scholarly journals Functional diversity for REST (NRSF) is defined by in vivo binding affinity hierarchies at the DNA sequence level

2009 ◽  
Vol 19 (6) ◽  
pp. 994-1005 ◽  
Author(s):  
A. W. Bruce ◽  
A. J. Lopez-Contreras ◽  
P. Flicek ◽  
T. A. Down ◽  
P. Dhami ◽  
...  
Keyword(s):  
Binding Affinity ◽  
Dna Sequence ◽  
Functional Diversity ◽  
In Vivo Binding

scholarly journals DNA thermodynamics shape chromosome organization and topology

2013 ◽  
Vol 41 (2) ◽  
pp. 548-553 ◽  
Author(s):  
Andrew A. Travers ◽  
Georgi Muskhelishvili
Keyword(s):  
Dna Sequence ◽  
Dna Sequences ◽  
Chromosome Organization ◽  
Topological Properties ◽  
Genetic Organization ◽  
And Topology ◽  
Dna Translocases

How much information is encoded in the DNA sequence of an organism? We argue that the informational, mechanical and topological properties of DNA are interdependent and act together to specify the primary characteristics of genetic organization and chromatin structures. Superhelicity generated in vivo, in part by the action of DNA translocases, can be transmitted to topologically sensitive regions encoded by less stable DNA sequences.

scholarly journals Aptardi predicts polyadenylation sites in sample-specific transcriptomes using high-throughput RNA sequencing and DNA sequence

2021 ◽  
Vol 12 (1) ◽  
Author(s):  
Ryan Lusk ◽  
Evan Stene ◽  
Farnoush Banaei-Kashani ◽  
Boris Tabakoff ◽  
Katerina Kechris ◽  
...  
Keyword(s):  
Rna Sequencing ◽  
Dna Sequence ◽  
Mammalian Species ◽  
Alternative Polyadenylation ◽  
Sequence Information ◽  
Rna Seq ◽  
Average Precision ◽  
Polyadenylation Sites ◽  
Dna Nucleotide Sequence

AbstractAnnotation of polyadenylation sites from short-read RNA sequencing alone is a challenging computational task. Other algorithms rooted in DNA sequence predict potential polyadenylation sites; however, in vivo expression of a particular site varies based on a myriad of conditions. Here, we introduce aptardi (alternative polyadenylation transcriptome analysis from RNA-Seq data and DNA sequence information), which leverages both DNA sequence and RNA sequencing in a machine learning paradigm to predict expressed polyadenylation sites. Specifically, as input aptardi takes DNA nucleotide sequence, genome-aligned RNA-Seq data, and an initial transcriptome. The program evaluates these initial transcripts to identify expressed polyadenylation sites in the biological sample and refines transcript 3′-ends accordingly. The average precision of the aptardi model is twice that of a standard transcriptome assembler. In particular, the recall of the aptardi model (the proportion of true polyadenylation sites detected by the algorithm) is improved by over three-fold. Also, the model—trained using the Human Brain Reference RNA commercial standard—performs well when applied to RNA-sequencing samples from different tissues and different mammalian species. Finally, aptardi’s input is simple to compile and its output is easily amenable to downstream analyses such as quantitation and differential expression.

scholarly journals Polarity-active NIR probes with strong two-photon absorption and ultrahigh binding affinity of insulin amyloid fibrils

2021 ◽  
Author(s):  
Li Li ◽  
Zheng Lv ◽  
Zhongwei Man ◽  
Zhenzhen Xu ◽  
YuLing Wei ◽  
...  
Keyword(s):  
Neurodegenerative Diseases ◽  
Binding Affinity ◽  
Fluorescent Probes ◽  
Amyloid Fibrils ◽  
Photon Absorption ◽  
Two Photon Absorption ◽  
Two Photon ◽  
Medical Diagnostic

Amyloid fibrils are associated with many neurodegenerative diseases. In-situ and in-vivo visualization of amyloid fibrils is important for medical diagnostic and requires fluorescent probes with both excitation and emission wavelengths in...

scholarly journals isoTarget: A Genetic Method for Analyzing the Functional Diversity of Splicing Isoforms In Vivo

Cell Reports ◽  
2020 ◽  
Vol 33 (6) ◽  
pp. 108361
Author(s):  
Hao Liu ◽  
Sarah Pizzano ◽  
Ruonan Li ◽  
Wenquan Zhao ◽  
Macy W. Veling ◽  
...  
Keyword(s):  
Functional Diversity ◽  
Genetic Method ◽  
Splicing Isoforms

scholarly journals Impaired in vivo binding of MeCP2 to chromatin in the absence of its DNA methyl-binding domain

2013 ◽  
Vol 41 (9) ◽  
pp. 4888-4900 ◽  
Author(s):  
D. P. Stuss ◽  
M. Cheema ◽  
M. K. Ng ◽  
A. Martinez de Paz ◽  
B. Williamson ◽  
...  
Keyword(s):  
Binding Domain ◽  
In Vivo Binding

scholarly journals Effect of Small-Molecule–Binding Affinity on Tumor Uptake In Vivo: A Systematic Study Using a Pretargeted Bispecific Antibody

2012 ◽  
Vol 11 (6) ◽  
pp. 1365-1372 ◽  
Author(s):  
Kelly Davis Orcutt ◽  
John J. Rhoden ◽  
Benjamin Ruiz-Yi ◽  
John V. Frangioni ◽  
K. Dane Wittrup
Keyword(s):  
Binding Affinity ◽  
Small Molecule ◽  
Systematic Study ◽  
Bispecific Antibody ◽  
Tumor Uptake

Comparison of [11C]diprenorphine and [11C]carfentanil in vivo binding to opiate receptors in man using a dual detector system

1994 ◽  
Vol 257 (1-2) ◽  
pp. 195-197 ◽  
Author(s):  
Victor L. Villemagne ◽  
J. James Frost ◽  
Robert F. Dannals ◽  
John R. Lever ◽  
Shuji Tanada ◽  
...  
Keyword(s):  
Opiate Receptors ◽  
Detector System ◽  
In Vivo Binding ◽  
Dual Detector
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