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Roles of Nucleotide Sequence Analysis in Human Genetics and Genomics
Published in Hajiya Mairo Inuwa, Ifeoma Maureen Ezeonu, Charles Oluwaseun Adetunji, Emmanuel Olufemi Ekundayo, Abubakar Gidado, Abdulrazak B. Ibrahim, Benjamin Ewa Ubi, Medical Biotechnology, Biopharmaceutics, Forensic Science and Bioinformatics, 2022
S. S. D. Mohammed, I. Abraham, D. Enoma, L. E. Okoror
Molecular phylogenetics can be defined as the process by which nucleotide and amino acid sequences are used to generate and elucidate the evolutionary relationship between two or more organisms (Human Evolution, 2020). The continuous increase in genomic sequence data set of diverse organisms has revolutionized the subject of phylogenetic with its impacts being appreciated globally. For example, the application of molecular phylogenetics has enabled research scientists to reveal the close relationship between Homo sapiens and Gorilla gorilla (2020). The paradigm shifts in human molecular phylogenetics that haze the line between population genetics and phylogenetics have occurred in recent years (Ting and Sterner, 2012; Jeffrey, 1993). The protein and DNA sequence give the most detailed and complete data for molecular phylogenetics. However, methods for sequencing proteins did not become regularly used until the late 1960s. Fast DNA sequencing also was not developed until about ten years after (Brown, 2002). The evolutionary relationships between humans and other primates have been clarified by the application of DNA phylogenetics. The detailed molecular data collected from the earliest immunological studies in 1960s (Goodman, 1962; Sarich and Wilson, 1967) has revealed that there is a single clade between gorillas, chimpanzees, and humans.
Pilot scale wastewater treatment, CO2 sequestration and lipid production using microalga, Neochloris aquatica RDS02
Published in International Journal of Phytoremediation, 2020
Silambarasan Tamil Selvan, Balasubramanian Velramar, Dhandapani Ramamurthy, Sendilkumar Balasundaram, Kanimozhi Sivamani
The Neochloris sp. microalgal genomic DNA was isolated and partial sequences the DNA using 18S rRNA sequencing method. The gene was amplified and it was found to be 466 bp. The molecular phylogenetic tree analysis indicated that this strain had a close relationship with N. aquatica (Figure 1C). The partial gene sequence of 18S rRNA of N. aquatica RDS02 was deposited in GenBank and got accession no. KJ7004761.1. Based on the molecular analysis, the isolated microalga has been confirmed as N. aquatica. Similarly, Jaiswar et al. (2017) have reported that the partially sequenced gene of 18S rRNA with 961 bp was amplified and confirmed as N. aquatica strain SJ-1. Gumbi et al. (2017) were examined the 461 bp genes were identified by18S rRNA sequencing and confirmed N. aquatica strain.
Characterization of nitrous oxide reduction by Azospira sp. HJ23 isolated from advanced wastewater treatment sludge
Published in Journal of Environmental Science and Health, Part A, 2020
Hyung-Joo Park, Ji Hyeon Kwon, Jeonghee Yun, Kyung-Suk Cho
To establish the identity of each pure colony, genomic DNA was extracted as follows. A portion of each pure colony was mixed with 15 μl of the sterilized water, and incubated for 3 min in a heating block at 95 °C. The incubation procedure was repeated three times. After the cellular debris was removed by centrifugation (7,500 × g), the DNA sample in the obtained supernatant was used as a template for PCR. The 340 F and 805 R primers (Table 1) were used for amplification to target the 16S rRNA gene.[31] The following PCR conditions were used: initial denaturation at 95 °C for 3 min; 35 cycles of denaturation at 95 °C for 30 s, annealing at 55 °C for 30 s, and extension at 72 °C for 30 s. A final extension step was performed at 72 °C for 5 min. The PCR products were sequenced by Macrogen (Seoul, South Korea). Sequence analysis through comparison with known DNA sequences was performed using the Basic Local Alignment Search Tool (BLAST) developed by the National Center for Biotechnology Information (NCBI). The sequence of the isolated strain HJ23 was deposited into the NCBI GenBank database under accession number MK568541. A molecular phylogenetic tree was constructed with the 16S rRNA sequences of the strain HJ23, inactivated N2O-reducing isolates, and known N2O-reducing bacteria using the Clustal X software package (version 2.1, http://www.clustal.org/clustal2/#Documentation.) and the neighbor-joining algorithm.
Integrating eco-technological approach for textile dye effluent treatment and carbon dioxide capturing from unicellular microalga Chlorella vulgaris RDS03: a synergistic method
Published in International Journal of Phytoremediation, 2023
Silambarasan Tamil Selvan, Balakumaran Manickam Dakshinamoorthi, Ravikumar Chandrasekaran, Sanjivkumar Muthusamy, Dhandapani Ramamurthy, Sendilkumar Balasundaram
A unicellular microalgal cell was isolated and inoculated in the sterilized bold basal media. The microalgae isolate was subjected to morphological characteristics identified using a light microscope, scanning electron microscope (SEM) and molecular identification (18S rRNA) methods. The microscopic observations were single cell, spherical-shaped, smooth surface, one large pyrenoid, 3-4 µm small size, dark green cells and identified as Chlorella sp. (Figures 1 and 2(a–b)). The genomic DNA was extracted from the isolated microalgal strain Chlorella sp., and amplified DNA was subjected to 18S rRNA sequencing. The sequenced gene size was 601 bp, and sequenced genes were analyzed. The molecular phylogenetic tree indicated that this strain was closely related to Chlorella vulgaris. These sequences were deposited in Genbank and assigned accession numbers (KT932639.1). The sequenced microalgal strain was confirmed as a Chlorella vulgaris strain (Figure 2(c)). Similarly, Jo et al. (2020) have documented the Chlorella vulgaris KNUA007 morphological features, spherical, 4–6 µm size, cup-shaped chloroplast and single smooth surface cell. Lortou and Gkelis (2019) have stated that Chlorella vulgaris TAU-MAC1110 strain morphological characteristics viz., spherical-shaped, smooth surface and large pyrenoid. Sharma et al. (2016) have reported morphologically identified green color, unicellular, spherical and 2–10 µm size by Chlorella vulgaris strain. Yanuhar et al. (2019) have documented 589 bp of genes partially sequenced by Chlorella vulgaris STB01. In addition, Jo et al. (2020) have examined the 612 bp of 18S rRNA sequenced genes identified from Chlorella vulgaris strain KNUA007.