mass spectrometer machine  (Syft Technologies)

Journal: Frontiers in Microbiology

Article Title: Subspecies Typing of Streptococcus agalactiae Based on Ribosomal Subunit Protein Mass Variation by MALDI-TOF MS

doi: 10.3389/fmicb.2019.00471

Figure Lengend Snippet: A representative MALDI-TOF mass spectrum of a Streptococcus agalactiae ST7 strain, covering the mass range between 4,000 Da and 22,000 Da. The arbitrary intensity values of the mass peaks are given on the y -axis. Dashed lines indicate the position of the 28 ribosomal subunit proteins (rsp) targeted in our analyses. (B) Assessment of mass spectra belonging to five Group B Streptococcus (GBS) isolates confirm in silico predicted mass shifts in three rsp (L35, L13, and S8). Green: Major rsp mass, yellow and orange: rsp mass variants. (C) In silico predicted molecular mass variation of 28 rsp across 796 GBS whole genome sequences. Ribosomal subunits proteins are ordered from left to right by increasing molecular weight. Green: Most abundant rsp mass allele; yellow, orange and blue: 2nd, 3 rd , and 4th most abundant rsp mass allele; Red: remaining rsp mass alleles.

Article Snippet: The MS measurements were carried out using a MALDI-TOF Mass Spectrometer Axima Confidence machine (Shimadzu-Biotech, Kyoto, Japan) with detection in the linear positive mode, allowing the interrogation of high molecular weight samples.

Techniques: In Silico, Molecular Weight

Journal: Frontiers in Microbiology

Article Title: Subspecies Typing of Streptococcus agalactiae Based on Ribosomal Subunit Protein Mass Variation by MALDI-TOF MS

doi: 10.3389/fmicb.2019.00471

Figure Lengend Snippet: FastTree phylogenetic tree based on core-genome analysis of 796 Group B Streptococcus whole genome sequences (WGS). Individual strains are annotated with their in silico determined ribosomal subunit proteins (rsp)-profile. For simplicity, only the six globally dominant rsp-profiles are shown (covering 83% of isolates in our WGS collection). Marked with asterisks are eight strains whose rsp-profile was miss-assigned due to limitation of MALDI-TOF MS resolution (i.e., 400 ppm). (Scale bar: nucleotide substitutions per site).

Article Snippet: The MS measurements were carried out using a MALDI-TOF Mass Spectrometer Axima Confidence machine (Shimadzu-Biotech, Kyoto, Japan) with detection in the linear positive mode, allowing the interrogation of high molecular weight samples.

Techniques: In Silico

Journal: Frontiers in Microbiology

Article Title: Subspecies Typing of Streptococcus agalactiae Based on Ribosomal Subunit Protein Mass Variation by MALDI-TOF MS

doi: 10.3389/fmicb.2019.00471

Figure Lengend Snippet: Validation of the established ribosomal subunit protein (rsp) typing scheme with MALDI-TOF MS measurements of in-house group B Streptococcus (GBS) isolates.

Article Snippet: The MS measurements were carried out using a MALDI-TOF Mass Spectrometer Axima Confidence machine (Shimadzu-Biotech, Kyoto, Japan) with detection in the linear positive mode, allowing the interrogation of high molecular weight samples.

Techniques: Sequencing

Journal: Agriculture, Ecosystems & Environment

Article Title: Cowpea ( Vigna unguiculata L. Walp) hosts several widespread bradyrhizobial root nodule symbionts across contrasting agro-ecological production areas in Kenya

doi: 10.1016/j.agee.2017.12.014

Figure Lengend Snippet: Dendrogram of an unsupervised hierarchical cluster analysis of rhizobial strains isolated from cowpea nodules based on Dice distances of mass spectral protein profiles of Matrix Assisted Laser Desorption/Ionization Time of Flight (MALDI-TOF) Mass Spectrometry (MS). Presence/absence of protein masses in the size range of mass-to charge ratio ( m / z ) 3000–12,000 was used. Strain origin is indicated in the strain identifiers (K: Kilifi, M: Mbeere). The strains 1–15 are from cultivated sites and the strains 16–20 from uncultivated sites. Reference strains were the isolates CBA from commercial Biofix inoculum (MEA Ltd. Nakuru, Kenya) and BK1 from a trap culture with soils from Burkina Faso. The scale bar shows the Dice distance in per cent.

Article Snippet: After co-crystallisation at room temperature, target plates were introduced into the MALDI-TOF Mass Spectrometer Axima™ Confidence machine (Shimadzu- Biotech Corp., Kyoto, Japan) for sample analysis.

Techniques: Isolation, Mass Spectrometry

Journal: Agriculture, Ecosystems & Environment

Article Title: Cowpea ( Vigna unguiculata L. Walp) hosts several widespread bradyrhizobial root nodule symbionts across contrasting agro-ecological production areas in Kenya

doi: 10.1016/j.agee.2017.12.014

Figure Lengend Snippet: (a) Frequency of occurrence of five Bradyrhizobium isolate groups from root nodules of cowpea at cultivated and uncultivated sites in the agro-ecological regions around Mbeere and Kilifi in Kenya. The isolate grouping is based on similarity clustering of mass spectral protein profiles as determined by Matrix Assisted Laser Desorption/ Ionization Time of Flight (MALDI-TOF) Mass Spectrometry (MS) . Sampling took place at 15 cultivated and 5 uncultivated sites in each agro-ecological region. (b) Rarefaction curves of the number of different groups of Bradyrhizobium in the two agro-ecological regions and cultivated and uncultivated sites . Number of isolates considered: Mbeere, cultivated: 66, uncultivated: 12; Kilifi, cultivated: 68, uncultivated: 25.

Article Snippet: After co-crystallisation at room temperature, target plates were introduced into the MALDI-TOF Mass Spectrometer Axima™ Confidence machine (Shimadzu- Biotech Corp., Kyoto, Japan) for sample analysis.

Techniques: Mass Spectrometry, Sampling

Journal: Agriculture, Ecosystems & Environment

Article Title: Cowpea ( Vigna unguiculata L. Walp) hosts several widespread bradyrhizobial root nodule symbionts across contrasting agro-ecological production areas in Kenya

doi: 10.1016/j.agee.2017.12.014

Figure Lengend Snippet: Correlative relationship between the occurrence of five similarity clusters of Bradyrhizobium root nodule isolates of cowpea and edaphic parameters as inferred by redundancy analysis (RDA). The biplot explains 96.3% of total variance in the dataset and is based on the presence/absence data of five similarity clusters of 156 Bradyrhizobium isolates, recovered from root nodules of cowpea plants growing in soil of 36 field sites. The vector sizes denote the strength of correlation and small angles indicate high correlation between environmental factors and/or cluster occurrence. Black arrows denote soil parameters, and blue arrows the Bradyrhizobium clusters, as characterized by similarity of MALDI-TOF MS protein mass spectra ( , a). Percentages on the axes show the fraction of total variance explained. Only environmental parameters significantly correlated to the occurrence of the Bradyrhizobium clusters are shown. The pH ( P < 0.05***), sand ( P < 0.01**), and clay ( P < 0.001*) concentrations, were those factors, which influenced Bradyrhizobium occurrence and symbiotic abundance. (For interpretation of the references to colour in this figure legend, the reader is referred to the web version of this article.)

Article Snippet: After co-crystallisation at room temperature, target plates were introduced into the MALDI-TOF Mass Spectrometer Axima™ Confidence machine (Shimadzu- Biotech Corp., Kyoto, Japan) for sample analysis.

Techniques: Plasmid Preparation