Weakly Confined Organic-Inorganic Halide Perovskite Quantum Dots as High-Purity Room-Temperature Single Photon Sources.

Colloidal perovskite quantum dots (PQDs) have emerged as highly promising single photon emitters for quantum information applications. Presently, most strategies have focused on leveraging quantum confinement to increase the nonradiative Auger recombination (AR) rate to enhance single-photon (SP) purity in all-inorganic CsPbBr3 QDs. However, this also increases the fluorescence intermittency. Achieving high SP purity and blinking mitigation simultaneously remains a significant challenge. Here, we transcend this limitation with room-temperature synthesized weakly confined hybrid organic-inorganic perovskite (HOIP) QDs. Superior single photon purity with a low g(2)(0) < 0.07 ± 0.03 and a nearly blinking-free behavior (ON-state fraction >95%) in 11 nm FAPbBr3 QDs are achieved at room temperature, attributed to their long exciton lifetimes (τX) and short biexciton lifetimes (τXX). The significance of the organic A-cation is further validated using the mixed-cation FAxCs1-xPbBr3. Theoretical calculations utilizing a combination of the Bethe-Salpeter (BSE) and k·p approaches point toward the modulation of the dielectric constants by the organic cations. Importantly, our findings provide valuable insights into an additional lever for engineering facile-synthesized room-temperature PQD single photon sources.

Digital PCR for the characterization of reference materials.

Well-characterized reference materials support harmonization and accuracy when conducting nucleic acid-based tests (such as qPCR); digital PCR (dPCR) can measure the absolute concentration of a specific nucleic acid sequence in a background of non-target sequences, making it ideal for the characterization of nucleic acid-based reference materials. National Metrology Institutes are increasingly using dPCR to characterize and certify their reference materials, as it offers several advantages over indirect methods, such as UV-spectroscopy. While dPCR is gaining widespread adoption, it requires optimization and has certain limitations and considerations that users should be aware of when characterizing reference materials. This review highlights the technical considerations of dPCR, as well as its role when developing and characterizing nucleic acid-based reference materials.

Quantitation and integrity evaluation of RNA genome in lentiviral vectors by direct reverse transcription-droplet digital PCR (direct RT-ddPCR).

Lentiviral vectors (LV) have proven to be powerful tools for stable gene delivery in both dividing and non-dividing cells. Approval of these LVs for use in clinical applications has been achieved by improvements in LV design. Critically important characteristics concerning quality control are LV titer quantification and the detection of impurities. However, increasing evidence concerning high variability in titration assays indicates poor harmonization of the methods undertaken to date. In this study, we developed a direct reverse transcription droplet digital PCR (Direct RT-ddPCR) approach without RNA extraction and purification for estimation of LV titer and RNA genome integrity. The RNA genome integrity was assessed by RT-ddPCR assays targeted to four distant regions of the LV genome. Results of the analyses showed that direct RT-ddPCR without RNA extraction and purification performs similarly to RT-ddPCR on purified RNA from 3 different LV samples, in terms of robustness and assay variance. Interestingly, these RNA titer results were comparable to physical titers by p24 antigen ELISA (enzyme-linked immunosorbent assay). Moreover, we confirmed the partial degradation or the incomplete RNA genomes in the prepared 3 LV samples. These results may partially explain the discrepancy of the LV particle titers to functional titers. This work not only demonstrates the feasibility of direct RT-ddPCR in determining LV titers, but also provides a method that can be easily adapted for RNA integrity assessment.

Insights to Carrier-Phonon Interactions in Lead Halide Perovskites via Multi-Pulse Manipulation.

A fundamental understanding of the hot-carrier dynamics in halide perovskites is crucial for unlocking their prospects for next generation photovoltaics. Presently, a coherent picture of the hot carrier cooling process remains patchy due to temporally overlapping contributions from many-body interactions, multi-bands, band gap renormalization, Burstein-Moss shift etc. Pump-push-probe (PPP) spectroscopy recently emerges as a powerful tool complementing the ubiquitous pump-probe (PP) spectroscopy in the study of hot-carrier dynamics. However, limited information from PPP on the initial excitation density and carrier temperature curtails its full potential. Herein, this work bridges this gap in PPP with a unified model that retrieves these essential hot carrier metrics like initial carrier density and carrier temperature under the push conditions, thus permitting direct comparison with traditional PP spectroscopy. These results are well-fitted by the phonon bottleneck model, from which the longitudinal optical phonon scattering time τLO , for MAPbBr3 and MAPbI3 halide perovskite thin film samples are determined to be 240 ± 10 and 370 ± 10 fs, respectively.

Plasma contains ultrashort single-stranded DNA in addition to nucleosomal cell-free DNA.

Plasma cell-free DNA is being widely explored as a biomarker for clinical screening. Currently, methods are optimized for the extraction and detection of double-stranded mononucleosomal cell-free DNA of ∼160bp in length. We introduce uscfDNA-seq, a single-stranded cell-free DNA next-generation sequencing pipeline, which bypasses previous limitations to reveal a population of ultrashort single-stranded cell-free DNA in human plasma. This species has a modal size of 50nt and is distinctly separate from mononucleosomal cell-free DNA. Treatment with single-stranded and double-stranded specific nucleases suggests that ultrashort cell-free DNA is primarily single-stranded. It is distributed evenly across chromosomes and has a similar distribution profile over functional elements as the genome, albeit with an enrichment over promoters, exons, and introns, which may be suggestive of a terminal state of genome degradation. The examination of this cfDNA species could reveal new features of cell death pathways or it can be used for cell-free DNA biomarker discovery.

Validation of ctDNA Quality Control Materials Through a Precompetitive Collaboration of the Foundation for the National Institutes of Health.

We report the results from a Foundation for the National Institutes of Health Biomarkers Consortium project to address the absence of well-validated quality control materials (QCMs) for circulating tumor DNA (ctDNA) testing. This absence is considered a cause of variance and inconsistencies in translating ctDNA results into clinical actions. METHODS: In this phase I study, QCMs with 14 clinically relevant mutations representing single nucleotide variants, insertions or deletions (indels), translocations, and copy number variants were sourced from three commercial manufacturers with variant allele frequencies (VAFs) of 5%, 2.5%, 1%, 0.1%, and 0%. Four laboratories tested samples in quadruplicate using two allele-specific droplet digital polymerase chain reaction and three (amplicon and hybrid capture) next-generation sequencing (NGS) panels. RESULTS: The two droplet digital polymerase chain reaction assays reported VAF values very close to the manufacturers' claimed concentrations for all QCMs. NGS assays reported most single nucleotide variants and indels, but not translocations, close to the expected VAF values. Notably, two NGS assays reported lower VAF than expected for all translocations in all QCM mixtures, possibly related to technical challenges detecting these variants. The ability to call ERBB2 copy number amplifications varied across assays. All three QCMs provided valuable insight into assay precision. Each assay across all variant types demonstrated dropouts at 0.1%, suggesting that the QCM can serve for testing of an assay's limit of detection with confidence claims for specific variants. CONCLUSION: These results support the utility of the QCM in testing ctDNA assay analytical performance. However, unique designs and manufacturing methods for the QCM, and variations in a laboratory's testing configuration, may require testing of multiple QCMs to find the best reagents for accurate result interpretation.

Reference standards for accurate validation and optimization of assays that determine integrated lentiviral vector copy number in transduced cells.

Lentiviral vectors (LV) have emerged as a robust technology for therapeutic gene delivery into human cells as advanced medicinal products. As these products are increasingly commercialized, there are concomitant demands for their characterization to ensure safety, efficacy and consistency. Standards are essential for accurately measuring parameters for such product characterization. A critical parameter is the vector copy number (VCN) which measures the genetic dose of a transgene present in gene-modified cells. Here we describe a set of clonal Jurkat cell lines with defined copy numbers of a reference lentiviral vector integrated into their genomes. Genomic DNA was characterized for copy number, genomic integrity and integration coordinates and showed uniform performance across independent quantitative PCR assays. Stability studies during continuous long-term culture demonstrated sustained renewability of the reference standard source material. DNA from the Jurkat VCN standards would be useful for control of quantitative PCR assays for VCN determination in LV gene-modified cellular products and clinical samples.

Structural Variation and Switchable Nonlinear Optical Behavior of Metal-Organic Frameworks.

Two europium metal-organic frameworks (MOFs) based on the same ligand, named as ZJU-23-Eu and ZJU-24-Eu, are selectively synthesized by fine-tuning solvent contents to tailor the coordination modes. Eu atoms are eight-coordinated and nine-coordinated in ZJU-23-Eu and ZJU-24-Eu respectively, and their frameworks vary in both spatial connectivity and symmetry. The ligand not only has multiphoton response but also suitable triplet energy level (19 998 cm-1 ) to sensitize Eu3+ . Thus ZJU-23-Eu exhibits characteristic emission of Eu3+ peaking at 614 nm via the energy transfer from the two-/three-photon excited ligand to Eu3+ , with its bidimensional layered structure benefiting this process. In contrast, the changed spatial connectivity in tridimensional ZJU-24-Eu narrows the distances between adjacent Eu3+ ions and reduces the density, resulting in poor two-photon excited fluorescence. Besides, noncentrosymmetric ZJU-24-Eu shows second harmonic generation (SHG) response with an intensity of ≈6.2 times relative to KH2 PO4 (KDP) microcrystalline powder while centrosymmetric ZJU-23-Eu cannot. These results have established two nonlinear optical (NLO) models based on MOFs to synchronously analyze the effects of two structural variables on different NLO behaviors, and provide ingenious ways to design MOF-based NLO devices with function on demand.

Halide perovskite nanocrystals for multiphoton applications.

Halide perovskite nanocrystals (NCs) are a unique class of NCs with novel properties distinct from those of traditional semiconductor NCs. These exceptional properties of defect tolerance, large absorption coefficients, high brightness, and narrow emission linewidths stem from their atypical band structure. Their facile synthesis and broad colour tunability have attracted widespread interest for application in light emitting devices and lasers. One fledging niche area is the field of multiphoton excited emission where their giant nonlinear optical action cross-sections are highly favorable for imaging applications. This Frontier article examines the state-of-the-art in perovskite NCs for multiphoton applications from the materials science and physics perspectives that include their synthesis and nonlinear optical characterization. Opportunities and challenges of these exceptional NCs as potential fluorescent labels for multiphoton deep tissue microscopy are also highlighted.

Controllable broadband multicolour single-mode polarized laser in a dye-assembled homoepitaxial MOF microcrystal.

Multicolour single-mode polarized microlasers with visible to near-infrared output have very important applications in photonic integration and multimodal biochemical sensing/imaging but are very difficult to realize. Here, we demonstrate a single crystal with multiple segments based on the host-guest metal-organic framework ZJU-68 hierarchically hybridized with different dye molecules generating controllable single-mode green, red, and near-infrared lasing, with the lasing mode mechanism revealed by computational simulation. The segmented and oriented assembly of different dye molecules within the ZJU-68 microcrystal causes it to act as a shortened resonator, enabling us to achieve dynamically controllable multicolour single-mode lasing with a low three-colour-lasing threshold of ~1.72 mJ/cm2 (approximately seven times lower than that of state-of-the-art designed heterostructure alloys, as reported by Fan F et al. (Nat. Nanotechnol. 10:796-803, 2015) considering the single pulse energy density) and degree of polarization >99.9%. Furthermore, the resulting three-colour single-mode lasing possesses the largest wavelength coverage of ~186 nm (ranging from ~534 to ~720 nm) ever reported. These findings may open a new route to the exploitation of multicolour single-mode micro/nanolasers constructed by MOF engineering for photonic and biochemical applications.

Stringent response interacts with the ToxR regulon to regulate Vibrio cholerae virulence factor expression.

The epidemic diarrheal disease cholera is caused by the Gram-negative bacterium Vibrio cholerae. V. cholerae virulence factors include the toxin-coregulated pilus (TCP) and cholera toxin, which are major factors responsible for host colonization and production of diarrhea. Expression of cholera toxin and TCP genes is controlled by the ToxR regulon. The ToxR regulon includes the transcriptional activators ToxR, TcpP, and ToxT. ToxT directly initiates transcription of the cholera toxin and TCP genes. TcpP and ToxR are necessary for expression of toxT. TcpP and ToxR activity requires TcpH and ToxS, respectively. Additionally, ToxR is able to directly initiate transcription of the cholera toxin genes independent of TcpP and ToxT. TCP is required early in infection to colonize the small intestine, then cholera toxin is expressed later in infection to produce diarrhea. We tested whether stringent response, the low nutrient stress response, was involved in regulation of virulence genes. Using an infant mouse model, we found that V. cholerae strains with deletions of the stringent response genes were unable to colonize the small intestine. We further tested these stringent response-null mutants and found that stringent response was necessary for TCP expression, although effects on cholera toxin expression were not significant. We then tested whether stringent response regulation of TCP occurred through the ToxR regulon. We found that stringent response induced toxT and tcpPH expression, while repressing toxRS. This differential regulation of ToxR and TcpP may explain the differential expression of TCP and cholera toxin in vivo.

Multilaboratory Assessment of a New Reference Material for Quality Assurance of Cell-Free Tumor DNA Measurements.

We conducted a multilaboratory assessment to determine the suitability of a new commercially available reference material with 40 cancer variants in a background of wild-type DNA at four different variant allele frequencies (VAFs): 2%, 0.50%, 0.125%, and 0%. The variants include single nucleotides, insertions, deletions, and two structural variations selected for their clinical importance and to challenge the performance of next-generation sequencing (NGS) methods. Fragmented DNA was formulated to simulate the size distribution of circulating wild-type and tumor DNA in a synthetic plasma matrix. DNA was extracted from these samples and characterized with different methods and multiple laboratories. The various extraction methods had differences in yield, perhaps because of differences in chemistry. Digital PCR assays were used to measure VAFs to compare results from different NGS methods. Comparable VAFs were observed across the different NGS methods. This multilaboratory assessment demonstrates that the new reference material is an appropriate tool to determine the analytical parameters of different measurement methods and to ensure their quality assurance.

Development and interlaboratory evaluation of a NIST Reference Material RM 8366 for EGFR and MET gene copy number measurements.

Background The National Institute of Standards and Technology (NIST) Reference Material RM 8366 was developed to improve the quality of gene copy measurements of EGFR (epidermal growth factor receptor) and MET (proto-oncogene, receptor tyrosine kinase), important targets for cancer diagnostics and treatment. The reference material is composed of genomic DNA prepared from six human cancer cell lines with different levels of amplification of the target genes. Methods The reference values for the ratios of the EGFR and MET gene copy numbers to the copy numbers of reference genes were measured using digital PCR. The digital PCR measurements were confirmed by two additional laboratories. The samples were also characterized using Next Generation Sequencing (NGS) methods including whole genome sequencing (WGS) at three levels of coverage (approximately 1 ×, 5 × and greater than 30 ×), whole exome sequencing (WES), and two different pan-cancer gene panels. The WES data were analyzed using three different bioinformatic algorithms. Results The certified values (digital PCR) for EGFR and MET were in good agreement (within 20%) with the values obtained from the different NGS methods and algorithms for five of the six components; one component had lower NGS values. Conclusions This study shows that NIST RM 8366 is a valuable reference material to evaluate the performance of assays that assess EGFR and MET gene copy number measurements.

Nanoscale fluorescent metal-organic framework composites as a logic platform for potential diagnosis of asthma.

Asthma is a common chronic disorder, and the decreased hydrogen sulfide (H2S) production in the lung has been considered as an early detection biomarker for asthma. However, the detection of H2S in biological systems remains a challenge; because it requires the designed sensors to have the following features: nanoscale size, good biocompatibility, real-time detection, high selectivity/sensitivity, and good water stability. Here, we propose the potential of using nanoscale fluorescent metal-organic framework (MOF) composites Eu3+/Ag+@UiO-66-(COOH)2 (hereafter denoted as EAUC) as a logic platform for tentative diagnosis of asthma by detecting the biomarker H2S. This INHIBIT logic gate based on Eu3+@UiO-66-(COOH)2 (EUC) can be produced by choosing Ag+ and H2S as inputs and by monitoring the fluorescent signal (I615) as an output. Our fluorescent studies indicate that the EAUC exhibits excellent selectivity, extreme sensitivity (limit of detection: 23.53 µM), and real-time in situ detection of H2S. Further, MTT analysis in PC12 cells shows that the EAUC possesses low cytotoxicity and favourable biocompatibility that are suitable for the detection of biomarker H2S in vivo, as demonstrated by the successful detection of spiked H2S in the diluted serum samples. This work represents the possibility of using MOF-based logic platform for tentative diagnosis of asthma in clinical medicine.

Broadband Extrinsic Self-Trapped Exciton Emission in Sn-Doped 2D Lead-Halide Perovskites.

As emerging efficient emitters, metal-halide perovskites offer the intriguing potential to the low-cost light emitting devices. However, semiconductors generally suffer from severe luminescence quenching due to insufficient confinement of excitons (bound electron-hole pairs). Here, Sn-triggered extrinsic self-trapping of excitons in bulk 2D perovskite crystal, PEA2 PbI4 (PEA = phenylethylammonium), is reported, where exciton self-trapping never occurs in its pure state. By creating local potential wells, isoelectronic Sn dopants initiate the localization of excitons, which would further induce the large lattice deformation around the impurities to accommodate the self-trapped excitons. With such self-trapped states, the Sn-doped perovskites generate broadband red-to-near-infrared (NIR) emission at room temperature due to strong exciton-phonon coupling, with a remarkable quantum yield increase from 0.7% to 6.0% (8.6 folds), reaching 42.3% under a 100 mW cm-2 excitation by extrapolation. The quantum yield enhancement stems from substantial higher thermal quench activation energy of self-trapped excitons than that of free excitons (120 vs 35 meV). It is further revealed that the fast exciton diffusion involves in the initial energy transfer step by transient absorption spectroscopy. This dopant-induced extrinsic exciton self-trapping approach paves the way for extending the spectral range of perovskite emitters, and may find emerging application in efficient supercontinuum sources.

Confinement of Perovskite-QDs within a Single MOF Crystal for Significantly Enhanced Multiphoton Excited Luminescence.

The development of the photostable higher-order multiphoton-excited (MPE) upconversion single microcrystalline material is fundamentally and technologically important, but very challenging. Here, up to five-photon excited luminescence in a host-guest metal-organic framework (MOF) and perovskite quantum dot (QD) hybrid single crystal ZJU-28⊃MAPbBr3 is shown via an in situ growth approach. Such a MOF strategy not only results in a high QD loading concentration, but also significantly diminishes the aggregation-caused quenching (ACQ) effect, provides effective surface passivation, and greatly reduces the contact of the QDs with the external bad atmosphere due to the confinement effect and protection of the framework. These advantages make the resulting ZJU-28⊃MAPbBr3 single crystals possess high PLQY of ≈51.1%, a high multiphoton action cross-sections that can rival the current highest record (measured in toluene solution), and excellent photostability. These findings liberate the excellent luminescence and nonlinear optical properties of perovskite QDs from the solution system to the solid single-crystal system, which provide a new avenue for the exploitation of high-performance multiphoton excited hybrid single microcrystal for future optoelectronic and micro-nano photonic integration applications.

Photonic functional metal-organic frameworks.

Metal-organic frameworks (MOFs) have emerged as particularly exciting inorganic-organic hybrid porous materials which can be simply self-assembled from their corresponding inorganic metal ions/clusters with organic linkers. MOFs can combine the inherent physical and chemical properties of both inorganic and organic photonic units due to their inorganic-organic hybrid nature. Furthermore, the pores within MOFs can also be utilized to encapsulate a large number of guest species as photonic units. The vast combination possibilities, synergistic effects, as well as controllable and ordered arrangements of multiple photonic units (MPUs) have distinguished MOFs from other inorganic and organic photonic materials and enabled them to be a promising platform to realize novel photonic functional applications. In this review, we summarize the recent and important progress in the design and construction of photonic MOFs, as well as their various applications in luminescence sensing, white-light emission, photocatalysis, nonlinear optics, lasing devices, data storage, and biomedicine. In addition, we highlight the construction strategy and the synergistic effects of MOFs towards achieving high performance and novel photonic functions. Finally, we also outline the challenges in these fields and put forward the prospects and directions for future development.

Assessment of Digital PCR as a Primary Reference Measurement Procedure to Support Advances in Precision Medicine.

BACKGROUND: Genetic testing of tumor tissue and circulating cell-free DNA for somatic variants guides patient treatment of many cancers. Such measurements will be fundamental in the future support of precision medicine. However, there are currently no primary reference measurement procedures available for nucleic acid quantification that would support translation of tests for circulating tumor DNA into routine use. METHODS: We assessed the accuracy of digital PCR (dPCR) for copy number quantification of a frequently occurring single-nucleotide variant in colorectal cancer (KRAS c.35G>A, p.Gly12Asp, from hereon termed G12D) by evaluating potential sources of uncertainty that influence dPCR measurement. RESULTS: Concentration values for samples of KRAS G12D and wild-type plasmid templates varied by <1.2-fold when measured using 5 different assays with varying detection chemistry (hydrolysis, scorpion probes, and intercalating dyes) and <1.3-fold with 4 commercial dPCR platforms. Measurement trueness of a selected dPCR assay and platform was validated by comparison with an orthogonal method (inductively coupled plasma mass spectrometry). The candidate dPCR reference measurement procedure showed linear quantification over a wide range of copies per reaction and high repeatability and interlaboratory reproducibility (CV, 2%-8% and 5%-10%, respectively). CONCLUSIONS: This work validates dPCR as an SI-traceable reference measurement procedure based on enumeration and demonstrates how it can be applied for assignment of copy number concentration and fractional abundance values to DNA reference materials in an aqueous solution. High-accuracy measurements using dPCR will support the implementation and traceable standardization of molecular diagnostic procedures needed for advancements in precision medicine.

Limitations of methods for measuring the concentration of human genomic DNA and oligonucleotide samples.

We compared different methods (absorbance, fluorescent dye-binding, and digital PCR) for measuring the concentrations of human genomic DNA from cultured cells and absorbance measurements of a synthetic DNA oligonucleotide. NIST Standard Reference Material (SRM) 2082, a pathlength absorbance standard, was used to benchmark the absorbance measurements done with microvolume spectrophotometers and a microvolume plate reader. Control absorbance values were measured on a high accuracy spectrophotometer and a NIST calibrated pathlength cuvette. Measurements of the human genomic DNA sample were done with several types of fluorescent dye binding assays using different DNA calibrators. The fluorescent dye binding methods gave different results for genomic DNA depending upon the type of DNA calibrator and the fluorescent dye that was used. The human genomic DNA sample was also characterized by using six different droplet digital PCR assays (amplicons located on different chromosomes) to measure the average copy number. Conversion of the digital PCR data to copy numbers was sensitive to the droplet size used for calculations and conversion to mass concentration was dependent upon the molecular weight of the human genome used for the calculations. The results from the different methods were compared and the caveats for each measurement method were discussed.

NIST Spectroscopic Measurement Standards.

Ultraviolet (UV) absorbance measurements provide a rapid and reliable method to determine protein concentrations. the National Institute of standards and technology (NIST) has developed Standard Reference Material (SRM) 2082 as a pathlength standard for UV absorbance measurements for use with the new generation of microvolume spectrophotometers and short-pathlength cuvettes. short pathlengths are used with high-concentration targets to ensure that absorbance values are within the optimal range. the short-pathlength instruments and cuvettes also reduce the required volumes to conserve valuable samples. the authors compared the results obtained with high-quality dual-beam spectrophotometers and short-pathlength cuvettes to the results obtained from a microvolume spectrophotometer and a microvolume plate reader. SRM 2082 can be used to accurately calculate pathlength values, thereby increasing the accuracy in subsequent measurements using the short-pathlength cuvettes and microvolume absorbance instruments. RM 8671 (reference material, the NISTmAb) can then be used to ensure the accuracy and reproducibility of protein concentration measurements by providing an industrially relevant reference material, a well-characterized monoclonal antibody.