| 1. |
- Beal, Jacob, et al.
(författare)
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Robust estimation of bacterial cell count from optical density
- 2020
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Ingår i: Communications Biology. - : Springer Science and Business Media LLC. - 2399-3642. ; 3:1
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Tidskriftsartikel (refereegranskat)abstract
- Optical density (OD) is widely used to estimate the density of cells in liquid culture, but cannot be compared between instruments without a standardized calibration protocol and is challenging to relate to actual cell count. We address this with an interlaboratory study comparing three simple, low-cost, and highly accessible OD calibration protocols across 244 laboratories, applied to eight strains of constitutive GFP-expressing E. coli. Based on our results, we recommend calibrating OD to estimated cell count using serial dilution of silica microspheres, which produces highly precise calibration (95.5% of residuals <1.2-fold), is easily assessed for quality control, also assesses instrument effective linear range, and can be combined with fluorescence calibration to obtain units of Molecules of Equivalent Fluorescein (MEFL) per cell, allowing direct comparison and data fusion with flow cytometry measurements: in our study, fluorescence per cell measurements showed only a 1.07-fold mean difference between plate reader and flow cytometry data.
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| 2. |
- Aspelin, Vidar, et al.
(författare)
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Counterintuitive Electrostatics upon Metal Ion Coordination to a Receptor with Two Homotopic Binding Sites
- 2022
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Ingår i: Journal of the American Chemical Society. - : American Chemical Society (ACS). - 1520-5126 .- 0002-7863. ; 144:7, s. 2921-2932
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Tidskriftsartikel (refereegranskat)abstract
- The consecutive binding of two potassium ions to a bis(18-crown-6) analogue of Tröger’s base (BCETB) in water was studied by isothermal titration calorimetry using four different salts, KCl, KI, KSCN, and K2SO4. A counterintuitive result was observed: the enthalpy change associated with the binding of the second ion is more negative than that of the first (ΔH°bind,2 < ΔH°bind,1). This remarkable finding is supported by continuum electrostatic theory as well as by atomic scale replica exchange molecular dynamics simulations, where the latter robustly reproduces experimental trends for all simulated salts, KCl, KI, and KSCN, using multiple force fields. While an enthalpic K+–K+attraction in water poses a small, but fundamentally important, contribution to the overall interaction, the probability of the collapsed conformation (COL) of BCETB, where both crown ether moieties (CEs) of BCETB are bent in toward the cavity, was found to increase successively upon binding of the first and second potassium ions. The promotion of the COL conformation reveals favorable intrinsic interactions between the potassium coordinated CEs, which further contribute to the observation that ΔH°bind,2 < ΔH°bind,1. While the observed trend is independent of the counterion, the origin of the significantly larger magnitude of the difference ΔH°bind,2 - ΔH°bind,1 observed experimentally for KSCN was studied in light of the weaker hydration of the thiocyanate anion, resulting in an enrichment of thiocyanate ions close to BCETB compared to the other studied counterions.
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| 3. |
- Jacobo-Martin, Alejandra, et al.
(författare)
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Resilient moth-eye nanoimprinted antireflective and self-cleaning TiO2 sputter-coated PMMA films
- 2022
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Ingår i: Applied Surface Science. - : Elsevier. - 0169-4332 .- 1873-5584. ; 585
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Tidskriftsartikel (refereegranskat)abstract
- Moth-eye nanostructures are amongst the most remarkable surfaces in nature because of their multi-functionality including antireflection, self-cleaning and bactericidal ability. Moth-eye surfaces consist of subwavelength arrays of tapered nanostructures, which are challenging to reproduce artificially. Nanoimprint lithography is probably one of the most suited technologies for this purpose. However, the poor mechanical resilience and durability of the polymeric nanocones when exposed to the environment, hinders their use in actual applications. To overcome these limitations, this work demonstrates the use of a thin oxide coating over the polymer moth-eye features imprinted on poly methyl methacrylate (PMMA) films. Particularly TiO2 conformal thin film coatings are deposited by unipolar pulsed dc magnetron sputtering over the antireflective nanopatterns acting as encapsulant. The coating, while preserving the antireflective properties, protects the nanostructures against mechanical scratching and improves substantially their thermal stability to over 250 ?. Furthermore, the TiO2 layer provides additional photoinduced self-cleaning functionality and at the same time it protects the matrix from UV photodegradation. The robust and durable antireflective surfaces developed here may find application on solar cells covers, flat panel displays or on optical components.
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| 4. |
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| 5. |
- Lidskog, Anna, et al.
(författare)
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Experimental and Computational Models for Side Chain Discrimination in Peptide–Protein Interactions
- 2021
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Ingår i: Chemistry - A European Journal. - : Wiley. - 0947-6539 .- 1521-3765. ; 27:42, s. 10883-10897
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Tidskriftsartikel (refereegranskat)abstract
- A bis(18-crown-6) Tröger's base receptor and 4-substituted hepta-1,7-diyl bisammonium salt ligands have been used as a model system to study the interactions between non-polar side chains of peptides and an aromatic cavity of a protein. NMR titrations and NOESY/ROESY NMR spectroscopy were used to analyze the discrimination of the ligands by the receptor based on the substituent of the ligand, both quantitatively (free binding energies) and qualitatively (conformations). The analysis showed that an all-anti conformation of the heptane chain was preferred for most of the ligands, both free and when bound to the receptor, and that for all of the receptor-ligand complexes, the substituent was located inside or partly inside of the aromatic cavity of the receptor. We estimated the free binding energy of a methyl- and a phenyl group to an aromatic cavity, via CH-π, and combined aromatic CH-π and π-π interactions to be −1.7 and −3.3 kJ mol−1, respectively. The experimental results were used to assess the accuracy of different computational methods, including molecular mechanics (MM) and density functional theory (DFT) methods, showing that MM was superior.
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| 6. |
- Murari, A., et al.
(författare)
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A control oriented strategy of disruption prediction to avoid the configuration collapse of tokamak reactors
- 2024
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Ingår i: Nature Communications. - 2041-1723 .- 2041-1723. ; 15:1
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Tidskriftsartikel (refereegranskat)abstract
- The objective of thermonuclear fusion consists of producing electricity from the coalescence of light nuclei in high temperature plasmas. The most promising route to fusion envisages the confinement of such plasmas with magnetic fields, whose most studied configuration is the tokamak. Disruptions are catastrophic collapses affecting all tokamak devices and one of the main potential showstoppers on the route to a commercial reactor. In this work we report how, deploying innovative analysis methods on thousands of JET experiments covering the isotopic compositions from hydrogen to full tritium and including the major D-T campaign, the nature of the various forms of collapse is investigated in all phases of the discharges. An original approach to proximity detection has been developed, which allows determining both the probability of and the time interval remaining before an incoming disruption, with adaptive, from scratch, real time compatible techniques. The results indicate that physics based prediction and control tools can be developed, to deploy realistic strategies of disruption avoidance and prevention, meeting the requirements of the next generation of devices.
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| 7. |
- Perez-Escobar, Oscar A., et al.
(författare)
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The origin and speciation of orchids
- 2024
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Ingår i: NEW PHYTOLOGIST. - 0028-646X .- 1469-8137.
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Tidskriftsartikel (refereegranskat)abstract
- Orchids constitute one of the most spectacular radiations of flowering plants. However, their origin, spread across the globe, and hotspots of speciation remain uncertain due to the lack of an up-to-date phylogeographic analysis. We present a new Orchidaceae phylogeny based on combined high-throughput and Sanger sequencing data, covering all five subfamilies, 17/22 tribes, 40/49 subtribes, 285/736 genera, and c. 7% (1921) of the 29 524 accepted species, and use it to infer geographic range evolution, diversity, and speciation patterns by adding curated geographical distributions from the World Checklist of Vascular Plants. The orchids' most recent common ancestor is inferred to have lived in Late Cretaceous Laurasia. The modern range of Apostasioideae, which comprises two genera with 16 species from India to northern Australia, is interpreted as relictual, similar to that of numerous other groups that went extinct at higher latitudes following the global climate cooling during the Oligocene. Despite their ancient origin, modern orchid species diversity mainly originated over the last 5 Ma, with the highest speciation rates in Panama and Costa Rica. These results alter our understanding of the geographic origin of orchids, previously proposed as Australian, and pinpoint Central America as a region of recent, explosive speciation.
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| 8. |
- Petkov, Valeri, et al.
(författare)
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Assessment of the Properties of two High-Temperature Thermosetting Polyimides
- 2022
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Ingår i: ECCM 2022 - Proceedings of the 20th European Conference on Composite Materials. - : EPFL Lausanne, Composite Construction Laboratory. ; , s. 8-15
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Konferensbidrag (övrigt vetenskapligt/konstnärligt)abstract
- A novel thermosetting polyimide, NEXIMID R300, is introduced and compared with the commercial MHT-R in terms of fracture toughness, thermal properties and ageing behaviour. The new R300 formulation has an altered chemical composition compared to the MHT-R, resulting in a reduced cross-linking density, and was presented as a less susceptible to cracking and a more processable alternative during composite manufacturing with resin transfer moulding. The study uses fracture toughness with single edge notched beam setup, DSC, dilatometry, weight loss measurements and optical microscopy for investigation of the neat resin properties of both material. A slight increase in fracture toughness and a decrease in glass transition temperature for the R300 formulation is observed.
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| 9. |
- Petkov, Valeri Ivanov, et al.
(författare)
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The Influence of Ethynyl In-Chain Crosslinkers on the Properties of 6FDA-Based Polyimides
- 2022
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Ingår i: Materials. - : MDPI. - 1996-1944. ; 16:1
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Tidskriftsartikel (refereegranskat)abstract
- Two 4,4′-(hexafluoroisopropylidene)diphthalic anhydride-based thermosetting polyimide formulations with varied amounts of crosslinking sites were compared to understand the influence of crosslinking density on fracture toughness, glass transition temperature and thermal oxidative stability. The thermal and mechanical properties of both materials were investigated through a series of single-edge notched beams, differential scanning calorimetry, dilatometry, weight loss, light optical microscopy and nanoindentation experiments. It was found out that the reduced crosslinking resulted in slightly increased fracture toughness but decreased the Tg of the material. No significant difference could be observed in the thermal oxidative stability with the experimental techniques considered.
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| 10. |
- Rodriguez-Espigares, Ismael, et al.
(författare)
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GPCRmd uncovers the dynamics of the 3D-GPCRome
- 2020
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Ingår i: Nature Methods. - : Springer Nature. - 1548-7091 .- 1548-7105. ; 17:8, s. 777-787
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Tidskriftsartikel (refereegranskat)abstract
- G-protein-coupled receptors (GPCRs) are involved in numerous physiological processes and are the most frequent targets of approved drugs. The explosion in the number of new three-dimensional (3D) molecular structures of GPCRs (3D-GPCRome) over the last decade has greatly advanced the mechanistic understanding and drug design opportunities for this protein family. Molecular dynamics (MD) simulations have become a widely established technique for exploring the conformational landscape of proteins at an atomic level. However, the analysis and visualization of MD simulations require efficient storage resources and specialized software. Here we present GPCRmd (http://gpcrmd.org/), an online platform that incorporates web-based visualization capabilities as well as a comprehensive and user-friendly analysis toolbox that allows scientists from different disciplines to visualize, analyze and share GPCR MD data. GPCRmd originates from a community-driven effort to create an open, interactive and standardized database of GPCR MD simulations.
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