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83 results for “Cheese”
Supplemental data for: Longitudinal, multi-platform metagenomics yields a high-quality genomic catalog and guides an in vitro model for cheese communities
<p><span>Microbiomes are intricately intertwined with human health, geochemical cycles, and food production. While many microbiomes of interest are highly complex and experimentally intractable, cheese rind microbiomes have proven powerful model systems for the study of microbial interactions. To provide a more comprehensive view of the genomic potential and temporal dynamics of cheese rind communities, we combine longitudinal, multi-platform metagenomics of three ripening washed-rind cheeses with whole genome sequencing of community isolates. Sequencing-based approaches revealed a highly reproducible microbial succession in each cheese, co-existence of closely related <em>Psychrobacter</em> species, and enabled the prediction of plasmid and phage diversity and their host associations. Combined with culture-based approaches, we established a genomic catalog and a paired 16-member in vitro washed rind cheese system. The combination of multi-platform metagenomic time-series data and an <em>in vitro</em> model provides a rich resource for further investigation of cheese rind microbiomes both computationally and experimentally. </span></p>
TMI cheese metagenomics sourmash output files
<p>Sourmash output files from signature sketches, compare, gather, and taxonomy of time-series cheese metagenomes generated using both short- and long-read sequencing technologies. Originally generated as part of the pub <a href="https://research.arcadiascience.com/pub/data-set-metagenomics-timecourse-cheese/release/1">"Paired long- and short-read metagenomics of cheese rind microbial communities at multiple time points"</a>. Analysis code of this data provided on Github at <a href="https://github.com/Arcadia-Science/metagenomics-of-cheese-rind-microbiomes">https://github.com/Arcadia-Science/metagenomics-of-cheese-rind-microbiomes</a>. </p> <p>To directly analyze this data, download and unzip the tarball. Clone the Github repository and point to the 2023-05-23-TMI-processed-data directory within a project using the `scripts/TMI-sourmash-explore.R` script. Install the packages used in the script if necessary. </p>
Cheese community and virome nucleoside mass spec from Arome
<p>These are files from LC-MS/MS analysis of nucleosides from cheese microbial communities and their viromes. For each run, we have uploaded the .mgf, .raw, and .ms1 files. We have also uploaded run descriptions, a first pass analysis from Arome, and the LC-MS/MS methods and exclusions lists. If you want to know more about the specific details of the cheeses that we sampled, please check out our pub "<a href="https://research.arcadiascience.com/pub/data-set-metagenomics-timecourse-cheese/release/1">Paired long- and short-read metagenomics of cheese rind microbial communities at multiple time points</a>". </p> <p>File list:</p> <p>Run data files: .raw, .mgf, .ms1 file types </p> <p>Run descriptions: arome_run_descriptions.csv</p> <p>First pass analysis from Arome: 20221209_Arcadia_Nucleo_HILIC_POS_quant_ALL_IDs.csv</p> <p>Exclusion lists: exclusionmasstable_1.csv, exclusionmasstable_2.csv</p> <p>Methods file: MethodSummary_POS1.txt</p>
A mould for the cheese known as "oscypek"
A wooden, two-piece, symmetrical mould for a spindle-shaped piece of rennet cheese – oscypek. It was probably made in 1922 by Jan Stoch from Podhale. It was still used in the 1970s. in a hut in Krywanie (a hill with the height of 809 m above sea level located in Orawa, through which the border between Poland and Slovakia passes). Then it was absorbed by the ethnographic collection of Magdalena and Stanisław Zapaśnik. In 2013, along with a collection of other cheese moulds, it was transferred to the ethnographic collections of the Tatra Museum in Zakopane. It represents a type of closed mould, a rarity in the collections of the Zakopane institution. ID no.:E/10898/a,b/MT Time of creation: 1922 (?) Museum: The Dr. Tytus Chałubiński Tatra Museum in Zakopane https://muzea.malopolska.pl/en/objects-list/1986 Digitalisation: Digitalisation: RDW MIC, Virtual Małopolska project Source: Objaverse 1.0 / Sketchfab
Cheese Consumption and Human Microvascular Function
ClinicalTrials.gov study NCT03376555. IPD Sharing: NO. Countries: 1. Publications: 1.
Supplemental data for: Longitudinal, multi-platform metagenomics yields a high-quality genomic catalog and guides an in vitro model for cheese communities
Open the record for dataset details and reuse information.
Soil microbiome dataset from the University of Wisconsin Arlington and Lancaster agricultural research stations and cheese maker and vegetable processor wastewater land application sites
Open the record for dataset details and reuse information.
Independent domestication events in the blue-cheese fungus Penicillium roqueforti
Open the record for dataset details and reuse information.
Bronze Age Cheese Strainer, Castilla-La Mancha
Ceramic strainer/cheese tray from the site of ??, , Castilla-La Mancha, Spain. Bronze Age. In the collection of the Ciudad Real Museum. Catalog number DO000414. Processed in Reality Capture from 933 images. . This work is part of the collaboration agreement signed in 2020 between the Junta de Comunidades de Castilla-La Mancha and Global Digital Heritage for the digitization of the Cultural Heritage of Castilla-La Mancha region. We want to publicly thank the collaboration of the Museum of Ciudad Real, especially by its director José Ignacio de la Torre. Source: Objaverse 1.0 / Sketchfab
Novel formulations for developing fresh hybrid cheese analogues utilizing fungal-fermented brewery side-stream flours
<p>Datasets corresponding to the main and supplementary material of the research article "<span>Novel formulations for developing fresh hybrid cheese analogues utilizing fungal-fermented brewery side-stream flours</span> ". This research paper was a result of a scientific project which was part of the European Union's HORIZON 2020 with the acronym SMARTPROTEIN. </p>
Supplement: Functional strain redundancy and persistent phage infection in a Swiss hard cheese starter culture
<p>Undefined starter cultures are bacterial communities used in cheese making. They are phenotypically stable and propagated under constant conditions in milk. This makes them interesting to understand the eco-evolutionary dynamics of microbial communities. While cheese starter cultures are known to be dominated by a few bacterial species, little is known about the composition, functional relevance, and temporal dynamics of strain-level diversity. Here, we applied shotgun metagenomics to analyze historical samples spanning 22 years and continuous propagation for 123 generations of an important Swiss cheese starter culture. We found that the bacterial community is highly stable and dominated by two species, Streptococcus thermophilus and Lactobacillus delbrueckii subsp. lactis. Each species is represented by a few coexisting strains. Genome sequencing, metabolomics analysis, and co-culturing experiments show that these strains are functionally redundant, but differ tremendously in their phage resistance potential. Moreover, we identified two highly abundant Streptococcus phages that seem to stably coexist in the community without any negative impact on bacterial growth or strain persistence, and despite the presence of a large diversity of matching CRISPR spacers. Our findings provide novel insights into strain-level diversity in domesticated microbial communities and highlight an important role of bacteria-phage interactions in cheese starter cultures. </p>
Effect of Herbal Extracts on the Survival of Staphylococcus aureus in Goats' Raw Milk Cheese
<p>Presented as e-Poster Flash Presentation; and in Book of Abstracts of the International Seminar ArtiSaneFood - Biopreservation and Risk Modelling Approaches. Bragança, Portugal (24-25 May 2023) (Page 54).</p>
Technological and antimicrobial properties of indigenous LAB from Portuguese artisanal goat cheeses
<p>Recording of the talk “Technological and antimicrobial properties of indigenous LAB from Portuguese artisanal goat cheeses” presented by Beatriz Nunes Silva at the Artisanal Foods and Bioactive Molecules Seminar, Médenine, Tunisia (19-21 December 2021).</p>
Fortified Cheese and Yogurt Products and Vitamin D Status in Young Children? Phase 2
ClinicalTrials.gov study NCT02387892. IPD Sharing: UNDECIDED. Countries: 1. Publications: 1.
Determine How Consumption of Dairy Fat as Cheese Influences Inflammation-Phase 2
ClinicalTrials.gov study NCT01803633. IPD Sharing: Not stated. Countries: 1. Publications: 7.
Effect of High Cheese Consumption on Metabolic Syndrome Risk Factors
ClinicalTrials.gov study NCT02616471. IPD Sharing: Not stated. Countries: 1. Publications: 1.
Jarlsberg Cheese Compared to Camembert Cheese
ClinicalTrials.gov study NCT04189796. IPD Sharing: NO. Countries: 1. Publications: 1.
Efficacy Comparison of Jarlsberg- and Norvegia Cheese on Bone Markers and Bone Mineral Density in Nordic Skiers
ClinicalTrials.gov study NCT06688032. IPD Sharing: NO. Countries: 1. Publications: 1.
Effect of Cheese on Cardiovascular Risk
ClinicalTrials.gov study NCT01739153. IPD Sharing: Not stated. Countries: 1. Publications: 1.
Cheese and Human Health
ClinicalTrials.gov study NCT01140165. IPD Sharing: Not stated. Countries: 1. Publications: 1.
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Allen Brain Atlas
Allen Brain Atlas is an Allen Institute collection of brain map atlases, datasets, APIs, and analysis tools covering mouse, human, and non-human primate brain resources.
Annotated Behaviour and Observability Dataset (ABODe)
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DANDI Archive for NWB datasets
DANDI is a BRAIN Initiative archive for publishing and sharing neurophysiology data, including electrophysiology, optophysiology, and behavioral data packaged as NWB and related standards.
International Brain Laboratory public data
The International Brain Laboratory public data releases expose standardized mouse decision-making experiments, including Neuropixels recordings, widefield calcium imaging, behavior, and session metadata accessed through the ONE API.
OpenNeuro
OpenNeuro is a free, open platform for sharing neuroimaging datasets, with public search, dataset pages, and download paths for web, S3, DataLad, and the OpenNeuro CLI.