrients such as glycogen likely contributes to the differential abundances of Gardnerella spp. Glycogen must be digested into smaller components for uptake, a process that depends on the combined action of glycogen-degrading enzymes. In this study, the ability of culture supernatants of 15 isolates of Gardnerella spp. to produce glucose, maltose, maltotriose, and maltotetraose from glycogen was demonstrated. Carbohydrate-active enzymes (CAZymes) were identified bioinformatically in Gardnerella proteomes using dbCAN2. Identified proteins included a single-domain α-amylase (EC 3.2.1.1) (encoded by all 15 isolates) and an α-amylase-pullulanase (EC 3.2.1.41) containing amylase, carbohydrate binding modules, and pullulanase domains (14/15 isolates). To verify the sequence-based functional predictions, the amylase and pullulanase domains of the α-amylase-pullulanase and the single-domain α-amylase were each produced in Escherichia coli. The α-amylase domain from the α-amylase-pullulanase released maltose, maltotriose, and maltotetraose from glycogen, and the pullulanase domain released maltotriose from pullulan and maltose from glycogen, demonstrating that the Gardnerella α-amylase-pullulanase is capable of hydrolyzing α-1,4 and α-1,6 glycosidic bonds. Similarly, the single-domain α-amylase protein also produced maltose, maltotriose, and maltotetraose from glycogen. Our findings show that Gardnerella spp. produce extracellular amylase enzymes as "public goods" that can digest glycogen into maltose, maltotriose, and maltotetraose that can be used by the vaginal microbiota. IMPORTANCE Increased abundance of Gardnerella spp. is a diagnostic characteristic of bacterial vaginosis, an imbalance in the human vaginal microbiome associated with troubling symptoms, and negative reproductive health outcomes, including increased transmission of sexually transmitted infections and preterm birth. Competition for nutrients is likely an important factor in causing dramatic shifts in the vaginal microbial community, but little is known about the contribution of bacterial enzymes to the metabolism of glycogen, a major food source available to vaginal bacteria. The significance of our research is characterizing the activity of enzymes conserved in Gardnerella species that contribute to the ability of these bacteria to utilize glycogen.

The pangenome of the wheat pathogen Pyrenophora tritici-repentis reveals novel transposons associated with necrotrophic effectors ToxA and ToxB.

BACKGROUND: In fungal plant pathogens, genome rearrangements followed by selection pressure for adaptive traits have facilitated the co-evolutionary arms race between hosts and their pathogens. Pyrenophora tritici-repentis (Ptr) has emerged recently as a foliar pathogen of wheat worldwide and its populations consist of isolates that vary in their ability to produce combinations of different necrotrophic effectors. These effectors play vital roles in disease development. Here, we sequenced the genomes of a global collection (40 isolates) of Ptr to gain insights into its gene content and genome rearrangements. RESULTS: A comparative genome analysis revealed an open pangenome, with an abundance of accessory genes (~ 57%) reflecting Ptr's adaptability. A clear distinction between pathogenic and non-pathogenic genomes was observed in size, gene content, and phylogenetic relatedness. Chromosomal rearrangements and structural organization, specifically around effector coding genes, were detailed using long-read assemblies (PacBio RS II) generated in this work in addition to previously assembled genomes. We also discovered the involvement of large mobile elements associated with Ptr's effectors: ToxA, the gene encoding for the necrosis effector, was found as a single copy within a 143-kb 'Starship' transposon (dubbed 'Horizon') with a clearly defined target site and target site duplications. 'Horizon' was located on different chromosomes in different isolates, indicating mobility, and the previously described ToxhAT transposon (responsible for horizontal transfer of ToxA) was nested within this newly identified Starship. Additionally, ToxB, the gene encoding the chlorosis effector, was clustered as three copies on a 294-kb element, which is likely a different putative 'Starship' (dubbed 'Icarus') in a ToxB-producing isolate. ToxB and its putative transposon were missing from the ToxB non-coding reference isolate, but the homolog toxb and 'Icarus' were both present in a different non-coding isolate. This suggests that ToxB may have been mobile at some point during the evolution of the Ptr genome which is contradictory to the current assumption of ToxB vertical inheritance. Finally, the genome architecture of Ptr was defined as 'one-compartment' based on calculated gene distances and evolutionary rates. CONCLUSIONS: These findings together reflect on the highly plastic nature of the Ptr genome which has likely helped to drive its worldwide adaptation and has illuminated the involvement of giant transposons in facilitating the evolution of virulence in Ptr.

Structural compositions and biological activities of cell wall polysaccharides in the rhizome, stem, and leaf of Polygonatum odoratum (Mill.) Druce.

Polygonatum odoratum is a perennial rhizomatous medicinal plant and different plant parts have been used in the treatment of various ailments. Herein, we have investigated the structural compositions of rhizome, leaf, and stem cell walls. We found 30-44% of polysaccharides in these wall preparations were cyclohexanediaminetetraacetic acid (CDTA) extractable, the proportion of heteromannans (HMs) in the rhizome is nearly three-fold compared to that of the leave and stem. The pectic polysaccharides of the rhizome are also structurally more diverse, with arabinans and type I and type II arabinogalactans being richest as shown by linkage study of the sodium carbonate (Na2CO3) extract. In addition, the 2-linked Araf was rhizome-specific, suggesting the cell walls in the rhizome had adapted to a more complex structure compared to that of the leaf and stem. Water-soluble polysaccharide fractions were also investigated, high proportion of Man as in 4-linked Manp indicated high proportion of HMs. The 21.4 kDa pectic polysaccharides and HMs derived from rhizome cell walls induced specific immune response in mice macrophage cells producing IL-1α and hematopoietic growth factors GM-CSF and G-CSF in vitro.