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1. Towards Standardizing Nomenclature in Huntingtons Disease Research.

Author

DiFiglia, Marian, DiFiglia, Marian, Leavitt, Blair, Macdonald, Douglas, Thompson, Leslie, DiFiglia, Marian, DiFiglia, Marian, Leavitt, Blair, Macdonald, Douglas, and Thompson, Leslie

Abstract

The field of Huntingtons disease research covers many different scientific disciplines, from molecular biology all the way through to clinical practice, and as our understanding of the disease has progressed over the decades, a great deal of different terminology has accrued. The field is also renowned for its collaborative spirit and use of standardized reagents, assays, datasets, models, and clinical measures, so the use of standardized terms is especially important. We have set out to determine, through a consensus exercise involving basic and clinical scientists working in the field, the most appropriate language to use across disciplines. Nominally, this article will serve as the style guide for the Journal of Huntingtons Disease (JHD), the only journal devoted exclusively to HD, and we lay out the preferred and standardized terminology and nomenclature for use in JHD publications. However, we hope that this article will also serve as a useful resource to the HD research community at large and that these recommended naming conventions will be adopted widely.

Published
2024

2. Behavioral deficits, early gliosis, dysmyelination and synaptic dysfunction in a mouse model of mucolipidosis IV.

Author

Grishchuk, Yulia, Grishchuk, Yulia, Sri, Sarmi, Rudinskiy, Nikita, Ma, Weiyuan, Stember, Katherine G, Cottle, Matthew W, Sapp, Ellen, Difiglia, Marian, Muzikansky, Alona, Betensky, Rebecca A, Wong, Andrew MS, Bacskai, Brian J, Hyman, Bradley T, Kelleher, Raymond J, Cooper, Jonathan D, Slaugenhaupt, Susan A, Grishchuk, Yulia, Grishchuk, Yulia, Sri, Sarmi, Rudinskiy, Nikita, Ma, Weiyuan, Stember, Katherine G, Cottle, Matthew W, Sapp, Ellen, Difiglia, Marian, Muzikansky, Alona, Betensky, Rebecca A, Wong, Andrew MS, Bacskai, Brian J, Hyman, Bradley T, Kelleher, Raymond J, Cooper, Jonathan D, and Slaugenhaupt, Susan A

Abstract

Mucolipidosis IV (MLIV) is caused by mutations in the gene MCOLN1. Patients with MLIV have severe neurologic deficits and very little is known about the brain pathology in this lysosomal disease. Using an accurate mouse model of mucolipidosis IV, we observed early behavioral deficits which were accompanied by activation of microglia and astrocytes. The glial activation that persisted during the course of disease was not accompanied by neuronal loss even at the late stage. In vivo [Ca(2+)]-imaging revealed no changes in resting [Ca(2+)] levels in Mcoln1(-/-) cortical neurons, implying their physiological health. Despite the absence of neuron loss, we observed alterations in synaptic plasticity, as indicated by elevated paired-pulse facilitation and enhanced long-term potentiation. Myelination deficits and severely dysmorphic corpus callosum were present early and resembled white matter pathology in mucolipidosis IV patients. These results indicate the early involvement of glia, and challenge the traditional view of mucolipidosis IV as an overtly neurodegenerative condition.

Published
2014

3. Behavioral deficits, early gliosis, dysmyelination and synaptic dysfunction in a mouse model of mucolipidosis IV.

Author

Grishchuk, Yulia, Grishchuk, Yulia, Sri, Sarmi, Rudinskiy, Nikita, Ma, Weiyuan, Stember, Katherine G, Cottle, Matthew W, Sapp, Ellen, Difiglia, Marian, Muzikansky, Alona, Betensky, Rebecca A, Wong, Andrew MS, Bacskai, Brian J, Hyman, Bradley T, Kelleher, Raymond J, Cooper, Jonathan D, Slaugenhaupt, Susan A, Grishchuk, Yulia, Grishchuk, Yulia, Sri, Sarmi, Rudinskiy, Nikita, Ma, Weiyuan, Stember, Katherine G, Cottle, Matthew W, Sapp, Ellen, Difiglia, Marian, Muzikansky, Alona, Betensky, Rebecca A, Wong, Andrew MS, Bacskai, Brian J, Hyman, Bradley T, Kelleher, Raymond J, Cooper, Jonathan D, and Slaugenhaupt, Susan A

Abstract

Mucolipidosis IV (MLIV) is caused by mutations in the gene MCOLN1. Patients with MLIV have severe neurologic deficits and very little is known about the brain pathology in this lysosomal disease. Using an accurate mouse model of mucolipidosis IV, we observed early behavioral deficits which were accompanied by activation of microglia and astrocytes. The glial activation that persisted during the course of disease was not accompanied by neuronal loss even at the late stage. In vivo [Ca(2+)]-imaging revealed no changes in resting [Ca(2+)] levels in Mcoln1(-/-) cortical neurons, implying their physiological health. Despite the absence of neuron loss, we observed alterations in synaptic plasticity, as indicated by elevated paired-pulse facilitation and enhanced long-term potentiation. Myelination deficits and severely dysmorphic corpus callosum were present early and resembled white matter pathology in mucolipidosis IV patients. These results indicate the early involvement of glia, and challenge the traditional view of mucolipidosis IV as an overtly neurodegenerative condition.

Published
2014

4. Guidelines for the use and interpretation of assays for monitoring autophagy in higher eukaryotes

Author

Klionsky, Daniel J., Abeliovich, Hagai, Agostinis, Patrizia, Agrawal, Devendra K., Aliev, Giumrakch, S. Askew, David, Baba, Misuzu, H. Baehrecke, Eric, A. Bahr, Ben, Ballabio, Andrea, A. Bamber, Bruce, C. Bassham, Diane, Bergamini, Ettore, Bi, Xiaoning, Biard-Piechaczyk, Martine, S. Blum, Janice, E. Breclesen, Dale, L. Brodsky, Jeffrey, H. Brumell, John, Brunk, Ulf T., Bursch, Wilfried, Camougrand, Nadine, Cebollero, Eduardo, Cecconi, Francesco, Chen, Yingyu, Chin, Lih-Shen, Choi, Augustine, T. Chu, Charleen, Chung, Jongkyeong, G. H. Clarke, Peter, S. B. Clark, Robert, G. Clarke, Steven, Clave, Corinne, L. Cleveland, John, Codogno, Patrice, I. Colombo, Maria, Coto-Montes, Ana, M. Cregg, James, Maria Cuervo, Ana, Debnath, Jayanta, Demarchi, Francesca, B. Dennis, Patrick, A. Dennis, Phillip, Deretic, Vojo, J. Devenish, Rodney, Di Sano, Federica, Fred Dice, J., DiFiglia, Marian, Dinesh-Kumar, Savithramma, W. Distelhorst, Clark, Djavaheri-Mergny, Mojgan, C. Dorsey, Frank, Droege, Wulf, Dron, Michel, A. Jr. Dunn, William, Duszenko, Michael, Tony Eissa, N., Elazar, Zvulun, Esclatine, Audrey, Eskelinen, Eeva-Liisa, Fesues, Laszlo, D. Finley, Kim, M. Fuentes, Jose, Fueyo, Juan, Fujisaki, Kozo, Galliot, Brigitte, Gao, Fen-Biao, A. Gewirtz, David, B. Gibson, Spencer, Gohla, Antje, L. Goldberg, Alfred, Gonzalez, Ramon, Gonzalez-Estevez, Cristina, Gorski, Sharon, A. Gottlieb, Roberta, Haussinger, Dieter, He, You-Wen, Heidenreich, Kim, A. Hill, Joseph, Hoyer-Hansen, Maria, Hu, Xun, Huang, Wei-Pang, Iwasaki, Akiko, Jaattela, Marja, T. Jackson, William, Jiang, Xuejun, Jin, Shengkan, Johansen, Terje, U. Jung, Jae, Kadowaki, Motoni, Kang, Chanhee, Kelekar, Ameeta, H. Kessel, David, A. K. W. Kiel, Jan, Pyo Kim, Hong, Kimchi, Adi, J. Kinsella, Timothy, Kiselyov, Kirill, Kitamoto, Katsuhiko, Knecht, Erwin, Komatsu, Masaaki, Kominami, Eiki, Kondo, Seiji, L. Kovacs, Attila, Kroemer, Guido, Kuan, Chia-Yi, Kumar, Rakesh, Kundu, Mondira, Landry, Jacques, Laporte, Marianne, Le, Weidong, Lei, Huan-Yao, J. Lenardo, Michael, Levine, Beth, Lieberman, Andrew, Lim, Kah-Leong, Lin, Fu-Cheng, Liou, Willisa, F. Liu, Leroy, Lopez-Berestein, Gabriel, Lopez-Otin, Carlos, Lu, Bo, F. Macleod, Kay, Malorni, Walter, Martinet, Wim, Matsuoka, Ken, Mautner, Josef, J. Meijer, Alfred, Melendez, Alicia, Michels, Paul, Miotto, Giovanni, P. Mistiaen, Wilhelm, Mizushima, Noboru, Mograbi, Baharia, Monastyrska, Iryna, N. Moore, Michael, I. Moreira, Paula, Moriyasu, Yuji, Motyl, Tomasz, Muenz, Christian, O. Murphy, Leon, I. Naqvi, Naweed, Neufeld, Thomas, Nishino, Ichizo, A. Nixon, Ralph, Noda, Takeshi, Nuernberg, Bernd, Ogawa, Michinaga, L. Oleinick, Nancy, J. Olsen, Laura, Ozpolat, Bulent, Paglin, Shoshana, E. Palmer, Glen, Papassideri, Issidora, Parkes, Miles, H. Perlmutter, David, Perry, George, Piacentini, Mauro, Pinkas-Kramarski, Ronit, Prescott, Mark, Proikas-Cezanne, Tassula, Raben, Nina, Rami, Abdelhaq, Reggiori, Fulvio, Rohrer, Baerbel, C. Rubinsztein, David, M. Ryan, Kevin, Sadoshima, Junichi, Sakagami, Hiroshi, Sakai, Yasuyoshi, Sandri, Marco, Sasakawa, Chihiro, Sass, Miklos, Schneider, Claudio, O. Seglen, Per, Seleverstov, Oleksandr, Settleman, Jeffre, J. Shacka, John, M. Shapiro, Irving, Sibirny, Andrei, C. M. Silva-Zacarin, Elaine, Simon, Hans-Uwe, Simone, Cristiano, Simonsen, Anne, A. Smith, Mark, Spanel-Borowski, Katharina, Srinivas, Vickram, Steeves, Meredith, Stenmark, Harald, E. Stromhaug, Per, S. Subauste, Carlos, Sugimoto, Seiichiro, Sulzer, David, Suzuki, Toshihiko, S. Swanson, Michele, Takeshita, Fumihiko, J. Talbot, Nicholas., Talloczy, Zsolt, Tanaka, Keiji, Tanaka, Kozo, Tanida, Isei, S. Taylor, Graham, Paul Taylor, J., Terman, Alexei, Tettamanti, Gianluca, B. Thompson, Craig, Thumm, Michael, M. Tolkovsky, Aviva, A. Tooze, Sharon, Truant, Ray, V. Tumanovska, Lesya, Uchiyama, Yasuo, Ueno, Takashi, L. Uzcategui, Nestor, van der Klei, Ida, C. Vaquero, Eva, Vellai, Tibor, W. Vogel, Michael, Wang, Hong-Gang, Webster, Paul, W. Wiley, John, Xi, Zhijun, Xiao, Gutian, Yahalom, Joachim, Yang, Jin-Ming, Yap, George, Yin, Xiao-Min, Yoshimori, Tamotsu, Yu, Li, Yue, Zhenyu, Yuzaki, Michisuke, Zabirnyk, Olga, Zheng, Xiaoxiang, Zhu, Xiongwei, L. Deter, Russell, Tabas, Ira, Klionsky, Daniel J., Abeliovich, Hagai, Agostinis, Patrizia, Agrawal, Devendra K., Aliev, Giumrakch, S. Askew, David, Baba, Misuzu, H. Baehrecke, Eric, A. Bahr, Ben, Ballabio, Andrea, A. Bamber, Bruce, C. Bassham, Diane, Bergamini, Ettore, Bi, Xiaoning, Biard-Piechaczyk, Martine, S. Blum, Janice, E. Breclesen, Dale, L. Brodsky, Jeffrey, H. Brumell, John, Brunk, Ulf T., Bursch, Wilfried, Camougrand, Nadine, Cebollero, Eduardo, Cecconi, Francesco, Chen, Yingyu, Chin, Lih-Shen, Choi, Augustine, T. Chu, Charleen, Chung, Jongkyeong, G. H. Clarke, Peter, S. B. Clark, Robert, G. Clarke, Steven, Clave, Corinne, L. Cleveland, John, Codogno, Patrice, I. Colombo, Maria, Coto-Montes, Ana, M. Cregg, James, Maria Cuervo, Ana, Debnath, Jayanta, Demarchi, Francesca, B. Dennis, Patrick, A. Dennis, Phillip, Deretic, Vojo, J. Devenish, Rodney, Di Sano, Federica, Fred Dice, J., DiFiglia, Marian, Dinesh-Kumar, Savithramma, W. Distelhorst, Clark, Djavaheri-Mergny, Mojgan, C. Dorsey, Frank, Droege, Wulf, Dron, Michel, A. Jr. Dunn, William, Duszenko, Michael, Tony Eissa, N., Elazar, Zvulun, Esclatine, Audrey, Eskelinen, Eeva-Liisa, Fesues, Laszlo, D. Finley, Kim, M. Fuentes, Jose, Fueyo, Juan, Fujisaki, Kozo, Galliot, Brigitte, Gao, Fen-Biao, A. Gewirtz, David, B. Gibson, Spencer, Gohla, Antje, L. Goldberg, Alfred, Gonzalez, Ramon, Gonzalez-Estevez, Cristina, Gorski, Sharon, A. Gottlieb, Roberta, Haussinger, Dieter, He, You-Wen, Heidenreich, Kim, A. Hill, Joseph, Hoyer-Hansen, Maria, Hu, Xun, Huang, Wei-Pang, Iwasaki, Akiko, Jaattela, Marja, T. Jackson, William, Jiang, Xuejun, Jin, Shengkan, Johansen, Terje, U. Jung, Jae, Kadowaki, Motoni, Kang, Chanhee, Kelekar, Ameeta, H. Kessel, David, A. K. W. Kiel, Jan, Pyo Kim, Hong, Kimchi, Adi, J. Kinsella, Timothy, Kiselyov, Kirill, Kitamoto, Katsuhiko, Knecht, Erwin, Komatsu, Masaaki, Kominami, Eiki, Kondo, Seiji, L. Kovacs, Attila, Kroemer, Guido, Kuan, Chia-Yi, Kumar, Rakesh, Kundu, Mondira, Landry, Jacques, Laporte, Marianne, Le, Weidong, Lei, Huan-Yao, J. Lenardo, Michael, Levine, Beth, Lieberman, Andrew, Lim, Kah-Leong, Lin, Fu-Cheng, Liou, Willisa, F. Liu, Leroy, Lopez-Berestein, Gabriel, Lopez-Otin, Carlos, Lu, Bo, F. Macleod, Kay, Malorni, Walter, Martinet, Wim, Matsuoka, Ken, Mautner, Josef, J. Meijer, Alfred, Melendez, Alicia, Michels, Paul, Miotto, Giovanni, P. Mistiaen, Wilhelm, Mizushima, Noboru, Mograbi, Baharia, Monastyrska, Iryna, N. Moore, Michael, I. Moreira, Paula, Moriyasu, Yuji, Motyl, Tomasz, Muenz, Christian, O. Murphy, Leon, I. Naqvi, Naweed, Neufeld, Thomas, Nishino, Ichizo, A. Nixon, Ralph, Noda, Takeshi, Nuernberg, Bernd, Ogawa, Michinaga, L. Oleinick, Nancy, J. Olsen, Laura, Ozpolat, Bulent, Paglin, Shoshana, E. Palmer, Glen, Papassideri, Issidora, Parkes, Miles, H. Perlmutter, David, Perry, George, Piacentini, Mauro, Pinkas-Kramarski, Ronit, Prescott, Mark, Proikas-Cezanne, Tassula, Raben, Nina, Rami, Abdelhaq, Reggiori, Fulvio, Rohrer, Baerbel, C. Rubinsztein, David, M. Ryan, Kevin, Sadoshima, Junichi, Sakagami, Hiroshi, Sakai, Yasuyoshi, Sandri, Marco, Sasakawa, Chihiro, Sass, Miklos, Schneider, Claudio, O. Seglen, Per, Seleverstov, Oleksandr, Settleman, Jeffre, J. Shacka, John, M. Shapiro, Irving, Sibirny, Andrei, C. M. Silva-Zacarin, Elaine, Simon, Hans-Uwe, Simone, Cristiano, Simonsen, Anne, A. Smith, Mark, Spanel-Borowski, Katharina, Srinivas, Vickram, Steeves, Meredith, Stenmark, Harald, E. Stromhaug, Per, S. Subauste, Carlos, Sugimoto, Seiichiro, Sulzer, David, Suzuki, Toshihiko, S. Swanson, Michele, Takeshita, Fumihiko, J. Talbot, Nicholas., Talloczy, Zsolt, Tanaka, Keiji, Tanaka, Kozo, Tanida, Isei, S. Taylor, Graham, Paul Taylor, J., Terman, Alexei, Tettamanti, Gianluca, B. Thompson, Craig, Thumm, Michael, M. Tolkovsky, Aviva, A. Tooze, Sharon, Truant, Ray, V. Tumanovska, Lesya, Uchiyama, Yasuo, Ueno, Takashi, L. Uzcategui, Nestor, van der Klei, Ida, C. Vaquero, Eva, Vellai, Tibor, W. Vogel, Michael, Wang, Hong-Gang, Webster, Paul, W. Wiley, John, Xi, Zhijun, Xiao, Gutian, Yahalom, Joachim, Yang, Jin-Ming, Yap, George, Yin, Xiao-Min, Yoshimori, Tamotsu, Yu, Li, Yue, Zhenyu, Yuzaki, Michisuke, Zabirnyk, Olga, Zheng, Xiaoxiang, Zhu, Xiongwei, L. Deter, Russell, and Tabas, Ira

Abstract

Research in autophagy continues to accelerate,1 and as a result many new scientists are entering the field. Accordingly, it is important to establish a standard set of criteria for monitoring macroautophagy in different organisms. Recent reviews have described the range of assays that have been used for this purpose.2,3 There are many useful and convenient methods that can be used to monitor macroautophagy in yeast, but relatively few in other model systems, and there is much confusion regarding acceptable methods to measure macroautophagy in higher eukaryotes. A key point that needs to be emphasized is that there is a difference between measurements that monitor the numbers of autophagosomes versus those that measure flux through the autophagy pathway; thus, a block in macroautophagy that results in autophagosome accumulation needs to be differentiated from fully functional autophagy that includes delivery to, and degradation within, lysosomes (in most higher eukaryotes) or the vacuole (in plants and fungi). Here, we present a set of guidelines for the selection and interpretation of the methods that can be used by investigators who are attempting to examine macroautophagy and related processes, as well as by reviewers who need to provide realistic and reasonable critiques of papers that investigate these processes. This set of guidelines is not meant to be a formulaic set of rules, because the appropriate assays depend in part on the question being asked and the system being used. In addition, we emphasize that no individual assay is guaranteed to be the most appropriate one in every situation, and we strongly recommend the use of multiple assays to verify an autophagic response.

Published
2008

5. Guidelines for the use and interpretation of assays for monitoring autophagy in higher eukaryotes

Author

Klionsky, Daniel J., Abeliovich, Hagai, Agostinis, Patrizia, Agrawal, Devendra K., Aliev, Giumrakch, S. Askew, David, Baba, Misuzu, H. Baehrecke, Eric, A. Bahr, Ben, Ballabio, Andrea, A. Bamber, Bruce, C. Bassham, Diane, Bergamini, Ettore, Bi, Xiaoning, Biard-Piechaczyk, Martine, S. Blum, Janice, E. Breclesen, Dale, L. Brodsky, Jeffrey, H. Brumell, John, Brunk, Ulf T., Bursch, Wilfried, Camougrand, Nadine, Cebollero, Eduardo, Cecconi, Francesco, Chen, Yingyu, Chin, Lih-Shen, Choi, Augustine, T. Chu, Charleen, Chung, Jongkyeong, G. H. Clarke, Peter, S. B. Clark, Robert, G. Clarke, Steven, Clave, Corinne, L. Cleveland, John, Codogno, Patrice, I. Colombo, Maria, Coto-Montes, Ana, M. Cregg, James, Maria Cuervo, Ana, Debnath, Jayanta, Demarchi, Francesca, B. Dennis, Patrick, A. Dennis, Phillip, Deretic, Vojo, J. Devenish, Rodney, Di Sano, Federica, Fred Dice, J., DiFiglia, Marian, Dinesh-Kumar, Savithramma, W. Distelhorst, Clark, Djavaheri-Mergny, Mojgan, C. Dorsey, Frank, Droege, Wulf, Dron, Michel, A. Jr. Dunn, William, Duszenko, Michael, Tony Eissa, N., Elazar, Zvulun, Esclatine, Audrey, Eskelinen, Eeva-Liisa, Fesues, Laszlo, D. Finley, Kim, M. Fuentes, Jose, Fueyo, Juan, Fujisaki, Kozo, Galliot, Brigitte, Gao, Fen-Biao, A. Gewirtz, David, B. Gibson, Spencer, Gohla, Antje, L. Goldberg, Alfred, Gonzalez, Ramon, Gonzalez-Estevez, Cristina, Gorski, Sharon, A. Gottlieb, Roberta, Haussinger, Dieter, He, You-Wen, Heidenreich, Kim, A. Hill, Joseph, Hoyer-Hansen, Maria, Hu, Xun, Huang, Wei-Pang, Iwasaki, Akiko, Jaattela, Marja, T. Jackson, William, Jiang, Xuejun, Jin, Shengkan, Johansen, Terje, U. Jung, Jae, Kadowaki, Motoni, Kang, Chanhee, Kelekar, Ameeta, H. Kessel, David, A. K. W. Kiel, Jan, Pyo Kim, Hong, Kimchi, Adi, J. Kinsella, Timothy, Kiselyov, Kirill, Kitamoto, Katsuhiko, Knecht, Erwin, Komatsu, Masaaki, Kominami, Eiki, Kondo, Seiji, L. Kovacs, Attila, Kroemer, Guido, Kuan, Chia-Yi, Kumar, Rakesh, Kundu, Mondira, Landry, Jacques, Laporte, Marianne, Le, Weidong, Lei, Huan-Yao, J. Lenardo, Michael, Levine, Beth, Lieberman, Andrew, Lim, Kah-Leong, Lin, Fu-Cheng, Liou, Willisa, F. Liu, Leroy, Lopez-Berestein, Gabriel, Lopez-Otin, Carlos, Lu, Bo, F. Macleod, Kay, Malorni, Walter, Martinet, Wim, Matsuoka, Ken, Mautner, Josef, J. Meijer, Alfred, Melendez, Alicia, Michels, Paul, Miotto, Giovanni, P. Mistiaen, Wilhelm, Mizushima, Noboru, Mograbi, Baharia, Monastyrska, Iryna, N. Moore, Michael, I. Moreira, Paula, Moriyasu, Yuji, Motyl, Tomasz, Muenz, Christian, O. Murphy, Leon, I. Naqvi, Naweed, Neufeld, Thomas, Nishino, Ichizo, A. Nixon, Ralph, Noda, Takeshi, Nuernberg, Bernd, Ogawa, Michinaga, L. Oleinick, Nancy, J. Olsen, Laura, Ozpolat, Bulent, Paglin, Shoshana, E. Palmer, Glen, Papassideri, Issidora, Parkes, Miles, H. Perlmutter, David, Perry, George, Piacentini, Mauro, Pinkas-Kramarski, Ronit, Prescott, Mark, Proikas-Cezanne, Tassula, Raben, Nina, Rami, Abdelhaq, Reggiori, Fulvio, Rohrer, Baerbel, C. Rubinsztein, David, M. Ryan, Kevin, Sadoshima, Junichi, Sakagami, Hiroshi, Sakai, Yasuyoshi, Sandri, Marco, Sasakawa, Chihiro, Sass, Miklos, Schneider, Claudio, O. Seglen, Per, Seleverstov, Oleksandr, Settleman, Jeffre, J. Shacka, John, M. Shapiro, Irving, Sibirny, Andrei, C. M. Silva-Zacarin, Elaine, Simon, Hans-Uwe, Simone, Cristiano, Simonsen, Anne, A. Smith, Mark, Spanel-Borowski, Katharina, Srinivas, Vickram, Steeves, Meredith, Stenmark, Harald, E. Stromhaug, Per, S. Subauste, Carlos, Sugimoto, Seiichiro, Sulzer, David, Suzuki, Toshihiko, S. Swanson, Michele, Takeshita, Fumihiko, J. Talbot, Nicholas., Talloczy, Zsolt, Tanaka, Keiji, Tanaka, Kozo, Tanida, Isei, S. Taylor, Graham, Paul Taylor, J., Terman, Alexei, Tettamanti, Gianluca, B. Thompson, Craig, Thumm, Michael, M. Tolkovsky, Aviva, A. Tooze, Sharon, Truant, Ray, V. Tumanovska, Lesya, Uchiyama, Yasuo, Ueno, Takashi, L. Uzcategui, Nestor, van der Klei, Ida, C. Vaquero, Eva, Vellai, Tibor, W. Vogel, Michael, Wang, Hong-Gang, Webster, Paul, W. Wiley, John, Xi, Zhijun, Xiao, Gutian, Yahalom, Joachim, Yang, Jin-Ming, Yap, George, Yin, Xiao-Min, Yoshimori, Tamotsu, Yu, Li, Yue, Zhenyu, Yuzaki, Michisuke, Zabirnyk, Olga, Zheng, Xiaoxiang, Zhu, Xiongwei, L. Deter, Russell, Tabas, Ira, Klionsky, Daniel J., Abeliovich, Hagai, Agostinis, Patrizia, Agrawal, Devendra K., Aliev, Giumrakch, S. Askew, David, Baba, Misuzu, H. Baehrecke, Eric, A. Bahr, Ben, Ballabio, Andrea, A. Bamber, Bruce, C. Bassham, Diane, Bergamini, Ettore, Bi, Xiaoning, Biard-Piechaczyk, Martine, S. Blum, Janice, E. Breclesen, Dale, L. Brodsky, Jeffrey, H. Brumell, John, Brunk, Ulf T., Bursch, Wilfried, Camougrand, Nadine, Cebollero, Eduardo, Cecconi, Francesco, Chen, Yingyu, Chin, Lih-Shen, Choi, Augustine, T. Chu, Charleen, Chung, Jongkyeong, G. H. Clarke, Peter, S. B. Clark, Robert, G. Clarke, Steven, Clave, Corinne, L. Cleveland, John, Codogno, Patrice, I. Colombo, Maria, Coto-Montes, Ana, M. Cregg, James, Maria Cuervo, Ana, Debnath, Jayanta, Demarchi, Francesca, B. Dennis, Patrick, A. Dennis, Phillip, Deretic, Vojo, J. Devenish, Rodney, Di Sano, Federica, Fred Dice, J., DiFiglia, Marian, Dinesh-Kumar, Savithramma, W. Distelhorst, Clark, Djavaheri-Mergny, Mojgan, C. Dorsey, Frank, Droege, Wulf, Dron, Michel, A. Jr. Dunn, William, Duszenko, Michael, Tony Eissa, N., Elazar, Zvulun, Esclatine, Audrey, Eskelinen, Eeva-Liisa, Fesues, Laszlo, D. Finley, Kim, M. Fuentes, Jose, Fueyo, Juan, Fujisaki, Kozo, Galliot, Brigitte, Gao, Fen-Biao, A. Gewirtz, David, B. Gibson, Spencer, Gohla, Antje, L. Goldberg, Alfred, Gonzalez, Ramon, Gonzalez-Estevez, Cristina, Gorski, Sharon, A. Gottlieb, Roberta, Haussinger, Dieter, He, You-Wen, Heidenreich, Kim, A. Hill, Joseph, Hoyer-Hansen, Maria, Hu, Xun, Huang, Wei-Pang, Iwasaki, Akiko, Jaattela, Marja, T. Jackson, William, Jiang, Xuejun, Jin, Shengkan, Johansen, Terje, U. Jung, Jae, Kadowaki, Motoni, Kang, Chanhee, Kelekar, Ameeta, H. Kessel, David, A. K. W. Kiel, Jan, Pyo Kim, Hong, Kimchi, Adi, J. Kinsella, Timothy, Kiselyov, Kirill, Kitamoto, Katsuhiko, Knecht, Erwin, Komatsu, Masaaki, Kominami, Eiki, Kondo, Seiji, L. Kovacs, Attila, Kroemer, Guido, Kuan, Chia-Yi, Kumar, Rakesh, Kundu, Mondira, Landry, Jacques, Laporte, Marianne, Le, Weidong, Lei, Huan-Yao, J. Lenardo, Michael, Levine, Beth, Lieberman, Andrew, Lim, Kah-Leong, Lin, Fu-Cheng, Liou, Willisa, F. Liu, Leroy, Lopez-Berestein, Gabriel, Lopez-Otin, Carlos, Lu, Bo, F. Macleod, Kay, Malorni, Walter, Martinet, Wim, Matsuoka, Ken, Mautner, Josef, J. Meijer, Alfred, Melendez, Alicia, Michels, Paul, Miotto, Giovanni, P. Mistiaen, Wilhelm, Mizushima, Noboru, Mograbi, Baharia, Monastyrska, Iryna, N. Moore, Michael, I. Moreira, Paula, Moriyasu, Yuji, Motyl, Tomasz, Muenz, Christian, O. Murphy, Leon, I. Naqvi, Naweed, Neufeld, Thomas, Nishino, Ichizo, A. Nixon, Ralph, Noda, Takeshi, Nuernberg, Bernd, Ogawa, Michinaga, L. Oleinick, Nancy, J. Olsen, Laura, Ozpolat, Bulent, Paglin, Shoshana, E. Palmer, Glen, Papassideri, Issidora, Parkes, Miles, H. Perlmutter, David, Perry, George, Piacentini, Mauro, Pinkas-Kramarski, Ronit, Prescott, Mark, Proikas-Cezanne, Tassula, Raben, Nina, Rami, Abdelhaq, Reggiori, Fulvio, Rohrer, Baerbel, C. Rubinsztein, David, M. Ryan, Kevin, Sadoshima, Junichi, Sakagami, Hiroshi, Sakai, Yasuyoshi, Sandri, Marco, Sasakawa, Chihiro, Sass, Miklos, Schneider, Claudio, O. Seglen, Per, Seleverstov, Oleksandr, Settleman, Jeffre, J. Shacka, John, M. Shapiro, Irving, Sibirny, Andrei, C. M. Silva-Zacarin, Elaine, Simon, Hans-Uwe, Simone, Cristiano, Simonsen, Anne, A. Smith, Mark, Spanel-Borowski, Katharina, Srinivas, Vickram, Steeves, Meredith, Stenmark, Harald, E. Stromhaug, Per, S. Subauste, Carlos, Sugimoto, Seiichiro, Sulzer, David, Suzuki, Toshihiko, S. Swanson, Michele, Takeshita, Fumihiko, J. Talbot, Nicholas., Talloczy, Zsolt, Tanaka, Keiji, Tanaka, Kozo, Tanida, Isei, S. Taylor, Graham, Paul Taylor, J., Terman, Alexei, Tettamanti, Gianluca, B. Thompson, Craig, Thumm, Michael, M. Tolkovsky, Aviva, A. Tooze, Sharon, Truant, Ray, V. Tumanovska, Lesya, Uchiyama, Yasuo, Ueno, Takashi, L. Uzcategui, Nestor, van der Klei, Ida, C. Vaquero, Eva, Vellai, Tibor, W. Vogel, Michael, Wang, Hong-Gang, Webster, Paul, W. Wiley, John, Xi, Zhijun, Xiao, Gutian, Yahalom, Joachim, Yang, Jin-Ming, Yap, George, Yin, Xiao-Min, Yoshimori, Tamotsu, Yu, Li, Yue, Zhenyu, Yuzaki, Michisuke, Zabirnyk, Olga, Zheng, Xiaoxiang, Zhu, Xiongwei, L. Deter, Russell, and Tabas, Ira

Abstract

Research in autophagy continues to accelerate,1 and as a result many new scientists are entering the field. Accordingly, it is important to establish a standard set of criteria for monitoring macroautophagy in different organisms. Recent reviews have described the range of assays that have been used for this purpose.2,3 There are many useful and convenient methods that can be used to monitor macroautophagy in yeast, but relatively few in other model systems, and there is much confusion regarding acceptable methods to measure macroautophagy in higher eukaryotes. A key point that needs to be emphasized is that there is a difference between measurements that monitor the numbers of autophagosomes versus those that measure flux through the autophagy pathway; thus, a block in macroautophagy that results in autophagosome accumulation needs to be differentiated from fully functional autophagy that includes delivery to, and degradation within, lysosomes (in most higher eukaryotes) or the vacuole (in plants and fungi). Here, we present a set of guidelines for the selection and interpretation of the methods that can be used by investigators who are attempting to examine macroautophagy and related processes, as well as by reviewers who need to provide realistic and reasonable critiques of papers that investigate these processes. This set of guidelines is not meant to be a formulaic set of rules, because the appropriate assays depend in part on the question being asked and the system being used. In addition, we emphasize that no individual assay is guaranteed to be the most appropriate one in every situation, and we strongly recommend the use of multiple assays to verify an autophagic response.

Published
2008

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