Education & Certifications

  • Master of Science, Stanford University, BIOE-MS (2014)
  • Bachelor of Science, University of California at Berkeley, Bioengineering (2012)

Stanford Advisors

All Publications

  • Controlling cell shape on hydrogels using lift-off protein patterning PLoS ONE Moeller, J., Denisin, A. K., Sim, J., Wilson, R. E., Ribeiro, A. J., Pruitt, B. L. 2018; 13 (1)
  • Controlling cell shape on hydrogels using lift-off patterning bioRxiv Moeller, J., Denisin, A. K., Sim, J., Wilson, R. E., Ribeiro, A. J., Pruitt, B. L. 2017

    View details for DOI 10.1101/111195

  • Single Molecule Force Measurements in Living Cells Reveal a Minimally Tensioned Integrin State. ACS nano Chang, A. C., Mekhdjian, A. H., Morimatsu, M., Denisin, A. K., Pruitt, B. L., Dunn, A. R. 2016: -?


    Integrins mediate cell adhesion to the extracellular matrix and enable the construction of complex, multicellular organisms, yet fundamental aspects of integrin-based adhesion remain poorly understood. Notably, the magnitude of the mechanical load experienced by individual integrins within living cells is unclear, due principally to limitations inherent to existing techniques. Here we use Förster resonance energy transfer-based molecular tension sensors to directly measure the distribution of loads experienced by individual integrins in living cells. We find that a large fraction of integrins bear modest loads of 1-3 pN, while subpopulations bearing higher loads are enriched within adhesions. Further, our data indicate that integrin engagement with the fibronectin synergy site, a secondary binding site specifically for α5β1 integrin, leads to increased levels of α5β1 integrin recruitment to adhesions but not to an increase in overall cellular traction generation. The presence of the synergy site does, however, increase cells' resistance to detachment by externally applied loads. We suggest that a substantial population of integrins experiencing loads well below their peak capacities can provide cells and tissues with mechanical integrity in the presence of widely varying mechanical loads.

    View details for PubMedID 27779848

  • Tuning the Range of Polyacrylamide Gel Stiffness for Mechanobiology Applications ACS APPLIED MATERIALS & INTERFACES Denisin, A. K., Pruitt, B. L. 2016; 8 (34): 21893-21902


    Adjusting the acrylamide monomer and cross-linker content in polyacrylamide gels controls the hydrogel stiffness, yet the reported elastic modulus for the same formulations varies widely and these discrepancies are frequently attributed to different measurement methods. Few studies exist that examine stiffness trends across monomer and cross-linker concentrations using the same characterization platform. In this work, we use Atomic Force Microscopy and analyze force-distance curves to derive the elastic modulus of polyacrylamide hydrogels. We find that gel elastic modulus increases with increasing cross-link concentration until an inflection point, after which gel stiffness decreases with increasing cross-linking. This behavior arises because of the formation of highly cross-linked clusters, which add inhomogeneity and heterogeneity to the network structure, causing the global network to soften even under high cross-linking conditions. We identify these inflection points for three different total polymer formulations. When we alter gelation kinetics by using a low polymerization temperature, we find that gels are stiffer when polymerized at 4 °C compared to room temperature, indicating a complex relationship between gel structure, elasticity, and network formation. We also investigate how gel stiffness changes during storage over 10 days and find that specific gel formulations undergo significant stiffening (1.55 ± 0.13), which may be explained by differences in gel swelling resulting from initial polymerization parameters. Taken together, our study emphasizes the importance of polyacrylamide formulation, polymerization temperature, gelation time, and storage duration in defining the structural and mechanical properties of the polyacrylamide hydrogels.

    View details for DOI 10.1021/acsami.5b09344

    View details for Web of Science ID 000382514100006

    View details for PubMedID 26816386

  • For whom the cells pull: Hydrogel and micropost devices for measuring traction forces. Methods Ribeiro, A. J., Denisin, A. K., Wilson, R. E., Pruitt, B. L. 2016; 94: 51-64


    While performing several functions, adherent cells deform their surrounding substrate via stable adhesions that connect the intracellular cytoskeleton to the extracellular matrix. The traction forces that deform the substrate are studied in mechanotrasduction because they are affected by the mechanics of the extracellular milieu. We review the development and application of two methods widely used to measure traction forces generated by cells on 2D substrates: (i) traction force microscopy with polyacrylamide hydrogels and (ii) calculation of traction forces with arrays of deformable microposts. Measuring forces with these methods relies on measuring substrate displacements and converting them into forces. We describe approaches to determine force from displacements and elaborate on the necessary experimental conditions for this type of analysis. We emphasize device fabrication, mechanical calibration of substrates and covalent attachment of extracellular matrix proteins to substrates as key features in the design of experiments to measure cell traction forces with polyacrylamide hydrogels or microposts. We also report the challenges and achievements in integrating these methods with platforms for the mechanical stimulation of adherent cells. The approaches described here will enable new studies to understand cell mechanical outputs as a function of mechanical inputs and advance the understanding of mechanotransduction mechanisms.

    View details for DOI 10.1016/j.ymeth.2015.08.005

    View details for PubMedID 26265073

    View details for PubMedCentralID PMC4746112

  • A Biotic Game Design Project for Integrated Life Science and Engineering Education PLOS BIOLOGY Cira, N. J., Chung, A. M., Denisin, A. K., Rensi, S., Sanchez, G. N., Quake, S. R., Riedel-Kruse, I. H. 2015; 13 (3)


    Engaging, hands-on design experiences are key for formal and informal Science, Technology, Engineering, and Mathematics (STEM) education. Robotic and video game design challenges have been particularly effective in stimulating student interest, but equivalent experiences for the life sciences are not as developed. Here we present the concept of a "biotic game design project" to motivate student learning at the interface of life sciences and device engineering (as part of a cornerstone bioengineering devices course). We provide all course material and also present efforts in adapting the project's complexity to serve other time frames, age groups, learning focuses, and budgets. Students self-reported that they found the biotic game project fun and motivating, resulting in increased effort. Hence this type of design project could generate excitement and educational impact similar to robotics and video games.

    View details for DOI 10.1371/journal.pbio.1002110

    View details for Web of Science ID 000352095700019

    View details for PubMedID 25807212

    View details for PubMedCentralID PMC4373802

  • Structural and molecular interrogation of intact biological systems. Nature Chung, K., Wallace, J., Kim, S., Kalyanasundaram, S., Andalman, A. S., Davidson, T. J., Mirzabekov, J. J., Zalocusky, K. A., Mattis, J., Denisin, A. K., Pak, S., Bernstein, H., Ramakrishnan, C., Grosenick, L., Gradinaru, V., Deisseroth, K. 2013; 497 (7449): 332-337


    Obtaining high-resolution information from a complex system, while maintaining the global perspective needed to understand system function, represents a key challenge in biology. Here we address this challenge with a method (termed CLARITY) for the transformation of intact tissue into a nanoporous hydrogel-hybridized form (crosslinked to a three-dimensional network of hydrophilic polymers) that is fully assembled but optically transparent and macromolecule-permeable. Using mouse brains, we show intact-tissue imaging of long-range projections, local circuit wiring, cellular relationships, subcellular structures, protein complexes, nucleic acids and neurotransmitters. CLARITY also enables intact-tissue in situ hybridization, immunohistochemistry with multiple rounds of staining and de-staining in non-sectioned tissue, and antibody labelling throughout the intact adult mouse brain. Finally, we show that CLARITY enables fine structural analysis of clinical samples, including non-sectioned human tissue from a neuropsychiatric-disease setting, establishing a path for the transmutation of human tissue into a stable, intact and accessible form suitable for probing structural and molecular underpinnings of physiological function and disease.

    View details for DOI 10.1038/nature12107

    View details for PubMedID 23575631

    View details for PubMedCentralID PMC4092167

  • Structural and molecular interrogation of intact biological systems. Nature Chung, K., Wallace, J., Kim, S., Kalyanasundaram, S., Andalman, A. S., Davidson, T. J., Mirzabekov, J. J., Zalocusky, K. A., Mattis, J., Denisin, A. K., Pak, S., Bernstein, H., Ramakrishnan, C., Grosenick, L., Gradinaru, V., Deisseroth, K. 2013; 497 (7449): 332-337

    View details for DOI 10.1038/nature12107

    View details for PubMedID 23575631

  • Hydrodynamic focusing for impedance-based detection of specifically bound microparticles and cells: Implications of fluid dynamics on tunable sensitivity Sensors and Actuators B: Chemical Gusphyl A Justin, Aleksandra K Denisin, Mansoor Nasir, Lisa C Shriver-Lake, Joel P Golden, Frances S Ligler 2012; 166-167: 386–393
  • Post-collection processing of Schirmer strip-collected human tear fluid impacts protein content ANALYST Denisin, A. K., Karns, K., Herr, A. E. 2012; 137 (21): 5088-5096


    We examine the impact of post-collection sample handling on the protein composition of human tear samples. In particular, we characterize diffusion-based protein extraction from Schirmer strips. These strips of filter paper membrane are the de facto standard for tear fluid collection and storage, with diffusion-based protein elution off the strip being the most widely reported protein extraction strategy. Nevertheless, the diffusion-based protein elution strategy remains uncharacterized regarding downstream functional protein assays. Here, the time-dependence, concentration-dependence, and repeatability of the diffusion-based protein recovery protocol are characterized. Levels of protein irrecoverable from the Schirmer strip and lost during sample handling are isolated and compared for several major tear proteins. Further, the impact of the Schirmer strip and sample handling on the downstream concentration of proteins ranging in molecular weight, surface charge, and surface hydropathicity is quantified. Diffusion-based protein extraction from Schirmer strips was observed to be protein-dependent. Schirmer strips retained tear proteins to varying extents: 14.2% of lysozyme, 9.5% of human serum albumin, 27.7% of secretory IgA, and 30.9% of mucin 4. Tear protein loss during sample handling ranged from 2% (lysozyme) to 41.2% (mucin 4). Strip retention of protein was observed to be associated with protein molecular weight and hydrophobic surface area. Greater sample handling loss was associated with increased hydrophobic surface area of model proteins. Surface charge or surface hydrophilicity was not significantly associated with protein loss. We therefore conclude that, although diffusion-based processing of Schirmer strip-collected tear samples is widely used, these protocols may result in total post-collection protein loss which is considerable, consistent, and protein-dependent. This loss alters the relative and absolute protein concentrations in the sample. A priori prediction of strip-losses for individual proteins does not appear to be facile, based on cursory knowledge of protein surface properties. Thus, we emphasize "spike and recover" control experiments to determine expected elution profiles for target proteins when using diffusion-based protein sample preparation for Schirmer strip-collected tear fluid.

    View details for DOI 10.1039/c2an35821b

    View details for Web of Science ID 000309427600030

    View details for PubMedID 22991688