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1.
J Am Heart Assoc ; 7(20): e010378, 2018 10 16.
Artigo em Inglês | MEDLINE | ID: mdl-30371266

RESUMO

Background The molecular mechanisms mediating postnatal loss of cardiac regeneration in mammals are not fully understood. We aimed to provide an integrated resource of mRNA , protein, and metabolite changes in the neonatal heart for identification of metabolism-related mechanisms associated with cardiac regeneration. Methods and Results Mouse ventricular tissue samples taken on postnatal day 1 (P01), P04, P09, and P23 were analyzed with RNA sequencing and global proteomics and metabolomics. Gene ontology analysis, KEGG pathway analysis, and fuzzy c-means clustering were used to identify up- or downregulated biological processes and metabolic pathways on all 3 levels, and Ingenuity pathway analysis (Qiagen) was used to identify upstream regulators. Differential expression was observed for 8547 mRNA s and for 1199 of 2285 quantified proteins. Furthermore, 151 metabolites with significant changes were identified. Differentially regulated metabolic pathways include branched chain amino acid degradation (upregulated at P23), fatty acid metabolism (upregulated at P04 and P09; downregulated at P23) as well as the HMGCS ( HMG -CoA [hydroxymethylglutaryl-coenzyme A] synthase)-mediated mevalonate pathway and ketogenesis (transiently activated). Pharmacological inhibition of HMGCS in primary neonatal cardiomyocytes reduced the percentage of BrdU-positive cardiomyocytes, providing evidence that the mevalonate and ketogenesis routes may participate in regulating the cardiomyocyte cell cycle. Conclusions This study is the first systems-level resource combining data from genomewide transcriptomics with global quantitative proteomics and untargeted metabolomics analyses in the mouse heart throughout the early postnatal period. These integrated data of molecular changes associated with the loss of cardiac regeneration may open up new possibilities for the development of regenerative therapies.


Assuntos
Coração/crescimento & desenvolvimento , Camundongos/crescimento & desenvolvimento , Aminoácidos de Cadeia Ramificada/metabolismo , Animais , Animais Recém-Nascidos/crescimento & desenvolvimento , Ácidos Graxos/metabolismo , Expressão Gênica/fisiologia , Coração/embriologia , Ventrículos do Coração , Corpos Cetônicos/biossíntese , Metabolômica , Ácido Mevalônico/metabolismo , Proteômica , RNA Mensageiro/genética , RNA Mensageiro/fisiologia , Transcriptoma/fisiologia
2.
Anal Chem ; 90(7): 4832-4839, 2018 04 03.
Artigo em Inglês | MEDLINE | ID: mdl-29513001

RESUMO

Raman spectroscopy is widely used for quantitative pharmaceutical analysis, but a common obstacle to its use is sample fluorescence masking the Raman signal. Time-gating provides an instrument-based method for rejecting fluorescence through temporal resolution of the spectral signal and allows Raman spectra of fluorescent materials to be obtained. An additional practical advantage is that analysis is possible in ambient lighting. This study assesses the efficacy of time-gated Raman spectroscopy for the quantitative measurement of fluorescent pharmaceuticals. Time-gated Raman spectroscopy with a 128 × (2) × 4 CMOS SPAD detector was applied for quantitative analysis of ternary mixtures of solid-state forms of the model drug, piroxicam (PRX). Partial least-squares (PLS) regression allowed quantification, with Raman-active time domain selection (based on visual inspection) improving performance. Model performance was further improved by using kernel-based regularized least-squares (RLS) regression with greedy feature selection in which the data use in both the Raman shift and time dimensions was statistically optimized. Overall, time-gated Raman spectroscopy, especially with optimized data analysis in both the spectral and time dimensions, shows potential for sensitive and relatively routine quantitative analysis of photoluminescent pharmaceuticals during drug development and manufacturing.


Assuntos
Corantes Fluorescentes/análise , Preparações Farmacêuticas/análise , Análise dos Mínimos Quadrados , Análise Espectral Raman , Fatores de Tempo
3.
PLoS One ; 6(5): e18841, 2011 May 09.
Artigo em Inglês | MEDLINE | ID: mdl-21573056

RESUMO

BACKGROUND: Low-density lipoprotein (LDL) particles, the major carriers of cholesterol in the human circulation, have a key role in cholesterol physiology and in the development of atherosclerosis. The most prominent structural components in LDL are the core-forming cholesteryl esters (CE) and the particle-encircling single copy of a huge, non-exchangeable protein, the apolipoprotein B-100 (apoB-100). The shape of native LDL particles and the conformation of native apoB-100 on the particles remain incompletely characterized at the physiological human body temperature (37 °C). METHODOLOGY/PRINCIPAL FINDINGS: To study native LDL particles, we applied cryo-electron microscopy to calculate 3D reconstructions of LDL particles in their hydrated state. Images of the particles vitrified at 6 °C and 37 °C resulted in reconstructions at ~16 Å resolution at both temperatures. 3D variance map analysis revealed rigid and flexible domains of lipids and apoB-100 at both temperatures. The reconstructions showed less variability at 6 °C than at 37 °C, which reflected increased order of the core CE molecules, rather than decreased mobility of the apoB-100. Compact molecular packing of the core and order in a lipid-binding domain of apoB-100 were observed at 6 °C, but not at 37 °C. At 37 °C we were able to highlight features in the LDL particles that are not clearly separable in 3D maps at 6 °C. Segmentation of apoB-100 density, fitting of lipovitellin X-ray structure, and antibody mapping, jointly revealed the approximate locations of the individual domains of apoB-100 on the surface of native LDL particles. CONCLUSIONS/SIGNIFICANCE: Our study provides molecular background for further understanding of the link between structure and function of native LDL particles at physiological body temperature.


Assuntos
Microscopia Crioeletrônica/métodos , Lipoproteínas LDL/ultraestrutura , Temperatura Corporal , Humanos
4.
Ann Med ; 41(6): 451-61, 2009.
Artigo em Inglês | MEDLINE | ID: mdl-19412820

RESUMO

BACKGROUND: There is an unmet need for a straightforward and cost-effective assessment of multiple lipoprotein risk factors for vascular diseases. AIMS: 1) To study the relation of various lipoprotein lipid and apolipoprotein (apo) measures on the Friedewald inputs, i.e. plasma triglycerides (TG), cholesterol (TC), and high-density lipoprotein cholesterol (HDL-C). 2) To build up regression models for the appropriate measures based solely on the Friedewald inputs. METHODS: Data were available for 1,775 plasma samples, from which very-low-density lipoprotein (VLDL), intermediate-density lipoprotein (IDL), low-density lipoprotein (LDL), and HDL were also isolated by ultracentrifugation. For HDL(2)-C and apolipoproteins, 343 and 247 samples were available, respectively. RESULTS: Accurate models were obtained for VLDL-TG (cross-validation r=0.98), LDL-C (r=0.91), HDL(2)-C (r=0.92), apoA-I (r=0.92), and apoB (r=0.95). A semi-quantitative model was obtained for IDL-C (r=0.78). Due to the anticipated role of IDL-C in atherosclerosis, it was still kept within the accepted models and pursued further. The associations of the estimates with premature deaths were studied in 4,084 patients with type 1 diabetes. The associations of IDL-C and LDL-C were markedly different, the best predictors of mortality being apoB, apoB to apoA-I ratio, and IDL-C. CONCLUSIONS: The new models allow identification of clinically relevant lipoprotein profiles with no added cost to the conventional Friedewald formula.


Assuntos
Doenças Cardiovasculares/epidemiologia , Diabetes Mellitus Tipo 1/sangue , Diabetes Mellitus Tipo 1/mortalidade , Lipoproteínas/sangue , Algoritmos , Doenças Cardiovasculares/etiologia , Colesterol/sangue , Colesterol/metabolismo , Diabetes Mellitus Tipo 1/complicações , Dislipidemias/complicações , Humanos , Lipoproteínas/metabolismo , Modelos Estatísticos , Análise de Regressão , Medição de Risco , Triglicerídeos/sangue , Triglicerídeos/metabolismo
6.
IEEE Trans Neural Syst Rehabil Eng ; 14(2): 190-3, 2006 Jun.
Artigo em Inglês | MEDLINE | ID: mdl-16792291

RESUMO

We characterized features of magnetoencephalographic (MEG) and electroencephalographic (EEG) signals generated in the sensorimotor cortex of three tetraplegics attempting index finger movements. Single MEG and EEG trials were classified offline into two classes using two different classifiers, a batch trained classifier and a dynamic classifier. Classification accuracies obtained with dynamic classifier were better, at 75%, 89%, and 91% in different subjects, when features were in the 0.5-3.0-Hz frequency band. Classification accuracies of EEG and MEG did not differ.


Assuntos
Encéfalo/fisiopatologia , Auxiliares de Comunicação para Pessoas com Deficiência , Eletroencefalografia/métodos , Magnetoencefalografia/métodos , Quadriplegia/fisiopatologia , Quadriplegia/reabilitação , Terapia Assistida por Computador/métodos , Inteligência Artificial , Análise por Conglomerados , Potenciais Evocados , Humanos , Masculino , Reconhecimento Automatizado de Padrão/métodos , Reprodutibilidade dos Testes , Sensibilidade e Especificidade , Software
7.
Artigo em Inglês | MEDLINE | ID: mdl-15531789

RESUMO

This paper proposes a new maximum likelihood approach for the deconvolution of identity and quantity of individual compounds based on the multicomponent mass spectra measured by mass spectrometry (MS). Mixture analysis of multicomponent mass spectra is, typically, based on a linear multicomponent mass spectrum model, where the compounds of the measured spectra to be solved are explicitly stated and assumed to be known. In many cases, however, the measured spectrum may contain unknown compounds that are not explicitly stated in the model and a commonly used least square (LS) solution fails. Moreover, a standard improvement over the LS method in these cases, namely the M-estimation (ME) approach, also suffers from this same problem. Our method overcomes the limitations of the LS and ME methods by modeling the effect of the unknown compound(s) to the residual of the linear model. The experimental results presented show that this new approach can separate more robustly the complex multicomponent mass spectra into their individual constituents compared to the LS and ME methods.


Assuntos
Misturas Complexas/análise , Funções Verossimilhança , Modelos Estatísticos , Espectrometria de Massas por Ionização por Electrospray/métodos , Espectrometria de Massas por Ionização por Electrospray/estatística & dados numéricos , Poluentes Atmosféricos/análise , Compostos Orgânicos/análise , Volatilização
8.
FEBS Lett ; 570(1-3): 107-13, 2004 Jul 16.
Artigo em Inglês | MEDLINE | ID: mdl-15251449

RESUMO

The need for high-throughput assays in molecular biology places increasing requirements on the applied signal processing and modelling methods. In order to be able to extract useful information from the measurements, the removal of undesirable signal characteristics such as random noise is required. This can be done in a quite elegant and efficient way by the minimum description length (MDL) principle, which treats and separates 'noise' from the useful information as that part in the data that cannot be compressed. In its current form the MDL denoising method assumes the Gaussian noise model but does not require any ad hoc parameter settings. It provides a basis for high-speed automated processing systems without requiring continual user interventions to validate the results as in the conventional signal processing methods. Our analysis of the denoising problem in mass spectrometry, capillary electrophoresis genotyping, and sequencing signals suggests that the MDL denoising method produces robust and intuitively appealing results sometimes even in situations where competing approaches perform poorly.


Assuntos
Eletroforese Capilar/métodos , Eletroforese/métodos , Espectrometria de Massas/métodos , Estatística como Assunto/métodos , Algoritmos , Calibragem , Microscopia Crioeletrônica , DNA Viral , Genótipo , Repetições de Microssatélites , Modelos Estatísticos , Modelos Teóricos , Distribuição Normal
9.
J Struct Biol ; 145(1-2): 41-51, 2004.
Artigo em Inglês | MEDLINE | ID: mdl-15065672

RESUMO

In order to make a high resolution model of macromolecular structures from cryo-electron microscope (cryo-EM) raw images one has to be precise at every processing step from particle picking to 3D image reconstruction. In this paper we propose a collection of novel methods for filtering cryo-EM images and for automatic picking of particles. These methods have been developed for two cases: (1) when particles can be identified and (2) when particle are not distinguishable. The advantages of these methods are demonstrated in standard purified protein samples and to generalize them we do not use any ad hoc presumption of the geometry of the particle projections. We have also suggested a filtering method to increase the signal-to-noise (S/N) ratio which has proved to be useful for other levels of reconstruction, i.e., finding orientations and 3D model reconstruction.


Assuntos
Microscopia Crioeletrônica/métodos , Aumento da Imagem/métodos , Processamento de Imagem Assistida por Computador/métodos , Proteínas/ultraestrutura , Algoritmos , Animais , Bacteriófago PRD1/química , Bacteriófago PRD1/ultraestrutura , Processamento Eletrônico de Dados/métodos , Hemocianinas/química , Hemocianinas/ultraestrutura , Imageamento Tridimensional , Modelos Estatísticos , Moluscos , Tamanho da Partícula , Reconhecimento Automatizado de Padrão , Probabilidade , Conformação Proteica , Proteínas/química , Virus Puumala/química , Design de Software , Proteínas Virais/química , Proteínas Virais/ultraestrutura
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