Methods of Evaluation in Orthopaedic Animal Research
Yuehuei H. An, Richard J. Friedman in Animal Models in Orthopaedic Research, 2020
The basic terminology given here is adapted from the reviews by Shore and Kaplan.251,252 A gene is a unit of heredity, consisting of a segment of chromosomal DNA that is required for production of a functional protein or RNA. The gene contains both coding and regulatory regions. A transgene is a foreign gene which has been spliced into an animals original genomic DNA. mRNA is a type of RNA that contains protein coding information. Nucleotide sequence refers to the order of nucleotides in a given segment of DNA or RNA. Translocation is the transfer of a portion of DNA from one chromosome to another. A probe is a DNA or RNA molecule that is labeled, or tagged, and can then be used to locate a complementary DNA or RNA strand through hybridization. Vectors are DNA molecules that are used as carrier molecules for cloned DNA sequences. They contain information which allows recombinant molecules to be replicated in host bacterial cells. A plasmid is a small circular double-stranded DNA molecule which is found in bacteria and replicates independently of the host chromosome. They are commonly used as vectors in molecular cloning. A recombinant DNA molecule is a DNA molecule containing segments of DNA from different origins, such as a piece of human DNA that has been joined to a plasmid DNA. A clone is a term used to describe identical segmental DNA molecules produced by recombinant DNA technique. Molecular cloning is a process by which a specific segment of DNA is isolated and then numerous identical copies, or clones, of that segment of DNA are generated.
ChIP-seq analysis
Altuna Akalin in Computational Genomics with R, 2020
As explained in Chapter 1, gene expression is controlled by a special class of genes called transcription factors - genes which control other genes. Transcription factor genes encode proteins which can bind to the DNA, and control whether a certain part of DNA will be transcribed (expressed), or stay silent (repressed). They program the expression patterns in each cell. Transcription factors contain DNA binding domains, which are specifically folded protein sequences which recognize specific DNA motifs (a short nucleotide sequence). Such sequence binding imparts transcription factors with specificity, transcription factors do not bind everywhere on the DNA, rather they are localized to short stretches which contain the corresponding DNA motif.
Oropharyngeal Tumours
John C Watkinson, Raymond W Clarke, Terry M Jones, Vinidh Paleri, Nicholas White, Tim Woolford in Head & Neck Surgery Plastic Surgery, 2018
This method relies on the use of a DNA probe labelled, for example, with a chromogen, the nucleotide sequence of which is complementary to the DNA sequence or gene under investigation. When applied to formalin-fixed paraffin embedded (FFPE) tumour samples, the probe will bind to the complementary sequence within the DNA of that tissue sample, thereby confirming its presence. The chromogen label allows the visualization of the bound probe by light microscopy. Kits are commercially available for the detection of HRHPV genotypes in FFPE tissue and are typically designed to detect the specific L1 gene sequences, variations of which determine the specific genotype. A positive test result is confirmed by the presence of a blue dot under light microscopy (Figure 13.6). This technique allows localization of the HPV DNA to the host cell nucleus and whilst a punctate staining pattern is suggestive of HPV DNA integration it does not amount to categorical proof of this.
Ethanol production from cassava starch by protoplast fusants of Wickerhamomyces anomalus and Galactomyces candidum
Published in Egyptian Journal of Basic and Applied Sciences, 2020
Tolulope Modupe Adeleye, Sharafadeen Olateju Kareem, Mobolaji O. Bankole, Olusegun Atanda, Abideen I. Adeogun
Figures 4 and 5 illustrate the molecular relationships between the parent and fusants yeasts as inferred from the sequences generated. The evolutionary history was inferred using the Neighbor-Joining method [33]. The optimal tree with the sum of branch length of 0.52913781 is shown. Percentage of replicate trees in which the associated taxa clustered together in the bootstrap test (1000 replicates) is shown next to the branches [34]. Branches corresponding to partitions reproduced in less than 50% bootstrap replicates were collapsed. The evolutionary distances were computed using the p-distance method [35] and are in the units of the number of base differences per site. The analysis involved five nucleotide sequences. Codon positions included were 1st+ 2nd+ 3rd+ Noncoding. All ambiguous positions were removed for each sequence pair. A total of 568 positions was obtained in the final dataset. Evolutionary analyses were conducted in MEGA 6 [36].
Nucleic acid-based electrochemical biosensors for rapid clinical diagnosis: advances, challenges, and opportunities
Published in Critical Reviews in Clinical Laboratory Sciences, 2022
Abu Hashem, M. A. Motalib Hossain, Ab Rahman Marlinda, Mohammad Al Mamun, Suresh Sagadevan, Zohreh Shahnavaz, Khanom Simarani, Mohd Rafie Johan
As a result, a research focus is to identify specialized bioreceptors. The target should be designed and compared with nucleotide sequences of other genes or species so that the target probe can distinguish it from possible interferences. For the design of a perfect probe, relevant nucleotide sequences can be retrieved from the National Center for Biotechnology Information (NCBI) (https://www.ncbi.nlm.nih.gov). The retrieved sequences are aligned using bioinformatics tools such as MEGA software to identify intra-species conserved and inter-species variable regions so the probe sequence that is designed matches completely with target species but has numerous mismatches with non-target species. Finally, the selected probe is checked for specificity between the closely related and distant species using the online Basic Local Alignment Search Tool (BLAST) in the NCBI database (http://blast. ncbi.nlm.nih.gov/Blast.cgi) so that the designed probe will be unique and hybridize with only target sequences. Repeated cycles are carried out until the specified sequence increases exponentially and low-affinity sequences are eliminated. Aptamers are capable of recognizing both small molecules and high-molecular-weight substances as well as complete cells. However, it is worth noting that aptamer commercialization is still in its early stages [103]. Thus, future improvements include developing novel bioreceptors and upgrading existing bioreceptors to cater to commercial needs.
HSP47: a potential target for fibrotic diseases and implications for therapy
Published in Expert Opinion on Therapeutic Targets, 2021
Pierre-Simon Bellaye, Olivier Burgy, Philippe Bonniaud, Martin Kolb
The most studied strategy to explore the impact of HSP47 inhibition in vivo is based on small interfering RNA (siRNA) blocking HSP47 expression. siRNA are double-stranded non-coding RNA molecules, typically 20–27 base pairs in length, which interferes with the expression of specific genes with complementary nucleotide sequences by degrading mRNA after transcription and/or preventing translation. This has demonstrated the anti-fibrotic potential in skin keloids, where siRNA targeting HSP47 reduced intra- and extracellular collagen levels in keloid fibroblasts [66]. In an animal model of subcutaneous implantation of human keloid dermal tissues, HSP47 downregulation reduced the volume of keloids and decreased collagen expression [67]. Similarly, Hagiwara et al. reported a protective effect of HSP47 inhibition by siRNA in vivo in several models of lung fibrosis [68,69]. In addition, HSP47 silencing using shRNA in a hepatic fibrosis model reduced collagen deposition in a dose-dependent manner [53].
Related Knowledge Centers
- Allele
- Directionality
- DNA
- Nucleobase
- Nucleotide
- Polymer
- Rna
- Sense
- Nucleic Acid Secondary Structure
- Nucleic Acid Tertiary Structure