Featured Publications

Jennifer Davis and colleagues use rainbow reporters to track cells.

Ying Zheng and colleagues demonstrate that engineered perfusable microvessel grafts enhance vascular remodeling and accelerate coronary perfusion, potentially supporting cardiac tissues after implantation.

Kim Woodrow and colleagues demonstrate a LCNP that has the potential to co-deliver ARVs and mAbs for eradicating HIV reservoirs.

Ruikang Wang and colleagues demonstrate that swept-source OCTA may represent a new and noninvasive method for detecting and monitoring disease activity in BSCR.

Charles Murry and colleagues demonstrate that remuscularization of the infarcted macaque heart with human myocardium provides durable improvement in left ventricular function.

Suzie Pun and colleagues We demonstrate transfection of both CD4+ and CD8+ primary human T cells with messenger RNA and plasmid DNA at efficiencies up to 25 and 18%, respectively, with similarly high viability.

Valerie Daggett and colleagues performed a comparative molecular dynamics study on the denatured states of two proteins, sharing nearly identical amino?acid sequences (88?%) but different topologies, namely an all?a?helical bundle protein named GA88 and an a+B?protein named GB88.

Lara Gamble and colleagues demonstrate that ToF-SIMS can be utilized to identify large-scale changes that occur in the tumor microenvironment and could thereby increase the understanding of tumor progression and the tumor microenvironment.

Patrick Stayton and colleagues demonstrate the versatility of the drugamer platform for engineering the intracellular pharmacokinetic profiles and its strong therapeutic activity in treating pulmonary intracellular infections.

Professor Xiaohu Gao and colleagues have created a new way to target prostate tumors that overcomes past challenges of designing effective drug delivery methods. This versatile nanocarrier design should offer opportunities for the clinical translation of therapies based on intracellularly acting biologics.

Professor Paul Yager's lab has created a method that enables optical-filter free mobile imaging for medical diagnostics, a first step towards enabling a new generation of highly sensitive, point-of-care fluorescence assays.

Professor Albert Folch's lab reports on the formulation, characterization, and SL application of a 3D?printable PDMS resin (3DP?PDMS) based on commercially available PDMS?methacrylate macromers, a high?efficiency photoinitiator and a high?absorbance photosensitizer. 3DP?PDMS resin enables assembly?free, automated, digital manufacturing of PDMS, which should facilitate the prototyping of devices for microfluidics, organ?on?chip platforms, soft robotics, flexible electronics, and sensors, among others.

Research Associate Professor Lara Gamble and colleagues report on a technique for characterizing the distribution and composition of chemical species through complex porous scaffolds. This approach could be widely applicable for ToF-SIMS analysis of scaffolds modified by multiple plasma processing techniques as well as alternative surface modification approaches.

Assistant Professor Ying Zheng and colleagues developed an engineered human vascular marrow niche to examine the three-dimensional cell interactions that direct hematopoietic cell trafficking. The platform provides a tool to advance study of the interactions between endothelial cells, marrow-derived fibroblasts and hematopoeitic cells that comprise the marrow vascular niche, and has potential for use in testing therapeutics and personalized medicine.

BioE faculty Charles Murry, Kelly Stevens and Ying Zheng, and interdisciplinary colleagues from across UW, investigated the properties of endothelial cells (ECs), isolated from four human major organs—the heart, lung, liver, and kidneys—in individual fetal tissues at three months' gestation, at gene expression, and at cellular function levels. Their findings showed the link between human EC heterogeneity and organ development and can be exploited therapeutically to contribute in organ regeneration, disease modeling, as well as guiding differentiation of tissue-specific ECs from human pluripotent stem cells.

Professor Gerald Pollack and colleagues report the formation of a ‘three-dimensional cell-like structured exclusion zone’ in water prepared by two different methods. Based on their findings of an electric potential difference between the heterogeneous structured water and the ordinary water, the researchers propose a new model to explain the relationship between heterogeneous, structured water and its electrical properties.

Researchers from Georg Seelig’s (Electrical Engineering, adjunct BioE) and Suzie Pun/Drew Sellers’ labs, and the Allen Institute for Brain Science, have developed a new single-cell RNA sequencing method that can reliably track gene activity in a tissue sample to the individual cell level.

The Bryers labs presents the effects of varying pore size of poly (2-hydroxyethyl methacrylate) (pHEMA) and poly(dimethylsiloxane) (PDMS, silicone) scaffolds on the maturation and in vivo enrichment of dendritic cells.

Researchers from Shaoyi Jiang's (BioE adjunct) lab demonstrate a zwitterionic polycarboxybetaine nanocage that can physically encase proteins while keeping their structure intact. This approach addresses the problem posed by efficacy loss of biotherapeutics due to undesirable immune response.

The Gao lab reports on the development of small, bifunctional chemical tags capable of transporting siRNA directly into the cytosol. The bifunctional tags consist of a siRNA-binding moiety that interacts with siRNA non-covalently, and a steroid domain that readily fuses with the mammalian cell membrane.

Deok-Ho Kim's lab demonstrates that biomimetic nanotopography and S1P can be combined to synergistically regulate the maturation and vascularization of engineered skeletal muscles.

The researchers compared area measurements for the same neovascular lesions imaged using swept source optical coherence tomography angiography (SS-OCTA) and enlarging scan patterns. The similarity in lesion area measurements across different scan patterns suggests that SS-OCTA imaging can be used to follow quantitatively the enlargement of choroidal neovascularization as the disease progresses.

Current approaches for topical vaginal administration of nanoparticles result in poor retention and extensive leakage. To overcome these challenges, the researchers developed a nanoparticle-releasing nanofiber delivery platform and evaluated its ability to improve nanoparticle retention in a murine model. In this first study of nanoparticle releasing fibers for drug delivery, they discovered that the system demonstrated 30-fold increased nanoparticle retention in the reproductive tract 24 hours following administration.

A new contrast agent for combined photoacoustic and ultrasound imaging is presented.

The researchers achieved high-throughput, quantitative characterization of protein–protein binding interactions without requiring purified recombinant proteins, by linking interaction strength with yeast mating. Using a next-generation sequencing output, they characterized protein networks consisting of thousands of pairwise interactions in a single tube and have demonstrated the effect of changing the binding environment.

The researchers demonstrate the application of crosslinking mass spectrometry to identify protein structural features and interactions in tissue samples, providing systems structural biology insight into protein complexes as they exist in the mouse heart. The extension of crosslinking mass spectrometry analysis into the realm of tissues opens the door to increasing understanding of protein structures and interactions within the context of the greater biological system.

The study's findings suggest that PiT-2 is involved in normal bone development and growth and plays roles in cortical and trabecular bone metabolism feasibly by regulating local phosphate transport and mineralization processes in the bone. Further studies that evaluate bone cell-specific loss of PiT-2 are now warranted and may yield insight into complex mechanisms of bone development and growth, leading to identification of new therapeutic options for patients with bone diseases.

This study validates a fast and sensitive HPLC–MS/MS method for direct quantification of intracellular dNTPs from tissue. Compared to existing methods, this study presents a faster and more sensitive method for dNTP quantification.

Stevens et al. fabricated artificial liver seeds in biomaterials that were able to grow after implantation into mice in response to liver injury, and began to carry out normal liver functions. The work offers an approach to study organ development and a possible strategy for organ engineering.

The researchers report a simple, universal "add-on" technology (EASE) that converts the ordinary sensitivities of common bioassays to extraordinary ones. They demonstrate that EASE facilitated increased sensitivity of ELISA-based detection of HIV, and enabled the direct visualization in tissues of the Zika virus and of low-abundance biomarkers for neurological diseases and cancer immunotherapy.

The researchers have designed small proteins that can inhibit the formation of biofilms, common sources of infection for hundreds of patients worldwide, especially with those who have implanted medical devices. Their designed anti-a-sheet peptides suppressed the formation of biofilm in S. aureus, a bacteria resistant to many drugs, by about half, and prevented aggregation of infectious proteins through their binding mechanism.

Dr. Kim and colleagues demonstrate a method for producing cardiac tissue scaffolds with anisotropic electroconductive properties using PEG-graphene substrates.

The researchers demonstrate a prototype of a self-contained, automated, disposable device for chemically amplified protein-based detection of influenza virus from nasal swab specimens. The device was tested in a clinical setting and was well received by patients and clinicians, further inspiring further optimization of the device.

The researchers propose a method to achieve enhanced immune response against viral infections in the female reproductive tract. They demonstrate that intravaginal pre-treatment with chitosan significantly facilitates translocation of nanoparticles across the the multilayered vaginal epithelium to target draining lymph nodes.

The researchers demonstrate a macromolecular therapeutic platform that provides sustained local delivery of ciprofloxacin. Their work addresses the unmet need for inhaled treatments for lung-based intracellular bacterial infections such as Franciscella tularensis pneumonia (tularemia), which are currently treated with oral or IV antibiotics that poorly achieve and sustain pulmonary drug bioavailability.

The researchers investigate whole cell and molecular level interactions that mediate contact guidance of phenotypically distinct carcinoma cells. By using nano-patterning techniques to produce substrates that facilitate detailed analysis, they identify a cellular mechanism of topographic sensing that can account for the diversity of responses across multiple cell phenotypes.