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Guidelines for the use and interpretation of assays for monitoring autophagy
- D. Klionsky, F. Abdalla, +498 authors Shengzhou or sheng-zhou wu
- Medicine, Biology
- 1 April 2012
These guidelines are presented for the selection and interpretation of methods for use by investigators who aim to examine macroautophagy and related processes, as well as for reviewers who need to provide realistic and reasonable critiques of papers that are focused on these processes. Expand
Guidelines for the use and interpretation of assays for monitoring autophagy (3rd edition)
There continues to be confusion regarding acceptable methods to measure autophagy, especially in multicellular eukaryotes, so it is important to update guidelines for monitoring autophagic activity in different organisms. Expand
A Systems Approach to Mapping DNA Damage Response Pathways
Interactions for which the target changed expression in wild-type cells in response to MMS but was nonresponsive in cells lacking the TF were identified and assembled into causal pathway models that provide global hypotheses of how signaling, transcription, and phenotype are integrated after damage. Expand
Trm9-catalyzed tRNA modifications link translation to the DNA damage response.
It is proposed that Trm9-specific tRNA modifications enhance codon-specific translation elongation and promote increased levels of key damage response proteins. Expand
A Quantitative Systems Approach Reveals Dynamic Control of tRNA Modifications during Cellular Stress
- Clement T. Y. Chan, Madhu Dyavaiah, M. DeMott, K. Taghizadeh, P. Dedon, T. Begley
- Biology, Chemistry
- PLoS genetics
- 1 December 2010
A highly precise mass spectrometric method is developed to quantify tRNA modifications in Saccharomyces cerevisiae and reveals several novel biosynthetic pathways for RNA modifications and led to the discovery of signature changes in the spectrum of t RNA modifications in the damage response to mechanistically different toxicants. Expand
Damage recovery pathways in Saccharomyces cerevisiae revealed by genomic phenotyping and interactome mapping.
- T. Begley, A. Rosenbach, T. Ideker, L. Samson
- Biology, Medicine
- Molecular cancer research : MCR
- 1 December 2002
A genomic phenotyping database identifying hundreds of Saccharomyces cerevisiae genes important for viable cellular recovery after mutagen exposure is generated and network mapping results demonstrate how systematic phenotypic assays may be linked directly to underlying molecular mechanisms. Expand
Mitochondria, Energetics, Epigenetics, and Cellular Responses to Stress
- D. Shaughnessy, K. McAllister, +16 authors F. Tyson
- Medicine, Biology
- Environmental health perspectives
- 15 August 2014
This work investigated the concept of bidirectional interactions between mitochondria and cellular pathways in response to environmental stress with a focus on epigenetic regulation, and examined DNA repair and DDR pathways as examples of biological processes that respond to exogenous insults through changes in homeostasis and altered mitochondrial function. Expand
Genome-wide responses to DNA-damaging agents.
This review highlights many of the studies that detail genome-wide responses to DNA-damaging agents and examines how these datasets have been used to build a systems view of cellular responses to damage. Expand
Hot spots for modulating toxicity identified by genomic phenotyping and localization mapping.
It is shown that many proteins associated with RNA polymerase II, macromolecular trafficking, and vacuole function can be counted among the many proteins that modulate carcinogen-induced toxicity. Expand
Global network analysis of phenotypic effects: Protein networks and toxicity modulation in Saccharomyces cerevisiae
- M. Said, T. Begley, A. Oppenheim, D. Lauffenburger, L. Samson
- Biology, Medicine
- Proceedings of the National Academy of Sciences…
- 17 December 2004
A global network investigation of the genotype/phenotype data set developed for the recovery of the yeast Saccharomyces cerevisiae from exposure to DNA-damaging agents is presented, enabling explicit study of how protein–protein interaction network characteristics may be associated with phenotypic functional effects. Expand