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1.  Crystallization and preliminary X-ray diffraction studies of the GhKCH2 motor domain: alteration of pH significantly improved the quality of the crystals 
The GhKCH2 motor domain was crystallized and the pH of the crystallization buffer was shown to have a significant effect on the crystal morphology and diffraction quality.
GhKCH2, a member of the kinesin superfamily, is a plant-specific microtubule-dependent motor protein from cotton with the ability to bind to both microtubules and microfilaments. Here, the motor domain of GhKCH2 (GhKCH2MD; amino acids 371–748) was overexpressed in Escherichia coli, purified and crystallized using the sitting-drop vapour-diffusion method. The pH of the crystallization buffer was shown to have a significant effect on the crystal morphology and diffraction quality. The crystals belonged to space group P212121, with unit-cell parameters a = 60.7, b = 78.6, c = 162.8 Å, α = β = γ = 90°. The Matthews coefficient and solvent content were calculated as 2.27 Å3 Da−1 and 45.87%, respectively. X-ray diffraction data for GhKCH2MD were collected on beamline BL17U1 at Shanghai Synchrotron Radiation Facility and processed to 2.8 Å resolution.
doi:10.1107/S1744309112016351
PMCID: PMC3388925  PMID: 22750868
kinesins; pH; crystal morphology; diffraction quality
2.  Characterization, Design, and Function of the Mitochondrial Proteome: From Organs to Organisms 
Journal of proteome research  2013;13(2):433-446.
Mitochondria are a common energy source for organs and organisms; their diverse functions are specialized according to the unique phenotypes of their hosting environment. Perturbation of mitochondrial homeostasis accompanies significant pathological phenotypes. However, the connections between mitochondrial proteome properties and function remain to be experimentally established on a systematic level. This uncertainty impedes the contextualization and translation of proteomic data to the molecular derivations of mitochondrial diseases. We present a collection of mitochondrial features and functions from four model systems, including two cardiac mitochondrial proteomes from distinct genomes (human and mouse), two unique organ mitochondrial proteomes from identical genetic codons (mouse heart and mouse liver), as well as a relevant metazoan out-group (drosophila). The data, composed of mitochondrial protein abundance and their biochemical activities, capture the core functionalities of these mitochondria. This investigation allowed us to redefine the core mitochondrial proteome from organs and organisms, as well as the relevant contributions from genetic information and hosting milieu. Our study has identified significant enrichment of disease-associated genes and their products. Furthermore, correlational analyses suggest that mitochondrial proteome design is primarily driven by cellular environment. Taken together, these results connect proteome feature with mitochondrial function, providing a prospective resource for mitochondrial pathophysiology and developing novel therapeutic targets in medicine.
doi:10.1021/pr400539j
PMCID: PMC4076470  PMID: 24070373
mitochondrial proteome; mitochondrial function; heart diseases; intergenomic; intragenomic; proteomic comparisons
3.  The signaling lipid PI(3,5)P2 stabilizes V1–Vo sector interactions and activates the V-ATPase 
Molecular Biology of the Cell  2014;25(8):1251-1262.
Certain stress-responsive changes in V-ATPase activity and assembly require the signaling lipid PI(3,5)P2. Purified Vo complexes bind preferentially to this lipid, and the cytosolic domain of one Vo subunit shows PI(3,5)P2-dependent recruitment to membranes in vivo. Lipid interactions with V-ATPases could provide compartment-specific regulation.
Vacuolar proton-translocating ATPases (V-ATPases) are highly conserved, ATP-driven proton pumps regulated by reversible dissociation of its cytosolic, peripheral V1 domain from the integral membrane Vo domain. Multiple stresses induce changes in V1-Vo assembly, but the signaling mechanisms behind these changes are not understood. Here we show that certain stress-responsive changes in V-ATPase activity and assembly require the signaling lipid phosphatidylinositol 3,5-bisphosphate (PI(3,5)P2). V-ATPase activation through V1-Vo assembly in response to salt stress is strongly dependent on PI(3,5)P2 synthesis. Purified Vo complexes preferentially bind to PI(3,5)P2 on lipid arrays, suggesting direct binding between the lipid and the membrane sector of the V-ATPase. Increasing PI(3,5)P2 levels in vivo recruits the N-terminal domain of Vo-sector subunit Vph1p from cytosol to membranes, independent of other subunits. This Vph1p domain is critical for V1-Vo interaction, suggesting that interaction of Vph1p with PI(3,5)P2-containing membranes stabilizes V1-Vo assembly and thus increases V-ATPase activity. These results help explain the previously described vacuolar acidification defect in yeast fab1∆ and vac14∆ mutants and suggest that human disease phenotypes associated with PI(3,5)P2 loss may arise from compromised V-ATPase stability and regulation.
doi:10.1091/mbc.E13-10-0563
PMCID: PMC3982991  PMID: 24523285
4.  Hydrogen-Rich Saline Promotes Survival of Retinal Ganglion Cells in a Rat Model of Optic Nerve Crush 
PLoS ONE  2014;9(6):e99299.
Objective
To investigate the effect of molecular hydrogen (H2) in a rat model subjected to optic nerve crush (ONC).
Methods
We tested the hypothesis that after optic nerve crush (ONC), retinal ganglion cell (RGC) could be protected by H2. Rats in different groups received saline or hydrogen-rich saline every day for 14 days after ONC. Retinas from animals in each group underwent measurements of hematoxylin and eosin (H&E) staining, cholera toxin beta (CTB) tracing, gamma synuclein staining, and terminal deoxynucleotidyltransferase-mediated dUTP nick end labeling (TUNEL) staining 2 weeks post operation. Flash visual evoked potentials (FVEP) and pupillary light reflex (PLR) were then tested to evaluate the function of optic nerve. The malondialdehyde (MDA) level in retina was evaluated.
Results
H&E, gamma synuclein staining and CTB tracing showed that the survival rate of RGCs in hydrogen saline-treated group was significantly higher than that in saline-treated group. Apoptosis of RGCs assessed by TUNEL staining were less observed in hydrogen saline-treated group. The MDA level in retina of H2 group was much lower than that in placebo group. Furthermore, animals treated with hydrogen saline showed better function of optic nerve in assessments of FVEP and PLR.
Conclusion
These results demonstrated that H2 protects RGCs and helps preserve the visual function after ONC and had a neuroprotective effect in a rat model subjected to ONC.
doi:10.1371/journal.pone.0099299
PMCID: PMC4051757  PMID: 24915536
5.  In vivo measurement of ALDH2 activity in rat liver ethanol model using dynamic MRSI of hyperpolarized [1-13C]pyruvate 
NMR in biomedicine  2012;26(6):607-612.
To date, measurements of the activity of aldehyde dehydrogenase-2 (ALDH2), a critical mitochondrial enzyme for eliminating certain cytotoxic aldehydes in the body and a promising target for drug development, have been largely limited to in vitro methods. Recent advancements in magnetic resonance spectroscopy (MRS) of hyperpolarized 13C-labeled substrates now provide a method to detect and image in vivo metabolic pathways with signal-to-noise ratio gains greater than 10,000 fold over conventional MRS techniques. However aldehydes, due to their toxicity and short T1 relaxation times, are generally poor targets for such 13C-labeled studies. In this work, we show that dynamic magnetic resonance spectroscopic imaging of hyperpolarized [1-13C]pyruvate and its conversion to [1-13C]lactate can provide an indirect in vivo measurement of ALDH2 activity via the concentration of NADH, a co-factor common to both the reduction of pyruvate to lactate and the oxidation of acetaldehyde to acetate. Results from a rat liver ethanol model (n = 9) show that changes in 13C-lactate labeling following the bolus injection of hyperpolarized pyruvate are highly correlated with changes in ALDH2 activity (R2=0.76).
doi:10.1002/nbm.2897
PMCID: PMC3634870  PMID: 23225495
hyperpolarized 13C; ALDH2 activity; liver; ethanol; pyruvate; lactate; NADH
6.  Identification of a Retroelement from the Resurrection Plant Boea hygrometrica That Confers Osmotic and Alkaline Tolerance in Arabidopsis thaliana 
PLoS ONE  2014;9(5):e98098.
Functional genomic elements, including transposable elements, small RNAs and non-coding RNAs, are involved in regulation of gene expression in response to plant stress. To identify genomic elements that regulate dehydration and alkaline tolerance in Boea hygrometrica, a resurrection plant that inhabits drought and alkaline Karst areas, a genomic DNA library from B. hygrometrica was constructed and subsequently transformed into Arabidopsis using binary bacterial artificial chromosome (BIBAC) vectors. Transgenic lines were screened under osmotic and alkaline conditions, leading to the identification of Clone L1-4 that conferred osmotic and alkaline tolerance. Sequence analyses revealed that L1-4 contained a 49-kb retroelement fragment from B. hygrometrica, of which only a truncated sequence was present in L1-4 transgenic Arabidopsis plants. Additional subcloning revealed that activity resided in a 2-kb sequence, designated Osmotic and Alkaline Resistance 1 (OAR1). In addition, transgenic Arabidopsis lines carrying an OAR1-homologue also showed similar stress tolerance phenotypes. Physiological and molecular analyses demonstrated that OAR1-transgenic plants exhibited improved photochemical efficiency and membrane integrity and biomarker gene expression under both osmotic and alkaline stresses. Short transcripts that originated from OAR1 were increased under stress conditions in both B. hygrometrica and Arabidopsis carrying OAR1. The relative copy number of OAR1 was stable in transgenic Arabidopsis under stress but increased in B. hygrometrica. Taken together, our results indicated a potential role of OAR1 element in plant tolerance to osmotic and alkaline stresses, and verified the feasibility of the BIBAC transformation technique to identify functional genomic elements from physiological model species.
doi:10.1371/journal.pone.0098098
PMCID: PMC4031123  PMID: 24851859
7.  Th22 Cell Is a Gradually Proved Potential Biomarker for Acute Coronary Syndrome 
Mediators of Inflammation  2014;2014:813926.
doi:10.1155/2014/813926
PMCID: PMC4034660  PMID: 24895489
8.  Comparative Functional Analysis of Wheat (Triticum aestivum) Zinc Finger-Containing Glycine-Rich RNA-Binding Proteins in Response to Abiotic Stresses 
PLoS ONE  2014;9(5):e96877.
Although the functional roles of zinc finger-containing glycine-rich RNA-binding proteins (RZs) have been characterized in several plant species, including Arabidopsis thaliana and rice (Oryza sativa), the physiological functions of RZs in wheat (Triticum aestivum) remain largely unknown. Here, the functional roles of the three wheat RZ family members, named TaRZ1, TaRZ2, and TaRZ3, were investigated using transgenic Arabidopsis plants under various abiotic stress conditions. Expression of TaRZs was markedly regulated by salt, dehydration, or cold stress. The TaRZ1 and TaRZ3 proteins were localized to the nucleus, whereas the TaRZ2 protein was localized to the nucleus, endoplasmic reticulum, and cytoplasm. Germination of all three TaRZ-expressing transgenic Arabidopsis seeds was retarded compared with that of wild-type seeds under salt stress conditions, whereas germination of TaRZ2- or TaRZ3-expressing transgenic Arabidopsis seeds was retarded under dehydration stress conditions. Seedling growth of TaRZ1-expressing transgenic plants was severely inhibited under cold or salt stress conditions, and seedling growth of TaRZ2-expressing plants was inhibited under salt stress conditions. By contrast, expression of TaRZ3 did not affect seedling growth of transgenic plants under any of the stress conditions. In addition, expression of TaRZ2 conferred freeze tolerance in Arabidopsis. Taken together, these results suggest that different TaRZ family members play various roles in seed germination, seedling growth, and freeze tolerance in plants under abiotic stress.
doi:10.1371/journal.pone.0096877
PMCID: PMC4011930  PMID: 24800811
9.  PLA1A2 platelet polymorphism predicts mortality in prediabetic subjects of the population based KORA S4-Cohort 
Objective
The genetic polymorphism concerning the ß3-subunit of platelet integrin receptor glycoprotein IIIa is held responsible for enhanced binding of adhesive proteins resulting in increased thrombogenic potential. Whether it is associated with mortality, HbA1c or platelet volume is tested prospectively in an epidemiological cohort.
Research design and methods
Population-based Cooperative Health Research in the Region of Augsburg (KORA) S4-Survey (N = 4,028) was investigated for prognostic value of PLA1A2-polymorphism regarding all-cause mortality, correlation with HbA1c, and mean platelet volume. Multivariate analysis was performed to investigate association between genotype and key variables.
Results
Prevalence of thrombogenic allele variant PLA2 was 15.0%. Multivariate analysis revealed no association between PLA1A2 polymorphism and mortality in the KORA-cohort. HbA1c was a prognostic marker of mortality in non-diabetic persons resulting in J-shaped risk curve with dip at HbA1c = 5.5% (37 mmol/mol), confirming previous findings regarding aged KORA-S4 participants (55–75 years). PLA1A2 was significantly associated with elevated HbA1c levels in diabetic patients (N = 209) and reduced mean platelet volume in general population. In non-diabetic participants (N = 3,819), carriers of PLA2 allele variant presenting with HbA1c > 5.5% (37 mmol/mol) showed higher relative risk of mortality with increasing HbA1c.
Conclusion
PLA1A2 polymorphism is associated with mortality in participants with HbA1c ranging from 5.5% (37 mmol/mol) to 6.5% (48 mmol/mol). Maintenance of euglycemic control and antiplatelet therapy are therefore regarded as effective primary prevention in this group.
doi:10.1186/1475-2840-13-90
PMCID: PMC4022397  PMID: 24886443
Glycated hemoglobin; Platelet glycoprotein receptor polymorphism; Mean platelet volume; All-cause mortality; Glycemic management; Epidemiology
10.  A Modified MuDPIT Separation Identified 4,488 Proteins in a System Wide Analysis of Quiescence in Yeast 
Journal of proteome research  2013;12(5):10.1021/pr400027m.
A modified multidimensional protein identification technology (MudPIT) separation was coupled to an LTQ Orbitrap Velos mass spectrometer and used to rapidly identify the near complete yeast proteome from a whole cell tryptic digest. This modified on-line two dimensional liquid chromatography separation consists of 39 strong cation exchange steps followed by a short 18.5 min reversed-phase (RP) gradient. A total of 4,269 protein identifications were made from 4,189 distinguishable protein families from yeast during log phase growth. The “Micro” MudPIT separation performed as well as a standard MudPIT separation in 40% less gradient time. The majority of the yeast proteome can now be routinely covered in less than a days’ time with high reproducibility and sensitivity. The newly devised separation method was used to detect changes in protein expression during cellular quiescence in yeast. An enrichment in the GO annotations ‘oxidation reduction’, ‘catabolic processing’ and ‘cellular response to oxidative stress’ was seen in the quiescent cellular fraction, consistent with their long lived stress resistant phenotypes. Heterogeneity was observed in the stationary phase fraction with a less dense cell population showing reductions in KEGG pathway categories of ‘Ribosome’ and ‘Proteasome’, further defining the complex nature of yeast populations present during stationary phase growth. In total 4,488 distinguishable protein families were identified in all cellular conditions tested.
doi:10.1021/pr400027m
PMCID: PMC3815592  PMID: 23540446
MudPIT; Saccharomyces cerevisiae; Quiescence
11.  Small molecules enable cardiac reprogramming of mouse fibroblasts with a single factor, Oct4 
Cell reports  2014;6(5):951-960.
Summary
It was recently shown that mouse fibroblasts could be reprogrammed into cells of a cardiac fate by forced expression of multiple transcription factors and microRNAs. To ultimately apply such reprogramming strategy for cell-based therapy or in vivo cardiac regeneration, reducing or eliminating the genetic manipulations by small molecules would be highly desirable. Here, we report the identification of a defined small-molecule cocktail that enables highly efficient conversion of mouse fibroblasts into cardiac cells with only one transcription factor, Oct4, without entering the pluripotent state. Small-molecule-induced cardiomyocytes spontaneously contract and exhibit a ventricular phenotype. Furthermore, such induced cardiomyocytes under our condition pass through a cardiac progenitor stage. This study lays the foundation for future pharmacological reprogramming approaches and provides a novel small-molecule condition to investigate the mechanisms underlying cardiac reprogramming process.
doi:10.1016/j.celrep.2014.01.038
PMCID: PMC4004339  PMID: 24561253
cardiac reprogramming; small molecules; screening
12.  Efficacy of novel antibacterial compounds targeting histidine kinase YycG protein 
Treating staphylococcal biofilm-associated infections is challenging. Based on the findings that compound 2 targeting the HK domain of Staphylococcus epidermidis YycG has bactericidal and antibiofilm activities against staphylococci, six newly synthesized derivatives were evaluated for their antibacterial activities. The six derivatives of compound 2 inhibited autophosphorylation of recombinant YycG′ and the IC50 values ranged from 24.2 to 71.2 μM. The derivatives displayed bactericidal activity against planktonic S. epidermidis or Staphylococcus aureus strains in the MIC range of 1.5–3.1 μM. All the derivatives had antibiofilm activities against the 6- and 24-h biofilms of S. epidermidis. Compared to the prototype compound 2, they had less cytotoxicity for Vero cells and less hemolytic activity for human erythrocytes. The derivatives showed antibacterial activities against clinical methicillin-resistant staphylococcal isolates. The structural modification of YycG inhibitors will assist the discovery of novel agents to eliminate biofilm infections and multidrug-resistant staphylococcal infections.
Electronic supplementary material
The online version of this article (doi:10.1007/s00253-014-5685-8) contains supplementary material, which is available to authorized users.
doi:10.1007/s00253-014-5685-8
PMCID: PMC4057637  PMID: 24737057
Staphylococcus epidermidis; Methicillin-resistant Staphylococcus aureus (MRSA); Antibacterial; Minimal inhibitory concentration (MIC); Minimal bactericidal concentration (MBC); Antibiofilm activity
13.  Detection of serum VEGF and MMP-9 levels by Luminex multiplexed assays in patients with breast infiltrative ductal carcinoma 
The aim of the present study was to assess the effect of the combined detection of serum vascular endothelial growth factor (VEGF) and matrix metalloproteinase-9 (MMP-9) by Luminex multiplexed assays for the diagnosis, treatment and prognosis of breast cancer. Preoperative levels of serum VEGF and MMP-9 were detected via a lipid chip-based method in 301 breast cancer cases, 83 breast fibroadenoma cases and 40 healthy adults. Postoperative levels of VEGF and MMP-9 were also detected in 118 breast cancer cases. The levels of serum VEGF and MMP-9 in patients with breast infiltrative ductal carcinoma (IDC) were higher than those in the breast fibroadenoma and healthy control groups (P<0.05); there was no statistically significant difference between the breast fibroadenoma and healthy groups (P>0.05). The levels of VEGF and MMP-9 were shown to correlate with the clinical stage, tumor size and the lymph node metastasis status. However, the levels were not associated with age or gender (P>0.05). In addition, the serum level of MMP-9 exhibited a significantly correlation with the VEGF level (r=0.601, P<0.001). Subgroup analysis revealed that in patients with IDC, serum levels of VEGF and MMP-9 prior to surgery were significantly higher than those following surgery (P<0.05). Therefore, the serum levels of VEGF and MMP-9 can be used as markers for the diagnosis of breast IDC and may also be valuable for the prediction of lymph nodes metastasis.
doi:10.3892/etm.2014.1685
PMCID: PMC4061234  PMID: 24944618
breast infiltrative ductal carcinoma; liquid chip-based method; vascular endothelial growth factor; matrix metalloproteinase-9
14.  Delivering MC3T3-E1 cells into injectable calcium phosphate cement through alginate-chitosan microcapsules for bone tissue engineering*  
Objective: To deliver cells deep into injectable calcium phosphate cement (CPC) through alginate-chitosan (AC) microcapsules and investigate the biological behavior of the cells released from microcapsules into the CPC. Methods: Mouse osteoblastic MC3T3-E1 cells were embedded in alginate and AC microcapsules using an electrostatic droplet generator. The two types of cell-encapsulating microcapsules were then mixed with a CPC paste. MC3T3-E1 cell viability was investigated using a Wst-8 kit, and osteogenic differentiation was demonstrated by an alkaline phosphatase (ALP) activity assay. Cell attachment in CPC was observed by an environment scanning electron microscopy. Results: Both alginate and AC microcapsules were able to release the encapsulated MC3T3-E1 cells when mixed with CPC paste. The released cells attached to the setting CPC scaffolds, survived, differentiated, and formed mineralized nodules. Cells grew in the pores concomitantly created by the AC microcapsules in situ within the CPC. At Day 21, cellular ALP activity in the AC group was approximately four times that at Day 7 and exceeded that of the alginate microcapsule group (P<0.05). Pores formed by the AC microcapsules had a diameter of several hundred microns and were spherical compared with those formed by alginate microcapsules. Conclusions: AC microcapsule is a promising carrier to release seeding cells deep into an injectable CPC scaffold for bone engineering.
doi:10.1631/jzus.B1300132
PMCID: PMC3989157  PMID: 24711359
Injectable scaffold; Calcium phosphate cement; Osteoblast; Microencapsulation; Cell release; Chitosan
15.  Ultrastructural Localization of Polygalacturonase in Ethylene-Stimulated Abscission of Tomato Pedicel Explants 
The Scientific World Journal  2014;2014:389896.
Polygalacturonase (PG) is crucial in plant organ abscission process. This paper investigated the cellular and subcellular localization of PG in ethylene-stimulated abscission of tomato pedicel explants. Confocal laser scanning microscopy of abscission zone sections with the fluorescent probe Cy3 revealed that PG was initially accumulated in parenchyma cells in cortical and vascular tissues after 8 h of ethylene treatment and then extended throughout the abscission zone when the abscission zone separated at 24 h after ethylene treatment. At the subcellular level, transmission electron microscopy with immunogold staining showed that PG showed abundant accumulation in the cortical and vascular tissues at 8 h after ethylene treatment, and the distribution area extended to the central parenchyma cells at 16 h after ethylene treatment. In addition, PGs were observed in the distal and proximal parts of the tomato pedicel explants throughout the abscission process. The results provided a visualized distribution of PG in the pedicel abscission zone and proved that PG was closely related to abscission.
doi:10.1155/2014/389896
PMCID: PMC3982476  PMID: 24790564
16.  Improvement of cellulose catabolism in Clostridium cellulolyticum by sporulation abolishment and carbon alleviation 
Background
Clostridium cellulolyticum can degrade lignocellulosic biomass, and ferment the soluble sugars to produce valuable chemicals such as lactate, acetate, ethanol and hydrogen. However, the cellulose utilization efficiency of C. cellulolyticum still remains very low, impeding its application in consolidated bioprocessing for biofuels production. In this study, two metabolic engineering strategies were exploited to improve cellulose utilization efficiency, including sporulation abolishment and carbon overload alleviation.
Results
The spo0A gene at locus Ccel_1894, which encodes a master sporulation regulator was inactivated. The spo0A mutant abolished the sporulation ability. In a high concentration of cellulose (50 g/l), the performance of the spo0A mutant increased dramatically in terms of maximum growth, final concentrations of three major metabolic products, and cellulose catabolism. The microarray and gas chromatography–mass spectrometry (GC-MS) analyses showed that the valine, leucine and isoleucine biosynthesis pathways were up-regulated in the spo0A mutant. Based on this information, a partial isobutanol producing pathway modified from valine biosynthesis was introduced into C. cellulolyticum strains to further increase cellulose consumption by alleviating excessive carbon load. The introduction of this synthetic pathway to the wild-type strain improved cellulose consumption from 17.6 g/l to 28.7 g/l with a production of 0.42 g/l isobutanol in the 50 g/l cellulose medium. However, the spo0A mutant strain did not appreciably benefit from introduction of this synthetic pathway and the cellulose utilization efficiency did not further increase. A technical highlight in this study was that an in vivo promoter strength evaluation protocol was developed using anaerobic fluorescent protein and flow cytometry for C. cellulolyticum.
Conclusions
In this study, we inactivated the spo0A gene and introduced a heterologous synthetic pathway to manipulate the stress response to heavy carbon load and accumulation of metabolic products. These findings provide new perspectives to enhance the ability of cellulolytic bacteria to produce biofuels and biocommodities with high efficiency and at low cost directly from lignocellulosic biomass.
doi:10.1186/1754-6834-7-25
PMCID: PMC3936895  PMID: 24555718
Clostridium cellulolyticum; Sporulation; spo0A; Cellulose catabolism; Isobutanol
17.  A genetic program promotes C. elegans longevity at cold temperatures via a thermosensitive TRP channel 
Cell  2013;152(4):806-817.
Summary
Both poikilotherms and homeotherms live longer at lower body temperatures, highlighting a general role of temperature reduction in lifespan extension. However, the underlying mechanisms remain unclear. One prominent model is that cold temperatures reduce the rate of chemical reactions, thereby slowing the rate of aging. This view suggests that cold-dependent lifespan extension is simply a passive thermodynamic process. Here, we challenge this view in C. elegans by showing that genetic programs actively promote longevity at cold temperatures. We find that TRPA-1, a cold-sensitive TRP channel, detects temperature drop in the environment to extend lifespan. This effect requires cold-induced, TRPA-1-mediated calcium influx and a calcium-sensitive PKC which signals to the transcription factor DAF-16/FOXO. Human TRPA1 can functionally substitute for worm TRPA-1 in promoting longevity. Our results reveal a new function for TRP channels, link calcium signaling to longevity, and importantly, demonstrate that genetic programs contribute to lifespan extension at cold temperatures.
doi:10.1016/j.cell.2013.01.020
PMCID: PMC3594097  PMID: 23415228
18.  LIN28 Is Involved in Glioma Carcinogenesis and Predicts Outcomes of Glioblastoma Multiforme Patients 
PLoS ONE  2014;9(1):e86446.
LIN28, an evolutionarily conversed RNA binding protein which can bind to the terminal loops of let-7 family microRNA precursors and block their processing to maturation, is highly expressed in several subsets of tumors that carry poor prognoses, such as ovarian carcinoma, hepatocellular carcinoma, colon carcinoma and germ cell carcinoma. However, there has been no study on the expression of LIN28 in glioma tissues or their importance as a prognostic predictor of glioma patients. This study aimed to examine the expression of LIN28 in glioma and correlate the results to patient outcome. We found that LIN28 expression was significantly higher in the group of patients with a poor prognosis compared to patients with a good prognosis by gene microarray. Log-rank analysis showed patients with higher LIN28 expression level in tumor had a shorter progression-free survival and overall survival times compared to those with lower LIN28 expression level. Similar results were also obtained from the tissue microarray analysis. Univariate and multivariate analyses showed high LIN28 expression was an independent prognostic factor for a shorter progression-free survival and overall survival in GBM patients. Furthermore in vitro experiments showed that down-regulation of LIN28 in U251 and U373 cells caused cell cycle arrest in the G1 phase, delayed cell proliferation, increased apoptosis, and resulted in fewer colonies compared to controls. Summarily, our data provides a potential target for cancer therapy as an approach to overcome the poor options currently available for GBM patients.
doi:10.1371/journal.pone.0086446
PMCID: PMC3901701  PMID: 24475120
19.  The Effect of Apigenin on Pharmacokinetics of Imatinib and Its Metabolite N-Desmethyl Imatinib in Rats 
BioMed Research International  2013;2013:789184.
The purpose of this study was to determine the effect of apigenin on the pharmacokinetics of imatinib and N-desmethyl imatinib in rats. Healthy male SD rats were randomly divided into four groups: A group (the control group), B group (the long-term administration of 165 mg/kg apigenin for 15 days), C group (a single dose of 165 mg/kg apigenin), and D group (a single dose of 252 mg/kg apigenin). The serum concentrations of imatinib and N-desmethyl imatinib were measured by HPLC, and pharmacokinetic parameters were calculated using DAS 3.0 software. The parameters of AUC(0−t), AUC(0−∞), Tmax, Vz/F, and CLz/F for imatinib in group B were different from those in group A (P < 0.05). Besides, MRT(0−t) and MRT(0−∞) in groups C and D differed distinctly from those in group A as well. The parameters of AUC(0−t) and Cmax for N-desmethyl imatinib in group C were significantly lower than those in group A (P < 0.05); however, compared with groups B and D, the magnitude of effect was modest. Those results indicated that apigenin in the short-term study inhibited the metabolism of imatinib and its metabolite N-desmethyl imatinib, while in the long-term study the metabolism could be accelerated.
doi:10.1155/2013/789184
PMCID: PMC3863468  PMID: 24369535
20.  SAMSN1 Is Highly Expressed and Associated with a Poor Survival in Glioblastoma Multiforme 
PLoS ONE  2013;8(11):e81905.
Objectives
To study the expression pattern and prognostic significance of SAMSN1 in glioma.
Methods
Affymetrix and Arrystar gene microarray data in the setting of glioma was analyzed to preliminarily study the expression pattern of SAMSN1 in glioma tissues, and Hieratical clustering of gene microarray data was performed to filter out genes that have prognostic value in malignant glioma. Survival analysis by Kaplan-Meier estimates stratified by SAMSN1 expression was then made based on the data of more than 500 GBM cases provided by The Cancer Genome Atlas (TCGA) project. At last, we detected the expression of SAMSN1 in large numbers of glioma and normal brain tissue samples using Tissue Microarray (TMA). Survival analysis by Kaplan-Meier estimates in each grade of glioma was stratified by SAMSN1 expression. Multivariate survival analysis was made by Cox proportional hazards regression models in corresponding groups of glioma.
Results
With the expression data of SAMSN1 and 68 other genes, high-grade glioma could be classified into two groups with clearly different prognoses. Gene and large sample tissue microarrays showed high expression of SAMSN1 in glioma particularly in GBM. Survival analysis based on the TCGA GBM data matrix and TMA multi-grade glioma dataset found that SAMSN1 expression was closely related to the prognosis of GBM, either PFS or OS (P<0.05). Multivariate survival analysis with Cox proportional hazards regression models confirmed that high expression of SAMSN1 was a strong risk factor for PFS and OS of GBM patients.
Conclusion
SAMSN1 is over-expressed in glioma as compared with that found in normal brains, especially in GBM. High expression of SAMSN1 is a significant risk factor for the progression free and overall survival of GBM.
doi:10.1371/journal.pone.0081905
PMCID: PMC3838348  PMID: 24278465
21.  The Detection of Orientation Continuity and Discontinuity by Cat V1 Neurons 
PLoS ONE  2013;8(11):e79723.
The orientation tuning properties of the non-classical receptive field (nCRF or “surround”) relative to that of the classical receptive field (CRF or “center”) were tested for 119 neurons in the cat primary visual cortex (V1). The stimuli were concentric sinusoidal gratings generated on a computer screen with the center grating presented at an optimal orientation to stimulate the CRF and the surround grating with variable orientations stimulating the nCRF. Based on the presence or absence of surround suppression, measured by the suppression index at the optimal orientation of the cells, we subdivided the neurons into two categories: surround-suppressive (SS) cells and surround-non-suppressive (SN) cells. When stimulated with an optimally oriented grating centered at CRF, the SS cells showed increasing surround suppression when the stimulus grating was expanded beyond the boundary of the CRF, whereas for the SN cells, expanding the stimulus grating beyond the CRF caused no suppression of the center response. For the SS cells, strength of surround suppression was dependent on the relative orientation between CRF and nCRF: an iso-orientation grating over center and surround at the optimal orientation evoked strongest suppression and a surround grating orthogonal to the optimal center grating evoked the weakest or no suppression. By contrast, the SN cells showed slightly increased responses to an iso-orientation stimulus and weak suppression to orthogonal surround gratings. This iso-/orthogonal orientation selectivity between center and surround was analyzed in 22 SN and 97 SS cells, and for the two types of cells, the different center-surround orientation selectivity was dependent on the suppressive strength of the cells. We conclude that SN cells are suitable to detect orientation continuity or similarity between CRF and nCRF, whereas the SS cells are adapted to the detection of discontinuity or differences in orientation between CRF and nCRF.
doi:10.1371/journal.pone.0079723
PMCID: PMC3836789  PMID: 24278163
22.  A Cell Cycle Phosphoproteome of the Yeast Centrosome 
Science (New York, N.Y.)  2011;332(6037):10.1126/science.1205193.
Centrosomes organize the bipolar mitotic spindle, and centrosomal defects cause chromosome instability. Protein phosphorylation modulates centrosome function, and we provide a comprehensive map of phosphorylation on intact yeast centrosomes (18 proteins). Mass spectrometry was used to identify 297 phosphorylation sites on centrosomes from different cell cycle stages. We observed different modes of phosphoregulation via specific protein kinases, phosphorylation site clustering, and conserved phosphorylated residues. Mutating all eight cyclin-dependent kinase (Cdk)–directed sites within the core component, Spc42, resulted in lethality and reduced centrosomal assembly. Alternatively, mutation of one conserved Cdk site within γ-tubulin (Tub4-S360D) caused mitotic delay and aberrant anaphase spindle elongation. Our work establishes the extent and complexity of this prominent posttranslational modification in centrosome biology and provides specific examples of phosphorylation control in centrosome function.
doi:10.1126/science.1205193
PMCID: PMC3825980  PMID: 21700874
23.  Concise Review: Chemical Approaches for Modulating Lineage-Specific Stem Cells and Progenitors 
This work summarizes recent progress in the use of small molecules for the expansion and generation of desirable lineage-restricted stem and progenitor cells in vitro and for selectively controlling cell fate of lineage-restricted stem and progenitor cells in vivo, thereby facilitating stem cell-based clinical applications. All of the examples listed suggest that small molecules can be used to facilitate the generation and expansion of desirable lineage-restricted stem and progenitor cells for various purposes, and selectively control the differentiation of lineage-restricted stem and progenitor cells in vitro and in vivo for therapeutics purposes.
Generation and manipulation of lineage-restricted stem and progenitor cells in vitro and/or in vivo are critical for the development of stem cell-based clinical therapeutics. Lineage-restricted stem and progenitor cells have many advantageous qualities, including being able to efficiently engraft and differentiate into desirable cell types in vivo after transplantation, and they are much less tumorigenic than pluripotent cells. Generation of lineage-restricted stem and progenitor cells can be achieved by directed differentiation from pluripotent stem cells or lineage conversion from easily obtained somatic cells. Small molecules can be very helpful in these processes since they offer several important benefits. For example, the risk of tumorigenesis is greatly reduced when small molecules are used to replace integrated transcription factors, which are widely used in cell fate conversion. Furthermore, small molecules are relatively easy to apply, optimize, and manufacture, and they can more readily be developed into conventional pharmaceuticals. Alternatively, small molecules can be used to expand or selectively control the differentiation of lineage-restricted stem and progenitor cells for desirable therapeutics purposes in vitro or in vivo. Here we summarize recent progress in the use of small molecules for the expansion and generation of desirable lineage-restricted stem and progenitor cells in vitro and for selectively controlling cell fate of lineage-restricted stem and progenitor cells in vivo, thereby facilitating stem cell-based clinical applications.
doi:10.5966/sctm.2012-0172
PMCID: PMC3667559  PMID: 23580542
Stem/progenitor cell; Differentiation; Hematopoietic stem cells; Neural stem cell; Stem cell expansion; T cell; Induced pluripotent stem cells; Mesenchymal stem cells; Self-renewal; Cell fate conversion
24.  Risk factors for early postoperative cognitive dysfunction after non-coronary bypass surgery in Chinese population 
Background
The present study was performed to investigate the incidence of early postoperative cognitive dysfunction (POCD) after non-coronary bypass surgery and the potential risk factors in Chinese population.
Methods
We performed a prospective study in a teaching tertiary hospital from May 2012 to August 2012. One hundred and seventy-six adult patients undergoing non-coronary bypass surgery were recruited. Mini-Mental State Examination (MMSE) score was evaluated before and 3 to 5 days after surgery. Patients with a MMSE score reduction of 2 was diagnosed with POCD.
Results
The general incidence of POCD was 33.0%, with no significant difference between the types of surgeries. In the univariate analysis, POCD associated factors included age, duration of surgery, anesthesia, cardiopulmonary bypass (CPB), cross-clamp and rewarming, and sevoflurane concentration. However, only age, cross-clamp duration and sevoflurane concentration were demonstrated to be independent risk factors for POCD.
Conclusion
Incidence of early POCD after non-coronary bypass surgery was relatively high in Chinese population. Advanced age, longer aortic cross-clamp duration and lower sevoflurane concentration was associated with a higher incidence of POCD.
doi:10.1186/1749-8090-8-204
PMCID: PMC3818927  PMID: 24175992
Postoperative cognitive dysfunction; Cardiovascular surgery; Risk factor; Sevoflurane
25.  Fabrication and evaluation of Bis-GMA/TEGDMA dental resins/composites containing halloysite nanotubes 
Objective
To investigate the reinforcement of Bis-GMA/TEGDMA dental resins (without conventional glass filler) and the corresponding composites (with conventional glass filler)containing vari ed mass fractions of halloysite nanotubes (HNTs).
Methods
Three dispersion methods were studied to separate the silanized halloysite as individual HNTs and to uniformly distribute them into dental matrices. Photopolymerization induced volumetric shrinkage was measured by using a mercury dilatometer. Real time near infrared spectroscopy was adopted to study the degree of vinyl double bond conversion and the photopolymerization rate. Mechanical properties of the composites were tested by a universal mechanical testing machine. Analysis of Variance (ANOVA) was used for the statistical analysis of the acquired data. Morphologies of halloysite/HNTs and representative fracture surfaces of the reinforced dental resins/composites were examined by SEM and TEM.
Results
Impregnation of small mass fractions (e.g., 1% and 2.5%) of the silanized HNTs in Bis-GMA/TEGDMA dental resins/composites improved mechanical properties significantly; however; large mass fractions (e.g., 5%) of impregnation did not further improve the mechanical properties. The impregnation of HNTs into dental resins/composites could result in two opposite effects: the reinforcing effect due to the highly separated and uniformly distributed HNTs, and the weakening effect due to the formation of HNT agglomerates/particles.
Significance
Uniform distribution of a small amount of well-separated silanized HNTs into Bis-GMA/TEGDMA dental resins/composites could result in substantial improvements on mechanical properties.
doi:10.1016/j.dental.2012.06.007
PMCID: PMC3432153  PMID: 22796038
Dental composites; Bis-GMA; TEGDMA; Halloysite nanotubes

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