Genomic mechanisms of climate adaptation in polyploid bioenergy switchgrass.

Long-term climate change and periodic environmental extremes threaten food and fuel security1 and global crop productivity2-4. Although molecular and adaptive breeding strategies can buffer the effects of climatic stress and improve crop resilience5, these approaches require sufficient knowledge of the genes that underlie productivity and adaptation6-knowledge that has been limited to a small number of well-studied model systems. Here we present the assembly and annotation of the large and complex genome of the polyploid bioenergy crop switchgrass (Panicum virgatum). Analysis of biomass and survival among 732 resequenced genotypes, which were grown across 10 common gardens that span 1,800 km of latitude, jointly revealed extensive genomic evidence of climate adaptation. Climate-gene-biomass associations were abundant but varied considerably among deeply diverged gene pools. Furthermore, we found that gene flow accelerated climate adaptation during the postglacial colonization of northern habitats through introgression of alleles from a pre-adapted northern gene pool. The polyploid nature of switchgrass also enhanced adaptive potential through the fractionation of gene function, as there was an increased level of heritable genetic diversity on the nondominant subgenome. In addition to investigating patterns of climate adaptation, the genome resources and gene-trait associations developed here provide breeders with the necessary tools to increase switchgrass yield for the sustainable production of bioenergy.

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.

A generalist-specialist trade-off between switchgrass cytotypes impacts climate adaptation and geographic range.

Polyploidy results from whole-genome duplication and is a unique form of heritable variation with pronounced evolutionary implications. Different ploidy levels, or cytotypes, can exist within a single species, and such systems provide an opportunity to assess how ploidy variation alters phenotypic novelty, adaptability, and fitness, which can, in turn, drive the development of unique ecological niches that promote the coexistence of multiple cytotypes. Switchgrass, Panicum virgatum, is a widespread, perennial C4 grass in North America with multiple naturally occurring cytotypes, primarily tetraploids (4×) and octoploids (8×). Using a combination of genomic, quantitative genetic, landscape, and niche modeling approaches, we detect divergent levels of genetic admixture, evidence of niche differentiation, and differential environmental sensitivity between switchgrass cytotypes. Taken together, these findings support a generalist (8×)­specialist (4×) trade-off. Our results indicate that the 8× represent a unique combination of genetic variation that has allowed the expansion of switchgrass' ecological niche and thus putatively represents a valuable breeding resource.

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.

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.

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-spatial-resolution φ-OFDR shape sensor based on multicore optical fiber with femtosecond-laser-induced permanent scatter arrays: publisher's note.

This publisher's note contains a correction to Opt. Lett.48, 3219 (2023)10.1364/OL.486644.

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.

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.

A Pleiotropic Flowering Time QTL Exhibits Gene-by-Environment Interaction for Fitness in a Perennial Grass.

Appropriate flowering time is a crucial adaptation impacting fitness in natural plant populations. Although the genetic basis of flowering variation has been extensively studied, its mechanisms in nonmodel organisms and its adaptive value in the field are still poorly understood. Here, we report new insights into the genetic basis of flowering time and its effect on fitness in Panicum hallii, a native perennial grass. Genetic mapping in populations derived from inland and coastal ecotypes identified flowering time quantitative trait loci (QTL) and many exhibited extensive QTL-by-environment interactions. Patterns of segregation within recombinant hybrids provide strong support for directional selection driving ecotypic divergence in flowering time. A major QTL on chromosome 5 (q-FT5) was detected in all experiments. Fine-mapping and expression studies identified a gene with orthology to a rice FLOWERING LOCUS T-like 9 (PhFTL9) as the candidate underlying q-FT5. We used a reciprocal transplant experiment to test for local adaptation and the specific impact of q-FT5 on performance. We did not observe local adaptation in terms of fitness tradeoffs when contrasting ecotypes in home versus away habitats. However, we observed that the coastal allele of q-FT5 conferred a fitness advantage only in its local habitat but not at the inland site. Sequence analyses identified an excess of low-frequency polymorphisms at the PhFTL9 promoter in the inland lineage, suggesting a role for either selection or population expansion on promoter evolution. Together, our findings demonstrate the genetic basis of flowering variation in a perennial grass and provide evidence for conditional neutrality underlying flowering time divergence.

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.

Fast all-fiber ultraviolet photodetector based on an Ag-decorated ZnO micro-pillar.

There are urgent demands of ultraviolet (UV) photodetectors with high sensitivity and fast response due to the wide application of ultraviolet light in the fields of medical treatment, space exploration, optical communication and semiconductor industry. The response speed of traditional ZnO-based UV photodetectors is always limited by the carrier mobility and electrical resistance caused by the external circuits. Utilizing the all-optical detection method may replace the complex circuit structure and effectively improve the response speed of photodetectors. Here, a fast-response fiber-optic UV photodetector is proposed, where a ZnO micro-pillar is fixed on the end face of a fiber-tip and acts as a Fabry-Pérot interferometer (FPI). Under the irradiation of UV light, the photo-generated carriers change the refractive index of the ZnO micro-pillar, leading to a redshift of the interference wavelengths of the ZnO FPI. To enhance this effect, a discontinuous Ag film with an island-like structure is coated on the surface of ZnO micro-pillars through magnetron sputtering, and therefore the sensitivity of the proposed device achieves to 1.13 nm/(W·cm-2), which is 3.9 times higher than that of without Ag-decoration, due to the intensification of photo-carrier change with the help of the Schottky junction formed between Ag film and ZnO micro-pillar. Meanwhile, since the response speed of the proposed device is mainly determined by the temporal RI change of ZnO micro-pillar, the fiber-optic UV photodetector also shows very fast response with a rise time of 35 ns and a decay time of 40 µs. The demonstrated structure takes full advantage of optical fiber devices, exhibiting compactness, flexibility, fast response and immune to electromagnetic interference, which paves a new way for the next generation of photodetection devices.

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.

Orthogonal single-mode helical Bragg gratings created in fiber cladding for vector bending measurement.

We demonstrate a novel, to the best of our knowledge, two-dimensional vector bending sensor based on orthogonal helical Bragg gratings inscribed in the cladding of a conventional single-mode fiber (SMF). The helical cladding fiber Bragg gratings (HCFBGs) are created by using a femtosecond laser direct writing technology and a quarter-pitch graded index fiber (GIF) is used in front of the HCFBGs to diverge the core mode into fiber cladding. In contrast to the multimode resonance observed in conventional cladding Bragg gratings inscribed by using a femtosecond laser point-by-point (PbP) or line-by-line (LbL) technology, the proposed HCFBGs exhibit stable narrowband single-mode Bragg resonance. An HCFBG with a low peak reflectivity of -50.77 dB and a narrow bandwidth of 0.66 nm was successfully fabricated by using a lateral offset of 45 µm between the HCFBG and the fiber core axis. Moreover, two orthogonal HCFBGs were fabricated in the SMF cladding and used for vector bending sensing. Strong orientation dependence could be seen in omnidirectional bending measurement, exhibiting a maximum bending sensitivity of up to 50.0 pm/m-1, which is comparable to that in a multicore FBG. In addition, both the orientation and amplitude of bending vector could be reconstructed by using the measured Bragg wavelength shifts in two orthogonal HCFBGs. As such, the proposed HCFBGs could be used in many applications, such as structural health monitoring, robotic arms, and medical instruments.

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.

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.

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.

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.