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Trends in Biotechnology
Published in Firdos Alam Khan, Biotechnology Fundamentals, 2020
DNA profiling is done to identify individuals on the basis of their respective DNA and genetic profiles. DNA profiles are encoded sets of numbers that mirror a person’s DNA makeup. DNA profiling is sequencing but that should not be confused with a full genome sequencing. Although 99.9% of human DNA sequences are the same in every person, there are sequence that are different in each individual. The unique sequencing can be measured by variable number tandem repeats (VNTR) in the DNA. It has been found that in closely related individuals VNTRs loci are very similar, whereas VNTRs are variable in unrelated individuals. The DNA profiling technique was first reported in 1985 by Sir Alec Jeffreys, University of Leicester, England. DNA fingerprinting is a technique to determine the possibility that genetic material came from a particular individual or group. In the case of plants such as grapes, researchers compared the similarities between different species of grapes and were able to piece together parent subspecies that could have contributed to the present prize-winning varieties.
Associations between Genetic Polymorphisms and Heart Rate Variability
Published in Herbert F. Jelinek, David J. Cornforth, Ahsan H. Khandoker, ECG Time Series Variability Analysis, 2017
Anne Voigt, Jasha W. Trompf, Mikhail Tamayo, Ethan Ng, Yuling Zhou, Yaxin Lu, Slade Matthews, Brett D. Hambly, Herbert F. Jelinek
Differences in the genetic sequence between individuals, or genetic polymorphisms, make up the foundation of diversity in biological organisms. Genetic polymorphisms require at least two variants in the population of a species, of which the least common one cannot be explained by recurrent mutations (Ford 1965). These polymorphisms have been studied using mostly restriction fragment length polymorphisms (RFLPs) and microsatellite markers. RFLP is based on the use of restriction enzymes, which cut the DNA sequence at a known position in order to compare the length of the sequence fragments between individuals (Botstein et al. 1980). RFLP was first used in 1983 for the mapping of the Huntington disease gene (Gusella et al. 1983). Micro- and mini-satellite markers (variable number of tandem repeats [VNTRs]) mark repetitive DNA sequences, which include repeated DNA motifs and have also been studied for gene mapping (Ellegren 2004).
DNA Structure, Sequencing, Synthesis, and Modification: Making Biology Molecular
Published in Richard J. Sundberg, The Chemical Century, 2017
By April, 2003, the 50th anniversary of the Watson–Crick double helix, the HGP had sequenced about 99.9% of the human genome with 400 gaps. There were some discrepancies between the HGP and WGS versions. According to analysis by Celera, about 2.7 million bp disagree. The HGP data is said to contain about 140 million base pairs that are redundant, while the Celera contains 50 million bp of such data. There are discrepancies between the two sets of data for about 200 bp. Continued refinement is being done. The final results provided some surprises. It turned out there were only around 25,000 genes, not 100,000. By way of comparison, C. elegans has about 20,000 and D. melanogaster about 14,000. The mouse genome is about 89% identical with that of humans. As the sequencing work proceeded, it became apparent that individual genes can make several proteins, overturning the one gene–one protein relationship. It also became apparent that all the sequenced genomes, human included, incorporated genes from ancient bacteria and single-cell organisms. The genetic material also contains many sequences that are not transcribed, which includes the extensive areas called tandem repeats.
Association of Genetic Polymorphisms of TERT with Telomere Length in Coke Oven Emissions-Exposed Workers
Published in International Journal of Environmental Health Research, 2022
Mengqing Yan, Shuai Cheng, Sihua Wang, Xiaoran Duan, Acquaye Reuben Mensah, Lei Li, Yuhong Zhang, Guoyu Li, Junfeng Zhao, Feifei Feng, Xiaoshan Zhou, Yongjun Wu, Yongli Yang, Wei Wang
Coke oven emissions (COE) contain volatile organic solvents and various particles, particularly polycyclic aromatic hydrocarbons (PAHs), which are highly toxic (Xin et al. 2014). Long-term exposure to PAHs induces oxidative stress, DNA damage, and chromosomal aberrations (Orjuela et al. 2010; Moorthy et al. 2015). Telomeres are non-coding DNA sequences composed of 5'-TTAGGG-3’ tandem repeats at the end of eukaryotic chromosomes. They are commonly associated with chromosome stability. Telomere shortening is associated with aging, and current studies suggest an important role of telomere structure, telomeric DNA damage, and telomere end-capping proteins during aging and in various age-associated disorders. A study involving 1628 coke-oven workers revealed that exposure to high PAHs levels accelerates shortening of the telomere length(Fu et al. 2018). Previous studies have also reported that shorter telomere lengths are associated with occupational exposure to COEs. In the same line, there exists an exposure-response relationship between COEs exposure and telomere damage(Wang et al. 2019). Nonetheless, changes in telomere length are primarily caused by a combined genetic and environmental effect.
Retrieving high-quality genomic DNA from formalin-fixed paraffin-embedded tissues for multiple molecular analyses
Published in Preparative Biochemistry & Biotechnology, 2022
Ha Thi Nguyen, Vinay Bharadwaj Tatipamula, Duy Ngoc Do, Thien Chi Huynh, Mai Kim Dang
Conventional PCR amplification using 100 ng of gDNA input followed by Sanger sequencing has been done for two markers KRAS (170 base-pairs, bp) and BRAF (224 bp) to detect the hot-spot mutations in these two loci in CRC patients. The primer sequences and PCR conditions are listed in Table 1. Additionally, conventional PCR was also performed for one primer pair, which amplifies a fragment of 725 bp of PIK3CA gene to investigate further the quality and amplificapacity of the extracted DNA samples. Multiplex-PCR for two sets of short tandem repeats (STR) markers have been performed and subjected to fragment analysis using ABI 3500 system (ABI, Thermo Scientific, Waltham, MA) to define the microsatellite instability (MSI) status of these CRC samples.[22] The technical details for PCR and fragment analysis are described in Table 1.
A hydroxyquinoline-appended ruthenium(II)-polypyridyl complex that induces and stabilizes G-quadruplex DNA
Published in Journal of Coordination Chemistry, 2019
Xuexue Xu, Shuang Wang, Yaxuan Mi, Huaqian Zhao, Zebao Zheng, Xiaolong Zhao
G-quadruplexes are functionally useful secondary DNA structures, comprising stacks of G-quartets that are stabilized through cyclic Hoogsteen hydrogen bonding [1, 2]. The G-quadruplex structures are abundant in human genome and are currently being regarded as appealing therapeutic targets [3–5]. Many G-rich regions such as proto-oncogenes of c-myc, c-kit and bcl-2 and telomeres have the ability to form G-quadruplexes [6–9]. It has been determined by crystallographic and NMR studies that human telomeric DNA consists of tandem repeats of sequence d[(TTAGGG)n] is rich in guanine residues and can fold into quadruplex structures [9]. The conversion of telomeric DNA to a G-quadruplex can inhibit the activity of telomerase, an enzyme inactive in most normal somatic cells, but overexpressed in above 85% of cancer cells and contributes to the immortality of these cells [10]. Thus, the design of small molecules that targets at the telomeric G-quadruplex is an active area in drug discovery.