Concordance analysis of microbial genomes

The set of proteins which are conserved across families of microbes contain important targets of new anti-microbial agents. We have developed a simple and efficient computational tool which determines concordances of putative gene products that show sets of proteins conserved across one set of user specified genomes and not present in another set of user specified genomes. The thresholds and the homology scoring criterion are selectable to allow the user to decide the stringency of the homologies. The system uses a relational database to store protein coding regions from different genomes, and to store the results of a complete comparison of all sequences against all sequences using the FASTA program. Using Web technology, the display of all the related proteins for a given sequence and calculation of multiple sequence alignments (using CLUSTALW) can be performed with the click of a button. The current database holds 97 365 sequences from 19 complete or partial genomes and 8798905 FASTA comparison results. A example concordance is presented which demonstrates that the target of the quinolone antibiotics could have been identified using this tool.     

A Golgi localization signal identified in the Menkes recombinant protein

Menkes disease arises from a genetic impairment in copper transport. The gene responsible for the phenotype has been identified as a copper transporting ATPase ( ATP7A ). Recently, the protein encoded by the ATP7A gene has been localized to the Golgi complex. In order to investigate the role of the Menkes disease protein in copper transport, recombinant constructs containing both the full-length open reading frame and an alternatively spliced form have been successfully expressed and localized in mammalian cells. Other studies of a patient with occipital horn syndrome, an allelic variant of Menkes disease, have demonstrated that only this alternatively spliced isoform and not the full-length form is expressed in this patient. The milder form of this patient's phenotype suggests that the alternatively spliced isoform has some functional role in copper transport. In the present study the full-length recombinant Menkes protein was shown by immunofluorescence to localize to the Golgi apparatus and the alternatively spliced form, lacking sequences for transmembrane domains 3 and 4 encoded by exon 10, was shown to localize to the endoplasmic reticulum. Using sequences from exon 10 fused to a non-Golgi reporter molecule, a 38 amino acid sequence containing transmembrane domain 3 of the Menkes protein was found to be sufficient for localization to the Golgi complex. Therefore, the protein sequence encoded by exon 10 may be responsible for this differential localization and both isoforms may be required for comprehensive transport of copper within the cell.     

Integrated MRI assessment of regional function and perfusion in canine myocardial infarction

A single integrated examination using regional measurements of perfusion from contrast-enhanced MRI and three-dimensional (3D) strain from tissue-tagged MRI was developed to differentiate infarcted myocardium from adjacent tissue with functional abnormalities. Ten dogs were studied at baseline and 10 days after a 2-hour occlusion of the left anterior descending coronary artery (LAD). Strain was determined using a 3D finite element model. Two-dimensional measurements of hypoenhancing regions were highly correlated with myocardial viability (r = 0.96). Signal intensity versus time curves obtained from contrast-enhanced MRI were used for quantitative perfusion analysis. The remote and adjacent noninfarcted tissue of the dogs with LAD occlusion, as well as the infarcted tissue, exhibited abnormal deformation patterns as compared to normal dogs (positive predictive value (PPV) of strain determination of infarction = 66%). Integration of contrast-enhanced MRI results with 3D strain analysis enabled the delineation of the myocardial infarction (PPV = 100%) from functionally compromised myocardium. This integrated cardiac examination shows promise for noninvasive serial assessment of potentially jeopardized noninfarcted myocardium to study the process of infarct remodeling and expansion.     

Steady-state cerebral glucose concentrations and transport in the human brain

Understanding the mechanism of brain glucose transport across the blood-brain barrier is of importance to understanding brain energy metabolism. The specific kinetics of glucose transport have been generally described using standard Michaelis-Menten kinetics. These models predict that the steady-state glucose concentration approaches an upper limit in the human brain when the plasma glucose level is well above the Michaelis-Menten constant for half-maximal transport, Kt. In experiments where steady-state plasma glucose content was varied from 4 to 30 mM, the brain glucose level was a linear function of plasma glucose concentration. At plasma concentrations nearing 30 mM, the brain glucose level approached 9 mM, which was significantly higher than predicted from the previously reported Kt of approximately 4 mM (p < 0.05). The high brain glucose concentration measured in the human brain suggests that ablumenal brain glucose may compete with lumenal glucose for transport. We developed a model based on a reversible Michaelis-Menten kinetic formulation of unidirectional transport rates. Fitting this model to brain glucose level as a function of plasma glucose level gave a substantially lower Kt of 0.6 +/- 2.0 mM, which was consistent with the previously reported millimolar Km of GLUT-1 in erythrocyte model systems. Previously reported and reanalyzed quantification provided consistent kinetic parameters. We conclude that cerebral glucose transport is most consistently described when using reversible Michaelis-Menten kinetics.     

Summary of the II International Symposium on Cytomegalovirus

Human cytomegalovirus (HCMV) is a highly species-specific DNA virus belonging to the Betaherpesvirinae subfamily of the herpesviridae family. Like other herpesviruses, primary infection with HCMV is followed by persistence of the virus in a latent form. The sites of latency are still largely undefined, but they probably include bone marrow progenitor cells and peripheral blood monocytes. From these sites, the virus can reactivate, resulting in renewed shedding of the virus, or, in immunocompromized persons, development of disease. Humans are the only reservoir of HCMV and transmission occurs by person-to-person contact. Infection with HCMV is common. In most developed countries, HCMV seroprevalence steadily increases after infancy and 10-20% of children are infected before puberty. In adults, the prevalence of antibodies ranges from 40 to 100%. Although HCMV has a world-wide distribution, infection with HCMV is more common in the developing countries and in areas of low socioeconomic conditions, which is predominantly related to the closeness of contacts within these populations. Except for a mononucleosis-like illness in some persons, infection with HCMV rarely causes disease in immunocompetent individuals. However, HCMV can cause severe morbidity and mortality in congenitally infected newborns and immunocompromized patients, most notably transplant-recipients and HIV-infected persons. This article provides a review of the information presented at the Second International Symposium on Cytomegalovirus organized and convened by The Macrae Group (New York City, NY) in Acapulco, Mexico on 24-28 April 1998. During this symposium, the state-of-the-art knowledge on diagnosis, treatment and prophylaxis of HCMV infections were discussed, and, based on this information, attempts to highlight the future directions in basic and clinical research areas that need to be stimulated to facilitate advancement in prevention and treatment of CMV disease.     

Synthesis and biological evaluation of certain new thiazolopyrimidines

A series of 5-methyl-3-phenyl thiazolo[5,4-e][1,2,4]triazolo[1,5-c] pyrimidin-2-thiones and 5-methyl-3-phenyl thiazolo[5,4-e]pyrimidino[3,4-b][1,2,4]triazin-2-thiones were prepared as potential antimicrobial and antitumor agents. Some of the tested compounds showed promising activity. The detailed synthesis, spectroscopic and biological data are reported.     

Kinetics of human erythrocyte acetylcholinesterase inhibition by a novel derivative of physostigmine: phenserine

The elastic properties of carotid arteries of spontaneously hypertensive rats (SHR) and normotensive controls (Wistar-Kyoto rats [WKY]) were examined in vivo, in situ, and in vitro. The changes of internal diameter were measured with a high-resolution A-mode echo-tracking device simultaneously with the intra-arterial pressure at the carotid. The internal diameter at mean arterial blood pressure (MBP) was substantially smaller in vitro than in vivo in SHR (-33.8%) and WKY (-48.3%). The arterial distensibility was lower in vitro in all arteries compared with in vivo conditions (SHR, -30.1%; WKY, -60.4%; at MBP) despite a reduced incremental elastic modulus in vitro (SHR, -56.9%; WKY, -45.1%; at MBP). However, the in vitro and in vivo measurements show consistent elastic behavior of the carotid arteries between both strains of rats. Carotid arteries from WKY were also examined in situ. Although no significant reduction in internal diameter could be observed in situ, distensibility was dramatically decreased (-87% at MBP). These results emphasize the importance of considering the original vascular geometry when determining elastic properties of arteries. We conclude that experimental conditions are likely to be a critical determinant for the assessment of the mechanical properties of conduit vessels.     

Structure and practice of institutional review boards in the United States

OBJECTIVE: The institutional review board (IRB) is a critical element in the protection of patients' and subjects' rights with regard to their participation in research protocols. The purpose of this study was to describe the structure and current practices of IRBs in the United States. METHODS: A self-administered questionnaire was mailed to the IRB chair of each U.S. hospital with a capacity of at least 400 beds (n = 907). The survey contained 21 questions outlining committee size and structure, review of research proposals, and policies concerning scientific misconduct. Chairs also were asked what advice they would offer a young investigator preparing a proposal for submission. RESULTS: A total of 488 surveys (54%) were returned; 447 of the responding institutions had an IRB committee. Committees had an average of 14 members, representing 27 medical specialties. Orthopedics had the least IRB representation (10% of committees), followed by emergency medicine (12%) and ophthalmology (15%). The majority of research proposals go through 5 specific steps once submitted for review. Common reasons for proposal rejection were improperly designed consent form (54%), poor study design (44%), unacceptable risk to subjects (34%), ethical or legal reasons (24%), and scientific merit (14%). When a research proposal is rejected, 86% of the responding IRBs assist the investigator in making appropriate revisions. Although a number of IRBs (17%) have dealt with scientific misconduct allegations, only 58% have a written policy regarding research integrity. CONCLUSION: Despite variations in committee structure and representation, IRBs have similar procedures for governing research. Investigators should be familiar with these procedures and are encouraged to discuss their proposal with an IRB representative prior to formal review.     

Diagnostic tools in the evaluation of patients with viral hepatitis undergoing liver transplantation

Familiarity with the diagnostic parameters of viral hepatitis is imperative in the liver transplantation arena. Chronic viral hepatitis B and C are among the most common categories of end-stage liver disease. The preoperative diagnosis, determination of recurrent infection, and the assessment of antiviral therapeutic efficacy are dependent on appropriate virological testing. Furthermore, liver transplant personnel are at a high risk for parenterally transmitted viral hepatitis infection. Knowledge and understanding of the serological patterns of acute and chronic viral hepatitis, as well as recognition of the immune status for one or more of these viruses, will facilitate prevention and treatment of viral hepatitis for these health care providers.