Calcium gradient-dependent and calcium gradient-independent phosphorylation of sarcoplasmic reticulum by orthophosphate. The role of magnesium.

Phosphorylation of the calcium-transport ATPase of skeletal muscle sarcoplasmic reticulum by inorganic phosphate was investigated in the presence or absence of a calcium gradient. The maximum phosphoprotein formation in the presence of a calcium gradient at 20 degrees C and pH 7.0 is approximately 4 nmol/mg sarcoplasmic reticulum protein, but only between 2.4 and 2.8 nmol/mg protein in the absence of a calcium gradient, using Ionophore X-537 A or phospholipase-A-treated sarcoplasmic reticulum vesicles. Maximum phosphoprotein formation independent of calcium gradient at 20 degrees C and pH 6.2 is in the range of 3.6--4 nmol/mg protein. Half-maximum phosphoprotein formation dependent on calcium gradient was achieved with 0.1--0.2 mM free orthophosphate at 10 mM free magnesium or at 0.1--0.2 mM free magnesium at 10 mM free orthophosphate. Phosphoprotein formation independent of calcium gradient is in accordance with a model which assumes, firstly, the formation of a ternary complex of the ATPase protein with orthophosphate and magnesium (E . Pi . Mg) in equilibrium with the phosphoprotein (E-Pi . Mg) and, secondly, an interdependence of both ions in the formation of the ternary complex. The apparent equilibrium constant was 0.6 and the apparent dissociation constants KMg, KMg', KPi and KPi' were 8.8, 1.9, 7.2 and 1.5 mM respectively, assuming a total concentration of the phosphorylation site per enzyme of 7 nmol/mg protein.     

Multiple Hypotheses in the Analysis of a Crossover Trial

Crossover trials are used in a variety of fields, such as medicine, biology, psychology, and some commercial goods investigations. The aim of this paper is to extend a methodology for multiple comparisons to the problem of testing in crossover trials with two treatments. These two treatments are given in two orderings, treatment A first or treatment B first. We perform inference on the effect of one treatment relative to the effect of the other, without assuming that these effects are independent of treatment ordering, using techniques from order-restricted inference and multiple comparisons, and compare to some existing multiple comparison tests.     

Small-sample confidence regions in exponential families

This article presents an algorithm for small-sample conditional confidence regions for two or more parameters for any discrete regression model in the generalized linear interactive model family. Regions are constructed by careful inversion of conditional hypothesis tests. This method presupposes the use of approximate or exact techniques for enumerating the sample space for some components of the vector of sufficient statistics conditional on other components. Such enumeration may be performed exactly or by exact or approximate Monte Carlo, including the algorithms of Kolassa and Tanner (1994, Journal of the American Statistical Association 89, 697-702; 1999, Biometrics 55, 246-251). This method also assumes that one can compute certain conditional probabilities for a fixed value of the parameter vector. Because of a property of exponential families, one can use this set of conditional probabilities to directly compute the conditional probabilities associated with any other value of the vector of the parameters of interest. This observation dramatically reduces the computational effort required to invert the hypothesis test to obtain the confidence region. To construct a region with confidence level 1 - alpha, the algorithm begins with a grid of values for the parameters of interest. For each parameter vector on the grid (corresponding to the current null hypothesis), one transforms the initial set of conditional probabilities using exponential tilting and then calculates the p value for this current null hypothesis. The confidence region is the set of parameter values for which the p value is at least alpha.     

Does Tinnitus Distress Depend on Age of Onset?

Objectives

Tinnitus is the perception of a sound in the absence of any physical source of it. About 5–15% of the population report hearing such a tinnitus and about 1–2% suffer from their tinnitus leading to anxiety, sleep disorders or depression. It is currently not completely understood why some people feel distressed by their tinnitus, while others don''t. Several studies indicate that the amount of tinnitus distress is associated with many factors including comorbid anxiety, comorbid depression, personality, the psychosocial situation, the amount of the related hearing loss and the loudness of the tinnitus. Furthermore, theoretical considerations suggest an impact of the age at tinnitus onset influencing tinnitus distress.

Methods

Based on a sample of 755 normal hearing tinnitus patients we tested this assumption. All participants answered a questionnaire on the amount of tinnitus distress together with a large variety of clinical and demographic data.

Results

Patients with an earlier onset of tinnitus suffer significantly less than patients with an onset later in life. Furthermore, patients with a later onset of tinnitus describe their course of tinnitus distress as more abrupt and distressing right from the beginning.

Conclusion

We argue that a decline of compensatory brain plasticity in older age accounts for this age-dependent tinnitus decompensation.     

Influence of sulfasalazine, 5-aminosalicylic acid and sulfapyridine on prostanoid synthesis and metabolism in rabbit colonic mucosa

The effects of sulfasalazine (SASP) and its cleavage products 5-aminosalicylic acid (5-ASA) and sulfapyridine (SP) on prostanoid (PG) synthesis and degradation were determined in rabbit colonic mucosa fractions in vitro. When the microsomal fraction was incubated with (14C)arachidonic acid, 10(-3) M SASP and SP did not markedly change the formation of labeled PGE2, PGF2 alpha, TxB2 and 6-keto-PGF1 alpha X 10(-4) M 5-ASA increased synthesis about 2.7-fold; the pattern of PG identified was unaltered. In the presence of the 10-fold higher concentration of 5-ASA, PG synthesis remained elevated at a similar level. When the cytosolic fraction was incubated with (3H)PGE2, 10(-3) M 5-ASA was without influence and 10(-3) M SP decreased slightly PGE2 breakdown. However, SASP showed a pronounced inhibitory effect at 10(-5) M and inhibition of PGE2 degradation was complete at 10(-3) M SASP. The results are compatible with the assumption that stimulation of PG synthesis by 5-ASA is related to therapeutic benefit in the treatment of ulcerative colitis.     

Proteome of the phytopathogen <Emphasis Type="Italic">Xanthomonas citri</Emphasis> subsp. <Emphasis Type="Italic">citri</Emphasis>: a global expression profile

Background  

Citrus canker is a disease caused by Xantomonas citri subsp.citri (Xac), and has emerged as one of the major threats to the worldwide citrus crop because it affects all commercial citrus varieties, decreases the production and quality of the fruits and can spread rapidly in citrus growing areas. In this work, the first proteome of Xac was analyzed using two methodologies, two-dimensional liquid chromatography (2D LC) and tandem mass spectrometry (MS/MS).     

Microarray-based maps of copy-number variant regions in European and sub-Saharan populations

The genetic basis of phenotypic variation can be partially explained by the presence of copy-number variations (CNVs). Currently available methods for CNV assessment include high-density single-nucleotide polymorphism (SNP) microarrays that have become an indispensable tool in genome-wide association studies (GWAS). However, insufficient concordance rates between different CNV assessment methods call for cautious interpretation of results from CNV-based genetic association studies. Here we provide a cross-population, microarray-based map of copy-number variant regions (CNVRs) to enable reliable interpretation of CNV association findings. We used the Affymetrix Genome-Wide Human SNP Array 6.0 to scan the genomes of 1167 individuals from two ethnically distinct populations (Europe, N=717; Rwanda, N=450). Three different CNV-finding algorithms were tested and compared for sensitivity, specificity, and feasibility. Two algorithms were subsequently used to construct CNVR maps, which were also validated by processing subsamples with additional microarray platforms (Illumina 1M-Duo BeadChip, Nimblegen 385K aCGH array) and by comparing our data with publicly available information. Both algorithms detected a total of 42669 CNVs, 74% of which clustered in 385 CNVRs of a cross-population map. These CNVRs overlap with 862 annotated genes and account for approximately 3.3% of the haploid human genome.We created comprehensive cross-populational CNVR-maps. They represent an extendable framework that can leverage the detection of common CNVs and additionally assist in interpreting CNV-based association studies.     

Approximate Monte Carlo conditional inference in exponential families

This article presents an algorithm for approximate frequentist conditional inference on two or more parameters for any regression model in the Generalized Linear Model (GLIM) family. We thereby extend highly accurate inference beyond the cases of logistic regression and contingency tables implimented in commercially available software. The method makes use of the double saddlepoint approximations of Skovgaard (1987, Journal of Applied Probability 24, 875-887) and Jensen (1992, Biometrika 79, 693-703) to the conditional cumulative distribution function of a sufficient statistic given the remaining sufficient statistics. This approximation is then used in conjunction with noniterative Monte Carlo methods to generate a sample from a distribution that approximates the joint distribution of the sufficient statistics associated with the parameters of interest conditional on the observed values of the sufficient statistics associated with the nuisance parameters. This algorithm is an alternate approach to that presented by Kolassa and Tanner (1994, Journal of the American Statistical Association 89, 697-702), in which a Markov chain is generated whose equilibrium distribution under certain regularity conditions approximates the joint distribution of interest. In Kolassa and Tanner (1994), the Gibbs sampler was used in conjunction with these univariate conditional distribution function approximations. The method of this paper does not require the construction and simulation of a Markov chain, thus avoiding the need to develop regularity conditions under which the algorithm converges and the need for the data analyst to check convergence of the particular chain. Examples involving logistic and truncated Poisson regression are presented.     

Absence of binding sites for the transport inhibitor nitrobenzylthioinosine on nucleoside transport-deficient mouse lymphoma cells

Cells of an adenosine-resistant clone (AE₁) of S49 mouse lymphoma cells were compared with cells of the parental line with respect to (a) characteristics of nucleoside transport, (b) high affinity binding of the inhibitor of nucleoside transport, nitrobenzylthionisine (NBMPR), and (c) the antiproliferative effects of the nucleoside antibiotics, tubercidin, arabinosyladenine and showdomycin. Rates of inward transport of uridine, thymidine, adenosine, 2′-deoxyadenosine, tubercidin, showdomycin, and arabinosyladenine in AE₁ cells were less than 1% of those in cells of the parental S49 line. The inhibitor of nucleoside transport, NBMPR, reduced rates of inward nucleoside transport in S49 cells to levels comparable to those seen in the transport-defective mutant. S49 cells possessed high affinity sites that bound NBMPR (6.6 · 10⁴ sites/cell, K_d  0.2 nM), whereas site-specific binding of NBMPR to AE₁ cells was not demonstrable, indicating that loss of nucleoside transport activity in AE₁ cells was accompanied by loss of the high affinity NBMPR binding sites. Relative to S49 cells, AE₁ cells were resistant to the antiproliferative effects of tubercidin and showdomycin, but differences between the two cell lines in sensitivity toward arabinosyladenine were minor, suggesting that nucleoside transport activity was required for cytotoxicity of tubercidin and showdomycin, but not for that of arabinosyladenine.