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53. Role of duplicate genes in genetic robustness against null mutations

Author

Gu, Zhenglong, Steinmetz, Lars M., Gu, Xun, Scharfe, Curt, Davis, Ronald W., and Li, Wen-Hsiung

Subjects
Environmental issues, Science and technology, Zoology and wildlife conservation
Abstract

Author(s): Zhenglong Gu [1, 2]; Lars M. Steinmetz [3, 2]; Xun Gu [4]; Curt Scharfe [3]; Ronald W. Davis [3]; Wen-Hsiung Li (corresponding author) [1] Deleting a gene in an [...]

Published
2003
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56. Spatial heterogeneity of glioblastoma cells reveals sensitivity to NAD+ depletion at tumor edge

Author

Yamashita, Daisuke, primary, Botta, Davide, additional, Cho, Hee Jin, additional, Guo, Xiaoxian, additional, Ozaki, Saya, additional, Flanary, Victoria L, additional, Sirota, Inna, additional, Gao, Mu, additional, Yamaguchi, Shinobu, additional, Nakano, Mayu A, additional, Zhou, Fen, additional, Zhou, Hongyi, additional, Kondo, Toru, additional, Kunieda, Takeharu, additional, Crossman, David K, additional, Kornblum, Harley I, additional, Gorospe, Myriam, additional, Nam, Do-Hyun, additional, Zamboni, Nicola, additional, Skolnick, Jeffrey, additional, Gu, Zhenglong, additional, Lund, Frances E, additional, and Nakano, Ichiro, additional

Published
2020
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60. Aberrant gut microbiota alters host metabolome and impacts renal failure in humans and rodents

Author

Wang, Xifan, primary, Yang, Songtao, additional, Li, Shenghui, additional, Zhao, Liang, additional, Hao, Yanling, additional, Qin, Junjie, additional, Zhang, Lian, additional, Zhang, Chengying, additional, Bian, Weijing, additional, Zuo, Li, additional, Gao, Xiu, additional, Zhu, Baoli, additional, Lei, Xin Gen, additional, Gu, Zhenglong, additional, Cui, Wei, additional, Xu, Xiping, additional, Li, Zhiming, additional, Zhu, Benzhong, additional, Li, Yuan, additional, Chen, Shangwu, additional, Guo, Huiyuan, additional, Zhang, Hao, additional, Sun, Jing, additional, Zhang, Ming, additional, Hui, Yan, additional, Zhang, Xiaolin, additional, Liu, Xiaoxue, additional, Sun, Bowen, additional, Wang, Longjiao, additional, Qiu, Qinglu, additional, Zhang, Yuchan, additional, Li, Xingqi, additional, Liu, Weiqian, additional, Xue, Rui, additional, Wu, Hong, additional, Shao, DongHua, additional, Li, Junling, additional, Zhou, Yuanjie, additional, Li, Shaochuan, additional, Yang, Rentao, additional, Pedersen, Oluf Borbye, additional, Yu, Zhengquan, additional, Ehrlich, Stanislav Dusko, additional, and Ren, Fazheng, additional

Published
2020
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65. Associations of Mitochondrial and Nuclear Mitochondrial Variants and Genes with Seven Metabolic Traits

Author

Kraja, Aldi T, Liu, Chunyu, Fetterman, Jessica L, Graff, Mariaelisa, Have, Christian Theil, Gu, Charles, Yanek, Lisa R, Feitosa, Mary F, Arking, Dan E, Chasman, Daniel I, Young, Kristin, Ligthart, Symen, Hill, W David, Weiss, Stefan, Luan, Jian'an, Giulianini, Franco, Li-Gao, Ruifang, Hartwig, Fernando P, Lin, Shiow J, Wang, Lihua, Richardson, Tom G, Yao, Jie, Fernandez, Eliana P, Ghanbari, Mohsen, Wojczynski, Mary K, Lee, Wen-Jane, Argos, Maria, Armasu, Sebastian M, Barve, Ruteja A, Ryan, Kathleen A, An, Ping, Baranski, Thomas J, Bielinski, Suzette J, Bowden, Donald W, Broeckel, Ulrich, Christensen, Kaare, Chu, Audrey Y, Corley, Janie, Cox, Simon R, Uitterlinden, Andre G, Rivadeneira, Fernando, Cropp, Cheryl D, Daw, E Warwick, Van Heemst, Diana, De Las Fuentes, Lisa, Gao, He, Tzoulaki, Ioanna, Ahluwalia, Tarunveer S, De Mutsert, Renée, Emery, Leslie S, Erzurumluoglu, A Mesut, Perry, James A, Fu, Mao, Forouhi, Nita G, Gu, Zhenglong, Hai, Yang, Harris, Sarah E, Hemani, Gibran, Hunt, Steven C, Irvin, Marguerite R, Jonsson, Anna E, Justice, Anne E, Kerrison, Nicola D, Larson, Nicholas B, Lin, Keng-Hung, Love-Gregory, Latisha D, Mathias, Rasika A, Lee, Joseph H, Nauck, Matthias, Noordam, Raymond, Ong, Ken K, Pankow, James, Patki, Amit, Pattie, Alison, Petersmann, Astrid, Qi, Qibin, Ribel-Madsen, Rasmus, Rohde, Rebecca, Sandow, Kevin, Schnurr, Theresia M, Sofer, Tamar, Starr, John M, Taylor, Adele M, Teumer, Alexander, Timpson, Nicholas J, De Haan, Hugoline G, Wang, Yujie, Weeke, Peter E, Williams, Christine, Wu, Hongsheng, Yang, Wei, Zeng, Donglin, Witte, Daniel R, Weir, Bruce S, Wareham, Nicholas J, Vestergaard, Henrik, Turner, Stephen T, Torp-Pedersen, Christian, Stergiakouli, Evie, Sheu, Wayne Huey-Herng, Rosendaal, Frits R, Ikram, M Arfan, Franco, Oscar H, Ridker, Paul M, Perls, Thomas T, Pedersen, Oluf, Nohr, Ellen A, Newman, Anne B, Linneberg, Allan, Langenberg, Claudia, Kilpeläinen, Tuomas O, Kardia, Sharon LR, Jørgensen, Marit E, Jørgensen, Torben, Sørensen, Thorkild IA, Homuth, Georg, Hansen, Torben, Goodarzi, Mark O, Deary, Ian J, Christensen, Cramer, Chen, Yii-Der Ida, Chakravarti, Aravinda, Brandslund, Ivan, Bonnelykke, Klaus, Taylor, Kent D, Wilson, James G, Rodriguez, Santiago, Davies, Gail, Horta, Bernardo L, Thyagarajan, Bharat, Rao, DC, Grarup, Niels, Davila-Roman, Victor G, Hudson, Gavin, Guo, Xiuqing, Arnett, Donna K, Hayward, Caroline, Vaidya, Dhananjay, Mook-Kanamori, Dennis O, Tiwari, Hemant K, Levy, Daniel, Loos, Ruth JF, Dehghan, Abbas, Elliott, Paul, Malik, Afshan N, Scott, Robert A, Becker, Diane M, De Andrade, Mariza, Province, Michael A, Meigs, James B, Rotter, Jerome I, North, Kari E, Epidemiology, Internal Medicine, Gastroenterology & Hepatology, Home Office, Medical Research Council (MRC), National Institute for Health Research, Imperial College Healthcare NHS Trust- BRC Funding, UK DRI Ltd, Luan, Jian'an [0000-0003-3137-6337], Erzurumluoglu, Mesut [0000-0003-1322-8138], Forouhi, Nita [0000-0002-5041-248X], Ong, Kenneth [0000-0003-4689-7530], Wareham, Nicholas [0000-0003-1422-2993], Langenberg, Claudia [0000-0002-5017-7344], and Apollo - University of Cambridge Repository

Subjects
insulin, HbA1c, MT-nDNA candidate genes, SUSCEPTIBILITY LOCI, Quantitative Trait Loci, 610 Medicine & health, ATHEROSCLEROSIS RISK, waist-to-hip ratio, PERIPHERAL-BLOOD, DNA, Mitochondrial, Article, HOMA-IR, Body Mass Index, Cohort Studies, BMI, 360 Social problems & social services, Adipocytes, Diabetes Mellitus, GLYCEMIC TRAITS, Humans, INDIVIDUALS REVEAL, GENOME-WIDE ASSOCIATION, glucose, Glycated Hemoglobin, Genetics & Heredity, Science & Technology, Waist-Hip Ratio, mtDNA, Genetic Variation, COMMON VARIANTS, HOMA-B, 11 Medical And Health Sciences, DNA COPY NUMBER, 06 Biological Sciences, BODY-MASS INDEX, mitochondria, Genes, Mitochondrial, Metabolism, ADIPOSE-TISSUE, Cardiovascular Diseases, Life Sciences & Biomedicine
Abstract

Mitochondria (MT), the major site of cellular energy production, are under dual genetic control by 37 mitochondrial DNA (mtDNA) genes and numerous nuclear genes (MT-nDNA). In the CHARGEmtDNA+ Consortium, we studied genetic associations of mtDNA and MT-nDNA associations with body mass index (BMI), waist-hip-ratio (WHR), glucose, insulin, HOMA-B, HOMA-IR, and HbA1c. This 45-cohort collaboration comprised 70,775 (insulin) to 170,202 (BMI) pan-ancestry individuals. Validation and imputation of mtDNA variants was followed by single-variant and gene-based association testing. We report two significant common variants, one in MT-ATP6 associated (p ≤ 5E-04) with WHR and one in the D-loop with glucose. Five rare variants in MT-ATP6, MT-ND5, and MT-ND6 associated with BMI, WHR, or insulin. Gene-based meta-analysis identified MT-ND3 associated with BMI (p ≤ 1E-03). We considered 2,282 MT-nDNA candidate gene associations compiled from online summary results for our traits (20 unique studies with 31 dataset consortia's genome-wide associations [GWASs]). Of these, 109 genes associated (p ≤ 1E-06) with at least 1 of our 7 traits. We assessed regulatory features of variants in the 109 genes, cis- and trans-gene expression regulation, and performed enrichment and protein-protein interactions analyses. Of the identified mtDNA and MT-nDNA genes, 79 associated with adipose measures, 49 with glucose/insulin, 13 with risk for type 2 diabetes, and 18 with cardiovascular disease, indicating for pleiotropic effects with health implications. Additionally, 21 genes related to cholesterol, suggesting additional important roles for the genes identified. Our results suggest that mtDNA and MT-nDNA genes and variants reported make important contributions to glucose and insulin metabolism, adipocyte regulation, diabetes, and cardiovascular disease.

Published
2019

68. Assembly and Analysis of the Genome Sequence of the Yeast Brettanomyces naardenensis CBS 7540

Author

Tiukova, Ievgeniia A., Jiang, Huifeng, Dainat, Jacques, Hoeppner, Marc P., Lantz, Henrik, Piskur, Jure, Sandgren, Mats, Nielsen, Jens, Gu, Zhenglong, Passoth, Volkmar, Tiukova, Ievgeniia A., Jiang, Huifeng, Dainat, Jacques, Hoeppner, Marc P., Lantz, Henrik, Piskur, Jure, Sandgren, Mats, Nielsen, Jens, Gu, Zhenglong, and Passoth, Volkmar

Abstract

Brettanomyces naardenensis is a spoilage yeast with potential for biotechnological applications for production of innovative beverages with low alcohol content and high attenuation degree. Here, we present the first annotated genome of B. naardenensis CBS 7540. The genome of B. naardenensis CBS 7540 was assembled into 76 contigs, totaling 11,283,072 nucleotides. In total, 5168 protein-coding sequences were annotated. The study provides functional genome annotation, phylogenetic analysis, and discusses genetic determinants behind notable stress tolerance and biotechnological potential of B. naardenensis.

Published
2019
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69. Associations of Mitochondrial and Nuclear Mitochondrial Variants and Genes with Seven Metabolic Traits

Author

Kraja, Aldi T., Liu, Chunyu, Fetterman, Jessica L., Graff, Mariaelisa, Have, Christian Theil, Gu, Charles, Yanek, Lisa R., Feitosa, Mary F., Arking, Dan E., Chasman, Daniel, I, Young, Kristin, Ligthart, Symen, Hill, W. David, Weiss, Stefan, Luan, Jian'an, Giulianini, Franco, Li-Gao, Ruifang, Hartwig, Fernando P., Lin, Shiow J., Wang, Lihua, Richardson, Tom G., Yao, Jie, Fernandez, Eliana P., Ghanbari, Mohsen, Wojczynski, Mary K., Lee, Wen-Jane, Argos, Maria, Armasu, Sebastian M., Barve, Ruteja A., Ryan, Kathleen A., An, Ping, Baranski, Thomas J., Bielinski, Suzette J., Bowden, Donald W., Broeckel, Ulrich, Christensen, Kaare, Chu, Audrey Y., Corley, Janie, Cox, Simon R., Uitterlinden, Andre G., Rivadeneira, Fernando, Cropp, Cheryl D., Daw, E. Warwick, van Heemst, Diana, de las Fuentes, Lisa, Gao, He, Tzoulaki, Ioanna, Ahluwalia, Tarunveer S., de Mutsert, Renee, Emery, Leslie S., Erzurumluoglu, A. Mesut, Perry, James A., Fu, Mao, Forouhi, Nita G., Gu, Zhenglong, Hai, Yang, Harris, Sarah E., Hemani, Gibran, Hunt, Steven C., Irvin, Marguerite R., Jonsson, Anna E., Justice, Anne E., Kernson, Nicola D., Larson, Nicholas B., Lin, Keng-Hung, Love-Gregory, Latisha D., Mathias, Rasika A., Lee, Joseph H., Nauck, Matthias, Noordam, Raymond, Ong, Ken K., Pankow, James, Patki, Amit, Pattie, Alison, Petersmann, Astrid, Qi, Qibin, Ribel-Madsen, Rasmus, Rohde, Rebecca, Sandow, Kevin, Schnurr, Theresia M., Sofer, Tamar, Starr, John M., Taylor, Adele M., Teumer, Alexander, Timpson, Nicholas J., de Haan, Hugoline G., Wang, Yujie, Weeke, Peter E., Williams, Christine, Wu, Hongsheng, Yang, Wei, Zeng, Donglin, Witte, Daniel R., Weir, Bruce S., Wareham, Nicholas J., Vestergaard, Henrik, Turner, Stephen T., Torp-Pedersen, Christian, Stergiakouli, Evie, Sheu, Wayne Huey-Hemg, Rosendaal, Frits R., Ikram, M. Arfan, Franco, Oscar H., Ridker, Paul M., Perls, Thomas T., Pedersen, Oluf, Nohr, Ellen A., Newman, Anne B., Linneberg, Allan, Langenberg, Claudia, Kilpelainen, Tuomas O., Kardia, Sharon L. R., Jørgensen, Marit E., Jørgensen, Torben, Sorensen, Thorkild I. A., Homuth, Georg, Hansen, Torben, Goodarzi, Mark O., Deary, Ian J., Christensen, Cramer, Chen, Yii-Der Ida, Chakravarti, Aravinda, Brandslund, Ivan, Bonnelykke, Klaus, Taylor, Kent D., Wilson, James G., Rodriguez, Santiago, Davies, Gail, Horta, Bernardo L., Thyagarajan, Bharat, Rao, D. C., Grarup, Niels, Davila-Roman, Victor G., Hudson, Gavin, Guo, Xiuqing, Arnett, Donna K., Hayward, Caroline, Vaidya, Dhananjay, Mook-Kanamori, Dennis O., Tiwari, Hemant K., Levy, Daniel, Loos, Ruth J. F., Dehghan, Abbas, Elliott, Paul, Malik, Afshan N., Scott, Robert A., Becker, Diane M., de Andrade, Mariza, Province, Michael A., Meigs, James B., Rotter, Jerome, I, North, Kari E., Kraja, Aldi T., Liu, Chunyu, Fetterman, Jessica L., Graff, Mariaelisa, Have, Christian Theil, Gu, Charles, Yanek, Lisa R., Feitosa, Mary F., Arking, Dan E., Chasman, Daniel, I, Young, Kristin, Ligthart, Symen, Hill, W. David, Weiss, Stefan, Luan, Jian'an, Giulianini, Franco, Li-Gao, Ruifang, Hartwig, Fernando P., Lin, Shiow J., Wang, Lihua, Richardson, Tom G., Yao, Jie, Fernandez, Eliana P., Ghanbari, Mohsen, Wojczynski, Mary K., Lee, Wen-Jane, Argos, Maria, Armasu, Sebastian M., Barve, Ruteja A., Ryan, Kathleen A., An, Ping, Baranski, Thomas J., Bielinski, Suzette J., Bowden, Donald W., Broeckel, Ulrich, Christensen, Kaare, Chu, Audrey Y., Corley, Janie, Cox, Simon R., Uitterlinden, Andre G., Rivadeneira, Fernando, Cropp, Cheryl D., Daw, E. Warwick, van Heemst, Diana, de las Fuentes, Lisa, Gao, He, Tzoulaki, Ioanna, Ahluwalia, Tarunveer S., de Mutsert, Renee, Emery, Leslie S., Erzurumluoglu, A. Mesut, Perry, James A., Fu, Mao, Forouhi, Nita G., Gu, Zhenglong, Hai, Yang, Harris, Sarah E., Hemani, Gibran, Hunt, Steven C., Irvin, Marguerite R., Jonsson, Anna E., Justice, Anne E., Kernson, Nicola D., Larson, Nicholas B., Lin, Keng-Hung, Love-Gregory, Latisha D., Mathias, Rasika A., Lee, Joseph H., Nauck, Matthias, Noordam, Raymond, Ong, Ken K., Pankow, James, Patki, Amit, Pattie, Alison, Petersmann, Astrid, Qi, Qibin, Ribel-Madsen, Rasmus, Rohde, Rebecca, Sandow, Kevin, Schnurr, Theresia M., Sofer, Tamar, Starr, John M., Taylor, Adele M., Teumer, Alexander, Timpson, Nicholas J., de Haan, Hugoline G., Wang, Yujie, Weeke, Peter E., Williams, Christine, Wu, Hongsheng, Yang, Wei, Zeng, Donglin, Witte, Daniel R., Weir, Bruce S., Wareham, Nicholas J., Vestergaard, Henrik, Turner, Stephen T., Torp-Pedersen, Christian, Stergiakouli, Evie, Sheu, Wayne Huey-Hemg, Rosendaal, Frits R., Ikram, M. Arfan, Franco, Oscar H., Ridker, Paul M., Perls, Thomas T., Pedersen, Oluf, Nohr, Ellen A., Newman, Anne B., Linneberg, Allan, Langenberg, Claudia, Kilpelainen, Tuomas O., Kardia, Sharon L. R., Jørgensen, Marit E., Jørgensen, Torben, Sorensen, Thorkild I. A., Homuth, Georg, Hansen, Torben, Goodarzi, Mark O., Deary, Ian J., Christensen, Cramer, Chen, Yii-Der Ida, Chakravarti, Aravinda, Brandslund, Ivan, Bonnelykke, Klaus, Taylor, Kent D., Wilson, James G., Rodriguez, Santiago, Davies, Gail, Horta, Bernardo L., Thyagarajan, Bharat, Rao, D. C., Grarup, Niels, Davila-Roman, Victor G., Hudson, Gavin, Guo, Xiuqing, Arnett, Donna K., Hayward, Caroline, Vaidya, Dhananjay, Mook-Kanamori, Dennis O., Tiwari, Hemant K., Levy, Daniel, Loos, Ruth J. F., Dehghan, Abbas, Elliott, Paul, Malik, Afshan N., Scott, Robert A., Becker, Diane M., de Andrade, Mariza, Province, Michael A., Meigs, James B., Rotter, Jerome, I, and North, Kari E.

Published
2019

72. TMIC-12. TUMOR EDGE-DESTINED CELLS IN GBM CELLS IN A CELL-INTRINSIC MECHANISM

Author

Yamashita, Daisuke, primary, Minata, Mutsuko, additional, Yu, Hai, additional, Zhang, Soujun, additional, Li, Chaoxi, additional, Flanary, Victoria, additional, Ghosh, Sadashib, additional, Lee, Yeri, additional, Cho, Heejin, additional, Botta, Davide, additional, Guo, Xiaoxian, additional, Ozaki, Saya, additional, Yamaguchi, Shinobu, additional, Komarova, Svetlana, additional, Bastola, Soniya, additional, Crossman, David, additional, Nabors, Louis, additional, Markert, James, additional, Gu, Zhenglong, additional, Skolnick, Jeffrey, additional, Zamboni, Nicola, additional, Lund, Frances, additional, Nam, Do-Hyun, additional, and Nakano, Ichiro, additional

Published
2019
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77. A novel FADS2 isoform identified in human milk fat globule suppresses FADS2 mediated Δ6-desaturation of omega-3 fatty acids

Author

Kothapalli, Kumar S.D., primary, Park, Hui Gyu, additional, Guo, Xiaoxian, additional, Sun, Xuepeng, additional, Zou, James, additional, Hyon, Stephanie S., additional, Qin, Xia, additional, Lawrence, Peter, additional, Ran-Ressler, Rinat R., additional, Zhang, Ji Yao, additional, Gu, Zhenglong, additional, and Brenna, J. Thomas, additional

Published
2018
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79. Acute Psychological Stress Triggers Circulating Cell-Free Mitochondrial DNA

Author

Trumpff, Caroline, primary, Marsland, Anna L., additional, Basualto-Alarcón, Carla, additional, Martin, James L., additional, Carroll, Judith E., additional, Sturm, Gabriel, additional, Vincent, Amy E., additional, Mosharov, Eugene V., additional, Gu, Zhenglong, additional, Kaufman, Brett A., additional, and Picard, Martin, additional

Published
2018
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82. Convergent and divergent genetic changes in the genome of Chinese and European pigs

Author

Wang, Jing, primary, Zou, Huiying, additional, Chen, Lei, additional, Long, Xi, additional, Lan, Jing, additional, Liu, Wenjie, additional, Ma, Li, additional, Wang, Chao, additional, Xu, Xinyu, additional, Ren, Liming, additional, Gu, Zhenglong, additional, Li, Ning, additional, Hu, Xiaoxiang, additional, Zhao, Yaofeng, additional, and Zhao, Yiqiang, additional

Published
2017
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83. A novel FADS2 isoform isolated from milk fat globules suppresses FADS2 mediated Δ6‐desaturation of omega‐3 fatty acids

Author

Kothapalli, Kumar, primary, Park, Hui Gyu, additional, Guo, Xiaoxian, additional, Sun, Xuepeng, additional, Zou, James, additional, Hyon, Stephanie S, additional, Qin, Xia, additional, Lawrence, Peter, additional, Ran‐Ressler, Rinat R, additional, Zhang, Ji Yao, additional, Gu, Zhenglong, additional, and Brenna, James Thomas, additional

Published
2017
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85. Glucomannan Hydrolysate Promotes Gut Proliferative Homeostasis and Extends Life Span in Drosophila melanogaster.

Author

Si, Yuan, Liu, Xi, Ye, Kaixiong, Bonfini, Alessandro, Hu, Xun Yang, Buchon, Nicolas, and Gu, Zhenglong

Subjects
DROSOPHILA melanogaster, LIFE spans, GLUCOMANNAN, PEPTIDE antibiotics, HOMEOSTASIS
Abstract

Dietary supplementation of glucomannan has been shown to have multiple health benefits, but its effect on life span has not been investigated. Here, we show that glucomannan hydrolysate (GMH) treatment extends mean life span of the model organism Drosophila melanogaster. To unravel the underlying mechanisms, we first examined the effect of GMH on the gut microbiota. We found that GMH treatment is associated with an elevated bacterial load in aged flies but overall has limited effects on the relative microbiota composition. We also demonstrated that GMH inhibits age-associated hyperproliferation of intestinal stem cells and thus delays the deterioration of gut integrity. Further analysis of the midgut transcriptome revealed that both EGFR/MAPK and JAK/STAT signaling pathways are suppressed in GMH groups. Multiple key regulators or effectors of EGFR/MAPK pathway, Ets21c, Mkp3, and Rho, are downregulated by GMH treatment. In the JAK/STAT pathway, major ligands (eg, Upd2 and Upd3) and negative feedback inhibitors (eg, Socs36e) are all significantly downregulated. Additionally, the expression of genes encoding antimicrobial peptides is elevated by GMH treatment. Taken together, our study shows that dietary supplementation of GMH can prolong life span, possibly through regulating gut proliferative homeostasis. [ABSTRACT FROM AUTHOR]

Published
2019
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89. RNA Sequencing: A Novel FADS2 Isoform Identified in Milk Fat Globule Suppresses FADS2 Mediated Delta 6‐Desaturation of Omega‐3 Fatty Acids

Author

Kothapalli, Kumar S.D, primary, Park, Hui Gyu, additional, Guo, Xiaoxian, additional, Sun, Xuepeng, additional, Zou, James, additional, Hyon, Stephanie S., additional, Qin, Xia, additional, Lawrence, Peter, additional, Ran‐Ressler, Rinat R., additional, Zhang, Ji Yao, additional, Gu, Zhenglong, additional, and Brenna, James Thomas, additional

Published
2016
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90. Positive Selection on a Regulatory Insertion–Deletion Polymorphism inFADS2Influences Apparent Endogenous Synthesis of Arachidonic Acid

Author

Kothapalli, Kumar S. D., primary, Ye, , Kaixiong, additional, Gadgil, Maithili S., additional, Carlson, Susan E., additional, O’Brien, Kimberly O., additional, Zhang, Ji Yao, additional, Park, Hui Gyu, additional, Ojukwu, Kinsley, additional, Zou, James, additional, Hyon, Stephanie S., additional, Joshi, Kalpana S., additional, Gu, Zhenglong, additional, Keinan, Alon, additional, and Brenna, J.Thomas, additional

Published
2016
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99. The baker's yeast diploid genome is remarkably stable in vegetative growth and meiosis.

Author

Nishant, K T, Wei, Wu, Mancera, Eugenio, Argueso, Juan Lucas, Schlattl, Andreas, Delhomme, Nicolas, Ma, Xin, Bustamante, Carlos D, Korbel, Jan O, Gu, Zhenglong, Steinmetz, Lars M, Alani, Eric, Nishant, K T, Wei, Wu, Mancera, Eugenio, Argueso, Juan Lucas, Schlattl, Andreas, Delhomme, Nicolas, Ma, Xin, Bustamante, Carlos D, Korbel, Jan O, Gu, Zhenglong, Steinmetz, Lars M, and Alani, Eric

Abstract

Accurate estimates of mutation rates provide critical information to analyze genome evolution and organism fitness. We used whole-genome DNA sequencing, pulse-field gel electrophoresis, and comparative genome hybridization to determine mutation rates in diploid vegetative and meiotic mutation accumulation lines of Saccharomyces cerevisiae. The vegetative lines underwent only mitotic divisions while the meiotic lines underwent a meiotic cycle every ∼20 vegetative divisions. Similar base substitution rates were estimated for both lines. Given our experimental design, these measures indicated that the meiotic mutation rate is within the range of being equal to zero to being 55-fold higher than the vegetative rate. Mutations detected in vegetative lines were all heterozygous while those in meiotic lines were homozygous. A quantitative analysis of intra-tetrad mating events in the meiotic lines showed that inter-spore mating is primarily responsible for rapidly fixing mutations to homozygosity as well as for removing mutations. We did not observe 1-2 nt insertion/deletion (in-del) mutations in any of the sequenced lines and only one structural variant in a non-telomeric location was found. However, a large number of structural variations in subtelomeric sequences were seen in both vegetative and meiotic lines that did not affect viability. Our results indicate that the diploid yeast nuclear genome is remarkably stable during the vegetative and meiotic cell cycles and support the hypothesis that peripheral regions of chromosomes are more dynamic than gene-rich central sections where structural rearrangements could be deleterious. This work also provides an improved estimate for the mutational load carried by diploid organisms.

Published
2010
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100. Front Cover: AuNP‐Modulated qPCR: An Optimized System for Detecting MIR Biophotons Released in DNA Replication (Chem. Eur. J. 8/2023).

Author

Yang, Yu, Peng, Daoling, Gu, Zhenglong, Jiang, Lei, and Song, Bo

Subjects
GOLD nanoparticles
Abstract

DNA replication, energy utilization efficiency, gold nanoparticles, MIR biophoton detection, qPCR Keywords: DNA replication; energy utilization efficiency; gold nanoparticles; MIR biophoton detection; qPCR EN DNA replication energy utilization efficiency gold nanoparticles MIR biophoton detection qPCR 1 1 1 02/13/23 20230207 NES 230207 B ATP, the cell energy currency b mostly produced by mitochondria, is conventionally regarded as releasing heat to drive biological reactions and processes. Front Cover: AuNP-Modulated qPCR: An Optimized System for Detecting MIR Biophotons Released in DNA Replication (Chem. Eur. J. 8/2023). [Extracted from the article]

Published
2023
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