Identification of protein interaction regions of VINC/NEAT1/Men epsilon RNA

The virus inducible non-coding RNA (VINC) was detected initially in the brain of mice infected with Japanese encephalitis virus (JEV) and rabies virus. VINC is also known as NEAT1 or Men epsilon RNA. It is localized in the nuclear paraspeckles of several murine as well as human cell lines and is essential for paraspeckle formation. We demonstrate that VINC interacts with the paraspeckle protein, P54nrb through three different protein interaction regions (PIRs) one of which (PIR-1) is localized near the 50 end while the other two (PIR-2, PIR-3) are localized near the 30 region of VINC. Our studies suggest that VINC may interact with P54nrb through a novel mechanism which is different from that reported for protein coding RNAs. (C) 2010 Federation of European Biochemical Societies. Published by Elsevier B. V. All rights reserved.

Modular design of synthetic protein mimics. Crystal structure of two seven-residue helical peptide segments linked by .epsilon.-aminocaproic acid

Two seven-residue helical segments, Val-Ala-Leu-Aib-Val-Ala-Leu, were linked synthetically with an epsilon-aminocaproic acid (Acp) linker with the intention of making a stable antiparallel helix-helix motif. The crystal structure of the linked peptide Boc-Val-Ala-Leu-Aib-Val-Ala-Leu-Acp-Val-Ala-Leu-Aib-Val-Ala-Leu-OMe (1) shows the two helices displaced laterally from each other by the linker, but the linker has not folded the molecule into a close-packed antiparallel conformation. Two strong intermolecular NH...O = C hydrogen bonds are formed between the top of the lower helix of one molecule and the bottom of the upper helix in a laterally adjacent molecule to give the appearance of an extended single helix. The composite peptide with Boc and OMe end groups, C76H137N15O18.H2O, crystallize in space group P2(1) with a = 8.802 (1) angstrom, b = 20.409 (4) angstrom, c = 26.315 (3) angstrom, and beta = 90.72 (1)degrees; overall agreement R = 7.86% for 5030 observed reflections (\F(o)\ > 3-sigma(F)); resolution = 0.93 angstrom. Limited evidence for a more compact conformation in solution consistent with an antiparallel helix arrangement is obtained by comparison of the HPLC retention times and CD spectra of peptide 1 with well-characterized continuous helices of similar length and sequence.

Ilmastonmuutoksen ääri-ilmiöihin liittyvän riskienhallinnan kustannus–hyötyanalyysi osana julkista päätöksentekoa. IRTORISKI-hankkeen loppuraportti.

IRTORISKI-hankkeessa tutkittiin, miten kustannus–hyötyanalyysin käyttöä ilmastonmuutoksen sopeutumissuunnittelussa voitaisiin helpottaa niin, että sitä pystyttäisiin hyödyntämään kustannustehokkaasti sekä ilmastonmuutokseen liittyvien vaarojen priorisoinnissa että ennaltaehkäisevien toimenpiteiden vertailussa. Tutkimuksessa käytettiin esimerkkitapauksina jokitulvaa ja rankkasateiden aiheuttamaa tulvaa kaupunkiolosuhteissa. Tapahtumapuuanalyysia laajennettiin siten, että siitä käyvät ilmi sekä suorat vahingot että lopulliset makrotaloudelliset vaikutukset. Arviot suorista taloudellisista vahingoista perustuivat aikaisempiin tutkimuksiin, kun taas makrotaloudellisia vaikutuksia simuloitiin yleisen tasapainon mallin avulla. Tapaustutkimusten valinnasta, tapahtumapuun käytöstä, sen laajennusosasta sekä lasketuista makrotaloudellisista vaikutuksista keskusteltiin sidosryhmien edustajien kanssa kolmessa asiantuntijaistunnossa.

Sään ääri-ilmiöt luonnollista vaihtelua kuvaavassa 1200-vuotisessa ilmastokokeessa

Tämän tutkielman tavoitteena oli selvittää erimittaisten sään ääri-ilmiöiden jaksojen (lämpötila ja sademäärä) ja sään ääri-ilmiöiden yhdistelmien esiintymistä sekä todennäköisyyttä Suomessa nykyisessä ilmastossa havaintojen (1950-2009) ja ilmaston sisäistä luonnollista vaihtelua kuvaavan ilmastomallikokeen, ns. Millennium0001-kontrolliajon (1200 vuotta) tulosten pohjalta. Tutkielmassa tarkastellaan sään ääri-ilmiöiden yhdistelmien esiintyvyyttä myös kirjallisuuden ja synoptisten tarkastelujen avulla sekä arvioidaan niiden esiintymisten mahdollisia muutoksia ilmaston lämmetessä. Aluksi tutkittiin, miten malliaineisto ja havainnot poikkeavat toisistaan tilastollisesti lämpötilojen ja sademäärien osalta, minkä jälkeen kontrolliajon tuottamia suureita korjattiin havaittua keskimääräistä ilmastoa vastaaviksi. Keskeiset tulokset johdettiin erimittaisille äärimmäisen kylmille tai kuumille jaksoille ja äärimmäisen sateisille jaksoille. Tutkitut kuukaudet olivat tammi- ja heinäkuu. Esimerkiksi vuorokauden keskilämpötila 25,5 °C ylittyy heinäkuussa keskimäärin suuren osan Etelä- ja Keski-Suomea peittävän hilaruudun (300 km x 300 km) alueella 0,2 %:n todennäköisyydellä, sademäärä 29,7 mm samoin 0,2 %:n todennäköisyydellä. Tammikuussa samassa hilapisteessä seitsemän vuorokauden kylmin jakso -30,2 °C ja sateisin jakso 50,1 mm toistuu kerran n. 500 vuodessa. Kuukauden keskilämpötiloille ja sademäärille tehtiin korrelaatioanalyysejä, joiden perusteella saatiin selville, että Suomessa vähäsateinen loppukevät (huhti-kesäkuu) tai pelkkä kesäkuu edesauttavat keskimääräistä lämpimämmän heinäkuun esiintymistä. Selityksenä voidaan pitää maaperän pientä kosteussisältöä. Korrelaatiot kesäkuun sademäärän ja heinäkuun keski- lämpötilojen välillä vaihtelivat -0,26 ja -0,36 välillä tilastollisen merkitsevyystason ollessa yli 99,9 %. Ilmastonmuutos muuttaa sään ääri-ilmiöiden esiintyvyyttä ja voi mahdollisesti lisätä sään ääri-ilmiöiden yhdistelmien todennäköisyyttä tai yhteiskunnan ja luonnon haavoittuvuutta ääri-ilmiöille tai niiden yhdistelmille. Ääri-ilmiöt voivat aiheuttaa mittavia vahinkoja niin yhteiskunnalle kuin luonnollekin, joten tällaisiin tapahtumiin olisi tärkeää voida varautua etukäteen mahdollisten tuhojen minimoimiseksi. Olisikin tärkeää lisätä tutkimusta tästä aiheesta.

Isolation and characterization of DNA polymerase epsilon from the silk glands of Bombyx mori

The silk gland of Bombyx mori, an endomitotically replicative tissue shows high levels of DNA polymerases alpha, delta, and epsilon activities. The ratio of polymerase alpha to that of delta plus epsilon is maintained at 1.1 to 1.3 in both the posterior and middle silk glands for the entire duration of late larval development. The three activities copurify in the initial stages of fractionation through phosphocellulose and DE52 but polymerase alpha gets resolved from the others on hydroxylapatite column. Separation between polymerase delta and epsilon is achieved by chromatography on QAE-Sephadex. DNA polymerase epsilon is a heterodimer comprising of 215- and 42-kDa subunits. The activity is maximum at pH 6.5 and the Km values for dNTPs vary between 3-9 microM. The enzyme possesses an intrinsically associated exonuclease activity which functions in the mismatch repair during DNA synthesis. Both polymerase and 3'-->5' exonuclease activities are associated with the 215-kDa subunit. By itself, DNA polymerase epsilon is processive and the catalytic activity is not enhanced by externally added bPCNA (Bombyx-proliferating cell nuclear antigen, an auxiliary protein for DNA polymerase delta). The enzyme resembles polymerase delta in having the exonuclease activity and in its response to aphidicolin or substrate analogs, but could be distinguished from the latter by its lack of response to the bPCNA and sensitivity to dimethyl sulfoxide. The two enzymes show partial immunological cross-reactivity with each other but no immunological relatedness to polymerase alpha. The absence of the repair enzyme DNA polymerase beta and the presence of substantial levels of polymerase epsilon in the silk glands suggest a possible role for the latter in DNA repair in that tissue.

The mean and turbulence structure simulation of the monsoon trough boundary layer using a one-dimensional model with e-l and e-epsilon closures

An attempt has been made here to study the sensitivity of the mean and the turbulence structure of the monsoon trough boundary layer to the choice of the constants in the dissipation equation for two stations Delhi and Calcutta, using one-dimensional atmospheric boundary layer model with e-epsilon turbulence closure. An analytical discussion of the problems associated with the constants of the dissipation equation is presented. It is shown here that the choice of the constants in the dissipation equation is quite crucial and the turbulence structure is very sensitive to these constants. The modification of the dissipation equation adopted by earlier studies, that is, approximating the Tke generation (due to shear and buoyancy production) in the epsilon-equation by max (shear production, shear + buoyancy production), can be avoided by a suitable choice of the constants suggested here. The observed turbulence structure is better simulated with these constants. The turbulence structure simulation with the constants recommended by Aupoix et al (1989) (which are interactive in time) for the monsoon region is shown to be qualitatively similar to the simulation obtained with the constants suggested here, thus implying that no universal constants exist to regulate dissipation rate. Simulations of the mean structure show little sensitivity to the type of the closure parameterization between e-l and e-epsilon closures. However the turbulence structure simulation with e-epsilon closure is far better compared to the e-l model simulations. The model simulations of temperature profiles compare quite well with the observations whenever the boundary layer is well mixed (neutral) or unstable. However the models are not able to simulate the nocturnal boundary layer (stable) temperature profiles. Moisture profiles are simulated reasonably better. With one-dimensional models, capturing observed wind variations is not up to the mark.

A k-epsilon model for turbulent weld pool convection in gas metal arc welding process

In this paper, we present a modified k - epsilon model capable of addressing turbulent weld-pool convection in a GMAW process, taking into account the morphology of the phase change interface during a Gas Metal Arc Welding (GMAW) process. A three-dimensional turbulence mathematical model has been developed to study the heat transfer and fluid flow within the weld pool by considering the combined effect of three driving forces, viz., buoyancy, Lorentz force and surface tension (Marangoni convection). Mass and energy transports by the droplets are considered through the thermal analysis of the electrode. The falling droplet's heat addition to the molten pool is considered to be a volumetric heat source distributed in an imaginary cylindrical cavity ("cavity model") within the weld pool. This nature of heat source distribution takes into account the momentum and the thermal, energy of the falling droplets. The numerically predicted weld pool dimensions both from turbulence and laminar models are then compared with the experimental post-weld results sectioned across the weld axis. The above comparison enables us to analyze the overall effects of turbulent convection on the nature of heat and fluid flow and hence on the weld pool shape/size during the arc welding processes.

Amine-functionalized multiwall carbon nanotubes impart osteoinductive and bactericidal properties in poly(epsilon-caprolactone) composites

Poly(epsilon-caprolactone) (PCL) is an aliphatic polyester widely used for biomedical applications but lacks the mechanical properties desired for many load-bearing orthopedic applications. The objective of this study was to prepare and characterize PCL composites incorporating multiwall carbon nanotubes (MWNTs) with different surface functional groups. PCL composites were prepared by melt-mixing with three different types of MWNTs: pristine (pMWNT), amine functionalized (aMWNT), and carboxyl functionalized (cMWNT). Melt rheology and scanning electron microscopy indicated good dispersion of the nanotubes in the matrix. Tensile strength and elastic modulus of the polymer was significantly increased by the incorporation of MWNTs and further enhanced by favorable interactions between PCL and aMWNTs. Thermal analysis revealed that MWNTs act as heterogeneous nucleation sites for crystallization of PCL and increase polymer crystallinity. Incorporation of functionalized MWNTs increased the surface water wettability of PCL. Osteoblast proliferation and differentiation was significantly enhanced on functionalized composites. aMWNT composites also exhibited the best bactericidal response. This study demonstrates that surface functionalization of MWNTs profoundly influences the properties of PCL and amine-functionalization offers the optimal combination of mechanical properties, osteogenesis and antimicrobial response. These results have important implications for designing nanocomposites for use in orthopedics.

Small strong epsilon nets

Let P be a set of n points in R-d. A point x is said to be a centerpoint of P if x is contained in every convex object that contains more than dn/d+1 points of P. We call a point x a strong centerpoint for a family of objects C if x is an element of P is contained in every object C is an element of C that contains more than a constant fraction of points of P. A strong centerpoint does not exist even for halfspaces in R-2. We prove that a strong centerpoint exists for axis-parallel boxes in Rd and give exact bounds. We then extend this to small strong epsilon-nets in the plane. Let epsilon(S)(i) represent the smallest real number in 0, 1] such that there exists an epsilon(S)(i)-net of size i with respect to S. We prove upper and lower bounds for epsilon(S)(i) where S is the family of axis-parallel rectangles, halfspaces and disks. (C) 2014 Elsevier B.V. All rights reserved.

epsilon-expansions near three dimensions from conformal field theory

We formally extend the CFT techniques introduced in arXiv: 1505.00963, to phi(2d0/d0-2) theory in d = d(0) dimensions and use it to compute anomalous dimensions near d(0) = 3, 4 in a unified manner. We also do a similar analysis of the O(N) model in three dimensions by developing a recursive combinatorial approach for OPE contractions. Our results match precisely with low loop perturbative computations. Finally, using 3-point correlators in the CFT, we comment on why the phi(3) theory in d(0) = 6 is qualitatively different.

Gamma -> Epsilon Martensite Transformation and Twinning Deformation in fcc Cobalt During Surface Mechanical Attrition Treatment

The deformation microstructure of face-centered cubic cobalt subjected to surface mechanical attrition treatment was studied as a function of strain levels. Strain-induced gamma --> epsilon transformation and twinning deformation were evidenced by transmission electron microscopy and were found to progress continuously in ultrafine and nanocrystalline grains as the strain increased.

Lehia ez perfektua-ri buruzko notak

Para quien es de utilidad: - Alumnos de Tª Microeconómica IV, curso 3º LE. - Alumnos de las asignaturas de Tª de Juegos y Organización Industrial del Máster en Economía: Instrumentos del Análisis Económico. Estas notas sobre competencia imperfecta están dedicadas al estudio de estructuras de mercado caracterizadas por la existencia de poder de mercado. Se estudia en primer lugar el monopolio, dedicando una atención especial a los diferentes tipos de discriminación de precios. A continuación se presenta la Tª de juegos no cooperativos y se muestra su utilidad para analizar diferentes fenómenos económicos caracterizados por la interdependencia estratégica. Finalmente, se estudian diferentes modelos de competencia oligopolística y la estabilidad de los acuerdos colusivos.

Completions of epsilon-dense partial Latin squares

A classical question in combinatorics is the following: given a partial Latin square $P$, when can we complete $P$ to a Latin square $L$? In this paper, we investigate the class of textbf{$epsilon$-dense partial Latin squares}: partial Latin squares in which each symbol, row, and column contains no more than $epsilon n$-many nonblank cells. Based on a conjecture of Nash-Williams, Daykin and H"aggkvist conjectured that all $frac{1}{4}$-dense partial Latin squares are completable. In this paper, we will discuss the proof methods and results used in previous attempts to resolve this conjecture, introduce a novel technique derived from a paper by Jacobson and Matthews on generating random Latin squares, and use this novel technique to study $ epsilon$-dense partial Latin squares that contain no more than $delta n^2$ filled cells in total.

In Chapter 2, we construct completions for all $ epsilon$-dense partial Latin squares containing no more than $delta n^2$ filled cells in total, given that $epsilon < frac{1}{12}, delta < frac{ left(1-12epsilonright)^{2}}{10409}$. In particular, we show that all $9.8 cdot 10^{-5}$-dense partial Latin squares are completable. In Chapter 4, we augment these results by roughly a factor of two using some probabilistic techniques. These results improve prior work by Gustavsson, which required $epsilon = delta leq 10^{-7}$, as well as Chetwynd and H"aggkvist, which required $epsilon = delta = 10^{-5}$, $n$ even and greater than $10^7$.

If we omit the probabilistic techniques noted above, we further show that such completions can always be found in polynomial time. This contrasts a result of Colbourn, which states that completing arbitrary partial Latin squares is an NP-complete task. In Chapter 3, we strengthen Colbourn's result to the claim that completing an arbitrary $left(frac{1}{2} + epsilonright)$-dense partial Latin square is NP-complete, for any $epsilon > 0$.

Colbourn's result hinges heavily on a connection between triangulations of tripartite graphs and Latin squares. Motivated by this, we use our results on Latin squares to prove that any tripartite graph $G = (V_1, V_2, V_3)$ such that begin{itemize} item $|V_1| = |V_2| = |V_3| = n$, item For every vertex $v in V_i$, $deg_+(v) = deg_-(v) geq (1- epsilon)n,$ and item $|E(G)| > (1 - delta)cdot 3n^2$ end{itemize} admits a triangulation, if $epsilon < frac{1}{132}$, $delta < frac{(1 -132epsilon)^2 }{83272}$. In particular, this holds when $epsilon = delta=1.197 cdot 10^{-5}$.

This strengthens results of Gustavsson, which requires $epsilon = delta = 10^{-7}$.

In an unrelated vein, Chapter 6 explores the class of textbf{quasirandom graphs}, a notion first introduced by Chung, Graham and Wilson cite{chung1989quasi} in 1989. Roughly speaking, a sequence of graphs is called "quasirandom"' if it has a number of properties possessed by the random graph, all of which turn out to be equivalent. In this chapter, we study possible extensions of these results to random $k$-edge colorings, and create an analogue of Chung, Graham and Wilson's result for such colorings.

Structural Characterization of Pro-inflammatory and Anti-inflammatory Immunoglobulin G Fc Proteins

Immunoglobulin G (IgG) is central in mediating host defense due to its ability to target and eliminate invading pathogens. The fragment antigen binding (Fab) regions are responsible for antigen recognition; however the effector responses are encoded on the Fc region of IgG. IgG Fc displays considerable glycan heterogeneity, accounting for its complex effector functions of inflammation, modulation and immune suppression. Intravenous immunoglobulin G (IVIG) is pooled serum IgG from multiple donors and is used to treat individuals with autoimmune and inflammatory disorders such as rheumatoid arthritis and Kawasaki’s disease, respectively. It contains all the subtypes of IgG (IgG1-4) and over 120 glycovariants due to variation of an Asparagine 297-linked glycan on the Fc. The species identified as the activating component of IVIG is sialylated IgG Fc. Comparisons of wild type Fc and sialylated Fc X-ray crystal structures suggests that sialylation causes an increase in conformational flexibility, which may be important for its anti-inflammatory properties.

Although glycan modifications can promote the anti-inflammatory properties of the Fc, there are amino acid substitutions that cause Fcs to initiate an enhanced immune response. Mutations in the Fc can cause up to a 100-fold increase in binding affinity to activating Fc gamma receptors located on immune cells, and have been shown to enhance antibody dependent cell-mediated cytotoxicity. This is important in developing therapeutic antibodies against cancer and infectious diseases. Structural studies of mutant Fcs in complex with activating receptors gave insight into new protein-protein interactions that lead to an enhanced binding affinity.

Together these studies show how dynamic and diverse the Fc region is and how both protein and carbohydrate modifications can alter structure, leading to IgG Fc’s switch from a pro-inflammatory to an anti-inflammatory protein.

II Workshop en Modelización Farmacocinética y Farmacodinámica. Aplicación del NONMEM para el desarrollo e interpretación de modelos FC/FD

Sesión I: Modelos FC/FD: Desarrollo e implementación de modelos. Sesión de exposición teórica seguida de realización y evaluación práctica: - Introducción al análisis farmacocinético con NONMEM: construcción de una base de datos y archivos control (Carmen Navarro Fontestad, Universitat de València). - Introducción al análisis farmacocinético con NONMEM: exploración, evaluación y validación de resultados de los modelos (Víctor Mangas Sanjuán, Universidad Miguel Hernández de Elche). Sesión II: Implementación de modelos farmacodinámicos en la modelización farmacocinética/farmacodinámica. Sesión de exposición teórica seguida de realización y evaluación práctica: - Iniciación al modelado de la respuesta farmacológica a través de NONMEM (Zinnia Parra-Guillén, Iñaki F. Trocóniz, Mª Jesús Garrido, Universidad de Navarra). - Iniciación al modelado de la respuesta farmacológica a través de NONMEM. Sesión práctica (Zinnia Parra-Guillén, Iñaki F. Trocóniz, Mª Jesús Garrido, Universidad de Navarra). Sesión III: Modelos FC/FD: Aplicaciones prácticas: - Modelos FC/FD para describir el efecto de antitumorales en el tamaño del tumor en modelos xenograft (Carlos Fernández Teruel, PharmaMar). - Modelos FC/FD en antibioterapia. Aplicación en profilaxis quirúrgica y pacientes críticos sometidos a técnicas continuas de reemplazo renal (Arantxa Isla, Universidad del País Vasco UPV/EHU). - Modelos FC/FD antihistamínicos. Caso práctico bilastina (Ignacio Ortega, FAES FARMA)