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Integrated Omics Technology for Basic and Clinical Research
Published in Jyoti Ranjan Rout, Rout George Kerry, Abinash Dutta, Biotechnological Advances for Microbiology, Molecular Biology, and Nanotechnology, 2022
Kuldeep Giri, Vinod Singh Bisht, Sudipa Maity, Kiran Ambatipudi
Biological databases are categorized according to the types of data they managed. They are divided into (1) DNA, (2) RNA, (3) protein, (4) expression, (5) pathway, (6) disease, (7) nomenclature, (8) literature and, (9) standard and ontology. For example, GenBank, a DNA database provides DNA sequences that are publicly available. Similarly, protein databases such as UniProt is a resourceful media for protein information. Another such database, known as Proteomics Identifications (Vizcaíno et al., 2016) database collects and stores experimentally validated MS-based identified proteins. Additionally, a database like ProGlycProt is a collection of experimentally characterized glycoproteins and glycosyltransferases of bacteria and archaea. Taken together, biological databases efficiently provide curated sources of information that could analyze massive data sets into big discovery (Zou et al., 2015).
Bioinformatics Analysis of Dysfunctional (Mutated) Proteins of Cardiac Ion Channels Underlying the Brugada Syndrome
Published in Qurban A. Memon, Shakeel Ahmed Khoja, Data Science, 2019
Carlos Polanco, Manlio F. Márquez, Vladimir N. Uversky, Thomas Buhse, Miguel Arias Estrada
This article comprises three sections: (i) A computational analysis of the degree of disorder of each BrS mutated protein as well as its association with other diseases, (ii) A bioinformatic characterization (through the PIM®) of the BrS mutated proteins, and their contrast with a large and diverse set of protein groups of different structural and functional types, with the objective to obtain a “fingerprint” of the BrS mutated protein set, and (iii) the use of this “fingerprint” on all of the reviewed proteins listed in the largest known public primary database UniProt containing protein sequence and functional information. We speculate that this characterization could be used for the rapid identification of this syndrome at early stages, potentially even before the development of major symptoms.
Loss of thermotolerance in antibiotic-resistant Acinetobacter baumannii
Published in International Journal of Environmental Health Research, 2021
Svjetlana Dekić Rozman, Ana Butorac, Rea Bertoša, Jasna Hrenović, Marina Markeš
The genome of A. baumannii codes for a variety of efflux pumps that actively remove antibiotics from the cell. The most significant are those pumps belonging to the resistance-nodulation-cell division (RND) superfamily of transporters. Three systems belonging to this superfamily have been identified thus far and associated with antibiotic resistance (AdeABC, AdeFGH, and AdeIJK) (Coyne et al. 2011; Li et al. 2015; Leus et al. 2018). The three-component structure enables the connection of the inner and outer membrane and works synergistically with the low permeability of the outer membrane (Leus et al. 2018). The structure of the efflux pumps is made of a membrane fusion protein (AdeA, AdeF, AdeI), protein transporters (AdeB, AdeG, AdeJ) and outer membrane factors (AdeC, AdeG, AdeK). The outer membrane factors provide the channel for the substances to cross the outer membrane and the membrane fusion proteins provide interactions between transporters and outer membrane factors (Leus et al. 2018). The efflux pumps AdeABC and AdeIJK have a broad substrate specificity including β-lactams. The downregulation of AdeA/AdeI family multidrug efflux protein expressed from adeI gene (UniProt Database, 2020), at elevated temperature suggests the decreased activity of efflux pumps especially the membrane fusion proteins that are responsible for the coupling of reactions separated in two different membranes (Leus et al. 2018).
Systems toxicology approach explores target-pathway relationship and adverse health impacts of ubiquitous environmental pollutant bisphenol A
Published in Journal of Toxicology and Environmental Health, Part A, 2022
Manigandan Nagarajan, Gobichettipalayam Balasubramaniam Maadurshni, Jeganathan Manivannan
In order to understand the system wide molecular effects and disease relationship of BPA targets, current study employed an enrichment analysis through EnrichR (http://amp.pharm.mssm.edu/Enrichr) tool, a comprehensive gene set enrichment analysis web server (Kuleshov et al. 2016). In the current study, the top 100 potential targets were subjected to pathway analysis. For suitable format, the top 100 protein identifiers were converted into their corresponding gene identifiers using ID mapping function of UniProt (https://www.uniprot.org/uploadlists/). For enrichment analysis, databases such as KEGG 2019 Human and OMIM disease modules were selected. Enriched terms were ordered based upon the combined score and considered as significant if adjusted P < .05.
Tailoring of recombinant FDH: effect of histidine tag location on solubility and catalytic properties of Chaetomium thermophilum formate dehydrogenase (CtFDH)
Published in Preparative Biochemistry & Biotechnology, 2019
Hacer Esen, Saadet Alpdağtaş, Mehmet Mervan Çakar, Barış Binay
The expression level of the fdh gene from C. thermophilum (DSM 1495, GenBank Accession Number EGS17433.1) was optimized by codon usage of E. coli and then it was synthesized based on the amino acid sequence (UniProt accession number:G0SGU4) by Genscript. Then, ∼1.1 kb fdh gene inserted into pET45b(+) vector between PstI and XhoI cloning sites and the process resulted with N-terminal His-tagged CtFDH (N-CtFDH). Then, the cloning sites were changed to NcoI and XhoI to get C-terminal His tagged CtFDH (C-CtFDH). Both of these processes were performed by Genscript, separately.