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1.  An atlas of DNA methylomes in porcine adipose and muscle tissues 
Nature communications  2012;3:850.
It is evident that epigenetic factors, especially DNA methylation, play essential roles in obesity development. Using pig as a model, here we investigated the systematic association between DNA methylation and obesity. We sampled eight variant adipose and two distinct skeletal muscle tissues from three pig breeds living within comparable environments but displaying distinct fat level. We generated 1,381 gigabases (Gb) of sequence data from 180 methylated DNA immunoprecipitation (MeDIP) libraries, and provided a genome-wide DNA methylation map as well as a gene expression map for adipose and muscle studies. The analysis showed global similarity and difference among breeds, sexes and anatomic locations, and identified the differentially methylated regions (DMRs). The DMRs in promoters are highly associated with obesity development via expression repression of both known obesity-related genes and novel genes. This comprehensive map provides a solid basis for exploring epigenetic mechanisms of adipose deposition and muscle growth.
doi:10.1038/ncomms1854
PMCID: PMC3508711  PMID: 22617290
2.  Genome-Wide Mapping of DNA Methylation in Chicken 
PLoS ONE  2011;6(5):e19428.
Cytosine DNA methylation is an important epigenetic modification termed as the fifth base that functions in diverse processes. Till now, the genome-wide DNA methylation maps of many organisms has been reported, such as human, Arabidopsis, rice and silkworm, but the methylation pattern of bird remains rarely studied. Here we show the genome-wide DNA methylation map of bird, using the chicken as a model organism and an immunocapturing approach followed by high-throughput sequencing. In both of the red jungle fowl and the avian broiler, DNA methylation was described separately for the liver and muscle tissue. Generally, chicken displays analogous methylation pattern with that of animals and plants. DNA methylation is enriched in the gene body regions and the repetitive sequences, and depleted in the transcription start site (TSS) and the transcription termination site (TTS). Most of the CpG islands in the chicken genome are kept in unmethylated state. Promoter methylation is negatively correlated with the gene expression level, indicating its suppressive role in regulating gene transcription. This work contributes to our understanding of epigenetics in birds.
doi:10.1371/journal.pone.0019428
PMCID: PMC3088676  PMID: 21573164
3.  Neuraminidase of Influenza A Virus Binds Lysosome-Associated Membrane Proteins Directly and Induces Lysosome Rupture 
Journal of Virology  2015;89(20):10347-10358.
ABSTRACT
As a recycling center, lysosomes are filled with numerous acid hydrolase enzymes that break down waste materials and invading pathogens. Recently, lysosomal cell death has been defined as “lysosomal membrane permeabilization and the consequent leakage of lysosome contents into cytosol.” Here, we show that the neuraminidase (NA) of H5N1 influenza A virus markedly deglycosylates and degrades lysosome-associated membrane proteins (LAMPs; the most abundant membrane proteins of lysosome), which induces lysosomal rupture, and finally leads to cell death of alveolar epithelial carcinoma A549 cells and human tracheal epithelial cells. The NA inhibitors peramivir and zanamivir could effectively block the deglycosylation of LAMPs, inhibit the virus cell entry, and prevent cell death induced by the H5N1 influenza virus. The NA of seasonal H1N1 virus, however, does not share these characteristics. Our findings not only reveal a novel role of NA in the early stage of the H5N1 influenza virus life cycle but also elucidate the molecular mechanism of lysosomal rupture crucial for influenza virus induced cell death.
IMPORTANCE The integrity of lysosomes is vital for maintaining cell homeostasis, cellular defense and clearance of invading pathogens. This study shows that the H5N1 influenza virus could induce lysosomal rupture through deglycosylating lysosome-associated membrane proteins (LAMPs) mediated by the neuraminidase activity of NA protein. NA inhibitors such as peramivir and zanamivir could inhibit the deglycosylation of LAMPs and protect lysosomes, which also further interferes with the H5N1 influenza virus infection at early stage of life cycle. This work is significant because it presents new concepts for NA's function, as well as for influenza inhibitors' mechanism of action, and could partially explain the high mortality and high viral load after H5N1 virus infection in human beings and why NA inhibitors have more potent therapeutic effects for lethal avian influenza virus infections at early stage.
doi:10.1128/JVI.01411-15
PMCID: PMC4580162  PMID: 26246576
4.  Effect of Root Moisture Content and Diameter on Root Tensile Properties 
PLoS ONE  2016;11(3):e0151791.
The stabilization of slopes by vegetation has been a topical issue for many years. Root mechanical characteristics significantly influence soil reinforcement; therefore it is necessary to research into the indicators of root tensile properties. In this study, we explored the influence of root moisture content on tensile resistance and strength with different root diameters and for different tree species. Betula platyphylla, Quercus mongolica, Pinus tabulaeformis, and Larix gmelinii, the most popular tree species used for slope stabilization in the rocky mountainous areas of northern China, were used in this study. A tensile test was conducted after root samples were grouped by diameter and moisture content. The results showedthat:1) root moisture content had a significant influence on tensile properties; 2) slightly loss of root moisture content could enhance tensile strength, but too much loss of water resulted in weaker capacity for root elongation, and consequently reduced tensile strength; 3) root diameter had a strong positive correlation with tensile resistance; and4) the roots of Betula platyphylla had the best tensile properties when both diameter and moisture content being controlled. These findings improve our understanding of root tensile properties with root size and moisture, and could be useful for slope stabilization using vegetation.
doi:10.1371/journal.pone.0151791
PMCID: PMC4803321  PMID: 27003872
5.  The decreased expression of electron transfer flavoprotein β is associated with tubular cell apoptosis in diabetic nephropathy 
Tubular injury is closely correlated with the development of progressive diabetic nephropathy (DN), particularly in cases of type 2 diabetes. The apoptosis of tubular cells has been recognized as a major cause of tubular atrophy, followed by tubulointerstitial fibrosis. Electron transfer flavoprotein β (ETFβ) is known as an important electron acceptor in energy metabolism, but its role in DN was not fully understood. In the present study, we examined the expression pattern of ETFβ using diabetic kidney samples and further investigated ETFβ involvement in tubular epithelial cell (TEC) apoptosis. Human renal biopsy specimens from patients with DN as well as a spontaneous rat model of diabetes using Otsuka Long-Evans Tokushima fatty (OLETF) rats, were employed in order to examine the expression of ETFβ and cell apoptosis in kidneys during the development of DN (for the rats, at 36 and 56 weeks of age respectively). Moreover, ETFβ siRNA was used to investigate the role of ETFβ in the apoptosis of renal tubular cells. Our present results showed that the expression of ETFβ in the kidneys was progressively decreased both in patients with DN and OLETF rats, which coincided with progressive renal injury and TEC apoptosis. In addition, the in vitro study demonstrated that knockdown of ETFβ caused apoptosis in tubular cells, as proven by the increased expression of pro-apoptotic proteins and TUNEL assay. Therefore, the findings of our present study suggest that ETFβ plays an important role in renal tubular cell apoptosis during the progression of DN.
doi:10.3892/ijmm.2016.2533
PMCID: PMC4829130  PMID: 27035869
electron transfer flavoprotein β; apoptosis; tubular injury; diabetic nephropathy
6.  ER stress and autophagy are involved in the apoptosis induced by cisplatin in human lung cancer cells 
Oncology Reports  2016;35(5):2606-2614.
Cisplatin [cis-diamminedichloroplatinum II (CDDP)] is one of the most classical and effective chemotherapeutic drugs for the treatment of cancers including lung cancer. However, the presence of cisplatin resistance in cancer lowers its curative effect and limits its usage in the clinic. The aim of the present study was to investigate the underlying mechanisms of cisplatin resistance in lung cancer involving endoplasmic reticulum (ER) stress and autophagy. In the present study, we detected the effect of cisplatin on cell viability, ER stress and autophagy in lung cancer cell lines A549 and H460. We also tested the effects of ER stress and autophagy on apoptosis induced by cisplatin. The results showed that cisplatin induced apoptosis, ER stress and autophagy in lung cancer cell lines. In addition, the inhibition of ER stress by 4-phenylbutyric acid (4-PBA) or tauroursodeoxycholic acid sodium (TUDC) enhanced cisplatin-induced apoptosis in the human lung cancer cells. Meanwhile, combination treatment with the autophagic inhibitor 3-methyladenine (3-MA) or chloroquine (CQ) further increased the apoptosis induced by cisplatin in the human lung cancer cells. The present study provides a novel treatment strategy - cisplatin in combination with an autophagic inhibitor or an ER stress inhibitor leads to increased apoptosis in human lung cancer cells.
doi:10.3892/or.2016.4680
PMCID: PMC4811398  PMID: 26985651
apoptosis; autophagy; ER stress; human lung cancer
7.  PTEN inhibits macrophage polarization from M1 to M2 through CCL2 and VEGF-A reduction and NHERF-1 synergism 
Cancer Biology & Therapy  2015;16(2):297-306.
PTEN has been studied in several tumor models as a tumor suppressor. In this study, we explored the role of PTEN in the inhibition state of polarized M2 subtype of macrophage in tumor microenvironment (TME) and the underlying mechanisms. To elucidate the potential effect in TME, RAW 264.7 macrophages and 4T1 mouse breast cancer cells were co-cultured to reconstruct tumor microenvironment. After PTEN was down-regulated with shRNA, the expression of CCL2 and VEGF-A, which are definited to promote the formation of M2 macrophages, have a dramatically increase on the level of both gene and protein in co-cultured RAW 264.7 macrophages. And at the same time, NHERF-1 (Na+/H+ exchanger regulating factor-1), another tumor suppressor has a similar tendency to PTEN. Q-PCR and WB results suggested that PTEN and NHERF-1 were consistent with one another no matter at mRNA or protein level when exposed to the same stimulus. Coimmunoprecipitation and immunofluorescence techniques confirmed that PTEN and NHERF-1 were coprecipitated, and NHERF-1 protein expression was properly reduced with rCCL2 effect. In addition, cell immunofluorescence images revealed a profound transferance, in co-cultured RAW 264.7 macrophages, an up-regulation of NHERF-1 could promote the PTEN marked expression on the cell membrane, and this form for the interaction was not negligible. These observations illustrate PTEN with a certain synergy of NHERF-1, as well as down-regulation of CCL2 suppressing M2 macrophage transformation pathway. The results suggest that the activation of PTEN and NHERF-1 may impede the evolution of macrophages beyond the M1 into M2 phenotype in tumor microenvironment.
doi:10.1080/15384047.2014.1002353
PMCID: PMC4622010  PMID: 25756512
CCL2; co-culture; NHERF-1; TAM; PTEN; transformation
8.  Large-scale production of functional human lysozyme from marker-free transgenic cloned cows 
Scientific Reports  2016;6:22947.
Human lysozyme is an important natural non-specific immune protein that is highly expressed in breast milk and participates in the immune response of infants against bacterial and viral infections. Considering the medicinal value and market demand for human lysozyme, an animal model for large-scale production of recombinant human lysozyme (rhLZ) is needed. In this study, we generated transgenic cloned cows with the marker-free vector pBAC-hLF-hLZ, which was shown to efficiently express rhLZ in cow milk. Seven transgenic cloned cows, identified by polymerase chain reaction, Southern blot, and western blot analyses, produced rhLZ in milk at concentrations of up to 3149.19 ± 24.80 mg/L. The purified rhLZ had a similar molecular weight and enzymatic activity as wild-type human lysozyme possessed the same C-terminal and N-terminal amino acid sequences. The preliminary results from the milk yield and milk compositions from a naturally lactating transgenic cloned cow 0906 were also tested. These results provide a solid foundation for the large-scale production of rhLZ in the future.
doi:10.1038/srep22947
PMCID: PMC4785527  PMID: 26961596
9.  Analysis of APC mutation in human ameloblastoma and clinical significance 
SpringerPlus  2016;5:314.
As a highly conserved signaling pathway, Wnt/β-catenin signal transduction pathway plays an important role in many processes. Either in the occurrence or development of tumor, activation of this pathway takes an important place. APC inhibits Wnt/β-catenin pathway to regulate cell proliferation and differentiation. This study aimed to investigate the function of cancer suppressor gene. PCR amplification and sequencing method was used to analyze APC mutations of human clinical specimens. The pathological specimens were collected for PCR and clear electrophoretic bands were obtained after electrophoresis. The gene sequence obtained after purification and sequencing analysis was compared with the known APC gene sequence (NM_000038.5). Base mutations at APC 1543 (T → C), APC-4564 (G → A), APC-5353 (T → G), APC-5550 (T → A) and APC-5969 (G → A) locus existed in 22 (27.5 %), 12 (15 %), 5 (6.25 %), 13 (16.25 %) and 12 patients (15 %), respectively. Gene mutations existed in ameloblastoma, and the mutation loci were 1543 locus (T → C), 4564 locus (G → A), 5353 locus (T → G), 5550 locus (T → A) and 5969 locus (G → A) 15 %, respectively. APC mutation plays a certain role in monitoring the tumor malignant degree as it may indicate the transition process of ameloblastoma malignant phenotype.
doi:10.1186/s40064-016-1904-3
PMCID: PMC4786515  PMID: 27065015
Wnt/β-catenin; Ameloblastoma; APC; Mutation
10.  Whole Grain Intake Reduces Pancreatic Cancer Risk 
Medicine  2016;95(9):e2747.
Abstract
Mounting evidence from epidemiology studies suggests that whole grain intake may reduce pancreatic cancer risk, but convincing evidence is scarce. We conducted a meta-analysis to assess the association between whole grain intake and pancreatic cancer risk.
Relevant observational studies were identified by searching PubMed, Embase, Scopus, and Cochrane library databases for the period from January 1980 to July 2015, with no restrictions. We calculated the summary odds ratios (ORs) for pancreatic cancer using random-effects model meta-analysis. Between-study heterogeneity was analyzed using the I2 statistic.
A total of 8 studies regarding whole grain intake were included in the meta-analysis. The pooled OR of pancreatic cancer for those with high versus low whole grain intake was 0.76 (95% confidence interval [CI], 0.64–0.91; P = 0.002). There was no significant heterogeneity across these studies (I2 = 11.7%; Pheterogeneity = 0.339). In the subgroup analysis by geographic area, the summary ORs of developing pancreatic cancer were 0.64 (95% CI, 0.53–0.79; P < 0.001; I2 = 0%; Pheterogeneity = 0.482) in the United States (n = 4) and 0.95 (95% CI, 0.63–1.43; P = 0.803; I2 = 45.6%; Pheterogeneity = 0.175) in Europe (n = 2). In the subgroup analysis by type of whole grain, the summary ORs were 0.72 (95% CI, 0.60–0.87; P = .001; I2 = 0; Pheterogeneity = 0.876) for grains (n = 4) and 0.74 (95% CI, 0.27–2.02; P = 0.554; I2 = 86.3%; Pheterogeneity = 0.007) for wheat (n = 2).
A high intake of whole grains was associated with a reduced risk of pancreatic cancer. Because of the absent of more cohort studies, further prospective studies need to be conducted to ensure conclusions that are more robust.
doi:10.1097/MD.0000000000002747
PMCID: PMC4782845  PMID: 26945361
11.  Low-Dose Intravenous Soybean Oil Emulsion for Prevention of Cholestasis in Preterm Neonates 
Background
Premature infants depend on intravenous fat emulsions to supply essential fatty acids and calories. The dose of soybean-based intravenous fat emulsions (S-IFE) has been associated with parenteral nutrition associated liver disease. This study’s purpose was to determine if low dose S-IFE is a safe and effective preventive strategy for cholestasis in preterm neonates.
Materials and Methods
This is a multicenter randomized controlled trial in infants with a gestation age (GA) ≤ 29 weeks. Subjects < 48 hours of life were randomized to receive a low (1g/kg/day) or control dose (approximately 3g/kg/day) of S-IFE. The primary outcome was cholestasis, defined as a direct bilirubin ≥ 15% of the total bilirubin at 28 days of life (DOL) or full enteral feeds, whichever was later, after 14 days of parenteral nutrition. Secondary outcomes included growth, length of hospital stay, death, and major neonatal morbidities.
Results
136 neonates (67 and 69 in the low and control group, respectively) were enrolled. Baseline characteristic were similar for the two groups. When the low group was compared to the control group, there was no difference in the primary outcome (69% vs. 63%, 95% CI (−0.1, 0.22), p=0.45). While the low group received less S-IFE and total calories over time compared to the control group (p<0.001 and p=0.03, respectively) weight, length and head circumference at 28 DOL, discharge, and over time were not different (p>0.2 for all).
Conclusion
Compared to the control dose, low dose S-IFE was not associated with a reduction in cholestasis or growth.
doi:10.1177/0148607114540005
PMCID: PMC4537394  PMID: 24963025
parenteral nutrition associated liver disease; growth; prematurity
12.  A Survey on Underwater Acoustic Sensor Network Routing Protocols 
Underwater acoustic sensor networks (UASNs) have become more and more important in ocean exploration applications, such as ocean monitoring, pollution detection, ocean resource management, underwater device maintenance, etc. In underwater acoustic sensor networks, since the routing protocol guarantees reliable and effective data transmission from the source node to the destination node, routing protocol design is an attractive topic for researchers. There are many routing algorithms have been proposed in recent years. To present the current state of development of UASN routing protocols, we review herein the UASN routing protocol designs reported in recent years. In this paper, all the routing protocols have been classified into different groups according to their characteristics and routing algorithms, such as the non-cross-layer design routing protocol, the traditional cross-layer design routing protocol, and the intelligent algorithm based routing protocol. This is also the first paper that introduces intelligent algorithm-based UASN routing protocols. In addition, in this paper, we investigate the development trends of UASN routing protocols, which can provide researchers with clear and direct insights for further research.
doi:10.3390/s16030414
PMCID: PMC4813989  PMID: 27011193
underwater acoustic sensor network; routing protocol; cross-layer design; intelligent algorithm based
13.  Rationally engineered Troponin C modulates in vivo cardiac function and performance in health and disease 
Nature Communications  2016;7:10794.
Treatment for heart disease, the leading cause of death in the world, has progressed little for several decades. Here we develop a protein engineering approach to directly tune in vivo cardiac contractility by tailoring the ability of the heart to respond to the Ca2+ signal. Promisingly, our smartly formulated Ca2+-sensitizing TnC (L48Q) enhances heart function without any adverse effects that are commonly observed with positive inotropes. In a myocardial infarction (MI) model of heart failure, expression of TnC L48Q before the MI preserves cardiac function and performance. Moreover, expression of TnC L48Q after the MI therapeutically enhances cardiac function and performance, without compromising survival. We demonstrate engineering TnC can specifically and precisely modulate cardiac contractility that when combined with gene therapy can be employed as a therapeutic strategy for heart disease.
Heart contraction, which is decreased in disease, is determined by Ca2+ binding to troponin C. Here, the authors combine a protein engineering approach with gene therapy to modulate heart contractility in mice with the use of rationally designed Troponin C variants, suggesting a new therapy for diseased hearts.
doi:10.1038/ncomms10794
PMCID: PMC4770086  PMID: 26908229
14.  Preparation and Characterization of Immobilized Lipase from Pseudomonas Cepacia onto Magnetic Cellulose Nanocrystals 
Scientific Reports  2016;6:20420.
Magnetic cellulose nanocrystals (MCNCs) were prepared and used as an enzyme support for immobilization of Pseudomonas cepacialipase (PCL). PCL was successfully immobilized onto MCNCs (PCL@MCNC) by a precipitation-cross-linking method. The resulting PCL@MCNC with a nanoscale size had high enzyme loading (82.2 mg enzyme/g) and activity recovery (95.9%). Compared with free PCL, PCL@MCNC exhibited significantly enhanced stability and solvent tolerance, due to the increase of enzyme structure rigidity. The observable optimum pH and temperature for PCL@MCNC were higher than those of free PCL. PCL@MCNC manifested relatively higher enzyme-substrate affinity and catalytic efficiency. Moreover, PCL@MCNC was capable of effectively catalyzing asymmetric hydrolysis of ketoprofenethyl ester with high yield of 43.4% and product e.e. of 83.5%. Besides, immobilization allowed PCL@MCNC reuse for at least 6 consecutive cycles retaining over 66% of its initial activity. PCL@MCNC was readily recycled by magnetic forces. Remarkably, the as-prepared nanobiocatalyst PCL@MCNC is promising for biocatalysis.
doi:10.1038/srep20420
PMCID: PMC4740797  PMID: 26843037
15.  The Application of Radiation Therapy to the Pediatric Preclinical Testing Program (PPTP): Results of a Pilot Study in Rhabdomyosarcoma 
Pediatric blood & cancer  2012;60(3):377-382.
Background
The Pediatric Preclinical Testing Program (PPTP) has been successfully used to determine the efficacy of novel agents against solid tumors by testing them within a mouse-flank in vivo model. To date, radiation therapy has not been applied to this system. We report on the feasibility and biologic outcomes of a pilot study using alveolar and embryonal rhabdomyosarcoma xeno-graft lines.
Procedures
We developed a high-throughput mouse-flank irradiation device that allows the safe delivery of radiotherapy in clinically relevant doses. For our pilot study, two rhabdomyosarcoma xenograft lines from the PPTP, Rh30 (alveolar) and Rh18 (embryonal) were selected. Using established methods, xenografts were implanted, grown to appropriate volumes, and were subjected to fractionated radiotherapy. Tumor response-rates, growth kinetics, and event-free survival time were measured.
Results
Once optimized, the rate of acute toxicity requiring early removal from study in 93 mice was only 3%. During the optimization phase, it was observed that the alveolar Rh30 xenograft line demonstrated a significantly greater radiation resistance than embryonal Rh18 in vivo. This finding was validated within the standardized 30 Gy treatment phase, resulting in overall treatment failure rates of 10% versus 60% for the embryonal versus alveolar subtype, respectively.
Conclusions
Our pilot study demonstrated the feasibility of our device which enables safe, clinically relevant focal radiation delivery to immunocompromised mice. It further recapitulated the expected clinical radiobiology.
doi:10.1002/pbc.24210
PMCID: PMC4733640  PMID: 22692929
fractionated radiotherapy; PPTP; preclinical testing; rhabdomyosarcoma; xenograft
16.  Circulating Neutrophil MicroRNAs as Biomarkers for the Detection of Lung Cancer 
Biomarkers in Cancer  2016;8:1-7.
Peripheral neutrophils are the predominant circulating leukocytes and an important component of innate and adaptive immune systems, which is a primary defense against cancer. MicroRNAs (miRNAs) can modulate neutrophil functions and play important roles in cancer pathogenesis by regulating neutrophil gene expression. To investigate if assessment of differential miRNA levels of peripheral neutrophils has the potential for diagnosis of non-small-cell lung cancer (NSCLC), we examine neutrophils of 15 patients with stage I NSCLC and 15 smokers without cancer. We identify five neutrophil miRNAs that have an abnormal level in patients with NSCLC versus smokers without cancer. In a training set of 82 patients with lung cancer and 73 controls, a set of two genes (miRs-26a-2-3p and 574-3p) are developed, producing 77.8% sensitivity and 78.1% specificity for NSCLC detection. Furthermore, in a testing set of 60 patients with lung cancer and 58 smokers, the performance of analyzing the two miRNAs for lung cancer detection is confirmed. This study for the first time shows that a neutrophil miRNA profile may serve as a new category of circulating biomarkers for the detection of NSCLC.
doi:10.4137/BIC.S37333
PMCID: PMC4725606  PMID: 26823654
microRNA; peripheral neutrophils; biomarkers; lung cancer; diagnosis
17.  The Association between Helicobacter pylori Infection and Chronic Hepatitis C: A Meta-Analysis and Trial Sequential Analysis 
Purpose. Helicobacter pylori is a common gastric disease-inducing pathogen. Although an increasing number of recent studies have shown that H. pylori is a risk factor for liver disease, the potential association between H. pylori infection and chronic hepatitis C still remains controversial. The aim of our meta-analysis was to evaluate a potential association between H. pylori infection and chronic hepatitis C. Methods. We searched the PubMed, Embase, CNKI, Web of Science, and the Cochrane Central Register of Controlled Trials (CENTRAL) databases between January 1, 1994, and May 1, 2015. Results. This study included a total of 1449 patients with chronic hepatitis C and 2377 control cases. The prevalence of H. pylori was significantly higher in patients with chronic hepatitis C than in those without chronic hepatitis C. The pooled odds ratio was 2.93. In a subgroup analysis, the odds ratios were 4.48 for hepatitis C virus- (HCV-) related cirrhosis and 5.45 for hepatocellular carcinoma. Conclusion. Our study found a strong association between H. pylori and chronic hepatitis C, particularly during the HCV progression stage; thus, we recommend active screening for H. pylori in patients with chronic hepatitis C.
doi:10.1155/2016/8780695
PMCID: PMC4745339  PMID: 26904112
18.  Characterization of the promoter region of the bovine long-chain acyl-CoA synthetase 1 gene: Roles of E2F1, Sp1, KLF15, and E2F4 
Scientific Reports  2016;6:19661.
The nutritional value and eating qualities of beef are enhanced when the unsaturated fatty acid content of fat is increased. Long-chain acyl-CoA synthetase 1 (ACSL1) plays key roles in fatty acid transport and degradation, as well as lipid synthesis. It has been identified as a plausible functional and positional candidate gene for manipulations of fatty acid composition in bovine skeletal muscle. In the present study, we determined that bovine ACSL1was highly expressed in subcutaneous adipose tissue and longissimus thoracis. To elucidate the molecular mechanisms involved in bovine ACSL1 regulation, we cloned and characterized the promoter region of ACSL1. Applying 5′-rapid amplification of cDNA end analysis (RACE), we identified multiple transcriptional start sites (TSSs) in its promoter region. Using a series of 5′ deletion promoter plasmids in luciferase reporter assays, we found that the proximal minimal promoter of ACSL1 was located within the region −325/−141 relative to the TSS and it was also located in the predicted CpG island. Mutational analysis and electrophoretic mobility shift assays demonstrated that E2F1, Sp1, KLF15 and E2F4 binding to the promoter region drives ACSL1 transcription. Together these interactions integrate and frame a key functional role for ACSL1 in mediating the lipid composition of beef.
doi:10.1038/srep19661
PMCID: PMC4726046  PMID: 26782942
19.  Analysis of a four generation family reveals the widespread sequence-dependent maintenance of allelic DNA methylation in somatic and germ cells 
Scientific Reports  2016;6:19260.
Differential methylation of the homologous chromosomes, a well-known mechanism leading to genomic imprinting and X-chromosome inactivation, is widely reported at the non-imprinted regions on autosomes. To evaluate the transgenerational DNA methylation patterns in human, we analyzed the DNA methylomes of somatic and germ cells in a four-generation family. We found that allelic asymmetry of DNA methylation was pervasive at the non-imprinted loci and was likely regulated by cis-acting genetic variants. We also observed that the allelic methylation patterns for the vast majority of the cis-regulated loci were shared between the somatic and germ cells from the same individual. These results demonstrated the interaction between genetic and epigenetic variations and suggested the possibility of widespread sequence-dependent transmission of DNA methylation during spermatogenesis.
doi:10.1038/srep19260
PMCID: PMC4713049  PMID: 26758766
20.  Cytokine levels contribute to the pathogenesis of minimal hepatic encephalopathy in patients with hepatocellular carcinoma via STAT3 activation 
Scientific Reports  2016;6:18528.
Hepatocellular carcinoma (HCC) patients were grouped according to the degree of encephalopathy, with healthy volunteers as controls. We investigated clinical presentation, protein and mRNA expression of 14 cytokines, and activation of six STAT proteins, the downstream signaling mediators. Levels of all 14 cytokines were significantly elevated in HCC patients with clinical hepatic encephalopathy. Statistical analysis showed that levels of IL-1β, IL-6, IFNγ, IL-17α, IFNλ2 and IFNλ3 were correlated with minimal hepatic encephalopathy (MHE). Multivariate regression analysis identified serum IL-6, IFNλ3 and IL-17α as independent risk factors for MHE. Increased mRNA levels of IL-6 and IFNγ were associated with MHE. Among the STAT proteins examined, only STAT3 was elevated in MHE. Treatment with a STAT3 inhibitor protected neurons from cytokine-induced apoptosis in vitro. In conclusion, this study identified potential biomarkers for MHE in HCC. The cytokines investigated may induce neural apoptosis via STAT3 in the pathogenesis of MHE in HCC.
doi:10.1038/srep18528
PMCID: PMC4725946  PMID: 26757951
21.  Impact of multiple bird partners on the seed dispersal effectiveness of China’s relic trees 
Scientific Reports  2016;6:17489.
Frugivorous birds generally exhibit an unequal contribution to dispersal effectiveness of plant species as a function of their habitat adaptation and body size. In our study, we compared the effectiveness of multiple bird species that contribute to the dispersal of the endangered relic Chinese yew, Taxus chinensis. Seven bird species dispersed T. chinensis seeds, with Picus canus, Turdus hortulorum, and Urocissa erythrorhyncha being the main dispersers. The quantity part of dispersal effectiveness was strongly influenced by two inherent characteristics of disperser species: body size and habitat adaptation. However, the quality part of dispersal effectiveness was only influenced by disperser type. For instance, small generalist birds and large specialist birds removed more seeds than other type dispersers. Moreover, small birds and specialist birds contributed slightly more to the dispersal quality of T. chinensis than large birds and generalist birds respectively; however, these differences were not significant. Our results suggest that dispersal effectiveness is affected by variety in the body size and habitat adaptation of different dispersers. Therefore, such variation should be incorporated into spatial and temporal management actions of relic plant species in patchy, human-disturbed habitats.
doi:10.1038/srep17489
PMCID: PMC4698718  PMID: 26725517
22.  Reproductive Outcomes and Nononcologic Complications After Radioactive Iodine Ablation for Well-Differentiated Thyroid Cancer 
Thyroid  2015;25(1):133-138.
Background: Radioactive iodine (RAI) ablation is frequently performed after initial surgery for well-differentiated thyroid cancer (WDTC). We examined the frequency and timing of childbirth as well as nononcologic complications after RAI ablation for WDTC on a population level.
Methods: A retrospective cohort study of 25,333 patients (18,850 women) with WDTC was performed using the California Cancer Registry and California Office of Statewide Health Planning and Development database, 1999–2008. The primary outcomes were birthrate and median time to first live birth among women of childbearing age. Secondary outcomes were nononcologic diagnoses occurring outside the acute setting (>30 days) after ablation.
Results: RAI ablation did not affect birthrate among women in the full dataset. However, in subgroup analyses, birthrate among women age 35–39 was significantly decreased in those who received RAI versus those who did not (11.5 versus 16.3 births per 1000 woman-years, p<0.001). Median time to first live birth after diagnosis of WDTC was prolonged among women who received RAI compared to those who did not (34.5 versus 26.1 months; p<0.0001). When 5-year age groups were examined individually, delay to first live birth was observed in women age 20–39 (p<0.05). This remained significant after adjustment for tumor characteristics, socioeconomic status, and marital status. The only nononcologic, nonreproductive adverse effect associated with RAI ablation was an increased rate of nasolacrimal stenosis (RR 3.44, p<0.0001).
Conclusions: RAI ablation is associated with delayed childbearing in women across most of the reproductive lifespan, and with decreased birthrate in the late reproductive years. The underlying mechanism likely involves physician recommendation to delay pregnancy, as well as a potential impact of RAI on both reproductive choice and reproductive health. Further investigation is merited.
doi:10.1089/thy.2014.0343
PMCID: PMC4291087  PMID: 25289542
23.  Purification and Characterization of Recombinant Human Lysozyme from Eggs of Transgenic Chickens 
PLoS ONE  2015;10(12):e0146032.
Transgenic chickens as bioreactors have several advantages, such as the simple establishment procedure, correct glycosylation profile of expressed proteins, etc. Lysozyme is widely used in food industry, livestock farming, and medical field as a replacement of antibiotics because of its antibacterial and complement system-modulating activity. In this study, we used RT-PCR, Western blot, and immunofluorescence to detect the expression of recombinant human lysozyme (rhLY) in the transgenic chicken. We demonstrated that the transgene of rhLY was genetically stable across different generations. We next optimized the purification procedure of rhLY from the transgenic eggs by utilizing two steps of cation-exchange chromatography and one gel-filtration chromatography. About 6 mg rhLY with the purity exceeding 90% was obtained from ten eggs, and the purification efficiency was about 75%. The purified rhLY had similar physicochemical and biological properties in molecular mass and antibacterial activity compared to the commercial human lysozyme. Additionally, both of them exhibited thermal stability at 60°C and tolerated an extensive pH range of 2 to 11. In conclusion, our study proved that the transgenic chickens we have previously generated were genetically stable and suitable for the production of active rhLY. We also provided a pipeline for purifying the recombinant proteins from transgenic eggs, which could be useful for other studies.
doi:10.1371/journal.pone.0146032
PMCID: PMC4694923  PMID: 26713728
24.  Preoperative Nutritional Therapy Reduces the Risk of Anastomotic Leakage in Patients with Crohn's Disease Requiring Resections 
Background. The rate of anastomotic leakage is high in surgeries for Crohn's disease, and therefore a temporary diverting stoma is often needed. We conducted this study to investigate whether preoperative nutritional therapy could reduce the risk of anastomotic leakage while decreasing the frequency of temporary stoma formation. Methods. This was a retrospective study. Patients requiring bowel resections due to Crohn's disease were reviewed. The rate of anastomotic leakage and temporary diverting stoma was compared between patients who received preoperative nutritional therapy and those on a normal diet before surgery. Possible predictive factors for anastomotic leakage were also analyzed. Results. One hundred and fourteen patients undergoing 123 surgeries were included. Patients in nutritional therapy (NT) group had a significantly lower level of C-reactive protein on the day before surgery. Patients in NT group suffered less anastomotic leakage (2.3% versus 17.9%, P = 0.023) and less temporary diverting stoma (22.8% versus 40.9%, P = 0.036). Serum albumin of the day before surgery ≤35 g/L and preoperative nutritional therapy were identified as factors which independently affected the rate of anastomotic leakage. Conclusion. Preoperative nutritional therapy reduced the risk of anastomotic leakage and the frequency of temporary diverting stoma formation in patients with Crohn's disease requiring resections.
doi:10.1155/2016/5017856
PMCID: PMC4706910  PMID: 26858749
25.  Genome-Wide Dynamic Profiling of Histone Methylation during Nuclear Transfer-Mediated Porcine Somatic Cell Reprogramming 
PLoS ONE  2015;10(12):e0144897.
The low full-term developmental efficiency of porcine somatic cell nuclear transfer (SCNT) embryos is mainly attributed to imperfect epigenetic reprogramming in the early embryos. However, dynamic expression patterns of histone methylation involved in epigenetic reprogramming progression during porcine SCNT embryo early development remain to be unknown. In this study, we characterized and compared the expression patterns of multiple histone methylation markers including transcriptionally repressive (H3K9me2, H3K9me3, H3K27me2, H3K27me3, H4K20me2 and H4K20me3) and active modifications (H3K4me2, H3K4me3, H3K36me2, H3K36me3, H3K79me2 and H3K79me3) in SCNT early embryos from different developmental stages with that from in vitro fertilization (IVF) counterparts. We found that the expression level of H3K9me2, H3K9me3 and H4K20me3 of SCNT embryos from 1-cell to 4-cell stages was significantly higher than that in the IVF embryos. We also detected a symmetric distribution pattern of H3K9me2 between inner cell mass (ICM) and trophectoderm (TE) in SCNT blastocysts. The expression level of H3K9me2 in both lineages from SCNT expanded blastocyst onwards was significantly higher than that in IVF counterparts. The expression level of H4K20me2 was significantly lower in SCNT embryos from morula to blastocyst stage compared with IVF embryos. However, no aberrant dynamic reprogramming of H3K27me2/3 occurred during early developmental stages of SCNT embryos. The expression of H3K4me3 was higher in SCNT embryos at 4-cell stage than that of IVF embryos. H3K4me2 expression in SCNT embryos from 8-cell stage to blastocyst stage was lower than that in the IVF embryos. Dynamic patterns of other active histone methylation markers were similar between SCNT and IVF embryos. Taken together, histone methylation exhibited developmentally stage-specific abnormal expression patterns in porcine SCNT early embryos.
doi:10.1371/journal.pone.0144897
PMCID: PMC4687693  PMID: 26683029

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