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Article ; Online: Human-vision-inspired cluster identification for single-molecule localization microscopy.

Chen, Lei / Liu, Qian / Chou, Keng C

2023 Volume 31, Issue 3, Page(s) 3459–3466

Abstract: Single-molecule localization microscopy has enabled scientists to visualize cellular structures at the nanometer scale. However, researchers are facing great challenges in analyzing images presented by point clouds. Existing algorithms for cluster ... ...

Abstract	Single-molecule localization microscopy has enabled scientists to visualize cellular structures at the nanometer scale. However, researchers are facing great challenges in analyzing images presented by point clouds. Existing algorithms for cluster identification are coordinate-based analyses requiring users to input cutoff thresholds based on the distance or density of the point cloud. These thresholds are often one's best guess with repeated visual inspections, making the cluster assignment user-dependent. Here, we present a cluster identification algorithm mimicking the modulation transfer function of human vision. This approach does not require any input parameters and produces visually satisfactory cluster assignments. We tested this algorithm by identifying the clusters of the fusion proteins of the Nipah virus on its host cells. This algorithm was further extended to analyze three-dimensional point clouds using virus-like particles as an example.
MeSH term(s)	Humans ; Microscopy/methods ; Single Molecule Imaging ; Algorithms
Language	English
Publishing date	2023-02-13
Publishing country	United States
Document type	Journal Article
ZDB-ID	1491859-6
ISSN	1094-4087 ; 1094-4087
ISSN (online)	1094-4087
ISSN	1094-4087
DOI	10.1364/OE.476486
Database	MEDical Literature Analysis and Retrieval System OnLINE

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Article: 3D structured illumination microscope using a spinning disk [Invited].

Zhang, Youchang / Asghari, Parisa / Scriven, David R L / Moore, Edwin D W / Chou, Keng C

Biomedical optics express

2023 Volume 14, Issue 11, Page(s) 5710–5719

Abstract: Three-dimensional (3D) structured illumination microscopy (SIM) improves spatial resolution by a factor of two in both lateral and axial directions. However, the adoption of 3D SIM is limited by low imaging speed, susceptibility to out-of-focus light, ... ...

Abstract	Three-dimensional (3D) structured illumination microscopy (SIM) improves spatial resolution by a factor of two in both lateral and axial directions. However, the adoption of 3D SIM is limited by low imaging speed, susceptibility to out-of-focus light, and likelihood of reconstruction errors. Here we present a novel approach for 3D SIM using a spinning disk. The disk generates a 3D lattice illumination pattern on the sample and optically reconstructs super-resolved images in real time. This technique achieves a 2-times resolution improvement with a speed up to 100 frames per second while physically rejecting 90% of the background signal.
Language	English
Publishing date	2023-10-11
Publishing country	United States
Document type	Journal Article
ZDB-ID	2572216-5
ISSN	2156-7085
ISSN	2156-7085
DOI	10.1364/BOE.499181
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Article ; Online: Structured illumination microscopy with a phase-modulated spinning disk for optical sectioning.

Zhang, Youchang / Asghari, Parisa / Scriven, David R L / Moore, Edwin D W / Chou, Keng C

Optics letters

2023 Volume 48, Issue 15, Page(s) 3933–3936

Abstract: Among various super-resolution microscopic techniques, structured illumination microscopy (SIM) stands out for live-cell imaging because of its higher imaging speed. However, conventional SIM lacks optical sectioning capability. Here we demonstrate a new, ...

Abstract	Among various super-resolution microscopic techniques, structured illumination microscopy (SIM) stands out for live-cell imaging because of its higher imaging speed. However, conventional SIM lacks optical sectioning capability. Here we demonstrate a new, to the best of our knowledge, approach using a phase-modulated spinning disk (PMSD) that enhances the optical sectioning capability of SIM. The PMSD consists of a pinhole array for confocal imaging and a transparent polymer layer for light phase modulation. The light phase modulation was designed to cancel the zeroth-order diffracted beam and create a sharp lattice illumination pattern using the interference of four first-order diffracted beams. In the detection optical path, the PMSD serves as a spatial filter to physically reject about 80% of the out-of-focus signals, an approach that allows for real-time optical reconstruction of super-resolved images with enhanced contrast. Furthermore, the simplicity of the design makes it easy to upgrade a conventional fluorescence microscope to a PMSD SIM system.
Language	English
Publishing date	2023-07-31
Publishing country	United States
Document type	Journal Article
ISSN	1539-4794
ISSN (online)	1539-4794
DOI	10.1364/OL.494655
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Article ; Online: Cardiomyocyte ryanodine receptor clusters expand and coalesce after application of isoproterenol.

Scriven, David R L / Johnsen, Anne Berit / Asghari, Parisa / Chou, Keng C / Moore, Edwin D W

The Journal of general physiology

2023 Volume 155, Issue 11

Abstract: Earlier work has shown that ventricular ryanodine receptors (RyR2) within a cluster rearrange on phosphorylation as well as with a number of other stimuli. Using dSTORM, we investigated the effects of 300 nmol/liter isoproterenol on RyR2 clusters. In rat ...

Abstract	Earlier work has shown that ventricular ryanodine receptors (RyR2) within a cluster rearrange on phosphorylation as well as with a number of other stimuli. Using dSTORM, we investigated the effects of 300 nmol/liter isoproterenol on RyR2 clusters. In rat ventricular cardiomyocytes, there was a symmetrical enlargement of RyR2 cluster areas, a decrease in the edge-to-edge nearest neighbor distance, and distribution changes that suggested movement to increase the cluster areas by coalescence. The surface area covered by the phosphorylated clusters was significantly greater than in the control cells, as was the cluster density. This latter change was accompanied by a decreased cluster fragmentation, implying that new tetramers were brought into the sarcoplasmic reticulum. We propose a possible mechanism to explain these changes. We also visualized individual RyR2 tetramers and confirmed our earlier electron-tomographic finding that the tetramers are in a disorganized but non-random array occupying about half of the cluster area. Multiclusters, cluster groups defined by the maximum distance between their members, were analyzed for various distances. At 100 nm, the areas occupied by the multiclusters just exceeded those of the single clusters, and more than half of the multiclusters had only a single subcluster that could initiate a spark. Phosphorylation increased the size of the multiclusters, markedly so for distances >100 nm. There was no relationship between the number of subclusters in a group and the area covered by it. We conclude that isoproterenol induces rapid, significant, changes in the molecular architecture of excitation-contraction coupling.
MeSH term(s)	Animals ; Rats ; Myocytes, Cardiac ; Ryanodine Receptor Calcium Release Channel ; Isoproterenol/pharmacology ; Excitation Contraction Coupling ; Cluster Analysis
Chemical Substances	Ryanodine Receptor Calcium Release Channel ; Isoproterenol (L628TT009W)
Language	English
Publishing date	2023-09-20
Publishing country	United States
Document type	Journal Article ; Research Support, Non-U.S. Gov't
ZDB-ID	3118-5
ISSN	1540-7748 ; 0022-1295
ISSN (online)	1540-7748
ISSN	0022-1295
DOI	10.1085/jgp.202213109
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Article: Conditional Generative Adversarial Network for Spectral Recovery to Accelerate Single-Cell Raman Spectroscopic Analysis

Ma, Xiangyun / Wang, Kaidi / Chou, Keng C. / Li, Qifeng / Lu, Xiaonan

Analytical chemistry. 2022 Jan. 03, v. 94, no. 2

2022

Abstract: Raman spectroscopy is a powerful tool to investigate cellular heterogeneity. However, Raman spectra for single-cell analysis are hindered by a low signal-to-noise ratio (SNR). Here, we demonstrate a simple and reliable spectral recovery conditional ... ...

Abstract	Raman spectroscopy is a powerful tool to investigate cellular heterogeneity. However, Raman spectra for single-cell analysis are hindered by a low signal-to-noise ratio (SNR). Here, we demonstrate a simple and reliable spectral recovery conditional generative adversarial network (SRGAN). SRGAN reduced the data acquisition time by 1 order of magnitude (i.e., 30 vs 3 s) by improving the SNR by a factor of ∼6. We classified five major foodborne bacteria based on single-cell Raman spectra to further evaluate the performance of SRGAN. Spectra processed using SRGAN achieved an identification accuracy of 94.9%, compared to 60.5% using unprocessed Raman spectra. SRGAN can accelerate spectral collection to improve the throughput of Raman spectroscopy and enable real-time monitoring of single living cells.
Keywords	Raman spectroscopy ; analytical chemistry ; data collection ; signal-to-noise ratio ; spectral analysis
Language	English
Dates of publication	2022-0103
Size	p. 577-582.
Publishing place	American Chemical Society
Document type	Article
ZDB-ID	1508-8
ISSN	1520-6882 ; 0003-2700
ISSN (online)	1520-6882
ISSN	0003-2700
DOI	10.1021/acs.analchem.1c04263
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Article ; Online: Campylobacter jejuni Antimicrobial Resistance Profiles and Mechanisms Determined Using a Raman Spectroscopy-Based Metabolomic Approach.

Ma, Luyao / Chen, Lei / Chou, Keng C / Lu, Xiaonan

Applied and environmental microbiology

2021 Volume 87, Issue 12, Page(s) e0038821

Abstract: Rapid identification of antimicrobial resistance (AMR) profiles and mechanisms is critical for clinical management and drug development. However, the current AMR detection approaches take up to 48 h to obtain a result. Here, we demonstrate a Raman ... ...

Abstract	Rapid identification of antimicrobial resistance (AMR) profiles and mechanisms is critical for clinical management and drug development. However, the current AMR detection approaches take up to 48 h to obtain a result. Here, we demonstrate a Raman spectroscopy-based metabolomic approach to rapidly determine the AMR profile of Campylobacter jejuni, a major cause of foodborne gastroenteritis worldwide. C. jejuni isolates with susceptible and resistant traits to ampicillin and tetracycline were subjected to different antibiotic concentrations for 5 h, followed by Raman spectral collection and chemometric analysis (i.e., second-derivative transformation analysis, hierarchical clustering analysis [HCA], and principal-component analysis [PCA]). The MICs obtained by Raman-2nd derivative transformation agreed with the reference agar dilution method for all isolates. The AMR profile of C. jejuni was accurately classified by Raman-HCA after treating bacteria with antibiotics at clinical susceptible and resistant breakpoints. According to PCA loading plots, susceptible and resistant strains showed different Raman metabolomic patterns for antibiotics. Ampicillin-resistant isolates had distinctive Raman signatures of peptidoglycan, which is related to cell wall synthesis. The ratio of saturated to unsaturated fatty acids in the lipid membrane layer of ampicillin-resistant isolates was higher than in susceptible ones, indicating more rigid envelope structure under ampicillin treatment. In comparison, tetracycline-resistant isolates exhibited prominent Raman spectral features associated with proteins and nucleic acids, demonstrating more active protein synthesis than susceptible strains with the presence of tetracycline. Taken together, Raman spectroscopy is a powerful metabolic fingerprinting technique for simultaneously revealing the AMR profiles and mechanisms of foodborne pathogens.
MeSH term(s)	Ampicillin/pharmacology ; Anti-Bacterial Agents/pharmacology ; Bacterial Proteins/metabolism ; Campylobacter jejuni/drug effects ; Campylobacter jejuni/metabolism ; Drug Resistance, Bacterial ; Lipid Metabolism/drug effects ; Metabolomics/methods ; Microbial Sensitivity Tests ; Nucleic Acids/metabolism ; Spectrum Analysis, Raman ; Tetracycline/pharmacology
Chemical Substances	Anti-Bacterial Agents ; Bacterial Proteins ; Nucleic Acids ; Ampicillin (7C782967RD) ; Tetracycline (F8VB5M810T)
Language	English
Publishing date	2021-05-26
Publishing country	United States
Document type	Journal Article ; Research Support, Non-U.S. Gov't
ZDB-ID	223011-2
ISSN	1098-5336 ; 0099-2240
ISSN (online)	1098-5336
ISSN	0099-2240
DOI	10.1128/AEM.00388-21
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Article ; Online: Conditional Generative Adversarial Network for Spectral Recovery to Accelerate Single-Cell Raman Spectroscopic Analysis.

Ma, Xiangyun / Wang, Kaidi / Chou, Keng C / Li, Qifeng / Lu, Xiaonan

Analytical chemistry

2022 Volume 94, Issue 2, Page(s) 577–582

Abstract	Raman spectroscopy is a powerful tool to investigate cellular heterogeneity. However, Raman spectra for single-cell analysis are hindered by a low signal-to-noise ratio (SNR). Here, we demonstrate a simple and reliable spectral recovery conditional generative adversarial network (SRGAN). SRGAN reduced the data acquisition time by 1 order of magnitude (i.e., 30 vs 3 s) by improving the SNR by a factor of ∼6. We classified five major foodborne bacteria based on single-cell Raman spectra to further evaluate the performance of SRGAN. Spectra processed using SRGAN achieved an identification accuracy of 94.9%, compared to 60.5% using unprocessed Raman spectra. SRGAN can accelerate spectral collection to improve the throughput of Raman spectroscopy and enable real-time monitoring of single living cells.
MeSH term(s)	Signal-To-Noise Ratio ; Single-Cell Analysis ; Spectrum Analysis, Raman/methods
Language	English
Publishing date	2022-01-03
Publishing country	United States
Document type	Journal Article ; Research Support, Non-U.S. Gov't
ZDB-ID	1508-8
ISSN	1520-6882 ; 0003-2700
ISSN (online)	1520-6882
ISSN	0003-2700
DOI	10.1021/acs.analchem.1c04263
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Article ; Online: The nanoscale organization of Nipah virus matrix protein revealed by super-resolution microscopy.

Liu, Qian T / Wang, Qian / Zhang, Youchang / Kliemke, Vicky / Liu, Qian / Chou, Keng C

Biophysical journal

2022 Volume 121, Issue 12, Page(s) 2290–2296

Abstract: The matrix proteins (M) of many enveloped RNA viruses mediate virus assembly and budding. However, it remains poorly understood how M are involved in virus budding and how they interact with envelope proteins. Here, we show that the expression level of ... ...

Abstract	The matrix proteins (M) of many enveloped RNA viruses mediate virus assembly and budding. However, it remains poorly understood how M are involved in virus budding and how they interact with envelope proteins. Here, we show that the expression level of Nipah (NiV) M in particles produced by the host cells deviates from a gamma distribution and does not reflect that of the host cells, indicating assembly of the NiV-M in the process. Our data reveal that NiV-M affects the circularity of the particles while the NiV envelope proteins do not. The organization of NiV envelope proteins on the membrane of the particles is similar to those that do not express NiV-M, suggesting that NiV-M does not directly interact with the envelope proteins during assembly and budding.
MeSH term(s)	Microscopy ; Nipah Virus/genetics ; Viral Envelope Proteins/metabolism ; Viral Matrix Proteins/metabolism ; Virion/metabolism ; Virus Assembly
Chemical Substances	Viral Envelope Proteins ; Viral Matrix Proteins
Language	English
Publishing date	2022-05-25
Publishing country	United States
Document type	Journal Article ; Research Support, Non-U.S. Gov't
ZDB-ID	218078-9
ISSN	1542-0086 ; 0006-3495
ISSN (online)	1542-0086
ISSN	0006-3495
DOI	10.1016/j.bpj.2022.05.026
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Article: Predicted Structure of Fully Activated Tas1R3/1R3′ Homodimer Bound to G Protein and Natural Sugars: Structural Insights into G Protein Activation by a Class C Sweet Taste Homodimer with Natural Sugars

Mafi, Amirhossein / Kim, Soo-Kyung / Chou, Keng C. / Güthrie, Brian / Goddard, William A.

Journal of the American Chemical Society. 2021 Sept. 29, v. 143, no. 40

2021

Abstract: The Tas1R3 G protein-coupled receptor constitutes the main component of sweet taste sensory response in humans via forming a heterodimer with Tas1R2 or a homodimer with Tas1R3. The Tas1R3/1R3′ homodimer serves as a low-affinity sweet taste receptor, ... ...

Abstract	The Tas1R3 G protein-coupled receptor constitutes the main component of sweet taste sensory response in humans via forming a heterodimer with Tas1R2 or a homodimer with Tas1R3. The Tas1R3/1R3′ homodimer serves as a low-affinity sweet taste receptor, stimulating gustducin G protein (GGᵤₛₜ) signaling in the presence of a high concentration of natural sugars. This provides an additional means to detect the taste of natural sugars, thereby differentiating the flavors between natural sugars and artificial sweeteners. We report here the predicted 3D structure of active state Tas1R3/1R3′ homodimer complexed with heterotrimeric GGᵤₛₜ and sucrose. We discovered that the GGᵤₛₜ makes ionic anchors to intracellular loops 1 and 2 of Tas1R3 while the Gα–α5 helix engages the cytoplasmic region extensively through salt bridge and hydrophobic interactions. We show that in the activation of this complex the Venus flytrap domains of the homodimer undergo a remarkable twist up to ∼100° rotation around the vertical axis to adopt a closed–closed conformation while the intracellular region relaxes to an open–open conformation. We find that binding of sucrose to the homodimer stabilizes a preactivated conformation with a largely open intracellular region that recruits and activates the GGᵤₛₜ. Upon activation, the Gα subunit spontaneously opens up the nucleotide-binding site, making nucleotide exchange facile for signaling. This activation of GGᵤₛₜ promotes the interdomain twist of the Venus flytrap domains. These structures and transformations could potentially be a basis for the design of new sweeteners with higher activity and less unpleasant flavors.
Keywords	Dionaea muscipula ; hydrophobicity ; sucrose ; sweetness ; taste ; taste receptors
Language	English
Dates of publication	2021-0929
Size	p. 16824-16838.
Publishing place	American Chemical Society
Document type	Article
ZDB-ID	3155-0
ISSN	1520-5126 ; 0002-7863
ISSN (online)	1520-5126
ISSN	0002-7863
DOI	10.1021/jacs.1c08839
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Article ; Online: Next-Generation Antimicrobial Resistance Surveillance System Based on the Internet-of-Things and Microfluidic Technique.

Ma, Luyao / He, Weidong / Petersen, Marlen / Chou, Keng C / Lu, Xiaonan

ACS sensors

2021 Volume 6, Issue 9, Page(s) 3477–3484

Abstract: Antimicrobial resistance (AMR) of foodborne pathogens is a global crisis in public health and economic growth. A real-time surveillance system is key to track the emergence of AMR bacteria and provides a comprehensive AMR trend from farm to fork. However, ...

Abstract	Antimicrobial resistance (AMR) of foodborne pathogens is a global crisis in public health and economic growth. A real-time surveillance system is key to track the emergence of AMR bacteria and provides a comprehensive AMR trend from farm to fork. However, current AMR surveillance systems, which integrate results from multiple laboratories using the conventional broth microdilution method, are labor-intensive and time-consuming. To address these challenges, we present the internet of things (IoT), including colorimetric-based microfluidic sensors, a custom-built portable incubator, and machine learning algorithms, to monitor AMR trends in real time. As a top priority microbe that poses risks to human health,
MeSH term(s)	Anti-Bacterial Agents/pharmacology ; Drug Resistance, Bacterial ; Humans ; Internet ; Microfluidics
Chemical Substances	Anti-Bacterial Agents
Language	English
Publishing date	2021-09-08
Publishing country	United States
Document type	Journal Article ; Research Support, Non-U.S. Gov't
ISSN	2379-3694
ISSN (online)	2379-3694
DOI	10.1021/acssensors.1c01453
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