Detection of selection signatures in dairy and beef cattle using high-density genomic information

peer-reviewedBackground Artificial selection for economically important traits in cattle is expected to have left distinctive selection signatures on the genome. Access to high-density genotypes facilitates the accurate identification of genomic regions that have undergone positive selection. These findings help to better elucidate the mechanisms of selection and to identify candidate genes of interest to breeding programs. Results Information on 705 243 autosomal single nucleotide polymorphisms (SNPs) in 3122 dairy and beef male animals from seven cattle breeds (Angus, Belgian Blue, Charolais, Hereford, Holstein-Friesian, Limousin and Simmental) were used to detect selection signatures by applying two complementary methods, integrated haplotype score (iHS) and global fixation index (FST). To control for false positive results, we used false discovery rate (FDR) adjustment to calculate adjusted iHS within each breed and the genome-wide significance level was about 0.003. Using the iHS method, 83, 92, 91, 101, 85, 101 and 86 significant genomic regions were detected for Angus, Belgian Blue, Charolais, Hereford, Holstein-Friesian, Limousin and Simmental cattle, respectively. None of these regions was common to all seven breeds. Using the FST approach, 704 individual SNPs were detected across breeds. Annotation of the regions of the genome that showed selection signatures revealed several interesting candidate genes i.e. DGAT1, ABCG2, MSTN, CAPN3, FABP3, CHCHD7, PLAG1, JAZF1, PRKG2, ACTC1, TBC1D1, GHR, BMP2, TSG1, LYN, KIT and MC1R that play a role in milk production, reproduction, body size, muscle formation or coat color. Fifty-seven common candidate genes were found by both the iHS and global FST methods across the seven breeds. Moreover, many novel genomic regions and genes were detected within the regions that showed selection signatures; for some candidate genes, signatures of positive selection exist in the human genome. Multilevel bioinformatic analyses of the detected candidate genes suggested that the PPAR pathway may have been subjected to positive selection. Conclusions This study provides a high-resolution bovine genomic map of positive selection signatures that are either specific to one breed or common to a subset of the seven breeds analyzed. Our results will contribute to the detection of functional candidate genes that have undergone positive selection in future studies.This study was financially supported by a grant from the Irish Department of Agriculture, Food and Marine Research Stimulus Fund (11/S/112), the Agricultural Science and Technology Innovation Program (No. ASTIP-IAS-TS-6) and the Natural Science Foundation of China (No. 31200927)

MASANet: Multi-Angle Self-Attention Network for Semantic Segmentation of Remote Sensing Images

As an important research direction in the field of pattern recognition, semantic segmentation has become an important method for remote sensing image information extraction. However, due to the loss of global context information, the effect of semantic segmentation is still incomplete or misclassified. In this paper, we propose a multi-angle self-attention network (MASANet) to solve this problem. Specifically, we design a multi-angle self-attention module to enhance global context information, which uses three angles to enhance features and takes the obtained three features as the inputs of self-attention to further extract the global dependencies of features. In addition, atrous spatial pyramid pooling (ASPP) and global average pooling (GAP) further improve the overall performance. Finally, we concatenate the feature maps of different scales obtained in the feature extraction stage with the corresponding feature maps output by ASPP to further extract multi-scale features. The experimental results show that MASANet achieves good segmentation performance on high-resolution remote sensing images. In addition, the comparative experimental results show that MASANet is superior to some state-of-the-art models in terms of some widely used evaluation criteria

Effect of Deformation Conditions on Mechanical Properties of Zr-based Metallic Glasses

In this paper, the effects of different strain rate(1×10-5 s-1, 5×10-5 s-1, 1×10-4 s-1, 5×10-4 s-1, 1×10-3 s-1) and aspect ratio(1:1, 1.5:1, 2:1, 2.5:1, 3:1) on mechanical properties of Zr-based metallic glasses at room temperature were investigated. The results indicate that as the strain rate increases, the plastic strain and compressive strength of the specimens gradually decrease. The specimen with the strain rate of 1×10-5 s-1 exhibits the higher plastic strain of 10.25 %, compressive strength of 2002 MPa and fracture strength of 1999 MPa. In addition, accompanied with the increase in aspect ratio, the plastic strain of the specimens declines from 25.42 % to 1.97 %, meanwhile, the compressive strength and fracture strength of the specimens also present declining trend

Dysregulation of circulating T follicular helper cell subsets and their potential role in the pathogenesis of syphilis

IntroductionThe role of the host immune response could be critical in the development of Treponema pallidum (Tp) infection in individuals with latent syphilis. This study aims to investigate the alterations in T follicular helper T (Tfh) cell balance among patients with secondary syphilis and latent syphilis.Methods30 healthy controls (HCs), 24 secondary syphilis patients and 41 latent syphilis patients were enrolled. The percentages of total Tfh, ICOS+ Tfh, PD-1+ Tfh, resting Tfh, effector Tfh, naïve Tfh, effector memory Tfh, central memory Tfh,Tfh1, Tfh2, and Tfh17 cells in the peripheral blood were all determined by flow cytometry.ResultsThe percentage of total Tfh cells was significantly higher in secondary syphilis patients compared to HCs across various subsets, including ICOS+ Tfh, PD-1+ Tfh, resting Tfh, effector Tfh, naïve Tfh, effector memory Tfh, central memory Tfh, Tfh1, Tfh2, and Tfh17 cells. However, only the percentages of ICOS+ Tfh and effector memory Tfh cells showed significant increases in secondary syphilis patients and decreases in latent syphilis patients. Furthermore, the PD-1+ Tfh cells, central memory Tfh cells, and Tfh2 cells showed significant increases in latent syphilis patients, whereas naïve Tfh cells and Tfh1 cells exhibited significant decreases in secondary syphilis patients when compared to the HCs. However, no significant change was found in resting Tfh and effector Tfh in HCs and secondary syphilis patients or latent syphilis patients.DiscussionDysregulated ICOS+ Tfh or effector memory Tfh cells may play an important role in immune evasion in latent syphilis patients

Quantitative assessment and case study of CO2 geological storage in deep coal seams

Geological storage of CO2 as an idea carbon reduction technology is expected to become an important means of mitigating the greenhouse effect. Therefore, quantitatively assessing the potential of geological storage of CO2 in deep coal seams and investigating the interaction between supercritical CO2 and deep coal rocks have become a hot research topic. Taking Jiulishan coal sample from Jiaozuo mining area in Henan, China as the experimental research object, we analyse the mechanism of supercritical CO2 adsorption and sequestration in deep coal seams, carry out CO2 isothermal adsorption experiments of the coal samples at 35 ℃ and 45 ℃, explain and correct the error of negative adsorption isotherms under high pressure, and obtain the actual adsorption amount of CO2 of the coal sample at different temperatures. Here, we propose a new method for calculating CO2 geological storage capacity, which can not only correct the storage capacity miscalculation caused by Gibbs adsorption, but also can accurately evaluate CO2 theory and effective storage capacity in different burial depths of coal seams. results show that: ① In theory, adsorption saturation means that all adsorption sites have been occupied, the volume and density of the adsorption phase have stabilized, and the adsorption amount should no longer changes. However, all adsorption isotherms measured in the laboratory show that the adsorption amount decreases with the increase of pressure under high-pressure saturation stage, which does not conform to the Langmuir adsorption principle. Therefore, the adsorption isotherm measured in the laboratory must be corrected before it can be applied to the assessment of CO2 storage capacity in deep coal seams; ② The CO2 storage capacity in coal mainly consists of the adsorption and free CO2 amount. The adsorption CO2 amount needs to be calculated using the adsorption phase density and Gibbs adsorption amount, while the free CO2 amount needs to know the pore volume occupied by the free phase in coal. It can only be calculated based on the total pore volume in coal minus the adsorption phase volume. Therefore, the adsorption phase is the decisive factor for accurately evaluating the adsorption and free CO2 storage capacity; ③ Using a modified CO2 geological storage quantification model and taking the 800-2000 m deep coal seam in the Xiuwu research area of Jiaozuo mining area as an example, it is calculated that The theoretical storage capacity of CO2 per unit mass of coal is 1.52−2.16 mmol/g, The total effective storage capacity is 11.19×109 m3, which is equivalent to 21.97 Mt. This case not only corrected the mass balance miscalculation of Gibbs adsorption data, but also considered the impact of adsorption phase occupying pore space on free storage capacity, and thus, it has important implication for improving the accuracy of predicting CO2 geological storage capacity in deep coal seams

c-Met inhibitor NVP-BVU972 induces antiviral protection and suppresses NF-κB-mediated inflammation

IntroductionInhibiting viral replication and limiting NF-κB-driven inflammation simultaneously is essential for better antiviral therapy, highlighting the urgent need for a single agent that achieves both functions.MethodsHere, we reported NVP-BVU972 (NVP), a selective c-Met inhibitor, induced a robust antiviral state and inhibited NF-κB-mediated inflammation.ResultsThe dual functions blocked replication of diverse RNA viruses (VSV, EMCV, MHV) and DNA viruses (HSV-1, VACV) and reduced systemic cytokine levels (Il1β, Il6, Tnfα) in vitro and in vivo. Mechanistically, we identified NVP reprogrammed inflammation-related loci by modulating both gene expression and chromatin accessibility, and chaetocin inhibition of H3K9 methylation reversed its antiviral activity.DiscussionThese findings unveil NVP as a promising host-directed agent that simultaneously limits viral propagation and reduces inflammation, and suggest repurposing NVP as a broad-spectrum antiviral

AAV2-mediated follistatin overexpression induces ovine primary myoblasts proliferation

BACKGROUND: Follistatin (FST) has been shown to bind to some TGF-β family members and can function as a potent myostatin (MSTN) antagonist. Recent studies have revealed that over-expression of FST by adeno-associated viruses increases muscle growth in mice, humans and nonhuman primates. In the present study, to determine the effect of FST on ovine primary myoblast (OPM) proliferation, FST was over-expressed using an adeno-associated virus serotype 2 (AAV 2) vector. RESULTS: Western blot results showed that AAV induced the expression of FST protein in transduced OPM cells. Real-time quantitative PCR results indicated that over-expression of FST resulted in a dramatic increase in Akt I and CDK2 expression and a decrease in p21 expression. Moreover, cell cycle analysis confirmed that FST down-regulated p21, a CDK inhibitor, and increased the level of CDK2 expression in OPM cells. Hence, follistatin positively regulated the G1 to S progression. Our results showed that FST induced proliferation through a down-regulation of p21, as only the p21 expression level was down-regulated as a result of FST over-expression in myoblasts, whereas no change was observed in the level of p57 expression. CONCLUSIONS: These results expanded our understanding of the regulation mechanism of FST in ovine primary myoblasts. Our results provide the first evidence that the AAV viral system can be used for gene transfer in ovine myoblast cells. Moreover, the results showed that an AAV vector can successfully induce the expression of FST in OPM cells in vitro. These findings demonstrated that FST over-expression induces proliferation through a down-regulation of the p21 gene under proliferating conditions