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PubMed2000

Identification of a 200- to 300-fold repetitive 529 bp DNA fragment in Toxoplasma gondii, and its use for diagnostic and quantitative PCR.

We have identified a novel 529bp fragment that is repeated 200- to 300-fold in the genome of Toxoplasma gondii. This 529bp fragment was utilised for the development of a very sensitive and specific PCR for diagnostic purposes, and a quantitative competitive-PCR for the evaluation of cyst numbers in the brains of chronically infected mice. The 529bp fragment was found in all 60 strains of T. gondii tested, and it discriminates DNA of T. gondii from that of other parasites. Toxoplasma gondii DNA was detected in amniotic fluid of patients, as well as in various tissues from infected mice. Polymerase chain reaction with the 529bp fragment was more sensitive than with the 35-copy B1 gene. For the quantitative competitive-PCR, a 410-bp competitor molecule was co-amplified with similar efficiency as the 529bp fragment. Quantitative competitive-PCR produced a linear relationship between the relative amounts of PCR product and the number of tachyzoites in the range of 10(2)-10(4) tachyzoites and 100-3000 tissue cysts. A highly significant correlation between visual counting of brain cysts and quantitative competitive-PCR was obtained in mice chronically infected with Toxoplasma. Thus, quantitative competitive-PCR with the 529bp fragment can be used as an alternative for the tedious visual counting of brain cysts in experimental animals. With the quantitative competitive-PCR, furthermore, we could confirm the copy number of the 529bp fragment in tachyzoites and estimate the number of bradyzoites per cyst.

Animals↗
PubMed2003

Habitat fragmentation resulting in overgrazing by herbivores.

Habitat fragmentation sometimes results in outbreaks of herbivorous insect and causes an enormous loss of primary production. It is hypothesized that the driving force behind such herbivore outbreaks is disruption of natural enemy attack that releases herbivores from top-down control. To test this hypothesis I studied how trophic community structure changes along a gradient of habitat fragmentation level using spatially implicit and explicit models of a tri-trophic (plant, herbivore and natural enemy) food chain. While in spatially implicit model number of trophic levels gradually decreases with increasing fragmentation, in spatially explicit model a relatively low level of habitat fragmentation leads to overgrazing by herbivore to result in extinction of the plant population followed by a total system collapse. This provides a theoretical support to the hypothesis that habitat fragmentation can lead to overgrazing by herbivores and suggests a central role of spatial structure in the influence of habitat fragmentation on trophic communities. Further, the spatially explicit model shows (i) that the total system collapse by the overgrazing can occur only if herbivore colonization rate is high; (ii) that with increasing natural enemy colonization rate, the fragmentation level that leads to the system collapse becomes higher, and the frequency of the collapse is lowered.

Animals↗
PubMed2002

Stone fragmentation during shock wave lithotripsy is improved by slowing the shock wave rate: studies with a new animal model.

PURPOSE: The current trend toward ungated shock wave lithotripsy means that more patients are being treated with shock waves delivered at a rapid rate (120 shock waves per minute or greater). However, no benefit of an increased shock wave rate has been shown and in vitro studies indicate that slowing the shock wave rate actually improves stone fragmentation. We tested the effect of the shock wave rate on stone comminution in a new animal model. MATERIALS AND METHODS: Gypsum model stones were inserted via upper pole percutaneous access into the lower pole calix of the kidneys of female pigs weighing approximately 100 pounds. Shock wave lithotripsy was performed (400 shock waves uninterrupted at 20 kV. and 30 or 120 shock waves per minute) 2 hours later using an unmodified HM3 lithotriptor (Dornier Medical Systems, Marietta, Georgia). After en bloc excision of the urinary tract stone fragments were collected and sieved through 2 mm. mesh. The particles were weighed and surface area was determined. RESULTS: Stones treated at 30 shock waves per minute broke more completely than stones treated at 120 shock waves per minute. The percent of fragments greater than 2 mm. was significantly higher for stones treated at the fast rate of 120 versus the slow rate of 30 shock waves per minute (mean +/- SEM 81% +/- 14% versus 45% +/- 12%, p <0.005). When stone fragmentation was expressed as the percent increase in fragment surface area, significantly greater fragmentation occurred at the slower than at the more rapid rate (327% +/- 63% versus 135% +/- 136%, p <0.02). CONCLUSIONS: Slowing the rate of shock wave administration during shock wave lithotripsy significantly improves the efficiency of stone fragmentation in vivo.

Animals↗
PubMed1994

Effect of alkaline citrate therapy on clearance of residual renal stone fragments after extracorporeal shock wave lithotripsy in sterile calcium and infection nephrolithiasis patients.

The natural history of post-extracorporeal shock wave lithotripsy residual stone fragments (clearance, growth and aggregation) is incompletely known, even though they are believed to constitute a risk in terms of new stone formation and persistent infection of the urinary tract. We addressed this issue and the hypothesis that alkaline citrate therapy improves residual stone fragment clearance in a 12-month followup study. There were 40 sterile calcium and 30 struvite stone patients with residual fragments after extracorporeal shock wave lithotripsy (diameter less than 5 mm.) consecutively enrolled and randomly assigned to a citrate therapy (6 to 8 gm. per day) or control (hygienic measures only) group. Infection stone patients also received adequate antibiotic therapy throughout the study. Among the patients in the untreated sterile group 21% and 32% were stone-free at 6 and 12 months, respectively. In the infection group these figures were 27% and 40%, respectively. Among the untreated sterile calcium stone patients in whom clearance was not achieved a high percentage experienced residual fragment growth or reaggregation. Citrate therapy significantly improved the stone clearance rate in the sterile (at 6 and 12 months 65% and 74% were stone-free, respectively) and infection (71% and 86%, respectively) stone patients, and prevented residual fragment growth or reaggregation in subjects in whom clearance was not achieved. The data show that growth and persistence are common in the natural history of residual stone fragments. Citrate ameliorated the outcome of these residual fragments by reducing the growth or agglomeration, and by increasing the clearance rate in calcium oxalate and in infection stone patients.

Adolescent↗
PubMed1987

An assessment of the pulsed dye laser for fragmenting calculi in the pig ureter.

The pulsed dye laser was used to fragment ureteric calculi in 10 pig ureters, compared to electrohydraulic disintegration in six pig ureters. The stones were impacted in the proximal ureter and approached by rigid ureteroscopy. Four ureters did not have stones impacted but had ureteroscopes passed. The stones were fragmented and the particles left to pass spontaneously. The degree of inflammatory reaction was graded at the site of fragmentation as well as in the middle and lower ureter. The degree of inflammation seen at the site of fragmentation was significantly less in the laser group than in the electrohydraulic group (p = 0.0027). It was noted that the degree of inflammation seen in the lower ureter was significantly greater than that seen at the site of fragmentation (p = 0.01), and that this grade of inflammation correlated well with the size of ureteroscope used (p = 0.0026). Further, the degree of dilatation of the ureter and pelvicalyceal system was significantly greater when the larger calibre ureteroscope had been used (p = 0.0056) ranging up to hydronephrosis with flattening of the papillae. If there is any parallel which can be drawn between the pig ureter and the human ureter then it suggests that ureteroscopy is more significant than the modality of fragmentation used. The contribution of the laser may therefore be more by the miniaturization of instrumentation which will be made possible than by any advantage it may have as a fragmenter.

Animals↗
PubMed1998

Degradation of fibrinogen and cross-linked fibrin by human neutrophil elastase generates D-like fragments detected by ELISA but not latex D-dimer test.

Recently, we observed that D-dimers are degraded by human neutrophil elastase (HNE) into two D-like fragments, reacting with the monoclonal antibody in an ELISA D-dimer test but not reacting with the corresponding latex D-dimer test. To investigate this in more detail, we studied the degradation of cross-linked fibrin and fibrinogen by plasmin and HNE to see if this resulted in D-fragments or D-like fragments. Degradation of fibrinogen, both by plasmin and HNE, resulted in D- and D-like fragments, respectively, detected by the ELISA D-dimer test. Degradation of cross-linked fibrin by plasmin and HNE also resulted in D- and D-like fragments, which were detected by the ELISA method. Intact D-dimers detected by the latex D-dimer test were only observed after degradation of cross-linked fibrin with plasmin. We conclude that during lysis of cross-linked fibrin as well as fibrinogen by plasmin and HNE, D-fragments, and D-like fragments, detected by the ELISA D-dimer test, are formed. Only during degradation of cross-linked fibrin by plasmin, intact D-dimers, detected by latex D-dimer test, are formed. The ELISA D-dimer test may therefore be used to detect fibrin and fibrinogen degradation products generated by the combined action of plasmin and HNE in sepsis and other conditions with increased HNE activity, while the latex D-dimer test may be used to detect plasmin derived intact D-dimers.

Animals↗
PubMed1992

Management of dislocated lens fragments during phacoemulsification.

BACKGROUND: Dislocation of nuclear lens fragments during phacoemulsification can lead to a high incidence of glaucoma, uveitis, and poor visual acuity. The correct approach to these patients is uncertain. The authors report on eight patients who underwent pars plana vitrectomy with removal of lens fragments. METHODS: Charts of eight consecutive patients who developed dislocation of nuclear lens fragments into the vitreous cavity during phacoemulsification were retrospectively reviewed. All patients underwent a standard three-port pars plana vitrectomy with removal of the dislocated nuclear fragments by pars plana fragmentation. After the vitrectomy, the retina was inspected with indirect ophthalmoscopy. Tears were treated with cryopexy. A fluid-air exchange and scleral buckle were performed when indicated. RESULTS: Retinal tears were located at the vitreous base in four of eight patients. After vitrectomy, visual acuity improved in all patients, with 7 of 8 patients achieving visual acuity of 20/40 or better. The type of pseudophakia did not influence the final visual acuity. There were no cases of glaucoma, uveitis, or macular edema with up to 22 months of follow-up. CONCLUSIONS: These results suggest that large nuclear fragments dislocated into the posterior segment during phacoemulsification can be removed safely with pars plana vitrectomy and lensectomy with an excellent visual prognosis. Attempts to remove lens fragments during the phacoemulsification through an anterior wound should be avoided because of excessive vitreous traction, leading to retinal break formation.

Aged↗
PubMed2002

Accuracy of AFM measurements of the contour length of DNA fragments adsorbed on mica in air and in aqueous buffer.

The measurement by atomic force microscope of the contour length of DNA fragments adsorbed on mica has been made as accurate as possible by revisiting the different steps of image acquisition and processing. In air, the DNA helical rise was estimated at 2.97 +/- 0.15 A per base pair (bp) (mean +/- standard deviation) by imaging a 648-bp DNA fragment and 2.95 +/- 0.14 A per bp for a 115-bp fragment. This confirms earlier observations suggesting that drying DNA fragments on mica in the presence of nickel induces limited conformational changes. At this point the exact nature of these conformational changes remains unknown. Simple hypotheses are the transconformation of stretches of the DNA molecules to the A-form of the double helix or alteration of the helix structure at the points of contact between DNA and mica. By contrast, in aqueous buffer, the measured helical rise was 3.14 +/- 0.15 A per bp for the 648-bp fragment and 3.17 +/- 0.13 A per bp for the 1115-bp fragment. Thus, measured helical rises do not depend on the fragment length and are significantly shorter than the 3.38 A per bp measured by crystallography, but close to the 3.18 A per bp found in NMR studies. These findings are discussed with respect to discrepancies in earlier results published in the literature.

Air↗
PubMed1998

Production of prostanoids via increased cyclo-oxygenase-2 expression in human amnion cells in response to low molecular weight hyaluronic acid fragment.

Increased concentrations of hyaluronic acid (HA) have been found in serum and at uterine cervix at term. In its native form, HA exists as a high molecular weight (MW) polymer, but during parturition a lower MW HA fragment accumulates. The aim of this study was to investigate the regulatory mechanisms responsible for increased amnion prostanoid production and cyclo-oxygenase (COX) expression in response to HA. Human term amnion cells in culture were exposed to native HA polymer (MW 2.2x106) and its fragment (MW 3.5x104). We have determined levels of prostanoids, prostaglandins E2 and F2alpha, in conditioned media using specific immunoassays. Expression of COX-1 and COX-2 was examined with Western blot. Results were analyzed for statistical significance with Mann-Whitney U-test. Human amnion cells treated with HA fragment (100 nmol/l) produced significantly more PGE2 (2.3+/-0.21 (mean+/-S.D.) pg/106 cells/24 h) than controls (0.34+/-0.03) or high MW HA-treated cells (1.2+/-0.21). Protein levels of COX-2, but not COX-1, were substantially increased in amnion cells treated with HA fragment. HA fragment-mediated prostanoid production is markedly diminished by pretreatment with indomethacin. Our results indicate that HA fragment, rather than physiologic native HA polymer, induces amnion cell-derived prostanoid production via increased COX-2 expression. COX-2-mediated prostanoid production is likely a key physiologic event in HA fragment-mediated cervical ripening and the labor onset.

Amnion↗
PubMed1992

A contig assembly program based on sensitive detection of fragment overlaps.

An effective computer program for assembling DNA fragments, the contig assembly program (CAP), has been developed. In the CAP program, a filter is used to eliminate quickly fragment pairs that could not possibly overlap, a dynamic programming algorithm is applied to compute the maximal-scoring overlapping alignment between each remaining pair of fragments, and a simple greedy approach is employed to assemble fragments in order of alignment scores. To identify the true fragment overlaps, the dynamic programming algorithm uses specially chosen sets of alignment parameters to tolerate sequencing errors and to penalize "mutational" changes between different copies of a repetitive sequence. The performance tests of the program on fragment data from genomic sequencing projects produced satisfactory results. The CAP program is efficient in computer time and memory; it took about 4 h to assemble a set of 1015 fragments into long contigs on a Sun workstation.

Algorithms↗
PubMed1999

The role of ursodeoxycholic acid in bile acid-mediated kidney fragment toxicity.

Elevated levels of bile acids are thought to play an important role in the renal failure of patients with obstructive jaundice undergoing surgery. In contrast, ursodeoxycholic acid (UDA) is widely used to improve cholestasis and has been proposed as protective bile acids and antioxidant. The present study employs kidney fragments to determine the role of reactive oxygen species (ROS) in the mechanism of toxicity of hydrophobic bile acids and to determine the nephroprotectant properties of UDA against the hydrophobic bile acids. The hydrophobic bile acids chenodeoxycholic (200 microM) and deoxycholic acid (200 microM) significantly (P<0.05) increased lactate dehydrogenase leakage (LDH) from glomerular fragments from 2.7+/-0.4 to 5.03+/-0.23 and 4.66+/-0.37 (micromol NADH consumed/min/mg protein) for chenodeoxycholic and deoxycholic acid respectively. Preincubating the fragments with UDA (500 microM) did not prevent the leakage of LDH caused by the bile acids. The level of lipid peroxidation was not increased in fragments exposed to either ursodeoxycholic (0-500 microM), lithocholic (0-100 microM), chenodeoxycholic (0-500 microM) or deoxycholic acid (0-500 microM). Furthermore UDA (500 microM) did not prevent the increase in lipid peroxidation caused by tert-butyl hydroperoxide (0-1000 microM) in the fragments. These results suggest that hydrophobic bile acids do not cause lipid peroxidation in kidney fragments and that UDA is neither capable of preventing the loss of membrane integrity induced by hydrophobic bile acids or acting as an antioxidant in kidney fragments.

Animals↗
PubMed2000

Fragmentation chemistry of [M + Cu]+ peptide ions containing an N-terminal arginine.

[M + Cu]+ peptide ions formed by matrix-assisted laser desorption/ionization from direct desorption off a copper sample stage have sufficient internal energy to undergo metastable ion dissociation in a time-of-flight mass spectrometer. On the basis of fragmentation chemistry of peptides containing an N-terminal arginine, we propose the primary Cu+ ion binding site is the N-terminal arginine with Cu+ binding to the guanidine group of arginine and the N-terminal amine. The principal decay products of [M + Cu]+ peptide ions containing an N-terminal arginine are [a(n) + Cu - H]+ and [b(n) + Cu - H]+ fragments. We show evidence to suggest that [a(n) + Cu - H]+ fragment ions are formed by elimination of CO from [b(n) + Cu - H]+ ions and by direct backbone cleavage. We conclude that Cu+ ionizes the peptide by attaching to the N-terminal arginine residue; however, fragmentation occurs remote from the Cu+ ion attachment site involving metal ion promoted deprotonation to generate a new site of protonation. That is, the fragmentation reactions of [M + Cu]+ ions can be described in terms of a "mobile proton" model. Furthermore, proline residues that are adjacent to the N-terminal arginine do not inhibit formation of [b(n) + Cu - H]+ ion, whereas proline residues that are distant to the charge carrying arginine inhibit formation of [b(n) + Cu - H]+ ions. An unusual fragment ion, [c(n) + Cu + H]+, is also observed for peptides containing lysine, glutamine, or asparagine in close proximity to the Cu+ carrying N-terminal arginine. Mechanisms for formation of this fragment ion are also proposed.

Arginine↗
PubMed2000

Electrospray mass spectrometry and fragmentation of N-linked carbohydrates derivatized at the reducing terminus.

Derivatives were prepared from N-linked glycans by reductive amination from 2-aminobenzamide, 2-aminopyridine, 3-aminoquinoline, 2-aminoacridone, 4-amino-N-(2-diethylaminoethyl)benzamide, and the methyl, ethyl, and butyl esters of 4-aminobenzoic acid. Their electrospray and collision-induced dissociation (CID) fragmentation spectra were examined with a Q-TOF mass spectrometer. The strongest signals were obtained from the [M + Na]+ ions for all derivatives except sugars derivatized with 4-amino-N-(2-diethylaminoethyl)benzamide which gave very strong doubly charged [M + H + Na]2+ ions. The strongest [M + Na]+ ion signals were obtained from the butyl ester of 4-aminobenzoic acid and the weakest from 2-aminopyridine. The most informative spectra were recorded from the [M + Li]+ or [M + Na]+ ions. These spectra were dominated by ions produced by sequence-revealing glycosidic cleavages and "internal" fragments. Linkage-revealing cross-ring cleavage ions were reasonably abundant, particularly from high-mannose glycans. Although the nature of the derivative was found to have little effect upon the fragmentation pattern, 3-aminoquinoline derivatives gave marginally more abundant cross-ring fragments than the other derivatives. [M + H]+ ions formed only glycosidic fragments with few, if any, cross-ring cleavage ions. Doubly charged molecular ions gave less informative spectra; singly charged fragments were weak, and molecular ions containing hydrogen ([M + 2H]2+ and [M + H + Na]2+) fragmented as the [M + H]+ singly charged ions with no significant cross-ring cleavages.

Amination↗
PubMed2001

Fragment mode analysis and its application to the vibrational normal modes of boron trichloride-ammonia and boron trichloride-pyridine complexes.

A method for expressing quantitatively the vibrational normal modes of a molecule in a basis set consisting of the normal vibrations (plus translations and rotations) of its constituent fragments is presented. The method is illustrated by describing the vibrational modes of BCl3-NH3 and BCl3-pyridine electron donor-acceptor complexes in terms of motions of BCl3 and either NH3 or pyridine. These complexes show examples of mixing between modes located on different fragments, mixing between modes of one fragment due to symmetry lowering, and the transformation of six fragment translations/rotations into vibrations of the complex. Although perturbation theory has been proposed to explain such examples of mode mixing, calculations imply that interactions between fragments of both complexes are too strong for perturbation theory to be generally applicable. In addition, the transformation of fragment rotations and/or translations into vibrations of the composite molecule will always occur and cannot be understood in detail by using perturbation theory. For the BCl3-pyridine complex, a band observed at 1107 cm(-1) is re-assigned as a combination of C-H in-plane bending and a ring-breathing mode of the pyridine fragment.

Ammonia↗
PubMed2003

Effect of habitat fragmentation on dispersal in the butterfly Proclossiana eunomia.

Comparison of dispersal rates of the bog fritillary butterfly between continuous and fragmented landscapes indicates that between patch dispersal is significantly lower in the fragmented landscape, while population densities are of the same order of magnitude. Analyses of the dynamics of the suitable habitat for the butterfly in the fragmented landscape reveal a severe, non linear increase in spatial isolation of patches over a time period of 30 years (i.e. 30 butterfly generations), but simulations of the butterfly metapopulation dynamics using a structured population model show that the lower dispersal rates in the fragmented landscape are far above the critical threshold leading to metapopulation extinction. These results indicate that changes in individual behaviour leading to the decrease of dispersal rates in the fragmented landscape were rapidly selected for when patch spatial isolation increased. The evidence of such an adaptive answer to habitat fragmentation suggests that dispersal mortality is a key factor for metapopulation persistence in fragmented landscapes. We emphasise that landscape spatial configuration and patch isolation have to be taken into account in the debate about large-scale conservation strategies.

Animals↗
PubMed2004

Preliminary study on the detection of the SARS-CoV specific target cDNA fragments by multiplex PCR.

The multiplex polymerase chain reaction (PCR) technique was applied to detect the SARS-CoV (severe acute respiratory syndrome-associated coronavirus) specific target cDNA fragments in the present study. The target cDNA fragments of SARS-CoV were synthesized artificially according to the genome sequence of SARS-CoV in GenBank submitted by The Chinese University of Hong Kong, and were used as simulated positive samples. Five primers recommended by World Health Organization (WHO) were used to amplify the fragments by single PCR and multiplex PCR. Three target cDNA fragments (121, 182 and 302 bp), as well as the three different combinations of any two of these fragments, were amplified by single PCR. The combination of these three fragments was amplified by multiplex PCR. The results indicated that the multiplex PCR technique could be applied to detect the SARS-CoV specific target cDNA fragments successfully.

Base Sequence↗
PubMed2002

Analysis of bromotryptophan and hydroxyproline modifications by high-resolution, high-accuracy precursor ion scanning utilizing fragment ions with mass-deficient mass tags.

Protein modifications are often detected by precursor ion scanning. When quadrupole TOF mass spectrometers are used for precursor ion scanning with high-resolution, high-accuracy fragment ion selection, "reporter" ions are required to have a unique mass within +/-0.04 Da or less instead of +/-0.5 Da on triple quadrupole mass spectrometers, the traditional instrument used for precursor ion scanning. Thus, characteristic fragment ions can be utilized even if other fragment ions have the same nominal mass as long as the characteristic fragment ions are slightly mass deficient as compared to the other fragments, i.e., when they have an inherent mass-deficient mass tag. Here, the immonium ions of bromotryptophan and hydroxyproline are described as two fragment ions characteristic for tryptophan-brominated and proline-hydroxylated peptides, respectively. The "reporter" ion of trytophan-brominated peptides is highly mass deficient due to the presence of bromine, thereby allowing the selective detection of these species and the distinction from other dipeptidic a-, b-, and y-fragment ions by high-resolution, high-accuracy precursor ion scanning. This strategy also enables the differentiation between precursors giving rise to the oxygen-containing immonium ion of hydroxyproline and precursors of the immonium ions of near-ubiquitous leucine/isoleucine. Both immonium ions have the same nominal mass of 86 Da, but the exact masses differ by less than 0.04 Da. High-resolution, high-accuracy precursor ion scanning enabled the identification of proline-hydroxylated and tryptophan-brominated species and the directed analysis of species carrying these modifications in a highly complex Conus textile conotoxin mixture. This lead to the characterization of one novel C. textile conotoxin containing a bromotryptophan residue and one novel C. textile conotoxin carrying two hydroxyproline residues.

Animals↗
PubMed2004

Influence of basic residue content on fragment ion peak intensities in low-energy collision-induced dissociation spectra of peptides.

The primary utility of trypsin digestion in proteomics is that it cleaves proteins at predictable locations, but it is also notable for yielding peptides that terminate in basic arginine and lysine residues. Tryptic peptides fragment in ion trap tandem mass spectrometry to produce prominent C-terminal y series ions. Alternative proteolytic digests may produce peptides that do not follow these rules. In this study, we examine 2568 peptides generated through proteinase K digestion, a technique that produces a greater diversity of basic residue content in peptides. We show that the position of basic residues within peptides influences the peak intensities of b and y series ions; a basic residue near the N-terminus of a peptide can lead to prominent b series peaks rather than the intense y series peaks associated with tryptic peptides. The effects of presence and position for arginine, lysine, and histidine are explored separately and in combination. Arg shows the most dominant effects followed by His and then by Lys. Fragment ions containing basic residues produce more intense peaks than those without basic residues. Doubly charged precursor ions have generally been modeled as producing only singly charged fragment ions, but fragment ions that contain two basic residues may accept both protons during fragmentation. By characterizing the influence of basic residues on gas-phase fragmentation of peptides, this research makes possible more accurate fragmentation models for peptide identification algorithms.

Algorithms↗