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PubMed2001

Unraveling peroxynitrite formation in biological systems.

Peroxynitrite promotes oxidative damage and is implicated in the pathophysiology of various diseases that involve accelerated rates of nitric oxide and superoxide formation. The unambiguous detection of peroxynitrite in biological systems is, however, difficult due to the combination of a short biological half-life, limited diffusion, multiple target molecule reactions, and participation of alternative oxidation/nitration pathways. In this review, we provide the conceptual framework and a comprehensive analysis of the current experimental strategies that can serve to unequivocally define the existence and quantitation of peroxynitrite in biological systems of different levels of organization and complexity.

Animals↗
PubMed2002

A single dose of lysergic acid diethylamide influences gene expression patterns within the mammalian brain.

Hallucinogenic drugs such as lysergic acid diethylamide (LSD) have profound effects on humans including hallucinations and detachment from reality. These remarkable behavioral effects have many similarities to the debilitating symptoms of neuropsychiatric disorders such as schizophrenia. The effects of hallucinogens are thought to be mediated by serotonin receptor activation; however, how these drugs elicit the unusual behavioral effects remains largely a mystery, despite much research. We have undertaken the first comprehensive analysis of gene expression influenced by acute LSD administration in the mammalian brain. These studies represent a novel approach to elucidate the mechanism of action of this class of drugs. We have identified a number of genes that are predicted to be involved in the processes of synaptic plasticity, glutamatergic signaling and cytoskeletal architecture. Understanding these molecular events will lead to new insights into the etiology of disorders whose behavioral symptoms resemble the temporary effects of hallucinogenic drugs, and also may ultimately result in new therapies.

Animals↗
PubMedDate not supplied

Evidence-based practice: an example related to the use of splinting in a patient with carpal tunnel syndrome.

The purpose of this article was to illustrate a limited search for evidence and its application in the context of a patient with CTS. The search was by no means exhaustive, as it was performed and interpreted in less than an hour. My conclusions are not definitive because my evidence was based almost exclusively on abstracts, and many key details about the studies are unknown. I do not know how closely my specific patient matches those in a particular study. My search allowed me, however, to make an informed response to a patient with legitimate questions. Integrating the evidence with my own clinical judgment and the patient's preferences kept me from being paralyzed in decision making by a lack of sufficient data. This intentionally quick and patient-specific search for evidence could be contrasted to a more complete and comprehensive analysis of evidence. A more complete search would be indicated for areas that represent common or frequent problems for a particular clinical setting, for which basic procedural guidelines might be developed.

Carpal Tunnel Syndrome↗
PubMed2000

Angiotensin II antagonists for hypertension: are there differences in efficacy?

We compared the antihypertensive efficacy of available drugs in the new angiotensin-II-antagonist (AIIA) class. The antihypertensive efficacy of losartan, valsartan, irbesartan, and candesartan was evaluated from randomized controlled trials (RCT) by performing a metaanalysis of 43 published RCT. These trials involved AIIA compared with placebo, other antihypertensive classes, and direct comparisons between AIIA. A weighted-average for diastolic and systolic blood pressure reduction with AIIA monotherapy, dose titration, and with addition of low-dose hydrochlorothiazide (HCTZ) were calculated. Weighted-average responder rates were also determined. The metaanalysis assessed a total of 11,281 patients. The absolute weighted-average reductions in diastolic (8.2 to 8.9 mm Hg) and systolic (10.4 to 11.8 mm Hg) blood pressure reductions (not placebo-corrected) for AIIA monotherapy were comparable for all AIIA. Responder rates for AIIA monotherapy were 48% to 55%. Dose titration resulted in slightly greater blood pressure reduction and an increase in responder rates to 53% to 63%. AIIA/hydrochlorothiazide combinations produced substantially greater reduction in systolic (16.1 to 20.6 mm Hg) and diastolic (9.9 to 13.6 mm Hg) blood pressure reductions than AIIA monotherapy and responder rates for AIIA/HCTZ combinations were 56% to 70%. This comprehensive analysis shows comparable antihypertensive efficacy within the AIIA class, a near-flat AIIA-dose response when titrating from starting to maximum recommended dose, and substantial potentiation of the antihypertensive effect with addition of HCTZ.

Angiotensin II↗
PubMed2002

Compartmentalized Eph receptor and ephrin expression in the thymus.

The maturation of T cells is an intricate process involving the interaction of developing thymocytes with discrete microenvironments within the thymus. Numerous studies have indicated that distinct thymic compartments provide signals required for each stage of thymocyte maturation. In this study we performed a comprehensive analysis of the expression patterns of Eph-A receptors and ephrins-A in the thymus using in situ hybridization and reverse transcription-polymerase chain reaction, and show that expression of these molecules is highly compartmentalized. Based on these expression patterns and the known mechanisms of action of Eph receptor/ephrin interactions in other organs, these data suggest that differential Eph receptor expression on discrete subsets of thymic stromal cells may be important in establishing compartment boundaries and preventing intermingling of stromal cell subtypes. Further, together with chemotactic signals such as those provided by chemokines, regulated Eph receptor/ephrin expression on thymocytes may play a role in thymocyte migration.

Cell Differentiation↗
PubMed2002

Alternative splicing of transcripts for the alpha 3 chain of mouse collagen VI: identification of an abundant isoform lacking domains N7-N10 in mouse and human.

Three distinct alpha chains form the collagen VI monomer, the alpha 3(VI) chain being much larger than the alpha 1(VI) and alpha 2(VI) chains. The alpha 3(VI) chain has 10 von Willebrand Factor type A domains of approximately 200 amino acids at the N-terminus (N1-N10) compared with only one such domain in the alpha 1(VI) and alpha 2(VI) chains. Domains N10, N9, N7 and N3 of the alpha 3(VI) chain are subject to alternative splicing in chick and/or human tissues, indicating the possibility of isoforms that have different functions depending on which N-terminal domains are included or excluded. In this study we have PCR amplified and sequenced mouse alpha 3(VI) cDNA encoding the N2-N10 domains. By reverse transcription-PCR using oligonucleotides spanning different regions of the cDNA we have undertaken a comprehensive analysis of alternative splicing of the alpha 3(VI) mRNA in embryonic and adult mouse tissues. We demonstrate that domains N10, N9 and N7 are also subject to alternative splicing in mouse tissues and in addition identify an abundant novel variant transcript that lacks all four N-terminal domains (N7-N10) in mouse tissues and human cells. We also identify less abundant transcripts that lack a large part of the N3 domain, and transcripts lacking the entire N5 domain. Using specific RNase protection assays we show that the shorter transcripts containing domains (N8+N7+N6), (N8+N6) and N6 are present at higher levels than transcripts containing the N10 and/or N9 domains, with tissue-specific variation in the levels of variant transcripts. These studies demonstrate a larger range of collagen VI protein variants than previously described.

5' Untranslated Regions↗
PubMed2000

The Drosophila genome.

The past year has been a spectacular one for Drosophila research. The sequencing and annotation of the Drosophila melanogaster genome has allowed a comprehensive analysis of the first three eukaryotes to be sequenced-yeast, worm and fly-including an analysis of the fly's influences as a model for the study of human disease. This year has also seen the initiation of a full-length cDNA sequencing project and the first analysis of Drosophila development using high-density DNA microarrays containing several thousand Drosophila genes. For the first time homologous recombination has been demonstrated in flies and targeted gene disruptions may not be far off.

Animals↗
PubMed2002

Alterations in p53 and pRb pathways and their prognostic significance in oesophageal cancer.

The pRb (p16-pRb-cyclin D1) and p53 (p53-MDM2-p21) pathways play a critical role in tumorigenesis. To evaluate which of these cell cycle regulatory proteins are related to patients' prognosis, a comprehensive analysis of alterations in these components was carried out in 100 ESCCs (oesophageal squamous cell carcinoma) using immunohistochemistry and correlated with clinicopathological parameters by univariate analysis. Overexpression of p53, MDM2 and cyclin D1 proteins was observed in 73, 42 and 67% of the cases, respectively, while loss of expression of p21, p16 and pRb was observed in 36, 45 and 75% of the cases, respectively. Multiple logistic regression analysis revealed that loss of p16 immunoreactivity was a significant risk factor for tumour stage (pT) (Odds Ratio (OR)=3.3), whereas the loss of pRb was a significant risk factor for nodal metastasis (pN) (OR=8.8). MDM2 overexpression emerged as the most significant risk factor for distant organ metastasis (pM) (OR=4.6). Of the ESCC patients who underwent oesophagectomy, 50 cases were followed-up for a maximum period of 44 months and median of 16 months. Survival analysis revealed that Cyclin D1 overexpression is an adverse prognosticator for disease-free survival, as well as overall survival, and tumour stage (pT) is an adverse prognosticator for disease-free survival. In conclusion, these data support a model of oesophageal cancer pathogenesis in which both the pRb and p53 pathways are inactivated and suggests an in-depth evaluation of the clinical utility of these putative markers is warranted.

Adult↗
PubMed2002

Strategic emphases for tropical diseases research: a TDR perspective.

Setting priorities for health research is a difficult task, especially for the neglected diseases of the poor. A new approach to priority setting for tropical diseases research has been adopted by the UNDP/World Bank/WHO Special Programme for Research and Training in Tropical Diseases (known as the TDR). Priorities are defined on the basis of a comprehensive analysis of research needs and research opportunities for each of the ten major tropical diseases in the TDR portfolio. The resulting strategic emphases matrix reflects the priorities for tropical diseases research from the perspective of the TDR. Its purpose is not to impose global research priorities, but we believe the results could be useful to other organizations.

Communicable Disease Control↗
PubMed2003

Tissue distribution, intracellular localization and proteolytic processing of rat 4-hydroxyphenylpyruvate dioxygenase.

4-hydroxyphenylpyruvate dioxygenase (HPD) is an important enzyme involved in tyrosine catabolism. HPD was shown to be identical to a protein named the F-antigen, exploited by immunologists because of its unique immunological properties. Congenital HPD deficiency is a rare, relatively benign condition known as hereditary type III tyrosinemia. Decreased expression of HPD is often observed in association with the severe type I tyrosinemia, and interestingly, inhibition of HPD activity seems to ameliorate the clinical symptoms of type I tyrosinemia. In this study we present a comprehensive analysis of tissue specific expression and intracellular localization of HPD in the rat. By combined use of in situ hybridization and immunohistochemistry we confirm previously known sites of expression in liver and kidney. In addition, we show that HPD is abundantly expressed in neurons in the cortex, cerebellum and hippocampus. By using immunoelectron microscopy and confocal laser scanning microscopy, we provide evidence that HPD contrary to earlier assumptions specifically localizes to membranes of the endoplasmic reticulum and the Golgi apparatus. Detailed mass spectrometric analyses of HPD purified from rat liver revealed N-terminal and C-terminal processing of HPD, and expression of recombinant HPD suggested that C-terminal processing enhances the enzymatic activity.

4-Hydroxyphenylpyruvate Dioxygenase↗
PubMed2001

Combined quality improvement ratio: a method for a more robust evaluation of changes in screening rates.

INTRODUCTION: It has been proposed that a ratio of the discordant cells from a McNemar's Chi-square table be used as a measure of quality improvement, and that this measure be called the Quality Improvement Ratio (QuIR). As proposed, patients enrolled in only one year of a two-year study are excluded from the McNemar's table of the QuIR. Since the original proposal of the McNemar's Chi-square in 1947 included application to matched pair data, a more comprehensive analysis would be possible if the single-year enrollees were matched into pairs. METHODS: Patients enrolled in only the first study year are matched and paired with patients enrolled in only the second study year. The pairs are matched on variables important to the disease or process being evaluated. The matched pairs are combined with the repeatedly measured subjects to increase the statistical power of the analysis. The Combined Quality Improvement Ratio (CQuIR) is demonstrated with parameters from the original articles, in a--Markov chain Monte-Carlo simulation, so a direct comparison can be made. RESULTS: CQuIR improved statistical power, especially in simulations of small populations. In some simulations the statistical power was double that of the QuIR alone. DISCUSSION: Although the QuIR provides important information, the CQuIR allows more of the data to be used to evaluate the effect of interventions in policy, delivery, and practice. The increase in statistical power of the CQuIR over the QuIR can facilitate successful evaluation of health care services.

Breast Neoplasms↗
PubMed2003

Operative parameters that predict the outcomes of hepatic transplantation.

BACKGROUND: A growing discrepancy between the number of patients awaiting liver transplantation and the number of organs available mandates the use of even marginal organ donors in whom there is major risk of suboptimal graft function. A comprehensive analysis of operative parameters on the outcomes of liver transplantation has not been reported. STUDY DESIGN: We analyzed the impact of 24 operative variables on the survival of 942 consecutive primary liver allografts performed at a single center from June 1992 through December 1997. Univariate and Cox proportional hazards analysis was used to identify those variables with independent prognostic significance in graft survival. Resource utilization for variables with multivariate significance was also analyzed. RESULTS: Of 12 intraoperative variables found to have significance in univariate analysis, three were significant by Cox multivariate analysis: 1) lack of immediate bile production by the graft intraoperatively, 2) platelet transfusion > or = 20 U, and 3) recipient urine output < or =2.0 mL/kg/h intraoperatively. Each of the three variables was associated with marked increases in hospital and Intensive Care Unit length of stay and hospital charges accrued during the admission for transplantation. CONCLUSION: We identified three operative parameters that predict a poor outcome after liver transplantation. The presence of these indicators suggests that early retransplantation should be considered. Early identification of grafts likely to have poor function might also provide an opportunity for therapeutic intervention to salvage graft function.

Adult↗
PubMed1999

Direct assessment of MHC class I binding by seven Ly49 inhibitory NK cell receptors.

Mouse NK cells express at least seven inhibitory Ly49 receptors. Here we employ a semiquantitative cell-cell adhesion assay as well as class I/peptide tetramers to provide a comprehensive analysis of specificities of Ly49 receptors for class I MHC molecules in eight MHC haplotypes. Different Ly49 receptors exhibited diverse binding properties. The degree of class I binding was related to the extent of functional inhibition. The tetramer studies demonstrated that neither glycosylation nor coreceptors were necessary for class I binding to Ly49 receptors and uncovered peptide-specific recognition by a Ly49 receptor. The results provide a foundation for interpreting and integrating many existing functional studies as well as for designing tests of NK cell development and self-tolerance.

Alleles↗
PubMed2002

Bud morphogenesis and the actin and microtubule cytoskeletons during budding in the corn smut fungus, Ustilago maydis.

Ustilago maydis is a dimorphic Basidiomycete fungus with a yeast-like form and a hyphal form. Here we present a comprehensive analysis of bud formation and the actin and microtubule cytoskeletons of the yeast-like form during the cell cycle. We show that bud morphogenesis entails a series of shape changes, initially a tubular or conical structure, culminating in a cigar-shaped cell connected to the mother cell by a narrow neck. Labelling of cells with concanavalin A demonstrated that growth occurs at bud tip. Indirect immunofluorescence studies revealed that the actin cytoskeleton consists of patches and cables that polarize to the presumptive bud site and the bud tip and an actin ring that forms at the neck region. Because the bud tip corresponds to the site of active cell wall growth, we hypothesize that actin is involved in secretion of cell wall components. The microtubule cytoskeleton has recently been shown to consist of a cytoplasmic network during interphase that disassembles at mitosis when a spindle and astral microtubules are formed. We have carried out studies of U. maydis cells synchronized by the microtubule-depolymerizing drug thiabendazole which allow us to construct a temporal sequence of steps in spindle formation and spindle elongation during the cell cycle. These studies suggest that astral microtubules may be involved in early stages of spindle orientation and migration of the nucleus into the bud and that the spindle pole bodies may be involved in reestablishment of the cytoplasmic microtubule network.

Actins↗
PubMed2001

Fungal genomics and pathogenicity.

The filamentous fungal genetics community has enthusiastically embraced the utilization of genomics technologies to resolve long-standing issues in fungal biology. For example, such technologies have been proposed to study the mechanics of tip growth, photoreception, gene silencing, the molecular basis of conidiation, the pathway leading to sexual reproduction, and mechanisms of pathogenesis. These studies have provided a refreshing change of pace in research on filamentous fungi, which has lagged behind that on other eukaryotes in the exploitation of genome-wide methodologies. Despite the late start, several fungal genome sequencing projects are underway. The resulting databases will allow the comprehensive analysis of developmental processes that are characteristic of fungi, including the molecular nature of pathogenicity. DNA databases underpin analyses of the fungal transcriptome, proteome, and metabolome. This combined information will contribute to our basic understanding of not only the mechanics of infection but also the evolution of pathogenicity.

Calcium-Binding Proteins↗
PubMed2002

Resistance of human fungal pathogens to antifungal drugs.

Resistance mechanisms can be engaged in clinically relevant fungal pathogens under different conditions when exposed to antifungal drugs. Over past years, active research was undertaken in the understanding of the molecular basis of antifungal drug resistance in these pathogens, and especially against the class of azole antifungals. The isolation of various alleles of the gene encoding the target of azoles has enabled correlation of the appearance of resistance with distinct mutations. Resistance mechanisms to azoles also converge to the upregulation of multidrug transporter genes, whose products have the capacity to extrude from cells several chemically unrelated antifungal agents and toxic compounds. Genome-wide studies of azole-resistant isolates are now permitting a more comprehensive analysis of the impact of resistance on gene expression, and may deliver new clues to their mechanisms. Several laboratories are also exploring, as well as possible alternative resistance pathways, the role of biofilm formation by several fungal species in the development of resistance to various antifungals, including azoles.

Antifungal Agents↗
PubMed2002

Strategic emphases for tropical diseases research: a TDR perspective.

Setting priorities for health research is a difficult task, especially for the neglected diseases of the poor. A new approach to priority setting for tropical diseases research has been adopted by the UNDP/World Bank/WHO Special Programme for Research and Training in Tropical Diseases (known as the TDR). Priorities are defined on the basis of a comprehensive analysis of research needs and research opportunities for each of the ten major tropical diseases in the TDR portfolio. The resulting strategic emphases matrix reflects the priorities for tropical diseases research from the perspective of the TDR. Its purpose is not to impose global research priorities, but we believe the results could be useful to other organizations.

Animals↗
PubMed2007

Role of mini-host models in the study of medically important fungi.

Mini-host models have emerged as simple experimental systems to study the pathogenesis and host innate immune responses in fungal invaders and also to test drug efficacy against these organisms. A growing number of medically important fungi, including Aspergillus spp, Candida spp, Cryptococcus spp, and species in the class Zygomycetes, have been shown to infect and kill invertebrates such as roundworms, fruit flies, and wax moths. These studies have shown that several genes implicated in the virulence of fungi in mammalian models also have a similarly important pathogenic role in mini-host organisms. These mini-host models provide a unique opportunity of simultaneously exploring the molecular mechanisms of fungal pathogenicity and candidate agents with antifungal activity. Furthermore, the fact that some of these mini-hosts have well-defined genetics and conserved innate immunity offers the advantage of a comprehensive analysis of the molecular aspects of host immune response. We examine the relevance, advantages, and pitfalls of experimental systems of fungal infections in various mini-hosts and compare them with what is known in experimental systems in mammalian animal models.

Animals↗