Stimulation of carbohydrate metabolising enzymes by synthetic hypertrehalosemic peptides in thoracic musculature of the American cockroach, Periplaneta americana.

The ability of the synthetic hypertrehalosemic peptides, HT-I and HT-II, to influence the activities of glycogen phosphorylase, trehalase and hexokinase via elevation of Ca++ and cAMP levels was examined in thoracic musculature of the American cockroach, Periplaneta americana. The peptides effect dose- and time-dependent activation of phosphorylase, trehalase and hexokinase activities that occur concomitantly with elevated levels of intracellular calcium. In addition, HT-I increases the accumulation of cyclic AMP in muscle cells.     

Fate of Labeled Hydroxamates During Iron Transport from Hydroxamate-Iron Chelates

The fate of the hydroxamic acid-iron transport cofactors during iron uptake from the (59)Fe(3+) chelates of the (3)H-labeled hydroxamates schizokinen and aerobactin was studied by assay of simultaneous incorporation of both (59)Fe(3+) and (3)H. In the schizokinen-producing organism Bacillus megaterium ATCC 19213 transport of (59)Fe(3+) from the (3)H-schizokinen-(59)Fe(3+) chelate at 37 C was accompanied by rapid uptake and release (within 2 min) of (3)H-schizokinen, although (3)H-schizokinen discharge was temperature-dependent and did not occur at 0 C. In the schizokinen-requiring strain B. megaterium SK11 similar release of (3)H-schizokinen occurred only at elevated concentrations of the double-labeled chelate; at lower chelate concentrations, (3)H-schizokinen remained cell-associated. Temperature-dependent uptake of deferri (iron-free) (3)H-schizokinen to levels equivalent to those incorporated from the chelate form was noted in strain SK11, but strain ATCC 19213 showed only temperature-independent binding of low concentrations of deferri (3)H-schizokinen. These results indicate an initial temperature-independent binding of the ferric hydroxamate which is followed rapidly by temperature-dependent transport of the chelate into the cell and an enzyme catalyzed separation of iron from the chelate. The resulting deferri hydroxamate is discharged from the cell only when a characteristic intracellular concentration of the hydroxamate is exceeded, which happens in the schizokinen-requiring strain only at elevated concentrations of the chelate. This strain also appears to draw the deferri hydroxamate into the cell by a temperature-dependent mechanism. The aerobactin-producing organism Aerobacter aerogenes 62-1 also demonstrated rapid initial uptake and temperature-dependent discharge of (3)H-aerobactin during iron transport from (3)H-aerobactin-(59)Fe(3+), suggesting a similar ferric hydroxamate transport system in this organism.     

Hydrogen exchange of lysozyme powders. Hydration dependence of internal motions

The rate of exchange of the labile hydrogens of lysozyme was measured by out-exchange of tritium from the protein in solution and from powder samples of varied hydration level, for pH 2, 3, 5, 7, and 10 at 25 degrees C. The dependence of exchange of powder samples on the level of hydration was the same for all pHs. Exchange increased strongly with increased hydration until reaching a rate of exchange that is constant above 0.15 g of H2O/g of protein (120 mol of H2O/mol of protein). This hydration level corresponds to coverage of less than half the protein surface with a monolayer of water. No additional hydrogen exchange was observed for protein powders with higher water content. Considered in conjunction with other lysozyme hydration data [Rupley, J. A., Gratton, E., & Careri, G. (1983) Trends Biochem. Sci. (Pers. Ed.) 8, 18-22], this observation indicates that internal protein dynamics are not strongly coupled to surface properties. The use of powder samples offers control of water activity through regulation of water vapor pressure. The dependence of the exchange rate on water activity was about fourth order. The order was pH independent and was constant from 114 to 8 mol of hydrogen remaining unexchanged/mol of lysozyme. These results indicate that the rate-determining step for protein hydrogen exchange is similar for all backbone amides and involves few water molecules. Powder samples were hydrated either by isopiestic equilibration, with a half-time for hydration of about 1 h, or by addition of solvent to rapidly reach final hydration. Samples hydrated slowly by isopiestic equilibration exhibited more exchange than was observed for samples of the same water content that had been hydrated rapidly by solvent addition. This difference can be explained by salt and pH effects on the nearly dry protein. Such effects would be expected to contribute more strongly during the isopiestic equilibration process. Solution hydrogen exchange measurements made for comparison with the powder measurements are in good agreement with published data. Rank order was proven the same for all pHs by solution pH jump experiments. The effect of ionic strength on hydrogen exchange was examined at pH 2 and pH 5 for protein solutions containing up to 1.0 M added salt. The influence of ionic strength was similar for both pHs and was complex in that the rate increased, but not monotonically, with increased ionic strength.     

Barley aleurone cells contain two types of vacuoles. Characterization Of lytic organelles by use of fluorescent probes

Light microscopy was used to study the structure and function of vacuoles in living protoplasts of barley (Hordeum vulgare cv Himalaya) aleurone. Light microscopy showed that aleurone protoplasts contain two distinct types of vacuole: the protein storage vacuole and a lysosome-like organelle, which we have called the secondary vacuole. Fluorescence microscopy using pH-sensitive fluorescent probes and a fluorogenic substrate for cysteine proteases showed that both protein storage vacuoles and secondary vacuoles are acidic, lytic organelles. Ratio imaging showed that the pH of secondary vacuoles was lower in aleurone protoplasts incubated in gibberellic acid than in those incubated in abscisic acid. Uptake of fluorescent probes into intact, isolated protein storage vacuoles and secondary vacuoles required ATP and occurred via at least two types of vanadate-sensitive, ATP-dependent tonoplast transporters. One transporter catalyzed the accumulation of glutathione-conjugated probes, and another transported probes not conjugated to glutathione.     

Modulation of octopamine-mediated production of cyclic AMP by phorbol-ester-sensitive protein kinase C in an insect cell line

The presence of protein kinase C (EC 2.7.1.37) in an insect cell line has been demonstrated. Phorbol 12-myristate 13-acetate (PMA), in micromolar concentrations, activated protein kinase C with a translocation of the enzyme from the cytosol to the particulate fraction. Cyclic AMP production in the presence of PMA, octopamine and a combination of both increased in a dose-dependent and time-dependent fashion. The biologically inactive 4 alpha-phorbol 12,13-didecanoate had no effect on protein kinase C activity or on octopamine-mediated cyclic AMP production. Pretreatment of the cells with pertussis toxin had no effect on the response of cells to octopamine or PMA. However, pretreatment with cholera toxin resulted in increased cyclic AMP production which was further enhanced when both cholera toxin and PMA were used in combination. Our data indicate that the octopamine-mediated cyclic AMP production is modulated by protein kinase C.     

Identifying rare and common disease associated variants in genomic data using Parkinson’s disease as a model

Background

Genome-wide association studies have been successful in identifying common genetic variants for human diseases. However, much of the heritable variation associated with diseases such as Parkinson’s disease remains unknown suggesting that many more risk loci are yet to be identified. Rare variants have become important in disease association studies for explaining missing heritability. Methods for detecting this type of association require prior knowledge on candidate genes and combining variants within the region. These methods may suffer from power loss in situations with many neutral variants or causal variants with opposite effects.

Results

We propose a method capable of scanning genetic variants to identify the region most likely harbouring disease gene with rare and/or common causal variants. Our method assigns a score at each individual variant based on our scoring system. It uses aggregate scores to identify the region with disease association. We evaluate performance by simulation based on 1000 Genomes sequencing data and compare with three commonly used methods. We use a Parkinson’s disease case–control dataset as a model to demonstrate the application of our method.Our method has better power than CMC and WSS and similar power to SKAT-O with well-controlled type I error under simulation based on 1000 Genomes sequencing data. In real data analysis, we confirm the association of α-synuclein gene (SNCA) with Parkinson’s disease (p = 0.005). We further identify association with hyaluronan synthase 2 (HAS2, p = 0.028) and kringle containing transmembrane protein 1 (KREMEN1, p = 0.006). KREMEN1 is associated with Wnt signalling pathway which has been shown to play an important role for neurodegeneration in Parkinson’s disease.

Conclusions

Our method is time efficient and less sensitive to inclusion of neutral variants and direction effect of causal variants. It can narrow down a genomic region or a chromosome to a disease associated region. Using Parkinson’s disease as a model, our method not only confirms association for a known gene but also identifies two genes previously found by other studies. In spite of many existing methods, we conclude that our method serves as an efficient alternative for exploring genomic data containing both rare and common variants.

Electronic supplementary material

The online version of this article (doi:10.1186/s12929-014-0088-9) contains supplementary material, which is available to authorized users.     

Impact of temperature on Na2Sr(PO4)F:Eu3+ phosphor

In this article, we report the synthesis of Na₂Sr_1‐x(PO₄)F:Eu_x phosphor via a combustion method. The influence of different annealing temperatures on the photoluminescence properties was investigated. The phosphor was excited at both 254 and 393 nm. Na₂Sr_1‐x(PO₄)F:Eu_x³⁺ phosphors emit strong orange and red color at 593 and 612 nm, respectively, under both excitation wavelengths. Na₂Sr_1‐x(PO₄)F:Eu_x³⁺ phosphors annealed at 1050°C showed stronger emission intensity compared with 600, 900 and 1200°C. Moreover, Na₂Sr_1‐x(PO₄)F:Eu_x³⁺ phosphor was found to be more intense when compared with commercial Y₂O₃:Eu³⁺ phosphor. Copyright © 2013 John Wiley & Sons, Ltd.     

Incorporating expression data in metabolic modeling: a case study of lactate dehydrogenase

Integrating biological information from different sources to understand cellular processes is an important problem in systems biology. We use data from mRNA expression arrays and chemical kinetics to formulate a metabolic model relevant to K562 erythroleukemia cells. MAP kinase pathway activation alters the expression of metabolic enzymes in K562 cells. Our array data show changes in expression of lactate dehydrogenase (LDH) isoforms after treatment with phorbol 12-myristate 13-acetate (PMA), which activates MAP kinase signaling. We model the change in lactate production which occurs when the MAP kinase pathway is activated, using a non-equilibrium, chemical-kinetic model of homolactic fermentation. In particular, we examine the role of LDH isoforms, which catalyse the conversion of pyruvate to lactate. Changes in the isoform ratio are not the primary determinant of the production of lactate. Rather, the total concentration of LDH controls the lactate concentration.     

Erratum

Neurotransmitter receptor trafficking and the regulation of synaptic strength. Traffic 2001:2(7):437–448.