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2.  Purification and Characterization of Flavonoids from the Leaves of Zanthoxylum bungeanum and Correlation between Their Structure and Antioxidant Activity 
PLoS ONE  2014;9(8):e105725.
Nine flavonoids were isolated and characterized from the leaves of Zanthoxylum bungeanum. Their structures were elucidated by spectroscopic techniques as quercetin (1), afzelin (2), quercitrin (3), trifolin (4), quercetin-3-O-β-D-glucoside (5), isorhamnetin 3-O-α-L-rhamnoside (6), hyperoside (7), vitexin (8) and rutin (9). All compounds were isolated from the leaves of Z. bungeanum for the first time. Five compounds (2, 4, 5, 6 and 8) were found for the first time in the genus Zanthoxylum. To learn the mechanisms underlying its health benefits, in vitro (DPPH, ABTS, FRAP and lipid peroxidation inhibition assays) and in vivo (protective effect on Escherichia coli under peroxide stress) antioxidant activities of the nine flavonoids were measured. Quercetin and quercetin glycosides (compounds 1, 3, 5, 7, 9) showed the highest antioxidant activity. Structure-activity relationships indicated that the -OH in 4′ position on the B ring and the -OH in 7 position on the A ring possessed high antioxidant activity; B ring and/or A ring with adjacent -OH groups could greatly increase their antioxidant ability. Also, due to the different structures of various flavonoids, they will certainly exhibit different antioxidant capacity when the reactions occur in solution or in oil-in-water emulsion. These findings suggest that Z. bungeanum leaves may have health benefits when consumed. It could become a useful supplement for pharmaceutical products and functional food ingredients in both nutraceutical and food industries as a potential source of natural antioxidants.
doi:10.1371/journal.pone.0105725
PMCID: PMC4144902  PMID: 25157400
3.  Wnt Pathway Activation Increases Hypoxia Tolerance during Development 
PLoS ONE  2014;9(8):e103292.
Adaptation to hypoxia, defined as a condition of inadequate oxygen supply, has enabled humans to successfully colonize high altitude regions. The mechanisms attempted by organisms to cope with short-term hypoxia include increased ATP production via anaerobic respiration and stabilization of Hypoxia Inducible Factor 1α (HIF-1α). However, less is known about the means through which populations adapt to chronic hypoxia during the process of development within a life time or over generations. Here we show that signaling via the highly conserved Wnt pathway impacts the ability of Drosophila melanogaster to complete its life cycle under hypoxia. We identify this pathway through analyses of genome sequencing and gene expression of a Drosophila melanogaster population adapted over >180 generations to tolerate a concentration of 3.5–4% O2 in air. We then show that genetic activation of the Wnt canonical pathway leads to increased rates of adult eclosion in low O2. Our results indicate that a previously unsuspected major developmental pathway, Wnt, plays a significant role in hypoxia tolerance.
doi:10.1371/journal.pone.0103292
PMCID: PMC4122365  PMID: 25093834
4.  Significantly increased monounsaturated lipids relative to polyunsaturated lipids in six types of cancer microenvironment are observed by mass spectrometry imaging 
Scientific Reports  2014;4:5959.
Six different types of cancer (i.e., breast, lung, colorectal, esophageal, gastric, and thyroid cancer) have high rates of incidence or mortality worldwide. It has been shown that activation of de novo lipogenesis is an early and common event in the cancer microenvironment. In this study, we performed lipid imaging and profiling for 134 tissue samples from six different types of cancer using matrix-assisted laser desorption/ionization-Fourier transform ion cyclotron resonance mass spectrometry, with 2,5-dihydroxybenzoic acid and 1,8-bis(dimethyl-amino)naphthalene as matrices in the positive and negative ion modes, respectively. Multivariate statistical analysis coupled with lipid distribution images revealed that significantly increased levels of monounsaturated fatty acids and monounsaturated phosphatidylcholines relative to polyunsaturated fatty acids and polyunsaturated phosphatidylcholines were observed in the cancer microenvironment compared with the adjacent normal tissue. The immunohistochemical assay indicated that fatty acid synthase, stearoyl-CoA desaturase-1, and choline kinase α were up-regulated in the cancer microenvironment compared with the adjacent normal tissue. Our findings suggest that de novo lipogenesis was activated in six types of cancer to promote a biosynthesis of lipids with monounsaturated acyl chains and to suppress a biosynthesis of polyunsaturated lipids in the cancer microenvironment.
doi:10.1038/srep05959
PMCID: PMC4121604  PMID: 25091112
5.  High Performance Relaxor-Based Ferroelectric Single Crystals for Ultrasonic Transducer Applications 
Sensors (Basel, Switzerland)  2014;14(8):13730-13758.
Relaxor-based ferroelectric single crystals Pb(Mg1/3Nb2/3)O3-PbTiO3 (PMN-PT) have drawn much attention in the ferroelectric field because of their excellent piezoelectric properties and high electromechanical coupling coefficients (d33∼2000 pC/N, kt∼60%) near the morphotropic phase boundary (MPB). Ternary Pb(In1/2Nb1/2)O3-Pb(Mg1/3Nb2/3)O3-PbTiO3 (PIN-PMN-PT) single crystals also possess outstanding performance comparable with PMN-PT single crystals, but have higher phase transition temperatures (rhombohedral to tetragonal Trt, and tetragonal to cubic Tc) and larger coercive field Ec. Therefore, these relaxor-based single crystals have been extensively employed for ultrasonic transducer applications. In this paper, an overview of our work and perspectives on using PMN-PT and PIN-PMN-PT single crystals for ultrasonic transducer applications is presented. Various types of single-element ultrasonic transducers, including endoscopic transducers, intravascular transducers, high-frequency and high-temperature transducers fabricated using the PMN-PT and PIN-PMN-PT crystals and their 2-2 and 1-3 composites are reported. Besides, the fabrication and characterization of the array transducers, such as phased array, cylindrical shaped linear array, high-temperature linear array, radial endoscopic array, and annular array, are also addressed.
doi:10.3390/s140813730
PMCID: PMC4178991  PMID: 25076222
PMN-PT; PIN-PMN-PT; single crystals; composites; ultrasonic transducers
6.  Fat Accumulation in the Liver of Obese Rats is Alleviated by Soy Protein Isolate through β-catenin signaling 
Obesity (Silver Spring, Md.)  2013;22(1):151-158.
Objectives
The current study aim to investigate the effects of SPI on Wnt/β-catenin signaling in the liver of obese rats, as well as the roles of this pathway in regulating the hepatic fat accumulation.
Design and Methods
Obese and lean Zucker rats were fed diets containing either casein or SPI as protein source for 17 weeks. Histology and biochemical analysis, real-time PCR, Western blot, immunostaining, short interfering RNA assay were performed for liver samples.
Results
Our study showed that fat content was significantly lowered in the liver of SPI-fed obese rats, accompanied by a reduction in hepatocellular vacuolation, compared to the casein-fed control. β-catenin protein level in the liver of obese rats was down-regulated compared to the lean group, indicating that the obese genotype exhibits an overall reduction in Wnt signaling. Importantly the repression of β-catenin in the obese rats was alleviated by feeding the SPI diet. siRNA treatment in rat hepatoma cells confirmed that silencing of β-catenin exacerbated fatty acid-induced fat accumulation, which implicated an important function of Wnt/β-catenin signaling in hepaticfat metabolism.
Conclusions
SPI intake restored β-catenin signaling and alleviated hepatic fat accumulation and liver damage in the obese rats.
doi:10.1002/oby.20421
PMCID: PMC3690171  PMID: 23512909
diet; hepatic fat; β-catenin signaling; SPI; obese Zucker rat
7.  A novel diagnostic algorithm for chronic and subacute cough 
Background
Cough remains the most common reason for patients to seek medical attention. We practised a novel diagnostic algorithm for chronic and subacute cough.
Methods
Chronic and subacute cough patients with normal chest X-ray results and without respiratory tract infections in the preceding eight weeks were recruited. The patients were divided into two groups: Group A, patients with typical symptoms and signs of postnasal drip syndrome (PNDS), asthma syndromes (AS) and gastroesophageal reflux disease (GERD); Group B, patients without the typical symptoms and signs. The two groups received targeted or sequential empirical trials of therapy according to the algorithm.
Results
Among the 524 patients available for analysis in Groups A and B, 436 (83.6%) were diagnosed to have PNDS (34.2%), AS (44.5%) and/or GERD (10.1%), among which 26 had two causes (6.0%) and 6 had three causes (1.4%). After empirical trials of therapy, 81.5% of the patients were diagnosed. The mean time for diagnosis was considerably shorter in Group A (13.1 ± 5.6 d) than in Group B (23.4 ± 7.2 d) (p < 0.01). The diagnosis rate of the first trial in Group A (54.1%) was significantly higher than that in Group B (28.6%, p < 0.01).
Conclusions
The proposed algorithm is a promising and practical approach to diagnose chronic and subacute cough.
doi:10.1186/2049-6958-9-33
PMCID: PMC4086183  PMID: 25006456
Asthma; Cough; Diagnosis; Gastroesophageal reflux disease; Postnasal drip syndrome
8.  Complete Genome Sequence of Canine Papillomavirus Type 11 
Genome Announcements  2014;2(3):e00529-14.
Papillomaviruses with the features of epitheliotropic, nonenveloped, circular, and double-stranded DNA belong to the family Papillomaviridae, which contributes to benign and malignant tumors in humans and animals. We report the whole-genome sequence of canine papillomavirus type 11 found at a pigmented plaque located on the skin of a mixed-breed bloodhound.
doi:10.1128/genomeA.00529-14
PMCID: PMC4038897  PMID: 24874662
9.  Use of Reprogrammed Cells to Identify Therapy for Respiratory Papillomatosis 
The New England journal of medicine  2012;367(13):1220-1227.
SUMMARY
A patient with a 20-year history of recurrent respiratory papillomatosis had progressive, bilateral tumor invasion of the lung parenchyma. We used conditional reprogramming to generate cell cultures from the patient’s normal and tumorous lung tissue. Analysis revealed that the laryngeal tumor cells contained a wild-type 7.9-kb human papillomavirus virus type 11 (HPV-11) genome, whereas the pulmonary tumor cells contained a 10.4-kb genome. The increased size of the latter viral genome was due to duplication of the promoter and oncogene regions. Chemosensitivity testing identified vorinostat as a potential therapeutic agent. At 3 months after treatment initiation, tumor sizes had stabilized, with durable effects at 15 months.
doi:10.1056/NEJMoa1203055
PMCID: PMC4030597  PMID: 23013073
10.  A case of horizontal gene transfer from Wolbachia to Aedes albopictus C6/36 cell line 
Mobile Genetic Elements  2014;4:e28914.
Horizontal gene transfer plays an essential role in evolution and ecological adaptation, yet this phenomenon has remained controversial, particularly where it occurs between prokaryotes and eukaryotes. There are a handful of reported examples of horizontal gene transfer occurring between prokaryotes and eukaryotes in the literature, with most of these documented cases pertaining to invertebrates and endosymbionts. However, the vast majority of these horizontally transferred genes were either eventually excluded or rapidly became nonfunctional in the recipient genome. In this study, we report the discovery of a horizontal gene transfer from the endosymbiont Wolbachia in the C6/36 cell line derived from the mosquito Aedes albopictus. Moreover, we report that this horizontally transferred gene displayed high transcription level. This finding and the results of further experimentation strongly suggest this gene is functional and has been expressed and translated into a protein in the mosquito host cells.
doi:10.4161/mge.28914
PMCID: PMC4013104  PMID: 24812591
horizontal gene transfer; endosymbiont; Wolbachia; mosquito; Aedes Albopictus; C6/36 cell line
11.  Ribosomal Protein S29 Regulates Metabolic Insecticide Resistance through Binding and Degradation of CYP6N3 
PLoS ONE  2014;9(4):e94611.
Background
Many diseases are transmitted by mosquitoes, including malaria, dengue fever, yellow fever, filariasis, and West Nile fever. Chemical control plays a major role in managing mosquito-borne diseases. However, excessive and continuous application of insecticides has caused the development of insecticide resistance in many species including mosquito, and this has become the major obstacle to controlling mosquito-borne diseases. Insecticide resistance is the result of complex polygenic inheritance, and the mechanisms are not well understood. Ribosomal protein RPS29 was found to be associated with DM resistance in our previous study. In this study, we aim to further investigate the involvement of RPS29 in deltamethrin resistance.
Methodology and Principal Findings
In this study, tandem affinity purification was used to identify proteins that can interact with RPS29. Among the candidate proteins, CYP6N3, a member of the CYP450 superfamily, was identified, and binding to RPS29 was confirmed in vitro and in vivo by GST pull-down and immunofluorescence. CCK-8 assay was used to investigate the RPS29-CTP6N3 interaction in relation to DM resistance. CYP6N3 overexpression significantly enhanced DM resistance and insect cell viability, but this was reversed by RPS29 overexpression. Western blot was used to study the mechanism of interaction between RPS29 and CYP6N3. RPS29 increases CYP6N3 protein degradation through the proteasome.
Conclusions and Significance
These observations indicate that CYP6N3, a novel RPS29-interacting partner, could stimulate deltamethrin resistance in mosquito cells and RPS29 overexpression targeted CYP6N3 for proteosomal degradation, abrogating the CYP6N3-associated resistence to deltamethrin. Our findings provide a novel mechanism associated with CYP450s mediated DM resistance.
doi:10.1371/journal.pone.0094611
PMCID: PMC3984272  PMID: 24728095
12.  Trypsin-Catalyzed Deltamethrin Degradation 
PLoS ONE  2014;9(3):e89517.
To explore if trypsin could catalyze the degradation of non-protein molecule deltamethrin, we compared in vitro hydrolytic reactions of deltamethrin in the presence and absence of trypsin with ultraviolet-visible (UV/Vis) spectrophotometry and gas chromatography-mass spectrometry (GC/MS). In addition, acute oral toxicity of the degradation products was determined in Wistar rats. The results show that the absorption peak of deltamethrin is around 264 nm, while the absorption peaks of deltamethrin degradation products are around 250 nm and 296 nm. In our GC setting, the retention time of undegraded deltamethrin was 37.968 min, while those of deltamethrin degradation products were 15.289 min and 18.730 min. The LD50 of deltamethrin in Wistar rats is 55 mg/kg, while that of deltamethrin degradation products is 3358 mg/kg in female rats and 1045 mg/kg in male rates (61-fold and 19-fold reductions in toxicity), suggesting that trypsin could directly degrade deltamethrin, which significantly reduces the toxicity of deltamethrin. These results expand people's understanding of the functions of proteases and point to potential applications of trypsin as an attractive agent to control residual pesticides in the environment and on agricultural products.
doi:10.1371/journal.pone.0089517
PMCID: PMC3940599  PMID: 24594869
13.  The Standard, Intervention Measures and Health Risk for High Water Iodine Areas 
PLoS ONE  2014;9(2):e89608.
Our study aims to clarify the population nutrient status in locations with different levels of iodine in the water in China; to choose effective measurements of water improvement(finding other drinking water source of iodine not excess) or non-iodised salt supply or combinations thereof; to classify the areas of elevated water iodine levels and the areas with endemic goiter; and to evaluate the risk factors of water iodine excess on pregnant women, lactating women and the overall population of women. From Henan, Hebei, Shandong and Shanxi province of China, for each of 50∼99 µg/L, 100∼149 µg/L, 150∼299 µg/L, and ≥300 µg/L water iodine level, three villages were selected respectively. Students of 6–12 years old and pregnant were sampled from villages of each water-iodine level of each province, excluded iodized salt consumer. Then the children's goiter volume, the children and pregnant's urinary iodine and water iodine were tested. In addition, blood samples were collected from pregnant women, lactating women and other women of reproductive age for each water iodine level in the Shanxi Province for thyroid function tests. These indicators should be matched for each person. When the water iodine exceeds 100 µg/L; the iodine nutrient of children are iodine excessive, and are adequate or more than adequate for the pregnant women. It is reasonable to define elevated water iodine areas as locations where the water iodine levels exceed 100 µg/L. The supply of non-iodised salt alone cannot ensure adequate iodine nutrition of the residents, and water improvement must be adopted, as well. Iodine excess increases the risk of certain thyroid diseases in women from one- to eightfold.
doi:10.1371/journal.pone.0089608
PMCID: PMC3938487  PMID: 24586909
14.  Whole genome sequencing of Ethiopian highlanders reveals conserved hypoxia tolerance genes 
Genome Biology  2014;15(2):R36.
Background
Although it has long been proposed that genetic factors contribute to adaptation to high altitude, such factors remain largely unverified. Recent advances in high-throughput sequencing have made it feasible to analyze genome-wide patterns of genetic variation in human populations. Since traditionally such studies surveyed only a small fraction of the genome, interpretation of the results was limited.
Results
We report here the results of the first whole genome resequencing-based analysis identifying genes that likely modulate high altitude adaptation in native Ethiopians residing at 3,500 m above sea level on Bale Plateau or Chennek field in Ethiopia. Using cross-population tests of selection, we identify regions with a significant loss of diversity, indicative of a selective sweep. We focus on a 208 kbp gene-rich region on chromosome 19, which is significant in both of the Ethiopian subpopulations sampled. This region contains eight protein-coding genes and spans 135 SNPs. To elucidate its potential role in hypoxia tolerance, we experimentally tested whether individual genes from the region affect hypoxia tolerance in Drosophila. Three genes significantly impact survival rates in low oxygen: cic, an ortholog of human CIC, Hsl, an ortholog of human LIPE, and Paf-AHα, an ortholog of human PAFAH1B3.
Conclusions
Our study reveals evolutionarily conserved genes that modulate hypoxia tolerance. In addition, we show that many of our results would likely be unattainable using data from exome sequencing or microarray studies. This highlights the importance of whole genome sequencing for investigating adaptation by natural selection.
doi:10.1186/gb-2014-15-2-r36
PMCID: PMC4054780  PMID: 24555826
15.  Incidence and Metastasis of Cutaneous Malignant Melanoma with Respect to ABO Blood Groups: A Case-Controlled Study in Northeast of China 
PLoS ONE  2014;9(2):e88096.
Background
ABO blood groups have been suggested to contribute to the development of certain tumors; however, the associations between ABO blood groups and the incidence and metastases of cutaneous malignant melanomas have not been fully evaluated in Chinese populations. Thus, we investigated these associations with a case-controlled study in northeast of China.
Methods
A total of 482 patients with cutaneous malignant melanoma and 3,068 healthy- controls were enrolled for the study between 2001 and 2012 at The Tumor Hospital of Harbin Medical University. A multivariate logistic model was used to evaluate adjusted odds ratios (ORs) and 95% confidence intervals (CI) for the incidence and metastases of cutaneous malignant melanoma.
Results
Blood type A individuals had higher tumor incidence and metastasis compared to those with blood type O (OR = 1.575; 95% CI = 1.208–2.053, p = 0.001; OR = 2.004; 95% CI = 1.032–3.889, p = 0.040), after adjusting for age, gender, smoking status and alcohol consumption.
Conclusions
Blood type A was associated with higher incidence and metastasis of cutaneous malignant melanoma but future studies are needed to examine the mechanisms linking cutaneous malignant melanoma to ABO blood types.
doi:10.1371/journal.pone.0088096
PMCID: PMC3917876  PMID: 24516588
16.  Ribose-phosphate pyrophosphokinase 1 (PRPS1) associated with deltamethrin resistance in Culex pipiens pallens 
Parasitology research  2012;112(2):847-854.
Ribose-phosphate pyrophosphokinase 1 (PRPS1) was identified and isolated as a differentially expressed gene between deltamethrin-susceptible (DS) and deltamethrin-resistant (DR) Culex pipiens pallens and Aedes albopictus C6/36 cell line through microarray and 2D-Gel. An open reading frame of PRPS1 cloned from C. pipiens pallens has 1,011 bp and encodes for a 336 amino acids protein which shares high homology with Culex quinquefasciatus. Real-time polymerase chain reaction was used to determine the transcript expression level of PRPS1 in DS and DR strains. The expression levels of PRPS1 were higher in DR laboratory strains and natural population JXZ-DR, JXZ-LDR. PRPS1 was also detected and expressed at all developmental stages of C. pipiens pallens and increased expression level in DR3 strain than DS strain in the third and fourth instar larvae, female and male stages. In addition, to further investigate the role of PRPS1 in deltamethrin resistance, PRPS1 was transiently expressed in A. albopictus C6/36 cells and detected by western blotting. Cells transfected with PRPS1 had an increased resistance to deltamethrin compared with control cells. These results suggested that the increased expression level of PRPS1 may play roles in the regulation of deltamethrin resistance.
doi:10.1007/s00436-012-3205-2
PMCID: PMC3720864  PMID: 23250545
17.  Genome sequence of Anopheles sinensis provides insight into genetics basis of mosquito competence for malaria parasites 
BMC Genomics  2014;15:42.
Background
Anopheles sinensis is an important mosquito vector of Plasmodium vivax, which is the most frequent and widely distributed cause of recurring malaria throughout Asia, and particularly in China, Korea, and Japan.
Results
We performed 454 next-generation sequencing and obtained a draft sequence of A. sinensis assembled into scaffolds spanning 220.8 million base pairs. Analysis of this genome sequence, we observed expansion and contraction of several immune-related gene families in anopheline relative to culicine mosquito species. These differences suggest that species-specific immune responses to Plasmodium invasion underpin the biological differences in susceptibility to Plasmodium infection that characterize these two mosquito subfamilies.
Conclusions
The A. sinensis genome produced in this study, provides an important resource for analyzing the genetic basis of susceptibility and resistance of mosquitoes to Plasmodium parasites research which will ultimately facilitate the design of urgently needed interventions against this debilitating mosquito-borne disease.
doi:10.1186/1471-2164-15-42
PMCID: PMC3901762  PMID: 24438588
Genome; Anopheles sinensis; Malaria
18.  Severe Hypoxia: Consequences to Neural Stem Cells and Neurons 
Journal of neurology research  2011;1(5):10.4021/jnr70w.
Background
Multiple neurological diseases result from a pathological hypoxia in the brain, resulting in various motor, sensory or cognitive sequelae. Understanding the response of neural stem cells (NSCs) and differentiated neurons to hypoxia will help better treat such diseases.
Methods
We exposed mouse embryonic primary neurons (PN) and neural stem cells to 1% O2 in vitro.
Results
Both cell types survived and retained their immunocyto-chemical markers, and neurons showed no obvious morphological changes. Microarray analysis showed that the number of genes with significantly altered expression levels was almost five-fold higher in NSCs compared to PN. NSCs displayed a clear block in G1/S phase of the cell cycle and a number of down-regulated cytokine genes. Various growth factors (e.g. neural growth factor, prolactin), involved in survival and proliferation, genes of the Notch pathway, and genes involved in glial differentiation, and cell-matrix adhesion were up-regulated. PN displayed a down-regulation of a number of genes involved in neuron-specific functions, in particular, transmitter-related (e.g. synaptic transmission, neurotransmitter transport and release, learning, adult behavior).
Conclusions
We conclude that hypoxia 1-down-regulates genes involved in multiple neuronal functions which can negatively impact learning and memory; 2-induces a cell cycle block in NSCs; 3-can precondition NSC towards a particular differentiation potential while maintaining them fully undifferentiated.
doi:10.4021/jnr70w
PMCID: PMC3858017  PMID: 24348887
Hypoxia; Neural stem cells; Cell cycle; Primary neuron; Neurotransmitter; Neuronal function
19.  Microcirculation Perfusion Monitor on the Back of the Health Volunteers 
Objective. To observe the dermal microcirculation blood perfusion characterization of meridians channels (acupoints). Methods. 20 healthy human subjects were monitored using Pericam Perfusion Speckle Imager (PSI) for the changes in dermal microcirculation blood perfusion on governor meridian and other respective dermal regions as a control. Result. The microcirculation blood perfusion on Governor Meridian is higher than its control area. Conclusion. The dermal microcirculation blood perfusion on certain parts of Governor Meridian of healthy human subjects showed specifics.
doi:10.1155/2013/590698
PMCID: PMC3863559  PMID: 24371463
20.  Long-Lasting Changes in DNA Methylation Following Short-Term Hypoxic Exposure in Primary Hippocampal Neuronal Cultures 
PLoS ONE  2013;8(10):e77859.
While the effects of hypoxia on gene expression have been investigated in the CNS to some extent, we currently do not know what role epigenetics plays in the transcription of many genes during such hypoxic stress. To start understanding the role of epigenetic changes during hypoxia, we investigated the long-term effect of hypoxia on gene expression and DNA methylation in hippocampal neuronal cells. Primary murine hippocampal neuronal cells were cultured for 7 days. Hypoxic stress of 1% O2, 5% CO2 for 24 hours was applied on Day 3, conditions we found to maximize cellular hypoxic stress response without inducing cell death. Cells were returned to normoxia for 4 days following the period of hypoxic stress. On Day 7, Methyl-Sensitive Cut Counting (MSCC) was used to identify a genome-wide methylation profile of the hippocampal cell lines to assess methylation changes resulting from hypoxia. RNA-Seq was also done on Day 7 to analyze changes in gene transcription. Phenotypic analysis showed that neuronal processes were significantly shorter after 1 day of hypoxia, but there was a catch-up growth of these processes after return to normoxia. Transcriptome profiling using RNA-Seq revealed 369 differentially expressed genes with 225 being upregulated, many of which form networks shown to affect CNS development and function. Importantly, the expression level of 59 genes could be correlated to the changes in DNA methylation in their promoter regions. CpG islands, in particular, had a strong tendency to remain hypomethylated long after hypoxic stress was removed. From this study, we conclude that short-term, sub-lethal hypoxia results in long-lasting changes to genome wide DNA methylation status and that some of these changes can be highly correlated with transcriptional modulation in a number of genes involved in functional pathways that have been previously implicated in neural growth and development.
doi:10.1371/journal.pone.0077859
PMCID: PMC3808424  PMID: 24205000
21.  Quantitative Evaluation of the Mitochondrial Proteomes of Drosophila melanogaster Adapted to Extreme Oxygen Conditions 
PLoS ONE  2013;8(9):e74011.
Mitochondria are the primary organelles that consume oxygen and provide energy for cellular activities. To investigate the mitochondrial mechanisms underlying adaptation to extreme oxygen conditions, we generated Drosophila strains that could survive in low- or high-oxygen environments (LOF or HOF, respectively), examined their mitochondria at the ultrastructural level via transmission electron microscopy, studied the activity of their respiratory chain complexes, and quantitatively analyzed the protein abundance responses of the mitochondrial proteomes using Isobaric tag for relative and absolute quantitation (iTRAQ). A total of 718 proteins were identified with high confidence, and 55 and 75 mitochondrial proteins displayed significant differences in abundance in LOF and HOF, respectively, compared with the control flies. Importantly, these differentially expressed mitochondrial proteins are primarily involved in respiration, calcium regulation, the oxidative response, and mitochondrial protein translation. A correlation analysis of the changes in the levels of the mRNAs corresponding to differentially regulated mitochondrial proteins revealed two sets of proteins with different modes of regulation (transcriptional vs. post-transcriptional) in both LOF and HOF. We believe that these findings will not only enhance our understanding of the mechanisms underlying adaptation to extreme oxygen conditions in Drosophila but also provide a clue in studying human disease induced by altered oxygen tension in tissues and cells.
doi:10.1371/journal.pone.0074011
PMCID: PMC3771901  PMID: 24069262
22.  Intravitreal Transplantation of Human Umbilical Cord Blood Stem Cells Protects Rats from Traumatic Optic Neuropathy 
PLoS ONE  2013;8(8):e69938.
Objectives
To treat traumatic optic neuropathy (TON) with transplantation of human umbilical cord blood stem cells (hUCBSC) and explore how transplanted stem cells participate in the neuron repairing process.
Methods
A total of 195 Sprague-Dawley rats were randomly assigned to three groups: sham-surgery, optic nerve injury, and stem cell transplant group. Optic nerve injury was established in rats by directly clamping the optic nerve for 30 seconds. hUCBSC was microinjected into the vitreous cavity of injured rats. Optic nerve function was evaluated by flash visual evoked potentials (F-VEP). Apoptosis in retina tissues was detected by TUNEL staining. GRP78 and CHOP gene expression was measured by RT-PCR.
Results
After injury, transplantation of hUCBSC significantly blunted a reduction in optic nerve function indicated by smaller decreases in amplitude and smaller increases in peak latency of F-VEP waveform compared to the injury alone group. Also, significant more in retinal ganglion cell (RGC) count and less in RGC apoptosis were detected after transplantation compared to injured rats. The protective effect correlated with upregulated GRP78 and downregulated CHOP mRNA expression.
Conclusion
Intravitreal transplantation of hUCBSCs significantly blunted a reduction in optic nerve function through increasing RGC survival and decreasing retinal cell apoptosis. The protective role of transplantation was associated with upregulation of GRP78 expression and downregulation of CHOP expression in retinal cells.
doi:10.1371/journal.pone.0069938
PMCID: PMC3734232  PMID: 23940534
23.  Cloning and characterization of prophenoloxidase A3 (proPOA3) from Culex pipiens pallens 
The prophenoloxidase subunit A3 (proPOA3) gene was cloned from Culex pipiens pallens, which had an open reading frame of 2,061 bp encoding a putative 686 amino acid protein. The deduced amino acid sequence shares 98% with proPOA3 from Cx. quinquefasciatus. ProPOA3 is expressed at all developmental stages of Cx. pipiens pallens. Significant negative correlation was observed between proPOA3 expression and deltamethrin resistance in resistant Cx. pipiens pallens. Furthermore, proPOA3 expression levels were significantly lower in deltamethrin-resistant mosquitoes than in susceptible mosquitoes collected at four locations in Eastern China. However, we did not find any substantial change in proPOA3 expression in field-collected resistant Anopheles mosquitoes. Moreover, overexpressing proPOA3 in C6/36 cells led to more sensitivity to deltamethrin treatment. In laboratory and field-collected resistant Cx. pipiens pallens, a valine to isoleucine mutation (769G>A) and two synonymous mutations (1116G>C and 1116G>A) were identified in proPOA3. In addition, the mutation frequency of 769G>A and 1116G>C increased gradually, which corresponded with raised deltamethrin resistance levels. Taken together, our study provides the first evidence that proPOA3 may play a role in the regulation of deltamethrin-resistance in Cx. pipiens pallens.
doi:10.1016/j.cbpb.2012.04.008
PMCID: PMC3365641  PMID: 22561195
Culex pipiens pallens; deltamethrin resistance; prophenoloxidase; mutation
24.  Divergent Human Papillomavirus Associated with Recurrent Respiratory Papillomatosis with Lung Involvement 
Genome Announcements  2013;1(4):e00474-13.
A divergent human papillomavirus (HPV), isolated from a lung lesion of a patient with recurrent respiratory papillomatosis, was fully cloned, sequenced, and genetically characterized. DNA analysis revealed that the HPV contained a 10.4-kb genome, with a duplication of 2,493 bp that includes partial L1-long control region (LCR)-E6-E7-partial E1 sequences.
doi:10.1128/genomeA.00474-13
PMCID: PMC3709150  PMID: 23846273
25.  Dissection of Mechanisms of a Chinese Medicinal Formula: Danhong Injection Therapy for Myocardial Ischemia/Reperfusion Injury In Vivo and In Vitro 
Traditional Chinese medicine uses a systemic treatment approach, targeting multiple etiological factors simultaneously. Danhong injection (DHI), a very popular Chinese medicine injection, is reported to be effective for many cardiovascular conditions. The primary active ingredients of DHI, and their systemic and interrelated mechanism have not been evaluated in an established myocardial ischemia/reperfusion (MI/R) model. We identified the main active constituents in DHI, including hydroxysafflor yellow A (A), salvianolic acid B (B), and danshensu (C), by HPLC fingerprint analysis and assessed their effect on MI/R rats and cardiomyocytes. These 3 compounds and DHI all decreased the levels of IL-1, TNF-α, and MDA, increased those of IL-10 and SOD activity in vivo and in vitro, and had antiapoptotic effects, as shown by flow cytometric analysis and TUNEL assay. Moreover, these compounds increased phosphorylation of Akt and ERK1/2 in cardiomyocytes. Interestingly, we found compound A exerted a more prominent anti-inflammatory effect than B and C, by decreasing NF-κB levels; compound B had more powerful antioxidative capacity than A and C, by increasing Nrf2 expression; compound C had stronger antiapoptotic ability than A and B, by lowering caspase-3 activity. Our results elucidate the mechanisms by which DHI protects against MI/R induced injury.
doi:10.1155/2013/972370
PMCID: PMC3686077  PMID: 23840272

Results 1-25 (59)