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At least 91 records · Page 5Linked to original sources
PubMed1993

Putative full-length clones of the genomic DNA segments of subterranean clover stunt virus and identification of the segment coding for the viral coat protein.

Subterranean clover stunt disease is an economically important aphid-borne virus disease affecting certain pasture and grain legumes in Australia. The virus associated with the disease, subterranean clover stunt virus (SCSV), was previously found to be representative of a new type of single-stranded DNA virus. Analysis of the virion DNA and restriction mapping of double-stranded cDNA synthesized from virion DNA suggested that SCSV has a segmented genome composed of 3 or 4 different species of circular ssDNA each of about 850-880 nucleotides. To further investigate the complexity of the SCSV genome, we have isolated the replicative form DNA from infected pea and from it prepared putative full-length clones representing the SCSV genome segments. Analysis of these clones by restriction mapping indicated that clones representing at least 4 distinct genomic segments were obtained. This method is thus suitable for generating an extensive genomic library of novel ssDNA viruses containing multiple genome segments such as SCSV and banana bunchy top virus. The N-terminal amino acid sequence and amino acid composition of the coat protein of SCSV were determined. Comparison of the amino acid sequence with partial DNA sequence data, and the distinctly different restriction maps obtained for the full-length clones suggested that only one of these clones contained the coat protein gene. The results confirmed that SCSV has a functionally divided genome composed of several distinct ssDNA circles each of about 1 kb.

Amino Acid Sequence↗
PubMed1997

Computer model analysis of the relationship of ST-segment and ST-segment/heart rate slope response to the constituents of the ischemic injury source.

The objective of the study was to investigate a proposed linear relationship between the extent of myocardial ischemic injury and the ST-segment/heart rate (ST/HR) slope by computer simulation of the injury sources arising in exercise electrocardiographic (ECG) tests. The extent and location of the ischemic injury were simulated for both single- and multivessel coronary artery disease by use of an accurate source-volume conductor model which assumes a linear relationship between heart rate and extent of ischemia. The results indicated that in some cases the ST/HR slope in leads II, aVF, and especially V5 may be related to the extent of ischemia. However, the simulations demonstrated that neither the ST-segment deviation nor the ST/HR slope was directly proportional to either the area of the ischemic boundary or the number of vessels occluded. Furthermore, in multivessel coronary artery disease, the temporal and spatial diversity of the generated multiple injury sources distorted the presumed linearity between ST-segment deviation and heart rate. It was concluded that the ST/HR slope and ST-segment deviation of the 12-lead ECG are not able to indicate extent of ischemic injury or number of vessels occluded.

Adult↗
PubMed1996

Multiple DNA and protein sequence alignment based on segment-to-segment comparison.

In this paper, a new way to think about, and to construct, pairwise as well as multiple alignments of DNA and protein sequences is proposed. Rather than forcing alignments to either align single residues or to introduce gaps by defining an alignment as a path running right from the source up to the sink in the associated dot-matrix diagram, we propose to consider alignments as consistent equivalence relations defined on the set of all positions occurring in all sequences under consideration. We also propose constructing alignments from whole segments exhibiting highly significant overall similarity rather than by aligning individual residues. Consequently, we present an alignment algorithm that (i) is based on segment-to-segment comparison instead of the commonly used residue-to-residue comparison and which (ii) avoids the well-known difficulties concerning the choice of appropriate gap penalties: gaps are not treated explicity, but remain as those parts of the sequences that do not belong to any of the aligned segments. Finally, we discuss the application of our algorithm to two test examples and compare it with commonly used alignment methods. As a first example, we aligned a set of 11 DNA sequences coding for functional helix-loop-helix proteins. Though the sequences show only low overall similarity, our program correctly aligned all of the 11 functional sites, which was a unique result among the methods tested. As a by-product, the reading frames of the sequences were identified. Next, we aligned a set of ribonuclease H proteins and compared our results with alignments produced by other programs as reported by McClure et al. [McClure, M. A., Vasi, T. K. & Fitch, W. M. (1994) Mol. Biol. Evol. 11, 571-592]. Our program was one of the best scoring programs. However, in contrast to other methods, our protein alignments are independent of user-defined parameters.

Algorithms↗
PubMed1996

Neutrophil nuclear segmentation in mild cobalamin deficiency: relation to metabolic tests of cobalamin status and observations on ethnic differences in neutrophil segmentation.

Neutrophil hypersegmentation is considered the most sensitive peripheral blood cell marker of cobalamin deficiency. However, its diagnostic value in the mild deficiency states that accompany most low cobalamin levels and its relation to metabolic test of cobalamin status are unknown. The authors compared neutrophil lobe averages and percent neutrophils with 5 or more lobes (%5+ lobes) in 169 subjects with their mean corpuscular volume (MCV) and serum cobalamin, methylmalonic acid (MMA), homocysteine, and folate levels and, in 65 cases, with the deoxyuridine suppression test (dUST). Only 9 subjects had hypersegmentation by lobe average and 20 subjects by %5+ lobes. They were not more often cobalamin-deficient than subjects without hypersegmentation. Moreover, only one of 34 subjects with dUST results diagnostic for cobalamin deficiency had neutrophil hypersegmentation. Both indices of neutrophil segmentation in the 169 subjects correlated significantly with homocysteine levels. They also showed weak inverse correlation with cobalamin levels, but did not correlate with MMA, folate, or MCV values. Cobalamin therapy for 6 months did not significantly change neutrophil lobe averages in 35 subjects with mild deficiency, compared with 8 nondeficient controls, and only marginally improved the %5+ lobes. A surprising, incidental observation was that blacks had significantly greater neutrophil segmentation by both criteria than did whites and others. This difference was unrelated to cobalamin or folate status. Our results indicate that dUST abnormalities precede all morphologic changes of deficiency, including hypersegmentation. Although a tendency exists for neutrophil segmentation to increase very slightly as some serum values, especially homocysteine, start to worsen in mild cobalamin deficiency, the metabolic changes precede overt hypersegmentation. Neutrophil nuclear segmentation is insufficiently sensitive in relation to metabolic evidence of deficiency to be used as a clinical tool in the diagnosis of mild cobalamin deficiency.

Asian People↗
PubMed1983

Cloning and sequence of UK bovine rotavirus gene segment 7: marked sequence homology with simian rotavirus gene segment 8.

The genome of the UK bovine rotavirus, which consists of eleven segments of dsRNA was polyadenylated and reverse-transcribed into cDNA. Complementary cDNA strands were annealed and the termini of the duplexes completed using DNA polymerase I. Full-length DNA copies of RNA segments 7, 8 and 9 were cloned into the Pst I site of pBR322 and a clone containing the entire gene 7 was identified and sequenced. Gene 7 is 1059 nucleotides in length and contains a single long open reading frame capable of coding for a protein of 317 amino-acids. The known gene product of segment 7 is a protein with an estimated molecular weight of 33,000 daltons. When the UK bovine rotavirus gene 7 sequence was compared with the published data for the homologous gene (segment 8) of the simian rotavirus SA11, it was found to be identical to it in size and the arrangement of the proposed coding and non-coding regions, and very similar in nucleotide sequence (88% homology). Most of the base changes are silent and the predicted amino-acid sequences are almost identical (96% homology).

Amino Acid Sequence↗
PubMed1983

The sequence of RNA segment 1 of influenza virus A/NT/60/68 and its comparison with the corresponding segment of strains A/PR/8/34 and A/WSN/33.

The complete nucleotide sequence of RNA segment 1 of influenza virus A/NT/60/68, corresponding to the PB2 protein, has been determined. It is 2341 nucleotides long, encoding a predicted product of 759 amino acids with a net charge of +27 1/2 at neutral pH. The predicted amino acid sequence has been compared to the equivalent sequences in influenza viruses A/PR/8/34 and A/WSN/33. Evolutionary divergence, assuming a direct lineage from A/PR/8/34 and allowing for "laboratory drift", is 0.08% per year. The alignment of RNA segment 10 of A/NT/60/68 with segments 1 and 3 is completed, confirming that it is a mosaic of regions from these two segments.

Amino Acid Sequence↗
PubMed1992

The nucleotide sequence of the M RNA segment of tomato spotted wilt virus, a bunyavirus with two ambisense RNA segments.

The complete sequence of the tomato spotted wilt virus (TSWV) M RNA segment has been determined. The RNA is 4821 nucleotides long and has an ambisense coding strategy similar to that of the S RNA segment. The M RNA segment contains two open reading frames (ORFs), one in the viral sense which encodes a protein with a predicted size of 33.6K, and one in the viral complementary sense which encodes the precursor to the G1 and G2 glycoproteins, with a predicted size of 127.4K. Both ORFs are expressed via the synthesis of subgenomic mRNAs that possibly terminate at a stable hairpin structure, located in the intergenic region. The precursor for the glycoproteins contains a sequence motif (RGD) which is characteristic of cellular attachment domains. Significant sequence homology was found between the G1 glycoproteins of members of the genus Bunyavirus and a corresponding region in the glycoprotein precursor of TSWV, indicating a close evolutionary relationship between these viruses. With the elucidation of the M RNA sequence, the complete nucleotide sequence of TSWV has been determined. TSWV represents the first member of the Bunyaviridae shown to contain two ambisense RNA segments.

Amino Acid Sequence↗
PubMed1992

Interference is controlled by segment 2 and possibly by segment 8 of the nondefective interfering influenza virus variant A/FM/1/47-MA.

On mouse adaption of A/FM/1/47, a variant, A/FM/1/47-MA (FM-MA), that had acquired the properties of increased virulence and interference was produced. Coinfection of cells with FM-MA and prototype strains of influenza virus yielded > 100-fold more FM-MA virus than prototype virus, whereas coinfection with the same prototype strains and the parental A/FM/1/47 virus produced equivalent yields, indicating that FM-MA had acquired mutations that confer the property of interference during mouse adaption. FM-MA is a nondefective interfering virus that grows to a high titer in vivo and in vitro. It has previously been shown that segments 4, 7, and 8 and possibly segment 5 account for the increased virulence. In this study we show by genetic analysis of FM-MA x A/HK/1/68 reassortants that segment 2, coding for the polymerase-associated protein PB1, and possibly segment 8, encoding the NS1 and NS2 proteins, control the ability of FM-MA to interfere. Interference could not be overcome by increasing the titer of the coinfecting strain, but delaying FM-MA infection by 4 to 6 h did avoid interference. During interference of A/HK/1/68, protein synthesis was inhibited by less than 65% throughout coinfection. Given the kinetics of interference and the small perturbation in protein synthesis, interference appeared to occur at the level of late genome replication or virus assembly. Virulence and interference in FM-MA were not linked. An interfering avirulent FM-MA x A/HK/1/68 reassortant, E07, was capable of protecting mice against lethal pneumonia due to a virulent noninterfering reassortant, H04.

Genetic Variation↗
PubMed1991

Site-specific recombination promoted by a short DNA segment of plasmid R1 and by a homologous segment in the terminus region of the Escherichia coli chromosome.

A short DNA segment located in the kanamycin resistance region of plasmid R1 promotes site-specific recombination and plasmid maintenance. This segment has been reduced to 100 bp and subsequently to 44 bp without losing these properties. It can recombine with a similar segment located in the terminus region of the Escherichia coli chromosome. It is proposed that this recombination is responsible for the plasmid maintenance properties of the R1 segment. The chromosomal site has been isolated; it also shows site-specific recombination activity. Sequence homologies were also found with a phage site-specific integration locus in the chromosome of Xanthomonas campestris and with the plasmid ColE1 site-specific recombination locus. The recombinase required in all these systems is probably XerC, an E. coli enzyme acting on the cer site of plasmid ColE1 for the conversion of plasmid dimers to monomers. It is postulated that site-specific recombination in the terminus region of the chromosome intervenes in the partitioning of the two daughter chromosomes.

Bacterial Proteins↗
PubMed1989

[ST-segment analysis in long-term ECG: amplitude and phase response of various systems in comparison with standard ECG and their effect on true original reproduction of ST segment depression].

Ambulatory ECG monitoring has been suggested as a method for the detection of transient myocardial ischemia. But it is still unclear how accurately ST-segment alterations can be detected with the different systems. Measurement of amplitude and phase response is a valid method to estimate the fidelity of reproduction of an ECG-signal. We investigated the direct-recording long-term ECG systems CardioData Mk4 with recorder PR3, CardioData Mk4 with Spacelabs recorder, DMI Eclipse with DMI Recorder, Reynolds Pathfinder II with Oxford replay PB2 and recorder MR-10 and Reynolds Pathfinder III with tracker in comparison to a standard ECG recorder Picker Schwarzer C6800. Amplitude vs frequency response curves were derived from input sinus waves ranging from 0.01 to 500 Hz. The phase response was measured with a phase-sensitive waveform at a frequency range from 0.05 to 10 Hz. To determine the distortion of the ST-segment on the actual ECG, we produced a standard PQRST-signal that was modified to provide flat ST-segment depressions from 0 to 0.5 mV at 0.05 mV increments. The low and high frequency cut-off of the amplitude response was found at 0.09 and 220 Hz with the standard ECG recorder. A phase shift of -30 degrees was detected at 0.07 Hz. ST-segment depressions of the test-ECG were reflected to the same extent. For the CardioData-System, both cassette recorders yielded lower and upper cut-off frequencies of 0.06 and 0.07, and 20 and 16 Hz, respectively. A phase shift of -30 degrees was found at 0.35 and 0.31 Hz, respectively.(ABSTRACT TRUNCATED AT 250 WORDS)

Arrhythmias, Cardiac↗
PubMed1986

Does complete revascularization by the conventional method truly provide the best possible results? Analysis of results and comparison with revascularization of infarct-prone segments (systematic segmental myocardial revascularization): the Sheba Study.

Myocardial revascularization is usually considered "complete" if all stenosed major coronaries are bypassed. Attempts were made to compare the results of this method with an approach by which each of the following five left ventricular infarct-prone segments is revascularized if ischemic: anteroseptal, anterolateral, posterosuperior, posteroinferior, and diaphragmatic. Two subsets of patients were studied. A total of 366 patients (Group A) who underwent aortacoronary bypass operations from 1980 to 1982 were followed up for a mean of 16.3 (6 to 43) months and were retrospectively divided into two groups: Group A1 (120 patients) had incomplete segmental revascularization (mean of 3.4 grafts per patient) and Group A2 (246 patients) had complete segmental revascularization (4.0 grafts per patient) (p less than 0.0001). Groups A1 and A2 were identical in all clinical and angiographic parameters: unstable angina, 60%; previous myocardial infarction, 70%; left main stenosis, 10%; and ejection fraction less than 30%, 2%. Overall operative mortality was 2.3%. Results in Groups A1 and A2, respectively, were as follows: operative mortality, 5.8% versus 0.8% (p less than 0.005); perioperative myocardial infarction, 6.9% versus 0.8% (p less than 0.0005); 35 month survival rate, 93.3% versus 97.9% (p less than 0.02); total freedom from symptoms, 54.1% versus 68.3% (p less than 0.025). In addition, 151 patients operated on in 1984 (Group B) were studied prospectively with regard to operative mortality and perioperative myocardial infarction, and the results were identical to those in Group A. Compared to conventional complete revascularization, complete segmental revascularization provides better results.

Adult↗
PubMed1979

[Signs of anterior segment ischemia following segmental external buckling (author's transl)].

The symptoms of an acute anterior segment necrosis are described as they might occur as a postoperative complication due to encircling procedures. Report about a patient presenting postoperatively signs of ischemia in the anterior segment following segmental external buckling. In this case the cylinder of the explant was 5 mm in diameter and extended over 2 quadrants of the globe. Discussion of the factors most likely causing this rare complication due to segmental external buckling.

Aged↗
PubMed1983

[Experimental study of changes in the pressure of the posterior segment of the eye under general anesthesia. Consequences for surgery of the anterior segment].

Animal studies were conducted to compare variations in intraocular (IOP) and posterior segment pressure (PSP) during general anesthesia to assess the role of PSP in the development of anesthesia for ophthalmological procedures. Anesthetic agents appear to have a marked effect on IOP during operations involving opening of hypertonic globe or examinations of children under general anesthesia, but their action on IOP has no significance during procedures requiring opening of the anterior chamber because of alteration of aqueous humor physiology. The PSP, defined as pressure in the posterior segment when the anterior segment is at atmospheric pressure, is the main factor affecting surgical conditions, a rise in PSP possibly resulting in typical complications of cataract surgery but having beneficial effects in corneal grafts for example. Posterior segment pressure cannot be studied in humans and an experimental model using rabbits under artificial ventilation following tracheotomy after general anesthesia was developed. Pressure gauges recorded arterial and central venous pressures and were connected to needles inserted in both eyes to monitor IOP and PSP, the latter from a needle passed into the anterior chamber through the cornea, which was incised over the needle to enable permanent drainage of aqueous humor. All pressures were recorded simultaneously and no correlations were observed between IOP and PSP after pentobarbitone, neosynephrine, succinylcholine, or asphyxia (interruption of ventilation and curarization). These findings suggest that IOP is not a valid measurement for assessment of anesthetic techniques, whereas PSP provides a better guideline for development of ophthalmological anesthesia.

Anesthesia, General↗
PubMed1994

[Structure of segmental tuft lesions in childhood IgA nephropathy--three dimensional analysis indicates development of segmental lesions].

The mechanisms responsible for the formation and development of segmental lesions of IgA nephropathy in children were studied by analysis of three dimensional reconstruction. Forty-eight segmental lesions from 15 cases (diffuse proliferative glomerulonephritis (DPGN) in 13 cases, focal glomerulonephritis (FGN) in 2 cases) were examined by light microscopy by analysis of serial sections (in average 26 sections/glomerulus). In tuft, three types of tuft lesions were defined by their chronisity: 1) endocapillary proliferation including exudative changes, 2) mesangial hypercellularity, 3) deposition of mesangial matrix with sclerosis. Extra-capillary lesions, namely crescent were also defined by their chronisity: 1) cellular, 2) fibrocellular, 3) fibrous. The structural relation in each tuft and endocapillary lesions were observed. Endocapillary proliferative lesions of tufts were closely associated with cellular crescent of extra-capillary lesions. In fibrocellular and fibrous crescents, the frequency of endocapillary proliferation in tufts were reduced, while the association of mesangial proliferation and sclerosis were increased. Nevertheless, endocapillary proliferation of tufts were still observed in 33% of fibrous crescent. We concluded that segmental lesions were originated by endocapillary tuft lesions leading to cellular crescents. The multifocal and repeated attack of endocapillary proliferative lesions within segmental sclerosis promotes further development of glomerular sclerosis in IgA nephropathy in children.

Adolescent↗
PubMed1993

[A case of bilateral synchronous renal cell carcinoma treated with partial nephrectomy with temporary occlusion of the segmental renal artery (segmental nephrectomy)].

We present a case of bilateral synchronous renal cell carcinoma. A 57-year-old man visited our hospital with a complaint of fever up. On ultrasonography and computerized tomography scan, a round tumor about 2.5 cm in diameter in the posterior portion of the right kidney and another tumor about 7 cm in diameter arising from the upper pole of the left kidney. Selective renal arteriogram showed that the inferior branch of the posterior segmental artery supplied blood to the right renal tumor. Left partial nephrectomy with temporary occlusion of the main renal artery and posterior segmental nephrectomy of the right kidney were performed at the same time. In patients with cancer confined to the posterior segment of the kidney, segmental nephrectomy can be performed while allowing unimpaired perfusion to the remainder of the kidney from the main renal artery.

Carcinoma, Renal Cell↗
PubMed1997

Anterior segment prosthesis development: retinal function following anterior segment removal.

Replacement of the entire anterior segment of the eye is a very ambitious and complex endeavor and it is not known whether the retina remains functional when the anterior structures have been removed. We used routine histo-pathologic evaluation and electroretinographic measurements to determine the structural and functional status of rabbit retinas following surgical removal of the internal anterior structures (iris, ciliary body, and lens) and replacement of the vitreous with silicone oil. In some cases, we were able to record both a scotopic and a photopic electroretinographic response as long as 15 weeks after complete removal of the internal anterior segment structures. Although many hurdles remain and more efficacious surgical techniques and biomaterials need to be developed, our results suggest that, in the rabbit, the retina may continue to function in the absence of critical anterior segment structures.

Animals↗
PubMed1986

Segmental differentiation in the leech nervous system: the genesis of cell number in the segmental ganglia of Haemopis marmorata.

In hirudinid leeches, the segmental ganglia associated with the sexual organs contain several hundred more neurons than other midbody ganglia. To determine whether this difference arises by differential cell addition or by differential cell death, cell counts were made in several segmental ganglia during the course of embryonic and postembryonic development. The results show that all ganglia behave equally in early development. In each case, at least 10-20% more cells than will make up the adult complement of about 400 neurons is generated, and by about 20 days of embryonic development cell loss brings the number down to about 400 cells. By about 30 days, when animals emerge from their cocoons, additional cells have begun to appear in the sex ganglia. The number of extra cells continue to increase gradually over the next several months, until the adult number of 600-700 neurons is attained. These observations indicate that at least some segmental differences in the size of neuronal populations are due to differential cell proliferation and that these differences can arise quite late in the maturation of an animal.

Animals↗
PubMed1991

Segmental differentiation in the leech central nervous system: proposed segmental homologs of the heart accessory neurons.

As part of an on-going study of segmental differentiation in the central nervous system (CNS) of the leech Hirudo medicinalis, a search was made for putative segmental homologs of the heart accessory (HA) neurons, which exist exclusively as a bilateral pair in the ganglia of the fifth and sixth body segments. As it is not yet feasible to obtain adequate cell lineage information in H. medicinalis, potential homologs of the HA neurons were determined using morphological, immunohistochemical, and electrophysiological criteria. Among cells in other body ganglia with somata in the same locations as HA neurons, a pair was found having extensive morphological and physiological similarities to HA neurons. These we have called HA-like (HAL) neurons. Adult HA and HAL neurons have closely related patterns of primary branching, in terms of shape, intraganglionic pathways taken, and extraganglionic projections. The number, location, and relative thickness of branches are also similar among these cells. In embryos 10 to 11 days old, HA and HAL neurons have virtually identical branching patterns, with primary and secondary branches of nearly uniform caliber. Differences in branch thickness develop gradually; by embryonic day 20, they resemble those found in adult neurons. Two features found to differ between HA and HAL neurons were the cell body diameter (larger for the HA cells) and the expression of antigens recognized by the monoclonal antibody Laz1-1 (absent at a detectable level in the HA neurons). At a physiological level, the HA and HAL neurons showed action potentials of similar size and shape, as well as inhibitory synaptic inputs from a common source, the heart interneurons (HN). The observations presented here suggest that there is a common developmental origin for the HA and HAL neurons, and hence that their fates are positionally determined by as yet unknown factors.

Aging↗