Article
Chemistry, Multidisciplinary
Adam Eordogh, Annabell Martin, Pablo Rivera-Fuentes
Summary: This study reports the development of functional probes that can operate at physiological pH and longer wavelengths compared to their predecessors. The probes are also compatible with HaloTag labeling, allowing for exceptionally long-term timelapse, single-molecule imaging of specific protein targets.
CHEMISTRY-A EUROPEAN JOURNAL
(2022)
Article
Chemistry, Multidisciplinary
Bryan J. Lampkin, Joshua A. Kritzer
Summary: Recent years have seen significant advancements in the design of organic fluorophores by restricting non-radiative decay pathways. In this study, we investigated benzothiadiazoles as turn-on fluorescent substrates, and by optimizing steric and electronic effects, we achieved improved turn-on dyes with a 136-fold increase in fluorescence over background.
CHEMICAL COMMUNICATIONS
(2023)
Article
Multidisciplinary Sciences
Stefan Niekamp, Nico Stuurman, Nan Zhang, Ronald D. Vale
Summary: The study reveals that during motility, the motor protein dynein exhibits variability in the movement between its domains, with the AAA ring and MTBDs not always stepping simultaneously and taking differently sized steps. This variability results in a large number of unexpected conformational states of dynein during motility. The flexibility between major dynein domains is found to be critical for dynein motility.
PROCEEDINGS OF THE NATIONAL ACADEMY OF SCIENCES OF THE UNITED STATES OF AMERICA
(2021)
Article
Chemistry, Analytical
Marketa Prochazkova, Eliska Kuchovska, Michael Killinger, Karel Kleparnik
Summary: In this study, a molecular probe based on Fo center dot rster resonance energy transfer (FRET) was designed and synthesized for investigating biological phenomena at a single-cell level. The probe utilizes a highly luminescent quantum dot (QD) as a donor and a specific peptide as a linker to a fluorophore or fluorescence quencher as an acceptor. The synthesized probe showed high reaction yield and specificity, and provided longer imaging times of caspases compared to commercial products.
ANALYTICA CHIMICA ACTA
(2023)
Review
Biotechnology & Applied Microbiology
Vikram Singh, Mukesh Jain
Summary: CRISPR-based imaging methods play a crucial role in studying the localization, interaction, and coordinated regulation of chromatin, genomic loci, RNAs, and proteins. These methods, utilizing various tools and technologies, have significantly improved the efficiency and clarity of imaging, offering insights into chromatin organization and dynamics, RNA visualization, and protein imaging for genome biology research.
CRITICAL REVIEWS IN BIOTECHNOLOGY
(2022)
Article
Physics, Fluids & Plasmas
Roberto N. Munoz, Laszlo Frazer, Gangcheng Yuan, Paul Mulvaney, Felix A. Pollock, Kavan Modi
Summary: It has been discovered that blinking quantum dots exhibit nontrivial memory, which cannot be detected using standard data analysis methods. This memory can be explained by various physical mechanisms such as chemical structure, intensity levels, and photon statistics.
Article
Optics
Gwiyeong Moon, Taehwang Son, Hajun Yoo, Changhun Lee, Hyunwoong Lee, Seongmin Im, Donghyun Kim
Summary: The interaction between single emitters and plasmonic structures can enhance optical properties but also causes distortion. By studying axially defocused images, the distortion can be explored and the precise positions of emitters can be retrieved, leading to improved localization accuracy.
LIGHT-SCIENCE & APPLICATIONS
(2023)
Article
Chemistry, Physical
Yuting Miao, Robert C. Boutelle, Anastasia Blake, Vigneshwaran Chandrasekaran, Chris J. Sheehan, Jennifer Hollingsworth, Daniel Neuhauser, Shimon Weiss
Summary: Plasmonic nano-objects have great potential in various applications. This study investigates the interaction between quantum dots (QDs) and L-shaped gold nanoantennas, and demonstrates that this strong interaction can induce polarization-dependent modifications to the QD emission intensity, polarization, and localization.
JOURNAL OF PHYSICAL CHEMISTRY LETTERS
(2022)
Article
Chemistry, Physical
Narima Eerqing, Hsin-Yu Wu, Sivaraman Subramanian, Serge Vincent, Frank Vollmer
Summary: This study developed an integrated optical setup that combines optoplasmonic and DNA-PAINT techniques for detecting oligonucleotides. The experimental results of both techniques were compared and complementary insights into single molecule processes were provided. Hybridisation events were observed in the same sample cell using fluorescence and optoplasmonic sensor signals, revealing the accumulation of irreversible hybridisation events in optoplasmonic sensing and the novel physicochemical mechanisms that stabilize DNA hybridisation on optically-excited plasmonic nanoparticles.
NANOSCALE HORIZONS
(2023)
Review
Biochemistry & Molecular Biology
Nitesh Kumar Podh, Sheetal Paliwal, Partha Dey, Ayan Das, Shruti Morjaria, Gunjan Mehta
Summary: Single-molecule imaging in live yeast cells has become a powerful tool for researchers to quantitatively measure cellular activities in real time, with significant progress made in recent years to provide important references for studying biological processes. Different labs have tailored imaging setups and data analysis pipelines to estimate biophysical parameters for various biological processes, reflecting a rich variety of experimental experiences.
JOURNAL OF MOLECULAR BIOLOGY
(2021)
Article
Chemistry, Multidisciplinary
Nazar Oleksiievets, Christeena Mathew, Jan Christoph Thiele, Jose Ignacio Gallea, Oleksii Nevskyi, Ingo Gregor, Andre Weber, Roman Tsukanov, Joerg Enderlein
Summary: This study compares the performance of wide-field and confocal FL-SMLM techniques in different spectral regions and provides practical advice.
Article
Chemistry, Physical
Cecilia Zaza, German Chiarelli, Ludovit P. Zweifel, Mauricio Pilo-Pais, Evangelos Sisamakis, Fabio Barachati, Fernando D. Stefani, Guillermo P. Acuna
Summary: Fluorescence Resonance Energy Transfer (FRET)-based approaches are unique tools for sensing the immediate surroundings and interactions of (bio)molecules. FRET imaging and Fluorescence Lifetime Imaging Microscopy (FLIM) enable the visualization of the spatial distribution of molecular interactions and functional states. However, conventional FLIM and FRET imaging provide average information over an ensemble of molecules within a diffraction-limited volume, which limits the spatial information, accuracy, and dynamic range of the observed signals. Here, an approach to obtain super-resolved FRET imaging based on single-molecule localization microscopy using an early prototype of a commercial time-resolved confocal microscope is demonstrated. DNA Points Accumulation for Imaging in Nanoscale Topography with fluorogenic probes provides a suitable combination of background reduction and binding kinetics compatible with the scanning speed of usual confocal microscopes. A single laser is used to excite the donor, a broad detection band is employed to retrieve both donor and acceptor emission, and FRET events are detected from lifetime information.
Review
Biochemistry & Molecular Biology
Eleonora Margheritis, Shirin Kappelhoff, Katia Cosentino
Summary: Pore-forming proteins (PFPs) are crucial in biological processes related to infection, immunity, cancer, and neurodegeneration, as they can form pores that disrupt the membrane and induce cell death. The exact mechanism of pore formation varies among PFPs, resulting in different pore structures with different functionalities. Recent studies have focused on using single-molecule imaging techniques to understand the molecular details of pore assembly, which are often obscured by ensemble measurements, and to determine pore structure and functionality. Uncovering the mechanistic elements of pore formation is essential for understanding the physiological role of PFPs and developing therapeutic strategies.
INTERNATIONAL JOURNAL OF MOLECULAR SCIENCES
(2023)
Article
Chemistry, Multidisciplinary
Yuqi Yang, Baolong Wang, Xu Zhang, Hongchuang Li, Sen Yue, Yifan Zhang, Yunhuang Yang, Maili Liu, Chaohui Ye, Peng Huang, Xin Zhou
Summary: In this study, acidity-activated graphene quantum dots-based nanotransformers (GQD NT) were developed as photosensitizer vehicles for long-period tumor imaging and repeated PDT. The GQD NT actively targeted tumor tissues and underwent loosening and enlargement in tumor acidity, enabling longer tumor retention. The GQD NT also generated mild hyperthermia upon laser irradiation, enhancing cell membrane permeability and promoting photosensitizer uptake. This study overcame the overdose obstacle in repeated PDT by using programmed deformation to enhance accumulation, retention, and release of photosensitizers in tumors.
ADVANCED MATERIALS
(2023)
Article
Nanoscience & Nanotechnology
Piotr Zdankowski, Lucia F. Lopez, Guillermo P. Acuna, Fernando D. Stefani
Summary: The localization of single fluorescent emitters is crucial for nanoscale physicochemical and biophysical measurements. MINFLUX and other related methods have achieved breakthroughs in resolution, enabling true nanoscale fluorescence nanoscopy and single-molecule tracking.
Review
Biochemical Research Methods
Wei Qin, Kelvin F. Cho, Peter E. Cavanagh, Alice Y. Ting
Summary: This article introduces the proximity labeling technology for studying and applying molecular interactions. By fusing baits with promiscuous enzymes, endogenous molecules interacting with them can be tagged and identified by mass spectrometry or nucleic acid sequencing. PL technology has been used to map protein-protein, protein-RNA, and protein-DNA interactions.
Article
Biochemistry & Molecular Biology
Ariana D. Sanchez, Tess C. Branon, Lauren E. Cote, Alexandros Papagiannakis, Xing Liang, Melissa A. Pickett, Kang Shen, Christine Jacobs-Wagner, Alice Y. Ting, Jessica L. Feldman
Summary: Microtubules are essential for cell transport, polarity, and division, and their organization is coordinated by microtubule-organizing centers. Non-centrosomal MTOCs like VAB-10B and WDR-62 play crucial roles in regulating microtubules and protein localization in cells. Understanding the functions of these non-centrosomal components expands our knowledge of cell biology and disease proteins.
Article
Multidisciplinary Sciences
Wei Qin, Samuel A. Myers, Dominique K. Carey, Steven A. Carr, Alice Y. Ting
Summary: Proximity labeling combined with organic-aqueous phase separation is a versatile approach for mapping and discovering proteins with novel functions in specific subcellular compartments. The method enables the identification of RNA binding proteins in the nucleus, nucleolus, and outer mitochondrial membrane.
NATURE COMMUNICATIONS
(2021)
Article
Biology
Robert Coukos, David Yao, Mateo Sanchez, Eric T. Strand, Meagan E. Olive, Namrata D. Udeshi, Jonathan S. Weissman, Steven A. Carr, Michael C. Bassik, Alice Y. Ting
Summary: The study demonstrates that gene perturbation technology combined with HiLITR tool can be used to explore protein trafficking processes by converting protein colocalization into a transcription factor driving expression of selected genes. By using HiLITR with FACS screening, genes that influence the trafficking of mitochondrial and ER tail-anchored proteins were identified, revealing the roles of SUMO E1 component SAE1 and EMC10 in mitochondrial and ER systems.
Article
Neurosciences
Qijing Xie, Jiefu Li, Hongjie Li, Namrata D. Udeshi, Tanya Svinkina, Daniel Orlin, Sayeh Kohani, Ricardo Guajardo, D. R. Mani, Chuanyun Xu, Tongchao Li, Shuo Han, Wei Wei, S. Andrew Shuster, David J. Luginbuhl, Stephen R. Quake, Swetha E. Murthy, Alice Y. Ting, Steven A. Carr, Liqun Luo
Summary: The transcription factor Acj6 regulates the precise dendrite targeting of Drosophila olfactory projection neurons by controlling the expression of cell-surface proteins. This study identifies specific cell-surface proteins that execute Acj6-regulated wiring decisions and demonstrates that Acj6 employs unique sets of these proteins in different neuron types for dendrite targeting. The combined expression of these proteins effectively rescues mutant phenotypes, highlighting the importance of Acj6 in controlling wiring specificity.
Article
Biochemical Research Methods
Elbegduuren Erdenee, Alice Y. Ting
Summary: LuCID is a novel calcium indicator and transcriptional calcium integrator that can real-time read out calcium dynamics in cells and convert the signal into stable gene expression. Its modular design enables it to read out other cellular events, making it an important tool for studying cells and cell populations utilizing calcium signaling.
ACS SYNTHETIC BIOLOGY
(2022)
Article
Biology
Kelvin F. Cho, Shawn M. Gillespie, Nicholas A. Kalogriopoulos, Michael A. Quezada, Martin Jacko, Michelle Monje, Alice Y. Ting
Summary: In this study, the researchers developed a transcriptional recorder called TRACC, which detects cell-cell contacts and converts them into stable gene expression. TRACC showed high specificity and sensitivity in detecting cell-cell contacts and was successfully used to study interactions between neurons and glioma.
Article
Biochemical Research Methods
Li-Chun Cheng, Xi Zhang, Kanishk Abhinav, Julie A. Nguyen, Sabyasachi Baboo, Salvador Martinez-Bartolome, Tess C. Branon, Alice Y. Ting, Esther Loose, John R. Yates, Larry Gerace
Summary: By using engineered biotin ligase TurboID and quantitative proteomics, this study explored the neighborhoods of Emerin and LBR in cultured mouse embryonic fibroblasts. The analysis revealed 232 high confidence proximity partners interacting selectively with Emerin and/or LBR, with 49 shared by both.
JOURNAL OF PROTEOME RESEARCH
(2022)
Article
Chemistry, Multidisciplinary
Matthew Ravalin, Heegwang Roh, Rahul Suryawanshi, G. Renuka Kumar, John E. Pak, Melanie Ott, Alice Y. Ting
Summary: The study presents a simplified and easily producible recombinant luminescent biosensor that can be used to detect SARS-CoV-2 antigen and virus in various assay formats, enabling detection using a cell phone camera.
JOURNAL OF THE AMERICAN CHEMICAL SOCIETY
(2022)
Article
Biochemistry & Molecular Biology
Rui Yang, Amanda S. Meyer, Ilia A. Droujinine, Namrata D. Udeshi, Yanhui Hu, Jinjin Guo, Jill A. McMahon, Dominique K. Carey, Charles Xu, Qiao Fang, Jihui Sha, Shishang Qin, David Rocco, James Wohlschlegel, Alice Y. Ting, Steven A. Carr, Norbert Perrimon, Andrew P. McMahon
Summary: Organ functions are specialized and interdependent. Secreted factors regulate organ development and maintain homeostasis through serum trafficking and inter-organ communication. This study introduces a BirA*G3 mouse strain that allows efficient labeling of proteins and enables tissue-specific biotinylation, providing insights into organ-specific secretory profiles and serum trafficking. The BirA*G3 mouse model enhances labelling efficiency and tissue specificity, facilitating a better understanding of secretory protein interplay in development, health, and disease.
Article
Neurosciences
S. Andrew Shuster, Jiefu Li, URee Chon, Miley C. Sinantha-Hu, David J. Luginbuhl, Namrata D. Udeshi, Dominique Kiki Carey, Yukari H. Takeo, Qijing Xie, Chuanyun Xu, D. R. Mani, Shuo Han, Alice Y. Ting, Steven A. Carr, Liqun Luo
Summary: A new method called iPEEL was developed to identify cell-surface proteomes in specific cell types in their native tissues. By applying iPEEL to studying developing and mature cerebellar Purkinje cells, researchers discovered differential enrichment in cell-surface proteomes with post-translational protein processing and synaptic functions in these cells. They also identified the critical role of Armh4 in Purkinje cell dendrite morphogenesis through in vivo loss-of-function screening. Disrupting Armh4's endocytosis augmented its effect on dendrite morphogenesis. This study highlights the importance of CSP profiling in native mammalian tissues for understanding cell-surface signaling regulations.
Article
Chemistry, Multidisciplinary
Heegwang Roh, Brigitte G. Dorner, Alice Y. Ting
Summary: The ability to deliver proteins and peptides across the plasma membrane into the cytosol of living mammalian cells has significant implications for basic science and medicine. In this study, we investigated the use of inactivated botulinum neurotoxin (BoNT) as a protein delivery platform, and found that nanobody-chimeric BoNTs can be selectively targeted to specific cells by replacing their natural receptor binding domain. These findings suggest that BoNT could be a versatile platform for targeted protein and peptide delivery into mammalian cells.
JOURNAL OF THE AMERICAN CHEMICAL SOCIETY
(2023)
Article
Biochemical Research Methods
Song-Yi Lee, Joleen S. Cheah, Boxuan Zhao, Charles Xu, Heegwang Roh, Christina K. Kim, Kelvin F. Cho, Namrata D. Udeshi, Steven A. Carr, Alice Y. Ting
Summary: The integration of light-responsive domains into proteins allows for control of protein localization, interactions, and function using light. In this study, we incorporated optogenetic control into proximity labeling, a technique for mapping organelles and interactomes in living cells. By introducing a light-sensitive LOV domain into the proximity labeling enzyme TurboID, we were able to control its labeling activity using low-power blue light. This approach, called 'LOV-Turbo', reduces background noise and allows for more precise labeling of proteins. Additionally, LOV-Turbo can be activated by bioluminescence resonance energy transfer from luciferase, enabling interaction-dependent proximity labeling.
Article
Biochemistry & Molecular Biology
Wei Qin, Joleen S. Cheah, Charles Xu, James Messing, Brian D. Freibaum, Steven Boeynaems, J. Paul Taylor, Namrata D. Udeshi, Steven A. Carr, Alice Y. Ting
Summary: The ability to map trafficking for thousands of endogenous proteins at once in living cells reveals biology currently invisible to microscopy and mass spectrometry. The method TransitID uses proximity labeling enzymes TurboID and APEX to map endogenous proteome trafficking with nanometer spatial resolution. TransitID allows for distinguishing protein populations based on their origin compartment or cell type.
Article
Biochemical Research Methods
Shimon M. Rosenthal, Tvisha Misra, Hala Abdouni, Tess C. Branon, Alice Y. Ting, Ian C. Scott, Anne-Claude Gingras
Summary: Researchers adapted proximity labeling for protein discovery in zebrafish, developing in vivo TurbolD and mini-Turbo labeling techniques. By providing biotin directly in the egg water, they demonstrated successful biotinylation of prey proteins after 12 hours, enabling time-resolved analysis of development.
MOLECULAR & CELLULAR PROTEOMICS
(2021)