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53. Labeling our way to a leaner America.

Author

Barnes, Stephanie

Subjects
Food labeling -- Laws, regulations and rules, Obesity -- Prevention, Government regulation, Labeling Education and Nutrition Act of 2009 (Draft), Nutrition Labeling and Education Act of 1990
Published
2010

55. Nitrous oxide‐induced myeloneuropathy

Author

Swart, Grace, primary, Blair, Christopher, additional, Lu, Zhong, additional, Yogendran, Solomon, additional, Offord, Joanna, additional, Sutherland, Emily, additional, Barnes, Stephanie, additional, Palavra, Natalie, additional, Cremer, Phillip, additional, Bolitho, Samuel, additional, and Michael Halmagyi, Gabor, additional

Published
2021
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57. 022 Nitrous oxide induced myelo-neuropathy

Author

Swart, Grace, primary, Blair, Christopher, additional, Lu, Zhong X, additional, Yogendran, Solomon, additional, Offord, Joanna, additional, Sutherland, Emily, additional, Barnes, Stephanie, additional, Palavra, Natalie, additional, Cremer, Phillip, additional, Bolitho, Samuel, additional, and Halmagyi, Gabor M, additional

Published
2021
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59. Spatial Multiplexing of Fluorescent Reporters for Imaging Signaling Network Dynamics

Author

Program in Media Arts and Sciences (Massachusetts Institute of Technology), McGovern Institute for Brain Research at MIT, Massachusetts Institute of Technology. Center for Neurobiological Engineering, Massachusetts Institute of Technology. Department of Electrical Engineering and Computer Science, Massachusetts Institute of Technology. Department of Biological Engineering, Massachusetts Institute of Technology. Department of Brain and Cognitive Sciences, Massachusetts Institute of Technology. Department of Biology, Koch Institute for Integrative Cancer Research at MIT, Howard Hughes Medical Institute, Linghu, Changyang, Johnson, Shannon L, Valdes, Pablo A, Shemesh, Or A, Park, Won Min, Park, Demian, Piatkevich, Kiryl D, Wassie, Asmamaw T, Liu, Yixi, An, Bobae, Barnes, Stephanie A, Celiker, Orhan T, Yao, Chun-Chen, Yu, Chih-Chieh Jay, Wang, Ru, Adamala, Katarzyna P, Bear, Mark F, Keating, Amy E, Boyden, Edward S, Program in Media Arts and Sciences (Massachusetts Institute of Technology), McGovern Institute for Brain Research at MIT, Massachusetts Institute of Technology. Center for Neurobiological Engineering, Massachusetts Institute of Technology. Department of Electrical Engineering and Computer Science, Massachusetts Institute of Technology. Department of Biological Engineering, Massachusetts Institute of Technology. Department of Brain and Cognitive Sciences, Massachusetts Institute of Technology. Department of Biology, Koch Institute for Integrative Cancer Research at MIT, Howard Hughes Medical Institute, Linghu, Changyang, Johnson, Shannon L, Valdes, Pablo A, Shemesh, Or A, Park, Won Min, Park, Demian, Piatkevich, Kiryl D, Wassie, Asmamaw T, Liu, Yixi, An, Bobae, Barnes, Stephanie A, Celiker, Orhan T, Yao, Chun-Chen, Yu, Chih-Chieh Jay, Wang, Ru, Adamala, Katarzyna P, Bear, Mark F, Keating, Amy E, and Boyden, Edward S

Abstract

© 2020 The Author(s) In order to analyze how a signal transduction network converts cellular inputs into cellular outputs, ideally one would measure the dynamics of many signals within the network simultaneously. We found that, by fusing a fluorescent reporter to a pair of self-assembling peptides, it could be stably clustered within cells at random points, distant enough to be resolved by a microscope but close enough to spatially sample the relevant biology. Because such clusters, which we call signaling reporter islands (SiRIs), can be modularly designed, they permit a set of fluorescent reporters to be efficiently adapted for simultaneous measurement of multiple nodes of a signal transduction network within single cells. We created SiRIs for indicators of second messengers and kinases and used them, in hippocampal neurons in culture and intact brain slices, to discover relationships between the speed of calcium signaling, and the amplitude of PKA signaling, upon receiving a cAMP-driving stimulus.

Published
2021

62. Sinus rhythm heart rate increase after atrial fibrillation ablation is associated with lower risk of arrhythmia recurrence

Author

Killu, Ammar M., primary, Witt, Chance M., additional, Sugrue, Alan M., additional, Vaidya, Vaibhav, additional, Monahan, Kristi H., additional, Barnes, Stephanie, additional, Lenz, Charles J., additional, Yogeswaran, Vidhushei, additional, Sun, Philip Y., additional, Hodge, David O., additional, Friedman, Paul A., additional, Packer, Douglas L., additional, and Asirvatham, Samuel J., additional

Published
2021
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68. Foldamer-based molecular recognition

Author

Prince, Ryan B., Barnes, Stephanie A., and Moore, Jeffrey S.

Subjects
Ligand binding (Biochemistry) -- Testimony, Molecular structure -- Research, Spectrum analysis -- Observations, Chemistry
Abstract

Issues concerning the study of conformationally ordered oligomers in solution for the development of a binding site for guest molecules are discussed. Use of induced circular dichroism spectroscopy reveals the reaction of an achiral oligomer with a chiral molecule indicating that binding occurs within the hydrophobic tubular cavity of the oligomer helix.

Published
2000

69. Decoding the Regulatory Genome: Quantitative Analysis of Transcriptional Regulation in Escherichia coli

Author

Barnes, Stephanie Loos, Barnes, Stephanie Loos, Barnes, Stephanie Loos, and Barnes, Stephanie Loos

Abstract

Over the past decades DNA sequencing has become significantly cheaper and faster, which has enabled the accumulation of a huge amount of genomic data. However, much of this genomic data is illegible to us. For noncoding regions of the genome in particular, it is difficult to determine what role is played by specific DNA sequences. Here we focus on regions of DNA that play a role in transcriptional regulation. We develop models and techniques that allow us to discover new regulatory sequences and better understand how DNA sequence determines regulatory output. We start by considering how quantitative models serve as a powerful tool for testing our understanding of biological systems. We apply a statistical mechanical framework that incorporates the Monod-Wyman-Changeux model to analyze the effects of allostery in simple repression, using the lac operon as a test case. By fitting our model to experimental data, we are able to determine the values of the unknown parameter values in our model. We then show that we can use the model to accurately predict the induction responses of an array of simple repression constructs with a variety of repressor copy numbers and repressor binding energies. Next, we consider how the DNA sequence of a promoter region can provide details about how the promoter is regulated. We begin by describing an approach for discovering regulatory architectures for promoters whose regulation has not previously been studied. We focus on six promoters from E. coli including three well-studied promoters (rel, mar, and lac) to serve as test cases. We use the massively parallel reporter assay Sort-Seq to identify transcription factor binding sites with base-pair resolution, determine the regulatory role of each binding site, and infer energy matrices for each binding site. Then, we use DNA affinity chromatography and mass spectrometry to identify each transcription factor. We conclude with an in vivo approach for analyzing the sequ

Published
2018

71. Lung tumor promotion by curcumin

Author

Dance-Barnes, Stephanie T., Kock, Nancy D., Moore, Joseph E., Lin, Elaine Y., Mosley, Libyadda J., DʼAgostino, Ralph B., Jr, McCoy, Thomas P., Townsend, Alan J., and Miller, Mark Steven

Published
2009

72. Microbiome-derived carnitine mimics as novel mediators of gut-brain axis communication

Author

Hulme, Heather, Meikle, Lynsey M., Strittmatter, Nicole, van der Hooft, Justin J.J., Swales, John, Bragg, Ryan A., Villar, Victor H., Ormsby, Michael J., Barnes, Stephanie, Brown, Sheila L., Dexter, Alex, Kamat, Maya T., Komen, Jasper C., Walker, Daniel, Milling, Simon, Osterweil, Emily K., MacDonald, Andrew S., Schofield, Chris J., Tardito, Saverio, Bunch, Josephine, Douce, Gillian, Edgar, Julia M., Edrada-Ebel, RuAngelie, Goodwin, Richard J.A., Burchmore, Richard, and Wall, Daniel M.

Abstract

Alterations to the gut microbiome are associated with various neurological diseases, yet evidence of causality and identity of microbiome-derived compounds that mediate gut-brain axis interaction remain elusive. Here, we identify two previously unknown bacterial metabolites 3-methyl-4-(trimethylammonio)butanoate and 4-(trimethylammonio)pentanoate, structural analogs of carnitine that are present in both gut and brain of specific pathogen–free mice but absent in germ-free mice. We demonstrate that these compounds are produced by anaerobic commensal bacteria from the family Lachnospiraceae (Clostridiales) family, colocalize with carnitine in brain white matter, and inhibit carnitine-mediated fatty acid oxidation in a murine cell culture model of central nervous system white matter. This is the first description of direct molecular inter-kingdom exchange between gut prokaryotes and mammalian brain cells, leading to inhibition of brain cell function.

Published
2020

73. Clinical and research applications of neuromuscular ultrasound in amyotrophic lateral sclerosis

Author

Barnes,Stephanie L and Simon,Neil G

Subjects
Degenerative Neurological and Neuromuscular Disease
Abstract

Stephanie L Barnes1,2, Neil G Simon31Department of Neurology, Concord Repatriation General Hospital, Concord, NSW, Australia; 2St Vincent’s Clinical School, School of Medicine, The University of Notre Dame Australia, Sydney, NSW, Australia; 3St Vincent’s Clinical School, Faculty of Medicine, University of New South Wales, Sydney, NSW, AustraliaAbstract: Amyotrophic lateral sclerosis (ALS) is a devastating neurodegenerative disorder characterized by dysfunction at multiple levels of the neuraxis. It remains a clinical diagnosis without a definitive diagnostic investigation. Electrodiagnostic testing provides supportive information and, along with imaging and biochemical markers, can help exclude mimicking conditions. Neuromuscular ultrasound has a valuable role in the diagnosis and monitoring of ALS and provides complementary information to clinical assessment and electrodiagnostic testing as well as insights into the underlying pathophysiology of this disease. This review highlights the evidence for ultrasound in the evaluation of bulbar, limb and respiratory musculature and peripheral nerves in ALS. Further research in this evolving area is required.Keywords: amyotrophic lateral sclerosis, ultrasound, clinical neurophysiology, biomarker, clinical trials

Published
2019

74. Microbiome-derived carnitine mimics as previously unknown mediators of gut-brain axis communication

Author

Hulme, Heather, Meikle, Lynsey M., Strittmatter, Nicole, van der Hooft, Justin J.J., Swales, John, Bragg, Ryan A., Villar, Victor H., Ormsby, Michael J., Barnes, Stephanie, Brown, Sheila L., Dexter, Alex, Kamat, Maya T., Komen, Jasper C., Walker, Daniel, Milling, Simon, Osterweil, Emily K., MacDonald, Andrew S., Schofield, Chris J., Tardito, Saverio, Bunch, Josephine, Douce, Gillian, Edgar, Julia M., Edrada-Ebel, Ru Angelie, Goodwin, Richard J.A., Burchmore, Richard, Wall, Daniel M., Hulme, Heather, Meikle, Lynsey M., Strittmatter, Nicole, van der Hooft, Justin J.J., Swales, John, Bragg, Ryan A., Villar, Victor H., Ormsby, Michael J., Barnes, Stephanie, Brown, Sheila L., Dexter, Alex, Kamat, Maya T., Komen, Jasper C., Walker, Daniel, Milling, Simon, Osterweil, Emily K., MacDonald, Andrew S., Schofield, Chris J., Tardito, Saverio, Bunch, Josephine, Douce, Gillian, Edgar, Julia M., Edrada-Ebel, Ru Angelie, Goodwin, Richard J.A., Burchmore, Richard, and Wall, Daniel M.

Abstract

Alterations to the gut microbiome are associated with various neurological diseases, yet evidence of causality and identity of microbiome-derived compounds that mediate gut-brain axis interaction remain elusive. Here, we identify two previously unknown bacterial metabolites 3-methyl-4-(trimethylammonio)butanoate and 4-(trimethylammonio)pentanoate, structural analogs of carnitine that are present in both gut and brain of specific pathogen-free mice but absent in germ-free mice. We demonstrate that these compounds are produced by anaerobic commensal bacteria from the family Lachnospiraceae (Clostridiales) family, colocalize with carnitine in brain white matter, and inhibit carnitine-mediated fatty acid oxidation in a murine cell culture model of central nervous system white matter. This is the first description of direct molecular inter-kingdom exchange between gut prokaryotes and mammalian brain cells, leading to inhibition of brain cell function.

Published
2020

75. Microbiome-derived carnitine mimics as previously unknown mediators of gut-brain axis communication

Author

Hulme, Heather, primary, Meikle, Lynsey M., additional, Strittmatter, Nicole, additional, van der Hooft, Justin J. J., additional, Swales, John, additional, Bragg, Ryan A., additional, Villar, Victor H., additional, Ormsby, Michael J., additional, Barnes, Stephanie, additional, Brown, Sheila L., additional, Dexter, Alex, additional, Kamat, Maya T., additional, Komen, Jasper C., additional, Walker, Daniel, additional, Milling, Simon, additional, Osterweil, Emily K., additional, MacDonald, Andrew S., additional, Schofield, Chris J., additional, Tardito, Saverio, additional, Bunch, Josephine, additional, Douce, Gillian, additional, Edgar, Julia M., additional, Edrada-Ebel, RuAngelie, additional, Goodwin, Richard J. A., additional, Burchmore, Richard, additional, and Wall, Daniel M., additional

Published
2020
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80. Riluzole

Author

Barnes, Stephanie

Published
1996

81. Supporting Information for 'Tuning transcriptional regulation through signaling: A predictive theory for allosteric induction'

Author

Razo-Mejia, Manuel, Barnes, Stephanie L., Belliveau, Nathan M., Chure, Griffin, Einav, Tal, Lewis, Mitchell, and Phillips, Rob

Subjects
allostery, microscopy, transcriptional regulation, statistical mechanics, bacteria, predictive models, image processing
Abstract

This is the additional supplemental information for "Tuning transcriptional regulation through signaling: A predictive theory for allosteric induction". In this document, we take a more in-depth dissection of the properties, applications, and nuances of our statistical mechanical model of allosteric transcriptional regulation.

Published
2018
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83. A mouse model featuring tissue-specific deletion of p53 and Brca1 gives rise to mammary tumors with genomic and transcriptomic similarities to human basal-like breast cancer

Author

Hollern, Daniel P., primary, Contreras, Cristina M., additional, Dance-Barnes, Stephanie, additional, Silva, Grace O., additional, Pfefferle, Adam D., additional, Xiong, Jessie, additional, Darr, David B., additional, Usary, Jerry, additional, Mott, Kevin R., additional, and Perou, Charles M., additional

Published
2018
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92. Repeatability, reproducibility, and accuracy of quantitative mri of the breast in the community radiology setting

Author

Sorace, Anna G., primary, Wu, Chengyue, additional, Barnes, Stephanie L., additional, Jarrett, Angela M., additional, Avery, Sarah, additional, Patt, Debra, additional, Goodgame, Boone, additional, Luci, Jeffery J., additional, Kang, Hakmook, additional, Abramson, Richard G., additional, Yankeelov, Thomas E., additional, and Virostko, John, additional

Published
2018
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95. Dynamic contrast-enhanced magnetic resonance imaging and diffusion-weighted magnetic resonance imaging for predicting the response of locally advanced breast cancer to neoadjuvant therapy: a meta-analysis

Author

Virostko, John, primary, Hainline, Allison, primary, Kang, Hakmook, primary, Arlinghaus, Lori R., primary, Abramson, Richard G., primary, Barnes, Stephanie L., primary, Blume, Jeffrey D., primary, Avery, Sarah, primary, Patt, Debra, primary, Goodgame, Boone, primary, Yankeelov, Thomas E., primary, and Sorace, Anna G., primary

Published
2017
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