Article
Chemistry, Physical
Ji-Hoon Lee, Joyce Han-Ching Chiu, Nicholas J. J. Ginga, Tasdiq Ahmed, M. D. Thouless, Yifan Liu, Shuichi Takayama
Summary: This study developed a three-layer tunable nanochannel system that enables non-electrophoretic linearization and immobilization of native chromatin. Through careful selection of self-blinking fluorescent dyes and nanochannel design, they achieved super-resolution imaging of the linearized chromatin using direct stochastic optical reconstruction microscopy (dSTORM). This work opens up a new avenue for collecting long-range and high-resolution epigenetic information as well as genetic information.
NANOSCALE HORIZONS
(2023)
Article
Biochemical Research Methods
David J. Schodt, Farzin Farzam, Sheng Liu, Keith A. Lidke
Summary: We introduce the Sequential Super-resolution Microscope (SeqSRM), a dedicated microscope for automated sequential localization microscopy. SeqSRM automates precise stage stabilization and data acquisition of user-selected cells, minimizing user interaction. We demonstrate that nanometer-scale changes in cell morphology can impact the fidelity of multi-target super-resolution reconstructions, but these shifts can be reliably detected and masked out using brightfield images. SeqSRM enables automated multi-target imaging without the need for multiple fluorophores, while accurately reflecting the relative organization of the targets.
BIOMEDICAL OPTICS EXPRESS
(2023)
Article
Biochemical Research Methods
Yevgeni Nogin, Tahir Detinis Zur, Sapir Margalit, Ilana Barzilai, Onit Alalouf, Yuval Ebenstein, Yoav Shechtman
Summary: A new computational method called DeepOM, which utilizes deep learning, is presented for efficient retrieval of genomic information from a single microscopic image of intact DNA molecules. The method employs a convolutional neural network trained on simulated images of labeled DNA molecules to improve the alignment success rate of DNA images to genomic references.
Article
Chemistry, Multidisciplinary
Gil Nifker, Assaf Grunwald, Sapir Margalit, Zuzana Tulpova, Yael Michaeli, Hagai Har-Gil, Noy Maimon, Elad Roichman, Leonie Schuetz, Elmar Weinhold, Yuval Ebenstein
Summary: Proteins and enzymes in the cell nucleus require physical access to their DNA target sites in order to perform genomic tasks such as gene activation and transcription. Chromatin accessibility is a central regulator of gene expression and holds essential information on the cell type and state. By utilizing a combination of E. coli Dam methyltransferase and a fluorescent cofactor analogue, we were able to generate fluorescent tags in accessible DNA regions within the cell nucleus, and then detect these accessible portions using single-molecule optical genome mapping in nanochannel arrays. This method allows for the characterization of long-range structural variations and their associated chromatin structure, resulting in the creation of whole-genome, allele-specific chromatin accessibility maps composed of long DNA molecules extended in silicon nanochannels.
Article
Chemistry, Multidisciplinary
Michael Holtmannspoetter, Eike Wienbeuker, Timo Dellmann, Isabelle Watrinet, Ana J. Garcia-Saez, Kai Johnsson, Rainer Kurre, Jacob Piehler
Summary: Self-labeling enzymes (SLE) like the HaloTag are valuable tools in high and super-resolution fluorescence microscopy. New fluorogenic substrates for SLE allow imaging with excess dye. Two engineered variants of HaloTag7 with restored dehalogenase activity, reHaloTagS (approx. 0.006 s(-1)) and reHaloTagF (approx. 0.055 s(-1)), showed different turnover kinetics in vitro. Imaging with reHaloTag labeling demonstrated 3-5 times enhanced photostability, and single molecule imaging enabled controlled and stable labeling density over extended periods. Combination with structured illumination allowed simultaneous visualization of single molecule diffusion and organellar dynamics. These applications showcase the potential of reHaloTag labeling in advancing fluorescence microscopy techniques.
ANGEWANDTE CHEMIE-INTERNATIONAL EDITION
(2023)
Article
Acoustics
Scott Schoen, Zhigen Zhao, Ashley Alva, Chengwu Huang, Shigao Chen, Costas Arvanitis
Summary: The generation of super-resolution ultrasound images through the localization of individual microbubbles has allowed for improved visualization of microvascular structure and flow. A method based on morphological image reconstruction has been proposed to increase peak detection and spatial resolution, with robustness to noise. This computationally efficient method shows promise for enhancing the capabilities of super-resolution ultrasound imaging.
IEEE TRANSACTIONS ON ULTRASONICS FERROELECTRICS AND FREQUENCY CONTROL
(2021)
Article
Materials Science, Multidisciplinary
Tiesheng Wang, Randy P. Sabatini, Bun Chan, Jingwei Hou, Vien T. Huynh, Nicholas Proschogo, Zixi Xie, Tan Wang, Long Gao, Jiaqi Zhang, Brian S. Hawkett, Ronald J. Clarke, Cameron J. Kepert, Vicki Chen, Girish Lakhwani, Deanna M. D'Alessandro
Summary: Nanoconfinement in metal-organic frameworks was used to oligomerize a fluorescent anthryl monomer, resulting in enhanced fluorescence emission. This study provides inspiration for the design of luminescent composites and encourages further exploration of molecules in nanoconfined spaces.
ACS MATERIALS LETTERS
(2021)
Review
Chemistry, Multidisciplinary
Alan M. Szalai, Cecilia Zaza, Fernando D. Stefani
Summary: The combination of super-resolution fluorescence microscopy and FRET has provided unique tools for studying biological systems and nanomaterials. The integration of these techniques has advanced super-resolution imaging and allowed for visualization of molecular interaction patterns with higher spatial resolution. Future perspectives include possible integration with next generation super-resolution techniques for true molecular-scale spatial resolution.
Article
Biochemical Research Methods
Yanlin Zhang, Mathieu Blanchette
Summary: In this study, we propose a deep learning framework called RefHiC-SR that utilizes a reference panel of Hi-C datasets to enhance the resolution of Hi-C data in a given study sample. Compared to tools that do not use reference samples, RefHiC-SR outperforms them across different cell types and sequencing depths, and enables high-accuracy mapping of structures such as loops and topologically associating domains.
Article
Computer Science, Hardware & Architecture
Seok Bong Yoo, Eung-Joo Lee
Summary: An optimal super-resolution imaging network based on object-adaptive optical point spread function estimation is proposed to address the issue of unknown optical blur in practical optical imaging systems. The network estimates the point spread function by a new object sharpness consistency cost in the dark channel domain and adaptively combines an object image sharpening network with the estimation. The performance of the proposed network is validated through experiments using various quantitative metrics.
IEEE CONSUMER ELECTRONICS MAGAZINE
(2021)
Article
Chemistry, Multidisciplinary
Shikha Dhiman, Teodora Andrian, Beatriz Santiago Gonzalez, Marrit M. E. Tholen, Yuyang Wang, Lorenzo Albertazzi
Summary: Characterization of newly synthesized materials is crucial in chemistry and nanotechnology, with standardized analytical techniques and novel technologies continually developing. The adoption of reporting standards like MIRIBEL aims to provide reproducible and reliable sample preparation for the scientific community. Super-resolution microscopy (SRM) shows potential to transition into a standard routine method for material characterization, but faces challenges in sample preparation, data analysis, and expensive instrumentation.
Article
Multidisciplinary Sciences
Erik Torstensson, Gaurav Goyal, Anna Johnning, Fredrik Westerlund, Tobias Ambjornsson
Summary: Optical DNA mapping (ODM) utilizes fluorescent labeling, stretching, and imaging of single DNA molecules to obtain sequence-specific fluorescence profiles, DNA barcodes, for DNA identification and detection of structural changes. This study introduces theoretical methods for analyzing DNA molecules with multiple label types and a novel assay for obtaining dual-labeled DNA barcodes. By simultaneously utilizing information from all labeling types, significant improvement in matching experimental barcodes to a theoretical database is demonstrated.
Article
Chemistry, Analytical
Guang Li, Qiqing Zhang
Summary: Single-molecule quantification using super-resolution imaging techniques has enabled the study of individual molecules as disease biomarkers. Counting is a simple and direct method for quantitative analysis, and utilizing higher spatial resolution to overcome counting errors is crucial for understanding intracellular mechanisms.
ANALYTICAL CHEMISTRY
(2021)
Article
Multidisciplinary Sciences
Xining Zhang, Yong Ge, Jin Chen, Feng Ling, Qunming Wang, Delin Du, Ru Xiang
Summary: Super-resolution mapping (SRM) is an important technology in remote sensing. To address the issues of existing models that only focus on spectral features, we propose a soft information-constrained network (SCNet) that leverages soft information as a spatial prior. SCNet generates more complete spatial details in complex areas, providing an effective means for producing high-quality and high-resolution mapping products from remote sensing images.
Article
Chemistry, Multidisciplinary
Florian Schueder, Juanita Lara-Gutierrez, Daniel Haas, Kai Sandvold Beckwith, Peng Yin, Jan Ellenberg, Ralf Jungmann
Summary: The researchers introduced a new super-resolution microscopy technique called pPAINT, which can sensitively detect the spatial proximity of biomolecules and has broad applications in cellular research.
ANGEWANDTE CHEMIE-INTERNATIONAL EDITION
(2021)
Article
Biochemistry & Molecular Biology
Vandana Singh, Pegah Johansson, Elina Ekedahl, Yii-Lih Lin, Ola Hammarsten, Fredrik Westerlund
Summary: In this study, single DNA molecule imaging using fluorescence microscopy was used to quantify DNA damage caused by the topoisomerase II poison etoposide. The researchers found a large variation in etoposide-induced DNA damage after in vitro treatment of blood cells from healthy individuals. The results further demonstrated that the etoposide-induced DNA damage was TopoII dependent.
BIOCHEMICAL AND BIOPHYSICAL RESEARCH COMMUNICATIONS
(2022)
Article
Infectious Diseases
K. K. Sriram, Elina Ekedahl, Ngoc Thi Bich Hoang, Tsegaye Sewunet, Bjorn Berglund, Ludwig Lundberg, Shoeib Nematzadeh, Maud Nilsson, Lennart E. Nilsson, Ngai Kien Le, Dien Minh Tran, Hakan Hanberger, Linus Olson, Mattias Larsson, Christian G. Giske, Fredrik Westerlund
Summary: The diversity of bla(NDM-1)-encoding plasmids from neonates at a large Vietnamese hospital was characterized using optical DNA mapping (ODM) and next-generation sequencing (NGS). The results showed that there were at least 10 different plasmids encoding bla(NDM-1) among the 18 isolates, indicating wide plasmid diversity. This study highlights the importance of ODM for plasmid analysis.
INTERNATIONAL JOURNAL OF ANTIMICROBIAL AGENTS
(2022)
Article
Dermatology
Miriam Karmon, Eli Kopel, Aviv Barzilai, Polina Geva, Eli Eisenberg, Erez Y. Levanon, Shoshana Greenberger
Summary: Atopic dermatitis (AD) is associated with reduced adenosine-to-inosine RNA editing, leading to impairment of the innate immune response and dysregulated type 1 interferon-mediated responses. This alteration in editing may play a role in the pathogenesis of AD as well as other autoimmune and inflammatory diseases, while not being observed in conditions like systemic lupus erythematosus and systemic sclerosis with IFN activation.
JOURNAL OF INVESTIGATIVE DERMATOLOGY
(2023)
Article
Nanoscience & Nanotechnology
John Andersson, Julia Jarlebark, K. K. Sriram, Andreas Schaefer, Rebekah Hailes, Chonnipa Palasingh, Bagus Santoso, Van-Truc Vu, Chun-Jun Huang, Fredrik Westerlund, Andreas Dahlin
Summary: In nanobiotechnology, controlling the interactions between biological molecules and surfaces is crucial. This study presents a simple method for passivating or selectively functionalizing silica surfaces, without the need for complex reactions. The modified surfaces show superior properties compared to existing options, with low fouling and the ability to detect specific molecules. This method is compatible with various surface-based sensors and analytical devices, making it highly valuable for the field of nanobiotechnology.
ACS APPLIED MATERIALS & INTERFACES
(2023)
Article
Biochemical Research Methods
Tomer D. Mann, Eli Kopel, Eli Eisenberg, Erez Y. Levanon
Summary: Adenosine-to-inosine RNA editing is essential for immune regulation and is associated with various pathological conditions. In this study, the authors characterized RNA editing in the heart and arteries and found increased editing in patients with atherosclerosis, cardiomyopathies, and heart failure. They identified a specific editing site in the IGFBP7 gene that is consistently elevated in these patients. These findings highlight the importance of RNA editing in cardiovascular diseases.
PLOS COMPUTATIONAL BIOLOGY
(2023)
Article
Chemistry, Multidisciplinary
Bjorn Altenburger, Carl Andersson, Sune Levin, Fredrik Westerlund, Joachim Fritzsche, Christoph Langhammer
Summary: This study introduces nanofluidic scattering microscopy to measure the activity of single nanoparticles during catalytic reactions. By detecting minuscule refractive index changes in the liquid, the concentration changes of reactants can be accurately measured. The turnover frequency of the particles is derived from the growth rate of gas bubbles formed during the reaction.
Article
Chemistry, Multidisciplinary
Jonathan Jeffet, Sayan Mondal, Amit Federbush, Nadav Tenenboim, Miriam Neaman, Jasline Deek, Yuval Ebenstein, Yohai Bar-Sinai
Summary: This article presents a method for multiplexed single-molecule detection and quantification of a selected panel of miRs. The method does not depend on sequencing, requires a small amount of blood, and provides fast results by directly analyzing native, unamplified miRs. It combines compact spectral imaging and a machine learning-based detection scheme, allowing simultaneous multiplexed classification of multiple miR targets.
Article
Genetics & Heredity
Rona Merdler-Rabinowicz, David Gorelik, Jiwoon Park, Cem Meydan, Jonathan Foox, Miriam Karmon, Hillel S. Roth, Roni Cohen-Fultheim, Galit Shohat-ophir, Eli Eisenberg, Eytan Ruppin, Christopher E. Mason, Erez Y. Levanon
Summary: This study analyzed the RNA sequences of COVID-19 infected individuals and observed a significant increase in global RNA editing activity in COVID-19 patients. The study also identified specific coding sites with higher editing activity and found that the increase in editing activity during the disease was temporary, returning to baseline levels after symptoms disappeared. These epigenetic changes may contribute to the immune system response and affect adverse outcomes in post-viral cases.
NAR GENOMICS AND BIOINFORMATICS
(2023)
Article
Biochemical Research Methods
Yevgeni Nogin, Tahir Detinis Zur, Sapir Margalit, Ilana Barzilai, Onit Alalouf, Yuval Ebenstein, Yoav Shechtman
Summary: A new computational method called DeepOM, which utilizes deep learning, is presented for efficient retrieval of genomic information from a single microscopic image of intact DNA molecules. The method employs a convolutional neural network trained on simulated images of labeled DNA molecules to improve the alignment success rate of DNA images to genomic references.
Article
Medicine, Research & Experimental
My Nyblom, Anna Johnning, Karolin Frykholm, Marie Wrande, Vilhelm Mueller, Gaurav Goyal, Miriam Robertsson, Albertas Dvirnas, Tsegaye Sewunet, K. K. Sriram, Tobias Ambjornsson, Christian G. Giske, Linus Sandegren, Erik Kristiansson, Fredrik Westerlund
Summary: We have developed a method to directly identify bacteria from patient samples, which can accurately identify different strains or subtypes. This method can be used for mixed bacterial samples and urine samples, providing fast diagnostic information for choosing the most suitable antibiotics and reducing the risk of death and suffering.
COMMUNICATIONS MEDICINE
(2023)
Article
Chemistry, Multidisciplinary
Patrick Finkelstein, Julia C. Reisenbauer, Bence B. Botlik, Ori Green, Andri Florin, Bill Morandi
Summary: We present a convenient method for inserting a nitrogen atom into indenes to produce isoquinolines. The reaction utilizes commercially available phenyliodine(iii) diacetate (PIDA) and ammonium carbamate as the nitrogen source, allowing for a wide range of isoquinoline synthesis. The protocol shows good tolerance towards various substitution patterns and commonly used functional groups. Moreover, it is applicable for the direct interconversion of cyclopentadienes into pyridines. Additionally, the strategy enables the synthesis of N-15 labelled isoquinolines using (NH4Cl)-N-15 as a commercial N-15 source.
Article
Chemistry, Multidisciplinary
Nima Sasanian, Rajhans Sharma, Quentin Lubart, K. K. Sriram, Marziyeh Ghaeidamini, Kevin D. Dorfman, Elin K. Esbjorner, Fredrik Westerlund
Summary: Amyloid fibrils play a central role in the pathology of many diseases and have significant structural polymorphism. A nanofluidic channel analysis technique was introduced to study single, fluorescently-labeled amyloid fibrils and determine their physical properties. The method allowed for accurate determination of fibril persistence length and revealed differences in physical properties between amyloid-beta(1-42) and alpha-synuclein fibrils.
Article
Infectious Diseases
Kk Sriram, Moa S. Wranne, Tsegaye Sewunet, Elina Ekedahl, Maarten Coorens, Teerawit Tangkoskul, Visanu Thamlikitkul, Christian G. Giske, Fredrik Westerlund
Summary: This study demonstrates the use of optical DNA mapping (ODM) to characterize plasmids carrying the colistin resistance gene mcr-1. The researchers successfully identified plasmids encoding mcr-1 and demonstrated the ability of ODM to identify resistance gene sites in small plasmids. They also propose a cut-and-stretch assay using surface-functionalized cover slips and a basic microscope to identify the mcr-1 gene in plasmid samples. These techniques could be valuable in identifying plasmids carrying antibiotic resistance in hospitals, particularly in low- and middle-income countries.
JAC-ANTIMICROBIAL RESISTANCE
(2022)
Meeting Abstract
Biophysics
Fredrik Westerlund
BIOPHYSICAL JOURNAL
(2022)
