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23rd International Conference on Miniaturized Systems for Chemistry and Life Sciences, MicroTAS 2019

作者： Carey, Thomas R. Hall, Jennifer Sohn, Lydia L. UC Berkeley-UCSF Graduate Program in Bioengineering United States UC Berkeley Molecular and Cell Biology United States UC Berkeley Mechanical Engineering United States

ISBN: (纸本)9781733419000

We present the theory, design, and proof-of-concept demonstration of a tumor-derived extracellular vesicle (EV) detection platform. Our platform detects EVs displaying specific surface antigens by electronically measuring the effective size increase of antibody-coated colloids when EVs specifically bind to them. We show that we can distinguish EVs derived from a lung cancer cell line (A549) and a non-malignant bronchial epithelial cell line (BEAS-2B) based on the CA12 surface marker. © 2019 CBMS-0001.

关键词： Tumors

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OLIGONucLEOTIDE FUNCTIONALIZED POLYACRYLAMIDE BEADS FOR AMPLIFICATION BASED BIOMARKER DETECTION 25

OLIGONUCLEOTIDE FUNCTIONALIZED POLYACRYLAMIDE BEADS FOR AMPL...

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25th International Conference on Miniaturized Systems for Chemistry and Life Sciences, MicroTAS 2021

作者： Chaves, Rodrigo Cotrim Streets, Aaron University of California BerkeleyCA United States UC Berkeley UCSF Graduate Program in Bioengineering CA United States

ISBN: (纸本)9781733419031

Single-cell quantitative biomarker analysis is a powerful technique for studying tissue heterogeneity, but commonly used staining techniques cannot detect markers with lower than 100 target molecules per cell [1]. Here we report a droplet microfluidic platform for encapsulation of samples in Polyacrylamide (PA) hydrogel beads, and staining for fluorescence analysis. This is achieved by functionalizing the PA with oligonucleotides designed to capture biomarkers of interest, and amplifying targets through PCR, enabling sensitive detection of DNA, RNA or protein molecules with low copy number for quantification of cellular populations with traditional flow cytometry. © 2021 MicroTAS 2021 - 25th International Conference on Miniaturized Systems for Chemistry and Life Sciences. All rights reserved.

关键词： Oligonucleotides

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Detection of proteoforms from single cells by multiplexed ion beam imaging 24

Detection of proteoforms from single cells by multiplexed io...

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24th International Conference on Miniaturized Systems for Chemistry and Life Sciences, MicroTAS 2020

作者： Lomeli, Gabriela Bosse, Marc Bendall, Sean C. Angelo, Michael Herr, Amy E. UC Berkeley UCSF Joint Graduate Program in Bioengineering CA United States Department of Bioengineering University of California Berkeley United States Department of Pathology Stanford University StanfordCA United States

ISBN: (纸本)9781733419017

Single-cell electrophoretic assays offer proteoform detection specificity, but target multiplexing can be further enhanced by transitioning from fluorescence to mass spectrometry imaging for readout. We report for the first time multiplexed ion beam imaging (MIBI) of isoelectrically separated proteoforms from single cells (scIEF). MIBI of scIEF enables the detection of proteoforms differing by a single charge unit. Additionally, we demonstrate that MIBI's ability to do multiple depth image acquisition-comparable to z-stack confocal imaging-enables us to disregard surface artefacts that would normally confound quantitation. © 2020 CBMS-0001

关键词： Depth profiling

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Linking physical phenotype to drug resistance: Single-cell mechanical measurements of acute promyelocytic Leukemia 23

Linking physical phenotype to drug resistance: Single-cell m...

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23rd International Conference on Miniaturized Systems for Chemistry and Life Sciences, MicroTAS 2019

作者： Li, Brian L. Maslan, Annie M. Streets, Aaron M. Sohn, Lydia L. UC Berkeley UCSF Graduate Program in Bioengineering Berkeley and San Francisco United States UC Berkeley Center for Computational Biology Berkeley United States UC Berkeley Biophysics Graduate Group Berkeley United States UC Berkeley Department of Mechanical Engineering Berkeley United States

ISBN: (纸本)9781733419000

Mechanical testing of cancer cells has established that certain pathophysiological phenotypes are strongly associated with abnormal cell mechanics. We used a microfluidic platform previously developed in our laboratory to perform rapid mechanical phenotyping of acute promyelocytic leukemia (APL) cells. These measurements revealed that drug-resistant APL cells exhibit more solid-like viscoelastic behavior compared to drug-responsive cells and that this mechanical difference could be due to chromatin condensation. Our work demonstrates that single-cell mechanical phenotyping could serve to predict drug-resistance in APL. © 2019 CBMS-0001.

关键词： Mechanical testing

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Creating an in vitro lung microenvironment via DNA-directed patterning to investigate the role of extracellular vesicles in metastasis 24

Creating an in vitro lung microenvironment via DNA-directed ...

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24th International Conference on Miniaturized Systems for Chemistry and Life Sciences, MicroTAS 2020

作者： Kitayama, Sean E. Sohn, Lydia L. UC Berkeley UCSF Graduate Program in Bioengineering BerkeleyCA United States Department of Mechanical Engineering University of California Berkeley BerkeleyCA United States

ISBN: (纸本)9781733419017

We present a novel in vitro heterogenous lung microenvironment fabricated using DNA-directed patterning, a lithographic method capable of controlled spatial and temporal presentation of cells and ligands with micron-scale precision. Designed using patient histology images, this alveolar microenvironment contains five cell types in an optimized co-culture system that has a number of advantages over existing in vivo models. Our optimized platform has the ability to answer questions about breast cancer metastasis, particularly about the role of extracellular vesicles in preparing the pre-metastatic niche in the secondary lung microenvironment. © 2020 CBMS-0001

关键词： Diseases

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Probing cytoskeleton dynamics with multi-directional topographical guidance 11

Probing cytoskeleton dynamics with multi-directional topogra...

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11th International Conference on Miniaturized Systems for Chemistry and Life Sciences, uTAS 2007

作者： Mai, Junyu Sun, Cheng Li, Song Zhang, Xiang NSF Nanoscale Science and Engineering Center United States UCSF UC Berkeley Joint Graduate Group in Bioengineering University of California Berkeley United States

We used microfabricated topographical guidance to manipulate the organization of a single cell cytoskeleton, and to probe a cell from multiple directions to study the molecular mechanisms regulating the coordination p... 详细信息

ISBN: (纸本)9780979806407

关键词： Surface topography

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MULTIPLEXED DNA-DIRECTED PATTERNING OF ANTIBODIES FOR SINGLE-CELL SURFACE MARKER ANALYSIS 25

MULTIPLEXED DNA-DIRECTED PATTERNING OF ANTIBODIES FOR SINGLE...

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25th International Conference on Miniaturized Systems for Chemistry and Life Sciences, MicroTAS 2021

作者： Kozminsky, Molly Scheideler, Olivia J. Li, Brian Liu, Nathaniel K. Sohn, Lydia L. California Institute of Quantitative Biosciences Berkeley United States UC Berkeley-UCSF Graduate Program in Bioengineering Berkeley and San Francisco United States UC Berkeley Department of Mechanical Engineering Berkeley United States

ISBN: (纸本)9781733419031

Cell surface marker expression is a ubiquitously measured property of single-cell phenotypes. However, measuring several markers with exogenous labels can be costly and complex. We applied a novel bioconjugation chemistry known as DNA-directed patterning to functionalize glass substrates with great specificity and flexibility. Combined with a newly-designed node-pore sensing device, we have developed a flexible and label-free platform for multiplexed surface-marker screening of single cells. In this work, we present our design and demonstrate our platform's capability to screen two example cell types for surface-marker expression. © 2021 MicroTAS 2021 - 25th International Conference on Miniaturized Systems for Chemistry and Life Sciences. All rights reserved.

关键词： DNA

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Miniscope3D:optimized single-shot miniature 3D fluorescence microscopy

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Light(Science & Applications) 2020年第1期9卷 367-379页

作者： Kyrollos Yanny Nick Antipa William Liberti Sam Dehaeck Kristina Monakhova Fanglin Linda Liu Konlin Shen Ren Ng Laura Waller UCB/UCSF Joint Graduate Program in Bioengineering University of CaliforniaBerkeleyCA 94720USA Department of Electrical Engineering&Computer Sciences University of CaliforniaBerkeleyCA 94720USA TIPs Department Universite libre de Bruxelles(ULB)1050 BrusselsBelgium

Miniature fluorescence microscopes are a standard tool in systems ***,widefield miniature microscopes capture only 2D information,and modifications that enable 3D capabilities increase the size and weight and have poor resolution outside a narrow depth ***,we achieve the 3D capability by replacing the tube lens of a conventional 2D Miniscope with an optimized multifocal phase mask at the objective’s aperture *** the phase mask at the aperture stop significantly reduces the size of the device,and varying the focal lengths enables a uniform resolution across a wide depth *** phase mask encodes the 3D fluorescence intensity into a single 2D measurement,and the 3D volume is recovered by solving a sparsity-constrained inverse *** provide methods for designing and fabricating the phase mask and an efficient forward model that accounts for the fieldvarying aberrations in miniature *** demonstrate a prototype that is 17mm tall and weighs 2.5 grams,achieving 2.76μm lateral,and 15μm axial resolution across most of the 900×700×390μm^(3) volume at 40 volumes per *** performance is validated experimentally on resolution targets,dynamic biological samples,and mouse brain *** with existing miniature single-shot volume-capture implementations,our system is smaller and lighter and achieves a more than 2×better lateral and axial resolution throughout a 10×larger usable depth *** microscope design provides single-shot 3D imaging for applications where a compact platform matters,such as volumetric neural imaging in freely moving animals and 3D motion studies of dynamic samples in incubators and lab-on-a-chip devices.

关键词： enable resolution narrow

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Developing a vision for executing scientifically useful virtual biomedical experiments

Developing a vision for executing scientifically useful virt...

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Agent-Directed Simulation Symposium, ADS 2016, Part of the 2016 Spring Simulation Multi-Conference, SpringSim 2016

作者： Petersen, Brenden K. Hunt, C. Anthony UC Berkeley-UCSF Graduate Program in Bioengineering University of California BerkeleyCA United States Department of Bioengineering and Therapeutic Sciences University of California San FranciscoCA United States

ISBN: (纸本)9781510824256

A virtual biomedical experiment (VBE) is a simulation of a wet-lab or clinical biomedical experiment. The goal of VBEs is to provide a scientifically useful method of in silico experimentation that can challenge concrete hypotheses and provide explanatory, mechanistic insight into the referent system. We envision virtual experimentation not as a supplement to traditional wet-lab experimentation, but rather as an essential part of the scientific method itself. The goal of this work is to lay preliminary groundwork for realizing this vision, through outlining requirements and describing agentbased models demonstrative of this vision. VBEs focus on reasoning by analogy;thus, a VBE includes model components analogous to particular relevant aspects of the referent experiment-from hypothesis formation to data analysis, and key concepts in between. We explore five exemplary categories of scientifically useful VBEs;hypothesis, experiment context, living counterparts, experiment agents, and measurements. We discuss how to develop model components of each category in the context of agent-based modeling. We highlight the importance of two overarching requirements: concreteness and modularity. Finally, we demonstrate this vision by describing an in silico liver model that partially fulfills the VBE vision and requirements, including components corresponding to each of the five VBE categories. © 2016 Society for Modeling & Simulation International (SCS).

关键词： Concretes

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Protein dot array patterning for study of cell adhesion and migration

Protein dot array patterning for study of cell adhesion and ...

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International Nano-Optoelectronic Workshop, iNOW

作者： Junyu, Mai Song, Li Xiang, Zhang NSF Nanoscale Science and Engineering Center UCSF/UC Berkeley Joint Graduate Group in Bioengineering Berkeley CA 94720 United States Department of Bioengineering UC Berkeley Berkeley CA 94720 United States NSF Nanoscale Science and Engineering Center UC Berkeley Berkeley CA 94720 United States

Fibronectin is patterned on silicone rubber surfaces in arrays of 2pm diameter dots using contact removal method. Cells are cultured on the patterned surface and their migration and the structure of actin cytoskeleton... 详细信息

ISBN: (纸本)1424415918

关键词： Proteins

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