Renal function in patients with significant tricuspid regurgitation: pathophysiological mechanisms and prognostic implications.

BACKGROUND: The pathophysiological mechanisms linking tricuspid regurgitation (TR) and chronic kidney disease (CKD) remain unknown. This study aimed to determine which pathophysiological mechanisms related to TR are independently associated with renal dysfunction and to evaluate the impact of renal impairment on long-term prognosis in patients with significant (≥ moderate) secondary TR. METHODS: A total of 1234 individuals (72 [IQR 63-78] years, 50% male) with significant secondary TR were followed up for the occurrence of all-cause mortality and the presence of significant renal impairment (eGFR of <60 mL min-1  1.73 m-2 ) at the time of baseline echocardiography. RESULTS: Multivariable analysis demonstrated that severe right ventricular (RV) dysfunction (TAPSE < 14 mm) was independently associated with the presence of significant renal impairment (OR 1.49, 95% CI 1.11 to 1.99, P = 0.008). Worse renal function was associated with a significant reduction in survival at 1 and 5 years (85% vs. 87% vs. 68% vs. 58% at 1 year, and 72% vs. 64% vs. 39% vs. 19% at 5 years, for stage 1, 2, 3 and 4-5 CKD groups, respectively, P < 0.001). The presence of severe RV dysfunction was associated with reduced overall survival in stage 1-3 CKD groups, but not in stage 4-5 CKD groups. CONCLUSIONS: Of the pathophysiological mechanisms identified by echocardiography that are associated with significant secondary TR, only severe RV dysfunction was independently associated with the presence of significant renal impairment. In addition, worse renal function according to CKD group was associated with a significant reduction in survival.

Comparison of two case difficulty assessment methods on cohorts of undergraduate dental students - a multi-centre study.

AIM: To compare the educational benefits and user friendliness of two anonymized endodontic case difficulty assessment (CDA) methods. METHODOLOGY: A cohort (n = 206) of fourth-year undergraduate dental students were recruited from four different Dental Schools and divided randomly into two groups (Group A and B). The participants assessed six test endodontic cases using anonymized versions of the American Association of Endodontists (AAE) case difficulty assessment form (AAE Endodontic Case Difficulty Assessment Form and Guidelines, 2006) and EndoApp, a web-based CDA tool. Group A (n = 107) used the AAE form for assessment of the first three cases, followed by EndoApp for the latter. Group B (n = 99) used EndoApp for the initial three cases and switched to the AAE form for the remainder. Data were collected online and analysed to assess participants' knowledge reinforcement and agreement with the recommendation generated. Statistical analysis was performed using the two-way mixed model anova, Cohen's Kappa (κ) and independent t-tests, with the levels of significance set at P < 0.05. Additionally, participants' feedback and preference for CDA was also gathered. RESULTS: There was a significant increase in knowledge reinforcement for the AAE form and EndoApp (P = 0.001) after assessment of the first three test cases. However, this increase was not significant (P = 0.842) between the CDA methods. Overall, the AAE form and EndoApp had slight (κ = 0.176, P < 0.001) and substantial (κ = 0.668, P < 0.001) levels of agreement, respectively, and the difference was statistically significant (P < 0.001). Participants' feedback on user friendliness favoured EndoApp for all parameters measured. EndoApp was preferred by 65% of the cohort, whereas only 11% chose the AAE form for CDA. CONCLUSIONS: Both the AAE form and EndoApp were beneficial for dental education. EndoApp was reliable in helping with decisions to treat or refer, and combined with user friendliness, it was the preferred choice for CDA.

Relationship between ventilatory constraint and muscle fatigue during exercise in COPD.

Dynamic hyperinflation and leg muscle fatigue are independently associated with exercise limitation in patients with chronic obstructive pulmonary disease (COPD). The aims of the present study were to examine 1) the relationship between these limitations and 2) the effect of delaying ventilatory limitation on exercise tolerance and leg muscle fatigue. In total, 11 patients with COPD (with a forced expiratory volume in one second of 52% predicted) completed two cycling bouts breathing either room air or heliox, and one bout breathing heliox but stopping at room air isotime. End-expiratory lung volume (EELV), leg muscle fatigue and exercise time were measured. On room air, end-exercise EELV was negatively correlated with leg fatigue. Heliox increased exercise time (from 346 to 530 s) and leg fatigue (by 15%). At isotime, there was no change in leg fatigue, despite a reduction in EELV compared with end-exercise, in both room air and heliox. The change in exercise time with heliox was best correlated with room air leg fatigue and end-inspiratory lung volume. Patients with chronic obstructive pulmonary disease who had greater levels of dynamic hyperinflation on room air had less muscle fatigue. These patients were more likely to increase exercise tolerance with heliox, which resulted in greater leg muscle fatigue.

EMAAS: an extensible grid-based rich internet application for microarray data analysis and management.

BACKGROUND: Microarray experimentation requires the application of complex analysis methods as well as the use of non-trivial computer technologies to manage the resultant large data sets. This, together with the proliferation of tools and techniques for microarray data analysis, makes it very challenging for a laboratory scientist to keep up-to-date with the latest developments in this field. Our aim was to develop a distributed e-support system for microarray data analysis and management. RESULTS: EMAAS (Extensible MicroArray Analysis System) is a multi-user rich internet application (RIA) providing simple, robust access to up-to-date resources for microarray data storage and analysis, combined with integrated tools to optimise real time user support and training. The system leverages the power of distributed computing to perform microarray analyses, and provides seamless access to resources located at various remote facilities. The EMAAS framework allows users to import microarray data from several sources to an underlying database, to pre-process, quality assess and analyse the data, to perform functional analyses, and to track data analysis steps, all through a single easy to use web portal. This interface offers distance support to users both in the form of video tutorials and via live screen feeds using the web conferencing tool EVO. A number of analysis packages, including R-Bioconductor and Affymetrix Power Tools have been integrated on the server side and are available programmatically through the Postgres-PLR library or on grid compute clusters. Integrated distributed resources include the functional annotation tool DAVID, GeneCards and the microarray data repositories GEO, CELSIUS and MiMiR. EMAAS currently supports analysis of Affymetrix 3' and Exon expression arrays, and the system is extensible to cater for other microarray and transcriptomic platforms. CONCLUSION: EMAAS enables users to track and perform microarray data management and analysis tasks through a single easy-to-use web application. The system architecture is flexible and scalable to allow new array types, analysis algorithms and tools to be added with relative ease and to cope with large increases in data volume.

Structure and function of the small ribozymes.

Recently, major advances have been made toward increasing our understanding of small ribozyme structure and function. The first general acid-base catalytic mechanism for a ribozyme has been defined. Shifted nucleotide pK(a) values have been found to be surprisingly frequent structural elements. Finally, the dynamic nature of RNA catalysis has been highlighted through new structural and biochemical information.

Combined EM/X-ray imaging yields a quasi-atomic model of the adenovirus-related bacteriophage PRD1 and shows key capsid and membrane interactions.

BACKGROUND: The dsDNA bacteriophage PRD1 has a membrane inside its icosahedral capsid. While its large size (66 MDa) hinders the study of the complete virion at atomic resolution, a 1.65-A crystallographic structure of its major coat protein, P3, is available. Cryo-electron microscopy (cryo-EM) and three-dimensional reconstruction have shown the capsid at 20-28 A resolution. Striking architectural similarities between PRD1 and the mammalian adenovirus indicate a common ancestor. RESULTS: The P3 atomic structure has been fitted into improved cryo-EM reconstructions for three types of PRD1 particles: the wild-type virion, a packaging mutant without DNA, and a P3-shell lacking the membrane and the vertices. Establishing the absolute EM scale was crucial for an accurate match. The resulting "quasi-atomic" models of the capsid define the residues involved in the major P3 interactions, within the quasi-equivalent interfaces and with the membrane, and show how these are altered upon DNA packaging. CONCLUSIONS: The new cryo-EM reconstructions reveal the structure of the PRD1 vertex and the concentric packing of DNA. The capsid is essentially unchanged upon DNA packaging, with alterations limited to those P3 residues involved in membrane contacts. These are restricted to a few of the N termini along the icosahedral edges in the empty particle; DNA packaging leads to a 4-fold increase in the number of contacts, including almost all copies of the N terminus and the loop between the two beta barrels. Analysis of the P3 residues in each quasi-equivalent interface suggests two sites for minor proteins in the capsid edges, analogous to those in adenovirus.

Specific DNA binding by different classes of human p53 mutants.

The p53 protein is a multifunctional transcription factor which orchestrates cellular responses to DNA damage, so helping to conserve genomic stability. It may also regulate genes involved in intercellular signalling, such as thrombospondin, a negative regulator of angiogenesis and metastatic spread. Activation of p53 target genes requires sequence-specific DNA binding, a function which maps to the central core of the protein. Missense point mutations within this domain inactivate p53 tumour suppressor function and involve either (i) DNA contact residues, or (ii) residues important for conformational structure. Using in vitro techniques we have analysed seven DNA contact mutants and 17 structural mutants known to occur in cancer. We show that DNA contact mutants can be carried into specific DNA interaction when co-expressed with wild type protein. For structural mutants, 9/17 retained DNA binding capacity and, with one exception, DNA binding correlated with conformational flexibility of the mutant protein. The exception was Asp281, which appeared essential for DNA interaction, probably due to its ability to form salt bridges with DNA contact residues Arg273 and Arg280. We suggest that different classes of p53 mutant may prove amenable to different strategies for restoration of wild type tumour suppressor function as means of anti-cancer therapy.

Dopamine release and metabolism in the rat striatum: an analysis by 'in vivo' brain microdialysis.

Brain microdialysis studies on the mechanisms underlying dopamine release in the rat striatum provide evidence that both exocytotic and carrier-dependent processes operate in vivo. While several releasers (potassium, veratrine, amphetamine, ouabain) utilize newly synthesized stores of dopamine, tyramine is uniquely sensitive to depletion of vesicular storage by reserpine. Extracellular DOPAC is closely associated with the newly synthesized pool of dopamine and experiments with selective monoamine oxidase inhibitors suggest that DOPAC is formed mainly by MAO-A. Recent work on the two dopamine receptors suggest that release by different mechanisms may selectively activate D1 or D2 receptor subtypes.

Structure-mapping of the hairpin ribozyme. Magnesium-dependent folding and evidence for tertiary interactions within the ribozyme-substrate complex.

We have used chemical modification analysis to probe the solution structure of the hairpin ribozyme. The modifying reagents dimethylsulfate, 1-cyclohexyl-N'-[2-(N-methylmorpholino) ethyl-carbodiimide-p-toluenesulfonate, kethoxal, diethylpyrocarbonate and (2,12-dimethyl-3,7,11,17- tetraazabicyclo [11.3.1]heptadeca-1(17),2,11,13,15-pentaenato) nickel(II) perchlorate were used to probe functional groups that participate in Watson-Crick and non-canonical base-pairs. Our results confirm the existence of four short helices (3 to 6 bp) within the ribozyme-substrate complex, and demonstrate that one intramolecular helix (helix 4) is comprised of three base-pairs rather than the previously suggested five. In the absence of magnesium, the ribozyme is observed to fold into its secondary structure. Upon addition of magnesium, a striking difference in chemical modification is observed, particularly at sites within the ribozyme's large internal loop (loop B) that are essential for catalytic function (bases 21 to 26). Moreover, magnesium-dependent folding clearly destabilizes an A-U base-pair in a region where a proposed bend is required to juxtapose the catalytically essential loops A and B. Upon addition of substrate, no changes are observed in the structure of helix 3, loop B or helix 4. However, strong protection of bases in the substrate-binding domain is observed, including those located across internal loop A. The modification data are consistent with the formation of a previously proposed tertiary structure motif within loop B that includes non-canonical G-A, A-U and A-A base-pairs, and that is identical with those identified by NMR analysis of loop E of 5 S rRNA and the sarcin/ricin loop of 28 S rRNA. Our results indicate that the hairpin ribozyme adopts a stable magnesium-dependent tertiary structure to which the substrate binds without inducing major conformational changes, and that substrate recognition is likely to involve non-canonical base-pairs between the ribozyme and substrate sequences adjacent to the cleavage site.

Solution structure of the conserved 16 S-like ribosomal RNA UGAA tetraloop.

The solution structure of the highly conserved UGAA tetraloop found at the 3' end of eukaryotic 16 S-like ribosomal RNA has been solved by nuclear magnetic resonance spectroscopy in the form of the 12 nucleotide hairpin 5'-GGUG[UGAA]CACC. The UGAA tetraloop displays a novel fold. The backbone turn occurs between the G and the third A in the loop, with the U and G in a 5' stack and the As in a 3' stacking arrangement. The loop is closed by a U-A mismatch in which the O2, 2'OH, and O4' groups of the U are within hydrogen bonding distance of the amino group of the A. The tetraloop does not make a uridine-turn, even though its sequence is identical to a U-turn found within the anticodon loop of tRNA(Phe). The hydrogen bonding pattern in the tetraloop provides insight into the function of base modifications found in vivo within this portion of 16 S-like rRNA.

Mutant ATP-binding RNA aptamers reveal the structural basis for ligand binding.

The solution structure of the ATP-binding RNA aptamer has recently been determined by NMR spectroscopy. The three-dimensional fold of the molecule is determined to a large extent by stacking and hydrogen bond interactions. In the course of the structure determination it was discovered that several highly conserved nucleotides in the binding pocket can be substituted while retaining binding under NMR conditions. These surprising findings allow a closer look at the interactions that determine stability and specificity of the aptamer as well as local structural features of the molecule. The binding properties of ATP binder mutants and modified ligand molecules are explored using NMR spectroscopy, column binding studies and molecular modeling. We present additional evidence and new insights regarding the network of hydrogen bonds that defines the structure and determines stability and specificity of the aptamer.

Bacteriophage PRD1 contains a labile receptor-binding structure at each vertex.

Bacteriophage PRD1 is a membrane-containing virus with an unexpected similarity to adenovirus. We mutagenized unassigned PRD1 genes to identify minor capsid proteins that could be structural or functional analogs to adenovirus proteins. We report here the identification of an amber mutant, sus525, in an essential PRD1 gene XXXI. The gene was cloned and the gene product was overexpressed and purified to near homogeneity. Analytical ultracentrifugation and gel filtration showed that P31 is a homopentamer of about 70 kDa. The protein was shown to be accessible on the virion surface and its absence in the sus525 particles led to the deficiency of two other viral coat proteins, protein P5 and the adsorption protein P2. Cryo-electron microscopy and image reconstruction of the sus525 particles indicate that these proteins are located on the capsid vertices, because in these particles the entire vertex structure was missing along with the peripentonal major capsid protein P3 trimers. Sus525 particles package DNA effectively but loose it upon purification. All of the PRD1 vertex structures are labile and potentially capable of mediating DNA delivery; this is in contrast to other dsDNA phages which employ a single vertex for packaging and delivery. We propose that this arises from a symmetry mismatch between protein P2 and the pentameric P31 in analogy to that between the adenovirus penton base and the receptor-binding spike.

Senescence in innate immune responses: reduced neutrophil phagocytic capacity and CD16 expression in elderly humans.

Elderly humans are more susceptible to bacterial infections because of declining immune status. We have investigated the effect of aging on neutrophil bactericidal responses, comparing neutrophil function in healthy, young (23-35 years) and elderly (>65 years) volunteers. Superoxide generation in response to fMLP was slightly increased in neutrophils from elderly donors, and serum from the elderly was able to opsonize E. coli efficiently. In contrast, phagocytic index was significantly lower in neutrophils from the elderly, compared with young donors (P<0.005). CD11a and CD11b expression was not affected by age, but CD16 was significantly reduced in neutrophils from elderly donors (P<0.0001). CD16 expression and phagocytic index were measured in the same neutrophils using FITC-labeled E. coli, PE-conjugated anti-CD16 antibody, and CD16 expression correlated with phagocytic index (r=0.83; P<0.05). In elderly patients with bacterial infection, CD16 expression remained low. We propose that reduced neutrophil CD16 expression and phagocytosis contribute to human immunesenescence.

Class-3 porin protein of Neisseria meningitidis: cloning and structure of the gene.

The gene coding for the class-3 protein of Neisseria meningitidis was cloned and sequenced. The deduced amino acid (aa) sequence was highly homologous (50-78%) to those of other neisserial porin proteins. Alignment of the aa sequence of five neisserial porin proteins pinpointed several regions of identity or near identity. These are assumed to be membrane-spanning beta-strands. A comparison of the homologies between these neisserial porins showed that the class-3 protein is most closely related to the Neisseria gonorrhoeae P1A protein.

Repeated sequences isolated from Bordetella pertussis induce DNA rearrangements and deletions at high frequency.

Two repeated sequences (RS) from Bordetella pertussis were cloned in Escherichia coli and sequenced. The RS, called RSBP1 and RSBP3, are highly homologous to other B. pertussis RS. The recombinant plasmids containing RSBP1 and RSBP3 or transposon-like structures of these elements were not stable but segregated plasmids with deletions or rearranged DNA. RS of B. pertussis seem to be able to stimulate both intra- and inter-genomic RecA-independent recombination events. In at least one case, the observed deletion had occurred precisely between the RS terminus and a site with sequence homology to the terminus. The high frequency rearrangements associated with the RS imply that the RS are transposable elements.

Neutrophil ageing and immunesenescence.

As humans age, their morbidity and mortality from infection increases, their response to vaccination declines and they have an increased incidence of inflammatory diseases and cancer. The reasons for these effects are clearly complex, but reduced efficiency of the innate and adaptive immune system is likely to be important in the pathology of old age. Age-related changes in the adaptive immune system are well-documented and include alterations in T cell phenotype and effector functions and a reduced ability of B cells to produce high affinity antibody. In contrast, the innate immune system has been less well researched and the perception amongst many immunogerontologists is that this branch of the immune system is only moderately affected by age. However, it is becoming increasingly clear that the adaptive and innate immune systems co-operate at several levels to ensure the optimal immune response and any decline in adaptive immunity will impact upon the function of the innate immune system and vice-versa. Here, we review the literature concerning intrinsic age-related changes in neutrophil responses and consider how changes in lymphocyte function with age might further compromise efficiency of neutrophil function.

On the epileptogenic effects of kainic acid and dihydrokainic acid in the dentate gyrus of the rat.

The in vivo effects of the acidic amino receptor agonist, kainic acid and the inhibitors of the uptake of glutamate, dihydrokainic acid and threo-3-hydroxyaspartate, on spontaneous activity and perforant path evoked field potentials were examined in the dentate gyrus of the rat. The effect of these compounds on extracellular levels of endogenous amino acids in the hippocampus was assessed simultaneously using in vivo microdialysis. Kainic acid (10-100 microM) and dihydrokainic acid (1-10 mM) both evoked epileptiform activity and an apparent loss of recurrent inhibition (as assessed using the paired-pulse technique). Extracellular increases in taurine, alanine and phosphoethanolamine were noted following administration of kainate (100 microM) and dihydrokainate (1-10 mM). An increase in extracellular glutamate and aspartate was also noted in rats treated with dihydrokainate (100 microM-10 mM). In contrast, threo-3-hydroxyaspartate did not induce epileptiform activity, suggesting that the epileptogenic effects of dihydrokainate and kainate are not mediated by inhibition of uptake. The effect of the N-methyl-D-aspartate receptor antagonist, D-2-amino-5-phosphonovalerate on these responses was studied. This compound attenuated the epileptiform activity and reversed the apparent loss of recurrent inhibition in response to both kainic acid and dihydrokainic acid. These data suggest that activation of N-methyl-D-aspartate receptors underlies the epileptogenic effects of both compounds, and the possible mechanisms which might be involved in this response are discussed.

Intracerebroventricular injection of a nitric oxide synthase inhibitor does not affect long-term slope potentiation in vivo.

Although there is evidence from in vitro studies to suggest that NO synthesis may be involved in the induction of hippocampal LTP, other in vitro studies and experiments conducted in vivo have provided conflicting results. In agreement with previous work conducted in this laboratory using an i.p. route of administration, this paper reports that i.c.v. injections of the NO synthase inhibitor, N omego-nitro-L-arginine methyl ester (L-NAME), at a dose sufficient to inhibit hippocampal NO synthase by 90-95%, failed to block the induction of LTP in the dentate gyrus in vivo (as measured by the change in the slope of the early rising phase of the field EPSP). The failure to block LTP occurred following both a strong and a weak tetanus. L-NAME injections did, however, result in a small but transient increase in the baseline slope of the field EPSP, a more prolonged enhancement of the baseline population spike, and a significant attenuation of spike potentiation induced by a strong tetanus. These results offer no support for the hypothesis that NO synthase is required for the induction of the synaptic component of LTP, but do suggest a role for NO in the control of cell excitability in the hippocampus.

A parametric study of the behavioral effects of phencyclidine in adult cats.

Five adult cats received four doses of phencyclidine to determine the behavioral effects of this compound. On alternate weeks the animals received control injections of saline vehicle. Dose-dependent behavioral changes occurred in three general categories (posture, locomotor activity and stereotyped head movements). In small doses (0.1 and 0.5 mg/kg), major postural effects consisted of head and body tremors and loss of hindlimb support. In larger doses (1.0 and 2.0 mg/kg), the postural effects occurred more rapidly and became more severe as animals lost both forelimb and hindlimb support and ultimately became immobile. Small doses of phencyclidine produced decreases in locomotor activity, followed by increases. Larger doses produced initial increases in activity. Increases in head movement stereotypies were produced by all doses of phencyclidine.

An analysis of the effects of excitatory amino acid receptor antagonists on evoked field potentials in the olfactory bulb.

The effects of excitatory amino acid antagonists on extracellular field potentials in the olfactory bulb produced by lateral olfactory tract stimulation were analysed in vivo. The compounds tested D-2-amino-5-phosphonovalerate, L-(+)2-amino-4-phosphonobutyrate, gamma-D-glutamylglycine, L-glutamic acid diethylester and cis-2,3-piperidine dicarboxylic acid, were administered by brain dialysis. Of the compounds tested, only cis-2,3 piperidine-dicarboxylic acid and gamma-D-glutamylglycine were able to suppress the synaptic excitation of granule cells. This pharmacological profile suggests the involvement of non-N-methyl-D-aspartate receptors. However, the suppression was accompanied by a reduction in the amplitude of the presynaptic volley. A second finding was that D-2-amino-5-phosphono-valerate and gamma-D-glutamyl glycine attenuated granule cell mediated inhibition of mitral cells, suggesting the involvement of N-methyl-D-aspartate-sensitive receptors. The possibility that mitral cells and that either centrifugal fibres, or an intrinsic olfactory bulb feedback loop might use an excitatory amino acid as its neurotransmitter is therefore discussed.