Miracle-dz/UniFAR-FTUs huggingface dataset:
Genome-Wide Identification and Analysis of Chitinase GH18 Gene Family in Mycogone perniciosa

Mycogone perniciosa causes wet bubble disease in Agaricus bisporus and various Agaricomycetes species. In a previous work, we identified 41 GH18 chitinase genes and other pathogenicity-related genes in the genome of M. perniciosa Hp10. Chitinases are enzymes that degrade chitin, and they have diverse functions in nutrition, morphogenesis, and pathogenesis. However, these important genes in M. perniciosa have not been fully characterized, and their functions remain unclear. Here, we performed a genome-wide analysis of M. perniciosa GH18 genes and analyzed the transcriptome profiles and GH18 expression patterns in M. perniciosa during the time course of infection in A. bisporus. Phylogenetic analysis of the 41 GH18 genes with those of 15 other species showed that the genes were clustered into three groups and eight subgroups based on their conserved domains. The GH18 genes clustered in the same group shared different gene structures but had the same protein motifs. All GH18 genes were localized in different organelles, were unevenly distributed on 11 contigs, and had orthologs in the other 13 species. Twelve duplication events were identified, and these had undergone both positive and purifying selection. The transcriptome analyses revealed that numerous genes, including transporters, cell wall degrading enzymes (CWDEs), cytochrome P450, pathogenicity-related genes, secondary metabolites, and transcription factors, were significantly upregulated at different stages of M. perniciosa Hp10 infection of A. bisporus. Twenty-three out of the 41 GH18 genes were differentially expressed. The expression patterns of the 23 GH18 genes were different and were significantly expressed from 3 days post-inoculation of M. perniciosa Hp10 in A. bisporus. Five differentially expressed GH18 genes were selected for RT-PCR and gene cloning to verify RNA-seq data accuracy. The results showed that those genes were successively expressed in different infection stages, consistent with the previous sequencing results. Our study provides a comprehensive analysis of pathogenicity-related and GH18 chitinase genes’ influence on M. perniciosa mycoparasitism of A. bisporus. Our findings may serve as a basis for further studies of M. perniciosa mycoparasitism, and the results have potential value for improving resistance in A. bisporus and developing efficient disease-management strategies to mitigate wet bubble disease.
Preparation and validation of monoclonal antibody-based indirect competitive ELISA for detecting testosterone levels

This paper presents the generation of monoclonal antibodies (mAbs) against testosterone (TES) through cell fusion technology, and the development of a mAb-based indirect competitive enzyme-linked immunosorbent assay (icELISA) method to detect TES residue in bovine edible tissues. Under optimal conditions, this assay exhibited a working range of 0.04–19 ng/mL, with half-maximum inhibition (IC50) and limit of detection values of 0.27 and 0.02 ng/mL, respectively. After three sample pretreatment procedures were checked, a simple dilution method was adopted for further use. The stabilisation studies demonstrated that the icELISA kits can be stored for at least 180 to 240 days, at 4°C and −20°C, respectively. When applied to bovine samples, the data from icELISA and gas chromatography coupled to mass spectrometry showed excellent correlation (r2=0.9923 in muscle, 0.9884 in liver and 0.9957 in kidney). Therefore, this assay has the potential to be incorporated into a quantitative monitoring programme for the rapid screening of TES residue in foods.
Assessing the Effects of β-Triketone Herbicides on the Soil Bacterial and hppd Communities: A Lab-to-Field Experiment

Maize cultivators often use β-triketone herbicides to prevent the growth of weeds in their fields. These herbicides target the 4-HPPD enzyme of dicotyledons. This enzyme, encoded by the hppd gene, is widespread among all living organisms including soil bacteria, which are considered as “non-target organisms” by the legislation. Within the framework of the pesticide registration process, the ecotoxicological impact of herbicides on soil microorganisms is solely based on carbon and nitrogen mineralization tests. In this study, we used more extensive approaches to assess with a lab-to-field experiment the risk of β-triketone on the abundance and the diversity of both total and hppd soil bacterial communities. Soil microcosms were exposed, under lab conditions, to 1× or 10× the recommended dose of sulcotrione or its commercial product, Decano®. Whatever the treatment applied, sulcotrione was fully dissipated from soil after 42 days post-treatment. The abundance and the diversity of both the total and the hppd bacterial communities were not affected by the herbicide treatments all along the experiment. Same measurements were led in real agronomical conditions, on three different fields located in the same area cropped with maize: one not exposed to any plant protection products, another one exposed to a series of plant protection products (PPPs) comprising mesotrione, and a last one exposed to different PPPs including mesotrione and tembotrione, two β-triketones. In this latter, the abundance of the hppd community varied over time. The diversity of the total and the hppd communities evolved over time independently from the treatment received. Only slight but significant transient effects on the abundance of the hppd community in one of the tested soil were observed. Our results showed that tested β-triketones have no visible impact toward both total and hppd soil bacteria communities.
Genome-Wide Association Study of Tan Spot Resistance in a Hexaploid Wheat Collection From Kazakhstan

Tan spot, caused by Pyrenophora tritici-repentis, is a serious foliar disease of wheat in Kazakhstan with reported yield losses as high as 50% during epidemic years. Here, we report the evaluation of a collection of 191 hexaploid spring and winter wheat lines for tan spot resistance and its underlying genetic architecture using genome-wide association study (GWAS). Our wheat collection comprised candidate varieties from Kazakhstan, Russia, and CIMMYT. It was genotyped using the DArTseq technology and phenotyped for resistance to tan spot at seedling and adult plant stages in Kazakhstan. DArTseq SNPs revealed high genetic diversity (average polymorphic information content = 0.33) in the panel and genome-wide linkage disequilibrium decay at 22 Mb (threshold r2 = 0.1). Principal component analysis revealed a clear separation of Eurasian germplasm from CIMMYT and IWWIP lines. GWAS identified 34 marker-trait associations (MTA) for resistance to tan spot and the amount of phenotypic variation explained by these MTA ranged from 4% to 13.7%. Our results suggest the existence of novel valuable resistant alleles on chromosomes 3BS, and 5DL and 6AL for resistance to Race 1 and Race 5, respectively, in addition to known genes tsn1 and tsc2. On chromosome 6AL, a genomic region spanning 3 Mb was identified conferring resistance to both Race 1 and Race 5. Epistatic interaction of associated loci was revealed on chromosomes 1B, 5B, 7B, 5A, and 6A contributing to additional variation of 3.2–11.7%. Twenty-five lines with the best allele combinations of SNPs associated with resistance to both races have been identified as candidates for future variety release and breeding. The results of the present study will be further validated in other independent genetic backgrounds to be able to use markers in breeding.
PROCEEDINGS OF THE 3RD INTERNATIONAL CONFERENCE ON MOLECULAR SIMULATION Quantum simulation for muoniated and deuterated methyl radicals in implicit water solvent: combined ab initio path integral molecular dynamics and the polarizable continuum model simulation study

We have combined ab initio path integral molecular dynamics (PIMD) simulation and the polarizable continuum model (PCM) method to efficiently incorporate solvent effects into nuclear quantum fluctuation of molecular systems. Our combined ab initio PIMD–PCM simulation was applied to muoniated and deuterated methyl radical immersed in implicit water solvent to gain information on solvent and isotope effects from one simulation run. We found that solvent effects lead to the bond elongation and a decrease in the magnitude of isotropic hyperfine coupling constants. These are consistent with the trends in conventional static calculations and experiments. In addition, the performance of cavity models (universal force field, united atom specified for Kohn–Sham and these hybrid models) and the conservation of the PIMD–PCMHamiltonian were accessed. We confirmed that solvent effects on nuclear quantum fluctuation are efficiently computed using our combined simulation of quantum solute in implicit solvent.
Characterisation of Cellulose Synthase Like F6 (CslF6) Mutants Shows Altered Carbon Metabolism in β-D-(1,3;1,4)-Glucan Deficient Grain in Brachypodium distachyon

Brachypodium distachyon is a small, fast growing grass species in the Pooideae subfamily that has become established as a model for other temperate cereals of agricultural significance, such as barley (Hordeum vulgare) and wheat (Triticum aestivum). The unusually high content in whole grains of β-D-(1,3;1,4)-glucan or mixed linkage glucan (MLG), considered a valuable dietary fibre due to its increased solubility in water compared with cellulose, makes B. distachyon an attractive model for these polysaccharides. The carbohydrate composition of grain in B. distachyon is interesting not only in understanding the synthesis of MLG, but more broadly in the mechanism(s) of carbon partitioning in cereal grains. Several mutants in the major MLG synthase, cellulose synthase like (CSL) F6, were identified in a screen of a TILLING population that show a loss of function in vitro. Surprisingly, loss of cslf6 synthase capacity appears to have a severe impact on survival, growth, and development in B. distachyon in contrast to equivalent mutants in barley and rice. One mutant, A656T, which showed milder growth impacts in heterozygotes shows a 21% (w/w) reduction in average grain MLG and more than doubling of starch compared with wildtype. The endosperm architecture of grains with the A656T mutation is altered, with a reduction in wall thickness and increased deposition of starch in larger granules than typical of wildtype B. distachyon. Together these changes demonstrate an alteration in the carbon storage of cslf6 mutant grains in response to reduced MLG synthase capacity and a possible cross-regulation with starch synthesis which should be a focus in future work in composition of these grains. The consequences of these findings for the use of B. distachyon as a model species for understanding MLG synthesis, and more broadly the implications for improving the nutritional value of cereal grains through alteration of soluble dietary fibre content are discussed.
Genetic Structure, Function, and Evolution of Capsule Biosynthesis Loci in Vibrio parahaemolyticus

Capsule-forming extracellular polysaccharides are crucial for bacterial host colonization, invasion, immune evasion, and ultimately pathogenicity. Due to warming ocean waters and human encroachment of coastal ecosystems, Vibrio parahaemolyticus has emerged as a globally important foodborne enteropathogen implicated in acute gastroenteritis, wound infections, and septic shock. Conventionally, the antigenic properties of lipopolysaccharide (LPS, O antigen) and capsular polysaccharide (CPS, K antigen) have provided a basis for serotyping V. parahaemolyticus, whereas disclosure of genetic elements encoding 13 O-serogroups have allowed molecular serotyping methods to be developed. However, the genetic structure of CPS loci for 71 K-serogroups has remained unidentified, limiting progress in understanding its roles in V. parahaemolyticus pathophysiology. In this study, we identified and characterized the genetic structure and their evolutionary relationship of CPS loci of 40 K-serogroups through whole genome sequencing of 443 V. parahaemolyticus strains. We found a distinct pattern of CPS gene cluster across different K-serogroups and expanded its new 3′-border by identifying glpX as a key gene conserved across all K-serogroups. A total of 217 genes involved in CPS biosynthesis were annotated. Functional contents and genetic structure of the 40 K-serogroups were analyzed. Based on inferences from species trees and gene trees, we proposed an evolution model of the CPS gene clusters of 40 K-serogroups. Horizontal gene transfer by recombination from other Vibrio species, gene duplication is likely to play instrumental roles in the evolution of CPS in V. parahaemolyticus. This is the first time, to the best of our knowledge, that a large scale of CPS gene clusters of different K-serogroups in V. parahaemolyticus have been identified and characterized in evolutionary contexts. This work should help advance understanding on the variation of CPS in V. parahaemolyticus and provide a framework for developing diagnostically relevant serotyping methods.
Spatial Epidemiology of Salmonellosis in Florida, 2009–2018

Non-typhoidal Salmonella enterica infections cause a high disease burden in the United States with an estimated 1.2 million illnesses annually. The state of Florida consistently has a relatively high incidence compared to other states in the United States. Nevertheless, studies regarding the epidemiology of nontyphoidal salmonellosis and its spatial and temporal patterns in Florida were rarely reported. We examined the spatial and temporal patterns of 62,947 salmonellosis cases reported to FL Health Charts between 2009 and 2018. Dominant serotypes circulating in Florida were also explored using whole genome sequencing (WGS) based serotype-prediction for 2,507 Salmonella isolates sequenced by the Florida Department of Health during 2017 and 2018. The representativeness of laboratory-sequenced isolates for reported cases was determined by regression modeling. The annual incidence rate of salmonellosis decreased from 36.0 per 100,000 population in 2009 to 27.8 per 100,000 in 2016, and gradually increased in 2017 and 2018. Increased use of culture-independent testing did not fully explain this increase. The highest incidence rate was observed in children, contributing 40.9% of total reported cases during this period. A seasonal pattern was observed with the incidence peaking in September and October, later than the national average pattern. Over these 10 years, the Northeast and Northwest regions of the state had higher reported incidence rates, while reported rates in the Southeast and South were gradually increasing over time. Serotypes were predicted based on WGS data in the EnteroBase platform. The top-five most prevalent serotypes in Florida during 2017–2018 were Enteritidis, Newport, Javiana, Sandiego and Braenderup. The highest percentage of isolates was from children under 5 years of age (41.4%), and stool (84.7%) was the major source of samples. A zero-inflated negative binomial regression model showed that the reported case number was a strong predictor for the number of lab-sequenced isolates in individual counties, and the geospatial distribution of sequenced isolates was not biased by other factors such as age group. The spatial and temporal patterns identified in this study along with the prevalence of different serotypes will be helpful for the development of efficient prevention and control strategies for salmonellosis in Florida.
Endosphere Microbiome and Metabolic Differences Between the Spots and Green Parts of Tricyrtis macropoda Leaves

Background Plant leaves are important organs for photosynthesis and biological energy production. The leaves of Tricyrtis macropoda have an unusual spotted pattern. However, whether the spots of T. macropoda affect the plant microbiome and metabolites is unclear. In this study, we compared differences in the endosphere microbiome and plant metabolites in green parts and spots and the effects of spots on the photosynthesis of leaves. Methods 16S/ITS sequences and metabolite spectra were obtained by high-throughput amplicon sequencing and ultra-high-performance liquid chromatography–high-resolution mass spectrometry, respectively. Changes in the diversity of the endophytic microbial community and metabolites were studied, and the effect of T. macropoda leaf spots on photosynthesis was examined by chlorophyll fluorescence. Results The results showed that the relative abundance of Cercospora fungi in the leaf spots of T. macropoda was significantly higher than that in the green parts (P < 0.05) while Colletotrichum fungi showed low abundance in the spots. Alkaloid and ketone metabolites were decreased in the green parts compared with the spots, and amino acids, organic acids, lipids, and other compounds were increased in the green parts compared with the spots. A combined analysis of microbial communities and metabolites showed a significant correlation between the endophytic fungal communities and metabolite production. The changes in these metabolites may cause changes in local leaf color. In addition, we found that the spot areas of T. macropoda can be photosynthetically normal. Conclusion This research showed the relationship between endophytic microorganisms and metabolites, and the findings advance our understanding of endophyte–plant interactions and provide a new direction for investigating the relationship between endophytes and phenotypes.
Vaccination and Infection of Swine With Salmonella Typhimurium Induces a Systemic and Local Multifunctional CD4+ T-Cell Response

The gram-negative facultative intracellular bacteria Salmonella Typhimurium (STM) often leads to subclinical infections in pigs, but can also cause severe enterocolitis in this species. Due to its high zoonotic potential, the pathogen is likewise dangerous for humans. Vaccination with a live attenuated STM strain (Salmoporc) is regarded as an effective method to control STM infections in affected pig herds. However, information on the cellular immune response of swine against STM is still scarce. In this study, we investigated the T-cell immune response in pigs that were vaccinated twice with Salmoporc followed by a challenge infection with a virulent STM strain. Blood- and organ-derived lymphocytes (spleen, tonsils, jejunal and ileocolic lymph nodes, jejunum, ileum) were stimulated in vitro with heat-inactivated STM. Subsequently, CD4+ T cells present in these cell preparations were analyzed for the production of IFN-γ, TNF-α, and IL-17A by flow cytometry and Boolean gating. Highest frequencies of STM-specific cytokine-producing CD4+ T cells were found in lamina propria lymphocytes of jejunum and ileum. Significant differences of the relative abundance of cytokine-producing phenotypes between control group and vaccinated + infected animals were detected in most organs, but dominated in gut and lymph node-residing CD4+ T cells. IL-17A producing CD4+ T cells dominated in gut and gut-draining lymph nodes, whereas IFN-γ/TNF-α co-producing CD4+ T cells were present in all locations. Additionally, the majority of cytokine-producing CD4+ T cells had a CD8α+CD27- phenotype, indicative of a late effector or effector memory stage of differentiation. In summary, we show that Salmonella-specific multifunctional CD4+ T cells exist in vaccinated and infected pigs, dominate in the gut and most likely contribute to protective immunity against STM in the pig.
Contributive Role of TNF-α to L-DOPA-Induced Dyskinesia in a Unilateral 6-OHDA Lesion Model of Parkinson’s Disease

Our present objective was to better characterize the mechanisms that regulate striatal neuroinflammation in mice developing L-DOPA-induced dyskinesia (LID). For that, we used 6-hydroxydopamine (6-OHDA)-lesioned mice rendered dyskinetic by repeated intraperitoneal injections of 3,4-dihydroxyphenyl-L-alanine (L-DOPA) and quantified ensuing neuroinflammatory changes in the dopamine-denervated dorsal striatum. LID development was associated with a prominent astrocytic response, and a more moderate microglial cell reaction restricted to this striatal area. The glial response was associated with elevations in two pro-inflammatory cytokines, tumor necrosis factor-α (TNF-α) and interleukin-1β. Treatment with the phytocannabinoid cannabidiol and the transient receptor potential vanilloid-1 (TRPV-1) channel antagonist capsazepine diminished LID intensity and decreased TNF-α levels without impacting other inflammation markers. To possibly reproduce the neuroinflammatory component of LID, we exposed astrocyte and microglial cells in culture to candidate molecules that might operate as inflammatory cues during LID development, i.e., L-DOPA, dopamine, or glutamate. Neither L-DOPA nor dopamine produced an inflammatory response in glial cell cultures. However, glutamate enhanced TNF-α secretion and GFAP expression in astrocyte cultures and promoted Iba-1 expression in microglial cultures. Of interest, the antidyskinetic treatment with cannabidiol + capsazepine reduced TNF-α release in glutamate-activated astrocytes. TNF-α, on its own, promoted the synaptic release of glutamate in cortical neuronal cultures, whereas cannabidiol + capsazepine prevented this effect. Therefore, we may assume that the release of TNF-α by glutamate-activated astrocytes may contribute to LID by exacerbating corticostriatal glutamatergic inputs excitability and maintaining astrocytes in an activated state through a self-reinforcing mechanism.
From BIDS-Formatted EEG Data to Sensor-Space Group Results: A Fully Reproducible Workflow With EEGLAB and LIMO EEG

Reproducibility is a cornerstone of scientific communication without which one cannot build upon each other’s work. Because modern human brain imaging relies on many integrated steps with a variety of possible algorithms, it has, however, become impossible to report every detail of a data processing workflow. In response to this analytical complexity, community recommendations are to share data analysis pipelines (scripts that implement workflows). Here we show that this can easily be done using EEGLAB and tools built around it. BIDS tools allow importing all the necessary information and create a study from electroencephalography (EEG)-Brain Imaging Data Structure compliant data. From there preprocessing can be carried out in only a few steps using EEGLAB and statistical analyses performed using the LIMO EEG plug-in. Using Wakeman and Henson (2015) face dataset, we illustrate how to prepare data and build different statistical models, a standard factorial design (faces ∗ repetition), and a more modern trial-based regression approach for the stimulus repetition effect, all in a few reproducible command lines.