Genome-wide association studies for the number of piglets born alive and dead in Dongliao black pigs.

Litter size (total number born) trait has a great impact on the economic success of pork production. The total number born consists of the number of piglets born alive and dead. To clarify the genetic background of litter size, genome-wide association studies were undertaken in the present study. Samples of DNA were collected and genotyped using the Porcine 50K BeadChip from 723 Dongliao Black sows. Using three different models (BLINK, FarmCPU, and MLM), a total of 155 significant SNPs were discovered, six of which had been reported in previous pig reproduction association studies. We suggest that rs81318434, located in the GLI3 gene, might be the promising candidate affecting litter size trait. Our findings may provide insights for uncovering the genetic mechanisms for the litter size of pigs.

Stereochemically Active Tin(II)-Induced Enhancement of Birefringence in SnII SnIV (PO4 )2 and SrSn(PO4 )PO2 (OH)2.

Two new tin(II) phosphates, SnII SnIV (PO4 )2 and SrSn(PO4 )PO2 (OH)2 , were synthesized by the high-temperature solution method and hydrothermal method, respectively. Theoretical study indicates that by introducing tin(II) with stereochemical activity lone pairs (SCALP) in metal phosphates, the birefringence was enhanced, 0.048@1064 nm for SnII SnIV (PO4 )2 and 0.080@1064 nm for SrSn(PO4 )PO2 (OH)2 .

PC-DOT: Improving genomic prediction ability of principal component regression by DOT product.

Principal component regression (PC regression) is a useful method developed for prediction based on a dimension-reducing strategy. Generally, the principal components (PCs) are added to the regression model one by one based on the eigenvalue (PC-Eigen). Considering that some PCs with large eigenvalues may be poorly associated with the response variable, the PC-Eigen may not be the best framework. Researchers previously tried to add PCs to the model based on their contribution to the sum of squares of the regression (PC-SS) and they found that the performance of PC-SS is generally lower than that of the PC-Eigen. A standard approach for selecting the optimal set of PCs remains a challenge. Here, from the cosine similarity theory, we postulated that we could rank the PCs by dot product, and this framework (we called PC-DOT) could help to preferentially extract PCs that are highly correlated with the response variable and meanwhile have a large eigenvalue. Based on one simulated and three real genomic datasets (a total of 15 traits), we tested the prediction ability of different frameworks. In general, the PC-DOT method showed a better performance than both PC-Eigen and PC-SS. To facilitate the application of PC, we attached a series of R codes for different frameworks (https://github.com/SUNHAO-JLU/Genome_Prediction-PC_DOT). In addition, the HAT matrix was used to reduce the compute complex in reference data during the cross-validation process. Our work may help researchers to better understand and carry out the PC regression model.

Detection of selection signatures in South African Mutton Merino sheep using whole-genome sequencing data.

The South African Mutton Merino (SAMM), a dual-purpose (meat and wool) sheep breed, is characterized by its excellent performance on growth, carcass traits and meat quality compared to other fine-wool Merino breeds. Nowadays, the SAMM breed has been widely used to cross with commercial and indigenous fine-wool or coarse-wool breeds to improve the growth and meat performance in many countries. To date, however, little is known about the genetic basis for its prominent characteristics. In this study, whole-genome sequences of 10 SAMM were sequenced and the selection signatures were analyzed together with those of 39 Australian Merino and Chinese Merino (wool-type Merino) by FST , iHS, and XP-EHH methods. In total, 313 genes in 277 regions were identified by at least 2 methods with the signal of selection and 21 of them were identified by all three methods. We highlighted a list of interesting genes, including GHR, LCORL, SMO, NCAPG, DCC, IBSP, PPARGC1A, PACRGL, PRDM5, XYLB, AHCYL2, TEFM, AFG1L, and FAM184B, which have been shown to be involved in growth, carcass traits, and meat quality by previous studies. Herein, GHR, encoding a transmembrane receptor for growth hormone, is the most notable one. We report the first study on selection signatures analysis of SAMM at whole-genome sequence level. These results provide new insights into the genetic mechanisms underlying the growth and carcass traits in SAMM.

Circular polarization analyzer based on surface plasmon polariton interference.

The determination of chirality of circularly polarized light (CPL) is of great significance to the development of various optical techniques. In this paper, a miniature circular polarization analyzer (CPA) based on surface plasmon polariton (SPP) interference is proposed. The proposed CPA consists of a micron scale long sub-wavelength slit and two groups of spatially arranged periodic sub-wavelength rectangular groove pairs, which are etched in a metal layer. Under the illumination of a CPL with a given chirality, the proposed CPA is capable of forming SPP-mediated interference fringes with different periods in far field. The chirality of CPL can be directly and quantitatively differentiated by the frequency value of the far field SPP-mediated interference fringes. Different from the existing SPP-based CPAs, the proposed CPA can directly image the chirality information in far field, avoiding near-field imaging of the SPP field.

Glycine alleviates fluoride-induced oxidative stress, apoptosis and senescence in a porcine testicular Sertoli cell line.

Glycine is a well-known free radical scavenger in the cellular antioxidant system that prevents oxidative damage and apoptosis. Excessive fluoride exposure is associated with multiple types of cellular damage in humans and animals. The objective of the present study was to investigate the protective effects of glycine on sodium fluoride (NaF) exposure and the possible underlying mechanisms in a porcine testicular Sertoli cell line model. Cellular viability and proliferation were examined following NaF exposure and glycine supplementation, and glycine dramatically ameliorated the decreases in NaF-induced porcine testicular Sertoli cell viability and proliferation. Further investigations revealed that glycine decreased NaF-induced intracellular reactive oxygen species production, DNA fragment accumulation and the apoptosis incidence in the porcine testicular Sertoli cell line; in addition, glycine improved mitochondrial function and ATP production. Notably, results of the SPiDER-ß-Gal analysis suggested that glycine alleviated NaF-induced cellular senescence and downregulated P53, P21, HMGA2 and P16INK4a gene expression in the porcine testicular Sertoli cell line. Collectively, the beneficial effects of glycine alleviate NaF-induced oxidative stress, apoptosis and senescence, and together with our previous findings, support the hypothesis that glycine plays an important role in protecting against NaF exposure-induced impairments in the porcine testicular Sertoli cell line.

Dynamical generation of multiple focal spot pairs with controllable position and polarization.

We report a flexible method to dynamically generate multiple sub-wavelength focal spot pairs with adjustable polarization, position and number at the focal plane of a high numerical aperture (NA) objective lens. The desired incident field on the pupil plane can be analytically derived by employing the time-reversed method combined with the dipole antenna radiation theory. The numerical simulations of the corresponding tightly focused field are conducted using the Richards-Wolf vectorial diffraction theory. The validity of the presented method is demonstrated through experimental generation of several designed pupil fields with a versatile vectorial optical field generator and characterization of the produced focused fields with Stokes parameter measurements.

Shift of the surface plasmon polariton interference pattern in symmetrical arc slit structures and its application to Rayleigh metallic particle trapping.

In symmetric nano/micro metal slit structures, interference patterns are produced by counter-propagating surface plasmon polaritons (SPPs) in the the center of structures, which can be employed to improve the resolution of microscopy and surface etching and to realize particle trapping. This paper focuses on the shift of the SPP interference patterns in the symmetric arc slit structures. The excitation models with one incident beam and two incident beams are established and analyzed respectively, and methods to shift the SPP interference patterns via adjusting the tilt angle and initial phase of the excitation beams are compared. The FDTD simulation results show that these methods can precisely shift the SPP interference patterns in the symmetrical arc slits. Compared to the linear slits, the SPP waves arising from arc slits are more strongly focused, resulting in a stronger gradient force. The characteristics of stronger focus and dynamic shifting of the focal spot give the symmetric arc slit structure unique advantages in the capture and transfer of the Rayleigh metallic particle.

Dynamic tailoring of an optical skyrmion lattice in surface plasmon polaritons: reply.

This is a Reply to the Comment by Meiler, Frank, and Giessen directed to a recent paper "Dynamic tailoring of an optical skyrmion lattice in surface plasmon polaritons" [Opt. Express28, 10320 (2020)10.1364/OE.384718] regarding to the existence of Bloch-type skyrmions in the magnetic field of surface plasmon polaritons.

Dynamic tailoring of an optical skyrmion lattice in surface plasmon polaritons.

A skyrmion is a topologically protected soliton with a spin structure on the micro/nano scale that has promising applications in magnetic information storage and spintronics devices. This study focuses on the optical skyrmion lattice structures created in the surface plasmon polaritons (SPPs) field. Both the Néel-type optical skyrmion lattice formed by the electric field vector and Bloch-type optical skyrmion lattice formed by the magnetic field vector are generated via exciting a hexagonal grating structure on the metal surface with six Gaussian optical spots. Such a multiple-spot excitation can be realized through tightly focusing a specially designed complex field with a high NA lens. Through introducing the phase difference of the excitation beams to shift the SPP standing waves, the shape and position of the optical skyrmion lattice can be dynamically controlled. Both the electric field vector and magnetic field vector are evaluated quantitatively based on the electric and magnetic field obtained by finite difference time domain (FDTD) simulation to demonstrate the validity and capability of the proposed technique.

miR-375 down-regulation of the rearranged L-myc fusion and hypoxia-induced gene domain protein 1A genes and effects on Sertoli cell proliferation.

OBJECTIVE: This study aimed to screen and identify the target genes of miR-375 in pig Sertoli (ST) cells and to elucidate the effect of miR-375 on the proliferation of ST cells. METHODS: In this study, bioinformatics software was used to predict and verify miR-375 target genes. Quantitative polymerase chain reaction (PCR) was used to detect the relationship between miR-375 and its target genes in ST cells. Enzyme-linked immunosorbent assay (ELISA) of rearranged L-myc fusion (RLF) and hypoxia-induced gene domain protein 1A (HIGD1A) was performed on porcine ST cells, which were transfected with a miR-375 mimics and inhibitor to verify the results. Dual luciferase reporter gene assays were performed to assess the interactions among miR-375, RLF, and HIGD1A. The effect of miR-375 on the proliferation of ST cells was analyzed by CellTiter 96 AQueous One Solution Cell Proliferation Assay (MTS). RESULTS: Five possible target genes of miR-375, including RLF, HIGD1A, colorectal cancer associated 2, POU class 3 homeobox 1, and WW domain binding protein 1 like, were found. The results of quantitative PCR suggested that mRNA expression of RLF and HIGD1A had a negative correlation with miR-375, indicating that RLF and HIGD1A are likely the target genes of miR-375. The ELISA results revealed that RLF and HIGD1A were negatively correlated with the miR-375 protein level. The luminescence results for the miR-375 group co-transfected with wild-type RLF and HIGD1A vector were significantly lower than those of the miR-375 group co-transfected with the blank vector or mutant RLF and HIGD1A vectors. The present findings suggest that RLF and HIGD1A are target genes of miR-375 and that miR-375 inhibits ST cell proliferation according to MTS analysis. CONCLUSION: It was speculated that miR-375 affects cell proliferation through its target genes, which play an important role in the development of testicular tissue.

Effect of halogen (Cl, Br) on the symmetry of flexible perovskite-related framework.

The perovskite structure is a good candidate for the design of functional materials. On the basis of the combination of B6O13 groups and XM6 (X = Cl, Br; M = alkali metals) octahedra, three new perovskite-related crystals Na3B6O10Cl, RbNa2B6O10Cl, and RbNa2B6O10Br have been synthesized by a high-temperature solution method for the first time. Na3B6O10Cl and RbNa2B6O10Cl are isostructural and crystallize in the noncentrosymmetric (NCS) space group P212121 (No. 19), while RbNa2B6O10Br belongs to the centrosymmetric (CS) space group Pnma (No. 62). The phenomenon that Cl-containing borates are not isostructural with corresponding Br-containing borates is extremely rare among borates. Detailed structure analysis suggests that the difference is owing to the effect of the halogen (Cl, Br) on the symmetry of the flexible perovskite-related framework. In addition, thermal analyses, IR spectroscopy, the UV-vis-NIR diffuse reflectance spectrum, and first-principles theoretical studies have also been performed on the three compounds.

Genome-wide methylation changes are associated with muscle fiber density and drip loss in male three-yellow chickens.

In eukaryotes, DNA methylation is an important epigenetic modification involved in gene expression regulation. Meat quality traits are complicated traits that are controlled by many genes. Changes in the methylation levels of certain genes controlling meat quality traits will inevitably affect their expression levels, thereby affecting meat quality. The objectives of this study were to investigate the differences in the DNA methylation level in pectoral muscle tissues using fluorescent-labeled methylation sensitive amplified polymorphism and their relationships with meat quality traits in three-yellow chickens. The results showed that the differences in the DNA methylation level had a highly significant effect on muscle fiber density and drip loss (P<0.01). However, no significant correlations were found between the DNA methylation levels and the other investigated traits (P>0.05).

Clinical study on microscopic syndrome differentiation and traditional Chinese medicine treatment for liver stomach disharmony in chronic gastritis.

BACKGROUND: Chronic gastritis (CG) is a common gastrointestinal disorder characterized by inflammation of the stomach lining. Liver-stomach disharmony (LSD) syndrome is believed to contribute to CG symptoms. AIM: To evaluate the efficacy and safety of microcosmic syndrome differentiation and Chinese herbal medicine (CHM) treatment in patients with CG and LSD syndrome. METHODS: Sixty-four patients with CG and LSD syndrome were randomly divided into two groups: The treatment group received CHM based on microcosmic syndrome differentiation and the control group received conventional Western medicine. The treatment course lasted 12 wk. The primary outcome was improvement in dyspeptic symptoms, measured using the Nepean Dyspepsia Index. The secondary outcomes included the improvement rate of endoscopic findings, histopathological findings, and microcosmic syndrome scores and the incidence of adverse events. RESULTS: After 12 wk of treatment, the treatment group showed significantly greater improvement in dyspeptic symptoms than the control group (93.75% vs 65.63%, P < 0.01). The treatment group also showed a significantly higher improvement rate in endoscopic findings than the control group (81.25% vs 53.13%, P < 0.05). The improvement rates of histopathological findings and microcosmic syndrome scores were not significantly different between the two groups (P > 0.05). No serious adverse events were observed in either group. CONCLUSION: Microcosmic syndrome differentiation and CHM treatment can effectively improve dyspeptic symptoms and endoscopic findings in patients with CG and LSD syndrome and have a good safety profile. Further studies with larger sample sizes and longer follow-up periods are required to confirm the long-term efficacy and mechanism of action of this treatment.

Whole genome sequencing identified genomic diversity and candidated genes associated with economic traits in Northeasern Merino in China.

Introduction: Northeast Merino (NMS) is a breed developed in Northeast China during the 1960s for wool and meat production. It exhibits excellent traits such as high wool yield, superior meat quality, rapid growth rate, robust disease resistance, and adaptability to cold climates. However, no studies have used whole-genome sequencing data to investigate the superior traits of NMS. Methods: In this study, we investigated the population structure, genetic diversity, and selection signals of NMS using whole-genome sequencing data from 20 individuals. Two methods (integrated haplotype score and composite likelihood ratio) were used for selection signal analysis, and the Fixation Index was used to explore the selection signals of NMS and the other two breeds, Mongolian sheep and South African meat Merino. Results: The results showed that NMS had low inbreeding levels, high genomic diversity, and a pedigree of both Merino breeds and Chinese local breeds. A total length of 14.09 Mb genomic region containing 287 genes was detected using the two methods. Further exploration of the functions of these genes revealed that they are mainly concentrated in wool production performance (IRF2BP2, MAP3K7, and WNT3), meat production performance (NDUFA9, SETBP1, ZBTB38, and FTO), cold resistance (DNAJC13, LPGAT1, and PRDM16), and immune response (PRDM2, GALNT8, and HCAR2). The selection signals of NMS and the other two breeds annotated 87 and 23 genes, respectively. These genes were also mainly focused on wool and meat production performance. Conclusion: These results provide a basis for further breeding improvement, comprehensive use of this breed, and a reference for research on other breeds.

Integrated microbiome-metabolome-genome axis data of Laiwu and Lulai pigs.

Excessive fat deposition can trigger metabolic diseases, and it is crucial to identify factors that can break the link between fat deposition and metabolic diseases. Healthy obese Laiwu pigs (LW) are high in fat content but resistant to metabolic diseases. In this study, we compared the fecal microbiome, fecal and blood metabolome, and genome of LW and Lulai pigs (LU) to identify factors that can block the link between fat deposition and metabolic diseases. Our results show significant differences in Spirochetes and Treponema, which are involved in carbohydrate metabolism, between LW and LU. The fecal and blood metabolome composition was similar, and some anti-metabolic disease components of blood metabolites were different between the two breeds of pigs. The predicted differential RNA is mainly enriched in lipid metabolism and glucose metabolism, which is consistent with the functions of differential microbiota and metabolites. The down-regulated gene RGP1 is strongly negatively correlated with Treponema. Our omics data would provide valuable resources for further scientific research on healthy obesity in both human and porcine.