On Building Parallel &; Grid Applications: Component Technology and Distributed Services

Software Component Frameworks are well known in the commercial business application world and now this technology is being explored with great interest as a way to build large-scale scientific applications on parallel computers. In the case of Grid systems, the current architectural model is based on the emerging web services framework. In this paper we describe progress that has been made on the Common Component Architecture model (CCA) and discuss its success and limitations when applied to problems in Grid computing. Our primary conclusion is that a component model fits very well with a services-oriented Grid, but the model of composition must allow for a very dynamic (both in space and in time) control of composition. We note that this adds a new dimension to conventional service workflow and it extends the “Inversion of Control” aspects of most component systems. Dennis Gannon is a professor of Computer Science at Indiana University. He received his Ph.D. in Computer Science from the University of Illinois in 1980 and his Ph.D. in Mathematics from the University of California in 1974. From 1980 to 1985, he was on the faculty at Purdue University. His research interests include software tools for high performance distributed systems and problem solving environments for scientific computation. Sriram Krishnan received his Ph.D. in Computer Science from Indiana University in 2004. He is currently in the Grid Development Group at the San Diego Supercomputer Center where he is working on designing a Web services based architecture for biomedical applications that is secure and scalable, and is conducive to the creation of complex workflows. He received my undergraduate degree in Computer Engineering from the University of Mumbai, India. Liang Fang is a Ph.D. student in Computer Science at Indiana University. His research interests include Grid computing, Web services, portals, their security and scalability issues. He is a Research Assistant in Computer Science at Indiana University, currently responsible for investigating authorization and other security solutions to the project of Linked Environments for Atmospheric Discovery (LEAD). Gopi Kandaswamy is a Ph.D. student in the Computer Science Department at Indiana University where he is current a Research Assistant. His research interests include Web services and workflow systems for the Grid. Yogesh Simmhan received his B.E. degree in Computer Science from Madras University, India in 2000, and is a doctoral candidate in Computer Science at Indiana University. He is currently working as a Research Assistant at Indiana University, investigating data management issues in the LEAD project. His interests lie in data provenance for workflow systems and its use in data quality estimation. Aleksander Slominski is a Ph.D. student in the Computer Science at Indiana University. His research interests include Grid and Web Services, streaming XML Pull Parsing and performance, Grid security, asynchronous messaging, events, and notifications brokers, component technologies, and workflow composition. He is currently working as a Research Assistant investigating creation and execution of dynamic workflows using Grid Process Execution Language (GPEL) based on WS-BPEL.     

Analysis of polymorphism of CTG repetitive sequences in the gene of myotonic dystrophy in human populations of the Volga-Ural region]

Distribution of CTG repetitive sequences in the myotonic dystrophy (MD) gene was analyzed in ten populations of the Volga-Ural region, including Tatars, Chuvashes, Maris, Udmurts, Mordovians, Komis, and four ethnogeographical groups of Bashkirs. A total of 25 alleles were found (9 to 14 in individual populations), with each allele containing 5 to 34 trinucleotide repeats. The allele frequency distribution had two peaks corresponding to alleles with 5 and 11-14 CTG repeats. The frequency of the (CTG)5 allele varied from 0.23 to 0.47 in Maris and Mordovians, respectively. Regarding the (CTG)11-14 alleles, those containing 13 and 12 trinucleotides were most frequent in all populations; their frequencies varied from 0.15 in Mordovians to 0.24 in Maris and Bashkirs from the Abzelilovskii raion (district). Alleles with large numbers of repeats (more than 30) were only found in Tatars and Bashkirs from the Abzelilovskii raion, where their frequency was 0.01. The data obtained were compared with those on other human populations from various regions of the world. In general, the populations of the Volga-Ural region took an intermediate position between European and Asian populations (although were somewhat more similar to the latter ones) with respect to the distribution of allelic frequencies of the CTG repetitive sequences. In individual populations, the number of genotypes varied from 13 to 27 in Mordovians and Bashkirs from the Ilishevskii raion, respectively. The observed heterozygosity was the highest (91%) in Udmurts and the lowest (58%) in Mordovians; the average heterozygosity was 81%. Such a high heterozygosity, as well as the revealed differentiation of the populations with respect to the distribution of the allelic frequencies of CTG repetitive sequences in the MD gene, allow this polymorphic DNA locus to be considered a highly informative genetic marker of populations.     

Metabolism of cholesterol, vitamin D3 and 20-hydroxyvitamin D3 incorporated into phospholipid vesicles by human CYP27A1

CYP27A1 is a mitochondrial cytochrome P450 which can hydroxylate vitamin D3 and cholesterol at carbons 25 and 26, respectively. The product of vitamin D3 metabolism, 25-hydroxyvitamin D3, is the precursor to the biologically active hormone, 1α,25-dihydroxyvitamin D3. CYP27A1 is attached to the inner mitochondrial membrane and substrates appear to reach the active site through the membrane phase. We have therefore examined the ability of bacterially expressed and purified CYP27A1 to metabolize substrates incorporated into phospholipid vesicles which resemble the inner mitochondrial membrane. We also examined the ability of CYP27A1 to metabolize 20-hydroxyvitamin D3 (20(OH)D3), a novel non-calcemic form of vitamin D derived from CYP11A1 action on vitamin D3 which has anti-proliferative activity on keratinocytes, leukemic and myeloid cells. CYP27A1 displayed high catalytic activity towards cholesterol with a turnover number (k(cat)) of 9.8 min(-1) and K(m) of 0.49 mol/mol phospholipid (510 μM phospholipid). The K(m) value of vitamin D3 was similar for that of cholesterol, but the k(cat) was 4.5-fold lower. 20(OH)D3 was metabolized by CYP27A1 to two major products with a k(cat)/K(m) that was 2.5-fold higher than that for vitamin D3, suggesting that 20(OH)D3 could effectively compete with vitamin D3 for catalysis. NMR and mass spectrometric analyses revealed that the two major products were 20,25-dihydroxyvitamin D3 and 20,26-dihydroxyvitamin D3, in almost equal proportions. Thus, the presence of the 20-hydroxyl group on the vitamin D3 side chain enables it to be metabolized more efficiently than vitamin D3, with carbon 26 in addition to carbon 25 becoming a major site of hydroxylation. Our study reports the highest k(cat) for the 25-hydroxylation of vitamin D3 by any human cytochrome P450 suggesting that CYP27A1 might be an important contributor to the synthesis of 25-hydroxyvitamin D3, particularly in tissues where it is highly expressed.     

Polymorphic markers for the angiotensinogen and angiotensin-converting enzyme in Yakuts. Lack of association with blood pressure level]

Allele frequency distributions of the insertion/deletion (I/D) polymorphism of the angiotensin-converting enzyme (ACE) gene and the M235T polymorphism of the angiotensinogen gene was studied in a random sample of the indigenous population of the Sakha Republic. The allelic variants of these genes did not showed an association with blood pressure in Yakuts.     

Photo-conversion of two epimers (20R and 20S) of pregna-5,7-diene-3β, 17α, 20-triol and their bioactivity in melanoma cells

Pregna-5,7-dienes and their hydroxylated derivatives can be formed in vivo when there is a deficiency in 7-dehydrocholesterol (7-DHC) Δ-reductase function, e.g., Smith-Lemli-Opitz syndrome (SLOS). Ultraviolet B (UVB) radiation induces photoconversion of 7-DHC to vitamin D₃, lumisterol₃ and tachysterol₃. Two epimers (20R and 20S) of pregna-5,7-diene-3β,17α,20-triol (4R and 4S, respectively) were synthesized and their UVB photo-conversion products identified as corresponding 9,10-secosteroids with vitamin D-like and tachysterol-like structures, and 5,7-dienes with inverted configuration at C-9 and C-10 (lumisterol-like). The number and character of the products and the dynamics of the process were dependent on the UVB dose. At high UVB doses, the formation of multiple oxidized derivatives of the primary products, and the formation of 5,7,9(11)-triene, were observed. The production of vitamin D-like, tachysterol-like and lumisterol-like derivatives was also observed in human skin treated with 4R and 4S, and subjected to UV irradiation, as shown by RP-HPLC. Newly synthesized compounds inhibited melanoma growth in dose dependent manner, and some of them showed equal or higher potency than 1,25(OH)₂D₃. In summary, we have characterized for the first time the products of UV induced conversion of pregna-5,7-diene-3β,17α,20-triols and documented that the newly synthesized compounds have antiproliferative properties against melanoma cells.     

CRH inhibits NF-kappa B signaling in human melanocytes

Corticotropin releasing hormone (CRH), a messenger of stress at the central level, is expressed in the epidermis where it operates within local equivalent of hypothalamo-pituitary axis. CRH inhibits NF-κB activity in human immortalized epidermal (PIG1) melanocytes. In melanocytes CRH stimulates pro-opiomelanocortin (POMC) mRNA and adrenocorticotropin (ACTH) peptide production. Knockdown of POMC levels by transfecting cells with antisense oligonucleotides blocks the effect of CRH on NF-κB signaling indicating that the above inhibition is indirect, e.g. through activation of POMC. We suggest that induction of POMC by CRH serves as a feedback mechanism to self-restrict inflammatory response in the skin.     

MSH binding in bomirski amelanotic hamster melanoma cells is stimulated by L-tyrosine

Bomirski Ab amelanotic melanoma cells have recently been shown to undergo striking phenotypic changes when precursors of the melanogenic pathway, L-tyrosine and L-dopa, are added to the culture medium. The changes include increased tyrosinase activity andde novo synthesis of melanosomes and melanin. L-tyrosine and L-dopa appeared to elicit these responses through separate but overlapping regulatory pathways. Here we show an additional effect of L-tyrosine: stimulation of MSH binding capacity. Cells cultured for 24–48 hours in the presence of 200 M L-tyrosine display a 3–4 fold increase in their ability to bind¹²⁵l--MSH. L-dopa did not stimulate MSH binding under the same conditions. In control experiments neither L-tyrosine nor L-dopa had any effect on insulin binding. The amelanotic cells respond to MSH with increased dendrite formation, increased tyrosinase activity without melanin production, and decreased growth rate.