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Glossary of scientific and technical terms in bioengineering and biological engineering
Published in Megh R. Goyal, Scientific and Technical Terms in Bioengineering and Biological Engineering, 2018
PFGE is an abbreviation for pulsed-field gel electrophoresis. PFGE is a technique used for the separation of large deoxyribonucleic acid (DNA) molecules by applying to a gel matrix an electric field that periodically changes direction.
Developing mitochondrial DNA field-compatible tests
Published in Critical Reviews in Environmental Science and Technology, 2022
Bidhan C. Dhar, Christina E. Roche, Jay F. Levine
Mitochondrial DNA genes are useful targets for polymerase chain reaction (PCR) assay development. Numerous nucleic acid based molecular techniques such as ribotyping, length heterogeneity PCR, terminal-restriction fragment length polymorphism, pulsed-field gel electrophoresis, amplified fragment length polymorphism, and southern blot analysis have their value for mtDNA detection but are tedious and dependent on expensive laboratory technology (Simpson et al., 2002). Several groups have developed microarray chip-based assays for mitochondrial and nuclear DNA detection (Dhar et al., 2015; Erdogan et al., 2001; Maitra et al., 2004; Vuong et al., 2013). These assays, however, require access to traditional laboratory instrumentation such as centrifuges and thermo-cyclers. Access to the needed instrumentation and laboratory infrastructure to take advantage of these technologies is often limited in developing countries, making the technologies inaccessible in many resource-constrained nations (Jani et al., 2014; Spooner et al., 2019). Skilled specimen collection and a secure, reliable framework for sample preservation and cold storage during transport is also needed and further limits the use of laboratory dependent technologies in economically challenged or remote communities. On-site sample-to-detection molecular assays are needed to accommodate fast and inexpensive environmental monitoring without expensive laboratory infrastructure, highly skilled staff, or cold storage.
Heavy metal remediation and resistance mechanism of Aeromonas, Bacillus, and Pseudomonas: A review
Published in Critical Reviews in Environmental Science and Technology, 2022
Ali Fakhar, Bushra Gul, Ali Raza Gurmani, Shah Masaud Khan, Shafaqat Ali, Tariq Sultan, Hassan Javed Chaudhary, Mazhar Rafique, Muhammad Rizwan
Recently, a high level of phylogenetic heterogeneity has been found during 16S rRNA gene sequence analysis, and various molecular techniques have been developed for identification of genus Bacillus. These techniques include (1) pulsed field gel electrophoresis (PFGE), (2) polymerase chain reaction (PCR), (3) random amplified polymorphism deoxyribonucleic acid (RAPD), (4) matrix-assisted laser desorption/ionization time of flight (MALDI-TOF), and (5) a PCR DNA replication process that amplifies small portions of DNA (amplicons) exponentially with the help of oligonucleotide primers and DNA polymerase (Grutsch et al., 2018; Jacob et al., 2018; Pornpukdeewattana, Jindaprasert, & Massa, 2020). B. aryabhattai AS6 was identified based on phenotypic characteristics, physio-biochemical tests, MALDI-TOF MS bio-typing, FAME analysis, and 16S rDNA sequence homology, and it was found to be As tolerant (Ghosh et al., 2018).
Interaction between bacterial enteric pathogens and aquatic macrophytes. Can Salmonella be internalized in the plants used in phytoremediation processes?
Published in International Journal of Phytoremediation, 2021
Filippo Chiudioni, Stefania Marcheggiani, Camilla Puccinelli, Laura Mancini
The identity of S. Napoli isolates from hydroponic solution, and parts of plants was checked by pulsed field gel electrophoresis (PFGE) according to the Pulsenet protocol (CDC 2017). Briefly, genomic DNA was digested with XbaI (New England Biolabs, Ipswich, MA, USA), and Salmonella enterica serovar Braenderup H9812 DNA was used as the molecular size marker. Dendrogram and cluster analyses were performed using algorithms included in the BioNumerics software package v.6.6 (Applied Math, Sint-Martens-Latem, Belgium). The percentage similarity between different chromosomal fingerprints had been scored using the Dice coefficient. The unweighted pair group method with arithmetic means (UPGMA) with a 1.00% tolerance limit and 1.00% optimization was used to generate the dendrogram.