scholarly journals Distributed chaos in DNA

2018 ◽  
Author(s):  
A. Bershadskii
Keyword(s):  
Arabidopsis Thaliana ◽  
Dna Sequence ◽  
Kam Theory ◽  
Translational Symmetry ◽  
Stacking Interactions ◽  
Dna Dynamics ◽  
Base Stacking ◽  
Genetic Sequencing ◽  
Model Plant ◽  
Human Genes

It is shown that distributed chaos, generated by Hamiltonian DNA dynamics with spontaneously broken time translational symmetry, imprints itself on the DNA sequence of Arabidopsis thaliana (a model plant for genetic sequencing and mapping) and of the NRXN1 and BRCA2 human genes (as an example). The base-stacking interactions in the DNA duplex, degenerate codon groups and a relation to the KAM theory have been discussed in this context.

scholarly journals A machine learning approach for accurate and real-time DNA sequence identification

BMC Genomics ◽  
2021 ◽  
Vol 22 (1) ◽  
Author(s):  
Yiren Wang ◽  
Mashari Alangari ◽  
Joshua Hihath ◽  
Arindam K. Das ◽  
M. P. Anantram
Keyword(s):  
Real Time ◽  
Dna Sequence ◽  
Single Molecule ◽  
Identification Accuracy ◽  
Measuring System ◽  
Identification System ◽  
Genetic Sequencing ◽  
Sequence Identification ◽  
Tree Classifier ◽  
Single Mismatch

Abstract Background The all-electronic Single Molecule Break Junction (SMBJ) method is an emerging alternative to traditional polymerase chain reaction (PCR) techniques for genetic sequencing and identification. Existing work indicates that the current spectra recorded from SMBJ experimentations contain unique signatures to identify known sequences from a dataset. However, the spectra are typically extremely noisy due to the stochastic and complex interactions between the substrate, sample, environment, and the measuring system, necessitating hundreds or thousands of experimentations to obtain reliable and accurate results. Results This article presents a DNA sequence identification system based on the current spectra of ten short strand sequences, including a pair that differs by a single mismatch. By employing a gradient boosted tree classifier model trained on conductance histograms, we demonstrate that extremely high accuracy, ranging from approximately 96 % for molecules differing by a single mismatch to 99.5 % otherwise, is possible. Further, such accuracy metrics are achievable in near real-time with just twenty or thirty SMBJ measurements instead of hundreds or thousands. We also demonstrate that a tandem classifier architecture, where the first stage is a multiclass classifier and the second stage is a binary classifier, can be employed to boost the single mismatched pair’s identification accuracy to 99.5 %. Conclusions A monolithic classifier, or more generally, a multistage classifier with model specific parameters that depend on experimental current spectra can be used to successfully identify DNA strands.

scholarly journals Fused Graphical Lasso Recovers Flowering Time Mutation Genes in Arabidopsis Thaliana

Inventions ◽  
2021 ◽  
Vol 6 (3) ◽  
pp. 52
Author(s):  
Rajan Kapoor ◽  
Aniruddha Datta ◽  
Michael Thomson
Keyword(s):  
Arabidopsis Thaliana ◽  
Crop Improvement ◽  
Phenotypic Traits ◽  
The Novel ◽  
Model Plant ◽  
Graphical Lasso ◽  
Analysis Strategy ◽  
Model Plant Arabidopsis Thaliana ◽  
Beneficial Traits ◽  
Delayed Flowering

Conventional breeding approaches that focus on yield under highly favorable nutrient conditions have resulted in reduced genetic and trait diversity in crops. Under the growing threat from climate change, the mining of novel genes in more resilient varieties can help dramatically improve trait improvement efforts. In this work, we propose the use of the joint graphical lasso for discovering genes responsible for desired phenotypic traits. We prove its efficiency by using gene expression data for wild type and delayed flowering mutants for the model plant. Arabidopsis thaliana shows that it recovers the mutation causing genes LNK1 and LNK2. Some novel interactions of these genes were also predicted. Observing the network level changes between two phenotypes can also help develop meaningful biological hypotheses regarding the novel functions of these genes. Now that this data analysis strategy has been validated in a model plant, it can be extended to crop plants to help identify the key genes for beneficial traits for crop improvement.

scholarly journals Bending and Base-Stacking Interactions in Double-Stranded DNA

1999 ◽  
Vol 82 (22) ◽  
pp. 4560-4563 ◽  
Author(s):  
Zhou Haijun ◽  
Zhang Yang ◽  
Ou-Yang Zhong-can
Keyword(s):  
Stacking Interactions ◽  
Base Stacking ◽  
Double Stranded Dna

A highly repeated DNA sequence in Arabidopsis thaliana

1986 ◽  
Vol 204 (3) ◽  
pp. 417-423 ◽  
Author(s):  
Jose M. Martinez-Zapater ◽  
Mark A. Estelle ◽  
Chris R. Somerville
Keyword(s):  
Arabidopsis Thaliana ◽  
Dna Sequence ◽  
Repeated Dna ◽  
Highly Repeated Dna ◽  
Repeated Dna Sequence

scholarly journals The scope of flavin-dependent reactions and processes in the model plant Arabidopsis thaliana

2021 ◽  
Vol 189 ◽  
pp. 112822
Author(s):  
Reinmar Eggers ◽  
Alexandra Jammer ◽  
Shalinee Jha ◽  
Bianca Kerschbaumer ◽  
Majd Lahham ◽  
...  
Keyword(s):  
Arabidopsis Thaliana ◽  
Model Plant ◽  
Model Plant Arabidopsis Thaliana ◽  
Plant Arabidopsis Thaliana

scholarly journals A short history of Arabidopsis thaliana (L.) Heynh. Columbia-0

2018 ◽  
Author(s):  
Marc Somssich
Keyword(s):  
Arabidopsis Thaliana ◽  
Short History ◽  
Model Plant ◽  
Natural Accession ◽  
History Of

75 Years ago Arabidopsis thaliana was first suggested as a Model Plant – But how did Arabidopsis Col-0 become the standard natural accession? This is a short history of Arabidopsis thaliana (L.) Heynh. Columbia-0.

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