Fredrik Westerlund
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View article: DOGMA: de novo assembly of densely labelled optical DNA maps using a matrix profile approach
DOGMA: de novo assembly of densely labelled optical DNA maps using a matrix profile approach Open
In optical genome mapping (OGM), large numbers of individual DNA maps—sequence-specific data series along single DNA molecules—are produced. Such individual maps have to be stitched together in a process called de novo OGM assembly in orde…
View article: Oligomerisation of Ku from Mycobacterium tuberculosis promotes DNA synapsis
Oligomerisation of Ku from Mycobacterium tuberculosis promotes DNA synapsis Open
Mycobacterium tuberculosis ( Mtb ), the causative agent of tuberculosis (TB), is estimated to infect nearly one-quarter of the global population. A key factor in its resilience and persistence is its robust DNA repair capacity. Non-homolog…
View article: Photophysical image analysis for sCMOS cameras: Noise modelling and estimation of background parameters in fluorescence-microscopy images
Photophysical image analysis for sCMOS cameras: Noise modelling and estimation of background parameters in fluorescence-microscopy images Open
Fluorescence microscopy is an effective tool for imaging biological samples, yet captured images often contain noises, including photon shot noise and camera read noise. To analyze biological samples accurately, separating background pixel…
View article: Strain-Level Typing of <i>Streptococcus pyogenes</i> Using Optical DNA Mapping
Strain-Level Typing of <i>Streptococcus pyogenes</i> Using Optical DNA Mapping Open
Streptococcus pyogenes, also known as group A Streptococcus (GAS), is a Gram-positive bacterial pathogen responsible for approximately 500,000 deaths globally per year. Therefore, surveillance of invasive GAS infections is of critical impo…
View article: Emergence of carbapenem-producing enterobacteriaceae (CPE) and other multidrug-resistant gram-negative bacteria in neonates at a tertiary-level NICU in Tanzania: a point prevalence study
Emergence of carbapenem-producing enterobacteriaceae (CPE) and other multidrug-resistant gram-negative bacteria in neonates at a tertiary-level NICU in Tanzania: a point prevalence study Open
Aim Multidrug-resistant (MDR) Gram-negative bacilli pose a significant threat in neonatal care. This study aimed to evaluate the point prevalence and molecular characteristics of intestinal MDR colonization in neonates at Muhimbili Nationa…
View article: MYC modulates TOP2A diffusion to promote substrate detection and activity
MYC modulates TOP2A diffusion to promote substrate detection and activity Open
Topoisomerases alleviate DNA supercoiling by cleaving and resealing DNA strands. Previously, we showed that the oncoprotein MYC recruits and stimulates topoisomerases to remove DNA entanglements generated by oncogenic transcription. Unders…
View article: A trackable trinuclear platinum complex for breast cancer treatment
A trackable trinuclear platinum complex for breast cancer treatment Open
Cancer remains a leading cause of death, with triple-negative breast cancer (TNBC) being particularly significant due to limited treatment options. As such, there is interest in anticancer polynuclear platinum(II) complexes, attributed to …
View article: A Platinum Butterfly Effect: Small Changes Turn an Anticancer Drug into a Non-toxic Metalloantibiotic with In Vivo Efficacy
A Platinum Butterfly Effect: Small Changes Turn an Anticancer Drug into a Non-toxic Metalloantibiotic with In Vivo Efficacy Open
Widespread resistance to all clinically used antibiotics has sparked investigations into alternative sources for novel and effective antimicrobial agents. Metal-based compounds (metalloantibiotics) have emerged as a promising class of pote…
View article: SmartTrap: Automated Precision Experiments with Optical Tweezers
SmartTrap: Automated Precision Experiments with Optical Tweezers Open
There is a trend in research towards more automation using smart systems powered by artificial intelligence. While experiments are often challenging to automate, they can greatly benefit from automation by reducing labor and increasing rep…
View article: Stained DNA Dot Detection (SD3): An automated tool for quantifying fluorescent features along single stretched DNA molecules
Stained DNA Dot Detection (SD3): An automated tool for quantifying fluorescent features along single stretched DNA molecules Open
The main information in DNA is its four-letter sequence that builds up the genetic information and that is traditionally read using sequencing methodologies. DNA can, however, also carry other important information, such as epigenetic mark…
View article: Expanding the DNA Damaging Potential of Artificial Metallo-Nucleases with Click Chemistry
Expanding the DNA Damaging Potential of Artificial Metallo-Nucleases with Click Chemistry Open
The preparation of new metallodrugs targeting DNA is of key therapeutic interest. Recently, the copper(I)-catalyzed azide-alkyne cycloaddition (CuAAC) "click chemistry" reaction has emerged as a promising approach for designing new artific…
View article: Biological Amyloids Chemically Damage DNA
Biological Amyloids Chemically Damage DNA Open
Amyloid fibrils are protein polymers noncovalently assembled through β-strands arranged in a cross-β structure. Biological amyloids were considered chemically inert until we and others recently demonstrated their ability to catalyze chemic…
View article: Design and <i>in vitr</i> <i>o</i> anticancer assessment of a click chemistry-derived dinuclear copper artificial metallo-nuclease
Design and <i>in vitr</i> <i>o</i> anticancer assessment of a click chemistry-derived dinuclear copper artificial metallo-nuclease Open
Copper compounds with artificial metallo-nuclease (AMN) activity are mechanistically unique compared to established metallodrugs. Here, we describe the development of a new dinuclear copper AMN, Cu2-BPL-C6 (BPL-C6 = bis-1,10-phenanthroline…
View article: High-throughput single-molecule nanofluidic studies on <i>B. subtilis</i> Rok protein interaction with DNA
High-throughput single-molecule nanofluidic studies on <i>B. subtilis</i> Rok protein interaction with DNA Open
Single-molecule methods offer powerful insights into DNA-protein interactions at the individual DNA molecule level. We developed an automated, high-throughput nanofluidic imaging platform to characterize DNA-protein complexes in solution. …
View article: Force-induced melting and S-DNA pathways for DNA overstretching exhibit distinct kinetics
Force-induced melting and S-DNA pathways for DNA overstretching exhibit distinct kinetics Open
It is widely appreciated that double stranded DNA (dsDNA) is subjected to strong and dynamic mechanical forces in cells. Under increasing tension B-DNA, the most stable double-stranded (ds) form of DNA, undergoes cooperative elongation int…
View article: Photophysical image analysis: Unsupervised probabilistic thresholding for images from electron-multiplying charge-coupled devices
Photophysical image analysis: Unsupervised probabilistic thresholding for images from electron-multiplying charge-coupled devices Open
We introduce the concept photophysical image analysis (PIA) and an associated pipeline for unsupervised probabilistic image thresholding for images recorded by electron-multiplying charge-coupled device (EMCCD) cameras. We base our approac…
View article: Exploring the conformational dynamics of the SARS-CoV-2 SL4 hairpin by combining optical tweezers and base analogues
Exploring the conformational dynamics of the SARS-CoV-2 SL4 hairpin by combining optical tweezers and base analogues Open
We characterize the stability, conformational dynamics, (un)folding pathways, as well as identify a promising drug–target site within the SL4 hairpin of the SARS-CoV-2 by combining base analogues and optical tweezers.
View article: Data compilation for "Label-free Imaging of Catalytic H2O2 Decomposition on Single Colloidal Pt Nanoparticles using Nanofluidic Scattering Microscopy"
Data compilation for "Label-free Imaging of Catalytic H2O2 Decomposition on Single Colloidal Pt Nanoparticles using Nanofluidic Scattering Microscopy" Open
Data compilation for "Label-free Imaging of Catalytic H2O2 Decomposition on Single Colloidal Pt Nanoparticles using Nanofluidic Scattering Microscopy" This data set contains raw and evaluated data for the publication mentioned above and is…
View article: Label-Free Imaging of Catalytic H<sub>2</sub>O<sub>2</sub> Decomposition on Single Colloidal Pt Nanoparticles Using Nanofluidic Scattering Microscopy
Label-Free Imaging of Catalytic H<sub>2</sub>O<sub>2</sub> Decomposition on Single Colloidal Pt Nanoparticles Using Nanofluidic Scattering Microscopy Open
Single-particle catalysis aims at determining factors that dictate the nanoparticle activity and selectivity. Existing methods often use fluorescent model reactions at low reactant concentrations, operate at low pressures, or rely on plasm…
View article: Data compilation for "Label-free Imaging of Catalytic H2O2 Decomposition on Single Colloidal Pt Nanoparticles using Nanofluidic Scattering Microscopy"
Data compilation for "Label-free Imaging of Catalytic H2O2 Decomposition on Single Colloidal Pt Nanoparticles using Nanofluidic Scattering Microscopy" Open
Data compilation for "Label-free Imaging of Catalytic H2O2 Decomposition on Single Colloidal Pt Nanoparticles using Nanofluidic Scattering Microscopy" This data set contains raw and evaluated data for the publication mentioned above and is…
View article: Photophysical image analysis: parameter estimation, thresholding and segmentation for images from electron-multiplying charge-coupled devices
Photophysical image analysis: parameter estimation, thresholding and segmentation for images from electron-multiplying charge-coupled devices Open
Images acquired in fluorescence microscopy are subject to two types of noise: stochasticity in the arrival of photons at the imaging camera and subsequent noise induced by the detection system of the camera. In here, we introduce the conce…
View article: Back Cover: A Click Chemistry‐Based Artificial Metallo‐Nuclease (Angew. Chem. Int. Ed. 38/2023)
Back Cover: A Click Chemistry‐Based Artificial Metallo‐Nuclease (Angew. Chem. Int. Ed. 38/2023) Open
A new click chemistry generated artificial metallonuclease is reported in the Research Article by Andrew Kellett et al. (e202305759). The oxidative DNA damaging properties of a polynuclear copper binding ligand called TC-Thio is demonstrat…
View article: CCDC 2192605: Experimental Crystal Structure Determination
CCDC 2192605: Experimental Crystal Structure Determination Open
An entry from the Cambridge Structural Database, the world’s repository for small molecule crystal structures. The entry contains experimental data from a crystal diffraction study. The deposited dataset for this entry is freely available …