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1.  Two unrelated patients with rare Crigler-Najjar syndrome type I: two novel mutations and a patient with loss of heterozygosity of UGT1A1 gene 
Crigler-Najjar syndrome type I (CN-I) is the most severe type of hereditary unconjugated hyperbilirubinemia. It is caused by homozygous or compound heterozygous mutations of the UDP-glycuronosyltransferase gene (UGT1A1) on chromosome 2q37. Two patients clinically diagnosed with CN-I were examined in this paper. We sequenced five exons and their flanking sequences, specifically the promoter region of UGT1A1, of the two patients and their parents. Quantitative real-time polymerase chain reaction (qRT-PCR) was used to determine the UGT1A1 gene copy number of one patient. In patient A, two mutations, c.239_245delCTGTGCC (p.Pro80HisfsX6; had not been reported previously) and c.1156G>T (p.Val386Phe), were identified. In patient B, we found that this patient had lost heterozygosity of the UGT1A1 gene by inheriting a deletion of one allele, and had a novel mutation c.1253delT (p.Met418ArgfsX5) in the other allele. In summary, we detected three UGT1A1 mutations in two CN-I patients: c.239_245delCTGTGCC (p.Pro80HisfsX6), c.1253delT (p.Met418ArgfsX5), and c.1156G>T (p.Val386Phe). The former two mutations are pathogenic; however, the pathogenic mechanism of c.1156G>T (p.Val386Phe) is unknown.
PMCID: PMC4076604  PMID: 24793765
Crigler-Najjar syndrome type I (CN-I); Hyperbilirubinemia; UDP-glycuronosyltransferase gene (UGT1A1); Mutation; Loss of heterozygosity
2.  Effect of dexmedetomidine on hippocampal neuron development and BDNF-TrkB signal expression in neonatal rats 
The study aimed to explore the effect of dexmedetomidine (DEX) on hippocampal neuron development process and on molecular expression of brain-derived neurotrophic factor (BDNF)-tyrosine receptor kinase B (TrkB) signaling pathway in neonatal rats. The hippocampal neuron cells were isolated from newborn neonatal rats and cultured in vitro. One control group and three treated groups with 1, 10, and 100 μmol/L DEX were used for the study. Cell activity and apoptosis were detected by the MTT and terminal deoxynucleotidyl transferase-mediated biotinylated uridine triphosphate (UTP) nick end labeling assays. The synaptophysin (SYN) and postsynaptic density 95 (PSD95) were detected by quantitative polymerase chain reaction. There was no difference in the viability of neuron cells among the different dose groups of DEX and the control group during days 2–10 (P>0.05). Compared to the control group, there was no significant difference (P>0.05) in the expressions of SYN and PSD95 in the groups treated with 1 and 10 μmol/L DEX, whereas significant difference in the expression was observed in the group treated with 100 μmol/L DEX (P<0.01). Compared with the control group, the expression of BDNF was significantly upregulated (P<0.05) in the group treated with 100 μmol/L DEX. There were no significant differences in TrkB expression among the four groups. The expression of p-N-methyl-D-aspartate receptor increased with an increase in the concentration of DEX; however, only the high dose revealed a significant upregulation compared with the control group. The neuroprotective effect of DEX may be achieved by upregulating the expression of BDNF and phosphorylation level of N-methyl-D-aspartate receptor.
PMCID: PMC5158139  PMID: 28003751
dexmedetomidine; hippocampal neuron; development; BDNF-TrkB
3.  Genetic evidence for an East Asian origin of Chinese Muslim populations Dongxiang and Hui 
Scientific Reports  2016;6:38656.
There is a long-going debate on the genetic origin of Chinese Muslim populations, such as Uygur, Dongxiang, and Hui. However, genetic information for those Muslim populations except Uygur is extremely limited. In this study, we investigated the genetic structure and ancestry of Chinese Muslims by analyzing 15 autosomal short tandem repeats in 652 individuals from Dongxiang, Hui, and Han Chinese populations in Gansu province. Both genetic distance and Bayesian-clustering methods showed significant genetic homogeneity between the two Muslim populations and East Asian populations, suggesting a common genetic ancestry. Our analysis found no evidence of substantial gene flow from Middle East or Europe into Dongxiang and Hui people during their Islamization. The dataset generated in present study are also valuable for forensic identification and paternity tests in China.
PMCID: PMC5141421  PMID: 27924949
4.  Self-patterning Gd nano-fibers in Mg-Gd alloys 
Scientific Reports  2016;6:38537.
Manipulating the shape and distribution of strengthening units, e.g. particles, fibers, and precipitates, in a bulk metal, has been a widely applied strategy of tailoring their mechanical properties. Here, we report self-assembled patterns of Gd nano-fibers in Mg-Gd alloys for the purpose of improving their strength and deformability. 1-nm Gd nano-fibers, with a 〈c〉-rod shape, are formed and hexagonally patterned in association with Gd segregations along dislocations that nucleated during hot extrusion. Such Gd-fiber patterns are able to regulate the relative activities of slips and twinning, as a result, overcome the inherent limitations in strength and ductility of Mg alloys. This nano-fiber patterning approach could be an effective method to engineer hexagonal metals.
PMCID: PMC5141485  PMID: 27924848
5.  Analysis of Heritability and Shared Heritability Based on Genome-Wide Association Studies for 13 Cancer Types 
Sampson, Joshua N. | Wheeler, William A. | Yeager, Meredith | Panagiotou, Orestis | Wang, Zhaoming | Berndt, Sonja I. | Lan, Qing | Abnet, Christian C. | Amundadottir, Laufey T. | Figueroa, Jonine D. | Landi, Maria Teresa | Mirabello, Lisa | Savage, Sharon A. | Taylor, Philip R. | Vivo, Immaculata De | McGlynn, Katherine A. | Purdue, Mark P. | Rajaraman, Preetha | Adami, Hans-Olov | Ahlbom, Anders | Albanes, Demetrius | Amary, Maria Fernanda | An, She-Juan | Andersson, Ulrika | Andriole, Gerald | Andrulis, Irene L. | Angelucci, Emanuele | Ansell, Stephen M. | Arici, Cecilia | Armstrong, Bruce K. | Arslan, Alan A. | Austin, Melissa A. | Baris, Dalsu | Barkauskas, Donald A. | Bassig, Bryan A. | Becker, Nikolaus | Benavente, Yolanda | Benhamou, Simone | Berg, Christine | Van Den Berg, David | Bernstein, Leslie | Bertrand, Kimberly A. | Birmann, Brenda M. | Black, Amanda | Boeing, Heiner | Boffetta, Paolo | Boutron-Ruault, Marie-Christine | Bracci, Paige M. | Brinton, Louise | Brooks-Wilson, Angela R. | Bueno-de-Mesquita, H. Bas | Burdett, Laurie | Buring, Julie | Butler, Mary Ann | Cai, Qiuyin | Cancel-Tassin, Geraldine | Canzian, Federico | Carrato, Alfredo | Carreon, Tania | Carta, Angela | Chan, John K. C. | Chang, Ellen T. | Chang, Gee-Chen | Chang, I-Shou | Chang, Jiang | Chang-Claude, Jenny | Chen, Chien-Jen | Chen, Chih-Yi | Chen, Chu | Chen, Chung-Hsing | Chen, Constance | Chen, Hongyan | Chen, Kexin | Chen, Kuan-Yu | Chen, Kun-Chieh | Chen, Ying | Chen, Ying-Hsiang | Chen, Yi-Song | Chen, Yuh-Min | Chien, Li-Hsin | Chirlaque, María-Dolores | Choi, Jin Eun | Choi, Yi Young | Chow, Wong-Ho | Chung, Charles C. | Clavel, Jacqueline | Clavel-Chapelon, Françoise | Cocco, Pierluigi | Colt, Joanne S. | Comperat, Eva | Conde, Lucia | Connors, Joseph M. | Conti, David | Cortessis, Victoria K. | Cotterchio, Michelle | Cozen, Wendy | Crouch, Simon | Crous-Bou, Marta | Cussenot, Olivier | Davis, Faith G. | Ding, Ti | Diver, W. Ryan | Dorronsoro, Miren | Dossus, Laure | Duell, Eric J. | Ennas, Maria Grazia | Erickson, Ralph L. | Feychting, Maria | Flanagan, Adrienne M. | Foretova, Lenka | Fraumeni, Joseph F. | Freedman, Neal D. | Beane Freeman, Laura E. | Fuchs, Charles | Gago-Dominguez, Manuela | Gallinger, Steven | Gao, Yu-Tang | Gapstur, Susan M. | Garcia-Closas, Montserrat | García-Closas, Reina | Gascoyne, Randy D. | Gastier-Foster, Julie | Gaudet, Mia M. | Gaziano, J. Michael | Giffen, Carol | Giles, Graham G. | Giovannucci, Edward | Glimelius, Bengt | Goggins, Michael | Gokgoz, Nalan | Goldstein, Alisa M. | Gorlick, Richard | Gross, Myron | Grubb, Robert | Gu, Jian | Guan, Peng | Gunter, Marc | Guo, Huan | Habermann, Thomas M. | Haiman, Christopher A. | Halai, Dina | Hallmans, Goran | Hassan, Manal | Hattinger, Claudia | He, Qincheng | He, Xingzhou | Helzlsouer, Kathy | Henderson, Brian | Henriksson, Roger | Hjalgrim, Henrik | Hoffman-Bolton, Judith | Hohensee, Chancellor | Holford, Theodore R. | Holly, Elizabeth A. | Hong, Yun-Chul | Hoover, Robert N. | Horn-Ross, Pamela L. | Hosain, G. M. Monawar | Hosgood, H. Dean | Hsiao, Chin-Fu | Hu, Nan | Hu, Wei | Hu, Zhibin | Huang, Ming-Shyan | Huerta, Jose-Maria | Hung, Jen-Yu | Hutchinson, Amy | Inskip, Peter D. | Jackson, Rebecca D. | Jacobs, Eric J. | Jenab, Mazda | Jeon, Hyo-Sung | Ji, Bu-Tian | Jin, Guangfu | Jin, Li | Johansen, Christoffer | Johnson, Alison | Jung, Yoo Jin | Kaaks, Rudolph | Kamineni, Aruna | Kane, Eleanor | Kang, Chang Hyun | Karagas, Margaret R. | Kelly, Rachel S. | Khaw, Kay-Tee | Kim, Christopher | Kim, Hee Nam | Kim, Jin Hee | Kim, Jun Suk | Kim, Yeul Hong | Kim, Young Tae | Kim, Young-Chul | Kitahara, Cari M. | Klein, Alison P. | Klein, Robert J. | Kogevinas, Manolis | Kohno, Takashi | Kolonel, Laurence N. | Kooperberg, Charles | Kricker, Anne | Krogh, Vittorio | Kunitoh, Hideo | Kurtz, Robert C. | Kweon, Sun-Seog | LaCroix, Andrea | Lawrence, Charles | Lecanda, Fernando | Lee, Victor Ho Fun | Li, Donghui | Li, Haixin | Li, Jihua | Li, Yao-Jen | Li, Yuqing | Liao, Linda M. | Liebow, Mark | Lightfoot, Tracy | Lim, Wei-Yen | Lin, Chien-Chung | Lin, Dongxin | Lindstrom, Sara | Linet, Martha S. | Link, Brian K. | Liu, Chenwei | Liu, Jianjun | Liu, Li | Ljungberg, Börje | Lloreta, Josep | Lollo, Simonetta Di | Lu, Daru | Lund, Eiluv | Malats, Nuria | Mannisto, Satu | Marchand, Loic Le | Marina, Neyssa | Masala, Giovanna | Mastrangelo, Giuseppe | Matsuo, Keitaro | Maynadie, Marc | McKay, James | McKean-Cowdin, Roberta | Melbye, Mads | Melin, Beatrice S. | Michaud, Dominique S. | Mitsudomi, Tetsuya | Monnereau, Alain | Montalvan, Rebecca | Moore, Lee E. | Mortensen, Lotte Maxild | Nieters, Alexandra | North, Kari E. | Novak, Anne J. | Oberg, Ann L. | Offit, Kenneth | Oh, In-Jae | Olson, Sara H. | Palli, Domenico | Pao, William | Park, In Kyu | Park, Jae Yong | Park, Kyong Hwa | Patiño-Garcia, Ana | Pavanello, Sofia | Peeters, Petra H. M. | Perng, Reury-Perng | Peters, Ulrike | Petersen, Gloria M. | Picci, Piero | Pike, Malcolm C. | Porru, Stefano | Prescott, Jennifer | Prokunina-Olsson, Ludmila | Qian, Biyun | Qiao, You-Lin | Rais, Marco | Riboli, Elio | Riby, Jacques | Risch, Harvey A. | Rizzato, Cosmeri | Rodabough, Rebecca | Roman, Eve | Roupret, Morgan | Ruder, Avima M. | de Sanjose, Silvia | Scelo, Ghislaine | Schned, Alan | Schumacher, Fredrick | Schwartz, Kendra | Schwenn, Molly | Scotlandi, Katia | Seow, Adeline | Serra, Consol | Serra, Massimo | Sesso, Howard D. | Setiawan, Veronica Wendy | Severi, Gianluca | Severson, Richard K. | Shanafelt, Tait D. | Shen, Hongbing | Shen, Wei | Shin, Min-Ho | Shiraishi, Kouya | Shu, Xiao-Ou | Siddiq, Afshan | Sierrasesúmaga, Luis | Sihoe, Alan Dart Loon | Skibola, Christine F. | Smith, Alex | Smith, Martyn T. | Southey, Melissa C. | Spinelli, John J. | Staines, Anthony | Stampfer, Meir | Stern, Marianna C. | Stevens, Victoria L. | Stolzenberg-Solomon, Rachael S. | Su, Jian | Su, Wu-Chou | Sund, Malin | Sung, Jae Sook | Sung, Sook Whan | Tan, Wen | Tang, Wei | Tardón, Adonina | Thomas, David | Thompson, Carrie A. | Tinker, Lesley F. | Tirabosco, Roberto | Tjønneland, Anne | Travis, Ruth C. | Trichopoulos, Dimitrios | Tsai, Fang-Yu | Tsai, Ying-Huang | Tucker, Margaret | Turner, Jenny | Vajdic, Claire M. | Vermeulen, Roel C. H. | Villano, Danylo J. | Vineis, Paolo | Virtamo, Jarmo | Visvanathan, Kala | Wactawski-Wende, Jean | Wang, Chaoyu | Wang, Chih-Liang | Wang, Jiu-Cun | Wang, Junwen | Wei, Fusheng | Weiderpass, Elisabete | Weiner, George J. | Weinstein, Stephanie | Wentzensen, Nicolas | White, Emily | Witzig, Thomas E. | Wolpin, Brian M. | Wong, Maria Pik | Wu, Chen | Wu, Guoping | Wu, Junjie | Wu, Tangchun | Wu, Wei | Wu, Xifeng | Wu, Yi-Long | Wunder, Jay S. | Xiang, Yong-Bing | Xu, Jun | Xu, Ping | Yang, Pan-Chyr | Yang, Tsung-Ying | Ye, Yuanqing | Yin, Zhihua | Yokota, Jun | Yoon, Ho-Il | Yu, Chong-Jen | Yu, Herbert | Yu, Kai | Yuan, Jian-Min | Zelenetz, Andrew | Zeleniuch-Jacquotte, Anne | Zhang, Xu-Chao | Zhang, Yawei | Zhao, Xueying | Zhao, Zhenhong | Zheng, Hong | Zheng, Tongzhang | Zheng, Wei | Zhou, Baosen | Zhu, Meng | Zucca, Mariagrazia | Boca, Simina M. | Cerhan, James R. | Ferri, Giovanni M. | Hartge, Patricia | Hsiung, Chao Agnes | Magnani, Corrado | Miligi, Lucia | Morton, Lindsay M. | Smedby, Karin E. | Teras, Lauren R. | Vijai, Joseph | Wang, Sophia S. | Brennan, Paul | Caporaso, Neil E. | Hunter, David J. | Kraft, Peter | Rothman, Nathaniel | Silverman, Debra T. | Slager, Susan L. | Chanock, Stephen J. | Chatterjee, Nilanjan
Studies of related individuals have consistently demonstrated notable familial aggregation of cancer. We aim to estimate the heritability and genetic correlation attributable to the additive effects of common single-nucleotide polymorphisms (SNPs) for cancer at 13 anatomical sites.
Between 2007 and 2014, the US National Cancer Institute has generated data from genome-wide association studies (GWAS) for 49 492 cancer case patients and 34 131 control patients. We apply novel mixed model methodology (GCTA) to this GWAS data to estimate the heritability of individual cancers, as well as the proportion of heritability attributable to cigarette smoking in smoking-related cancers, and the genetic correlation between pairs of cancers.
GWAS heritability was statistically significant at nearly all sites, with the estimates of array-based heritability, hl 2, on the liability threshold (LT) scale ranging from 0.05 to 0.38. Estimating the combined heritability of multiple smoking characteristics, we calculate that at least 24% (95% confidence interval [CI] = 14% to 37%) and 7% (95% CI = 4% to 11%) of the heritability for lung and bladder cancer, respectively, can be attributed to genetic determinants of smoking. Most pairs of cancers studied did not show evidence of strong genetic correlation. We found only four pairs of cancers with marginally statistically significant correlations, specifically kidney and testes (ρ = 0.73, SE = 0.28), diffuse large B-cell lymphoma (DLBCL) and pediatric osteosarcoma (ρ = 0.53, SE = 0.21), DLBCL and chronic lymphocytic leukemia (CLL) (ρ = 0.51, SE =0.18), and bladder and lung (ρ = 0.35, SE = 0.14). Correlation analysis also indicates that the genetic architecture of lung cancer differs between a smoking population of European ancestry and a nonsmoking Asian population, allowing for the possibility that the genetic etiology for the same disease can vary by population and environmental exposures.
Our results provide important insights into the genetic architecture of cancers and suggest new avenues for investigation.
PMCID: PMC4806328  PMID: 26464424
6.  Class I HDACs specifically regulate E‐cadherin expression in human renal epithelial cells 
Epithelial‐mesenchymal transition (EMT) and renal fibrosis are closely involved in chronic kidney disease. Inhibition of histone deacetylase (HDAC) has an anti‐fibrotic effect in various diseases. However, the pathophysiological role of isoform‐specific HDACs or class‐selective HDACs in renal fibrosis remains unknown. Here, we investigated EMT markers and extracellular matrix (ECM) proteins in a human proximal tubular cell line (HK‐2) by using HDAC inhibitors or by knockdown of class I HDACs (HDAC1, 2, 3 and 8). Trichostatin A (TSA), MS275, PCI34051 and LMK235 inhibited ECM proteins such as collagen type I or fibronectin in transforming growth factor β1 (TGF‐β1)‐induced HK2 cells. However, restoration of TGF‐β1‐induced E‐cadherin down‐regulation was only seen in HK‐2 cells treated with TSA or MS275, but not with PCI34051, whereas TGF‐β1‐induced N‐cadherin expression was not affected by the inhibitors. ECM protein and EMT marker levels were prevented or restored by small interfering RNA transfection against HDAC8, but not against other class I HDACs (HDAC1, 2 and 3). E‐cadherin regulation is mediated by HDAC8 expression, but not by HDAC8 enzyme activity. Thus, class I HDACs (HDAC1, 2, 3 and 8) play a major role in regulating ECM and EMT, whereas class IIa HDACs (HDAC4 and 5) are less effective.
PMCID: PMC5134402  PMID: 27420561
class I HDAC; epithelial‐mesenchymal transition (EMT); renal fibrosis; HK‐2 cells; E‐cadherin
7.  Piceatannol Attenuates Renal Fibrosis Induced by Unilateral Ureteral Obstruction via Downregulation of Histone Deacetylase 4/5 or p38-MAPK Signaling 
PLoS ONE  2016;11(11):e0167340.
Piceatannol, a resveratrol metabolite, is a phenolic compound found in red wine and grapes. We investigated the effect of piceatannol on renal fibrosis and histone deacetylase (HDAC) expression in a mouse model of unilateral ureteral obstruction (UUO). Fibrosis was established by UUO and piceatannol was intraperitoneally injected for 2 weeks. Piceatannol suppressed extracellular matrix (ECM) protein deposition including collagen type I and fibronectin as well as connective tissue growth factor (CTGF) and α-smooth muscle actin (α-SMA) in UUO kidneys. However, the expressions of epithelial-mesenchymal transition (EMT) marker genes, such as N-cadherin and E-cadherin, were not changed in the kidneys after UUO. Masson’s trichrome staining and fluorescence immunostaining showed that piceatannol administration attenuated collagen deposition in UUO kidneys. HDAC1, HDAC4, HDAC5, HDAC6, and HDAC10 protein expression was upregulated in UUO kidneys, whereas that of HDAC8 was downregulated. Piceatannol treatment significantly reduced HDAC4 and HDAC5 protein expression. Further, piceatannol attenuated phosphorylation of p38 mitogen-activated protein kinase (p38-MAPK) in UUO kidneys, but not that of transforming growth factor beta1-Smad2/3. These results suggest that class I HDACs and class IIa/b HDACs are involved in renal fibrosis development. Piceatannol may be a beneficial therapeutic agent for treating renal fibrosis via reduction of HDAC4 and HDAC5 protein expression or suppression of the p38-MAPK signaling pathway.
PMCID: PMC5130266  PMID: 27902771
8.  The anti-Staphylococcus aureus activity of the phenanthrene fraction from fibrous roots of Bletilla striata 
Bletillae Rhizoma, the tuber of Bletilla striata, has been used in Chinese traditional medicine to treat infectious diseases. Chemical studies indicated that phenanthrene was one of the most important components of the herb, with a broad spectrum of antibiotic activity against Gram-positive bacteria. The objective of this study was to further characterize the antibacterial activity of the phenanthrene fraction from the fibrous root of the pseudobulb of B. striata.
The phenanthrene fraction (EF60) from the ethanol extract of fibrous roots of Bletilla striata pseudobulbs was isolated using polyamide column chromatography. The antibacterial activity of the fraction was evaluated in vitro using a 96-well microtiter plate and microbroth dilution method. The cytotoxicity of EF60 against mammalian cells was tested by hemolysis and MTT assays.
EF60 was obtained using alcohol extraction and polyamide column chromatography, with a yield of 14.9 g per 1 kg of the fibrous roots of B. striata. In vitro tests indicated that EF60 was active against all tested strains of Staphylococcus aureus, including clinical isolates and methicillin-resistant S. aureus (MRSA). The minimum inhibitory concentration (MIC) values of EF60 against these pathogens ranged from 8 to 64 μg/mL. Minimum bactericidal concentration tests demonstrated that EF60 was bactericidal against S. aureus 3304 and ATCC 29213 and was bacteriostatic against S. aureus 3211, ATCC 25923, and ATCC 43300. Consistently, the time-kill assay indicated that EF60 could completely kill S. aureus ATCC 29213 at 2× the MIC within 3 h but could kill less than two logarithmic units of ATCC 43300, even at 4× the MIC within 24 h. The postantibiotic effects (PAE) of EF60 (4× MIC) against strains 29213 and 43300 were 2.0 and 0.38 h, respectively. Further studies indicated that EF60 (160 μg/mL) showed no cytotoxicity against human erythrocytes, and was minimally toxic to Human Umbilical Vein Endothelial Cells with an IC50 of 75 μg/mL.
Our studies indicated that EF60 is worthy of further investigation as a potential phytotherapeutic agent for treating infections caused by S. aureus and MRSA.
Electronic supplementary material
The online version of this article (doi:10.1186/s12906-016-1488-z) contains supplementary material, which is available to authorized users.
PMCID: PMC5129615  PMID: 27899152
Bletillae Rhizom; Gram-positive bacteria; Antibacterial; Time-kill assays; Postantibiotic effect
9.  Non-uniform Evolving Hypergraphs and Weighted Evolving Hypergraphs 
Scientific Reports  2016;6:36648.
Firstly, this paper proposes a non-uniform evolving hypergraph model with nonlinear preferential attachment and an attractiveness. This model allows nodes to arrive in batches according to a Poisson process and to form hyperedges with existing batches of nodes. Both the number of arriving nodes and that of chosen existing nodes are random variables so that the size of each hyperedge is non-uniform. This paper establishes the characteristic equation of hyperdegrees, calculates changes in the hyperdegree of each node, and obtains the stationary average hyperdegree distribution of the model by employing the Poisson process theory and the characteristic equation. Secondly, this paper constructs a model for weighted evolving hypergraphs that couples the establishment of new hyperedges, nodes and the dynamical evolution of the weights. Furthermore, what is obtained are respectively the stationary average hyperdegree and hyperstrength distributions by using the hyperdegree distribution of the established unweighted model above so that the weighted evolving hypergraph exhibits a scale-free behavior for both hyperdegree and hyperstrength distributions.
PMCID: PMC5109229  PMID: 27845334
10.  Maternal High Estradiol Exposure is Associated with Elevated Thyroxine and Pax8 in Mouse Offspring 
Scientific Reports  2016;6:36805.
Our previous studies have shown that maternal high estradiol (E2) environment increased the risk of thyroid dysfunction in offspring. However, the mechanism involved remains unexplored. To evaluate the thyroid function of offspring after high E2 exposure and to explore the underlying mechanism, we established a high E2 mouse model of early pregnancy, and detected thyroid hormones of their offspring. In thyroids of offspring, the expressions of Tg, Nis, Tpo, Pax8, and Titf1 and CpG island methylation status of Pax8 and genes involved in methylation were analyzed. We found that thyroxine (T4) and FT4 levels of offspring were obviously increased in the high-E2 group, especially in females. In both 3- and 8-week-old offspring of the high-E2 group, Pax8 was significantly up-regulated in thyroid glands, accompanied by the abnormal CpG island methylation status in the promoter region. Furthermore, Dnmt3a and Mbd1 were obviously down-regulated in thyroids of the high E2 group. Besides, the disturbance of thyroid function in females was more severe than that in males, implying that the effects were related to gender. In summary, our study indicated that maternal high E2 exposure disturbed the thyroid function of offspring through the dysregulation and abnormal DNA methylation of Pax8.
PMCID: PMC5101534  PMID: 27827435
11.  A new statistical framework for genetic pleiotropic analysis of high dimensional phenotype data 
BMC Genomics  2016;17:881.
The widely used genetic pleiotropic analyses of multiple phenotypes are often designed for examining the relationship between common variants and a few phenotypes. They are not suited for both high dimensional phenotypes and high dimensional genotype (next-generation sequencing) data.
To overcome limitations of the traditional genetic pleiotropic analysis of multiple phenotypes, we develop sparse structural equation models (SEMs) as a general framework for a new paradigm of genetic analysis of multiple phenotypes. To incorporate both common and rare variants into the analysis, we extend the traditional multivariate SEMs to sparse functional SEMs. To deal with high dimensional phenotype and genotype data, we employ functional data analysis and the alternative direction methods of multiplier (ADMM) techniques to reduce data dimension and improve computational efficiency.
Using large scale simulations we showed that the proposed methods have higher power to detect true causal genetic pleiotropic structure than other existing methods. Simulations also demonstrate that the gene-based pleiotropic analysis has higher power than the single variant-based pleiotropic analysis. The proposed method is applied to exome sequence data from the NHLBI’s Exome Sequencing Project (ESP) with 11 phenotypes, which identifies a network with 137 genes connected to 11 phenotypes and 341 edges. Among them, 114 genes showed pleiotropic genetic effects and 45 genes were reported to be associated with phenotypes in the analysis or other cardiovascular disease (CVD) related phenotypes in the literature.
Our proposed sparse functional SEMs can incorporate both common and rare variants into the analysis and the ADMM algorithm can efficiently solve the penalized SEMs. Using this model we can jointly infer genetic architecture and casual phenotype network structure, and decompose the genetic effect into direct, indirect and total effect. Using large scale simulations we showed that the proposed methods have higher power to detect true causal genetic pleiotropic structure than other existing methods.
Electronic supplementary material
The online version of this article (doi:10.1186/s12864-016-3169-1) contains supplementary material, which is available to authorized users.
PMCID: PMC5100198  PMID: 27821073
Structural equations; Causal inference; Multiple phenotypes; Quantitative trait; Next-generation sequencing; Pleiotropic analysis
12.  Phenanthrene and Pyrene Modify the Composition and Structure of the Cultivable Endophytic Bacterial Community in Ryegrass (Lolium multiflorum Lam) 
This study provides new insights into the dynamics of bacterial community structure during phytoremediation. The communities of cultivable autochthonous endophytic bacteria in ryegrass exposed to polycyclic aromatic hydrocarbons (PAHs) were investigated with regard to their potential to biodegrade PAHs. Bacterial counts and 16S rRNA gene sequence were used in the microbiological evaluation. A total of 33 endophytic bacterial strains were isolated from ryegrass plants, which represented 15 different genera and eight different classes, respectively. Moreover, PAH contamination modified the composition and structure of the endophytic bacterial community in the plants. Bacillus sp., Pantoea sp., Pseudomonas sp., Arthrobacter sp., Pedobacter sp. and Delftia sp. were only isolated from the seedlings exposed to PAHs. Furthermore, the dominant genera in roots shifted from Enterobacter sp. to Serratia sp., Bacillus sp., Pantoea sp., and Stenotrophomonas sp., which could highly biodegrade phenanthrene (PHE). However, the diversity of endophytic bacterial community was decreased by exposure to the mixture of PAHs, and increased by respective exposure to PHE and pyrene (PYR), while the abundance was increased by PAH exposure. The results clearly indicated that the exposure of plants to PAHs would be beneficial for improving the effectiveness of phytoremediation of PAHs.
PMCID: PMC5129291  PMID: 27827894
community structure; cultivable endophytic bacteria; diversity; biodegradation; polycyclic aromatic hydrocarbons
13.  Developmental Toxicity of Carbon Quantum Dots to the Embryos/Larvae of Rare Minnow (Gobiocypris rarus) 
BioMed Research International  2016;2016:4016402.
The toxic effects of CDs on rare minnow (Gobiocypris rarus) embryos at different developmental stages were investigated. The results showed that rare minnow embryos had decreased spontaneous movements, body length, increased heart rate, pericardial edema, yolk sac edema, tail/spinal curvature, various morphological malformations, and decreased hatching rate. Biochemical analysis showed the CDs exposure significantly inhibited the activity of Na+/K+-ATPase and Ca2+-ATPase and increased the MDA contents and the activity of SOD, CAT, and GPX. Further examination suggested that the CDs exposure induced serious embryonic cellular DNA damage. Moreover, the CDs exposure induced upregulation of development related genes (Wnt8a and Mstn) along with the downregulation of Vezf1. Overall, the present study revealed that the CDs exposure has significant development toxicity on rare minnow embryos/larvae. Mechanistically, this toxicity might result from the pressure of induced oxidative stress coordinate with the dysregulated development related gene expression mediated by the CDs exposure.
PMCID: PMC5107864  PMID: 27872851
14.  Evolutionary trajectories of snake genes and genomes revealed by comparative analyses of five-pacer viper 
Nature Communications  2016;7:13107.
Snakes have numerous features distinctive from other tetrapods and a rich history of genome evolution that is still obscure. Here, we report the high-quality genome of the five-pacer viper, Deinagkistrodon acutus, and comparative analyses with other representative snake and lizard genomes. We map the evolutionary trajectories of transposable elements (TEs), developmental genes and sex chromosomes onto the snake phylogeny. TEs exhibit dynamic lineage-specific expansion, and many viper TEs show brain-specific gene expression along with their nearby genes. We detect signatures of adaptive evolution in olfactory, venom and thermal-sensing genes and also functional degeneration of genes associated with vision and hearing. Lineage-specific relaxation of functional constraints on respective Hox and Tbx limb-patterning genes supports fossil evidence for a successive loss of forelimbs then hindlimbs during snake evolution. Finally, we infer that the ZW sex chromosome pair had undergone at least three recombination suppression events in the ancestor of advanced snakes. These results altogether forge a framework for our deep understanding into snakes' history of molecular evolution.
Snakes have many characteristics that distinguish them from their relatives. Here, Yin et al. sequence the genome of the five-pacer viper, Deinagkistrodon acutus, and use comparative genomic analyses to elucidate the evolution of transposable elements, developmental genes and sex chromosomes in snakes.
PMCID: PMC5059746  PMID: 27708285
15.  Gallic acid prevents isoproterenol-induced cardiac hypertrophy and fibrosis through regulation of JNK2 signaling and Smad3 binding activity 
Scientific Reports  2016;6:34790.
Gallic acid, a type of phenolic acid, has been shown to have beneficial effects in inflammation, vascular calcification, and metabolic diseases. The present study was aimed at determining the effect and regulatory mechanism of gallic acid in cardiac hypertrophy and fibrosis. Cardiac hypertrophy was induced by isoproterenol (ISP) in mice and primary neonatal cardiomyocytes. Gallic acid pretreatment attenuated concentric cardiac hypertrophy. It downregulated the expression of atrial natriuretic peptide, brain natriuretic peptide, and beta-myosin heavy chain in vivo and in vitro. Moreover, it prevented interstitial collagen deposition and expression of fibrosis-associated genes. Upregulation of collagen type I by Smad3 overexpression was observed in cardiac myoblast H9c2 cells but not in cardiac fibroblasts. Gallic acid reduced the DNA binding activity of phosphorylated Smad3 in Smad binding sites of collagen type I promoter in rat cardiac fibroblasts. Furthermore, it decreased the ISP-induced phosphorylation of c-Jun N-terminal kinase (JNK) and extracellular signal regulated kinase (ERK) protein in mice. JNK2 overexpression reduced collagen type I and Smad3 expression as well as GATA4 expression in H9c2 cells and cardiac fibroblasts. Gallic acid might be a novel therapeutic agent for the prevention of cardiac hypertrophy and fibrosis by regulating the JNK2 and Smad3 signaling pathway.
PMCID: PMC5050511  PMID: 27703224
16.  Ultraviolet-B Radiation (UV-B) Relieves Chilling-Light-Induced PSI Photoinhibition And Accelerates The Recovery Of CO2 Assimilation In Cucumber (Cucumis sativus L.) Leaves 
Scientific Reports  2016;6:34455.
Ultraviolet-B radiation (UV-B) is generally considered to negatively impact the photosynthetic apparatus and plant growth. UV-B damages PSII but does not directly influence PSI. However, PSI and PSII successively drive photosynthetic electron transfer, therefore, the interaction between these systems is unavoidable. So we speculated that UV-B could indirectly affect PSI under chilling-light conditions. To test this hypothesis, the cucumber leaves were illuminated by UV-B prior or during the chilling-light treatment, and the leaves were then transferred to 25 °C and low-light conditions for recovery. The results showed that UV-B decreased the electron transfer to PSI by inactivating the oxygen-evolving complex (OEC), thereby protecting PSI from chilling-light-induced photoinhibition. This effect advantages the recoveries of PSI and CO2 assimilation after chilling-light stress, therefore should minimize the yield loss caused by chilling-light stress. Because sunlight consists of both UV-B and visible light, we suggest that UV-B-induced OEC inactivation is critical for chilling-light-induced PSI photoinhibition in field. Moreover, additional UV-B irradiation is an effective strategy to relieve PSI photoinhibition and yield loss in protected cultivation during winter. This study also demonstrates that minimizing the photoinhibition of PSI rather than that of PSII is essential for the chilling-light tolerance of the plant photosynthetic apparatus.
PMCID: PMC5043378  PMID: 27686324
17.  The Evolution of Hyperedge Cardinalities and Bose-Einstein Condensation in Hypernetworks 
Scientific Reports  2016;6:33651.
To depict the complex relationship among nodes and the evolving process of a complex system, a Bose-Einstein hypernetwork is proposed in this paper. Based on two basic evolutionary mechanisms, growth and preference jumping, the distribution of hyperedge cardinalities is studied. The Poisson process theory is used to describe the arrival process of new node batches. And, by using the Poisson process theory and a continuity technique, the hypernetwork is analyzed and the characteristic equation of hyperedge cardinalities is obtained. Additionally, an analytical expression for the stationary average hyperedge cardinality distribution is derived by employing the characteristic equation, from which Bose-Einstein condensation in the hypernetwork is obtained. The theoretical analyses in this paper agree with the conducted numerical simulations. This is the first study on the hyperedge cardinality in hypernetworks, where Bose-Einstein condensation can be regarded as a special case of hypernetworks. Moreover, a condensation degree is also discussed with which Bose-Einstein condensation can be classified.
PMCID: PMC5037361  PMID: 27669903
18.  Mechanisms of fibrosis in acute liver failure 
Liver International  2015;35(7):1877-1885.
Background & Aims
Acute liver failure (ALF) is a condition with high mortality and morbidity. Fibrosis in chronic liver disease was extensively researched, whereas fibrosis and underlying mechanism in acute liver failure remains unclear.
Hepatitis B virus related ALF patients were recruited to investigate if there was ongoing fibrosis by liver histology and liver stiffness measurement(LSM) analysis as well as fibrosis markers assay. Sera HMGB1 were kinetically detected in progression and remission stage of ALF. Hepatic stellate cell(HSC) activation by HMGB1 was explored by testing mRNA and protein level of α‐SMA and collagen 1a1 by using qPCR and western blot. Autophagy induction by HMGB1 was explored by LC3‐II conversion, autophagy flux and fluorescence.
Firstly, ongoing fibrosis in progression stage of ALF was confirmed by histological analysis, LS measurement as well as fibrosis markers detection. HSC activation and autophagy induction in explanted liver tissue also revealed. Next, kinetic monitoring sera HMGB1 revealed elevated HMGB1 in progression stage of ALF vs HBsAg carrier, and drop back to base level in remission stage. Thirdly, rHMGB1 dose dependently activated HSCs, as indicated by increased mRNA and proteins level in α‐SMA and collagen 1a1. Moreover, autophagy was induced in HSC treated with rHMGB1, as illustrated by increased LC3 lipidation, elevated autophagy flux and GFP‐LC3 puncta.
Acute liver failure is accompanied by ongoing fibrosis, HSC activation and autophagy induction. Increased HMGB1 activates HSC via autophagy induction. Those findings integrate HMGB1, HSCs activation, autophagy into a common framework that underlies the fibrosis in ALF.
PMCID: PMC5024020  PMID: 25388426
acute liver failure; autophagy; fibrosis; hepatic stellate cell; hepatitis B virus; high mobility group box 1
19.  Y chromosome haplogroups based genome-wide association study pinpoints revelation for interactions on non-obstructive azoospermia 
Scientific Reports  2016;6:33363.
The Y chromosome has high genetic variability with low rates of parallel and back mutations, which make up the most informative haplotyping system. To examine whether Y chromosome haplogroups (Y-hgs) could modify the effects of autosomal variants on non-obstructive azoospermia (NOA), based on our previous genome-wide association study (GWAS), we conducted a genetic interaction analysis in GWAS subjects. Logistic regression analysis demonstrated a protective effect of Y-hg O3e* on NOA. Then, we explored the potential interaction between Y-hg O3e* and autosomal variants. Our results demonstrated that there was a suggestively significant interaction between Y-hg O3e* and rs11135484 on NOA (Pinter = 9.89 × 10−5). Bioinformatic analysis revealed that genes annotated by significant single nucleotide polymorphisms (SNPs) were mainly enriched in immunological pathways. This is the first study of interactions between Y-hgs and autosomal variants on a genome-wide scale, which addresses the missing heritability in spermatogenic impairment and sheds new light on the pathogenesis of male infertility.
PMCID: PMC5024297  PMID: 27628680
20.  Silencing of Prrx1b suppresses cellular proliferation, migration, invasion and epithelial–mesenchymal transition in triple‐negative breast cancer 
Triple‐negative breast cancer (TNBC) is a highly aggressive tumour subtype associated with poor prognosis. The mechanisms involved in TNBC progression remains largely unknown. To date, there are no effective therapeutic targets for this tumour subtype. Paired‐related homeobox 1b (Prrx1b), one of major isoforms of Prrx1, has been identified as a new epithelial–mesenchymal transition (EMT) inducer. However, the function of Prrx1b in TNBC has not been elucidated. In this study, we found that Prrx1b was significantly up‐regulated in TNBC and associated with tumour size and vascular invasion of breast cancer. Silencing of Prrx1b suppressed the proliferation, migration and invasion of basal‐like cancer cells. Moreover, silencing of Prrx1b prevented Wnt/β‐catenin signaling pathway and induced the mesenchymal‐epithelial transition (MET). Taken together, our data indicated that Prrx1b may be an important regulator of EMT in TNBC cells and a new therapeutic target for interventions against TNBC invasion and metastasis.
PMCID: PMC4988287  PMID: 27027510
triple‐negative breast cancer; paired‐related homeobox 1b; epithelial–mesenchymal transition; proliferation; invasion
21.  TNF-α Promoter Polymorphisms Predict the Response to Etanercept More Powerfully than that to Infliximab/Adalimumab in Spondyloarthritis 
Scientific Reports  2016;6:32202.
While previous studies have researched in association analyses between TNFα promoter polymorphisms and responses to TNF blockers in spondyloarthritis patients, their results were conflicting. Therefore, we aimed to determine whether TNFα promoter polymorphisms could predict response to TNF blockers and find the source of heterogeneity. Data were extracted and analyzed from published articles and combined with our unpublished data. We found that the greatest potential sources of heterogeneity in the results were gender ratio, disease type, continents, and TNF blockers. Then Stratification analysis showed that the TNFα −308 G allele and the −238 G allele predicted a good response to TNF blockers (OR = 2.64 [1.48–4.73]; 2.52 [1.46–4.37]). However, G alleles of TNFα −308 and −238 could predict the response to etanercept (OR = 4.02 [2.24–7.23]; 5.17 [2.29–11.67]) much more powerfully than the response to infiliximab/adalimumab (OR = 1.68 [1.02–2.78]; 1.28 [0.57–2.86]). TNFα −857 could not predict the response in either subgroup. Cumulative meta-analysis performed in ankylosing spondylitis patients presented the odds ratio decreased with stricter response criteria. In conclusion, TNFα −308 A/G and −238 A/G are more powerful to predict the response to Etanercept and it is dependent on the criteria of response.
PMCID: PMC5006048  PMID: 27578555
22.  Identification of the protective effects of traditional medicinal plants against SDS-induced Drosophila gut damage 
Traditional medicinal plants are widely used as immunomodulatory medicines that help improve health. A total of 50 different plants used for the treatment of toxicity were screened for their in vivo protective effects. Flies were fed a standard cornmeal-yeast medium (control group) or the standard medium containing medicinal plant extracts (experimental groups). Assessment of the survival rate was performed by feeding flies with toxic compounds. Gut epithelial cells were analyzed for cell proliferation and death by green fluorescent protein antibodies and 7-aminoactinomycin D staining under the microscope. The expression of antimicrobial peptides (AMPs) was evaluated by the quantitative polymerase chain reaction and the results revealed that after feeding the flies with toxic compounds, aqueous extracts from Codonopsis pilosula (Franch.) Nannf (C. pilosula), Saussurea lappa (Decne.) C.B.Clarke (S. lappa), Imperata cylindrica Beauv.var.major (Nees) C.E. Hubb. (I. cylindrical var. major) and Melia toosendan Sied. Et Zucc. (M.toosendan) increased the fly survival rate, reduced epithelial cell death and improved gut morphology. In addition, C. pilosula extracts induced the antimicrobial peptide levels (Dpt and Mtk) following treatment with sodium dodecyl sulfate (SDS). However, these extracts were not observed to increase SDS-induced cell proliferation in vivo. These results indicate that there are strong protective effects in extracts of C. pilosula, S. lappa, I. cylindrical var. major and M. toosendan on Drosophila intestinal cells among 50 medicinal plants.
PMCID: PMC5038347  PMID: 27698771
traditional medicinal plant; gut immunity; survival; Drosophila melanogaster cell death
23.  Trastuzumab improves locoregional control in HER2-positive breast cancer patients following adjuvant radiotherapy 
Medicine  2016;95(32):e4230.
The benefit of adjuvant trastuzumab in disease-free and overall survival for human epidermal receptor 2–positive (HER2+) breast cancer patients is well established. However, the effect of trastuzumab on locoregional control remains unclear, particularly in patients treated with adjuvant radiotherapy (RT). In this study, we investigated the locoregional benefit of trastuzumab in patients with HER2+ breast cancer after adjuvant RT.
Using a single institutional database, we identified 278 patients with stage II/III invasive HER2+ breast tumors receiving adjuvant RT between January 2008 and July 2011. We compared the locoregional outcomes of 134 patients who received trastuzumab to 144 patients without trastuzumab within the same period. Clinical and biological factors that might impact on the locoregional benefit of trastuzumab were also assessed.
At the median follow-up of 45 months, trastuzumab significantly lowered the risk of locoregional recurrence (LRR) with a 3-year LRR rate of 2.4% versus 7.5% for the cohort with and without trastuzumab (P = 0.019). Trastuzumab was associated with a more significant locoregional benefit in the hormone receptor–positive (HR+)/HER2+ subgroup, with a 3-year LRR of 0% versus 6.7% in the cohort with and without trastuzumab (P = 0.027). For HR−/HER2+ breast tumor patients, the 3-year LRR rate was still lower for the cohort with trastuzumab (4.7% vs 8.6%). However, statistical significance was not found (P = 0.179). Both univariate and multivariate analyses confirmed that trastuzumab treatment was the only significant predictive factor for LRR (hazard ratio, 4.05; 95% confidence interval, 1.07–15.35; P = 0.039).
Adjuvant trastuzumab in addition to RT is associated with significant reduced LRR risk in HER2+ breast cancer.
PMCID: PMC4985293  PMID: 27512838
adjuvant radiotherapy; breast cancer; HER2+; locoregional benefit; trastuzumab
24.  MtDNA analysis reveals enriched pathogenic mutations in Tibetan highlanders 
Scientific Reports  2016;6:31083.
Tibetan highlanders, including Tibetans, Monpas, Lhobas, Dengs and Sherpas, are considered highly adaptive to severe hypoxic environments. Mitochondrial DNA (mtDNA) might be important in hypoxia adaptation given its role in coding core subunits of oxidative phosphorylation. In this study, we employed 549 complete highlander mtDNA sequences (including 432 random samples) to obtain a comprehensive view of highlander mtDNA profile. In the phylogeny of a total of 36,914 sequences, we identified 21 major haplogroups representing founding events of highlanders, most of which were coalesced in 10 kya. Through founder analysis, we proposed a three-phase model of colonizing the plateau, i.e., pre-LGM Time (30 kya, 4.68%), post-LGM Paleolithic Time (16.8 kya, 29.31%) and Neolithic Time (after 8 kya, 66.01% in total). We observed that pathogenic mutations occurred far more frequently in 22 highlander-specific lineages (five lineages carrying two pathogenic mutations and six carrying one) than in the 6,857 haplogroups of all the 36,914 sequences (P = 4.87 × 10−8). Furthermore, the number of possible pathogenic mutations carried by highlanders (in average 3.18 ± 1.27) were significantly higher than that in controls (2.82 ± 1.40) (P = 1.89 × 10−4). Considering that function-altering and pathogenic mutations are enriched in highlanders, we therefore hypothesize that they may have played a role in hypoxia adaptation.
PMCID: PMC4976311  PMID: 27498855
25.  Use of serum albumin and activities of daily living to predict mortality in long-lived individuals over 95 years of age: a population-based study 
Age  2015;37(4):73.
Both activities of daily living (ADL) and some blood biomarkers (such as albumin) have been associated with mortality in very elderly people, but scarce data is available on the predictive performance of them in isolation or in combination, which is important for clinicians in decision making. Here, based on prospective mortality data over a 6-year follow-up period from 433 long-lived individuals (LLIs) aged 95+ years in the Rugao longevity cohort, we aimed to evaluate Cox proportional hazard ratios (HRs) and discriminative power (ROC curve) of 14 biomarkers and ADL for all-cause mortality. We found that six biomarkers (total triglyceride, albumin, low-density lipoprotein cholesterol, platelet count, lymphocyte count, and neutrophil count) were associated with mortality with a p < .10 in the univariate model. Significant associations of albumin and neutrophil count with mortality were observed when they were simultaneously included in a multivariate model, with HRs of 0.97 (95 % CI 0.94, 0.99; p = .005) and 1.09 (95 % CI 1.00, 1.18; p = .043). With respect to ADL, the corresponding HR was 1.10 (95 % CI 1.07, 1.14; p < .001). Low albumin (<40 g/L) combined with ADL dependent had a significantly increased mortality risk (HR = 2.19; 95 % CI 1.63, 2.95). Albumin and ADL separately showed good discriminative accuracies (area under the curve [AUC] = 0.68 and 0.66, respectively), and their combination had an increased predictive utility (AUC = 0.73). In conclusion, both albumin and ADL are efficient predictors of all-cause mortality in long-lived populations and their combination further increases discriminative power. The preliminary findings, if validated and translated, would help clinicians to identify the elderly people at varying mortality risk.
PMCID: PMC4503704  PMID: 26178970
Activities of daily living; Serum albumin; Long-lived individuals; Mortality

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