Research Tools

We utilize in vitro to in vivo models, as well as neuroscience, nanotechnology, data science, confocal microscopy, and biophysical tools to study the brain microenvironment, nanoparticle transport, and therapeutic effectiveness. Read more about our work in developing and applying these tools!

Data science tools to advance neuroscience and neurotherapeutics

The cellular and extracellular architecture of brain tissue is critical for homeostasis, but changes occur frequently due to aging, disease, or injury. To study these changes, biological imaging techniques are used to generate large amounts of data across multiple spatial and temporal dimensions. Modern data science techniques, including machine learning and artificial intelligence (ML/AI), provide a new toolkit to maximize the data collected through these techniques and gain deeper insight into how the brain changes by connecting datasets. We have applied ML/AI to MPT data. We showed the ability to predict local viscosity with 75% accuracy, nanoparticle size with 90% accuracy, and protein adhesion and cell internalization (which currently have no existing theoretical models) with 89% accuracy. We have also applied a boosted decision tree ML model to MPT data from nanoparticle diffusion in OWH slices to predict brain age. With cell imaging data, we have applied unsupervised ML to quantify cellular morphological features. In analyzing effectiveness of different therapies for term brain injury, we showed that ML-based classification of microglia morphological shifts in response to injury predicted the neuroprotective response to each therapy, with different morphologies associated with different treatment responses.

Representative publications:

Curtis C., Rokem A., Nance E.* Diff_classifier: Particle tracking parallelization. Journal Open Source Software 4(36):989 doi: 10.21105.joss.00989

Curtis C.D., McKenna M., Pontes C., Toghani D., Choe A., Nance E.* Predicting in situ nanoparticle behavior using multiple particle tracking and artificial neural networks. Nanoscale (2019) Nov 28; 11(46):22515-22530. doi: 10.1039/c9nr06327g

McKenna M., Shackelford D., Ferreira Pontes C., Ball B.K., Nance E.* Multiple particle tracking detects changes in brain extracellular matrix structure and predicts neurodevelopmental age. ACS Nano (2021) 15(5):8559-8573; doi: 10.1021/acsnano.1c00394

Schimek N., Wood T., Beck D.A.C., Toghani A., McKenna M., Nance E.* High fidelity predictions of diffusion in the brain microenvironment. Biophys J. (2024), Vol 123, Issue 22, 3935 – 3950. doi: 10.1016/j.bpj.2024.10.005

Wood T.R., Hildahl K., Helmbrecht H., Corry K.A., Moralejo D.H., Kolnik S.E., Prater K.E., Juul S.E., Nance E.* A ferret brain slice model of oxygen-glucose deprivation captures regional responses to perinatal injury and treatment associated with specific microglial phenotypes. Bioeng & Transl. Med (2021) e10265; doi: 10.1002/btm2.10265

DS ML

Imaging

Imaging methods to increase quantitative analysis of biological phenomena

Confocal microscopy is a powerful tool but often considered quantitative. We have focused on developing more robust image processing methods to increase the quantitative reliability and reproducibility of confocal microscopy. We have developed live cell and nanoparticle imaging techniques in partnership with Nikon and Hamamatsu to capture real-time processes in living brain tissue. Lastly, we have developed imaging and quantification methods to study transport and fate of biologically relevant entities - such as drug delivery systems and extracellular vesicles - and to measure permeability of epithelial and endothelial layers in engineered systems and in vivo models. Specifically, we have worked with collaborators to use nanoparticle probes for studying extracellular vesicle trafficking, and for measuring vascular construct permeability and epithelial permeability, particularly in the cervical-vaginal tract.

Representative publications:

Nance E.* Brain penetrating nanoparticles for analysis of the brain microenvironment. Methods Mol. Biol. (2017) 1570:91-104. doi: 10.1007/978-1-4939-6840-4_6

Helmbrecht H., Lin T-J., Janakiraman S., Decker K., Nance E.* Prevalence and practices of immunofluorescent cell image processing: a systematic review. Front. Cell Neurosci. (2023) 17:1188858;; doi: 10.3389/fncel.2023.1188858

Zhang M., Vojtech L., Ye Z., Hladik F., Nance E.* Quantum dot labeling and visualization of extracellular vesicles. ACS Applied Nano Materials (2020) June 15; 7(3):7211-7222. doi: 10.1021/acsanm.0c01553

Millik S.C., Dostie A.M., Karis D.G., Smith P.T., Mckenna M., Chan N., Curtis C.D., Nance E., Theberge A.B., Nelson A.* 3D printed coaxial nozzles for the extrusion of hydrogel tubes toward modeling vascular endothelium. Biofabrication (2019) Jul 12; 11(4):045009. doi: 10.1088/1758-5090/ab2b4d

Vornhagen J., Armistead B., Quach P., Santana-Ufret V., Boldenow E., Alishetti V., Melief C., Ngo L.Y., Whidbey C., Doran K.S., Curtis C.1, Nance E., Rajagopal L.* Group B streptococcus exploits vaginal epithelial exfoliation for ascending infection. J. Clinical Investigation (2018) May 1; 128(5):1985-1999. doi: 10.1172/JCI97043

MPT

Multiple particle tracking of nanoparticle probes

Multiple particle tracking (MPT) is a powerful analytical tool that has been used in fields ranging from aeronautics to oceanography allowing researchers to collect spatial and velocity information of moving objects from video datasets. MPT tracks the movement of up to thousands of nanoparticles simultaneously with high resolution. Experimentally, MPT typically involves in vivo injection or ex vivo or in vitro topical application of fluorescent nanoparticles that are subsequently tracked via microscopy. Open-source software packages can then be used to calculate the trajectory coordinates and mean-square displacement values for each nanoparticle. We have applied MPT across a variety of use cases to probe the brain microstructure. We have identified the range of available pore sizes in the brain for nanoprobes to access and used MPT to study changes in diffusion in response to varying degrees of insult or stimuli, showing that for example, increased disease severity results in increased diffusive capability in the presence of ischemia. We have also used MPT to assess whether therapeutic entities, such as nanoparticles, small molecules, or extracellular vesicles, are capable of diffusing - and thus penetrating - within the brain parenchyma. MPT has helped us characterize the microrheology of the brain microenvironment and also define critical design constraints for effective nano-based therapeutic delivery in the brain.

Representative publications:

Nance E., Woodworth G., Sailor K., Shih T-Y, Swaminathan G., Xiang D., Eberhart C., Hanes J.* A dense poly(ethylene glycol) coating improves penetration of large polymeric nanoparticles within brain tissue. Sci. Transl. Med. (2012) Aug 29; 4(149):149ra119. doi: 10.1126/scitranslmed.3003594. **Selected Cover Image

Curtis C. Toghani D., Wong B., Nance E.* Colloidal stability as a determinant of nanoparticle behavior in the brain. Colloids and Surfaces B: Biointerfaces (2018) 170, 673-682. doi: 10.1016/j.colsurfb.2018.06.050

Joseph A., Motchoffo Simo G., Gao T., Alhindi N., Xu N., Graham D.J., Gamble L.J., Nance E.* Surfactants influence polymeric nanoparticle fate in the brain. Biomaterials (2021) 277: 121086; doi: 10.1016/j.biomaterials.2021.121086