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Three-Dimensional Free-Breathing Ultrashort Echo Time (UTE) 1H MRI Regional Ventilation: Comparison With Hyperpolarized 129Xe MRI and Pulmonary Function Testing in Healthy Volunteers and People With Cystic Fibrosis

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NMR in Biomedicine 2025年第6期38卷 e70033页

作者： Tan, Fei Eddy, Rachel L. Diamond, Vanessa M. Rayment, Jonathan H. Larson, Peder E. Z. UC Berkeley–UCSF Graduate Program in Bioengineering University of California Berkeley BerkeleyCA United States Department of Radiology and Biomedical Imaging University of California San Francisco San FranciscoCA United States BC Children's Hospital Research Institute Vancouver Canada Centre for Heart Lung Innovation University of British Columbia Vancouver Canada Department of Pediatrics University of British Columbia Vancouver Canada

MRI can provide localized assessment of lung function for monitoring people with lung disease. Hyperpolarized 129Xe MRI directly images pulmonary gas distribution but requires specialized hardware. Conventional 1H MRI acquisitions can also provide functional maps using free-breathing approaches. The purpose of this study is to evaluate regional ventilation derived from 3D ultrashort echo-time (UTE) 1H MRI using Motion-Compensated Low-Rank constrained reconstruction (MoCoLoR), by comparing against 129Xe MRI and pulmonary function testing as reference-standard. The study is retrospective in design. The study included 57 participants (25.4 ± 15.8 years, 35 males and 22 females): 12 healthy volunteers, 20 pediatric, and 25 adult people with cystic fibrosis (CF) scanned between January 2022 and February 2023. Field strength/sequence: 3T;129Xe: 2D multislice spoiled gradient-recalled sequence;UTE 1H: variable-density 3D radial sequence. K-means-based 129Xe ventilation defect percent (VDP), forced expiratory volume in 1 s (FEV1), and lung clearance index (LCI) were evaluated against UTE 1H VDP from a modified k-means method. The correspondence of ventilation defect maps from 129Xe and UTE 1H was also evaluated. Statistical tests included the Pearson correlation coefficient (r) and t tests, with p 129Xe and UTE 1H VDP were significantly correlated (r = 0.64, p = (Formula presented.)). Bland–Altman analysis showed a bias of −0.05 (p = (Formula presented.)) and limits of agreement of (0.07, −0.17). The Dice spatial accuracy of the UTE-based ventilation defect regions using 129Xe as reference was 0.64 ± 0.05. UTE 1H VDP was significantly correlated with FEV1 (r = −0.54, p = (Formula presented.)) and LCI (r = 0.48, p = (Formula presented.)) and was significantly different between healthy and CF participants (p = 0.017), although the correlations and differences were stronger for 129Xe VDP. UTE 1H VDP correlated with 129Xe VDP, FEV1, and LCI, and demonstrated high, consistent Di

关键词： Magnetic resonance imaging

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Subcellular western blotting of single cells

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Microsystems & Nanoengineering 2017年第1期3卷 405-413页

作者： Kevin A.Yamauchi Amy E.Herr Department of Bioengineering University of CaliforniaBerkeleyCA 94720USA The UC Berkeley—UCSF Graduate Program in Bioengineering University of CaliforniaBerkeleyCA 94720USA

Although immunoassays are the de facto standard for determining subcellular protein localization in individual cells,antibody probe cross-reactivity and fixation artifacts remain confounding *** enhance selectivity while providing single-cell resolution,we introduce a subcellular western blotting technique capable of separately assaying proteins in the 14 pL cytoplasm and 2 pL nucleus of individual *** confer precision fluidic control,we describe a passive multilayer microdevice that leverages the rapid transport times afforded by *** isolating single cells in microwells,we apply single-cell differential detergent fractionation to lyse and western blot the cytoplasmic lysate,whereas the nucleus remains intact in the ***,we lyse the intact nucleus and western blot the nuclear *** index each protein analysis to the originating subcellular compartment,we utilize bi-directional electrophoresis,a multidimensional separation that assays the lysate from each compartment in a distinct region of the separation ***-cell bi-directional electrophoresis eliminates the need for semi-subjective image segmentation algorithms required in *** subcellular,single-cell western blot is demonstrated for six targets per cell,and successfully localizes spliceosome-associated proteins solubilized from large protein and RNA complexes,even for closely sized proteins(a 7 kDa difference).Measurement of NF-κB translocation dynamics in unfixed cells at 15-min intervals demonstrates reduced technical variance compared with *** chemical cytometry assay directly measures the nucleocytoplasmic protein distribution in individual unfixed cells,thus providing insight into protein signaling in heterogeneous cell populations.

关键词： cytometry microfluidic design proteomics single-cell analysis

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10 Minute western blotting with 54-plex throughput for clinical confirmatory hiv diagnosis in human serum

10 Minute western blotting with 54-plex throughput for clini...

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16th International Conference on Miniaturized Systems for Chemistry and Life Sciences, MicroTAS 2012

作者： Hughes, Alex J. Herr, Amy E. UC Berkeley UCSF Graduate Program in Bioengineering United States UC Berkeley Bioengineering United States

ISBN: (纸本)9780979806452

We translate western blotting to a microchip workflow that cuts conventional assay times from 3-18 hours to 10-60 min with up to 5-plex analyte detection and 54-plex channel throughput. An engineered photoactive protein capture matrix with tunable porosity (PACTgel) constitutes 1) a spatially addressable denaturing polyacrylamide gel electrophoresis (SDS-PAGE) separation matrix compatible with mask-based visible light photopatterning and 2) a UV light-toggled protein capture matrix with unprecedented capture efficiency (>75%). We report the first 10 minute western blot consisting of protein sizing and immunoaffinity detection in a single microchannel, and validate a rapid confirmatory HIV diagnostic using human serum. Our capability for rapid confirmatory HIV diagnosis at the point of care has the potential to circumvent the western blotting bottleneck in the current diagnostic pipeline.

关键词： Proteins

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Photo-clickable separation gels enable targeted proteomics of cancer biomarker isoforms: A 'single channel, multi-stage' strategy

Photo-clickable separation gels enable targeted proteomics o...

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15th International Conference on Miniaturized Systems for Chemistry and Life Sciences 2011, MicroTAS 2011

作者： Hughes, Alex J. Herr, Amy E. UC Berkeley UCSF Graduate Program in Bioengineering United States UC Berkeley Bioengineering United States

ISBN: (纸本)9781618395955

We introduce a 'hands free' proteomic tool with the potential to radically transform the status quo of cancer protein bi-omarker validation. Here, we focus on a challenging and broadly relevant target in this analyte class - the prostate cancer marker prostate-specific antigen (PSA). We introduce light-activatable, volume accessible polyacrylamide separation gels (LAVAgels) that capture electrophoretically separated PSA isoforms within a highly multiplexed (16-channel) microfluidic assay format. The 3D LAVAgel matrix offers unprecedented target capture duty, with capture efficiencies greater than 100fold higher than for existing surface chemistries. Our optofluidic separations strategy harnesses tremendous micro/nanoscale transport advantages to yield unmatched speed and efficiency - major barriers to realizing high-throughput proteomics.

关键词： Microfluidics

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Resistive-pulse sensing tumor-derived exosome detection device for resrouce-limited settings 21

Resistive-pulse sensing tumor-derived exosome detection devi...

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21st International Conference on Miniaturized Systems for Chemistry and Life Sciences, MicroTAS 2017

作者： Carey, Thomas R. Yu, Connie W. Sohn, Lydia L. UC Berkeley-UCSF Graduate Program in Bioengineering United States UC Berkeley Bioengineering United States UC Berkeley Mechanical Engineering United States

ISBN: (纸本)9780692941836

We present the theory, design, and initial characterization of a tumor-derived exosome detection platform based on resistive-pulse sensing to enable cost-effective, point-of-care cancer screening. Our platform detects exosomes displaying a specific surface antigen by electronically measuring the effective size increase that occurs when exosomes bind to colloids functionalized with a specific antibody. We have demonstrated that our device can distinguish antibody-functionalized colloids from similar colloids incubated with SKBR3-derived exosomes. © 17CBMS-0001.

关键词： Colloids

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Regulation of vascular smooth muscle cells and mesenchymal stem cells by mechanical strain

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MCB Molecular and Cellular Biomechanics 2006年第1期3卷 21-34页

作者： Kurpinski, Kyle Park, Jennifer Thakar, Rahul G. Li, Song Department of Bioengineering University of California at Berkeley Berkeley CA United States Joint Graduate Program in Bioengineering UC Berkeley Berkeley CA United States Joint Graduate Program in Bioengineering UC San Francisco San Francisco CA United States

Vascular smooth muscle cells (SMCs) populate in the media of the blood vessel, and play an important role in the control of vasoactivity and the remodeling of the vessel wall. Blood vessels are constantly subjected to hemodynamic stresses, and the pulsatile nature of the blood flow results in a cyclic mechanical strain in the vessel walls. Accumulating evidence in the past two decades indicates that mechanical strain regulates vascular SMC phenotype, function and matrix remodeling. Bone marrow mesenchymal stem cell (MSC) is a potential cell source for vascular regeneration therapy, and may be used to generate SMCs to construct tissue-engineered vascular grafts for blood vessel replacements. In this review, we will focus on the effects of mechanical strain on SMCs and MSCs, e.g., cell phenotype, cell morphology, cytoskeleton organization, gene expression, signal transduction and receptor activation. We will compare the responses of SMCs and MSCs to equiaxial strain, uniaxial strain and mechanical strain in three-dimensional culture. Understanding the hemodynamic regulation of SMC and MSC functions will provide a basis for the development of new vascular therapies and for the construction of tissue-engineered vascular, grafts. Copyright © 2006 Tech Science Press.

关键词： Muscle

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Resistive-pulse sensing tumor-derived exosome detection device 22

Resistive-pulse sensing tumor-derived exosome detection devi...

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22nd International Conference on Miniaturized Systems for Chemistry and Life Sciences, MicroTAS 2018

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

ISBN: (纸本)9781510897571

We present the theory, design, and proof-of-concept demonstration of a tumor-derived exosome detection platform that enables non-invasive, cost-effective, point-of-care cancer screening. Our platform detects exosomes displaying a specific surface antigen by electronically measuring through node-pore sensing the effective size increase that occurs when exosomes bind to colloids functionalized with specific antibodies. We have demonstrated that our platform can differentially detect exosomes derived from A549 cells (a non-small cell lung cancer cell line) and BEAS-2B cells (a non-malignant bronchial epithelial cell line). Copyright © (2018) by Chemical and Biological Microsystems Society. All rights reserved.

关键词： Tumors

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Multiplexed resistive-pulse sensing through coded node⇓pore channel geometry 24

Multiplexed resistive-pulse sensing through coded node⇓pore...

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

作者： Cotner, Kristen L. Sohn, Lydia L. 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)9781733419017

Node-pore sensing (NPS) is a versatile label-free microfluidic platform to measure a variety of cell phenotypes. Yet the single-channel nature of NPS limits throughput and precludes integration with components such as cell sorting. Here we demonstrate a novel multichannel NPS design by encoding the channels with Barker and Gold codes to modulate the current pulse. Particle events are detected through matched-filter detection and successive interference cancellation (SIC), resolving overlapping signals in the same channel and across separate channels. © 2020 CBMS-0001

关键词： Matched filters

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Node-pore sensing device to detect tumor-derived extracellular vesicles 23

Node-pore sensing device to detect tumor-derived extracellul...

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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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