Experimental demonstration on 400†nm-scale bandwidth optical parametric chirped-pulse amplification based on mixed cascaded crystals.

We present an optical parametric chirped-pulse amplification (OPCPA) based on mixed cascaded crystals, taking advantage of the unique parametric phase-matching of lithium triborate (LiB3O5, LBO) and yttrium calcium oxyborate ((YCa4O(BO3)3, YCOB) crystals. The OPCPA properties of LBO at 880 nm and YCOB at 750 nm are studied respectively. After amplification by two LBO and two YCOB crystals, a total signal gain of 108 and spectral bandwidth close to 400 nm is obtained. After accurate dispersion compensation with a grating-pair compressor and chirped mirror compensator, a pulse duration of 9.4 fs is obtained by a SHG-frequency-resolved optical grating (FROG). This approach will be of great significance in high energy amplifier for high peak power few-cycle laser sources.

Photothermal vortex interferometer with azimuthal complex spectra analysis for the measurement of laser-induced nanoscale thermal lens dynamics.

A photothermal vortex interferometer (PTVI) is proposed to fill the gap of full-field measurement of the laser-induced nanoscale thermal lens dynamics of optical elements. The PTVI produces a multi-ring petal-like interferogram by the coaxial coherent superposition of the high-order conjugated Laguerre-Gaussian beams. The non-uniform optical path change (OPC) profile resulting from the thermal lens causes the petals of the interferogram at the different radii to shift by the different azimuths. To demodulate such an interferogram, an azimuthal complex spectra analysis is presented by using a camera with a pixelated multi-ring pattern written on its sensor to extract multiple azimuthal intensity profiles synchronously from the interferogram. Therefore, the OPC profile can be determined dynamically from the complex spectra of the azimuthal intensity profiles at the main frequency components. An analytical thermophysical model of the thermal lens is given, and the basic principle of the azimuthal complex spectra analysis is revealed. A proof-of-concept experiment is demonstrated using a N-BK7 glass sample heated by a pump laser. The results verified that the PTVI achieves the measurement accuracy of 47 pm with a standard deviation of 358 pm (3σ) and can be used for full-field measurement of the nanoscale OPC profile caused by the thermal lens dynamics. Due to the picometer-scale accuracy of the PTVI, the absorption coefficient and thermal diffusivity of the glass sample were determined to be A0 = 0.126 m-1 and D = 5.63 × 10-7 m2 s-1, respectively, which agree with the nominal ones of A0 = 0.129 m-1 and D = 5.17 × 10-7 m2 s-1. Although the PTVI is only suitable for measuring the rotationally symmetric OPC, it shows less computation burden and hardware complexity, and it is proved to be a highly sensitive and effective tool in studying optical, thermo-physical, and mechanical properties of optical elements.

Development of a confocal line-scan laser scattering probe for dark-field surface defects detection of transmissive optics.

Dark-field detection has long been used to identify micron/submicron-sized surface defects benefiting from the broadening effect of the actual defect size caused by light scattering. However, the back-side scattering of a transmissive optical slab is inevitably confused with the front-side scattering phenomenon, resulting in deterioration of the signal-to-noise ratio (SNR) of the scattering signal and false alarms for real defect detection. To this end, a confocal line-scan laser scattering probe equipped with optical sectioning ability is proposed to separate the back-side scattering from the front-side scattering. The optical sectioning ability is realized through a confocal light scattering collector, which overcomes the restriction imposed on the numerical aperture (NA) and the field of view (FOV), reaching an FOV length of 90 mm and NA of 0.69. The line-scan principle of the probe protects itself from crosstalk because it produces only a laser spot on the tested surface in an instant. Experimental results verified that the probe has a line-scan length of 90 mm with a uniformity better than 98%, an rms electronic noise of 3.4 mV, and an rms background noise of 6.4 mV with laser on. The probe can reject the false back-side scattering light for a 2 mm thick fused silica slab at 17.1 dB SNR and operate at a high imaging efficiency of 720 mm2/s with a minimum detectability limit of 1.4 µm at 12 dB SNR. This work put forward an effective method with great application value for submicron-sized defect detection in transmissive optics.

Genomic analyses of wild argali, domestic sheep, and their hybrids provide insights into chromosome evolution, phenotypic variation, and germplasm innovation.

Understanding the genetic mechanisms of phenotypic variation in hybrids between domestic animals and their wild relatives may aid germplasm innovation. Here, we report the high-quality genome assemblies of a male Pamir argali (O ammon polii, 2n = 56), a female Tibetan sheep (O aries, 2n = 54), and a male hybrid of Pamir argali and domestic sheep, and the high-throughput sequencing of 425 ovine animals, including the hybrids of argali and domestic sheep. We detected genomic synteny between Chromosome 2 of sheep and two acrocentric chromosomes of argali. We revealed consistent satellite repeats around the chromosome breakpoints, which could have resulted in chromosome fusion. We observed many more hybrids with karyotype 2n = 54 than with 2n = 55, which could be explained by the selfish centromeres, the possible decreased rate of normal/balanced sperm, and the increased incidence of early pregnancy loss in the aneuploid ewes or rams. We identified genes and variants associated with important morphological and production traits (e.g., body weight, cannon circumference, hip height, and tail length) that show significant variations. We revealed a strong selective signature at the mutation (c.334C > A, p.G112W) in TBXT and confirmed its association with tail length among sheep populations of wide geographic and genetic origins. We produced an intercross population of 110 F2 offspring with varied number of vertebrae and validated the causal mutation by whole-genome association analysis. We verified its function using CRISPR-Cas9 genome editing. Our results provide insights into chromosomal speciation and phenotypic evolution and a foundation of genetic variants for the breeding of sheep and other animals.

A laser wakefield acceleration facility using SG-II petawatt laser system.

Laser wakefield acceleration (LWFA) using PW-class laser pulses generally requires cm-scale laser-plasma interaction Rayleigh length, which can be realized by focusing such pulses inside a long underdense plasma with a large f-number focusing optic. Here, we present a new PW-based LWFA instrument at the SG-II 5 PW laser facility, which employs f/23 focusing. The setup also adapted an online probing of the plasma density via Nomarski interferometry using a probe laser beam having 30 fs pulse duration. By focusing 1-PW, 30-fs laser pulses down to a focal spot of 230 µm, the peak laser intensity reached a mild-relativistic level of 2.6 × 1018 W/cm2, a level modest for standard LWFA experiments. Despite the large aspect ratio of >25:1 (transverse to longitudinal dimensions) of the laser pulse, electron beams were observed in our experiment only when the laser pulse experienced relativistic self-focusing at high gas-pressure thresholds, corresponding to plasma densities higher than 3 × 1018 cm-3.

Simple single-shot complete spatiotemporal intensity and phase measurement of an arbitrary ultrashort pulse using coherent modulation imaging.

We propose a simple single-shot spatiotemporal measurement technique called coherent modulation imaging for the spatio-spectrum (CMISS), which reconstructs the full three-dimensional high-resolution characteristics of ultrashort pulses based on frequency-space division and coherent modulation imaging. We demonstrated it experimentally by measuring the spatiotemporal amplitude and phase of a single pulse with a spatial resolution of 44 µm and a phase accuracy of 0.04 rad. CMISS has good potential for high-power ultrashort-pulse laser facilities and can measure even spatiotemporally complicated pulses with important applications.

Whole-genome sequence analysis unveils different origins of European and Asiatic mouflon and domestication-related genes in sheep.

The domestication and subsequent development of sheep are crucial events in the history of human civilization and the agricultural revolution. However, the impact of interspecific introgression on the genomic regions under domestication and subsequent selection remains unclear. Here, we analyze the whole genomes of domestic sheep and their wild relative species. We found introgression from wild sheep such as the snow sheep and its American relatives (bighorn and thinhorn sheep) into urial, Asiatic and European mouflons. We observed independent events of adaptive introgression from wild sheep into the Asiatic and European mouflons, as well as shared introgressed regions from both snow sheep and argali into Asiatic mouflon before or during the domestication process. We revealed European mouflons might arise through hybridization events between a now extinct sheep in Europe and feral domesticated sheep around 6000-5000 years BP. We also unveiled later introgressions from wild sheep to their sympatric domestic sheep after domestication. Several of the introgression events contain loci with candidate domestication genes (e.g., PAPPA2, NR6A1, SH3GL3, RFX3 and CAMK4), associated with morphological, immune, reproduction or production traits (wool/meat/milk). We also detected introgression events that introduced genes related to nervous response (NEURL1), neurogenesis (PRUNE2), hearing ability (USH2A), and placental viability (PAG11 and PAG3) into domestic sheep and their ancestral wild species from other wild species.

Sensitivity enhancement in photothermal interferometry by balanced detection of the complex response to moving excitation.

The sensitivity of photothermal detection relies on both the magnitude of the response of a sample to excitation and the way the response is sensed. We propose a highly sensitive photothermal interferometry by addressing the above two issues. One is the use of moving excitation to enable a different manner in sample heating and cooling, which results in a strong thermoelastic response of the sample. The other is the use of a balanced Mach-Zehnder interferometer with a defocused probe beam to sense the complex response induced by the phase delays taking place at the sample surface and in the surrounding air. The method was verified experimentally with a Nd-doped glass to have 68-fold sensitivity enhancement over the classical photothermal common-path interferometry.

Experimental demonstration of 1011 temporal contrast in pure nanosecond optical parametric chirped pulse amplifiers.

The temporal contrast of ultrashort and ultraintense laser pulses can significantly influence the laser-plasma interactions. As the optical parametric chirped pulse amplification (OPCPA) has been widely adopted in these laser facilities, the inherent optical parametric fluorescence, exhibiting a pedestal in the time window of the pump pulse, has become a significant problem. In this paper, we investigated experimentally its influence on the contrast of the compressed pulses at 808 nm using a multistage OPCPA amplifier. Compared to the highest value of 108 ever reported in the literature for such a type of regime, by adjusting the pump energy allocation between OPCPA stages and controlling the gain of small signal regime, we for the first time, to the best of our knowledge, realized a 1011 temporal contrast in a pure nanosecond OPCPA design at a gain exceeding 7×108, without adopting any other noise cleaning methods, such as picosecond OPCPA, cross-polarized wave generation, etc. This indicates that the OPCPA has a very significant potential for contrast improvement and to become a candidate for the future high-energy amplifiers in ultrashort high-power laser facilities.

Historical Introgression from Wild Relatives Enhanced Climatic Adaptation and Resistance to Pneumonia in Sheep.

How animals, particularly livestock, adapt to various climates and environments over short evolutionary time is of fundamental biological interest. Further, understanding the genetic mechanisms of adaptation in indigenous livestock populations is important for designing appropriate breeding programs to cope with the impacts of changing climate. Here, we conducted a comprehensive genomic analysis of diversity, interspecies introgression, and climate-mediated selective signatures in a global sample of sheep and their wild relatives. By examining 600K and 50K genome-wide single nucleotide polymorphism data from 3,447 samples representing 111 domestic sheep populations and 403 samples from all their seven wild relatives (argali, Asiatic mouflon, European mouflon, urial, snow sheep, bighorn, and thinhorn sheep), coupled with 88 whole-genome sequences, we detected clear signals of common introgression from wild relatives into sympatric domestic populations, thereby increasing their genomic diversities. The introgressions provided beneficial genetic variants in native populations, which were significantly associated with local climatic adaptation. We observed common introgression signals of alleles in olfactory-related genes (e.g., ADCY3 and TRPV1) and the PADI gene family including in particular PADI2, which is associated with antibacterial innate immunity. Further analyses of whole-genome sequences showed that the introgressed alleles in a specific region of PADI2 (chr2: 248,302,667-248,306,614) correlate with resistance to pneumonia. We conclude that wild introgression enhanced climatic adaptation and resistance to pneumonia in sheep. This has enabled them to adapt to varying climatic and environmental conditions after domestication.

Paternal Origins and Migratory Episodes of Domestic Sheep.

The domestication and subsequent global dispersal of livestock are crucial events in human history, but the migratory episodes during the history of livestock remain poorly documented [1-3]. Here, we first developed a set of 493 novel ovine SNPs of the male-specific region of Y chromosome (MSY) by genome mapping. We then conducted a comprehensive genomic analysis of Y chromosome, mitochondrial DNA, and whole-genome sequence variations in a large number of 595 rams representing 118 domestic populations across the world. We detected four different paternal lineages of domestic sheep and resolved, at the global level, their paternal origins and differentiation. In Northern European breeds, several of which have retained primitive traits (e.g., a small body size and short or thin tails), and fat-tailed sheep, we found an overrepresentation of MSY lineages y-HC and y-HB, respectively. Using an approximate Bayesian computation approach, we reconstruct the demographic expansions associated with the segregation of primitive and fat-tailed phenotypes. These results together with archaeological evidence and historical data suggested the first expansion of early domestic hair sheep and the later expansion of fat-tailed sheep occurred ∼11,800-9,000 years BP and ∼5,300-1,700 years BP, respectively. These findings provide important insights into the history of migration and pastoralism of sheep across the Old World, which was associated with different breeding goals during the Neolithic agricultural revolution.

Whole-genome resequencing of wild and domestic sheep identifies genes associated with morphological and agronomic traits.

Understanding the genetic changes underlying phenotypic variation in sheep (Ovis aries) may facilitate our efforts towards further improvement. Here, we report the deep resequencing of 248 sheep including the wild ancestor (O. orientalis), landraces, and improved breeds. We explored the sheep variome and selection signatures. We detected genomic regions harboring genes associated with distinct morphological and agronomic traits, which may be past and potential future targets of domestication, breeding, and selection. Furthermore, we found non-synonymous mutations in a set of plausible candidate genes and significant differences in their allele frequency distributions across breeds. We identified PDGFD as a likely causal gene for fat deposition in the tails of sheep through transcriptome, RT-PCR, qPCR, and Western blot analyses. Our results provide insights into the demographic history of sheep and a valuable genomic resource for future genetic studies and improved genome-assisted breeding of sheep and other domestic animals.

Ultra-broadband high conversion efficiency optical parametric chirped-pulse amplification based on YCOB crystals.

We present a high efficiency and ultra-broadband optical parametric chirped-pulse amplification (OPCPA) system fully based on yttrium calcium oxyborate (YCOB) crystals. The OPCPA properties of YCOB at 808 nm are studied for both high gain and saturated amplification. The non-collinear angle is finely tuned to study the variation of gain spectrum at a certain phase-matching angle of YCOB crystals. After amplification by four YCOB crystals, a total signal gain of 0.9×109 is obtained and the FWHM spectral bandwidth is still over 100 nm. An amplified signal pulse of 182 mJ is achieved with pump energy of 440 mJ in the saturated amplification stage and the conversion efficiency is about 40%. After a four-grating compressor, a pulse duration of 20 fs is measured by a second-order autocorrelator.

Temporal contrast enhancement of ultrashort pulses using a spatiotemporal plasma-lens filter.

The spatiotemporal plasma-lens filter proposed here enhances the temporal contrast of the ultrashort pulse laser by combining plasma optics and spatial filtering. Experimentally, the spatiotemporal plasma-lens filter has improved the temporal contrast by 2 orders of magnitude with 80% laser transmission efficiency under a 1 Hz repetitive laser operation. Not only were the pre-pulse and the pedestal cleaned out, but also the rising edge of the main pulse was sharpened.

Dynamic chromatic aberration pre-compensation scheme for ultrashort petawatt laser systems.

A novel chromatic aberration pre-compensation scheme for ultrashort petawatt laser systems was proposed. The pre-compensation scheme consists of a convex lens, group of concave lenses, and a spherical reflector combined with a conventional vacuum chamber. It provides a versatile method to accurately compensate the chromatic aberration of an entire laser system via controlling the amount of propagation time delay (PTD) induced by the compensator without changing the input and output beam size. A compensator, tailored based on the proposed scheme, was designed and experimentally evaluated for the Shen-Guang-II 5PW (SG-II 5PW) laser system at Shanghai Institute of Optics and Fine Mechanics (SIOM). The experimental results verified that chromatic aberration in the laser system was almost fully compensated: the size of laser beam focused by an f/2.42 off-axis parabolic mirror (OAP) was reduced tremendously from 32×18µm2to about 4×4µm2at full width at half maximum (FWHM). The proposed scheme provides the flexibility to accurately correct chromatic aberration in high-power laser systems within a wide dynamic range.

The Genome Landscape of Tibetan Sheep Reveals Adaptive Introgression from Argali and the History of Early Human Settlements on the Qinghai-Tibetan Plateau.

Tibetan sheep are the most common and widespread domesticated animals on the Qinghai-Tibetan Plateau (QTP) and have played an essential role in the permanent human occupation of this high-altitude region. However, the precise timing, route, and process of sheep pastoralism in the QTP region remain poorly established, and little is known about the underlying genomic changes that occurred during the process. Here, we investigate the genomic variation in Tibetan sheep using whole-genome sequences, single nucleotide polymorphism arrays, mitochondrial DNA, and Y-chromosomal variants in 986 samples throughout their distribution range. We detect strong signatures of selection in genes involved in the hypoxia and ultraviolet signaling pathways (e.g., HIF-1 pathway and HBB and MITF genes) and in genes associated with morphological traits such as horn size and shape (e.g., RXFP2). We identify clear signals of argali (Ovis ammon) introgression into sympatric Tibetan sheep, covering 5.23-5.79% of their genomes. The introgressed genomic regions are enriched in genes related to oxygen transportation system, sensory perception, and morphological phenotypes, in particular the genes HBB and RXFP2 with strong signs of adaptive introgression. The spatial distribution of genomic diversity and demographic reconstruction of the history of Tibetan sheep show a stepwise pattern of colonization with their initial spread onto the QTP from its northeastern part ∼3,100 years ago, followed by further southwest expansion to the central QTP ∼1,300 years ago. Together with archeological evidence, the date and route reveal the history of human expansions on the QTP by the Tang-Bo Ancient Road during the late Holocene. Our findings contribute to a depth understanding of early pastoralism and the local adaptation of Tibetan sheep as well as the late-Holocene human occupation of the QTP.

Broadband main OPCPA amplifier at 808 nm wavelength in high deuterated DKDP crystals.

The optical aperture of ultrashort extreme intensity laser facilities, which reach 10 PW, will be beyond several hundred millimeters. DKDP is by now the only nonlinear crystal that can be grown to such diameter and used in the main optical parametric chirped-pulse amplification (OPCPA) amplifier of such a laser system. Here, at the signal wavelength of 808 nm for the first time, we experimentally present a broadband OPCPA system that consists of a pre-amplifier in BBO crystals and a main OPCPA amplifier in two 95% deuterated DKDP crystals. The final amplified spectrum bandwidth exceeds 50 nm, and a compressed pulse duration of 27 fs has been measured. The conversion efficiency of the main OPCPA amplifier reached 24%, and a net signal gain of 13 was obtained. For the high energy OPCPA amplifier, the influence due to partial absorption on the idler pulses in DKDP crystal is theoretically analyzed. The results indicate the potential utilization of high deuterated DKDP for the main OPCPA amplifiers in a multi-petawatt laser system at 808 nm wavelength.

Genome-Wide Association Analyses Highlight the Potential for Different Genetic Mechanisms for Litter Size Among Sheep Breeds.

Reproduction is an important trait in sheep breeding as well as in other livestock. However, despite its importance the genetic mechanisms of litter size in domestic sheep (Ovis aries) are still poorly understood. To explore genetic mechanisms underlying the variation in litter size, we conducted multiple independent genome-wide association studies in five sheep breeds of high prolificacy (Wadi, Hu, Icelandic, Finnsheep, and Romanov) and one low prolificacy (Texel) using the Ovine Infinium HD BeadChip, respectively. We identified different sets of candidate genes associated with litter size in different breeds: BMPR1B, FBN1, and MMP2 in Wadi; GRIA2, SMAD1, and CTNNB1 in Hu; NCOA1 in Icelandic; INHBB, NF1, FLT1, PTGS2, and PLCB3 in Finnsheep; ESR2 in Romanov and ESR1, GHR, ETS1, MMP15, FLI1, and SPP1 in Texel. Further annotation of genes and bioinformatics analyses revealed that different biological pathways could be involved in the variation in litter size of females: hormone secretion (FSH and LH) in Wadi and Hu, placenta and embryonic lethality in Icelandic, folliculogenesis and LH signaling in Finnsheep, ovulation and preovulatory follicle maturation in Romanov, and estrogen and follicular growth in Texel. Taken together, our results provide new insights into the genetic mechanisms underlying the prolificacy trait in sheep and other mammals, suggesting targets for selection where the aim is to increase prolificacy in breeding projects.

Genomic Reconstruction of the History of Native Sheep Reveals the Peopling Patterns of Nomads and the Expansion of Early Pastoralism in East Asia.

China has a rich resource of native sheep (Ovis aries) breeds associated with historical movements of several nomadic societies. However, the history of sheep and the associated nomadic societies in ancient China remains poorly understood. Here, we studied the genomic diversity of Chinese sheep using genome-wide SNPs, mitochondrial and Y-chromosomal variations in > 1,000 modern samples. Population genomic analyses combined with archeological records and historical ethnic demographics data revealed genetic signatures of the origins, secondary expansions and admixtures, of Chinese sheep thereby revealing the peopling patterns of nomads and the expansion of early pastoralism in East Asia. Originating from the Mongolian Plateau ∼5,000‒5,700 years ago, Chinese sheep were inferred to spread in the upper and middle reaches of the Yellow River ∼3,000‒5,000 years ago following the expansions of the Di-Qiang people. Afterwards, sheep were then inferred to reach the Qinghai-Tibetan and Yunnan-Kweichow plateaus ∼2,000‒2,600 years ago by following the north-to-southwest routes of the Di-Qiang migration. We also unveiled two subsequent waves of migrations of fat-tailed sheep into northern China, which were largely commensurate with the migrations of ancestors of Hui Muslims eastward and Mongols southward during the 12th‒13th centuries. Furthermore, we revealed signs of argali introgression into domestic sheep, extensive historical mixtures among domestic populations and strong artificial selection for tail type and other traits, reflecting various breeding strategies by nomadic societies in ancient China.

Whole-Genome Sequencing of Native Sheep Provides Insights into Rapid Adaptations to Extreme Environments.

Global climate change has a significant effect on extreme environments and a profound influence on species survival. However, little is known of the genome-wide pattern of livestock adaptations to extreme environments over a short time frame following domestication. Sheep (Ovis aries) have become well adapted to a diverse range of agroecological zones, including certain extreme environments (e.g., plateaus and deserts), during their post-domestication (approximately 8-9 kya) migration and differentiation. Here, we generated whole-genome sequences from 77 native sheep, with an average effective sequencing depth of ∼5× for 75 samples and ∼42× for 2 samples. Comparative genomic analyses among sheep in contrasting environments, that is, plateau (>4,000 m above sea level) versus lowland (<100 m), high-altitude region (>1500 m) versus low-altitude region (<1300 m), desert (<10 mm average annual precipitation) versus highly humid region (>600 mm), and arid zone (<400 mm) versus humid zone (>400 mm), detected a novel set of candidate genes as well as pathways and GO categories that are putatively associated with hypoxia responses at high altitudes and water reabsorption in arid environments. In addition, candidate genes and GO terms functionally related to energy metabolism and body size variations were identified. This study offers novel insights into rapid genomic adaptations to extreme environments in sheep and other animals, and provides a valuable resource for future research on livestock breeding in response to climate change.