32 research outputs found
Rhizopus stolonifer Exhibits Necrotrophic Behavior when Causing Soft Rot in Ripe Fruit
No full textAcknowledgments
We thank Yiduo Wei and Stefan Petrasch for assisting us with data analysis and interpretation; Manon Paineau for providing advice on optimizing the bioinformatic pipeline; and Carlos Carachure, Juniper Piedmont, and Annie Willett for their review of the manuscript's narrative.
Author contributions: B.B.-U. designed the study. B.B.-U., A.M.-C., and R.F.-B. designed the methodology. S.D.M.-P., A.M.-C., S.R.-P., R.F.-B., C.J.S., A.S., E.G.-B., and P.M.R. conducted the experiments. S.D.M.-P., A.M.-C., and C.J.S. conducted genomic and transcriptomic analyses. B.B.-U., S.D.M.-P., and A.M.-C. carried out data analysis and interpretation of results. B.B.-U. and S.D.M.-P. wrote the manuscript, with contributions and revisions from all co-authors. B.B.-U. and D.C. provided funding and resources and coordinated the study.
Funding: Support was provided by the College of Agriculture and Environmental Sciences and the Department of Plant Sciences at the University of California, Davis as start-up funding to B. Blanco-Ulate; and the Department of Plant Sciences, University of California, Davis, funded by endowments, particularly the James Monroe McDonald Endowment, administered by the Division of Agriculture and Natural Resources, University of California as a graduate student award to S. D. Mesquida-Pesci. The project leading to these results received funding from the “La Caixa” Foundation (ID 100010434; under the agreement LCF/BQ/AA19/11720034) to S. D. Mesquida-Pesci.
The author(s) declare no conflict of interest.Rhizopus stolonifer is known for causing soft rot in fruits and vegetables during postharvest. Although it has traditionally been considered a saprophyte, it appears to behave more like a necrotrophic pathogen. In this study, we propose that R. stolonifer invades host tissues by actively killing host cells and overcoming the host defense mechanisms, as opposed to growing saprophytically on decaying plant matter. We tested this hypothesis by characterizing R. stolonifer infection strategies when infecting four fruit hosts (tomato, grape, strawberry, and plum). We started by generating a high-quality genome assembly for R. stolonifer using PacBio sequencing. This led to a genome size of 45.02 Mb, an N50 of 2.87 Mb, and 12,644 predicted loci with protein-coding genes. Next, we performed a transcriptomic analysis to identify genes that R. stolonifer preferentially uses when growing in fruit versus culture media. We categorized these infection-related genes into clusters according to their expression patterns during the interaction with the host. Based on the expression data, we determined that R. stolonifer has a core infection toolbox consisting of strategies typical of necrotrophs, which includes a set of 33 oxidoreductases, 7 proteases, and 4 cell wall-degrading enzymes to facilitate tissue breakdown and maceration across various hosts. This study provides new genomic resources for R. stolonifer and advances the knowledge of Rhizopus–fruit interactions, which can assist in formulating effective and sustainable integrated pest management approaches for soft rot prevention.University of CaliforniaFundación "La Caixa"Depto. de Genética, Fisiología y MicrobiologíaFac. de Ciencias BiológicasTRUEpu
An Event-B Approach to Data Sharing Agreements
No full textThe original publication is available at www.springerlink.com.International audienceA Data Sharing Agreement (DSA) is a contract among two or more principals regulating how they share data. Agreements are usually represented as a set of clauses expressed using the deontic notions of obligation, prohibition and permission. In this paper, we present how to model DSAs using the Event-B specification language. Agreement clauses are modelled as temporal-logic formulas that preserve the intuitive meaning of the deontic operators, and constrain the actions that a principal can execute.We have exploited the ProB animator and model checker in order to verify that a system behaves according to its associated DSA and to validate that principals' actions are in agreement with the DSA clauses
OWL-S Atomic services composition with SWRL rules
No full textThis paper presents a method for encoding OWL-S atomic processes by means of SWRL rules and composing them using a backward search planning algorithm. A description of the preliminary prototype implementation is also presented
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Effect of Weather on the Die-Off of Escherichia coli and Attenuated Salmonella enterica Serovar Typhimurium on Preharvest Leafy Greens following Irrigation with Contaminated Water
No full textThe Food Safety Modernization Act (FSMA) includes a time-to-harvest interval following the application of noncompliant water to preharvest produce to allow for microbial die-off. However, additional scientific evidence is needed to support this rule. This study aimed to determine the impact of weather on the die-off rate of Escherichia coli and Salmonella on spinach and lettuce under field conditions. Standardized, replicated field trials were conducted in California, New York, and Spain over 2 years. Baby spinach and lettuce were grown and inoculated with an ∼104-CFU/ml cocktail of E. coli and attenuated Salmonella Leaf samples were collected at 7 time points (0 to 96 h) following inoculation; E. coli and Salmonella were enumerated. The associations of die-off with study design factors (location, produce type, and bacteria) and weather were assessed using log-linear and biphasic segmented log-linear regression. A segmented log-linear model best fit die-off on inoculated leaves in most cases, with a greater variation in the segment 1 die-off rate across trials (-0.46 [95% confidence interval {95% CI}, -0.52, -0.41] to -6.99 [95% CI, -7.38, -6.59] log10 die-off/day) than in the segment 2 die-off rate (0.28 [95% CI, -0.20, 0.77] to -1.00 [95% CI, -1.16, -0.85] log10 die-off/day). A lower relative humidity was associated with a faster segment 1 die-off and an earlier breakpoint (the time when segment 1 die-off rate switches to the segment 2 rate). Relative humidity was also found to be associated with whether die-off would comply with FSMA's specified die-off rate of -0.5 log10 die-off/day.IMPORTANCE The log-linear die-off rate proposed by FSMA is not always appropriate, as the die-off rates of foodborne bacterial pathogens and specified agricultural water quality indicator organisms appear to commonly follow a biphasic pattern with an initial rapid decline followed by a period of tailing. While we observed substantial variation in the net culturable population levels of Salmonella and E. coli at each time point, die-off rate and FSMA compliance (i.e., at least a 2 log10 die-off over 4 days) appear to be impacted by produce type, bacteria, and weather; die-off on lettuce tended to be faster than that on spinach, die-off of E. coli tended to be faster than that of attenuated Salmonella, and die-off tended to become faster as relative humidity decreased. Thus, the use of a single die-off rate for estimating time-to-harvest intervals across different weather conditions, produce types, and bacteria should be revised
Hydrogen sulfide is neuroprotective in Alzheimer’s disease by sulfhydrating GSK3β and inhibiting Tau hyperphosphorylation
No full textThis is the author accepted manuscript. The final version is available from the National Academy of Sciences via the DOI in this recordData Availability. All study data are included in the article and supporting
information.Alzheimer’s disease (AD), the most common cause of dementia and neurodegeneration in the elderly, is characterized by deterioration of memory and executive and motor functions. Neuropathologic hallmarks of AD include neurofibrillary tangles (NFTs), paired helical filaments, and amyloid plaques. Mutations in the microtubule-associated protein Tau, a major component of the NFTs, cause its hyperphosphorylation in AD. We have shown that signaling by the gaseous molecule hydrogen sulfide (H2S) is dysregulated during aging. H2S signals via a posttranslational modification termed sulfhydration/persulfidation, which participates in diverse cellular processes. Here we show that cystathionine γ-lyase (CSE), the biosynthetic enzyme for H2S, binds wild type Tau, which enhances its catalytic activity. By contrast, CSE fails to bind Tau P301L, a mutant that is present in the 3xTg-AD mouse model of AD. We further show that CSE is depleted in 3xTg-AD mice as well as in human AD brains, and that H2S prevents hyperphosphorylation of Tau by sulfhydrating its kinase, glycogen synthase kinase 3β (GSK3β). Finally, we demonstrate that sulfhydration is diminished in AD, while administering the H2S donor sodium GYY4137 (NaGYY) to 3xTg-AD mice ameliorates motor and cognitive deficits in AD.US Public Health Service GrantAmerican Heart Association (AHA)–Allen Initiative in Brain Health and Cognitive ImpairmentMedical Research Council (MRC)European Union Horizon 202
Genome-wide association scan meta-analysis identifies three loci influencing adiposity and fat distribution
No full textTo identify genetic loci influencing central obesity and fat distribution, we performed a meta-analysis of 16 genome-wide association studies (GWAS, N = 38,580) informative for adult waist circumference (WC) and waist–hip ratio (WHR). We selected 26 SNPs for follow-up, for which the evidence of association with measures of central adiposity (WC and/or WHR) was strong and disproportionate to that for overall adiposity or height. Follow-up studies in a maximum of 70,689 individuals identified two loci strongly associated with measures of central adiposity; these map near TFAP2B (WC, P = 1.9×10?11) and MSRA (WC, P = 8.9×10?9). A third locus, near LYPLAL1, was associated with WHR in women only (P = 2.6×10?8). The variants near TFAP2B appear to influence central adiposity through an effect on overall obesity/fat-mass, whereas LYPLAL1 displays a strong female-only association with fat distribution. By focusing on anthropometric measures of central obesity and fat distribution, we have identified three loci implicated in the regulation of human adiposit
Diversity of Methylobacterium Species Associated with New Zealand Native Plants
No full textThe genus Methylobacterium are pink-pigmented facultative methylotrophs (PPFMs), and are abundant colonizers of the phyllosphere, due to the availability of methanol, a waste product of pectin metabolism during plant cell division. Besides methanol cycling, Methylobacterium has important effects on plant health. The phyllosphere is an extreme environment with a landscape that is heterogeneous, continuously changing as the plant grows, and is exposed to very high ultra violet irradiation. Geographically, New Zealand has been isolated for over a million years, has a biologically diverse group of species, and is considered a biodiversity hotspot, with most of the native plants being endemic. We hypothesize that NZ native plants harbor diverse groups of Methylobacterium species, and to test this we aimed to isolate Methylobacterium species from the phyllosphere of native New Zealand plants. A leaf imprinting technique using methanol supplemented AMS agar media was used to isolate bacteria and diversity was determined using a combination of ARDRA, 16S rRNA gene sequencing and phylogenetic analysis. Methylobacterium spp. were successfully isolated from 19 of the 21 plant species used in this study. Eleven Methylobacterium species have been identified in association with the phyllosphere of native NZ plants: M. adhaesivum, M. brachiatum, M. komagatae, M. marchantiae, M. mesophilicum, M. phyllosphaerae, M. fujisawaense, M. oryzae, M. radiotolerans, M. tardum and M. zatmanii, with the first six being the most frequently isolated from more plant species. In this study other α, β, γ-proteobacterial species were also isolated: Hyphomicrobium, Methylopila, Rhizobium, Achromobacter, Methylophilus, Ramlibacter and Xanthomonas; Janibacter melonis (Actinomycetes); Niastella populi (Bacteroidetes) and Paenibacillus lautus (Firmicutes), highlighting the presence of potential novel methanol utilizer within the ecosystem. Results from this study indicate that Methylobacterium are abundant and dominant members of the NZ phyllosphere environment, with species diversity and composition dependent on the host plant species
