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1.
J Comput Aided Mol Des ; 32(8): 869-876, 2018 08.
Artigo em Inglês | MEDLINE | ID: mdl-30084079

RESUMO

Research on biology has seen significant advances with the use of molecular dynamics (MD) simulations. The MD methodology enables explanation and discovery of molecular mechanisms in a wide range of natural processes and biological systems. The need to readily share the ever-increasing amount of MD data has been hindered by the lack of specialized bioinformatic tools. The difficulty lies in the efficient management of the data, i.e., in sending and processing 3D information for its visualization. In this work, we present HTMoL, a plug-in-free, secure GPU-accelerated web application specifically designed to stream and visualize MD trajectory data on a web browser. Now, individual research labs can publish MD data on the Internet, or use HTMoL to profoundly improve scientific reports by including supplemental MD data in a journal publication. HTMoL can also be used as a visualization interface to access MD trajectories generated on a high-performance computer center directly. Furthermore, the HTMoL architecture can be leveraged with educational efforts to improve learning in the fields of biology, chemistry, and physics.


Assuntos
Simulação de Dinâmica Molecular , Proteínas/química , Internet , Lignanas , Conformação Proteica , Software , Termodinâmica , Interface Usuário-Computador
2.
Sci Rep ; 8(1): 6303, 2018 Apr 16.
Artigo em Inglês | MEDLINE | ID: mdl-29657314

RESUMO

A correction to this article has been published and is linked from the HTML and PDF versions of this paper. The error has not been fixed in the paper.

3.
Proc Natl Acad Sci U S A ; 115(8): E1876-E1885, 2018 02 20.
Artigo em Inglês | MEDLINE | ID: mdl-29432159

RESUMO

Emerging findings suggest that compromised cellular bioenergetics and DNA repair contribute to the pathogenesis of Alzheimer's disease (AD), but their role in disease-defining pathology is unclear. We developed a DNA repair-deficient 3xTgAD/Polß+/- mouse that exacerbates major features of human AD including phosphorylated Tau (pTau) pathologies, synaptic dysfunction, neuronal death, and cognitive impairment. Here we report that 3xTgAD/Polß+/- mice have a reduced cerebral NAD+/NADH ratio indicating impaired cerebral energy metabolism, which is normalized by nicotinamide riboside (NR) treatment. NR lessened pTau pathology in both 3xTgAD and 3xTgAD/Polß+/- mice but had no impact on amyloid ß peptide (Aß) accumulation. NR-treated 3xTgAD/Polß+/- mice exhibited reduced DNA damage, neuroinflammation, and apoptosis of hippocampal neurons and increased activity of SIRT3 in the brain. NR improved cognitive function in multiple behavioral tests and restored hippocampal synaptic plasticity in 3xTgAD mice and 3xTgAD/Polß+/- mice. In general, the deficits between genotypes and the benefits of NR were greater in 3xTgAD/Polß+/- mice than in 3xTgAD mice. Our findings suggest a pivotal role for cellular NAD+ depletion upstream of neuroinflammation, pTau, DNA damage, synaptic dysfunction, and neuronal degeneration in AD. Interventions that bolster neuronal NAD+ levels therefore have therapeutic potential for AD.


Assuntos
Doença de Alzheimer , Modelos Animais de Doenças , NAD/farmacologia , Niacinamida/análogos & derivados , Animais , Disfunção Cognitiva , Dano ao DNA , Regulação da Expressão Gênica/efeitos dos fármacos , Masculino , Camundongos , Camundongos Transgênicos , Neurogênese/efeitos dos fármacos , Niacinamida/farmacologia , Compostos de Piridínio , Sirtuína 3/genética , Sirtuína 3/metabolismo , Sirtuínas/genética , Sirtuínas/metabolismo , Proteínas tau/metabolismo
4.
Sci Rep ; 7(1): 1756, 2017 05 11.
Artigo em Inglês | MEDLINE | ID: mdl-28496155

RESUMO

MicroRNAs are key non-coding RNA molecules that play a relevant role in the regulation of gene expression through translational repression and/or transcript cleavage during normal development and physiological adaptation processes like stress. Quantitative reverse transcription polymerase chain reaction (RT-qPCR) has become the approach normally used to determine the levels of microRNAs. However, this approach needs the use of endogenous reference. An improper selection of endogenous references can result in confusing interpretation of data. The aim of this study was to identify and validate appropriate endogenous reference miRNA genes for normalizing RT-qPCR survey of miRNAs expression in four different tissues of Atlantic salmon, under handling and confinement stress conditions associated to early or primary stress response. Nine candidate reference normalizers, including microRNAs and nuclear genes, normally used in vertebrate microRNA expression studies were selected from literature, validated by RT-qPCR and analyzed by the algorithms geNorm and NormFinder. The results revealed that the ssa-miR-99-5p gene was the most stable overall and that ssa-miR-99-5p and ssa-miR-23a-5p genes were the best combination. Moreover, the suitability of ssa-miR-99-5p and ssa-miR-23a-5p as endogeneuos reference genes was demostrated by the expression analysis of ssa-miR-193-5p gene.


Assuntos
MicroRNAs/genética , Salmo salar/genética , Estresse Fisiológico/genética , Animais , Regulação da Expressão Gênica , Estudos de Associação Genética , Hidrocortisona/sangue , MicroRNAs/metabolismo , Padrões de Referência , Salmo salar/sangue
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