Search results for "bioinformatics"

2015

AbstractAtomic manipulation in the scanning tunnelling microscopy, conventionally a tool to build nanostructures one atom at a time, is here employed to enable the atomic-scale imaging of a model low-dimensional system. Specifically, we use low-temperature STM to investigate an ultra thin film (4 atomic layers) of potassium created by epitaxial growth on a graphite substrate. The STM images display an unexpected honeycomb feature, which corresponds to a real-space visualization of the Wigner-Seitz cells of the close-packed surface K atoms. Density functional simulations indicate that this behaviour arises from the elastic, tip-induced vertical manipulation of potassium atoms during imaging,…

Estimation of recombinant protein production in Pichia pastoris base don a constraint-based model

2012

[EN] A previously validated constraint based model and possibilistic MFA have been used to design a simple estimator of protein production rate in Pichia pastoris cultures. A structured model of the yeast P. pastoris metabolism is used to predict the balance of key energetic equivalents such as ATP from available measurements, mainly substrate consumption, gases exchange rates and biomass specific growth. It has been shown that ATP flux can be related to biomass growth and protein productivity specific rates by linear regression. Cross-validation has been applied for robust parameter fitting on the basis of chemostat, steady-state experimental conditions. In this way, protein estimation can…

MicroRNA-Based Therapeutic Perspectives in Myotonic Dystrophy

2019

Myotonic dystrophy involves two types of chronically debilitating rare neuromuscular diseases: type 1 (DM1) and type 2 (DM2). Both share similarities in molecular cause, clinical signs, and symptoms with DM2 patients usually displaying milder phenotypes. It is well documented that key clinical symptoms in DM are associated with a strong mis-regulation of RNA metabolism observed in patient’s cells. This mis-regulation is triggered by two leading DM-linked events: the sequestration of Muscleblind-like proteins (MBNL) and the mis-regulation of the CUGBP RNA-Binding Protein Elav-Like Family Member 1 (CELF1) that cause significant alterations to their important functions in RNA processing. It ha…

Multivariate analysis in the identification of biological targets for designed molecular structures: The BIOTA protocol

2013

In this work the new protocol BIOlogical Target Assignation (BIOTA) for the prediction of the biological target from molecular structures is proposed. BIOTA is based on the Principal Components Analysis (PCA) application on a matrix of ligands versus molecular descriptors. The application of BIOTA could allow to hypothesize the mechanism of action of a candidate drug prior to its biological evaluation or to repurpose old drugs. The protocol can be fine-tuned by choosing opportune targets (biological or not) and molecular descriptors, and it can be useful in every fields in with it is possible to collect set of compounds with known properties. The robustness of the protocol depends from diff…

Improving protein secondary structure predictions by prediction fusion

2009

Protein secondary structure prediction is still a challenging problem at today. Even if a number of prediction methods have been presented in the literature, the various prediction tools that are available on-line produce results whose quality is not always fully satisfactory. Therefore, a user has to know which predictor to use for a given protein to be analyzed. In this paper, we propose a server implementing a method to improve the accuracy in protein secondary structure prediction. The method is based on integrating the prediction results computed by some available on-line prediction tools to obtain a combined prediction of higher quality. Given an input protein p whose secondary struct…

Study of the Viral and Microbial Communities Associated With Crohn's Disease: A Metagenomic Approach

2013

OBJECTIVES: This study aimed to analyze and compare the diversity and structure of the viral and microbial communities in fecal samples from a control group of healthy volunteers and from patients affected by Crohn's disease (CD). METHODS: Healthy adult controls (n=8) and patients affected by ileocolic CD (n=11) were examined for the viral and microbial communities in their feces and, in one additional case, in the intestinal tissue. Using two different approaches, we compared the viral and microbial communities in several ways: by group (patients vs. controls), entity (viruses vs. bacteria), read assembly (unassembled vs. assembled reads), and methodology (our approach vs. an existing pipe…

Two genomes of highly polyphagous lepidopteran pests (Spodoptera frugiperda, Noctuidae) with different host-plant ranges

2017

International audience; Emergence of polyphagous herbivorous insects entails significant adaptation to recognize, detoxify and digest a variety of host-plants. Despite of its biological and practical importance - since insects eat 20% of crops - no exhaustive analysis of gene repertoires required for adaptations in generalist insect herbivores has previously been performed. The noctuid moth Spodoptera frugiperda ranks as one of the world’s worst agricultural pests. This insect is polyphagous while the majority of other lepidopteran herbivores are specialist. It consists of two morphologically indistinguishable strains (“C” and “R”) that have different host plant ranges. To describe the evol…

Dimethyl 4,4'-(diazenedi-yl)dibenzoate at 100 K.

2013

In the asymmetric part of the unit cell of the title compound, C16H14N2O4, there are two chemically equivalent but crystallographic independent half molecules. The geometric centre of each complete molecule lies on a crystallographic inversion centre. Both molecules are almost planar [mean deviations of atoms in the two molecules are 0.032 (2) and 0.044 (2) Å] and their geometries are similar. In the crystal, molecules are arranged in columns along theaaxis. There are no intermolecular donor–acceptor distances shorter than 3.4 Å.

1,1′-[2,3,5,6-Tetramethyl-p-phenylenebis(methyleneoxy)]di-1H-benzotriazole

2009

The complete molecule of the title compound, C(24)H(24)N(6)O(2), is generated by a crystallographic inversion centre. The benzotriazole rings form dihedral angles of 2.10 (7)° with the central aromatic ring. The crystal packing is consolidated by π-π inter-actions, with centroid-centroid distances of 3.6234 (10) Å, together with weak C-H⋯π inter-actions.

Bis[3-methyl-5-(pyridin-2-yl)-1H-pyrazol-4-yl] selenide methanol hemisolvate

2014

The asymmetric unit of the title compound, C18H16N6Se·0.5CH3OH, contains two independent molecules of bis[3-methyl-5-(pyridin-2-yl)-1H-pyrazol-4-yl] selenide with similar C—Se—C bond angles [99.30 (14) and 98.26 (13)°], and a methanol molecule of solvation. In one molecule, the dihedral angles between pyrazole and neighbouring pyridine rings are 18.3 (2) and 15.8 (2)°, and the corresponding angles in the other molecule are 13.5 (2) and 8.3 (2)°. In the crystal, the selenide and solvent molecules are linked by classical O—H...N and N—H...N hydrogen bonds, as well as by weak C—H...O and C—H...π interactions, forming a three-dimensional supramolecular architecture.