S. Ling, Y. Zhu, D. Lan, D. S. Li, H. Pang, Y. Wang, D. Li, R. Wei, H. Zhang, C. D. Wang, Y. D. Hu
The giant panda, Ailuropoda melanoleuca (Ursidae), has a unique bamboo-based diet; however, this low-energy intake has been sufficient to maintain the metabolic processes of this species since the fourth ice age. As mitochondria are the main sites for energy metabolism in animals, the protein-coding genes involved in mitochondrial respiratory chains, particularly cytochrome c oxidase subunit II (COX2), which is the rate-limiting enzyme in electron transfer, could play an important role in giant panda metabolism. Therefore, the present study aimed to isolate, sequence, and analyze the COX2 DNA from individuals kept at the Giant Panda Protection and Research Center, China, and compare these sequences with those of the other Ursidae family members. Multiple sequence alignment showed that the COX2 gene had three point mutations that defined three haplotypes, with 60% of the sequences corresponding to haplotype I. The neutrality tests revealed that the COX2 gene was conserved throughout evolution, and the maximum likelihood phylogenetic analysis, using homologous sequences from other Ursidae species, showed clustering of the COX2 sequences of giant pandas, suggesting that this gene evolved differently in them.
{"title":"Analysis of the cytochrome c oxidase subunit II (COX2) gene in giant panda, Ailuropoda melanoleuca.","authors":"S. Ling, Y. Zhu, D. Lan, D. S. Li, H. Pang, Y. Wang, D. Li, R. Wei, H. Zhang, C. D. Wang, Y. D. Hu","doi":"10.4238/gmr16019158","DOIUrl":"https://doi.org/10.4238/gmr16019158","url":null,"abstract":"The giant panda, Ailuropoda melanoleuca (Ursidae), has a unique bamboo-based diet; however, this low-energy intake has been sufficient to maintain the metabolic processes of this species since the fourth ice age. As mitochondria are the main sites for energy metabolism in animals, the protein-coding genes involved in mitochondrial respiratory chains, particularly cytochrome c oxidase subunit II (COX2), which is the rate-limiting enzyme in electron transfer, could play an important role in giant panda metabolism. Therefore, the present study aimed to isolate, sequence, and analyze the COX2 DNA from individuals kept at the Giant Panda Protection and Research Center, China, and compare these sequences with those of the other Ursidae family members. Multiple sequence alignment showed that the COX2 gene had three point mutations that defined three haplotypes, with 60% of the sequences corresponding to haplotype I. The neutrality tests revealed that the COX2 gene was conserved throughout evolution, and the maximum likelihood phylogenetic analysis, using homologous sequences from other Ursidae species, showed clustering of the COX2 sequences of giant pandas, suggesting that this gene evolved differently in them.","PeriodicalId":189314,"journal":{"name":"Genetics and molecular research : GMR","volume":"50 1","pages":"0"},"PeriodicalIF":0.0,"publicationDate":"2017-01-23","publicationTypes":"Journal Article","fieldsOfStudy":null,"isOpenAccess":false,"openAccessPdf":"","citationCount":null,"resultStr":null,"platform":"Semanticscholar","paperid":"116765460","PeriodicalName":null,"FirstCategoryId":null,"ListUrlMain":null,"RegionNum":0,"RegionCategory":"","ArticlePicture":[],"TitleCN":null,"AbstractTextCN":null,"PMCID":"","EPubDate":null,"PubModel":null,"JCR":null,"JCRName":null,"Score":null,"Total":0}
Wenyi Yang, G. Shi, Liping Wu, Shutang Wei, Y. Huang, Lixia Tan, R. Yang, Chunxiao Yan, E. Guo, Hangyu Wang, J. Tong, Y. Dong, Dazheng Han
We aimed to evaluate the specificity of 12 tumor markers related to colon carcinoma and identify the most sensitive index. Bhattacharyya distance was used to evaluate the index. Then, different index combinations were used to establish a support vector machine (SVM) diagnosis model of malignant colon carcinoma. The accuracy of the model was checked. High accuracy was assumed to indicate the high specificity of the index. The Bhattacharyya distances of carcinoembryonic antigen, neuron-specific enolase, alpha-feto protein, and CA724 were the largest, and those of CYFRA21-І, CA125, and UGT1A83 were the second largest. The specificity of the combination of the above seven indexes was higher than that of other combinations, and the accuracy of the established SVM identification model was high. Using Bhattacharyya distance detection and establishing an SVM model based on different serum marker combinations can increase diagnostic accuracy, providing a theoretical basis for application of mathematical models in cancer diagnosis.
{"title":"Analysis of specific serum markers of colon carcinoma using a Bhattacharyya-based support vector machine.","authors":"Wenyi Yang, G. Shi, Liping Wu, Shutang Wei, Y. Huang, Lixia Tan, R. Yang, Chunxiao Yan, E. Guo, Hangyu Wang, J. Tong, Y. Dong, Dazheng Han","doi":"10.4238/gmr16019521","DOIUrl":"https://doi.org/10.4238/gmr16019521","url":null,"abstract":"We aimed to evaluate the specificity of 12 tumor markers related to colon carcinoma and identify the most sensitive index. Bhattacharyya distance was used to evaluate the index. Then, different index combinations were used to establish a support vector machine (SVM) diagnosis model of malignant colon carcinoma. The accuracy of the model was checked. High accuracy was assumed to indicate the high specificity of the index. The Bhattacharyya distances of carcinoembryonic antigen, neuron-specific enolase, alpha-feto protein, and CA724 were the largest, and those of CYFRA21-І, CA125, and UGT1A83 were the second largest. The specificity of the combination of the above seven indexes was higher than that of other combinations, and the accuracy of the established SVM identification model was high. Using Bhattacharyya distance detection and establishing an SVM model based on different serum marker combinations can increase diagnostic accuracy, providing a theoretical basis for application of mathematical models in cancer diagnosis.","PeriodicalId":189314,"journal":{"name":"Genetics and molecular research : GMR","volume":"1 1","pages":"0"},"PeriodicalIF":0.0,"publicationDate":"2017-01-23","publicationTypes":"Journal Article","fieldsOfStudy":null,"isOpenAccess":false,"openAccessPdf":"","citationCount":null,"resultStr":null,"platform":"Semanticscholar","paperid":"124648647","PeriodicalName":null,"FirstCategoryId":null,"ListUrlMain":null,"RegionNum":0,"RegionCategory":"","ArticlePicture":[],"TitleCN":null,"AbstractTextCN":null,"PMCID":"","EPubDate":null,"PubModel":null,"JCR":null,"JCRName":null,"Score":null,"Total":0}
With the expanding demand for genetically modified (GM) rice, its safety evaluation is of great significance. Therefore, this study was carried out to assess the acute cytotoxicity of the whole protein extract from GM rice Bar68-1 in Mus musculus lymphocytes in vitro. Cell viability was determined by Cell Counting Kit-8 (CCK-8) and Neutral Red Uptake (NRU) tests. CCK-8 tests was carried out according to the manufacturer's instructions. Cell dehydrogenase (catalytic redox enzymes) activity was spectrophotometrically determined at 450 nm. The tests result were recorded immediately. NRU tests were completed under yellow light in a dark room according to an improved protocol. Lysosomal uptake of neutral red was spectrophotometrically determined at 540 nm and the results were recorded immediately. The results showed that the survival rate of M. musculus lymphocytes in the positive control group was significantly less than in the blank control group (P < 0.05). Moreover, an exposure- time-effect relationship was observed in the positive control group with CCK-8 and NRU tests. There was no significant difference in survival rate between GM rice Bar68-1group and non-GM rice D68 group (P > 0.05). The GM rice Bar68-1 group also did not show a higher survival rate than non-GM rice D68 group (P > 0.05). These results suggested that the whole protein extract from Bar68-1 and D68 were equivalent in their cytotoxicity, and GM rice Bar68-1 had no acute cytotoxic effect on M. musculus lymphocytes in vitro.
{"title":"Cytotoxicity evaluation of the whole protein extract from Bar-transgenic rice on Mus musculus lymphocytes.","authors":"X. B. Lu","doi":"10.4238/gmr16019331","DOIUrl":"https://doi.org/10.4238/gmr16019331","url":null,"abstract":"With the expanding demand for genetically modified (GM) rice, its safety evaluation is of great significance. Therefore, this study was carried out to assess the acute cytotoxicity of the whole protein extract from GM rice Bar68-1 in Mus musculus lymphocytes in vitro. Cell viability was determined by Cell Counting Kit-8 (CCK-8) and Neutral Red Uptake (NRU) tests. CCK-8 tests was carried out according to the manufacturer's instructions. Cell dehydrogenase (catalytic redox enzymes) activity was spectrophotometrically determined at 450 nm. The tests result were recorded immediately. NRU tests were completed under yellow light in a dark room according to an improved protocol. Lysosomal uptake of neutral red was spectrophotometrically determined at 540 nm and the results were recorded immediately. The results showed that the survival rate of M. musculus lymphocytes in the positive control group was significantly less than in the blank control group (P < 0.05). Moreover, an exposure- time-effect relationship was observed in the positive control group with CCK-8 and NRU tests. There was no significant difference in survival rate between GM rice Bar68-1group and non-GM rice D68 group (P > 0.05). The GM rice Bar68-1 group also did not show a higher survival rate than non-GM rice D68 group (P > 0.05). These results suggested that the whole protein extract from Bar68-1 and D68 were equivalent in their cytotoxicity, and GM rice Bar68-1 had no acute cytotoxic effect on M. musculus lymphocytes in vitro.","PeriodicalId":189314,"journal":{"name":"Genetics and molecular research : GMR","volume":"95 1","pages":"0"},"PeriodicalIF":0.0,"publicationDate":"2017-01-23","publicationTypes":"Journal Article","fieldsOfStudy":null,"isOpenAccess":false,"openAccessPdf":"","citationCount":null,"resultStr":null,"platform":"Semanticscholar","paperid":"123401802","PeriodicalName":null,"FirstCategoryId":null,"ListUrlMain":null,"RegionNum":0,"RegionCategory":"","ArticlePicture":[],"TitleCN":null,"AbstractTextCN":null,"PMCID":"","EPubDate":null,"PubModel":null,"JCR":null,"JCRName":null,"Score":null,"Total":0}
Microarray gene expression technology provides a systematic approach to patient classification. However, microarray data pose a great computational challenge owing to their large dimensionality, small sample sizes, and potential correlations among genes. A recent study has shown that gene-gene correlations have a positive effect on the accuracy of classification models, in contrast to some previous results. In this study, a recently developed correlation-based classifier, the ensemble of random subspace (RS) Fisher linear discriminants (FLDs), was utilized. The impact of gene-gene correlations on the performance of this classifier and other classifiers was studied using simulated datasets and real datasets. A cross-validation framework was used to evaluate the performance of each classifier using the simulated datasets or real datasets, and misclassification rates (MRs) were computed. Using the simulated data, the average MRs of the correlation-based classifiers decreased as the correlations increased when there were more correlated genes. Using real data, the correlation-based classifiers outperformed the non-correlation-based classifiers, especially when the gene-gene correlations were high. The ensemble RS-FLD classifier is a potential state-of-the-art computational method. The correlation-based ensemble RS-FLD classifier was effective and benefited from gene-gene correlations, particularly when the correlations were high.
{"title":"Correlation-based linear discriminant classification for gene expression data.","authors":"M. Pan, J. Zhang","doi":"10.4238/gmr16019357","DOIUrl":"https://doi.org/10.4238/gmr16019357","url":null,"abstract":"Microarray gene expression technology provides a systematic approach to patient classification. However, microarray data pose a great computational challenge owing to their large dimensionality, small sample sizes, and potential correlations among genes. A recent study has shown that gene-gene correlations have a positive effect on the accuracy of classification models, in contrast to some previous results. In this study, a recently developed correlation-based classifier, the ensemble of random subspace (RS) Fisher linear discriminants (FLDs), was utilized. The impact of gene-gene correlations on the performance of this classifier and other classifiers was studied using simulated datasets and real datasets. A cross-validation framework was used to evaluate the performance of each classifier using the simulated datasets or real datasets, and misclassification rates (MRs) were computed. Using the simulated data, the average MRs of the correlation-based classifiers decreased as the correlations increased when there were more correlated genes. Using real data, the correlation-based classifiers outperformed the non-correlation-based classifiers, especially when the gene-gene correlations were high. The ensemble RS-FLD classifier is a potential state-of-the-art computational method. The correlation-based ensemble RS-FLD classifier was effective and benefited from gene-gene correlations, particularly when the correlations were high.","PeriodicalId":189314,"journal":{"name":"Genetics and molecular research : GMR","volume":"153 1-4","pages":"0"},"PeriodicalIF":0.0,"publicationDate":"2017-01-23","publicationTypes":"Journal Article","fieldsOfStudy":null,"isOpenAccess":false,"openAccessPdf":"","citationCount":null,"resultStr":null,"platform":"Semanticscholar","paperid":"120928572","PeriodicalName":null,"FirstCategoryId":null,"ListUrlMain":null,"RegionNum":0,"RegionCategory":"","ArticlePicture":[],"TitleCN":null,"AbstractTextCN":null,"PMCID":"","EPubDate":null,"PubModel":null,"JCR":null,"JCRName":null,"Score":null,"Total":0}
This study aimed to evaluate the clinical significance of diffusion tensor imaging (DTI) in the early diagnosis of pyramidal tract Wallerian degeneration (WD) and assessment of neurological recovery following cerebral infarction. This study included 23 patients with acute cerebral infarction and 10 healthy adult controls. All participants underwent both magnetic resonance imaging (MRI) and DTI scans. DTI images were analyzed using the Functional MRI of the Brain Software Library to determine the regions of interest (ROI) and obtain the mean diffusivity (MD) and fractional anisotropy (FA) value for each ROI. The correlation between FA or MD and postinfarction functional recovery of the nervous system was further analyzed to assess the feasibility of using a DTI scan in the evaluation of functional recovery of the nervous system in patients with cerebral infarction. DTI may be useful in detecting signals of early postinfarction pyramidal tract WD and is useful for the evaluation of postinfarction neurological recovery. Cerebral lesions were detected using MRI in all patients. It was found that in some patients, the FA value of the ipsilateral pyramidal tract on DTI was decreased as early as day 3 after the onset of infarction and in all patients by day 7. Subsequent correlation studies showed that the FA value of the ipsilateral pyramidal tract on day 13 was negatively correlated with the National Institutes of Health Stroke Scale score, but positively correlated with the Barthel Index, motricity index, and modified Rankin Scale scores.
{"title":"An assessment of the correlation between early postinfarction pyramidal tract Wallerian degeneration and nerve function recovery using diffusion tensor imaging.","authors":"A. Guo, F. Hao, L. Liu, B. Wang, X. Jiang","doi":"10.4238/gmr16019035","DOIUrl":"https://doi.org/10.4238/gmr16019035","url":null,"abstract":"This study aimed to evaluate the clinical significance of diffusion tensor imaging (DTI) in the early diagnosis of pyramidal tract Wallerian degeneration (WD) and assessment of neurological recovery following cerebral infarction. This study included 23 patients with acute cerebral infarction and 10 healthy adult controls. All participants underwent both magnetic resonance imaging (MRI) and DTI scans. DTI images were analyzed using the Functional MRI of the Brain Software Library to determine the regions of interest (ROI) and obtain the mean diffusivity (MD) and fractional anisotropy (FA) value for each ROI. The correlation between FA or MD and postinfarction functional recovery of the nervous system was further analyzed to assess the feasibility of using a DTI scan in the evaluation of functional recovery of the nervous system in patients with cerebral infarction. DTI may be useful in detecting signals of early postinfarction pyramidal tract WD and is useful for the evaluation of postinfarction neurological recovery. Cerebral lesions were detected using MRI in all patients. It was found that in some patients, the FA value of the ipsilateral pyramidal tract on DTI was decreased as early as day 3 after the onset of infarction and in all patients by day 7. Subsequent correlation studies showed that the FA value of the ipsilateral pyramidal tract on day 13 was negatively correlated with the National Institutes of Health Stroke Scale score, but positively correlated with the Barthel Index, motricity index, and modified Rankin Scale scores.","PeriodicalId":189314,"journal":{"name":"Genetics and molecular research : GMR","volume":"17 1","pages":"0"},"PeriodicalIF":0.0,"publicationDate":"2017-01-23","publicationTypes":"Journal Article","fieldsOfStudy":null,"isOpenAccess":false,"openAccessPdf":"","citationCount":null,"resultStr":null,"platform":"Semanticscholar","paperid":"131989996","PeriodicalName":null,"FirstCategoryId":null,"ListUrlMain":null,"RegionNum":0,"RegionCategory":"","ArticlePicture":[],"TitleCN":null,"AbstractTextCN":null,"PMCID":"","EPubDate":null,"PubModel":null,"JCR":null,"JCRName":null,"Score":null,"Total":0}
F. L. Araujo, Marcos Vinicius B M Siqueira, C. Grando, João Paulo Gomes Viana, J. B. Pinheiro, A. Alves-Pereira, J. B. Campos, P. Brancalion, M. Zucchi
Guaçatonga (Casearia sylvestris) is a native plant of the Atlantic Forest, with high medicinal potential and relevance for reforestation programs. The aim of this study was to characterize, with microsatellite markers, two populations of C. sylvestris from remaining areas of the Atlantic Forest in the State of São Paulo. High allelic variation was found in both populations (NA = 101 and 117; AR = 12.5 and 14.4), although with high endogamy coefficients (f = 0.640 and 0.363). Estimates of genetic structure suggested the presence of considerable genetic divergence between the populations (FST = 0.103); however, there was no spatial genetic structure within the populations. Genetic divergence may have occurred due to decreased gene flow between the fragmented populations as the result of deforestation. The results of this study demonstrate the importance of genetic diversity and its characterization in native plants within remaining forest areas for the management and restoration of such areas.
{"title":"Genetic diversity of Casearia sylvestris populations in remnants of the Atlantic Forest.","authors":"F. L. Araujo, Marcos Vinicius B M Siqueira, C. Grando, João Paulo Gomes Viana, J. B. Pinheiro, A. Alves-Pereira, J. B. Campos, P. Brancalion, M. Zucchi","doi":"10.4238/gmr16019105","DOIUrl":"https://doi.org/10.4238/gmr16019105","url":null,"abstract":"Guaçatonga (Casearia sylvestris) is a native plant of the Atlantic Forest, with high medicinal potential and relevance for reforestation programs. The aim of this study was to characterize, with microsatellite markers, two populations of C. sylvestris from remaining areas of the Atlantic Forest in the State of São Paulo. High allelic variation was found in both populations (NA = 101 and 117; AR = 12.5 and 14.4), although with high endogamy coefficients (f = 0.640 and 0.363). Estimates of genetic structure suggested the presence of considerable genetic divergence between the populations (FST = 0.103); however, there was no spatial genetic structure within the populations. Genetic divergence may have occurred due to decreased gene flow between the fragmented populations as the result of deforestation. The results of this study demonstrate the importance of genetic diversity and its characterization in native plants within remaining forest areas for the management and restoration of such areas.","PeriodicalId":189314,"journal":{"name":"Genetics and molecular research : GMR","volume":"167 1","pages":"0"},"PeriodicalIF":0.0,"publicationDate":"2017-01-23","publicationTypes":"Journal Article","fieldsOfStudy":null,"isOpenAccess":false,"openAccessPdf":"","citationCount":null,"resultStr":null,"platform":"Semanticscholar","paperid":"122624462","PeriodicalName":null,"FirstCategoryId":null,"ListUrlMain":null,"RegionNum":0,"RegionCategory":"","ArticlePicture":[],"TitleCN":null,"AbstractTextCN":null,"PMCID":"","EPubDate":null,"PubModel":null,"JCR":null,"JCRName":null,"Score":null,"Total":0}
M. A. Rosales-Reynoso, L. Wence-Chávez, A. R. Arredondo-Valdez, S. Dumois-Petersen, Patricio Barros-Núñez, M. Gallegos-Arreola, S. Flores-Martínez, José Sánchez-Corona
PPARD encodes for peroxisome proliferator-activated receptor delta, which plays a significant role in controlling lipid metabolism, atherosclerosis, inflammation, cancer growth, progression, and apoptosis. Accumulated evidence suggests that the polymorphism rs2016520 in PPARD is associated with lipid metabolism, obesity, metabolic syndrome, and type 2 diabetes mellitus. The aim of this study was to determine whether the single nucleotide polymorphism +294T/C (rs2016520) in PPARD is associated with colorectal cancer (CRC) in the Mexican population. Genomic DNA from 178 CRC patients and 97 healthy blood donors was analyzed. The polymorphism was identified by the polymerase chain reaction-restriction fragment length polymorphism method. Results demonstrated that patients with the T/C genotype for the +294T/C (rs2016520) polymorphism present a protective role against CRC [odds ratio (OR) = 0.39; 95% confidence interval (CI) = 0.22-0.69; P = 0.0008]. This association was also evident for the T/C genotype in the stratified analysis by tumor-node-metastasis stages I+II (OR = 0.26, P = 0.0332) and III+IV (OR = 0.44, P = 0.0067). However, in the stratified analysis by tumor location, we observed an increased risk of rectal cancer (OR = 7.57, P = 0.0403) vs colon cancer (OR = 4.87, P = 0.234) in patients carrying the C/C genotype and under the dominant and recessive models of inheritance. In conclusion, for the first time, the association between the +294T/C (rs2016520) polymorphism and colorectal cancer has been studied in Mexican patients. Our results reveal that variations in PPARD may play a significant role in genetic susceptibility to colorectal cancer.
PPARD编码过氧化物酶体增殖物激活受体，在控制脂质代谢、动脉粥样硬化、炎症、癌症生长、进展和细胞凋亡中起重要作用。越来越多的证据表明PPARD中rs2016520多态性与脂质代谢、肥胖、代谢综合征和2型糖尿病有关。本研究的目的是确定PPARD中单核苷酸多态性+294T/C (rs2016520)是否与墨西哥人群的结直肠癌(CRC)相关。分析了178例结直肠癌患者和97名健康献血者的基因组DNA。采用聚合酶链反应-限制性片段长度多态性法鉴定其多态性。结果表明，T/C基因型+294T/C (rs2016520)多态性的患者对CRC具有保护作用[优势比(OR) = 0.39;95%置信区间(CI) = 0.22-0.69;P = 0.0008]。在肿瘤淋巴结转移分期I+II (OR = 0.26, P = 0.0332)和III+IV (OR = 0.44, P = 0.0067)的分层分析中，T/C基因型的相关性也很明显。然而，在肿瘤位置分层分析中，我们观察到携带C/C基因型的患者在显性和隐性遗传模式下患直肠癌的风险(OR = 7.57, P = 0.0403)高于结肠癌(OR = 4.87, P = 0.234)。总之，我们首次在墨西哥患者中研究了+294T/C (rs2016520)多态性与结直肠癌之间的关系。我们的研究结果表明PPARD的变异可能在结直肠癌的遗传易感性中起重要作用。
{"title":"Protective role of +294 T/C (rs2016520) polymorphism of PPARD in Mexican patients with colorectal cancer.","authors":"M. A. Rosales-Reynoso, L. Wence-Chávez, A. R. Arredondo-Valdez, S. Dumois-Petersen, Patricio Barros-Núñez, M. Gallegos-Arreola, S. Flores-Martínez, José Sánchez-Corona","doi":"10.4238/gmr16019324","DOIUrl":"https://doi.org/10.4238/gmr16019324","url":null,"abstract":"PPARD encodes for peroxisome proliferator-activated receptor delta, which plays a significant role in controlling lipid metabolism, atherosclerosis, inflammation, cancer growth, progression, and apoptosis. Accumulated evidence suggests that the polymorphism rs2016520 in PPARD is associated with lipid metabolism, obesity, metabolic syndrome, and type 2 diabetes mellitus. The aim of this study was to determine whether the single nucleotide polymorphism +294T/C (rs2016520) in PPARD is associated with colorectal cancer (CRC) in the Mexican population. Genomic DNA from 178 CRC patients and 97 healthy blood donors was analyzed. The polymorphism was identified by the polymerase chain reaction-restriction fragment length polymorphism method. Results demonstrated that patients with the T/C genotype for the +294T/C (rs2016520) polymorphism present a protective role against CRC [odds ratio (OR) = 0.39; 95% confidence interval (CI) = 0.22-0.69; P = 0.0008]. This association was also evident for the T/C genotype in the stratified analysis by tumor-node-metastasis stages I+II (OR = 0.26, P = 0.0332) and III+IV (OR = 0.44, P = 0.0067). However, in the stratified analysis by tumor location, we observed an increased risk of rectal cancer (OR = 7.57, P = 0.0403) vs colon cancer (OR = 4.87, P = 0.234) in patients carrying the C/C genotype and under the dominant and recessive models of inheritance. In conclusion, for the first time, the association between the +294T/C (rs2016520) polymorphism and colorectal cancer has been studied in Mexican patients. Our results reveal that variations in PPARD may play a significant role in genetic susceptibility to colorectal cancer.","PeriodicalId":189314,"journal":{"name":"Genetics and molecular research : GMR","volume":"33 1","pages":"0"},"PeriodicalIF":0.0,"publicationDate":"2017-01-23","publicationTypes":"Journal Article","fieldsOfStudy":null,"isOpenAccess":false,"openAccessPdf":"","citationCount":null,"resultStr":null,"platform":"Semanticscholar","paperid":"128110977","PeriodicalName":null,"FirstCategoryId":null,"ListUrlMain":null,"RegionNum":0,"RegionCategory":"","ArticlePicture":[],"TitleCN":null,"AbstractTextCN":null,"PMCID":"","EPubDate":null,"PubModel":null,"JCR":null,"JCRName":null,"Score":null,"Total":0}
D. Song, X. Xiong, W. Tu, W. Yao, H. Liang, F. J. Chen, Z. He
Lettuce (Lactuca sativa L.) is an annual plant of the daisy family, Asteraceae, with high food and medicinal value. However, the crop is susceptible to several viruses that are transmitted by aphids and is highly vulnerable to post-harvest diseases, as well as insect and mammal pests and fungal and bacterial diseases. Here, the rabbit defensin gene NP-1 was transferred into lettuce by Agrobacterium-mediated transformation to obtain a broad-spectrum disease-resistant lettuce. Transgenic lettuce plants were selected and regenerated on selective media. The presence of the NP-1 gene in these plants was confirmed by western blot analyses. Resistance tests revealed native defensin NP-1 expression conferred partial resistance to Bacillus subtilis and Pseudomonas aeruginosa, which suggests new possibilities for lettuce disease resistance.
{"title":"Transfer and expression of the rabbit defensin NP-1 gene in lettuce (Lactuca sativa).","authors":"D. Song, X. Xiong, W. Tu, W. Yao, H. Liang, F. J. Chen, Z. He","doi":"10.4238/gmr16019333","DOIUrl":"https://doi.org/10.4238/gmr16019333","url":null,"abstract":"Lettuce (Lactuca sativa L.) is an annual plant of the daisy family, Asteraceae, with high food and medicinal value. However, the crop is susceptible to several viruses that are transmitted by aphids and is highly vulnerable to post-harvest diseases, as well as insect and mammal pests and fungal and bacterial diseases. Here, the rabbit defensin gene NP-1 was transferred into lettuce by Agrobacterium-mediated transformation to obtain a broad-spectrum disease-resistant lettuce. Transgenic lettuce plants were selected and regenerated on selective media. The presence of the NP-1 gene in these plants was confirmed by western blot analyses. Resistance tests revealed native defensin NP-1 expression conferred partial resistance to Bacillus subtilis and Pseudomonas aeruginosa, which suggests new possibilities for lettuce disease resistance.","PeriodicalId":189314,"journal":{"name":"Genetics and molecular research : GMR","volume":"18 1","pages":"0"},"PeriodicalIF":0.0,"publicationDate":"2017-01-23","publicationTypes":"Journal Article","fieldsOfStudy":null,"isOpenAccess":false,"openAccessPdf":"","citationCount":null,"resultStr":null,"platform":"Semanticscholar","paperid":"133652132","PeriodicalName":null,"FirstCategoryId":null,"ListUrlMain":null,"RegionNum":0,"RegionCategory":"","ArticlePicture":[],"TitleCN":null,"AbstractTextCN":null,"PMCID":"","EPubDate":null,"PubModel":null,"JCR":null,"JCRName":null,"Score":null,"Total":0}
L. Rocha, G. A. Silva, F. O. Bustamante, R. A. D. Silveira, A. Mittlemann, V. H. Techio
Analyses carried out with fluorescence in situ hybridization (FISH) in C-metaphases of the Lolium-Festuca complex have shown the occurrence of spontaneous fragile sites (FSs) in 45S rDNA regions. FSs are expressed as gaps but they do not result in breaks or chromosomal fragments in these species. These gaps have high DNA condensation observed as thin chromatin fibers that connect the apparent segments of the fragile chromosome, allowing for genomic stability. Assessing the behavior of these regions in the cell cycle of Lolium and Festuca species may lead to a better understanding of the dynamics that preserve stability during cell division. Furthermore, it is interesting to track the dynamics of chromosomes bearing 45S rDNA sites in the cell cycle as well as to observe the expression of FSs with no effect of the mitotic block. We observed variation in both the number and size of 45S FISH signals from the S/G2 phases of interphase and from prophase to anaphase where gaps in 45S rDNA sites also were observed. The change in the degree of condensation of the 45S site begins in the S/G2 phase and appears to be related to the transcriptional demand. Taking into account that the number of 45S rDNA sites tends to be re-established when cells reach telophase, we suggest that the chromatin fiber goes back to the normal condensation level to the anaphase (after segregation), allowing for the approximation of chromosome segments and ensuring dynamics that favor the genomic stability of these species.
{"title":"Dynamics of 45S rDNA sites in the cell cycle: fragile sites and chromosomal stability in Lolium and Festuca.","authors":"L. Rocha, G. A. Silva, F. O. Bustamante, R. A. D. Silveira, A. Mittlemann, V. H. Techio","doi":"10.4238/gmr16019156","DOIUrl":"https://doi.org/10.4238/gmr16019156","url":null,"abstract":"Analyses carried out with fluorescence in situ hybridization (FISH) in C-metaphases of the Lolium-Festuca complex have shown the occurrence of spontaneous fragile sites (FSs) in 45S rDNA regions. FSs are expressed as gaps but they do not result in breaks or chromosomal fragments in these species. These gaps have high DNA condensation observed as thin chromatin fibers that connect the apparent segments of the fragile chromosome, allowing for genomic stability. Assessing the behavior of these regions in the cell cycle of Lolium and Festuca species may lead to a better understanding of the dynamics that preserve stability during cell division. Furthermore, it is interesting to track the dynamics of chromosomes bearing 45S rDNA sites in the cell cycle as well as to observe the expression of FSs with no effect of the mitotic block. We observed variation in both the number and size of 45S FISH signals from the S/G2 phases of interphase and from prophase to anaphase where gaps in 45S rDNA sites also were observed. The change in the degree of condensation of the 45S site begins in the S/G2 phase and appears to be related to the transcriptional demand. Taking into account that the number of 45S rDNA sites tends to be re-established when cells reach telophase, we suggest that the chromatin fiber goes back to the normal condensation level to the anaphase (after segregation), allowing for the approximation of chromosome segments and ensuring dynamics that favor the genomic stability of these species.","PeriodicalId":189314,"journal":{"name":"Genetics and molecular research : GMR","volume":"22 1","pages":"0"},"PeriodicalIF":0.0,"publicationDate":"2017-01-23","publicationTypes":"Journal Article","fieldsOfStudy":null,"isOpenAccess":false,"openAccessPdf":"","citationCount":null,"resultStr":null,"platform":"Semanticscholar","paperid":"129914768","PeriodicalName":null,"FirstCategoryId":null,"ListUrlMain":null,"RegionNum":0,"RegionCategory":"","ArticlePicture":[],"TitleCN":null,"AbstractTextCN":null,"PMCID":"","EPubDate":null,"PubModel":null,"JCR":null,"JCRName":null,"Score":null,"Total":0}
The objective of this study was to investigate the effect of downregulating long non-coding RNAs (lncRNAs) on the reversal of cisplatin resistance in CP70 ovarian cancer cells, and to identify the underlying mechanism(s) of action. An lncRNA microarray was performed to screen for downregulated lncRNAs in cisplatin-resistant CP70 cells. Expression levels of these lncRNAs were then verified in SKOV3 and SKOV3/DDP cells. Quantitative polymerase chain reaction was conducted to identify the lncRNA most downregulated, which was then synthesized and transfected into CP70 cells. To assess the viability and migration ability of these transfected CP70 cells, methyl thiazolyl tetrazolium and Transwell assays were carried out. In addition, expression levels of apoptosis-related proteins were examined by western blotting. The lncRNA microarray analysis and qPCR identified seven lncRNAs that were significantly downregulated. Transfection of lncRNA ENST00000457645 into CP70 cells markedly inhibited viability and migration ability, and significantly increased expression of apoptotic proteins such as Bax and cleaved caspase-3. lncRNA ENST00000457645 negatively affects the viability and migration of cisplatin-resistant CP70 ovarian cancer cells. The mechanism responsible involves modification of apoptotic protein expression.
{"title":"Long non-coding RNA ENST00000457645 reverses cisplatin resistance in CP70 ovarian cancer cells.","authors":"H. Yan, J. Xia, F. Feng","doi":"10.4238/gmr16019411","DOIUrl":"https://doi.org/10.4238/gmr16019411","url":null,"abstract":"The objective of this study was to investigate the effect of downregulating long non-coding RNAs (lncRNAs) on the reversal of cisplatin resistance in CP70 ovarian cancer cells, and to identify the underlying mechanism(s) of action. An lncRNA microarray was performed to screen for downregulated lncRNAs in cisplatin-resistant CP70 cells. Expression levels of these lncRNAs were then verified in SKOV3 and SKOV3/DDP cells. Quantitative polymerase chain reaction was conducted to identify the lncRNA most downregulated, which was then synthesized and transfected into CP70 cells. To assess the viability and migration ability of these transfected CP70 cells, methyl thiazolyl tetrazolium and Transwell assays were carried out. In addition, expression levels of apoptosis-related proteins were examined by western blotting. The lncRNA microarray analysis and qPCR identified seven lncRNAs that were significantly downregulated. Transfection of lncRNA ENST00000457645 into CP70 cells markedly inhibited viability and migration ability, and significantly increased expression of apoptotic proteins such as Bax and cleaved caspase-3. lncRNA ENST00000457645 negatively affects the viability and migration of cisplatin-resistant CP70 ovarian cancer cells. The mechanism responsible involves modification of apoptotic protein expression.","PeriodicalId":189314,"journal":{"name":"Genetics and molecular research : GMR","volume":"63 1","pages":"0"},"PeriodicalIF":0.0,"publicationDate":"2017-01-23","publicationTypes":"Journal Article","fieldsOfStudy":null,"isOpenAccess":false,"openAccessPdf":"","citationCount":null,"resultStr":null,"platform":"Semanticscholar","paperid":"130498766","PeriodicalName":null,"FirstCategoryId":null,"ListUrlMain":null,"RegionNum":0,"RegionCategory":"","ArticlePicture":[],"TitleCN":null,"AbstractTextCN":null,"PMCID":"","EPubDate":null,"PubModel":null,"JCR":null,"JCRName":null,"Score":null,"Total":0}
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