Genome visualization in space

Phylogeny is an important field to understand evolution and the organization of life. However, most methods depend highly on manual study and analysis, making the construction of phylogeny error prone. Linear Algebra methods are known to be efficient to deal with the semantic relationships between a large number of elements in spaces of high dimensionality. Therefore, they can be useful to help the construction of phylogenetic trees. The ability to visualize the relationships between genomes is crucial in this process. In this paper, a linear algebra method, followed by optimization, is used to generate a visualization of a set of complete genomes. Using the proposed method we were able to visualize the relationships of 64 complete mitochondrial genomes, organized as six different groups, and of 31 complete mitochondrial genomes of mammals, organized as nine different groups. The prespecified groups could be seen clustered together in the visualization, and similar species were represented close together. Besides, there seems to be an evolutionary influence in the organization of the graph

Molecular dynamics simulation of silver nanoparticles in a europium doped sodosilicate glass

Molecular dynamics simulation is applied to an europium doped sodosilicate glass containing silver [(Na–Ag)2O–SiO2–Eu2O3]. The silver is implanted in substitution of Na, simulating an ionic exchange. For ionic interactions a modified Born–Mayer–Huggins potential was employed. For the Ag–Ag interaction, a Lennard-Jones (LJ) potential is applied, while for the Eu–Ag interaction, a modified LJ potential is introduced. The particle size increases with the annealing treatment and follows a lognormal law. After 75 ps the average particle size reaches 5.8 atoms (4.8 for Ag and 1.0 for Eu), and it is found that the europium is preferentially situated on these nanoclusters

Selection of carioca type common bean lines with anthracnose and angular leaf spot-resistance.

Objective of the present study was to select common bean lines with the traits anthracnose and angular leaf spot-resistance, high yield, Carioca type grains and an upright plant type. One hundred and fifty-three lines were selected from five segregating families derived from backcrosses using G2333 (donor parent) and the lines ESAL 696 and CI 140 (recurrent parents). The lines were evaluated and selected in three seasons under inoculation with the races 2047, 1545 and 81 of C. lindemuthianum and also tested with the SCAR marker of allele Co-5. Lines with high grain yield, Carioca type grains, upright plant type, and anthracnose-resistance were selected. The SCAR marker was not effective for the selection of resistant lines with Co-5 allele. No angular leaf spot-resistant lines were identified

Prediction of drug targets in human pathogens

The identification of new and druggable targets in bacteria is a critical endeavour in pharmaceutical research of novel antibiotics to fight infectious agents. The rapid emergence of resistant bacteria makes today's antibiotics more and more ineffective, consequently increasing the need for new pharmacological targets and novel classes of antibacterial drugs. A new model that combines the singular value decomposition technique with biological filters comprised of a set of protein properties associated with bacterial drug targets and similarity to protein-coding essential genes of E. coli has been developed to predict potential drug targets in the Enterobacteriaceae family [1]. This model identified 99 potential target proteins amongst the studied bacterial family, exhibiting eight different functions that suggest that the disruption of the activities of these proteins is critical for cells. Out of these candidates, one was selected for target confirmation. To find target modulators, receptor-based pharmacophore hypotheses were built and used in the screening of a virtual library of compounds. Postscreening filters were based on physicochemical and topological similarity to known Gram-negative antibiotics and applied to the retrieved compounds. Screening hits passing all filters were docked into the proteins catalytic groove and 15 of the most promising compounds were purchased from their chemical vendors to be experimentally tested in vitro. To the best of our knowledge, this is the first attempt to rationalize the search of compounds to probe the relevance of this candidate as a new pharmacological target

Identificação de QTLs ligados a resistência ao crestamento bacteriano em Phaseolus vulgaris.

O objetivo deste trabalho foi identificar QTLs associados à resistência do feijoeiro ao crestamento bacteriano comum, a fim de auxiliar a seleção com marcadores

Criação em larga escala de Biomphalaria tenagophila

An efficient method for breeding Biomphalaria tenagophila (Taim lineage/RS) was developed over a 5-year-period (2005-2010). Special facilities were provided which consisted of four cement tanks (9.4 x 0.6 x 0.22 m), with their bottom covered with a layer of sterilized red earth and calcium carbonate. Standard measures were adopted, as follows: each tank should contain an average of 3000 specimens, and would be provided with a daily ration of 35,000 mg complemented with lettuce. A green-house effect heating system was developed which constituted of movable dark canvas covers, which allowed the temperature to be controlled between 20 - 24 ºC. This system was essential, especially during the coldest months of the year. Approximately 27,000 specimens with a diameter of 12 mm or more were produced during a 14-month-period. The mortality rates of the newly-hatched and adult snails were 77% and 37%, respectively. The follow-up of the development system related to 310 specimens of B. tenagophila demonstrated that 70-day-old snails reached an average of 17.0 ± 0.9 mm diameter. The mortality rates and the development performance of B. tenagophila snails can be considered as highly satisfactory, when compared with other results in literature related to works carried out with different species of the genus Biomphalaria, under controlled laboratory conditions.Foi desenvolvido um método eficiente de criação em larga escala de Biomphalaria tenagophila (linhagem Taim/RS) durante o período de 2005-2010. Foi concebida uma instalação que consiste de quatro tanques de alvenaria (9,4 x 0,6 x 0,22) com fundos recobertos por uma mistura constituída de terra vermelha esterilizada e carbonato de cálcio. Foi padronizado que cada tanque de criação conteria em média 3.000 exemplares e receberia diariamente 35.000 mg de ração e alface como complemento. O desenvolvimento de um sistema de aquecimento por efeito estufa constituído de lonas escuras móveis permitiu controlar a temperatura entre 20 a 24 ºC, sistema essencial principalmente nos meses mais frios. Durante o período de 14 meses foram produzidos aproximadamente 27.000 exemplares com diâmetros superiores a 12 mm. As taxas de mortalidade dos caramujos recém-eclodidos e adultos foram de 77% e 37%, respectivamente. O acompanhamento do ritmo de crescimento de 310 B. tenagophila demonstrou que caramujos com 70 dias de idade alcançaram em média 17,0 ± 0,9 mm de diâmetro. As taxas de mortalidade e o desempenho de crescimento de caramujos do gênero B. tenagophila podem ser considerados altamente satisfatórios, comparando-se com os resultados da literatura realizados com espécies do gênero Biomphalaria em condições controladas de laboratório

Enhancement of carrier lifetimes in type-II quantum dot/quantum well hybrid structures

FAPESP - FUNDAÇÃO DE AMPARO À PESQUISA DO ESTADO DE SÃO PAULOCNPQ - CONSELHO NACIONAL DE DESENVOLVIMENTO CIENTÍFICO E TECNOLÓGICOCAPES - COORDENAÇÃO DE APERFEIÇOAMENTO DE PESSOAL DE NÍVEL SUPERIORWe investigate optical transitions and carrier dynamics in hybrid structures containing type-I GaAs/AlGaAs quantum wells (QWs) and type-II GaSb/AlGaAs quantum dots (QDs). We show that the optical recombination of photocreated electrons confined in the QWs with holes in the QDs and wetting layer can be modified according to the QW/QD spatial separation. In particular, for low spacer thicknesses, the QW optical emission can be suppressed due to the transference of holes from the QW to the GaSb layer, favoring the optical recombination of spatially separated carriers, which can be useful for optical memory and solar cell applications. Time-resolved photoluminescence (PL) measurements reveal non-exponential recombination dynamics. We demonstrate that the PL transients can only be quantitatively described by considering both linear and quadratic terms of the carrier density in the bimolecular recombination approximation for type-II semiconductor nanostructures. We extract long exciton lifetimes from 700 ns to 5 mu s for QDs depending on the spacer layer thickness. Published by AIP Publishing.We investigate optical transitions and carrier dynamics in hybrid structures containing type-I GaAs/AlGaAs quantum wells (QWs) and type-II GaSb/AlGaAs quantum dots (QDs). We show that the optical recombination of photocreated electrons confined in the QWs with holes in the QDs and wetting layer can be modified according to the QW/QD spatial separation. In particular, for low spacer thicknesses, the QW optical emission can be suppressed due to the transference of holes from the QW to the GaSb layer, favoring the optical recombination of spatially separated carriers, which can be useful for optical memory and solar cell applications. Time-resolved photoluminescence (PL) measurements reveal non-exponential recombination dynamics. We demonstrate that the PL transients can only be quantitatively described by considering both linear and quadratic terms of the carrier density in the bimolecular recombination approximation for type-II semiconductor nanostructures. We extract long exciton lifetimes from 700 ns to 5 mu s for QDs depending on the spacer layer thickness.120817FAPESP - FUNDAÇÃO DE AMPARO À PESQUISA DO ESTADO DE SÃO PAULOCNPQ - CONSELHO NACIONAL DE DESENVOLVIMENTO CIENTÍFICO E TECNOLÓGICOCAPES - COORDENAÇÃO DE APERFEIÇOAMENTO DE PESSOAL DE NÍVEL SUPERIORFAPESP - FUNDAÇÃO DE AMPARO À PESQUISA DO ESTADO DE SÃO PAULOCNPQ - CONSELHO NACIONAL DE DESENVOLVIMENTO CIENTÍFICO E TECNOLÓGICOCAPES - COORDENAÇÃO DE APERFEIÇOAMENTO DE PESSOAL DE NÍVEL SUPERIOR2012/11382-9 , 2014/17141-9Sem informaçãoSem informaçã