Gene/Protein Disease Symptom Drug Enzyme Compound
Pivot Concepts: Gene/Protein Disease Symptom Drug Enzyme Compound   Target Concepts: Gene/Protein Disease Symptom Drug Enzyme Compound

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Query: EC:3.1.30.2 (endonuclease)
18,621 document(s) hit in 31,850,051 MEDLINE articles (0.00 seconds)

Stickler syndrome is one of the milder phenotypes resulting from mutations in the gene that encodes type-II collagen, COL2A1. All COL2A1 mutations known to cause Stickler syndrome result in the formation of a premature termination codon within the type-II collagen gene. COL2A1 has 10 in-frame CGA codons, which can mutate to TGA STOP codons via a methylation-deamination mechanism. We have analyzed these sites in genomic DNA from a panel of 40 Stickler syndrome patients to test the hypothesis that mutations that cause Stickler syndrome preferentially occur at these bases. Polymerase chain reaction (PCR) amplification of genomic DNA containing each of the in-frame CGA codons was done by one of two methods: either using primers that amplify DNA that includes the CGA codon, or using allele-specific primers that either amplify normal sequence containing a CGA codon or amplify a mutant sequence containing a TGA codon. Analysis of PCR products by restriction endonuclease digestion or sequencing demonstrated the presence of a normal or mutated codon. TGA mutations were identified in eight patients, at five of the 10 in-frame CGA codons. The identification of these mutations in eight of 40 patients demonstrates that these sites are common sites for mutations in individuals with Stickler syndrome and, we propose, should be analyzed as a first step in the search for mutations that result in this disorder.
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PMID:Rapid determination of COL2A1 mutations in individuals with Stickler syndrome: analysis of potential premature termination codons. 1098 70

The genomic DNA of four Autographa californica multinucleocapsid nucleopolyhedrovirus (AcMNPV) variants isolated from Galleria mellonella, Spodoptera exigua, Spodoptera litura and Xestia c-nigrum was analyzed in comparison with the AcMNPV E2 strain. Restriction endonuclease analysis revealed a deletion and an insertion in collinear regions of the four variants. Polymerase chain reaction analysis indicated that, in the four variants, the deletion occurred in the region corresponding to AcMNPV C6 ORF86 (pnk/pnl). Also the insertion, with a length of approximately 1.1 kb, was commonly identified in the fragments corresponding to the PstI-J fragment (18.5 m.u.-21.2 m.u.) of AcMNPV E2. Sequencing analysis of the variant from S. litura showed that the insertion contains an additional open reading frame encoding 322 amino acids between homologues of AcMNPV ORF30 and ORF31 (the superoxide dismutase gene). This ORF has 82.8% amino acid identity to Bombyx mori NPV T3 ORF 22 (bro-a, one of the baculovirus repeated ORFs) and thus, it was named Splt-bro-a. Southern blot hybridization study indicated that the other three variants also contain Splt-bro-a homologue. In addition, the labeled Splt-bro-a gene weakly hybridized to the PstI-D fragment (99.0 m.u.-8.0 m.u.) of AcMNPV E2. This fragment contains AcMNPV ORF2, a member of bro family. The signal was also observed on the corresponding fragment of the four variants. This result suggested that two bro genes are present in the four variants, although AcMNPV E2 and C6 are known to contain a single bro gene.
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PMID:Identification of insertion and deletion genes in Autographa californica nucleopolyhedrovirus variants isolated from Galleria mellonella, Spodoptera exigua, Spodoptera litura and Xestia c-nigrum. 1112 32

Terminal Restriction Fragment Length Polymorphism (T-RFLP) or Fluorescent Polymerase Chain Reaction/Restriction Fragment Length Polymorphism (FluRFLP) have made a significant impact on the way in which PCR products amplified from mixed community DNA extracts have been assessed. Technically, these approaches are essentially the same. PCR products are generated that contain at one 5' end label, typically a fluorescent moiety, that will be detected by a DNA sequencing machine. Upon digestion using a specific restriction endonuclease, labeled and unlabeled fragments are generated. This restriction endonuclease is chosen such that following this digestion, each labeled fragment corresponds to a different sequence variant. During electrophoretic separation, the DNA sequencing machine detects only these labeled fragments and therefore detects only the sequence variants. The aim of this article is to describe the protocols and demonstrate that this profiling can be performed using different DNA sequencing machines. The analysis and applications of this approach are also discussed.
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PMID:Terminal restriction fragment length polymorphism monitoring of genes amplified directly from bacterial communities in soils and sediments. 1125 10

Distinct strains of Mycobacterium avium subsp. paratuberculosis with a tendency to segregate in either sheep, or cattle and other ruminants, have been described and are known as S and C strains, respectively. These strains can be distinguished by a polymorphism in the IS1311 element and other DNA-based methods. C strains are relatively easy to culture from tissues and faeces of animals with paratuberculosis but S strains are difficult to culture. A retrospective survey of archival formalin-fixed paraffin-embedded tissue samples from culture negative Australian paratuberculous cattle was undertaken to determine whether infection in these cases was due to S strains. Polymerase chain reaction and restriction endonuclease analysis of the amplified product was used to identify the polymorphism in IS1311. Three cases of bovine paratuberculosis due to S strain were confirmed from three different farms. A serological survey led to the identification of a further two cases on one of these farms. S strains were also identified in archival tissues from paratuberculous sheep and cattle from Iceland, confirming epidemiological and microbiological evidence that paratuberculosis in Iceland was due to S strain following importation of infected sheep from Europe. In each bovine case in both Iceland and Australia there had been direct or indirect contact of calves with paratuberculous sheep. We were unable to determine whether S strains had established endemic infection in cattle or whether repeated infection from sheep had occurred. Limited epidemiological evidence suggests that transmission of S strains to cattle in Australia has been uncommon under extensive grazing conditions. In Iceland, different husbandry practices appear to have favoured transmission of S strains to cattle.
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PMID:Molecular epidemiological confirmation and circumstances of occurrence of sheep (S) strains of Mycobacterium avium subsp. paratuberculosis in cases of paratuberculosis in cattle in Australia and sheep and cattle in Iceland. 1126 91

In a pilot study Double Repetitive Element-Polymerase Chain Reaction 20 clinical isolates of Mycobacterium tuberculosis from Guatemala and 49 strains from Prague were typed. This technique is based on direct evidence of repetitive elements IS6110 or PGRS and does not require DNA purification, digestion by endonuclease nor Southern blot hybridization. Preliminary examination of Guatemalian strains revealed a striking identity or similarity of DRE-PCR profiles while the Prague strains were characterized by conspicuous polymorphism. The Prague strains were examined in a total number of 13 series of electrophoreograms and subsequently subjected to automated analysis with GelCompar software. The DRE-PCR method is suitable for screening of a major number of clinical isolates of M. tuberculosis in laboratories equipped with a minimum of technical facilities for the PCR method, furthermore it requires facilities for synthesis of the necessary primers and at least basic knowledge of molecular biology.
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PMID:[DRE-PCR (Double Repetitive Element-Polymerase Chain Reaction)--a new molecular-epidemiologic method in the detection of tuberculosis]. 1132 32

Replication of kinetoplast DNA minicircles in Crithidia fasciculata occurs by a unidirectional mechanism involving continuous synthesis of one strand (L strand) and discontinuous synthesis of the complementary strand (H strand). L-strands are initiated by RNA priming at alternate origins (A and B) resulting in daughter molecules with a single nick or gap in the L strand at either ori A or ori B. Some of the gapped molecules contain ribonucleotides at the 5' side of the gap. We have investigated the ability of recombinant forms of kinetoplast replication proteins, DNA polymerase beta and structure specific endonuclease 1, to repair gaps in a model minicircle substrate. Structure specific endonuclease 1 was shown to efficiently remove all ribonucleotides from the 5' side of the model substrate by stepwise cleavage of the RNA primer. Polymerase beta was then able to extend the 3' terminus of the gap to yield a nicked molecule capable of covalent joining by a DNA ligase. These results demonstrate that the nuclease and polymerase enzymes present at antipodal protein complexes flanking the kinetoplast disk are capable of complete RNA primer removal and subsequent gap filling of newly synthesized minicircle L strands.
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PMID:RNA primer removal and gap filling on a model minicircle replication intermediate. 1137 40

Polymerase chain reaction with subsequent SSCP (single-strand DNA conformational polymorphism) and restriction (BselI restriction endonuclease) analyses were used to type the DNA samples of affected individuals and their relatives from 23 Russian families with high risk of spinal muscular atrophy (SMA) residing in the northwestern region of Russia. Deletions of exon 7 of the SMN gene were found in 96% of the individuals examined. The frequency of homozygous deletion of exons 7 and 8 of the SMN1 gene was 65%. The frequency of homozygous isolated deletion of the SMN1 gene exon 7 among the SMA patients was 4.3%. Homozygous deletion of exon 5 of the NAIP gene was found in 22% of SMA patients. In SMA patients, a total of seven deletion types involving the SMN1, NAIP, and SMN2 genes were detected. Deletion of exons 7 and 8 of the SMN1 gene was the most common mutation associated with SMA in patients from the northwestern Russia.
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PMID:[Analysis of deletional damage in SMN1, SMN2, and NAIP genes in patients with spinal muscular atrophy in the northwestern region of Russia]. 1164 17

The current model for influenza virus mRNA transcription involves the sequential interaction of the viral polymerase with the 5'- and 3'-ends of vRNA, with each RNA-protein interaction triggering a polymerase function necessary for cap-primed transcription. Here we show that the order in which this ternary complex is assembled is in fact important. Polymerase bound simultaneously to a pre-annealed duplex of the 5'- and 3'-ends of vRNA had greatly increased levels of primer binding and endonuclease activities compared to a sequentially assembled complex. Increased primer binding was due to the activation of a high affinity binding site with a preference for primer length RNAs. This correlated with enhanced levels of cap-primed transcription. Polymerase that was bound initially to just 5' vRNA had low primer binding activity, but was endonucleolytically active. Neither activity was significantly increased by the subsequent addition of 3' vRNA, and this sequentially assembled complex had correspondingly low mRNA transcription activity. Nevertheless, both routes of assembly led to complexes that were highly competent for dinucleotide ApG-primed transcription. Therefore, polymerase complexes assembled on pre-annealed 5' and 3' terminal viral RNA sequences have distinct properties from those assembled by sequential loading of polymerase onto the 5'-end followed by the 3'-end. This suggests a mechanism by which the virus couples transcription initiation and termination during mRNA transcription.
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PMID:Activation of influenza virus RNA polymerase by the 5' and 3' terminal duplex of genomic RNA. 1262 3

The tumor suppressor p53 protein stimulates nuclear base excision repair (BER) in vitro. In response to certain cellular stresses, p53 translocates to mitochondria, where it can trigger an apoptotic response. However, a potential role for p53 in modulating mitochondrial DNA repair has not yet been examined. In this study, we show that p53 also modulates mitochondrial BER. Uracil-initiated BER incorporation, which measures flux through the entire BER pathway, was lower in mitochondrial extracts from nonstressed p53 knockout mice than in wild type. The addition of recombinant p53 complemented the BER incorporation in p53 knockout extracts and stimulated BER in wt extracts. The activities of three major mitochondrial DNA glycosylases were similar in extracts from wild-type and knockout animals. Likewise, AP endonuclease activity was unaffected by the absence of p53. Gel shift experiments with recombinant p53 demonstrated that p53 did not bind to the uracil-containing substrate used in the repair assay. Polymerase gamma gap-filing activity was less efficient in p53 knockout extracts, but it was complemented with the addition of recombinant p53. Thus, we conclude that p53 may participate in mtBER by stimulating the repair synthesis incorporation step.
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PMID:p53 functions in the incorporation step in DNA base excision repair in mouse liver mitochondria. 1520 69

The parasitoid, Peristenus howardi Shaw (Hymenoptera: Braconidae) has been found to parasitize a large proportion of Lygus species in some Washington and Idaho alfalfa seed fields. During 2002-2003 a survey was conducted to estimate the proportion of Lygus spp. (Hemiptera: Miridae) parasitized and the amountof that parasitism attributable to P. howardi in crop and non-crop plants attacked by Lygus in the alfalfa seed growing region of southwestern Idaho and eastern Oregon. Percentage parasitism was estimated from dissection of field-collected Lygus nymphs. Polymerase chain reaction (PCR) was used to amplify DNA extracted from parasitoid larvae followed by restriction endonuclease digestion of PCR products to distinguish P. howardi from other potentially co-occurring Peristenus species. Peak parasitism of Lygus nymphs occurred between the first and third weeks of July for both years for all host plants sampled. Of the parasitoid larvae recovered from Lygus nymphs in our study, 75% to 80% tested positive as Peristenus spp. and 76% of these matched the endonuclease digestion banding pattern for P. howardi. The identity of the remaining 20% to 25% of the parasitoids is not known.
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PMID:Parasitism of Lygus spp. nymphs by the parasitoid wasp, Peristenus howardi, in the alfalfa seed-growing region of the Pacific Northwest. 1711 26


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