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A Cooper

Publications and source records attributed to A Cooper.

At least 55 records · Page 3Linked to original sources
PubMed2001

Soybean genomic survey: BAC-end sequences near RFLP and SSR markers.

We are building a framework physical infrastructure across the soybean genome by using SSR (simple sequence repeat) and RFLP (restriction fragment length polymorphism) markers to identify BACs (bacterial artificial chromosomes) from two soybean BAC libraries. The libraries were prepared from two genotypes, each digested with a different restriction enzyme. The BACs identified by each marker were grouped into contigs. We have obtained BAC- end sequence from BACs within each contig. The sequences were analyzed by the University of Minnesota Center for Computational Genomics and Bioinformatics using BLAST algorithms to search nucleotide and protein databases. The SSR-identified BACs had a higher percentage of significant BLAST hits than did the RFLP-identified BACs. This difference was due to a higher percentage of hits to repetitive-type sequences for the SSR-identified BACs that was offset in part, however, by a somewhat larger proportion of RFLP-identified significant hits with similarity to experimentally defined genes and soybean ESTs (expressed sequence tags). These genes represented a wide range of metabolic functions. In these analyses, only repetitive sequences from SSR-identified contigs appeared to be clustered. The BAC-end sequences also allowed us to identify microsynteny between soybean and the model plants Arabidopsis thaliana and Medicago truncatula. This map-based approach to genome sampling provides a means of assaying soybean genome structure and organization.

Algorithms↗
PubMed2001

The impact of prostate biopsy on patient well-being: a prospective study of voiding impairment.

PURPOSE: We studied the possible association of transrectal ultrasound guided prostate biopsy with voiding impairment. MATERIALS AND METHODS: A total of 211 consecutive patients were prospectively enrolled. International Prostate Symptom Score (I-PSS), subjective voiding complaints and retention were recorded in 3 personal interviews before biopsy, and on postoperative days 7 and 30. RESULTS: Of the 204 patients who voided via the urethra at biopsy 52 (25%) reported subjective voiding impairment on postoperative day 7, including 12% who defined difficult voiding as mild-1 to 2 points on a 0 to 5 scale, 8% as moderate-3/5 and 5% as severe-4 to 5/5. In 5 of the latter cases (2.5%) acute urinary retention necessitated urethral catheter insertion. Transition zone volume, which was 42 ml. or larger in all patients in urinary retention, was the only independent variable associated with patient report of subjective difficult voiding and acute urinary retention during week 1 after biopsy (p = 0.03). Baseline I-PSS greater than 20 points indicated a risk of an acute transient increase in I-PSS on postoperative day 7. CONCLUSIONS: Transient voiding impairment may be precipitated by ultrasound guided prostate biopsy. To decrease this morbidity appropriate evaluation and possible treatment for bladder outlet obstruction are justified in patients with a larger transition zone and in those with preoperative baseline I-PSS greater than 20 points.

Adult↗
PubMed2000

The TolA-recognition site of colicin N. ITC, SPR and stopped-flow fluorescence define a crucial 27-residue segment.

Colicins translocate across the Escherichia coli outer membrane and periplasm by interacting with several receptors. After first binding to the outer membrane surface receptors via their central region, they interact with TolA or TonB proteins via their N-terminal region. Colicin N residues critical to TolA binding have been discovered, but the full extent of any colicin TolA site is unknown. We present, for the first time, a fully mapped TolA binding site for a colicin. It was determined through the use of alanine-scanning mutants, glutathione S-transferase fusion peptides and Biacore/fluorescence binding studies. The minimal TolA binding region is 27 residues and of similar size to the TolA binding region of bacteriophage g3p-D1 protein. Stopped-flow kinetic studies show that the binding to TolA follows slow association kinetics. The role of other E. coli Tol proteins in colicin translocation was also investigated. Isothermal titration microcalorimetry (ITC) and in vivo studies conclusively show that colicin N translocation does not require the presence of TolB. ITC also demonstrated colicin A interaction with TolB, and that colicin A in its native state does not interact with TolAII-III. Colicin N does not bind TolR-II. The TolA protein is shown to be unsuitable for direct immobilisation in Biacore analysis.

Amino Acid Sequence↗
PubMed2000

Heat capacity of hydrogen-bonded networks: an alternative view of protein folding thermodynamics.

Large changes in heat capacity (deltaCp) have long been regarded as the characteristic thermodynamic signature of hydrophobic interactions. However, similar effects arise quite generally in order-disorder transitions in homogeneous systems, particularly those comprising hydrogen-bonded networks, and this may have significance for our understanding of protein folding and other biomolecular processes. The positive deltaCp associated with unfolding of globular proteins in water, thought to be due to hydrophobic interactions, is also typical of the values found for the melting of crystalline solids, where the effect is greatest for the melting of polar compounds, including pure water. This suggests an alternative model of protein folding based on the thermodynamics of phase transitions in hydrogen-bonded networks. Folded proteins may be viewed as islands of cooperatively-ordered hydrogen-bonded structure, floating in an aqueous network of less-well-ordered H-bonds in which the degree of hydrogen bonding decreases with increasing temperature. The enthalpy of melting of the protein consequently increases with temperature. A simple algebraic model, based on the overall number of protein and solvent hydrogen bonds in folded and unfolded states, shows how deltaCp from this source could match the hydrophobic contribution. This confirms the growing view that the thermodynamics of protein folding, and other interactions in aqueous systems, are best described in terms of a mixture of polar and non-polar effects in which no one contribution is necessarily dominant.

Algorithms↗
PubMed2000

Population genetics of ice age brown bears.

The Pleistocene was a dynamic period for Holarctic mammal species, complicated by episodes of glaciation, local extinctions, and intercontinental migration. The genetic consequences of these events are difficult to resolve from the study of present-day populations. To provide a direct view of population genetics in the late Pleistocene, we measured mitochondrial DNA sequence variation in seven permafrost-preserved brown bear (Ursus arctos) specimens, dated from 14,000 to 42,000 years ago. Approximately 36,000 years ago, the Beringian brown bear population had a higher genetic diversity than any extant North American population, but by 15,000 years ago genetic diversity appears similar to the modern day. The older, genetically diverse, Beringian population contained sequences from three clades now restricted to local regions within North America, indicating that current phylogeographic patterns may provide misleading data for evolutionary studies and conservation management. The late Pleistocene phylogeographic data also indicate possible colonization routes to areas south of the Cordilleran ice sheet.

Alaska↗
PubMed2000

Predicting inpatient mortality for pediatric trauma patients with blunt injuries: a better alternative.

PURPOSE: The aim of this study was to identify significant independent predictors of inpatient mortality rates for pediatric victims of blunt trauma and to develop a formula for predicting the probability of inpatient mortality for these patients. METHODS: Emergency department and inpatient data from 2,923 pediatric victims of blunt injury in the New York State Trauma Registry in 1994 and 1995 were used to explore the relationship between patient risk factors and mortality rate. A stepwise logistic regression model with P<.05 was developed using survival status asthe dependent variable. Independent variables included are elements of the Pediatric Trauma Score (PTS), additional elements from the Revised Trauma Score (RTS), the motor response and eye opening components of the Glasgow Coma Scale (GCS), age-specific systolic blood pressure, the AVPU score, and 2 measures of anatomic injury severity (the Injury Severity Score [ISS] and the International Classification of Disease, Ninth Revision-based Injury Severity Score [ICISS]). RESULTS: The only significant independent predictors of severity that emerged were the ICISS, no motor response (best motor response = 1) from the GCS, and the unresponsive component from the AVPU score. The statistical model exhibited an excellent fit (C statistic = .964). The specificity associated with the prediction of inpatient mortality rate based on the presence of 1 or more of these risk factors was .926, and the sensitivity was .944. CONCLUSION: The best independent predictors of inpatient mortality rate for pediatric trauma patients with blunt injuries include variables not specifically contained in the PTS or the RTS: ICISS, no motor response (best motor response = 1) from the GCS, and the unresponsive component of the AVPU score.

Child↗
PubMed2000

Effect of 1-(gamma)linolenyl-3-eicosapentaenoyl propane diol on the growth of human pancreatic carcinoma in vitro and in vivo.

Essential fatty acids such as (gamma)linolenic (GLA) and eicosapentaenoic (EPA) acids have been proposed as anticancer drugs. The aim of this study was to test the effect of a lipid emulsion containing both GLA and EPA in a novel chemical formulation of 1-(gamma)linolenyl-3-eicosapentaenoyl propane diol on the growth of human pancreatic carcinoma in vitro and in nude mice. This compound had a dose-dependent growth-inhibitory effect on human pancreatic cancer cell lines MIA PaCa-2 and Panc-1 in vitro. The concentration necessary for 50% growth inhibition was 25 micromol/l for MIA PaCa-2 and 68 micromol/l for Panc-1 (95% CI 20-29 and 59-77 micromol/l respectively). Nude mice bearing subcutaneous pancreatic tumours produced with the MIA PaCa-2 cell line were treated with the maximum tolerated dose (6.75 mg GLA and 7.3 mg EPA per g of body weight) administered over 10 days by daily intravenous (i.v.) bolus injections. No antitumour effect or major alteration in tumour lipid fatty acid composition was seen in comparison with control animals. Concurrent treatment with parenteral iron (iron saccharate, 5 microg/gram body weight daily) did not make a significant difference. Further improvements in fatty acid delivery mechanisms are necessary before they can become useful anticancer agents.

Animals↗
PubMed2000

Polymorphism of the transforming growth factor-beta 1 gene correlates with the development of coronary vasculopathy following cardiac transplantation.

BACKGROUND: Expression of transforming growth factor-beta1 (TGF-beta1) is central to vascular repair due to its effects on smooth muscle cell, monocyte/macrophage, leucocyte, and extracellular matrix accumulation and proliferation. Genetic polymorphism at position +915 of the TGF-beta1 gene determines the degree of cytokine production in response to injury. We investigated this allelic variation on the development of cardiac transplant-related coronary vasculopathy (CV). METHODS: Using sequence-specific primers to the TGF-beta1 gene region of interest, a polymerase chain reaction (PCR) and gel electrophoresis identified the genotype in 129 cardiac transplant recipients. An association was sought between the presence of a high- (GG) or low/intermediate-producing (CC/GC) genotype and the development of coronary vasculopathy diagnosed by coronary angiography. RESULTS: C allele carriers made up 10.9% of the recipient population but were significantly less likely to develop coronary vasculopathy (p = 0. 0361). Mean time to diagnosis was 1240.5 days in G homozygotes relative to 2266.5 days in C allele carriers (p = 0.002). Pre- and 1-year posttransplant clinical variables were equivalent between the 2 groups. Multivariate analysis identified the GG genotype (p = 0. 042, hazard ratio 3.01, [95% CI, 1.056-10.99]), donor age (p = 0.002, hazard ratio 1.063, [95% CI, 1.029-1.097]), and number of acute-rejection episodes of grade 3 or greater in the first year (p = 0.029, hazard ratio 1.11, [95% CI, 1.05-1.26]) as significant predictors of vasculopathy. CONCLUSION: This study demonstrates a correlation between a high-producing TGF-beta1 genotype and an earlier onset of cardiac-transplant coronary vasculopathy. This gives an important insight into the pathophysiology of cardiac transplant vasculopathy and suggests new treatment options.

Adult↗
PubMed2000

The ABA-1 allergen of Ascaris lumbricoides: sequence polymorphism, stage and tissue-specific expression, lipid binding function, and protein biophysical properties.

The ABA-1 protein of Ascaris lumbricoides (of humans) and Ascaris suum (of pigs) is abundant in the pseudocoelomic fluid of the parasites and also appears to be released by the tissue-parasitic larvae and the adult stages. The genes encoding the polyprotein precursor of ABA-1 (aba-1) were found to be arranged similarly in the two taxa, comprising tandemly repeating units encoding a large polyprotein which is cleaved to yield polypeptides of approximately 15 kDa which fall into 2 distinct classes, types A and B. The polyprotein possibly comprises only 10 units. The aba-1 gene of A. lumbricoides is polymorphic, and the majority of substitutions observed occur in or near predicted loop regions in the encoded proteins. mRNA for ABA-1 is present in infective larvae within the egg, and in all parasitic stages, but was not detectable in unembryonated eggs. ABA-1 mRNA was confined to the gut of adult parasites, and not in body wall or reproductive tissues. Recombinant protein representing a single A-type unit for the A. lumbricoides aba-1 gene was produced and found to bind retinol (Vitamin A) and a range of fatty acids, including the pharmacologically active lipids lysophosphatidic acid, lysoplatelet activating factor, and there was also evidence of binding to leukotrienes. It failed to bind to any of the anthelmintics screened. Differential Scanning Calorimetry showed that the recombinant protein was highly stable, and unfolded in a single transition at 90.4 degrees C. Analysis of the transition indicated that the protein occurs as a dimer and that the dimer dissociates simultaneously with the unfolding of the monomer units.

Allergens↗
PubMed2000

A randomised placebo controlled trial of the effects of tibolone on blood pressure and lipids in hypertensive women.

The effects of hormone replacement therapy in hypertensive women are controversial. This randomised placebo controlled trial assessed the effect of tibolone 2.5 mg on blood pressure and fasting plasma lipids in 29 hypertensive postmenopausal women over 6 months using a 2:1 randomisation to tibolone. The primary clinical end-point was mean office blood pressure. At 6 months systolic blood pressure declined by 5.30 +/- 2.87% vs 4.94 +/- 3.37% whilst diastolic blood pressure declined 5.38 +/- 2.65% vs 0.85 +/- 3.69% on tibolone and placebo respectively. These differences were not statistically significant. Triglycerides decreased by 33.3 +/- 6.1% vs 7.6 +/- 7.9% (P < 0.01) and high-density lipoprotein (HDL)-cholesterol by 21.7 +/- 3.8% vs 2.4 +/- 2.6% (P < 0.01) with tibolone as opposed to placebo. No significant differences were observed in total cholesterol, low-density lipoprotein (LDL)-cholesterol and lipoprotein (a). Fibrinogen levels were reduced by 13.6 +/- 6.8% on tibolone compared to a 19.3 +/- 15.4% rise (P < 0.05) on placebo. This study suggests that tibolone has no deleterious effect on blood pressure in women with hypertension but has contrasting effects on biochemical risk factors. Large-scale studies are required to determine the overall effect of tibolone on cardiovascular morbidity and mortality.

Antihypertensive Agents↗
PubMed2000

Bactericidal action of high-power Nd:YAG laser light on Escherichia coli in saline suspension.

Infra-red light (1064 nm) from a high-power Nd:YAG laser caused more than 90% loss of viability of Escherichia coli during exposures that raised the temperature of PBS suspensions of the bacteria to 50 C in a thermocouple-equipped cuvette. In contrast, there was minimal loss of viability after heating the same suspensions to 50 degrees C in a water-bath, or in a PCR thermal cycler. The mechanism of laser killing at 50 degrees C was explored by differential scanning calorimetry, by laser treatment of transparent and turbid bacterial suspensions, and by optical absorbency studies of E. coli suspensions at 1064 nm. Taken together, the data suggested that the bactericidal action of Nd:YAG laser light at 50 degrees C was due partly to thermal heating and partly to an additional, as yet undefined, mechanism. Scanning electron microscopy revealed localized areas of surface damage on laser-exposed E. coli cells.

Colony Count, Microbial↗
PubMed2000

An examination of the volume-mortality relationship for New York State trauma centers.

OBJECTIVES: New York State Trauma Registry data were analyzed to determine whether there is a significant relationship between the volume of trauma patients treated by a trauma center and its risk-adjusted inpatient mortality rate. METHODS: Stepwise logistic regression was used to identify significant independent predictors of mortality, their weights, and the probability of in-hospital mortality for each patient. These data were then used to calculate risk-adjusted mortality rates for various ranges of hospital volume. Ranges were identified on the basis of homogeneity of mortality rates, the number of hospitals in each range, and the number of patients in each range. Three volume measures were used: (1) total annual volume of trauma cases > or = 1200 and total annual volume > or = 240 for patients with Injury Severity Score (ISS) > or = 15 (equivalent to American College of Surgeons [ACS] criteria), (2) total annual volume of patients with ISS > or = 15, and (3) total annual volume of cases in the Registry (approximately, inpatients with ISS > or = 9). RESULTS: Results show that the 35 New York State trauma centers not meeting the ACS criteria had lower, but not significantly lower, observed and risk-adjusted mortality rates (7.62% and 8.25%, respectively) than the corresponding rates for the 8 New York State trauma centers that met the ACS criteria (9.36% and 8.83%, respectively). Regarding the other two criteria, hospital ranges representing lower annual volumes tended to have somewhat lower, although not significantly lower, observed and risk-adjusted mortality rates. For example, using a total annual volume for patients with ISS > or = 15, the risk-adjusted mortality rates for the volume ranges 1-150, 151-250, and 251+ were 7.78%, 9.23%, and 8.70%, respectively. CONCLUSIONS: We were unable to document an inverse relationship between hospital volume and inpatient mortality rate for trauma centers in New York State. Volume criteria should not be considered indicators of the quality of trauma care.

Age Distribution↗
PubMed2000

Accounting for intubation status in predicting mortality for victims of motor vehicle crashes.

BACKGROUND: Two of the important predictors of mortality for trauma patients are the Glasgow Coma Scale and the respiratory rate. However, for intubated patients, the verbal response component of the Glasgow Coma Scale and the respiratory rate cannot be accurately obtained. This study extends previous work that attempts to predict mortality accurately for intubated patients without using verbal response and respiratory rate. METHODS: The New York State Trauma Registry was used to identify 1994 and 1995 victims of motor vehicle crashes (MVCs). For the subset of patients who were not intubated, we developed two statistical models to predict mortality: one did not contain verbal response or respiratory rate, and the other contained a predicted verbal response. These were compared with a model that did include verbal response and respiratory rate. We also compared the predictive abilities of the first two models for all MVC patients (intubated and nonintubated) and determined the extent to which intubated patients were at increased risk of dying in the hospital after having adjusted for other predictors of mortality. RESULTS: For nonintubated patients, the statistical model without verbal response and the model with predicted verbal response had slightly better discrimination and worse calibration than the model that included verbal response and respiratory rate. Predicted verbal response did not improve the strength of the model without verbal response. For all MVC patients (intubated and nonintubated), predicted verbal response was not a significant predictor of mortality when used in combination with the other predictors. Intubation status was a significant predictor, with intubated patients having a higher probability of dying in the hospital than patients with otherwise identical risk factors. CONCLUSION: Inpatient mortality for intubated MVC patients can be accurately predicted without respiratory rate or verbal response. There appears to be no need for predicted verbal response to be part of the prediction formula, but intubation status is an important independent predictor of mortality and should be used in statistical models that predict mortality for MVC patients.

Accidents, Traffic↗
PubMed2000

Chest pain in the emergency department.

The assessment of patients with chest pain is challenging for any emergency physician because of the spectrum of illness covered by this symptom. Patients may have a serious life-threatening condition or a trivial self-limiting illness. This article presents an approach to the assessment and early management of patients presenting with acute non-traumatic chest pain in the emergency department.

Acute Disease↗
PubMed2000

Cloning and characterization of the murine coagulation factor X gene.

The gene encoding murine coagulation factor X (fX) was isolated and characterized from a lamdaFIX II library generated from murine genomic DNA. The 20130 bp sequence contains 18049 nucleotides that extend from the initiating methionine to the polyadenylation site. 1056 nucleotides 5' of the start codon were determined and contain putative start sites for the FX mRNA as well as sites for binding of putative transcription factors. The sequence extends 1024 3' of the polyadenylation site. The gene contains 8 exons and 7 introns which were determined by comparing the mouse FX cDNA and gene sequences. The exonic structure of the gene is similar to that of the other mammalian vitamin K-dependent serine proteases of the coagulation system. These include an exon encoding the prepropepetide, the gla-domain, a short helical stack, two exons for the two EGF domains, the activation pepetide, and two exons encoding the serine protease domain. The 5' sequence of the mouse FX gene overlaps with the 3' region of the FVII gene indicating that the murine FVII and FX gene are arranged in a head to tail arrangement as they are in humans.

Animals↗
PubMed2000

Are women discriminated against for lipid lowering therapy? Results from a prospective cohort of women with coronary artery disease.

The objective of the study was to compare the lipid management of men and women with documented coronary artery disease in 587 patients (433 men and 154 women) undergoing coronary angiography between 1991 and 1995. A fasting total cholesterol (TC) was measured in all patients on the morning of angiography. A postal/telephone follow-up was carried out one year after angiography in a subpopulation of 278 patients (194 men and 84 women) who were not taking lipid-lowering therapy (LLT) or whose TC was > 5.2 mmol/l at the time of angiography. At baseline, mean TC was 5.89 mmol/l (SE 0.06) in the men and 6.47 mmol/l (SE 0.09) in the women (p = < 0.0001). Action or recommendation to institute LLT was taken in 141 (32.7%) men and 62 (40.3%) women (p = 0.09). In the follow-up population, comparing men with women, 74 (38.3%) vs 39 (46.4%) were taking LLT (p = 0.21); 56 (28.9%) vs 26 (31.0%) had not undergone repeat TC testing (p = 0.73); when performed, repeat TC was 5.75 (0.09) mmol/l vs 5.64 (0.16) mmol/l (p = 0.53); mean decrease in TC between baseline and follow-up was 0.86 (0.10) mmol/l vs 1.01 (0.21) mmol/l (p = 0.51). There was no significant gender difference in lipid management either at the time of coronary angiography or subsequent follow-up, although the level of lipid-lowering drug use remained inadequate in both sexes.

Cholesterol↗
PubMed1999

Quantitation of metal ion and DNA junction binding to the Holliday junction endonuclease Cce1.

Cce1 is a magnesium-dependent Holliday junction endonuclease involved in the resolution of recombining mitochondrial DNA in Saccharomyces cerevisiae. Cce1 binds four-way DNA junctions as a dimer, opening the junction into an extended, 4-fold symmetric structure, and resolves junctions by the introduction of paired nicks in opposing strands at the point of strand exchange. In the present study, we have examined the interactions of wild-type Cce1 with a noncleavable four-way DNA junction and metal ions (Mg(2+) and Mn(2+)) using isothermal titration calorimetry, EPR, and gel electrophoresis techniques. Mg(2+) or Mn(2+) ions bind to Cce1 in the absence of DNA junctions with a stoichiometry of two metal ions per Cce1 monomer. Cce1 binds to four-way junctions with a stoichiometry of two Cce1 dimers per junction molecule in the presence of EDTA, and one dimer of Cce1 per junction in 15 mM magnesium. The presence of 15 mM Mg(2+) dramatically reduces the affinity of Cce1 for four-way DNA junctions, by about 900-fold. This allows an estimation of DeltaG degrees for stacking of four-way DNA junction 7 of -4.1 kcal/mol, consistent with the estimate of -3.3 to -4.5 kcal/mol calculated from branch migration and NMR experiments [Overmars and Altona (1997) J. Mol. Biol. 273, 519-524; Panyutin et al. (1995) EMBO J. 14, 1819-1826]. The striking effect of magnesium ions on the affinity of Cce1 binding to the four-way junction is predicted to be a general one for proteins that unfold the stacked X-structure of the Holliday junction on binding.

Binding Sites↗