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Kearns–Sayre syndrome
Published in William L. Nyhan, Georg F. Hoffmann, Aida I. Al-Aqeel, Bruce A. Barshop, Atlas of Inherited Metabolic Diseases, 2020
William L. Nyhan, Georg F. Hoffmann, Aida I. Al-Aqeel, Bruce A. Barshop
A 4.9-kb deletion and heteroplasmy has been observed in wild mice [32]. It has been thought that deletions in a region between two areas of direct repeats could occur through slip-replication, in which, following a break at the first direct repeat the first repeat pairs with the second direct repeat (Figure 54.6).
Mobile DNA Sequences and Their Possible Role in Evolution
Published in S. K. Dutta, DNA Systematics, 2019
Georgii P. Georgiev, Yurii V. Ilyin, Alexei P. Ryskov, Tatiana I. Gerasimova
It is of interest that different repetitive DNA elements, in some respect, interact with one another, giving new composite transposon-like elements. For example, neither the mouse BAM5 element69 nor the mouse R element70 is surrounded by direct repeats, whereas their linked entity (Bam 5 + R) is surrounded by a 15 bp direct repeat.71
Instability of Human Mitochondrial DNA, Nuclear Genes and Diseases
Published in Shamim I. Ahmad, Handbook of Mitochondrial Dysfunction, 2019
Another way of looking at mtDNA deletions is to determine the presence and type of border repeats flanking the deletion. In most deletions, border repeats are present and they can be exact – when the sequence on both sides of the deletion is identical or indirect – when two flanking sequences are similar but not identical. The length of the repeat is from four to fourteen nucleotides according to MITOMAP. It is worth mentioning that the controversy exists whether, in the case of short (a few nucleotide long), direct repeat we are dealing just with short direct repeat or whether there is long (up to 50 nucleotides), indirect repeat consisting of a series of short ones divided by nonhomologous regions65.
T cell repertoire to citrullinated self-peptides in healthy humans is not confined to the HLA-DR SE alleles; Targeting of citrullinated self-peptides presented by HLA-DP4 for tumour therapy
Published in OncoImmunology, 2019
Victoria A Brentville, Peter Symonds, Katherine W Cook, Ian Daniels, Tracy Pitt, Mohamed Gijon, Poonam Vaghela, Wei Xue, Sabaria Shah, Rachael L Metheringham, Lindy G Durrant
To generate the plasmid pVITRO2 Human HLA-DP4, the nucleotide sequence encoding the full length human HLA-DPA*0103 α chain flanked by FspI/EcoRI and the HLA-DPB*0401 β chain flanked by BamHI/SalI restriction sites were synthesized (Eurofins MWG). Following sequence confirmation, the HLA-DPA*0103 chain was cloned into the FspI/EcoRI mcs2 of the vector pVITRO2-hygro-mcs (Invivogen). The HLA-DPB*0401 chain was subsequently inserted into the BamHI/SalI mcs1 of the mammalian expression vector alongside the alpha HLA-DPA*0103 chain present within mcs2. To construct the IFNγ inducible plasmid pDCGAS Human HLA-DP4, the HLA-DPA*0103α and HLA-DPB*0401β chains, were sequentially cloned into the pDCGAS chimeric HLA-DR401 plasmid in replacement of the chimeric DR4 chains described elsewhere.9 The IFNγ inducible promoter within this plasmid consists of a TATA box and the GAS (IFNγ activated sequence) direct repeat enhancer element that in the presence of IFNγ drives expression of the HLA-DP401 chains within the pDCOrig vector backbone. After sequence confirmation endotoxin-free plasmid DNA was generated using the endofree Qiagen maxiprep kit (Qiagen, Crawley).
Tuberculosis in the 21th century: Current status of diagnostic methods
Published in Experimental Lung Research, 2018
Patrícia Poeta, Vanessa Silva, Andreia Guedes, José Eduardo Pereira, Ana Cláudia Coelho, Gilberto Igrejas
Spoligotyping and Line Probe Assays (LPA) are Polymerase Chain Reaction (PCR) based methods. Spoligotyping is membrane-based reverse-line blotting method designed not only for the diagnosis of TB, but also to investigate which strain of M. tuberculosis is present. This method shows the presence of unique spacer sequences located between the direct-repeat sequences of the Clustered Regularly Interspersed Short Palindromic Repeat region of M. tuberculosis genomes.17 However it is necessary to make a bacterial culture with specificity (about 96%) and high sensitivity (about 98%) when used with clinical specimens. This methodology’s application enables rapid diagnosis, assess the transmission of the disease and prevent its dissemination.18,19 Two LPAs are commercially available for the diagnosis of TB in samples from patients.20–22 In a study conducted by Singh et al.23 the sensitivity and specificity of LPA was 68.4% and 89.3% respectively, whereas the sensitivity and specificity for detecting resistance to RIF were 100% and 99.24% and for resistance to isoniazid were 97.62% and 98.55%, respectively.23 Another study verified the LPA ability to detect MTB in extrapulmonary tuberculosis when the results were negative for sputum smear and found that culture positivity was found in 21.3% of specimens; and of these 95.48% were found to be MTB. Among the MTB detected 3.9% were RIF resistant and 13.3% were Isoniazid resistant.24
Porphyromonas gingivalis and its CRISPR-Cas system
Published in Journal of Oral Microbiology, 2019
Previously, the structure of the cas gene in P. gingivalis was reported to be conserved at two CRISPR loci, type 1-C and III-B [24]. By using the online software CRISPR finger (http://crispr.i2bc.paris-saclay.fr/Server) strain F0569 was found to have the highest number of CRISPR arrays (Table 3), but this strain did not have the highest number of Cas proteins [23]. The length of the direct repeat (DR) elements ranged from 23 to 47 bps among all the CRISPR arrays detected while the number of DRs in the arrays varied from five to 121 copies. The closely related strains ATCC33277 and 381 had three copies of almost identical CRISPR arrays with 121 DR sequences and 120 spacer sequences.