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Published in Michael Hehenberger, Zhi Xia, Huanming Yang, Our Animal Connection, 2020
Michael Hehenberger, Zhi Xia, Huanming Yang
They endure numerous strains of pathogenic bacteria in their saliva and easily recover from wounds inflicted by other dragons, reflecting an exceptional innate immune defense. Scientists224 from George Mason University (Manassas, VA), Virginia Polytechnic Institute (Blacksburgh, VA), and the University of Florida (Gainesville, FL), have combined partial de novo peptide sequencing with transcriptome assembly to identify antimicrobial peptides from Komodo dragon blood plasma. They identified 48 novel potential antimicrobial peptides. All but one of the identified peptides were derived from histone proteins, defined as highly alkaline proteins found in eukaryotic cell nuclei. They are the chief protein components of chromatin, acting as “spools” around which DNA winds. Without histones, the unwound DNA in chromosomes would be very long: for example, each human diploid cell (containing 23 pairs of chromosomes) has about 1.8 m of (unwound) DNA. In its “wound” state, however, the diploid cell contains only about 90 µm (0.09 mm) of chromatin. Histones are also playing a role in gene regulation.
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Published in Michael Hehenberger, Zhi Xia, Our Animal Connection, 2019
They endure numerous strains of pathogenic bacteria in their saliva and easily recover from wounds inflicted by other dragons, reflecting an exceptional innate immune defense. Scientists224 from George Mason University (Manassas, VA), Virginia Polytechnic Institute (Blacksburgh, VA), and the University of Florida (Gainesville, FL), have combined partial de novo peptide sequencing with transcriptome assembly to identify antimicrobial peptides from Komodo dragon blood plasma. They identified 48 novel potential antimicrobial peptides. All but one of the identified peptides were derived from histone proteins, defined as highly alkaline proteins found in eukaryotic cell nuclei. They are the chief protein components of chromatin, acting as “spools” around which DNA winds. Without histones, the unwound DNA in chromosomes would be very long: for example, each human diploid cell (containing 23 pairs of chromosomes) has about 1.8 m of (unwound) DNA. In its “wound” state, however, the diploid cell contains only about 90 μm (0.09 mm) of chromatin. Histones are also playing a role in gene regulation.
New Tools for Bioprocess Analysis and Optimization of Microbial Fuel Production
Published in Farshad Darvishi Harzevili, Serge Hiligsmann, Microbial Fuels, 2017
Isabelle France George, Philippe Bogaerts, Dimitri Gilis, Marianne Rooman, Jean-François Flot
Metaproteomics is the large-scale characterization of the entire protein complement of environmental microbiomes at a given point in time (Wilmes et al. 2015). Compared with metatranscriptomics, it takes into account posttranslational events. Proteins are extracted from the environmental sample, fractionated, separated using liquid chromatography (LC), and detected with tandem mass spectrometry (MS/MS) (VerBerkmoes et al. 2009). This protocol has not changed much for the last decade, after spectacular progress in analytical capacities. In about a year, proteomics moved from separation of proteins by two-dimensional (2D) polyacrylamide gel electrophoresis, in-gel enzymatic digestion, identification of a few proteins by LC-MS/MS, and de novo peptide sequencing to the identification of thousands of proteins by the above-mentioned pipeline (Wilmes et al. 2015). As other omic techniques, metaproteomics is facing technical challenges, including (1) cell lysis and quantitative protein extraction from complex matrices, (2) standardized protein fractionation methods exploiting both molecular weight and charge, (3) the need for mass spectrometers with faster scan speeds and higher mass accuracies, and (4) the need for good reference databases (sample-derived metagenomic and metatranscriptomic datasets rather than public protein databases) (Wilmes et al. 2015). Solutions to these challenges already exist, but they are not routinely applied to metaproteomic studies yet (Wilmes et al. 2015). One exception might be coupling metaproteomics to metagenomics to analyze the same sample, an approach called “community proteogenomics” (VerBerkmoes et al. 2009). This procedure is now widely applied, since its usefulness to improve protein identification was proved over and over. It is based on the construction of a protein sequence database from the sequenced metagenome. In silico trypsin digest is performed on the predicted proteins, resulting in a peptide database. MS/MS spectra are then matched to the peptides in the database, and after filtering, a list of identified peptides is obtained. Peptides that are present in only one protein in the whole database can be unambiguously tracked back to their corresponding protein, and thus permit reliable protein identification, and hopefully the microbial species it is derived from. In addition, in case the protein mixture was fractionated (into extracellular, soluble, and membrane fractions) after the initial extraction, information about protein localization is available. There are other difficulties linked to the application of metaproteomics to complex communities, like detection of strain variability (amino acid substitutions) and follow-up of protein turnover in highly dynamic microbial assemblages (VerBerkmoes et al. 2009).
Kurstakin molecules facilitate diesel oil assimilation by Acinetobacter haemolyticus strain 2SA through overexpression of alkane hydroxylase genes
Published in Environmental Technology, 2021
Mamadou Malick Diallo, Caner Vural, Umut Şahar, Guven Ozdemir
Tandem mass spectrometry (MS/MS) plays an important role in de novo peptide sequencing. Basic hydrolysis of the lipopeptide extract using 1 M NaOH for 24 h at room temperature gave a protonated pseudo molecular ion at m/z 927. The lactone ring opening by hydrolysis (24 h) of the lipopeptide shifted molecular mass of 907–927 [24]. Open form of the lipopeptide provides more information about the amino acid sequence in MS/MS fragmentation. MS/MS chromatograms spectra of two lipopeptides obtained on the Ion Trap instrument are shown in Figure 2. The protonated pseudo molecular ion at m/z 927, which is open form, generates fragments at m/z 779, 650, 632, 629, 501, 414. These ions have already characterized in the literatures before [24,26]. For example, fragment ion in this study at m/z 414 reflects [His-Glu-Glu]+, and that at m/z 501 gives information about [Ser-His-Glu-Glu] + . The difference between these two ions is 87 Da, which is corresponding to Serine amino acid. The other protonated pseudo molecular ion at m/z 924 was also studied using MRM system. This lipopeptide could be the linear C13 Kurstakin means that there is no lactone ring on molecular chain. The observed fragment ions of precursor m/z 924.3 were m/z 778, 632, 499, 481, 412. All these fragment ions provide a reasonable match to the sequence of Fatty Acid-Thr-Gly-Ala-Ser-His-Gln-Gln amino acids which were strongly supported by the MS data and a previous report of lipopeptides of similar structure [35–38].