Identification of pesticide-degrading Pseudomonas strains as poly-β-hydroxybutyrate producers

Polyhydroxybutyrate (PHB) is an ecological promising substitute for polypropylene because it is biocompatible, biodegradable and can be produced by renewable sources. This study investigated PHB accumulation on pesticide-degrading Pseudomonas. 14 strains of pesticide-degrading Pseudomonas isolated from subtropical lowland soil in southern Brazil were analyzed using optical microscopy. Lipid inclusions were identified in four strains, and three of them, which degraded the pesticide carbofuran, had extensive granules accumulation which was detected by transmission electron microscopy. These strains were cultivated in a shaker at 28°C and the polymer was characterized by Fourier transform infrared (FTIR) spectroscopy. Strain CMM43 had the best accumulation after 48 h. The biopolymer was identified as poly-β-hydroxybutyrate.Key words: Polyhydroxybutyrate (PHB), pesticide-degrading Pseudomonas sp., microscopy, subtropical lowland soil

Segmentation and Classification of Cine-MR Images Using Fully Convolutional Networks and Handcrafted Features

Three-dimensional cine-MRI is of crucial importance for assessing the cardiac function. Features that describe the anatomy and function of cardiac structures (e.g. Left Ventricle (LV), Right Ventricle (RV), and Myocardium(MC)) are known to have significant diagnostic value and can be computed from 3D cine-MR images. However, these features require precise segmentation of cardiac structures. Among the fully automated segmentation methods, Fully Convolutional Networks (FCN) with Skip Connections have shown robustness in medical segmentation problems. In this study, we develop a complete pipeline for classification of subjects with cardiac conditions based on 3D cine-MRI. For the segmentation task, we develop a 2D FCN and introduce Parallel Paths (PP) as a way to exploit the 3D information of the cine-MR image. For the classification task, 125 features were extracted from the segmented structures, describing their anatomy and function. Next, a two-stage pipeline for feature selection using the LASSO method is developed. A subset of 20 features is selected for classification. Each subject is classified using an ensemble of Logistic Regression, Multi-Layer Perceptron, and Support Vector Machine classifiers through majority voting. The Dice Coefficient for segmentation was 0.95+-0.03, 0.89+-0.13, and 0.90+-0.03 for LV, RV, and MC respectively. The 8-fold cross validation accuracy for the classification task was 95.05% and 92.77% based on ground truth and the proposed methods segmentations respectively. The results show that the PPs increase the segmentation accuracy, by exploiting the spatial relations. Moreover, the classification algorithm and the features showed discriminability while keeping the sensitivity to segmentation error as low as possible.Comment: 9 pages, 3 figures, 2 tables. Was accepted to the ACDC challenge, MICCAI 2017 (not attended

Influência de diferentes extratos de levedura (insumos) no crescimento celular de Xanthomonas arboricola pv pruni cepa 101/ Influence of different yeast extracts (inputs) on the cell growth of Xanthomonas arboricola pv pruni strain 101

Xantana é um heteropolissacarídeo produzido por bactérias do gênero Xanthomonas. Esse biopolímero desempenha diversas funções de grande importância para indústrias de variados setores. O processo de produção de xantana é realizado em duas etapas: crescimento celular e produção do biopolímero, e ambas são importantes para a obtenção de xantana com rendimento e qualidade satisfatórios, os quais são influenciados por diferentes fatores, dentre eles os meios de cultivo utilizados. Objetivou-se avaliar o crescimento bacteriano de Xanthomonas arboricola pv pruni cepa 101 em meio de cultivo complexo YM adicionado de diferentes extratos de levedura, sendo um tradicional - controle (1) - e outros alternativos de menor custo - 560PW (2), 810PW (3), 845MG (4), 851MG (5), 861PW (6) - e relacionar com o teor de nitrogênio fornecido. Avaliou-se o crescimento celular (UFC.mL-1) e o teor de nitrogênio (mg.dL-1) nos tempos 24 h e em 0 e 24 h de crescimento celular, respectivamente. Não observou-se diferença estatística entre a concentração celular final obtida com extrato controle e os extratos alternativos. A concentração celular final variou entre 3,1 × 1010 a 5,2 × 1010 UFC.mL-1. O uso dos extratos de levedura 4, 6 e o controle resultaram em maior disponibilidade de nitrogênio no meio de cultivo no tempo inicial e ao final, e têm potencial para propiciar um maior crescimento celular. Observou-se aumento no teor de nitrogênio no tempo final, provavelmente devido à hidrólise celular parcial.  O teor inicial de nitrogênio variou de 9,11 a 12,04 e o final de 31,41 a 47,51 mg.dL-1, respectivamente. Os diferentes extratos de levedura avaliados são substitutos adequados para o crescimento celular da bactéria X. arboricola pv pruni cepa 101, e provavelmente para outras cepas da espécie, com resultados equivalentes ao obtido com o extrato controle

Produção de xantana pruni em meios alternativos adicionados de água de parboilização de arroz

O objetivo deste estudo foi investigar os efeitos, no crescimento celular e produção de xantana, da utilização da água de parboilização de arroz, peptona e extrato de levedura como componentes no meio de cultura para o crescimento celular da Xanthomonas arboricola, espécie utilizada pelo grupo de pesquisa do laboratório de Biopolímeros do CDTec, Núcleo de Biotecnologia, da Universidade Federal de Pelotas, e produção da goma xantana. Buscou-se avaliar a viabilidade, analisando

Influencia de la agitación y la aireación en la producción de xantano por Xanthomonas campestris pv. pruni cepa 101

Se evaluó la producción, viscosidad y composición química del xantano sintetizado por la bacteria Xanthomonas campestris pv. pruni cepa 101 en un fermentador. Durante el proceso se controló el pH y se determinaron el coeficiente de transferencia de masa de oxígeno (kLa) y la producción de masa celular seca. Los cultivos se realizaron en un fermentador de 3 l variando la aireación y la agitación, en las siguientes condiciones: (A) 300 rpm, 3 vvm y (B) 200 rpm, 2 vvm; a 28 °C. Nuestros resultados mostraron que la producción de goma fue dependiente del kLa, con un rendimiento máximo de 8,15 g/l a 300 rpm y 3 vvm a las 54 h de fermentación, kLa de 21,4/h, mientras que la producción de biomasa no se afectó. Todas las soluciones acuosas de xantano al 3% (m/v) sintetizadas presentaron comportamiento pseudoplástico. La mayor viscosidad se alcanzó en la condición de aireación/agitación más intensa. Todas las muestras de xantano contenían glucosa, manosa, ramnosa y ácido glucurónico como constituyentes principales. La mayor tasa de agitación y aireación utilizada en la condición A (300 rpm y 3 vvm) influyó favorablemente en el rendimiento y la viscosidad del xantano producido por la bacteria X. campestris pv. pruni 101 a diferentes tiempos de fermentación.Production, viscosity, and chemical composition of xanthan synthesized by bacterium Xanthomonas campestris pv pruni strain 101 were evaluated in bioreactor systems. During the process, the volumetric oxygen mass transfer coefficient (kLa) and the biomass were determined and the pH was monitored. The cultures were grown in a 3 l bioreactor, with aeration and agitation varying as follows: conditions (A) 300 rpm, 3 vvm and (B) 200 rpm, 2 vvm, at 28 °C. Our results showed that gum production was dependent on kLa, with a maximum yield of 8.15 g/l at 300 rpm, 3 vvm, 54 h of fermentation, kLa 21.4/h, while biomass was not affected. All aqueous solutions of 3% (w/v) xanthans synthesized showed a pseudoplastic behavior. The highest viscosity was reached under the strongest aeration/agitation conditions. All xanthan samples contained glucose, mannose, rhamnose, and glucuronic acid as their main components. The highest agitation and aeration rates used under condition A (300 rpm and 3 vvm) favorably influenced the yield and viscosity of the xanthan produced by bacterium X. campestris pv pruni 101 at different fermentation times

Influencia de la agitación y la aireación en la producción de xantano por Xanthomonas campestris pv. pruni cepa 101

Se evaluó la producción, viscosidad y composición química del xantano sintetizado por la bacteria Xanthomonas campestris pv. pruni cepa 101 en un fermentador. Durante el proceso se controló el pH y se determinaron el coeficiente de transferencia de masa de oxígeno (kLa) y la producción de masa celular seca. Los cultivos se realizaron en un fermentador de 3 l variando la aireación y la agitación, en las siguientes condiciones: (A) 300 rpm, 3 vvm y (B) 200 rpm, 2 vvm; a 28 °C. Nuestros resultados mostraron que la producción de goma fue dependiente del kLa, con un rendimiento máximo de 8,15 g/l a 300 rpm y 3 vvm a las 54 h de fermentación, kLa de 21,4/h, mientras que la producción de biomasa no se afectó. Todas las soluciones acuosas de xantano al 3% (m/v) sintetizadas presentaron comportamiento pseudoplástico. La mayor viscosidad se alcanzó en la condición de aireación/agitación más intensa. Todas las muestras de xantano contenían glucosa, manosa, ramnosa y ácido glucurónico como constituyentes principales. La mayor tasa de agitación y aireación utilizada en la condición A (300 rpm y 3 vvm) influyó favorablemente en el rendimiento y la viscosidad del xantano producido por la bacteria X. campestris pv. pruni 101 a diferentes tiempos de fermentación.Production, viscosity, and chemical composition of xanthan synthesized by bacterium Xanthomonas campestris pv pruni strain 101 were evaluated in bioreactor systems. During the process, the volumetric oxygen mass transfer coefficient (kLa) and the biomass were determined and the pH was monitored. The cultures were grown in a 3 l bioreactor, with aeration and agitation varying as follows: conditions (A) 300 rpm, 3 vvm and (B) 200 rpm, 2 vvm, at 28 °C. Our results showed that gum production was dependent on kLa, with a maximum yield of 8.15 g/l at 300 rpm, 3 vvm, 54 h of fermentation, kLa 21.4/h, while biomass was not affected. All aqueous solutions of 3% (w/v) xanthans synthesized showed a pseudoplastic behavior. The highest viscosity was reached under the strongest aeration/agitation conditions. All xanthan samples contained glucose, mannose, rhamnose, and glucuronic acid as their main components. The highest agitation and aeration rates used under condition A (300 rpm and 3 vvm) favorably influenced the yield and viscosity of the xanthan produced by bacterium X. campestris pv pruni 101 at different fermentation times