| 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. |
- Li, Mian, et al.
(författare)
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Halogenated Ti3C2 MXenes with Electrochemically Active Terminals for High-Performance Zinc Ion Batteries
- 2021
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Ingår i: ACS Nano. - : AMER CHEMICAL SOC. - 1936-0851 .- 1936-086X. ; 15:1, s. 1077-1085
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Tidskriftsartikel (refereegranskat)abstract
- The class of two-dimensional metal carbides and nitrides known as MXenes offer a distinct manner of property tailoring for a wide range of applications. The ability to tune the surface chemistry for expanding the property space of MXenes is thus an important topic, although experimental exploration of surface terminals remains a challenge. Here, we synthesized Ti3C2 MXene with unitary, binary, and ternary halogen terminals, e.g., -Cl, -Br, -I, -BrI, and -ClBrI, to investigate the effect of surface chemistry on the properties of MXenes. The electrochemical activity of Br and I elements results in the extraordinary electrochemical performance of the MXenes as cathodes for aqueous zinc ion batteries. The -Br- and -I-containing MXenes, e.g., Ti3C2Br2 and Ti3C2I2, exhibit distinct discharge platforms with considerable capacities of 97.6 and 135 mA.g(-1). Ti3C2 (BrI) and Ti3C2 (ClBrI) exhibit dual discharge platforms with capacities of 117.2 and 106.7 mAh.g(-1). In contrast, the previously discovered MXenes Ti3C2Cl2 and Ti3C2 (OF) exhibit no discharge platforms and only similar to 50% of capacities and energy densities of Ti3C2Br2. These results emphasize the effectiveness of the Lewis-acidic-melt etching route for tuning the surface chemistry of MXenes and also show promise for expanding the MXene family toward various applications.
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| 3. |
- Ding, Haoming, et al.
(författare)
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Chemical scissor-mediated structural editing of layered transition metal carbides
- 2023
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Ingår i: Science. - : AMER ASSOC ADVANCEMENT SCIENCE. - 0036-8075 .- 1095-9203. ; 379:6637, s. 1130-1135
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Tidskriftsartikel (refereegranskat)abstract
- Intercalated layered materials offer distinctive properties and serve as precursors for important two-dimensional (2D) materials. However, intercalation of non-van der Waals structures, which can expand the family of 2D materials, is difficult. We report a structural editing protocol for layered carbides (MAX phases) and their 2D derivatives (MXenes). Gap-opening and species-intercalating stages were respectively mediated by chemical scissors and intercalants, which created a large family of MAX phases with unconventional elements and structures, as well as MXenes with versatile terminals. The removal of terminals in MXenes with metal scissors and then the stitching of 2D carbide nanosheets with atom intercalation leads to the reconstruction of MAX phases and a family of metal-intercalated 2D carbides, both of which may drive advances in fields ranging from energy to printed electronics.
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| 4. |
- Ding, Haoming, et al.
(författare)
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Synthesis of MAX phases Nb2CuC and Ti2(Al0.1Cu0.9)N by A-site replacement reaction in molten salts
- 2019
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Ingår i: Materials Research Letters. - : Taylor & Francis. - 2166-3831. ; 7:12, s. 510-516
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Tidskriftsartikel (refereegranskat)abstract
- New MAX phases Ti2(AlxCu1−x)N and Nb2CuC were synthesized by A-site replacement by reacting Ti2AlN and Nb2AlC, respectively, with CuCl2 or CuI molten salt. X-ray diffraction, scanning electron microscopy, and atomically resolved scanning transmission electron microscopy showed complete A-site replacement in Nb2AlC, which lead to the formation of Nb2CuC. However, the replacement of Al in Ti2AlN phase was only close to complete at Ti2(Al0.1Cu0.9)N. Density-functional theory calculations corroborated the structural stability of Nb2CuC and Ti2CuN phases. Moreover, the calculated cleavage energy in these Cu-containing MAX phases are weaker than in their Al-containing counterparts.The preparation of MAX phases Nb2CuC and Ti2(Al0.1Cu0.9)N were realized by A-site replacement in Ti2AlN and Nb2AlN, respectively.
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| 5. |
- Li, Mian, et al.
(författare)
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Element Replacement Approach by Reaction with Lewis Acidic Molten Salts to Synthesize Nanolaminated MAX Phases and MXenes
- 2019
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Ingår i: Journal of the American Chemical Society. - : AMER CHEMICAL SOC. - 0002-7863 .- 1520-5126. ; 141:11, s. 4730-4737
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Tidskriftsartikel (refereegranskat)abstract
- Nanolaminated materials are important because of their exceptional properties and wide range of applications. Here, we demonstrate a general approach to synthesizing a series of Zn-based MAX phases and Cl-terminated MXenes originating from the replacement reaction between the MAX phase and the late transition-metal halides. The approach is a top-down route that enables the late transitional element atom (Zn in the present case) to occupy the A site in the pre-existing MAX phase structure. Using this replacement reaction between the Zn element from molten ZnCl2 and the Al element in MAX phase precursors (Ti3AlC2, Ti2AlC, Ti2AlN, and V2AlC), novel MAX phases Ti3ZnC2, Ti2ZnC, Ti2ZnN, and V2ZnC were synthesized. When employing excess ZnCl2, Cl-terminated MXenes (such as Ti3C2Cl2 and Ti2CCl2) were derived by a subsequent exfoliation of Ti3ZnC2 and Ti2ZnC due to the strong Lewis acidity of molten ZnCl2. These results indicate that A-site element replacement in traditional MAX phases by late transition-metal halides opens the door to explore MAX phases that are not thermodynamically stable at high temperature and would be difficult to synthesize through the commonly employed powder metallurgy approach. In addition, this is the first time that exclusively Cl-terminated MXenes were obtained, and the etching effect of Lewis acid in molten salts provides a green and viable route to preparing MXenes through an HF-free chemical approach.
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| 6. |
- Li, Shiyu, et al.
(författare)
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Docking and Activity of DNA Polymerase on Solid-State Nanopores
- 2022
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Ingår i: ACS Sensors. - : American Chemical Society (ACS). - 2379-3694. ; 7:5, s. 1476-1483
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Tidskriftsartikel (refereegranskat)abstract
- Integration of motor enzymes with biological nanopores has enabled commercial DNA sequencing technology; yet studies of the similar principle applying to solid-state nanopores are limited. Here, we demonstrate the real-life monitoring of phi29 DNA polymerase (DNAP) docking onto truncated-pyramidal nanopore (TPP) arrays through both electrical and optical readout. To achieve effective docking, atomic layer deposition of hafnium oxide is employed to reduce the narrowest pore opening size of original silicon (Si) TPPs to sub-10 nm. On a single TPP with pore opening size comparable to DNAP, ionic current measurements show that a polymerase-DNA complex can temporally dock onto the TPP with a certain docking orientation, while the majority become translocation events. On 5-by-5 TPP arrays, a label-free optical detection method using Ca2+ sensitive dye, are employed to detect the docking dynamics of DNAP. The results show that this label-free detection strategy is capable of accessing the docking events of DNAP on TPP arrays. Finally, we examine the activity of docked DNAP by performing on-site rolling circle amplification to synthesize single-stranded DNA (ssDNA), which serves as a proof-of-concept demonstration of utilizing this docking scheme for emerging nanopore sensing applications.
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| 7. |
- Li, Shiyu, et al.
(författare)
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Dynamics of DNA Clogging in Hafnium Oxide Nanopores
- 2020
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Ingår i: Journal of Physical Chemistry B. - : American Chemical Society (ACS). - 1520-6106 .- 1520-5207. ; 124:51, s. 11573-11583
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Tidskriftsartikel (refereegranskat)abstract
- Interfacing solid-state nanopores with biological systems has been exploited as a versatile analytical platform for analysis of individual biomolecules. Although clogging of solid-state nanopores due to nonspecific interactions between analytes and pore walls poses a persistent challenge in attaining the anticipated sensing efficacy, insufficient studies focus on elucidating the clogging dynamics. Herein, we investigate the DNA clogging behavior by passing double-stranded (ds) DNA molecules of different lengths through hafnium oxide(HfO2)-coated silicon (Si) nanopore arrays, at different bias voltages and electrolyte pH values. Employing stable and photoluminescent-free HfO2/Si nanopore arrays permits a parallelized visualization of DNA clogging with confocal fluorescence microscopy. We find that the probability of pore clogging increases with both DNA length and bias voltage. Two types of clogging are discerned: persistent and temporary. In the time-resolved analysis, temporary clogging events exhibit a shorter lifetime at higher bias voltage. Furthermore, we show that the surface charge density has a prominent effect on the clogging probability because of electrostatic attraction between the dsDNA and the HfO2 pore walls. An analytical model based on examining the energy landscape along the DNA translocation trajectory is developed to qualitatively evaluate the DNA–pore interaction. Both experimental and theoretical results indicate that the occurrence of clogging is strongly dependent on the configuration of translocating DNA molecules and the electrostatic interaction between DNA and charged pore surface. These findings provide a detailed account of the DNA clogging phenomenon and are of practical interest for DNA sensing based on solid-state nanopores.
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| 8. |
- Li, Shiyu, 1991-
(författare)
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Engineering Surfaces of Solid-State Nanopores for Biomolecule Sensing
- 2021
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Konstnärligt arbete (övrigt vetenskapligt/konstnärligt)abstract
- Nanopores have emerged as a special class of single-molecule analytical tool that offers immense potential for sensing and characterizing biomolecules such as nucleic acids and proteins. As an alternative to biological nanopores, solid-state nanopores present remarkable versatility due to their wide-range tunability in pore geometry and dimension as well as their excellent mechanical robustness and stability. However, being intrinsically incompatible with biomolecules, surfaces of inorganic solids need be modified to provide desired functionalities for real-life sensing purposes. In this thesis, we presented an exploration of various surface engineering strategies and an examination of several surface associated phenomena pertaining specifically to solid-state nanopores. Based on the parallel sensing concept using arrayed pores, optical readout is mainly employed throughout the whole study.For the surface engineering aspect, a list of approaches was explored. A versatile surface patterning strategy for immobilization of biomolecules was developed based on selective poly(vinylphosphonic acid) passivation and electron beam induced deposition technique. This scheme was then implemented on nanopore arrays for nanoparticle localization. In addition, vesicle rupture-based lipid bilayer coating was adapted to truncated-pyramidal nanopores, which was shown to be effective for the minimizing DNA-pore interaction. Further, HfO2 coating by means of atomic layer deposition was employed to prevent the erosion of Si-based pores and to shrink the pore diameter, which enabled reliable investigations of DNA clogging and DNA polymerase docking.For the surface associated phenomena, several findings were made. The lipid bilayer formation on truncated pyramidal nanopores via instantaneous rupture of individual vesicles was quantified based on combined ionic current monitoring and optical observation. The probability of pore clogging appeared to linearly increase with the length of DNA strands and applied bias voltage, which could be attributed a higher probability of knotting and/or folding of longer DNA strands and more frequent translocation events at higher voltage. A free-energy based analytical model was proposed to evaluate the DNA-pore interaction and to interpret observed clogging behavior. Finally, docking of DNA polymerase on nanopore arrays was demonstrated using label-free optical method based on Ca2+ indicator dyes, which may open the avenue to sequencing-by-synthesis enabled by the docked polymerase.
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| 9. |
- Li, Shiyu, et al.
(författare)
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Label-Free Optical Detection of DNA Polymerase Docking on Solid-State Nanopore Arrays
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Annan publikation (övrigt vetenskapligt/konstnärligt)abstract
- Integration of motor enzymes with biological nanopores has enabled commercial DNA sequencing, yet studies of the similar principle applying to solid-state nanopores are limited. Here, we demonstrate the label-free optical detection of phi29 DNA polymerase (DNAP) docking onto truncated-pyramidal nanopores (TPP). Atomic layer deposition of hafnium oxide is employed to shrink the pore opening size of original silicon (Si) TPP to sub-10 nm. Ionic current measurements of single TPP of an opening size comparable to DNAP show that polymerase-DNA complexes can temporally dock onto the TPP with a certain docking orientation, while the majority are translocation events. A label-free optical detection method using Ca2+ sensitive dye is employed to detect the docking of DNAP on 5-by-5 nanopore arrays. The results of the proof-of-concept experiment show that this label-free detection strategy is capable of accessing the docking events of DNAP on solid-state nanopore arrays.
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| 10. |
- Li, Shiyu, et al.
(författare)
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Nanoarrays on Passivated Aluminum Surface for Site-Specific Immobilization of Biomolecules
- 2018
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Ingår i: ACS Applied Bio Materials. - : American Chemical Society (ACS). - 2576-6422. ; 1:1, s. 125-135
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Tidskriftsartikel (refereegranskat)abstract
- The rapid development of biosensing platforms for highly sensitive and specific detection raises the desire of precise localization of biomolecules onto various material surfaces. Aluminum has been strategically employed in the biosensor system due to its compatibility with CMOS technology and its optical and electrical properties such as prominent propagation of surface plasmons. Herein, we present an adaptable method for preparation of carbon nanoarrays on aluminum surface passivated with poly(vinylphosphonic acid) (PVPA). The carbon nanoarrays were defined by means of electron beam induced deposition (EBID) and they were employed to realize site-specific immobilization of target biomolecules. To demonstrate the concept, selective streptavidin/neutravidin immobilization on the carbon nanoarrays was achieved through protein physisorption with a significantly high contrast of the carbon domains over the surrounding PVPA-modified aluminum surface. By adjusting the fabrication parameters, local protein densities could be varied on similarly sized nanodomains in a parallel process. Moreover, localization of single 40 nm biotinylated beads was achieved by loading them on the neutravidin-decorated nanoarrays. As a further demonstration, DNA polymerase with a streptavidin tag was bound to the biotin-beads that were immobilized on the nanoarrays and in situ rolling circle amplification (RCA) was subsequently performed. The observation of organized DNA arrays synthesized by RCA verified the nanoscale localization of the enzyme with retained biological activity. Hence, the presented approach could provide a flexible and universal avenue to precise localizing various biomolecules on aluminum surface for potential biosensor and bioelectronic applications.
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