We use a combination of experimental and computational approaches to reverse-engineer pattern formation and tissue morphogenesis, growth control, and regeneration to inspire new ways to treat human diseases, such as cancer, and to accelerate wound healing and regeneration.
We are looking for talented and motivated graduate students and post-doctoral researchers with interests in either two areas: 1. Synthetic or quantitative biology of multicellular systems; and 2. Computational modeling of cell signaling or systems identification.
Interested undergraduates and potential graduates and post-doctoral researchers are welcome to inquire about available positions in the lab. Please note that undergraduate research positions require a 15 hour per week commitment to the research project.
Congratulations to Dharsan Soundarrajan for passing his Ph.D. candidacy exam!
Collaborative work with Saverio Gentile entitled “Potassium channel activity controls breast cancer metastasis by affecting β-catenin signaling” is now published in Cell Death and Disease!
Our work on decoding calcium signaling dynamics at the organ-level is accepted published in Biophysical Journal! The work is entitled, “Decoding Calcium Signaling Dynamics during Drosophila Wing Disc Development.”Way to go everyone!
We officially welcome Francisco Huizar, who is pursuing a Bioengineering Ph.D. program, to the lab!
Congratulations to Dr. Pavel Brodskiy on his successful dissertation defense. Well done!
Our short perspective on the new field of synthetic developmental biology is highlighted at Science Trends.
Ulises, Ana, Mark and Anthony all provide research updates at group meeting. It was great having you guys join our group for the summer!
Summer lab picnic: Lots of fun!
Dr. Zartman is promoted to Associate Professor (effective July 2018).
Dr. Zartman named as a 2018 Rising Star by the BMES Cellular and Molecular Bioengineering Special Interest Group working group.
We welcome Mascha and Ramezan to our group! Welcome
We welcome Nilay and Vijay to our group! Welcome!
October 6, 2017: Congratulations to Cody Narciso for successfully defending his dissertation. Way to go, Dr. Narciso!
Current: We are looking for talented post-doctoral researchers with experience in either two areas:
1. Molecular cell biology and advanced Drosophila genetics
2. Computational modeling of cell signaling or systems identification
We are also looking for lab technicians with expertise in Drosophila and cell biology. Please contact Professor Zartman directly.
We have been awarded a NIH R35 grant entitled: “Regulation and Function of Multicellular Calcium Signaling in Epithelial Growth and Regeneration.” In this research program we seek to discover the underlying principles of integrative cell communication mediated by calcium signaling.
A long-term goal of this research is to learn how to manipulate calcium signaling to control cellular functions such as growth, motility, or death. Such knowledge will inspire methods to regulate cell differentiation for stem cell engineering applications or to stop metastatic cancers.
Our work “Release of Applied Mechanical Loading Stimulates Intercellular Calcium Waves in Drosophila Wing Disc” in Biophysical Journal is now online. This work was highlighted as a “New and Notable” by the journal!
July 17, 2017: Our work with the Alber, Goodson and Weisel groups to identify efficient tissue clearing method for whole blood clots is now published at Biomedical Optics Express! This work has been highlighted at EurekAlert and Science Daily.
July 10, 2017: Our collaborator Jochen Kursawe (Oxford University) visited us and also gave a seminar talk: Quantitative approaches to investigating epithelial morphogenesis
April 8, 2017: We are co-organizing the 5th Midwest Q-Bio Symposium @ University of Notre Dame. It was a great turnout!
March 2017: Contratulations to Paulina Eberts for her National Science Foundation Gradute Fellowship award!
Paulina was selected as an undergraduate student in chemical engineering. Her thesis is “Extension of Non-destructive 3D Immunostaining to Paraffin Embedded Tissues.”
November 2016: Our collaborative work is now published in Interface! Robust cell tracking in epithelial tissues through identification of maximum common subgraphs. Congratulations especially to lead author Jochen Kursawe.
November 2016: We welcome two new members to the lab: Jamison Jangula and Dharsan Soundarrajan.
July 2016: Congratulations to Pavel! He was selected as an Walther Cancer Foundation Interdisciplinary Interface Training Project (IITP) fellow through the Harper Cancer Research Institute.
June 7, 2016: Congratulations, Dr. Miranda Burnette! Great job on your dissertation defense. Way to go!
May 2016: Megan, welcome to the lab! Megan Levis joins the group.
March 1 2016: We have been awarded an NSF CAREER award for our project, “Integrative Analysis for Reverse Engineering Embryonic Pattern Repair Mechanisms.”
March 1 2016: In collaboration with the Hoelzle and Zhang labs, a short communication describing on-chip 3D tissue histology for microbiopsies is now online in Biomicrofluidics. Great work team! Links to the press release is found here.
February 26, 2016: Congratulations to Qinfeng Wu for passing his Ph.D. Candidacy exam. Way to go!
A collaborative study with the Fletcher and Baker groups on the capabilities and limitations of tissue size control through passive mechanical forces is now in press in PLOS Computational Biology!
Our study examining the spatiotemporal dynamics of calcium flashes due to local wounding is now online.
July 2015: Congratulations to Cody Narciso, who was named a 2015/16 Berry Family Foundation Graduate Fellowships in Advanced Diagnostics & Therapeutics. See more at here.
From the CBE Website: “Qinfeng Wu, a graduate student in the Department of Chemical and Biomolecular Engineering, was one of the 2015 winners in the annual Research Like a Champion competition. Sponsored by the Harper Cancer Research Institute, the competition is open to individual students/student groups across all disciplines of the University. Participants submit innovative approaches to the fight against cancer. The submitted proposals address causes, treatment, or prevention of the disease.
Wu’s winning project, “Cell Competition in Breast Cancer: Functional Identification of Genes that Determine Whether Breast Cancer Cells Out-compete Breast Epithelial Cells,” focuses on how breast cancer cells avoid tumor suppression treatments and beat out normal cells for nutrients, as well as how best to identify and change the mechanisms through which this cell competition occurs.”
April 2015: Congratulations to the start-up Enlightened Diagnostics, Inc. on their achievements at the McCloskey Business Plan competition and at the Rice Business Plan Competition. For a description of their success, click here.
February 2015: Congratulations to the Englightened Diagnostics team on their victory at the Cardinal Challenge business plan competition! The team is presenting on a novel 3-D imaging platform developed iin collaboration with the Hoelzle and Zhang labs to improve the amount of information available for clinicians from biopsies.
January 2015: Cody passed his Candidacy exam. Congratulations!
July 2014: Miranda publishes her chemically defined medium for long-term maintenance and growth of Drosophila cells. The first truly chemically defined medium for Drosophila cell culture. In addition, the paper highlights a strategy for rationale media design. Congratulations!
April 15, 2014: Cody Narciso and Kyle Cowdrick (Mentor: Siyuan Zhang) win the Harper Cancer Research Institute’s“Research Like A Champion” Award. Congratulations!
January 30, 2014: Miranda passes her Candidacy exam. Congratulations!
December 12, 2013: Lab Christmas party. Merry Christmas and Happy New Year!
Pavel Brodskiy and Qinfeng (Austin) Wu officially join the group. Welcome!
June 11, 2013: Jessica Freeman selected as a HCRI Summer Undergraduate Research Fellow. Congratulations Jessica!
March 4, 2013: Cody Narciso presented at the Workshop on Physical Approaches to Studying the Cytoskeleton and Cell Motility: https://www3.nd.edu/~icsb/Workshop_2013/.
January 12-16, 2013: Miranda presented a poster at SLAS 2013: Miranda Burnette, Jonathan Chen, and Jeremiah Zartman, Combinatorial Inverse Drug Screen Pipeline to Probe Epithelial Wound Healing in a Model Genetic Organ Culture System. SLAS 2013. January 12-16, 2013.
October 2012: Cody Narciso joins the lab. Welcome!
March 2012: Teresa Brito-Robinson joins the lab. Welcome!
January 2012: Lab officially opens. Miranda Burnette joins the lab. Welcome!
To be updated.
Simplified microfluidics and bioprinting systems for research and education.
PhD. Assistant Professor Biology Department, St. John Fisher College
Tuesday, August 8, 4-5 pm
Widespread adoption of novel research technologies is often hampered by cost and lack of equipment and expertise. Overcoming these hurdles can prove challenging. For example, improved protocols that produce reliable results may manage to reduce production time and cost of materials, but may still require procedures and/or the use of equipment not commonly available to most research and teaching laboratories. On the other hand, the quality and/or reproducibility of results obtained using low cost approaches may be compromised by the use of unreliable materials. Our goal is to provide research groups and educational settings with microfluidics and bioprinting systems that are both reliable and affordable. In the area of microfludics we describe a type of device that makes exclusive use of consumer-grade components and equipment. The user-designed devices consist of as little as three layers of a polymer film, with microchannels shaped by an inexpensive craft cutter, and sealed by thermal lamination. The chips are flexible and ten to thirty-times thinner than the common PDMS/ glass alternative. Fabrication time is in the order of minutes (allowing for rapid iteration), and the method requires very little training. In the area of bioprinting we make use of a consumer-grade 3D printer fitted with a heated nozzle which delivers a biocompatible hydrogel that sets as it comes into contact with a cooled surface. Our objective is to produce scaffolds in a variety of shapes that promote 3-dimensional arrangements of cells in culture. In summary, our systems lower the barrier-to-entry for robust microfluidic devices and biocompatible tissue scaffolds, facilitating the adoption of formerly out-of-reach technologies.
Monday, July 10 3 – 4 PM,
McCourtney Hall Conference Room 203
Quantitative approaches to investigating epithelial morphogenesis
Jochen Kursawe, University of Oxford, Oxford
Recently, the experimental study of morphogenesis has thrived due to a rise in quantitative methods. The resulting avalanche of quantitative data requires us to rethink the scientific method. We need to design quantitative hypotheses through mathematical models, make quantitative experimental predictions, devise methods for quantitative data analysis, and design methods for quantitative inference using models and data. This work aims to enable this transition for the integrative analysis of morphogenesis in epithelia. We conduct the first systematic numerical analysis of a widely used cell-based model of epithelia, the vertex model, and estimate to what extent quantitative model predictions may be influenced by parameter values and implementation details. We then apply this model to a key question in developmental biology by constructing a quantitative theory for tissue size control in the embryonic epidermis of the fruit fly Drosophila, using the model to predict the outcomes of future experiments. We further devise a method for estimating mechanical parameters of vertex models from imaging data and quantifying the uncertainty associated with such estimates. Finally, we propose a novel algorithm for robust cell tracking in live-imaging microscopy videos of epithelial tissues that illustrates how graph theoretic concepts may be used to overcome challenges in quantitative data analysis. Together, these contributions will enable the quantitative study of epithelia for a wide range of applications.
Christmas dinner with the lab group – December 6, 2012 at J.W. Chen’s. Lot’s of fun!
Lab Picnic was held on May 2013.