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A DNA sequencer is a scientific instrument used to automate the DNA sequencing process. Given a sample of DNA, a DNA sequencer is used to determine the order of the four bases: G (guanine), C (cytosine), A (adenine) and T (thymine). This is then reported as a text string, called a read. Some DNA sequencers can be also considered optical instruments as they analyze light signals originating from fluorochromes attached to nucleotides.
A nanopore is a pore of nanometer size. It may, for example, be created by a pore-forming protein or as a hole in synthetic materials such as silicon or graphene.
Nanopore sequencing is a third generation approach used in the sequencing of biopolymers — specifically, polynucleotides in the form of DNA or RNA.
DNA sequencing is the process of determining the nucleic acid sequence – the order of nucleotides in DNA. It includes any method or technology that is used to determine the order of the four bases: adenine, guanine, cytosine, and thymine. The advent of rapid DNA sequencing methods has greatly accelerated biological and medical research and discovery.
Alpha-toxin, also known as alpha-hemolysin (Hla), is the major cytotoxic agent released by bacterium Staphylococcus aureus and the first identified member of the pore forming beta-barrel toxin family. This toxin consists mostly of beta sheets (68%) with only about 10% alpha helices. The hly gene on the S. aureus chromosome encodes the 293 residue protein monomer, which forms heptameric units on the cellular membrane to form a complete beta barrel pore. This structure allows the toxin to perform its major function, development of pores in the cellular membrane, eventually causing cell death.
Cornelis "Cees" Dekker is a Dutch physicist, and Distinguished University Professor at Delft University of Technology. He is known for his research on carbon nanotubes, single-molecule biophysics, and nanobiology.
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Synaptotagmin-13 is a protein that in humans is encoded by the SYT13 gene.
Epigenomics is the study of the complete set of epigenetic modifications on the genetic material of a cell, known as the epigenome. The field is analogous to genomics and proteomics, which are the study of the genome and proteome of a cell. Epigenetic modifications are reversible modifications on a cell's DNA or histones that affect gene expression without altering the DNA sequence. Epigenomic maintenance is a continuous process and plays an important role in stability of eukaryotic genomes by taking part in crucial biological mechanisms like DNA repair. Plant flavones are said to be inhibiting epigenomic marks that cause cancers. Two of the most characterized epigenetic modifications are DNA methylation and histone modification. Epigenetic modifications play an important role in gene expression and regulation, and are involved in numerous cellular processes such as in differentiation/development and tumorigenesis. The study of epigenetics on a global level has been made possible only recently through the adaptation of genomic high-throughput assays.
A protocell is a self-organized, endogenously ordered, spherical collection of lipids proposed as a rudimentary precursor to cells during the origin of life. A central question in evolution is how simple protocells first arose and how their progeny could diversify, thus enabling the accumulation of novel biological emergences over time. Although a functional protocell has not yet been achieved in a laboratory setting, the goal to understand the process appears well within reach.
Whole genome sequencing (WGS) is the process of determining the entirety, or nearly the entirety, of the DNA sequence of an organism's genome at a single time. This entails sequencing all of an organism's chromosomal DNA as well as DNA contained in the mitochondria and, for plants, in the chloroplast.
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Oxford Nanopore Technologies plc is a UK-based company which develops and sells nanopore sequencing products for the direct, electronic analysis of single molecules. It is listed on the London Stock Exchange and is a constituent of the FTSE 250 Index.
Third-generation sequencing is a class of DNA sequencing methods which produce longer sequence reads, under active development since 2008.
Cynthia J. Burrows is an American chemist, currently a distinguished professor in the department of chemistry at the University of Utah, where she is also the Thatcher Presidential Endowed Chair of Biological Chemistry. Burrows was the Senior Editor of the Journal of Organic Chemistry (2001-2013) and became Editor-in-Chief of Accounts of Chemical Research in 2014.,,
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Karen Elizabeth Hayden Miga is an American geneticist who co-leads the Telomere-to-Telomore (T2T) consortium that released fully complete assembly of the human genome in March 2022. She is an associate professor of biomolecular engineering at the University of California, Santa Cruz and Associate Director of Human Pangenomics at the UC Santa Cruz Genomics Institute. She was named as "One to Watch" in the 2020 Nature's 10 and one of Time 100’s most influential people of 2022.
Nucleosome Occupancy and Methylome Sequencing (NOMe-seq) is a genomics technique used to simultaneously detect nucleosome positioning and DNA methylation... This method is an extension of bisulfite sequencing, which is the gold standard for determining DNA methylation. NOMe-seq relies on the methyltransferase M.CviPl, which methylates cytosines in GpC dinucleotides unbound by nucleosomes or other proteins, creating a nucleosome footprint. The mammalian genome naturally contains DNA methylation, but only at CpG sites, so GpC methylation can be differentiated from genomic methylation after bisulfite sequencing. This allows simultaneous analysis of the nucleosome footprint and endogenous methylation on the same DNA molecules. In addition to nucleosome foot-printing, NOMe-seq can determine locations bound by transcription factors. Nucleosomes are bound by 147 base pairs of DNA whereas transcription factors or other proteins will only bind a region of approximately 10-80 base pairs. Following treatment with M.CviPl, nucleosome and transcription factor sites can be differentiated based on the size of the unmethylated GpC region.
References
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- ↑ "David W. Deamer's "Origin of Life" published in Persian". Tehran Times. 2024-06-12. Retrieved 2025-01-06.
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- ↑ Deamer, David (2011). First life : discovering the connections between stars, cells, and how life began. Berkeley, CA, US: University of California Press. ISBN 9780520274457. OCLC 727950391.
- ↑ USpatent 5795782,Church, George; Deamer, David W.; Branton, Daniel; Baldarelli, Richard; Kasianowicz, John,"Characterization of Individual Polymer Molecules Based on Monomer-Interface Interactions",issued August 18, 1998, assigned to President and Fellows of Harvard College
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- ↑ Akeson, M.; Deamer, D.W. (1991). "Proton conductance in the gramicidin water wire: Model for proton conductance in the FoF1 ATPase?". Biophysical Journal. 60 (1): 101–109. doi:10.1016/s0006-3495(91)82034-3. PMC 1260042 . PMID 1715764.
- ↑ Kasianowicz, J.; Brandin, E.; Branton, D.; Deamer, D.W. (1996). "Characterization of individual polynucleotide molecules using a membrane channel" (PDF). Proceedings of the National Academy of Sciences USA. 93 (24): 13770–13773. Bibcode:1996PNAS...9313770K. doi: 10.1073/pnas.93.24.13770 . PMC 19421 . PMID 8943010.
- ↑ Akeson, M.; Branton, D.; Kasianowicz, J.J.; Brandin, E.; Deamer, D.W. (1999). "Microsecond time-scale discrimination among polycytidylic acid, polyadenylic acid, and polyuridylic acid as homopolymers or as segments within single RNA molecules". Biophysical Journal. 77 (6): 3227–3233. Bibcode:1999BpJ....77.3227A. doi:10.1016/s0006-3495(99)77153-5. PMC 1300593 . PMID 10585944.
- ↑ "Oxford Nanopore Technology" . Retrieved 17 December 2015.
- ↑ Loman, N.J.; Quick, J.; Simpson, J.T. (2015). "A complete bacterial genome assembled de novo using only nanopore sequencing data". Nature Methods. 12 (8): 733–735. doi:10.1038/nmeth.3444. PMID 26076426. S2CID 15053702.
- ↑ Regalado, Antonio; Quick, J.; Simpson, J.T. (2014-09-17). "Radical New DNA Sequencer Finally Gets into Researchers' Hands". MIT Technology Review. Retrieved 2019-03-26.
- ↑ Hayden, Antonio; Quick, J.; Simpson, J.T. (2015). "Pint-sized DNA sequencer impresses first users". Nature. 521 (7550): 15–16. Bibcode:2015Natur.521...15C. doi: 10.1038/521015a . PMID 25951262.
- ↑ Zon, Jerry; Quick, J.; Simpson, J.T. (2015-09-15). "Nanopore Sequencing: 20 Years On". Zone in With Zon: What's Trending in Nucleic Acid Research. Retrieved 2019-03-26.
- ↑ Krol, Aaron; Quick, J.; Simpson, J.T. (2014-12-22). "Nanopore Sequencing Is Here to Stay". Bio-IT World. Retrieved 2019-03-26.
- ↑ Stephens, Tim; Writer 459-2495, Staff. "UCSC chemist explores the membranous origins of the first living cell". UC Santa Cruz News. Retrieved 2025-01-06.
{{cite web}}: CS1 maint: numeric names: authors list (link) - ↑ Djokic, Martin J. Van Kranendonk, David W. Deamer, Tara (2017-08-01). "Life on Earth Came from a Hot Volcanic Pool, Not the Sea, New Evidence Suggests". Scientific American. Retrieved 2025-01-06.
{{cite web}}: CS1 maint: multiple names: authors list (link)
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