Enterprise architecture – the foundation for a strategy

Artikkeli selostaa kokonaisarkkitehtuurin käsitettä ja Kansallinen digitaalinen kirjasto -hankkeen kokonaisarkkitehtuurin laatimista. Kokonaisarkkitehtuuri on tietohallinnon strategisen suunnittelun ja johtamisen väline, mutta sillä on monia käytännöllisempia käyttötarkoituksia esimerkiksi tietojärjestelmien kehittämisessä. Kansallinen digitaalinen kirjasto on opetus- ja kulttuuriministeriön tavoitteena on varmistaa kulttuurin ja tieteen digitaalisten tietovarantojen tehokas ja laadukas hallinta, jakelu ja pitkäaikaissäilytys. Lisäksi hankkeessa edistetään kulttuuriperintö- ja asiakirja-aineistojen digitointia.

Yksinkertainen on kaunista

Yksinkertaisuus on vahva induktiivisen päättelyn periaate. Se on läsnä monessa arkielämän tilanteessa epäformaalina peukalosääntönä, jonka mukaan yksinkertaisin selitys on paras. Yksinkertaisuuden periaatetta, eli Okkamin partaveistä, voidaan soveltaa myös tilastollisen päättelyn pohjana. Sen formaali versio, niin sanottu lyhimmän kuvauspituuden periaate (MDL-periaate), asettaa vaihtoehtoiset hypoteesit paremmuusjärjestykseen sen mukaan, mikä niistä mahdollistaa aineiston lyhimmän kuvauksen, kun kuvaus sisältää myös itse hypoteesin. Kuvauspituuden määrittämiseksi sovelletaan informaatioteorian ja tiedon tiivistämisen menetelmiä. Esitän tässä kirjoituksessa joitakin informaatioteorian käsitteitä. Kirjoituksen jälkipuoliskolla käydään läpi MDL-periaatteen alkeita.

The gasification of wood-char spheres in CO2---N2 mixtures: analysis and experiments

The gasification of charcoal spheres in an atmosphere of carbon-dioxide-nitrogen mixture involving diffusion and reactions in the pores is modelled and the results are compared with experiments of Standish and Tanjung and those performed in the laboratory on wood-char spheres to determine the effects of diameter, density, gas composition and flow. The results indicate that the conversion time, t(c) approximately d1.03 for large particles (> 5 mm), departing substantially from the t(c) approximately d2 law valid for diffusion limited conditions. The computational studies indicate that the kinetic limit for the particle is below 100 mum. The conversion time varies inversely as the initial char density as expected in the model. Predictions from the model show that there is no significant change in conversion time up to 60% N2 consistent with the CO2-N2 experiments. The variation of diameter and density with time are predicted. The peculiar dependence of conversion time on flow velocity in the experiments is sought to be explained by opposing free and forced convection heat transfer and the attempt is only partly successful. The studies also indicate that the dependence on the CO concentration with low CO2 is significant, indicating the need for multistep reaction mechanism against the generally accepted single-step reaction.

Diperoxovanadate can substitute for H(2)O(2) at much lower concentration in inducing features of premature cellular senescence in mouse fibroblasts (NIH3T3)

Stress induced premature senescence (SIPS) in mammalian cells is an accelerated ageing response and experimentally obtained on treatment of cells with high concentrations of H(2)O(2), albeit at sub-lethal doses, because H(2)O(2) gets depleted by abundant cellular catalase. In the present study diperoxovanadate (DPV) was used as it is known to be stable at physiological pH, to be catalase-resistant and to substitute for H(2)O(2) in its activities at concentrations order of magnitudes lower. On treating NIH3T3 cells with DPV, SIPS-like morphology was observed along with an immediate response of rounding of the cells by disruption of actin cytoskeleton and transient G2/M arrest. DPV could bring about growth arrest and senescence associated features at 25 mu M dose, which were not seen with similar doses of either H(2)O(2) or vanadate. A minimal dose of 150 mu M of H(2)O(2) was required to induce similar affects as 25 mu M DPV. Increase in senescent associated markers such as p21, HMGA2 and PAI-1 was more prominent in DPV treated cells compared to similar dose of H(2)O(2). DPV-treated cells showed marked relocalization of Cyclin D1 from nucleus to cytoplasm. These results indicate that DPV, stable inorganic peroxide, is more efficient in inducing SIPS at lower concentrations compared to H(2)O(2). (C) 2011 Elsevier Ireland Ltd. All rights reserved.

Design and Characterization of Stabilized Derivatives of Human CD4D12 and CD4D1

CD4 is present on the surface of T-lymphocytes and is the primary cellular receptor for HIV-1. CD4 consists of a cytoplasmic tail, one transmembrane region, and four extracellular domains, D1-D4. A construct consisting of the first two domains of CD4 (CD4D12) is folded and binds gp120 with similar affinity as soluble 4-domain CD4 (sCD4). However, the first domain alone (CD4D1) was previously shown to be largely unfolded and had 3-fold weaker affinity for gp120 when compared to sCD4 [Sharma, D.; et al. (2005) Biochemistry 44, 16192-16202]. We now report the design and characterization of three single-site mutants of CD4D12 (G6A, L51I, and V86L) and one multisite mutant of CD4D1 (G6A/L511/L5K/F98T). G6A, L51I, and V86L are cavity-filling mutations while L5K and F98T are surface mutations which were introduced to minimize the aggregation of CD4D1 upon removal of the second domain. Two mutations, G6A and V86L in CD4D12 increased the stability and yield of the protein relative to the wild-type protein. The mutant CD4D1 (CD4D1a) with the 4 mutations was folded and more stable compared to the original CD4D1, but both bound gp120 with comparable affinity. In in vitro neutralization assays, both CD4D1a and G6A-CD4D12 were able to neutralize diverse HIV-1 viruses with similar IC(50)s as 4-domain CD4. These stabilized derivatives of human CD4 can be useful starting points for the design of other more complex viral entry inhibitors.

Modulation of Catalytic Activity in Multi-Domain Protein Tyrosine Phosphatases

Signaling mechanisms involving protein tyrosine phosphatases govern several cellular and developmental processes. These enzymes are regulated by several mechanisms which include variation in the catalytic turnover rate based on redox stimuli, subcellular localization or protein-protein interactions. In the case of Receptor Protein Tyrosine Phosphatases (RPTPs) containing two PTP domains, phosphatase activity is localized in their membrane-proximal (D1) domains, while the membrane-distal (D2) domain is believed to play a modulatory role. Here we report our analysis of the influence of the D2 domain on the catalytic activity and substrate specificity of the D1 domain using two Drosophila melanogaster RPTPs as a model system. Biochemical studies reveal contrasting roles for the D2 domain of Drosophila Leukocyte antigen Related (DLAR) and Protein Tyrosine Phosphatase on Drosophila chromosome band 99A (PTP99A). While D2 lowers the catalytic activity of the D1 domain in DLAR, the D2 domain of PTP99A leads to an increase in the catalytic activity of its D1 domain. Substrate specificity, on the other hand, is cumulative, whereby the individual specificities of the D1 and D2 domains contribute to the substrate specificity of these two-domain enzymes. Molecular dynamics simulations on structural models of DLAR and PTP99A reveal a conformational rationale for the experimental observations. These studies reveal that concerted structural changes mediate inter-domain communication resulting in either inhibitory or activating effects of the membrane distal PTP domain on the catalytic activity of the membrane proximal PTP domain.

Inter-domain interactions influence the stability and catalytic activity of the bi-domain protein tyrosine phosphatase PTP99A

The two protein tyrosine phosphatase (PTP) domains in bi-domain PTPs share high sequence and structural similarity. However, only one of the two PIP domains is catalytically active. Here we describe biochemical studies on the two tandem PTP domains of the bi-domain PTP, PTP99A. Phosphatase activity, monitored using small molecule as well as peptide substrates, revealed that the inactive (D2) domain activates the catalytic (D1) domain. Thermodynamic measurements suggest that the inactive D2 domain stabilizes the bi-domain (D1-D2) protein. The mechanism by which the D2 domain activates and stabilizes the bi-domain protein is governed by few interactions at the inter-domain interface. In particular, mutating Lys990 at the interface attenuates inter-domain communication. This residue is located at a structurally equivalent location to the so-called allosteric site of the canonical single domain PIP, PTP1B. These observations suggest functional optimization in bi-domain PTPs whereby the inactive PTP domain modulates the catalytic activity of the bi-domain enzyme. (C) 2012 Elsevier B.V. All rights reserved.

Oncogenic MicroRNA-155 Down-regulates Tumor Suppressor CDC73 and Promotes Oral Squamous Cell Carcinoma Cell Proliferation IMPLICATIONS FOR CANCER THERAPEUTICS

The CDC73 gene is mutationally inactivated in hereditary and sporadic parathyroid tumors. It negatively regulates beta-catenin, cyclin D1, and c-MYC. Down-regulation of CDC73 has been reported in breast, renal, and gastric carcinomas. However, the reports regarding the role of CDC73 in oral squamous cell carcinoma (OSCC) are lacking. In this study we show that CDC73 is down-regulated in a majority of OSCC samples. We further show that oncogenic microRNA-155 (miR-155) negatively regulates CDC73 expression. Our experiments show that the dramatic up-regulation of miR-155 is an exclusive mechanism for down-regulation of CDC73 in a panel of human cell lines and a subset of OSCC patient samples in the absence of loss of heterozygosity, mutations, and promoter methylation. Ectopic expression of miR-155 in HEK293 cells dramatically reduced CDC73 levels, enhanced cell viability, and decreased apoptosis. Conversely, the delivery of a miR-155 antagonist (antagomir-155) to KB cells overexpressing miR-155 resulted in increased CDC73 levels, decreased cell viability, increased apoptosis, and marked regression of xenografts in nude mice. Cotransfection of miR-155 with CDC73 in HEK293 cells abrogated its pro-oncogenic effect. Reduced cell proliferation and increased apoptosis of KB cells were dependent on the presence or absence of the 3'-UTR in CDC73. In summary, knockdown of CDC73 expression due to overexpression of miR-155 not only adds a novelty to the list of mechanisms responsible for its down-regulation in different tumors, but the restoration of CDC73 levels by the use of antagomir-155 may also have an important role in therapeutic intervention of cancers, including OSCC.

Synthesis and Electron Microscopy of Superalloy Nanowires

An electrodeposition based methodology for synthesizing Ni-Cr-Fe nanowires is provided. As-synthesized nanowires were 200 nm in diameter and more than 5 mu m in length. Detailed characterization of the nanowires using electron microscopy technique revealed an amorphous microstructure for the nanowires with uniform distribution of Ni, Fe and Cr atoms. Annealing of the nanowire using the electron beam inside electron microscope resulted in gradual crystallization of amorphous microstructure into a nanocrystalline one which illustrated the potential for microstructural engineering of the nanowires. (C) 2014 The Electrochemical Society. All rights reserved.

NrichD database: sequence databases enriched with computationally designed protein-like sequences aid in remote homology detection

NrichD ( ext-link-type=''uri'' xlink:href=''http://proline.biochem.iisc.ernet.in/NRICHD/'' xlink:type=''simple''>http://proline.biochem.iisc.ernet.in/NRICHD/)< /named-content> is a database of computationally designed protein-like sequences, augmented into natural sequence databases that can perform hops in protein sequence space to assist in the detection of remote relationships. Establishing protein relationships in the absence of structural evidence or natural `intermediately related sequences' is a challenging task. Recently, we have demonstrated that the computational design of artificial intermediary sequences/linkers is an effective approach to fill naturally occurring voids in protein sequence space. Through a large-scale assessment we have demonstrated that such sequences can be plugged into commonly employed search databases to improve the performance of routinely used sequence search methods in detecting remote relationships. Since it is anticipated that such data sets will be employed to establish protein relationships, two databases that have already captured these relationships at the structural and functional domain level, namely, the SCOP database and the Pfam database, have been `enriched' with these artificial intermediary sequences. NrichD database currently contains 3 611 010 artificial sequences that have been generated between 27 882 pairs of families from 374 SCOP folds. The data sets are freely available for download. Additional features include the design of artificial sequences between any two protein families of interest to the user.

A carboxy terminal domain of the L protein of rinderpest virus possesses RNA triphosphatase activity - The first enzyme in the viral mRNA capping pathway

The large protein L of negative-sense RNA viruses is a multifunctional protein involved in transcription and replication of genomic RNA. It also possesses enzymatic activities involved in capping and methylation of viral mRNAs. The pathway for mRNA capping followed by the L protein of the viruses in the Morbillivirus genus has not been established, although it has been speculated that these viruses may follow the unconventional capping pathway as has been shown for some viruses of Rhabdoviridae family. We had earlier shown that the large protein L of Rinderpest virus expressed as recombinant L-P complex in insect cells as well as the ribonucleoprotein complex from purified virus possesses RNA triphosphatase (RTPase) and guanylyltransferase activities, in addition to RNA dependent RNA polymerase activity. In the present work, we demonstrate that RTPase as well as nucleoside triphosphatase (NTPase) activities are exhibited by a subdomain of the L protein in the C terminal region (a.a. 1640 1840). The RTPase activity depends absolutely on a divalent cation, either magnesium or manganese. Both the RTPase and NTPase activities of the protein show dual metal specificity. Two mutant proteins having alanine mutations in the glutamic acid residues in motif-A of the RTPase domain did not show RTPase activity, while exhibiting reduced NTPase activity suggesting overlapping active sites for the two enzymatic functions. The RTPase and NTPase activities of the L subdomain resemble those of the Vaccinia capping enzyme D1 and the baculovirus LEF4 proteins. (C) 2015 Elsevier Inc. All rights reserved.

Efecto de tres periodos de suministro de alimento de retiro en broilers en la Empresa Tip-Top industrial, S.A.

En el presente estudio se evaluaron tres periodos de alimento de retiro o acabado en broilers (o, 3, 6 y 9 días antes de la matanza) el cual contiene 3,225 kcal EM/kg de alimento y 19% de proteína, ajustándose a los requerimientos nutricionales recomendados por Arbor Acres Farm Inc., (1992), en especial a la proporción energia-proteina. La evaluación tuvo lugar en la Granja Buenos Aires propiedad de la Empresa Tip-Top Industrial, S.A., con una duración de 42 días, en donde se utilizaron 800 pollos de engorde sin sexar (mixtos) de la línea Peterson-Arbor Acres de un día de edad, dichos pollos fueron distribuidos aleatoriamente en cuatro tratamientos: T1 suministro de alimento de retiro por nueve días), T2 suministro de alimento de retiro por seis días), T3, (Suministro de alimento de retiro por tres días) y T4 (testigo, con cero días de alimento de retiro), con cuatro repeticiones cada uno, distribuidos en un Diseño completamente al Azar sometidos a la prueba de rangos múltiples de Duncan. Las variables estudiadas fueron: consumo de alimento, peso vivo, ganancia de peso, conversión alimenticia, mortalidad vs viabilidad, rendimiento en la canal, análisis económico. No se encontraron diferencias significativas (P<0.05) entre los tratamientos al final del ensayo para el consumo de alimento, conversión alimenticia y costo de alimento, pero no así ara peso vivo y ganancia de peso. El porcentaje de mortalidad acumulada total fue de 2.5% y los rendimientos de la canal fueron: (90.74)T1 (88.98)T2, (85.86)T3,y (90.31)T4, Se corolo que el periodo de suministro de alimento de retiro que permitió los mejores pesos vivos, ganancias de pesos y conversiones alimenticias fue el periodo de tres días (T3), sin embargo, obtuvo el mayor consumo total para generar un peso promedio en la canal de 3.34 lbs, además, presentó el mayor costo alimenticio entre los tratamientos experimentales (T1, T2, T3) y bajo rendimiento en la canal, contrario al T1 que aunque los parámetros productivos fueron menores que el T3 obtuvo el mayor rendimiento en la canal con un menor costo alimenticio. El alimento de retiro no ejerció efecto sobre las variables estudiadas lo que demuestra que dicho alimento pueda ser una alternativa viable para disminuir costo alimenticio.

Influencia de diferentes periodos de destete en conejas primiparas en el municipio de Diriamba, Departamento de Carazo, Nicaragua

Este trabajo fue realizado en la Quinta "Myriam", ubicada en el municipio de Diriamba, departamento de Carazo, Nicaragua, propiedad del Dr. Jorge Ferreira. La ubicación geográfica del municipio está comprendida entre los 11° 50' y 12° 00' de Latitud Norte y entre los 86° 00' y 86° 15' de Longitud Oeste, cuenta con una elevación de 551 m.s.n.m., los datos meteorológicos de la zona en los últimos cuatro años (90-93) en cuanto a temperatura, humedad relativa y precipitación promedio fueron: 23.8 °C, 84% y 1184,5 mm respectivamente, (INETER, Departamento de Estadística, 1993). En el presente ensayo, se utilizó un diseño estadístico completamente aleatorizado (DCA), mediante el cual se evaluó el efecto de 3 tratamientos (15, 30 y 45 días de destete) sobre las variables Peso de la Camada al Destete (PCD), Peso de la Madre al Destete (PMD), Peso de la Madre al Segundo Parto (PSP), Ganancia Media Diaria del Parto 1 al Parto 2 (GMDp 1.P2) , con 4 repeticiones por tratamiento, éstas repeticiones estuvieron constituidas por conejas primíparas, las cuales tuvieron un peso que osciló entre 3 - 3.18 kg. y edad homogénea de 7 meses. Las variables fueron sometidas a la prueba de Duncan para determinar la superioridad en rango por tratamiento. Mediante el análisis de varianza se encontró que el efecto de los tratamientos resultó ser altamente significativo sobre la variable Peso de la Camada al Destete (PCD) (P0.01), significativo sobre las variables Peso de la Madre al Segundo Parto (PSP) y Ganancia Media Diaria del Parto 1 al Parto 2 (GMD p 1.P2) (P0.1) y no significativo sobre la variable Peso de la Madre al Destete (PMD) (NS). El efecto de la covariable Peso al Primer Parto (P1P) resultó ser altamente significativo sobre las variables Peso de la Madre al Destete (PMD) y Peso de la Madre al Segundo Parto (PSP) (P0.01). Después de someter las variables a la prueba de DUNCAN se encontraron los siguientes promedios por tratamiento: Peso de la Camada al Destete (PCD) ; T.15 días 1.538 kg P.V.(C), T.30 días 3.360 kg P.V. (B), T.45 días 4.523 kg P.V. (A), Peso de la Madre al Destete (PMD); T.15 días 3.649 kg P.V. (A) T.30 días 3.549 kg P.V. (A), T.45 dias 3.493 kg P.V.(A). Peso de la Madre al Segundo Parto (PSP); T.15 días 3. 449 kg P.V. (B), T.30 días 3.628 kg P.V. (AB), T.45 días 3.777 kg P.V.(A). Ganancia Media Diaria del Parto 1 al Parto 2 (GMD p 1.P2) T .15 días (2.071 g (B), T.30 días 2.718 g (AB), T.45 días 2. 975 g (A). Los promedios y desviaciones standard para las variables Ganancia Media Diaria del Parto 1 al Destete 1 (GMDp1-D1)y Ganancia Media Diaria del Destete l al Parto 2 (GMDD1.P2) por tratamiento fueron: GMD P1-D1; T.l5 días 3.84 g ± 0.50 g, T.30 días 2.54 g ± 0.64 g, T.45 días 2.37 g ± 0.72 g. GMD D1-P2; T.l5 días 2.26 g ± 0.54 g, T.30 días 3.17 g ± 0.74 g, T.45 días 3.93 g ± 0.28 g. Se encontró que el alimento tipo único suministrado a los animales bajo experimentación, cumplió con los requerimientos nutricionales de la especie estudiada. Los costos encontrados por hembra, por tratamiento, fueron C$ 197.21 destete de 15 días, C$ 220.28 destete de 30 días, C$ 243 .1.4 destete de 45 días. Los costos por gazapo destetado fueron de C$ 5.48 destete de 15 días, C$ 6.12 destete de 30 días, C$ 8.10 destete de 45 días.