Polymorphisms in Epigenetic and Meat Quality Related Genes in Fourteen Cattle Breeds and Association with Beef Quality and Carcass Traits

Liu, Xuan,Usman, Tahir,Wang, Yachun,Wang, Zezhao,Xu, Xianzhou,Wu, Meng,Zhang, Yi,Zhang, Xu,Li, Qiang,Liu, Lin,Shi, Wanhai,Qin, Chunhua,Geng, Fanjun,Wang, Congyong,Tan, Rui,Huang, Xixia,Liu, Airong,Wu, Asian Australasian Association of Animal Productio 2015 Animal Bioscience Vol.28 No.4

Improvement for carcass traits related to beef quality is the key concern in beef production. Recent reports found that epigenetics mediates the interaction of individuals with environment and nutrition. The present study was designed to analyze the genetic effect of single nucleotide polymorphisms (SNPs) in seven epigenetic-related genes (DNMT1, DNMT3a, DNMT3b, DNMT3L, Ago1, Ago2, and HDAC5) and two meat quality candidate genes (CAPN1 and PRKAG3) on fourteen carcass traits related to beef quality in a Snow Dragon beef population, and also to identify SNPs in a total of fourteen cattle populations. Sixteen SNPs were identified and genotyped in 383 individuals sampled from the 14 cattle breeds, which included 147 samples from the Snow Dragon beef population. Data analysis showed significant association of 8 SNPs within 4 genes related to carcass and/or meat quality traits in the beef populations. SNP1 (13154420A>G) in exon 17 of DNMT1 was significantly associated with rib-eye width and lean meat color score (p<0.05). A novel SNP (SNP4, 76198537A>G) of DNMT3a was significantly associated with six beef quality traits. Those individuals with the wild-type genotype AA of DNMT3a showed an increase in carcass weight, chilled carcass weight, flank thicknesses, chuck short rib thickness, chuck short rib score and in chuck flap weight in contrast to the GG genotype. Five out of six SNPs in DNMT3b gene were significantly associated with three beef quality traits. SNP15 (45219258C>T) in CAPN1 was significantly associated with chuck short rib thickness and lean meat color score (p<0.05). The significant effect of SNP15 on lean meat color score individually and in combination with each of other 14 SNPs qualify this SNP to be used as potential marker for improving the trait. In addition, the frequencies of most wild-type alleles were higher than those of the mutant alleles in the native and foreign cattle breeds. Seven SNPs were identified in the epigenetic-related genes. The SNP15 in CAPN1 could be used as a powerful genetic marker in selection programs for beef quality improvement in the Snow Dragon Beef population.

Liquid/Liquid Interfacial Fabrication of Thermosensitive and Catalytically Active Ag Nanoparticle-Doped Block Copolymer Composite Foam Films

Liu, Mei,Wang, Qian,Geng, Yuanyuan,Wang, Changwei,Lee, Yong-Ill,Hao, Jingcheng,Liu, Hong-Guo American Chemical Society 2014 Langmuir Vol.30 No.34

<P>An aqueous solution of AgNO<SUB>3</SUB> (upper phase) and a DMF/CHCl<SUB>3</SUB> solution of polystyrene-<I>b</I>-poly(acryl acid)-<I>b</I>-polystyrene (PS-<I>b</I>-PAA-<I>b</I>-PS) or PS-<I>b</I>-PAA-<I>b</I>-PS/1,6-diaminohexane (DAH) (lower phase) constituted a planar liquid/liquid interface. The lower phase gradually transformed to a water-in-oil (W/O) emulsion via spontaneous emulsification due to the “ouzo effect”. Polymer molecules, DAH molecules, and Ag<SUP>+</SUP> ions assembled into microcapsules around emulsion droplets that adsorbed at the planar liquid/liquid interface, resulting in formation of a foam film. DAH acted as a cross-linker during this process. Transmission electron microscopic observations indicated that Ag nanoclusters that were generated through reduction of Ag<SUP>+</SUP> ions by DMF were homogeneously dispersed in the walls of the foam structure. X-ray photoelectron spectroscopic investigations revealed that Ag(I) and Ag(0) coexisted in the film, and Ag(I) transformed to Ag(0) after further treatment. The film formed without DAH was not stable, while the film formed with DAH was very stable due to intermolecular attraction between PAA and DAH and formation of amides, as revealed by FTIR spectra. The film formed with DAH exhibited high and durable catalytic activity for hydrogenation of nitro compounds and, very interestingly, exhibited thermoresponsive catalytic behavior.</P><P><B>Graphic Abstract</B> <IMG SRC='http://pubs.acs.org/appl/literatum/publisher/achs/journals/content/langd5/2014/langd5.2014.30.issue-34/la502738j/production/images/medium/la-2014-02738j_0012.gif'></P><P><A href='http://pubs.acs.org/doi/suppl/10.1021/la502738j'>ACS Electronic Supporting Info</A></P>

Study on Importance Function for Particle Filter

Liu Lu,Meng Yang,Shu Geng,Shu-fen Wang,Yong-hui Wang 보안공학연구지원센터 2015 International Journal of Multimedia and Ubiquitous Vol.10 No.2

As an important nonlinear filter theory, particle filter is a heated issue in domestic and foreign researches. The option of importance density is one of the key steps of particle filter algorithm. The proper option of importance density can minish the negative influence of filter algorithm caused by degeneracy problem. This paper introduces several widely-used options of importance density systemically, and analyzes their features and applied perspectives respectively. The paper also advances a comprehensive method of importance density, analyzes its technical features, explores the adjudgement and improvement of this method based on various performance, and finally puts forward the necessary further study according to the engineer requirements.

Identification of onlline users' type based on clustering

Geng Peng,Tianqi Li,Fan Liu,Ying Liu,Benfu Lv 인하대학교 정석물류통상연구원 2009 인하대학교 정석물류통상연구원 학술대회 Vol.2009 No.10

User’s browsing on shopping websites is a complicated process which is affected by many factors. The users with different purposes and backgrounds tend to show different behavioral characteristics and shopping intentions, which areal hidden in weblog data of the sites. In this paper, we firstly introduce the method of data mining to cluster a month weblog data of a publishing house website, and then identify four types of online users: purchasing, browsing, information accumulating, and superficiality. Finally, we give an explanation for each type user in detail. The study of this paper could be used to improve marketing plans and shopping experiences of sites.

Differential Protein Expression Profile Between CD20 Positive and Negative Cells of the NCI-H929 Cell Line

Geng, Chuan-Ying,Liu, Nian,Yang, Guang-Zhong,Liu, Ai-Jun,Leng, Yun,Wang, Hui-Juan,Li, Li-Hong,Wu, Yin,Li, Yan-Chen,Chen, Wen-Ming Asian Pacific Journal of Cancer Prevention 2012 Asian Pacific journal of cancer prevention Vol.13 No.11

At present, multiple myeloma (MM) remains an incurable disease and cologenic cells may be responsible for disease relapse. It has been proposed that CD20+/CD138- NCI-H929 cells could be hallmarks of MM clonogenic cells. Here, the immunology phenotype of NCI-H929 cells is described. Only a small population of CD20+/CD138- cells (<1%) was found in the NCI-H929 cell line, but CD20+/CD138- cells were not detected. We found that CD20+/CD138+ cells were able to exhibit cologenic capacity by colony formation assay and continuous passage culture. Proteins were analyzed by 1D-SDS-PAGE and TMT based quantitative differential liquid chromatography tandem mass spectrometry (LC-MS/MS). 1,082 non-redundant proteins were identified, 658 of which were differentially expressed with at least a 1.5-fold difference. 205 proteins in CD20+ cells were expressed at higher levels and 453 proteins were at lower levels compared with CD20- cells. Most proteins had catalytic and binding activity and mainly participated in metabolic processes, cell communication and molecular transport. These results proved that there are different biological features and protein expression profile between CD20+ and CD20- cells in the NCI-H929 cell line.

Fabrication of Composite Polymer Foam Films at the Liquid/Liquid Interface through Emulsion-Directed Assembly and Adsorption Processes

Geng, Yuanyuan,Liu, Mei,Tong, Kun,Xu, Jian,Lee, Yong-Ill,Hao, Jingcheng,Liu, Hong-Guo American Chemical Society 2014 Langmuir Vol.30 No.8

<P>The foam films of polystyrene-<I>b</I>-poly(acrylic acid)-<I>b</I>-polystyrene (PS-<I>b</I>-PAA-<I>b</I>-PS) doped with Cd(II) or Pb(II) species were fabricated at the planar liquid/liquid interfaces between a DMF/chloroform (v/v: 1/1) solution of the polymer and aqueous solutions containing cadmium acetate or lead acetate at ambient temperature. Optical microscopic observation shows the thin film is uniform on a larger length scale. Transmission electron microscopic (TEM) investigations reveal that the foam films are made up of microcapsules with the size of several hundreds of nanometers to micrometers. The walls of the microcapsules have a layered structure decorating with nanofibers and hollow nanospheres, where numerous inorganic fine nanoparticles are dispersed homogeneously. The film formation is a result of emulsion droplet-templated assembly and adsorption of the formed microcapsules at the planar liquid/liquid interface. Because of the miscibility of DMF with chloroform and water, DMF migrates to the aqueous phase while water migrates to the organic phase across the interface, resulting in the formation of a W/O emulsion, as revealed by optical microscopic observation, freeze fracture transmission electron microscopic (FF-TEM) observation, and dynamic laser scattering (DLS) investigation. The triblock copolymer molecules and the inorganic species adsorb and self-assemble around the emulsion drops, leading to the formation of the composite microcapsules. X-ray photoelectron spectroscopic (XPS) and FTIR spectroscopic results indicate that two kinds of Cd(II) or Pb(II) species, metal oxide or hydroxide, resulting from the hydrolysis of the metal ions and the coordinated metal ions to the carboxyl groups coexist in the formed thin films, which transform to metal sulfide completely after treating with hydrogen sulfide to get metal sulfide nanoparticle-doped polymer thin films.</P><P><B>Graphic Abstract</B> <IMG SRC='http://pubs.acs.org/appl/literatum/publisher/achs/journals/content/langd5/2014/langd5.2014.30.issue-8/la500187d/production/images/medium/la-2014-00187d_0012.gif'></P><P><A href='http://pubs.acs.org/doi/suppl/10.1021/la500187d'>ACS Electronic Supporting Info</A></P>

Condition monitoring of inverter power devices based on electromagnetic acoustic emissions

Fei Liu,Chenghao Zeng,Liang Cheng,Yunze He,Yun Bai,Xuefeng Geng,Songyuan Liu,Dantong Ren,Lei Wang 전력전자학회 2022 JOURNAL OF POWER ELECTRONICS Vol.22 No.12

Unlike conventional voltage and current sensing, this paper studies the use of acoustic emission signals to detect the condition of the power device for a DC–AC inverter. As a relatively new method for monitoring power devices, there are some unknown phenomena in acoustic emissions (also called mechanical stress wave). Therefore, the authors present an experimental setup that is used to analyze acoustic emission signals. Based on experimental results, some interesting points have been found: (1) The generation of a mechanical stress wave is verified for the first time. (2) The time-domain peak value, energy, and rise time of the mechanical stress wave at the turn-on time of a power device are barely affected by the load. Meanwhile, these values decrease with an increase of the load at the turn-off time. (3) The frequency-domain peak value of the mechanical stress wave tends to decrease with an increase of the load, and the peak frequency is barely affected by the load. These mechanical stress analysis results can be utilized for condition monitoring in many applications.

Autophagy of bovine mammary epithelial cell induced by intracellular Staphylococcus aureus

Na Geng,Kangping Liu,Jianwei Lu,Yuliang Xu,Xiaozhou Wang,Run Wang,Jianzhu Liu,Yongxia Liu,Bo Han 한국미생물학회 2020 The journal of microbiology Vol.58 No.4

Bovine mastitis is a common disease in the dairy industry that causes great economic losses. As the primary pathogen of contagious mastitis, Staphylococcus aureus (S. aureus) can invade bovine mammary epithelial cells, thus evading immune defenses and resulting in persistent infection. Recently, autophagy has been considered an important mechanism for host cells to clear intracellular pathogens. In the current study, autophagy caused by S. aureus was detected, and the correlation between autophagy and intracellular S. aureus survival was assessed. First, a model of intracellular S. aureus infection was established. Then, the autophagy of MAC-T cells was evaluated by confocal microscopy and western blot. Moreover, the activation of the PI3K-Akt-mTOR and ERK1/2 signaling pathways was determined by western blot. Finally, the relationship between intracellular bacteria and autophagy was analyzed by using autophagy regulators (3-methyladenine [3-MA], rapamycin [Rapa] and chloroquine [CQ]). The results showed that S. aureus caused obvious induction of autophagosome formation, transformation of LC3I/II, and degradation of p62/SQSTM1 in MAC-T cells; furthermore, the PI3K-Akt-mTOR and ERK1/2 signaling pathways were activated. The number of intracellular S. aureus increased significantly with autophagy activation by rapamycin, whereas the number decreased when the autophagy flux was inhibited by chloroquine. Therefore, this study indicated that intracellular S. aureus can induce autophagy and utilize it to survive in bovine mammary epithelial cells.

Polymorphisms in Epigenetic and Meat Quality Related Genes in Fourteen Cattle Breeds and Association with Beef Quality and Carcass Traits

Xuan Liu,Tahir Usman,Yachun Wang,Zezhao Wang,Xianzhou Xu,Meng Wu,Yi Zhang,Xu Zhang,Qiang Li,Lin Liu,Wanhai Shi,Chunhua Qin,Fanjun Geng,Congyong Wang,Rui Tan,Xixia Huang,Airong Liu,Hongjun Wu,Shixin Ta 아세아·태평양축산학회 2015 Animal Bioscience Vol.28 No.4

Improvement for carcass traits related to beef quality is the key concern in beef production. Recent reports found that epigenetics mediates the interaction of individuals with environment and nutrition. The present study was designed to analyze the genetic effect of single nucleotide polymorphisms (SNPs) in seven epigenetic-related genes (DNMT1, DNMT3a, DNMT3b, DNMT3L, Ago1, Ago2, and HDAC5) and two meat quality candidate genes (CAPN1 and PRKAG3) on fourteen carcass traits related to beef quality in a Snow Dragon beef population, and also to identify SNPs in a total of fourteen cattle populations. Sixteen SNPs were identified and genotyped in 383 individuals sampled from the 14 cattle breeds, which included 147 samples from the Snow Dragon beef population. Data analysis showed significant association of 8 SNPs within 4 genes related to carcass and/or meat quality traits in the beef populations. SNP1 (13154420A>G) in exon 17 of DNMT1 was significantly associated with rib-eye width and lean meat color score (p<0.05). A novel SNP (SNP4, 76198537A>G) of DNMT3a was significantly associated with six beef quality traits. Those individuals with the wild-type genotype AA of DNMT3a showed an increase in carcass weight, chilled carcass weight, flank thicknesses, chuck short rib thickness, chuck short rib score and in chuck flap weight in contrast to the GG genotype. Five out of six SNPs in DNMT3b gene were significantly associated with three beef quality traits. SNP15 (45219258C>T) in CAPN1 was significantly associated with chuck short rib thickness and lean meat color score (p<0.05). The significant effect of SNP15 on lean meat color score individually and in combination with each of other 14 SNPs qualify this SNP to be used as potential marker for improving the trait. In addition, the frequencies of most wild-type alleles were higher than those of the mutant alleles in the native and foreign cattle breeds. Seven SNPs were identified in the epigenetic-related genes. The SNP15 in CAPN1 could be used as a powerful genetic marker in selection programs for beef quality improvement in the Snow Dragon Beef population.

Identification and expression profiles of chitin deacetylase genes in the rice leaf folder, Cnaphalocrocis medinalis

Hai-Zhong Yu,Ming-Hui Liu,Xue-Yang Wang,Xin Yang,Wan-Ling Wang,Lei Geng,Dong Yu,Xue-Lan Liu,Gui-Ying Liu,Jia-Ping Xu 한국응용곤충학회 2016 Journal of Asia-Pacific Entomology Vol.19 No.3

Chitin deacetylase (CDA) is an insect chitin degradation enzyme that catalyzes the deacetylation of chitin to form chitosan. In this study, combination of rapid-amplification of cDNA ends (RACE) technology with Cnaphalocrocis medinalis transcriptome database analysis revealed the presence of at least five C. medinalis CDAs (CmCDAs), which were CmCDA1, CmCDA2, CmCDA4, CmCDA5, and CmCDA6. The cDNA sequences of CmCDA1, CmCDA2, and CmCDA4 hadwhole open reading frame (ORF) for further analysis. Phylogenetic analysis indicated that insect CDAs could be categorized into five groups. CmCDAs' structural domain analysis revealed that all three CDAs contained the chitin deacetylase-like catalytic domain. CmCDA1 and CmCDA2 belong to Group I because they both contain the chitin-binding peritrophin-A domain (ChBD), low-density lipoprotein receptor class A domain (LDLa), and chitin deacetylase-like catalytic domain. CmCDA4 only contains ChBD and chitin deacetylase-like catalytic domain thus belongs to Group III. Tissue and developmental stage expression analysis showed that the expression levels of CmCDA1, CmCDA2, and CmCDA4 are significantly higher in the head than other tissues and also significantly higher in adults than in larvae. CmCDA5 had significantly higher expression in the integument than other tissues, suggesting potential roles in the process of degradation of chitin. In contrast, CmCDA5 showed relatively high expression in larvae. In conclusion, this study analyzed the cDNA sequences of three CDA genes and determined their expression and molecular characteristics, which provided a new sequence resource and improved the development of bio-pesticides and the biological pest control and contributed to management of this important agricultural pest.