Parallelization of ARACNe, an Algorithm for the Reconstruction of Gene Regulatory Networks

[Abstract] Gene regulatory networks are graphical representations of molecular regulators that interact with each other and with other substances in the cell to govern the gene expression. There are different computational approaches for the reverse engineering of these networks. Most of them require all gene-gene evaluations using different mathematical methods such as Pearson/Spearman correlation, Mutual Information or topology patterns, among others. The Algorithm for the Reconstruction of Accurate Cellular Networks (ARACNe) is one of the most effective and widely used tools to reconstruct gene regulatory networks. However, the high computational cost of ARACNe prevents its use over large biologic datasets. In this work, we present a hybrid MPI/OpenMP parallel implementation of ARACNe to accelerate its execution on multi-core clusters, obtaining a speedup of 430.46 using as input a dataset with 41,100 genes and 108 samples and 32 nodes (each of them with 24 cores).Ministerio de Economía y Competitividad; TIN2016-75845-PXunta de Galicia; ED431G/01Xunta de Galicia; ED431C 2017/0

Response surface optimization of the culture medium for production of elastin-like polymers by E. coli

ASTM program POCI 2010 (project POCI/CTM/57177/2004) suported by FEDER and FCTElastin-Like Polymers (ELP`s), a family of proteins based on repetitive pentapeptide sequences known by their smart and extremely biocompatible behavior (1, 2), are of great interest to our research group. Ongoing work using E. coli as the expression system, strongly suggests that the biomass and polymer production are closely related. The Response Surface Methodology (RSM) is a collection of mathematical and statistical techniques useful for the modeling and analysis of problems, in which a response of interest is influenced by several variables and the objective is to optimize this response, in a suitable set of experiments (3). This strategy was employed in order to improve the production of both, biomass and ELP`s, in an auto induction medium previously designed by us (adapted from Terrific Broth and Phosphate Buffer Glycerol). The nutrients yeast extract, lactose and glycerol were the factors subjected to this statistical treatment. Knowing that glycerol and lactose are, respectively, sub-products of biodiesel production and dairy industry, the use of these compounds is highly favorable for the design of a sustainable scale-up procedure. On the other hand, yeast extract was selected in order to maximize the final yield due to it`s described importance in the boost of production. The validation of the model obtained was achieved and allowed the optimization of biomass levels.info:eu-repo/semantics/publishedVersio

Contributions of cryptochromes and phototropins to stomatal opening through the day

The UV-A/blue photoreceptors phototropins and cryptochromes are both known to contribute to stomatal opening (∆gs) in blue light. However, their relative contributions to maintenance of gs in blue light through the whole photoperiod remains unknown. To elucidate this question, Arabidopsis phot1 phot2 and cry1 cry2 mutants (MTs) and their respective wild types (WTs) were irradiated with 200 μmol m-2 s-1 of blue-, green- or red-light (BL, GL or RL) throughout a 11-hour photoperiod. Stomatal conductance (gs) was higher under BL, than under RL or GL. Under RL, gs was not affected by either of the photoreceptor mutations, but under GL gs was slightly lower in cry1 cry2 than its WT. Under BL, the presence of phototropins was essential for rapid stomatal opening at the beginning of the photoperiod, while maximal stomatal opening beyond 3 h of irradiation required both phototropins and cryptochromes. Time courses of whole-plant net carbon assimilation rate (Anet) and the effective quantum yield of photosystem II photochemistry (ΦPSII) were consistent with an Anet-independent contribution of BL on gs both in phot1 phot2 and cry1 cry2 mutants. The changing roles of phototropins and cryptochromes through the day may allow more flexible coordination between gs and Anet.Peer reviewe

Comparative genomic analysis of light-regulated transcripts in the Solanaceae

<p>Abstract</p> <p>Background</p> <p>Plants use different light signals to adjust their growth and development to the prevailing environmental conditions. Studies in the model species <it>Arabidopsis thaliana </it>and rice indicate that these adjustments are mediated by large changes in the transcriptome. Here we compared transcriptional responses to light in different species of the Solanaceae to investigate common as well as species-specific changes in gene expression.</p> <p>Results</p> <p>cDNA microarrays were used to identify genes regulated by a transition from long days (LD) to short days (SD) in the leaves of potato and tobacco plants, and by phytochrome B (phyB), the photoreceptor that represses tuberization under LD in potato. We also compared transcriptional responses to photoperiod in <it>Nicotiana tabacum </it>Maryland Mammoth (MM), which flowers only under SD, with those of <it>Nicotiana sylvestris</it>, which flowers only under LD conditions. Finally, we identified genes regulated by red compared to far-red light treatments that promote germination in tomato.</p> <p>Conclusion</p> <p>Most of the genes up-regulated in LD were associated with photosynthesis, the synthesis of protective pigments and the maintenance of redox homeostasis, probably contributing to the acclimatization to seasonal changes in irradiance. Some of the photoperiodically regulated genes were the same in potato and tobacco. Others were different but belonged to similar functional categories, suggesting that conserved as well as convergent evolutionary processes are responsible for physiological adjustments to seasonal changes in the Solanaceae. A β-ZIP transcription factor whose expression correlated with the floral transition in <it>Nicotiana </it>species with contrasting photoperiodic responses was also regulated by photoperiod and phyB in potato, and is a candidate gene to act as a general regulator of photoperiodic responses. Finally, <it>GIGANTEA</it>, a gene that controls flowering time in <it>Arabidopsis thaliana </it>and rice, was regulated by photoperiod in the leaves of potato and tobacco and by red compared to far-light treatments that promote germination in tomato seeds, suggesting that a conserved light signaling cascade acts across developmental contexts and species.</p

Portuguese ornamental stones

Portugal produces a great diversity of ornamental stones. Besides the internationally known white and pink marbles, also light cream limestones are produced, as well as grey, yellow and pink granites, and dark grey slates. From these, limestones are the most request variety today, especially by the Chinese market

Relationship of stearic acid content to total fatin beef carcass

Se determinó la composición en ácidos grasos de grasa subcutáneas, intermusculares y de cavidad y de los lípidos de los músculos psoas mayor y semitendinoso de 37 novillos cruzas entre 383 y 544 kg. de peso vivo y con grados variables de gordura.. Se relacionó la concentración en ácidos esteárico en los diversos tejidos estudiados, con las cantidades de grasa depositada en los diversos lugares anatómicos, así como con sus respectivas contribuciones relativas a la grasa total. Diferencias importantes aparecieron en la composición en ácidos grasos de los lípidos, de depósitos e intramusculares de novillos entre 24-30 meses de edad. Los valores en ácido esteárico (Cl 8:0) oscilaron entre 5,3 a 40 % indicando gran variabilidad en composición. Los niveles de ácido palmitoléico y oléico también fueron muy distintos. Los ácidos mirístico y linoléico presentaron valores más parejos. Las concentraciones de Cl 8 0. estuvieron muy relacionados en los diversos lugares analizados pero con diversos grados de significación estadística. La relación Cl 8 :1 /Cl 8 0 considerada como índice de capacidad de desaturacién fue máxima en grasas subcutáneas y mínima en grasas de cavidad (comparando las grasas intermusculares valores intermedios).The fatty acid composition of the subcutaneous, intermuscular and cavity fats of crossbred steers have been determinated. The fatty acid composition of intramuscular fats of psoas major and semitendinosus muscles also were determinated The stearic acid (C18 0.) content in the different fats varied from 5,3 to 40 O/O and was significantly correlated in the different places studied. The ratio C18 i/C18 0, a reflection of desaturase activity, was higher in subcutaoeous fata as compared with cavity fata lo the intramuscular fat of the semitendinosus muscle was higher than in the psoas mayor. The total dissectable fat was significantly correlated with the C18:0 acid content lo the different place except in subscapular and psoas mayor fats. Subcutaoeous (ar ll-l2th rib), ladney and omental fats stearic acid cootent were highly correlated (r,70 p 0,001) The total lat was related negatively or positively with the relative contribution of the different depots. Intermuscular, cod and brisket fats decrease relatively to total fat but subcutaneous and ltidney fats increase.Facultad de Ciencias Veterinaria

Relationship of stearic acid content to total fatin beef carcass

Se determinó la composición en ácidos grasos de grasa subcutáneas, intermusculares y de cavidad y de los lípidos de los músculos psoas mayor y semitendinoso de 37 novillos cruzas entre 383 y 544 kg. de peso vivo y con grados variables de gordura.. Se relacionó la concentración en ácidos esteárico en los diversos tejidos estudiados, con las cantidades de grasa depositada en los diversos lugares anatómicos, así como con sus respectivas contribuciones relativas a la grasa total. Diferencias importantes aparecieron en la composición en ácidos grasos de los lípidos, de depósitos e intramusculares de novillos entre 24-30 meses de edad. Los valores en ácido esteárico (Cl 8:0) oscilaron entre 5,3 a 40 % indicando gran variabilidad en composición. Los niveles de ácido palmitoléico y oléico también fueron muy distintos. Los ácidos mirístico y linoléico presentaron valores más parejos. Las concentraciones de Cl 8 0. estuvieron muy relacionados en los diversos lugares analizados pero con diversos grados de significación estadística. La relación Cl 8 :1 /Cl 8 0 considerada como índice de capacidad de desaturacién fue máxima en grasas subcutáneas y mínima en grasas de cavidad (comparando las grasas intermusculares valores intermedios).The fatty acid composition of the subcutaneous, intermuscular and cavity fats of crossbred steers have been determinated. The fatty acid composition of intramuscular fats of psoas major and semitendinosus muscles also were determinated The stearic acid (C18 0.) content in the different fats varied from 5,3 to 40 O/O and was significantly correlated in the different places studied. The ratio C18 i/C18 0, a reflection of desaturase activity, was higher in subcutaoeous fata as compared with cavity fata lo the intramuscular fat of the semitendinosus muscle was higher than in the psoas mayor. The total dissectable fat was significantly correlated with the C18:0 acid content lo the different place except in subscapular and psoas mayor fats. Subcutaoeous (ar ll-l2th rib), ladney and omental fats stearic acid cootent were highly correlated (r,70 p 0,001) The total lat was related negatively or positively with the relative contribution of the different depots. Intermuscular, cod and brisket fats decrease relatively to total fat but subcutaneous and ltidney fats increase.Facultad de Ciencias Veterinaria

Sistema de presentación de antígenos basado en el virus de la sharka

Referencia OEPM: P9800623.-- Fecha de solicitud: 24/03/1998.-- Titulares: Inmunología y Genética Aplicada, S.A., Consejo Superior de Investigaciones Científicas (CSIC).El sistema de presentación de antígenos heterólogos basado en el virus de la sharka (PPV) comprende una partícula de PPV quimérica formada por ensamblaje de la proteína de la cápsida (CP) de PPV modificada que contiene, al menos, un antígeno heterólogo en dicha CP modificada, estando dicho antígeno dispuesto en la superficie exterior de dicha partícula viral de PPV. Preferentemente, dicho antígeno heterólogo se encuentra en el extremo amino terminal de la CP modificada de PPV. En una realización concreta se describe la construcción de un sistema de presentación de un epítopo inmunológicamente activo derivado de la proteína VP2 del parvovirus canino (CPV). Estos sistemas de presentación de antígenos tienen utilidad en diagnóstico y vacunas.Peer reviewe

Construction and bioproduction of a "green" synthetic protein-based polymer exhibiting a smart behaviour

Natural occurring elastomeric proteins occur in a wide range of biological systems, fulfilling precise functional roles [Tatham and Shewry, 2000]. Their properties are due to the presence of short repeating oligopeptide sequences contained in fibrous proteins, such as silk fibroin (GAGAGS) and mammalian elastin (VPGVG). Elastin is widely distributed in vertebrate tissues, acting statically in dermis to resist long-term forces and dynamically in arteries to store and release energy rapidly. Natural silk from Bombyx mori (silkworm) has been used for centuries either in textile industry or as biomedical suture material, exhibiting impressive mechanical properties as well as high biocompatibility [Kim et al, 2004]. With the development of protein engineering and nano(bio)technologies in general, it is now possible to use amino acids to design and produce genetically engineered Protein-Based Polymers (PBPs) fully biodegradable that simulate the properties of natural occurring proteins . With the advance in recombinant DNA technology it is possible to precisely control the composition, sequence and length of large molecular weight PBPs [Haider et al, 2000]. Recombinant Elastin-Like Polymers (ELPs) are biopolymers based on the aminoacid sequence VPGXG (V-valine, P-proline, G-glycine), where X, termed the guest residue, is any naturally occurring aminoacid except proline. The most striking feature of the ELPs is their Inverse Temperature Transition (ITT) behaviour. Below a specific critical temperature (Tt) and in the presence of water they are soluble, with the polymer chains relatively extended in a disordered state and fully hydrated mainly by hydrophobic hydration. Above the Tt, the polymer chains hydrophobically fold and adopt a dynamic structure, called β-spiral, stabilized by hydrophobic contacts . The ability of ELPs to self-assemble into nanostructures in response to environmental changes allows their utilization in many devices such as microparticles for controlled drug delivery systems or nanosensors. The polymer poly(VPAVG), a ELP where the central glycine (G) is substituted by a L-alanine (A), was chemically synthesized by Rodríguez-Cabello and co-workers and described by Urry as having thermoplastic properties. These groups reported its characterization, demonstrating its extreme biocompatibility both in vitro and in vivo, as well as the ability to self-assemble, forming microparticles that can entrap active substances during the self-assembling process [Herrero-Vanrell et al, 2005; Rincón et al, 2006]. In the present work a new thermal responsive, biologically synthesized ELP based on the (VPAVG)220 sequence was produced, by recurring to standard molecular genetic tools and, as expected, the polymer displayed an inverse temperature transition (Tt) which could be explored as a purification step. Additionally, the purified polymer (VPAVG)220 showed the ability to self-associate at physiological temperature forming aggregates. The culture media and fermentation conditions were optimized using a Central Composite Design (CCD) approach while exploring the use of low cost carbon sources like lactose and glycerol. Sequence and purity of (VPAVG)220 was confirmed by MALDI TOF analysis and purified polymer was subjected to thermal and physical characterization. Due to its self-assembling behaviour near 34 ºC stable spherical microparticles of a ~1μm diameter were obtained, ready solubilized when a strong undercooling was achieved. Moreover, we have constructed and produced a new set of copolymers (Silk-ElastinLike Polymers – SELPs) consisting of flexible ELP and crystalline silk-like blocks (GAGAGS) at different proportions. By this strategy it was possible to produce a variety of biomaterials with diverse physical properties, such as viscosity and gelation time depending on the number of elastin-blocks and silk-like blocks, respectively [Megeed et al, 2000]. The stability of these SELPs in combination with their biocompatibility and unique mechanical properties, provide the basis of their exploitation for biomedical applications