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1.  Elevation of brain magnesium prevents synaptic loss and reverses cognitive deficits in Alzheimer’s disease mouse model 
Molecular Brain  2014;7(1):65.
Background
Profound synapse loss is one of the major pathological hallmarks associated with Alzheimer’s disease, which might underlie memory impairment. Our previous work demonstrates that magnesium ion is a critical factor in controlling synapse density/plasticity. Here, we tested whether elevation of brain magnesium, using a recently developed compound (magnesium-L-threonate, MgT), can ameliorate the AD-like pathologies and cognitive deficits in the APPswe/PS1dE9 mice, a transgenic mouse model of Alzheimer’s disease.
Results
MgT treatment reduced Aβ-plaque, prevented synapse loss and memory decline in the transgenic mice. Strikingly, MgT treatment was effective even when the treatment was given to the mice at the end-stage of their Alzheimer’s disease-like pathological progression. To explore how elevation of brain magnesium ameliorates the AD-like pathologies in the brain of transgenic mice, we studied molecules critical for APP metabolism and signaling pathways implicated in synaptic plasticity/density. In the transgenic mice, the NMDAR signaling pathway was downregulated, while the BACE1 expression were upregulated. MgT treatment prevented the impairment of these signaling pathways, stabilized BACE1 expression and reduced sAPPβ and β-CTF in the transgenic mice. At the molecular level, elevation of extracellular magnesium prevented the high Aβ-induced reductions in synaptic NMDARs by preventing calcineurin overactivation in hippocampal slices.
Conclusions
Our results suggest that elevation of brain magnesium exerts substantial synaptoprotective effects in a mouse model of Alzheimer’s disease, and hence it might have therapeutic potential for treating Alzheimer’s disease.
Electronic supplementary material
The online version of this article (doi:10.1186/s13041-014-0065-y) contains supplementary material, which is available to authorized users.
doi:10.1186/s13041-014-0065-y
PMCID: PMC4172865  PMID: 25213836
Alzheimer’s disease; Brain magnesium; Synaptoprotection; NMDAR signaling; BACE1
3.  Direct reprogramming of Sertoli cells into multipotent neural stem cells by defined factors 
Cell Research  2011;22(1):208-218.
Multipotent neural stem/progenitor cells hold great promise for cell therapy. The reprogramming of fibroblasts to induced pluripotent stem cells as well as mature neurons suggests a possibility to convert a terminally differentiated somatic cell into a multipotent state without first establishing pluripotency. Here, we demonstrate that Sertoli cells derived from mesoderm can be directly converted into a multipotent state that possesses neural stem/progenitor cell properties. The induced neural stem/progenitor cells (iNSCs) express multiple NSC-specific markers, exhibit a global gene-expression profile similar to normal NSCs, and are capable of self-renewal and differentiating into glia and electrophysiologically functional neurons. iNSC-derived neurons stain positive for tyrosine hydroxylase (TH), γ-aminobutyric acid, and choline acetyltransferase. In addition, iNSCs can survive and generate synapses following transplantation into the dentate gyrus. Generation of iNSCs may have important implications for disease modeling and regenerative medicine.
doi:10.1038/cr.2011.175
PMCID: PMC3351918  PMID: 22064700
direct conversion; neural stem cell; multipotent; transdifferentiation; transplantation
4.  Peripheral Nerve Injury Leads to Working Memory Deficits and Dysfunction of the Hippocampus by Upregulation of TNF-α in Rodents 
Neuropsychopharmacology  2011;36(5):979-992.
Patients with chronic pain usually suffer from working memory deficits, which may decrease their intellectual ability significantly. Despite intensive clinical studies, the mechanism underlying this form of memory impairment remains elusive. In this study, we investigated this issue in the spared nerve injury (SNI) model of neuropathic pain, a most common form of chronic pain. We found that SNI impaired working memory and short-term memory in rats and mice. To explore the potential mechanisms, we studied synaptic transmission/plasticity in hippocampus, a brain region critically involved in memory function. We found that frequency facilitation, a presynaptic form of short-term plasticity, and long-term potentiation at CA3–CA1 synapses were impaired after SNI. Structurally, density of presynaptic boutons in hippocampal CA1 synapses was reduced significantly. At the molecular level, we found that tumor necrosis factor-α (TNF-α) increased in cerebrospinal fluid, in hippocampal tissue and in plasma after SNI. Intracerebroventricular or intrahippocampal injection of recombinant rat TNF mimicked the effects of SNI in naive rats, whereas inhibition of TNF-α or genetic deletion of TNF receptor 1 prevented both memory deficits and synaptic dysfunction induced by SNI. As TNF-α is critical for development of neuropathic pain, we suggested that the over-production of TNF-α following peripheral nerve injury might lead to neuropathic pain and memory deficits, simultaneously.
doi:10.1038/npp.2010.236
PMCID: PMC3077267  PMID: 21289602
spared nerve injury; chronic neuropathic pain; working memory; long-term potentiation; presynaptic boutons; tumor necrosis factor-α; pain/analgesics; learning & memory; neuropharmacology; plasticity; peripheral nerve injury; chronic neuropathic pain; working memory; long-term potentiation; presynaptic boutons; tumor necrosis factor alpha
5.  MM-ChIP enables integrative analysis of cross-platform and between-laboratory ChIP-chip or ChIP-seq data 
Genome Biology  2011;12(2):R11.
The ChIP-chip and ChIP-seq techniques enable genome-wide mapping of in vivo protein-DNA interactions and chromatin states. The cross-platform and between-laboratory variation poses a challenge to the comparison and integration of results from different ChIP experiments. We describe a novel method, MM-ChIP, which integrates information from cross-platform and between-laboratory ChIP-chip or ChIP-seq datasets. It improves both the sensitivity and the specificity of detecting ChIP-enriched regions, and is a useful meta-analysis tool for driving discoveries from multiple data sources.
doi:10.1186/gb-2011-12-2-r11
PMCID: PMC3188793  PMID: 21284836
6.  Transcriptional Regulation and Adaptation to a High-Fiber Environment in Bacillus subtilis HH2 Isolated from Feces of the Giant Panda 
PLoS ONE  2015;10(2):e0116935.
In the giant panda, adaptation to a high-fiber environment is a first step for the adequate functioning of intestinal bacteria, as the high cellulose content of the gut due to the panda's vegetarian appetite results in a harsh environment. As an excellent producer of several enzymes and vitamins, Bacillus subtilis imparts various advantages to animals. In our previous study, we determined that several strains of B. subtilis isolated from pandas exhibited good cellulose decomposition ability, and we hypothesized that this bacterial species can survive in and adapt well to a high-fiber environment. To evaluate this hypothesis, we employed RNA-Seq technology to analyze the differentially expressed genes of the selected strain B. subtilis HH2, which demonstrates significant cellulose hydrolysis of different carbon sources (cellulose and glucose). In addition, we used bioinformatics software and resources to analyze the functions and pathways of differentially expressed genes. Interestingly, comparison of the cellulose and glucose groups revealed that the up-regulated genes were involved in amino acid and lipid metabolism or transmembrane transport, both of which are involved in cellulose utilization. Conversely, the down-regulated genes were involved in non-essential functions for bacterial life, such as toxin and bacteriocin secretion, possibly to conserve energy for environmental adaptation. The results indicate that B. subtilis HH2 triggered a series of adaptive mechanisms at the transcriptional level, which suggests that this bacterium could act as a probiotic for pandas fed a high-fiber diet, despite the fact that cellulose is not a very suitable carbon source for this bacterial species. In this study, we present a model to understand the dynamic organization of and interactions between various functional and regulatory networks for unicellular organisms in a high-fiber environment.
doi:10.1371/journal.pone.0116935
PMCID: PMC4319723  PMID: 25658435
7.  Heterosis and Combining Ability Estimates in Isoflavone Content Using Different Parental Soybean Accessions: Wild Soybean, a Valuable Germplasm for Soybean Breeding 
PLoS ONE  2015;10(1):e0114827.
Isoflavone, a group of secondary metabolites in soybean, is beneficial to human health. Improving isoflavone content in soybean seeds has become one of the most important breeding objectives. However, the narrow genetic base of soybean cultivars hampered crop improvement. Wild soybean is an extraordinarily important gene pool for soybean breeding. In order to select an optimal germplasm for breeding programs to increase isoflavone concentration, 36 F1 soybean progenies from different parental accessions (cultivars, wild, Semi-wild and Interspecific) with various total isoflavone (TIF) concentration (High, Middle, Low) were analyzed for their isoflavone content. Results showed that male parents, except for Cultivars, showed positive GCA effects. In particular, wild soybean had higher positive GCA effects for TIF concentration. Both MP and BP heterosis value declined in the hybrid in which male parents were wild soybean, semi-wild soybean, interspecific offspring and cultivar in turn. In general, combining ability and heterosis in hybrids which had relative higher TIF concentration level parents showed better performance than those which had lower TIF concentration level parents. These results indicated characteristics of isoflavone content were mainly governed by additive type of gene action, and wild relatives could be utilized for breeding of soybean cultivars with this trait. A promising combination was found as the best potential hybrid for isoflavone content improvement.
doi:10.1371/journal.pone.0114827
PMCID: PMC4301644  PMID: 25607952
8.  A derivative of chrysin suppresses two-stage skin carcinogenesis by inhibiting mitogen- and stress-activated kinase 1 
Mitogen-activated and stress-activated kinase 1 (MSK1) is a nuclear serine/threonine protein kinase that acts downstream of both ERKs and p38 MAP kinases in response to stress or mitogenic extracellular stimuli. Increasing evidence has shown that MSK1 is closely associated with malignant transformation and cancer development. MSK1 should be an effective target for cancer chemoprevention and chemotherapy. However, very few MSK1 inhibitors, especially natural compounds, have been reported. We used virtual screening of a natural products database and the active conformation of the C-terminal kinase domain of MSK1 (PDB id 3KN) as the receptor structure to identify chrysin and its derivative, compound 69407, as inhibitors of MSK1. Compared with chrysin, compound 69407 more strongly inhibited proliferation and TPA-induced neoplastic transformation of JB6 P+ cells with lower cytotoxicity. Western blot data demonstrated that compound 69407 suppressed phosphorylation of the MSK1 downstream effector histone H3 in intact cells. Knocking down the expression of MSK1 effectively reduced the sensitivity of JB6 P+ cells to compound 69407. Moreover, topical treatment with compound 69407 prior to TPA application significantly reduced papilloma development in terms of number and size in a two-stage mouse skin carcinogenesis model. The reduction in papilloma development was accompanied by the inhibition of histone H3 phosphorylation at Ser10 in tumors extracted from mouse skin. The results indicated that compound 69407 exerts inhibitory effects on skin tumorigenesis by directly binding with MSK1 and attenuates the MSK1/histone H3 signaling pathway, which makes it an ideal chemopreventive agent against skin cancer.
doi:10.1158/1940-6207.CAPR-13-0133
PMCID: PMC3947278  PMID: 24169959
neoplastic transformation; MSK inhibitor; natural compound; chemoprevention; skin carcinogenesis
9.  Automatic Segmentation of the Left Ventricle in Cardiac MRI Using Local Binary Fitting Model and Dynamic Programming Techniques 
PLoS ONE  2014;9(12):e114760.
Segmentation of the left ventricle is very important to quantitatively analyze global and regional cardiac function from magnetic resonance. The aim of this study is to develop a novel algorithm for segmenting left ventricle on short-axis cardiac magnetic resonance images (MRI) to improve the performance of computer-aided diagnosis (CAD) systems. In this research, an automatic segmentation method for left ventricle is proposed on the basis of local binary fitting (LBF) model and dynamic programming techniques. The validation experiments are performed on a pool of data sets of 45 cases. For both endo- and epi-cardial contours of our results, percentage of good contours is about 93.5%, the average perpendicular distance are about 2 mm. The overlapping dice metric is about 0.91. The regression and determination coefficient between the experts and our proposed method on the LV mass is 1.038 and 0.9033, respectively; they are 1.076 and 0.9386 for ejection fraction (EF). The proposed segmentation method shows the better performance and has great potential in improving the accuracy of computer-aided diagnosis systems in cardiovascular diseases.
doi:10.1371/journal.pone.0114760
PMCID: PMC4263664  PMID: 25500580
10.  Protein Profiling of Preeclampsia Placental Tissues 
PLoS ONE  2014;9(11):e112890.
Preeclampsia is a multi-system disorder involved in pregnancy without an effective treatment except delivery. The precise pathogenesis of this complicated disorder is still not completely understood. The objective of this study is to evaluate the alterations of protein expression and phosphorylations that are important in regulating placental cell function in preterm and term preeclampsia. Using the Protein Pathway Array, 38 proteins in placental tissues were found to be differentially expressed between preterm preeclampsia and gestational age matched control, while 25 proteins were found to be expressed differentially between term preeclampsia and matched controls. Among these proteins, 16 proteins and their associated signaling pathways overlapped between preterm and term preeclampsia, suggesting the common pathogenesis of two subsets of disease. On the other hand, many proteins are uniquely altered in either preterm or term preeclampsia and correlated with severity of clinical symptoms and outcomes, therefore, providing molecular basis for these two subsets of preeclampsia. Furthermore, the expression levels of some of these proteins correlated with neonatal small for gestational age (PAI-1 and PAPP-A) and adverse outcomes (Flt-1) in women with preterm preeclampsia. These proteins could potentially be used as candidate biomarkers for predicting outcomes of preeclampsia.
doi:10.1371/journal.pone.0112890
PMCID: PMC4231077  PMID: 25392996
11.  Global lung cancer risk from PAH exposure highly depends on emission sources and individual susceptibility 
Scientific Reports  2014;4:6561.
The health impacts of polycyclic aromatic hydrocarbons (PAHs), the most concerning organic pollutants, depend not only on the locations and strengths of emission sources, but also on individual susceptibility. Moreover, trans-boundary transport makes them a global concern. In this study, a comprehensive analysis of the global health impacts of polycyclic aromatic hydrocarbons (PAHs) in ambient air is presented. Model resolution is critical in exposure modelling. Globally, incremental lifetime lung cancer risk (ILCR) induced by ambient PAH exposure is 3.1 × 10−5. If the individual susceptibility was not taken into consideration, the overall risk would be underestimated by 55% and the proportion of highly vulnerable population would be underestimated by more than 90%. Emphasizing on individual susceptibility, our study provides an instrumental revision of current risk assessment methodology. In terms of lung cancer risk, the most important sources are combustion of biomass fuels (40%) and fossil fuels (14%) in the residential/commercial sector, coke (13%) and aluminium (12%) production, and motor vehicles (9%). PAHs can travel long distance globally especially within the Eurasian continent. Still, the risk is dominantly contributed by local.
doi:10.1038/srep06561
PMCID: PMC4190535  PMID: 25297709
12.  Resveratrol Inhibits the TRIF-Dependent Pathway by Upregulating Sterile Alpha and Armadillo Motif Protein, Contributing to Anti-Inflammatory Effects after Respiratory Syncytial Virus Infection 
Journal of Virology  2014;88(8):4229-4236.
ABSTRACT
Respiratory syncytial virus (RSV) is the most important cause of lower respiratory tract infection in young children and the leading cause of infant hospitalization worldwide. Uncontrolled response to RSV is mediated by a toll-like receptor (TLR)-mediated immune response. Resveratrol possesses anti-RSV activity and is an inhibitor of the TRIF/TBK1/IRF-3 complex. We hypothesize that resveratrol inhibits the TRIF-dependent pathway through upregulation of SARM post-RSV infection. BALB/c mice were infected with RSV and were injected with resveratrol 1 h postinoculation. SARM short interfering RNA was administered to RSV-infected and resveratrol-treated mice. Lung function was measured by whole-body plethysmography, lung histopathology was examined, and lymphocytes in bronchoalveolar lavage fluid were quantified. SARM and TRIF protein expression were detected in the lung by Western blot analyses. The expression of gamma interferon in bronchoalveolar lavage fluid (BALF) was evaluated by enzyme-linked immunosorbent assay (ELISA). SARM expression was reduced and TRIF expression was increased after infection with RSV. Resveratrol increased SARM expression and decreased TRIF expression after RSV infection. SARM knockdown in resveratrol-treated mice enhanced gamma interferon production, RSV-induced airway inflammation, and airway hyperresponsiveness (AHR). Resveratrol decreased TRIF expression and prevented the RSV-mediated reduction of SARM expression. Resveratrol-mediated inhibition of the TRIF-dependent pathway may be dependent on SARM expression.
IMPORTANCE Our study provides insights into the regulation of innate immunity in response to RSV infection. The results suggest that resveratrol-mediated alterations in SARM have therapeutic potential against RSV immunopathology caused by deregulation of the TLR-mediated immune response. Ultimately, improved insight into the complex interplay between TLR adaptor proteins and the occurrence of severe RSV infection might lead to novel therapeutic treatment strategies, such as TLR adjuvants.
doi:10.1128/JVI.03637-13
PMCID: PMC3993725  PMID: 24478430
13.  Martensitic transformation of FeNi nanofilm induced by interfacial stress generated in FeNi/V nanomultilayered structure 
Nanoscale Research Letters  2014;9(1):440.
FeNi/V nanomultilayered films with different V layer thicknesses were synthesized by magnetron sputtering. By adjusting the thickness of the V layer, different interfacial compressive stress were imposed on FeNi layers and the effect of interfacial stress on martensitic transformation of the FeNi film was investigated. Without insertion of V layers, the FeNi film exhibits a face-centered cubic (fcc) structure. With the thickness of V inserted layers up to 1.5 nm, under the coherent growth structure in FeNi/V nanomultilayered films, FeNi layers bear interfacial compressive stress due to the larger lattice parameter relative to V, which induces the martensitic transformation of the FeNi film. As the V layer thickness increases to 2.0 nm, V layers cannot keep the coherent growth structure with FeNi layers, leading to the disappearance of interfacial compressive stress and termination of the martensitic transformation in the FeNi film. The interfacial compressive stress-induced martensitic transformation of the FeNi nanofilm is verified through experiment. The method of imposing and modulating the interfacial stress through the epitaxial growth structure in the nanomultilayered films should be noticed and utilized.
doi:10.1186/1556-276X-9-440
PMCID: PMC4154052  PMID: 25232296
FeNi alloy; Multilayer thin films; Martensitic phase transformation; Interfacial stress; Epitaxial growth
14.  Meta-analysis of GSTM1 null genotype and lung cancer risk in Asians 
Background
Several molecular epidemiological studies have been conducted to examine the association between glutathione S-transferase M 1 (GSTM1) null genotype and lung cancer in Asians; however, the conclusions remained controversial. We therefore performed an extensive meta-analysis on 31 published case-control studies with a total of 5347 lung cancer cases and 6072 controls.
Material/Methods
PubMed and EMBASE were searched to identify case-control studies investigating the associations of GSTM1 null genotype with risk of lung cancer in Asians. Odds ratios (ORs) with 95% confidence intervals (CIs) were used to assess the strength of association between lung cancer risk and polymorphism of GSTM1.
Results
GSTM1 null genotype was significantly associated with lung cancer risk (OR=1.43; 95% CI, 1.30–1.58). This result remained statistically significant when the adjusted ORs were combined (OR=1.38; 95% CI, 1.23–1.54). In the subgroup analysis by sex, there were significant associations in women and men. When stratifying for histology, this genotype showed increased adenocarcinoma risk and squamous cell carcinoma risk. In the subgroup analysis stratified by smoking status, lung cancer risk was increased in both smokers and non-smokers.
Conclusions
This study suggests that GSTM1 null genotype is a risk factor for lung cancer in Asians.
doi:10.12659/MSM.890490
PMCID: PMC4111653  PMID: 25033877
Meta-Analysis; Lung Neoplasms - genetics; Polymorphism; Genetic - genetics
15.  Global atmospheric emissions of polycyclic aromatic hydrocarbons from 1960 to 2008 and future predictions 
Environmental science & technology  2013;47(12):6415-6424.
Global atmospheric emissions of 16 polycyclic aromatic hydrocarbons (PAHs) from 69 major sources were estimated for a period from 1960 to 2030. Regression models and a technology split method were used to estimate country and time specific emission factors, resulting in a new estimate of PAH emission factor variation among different countries and over time. PAH emissions in 2007 were spatially resolved to 0.1°× 0.1° grids based on a newly developed global high-resolution fuel combustion inventory (PKU-FUEL-2007). The global total annual atmospheric emission of 16 PAHs in 2007 was 504 Gg (331-818 Gg, as interquartile range), with residential/commercial biomass burning (60.5%), open-field biomass burning (agricultural waste burning, deforestation, and wildfire, 13.6%), and petroleum consumption by on-road motor vehicles (12.8%) as the major sources. South (87 Gg), East (111 Gg), and Southeast Asia (52 Gg) were the regions with the highest PAH emission densities, contributing half of the global total PAH emissions. Among the global total PAH emissions, 6.19% of the emissions were in the form of high molecular weight carcinogenic compounds and the percentage of the carcinogenic PAHs was higher in developing countries (6.22%) than in developed countries (5.73%), due to the differences in energy structures and the disparities of technology. The potential health impact of the PAH emissions was greatest in the parts of the world with high anthropogenic PAH emissions, because of the overlap of the high emissions and high population densities. Global total PAH emissions peaked at 592 Gg in 1995 and declined gradually to 499 Gg in 2008. Total PAH emissions from developed countries peaked at 122 Gg in the early 1970s and decreased to 38 Gg in 2008. Simulation of PAH emissions from 2009 to 2030 revealed that PAH emissions in developed and developing countries would decrease by 46-71% and 48-64%, respectively, based on the six IPCC SRES scenarios.
doi:10.1021/es400857z
PMCID: PMC3753807  PMID: 23659377
Polycyclic aromatic hydrocarbons; global emission; source profile; time trend
16.  Acetylation-Mediated Proteasomal Degradation of Core Histones during DNA Repair and Spermatogenesis 
Cell  2013;153(5):1012-1024.
SUMMARY
Histone acetylation plays critical roles in chromatin remodeling, DNA repair, and epigenetic regulation of gene expression, but the underlying mechanisms are unclear. Proteasomes usually catalyze ATP- and polyubiquitin-dependent proteolysis. Here we show that the proteasomes containing the activator PA200 catalyze the polyubiquitin-independent degradation of histones. Most proteasomes in mammalian testes (“spermatoproteasomes”) contain a spermatid/sperm-specific α-subunit α4s/PSMA8 and/or the catalytic β-subunits of immunoproteasomes in addition to PA200. Deletion of PA200 in mice abolishes acetylation-dependent degradation of somatic core histones during DNA double-strand breaks, and delays core histone disappearance in elongated spermatids. Purified PA200 greatly promotes ATP-independent proteasomal degradation of the acetylated core histones, but not polyubiquitinated proteins. Furthermore, acetylation on histones is required for their binding to the bromodomain-like regions in PA200 and its yeast ortholog, Blm10. Thus, PA200/Blm10 specifically targets the core histones for acetylation-mediated degradation by proteasomes, providing mechanisms by which acetylation regulates histone degradation, DNA repair, and spermatogenesis.
doi:10.1016/j.cell.2013.04.032
PMCID: PMC3983474  PMID: 23706739
17.  Effect of Hematoporphyrin Monomethyl Ether-Sonodynamic Therapy (HMME-SDT) on Hypertrophic Scarring 
PLoS ONE  2014;9(1):e86003.
Objective
The aim of the present study was to explore the potential for hematoporphyrin monomethyl ether-Sonodynamic Therapy (HMME-SDT) treatment of hypertrophic scars within rabbit ears.
Methods
60 white rabbits were randomly divided into five groups: 1) untreated controls, 2) lesioned, 3) lesioned + HMME, 4) lesioned + US (Ultrasound), and 5) lesioned +HMME-SDT. After induction of a lesion upon the ears of the rabbits, hypertrophic scars were assessed at 14, 28, 42 and 56 days post-lesion +/− treatment. Assessments consisted of visual inspection in the change of the skin, scar formation pathological morphology by hematoxylin and eosin (HE) staining technique with optical microscopy, calculation of a hypertrophic index, fibroblastic density measures, and observation of collagen changes in the scar tissue by Van Gieson's (VG)Stain along with calculation of collagen area density.
Results
With continued HMME-SDT treatment there was a gradual improvement in all parameters over the duration of the experiment. The lesion-induced scars of rabbits receiving HMME-SDT treatment were soft, the size was reduced, hyperplasia was flat and the color pale. The fibroblasts and collagens were reduced and the collagens were light red, sparse and orderly. The hypertrophic index was reduced, since the fibroblastic density was lowered and collagen area density was decreased.
Conclusion
HMME is an effective sonosensitizer and the combination of HMME-SDT treatment can exert significant benefits in reducing the formation of hypertrophic scars.
doi:10.1371/journal.pone.0086003
PMCID: PMC3897560  PMID: 24465834
18.  New understanding of hardening mechanism of TiN/SiNx-based nanocomposite films 
Nanoscale Research Letters  2013;8(1):427.
In order to clarify the controversies of hardening mechanism for TiN/SiNx-based nanocomposite films, the microstructure and hardness for TiN/SiNx and TiAlN/SiNx nanocomposite films with different Si content were studied. With the increase of Si content, the crystallization degree for two series of films firstly increases and then decreases. The microstructural observations suggest that when SiNx interfacial phase reaches to a proper thickness, it can be crystallized between adjacent TiN or TiAlN nanocrystallites, which can coordinate misorientations between nanocrystallites and grow coherently with them, resulting in blocking of the dislocation motions and hardening of the film. The microstructure of TiN/SiNx-based nanocomposite film can be characterized as the nanocomposite structure with TiN-based nanocrystallites surrounded by crystallized SiNx interfacial phase, which can be denoted by nc-TiN/c-SiNx model ('c’ before SiNx means crystallized) and well explain the coexistence between nanocomposite structure and columnar growth structure within the TiN/SiNx-based film.
doi:10.1186/1556-276X-8-427
PMCID: PMC3856532  PMID: 24134611
TiN/SiNx film; Nanocomposite; Hardening mechanism; Microstructure
19.  Neurotransmitter substance P mediates pancreatic cancer perineural invasion via NK-1R in cancer cells 
Molecular cancer research : MCR  2013;11(3):294-302.
Pancreatic cancer significantly affects the quality of life due to the severe abdominal pain. However, the underlying mechanism is not clear. This study aimed to determine the relationship between substance P (SP) and pancreatic cancer perineural invasion (PNI) as well as mechanism of SP mediating pancreatic cancer PNI which cause pain in patients with pancreatic cancer. Human pancreatic cancer cells MIA PaCa-2, BxPC-3 and newborn dorsal root ganglions (DRGs) were used to determine the expression of SP or NK-1R in pancreatic cancer cells and DRGs cells by QT-PCR and Western blotting. The effects of SP on pancreatic cancer cell proliferation and invasion were analyzed using MTT assay and Transwell matrigel invasion assay, respectively. Alterations in the neurotropism of pancreatic cancer cells were assessed by co-culture system which mimics the interaction of tumor/neuron in vivo. SP is not only widely distributed in the neurite outgrowth from newborn DRGs but also expressed in MIA PaCa-2 and BxPC-3 cells. NK-1R is found to be overexpressed in the pancreatic cancer cell lines MIA PaCa-2 and BxPC-3. SP induces cancer cell proliferation and invasion and the expression of MMP-2 in pancreatic cancer cells; and NK-1R antagonists inhibit these effects. Furthermore, SP is also able to promote neurite outgrowth and the migration of pancreatic cancer cell cluster to the DRGs, which is blocked by NK-1R antagonists in the co-culture model. Our results suggest that SP plays an important role in the development of pancreatic cancer metastasis and PNI, and blocking the SP/NK-1R signaling system is a novel strategy for the treatment of pancreatic cancer.
doi:10.1158/1541-7786.MCR-12-0609
PMCID: PMC3709020  PMID: 23345604
Substance P (SP); NK-1 receptor (NK-1R); pancreatic cancer; perineural invasion (PNI)
20.  Identification and Characterization of the First Escherichia coli Strain Carrying NDM-1 Gene in China 
PLoS ONE  2013;8(6):e66666.
New Delhi metallo-β-lactamase-1 (NDM-1), an acquired class B carbapenemase, is a significant clinical threat due to its extended hydrolysis of β-lactams including carbapenems. In this study, we identified the first confirmed clinical isolate of Escherichia coli BJ01 harboring blaNDM-1 in China. The isolate is highly resistant to all tested antimicrobials except polymyxin. blaNDM-1, blaCTX-M-57, and blaTEM-1 were identified in the isolate. blaNDM-1 was transferable to E. coli EC600 and DH5α in both plasmid conjugation experiments and plasmid transformation tests. BJ01 was identified as a new sequence type, ST224, by multilocus sequence typing. Analysis of genetic environment shows complex transposon-like structures surrounding the blaNDM-1 gene. Genetic analysis revealed that the region flanking blaNDM-1 was very similar to previously identified NDM-positive Acinetobacter spp. isolated in China. The findings of this study raise attention to the emergence and spread of NDM-1-carrying Enterobacteriaceae in China.
doi:10.1371/journal.pone.0066666
PMCID: PMC3677923  PMID: 23762496
21.  Stem cells and small molecule screening: haploid embryonic stem cells as a new tool 
Acta Pharmacologica Sinica  2013;34(6):725-731.
Stem cells can both self-renew and differentiate into various cell types under certain conditions, which makes them a good model for development and disease studies. Recently, chemical approaches have been widely applied in stem cell biology by promoting stem cell self-renewal, proliferation, differentiation and somatic cell reprogramming using specific small molecules. Conversely, stem cells and their derivatives also provide an efficient and robust platform for small molecule and drug screening. Here, we review the current research and applications of small molecules that modulate stem cell self-renewal and differentiation and improve reprogramming, as well as the applications that use stem cells as a tool for small molecule screening. Moreover, we introduce the recent advance in haploid embryonic stem cells research. Haploid embryonic stem cells maintain haploidy and stable growth over extensive passages, possess the ability to differentiate into all three germ layers in vitro and in vivo, and contribute to the germlines of chimeras when injected into blastocysts. Androgenetic haploid stem cells can also be used in place of sperm to produce fertile progeny after intracytoplasmic injection into mature oocytes. Such characteristics demonstrate that haploid stem cells are a new approach for genetic studies at both the cellular and animal levels and that they are a valuable platform for future small molecule screening.
doi:10.1038/aps.2013.26
PMCID: PMC4002892  PMID: 23645011
small molecules; stem cells; haploid embryonic stem cells; induced pluripotent stem cell (iPS); drug screening
22.  CistromeMap: a knowledgebase and web server for ChIP-Seq and DNase-Seq studies in mouse and human 
Bioinformatics  2012;28(10):1411-1412.
Summary: Transcription and chromatin regulators, and histone modifications play essential roles in gene expression regulation. We have created CistromeMap as a web server to provide a comprehensive knowledgebase of all of the publicly available ChIP-Seq and DNase-Seq data in mouse and human. We have also manually curated metadata to ensure annotation consistency, and developed a user-friendly display matrix for quick navigation and retrieval of data for specific factors, cells and papers. Finally, we provide users with summary statistics of ChIP-Seq and DNase-Seq studies.
Availability: Freely available on the web at http://cistrome.dfci.harvard.edu/pc/
Contact: yzhang@tongji.edu.cn; xsliu@jimmy.harvard.edu
doi:10.1093/bioinformatics/bts157
PMCID: PMC3348563  PMID: 22495751
23.  A functional variomics tool for discovering drug resistance genes and drug targets 
Cell reports  2013;3(2):577-585.
Comprehensive discovery of genetic mechanisms of drug resistance and identification of in vivo drug targets represent significant challenges. Here we present a functional variomics technology in the model organism Saccharomyces cerevisiae. This tool analyzes numerous genetic variants and effectively tackles both problems simultaneously. Using this tool, we discovered almost all genes that, due to mutations or modest overexpression, confer resistance to rapamycin, cycloheximide, and amphotericin B. Most significant among the resistance genes were drug targets, including multiple targets of a given drug. With amphotericin B, we discovered the highly conserved membrane protein Pmp3 as a potent resistance factor and a possible novel target. Widespread application of this tool should allow rapid identification of conserved resistance mechanisms and targets of many more compounds. New genes and alleles that confer resistance to other stresses can also be discovered. Similar tools in other systems such as human cell lines will also be useful.
doi:10.1016/j.celrep.2013.01.019
PMCID: PMC3594652  PMID: 23416056
24.  Unfolded Protein Response and Activated Degradative Pathways Regulation in GNE Myopathy 
PLoS ONE  2013;8(3):e58116.
Although intracellular beta amyloid (Aβ) accumulation is known as an early upstream event in the degenerative course of UDP-N-acetylglucosamine 2-epimerase/N-acetylmannosamine kinase (GNE) myopathy, the process by which Aβdeposits initiate various degradative pathways, and their relationship have not been fully clarified. We studied the possible secondary responses after amyloid beta precursor protein (AβPP) deposition including unfolded protein response (UPR), ubiquitin proteasome system (UPS) activation and its correlation with autophagy system. Eight GNE myopathy patients and five individuals with normal muscle morphology were included in this study. We performed immunofluorescence and immunoblotting to investigate the expression of AβPP, phosphorylated tau (p-tau) and endoplasmic reticulum molecular chaperones. Proteasome activities were measured by cleavage of fluorogenic substrates. The expression of proteasome subunits and linkers between proteasomal and autophagy systems were also evaluated by immunoblotting and relative quantitative real-time RT-PCR. Four molecular chaperones, glucose-regulated protein 94 (GRP94), glucose-regulated protein 78 (GRP78), calreticulin and calnexin and valosin containing protein (VCP) were highly expressed in GNE myopathy. 20S proteasome subunits, three main proteasome proteolytic activities, and the factors linking UPS and autophagy system were also increased. Our study suggests that AβPP deposition results in endoplasmic reticulum stress (ERS) and highly expressed VCP deliver unfolded proteins from endoplasmic reticulum to proteosomal system which is activated in endoplasmic reticulum associated degradation (ERAD) in GNE myopathy. Excessive ubiquitinated unfolded proteins are exported by proteins that connect UPS and autophagy to autophagy system, which is activated as an alternative pathway for degradation.
doi:10.1371/journal.pone.0058116
PMCID: PMC3589370  PMID: 23472144

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