PubMed Health⌕ Search

Biomedical subjects

A Cooper

Publications and source records attributed to A Cooper.

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

A molecular analysis of dietary diversity for three archaic Native Americans.

DNA was extracted from three fecal samples, more than 2,000 years old, from Hinds Cave, Texas. Amplification of human mtDNA sequences showed their affiliation with contemporary Native Americans, while sequences from pronghorn antelope, bighorn sheep, and cottontail rabbit allowed these animals to be identified as part of the diet of these individuals. Furthermore, amplification of chloroplast DNA sequences identified eight different plants as dietary elements. These archaic humans consumed 2-4 different animal species and 4-8 different plant species during a short time period. The success rate for retrieval of DNA from paleofeces is in strong contrast to that from skeletal remains where the success rate is generally low. Thus, human paleofecal remains represent a source of ancient DNA that significantly complements and may in some cases be superior to that from skeletal tissue.

Animals↗
PubMed2001

Complete mitochondrial genome sequences of two extinct moas clarify ratite evolution.

The origin of the ratites, large flightless birds from the Southern Hemisphere, along with their flighted sister taxa, the South American tinamous, is central to understanding the role of plate tectonics in the distributions of modern birds and mammals. Defining the dates of ratite divergences is also critical for determining the age of modern avian orders. To resolve the ratite phylogeny and provide biogeographical data to examine these issues, we have here determined the first complete mitochondrial genome sequences of any extinct taxa--two New Zealand moa genera--along with a 1,000-base-pair sequence from an extinct Madagascan elephant-bird. For comparative data, we also generated 12 kilobases of contiguous sequence from the kiwi, cassowary, emu and two tinamou genera. This large dataset allows statistically precise estimates of molecular divergence dates and these support a Late Cretaceous vicariant speciation of ratite taxa, followed by the subsequent dispersal of the kiwi to New Zealand. This first molecular view of the break-up of Gondwana provides a new temporal framework for speciation events within other Gondwanan biota and can be used to evaluate competing biogeographical hypotheses.

Animals↗
PubMed2001

Thermodynamics of ion-induced RNA folding in the hammerhead ribozyme: an isothermal titration calorimetric study.

The hammerhead ribozyme undergoes a well-defined two-stage conformational folding process, induced by the binding of magnesium ions. In this study, we have used isothermal titration calorimetry to analyze the thermodynamics of magnesium binding and magnesium ion-induced folding of the ribozyme. Binding to the natural sequence ribozyme is strongly exothermic and can be analyzed in terms of sequential interaction at two sites with association constants K(A) = 480 and 2840 M(-1). Sequence variants of the hammerhead RNA give very different isothermal titration curves. An A14G variant that cannot undergo ion-induced folding exhibits endothermic binding. By contrast, a deoxyribose G5 variant that can undergo only the first of the two folding transitions gives a complex titration curve. However, despite these differences the ITC data for all three species can be analyzed in terms of the sequential binding of magnesium ions at two sites. While the binding affinities are all in the region of 10(3) M(-1), corresponding to free energies of Delta G degrees = -3.5 to -4 kcal mol(-1), the enthalpic and entropic contributions show much greater variation. The ITC experiments are in good agreement with earlier conformational studies of the folding of the ion-induced folding of the hammerhead ribozyme.

Adenine↗
PubMed2001

Induction of strong hepatitis B virus (HBV) specific T helper cell and cytotoxic T lymphocyte responses by therapeutic vaccination in the trimera mouse model of chronic HBV infection.

Humanized BALB/c mice (termed trimera mice) conditioned by lethal total body irradiation and bone marrow transplantation from SCID mice have been described to support rapid engraftment of human peripheral blood mononuclear cells (PBMC) and the induction of strong B and T cell responses after immunization in vivo. Moreover, these mice can be infected with the hepatitis B and C viruses (HBV, HCV). The current study employed this model to study therapeutic vaccination approaches against the HBV. Thus, strong primary Th cell responses against the HBV core (HBc) and the Borrelia burgdorferi control antigen were induced by transfer of antigen-loaded dendritic cells together with autologous PBMC from HBV-naive donors as well as by vaccination with high doses of antigen or a DNA plasmid encoding for HBcAg. Moreover, primary peptide-specific CTL responses against the immunodominant epitope HBc(18 - 27) were induced by HBc particle or DNA vaccination of chimera engrafted with HBV-naive PBMC. Finally, strong HBc-specific Th cell and antibody responses were induced by HBc or DNA vaccination of mice reconstituted with PBMC from a chronic HBV patient. Thus, since HBc represents the immunodominant antigen in self-limited HBV infection, HBc particles or DNA vectors are good candidates for therapeutic vaccination, that will be further studied in our model and clinical studies.

Animals↗
PubMed2001

Co-existence of lysosomal storage diseases in a consanguineous family.

Lysosomal storage diseases are rare and coexistence of more than one in a family can present a diagnostic challenge as illustrated by this study. The index case born to consanguineous Asian parents presented with developmental delay. Investigations led to an incidental finding of Fabry disease. After numerous additional investigations over a year, a second diagnosis of aspartylglucosaminuria (AGU) was made. A family history of renal disease and developmental delay was disclosed. The sister and first cousin of the index case were diagnosed as homozygous for AGU, but do not have Fabry disease. The younger brother has since been diagnosed with both Fabry disease and AGU. Another cousin has learning difficulties and fits, but is heterozygous for AGU, and possibly has another uncharacterised autosomal recessive disorder. In a family with consanguinity when the clinical picture in an individual is not fully explained by the presence of one rare metabolic disease, it is essential to investigate further for the presence of others.

Acetylglucosamine↗
PubMed2001

Prehospital endotracheal intubation for severe head injury in children: a reappraisal.

Controversy exists regarding the efficacy of prehospital assisted ventilation by endotracheal intubation (ETI) versus bag-valve-mask (BVM) in serious pediatric head injury. The National Pediatric Trauma Registry (NPTR-3) data set was analyzed to examine this question. NPTR-3 (n = 31,464) was queried regarding the demographics, injury mechanism, injury severity, prehospital interventions, transport mode, mortality rate, injury complications, procedure and equipment failure or complications, and functional outcome of seriously head-injured patients (n = 578) with comparable injury mechanisms and injury severity who received endotracheal intubation (ETI) (n = 479; 83%) versus those who received BVM (n = 99; 17%). Mortality rate was virtually identical between the 2 groups (ETI = 48%, BVM = 48%), although children receiving ETI were significantly older (P < .01), more often transported by helicopter (P < .01), and more often received intravenous fluid in the field (P < .05). However, injury complications affecting nearly every body system or organ (except kidney, gut, and skin) occurred less often in children receiving ETI (ETI = 58%, BVM = 71%, P < .05). Procedure and equipment failure or complications, and functional outcome, were similar between the 2 groups. Prehospital endotracheal intubation appears to offer no demonstrable survival or functional advantage when compared with prehospital bag-valve-mask for prehospital assisted ventilation in serious pediatric head injury. Injury complications appear to occur somewhat less often among patients intubated in the field.

Adolescent↗
PubMed2001

Overcoming methodological concerns in the investigation of online sexual activities.

Online Sexual Activity (OSA) is an important and growing phenomenon. Prior research in this area has been criticized on methodological grounds. This study examines the reliability of Internet research regarding online sexual activities by comparing a selected random sample to a convenience sample. Participation in the selected random sample was limited to every 1,000th visitor to the MSNBC website in June 2000. Participation in the convenience sample was available to anyone with access to the Internet during the same time period. Most differences between these samples indicated that, relative to a selected random sample, a significantly greater proportion of Internet users in the convenience sample had a heavier involvement with OSA, including online sexual difficulties. We discuss the methodological and clinical implications of this finding.

Adult↗
PubMed2001

Follicular fluid responds endothermically to aqueous dilution.

BACKGROUND: Studies suggest that ovarian follicles are cooler than their surrounding tissues. The mechanism of this remarkable phenomenon is unclear. We postulate that endothermic reactions accompany the growth-associated hydration of follicular fluid. METHODS: We performed two types of experiment, using human and animal follicular fluids. In the first, saline (50 microl) was injected into follicular fluid (500 microl) held in an equilibrated incubator, with monitoring of sample temperature. In the second, an adiabatic microcalorimeter recorded thermal shifts after injection of buffer (10 microl) into previously dialysed samples (1.4 ml). The relevance of changes observed was assessed by mathematical modelling. RESULTS: In the incubator study, 9/17 bovine and 6/12 human fluids showed a temperature fall (0.05-0.2 degrees C). Cooling was delayed by up to 2 min but sustained for 7-25 min. Remaining fluids showed no change. In the microcalorimeter, 4/9 human, 4/6 bovine, 5/5 porcine and 1/4 equine samples showed an endothermic response. Remaining samples showed either no response (bovine) or exothermy (human, equine). Pre-concentration of human follicular fluid amplified the endothermy or reversed the exothermy. Modelling indicated that the incubator-type response was of appropriate magnitude to explain follicular hypothermy. CONCLUSION: Follicular fluid responds endothermically to aqueous dilution and may contribute to follicular cooling during growth.

Animals↗
PubMed2001

Physicochemical consequences of the perdeuteriation of glutathione S-transferase from S. japonicum.

Glutathione S:-transferase (GST) from Schistosoma japonicum has been prepared in both normal protiated (pGST) and fully deuteriated (dGST) form by recombinant DNA technology. Electrospray mass spectrometry showed that the level of deuteriation in dGST was 96% and was homogeneous across the sample. This result is attributed to the use of a deuterium-tolerant host Escherichia coli strain in the preparation of the protein. 10 heteroatom-bound deuteriums (in addition to the carbon-bound deuteriums) were resistant to exchange when dGST was incubated in protiated buffer. The physicochemical and biological properties of the two proteins were compared. dGST was relatively less stable to heat denaturation and to proteolytic cleavage than was pGST. The midpoint transition temperature for pGST was 54.9 degrees C, whereas that for dGST was 51.0 degrees C. Static light-scattering measurements revealed that the association behavior of dGST is also different from that of pGST. The perdeuteriated enzyme shows a tendency to associate into dimers of the fundamental dimer. This is in contrast with results that have been obtained for other perdeuteriated proteins in which perdeuteriation has been shown to promote dissociation of aggregates. dGST showed a similar K(m) to pGST; similar results had been obtained previously with bacterial alkaline phosphatase. However, whereas the alkaline phosphatase showed a reduced rate of catalysis on deuteriation, dGST exhibited a slightly higher rate of catalysis than pGST. It is clear that the bulk substitution of deuterium for protium has significant effects on the properties of proteins. Until many more examples have been studied, it will be difficult to predict these effects for any given protein. Nevertheless, deuteriation represents an intriguing method of preparing functional analogs of recombinant proteins.

Animals↗
PubMed2001

Biochemical and X-ray crystallographic studies on shikimate kinase: the important structural role of the P-loop lysine.

Shikimate kinase, despite low sequence identity, has been shown to be structurally a member of the nucleoside monophosphate (NMP) kinase family, which includes adenylate kinase. In this paper we have explored the roles of residues in the P-loop of shikimate kinase, which forms the binding site for nucleotides and is one of the most conserved structural features in proteins. In common with many members of the P-loop family, shikimate kinase contains a cysteine residue 2 amino acids upstream of the essential lysine residue; the side chains of these residues are shown to form an ion pair. The C13S mutant of shikimate kinase was found to be enzymatically active, whereas the K15M mutant was inactive. However, the latter mutant had both increased thermostability and affinity for ATP when compared to the wild-type enzyme. The structure of the K15M mutant protein has been determined at 1.8 A, and shows that the organization of the P-loop and flanking regions is heavily disturbed. This indicates that, besides its role in catalysis, the P-loop lysine also has an important structural role. The structure of the K15M mutant also reveals that the formation of an additional arginine/aspartate ion pair is the most likely reason for its increased thermostability. From studies of ligand binding it appears that, like adenylate kinase, shikimate kinase binds substrates randomly and in a synergistic fashion, indicating that the two enzymes have similar catalytic mechanisms.

2,2'-Dipyridyl↗
PubMed2001

High resolution CISS imaging of the spine.

Spatial resolution remains one of the major problems and goals in spinal imaging. The high spatial resolution afforded by a novel sequence, constructive interference in steady state (CISS), provides a further refinement to MRI, the modality of choice in the investigation of suspected intraspinal pathology. Both complex and subtle abnormalities are more fully elucidated using CISS. It is now used in our institution as an adjunct to conventional imaging sequences in the diagnostic evaluation of complex intraspinal pathology. The anatomical information provided by CISS is of particular value in planning surgical interventions, most notably in the management of intraaxial and extraaxial cystic abnormalities, dysraphic malformations and disturbances of cerebrospinal fluid circulation, including post-traumatic and post-surgical scarring.

Arachnoiditis↗
PubMed2001

Attitudes, practices, and preferences of pediatricians regarding initiation of hepatitis B immunization at birth.

OBJECTIVES: To explore practices and attitudes of pediatricians toward administration of the first dose of hepatitis B vaccine to infants, and to identify factors influencing the decision of pediatricians to initiate immunization at birth versus at 1 to 2 months of age. METHODS: A random sample of 600 pediatricians obtained from the American Academy of Pediatrics membership database was surveyed by mail. RESULTS: Three hundred eighty (68%) of the 563 pediatricians who were located responded to the survey. Of these 380 pediatricians, 279 provided routine immunizations to children. Of the 270 pediatricians who vaccinated children with hepatitis B vaccine and indicated their practice regarding the birth dose, 50% offered the first dose of hepatitis B vaccine at birth to all infants; the rest either offered the vaccine at birth only to infants of hepatitis B surface antigen-positive mothers and mothers whose serostatus is unknown, or did not offer the birth dose to any infants at all. Practicing in the inner city, working for a medical school or government hospital, and living in a state with universal immunization supply policies were associated with the respondent giving the birth dose. The strongest perceived barriers to giving the birth dose in the hospital were the difficulty tracking these vaccines (39%), the increased cost (27%), and the lack of reimbursement from insurance companies (26%). If a combination vaccine that includes hepatitis B; diphtheria, tetanus, pertussis (diphtheria and tetanus toxoids and acellular pertussis vaccine); and polio (inactivated poliovirus vaccine) antigens become available in the near future, then 38% of physicians who currently give the birth dose to all infants would prefer to wait until 2 months of age to initiate hepatitis B immunization. CONCLUSIONS: Efforts to achieve high implementation of hepatitis B birth dose administration may falter once a hepatitis B-containing pentavalent combination vaccine becomes available. Programmatic efforts should ensure prevention of perinatal hepatitis B virus transmission through universal prenatal hepatitis B surface antigen screening and immunoprophylaxis of high-risk newborn infants.

Health Knowledge, Attitudes, Practice↗
PubMed2001

The South African National Non-Natural Mortality Surveillance System--rationale, pilot results and evaluation.

BACKGROUND: While individual mortuaries have recorded data for non-natural deaths in time-limited studies, there have been no systematic efforts to draw forensic-medical services and state mortuaries into a nationwide fatal injury surveillance system. Beginning in June 1998, the National Non-Natural Mortality Surveillance System (NMSS) commenced pilot operation. OBJECTIVE: To evaluate the NMSS and illustrate its utility from sample findings. DESIGN: Data entered into the system by mortuary staff were checked against a random sample of cases for which separate forms were completed by an independent researcher. Process observations and follow-up with data users were used to assess the system's acceptability, timeliness and data usefulness. SETTING: Eighteen mortuaries in six provinces representing approximately 35,000 cases per year, or around 50% of all non-natural deaths. PARTICIPANTS: The National Departments of Health; Safety and Security; and Arts, Culture, Science and Technology; national and provincial forensic medico-legal services; the South African Police Services; universities and science research councils. MAIN OUTCOME MEASURES: Surveillance system simplicity, flexibility, acceptability, sensitivity, positive predictive value, representativeness, timeliness, data usefulness and resources. RESULTS: The NMSS was established at 10 target sites. Lack of equipment, personnel resistance, and closure of some mortuaries prevented implementation in the remaining eight mortuaries. Sensitivity was internally assessed and ranged from 65% to 95% for manner of death. Positive predictive value was also internally measured, and ranged from 74% to 80% for manner of death and from 71% to 82% for mechanism of death. Timeliness was good, and basic reports covering most items were available 6 weeks after a case had been examined. While staff found the system simple, acceptability depended on the individuals involved at different mortuaries, and the system was compromised to some extent by bureaucratic barriers. End users found the data to be of great value. NMSS set-up costs totalled approximately R26,000 per mortuary, and it is estimated that maintenance costs will be R8.00 per case registered. CONCLUSIONS: With minimal resources, the NMSS uses existing investigative procedures to describe and report the epidemiology of fatal injuries. The pilot study demonstrates the feasibility of the system, and identifies the need to remove organisational constraints and individual barriers if it is to be sustained and expanded beyond the pilot sites.

Accidents↗
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↗