Rhodamine-based fluorescent probe for dynamic STED imaging of mitochondria.

Stimulated emission depletion (STED) microscopy holds tremendous potential and practical implications in the field of biomedicine. However, the weak anti-bleaching performance remains a major challenge limiting the application of STED fluorescent probes. Meanwhile, the main excitation wavelengths of most reported STED fluorescent probes were below 500 nm or above 600 nm, and few of them were between 500-600 nm. Herein, we developed a new tetraphenyl ethylene-functionalized rhodamine dye (TPERh) for mitochondrial dynamic cristae imaging that was rhodamine-based with an excitation wavelength of 560 nm. The TPERh probe exhibits excellent anti-bleaching properties and low saturating stimulated radiation power in mitochondrial STED super-resolution imaging. Given these outstanding properties, the TPERh probe was used to measure mitochondrial deformation, which has positive implications for the study of mitochondria-related diseases.

Highly birefringent side-hole fiber Bragg grating for high-temperature pressure sensing.

We demonstrate a novel, to the best of our knowledge, high-temperature pressure sensor based on a highly birefringent fiber Bragg grating (Hi-Bi FBG) fabricated in a dual side-hole fiber (DSHF). The Hi-Bi FBG is generated by a femtosecond laser directly written sawtooth structure in the DSHF cladding along the fiber core through the slow axis (i.e., the direction perpendicular to the dual-hole axis). The sawtooth structure serves as an in-fiber stressor and also generates Bragg resonance due to its periodicity. The DSHF was etched by hydrofluoric acid to increase its pressure sensitivity, and the diameter of two air holes was enlarged from 38.2 to 49.6 µm. A Hi-Bi FBG with a birefringence of up to 1.8 × 10-3 was successfully created in the etched DSHF. Two distinct reflection peaks could be observed by using a commercial FBG interrogator. Moreover, pressure measurement from 0 to 3 MPa at a high temperature of 700°C was conducted by monitoring the birefringence-induced peak splits and achieved a high-pressure sensitivity of -21.2 pm/MPa. The discrimination of the temperature and pressure could be realized by simultaneously measuring the Bragg wavelength shifts and peak splits. Furthermore, a wavelength-division-multiplexed (WDM) Hi-Bi FBG array was also constructed in the DSHF and was used for quasi-distributed high-pressure sensing up to 3 MPa. As such, the proposed femtosecond laser-inscribed Hi-Bi FBG is a promising tool for high-temperature pressure sensing in harsh environments, such as aerospace vehicles, nuclear reactors, and petrochemical industries.

High-temperature strain sensor based on sapphire fiber Bragg grating.

Sapphire fiber Bragg grating (SFBG) is a promising high-temperature strain sensor due to its melting point of 2045°C. However, the study on the long-term stability of SFBG under high temperature with an applied strain is still missing. In this paper, we reported for the first time to our knowledge on the critical temperature point of plastic deformation of the SFBG and demonstrated that the SFBG strain sensor can operate stably below 1200°C. At first, we experimentally investigated the topography and the spectral characteristics of the SFBG at different temperatures (i.e., 25°C, 1180°C, and 1600°C) with applied 650 µÎµ. The reflection peak of the SFBG exhibits a redshift of about 15 nm and broadens gradually within 8 h at 1600°C, and the tensile force value decreases by 0.60 N in this process. After the test, the diameter of the SFBG region decreases from 100 to 88.6 µm, and the grating period is extended from 1.76 to 1.79 µm. This indicates that the plastic deformation of the SFBG happened indeed, and it was elongated irreversibly. Moreover, the stability of the Bragg wavelength of the SFBG under high temperature with the applied strain was evaluated. The result demonstrates the SFBG can be used to measure strain reliably below 1200°C. Furthermore, the strain experiments of SFBG at 25°C, 800°C, and 1100°C have been carried out. A linear fitting curve with high fitness (R2 > 0.99) and a lower strain measurement error (<15 µÎµ) can be obtained. The aforementioned results make SFBG promising for high-temperature strain sensing in many fields, such as, power plants, gas turbines, and aerospace vehicles.

Exploring the effect of photobiomodulation and gamma visual stimulation induced by 808 nm and visible LED in Alzheimer's disease mouse model.

Although photobiomodulation (PBM) and gamma visual stimulatqion (GVS) have been overwhelmingly explored in the recent time as a possible light stimulation (LS) means of Alzheimer's disease (AD) therapy, their effects have not been assessed at once. In our research, the AD mouse model was stimulated using light with various parameters [continuous wave (PBM) or 40 Hz pulsed visible LED (GVS) or 40 Hz pulsed 808 nm LED (PBM and GVS treatment)]]. The brain slices collected from the LS treated AD model mice were evaluated using (i) fluorescence microscopy to image thioflavine-S labeled amy-loid-ß (Aß) plaques (the main hallmark of AD), or (ii) two-photon excited fluorescence (TPEF) imaging of unlabeled Aß plaques, showing that the amount of Aß plaques was reduced after LS treatment. The imaging results correlated well with the results of Morris water maze (MWM) test, which demonstrated that the spatial learning and memory abilities of LS treated mice were noticeably higher than those of untreated mice. The LS effect was also assessed by in vivo nonlinear optical imaging, revealing that the cerebral amyloid angiopathy decreased spe-cifically as a result of 40 Hz pulsed 808 nm irradiation, on the contrary, the angiopathy reversed after visible 40 Hz pulsed light treatment. The obtained results provide useful reference for further optimization of the LS (PBM or GVS) parameters to achieve efficient phototherapy of AD.

In Vivo High-Contrast Biomedical Imaging in the Second Near-Infrared Window Using Ultrabright Rare-Earth Nanoparticles.

Intravital luminescence imaging in the second near-infrared window (NIR-II) enables noninvasive deep-tissue imaging with high spatiotemporal resolution of live mammals because of the properties of suppressed light scattering and diminished autofluorescence in the long-wavelength region. Herein, we present the synthesis of a downconversion luminescence rare-earth nanocrystal with a core-shell-shell structure (NaYF4@NaYbF4:Er,Ce@NaYF4:Ca). The structure efficiently maximized the doping concentration of the sensitizers and increased Er3+ luminescence while preventing cross relaxation. Furthermore, Ce3+ doping in the middle layer efficiently limited the upconversion pathway and increased downconversion by 24-fold to produce bright 1550 nm luminescence under 975 nm excitation. Finally, optimizing the inert shell coating of NaYF4:Ca and liposome encapsulation reduced the luminescence quenching impact by water and improved biological metabolism. Thus, our synthesized biocompatible, ultrabright NIR-II probes provide high contrast and resolution for through-scalp and through-skull luminescence imaging of mice cerebral vasculature without craniotomy as well as imaging of mouse hindlimb microvessels.

Ultraviolet sensing based on an in-fiber ZnO microwire constructed Mach-Zehnder interferometer.

We propose a Mach-Zehnder interferometer based on an in-fiber ZnO microwire structure for ultraviolet sensing. The device undergoes femtosecond laser micromachining and chemical etching on a single-mode optical fiber initially, creating a microgroove that extends to half of the core's depth, into which a single ZnO microwire is transferred. The ZnO microwire and the remaining core are used as the sensing arm and the reference arm, respectively, forming a Mach-Zehnder interferometer. To enhance the stability and the sensitivity, ZnO nanoparticles are filled into the microgroove after the ZnO microwire is transferred. The fabricated device exhibits a sensitivity of 0.86 nm/(W·cm-2) for ultraviolet sensing, along with a response time of 115 ns (rise time) and 133 µs (decay time), respectively. The proposed sensor exhibits good ultraviolet sensitivity, offering a novel approach for ultraviolet sensing technology.

Two-dimensional nanomaterials as enhanced surface plasmon resonance sensing platforms: Design perspectives and illustrative applications.

Both increasing demand for ultrasensitive detection in the scientific community and significant new breakthroughs in materials science field have inspired and promoted the development of new-generation multifunctional plasmonic sensing platforms by adopting promising plasmonic nanomaterials. Recently, high-quality surface plasmon resonance (SPR) sensors, assisted by two dimensional (2D) nanomaterials including 2D van der Waals (vdWs) materials (such as graphene/graphene oxide, transition metal dichalcogenides (TMDs), phosphorene, antimonene, tellurene, MXenes, and metal oxides), 2D metal-organic frameworks (MOFs), 2D hyperbolic metamaterials (HMMs), and 2D optical metasurfaces, have emerged as a class of novel plasmonic sensing platforms that show unprecedented detection sensitivity and impressive performance. This review of recent progress in 2D nanomaterials-enhanced SPR platforms will highlight their compelling plasmonic enhancement features, working mechanisms, and design methodologies, as well as discuss illustrative practical applications. Hence, it is of great importance to describe the latest research progress in 2D nanomaterials-enhanced SPR sensing cases. In this review, we present some concepts of SPR enhanced by 2D nanomaterials, including the basic principles of SPR, signal modulation approaches, and working enhancement mechanisms for various 2D materials-enhanced SPR systems. In addition, we also demonstrate a detailed categorization of 2D nanomaterials-enhanced SPR sensing platforms and comment on their ability to realize ultrasensitive SPR detection. Finally, we conclude with future perspectives for exploring a new generation of 2D nanomaterials-based sensors.

JGI Plant Gene Atlas: an updateable transcriptome resource to improve functional gene descriptions across the plant kingdom.

Gene functional descriptions offer a crucial line of evidence for candidate genes underlying trait variation. Conversely, plant responses to environmental cues represent important resources to decipher gene function and subsequently provide molecular targets for plant improvement through gene editing. However, biological roles of large proportions of genes across the plant phylogeny are poorly annotated. Here we describe the Joint Genome Institute (JGI) Plant Gene Atlas, an updateable data resource consisting of transcript abundance assays spanning 18 diverse species. To integrate across these diverse genotypes, we analyzed expression profiles, built gene clusters that exhibited tissue/condition specific expression, and tested for transcriptional response to environmental queues. We discovered extensive phylogenetically constrained and condition-specific expression profiles for genes without any previously documented functional annotation. Such conserved expression patterns and tightly co-expressed gene clusters let us assign expression derived additional biological information to 64 495 genes with otherwise unknown functions. The ever-expanding Gene Atlas resource is available at JGI Plant Gene Atlas (https://plantgeneatlas.jgi.doe.gov) and Phytozome (https://phytozome.jgi.doe.gov/), providing bulk access to data and user-specified queries of gene sets. Combined, these web interfaces let users access differentially expressed genes, track orthologs across the Gene Atlas plants, graphically represent co-expressed genes, and visualize gene ontology and pathway enrichments.

Super-Resolution Second-Harmonic Generation Imaging with Multifocal Structured Illumination Microscopy.

Second-harmonic generation (SHG) is a noninvasive imaging technique that enables the exploration of physiological structures without the use of an exogenous label. However, traditional SHG imaging is limited by optical diffraction, which restricts the spatial resolution. To break this limitation, we developed a novel approach called multifocal structured illumination microscopy-SHG (MSIM-SHG). By combination of SHG with MSIM, SHG-based super-resolution imaging of material molecules can be achieved, and this SHG super-resolution imaging has a wide range of applications for biological tissues and cells. MSIM-SHG achieved a lateral full width at half-maximum (fwhm) of 147 ± 13 nm and an axial fwhm of 493 ± 47 nm by imaging zinc oxide (ZnO) particles. Furthermore, MSIM-SHG was utilized to quantify collagen fiber alignment in various tissues such as the ovary, muscle, heart, kidney, and cartilage, demonstrating its feasibility for identifying collagen characteristics. MSIM-SHG has potential as a powerful tool for clinical diagnosis and biological research.

Dynamic Volumetric Imaging of Mouse Cerebral Blood Vessels In Vivo with an Ultralong Anti-Diffracting Beam.

Volumetric imaging of a mouse brain in vivo with one-photon and two-photon ultralong anti-diffracting (UAD) beam illumination was performed. The three-dimensional (3D) structure of blood vessels in the mouse brain were mapped to a two-dimensional (2D) image. The speed of volumetric imaging was significantly improved due to the long focal length of the UAD beam. Comparing one-photon and two-photon UAD beam volumetric imaging, we found that the imaging depth of two-photon volumetric imaging (80 µm) is better than that of one-photon volumetric imaging (60 µm), and the signal-to-background ratio (SBR) of two-photon volumetric imaging is two times that of one-photon volumetric imaging. Therefore, we used two-photon UAD volumetric imaging to perform dynamic volumetric imaging of mouse brain blood vessels in vivo, and obtained the blood flow velocity.

ReS2 Nanoflowers-Assisted Confined Growth of Gold Nanoparticles for Ultrasensitive and Reliable SERS Sensing.

ReS2, as a new member of transition metal dichalcogenides (TMDCs), has emerged as a promising substrate for semiconductor surface-enhanced Raman spectroscopy (SERS) due to its unique optoelectronic properties. Nevertheless, the sensitivity of the ReS2 SERS substrate poses a significant challenge to its widespread application in trace detection. In this work, we present a reliable approach for constructing a novel ReS2/AuNPs SERS composite substrate, enabling ultrasensitive detection of trace amounts of organic pesticides. We demonstrate that the porous structures of ReS2 nanoflowers can effectively confine the growth of AuNPs. By precisely controlling the size and distribution of AuNPs, numerous efficient and densely packed "hot spots" were created on the surface of ReS2 nanoflowers. As a result of the synergistic enhancement of the chemical and electromagnetic mechanisms, the ReS2/AuNPs SERS substrate demonstrates high sensitivity, good reproducibility, and superior stability in detecting typical organic dyes such as rhodamine 6G and crystalline violet. The ReS2/AuNPs SERS substrate shows an ultralow detection limit of 10-10 M and a linear detection of organic pesticide molecules within 10-6-10-10 M, which is significantly lower than the EU Environmental Protection Agency regulation standards. The strategy of constructing ReS2/AuNPs composites would contribute to the development of highly sensitive and reliable SERS sensing platforms for food safety monitoring.

High-spatial-resolution φ-OFDR shape sensor based on multicore optical fiber with femtosecond-laser-induced permanent scatter arrays.

An optical fiber φ-OFDR shape sensor with a submillimeter spatial resolution of 200 µm was demonstrated by using femtosecond-laser-induced permanent scatter array (PS array) multicore fiber (MCF). A PS array was successfully inscribed in each slightly twisted core of the 400-mm-long MCF. The two-dimensional (2D) and three-dimensional (3D) shapes of the PS-array-inscribed MCF were successfully reconstructed by using PS-assisted φ-OFDR, vector projections, and the Bishop frame based on the PS-array-inscribed MCF. The minimum reconstruction error per unit length of the 2D and 3D shape sensor was 2.21% and 1.45%, respectively.

Tunable mode convertor based on fiber Bragg grating inscribed in graded-index nine-mode fiber.

A tunable mode convertor is experimentally demonstrated based on a fiber Bragg grating (FBG), which is fabricated in a graded-index nine-mode fiber by using a femtosecond laser. Nine linearly polarized (LP) modes were excited and the coupling efficiency of them can reach 90%. By adjusting the polarization controller, the ±1st-, ±2nd-, ±3rd-, and ±4th-order orbital angular momentum (OAM) modes were excited, which means the OAM tuning of 0-±1ℏ, 0-±2ℏ, 0-±3ℏ, and 0-±4ℏ were achieved. LP21/LP02, LP31/LP12, LP41/LP22/LP03 modes were successfully tuned at 1556.00 nm, 1555.10 nm, and 1554.25 nm by twisting the FBG, respectively. Moreover, combined with polarization and torsion control, the tuning between 0th- and -2nd-order OAM has been realized, which is converted from the tuning between LP02 and LP21. By using this method, the OAM tuning of ±1-±3ℏ and ±4-0-±2ℏ may be further realized theoretically.

Fiber-integrated cantilever-based nanomechanical biosensors as a tool for rapid antibiotic susceptibility testing.

There is an urgent need for developing rapid and affordable antibiotic susceptibility testing (AST) technologies to inhibit the overuse of antibiotics. In this study, a novel microcantilever nanomechanical biosensor based on Fabry-Pérot interference demodulation was developed for AST. To construct the biosensor, a cantilever was integrated with the single mode fiber in order to form the Fabry-Pérot interferometer (FPI). After the attachment of bacteria on the cantilever, the fluctuations of cantilever caused by the bacterial movements were detected by monitoring the changes of resonance wavelength in the interference spectrum. We applied this methodology to Escherichia coli and Staphylococcus aureus, showing the amplitude of cantilever's fluctuations was positively related on the quantity of bacteria immobilized on the cantilever and associated with the bacterial metabolism. The response of bacteria to antibiotics was dependent on the types of bacteria, the types and concentrations of antibiotics. Moreover, the minimum inhibitory and bactericidal concentrations for Escherichia coli were obtained within 30 minutes, demonstrating the capacity of this method for rapid AST. Benefiting from the simplicity and portability of the optical fiber FPI-based nanomotion detection device, the developed nanomechanical biosensor in this study provides a promising technique for AST and a more rapid alternative for clinical laboratories.

Multifunctional carbon dots for glutathione detection and Golgi imaging.

Glutathione (GSH) is present in almost every cell in the body and plays various integral roles in many biological processes. The Golgi apparatus is a eukaryotic organelle for the biosynthesis, intracellular distribution, and secretion of various macromolecules; however, the mechanism of GSH in the Golgi apparatus has not been fully elucidated. Here, specific and sensitive sulfur-nitrogen co-doped carbon dots (SNCDs) with orange-red fluorescence was synthesized for the detection of GSH in the Golgi apparatus. The SNCDs have a Stokes shift of 147 nm and excellent fluorescence stability, and they exhibited excellent selectivity and high sensitivity to GSH. The linear response of the SNCDs to GSH was in the range of 10-460 µM (LOD = 0.25 µΜ). More importantly, we used SNCDs with excellent optical properties and low cytotoxicity as probes, and successfully realized golgi imaging in HeLa cells and GSH detection at the same time.

Transcriptome and DNA methylome divergence of inflorescence development between 2 ecotypes in Panicum hallii.

The morphological diversity of the inflorescence determines flower and seed production, which is critical for plant adaptation. Hall's panicgrass (Panicum hallii, P. hallii) is a wild perennial grass that has been developed as a model to study perennial grass biology and adaptive evolution. Highly divergent inflorescences have evolved between the 2 major ecotypes in P. hallii, the upland ecotype (P. hallii var hallii, HAL2 genotype) with compact inflorescence and large seed and the lowland ecotype (P. hallii var filipes, FIL2 genotype) with an open inflorescence and small seed. Here we conducted a comparative analysis of the transcriptome and DNA methylome, an epigenetic mark that influences gene expression regulation, across different stages of inflorescence development using genomic references for each ecotype. Global transcriptome analysis of differentially expressed genes (DEGs) and co-expression modules underlying the inflorescence divergence revealed the potential role of cytokinin signaling in heterochronic changes. Comparing DNA methylome profiles revealed a remarkable level of differential DNA methylation associated with the evolution of P. hallii inflorescence. We found that a large proportion of differentially methylated regions (DMRs) were located in the flanking regulatory regions of genes. Intriguingly, we observed a substantial bias of CHH hypermethylation in the promoters of FIL2 genes. The integration of DEGs, DMRs, and Ka/Ks ratio results characterized the evolutionary features of DMR-associated DEGs that contribute to the divergence of the P. hallii inflorescence. This study provides insights into the transcriptome and epigenetic landscape of inflorescence divergence in P. hallii and a genomic resource for perennial grass biology.

Simultaneous measurement of humidity and temperature based on fiber-tip microcantilever cascaded with fiber Bragg grating.

We demonstrated a hybrid sensor of fiber Bragg grating (FBG) and Fabry-Perot interferometer (FPI) based on fiber-tip microcantilever for simultaneous measurement of temperature and humidity. The FPI was developed using femtosecond (fs) laser-induced two-photon polymerization to print the polymer microcantilever at the end of a single-mode fiber, achieving a humidity sensitivity of 0.348 nm/%RH (40% to 90%, when temperature = 25 °C ± 0.1 °C), and a temperature sensitivity of -0.356 nm/°C (25 to 70 °C, when RH% = 40% ± 1%). The FBG was line-by-line inscribed in the fiber core by fs laser micromachining, with a temperature sensitivity of 0.012 nm/ °C (25 to 70 °C, when RH% = 40% ± 1%). As the shift of FBG-peak on the reflection spectra is only sensitive to temperature rather than humidity, the ambient temperature can be directly measured by the FBG. The output of FBG can also be utilized as temperature compensation for FPI-based humidity measurement. Thus, the measured result of relative humidity can be decoupled from the total shift of FPI-dip, achieving the simultaneous measurement of humidity and temperature. Gaining the advantages of high sensitivity, compact size, easy packaging, and dual parameter measurement, this all-fiber sensing probe is anticipated to be applied as the key component for various applications involving the simultaneous measurement of temperature and humidity.

Free-space creation of a perfect vortex beam with fractional topological charge.

Perfect vortex beams can only propagate stably with integer topological charges. Thus, creating perfect fractional vortex beams capable of stable propagation in free space, as perfect integer vortex beams, is crucial. This study proposed perfect vortex beams carrying fractional topological charge of l + 0.5, which are special solutions of the wave equation, and can maintain stable propagation with physical laws same as integer topological charge. Perfect fractional vortex beams were created in free space, which can break the cognition of traditional fractional perfect vortex beams and promote the development of scientific fields such as optical communication, quantum sensing, and optical imaging.

Optimized femtosecond laser direct-written fiber Bragg gratings with high reflectivity and low loss.

We propose and experimentally demonstrate a femtosecond laser plane-by-plane (Pl-b-Pl) technology for inscription of high-quality fiber Bragg gratings (FBGs). The spherical aberration (SA) was introduced to elongate the focal volume, and then combined with the scanning process, an expanded rectangular refractive index modification (RIM) region can be achieved. Such RIM regions exhibit a length of 15 µm and a width of 14 µm. Note that it consists of a negative region and a positive region. We have systematically studied the influence of the overlap between the RIM region and fiber core on the spectrum of FBG. After optimizing, the core of a conventional single-mode fiber (SMF) is covered completely by using the positive RIM region, resulting in a significant enhancement of the coupling strength coefficient (i.e., 3177.6 m-1). A 500 µm long FBG assembled by using these RIM regions can achieve a high reflectivity of 95.83%. Moreover, the cladding mode resonances in transmission spectrum are suppressed thoroughly, since the localized effect in RIM region was avoided. In addition, this FBG exhibits a high birefringence of 2.13 × 10-4. Therefore, the proposed fabrication method can be used to inscribe high-quality FBGs that could be used in many fields such as communication, fiber laser, polarization-selective filtering and multi-parameter sensing.