Affinity Purification of Embryo Proteins Phosphorylated on Tyrosine In Vitro*

Fertilization of the sea urchin egg is accompanied by activation of one or more protein tyrosine kinases which have been shown to phosphorylate a restricted set of egg proteins in vitro. In order to characterize these tyrosine kinase substrates, we have used an antibody specific for phosphotyrosine to prepare an immunoaffinity column capable of binding phosphotyrosine containing proteins. This column bound five ³²P-labelled proteins from detergent extracts of embryo membranes phosphorylated in vitro. All were very tightly membrane associated, requiring detergent solubilization. Phosphoamino acid analysis revealed that each of these proteins was phosphorylated exclusively on tyrosine, indicating that they do not act as substrates for other classes of protein kinases.     

Facilitated diffusion of myoglobin and creatine kinase and reaction-diffusion constraints of aerobic metabolism under steady-state conditions in skeletal muscle

The roles of creatine kinase (CK) and myoglobin (Mb) on steady-state facilitated diffusion and temporal buffering of ATP and oxygen, respectively, are assessed within the context of a reaction-diffusion model of muscle energetics. Comparison of the reaction-diffusion model with experimental data from a wide range of muscle fibers shows that the experimentally observed skeletal muscle fibers are generally not limited by diffusion, and the model further indicates that while some muscle fibers operate near the edge of diffusion limitation, no detectable effects of Mb and CK on the effectiveness factor, a measure of diffusion constraints, are observed under steady-state conditions. However, CK had a significant effect on average ATP concentration over a wide range of rates and length scales within the reaction limited regime. The facilitated diffusion functions of Mb and CK become observable in the model for larger size cells with low mitochondrial volume fraction and for low boundary O(2) concentration and high ATP demand, where the fibers may be limited by diffusion. From the transient analysis it may be concluded that CK primarily functions to temporally buffer ATP as opposed to facilitating diffusion while Mb has a small temporal buffering effect on oxygen but does not play any significant role in steady-state facilitated diffusion in skeletal muscle fibers under most physiologically relevant regions.     

Diffusional constraints on energy metabolism in skeletal muscle

Aerobic metabolic flux depends on the diffusion of high-energy phosphate molecules (e.g., ATP and phosphocreatine) from the mitochondria to cellular ATPases, as well as the diffusion of other molecules (e.g., ADP, Pi) back to the mitochondria. Here, we develop an approach for evaluating the influence of intracellular metabolite diffusion on skeletal muscle aerobic metabolism through the application of the effectiveness factor (η). This parameter provides an intuitive and informative means of quantifying the extent to which diffusion limits metabolic flux. We start with the classical approach assuming an infinite supply of substrate at the fiber boundary, and we expand this model to ultimately include nonlinear boundary and homogeneous reactions. Comparison of the model with experimental data from a wide range of skeletal muscle types reveals that most muscle fibers are not substantially limited by diffusion (η close to unity), but many are on the brink of rather substantial diffusion limitation. This implies that intracellular metabolite diffusion does not dramatically limit aerobic metabolic flux in most fibers, but it likely plays a role in limiting the evolution of muscle fiber design and function.     

Definition of common carotid wall thickness affects risk classification in relation to degree of internal carotid artery stenosis: the Plaque At RISK (PARISK) study

Background

Mean or maximal intima-media thickness (IMT) is commonly used as surrogate endpoint in intervention studies. However, the effect of normalization by surrounding or median IMT or by diameter is unknown. In addition, it is unclear whether IMT inhomogeneity is a useful predictor beyond common wall parameters like maximal wall thickness, either absolute or normalized to IMT or lumen size. We investigated the interrelationship of common carotid artery (CCA) thickness parameters and their association with the ipsilateral internal carotid artery (ICA) stenosis degree.

Methods

CCA thickness parameters were extracted by edge detection applied to ultrasound B-mode recordings of 240 patients. Degree of ICA stenosis was determined from CT angiography.

Results

Normalization of maximal CCA wall thickness to median IMT leads to large variations. Higher CCA thickness parameter values are associated with a higher degree of ipsilateral ICA stenosis (p?<?0.001), though IMT inhomogeneity does not provide extra information. When the ratio of wall thickness and diameter instead of absolute maximal wall thickness is used as risk marker for having moderate ipsilateral ICA stenosis (>50%), 55 arteries (15%) are reclassified to another risk category.

Conclusions

It is more reasonable to normalize maximal wall thickness to end-diastolic diameter rather than to IMT, affecting risk classification and suggesting modification of the Mannheim criteria.

Trial registration

Clinical trials.gov NCT01208025.

     

Maximum likelihood estimation of the heterogeneity of substitution rate among nucleotide sites

This paper presents a maximum likelihood approach to estimating the variation of substitution rate among nucleotide sites. We assume that the rate varies among sites according to an invariant+gamma distribution, which has two parameters: the gamma parameter alpha and the proportion of invariable sites theta. Theoretical treatments on three, four, and five sequences have been conducted, and computer program have been developed. It is shown that rho = (1 + theta alpha)/(1 + alpha) is a good measure for the rate heterogeneity among sites. Extensive simulations show that (1) if the proportion of invariable sites is negligible, i.e., theta = 0, the gamma parameter alpha can be satisfactorily estimated, even with three sequences; (2) if the proportion of invariable sites is not negligible, the heterogeneity rho can still be suitably estimated with four or more sequences; and (3) the distances estimated by the proposed method are almost unbiased and are robust against violation of the assumption of the invariant + gamma distribution.      

Preparation of plasma membranes from fertilized sea urchin eggs

A new method is presented for preparation of highly purified plasma membranes from fertilized sea urchin eggs. The purified plasma membranes are in vesicle form and are highly enriched in ouabain inhibitable, Na+/K+ ATPase activity. Analysis of membrane proteins by sodium dodecyl sulfate-gel electrophoresis indicates that several high-molecular-weight proteins characteristic of plasma membranes from unfertilized eggs are absent in plasma membranes from fertilized eggs.     

Transformation of Neurospora crassa with the cloned am (glutamate dehydrogenase) gene.

We used DNA containing the am gene of Neurospora crassa, cloned in the lambda replacement vector lambdaL-47 (this clone is designated lambdaC-10), and plasmid vector subclones of this DNA to transform am deletion and point mutant strains. By means of subcloning, all sequences required for transformation to am prototrophy and expression of glutamate dehydrogenase have been shown to reside on a 2.5-kilobase BamHI fragment. We also characterized several am+ strains that were obtained after transformation with lambdaC-10. These strains showed Mendelian segregation of the am+ gene, although less than 50% of the transformed strains showed the normal linkage relationship of am with inl. In all cases tested, the strains had incorporated lambda DNA as well. The lambda DNA also showed a Mendelian segregation pattern. In one case, the incorporation of am DNA in a novel position was associated with a mutagenic event producing a strain with a very tight colonial morphology. In all cases in which the am+ gene had become the resident of a new chromosome, glutamate dehydrogenase was produced to only 10 to 20% of the wild-type levels.