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1.  The methyl-CpG-binding protein MBD7 facilitates active DNA demethylation to limit DNA hyper-methylation and transcriptional gene silencing 
Molecular cell  2015;57(6):971-983.
SUMMARY
DNA methylation is a conserved epigenetic mark that plays important roles in plant and vertebrate development, genome stability, and gene regulation. Canonical Methyl-CpG-Binding Domain (MBD) proteins are important interpreters of DNA methylation that recognize methylated CG sites and recruit chromatin remodelers, histone deacetylases and histone methyltransferases to repress transcription. Here, we show that Arabidopsis MBD7 and Increased DNA Methylation 3 (IDM3) are anti-silencing factors that prevent gene repression and DNA hypermethylation. MBD7 preferentially binds to highly methylated, CG-dense regions and physically associates with other anti-silencing factors, including the histone acetyltransferase IDM1 and the alpha-crystallin domain proteins IDM2 and IDM3. IDM1 and IDM2 were previously shown to facilitate active DNA demethylation by the 5-methylcytosine DNA glycosylase/lyase ROS1. Thus, MBD7 tethers the IDM proteins to methylated DNA, which enables the function of DNA demethylases that in turn limit DNA methylation and prevent transcriptional gene silencing.
doi:10.1016/j.molcel.2015.01.009
PMCID: PMC4369450  PMID: 25684209
MBD; IDM1; anti-silencing; DNA methylation; transposable elements
2.  Bioprobes Based on Aptamer and Silica Fluorescent Nanoparticles for Bacteria Salmonella typhimurium Detection 
In this study, we have developed an efficient method based on single-stranded DNA (ssDNA) aptamers along with silica fluorescence nanoparticles for bacteria Salmonella typhimurium detection. Carboxyl-modified Tris(2,2′-bipyridyl)dichlororuthenium(II) hexahydrate (RuBPY)-doped silica nanoparticles (COOH-FSiNPs) were prepared using reverse microemulsion method, and the streptavidin was conjugated to the surface of the prepared COOH-FSiNPs. The bacteria S. typhimurium was incubated with a specific ssDNA biotin-labeled aptamer, and then the aptamer-bacteria conjugates were treated with the synthetic streptavidin-conjugated silica fluorescence nanoprobes (SA-FSiNPs). The results under fluorescence microscopy show that SA-FSiNPs can be applied effectively for the labeling of bacteria S. typhimurium with great photostable property. To further verify the specificity of SA-FSiNPs out of multiple bacterial conditions, variant concentrations of bacteria mixtures composed of bacteria S. typhimurium, Escherichia coli, and Bacillus subtilis were treated with SA-FSiNPs.
In addition, the feasibility of SA-FSiNPs for bacteria S. typhimurium detection in chicken samples was assessed. All the results display that the established aptamer-based nanoprobes exhibit the superiority for bacteria S. typhimurium detection, which is referentially significant for wider application prospects in pathogen detection.
Electronic supplementary material
The online version of this article (doi:10.1186/s11671-016-1359-z) contains supplementary material, which is available to authorized users.
doi:10.1186/s11671-016-1359-z
PMCID: PMC4794472  PMID: 26983430
Bacteria Salmonella typhimurium; Aptamer; Silica; Fluorescent nanoprobes
3.  Stability of titania nanotube arrays in aqueous environment and the related factors 
Scientific Reports  2016;6:23065.
Titania nanotube arrays (NTAs) on titanium (Ti) fabricated by electrochemical anodization have attracted tremendous interest for diverse applications, of which most perform in aqueous environment or related to interaction with water. The NTAs are widely studied however the related factor of stability of NTAs when applied in such environment has rarely been concerned. We report that the annealed anatase NTAs are stable but the non-annealed amorphous NTAs are unstable to undergo specific structural change accompanied with a process of amorphous TiO2 dissolution and anatase TiO2 recrystallization. Quite unexpectedly, the non-annealed NTAs still show good stability without structural change in the cell culture media, possibly due to the presence of inorganics that may interfere with the TiO2 dissolution/redeposition process. The pH value of the aqueous environment is not a determinant factor for the structural change for non-annealed NTAs or not, while the temperature and the existence of F− can accelerate the structural change process. F− may play a very important role in the change process.
doi:10.1038/srep23065
PMCID: PMC4785341  PMID: 26960922
4.  Type One Protein Phosphatase 1 and Its Regulatory Protein Inhibitor 2 Negatively Regulate ABA Signaling 
PLoS Genetics  2016;12(3):e1005835.
The phytohormone abscisic acid (ABA) regulates plant growth, development and responses to biotic and abiotic stresses. The core ABA signaling pathway consists of three major components: ABA receptor (PYR1/PYLs), type 2C Protein Phosphatase (PP2C) and SNF1-related protein kinase 2 (SnRK2). Nevertheless, the complexity of ABA signaling remains to be explored. To uncover new components of ABA signal transduction pathways, we performed a yeast two-hybrid screen for SnRK2-interacting proteins. We found that Type One Protein Phosphatase 1 (TOPP1) and its regulatory protein, At Inhibitor-2 (AtI-2), physically interact with SnRK2s and also with PYLs. TOPP1 inhibited the kinase activity of SnRK2.6, and this inhibition could be enhanced by AtI-2. Transactivation assays showed that TOPP1 and AtI-2 negatively regulated the SnRK2.2/3/6-mediated activation of the ABA responsive reporter gene RD29B, supporting a negative role of TOPP1 and AtI-2 in ABA signaling. Consistent with these findings, topp1 and ati-2 mutant plants displayed hypersensitivities to ABA and salt treatments, and transcriptome analysis of TOPP1 and AtI-2 knockout plants revealed an increased expression of multiple ABA-responsive genes in the mutants. Taken together, our results uncover TOPP1 and AtI-2 as negative regulators of ABA signaling.
Author Summary
The phytohormone abscisic acid (ABA) regulates multiple developmental processes such as seed dormancy, germination, root/shoot growth, flowering and senescence in plants. Although the core ABA perception and signaling pathway has been elucidated, the complexity of the pathway remains to be exploited. In the present work, we uncovered two new proteins, TOPP1 and its regulatory protein AtI-2, interact with both ABA receptor PYLs and their downstream positive regulator SnRK2s. In addition to their physical interaction, TOPP1 could inhibit the kinase activity of SnRK2s and this inhibition could be further enhanced by AtI-2, which is likely due to a promotion of the interaction between TOPP1 and SnRK2s by AtI-2. topp1 and ati-2 mutants exhibited hypersensitivity to ABA and salt treatments; and transcriptome studies revealed multiple ABA-responsive genes were up-regulated in the mutants. In summary, our work identified two new components, TOPP1 and AtI-2, and characterized their negative roles in ABA signaling.
doi:10.1371/journal.pgen.1005835
PMCID: PMC4778861  PMID: 26943172
5.  HOS1 Regulates Argonaute1 by Promoting the Transcription of the MicroRNA Gene MIR168b in Arabidopsis 
Summary
Proper accumulation and function of miRNAs is essential for plant growth and development. While core components of the miRNA biogenesis pathway and miRNA-induced silencing complex have been well characterized, cellular regulators of miRNAs remain to be fully explored. Here we report that HIGH EXPRESSION OF OSMOTICALLY RESPONSIVE GENES1 (HOS1) is a regulator of an important miRNA, mi168a/b, that targets the ARGONAUTE 1 (AGO1) gene in Arabidopsis. HOS1 functions to regulate plant cold stress responses as an ubiquitin E3 ligase, associate with the nuclear pores to regulate mRNA export and circadian clock and flowering time by binding to chromatin of the flowering regulator FLC. We isolated a loss-of-function Arabidopsis mutant of HOS1 in a genetic screen for enhancers of sic-1, which is defective in miRNA biogenesis. Like other hos1 mutant alleles, the new hos1-7 mutant allele flowered early and was smaller in stature than the wild type. Dysfunction in HOS1 reduced the abundance of miR168a/b but not of other miRNAs. In hos1 mutants, pri-MIR168b and pre-MIR168b levels were decreased, and RNA polymerase II occupancy was reduced at the promoter of MIR168b but not MIR168a. Chromatin immunoprecipitation assays revealed HOS1 protein is enriched at the chromatin of the MIR168b promoter. The reduced miR168a/b level in hos1 mutants results in an increase in the mRNA and protein levels of its target gene, AGO1. Our results reveal that HOS1 regulates miR168a/b and AGO1 levels in Arabidopsis by maintaining proper transcription of MIR168b.
doi:10.1111/tpj.12772
PMCID: PMC4355216  PMID: 25619693
gene expression; transcriptional regulation; MicroRNA; MIR168b; high expression of osmotically responsive gene 1; Arabidopsis thaliana
6.  A novel M2e-multiple antigenic peptide providing heterologous protection in mice 
Journal of Veterinary Science  2016;17(1):71-78.
Swine influenza viruses (SwIVs) cause considerable morbidity and mortality in domestic pigs, resulting in a significant economic burden. Moreover, pigs have been considered to be a possible mixing vessel in which novel strains loom. Here, we developed and evaluated a novel M2e-multiple antigenic peptide (M2e-MAP) as a supplemental antigen for inactivated H3N2 vaccine to provide cross-protection against two main subtypes of SwIVs, H1N1 and H3N2. The novel tetra-branched MAP was constructed by fusing four copies of M2e to one copy of foreign T helper cell epitopes. A high-yield reassortant H3N2 virus was generated by plasmid based reverse genetics. The efficacy of the novel H3N2 inactivated vaccines with or without M2e-MAP supplementation was evaluated in a mouse model. M2e-MAP conjugated vaccine induced strong antibody responses in mice. Complete protection against the heterologous swine H1N1 virus was observed in mice vaccinated with M2e-MAP combined vaccine. Moreover, this novel peptide confers protection against lethal challenge of A/Puerto Rico/8/34 (H1N1). Taken together, our results suggest the combined immunization of reassortant inactivated H3N2 vaccine and the novel M2e-MAP provided cross-protection against swine and human viruses and may serve as a promising approach for influenza vaccine development.
doi:10.4142/jvs.2016.17.1.71
PMCID: PMC4808646  PMID: 27051342
H3N2; M2e-multiple antigenic peptide; high-yield; inactivated vaccine; swine influenza virus
7.  Discovery of novel PDE9 inhibitors capable of inhibiting Aβ aggregation as potential candidates for the treatment of Alzheimer’s disease 
Scientific Reports  2016;6:21826.
Recently, phosphodiesterase-9 (PDE9) inhibitors and biometal-chelators have received much attention as potential therapeutics for the treatment of Alzheimer’s disease (AD). Here, we designed, synthesized, and evaluated a novel series of PDE9 inhibitors with the ability to chelate metal ions. The bioassay results showed that most of these molecules strongly inhibited PDE9 activity. Compound 16 showed an IC50 of 34 nM against PDE9 and more than 55-fold selectivity against other PDEs. In addition, this compound displayed remarkable metal-chelating capacity and a considerable ability to halt copper redox cycling. Notably, in comparison to the reference compound clioquinol, it inhibited metal-induced Aβ1-42 aggregation more effectively and promoted greater disassembly of the highly structured Aβ fibrils generated through Cu2+-induced Aβ aggregation. These activities of 16, together with its favorable blood-brain barrier permeability, suggest that 16 may be a promising compound for treatment of AD.
doi:10.1038/srep21826
PMCID: PMC4766439  PMID: 26911795
8.  Oscillating primary transcripts harbor miRNAs with circadian functions 
Scientific Reports  2016;6:21598.
The roles of miRNAs as important post-transcriptional regulators in the circadian clock have been suggested in several studies. But the search for circadian miRNAs has led to disparate results. Here we demonstrated that at least 57 miRNA primary transcripts are rhythmically transcribed in mouse liver. Most of these transcripts are under the regulation of circadian transcription factors such as BMAL1/CLOCK and REV-ERBα/β. However, the mature miRNAs derived from these transcripts are either not oscillating or oscillating at low amplitudes, which could explain the inconsistency of different circadian miRNA studies. In order to show that these circadian primary transcripts can give rise to miRNAs with circadian functions, we over-expressed one of them, miR-378, in mouse by adenovirus injection. We found a significant over-representation of circadian oscillating genes under-expressed by miR-378 over-expression in liver. In particular, we observed that miR-378 modulates the oscillation amplitudes of Cdkn1a in the control of cell cycle and Por in the regulation of oxidation reduction by forming partnership with different circadian transcription factors. Our study suggests that circadian transcription of miRNA at primary transcript level can be a good indicator for circadian miRNA functions.
doi:10.1038/srep21598
PMCID: PMC4761921  PMID: 26898952
9.  De novo transcriptome sequencing and gene expression profiling of spinach (Spinacia oleracea L.) leaves under heat stress 
Scientific Reports  2016;6:19473.
Spinach (Spinacia oleracea) has cold tolerant but heat sensitive characteristics. The spinach variety ‘Island,’ is suitable for summer periods. There is lack molecular information available for spinach in response to heat stress. In this study, high throughput de novo transcriptome sequencing and gene expression analyses were carried out at different spinach variety ‘Island’ leaves (grown at 24 °C (control), exposed to 35 °C for 30 min (S1), and 5 h (S2)). A total of 133,200,898 clean reads were assembled into 59,413 unigenes (average size 1259.55 bp). 33,573 unigenes could match to public databases. The DEG of controls vs S1 was 986, the DEG of control vs S2 was 1741 and the DEG of S1 vs S2 was 1587. Gene Ontology (GO) and pathway enrichment analysis indicated that a great deal of heat-responsive genes and other stress-responsive genes were identified in these DEGs, suggesting that the heat stress may have induced an extensive abiotic stress effect. Comparative transcriptome analysis found 896 unique genes in spinach heat response transcript. The expression patterns of 13 selected genes were verified by RT-qPCR (quantitative real-time PCR). Our study found a series of candidate genes and pathways that may be related to heat resistance in spinach.
doi:10.1038/srep19473
PMCID: PMC4746569  PMID: 26857466
10.  Alteration of the DNA methylation status of donor cells impairs the developmental competence of porcine cloned embryos 
Nuclear reprogramming induced by somatic cell nuclear transfer is an inefficient process, and donor cell DNA methylation status is thought to be a major factor affecting cloning efficiency. Here, the role of donor cell DNA methylation status regulated by 5-aza-2'-deoxycytidine (5-aza-dC) or 5-methyl-2'-deoxycytidine-5'-triphosphate (5-methyl-dCTP) in the early development of porcine cloned embryos was investigated. Our results showed that 5-aza-dC or 5-methyl-dCTP significantly reduced or increased the global methylation levels and altered the methylation and expression levels of key genes in donor cells. However, the development of cloned embryos derived from these cells was reduced. Furthermore, disrupted pseudo-pronucleus formation and transcripts of early embryo development-related genes were observed in cloned embryos derived from these cells. In conclusion, our results demonstrated that alteration of the DNA methylation status of donor cells by 5-aza-dC or 5-methyl-dCTP disrupted nuclear reprogramming and impaired the developmental competence of porcine cloned embryos.
doi:10.1262/jrd.2015-048
PMCID: PMC4768780  PMID: 26537205
DNA methylation; Donor cell; Nuclear reprogramming; Somatic cell nuclear transfer; Pig
11.  Ex vivo expanded human circulating Vδ1 γδT cells exhibit favorable therapeutic potential for colon cancer 
Oncoimmunology  2015;4(3):e992749.
Gamma delta T (γδT) cells are innate-like lymphocytes with strong, MHC-unrestricted cytotoxicity against cancer cells and show a promising prospect in adoptive cellular immunotherapy for various malignancies. However, the clinical outcome of commonly used Vγ9Vδ2 γδT (Vδ2 T) cells in adoptive immunotherapy for most solid tumors is limited. Here, we demonstrate that freshly isolated Vδ1 γδT (Vδ1 T) cells from human peripheral blood (PB) exhibit more potent cytotoxicity against adherent and sphere-forming human colon cancer cells than Vδ2 T cells in vitro. We also develop an optimized protocol to preferentially expand Vδ1 T cells isolated from PB of both healthy donors and colon cancer patients by in vitro short-term culture with phytohemagglutinin (PHA) and interleukin-7 (IL-7). Expanded Vδ1 T cells highly expressed cytotoxicity-related molecules, chemokine receptors and cytokines with enhanced cytolytic effect against adherent and sphere-forming colon cancer cells in a cell-to-cell contact dependent manner. In addition, PHA and IL-7 expanded Vδ1 T cells showed proliferation and survival advantage partly through an IL-2 signaling pathway. Furthermore, ex vivo expanded Vδ1 T cells also restrained the tumor growth and prolonged the tumor-burdened survival of human colon carcinoma xenografted mice. Our findings suggest that human PB Vδ1 T cells expanded by PHA and IL-7 are a promising candidate for anticancer adoptive immunotherapy for human solid tumors such as colon cancer.
doi:10.4161/2162402X.2014.992749
PMCID: PMC4404819  PMID: 25949914
adoptive cellular immunotherapy; cytotoxicity; human colon cancer; human PB Vδ1 T cells; human PB Vδ2 T cells; Antigens, Ags; CCSCs, colon cancer stem cells; FACS, fluorescence activated cell sorting; FCM, flow cytometry; γδT cells, gamma delta T cells; IL-7, interleukin-7; MACS, magnetic activated cell sorting; PB, peripheral blood; PHA, phytohemagglutinin; PBMCs, peripheral blood mononuclear cells; Vδ2 T cells, Vγ9Vδ2 γδT cells; Vδ1 T cells, Vδ1 γδT cells; Zol, Zoledronate.
12.  γδT17 Cells Promote the Accumulation and Expansion of Myeloid-Derived Suppressor Cells in Human Colorectal Cancer 
Immunity  2014;40(5):785-800.
SUMMARY
Development of cancer has been linked to chronic inflammation, particularly via interleukin-23 (IL-23) and IL-17 signaling pathways. However, the cellular source of IL-17 and underlying mechanisms by which IL-17-producing cells promote human colorectal cancer (CRC) remain poorly defined. Here, we demonstrate that innate γδT (γδT17) cells are the major cellular source of IL-17 in human CRC. Microbial products elicited by tumorous epithelial barrier disruption correlated with inflammatory dendritic cell (inf-DC) accumulation and γδT17 polarization in human tumors. Activated inf-DCs induced γδT17 cells to secrete IL-8, tumor necrosis factor alpha, and GM-CSF with a concomitant accumulation of immunosuppressive PMN-MDSCs in the tumor. Importantly, γδT17 cell infiltration positively correlated with tumor stages and other clinicopathological features. Our study uncovers an inf-DC-γδT17-PMN-MDSC regulatory axis in human CRC that correlates MDSC-meditated immunosuppression with tumor-elicited inflammation. These findings suggest that γδT17 cells might be key players in human CRC progression and have the potential for treatment or prognosis prediction.
doi:10.1016/j.immuni.2014.03.013
PMCID: PMC4716654  PMID: 24816404
13.  Comparison of mammography and ultrasound in detecting residual disease following bioptic lumpectomy in breast cancer patients 
Molecular and Clinical Oncology  2016;4(3):419-424.
Surgical biopsy is a method for diagnosing breast cancer. The aim of this study was to prospectively evaluate the relative accuracies of mammography (MMG) and ultrasound (US) in predicting residual disease following bioptic lumpectomy. Each prediction method was compared with the gold standard of surgical pathology. The results of MMG and US from 312 consecutive breast cancer patients diagnosed by surgical excision were analyzed. All the patients underwent re-excision mastectomy or lumpectomy and the imaging results were compared with the histopathological findings. The accuracy and sensitivity of each modality were investigated. A total of 312 patients with 312 primary breast cancers were investigated. Residual disease was identified in 118 patients. Of the 118 cases with residual disease, MMG and US were able to detect 77 (65.3%) and 32 (27.1%), respectively (chi-square P<0.001). MMG was also more sensitive compared with US in estimating residual ductal carcinoma in situ (DCIS) (94.2 vs. 33.3%, respectively; P<0.001). MMG was more accurate compared with US in detecting residual disease following bioptic lumpectomy and the diagnostic accuracy of MMG was associated with the presence of residual DCIS.
doi:10.3892/mco.2016.729
PMCID: PMC4774526  PMID: 26998296
mammography; ultrasound; residual disease; lumpectomy; breast cancer
14.  Outcomes of Surgical Repair for Persistent Truncus Arteriosus from Neonates to Adults: A Single Center's Experience 
PLoS ONE  2016;11(1):e0146800.
Objective
This study aimed to report our experiences with surgical repair in patients of all ages with persistent truncus arteriosus.
Methods
From July 2004 to July 2014, 50 consecutive patients with persistent truncus arteriosus who underwent anatomical repair were included in the retrospective review. Median follow-up time was 3.4 years (range, 3 months to 10 years).
Results
Fifty patients underwent anatomical repair at a median age of 19.6 months (range, 20 days to 19.1 years). Thirty patients (60%) were older than one year. The preoperative pulmonary vascular resistance and mean pulmonary artery pressure were 4.1±2.1 (range, 0.1 to 8.9) units.m2 and 64.3±17.9 (range, 38 to 101) mmHg, respectively. Significant truncal valve regurgitation was presented in 14 (28%) patients. Hospital death occurred in 3 patients, two due to pulmonary hypertensive crisis and the other due to pneumonia. Three late deaths occurred at 3, 4 and 11 months after surgery. The actuarial survival rates were 87.7% and 87.7% at 1 year and 5 years, respectively. Multivariate analysis identified significant preoperative truncal valve regurgitation was a risk factor for overall mortality (odds ratio, 7.584; 95%CI: 1.335–43.092; p = 0.022). Two patients required reoperation of truncal valve replacement. One patient underwent reintervention for conduit replacement. Freedom from reoperation at 5 years was 92.9%. At latest examination, there was one patient with moderate-to-severe truncal valve regurgitation and four with moderate. Three patients had residual pulmonary artery hypertension. All survivors were in New York Heart Association class I-II.
Conclusions
Complete repair of persistent truncus arteriosus can be achieved with a relatively low mortality and acceptable early- and mid-term results, even in cases with late presentation. Significant preoperative truncal valve regurgitation remains a risk factor for overall mortality. The long-term outcomes warrant further follow-up.
doi:10.1371/journal.pone.0146800
PMCID: PMC4713837  PMID: 26752522
15.  Both diet and gene mutation induced obesity affect oocyte quality in mice 
Scientific Reports  2016;6:18858.
Obesity was shown to cause reproductive dysfunctions such as reduced conception, infertility and early pregnancy loss. However, the possible effects of obesity on oocyte quality are still not fully understood. In this study we investigated the effects of both diet and gene mutation induced obesity on impairments in mouse oocyte polarization, oxidative stress, and epigenetic modifications. Our results showed that high-fat diet induced obesity (HFD) and gene mutation induced obesity (ob/ob) could both impair oocyte meiotic maturation, disrupt spindle morphology, and reduce oocyte polarity. Oocytes from obese mice underwent oxidative stress, as shown by high DHE and ROS levels. Abnormal mitochondrial distributions and structures were observed in oocytes from obese groups of mice and early apoptosis signals were detected, which suggesting that oxidative stress had impaired mitochondrial function and resulted in oocyte apoptosis. Our results also showed that 5 mC levels and H3K9 and H3K27 methylation levels were altered in oocytes from obese mice, which indicated that DNA methylation and histone methylation had been affected. Our results showed that both HFD and ob/ob induced obesity affected oocyte maturation and that oxidative stress-induced early apoptosis and altered epigenetic modifications may be the reasons for reduced oocyte quality in obese mice.
doi:10.1038/srep18858
PMCID: PMC4702149  PMID: 26732298
16.  The Sequence Characteristics and Expression Models Reveal Superoxide Dismutase Involved in Cold Response and Fruiting Body Development in Volvariella volvacea 
As the first defence for cells to counteract the toxicity of active oxygen, superoxide dismutase (SOD) plays an important role in the response of living organisms to stress and cell differentiation. One extracellular Cu-ZnSOD (ecCu-ZnSOD), and two MnSODs, were identified based on the Volvariella volvacea genome sequence. All three genes have complicated alternative splicing modes during transcription; only when the fourth intron is retained can the Vv_Cu-Znsod1 gene be translated into a protein sequence with SOD functional domains. The expression levels of the three sod genes in the pilei are higher than in the stipe. The Vv_Cu-Znsod1 and the Vv_Mnsod2 are co-expressed in different developmental stages of the fruiting body, with the highest level of expression in the pilei of the egg stage, and they show a significant, positive correlation with the efficiency of karyogamy, indicating the potential role of these two genes during karyogamy. The expression of the ecCu-Znsod and two Vv_Mnsod genes showed a significant up-regulated when treated by cold stress for one hour; however, the lack of the intracellular Cu-ZnSOD encoding gene (icCu-Znsod) and the special locus of the ecCu-Znsod gene initiation codon suggested a possible reason for the autolysis phenomenon of V. volvacea in cold conditions.
doi:10.3390/ijms17010034
PMCID: PMC4730280  PMID: 26784168
straw mushroom; alternative splicing modes; gene differential expression; cold stress; fruiting-body development
17.  13C Tracer Studies of Metabolism in Mouse Tumor Xenografts 
Bio-protocol  2015;5(22):bio-protocol.org/e1650.
Mice are widely used for human tumor xenograft studies of cancer development and drug efficacy and toxicity. Stable isotope tracing coupled with metabolomic analysis is an emerging approach for assaying metabolic network activity. In mouse models there are several routes of tracer introduction, which have particular advantages and disadvantages that depend on the model and the questions addressed. This protocol describes the bolus i.v. route via repeated tail vein injections of solutions of stable isotope enriched tracers including 13C6-glucose and 13C5,15N2-glutamine. Repeated injections give higher enrichments and over longer labeling periods than a single bolus. Multiple injections of glutamine are necessary to achieve adequate enrichment in engrafted tumors.
PMCID: PMC4675468  PMID: 26693168
18.  IL30 (IL27p28) attenuates liver fibrosis through inducing NKG2D-Rae1 interaction between NKT and activated hepatic stellate cells 
Hepatology (Baltimore, Md.)  2014;60(6):2027-2039.
Chronic hepatic diseases such as cirrhosis, hepatocellular carcinoma and virus mediated immunopathogenic infections are affecting billions of people worldwide. These diseases commonly initiate with fibrosis. Owing to the various side effects of anti-fibrotic therapy and the difficulty of diagnosing asymptomatic patients, suitable medication remains a major concern. To overcome this drawback, the use of cytokine-based sustained therapy might be a suitable alternative with minimal side effects. Here, we studied the therapeutic efficacy and potential mechanisms of IL30 as anti-fibrosis therapy in murine liver fibrosis models. Carbon tetrachloride (CCl4) mixed with corn oil at a ratio 1:3 was injected intraperitoneally (IP) 1µl/gm body weight twice per week for 1 month or 3,5-diethoxycarbonyl-1,4-dihydrocollidine (DDC) 0.1% (wt/wt) Purnima 5015 Chow was fed for 3 weeks to induce liver fibrosis. Either control vector (pCtr) or pIL30 was injected hydrodynamically once per week. A significant decrease in collagen deposition and reduced expression of α-smooth muscle Actin (αSMA) protein indicated that IL30–based gene therapy dramatically reduced bridging fibrosis that was induced by CCl4 or DDC. Immunophenotyping and knockout studies showed that IL30 recruits NKT cells to the liver to decrease activated hepatic stellate cells (HSCs) significantly and ameliorate liver fibrosis. Both flow cytometric and antibody mediated neutralization studies showed NKT cells alleviate liver fibrosis in an NKG2D dependent manner. Furthermore, chronic treatment with CCl4 showed inducible surface expression of the NKG2D ligand Rae1 on activated HSCs as compared to quiescent ones.
Taken together, our results show that highly target specific liver NKT cells selectively remove activated HSCs via an NKG2D-Rae1 interaction to ameliorate liver fibrosis after IL30 treatment.
doi:10.1002/hep.27392
PMCID: PMC4245364  PMID: 25351459
IL30; NKT; NKG2D; Rae1; CCl4
19.  Reduction of blood pressure by store‐operated calcium channel blockers 
Abstract
The voltage‐operated Ca2+ channels (VOCC), which allow Ca2+ influx from the extracellular space, are inhibited by anti‐hypertensive agents such as verapamil and nifedipine. The Ca2+ entering from outside into the cell triggers Ca2+ release from the sarcoplasmic reticulum (SR) stores. To refill the depleted Ca2+ stores in the SR, another type of Ca2+ channels in the cell membrane, known as store‐operated Ca2+ channels (SOCC), are activated. These SOCCs are verapamil and nifedipine resistant, but are SKF 96465 (SK) and gadolinium (Gd3+) sensitive. Both SK and Gd3+ have been shown to reduce [Ca2+]i in the smooth muscle, but their effects on blood pressure have not been reported. Our results demonstrated that both SK and Gd3+ produced a dose‐dependent reduction in blood pressure in rat. The combination of SK and verapamil produced an additive action in lowering the blood pressure. Furthermore, SK, but not Gd3+ suppressed proliferation of vascular smooth muscle cells in the absence or presence of lysophosphatidic acid (LPA). SK decreased the elevation of [Ca2+]i induced by LPA, endothelin‐1 (ET‐1) and angiotensin II (Ang II), but did not affect the norepinephrine (NE)‐evoked increase in [Ca2+]i. On the other hand, Gd3+ inhibited the LPA and Ang II induced change in [Ca2+]i, but had no effect on the ET‐1 and NE induced increase in [Ca2+]i. The combination of verapamil and SK abolished the LPA‐ or adenosine‐5′‐triphosphate (ATP)‐induced [Ca2+]i augmentation. These results suggest that SOCC inhibitors, like VOCC blocker, may serve as promising drugs for the treatment of hypertension.
doi:10.1111/jcmm.12684
PMCID: PMC4687696  PMID: 26471725
Ca2+ antagonists; antihypertensive agents; intracellular Ca2+; cell proliferation; hypertension
20.  A safety study of transumbilical single incision versus conventional laparoscopic surgery for colorectal cancer: study protocol for a randomized controlled trial 
Trials  2015;16:539.
Background
Single-incision laparoscopic surgery (SILS) is an emerging minimally invasive surgery to reduce abdominal incisions. However, despite the increasing clinical application of SILS, no evidence from large-scale, randomized controlled trials is available for assessing the feasibility, short-term safety, oncological safety, and potential benefits of SILS compared with conventional laparoscopic surgery (CLS) for colorectal cancer.
Methods/Design
This is a single-center, open-label, noninferiority, randomized controlled trial. A total of 198 eligible patients will be randomly assigned to transumbilical single incision plus one port laparoscopic surgery (SILS plus one) group or to a CLS group at a 1:1 ratio. Patients ranging in age from 18 to 80 years with rectosigmoid cancer diagnosed as cT1-4aN0-2 M0 and a tumor size no larger than 5 cm are considered eligible. The primary endpoint is early morbidity, as evaluated by an independent investigator. Secondary outcomes include operative outcomes (operative time, estimated blood loss, and incision length), pathologic outcomes (tumor size, length of proximal and distal resection margins, and number of harvested lymph nodes), postoperative inflammatory and immune responses (white blood cells [WBC], neutrophil percentage [NE %], C-reactive protein [CRP], interleukin-6 [IL-6], and tumor necrosis factor-α [TNF-α]), postoperative recovery (time to first ambulation, flatus, liquid diet, soft diet, and duration of hospital stay), pain intensity, body image and cosmetic assessment, 3-year disease free survival (DFS), and 5-year overall survival (OS). Follow-up visits are scheduled for 1 and 3 months after surgery, then every 3 months for the first 2 years and every 6 months for the next 3 years.
Discussion
This trial will provide valuable clinical evidence for the objective assessment of the feasibility, safety, and potential benefits of SILS plus one compared with CLS for the radical resection of rectosigmoid cancer. The hypothesis is that SILS plus one is feasible for the radical resection of rectosigmoid cancer and offers short-term safety and long-term oncological safety comparable to that of CLS, and that SILS plus one offers better cosmetic results and faster convalescence compared to CLS.
Trial registration
ClinicalTrials.gov: NCT02117557 (registered on 16 April 2014).
Electronic supplementary material
The online version of this article (doi:10.1186/s13063-015-1067-5) contains supplementary material, which is available to authorized users.
doi:10.1186/s13063-015-1067-5
PMCID: PMC4663734  PMID: 26620555
Colorectal cancer; laparoscopy; single incision; SILS; rectosigmoid; transumbilical; randomized controlled trial; study protocol
21.  Ginger-derived nanoparticles protect against alcohol-induced liver damage 
Journal of Extracellular Vesicles  2015;4:10.3402/jev.v4.28713.
Daily exposure of humans to nanoparticles from edible plants is inevitable, but significant advances are required to determine whether edible plant nanoparticles are beneficial to our health. Additionally, strategies are needed to elucidate the molecular mechanisms underlying any beneficial effects. Here, as a proof of concept, we used a mouse model to show that orally given nanoparticles isolated from ginger extracts using a sucrose gradient centrifugation procedure resulted in protecting mice against alcohol-induced liver damage. The ginger-derived nanoparticle (GDN)–mediated activation of nuclear factor erythroid 2-related factor 2 (Nrf2) led to the expression of a group of liver detoxifying/antioxidant genes and inhibited the production of reactive oxygen species, which partially contributes to the liver protection. Using lipid knock-out and knock-in strategies, we further identified that shogaol in the GDN plays a role in the induction of Nrf2 in a TLR4/TRIF-dependent manner. Given the critical role of Nrf2 in modulating numerous cellular processes, including hepatocyte homeostasis, drug metabolism, antioxidant defenses, and cell-cycle progression of liver, this finding not only opens up a new avenue for investigating GDN as a means to protect against the development of liver-related diseases such as alcohol-induced liver damage but sheds light on studying the cellular and molecular mechanisms underlying interspecies communication in the liver via edible plant–derived nanoparticles.
doi:10.3402/jev.v4.28713
PMCID: PMC4662062  PMID: 26610593
ginger nanoparticles; shogaol; Nrf2 detoxic effect; TLR4/TRIF pathway; alcoholic liver injury
22.  MAE4, an eLtaS monoclonal antibody, blocks Staphylococcus aureus virulence 
Scientific Reports  2015;5:17215.
Staphylococcus aureus causes a wide range of infectious diseases. Treatment of these infections has become increasingly difficult due to the widespread emergence of antibiotic-resistant strains; therefore, it is essential to explore effective alternatives to antibiotics. A secreted protein of S. aureus, known as eLtaS, is an extracellular protein released from the bacterial membrane protein, LtaS. However, the role of eLtaS in S. aureus pathogenesis remains largely unknown. Here we show eLtaS dramatically aggravates S. aureus infection by binding to C3b and then inhibiting the phagocytosis of C3b-deposited S. aureus. Furthermore, we developed a monoclonal antibody against eLtaS, MAE4, which neutralizes the activity of eLtaS and blocks staphylococcal evasion of phagocytosis. Consequently, MAE4 is capable of protecting mice from lethal S. aureus infection. Our findings reveal that targeting of eLtaS by MAE4 is a potential therapeutic strategy for the treatment of infectious diseases caused by S. aureus.
doi:10.1038/srep17215
PMCID: PMC4657049  PMID: 26599734
23.  SPOP E3 Ubiquitin Ligase Adaptor Epigenetically Promotes Cellular Senescence by Degrading the SENP7 deSUMOylase. 
Cell reports  2015;13(6):1183-1193.
Summary
The SPOP gene, encoding an E3 ubiquitin ligase adaptor, is frequently mutated in a number of cancer types such as prostate. However, the mechanisms by which SPOP functions as a tumor suppressor remain poorly understood. Here we show that SPOP promotes senescence, an important tumor suppression mechanism, by targeting the SENP7 deSUMOylase for degradation. SPOP is upregulated during senescence. This correlates with ubiquitin-mediated degradation of SENP7, which promotes senescence by increasing HP1α sumoylation and the associated epigenetic gene silencing. Ectopic wild-type SPOP, but not its cancer-associated mutants, drives senescence. Conversely, SPOP knockdown overcomes senescence. These phenotypes correlate with ubiquitination and degradation of SENP7, and HP1α sumoylation, subcellular re-localization and its associated gene silencing. Furthermore, SENP7 is expressed at higher levels in prostate tumor specimens with SPOP mutation (n=13) compared to those with wild-type SPOP (n=80). In summary, SPOP acts as a tumor suppressor by promoting senescence through degrading SENP7.
Graphical abstract
doi:10.1016/j.celrep.2015.09.083
PMCID: PMC4644472  PMID: 26527005
24.  Honokiol inhibits bladder tumor growth by suppressing EZH2/miR-143 axis 
Oncotarget  2015;6(35):37335-37348.
The oncoprotein EZH2, as a histone H3K27 methyltransferase, is frequently overexpressed in various cancer types. However, the mechanisms underlying its role in urinary bladder cancer (UBC) cells have not yet fully understood. Herein, we reported that honokiol, a biologically active biphenolic compound isolated from the Magnolia officinalis inhibited human UBC cell proliferation, survival, cancer stemness, migration, and invasion, through downregulation of EZH2 expression level, along with the reductions of MMP9, CD44, Sox2 and the induction of tumor suppressor miR-143. Either EZH2 overexpression or miR-143 inhibition could partially reverse honokiol-induced cell growth arrest and impaired clonogenicity. Importantly, it was first revealed that EZH2 could directly bind to the transcriptional regulatory region of miR-143 and repress its expression. Furthermore, honokiol treatment on T24 tumor xenografts confirmed its anticancer effects in vivo, including suppression tumor growth and tumor stemness, accompanied by the dysregulation of EZH2 and miR-143 expressions. Our data suggest a promising therapeutic option to develop drugs targeting EZH2/miR-143 axis, such as honokiol, for bladder cancer treatment.
PMCID: PMC4741933  PMID: 26484567
honokiol; bladder cancer; EZH2; microRNA
25.  Comparative functional genomics of adaptation to muscular disuse in hibernating mammals 
Molecular ecology  2014;23(22):5524-5537.
Hibernation is an energy saving adaptation that involves a profound suppression of physical activity that can continue for 6-8 months in highly seasonal environments. While immobility and disuse generate muscle loss in most mammalian species, in contrast, hibernating bears and ground squirrels demonstrate limited muscle atrophy over the prolonged periods of physical inactivity during winter suggesting that hibernating mammals have adaptive mechanisms to prevent disuse muscle atrophy. To identify common transcriptional programs that underlie molecular mechanisms preventing muscle loss, we conducted a large-scale gene expression screen in hind limb muscles comparing hibernating and summer active black bears and arctic ground squirrels using custom 9,600 probe cDNA microarrays. A molecular pathway analysis showed an elevated proportion of over-expressed genes involved in all stages of protein biosynthesis and ribosome biogenesis in muscle of both species during torpor of hibernation that suggests induction of translation at different hibernation states. The induction of protein biosynthesis likely contributes to attenuation of disuse muscle atrophy through the prolonged periods of immobility of hibernation. The lack of directional changes in genes of protein catabolic pathways does not support the importance of metabolic suppression for preserving muscle mass during winter. Coordinated reduction of multiple genes involved in oxidation reduction and glucose metabolism detected in both species is consistent with metabolic suppression and lower energy demand in skeletal muscle during inactivity of hibernation.
doi:10.1111/mec.12963
PMCID: PMC4245363  PMID: 25314618
protein biosynthesis; hibernation; black bear; arctic ground squirrel; functional genomics; gene expression

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