Double helix point spread function with variable spacing for precise 3D particle localization.

To extend the axial depth of nanoscale 3D-localization microscopy, we propose here a splicing-type vortex singularities (SVS) phase mask, which has been meticulously optimized with a Fresnel approximation imaging inverse operation. The optimized SVS DH-PSF has proven to have high transfer function efficiency with adjustable performance in its axial range. The axial position of the particle was computed by using both the main lobes' spacing and the rotation angle, an improvement of the localization precision of the particle. Concretely, the proposed optimized SVS DH-PSF, with a smaller spatial extent, can effectively reduce the overlap of nanoparticle images and realize the 3D localization of multiple nanoparticles with small spacing, with respect to PSFs for large axial 3D localization. Finally, we successfully conducted extensive experiments on 3D localization for tracking dense nanoparticles at 8µm depth with a numerical aperture of 1.4, demonstrating its great potential.

Phase-based reconstruction optimization method for digital holographic measurement of microstructures.

Digital holography has transformative potential in measuring stacked-chip microstructures due to its noninvasive, single-shot, full-field characteristics. However, uncertainties in reconstruction distance inevitably lead to resolving blur and reconstruction distortion. Herein, we propose a phase-based reconstruction optimization method that consists of a phase-evaluation function and a structured surface-characterization model. Our proposed method involves setting a reconstruction distance range, obtaining phase information using sliced numerical reconstruction, and optimizing the reconstruction distance by finding the extreme value of the function, which identifies the focal plane of the reconstructed image. The structure of the surface topography is then characterized using the characterization model. We perform simulations of the recording, reconstruction, and characterization to verify the effectiveness of the proposed method. To further demonstrate the approach, a simple holographic recording system is constructed to measure a standard resolution target, and the measurement results are compared with a commercial instrument. The simulation and experiment demonstrate, respectively, 31.16% and 34.41% improvement in step-height characterization accuracy.

Phase optimization algorithm for 3D particle localization with large axial depth.

We propose an optimization algorithm based on Fresnel approximation (FA) imaging to optimize an extended-axial-depth point spread function (PSF) for 3D particle localization. The transfer function efficiency of the PSF is improved by repeatedly imposing constraints in the object plane, the spatial domain, and the Fourier domain. During the iterative calculation, the effective photon number or Cramer-Rao lower bound is used as the termination condition of the iteration. The algorithm allows flexible adjustment of the peak intensity ratio of the two main lobes. Moreover, the transfer function efficiency can be balanced by increasing the weight of the modulation function of the expected PSF at each axial position. The twin-Airy (TA) PSF optimized by the FA optimization algorithm does not require complex post-processing, whereas post-processing is an essential step for the unoptimized TA-PSF. The optimization algorithm is significant for extended-axial-depth PSFs used for 3D particle localization, as it improves localization precision and temporal resolution.

Splicing exponential point spread function design for localization of nanoparticles.

We propose a point spread function for three-dimensional localization of nanoparticles. The axial detection range of the point spread function can be simply changed by adjusting the design parameters. In addition, the spatial extent of the point spread function can also be changed by adjusting the design parameters, which is an advantage other point spread functions do not have. We used our point spread functions and the existing point spread functions for dense multi-particle imaging, which proved the advantage that the point spread function with a smaller spatial extent we designed can effectively reduce the overlap between the point spread functions. The three-dimensional process of the fluorescent microsphere penetrating HT-22 cell membrane was successfully recorded, which verified the effectiveness of this method.

Particles 3D tracking with large axial depth by using the 2π-DH-PSF.

We propose a 2π-double-helix point spread function (2π-DH-PSF) using the Fresnel zone approach that can rotate 2π rad. When 16 Fresnel zones are used, the particles can be tracked in the axial range of 10 µm in a 100× microscopy imaging system (NA=1.4, λ=514nm). We measured the diffusion coefficient of nanospheres in different concentrations of glycerol with the 2π-DH-PSF, and the error between the measured results and theoretical value was within 10%, indicating the superior performance of 2π-DH-PSF in 3D localization imaging of nanoparticles. When combined with the defocus phase, the rotation angle can reach 4π rad, four times that of the conventional DH-PSF.

Three-dimensional diffusion coefficient measurement by a large depth-of-field rotating point spread function.

A prominent challenge in single-molecule localization microscopy is the real-time, fast, and accurate localization of nano-objects moving in three-dimensional (3D) samples. A well-established method for 3D single-molecule localization is the double-helix pointspread-function (DH-PSF) engineering, which uses additional optical elements to make the PSF exhibit different rotation angles with different nanoparticle depths. However, the compact main lobe size, effective detection depth, and precise conversion between rotation angle and depth are necessary, posing challenges to the DH-PSF generation method. Here we generate a more compact DH-PSF using Fresnel-zone-based spiral phases, and the pure phase mask achieves high transmission efficiency. The final generated DH-PSFs have a linear rotation rate at each axial position, showing a more accurate rotation angle and depth conversion. The Cramer-Rao lower limit calculation results show that the axial depth of DH-PSF extends to ∼11µm with an axial localization precision of ∼45nm at 3000 photons and average background noise of 15. We measured the diffusion coefficient of nanospheres in different concentrations of glycerol using the generated DH-PSF. The measured results are within 6% error from the theoretical values, indicating the superior performance of the DH-PSF for nanoparticle diffusion coefficient measurements.

Draft genome of the wheat A-genome progenitor Triticum urartu.

Bread wheat (Triticum aestivum, AABBDD) is one of the most widely cultivated and consumed food crops in the world. However, the complex polyploid nature of its genome makes genetic and functional analyses extremely challenging. The A genome, as a basic genome of bread wheat and other polyploid wheats, for example, T. turgidum (AABB), T. timopheevii (AAGG) and T. zhukovskyi (AAGGA(m)A(m)), is central to wheat evolution, domestication and genetic improvement. The progenitor species of the A genome is the diploid wild einkorn wheat T. urartu, which resembles cultivated wheat more extensively than do Aegilops speltoides (the ancestor of the B genome) and Ae. tauschii (the donor of the D genome), especially in the morphology and development of spike and seed. Here we present the generation, assembly and analysis of a whole-genome shotgun draft sequence of the T. urartu genome. We identified protein-coding gene models, performed genome structure analyses and assessed its utility for analysing agronomically important genes and for developing molecular markers. Our T. urartu genome assembly provides a diploid reference for analysis of polyploid wheat genomes and is a valuable resource for the genetic improvement of wheat.

ISIR and its human homolog gene AK131315 strengthen LPS-induced inflammation and acute lung injury by promoting TAK1-dependent NF-κB and MAPK signaling.

Acute lung injury (ALI), a critical complication observed in various clinical disorders, is characterized by widespread inflammation, neutrophil infiltration, and proinflammatory cytokine production. This study showed that the recently identified non-coding RNA ISIR and its human homolog gene AK131315 played a role in regulating lipopolysaccharide (LPS)-induced inflammatory responses. ISIR and AK131315 increased the production of inflammatory cytokines in LPS-stimulated macrophages, and exogenous ISIR aggravated LPS-induced lung inflammation in an animal model of ALI. Mechanistically, ISIR promoted LPS-triggered NF-κB and MAPK signaling and the transcription of proinflammatory cytokines by enhancing TAK1 activation. Furthermore, a significant correlation was observed between AK131315 expression and pulmonary infectious caused by Gram-negative bacteria, suggesting that AK131315 plays an important role in bacterial infections. Altogether, these findings indicate that ISIR regulates LPS-induced inflammation and AK131315 is involved in the pathogenesis of bacterial infections.

The Role of ASIC1a in Epilepsy: A Potential Therapeutic Target.

BACKGROUND: Epilepsy represents one of the most common brain diseases among humans. Tissue acidosis is a common phenomenon in epileptogenic foci. Moreover, its role in epileptogenesis remains unclear. Acid-sensing ion channel-1a (ASIC1a) represents a potential way to assess new therapies. ASIC1a, mainly expressed in the mammalian brain, is a type of protein-gated cation channel. It has been shown to play an important role in the pathological mechanism of various diseases, including stroke, epilepsy, and multiple sclerosis. METHODS: Data were collected from Web of Science, Medline, PubMed, through searching for these keywords: "Acid-sensing ion channels 1a" or "ASIC1a" and "epilepsy" or "seizure". RESULTS: The role of ASIC1a in epilepsy remains controversial; it may represent a promising therapeutic target of epilepsy. CONCLUSION: This review is intended to provide an overview of the structure, trafficking, and molecular mechanisms of ASIC1a in order to elucidate the role of ASIC1a in epilepsy further.

Vinpocetine Protects Against Cerebral Ischemia-Reperfusion Injury by Targeting Astrocytic Connexin43 via the PI3K/AKT Signaling Pathway.

Vinpocetine (Vinp) is known for its neuroprotective properties. However, the protective mechanism of Vinp against cerebral ischemia/reperfusion (I/R) injury should be further explored. This study was designed to investigate the neuroprotective effects of Vinp against oxygen-glucose deprivation/reoxygenation (OGD/R) injury in vitro and cerebral I/R injury in vivo and explore whether this mechanism would involve enhancement of astrocytic connexin 43 (Cx43) expression via the phosphatidylinositol 3-kinase/protein kinase B (PI3K/AKT) pathway. In vitro, we detected astrocytic viability and extracellular nitric oxide by an assay kit, intracellular reactive oxygen species by a DCFH-DA probe, inflammation and apoptosis-related protein expression by immunofluorescence staining, and the astrocytic apoptosis rate by flow cytometry. In vivo, we measured the cerebral infarction volume, superoxide dismutase activity, malondialdehyde content, and the expression of inflammation and apoptosis-related proteins. The results indicated that Vinp ameliorated the detrimental outcome of I/R injury. Vinp attenuated astrocytic injury induced by OGD/R and reduced cerebral infarction volume and cerebral edema in rats with cerebral I/R injury. Moreover, Vinp reduced oxidative stress, inflammation, and apoptosis induced by cerebral I/R injury in brain tissues. Meanwhile, Vinp increased p-Cx43 and p-AKT expression, and the p-Cx43/Cx43 and p-AKT/AKT ratio, which was decreased by cerebral I/R injury. Coadministration of PI3K inhibitors LY294002 and BKM120 blunted the effects of Vinp. This study suggests that Vinp protects against cerebral I/R injury via Cx43 phosphorylation by activating the PI3K/AKT pathway.