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Biomedical subjects

T Collins

Publications and source records attributed to T Collins.

At least 19 recordsLinked to original sources
PubMed2006

Cold-adapted enzymes from marine Antarctic microorganisms.

The Antarctic marine environment is characterized by challenging conditions for the survival of native microorganisms. Indeed, next to the temperature effect represented by the Arrhenius law, the viscosity of the medium, which is also significantly enhanced by low temperatures, contributes to slow down reaction rates. This review analyses the different challenges and focuses on a key element of life at low temperatures: cold-adapted enzymes. The molecular characteristics of these enzymes are discussed as well as the adaptation strategies which can be inferred from the comparison of their properties and three-dimensional structures with those of their mesophilic counterparts. As these enzymes display a high specific activity at low and moderate temperatures associated with a relatively high thermosensitivity, the interest in these properties is discussed with regard to their current and possible applications in biotechnology.

Adaptation, Physiological↗
PubMed2006

Oligosaccharide binding in family 8 glycosidases: crystal structures of active-site mutants of the beta-1,4-xylanase pXyl from Pseudoaltermonas haloplanktis TAH3a in complex with substrate and product.

The structures of inactive mutants D144A and E78Q of the glycoside hydrolase family 8 (GH-8) endo-beta-1,4-d-xylanase (pXyl) from the Antarctic bacterium Pseudoalteromonas haloplanktis TAH3a in complex with its substrate xylopentaose (at 1.95 A resolution) and product xylotriose (at 1.9 A resolution) have been determined by X-ray crystallography. A detailed comparative analysis of these with the apo-enzyme and with other GH-8 structures indicates an induced fit mechanism upon ligand binding whereby a number of conformational changes and, in particular, a repositioning of the proton donor into a more catalytically competent position occurs. This has also allowed for the description of protein-ligand interactions in this enzyme and for the demarcation of subsites -3 to +3. An in-depth analysis of each of these subsites gives an insight into the structure-function relationship of this enzyme and the basis of xylose/glucose discrimination in family 8 glycoside hydrolases. Furthermore, the structure of the -1/+1 subsite spanning complex reveals that the substrate is distorted from its ground state conformation. Indeed, structural analysis and in silico docking studies indicate that substrate hydrolysis in GH-8 members is preceded by a conformational change, away from the substrate ground-state chair conformation, to a pretransition state local minimum (2)S(O) conformation.

Binding Sites↗
PubMed2005

Study of the active site residues of a glycoside hydrolase family 8 xylanase.

Site-directed mutagenesis and a comparative characterisation of the kinetic parameters, pH dependency of activity and thermal stability of mutant and wild-type enzymes have been used in association with crystallographic analysis to delineate the functions of several active site residues in a novel glycoside hydrolase family 8 xylanase. Each of the residues investigated plays an essential role in this enzyme: E78 as the general acid, D281 as the general base and in orientating the nucleophilic water molecule, Y203 in maintaining the position of the nucleophilic water molecule and in structural integrity and D144 in sugar ring distortion and transition state stabilization. Interestingly, although crystal structure analyses and the pH-activity profiles clearly identify the functions of E78 and D281, substitution of these residues with their amide derivatives results in only a 250-fold and 700-fold reduction in their apparent k(cat) values, respectively. This, in addition to the observation that the proposed general base is not conserved in all glycoside hydrolase family 8 enzymes, indicates that the mechanistic architecture in this family of inverting enzymes is more complex than is conventionally believed and points to a diversity in the identity of the mechanistically important residues as well as in the arrangement of the intricate microenvironment of the active site among members of this family.

Binding Sites↗
PubMed2005

Health policy analysis: a simple tool for policy makers.

Policy analysis is not an easy task. Its scope is broad and can include both the analysis of policy process and the analysis of policy content. This paper is concerned with the analysis of policy content and offers some practical guidance regarding how to analyse health policy and link it to health outcomes. An eight-step framework for policy analysis is proposed that public health policy makers and public health practitioners may find especially useful due to its simplicity.

Decision Making, Organizational↗
PubMed2004

Transition from film to electronic media in the first-year medical school gross anatomy lab.

For the benefit of the first-year gross anatomy students, we digitized and published on a Web site images that had been collected over a 30-year period. We provided a CD-ROM (compact disk, read-only media) containing the image set in higher quality format to students and faculty. We supplemented basic images with hot topics such as CT angiography, virtual colonography, computer-aided diagnosis, and 3D post-processing. Full motion video and moving JPEG (Joint Photo Expert Group) animations were integrated into the atlas. On the post course questionnaire medical students reported that the images on CD-ROM were helpful during the course and for review prior to examinations. Faculty and medical students used the CD-ROM for problem-based learning sections and facilitator training. The images were clear and easily projected during review sessions and were useful for the small group sessions, where they served as examples of normal anatomy.

Anatomy, Cross-Sectional↗
PubMed2004

Some like it cold: biocatalysis at low temperatures.

In the last few years, increased attention has been focused on a class of organisms called psychrophiles. These organisms, hosts of permanently cold habitats, often display metabolic fluxes more or less comparable to those exhibited by mesophilic organisms at moderate temperatures. Psychrophiles have evolved by producing, among other peculiarities, "cold-adapted" enzymes which have the properties to cope with the reduction of chemical reaction rates induced by low temperatures. Thermal compensation in these enzymes is reached, in most cases, through a high catalytic efficiency associated, however, with a low thermal stability. Thanks to recent advances provided by X-ray crystallography, structure modelling, protein engineering and biophysical studies, the adaptation strategies are beginning to be understood. The emerging picture suggests that psychrophilic enzymes are characterized by an improved flexibility of the structural components involved in the catalytic cycle, whereas other protein regions, if not implicated in catalysis, may be even more rigid than their mesophilic counterparts. Due to their attractive properties, i.e., a high specific activity and a low thermal stability, these enzymes constitute a tremendous potential for fundamental research and biotechnological applications.

Adaptation, Physiological↗
PubMed2004

A perspective on cold enzymes: current knowledge and frequently asked questions.

Studies on psychrophilic enzymes to determine the structural features important for cold-activity have attracted increased attention in the last few years. This enhanced interest is due to the attractive properties of such proteins, i.e. a high specific activity and a low thermal stability, and thus, these enzymes constitute a tremendous potential for fundamental research and biotechnological applications. This review examines the impact of low temperatures on life, the diversity of adaptation to counteract these effects and gives an overview of the features proposed to account for low thermal stability and cold-activity, following the chronological order of the catalytic cycle phases. Moreover, we present an overview of recent techniques used in the analysis of the flexibility of a protein structure which is an important concept in cold-adaptation; an overview of biotechnological potential of psychrophilic enzymes and finally, a few frequently asked questions about cold-adaptation and their possible answers.

Adaptation, Physiological↗
PubMed2002

Evidence based medicine in clinical practice: how to advise patients on the influence of age on the outcome of surgical anterior cruciate ligament reconstruction: a review of the literature.

OBJECTIVE: To determine, using a literature search, whether patient age influences the outcome of surgical reconstruction of a torn anterior cruciate ligament. METHODS: Medline (1966 to present) was searched using the PubMed interface, Embase (1974 to present) using the Datastar system, and the Cochrane Library at the Update Software web site. Papers retrieved from the three databases were independently assessed by two reviewers using preliminary inclusion criteria. Reference lists of papers satisfying the preliminary criteria were then scanned and appropriate papers reviewed. Any new papers in turn had their reference lists scanned, this process continuing until no new papers were identified. Final inclusion criteria were then applied to all papers satisfying the preliminary inclusion criteria. RESULTS: The initial search identified 661 papers. Exclusion of duplicates produced 536 unique papers. Medline contained 445, Embase 185, and the Cochrane Library 31. Of the 536, 523 were assessed by abstract and 12 by full text; one paper was not retrieved. Application of the preliminary inclusion criteria produced 33 papers. Their reference lists contained 950 references. Scanning of these added six new papers to the dataset. These six had their reference lists assessed; no new papers were identified. Four of the 39 papers in the completed dataset satisfied the final inclusion criteria. There was wide variation in the total number of subjects in the four studies, ranging from 22 to 203 patients. The total number of different outcome measures was 17; only one measure was used by all four studies. None of the objective outcome measures showed any significant difference between age groups, and the subjective measures, which did show differences, were contradictory. A total of 108 interlibrary loans were requested, by a full time researcher, at a total cost of 432.00 Irish pounds over a 10 week period. CONCLUSIONS: When advising patients on the outcome of anterior cruciate ligament reconstruction, age should not be considered in isolation. In the absence of relevant guidelines, meta-analyses, or systematic reviews, the application of evidence based medicine to clinical practice has significant resource implications.

Adult↗
PubMed2002

Differences in immunocontraceptive responses in white-tailed deer (Odocoileus virginianus) and goats (Capra hircus).

Thirteen deer (Odocoileus virginianus) and three goats (Capra hircus) were given an initial immunization of 300 microg porcine zona pellucida (PZP) combined with 50 mg synthetic trehalose dicorynomycolate ml(-1) (STDCM) in drakeol i.m. in the semitendinosus and semimembranosus muscles. This immunization was followed by two booster injections of 300 microg PZP, 2 weeks apart. The vaccinations were made from the same purified batch of PZP and lot of adjuvant. All the doses were made at the same time and injected on the same day. The immune response was quantified by measuring serum anti-PZP IgG antibody concentration by ELISA. The results showed that the mean serum IgG concentration of the deer increased from 0.000 +/- 0.003 to 0.083 +/- 0.023 absorbance units, whereas in the goats the mean IgG concentration increase was from 0.044 +/- 0.019 to 1.245 +/- 0.774 absorbance units. Both the goats and deer showed a significant increase in IgG concentration (P < 0.05) after the final booster injection compared with preimmune serum. The final goat IgG concentration was significantly (P < 0.05) higher than that of the deer. If PZP and Freund's adjuvant are administered to deer, immunocontraception is achieved, but the IgG concentration in the deer in this study did not appear to be compatible with immunocontraception.

Animals↗
PubMed2001

Extinguishing Egr-1-dependent inflammatory and thrombotic cascades after lung transplantation.

Hypoxic induction of the early growth response-1 (Egr-1) transcription factor initiates proinflammatory and procoagulant gene expression. Orthotopic/isogeneic rat lung transplantation triggers Egr-1 expression and nuclear DNA binding activity corresponding to Egr-1, which leads to increased expression of downstream target genes such as interleukin-1b, tissue factor, and plasminogen activator inhibitor-1. The devastating functional consequences of Egr-1 up-regulation in this setting are prevented by treating donor lungs with a phosphorothioate antisense oligodeoxyribonucleotide directed against the Egr-1 translation initiation site, which blocks expression of Egr-1 and its gene targets. Post-transplant graft leukostasis, inflammation, and thrombosis are consequently diminished, with marked improvement in graft function and recipient survival. Blocking expression of a proximal transcription factor, which activates deleterious inflammatory and coagulant effector mechanisms, is an effective molecular strategy to improve organ preservation.

Animals↗
PubMed2001

I kappa B kinase is critical for TNF-alpha-induced VCAM1 gene expression in renal tubular epithelial cells.

The expression of VCAM1 is up-regulated in renal proximal tubular epithelial cells (TEC) in a variety of inflammatory renal diseases, a prominent example of which is acute renal allograft rejection. VCAM1 may play an important role in these diseases because it binds to the integrins very late Ag-4 and alpha(4)beta(7) on lymphocytes and monocytes, thereby providing a potential mechanism to recruit these leukocytes to sites of inflammation. The molecular mechanisms underlying VCAM1 regulation in renal TEC are essentially unknown. We now report that VCAM1 mRNA is dramatically up-regulated in C1, a cell line derived from renal TEC, on exposure to TNF-alpha. Two NF-kappaB binding sites in the VCAM1 promoter are critical for the TNF-alpha-induced VCAM1 transcriptional up-regulation, and both sites bind to p65-p50 NF-kappaB complexes. TNF-alpha induces activation of inhibitor of NF-kappaB (IkappaB) kinase-beta (IKK-beta), a protein kinase that phosphorylates the NF-kappaB inhibitor IkappaB, and thereby targets the latter for degradation via the ubiquitin-proteasome pathway. Moreover, dominant negative versions of IKK inhibit TNF-alpha activation of a VCAM1 promoter reporter. We conclude that the IKK/NF-kappaB pathway is critical in the TNF-alpha-induced up-regulation of VCAM1 mRNA in renal TEC.

Animals↗
PubMed2001

Proper coronary vascular development and heart morphogenesis depend on interaction of GATA-4 with FOG cofactors.

GATA-family transcription factors are critical to the development of diverse tissues. In particular, GATA-4 has been implicated in formation of the vertebrate heart. As the mouse Gata-4 knock-out is early embryonic lethal because of a defect in ventral morphogenesis, the in vivo function of this factor in heart development remains unresolved. To search for a requirement for Gata4 in heart development, we created mice harboring a single amino acid replacement in GATA-4 that impairs its physical interaction with its presumptive cardiac cofactor FOG-2. Gata4(ki/ki) mice die just after embryonic day (E) 12.5 exhibiting features in common with Fog2(-/-) embryos as well as additional semilunar cardiac valve defects and a double-outlet right ventricle. These findings establish an intrinsic requirement for GATA-4 in heart development. We also infer that GATA-4 function is dependent on interaction with FOG-2 and, very likely, an additional FOG protein for distinct aspects of heart formation.

Amino Acid Sequence↗
PubMed2001

The use of tat and env sequences from human immunodeficiency virus 1 in phylogenetic epidemiological studies.

Using nucleotide sequences from the first exon of the tat gene of the human immunodeficiency virus 1 (HIV-1), we tested the hypothesis that a Florida dentist (a common source) infected five of his patients in the course of dental procedures against the null hypothesis that the dentist and each individual of the dental group independently acquired the virus within the local community. This novel approach of analyzing the tat gene region was used because it may, in some circumstances, be more informative for phylogenetic epidemiology than the more commonly used C2-V3 envelope gene region. The first exon of the tat gene was polymerase chain reaction (PCR)-amplified and directly sequenced from uncultured peripheral blood mononuclear cells. Patient's sequences were compared with sequences from six HIV-1 infected heterosexual couples unrelated to the dentist or the five patients, but from the same general geographic area. In addition, a sixth infected dental patient, previously inferred to have acquired HIV-1 from a source other than the dentist, was included. Multiple phylogenetic analyses demonstrated that the sequences of the five patients were significantly more closely related to each other than to sequences of the controls. Our results using tat sequences, combined with envelope sequence data, strongly support a common phylogenetic epidemiological relationship among these five patients, and the HIV-1 infected dentist who treated them. Correct recovery of known epidemiological relationships among couples included in the analysis further strengthens this conclusion.

Base Sequence↗
PubMed2001

Reduction in QT dispersion with rheolytic thrombectomy in acute myocardial infarction: evidence of electrial stability with reperfusion therapy.

An increase in QT dispersion (QTd) is associated with myocardial ischemia and may serve as a marker of ischemia and ventricular arrhythmia. We studied the effect of early reperfusion with rheolytic thrombectomy using an angiojet catheter (Possis, Minneapolis, MN) on QTd in 12 patients who presented with acute myocardial infarction. QTd and QT dispersion, rate-corrected for RR interval, were significantly reduced from 57 +/- 16 and 68 +/- 13 msec before reperfusion to 34 +/- 16 and 44 +/- 19 msec after reperfusion respectively (mean +/- SD; P < 0.002 and P < 0.0008, respectively). Successful reperfusion with rheolytic thrombectomy reduces QTd and may confer electrical stability to vulnerable myocardium. Reduction in indexes of repolarization inhomogeneity with reperfusion may serve as a noninvasive marker of coronary patency.

Aged↗
PubMed2001

Did psychrophilic enzymes really win the challenge?

Organisms living in permanently cold environments, which actually represent the greatest proportion of our planet, display at low temperatures metabolic fluxes comparable to those exhibited by mesophilic organisms at moderate temperatures. They produce cold-evolved enzymes partially able to cope with the reduction in chemical reaction rates and the increased viscosity of the medium induced by low temperatures. In most cases, the adaptation is achieved through a reduction in the activation energy, leading to a high catalytic efficiency, which possibly originates from an increased flexibility of either a selected area of or the overall protein structure. This enhanced plasticity seems in return to be responsible for the weak thermal stability of cold enzymes. These particular properties render cold enzymes particularly useful in investigating the possible relationships existing between stability, flexibility, and specific activity and make them potentially unrivaled for numerous biotechnological tasks. In most cases, however, the adaptation appears to be far from being fully achieved.

Adaptation, Physiological↗