Substrate specificity of human ceramide kinase

Previous studies in our laboratory have established ceramide kinase (CERK) as a critical mediator of eicosanoid synthesis. To date, CERK has not been well characterized in vitro. In this study, we investigated the substrate specificity of CERK using baculovirus-expressed human CERK (6 x His) and a newly designed assay based on mixed micelles of Triton X-100. The results indicate that the ability of CERK to recognize ceramide as a substrate is stereospecific. A minimum of a 12 carbon acyl chain was required for normal CERK activity, and the 4-5 trans double bond was important for substrate recognition. A significant discrimination by CERK was not observed between ceramides with long saturated and long unsaturated fatty acyl chains. Methylation of the primary hydroxyl group resulted in a loss of activity, confirming that CERK produces ceramide-1-phosphate versus ceramide-3-phosphate. In addition, methylation of the secondary hydroxyl group drastically decreased the phosphorylation by CERK. These results also indicated that the free hydrogen of the secondary amide group is critical for substrate recognition. Lastly, the sphingoid chain was also required for substrate recognition by CERK. Together, these results indicate a very high specificity for substrate recognition by CERK, explaining the use of ceramide and not sphingosine or diacylglycerol as substrates.     

PHACCS,an online tool for estimating the structure and diversity of uncultured viral communities using metagenomic information

Background  

Phages, viruses that infect prokaryotes, are the most abundant microbes in the world. A major limitation to studying these viruses is the difficulty of cultivating the appropriate prokaryotic hosts. One way around this limitation is to directly clone and sequence shotgun libraries of uncultured viral communities (i.e., metagenomic analyses). PHACCS, Phage Communities from Contig Spectrum, is an online bioinformatic tool to assess the biodiversity of uncultured viral communities. PHACCS uses the contig spectrum from shotgun DNA sequence assemblies to mathematically model the structure of viral communities and make predictions about diversity.     

Modeling tubular shapes in the inner mitochondrial membrane

The inner mitochondrial membrane has been shown to have a novel structure that contains tubular components whose radii are of the order of 10 nm as well as comparatively flat regions. The structural organization of mitochondria is important for understanding their functionality. We present a model that can account, thermodynamically, for the observed size of the tubules. The model contains two lipid constituents with different shapes. They are allowed to distribute in such a way that the composition differs on the two sides of the tubular membrane. Our calculations make two predictions: (1) there is a pressure difference of 0.2 atmospheres across the inner membrane as a necessary consequence of the experimentally observed tubule radius of 10 nm, and (2) migration of differently shaped lipids causes concentration variations of the order of 7% between the two sides of the tubular membrane.     

A 30 kb region of the Epstein-Barr virus genome is colinear with the rearranged human immunoglobulin gene loci: implications for a "ping-pong evolution" model for persisting viruses and their hosts. A review

The left part of the Epstein-Barr virus (EBV) genome exhibits a strong colinearity of structural and functional elements with the immunoglobulin (Ig) gene loci which is only partially reflected in nucleotide sequence homologies. We propose that this colinearity may be the result of an inter-dependent co-evolution of the immunoglobulin loci together with EBV. Our observation could help elucidating the mechanisms of somatic hypermutation, explaining the ability of EBV to accidentally cause tumors, and shedding more light on the general mechanisms of viral and organismal evolution. We suggest that persisting viruses served as a complement for the organismal germline like in a ping-pong game and outline The Ping-Pong Evolution Hypothesis.     

The binding of the RyR2 calcium channel to its gating protein FKBP12.6 is oppositely affected by ARVD2 and VTSIP mutations

Arrhythmogenic right ventricular dysplasia/cardiomyopathy type 2 (ARVD2, OMIM 600996) and stress-induced polymorphic ventricular tachycardia (VTSIP, OMIM 604772) are two cardiac diseases causing juvenile sudden death, both associated with mutations in the RyR2 calcium channel. By using a quantitative yeast two-hybrid system, we show that VTSIP- and ARVD2-associated point mutations influence positively and negatively, respectively, the binding of RyR2 to its gating protein FKBP12.6. These findings suggest that ARVD2 mutations increase RyR2-mediated calcium release to cytoplasm, while VTSIP mutations do not affect significantly cytosolic calcium levels, thereby explaining the clinical differences between the two diseases. The present two-hybrid system appears to be an efficient molecular tool to assay the binding of FKBP12s proteins to both cardiac RyR2 and skeletal muscle RyR1 isoforms, circumventing the full-length expression of this class of giant channels. We also provide evidence of the suitability of this system to test new drugs that target RyRs-FKBP12s interactions and do not affect yeast growth.     

Pyrimidine homonucleoside analogues from 2,5-anhydroaldose derivatives

3,4-Di-O-acetyl-2,5-anhydro-D-xylose diisobutyl dithioacetal (1) reacts with bromine to give a monobromo derivative which, on condensation with 2,4-diethoxy-pyrimidine or its 5-methyl analogue, affords the protected nucleoside derivatives 4 and 11, respectively; ammonolysis of 4 gave the cytosine “homonucleoside” 7, and hydrolysis of 11 gave the thymine “homonucleoside” 12. The same type of “homonucleoside” may be produced by cyclization of the sugar chain in a suitable acyclic-sugar nucleoside, as in the conversion of 1-S-ethyl-1-thio-1-(uracil-1-yl)-D-xylitol (16, obtained from tetra-O-acetyl-D-xylose diethyl dithioacetal, 9), by the action of one molar equivalent of p-toluenesulfonyl chloride, into a homonucleoside isolated as its diacetate 17; acyclic-sugar derivatives not susceptible to such cyclization afford instead the 5-p-toluenesulfonates, as exemplified by the conversion of the D-arabino analogue (13) of 16 into the 5′-ester 14. When cyclohexene is used to remove the excess of bromine in the preparation of nucleoside analogues from dithioacetals, the alkylsulfenyl bromide produced may react, by way of its cyclohexene adduct, with the hoterocyclic base to give cyclohexane-base adducts, for example, compounds 6 and 10.     

Stable Isotope Signatures of Middle Palaeozoic Ahermatypic Rugose Corals – Deciphering Secondary Alteration,Vital Fractionation Effects,and Palaeoecological Implications

This study investigates stable isotope signatures of five species of Silurian and Devonian deep-water, ahermatypic rugose corals, providing new insights into isotopic fractionation effects exhibited by Palaeozoic rugosans, and possible role of diagenetic processes in modifying their original isotopic signals. To minimize the influence of intraskeletal cements on the observed signatures, the analysed specimens included unusual species either devoid of large intraskeletal open spaces (''button corals'': Microcyclus, Palaeocyclus), or typified by particularly thick corallite walls (Calceola). The corals were collected at four localities in the Holy Cross Mountains (Poland), Mader Basin (Morocco) and on Gotland (Sweden), representing distinct diagenetic histories and different styles of diagenetic alteration. To evaluate the resistance of the corallites to diagenesis, we applied various microscopic and trace element preservation tests. Distinct differences between isotopic compositions of the least-altered and most-altered skeleton portions emphasise a critical role of material selection for geochemical studies of Palaeozoic corals. The least-altered parts of the specimens show marine or near-marine stable isotope signals and lack positive correlation between δ¹³C and δ¹⁸O. In terms of isotopic fractionation mechanisms, Palaeozoic rugosans must have differed considerably from modern deep-water scleractinians, typified by significant depletion in both ¹⁸O and ¹³C, and pronounced δ¹³C-δ¹⁸O co-variance. The fractionation effects exhibited by rugosans seem similar rather to the minor isotopic effects typical of modern non-scleractinian corals (octocorals and hydrocorals). The results of the present study add to growing evidence for significant differences between Scleractinia and Rugosa, and agree with recent studies indicating that calcification mechanisms developed independently in these two groups of cnidarians. Consequently, particular caution is needed in using scleractinians as analogues in isotopic studies of extinct coral lineages. Answering some of the pertinent palaeoecological questions, such as that of the possibility of photosymbiosis in Palaeozoic corals, may not be possible based on stable isotope data.     

The Extended Oxygen Window Concept for Programming Saturation Decompressions Using Air and Nitrox

Saturation decompression is a physiological process of transition from one steady state, full saturation with inert gas at pressure, to another one: standard conditions at surface. It is defined by the borderline condition for time spent at a particular depth (pressure) and inert gas in the breathing mixture (nitrogen, helium). It is a delicate and long lasting process during which single milliliters of inert gas are eliminated every minute, and any disturbance can lead to the creation of gas bubbles leading to decompression sickness (DCS). Most operational procedures rely on experimentally found parameters describing a continuous slow decompression rate. In Poland, the system for programming of continuous decompression after saturation with compressed air and nitrox has been developed as based on the concept of the Extended Oxygen Window (EOW). EOW mainly depends on the physiology of the metabolic oxygen window—also called inherent unsaturation or partial pressure vacancy—but also on metabolism of carbon dioxide, the existence of water vapor, as well as tissue tension. Initially, ambient pressure can be reduced at a higher rate allowing the elimination of inert gas from faster compartments using the EOW concept, and maximum outflow of nitrogen. Then, keeping a driving force for long decompression not exceeding the EOW allows optimal elimination of nitrogen from the limiting compartment with half-time of 360 min. The model has been theoretically verified through its application for estimation of risk of decompression sickness in published systems of air and nitrox saturation decompressions, where DCS cases were observed. Clear dose-reaction relation exists, and this confirms that any supersaturation over the EOW creates a risk for DCS. Using the concept of the EOW, 76 man-decompressions were conducted after air and nitrox saturations in depth range between 18 and 45 meters with no single case of DCS. In summary, the EOW concept describes physiology of decompression after saturation with nitrogen-based breathing mixtures.