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Chloroplast DNA and Phylogenetic Relationships
Published in S. K. Dutta, DNA Systematics, 2019
Although restriction map comparisons can also be useful in evaluating relationships at the genus and family levels, the greatest progress in molecular systematics research above the genus level, particularly above the family level, will come through comparative DNA sequencing. With continuing improvements in the efficiency and ease of DNA sequencing, it is predicted that this technique will increasingly be used to answer questions of plant phylogeny. The ability to focus sequencing efforts on especially conserved11–13,85,86 chloroplast genes should ultimately lead to unparalleled insight into the pattern of divergence and diversification of major plant taxa.
Muscle, Bone, and Skin Disorders
Published in Victor A. Bernstam, Pocket Guide to GENE LEVEL DIAGNOSTICS in Clinical Practice, 2019
Using probes for CKMM, apo C-II, and the repair genes ERCC-1 and ERCC-2, and separation of large-sized DNA restriction fragments by field inversion gel electrophoresis, a long-range restriction map of the 19q13 region has been constructed.
The Gene for t-PA
Published in Cornelis Kluft, Tissue-Type Plasminogen Activator (t-PA): Physiological and Clinical Aspects, 1988
Tor Ny, Monica Ohlsson, Leif Strandberg
All the findings about the t-PA gene from the different groups are in good agreement. There are no major discrepancies in the restriction maps from the various laboratories, and the few differences in the DNA sequence found are most easily understood as minor polymorphisms. This consistency between the different t-PA gene isolates indicates that there is only one t-PA gene in the human genome and that the different isolates represent a continuous stretch of DNA of the human genome. One cosmid clone carrying about 40KB of human DNA was introduced into mouse L cells.21 Since these cells produce human t-PA protein, this clone most likely carries the entire t-PA coding region together with the regulatory elements necessary for its expression. Other isolates of t-PA genes are either incomplete, 14,20 or are contained on separate lambda phages.22
Host immune response mediates changes in cagA copy number and virulence potential of Helicobacter pylori
Published in Gut Microbes, 2022
Sungil Jang, Lori M. Hansen, Hanfu Su, Jay V. Solnick, Jeong-Heon Cha
To identify variation of cagA copy number in H. pylori population isolated from mice, Southern blot was performed as previously described.61 Briefly, H. pylori genomic DNA was digested with restriction enzyme SspI (New England Biolabs) for 2 h, then separated on a 0.5% agarose gel overnight at 0.75 V/cm. Separated DNA fragments were then transferred to a nylon membrane. Part of cagA gene of H. pylori strain PMSS1 was PCR-amplified using primers D008 and R008 (Table 2). The resulting 298-bp fragment was labeled with biotin using a North2South biotin Random Prime Labeling kit (Thermo Scientific) and used as a probe for Southern blot. Hybridization and detection were performed using North2South chemiluminescent hybridization and detection kit according to the manufacturer’s instructions. cagA copy numbers were determined based on fragment size and the known restriction map of the cagA locus.
Local recurrence rate in patients with colorectal cancer liver metastasis after wedge resection or percutaneous radiofrequency ablation
Published in International Journal of Hyperthermia, 2018
Naïk Vietti Violi, Rafael Duran, Nicolas Demartines, Christine Sempoux, Boris Guiu, Pierre E. Bize, Nathalie Sala, Nermin Halkic, Jean-Francois Knebel, Alban Denys
All available radiological exams were reviewed to identify LR, which was considered on a lesion-by-lesion basis and was defined as the appearance of a new lesion with tumoural characteristics (MDCT: a nodule with peripheral enhancement on the portal venous phase; MRI: high signal on B800 DWI and diffusion restriction on restriction MAP, arterial and portal enhancement, moderate to high signal on T2-weighted images) at the location of the initial lesion or in direct contact with the RFA scar or WR margin [12] (Figure 3). Hepatic recurrence was defined as newly identified lesions in the hepatic parenchyma (except in direct contact to the resected/ablated area). Based on the imaging follow-up and patient data, extrahepatic recurrence was defined as newly identified extrahepatic metastases.
Improving post-natal detection of mitochondrial DNA mutations
Published in Expert Review of Molecular Diagnostics, 2020
Giulia Barcia, Zahra Assouline, Maryse Magen, Alessandra Pennisi, Agnès Rötig, Arnold Munnich, Jean-Paul Bonnefont, Julie Steffann
When the mutation does not modify the restriction map, PCR amplification can be carried out using the Allele Creating Restriction Site (ACRS) method. Fluorescent PCR focusing on the region is performed, with a limited number of PCR cycles to stay in the exponential phase of the PCR, in order to avoid the preferential amplification of one type of mtDNA molecules over another. Cross hybridization of oligonucleotide primers to genomic DNA is ruled out by PCR amplification on mtDNA-less Rho0 cells [22].