An official website of the United States government
Abstract The global health threat posed by the Monkeypox virus (Mpox) requires swift, simple, and accurate detection methods for effective management, emphasizing the growing necessity for decentralized point-of-care (POC) diagnostic solutions. The clustered regularly interspaced short palindromic repeats (CRISPR), initially known for its effective nucleic acid detection abilities, presents itself as an attractive diagnostic strategy. CRISPR offers exceptional sensitivity, single-base specificity, and programmability. Here, we reviewed the latest developments in CRISPR-based POC devices and testing strategies for Mpox detection. We explored the crucial role of genetic sequencing in designing crRNA for CRISPR reaction and understanding Mpox transmission and mutations. Additionally, we showed the integration of CRISPR-Cas12 strategy with pre-amplification and amplification-free methods. Our study also focused on the significant role of Cas12 proteins and the effectiveness of Cas12 coupled with recombinase polymerase amplification (RPA) for Mpox detection. We envision the future prospects and challenges, positioning CRISPR-Cas12-based POC devices as a frontrunner in the next generation of molecular biosensing technologies.
more »
« less
A non-enzyme cascade amplification strategy for colorimetric assay of disease biomarkers
A non-enzyme cascade amplification strategy, based on the dissolution of Ag nanoparticles and a Pt nanocube-catalyzed reaction, for colorimetric assay of disease biomarkers was developed. This strategy overcomes the intrinsic limitations of enzymes involved in conventional enzymatic amplification techniques, thanks to the utilization of noble-metal nanostructures with superior properties.
more »
« less
- Award ID(s):
- 1651307
- PAR ID:
- 10048855
- Date Published:
- Journal Name:
- Chemical Communications
- Volume:
- 53
- Issue:
- 65
- ISSN:
- 1359-7345
- Page Range / eLocation ID:
- 9055 to 9058
- Format(s):
- Medium: X
- Sponsoring Org:
- National Science Foundation
More Like this
-
-
The time-marching strategy, which propagates the solution from one time step to the next, is a natural strategy for solving time-dependent differential equations on classical computers, as well as for solving the Hamiltonian simulation problem on quantum computers. For more general homogeneous linear differential equations d d t | ψ ( t ) ⟩ = A ( t ) | ψ ( t ) ⟩ , | ψ ( 0 ) ⟩ = | ψ 0 ⟩ , a time-marching based quantum solver can suffer from exponentially vanishing success probability with respect to the number of time steps and is thus considered impractical. We solve this problem by repeatedly invoking a technique called the uniform singular value amplification, and the overall success probability can be lower bounded by a quantity that is independent of the number of time steps. The success probability can be further improved using a compression gadget lemma. This provides a path of designing quantum differential equation solvers that is alternative to those based on quantum linear systems algorithms (QLSA). We demonstrate the performance of the time-marching strategy with a high-order integrator based on the truncated Dyson series. The complexity of the algorithm depends linearly on the amplification ratio, which quantifies the deviation from a unitary dynamics. We prove that the linear dependence on the amplification ratio attains the query complexity lower bound and thus cannot be improved in the worst case. This algorithm also surpasses existing QLSA based solvers in three aspects: (1) A ( t ) does not need to be diagonalizable. (2) A ( t ) can be non-smooth, and is only of bounded variation. (3) It can use fewer queries to the initial state | ψ 0 ⟩ . Finally, we demonstrate the time-marching strategy with a first-order truncated Magnus series, which simplifies the implementation compared to high-order truncated Dyson series approach, while retaining the aforementioned benefits. Our analysis also raises some open questions concerning the differences between time-marching and QLSA based methods for solving differential equations.more » « less
-
Log-structured merge (LSM) trees offer efficient ingestion by appending incoming data, and thus, are widely used as the storage layer of production NoSQL data stores. To enable competitive read performance, LSM-trees periodically re-organize data to form a tree with levels of exponentially increasing capacity, through iterative compactions. Compactions fundamentally influence the performance of an LSM-engine in terms of write amplification, write throughput, point and range lookup performance, space amplification, and delete performance. Hence, choosing the appropriate compaction strategy is crucial and, at the same time, hard as the LSM-compaction design space is vast, largely unexplored, and has not been formally defined in the literature. As a result, most LSM-based engines use a fixed compaction strategy, typically hand-picked by an engineer, which decides how and when to compact data. In this paper, we present the design space of LSM-compactions, and evaluate state-of-the-art compaction strategies with respect to key performance metrics. Toward this goal, our first contribution is to introduce a set of four design primitives that can formally define any compaction strategy: (i) the compaction trigger, (ii) the data layout, (iii) the compaction granularity, and (iv) the data movement policy. Together, these primitives can synthesize both existing and completely new compaction strategies. Our second contribution is to experimentally analyze 10 compaction strategies. We present 12 observations and 7 high-level takeaway messages, which show how LSM systems can navigate the compaction design space.more » « less
-
Foodborne bacteria have persisted as a significant threat to public health and to the food and agriculture industry. Due to the widespread impact of these pathogens, there has been a push for the development of strategies that can rapidly detect foodborne bacteria on-site. Shiga toxin-producing E. coli strains (such as E. coli O157:H7, E. coli O121, and E. coli O26) from contaminated food have been a major concern. They carry genes stx1 and/or stx2 that produce two toxins, Shiga toxin 1 and Shiga toxin 2, which are virulent proteins. In this work, we demonstrate the development of a rapid test based on an isothermal recombinase polymerase amplification reaction for two Shiga toxin genes in a single reaction. Results of the amplification reaction are visualized simultaneously for both Shiga toxins on a single lateral flow paper strip. This strategy targets the DNA encoding Shiga toxin 1 and 2, allowing for broad detection of any Shiga toxin-producing bacterial species. From sample to answer, this method can achieve results in approximately 35 min with a detection limit of 10 CFU/mL. This strategy is sensitive and selective, detecting only Shiga toxin-producing bacteria. There was no interference observed from non-pathogenic or pathogenic non-Shiga toxin-producing bacteria. A detection limit of 10 CFU/mL for Shiga toxin-producing E. coli was also obtained in a food matrix. This strategy is advantageous as it allows for timely identification of Shiga toxin-related contamination for quick initial food contamination assessments.more » « less
-
Abstract Novel methods that enable sensitive, accurate and rapid detection of RNA would not only benefit fundamental biological studies but also serve as diagnostic tools for various pathological conditions, including bacterial and viral infections and cancer. Although highly sensitive, existing methods for RNA detection involve long turn‐around time and extensive capital equipment. Here, an ultrasensitive and amplification‐free RNA quantification method is demonstrated by integrating CRISPR‐Cas13a system with an ultrabright fluorescent nanolabel, plasmonic fluor. This plasmonically enhanced CRISPR‐powered assay exhibits nearly 1000‐fold lower limit‐of‐detection compared to conventional assay relying on enzymatic reporters. Using a xenograft tumor mouse model, it is demonstrated that this novel bioassay can be used for ultrasensitive and quantitative monitoring of cancer biomarker (lncRNA H19). The novel biodetection approach described here provides a rapid, ultrasensitive, and amplification‐free strategy that can be broadly employed for detection of various RNA biomarkers, even in resource‐limited settings.more » « less
- Free Publicly Accessible Full Text
-
Accepted Manuscript1.0
- Journal Article:
- https://doi.org/10.1039/C7CC04521B
