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Methods in molecular exercise physiology
Published in Adam P. Sharples, James P. Morton, Henning Wackerhage, Molecular Exercise Physiology, 2022
Adam P. Sharples, Daniel C. Turner, Stephen Roth, Robert A. Seaborne, Brendan Egan, Mark Viggars, Jonathan C. Jarvis, Daniel J. Owens, Jatin G. Burniston, Piotr P. Gorski, Claire E. Stewart
Once created, DNA sequencing libraries usually undergo a sequencing process known as ‘sequencing by synthesis’. First, the DNA library sample is transferred to a flowcell which is placed in the sequencing platform. The single-stranded DNA (ssDNA) fragments then adhere to the flowcell via hybridisation of the adapter regions (as described directly above). The attached DNA strands are then amplified to create ‘clusters’ of the exact same ssDNA molecules – these represent the template strand. Sequencing by synthesis is then performed by the creation of a copy strand of DNA, where fluorescently labelled nucleotides of different colours are added in a stepwise manner, each giving off a different coloured fluorescence signal depending on the nucleotide (e.g. the four nucleotides have four different colours). Depending on the length of the DNA libraries, this process is repeated until the entire DNA length has been sequenced. At the end of the sequencing process, the original DNA fragment will now be computationally identified in a series of nucleotide sequences. These computational sequences are commonly referred to as sequencing reads.
Food Interactions, Sirtuins, Genes, Homeostasis, and General Discussion
Published in Chuong Pham-Huy, Bruno Pham Huy, Food and Lifestyle in Health and Disease, 2022
Chuong Pham-Huy, Bruno Pham Huy
A gene, the basic physical and functional unit of heredity, is made up of deoxyribonucleic acid (DNA). (103–107). A gene is a sequence of nucleotides in a particular nucleic acid (104). The nucleotide is the structural unit of a nucleic acid. It is comprised of phosphoric acid, sugar (5-carbon), and a nitrogenous base. The chains of nucleotides in a nucleic acid are linked by 3′, 5′ phosphodiester linkages (104). Genes control identifiable traits of an organism. Genes are segments of DNA that contain the code for a specific protein that functions in one or more types of cells in the body (106). The information stored in DNA is arranged in hereditary units, now known as genes, that control identifiable traits of an organism. In the process of transcription, the information stored in DNA is copied into ribonucleic acid (RNA), which has three distinct roles in protein synthesis (107). Some genes contain all the information necessary to synthesize a protein (enzyme). However, many genes do not code for proteins (105). In humans, genes vary in size from a few hundred DNA bases to more than 2 million DNA bases (105). Humans have about 20,000 to 25,000 genes (105–106).
An Analysis of Protein Interaction and Its Methods, Metabolite Pathway and Drug Discovery
Published in Ayodeji Olalekan Salau, Shruti Jain, Meenakshi Sood, Computational Intelligence and Data Sciences, 2022
Protein sequence alignment is used to know the importance of the homology detection, to predict the various features of a protein and to know the homologous structure. This alignment helps to predict the difference between the structure and the template of the sequence. In sequence alignment, BLAST and FASTA are the basic operations. The operations required to be performed level-wise are sequence identification, searching data in database, detection of homology, alignment of the sequences and updation of the structural information. Figure 13.4 shows the categorization of the sequence alignment. The recent versions of the instrument experiments with the help of NMR and X-ray crystallography are used to store the information of the isolation. These data are input to various algorithms to align the sequences effectively. Three types of alignments are available: single, pairwise and multiple sequence alignments.
Diversity in matrilineages among the Jomon individuals of Japan
Published in Annals of Human Biology, 2023
Fuzuki Mizuno, Yasuhiro Taniguchi, Osamu Kondo, Michiko Hayashi, Kunihiko Kurosaki, Shintaroh Ueda
High-throughput sequencing technologies developed in recent decades have enabled us to acquire a large number of nucleotide and genome-wide sequences. In addition, their costs have decreased dramatically. As a result, ancient genome analysis is not restricted to well-preserved ancient human samples anymore but can be used for a wide range of ancient human samples. Since maternally inherited mitochondrial DNA/genome exhibits significant differences in nucleotide sequence among individuals, it has been used as a valuable index not only for individual identification of maternal relationships but also for genetic relationships among human populations. Here, we aimed to determine the entire nucleotide sequences of the mitochondrial genome (mitogenome) of an ancient human individual remains excavated from an 8200–8600 cal BP Initial Jomon archaeological site, the Iyai rock shelter site in Gunma Prefecture, central Honshu, Japan. We also investigated the matrilineal relationships among seven individuals. Although multiple haplogroup data were determined by PCR genotyping alone, we specifically compared the occurrence of mitochondrial haplogroups in the Jomon period from temporal and regional perspectives.
Facing urosepsis- the most deadly of all urological diseases
Published in Scandinavian Journal of Urology, 2022
Truls E. Bjerklund Johansen, Tommaso Cai
The SIRS definition uses central hemodynamic data and respiration rate as diagnostic criteria for sepsis together with body temperature and levels of white blood cells. For the two criteria most typically related to the immune response, the values can be either significantly higher or lower than normal. Current definitions recognize sepsis as a dysregulated immune response. In 1994, an expert committee of the European Society of Intensive Care Medicine developed the SOFA score [3]. The committee recognized that organs tend to fail in an order or sequence and introduced the term ‘sequential’. They also recognized that disease progression may occur rapidly and recommended that antibiotic treatment and source control, for example inserting a nephrostomy tube in case of obstructive pyelonephritis, should take place within one hour after diagnosis [4].
The evolving role of genetics in ophthalmology
Published in Ophthalmic Genetics, 2021
Natario L. Couser, Brian P. Brooks, Arlene V. Drack, Suma P. Shankar
On October 1, 1990, an international consortium of researchers began the task to sequence and map all three billion base pairs of the human genome (1). Thirteen years and billions of dollars later this biomedical odyssey, the Human Genome Project, was 99% complete. Notwithstanding this astonishing collaborative feat, the clinical molecular diagnostics landscape was in an early infancy stage in 2003; genome sequencing was exceedingly costly, slow and not readily available for widespread clinical applications. Advances in molecular genetics over the past three decades have helped identify a substantial number of genetic variants and conditions known to contribute to eye diseases, and now individual patient analysis can be readily performed in a clinically useful window (2). With this progression of knowledge, the roles of genetics and ophthalmology in patient care have become increasingly intertwined, and the necessity for subspecialists in the field of ophthalmic genetics is of paramount importance.