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Biomedical subjects

T E Clarke

Publications and source records attributed to T E Clarke.

11 recordsLinked to original sources
PubMed2001

Rapid evolution in the Nebria gregaria group (Coleoptera: Carabidae) and the paleogeography of the Queen Charlotte Islands.

Morphological differentiation in the ground beetles of the Nebria gregaria group, found on the Queen Charlotte Islands, has been used as support for the glacial refugium proposed for the northwest coast of North America. Two members of this species group, N. charlottae and N. louiseae, are restricted to cobble beaches in this archipelago. A third, N. haida, is found only in alpine regions of the archipelago and the adjacent mainland. The remaining two species of the gregaria group, N. lituyae and N. gregaria, show highly restricted distributions in the mountains of the Alaska panhandle and on the beaches of the Aleutian Islands, respectively. To determine the relationships of the five species, we conducted phylogenetic analyses on nucleotide sequence data obtained from five regions of the mitochondrial DNA. In total, 1835 bp were analyzed. The results suggest that one species, N. lituyae, does not belong in the gregaria group, and that only seven mutations separated the two most divergent of the four remaining species. We also conducted random amplified polymorphic DNA fingerprinting analyses on genomic DNA extracted from the five species. Analyses of genetic diversity revealed a lack of molecular differentiation among the Queen Charlotte species, suggesting that these populations may be postglacial in origin and that together N. gregaria, N. charlottae, N. louiseae, and N. haida might represent local variations of a single species. These results are consistent with conclusions derived for the morphological and genetical differentiation among Gasterosteus populations in the archipelago.

Animals↗
PubMed2001

Structural biology of bacterial iron uptake systems.

Numerous bacterial proteins are involved in microbial iron uptake and transport and considerable variation has been found in the uptake schemes used by different bacterial species. However, whether extracting iron from host proteins such as transferrin, lactoferrin or hemoglobin or importing low molecular weight iron-chelating compounds such as heme, citrate or siderophores, Gram-negative pathogenic bacteria typically employ a specific outer membrane receptor, a periplasmic binding protein and two inner membrane associated proteins: a transporter coupled with an ATP-hydrolyzing protein. Often, studies have shown that proteins with similar function but little amino acid sequence homology are structurally related. Elucidation of the structures of the Escherichia coli outer membrane siderophore transport proteins FepA and FhuA have provided the first insights into the conformational changes required for ligand transport through the bacterial outer membrane. The variations between the structures of the prototypical periplasmic ferric binding protein FbpA from Neisseria and Haemophilus influenzae and the unusual E coli periplasmic siderophore binding protein FhuD reveal that the different periplasmic ligand binding proteins exercise distinct mechanisms for ligand binding and release. The structure of the hemophore HasA from Serratia marcescens shows how heme may be extracted and utilized by the bacteria. Other biochemical evidence also shows that the proteins that provide energy for iron transport at the outer membrane, such as the TonB-ExbB-ExbD system, are structurally very similar across bacterial species. Likewise, the iron-sensitive gene regulatory protein Fur is found in most bacteria. To date, no structural information is available for Fur, but the structure for the related protein DxtR has been determined. Together, these three-dimensional structures complement our knowledge of iron transport systems from other pathogenic bacteria, including Pseudomonas aeruginosa, which has a number of homologous iron uptake proteins. More importantly, the current structures for iron transport proteins provide rational starting points for design of novel antimicrobial agents.

Bacteria↗
PubMed2000

Comparative modeling studies of the calmodulin-like domain of calcium-dependent protein kinase from soybean.

Calmodulin-like domain protein kinases (CDPKs) represent a new class of calcium-dependent protein-phosphorylating enzymes that are not activated by calmodulin or phospholipid compounds. They have been found exclusively in plant and protozoal tissues. CDPKs are typified by four distinct domains: an N-terminal leader sequence, a protein kinase (PK) domain, a calmodulin-like domain (CLD), and a junction domain (JD) between the PK domain and CLD. Structural characterization of the CLD of CDPKalpha from soybean was undertaken based on the amino acid sequence homology of CLD to the structurally well-characterized calmodulin (CaM) family of structures. Tertiary models of apo-CLD, Ca(2+)-CLD complex, and intermolecularly bound Ca(2+)-CLD-JD complexes were obtained via automated and non-automated homology building methods. The resulting structures were compared and validated based on energy differences, phi-psi angle distribution, solvent accessibility, and hydrophobic potential. Circular dichroism, one-dimensional, and two-dimensional nuclear magnetic resonance spectroscopy studies of the CLD and peptides encompassing the JD provide experimental support to the models. The results suggest that there is a possible interaction between the CLD and JD domain similar to that of the CaM/calmodulin-dependent protein kinase II system. At low Ca(2+) levels, the JD may act as an autoinhibitory domain for kinase activity, and during calcium activation an intramolecular CLD-JD complex may form, relieving inhibition of the PK domain. Interactions between the JD and the C terminus of the CLD appear to be particularly important. The outcome of this study supports an intramolecular binding model for calcium activation of CDPK, although not exclusively.

Amino Acid Sequence↗
PubMed2000

The structure of the ferric siderophore binding protein FhuD complexed with gallichrome.

Siderophore binding proteins play a key role in the uptake of iron in many gram-positive and gram-negative bacteria. FhuD is a soluble periplasmic binding protein that transports ferrichrome and other hydroxamate siderophores. The crystal structure of FhuD from Escherichia coli in complex with the ferrichrome homolog gallichrome has been determined at 1.9 ¿ resolution, the first structure of a periplasmic binding protein involved in the uptake of siderophores. Gallichrome is held in a shallow pocket lined with aromatic groups; Arg and Tyr side chains interact directly with the hydroxamate moieties of the siderophore. FhuD possesses a novel fold, suggesting that its mechanisms of ligand binding and release are different from other structurally characterized periplasmic ligand binding proteins.

Bacterial Outer Membrane Proteins↗
PubMed1985

The effect of varied stride rate upon shank deceleration in running.

The purpose of this study was to determine the effects of systematic changes in stride rate and length at a given running speed on the peak shank deceleration (PSD) experienced during ground contact. Data were collected from 10 well-trained subjects as they ran on a treadmill at a pace of 3.8 m s-1 (7-min mile-1). Shank deceleration was measured by a lightweight accelerometer which was tightly attached over the distal medial tibia. High-speed films (200 Hz) were taken from a side view to quantify modifications in sagittal plane movement which might have accompanied the stride rate changes. Five stride rate conditions were randomly presented - 10% slower, 5% slower, normal, 5% faster and 10% faster. Average PSD was computed from 10 steps during each condition and testing was repeated on three different occasions. For each session, PSD observed for each condition was normalized to that observed at the normal stride rate in order to minimize the effects of variations in attachment of the accelerometer between and within subjects. The normalized PSD results at each stride rate tested were - normal = 1.0, 10% slower = 1.09, 5% slower = 1.03, 5% faster = 0.96 and 10% faster = 0.91. Significant differences were found between all these means except normal and 5% slower. The kinematic analysis revealed non-significant results for hip, knee and ankle joint angles at touchdown for the various stride rates. Application of the findings to existing analytical models indicated that, for a given running speed, peak impact forces in the ankle and knee joints decreased as stride rate increased.

Acceleration↗
PubMed1983

Effects of shoe cushioning upon ground reaction forces in running.

To determine the effects of widely varying amounts of cushioning upon vertical force (VF) parameters, ten male subjects, (mean weight = 68.0 kg) ran at a speed of 4.5 m . s-1 (6 min/mile pace) and contacted a Kistler force platform. Two shoes were tested: a hard one and a softer shoe that had 50% more cushioning as measured by an instrumented impact tester. Five right footfalls were collected for each shoe on each subject during which the ground reaction forces were sampled at 500 HZ using a PDP 11/34 minicomputer. Eight parameters from the VF data obtained for each trial were selected for analysis and compared statistically using a paired difference t test. It was found [force magnitudes expressed in multiples of body weight (BW)] that the time to the vertical force impact peak (VFIP) was significantly longer (hard = 22.5 ms, soft = 26.6 ms) in the soft shoe; however, no differences were seen in the magnitudes (hard = 2.30 BW, soft = 2.34 BW). The minimum after the VFIP was also significantly delayed in the soft shoe (hard = 33.8 ms, soft = 37.9 ms) and was significantly greater in the soft shoe (hard = 1.46 BW, soft = 1.90 BW). The peak VF propulsive force occurred statistically at the same time in both shoes (hard = 85.7 ms, soft = 84.0 ms), but was significantly greater in the soft shoe (hard = 2.73 BW, soft = 2.83 BW).(ABSTRACT TRUNCATED AT 250 WORDS)

Biomechanical Phenomena↗
PubMed1983

The effects of shoe design parameters on rearfoot control in running.

Control of the amount and/or rate of pronation of the foot which occurs during distance running has been cited as an important consideration for runners when selecting a running shoe. In this study, high-speed movie film was taken from the rear while 10 subjects ran on a treadmill at a pace of 3.8 m X s-1. These subjects wore 36 different shoes in combinations of three midsole hardnesses, three heel flares, and four heel heights. The film data were digitized and used to determine the eversion or inversion of the heel relative to the lower leg throughout foot contact. Because eversion of the foot is a component of pronation it was used as a predictor of how much pronation was occurring. It was found that shoes with soft midsoles (25 durometer, Shore A scale) allowed significantly more maximum pronation (MP) and total rearfoot movement (TRM) than shoes with either medium (35 durometer) or hard (45 durometer) midsoles. Shoes with 0 degrees heel flare allowed significantly more MP and TRM than shoes with either 15 degrees or 30 degrees heel flares. Heel height was found to have no significant effect on either MP or TRM. These data provide guidelines for the construction of running shoes designed to limit rearfoot movement.

Biomechanical Phenomena↗
PubMed1978

Legg-Perthes disease in children less than four years old.

In children with Legg-Perthes disease who were less than four years old, better results were seen after treatment by recumbency and abduction bracing than with no treatment. All results were better in children having mild epiphyseal involvement (Catterall Groups I and II) than in those with more extensive disease.

Age Factors↗
PubMed1978

CHA as an ecclesial community.

In discussing the CHA Study Committee's description of the CHA as an ecclesial community, Fr. Clarke explains why the committee chose this particular description and outlines in theological and pastoral terms what accepting this concept means for the present and future activities of CHA.

Catholicism↗