Ultrasensitive detection of Salmonella typhi using a PAM-free Cas14a-based biosensor.

The effectiveness of Clustered Regularly Interspaced Short Palindromic Repeats (CRISPR)-Cas14a1, widely utilized for pathogenic microorganism detection, has been limited by the requirement of a protospacer adjacent motif (PAM) on the target DNA strands. To overcome this limitation, this study developed a Single Primer isothermal amplification integrated-Cas14a1 biosensor (SPCas) for detecting Salmonella typhi that does not rely on a PAM sequence. The SPCas biosensor utilizes a novel primer design featuring an RNA-DNA primer and a 3'-biotin-modified primer capable of binding to the same single-stranded DNA (ssDNA) in the presence of the target gene. The RNA-DNA primer undergoes amplification and is blocked at the biotin-modified end. Subsequently, strand replacement is initiated to generate ssDNA assisted by RNase H and Bst enzymes, which activate the trans-cleavage activity of Cas14a1 even in the absence of a PAM sequence. Leveraging both cyclic chain replacement reaction amplification and Cas14a1 trans-cleavage activity, the SPCas biosensor exhibits a remarkable diagnostic sensitivity of 5 CFU/mL. Additionally, in the assessment of 20 milk samples, the SPCas platform demonstrated 100% diagnostic accuracy, which is consistent with the gold standard qPCR. This platform introduces a novel approach for developing innovative CRISPR-Cas-dependent biosensors without a PAM sequence.

Development of an inducible Cas9 nickase and PAM-free Cas12a platform for bacterial diagnostics.

Rapid, efficient, specific and sensitive diagnostic techniques are critical for selecting appropriate treatments for drug-resistant bacterial infections. To address this challenge, we have developed a novel diagnostic method, called the Dual-Cas Tandem Diagnostic Platform (DTDP), which combines the use of Cas9 nickase (Cas9n) and Cas12a. DTDP works by utilizing the Cas9n-sgRNA complex to create a nick in the target strand's double-stranded DNA (dsDNA). This prompts DNA polymerase to displace the single-stranded DNA (ssDNA) and leads to cycles of DNA replication through nicking, displacement, and extension. The ssDNA is then detected by the Cas12a-crRNA complex (which is PAM-free), activating trans-cleavage and generating a fluorescent signal from the fluorescent reporter. DTDP exhibits a high sensitivity (1 CFU/mL or 100 ag/µL), high specificity (specifically to MRSA in nine pathogenic species), and excellent accuracy (100%). The dual RNA recognition process in our method improves diagnostic specificity by decreasing the limitations of Cas12a in detecting dsDNA protospacer adjacent motifs (PAMs) and leverages multiple advantages of multi-Cas enzymes in diagnostics. This novel approach to pathogenic microorganism detection has also great potential for clinical diagnosis.

Mechanisms of Scaling Effect for Emerging Nanoscale Interconnect Materials.

The resistivity of Cu interconnects increases rapidly with continuously scaling down due to scatterings, causing a major challenge for future nodes in M0 and M1 layers. Here, A Boltzmann-transport-equation-based Monte Carlo simulator, including all the major scattering mechanisms of interconnects, is developed for the evaluation of electron transport behaviors. Good agreements between our simulation and the experimental results are achieved for Cu, Ru, Co, and W, from bulk down to 10 nm interconnects. The line resistance values of the four materials with the inclusion of liner and barrier thicknesses are calculated in the same footprint for a fair comparison. The impact of high aspect ratio on resistivity is analyzed for promising buried power rail materials, such as Ru and W. Our results show that grain boundary scattering plays the most important role in nano-scale interconnects, followed by surface roughness and plasma excimer scattering. Surface roughness scattering is the origin of the resistivity decrease for high-aspect-ratio conductive rails. In addition, the grain sizes for the technical nodes of different materials are extracted and the impact of grain size on resistivity is analyzed.

Free zinc determines the formability of the vesicular dense core in diabetic beta cells.

During the progression of type 2 diabetes, total body zinc deficiency disrupts the formability of the electron-dense core in beta-cell vesicles, but the mechanism is unclear. Using fluorescence imaging, transmission electron microscopy and pharmacokinetics assays, we established a strong link between an increasing concentration of free zinc and the formability enhancement of the dense core electron density. Thus, our results highlight a mechanism by which zinc supplementation enhances the maturation of dense cores and restores the secretion of insulin in two diabetic mouse models both in vitro and in vivo. This study provides a potential research direction for investigating the etiology and nutrition of zinc in the management of type 2 diabetes.

Imaging elemental events of store-operated Ca2+ entry in invading cancer cells with plasmalemmal targeted sensors.

STIM1- and Orai1-mediated store-operated Ca2+ entry (SOCE) constitutes the major Ca2+ influx in almost all electrically non-excitable cells. However, little is known about the spatiotemporal organization at the elementary level. Here, we developed Orai1-tethered or palmitoylated biosensor GCaMP6f to report subplasmalemmal Ca2+ signals. We visualized spontaneous discrete and long-lasting transients ('Ca2+ glows') arising from STIM1-Orai1 in invading melanoma cells. Ca2+ glows occurred preferentially in single invadopodia and at sites near the cell periphery under resting conditions. Re-addition of external Ca2+ after store depletion elicited spatially synchronous Ca2+ glows, followed by high-rate discharge of asynchronous local events. Knockout of STIM1 or expression of the dominant-negative Orai1-E106A mutant markedly decreased Ca2+ glow frequency, diminished global SOCE and attenuated invadopodial formation. Functionally, invadopodial Ca2+ glows provided high Ca2+ microdomains to locally activate Ca2+/calmodulin-dependent Pyk2 (also known as PTK2B), which initiates the SOCE-Pyk2-Src signaling cascade required for invasion. Overall, the discovery of elemental Ca2+ signals of SOCE not only unveils a previously unappreciated gating mode of STIM1-Orai1 channels in situ, but also underscores a critical role of the spatiotemporal dynamics of SOCE in orchestrating complex cell behaviors such as invasion. This article has an associated First Person interview with the first author of the paper.

Fascin induces melanoma tumorigenesis and stemness through regulating the Hippo pathway.

BACKGROUND: Fascin is a F-actin bundling protein and its overexpression is correlated with poor prognosis and increases metastatic potential in a number of cancers. But underlying function and mechanism of fascin on tumorigenesis in melanoma remain elusive. METHODS: The melanoma cell lines WM793 and WM39 were employed for the soft agar and sphere formation assay. Quantitative RT-PCR and Western blot were performed for identifying the gene expression at mRNA and protein levels, respectively. Co-IP and in vitro GST pulldown experiments were used to test the interaction between fascin and MST2. RESULTS: Fascin regulates tumorigenesis and cancer cell stemness in melanoma through inhibition of the Hippo pathway kinase MST2 and the activation of transcription factor TAZ. Our data showed that fascin interacts with the kinase domain of MST2 to inhibit its homodimer formation and kinase activity. Depletion of fascin led to increase of p-LATS level and decrease of TAZ, but not YAP. We also demonstrated that fascin regulates melanoma tumorigenesis independent of its actin-bundling activity. CONCLUSIONS: Fascin is a new regulator of the MST2-LATS-TAZ pathway and plays a critical role in melanoma tumorigenesis. Inhibition of fascin reduces melanoma tumorigenesis and stemness, and thus fascin could be a potential therapeutic target for this malignancy.