Development and Application of High-density SNP Arrays in Genomic Studies of Domestic Animals

Fan, Bin,Du, Zhi-Qiang,Gorbach, Danielle M.,Rothschild, Max F. Asian Australasian Association of Animal Productio 2010 Animal Bioscience Vol.23 No.7

In the past decade, there have been many advances in whole-genome sequencing in domestic animals, as well as the development of "next-generation" sequencing technologies and high-throughput genotyping platforms. Consequently, these advances have led to the creation of the high-density SNP array as a state-of-the-art tool for genetics and genomics analyses of domestic animals. The emergence and utilization of SNP arrays will have significant impacts not only on the scale, speed, and expense of SNP genotyping, but also on theoretical and applied studies of quantitative genetics, population genetics and molecular evolution. The most promising applications in agriculture could be genome-wide association studies (GWAS) and genomic selection for the improvement of economically important traits. However, some challenges still face these applications, such as incorporating linkage disequilibrium (LD) information from HapMap projects, data storage, and especially appropriate statistical analyses on the high-dimensional, structured genomics data. More efforts are still needed to make better use of the high-density SNP arrays in both academic studies and industrial applications.

Bidirectional two-sample mendelian randomization analysis identifies causal associations between age at menarche and sarcopenia-related traits

Fan Wei,Gu Peng,Pu Bin,Yue Dan,Xin Qiao,Zheng XiaoHui,Zeng ZhanPeng,Fan Shaoyong 한국유전학회 2023 Genes & Genomics Vol.45 No.8

Background Observational studies have shown that the age of menarche is associated with sarcopenia, but confounding factors make the causal relationship difficult to infer. Objective Therefore, we conducted a bidirectional two-sample Mendelian randomized (MR) analysis to evaluate the potential causal relationship between age at menarche and sarcopenia-related traits (hand grip strength, lean mass, walking pace). Methods We obtained the latest aggregate statistics from the Genome-wide association studies (GWAS) database on the age of menarche of 182,416 participants from ReproGen, the appendicular lean mass of 244,730 participants from EMBL’s European Bioinformatics Institute, the left-hand grip strength of 401,026 participants, the right-hand grip strength of 461,089 participants and the usual walking pace of 459,915 participants from the UK Biobank. The inverse variance weighting (IVW) method and other MR methods were used to evaluate the bidirectional causal relationship between the age of menarche and sarcopenia. Results The forward MR results showed that the age of menarche predicted by the gene was positively correlated with left-hand grip strength (IVWβ=0.041, P = 2.00 × 10−10), right-hand grip strength (IVWβ=0.053, P = 1.97 × 10−18), appendicular lean mass (IVWβ=0.012, P = 4.38 × 10−13) and usual walking pace (IVWβ=0.033, P = 1.62 × 10−8).In the reverse MR analysis, we also found that the usual walking pace was positively correlated with the age of menarche predicted by genes (IVWβ=0.532, P = 1.65 × 10−4). Still, there was no causal relationship between grip strength and appendicular lean mass and the age at menarche. Conclusion Our results show that earlier menarche will increase the risk of sarcopenia. In addition, people with higher muscle function tend to have menarche later. These findings may provide a reference for prevention strategies and interventions for menarche in advance and sarcopenia.

The role of ginsenoside Rb1, a potential natural glutathione reductase agonist, in preventing oxidative stress-induced apoptosis of H9C2 cells

Fan, Hui-Jie,Tan, Zhang-Bin,Wu, Yu-Ting,Feng, Xiao-Reng,Bi, Yi-Ming,Xie, Ling-Peng,Zhang, Wen-Tong,Ming, Zhi,Liu, Bin,Zhou, Ying-Chun The Korean Society of Ginseng 2020 Journal of Ginseng Research Vol.44 No.2

Background: Oxidative stress-induced cardiomyocytes apoptosis is a key pathological process in ischemic heart disease. Glutathione reductase (GR) reduces glutathione disulfide to glutathione (GSH) to alleviate oxidative stress. Ginsenoside Rb1 (GRb1) prevents the apoptosis of cardiomyocytes; however, the role of GR in this process is unclear. Therefore, the effects of GRb1 on GR were investigated in this study. Methods: The antiapoptotic effects of GRb1 were evaluated in H9C2 cells by 3-(4,5-dimethylthiazol-2-yl)-2,5-diphenyltetrazolium bromide, annexin V/propidium iodide staining, and Western blotting. The antioxidative effects were measured by a reactive oxygen species assay, and GSH levels and GR activity were examined in the presence and absence of the GR inhibitor 1,3-bis-(2-chloroethyl)-1-nitrosourea. Molecular docking and molecular dynamics simulations were used to investigate the binding of GRb1 to GR. The direct influence of GRb1 on GR was confirmed by recombinant human GR protein. Results: GRb1 pretreatment caused dose-dependent inhibition of tert-butyl hydroperoxide-induced cell apoptosis, at a level comparable to that of the positive control N-acetyl-L-cysteine. The binding energy between GRb1 and GR was positive (-6.426 kcal/mol), and the binding was stable. GRb1 significantl reduced reactive oxygen species production and increased GSH level and GR activity without altering GR protein expression in H9C2 cells. Moreover, GRb1 enhanced the recombinant human GR protein activity in vitro, with a half-maximal effective concentration of ≈2.317 μM. Conversely, 1,3-bis-(2-chloroethyl)-1-nitrosourea co-treatment significantly abolished the GRb1's apoptotic and antioxidative effects of GRb1 in H9C2 cells. Conclusion: GRb1 is a potential natural GR agonist that protects against oxidative stress-induced apoptosis of H9C2 cells.

Structural Characterization and Optical Properties of Sol-gel-derived Polycrystalline Pb(Zr0.35Ti0.65)O3 Thin Films

Fan Zhang,Rong-Jun Zhang,Zi YiWang,Yu-Xiang Zheng,Song-You Wang,Hai-Bin Zhao,Liang-Yao Chen,Xiao Bin Liu,An Quan Jiang 한국물리학회 2013 THE JOURNAL OF THE KOREAN PHYSICAL SOCIETY Vol.63 No.1

Polycrystalline Pb(Zr0.35Ti0.65)O3 thin films prepared on Pt/Ti/SiO2/Si substrate by using solgel technique were characterized by using X-ray diffraction (XRD) and atomic force microscopy (AFM). The optical properties of the films were investigated by using spectroscopic ellipsometry (SE) with a four-phase optical model, air/roughness layer/PZT layer/Pt layer in the spectral range of 300 - 800 nm. The optical band gap of the films calculated following the Tauc’s Law was smaller than that of an amorphous PZT thin film with some microcrystals existing on the surface. The result indicates that the quantum-size effect leads to an increase in band gap when the crystalline dimensions become very small.

The role of ginsenoside Rb1, a potential natural glutathione reductase agonist, in preventing oxidative stress-induced apoptosis of H9C2 cells

Hui-Jie Fan,Zhang-Bin Tan,Yu-Ting Wu,Xiao-Reng Feng,Yi-Ming Bi,Ling-Peng Xie,Wen-Tong Zhang,Zhi Ming,Bin Liu,Ying-Chun Zhou 고려인삼학회 2020 Journal of Ginseng Research Vol.44 No.2

Background: Oxidative stress-induced cardiomyocytes apoptosis is a key pathological process inischemic heart disease. Glutathione reductase (GR) reduces glutathione disulfide to glutathione (GSH) toalleviate oxidative stress. Ginsenoside Rb1 (GRb1) prevents the apoptosis of cardiomyocytes; however,the role of GR in this process is unclear. Therefore, the effects of GRb1 on GR were investigated in thisstudy. Methods: The antiapoptotic effects of GRb1 were evaluated in H9C2 cells by 3-(4,5-dimethylthiazol-2-yl)-2,5-diphenyltetrazolium bromide, annexin V/propidium iodide staining, and Western blotting. Theantioxidative effects were measured by a reactive oxygen species assay, and GSH levels and GR activitywere examined in the presence and absence of the GR inhibitor 1,3-bis-(2-chloroethyl)-1-nitrosourea. Molecular docking and molecular dynamics simulations were used to investigate the binding of GRb1 toGR. The direct influence of GRb1 on GR was confirmed by recombinant human GR protein. Results: GRb1 pretreatment caused dose-dependent inhibition of tert-butyl hydroperoxide-induced cellapoptosis, at a level comparable to that of the positive control N-acetyl-L-cysteine. The binding energybetween GRb1 and GR was positive ( 6.426 kcal/mol), and the binding was stable. GRb1 significantlyreduced reactive oxygen species production and increased GSH level and GR activity without altering GRprotein expression in H9C2 cells. Moreover, GRb1 enhanced the recombinant human GR protein activityin vitro, with a half-maximal effective concentration of z2.317 mM. Conversely, 1,3-bis-(2-chloroethyl)-1-nitrosourea co-treatment significantly abolished the GRb1’s apoptotic and antioxidative effects of GRb1in H9C2 cells. Conclusion: GRb1 is a potential natural GR agonist that protects against oxidative stresseinducedapoptosis of H9C2 cells.

Optical Anisotropy in Micromechanically Rolled Carbon Nanotube Forest

Mohd Asyraf bin Mohd Razib,Masud Rana,Tanveer Saleh,Harrison Fan,Andrew Koch,Alireza Nojeh,Kenichi Takahata,Asan Gani Bin Abdul Muthalif 대한금속·재료학회 2017 ELECTRONIC MATERIALS LETTERS Vol.13 No.5

The bulk appearance of arrays of vertically aligned carbonnanotubes (VACNT arrays or CNT forests) is dark as theyabsorb most of the incident light. In this paper, two postprocessingtechniques have been described where the CNTforest can be patterned by selective bending of the tips of thenanotubes using a rigid cylindrical tool. A tungsten tool wasused to bend the vertical structure of CNTs with predefinedparameters in two different ways as stated above: bendingusing the bottom surface of the tool (micromechanicalbending (M2B)) and rolling using the side of the tool(micromechanical rolling (M2R)). The processed zone wasinvestigated using a Field Emission Scanning ElectronMicroscope (FESEM) and optical setup to reveal the surfacemorphology and optical characteristics of the patterned CNTson the substrate. Interestingly, the polarized optical reflection from the micromechanical rolled (M2R) sample was found to besignificantly influenced by the rotation of the sample. It was observed that, if the polarization of the light is parallel to thealignment of the CNTs, the reflectance is at least 2 x higher than for the perpendicular direction. Furthermore, the reflectancevaried almost linearly with good repeatability (~10%) as the processed CNT forest sample was rotated from 0° to 90°.

Fabrication of recyclable UiO-66-NH2/PVDF hybrid fibrous membrane for Cr(VI) removal in wastewater

Fan Yu,Liusha Cen,Caihong Lei,Feichao Zhu,Lan Zhou,Hailin Zhu,Bin Yu 한국공업화학회 2023 Journal of Industrial and Engineering Chemistry Vol.123 No.-

Efficient and recyclable water treatment technology plays a vital role in practical application of Cr(Ⅵ)removal. Zr-based metal–organic framework (UiO-66-NH2) is widely used in wastewater treatmentdue to its water stability. Powdery UiO-66-NH2 has disadvantages of easy aggregation, reclamation difficultyand secondary pollution. In this work, UiO-66-NH2 was successfully loaded on electrospunpolyvinylidene fluoride (PVDF) fibers by in-situ growth to achieve efficient adsorption and photoreductionof Cr(Ⅵ). Grooved surface of PVDF fibers and truncated octahedron shape of UiO-66-NH2 ensuredthe loading uniformity and firmness. The loading rate and size of UiO-66-NH2 crystals increased withthe amount of trifluoroacetic acid (TFA) in the preparation process. Meantime, the introduction of TFAin synthesis was conducive to the separation efficiency of photogenerated carries. When the additionamount of TFA was 5 ml, UiO-PVDF-3 with loading rate of 44.8% exhibited best Cr(VI) adsorption andphotocatalysis performance. For the pure adsorption process, the adsorption capacity of UiO-PVDF-3 at90 min was 3.76 mg/cm2, and the corresponding removal rate was 95.8%. When visible light was applied,the Cr(VI) removal rate for UiO-PVDF-3 reached to about 95.0% at 45 min. Furthermore, regenerationexperiments showed UiO-PVDF-3 had excellent adsorption and photocatalysis reusability. Based on thismethod, synthesized UiO-66-NH2/PVDF hybrid membrane as a bifunctional material for adsorption andphotocatalysis realizes the reuse of UiO-66-NH2 crystals conveniently and avoids secondary pollutionduring Cr(VI) wastewater treatment.

Effect of Soyabean Isoflavones Exposure on Onset of Puberty, Serum Hormone Concentration and Gene Expression in Hypothalamus, Pituitary Gland and Ovary of Female Bama Miniature Pigs

Fan, Juexin,Zhang, Bin,Li, Lili,Xiao, Chaowu,Oladele, Oso Abimbola,Jiang, Guoli,Ding, Hao,Wang, Shengping,Xing, Yueteng,Xiao, Dingfu,Yin, Yulong Asian Australasian Association of Animal Productio 2015 Animal Bioscience Vol.28 No.11

This study was to investigate the effect of soyabean isoflavones (SIF) on onset of puberty, serum hormone concentration, and gene expression in hypothalamus, pituitary and ovary of female Bama miniature pigs. Fifty five, 35-days old pigs were randomly assigned into 5 treatment groups consisting of 11 pigs per treatment. Results showed that dietary supplementation of varying dosage (0, 250, 500, and 1,250 mg/kg) of SIF induced puberty delay of the pigs with the age of puberty of pigs fed basal diet supplemented with 1,250 mg/kg SIF was significantly higher (p<0.05) compared to control. Supplementation of SIF or estradiol valerate (EV) reduced (p<0.05) serum gonadotrophin releasing hormone and luteinizing hormone concentration, but increased follicle-stimulating hormone concentration in pigs at 4 months of age. The expression of KiSS-1 metastasis-suppressor (KISS1), steroidogenic acute regulatory protein (StAR) and 3-beta-hydroxysteroid dehydrogenase/delta-5-delta-4 isomerase ($3{\beta}-HSD$) was reduced (p<0.01) in SIF-supplemented groups. Expression of gonadotropin-releasing hormone receptor in the pituitary of miniature pigs was reduced (p<0.05) compared to the control when exposed to 250, 1,250 mg/kg SIF and EV. Pigs on 250 mg/kg SIF and EV also showed reduced (p<0.05) expression of cytochrome P450 19A1 compared to the control. Our results indicated that dietary supplementation of SIF induced puberty delay, which may be due to down-regulation of key genes that play vital roles in the synthesis of steroid hormones.

Ratiometric and discriminative visualization of autophagic processes with a novel dual-responded lysosome-specific fluorescent probe

Fan Zheng,Yeshuo Ma,Jipeng Ding,Shuai Huang,Shengwang Zhang,Xueyan Huang,Bin Feng,Hongliang Zeng,Fei Chen,Wenbin Zeng 한국생체재료학회 2023 생체재료학회지 Vol.27 No.00

Background Autophagy is a critical self-eating pathway involved in numerous physiological and pathological processes. Lysosomal degradation of dysfunctional organelles and invading microorganisms is central to the autophagy mechanism and essential for combating disease-related conditions. Therefore, monitoring fluctuations in the lysosomal microenvironment is vital for tracking the dynamic process of autophagy. Although much effort has been put into designing probes for measuring lysosomal viscosity or pH separately, there is a need to validate the concurrent imaging of the two elements to enhance the understanding of the dynamic progression of autophagy. Methods Probe HFI was synthesized in three steps and was developed to visualize changes in viscosity and pH within lysosomes for real-time autophagy tracking. Then, the spectrometric determination was carried out. Next, the probe was applied to image autophagy in cells under nutrient-deprivation or external stress. Additionally, the performance of HFI to monitor autophagy was employed to evaluate acetaminophen-induced liver injury. Results We constructed a ratiometric dual-responsive probe, HFI, with a large Stokes shift over 200 nm, dualwavelength emission, and small background interference. The ratiometric fluorescent signal (R = I610/I460) of HFI had an excellent correlation with both viscosity and pH. More importantly, high viscosity and low pH had a synergistic promotion effect on the emission intensity of HFI, which enabled it to specially lit lysosomes without disturbing the inherent microenvironment. We then successfully used HFI to monitor intracellular autophagy induced by starvation or drugs in real-time. Interestingly, HFI also enabled us to visualize the occurrence of autophagy in the liver tissue of a DILI model, as well as the reversible effect of hepatoprotective drugs on this event. Conclusions In this study, we developed the first ratiometric dual-responsive fluorescent probe, HFI, for real-time revealing autophagic details. It could image lysosomes with minimal perturbation to their inherent pH, allowing us to track changes in lysosomal viscosity and pH in living cells. Ultimately, HFI has great potential to serve as a useful indicator for autophagic changes in viscosity and pH in complex biological samples and can also be used to assess drug safety.

A Simplified Method to Predict Damage of Axially-Loaded Circular RC Columns Under Lateral Impact Loading

Bin Liu,Wei Fan,Xu Huang,Xudong Shao,Lijing Kang 한국콘크리트학회 2020 International Journal of Concrete Structures and M Vol.14 No.4

Detailed finite element (FE) models are often employed to predict the impact responses of reinforced concrete (RC) columns. However, they always require substantial investments of time and effort in modeling and analysis so that they are not widely used in practice, particularly in preliminary designs. Moreover, although some simplified models have been established for beams and slabs under impact loading, few attempts have been made on modeling RC columns. For these reasons, this paper proposes a simplified modeling method to accurately capture the impact-induced response and damage of circular RC columns. In the proposed method, a two-degree-of-freedom (DOF) system was used to describe the interaction between the impactor and the impacted column. The formulas, and procedure to estimate the force-deformation relationship with strain-rate effects were presented according to the section-based analysis. The influence of the unloading stiffness on the residual deformation was addressed, and the method to determine the unloading stiffness of circular columns was proposed. Furthermore, a fiber-based beam-column element modeling method was developed to estimate the force-deformation relationship of the columns with strain-rate effects. The proposed simplified method was demonstrated by the drop-hammer impact tests to be capable of predicting the impact response of RC columns well. Its accuracy in the residual deformation is superior to that of the detailed FE simulation. Parametric studies were performed to investigate the damage characteristics of axially-loaded circular RC columns under various impact scenarios.