Phylogenomics and divergence pattern of Polygonatum (Asparagaceae: Polygonateae) in the north temperate region.

Polygonatum is the largest genus of tribe Polygonateae (Asparagaceae) and is widely distributed in the temperate Northern Hemisphere, especially well diversified in southwestern China to northeastern Asia. Phylogenetic relationships of many species are still controversial. Hence it is necessary to clarify their phylogenetic relationships and infer possible reticulate relationships for the genus. In this study, genome-wide data of 43 species from Polygonatum and its closely related taxa were obtained by Hyb-Seq sequencing. The phylogenetic trees constructed from genome-wide nuclear and chloroplast sequences strongly supported the monophyly of Polygonatum with division into three major clades. A high level of incongruence was detected between nuclear and chloroplast trees as well as among gene trees within the genus, but all occurred within each major clade. However, introgression tests and reticulate evolution analyses revealed low level of gene flow and weak introgression events in the genus, suggesting hybridization and introgression were not dominant during the evolutionary diversification of Polygonatum in the Northern Hemisphere. This study provides important insights into reconstructing evolutionary relationships and speciation pattern of taxa from the north temperate flora.

Whole-genome resequencing uncovers diversity and selective sweep in Kazakh cattle.

The Kazakh cattle in the Xinjiang Uygur Autonomous Region of China are highly adaptable and have multiple uses, including milk and meat production, and use as draft animals. They are an excellent original breed that could be enhanced by breeding and hybrid improvement. However, the genomic diversity and signature of selection underlying the germplasm characteristics require further elucidation. Herein, we evaluated 26 Kazakh cattle genomes in comparison with 103 genomes of seven other cattle breeds from regions around the world to assess the Kazakh cattle genetic variability. We revealed that the relatively low linkage disequilibrium at large SNP distances was strongly correlated with the largest effective population size among Kazakh cattle. Using population structural analysis, we next demonstrated a taurine lineage with restricted Bos indicus introgression among Kazakh cattle. Notably, we identified putative selected genes associated with resistance to disease and body size within Kazakh cattle. Together, our findings shed light on the evolutionary history and breeding profile of Kazakh cattle, as well as offering indispensable resources for germplasm resource conservation and crossbreeding program implementation.

SE-VisionTransformer: Hybrid Network for Diagnosing Sugarcane Leaf Diseases Based on Attention Mechanism.

Sugarcane is an important raw material for sugar and chemical production. However, in recent years, various sugarcane diseases have emerged, severely impacting the national economy. To address the issue of identifying diseases in sugarcane leaf sections, this paper proposes the SE-VIT hybrid network. Unlike traditional methods that directly use models for classification, this paper compares threshold, K-means, and support vector machine (SVM) algorithms for extracting leaf lesions from images. Due to SVM's ability to accurately segment these lesions, it is ultimately selected for the task. The paper introduces the SE attention module into ResNet-18 (CNN), enhancing the learning of inter-channel weights. After the pooling layer, multi-head self-attention (MHSA) is incorporated. Finally, with the inclusion of 2D relative positional encoding, the accuracy is improved by 5.1%, precision by 3.23%, and recall by 5.17%. The SE-VIT hybrid network model achieves an accuracy of 97.26% on the PlantVillage dataset. Additionally, when compared to four existing classical neural network models, SE-VIT demonstrates significantly higher accuracy and precision, reaching 89.57% accuracy. Therefore, the method proposed in this paper can provide technical support for intelligent management of sugarcane plantations and offer insights for addressing plant diseases with limited datasets.

Plastid phylogenomic analyses of the Selaginella sanguinolenta group (Selaginellaceae) reveal conflict signatures resulting from sequence types, outlier genes, and pervasive RNA editing.

Different from the generally conserved plastomes (plastid genomes) of most land plants, the Selaginellaceae plastomes exhibit dynamic structure, high GC content and high substitution rates. Previous plastome analyses identified strong conflict on several clades in Selaginella, however the factors causing the conflictions and the impact on the phylogenetic inference have not been sufficiently investigated. Here, we dissect the distribution of phylogenetic signals and conflicts in Selaginella sanguinolenta group, the plastome of which is DR (direct repeats) structure and with genome-wide RNA editing. We analyzed the data sets including 22 plastomes representing all species of the S. sanguinolenta group, covering the entire geographical distribution from the Himalayas to Siberia and the Russian Far East regions. We recovered four different topologies by applying multispecies coalescent (ASTRAL) and concatenation methods (IQ-TREE and RAxML) on four data sets of PC (protein-coding genes), NC (non-coding sequences), PCN (the concatenated PC and NC), and RC (predicted RNA editing sites "C" were corrected by "T"), respectively. Six monophyletic clades, S. nummularifolia clade, S. rossii clade, S. sajanensis clade, S. sanguinolenta I clade, S. sanguinolenta II clade, and S. sanguinolenta III clade, were consistently resolved and supported by the characteristics of GC content, RNA editing frequency, and gene content. However, the relationships among these clades varied across the four topologies. To explore the underlying causes of the uncertainty, we compared the phylogenetic signals of the four topologies. We identified that the sequence types (coding versus non-coding), outlier genes (genes with extremely high |ΔGLS| values), and C-to-U RNA editing frequency in the protein-coding genes were responsible for the unstable phylogenomic relationship. We further revealed a significant positive correlation between the |ΔGLS| values and the variation coefficient of the RNA editing number. Our results demonstrated that the coalescent method performed better than the concatenation method in overcoming the problems caused by outlier genes and extreme RNA editing events. Our study particularly focused on the importance of exploring the plastid phylogenomic conflicts and suggested conducting concatenated analyses cautiously when adopting organelle genome data.

Self-pulsations in a microcavity Brillouin laser.

We demonstrate a new, to the best of our knowledge, kind of self-pulsation in a microcavity Brillouin laser. This specific self-pulsation is generated by the interplay between the Brillouin lasing and the thermo-optic effect in an optical microcavity. Intriguingly, the self-pulsation behaviors are simultaneously present in both forward input pump and backward Brillouin lasing emission. By developing a coupled-mode theory, our numerical simulations display an excellent agreement with the experimental results.

High-power, low-noise Brillouin laser on a silicon chip.

We realize a chip-based Brillouin microlaser with remarkable features of high power and low noise using a microtoroid resonator. Our Brillouin microlaser is able to output a power of up to 126 mW with a fundamental linewidth down to 245 mHz. Additionally, in the course of Brillouin lasing we observe an intriguing power saturation-like effect, which can be attributed to complex thermo-optic-effect-induced mode mismatch between the pump and Brillouin modes. To have a quantitative understanding of this phenomenon, we develop a model by simultaneously considering Brillouin lasing and the thermo-optic effect occurring in the microcavity. Of importance, our theoretical results match well with experimentally measured data.

Genomic landscape of a mouse model of diffuse-type gastric adenocarcinoma.

BACKGROUND: There is a need for a model of diffuse-type gastric cancer that captures the features of the disease, facilitates the study of its mechanisms, and aids the development of potential therapies. One such model may be Cdh1 and Trp53 double conditional knockout (DCKO) mice, which have histopathological features similar to those of human diffuse-type gastric cancer. However, a genomic profile of this mouse model has yet to be completed. METHODS: Whole-genome sequences of tumors from eight DCKO mice were analyzed and their molecular features were compared with those of human gastric adenocarcinoma. RESULTS: DCKO mice gastric cancers harbored single nucleotide variations and indel patterns comparable to those of human genomically stable gastric cancers, whereas their copy number variation fraction and ploidy were more similar to human chromosomal instability gastric cancers (perhaps due to Trp53 knockout). Copy number variations dominated changes in cancer-related genes in DCKO mice, with typical high-level amplifications observed for oncogenic drivers, e.g., Myc, Ccnd1, and Cdks, as well as gastrointestinal transcription factors, e.g., Gata4, Foxa1, and Sox9. Interestingly, frequent alterations in gastrointestinal transcription factors in DCKO mice indicated their potential role in tumorigenesis. Furthermore, mouse gastric cancer had a reproducible but smaller number of mutational signatures than human gastric cancer, including the potentially acid-related signature 17, indicating shared tumorigenic etiologies in humans and mice. CONCLUSIONS: Cdh1/Trp53 DCKO mice have similar genomic features to those found in human gastric cancer; hence, this is a suitable model for further studies of diffuse-type gastric cancer mechanisms and therapies.

A 67-bp variable duplication in the promoter region of the ADIPOQ is associated with milk traits in Xinjiang brown cattle.

Adiponectin, also known as ADIPOQ, is a hormone protein secreted by adipocytes. The ADIPOQ gene is expressed primarily in adipose tissue, and the encoded protein circulates in the bloodstream and has the potential to regulate both animal fat metabolism and hormone production. Our previous work uncovered a 67-bp variable duplication in the promoter region of ADIPOQ, which reduced the basal transcriptional activity of ADIPOQ in the 3T3_L1 cell and also inhibits the ADIPOQ mRNA expression in adipose tissue. Accordingly, the present study aimed to identify the relationship between the 67-bp structural variations in ADIPOQ promoter region and the milk traits of Xinjiang brown cattle (XJBC). The results revealed two genotypes, DD and ID, in the XJBC, and minor allelic frequency (MAF) for the 'I' allele was more than 1%. Moreover, the association analysis revealed that the 67-bp duplication in the promoter region of the ADIPOQ gene was significantly correlated with the 305 days of milk production volume, fat yield, and milk fat percentage in the XJBC (p < 0.05). These results obtained in this study suggested that the identified variable duplication could be considered as the potential genetic marker for improving milk traits of XJBC.

Brillouin-Kerr Soliton Frequency Combs in an Optical Microresonator.

By generating a Brillouin laser in an optical microresonator, we realize a soliton Kerr microcomb through exciting the Kerr frequency comb using the generated Brillouin laser in the same cavity. The intracavity Brillouin laser pumping scheme enables us to access the soliton states with a blue-detuned input pump. Because of the ultranarrow linewidth and the low-noise properties of the generated Brillouin laser, the observed soliton microcomb exhibits narrow-linewidth comb lines and stable repetition rate. Also, we demonstrate a low-noise microwave signal with phase noise of -49 dBc/Hz at 10 Hz, -130 dBc/Hz at 10 kHz, and -149 dBc/Hz at 1 MHz offsets for a 10.43 GHz carrier with only a free-running input pump. The easy operation of the Brillouin-Kerr soliton microcomb with excellent performance makes our scheme promising for practical applications.

Effects of eight InDel variants in FHIT on milk traits in Xinjiang brown cattle.

In our previous genome-wide association study (GWAS), we identified the fragile histidine triad diadenosine triphosphatase (FHIT) gene in Xinjiang brown cattle (XJBC) as a candidate gene associated with cattle productive traits, with potential application in mark-assisted selection (MAS) in cattle breeding. FHIT is a prototype of a class of tumor suppressor genes that contain genomic loci mapped to common fragile loci. Here, 388 healthy and unrelated XJBC were selected to identify insertion/deletion (InDel) variants in the bovine FHIT and assess their effects on milk traits. Eight of the thirteen InDel loci were found to be polymorphic in FHIT. The polymorphism information content of the eight loci ranged from 0.061 to 0.375. The correlation analysis showed that all the new InDel variants were significantly related to six different milk traits (p < 0.05). The following variants presented a significant relationship with productive traits: P2-23bp with the 305 milk yield (p = 0.005) in the sixth parity; P3-24bp with the milk fat yield (p = 0.009) in the third parity; P5-21bp with the somatic cell score (p = 0.001) in the first parity and with the milk protein percentage (p = 0.002) in the sixth parity; and P7-26bp with the somatic cell score (p = 0.003) in the sixth parity. These findings will help evaluate InDel genotypes, within and between cattle breeds and identify potential target loci to accelerate progress in MAS in cattle breeding.

Genome-wide association study of milk and reproductive traits in dual-purpose Xinjiang Brown cattle.

BACKGROUND: Dual-purpose cattle are more adaptive to environmental challenges than single-purpose dairy or beef cattle. Balance among milk, reproductive, and mastitis resistance traits in breeding programs is therefore more critical for dual-purpose cattle to increase net income and maintain well-being. With dual-purpose Xinjiang Brown cattle adapted to the Xinjiang Region in northwestern China, we conducted genome-wide association studies (GWAS) to dissect the genetic architecture related to milk, reproductive, and mastitis resistance traits. Phenotypic data were collected for 2410 individuals measured during 1995-2017. By adding another 445 ancestors, a total of 2855 related individuals were used to derive estimated breeding values for all individuals, including the 2410 individuals with phenotypes. Among phenotyped individuals, we genotyped 403 cows with the Illumina 150 K Bovine BeadChip. RESULTS: GWAS were conducted with the FarmCPU (Fixed and random model circulating probability unification) method. We identified 12 markers significantly associated with six of the 10 traits under the threshold of 5% after a Bonferroni multiple test correction. Seven of these SNPs were in QTL regions previously identified to be associated with related traits. One identified SNP, BovineHD1600006691, was significantly associated with both age at first service and age at first calving. This SNP directly overlapped a QTL previously reported to be associated with calving ease. Within 160 Kb upstream and downstream of each significant SNP identified, we speculated candidate genes based on functionality. Four of the SNPs were located within four candidate genes, including CDH2, which is linked to milk fat percentage, and GABRG2, which is associated with milk protein yield. CONCLUSIONS: These findings are beneficial not only for breeding through marker-assisted selection, but also for genome editing underlying the related traits to enhance the overall performance of dual-purpose cattle.

Compared the physiological response of two petroleum tolerant-contrasting plants to petroleum stress.

Petroleum not only benefits the world economy but also contaminates the soil. In order to select the plants tolerant to petroleum, the physiological response of two petroleum tolerant-contrasting plants, Mirabilis jalapa and Orychophragmus violace, were investigated in variation of petroleum-contaminated soils (0, 5, 10, 20, and 40 g petroleum per kg soil) for 120 d. Petroleum degradation rate, seeds germination rate, free proline, and superoxide dismutase and peroxidase activities of M. jalapa were higher than that of O. violace under petroleum stress. However, the decrease rate of soluble protein, plant height, chlorophyll, and root fresh weight was greater in O. violace as compared to M. jalapa. Pearson correlation coefficient analysis was conducted, which indicated that the higher tolerance of M. jalapa was correlated with the higher level of free proline and antioxidative enzyme activities. Besides, the 10 g petroleum per kg soil may be appropriate for petroleum-tolerant plants selection, in which petroleum significantly restrain growth in O. violace but not in M. jalapa.

Rapid and enzyme-free nucleic acid detection based on exponential hairpin assembly in complex biological fluids.

Herein, we have developed a rapid and enzyme-free nucleic acid amplification detection method that combined the exponential self-assembly of four DNA hairpins and the FRET pair Cy3 and Cy5. This strategy was very ingenious and rapid, and could detect nucleic acids at concentrations as low as 10 pM in 15 min in biological fluids.

Detection of thrombin based on aptamer isothermal exponential signal amplification technique.

In this report, a strategy based on an aptameric molecule switch to realize homogeneous and isothermal signal exponential amplification and protein detection has been described. This method was simple and sensitive, allowing detection of as low as 2.6 × 10(-12) M thrombin.

Fault-tolerant controller design based on adaptive backstepping for tower cranes with actuator faults.

Due to the widespread application and significant investment required for a single crane, there is an increased emphasis on crane safety and service life. Fault-tolerant control as an effective solution to unexpected faults has been widely studied recently. However, most fault-tolerant control methods require redundant actuators or a complex design process, which is unsuitable for the tower crane. Following these problems, a fault-tolerant controller based on an adaptive backstepping technique is proposed. Firstly, the system states are reconstructed and written as a cascade system. Secondly, a fixed-time convergence optimized backstepping controller is proposed to achieve smooth control of the tower crane without generating sudden or abrupt values. Then, an adaptive approach has been proposed to update fault parameters for the crane system in case of a sudden fault occurrence. Finally, after conducting comparison tests, it has been determined that the proposed controller not only performs exceptionally well in terms of position accuracy and swing elimination, but also maintains a satisfactory control performance when faced with sudden faults.

Strong interactions between solitons and background light in Brillouin-Kerr microcombs.

Dissipative Kerr-soliton combs are laser pulses regularly sustained by a localized solitary wave on top of a continuous-wave background inside a nonlinear resonator. Usually, the intrinsic interactions between the background light and solitons are weak and localized. Here, we demonstrate a strong interaction between the generated soliton comb and the background light in a Brillouin-Kerr microcomb system. This strong interaction enables the generation of a monostable single-soliton microcomb on a silicon chip. Also, new phenomena related to soliton physics including solitons hopping between different states as well as controlling the formations of the soliton states by the pump power, are observed owing to such strong interaction. Utilizing this monostable single-soliton microcomb, we achieve the 100% deterministic turnkey operation successfully without any feedback controls. Importantly, it allows to output turnkey ultra-low-noise microwave signals using a free-running pump.

Comparative Study of Bacterial Microbiota Differences in the Rumen and Feces of Xinjiang Brown and Holstein Cattle.

Xinjiang Brown cattle are a unique and widely distributed breed of dual-purpose cattle in the Xinjiang area of China, whose milk production performance differs from Holstein cattle. It has been known that variations in bacterial species of the gastrointestinal tract influence milk protein, fat, and lactose synthesis. However, the microbiota differences between Xinjiang Brown and Holstein cattle are less known. This study aims to compare the bacterial community composition of the rumen and feces of these two cattle breeds under the same dietary and management conditions. The 16s rRNA sequencing data and milk production of 18 Xinjiang Brown cows and 20 Holstein cows on the same farm were obtained for analysis. The results confirmed differences in milk production between Xinjiang Brown and Holstein cattle. Microbiota with different relative abundance between these two cattle breeds were identified, and their biological functions might be related to milk synthesis. This study increases the understanding of the differences in microbiota between Xinjiang Brown and Holstein cattle and might provide helpful information for microbiota composition optimization of these dairy cattle.

Genomic prediction based on a joint reference population for the Xinjiang Brown cattle.

Introduction: Xinjiang Brown cattle constitute the largest breed of cattle in Xinjiang. Therefore, it is crucial to establish a genomic evaluation system, especially for those with low levels of breed improvement. Methods: This study aimed to establish a cross breed joint reference population by analyzing the genetic structure of 485 Xinjiang Brown cattle and 2,633 Chinese Holstein cattle (Illumina GeneSeek GGP bovine 150 K chip). The Bayes method single-step genome-wide best linear unbiased prediction was used to conduct a genomic evaluation of the joint reference population for the milk traits of Xinjiang Brown cattle. The reference population of Chinese Holstein cattle was randomly divided into groups to construct the joint reference population. By comparing the prediction accuracy, estimation bias, and inflation coefficient of the validation population, the optimal number of joint reference populations was determined. Results and Discussion: The results indicated a distinct genetic structure difference between the two breeds of adult cows, and both breeds should be considered when constructing multi-breed joint reference and validation populations. The reliability range of genome prediction of milk traits in the joint reference population was 0.142-0.465. Initially, it was determined that the inclusion of 600 and 900 Chinese Holstein cattle in the joint reference population positively impacted the genomic prediction of Xinjiang Brown cattle to certain extent. It was feasible to incorporate the Chinese Holstein into Xinjiang Brown cattle population to form a joint reference population for multi-breed genomic evaluation. However, for different Xinjiang Brown cattle populations, a fixed number of Chinese Holstein cattle cannot be directly added during multi-breed genomic selection. Pre-evaluation analysis based on the genetic structure, kinship, and other factors of the current population is required to ensure the authenticity and reliability of genomic predictions and improve estimation accuracy.

Estimation of Genetic Parameters for Early Growth Traits in Luzhong Mutton Sheep.

In this study, six different animal models were fitted, and the constrained maximum likelihood method was used to assess the genetic parameters and genetic trends of early growth traits in Luzhong mutton sheep. The experimental data of this study included the newborn weight (BWT, N = 2464), weaning weight (WWT, N = 2923), weight at 6 months of age (6WT, N = 2428), average daily weight gain from birth to weaning (ADG1, N = 2424), and average daily weight gain from weaning to 6 months of age (ADG2, N = 1836) in Luzhong mutton sheep (2015~2019). The best model for the genetic parameters of the five traits in Luzhong mutton sheep was identified as Model 4 using the Akaike information criterion (AIC) and likelihood ratio test (LRT) methods, in which the estimated values of direct heritability for the BWT, WWT, 6WT, ADG1, and ADG2 were 0.156 ± 0.057, 0.547 ± 0.031, 0.653 ± 0.031, 0.531 ± 0.035, and 0.052 ± 0.046, respectively, and the values for maternal heritability were 0.201 ± 0.100, 0.280 ± 0.047, 0.197 ± 0.053, 0.275 ± 0.052, and 0.081 ± 0.092, respectively. The genetic correlation between the ADG2 and WWT was negative, and the genetic and phenotypic correlations among the remaining traits were positive. In this study, maternal effects had a more significant influence on early growth traits in Luzhong mutton sheep. In conclusion, to effectively improve the accuracy of genetic parameter estimation, maternal effects must be fully considered to ensure more accurate and better breeding planning.

DNA methylation patterns in the peripheral blood of Xinjiang brown cattle with variable somatic cell counts.

The use of wide-ranging dairy herd improvement (DHI) measurements has resulted in the investigation of somatic cell count (SCC) and the identification of many genes associated with mastitis resistance. In this study, blood samples of Xinjiang brown cattle with different SCCs were collected, and genome-wide DNA methylation was analyzed by MeDIP-seq. The results showed that peaks were mostly in intergenic regions, followed by introns, exons, and promoters. A total of 1,934 differentially expressed genes (DEGs) associated with mastitis resistance in Xinjiang brown cattle were identified. The enrichment of differentially methylated CpG islands of the TRAPPC9 and CD4 genes was analyzed by bisulfate genome sequencing. The methylation rate of differentially methylated CpGs was higher in the TRAPPC9 gene of cattle with clinical mastitis (mastitis group) compared with healthy cattle (control group), while methylation of differentially methylated CpGs was significantly lower in CD4 of the mastitis group compared with the control group. RT-qRCR analysis showed that the mastitis group had significantly reduced expression of CD4 and TRAPPC9 genes compared to the control group (p < 0.05). Furthermore, Mac-T cells treated with lipopolysaccharide and lipoteichoic acid showed significant downregulation of the TRAPPC9 gene in the mastitis group compared with the control group. The identified epigenetic biomarkers provide theoretical reference for treating cow mastitis, breeding management, and the genetic improvement of mastitis resistance in Xinjiang brown cattle.