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Automated Tracing of Adsorbed DNA Molecules with Curvature Using B-Splines

Stenström, Terje LU (2017) FYTK02 20171
Computational Biology and Biological Physics
Abstract
Barcoding is a coarse-grained optical DNA sequencing method, where DNA molecules are stained with fluorescent dyes to create sequence-dependent patterns similar to barcodes. For DNA adsorbed onto a glass surface, we need to be able to trace out these molecules for barcode extraction. We show that B-splines can be used to approximate the shape of adsorbed DNA molecules with curvature and present a basic algorithm that can be automated. We focus on single molecules and test our algorithm on a couple of examples.
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Antibiotics are a vital component in modern medicine, used in prevention and treatment of bacterial infections. But, because of their extensive (mis)use, bacteria are starting to develop a resistance against several common antibiotics. Rapid detection of genes that implement antibiotic resistance (ABR) in bacteria is key in impeding this trend. Genes that implement ABR in bacteria are usually located in so-called plasmids, circular DNA segments that act as supplements to the bacterium's genome. These genetic entities are not essential for the survival of the bacterium, but carry genes that might become useful under certain conditions, such as being exposed to harmful substances. Plasmids are notorious for spreading and mutating fast,... (More)
Antibiotics are a vital component in modern medicine, used in prevention and treatment of bacterial infections. But, because of their extensive (mis)use, bacteria are starting to develop a resistance against several common antibiotics. Rapid detection of genes that implement antibiotic resistance (ABR) in bacteria is key in impeding this trend. Genes that implement ABR in bacteria are usually located in so-called plasmids, circular DNA segments that act as supplements to the bacterium's genome. These genetic entities are not essential for the survival of the bacterium, but carry genes that might become useful under certain conditions, such as being exposed to harmful substances. Plasmids are notorious for spreading and mutating fast, making conventional DNA sequencing methods, which require samples to be grown in laboratories, too slow and unreliable for hospital use. Barcoding is a DNA sequencing method, where DNA molecules are stained with fluorescent dyes to create sequence-dependent patterns similar to barcodes. From these patterns, we can detect DNA sequences that indicate the presence of ABR genes. This method allows information about the inner structure of the DNA to be revealed from single molecules, meaning that no growing of samples is required. In collaboration with Westerlund’s group at Chalmers University, we are working on developing an automated barcode extraction device, where DNA molecules are adsorbed onto a glass surface and recorded with a cell phone camera. Automated barcode extraction algorithms have been developed for DNA in nanochannels, using line detection to detect straight lines in an image. But, because adsorbed DNA molecules tend to be more or less curved, we need a method for approximating their shape in order to extract the barcodes. Here, we present a basic algorithm that can be automated, using B-splines to approximate the shape of adsorbed DNA molecules. The main reason we are interested in B-splines is because these curves can take on all sorts of complicated shapes. We show that B-splines have excellent potential being used for automated tracing of adsorbed DNA molecules with curvature. (Less)
Please use this url to cite or link to this publication:
author
Stenström, Terje LU
supervisor
organization
course
FYTK02 20171
year
type
M2 - Bachelor Degree
subject
language
English
id
8922604
date added to LUP
2017-08-28 13:56:33
date last changed
2017-10-06 16:04:06
@misc{8922604,
  abstract     = {Barcoding is a coarse-grained optical DNA sequencing method, where DNA molecules are stained with fluorescent dyes to create sequence-dependent patterns similar to barcodes. For DNA adsorbed onto a glass surface, we need to be able to trace out these molecules for barcode extraction. We show that B-splines can be used to approximate the shape of adsorbed DNA molecules with curvature and present a basic algorithm that can be automated. We focus on single molecules and test our algorithm on a couple of examples.},
  author       = {Stenström, Terje},
  language     = {eng},
  note         = {Student Paper},
  title        = {Automated Tracing of Adsorbed DNA Molecules with Curvature Using B-Splines},
  year         = {2017},
}