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PubMed1997

Morphological variation of nonreentrant idiopathic ventricular tachycardia originating from the right ventricular outflow tract and effect of radiofrequency lesion.

RF catheter ablation was performed in 16 patients with nonreentrant idiopathic VT originating from the RVOT. All documented VT was monomorphic, but subtle morphological variation in the VT-QRS complex was observed in 10 (63%) of 16 patients. Through endocardial mapping, VT origin was determined within a narrow site (< 0.5 x 0.5 cm) in 4 of the 10 patients with the morphological variation. In the other 6 of 10 patients, the origin extended to an area of > 0.5 x 0.5 cm. In VT with morphological variation, the local electrogram at the site of VT origin also showed variation in morphology and activation sequence. For VT of narrow origin, RF application to the site eliminated the VT. However, in VT from a wide arrhythmogenic area, RF current had to be delivered to 3-7 distinct sites to cover the possible origin, and specific QRS configuration of VT and/or PVC was ablated at each of the earliest activation site. All but one VT were successfully ablated by RF current. Subtle morphological variation was frequent in this type of VT, and about half were associated with a wide arrhythmogenic area. Precise mapping and analysis of the efficacy of each RF application might be helpful to better understand the relationship between subtle changes of VT-QRS morphology and their origins.

Adult↗

PubMed2000

Color-coded duplex ultrasonography of the origin of the vertebral artery: normal values of flow velocities.

The introduction of color-coded duplex ultrasonography has improved the ease of performing ultrasound investigations of the vertebral arteries. So far, normal values of flow velocities have been reported only for the intertransverse region of the vertebral artery (V2 segments). Atherosclerotic disease at the origin of the vertebral arteries (V0 segment) is frequent and is one of the risk factors for vertebrobasilar ischemic disease. Normal values of flow velocities of the vertebral artery origin are needed to assess pathologic findings, such as vertebral artery origin stenosis or dissection. The aim of this study was to describe the normal flow velocities of vertebral artery origin (V0 segment) and the pre- (V1 segment) and intertransverse (V2 segment) part in 50 age-matched neurologic patients (mean age 54) without ischemic cerebral disease. The V0 segment could be visualized in 46 persons (92%) on the right side and in 43 (86%) on the left. The peak systolic blood velocity ranged from 30 to 100 cm/s (mean 63.6 +/- 17.5 cm/s), and end-diastolic blood velocity ranged from 10 to 35 cm/s (mean 16.1 +/- 5.1 cm/s). Analysis of side-to-side differences showed no significant differences of flow velocities in all subjects. It is concluded that color duplex ultrasonography is a feasible method to insonate the origin of the vertebral artery, and that nomogram data could be established. It is suggested that color-coded duplex ultrasonography of the vertebral artery origin should be performed in all patients with clinical symptoms or signs of vertebrobasilar ischemic disease. Nevertheless, further studies are needed to determine the normal and pathologic values of flow velocities of the vertebral artery origin and their reproducibility.

Adult↗

PubMed1992

A yeast chromosomal origin of DNA replication defined by multiple functional elements.

Although it has been demonstrated that discrete origins of DNA replication exist in eukaryotic cellular chromosomes, the detailed organization of a eukaryotic cellular origin remains to be determined. Linker substitution mutations were constructed across the entire Saccharomyces cerevisiae chromosomal origin, ARS1. Functional studies of these mutants revealed one essential element (A), which includes a match to the ARS consensus sequence, and three additional elements (B1, B2, and B3), which collectively are also essential for origin function. These four elements arranged exactly as in ARS1, but surrounded by completely unrelated sequence, functioned as an efficient origin. Element B3 is the binding site for the transcription factor-origin binding protein ABF1. Other transcription factor binding sites substitute for the B3 element and a trans-acting transcriptional activation domain is required. The multipartite nature of a chromosomal replication origin and the role of transcriptional activators in its function present a striking similarity to the organization of eukaryotic promoters.

Amino Acid Sequence↗

PubMed1989

Replication origins of single-stranded-DNA plasmid pUB110.

The two replication origins of plasmid pUB110 have been characterized. The site of initiation of DNA replication at the plus origin was mapped to within an 8-base-pair sequence. DNA synthesis initiated at the origin was made to terminate precociously in an inserted sequence of 18 base pairs that is homologous to a sequence in the origin. This suggests that pUB110 replicates as a rolling circle. The minus origin of plasmid pUB110 has been characterized, and the minimal sequence required for function has been determined. As with other minus origins, activity is orientation specific with respect to the direction of replication. Its activity is sensitive to rifampin in vivo, suggesting that RNA polymerase catalyzes single-strand to double-strand conversion. Unlike all other plasmids of gram-positive bacteria thus far described, the pUB110 minus origin is functional in more than one host.

Base Sequence↗

PubMed1990

A single DnaA box is sufficient for initiation from the P1 plasmid origin.

The P1 plasmid replication origin requires the host DnaA protein for function. Two DnaA-binding boxes lie in tandem within the previously defined minimal origin, constituting its left boundary. Three more boxes lie 200 base pairs to the right of these, in the leader region for the P1 repA gene. We show that either set alone is active for origin function. One of the two origin boxes is relatively inactive. Constructs with just one of the five boxes are active for specific origin function as long as the box conforms exactly to the published consensus. This single consensus box is functional when placed either to the left or right of the core origin sequences. The flexibility shown by this system suggests that the boxes play a role different from those in the host oriC origin, where the number and position of boxes are critical.

Bacterial Proteins↗

PubMed1991

Characterization of a phage-plasmid hybrid (phasyl) with two independent origins of replication isolated from Escherichia coli.

The phage-plasmid hybrid phasyl can replicate as a phage in the presence of a filamentous phage of Escherichia coli (M13, fl, fd). The extragenic region of phasyl shows homology with the plus and the minus origins of filamentous phages. Insertion of a Cmr fragment into the plus origin or of a Kmr fragment into the minus origin resulted in a reduced transduction frequency, while insertion into other parts of the extragenic region did not. This suggests that phagelike replication of phasyl is mediated by an origin that coincides with the two homologous elements in the extragenic region. Autonomous replication of phasyl occurs from a second origin (oriA) that is located between positions 297 and 636. This fragment mediates replication if the Arp protein is supplied in trans. Arp is the only phage-encoded protein and is essential for plasmidlike replication. No sequence homology to other known origins was found. Phasyl derivatives with either one of the two origins inactivated can be rescued via the alternative replication mode, suggesting that the two replication pathways are independent.

Base Sequence↗

PubMed1993

Evidence of two levels of control of P1 oriR and host oriC replication origins by DNA adenine methylation.

A mutant mini-P1 plasmid with increased copy number can be established in Dam- strains of Escherichia coli, where mini-P1 plasmid replication is normally blocked. Comparison of this plasmid and a plasmid driven by the host oriC replication origin showed that both origins are subject to control by methylation at two different levels. First, both origins appear to be subject to negative regulation acting at the level of hemimethylation. This probably involves the sequestration of the hemimethylated DNA produced by replication, as has been previously described for oriC. Second, both origins show a positive requirement for adenine methylation for efficient function in vivo. This conclusion is supported by the behavior of the P1 origin in an improved in vitro replication system. In vitro, where sequestration of hemimethylated DNA is not expected to occur, the hemimethylated P1 origin DNA was fully functional as a template. However, the activity of fully unmethylated DNA was severely restricted in comparison with that of either of the methylated forms. This in vitro uncoupling of the two effects of origin methylation suggests that two separate mechanisms are involved.

Adenine↗

PubMed2000

Bacillus subtilis SMC is required for proper arrangement of the chromosome and for efficient segregation of replication termini but not for bipolar movement of newly duplicated origin regions.

SMC protein is required for chromosome condensation and for the faithful segregation of daughter chromosomes in Bacillus subtilis. The visualization of specific sites on the chromosome showed that newly duplicated origin regions in growing cells of an smc mutant were able to segregate from each other but that the location of origin regions was frequently aberrant. In contrast, the segregation of replication termini was impaired in smc mutant cells. This analysis was extended to germinating spores of an smc mutant. The results showed that during germination, newly duplicated origins, but not termini, were able to separate from each other in the absence of SMC. Also, DAPI (4',6'-diamidino-2-phenylindole) staining revealed that chromosomes in germinating spores were able to undergo partial or complete replication but that the daughter chromosomes were blocked at a late stage in the segregation process. These findings were confirmed by time-lapse microscopy, which showed that after duplication in growing cells the origin regions underwent rapid movement toward opposite poles of the cell in the absence of SMC. This indicates that SMC is not a required component of the mitotic motor that initially drives origins apart after their duplication. It is also concluded that SMC is needed to maintain the proper layout of the chromosome in the cell and that it functions in the cell cycle after origin separation but prior to complete segregation or replication of daughter chromosomes. It is proposed here that chromosome segregation takes place in at least two steps: an SMC-independent step in which origins move apart and a subsequent SMC-dependent step in which newly duplicated chromosomes condense and are thereby drawn apart.

Bacillus subtilis↗

PubMed1986

DNA requirements at the bacteriophage G4 origin of complementary-strand DNA synthesis.

An in vivo assay was used to define the DNA requirements at the bacteriophage G4 origin of complementary-strand DNA synthesis (G4 origin). This assay made use of an origin-cloning vector, mRZ1000, a defective M13 recombinant phage deleted for its natural origin of complementary-strand DNA synthesis. The minimal DNA sequence of the G4 genome sufficient for the restoration of normal M13 growth parameters was determined to be 139 bases long, located between positions 3868 and 4007. This G4-M13 construct was also found to give rise to proper initiation of complementary-strand synthesis in vitro. The cloned DNA sequence contains all the regions of potential secondary structure which have been implicated in primase-dependent replication initiation as well as additional sequence information. To address the role of one region which potentially forms a DNA secondary structure, the DNA sequence internal to the G4 origin was altered by site-directed mutagenesis. A 3-base insertion at the AvaII site as well as a 17-base deletion between the AvaI and AvaII sites both resulted in loss of origin function. The 17-base deletion was also generated within the G4 genome and found to dramatically reduce the infectious growth rate of the resulting phage. These results are discussed with respect to the role of the G4 origin as the recognition site for primase-dependent replication initiation and its possible role in stage II replication.

Base Sequence↗

PubMed1995

cis-Acting components of human papillomavirus (HPV) DNA replication: linker substitution analysis of the HPV type 11 origin.

Papillomavirus DNA replication requires the viral trans-acting factors E1 and E2 in addition to the host cell's general replication machinery. The origins of DNA replication in bovine and human papillomavirus genomes have been localized to a specific part of the upstream regulatory region (URR) which includes recognition sites for E1 and E2 proteins. To fine map cis-acting elements influencing human papillomavirus type 11 (HPV-11) DNA replication and to determine the relative contributions of such sites, we engineered consecutive linker substitution mutations across a region of 158 bp in the HPV-11 origin and tested mutant origins for replication function in a cell-based transient replication assay. Our results both confirm and extend the findings of others. E2 binding sites are the major cis components of HPV-11 DNA replication, and there is evidence for synergy between these sites. Differential capacity of the three E2 binding sites within the origin to affect replication may be attributed, at least in part, to context. At least one E2 binding site is essential for replication. The imperfect AT-rich palindrome of the E1 helicase binding site is not essential since replication occurs even in the absence of this sequence. However, replication is enhanced by the presence of the palindromic sequence in the HPV-11 origin. Sequence components adjacent to the E1 and E2 binding sites, comprising AT-rich and purine-rich elements and the consensus TATA box sequence, probably contribute to the overall efficiency of replication, though they are nonessential. None of the other cis elements of the HPV-11 origin region analyzed seems to influence replication significantly in the system described. The HPV-11 origin of DNA replication therefore differs from those of the other papovaviruses, simian virus 40 and polyomavirus, inasmuch as an intact helicase binding site and adjacent AT-rich components, while influential, are not absolutely essential.

Animals↗

PubMed1997

The N-terminal side of the origin-binding domain of simian virus 40 large T antigen is involved in A/T untwisting.

We investigated the role of the N-terminal side of simian virus 40 (SV40) large T antigen's origin-binding domain in the initiation of virus DNA replication by analyzing the biochemical activities of mutants containing single point substitutions or deletions in this region. Four mutants with substitutions at residues between 121 and 135 were partially defective in untwisting the A/T-rich track on the late side of the origin but were normal in melting the imperfect palindrome (IP) region on the early side. Deletion of the N-terminal 109 amino acids had no effect on either activity, whereas a longer deletion, up to residue 123, greatly reduced A/T untwisting but not IP melting. These results indicate that the region from residue 121 to 135 is important for A/T untwisting but not for IP melting and demonstrate that these activities are separable. Two point substitution mutants (126PS and 135PL) were characterized further by testing them for origin DNA binding, origin unwinding, oligomerization, and helicase activity. These two mutants were completely defective in origin (form U(R)) unwinding but normal in the other activities. Our results demonstrate that a failure to normally untwist the A/T track is correlated with a defect in origin unwinding. Further, they indicate that some mutants with substitutions in the region from residue 121 to 135 interact with origin DNA incorrectly, perhaps by failing to make appropriate contacts with the A/T-rich DNA.

Antigens, Polyomavirus Transforming↗

PubMed1991

Evidence suggesting that the ARS elements associated with silencers of the yeast mating-type locus HML do not function as chromosomal DNA replication origins.

The silent mating-type loci of Saccharomyces cerevisiae, HML and HMR, are flanked by transcriptional silencers that have ARS activity (i.e., they function as replication origins when in plasmids). To test whether these ARS elements are chromosomal origins, we mapped origins near HML (close to the left telomere of chromosome III). Our results indicate that the HML-associated ARS elements either do not function as chromosomal replication origins or do so at a frequency below our detection level, suggesting that replication from a silencer-associated origin in each S phase is not essential for the maintenance of transcriptional repression at HML. Our results also imply that the ability of a DNA fragment to function as an ARS element in a plasmid does not ensure its ability to function as an efficient chromosomal replication origin. Telomere proximity is not responsible for inactivating these ARS elements, because they are not detectably functional as chromosomal origins even in genetically modified strains in which they are far from the telomere.

Chromosome Mapping↗

PubMed1997

Renal artery origins: best angiographic projection angles.

PURPOSE: To determine the best projection angles for imaging the renal artery origins in profile. MATERIALS AND METHODS: A mathematical model of the anatomy at the renal artery origins in the transverse plane was used to analyze the amount of aortic lumen that projects over the renal artery origins at various projection angles. Computed tomographic (CT) angiographic data about the location of 400 renal artery origins in 200 patients were statistically analyzed. RESULTS: In patients with an abdominal aortic diameter no larger than 3.0 cm, approximately 0.5 mm of the proximal part of the renal artery and origin may be hidden from view if there is a projection error of +/-10 degrees from the ideal image. A combination of anteroposterior and 20 degrees and 40 degrees left anterior oblique projections resulted in a 92% yield of images that adequately profiled the renal artery origins. Right anterior oblique projections resulted in the least useful images. CONCLUSION: An error in projection angle of +/-10 degrees is acceptable for angiographic imaging of the renal artery origins. Patients sex, site of interest (left or right artery), and local diameter of the abdominal aorta are important factors to consider.

Angiography↗

PubMed1978

A rare origin of the superior thyroid artery.

In the course of a classroom dissection of a negro male (height: 167 cm; weight: 56.8 kg), and anomalous right superior thyroid artery was noted. It arose from the common carotid artery 27 mm proximal to the bifurcation into external and internal carotids. Previous reports indicate that the incidence of origin of the superior thyroid from the common carotid or its bifurcation varies from 5 to 45%, depending on the population sampled. Moreover, a low origin is more common in females than males, and appears approximately twice as often on the left as on the right. Previous reports also indicate that the origin is only very rarely more than 1 cm proximal to the bifurcation, only one case having been reported of an origin 25 mm proximal. The present case appears to be the most proximal origin so far recorded, and the first far proximal origin in negroes. The implications of such a low origin for surgical approach to the thyroid are considerable.

Aged↗

PubMed2006

On the origin of microbial ORFans: quantifying the strength of the evidence for viral lateral transfer.

BACKGROUND: The origin of microbial ORFans, ORFs having no detectable homology to other ORFs in the databases, is one of the unexplained puzzles of the post-genomic era. Several hypothesis on the origin of ORFans have been suggested in the last few years, most of which based on selected, relatively small, subsets of ORFans. One of the hypotheses for the origin of ORFans is that they have been acquired thru lateral transfer from viruses. Here we carry out a comprehensive, genome-wide study on the origins of ORFans to quantify the strength of current evidence supporting this hypothesis. RESULTS: We performed similarity searches by querying all current ORFans against the public virus protein database. Surprisingly, we found that only 2.8% of all microbial ORFans have detectable homologs in viruses, while the percentage of non-ORFans with detectable homologs in viruses is 7.9%, a significantly higher figure. This suggests that the current evidence for the origin of ORFans from lateral transfer from viruses is at best weak. However, an analysis of individual genomes revealed a number of organisms with much higher percentages, many of them belonging to the Firmicutes and Gamma-proteobacteria. We provide evidence suggesting that the current virus database may be biased towards those viruses attacking Firmicutes and Gamma-proteobacteria. CONCLUSION: We conclude that as more viral genomes are sequenced, more microbial ORFans will find homologs in viruses, but this trend may vary much for individual genomes. Thus, lateral transfer from viruses alone is unlikely to explain the origin of the majority of ORFans in the majority of prokaryotes and consequently, other, not necessarily exclusive, mechanisms are likely to better explain the origin of the increasing number of ORFans.

Bacteria↗

PubMed2006

Tracing the origin of functional and conserved domains in the human proteome: implications for protein evolution at the modular level.

BACKGROUND: The functional repertoire of the human proteome is an incremental collection of functions accomplished by protein domains evolved along the Homo sapiens lineage. Therefore, knowledge on the origin of these functionalities provides a better understanding of the domain and protein evolution in human. The lack of proper comprehension about such origin has impelled us to study the evolutionary origin of human proteome in a unique way as detailed in this study. RESULTS: This study reports a unique approach for understanding the evolution of human proteome by tracing the origin of its constituting domains hierarchically, along the Homo sapiens lineage. The uniqueness of this method lies in subtractive searching of functional and conserved domains in the human proteome resulting in higher efficiency of detecting their origins. From these analyses the nature of protein evolution and trends in domain evolution can be observed in the context of the entire human proteome data. The method adopted here also helps delineate the degree of divergence of functional families occurred during the course of evolution. CONCLUSION: This approach to trace the evolutionary origin of functional domains in the human proteome facilitates better understanding of their functional versatility as well as provides insights into the functionality of hypothetical proteins present in the human proteome. This work elucidates the origin of functional and conserved domains in human proteins, their distribution along the Homo sapiens lineage, occurrence frequency of different domain combinations and proteome-wide patterns of their distribution, providing insights into the evolutionary solution to the increased complexity of the human proteome.

Animals↗

PubMed2006

Origin and evolution of the peroxisomal proteome.

BACKGROUND: Peroxisomes are ubiquitous eukaryotic organelles involved in various oxidative reactions. Their enzymatic content varies between species, but the presence of common protein import and organelle biogenesis systems support a single evolutionary origin. The precise scenario for this origin remains however to be established. The ability of peroxisomes to divide and import proteins post-translationally, just like mitochondria and chloroplasts, supports an endosymbiotic origin. However, this view has been challenged by recent discoveries that mutant, peroxisome-less cells restore peroxisomes upon introduction of the wild-type gene, and that peroxisomes are formed from the Endoplasmic Reticulum. The lack of a peroxisomal genome precludes the use of classical analyses, as those performed with mitochondria or chloroplasts, to settle the debate. We therefore conducted large-scale phylogenetic analyses of the yeast and rat peroxisomal proteomes. RESULTS: Our results show that most peroxisomal proteins (39-58%) are of eukaryotic origin, comprising all proteins involved in organelle biogenesis or maintenance. A significant fraction (13-18%), consisting mainly of enzymes, has an alpha-proteobacterial origin and appears to be the result of the recruitment of proteins originally targeted to mitochondria. Consistent with the findings that peroxisomes are formed in the Endoplasmic Reticulum, we find that the most universally conserved Peroxisome biogenesis and maintenance proteins are homologous to proteins from the Endoplasmic Reticulum Assisted Decay pathway. CONCLUSION: Altogether our results indicate that the peroxisome does not have an endosymbiotic origin and that its proteins were recruited from pools existing within the primitive eukaryote. Moreover the reconstruction of primitive peroxisomal proteomes suggests that ontogenetically as well as phylogenetically, peroxisomes stem from the Endoplasmic Reticulum. REVIEWERS: This article was reviewed by Arcady Mushegian, Gáspár Jékely and John Logsdon. OPEN PEER REVIEW: Reviewed by Arcady Mushegian, Gáspar Jékely and John Logsdon. For the full reviews, please go to the Reviewers' comments section.

Journal Article↗

PubMed2005

[Role of esophageal provocative tests in the investigation of patients with chest pain of undetermined origin].

BACKGROUND: Traditional methods employed in esophageal investigation of patients with chest pain of undetermined origin includes upper endoscopy, esophageal manometry and pH monitoring. These methods many times disclose abnormalities that can only be enrolled as the possible cause of chest pain. Provocative tests can reproduce pain in the laboratory, establishing its esophageal origin. OBJECTIVES: Determine the positivity of acid perfusion test, edrophonium and balloon distension in patients with chest pain of undetermined origin and compare with results of traditional exams, establishing the gain for the diagnosis of esophageal pain. RESULTS: Forty patients with chest pain of undetermined origin (normal coronary angiography), 80% female, mean age of 54.7 years were submitted to traditional exams and provocative tests. Upper endoscopy disclosed erosive esophagitis in two (5%) and peptic ulcer in one (2.5%), esophageal manometry was abnormal in 60%. pH monitoring was abnormal in 14 (35%) with a positive symptom index in 7. Chest pain was considered of proved esophageal origin by traditional exams in 7 (17.5%) patients with a positive symptom index and of probable esophageal origin in 19 (47.5%) being 8 with gastroesophageal reflux disease and 11 abnormal esophageal motility. In 14 (35%) an esophageal origin could not be demonstrated. The acid perfusion test was positive in 10 (25%), edrophonium test in 8 (20%) and balloon distension test in 15 (37.5%) and at least one provocative test was positive in 23 (57.5%) patients. The introduction of provocative tests allowed the diagnosis of proved esophageal pain in 12 of 19 (63.1%) patients with probable esophageal pain and in 6 of 14 (42.8%) with normal or inconclusive traditional exams what represented a diagnostic gain of 45% (18/40). Two patients had negative provocative tests and a positive symptom index, making a total of 25 (62.5%) patients with proved esophageal pain.

Adult↗