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Molecular Advances in Bioremediation of Hexavalent Chromium from Soil and Wastewater
Published in Maulin P. Shah, Removal of Refractory Pollutants from Wastewater Treatment Plants, 2021
Aditi Nag, Devendra Sharma, Sudipti Arora
Our group obtained six isolates which were able to tolerate and survive on a 0.2% Cr concentration. These isolates were further categorized into three categories as the isolates giving an optimal reduction of Cr on less (0.1% Cr) to more (0.25% Cr) concentrated exposures than the initial concentration of Cr in the growth medium. Genomic DNA was isolated from the isolates of each category and the variable region of 16s rDNA was amplified using two universal primers (see Figure 7.1a). Universal primers are those which are designed against the conserved sequences and therefore are likely to amplify sequences even from the yet unidentified and unsequenced genomes. An alternate method is to prepare a molecular profile of rapidly amplified polymorphic DNA (RAPD), which is a technique in which random primers are used to amplify DNA fragments in unknown isolates. This random amplification gives very specific bands for a particular species as well as various strains of microorganisms. Thus, unique molecular profiles can be created to specifically identify any microorganism even to their strains (see Figure 7.1b).
The Genetic Resources as an Inexhaustible Source of Biodiversity in Tajikistan
Published in Hasnain Nangyal, Muhammad Saleem Khan, Environmental Pollution, Biodiversity, and Sustainable Development, 2020
N. Firuza, H. Nangyal, A. Nawaz, M. S. Khan
Depending on the nature of the primers and method for identifying the amplification products are several types of PCR-analysis. First, there was a method of randomly selected DNA sequences [randomly amplified polymorphic DNA (RAPD)], which uses a standard set of primers, amplification products are separated by electrophoresis and stained. Embodiments RAPD primers differ in length, the ratio of primer/template DNA and gel separation of the amplification products. RAPD analysis requires a minimum amount of DNA (10 ng per reaction) and do not need to know in advance exactly what the DNA sequence to be amplified. The method is very simple to perform, although it requires strict standardization of amplification conditions.
Advances in Microbial Molecular Biology
Published in Gustavo Molina, Zeba Usmani, Minaxi Sharma, Abdelaziz Yasri, Vijai Kumar Gupta, Microbes in Agri-Forestry Biotechnology, 2023
Deborah Catharine de Assis Leite, Naiana Cristine Gabiatti
Molecular phenotypes, generated from RAPD, can be used to diagnose different taxonomic levels, and may be able to discriminate even intraspecific levels. Di Cello et al. (1997) applied RAPD methodology to study changes in the population structure of Burkholderia cepacia during the growth of corn plants. The authors showed the high degree of genetic diversity among the isolates. In the initial stages of plant growth, the diversity presented was greater compared to the last stages at the end of maturation. The most possible reason attributed for this variation is the greater instability of an ecosystem with young plants compared to developed plants.
Lemna minor, a hyperaccumulator shows elevated levels of Cd accumulation and genomic template stability in binary application of Cd and Ni: a physiological and genetic approach
Published in International Journal of Phytoremediation, 2021
Ibrahim Ilker Ozyigit, Lutfi Arda, Bestenur Yalcin, Ibrahim Ertugrul Yalcin, Bihter Ucar, Asli Hocaoglu-Ozyigit
Amplifications of random DNA fragments of genomic material using single primers consisting random nucleotide sequences under low-annealing conditions can be achieved through application of a PCR-based technique known as Random Amplification of Polymorphic DNA (RAPD) (Dogan et al.2012; Erturk et al.2013; Ozyigit, Yilmaz, et al.2016). Obtaining of amplifications of regions in genomic DNA by this technique depends on using approximate 10 nucleotide long multiple random primers and gel electrophoresis and visualization of the amplified PCR products follow the amplification step (Huybrechts et al.2019). Specifying of the identities of species used for agricultural purposes, determination of genetic diversity in species, and the construction of phylogenetic relationships between species are common practices done by RAPD, and it is also employed for detection of genotoxicity due to disposal of suspicious chemicals (Cenkci et al.2009; Cenkci and Dogan 2015; Filiz et al.2015; Ozyigit et al.2019). In addition, RAPD is a suitable technique to determine various damages and mutations including rearrangements, point mutations, insertions and deletions of DNA, and ploidy changes in genomic DNA arisen due to genotoxic factors found in exceeding amounts in the environments (Erturk et al.2013; Ozyigit, Dogan, et al.2016).
Genetic Variability of Klebsiella Variicola by RAPD-PCR Technique and Bioremoval of Pb2+ and Cd2+ from Simulated Contaminated Soils
Published in Soil and Sediment Contamination: An International Journal, 2022
Yetunde Mutiat Feruke-Bello, Gbolahan Babalola, Olu Odeyemi
RAPD is used in surveying genomic DNA to detect various types of DNA damage and mutations; they might signify the foundation of new biomarker method for the detection of DNA impairment and mutations in the cells of organisms (Atienzar et al. 2000; Savva 1998).