DNA differential diagnosis of human taeniid cestodes by base excision sequence scanning thymine-base reader analysis with mitochondrial genes.
Ontology highlight
ABSTRACT:
SUBMITTER: Yamasaki H
PROVIDER: S-EPMC130864 | biostudies-literature | 2002 Oct
REPOSITORIES: biostudies-literature
Publications
DNA differential diagnosis of human taeniid cestodes by base excision sequence scanning thymine-base reader analysis with mitochondrial genes.
Yamasaki Hiroshi H Nakao Minoru M Sako Yasuhito Y Nakaya Kazuhiro K Sato Marcello Otake MO Mamuti Wulamu W Okamoto Munehiro M Ito Akira A
Journal of clinical microbiology 20021001 10
For DNA differential diagnosis of human Taenia cestodes, a base excision sequence scanning thymine-base method using the cytochrome c oxidase subunit I and cytochrome b genes as targets was used. The characteristic thymine-base peak profiles provide four distinct types, unique for T. saginata, T. asiatica, and two genotypes of T. solium. This approach provides a useful tool for the identification and diagnosis of human taeniid cestodes without DNA sequencing if nucleotide sequence databases are ...[more]
Similar Datasets
Project description:Taenia saginata, T. solium, and T. asiatica are causative agents of taeniasis in humans. The difficulty of morphological identification of human taeniids can lead to misdiagnosis or confusion. To overcome this problem, several molecular methods have been developed, but use of these tends to be time-consuming. Here, a rapid and high-throughput pyrosequencing approach was developed for the identification of three human taeniids originating from various countries. Primers targeting the mitochondrial cytochrome c oxidase subunit 1 (cox1) gene of the three Taenia species were designed. Variations in a 26-nucleotide target region were used for identification. The reproducibility and accuracy of the pyrosequencing technology was confirmed by Sanger sequencing. This technique will be a valuable tool to distinguish between sympatric human taeniids that occur in Thailand, Asia and Pacific countries. This method could potentially be used for the molecular identification of the taeniid species that might be associated with suspicious cysts and lesions, or cyst residues in humans or livestock at the slaughterhouse.
| S-EPMC4063941 | biostudies-literature
Project description:Our knowledge of parasites in wildlife remains limited, primarily due to restricted access to samples, especially of parasites from protected species. This present study contributes to the comprehension of the enigmatic world of helminths of African wild mammals and cestode biodiversity by combining both molecular and morphological analysis. Cestode samples were opportunistically collected from 77 individual definitive hosts in South Africa, Namibia and Ethiopia, encompassing 15 different species of wild African carnivores and additionally domestic cats. The analysis revealed 32 different cyclophyllidean species of which 21 (65.6 %) represent previously unknown genetic entities. They belong to the families Mesocestoididae, Hymenolepididae, Dipylidiidae and Taeniidae. Here we cover the non-taeniid cestodes, while the taeniids will be addressed in a separate publication. Three of the non-taeniid species uncovered in this study could be assigned to the genus Mesocestoides and were isolated from servals and domestic cats. The white-tailed mongoose was found to be a suitable host for a species belonging to the Hymenolepididae, which was identified as Pseudandrya cf. mkuzii. Both feline and canine genotypes of Dipylidium caninum were detected in domestic cats, the canine genotype also in an African wolf. In addition to these, a novel species of Dipylidium was discovered in an aardwolf. Lastly, four distinct species of Joyeuxiella were found in this study, revealing a cryptic species complex and emphasizing the need for a taxonomic reassessment of this genus. Despite the limited scope of our study in terms of geography and sample size, the results highlight that biodiversity of cestodes in African wild mammals is grossly under-researched and follow-up studies are urgently required, in particular linking morphology to gene sequences.
| S-EPMC11002657 | biostudies-literature
Project description:5-Fluorouracil (5-FU), a chemotherapeutic drug commonly used in cancer treatment, imbalances nucleotide pools, thereby favoring misincorporation of uracil and 5-FU into genomic DNA. The processing of these bases by DNA repair activities was proposed to cause DNA-directed cytotoxicity, but the underlying mechanisms have not been resolved. In this study, we investigated a possible role of thymine DNA glycosylase (TDG), one of four mammalian uracil DNA glycosylases (UDGs), in the cellular response to 5-FU. Using genetic and biochemical tools, we found that inactivation of TDG significantly increases resistance of both mouse and human cancer cells towards 5-FU. We show that excision of DNA-incorporated 5-FU by TDG generates persistent DNA strand breaks, delays S-phase progression, and activates DNA damage signaling, and that the repair of 5-FU-induced DNA strand breaks is more efficient in the absence of TDG. Hence, excision of 5-FU by TDG, but not by other UDGs (UNG2 and SMUG1), prevents efficient downstream processing of the repair intermediate, thereby mediating DNA-directed cytotoxicity. The status of TDG expression in a cancer is therefore likely to determine its response to 5-FU-based chemotherapy.
| S-EPMC2671560 | biostudies-literature
Project description:TDG (thymine DNA glycosylase) is an essential multifunctional enzyme involved in DNA base excision repair, DNA demethylation and transcription regulation. TDG is the predominant enzyme that removes thymine from T/G mispair, which arises due to deamination of 5-methyl-cytosine at the CpG dinucleotide, thereby preventing C to T mutations. SIRT1 is a member of class III NAD+-dependent histone/protein deacetylases. In the present study, we demonstrate that SIRT1 interacts with residues 67-110 of hTDG (human TDG). In addition, SIRT1 enhances TDG glycosylase activity and deacetylates acetylated TDG. TDG acetylation weakens its interaction with SIRT1. Although acetylated TDG has reduced glycosylase activity towards T/G, 5-formylcytosine/G and 5-carboxylcytosine/G, it has a stronger activity towards a 5-fluorouracil/G substrate as compared with unmodified TDG. SIRT1 weakly stimulates acetylated hTDG activity towards T/G, 5-formylcytosine/G and 5-carboxylcytosine/G as compared with control hTDG. Sirt1-knockout mouse embryonic fibroblast cells have higher levels of TDG expression and acetylation. The physical and functional interactions between SIRT1 and TDG may mediate DNA repair, gene expression and FU (5-fluorouracil)-mediated cytotoxicity.
| S-EPMC4465237 | biostudies-literature
Project description:DNA methylation is a major epigenetic mechanism for gene silencing. Whereas methyltransferases mediate cytosine methylation, it is less clear how unmethylated regions in mammalian genomes are protected from de novo methylation and whether an active demethylating activity is involved. Here, we show that either knockout or catalytic inactivation of the DNA repair enzyme thymine DNA glycosylase (TDG) leads to embryonic lethality in mice. TDG is necessary for recruiting p300 to retinoic acid (RA)-regulated promoters, protection of CpG islands from hypermethylation, and active demethylation of tissue-specific developmentally and hormonally regulated promoters and enhancers. TDG interacts with the deaminase AID and the damage response protein GADD45a. These findings highlight a dual role for TDG in promoting proper epigenetic states during development and suggest a two-step mechanism for DNA demethylation in mammals, whereby 5-methylcytosine and 5-hydroxymethylcytosine are first deaminated by AID to thymine and 5-hydroxymethyluracil, respectively, followed by TDG-mediated thymine and 5-hydroxymethyluracil excision repair.
| S-EPMC3230223 | biostudies-literature
Project description:Tibetan foxes (Vulpes ferrilata) have been confirmed as the main wild definitive hosts in echinococcosis transmission in the eastern Tibetan Plateau. However, little information is available about the epidemiology in wildlife from the perspective of the Taeniidae family, which is essential knowledge in understanding the epidemiology and phylogeography of cestode species in the Tibetan plateau. Therefore, in this study, we used copro-PCR techniques, by amplifying nad1 and cox1 gene fragments, to detect the taeniid species from Tibetan fox feces collected in Shiqu County, (Sichuan Province, China), eastern Tibetan Plateau. Phylogenetic relationships between amplified sequences and existed Taenia species genotypes were evaluated. Then, the maximum prevalence (positive PCR results from at least one primer pair) and the conservative prevalence (positive PCR results from at least two primer pairs) were calculated. Thirty-six Tibetan fox feces were analyzed. Echinococcus multilocularis (conservative prevalence ± 95% CI: 22.2% ± 13.6%; maximum prevalence ± 95% CI: 33.3% ± 15.4%) and E. shiquicus (2.8 ± 5.4%; 8.3 ± 9.0%) was detected. Meanwhile, DNA fragments of T. polyacantha were detected with high similarity to NCBI sequences (cox1, 94.0%) and to the larva sample DNA sequenced in this study (93.4%), and were supported by phylogenetic analysis. Thus, T. polyacantha might infect Tibetan foxes (5.6% ± 7.5%, 11.1% ± 10.3%). Our limited findings in the epidemiology of parasitic Taenia species suggest that sylvatic transmission cycles for a more species-rich Taeniid community must be established between wild canids and small mammals than just for the two Echinococcus species. Besides, discrepancies in different primer pairs in detecting the taeniid species were evaluated. The sensitivity of some widely used universal primer pairs was poor in detecting Taenia species from canid copro-DNA samples. It is still challenging to the development of effective taeniid species-specific molecular markers especially for non-zoonotic species.
| S-EPMC7369422 | biostudies-literature
Project description:Mitochondrial transcription factor A (TFAM) is an essential component of mitochondrial nucleoids. TFAM plays an important role in mitochondrial transcription and replication. TFAM has been previously reported to inhibit nucleotide excision repair (NER) in vitro but NER has not yet been detected in mitochondria, whereas base excision repair (BER) has been comprehensively characterized in these organelles. The BER proteins are associated with the inner membrane in mitochondria and thus with the mitochondrial nucleoid, where TFAM is also situated. However, a function for TFAM in BER has not yet been investigated. This study examines the role of TFAM in BER. In vitro studies with purified recombinant TFAM indicate that it preferentially binds to DNA containing 8-oxoguanines, but not to abasic sites, uracils, or a gap in the sequence. TFAM inhibited the in vitro incision activity of 8-oxoguanine DNA glycosylase (OGG1), uracil-DNA glycosylase (UDG), apurinic endonuclease 1 (APE1), and nucleotide incorporation by DNA polymerase ? (pol ?). On the other hand, a DNA binding-defective TFAM mutant, L58A, showed less inhibition of BER in vitro. Characterization of TFAM knockdown (KD) cells revealed that these lysates had higher 8oxoG incision activity without changes in ?OGG1 protein levels, TFAM KD cells had mild resistance to menadione and increased damage accumulation in the mtDNA when compared to the control cells. In addition, we found that the tumor suppressor p53, which has been shown to interact with and alter the DNA binding activity of TFAM, alleviates TFAM-induced inhibition of BER proteins. Together, the results suggest that TFAM modulates BER in mitochondria by virtue of its DNA binding activity and protein interactions.
| S-EPMC2955416 | biostudies-literature
Project description:Interstrand crosslinks (ICLs) are covalent lesions formed by cisplatin. The mechanism for the processing and removal of ICLs by DNA repair proteins involves nucleotide excision repair (NER), homologous recombination (HR) and fanconi anemia (FA) pathways. In this report, we monitored the processing of a flanking uracil adjacent to a cisplatin ICL by the proteins involved in the base excision repair (BER) pathway. Using a combination of extracts, purified proteins, inhibitors, functional assays and cell culture studies, we determined the specific BER proteins required for processing a DNA substrate with a uracil adjacent to a cisplatin ICL. Uracil DNA glycosylase (UNG) is the primary glycosylase responsible for the removal of uracils adjacent to cisplatin ICLs, whereas other uracil glycosylases can process uracils in the context of undamaged DNA. Repair of the uracil adjacent to cisplatin ICLs proceeds through the classical BER pathway, highlighting the importance of specific proteins in this redundant pathway. Removal of uracil is followed by the generation of an abasic site and subsequent cleavage by AP endonuclease 1 (APE1). Inhibition of either the repair or redox domain of APE1 gives rise to cisplatin resistance. Inhibition of the lyase domain of Polymerase β (Polβ) does not influence cisplatin cytotoxicity. In addition, lack of XRCC1 leads to increased DNA damage and results in increased cisplatin cytotoxicity. Our results indicate that BER activation at cisplatin ICLs influences crosslink repair and modulates cisplatin cytotoxicity via specific UNG, APE1 and Polβ polymerase functions.
| S-EPMC5328804 | biostudies-literature
Project description:DNA double-strand breaks induced by ionizing radiation are often accompanied by ancillary oxidative base damage that may prevent or delay their repair. In order to better define the features that make some DSBs repair-resistant, XLF-dependent nonhomologous end joining of blunt-ended DSB substrates having the oxidatively modified nonplanar base thymine glycol at the first (Tg1), second (Tg2), third (Tg3) or fifth (Tg5) positions from one 3' terminus, was examined in human whole-cell extracts. Tg at the third position had little effect on end-joining even when present on both ends of the break. However, Tg as the terminal or penultimate base was a major barrier to end joining (>10-fold reduction in ligated products) and an absolute barrier when present at both ends. Dideoxy trapping of base excision repair intermediates indicated that Tg was excised from Tg1, Tg2 and Tg3 largely if not exclusively after DSB ligation. However, Tg was rapidly excised from the Tg5 substrate, resulting in a reduced level of DSB ligation, as well as slow concomitant resection of the opposite strand. Ligase reactions containing only purified Ku, XRCC4, ligase IV and XLF showed that ligation of Tg3 and Tg5 was efficient and only partially XLF-dependent, whereas ligation of Tg1 and Tg2 was inefficient and only detectable in the presence of XLF. Overall, the results suggest that promoting ligation of DSBs with proximal base damage may be an important function of XLF, but that Tg can still be a major impediment to repair, being relatively resistant to both trimming and ligation. Moreover, it appears that base excision repair of Tg can sometimes interfere with repair of DSBs that would otherwise be readily rejoined.
| S-EPMC4851560 | biostudies-literature
Project description:Mitochondria are highly specialised organelles required for key cellular processes including ATP production through cellular respiration and controlling cell death via apoptosis. Unlike other organelles, mitochondria contain their own DNA genome which encodes both protein and RNA required for cellular respiration. Each cell may contain hundreds to thousands of copies of the mitochondrial genome, which is essential for normal cellular function - deviation of mitochondrial DNA (mtDNA) copy number is associated with cellular ageing and disease. Furthermore, mtDNA lesions can arise from both endogenous or exogenous sources and must either be tolerated or corrected to preserve mitochondrial function. Importantly, replication of damaged mtDNA can lead to stalling and introduction of mutations or genetic loss, mitochondria have adapted mechanisms to repair damaged DNA. These mechanisms rely on nuclear-encoded DNA repair proteins that are translocated into the mitochondria. Despite the presence of many known nuclear DNA repair proteins being found in the mitochondrial proteome, it remains to be established which DNA repair mechanisms are functional in mammalian mitochondria. Here, we summarise the existing and emerging research, alongside examining proteomic evidence, demonstrating that mtDNA damage can be repaired using Base Excision Repair (BER), Homologous Recombination (HR) and Microhomology-mediated End Joining (MMEJ). Critically, these repair mechanisms do not operate in isolation and evidence for interplay between pathways and repair associated with replication is discussed. Importantly, characterising non-canonical functions of key proteins and understanding the bespoke pathways used to tolerate, repair or bypass DNA damage will be fundamental in fully understanding the causes of mitochondrial genome mutations and mitochondrial dysfunction.
| S-EPMC8527207 | biostudies-literature