GRIFFIN: a system for predicting GPCR–G-protein coupling selectivity using a support vector machine and a hidden Markov model

We describe a novel system, GRIFFIN (G-protein and Receptor Interaction Feature Finding INstrument), that predicts G-protein coupled receptor (GPCR) and G-protein coupling selectivity based on a support vector machine (SVM) and a hidden Markov model (HMM) with high sensitivity and specificity. Based on our assumption that whole structural segments of ligands, GPCRs and G-proteins are essential to determine GPCR and G-protein coupling, various quantitative features were selected for ligands, GPCRs and G-protein complex structures, and those parameters that are the most effective in selecting G-protein type were used as feature vectors in the SVM. The main part of GRIFFIN includes a hierarchical SVM classifier using the feature vectors, which is useful for Class A GPCRs, the major family. For the opsins and olfactory subfamilies of Class A and other minor families (Classes B, C, frizzled and smoothened), the binding G-protein is predicted with high accuracy using the HMM. Applying this system to known GPCR sequences, each binding G-protein is predicted with high sensitivity and specificity (>85% on average). GRIFFIN () is freely available and allows users to easily execute this reliable prediction of G-proteins

TÉCNICAS PARA VISUALIZAR INFORMAÇÃO E EXTRAIR CONHECIMENTO DE BASES DE INFORMAÇÕES: ESTUDO DE CASO DAS PRODUÇÕES DOS PROFESSORES DO PPGI-UFES

A Visualização é uma parte muito importante para conseguir a compreensão real da informação e para extrair conhecimentos relevantes. Portanto, a técnica para visualizar a informação selecionada deve ser compatível com o conteúdo que se vai apresentar. A proposta desta dissertação é apresentar um site que integre diversas Técnicas de Visualização criadas, que sejam fáceis, rápidas, entendíveis, dinâmicas e adaptáveis, dos temas desenvolvidos pelos integrantes de um grupo de pesquisa, durante alguns períodos. Essas técnicas são construídas tomando por base principalmente as palavras-chave e títulos das Produções Bibliográficas, representando assim a evolução dos temas pesquisados ao longo do tempo, entre outras coisas

Novel, Objective, Multivariate Biomarkers Composed of Plasma Amino Acid Profiles for the Diagnosis and Assessment of Inflammatory Bowel Disease

BACKGROUND: Inflammatory bowel disease (IBD) is a chronic intestinal disorder that is associated with a limited number of clinical biomarkers. In order to facilitate the diagnosis of IBD and assess its disease activity, we investigated the potential of novel multivariate indexes using statistical modeling of plasma amino acid concentrations (aminogram). METHODOLOGY AND PRINCIPAL FINDINGS: We measured fasting plasma aminograms in 387 IBD patients (Crohn's disease (CD), n = 165; ulcerative colitis (UC), n = 222) and 210 healthy controls. Based on Fisher linear classifiers, multivariate indexes were developed from the aminogram in discovery samples (CD, n = 102; UC, n = 102; age and sex-matched healthy controls, n = 102) and internally validated. The indexes were used to discriminate between CD or UC patients and healthy controls, as well as between patients with active disease and those in remission. We assessed index performances using the area under the curve of the receiver operating characteristic (ROC AUC). We observed significant alterations to the plasma aminogram, including histidine and tryptophan. The multivariate indexes established from plasma aminograms were able to distinguish CD or UC patients from healthy controls with ROC AUCs of 0.940 (95% confidence interval (CI): 0.898-0.983) and 0.894 (95%CI: 0.853-0.935), respectively in validation samples (CD, n = 63; UC, n = 120; healthy controls, n = 108). In addition, other indexes appeared to be a measure of disease activity. These indexes distinguished active CD or UC patients from each remission patients with ROC AUCs of 0.894 (95%CI: 0.853-0.935) and 0.849 (95%CI: 0.770-0.928), and correlated with clinical disease activity indexes for CD (r(s) = 0.592, 95%CI: 0.385-0.742, p<0.001) or UC (r(s) = 0.598, 95%CI: 0.452-0.713, p<0.001), respectively. CONCLUSIONS AND SIGNIFICANCE: In this study, we demonstrated that established multivariate indexes composed of plasma amino acid profiles can serve as novel, non-invasive, objective biomarkers for the diagnosis and monitoring of IBD, providing us with new insights into the pathophysiology of the disease

A novel strategy for enrichment and isolation of osteoprogenitor cells from induced pluripotent stem cells based on surface marker combination.

In this study, we developed a new method to stimulate osteogenic differentiation in tissue-nonspecific alkaline phosphatase (TNAP)-positive cells liberated from human induced pluripotent stem cells (hiPSCs)-derived embryoid bodies (EBs) with 14 days long TGF-β/IGF-1/FGF-2 treatment. TNAP is a marker protein of osteolineage cells. We analyzed and isolated TNAP-positive and E-cadherin-negative nonepithelial cells by fluorescence-activated cell sorting. Treating the cells with a combination of transforming growth factor (TGF)-β, insulin-like growth factor (IGF)-1, and fibroblast growth factor (FGF)-2 for 14 days greatly enhanced TNAP expression and maximized expression frequency up to 77.3%. The isolated cells expressed high levels of osterix, which is an exclusive osteogenic marker. Culturing these TNAP-positive cells in osteoblast differentiation medium (OBM) led to the expression of runt-related transcription factor 2, type I collagen, bone sialoprotein, and osteocalcin (OCN). These cells responded to treatment with activated vitamin D3 by upregulating OCN. Furthermore, in OBM they were capable of generating many mineralized nodules with strong expression of receptor activator of NF-kappaB ligand and sclerostin (SOST). Real-time RT-PCR showed a significant increase in the expression of osteocyte marker genes, including SOST, neuropeptide Y, and reelin. Scanning electron microscopy showed dendritic morphology. Examination of semi-thin toluidine blue-stained sections showed many interconnected dendrites. Thus, TNAP-positive cells cultured in OBM may eventually become terminally differentiated osteocyte-like cells. In conclusion, treating hiPSCs-derived cells with a combination of TGF-β, IGF-1, and FGF-2 generated TNAP-positive cells at high frequency. These TNAP-positive cells had a high osteogenic potential and could terminally differentiate into osteocyte-like cells. The method described here may reveal new pathways of osteogenesis and provide a novel tool for regenerative medicine and drug development

Plasma Amino Acid Profile in Severely Frail Elderly Patients in Japan

Summary: Background: Severe frailty, which is the highest level of frailty, leads to multiple health impairments that may individually affect the plasma-free amino acid (PFAA) profile. However, the PFAA profile of severely frail patients has not been clarified. The aim of this study was to describe the PFAA profile of severely frail elderly patients. Methods: Elderly patients (aged ≥65 years) who were admitted to the Nukada Institute for Medical and Biological Research (Chiba, Japan) were included. Severe frailty was defined using the Canadian Study of Health and Aging Clinical Frailty Scale. Subjects were divided into non-frail and severely frail groups. The PFAA profile and clinical characteristics of the subjects were analyzed. Results: Compared to the non-frail group (n = 31), the severely frail group (n = 28) had lower body mass index (BMI), serum albumin, serum prealbumin, hemoglobin, and blood pressure and higher C-reactive protein. Seventy-nine percent of severely frail patients had cognitive impairment. Severely frail patients had significantly lower essential amino acid (EAA) plasma concentrations than non-frail patients. Multiple linear regression analysis identified that valine (p = 0.005) was strongly associated with BMI. Valine (p = 0.004), leucine (p = 0.004), tryptophan (p = 0.006), lysine (p < 0.001), and total EAA (p < 0.001) levels were significantly associated with serum prealbumin levels. Conclusion: Severely frail patients had multiple health impairments. BMI and nutritional status were most significantly associated with low EAA levels. Keywords: body mass index, elderly, frailty, nutritional status, prealbumi

Primers used for RT-PCR.

<p>Primers used for RT-PCR.</p