Search tips
Search criteria

Results 1-25 (397)

Clipboard (0)

Select a Filter Below

more »
Year of Publication
more »
1.  Backbone resonance assignments of the 42 kDa enzyme arginine kinase in the transition state analogue form 
Biomolecular NMR assignments  2013;8(2):335-338.
Nearly complete backbone resonance assignments for the 357 residue, 42 kDa enzyme arginine kinase in a transition state analogue (TSA) complex are presented. The TSA is a quaternary complex of arginine kinase, MgADP, arginine, and nitrate. About 93% (320 of 344) of the non-proline backbone amides were assigned using an enzyme enriched with 2H,13C, and 15N in combination with three enzyme samples prepared with a single 15N-labeled amino acid (K, L, and R). The amide assignments will provide the foundation for investigating the dynamics of arginine kinase when in a TSA complex.
PMCID: PMC3906217  PMID: 23893440
Arginine kinase; phosphagen kinase; NMR spectroscopy; resonance assignment; enzyme dynamics; transition state analogue
2.  Quercetin attenuates doxorubicin cardiotoxicity by modulating Bmi-1 expression 
British Journal of Pharmacology  2014;171(19):4440-4454.
Background and Purpose
Doxorubicin-based chemotherapy induces cardiotoxicity, which limits its clinical application. We previously reported the protective effects of quercetin against doxorubicin-induced hepatotoxicity. In this study, we tested the effects of quercetin on the expression of Bmi-1, a protein regulating mitochondrial function and ROS generation, as a mechanism underlying quercetin-mediated protection against doxorubicin-induced cardiotoxicity.
Experimental Approach
Effects of quercetin on doxorubicin-induced cardiotoxicity was evaluated using H9c2 cardiomyocytes and C57BL/6 mice. Changes in apoptosis, mitochondrial function, oxidative stress and related signalling were evaluated in H9c2 cells. Cardiac function, serum enzyme activity and reactive oxygen species (ROS) generation were measured in mice after a single injection of doxorubicin with or without quercetin pre-treatment.
Key Results
In H9c2 cells, quercetin reduced doxorubicin-induced apoptosis, mitochondrial dysfunction, ROS generation and DNA double-strand breaks. The quercetin-mediated protection against doxorubicin toxicity was characterized by decreased expression of Bid, p53 and oxidase (p47 and Nox1) and by increased expression of Bcl-2 and Bmi-1. Bmi-1 siRNA abolished the protective effect of quercetin against doxorubicin-induced toxicity in H9c2 cells. Furthermore, quercetin protected mice from doxorubicin-induced cardiac dysfunction that was accompanied by reduced ROS levels and lipid peroxidation, but enhanced the expression of Bmi-1 and anti-oxidative superoxide dismutase.
Conclusions and Implications
Our results demonstrate that quercetin decreased doxorubicin-induced cardiotoxicity in vitro and in vivo by reducing oxidative stress by up-regulation of Bmi-1 expression. The findings presented in this study have potential applications in preventing doxorubicin-induced cardiomyopathy.
PMCID: PMC4209150  PMID: 24902966
3.  An Unexpected Deamination Reaction after Hydrolysis of the Pyrimidine (6-4) Pyrimidone Photoproduct 
Organic Letters  2014;16(19):5076-5079.
Pyrimidine (6-4) pyrimidone photoproduct (6-4PP), a common DNA photolesion formed under solar irradiation, was indicated to hydrolyze under strong basic conditions, breaking the N3–C4 bond at the 5′-thymine. The reanalysis of this reaction revealed that the resulting water adduct may not be stable as previously proposed; it readily undergoes an esterification reaction induced by the 5-OH group at 6-4PP to form a five-membered ring, eliminating a molecule of ammonia.
PMCID: PMC4184442  PMID: 25250878
4.  Postoperative external beam irradiation with and without brachytherapy in pelvic node-positive IB1-IIA2 cervical cancer patients: a retrospective clinical study 
This study assessed the survival outcomes and recurrent patterns in pelvic node-positive IB1-IIA2 cervical cancer patients treated with postoperative external beam irradiation with or without vaginal brachytherapy.
The records of 1149 cervical cancer patients received radical surgery between February 2008 and March 2010 were retrospectively reviewed. 126 stages IB1-IIA2 patients with positive pelvic lymph node (LN) were included and a total of 113 patients who received different postoperative radiation therapy were identified and analyzed. Of the enrolled patients, 55 patients received pelvic external beam radiotherapy (EBRT) without vaginal brachytherapy and 58 patients received pelvic EBRT with vaginal brachytherapy. Treatment-related toxicities were evaluated. Progression-free survival (PFS) and overall survival (OS) were analyzed using Kaplan-Meier estimates and statistical significance was determined using the log-rank test.
With a median follow-up of 47 months (range: 10–61 months), the group which had pelvic EBRT with brachytherapy had a significantly improved 5-year PFS rate (P = 0.044), but no significant difference in 5-year overall survival was found between the two groups (P = 0.437). In patients treated without brachytherapy, the most common site of relapse was the pelvis. No significant differences were found regards to acute and chronic radiation toxicities, including myelosuppression, dermatitis, enterocolitis, proctitis and cystitis (P = 0.485, 0.875, 0.671, 0.459 and 0.969 respectively) between the groups of pelvic EBRT with and without vaginal brachytherapy.
Treated with pelvic EBRT in combination with vaginal brachytherapy, cervical cancer patients with positive pelvic lymph node had a reduced risk of locoregional recurrence without increased side effects compared with patients treated with pelvic EBRT without vaginal brachytherapy.
PMCID: PMC4574344  PMID: 26377326
5.  Tetrandrine suppresses proliferation, induces apoptosis, and inhibits migration and invasion in human prostate cancer cells 
Asian Journal of Andrology  2015;17(5):850-853.
Tetrandrine (TET), a traditional Chinese medicine, exerts remarkable anticancer activity on various cancer cells. However, little is known about the effect of TET on human prostate cancer cells, and the mechanism of function of TET on prostate cancer has not yet been elucidated. To investigate the effects of TET on the suppression of proliferation, induction of apoptosis, and inhibition of migration and invasion in human prostate cancer cell lines, DU145 and PC-3. Inhibition of growth was determined by 3-(4,5-dimethylthiazol-2-yl)-2,5-diphenyltetrazolium bromide assay and clone formation assay, and flow cytometry analysis was performed to detect the induction of apoptosis. Activation of poly (ADP-ribose) polymerase, caspase-3, Akt, phospho-Akt, Bcl-2, and Bax was analyzed by Western blotting. Wound healing assay and transwell migration assay were used to evaluate the effect of TET on migration and invasion of cancer cells. TET inhibited the growth of DU145 and PC–3 cells in a dose- and time-dependent manner. Cell cloning was inhibited in the presence of TET in DU145 and PC-3 cells. TET suppressed the migration of DU145 and PC-3 cells. Transwell invasion assay showed that TET significantly weakened invasion capacity of DU145 and PC-3 cells. TET exhibited strong inhibitory effect on proliferation, migration, and invasion of prostate cancer cells. In addition, TET induced apoptosis in a dose-dependent manner by activating the caspase cascade and inhibiting phosphoinositide 3-kinase-Akt signal pathway. The accumulating evidence suggests that TET could be a potential therapeutic candidate against prostate cancer in a clinical setting.
PMCID: PMC4577603  PMID: 25677131
apoptosis; invasion; migration; proliferation; prostate cancer; tetrandrine
6.  Prognostic value and clinicopathological significance of epithelial cadherin expression in non-small cell lung cancer 
Thoracic Cancer  2015;6(5):589-596.
Epithelial cadherin (E-cadherin), a calcium-dependent cell-cell adhesion molecule, as an important adhesion and signaling pathway mediator plays key roles in the maintenance of tissue integrity. However, the available results of E-cadherin expression and its prognostic value on non-small cell lung cancer (NSCLC) remain controversial. Therefore, a meta-analysis of published studies investigating the prognostic value of E-cadherin expression and its association with clinicopathological characteristics with NSCLC was performed.
A literature search via PubMed, EMBASE, and MEDLINE (Ovid) databases was conducted. Data from eligible studies were extracted. Statistical analysis was performed using STATA 12.0.
A total of 2412 patients from 15 studies were included in the meta-analysis. The results showed that the pooled hazard ratio (HR) for overall survival was 0.55 (95% confidence interval [CI]: 0.44–0.69) by univariate analysis and 0.68 (95% CI: 0.43–1.08) by multivariate analysis. In addition, the results showed a significant association between E-cadherin expression and the presence of lymph node metastasis (odds ratio = 0.37, 95% CI=0.05–0.69, P = 0.001).
Our study showed that positive expression of E-cadherin was associated with a favorable prognosis in patients with NSCLC, and might act as an inhibition factor of metastasis. However, adequately designed prospective studies are required to confirm this finding.
PMCID: PMC4567004  PMID: 26445607
E-cadherin; meta-analysis; metastasis; non-small cell lung cancer (NSCLC); overall survival (OS)
7.  CYP450 Enzyme-Mediated Metabolism of TCAS and Its Inhibitory and Induced Effects on Metabolized Enzymes in Vitro 
In this study, we investigated the enzymes catalyzing the phaseⅠmetabolism of thiacalixarene (TCAS) based on in vitro system including cDNA-expressed P450 enzymes, human liver microsomes plus inhibitors and monoclonal antibodies. In addition, the inhibitory potential of TCAS on major CYP450 drug metabolizing enzymes (CYP1A2, CYP2C9, CYP2B6, CYP2D6 and CYP3A4) was assessed. The results showed that CYP1A2 and CYP2C9 mediated TCAS hydroxylation. IC50 values for TCAS in rat and human liver microsomes were greater than 50 µM, and it demonstrated a weak inhibition of rat and human CYP450 enzymes. Finally, sandwiched hepatocytes were used to evaluate the induction of CYP1A and CYP3A to define the function of TCAS in vivo. The results showed that incubation of TCAS at different concentrations for 72 h failed to induce CYP1A and CYP3A. However, incubation of the cells with 50 and 100 µM TCAS caused a profound decrease in the activities of CYP1A and CYP3A, which was probably due to cytotoxic effects, suggesting that exposure to TCAS might be a health concern.
PMCID: PMC4586642  PMID: 26404338
thiacalix[4]arene tetrasulfonate; CYP450; hepatocyte; metabolism
8.  Reactivity of Damaged Pyrimidines: DNA Cleavage via Hemiaminal Formation at the C4 Positions of the Saturated Thymine of Spore Photoproduct and Dihydrouridine 
Journal of the American Chemical Society  2014;136(37):12938-12946.
Described here are mechanistic details of the chemical reactivities of two modified/saturated pyrimidine residues that represent naturally occurring forms of DNA damage: 5-thyminyl-5,6-dihydrothymine, commonly referred to as the “spore photoproduct” (SP), and 5,6-dihydro-2′-deoxyuridine (dHdU), formed via ionizing radiation damage to cytosine under anoxic conditions and also serving as a general model of saturated pyrimidine residues. It is shown that due to the loss of the pyrimidine C5–C6 double bond and consequent loss of ring aromaticity, the C4 position of both these saturated pyrimidines is prone to the formation of a hemiaminal intermediate via water addition. Water addition is facilitated by basic conditions; however, it also occurs at physiological pH at a slower rate. The hemiaminal species so-formed subsequently converts to a ring-opened hydrolysis product through cleavage of the pyrimidine N3–C4 bond. Further decomposition of this ring-opened product above physiological pH leads to DNA strand break formation. Taken together, these results suggest that once the aromaticity of a pyrimidine residue is lost, the C4 position becomes a “hot spot” for the formation of a tetrahedral intermediate, the decay of which triggers a cascade of elimination reactions that can under certain conditions convert a simple nucleobase modification into a DNA strand break.
PMCID: PMC4183628  PMID: 25127075
9.  The roles of ERAS during cell lineage specification of mouse early embryonic development 
Open Biology  2015;5(8):150092.
Eras encodes a Ras-like GTPase protein that was originally identified as an embryonic stem cell-specific Ras. ERAS has been known to be required for the growth of embryonic stem cells and stimulates somatic cell reprogramming, suggesting its roles on mouse early embryonic development. We now report a dynamic expression pattern of Eras during mouse peri-implantation development: its expression increases at the blastocyst stage, and specifically decreases in E7.5 mesoderm. In accordance with its expression pattern, the increased expression of Eras promotes cell proliferation through controlling AKT activation and the commitment from ground to primed state through ERK activation in mouse embryonic stem cells; and the reduced expression of Eras facilitates primitive streak and mesoderm formation through AKT inhibition during gastrulation. The expression of Eras is finely regulated to match its roles in mouse early embryonic development during which Eras expression is negatively regulated by the β-catenin pathway. Thus, beyond its well-known role on cell proliferation, ERAS may also play important roles in cell lineage specification during mouse early embryonic development.
PMCID: PMC4554925  PMID: 26269429
Eras; primitive streak; mesoderm; embryonic stem cells; cell lineage
10.  Effect of Iodine Intake on p14ARF and p16INK4a Expression in Thyroid Papillary Carcinoma in Rats 
Iodine intake is related to thyroid disease. This study investigated the effect of the amount of iodine intake on p14ARF and p16INK4a expression of thyroid papillary carcinoma in rats.
A cohort of 240 SD rats were randomly divided into control group, low iodine, normal iodine, and high iodine groups (n=60 per group). We inoculated 2×105 papillary thyroid carcinoma (PTC) cells on the left side of the thyroid gland. After 6 and 12 weeks, serum thyroid hormone level and urine iodine level were measured in addition to morphological observations of tumor tissues. Expression of p14ARF, p16INK4a was detected by immunohistochemical staining.
The expression of p14ARF, p16INK4a, FT3, and FT4 levels in all iodine-treated animals were significantly lower than in the control group, while TSH level was significantly higher (P<0.05). Compared to the normal iodine group, the low and high groups had lower p14ARF and p16INK4a expression, lower FT3 and FT4 levels, higher TSH levels, and heavier tumors (P<0.05). In a further between-group comparison, p14ARF and p16INK4a expression and FT3 and FT4 levels at 12 weeks were lower than at 6 weeks. Expression of p14ARF and p16INK4a were positively correlated with FT3 and FT4, and negatively correlated with TSH and tumor weight.
Low and high iodine diet intake could reduce p14ARF and p16INK4a expressions and promote tumor development.
PMCID: PMC4532191  PMID: 26248224
Genes, p16; Iodine; Thyroiditis, Suppurative; Tumor Suppressor Protein p14ARF
11.  Optical-Resolution Photoacoustic Microscopy for Volumetric and Spectral Analysis of Histological and Immunochemical Samples** 
Optical-resolution photoacoustic microscopy (OR-PAM) is an imaging modality with superb penetration depth and excellent absorption contrast. Here we demonstrate, for the first time, that this technique can advance quantitative analysis of conventional chromogenic histochemistry. Because OR-PAM can quantify the absorption contrast at different wavelengths, it is feasible to spectrally resolve the specific biomolecules involved in a staining color. Furthermore, the tomographic capability of OR-PAM allows for non-invasive volumetric imaging of a thick sample without microtoming it. By immunostaining the sample with different chromogenic agents, we further demonstrated the ability of OP-PAM to resolve different types of cells in a co-culture sample with imaging depths up to 1 mm. Taken together, the integration of OR-PAM with (immuno)histochemistry offers a simple and versatile technique with broad applications in cell biology, pathology, tissue engineering, and related biomedical studies.
PMCID: PMC4116434  PMID: 24961608
photoacoustic microscopy; biomedical imaging; histochemistry; cell biology; tissue engineering
12.  Monitoring brain development of chick embryos in vivo using 3.0 T MRI: subdivision volume change and preliminary structural quantification using DTI 
Magnetic resonance imaging (MRI) has many advantages in the research of in vivo embryonic brain development, specifically its noninvasive aspects and ability to avoid skeletal interference. However, few studies have focused on brain development in chick, which is a traditional animal model in developmental biology. We aimed to serially monitor chick embryo brain development in vivo using 3.0 T MRI.
Ten fertile Hy-line white eggs were incubated and seven chick embryo brains were monitored in vivo and analyzed serially from 5 to 20 days during incubation using 3.0 T MRI. A fast positioning sequence was pre-scanned to obtain sagittal and coronal brain planes corresponding to the established atlas. T2-weighted imaging (T2WI) was performed for volume estimation of the whole brain and subdivision (telencephalon, cerebellum, brainstem, and lateral ventricle [LV]); diffusion tensor imaging (DTI) was used to reflect the evolution of neural bundle structures.
The chick embryos’ whole brain and subdivision grew non-linearly over time; the DTI fractional anisotropy (FA) value within the telencephalon increased non-linearly as well. All seven scanned eggs hatched successfully.
MRI avoids embryonic sacrifice in a way that allows serial monitoring of longitudinal developmental processes of a single embryo. Feasibility for analyzing subdivision of the brain during development, and adding structural information related to neural bundles, makes MRI a powerful tool for exploring brain development.
PMCID: PMC4513430  PMID: 26208519
Chick embryo; Brain development; In vivo; Magnetic resonance imaging; Diffusion tensor imaging
13.  Targeting BTK with Ibrutinib in Relapsed or Refractory Mantle-Cell Lymphoma 
The New England journal of medicine  2013;369(6):507-516.
Bruton's tyrosine kinase (BTK) is a mediator of the B-cell–receptor signaling pathway implicated in the pathogenesis of B-cell cancers. In a phase 1 study, ibrutinib, a BTK inhibitor, showed antitumor activity in several types of non-Hodgkin's lymphoma, including mantle-cell lymphoma.
In this phase 2 study, we investigated oral ibrutinib, at a daily dose of 560 mg, in 111 patients with relapsed or refractory mantle-cell lymphoma. Patients were enrolled into two groups: those who had previously received at least 2 cycles of bortezomib therapy and those who had received less than 2 complete cycles of bortezomib or had received no prior bortezomib therapy. The primary end point was the overall response rate. Secondary end points were duration of response, progression-free survival, overall survival, and safety.
The median age was 68 years, and 86% of patients had intermediate-risk or high-risk mantle-cell lymphoma according to clinical prognostic factors. Patients had received a median of three prior therapies. The most common treatment-related adverse events were mild or moderate diarrhea, fatigue, and nausea. Grade 3 or higher hematologic events were infrequent and included neutropenia (in 16% of patients), thrombocytopenia (in 11%), and anemia (in 10%). A response rate of 68% (75 patients) was observed, with a complete response rate of 21% and a partial response rate of 47%; prior treatment with bortezomib had no effect on the response rate. With an estimated median follow-up of 15.3 months, the estimated median response duration was 17.5 months (95% confidence interval [CI], 15.8 to not reached), the estimated median progression-free survival was 13.9 months (95% CI, 7.0 to not reached), and the median overall survival was not reached. The estimated rate of overall survival was 58% at 18 months.
Ibrutinib shows durable single-agent efficacy in relapsed or refractory mantle-cell lymphoma. (Funded by Pharmacyclics and others; number, NCT01236391.)
PMCID: PMC4513941  PMID: 23782157
14.  A β-Fluoroamine Inhibitor of Purine Nucleoside Phosphorylase 
Journal of medicinal chemistry  2008;51(18):5880-5884.
The potent immucillin purine nucleoside phosphorylase (PNP) inhibitors F-DADMe-ImmH [(3S,4S)−3], and [(3R,4R)−3] are synthesized in seven steps. Cycloaddition to a fluoroalkene and an enzymic resolution are the key features of the construction of the fluoropyrrolidines 11, from which the immucillins are assembled by use of a three-component Mannich reaction. Slow-onset binding constants (Ki∗) for [(3S,4S)−3] and [(3R,4R)−3] with human PNP are 0.032 and 1.82 nM, respectively. F-DADMe-ImmH [(3S,4S)−3] exhibits oral availability in mice at doses as low as 0.2 mg/kg.
PMCID: PMC4508846  PMID: 18800772
15.  Delta Inulin Adjuvant Enhances Plasmablast Generation, Expression of Activation-Induced Cytidine Deaminase and B-Cell Affinity Maturation in Human Subjects Receiving Seasonal Influenza Vaccine 
PLoS ONE  2015;10(7):e0132003.
There is a major need for new adjuvants to improve the efficacy of seasonal and pandemic influenza vaccines. Advax is a novel polysaccharide adjuvant based on delta inulin that has been shown to enhance the immunogenicity of influenza vaccine in animal models and human clinical trials. To better understand the mechanism for this enhancement, we sought to assess its effect on the plasmablast response in human subjects. This pilot study utilised cryopreserved 7 day post-vaccination (7dpv) peripheral blood mononuclear cell samples obtained from a subset of 25 adult subjects from the FLU006-12 trial who had been immunized intramuscularly with a standard dose of 2012 trivalent inactivated influenza vaccine (TIV) alone (n=9 subjects) or combined with 5mg (n=8) or 10mg (n=8) of Advax adjuvant. Subjects receiving Advax adjuvant had increased 7dpv plasmablasts, which in turn exhibited a 2-3 fold higher rate of non-silent mutations in the B-cell receptor CDR3 region associated with higher expression of activation-induced cytidine deaminase (AID), the major enzyme controlling BCR affinity maturation. Together, these data suggest that Advax adjuvant enhances influenza immunity in immunized subjects via multiple mechanisms including increased plasmablast generation, AID expression and CDR3 mutagenesis resulting in enhanced BCR affinity maturation and increased production of high avidity antibody. How Advax adjuvant achieves these beneficial effects on plasmablasts remains the subject of ongoing investigation.
Trial Registration
Australia New Zealand Clinical Trials Register ACTRN12612000709842
PMCID: PMC4503308  PMID: 26177480
16.  Superovulation Induced Changes of Lipid Metabolism in Ovaries and Embryos and Its Probable Mechanism 
PLoS ONE  2015;10(7):e0132638.
This research was intended to investigate the fetal origins of changed birth weight of the offspring born through assisted reproductive technology (ART). The association between hormone and lipid metabolism or body weight has been generally accepted, and as the basic and specific treatment in ART procedure, gonadotropin stimulation might have potential effects on intrauterine lipid metabolism. In our studies, the mice were superovulated with two doses of gonadotropin. The cholesterol metabolism in ovaries and the triglyceride metabolism in embryos were analyzed. The results showed gonadotropin probably accelerated luteinization and induced a longer time follicle development and ovulation, which resulted in histological and morphological alteration of ovary, and increased the cholesterol content and the expressions of steroidogenesis-related genes. In embryos, gonadotropin increased lipid accumulation and decreased fatty acid synthesis in a dose-dependent manner. Moreover, the changes of fatty acid composition were also shown in superovulation groups. Our studies firstly provided the evidence that the superovulation might affect the maternal and fetal lipid metabolism. These variations of lipid metabolism in our results may be associated with birth weight of ART infants.
PMCID: PMC4500408  PMID: 26167919
17.  Slit2 as a β-catenin/Ctnnb1-dependent retrograde signal for presynaptic differentiation 
eLife  null;4:e07266.
Neuromuscular junction formation requires proper interaction between motoneurons and muscle cells. β-Catenin (Ctnnb1) in muscle is critical for motoneuron differentiation; however, little is known about the relevant retrograde signal. In this paper, we dissected which functions of muscle Ctnnb1 are critical by an in vivo transgenic approach. We show that Ctnnb1 mutant without the transactivation domain was unable to rescue presynaptic deficits of Ctnnb1 mutation, indicating the involvement of transcription regulation. On the other hand, the cell-adhesion function of Ctnnb1 is dispensable. We screened for proteins that may serve as a Ctnnb1-directed retrograde factor and identified Slit2. Transgenic expression of Slit2 specifically in the muscle was able to diminish presynaptic deficits by Ctnnb1 mutation in mice. Slit2 immobilized on beads was able to induce synaptophysin puncta in axons of spinal cord explants. Together, these observations suggest that Slit2 serves as a factor utilized by muscle Ctnnb1 to direct presynaptic differentiation.
eLife digest
Motor nerves are like electrical wires that connect our spinal cord to the muscles in our body. These nerves communicate with muscles across a connection called the neuromuscular junction. To first form a neuromuscular junction, the motor nerves and muscles each produce molecular cues that tell each other to do their part to build a connection. Beta-catenin in the muscle is known to regulate motor nerve development. However, beta-catenin has two different roles: it helps to coordinate whether neighboring cells stick together, and it can regulate which genes are ‘transcribed’ to produce proteins. It was not known which of these roles is necessary for forming neuromuscular junctions.
Wu, Barik et al. now investigate this question by creating mice with mutant forms of beta-catenin in their muscles. Some mice had muscle beta-catenin that could not help cells stick together, and others had beta-catenin that could not control gene transcription. Only mutations that affected the ability of beta-catenin to control transcription caused abnormalities in the neuromuscular junction. However, these problems could be fixed by adding either normal beta-catenin or the mutant form that cannot help cells stick together.
Wu, Barik et al. then used molecular tools to explore which genes are turned on by beta-catenin. The experiments showed that beta-catenin causes muscle fibers to produce a protein called Slit2—a developmental cue that controls where neurons grow. Furthermore, the neuromuscular junction defects found in mice without beta-catenin in their muscles could be reduced by making the muscle fibers produce more Slit2. However, not all defects in beta-catenin mutant mice are rescued by Slit2. Future research is needed to identify other beta-catenin-controlled signals and to determine whether such a pathway is altered in neuromuscular disorders.
PMCID: PMC4498096  PMID: 26159615
Ctnnb1; Wnt; NMJ; mouse
18.  Hydrogen sulfide protects spinal cord and induces autophagy via miR-30c in a rat model of spinal cord ischemia-reperfusion injury 
Hydrogen sulfide (H2S), a novel gaseous mediator, has been recognized as an important neuromodulator and neuroprotective agent in the nervous system. The present study was undertaken to study the effects of exogenous H2S on ischemia/reperfusion (I/R) injury of spinal cord and the underlying mechanisms.
The effects of exogenous H2S on I/R injury were examined by using assessment of hind motor function, spinal cord infarct zone by Triphenyltetrazolium chloride (TTC) staining. Autophagy was evaluated by expressions of Microtubule associated protein 1 light chain 3 (LC3) and Beclin-1 which were determined by using Quantitative Real-Time PCR and Western blotting, respectively.
Compared to I/R injury groups, H2S pretreatment had reduced spinal cord infarct zone, improved hind motor function in rats. Quantitative Real-Time PCR or Western blotting results showed that H2S pretreatment also downregulated miR-30c expression and upregulated Beclin-1 and LC3II expression in spinal cord. In vitro, miR-30c was showed to exert negative effect on Beclin-1 expression by targeting its 3’UTR in SY-SH-5Y cells treated with Oxygen, Glucose Deprivation (OGD). In rat model of I/R injury, pretreatment of pre-miR-30c or 3-MA (an inhibitor for autophagy) can abrogated spinal cord protective effect of H2S.
H2S protects spinal cord and induces autophagy via miR-30c in a rat model of spinal cord hemia-reperfusion injury.
PMCID: PMC4491897  PMID: 26149869
Autophagy; Beclin-1; miR-30c; Microtubule associated protein 1 light chain 3 (LC3); Oxygen glucose deprivation (OGD)
19.  Effect of Acute Hypercapnia on Outcomes and Predictive Risk Factors for Complications among Patients Receiving Bronchoscopic Interventions under General Anesthesia 
PLoS ONE  2015;10(7):e0130771.
The aim of this study is to investigate the effect of acute hypercapnia on surgery outcomes among patients receiving bronchoscopic interventions under general anesthesia. Furthermore, independent predictive factors for surgery complications were analyzed.
A total of 323 patients with airway stenosis were enrolled in this retrospective study. Each patient underwent interventional rigid bronchoscopy under general anesthesia. Arterial blood gas (ABG) was measured intraoperatively. In light of PaCO2 levels in ABG, patients were divided into three groups: Group C (control) (PaCO2:≤ 60 mmHg), Group M (moderate) (PaCO2:61–100 mmHg), and Group S (severe) (PaCO2: >100 mmHg). Parameters, including PaO2 levels and recovery delays, were compared across three groups. Complications among patients receiving bronchoscopic interventions were evaluated as well. Independent predictive factors for surgery related complications were analyzed by multivariable regression method.
Significant differences in weight (p=0.04), ASA IV (p=0.008), dyspnea index (p=0.003),COPD (p=0.02), dynamic airway collapse (p=0.002), severe stenosis severity (p=0.02), and stenosis locations among three groups were observed. Mild (PaCO2:~60 mmHg) to moderate (PaCO2:60–100 mmHg) hypercapnia was not associated with delayed recovery, whereas severe hypercapnia (PaCO2:>100 mmHg) was associated with delayed recovery, as well as declined PaO2 (p=0.00) and elevated blood glucose levels (p=0.00). The complications of bronchoscopic interventions included postoperative congestive heart failure (14 cases, 4.3%), tracheorrhagia (8 cases, 2.5%), delayed recovery (19 cases, 5.9%), and transfers to ICU after surgery (10 cases, 3.1%). The multivariable regression analysis showed that procedure duration (p=0.003), lobectomy (p=0.007), dynamic airway collapse (p=0.01), severe bronchial stenosis (p=0.01) and hypercapnia (p=0.02) were independent predictive factors for surgery related complications.
Acute hypercapnia lower than 100 mmHg was not associated with detrimental consequences, whereas severe hypercapnia (PaCO2: >100 mmHg) was associated with lower levels of PaO2. Hypercapnia was an independent predictive factor for bronchoscopic intervention complication, which may help physicians to optimize the therapeutic choices.
PMCID: PMC4492548  PMID: 26147645
20.  PKA turnover by the REGγ-proteasome modulates FoxO1 cellular activity and VEGF-induced angiogenesis 
The REGγ-proteasome serves as a short-cut for the destruction of certain intact mammalian proteins in the absence of ubiquitin-and ATP. The biological roles of the proteasome activator REGγ are not completely understood. Here we demonstrate that REGγ controls degradation of protein kinase A catalytic subunit-α (PKAca) both in primary human umbilical vein endothelial cells (HUVECs) and mouse embryonic fibroblast cells (MEFs). Accumulation of PKAca in REGγ-deficient HUVECs or MEFs results in phosphorylation and nuclear exclusion of the transcription factor FoxO1, indicating that REGγ is involved in preserving FoxO1 transcriptional activity. Consequently, VEGF-induced expression of the FoxO1 responsive genes, VCAM-1 and E-Selectin, was tightly controlled by REGγ in a PKA dependent manner. Functionally, REGγ is crucial for the migration of HUVECs. REGγ−/− mice display compromised VEGF-instigated neovascularization in cornea and aortic ring models. Implanted matrigel plugs containing VEGF in REGγ−/− mice induced fewer capillaries than in REGγ+/+ littermates. Taken together, our study identifies REGγ as a novel angiogenic factor that plays an important role in VEGF-induced expression of VCAM-1 and E-Selectin by antagonizing PKA signaling. Identification of the REGγ–PKA–FoxO1 pathway in endothelial cells (ECs) provides another potential target for therapeutic intervention in vascular diseases.
PMCID: PMC4237316  PMID: 24560667
Angiogenesis; E-Selectin; FoxO1; PKAca; REGγ; VCAM-1
21.  Overexpression of eukaryotic translation initiation factor 4E-binding protein 1 induces the alteration of immune status in H1299 lung cancer cells 
Thoracic Cancer  2015;6(4):427-432.
Eukaryotic translation initiation factor 4E-binding protein 1 (4E-BP1) is an important factor regulating protein translation. It also impacts proliferation, apoptosis, invasion, and the cell cycle of cancer cells. The aim of this study was to investigate the relationship between 4E-BP1 and human immune status, recognizing immunomodulatory molecules involved in the overexpression of 4E-BP1.
A lentivirus expression system was used to overexpress 4E-BP1 in the H1299 cell line. Western blot was performed to investigate the expression level of 4E-BP1 and P-4E-BP1, and quantitative polymerase chain reaction was used to quantify gene expression of immunomodulatory molecules.
The expression level of 4E-BP1 increased significantly after lentivirus infection (P < 0.05). Overexpression of 4E-BP1 upregulated the expression of interleukin (IL)-1β (P < 0.05), IL-5 (P < 0.001), IL-23 (P < 0.001), macrophage inflammatory protein-1β (P < 0.001), Eota-3 (P < 0.05), and MCP-4 (P < 0.05). Most of the increases were observed at the seventh day. The variation trend of IL-10, cell division cycle protein 2, proliferating cell nuclear antigen, and phosphatase and tensin homolog was not clear.
Overexpression of 4E-BP1 altered immune status by upregulating the expression of a series of immunomodulatory molecules, indicating that 4E-BP1 could serve as a potential therapeutic target against cancer.
PMCID: PMC4511320  PMID: 26273397
4E-BP1; chemokines; immune system; interleukins; lung neoplasms
22.  Modularized Functions of the Fanconi Anemia Core Complex 
Cell reports  2014;7(6):1849-1857.
The Fanconi Anemia (FA) core complex provides the essential E3 ligase function for the FA pathway activation through the spatially defined FANCD2 ubiquitination. Of the seven FA gene products forming the core complex, FANCL possesses a RING domain with demonstrated E3 ligase activity. The other six components have no clearly defined roles. Through epistatic analyses, we identified three functional modules in the FA core complex: a catalytic module consisting of FANCL, FANCB, and FAAP100 is absolutely required for the E3 ligase function; the FANCA-FANCG-FAAP20 module and the FANCC-FANCE-FANCF module provide non-redundant and ancillary functions supporting the chromatin and DNA damage association of the catalytic module. Disruption of the catalytic module renders total loss of the core complex function whereas loss of any ancillary module component does not. Our work revealed the roles of several FA gene products with previously undefined functions and a modularized assembly of the FA core complex.
PMCID: PMC4157997  PMID: 24910428
23.  PlantOrDB: a genome-wide ortholog database for land plants and green algae 
BMC Plant Biology  2015;15:161.
Genes with different functions are originally generated from some ancestral genes by gene duplication, mutation and functional recombination. It is widely accepted that orthologs are homologous genes evolved from speciation events while paralogs are homologous genes resulted from gene duplication events.With the rapid increase of genomic data, identifying and distinguishing these genes among different species is becoming an important part of functional genomics research.
Using 35 plant and 6 green algal genomes from Phytozome v9, we clustered 1,291,670 peptide sequences into 49,355 homologous gene families in terms of sequence similarity. For each gene family, we have generated a peptide sequence alignment and phylogenetic tree, and identified the speciation/duplication events for every node within the tree. For each node, we also identified and highlighted diagnostic characters that facilitate appropriate addition of a new query sequence into the existing phylogenetic tree and sequence alignment of its best matched gene family. Based on a desired species or subgroup of all species, users can view the phylogenetic tree, sequence alignment and diagnostic characters for a given gene family selectively. PlantOrDB not only allows users to identify orthologs or paralogs from phylogenetic trees, but also provides all orthologs that are built using Reciprocal Best Hit (RBH) pairwise alignment method. Users can upload their own sequences to find the best matched gene families, and visualize their query sequences within the relevant phylogenetic trees and sequence alignments.
PlantOrDB ( is a genome-wide ortholog database for land plants and green algae. PlantOrDB offers highly interactive visualization, accurate query classification and powerful search functions useful for functional genomic research.
Electronic supplementary material
The online version of this article (doi:10.1186/s12870-015-0531-4) contains supplementary material, which is available to authorized users.
PMCID: PMC4481079  PMID: 26112452
Homolog; Ortholog; Paralog; Database; Land plants; Green algae; Gene family; PlantOrDB
24.  Cancer-associated fibroblasts provide a suitable microenvironment for tumor development and progression in oral tongue squamous cancer 
Oral tongue squamous cell carcinoma (OTSCC) is still associated with a poor prognosis due to local recurrence and metastasis. Cancer-associated fibroblasts (CAFs) play an important role in the complex processes of cancer stroma interaction and tumorigenesis. This study aims to determine the role of CAFs in the development and progression of OTSCC.
Immunohistochemistry was performed to evaluate the frequency and distribution of CAFs in 178 paraffin specimens from patients with OTSCC. Immunofluorescence, a cell proliferation assay, flow cytometry, migration and invasion assays and western blot analysis were used to study the effects of CAFs and the corresponding conditioned medium (CM) on the proliferation and invasion of OTSCC cell lines.
Statistical analysis showed a strong correlation between the frequency and distribution of CAFs and the clinicopathological characteristics of patients with cN0 OTSCC, including pathological stage (P = 0.001), T classification (P = 0.001), and N classification (P = 0.009). Survival analysis demonstrated a negative correlation of the frequency and distribution of CAFs with the overall survival and disease-free survival of patients with cN0 tongue squamous cell cancer (P = 0.009, 0.002, respectively); Cox regression analysis showed that the presence of CAFs (relative risk: 2.113, CI 1.461–3.015, P = 0.023) is an independent prognostic factor. A functional study demonstrated that CAFs and CM from CAFs could promote the growth, proliferation, mobility, invasion and even Epithelial Mesenchymal Transition (EMT) of OTSCC cells compared with NFs and CM from NFs.
CAFs were an independent prognostic factor for patients with OTSCC. Compared with NFs, CAFs and their CM have the ability to promote the growth, proliferation, metastasis and even EMT of OTSCC cells.
Electronic supplementary material
The online version of this article (doi:10.1186/s12967-015-0551-8) contains supplementary material, which is available to authorized users.
PMCID: PMC4475624  PMID: 26094024
Oral tongue squamous cell cancer; Microenvironment; Cancer-associated fibroblast; Progression
25.  Context-Aware Reviewer Assignment for Trust Enhanced Peer Review 
PLoS ONE  2015;10(6):e0130493.
Reviewer assignment is critical to peer review systems, such as peer-reviewed research conferences or peer-reviewed funding applications, and its effectiveness is a deep concern of all academics. However, there are some problems in existing peer review systems during reviewer assignment. For example, some of the reviewers are much more stringent than others, leading to an unfair final decision, i.e., some submissions (i.e., papers or applications) with better quality are rejected. In this paper, we propose a context-aware reviewer assignment for trust enhanced peer review. More specifically, in our approach, we first consider the research area specific expertise of reviewers, and the institution relevance and co-authorship between reviewers and authors, so that reviewers with the right expertise are assigned to the corresponding submissions without potential conflict of interest. In addition, we propose a novel cross-assignment paradigm, and reviewers are cross-assigned in order to avoid assigning a group of stringent reviewers or a group of lenient reviewers to the same submission. More importantly, on top of them, we propose an academic CONtext-aware expertise relevanCe oriEnted Reviewer cross-assignmenT approach (CONCERT), which aims to effectively estimate the “true” ratings of submissions based on the ratings from all reviewers, even though no prior knowledge exists about the distribution of stringent reviewers and lenient reviewers. The experiments illustrate that compared with existing approaches, our proposed CONCERT approach can less likely assign more than one stringent reviewers or lenient reviewers to a submission simultaneously and significantly reduce the influence of ratings from stringent reviewers and lenient reviewers, leading to trust enhanced peer review and selection, no matter what kind of distributions of stringent reviewers and lenient reviewers are.
PMCID: PMC4474895  PMID: 26090849

Results 1-25 (397)