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59 results for “MALDI-TOF”
Native American use of cetaceans in pre-contact Oregon: Biomolecular and taphonomic analyses illuminate human-cetacean relationships: MALDI-TOF data
<p><span>This study characterizes how Native Americans living on the Oregon coast used whales and small cetaceans prior to European contact. We present an original analysis of a large subsample of archaeological cetacean remains from the Palmrose (35CLT47) site and new identifications from the previously analyzed Par-Tee (35CLT20) and Tahkenitch Landing (35DO130) sites. Using zooarchaeological and biomolecular analyses we report species presence and modification patterns to characterize use. Grays (<em>Eschrichtius</em> <em>robustus</em>) and humpbacks (<em>Megaptera</em> <em>novaeangliae</em>) were the most commonly identified whale species and a preferred source of food, oil, bone for tool manufacture, and possibly ligaments for sinew. Dolphins and porpoises, especially harbor porpoise (<em>Phocoena</em> <em>phocoena</em>), were a source of food and possibly bone for tool manufacture. While opportunistic hunting may have occurred, the presence of species such as blue (<em>Balaenoptera</em> <em>musculus</em>) and Cuvier's beaked (<em>Ziphius</em> <em>cavirostris</em>) whales suggest collection of beached animals was an important acquisition strategy. Our study demonstrates the value of biomolecular analyses for improved species identifications/understanding of species richness, and the value of zooarchaeological analysis to fully understand dietary and cultural contributions of cetaceans to precontact lifeways on the Oregon coast.</span></p>
DRIAMS: Database of Resistance Information on Antimicrobials and MALDI-TOF Mass Spectra
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MALDI-TOF MS data: Species delimitation of Hexacorallia and Octocorallia around Iceland using nuclear and mitochondrial DNA and proteome fingerprinting
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Native American use of cetaceans in pre-contact Oregon: Biomolecular and taphonomic analyses illuminate human-cetacean relationships: MALDI-TOF data
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Data from: Comparison of rapid biodiversity assessment of meiobenthos using MALDI-TOF MS and metabarcoding
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MALDI-TOF MS spectra of archaeological whale bone specimens from Atlantic Europe
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A comparison of minimally-invasive sampling techniques for ZooMS analysis of bone artifacts: MALDI-TOF mass spectra
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Machine learning in mass spectrometry: A MALDI-TOF MS approach to phenotypic antibacterial screening
<p>Dataset relating to the publication:</p> <p>Machine learning in mass spectrometry: A MALDI-TOF MS approach to phenotypic antibacterial screening</p> <p>by Luuk Nico van Oosten and Christian D. Klein</p> <p>Published in the Journal of Medicinal Chemistry, 2020</p> <p><strong>Important notice:</strong></p> <p><strong>The data are free to use for non-commercial, academic purposes, provided that the original source is<br> cited and the authors and the publication are credited in any derivative work.</strong></p> <p><strong>A patent application has been filed for the method described by van Oosten and Klein, which uses mass<br> spectrometry and machine learning to identify the pharmacological or other effects of compounds on cell<br> cultures and other biological systems.</strong></p> <p>Therefore, a license for the commercial use of the method must be negotiated by contacting either</p> <p>Anke Faller<br> Universität Heidelberg<br> Dezernat Forschung<br> Rechts- und Strukturfragen der Forschungsförderung<br> Seminarstraße 2, 69117 Heidelberg<br> Tel. +49 6221 54-12611<br> anke.faller(at)zuv.uni-heidelberg.de</p> <p>or</p> <p>Prof. Dr. C. Klein; c.klein(at)uni-heidelberg.de<br> Medicinal Chemistry<br> Institute of Pharmacy and Molecular Biotechnology IPMB<br> Heidelberg University, INF 364<br> D-69120 Heidelberg<br> Germany<br> Phone: ++49-6221-54-4875<br> FAX : ++49-6221-54-6430</p> <p> </p>
Data from: Revealing higher than expected diversity of Harpacticoida (Crustacea:Copepoda) in the North Sea using MALDI-TOF MS and molecular barcoding
The North Sea is one of the most extensively studied marine regions of the world. Hence, large amounts of molecular data for species identification are available in public repositories, and expectations to find numerous new species in this well-known region are rather low. However, molecular reference data for harpacticoid copepods from this area in particular but also for this group in general is scarce. By assessing COI barcodes and MALDI-TOF mass spectra for this group of small crustaceans, it was discovered that there is a huge unknown diversity in this area. In total, COI sequences for 548 specimens from 115 species of harpacticoid copepods are presented. Over 19% of these were new to science and ten MOTUs were found to be part of cryptic species complexes. MALDI-TOF mass spectra were assessed for 622 specimens from 75 species. Because results were in concordance with species delimitation by COI barcoding and also enabled recognition of possible cryptic species, the discriminative power of this technique for biodiversity assessments is highlighted. Findings imply, species diversity in this group may be largely underestimated and total species number can be expected to be much higher than previously assumed.
Data from: Rapid MALDI-TOF mass spectrometry strain typing during a large outbreak of Shiga-Toxigenic Escherichia coli
Background: In 2011 northern Germany experienced a large outbreak of Shiga-Toxigenic Escherichia coli O104:H4. The large amount of samples sent to microbiology laboratories for epidemiological assessment highlighted the importance of fast and inexpensive typing procedures. We have therefore evaluated the applicability of a MALDI-TOF mass spectrometry based strategy for outbreak strain identification. Methods: Specific peaks in the outbreak strain's spectrum were identified by comparative analysis of archived pre-outbreak spectra that had been acquired for routine species-level identification. Proteins underlying these discriminatory peaks were identified by liquid chromatography tandem mass spectrometry and validated against publicly available databases. The resulting typing scheme was evaluated against PCR genotyping with 294 E. coli isolates from clinical samples collected during the outbreak. Results: Comparative spectrum analysis revealed two characteristic peaks at m/z 6711 and m/z 10883. The underlying proteins were found to be of low prevalence among genome sequenced E. coli strains. Marker peak detection correctly classified 292 of 293 study isolates, including all 104 outbreak isolates. Conclusions: MALDI-TOF mass spectrometry allowed for reliable outbreak strain identification during a large outbreak of Shiga-Toxigenic E. coli. The applied typing strategy could probably be adapted to other typing tasks and might facilitate epidemiological surveys as part of the routine pathogen identification workflow.
Custom MALDI-TOF Mass Spectrometric Database for identification of environmental Burkholderia and related genera
<p class="CxSpFirst">Success of microbial natural products discovery programs is dependent on quick and concise discrimination between isolates from diverse environments. However, laboratory isolation and identification of priority genera using current 16S rRNA PCR-based methods is both challenging and time-consuming. In clinical settings, MALDI-TOF MS is used to rapidly identify unknown bacterial pathogens, yet this has not been widely adapted for isolation of environmental bacteria. To expedite isolation of Gram-negative proteobacterial order Burkholderiales, we have created a main spectral (MSP) library for the Bruker Biotyper MALDI mass spectrometer that includes 95 entries of <i>Burkholderia, Caballeronia, Paraburkholderia,</i> and other environmentally related genera. We tested the effectiveness of the reference library by analyzing 49 unknown environmental isolate strains before comparing to results of traditional 16S sequencing. The MALDI Biotyper correctly identified all strains to the genus level when sufficient reference spectra were available. This dataset is freely available to the scientific research community for use in taxonomic assignments of environmentally-derived bacteria from the order Burkholderiales.</p>
Data from: Rapid species-level identification of vaginal and oral lactobacilli using MALDI-TOF MS analysis and 16S rDNA sequencing
Background: Lactobacillus represents a large genus with different implications for the human host. Specific lactobacilli are considered to maintain vaginal health and to protect from urogenital infection. The presence of Lactobacillus species in carious lesions on the other hand is associated with progressive caries. Despite their clinical significance, species-level identification of lactobacilli still poses difficulties and mostly involves a combination of different phenotypic and genotypic methods. This study evaluated rapid MALDI-TOF MS analysis of vaginal and oral Lactobacillus isolates in comparison to 16S rDNA analysis. Results: Both methods were used to analyze 77 vaginal and 21 oral Lactobacillus isolates. The concordance of both methods was at 96% with five samples discordantly identified. Fifteen different Lactobacillus species were found in the vaginal samples, primarily L. iners, L. crispatus, L. jensenii and L. gasseri. In the oral samples 11 different species were identified, mostly L. salivarius, L. gasseri, L. rhamnosus and L. paracasei. Overall, the species found belonged to six different phylogenetic groups. For several samples, MALDI-TOF MS analysis only yielded scores indicating genus-level identification. However, in most cases the species found agreed with the 16S rDNA analysis result. Conclusion: MALDI-TOF MS analysis proved to be a reliable and fast tool to identify lactobacilli to the species level. Even though some results were ambiguous while 16S rDNA sequencing yielded confident species identification, accuracy can be improved by extending reference databases. Thus, mass spectra analysis provides a suitable method to facilitate monitoring clinically relevant Lactobacillus species.
Identification of Protein Markers of Epidemiological and Clinical Interest by MALDI-TOF
ClinicalTrials.gov study NCT03626987. IPD Sharing: NO. Countries: 1. Publications: 1.
Microbiological Evaluation of Single Versus Multiple Visits Regeneration Using MALDI-TOF Mass Spectrometry
ClinicalTrials.gov study NCT04533074. IPD Sharing: Not stated. Countries: 1. Publications: 18.
Proteomic Approach Using Matrix-assisted Laser Desorption/Ionization Tandem Time-of-flight (MALDI-TOF/TOF) of Tumor Response in Rectal Carcinoma After Radiochemotherapy
ClinicalTrials.gov study NCT00855946. IPD Sharing: Not stated. Countries: 1. Publications: 34.
Data from: Effects of sample fixation on specimen identification in biodiversity assemblies based on proteomic data (MALDI-TOF)
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Data from: Rapid species-level identification of vaginal and oral lactobacilli using MALDI-TOF MS analysis and 16S rDNA sequencing
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Data from: Rapid MALDI-TOF mass spectrometry strain typing during a large outbreak of Shiga-Toxigenic Escherichia coli
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Data from: Revealing higher than expected diversity of Harpacticoida (Crustacea:Copepoda) in the North Sea using MALDI-TOF MS and molecular barcoding
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Custom MALDI-TOF Mass Spectrometric Database for identification of environmental Burkholderia and related genera
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