Source code of PSI-VBS module based on CAMx v6.3

This is a modified Volatility Basis Set (VBS) module based on the regional air quality model CAMx v6.3 (Ramboll Environ 2016, http://www.camx.com/) More information can be found on Jiang, J., Aksoyoglu, S., et al.: Sources of organic aerosols in Europe: A modelling study using CAMx with modified volatility basis set scheme, Atmos. Chem. Phys.,2019 Features - Extend and split the standard VBS scheme to enable source apportionment for POA and SOA.   - Adjust the yields for the new diesel vehicles and oxidation rate of SOA from biomass burning.    </p

Dataset for "Sources of organic aerosols in Europe: A modelling study using CAMx with modified volatility basis set scheme"

Model data for figures in the publication "Sources of organic aerosols in Europe: A modelling study using CAMx with modified volatility basis set scheme" Jiang, J., Aksoyoglu, S., El-Haddad, I., Ciarelli, G., Denier van der Gon, H. A. C., Canonaco, F., Gilardoni, S., Paglione, M., Minguillón, M. C., Favez, O., Zhang, Y., Marchand, N., Hao, L., Virtanen, A., Florou, K., O’Dowd, C., Ovadnevaite, J., Baltensperger, U., and Prévôt, A. S. H.: Sources of organic aerosols in Europe: A modelling study using CAMx with modified volatility basis set scheme, Atmos. Chem. Phys., 2019.  All the data are stored in .mat file, and the variable names are self-explanatory.      </p

Graphene Fluorescence Resonance Energy Transfer Aptasensor for the Thrombin Detection

Combining nanomaterials and biomolecule recognition units is promising in developing novel clinic diagnostic and protein analysis techniques. In this work, a highly sensitive and specific fluorescence resonance energy transfer (FRET) aptasensor for thrombin detection is developed based on the dye labeled aptamer assembled graphene. Due to the noncovalent assembly between aptamer and graphene, fluorescence quenching of the dye takes place because of FRET. The addition of thrombin leads to the fluorescence recovery due to the formation of quadruplex−thrombin complexes which have weak affinity to graphene and keep the dyes away from graphene surface. Because of the high fluorescence quenching efficiency, unique structure, and electronic properties of graphene, the graphene aptasensor exhibits extraordinarily high sensitivity and excellent specificity in both buffer and blood serum. A detection limit as low as 31.3 pM is obtained based on the graphene FRET aptasensor, which is two orders magnitude lower than those of fluorescent sensors based on carbon nanotubes. The excellent performance of FRET aptasensor based on graphene will also be ascribed to the unique structure and electronic properties of graphene

Fluorogen-Activating-Protein-Loaded Tantalum Oxide Nanoshells for in Vivo On-Demand Fluorescence/Photoacoustic Imaging

Optical imaging of targeted compartments within living animals has been widely adopted in many research areas. In particular, various fluorescence-based probes and emerged photoacoustic molecules that enable sensitive and specific imaging through tissue have greatly advanced clinically relevant studies. However, delivery and signal penetration have placed requirements on the performance of conventional optical probes. Here, we use hallow tantalum oxide (TaOx) nanoparticles to enclose fluorogen-activating protein (FAP) for the in vivo fluorescence and photoacoustic imaging of cancer cells. We found that the TaOx shell can provide a natural cover for the enclosed fluorogen/FAP complexes, protecting them from photobleaching and common biodegradation. Moreover, we have developed a near-infrared excitable tetrafluorinated photoacoustic fluorogen for the specific and persistent photoacoustic imaging of tumors. We believe that this enclosing and delivery strategy of optical biomolecules will be an attractive alternative for bioimaging

Ligand-Induced Divergent Evolution of ZnSe Magic Sized Clusters

Alkylamine ligand-induced evolutions of ZnSe magic sized clusters (MSCs) toward divergent products have been discovered for the first time. With correspondingly assigned molecular structures, the same ZnSe MSC was found to undergo either single-atom growth or dissolution through the elaborate tailoring of alkylamine ligands

Rolling Circle Amplification Combined with Gold Nanoparticle Aggregates for Highly Sensitive Identification of Single-Nucleotide Polymorphisms

A highly sensitive and specific colorimetry-based rolling circle amplification (RCA) assay method for single-nucleotide polymorphism genotyping has been developed. A circular template is generated by ligation upon the recognition of a point mutation on DNA targets. An RCA amplification is then initiated using the circular template in the presence of Phi29 polymerase. The RCA product can be digested by a restricting endonuclease, and the cleaved DNA fragments can mediate the aggregation of gold nanoparticle-tagged DNA probes. This causes a colorimetric change of the solution as the indicator of the mutation occurrence, which can be detected using UV−vis spectroscopy or viewed by naked eyes. On the basis of the high amplification efficiency of Phi29 polymerase, a mutated target of ∼70 fM can be detected in this assay. In addition, the protection of the circle template using phosphorothioated nucleotides allows the digestion reaction to be performed simultaneously in RCA. Moreover, DNA ligase offers high fidelity in distinguishing the mismatched bases at the ligation site, resulting in positive detection of mutant targets even when the ratio of the wild-type to the mutant is 10 000:1. The developed RCA-based colorimetric detection scheme was demonstrated for SNP typing of β-thalassemia gene at position −28 in genomic DNA

Inhibition of dsDNA-Templated Copper Nanoparticles by Pyrophosphate as a Label-Free Fluorescent Strategy for Alkaline Phosphatase Assay

On the basis of the inhibition of double strand DNA (dsDNA)-templated fluorescent copper nanoparticles (CuNPs) by pyrophosphate (PPi), a novel label-free turn-on fluorescent strategy to detect alkaline phosphatase (ALP) under physiological conditions has been developed. This method relies on the strong interaction between PPi and Cu²⁺, which would hamper the effective formation of fluorescent CuNPs, leading to low fluorescence intensity. The ALP-catalyzed PPi hydrolysis would disable the complexation between Cu²⁺ and PPi, facilitating the formation of fluorescent CuNPs through the reduction by ascorbate in the presence of dsDNA templates. Thus, the fluorescence intensity was recovered, and the fluorescence enhancement was related to the concentration of ALP. This method is cost-effective and convenient without any labels or complicated operations. The present strategy exhibits a high sensitivity and the turn-on mode provides a high selectivity for the ALP assay. Additionally, the inhibition effect of phosphate on the ALP activity was also studied. The proposed method using a PPi substrate may hold a potential application in diagnosis of ALP-related diseases or evaluation of ALP functions in biological systems

Spatiotemporally Resolved Protein Detection in Live Cells Using Nanopore Biosensors

Spatiotemporal detection of proteins in living cells is a persistent challenge but is the key to understanding their cellular biology and developing theranostic technologies. We develop a dual-nanopore biosensor using affinity-tunable peptide probes, which enables label-free and spatiotemporal monitoring of protein abundance and its concentration change in single live cells. We demonstrate that by screening for peptide probes with tunable affinities, the nanopore modified with a medium-affinity peptide allowed reversible and sensitive detection of the protein kinase A (PKA) catalytic subunit with a detection limit of 0.04 nM. The sensor is shown to have the ability to effectively eliminate interferences from cell membrane resistance and coexisting species in live cell detection. Moreover, our sensor is successfully implemented in monitoring of dynamic PKA activity changes (PKA catalytic subunit dynamic concentration changes) under different stimulations in single live cells. Our design may provide a paradigm for developing nanopore biosensors for spatiotemporally resolved protein analysis in live cells

Real-Time Monitoring of Exosomes Secretion from Single Cell Using Dual-Nanopore Biosensors

Exosomes secreted from cells carry rich information from their parent cells, representing a promising biomarker for investigation of diseases. We develop a dual-nanopore biosensor using DNA aptamers to specifically recognize CD63 protein on the exosome’s surface, which enables label-free exosome detection based on ionic current change. The sensor allows for sensitive detection of exosomes with a detection limit of 3.4 × 106 particles/mL. The dual-nanopore biosensor was able to form an intrapipette electric circuit for ionic current measurement due to its unique structure, which is crucial to achieve detection of exosome secretion from a single cell. We utilized a microwell array chip to entrap a single cell into a confined microwell with small volume, enabling the accumulation of exosomes with high concentration. The dual-nanopore biosensor was positioned into the microwell with a single cell, and monitoring of exosome secretion from a single cell in different cell lines and under different stimulations has been achieved. Our design may provide a useful platform for developing nanopore biosensors for detecting cell secretions from a single living cell