Photoacoustic technology in combination with molecular imaging is a highly effective method for accurately diagnosing brain glioma. For glioma detection at a deeper site, contrast agents with higher photoacoustic imaging sensitivity are needed. Herein, we report a MoS2-ICG hybrid with indocyanine green (ICG) conjugated to the surface of MoS2 nanosheets. The hybrid significantly enhanced photoacoustic imaging sensitivity compared to MoS2 nanosheets. This conjugation results in remarkably high optical absorbance across a broad near-infrared spectrum, redshifting of the ICG absorption peak and photothermal/photoacoustic conversion efficiency enhancement of ICG. A tumor mass of 3.5 mm beneath the mouse scalp was clearly visualized by using MoS2-ICG as a contrast agent for the in vivo photoacoustic imaging of orthotopic glioma, which is nearly twofold deeper than the tumors imaged in our previous report using MoS2 nanosheet. Thus, combined with its good stability and high biocompatibility, the MoS2-ICG hybrid developed in this study has a great potential for high-efficiency tumor molecular imaging in translational medicine.

Next-generation sequencing has yielded a vast amount of cattle genomic data for global characterization of population genetic diversity and identification of genomic regions under natural and artificial selection. However, efficient storage, querying, and visualization of such large datasets remain challenging. Here, we developed a comprehensive database, the Bovine Genome Variation Database (BGVD). It provides six main functionalities: gene search, variation search, genomic signature search, Genome Browser, alignment search tools, and the genome coordinate conversion tool. BGVD contains information on genomic variations comprising ~60.44 M SNPs, ~6.86 M indels, 76,634 CNV regions, and signatures of selective sweeps in 432 samples from modern cattle worldwide. Users can quickly retrieve distribution patterns of these variations for 54 cattle breeds through an interactive source of breed origin map, using a given gene symbol or genomic region for any of the three versions of the bovine reference genomes (ARS-UCD1.2, UMD3.1.1, and Btau 5.0.1). Signals of selection sweep are displayed as Manhattan plots and Genome Browser tracks. To further investigate and visualize the relationships between variants and signatures of selection, the Genome Browser integrates all variations, selection data, and resources, from NCBI, the UCSC Genome Browser, and Animal QTLdb. Collectively, all these features make the BGVD a useful archive for in-depth data mining and analyses of cattle biology and cattle breeding on a global scale. BGVD is publicly available at http://animal.nwsuaf.edu.cn/BosVar.

Recently, we developed an integrated optical-resolution (OR) and acoustic-resolution (AR) PAM, which has multiscale imaging capability using different resolutions. However, limited by the scanning method, a tradeoff exists between the imaging speed and field of view, which impedes its wider applications. Here, we present an improved multiscale PAM which achieves high-speed wide-field imaging based on a homemade polygon scanner. Encoder trigger mode was proposed to avoid jittering of the polygon scanner during imaging. Distortions caused by polygon scanning were analyzed theoretically and compared with traditional types of distortions in optical-scanning PAM. Then a depth correction method was proposed and verified to compensate for the distortions. System characterization of OR-PAM and AR-PAM was performed prior to in vivo imaging. Blood reperfusion of an in vivo mouse ear was imaged continuously to demonstrate the feasibility of the multiscale PAM for high-speed imaging. Results showed that the maximum B-scan rate could be 14.65 Hz in a fixed range of 10 mm. Compared with our previous multiscale system, the imaging speed of the improved system was increased by a factor of 12.35. In vivo imaging of a subcutaneously inoculated B-16 melanoma of a mouse was performed. Results showed that the blood vasculature around the melanoma could be resolved and the melanoma could be visualized at a depth up to 1.6 mm using the multiscale PAM.

Domestic yak, cattle, and their hybrids are fundamental to herder survival at high altitudes on the Tibetan Plateau. However, little is known about their history. Bos remains are uncommon in this region, and ancient domestic yak have not been securely identified. To identify Bos taxa and investigate their initial management, we conducted zooarchaeological analyses of 193 Bos specimens and sequenced five nuclear genomes from recently excavated assemblages at Bangga. Morphological data indicated that more cattle than yak were present. Ancient mitochondrial DNA and nuclear genome sequences identified taurine cattle and provided evidence for domestic yak and yak-cattle hybridization ~2500 years ago. Reliance on diverse Bos species and their hybrid has increased cattle adaptation and herder resilience to plateau conditions. Ancient cattle and yak at Bangga were closely related to contemporary livestock, indicating early herder legacies and the continuity of cattle and yak husbandry on the Tibetan Plateau.

Chinese Yunling black goats and African Nubian goats are divergent breeds showing significant differences in body size, milk production, and environmental adaptation. However, the genetic mechanisms underlying these phenotypic differences remain to be elucidated. In this report, we provide a detailed portrait of allele-specific expression (ASE) from 54 RNA-Seq analyses across six tissues from nine F1 hybrid offspring generated by crossing the two breeds combined with 13 genomes of the two breeds. We identified a total of 524 genes with ASE, which are involved in bone development, muscle cell differentiation, and the regulation of lipid metabolic processes. We further found that 38 genes with ASE were also under directional selection by comparing 13 genomes of the two breeds; these 38 genes play important roles in metabolism, immune responses, and the adaptation to hot and humid environments. In conclusion, our study shows that the exploration of genes with ASE in F1 hybrids provides an efficient way to understand the genetic basis underlying the phenotypic differences of two diverse goat breeds.

Spermatogenesis is a complex biological process regulated by well-coordinated gene regulation, including MicroRNAs (miRNAs). miRNAs are endogenous non-coding ribonucleic acids (ncRNAs) that mainly regulate the gene expression at post-transcriptional levels. Several studies have reported miRNAs expression in bull sperm and the process of spermatogenic arrest in cattle and yak. However, studies for the identification of differential miRNA expression and its mechanisms during the developmental stages of testis still remain uncertain. In the current study, we comprehensively analyzed the expression of miRNA in bovine testes at neonatal (3 days after birth, n = 3) and mature (13 months, n = 3) stages by RNA-seq. Moreover, the role of bta-miR-146b was also investigated in regulating the proliferation and apoptosis of bovine male germline stem cells (mGSCs) followed by a series of experiments. A total of 652 miRNAs (566 known and 86 novel miRNAs) were identified, whereas 223 miRNAs were differentially expressed between the two stages. Moreover, an elevated expression level of bta-miR-146b was found in bovine testis among nine tissues, and the functional studies indicated that the overexpression of bta-miR-146b inhibited the proliferation of bovine mGSCs and promoted apoptosis. Conversely, regulation of bta-miR-146b inhibitor promoted bovine mGSCs proliferation. This study provides a basis for understanding the regulation roles of miRNAs in bovine testis development and spermatogenesis.

Chaka sheep, named after Chaka Salt Lake, are adapted to a harsh, highly saline environment. They are known for their high-grade meat quality and are a valuable genetic resource in China. Furthermore, the Chaka sheep breed has been designated a geographical symbol of agricultural products by the Chinese Ministry of Agriculture.

With the inexorable rise of global temperature, heat stress deserves more and more attention in livestock agriculture. Previous studies have shown that the mechanistic target of rapamycin (MTOR) (NC_037343.1:c.2062G>C) gene contributes to the repair of DNA damage repair and is associated with the adaptation of camels in dry and hot environments. However, it is unknown whether this mutation is related to the heat tolerance of Chinese cattle. In this study, PCR and sequencing were used to type the mutation locus in 1030 individuals of 37 cattle breeds. The analysis results showed that the frequency of G allele of the locus gradually diminished from the northern group to the southern group of native Chinese cattle, whereas the frequency of the C allele showed an opposite pattern, displaying a significant geographical difference across native Chinese cattle breeds. Additionally, an analysis of the locus in Chinese indigenous cattle revealed that this SNP was significantly associated with mean annual temperature (T), relative humidity (RH) and temperature humidity index (THI) (p < 0.01), suggesting that cattle with C allele was distributed in regions with higher T, RH and THI. In conclusion, this study proved that the mutation of MTOR gene in Chinese cattle could be associated with the heat tolerance.

SLC45A2 is involved in the synthesis of melanin transporters. We investigated the association between single nucleotide polymorphisms (SNPs) of the SLC45A2 gene and humidity and hot conditions in indigenous cattle habitat. According to the Bovine Genome Variation Database and Selective Signatures (BGVD), we explored the frequency distribution of a missense mutation (NC_037347.1: c.1543A > G, p.ser515gly) in the SLC45A2 gene in Chinese indigenous cattle. This variation from serine to glycine caused a significant change in the protein modeling structure. PCR and partial DNA sequencing were used to genotype 541 individuals, including 28 Chinese indigenous cattle breeds as well as Angus and zebu. From our results, the mutant allele frequency of this SNP in Chinese native cattle increases gradually from north to south, which is consistent with the distribution of climatic conditions in China. In addition, according to association analysis of a missense mutation (NC_037347.1: c.1543A > G) (rs525805167) in Chinese cattle, it is closely related to the annual average temperature (T), relative humidity (RH), temperature and humidity index (THI) and solar radiation time (P < 0.01). Based on the statistical analysis of the data, we assumed that rs525805167 was associated with heat tolerance traits. Simple Summary: The characteristics of Chinese indigenous cattle are closely related to their climatic environment. In China, Bos taurus is mainly distributed in the northern regions; Bos indicus is mainly distributed in southern China. In addition, the average temperature is higher in the south than in the north, and there are many mixed ancestry breeds of B. taurus and B. indicus in the middle area. The SLC45A2 gene is related to melanin synthesis, which may be closely related to heat tolerance in cattle. The purpose of our study was to investigate whether the SLC45A2 gene is related to heat tolerance in Chinese indigenous cattle.

The single nucleotide polymorphisms (SNPs) and copy number variations (CNVs) are two major genomic variants, which play crucial roles in evolutionary and phenotypic diversity.

Structural variations (SVs) in individual genomes are major determinants of complex traits, including adaptability to environmental variables. The Mongolian and Hainan cattle breeds in East Asia are of taurine and indicine origins that have evolved to adapt to cold and hot environments, respectively. However, few studies have investigated SVs in East Asian cattle genomes and their roles in environmental adaptation, and little is known about adaptively introgressed SVs in East Asian cattle.

Cattle domestication and the complex histories of East Asian cattle breeds warrant further investigation. Through analysing the genomes of 49 modern breeds and eight East Asian ancient samples, worldwide cattle are consistently classified into five continental groups based on Y-chromosome haplotypes and autosomal variants. We find that East Asian cattle populations are mainly composed of three distinct ancestries, including an earlier East Asian taurine ancestry that reached China at least ~3.9 kya, a later introduced Eurasian taurine ancestry, and a novel Chinese indicine ancestry that diverged from Indian indicine approximately 36.6-49.6 kya. We also report historic introgression events that helped domestic cattle from southern China and the Tibetan Plateau achieve rapid adaptation by acquiring ~2.93% and ~1.22% of their genomes from banteng and yak, respectively. Our findings provide new insights into the evolutionary history of cattle and the importance of introgression in adaptation of cattle to new environmental challenges in East Asia.

We report genome characterization of three native Chinese cattle breeds discovering ~34.3 M SNPs and ~3.8 M InDels using whole genome resequencing. On average, 10.4 M SNPs were shared amongst the three cattle breeds, whereas, 3.0 M, 4.9 M and 5.8 M were specific to LQ, WN and WS breeds, respectively. Gene ontology (GO)analysis revealed four immune response-related GO terms were over represented in all samples, while two immune signaling pathways were significantly over-represented in WS cattle. Altogether, we found immune related genes (PGLYRP2, ROMO1, FYB2, CD46, TSC1) in the three cattle breeds. Our study provides insights into the genetic basis of Chinese indicine adaptation to the tropic and subtropical environment, and provides a valuable resource for further investigations of genetic characteristics of the three breeds.

Guangxi Province, in the southwest of China, is one of the putative migratory corridors or domestication centers for swamp buffalo. In this study, we investigated the evolutionary status of two Guangxi native buffalo breeds (Fuzhong buffalo, n = 15; Xilin buffalo, n = 25) based on the complete mitogenome sequencing. Our results revealed rich genetic diversity in the two buffalo breeds. We detected five haplogroups (SA1, SA2, SB1, SB2, SB3) in the two Guangxi buffalo breeds, and the haplogroup SB3 in the Fuzhong buffalo. Our results showed that the haplogroup SA1 was associated with the major domestication event that involved population expansion in Guangxi buffalo. In conclusion, our findings revealed a high level of maternal genetic diversity and the phylogenetic pattern of the two Guangxi buffalo breeds.

Quantitative analysis of tumor vessels is of great significance for tumor staging and diagnosis. Photoacoustic imaging (PAI) has been proven to be an effective way to visualize comprehensive tumor vascular networks in three-dimensional (3D) volume, while previous studies only quantified the vessels projected in one plane. In this study, tumor vessels were segmented and quantified in a full 3D framework. It had been verified in the phantom experiments that the 3D quantification results have better accuracy than 2D. Furthermore, in vivo vessel images were quantified by 2D and 3D quantification methods respectively. And the difference between these two results is significant. In this study, complete vessel segmentation and quantification method within a 3D framework was implemented, which showed obvious advantage in the analysis accuracy of 3D photoacoustic images, and potentially improve tumor study and diagnosis.

Local wild bovids have been determined to be important prey on the northeastern Tibetan Plateau (NETP), where hunting game was a major subsistence strategy until the late Neolithic, when farming lifestyles dominated in the neighboring Loess Plateau. However, the species affiliation and population ecology of these prehistoric wild bovids in the prehistoric NETP remain unknown. Ancient DNA (aDNA) analysis is highly informative in decoding this puzzle. Here, we applied aDNA analysis to fragmented bovid and rhinoceros specimens dating ∼5,200 y B.P. from the Neolithic site of Shannashuzha located in the marginal area of the NETP. Utilizing both whole genomes and mitochondrial DNA, our results demonstrate that the range of the present-day tropical gaur (Bos gaurus) extended as far north as the margins of the NETP during the late Neolithic from ∼29°N to ∼34°N. Furthermore, comparative analysis with zooarchaeological and paleoclimatic evidence indicated that a high summer temperature in the late Neolithic might have facilitated the northward expansion of tropical animals (at least gaur and Sumatran-like rhinoceros) to the NETP. This enriched the diversity of wildlife, thus providing abundant hunting resources for humans and facilitating the exploration of the Tibetan Plateau as one of the last habitats for hunting game in East Asia.

Dabieshan cattle are a typical breed of southern Chinese cattle that have the characteristics of muscularity, excellent meat quality and tolerance to temperature and humidity. Based on 148 whole-genome data, our analysis disclosed the ancestry components of Dabieshan cattle with Chinese indicine (0.857) and East Asian taurine (0.139). The Dabieshan genome demonstrated a higher genomic diversity compared with the other eight populations, supported by the observed nucleotide diversity, linkage disequilibrium decay and runs of homozygosity. The candidate genes were detected by a selective sweep, which might relate to the fertility (GPX5, GPX6), feed efficiency (SLC2A5), immune response (IGLL1, BOLA-DQA2, BOLA-DQB), heat resistance (DnaJC1, DnaJC13, HSPA4), fat deposition (MLLT10) and the coat color (ASIP). We also identified the "East Asian taurine-like" segments in Dabieshan cattle, which might contribute to meat quality traits. The results revealed by the unique and valuable genomic data can build a foundation for the genetic improvement and conservation of genetic resources for indigenous cattle breeds.

Bread wheat is one of the most important and broadly studied crops. However, due to the complexity of its genome and incomplete genome collection of wild populations, the bread wheat genome landscape and domestication history remain elusive.

We investigated the effects of housing systems and dietary glucose oxidase (GOD) on the growth performance and intestinal health of Beijing You chickens (BYC). The experiment was designed as a factorial arrangement of 2 housing systems × 2 dietary treatments. Chickens were fed a basal diet or a diet with 200 U/kg GOD and were reared on the floor with deep litter or in the cages. Compared with the litter floor groups, the decreased average daily feed intake of 1 to 42 d, decreased feed conversion ratio (FCR), improved average daily gain of 42 to 77 d, and the whole period were identified in the cage rearing groups (P < 0.05). The FCR of 42 to 77 d and the whole period, the 42-d ileal pH, and 77-d jejunal and ileal pH decreased with the supplement of GOD (P < 0.05). Additionally, 16S rRNA gene of ileum contents was sequenced by high-throughput sequencing. Sequencing data indicated that the Firmicutes phylum of 42 d and the Bacteroidetes phylum were significantly higher in the litter group with GOD supplement (P < 0.05). The jejunal Occludin, Mucin-2 mRNA expression levels were higher in the litter floor groups than those in the cage rearing groups on 42 d (P < 0.05). The Mucin-2 and TNF-α mRNA expression levels increased with cage rearing on 77 d (P < 0.05). The Occludin and TLR-4 mRNA expression levels increased with the supplementation of GOD on 77 d (P < 0.05). Moreover, the upregulation effects of Occludin and ZO-1 mRNA expression levels were more obvious in the litter floor group fed with GOD diet on 77 d (P < 0.05). The serum endotoxin content of 42-day-old cage rearing groups were higher than that of the litter floor groups, and the serum endotoxin content significantly decreased with the supplement of GOD on 77 d. The results indicated that the litter floor systems were beneficial to the development of intestinal barrier junction in the early stage, but the cage systems were more conducive to the growth performance of BYC. The dietary GOD could inhibit the harmful bacteria and promote the beneficial bacteria, which might be related to the improvement of the growth performance and intestinal barrier function.

As a stimulating point in acupuncture, acupoint has unique microcirculatory features, and its dynamics vary greatly depending on health status. Acupoint sensitization is defined as the transformation of an acupoint from a "silenced status" (healthy) to an "activated status" (disease). Our previous study demonstrated that acupoint sensitization is associated with an increase in the level of local blood perfusion. However, the structural changes in microcirculation during acupoint sensitization have yet to be elucidated because the high-resolution microcirculation imaging of acupoints has been difficult to obtain. In this study, the structural changes in microcirculation at the Zusanli (ST36), Yanglingquan (GB34) and nonacupoint sites on days 0, 7 and 21 were dynamically observed during acupoint sensitization in an experimental knee osteoarthritis mouse model by using optical-resolution photoacoustic microscopy. The results showed that no significant differences in microvessel density, the distribution of vessel diameters or vascular tortuosity were observed at the GB34, ST36 or nonacupoint sites among days 0, 7 and 21. We proposed that acupoint sensitization may not be associated with the structural changes in microcirculation and that the microcirculatory changes during acupoint sensitization are more likely to be functional. The functional characteristics of the sensitized acupoints warrant further investigation.