RESUMO
In this study, a software tool (IFGFA) for identification of featured genes from gene expression data based on latent factor analysis was developed. Despite the availability of computational methods and statistical models appropriate for analyzing special genomic data, IFGFA provides a platform for predicting colon cancer-related genes and can be applied to other cancer types. The computational framework behind IFGFA is based on the well-established Bayesian factor and regression model and prior knowledge about the gene from OMIM. We validated the predicted genes by analyzing somatic mutations in patients. An interface was developed to enable users to run the computational framework efficiently through visual programming. IFGFA is executable in a Windows system and does not require other dependent software packages. This program can be freely downloaded at http://www.fupage.org/downloads/ifgfa.zip.
Assuntos
Análise Fatorial , Perfilação da Expressão Gênica/métodos , Software , Algoritmos , Teorema de Bayes , Neoplasias do Colo/diagnóstico , Neoplasias do Colo/genética , Biologia Computacional/métodos , Humanos , Análise de Sequência com Séries de Oligonucleotídeos/métodos , Análise de Sequência de DNA/métodos , TranscriptomaRESUMO
We evaluated the effect of puerarin on spatial learning and memory ability of mice with chronic alcohol poisoning. A total of 30 male C57BL/6 mice were randomly divided into model, puerarin, and control groups (n=10 each). The model group received 60% (v/v) ethanol by intragastric administration followed by intraperitoneal injection of normal saline 30 min later. The puerarin group received intragastric 60% ethanol followed by intraperitoneal puerarin 30 min later, and the control group received intragastric saline followed by intraperitoneal saline. Six weeks after treatment, the Morris water maze and Tru Scan behavioral tests and immunofluorescence staining of cerebral cortex and hippocampal neurons (by Neu-N) and microglia (by Ib1) were conducted. Glutamic acid (Glu) and gamma amino butyric acid (GABA) in the cortex and hippocampus were assayed by high-performance liquid chromatography (HPLC), and tumor necrosis factor (TNF)-α and interleukin (IL)-1β were determined by ELISA. Compared with mice in the control group, escape latency and distance were prolonged, and spontaneous movement distance was shortened (P<0.05) by puerarin. The number of microglia was increased in both the cortex and hippocampal dentate gyrus (P<0.01), and neurons were reduced only in the hippocampal dentate gyrus (P<0.01) in puerarin-treated mice. In the model group, Glu and GABA levels decreased (P<0.05), and Glu/GABA, TNF-α, and IL-1β increased (P<0.01) with puerarin treatment, returning to near normal levels. In conclusion, puerarin protected against the effects of chronic alcohol poisoning on spatial learning and memory ability primarily because of anti-inflammatory activity and regulation of the balance of Glu and GABA.
Assuntos
Animais , Masculino , Etanol/intoxicação , Isoflavonas/uso terapêutico , Aprendizagem em Labirinto/efeitos dos fármacos , Transtornos da Memória/prevenção & controle , Fármacos Neuroprotetores/uso terapêutico , Memória Espacial/efeitos dos fármacos , Vasodilatadores/uso terapêutico , Alcoolismo/complicações , Cromatografia Líquida de Alta Pressão , Córtex Cerebral/química , Córtex Cerebral/efeitos dos fármacos , Ensaio de Imunoadsorção Enzimática , Ácido Glutâmico/análise , Interleucina-1beta/análise , Isoflavonas/farmacologia , Transtornos da Memória/induzido quimicamente , Transtornos da Memória/tratamento farmacológico , Microglia/efeitos dos fármacos , Fármacos Neuroprotetores/farmacologia , Distribuição Aleatória , Fatores de Tempo , Resultado do Tratamento , Fator de Necrose Tumoral alfa/análise , Vasodilatadores/farmacologia , Ácido gama-Aminobutírico/análiseRESUMO
We evaluated the effect of puerarin on spatial learning and memory ability of mice with chronic alcohol poisoning. A total of 30 male C57BL/6 mice were randomly divided into model, puerarin, and control groups (n=10 each). The model group received 60% (v/v) ethanol by intragastric administration followed by intraperitoneal injection of normal saline 30 min later. The puerarin group received intragastric 60% ethanol followed by intraperitoneal puerarin 30 min later, and the control group received intragastric saline followed by intraperitoneal saline. Six weeks after treatment, the Morris water maze and Tru Scan behavioral tests and immunofluorescence staining of cerebral cortex and hippocampal neurons (by Neu-N) and microglia (by Ib1) were conducted. Glutamic acid (Glu) and gamma amino butyric acid (GABA) in the cortex and hippocampus were assayed by high-performance liquid chromatography (HPLC), and tumor necrosis factor (TNF)-α and interleukin (IL)-1ß were determined by ELISA. Compared with mice in the control group, escape latency and distance were prolonged, and spontaneous movement distance was shortened (P<0.05) by puerarin. The number of microglia was increased in both the cortex and hippocampal dentate gyrus (P<0.01), and neurons were reduced only in the hippocampal dentate gyrus (P<0.01) in puerarin-treated mice. In the model group, Glu and GABA levels decreased (P<0.05), and Glu/GABA, TNF-α, and IL-1ß increased (P<0.01) with puerarin treatment, returning to near normal levels. In conclusion, puerarin protected against the effects of chronic alcohol poisoning on spatial learning and memory ability primarily because of anti-inflammatory activity and regulation of the balance of Glu and GABA.
Assuntos
Etanol/intoxicação , Isoflavonas/uso terapêutico , Aprendizagem em Labirinto/efeitos dos fármacos , Transtornos da Memória/prevenção & controle , Fármacos Neuroprotetores/uso terapêutico , Memória Espacial/efeitos dos fármacos , Vasodilatadores/uso terapêutico , Alcoolismo/complicações , Animais , Córtex Cerebral/química , Córtex Cerebral/efeitos dos fármacos , Cromatografia Líquida de Alta Pressão , Ensaio de Imunoadsorção Enzimática , Ácido Glutâmico/análise , Interleucina-1beta/análise , Isoflavonas/farmacologia , Masculino , Transtornos da Memória/induzido quimicamente , Transtornos da Memória/tratamento farmacológico , Camundongos Endogâmicos C57BL , Microglia/efeitos dos fármacos , Fármacos Neuroprotetores/farmacologia , Distribuição Aleatória , Fatores de Tempo , Resultado do Tratamento , Fator de Necrose Tumoral alfa/análise , Vasodilatadores/farmacologia , Ácido gama-Aminobutírico/análiseRESUMO
Mexican petunia (Ruellia brittoniana) is an herbaceous flowering perennial with strikingly colored flowers, widely cultivated commercially as a potted plant and a popular garden plant. In July of 2010, root and stem rot that caused death was observed on Mexican petunia at the flower nursery of the Council of Agriculture & Chiayi County in Taiwan. Plants had rotted and girdled stem bases. Necrotic areas were covered with fans of white mycelium as well as abundant spherical sclerotia. A fungus was isolated from infected tissue and sclerotia, and maintained on potato dextrose agar (PDA) plates incubated at 25°C without light. Colonies were white, cottony, often forming fans; pure cultures were prepared by transferring hyphal tips to PDA. Sclerotia formed after 10 days, initially white becoming dark brown with age, and 0.5 to 0.6 mm in diameter. To confirm identity of the causal fungus, the complete internal transcribed spacer (ITS) rDNA region of the causal fungus was amplified using the primers ITS4 and ITS5 (2) and sequenced. The resulting sequence of 687 bp was uploaded in NCBI. The sequence was 98% similar to sequences of Athelia rolfsii (Sclerotium rolfsii) in NCBI (Accession No. JN543691.1). Koch's postulates were performed using two inoculation techniques. The soil near the base of healthy Mexican petunia plants (four plants per pot) were exposed to recently matured sclerotia (10 sclerotia per plant) developed from pure fungal cultures or 10-mm-diameter agar plugs of mycelium (one plug per plant). Noninoculated plants, in a separate pot, were used as a control. All plants were incubated in a growth chamber at 28 to 33°C. Disease symptoms occurred on all inoculated plants by 5 to 7 days and included yellowing of leaves, basal stem rot, and wilt. Ten days after inoculation, inoculated plants were dead whereas control plants remained healthy. The pathogenicity test was repeated twice with similar results and S. rolfsii was reisolated from infected plants in each test. The pathogen has been reported to cause substantial loss of Mexican petunia in Louisiana (1). The disease is becoming more common in Taiwan and could cause losses in Mexican petunia production. To our knowledge, this is the first report of disease on Mexican petunia caused by S. rolfsii in Taiwan. References: (1) G. E. Holcomb. Plant Dis. 88:770, 2004. (2) T. J. White et al. Page 315 in: PCR Protocols: A Guide to Methods and Applications. M. A. Innis et al., eds. Academic Press, 1990.