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2009 Spring Simulation Multiconference, SpringSim 2009

作者： Lam, Tai Ning Ropella, Glen E. P. Hunt, C. Anthony Graduate Program in Pharmaceutical Sciences and Pharmacogenomics University of California San Francisco United States Department of Bioengineering and Therapeutic Sciences BioSystems Group University of California 513 Parnassus Ave. San FranciscoCA United States Tempus Dictum Inc. United States

To facilitate integration and reconciliation between similar experiments, we need relativistic analogues that can be independent of experimental protocols;yet reasonably represent biological components and interactions among them, along with hypothesized mechanistic details. We designed, constructed and validated an analogue of a recirculating, isolated perfused liver used in a study of drug interactions between digoxin, rifampicin and quinidine. We believe these analogues can evolve into executable biological knowledge embodiments that provide concrete instances of knowledge and means to falsify mechanistic hypotheses.

关键词： Drug interactions

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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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Novel techniques for large-scale manipulations of cortical networks in non-human primates

Novel techniques for large-scale manipulations of cortical n...

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Annual International Conference of the IEEE Engineering in Medicine and Biology Society

作者： Azadeh Yazdan-Shahmorad Daniel B. Silversmith Philip N. Sabes University of California San Francisco San Francisco CA US UC Berkeley – UCSF Graduate Program in Bioengineering San Francisco CA 94158 USA

Optogenetics is a powerful tool that enables millisecond-level control of the activity of specific groups of neurons. Furthermore, it has the great advantage of artifact free recordings. These characteristics make this technique ideal for relating brain function to behavior in animals with great behavioral capabilities such as non-human primates (NHPs). We recently introduced a practical, stable interface for optogenetic stimulation and recording of large-scale cortical circuits in NHPs. Here we present the various potentials of this interface for studying circuits and connectivity at a large-scale and for relating it to behavior.

关键词： Frequency modulation Oscillators Time series analysis Couplings Electrical stimulation

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De novo protein fold families expand the designable ligand binding site space

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PLoS Computational Biology 2021年第11期17卷 e1009620-e1009620页

作者： Pan, Xingjie Kortemme, Tanja Department of Bioengineering and Therapeutic Sciences University of California San Francisco San FranciscoCA United States UC Berkeley-UCSF Graduate Program in Bioengineering University of California San Francisco San FranciscoCA United States University of California San Francisco San FranciscoCA United States Chan Zuckerberg Biohub San FranciscoCA United States

A major challenge in designing proteins de novo to bind user-defined ligands with high affinity is finding backbones structures into which a new binding site geometry can be engineered with high precision. Recent advances in methods to generate protein fold families de novo have expanded the space of accessible protein structures, but it is not clear to what extend de novo proteins with diverse geometries also expand the space of designable ligand binding functions. We constructed a library of 25,806 high-quality ligand binding sites and developed a fast protocol to place ("match") these binding sites into both naturally occurring and de novo protein families with two fold topologies: Rossman and NTF2. Each matching step involves engineering new binding site residues into each protein "scaffold", which is distinct from the problem of comparing already existing binding pockets. 5,896 and 7,475 binding sites could be matched to the Rossmann and NTF2 fold families, respectively. De novo designed Rossman and NTF2 protein families can support 1,791 and 678 binding sites that cannot be matched to naturally existing structures with the same topologies, respectively. While the number of protein residues in ligand binding sites is the major determinant of matching success, ligand size and primary sequence separation of binding site residues also play important roles. The number of matched binding sites are power law functions of the number of members in a fold family. Our results suggest that de novo sampling of geometric variations on diverse fold topologies can significantly expand the space of designable ligand binding sites for a wealth of possible new protein functions. © 2021 Pan, Kortemme. This is an open access article distributed under the terms of the Creative Commons Attribution License, which permits unrestricted use, distribution, and reproduction in any medium, provided the original author and source are credited.

关键词： Topology

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A comparison of coil combination strategies in 3D multi-channel MRSI reconstruction for patients with brain tumors (vol 31, e3929, 2018)

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NMR IN BIOMEDICINE 2018年第12期31卷 e3929-e3929页

作者： Vareth, M. Lupo, J. M. Larson, P. E. Z. Nelson, S. J. UC Berkeley-UCSF Graduate Program in Bioengineering University of California Berkeley and University of California San Francisco California USA Surbeck Laboratory of Advanced Imaging Department of Radiology and Biomedical Imaging University of California San Francisco California USA UC Berkeley-UCSF Graduate Program in Bioengineering University of California Berkeley and University of California San Francisco California USA Surbeck Laboratory of Advanced Imaging Department of Radiology and Biomedical Imaging University of California San Francisco California USA UC Berkeley-UCSF Graduate Program in Bioengineering University of California Berkeley and University of California San Francisco California USA Surbeck Laboratory of Advanced Imaging Department of Radiology and Biomedical Imaging University of California San Francisco California USA UC Berkeley-UCSF Graduate Program in Bioengineering University of California Berkeley and University of California San Francisco California USA Surbeck Laboratory of Advanced Imaging Department of Radiology and Biomedical Imaging University of California San Francisco California USA

The goal of this study was to find the most robust algorithm for a phase‐sensitive coil combination of 3D single‐cycle and lactate‐edited, multi‐channel H‐1 point‐resolved spectroscopy (PRESS) localized echo planar spectroscopic imaging (EPSI) data for clinical applications in the brain. Data were acquired over 5-10 minutes at 3T using 8‐ or 32‐channel array coils. Peak referencing with residual water and N‐acetyl‐aspartate, first‐point phasing, generalized least squared (GLS) and whitened singular‐value decomposition (WSVD) combination algorithms were evaluated relative to unsuppressed water with data from a phantom, six volunteers and 55 patients with brain tumors. Comparison metrics were signal‐to‐noise ratio, coefficient of variance and percent signal increase. Where residual water was present, using it as a reference peak for phasing and weighting factors from an imaging calibration scan gave the best overall performance. Greater improvement was seen for large selected volumes (>720 cm³) and for the 32‐channel array (25%) compared with the 8‐channel array (19%). Applying voxel‐by‐voxel phase corrections produced a larger increase in performance for the 32‐ versus 8‐channel coil. We conclude that, for clinically relevant 3D H‐1 PRESS localized EPSI studies, the most robust technique employed individual phase maps generated from high residual water and individual amplitude maps generated from calibration scans.

关键词： coil combination techniques first‐point phasing GLS lactate editing multichannel EPSI peak referencing PRESS localization WSVD

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DEVELOPING A DIGITAL TWIN FOR SINGLE-CELL MECHANICAL PHENOTYPING MICROFLUIDIC DEVICES 26

DEVELOPING A DIGITAL TWIN FOR SINGLE-CELL MECHANICAL PHENOTY...

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26th International Conference on Miniaturized Systems for Chemistry and Life Sciences, MicroTAS 2022

作者： Roychowdhury, Sayan Mahmud, Samreen T. Puleri, Daniel F. Lai, Andre Rex, Rachel Li, Brian Sohn, Lydia L. Randles, Amanda Department of Biomedical Engineering Duke University United States UC Berkeley-UC San Francisco Graduate Program in Bioengineering University of California Berkeley United States Department of Mechanical Engineering University of California Berkeley United States

ISBN: (纸本)9781733419048

Microfluidics can be used to characterize individual cells in a population based on their mechanical traits. In this work, we digitally replicate the microfluidic device developed by Li et al. [1] and perform simulations of a representative AP-1060 cell. We show that the numerical model is able to recover whole-cell deformability index, a metric used to quantify the resistance of cells to compressive deformation, within 3% of the experimental average. These results pave the way for future studies which utilize experimental and computational approaches to optimize geometric design parameters, complement signal analysis, and enhance the acquisition of mechanical information. © 2022 MicroTAS 2022 - 26th International Conference on Miniaturized Systems for Chemistry and Life Sciences. All rights reserved.

关键词： Fluid structure interaction

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Towards Next-Generation Proteomic Assays: Functional Materials as Sieving Matrices and Binding Scaffolds

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MRS Online Proceedings Library 2011年第1期1415卷 7-15页

作者： Samuel Q. Tia Alex J. Hughes Kelly Karns M. Kursad Araz Mei He Dohyun Kim Amy E. Herr University of California Berkeley Bioengineering Berkeley U.S.A. Graduate Program in Bioengineering University of California Berkeley/University of California San Francisco Berkeley U.S.A.

Next-generation bioanalytical approaches for protein-level measurements are advanced by the integration capacity of microfluidic design strategies, as well as the fine fluid and material control possible. Photopatterning of polymers within fluidic volumes is a key tool in the suite of technologies available for seamless integration of assay measurement modalities, as well as rapid target detection. Here, we overview recent advances in heterogeneous and homogeneous immunoassays using functional polymers, electrophoretic transport, and microdevices.

关键词： polymer devices fluidics

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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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Clinical anthropometrics and body composition from 3D whole-body surface scans (vol 70, pg 1265, 2016)

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EUROPEAN JOURNAL OF CLINICAL NUTRITION 2021年第3期75卷 574-574页

作者： Ng, B. K. Hinton, B. J. Fan, B. Kanaya, A. M. Shepherd, J. A. Department of Radiology and Biomedical Imaging University of California San Francisco San Francisco USA The UC Berkeley—UCSF Graduate Program in Bioengineering San Francisco USA Department of Medicine University of California San Francisco San Francisco USA

A Correction to this paper has been published: https://***/10.1038/s41430-020-00808-y

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Perception of 3-D layout in stereo displays

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Information Display 2009年第1期25卷 12-16页

作者： Banks, Martin S. Held, Robert T. Girshick, Ahna R. Science Program School of Optometry University of California at Berkeley Berkeley CA United States Joint Graduate Group in Bioengineering University of California San Francisco CA United States University of California at Berkeley Berkeley CA United States Department of Psychology Center for Neural Science New York University New York NY United States

As stereoscopic displays become more commonplace, it is more important than ever for those displays to create a faithful impression of the 3-D structure of the object or scene being portrayed. This article reviews cur... 详细信息

关键词： Chemicals

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