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1.  IL-9 Regulates Allergen-Specific Th1 Responses in Allergic Contact Dermatitis 
The cytokine IL-9, derived primarily from T-helper (Th)-9 lymphocytes, promotes expansion of the Th2 subset and is implicated in the mechanisms of allergic asthma. We hypothesize that IL-9 also plays a role in human allergic contact dermatitis (ACD). To investigate this hypothesis, skin biopsy specimens of positive patch test sites from non-atopic patients were assayed using qPCR and immunohistochemistry. Along with Th2 associated cytokines, IFN-γ, IL-4, and IL-17A, expression of IL-9, and PU.1, a Th9-associated transcription factor, were elevated when compared to paired normal skin. Immunohistochemistry on ACD skin biopsies identified PU.1+CD3+, and PU.1+CD4+ cells, consistent with Th9 lymphocytes, in the inflammatory infiltrate. PBMC from nickel-allergic patients, but not non-allergic controls, show significant IL-9 production in response to nickel. Blocking studies with monoclonal antibodies to HLA-DR (but not HLA-A, B, C) or chloroquine significantly reduced this nickel-specific IL-9 production. Additionally, blockade of IL-9 or IL-4 enhanced allergen-specific IFN-γ production. A contact hypersensitivity model using IL-9−/− mice, shows enhanced Th1 lymphocyte immune responses, when compared to WT mice, consistent with our human in vitro data. This study demonstrates that IL-9, through its direct effects on Th1 and ability to promote IL-4 secretion, has a regulatory role for Th1 lymphocytes in ACD.
doi:10.1038/jid.2014.61
PMCID: PMC4303591  PMID: 24487305
2.  Himalayan fossils of the oldest known pantherine establish ancient origin of big cats 
Pantherine felids (‘big cats’) include the largest living cats, apex predators in their respective ecosystems. They are also the earliest diverging living cat lineage, and thus are important for understanding the evolution of all subsequent felid groups. Although the oldest pantherine fossils occur in Africa, molecular phylogenies point to Asia as their region of origin. This paradox cannot be reconciled using current knowledge, mainly because early big cat fossils are exceedingly rare and fragmentary. Here, we report the discovery of a fossil pantherine from the Tibetan Himalaya, with an age of Late Miocene–Early Pliocene, replacing African records as the oldest pantherine. A ‘total evidence’ phylogenetic analysis of pantherines indicates that the new cat is closely related to the snow leopard and exhibits intermediate characteristics on the evolutionary line to the largest cats. Historical biogeographic models provide robust support for the Asian origin of pantherines. The combined analyses indicate that 75% of the divergence events in the pantherine lineage extended back to the Miocene, up to 7 Myr earlier than previously estimated. The deeper evolutionary origin of big cats revealed by the new fossils and analyses indicate a close association between Tibetan Plateau uplift and diversification of the earliest living cats.
doi:10.1098/rspb.2013.2686
PMCID: PMC3843846  PMID: 24225466
first appearance; Himalaya; Pantherinae; Felidae; Miocene; Asia
3.  New Meroterpenoids from the Endophytic Fungus Aspergillus flavipes AIL8 Derived from the Mangrove Plant Acanthus ilicifolius 
Marine Drugs  2015;13(1):237-248.
Four new meroterpenoids (2–5), along with three known analogues (1, 6, and 7) were isolated from mangrove plant Acanthus ilicifolius derived endophytic fungus Aspergillus flavipes. The structures of these compounds were elucidated by NMR and MS analysis, the configurations were assigned by CD data, and the stereochemistry of 1 was confirmed by X-ray crystallography analysis. A possible biogenetic pathway of compounds 1–7 was also proposed. All compounds were evaluated for antibacterial and cytotoxic activities.
doi:10.3390/md13010237
PMCID: PMC4306934  PMID: 25574738
meroterpenoid; Aspergillus flavipes; endophytic fungus
4.  Nerve growth factor for Bell’s palsy: A meta-analysis 
A meta-analysis was performed to evaluate the efficacy and safety of nerve growth factor (NGF) in the treatment of Bell’s palsy. PubMed, the Cochrane Central Register of Controlled Trials, Embase and a number of Chinese databases, including the China National Knowledge Infrastructure, China Biology Medicine disc, VIP Database for Chinese Technical Periodicals and Wan Fang Data, were used to collect randomised controlled trials (RCTs) of NGF for Bell’s palsy. The span of the search covered data from the date of database establishment until December 2013. The included trials were screened comprehensively and rigorously. The efficacies of NGF were pooled via meta-analysis performed using Review Manager 5.2 software. Odds ratios (ORs) and 95% confidence intervals (CIs) were calculated using the fixed-effects model. The meta-analysis of eight RCTs showed favorable effects of NGF on the disease response rate (n=642; OR, 3.87; 95% CI, 2.13–7.03; P<0.01; I2=0%). However, evidence supporting the effectiveness of NGF for the treatment of Bell’s palsy is limited. The number and quality of trials are too low to form solid conclusions. Further meticulous RCTs are required to overcome the limitations identified in the present study.
doi:10.3892/etm.2014.2100
PMCID: PMC4280984  PMID: 25574223
nerve growth factor; Bell’s palsy; meta-analysis
5.  Biosafe Nanoscale Pharmaceutical Adjuvant Materials 
Journal of biomedical nanotechnology  2014;10(9):2393-2419.
Thanks to developments in the field of nanotechnology over the past decades, more and more biosafe nanoscale materials have become available for use as pharmaceutical adjuvants in medical research. Nanomaterials possess unique properties which could be employed to develop drug carriers with longer circulation time, higher loading capacity, better stability in physiological conditions, controlled drug release, and targeted drug delivery. In this review article, we will review recent progress in the application of representative organic, inorganic and hybrid biosafe nanoscale materials in pharmaceutical research, especially focusing on nanomaterial-based novel drug delivery systems. In addition, we briefly discuss the advantages and notable functions that make these nanomaterials suitable for the design of new medicines; the biosafety of each material discussed in this article is also highlighted to provide a comprehensive understanding of their adjuvant attributes.
doi:10.1166/jbn.2014.1898
PMCID: PMC4242152  PMID: 25429253
Drug Delivery; Adjuvant Nanomaterials; Biosafe; Multifunction; Nanoparticle; Controlled Release
6.  Development of reverse-transcription loop-mediated isothermal amplification assay for rapid detection of novel avian influenza A (H7N9) virus 
BMC Microbiology  2014;14(1):271.
Background
The emerged human infection with avian influenza A (H7N9) virus in China since 2013 has aroused global concerns. There is great demand for simple and rapid diagnostic method for early detection of H7N9 to provide timely treatment and disease control. The aim of the current study was to develop a rapid, accurate and feasible reverse-transcription loop-mediated isothermal amplification (RT-LAMP) assay for detection of H7N9 virus.
Results
The detection limits of the H7- and N9-specific RT-LAMP assay were both approximately 0.2 PFU per reaction. No cross-reactivity was observed with other subtype of influenza viruses or common respiratory viral pathogens. The assay worked well with clinical specimens from patients and chickens, and exhibited high specificity and sensitivity.
Conclusions
The H7/N9 specific RT-LAMP assay was sensitive and accurate, which could be a useful alternative in clinical diagnostics of influenza A (H7N9) virus, especially in the hospitals and laboratories without sophisticated diagnostic systems.
doi:10.1186/s12866-014-0271-x
PMCID: PMC4234856  PMID: 25394781
Influenza virus; H7N9 subtype; Reverse transcription-loop-mediated isothermal amplification; Molecular diagnosis
7.  Identification of single-stranded and double-stranded dna binding proteins based on protein structure 
BMC Bioinformatics  2014;15(Suppl 12):S4.
Background
Protein-DNA interactions are essential for many biological processes. However, the structural mechanisms underlying these interactions are not fully understood. DNA binding proteins can be classified into double-stranded DNA binding proteins (DSBs) and single-stranded DNA binding proteins (SSBs), and they take part in different biological functions. DSBs usually act as transcriptional factors to regulate the genes' expressions, while SSBs usually play roles in DNA replication, recombination, and repair, etc. Understanding the binding specificity of a DNA binding protein is helpful for the research of protein functions.
Results
In this paper, we investigated the differences between DSBs and SSBs on surface tunnels as well as the OB-fold domain information. We detected the largest clefts on the protein surfaces, to obtain several features to be used for distinguishing the potential interfaces between SSBs and DSBs, and compared its structure with each of the six OB-fold protein templates, and use the maximal alignment score TM-score as the OB-fold feature of the protein, based on which, we constructed the support vector machine (SVM) classification model to automatically distinguish these two kinds of proteins, with prediction accuracy of 87%,83% and 83% for HOLO-set, APO-set and Mixed-set respectively.
Conclusions
We found that they have different ranges of tunnel lengths and tunnel curvatures; moreover, the alignment results with OB-fold templates have also found to be the discriminative feature of SSBs and DSBs. Experimental results on 10-fold cross validation indicate that the new feature set are effective to describe DNA binding proteins. The evaluation results on both bound (DNA-bound) and non-bound (DNA-free) proteins have shown the satisfactory performance of our method.
doi:10.1186/1471-2105-15-S12-S4
PMCID: PMC4243121  PMID: 25474071
8.  Characterization of the sequence and expression pattern of LFY homologues from dogwood species (Cornus) with divergent inflorescence architectures 
Annals of Botany  2013;112(8):1629-1641.
Background and Aims LFY
homologues encode transcription factors that regulate the transition from vegetative to reproductive growth in flowering plants and have been shown to control inflorescence patterning in model species. This study investigated the expression patterns of LFY homologues within the diverse inflorescence types (head-like, umbel-like and inflorescences with elongated internodes) in closely related lineages in the dogwood genus (Cornus s.l.). The study sought to determine whether LFY homologues in Cornus species are expressed during floral and inflorescence development and if the pattern of expression is consistent with a function in regulating floral development and inflorescence architectures in the genus.
Methods
Total RNAs were extracted using the CTAB method and the first-strand cDNA was synthesized using the SuperScript III first-strand synthesis system kit (Invitrogen). Expression of CorLFY was investigated by RT–PCR and RNA in situ hybridization. Phylogenetic analyses were conducted using the maximum likelihood methods implemented in RAxML-HPC v7.2.8.
Key Results
cDNA clones of LFY homologues (designated CorLFY) were isolated from six Cornus species bearing different types of inflorescence. CorLFY cDNAs were predicted to encode proteins of approximately 375 amino acids. The detection of CorLFY expression patterns using in situ RNA hybridization demonstrated the expression of CorLFY within the inflorescence meristems, inflorescence branch meristems, floral meristems and developing floral organ primordia. PCR analyses for cDNA libraries derived from reverse transcription of total RNAs showed that CorLFY was also expressed during the late-stage development of flowers and inflorescences, as well as in bracts and developing leaves. Consistent differences in the CorLFY expression patterns were not detected among the distinct inflorescence types.
Conclusions
The results suggest a role for CorLFY genes during floral and inflorescence development in dogwoods. However, the failure to detect expression differences between the inflorescence types in the Cornus species analysed suggests that the evolutionary shift between major inflorescence types in the genus is not controlled by dramatic alterations in the levels of CorLFY gene transcript accumulation. However, due to spatial, temporal and quantitative limitations of the expression data, it cannot be ruled out that subtle differences in the level or location of CorLFY transcripts may underlie the different inflorescence architectures that are observed across these species. Alternatively, differences in CorLFY protein function or the expression or function of other regulators (e.g. TFL1 and UFO homologues) may support the divergent developmental trajectories.
doi:10.1093/aob/mct202
PMCID: PMC3828947  PMID: 24052556
Cornus; dogwood; inflorescence evolution; LFY homologues; CorLFY expression; RT–PCR; in situ hybridization
9.  The miR-545/374a Cluster Encoded in the Ftx lncRNA is Overexpressed in HBV-Related Hepatocellular Carcinoma and Promotes Tumorigenesis and Tumor Progression 
PLoS ONE  2014;9(10):e109782.
Hepatitis B virus (HBV) infection is a major risk factor for hepatocellular carcinoma (HCC). Previous studies have shown several long noncoding RNAs (lncRNAs) play various roles in HCC progression, but no research has focused on the expression pattern of microRNA clusters encoded in lncRNAs. The Ftx gene encodes a lncRNA which harbors 2 clusters of microRNAs in its introns, the miR-374b/421 cluster and the miR-545/374a cluster. To date, no research has focused on the role of the miR-545/374a and miR-374b/421 clusters in HBV-related HCC. In this study, 66 pairs of HBV-related HCC tissue and matched non-cancerous liver tissue specimens were analyzed for the expression of the Ftx microRNA clusters. Our results showed that the miR-545/374a cluster was upregulated in HBV-HCC tissue and significantly correlated with prognosis-related clinical features, including histological grade, metastasis and tumor capsule. Transfection studies with microRNA mimics and inhibitors revealed that miR-545/374a expression promoted in vitro cell proliferation, cell migration and invasion. The wild-type HBV-genome-containing plasmid or full-length HBx protein encoding plasmid was transfected into the Bel-7402 cell line and observed for their influence on miR-545/374a expression. We found that transfection of the HBV genome or HBx alone resulted in an increase in miR-545/374a expression. Next, by monitoring the expression of sera miR-545/374a before and after surgical tumor excision, we found serum miR-545/374a was tumor-derived and exhibited a sharp decrease 25 days after tumor excision. We also examined the gender-based difference in miR-545/374a expression among HCC patients and utilized microRNA target prediction software to find the targets of miR-545/374a. One of these targets, namely estrogen-related receptor gamma (ESRRG) was inversely correlated with miR-545 expression. In conclusion, the overexpression of miR-545/374a cluster located in the Ftx lncRNA is partially responsible for a poor prognosis, and monitoring sera levels of miR-545/374a may be a useful diagnostic marker for HCC.
doi:10.1371/journal.pone.0109782
PMCID: PMC4192320  PMID: 25299640
10.  Short-Term Continuous Subcutaneous Insulin Infusion Combined with Insulin Sensitizers Rosiglitazone, Metformin, or Antioxidant α-Lipoic Acid in Patients with Newly Diagnosed Type 2 Diabetes Mellitus 
Diabetes Technology & Therapeutics  2013;15(10):859-869.
Abstract
Background
Short-term continuous subcutaneous insulin infusion (CSII) in patients with newly diagnosed type 2 diabetes has been proved effective in improving metabolic control and β-cell function, thus inducing long-term drug-free remission. A randomized controlled trial was conducted to investigate whether CSII in combination with rosiglitazone, metformin, or α-lipoic acid separately brings about extra benefits.
Patients and Methods
One hundred sixty patients with newly diagnosed type 2 diabetes were randomized to one of four treatment groups: CSII alone, CSII in combination with rosiglitazone or metformin for 3 months, or CSII with α-lipoic acid intravenous infusion for 2 weeks. Duration of CSII treatment was identical in the four groups. Glucose and lipid profiles, homeostasis model assessment (HOMA) indices, acute insulin response (AIR), intramyocellular lipid (IMCL) level, and malondialdehyde level were compared before and after intervention.
Results
The near-normoglycemia rate at the third month in CSII alone and that in combination with rosiglitazone, metformin, or α-lipoic acid was 72.5%, 87.5%, 90%, and 75%, respectively (metformin group vs. CSII alone, P=0.045). The metformin group achieved euglycemia in a shorter time (2.6±1.3 vs. 3.7±1.8 days, P=0.020) with less daily insulin dosage and was more powerful in lowering total cholesterol, increasing AIR and HOMA β-cell function, whereas reduction of IMCL in the soleus was more obvious in the rosiglitazone group but not in the metformin group. The efficacy of combination with α-lipoic acid was similar to that of CSII alone.
Conclusions
Short-term CSII in combination with rosiglitazone or metformin is superior to CSII alone, yet the efficacy of the two differs in some way, whereas that with α-lipoic acid might not have an additive effect.
doi:10.1089/dia.2013.0013
PMCID: PMC3781121  PMID: 23991629
11.  Sinulolides A–H, New Cyclopentenone and Butenolide Derivatives from Soft Coral Sinularia sp. 
Marine Drugs  2014;12(10):5316-5327.
Eight new compounds, sinulolides A–H (1–8), along with two known compounds, α-methoxy-2,3-dimethyl-butenolide (9) and sinularone D (10), were isolated from the soft coral Sinularia sp. The structures of these compounds were elucidated on the basis of extensive spectroscopic analysis. The absolute configurations were determined on the basis of electronic circular dichroism (ECD) data analysis. Compounds 5 and 10 exhibited moderate effects for the inhibition of NF-κB activation.
doi:10.3390/md12105316
PMCID: PMC4210901  PMID: 25342460
soft coral; Sinularia sp.; sinulolide; NF-κB
12.  MicroRNA-339-5p inhibits colorectal tumorigenesis through regulation of the MDM2/p53 signaling 
Oncotarget  2014;5(19):9106-9117.
Tumor suppressor p53 plays a central role in tumor suppression. To ensure its proper function, the levels and activity of p53 are under a tight regulation in cells. MicroRNAs are short non-coding RNAs that play an important role in regulation of gene expression. Recently, microRNA-339-5p has been reported to be frequently down-regulated in colorectal cancer, and furthermore, its down-regulation is associated with poor prognosis in cancer patients, which strongly suggests a tumor suppressive function of microRNA-339-5p in colorectal cancer. In this study, we found that microRNA-339-5p directly represses the expression of MDM2, a key negative regulator of p53, through binding to MDM2 3′-UTR in colorectal cancer cells. Through the down-regulation of MDM2, microRNA-339-5p increases p53 protein levels and functions, including p53 transcriptional activity and p53-mediated apoptosis and senescence in response to stress. Furthermore, microRNA-339-5p inhibits the migration and invasion of colorectal cancer cells and the growth of colorectal xenograft tumors in a largely p53-dependent manner. Our results highlighted an important role of microRNA-339-5p in suppression of colorectal tumorigenesis, and also revealed that regulating the p53 function is an important mechanism for microRNA-339-5p in tumor suppression.
PMCID: PMC4253422  PMID: 25193859
microRNA-339-5p; colorectal cancer; p53; migration; invasion; tumorigenesis
13.  Colonization on Root Surface by a Phenanthrene-Degrading Endophytic Bacterium and Its Application for Reducing Plant Phenanthrene Contamination 
PLoS ONE  2014;9(9):e108249.
A phenanthrene-degrading endophytic bacterium, Pn2, was isolated from Alopecurus aequalis Sobol grown in soils contaminated with polycyclic aromatic hydrocarbons (PAHs). Based on morphology, physiological characteristics and the 16S rRNA gene sequence, it was identified as Massilia sp. Strain Pn2 could degrade more than 95% of the phenanthrene (150 mg·L−1) in a minimal salts medium (MSM) within 48 hours at an initial pH of 7.0 and a temperature of 30°C. Pn2 could grow well on the MSM plates with a series of other PAHs, including naphthalene, acenaphthene, anthracene and pyrene, and degrade them to different degrees. Pn2 could also colonize the root surface of ryegrass (Lolium multiflorum Lam), invade its internal root tissues and translocate into the plant shoot. When treated with the endophyte Pn2 under hydroponic growth conditions with 2 mg·L−1 of phenanthrene in the Hoagland solution, the phenanthrene concentrations in ryegrass roots and shoots were reduced by 54% and 57%, respectively, compared with the endophyte-free treatment. Strain Pn2 could be a novel and useful bacterial resource for eliminating plant PAH contamination in polluted environments by degrading the PAHs inside plants. Furthermore, we provide new perspectives on the control of the plant uptake of PAHs via endophytic bacteria.
doi:10.1371/journal.pone.0108249
PMCID: PMC4172705  PMID: 25247301
14.  HIV Transmission among Men Who Have Sex with Men due to Condom Failure 
PLoS ONE  2014;9(9):e107540.
Background
Despite preventive efforts, HIV incidence remains high among men who have sex with men (MSM) in industrialized countries. Condoms are an important element in prevention but, given the high frequency of condom use and their imperfect effectiveness, a substantial number and proportion of HIV transmissions may occur despite condoms. We developed a model to examine this hypothesis.
Methods
We used estimates of annual prevalent and incident HIV infections for MSM in Ontario. For HIV-negative men, we applied frequencies of sexual episodes and per-contact HIV transmission risks of receptive and insertive anal sex with and without a condom and oral sex without a condom. We factored in the proportion of HIV-infected partners receiving antiretroviral therapy and its impact in reducing transmissibility. We used Monte-Carlo simulation to determine the plausible range for the proportion of HIV transmissions for each sexual practice.
Results
Among Ontario MSM in 2009, an estimated 92,963 HIV-negative men had 1,184,343 episodes of anal sex with a condom and 117,133 anal sex acts without a condom with an HIV-positive partner. Of the 693 new HIV infections, 51% were through anal sex with a condom, 33% anal sex without a condom and 16% oral sex. For anal sex with a condom, the 95% confidence limits were 17% and 77%.
Conclusions
The proportion of HIV infections related to condom failure appears substantial and higher than previously thought. That 51% of transmissions occur despite condom use may be conservative (i.e. low) since we used a relatively high estimate (87.1%) for condom effectiveness. If condom effectiveness were closer to 70%, a value estimated from a recent CDC study, the number and proportion of HIV transmissions occurring despite condom use would be much higher. Therefore, while condom use should continue to be promoted and enhanced, this alone is unlikely to stem the tide of HIV infection among MSM.
doi:10.1371/journal.pone.0107540
PMCID: PMC4161430  PMID: 25211493
15.  A Ranking Procedure by Incomplete Pairwise Comparisons Using Information Entropy and Dempster-Shafer Evidence Theory 
The Scientific World Journal  2014;2014:904596.
Decision-making, as a way to discover the preference of ranking, has been used in various fields. However, owing to the uncertainty in group decision-making, how to rank alternatives by incomplete pairwise comparisons has become an open issue. In this paper, an improved method is proposed for ranking of alternatives by incomplete pairwise comparisons using Dempster-Shafer evidence theory and information entropy. Firstly, taking the probability assignment of the chosen preference into consideration, the comparison of alternatives to each group is addressed. Experiments verified that the information entropy of the data itself can determine the different weight of each group's choices objectively. Numerical examples in group decision-making environments are used to test the effectiveness of the proposed method. Moreover, the divergence of ranking mechanism is analyzed briefly in conclusion section.
doi:10.1155/2014/904596
PMCID: PMC4163326  PMID: 25250393
16.  A computational model to predict bone metastasis in breast cancer by integrating the dysregulated pathways 
BMC Cancer  2014;14(1):618.
Background
Although there are a lot of researches focusing on cancer prognosis or prediction of cancer metastases, it is still a big challenge to predict the risks of cancer metastasizing to a specific organ such as bone. In fact, little work has been published for such a purpose nowadays.
Methods
In this work, we propose a Dysregulated Pathway Based prediction Model (DPBM) built on a merged data set with 855 samples. First, we use bootstrapping strategy to select bone metastasis related genes. Based on the selected genes, we then detect out the dysregulated pathways involved in the process of bone metastasis via enrichment analysis. And then we use the discriminative genes in each dysregulated pathway, called as dysregulated genes, to construct a sub-model to forecast the risk of bone metastasis. Finally we combine all sub-models as an ensemble model (DPBM) to predict the risk of bone metastasis.
Results
We have validated DPBM on the training, test and independent sets separately, and the results show that DPBM can significantly distinguish the bone metastases risks of patients (with p-values of 3.82E-10, 0.00007 and 0.0003 on three sets respectively). Moreover, the dysregulated genes are generally with higher topological coefficients (degree and betweenness centrality) in the PPI network, which means that they may play critical roles in the biological functions. Further functional analysis of these genes demonstrates that the immune system seems to play an important role in bone-specific metastasis of breast cancer.
Conclusions
Each of the dysregulated pathways that are enriched with bone metastasis related genes may uncover one critical aspect of influencing the bone metastasis of breast cancer, thus the ensemble strategy can help to describe the comprehensive view of bone metastasis mechanism. Therefore, the constructed DPBM is robust and able to significantly distinguish the bone metastases risks of patients in both test set and independent set. Moreover, the dysregulated genes in the dysregulated pathways tend to play critical roles in the biological process of bone metastasis of breast cancer.
Electronic supplementary material
The online version of this article (doi:10.1186/1471-2407-14-618) contains supplementary material, which is available to authorized users.
doi:10.1186/1471-2407-14-618
PMCID: PMC4161863  PMID: 25163697
Bone metastasis; Breast cancer; Dysregulated pathways; Prediction model; Immune system
17.  Correlations of lysyl oxidase with MMP2/MMP9 expression and its prognostic value in non-small cell lung cancer 
Lysyl oxidase (LOX) has been reported to regulate tumor metastasis and has been found to involve in modification of extracellular matrix (ECM) in the context of tumorigenesis. The aim of this study is to determine the prognostic significance of LOX in non-small cell lung cancer (NSCLC) patients and to examine the correlation between LOX expression and ECM remodeling-associated MMP2/MMP9 in NSCLC tissues. The mRNA expression of LOX, MMP2 and MMP9 was investigated by quantitative real-time reverse transcriptase-polymerase chain reaction (qRT-PCR) in 30 NSCLC patients. The protein expression of LOX was measured by immunohistochemistry (IHC) in 110 paraffin-embedded tissues with NSCLC and the protein expression of MMP2/MMP9 was measured by in 30 NSCLC patients. The correlation between LOX expression and clinical parameters and MMP2/MMP9 was analyzed by appropriate statistics. The Kaplan-Meier method, univariate and multivariate regression analysis was used to analyze the correlation between LOX expression and overall survival (OS). The relative mRNA expression or protein expression of LOX were significantly higher in NSCLC tumor tissues than in the corresponding noncancerous tissues (P < 0.05). High LOX expression was significantly associated with MMP2, MMP9, tumor size, lymph node metastasis, pathological stage and OS (P < 0.05). Univariate and multivariate analysis showed that LOX was an independent prognostic factor for OS. Our results indicate that LOX may play a role in the metastasis of NSCLC by promoting MMP2/MMP9 expression. LOX expression is an independent prognostic factor in OS in NSCLC.
PMCID: PMC4203220  PMID: 25337249
LOX; NSCLC; prognosis; ECM
18.  Moderate-Intensity Rotating Magnetic Fields Do Not Affect Bone Quality and Bone Remodeling in Hindlimb Suspended Rats 
PLoS ONE  2014;9(7):e102956.
Abundant evidence has substantiated the positive effects of pulsed electromagnetic fields (PEMF) and static magnetic fields (SMF) on inhibiting osteopenia and promoting fracture healing. However, the osteogenic potential of rotating magnetic fields (RMF), another common electromagnetic application modality, remains poorly characterized thus far, although numerous commercial RMF treatment devices have been available on the market. Herein the impacts of RMF on osteoporotic bone microarchitecture, bone strength and bone metabolism were systematically investigated in hindlimb-unloaded (HU) rats. Thirty two 3-month-old male Sprague-Dawley rats were randomly assigned to the Control (n = 10), HU (n = 10) and HU with RMF exposure (HU+RMF, n = 12) groups. Rats in the HU+RMF group were subjected to daily 2-hour exposure to moderate-intensity RMF (ranging from 0.60 T to 0.38 T) at 7 Hz for 4 weeks. HU caused significant decreases in body mass and soleus muscle mass of rats, which were not obviously altered by RMF. Three-point bending test showed that the mechanical properties of femurs in HU rats, including maximum load, stiffness, energy absorption and elastic modulus were not markedly affected by RMF. µCT analysis demonstrated that 4-week RMF did not significantly prevent HU-induced deterioration of femoral trabecular and cortical bone microarchitecture. Serum biochemical analysis showed that RMF did not significantly change HU-induced decrease in serum bone formation markers and increase in bone resorption markers. Bone histomorphometric analysis further confirmed that RMF showed no impacts on bone remodeling in HU rats, as evidenced by unchanged mineral apposition rate, bone formation rate, osteoblast numbers and osteoclast numbers in cancellous bone. Together, our findings reveal that RMF do not significantly affect bone microstructure, bone mechanical strength and bone remodeling in HU-induced disuse osteoporotic rats. Our study indicates potentially obvious waveform-dependent effects of electromagnetic fields-stimulated osteogenesis, suggesting that RMF, at least in the present form, might not be an optimal modality for inhibiting disuse osteopenia/osteoporosis.
doi:10.1371/journal.pone.0102956
PMCID: PMC4105536  PMID: 25047554
19.  Directed Evolution of an LBP/CD14 Inhibitory Peptide and Its Anti-Endotoxin Activity 
PLoS ONE  2014;9(7):e101406.
Background
LPS-binding protein (LBP) and its ligand CD14 are located upstream of the signaling pathway for LPS-induced inflammation. Blocking LBP and CD14 binding might prevent LPS-induced inflammation. In previous studies, we obtained a peptide analog (MP12) for the LBP/CD14 binding site and showed that this peptide analog had anti-endotoxin activity. In this study, we used in vitro directed evolution for this peptide analog to improve its in vivo and in vitro anti-endotoxin activity.
Methods
We used error-prone PCR (ep-PCR) and induced mutations in the C-terminus of LBP and attached the PCR products to T7 phages to establish a mutant phage display library. The positive clones that competed with LBP for CD14 binding was obtained by screening. We used both in vivo and in vitro experiments to compare the anti-endotoxin activities of a polypeptide designated P1 contained in a positive clone and MP12.
Results
11 positive clones were obtained from among target phages. Sequencing showed that 9 positive clones had a threonine (T) to methionine (M) mutation in amino acid 287 of LBP. Compared to polypeptide MP12, polypeptide P1 significantly inhibited LPS-induced TNF-α expression and NF-κB activity in U937 cells (P<0.05). Compared to MP12, P1 significantly improved arterial oxygen pressure, an oxygenation index, and lung pathology scores in LPS-induced ARDS rats (P<0.05).
Conclusion
By in vitro directed evolution of peptide analogs for the LBP/CD14 binding site, we established a new polypeptide (P1) with a threonine (T)-to-methionine (M) mutation in amino acid 287 of LBP. This polypeptide had high anti-endotoxin activity in vitro and in vivo, which suggested that amino acid 287 in the C-terminus of LBP may play an important role in LBP binding with CD14.
doi:10.1371/journal.pone.0101406
PMCID: PMC4098906  PMID: 25025695
20.  Pushing the resolution of photolithography down to 15nm by surface plasmon interference 
Scientific Reports  2014;4:5618.
A deep ultraviolet plasmonic structure is designed and a surface plasmon interference lithography method using the structure is proposed to generate large-area periodic nanopatterns. By exciting the anti-symmetric coupled surface plasmon polaritons in the structure, ultrahigh resolution periodic patterns can be formed in a photoresist. The resolution of the generated patterns can be tuned by changing the refractive index and thickness of the photoresist. We demonstrate numerically that one-dimensional and two-dimensional patterns with a half-pitch resolution of 14.6 nm can be generated in a 25 nm-thick photoresist by using the structure under 193 nm illumination. Furthermore, the half-pitch resolution of the generated patterns can be down to 13 nm if high refractive index photoresists are used. Our findings open up an avenue to push the half-pitch resolution of photolithography towards 10 nm.
doi:10.1038/srep05618
PMCID: PMC4085591  PMID: 25001238
21.  Differences of Urinary Arsenic Metabolites and Methylation Capacity between Individuals with and without Skin Lesions in Inner Mongolia, Northern China 
Incomplete arsenic (As) methylation has been considered a risk factor of As-related diseases. This study aimed to examine the difference of urinary As metabolites and the methylation capacity between subjects with and without skin lesions. Urinary inorganic arsenic (iAs), monomethylarsonic acid (MMA), and dimethylarsinic acid (DMA) were analyzed. The percentage of each As species (iAs%, MMA%, and DMA%), the primary methylation index (PMI) and secondary methylation index (SMI) were calculated. The results showed that subjects with skin lesions have higher levels of urinary iAs (99.08 vs. 70.63 μg/g Cr, p = 0.006) and MMA (69.34 vs. 42.85 μg/g Cr, p = 0.016) than subjects without skin lesions after adjustment for several confounders. Significant differences of urianry MMA% (15.49 vs. 12.11, p = 0.036) and SMI (0.74 vs. 0.81, p = 0.025) were found between the two groups. The findings of the present study suggest that subjects with skin lesions may have a lower As methylation capacity than subjects without skin lesions.
doi:10.3390/ijerph110707319
PMCID: PMC4113878  PMID: 25046631
arsenic; groundwater; skin lesion; methylation capacity; metabolism
22.  Tumor suppressor p53 negatively regulates glycolysis stimulated by hypoxia through its target RRAD 
Oncotarget  2014;5(14):5535-5546.
Cancer cells display enhanced glycolysis to meet their energetic and biosynthetic demands even under normal oxygen concentrations. Recent studies have revealed that tumor suppressor p53 represses glycolysis under normoxia as a novel mechanism for tumor suppression. As the common microenvironmental stress for tumors, hypoxia drives the metabolic switch from the oxidative phosphorylation to glycolysis, which is crucial for survival and proliferation of cancer cells under hypoxia. The p53's role and mechanism in regulating glycolysis under hypoxia is poorly understood. Here, we found that p53 represses hypoxia-stimulated glycolysis in cancer cells through RRAD, a newly-identified p53 target. RRAD expression is frequently decreased in lung cancer. Ectopic expression of RRAD greatly reduces glycolysis whereas knockdown of RRAD promotes glycolysis in lung cancer cells. Furthermore, RRAD represses glycolysis mainly through inhibition of GLUT1 translocation to the plasma membrane. Under hypoxic conditions, p53 induces RRAD, which in turn inhibits the translocation of GLUT1 and represses glycolysis in lung cancer cells. Blocking RRAD by siRNA greatly abolishes p53's function in repressing glycolysis under hypoxia. Taken together, our results revealed an important role and mechanism of p53 in antagonizing the stimulating effect of hypoxia on glycolysis, which contributes to p53's function in tumor suppression.
PMCID: PMC4170611  PMID: 25114038
p53; glycolysis; RRAD; hypoxia; lung cancer
23.  Isolation, plant colonization potential, and phenanthrene degradation performance of the endophytic bacterium Pseudomonas sp. Ph6-gfp 
Scientific Reports  2014;4:5462.
This investigation provides a novel method of endophyte-aided removal of polycyclic aromatic hydrocarbons (PAHs) from plant bodies. A phenanthrene-degrading endophytic bacterium Pseudomonas sp. Ph6 was isolated from clover (Trifolium pratense L.) grown in a PAH-contaminated site. After being marked with the GFP gene, the colonization and distribution of strain Ph6-gfp was directly visualized in plant roots, stems, and leaves for the first time. After ryegrass (Lolium multiflorum Lam.) roots inoculation, strain Ph6-gfp actively and internally colonized plant roots and transferred vertically to the shoots. Ph6-gfp had a natural capacity to cope with phenanthrene in vitro and in planta. Ph6-gfp degraded 81.1% of phenanthrene (50 mg·L−1) in a culture solution within 15 days. The inoculation of plants with Ph6-gfp reduced the risks associated with plant phenanthrene contamination based on observations of decreased concentration, accumulation, and translocation factors of phenanthrene in ryegrass. Our results will have important ramifications in the assessment of the environmental risks of PAHs and in finding ways to circumvent plant PAH contamination.
doi:10.1038/srep05462
PMCID: PMC4071310  PMID: 24964867
24.  In Vitro Characterization of Human Adenovirus Type 55 in Comparison with Its Parental Adenoviruses, Types 11 and 14 
PLoS ONE  2014;9(6):e100665.
Human adenovirus type 55 (HAdV-B55) represents a re-emerging human pathogen, and this adenovirus has been reported to cause outbreaks of acute respiratory diseases among military trainees and in school populations around the world. HAdV-B55 has been revealed to have evolved from homologous recombination between human adenovirus type 14 (HAdV-B14) and type 11 (HAdV-B11), but it presents different clinical manifestations from parental virus HAdV-B11. In the present paper, we report the distinct biological features of HAdV-B55 in comparison with the parental viruses HAdV-B11 and HAdV-B14 in cell cultures. The results showed that HAdV-B55 replicated well in various cells, similar to HAdV-B11 and HAdV-B14, but that its processing had a slower and milder cytopathic effect in the early stages of infection. Viral fitness analysis showed that HAdV-B55 exhibited higher levels of replication in respiratory cells than did either of its parents. Cytotoxicity and apoptosis analyses in A549 cells indicated that HAdV-B55 was less cytotoxic than HAdV-B11 and HAdV-B14 were and induced milder apoptosis. Finally, thermal sensitivity analysis revealed that HAdV-B55 exhibited lower thermostability than did either HAdV-B11 or HAdV-B14, which may limit the transmission of HAdV-B55 in humans. Together, the findings described here expand current knowledge about this re-emerging recombinant HAdV, shedding light on the pathogenesis of HAdV-B55.
doi:10.1371/journal.pone.0100665
PMCID: PMC4067339  PMID: 24956280
25.  Tumor-Associated Mutant p53 Drives the Warburg Effect 
Nature communications  2013;4:2935.
Tumor cells primarily utilize aerobic glycolysis for energy production, a phenomenon known as the Warburg effect. Its mechanism is not well-understood. The tumor suppressor gene p53 is frequently mutated in tumors. Many tumor-associated mutant p53 (mutp53) proteins not only lose tumor suppressive function, but also gain new oncogenic functions that are independent of wild type p53, defined as mutp53 gain-of-function (GOF). Here we show that tumor-associated mutp53 stimulates the Warburg effect in cultured cells and mutp53 knock-in mice as a new mutp53 GOF. Mutp53 stimulates the Warburg effect through promoting GLUT1 translocation to plasma membrane, which is mediated by the activated RhoA and its downstream effector ROCK. Inhibition of the RhoA/ROCK/GLUT1 signaling largely abolishes mutp53 GOF in stimulating the Warburg effect. Furthermore, inhibition of glycolysis in tumor cells greatly compromises mutp53 GOF in promoting tumorigenesis. Thus, our results reveal a new mutp53 GOF and a mechanism for controlling the Warburg effect.
doi:10.1038/ncomms3935
PMCID: PMC3969270  PMID: 24343302

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