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Biomedical subjects

A Cooper

Publications and source records attributed to A Cooper.

At least 73 records · Page 4Linked to original sources

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↗

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↗

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↗

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↗

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↗

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↗

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↗

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↗

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↗

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↗

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↗

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↗

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↗

Relationships of the extinct moa-nalos, flightless Hawaiian waterfowl, based on ancient DNA.

The extinct moa-nalos were very large, flightless waterfowl from the Hawaiian islands. We extracted, amplified and sequenced mitochondrial DNA from fossil moa-nalo bones to determine their systematic relationships and lend insight into their biogeographical history. The closest living relatives of these massive, goose-like birds are the familiar dabbling ducks (tribe Anatini). Moa-nalos, however, are not closely related to any one extant species, but represent an ancient lineage that colonized the Hawaiian islands and evolved flightlessness long before the emergence of the youngest island, Hawaii, from which they are absent. Ancient DNA yields a novel hypothesis for the relationships of these bizarre birds, whereas the evidence of phylogeny in morphological characters was obscured by the evolutionary transformation of a small, volant duck into a giant, terrestrial herbivore.

Animals↗

Homing in on the role of transition metals in the HNH motif of colicin endonucleases.

The cytotoxic domain of the bacteriocin colicin E9 (the E9 DNase) is a nonspecific endonuclease that must traverse two membranes to reach its cellular target, bacterial DNA. Recent structural studies revealed that the active site of colicin DNases encompasses the HNH motif found in homing endonucleases, and bound within this motif a single transition metal ion (either Zn(2+) or Ni(2+)) the role of which is unknown. In the present work we find that neither Zn(2+) nor Ni(2+) is required for DNase activity, which instead requires Mg(2+) ions, but binding transition metals to the E9 DNase causes subtle changes to both secondary and tertiary structure. Spectroscopic, proteolytic, and calorimetric data show that, accompanying the binding of 1 eq of Zn(2+), Ni(2+), or Co(2+), the thermodynamic stability of the domain increased substantially, and that the equilibrium dissociation constant for Zn(2+) was less than or equal to nanomolar, while that for Co(2+) and Ni (2+) was micromolar. Our data demonstrate that the transition metal is not essential for colicin DNase activity but rather serves a structural role. We speculate that the HNH motif has been adapted for use by endonuclease colicins because of its involvement in DNA recognition and because removal of the bound metal ion destabilizes the DNase domain, a likely prerequisite for its translocation across bacterial membranes.

Bacterial Proteins↗

Formation and biochemical characterization of tube/pelle death domain complexes: critical regulators of postreceptor signaling by the Drosophila toll receptor.

In Drosophila, the Toll receptor signaling pathway is required for embryonic dorso-ventral patterning and at later developmental stages for innate immune responses. It is thought that dimerization of the receptor by binding of the ligand spätzle causes the formation of a postreceptor activation complex at the cytoplasmic surface of the membrane. Two components of this complex are the adaptor tube and protein kinase pelle. These proteins both have "death domains", protein interaction motifs found in a number of signaling pathways, particularly those involved in apoptotic cell death. It is thought that pelle is bound by tube during formation of the activation complexes, and that this interaction is mediated by the death domains. In this paper, we show using the yeast two-hybrid system that the wild-type tube and pelle death domains bind together. Mutant tube proteins which do not support signaling in the embryo are also unable to bind pelle in the 2-hybrid assay. We have purified proteins corresponding to the death domains of tube and pelle and show that these form corresponding heterodimeric complexes in vitro. Partial proteolysis reveals a smaller core consisting of the minimal death domain sequences. We have studied the tube/pelle interaction with the techniques of surface plasmon resonance, analytical ultracentrifugation and isothermal titration calorimetry. These measurements produce a value of K(d) for the complex of about 0.5 microM.

Amino Acid Sequence↗

A family IIb xylan-binding domain has a similar secondary structure to a homologous family IIa cellulose-binding domain but different ligand specificity.

BACKGROUND: Many enzymes that digest polysaccharides contain separate polysaccharide-binding domains. Structures have been previously determined for a number of cellulose-binding domains (CBDs) from cellulases. RESULTS: The family IIb xylan-binding domain 1 (XBD1) from Cellulomonas fimi xylanase D is shown to bind xylan but not cellulose. Its structure is similar to that of the homologous family IIa CBD from C. fimi Cex, consisting of two four-stranded beta sheets that form a twisted 'beta sandwich'. The xylan-binding site is a groove made from two tryptophan residues that stack against the faces of the sugar rings, plus several hydrogen-bonding polar residues. CONCLUSIONS: The biggest difference between the family IIa and IIb domains is that in the former the solvent-exposed tryptophan sidechains are coplanar, whereas in the latter they are perpendicular, forming a twisted binding site. The binding sites are therefore complementary to the secondary structures of the ligands cellulose and xylan. XBD1 and CexCBD represent a striking example of two proteins that have high sequence similarity but a different function.

Amino Acid Sequence↗

Independently melting modules and highly structured intermodular junctions within complement receptor type 1.

A segment of complement receptor type 1 (CR1) corresponding to modules 15-17 was overexpressed as a functionally active recombinant protein with N-glycosylation sites ablated by mutagenesis (referred to as CR1 approximately 15-17(-)). A protein consisting of modules 15 and 16 and another corresponding to module 16 were also overexpressed. Comparison of heteronuclear nuclear magnetic resonance (NMR) spectra for the single, double, and triple module fragments indicated that module 16 makes more extensive contacts with module 15 than with module 17. A combination of NMR, differential scanning calorimetry, circular dichroism, and tryptophan-derived fluorescence indicated a complex unfolding pathway for CR1 approximately 15-17(-). As temperature or denaturant concentration was increased, the 16-17 junction appeared to melt first, followed by the 15-16 junction, and module 17 itself; finally, modules 15 and 16 became denatured. Modules 15 and 16 adopted an intermediate state prior to total denaturation. These results are compared with a previously published study [Clark, N. S., Dodd, I, Mossakowska, D. E., Smith, R. A. G., and Gore, M. G. (1996) Protein Eng. 9, 877-884] on a fragment consisting of the N-terminal three CR1 modules which appeared to melt as a single unit.

Amino Acid Sequence↗