Selected Publications

2024

Emergence of dauer larvae in Caenorhabditis elegans disrupts continuity of host-microbiome interactions
Rahul Bodkhe, Kenneth Trang, Sabrina Hammond, Da Kyung Jung, Michael Shapira
FEMS Microbiology Ecology (2024) | Article

 
Video Summery of Choi et al.,: Investigating the Role of Gut Microbes in Aging and Disease Using Tiny Worms
Rebecca Choi, Rahul Bodkhe, Barbara Pees, Dan Kim, Maureen Berg, David Monnin, Juhyun Cho, Vivek Narayan, Ethan Deller, Cathy Savage-Dunn and Michael Shapira
SciTube (2024) | Article

 
An Enterobacteriaceae bloom in aging animals is restrained by the gut microbiome
Rebecca Choi, Rahul Bodkhe, Barbara Pees, Dan Kim, Maureen Berg, David Monnin, Juhyun 3 Cho, Vivek Narayan, Ethan Deller, Cathy Savage-Dunn and Michael Shapira
Aging Biology 2: (2024) | Article

 

2023

Identification of intestinal mediators of Caenorhabditis elegans DBL-1/BMP immune signaling shaping gut microbiome composition
Kenneth Trang, Barbara Pees, Siavash Karimzadegan, Rahul Bodkhe, Sabrina Hammond, Michael Shapira
BioRXiv /2023.10.26.564221: (2023) Abstract | Article
[ Request by emailing mshapira@berkeley.edu ]

 
Microbiome remodeling through bacterial competition and host behavior enables rapid adaptation to environmental toxins
Dan J Kim, Olga Maria Pérez-Carrascal, Catherin DeSousa, Da Kyung Jung, Seneca Bohley, Lila Wijaya, Kenneth Trang, Sarah El Khoury, Michael Shapira
BioXiv (2023) | Article

 

2022

Compost microcosms as microbially diverse natural-like environments for microbiome research in C. elegans.
Trang, K., Bodkhe, R. and Shapira, M.
Journal of Visualized Experiments 187: (2022) Abstract | Article
[ Request by emailing mshapira@berkeley.edu ]

 
Host Preference of Beneficial Commensals in a Microbially-Diverse Environment
Olga M Pérez-Carrascal, Rebecca Choi, Méril Massot, Barbara Pees, Vivek Narayan and Michael Shapira
Frontiers in Cellular and Infection Microbiology 12: 795343 (2022) Abstract | Article

 

2021

mir-71 mediates age-dependent opposing contributions of the stress-activated kinase KGB-1 in Caenorhabditis elegans
Cyrus Ruediger, Siavash Karimzadegan, Sonya Lin, Michael Shapira
Genetics (2021) Abstract | Article

 

2020

Interactions with a Complex Microbiota Mediate a Trade-Off between the Host Development Rate and Heat Stress Resistance
Samuel Slowinski, Isabella Ramirez, Vivek Narayan, Medha Somayaji, Maya Para, Sarah Pi, Niharika Jadeja, Siavash Karimzadegan, Barbara Pees and Michael Shapira
Microorganisms 8: 1781 (2020) Abstract | Article
[ Request by emailing mshapira@berkeley.edu ]

 
CeMbio - The Caenorhabditis elegans Microbiome Resource
Philipp Dirksen, Adrien Assié, Johannes Zimmermann, Fan Zhang, Adina-Malin Tietje, Sarah Arnaud Marsh, Marie-Anne Félix, Michael Shapira, Christoph Kaleta, Hinrich Schulenburg, Buck Samuel
G3 (2020) Abstract | Article
[ Request by emailing mshapira@berkeley.edu ]

 
Extra-intestinal regulation of the gut microbiome: The case of C. elegans TGFβ/SMA signalling
Rebecca Choi, Dan Kim, Stacy Li, Meril Massot, Vivek Narayan, Samuel Slowinski, Hinrich Schulenburg, Michael Shapira
Book chapter in Cellular Dialogues in the Holobiont, in press (2020)
[ Request by emailing mshapira@berkeley.edu ]

 

2019

TGFβ/BMP signaling determines abundance and contributions of C. elegans gut commensals
Maureen Berg, David Monnin, Juhyun Cho, Lydia Nelson, Alex Crits-Christoph, and Michael Shapira
Nature Communications 10(1): 604 (2019) Abstract | Article

 

2018

Integration of Stress Signaling in Caenorhabditis elegans Through Cell Non-autonomous Contributions of the JNK Homolog KGB-1
Limeng Liu, Cyrus Ruediger and Michael Shapira
Genetics 210(4): 1317-1328 (2018) Abstract | Article

 

2017

Caenorhabditis elegans as a Model for Microbiome Research
Zhang F, Berg M, Dierking K, Félix MA, Shapira M, Samuel BS, Schulenberg H.
Frontiers in Microbiology 8: 485 (2017) Abstract | Article

 
Host-microbiota interactions in Caenorhabditis elegans and their significance
Shapira, M.
Current Opinion in Microbiology 38: 142-147 (2017) Abstract | Article

 
Adaptation from Within or from Without: A Reply to Rodrigo et al.
Shapira, M.
Trends in Ecology and Evolution 32(2): 85 (2017) Abstract | Article

 

2016

The nematode Caenorhabditis elegans survives subfreezing temperatures in an isochoric system
Mikus H, Miller A, Nastase G, Serban A, Shapira M, Rubinsky B
Biochem Biophys Res Commun 477(3): 410-405 (2016) Abstract | Article

 
Assembly of the Caenorhabditis elegans gut microbiota from diverse soil microbial environments
Berg M, Stenuit B, Ho J, Wang A, Parke C, Knight M, Alvarez-Cohen L, Shapira M.
ISME J 10(8): 1998-2009 (2016) Abstract | Article

 
FOS-1 functions as a transcriptional activator downstream of the C. elegans JNK homolog KGB-1
Zhang Z, Liu L, Twumasi-Boateng K, Block DH, Shapira M.
Cell Signal (2016) Abstract

 
Host-Specific Functional Significance of Caenorhabditis Gut Commensals
Berg M, Zhou XY, Shapira M.
Frontiers in Microbiology 7: 1622 (2016) Abstract | Article

 
Gut Microbiotas and Host Evolution: Scaling Up Symbiosis
Shapira, M.
Trends in Ecology and Evolution 31(7): 539-549 (2016) Abstract | Article

 

2015

The Developmental Intestinal Regulator ELT-2 Controls p38-Dependent Immune Responses in Adult C. elegans
Block DH, Twumasi-Boateng K, Kang HS, Carlisle JA, Hanganu A, Lai TY, Shapira M.
Plos Genetics 11(5): e1005265 (2015) Abstract | Article

 
GATA transcription factors as tissue-specific master regulators for induced responses
Block, D.H. and Shapira, M.
Worm 4(4): e1118607 (2015) Abstract | Article

 

2014

Automated separation of C. elegans variably colonized by a bacterial pathogen
Twumasi-Boateng, K., Berg, M., and Shapira, M
J Vis Exp Mar 21: 85 (2014) Abstract | Article

 

2013

Association with soil bacteria enhances p38-dependent infection resistance in C. elegans
Montalvo-Katz, S., Huang, H. Appel, M.D., Berg, M. and Shapira, M
Infection and Immunity 81(2): 514-20 (2013) Abstract | Article

 

2012

An age-dependent reversal in the protective capacities of JNK signaling shortens C. elegans lifespan
Twumasi-Boateng, K., Wang, T., Tsai, L., Lee, K.L., Salehpour, A., Bhat, S., Tan, M.W. and Shapira, M.
Aging Cell 11(4): 659-67 (2012) Abstract | Article

 
Dissociation of immune responses from pathogen colonization supports pattern recognition in C. elegans
Twumasi-Boateng, K. and Shapira, M.
Plos ONE 7(4): e35400 (2012) Abstract | Article

 

2011

Genetic and molecular analysis of nematode-microbe interactions
Tan, M.W. and Shapira, M.
Cell Microbiol 11(4): 497-507 (2011) Abstract | Article

 

2010

Stress effects on immunity in vertebrates and invertebrates. In Stress: from molecules to behavior. A comprehensive analysis of the neurobiology of stress responses
Shapira M.
Book. Wiley Publishing (2010)

 

2008

Genetic analysis of C. elegans innate immunity
Shapira, M. and Tan, M.W.
Methods in Molecular Biology 415: 429-42 (2008) Abstract | Article

 

2007

C. elegans pgp-5 is involved in resistance to bacterial infection and heavy metal and its regulation requires TIR-1 and a p38 MAP kinase cascade
Kurz, C.L., Shapira, M., Chen, K., Baillie, D.L. and Tan, M.W.
Biochem. Biophys. Res. Commun. 363(2): 438-43 (2007) Abstract | Article

 

2006

A conserved role for a GATA transcription factor in regulating epithelial innate immune responses
Shapira, M. Hamlin, B.J., Rong, J., Chen, K., Ronen, M. and Tan, M.W.
PNAS 103: 14086-14091 (2006) Abstract | Article

 

2004

Disruption of yeast forkhead-associated cell cycle transcription by oxidative stress
Shapira, M. Segal, E. and Botstein, D.
Mol. Biol. Cell 15: 5659-5669 (2004) | Article

 

2003

Module Networks: Discovering Regulatory Modules and their Condition Specific Regulators from Gene Expression Data
Segal, E., Shapira, M., Regev, A., Pe’er, D., Botstein, D., Koller, D and Friedman, N.
Nature Genetics 34(2): 166-176 (2003) Abstract

 

2001

Changes in neuronal acetylcholinesterase gene expression and division of labor in honey bee colonies
Shapira, M, Thompson, C.K., Soreq, H. and Robinson, G.
J Mol Neurosc 17: 1-12 (2001) Abstract | Article

 

2000

A transcription-activating polymorphism in the ACHE promoter associated with acute sensitivity to anti-acetylcholinesterases
Shapira, M., Tur-Kaspa, I., Bosgraaf, L., Livni, N., Grant, A.D., Grisaru, D., Korner, M., Ebstein, R.P. and Soreq, H.
Hum Mol Gen 9(9): 1273-81 (2000) Abstract | Article

 

1994

Transgenic engineering of neuromuscular junctions in Xenopus laevis embryos transiently overexpressing key cholinergic proteins
Shapira, M., Seidman, S., Sternfeld, M., Timberg, R., Kaufer, D., Patrick J. and Soreq, H
PNAS 91: 9072-6 (1994) | Article