| 1. |
- Dahlberg, Tobias, 1990-
(författare)
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KNOW YOUR ENEMY : Characterizing Pathogenic Biomaterials Using Laser Tweezers
- 2022
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Doktorsavhandling (övrigt vetenskapligt/konstnärligt)abstract
- Diseases caused by pathogenic agents such as bacteria and viruses result in devastating costs on personal and societal levels. However, it is not just the emergence of new diseases that is problematic. Antibiotic resistance among bacteria makes uncomplicated infections difficult and lethal. Resilient disease-causing spores spread in hospitals, the food industry, and water supplies requiring effective detection and disinfection methods. Further, we face complex neurological diseases where no effective treatment or diagnostic methods exist. Thus, we must increase our fundamental understanding of these diseases to develop effective diagnostic, detection, disinfection, and treatment methods.Classically, the methods used for detecting and studying the underlying mechanics of pathogenic agents work on a large scale, measuring the average macroscopic behavior and properties of these pathogens. However, just as with humans, the average behavior is not always representative of individual behavior. Therefore, it is also essential to investigate the characteristics of these pathogens on a single cell or particle level. This thesis develops and applies optical techniques to characterize pathogenic biomaterial on a single cell or particle level. At the heart of all these studies is our Optical Tweezers (OT) instrument. OT are a tool that allows us to reach into the microscopic world and interact with it. Finally, by combining OT with other experimental techniques, we can chemically characterize biomaterials and develop assays that mimic different biological settings. Using these tools, we investigate bacterial adhesion, disinfection, and detection of pathogenic spores and proteins.Hopefully, the insights of these studies can lessen the burden on society caused by diseases by helping others develop effective treatment, diagnostic, detection, and disinfection methods in the future.
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| 2. |
- Dahlberg, Tobias, 1990-, et al.
(författare)
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Unveiling molecular interactions that stabilize bacterial adhesion pili
- 2022
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Ingår i: Biophysical Journal. - : Biophysical Society. - 0006-3495 .- 1542-0086. ; 121:11, s. 2096-2106
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Tidskriftsartikel (refereegranskat)abstract
- Adhesion pili assembled by the chaperone-usher pathway are superelastic helical filaments on the surface of bacteria, optimized for attachment to target cells. Here, we investigate the biophysical function and structural interactions that stabilize P pili from uropathogenic bacteria. Using optical tweezers, we measure P pilus subunit-subunit interaction dynamics and show that pilus compliance is contour-length dependent. Atomic details of subunit-subunit interactions of pili under tension are shown using steered molecular dynamics (sMD) simulations. sMD results also indicate that the N-terminal “staple” region of P pili, which provides interactions with pilins that are four and five subunits away, significantly stabilizes the helical filament structure. These data are consistent with previous structural data, and suggest that more layer-to-layer interactions could compensate for the lack of a staple in type 1 pili. This study informs our understanding of essential structural and dynamic features of adhesion pili, supporting the hypothesis that the function of pili is critically dependent on their structure and biophysical properties.
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| 3. |
- Doran, Matthew, et al.
(författare)
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CS20 bridge the gap between class 1 and class 5 bacterial adhesion pili
- 2022
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Ingår i: Biophysical Journal. - : Cell press. - 0006-3495 .- 1542-0086. ; 121:3, suppl. 1, s. 168a-168a
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Tidskriftsartikel (refereegranskat)abstract
- Enterotoxigenic Escherichia coli (ETEC) are pathogenic bacteria that cause diarrheal disease that disrupts the nutrition and the growth of children under the age of 5 and causes illness in travelers to countries where these bacteria are endemic. ETEC express long thin helical filaments on their surface, ∼1 micron long and 8 nm in diameter, called pili or fimbriae. Often essential virulence factors, these filaments, including ETEC CS20 pili, are composed of approximately 1,000 copies of the major pilin protein and one copy of a tip protein that provides binding specificity. While the structures of ETEC pili from different strains are similar, there are critical differences that alter their biophysical properties.ETEC express Class 1 and/or Class 5 pilins. The Class 1 CS20 pilin, CsbA, is genetically similar to FimA from Type 1 pili that are expressed on many strains of Escherichia coli, including bacteria that infect the urinary tract or the gastrointestinal tract, and also to PapA pilins expressed on bacteria that infect the kidneys. Thus, despite CS20 being expressed on ETEC, its pilin is genetically distant from the Class 5 CFA/I pilin, CfaB, the most commonly expressed ETEC pilin.We show here the three-dimensional structure and surface coulombic charge of CS20 pili, determined at 3.4 Å resolution by electron cryomicroscopy (cryo-EM). Our force spectroscopy data show that CS20 pili have a helix unwinding force that is twice that of CFA/I pili, and half that of Type 1 pili. Molecular dynamics simulations are further used to unveil features along the unwinding pathway at an atomistic scale. We see that CS20 pili bridge the genetic and environmental gap between Class 1 and Class 5 adhesion pili that are expressed on pathogenic bacteria.
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| 4. |
- Doran, Matthew H., et al.
(författare)
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Three structural solutions for bacterial adhesion pilus stability and superelasticity
- 2023
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Ingår i: Structure. - : Elsevier. - 0969-2126 .- 1878-4186.
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Tidskriftsartikel (refereegranskat)abstract
- Bacterial adhesion pili are key virulence factors that mediate host-pathogen interactions in diverse epithelial environments. Deploying a multimodal approach, we probed the structural basis underpinning the biophysical properties of pili originating from enterotoxigenic (ETEC) and uropathogenic bacteria. Using cryo-electron microscopy we solved the structures of three vaccine target pili from ETEC bacteria, CFA/I, CS17, and CS20. Pairing these and previous pilus structures with force spectroscopy and steered molecular dynamics simulations, we find a strong correlation between subunit-subunit interaction energies and the force required for pilus unwinding, irrespective of genetic similarity. Pili integrate three structural solutions for stabilizing their assemblies: layer-to-layer interactions, N-terminal interactions to distant subunits, and extended loop interactions from adjacent subunits. Tuning of these structural solutions alters the biophysical properties of pili and promotes the superelastic behavior that is essential for sustained bacterial attachment.
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| 5. |
- Jonsmoen, Unni Lise, et al.
(författare)
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Endospore pili - flexible, stiff and sticky nanofibers
- 2023
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Ingår i: Biophysical Journal. - : Elsevier. - 0006-3495 .- 1542-0086. ; 122:13, s. 2696-2706
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Tidskriftsartikel (refereegranskat)abstract
- Species belonging to the Bacillus cereus group form endospores (spores) whose surface is decorated with micrometers-long and nanometers-wide endospore appendages (Enas). The Enas have recently been shown to represent a completely novel class of Gram-positive pili. They exhibit remarkable structural properties making them extremely resilient to proteolytic digestion and solubilization. However, little is known about their functional and biophysical properties. In this work, we apply optical tweezers to manipulate and assess how wild type and Ena-depleted mutant spores immobilize on a glass surface. Further, we utilize optical tweezers to extend S-Ena fibers to measure their flexibility and tensile stiffness. Finally, by oscillating single spores, we examine how the exosporium and Enas affect spores’ hydrodynamic properties. Our results show that S-Enas (μm long pili) are not as effective as L-Enas in immobilizing spores to glass surfaces but are involved in forming spore to spore connections, holding the spores together in a gel-like state. The measurements also show that S-Enas are flexible but tensile stiff fibers, which support structural data suggesting that the quaternary structure is composed of subunits arranged in a complex to produce a bendable fiber (helical turns can tilt against each other) with limited axial fiber extensibility. Lastly, the results show that the hydrodynamic drag is 1.5-times higher for wild type spores expressing S- and L-Enas compared to mutant spores expressing only L-Enas or ”bald spores” lacking Ena, and 2-times higher compared to spores of the exosporium deficient strain. This study unveils novel findings on the biophysics of S- and L-Enas, their role in spore aggregation, binding of spores to glass, and their mechanical behavior upon exposure to drag forces.
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| 6. |
- Malyshev, Dmitry, et al.
(författare)
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Reactive oxygen species generated by infrared laser light in optical tweezers inhibits the germination of bacterial spores
- 2022
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Ingår i: Journal of Biophotonics. - : John Wiley & Sons. - 1864-063X .- 1864-0648. ; 15:8
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Tidskriftsartikel (refereegranskat)abstract
- Bacterial spores are highly resistant to heat, radiation and various disinfection chemicals. The impact of these on the biophysical and physicochemical properties of spores can be studied on the single-cell level using optical tweezers. However, the effect of the trapping laser on spores' germination rate is not fully understood. In this work, we assess the impact of 1064 nm laser light on the germination of Bacillus thuringiensis spores. The results show that the germination rate of spores after laser exposure follows a sigmoid dose-response relationship, with only 15% of spores germinating after 20 J of laser light. Under anaerobic growth conditions, the percentage of germinating spores at 20 J increased to 65%. The results thereby indicate that molecular oxygen is a major contributor to the germination-inhibiting effect observed. Thus, our study highlights the risk for optical trapping of spores and ways to mitigate it.
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| 7. |
- Nilsson, Daniel, et al.
(författare)
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Patient-specific brain arteries molded as a flexible phantom model using 3D printed water-soluble resin
- 2022
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Ingår i: Scientific Reports. - : Nature Publishing Group. - 2045-2322. ; 12
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Tidskriftsartikel (refereegranskat)abstract
- Visualizing medical images from patients as physical 3D models (phantom models) have many roles in the medical field, from education to preclinical preparation and clinical research. However, current phantom models are generally generic, expensive, and time-consuming to fabricate. Thus, there is a need for a cost- and time-efficient pipeline from medical imaging to patient-specific phantom models. In this work, we present a method for creating complex 3D sacrificial molds using an off-the-shelf water-soluble resin and a low-cost desktop 3D printer. This enables us to recreate parts of the cerebral arterial tree as a full-scale phantom model (10×6×410×6×4 cm) in transparent silicone rubber (polydimethylsiloxane, PDMS) from computed tomography angiography images (CTA). We analyzed the model with magnetic resonance imaging (MRI) and compared it with the patient data. The results show good agreement and smooth surfaces for the arteries. We also evaluate our method by looking at its capability to reproduce 1 mm channels and sharp corners. We found that round shapes are well reproduced, whereas sharp features show some divergence. Our method can fabricate a patient-specific phantom model with less than 2 h of total labor time and at a low fabrication cost.
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| 8. |
- Pakharukova, Natalia, et al.
(författare)
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Archaic chaperone-usher pili self-secrete into superelastic zigzag springs
- 2022
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Ingår i: Nature. - : Nature Publishing Group. - 0028-0836 .- 1476-4687. ; 609:7926, s. 335-340
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Tidskriftsartikel (refereegranskat)abstract
- Adhesive pili assembled via the chaperone-usher pathway (CUP) are hair-like appendages that mediate host tissue colonization and biofilm formation of Gram-negative bacteria 1-3. Archaic CUP pili, the most diverse and widespread CUP adhesins, are promising vaccine and drug targets due to their prevalence in the most troublesome multidrug-resistant (MDR) pathogens 1,4,5. However, their architecture and assembly-secretion process remain unknown. Here, we present the 3.4 Å resolution cryo-electron microscopy structure of the prototypical archaic Csu pilus that mediates biofilm formation of Acinetobacter baumannii, a notorious MDR nosocomial pathogen. In contrast to the thick helical tubes of the classical type 1 and P pili, archaic pili assemble into a conceptually novel ultrathin zigzag architecture secured by an elegant clinch mechanism. The molecular clinch provides the pilus with high mechanical stability as well as superelasticity, a property observed now for the first time in biomolecules, while enabling a more economical and faster pilus production. Furthermore, we demonstrate that clinch formation at the cell surface drives pilus secretion through the outer membrane. These findings suggest that clinch-formation inhibitors might represent a new strategy to fight MDR bacterial infections.
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| 9. |
- Patkowski, Jonasz B., et al.
(författare)
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The F-pilus biomechanical adaptability accelerates conjugative dissemination of antimicrobial resistance and biofilm formation
- 2023
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Ingår i: Nature Communications. - : Springer Nature. - 2041-1723. ; 14
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Tidskriftsartikel (refereegranskat)abstract
- Conjugation is used by bacteria to propagate antimicrobial resistance (AMR) in the environment. Central to this process are widespread conjugative F-pili that establish the connection between donor and recipient cells, thereby facilitating the spread of IncF plasmids among enteropathogenic bacteria. Here, we show that the F-pilus is highly flexible but robust at the same time, properties that increase its resistance to thermochemical and mechanical stresses. By a combination of biophysical and molecular dynamics methods, we establish that the presence of phosphatidylglycerol molecules in the F-pilus contributes to the structural stability of the polymer. Moreover, this structural stability is important for successful delivery of DNA during conjugation and facilitates rapid formation of biofilms in harsh environmental conditions. Thus, our work highlights the importance of F-pilus structural adaptations for the efficient spread of AMR genes in a bacterial population and for the formation of biofilms that protect against the action of antibiotics.
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| 10. |
- Öberg, Rasmus, et al.
(författare)
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Monitoring bacterial spore metabolic activity using heavy water-induced Raman peak evolution
- 2023
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Ingår i: The Analyst. - : Royal Society of Chemistry. - 0003-2654 .- 1364-5528. ; 148:9, s. 2141-2148
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Tidskriftsartikel (refereegranskat)abstract
- Endospore-forming bacteria are associated with food spoilage, food poisoning, and infection in hospitals. Therefore, methods to monitor spore metabolic activity and verify sterilization are of great interest. However, current methods for tracking metabolic activity are time-consuming and resource intensive. This work investigates isotope labeling and Raman microscopy as a low-cost rapid alternative. Specifically, we monitor the Raman spectrum of enterotoxic \textit{B. cereus} spores undergoing germination and cell division in D2O-infused broth. During germination and cell division, water is metabolized and deuterium from the broth is incorporated into proteins and lipids, resulting in the appearance of a Raman peak related to C-D bonds at 2190 cm-1. We find that a significant C-D peak appears after 2 h of incubation at 37◦C. Further, we found that the peak appearance coincides with the observed first cell division indicating little metabolic activity during germination. Lastly, the germination and cell growth rate of spores were not affected by adding 30 % heavy water to the broth. This shows the potential for real-time monitoring of metabolic activity from a bacterial spore to a dividing cell. In conclusion, our work proposes tracking the evolution of the C-D Raman peak in spores incubated with D2O-infused broth as an effective and time-, and cost-efficient method to monitor the outgrowth of a spore population, simultaneously allowing us to track for how long the bacteria have grown and divided.
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