Welcome
The Biophysics and Biophotonics group is located in the Department of Physics at Umeå University. The head of the group is Magnus Andersson (ResearchGate profile here). We mainly develop and apply photonic techniques to study biological processes. For more than 20 years, we have developed optical tweezers that are used for micromanipulation, force spectroscopy, and Raman spectroscopy measurements. We also develop image-processing algorithms, machine learning tools, and software for tracking organisms. In addition, we develop microfluidic systems using 3D-printing technology as well as digital holographic microscopy imaging techniques. We are also a partner in the Umeå Center for Microbial Research (UCMR).
Recent News
Major happenings 2024:
Paper out: Segmentation and Characterization of Macerated Fibers and Vessels Using Deep Learning (2024) Plant Method
Paper out: The role of endospore appendages in spore-spore contacts in pathogenic Bacillus cereus group (2024) Environmental Microbiology
Paper out: Evaluating Bacterial Spore Preparation Methods for Scanning Electron Microscopy (2024) Microscopy & Microanalysis
Paper out: Assessing CaDPA Levels, Metabolic Activity, and Spore Detection through Deuterium Labeling (2024) The Analyst
Paper out: UV-induced Spectral and Morphological Changes in Bacterial Spores for Inactivation Assessment (2024) The Journal of Physical Chemistry
Paper out: Characterization of carfentanil and thiofentanil using surface‐enhanced Raman spectroscopy and density functional theory (2024) Journal of Raman Spectroscopy
Preprint out: Advancing Spore Detection: Sers-Based Detection of the Biomarker Dipicolinic Acid Using Gold Nanorods (2024) SSNR
Preprint out: Attention-Driven UNet Enhancement for Accurate Segmentation of Growing Bacteria in Microscopy (2024) Research Square
A new ToxTrac version has been released, the fastest free Software for animal-tracking, downloaded >29 000 times!
We hosted the first Research Workshop on Bacillus in Clinical and Agricultural Environments at Umeå University.
Major happenings 2023:
Paper out: The F-pilus biomechanical adaptability accelerates conjugative dissemination (2023) Nature Communications
Paper out: Hypervirulent R20291 Clostridioides difficile spores show disinfection resilience to sodium hypochlorite (2023) BMC Microbiology
Paper out: Endospore pili - flexible, stiff and sticky nanofibers (2023) Biophysical Journal
Paper out: A lab-on-a-chip utilizing microwaves for bacterial spore disruption and detection (2023) Biosensors and Bioelectronics
Paper out: Bioprinted Schwann and mesenchymal stem cell co-cultures for enhanced spatial control of neurite outgrowth (2023) Gels
Paper out: Polydopamine-coated two-dimensional nanomaterials as high-affinity photothermal signal tag towards dual-signal detection of Salmonella typhimurium by lateral flow immunoassay (2023) Chemical Engineering Journal
Paper out: Design of a low-voltage dielectrophoresis lab-on-the chip to separate tumor and blood cells (2023) Microfluidics and Nanofluidics
Paper out: Three structural solutions for bacterial adhesion pilus stability and superelasticity (2023) Structure
Paper out: Monitoring bacterial spore metabolic activity using heavy water-induced Raman peak evolution (2023) Analyst
Paper out: Physico-chemical characterization of single bacteria and spores using optical tweezers (2023) Research in Microbiology
Paper out: Fabricating a dielectrophoretic microfluidic device using 3D-printed moulds and silver conductive paint (2023) Scientific reports
Paper out: A hybrid CNN-Random Forest algorithm for bacterial spore segmentation and classification in TEM images (2023) Scientific reports
Preprint out: Design and fabrication of a passive micromixer for synthesizing nanoparticles (2023)
Preprint out: A community-curated, global atlas of Bacillus cereus sensu lato genomes for epidemiological surveillance (2023) bioRxiv
We have 20 years experience in developing optical tweezers instrumentation. Our user-friendly optical tweezers instrument, in which we also have integrated a Raman spectrometer, allows for sub-pN force measurements. With this instrument, we can perform micromanipulation, force spectroscopy, dynamic forces spectroscopy, and laser Raman spectroscopy of single cells.
We have developed the fasted tracking program for animals and objects. Easy to install and use. Downloaded it free from and follow our updates at Sourceforge. Instruction movies available on youtube! >29 000 downloads and >370 citations since 2018!
Using optical tweezers, we characterize the biomechanical properties of bacterial adhesion pili to better understand how pathogenic bacteria are able to stick to host surfaces. So far we have assessed typical uropathogenic-related pili such as; type 1, P, S1, S2, F1C and enterotoxic, CFA/I, CS2, CS20. Read our latest PNAS 2021 paper here, the latest Nature 2022 paper here, and the latest Nature Communication 2023 paper here.
We have developed a method to fabricate micro-fluidic flow chambers in polydimethylsiloxane (PDMS) by 3D-printing water-soluble polyvinyl alcohol (PVA) filaments as master scaffolds. The scaffolds are first embedded in the PDMS and later residue-free dissolved in water leaving an inscription of the scaffolds in the hardened PDMS. These flow channels are perfectly transparent, biocompatible and can be used for microscopic applications without further treatment. Our protocols facilitate an easy, fast and adaptable production of micro-fluidic channel designs that are cost-effective, do not require specialized training and can be used for a variety of cell and bacterial assays. To help readers reproduce our micro-fluidic devices, we provide: full preparation protocols, 3D-printing CAD files for channel scaffolds and our custom-made molding device,
The Phantom Brain - A new tool in the toolbox of neurological research
We are developing new methods for creating flow devices in silicone rubber by using 3D printing techniques. Here we demonstrate the capability of our method by recreating the cerebral vascular network as a patient-specific phantom model. This technology can help advance research in the field of e.g. neurological disorders by allowing invasive measurement techniques not previously possible when working on patients. This work is explained in-depth in this paper.
Characterization of spores using Laser Tweezers Raman spectroscopy
Spore-forming bacteria that cause diseases, food spoilage and poisoning, pose a particularly hazardous danger in our society. When in spore form, they can survive harsh conditions. For example, strains of genus Bacillus, which cause anthrax and food poisoning, can stay dormant for several decades in the soil. They can sustain over 100 °C for hours, and resist gamma radiation as well as a plethora of disinfection chemicals. Thus, spores´ possibility to stay dormant and their robustness is a challenge for healthcare, the food, and the dairy industry. In this project we investigate means to kill spores.
We characterize individual bacterial spores using Laser Tweezers Raman Spectroscopy (LTRS). Raman bands specifically represent chemical content that depends on the chemical composition. One can thus identify proteins, lipids, DNA none-invasive. In one of our projects we are interested in understanding how common disinfection chemicals affect bacterial spores body composition. Check the results in our Analytical Chemistry 2021 paper here.
Dseg - Matlab program for segmentation and analysis of filamentous structures
Analysis of numerous filamentous structures in an image is often limited by the ability of algorithms to accurately segment complex structures or structures within a dense population. To overcome these issues we present DSeg; an image analysis program designed to process time-series image data, as well as single images, to segment filamentous structures. DSeg includes automatic segmentation, tools for analysis, and drift correction, and outputs statistical data such as persistence length, growth rate, and growth direction. The program is available here: Sourceforge.
Research Workshop on Bacillus in Clinical and Agricultural Environments
29 February - 1 March 2024
This workshop seeks to unite researchers actively engaged in Bacillus research, as well as those entering the field with relevant expertise in associated domains. The primary objective is to facilitate the exchange of insights and ideas and foster fresh collaborations and synergistic efforts. In particular, the focus of the workshop will be on infection biology and the impact of Bacillus in the “real world” (e.g., in clinical, agricultural, and food industry settings). Finally, the workshop aims to highlight the biosecurity challenges of anthrax.
Sessions
1. Spore Germination
2. Bacillus spore and cellular architecture
3. Bacillus in Food & Industry
4. Environmental Decontamination of Bacillus
