Run-Length Encoding Graphic Rules Applied to DNA-Coded Images and Animation Editable by Polymerase Chain Reactions

2015 ◽  
Vol 19 (1) ◽  
pp. 5-10 ◽  
Author(s):  
Yuki Hara ◽  
◽  
Tomonori Kawano
Keyword(s):  
Image Coding ◽  
Image Data ◽  
Chain Reaction ◽  
Run Length ◽  
Noncoding Regions ◽  
Chain Reactions ◽  
Polymerase Chain Reactions ◽  
Coding Regions ◽  
Polymerase Chain ◽  
Coded Images

We previously proposed novel designs for artificial genes as media for storing digitally compressed image data, specifically for biocomputing by analogy to natural genes mainly used to encode proteins. A run-length encoding (RLE) rule had been applied in DNA-based image data processing, to form coding regions, and noncoding regions were created as space for designing biochemical editing. In the present study, we apply the RLE-based image-coding rule to creation of DNAbased animation. This article consisted of three parts: (i) a theoretical review of RLE-based image coding by DNA, (ii) a technical proposal for biochemical editing of DNA-coded images using the polymerase chain reaction, and (iii) a minimal demonstration of DNAbased animation using simple model images encoded on short DNA molecules.

Investigation of Mutations in Exon 12 Of MYH7, 16 Of β-MYBPC3 and 2 Of TCAP Gene in Dogs with Dilated Cardiomyopathy using PCR-SSCP Technique

2021 ◽  
Author(s):  
R.B. Vishnurahav ◽  
S. Ajithkumar ◽  
Usha Narayana Pillai ◽  
N. Madhvan Unny ◽  
K.D. John Martin ◽  
...  
Keyword(s):  
Polymerase Chain Reaction ◽  
Dilated Cardiomyopathy ◽  
Genetic Alterations ◽  
Chain Reaction ◽  
Multifunctional Protein ◽  
Chain Reactions ◽  
Polymerase Chain Reactions ◽  
Intron 1 ◽  
Cardiac Disorders ◽  
Polymerase Chain

Background: Dilated cardiomyopathy is the important myocardial disease and one of the most common cause of death in the medium to large size dog breeds worldwide. The disease is characterized by dilatation of cardiac chambers and thinning of walls leads to systolic failure. Mutations in some sarcomere genes leads to cardiomyopathy in humans. Sarcomere is an important multifunctional protein network involved in the signal reception and transduction. Mutations in β-MYH7, MYBPC3 and TCAP genes produce alterations in the morphology of heart (hypertrophy or dilatation).Methods: In this study twenty apparently healthy and twenty five dogs with dilated cardiomyopathy (DCM) were selected from patients reported or referred to University Veterinary Hospital and Teaching Veterinary Clinical Complex, Mannuthy (2015-2017) based on the clinical examination, radiographic, electrocardiographic, haematobiochemical and echocardiographic studies cardiac disorders (Dilated cardiomyopathy and hypertrophic cardiomyopathy) were confirmed.Result: In the present study we investigated genetic alterations of exon 12 of MYH7, 16 of β-MYBPC3 and 2 of TCAP gene in dogs by polymerase chain reaction -single stranded confirmation of polymorphism (PCR-SSCP). Polymerase chain reactions were analysed using acrylamide gel and samples with different pattern of bands were sequenced. Polymerase chain reaction-SSCP showed different migration of band pattern in the intron 1 of TCAP gene in one sample.

Detection of rye chromosome 2R using the polymerase chain reaction and sequence-specific DNA primers

Genome ◽  
1994 ◽  
Vol 37 (1) ◽  
pp. 19-22 ◽  
Author(s):  
J.-H. Lee ◽  
R. A. Graybosch ◽  
D. J. Lee
Keyword(s):  
Polymerase Chain Reaction ◽  
Wheat Chromosome ◽  
Specific Marker ◽  
Chain Reaction ◽  
Chain Reactions ◽  
Polymerase Chain Reactions ◽  
Pcr Product ◽  
Polymerase Chain ◽  
Wheat Lines ◽  
Dna Primers

Sequences derived from a rye gamma secalin gene were used as primers in polymerase chain reactions using DNA obtained from a series of wheat and triticale genetic stocks. A 473-bp fragment, the predicted size based on the distance between the selected primers, was found only in rye, triticales, and wheat lines carrying rye chromosome 2RS. Use of triticale lines with various wheat chromosome substitutions confirmed the chromosomal origin of the rye-specific marker. The presence of the 473-bp PCR product was always associated with the production of 75K secalins in grain samples. Thus, the primer sequences, and the clone of origin (pSC503), were both derived from the SEC-2 locus of rye chromosome 2RS.Key words: wheat (Triticum aestivum), rye (Secale cereale), chromosomal translocations, chromosomal substitutions, DNA polymerase chain reaction, sequence-specific primers.

scholarly journals ABO glycosyltransferase genotyping by polymerase chain reaction using sequence-specific primers

Blood ◽  
1996 ◽  
Vol 88 (5) ◽  
pp. 1852-1856 ◽  
Author(s):  
C Gassner ◽  
A Schmarda ◽  
W Nussbaumer ◽  
D Schonitzer
Keyword(s):  
Pcr Amplification ◽  
Abo Blood Groups ◽  
Chain Reaction ◽  
Specific Primers ◽  
Chain Reactions ◽  
Polymerase Chain Reactions ◽  
Serological Typing ◽  
Modern Molecular Biology ◽  
Specific Nucleotide Sequence ◽  
Polymerase Chain

Serological typing for the classical ABO blood groups is routinely performed using anti-A and anti-B antisera of polyclonal or monoclonal origin, which are able to distinguish four phenotypes (A, B, AB, and O). Modern molecular biology methods offer the possibility of direct ABO genotyping without the need for family investigations. Typing can be done with small amounts of DNA and without detection of blood group molecules on the surface of red blood cells. We developed a system of eight polymerase chain reactions (PCR) to detect specific nucleotide sequence differences between the ABO alleles O1, O2, A1, A2, and B. PCR amplification using sequence-specific primers and detection of amplification products by agarose gel electrophoresis is one of the fastest genotyping methods and is easy to handle. With our method we tested the A1,2BO1,2 genotypes of 300 randomly chosen persons out of a pool of platelet donors and found the results to be consistent with ABO glycosyltransferase phenotypes. We also identified a presumably new ABO allele, which may be the result of a crossing-over event between alleles O1 and A2.

scholarly journals ABO glycosyltransferase genotyping by polymerase chain reaction using sequence-specific primers

Blood ◽  
1996 ◽  
Vol 88 (5) ◽  
pp. 1852-1856 ◽  
Author(s):  
C Gassner ◽  
A Schmarda ◽  
W Nussbaumer ◽  
D Schonitzer
Keyword(s):  
Pcr Amplification ◽  
Abo Blood Groups ◽  
Chain Reaction ◽  
Specific Primers ◽  
Chain Reactions ◽  
Polymerase Chain Reactions ◽  
Serological Typing ◽  
Modern Molecular Biology ◽  
Specific Nucleotide Sequence ◽  
Polymerase Chain

Abstract Serological typing for the classical ABO blood groups is routinely performed using anti-A and anti-B antisera of polyclonal or monoclonal origin, which are able to distinguish four phenotypes (A, B, AB, and O). Modern molecular biology methods offer the possibility of direct ABO genotyping without the need for family investigations. Typing can be done with small amounts of DNA and without detection of blood group molecules on the surface of red blood cells. We developed a system of eight polymerase chain reactions (PCR) to detect specific nucleotide sequence differences between the ABO alleles O1, O2, A1, A2, and B. PCR amplification using sequence-specific primers and detection of amplification products by agarose gel electrophoresis is one of the fastest genotyping methods and is easy to handle. With our method we tested the A1,2BO1,2 genotypes of 300 randomly chosen persons out of a pool of platelet donors and found the results to be consistent with ABO glycosyltransferase phenotypes. We also identified a presumably new ABO allele, which may be the result of a crossing-over event between alleles O1 and A2.

scholarly journals Detection of Bovine Leukemia Virus in Blood and Milk by Nested and Real-Time Polymerase Chain Reactions

2003 ◽  
Vol 15 (1) ◽  
pp. 72-76 ◽  
Author(s):  
Christopher J. Kuckleburg ◽  
Christopher C. Chase ◽  
Eric A. Nelson ◽  
Salvatore A. E. Marras ◽  
Matthew A. Dammen ◽  
...  
Keyword(s):  
Polymerase Chain Reaction ◽  
Early Detection ◽  
Real Time ◽  
Bovine Leukemia Virus ◽  
Leukemia Virus ◽  
Chain Reaction ◽  
Nested Polymerase Chain Reaction ◽  
Chain Reactions ◽  
Polymerase Chain Reactions ◽  
Polymerase Chain

Concerns about retroviruses in livestock and products derived from them have necessitated the development of tests to detect the bovine leukemia virus (BLV) in blood and milk from cattle. Dairy cattle ( n = 101) from 5 different geographical areas were used for this study. A nested polymerase chain reaction (PCR) identified 98% of BLV seropositive cattle ( n = 80) from blood and 65% from milk, whereas real-time PCR detected 94% of BLV seropositive cattle from blood and 59% from milk. Bovine leukemia virus was also detected by PCR in approximately 10% of seronegative cattle ( n = 21), most likely because of early detection before seroconversion.

scholarly journals A Guide to Cloning the Products of Polymerase Chain Reactions

2021 ◽  
Vol 2021 (9) ◽  
pp. pdb.top101345
Author(s):  
Michael R. Green ◽  
Joseph Sambrook
Keyword(s):  
Polymerase Chain Reaction ◽  
Chain Reaction ◽  
Site Specific ◽  
Site Specific Recombination ◽  
Chain Reactions ◽  
Polymerase Chain Reactions ◽  
Polymerase Chain

This introduction outlines various methods to clone amplified DNAs and to facilitate the construction of complex multicomponent genetic units. Because of the ease with which the termini of amplified DNAs can be tailored by polymerase chain reaction (PCR), many of the methods outlined here use PCR not only to synthesize DNAs but also to link them together into purpose-designed constructs. The most recent refinements however have been the development of modular genetic units that can be harnessed to target DNAs not by PCR but by site-specific recombination enzymes.

The phenanthroimidazole-based dizinc(ii) complex as a fluorescent probe for the pyrophosphate ion as generated in polymerase chain reactions and pyrosequencing

2015 ◽  
Vol 44 (9) ◽  
pp. 3930-3933 ◽  
Author(s):  
Sellamuthu Anbu ◽  
Subban Kamalraj ◽  
Anup Paul ◽  
Chelliah Jayabaskaran ◽  
Armando J. L. Pombeiro
Keyword(s):  
Detection Limit ◽  
Fluorescent Probe ◽  
Chain Reaction ◽  
Dna Polymerization ◽  
Chain Reactions ◽  
Polymerase Chain Reactions ◽  
Low Detection Limit ◽  
Polymerase Chain ◽  
Polymerization Chain

The phenanthroimidazole-based dizinc(II) complex is an efficient fluorescent probe for the pyrophosphate ion (PPi) in water with a very low detection limit, and also used to detect PPi released from DNA polymerization chain reaction.

Identification of Clavibacter michiganensis subsp. sepedonicus using the polymerase chain reaction

1994 ◽  
Vol 40 (2) ◽  
pp. 148-151 ◽  
Author(s):  
Giuseppe Firrao ◽  
Romano Locci
Keyword(s):  
Polymerase Chain Reaction ◽  
Clavibacter Michiganensis ◽  
Chain Reaction ◽  
Chain Reactions ◽  
Polymerase Chain Reactions ◽  
Clavibacter Michiganensis Subsp ◽  
Ring Rot ◽  
Dna Fragment ◽  
Polymerase Chain ◽  
Polymerase Chain Reaction Primers

From the sequence of a subcloned DNA fragment of a highly conserved plasmid of Clavibacter michiganensis subsp. sepedonicus a pair of oligonucleotides were devised for use as polymerase chain reaction primers. The primer sequences do not show significant homology with any other sequence deposited in public databases. Polymerase chain reactions carried out using this primer pair and untreated cells of all strains of C. michiganensis sepedonicus tested resulted in the amplification of a DNA fragment of about 670 base pairs. No amplification was observed when bacteria belonging to other species were submitted to polymerase chain reaction under the same conditions. The detection limit of the assay was 4 × 103 bacteria.Key words: detection, potato ring rot, Corynebacterium sepedonicum.

scholarly journals NGS-PrimerPlex: High-throughput primer design for multiplex polymerase chain reactions

2020 ◽  
Vol 16 (12) ◽  
pp. e1008468
Author(s):  
Andrey Kechin ◽  
Viktoria Borobova ◽  
Ulyana Boyarskikh ◽  
Evgeniy Khrapov ◽  
Sergey Subbotin ◽  
...  
Keyword(s):  
Foodborne Pathogens ◽  
Primer Design ◽  
Nucleotide Polymorphisms ◽  
Chain Reactions ◽  
Targeted Next Generation Sequencing ◽  
Polymerase Chain Reactions ◽  
Coding Regions ◽  
Gene Coding ◽  
Polymerase Chain ◽  
Next Generation Sequencing Ngs

Multiplex polymerase chain reaction (PCR) has multiple applications in molecular biology, including developing new targeted next-generation sequencing (NGS) panels. We present NGS-PrimerPlex, an efficient and versatile command-line application that designs primers for different refined types of amplicon-based genome target enrichment. It supports nested and anchored multiplex PCR, redistribution among multiplex reactions of primers constructed earlier, and extension of existing NGS-panels. The primer design process takes into consideration the formation of secondary structures, non-target amplicons between all primers of a pool, primers and high-frequent genome single-nucleotide polymorphisms (SNPs) overlapping. Moreover, users of NGS-PrimerPlex are free from manually defining input genome regions, because it can be done automatically from a list of genes or their parts like exon or codon numbers. Using the program, the NGS-panel for sequencing the LRRK2 gene coding regions was created, and 354 DNA samples were studied successfully with a median coverage of 97.4% of target regions by at least 30 reads. To show that NGS-PrimerPlex can also be applied for bacterial genomes, we designed primers to detect foodborne pathogens Salmonella enterica, Escherichia coli O157:H7, Listeria monocytogenes, and Staphylococcus aureus considering variable positions of the genomes.

scholarly journals NGS-PrimerPlex: high-throughput primer design for multiplex polymerase chain reactions

2020 ◽  
Author(s):  
Andrey Kechin ◽  
Viktoria Borobova ◽  
Ulyana Boyarskikh ◽  
Evgeniy Khrapov ◽  
Sergey Subbotin ◽  
...  
Keyword(s):  
Multiplex Pcr ◽  
Primer Design ◽  
Supplementary Information ◽  
Target Enrichment ◽  
Chain Reactions ◽  
Polymerase Chain Reactions ◽  
Coding Regions ◽  
Gene Coding ◽  
Targeted Ngs ◽  
Polymerase Chain

AbstractSummaryMultiplex PCR has multiple applications in molecular biology, including developing new targeted NGS-panels. We present NGS-PrimerPlex, an efficient and versatile command-line application that designs primers for different refined types of amplicon-based genome target enrichment. It supports nested and anchored multiplex PCR, redistribution among multiplex reactions of primers constructed earlier and extension of existing NGS-panels. The primer design process takes into consideration formation of secondary structures, non-target amplicons between all primers of a pool, primers and high-frequent genome SNPs overlapping. Moreover, users of NGS-PrimerPlex are free from manually defining input genome regions, because it can be done automatically from a list of genes or their parts like exon or codon numbers. Using the program, NGS-panel for sequencing the LRRK2 gene coding regions was created, and 354 DNA samples were studied successfully with median coverage of 97.4% of target regions by at least 30 reads.Availability and implementationNGS-PrimerPlex is open-source and freely available at https://github.com/aakechin/NGS-PrimerPlex/[email protected] informationSupplementary data

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