Functional mechanisms for diabetic nephropathy-associated genetic variants

Hong Xu,Chengxin Gong,Yonghu Xu,Yongfang Fan,Xingzi Liu,Chaopeng Xiong,Luling He,Changle Liu,Shenqiang Rao,Wen Xiao,Lu Ding,Lan Tang,Fangfang Hu,Mengqi Xiong,Mei Yang,Shangdong Liang 한국유전학회 2016 Genes & Genomics Vol.38 No.7

Diabetic nephropathy (DN) is one of the major complications of diabetes. A tremendous amount of genetic variations have been identified to be associated with DN. However, most of them only generate from statistical associations at the DNA level, generally without direct functional evidence regarding their association mechanisms underlying DN. Based on the publicly available datasets and resources, this study performed integrative analyses (expression quantitative trait loci analysis, differential gene expression analysis and functional prediction analysis) to detect the molecular functional mechanisms underlying the associations for DN. Among 150 selected (P\E-4) genetic associations that were archived in the public databases, two single nucleotide polymorphisms (SNPs) (rs3135377 and rs9469220) have been found to act as cis-effect regulators of the ‘‘identified’’ gene (HLADRA and HLA-DRB1). These eQTL genes have differential expression signals in the DN-associated cell groups. These SNPs were predicted as regulatory sites by utilizing online prediction tools. Our data suggest potential mechanistic links underlying the association between DN and two identified SNPs. These results could help us to have a deeper understanding of the functional relevance of genetic variants with susceptibility to DN, which is useful for pursuit of in-depth validation studies to dissect their involvements and molecular functional mechanisms in DN.

Comparative energy content and amino acid digestibility of barley obtained from diverse sources fed to growing pigs

Hong Liang Wang,Meng Shi,Xiao Xu,Xiao Kang Ma,Ling Liu,Xiang Shu Piao 아세아·태평양축산학회 2017 Animal Bioscience Vol.30 No.7

Objective: Two experiments were conducted to determine the content of digestible energy (DE) and metabolizable energy (ME) as well as the apparent ileal digestibility (AID) and standardized ileal digestibility (SID) of crude protein (CP) and amino acids (AA) in barley grains obtained from Australia, France or Canada. Methods: In Exp. 1, 18 growing barrows (Duroc×Landrace×Yorkshire; 31.5±3.2 kg) were individually placed in stainless-steel metabolism crates (1.4×0.7×0.6 m) and randomly allotted to 1 of 3 test diets. In Exp. 2, eight crossbred pigs (30.9±1.8 kg) were allotted to a replicate 3×4 Youden Square designed experiment with three periods and four diets. Two pigs received each diet during each test period. The diets included one nitrogen-free diet and three test diets. Results: The relative amounts of gross energy (GE), CP, and all AA in the Canadian barley were higher than those in Australian and French barley while higher concentrations of neutral detergent fiber, acid detergent fiber, total dietary fiber, insoluble dietary fiber and β-glucan as well as lower concentrations of GE and ether extract were observed in the French barley compared with the other two barley sources. The DE and ME as well as the SID of histidine, isoleucine, leucine and phenylalanine in Canadian barley were higher (p<0.05) than those in French barley but did not differ from Australian barley. Conclusion: Differences in the chemical composition, energy content and the SID and AID of AA were observed among barley sources obtained from three countries. The feeding value of barley from Canada and Australia was superior to barley obtained from France which is important information in developing feeding systems for growing pigs where imported grains are used.

Metastasis associated genomic aberrations in stage II rectal cancer

Hong Zhao,Zhi-Zhou Shi,Rui Jiang,Dong-Bing Zhao,Hai-Tao Zhou,Jian-Wei Liang,Xin-Yu Bi,Jian-Jun Zhao,Zhi-Yu Li,Jian-Guo Zhou,Zhen Huang,Ye-Fan Zhang,Jian Wang,Xin Xu,Yan Cai,Ming-Rong Wang,Yu Zhang 한국유전학회 2016 Genes & Genomics Vol.38 No.11

Genomic aberrations of rectal carcinoma, especially DNA copy number changes associated with metastasis were largely unclear. We aim to identify the metastasis associated biomarkers in stage II rectal cancer. Formalin-fixed, paraffin-embedded primary tumor tissues of stage II rectal carcinoma were analyzed by array-based comparative genomic hybridization, and genomic aberrations were identified by Genomic Workbench and SAM software. Copy number changes and mRNA expressions were validated by Real-time PCR in an independent rectal cancer samples. The results showed that the most frequent gains in stage II rectal cancer were at 1q21.2-q23.1, 3p21.31, 11q12.2-q23.3, 12q24.11-q24.31, 12q13.11-q14.1 and losses in 18q11.2-q23, 17q21.33-q22, 13q31.1-q31.3, 21q21.1-q21.3, 8p23.3-p23.1 and 4q22.1-q23. Twenty-two amplifications and five homozygous deletions were also identified. We further found that S100A1 (1q21.3-q23.1), MCM7 (7q22.1) and JUND (19p13.11) were amplified and overexpressed in stage II rectal cancer. Interestingly, the genomic aberrations affected 14 signaling pathways including VEGF signaling pathway and fatty acid metabolism. Most importantly, loss of 13q31.1-q34 and gain of 1q44 were associated with distant metastasis. Our results indicated that these metastasis associated genomic changes may be useful to reveal the pathogenesis of rectal cancer metastasis and identify candidate biomarkers.

EST-SSRs characterization and in-silico alignments with linkage map SSR loci in Grape (Vitis L.) genome

Hong Huang,Xia Xu,Xiaoqin Yang,Shuang Liang,Jiao Wu,Jiang Lu 한국유전학회 2012 Genes & Genomics Vol.34 No.1

11,581 grape (Vitis L.) EST-SSRs were produced and characterized from a total of 381,609 grape ESTs. Among the EST-SSRs, the tri repeat (5,560, 45.4%) represented the most abundant class of microsatellites in grape EST. Most of grape EST-SSR motifs fall within 18-24 bps in length. The EST-SSRs tri- repeats occurred a higher percentage in 5'-end (59.3%) than in 3'-end (48.3%). And EST-SSR tri- repeats had abundant codon repeats for putative amino acid runs as Proline, Arginine in grape ESTs. To better utilizing these markers, 142 of newly developed and validated EST SSR loci as well as 223 linkage map SSR loci were in silico aligned and mapped in grape genome. The orders of these SSR loci in the chromosomal physical locations and in the linkage groups were compared, and about twenty linkage map loci positions were switched or rearranged in grape genome. The EST-SSR markers extended the linkage map in grape genome. The method of in silico mapping reported in this study provided an initial collection for grape mapping resources. This approach offers great opportunities to understand the genetic variations in nucleotide sequences differences in physical map,and genetic recombination in linkage maps, as well as benefits for markers enrichment in a specific grape genome region for fine mapping or QTL mapping.

Partial dehulling increases the energy content and nutrient digestibility of barley in growing pigs

Hong Liang Wang,Meng Shi,Xiao Xu,Long Pan,Ling Liu,Xiang Shu Piao 아세아·태평양축산학회 2017 Animal Bioscience Vol.30 No.4

Objective: The hull attached to the barley kernel can be mechanically removed thus reducing the fiber content of the barley. This experiment was carried out to evaluate the effects of partial dehulling on the nutrient digestibility as well as the digestible energy (DE) and metabolizable energy (ME) content of barley in pigs. Methods: Two hulled barley samples (high fiber barley [HF] and low fiber barley [LF]) with either high or low fiber contents were obtained from the Hubei and Jiangsu Provinces of China. A portion of the two barleys was mechanically dehulled (dehulled high fiber barley [DHF] and dehulled low fiber barley [DLF]). Thirty barrows (initial BW = 31.5±3.2 kg) were assigned to one of five diets in a randomized complete block design. The five diets consisted of 96.9% corn, HF, LF, DHF, or DLF supplemented with 3.1% minerals and vitamins. Each diet was fed to six barrows housed in individual metabolism crates for a 10-d acclimation period followed by a 5-day total but separate collection of feces and urine. Results: The daily loss of gross energy (GE) in feces was lower (p<0.01) for pigs fed DHF than for those fed HF. The daily N intake and fecal N loss were lowest (p<0.01) for pigs fed the corn diet. The DE and ME as well as the apparent total tract digestibility (ATTD) of dry matter, GE, organic matter, neutral detergent fiber (NDF) and acid detergent fiber (ADF) of DHF or DLF were higher (p<0.01) than the values in HF and LF, respectively while the values except the ATTD of NDF and ADF in DLF were higher (p<0.01) than the values in DHF and were comparable to corn. Conclusion: The DE and ME contents as well as the ATTD of nutrients in both DHF and DLF barley were improved compared with the HF and LF barley. Moreover, the nutritive value of DLF barley was comparable to the yellow-dent corn used in the study.

Vibration performance characteristics of a long-span and light-weight concrete floor under human-induced loads

Liang Cao,Jie-Peng Liu,Xu-Hong Zhou,Y. Frank Chen 국제구조공학회 2018 Structural Engineering and Mechanics, An Int'l Jou Vol.65 No.3

An extensive research was undertaken to study the vibration serviceability of a long-span and light-weight floor subjected to human loading experimentally and numerically. Specifically, heel-drop test was first conducted to capture the floor’s natural frequencies and damping ratios, followed by jumping and running tests to obtain the acceleration responses. In addition, numerical simulations considering walking excitation were performed to further evaluate the vibration performance of a multi-panel floor under different loading cases and walking rates. The floor is found to have a high frequency (11.67 Hz) and a low damping ratio (2.32%). The comparison of the test results with the published data from the 1997 AISC Design Guide 11 indicates that the floor exhibits satisfactory vibration perceptibility overall. The study results show that the peak acceleration is affected by the walking path, walking rate, and adjacent structure. A simpler loading case may be considered in design in place of a more complex one.

Synthesis, Structures and Properties of Three Metal-organic Frameworks Based on 3-(4-((1H-imidazol-1-yl)methyl)phenyl)acrylic Acid

Liang, Peng,Ren, Tian-Tian,Tian, Wei-Man,Xu, Wen-Jia,Pan, Gang-Hong,Yin, Xian-Hong Korean Chemical Society 2014 Bulletin of the Korean Chemical Society Vol.35 No.1

Three new transition metal complexes based on Ozagrel $[Cu(Ozagrel)]_n$ (1), $[Zn(Ozagrel)(Cl)]_n$ (2), ${[Mn_2-(Ozagrel)(1,4-ndc)_2]{\cdot}(H_2O)}_n$ (3), (Ozagrel = 3-(4-((1H-imidazol-1-yl)methyl)phenyl)acrylic acid; 1,4-ndc = 1,4-Naphthalenedicarboxylic acid) have been hydrothermally synthesized and characterized by elemental analyse, IR, TG, PXRD, electrochemical analysis and single crystal X-ray diffraction. X-ray structure analysis reveals that 1 and 3 are 3D coordination polymers, while complex 2 is a two-dimensional network polymer, the 2D layers are further packed into 3D supramolecular architectures that are connected through hydrogen bonds. The electrochemistry of 1-3 was studied by cyclic voltammetry in methanol and water using a glassy carbon working electrode. Also, thermal decomposition process and powder X-ray diffraction of complexes were investigated.

Transcriptome sequencing and analysis of sweet osmanthus (Osmanthus fragrans Lour.)

Hong Na Mu,Liang Gui Wang,Huo Gen Li,Xiu Lian Yang,Tao Ze Sun,Chen Xu 한국유전학회 2014 Genes & Genomics Vol.36 No.6

Osmanthus fragrans is a woody, evergreenspecies of shrubs and small trees that is extensively plantedin sub-tropical and temperate climates as an ornamentalplant in gardens and for its health benefits. The flower colorranges from ivory to orange to pink among different varietiesand even color difference during the whole blossom inthe sweet osmanthus. Sweet osmanthus is widely cultivatedthroughout China and other countries due to its prominentfragrance, colorful flowers, and medicinal properties. However, the scanty genomic resources in the Olea familyhave greatly hindered further exploration of its geneticmechanism on these economically important traits. In thisstudy, transcriptome sequencing of O. fragrans was performedusing the Illumina HighSeqTM2000 sequencingplatform. Next generation sequencing (NGS) of the transcriptomeof O. fragrans produced 31.7G of clean bases(211,266,818 clean reads) that were assembled into256,774 transcripts and 117,595 unigenes. Of them, 197and 237 candidate genes involved in fragrance and pigmentbiosynthesis respectively were identified based on functionannotation. Meanwhile, 1 unnamed protein and 468 functionalunknown genes were also identified. Furthermore,mRNA sequencing expression profiling of O. fragranswere compared to previous genes’. In summary, thiscomprehensive transcriptome dataset allows the identificationof genes associated with several major metabolicpathways and provides a useful public information platformfor further functional genomic studiesin O. fragransLour.

Observation of the topological surface state in the nonsymmorphic topological insulator KHgSb

Liang, A. J.,Jiang, J.,Wang, M. X.,Sun, Y.,Kumar, N.,Shekhar, C.,Chen, C.,Peng, H.,Wang, C. W.,Xu, X.,Yang, H. F.,Cui, S. T.,Hong, G. H.,Xia, Y.-Y.,Mo, S.-K.,Gao, Q.,Zhou, X. J.,Yang, L. X.,Felser, C. American Physical Society 2017 Physical review. B Vol.96 No.16

<P>Topological insulators represent unusual topological quantum states, typically with gapped bulk band structure but gapless surface Dirac fermions protected by time-reversal symmetry. Recently, a distinct kind of topological insulator resulting from nonsymmorphic crystalline symmetry was proposed in the KHgX (X = As, Sb, Bi) compounds. Unlike regular topological crystalline insulators, the nonsymmorphic glide-reflection symmetry in KHgX guarantees the appearance of an exotic surface fermion with hourglass shape dispersion (where two pairs of branches switch their partners) residing on its (010) side surface, contrasting to the usual two-dimensional Dirac fermion form. Here, by using high-resolution angle-resolved photoemission spectroscopy, we systematically investigate the electronic structures of KHgSb on both (001) and (010) surfaces and reveal the unique in-gap surface states on the (010) surface with delicate dispersion consistent with the 'hourglass Fermion' recently proposed. Our experiment strongly supports that KHgSb is a nonsymmorphic topological crystalline insulator with hourglass fermions, which serves as an important step to the discovery of unique topological quantum materials and exotic fermions protected by nonsymmorphic crystalline symmetry.</P>

MicroRNA-155 Expression has Prognostic Value in Patients with Non-small Cell Lung Cancer and Digestive System Carcinomas

Xu, Tong-Peng,Zhu, Can-Hong,Zhang, Jian,Xia, Rui,Wu, Feng-Lei,Han, Liang,Shen, Hua,Liu, Ling-Xiang,Shu, Yong-Qian Asian Pacific Journal of Cancer Prevention 2013 Asian Pacific journal of cancer prevention Vol.14 No.12

Objective: Published data have shown that microRNAs (miRNAs) could play a potential role as diagnostic and prognostic indicators in cancers. Data for the predictive value of microRNA-155 are inconclusive. The aim of the present analysis was therefore to evaluate the role of miR-155 in prognosis for patients with a variety of carcinomas. Methods: Relevant studies were identified by searching PubMed and EMBASE. Data were extracted from studies comparing overall survival (OS), recurrence-free survival (RFS) or cancer-specific survival (CSS) in patients with carcinoma with higher miR-155 expression and those with lower levels. The pooled hazard ratios (HRs) and 95% confidence intervals (CIs) of miR-155 for clinical outcome were calculated. Results: A total of 15 studies were included. The pooled hazard ratio (HR) for OS of higher miR-155 expression in cancerous tissue was 1.89 (95% CI: 1.20-2.99, P=0.006), which could markedly predict poorer survival in general cancer. For RFS/CSS, elevated miR-155 was also associated with poor prognosis of cancer (HR=1.50, 95% CI: 1.10-2.05, P=0.01). On subgroup analysis, the pooled HR for OS in non-small cell lung cancer (NSCLC) was 2.09 (95% CI: 0.68-6.41, P > 0.05), but for RFS/CSS was 1.28 (95% CI: 1.05-1.55, P=0.015), with statistical significance; the pooled HRs for OS and RFS/CSS in digestive system neoplasms were 3.04 (95% CI: 1.48-6.24, P=0.003) and 2.61 (95% CI: 1.98-3.42, P<0.05), respectively. Conclusions: The results indicated that the miR-155 expression level plays a prognostic role in patients with cancer, especially NSCLCs and digestive system carcinomas.