GNPS - Paenibacillus in spent coffee grounds
Ontology highlight
ABSTRACT:
INSTRUMENT(S): Q Exactive|MS:1001911
ORGANISM(S): 1206781|paenibacillus Alvei 1087481|paenibacillus Peoriae 1406|paenibacillus Polymyxa
SUBMITTER: 
Alexander Aksenov Pieter C Dorrestein
PROVIDER: MSV000087141 | GNPS | Wed Mar 31 22:52:00 BST 2021
REPOSITORIES: GNPS
Similar Datasets
Project description:Cultures of Paenibacillus peoriae DSM 8320 NCBI:txid1087481 | Pseudomonas fluorescens DSM 106121 NCBI:txid294 and unknown Paenibacillus strain on ground coffee. Extracts of 50% MeOH:water analyzed by LC-MS/MS performed in an UltiMate 3000 UPLC system (Thermo Scientific) using a Kinetex 1.7 um C18 reversed phase UHPLC column (50 X 2.1 mm) and Maxis Impact Q-TOF mass spectrometer (Bruker Daltonics) equipped with ESI source. Data was acquired in negative ion mode.
2020-11-18 | MSV000086478 | GNPS
Project description:Cultures of Paenibacillus peoriae DSM 8320 NCBI:txid1087481 | Pseudomonas fluorescens DSM 106121 NCBI:txid294 and unknown Paenibacillus strain on ground coffee. Extracts of 50% MeOH:water analyzed by LC-MS/MS performed in an UltiMate 3000 UPLC system (Thermo Scientific) using a Kinetex 1.7 um C18 reversed phase UHPLC column (50 X 2.1 mm) and Maxis Impact Q-TOF mass spectrometer (Bruker Daltonics) equipped with ESI source. Data was acquired in positive ion mode.
2020-11-18 | MSV000086477 | GNPS
Project description:Coffee leaf miner is an important plague in coffee crops. Using subtracted cDNA libraries and nylon filter arrays, we analyzed the expression profile of 1536 expressed sequence tags (ESTs) of coffee plants from an hybrid progeny (C. arabica x C. racemosa), containg resistant (R) and susceptible plants (S) to the infestation of coffee leaf miner. Leaf discs were collected from non-infested plants (R control - RC; S control - SC), infested plants after moth oviposition (R oviposition - Ro; S oviposition - So) and infested after larvar eclosion (R eclosion - Re; S eclosion - Se). Isolation and characterization of Coffea genes induced during coffee leaf miner (Leucoptera coffeella) infestation. Plant Science 169(2):351-360 Keywords: ordered
2005-08-15 | GSE2045 | GEO
Project description:Coffee leaf miner is an important plague in coffee crops. Using subtracted cDNA libraries and nylon filter arrays, we analyzed the expression profile of 1536 expressed sequence tags (ESTs) of coffee plants from an hybrid progeny (C. arabica x C. racemosa), containg resistant (R) and susceptible plants (S) to the infestation of coffee leaf miner. Leaf discs were collected from non-infested plants (R control - RC; S control - SC), infested plants after moth oviposition (R oviposition - Ro; S oviposition - So) and infested after larvar eclosion (R eclosion - Re; S eclosion - Se). Isolation and characterization of Coffea genes induced during coffee leaf miner (Leucoptera coffeella) infestation. Plant Science 169(2):351-360
2010-06-09 | E-GEOD-2045 | biostudies-arrayexpress
Project description:A summary of the work associated to these microarrays is the following: Background: Phenolic compounds present in coffee are antioxidants in vitro that might protect against cardiovascular disease and certain types of cancer in humans. Objective: Our aim was to identify differentially expressed genes upon incubation of HT-29 human colon cancer cells with instant caffeinated coffee (ICC) or caffeic acid (CA) using microarrays. Results: In HT-29 cells incubated with ICC, 77 genes were overexpressed whereas 162 were underexpressed. Upon incubation with CA, 12 genes were overexpressed whereas 33 were underexpressed. A list of five overexpressed genes and eleven underexpressed genes were found in common between the two conditions and was use to construct a biological association network. In the generated network, STAT5B and ATF-2 appeared as highly interconnected nodes. STAT5B overexpression was confirmed at the mRNA and protein levels. For ATF-2, the changes in mRNA levels were confirmed for both ICC and CA, whereas the decrease in protein levels was only observed in CA-treated cells. The levels of cyclin D1, a target gene for both STAT5B and ATF-2 transcription factors, decreased dramatically in breast cancer cells treated with CA or ICC. Conclusions: Coffee polyphenols are able to affect gene expression in cancer cells through the modulation of STA5B and ATF-2 transcription factors. The aim of our study was to evaluate, by using whole genome microarrays, the effects of one cup of coffee, either regular caffeinated coffee or a coffee polyphenol, such as caffeic acid, on HT-29 gene expression, Three experimental approaches were conducted to assess the effects of coffee on HT29 cells. I) Incubation with non cytotoxic concentrations of ICC (7 µg/mL) for 24h. (Group ICC); II) Incubation with non cytotoxic concentrations of CA (1.68 µg/mL) for 24h. (Group CA); III) non treatment of HT-29 to refered as a control (Group CNT). Triplicate samples were hybridized for each experimental condition (9 samples in total). The samples provided were analyzed using the specific software GeneSpring GX.
2013-05-29 | E-GEOD-35382 | biostudies-arrayexpress
Project description:Paenibacillus alvei DSM 29 Genome sequencing and assembly
| PRJNA170044 | ENA
Project description:Paenibacillus larvae, the causal agent of American Foulbrood disease (AFB), affects honeybee health worldwide. The present study investigates the transcriptional response of this Gram-positive, endospore-forming bacterium to bodily fluids from honeybee larvae. Four different conditions were evaluated with a loop design: sampling of in vitro grown P. larvae cultures one or four hours after addition of larval fluids or BHIT-broth (C1, T1, C4, T4).
2014-12-22 | GSE37481 | GEO
Project description:A summary of the work associated to these microarrays is the following: Background: Phenolic compounds present in coffee are antioxidants in vitro that might protect against cardiovascular disease and certain types of cancer in humans. Objective: Our aim was to identify differentially expressed genes upon incubation of HT-29 human colon cancer cells with instant caffeinated coffee (ICC) or caffeic acid (CA) using microarrays. Results: In HT-29 cells incubated with ICC, 77 genes were overexpressed whereas 162 were underexpressed. Upon incubation with CA, 12 genes were overexpressed whereas 33 were underexpressed. A list of five overexpressed genes and eleven underexpressed genes were found in common between the two conditions and was use to construct a biological association network. In the generated network, STAT5B and ATF-2 appeared as highly interconnected nodes. STAT5B overexpression was confirmed at the mRNA and protein levels. For ATF-2, the changes in mRNA levels were confirmed for both ICC and CA, whereas the decrease in protein levels was only observed in CA-treated cells. The levels of cyclin D1, a target gene for both STAT5B and ATF-2 transcription factors, decreased dramatically in breast cancer cells treated with CA or ICC. Conclusions: Coffee polyphenols are able to affect gene expression in cancer cells through the modulation of STA5B and ATF-2 transcription factors.
2013-05-29 | GSE35382 | GEO
Project description:The present study was conducted to evaluate the effects of the intake of three types of coffee (caffeinated, decaffeinated, and green unroasted coffee) on the livers of C57BL/6J mice fed a high-fat diet, and to extensively elucidate the physiological responses to coffee intake by analysing the findings obtained from a comprehensive transcriptomic analysis using DNA microarrays. The present study was conducted to evaluate the effects of the intake of three types of coffee (caffeinated, decaffeinated, and green unroasted coffee) on the livers of C57BL/6J mice fed a high-fat diet, and to extensively elucidate the physiological responses to coffee intake by analysing the findings obtained from a comprehensive transcriptomic analysis using DNA microarrays.
2013-12-10 | GSE53131 | GEO
Project description:The following strains of Paenibacillus larvae classified as ERIC I-IV genotypes (pl1-pl4) were used in the study: ERIC I - DSM-7030; ERIC II - DSM-25430; ERIC III - LMG-16252; and ERIC IV - DSM-3615.
The 7 biological replicates (a-g) of the exoprotein fractions prepared from each ERIC genotype were used in the nanoLC-MS/MS analysis.
All 28 samples were consecutively analyzed using an OrbitrapTM FusionTM Tribrid q-OT-IT mass spectrometer.
To improve the protein identification and easy exclude contaminants from the medium, we considered the proteins that could originate from the yeast extract and Mueller-Hinton broth (contains beef fusion and casein peptone-acidic hydrolysate) in analyzing the MS data. Thus, we included the sequences related to Saccharomyces cerevisiae and Bos taurus, respectively, to the list of contaminants in MaxQuant. The contaminants.fasta file is provided. Futhermore, we provide the database (uniprot-paenibacillus+larvae.fasta) used for the identification of P. larvae proteins created of different strains of P. larvae.
The sequences were downloaded of UniProt on 12.03.2019.
Finally, the compressed (zipped) folder "combined" is provided.
The data were analyzed in MaxQuant v1.6.3.4.
2019-03-27 | MSV000083636 | MassIVE