All Publications

  • Ultrafast epithelial contractions provide insights into contraction speed limits and tissue integrity. Proceedings of the National Academy of Sciences of the United States of America Armon, S., Bull, M. S., Aranda-Diaz, A., Prakash, M. 2018


    By definition of multicellularity, all animals need to keep their cells attached and intact, despite internal and external forces. Cohesion between epithelial cells provides this key feature. To better understand fundamental limits of this cohesion, we study the epithelium mechanics of an ultrathin (25 mum) primitive marine animal Trichoplax adhaerens, composed essentially of two flat epithelial layers. With no known extracellular matrix and no nerves or muscles, T. adhaerens has been claimed to be the "simplest known living animal," yet is still capable of coordinated locomotion and behavior. Here we report the discovery of the fastest epithelial cellular contractions known in any metazoan, to be found in T. adhaerens dorsal epithelium (50% shrinkage of apical cell area within one second, at least an order of magnitude faster than other known examples). Live imaging reveals emergent contractile patterns that are mostly sporadic single-cell events, but also include propagating contraction waves across the tissue. We show that cell contraction speed can be explained by current models of nonmuscle actin-myosin bundles without load, while the tissue architecture and unique mechanical properties are softening the tissue, minimizing the load on a contracting cell. We propose a hypothesis, in which the physiological role of the contraction dynamics is to resist external stresses while avoiding tissue rupture ("active cohesion"), a concept that can be further applied to engineering of active materials.

    View details for PubMedID 30309963

  • Robust Synthetic Circuits for Two-Dimensional Control of Gene Expression in Yeast ACS SYNTHETIC BIOLOGY Aranda-Diaz, A., Mace, K., Zuleta, I., Harrigan, P., El-Samad, H. 2017; 6 (3): 545-554


    Cellular phenotypes are the result of complex interactions between many components. Understanding and predicting the system level properties of the resulting networks requires the development of perturbation tools that can simultaneously and independently modulate multiple cellular variables. Here, we develop synthetic modules that use different arrangements of two transcriptional regulators to achieve either concurrent and independent control of the expression of two genes, or decoupled control of the mean and variance of a single gene. These modules constitute powerful tools to probe the quantitative attributes of network wiring and function.

    View details for DOI 10.1021/acssynbio.6b00251

    View details for Web of Science ID 000397080300019

    View details for PubMedCentralID PMC5507677

  • Ceapins are a new class of unfolded protein response inhibitors, selectively targeting the ATF6 alpha branch ELIFE Gallagher, C. M., Garri, C., Cain, E. L., Ang, K., Wilson, C. G., Chen, S., Hearn, B. R., Jaishankar, P., Aranda-Diaz, A., Arkin, M. R., Renslo, A. R., Walter, P. 2016; 5


    The membrane-bound transcription factor ATF6α plays a cytoprotective role in the unfolded protein response (UPR), required for cells to survive ER stress. Activation of ATF6α promotes cell survival in cancer models. We used cell-based screens to discover and develop Ceapins, a class of pyrazole amides, that block ATF6α signaling in response to ER stress. Ceapins sensitize cells to ER stress without impacting viability of unstressed cells. Ceapins are highly specific inhibitors of ATF6α signaling, not affecting signaling through the other branches of the UPR, or proteolytic processing of its close homolog ATF6β or SREBP (a cholesterol-regulated transcription factor), both activated by the same proteases. Ceapins are first-in-class inhibitors that can be used to explore both the mechanism of activation of ATF6α and its role in pathological settings. The discovery of Ceapins now enables pharmacological modulation all three UPR branches either singly or in combination.

    View details for DOI 10.7554/eLife.11878

    View details for Web of Science ID 000380847300001

    View details for PubMedID 27435960

    View details for PubMedCentralID PMC4954757

  • Delayed Ras/PKA signaling augments the unfolded protein response PROCEEDINGS OF THE NATIONAL ACADEMY OF SCIENCES OF THE UNITED STATES OF AMERICA Pincus, D., Aranda-Diaz, A., Zuleta, I. A., Walter, P., El-Samad, H. 2014; 111 (41): 14800–14805


    During environmental, developmental, or genetic stress, the cell's folding capacity can become overwhelmed, and misfolded proteins can accumulate in all cell compartments. Eukaryotes evolved the unfolded protein response (UPR) to counteract proteotoxic stress in the endoplasmic reticulum (ER). Although the UPR is vital to restoring homeostasis to protein folding in the ER, it has become evident that the response to ER stress is not limited to the UPR. Here, we used engineered orthogonal UPR induction, deep mRNA sequencing, and dynamic flow cytometry to dissect the cell's response to ER stress comprehensively. We show that budding yeast augments the UPR with time-delayed Ras/PKA signaling. This second wave of transcriptional dynamics is independent of the UPR and is necessary for fitness in the presence of ER stress, partially due to a reduction in general protein synthesis. This Ras/PKA-mediated effect functionally mimics other mechanisms, such as translational control by PKR-like ER kinase (PERK) and regulated inositol-requiring enzyme 1 (IRE1)-dependent mRNA decay (RIDD), which reduce the load of proteins entering the ER in response to ER stress in metazoan cells.

    View details for DOI 10.1073/pnas.1409588111

    View details for Web of Science ID 000342922000049

    View details for PubMedID 25275008

    View details for PubMedCentralID PMC4205644

  • Dynamic characterization of growth and gene expression using high-throughput automated flow cytometry NATURE METHODS Zuleta, I. A., Aranda-Diaz, A., Li, H., El-Samad, H. 2014; 11 (4): 443-+


    Cells adjust to changes in environmental conditions using complex regulatory programs. These cellular programs are the result of an intricate interplay between gene expression, cellular growth and protein degradation. Technologies that enable simultaneous and time-resolved measurements of these variables are necessary to dissect cellular homeostatic strategies. Here we report the development of an automated flow cytometry robotic setup that enables real-time measurement of precise and simultaneous relative growth and protein synthesis rates of multiplexed microbial populations across many conditions. These measurements generate quantitative profiles of dynamically evolving protein synthesis and degradation rates. We demonstrate this setup in the context of gene regulation of the unfolded protein response (UPR) of Saccharomyces cerevisiae and uncover a dynamic and complex landscape of gene expression, growth dynamics and proteolysis following perturbations.

    View details for DOI 10.1038/nmeth.2879

    View details for Web of Science ID 000333749900028

    View details for PubMedID 24608180

    View details for PubMedCentralID PMC4016179