Ethnobotany Post-Genomic Horizons and Multidisciplinary Approaches for Herbal Medicine Exploration: An Overview
T. Pullaiah, K. V. Krishnamurthy, Bir Bahadur in Ethnobotany of India, 2017
Bioinformatics act as an essential tool for the identification of genes and its pathways that correlate with important bioactive secondary metabolites in medicinal plants. The International Ethnobotany Database (ebDB), NAPALERT and USDA maintain a database for medicinal plants. The majority of genomics resources for plants have come from ESTs. Transcriptlevel information could be valuable to molecular biology-based research relative to medicinal plants. Bioinformatics approaches can be used to create coexpression networks from transcriptome data, providing possible leads to gene discovery in related plant species. In particular, the use of comparative genomics provides basis for exchange of information among the different species (Sharma and Sarkar, 2013).
“Omics” Technologies in Vaccine Research
Mesut Karahan in Synthetic Peptide Vaccine Models, 2021
Another strategy to discover potential antigens and virulence factors is comparison of the genomes of pathogenic and non-pathogenic strains of the same species via comparative genome analysis. Thus, the genes responsible for pathogenesis can be identified (Serruto et al. 2009). The biological trends can be identified and characterized via comparison of large-scale genomes to understand a particular phenomenon or to highlight an interesting exception. The comparative genomics can be used to discover the patterns common among bacteria and the increasing number of published genomes strengthens it. These patterns cover the distribution of structural properties, relative amounts of specific genes, and the differential expression of the encoded proteins under varying conditions (Barocchi, Censini, and Rappuoli 2007).
The Future of Endotoxin Research
Helmut Brade, Steven M. Opal, Stefanie N. Vogel, David C. Morrison in Endotoxin in Health and Disease, 2020
Comparative genomics will provide new insights into the molecular pathogenesis of disease and provide new targets for therapeutic intervention. The availability of the molecular “blueprints” for each invasive microbial organism will give forthcoming investigators an enormous advantage over bacterial pathogens. The mechanisms by which pathogens evade host defenses and cause disease can now be characterized in precise molecular detail. Promising new vaccine targets, novel chemotherapeutic agents, and improved methods to avoid microbial injury should lead to substantial advances for the health of humankind in the near future. There is, therefore, considerable reason for optimism if scientists and policymakers proceed wisely in an organized, ethical, and logical manner.
Genomic characterization of four Escherichia coli strains isolated from oral lichen planus biopsies
Published in Journal of Oral Microbiology, 2021
Huitae Min, Keumjin Baek, Ahreum Lee, Yeong-Jae Seok, Youngnim Choi
After selection of genomes, comparative genomic analyses were performed using ChunLab’s comparative genomics tools (https://www.ezbiocloud.net/genome/view_myCGData). Pangenome orthologous groups (POGs) were determined by the reciprocal best hit (RBH) method [28] using UBLAST [17] with an e-value threshold of 1e−6 and an open reading frame (ORF)-independent method [29] using nucleotide sequences with cut-off values of 70% of minimum gene coverage. Venn diagrams of the calculated POGs were constructed using the jvenn tool [30]. A pairwise ortholog matrix (POM) table was generated by complete calculation of pairwise ortholog detection within the dataset of select strains. The existence of genomic islands (GIs), which provide evidence of horizontal gene transfer, was confirmed only if the genomic region contained five or more consecutive CDSs in a contig, and the same pattern was observed across the four OLP strains but not in the K-12 MG1655 strain, as previously described [31].
Marine biofilm bacterial community response and carbon steel loss following Deepwater Horizon spill contaminant exposure
Published in Biofouling, 2019
Rachel L. Mugge, Jason S. Lee, Treva T. Brown, Leila J. Hamdan
For 16S gene amplification and sequencing, samples were analyzed at the Centre for Comparative Genomics and Evolutionary Bioinformatics at the Integrated Microbiome Resource at Dalhousie University. PCR amplification and 16S rRNA sequencing protocols are described in Comeau et al. (2011). Gene amplification targeted the V6-V8 variable region for bacteria using the fusion primers B969F (ACGCGHNRAACCTTACC) and BA1406R (ACGGGCRGTGWGTRCAA). These primers were selected to target the V6-V8 variable region because they provide a more accurate estimate of marine microbial communities and can distinguish a higher resolution of marine taxa (Parada et al. 2016). PCR reactions were pooled, cleaned and normalized using the Invitrogen SequalPrep 96-well Plate Kit. The Illumina MiSeq (San Diego, CA, USA) platform generated paired-end sequences of ∼440–450 base pairs.
Omics of antimicrobials and antimicrobial resistance
Published in Expert Opinion on Drug Discovery, 2019
Vladislav M. Chernov, Olga A. Chernova, Alexey A. Mouzykantov, Leonid L. Lopukhov, Rustam I. Aminov
There appear to be a number of obstacles in the application of omics technologies to antimicrobial drug discovery. One of the most important obstacles is the identification of prospective bacterial cell targets [128]. The original assumption was that comparative genomics, using the identification of a core genome of species [129] and/or the use of mutagenesis techniques (Tn-seq, INseq, HITS) [77,78] would identify important genes that are critical for microbial growth and/or virulence. Then, 3D structure modeling platforms would be used to screen for potential inhibitors [130]. However, because the number of genes identified appears to be extremely high and there is uncertainty about the function of many hypothetical genes, their usefulness as targets has remained questionable. In addition, successful in silico structure modeling is not always translated into a successful in vivo result [131].
Related Knowledge Centers
- Conserved Sequence
- DNA
- Evolution
- Genome
- Genomics
- Regulatory Sequence
- Synteny
- Nucleic Acid Sequence
- Gene
- Sequence Homology