Molecular cloning and homology modelling of a subtilisin-like serine protease from the marine fungus, Engyodontium album BTMFS10

An alkaline protease gene (Eap) was isolated for the first time from a marine fungus, Engyodontium album. Eap consists of an open reading frame of 1,161 bp encoding a prepropeptide consisting of 387 amino acids with a calculated molecular mass of 40.923 kDa. Homology comparison of the deduced amino acid sequence of Eap with other known proteins indicated that Eap encode an extracellular protease that belongs to the subtilase family of serine protease (Family S8). A comparative homology model of the Engyodontium album protease (EAP) was developed using the crystal structure of proteinase K. The model revealed that EAP has broad substrate specificity similar to Proteinase K with preference for bulky hydrophobic residues at P1 and P4. Also, EAP is suggested to have two disulfide bonds and more than two Ca2? binding sites in its 3D structure; both of which are assumed to contribute to the thermostable nature of the protein.

Identification of models using failure rate and mean residual life of doubly truncated random variables

In this paper, we study the relationship between the failure rate and the mean residual life of doubly truncated random variables. Accordingly, we develop characterizations for exponential, Pareto 11 and beta distributions. Further, we generalize the identities for fire Pearson and the exponential family of distributions given respectively in Nair and Sankaran (1991) and Consul (1995). Applications of these measures in file context of lengthbiased models are also explored

On conduction mechanism in paramagnetic phase of Gd based manganites

Materials belonging to the family of manganites are technologically important since they exhibit colossal magneto resistance. A proper understanding of the transport properties is very vital in tailoring the properties. A heavy rare earth doped manganite like Gd0·7Sr0·3MnO3 is purported to be exhibiting unusual properties because of smaller ionic radius of Gd. Gd0·7Sr0·3MnO3 is prepared by a wet solid state reaction method. The conduction mechanism in such a compound has been elucidated by subjecting the material to low temperature d.c. conductivity measurement. It has been found that the low band width material follows a variable range hopping (VRH) model followed by a small polaron hopping (SPH) model. The results are presented here

Synthesis and Photoluminescence Properties of Novel Red Phosphors for White Light Emitting Diode Applications

Several series of Eu3+ based red emitting phosphor materials were synthesized using solid state reaction route and their properties were characterized. The present studies primarily investigated the photoluminescence properties of Eu3+ in a family of closely related host structure with a general formula Ln3MO7. The results presented in the previous chapters throws light to a basic understanding of the structure, phase formation and the photoluminescence properties of these compounds and their co-relations. The variation in the Eu3+ luminescence properties with different M cations was studied in Gd3-xMO7 (M = Nb, Sb, Ta) system.More ordering in the host lattice and more uniform distribution of Eu3+ ions resulting in the increased emission properties were observed in tantalate system.Influence of various lanthanide ion (Lu, Y, Gd, La) substitutions on the Eu3+ photoluminescence properties in Ln3MO7 host structures was also studied. The difference in emission profiles with different Ln ions demonstrated the influence of long range ordering, coordination of cations and ligand polarizability in the emission probabilities, intensity and quantum efficiency of these phosphor materials. Better luminescence of almost equally competing intensities from all the 4f transitions of Eu3+ was noticed for La3TaO7 system. Photoluminescence properties were further improved in La3TaO7 : Eu3+ phosphors by the incorporation of Ba2+ ions in La3+ site. New red phosphor materials Gd2-xGaTaO7 : xEu3+ exhibiting intense red emissions under UV excitation were prepared. Optimum doping level of Eu3+ in these different host lattices were experimentally determined. Some of the prepared samples exhibited higher emission intensities than the standard Y2O3 : Eu3+ red phosphors. In the present studies, Eu3+ acts as a structural probe determining the coordination and symmetry of the atoms in the host lattice. Results from the photoluminescence studies combined with the powder XRD and Raman spectroscopy investigations helped in the determination of the correct crystal structures and phase formation of the prepared compounds. Thus the controversy regarding the space groups of these compounds could be solved to a great extent. The variation in the space groups with different cation substitutions were discussed. There was only limited understanding regarding the various influential parameters of the photoluminescence properties of phosphor materials. From the given studies, the dependence of photoluminescence properties on the crystal structure and ordering of the host lattice, site symmetries, polarizability of the ions, distortions around the activator ion, uniformity in the activator distribution, concentration of the activator ion etc. were explained. Although the presented work does not directly evidence any application, the materials developed in the studies can be used for lighting applications together with other components for LED lighting. All the prepared samples were well excitable under near UV radiation. La3TaO7 : 0.15Eu3+ phosphor with high efficiency and intense orange red emissions can be used as a potential red component for the realization of white light with better color rendering properties. Gd2GaTaO7 : Eu3+, Bi2+ red phosphors give good color purity matching to NTSC standards of red. Some of these compounds exhibited higher emission intensities than the standard Y2O3 : Eu3+ red phosphors. However thermal stability and electrical output using these compounds should be studied further before applications. Based on the studies in the closely related Ln3MO7 structures, some ideas on selecting better host lattice for improved luminescence properties could be drawn. Analyzing the CTB position and the number of emission splits, a general understanding on the doping sites can be obtained. These results could be helpful for phosphor designs in other host systems also, for enhanced emission intensity and efficiency.

Solution properties of the de Branges differential recurrence equation

In this 1984 proof of the Bieberbach and Milin conjectures de Branges used a positivity result of special functions which follows from an identity about Jacobi polynomial sums thas was published by Askey and Gasper in 1976. The de Branges functions Tn/k(t) are defined as the solutions of a system of differential recurrence equations with suitably given initial values. The essential fact used in the proof of the Bieberbach and Milin conjectures is the statement Tn/k(t)<=0. In 1991 Weinstein presented another proof of the Bieberbach and Milin conjectures, also using a special function system Λn/k(t) which (by Todorov and Wilf) was realized to be directly connected with de Branges', Tn/k(t)=-kΛn/k(t), and the positivity results in both proofs Tn/k(t)<=0 are essentially the same. In this paper we study differential recurrence equations equivalent to de Branges' original ones and show that many solutions of these differential recurrence equations don't change sign so that the above inequality is not as surprising as expected. Furthermore, we present a multiparameterized hypergeometric family of solutions of the de Branges differential recurrence equations showing that solutions are not rare at all.

A Note on the Generalization Performance of Kernel Classifiers with Margin

We present distribution independent bounds on the generalization misclassification performance of a family of kernel classifiers with margin. Support Vector Machine classifiers (SVM) stem out of this class of machines. The bounds are derived through computations of the $V_gamma$ dimension of a family of loss functions where the SVM one belongs to. Bounds that use functions of margin distributions (i.e. functions of the slack variables of SVM) are derived.

Multiclass Classification of SRBCTs

A novel approach to multiclass tumor classification using Artificial Neural Networks (ANNs) was introduced in a recent paper cite{Khan2001}. The method successfully classified and diagnosed small, round blue cell tumors (SRBCTs) of childhood into four distinct categories, neuroblastoma (NB), rhabdomyosarcoma (RMS), non-Hodgkin lymphoma (NHL) and the Ewing family of tumors (EWS), using cDNA gene expression profiles of samples that included both tumor biopsy material and cell lines. We report that using an approach similar to the one reported by Yeang et al cite{Yeang2001}, i.e. multiclass classification by combining outputs of binary classifiers, we achieved equal accuracy with much fewer features. We report the performances of 3 binary classifiers (k-nearest neighbors (kNN), weighted-voting (WV), and support vector machines (SVM)) with 3 feature selection techniques (Golub's Signal to Noise (SN) ratios cite{Golub99}, Fisher scores (FSc) and Mukherjee's SVM feature selection (SVMFS))cite{Sayan98}.

Functional studies of the deubiquitinating enzymes USP19, USP4 and UCH-L1

El marcaje de proteínas con ubiquitina, conocido como ubiquitinación, cumple diferentes funciones que incluyen la regulación de varios procesos celulares, tales como: la degradación de proteínas por medio del proteosoma, la reparación del ADN, la señalización mediada por receptores de membrana, y la endocitosis, entre otras (1). Las moléculas de ubiquitina pueden ser removidas de sus sustratos gracias a la acción de un gran grupo de proteasas, llamadas enzimas deubiquitinizantes (DUBs) (2). Las DUBs son esenciales para la manutención de la homeostasis de la ubiquitina y para la regulación del estado de ubiquitinación de diferentes sustratos. El gran número y la diversidad de DUBs descritas refleja tanto su especificidad como su utilización para regular un amplio espectro de sustratos y vías celulares. Aunque muchas DUBs han sido estudiadas a profundidad, actualmente se desconocen los sustratos y las funciones biológicas de la mayoría de ellas. En este trabajo se investigaron las funciones de las DUBs: USP19, USP4 y UCH-L1. Utilizando varias técnicas de biología molecular y celular se encontró que: i) USP19 es regulada por las ubiquitin ligasas SIAH1 y SIAH2 ii) USP19 es importante para regular HIF-1α, un factor de transcripción clave en la respuesta celular a hipoxia, iii) USP4 interactúa con el proteosoma, iv) La quimera mCherry-UCH-L1 reproduce parcialmente los fenotipos que nuestro grupo ha descrito previamente al usar otros constructos de la misma enzima, y v) UCH-L1 promueve la internalización de la bacteria Yersinia pseudotuberculosis.

New Ruthenium complexes containing N, P and S-donor type of ligands: coordination chemistry, characterization and application to asymetric and non-asymetric catalysis

Síntesi de nous complexos de Ruteni amb lligands no quirals que tenen per fórmula [Ru(phen)([9]aneS3)X] (on X = H2O, py i MeCN). Caracterització espectroscòpica electroquímica i estructural d'aquesta família de complexos. Estudi de les seves propietats catalítiques en front a l'oxidació de substrats orgànics com l'alcohol benzílic en reaccions d'electrocatàlisi. Avaluació cinètica dels mecanismes de substitució entre els complexos Ru-py i Ru-MeCN. Generació d'un interruptor molecular foto-induït. Síntesi de nous complexos quirals de Ru atropoisomèricament purs amb lligands oxazolínics que tenen per fórmula [Ru(trpy)(Ph-box-R)X] on (X = Cl, H2O, py, MeCN, 2-OH-py). Caracterització estructural exhaustiva en estat sòlid (Raig-X) en solució (RMN) i en fase gas (càlculs DFT). Avaluació de la seva activitat catalítica en reaccions asimmetriques d'epoxidació de substrats proquirals. Síntesi de nous lligands polipiridílics quirals amb simetria C3. Estudi de la seva química de coordinació i avaluació de la seva activitat catalítica en reaccions asimmetriques d'oxidació i reducció.

Rational modification of the hierarchy of intermolecular interactions in molecular crystal structures by using tunable halogen bonds

A family of 16 isomolecular salts (3-XpyH)(2)[MX'(4)] (3-XpyH=3-halopyridinium; M=Co, Zn; X=(F), Cl, Br, (I); X'=Cl, Br, I) each containing rigid organic cations and tetrahedral halometallate anions has been prepared and characterized by X-ray single crystal and/or powder diffraction. Their crystal structures reflect the competition and cooperation between non-covalent interactions: N-H center dot center dot center dot X'-M hydrogen bonds, C-X center dot center dot center dot X'-M halogen bonds and pi-pi stacking. The latter are essentially unchanged in strength across the series, but both halogen bonds and hydrogen bonds are modified in strength upon changing the halogens involved. Changing the organic halogen (X) from F to I strengthens the C-X center dot center dot center dot X'-M halogen bonds, whereas an analogous change of the inorganic halogen (X') weakens both halogen bonds and N-H center dot center dot center dot X'-M hydrogen bonds. By so tuning the strength of the putative halogen bonds from repulsive to weak to moderately strong attractive interactions, the hierarchy of the interactions has been modified rationally leading to systematic changes in crystal packing. Three classes of crystal structure are obtained. In type A (C-F center dot center dot center dot X'-M) halogen bonds are absent. The structure is directed by N-H center dot center dot center dot X'-M hydrogen bonds and pi-stacking interactions. In type B structures, involving small organic halogens (X) and large inorganic halogens (X'), long (weak) C-X center dot center dot center dot X'-M interactions are observed with type I halogen-halogen interaction geometries (C-X center dot center dot center dot X' approximate to X center dot center dot center dot X'-M approximate to 155 degrees), but hydrogen bonds still dominate. Thus, minor but quite significant perturbations from the type A structure arise. In type C, involving larger organic halogens (X) and smaller inorganic halogens (X'), stronger halogen bonds are formed with a type II halogen-halogen interaction geometry (C-X center dot center dot center dot X' approximate to 180 degrees; X center dot center dot center dot X'-M approximate to 110 degrees) that is electrostatically attractive. The halogen bonds play a major role alongside hydrogen bonds in directing the type C structures, which as a result are quite different from type A and B.

Lys-gamma3-MSH: a global regulator of hormone sensitive lipase activity?

Gamma-melanocyte stimulating hormone (gamma-MSH) is a peptide derived from the ACTH precursor, pro-opiomelanocortin (POMC), and belongs to a family of peptides called the melanocortins that also comprises alpha- and beta-MSH. Although conserved in tetrapods, the biological role of gamma-MSH remains largely undefined. It has been demonstrated previously that gamma-MSH is involved in the regulating the activity of hormone sensitive lipase (HSL) activity in the adrenal and more recently, in the adipocyte. It has been shown also to have effects on the cardiovascular and renal systems. This short review will provide a brief overview of the role of gamma-MSH in the adrenal and the more recent report that it can also regulate HSL function in the adipocyte. We also present some preliminary data purporting a direct role for Lys-gamma(3)-MSH in the regulation of HSL phosphorylation in the heart. Taken together these data suggest that gamma-MSH peptides might play a more widespread role in lipid and cholesterol utilization.

Polymer-drug conjugates for combination anticancer therapy: investigating the mechanism of action.

We developed a family of polymer-drug conjugates carrying the combination of the anticancer agent epirubicin (EPI) and nitric oxide (NO). EPI-PEG-(NO)8, carrying the highest content of NO, displayed greater activity in Caco-2 cells while it decreased toxicity against endothelium cells and cardiomyocytes with respect to free EPI. FACS and confocal microscopy confirmed conjugates internalization. Light scattering showed formation of micelle whose size correlated with internalization rate. EPI-PEG-(NO)8 showed increased bioavailability in mice compared to free EPI.

Dynamic load balancing for the distributed mining of molecular structures

In molecular biology, it is often desirable to find common properties in large numbers of drug candidates. One family of methods stems from the data mining community, where algorithms to find frequent graphs have received increasing attention over the past years. However, the computational complexity of the underlying problem and the large amount of data to be explored essentially render sequential algorithms useless. In this paper, we present a distributed approach to the frequent subgraph mining problem to discover interesting patterns in molecular compounds. This problem is characterized by a highly irregular search tree, whereby no reliable workload prediction is available. We describe the three main aspects of the proposed distributed algorithm, namely, a dynamic partitioning of the search space, a distribution process based on a peer-to-peer communication framework, and a novel receiverinitiated load balancing algorithm. The effectiveness of the distributed method has been evaluated on the well-known National Cancer Institute’s HIV-screening data set, where we were able to show close-to linear speedup in a network of workstations. The proposed approach also allows for dynamic resource aggregation in a non dedicated computational environment. These features make it suitable for large-scale, multi-domain, heterogeneous environments, such as computational grids.

Breeding distribution and population decline of globally threatened Grey-necked Picathartes Picathartes oreas in Mbam Minkom Mountain Forest, southern Cameroon

The Grey-necked Picathartes Picathartes oreas, considered 'Vulnerable', is an enigmatic ground-dwelling bird endemic to the central African equatorial rainforest and belongs to a family of only two species. Its distribution extends to the two Endemic Bird Areas within Cameroon (Guinea Congo forest biome and Cameroon mountain arc) and its population is thought to be in decline throughout its range due to increasing habitat fragmentation and disturbance. During March-April 2003 and June and October 2007 we surveyed Grey-necked Picathartes in the north-western region of the Mbam Minkom Mountain Forest. In January-March 2006 we surveyed the entire mountain range and found go breeding and 24 potential breeding sites, mostly located on the western slopes. From the complete survey, we estimated the population at 44 breeding individuals. Populations were highest in the north-west region but had apparently declined from 40 breeding individuals in 2003 to 20 in 2007. This region accounted for 41% of the entire population on the mountain range during the 2006 survey. The Mbam Minkom/Kala Important Bird Area was designated based on the presence of Grey-necked Picathartes but is under high pressure of imminent destruction from agricultural encroachment and illegal timber exploitation. These results have important implications for decision making in delimiting forest boundaries and core areas for protection in the development of management plans. We suggest possible remedial actions, appropriate repeatable methods for future monitoring and opportunities for community involvement in the management and conservation of the site.

Asymptotic normality in mixtures of power series distributions

The problem of estimating the individual probabilities of a discrete distribution is considered. The true distribution of the independent observations is a mixture of a family of power series distributions. First, we ensure identifiability of the mixing distribution assuming mild conditions. Next, the mixing distribution is estimated by non-parametric maximum likelihood and an estimator for individual probabilities is obtained from the corresponding marginal mixture density. We establish asymptotic normality for the estimator of individual probabilities by showing that, under certain conditions, the difference between this estimator and the empirical proportions is asymptotically negligible. Our framework includes Poisson, negative binomial and logarithmic series as well as binomial mixture models. Simulations highlight the benefit in achieving normality when using the proposed marginal mixture density approach instead of the empirical one, especially for small sample sizes and/or when interest is in the tail areas. A real data example is given to illustrate the use of the methodology.