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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.
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.
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.
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.
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.
PMCID: PMC4243764  PMID: 25349902
Protein-protein interaction network; Protein complexes; Gene Ontology; Supervised learning
2.  Antibodies VRC01 and 10E8 neutralize HIV-1 with high breadth and potency even with immunoglobulin-framework regions substantially reverted to germline 
Antibodies capable of effectively neutralizing HIV-1 generally exhibit very high levels of somatic hypermutation, both in their complementarity-determining and framework-variable regions. In many cases, full reversion of the antibody framework mutations back to germline has been shown to result in substantial to complete loss of HIV-1 neutralizing activity. However, it is currently not known whether all or most of the observed framework mutations are necessary, or whether a small subset of these mutations may be sufficient for broad and potent neutralization. To address this issue and to explore the dependence of neutralization activity on the level of somatic hypermutation in antibody framework, we applied a computationally guided framework reversion procedure to two broadly neutralizing anti-HIV-1 antibodies, VRC01 and 10E8, which target two different HIV-1 sites of vulnerability. Antibody variants in which up to 78% (38 out of 49 for VRC01) and 89% (31 out of 35 for 10E8) of framework mutations were reverted to germline retained breadth and potency within 3-fold of the mature antibodies when evaluated on a panel of 21-diverse viral strains. Further, a VRC01 variant with a ~50% framework-reverted light chain showed a 2-fold improvement in potency over the mature antibody. Our results indicate that only a small number of antibody-framework mutations may be sufficient for high breadth and potency of HIV-1 neutralization by antibodies VRC01 and 10E8. Partial framework revertants of HIV-1 broadly neutralizing antibodies may present advantages over their highly mutated counterparts as antibody therapeutics and as targets for immunogen design.
PMCID: PMC4140862  PMID: 24391217
4.  Development and Characterization of a Novel Fusion Protein of a Mutated Granulocyte Colony-Stimulating Factor and Human Serum Albumin in Pichia pastoris 
PLoS ONE  2014;9(12):e115840.
The purpose of the present work was to develop a novel, long-acting and potent human serum albumin/granulocyte colony stimulating factor (HSA/G-CSF) therapeutic fusion protein. The novel fusion protein, called HMG, was constructed by genetically fusing mutated human derived G-CSF (mG-CSF) to the C-terminal of HSA and then prepared in Pichia pastoris. The molecular mass of HMG was about 85 kDa and the isoelectric point was 5.3. Circular dichroism spectroscopy suggested that mG-CSF retained nearly all of its native secondary structure, regardless of fusion. The binding capabilities of mG-CSF moiety to G-CSF receptor and HSA moiety to warfarin showed very little change after fusing. The bioactivity of HMG (11.0×106 IU/mg) was more than twice that of rHSA/G-CSF (4.6×106 IU/mg). A mutation was made at the 718th amino acid of HMG, substituting Ala for Thr, to investigate the glycosylation of HMG expressed in P. pastoris. Data indicated that HMG was modified at Thr718, speculatively with the addition of a mannose chain. In conclusion, a novel HSA/G-CSF fusion protein was successfully constructed based on a mutated G-CSF. This protein showed more potent bioactivity than rHSA/G-CSF and thus may be a suitable long-acting G-CSF.
PMCID: PMC4275271  PMID: 25535738
5.  Cancer survivors’ perspectives and experience on western medicine and traditional Chinese medicine treatment and rehabilitation: a qualitative study 
In the People’s Republic of China, both western medicine (WM) and traditional Chinese medicine (TCM) are the main treatment and rehabilitation options for cancer patients. This study aimed to explore cancer survivors’ perspectives and experience of treatment and rehabilitation, in order to promote patient-centered activities of treatment and rehabilitation.
Using a qualitative research approach, 68 cancer survivors were recruited from eight community cancer rehabilitation organizations in Shanghai, People’s Republic of China. Eight focus group interviews were conducted. All these interviews were transcribed verbatim, and the data were analyzed by theme analysis.
WM was the main choice in treatment phase though study participants noted more side effects. TCM was primarily used in the recovery phase. The lack of communication between doctors and cancer patients appears to affect treatment adherence and impair the doctor–patient relationship. WM was expensive for diagnostic procedures and treatment, while the cumulative costs of frequent use of TCM in the long rehabilitation period were also high. Both treatment options created significant perceived economic burden on patients. Conflicting information about dietary supplements tended to make cancer survivors confused.
Improving the communication between doctors and cancer patients helps to ameliorate cancer patient adherence and the effect of treatments. It is essential to educate cancer patients about the effect and cost of both WM and traditional TCM. Meanwhile, marketing management and guidance to consumers regarding use of dietary supplements in the cancer rehabilitation field are also necessary.
PMCID: PMC4274133  PMID: 25565779
preference; adherence; cancer survivor education; focus group interview
6.  Functional Role of Calstabin2 in Age-related Cardiac Alterations 
Scientific Reports  2014;4:7425.
Calstabin2 is a component of the cardiac ryanodine receptor (RyR2) macromolecular complex, which modulates Ca2+ release from the sarcoplasmic reticulum in cardiomyocytes. Previous reports implied that genetic deletion of Calstabin2 leads to phenotypes related to cardiac aging. However, the mechanistic role of Calstabin2 in the process of cardiac aging remains unclear. To assess whether Calstabin2 is involved in age-related heart dysfunction, we studied Calstabin2 knockout (KO) and control wild-type (WT) mice. We found a significant association between deletion of Calstabin2 and cardiac aging. Indeed, aged Calstabin2 KO mice exhibited a markedly impaired cardiac function compared with WT littermates. Calstabin2 deletion resulted also in increased levels of cell cycle inhibitors p16 and p19, augmented cardiac fibrosis, cell death, and shorter telomeres. Eventually, we demonstrated that Calstabin2 deletion resulted in AKT phosphorylation, augmented mTOR activity, and impaired autophagy in the heart. Taken together, our results identify Calstabin2 as a key modulator of cardiac aging and indicate that the activation of the AKT/mTOR pathway plays a mechanistic role in such a process.
PMCID: PMC4262885  PMID: 25502776
7.  Surfactant-free synthesis of Cu2O hollow spheres and their wavelength-dependent visible photocatalytic activities using LED lamps as cold light sources 
Nanoscale Research Letters  2014;9(1):624.
A facile synthesis route of cuprous oxide (Cu2O) hollow spheres under different temperatures without the aid of a surfactant was introduced. Morphology and structure varied as functions of reaction temperature and duration. A bubble template-mediated formation mechanism was proposed, which explained the reason of morphology changing with reaction temperature. The obtained Cu2O hollow spheres were active photocatalyst for the degradation of methyl orange under visible light. A self-designed equipment of light emitting diode (LED) cold light sources with the wavelength of 450, 550, and 700 nm, respectively, was used for the first time in the photocatalysis experiment with no extra heat introduced. The most suitable wavelength for Cu2O to photocatalytic degradation is 550 nm, because the light energy (2.25 eV) is closest to the band gap of Cu2O (2.17 eV). These surfactant-free synthesized Cu2O hollow spheres would be highly attractive for practical applications in water pollutant removal and environmental remediation.
PMCID: PMC4256968  PMID: 25489279
Cuprous oxide; Hollow spheres; Surfactant-free; Photocatalysis; LED cold light sources
8.  Angiogenesis effect of therapeutic ultrasound on ischemic hind limb in mice 
Although significant progress in bypass surgery and catheter intervention against peripheral artery disease, the number of severe critical limb ischemia (CLI) patients is increasing. Thus, it is crucial to develop new, non-invasive therapeutic strategies. The purpose of this study was to determine the mechanism of therapeutic ultrasound (TUS) on ischemic angiogenesis using mouse model of hindlimb ischemia and the cellular/molecular mechanisms underlying TUS-related neovascularization. The hindlimb ischemic mice were exposed to extracorporeal TUS for 3, 6, 9 minute per day (1 MHz, 0.3 W/cm2) until day 14 after left femoral artery ligation. Increased blood perfusion and capillary density were determined following 9 min of TUS compared with ischemic group. Moreover, TUS treatment increased the protein levels of vascular endothelial growth factor (VEGF), hypoxic inducible factor-1α (HIF-1α), endothelial nitric oxide synthase (eNOS) and p-Akt in vivo. TUS promoted capillary-like tube formation, migration and motility of human umbilical venous endothelial cells (HUVECs). Furthermore, the protein expressions of VEGF, eNOS and p-Akt were increased after TUS treatment. In conclusion, TUS therapy promotes postnatal neovascularization through multiple angiogenic pathways in mice model of ischemic hindlimb.
PMCID: PMC4297338  PMID: 25628781
Therapeutic ultrasound; angiogenesis; critical limb ischemia; VEGF
10.  Mouse dead end 1-β interacts with c-Jun and stimulates activator protein 1 transactivation 
Molecular Medicine Reports  2014;11(3):1701-1707.
Dead end 1 (DND1), important for maintaining the viability of primordial germ cells, is the first protein containing an RNA recognition motif that has been directly implicated as a heritable cause of spontaneous tumorigenesis. In the present study, c-Jun was identified through yeast two-hybrid screening of a 10.5-day old mouse embryo cDNA library as one of the proteins which interact with DND1-β. The interaction between DND1-β and c-Jun was demonstrated to occur by glutathione S-transferase pull-down and co-immunoprecipitation. Using confocal microscopy, DND1-β was found to be specifically expressed in GC-1 spermatogonia cells, mainly in the nuclei. When transfected into GC-1 cells, DND1-β and c-Jun were demonstrated to be co-localized principally in the nuclei. Furthermore, in a dual luciferase reporter assay, the transcriptional activity of activator protein 1 was demonstrated to be significantly increased by co-transfection with DND1-β and c-Jun plasmids in GC-1 cells. The identification and confirmation of an additional protein interacting with DND1-β facilitates the investigation of the functions and molecular mechanisms of DND1.
PMCID: PMC4270339  PMID: 25405725
dead end 1-β; c-Jun; activator protein-1; yeast two-hybrid; interaction; immunoprecipitation; glutathione 3-transferase pull-down
11.  Polyethylene glycol–polylactic acid nanoparticles modified with cysteine–arginine–glutamic acid–lysine–alanine fibrin-homing peptide for glioblastoma therapy by enhanced retention effect 
For a nanoparticulate drug-delivery system, crucial challenges in brain-glioblastoma therapy are its poor penetration and retention in the glioblastoma parenchyma. As a prevailing component in the extracellular matrix of many solid tumors, fibrin plays a critical role in the maintenance of glioblastoma morphology and glioblastoma cell differentiation and proliferation. We developed a new drug-delivery system by conjugating polyethylene glycol–polylactic acid nanoparticles (NPs) with cysteine–arginine–glutamic acid–lysine–alanine (CREKA; TNPs), a peptide with special affinity for fibrin, to mediate glioblastoma-homing and prolong NP retention at the tumor site. In vitro binding tests indicated that CREKA significantly enhanced specific binding of NPs with fibrin. In vivo fluorescence imaging of glioblastoma-bearing nude mice, ex vivo brain imaging, and glioblastoma distribution demonstrated that TNPs had higher accumulation and longer retention in the glioblastoma site over unmodified NPs. Furthermore, pharmacodynamic results showed that paclitaxel-loaded TNPs significantly prolonged the median survival time of intracranial U87 glioblastoma-bearing nude mice compared with controls, Taxol, and NPs. These findings suggested that TNPs were able to target the glioblastoma and enhance retention, which is a valuable strategy for tumor therapy.
PMCID: PMC4235507  PMID: 25419130
CREKA peptide; nanoparticles; retention effect; paclitaxel; glioblastoma
12.  Hydroxyapatite-Coated Sillicone Rubber Enhanced Cell Adhesion and It May Be through the Interaction of EF1β and γ-Actin 
PLoS ONE  2014;9(11):e111503.
Silicone rubber (SR) is a common soft tissue filler material used in plastic surgery. However, it presents a poor surface for cellular adhesion and suffers from poor biocompatibility. In contrast, hydroxyapatite (HA), a prominent component of animal bone and teeth, can promote improved cell compatibility, but HA is an unsuitable filler material because of the brittleness in mechanism. In this study, using a simple and economical method, two sizes of HA was applied to coat on SR to counteract the poor biocompatibility of SR. Surface and mechanical properties of SR and HA/SRs confirmed that coating with HA changes the surface topology and material properties. Analysis of cell proliferation and adhesion as well as measurement of the expression levels of adhesion related molecules indicated that HA-coated SR significantly increased cell compatibility. Furthermore, mass spectrometry proved that the biocompatibility improvement may be related to elongation factor 1-beta (EF1β)/γ-actin adjusted cytoskeletal rearrangement.
PMCID: PMC4227678  PMID: 25386892
13.  Integrating PPI datasets with the PPI data from biomedical literature for protein complex detection 
BMC Medical Genomics  2014;7(Suppl 2):S3.
Protein complexes are important for understanding principles of cellular organization and function. High-throughput experimental techniques have produced a large amount of protein-protein interactions (PPIs), making it possible to predict protein complexes from protein-protein interaction networks. On the other hand, the rapidly growing biomedical literature provides a significantly large and readily available source of interaction data, which can be integrated into the protein network for better complex detection performance.
We present an approach of integrating PPI datasets with the PPI data from biomedical literature for protein complex detection. The approach applies a sophisticated natural language processing system, PPIExtractor, to extract PPI data from biomedical literature. These data are then integrated into the PPI datasets for complex detection.
The experimental results of the state-of-the-art complex detection method, ClusterONE, on five yeast PPI datasets verify our method's effectiveness: compared with the original PPI datasets, the average improvements of 3.976 and 5.416 percentage units in the maximum matching ratio (MMR) are achieved on the new networks using the MIPS and SGD gold standards, respectively. In addition, our approach also proves to be effective for three other complex detection algorithms proposed in recent years, i.e. CMC, COACH and RRW.
The rapidly growing biomedical literature provides a significantly large, readily available and relatively accurate source of interaction data, which can be integrated into the protein network for better protein complex detection performance.
PMCID: PMC4243118  PMID: 25350598
Protein-protein interaction network; Protein complexes; Information extraction; Text mining
14.  Combined Effects of Admission Serum Creatinine Concentration with Age and Gender on the Prognostic Significance of Subjects with Acute ST-Elevation Myocardial Infarction in China 
PLoS ONE  2014;9(10):e108986.
to explore the impact of admission serum creatinine concentration on the in-hospital mortality and its interaction with age and gender in patients with acute ST-segment elevation myocardial infarction (STEMI) in China.
1424 acute STEMI patients were enrolled in the study. Anthropometric and laboratory measurements were collected from every patient. A Cox proportional hazards regression model was used to determine the relationships between the admission serum creatinine level (Cr level), age, sex and the in-hospital mortality. A crossover analysis and a stratified analysis were used to determine the combined impact of Cr levels with age and gender.
Female (HR 1.687, 95%CI 1.051∼2.708), elevated Cr level (HR 5.922, 95%CI 3.780∼9,279) and old age (1.692, 95%CI 1.402∼2.403) were associated with a high risk of death respectively. After adjusting for other confounders, the renal dysfunction was still independently associated with a higher risk of death (HR 2.48, 95% CI 1.32∼4.63), while female gender (HR 1.19, 95%CI 0.62∼2.29) and old age (HR 1.77, 95%CI 0.92∼3.37) was not. In addition, crossover analysis revealed synergistic effects between elevated Cr level and female gender (SI = 3.01, SIM = 2.10, AP = 0.55). Stratified analysis showed that the impact of renal dysfunction on in-hospital mortality was more pronounced in patients <60 years old (odds ratios 11.10, 95% CI 3.72 to 33.14) compared with patients 60 to 74 years old (odds ratios 5.18, 95% CI 2.48∼10.83) and patients ≥75years old (odds ratios 3.99, 95% CI 1.89 to 8.42).
Serum Cr concentration on admission was a strong predictor for in-hospital mortality among Chinese acute STEMI patients especially in the young and the female.
PMCID: PMC4193830  PMID: 25303229
15.  Comparison of lower extremity atherosclerosis in diabetic and non-diabetic patients using multidetector computed tomography 
Lower extremity atherosclerosis (LEA) is among the most serious diabetic complications and leads to non-traumatic amputations. The recently developed dual-source CT (DSCT) and 320- multidetector computed tomography (MDCT) may help to detect plaques more precisely. The aim of our study was to evaluate the differences in LEA between diabetic and non-diabetic patients using MDCT angiography.
DSCT and 320-MDCT angiographies of the lower extremities were performed in 161 patients (60 diabetic and 101 non-diabetic). The plaque type, distribution, shape and obstructive natures were compared.
Compared with non-diabetic patients, diabetic patients had higher peripheral neuropathy, history of cerebrovasuclar infarction and hypertension rates. A total of 2898 vascular segments were included in the analysis. Plaque and stenosis were detected in 681 segments in 60 diabetic patients (63.1%) and 854 segments in 101 non-diabetic patients (46.9%; p <0.05). Regarding these plaques, diabetic patients had a higher incidence of mixed plaques (34.2% vs. 27.1% for non-diabetic patients). An increased moderate stenosis rate and decreased occlusion rate were observed in diabetic patients relative to non-diabetic patients (35.8% vs. 28.3%; and 6.6% vs. 11.4%; respectively). In diabetic patients, 362 (53.2%) plaques were detected in the distal lower leg segments, whereas in non-diabetic patients, 551 (64.5%) plaques were found in the proximal upper leg segments. The type IV plaque shape, in which the full lumen was involved, was detected more frequently in diabetic patients than in non-diabetic patients (13.1% vs. 8.2%).
Diabetes is associated with a higher incidence of plaque, increased incidence of mixed plaques, moderate stenosis and localisation primarily in the distal lower leg segments. The advanced and non-invasive MDCT could be used for routine preoperative evaluations of LEA.
PMCID: PMC4182836  PMID: 25252783
Diabetes mellitus; Lower extremity; Atherosclerosis; Computed tomography; Angiography
16.  Vaccine-Induced Env V1–V2 IgG3 Correlates with Lower HIV-1 Infection Risk and Declines Soon After Vaccination 
Science translational medicine  2014;6(228):228ra39.
HIV-1–specific immunoglobulin G (IgG) subclass antibodies bind to distinct cellular Fc receptors. Antibodies of the same epitope specificity but of a different subclass therefore can have different antibody effector functions. The study of IgG subclass profiles between different vaccine regimens used in clinical trials with divergent efficacy outcomes can provide information on the quality of the vaccine-induced B cell response. We show that HIV-1–specific IgG3 distinguished two HIV-1 vaccine efficacy studies (RV144 and VAX003 clinical trials) and correlated with decreased risk of HIV-1 infection in a blinded follow-up case-control study with the RV144 vaccine. HIV-1–specific IgG3 responses were not long-lived, which was consistent with the waning efficacy of the RV144 vaccine. These data suggest that specific vaccine-induced HIV-1 IgG3 should be tested in future studies of immune correlates in HIV-1 vaccine efficacy trials.
PMCID: PMC4116665  PMID: 24648342
17.  TGF-β upregulates CD70 expression and induces exhaustion of effector memory T cells in B-cell non-Hodgkin’s lymphoma 
Leukemia  2014;28(9):1872-1884.
Transforming growth factor beta (TGF-β) plays an important role in mediating T-cell suppression in B-cell non-Hodgkin lymphoma (NHL). However, the underlying mechanism responsible for TGF-β-mediated inhibition of effector memory T (Tm) cells is largely unknown. As reported here, we show that exhaustion is a major mechanism by which TGF-β inhibits Tm cells, and TGF-β mediated exhaustion is associated with upregulation of CD70. We found that TGF-β upregulates CD70 expression on effector Tm cells while it preferentially induces Foxp3 expression in naïve T cells. CD70 induction by TGF-β is Smad3-dependent and involves IL-2/Stat5 signaling. CD70+ T cells account for TGF-β-induced exhaustion of effector Tm cells. Both TGF-β-induced and preexisting intratumoral CD70+ effector Tm cells from B-cell NHL have an exhausted phenotype and express higher levels of PD-1 and TIM-3 compared to CD70− T cells. Signaling transduction, proliferation and cytokine production are profoundly decreased in these cells and they are highly susceptible to apoptosis. Clinically, intratumoral CD70-expressing T cells are prevalent in follicular B-cell lymphoma (FL) biopsy specimens, and increased numbers of intratumoral CD70+ T cells correlate with an inferior patient outcome. These findings confirm TGF-β-mediated effector Tm cell exhaustion as an important mechanism of immune suppression in B-cell NHL.
PMCID: PMC4145058  PMID: 24569779
TGF-β; CD70; T-cell exhaustion; B-cell non-Hodgkin lymphoma
18.  Assessing Right Ventricular Function in Patients with Hypertrophic Cardiomyopathy with Cardiac MRI: Correlation with the New York Heart Function Assessment (NYHA) Classification 
PLoS ONE  2014;9(9):e104312.
To determine whether 3.0-T magnetic resonance imaging (MRI) could assess right ventricular (RV) function in patients with hypertrophic cardiomyopathy (HCM), and if this assessment is correlated with the New York Heart Function Assessment (NYHA) classification.
Materials and Methods
Forty-six patients with HCM and 23 normal individuals were recruited. Left and right ventricular function parameters including end-diastolic and end-systolic volumes (EDV, ESV), stroke volume (SV) and ejection fraction (EF) and dimensions were measured and compared using 3.0-T MRI. RV function parameters between HCM patients and controls were compared using independent sample t tests. A one way ANOVA test with Bonferroni correction was used to determine significant differences among different NYHA groups. Receiver operating characteristic analyses calculated the sensitivity and specificity of RV dysfunction on MRI for the prediction of HCM severity.
Statistical analysis revealed significant differences of left ventricular (LV) and RV volumetric values and masses between the HCM patients and controls (all p<0.05). Within the HCM group, the simultaneously decreased maximum RVEDD correlated well with the LVEDD (r = 0.53; p<0.001). The function and dimension parameters among Class I to III were not determined to be significantly different (all p>0.05). However, significant differences between the Class IV and I-III groups (all P<0.0167) indicated that the diastolic and systolic function in both the RV and LV were impaired in Class IV patients. ROC analyses identified the EDV, ESV and EDD of both the LV and RV with a high sensitivity cutoff value to predict the HCM patients with severe heart failure (Class IV) with high sensitivity and specificity.
RV involvements were comparable to those of LV global function impairments in patients with HCM. The presence of RV dysfunction and decreased dimension on the MRI helped to predict the severe symptomatic HCM with high sensitivity and specificity.
PMCID: PMC4152157  PMID: 25180597
19.  NrdH Redoxin Enhances Resistance to Multiple Oxidative Stresses by Acting as a Peroxidase Cofactor in Corynebacterium glutamicum 
NrdH redoxins are small protein disulfide oxidoreductases behaving like thioredoxins but sharing a high amino acid sequence similarity to glutaredoxins. Although NrdH redoxins are supposed to be another candidate in the antioxidant system, their physiological roles in oxidative stress remain unclear. In this study, we confirmed that the Corynebacterium glutamicum NrdH redoxin catalytically reduces the disulfides in the class Ib ribonucleotide reductases (RNR), insulin and 5,5′-dithiobis-(2-nitrobenzoic acid) (DTNB), by exclusively receiving electrons from thioredoxin reductase. Overexpression of NrdH increased the resistance of C. glutamicum to multiple oxidative stresses by reducing ROS accumulation. Accordingly, elevated expression of the nrdH gene was observed when the C. glutamicum wild-type strain was exposed to oxidative stress conditions. It was discovered that the NrdH-mediated resistance to oxidative stresses was largely dependent on the presence of the thiol peroxidase Prx, as the increased resistance to oxidative stresses mediated by overexpression of NrdH was largely abrogated in the prx mutant. Furthermore, we showed that NrdH facilitated the hydroperoxide reduction activity of Prx by directly targeting and serving as its electron donor. Thus, we present evidence that the NrdH redoxin can protect against the damaging effects of reactive oxygen species (ROS) induced by various exogenous oxidative stresses by acting as a peroxidase cofactor.
PMCID: PMC3957609  PMID: 24375145
20.  A homolog of glyceraldehyde-3-phosphate dehydrogenase from Riemerella anatipestifer is an extracellular protein and exhibits biological activity*  
Riemerella anatipestifer is the causative agent of septicemia anserum exsudativa in ducks. Its pathogenesis and virulence factors are still unclear. The glycolytic enzyme, glyceraldehyde-3-phosphate dehydrogenase (GAPDH), an anchorless and multifunctional protein on the surface of several pathogenic microorganisms, is involved in virulence and adhesion. Whether homologs of GAPDH exist, and display similar characteristics in R. anatipestifer (RaGAPDH) has not been determined. In our research, the RaGAPDH activity from various R. anatipestifer isolates was confirmed. Twenty-two gapdh genes from genomic DNA of R. anatipestifer isolates were cloned and sequenced for phylogenetic analysis. The distribution of RaGAPDH in R. anatipestifer CZ2 strain was confirmed by antisera to recombinant RaGAPDH. The ability of purified RaGAPDH to bind host proteins was analyzed by solid-phase ligand-binding assay. Results revealed that all R. anatipestifer isolates showed different levels of GAPDH activity except four strains, which contained a gapdh-like gene. The gapdh of R. anatipestifer, which is located phylogenetically in the same branch as enterohemorrhagic Escherichia coli (EHEC), belonged to class I GAPDH, and encoded a 36.7-kDa protein. All RaGAPDH-encoding gene sequences from field isolates of R. anatipestifer displayed 100% homology. The RaGAPDH localized on the extracellular membrane of several R. anatipestifer strains. Further, it was released into the culture medium, and exhibited GAPDH enzyme activity. We also confirmed the binding of RaGAPDH to plasminogen and fibrinogen. These results demonstrated that GAPDH was present in R. anatipestifer, although not in all strains, and that RaGAPDH might contribute to the microorganism’s virulence.
PMCID: PMC4162879  PMID: 25183032
Riemerella anatipestifer; Glyceraldehyde-3-phosphate dehydrogenase (GAPDH); Extracellular protein
21.  Risk factors associated with missed colorectal flat adenoma: A multicenter retrospective tandem colonoscopy study 
World Journal of Gastroenterology : WJG  2014;20(31):10927-10937.
AIM: To determine the miss rate for colorectal flat adenomas during colonoscopy and the risk factors.
METHODS: Flat adenomas are frequently missed during colonoscopy. However, the risk factors that influence their miss rates are unclear. This was a multicenter, retrospective study in which patients diagnosed with colorectal adenomas at a diagnostic colonoscopy and followed within 3 mo by a second therapeutic colonoscopy were pooled out from the established database. The “per-patient” and “per-adenoma” adenoma miss rates (AMR) for overall adenomas and flat adenomas, and patient-, adenoma-, and procedure-related risk factors potentially associated with the “per-adenoma” AMR for flat adenomas were determined.
RESULTS: Chromoscopy and high-definition colonoscopy were not taken under consideration in the study. Among 2093 patients with colorectal adenomas, 691 (33.0%) were diagnosed with flat adenomas, 514 with concomitant protruding adenomas and 177 without. The “per-patient” AMR for flat adenomas was 43.3% (299/691); the rates were 54.3% and 11.3%, respectively, for those with protruding adenomas and those without (OR = 9.320, 95%CI: 5.672-15.314, χ2 = 99.084, P < 0.001). The “per-adenoma” AMR for flat adenomas was 44.3% (406/916). In multivariate analysis, older age, presence of concomitant protruding adenomas, poor bowel preparation, smaller adenoma size, location at the right colon, insufficient experience of the colonoscopist, and withdrawal time < 6 min were associated with an increased “per-adenoma” AMR for flat adenomas. The AMR for flat adenomas was moderately correlated with that for overall adenomas (r = 0.516, P < 0.0001). The AMR for flat adenomas during colonoscopy was high.
CONCLUSION: Patient’s age, concomitant protruding adenomas, bowel preparation, size and location of adenomas, proficiency of the colonoscopist, and withdrawal time are factors affecting the “per-adenoma” AMR for flat adenomas.
PMCID: PMC4138473  PMID: 25152596
Flat adenoma; Colorectal cancer; Miss rate; Risk factor; Colonoscopy
22.  Tumor Bioengineering Using a Transglutaminase Crosslinked Hydrogel 
PLoS ONE  2014;9(8):e105616.
Development of a physiologically relevant 3D model system for cancer research and drug development is a current challenge. We have adopted a 3D culture system based on a transglutaminase-crosslinked gelatin gel (Col-Tgel) to mimic the tumor 3D microenvironment. The system has several unique advantages over other alternatives including presenting cell-matrix interaction sites from collagen-derived peptides, geometry-initiated multicellular tumor spheroids, and metabolic gradients in the tumor microenvironment. Also it provides a controllable wide spectrum of gel stiffness for mechanical signals, and technical compatibility with imaging based screening due to its transparent properties. In addition, the Col-Tgel provides a cure-in-situ delivery vehicle for tumor xenograft formation in animals enhancing tumor cell uptake rate. Overall, this distinctive 3D system could offer a platform to more accurately mimic in vivo situations to study tumor formation and progression both in vitro and in vivo.
PMCID: PMC4136878  PMID: 25133673
23.  Antisense knockdown of pyruvate dehydrogenase kinase promotes the neutral lipid accumulation in the diatom Phaeodactylum tricornutum 
Microbial Cell Factories  2014;13(1):100.
Microalgae have been an emerging biofuel resource; however, the germplasm improvement has been slow due to the lack of molecular tools. Pyruvate dehydrogenase kinase (PDK) deactivates the pyruvate dehydrogenase complex (PDC) which catalyzes the oxidative decarboxylation of pyruvate. Acetyl-CoA production via PDC is important in plant tissues that are active in fatty acid synthesis.
A 1261-bp cDNA of a putative PDK gene (PtPDK) was cloned from a diatom Phaeodactylum tricornutum, and PtPDK antisense knockdown transgenic diatoms were generated. Both PtPDK transcript abundance and enzyme activity were reduced significantly due to antisense knockdown of PtPDK. Neutral lipid content of transgenic diatom cells increased up to 82% as determined by Nile red staining, and fatty acid composition was not altered. Transgenic cells showed slightly lower growth rate but similar cell size with the wild type, hence retaining similar biomass productivity.
This work first obtained a successful engineered diatom regulating a key gene involved in lipid metabolism. Our findings also provide powerful indications in enhancing microalgal lipid production by metabolic engineering for biofuel industry.
PMCID: PMC4251698  PMID: 25106441
Microalga; Pyruvate dehydrogenase kinase; Antisense; Lipid; Biofuel
24.  Nitrogenase Reduction of Carbon-Containing Compounds 
Biochimica et biophysica acta  2013;1827(0):1102-1111.
Nitrogenase is an enzyme found in many bacteria and archaea that catalyzes biological dinitrogen fixation, the reduction of N2 to NH3, accounting for the major input of fixed nitrogen into the biogeochemical N cycle. In addition to reducing N2 and protons, nitrogenase can reduce a number of small, non-physiological substrates. Among these alternative substrates are included a wide array of carbon containing compounds. These compounds have provided unique insights into aspects of the nitrogenase mechanism. Recently, it was shown that carbon monoxide (CO) and carbon dioxide (CO2) can also be reduced by nitrogenase to yield hydrocarbons, opening new insights into the mechanism of small molecule activation and reduction by this complex enzyme as well as providing clues for the design of novel molecular catalysts.
PMCID: PMC3714343  PMID: 23597875
25.  Immunological and Virological Mechanisms of Vaccine-Mediated Protection Against SIV and HIV 
Nature  2013;505(7484):502-508.
A major challenge for the development of a highly effective AIDS vaccine is the identification of mechanisms of protective immunity. To address this question, we used a non-human primate challenge model with simian immunodeficiency virus (SIV). We show that antibodies to the SIV Envelope are necessary and sufficient to prevent infection. Moreover, sequencing of viruses from breakthrough infections revealed selective pressure against neutralization-sensitive viruses; we identified a two amino acid signature that alters antigenicity and confers neutralization resistance. A similar signature confers resistance of HIV-1 to neutralization by monoclonal antibodies against variable regions 1 and 2 (V1V2), suggesting that SIV and HIV share a fundamental mechanism of immune escape from vaccine- or naturally-elicited antibodies. These analyses provide insight into the limited efficacy seen in HIV vaccine trials.
PMCID: PMC3946913  PMID: 24352234

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