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1.  Inhibition of IAPP aggregation by insulin depends on the insulin oligomeric state regulated by zinc ion concentration 
Scientific Reports  2015;5:8240.
While islet amyloid polypeptide (IAPP) aggregation is associated with β-cell death in type-II diabetes (T2D), environmental elements of β-cell granules — e.g. high concentrations of insulin and Zn2+ — inhibit IAPP aggregation in healthy individuals. The inhibition by insulin is experimentally known, but the role of Zn2+ is controversial as both correlations and anti-correlations at the population level are observed between T2D risk and the activity of a β-cell specific zinc ion transporter, ZnT8. Since Zn2+ concentration determines insulin oligomer equilibrium, we computationally investigated interactions of IAPP with different insulin oligomers and compared with IAPP homodimer formation. We found that IAPP binding with insulin oligomers competes with the formation of both higher-molecular-weight insulin oligomers and IAPP homodimers. Therefore, zinc deficiency due to loss-of-function ZnT8 mutations shifts insulin oligomer equilibrium toward zinc-free monomers and dimers, which bind IAPP monomers more efficiently compared to zinc-bound hexamers. The hetero-molecular complex formation prevents IAPP from self-association and subsequent aggregation, reducing T2D risk.
doi:10.1038/srep08240
PMCID: PMC4316164  PMID: 25649462
2.  Long-Term Treatment of Clonidine, Atenolol, Amlodipine and Dihydrochlorothiazide, but Not Enalapril, Impairs the Sexual Function in Male Spontaneously Hypertensive Rats 
PLoS ONE  2015;10(1):e0116155.
This study was designed to investigate the impact of representative antihypertensive drugs of 5 classes on the sexual function in male spontaneously hypertensive rats (SHR) at doses that achieved similar blood pressure (BP) reduction. The experiment was performed in 6 groups of male SHR. The dose are 20 μg/kg/day for clonidine, 3 mg/kg/day for enalapril, 20 mg/kg/day for atenolol, 2 mg/kg/day for amlodipine, and 10 mg/kg/day for dihydrochlorothiazide. SHR were treated for 3 months, and then the penile erection and sexual behavior were detected. After BP recording, SHR were killed to evaluate the organ-damage, weight of accessory sex organs and levels of follicle-stimulating hormone (FSH), luteinizing hormone (LH) and testosterone in serum. Five drugs had the similar efficacy on BP reduction. All drugs except of enalapril, significantly prolonged the mount latency, and decreased the mount frequency (P<0.05). Clonidine also reduced the conception rate (45% vs. 80% in control group, P<0.05). Amlodipine and dihydrochlorothiazide significantly increased the testosterone level (0.79±0.30, 0.80±0.34 vs. 0.49±0.20 in control group, unit: ng/dl, P<0.05). Enalapril, atenolol and amlodipine also significantly decreased the BP variability (systolic, 8.2±2.5, 7.6±1.8, 8.9±2.0 vs. 12.2±3.8 in control group, unit: mm Hg). All these drugs significantly decreased the organ-damage (P<0.05). In conclusion, long-term treatment with 5 common antihypertensive drugs possessed obvious organ protection in SHR. Clonidine, atenolol, amlodipine and dihydrochlorothiazide, but not enalapril, impair sexual function.
doi:10.1371/journal.pone.0116155
PMCID: PMC4304790  PMID: 25615941
3.  Formation of Graphene Grain Boundaries on Cu(100) Surface and a Route Towards Their Elimination in Chemical Vapor Deposition Growth 
Scientific Reports  2014;4:6541.
Grain boundaries (GBs) in graphene prepared by chemical vapor deposition (CVD) greatly degrade the electrical and mechanical properties of graphene and thus hinder the applications of graphene in electronic devices. The seamless stitching of graphene flakes can avoid GBs, wherein the identical orientation of graphene domain is required. In this letter, the graphene orientation on one of the most used catalyst surface — Cu(100) surface, is explored by density functional theory (DFT) calculations. Our calculation demonstrates that a zigzag edged hexagonal graphene domain on a Cu(100) surface has two equivalent energetically preferred orientations, which are 30 degree away from each other. Therefore, the fusion of graphene domains on Cu(100) surface during CVD growth will inevitably lead to densely distributed GBs in the synthesized graphene. Aiming to solve this problem, a simple route, that applies external strain to break the symmetry of the Cu(100) surface, was proposed and proved efficient.
doi:10.1038/srep06541
PMCID: PMC4187007  PMID: 25286970
4.  Direct observation of a single nanoparticle-ubiquitin corona formation 
Nanoscale  2013;5(19):9162-9169.
The advancement of nanomedicine and the increasing applications of nanoparticles in consumer products have led to administered biological exposure and unintentional environmental accumulation of nanoparticles, causing concerns over the biocompatibility and sustainability of nanotechnology. Upon entering physiological environments, nanoparticles readily assume the form of a nanoparticle-protein corona that dictates their biological identity. Consequently, understanding the structure and dynamics of nanoparticle-protein corona is essential for predicting the fate, transport, and toxicity of nanomaterials in living systems and for enabling the vast applications of nanomedicine. Here we combined multiscale molecular dynamics simulations and complementary experiments to characterize the silver nanoparticle-ubiquitin corona formation. Notably, ubiquitins competed with citrates for the nanoparticle surface, governed by specific electrostatic interactions. Under a high protein/nanoparticle stoichiometry, ubiquitins formed a multi-layer corona on the particle surface. The binding exhibited an unusual stretched-exponential behavior, suggesting a rich binding kinetics. Furthermore, the binding destabilized the α-helices while increasing the β-sheets of the proteins. This study revealed the atomic and molecular details of the structural and dynamic characteristics of nanoparticle-protein corona formation.
doi:10.1039/c3nr02147e
PMCID: PMC4037870  PMID: 23921560
5.  Predicting binding affinity of CSAR ligands using both structure-based and ligand-based approaches 
We report on the prediction accuracy of ligand-based (2D QSAR) and structure-based (MedusaDock) methods used both independently and in consensus for ranking the congeneric series of ligands binding to three protein targets (UK, ERK2, and CHK1) from the CSAR 2011 benchmark exercise. An ensemble of predictive QSAR models was developed using known binders of these three targets extracted from the publicly-available ChEMBL database. Selected models were used to predict the binding affinity of CSAR compounds towards the corresponding targets and rank them accordingly; the overall ranking accuracy evaluated by Spearman correlation was as high as 0.78 for UK, 0.60 for ERK2, and 0.56 for CHK1, placing our predictions in top-10% among all the participants. In parallel, MedusaDock designed to predict reliable docking poses was also used for ranking the CSAR ligands according to their docking scores; the resulting accuracy (Spearman correlation) for UK, ERK2, and CHK1 were 0.76, 0.31, and 0.26, respectively. In addition, performance of several consensus approaches combining MedusaDock and QSAR predicted ranks altogether has been explored; the best approach yielded Spearman correlation coefficients for UK, ERK2, and CHK1 of 0.82, 0.50, and 0.45, respectively. This study shows that (i) externally validated 2D QSAR models were capable of ranking CSAR ligands at least as accurately as more computationally intensive structure-based approaches used both by us and by other groups and (ii) ligand-based QSAR models can complement structure-based approaches by boosting the prediction performances when used in consensus.
doi:10.1021/ci400216q
PMCID: PMC3779696  PMID: 23809015
6.  Genetics of rheumatoid arthritis contributes to biology and drug discovery 
Okada, Yukinori | Wu, Di | Trynka, Gosia | Raj, Towfique | Terao, Chikashi | Ikari, Katsunori | Kochi, Yuta | Ohmura, Koichiro | Suzuki, Akari | Yoshida, Shinji | Graham, Robert R. | Manoharan, Arun | Ortmann, Ward | Bhangale, Tushar | Denny, Joshua C. | Carroll, Robert J. | Eyler, Anne E. | Greenberg, Jeffrey D. | Kremer, Joel M. | Pappas, Dimitrios A. | Jiang, Lei | Yin, Jian | Ye, Lingying | Su, Ding-Feng | Yang, Jian | Xie, Gang | Keystone, Ed | Westra, Harm-Jan | Esko, Tõnu | Metspalu, Andres | Zhou, Xuezhong | Gupta, Namrata | Mirel, Daniel | Stahl, Eli A. | Diogo, Dorothée | Cui, Jing | Liao, Katherine | Guo, Michael H. | Myouzen, Keiko | Kawaguchi, Takahisa | Coenen, Marieke J.H. | van Riel, Piet L.C.M. | van de Laar, Mart A.F.J. | Guchelaar, Henk-Jan | Huizinga, Tom W.J. | Dieudé, Philippe | Mariette, Xavier | Bridges, S. Louis | Zhernakova, Alexandra | Toes, Rene E.M. | Tak, Paul P. | Miceli-Richard, Corinne | Bang, So-Young | Lee, Hye-Soon | Martin, Javier | Gonzalez-Gay, Miguel A. | Rodriguez-Rodriguez, Luis | Rantapää-Dahlqvist, Solbritt | Ärlestig, Lisbeth | Choi, Hyon K. | Kamatani, Yoichiro | Galan, Pilar | Lathrop, Mark | Eyre, Steve | Bowes, John | Barton, Anne | de Vries, Niek | Moreland, Larry W. | Criswell, Lindsey A. | Karlson, Elizabeth W. | Taniguchi, Atsuo | Yamada, Ryo | Kubo, Michiaki | Liu, Jun S. | Bae, Sang-Cheol | Worthington, Jane | Padyukov, Leonid | Klareskog, Lars | Gregersen, Peter K. | Raychaudhuri, Soumya | Stranger, Barbara E. | De Jager, Philip L. | Franke, Lude | Visscher, Peter M. | Brown, Matthew A. | Yamanaka, Hisashi | Mimori, Tsuneyo | Takahashi, Atsushi | Xu, Huji | Behrens, Timothy W. | Siminovitch, Katherine A. | Momohara, Shigeki | Matsuda, Fumihiko | Yamamoto, Kazuhiko | Plenge, Robert M.
Nature  2013;506(7488):376-381.
A major challenge in human genetics is to devise a systematic strategy to integrate disease-associated variants with diverse genomic and biological datasets to provide insight into disease pathogenesis and guide drug discovery for complex traits such as rheumatoid arthritis (RA)1. Here, we performed a genome-wide association study (GWAS) meta-analysis in a total of >100,000 subjects of European and Asian ancestries (29,880 RA cases and 73,758 controls), by evaluating ~10 million single nucleotide polymorphisms (SNPs). We discovered 42 novel RA risk loci at a genome-wide level of significance, bringing the total to 1012–4. We devised an in-silico pipeline using established bioinformatics methods based on functional annotation5, cis-acting expression quantitative trait loci (cis-eQTL)6, and pathway analyses7–9 – as well as novel methods based on genetic overlap with human primary immunodeficiency (PID), hematological cancer somatic mutations and knock-out mouse phenotypes – to identify 98 biological candidate genes at these 101 risk loci. We demonstrate that these genes are the targets of approved therapies for RA, and further suggest that drugs approved for other indications may be repurposed for the treatment of RA. Together, this comprehensive genetic study sheds light on fundamental genes, pathways and cell types that contribute to RA pathogenesis, and provides empirical evidence that the genetics of RA can provide important information for drug discovery.
doi:10.1038/nature12873
PMCID: PMC3944098  PMID: 24390342
7.  Rhesus monkey is a new model of secondary lymphedema in the upper limb 
Objective: This study is to establish the rhesus monkey model of lymphedema in the upper limbs, and assess the suitability of this model. Methods: An animal model of lymphedema was established by the combined irradiation and surgical techniques in the upper limbs of these rhesus monkeys. Physical examination, high-resolution MR lymphangiography, bioelectrical impedance analysis (BIA), and immunohistochemical staining were performed to determine the severity of the edema in the upper limbs of the animal model. Results: Our results from physical examination indicated that the rhesus monkey model present with typical appearance and features of lymphedema. MR lymphangiography further demonstrated pathologically modified lymphatic vessels in our rhesus monkey model. BIA revealed increased water content in the upper limb in these rhesus monkeys, which was in line with the pathology of lymphedema. Immunohistochemical staining showed the curvature of the lymphatic vessels in the rhesus monkey model, typical pathological changes in lymphedema. Conclusion: Rhesus monkey lymphedema model provides a more consistent background to elucidate the pathophysiology of the disease. This new model would help to increase our understanding of acquired upper limb lymphedema, and promote the development of new treatments for this intractable disorder.
PMCID: PMC4203178  PMID: 25337207
Secondary lymphedema; rhesus monkeys; upper extremity; breast cancer; animal model
8.  Protein Kinase D3 Is Essential for Prostratin-Activated Transcription of Integrated HIV-1 Provirus Promoter via NF-κB Signaling Pathway 
BioMed Research International  2014;2014:968027.
Prostratin has been proposed as a promising reagent for eradicating the latent HIV-1 provirus by inducing HIV-1 transcription activation. The molecular mechanism of this activation, however, is far from clear. Here, we show that the protein kinase D3 (PKD3) is essential for prostratin-induced transcription activation of latent HIV-1 provirus. First, silencing PKD3, but not the other members of PKD family, blocked prostratin-induced transcription of HIV-1. Second, overexpressing the constitutively active form of PKD3, but not the wild-type or kinase-dead form of PKD3, augmented the expression of HIV-1. Consistent with this observation, we found that prostratin could trigger PKD3 activation by inducing the phosphorylation of its activation loop. In addition, we identified PKCε of the novel PKC subfamily as the upstream kinase for this phosphorylation. Finally, the activation effect of PKD3 on HIV-1 transcription was shown to depend on the presence of κB element and the prostratin-induced activation of NF-κB, as indicated by the fact that silencing PKD3 blocked prostratin-induced NF-κB activation and NF-κB-dependent HIV-1 transcription. Therefore, for the first time, PKD3 is implicated in the transcription activation of latent HIV-1 provirus, and our results revealed a molecular mechanism of prostratin-induced HIV-1 transcription via PKCε/PKD3/NF-κB signaling pathway.
doi:10.1155/2014/968027
PMCID: PMC4127265  PMID: 25136641
9.  Genome-wide analysis of alternative splicing of pre-mRNA under salt stress in Arabidopsis 
BMC Genomics  2014;15(1):431.
Background
Alternative splicing (AS) of precursor mRNA (pre-mRNA) is an important gene regulation process that potentially regulates many physiological processes in plants, including the response to abiotic stresses such as salt stress.
Results
To analyze global changes in AS under salt stress, we obtained high-coverage (~200 times) RNA sequencing data from Arabidopsis thaliana seedlings that were treated with different concentrations of NaCl. We detected that ~49% of all intron-containing genes were alternatively spliced under salt stress, 10% of which experienced significant differential alternative splicing (DAS). Furthermore, AS increased significantly under salt stress compared with under unstressed conditions. We demonstrated that most DAS genes were not differentially regulated by salt stress, suggesting that AS may represent an independent layer of gene regulation in response to stress. Our analysis of functional categories suggested that DAS genes were associated with specific functional pathways, such as the pathways for the responses to stresses and RNA splicing. We revealed that serine/arginine-rich (SR) splicing factors were frequently and specifically regulated in AS under salt stresses, suggesting a complex loop in AS regulation for stress adaptation. We also showed that alternative splicing site selection (SS) occurred most frequently at 4 nucleotides upstream or downstream of the dominant sites and that exon skipping tended to link with alternative SS.
Conclusions
Our study provided a comprehensive view of AS under salt stress and revealed novel insights into the potential roles of AS in plant response to salt stress.
Electronic supplementary material
The online version of this article (doi:10.1186/1471-2164-15-431) contains supplementary material, which is available to authorized users.
doi:10.1186/1471-2164-15-431
PMCID: PMC4079960  PMID: 24897929
Alternative splicing; Pre-mRNA; SR proteins; Salt stress; Arabidopsis thaliana
10.  Involvement of arterial baroreflex in the protective effect of dietary restriction against stroke 
Dietary restriction (DR) protects against neuronal dysfunction and degeneration, and reduces the risk of ischemic stroke. This study examined the role of silent information regulator T1 (SIRT1) and arterial baroreflex in the beneficial effects of DR against stroke, using two distinct stroke models: stroke-prone spontaneously hypertensive rats (SP-SHRs) and Sprague-Dawley (SD) rats with middle cerebral artery occlusion (MCAO). Sirt1 knockout (KO) mice were used to examine the involvement of sirt1. Sinoaortic denervation was used to inactivate arterial baroreflex. Dietary restriction was defined as 40% reduction of dietary intake. Briefly, DR prolonged the life span of SP-SHRs and reduced the infarct size induced by MCAO. Dietary restriction also improved the function arterial baroreflex, decreased the release of proinflammatory cytokines, and reduced end-organ damage. The beneficial effect of DR on stroke was markedly attenuated by blunting arterial baroreflex. Lastly, the infarct area in sirt1 KO mice was significantly larger than in the wild-type mice. However, the beneficial effect of DR against ischemic injury was still apparent in sirt1 KO mice. Accordingly, arterial baroreflex, but not sirt1, is important in the protective effect of DR against stroke.
doi:10.1038/jcbfm.2013.28
PMCID: PMC3677110  PMID: 23443169
arterial baroreflex; dietary restriction; sirt1; stroke
11.  Arterial Baroreflex Dysfunction Impairs Ischemia‐Induced Angiogenesis 
Background
Endothelium‐derived acetylcholine (eACh) plays an important role in the regulation of vascular actions in response to hypoxia, whereas arterial baroreflex (ABR) dysfunction impairs the eACh system. We investigated the effects of ABR dysfunction on ischemia‐induced angiogenesis in animal models of hindlimb ischemia with a special focus on eACh/nicotinic ACh receptor (nAChR) signaling activation.
Methods and Results
Male Sprague‐Dawley rats were randomly assigned to 1 of 3 groups that received (1) sham operation (control group), (2) sinoaortic denervation (SAD)‐induced ABR dysfunction (SAD group), or (3) SAD rats on diet with an acetylcholinesterase inhibitor pyridostigmine (30 mg/kg per day, SAD+Pyr group). After 4 weeks of the SAD intervention, unilateral limb ischemia was surgically induced in all animals. At postoperative day 14, SAD rats exhibited impaired angiogenic action (skin temperature and capillary density) and decreased angiogenic factor expressions (vascular endothelial growth factor [VEGF] and hypoxic inducible factor [HIF]‐1α) in ischemic muscles. These changes were restored by acetylcholinesterase inhibition. Rats with ABR dysfunction had lower eACh levels than did control rats, and this effect was recovered in SAD+Pyr rats. In α7‐nAChR knockout mice, pyridostigmine improved ischemia‐induced angiogenic responses and increased the levels of VEGF and HIF‐1α. Moreover, nicotinic receptor blocker inhibited VEGF expression and VEGF receptor 2 phosphorylation (p‐VEGFR2) induced by ACh analog.
Conclusions
Thus, ABR dysfunction appears to impair ischemia‐induced angiogenesis through the reduction of eACh/α7‐nAChR‐dependent and ‐independent HIF‐1α/VEGF‐VEGFR2 signaling activation.
doi:10.1161/JAHA.114.000804
PMCID: PMC4309071  PMID: 24820655
acetylcholinesterase inhibitor; angiogenesis; arterial baroreflex; non‐neural cholinergic system; peripheral vascular disease
12.  De Novo Characterization of the Spleen Transcriptome of the Large Yellow Croaker (Pseudosciaena crocea) and Analysis of the Immune Relevant Genes and Pathways Involved in the Antiviral Response 
PLoS ONE  2014;9(5):e97471.
The large yellow croaker (Pseudosciaena crocea) is an economically important marine fish in China. To understand the molecular basis for antiviral defense in this species, we used Illumia paired-end sequencing to characterize the spleen transcriptome of polyriboinosinic:polyribocytidylic acid [poly(I:C)]-induced large yellow croakers. The library produced 56,355,728 reads and assembled into 108,237 contigs. As a result, 15,192 unigenes were found from this transcriptome. Gene ontology analysis showed that 4,759 genes were involved in three major functional categories: biological process, cellular component, and molecular function. We further ascertained that numerous consensus sequences were homologous to known immune-relevant genes. Kyoto Encyclopedia of Genes and Genomes orthology mapping annotated 5,389 unigenes and identified numerous immune-relevant pathways. These immune-relevant genes and pathways revealed major antiviral immunity effectors, including but not limited to: pattern recognition receptors, adaptors and signal transducers, the interferons and interferon-stimulated genes, inflammatory cytokines and receptors, complement components, and B-cell and T-cell antigen activation molecules. Moreover, the partial genes of Toll-like receptor signaling pathway, RIG-I-like receptors signaling pathway, Janus kinase-Signal Transducer and Activator of Transcription (JAK-STAT) signaling pathway, and T-cell receptor (TCR) signaling pathway were found to be changed after poly(I:C) induction by real-time polymerase chain reaction (PCR) analysis, suggesting that these signaling pathways may be regulated by poly(I:C), a viral mimic. Overall, the antivirus-related genes and signaling pathways that were identified in response to poly(I:C) challenge provide valuable leads for further investigation of the antiviral defense mechanism in the large yellow croaker.
doi:10.1371/journal.pone.0097471
PMCID: PMC4018400  PMID: 24820969
13.  hSulf-1 inhibits cell proliferation and migration and promotes apoptosis by suppressing stat3 signaling in hepatocellular carcinoma 
Oncology Letters  2014;7(4):963-969.
Human sulfatase-1 (hSulf-1) has been shown to desulfate cellular heparin sulfate proteoglycans and modulate several growth factors and cytokines. However, hSulf-1 has not been previously shown to mediate the signal transducer and activator of transcription 3 (stat3) signaling pathway, which is known to regulate cell proliferation, motility and apoptosis. The present study investigated the role of hSulf-1 in stat3 signaling in hepatocellular cancer. hSulf-1 expression vector and stat3 small interfering RNA (siRNA) were constructed to control the expression of hSulf-1 and stat3 in HepG2 cells. hSulf-1 was found to inhibit the phosphorylation of stat3 and downregulate its targeted protein. MTT and Transwell chamber assays, as well as Annexin V/propidium iodide double-staining methods, were used to examine the effects of hSulf-1 on stat3-mediated motility, proliferation and apoptosis in HepG2 cells. Transfection with hSulf-1 cDNA and/or stat3 siRNA inhibited cell proliferation and motility, concurrent with G0/G1 and G2/M phase cell cycle arrest and apoptosis. Overall, the results of the current study suggested that hSulf-1 functions as a negative regulator of proliferation and migration and as a positive regulator of apoptosis in hepatocellular carcinoma, at least partly via the downregulation of stat3 signaling.
doi:10.3892/ol.2014.1848
PMCID: PMC3961425  PMID: 24944651
human sulfatase-1; hepatocellular carcinoma; stat3 signaling
14.  Statistical analysis of SHAPE-directed RNA secondary structure modeling 
Biochemistry  2013;52(4):596-599.
The ability to predict RNA secondary structure is fundamental for understanding and manipulating RNA function. The structural information obtained from selective 2'-hydroxyl acylation analyzed by primer extension (SHAPE) experiments greatly improves the accuracy of RNA secondary structure prediction. Recently, Das and colleagues [Kladwang et al., Biochemistry 50:8049 (2011)] proposed a “bootstrapping” approach to estimate the variance and helix-by-helix confidence levels of predicted secondary structures based on resampling (randomizing and summing) the measured SHAPE data. We show that the specific resampling approach described by Kladwang et al. introduces systematic errors and underestimates confidence in secondary structure prediction using SHAPE data. Instead, a leave-data-out jackknife approach better estimates the influence of a given experimental dataset on SHAPE-directed secondary structure modeling. Even when 35% of the data were left out in the jackknife approach, the confidence levels of SHAPE-directed secondary structure prediction were significantly higher than those calculated by Das and colleagues using bootstrapping. Helix confidence levels were thus significantly underestimated in the recent study, and resampling approach implemented by Kladwang et al. is not an appropriate metric for assigning confidences in SHAPE-directed secondary structure modeling.
doi:10.1021/bi300756s
PMCID: PMC3558531  PMID: 23286327
15.  Biobutanol production in a Clostridium acetobutylicum biofilm reactor integrated with simultaneous product recovery by adsorption 
Background
Clostridium acetobutylicum can propagate on fibrous matrices and form biofilms that have improved butanol tolerance and a high fermentation rate and can be repeatedly used. Previously, a novel macroporous resin, KA-I, was synthesized in our laboratory and was demonstrated to be a good adsorbent with high selectivity and capacity for butanol recovery from a model solution. Based on these results, we aimed to develop a process integrating a biofilm reactor with simultaneous product recovery using the KA-I resin to maximize the production efficiency of biobutanol.
Results
KA-I showed great affinity for butanol and butyrate and could selectively enhance acetoin production at the expense of acetone during the fermentation. The biofilm reactor exhibited high productivity with considerably low broth turbidity during repeated batch fermentations. By maintaining the butanol level above 6.5 g/L in the biofilm reactor, butyrate adsorption by the KA-I resin was effectively reduced. Co-adsorption of acetone by the resin improved the fermentation performance. By redox modulation with methyl viologen (MV), the butanol-acetone ratio and the total product yield increased. An equivalent solvent titer of 96.5 to 130.7 g/L was achieved with a productivity of 1.0 to 1.5 g · L-1 · h-1. The solvent concentration and productivity increased by 4 to 6-fold and 3 to 5-fold, respectively, compared to traditional batch fermentation using planktonic culture.
Conclusions
Compared to the conventional process, the integrated process dramatically improved the productivity and reduced the energy consumption as well as water usage in biobutanol production. While genetic engineering focuses on strain improvement to enhance butanol production, process development can fully exploit the productivity of a strain and maximize the production efficiency.
doi:10.1186/1754-6834-7-5
PMCID: PMC3891980  PMID: 24401161
Biofilm reactor; Clostridium acetobutylicum; Simultaneous product recovery; Acetoin; Adsorption; Redox modulation
16.  Dynamic regulation of genome-wide pre-mRNA splicing and stress tolerance by the Sm-like protein LSm5 in Arabidopsis 
Genome Biology  2014;15(1):R1.
Background
Sm-like proteins are highly conserved proteins that form the core of the U6 ribonucleoprotein and function in several mRNA metabolism processes, including pre-mRNA splicing. Despite their wide occurrence in all eukaryotes, little is known about the roles of Sm-like proteins in the regulation of splicing.
Results
Here, through comprehensive transcriptome analyses, we demonstrate that depletion of the Arabidopsis supersensitive to abscisic acid and drought 1 gene (SAD1), which encodes Sm-like protein 5 (LSm5), promotes an inaccurate selection of splice sites that leads to a genome-wide increase in alternative splicing. In contrast, overexpression of SAD1 strengthens the precision of splice-site recognition and globally inhibits alternative splicing. Further, SAD1 modulates the splicing of stress-responsive genes, particularly under salt-stress conditions. Finally, we find that overexpression of SAD1 in Arabidopsis improves salt tolerance in transgenic plants, which correlates with an increase in splicing accuracy and efficiency for stress-responsive genes.
Conclusions
We conclude that SAD1 dynamically controls splicing efficiency and splice-site recognition in Arabidopsis, and propose that this may contribute to SAD1-mediated stress tolerance through the metabolism of transcripts expressed from stress-responsive genes. Our study not only provides novel insights into the function of Sm-like proteins in splicing, but also uncovers new means to improve splicing efficiency and to enhance stress tolerance in a higher eukaryote.
doi:10.1186/gb-2014-15-1-r1
PMCID: PMC4053965  PMID: 24393432
17.  Ketanserin improves cardiac performance after myocardial infarction in spontaneously hypertensive rats partially through restoration of baroreflex function 
Acta Pharmacologica Sinica  2013;34(12):1508-1514.
Aim:
Baroreflex dysfunction is associated with a higher rate of sudden death after myocardial infarction (MI). Ketanserin enhances baroreflex function in rats. The present work was designed to examine whether ketanserin improves the post-MI cardiac function and to explore the possible mechanism involved.
Methods:
Spontaneously hypertensive rats (SHR) were treated with ketanserin (0.3 mg·kg−1·d−1). Two weeks later, blood pressure and baroreflex function were measured, followed by a ligation of the left coronary artery. The expressions of vesicular acetylcholine transporter (VAChT) and α7 nicotinic acetylcholine receptor (α7-nAChR) in ischemic myocardium, angiogenesis, cardiac function, and left ventricular (LV) remodeling were evaluated subsequently.
Results:
Ketanserin significantly improved baroreflex sensitivity (0.62±0.21 vs 0.34±0.12 ms/mmHg, P<0.01) and vagal tonic activity (heart rate changes in response to atropine, 54.8±16.2 vs 37.6±13.4 bpm, P<0.01) without affecting the blood pressure or basic heart rate in SHR. Treatment of SHR with ketanserin prominently improved cardiac function and alleviated LV remodeling, as reflected by increases in the ejection fraction, fractional shortening, and LV systolic pressure as well as decreases in LV internal diameter and LV relative weight. The capillary density, vascular endothelial growth factor expression, and blood flow in the ischemic myocardium were significantly higher in the ketanserin-treated group. In addition, ketanserin markedly increased the expression of VAChT and α7-nAChR in ischemic myocardium.
Conclusion:
Ketanserin improved post-MI cardiac function and angiogenesis in ischemic myocardium. The findings provide a mechanistic basis for restoring baroreflex function using ketanserin in the treatment of MI.
doi:10.1038/aps.2013.147
PMCID: PMC4002568  PMID: 24241347
ketanserin; myocardial infarction; baroreflex; angiogenesis; α7-nAChR
18.  Nitrotyrosine Level Was Associated with Mortality in Patients with Acute Kidney Injury 
PLoS ONE  2013;8(11):e79962.
Background
To examine the characteristics of oxidative stress in patients with acute kidney injury (AKI) and investigate the association between plasma nitrotyrosine levels and 90-day mortality in patients with AKI.
Methodology/Principal Findings
158 patients with hospital-acquired AKI were recruited to this prospective cohort study according to RIFLE (Risk, Injury, Failure, Lost or End Stage Kidney) criteria. Twelve critically ill patients without AKI and 15 age and gender-matched healthy subjects served as control. Plasma 3-nitrotyrosine was analyzed in relation to 90-day all cause mortality of patients with AKI. The patients with AKI were followed up for 90 days and grouped according to median plasma 3-nitrotyrosine concentrations. Highest 3-NT/Tyr was detected in patients with AKI compared with healthy subjects, and critically ill patients without AKI (ANOVA p<0.001). The 90-day survival curves of patients with high 3-NT/Tyr showed significant differences compared with the curves of individuals with low 3-NT/Tyr (p = 0.001 by log rank test). Multivariate analysis (Cox regression) revealed that 3-NT/Tyr (p = 0.025) was independently associated with mortality after adjustment for age, gender, sepsis and Acute Physiology and Chronic Health Evaluation (APACHE) II score.
Conclusions/Significance
There is excess plasma protein oxidation in patients with AKI, as evidenced by increased nitrotyrosine content. 3-NT/Tyr level was associated with mortality of AKI patients independent of the severity of illness.
doi:10.1371/journal.pone.0079962
PMCID: PMC3835782  PMID: 24278225
19.  Association of increased serum glycated albumin levels with low coronary collateralization in type 2 diabetic patients with stable angina and chronic total occlusion 
Background
We investigated whether serum glycated albumin (GA) levels are related to coronary collateralization in type 2 diabetic patients with chronic total occlusion.
Methods
Blood levels of GA and glycosylated hemoglobin (HbA1c) were determined in 317 diabetic and 117 non-diabetic patients with stable angina and angiographic total occlusion of at least one major coronary artery. The degree of collaterals supplying the distal aspect of a total occlusion from the contra-lateral vessel was graded as low (Rentrop score of 0 or 1) or high collateralization (Rentrop score of 2 or 3).
Results
For diabetic patients, GA (21.2 ± 6.5% vs. 18.7 ± 5.6%, P < 0.001) but not HbA1c levels (7.0 ± 1.1% vs. 6.8 ± 1.3%, P = 0.27) was significantly elevated in low collateralization than in high collateralization group, and correlated inversely with Rentrop score (Spearmen’s r = -0.28, P < 0.001; Spearmen’s r = -0.10, P = 0.09, respectively). There was a trend towards a larger area under the curve of GA compared with that of HbA1c for detecting the presence of low collateralization (0.64 vs. 0.58, P = 0.15). In non-diabetic patients, both GA and HbA1c levels did not significantly differ regardless the status of coronary collateralization. In multivariable analysis, female gender, age > 65 years, smoke, non-hypertension, duration of diabetes > 10 years, metabolic syndrome, eGFR < 90 ml/min/1.73 m2, and GA > 18.3% were independently determinants for low collateralization in diabetic patients.
Conclusions
Increased GA levels in serum are associated with impaired collateral growth in type 2 diabetic patients with stable angina and chronic total occlusion.
doi:10.1186/1475-2840-12-165
PMCID: PMC4225762  PMID: 24209601
Glycated albumin; Coronary collateralization; Diabetes
20.  MicroRNA-124 mediates the cholinergic anti-inflammatory action through inhibiting the production of pro-inflammatory cytokines 
Cell Research  2013;23(11):1270-1283.
The vagus nerve can control inflammatory response through a 'cholinergic anti-inflammatory pathway', which is mediated by the α7-nicotinic acetylcholine receptor (α7nAChR) on macrophages. However, the intracellular mechanisms that link α7nAChR activation and pro-inflammatory cytokine production remain not well understood. In this study, we found that miR-124 is upregulated by cholinergic agonists in LPS-exposed cells and mice. Utilizing miR-124 mimic and siRNA knockdown, we demonstrated that miR-124 is a critical mediator for the cholinergic anti-inflammatory action. Furthermore, our data indicated that miR-124 modulates LPS-induced cytokine production by targeting signal transducer and activator of transcription 3 (STAT3) to decrease IL-6 production and TNF-α converting enzyme (TACE) to reduce TNF-α release. These results also indicate that miR-124 is a potential therapeutic target for the treatment of inflammatory diseases.
doi:10.1038/cr.2013.116
PMCID: PMC3817544  PMID: 23979021
micorRNA-124; cholinergic anti-inflammatory action; α7nAChR; macrophages; septic shock; STAT3; TACE
21.  The positive correlations of apolipoprotein E with disease activity and related cytokines in systemic lupus erythematosus 
Diagnostic Pathology  2013;8:175.
Background
The aim of this study is to investigate the expression of apolipoprotein E (apoE) and the relationship between apoE and disease activity of SLE, and the possible effects of glucocorticoid on apoE and other cytokines activities in SLE patients.
Methods
Forty treatment-naïve SLE patients and forty matched healthy controls were studied. All the SLE patients received prednisone 1 mg/kg/day for 28 consecutive days. The sera levels of apoE and related cytokines were evaluated by ELISA. The expression of apoE mRNA in peripheral blood mononuclear cells (PBMCs) was determined by real-time PCR.
Results
Compared with healthy controls, the relative expression levels of ApoE proteins and sera levels were significantly up-regulated in active SLE patients. ApoE sera concentrations positively correlated with SLEDAI, anti-dsDNA antibody and the related cytokines including IL-6, IFN-γ and IL-10, and uncorrelated with the concentration of total cholesterol (TC) and triglyceride (TG) in SLE patients. After 4 weeks prednisone treatment, the relative mRNA expression of apoE and the serum levels of apoE and related cytokines decreased.
Conclusions
ApoE correlated with disease activity and related cytokines in SLE patients. Glucocorticoid can down-regulate the expressions of apoE and related cytokines.
Virtual slide
The virtual slide(s) for this article can be found here:http://www.diagnosticpathology.diagnomx.eu/vs/1646714011077325
doi:10.1186/1746-1596-8-175
PMCID: PMC4231472  PMID: 24144108
Systemic lupus erythematosus; Apolipoprotein E; Anti-inflammatory cytokine; SLEDAI
22.  Reversible Loss of Bernal Stacking during the Deformation of Few-Layer Graphene in Nanocomposites 
ACS Nano  2013;7(8):7287-7294.
The deformation of nanocomposites containing graphene flakes with different numbers of layers has been investigated with the use of Raman spectroscopy. It has been found that there is a shift of the 2D band to lower wavenumber and that the rate of band shift per unit strain tends to decrease as the number of graphene layers increases. It has been demonstrated that band broadening takes place during tensile deformation for mono- and bilayer graphene but that band narrowing occurs when the number of graphene layers is more than two. It is also found that the characteristic asymmetric shape of the 2D Raman band for the graphene with three or more layers changes to a symmetrical shape above about 0.4% strain and that it reverts to an asymmetric shape on unloading. This change in Raman band shape and width has been interpreted as being due to a reversible loss of Bernal stacking in the few-layer graphene during deformation. It has been shown that the elastic strain energy released from the unloading of the inner graphene layers in the few-layer material (∼0.2 meV/atom) is similar to the accepted value of the stacking fault energies of graphite and few layer graphene. It is further shown that this loss of Bernal stacking can be accommodated by the formation of arrays of partial dislocations and stacking faults on the basal plane. The effect of the reversible loss of Bernal stacking upon the electronic structure of few-layer graphene and the possibility of using it to modify the electronic structure of few-layer graphene are discussed.
doi:10.1021/nn402830f
PMCID: PMC3789269  PMID: 23899378
graphene; Bernal stacking; nanocomposites; Raman spectroscopy; deformation
23.  Manageable N-doped Graphene for High Performance Oxygen Reduction Reaction 
Scientific Reports  2013;3:2771.
Catalysts for oxygen reduction reaction (ORR) are at the heart of key green-energy fuel cell technology. N-doped graphene is a potential metal-free electrode with much better electrocatalytic activity, long-term stability, and tolerance to crossover effect than expensive platinum-based electrocatalysts. Here, we report a feasible direct-synthesis method in preparing N-graphene with manageable N contents in a large scale. The resultant N-graphene used as electrocatalysts exhibits similar catalytic activity but superior stability compared to commercial Pt/C for ORR in an alkaline solution. It was found that their electrocatalytic activities were demonstrated to depend largely on N-doping content. When nitrogen content reaches a high value at about 24–25%, ORR reaction exhibits a favorable formation of water via a four-electron pathway. Furthermore, the effect of pyrolysis temperature and precursor on the activity of N-graphene is systematically analyzed, and may shed some light on the principle of choosing appropriate way for preparing N-graphene.
doi:10.1038/srep02771
PMCID: PMC3783894  PMID: 24067782
24.  Exome sequencing identifies MXRA5 as a novel cancer gene frequently mutated in non–small cell lung carcinoma from Chinese patients 
Carcinogenesis  2012;33(9):1797-1805.
Lung cancer has become the top killer among malignant tumors in China and is significantly associated with somatic genetic alterations. We performed exome sequencing of 14 non–small cell lung carcinomas (NSCLCs) with matched adjacent normal lung tissues extracted from Chinese patients. In addition to the lung cancer–related genes (TP53, EGFR, KRAS, PIK3CA, and ROS1), this study revealed “novel” genes not previously implicated in NSCLC. Especially, matrix-remodeling associated 5 was the second most frequently mutated gene in NSCLC (first is TP53). Subsequent Sanger sequencing of matrix-remodeling associated 5 in an additional sample set consisting of 52 paired tumor-normal DNA samples revealed that 15% of Chinese NSCLCs contained somatic mutations in matrix-remodeling associated 5. These findings, together with the results from pathway analysis, strongly indicate that altered extracellular matrix-remodeling may be involved in the etiology of NSCLC.
doi:10.1093/carcin/bgs210
PMCID: PMC3514907  PMID: 22696596
25.  Local unfolding of Cu, Zn Superoxide Dismutase monomer determines the morphology of fibrillar aggregates 
Journal of Molecular Biology  2011;421(4-5):548-560.
Aggregation of Cu, Zn Superoxide Dismutase (SOD1) is often found in Amyotrophic Lateral Sclerosis (ALS) patients. The fibrillar aggregates formed by wildtype and various disease-associated mutants have recently been found to have distinct cores and morphologies. Previous computational and experimental studies of wildtype SOD1 suggest that the apo-monomer, highly aggregation-prone, displays substantial local unfolding dynamics. The residual folded structure of locally unfolded apoSOD1 corresponds to peptide segments forming the aggregation core as identified by a combination of proteolysis and mass spectroscopy. Therefore, we hypothesize that the destabilization of apoSOD1 caused by various mutations leads to distinct local unfolding dynamics. The partially unfolded structure, exposing the hydrophobic core and backbone hydrogen bond donors and acceptors, is prone to aggregate. The peptide segments in the residual folded structures form the “building block” for aggregation, which in turn determines the morphology of the aggregates. To test this hypothesis, we apply a multiscale simulation approach to study the aggregation of three typical SOD1 variants: wildtype, G37R, and I149T. Each of these SOD1 variants has distinct peptide segments forming the core structure and features different aggregate morphologies. We perform atomistic molecular dynamics simulations to study the conformational dynamics of apoSOD1 monomer, and coarse-grained molecular dynamics simulations to study the aggregation of partially unfolded SOD1 monomers. Our computational studies of monomer local unfolding and the aggregation of different SOD1 variants are consistent with experiments, supporting the hypothesis of the formation of aggregation “building blocks” via apo-monomer local unfolding as the mechanism of SOD1 fibrillar aggregation.
doi:10.1016/j.jmb.2011.12.029
PMCID: PMC3320695  PMID: 22210350
SOD1 misfolding and aggregation; fibrillar aggregate; aggregation building block; molecular dynamics; multiscale modeling

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