A5064644435- Advanced Electron Microscopy Techniques and Applications
- Electron and X-Ray Spectroscopy Techniques
- RNA and protein synthesis mechanisms
- Extracellular vesicles in disease
- MicroRNA in disease regulation
- Advanced Fluorescence Microscopy Techniques
- Lipid Membrane Structure and Behavior
- Diabetes, Cardiovascular Risks, and Lipoproteins
- Near-Field Optical Microscopy
- Molecular Biology Techniques and Applications
- Monoclonal and Polyclonal Antibodies Research
- Force Microscopy Techniques and Applications
- Cancer Mechanisms and Therapy
- Microfluidic and Bio-sensing Technologies
- Advanced biosensing and bioanalysis techniques
- Integrated Circuits and Semiconductor Failure Analysis
- Lipoproteins and Cardiovascular Health
- Cancer Research and Treatments
- CRISPR and Genetic Engineering
- Cancer Genomics and Diagnostics
- Cellular transport and secretion
- Cholesterol and Lipid Metabolism
- Cancer therapeutics and mechanisms
- Nanopore and Nanochannel Transport Studies
- Environmental DNA in Biodiversity Studies
Oregon Health & Science University
2019-2025
Lawrence Berkeley National Laboratory
2012-2016
Commonly used methods for determining protein structure, including X-ray crystallography and single-particle reconstruction, often provide a single unique three-dimensional (3D) structure. However, in these methods, the dynamics flexibility/fluctuation remain mostly unknown. Here, we utilized advances electron tomography (ET) to study antibody flexibility fluctuation through structural determination of individual particles rather than averaging multiple together. Through individual-particle...
Abstract Exosomes are secreted to the extracellular milieu when multivesicular endosomes (MVEs) dock and fuse with plasma membrane. However, MVEs also known lysosomes for degradation. How directed membrane exosome secretion rather than is unclear. Here we report that a conversion of phosphatidylinositol-3-phosphate (PI(3)P) phosphatidylinositol-4-phosphate (PI(4)P) catalyzed sequentially by Myotubularin 1 (MTM1) phosphatidylinositol 4-kinase type IIα (PI4KIIα) on surface mediates recruitment...
Structural determination of proteins is rather challenging for with molecular masses between 40 - 200 kDa. Considering that more than half natural have a mass kDa1,2, robust and high-throughput method nanometer resolution capability needed. Negative staining (NS) electron microscopy (EM) an easy, rapid, qualitative approach which has frequently been used in research laboratories to examine protein structure protein-protein interactions. Unfortunately, conventional NS protocols often generate...
Abstract Cholesteryl ester transfer protein (CETP) mediates the of cholesterol esters (CE) from atheroprotective high-density lipoproteins (HDL) to atherogenic low-density (LDL). CETP inhibition has been regarded as a promising strategy for increasing HDL levels and subsequently reducing risk cardiovascular diseases (CVD). Although crystal structure is known, little known regarding how binds HDL. Here, we investigated various HDL-like particles interact with by electron microscopy molecular...
Abstract DNA points accumulation for imaging in nanoscale topography (DNA-PAINT) facilitates multiplexing superresolution microscopy but is practically limited by slow speed. To address this issue, we propose the additions of ethylene carbonate (EC) to buffer, sequence repeats docking strand, and a spacer between strand affinity agent. Collectively termed DNA-PAINT-ERS (E = EC, R Repeating sequence, S Spacer), these strategies can be easily integrated into current DNA-PAINT workflows both...
Upregulation of Cyclin E1 and subsequent activation CDK2 accelerates cell cycle progression from G1 to S phase is a common oncogenic driver in gynecological malignancies. WEE1 kinase counteracts the effects E1/CDK2 by regulating multiple checkpoints. Here we characterized relationship between sensitivity selective inhibitor azenosertib. We found that ovarian cancer lines with high levels endogenous expression or forced overexpression were exquisitely sensitive azenosertib these results...
Accurate visualization and quantification of homologous recombination (HR)-associated foci in readily available patient samples are critical for identifying patients with HR deficiency (HRD) when they present care to guide polyADP ribose polymerase (PARP) inhibitors (PARPi) or platinum-based therapies. Immunofluorescence (IF) assays have the potential accurately visualize DNA repair processes as punctate within nucleus. To ensure precise HRD assessment, we developed MAP-HR, (Machine-learning...
Peptides show much promise as potent and selective drug candidates. Fusing peptides to a scaffold monoclonal antibody produces conjugated which has the advantages of peptide activity yet also pharmacokinetics determined by antibody. However, often poor binding affinity antigens that may be related unknown structural changes. The study conformational change is difficult conventional techniques because fluctuation under equilibrium results in multiple structures co-existing. Here, we employed...
Structural determination of proteins is rather challenging for with molecular masses between 40 - 200 kDa. Considering that more than half natural have a mass kDa1,2, robust and high-throughput method nanometer resolution capability needed. Negative staining (NS) electron microscopy (EM) an easy, rapid, qualitative approach which has frequently been used in research laboratories to examine protein structure protein-protein interactions. Unfortunately, conventional NS protocols often generate...
The discovery and utility of clinically relevant circulating biomarkers depend on standardized methods that minimize preanalytical errors. Despite growing interest in studying extracellular vesicles (EVs) cell-free messenger RNA (cf-mRNA) as potential biomarkers, how blood processing freeze/thaw impacts the profiles these analytes plasma was not thoroughly understood. We utilized flow cytometric analysis to examine effect differential centrifugation a cycle EV profiles. Utilizing cytometry...
Abstract Extracellular vesicles (EVs) have been shown as key mediators of extracellular small RNA transport. However, carriers cell-free messenger (cf-mRNA) in human biofluids and their association with cancer remain poorly understood. Here, we performed a transcriptomic analysis size-fractionated plasma from lung cancer, liver multiple myeloma, healthy donors. Morphology size distribution showed the successful separation large medium particles other soluble protein fractions. We developed...
Cholesteryl ester transfer protein (CETP) mediates cholesteryl (CE) from the atheroprotective high density lipoprotein (HDL) cholesterol to atherogenic low cholesterol. In past decade, this property has driven development of CETP inhibitors, which have been evaluated in large scale clinical trials for treating cardiovascular diseases. Despite pharmacological interest, little is known about fundamental mechanism CE transfer. Recent electron microscopy (EM) experiments suggested a tunnel...
Fluorescence nanoscopy has become increasingly powerful for biomedical research, but it historically afforded a small field-of-view (FOV) of around 50 μm × at once and more recently up to ∼200 200 μm. Efforts further increase the FOV in fluorescence have thus far relied on use fabricated waveguide substrates, adding cost sample constraints applications. Here we report PRism-Illumination Microfluidics-Enhanced DNA-PAINT (PRIME-PAINT) multiplexed across millimeter-scale FOVs. Built upon...
Abstract Cholesteryl ester transfer protein (CETP) mediates the net of cholesteryl esters (CEs) from atheroprotective high‐density lipoproteins (HDLs) to atherogenic low‐density (LDLs) or very‐low‐density (VLDLs). Inhibition CETP raises HDL cholesterol (good cholesterol) levels and reduces LDL (bad levels, making it a promising drug target for prevention treatment coronary heart disease. Although crystal structure has been determined, molecular mechanism mediating CEs is still unknown, even...
Abstract Knowledge of three-dimensional (3D) structures each individual particles asymmetric and flexible proteins is essential in understanding those proteins’ functions; but their are difficult to determine. Electron tomography (ET) provides a tool for imaging single unique biological object from series tilted angles, it challenging image protein reconstruction due the imperfect mechanical control capability specimen goniometer under both medium high magnification (approximately...
Abstract In syngeneic murine breast cancer models, poly ADP-ribose polymerase inhibitor (PARPi) and anti-PD-L1 combinations induce deep, sustained responses independent of BRCA1/2 mutation status. We therefore investigated this combination in the AMTEC clinical trial, which a one-month olaparib run-in was followed by combined durvalumab participants with wild-type metastatic triple negative cancer. To characterize adaptive to monotherapy, paired biopsies taken before during PARPi lead-in...
Recent work suggests that Ras small GTPases interact with the anionic lipid phosphatidylserine (PS) in an isoform-specific manner, direct implications for their biological functions. Studies on PS-Ras associations cells, however, have relied immuno-EM imaging of membrane sheets. To study spatial relationships intact we combined use Lact-C2-GFP, a biosensor PS, multicolor super resolution based DNA-PAINT. At ~20 nm resolution, resulting images clearly show nonuniform molecular distribution PS...
Apolipoprotein A-I (apo A-I), the major protein component of high-density lipoprotein, has been proven inversely correlated to cardiovascular risk in past decades. The lipid-free state apo is initial stage which binds lipids forming lipoprotein. Molecular models have reported by methods like X-ray crystallography and chemical cross-linking/mass spectrometry (CCL/MS). Through structural analysis we found that those current had limited consistency with other experimental results, such as from...
Abstract Fluorescence nanoscopy has become increasingly powerful for biomedical research, but it historically afforded a small field-of-view (FOV) around 50 µm x at once and more recently up to ~200 200 µm. Efforts further increase the FOV in fluorescence have thus far relied on use of fabricated waveguide substrates, adding cost sample constraints applications. Here we report PRism-Illumination Microfluidics-Enhanced DNA-PAINT (PRIME-PAINT) multiplexed across millimeter-scale FOVs. Built...
Abstract PARP inhibitors (PARPi) as monotherapy are approved in a wide variety of cancers that show genetic alterations result homologous recombination repair (HRR) deficiency. Current genomic scar tests for HRR deficiency (HRD) predictive response to PARPi on population scale but they may fail provide real-time functional status an individual. RAD51 is critical DNA factor functions safeguard the integrity genome and could be useful patient selection biomarker response.During HRR, forms...
Abstract Over the last few years, spatial multi-omics platforms have emerged as a powerful tool for characterizing cancer biology in multiple dimensions. Notably, these systems typically rely on multiplex immunolabeling. Conventionally, multiplexing is accomplished through carefully selecting primary antibodies from different animal species, and combination with their corresponding polyclonal secondary antibodies. However, given practical complication related to species availability of...