Navegando por Autor "Pupin, Breno"

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    Evaluation of hydrogel use in the development of Rapanea ferruginea with water restriction by vibrational Fourier Transform Infrared Spectroscopy (FTIR-UATR)
    (SciELO) Pereira, Douglas Cubas; Pupin, Breno; Sakane, Kumiko Koibuchi
    This study evaluated the use of hydrogel on the development of Rapanea ferruginea under water restriction through Vibrational Fourier Transform Infrared Spectroscopy (FTIR-UATR). Seedlings of approximately 30 cm height were transferred in pots with 3 L of soil. The group of seedlings was separated into 5 different triplicate treatments according to the amount of hydrogel, as follows: H1 (25%), H2 (20%), H3 (15%), H4 (10%) and S (control without hydrogel). The applied hydrogel was mixed homogeneously with the soil. All treatments were irrigated with 40 mL of water. FTIR spectra were obtained from fresh leaves collected during 13 months of monitoring. The correlation of the hydroxyl (water) band with the main biomolecules between treatments with the control was evaluated using the Mann-Whitney test (p<0.05). The biomolecule bands were subjected to principal component analysis (PCA) and hierarchical clustering analysis (HCA). The results indicate a significant correlation of the water band with the lipid, hemicellulose, cell wall and starch components in the species. The use of hydrogel resulted in a significant difference in the water absorption band in relation to the control group through the Mann-Whitney test and in biomolecules as the HCA and PCA analysis suggested. The best development was observed in groups H4 (10%), H2 (20%) and H3 (15%). The use of hydrogel positively influences the biomolecular development of the Rapanea ferruginea and monitoring is viable by FTIR.
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    Expression data of FOS and JUN genes and FTIR spectra provide diagnosis of thyroid carcinoma
    (Elsevier) Queiroz, João Paulo da Silva; Pupin, Breno; Bhattacharjee, Tanmoy Tapobrata; Uno, Miyuki; Chammas, Roger; Kulcsar, Marco Aurélio Vamondes; Canevari, Renata de Azevedo
    We explore the feasibility of using FOS and JUN gene expression and ATR-FTIR for diagnosis of thyroid cancer. For the study, 38 samples (6 non-neoplastic (NN), 10 papillary thyroid carcinoma (PTC), 7 follicular thyroid carcinoma (FTC), and 15 benign tumors (BT) were subjected to RNA extraction followed by quantitative real time PCR (qRT-PCR) and 30 samples (5 NN, 9 PTC, 5 FTC, and 11 BT) were used for Attenuated Total Reflectance – Fourier Transform Infrared (ATR-FTIR) followed by multivariate analysis. Of the above, 20 samples were used for both gene expression and ATR-FTIR studies. We found FOS and JUN expression in malignant tumor samples to be significantly lower than NN and benign. ATR-FIR after multivariate analysis could identify the difficult to diagnose FTC with 93 % efficiency. Overall, results suggest the diagnostic potential of molecular biology techniques combined with ATR-FTIR spectroscopy in differentiated thyroid carcinomas (PTC and FTC) and BT.
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    PCR-RFLP and FTIR-based detection of high-risk human papilloma virus for cervical cancer screening and prevention
    (Elsevier) Melo, Igor Martins Alves; Viana, Magda Rogéria Pereira; Pupin, Breno; Bhattacharjee, Tanmoy Tapobrata; Canevari, Renata de Azevedo
    Background: Approximately 70% of cervical carcinoma cases show the presence of high-risk Human Papilloma Virus (HPV), especially HPV-16 and HPV-18, and can be used to stratify high risk patients from low risk and healthy. Currently, molecular biology techniques such as polymerase chain reaction (PCR) are used to identify the presence of virus in patient samples. While the methodology is highly sensitive, it is labor intensive and timeconsuming. Alternative techniques, such as vibrational spectroscopy, has been suggested as a possible rapid alternative. Therefore, in this study, we evaluate the efficiency of cervical fluid Fourier Transform Infrared spectroscopy (FTIR) in patient risk stratification informed by PCR. Methods: Cervical fluid samples (n = 91) were obtained from patients who have undergone routine Papanicolaou (Pap) test. Viral genome was identified and classified as high/low-risk by PCR-Restriction Fragment Length Polymorphism (PCR-RFLP). FTIR spectra were acquired from samples identified by PCR-RFLP as No-HPV (n = 10), high-risk HPV (n = 7), and low-risk HPV (n = 7). Results: Of the 91 samples, was detected the viral genome by PCR in 36 samples. Of these 36 samples, nine samples were identified to contain high-risk HPV (HR-HPV) and nine samples were found to have low-risk HPV (LR-HPV). The FTIR spectra acquired from No-HPV, LR-HPV, and HR-HPV showed differences in 1069, 1437, 1555, 1647, 2840, 2919, and 3287 cm-1 bands. Principal Component Analysis (PCA) showed distinct clusters for No-HPV and HR-HPV and No-HPV and LR-HPV, but there was significant overlap in the clusters of HR-HPV and LR-HPV. PCA-Linear Discriminant Analysis (PC-LDA) after Leave One Out Cross Validation (LOOCV) classified No-HPV from HR-HPV and No-HPV from LR-HPV with 100% efficiency in the 1400-1800 cm-1 spectral range. LOOCV classifications for LR-HPV and HR-HPV from each other were 71 and 75%, respectively, in the 2800-3400 cm-1 spectral range. Conclusions: The results highlight the high sensitivity of PCR-RFLP in HPV identification and show that FTIR can classify samples identified as healthy, low, and high-risk samples by PCR-RFLP. General significance: We show the possibility of using FTIR for initial cervical cancer risk stratification followed by detailed PCR-RFLP investigations for suspect cases.