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Liu WT, Xu ZL, Mou XQ, Zhang BH, Bao W, Wang SH, Lee D, Lei LS, Zhang K. The synthesis of cycloalka[b]furans via an Au(i)-catalyzed tandem reaction of 3-yne-1,2-diols. Org Biomol Chem 2017; 15:6333-6337. [DOI: 10.1039/c7ob01179b] [Citation(s) in RCA: 4] [Impact Index Per Article: 0.6] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/21/2022]
Abstract
A rapid and convenient approach toward substituted cycloalka[b]furan compounds has been developed via an Au(i)-catalyzed cyclization/1,2-rearrangement/aromatization cascade.
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Zhang BH, Lei LS, Liu SZ, Mou XQ, Liu WT, Wang SH, Wang J, Bao W, Zhang K. Zinc-promoted cyclization of tosylhydrazones and 2-(dimethylamino)malononitrile: an efficient strategy for the synthesis of substituted 1-tosyl-1H-pyrazoles. Chem Commun (Camb) 2017; 53:8545-8548. [DOI: 10.1039/c7cc04610c] [Citation(s) in RCA: 34] [Impact Index Per Article: 4.9] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/21/2022]
Abstract
An efficient strategy for the synthesis of substituted 1-tosyl-1H-pyrazoles has been developed through a cyclization reaction of tosylhydrazones with 2-(dimethylamino)malononitrile.
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Liu WT, Yang CC, Chen RK, Jwo WS, Wu CW, Ting WY, Shung DP, Liu CC, Chen JJW. RiceATM: a platform for identifying the association between rice agronomic traits and miRNA expression. DATABASE-THE JOURNAL OF BIOLOGICAL DATABASES AND CURATION 2016; 2016:baw151. [PMID: 28025342 PMCID: PMC5199133 DOI: 10.1093/database/baw151] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.1] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Subscribe] [Scholar Register] [Received: 04/01/2016] [Revised: 10/21/2016] [Accepted: 10/24/2016] [Indexed: 11/12/2022]
Abstract
MicroRNAs (miRNAs) are known to play critical roles in plant development and stress-response regulation, and they frequently display multi-targeting characteristics. The control of defined rice phenotypes occurs through multiple genes; however, evidence demonstrating the relationship between agronomic traits and miRNA expression profiles is lacking. In this study, we investigated eight yield-related traits in 187 local rice cultivars and profiled the expression levels of 193 miRNAs in these cultivars using microarray analyses. By integrating the miRBase database, the rice annotation project database, and the miRanda and psRNATarget web servers, we constructed a database (RiceATM) that can be employed to investigate the association between rice agronomic traits and miRNA expression. The functions of this platform include phenotype selection, sample grouping, microarray data pretreatment, statistical analysis and target gene predictions. To demonstrate the utility of RiceATM, we used the database to identify four miRNAs associated with the heading date and validated their expression trends in the cultivars with early or late heading date by real-time PCR. RiceATM is a useful tool for researchers seeking to characterize the role of certain miRNAs for a specific phenotype and discover potential biomarkers for breeding or functional studies. Database URL: http://syslab3.nchu.edu.tw/rice/
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Wang M, Carver JJ, Phelan VV, Sanchez LM, Garg N, Peng Y, Nguyen DD, Watrous J, Kapono CA, Luzzatto-Knaan T, Porto C, Bouslimani A, Melnik AV, Meehan MJ, Liu WT, Crüsemann M, Boudreau PD, Esquenazi E, Sandoval-Calderón M, Kersten RD, Pace LA, Quinn RA, Duncan KR, Hsu CC, Floros DJ, Gavilan RG, Kleigrewe K, Northen T, Dutton RJ, Parrot D, Carlson EE, Aigle B, Michelsen CF, Jelsbak L, Sohlenkamp C, Pevzner P, Edlund A, McLean J, Piel J, Murphy BT, Gerwick L, Liaw CC, Yang YL, Humpf HU, Maansson M, Keyzers RA, Sims AC, Johnson AR, Sidebottom AM, Sedio BE, Klitgaard A, Larson CB, P CAB, Torres-Mendoza D, Gonzalez DJ, Silva DB, Marques LM, Demarque DP, Pociute E, O'Neill EC, Briand E, Helfrich EJN, Granatosky EA, Glukhov E, Ryffel F, Houson H, Mohimani H, Kharbush JJ, Zeng Y, Vorholt JA, Kurita KL, Charusanti P, McPhail KL, Nielsen KF, Vuong L, Elfeki M, Traxler MF, Engene N, Koyama N, Vining OB, Baric R, Silva RR, Mascuch SJ, Tomasi S, Jenkins S, Macherla V, Hoffman T, Agarwal V, Williams PG, Dai J, Neupane R, Gurr J, Rodríguez AMC, Lamsa A, Zhang C, Dorrestein K, Duggan BM, Almaliti J, Allard PM, Phapale P, Nothias LF, Alexandrov T, Litaudon M, Wolfender JL, Kyle JE, Metz TO, Peryea T, Nguyen DT, VanLeer D, Shinn P, Jadhav A, Müller R, Waters KM, Shi W, Liu X, Zhang L, Knight R, Jensen PR, Palsson BO, Pogliano K, Linington RG, Gutiérrez M, Lopes NP, Gerwick WH, Moore BS, Dorrestein PC, Bandeira N. Sharing and community curation of mass spectrometry data with Global Natural Products Social Molecular Networking. Nat Biotechnol 2016. [PMID: 27504778 DOI: 10.1038/nbt.3597.sharing] [Citation(s) in RCA: 3] [Impact Index Per Article: 0.4] [Reference Citation Analysis] [Abstract] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 03/16/2023]
Abstract
The potential of the diverse chemistries present in natural products (NP) for biotechnology and medicine remains untapped because NP databases are not searchable with raw data and the NP community has no way to share data other than in published papers. Although mass spectrometry (MS) techniques are well-suited to high-throughput characterization of NP, there is a pressing need for an infrastructure to enable sharing and curation of data. We present Global Natural Products Social Molecular Networking (GNPS; http://gnps.ucsd.edu), an open-access knowledge base for community-wide organization and sharing of raw, processed or identified tandem mass (MS/MS) spectrometry data. In GNPS, crowdsourced curation of freely available community-wide reference MS libraries will underpin improved annotations. Data-driven social-networking should facilitate identification of spectra and foster collaborations. We also introduce the concept of 'living data' through continuous reanalysis of deposited data.
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Wang M, Carver JJ, Phelan VV, Sanchez LM, Garg N, Peng Y, Nguyen DD, Watrous J, Kapono CA, Luzzatto-Knaan T, Porto C, Bouslimani A, Melnik AV, Meehan MJ, Liu WT, Crüsemann M, Boudreau PD, Esquenazi E, Sandoval-Calderón M, Kersten RD, Pace LA, Quinn RA, Duncan KR, Hsu CC, Floros DJ, Gavilan RG, Kleigrewe K, Northen T, Dutton RJ, Parrot D, Carlson EE, Aigle B, Michelsen CF, Jelsbak L, Sohlenkamp C, Pevzner P, Edlund A, McLean J, Piel J, Murphy BT, Gerwick L, Liaw CC, Yang YL, Humpf HU, Maansson M, Keyzers RA, Sims AC, Johnson AR, Sidebottom AM, Sedio BE, Klitgaard A, Larson CB, P. CAB, Torres-Mendoza D, Gonzalez DJ, Silva DB, Marques LM, Demarque DP, Pociute E, O'Neill EC, Briand E, Helfrich EJN, Granatosky EA, Glukhov E, Ryffel F, Houson H, Mohimani H, Kharbush JJ, Zeng Y, Vorholt JA, Kurita KL, Charusanti P, McPhail KL, Nielsen KF, Vuong L, Elfeki M, Traxler MF, Engene N, Koyama N, Vining OB, Baric R, Silva RR, Mascuch SJ, Tomasi S, Jenkins S, Macherla V, Hoffman T, Agarwal V, Williams PG, Dai J, Neupane R, Gurr J, Rodríguez AMC, Lamsa A, Zhang C, Dorrestein K, Duggan BM, Almaliti J, Allard PM, Phapale P, Nothias LF, Alexandrov T, Litaudon M, Wolfender JL, Kyle JE, Metz TO, Peryea T, Nguyen DT, VanLeer D, Shinn P, Jadhav A, Müller R, Waters KM, Shi W, Liu X, Zhang L, Knight R, Jensen PR, Palsson BO, Pogliano K, Linington RG, Gutiérrez M, Lopes NP, Gerwick WH, Moore BS, Dorrestein PC, Bandeira N. Sharing and community curation of mass spectrometry data with Global Natural Products Social Molecular Networking. Nat Biotechnol 2016; 34:828-837. [PMID: 27504778 PMCID: PMC5321674 DOI: 10.1038/nbt.3597] [Citation(s) in RCA: 2320] [Impact Index Per Article: 290.0] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/11/2015] [Accepted: 05/10/2016] [Indexed: 12/14/2022]
Abstract
The potential of the diverse chemistries present in natural products (NP) for biotechnology and medicine remains untapped because NP databases are not searchable with raw data and the NP community has no way to share data other than in published papers. Although mass spectrometry (MS) techniques are well-suited to high-throughput characterization of NP, there is a pressing need for an infrastructure to enable sharing and curation of data. We present Global Natural Products Social Molecular Networking (GNPS; http://gnps.ucsd.edu), an open-access knowledge base for community-wide organization and sharing of raw, processed or identified tandem mass (MS/MS) spectrometry data. In GNPS, crowdsourced curation of freely available community-wide reference MS libraries will underpin improved annotations. Data-driven social-networking should facilitate identification of spectra and foster collaborations. We also introduce the concept of 'living data' through continuous reanalysis of deposited data.
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Mou XQ, Xu ZL, Xu L, Wang SH, Zhang BH, Zhang D, Wang J, Liu WT, Bao W. The Synthesis of Multisubstituted Pyrroles via a Copper-Catalyzed Tandem Three-Component Reaction. Org Lett 2016; 18:4032-5. [DOI: 10.1021/acs.orglett.6b01883] [Citation(s) in RCA: 28] [Impact Index Per Article: 3.5] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/18/2022]
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Liu LL, Zhao CL, Liu WT, Wang Y, Shen DH. [Clinicopathologic features and molecular genetics of alveolar rhabdomyosarcoma]. ZHONGHUA BING LI XUE ZA ZHI = CHINESE JOURNAL OF PATHOLOGY 2016; 45:411-2. [PMID: 27256052 DOI: 10.3760/cma.j.issn.0529-5807.2016.06.013] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Subscribe] [Scholar Register] [Indexed: 11/05/2022]
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Wang J, Mou XQ, Zhang BH, Liu WT, Yang C, Xu L, Xu ZL, Wang SH. A metal-free addition/dearomatization–cyclization/decarboxylation cascade of aryl 3-arylpropiolate toward the synthesis of 1,1-diaryl-2-alkyl-substituted ethylenes. Tetrahedron Lett 2016. [DOI: 10.1016/j.tetlet.2016.02.013] [Citation(s) in RCA: 10] [Impact Index Per Article: 1.3] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/15/2022]
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Huang HC, Liu WT, Hua KS, Hung HC, Tsai JY, Kuo SC, Huang LJ, Gean PW. α-Carboline derivative TJY-16 inhibits tumor growth by inducing G2/M cell cycle arrest in glioma cells. J Biomed Sci 2016; 23:10. [PMID: 26786523 PMCID: PMC4717554 DOI: 10.1186/s12929-016-0222-y] [Citation(s) in RCA: 7] [Impact Index Per Article: 0.9] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/29/2015] [Accepted: 01/11/2016] [Indexed: 01/21/2023] Open
Abstract
Background Glioblastoma multiforme (GBM) is the most lethal primary brain tumors which remains difficult to cure despite advances in surgery, radiotherapy and chemotherapy. Therefore, the development of new drug is urgently needed. α-carboline derivatives were usually isolated from marine animals such as Britannia marine tunicate Dendrodoa grossularia and Indonesian ascidian Polycarpa aurata. In this study, we have synthesized several α-carboline compounds and examined their anti-glioma activities. Results We report that among α-carboline derivatives TJY-16 (6-acetyl-9-(3,4,5-trimethoxybenzyl)-9H-pyrido[2,3-b] indole) is the most potent α-carboline analog to induce glioma cell death with IC50 value of around 50 nM. TJY-16 decreased cell viability of glioma cells in a concentration- and time-dependent manner. Trypan blue exclusion assay showed that the reduction of cell viability was due to both cell growth inhibition and cell death. Flow cytometric analysis showed that TJY-16 induced G2/M cell cycle arrest followed by induction of sub-G1 phase. Hoechst staining detected the apoptotic features such as nuclear shrinkage and DNA condensation. Western blot analysis showed the increased level of cleaved caspase-3. The activation of caspase-8 and depolarization of mitochondrial membrane potential (ΔΨm) indicated that both extrinsic and intrinsic apoptotic pathways were involved in TJY-16-induced apoptosis. TJY-16 effectively inhibited tumor growth and induced caspase-3 activation in the xenograft tumor model of U87 glioma cells. Conclusions Our results suggest that TJY-16 may kill glioma cells by inducing G2/M cell cycle arrest followed by apoptosis. Thus, TJY-16 is a promising agent for the treatment of malignant gliomas.
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Oyama KI, Hsu YW, Jiang GS, Chen WH, Cheng CZ, Fang HK, Liu WT. Electron temperature and density probe for small aeronomy satellites. THE REVIEW OF SCIENTIFIC INSTRUMENTS 2015; 86:084703. [PMID: 26329217 DOI: 10.1063/1.4927342] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 06/05/2023]
Abstract
A compact and low power consumption instrument for measuring the electron density and temperature in the ionosphere has been developed by modifying the previously developed Electron Temperature Probe (ETP). A circuit block which controls frequency of the sinusoidal signal is added to the ETP so that the instrument can measure both T(e) in low frequency mode and N(e) in high frequency mode from the floating potential shift of the electrode. The floating potential shift shows a minimum at the upper hybrid resonance frequency (f(UHR)). The instrument which is named "TeNeP" can be used for tiny satellites which do not have enough conductive surface area for conventional DC Langmuir probe measurements. The instrument also eliminates the serious problems associated with the contamination of satellite surface as well as the sensor electrode.
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Wang YF, Liu WT, Chen CY, Ke HP, Jiang HL, Chen XL, Shi SY, Wei W, Zhang XN. Anti-osteoporosis activity of red yeast rice extract on ovariectomy-induced bone loss in rats. GENETICS AND MOLECULAR RESEARCH 2015; 14:8137-46. [PMID: 26345740 DOI: 10.4238/2015.july.27.2] [Citation(s) in RCA: 8] [Impact Index Per Article: 0.9] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/03/2022]
Abstract
Osteoporosis is the most common bone disease, affecting millions of people worldwide and leading to significant morbidity and high costs. Monacolin K, an extract of red yeast rice (RYR, Hongqu), plays important roles in the management of dyslipidemia, coronary heart disease, and diabetes. Our study aimed to investigate the protective effect of monacolin K on ovariectomy-induced bone loss in rats. Fifty female Sprague-Dawley rats were randomly divided into a sham-operated and five ovariectomized (OVX) groups: OVX with vehicle, OVX with fluvastatin, and OVX with RYR extract of three graded doses. Bone mineral density (BMD), biochemical markers, and cell viability were analyzed by dual energy X-ray absorptiometry, enzyme-linked immunosorbent assay, and 3(4,5-dimethylthiazol-2-yl)-2,5-diphenyl tetrazolium bromide (MTT) assays. Gene expression was evaluated by real-time polymerase chain reaction amplification and western blot. Our results showed that administration of RYR extract markedly increased the bone mineral density in OVX rats. Moreover, RYR extract decreased the levels of bone turnover markers, including osteocalcin and tartrate resistant acid phosphatase activity. The MMT assay revealed that RYR extract treatment significantly improved the osteoblast viabilities in a dose-dependent manner (P < 0.05). At the molecular level, we further demonstrated that RYR extract enhanced the expression of Bmp2 and Bmp4 both at the mRNA and protein levels. Collectively, these data suggested RYR extract could protect against osteoporosis in ovariectomized rats, most likely through activation of BMP2/4 expression.
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Liu YP, Lee JJ, Lai TC, Lee CH, Hsiao YW, Chen PS, Liu WT, Hong CY, Lin SK, Ping Kuo MY, Lu PJ, Hsiao M. Suppressive function of low-dose deguelin on the invasion of oral cancer cells by downregulating tumor necrosis factor alpha-induced nuclear factor-kappa B signaling. Head Neck 2015; 38 Suppl 1:E524-34. [PMID: 25784049 DOI: 10.1002/hed.24034] [Citation(s) in RCA: 24] [Impact Index Per Article: 2.7] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Accepted: 03/05/2015] [Indexed: 12/16/2022] Open
Abstract
BACKGROUND Deguelin has both antiproliferation and antimetastasis activities. However, high-dose deguelin elicits many undesired side effects. The purpose of this study was to investigate whether the low-dose deguelin can prevent the metastasis of oral cancer. METHODS The dose effects of deguelin on metastasis of oral cancer cells were analyzed by in vitro invasion assay and an orthotropic xenograft mouse model. The involvement of tumor necrosis factor alpha (TNF-α)-induced nuclear factor-kappa B (NF-κB) signaling was examined by Western blot and reporter assay. RESULTS Low-dose deguelin, which has minimal cytotoxicity, significantly inhibited the invasion and migration of oral cancer cells. These inhibitory effects of low-dose deguelin were mediated by suppressing TNF-α-induced activation of IκB kinase leading to the inhibition of IκB phosphorylation, NF-κB transcriptional activity, and matrix metalloproteinase-2 (MMP2) expression. The low-dose deguelin treatment significantly inhibited tumor growth and invasion without systemic toxicity. CONCLUSION The low-dose deguelin suppressed the invasion and migration of oral cancer by downregulating TNF-α-induced NF-κB signaling. © 2015 Wiley Periodicals, Inc. Head Neck 38: E524-E534, 2016.
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Yang YY, Liu LY, Guo LL, Lv YL, Zhang GM, Lei J, Liu WT, Xiong YY, Wen HM. Seasonal concentrations, contamination levels, and health risk assessment of arsenic and heavy metals in the suspended particulate matter from an urban household environment in a metropolitan city, Beijing, China. ENVIRONMENTAL MONITORING AND ASSESSMENT 2015; 187:409. [PMID: 26048587 DOI: 10.1007/s10661-015-4611-6] [Citation(s) in RCA: 6] [Impact Index Per Article: 0.7] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Received: 11/09/2014] [Accepted: 05/19/2015] [Indexed: 06/04/2023]
Abstract
The levels and health risks of arsenic and heavy metals (As, Ba, Cd, Co, Cr, Cu, Mn, Ni, Pb, and Zn) in the suspended particulate matter (SPM) collected from an urban household environment in Beijing of China for 12 months were investigated. The mean concentrations of the studied toxic elements were higher and lower than crustal abundance and PM2.5 in the urban outdoors of Beijing. The concentrations of the studied elements displayed significant seasonality. The highest concentrations of the total elements occurred in winter, followed by autumn, while the lowest concentrations were recorded in summer. Based on the calculated values of enrichment factor (EF) and geoaccumulation index (Igeo), the levels for As and Cu were heavily contaminated, while those for Cd, Pb, and Zn were extremely contaminated. As and Pb might pose risks to children and adults via ingestion exposure. The accumulative risks of multi-elements resulted from dermal contact and inhalation exposures were not negligible. More attention should be paid to reducing the non-carcinogenic and carcinogenic health risks posed by the toxic elements bound to urban household SPM particles via ingestion, inhalation, and dermal contact exposure.
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Tsai HW, Yaghoubi A, Chan TC, Wang CC, Liu WT, Liao CN, Lu SY, Chen LJ, Chueh YL. Electrochemical synthesis of ultrafast and gram-scale surfactant-free tellurium nanowires by gas-solid transformation and their applications as supercapacitor electrodes for p-doping of graphene transistors. NANOSCALE 2015; 7:7535-7539. [PMID: 25832197 DOI: 10.1039/c5nr00876j] [Citation(s) in RCA: 7] [Impact Index Per Article: 0.8] [Reference Citation Analysis] [Abstract] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 06/04/2023]
Abstract
We herein report a gas-solid transformation mechanism for the surfactant-free synthesis of Te NWs at room temperature by electrolysis of bulk Bi2Te3 using H2Te gas. Te NWs, with an average diameter below 20 nm, grow along the [001] direction due to the unique spiral chains in the crystal structure and show an enhanced Raman scattering effect, a broad absorption band over the range of 350-750 nm and an emission band over the range of 400-700 nm in the photoluminescence spectrum. In terms of device applications, we demonstrate how Te NWs can be directly applied as a p-type dopant source in order to shift the Dirac point in ambipolar field effect graphene transistors. Finally, the favorable capacitive properties of Te NWs are established as supercapacitor electrodes with negligible internal resistance and excellent electrochemical reversibility and a specific capacitance of 24 F g(-1).
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Yu HC, Huang KY, Lu MC, Huang HL, Liu WT, Lee WC, Liu SQ, Huang HB, Lai NS. Characterization of the recognition specificity of BH2, a monoclonal antibody prepared against the HLA-B27 heavy chain. Int J Mol Sci 2015; 16:8142-50. [PMID: 25872138 PMCID: PMC4425072 DOI: 10.3390/ijms16048142] [Citation(s) in RCA: 2] [Impact Index Per Article: 0.2] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/30/2015] [Revised: 03/18/2015] [Accepted: 04/03/2015] [Indexed: 12/22/2022] Open
Abstract
BH2, a monoclonal antibody prepared against the denatured human leukocytic antigen-B27 heavy chain (HLA-B27 HC), can immunoprecipitate the misfolded HLA-B27 HC complexed with Bip in the endoplasmic reticulum and recognize the homodimerized HLA-B27 HC that is often observed on the cell membrane of patients suffered from ankylosing spondylitis (AS). However, the recognition specificity of BH2 toward the other molecules of HLA-B type and toward the different types of HLA molecules remained uncharacterized. In this study, we carried out the HLA-typing by using the Luminex Technology to characterize the recognition specificity of BH2 and analyzed the binding domain of HLA-B27 HC by BH2. Our results indicated that BH2 preferably binds to molecules of HLA-B and -C rather than HLA-A and the binding site is located within the α2 domain of HLA-B27 HC.
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Liu WT, Lin CH, Hsiao M, Gean PW. Minocycline inhibits the growth of glioma by inducing autophagy. Autophagy 2014; 7:166-75. [DOI: 10.4161/auto.7.2.14043] [Citation(s) in RCA: 59] [Impact Index Per Article: 5.9] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/19/2022] Open
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Moree WJ, McConnell OJ, Nguyen DD, Sanchez LM, Yang YL, Zhao X, Liu WT, Boudreau PD, Srinivasan J, Atencio L, Ballesteros J, Gavilán RG, Torres-Mendoza D, Guzmán HM, Gerwick WH, Gutiérrez M, Dorrestein PC. Microbiota of healthy corals are active against fungi in a light-dependent manner. ACS Chem Biol 2014; 9:2300-8. [PMID: 25058318 PMCID: PMC4201335 DOI: 10.1021/cb500432j] [Citation(s) in RCA: 49] [Impact Index Per Article: 4.9] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/24/2022]
Abstract
![]()
Coral
reefs are intricate ecosystems that harbor diverse organisms,
including 25% of all marine fish. Healthy corals exhibit a complex
symbiosis between coral polyps, endosymbiotic alga, and an array of
microorganisms, called the coral holobiont. Secretion of specialized
metabolites by coral microbiota is thought to contribute to the defense
of this sessile organism against harmful biotic and abiotic factors.
While few causative agents of coral diseases have been unequivocally
identified, fungi have been implicated in the massive destruction
of some soft corals worldwide. Because corals are nocturnal feeders,
they may be more vulnerable to fungal infection at night, and we hypothesized
that the coral microbiota would have the capability to enhance their
defenses against fungi in the dark. A Pseudoalteromonas sp. isolated from a healthy octocoral displayed light-dependent
antifungal properties when grown adjacent to Penicilliumcitrinum (P. citrinum) isolated
from a diseased Gorgonian octocoral. Microbial MALDI-imaging mass
spectrometry (IMS) coupled with molecular network analyses revealed
that Pseudoalteromonas produced higher levels of
antifungal polyketide alteramides in the dark than in the light. The
alteramides were inactivated by light through a photoinduced intramolecular
cyclization. Further NMR studies led to a revision of the stereochemical
structure of the alteramides. Alteramide A exhibited antifungal properties
and elicited changes in fungal metabolite distributions of mycotoxin
citrinin and citrinadins. These data support the hypothesis that coral
microbiota use abiotic factors such as light to regulate the production
of metabolites with specialized functions to combat opportunistic
pathogens at night.
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Hour MJ, Liu WT, Lu IC, Kuo SC, Gean PW. Aggravated DNA damage as a basis for enhanced glioma cell killing by MJ-66 in combination with minocycline. Am J Cancer Res 2014; 4:474-483. [PMID: 25232489 PMCID: PMC4163612] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/31/2014] [Accepted: 08/15/2014] [Indexed: 06/03/2023] Open
Abstract
Despite recent advances in the treatment of malignant glomas, the prognosis of patients remains very poor and more efficient therapeutic approaches are urgently needed. In the present study, we investigated whether 2-(naphthalene-1-yl)-6-pyrrolidinyl-4-quinazolinone (MJ-66), a synthetic quinazolinone analog, induces glioma cell death through DNA damage. Treatment of C6 glioma cells with MJ-66 resulted in a time-dependent increase in γ-H2AX and increased the appearance of nuclear γ-H2AX foci. MJ-66 interfered with G2/M DNA damage checkpoint through increasing phosphorylated levels of Chk1 and Cdc25C. UCN-01, a Chk1 inhibitor, reversed MJ-66-induced activation of Cdc25C and caspase 3. MJ-66 inhibited tumor growth and prolonged survival time in intracranial glioma xenograft model. The combination of MJ-66 and Mino enhanced DNA damage and synergistically inhibited tumor growth and prolonged survival time in intracranial glioma xenograft model. These results suggest that the combination of MJ-66 and Mino may be developed as a new therapeutic strategy against malignant gliomas.
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Mohimani H, Liu WT, Kersten R, Moore BS, Dorrestein PC, Pevzner PA. NRPquest: Coupling Mass Spectrometry and Genome Mining for Nonribosomal Peptide Discovery. JOURNAL OF NATURAL PRODUCTS 2014; 77:1902-9. [PMID: 25116163 PMCID: PMC4143176 DOI: 10.1021/np500370c] [Citation(s) in RCA: 65] [Impact Index Per Article: 6.5] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Subscribe] [Scholar Register] [Received: 04/29/2014] [Indexed: 05/31/2023]
Abstract
Nonribosomal peptides (NRPs) such as vancomycin and daptomycin are among the most effective antibiotics. While NRPs are biomedically important, the computational techniques for sequencing these peptides are still in their infancy. The recent emergence of mass spectrometry techniques for NRP analysis (capable of sequencing an NRP from small amounts of nonpurified material) revealed an enormous diversity of NRPs. However, as many NRPs have nonlinear structure (e.g., cyclic or branched-cyclic peptides), the standard de novo sequencing tools (developed for linear peptides) are not applicable to NRP analysis. Here, we introduce the first NRP identification algorithm, NRPquest, that performs mutation-tolerant and modification-tolerant searches of spectral data sets against a database of putative NRPs. In contrast to previous studies aimed at NRP discovery (that usually report very few NRPs), NRPquest revealed nearly a hundred NRPs (including unknown variants of previously known peptides) in a single study. This result indicates that NRPquest can potentially make MS-based NRP identification as robust as the identification of linear peptides in traditional proteomics.
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Liu WT, Chen C, Lu IC, Kuo SC, Lee KH, Chen TL, Song TS, Lu YL, Gean PW, Hour MJ. MJ-66 induces malignant glioma cells G2/M phase arrest and mitotic catastrophe through regulation of cyclin B1/Cdk1 complex. Neuropharmacology 2014; 86:219-27. [PMID: 25107587 DOI: 10.1016/j.neuropharm.2014.07.014] [Citation(s) in RCA: 19] [Impact Index Per Article: 1.9] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/20/2014] [Revised: 07/12/2014] [Accepted: 07/24/2014] [Indexed: 02/06/2023]
Abstract
Malignant gliomas are among the most devastating cancers as they are resistant to many kinds of treatment. Despite recent advances in the diagnosis and treatment, the prognosis of patients remains very poor and the development of new drug is urgently needed. Here, we report that a synthetic quinazolinone analog 2-(naphthalene-1-yl)-6-pyrrolidinyl-4-quinazolinone (MJ-66) induced glioma cell death. Immunofluorescence staining showed that MJ-66-induced cell death was associated with multinucleated phenotype and multipolar spindles that were typical characteristics of mitotic catastrophe. Flow cytometry analysis revealed that MJ-66 caused glioma cell cycle arrest at G2/M phase and increased the proportion of polyploidy cells. Western blotting indicated that the expression of cyclin B1, Cdk1 pY15 and Cdk1 increased after treatment with MJ-66. MJ-66 effectively inhibited tumor growth and induced apoptosis in the xenograft animal model of U87 human glioma cells. Together, these results suggest that MJ-66 inhibited malignant gliomas growth through inducing mitotic catastrophe by interference with G2/M cell cycle checkpoint which may open a new avenue for the treatment of malignant gliomas.
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Mohimani H, Kersten RD, Liu WT, Wang M, Purvine SO, Wu S, Brewer HM, Pasa-Tolic L, Bandeira N, Moore BS, Pevzner PA, Dorrestein PC. Automated genome mining of ribosomal peptide natural products. ACS Chem Biol 2014; 9:1545-51. [PMID: 24802639 PMCID: PMC4215869 DOI: 10.1021/cb500199h] [Citation(s) in RCA: 102] [Impact Index Per Article: 10.2] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/22/2022]
Abstract
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Ribosomally synthesized and posttranslationally
modified peptides
(RiPPs), especially from microbial sources, are a large group of bioactive
natural products that are a promising source of new (bio)chemistry
and bioactivity.1 In light of exponentially
increasing microbial genome databases and improved mass spectrometry
(MS)-based metabolomic platforms, there is a need for computational
tools that connect natural product genotypes predicted from microbial
genome sequences with their corresponding chemotypes from metabolomic
data sets. Here, we introduce RiPPquest, a tandem mass spectrometry
database search tool for identification of microbial RiPPs, and apply
it to lanthipeptide discovery. RiPPquest uses genomics to limit search
space to the vicinity of RiPP biosynthetic genes and proteomics to
analyze extensive peptide modifications and compute p-values of peptide-spectrum
matches (PSMs). We highlight RiPPquest by connecting multiple RiPPs
from extracts of Streptomyces to their gene clusters
and by the discovery of a new class III lanthipeptide, informatipeptin,
from Streptomyces viridochromogenes DSM 40736 to
reflect that it is a natural product that was discovered by mass spectrometry
based genome mining using algorithmic tools rather than manual inspection
of mass spectrometry data and genetic information. The presented tool
is available at cyclo.ucsd.edu.
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Liu G, Bakker GL, Li S, Vreeburg JHG, Verberk JQJC, Medema GJ, Liu WT, Van Dijk JC. Pyrosequencing reveals bacterial communities in unchlorinated drinking water distribution system: an integral study of bulk water, suspended solids, loose deposits, and pipe wall biofilm. ENVIRONMENTAL SCIENCE & TECHNOLOGY 2014; 48:5467-76. [PMID: 24766451 DOI: 10.1021/es5009467] [Citation(s) in RCA: 131] [Impact Index Per Article: 13.1] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 05/08/2023]
Abstract
The current understanding of drinking water distribution system (DWDS) microbiology is limited to pipe wall biofilm and bulk water; the contributions of particle-associated bacteria (from suspended solids and loose deposits) have long been neglected. Analyzing the composition and correlation of bacterial communities from different phases helped us to locate where most of the bacteria are and understand the interactions among these phases. In the present study, the bacteria from four critical phases of an unchlorinated DWDS, including bulk water, pipe wall biofilm, suspended solids, and loose deposits, were quantified and identified by adenosine triphosphate analysis and pyrosequencing, respectively. The results showed that the bulk water bacteria (including the contribution of suspended solids) contributed less than 2% of the total bacteria. The bacteria associated with loose deposits and pipe wall biofilm that accumulated in the DWDS accounted for over 98% of the total bacteria, and the contributions of bacteria in loose deposits and pipe wall biofilm were comparable. Depending on the amount of loose deposits, its contribution can be 7-fold higher than the pipe wall biofilm. Pyrosequencing revealed relatively stable bacterial communities in bulk water, pipe wall biofilm, and suspended solids throughout the distribution system; however, the communities present in loose deposits were dependent on the amount of loose deposits locally. Bacteria within the phases of suspended solids, loose deposits, and pipe wall biofilm were similar in phylogenetic composition. The bulk water bacteria (dominated by Polaromonas spp.) were clearly different from the bacteria from the other three phases (dominated by Sphingomonas spp.). This study highlighted that the integral DWDS ecology should include contributions from all of the four phases, especially the bacteria harbored by loose deposits. The accumulation of loose deposits and the aging process create variable microenvironments inside loose deposits structures for bacteria to grow. Moreover, loose deposits protect the associated bacteria from disinfectants, and due to their mobility, the associated bacteria reach taps easily.
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Lin YS, Huang HL, Liu WT, Lin TH, Huang HB. Identification of the high molecular weight isoform of phostensin. Int J Mol Sci 2014; 15:1068-79. [PMID: 24434620 PMCID: PMC3907856 DOI: 10.3390/ijms15011068] [Citation(s) in RCA: 5] [Impact Index Per Article: 0.5] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/11/2013] [Revised: 12/31/2013] [Accepted: 01/06/2014] [Indexed: 11/16/2022] Open
Abstract
Phostensin is encoded by KIAA1949. 5′-RACEanalysis has been used to identify the translation start site of phostensin mRNA, indicating that it encodes 165 amino acids with an apparent molecular weight of 26 kDa on SDS-PAGE. This low-molecular-weight phostensin is present in human peripheral blood mononuclear cells and many leukemic cell lines. Phostensin is a protein phosphatase-1(PP1) binding protein. It also contains one actin-binding motif at its C-terminal region and binds to the pointed ends of actin filaments, modulating actin dynamics. In the current study, a high-molecular-weight phostensin is identified by using immunoprecipitationin combination with a proteomic approach. This new species of phostensin is also encoded by KIAA1949 and consists of 613 amino acids with an apparent molecular weight of 110 kDa on SDS-PAGE. The low-molecular-weight and high-molecular-weight phostensins were named as phostensin-α and phostensin-β, respectively. Although phostensin-α is the C-terminal region of phostensin-β, it is not degraded from phostensin-β. Phostensin-β is capable of associating with PP1 and actin filaments, and is present in many cell lines.
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Liu WT, Lamsa A, Wong WR, Boudreau PD, Kersten R, Peng Y, Moree WJ, Duggan BM, Moore BS, Gerwick WH, Linington RG, Pogliano K, Dorrestein PC. MS/MS-based networking and peptidogenomics guided genome mining revealed the stenothricin gene cluster in Streptomyces roseosporus. J Antibiot (Tokyo) 2013; 67:99-104. [PMID: 24149839 DOI: 10.1038/ja.2013.99] [Citation(s) in RCA: 57] [Impact Index Per Article: 5.2] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/27/2013] [Revised: 07/24/2013] [Accepted: 07/27/2013] [Indexed: 02/06/2023]
Abstract
Most (75%) of the anti-infectives that save countless lives and enormously improve quality of life originate from microbes found in nature. Herein, we described a global visualization of the detectable molecules produced from a single microorganism, which we define as the 'molecular network' of that organism, followed by studies to characterize the cellular effects of antibacterial molecules. We demonstrate that Streptomyces roseosporus produces at least four non-ribosomal peptide synthetase-derived molecular families and their gene subnetworks (daptomycin, arylomycin, napsamycin and stenothricin) were identified with different modes of action. A number of previously unreported analogs involving truncation, glycosylation, hydrolysis and biosynthetic intermediates and/or shunt products were also captured and visualized by creation of a map through MS/MS networking. The diversity of antibacterial compounds produced by S. roseosporus highlights the importance of developing new approaches to characterize the molecular capacity of an organism in a more global manner. This allows one to more deeply interrogate the biosynthetic capacities of microorganisms with the goal to streamline the discovery pipeline for biotechnological applications in agriculture and medicine. This is a contribution to a special issue to honor Chris Walsh's amazing career.
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Liu WT, Huang CY, Lu IC, Gean PW. Inhibition of glioma growth by minocycline is mediated through endoplasmic reticulum stress-induced apoptosis and autophagic cell death. Neuro Oncol 2013; 15:1127-41. [PMID: 23787763 DOI: 10.1093/neuonc/not073] [Citation(s) in RCA: 30] [Impact Index Per Article: 2.7] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 01/01/2023] Open
Abstract
BACKGROUND We have reported that minocycline (Mino) induced autophagic death in glioma cells. In the present study, we characterize the upstream regulators that control autophagy and switch cell death from autophagic to apoptotic. METHODS Western blotting and immunofluorescence were used to detect the expressions of eukaryotic translation initiation factor 2α (eIF2α), transcription factor GADD153 (CHOP), and glucose-regulated protein 78 (GRP78). Short hairpin (sh)RNA was used to knock down eIF2α or CHOP expression. Autophagy was assessed by the conversion of light chain (LC)3-I to LC3-II and green fluorescent protein puncta formation. An intracranial mouse model and bioluminescent imaging were used to assess the effect of Mino on tumor growth and survival time of mice. RESULTS The expression of GRP78 in glioma was high, whereas in normal glia it was low. Mino treatment increased GRP78 expression and reduced binding of GRP78 with protein kinase-like endoplasmic reticulum kinase. Subsequently, Mino increased eIF2α phosphorylation and CHOP expression. Knockdown of eIF2α or CHOP reduced Mino-induced LC3-II conversion and glioma cell death. When autophagy was inhibited, Mino induced cell death in a caspase-dependent manner. Rapamycin in combination with Mino produced synergistic effects on LC3 conversion, reduction of the Akt/mTOR/p70S6K pathway, and glioma cell death. Bioluminescent imaging showed that Mino inhibited the growth of glioma and prolonged survival time and that these effects were blocked by shCHOP. CONCLUSIONS Mino induced autophagy by eliciting endoplasmic reticulum stress response and switched cell death from autophagy to apoptosis when autophagy was blocked. These results coupled with clinical availability and a safe track record make Mino a promising agent for the treatment of malignant gliomas.
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