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1.  Preparation and Identification of Monoclonal Antibodies Against ω-Conotoxin MVIIA 
ω-Conotoxins MVIIA (ω-CTX MVIIA) is a peptide with 25 amino acid residues. It is a selective and reversible N-type voltage-gated calcium channel blocker, which could be used as an analgesic for pain. To date, there are no monoclonal antibodies (MAb) for immunoassay against ω-conotoxin MVIIA. In this study, an MAb against ω-conotoxin MVIIA was prepared. The conotoxin-coding DNA sequence was chemically synthesized and cloned into expression vector pGEX-6p-1 and pET32a (+), respectively. The fusion protein GST-CTX was expressed and purified, and was used to immunize BALB/c mice for preparing the anti-CTX antibody. The spleen cells were fused with SP2/0 myeloma cells after the titer of antiserum was detected and qualified. After being screened by indirect ELISA and cloned by limiting dilution, a hybridoma named 4A12, which produces monoclonal antibody specifically against ω-CTX MVIIA, was successfully obtained. It was found that there are 102 chromosomes in the 4A12 cell, and the subclass for the MAb is IgM. The MAb affinity against ω-CTX MVIIA was 7.33×109 L/mol, and the cross-reaction test showed that the MAb specifically bound ω-CTX MVIIA. The MAb could be used as a specific antagonist for ω-CTX MVIIA in the physiological study on the CaV channels in the nervous system.
doi:10.1089/mab.2014.0019
PMCID: PMC4151065  PMID: 25171005
2.  No evidence that selection has been less effective at removing deleterious mutations in Europeans than in Africans 
Nature genetics  2015;47(2):126-131.
Non-African populations have experienced size reductions in the time since their split from West Africans, leading to the hypothesis that natural selection to remove weakly deleterious mutations has been less effective in the history of non-Africans. To test this hypothesis, we measured the per-genome accumulation of non-synonymous substitutions across diverse pairs of populations. We find no evidence for a higher load of deleterious mutations in non-Africans. However, we detect significant differences among more divergent populations, as archaic Denisovans have accumulated non-synonymous mutations faster than either modern humans or Neanderthals. To reconcile these findings with patterns that have been interpreted as evidence of less effective removal of deleterious mutations in non-Africans than in West Africans, we use simulations to show that the observed patterns are not likely to reflect changes in the effectiveness of selection after the populations split, and instead are likely to be driven by other population genetic factors.
doi:10.1038/ng.3186
PMCID: PMC4310772  PMID: 25581429
3.  Integration of metabolic activation with a predictive toxicogenomics signature to classify genotoxic versus non-genotoxic chemicals in human TK6 cells 
The use of integrated approaches in genetic toxicology, including the incorporation of gene expression data to determine the molecular pathways involved in the response, is becoming more common. In a companion paper, a genomic biomarker was developed in human TK6 cells to classify chemicals as genotoxic or non-genotoxic. Because TK6 cells are not metabolically competent, we set out to broaden the utility of the biomarker for use with chemicals requiring metabolic activation. Specifically, chemical exposures were conducted in the presence of rat liver S9. The ability of the biomarker to classify genotoxic (benzo[a]pyrene, BaP; aflatoxin B1, AFB1) and non-genotoxic (dexamethasone, DEX; phenobarbital, PB) agents correctly was evaluated. Cells were exposed to increasing chemical concentrations for 4h and collected 0h, 4h and 20h post-exposure. Relative survival, apoptosis, and micronucleus frequency were measured at 24h. Transcriptome profiles were measured with Agilent microarrays. Statistical modeling and bioinformatics tools were applied to classify each chemical using the genomic biomarker. BaP and AFB1 were correctly classified as genotoxic at the mid- and high concentrations at all three time points, whereas DEX was correctly classified as non-genotoxic at all concentrations and time points. The high concentration of PB was misclassified at 24h, suggesting that cytotoxicity at later time points may cause misclassification. The data suggest that the use of S9 does not impair the ability of the biomarker to classify genotoxicity in TK6 cells. Finally, we demonstrate that the biomarker is also able to accurately classify genotoxicity using a publicly available dataset derived from human HepaRG cells.
doi:10.1002/em.21940
PMCID: PMC4506226  PMID: 25733247
genetic toxicology; genomic biomarker; TGx-28.65 classifier; gene expression microarray; micronucleus
4.  Caspase-1 inhibitor ameliorates experimental autoimmune myasthenia gravis by innate dendric cell IL-1-IL-17 pathway 
Background
IL-1β has been shown to play a pivotal role in autoimmunity. Cysteinyl aspartate-specific proteinase-1 (caspase-1) inhibitor may be an important drug target for autoimmune diseases. However, the effects of caspase-1 inhibitor on myasthenia gravis (MG) remain undefined.
Methods
To investigate the effects of caspase-1 inhibitor on experimental autoimmune myasthenia gravis (EAMG), an animal model of MG, caspase-1 inhibitor was administered to Lewis rats immunized with region 97–116 of the rat AChR α subunit (R97-116 peptide) in complete Freund’s adjuvant. The immunophenotypical characterization by flow cytometry and the levels of autoantibody by ELISA were carried out to evaluate the neuroprotective effect of caspase-1 inhibitor.
Results
We found that caspase-1 inhibitor improved EAMG clinical symptom, which was associated with decreased IL-17 production by CD4+ T cells and γδ T cells, lower affinity of anti-R97-116 peptide IgG. Caspase-1 inhibitor decreased expression of CD80, CD86, and MHC class II on DCs, as well as intracellular IL-1β production from DCs. In addition, caspase-1 inhibitor treatment inhibited R97-116 peptide-specific cell proliferation and decreased follicular helper T cells relating to EAMG development.
Conclusions
Our results suggest that caspase-1 inhibitor ameliorates experimental autoimmune myasthenia gravis by innate DC IL-1-IL-17 pathway and provides new evidence that caspase-1 is an important drug target in the treatment of MG and other autoimmune diseases.
doi:10.1186/s12974-015-0334-4
PMCID: PMC4470006  PMID: 26071315
Caspase-1 inhibitor; IL-1β; Dendric cell; Th17 cell; Follicular helper T cell; Experimental autoimmune myasthenia gravis
5.  Modulation of fatty acid and bile acid metabolism by PPARα protects against alcoholic liver disease 
Background
Chronic alcohol intake affects liver function and causes hepatic pathological changes. It has been shown that peroxisome proliferator-activated receptor α (PPARα)-null mice developed more pronounced hepatic changes than wild type (WT) mice after chronic exposure to a diet containing 4% alcohol. The remarkable similarity between the histopathology of ALD in Ppara-null model and in humans, and the fact that PPARα expression and activity in human liver are less than one-tenth of those in WT mouse liver make Ppara-null a good system to investigate ALD.
Methods
In this study, the Ppara-null model was used to elucidate the dynamic regulation of PPARα activity during chronic alcohol intake. Hepatic transcriptomic and metabolomic analyses were used to examine alterations of gene expression and metabolites associated with pathological changes. The changes triggered by alcohol consumption on gene expression and metabolites in Ppara-null mice were compared with those in wild-type mice.
Results
The results showed that in the presence of PPARα, three major metabolic pathways in mitochondria, namely the fatty acid β-oxidation, the tricarboxylic acid cycle (TCA) and the electron transfer chain, were induced in response to two-month alcohol feeding, while these responses were greatly reduced in the absence of PPARα. In line with the transcriptional modulations of these metabolic pathways, lipidomic profiling showed consistent accumulation of triglycerides in Ppara-null mice, a robust increase of hepatic cholic acid and its derivatives, and a strong induction of fibrogenesis genes exclusively in alcohol-fed Ppara-null mice.
Conclusions
These observations indicate that PPARα plays a protective role to enhance mitochondrial function in response to chronic alcohol consumption by adaptive transcriptional activation and suggest that activation of this nuclear receptor may be of therapeutic value in the treatment of ALD.
doi:10.1111/acer.12424
PMCID: PMC4047177  PMID: 24773203
Ppara-null mice; fibrogenesis; metabolic pathways; transcriptomics; metabolomics
6.  Recent Advances on Building Information Modeling 
The Scientific World Journal  2015;2015:786598.
doi:10.1155/2015/786598
PMCID: PMC4454765  PMID: 26090516
7.  Kinetics of plasma microRNA-499 expression in acute myocardial infarction 
Journal of Thoracic Disease  2015;7(5):890-896.
Background
MicroRNA (miRNA) is reported to be present in human plasma and has been increasingly suggested as a biomarker for diseases. Our study aimed to investigate the kinetics of cardiac-specific microR-499 (miR-499) in acute myocardial infarction (AMI).
Methods
Circulating concentrations of cardiac enriched miR-499 were measured by quantitative PCR in 73 patients with acute coronary syndrome (ACS), including 53 with AMI and 20 with unstable angina (UA). Thirty healthy subjects were used as controls. Plasma samples in AMI group were obtained immediately after admission and at 12 h, 24 h, 3 d and 7 d after onset of symptoms. Plasma samples in UA and healthy control groups were collected immediately after admission. The severity and extent of coronary stenotic lesions were evaluated on the basis of coronary angiography using Gensini score.
Results
miR-499 expression levels were significantly higher in the 53 AMI patients than in the 20 UA patients and 30 healthy controls immediately after admission (P<0.01). A measurable increase in miR-499 levels was observed in AMI patients within 24 h of the last onset of chest pain and the levels returned to the baseline after 7 d. Plasma miR-499 levels in the patients with AMI were positively-correlated with cTnI (r=0.384, P<0.01) and CK-MB (r=0.402, P<0.01). In addition, miR-499 levels in AMI patients with two- and three-vessel coronary artery disease (CAD) were significantly higher than those in patients with single-vessel CAD (P<0.05). Gensini scores were used to evaluate the severity of coronary stenosis. miR-499 were positively correlated with Gensini scores (r=0.52, P<0.01). miR-499 levels at admission were significantly higher than that those 24 h after percutaneous coronary intervention (PCI) in AMI patients (P<0.01) and were negatively correlated with LVEF (r=0.36, P=0.008).
Conclusions
Cardiac-specific miRNA-499 levels were found to be linearly proportional to myocardial damage. MiRNA-499 might prove to be a new biomarker for AMI and a predictor of the risk of myocardial ischemia.
doi:10.3978/j.issn.2072-1439.2014.11.32
PMCID: PMC4454849  PMID: 26101645
MicroRNA (miRNA); acute myocardial infarction (AMI); biomarker
8.  Astrocyte-like cells differentiated from a novel population of CD45-positive cells in adult human peripheral blood 
Cell Biology International  2014;39(1):84-93.
We have previously reported a novel CD45-positive cell population called peripheral blood insulin-producing cells (PB-IPCs) and its unique potential for releasing insulin in vitro. Despite the CD45-positive phenotype and self-renewal ability, PB-IPCs are distinguished from hemopoietic and endothelial progenitor cells (EPCs) by some characteristics, such as a CD34-negative phenotype and different culture conditions. We have further identified the gene profiles of the embryonic and neural stem cells, and these profiles include Sox2, Nanog, c-Myc, Klf4, Notch1 and Mash1. After treatment with all-trans retinoic acid (ATRA) in vitro, most PB-IPCs exhibited morphological changes that included the development of elongated and branched cell processes. In the process of induction, the mRNA expression of Hes1 was robustly upregulated, and a majority of cells acquired some astrocyte-associated specific phenotypes including anti-glial fibrillary acidic protein (GFAP), CD44, Glutamate-aspartate transporter (GLAST) and S100β. In spite of the deficiency of glutamate uptaking, the differentiated cells significantly relaxed the regulation of the expression of brain-derived neurotrophic factor (BDNF) mRNA. This finding demonstrates that PB-IPCs could be induced into a population of astrocyte-like cells and enhanced the neurotrophic potential when the state of proliferation was limited by ATRA, which implies that this unique CD45+ cell pool may have a protective role in some degenerative diseases of the central nervous system (CNS).
doi:10.1002/cbin.10355
PMCID: PMC4410680  PMID: 25077697
all-trans retinoic acid; astrocytes; differentiation; human peripheral blood; insulin-producing cells
9.  Using Visualized Matrix Effects to Develop and Improve LC-MS/MS Bioanalytical Methods, Taking TRAM-34 as an Example 
PLoS ONE  2015;10(4):e0118818.
Matrix effects (MEs) continue to be an obstacle in the development of the LC-MS/MS method, with phospholipids being the major cause of MEs. Changing the mobile phase has been a common strategy to reduce MEs; however, the underlying mechanism is unclear. "In-source multiple-reaction monitoring" (IS-MRM) for glycerophosphocholines (PCs) has been commonly applied in many bioanalytical methods. "Visualized MEs" is a suitable term to describe the application of IS-MRM to visualize the elution pattern of phospholipids. We selected a real case to discuss the relationship of MEs and phospholipids in different mobile phases by quantitative, qualitative, and visualized MEs in LC-MS/MS bioanalysis. The application of visualized MEs not only predicts the ion-suppression zone but also helps in selecting an appropriate (1) mobile phase, (2) column, (3) needle wash solvent for the residue of analyte and phospholipids, and (4) evaluates the clean-up efficiency of sample preparation. The TRAM-34 LC-MS/MS method, improved by using visualized MEs, was shown to be a precise and accurate analytical method. All data indicated that the use of visualized MEs indeed provided useful information about the LC-MS/MS method development and improvement. In this study, an integrative approach for the qualitative, quantitative, and visualized MEs was used to decipher the complexity of MEs.
doi:10.1371/journal.pone.0118818
PMCID: PMC4409340  PMID: 25909956
10.  Hair regrowth in alopecia areata patients following Stem Cell Educator therapy 
BMC Medicine  2015;13:87.
Background
Alopecia areata (AA) is one of the most common autoimmune diseases and targets the hair follicles, with high impact on the quality of life and self-esteem of patients due to hair loss. Clinical management and outcomes are challenged by current limited immunosuppressive and immunomodulating regimens.
Methods
We have developed a Stem Cell Educator therapy in which a patient’s blood is circulated through a closed-loop system that separates mononuclear cells from the whole blood, allows the cells to briefly interact with adherent human cord blood-derived multipotent stem cells (CB-SC), and returns the “educated” autologous cells to the patient’s circulation. In an open-label, phase 1/phase 2 study, patients (N = 9) with severe AA received one treatment with the Stem Cell Educator therapy. The median age was 20 years (median alopecic duration, 5 years).
Results
Clinical data demonstrated that patients with severe AA achieved improved hair regrowth and quality of life after receiving Stem Cell Educator therapy. Flow cytometry revealed the up-regulation of Th2 cytokines and restoration of balancing Th1/Th2/Th3 cytokine production in the peripheral blood of AA subjects. Immunohistochemistry indicated the formation of a “ring of transforming growth factor beta 1 (TGF-β1)” around the hair follicles, leading to the restoration of immune privilege of hair follicles and the protection of newly generated hair follicles against autoimmune destruction. Mechanistic studies revealed that co-culture with CB-SC may up-regulate the expression of coinhibitory molecules B and T lymphocyte attenuator (BTLA) and programmed death-1 receptor (PD-1) on CD8β+NKG2D+ effector T cells and suppress their proliferation via herpesvirus entry mediator (HVEM) ligands and programmed death-1 ligand (PD-L1) on CB-SCs.
Conclusions
Current clinical data demonstrated the safety and efficacy of the Stem Cell Educator therapy for the treatment of AA. This innovative approach produced lasting improvement in hair regrowth in subjects with moderate or severe AA.
Trial registration
ClinicalTrials.gov, NCT01673789, 21 August 2012
doi:10.1186/s12916-015-0331-6
PMCID: PMC4417286  PMID: 25896390
Alopecia areata; Autoimmune; Stem Cell Educator; Immune modulation; Hair regrowth
11.  Towards Effective and Efficient Patient-Specific Quality Assurance for Spot Scanning Proton Therapy 
Cancers  2015;7(2):631-647.
An intensity-modulated proton therapy (IMPT) patient-specific quality assurance (PSQA) program based on measurement alone can be very time consuming due to the highly modulated dose distributions of IMPT fields. Incorporating independent dose calculation and treatment log file analysis could reduce the time required for measurements. In this article, we summarize our effort to develop an efficient and effective PSQA program that consists of three components: measurements, independent dose calculation, and analysis of patient-specific treatment delivery log files. Measurements included two-dimensional (2D) measurements using an ionization chamber array detector for each field delivered at the planned gantry angles with the electronic medical record (EMR) system in the QA mode and the accelerator control system (ACS) in the treatment mode, and additional measurements at depths for each field with the ACS in physics mode and without the EMR system. Dose distributions for each field in a water phantom were calculated independently using a recently developed in-house pencil beam algorithm and compared with those obtained using the treatment planning system (TPS). The treatment log file for each field was analyzed in terms of deviations in delivered spot positions from their planned positions using various statistical methods. Using this improved PSQA program, we were able to verify the integrity of the data transfer from the TPS to the EMR to the ACS, the dose calculation of the TPS, and the treatment delivery, including the dose delivered and spot positions. On the basis of this experience, we estimate that the in-room measurement time required for each complex IMPT case (e.g., a patient receiving bilateral IMPT for head and neck cancer) is less than 1 h using the improved PSQA program. Our experience demonstrates that it is possible to develop an efficient and effective PSQA program for IMPT with the equipment and resources available in the clinic.
doi:10.3390/cancers7020631
PMCID: PMC4491675  PMID: 25867000
spot scanning proton therapy; IMPT; SFO; SFIB; patient specific QA
12.  Ancient human genomes suggest three ancestral populations for present-day Europeans 
Lazaridis, Iosif | Patterson, Nick | Mittnik, Alissa | Renaud, Gabriel | Mallick, Swapan | Kirsanow, Karola | Sudmant, Peter H. | Schraiber, Joshua G. | Castellano, Sergi | Lipson, Mark | Berger, Bonnie | Economou, Christos | Bollongino, Ruth | Fu, Qiaomei | Bos, Kirsten I. | Nordenfelt, Susanne | Li, Heng | de Filippo, Cesare | Prüfer, Kay | Sawyer, Susanna | Posth, Cosimo | Haak, Wolfgang | Hallgren, Fredrik | Fornander, Elin | Rohland, Nadin | Delsate, Dominique | Francken, Michael | Guinet, Jean-Michel | Wahl, Joachim | Ayodo, George | Babiker, Hamza A. | Bailliet, Graciela | Balanovska, Elena | Balanovsky, Oleg | Barrantes, Ramiro | Bedoya, Gabriel | Ben-Ami, Haim | Bene, Judit | Berrada, Fouad | Bravi, Claudio M. | Brisighelli, Francesca | Busby, George B. J. | Cali, Francesco | Churnosov, Mikhail | Cole, David E. C. | Corach, Daniel | Damba, Larissa | van Driem, George | Dryomov, Stanislav | Dugoujon, Jean-Michel | Fedorova, Sardana A. | Romero, Irene Gallego | Gubina, Marina | Hammer, Michael | Henn, Brenna M. | Hervig, Tor | Hodoglugil, Ugur | Jha, Aashish R. | Karachanak-Yankova, Sena | Khusainova, Rita | Khusnutdinova, Elza | Kittles, Rick | Kivisild, Toomas | Klitz, William | Kučinskas, Vaidutis | Kushniarevich, Alena | Laredj, Leila | Litvinov, Sergey | Loukidis, Theologos | Mahley, Robert W. | Melegh, Béla | Metspalu, Ene | Molina, Julio | Mountain, Joanna | Näkkäläjärvi, Klemetti | Nesheva, Desislava | Nyambo, Thomas | Osipova, Ludmila | Parik, Jüri | Platonov, Fedor | Posukh, Olga | Romano, Valentino | Rothhammer, Francisco | Rudan, Igor | Ruizbakiev, Ruslan | Sahakyan, Hovhannes | Sajantila, Antti | Salas, Antonio | Starikovskaya, Elena B. | Tarekegn, Ayele | Toncheva, Draga | Turdikulova, Shahlo | Uktveryte, Ingrida | Utevska, Olga | Vasquez, René | Villena, Mercedes | Voevoda, Mikhail | Winkler, Cheryl | Yepiskoposyan, Levon | Zalloua, Pierre | Zemunik, Tatijana | Cooper, Alan | Capelli, Cristian | Thomas, Mark G. | Ruiz-Linares, Andres | Tishkoff, Sarah A. | Singh, Lalji | Thangaraj, Kumarasamy | Villems, Richard | Comas, David | Sukernik, Rem | Metspalu, Mait | Meyer, Matthias | Eichler, Evan E. | Burger, Joachim | Slatkin, Montgomery | Pääbo, Svante | Kelso, Janet | Reich, David | Krause, Johannes
Nature  2014;513(7518):409-413.
We sequenced the genomes of a ~7,000 year old farmer from Germany and eight ~8,000 year old hunter-gatherers from Luxembourg and Sweden. We analyzed these and other ancient genomes1–4 with 2,345 contemporary humans to show that most present Europeans derive from at least three highly differentiated populations: West European Hunter-Gatherers (WHG), who contributed ancestry to all Europeans but not to Near Easterners; Ancient North Eurasians (ANE) related to Upper Paleolithic Siberians3, who contributed to both Europeans and Near Easterners; and Early European Farmers (EEF), who were mainly of Near Eastern origin but also harbored WHG-related ancestry. We model these populations’ deep relationships and show that EEF had ~44% ancestry from a “Basal Eurasian” population that split prior to the diversification of other non-African lineages.
doi:10.1038/nature13673
PMCID: PMC4170574  PMID: 25230663
13.  Serum Metabolites as Potential Biomarkers for Diagnosis of Knee Osteoarthritis 
Disease Markers  2015;2015:684794.
Knee osteoarthritis (OA) is a highly prevalent chronic degenerative joint disease that mainly affects the elderly population. The aim of this study was to investigate serum signature metabolites as potential biomarkers for early diagnosis of knee OA. Global serum metabolic profiles of 40 patients with knee OA and 20 healthy controls (HC) were analyzed by ultra-performance liquid chromatography coupled to mass spectrometry. An OA-specific metabolic profile was established that can clearly discriminate patients with OA from HCs. Fourteen metabolites that are involved in the metabolism of amino acids, purine, energy, glycolysis, fatty acids, and lipids were significantly altered in patients with OA compared to HCs. These metabolites could be potentially used as biomarkers for the diagnosis of knee OA.
doi:10.1155/2015/684794
PMCID: PMC4378325  PMID: 25861152
14.  Src regulates angiogenic factors and vascular permeability after focal cerebral ischemia-reperfusion 
Neuroscience  2014;262:118-128.
Developing new strategies to treat cerebral ischemic-reperfusion injury will require a better understanding of the mechanisms that underlie vascular permeability. In this study we examined the temporal expression of Src and angiogenic factors in rat brain after focal cerebral ischemia and reperfusion and analyzed the relationships among those factors. We also investigated the effect of Src inhibitor PP1 in ischemic reperfusion. Rats were subjected to middle cerebral artery occlusion for 90 min followed by reperfusion with or without PP1 treatment. Src mRNA increased at 3 h after reperfusion and then gradually declined. Phosphorylation of Src at Y418 displayed a biphasic increase. Phosphorylation increased as early as 3 h and peaked at 6 h; after decreasing, it peaked again at 3 to 7 days. Increases in Src mRNA and phosphorylation correlated positively with levels of vascular endothelial growth factor (VEGF) and angiopoietin-2 (Ang-2), and negatively with levels of angiopoietin-1 (Ang-1) and zonula occludens-1 (ZO-1). Changes in the expression of these factors correlated with the progress of vascular permeability, especially early after reperfusion. Hence, dynamic temporal changes in Src Y418 phosphorylation may modulate vascular permeability after cerebral ischemia and reperfusion. PP1 effectively decreased Src Y418 phosphorylation and the expression of VEGF and Ang-2 and increased the expression of Ang-1 and ZO-1. It also reduced cerebral infarct size and neurologic dysfunction. Therefore, Src may represent a new therapeutic target for reducing tissue damage caused by increased vascular permeability.
doi:10.1016/j.neuroscience.2013.12.060
PMCID: PMC3943922  PMID: 24412374
angiogenic factors; cerebral ischemia; PP1; Src; vascular permeability; zonula occludens-1
15.  First-principles calculations of perpendicular magnetic anisotropy in Fe1−xCox/MgO(001) thin films 
The perpendicular magnetic anisotropy (PMA) of Fe1−xCox thin films on MgO(001) was investigated via first-principles density-functional calculations. Four different configurations were considered based on their ground states: Fe/MgO, Fe12Co4/MgO, Fe10Co6/MgO, and Fe8Co8/MgO. As the Co composition increases, the amplitude of PMA increases first from Fe/MgO to Fe12Co4/MgO, and then decreases in Fe10Co6/MgO; finally, the magnetic anisotropy becomes horizontal in Fe8Co8/MgO. Analysis based on the second-order perturbation of the spin-orbit interaction was carried out to illustrate the contributions from Fe and Co atoms to PMA, and the differential charge density was calculated to give an intuitive comparison of 3d orbital occupancy. The enhanced PMA in Fe12Co4/MgO is ascribed to the optimized combination of occupied and unoccupied 3d states around the Fermi energy from both interface Fe and Co atoms, while the weaker PMA in Fe10Co6/MgO is mainly attributed to the modulation of the interface Co-dxy orbital around the Fermi energy. By adjusting the Co composition in Fe1−xCox, the density of states of transitional metal atoms will be modulated to optimize PMA for future high-density memory application.
doi:10.1186/s11671-015-0825-3
PMCID: PMC4385311  PMID: 25852418
First-principles calculations; FeCo/MgO; Perpendicular magnetic anisotropy
16.  Circulating miR-499 are novel and sensitive biomarker of acute myocardial infarction 
Journal of Thoracic Disease  2015;7(3):303-308.
Background
miRNAs are known to play a crucial role in cardiac development, and the expression of miRNA is altered in the diseased heart. The aim of this study was to investigate the value of plasma microRNA-499 (miR-499) as a novel biomarker for early diagnosis of acute myocardial infarction (AMI).
Methods
Enrolled in this study were 227 patients with chest pain on presentation to the departments of emergency and cardiology of Wuxi Second People’s Hospital between October 2011 and May 2014. Additional 100 healthy individuals who received physical examination in the same hospital during the same period were used as control. Plasma was collected at admission, and the abundance of miR-499 was measured using reverse transcriptase-polymerase chain reaction (RT-PCR).
Results
MiR-499 was significantly elevated in 142 patients diagnosed with AMI as compared with 85 patients in non-AMI group and 100 subjects in healthy control group. Plasma miR-499 were already detectable in the plasma as early as 1 h after onset of chest pain in AMI patients, and continued to increase gradually without any sign of decreasing tendency within 9 h in AMI patients. miR-499 was highly positively correlated with the serum creatine kinase-MB (CK-MB) and cTnI. The area under the curve (AUC) of miR-499 for the diagnosis of AMI was 0.86, with an optimal cut-off value of 4.79, sensitivity of 80%, and specificity of 80.28%.
Conclusions
miR-499 was shown to substantially increase the diagnostic accuracy of CK-MB and cTnI in the diagnosis of AMI, and therefore it may prove to be a useful marker for early diagnosis of AMI.
doi:10.3978/j.issn.2072-1439.2015.02.05
PMCID: PMC4387434  PMID: 25922707
microRNA (miR); acute myocardial infarction (AMI); early diagnosis; biomarker
17.  Design and Application of a Novel High-throughput Screening Technique for 1-Deoxynojirimycin 
Scientific Reports  2015;5:8563.
High-throughput screening techniques for small molecules can find intensive applications in the studies of biosynthesis of these molecules. A sensitive, rapid and cost-effective technique that allows high-throughput screening of endogenous production of the natural iminosugar 1-deoxynojirimycin (1-DNJ), an α-glucosidase inhibitor relevant to the pharmaceutical industry, was developed in this study, based on the inhibitory effects of 1-DNJ on the activity of the β-glycosidase LacS from Sulfolobus solfataricus. This technique has been demonstrated effective in engineering both the key enzyme and the expression levels of enzymes in the 1-DNJ biosynthetic pathway from Bacillus atrophaeus cloned in E. coli. Higher biosynthetic efficiency was achieved using directed evolution strategies.
doi:10.1038/srep08563
PMCID: PMC4338435  PMID: 25708517
18.  Performance evaluation of multi-junction solar cells by spatially resolved electroluminescence microscopy 
An electroluminescence microscopy combined with a spectroscopy was developed to visually analyze multi-junction solar cells. Triple-junction solar cells with different conversion efficiencies were characterized by using this system. The results showed that the mechanical damages and material defects in solar cells can be clearly distinguished, indicating a high-resolution imaging. The external quantum efficiency (EQE) measurements demonstrated that different types of defects or damages impacted cell performance in various degrees and the electric leakage mostly degraded the EQE. Meanwhile, we analyzed the relationship between electroluminescence intensity and short-circuit current density JSC. The results indicated that the gray value of the electroluminescence image corresponding to the intensity was almost proportional to JSC. This technology provides a potential way to evaluate the current matching status of multi-junction solar cells.
doi:10.1186/s11671-014-0719-9
PMCID: PMC4385041  PMID: 25852337
Multi-junction solar cells; Electroluminescence imaging; Quantum efficiency; Current matching
19.  The fate of recent duplicated genes following a fourth-round whole genome duplication in a tetraploid fish, common carp (Cyprinus carpio) 
Scientific Reports  2015;5:8199.
Whole genome duplication (WGD) results in extensive genetic redundancy. In plants and yeast, WGD is followed by rapid gene deletions and intense expression differentiation with slow functional divergence. However, the early evolution of the gene differentiation processes is poorly understood in vertebrates because almost all studied WGDs are extremely ancient, and the genomes have returned to a diploid status. Common carp had a very recent fourth round of WGD dated to 8 million years ago. It therefore constitutes an ideal model to study early-stage functional divergence and expression differentiation in vertebrates. We identified 1,757 pairs of recently duplicated genes (RDGs) originating from this specific WGD and found that most ancestral genes were retained in duplicate. Most RDGs were conserved and under selective pressure. Gene expression analysis across six tissues revealed that 92.5% of RDG pairs were co-expressed in at least one tissue and that the expression of nearly half pairs ceased to be strongly correlated, indicating slow spatial divergence but rapid expression dissociation. Functional comparison revealed that 25% of pairs had functional divergence, of which neo- and sub-functionalization were the main outcomes. Our analysis revealed slow gene loss but rapid and intense expression and function differentiation after WGD.
doi:10.1038/srep08199
PMCID: PMC4314655  PMID: 25645996
20.  Genetic history of an archaic hominin group from Denisova Cave in Siberia 
Nature  2010;468(7327):1053-1060.
Using DNA extracted from a finger bone found in Denisova Cave in southern Siberia, we have sequenced the genome of an archaic hominin to about 1.9-fold coverage. This individual is from a group that shares a common origin with Neanderthals. This population was not involved in the putative gene flow from Neanderthals into Eurasians; however, the data suggest that it contributed 4–6% of its genetic material to the genomes of present-day Melanesians. We designate this hominin population ‘Denisovans’ and suggest that it may have been widespread in Asia during the Late Pleistocene epoch. A tooth found in Denisova Cave carries a mitochondrial genome highly similar to that of the finger bone. This tooth shares no derived morphological features with Neanderthals or modern humans, further indicating that Denisovans have an evolutionary history distinct from Neanderthals and modern humans.
doi:10.1038/nature09710
PMCID: PMC4306417  PMID: 21179161
21.  Dietary Flavonoids Modulate CYP2C to Improve Drug Oral Bioavailability and Their Qualitative/Quantitative Structure–Activity Relationship 
The AAPS Journal  2014;16(2):258-268.
This study aims to improve the drug oral bioavailability by co-administration with flavonoid inhibitors of the CYP2C isozyme and to establish qualitative and quantitative (QSAR) structure–activity relationships (SAR) between flavonoids and CYP2C. A total of 40 naturally occurring flavonoids were screened in vitro for CYP2C inhibition. Enzyme activity was determined by measuring conversion of tolbutamide to 4-hydroxytolbutamide by rat liver microsomes. The percent inhibition and IC50 of each flavonoid were calculated and used to develop SAR and QSAR. The most effective flavonoid was orally co-administered in vivo with a cholesterol-reducing drug, fluvastatin, which is normally metabolized by CYP2C. The most potent CYP2C inhibitor identified in vitro was tamarixetin (IC50 = 1.4 μM). This flavonoid enhanced the oral bioavailability of fluvastatin in vivo, producing a >2-fold increase in the area under the concentration–time curve and in the peak plasma concentration. SAR analysis indicated that the presence of a 2,3-double bond in the C ring, hydroxylation at positions 5, 6, and 7, and glycosylation had important effects on flavonoid–CYP2C interactions. These findings should prove useful for predicting the inhibition of CYP2C activity by other untested flavonoid-like compounds. In the present study, tamarixetin significantly inhibited CYP2C activity in vitro and in vivo. Thus, the use of tamarixetin could improve the therapeutic efficacy of drugs with low bioavailability.
doi:10.1208/s12248-013-9549-4
PMCID: PMC3933575  PMID: 24431079
bioavailability; CYP2C; flavonoid; structure–activity relationship; tamarixetin
22.  Dosimetric benefits of robust treatment planning for intensity modulated proton therapy for base-of-skull cancers 
Practical radiation oncology  2014;4(6):384-391.
Purpose
The clinical advantage of intensity modulated proton therapy (IMPT) may be diminished by range and patient setup uncertainties. We evaluated the effectiveness of robust optimization that incorporates uncertainties into the treatment planning optimization algorithm for treatment of base of skull cancers.
Methods and materials
We compared 2 IMPT planning methods for 10 patients with base of skull chordomas and chondrosarcomas: (1) conventional optimization, in which uncertainties are dealt with by creating a planning target volume (PTV); and (2) robust optimization, in which uncertainties are dealt with by optimizing individual spot weights without a PTV. We calculated root-mean-square deviation doses (RMSDs) for every voxel to generate RMSD volume histograms (RVHs). The area under the RVH curve was used for relative comparison of the 2 methods’ plan robustness. Potential benefits of robust planning, in terms of target dose coverage and homogeneity and sparing of organs at risk (OARs) were evaluated using established clinical metrics. Then the plan evaluation metrics were averaged and compared with 2-sided paired t tests. The impact of tumor volume on the effectiveness of robust optimization was also analyzed.
Results
Relative to conventionally optimized plans, robustly optimized plans were less sensitive for both targets and OARs. In the nominal scenario, robust and conventional optimization resulted in similar D95% doses (D95% clinical target volume [CTV]: 63.3 and 64.8 Gy relative biologic effectiveness [RBE]), P <.01]) and D5%-D95% (D5%-D95% CTV: 8.0 and 7.1 Gy[RBE], [P < .01); irradiation of OARs was less with robust optimization (brainstem V60: 0.076 vs 0.26 cm3 [P <.01], left temporal lobe V70: 0.22 vs 0.41 cm3, [P = .068], right temporal lobe V70: 0.016 vs 0.11 cm3, [P = .096], left cochlea Dmean: 28.1 vs 30.1 Gy[RBE], [P = .023], right cochlea Dmean: 23.7 vs 25.2 Gy [RBE], [P = .059]). Results in the worst-case scenario were analogous.
Conclusions
Robust optimization is effective for creating clinically feasible IMPT plans for tumors of the base of skull.
doi:10.1016/j.prro.2013.12.001
PMCID: PMC4238033  PMID: 25407859
23.  Draft Genome Sequence of the Cellulolytic Bacterium Clavibacter sp. CF11, a Strain Producing Cold-Active Cellulase 
Genome Announcements  2015;3(1):e01304-14.
Clavibacter sp. strain CF11, which was isolated from soil at a tomato-planting greenhouse in Inner Mongolia, North China, has a high capability for producing cold-active cellulase at low temperatures. Here, we report the draft genome sequence of strain CF11, which comprises 2,437 protein-coding sequences and 49 RNA-coding sequences.
doi:10.1128/genomeA.01304-14
PMCID: PMC4293624  PMID: 25555737
24.  Effects of rapamycin against paraquat-induced pulmonary fibrosis in mice*  
Background and aims: Ingestion of paraquat (PQ), a widely used herbicide, can cause severe toxicity in humans, leading to a poor survival rate and prognosis. One of the main causes of death by PQ is PQ-induced pulmonary fibrosis, for which there are no effective therapies. The aim of this study was to evaluate the effects of rapamycin (RAPA) on inhibiting PQ-induced pulmonary fibrosis in mice and to explore its possible mechanisms. Methods: Male C57BL/6J mice were exposed to either saline (control group) or PQ (10 mg/kg body weight, intraperitoneally; test group). The test group was divided into four subgroups: a PQ group (PQ-exposed, non-treated), a PQ+RAPA group (PQ-exposed, treated with RAPA at 1 mg/kg intragastrically), a PQ+MP group (PQ-exposed, treated with methylprednisolone (MP) at 30 mg/kg intraperitoneally), and a PQ+MP+RAPA group (PQ-exposed, treated with MP at 30 mg/kg intraperitoneally and with RAPA at 1 mg/kg intragastrically). The survival rate and body weight of all the mice were recorded every day. Three mice in each group were sacrificed at 14 d and the rest at 28 d after intoxication. Lung tissues were excised and stained with hematoxylin-eosin (H&E) and Masson’s trichrome stain for histopathological analysis. The hydroxyproline (HYP) content in lung tissues was detected using an enzyme-linked immunosorbent assay (ELISA) kit. The expression of transforming growth factor-β1 (TGF-β1) and α-smooth muscle actin (α-SMA) in lung tissues was detected by immunohistochemical staining and Western blotting. Results: A mice model of PQ-induced pulmonary fibrosis was established. Histological examination of lung tissues showed that RAPA treatment moderated the pathological changes of pulmonary fibrosis, including alveolar collapse and interstitial collagen deposition. HYP content in lung tissues increased soon after PQ intoxication but had decreased significantly by the 28th day after RAPA treatment. Immunohistochemical staining and Western blotting showed that RAPA treatment significantly down-regulated the enhanced levels of TGF-β1 and α-SMA in lung tissues caused by PQ exposure. However, RAPA treatment alone could not significantly ameliorate the lower survival rate and weight loss of treated mice. MP treatment enhanced the survival rate, but had no significant effects on attenuating PQ-induced pulmonary fibrosis or reducing the expression of TGF-β1 and α-SMA. Conclusions: This study demonstrates that RAPA treatment effectively suppresses PQ-induced alveolar collapse and collagen deposition in lung tissues through reducing the expression of TGF-β1 and α-SMA. Thus, RAPA has potential value in the treatment of PQ-induced pulmonary fibrosis.
doi:10.1631/jzus.B1400229
PMCID: PMC4288945  PMID: 25559956
Paraquat; Pulmonary fibrosis; Rapamycin; Transforming growth factor-β1; α-Smooth muscle actin; Methylprednisolone
25.  Ionizing Radiation Impairs T Cell Activation by Affecting Metabolic Reprogramming 
Ionizing radiation has a variety of acute and long-lasting adverse effects on the immune system. Whereas measureable effects of radiation on immune cell cytotoxicity and population change have been well studied in human and animal models, little is known about the functional alterations of the surviving immune cells after ionizing radiation. The objective of this study was to delineate the effects of radiation on T cell function by studying the alterations of T cell receptor activation and metabolic changes in activated T cells isolated from previously irradiated animals. Using a global metabolomics profiling approach, for the first time we demonstrate that ionizing radiation impairs metabolic reprogramming of T cell activation, which leads to substantial decreases in the efficiency of key metabolic processes required for activation, such as glucose uptake, glycolysis, and energy metabolism. In-depth understanding of how radiation impacts T cell function highlighting modulation of metabolism during activation is not only a novel approach to investigate the pivotal processes in the shift of T cell homeostasis after radiation, it also may lead to new targets for therapeutic manipulation in the combination of radiotherapy and immune therapy. Given that appreciable effects were observed with as low as 10 cGy, our results also have implications for low dose environmental exposures.
doi:10.7150/ijbs.12009
PMCID: PMC4466454  PMID: 26078715
metabolic reprogramming; metabolomics; mass spectrometry; UPLC-QTOF; ionizing radiation; TCR activation

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