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1.  Predicting protein complex in protein interaction network - a supervised learning based method 
BMC Systems Biology  2014;8(Suppl 3):S4.
Background
Protein complexes are important for understanding principles of cellular organization and function. High-throughput experimental techniques have produced a large amount of protein interactions, making it possible to predict protein complexes from protein -protein interaction networks. However, most of current methods are unsupervised learning based methods which can't utilize the information of the large amount of available known complexes.
Methods
We present a supervised learning-based method for predicting protein complexes in protein - protein interaction networks. The method extracts rich features from both the unweighted and weighted networks to train a Regression model, which is then used for the cliques filtering, growth, and candidate complex filtering. The model utilizes additional "uncertainty" samples and, therefore, is more discriminative when used in the complex detection algorithm. In addition, our method uses the maximal cliques found by the Cliques algorithm as the initial cliques, which has been proven to be more effective than the method of expanding from the seeding proteins used in other methods.
Results
The experimental results on several PIN datasets show that in most cases the performance of our method are superior to comparable state-of-the-art protein complex detection techniques.
Conclusions
The results demonstrate the several advantages of our method over other state-of-the-art techniques. Firstly, our method is a supervised learning-based method that can make full use of the information of the available known complexes instead of being only based on the topological structure of the PIN. That also means, if more training samples are provided, our method can achieve better performance than those unsupervised methods. Secondly, we design the rich feature set to describe the properties of the known complexes, which includes not only the features from the unweighted network, but also those from the weighted network built based on the Gene Ontology information. Thirdly, our Regression model utilizes additional "uncertainty" samples and, therefore, becomes more discriminative, whose effectiveness for the complex detection is indicated by our experimental results.
doi:10.1186/1752-0509-8-S3-S4
PMCID: PMC4243764  PMID: 25349902
Protein-protein interaction network; Protein complexes; Gene Ontology; Supervised learning
2.  Identification of a Key Catalytic Intermediate Demonstrates that Nitrogenase is Activated by the Reversible Exchange of N2 for H2 
Freeze-quenching nitrogenase during turnover with N2 traps an S = ½ intermediate that was shown by ENDOR and EPR spectroscopy to contain N2 or a reduction product bound to the active-site molybdenum-iron cofactor (FeMo-co). To identify this intermediate (termed here EG), we turned to a quench-cryoannealing relaxation protocol. The trapped state is allowed to relax to the resting E0 state in frozen medium at a temperature below the melting temperature; relaxation is monitored by periodically cooling the sample to cryogenic temperature for EPR analysis. During −50°C cryoannealing of EG prepared under turnover conditions in which the concentrations of N2 and H2 ([H2], [N2]) are systematically and independently varied, the rate of decay of EG is accelerated by increasing [H2] and slowed by increasing [N2] in the frozen reaction mixture; correspondingly, the accumulation of EG is greater with low [H2] and/or high [N2]. The influence of these diatomics identifies EG as the key catalytic intermediate formed by reductive elimination (re) of H2 with concomitant N2 binding, a state in which FeMo-co binds the components of diazene (an N-N moiety, perhaps N2 and two [e−/H+] or diazene itself). This identification combines with an earlier study to demonstrate that nitrogenase is activated for N2 binding and reduction through the thermodynamically and kinetically reversible reductive-elimination/oxidative-addition exchange of N2 and H2, with an implied limiting stoichiometry of eight electrons/protons for the reduction of N2 to two NH3.
doi:10.1021/jacs.5b00103
PMCID: PMC4374740  PMID: 25741750
3.  Hierarchical TiO2 spheres as highly efficient polysulfide host for lithium-sulfur batteries 
Scientific Reports  2016;6:22990.
Hierarchical TiO2 micron spheres assembled by nano-plates were prepared through a facile hydrothermal route. Chemical tuning of the TiO2 through hydrogen reduction (H-TiO2) is shown to increase oxygen-vacancy density and thereby modifies the electronic properties. H-TiO2 spheres with a polar surface serve as the surface-bound intermediates for strong polysulfides binding. Under the restricting and recapturing effect, the sulfur cathode could deliver a high reversible capacity of 928.1 mA h g−1 after 50 charge-discharge cycles at a current density of 200 mA g−1. The H-TiO2 additive developed here is practical for restricting and recapturing the polysulfide from the electrolyte.
doi:10.1038/srep22990
PMCID: PMC4786857  PMID: 26965058
4.  The role of Card9 overexpression in peripheral blood mononuclear cells from patients with aseptic acute pancreatitis 
Abstract
Activated mononuclear cells are an early event in the course of severe acute pancreatitis (SAP). To date, the molecular mechanism triggering peripheral blood mononuclear cells (PBMCs) is poorly understood. The aim of this paper was to determine the potential role of Card9 in SAP. We collected data from 72 subjects between January 2013 and June 2014. Subsequently, PBMCs were isolated on day 1, 3 and 5 of pancreatitis. Immunofluorescence staining, quantitative real‐time PCR, Western blotting, immunoprecipitation and ELISA were used to determine the role of Card9 in SAP. Microbial culture showed that SAP patients at the early period did not develop any bacteria and fungi infection. Card9 expression in SAP patients was higher than that in mild acute pancreatitis and volunteer healthy controls, up to the peak on day 1. The monocyte‐derived cytokines interleukin (IL)‐17, IL‐1β, IL‐6 and tumour necrosis factor‐α mediated by the induction of Card9 markedly increased in SAP patients compared with the control group. Furthermore, the inducible formation of Card9‐Bcl10 complex was found in PBMCs, which may be involved in nuclear factor kappa B (NF‐κB) and p38 activation in SAP. Receiver operating characteristic curve indicated that Card9 levels had a high sensitivity of 87.5% and specificity of 67.7%, showing the close correlation with SAP patients. Card9 overexpression was firstly found in aseptic SAP, which may be played an important role in NF‐κB and p38 activation in PBMCs. It also provided the new insights into therapeutic interventions by targeting monocytes activation in SAP patients.
doi:10.1111/jcmm.12738
PMCID: PMC4759462  PMID: 26893103
Card9 overexpression; peripheral blood mononuclear cells; acute pancreatitis; non‐infection inflammation
5.  Biochemical and Metabolic Changes in Arsenic Contaminated Boehmeria nivea L. 
BioMed Research International  2016;2016:1423828.
Arsenic (As) is identified by the EPA as the third highest toxic inorganic contaminant. Almost every 9th or 10th human in more than 70 countries including mainland China is affected by As. Arsenic along with other toxins not only affects human life but also creates alarming situations such as the deterioration of farm lands and desertion of industrial/mining lands. Researchers and administrators have agreed to opt for phytoremediation of As over costly cleanups. Boehmeria nivea L. can soak up various heavy metals, such as Sb, Cd, Pb, and Zn. But the effect of As pollution on the biology and metabolism of B. nivea has been somewhat overlooked. This study attempts to evaluate the extent of As resistance, chlorophyll content, and metabolic changes in As-polluted (5, 10, 15, and 20 mg L−1 As) B. nivea in hydroponics. Toxic effects of As in the form of inhibited growth were apparent at the highest level of added As. The significant changes in the chlorophyll, electrolyte leakage, and H2O2, significant increases in As in plant parts, catalase (CAT), and malondialdehyde (MDA), with applied As revealed the potential of B. nivea for As decontamination. By employing the metabolic machinery of B. nivea, As was sustainably removed from the contaminated areas.
doi:10.1155/2016/1423828
PMCID: PMC4789022  PMID: 27022603
6.  Broadly Neutralizing Human Immunodeficiency Virus Type 1 Antibody Gene Transfer Protects Nonhuman Primates from Mucosal Simian-Human Immunodeficiency Virus Infection 
Journal of Virology  2015;89(16):8334-8345.
ABSTRACT
Broadly neutralizing antibodies (bnAbs) can prevent lentiviral infection in nonhuman primates and may slow the spread of human immunodeficiency virus type 1 (HIV-1). Although protection by passive transfer of human bnAbs has been demonstrated in monkeys, durable expression is essential for its broader use in humans. Gene-based expression of bnAbs provides a potential solution to this problem, although immune responses to the viral vector or to the antibody may limit its durability and efficacy. Here, we delivered an adeno-associated viral vector encoding a simianized form of a CD4bs bnAb, VRC07, and evaluated its immunogenicity and protective efficacy. The expressed antibody circulated in macaques for 16 weeks at levels up to 66 μg/ml, although immune suppression with cyclosporine (CsA) was needed to sustain expression. Gene-delivered simian VRC07 protected against simian-human immunodeficiency virus (SHIV) infection in monkeys 5.5 weeks after treatment. Gene transfer of an anti-HIV antibody can therefore protect against infection by viruses that cause AIDS in primates when the host immune responses are controlled.
IMPORTANCE Sustained interventions that can prevent HIV-1 infection are needed to halt the spread of the HIV-1 pandemic. The protective capacity of anti-HIV antibody gene therapy has been established in mouse models of HIV-1 infection but has not been established for primates. We show here a proof-of-concept that gene transfer of anti-HIV antibody genes can protect against infection by viruses that cause AIDS in primates when host immune responses are controlled.
doi:10.1128/JVI.00908-15
PMCID: PMC4524228  PMID: 26041300
7.  Relationship between diagonal earlobe creases and coronary artery disease as determined via angiography 
BMJ Open  2016;6(2):e008558.
Objective
This study was designed to examine the prevalence of unilateral and bilateral diagonal earlobe creases (DELCs) with respect to the diagnosis of coronary heart disease (CHD).
Methods
A total of 558 consecutive participants (402 males and 156 females) aged 36–91 years who underwent coronary angiography were enrolled in this study. The participants were classified as being without a DELC, having a unilateral DELC and having bilateral DELCs; participants with either a unilateral DELC or bilateral DELCs were defined as participants with DELCs. Significant CHD was defined as at least one major vessel with >50% stenosis, and coronary atherosclerosis severity was defined using the Gensini scoring system.
Results
In the present study, bilateral DELCs were more frequently among male (p=0.001), CHD (p=0.000), older people (p=0.000) and those with more severe coronary artery atherosclerosis (p=0.000). The results of the multiple regression analyses indicated that DELCs (OR, 4.861; 95% CI 3.093 to 7.642, p=0.000) remained independently associated with a risk of CHD. It was assumed that participants without a DELC have a certain background risk for CHD (OR is assumed to be 1); the results of the multivariate logistic regression indicated that the relative risk of CHD among participants with bilateral DELCs was 5.690 among all participants (OR, 5.690; 95% CI 3.450 to 9.384, p=0.000), 5.436 among male participants (OR, 5.436; 95% CI 2.808 to 10.523, p=0.000) and 7.148 among female participants (OR, 7.148; 95% CI 3.184 to 16.049, p=0.000). Moreover, a positive association between DELC and age (SI=1.21, SIM=1.65, AP =0.132), gender (SI=2.09, SIM=0.81, AP=0.49) and smoking status (SI=1.49, SIM=0.73, AP=0.29) was found, respectively.
Conclusions
The results of the present study indicated that DELCs are a simple and a feasible means of identifying CHD. However, the exact mechanism underlying the relationship between DELCs and CHD warrants further study.
doi:10.1136/bmjopen-2015-008558
PMCID: PMC4762085  PMID: 26868940
CARDIOLOGY
8.  From competency to dormancy: a 3D model to study cancer cells and drug responsiveness 
Background
The heterogeneous and dynamic tumor microenvironment has significant impact on cancer cell proliferation, invasion, drug response, and is probably associated with entering dormancy and recurrence. However, these complex settings are hard to recapitulate in vitro.
Methods
In this study, we mimic different restriction forces that tumor cells are exposed to using a physiologically relevant 3D model with tunable mechanical stiffness.
Results
Breast cancer MDA-MB-231, colon cancer HCT-116 and pancreatic cancer CFPAC cells embedded in the stiffer gels exhibit a changed morphology and cluster formation, prolonged doubling time, and a slower metabolism rate, recapitulating the pathway from competency to dormancy. Altering environmental restriction allows them to re-enter and exit dormant conditions and change their sensitivities to drugs such as paclitaxol and gemcitabine. Cells surviving drug treatments can still regain competent growth and form tumors in vivo.
Conclusion
We have successfully developed an in vitro 3D model to mimic the effects of matrix restriction on tumor cells and this high throughput model can be used to study tumor cellular functions and their drug responses in their different states. This all in one platform may aid effective drug development.
doi:10.1186/s12967-016-0798-8
PMCID: PMC4743174  PMID: 26847768
3D cell culture; Microenvironment; Drug response; Dormancy; Competency
9.  Simultaneous-Fault Diagnosis of Gearboxes Using Probabilistic Committee Machine 
This study combines signal de-noising, feature extraction, two pairwise-coupled relevance vector machines (PCRVMs) and particle swarm optimization (PSO) for parameter optimization to form an intelligent diagnostic framework for gearbox fault detection. Firstly, the noises of sensor signals are de-noised by using the wavelet threshold method to lower the noise level. Then, the Hilbert-Huang transform (HHT) and energy pattern calculation are applied to extract the fault features from de-noised signals. After that, an eleven-dimension vector, which consists of the energies of nine intrinsic mode functions (IMFs), maximum value of HHT marginal spectrum and its corresponding frequency component, is obtained to represent the features of each gearbox fault. The two PCRVMs serve as two different fault detection committee members, and they are trained by using vibration and sound signals, respectively. The individual diagnostic result from each committee member is then combined by applying a new probabilistic ensemble method, which can improve the overall diagnostic accuracy and increase the number of detectable faults as compared to individual classifiers acting alone. The effectiveness of the proposed framework is experimentally verified by using test cases. The experimental results show the proposed framework is superior to existing single classifiers in terms of diagnostic accuracies for both single- and simultaneous-faults in the gearbox.
doi:10.3390/s16020185
PMCID: PMC4801562  PMID: 26848665
simultaneous-fault diagnosis; Hilbert-Huang transform; pairwise-coupling probabilistic committee machine
10.  A cotton miRNA is involved in regulation of plant response to salt stress 
Scientific Reports  2016;6:19736.
The present study functionally identified a new microRNA (microRNA ovual line 5, miRNVL5) with its target gene GhCHR from cotton (Gossypium hirsutum). The sequence of miRNVL5 precursor is 104 nt long, with a well developed secondary structure. GhCHR contains two DC1 and three PHD Cys/His-rich domains, suggesting that GhCHR encodes a zinc-finger domain-containing transcription factor. miRNVL5 and GhCHR express at various developmental stages of cotton. Under salt stress (50–400 mM NaCl), miRNVL5 expression was repressed, with concomitant high expression of GhCHR in cotton seedlings. Ectopic expression of GhCHR in Arabidopsis conferred salt stress tolerance by reducing Na+ accumulation in plants and improving primary root growth and biomass. Interestingly, Arabidopsis constitutively expressing miRNVL5 showed hypersensitivity to salt stress. A GhCHR orthorlous gene At2g44380 from Arabidopsis that can be cleaved by miRNVL5 was identified by degradome sequencing, but no confidential miRNVL5 homologs in Arabidopsis have been identified. Microarray analysis of miRNVL5 transgenic Arabidopsis showed six downstream genes (CBF1, CBF2, CBF3, ERF4, AT3G22920, and AT3G49200), which were induced by salt stress in wild-type but repressed in miRNVL5-expressing Arabidopsis. These results indicate that miRNVL5 is involved in regulation of plant response to salt stress.
doi:10.1038/srep19736
PMCID: PMC4728436  PMID: 26813144
11.  Three-dimensional skeleton networks of graphene wrapped polyaniline nanofibers: an excellent structure for high-performance flexible solid-state supercapacitors 
Scientific Reports  2016;6:19777.
Thin, robust, lightweight, and flexible supercapacitors (SCs) have aroused growing attentions nowadays due to the rapid development of flexible electronics. Graphene-polyaniline (PANI) hybrids are attractive candidates for high performance SCs. In order to utilize them in real devices, it is necessary to improve the capacitance and the structure stability of PANI. Here we report a hierarchical three-dimensional structure, in which all of PANI nanofibers (NFs) are tightly wrapped inside reduced graphene oxide (rGO) nanosheet skeletons, for high-performance flexible SCs. The as-fabricated film electrodes with this unique structure showed a highest gravimetric specific capacitance of 921 F/g and volumetric capacitance of 391 F/cm3. The assembled solid-state SCs gave a high specific capacitance of 211 F/g (1 A/g), a high area capacitance of 0.9 F/cm2, and a competitive volumetric capacitance of 25.6 F/cm3. The SCs also exhibited outstanding rate capability (~75% retention at 20 A/g) as well as excellent cycling stability (100% retention at 10 A/g for 2000 cycles). Additionally, no structural failure and loss of performance were observed under the bending state. This structure design paves a new avenue for engineering rGO/PANI or other similar hybrids for high performance flexible energy storage devices.
doi:10.1038/srep19777
PMCID: PMC4726342  PMID: 26795067
12.  Acute Targeting of General Transcription Factor IIB Restricts Cardiac Hypertrophy via Selective Inhibition of Gene Transcription 
Circulation. Heart failure  2014;8(1):138-148.
Background
We previously reported that specialized and housekeeping genes are differentially regulated via de novo recruitment and pause-release of RNA polymerase II (pol II), respectively, during cardiac hypertrophy. However, the significance of this finding remains to be examined. Therefore, the purpose of this study was to determine the mechanisms that differentially regulate these gene groups and exploit them for therapeutic targeting.
Methods and Results
Here we show that general transcription factor IIB (TFIIB) and cyclin-dependent kinase 9 are upregulated during hypertrophy, both targeted by miR-1, and play preferential roles in regulating those two groups of genes. Chromatin immunoprecipitation-sequencing reveals that TFIIB is constitutively bound to all paused, housekeeping, promoters, whereas, de novo recruitment of TFIIB and pol II is required for specialized genes that are induced during hypertrophy. We exploited this dichotomy to acutely inhibit induction of the latter set, which encompasses cardiomyopathy, immune reaction, and extracellular matrix genes, using locked nucleic acid (LNA)-modified antisense TFIIB oligonucleotide treatment. This resulted in suppression of all specialized genes, while sparing the housekeeping ones, and, thus, attenuated pathological hypertrophy.
Conclusions
The data for the first time reveal distinct general transcription factor IIB dynamics that regulate specialized vs. housekeeping genes during cardiac hypertrophy. Thus, by acutely targeting TFIIB we were able to selectively inhibit the former set of genes and ameliorate pressure overload hypertrophy. We also demonstrate the feasibility of acutely and reversibly targeting cardiac mRNA for therapeutic purposes using LNA-modified antisense oligonucleotides.
doi:10.1161/CIRCHEARTFAILURE.114.001660
PMCID: PMC4401077  PMID: 25398966
transcription; hypertrophy; general transcription factor IIB; chromatin immunoprecipitation
13.  Characterization of Full-Length Genomes of Hepatitis B Virus Quasispecies in Sera of Patients at Different Phases of Infection 
Journal of Clinical Microbiology  2015;53(7):2203-2214.
Hepatitis B virus (HBV) infection results in different clinical presentation due to different levels of immune response. Our study aimed to characterize HBV full-length genome quasispecies (QS) in patients with different phases of infection to better understand its pathogenesis. Forty treatment-naive HBV-infected patients were enrolled, including 10 cases of acute hepatitis B (AHB), 9 cases of immunotolerant (IT) HBV carriers, 11 cases of chronic hepatitis B (CHB), and 10 cases of acute-on-chronic liver failure (ACLF). The present study was conducted by clone-based sequencing. QS heterogeneity within each open reading frame was calculated. The mutation frequency index (MFI) and amino acid variations within the large HBsAg, HBcAg, and HBxAg regions were analyzed based on the different infection phases. In total, 606 HBV full-length sequences were obtained. HBV QS had higher heterogeneity in ACLF and CHB than that in IT among chronically infected individuals. AHB patients had the lower QS heterogeneity at onset than those with chronic infection. ACLF patients had the highest frequency of mutations in the core promoter and precore region. A triple mutation (A1762T/G1764A/G1896A) was observed more frequently in genotype C than in genotype B. The MFI indicated that specific peptides of the studied regions had more frequent mutations in ACLF. Furthermore, several amino acid variations, known as T- and B-cell epitopes, were potentially associated with the immunoactive phase of infection. More HBV genome mutations and deletions were observed in patients with more severe diseases, particularly in specific regions of the core and preS regions, the clinical significance and mechanism of which need to be further investigated.
doi:10.1128/JCM.00068-15
PMCID: PMC4473231  PMID: 25926495
14.  Spatiotemporal expression of Nogo-66 receptor after focal cerebral ischemia 
Neural Regeneration Research  2016;11(1):132-136.
NgR, the receptor for the neurite outgrowth inhibitor Nogo-66, plays a critical role in the plasticity and regeneration of the nervous system after injury such as ischemic stroke. In the present study, we used immunohistochemistry to investigate the regional expression of NgR in rat brain following middle cerebral artery occlusion (MCAO). NgR protein expression was not observed in the center of the lesion, but was elevated in the marginal zone compared with control and sham-operated rats. The cerebral cortex and hippocampus (CA1, CA2, and CA3) showed the greatest expression of NgR. Furthermore, NgR expression was higher in the ipsilesional hemisphere than on the control side in the same coronal section. Although time-dependent changes in NgR expression across brain regions had their own characteristics, the overall trend complied with the following rules: NgR expression changes with time showed two peaks and one trough; the first peak in expression appeared between 1 and 3 days after MCAO; expression declined at 5 days; and the second peak occurred at 28 days.
doi:10.4103/1673-5374.175059
PMCID: PMC4774206  PMID: 26981102
nerve regeneration; focal cerebral ischemia; cerebral cortex; hippocampus; NgR; Nogo-A; immunohistochemistry; neural regeneration
15.  Individual Variability and Test-Retest Reliability Revealed by Ten Repeated Resting-State Brain Scans over One Month 
PLoS ONE  2015;10(12):e0144963.
Individual differences in mind and behavior are believed to reflect the functional variability of the human brain. Due to the lack of a large-scale longitudinal dataset, the full landscape of variability within and between individual functional connectomes is largely unknown. We collected 300 resting-state functional magnetic resonance imaging (rfMRI) datasets from 30 healthy participants who were scanned every three days for one month. With these data, both intra- and inter-individual variability of six common rfMRI metrics, as well as their test-retest reliability, were estimated across multiple spatial scales. Global metrics were more dynamic than local regional metrics. Cognitive components involving working memory, inhibition, attention, language and related neural networks exhibited high intra-individual variability. In contrast, inter-individual variability demonstrated a more complex picture across the multiple scales of metrics. Limbic, default, frontoparietal and visual networks and their related cognitive components were more differentiable than somatomotor and attention networks across the participants. Analyzing both intra- and inter-individual variability revealed a set of high-resolution maps on test-retest reliability of the multi-scale connectomic metrics. These findings represent the first collection of individual differences in multi-scale and multi-metric characterization of the human functional connectomes in-vivo, serving as normal references for the field to guide the use of common functional metrics in rfMRI-based applications.
doi:10.1371/journal.pone.0144963
PMCID: PMC4694646  PMID: 26714192
16.  Periodic-peristole agitation for process enhancement of butanol fermentation 
Background
Mass transfer plays an important role in determining the efficiency of the biofuel conversion. However, adverse effect of shear stress from traditional agitation inhibits the cell growth and production of biofuels. How to enhance the mass transfer with less adverse effect is considered as one of the important bioengineering issues.
Results
In this study, a novel agitation type, named periodic-peristole was applied to butanol fermentation with Clostridium acetobutylicum ATCC 824. Meanwhile, the enhancement mechanism was studied. Initially, the fermentation performance of periodic-peristole agitation was compared with the traditional Rushton impeller and stationary cultivation. Result showed that the biomass, butanol and total solvent in periodic-peristole group (PPG) was enhanced to 1.92-, 2.06-, and 2.4-fold of those in the traditional Rushton impeller group (TIG), as well as 1.64-, 1.19- and 1.41-fold of those in the stationary group (SG). Subsequently, to get in-depth insight into enhancement mechanism, hydromechanics analysis and metabolic flux analysis (MFA) were carried out. The periodic-peristole agitation exhibits significant difference on velocity distribution, shear force, and mixing efficiency from the traditional Rushton impeller agitation. And the shear force in PPG is only 74 % of that in TIG. According to MFA result, fructose 6-phosphate, pyruvate, acetyl-CoA, oxaloacetate and α-ketoglutarate were determined the key nodes of cells in response to hydrodynamic mechanical stress. Based on such key information, rational enhancement strategies were proposed and butanol production was further improved.
Conclusion
The agitation associated with three issues which resulted in significant changes in cell metabolic behaviors: first, a rebalanced redox status; second, the energy (ATP) acquirement and consumption; third, the tolerance mechanism of the cell for survival of solvent. Periodic-peristole agitation provides an answer to address a long-standing problem of biofuel engineering. Key information derived from current study deepens the understanding of agitation, which can guide the designment of new bioreactors and development of enhancement strategies for biofuel refinery.
Electronic supplementary material
The online version of this article (doi:10.1186/s13068-015-0409-6) contains supplementary material, which is available to authorized users.
doi:10.1186/s13068-015-0409-6
PMCID: PMC4689062  PMID: 26702300
Periodic-peristoleagitation; Butanol; Hydrodynamic analysis; Metabolic flux analysis; Enhancement mechanism of agitation; Rational enhancement strategy
17.  Molecular Properties and Functional Divergence of the Dehydroascorbate Reductase Gene Family in Lower and Higher Plants 
PLoS ONE  2015;10(12):e0145038.
Dehydroascorbate reductase (DHAR), which reduces oxidized ascorbate, is important for maintaining an appropriate ascorbate redox state in plant cells. To date, genome-wide molecular characterization of DHARs has only been conducted in bryophytes (Physcomitrella patens) and eudicots (e.g. Arabidopsis thaliana). In this study, to gain a general understanding of the molecular properties and functional divergence of the DHARs in land plants, we further conducted a comprehensive analysis of DHARs from the lycophyte Selaginella moellendorffii, gymnosperm Picea abies and monocot Zea mays. DHARs were present as a small gene family in all of the land plants we examined, with gene numbers ranging from two to four. All the plants contained cytosolic and chloroplastic DHARs, indicating dehydroascorbate (DHA) can be directly reduced in the cytoplasm and chloroplast by DHARs in all the plants. A novel vacuolar DHAR was found in Z. mays, indicating DHA may also be reduced in the vacuole by DHARs in Z. mays. The DHARs within each species showed extensive functional divergence in their gene structures, subcellular localizations, and enzymatic characteristics. This study provides new insights into the molecular characteristics and functional divergence of DHARs in land plants.
doi:10.1371/journal.pone.0145038
PMCID: PMC4687524  PMID: 26684301
18.  GTPase Activating Protein (Sh3 Domain) Binding Protein 1 Regulates the Processing of MicroRNA-1 during Cardiac Hypertrophy 
PLoS ONE  2015;10(12):e0145112.
Background
MicroRNAs (miR) are small, posttranscriptional regulators, expressed as part of a longer primary transcript, following which they undergo nuclear and cytoplasmic processing by Drosha and Dicer, respectively, to form the functional mature ~20mer that gets incorporated into the silencing complex. Others and we have shown that mature miR-1 levels decrease with pressure-induced cardiac hypertrophy, however, there is little or no change in the primary transcript encompassing miR-1 stem-loop, suggesting critical regulatory step in microRNA processing. The objective of this study was to investigate the underlying mechanisms regulating miR-1 expression in cardiomyocytes.
Results
Here we report that GTPase–activating protein (SH3 domain) binding protein 1 (G3bp1), an endoribonuclease regulates miR-1 processing in cardiomyocytes. G3bp1 is upregulated during cardiac hypertrophy and restricts miR-1 processing by binding to its consensus sequence in the pre-miR-1-2 stem-loop. In accordance, exogenous G3bp1 is sufficient to reduce miR-1 levels, along with derepression of miR-1 targets; General transcription factor IIB (Gtf2b), cyclin dependent factor 9 (Cdk9) and eukaryotic initiation factor 4E (Eif4e). While Cdk9 and Gtf2b are essential for transcription, Eif4e is required for translation. Thus, downregulation of miR-1 is necessary for increase in these molecules. Similar to miR-1 knockdown, G3bp1 overexpression is not sufficient for development of cardiac hypertrophy. Conversely, knockdown of G3bp1 in hypertrophying cardiomyocytes inhibited downregulation of miR-1 and upregulation of its targets along with restricted hypertrophy, suggesting that G3bp1 is necessary for development of cardiac hypertrophy. These results indicate that G3bp1-mediated inhibition of miR-1 processing with growth stimulation results in decrease in mature miR-1 and, thereby, an increase of its targets, which play fundamental roles in the development of hypertrophy.
Conclusion
G3bp1 posttranscriptionally regulates miRNA-1 processing in the heart, and G3bp1 mediated downregulation of mature miRNA-1 levels is required for the derepression of its targets and increase in gene expression during cardiac hypertrophy.
doi:10.1371/journal.pone.0145112
PMCID: PMC4684496  PMID: 26675618
19.  In vitro controlled release of cisplatin from gold-carbon nanobottles via cleavable linkages 
Carbon nanotubes’ (CNTs) hollow interior space has been explored for biomedical applications, such as drug repository against undesirable inactivation. To further devise CNTs as smart material for controlled release of cargo molecules, we propose the concept of “gold-carbon nanobottles”. After encapsulating cis-diammineplatinum(II) dichloride (cisplatin, CDDP) in CNTs, we covalently attached gold nanoparticles (AuNPs) at the open-tips of CNTs via different cleavable linkages, namely hydrazine, ester, and disulfide-containing linkages. Compared with our previous study in which more than 80% of CDDP leaked from CNTs in 2 hours, AuNPs were found to significantly decrease such spontaneous release to <40%. In addition, CDDP release from AuNP-capped CNTs via disulfide linkage was selectively enhanced by twofolds in reducing conditions (namely with 1 mM dithiothreitol [DTT]), which mimic the intracellular environment. We treated human colon adenocarcinoma cells HCT116 with our CDDP-loaded gold-carbon nanobottles and examined the cell viability using lactate dehydrogenase assay. Interestingly, we found that our nanobottles with cleavable disulfide linkage exerted stronger cytotoxic effect in HCT116 compared with normal human fetal lung fibroblast cells IMR-90. Therefore, we infer that our nanobottles strategy with inbuilt disulfide linkage could attain selective release of payload in highly reductive tumor tissues while avoiding collateral damage to normal tissues.
doi:10.2147/IJN.S93810
PMCID: PMC4687722  PMID: 26719686
carbon nanotubes; surface functionalization; cleavable bonds; cisplatin; drug delivery
20.  Identification of the Replication Origins from Cyanothece ATCC 51142 and Their Interactions with the DnaA Protein: From In Silico to In Vitro Studies 
Based on the complete genome of Cyanothece ATCC 51142, the oriCs of both the circular and linear chromosomes in Cyanothece ATCC 51142 have been predicted by utilizing a web-based system Ori-Finder. Here, we provide experimental support for the results of Ori-Finder to identify the replication origins of Cyanothece ATCC 51142 and their interactions with the initiator protein, DnaA. The two replication origins are composed of three characteristically arranged DnaA boxes and an AT-rich stretch, and the oriC in the circular chromosome is followed by the dnaN gene. The dnaA gene is located downstream of the origin of the circular chromosome and it expresses a typical DnaA protein that is divided into four domains (I, II, III, IV), as with other members of the DnaA protein family. We purify DnaA (IV) and characterize the interaction of the purified protein with the replication origins, so as to offer experimental support for the prediction. The results of the electrophoretic mobility shift assay and DNase I footprint assay demonstrate that the C-terminal domain of the DnaA protein from Cyanothece ATCC 51142 specifically binds the oriCs of both the circular and linear chromosomes, and the DNase I footprint assay demonstrates that DnaA (IV) exhibits hypersensitive affinity with DnaA boxes in both oriCs.
doi:10.3389/fmicb.2015.01370
PMCID: PMC4674748  PMID: 26696980
DnaA; DnaA (IV); DNA binding; origin of chromosomal replication (oriC); initiation complex; Cyanothece ATCC 51142
21.  Sustained Delivery of a Broadly Neutralizing Antibody in Nonhuman Primates Confers Long-Term Protection against Simian/Human Immunodeficiency Virus Infection 
Journal of Virology  2015;89(11):5895-5903.
ABSTRACT
Pathogen-specific neutralizing antibodies protect against many viral infections and can potentially prevent human immunodeficiency virus (HIV) transmission in humans. However, neutralizing antibodies have so far only been shown to protect nonhuman primates (NHP) against lentiviral infection when given shortly before challenge. Thus, the clinical utility and feasibility of passive antibody transfer to confer long-term protection against HIV-1 are still debated. Here, we investigate the potential of a broadly neutralizing HIV-1 antibody to provide long-term protection in a NHP model of HIV-1 infection. A human antibody was simianized to avoid immune rejection and used to sustain therapeutic levels for ∼5 months. Two months after the final antibody administration, animals were completely protected against viral challenge. These findings demonstrate the feasibility and potential of long-term passive antibody for protection against HIV-1 in humans and provide a model to test antibody therapies for other diseases in NHP.
IMPORTANCE Antibodies against HIV are potential drugs that may be able to prevent HIV infection in humans. However, the long-term protective capacity of antibodies against HIV has not been assessed. Here, we repetitively administered a macaque version of a human anti-HIV antibody to monkeys, after which the antibody persisted in the blood for >5 months. Moreover, the antibody could be sustained at protective levels for 108 days, conferring protection 52 days after the last dose in a monkey model of HIV infection. Thus, passive antibody transfer can provide durable protection against infection by viruses that cause AIDS in primates.
doi:10.1128/JVI.00210-15
PMCID: PMC4442454  PMID: 25787288
22.  Long-term dietary supplementation with saury oil attenuates metabolic abnormalities in mice fed a high-fat diet: combined beneficial effect of omega-3 fatty acids and long-chain monounsaturated fatty acids 
Background
Pacific saury is a common dietary component in East Asia. Saury oil contains considerable levels of n-3 unsaturated fatty acids (PUFA) and long-chain monounsaturated fatty acids (LCMUFA) with aliphatic tails longer than 18 carbons. In our previous study, consumption of saury oil for 4 to 6 wk improved insulin sensitivity and the plasma lipid profile in mice. However, the long-term effects of saury oil on metabolic syndrome (MetS) risk factors remain to be demonstrated. In the current study, we examined the long-term effects of saury oil on mice fed a high-fat diet, and compared the effect of n-3 PUFA EPA and LCMUFA on MetS risk factor in diet-induced obese mice.
Methods and Results
In Experiment 1, male C57BL/6 J mice were fed either a 32 % lard diet (control) or a diet containing 22 % lard plus 10 % saury oil (saury oil group) for 18 weeks. Although no differences were found in body weight and energy expenditure between the control and saury oil groups, the saury oil diet decreased plasma insulin, non–HDL cholesterol, hepatic steatosis, and adipocyte size, and altered levels of mRNA transcribed from genes involved in insulin signaling and inflammation in adipose tissue. Organ and plasma fatty acid profile analysis revealed that consumption of saury oil increased n-3 PUFA and LCMUFA (especially n-11 LCMUFA) levels in multiple organs, and decreased the fatty acid desaturation index (C16:1/C16:0; C18:1/C18:0) in liver and adipose tissue. In Experiment 2, male C57BL/6 J mice were fed a 32 % lard diet (control), a diet containing 28 % lard plus 4 % EPA (EPA group), or a diet containing 20 % lard plus 12 % LCMUFA concentrate (LCMUFA group) for 8 weeks. EPA or LCMUFA intake increased organ levels of EPA and LCMUFA, respectively. Consumption of EPA reduced plasma lipid levels and hepatic lipid deposition, and decreased the fatty acid desaturation index in liver and adipose tissue. Consumption of LCMUFA decreased plasma non–HDL cholesterol, improved hyperinsulinemia, and decreased the fatty acid desaturation index in adipose tissue. EPA accumulated mainly in liver, and LCMUFA (especially n-11 LCMUFA) accumulated mainly in white adipose tissue, suggesting their possible individual biological effects for improving MetS.
Conclusion
Our results suggest that saury oil-mediated improvement of metabolic syndrome in diet-induced obese mice may possibly be due to a combined effect of n-3 PUFA and LCMUFA.
Electronic supplementary material
The online version of this article (doi:10.1186/s12944-015-0161-8) contains supplementary material, which is available to authorized users.
doi:10.1186/s12944-015-0161-8
PMCID: PMC4666194  PMID: 26627187
23.  Live Bird Exposure among the General Public, Guangzhou, China, May 2013 
PLoS ONE  2015;10(12):e0143582.
Background
A novel avian-origin influenza A(H7N9) caused a major outbreak in Mainland China in early 2013. Exposure to live poultry was believed to be the major route of infection. There are limited data on how the general public changes their practices regarding live poultry exposure in response to the early outbreak of this novel influenza and the frequency of population exposure to live poultry in different areas of China.
Methodology
This study investigated population exposures to live birds from various sources during the outbreak of H7N9 in Guangzhou city, China in 2013 and compared them with those observed during the 2006 influenza A(H5N1) outbreak. Adults were telephone-interviewed using two-stage sampling, stratified by three residential areas of Guangzhou: urban areas and two semi-rural areas in one of which (Zengcheng) A(H7N9) virus was detected in a chicken from wet markets. Logistic regression models were built to describe practices protecting against avian influenza, weighted by age and gender, and then compare these practices across residential areas in 2013 with those from a comparable 2006 survey.
Principal Findings
Of 1196 respondents, 45% visited wet markets at least daily and 22.0% reported buying live birds from wet markets at least weekly in April-May, 2013, after the H7N9 epidemic was officially declared in late March 2013. Of those buying live birds, 32.3% reported touching birds when buying and 13.7% would slaughter the poultry at home. Although only 10.1% of the respondents reported raising backyard birds, 92.1% of those who did so had physical contact with the birds they raised. Zengcheng respondents were less likely to report buying live birds from wet markets, but more likely to buy from other sources when compared to urban respondents. Compared with the 2006 survey, the prevalence of buying live birds from wet markets, touching when buying and slaughtering birds at home had substantially declined in the 2013 survey.
Conclusion/Significance
Although population exposures to live poultry were substantially fewer in 2013 compared to 2006, wet markets and backyard poultry remained the two major sources of live bird exposures for the public in Guangzhou in 2013. Zengcheng residents seemed to have reduced buying live birds from wet markets but not from other sources in response to the detection of H7N9 virus in wet markets.
doi:10.1371/journal.pone.0143582
PMCID: PMC4666652  PMID: 26623646
24.  The association of TGFB1 genetic polymorphisms with high myopia: a systematic review and meta-analysis 
Objective: The TGFB1 gene is among the most studied genes in high myopia due to its role in scleral remodeling. But reported findings of association on TGFB1 and high myopia are inconsistent. This present study is to evaluate the association of TGFB1 polymorphisms and high myopia. Methods: A comprehensive literature search was conducted on studies published up to April 5, 2015. Summary odds ratios (ORs) and 95% confidence intervals were analyzed. Heterogeneity across studies was evaluated by Cochran Q statistic test and the I2 index. Sensitivity analyses were conducted by the approach of one-study remove to assess the influence of single study on the combined effect. Results: Eight studies were included in this study for meta-analysis. Rs1982073 was associated with high myopia in dominant model (OR=1.64; 95% CI=1.04~2.58; P<0.05), heterozygous model (OR=1.54; 95% CI=1.02~2.33; P<0.05), homozygous model (OR=1.90; 95% CI=1.01~3.55; P=0.05) and allelic model (OR=1.36; 95% CI=1.01~1.84; P=0.05). However, there was no statistical significance when Bonferroni correction was considered. Rs4803455 was associated with high myopia in recessive model (OR=0.40; 95% CI=0.25~0.64; P<0.01) and homozygous model (OR=0.42; 95% CI=0.26~0.68; P<0.01). Rs1800469 was associated with high myopia in allelic model (OR=0.78; 95% CI=0.64~0.96; P<0.05). And the associations can withstand Bonferroni correction in models mentioned above when referring to rs4803455 (P<0.01) and rs1800469 (P<0.05). Conclusions: Meta-analysis of existing data revealed a suggestive association of TGFB1 rs1982073 and rs4803455 with high myopia.
PMCID: PMC4723797  PMID: 26884952
Transforming growth factor beta1; single nucleotide polymorphism; high myopia
25.  Endoscopic biopsy of a B-cell lymphoma involving the entire ventricular system: A case report 
A 62-year-old male suffering from vomiting and mild preceding nausea for 15 days was examined in the present case report. Magnetic resonance imaging revealed a homogeneously enhancing cluster-like lesion involving the lateral, third and fourth ventricles. An endoscopic biopsy was performed, and histopathological examination led to the diagnosis of a high-grade diffuse large B-cell lymphoma. To the best of our knowledge, the present study reports the first case of a primary lymphoma involving the entire ventricular system. Therefore, primary lymphomas should be considered in the list of ventricular tumors. An endoscopic biopsy requires minimal invasion to obtain an adequate tissue sample, and frequently leads to the correct diagnosis and subsequent treatment protocols.
doi:10.3892/etm.2015.2861
PMCID: PMC4726988  PMID: 26889262
intraventricular tumor; fourth ventricle; B cell; high-grade

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