60 research outputs found
Systematic interaction network filtering identifies CRMP1 as a novel suppressor of huntingtin misfolding and neurotoxicity
Assemblies of huntingtin (HTT) fragments with expanded polyglutamine (polyQ) tracts are a pathological hallmark of Huntington's disease (HD). The molecular mechanisms by which these structures are formed and cause neuronal dysfunction and toxicity are poorly understood. Here, we utilized available gene expression data sets of selected brain regions of HD patients and controls for systematic interaction network filtering in order to predict disease-relevant, brain region-specific HTT interaction partners. Starting from a large protein-protein interaction (PPI) data set, a step-by-step computational filtering strategy facilitated the generation of a focused PPI network that directly or indirectly connects 13 proteins potentially dysregulated in HD with the disease protein HTT. This network enabled the discovery of the neuron-specific protein CRMP1 that targets aggregation-prone, N-terminal HTT fragments and suppresses their spontaneous self-assembly into proteotoxic structures in various models of HD. Experimental validation indicates that our network filtering procedure provides a simple but powerful strategy to identify disease-relevant proteins that influence misfolding and aggregation of polyQ disease proteins.DFG [SFB740, 740/2-11, SFB618, 618/3-09, SFB/TRR43 A7]; BMBF(NGFN-Plus) [01GS08169-73, 01GS08150, 01GS08108]; HDSA Coalition for the Cure; EU (EuroSpin) [Health-F2-2009-241498, HEALTH-F2-2009-242167]; Helmholtz Association (MSBN, HelMA) [HA-215]; FCT [IF/00881/2013]info:eu-repo/semantics/publishedVersio
Ferramentas de processamento digital de imagem para imagens neuronais
Mestrado em Biomedicina MolecularOs neurónios são celulas especializadas do Sistema Nervoso, cujas funções
se baseiam na correta formação de três compartimentos subcelulares
primários – corpo celular, axónio e dendrites – e na rede neuronal que formam
para passar a informação entre si.
A análise quantitativa das caracterÃsticas destas estruturas pode ser usada
para estudar a relação entre a morfologia e função neuronal, e monitorizar
alterações que ocorram em células individuais ou ao nÃvel da rede, que se
possam correlacionar com doenças neurológicas.
Nesta tese foi efetuada uma pesquisa de ferramentas digitais disponÃveis
dedicadas ao processamento e análise de imagens neuronais, com enfoque na
sua aplicabilidade para analisar as nossas bioimagens neuronais de
fluorescência adquiridas no dia-a-dia. Nos programas selecionados (NeuronJ,
NeurphologyJ e NeuriteQuant) foi primeiro avaliada a necessidade de preprocessamento,
e os programas foram subsequentemente utilizados em
conjuntos de imagens de culturas primárias de córtex de rato para comparar a
sua eficácia no processamento destas bioimagens. Os dados obtidos com os
vários programas foram comparados com a análise manual usando o ImageJ
como ferramenta de análise.
Os resultados demonstraram que o programa que aparenta funcionar melhor
com as nossas imagens de fluorescência é o NeuriteQuant, porque é
automático e dá resultados globalmente semelhantes aos da análise manual,
especialmente na avaliação do Comprimento das Neurites por célula. Uma das
desvantagens é que a quantificação da ramificação das neurites não dá
resultados satisfatórios e deve continuar a ser realizada manualmente.
Também realizamos uma pesquisa de ferramentas de processamento de
imagem dedicada a imagens de contraste de fase, mas poucos programas
foram encontrados. Estas imagens são mais fáceis de obter e mais acessÃveis
economicamente, contudo são mais difÃceis de analisar devido à s suas
caracterÃsticas intrÃnsecas.
Para contornar esta lacuna, estabeleceu-se e otimizou-se uma sequência de
processamento e análise para melhor extrair informação neuronal relevante de
imagens de contraste de fase utilizando o programa ImageJ.
A sequência desenvolvida, na forma de uma macro do ImageJ designada
NeuroNet, foi aplicada a imagens de contraste de fase de culturas neuronais
em diferentes dias de diferenciação, na presença ou ausência de um inibidor
farmacológico, com o objetivo de responder a uma questão cientÃfica.
A macro NeuroNet desenvolvida provou ser útil para analisar estas
bioimagens, existindo contudo espaço para ser aperfeiçoada.Neurons are specialized cells of the Nervous System, with their function being
based on the formation of the three primary sub cellular compartments – soma,
axons, and dendrites – and on the neuritic network they form to contact and
pass information to each other.
The quantitative analysis of the characteristics of these structures can be used
to study the relation between neuronal morphology and function, and to monitor
distortions occurring in individual cells or at the network level that may correlate
with neurological diseases.
In this thesis a survey of freely available digital tools dedicated to neuronal
images processing and analysis was made with an interest in their applicability
to analyse our routinely acquired neuronal fluorescent bioimages. The selected
program´ (NeuronJ, NeurphologyJ and NeuriteQuant) preprocessing
requirements were first evaluated, and the programs were subsequently
applied to a set of images of rat cortical neuronal primary cultures in order to
compare their effectiveness in bioimage processing. Data obtained with the
various programs was compared to the manual analysis of the images using
the ImageJ analysis tool.
The result show that the program that seems to work better with our
fluorescence images is NeuriteQuant, since it is automatic and gives overall
results more similar to the manual analysis. This is particularly true for the
evaluation of the Neurite Length per Cell. One of the drawbacks is that the
quantification of neuritic ramification does not give satisfactory results and is
better to be performed manually.
We also performed a survey of digital image processing tools dedicated to
phase contrast microphotographs, but very few programs were found. These
images are easier to obtain and more affordable in economic terms, however
they are harder to analyse due to their intrinsic characteristics.
To surpass this gap we have established and optimized a sequence of steps to
better extract relevant information of neuronal phase contrast images using
ImageJ.
The work-flow developed, in the form of an ImageJ macro named NeuroNet,
was then used to answer a scientific question by applying it to phase contrast
images of neuronal cultures at different differentiating days, in the presence or
absence of a pharmacological inhibitor.
The developed macro NeuroNet proved to be useful to analyse the images
however there is still space to improvement
NASA Center for Intelligent Robotic Systems for Space Exploration
NASA's program for the civilian exploration of space is a challenge to scientists and engineers to help maintain and further develop the United States' position of leadership in a focused sphere of space activity. Such an ambitious plan requires the contribution and further development of many scientific and technological fields. One research area essential for the success of these space exploration programs is Intelligent Robotic Systems. These systems represent a class of autonomous and semi-autonomous machines that can perform human-like functions with or without human interaction. They are fundamental for activities too hazardous for humans or too distant or complex for remote telemanipulation. To meet this challenge, Rensselaer Polytechnic Institute (RPI) has established an Engineering Research Center for Intelligent Robotic Systems for Space Exploration (CIRSSE). The Center was created with a five year $5.5 million grant from NASA submitted by a team of the Robotics and Automation Laboratories. The Robotics and Automation Laboratories of RPI are the result of the merger of the Robotics and Automation Laboratory of the Department of Electrical, Computer, and Systems Engineering (ECSE) and the Research Laboratory for Kinematics and Robotic Mechanisms of the Department of Mechanical Engineering, Aeronautical Engineering, and Mechanics (ME,AE,&M), in 1987. This report is an examination of the activities that are centered at CIRSSE
A Y2H-seq approach defines the human protein methyltransferase interactome
To accelerate high-density interactome mapping, we developed a yeast two-hybrid interaction screening approach involving short-read second-generation sequencing (Y2H-seq) with improved sensitivity and a quantitative scoring readout allowing rapid interaction validation. We applied Y2H-seq to investigate enzymes involved in protein methylation, a largely unexplored post-translational modification. The reported network of 523 interactions involving 22 methyltransferases or demethylases is comprehensively annotated and validated through coimmunoprecipitation experiments and defines previously undiscovered cellular roles of nonhistone protein methylation
FPGA design methodology for industrial control systems—a review
This paper reviews the state of the art of fieldprogrammable gate array (FPGA) design methodologies with a focus on industrial control system applications. This paper starts with an overview of FPGA technology development, followed by a presentation of design methodologies, development tools and relevant CAD environments, including the use of portable hardware description languages and system level programming/design tools. They enable a holistic functional approach with the major advantage of setting up a unique modeling and evaluation environment for complete industrial electronics systems. Three main design rules are then presented. These are algorithm refinement, modularity, and systematic search for the best compromise between the control performance and the architectural constraints. An overview of contributions and limits of FPGAs is also given, followed by a short survey of FPGA-based intelligent controllers for modern industrial systems. Finally, two complete and timely case studies are presented to illustrate the benefits of an FPGA implementation when using the proposed system modeling and design methodology. These consist of the direct torque control for induction motor drives and the control of a diesel-driven synchronous stand-alone generator with the help of fuzzy logic
Direct neural-network hardware-implementation algorithm
An algorithm for compact neural network hardware implementation is presented, which exploits special properties of the Boolean functions describing the operation of artificial neurones with step activation function. The algorithm contains three steps: ANN mathematical model digitisation, conversion of the digitised model into a logic gate structure, and hardware optimisation by elimination of redundant logic gates. A set of C++ programs automates algorithm implementation, generating optimised VHDL code. This strategy bridges the gap between ANN design software and hardware design packages (Xilinx). Although the method is directly applicable only to neurones with step activation functions, it can be extended to sigmoidal functions
Identification of human proteins that modify misfolding and proteotoxicity of pathogenic ataxin-1
Proteins with long, pathogenic polyglutamine (polyQ) sequences have an enhanced propensity to spontaneously misfold and self-assemble into insoluble protein aggregates. Here, we have identified 21 human proteins that influence polyQ-induced ataxin-1 misfolding and proteotoxicity in cell model systems. By analyzing the protein sequences of these modifiers, we discovered a recurrent presence of coiled-coil (CC) domains in ataxin-1 toxicity enhancers, while such domains were not present in suppressors. This suggests that CC domains contribute to the aggregation- and toxicity-promoting effects of modifiers in mammalian cells. We found that the ataxin-1–interacting protein MED15, computationally predicted to possess an N-terminal CC domain, enhances spontaneous ataxin-1 aggregation in cell-based assays, while no such effect was observed with the truncated protein MED15ΔCC, lacking such a domain. Studies with recombinant proteins confirmed these results and demonstrated that the N-terminal CC domain of MED15 (MED15CC) per se is sufficient to promote spontaneous ataxin-1 aggregation in vitro. Moreover, we observed that a hybrid Pum1 protein harboring the MED15CC domain promotes ataxin-1 aggregation in cell model systems. In strong contrast, wild-type Pum1 lacking a CC domain did not stimulate ataxin-1 polymerization. These results suggest that proteins with CC domains are potent enhancers of polyQ-mediated protein misfolding and aggregation in vitro and in vivo
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