151
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An improved and reproducible protocol for the extraction of high quality fungal RNA from plant biomass substrates. Fungal Genet Biol 2014; 72:201-206. [PMID: 24951842 DOI: 10.1016/j.fgb.2014.06.001] [Citation(s) in RCA: 17] [Impact Index Per Article: 1.7] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 02/12/2014] [Revised: 05/20/2014] [Accepted: 06/08/2014] [Indexed: 11/23/2022]
Abstract
Isolation of high quantity and quality RNA is a crucial step in the detection of meaningful gene expression data. Obtaining intact fungal RNA from complex lignocellulosic substrates is often difficult, producing low integrity RNA which perform poorly in downstream applications. In this study we developed an RNA extraction method using CsCl centrifugation procedure, modified from previous reports and adapted for isolation of RNA from plant biomass. This method provided high level of integrity and good quantity of RNA which were suitable for reliable analyses of gene expression and produced consistent and reproducible results.
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152
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Nacul L, O’Donovan DG, Lacerda EM, Gveric D, Goldring K, Hall A, Bowman E, Pheby D. Considerations in establishing a post-mortem brain and tissue bank for the study of myalgic encephalomyelitis/chronic fatigue syndrome: a proposed protocol. BMC Res Notes 2014; 7:370. [PMID: 24938650 PMCID: PMC4076507 DOI: 10.1186/1756-0500-7-370] [Citation(s) in RCA: 8] [Impact Index Per Article: 0.8] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/02/2013] [Accepted: 06/02/2014] [Indexed: 01/13/2023] Open
Abstract
BACKGROUND Our aim, having previously investigated through a qualitative study involving extensive discussions with experts and patients the issues involved in establishing and maintaining a disease specific brain and tissue bank for myalgic encephalomyelitis/chronic fatigue syndrome (ME/CFS), was to develop a protocol for a UK ME/CFS repository of high quality human tissue from well characterised subjects with ME/CFS and controls suitable for a broad range of research applications. This would involve a specific donor program coupled with rapid tissue collection and processing, supplemented by comprehensive prospectively collected clinical, laboratory and self-assessment data from cases and controls. FINDINGS We reviewed the operations of existing tissue banks from published literature and from their internal protocols and standard operating procedures (SOPs). On this basis, we developed the protocol presented here, which was designed to meet high technical and ethical standards and legal requirements and was based on recommendations of the MRC UK Brain Banks Network. The facility would be most efficient and cost-effective if incorporated into an existing tissue bank. Tissue collection would be rapid and follow robust protocols to ensure preservation sufficient for a wide range of research uses. A central tissue bank would have resources both for wide-scale donor recruitment and rapid response to donor death for prompt harvesting and processing of tissue. CONCLUSION An ME/CFS brain and tissue bank could be established using this protocol. Success would depend on careful consideration of logistic, technical, legal and ethical issues, continuous consultation with patients and the donor population, and a sustainable model of funding ideally involving research councils, health services, and patient charities. This initiative could revolutionise the understanding of this still poorly-understood disease and enhance development of diagnostic biomarkers and treatments.
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Affiliation(s)
- Luis Nacul
- London School of Hygiene & Tropical Medicine, ITD/CRD/International Centre for Evidence in Disability, K/490, Keppel Street, WC1E 7HT London, UK
| | - Dominic G O’Donovan
- Department of Histopathology, Box 235 Level 5 John Bonnett Clincal Laboratories, Addenbrooke’s Hospital, Hills Road, CB1 0QQ Cambridge, UK
| | - Eliana M Lacerda
- London School of Hygiene & Tropical Medicine, ITD/CRD/International Centre for Evidence in Disability, K/490, Keppel Street, WC1E 7HT London, UK
| | - Djordje Gveric
- The UK Multiple Sclerosis and Parkinson’s Disease Tissue Banks, Hammersmith Campus, Imperial College, 160 Du Cane Road, W12 0NN London, UK
| | - Kirstin Goldring
- UCL-RFH BioBank, Royal Free Hospital, 1st Floor, Rowland Hill Street, NW3 2PF Hampstead, UK
| | - Alison Hall
- PHG Foundation, 2 Wort’s Causeway, Cambridge CB1 8RN, UK
| | - Erinna Bowman
- London School of Hygiene & Tropical Medicine, ITD/CRD/International Centre for Evidence in Disability, K/490, Keppel Street, WC1E 7HT London, UK
| | - Derek Pheby
- Faculty of Health and Society, Buckinghamshire New University, Uxbridge Campus, 106, Oxford Road, Uxbridge, Middlesex UB8 1NA, USA
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153
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Grasso D, Garcia MN, Hamidi T, Cano C, Calvo E, Lomberk G, Urrutia R, Iovanna JL. Genetic inactivation of the pancreatitis-inducible gene Nupr1 impairs PanIN formation by modulating Kras(G12D)-induced senescence. Cell Death Differ 2014; 21:1633-41. [PMID: 24902898 PMCID: PMC4158688 DOI: 10.1038/cdd.2014.74] [Citation(s) in RCA: 38] [Impact Index Per Article: 3.8] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/12/2013] [Revised: 04/01/2014] [Accepted: 04/30/2014] [Indexed: 12/29/2022] Open
Abstract
Nuclear protein 1 (Nupr1), a small chromatin protein, has a critical role in cancer development, progression and resistance to therapy. Previously, we had demonstrated that Nupr1 cooperates with KrasG12D to induce pancreas intraepithelial neoplasias (PanIN) formation and pancreatic ductal adenocarcinoma development in mice. However, the molecular mechanisms by which Nupr1 influences Kras-mediated preneoplastic growth remain to be fully characterized. In the current study, we report evidence supporting a role for Nupr1 as a gene modifier of KrasG12D-induced senescence, which must be overcome to promote PanIN formation. We found that genetic inactivation of Nupr1 in mice impairs Kras-induced PanIN, leading to an increase in β-galactosidase-positive cells and an upregulation of surrogate marker genes for senescence. More importantly, both of these cellular and molecular changes are recapitulated by the results of mechanistic experiments using RNAi-based inactivation of Nupr1 in human pancreatic cancer cell models. In addition, the senescent phenotype, which results from Nupr1 inactivation, is accompanied by activation of the FoxO3a-Skp2-p27Kip1-pRb-E2F pathway in vivo and in vitro. Thus, combined, these results show, for the first time, that Nupr1 aids oncogenic Kras to bypass senescence in a manner that cooperatively promotes PanIN formation. Besides its mechanistic importance, this new knowledge bears medical relevance as it delineates early pathobiological events that may be targeted in the future as a means to interfere with the formation of preneoplastic lesions early during pancreatic carcinogenesis.
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Affiliation(s)
- D Grasso
- Centre de Recherche en Cancérologie de Marseille (CRCM), INSERM U1068, CNRS UMR 7258, Aix-Marseille Université and Institut Paoli-Calmettes, Parc Scientifique et Technologique de Luminy, Marseille, France
| | - M N Garcia
- Centre de Recherche en Cancérologie de Marseille (CRCM), INSERM U1068, CNRS UMR 7258, Aix-Marseille Université and Institut Paoli-Calmettes, Parc Scientifique et Technologique de Luminy, Marseille, France
| | - T Hamidi
- Centre de Recherche en Cancérologie de Marseille (CRCM), INSERM U1068, CNRS UMR 7258, Aix-Marseille Université and Institut Paoli-Calmettes, Parc Scientifique et Technologique de Luminy, Marseille, France
| | - C Cano
- Centre de Recherche en Cancérologie de Marseille (CRCM), INSERM U1068, CNRS UMR 7258, Aix-Marseille Université and Institut Paoli-Calmettes, Parc Scientifique et Technologique de Luminy, Marseille, France
| | - E Calvo
- Molecular Endocrinology and Oncology Research Center, CHUL Research Center, Quebec City, QC, Canada
| | - G Lomberk
- Laboratory of Epigenetics and Chromatin Dynamics, Gastroenterology Research Unit, Departments of Biochemistry and Molecular Biology, Biophysics, and Medicine, Mayo Clinic, Rochester, MN, USA
| | - R Urrutia
- Laboratory of Epigenetics and Chromatin Dynamics, Gastroenterology Research Unit, Departments of Biochemistry and Molecular Biology, Biophysics, and Medicine, Mayo Clinic, Rochester, MN, USA
| | - J L Iovanna
- Centre de Recherche en Cancérologie de Marseille (CRCM), INSERM U1068, CNRS UMR 7258, Aix-Marseille Université and Institut Paoli-Calmettes, Parc Scientifique et Technologique de Luminy, Marseille, France
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154
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Cano CE, Hamidi T, Garcia MN, Grasso D, Loncle C, Garcia S, Calvo E, Lomberk G, Dusetti N, Bartholin L, Urrutia R, Iovanna JL. Genetic inactivation of Nupr1 acts as a dominant suppressor event in a two-hit model of pancreatic carcinogenesis. Gut 2014; 63:984-95. [PMID: 24026351 DOI: 10.1136/gutjnl-2013-305221] [Citation(s) in RCA: 31] [Impact Index Per Article: 3.1] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Submit a Manuscript] [Subscribe] [Scholar Register] [Indexed: 12/12/2022]
Abstract
BACKGROUND Nuclear protein 1 (Nupr1) is a major factor in the cell stress response required for Kras(G12D)-driven formation of pancreatic intraepithelial neoplastic lesions (PanINs). We evaluated the relevance of Nupr1 in the development of pancreatic cancer. METHODS We investigated the role of Nupr1 in pancreatic ductal adenocarcinoma (PDAC) progression beyond PanINs in Pdx1-cre;LSL-Kras(G12D);Ink4a/Arf(fl/fl)(KIC) mice. RESULTS Even in the context of the second tumorigenic hit of Ink4a/Arf deletion, Nupr1 deficiency led to suppression of malignant transformation involving caspase 3 activation in premalignant cells of KIC pancreas. Only half of Nupr1-deficient;KIC mice achieved PDAC development, and incident cases survived longer than Nupr1(wt);KIC mice. This was associated with the development of well-differentiated PDACs in Nupr1-deficient;KIC mice, which displayed enrichment of genes characteristic of the recently identified human classical PDAC subtype. Nupr1-deficient;KIC PDACs also shared with human classical PDACs the overexpression of the Kras-activation gene signature. In contrast, Nupr1(wt);KIC mice developed invasive PDACs with enriched gene signature of human quasi-mesenchymal (QM) PDACs. Cells derived from Nupr1-deficient;KIC PDACs growth in an anchorage-independent manner in vitro had higher aldehyde dehydrogenase activity and overexpressed nanog, Oct-4 and Sox2 transcripts compared with Nupr1(wt);KIC cells. Moreover, Nupr1-deficient and Nurpr1(wt);KIC cells differed in their sensitivity to the nucleoside analogues Ly101-4b and WJQ63. Together, these findings show the pivotal role of Nupr1 in both the initiation and late stages of PDAC in vivo, with a potential impact on PDAC cell stemness. CONCLUSIONS According to Nupr1 status, KIC mice develop tumours that phenocopy human classical or QM-PDAC, respectively, and present differential drug sensitivity, thus becoming attractive models for preclinical drug trials.
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Affiliation(s)
- Carla E Cano
- Centre de Recherche en Carcérologie de Marseille (CRCM), INSERM UMR 1068, CNRS UMR 7258, Aix-Marseille University and Institut Paoli-Calmettes, Parc Scientifique et Technologique de Luminy, , Marseille, France
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Effect of a Liver X Receptor Agonist on Deposition and Lymphatic Absorption of Plant Sterols in Stroke-Prone Spontaneously Hypertensive Rats Having a Mutation in ATP-Binding Cassette Transporter G5. Biosci Biotechnol Biochem 2014; 75:2359-63. [DOI: 10.1271/bbb.110554] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.1] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/31/2022]
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156
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Kefir fermented milk and kefiran promote growth of Bifidobacterium bifidum PRL2010 and modulate its gene expression. Int J Food Microbiol 2014; 178:50-9. [DOI: 10.1016/j.ijfoodmicro.2014.02.024] [Citation(s) in RCA: 50] [Impact Index Per Article: 5.0] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/08/2013] [Revised: 01/21/2014] [Accepted: 02/27/2014] [Indexed: 12/28/2022]
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157
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Albarouki E, Schafferer L, Ye F, von Wirén N, Haas H, Deising HB. Biotrophy-specific downregulation of siderophore biosynthesis in Colletotrichum graminicola is required for modulation of immune responses of maize. Mol Microbiol 2014; 92:338-55. [PMID: 24674132 PMCID: PMC4235341 DOI: 10.1111/mmi.12561] [Citation(s) in RCA: 36] [Impact Index Per Article: 3.6] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Accepted: 02/18/2014] [Indexed: 12/01/2022]
Abstract
The hemibiotrophic maize pathogen Colletotrichum graminicola synthesizes one intracellular and three secreted siderophores. eGFP fusions with the key siderophore biosynthesis gene, SID1, encoding l-ornithine-N(5) -monooxygenase, suggested that siderophore biosynthesis is rigorously downregulated specifically during biotrophic development. In order to investigate the role of siderophores during vegetative development and pathogenesis, SID1, which is required for synthesis of all siderophores, and the non-ribosomal peptide synthetase gene NPS6, synthesizing secreted siderophores, were deleted. Mutant analyses revealed that siderophores are required for vegetative growth under iron-limiting conditions, conidiation, ROS tolerance, and cell wall integrity. Δsid1 and Δnps6 mutants were hampered in formation of melanized appressoria and impaired in virulence. In agreement with biotrophy-specific downregulation of siderophore biosynthesis, Δsid1 and Δnps6 strains were not affected in biotrophic development, but spread of necrotrophic hyphae was reduced. To address the question why siderophore biosynthesis is specifically downregulated in biotrophic hyphae, maize leaves were infiltrated with siderophores. Siderophore infiltration alone did not induce defence responses, but formation of biotrophic hyphae in siderophore-infiltrated leaves caused dramatically increased ROS formation and transcriptional activation of genes encoding defence-related peroxidases and PR proteins. These data suggest that fungal siderophores modulate the plant immune system.
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Affiliation(s)
- Emad Albarouki
- Martin-Luther-Universität Halle-Wittenberg, Interdisziplinäres Zentrum für Nutzpflanzenforschung (IZN), Betty-Heimann-Str. 3, D-06120, Halle (Saale), Germany; Martin-Luther-Universität Halle-Wittenberg, Institut für Agrar- und Ernährungswissenschaften, Phytopathologie und Pflanzenschutz, Betty-Heimann-Str. 3, D-06120, Halle (Saale), Germany
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158
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Guo W, Tang H, Zhang L. Lycopene cyclase and phytoene synthase activities in the marine yeast Rhodosporidium diobovatum are encoded by a single gene crtYB. J Basic Microbiol 2014; 54:1053-61. [PMID: 24677129 DOI: 10.1002/jobm.201300920] [Citation(s) in RCA: 11] [Impact Index Per Article: 1.1] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/18/2013] [Accepted: 01/26/2014] [Indexed: 11/05/2022]
Abstract
crtYB, encoding lycopene cyclase and phytoene synthase was cloned from Rhodosporidium diobovatum ATCC 2527 by rapid amplification of cDNA ends method. The full-length cDNA of crtYB is 2, 330 bp and contains eight introns. The gene products is a 594 amino acids, with a predicted molecular mass of 65.63 kDa and a pI of 6.73. The N-terminus of the protein contains six transmembrane regions, which has been characterized as a lycopene beta-cyclase. The C-terminal half has squalene and phytoene synthase signatures that identified as phytoene synthetase. By heterologous complementary detection of this gene in E. coli and HPLC analysis, the regions responsible for phytoene synthesis and lycopene cyclization were localized within the protein.
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Affiliation(s)
- Wenjing Guo
- Key Discipline of Biological Engineering of Hebei Province, College of Life Sciences, Hebei University, Baoding, China; Key Laboratory of Microbial Diversity Research and Application of Hebei Province, College of Life Sciences, Hebei University, Baoding, China
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159
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Impact of IGF-I release kinetics on bone healing: a preliminary study in sheep. Eur J Pharm Biopharm 2014; 85:99-106. [PMID: 23958321 DOI: 10.1016/j.ejpb.2013.03.004] [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: 12/14/2012] [Revised: 03/11/2013] [Accepted: 03/12/2013] [Indexed: 11/20/2022]
Abstract
Spatiotemporal release of growth factors from a delivery device can profoundly affect the efficacy of bone growth induction. Here, we report on a delivery platform based on the encapsulation of insulin-like growth factor I (IGF-I) in different poly(D,L-lactide) (PLA) and poly(D,L-lactide-co-glycolide) (PLGA) microsphere (MS) formulations to control IGF-I release kinetics. In vitro IGF-I release profiles generally exhibited an initial burst (14-36% of total IGF-I content), which was followed by a more or less pronounced dormant phase with little release (2 to 34 days), and finally, a third phase of re-increased IGF-I release. The osteoinductive potential of these different IGF-I PL(G)A MS formulations was tested in studies using 8-mm metaphyseal drill hole bone defects in sheep. Histomorphometric analysis at 3 and 6 weeks after surgery showed that new bone formation was improved in the defects locally treated with IGF-I PL(G)A MS (n=5) as compared to defects filled with IGF-I-free PL(G)A MS (n=4). The extent of new bone formation was affected by the particular release kinetics, although a definitive relationship was not evident. Local administration of IGF-I resulted in down-regulation of inflammatory marker genes in all IGF-I treated defects. The over-expression of growth factor genes in response to IGF-I delivery was restricted to formulations that produced osteogenic responses. These experiments demonstrate the osteoinductive potential of sustained IGF-I delivery and show the importance of delivery kinetics for successful IGF-I-based therapies.
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160
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Kato H, Saito T, Ito H, Komeda Y, Kato A. Overexpression of the TIR-X gene results in a dwarf phenotype and activation of defense-related gene expression in Arabidopsis thaliana. JOURNAL OF PLANT PHYSIOLOGY 2014; 171:382-8. [PMID: 24594389 DOI: 10.1016/j.jplph.2013.12.002] [Citation(s) in RCA: 7] [Impact Index Per Article: 0.7] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Received: 09/05/2013] [Revised: 11/30/2013] [Accepted: 12/03/2013] [Indexed: 05/03/2023]
Abstract
The Arabidopsis genome encodes various proteins with a Toll/interleukin-1 receptor (TIR) domain. Many of these proteins also contain nucleotide-binding site (NBS) and leucine-rich repeat (LRR) domains and function as resistance (R) proteins. However, the protein encoded by At2g32140 (a TIR-X gene) contains a TIR domain but lacks NBS and LRR domains. We found that transgenic plants overexpressing At2g32140 displayed a dwarf phenotype and showed increased expression of defense-related genes. In general, the growth defect caused by activation of defense responses is suppressed under high-temperature conditions. However, transgenic plants overexpressing At2g32140 displayed a much stronger dwarf phenotype at 28°C than at 22°C. This dwarf phenotype was suppressed under the combination with known salicylic-acid pathway mutants. These findings suggest that At2g32140 encodes a protein involved in the plant defense response.
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Affiliation(s)
- Hiroaki Kato
- Biosystems Science Course, Graduate School of Life Science, Hokkaido University, Sapporo 060-0810, Japan
| | - Tamao Saito
- Department of Materials and Life Sciences, Faculty of Science and Technology, Sophia University, Chiyoda-ku, Tokyo 120-8554, Japan
| | - Hidetaka Ito
- Department of Biological Sciences, Faculty of Science, Hokkaido University, Sapporo 060-0810, Japan; Japan Science and Technology Agency, PRESTO, Kawaguchi, Saitama 332-0012, Japan
| | - Yoshibumi Komeda
- Department of Biological Sciences, Graduate School of Science, The University of Tokyo, Hongo, Tokyo 113-0033, Japan
| | - Atsushi Kato
- Department of Biological Sciences, Faculty of Science, Hokkaido University, Sapporo 060-0810, Japan.
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161
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Borirak O, Bekker M, Hellingwerf KJ. Molecular physiology of the dynamic regulation of carbon catabolite repression in Escherichia coli. MICROBIOLOGY-SGM 2014; 160:1214-1223. [PMID: 24603062 DOI: 10.1099/mic.0.077289-0] [Citation(s) in RCA: 4] [Impact Index Per Article: 0.4] [Reference Citation Analysis] [Abstract] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 11/18/2022]
Abstract
We report on the use of the chemostat as an optimal device to create time-invariant conditions that allow accurate sampling for various omics assays in Escherichia coli, in combination with recording of the dynamics of the physiological transition in the organism under study that accompany the initiation of glucose repression. E. coli cells respond to the addition of glucose not only with the well-known transcriptional response, as was revealed through quantitative PCR analysis of the transcript levels of key genes from the CRP (cAMP receptor protein) regulon, but also with an increased growth rate and a transient decrease in the efficiency of its aerobic catabolism. Less than half of a doubling time is required for the organism to recover to maximal values of growth rate and efficiency. Furthermore, calculations based on our results show that the specific glucose uptake rate (qs) and the H(+)/e(-) ratio increase proportionally, up to a growth rate of 0.4 h(-1), whilst biomass yield on glucose (Yx / s) drops during the first 15 min, followed by a gradual recovery. Surprisingly, the growth yields after the recovery phase show values even higher than the maximum theoretical yield. Possible explanations for these high yields are discussed.
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Affiliation(s)
- Orawan Borirak
- Swammerdam Institute for Life Science and Netherlands Institute for System Biology, University of Amsterdam, Amsterdam, The Netherlands
| | - Martijn Bekker
- Swammerdam Institute for Life Science and Netherlands Institute for System Biology, University of Amsterdam, Amsterdam, The Netherlands
| | - Klaas J Hellingwerf
- Swammerdam Institute for Life Science and Netherlands Institute for System Biology, University of Amsterdam, Amsterdam, The Netherlands
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162
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Purification of nucleic acids using isotachophoresis. J Chromatogr A 2014; 1335:105-20. [DOI: 10.1016/j.chroma.2013.12.027] [Citation(s) in RCA: 70] [Impact Index Per Article: 7.0] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/21/2013] [Revised: 12/04/2013] [Accepted: 12/07/2013] [Indexed: 12/30/2022]
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163
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Boucher E, Provost PR, Tremblay Y. Ontogeny of adrenal-like glucocorticoid synthesis pathway and of 20α-hydroxysteroid dehydrogenase in the mouse lung. BMC Res Notes 2014; 7:119. [PMID: 24580729 PMCID: PMC3944916 DOI: 10.1186/1756-0500-7-119] [Citation(s) in RCA: 12] [Impact Index Per Article: 1.2] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/17/2013] [Accepted: 02/24/2014] [Indexed: 11/10/2022] Open
Abstract
BACKGROUND Glucocorticoids exert recognized positive effects on lung development. The genes involved in the classical pathway of glucocorticoid synthesis normally occurring in adrenals were found to be expressed on gestation day (GD) 15.5 in the developing mouse lung. Recently, expression of two of these genes was also detected on GD 17.5 suggesting a more complex temporal regulation than previously expected. Here, we deepen the knowledge on expression of "adrenal" glucocorticoid synthesis genes in the mouse lung during the perinatal period and we also study expression of the gene encoding for the steroid inactivating enzyme 20α-hydroxysteroid dehydrogenase (20α-HSD). RESULTS We performed an ontogenic study of P450scc, 3β-hydroxysteroid dehydrogenase/Δ5-Δ4 isomerase 1 (3β-HSD1), 21-hydroxylase, 11β-hydroxylase, 11β-HSD1, and 11β-HSD2 expression up to post natal day (PN) 15. The substrate (progesterone) and the product (deoxycorticosterone) of 21-hydroxylase are substrates of 20α-HSD, thus 20α-HSD (Akr1c18) gene expression was investigated. In lung samples collected between GD 15.5 and PN 15, 11β-hydroxylase was only detected on GD 15.5. In contrast, all the other tested genes were expressed throughout the analyzed period with different temporal expression patterns. P450scc, 21-hydroxylase, 20α-HSD and 11β-HSD2 mRNA levels increased after birth with different patterns including an increase from PN 3 with a possible sex difference for 21-hydroxylase mRNA. Also, the 21-hydroxylase protein was observed by Western blot in perinatal lungs with higher levels after birth. CONCLUSION Progesterone is present at high levels during gestation and the product of 21-hydroxylase, deoxycorticosterone, can bind the glucocorticoid receptor with an affinity close to that of corticosterone. Detection of 21-hydroxylase at the protein level during antenatal lung development is the first evidence that the adrenal-like glucocorticoid synthesis pathway detected during lung development has the machinery to produce glucocorticoids in the fetal lung. Glucocorticoids from lung 21-hydroxylase appear to modulate lung ontogenesis through paracrine/intracrine actions.
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Affiliation(s)
| | | | - Yves Tremblay
- Reproduction, mother and youth health, Centre de recherche du CHU de Québec, Québec, QC, Canada.
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164
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Fiebig C, Kretzschmar F, Sprenger I, Link G. Sequence Characteristics and Transcripts ofrbcSGenes fromBrassica napus: Temporal and Spatial Expression During Crucifer Seedling Morphogenesis*. ACTA ACUST UNITED AC 2014. [DOI: 10.1111/j.1438-8677.1990.tb00158.x] [Citation(s) in RCA: 8] [Impact Index Per Article: 0.8] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/28/2022]
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165
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Seo Y, Ichida D, Sato S, Kuroki K, Kishida T. An improved method for the diatom test utilizing DNA binding ability of silica. J Forensic Sci 2014; 59:779-84. [PMID: 24502836 DOI: 10.1111/1556-4029.12390] [Citation(s) in RCA: 4] [Impact Index Per Article: 0.4] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/22/2012] [Revised: 02/28/2013] [Accepted: 03/17/2013] [Indexed: 11/29/2022]
Abstract
In order to devise a better forensic test for diatoms, the DNA binding ability of the diatom frustule constructing by silica, in the presence of chaotropic ions were utilized. It was proved that the diatoms were able to be captured via λDNA using silica-coated magnetic beads (Mag beads), followed by isolation and purification from the Mag beads as a solid phase by substituting the chaotropic agent with ultrapure water. Five cases of drowning, three in freshwater and two in seawater, were applied to the present method and similar results as the usual diatom test were obtained. Specimens of lung and other organs were rendered clearly visible, with elimination of foreign impurities. The present method appears applicable for detection of diatoms indirectly using PCR amplification of bound DNA or directly staining of the DNA.
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Affiliation(s)
- Yasuhisa Seo
- Department of Forensic Medicine, Oita University Faculty of Medicine, Hasama-machi, Yufu City, Oita, 879-5593, Japan
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166
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Tanaka Y, Nagao K, Nakagiri H, Nagaso T, Iwasa Y, Mori H, Asahina M, Imaizumi K, Sato M. Unavailability of liver triacylglycerol increases serum cholesterol concentration induced by dietary cholesterol in exogenously hypercholesterolemic (ExHC) rats. Lipids Health Dis 2014; 13:19. [PMID: 24450544 PMCID: PMC3902423 DOI: 10.1186/1476-511x-13-19] [Citation(s) in RCA: 2] [Impact Index Per Article: 0.2] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/25/2013] [Accepted: 01/14/2014] [Indexed: 11/10/2022] Open
Abstract
BACKGROUND Exogenously hypercholesterolemic (ExHC) rats develop hypercholesterolemia and low hepatic triacylglycerol (TAG) levels when dietary cholesterol is loaded. The responsible gene Smek2 was identified via linkage analysis using the original strain Sprague-Dawley (SD) rats. In this study, we compared SD and ExHC rats to investigate a relationship between hypercholesterolemia and the low hepatic TAG levels observed in ExHC rats. METHODS Male 4-weeks-old ExHC and SD rats were fed a 1% cholesterol diet for 1 week. Serum and liver parameters were analyzed. Gene expression and enzyme activities related to TAG metabolism were also assessed. RESULTS We reproducibly observed higher serum cholesterol and lower hepatic TAG levels in ExHC rats than in SD rats. Golgi apparatus in the livers of ExHC rats secreted β-very-low-density lipoprotein (β-VLDL) that had higher cholesterol ester (CE) and lower TAG content than those in the β-VLDL secreted by SD rats. Gene expression related to fatty acid and TAG synthesis in ExHC rats was lower than that in SD rats. Enzymatic activities for fatty acid synthesis were also relatively lower in ExHC rats. Moreover, the fatty acid composition of hepatic and serum CE in ExHC rats showed that these CEs were not modified after secretion from the liver despite the similar activities of serum lecithin-cholesterol acyltransferase (LCAT) in ExHC rats to those in SD rats. CONCLUSIONS Low production of liver TAG and secretion of CE-rich, TAG-poor β-VLDL without modification by LCAT in the circulation contributed to hypercholesterolemia induced by dietary cholesterol in ExHC rats.
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Affiliation(s)
- Yasutake Tanaka
- Laboratory of Nutrition Chemistry, Division of Bioresource and Bioenvironmental Sciences, Graduate School, Kyushu University, 6-10-1 hakozaki, higashi-ku, Fukuoka 812-8581, Japan
| | - Koji Nagao
- Laboratory of Nutrition Chemistry, Division of Bioresource and Bioenvironmental Sciences, Graduate School, Kyushu University, 6-10-1 hakozaki, higashi-ku, Fukuoka 812-8581, Japan
| | - Hideaki Nakagiri
- Laboratory of Nutrition Chemistry, Division of Bioresource and Bioenvironmental Sciences, Graduate School, Kyushu University, 6-10-1 hakozaki, higashi-ku, Fukuoka 812-8581, Japan
| | - Toshirou Nagaso
- Laboratory of Nutrition Chemistry, Division of Bioresource and Bioenvironmental Sciences, Graduate School, Kyushu University, 6-10-1 hakozaki, higashi-ku, Fukuoka 812-8581, Japan
| | - Yasue Iwasa
- Laboratory of Nutrition Chemistry, Division of Bioresource and Bioenvironmental Sciences, Graduate School, Kyushu University, 6-10-1 hakozaki, higashi-ku, Fukuoka 812-8581, Japan
| | - Haruhiko Mori
- Laboratory of Nutrition Chemistry, Division of Bioresource and Bioenvironmental Sciences, Graduate School, Kyushu University, 6-10-1 hakozaki, higashi-ku, Fukuoka 812-8581, Japan
| | - Makoto Asahina
- Laboratory of Nutrition Chemistry, Division of Bioresource and Bioenvironmental Sciences, Graduate School, Kyushu University, 6-10-1 hakozaki, higashi-ku, Fukuoka 812-8581, Japan
| | - Katsumi Imaizumi
- Laboratory of Nutrition Chemistry, Division of Bioresource and Bioenvironmental Sciences, Graduate School, Kyushu University, 6-10-1 hakozaki, higashi-ku, Fukuoka 812-8581, Japan
| | - Masao Sato
- Laboratory of Nutrition Chemistry, Division of Bioresource and Bioenvironmental Sciences, Graduate School, Kyushu University, 6-10-1 hakozaki, higashi-ku, Fukuoka 812-8581, Japan
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Li Z, Roccatano D, Lorenz M, Martinez R, Schwaneberg U. Insights on activity and stability of subtilisin E towards guanidinium chloride and sodium dodecylsulfate. J Biotechnol 2014; 169:87-94. [DOI: 10.1016/j.jbiotec.2013.11.001] [Citation(s) in RCA: 8] [Impact Index Per Article: 0.8] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/21/2013] [Revised: 10/17/2013] [Accepted: 11/03/2013] [Indexed: 11/25/2022]
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168
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Shu C, Sun S, Chen J, Chen J, Zhou E. Comparison of different methods for total RNA extraction from sclerotia of Rhizoctonia solani. ELECTRON J BIOTECHN 2014. [DOI: 10.1016/j.ejbt.2013.12.009] [Citation(s) in RCA: 11] [Impact Index Per Article: 1.1] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 10/25/2022] Open
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Park MR, Wang YH, Hasenstein KH. Profiling Gene Expression in Germinating Brassica Roots. PLANT MOLECULAR BIOLOGY REPORTER 2014; 32:541-548. [PMID: 24563578 PMCID: PMC3926982 DOI: 10.1007/s11105-013-0668-y] [Citation(s) in RCA: 4] [Impact Index Per Article: 0.4] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 05/29/2023]
Abstract
Based on previously developed solid-phase gene extraction (SPGE) we examined the mRNA profile in primary roots of Brassica rapa seedlings for highly expressed genes like ACT7 (actin7), TUB (tubulin1), UBQ (ubiquitin), and low expressed GLK (glucokinase) during the first day post-germination. The assessment was based on the mRNA load of the SPGE probe of about 2.1 ng. The number of copies of the investigated genes changed spatially along the length of primary roots. The expression level of all genes differed significantly at each sample position. Among the examined genes ACT7 expression was most even along the root. UBQ was highest at the tip and root-shoot junction (RS). TUB and GLK showed a basipetal gradient. The temporal expression of UBQ was highest in the MZ 9 h after primary root emergence and higher than at any other sample position. Expressions of GLK in EZ and RS increased gradually over time. SPGE extraction is the result of oligo-dT and oligo-dA hybridization and the results illustrate that SPGE can be used for gene expression profiling at high spatial and temporal resolution. SPGE needles can be used within two weeks when stored at 4 °C. Our data indicate that gene expression studies that are based on the entire root miss important differences in gene expression that SPGE is able to resolve for example growth adjustments during gravitropism.
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Affiliation(s)
- Myoung Ryoul Park
- Department of Biology, University of Louisiana, Lafayette, LA 70504 USA
| | - Yi-Hong Wang
- Department of Biology, University of Louisiana, Lafayette, LA 70504 USA
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170
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Abstract
Ferritin L (FTL) and ferritin H (FTH) subunits are responsible for intracellular iron storage. Serum ferritin levels are not only dependant on body iron stores. Aims of the present study are to demonstrate nature, source, and major regulatory mediators of serum ferritin in an animal model of acute-phase (AP) response. Animals (rats, wild-type [WT] mice, and interleukin [IL]-6ko mice) were injected with turpentine oil (TO) intra-muscularity to induce a sterile abscess and sacrificed at different time points afterward. Rat hepatocytes were isolated for cell culture and, after reaching confluence, stimulated with major AP cytokines to induce AP conditions. We found a significantly increased expression of both ferritin subunits in liver at mRNA and protein levels during AP response. In the serum of both control and TO-injected rats, only FTL was detectable by Western blotting, whereas no increase in serum FTL was measured by Western blot or enzyme-linked immunosorbent assay. An increase in protein expression of FTL and FTH was observed in lysates of rat hepatocytes after treatment with IL-6, IL-1β, and tumor necrosis factor-α; however, only FTL was increasingly released into supernatant. In both TO-injected rats and WT mice, a dramatic increase in serum IL-6 levels was observed, along with an increased amount of hepatic ferritin subunits. However, an increase of hepatic FTL but not of FTH protein expression was observed in IL-6ko mice after TO injection. Our data demonstrate that FTL is the only rat serum ferritin whose release into circulation from the hepatocytes is increased by the effect of AP cytokines (e.g., IL-6). In contrast, FTH expression is intracellular in both under physiological and AP conditions.
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171
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Secq V, Mallmann C, Gironella M, Lopez B, Closa D, Garcia S, Christa L, Montalto G, Dusetti N, Iovanna JL. PAP/HIP protein is an obesogenic factor. J Cell Physiol 2013; 229:225-31. [PMID: 23881718 DOI: 10.1002/jcp.24438] [Citation(s) in RCA: 4] [Impact Index Per Article: 0.4] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/16/2013] [Accepted: 07/16/2013] [Indexed: 12/19/2022]
Abstract
In this article we report the obesogenic role of the acute phase protein PAP/HIP. We found that the transgenic TgPAP/HIP mice develop spontaneous obesity under standard nutritional conditions, with high levels of glucose, leptin, and LDL and low levels of triglycerides and HDL in blood. Accordingly, PAP/HIP-deficient mice are skinny under standard nutritional conditions. We also found that expression of PAP/HIP is induced in intestinal epithelial cells in response to gavage with olive oil and this induction is AG490 sensitive. We demonstrated that incubation of 3T3-L1 preadipocytes with a low concentration as 1 ng/ml of recombinant PAP/HIP results in accelerated BrdU incorporation in vitro. PAP/HIP-dependent adipocytes growth is sensitive to the MEK inhibitor U0126. Finally, patients with severe obesity present higher blood levels of PAP/HIP than non-obese control individuals. Altogether our data suggest that PAP/HIP could be a mediator of fat tissue development, released by the intestine and induced by the presence of food into the gut.
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Affiliation(s)
- Veronique Secq
- Centre de Recherche en Carcérologie de Marseille (CRCM), INSERM UMR 1068, CNRS UMR 7258, Aix-Marseille University and Institut Paoli-Calmettes, Parc Scientifique et Technologique de Luminy, Marseille, France
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172
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Miyazaki M, Araki M, Okamura K, Ishibashi Y, Yuasa T, Iwaya-Inoue M. Assimilate translocation and expression of sucrose transporter, OsSUT1, contribute to high-performance ripening under heat stress in the heat-tolerant rice cultivar Genkitsukushi. JOURNAL OF PLANT PHYSIOLOGY 2013; 170:1579-84. [PMID: 23910376 DOI: 10.1016/j.jplph.2013.06.011] [Citation(s) in RCA: 10] [Impact Index Per Article: 0.9] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Received: 03/26/2013] [Revised: 06/18/2013] [Accepted: 06/18/2013] [Indexed: 05/08/2023]
Abstract
High temperature reduces the grain quality of rice, a situation likely to become more frequent because of global warming. We studied the effects of high-temperature stress on grain quality of heat-tolerant cultivar 'Genkitsukushi' and heat-sensitive cultivar 'Tsukushiroman'. When day/night temperatures were 31/26 °C from heading until maturity, the grain quality of 'Genkitsukushi' was rated at the first inspection grade (high quality), whereas 'Tsukushiroman' showed a remarkable increase in the percentage of white immature kernels (low quality). Nonstructural carbohydrate content in the stem of 'Genkitsukushi' the early maturation was significantly higher than in 'Tsukushiroman' and greatly decreased under high temperature. From 14 to 21 days after heading, the expression of the sucrose transporter gene, OsSUT1, was higher in the stem of 'Genkitsukushi' grown under high temperature than in 'Tsukushiroman'. In addition, the expression of OsSUT1 in the grains of 'Genkitsukushi' was significantly higher than in 'Tsukushiroman' during the ripening period. These results indicate that sugar transport functions more effectively in 'Genkitsukushi' than in 'Tsukushiroman', and that the effectiveness of sugar transport contributes to maintaining high grain quality in 'Genkitsukushi' under high-temperature conditions.
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Affiliation(s)
- Masayuki Miyazaki
- Fukuoka Agricultural Research Center, Chikushino, Fukuoka 818-8549, Japan; Crop Science Laboratory, Faculty of Agriculture, Kyushu University, 6-10-1 Hakozaki, Higashi-ku, Fukuoka 812-8581, Japan
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173
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Naz N, Ahmad S, Cameron S, Moriconi F, Rave-Fränk M, Christiansen H, Hess CF, Ramadori G, Malik IA. Differential regulation of ferritin subunits and iron transport proteins: an effect of targeted hepatic X-irradiation. BIOMED RESEARCH INTERNATIONAL 2013; 2013:353106. [PMID: 24693535 PMCID: PMC3874337 DOI: 10.1155/2013/353106] [Citation(s) in RCA: 4] [Impact Index Per Article: 0.4] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Download PDF] [Figures] [Subscribe] [Scholar Register] [Received: 08/05/2013] [Accepted: 10/09/2013] [Indexed: 01/23/2023]
Abstract
The current study aimed to investigate radiation-induced regulation of iron proteins including ferritin subunits in rats. Rat livers were selectively irradiated in vivo at 25 Gy. This dose can be used to model radiation effects to the liver without inducing overt radiation-induced liver disease. Sham-irradiated rats served as controls. Isolated hepatocytes were irradiated at 8 Gy. Ferritin light polypeptide (FTL) was detectable in the serum of sham-irradiated rats with an increase after irradiation. Liver irradiation increased hepatic protein expression of both ferritin subunits. A rather early increase (3 h) was observed for hepatic TfR1 and Fpn-1 followed by a decrease at 12 h. The increase in TfR2 persisted over the observed time. Parallel to the elevation of AST levels, a significant increase (24 h) in hepatic iron content was measured. Complete blood count analysis showed a significant decrease in leukocyte number with an early increase in neutrophil granulocytes and a decrease in lymphocytes. In vitro, a significant increase in ferritin subunits at mRNA level was detected after irradiation which was further induced with a combination treatment of irradiation and acute phase cytokine. Irradiation can directly alter the expression of ferritin subunits and this response can be strongly influenced by radiation-induced proinflammatory cytokines. FTL can be used as a serum marker for early phase radiation-induced liver damage.
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Affiliation(s)
- Naila Naz
- Department of Gastroenterology and Endocrinology, University Medical Center, Georg-August University, Robert-Koch Straße 40, 37075 Göttingen, Germany
- Department of Radiation Therapy and Radiooncology, University Medical Center, Georg-August University, Robert-Koch-Straße 40, 37075 Göttingen, Germany
| | - Shakil Ahmad
- Department of Gastroenterology and Endocrinology, University Medical Center, Georg-August University, Robert-Koch Straße 40, 37075 Göttingen, Germany
| | - Silke Cameron
- Department of Gastroenterology and Endocrinology, University Medical Center, Georg-August University, Robert-Koch Straße 40, 37075 Göttingen, Germany
| | - Federico Moriconi
- Department of Gastroenterology and Endocrinology, University Medical Center, Georg-August University, Robert-Koch Straße 40, 37075 Göttingen, Germany
| | - Margret Rave-Fränk
- Department of Radiation Therapy and Radiooncology, University Medical Center, Georg-August University, Robert-Koch-Straße 40, 37075 Göttingen, Germany
| | - Hans Christiansen
- Department of Radiation Therapy and Radiooncology, University Medical Center, Georg-August University, Robert-Koch-Straße 40, 37075 Göttingen, Germany
- Department of Radiation Oncology, Medizinische Hochschule Hannover, Carl-Neuberg Straße, 30625 Hannover, Germany
| | - Clemens Friedrich Hess
- Department of Radiation Therapy and Radiooncology, University Medical Center, Georg-August University, Robert-Koch-Straße 40, 37075 Göttingen, Germany
| | - Giuliano Ramadori
- Department of Gastroenterology and Endocrinology, University Medical Center, Georg-August University, Robert-Koch Straße 40, 37075 Göttingen, Germany
| | - Ihtzaz A. Malik
- Department of Gastroenterology and Endocrinology, University Medical Center, Georg-August University, Robert-Koch Straße 40, 37075 Göttingen, Germany
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Yurkovetskiy L, Burrows M, Khan AA, Graham L, Volchkov P, Becker L, Antonopoulos D, Umesaki Y, Chervonsky AV. Gender bias in autoimmunity is influenced by microbiota. Immunity 2013; 39:400-12. [PMID: 23973225 DOI: 10.1016/j.immuni.2013.08.013] [Citation(s) in RCA: 645] [Impact Index Per Article: 58.6] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/27/2013] [Accepted: 05/24/2013] [Indexed: 12/14/2022]
Abstract
Gender bias and the role of sex hormones in autoimmune diseases are well established. In specific pathogen-free nonobese diabetic (NOD) mice, females have 1.3-4.4 times higher incidence of type 1 diabetes (T1D). Germ-free (GF) mice lost the gender bias (female-to-male ratio 1.1-1.2). Gut microbiota differed in males and females, a trend reversed by male castration, confirming that androgens influence gut microbiota. Colonization of GF NOD mice with defined microbiota revealed that some, but not all, lineages overrepresented in male mice supported a gender bias in T1D. Although protection of males did not correlate with blood androgen concentration, hormone-supported expansion of selected microbial lineages may work as a positive-feedback mechanism contributing to the sexual dimorphism of autoimmune diseases. Gene-expression analysis suggested pathways involved in protection of males from T1D by microbiota. Our results favor a two-signal model of gender bias, in which hormones and microbes together trigger protective pathways.
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Affiliation(s)
- Leonid Yurkovetskiy
- Committee on Microbiology, The University of Chicago, Chicago, IL 60637, USA
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175
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Transcription of a mitochondrial plasmid during senescence in Podospora anserina. Curr Genet 2013; 7:457-64. [PMID: 24173452 DOI: 10.1007/bf00377611] [Citation(s) in RCA: 10] [Impact Index Per Article: 0.9] [Reference Citation Analysis] [Abstract] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/31/1983] [Indexed: 10/26/2022]
Abstract
In the ascomycete fungus Podospora anserina, cellular senescence is characterized by the excision, circularization, and amplification of specific segments of the non-senescent mitochondrial genome. During senescence, various plasmids can be found in the mitochondria, and different senescent events produce different plasmid populations. In this paper we have examined the transcriptional activity of one mitochondrial plasmid (α-sen DNA) and have contrasted this with the non-senescent mitochondrial genome of rapidly (A(+)) and slowly (s(+)) senescing races. In non-senescent and senescent mitochondria we observe two RNAs which are homologous to α-sen DNA and to the parental locus on the native genome. These are 2.4 and 2.5 kb long and have different 5' ends while overlapping throughout most of their lengths. They may represent different transcripts for α-sen DNA and the parental genome and indicate that excision of the plasmid begins 450 bp from the 5' end of the genomic coding sequence. Transcription of the α-sen DNA plasmid appears to be active in both senescent and in non-senescent mycelia.
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176
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Mahmood SF, Gruel N, Chapeaublanc E, Lescure A, Jones T, Reyal F, Vincent-Salomon A, Raynal V, Pierron G, Perez F, Camonis J, Del Nery E, Delattre O, Radvanyi F, Bernard-Pierrot I. A siRNA screen identifies RAD21, EIF3H, CHRAC1 and TANC2 as driver genes within the 8q23, 8q24.3 and 17q23 amplicons in breast cancer with effects on cell growth, survival and transformation. Carcinogenesis 2013; 35:670-82. [PMID: 24148822 DOI: 10.1093/carcin/bgt351] [Citation(s) in RCA: 39] [Impact Index Per Article: 3.5] [Reference Citation Analysis] [Abstract] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 02/02/2023] Open
Abstract
RNA interference has boosted the field of functional genomics, by making it possible to carry out 'loss-of-function' screens in cultured cells. Here, we performed a small interfering RNA screening, in three breast cancer cell lines, for 101 candidate driver genes overexpressed in amplified breast tumors and belonging to eight amplicons on chromosomes 8q and 17q, investigating their role in cell survival/proliferation. This screening identified eight driver genes that were amplified, overexpressed and critical for breast tumor cell proliferation or survival. They included the well-described oncogenic driver genes for the 17q12 amplicon, ERBB2 and GRB7. Four of six other candidate driver genes-RAD21 and EIF3H, both on chromosome 8q23, CHRAC1 on chromosome 8q24.3 and TANC2 on chromosome 17q23-were confirmed to be driver genes regulating the proliferation/survival of clonogenic breast cancer cells presenting an amplification of the corresponding region. Indeed, knockdown of the expression of these genes decreased cell viability, through both cell cycle arrest and apoptosis induction, and inhibited the formation of colonies in anchorage-independent conditions, in soft agar. Strategies for inhibiting the expression of these genes or the function of the proteins they encode are therefore of potential value for the treatment of breast cancers presenting amplifications of the corresponding genomic region.
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177
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Lamming DW, Demirkan G, Boylan JM, Mihaylova MM, Peng T, Ferreira J, Neretti N, Salomon A, Sabatini DM, Gruppuso PA. Hepatic signaling by the mechanistic target of rapamycin complex 2 (mTORC2). FASEB J 2013; 28:300-15. [PMID: 24072782 DOI: 10.1096/fj.13-237743] [Citation(s) in RCA: 59] [Impact Index Per Article: 5.4] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/22/2022]
Abstract
The mechanistic target of rapamycin (mTOR) exists in two complexes that regulate diverse cellular processes. mTOR complex 1 (mTORC1), the canonical target of rapamycin, has been well studied, whereas the physiological role of mTORC2 remains relatively uncharacterized. In mice in which the mTORC2 component Rictor is deleted in liver [Rictor-knockout (RKO) mice], we used genomic and phosphoproteomic analyses to characterize the role of hepatic mTORC2 in vivo. Overnight food withdrawal followed by refeeding was used to activate mTOR signaling. Rapamycin was administered before refeeding to specify mTORC2-mediated events. Hepatic mTORC2 regulated a complex gene expression and post-translational network that affects intermediary metabolism, ribosomal biogenesis, and proteasomal biogenesis. Nearly all changes in genes related to intermediary metabolic regulation were replicated in cultured fetal hepatocytes, indicating a cell-autonomous effect of mTORC2 signaling. Phosphoproteomic profiling identified mTORC2-related signaling to 144 proteins, among which were metabolic enzymes and regulators. A reduction of p38 MAPK signaling in the RKO mice represents a link between our phosphoproteomic and gene expression results. We conclude that hepatic mTORC2 exerts a broad spectrum of biological effects under physiological conditions. Our findings provide a context for the development of targeted therapies to modulate mTORC2 signaling.
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Affiliation(s)
- Dudley W Lamming
- 3Division of Pediatric Endocrinology, Rhode Island Hospital, 593 Eddy Street, Providence, RI 02903, USA.
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178
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Resnyk CW, Carré W, Wang X, Porter TE, Simon J, Le Bihan-Duval E, Duclos MJ, Aggrey SE, Cogburn LA. Transcriptional analysis of abdominal fat in genetically fat and lean chickens reveals adipokines, lipogenic genes and a link between hemostasis and leanness. BMC Genomics 2013; 14:557. [PMID: 23947536 PMCID: PMC3765218 DOI: 10.1186/1471-2164-14-557] [Citation(s) in RCA: 63] [Impact Index Per Article: 5.7] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/29/2013] [Accepted: 08/12/2013] [Indexed: 12/15/2022] Open
Abstract
Background This descriptive study of the abdominal fat transcriptome takes advantage of two experimental lines of meat-type chickens (Gallus domesticus), which were selected over seven generations for a large difference in abdominal (visceral) fatness. At the age of selection (9 wk), the fat line (FL) and lean line (LL) chickens exhibit a 2.5-fold difference in abdominal fat weight, while their feed intake and body weight are similar. These unique avian models were originally created to unravel genetic and endocrine regulation of adiposity and lipogenesis in meat-type chickens. The Del-Mar 14K Chicken Integrated Systems microarray was used for a time-course analysis of gene expression in abdominal fat of FL and LL chickens during juvenile development (1–11 weeks of age). Results Microarray analysis of abdominal fat in FL and LL chickens revealed 131 differentially expressed (DE) genes (FDR≤0.05) as the main effect of genotype, 254 DE genes as an interaction of age and genotype and 3,195 DE genes (FDR≤0.01) as the main effect of age. The most notable discoveries in the abdominal fat transcriptome were higher expression of many genes involved in blood coagulation in the LL and up-regulation of numerous adipogenic and lipogenic genes in FL chickens. Many of these DE genes belong to pathways controlling the synthesis, metabolism and transport of lipids or endocrine signaling pathways activated by adipokines, retinoid and thyroid hormones. Conclusions The present study provides a dynamic view of differential gene transcription in abdominal fat of chickens genetically selected for fatness (FL) or leanness (LL). Remarkably, the LL chickens over-express a large number of hemostatic genes that could be involved in proteolytic processing of adipokines and endocrine factors, which contribute to their higher lipolysis and export of stored lipids. Some of these changes are already present at 1 week of age before the divergence in fatness. In contrast, the FL chickens have enhanced expression of numerous lipogenic genes mainly after onset of divergence, presumably directed by multiple transcription factors. This transcriptional analysis shows that abdominal fat of the chicken serves a dual function as both an endocrine organ and an active metabolic tissue, which could play a more significant role in lipogenesis than previously thought.
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Affiliation(s)
- Christopher W Resnyk
- Department of Animal and Food Sciences, University of Delaware, Newark, DE 19716, USA
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Bahls M, Bidwell CA, Hu J, Tellez A, Kaluza GL, Granada JF, Krueger CG, Reed JD, Laughlin MH, Van Alstine WG, Newcomer SC. Gene expression differences during the heterogeneous progression of peripheral atherosclerosis in familial hypercholesterolemic swine. BMC Genomics 2013; 14:443. [PMID: 23822099 PMCID: PMC3716534 DOI: 10.1186/1471-2164-14-443] [Citation(s) in RCA: 10] [Impact Index Per Article: 0.9] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/18/2012] [Accepted: 06/18/2013] [Indexed: 01/17/2023] Open
Abstract
BACKGROUND The heterogeneous progression of atherosclerotic disease in the peripheral arteries is currently not well understood. In humans, artery specific disease progression is partly attributed to the local hemodynamic environments. However, despite similar hemodynamic environments, porcine brachial arteries are protected while femoral arteries are highly susceptible to advanced lesion formation. The aim of this investigation was to determine whether artery specific gene expression patterns contribute to the uneven distribution of peripheral arterial disease (PAD) in Rapacz Familial-Hypercholesterolemic (FHC) swine. RESULTS Histological results confirmed rapid atherosclerotic disease progression in femoral but not brachial arteries. A total of 18,922 probe sets had sufficient signal abundance. A main effect for age and artery was observed for 1784 and 1256 probe sets, respectively. A significant age x artery interaction was found for 184 probe sets. Furthermore, comparison between arteries found a decrease from 714 to 370 differentially expressed transcripts from nine months to two years of age. Gene ontology analysis of the 56 genes with a main effect for artery and an age x artery interaction identified vascular smooth muscle contraction as enhanced biological signaling pathway. CONCLUSION This is the first investigation to report that the total number of differential genes decreases with diverging atherosclerotic disease pattern between porcine brachial and femoral arteries.
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Affiliation(s)
- Martin Bahls
- Department of Health and Kinesiology, Purdue University, West Lafayette, IN, USA.
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180
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Liu X, Harada S. RNA isolation from mammalian samples. CURRENT PROTOCOLS IN MOLECULAR BIOLOGY 2013; Chapter 4:Unit 4.16. [PMID: 23821441 DOI: 10.1002/0471142727.mb0416s103] [Citation(s) in RCA: 10] [Impact Index Per Article: 0.9] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 06/02/2023]
Abstract
RNA can be extracted from cultured cells, peripheral blood, bone marrow, plasma, serum, body fluids, and fresh or frozen tissues. RNA can also be extracted from formalin-fixed paraffin-embedded (FFPE) tissues. Methods for RNA extraction can be divided into three groups: phenol/chloroform extraction, silica spin-column absorption, and isopycnic gradient centrifugation. Two different RNA isolation procedures are described in this unit. The first basic protocol describes a one-step isolation involving monophasic lysis with guanidine isothiocyanate and phenol followed by chloroform extraction. The second basic protocol describes a silica-column separation method for RNA isolation.
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Affiliation(s)
- Ximeng Liu
- Department of Pathology, University of Alabama at Birmingham, Birmingham, AL, USA
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Derricks KE, Rich CB, Buczek-Thomas JA, Nugent MA. Ascorbate enhances elastin synthesis in 3D tissue-engineered pulmonary fibroblasts constructs. Tissue Cell 2013; 45:253-60. [PMID: 23648172 DOI: 10.1016/j.tice.2013.03.001] [Citation(s) in RCA: 10] [Impact Index Per Article: 0.9] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/24/2012] [Revised: 02/14/2013] [Accepted: 03/13/2013] [Indexed: 12/19/2022]
Abstract
Extracellular matrix remodeling is a continuous process that is critical to maintaining tissue homeostasis, and alterations in this process have been implicated in chronic diseases such as atherosclerosis, lung fibrosis, and emphysema. Collagen and elastin are subject to ascorbate-dependent hydroxylation. While this post-translational modification in collagen is critical for function, the role of hydroxylation of elastin is not well understood. A number of studies have indicated that ascorbate leads to reduced elastin synthesis. However, these studies were limited to analysis of cells grown under traditional 2D tissue culture conditions. To investigate this process we evaluated elastin and collagen synthesis in primary rat neonatal pulmonary fibroblasts in response to ascorbate treatment in traditional 2D culture and within 3D cross-linked gelatin matrices (Gelfoam). We observed little change in elastin or collagen biosynthesis in standard 2D cultures treated with ascorbate, yet observed a dramatic increase in elastin protein and mRNA levels in response to ascorbate in 3D cell-Gelfoam constructs. These data suggest that the cell-ECM architecture dictates pulmonary cell response to ascorbate, and that approaches aimed toward stimulating ECM repair or engineering functional cell-derived matrices should consider all aspects of the cellular environment.
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Affiliation(s)
- Kelsey E Derricks
- Department of Medicine, Boston University School of Medicine, Boston, MA, United States
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Mun SH, Won HY, Hernandez P, Aguila HL, Lee SK. Deletion of CD74, a putative MIF receptor, in mice enhances osteoclastogenesis and decreases bone mass. J Bone Miner Res 2013; 28:948-59. [PMID: 23044992 PMCID: PMC3563845 DOI: 10.1002/jbmr.1787] [Citation(s) in RCA: 36] [Impact Index Per Article: 3.3] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Submit a Manuscript] [Subscribe] [Scholar Register] [Received: 06/05/2012] [Revised: 09/26/2012] [Accepted: 10/01/2012] [Indexed: 12/24/2022]
Abstract
CD74 is a type II transmembrane protein that can act as a receptor for macrophage migration inhibitory factor (MIF) and plays a role in MIF-regulated responses. We reported that MIF inhibited osteoclast formation and MIF knockout (KO) mice had decreased bone mass. We therefore examined if CD74 was involved in the ability of MIF to alter osteoclastogenesis in cultured bone marrow (BM) from wild-type (WT) and CD74-deficient (KO) male mice. We also measured the bone phenotype of CD74 KO male mice. Bone mass in the femur of 8-week-old mice was measured by micro-computed tomography and histomorphometry. Bone marrow cells from CD74 KO mice formed 15% more osteoclast-like cells (OCLs) with macrophage colony-stimulating factor (M-CSF) and receptor activator of NF-κB ligand (RANKL) (both at 30 ng/mL) compared to WT. Addition of MIF to WT cultures inhibited OCL formation by 16% but had no effect on CD74KO cultures. The number of colony forming unit granulocyte-macrophage (CFU-GM) in the bone marrow of CD74 KO mice was 26% greater than in WT controls. Trabecular bone volume (TBV) in the femurs of CD74 KO male mice was decreased by 26% compared to WT. In addition, cortical area and thickness were decreased by 14% and 11%, respectively. Histomorphometric analysis demonstrated that tartrate-resistant acid phosphatase (TRAP)(+) osteoclast number and area were significantly increased in CD74 KO by 35% and 43%, respectively compared to WT. Finally, we examined the effect of MIF on RANKL-induced-signaling pathways in bone marrow macrophage (BMM) cultures. MIF treatment decreased RANKL-induced nuclear factor of activated T cells, cytoplasmic 1 (NFATc1) and c-Fos protein in BMM cultures by 70% and 41%, respectively. Our data demonstrate that CD74 is required for MIF to affect in vitro osteoclastogenesis. Further, the bone phenotype of CD74 KO mice is similar to that of MIF KO mice. MIF treatment of WT cultures suppressed RANKL-induced activator protein 1 (AP-1) expression, which resulted in decreased osteoclast differentiation in vitro. We propose that CD74 plays a critical role in the MIF inhibition of osteoclastogenesis.
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Affiliation(s)
- Se Hwan Mun
- UCONN Center on Aging, University of Connecticut Health Center, Farmington, CT 06030-1835, USA
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183
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Imsirovic J, Derricks K, Buczek-Thomas JA, Rich CB, Nugent MA, Suki B. A novel device to stretch multiple tissue samples with variable patterns: application for mRNA regulation in tissue-engineered constructs. BIOMATTER 2013; 3:24650. [PMID: 23628870 PMCID: PMC3749279 DOI: 10.4161/biom.24650] [Citation(s) in RCA: 14] [Impact Index Per Article: 1.3] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Subscribe] [Scholar Register] [Indexed: 12/27/2022]
Abstract
A broad range of cells are subjected to irregular time varying mechanical stimuli within the body, particularly in the respiratory and circulatory systems. Mechanical stretch is an important factor in determining cell function; however, the effects of variable stretch remain unexplored. In order to investigate the effects of variable stretch, we designed, built and tested a uniaxial stretching device that can stretch three-dimensional tissue constructs while varying the strain amplitude from cycle to cycle. The device is the first to apply variable stretching signals to cells in tissues or three dimensional tissue constructs. Following device validation, we applied 20% uniaxial strain to Gelfoam samples seeded with neonatal rat lung fibroblasts with different levels of variability (0%, 25%, 50% and 75%). RT-PCR was then performed to measure the effects of variable stretch on key molecules involved in cell-matrix interactions including: collagen 1α, lysyl oxidase, α-actin, β1 integrin, β3 integrin, syndecan-4, and vascular endothelial growth factor-A. Adding variability to the stretching signal upregulated, downregulated or had no effect on mRNA production depending on the molecule and the amount of variability. In particular, syndecan-4 showed a statistically significant peak at 25% variability, suggesting that an optimal variability of strain may exist for production of this molecule. We conclude that cycle-by-cycle variability in strain influences the expression of molecules related to cell-matrix interactions and hence may be used to selectively tune the composition of tissue constructs.
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Affiliation(s)
- Jasmin Imsirovic
- Department of Biomedical Engineering; Boston University; Boston, MA USA
| | - Kelsey Derricks
- Department of Biochemistry; Boston University School of Medicine; Boston, MA USA
| | - Jo Ann Buczek-Thomas
- Department of Biochemistry; Boston University School of Medicine; Boston, MA USA
| | - Celeste B Rich
- Department of Biochemistry; Boston University School of Medicine; Boston, MA USA
| | - Matthew A Nugent
- Department of Biomedical Engineering; Boston University; Boston, MA USA; Department of Biochemistry; Boston University School of Medicine; Boston, MA USA
| | - Béla Suki
- Department of Biomedical Engineering; Boston University; Boston, MA USA
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Atanasova L, Crom SL, Gruber S, Coulpier F, Seidl-Seiboth V, Kubicek CP, Druzhinina IS. Comparative transcriptomics reveals different strategies of Trichoderma mycoparasitism. BMC Genomics 2013; 14:121. [PMID: 23432824 PMCID: PMC3599271 DOI: 10.1186/1471-2164-14-121] [Citation(s) in RCA: 148] [Impact Index Per Article: 13.5] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/10/2012] [Accepted: 02/19/2013] [Indexed: 01/27/2023] Open
Abstract
BACKGROUND Trichoderma is a genus of mycotrophic filamentous fungi (teleomorph Hypocrea) which possess a bright variety of biotrophic and saprotrophic lifestyles. The ability to parasitize and/or kill other fungi (mycoparasitism) is used in plant protection against soil-borne fungal diseases (biological control, or biocontrol). To investigate mechanisms of mycoparasitism, we compared the transcriptional responses of cosmopolitan opportunistic species and powerful biocontrol agents Trichoderma atroviride and T. virens with tropical ecologically restricted species T. reesei during confrontations with a plant pathogenic fungus Rhizoctonia solani. RESULTS The three Trichoderma spp. exhibited a strikingly different transcriptomic response already before physical contact with alien hyphae. T. atroviride expressed an array of genes involved in production of secondary metabolites, GH16 ß-glucanases, various proteases and small secreted cysteine rich proteins. T. virens, on the other hand, expressed mainly the genes for biosynthesis of gliotoxin, respective precursors and also glutathione, which is necessary for gliotoxin biosynthesis. In contrast, T. reesei increased the expression of genes encoding cellulases and hemicellulases, and of the genes involved in solute transport. The majority of differentially regulated genes were orthologues present in all three species or both in T. atroviride and T. virens, indicating that the regulation of expression of these genes is different in the three Trichoderma spp. The genes expressed in all three fungi exhibited a nonrandom genomic distribution, indicating a possibility for their regulation via chromatin modification. CONCLUSION This genome-wide expression study demonstrates that the initial Trichoderma mycotrophy has differentiated into several alternative ecological strategies ranging from parasitism to predation and saprotrophy. It provides first insights into the mechanisms of interactions between Trichoderma and other fungi that may be exploited for further development of biofungicides.
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Affiliation(s)
- Lea Atanasova
- Research Area Biotechnology and Microbiology, Institute of Chemical Engineering, Vienna University of Technology, Gumpendorferstrasse 1a, A-1060, Vienna, Austria
| | - Stephane Le Crom
- École normale supérieure, Institut de Biologie de l’ENS, IBENS, F-75005, Paris, France
- Inserm, U1024, F-75005, Paris, France
- CNRS, UMR 8197, F-75005, Paris, France
- UPMC Univ Paris 06, UMR7622, Laboratoire de Biologie du Développement, 9 quai St. Bernard, F-75005, Paris, France
- CNRS, UMR7622, Laboratoire de Biologie du Développement, 9 quai St. Bernard, F-75005, Paris, France
| | - Sabine Gruber
- Research Area Biotechnology and Microbiology, Institute of Chemical Engineering, Vienna University of Technology, Gumpendorferstrasse 1a, A-1060, Vienna, Austria
| | - Fanny Coulpier
- École normale supérieure, Institut de Biologie de l’ENS, IBENS, F-75005, Paris, France
- Inserm, U1024, F-75005, Paris, France
- CNRS, UMR 8197, F-75005, Paris, France
| | - Verena Seidl-Seiboth
- Research Area Biotechnology and Microbiology, Institute of Chemical Engineering, Vienna University of Technology, Gumpendorferstrasse 1a, A-1060, Vienna, Austria
| | - Christian P Kubicek
- Research Area Biotechnology and Microbiology, Institute of Chemical Engineering, Vienna University of Technology, Gumpendorferstrasse 1a, A-1060, Vienna, Austria
- Austrian Center of Industrial Biotechnology (ACIB), GmBH c/o Institute of Chemical Engineering, Vienna University of Technology, Gumpendorferstrasse 1a, A-1060, Vienna, Austria
| | - Irina S Druzhinina
- Research Area Biotechnology and Microbiology, Institute of Chemical Engineering, Vienna University of Technology, Gumpendorferstrasse 1a, A-1060, Vienna, Austria
- Austrian Center of Industrial Biotechnology (ACIB), GmBH c/o Institute of Chemical Engineering, Vienna University of Technology, Gumpendorferstrasse 1a, A-1060, Vienna, Austria
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Strengthened glycolysis under hypoxia supports tumor symbiosis and hexosamine biosynthesis in pancreatic adenocarcinoma. Proc Natl Acad Sci U S A 2013; 110:3919-24. [PMID: 23407165 DOI: 10.1073/pnas.1219555110] [Citation(s) in RCA: 302] [Impact Index Per Article: 27.5] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/15/2022] Open
Abstract
Pancreatic ductal adenocarcinoma is one of the most intractable and fatal cancer. The decreased blood vessel density displayed by this tumor not only favors its resistance to chemotherapy but also participates in its aggressiveness due to the consequent high degree of hypoxia. It is indeed clear that hypoxia promotes selective pressure on malignant cells that must develop adaptive metabolic responses to reach their energetic and biosynthetic demands. Here, using a well-defined mouse model of pancreatic cancer, we report that hypoxic areas from pancreatic ductal adenocarcinoma are mainly composed of epithelial cells harboring epithelial-mesenchymal transition features and expressing glycolytic markers, two characteristics associated with tumor aggressiveness. We also show that hypoxia increases the "glycolytic" switch of pancreatic cancer cells from oxydative phosphorylation to lactate production and we demonstrate that increased lactate efflux from hypoxic cancer cells favors the growth of normoxic cancer cells. In addition, we show that glutamine metabolization by hypoxic pancreatic tumor cells is necessary for their survival. Metabolized glucose and glutamine converge toward a common pathway, termed hexosamine biosynthetic pathway, which allows O-linked N-acetylglucosamine modifications of proteins. Here, we report that hypoxia increases transcription of hexosamine biosynthetic pathway genes as well as levels of O-glycosylated proteins and that O-linked N-acetylglucosaminylation of proteins is a process required for hypoxic pancreatic cancer cell survival. Our results demonstrate that hypoxia-driven metabolic adaptive processes, such as high glycolytic rate and hexosamine biosynthetic pathway activation, favor hypoxic and normoxic cancer cell survival and correlate with pancreatic ductal adenocarcinoma aggressiveness.
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186
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Development of a rapid total nucleic acid extraction method for the isolation of hepatitis A virus from fresh produce. Int J Food Microbiol 2013; 161:143-50. [DOI: 10.1016/j.ijfoodmicro.2012.12.007] [Citation(s) in RCA: 17] [Impact Index Per Article: 1.5] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/26/2012] [Revised: 12/12/2012] [Accepted: 12/19/2012] [Indexed: 01/09/2023]
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Functional analyses of Trichoderma reesei LAE1 reveal conserved and contrasting roles of this regulator. G3-GENES GENOMES GENETICS 2013; 3:369-78. [PMID: 23390613 PMCID: PMC3564997 DOI: 10.1534/g3.112.005140] [Citation(s) in RCA: 93] [Impact Index Per Article: 8.5] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Subscribe] [Scholar Register] [Received: 11/29/2012] [Accepted: 12/23/2012] [Indexed: 11/25/2022]
Abstract
The putative methyltransferase LaeA is a global regulator that affects the expression of multiple secondary metabolite gene clusters in several fungi, and it can modify heterochromatin structure in Aspergillus nidulans. We have recently shown that the LaeA ortholog of Trichoderma reesei (LAE1), a fungus that is an industrial producer of cellulase and hemicellulase enzymes, regulates the expression of cellulases and polysaccharide hydrolases. To learn more about the function of LAE1 in T. reesei, we assessed the effect of deletion and overexpression of lae1 on genome-wide gene expression. We found that in addition to positively regulating 7 of 17 polyketide or nonribosomal peptide synthases, genes encoding ankyrin-proteins, iron uptake, heterokaryon incompatibility proteins, PTH11-receptors, and oxidases/monoxygenases are major gene categories also regulated by LAE1. chromatin immunoprecipitation sequencing with antibodies against histone modifications known to be associated with transcriptionally active (H3K4me2 and -me3) or silent (H3K9me3) chromatin detected 4089 genes bearing one or more of these methylation marks, of which 75 exhibited a correlation between either H3K4me2 or H3K4me3 and regulation by LAE1. Transformation of a laeA-null mutant of A. nidulans with the T. reesei lae1 gene did not rescue sterigmatocystin formation and further impaired sexual development. LAE1 did not interact with A. nidulans VeA in yeast two-hybrid assays, whereas it interacted with the T. reesei VeA ortholog, VEL1. LAE1 was shown to be required for the expression of vel1, whereas the orthologs of velB and VosA are unaffected by lae1 deletion. Our data show that the biological roles of A. nidulans LaeA and T. reesei LAE1 are much less conserved than hitherto thought. In T. reesei, LAE1 appears predominantly to regulate genes increasing relative fitness in its environment.
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Kaitaniemi S, Grön K, Elovaara H, Salmi M, Jalkanen S, Elima K. Functional modulation of vascular adhesion protein-1 by a novel splice variant. PLoS One 2013; 8:e54151. [PMID: 23349812 PMCID: PMC3548902 DOI: 10.1371/journal.pone.0054151] [Citation(s) in RCA: 8] [Impact Index Per Article: 0.7] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/15/2012] [Accepted: 12/07/2012] [Indexed: 12/22/2022] Open
Abstract
Vascular Adhesion Protein-1 (VAP-1) is an endothelial adhesion molecule belonging to the primary amine oxidases. Upon inflammation it takes part in the leukocyte extravasation cascade facilitating transmigration of leukocytes into the inflamed tissue. Screening of a human lung cDNA library revealed the presence of an alternatively spliced shorter transcript of VAP-1, VAP-1Δ3. Here, we have studied the functional and structural characteristics of VAP-1Δ3, and show that the mRNA for this splice variant is expressed in most human tissues studied. In comparison to the parent molecule this carboxy-terminally truncated isoform lacks several of the amino acids important in the formation of the enzymatic groove of VAP-1. In addition, the conserved His684, which takes part in coordinating the active site copper, is missing from VAP-1Δ3. Assays using the prototypic amine substrates methylamine and benzylamine demonstrated that VAP-1Δ3 is indeed devoid of the semicarbazide-sensitive amine oxidase (SSAO) activity characteristic to VAP-1. When VAP-1Δ3-cDNA is transfected into cells stably expressing VAP-1, the surface expression of the full-length molecule is reduced. Furthermore, the SSAO activity of the co-transfectants is diminished in comparison to transfectants expressing only VAP-1. The observed down-regulation of both the expression and enzymatic activity of VAP-1 may result from a dominant-negative effect caused by heterodimerization between VAP-1 and VAP-1Δ3, which was detected in co-immunoprecipitation studies. This alternatively spliced transcript adds thus to the repertoire of potential regulatory mechanisms through which the cell-surface expression and enzymatic activity of VAP-1 can be modulated.
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Affiliation(s)
- Sam Kaitaniemi
- MediCity Research Laboratory, University of Turku, Turku, Finland
- Department of Microbiology and Immunology, University of Turku, Turku, Finland
| | - Kirsi Grön
- MediCity Research Laboratory, University of Turku, Turku, Finland
| | - Heli Elovaara
- MediCity Research Laboratory, University of Turku, Turku, Finland
| | - Marko Salmi
- MediCity Research Laboratory, University of Turku, Turku, Finland
- Department of Medical Biochemistry and Genetics, University of Turku, Turku, Finland
| | - Sirpa Jalkanen
- MediCity Research Laboratory, University of Turku, Turku, Finland
- Department of Microbiology and Immunology, University of Turku, Turku, Finland
| | - Kati Elima
- MediCity Research Laboratory, University of Turku, Turku, Finland
- Department of Medical Biochemistry and Genetics, University of Turku, Turku, Finland
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Sharma P, Ryu MH, Basu S, Maltby SA, Yeganeh B, Mutawe MM, Mitchell RW, Halayko AJ. Epithelium-dependent modulation of responsiveness of airways from caveolin-1 knockout mice is mediated through cyclooxygenase-2 and 5-lipoxygenase. Br J Pharmacol 2013; 167:548-60. [PMID: 22551156 DOI: 10.1111/j.1476-5381.2012.02014.x] [Citation(s) in RCA: 15] [Impact Index Per Article: 1.4] [Reference Citation Analysis] [Abstract] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/29/2022] Open
Abstract
BACKGROUND AND PURPOSE Acute silencing of caveolin-1 (Cav-1) modulates receptor-mediated contraction of airway smooth muscle. Moreover, COX-2- and 5-lipoxygenase (5-LO)-derived prostaglandin and leukotriene biosynthesis can influence smooth muscle reactivity. COX-2 half-life can be prolonged through association with Cav-1. We suggested that lack of Cav-1 modulated levels of COX-2 which in turn modulated tracheal contraction, when arachidonic acid signalling was disturbed by inhibition of COX-2. EXPERIMENTAL APPROACH Using tracheal rings from Cav-1 knockout (KO) and wild-type mice (B6129SF2/J), we measured isometric contractions to methacholine and used PCR, immunoblotting and immunohistology to monitor expression of relevant proteins. KEY RESULTS Tracheal rings from Cav-1 KO and wild-type mice exhibited similar responses, but the COX-2 inhibitor, indomethacin, increased responses of tracheal rings from Cav-1 KO mice to methacholine. The phospholipase A₂ inhibitor, eicosatetraynoic acid, which inhibits formation of both COX-2 and 5-LO metabolites, had no effect on wild-type or Cav-1 KO tissues. Indomethacin-mediated hyperreactivity was ablated by the LTD₄ receptor antagonist (montelukast) and 5-LO inhibitor (zileuton). The potentiating effect of indomethacin on Cav-1 KO responses to methacholine was blocked by epithelial denudation. Immunoprecipitation showed that COX-2 binds Cav-1 in wild-type lungs. Immunoblotting and qPCR revealed elevated levels of COX-2 and 5-LO protein, but not COX-1, in Cav-1 KO tracheas, a feature that was prevented by removal of the epithelium. CONCLUSION AND IMPLICATIONS The indomethacin-induced hypercontractility observed in Cav-1 KO tracheas was linked to increased expression of COX-2 and 5-LO, which probably enhanced arachidonic acid shunting and generation of pro-contractile leukotrienes when COX-2 was inhibited.
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Affiliation(s)
- Pawan Sharma
- Department of Physiology, University of Manitoba, Winnipeg, MB, Canada
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190
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Jensen K, Günther J, Talbot R, Petzl W, Zerbe H, Schuberth HJ, Seyfert HM, Glass EJ. Escherichia coli- and Staphylococcus aureus-induced mastitis differentially modulate transcriptional responses in neighbouring uninfected bovine mammary gland quarters. BMC Genomics 2013; 14:36. [PMID: 23324411 PMCID: PMC3598231 DOI: 10.1186/1471-2164-14-36] [Citation(s) in RCA: 84] [Impact Index Per Article: 7.6] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/21/2012] [Accepted: 01/15/2013] [Indexed: 12/31/2022] Open
Abstract
Background The most important disease of dairy cattle is mastitis, caused by the infection of the mammary gland by various micro-organisms. Although the transcriptional response of bovine mammary gland cells to in vitro infection has been studied, the interplay and consequences of these responses in the in vivo environment of the mammary gland are less clear. Previously mammary gland quarters were considered to be unaffected by events occurring in neighbouring quarters. More recently infection of individual quarters with mastitis causing pathogens, especially Escherichia coli, has been shown to influence the physiology of neighbouring uninfected quarters. Therefore, the transcriptional responses of uninfected mammary gland quarters adjacent to quarters infected with two major mastitis causing pathogens, E. coli and Staphylococcus aureus, were compared. Results The bacteriologically sterile, within-animal control quarters exhibited a transcriptional response to the infection of neighbouring quarters. The greatest response was associated with E. coli infection, while a weaker, yet significant, response occurred during S. aureus infection. The transcriptional responses of these uninfected quarters included the enhanced expression of many genes previously associated with mammary gland infections. Comparison of the transcriptional response of uninfected quarters to S. aureus and E. coli infection identified 187 differentially expressed genes, which were particularly associated with cellular responses, e.g. response to stress. The most affected network identified by Ingenuity Pathway analysis has the immunosuppressor transforming growth factor beta 1 (TGFB1) at its hub and largely consists of genes more highly expressed in control quarters from S. aureus infected cows. Conclusions Uninfected mammary gland quarters reacted to the infection of neighbouring quarters and the responses were dependent on pathogen type. Therefore, bovine udder quarters exhibit interdependence and should not be considered as separate functional entities. This suggests that mastitis pathogens not only interact directly with host mammary cells, but also influence discrete sites some distance away, which will affect their response to the subsequent spread of the infection. Understanding the underlying mechanisms may provide further clues for ways to control mammary gland infections. These results also have implications for the design of experimental studies investigating immune regulatory mechanisms in the bovine mammary gland.
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Affiliation(s)
- Kirsty Jensen
- Division of Infection & Immunity, The Roslin Institute and Royal (Dick) School of Veterinary Studies, University of Edinburgh, Easter Bush, Midlothian EH25 9RG, UK.
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Arai T, Kim HJ, Hirako S, Nakasatomi M, Chiba H, Matsumoto A. Effects of dietary fat energy restriction and fish oil feeding on hepatic metabolic abnormalities and insulin resistance in KK mice with high-fat diet-induced obesity. J Nutr Biochem 2013; 24:267-73. [DOI: 10.1016/j.jnutbio.2012.06.002] [Citation(s) in RCA: 10] [Impact Index Per Article: 0.9] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/31/2011] [Revised: 06/01/2012] [Accepted: 06/02/2012] [Indexed: 12/22/2022]
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192
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Ishibashi Y, Koda Y, Zheng SH, Yuasa T, Iwaya-Inoue M. Regulation of soybean seed germination through ethylene production in response to reactive oxygen species. ANNALS OF BOTANY 2013; 111:95-102. [PMID: 23131300 PMCID: PMC3523653 DOI: 10.1093/aob/mcs240] [Citation(s) in RCA: 56] [Impact Index Per Article: 5.1] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Received: 07/08/2012] [Accepted: 10/03/2012] [Indexed: 05/20/2023]
Abstract
BACKGROUND AND AIMS Despite their toxicity, reactive oxygen species (ROS) play important roles in plant cell signalling pathways, such as mediating responses to stress or infection and in programmed cell death, at lower levels. Although studies have indicated that hydrogen peroxide (H(2)O(2)) promotes seed germination of several plants such as Arabidopsis, barley, wheat, rice and sunflower, the role of H(2)O(2) in soybean seed germination is not well known. The aim of this study therefore was to investigate the relationships between ROS, plant hormones and soybean seed germination. METHODS An examination was made of soybean seed germination, the expression of genes related to ethylene biosynthesis, endogenous ethylene contents, and the number and area of cells in the root tip, using N-acetylcysteine, an antioxidant, to counteract the effect of ROS. KEY RESULTS H(2)O(2) promoted germination, which N-acetylcysteine suppressed, suggesting that ROS are involved in the regulation of soybean germination. H(2)O(2) was produced in the embryonic axis after imbibition. N-Acetylcysteine suppressed the expression of genes related to ethylene biosynthesis and the production of endogenous ethylene. Interestingly, ethephon, which is converted to ethylene, and H(2)O(2) reversed the suppression of seed germination by N-acetylcysteine. Furthermore, morphological analysis revealed that N-acetylcysteine suppressed cell elongation at the root tip, and this suppression was also reversed by ethephon or H(2)O(2) treatments, as was the case in germination. CONCLUSIONS In soybean seeds, ROS produced in the embryonic axis after imbibition induce the production of endogenous ethylene, which promotes cell elongation in the root tip. This appears to be how ROS regulate soybean seed germination.
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Affiliation(s)
- Yushi Ishibashi
- Crop Science Laboratory, Faculty of Agriculture, Kyushu University, 6-10-1 Hakozaki, Higashi-ku, Fukuoka 812-8581, Japan.
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Morris KL, Zemel MB. Effect of Dietary Carbohydrate Source on the Development of Obesity inAgoutiTransgenic Mice**. ACTA ACUST UNITED AC 2012; 13:21-35. [PMID: 15761160 DOI: 10.1038/oby.2005.5] [Citation(s) in RCA: 9] [Impact Index Per Article: 0.8] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/09/2022]
Abstract
OBJECTIVES Our objective was to evaluate the effects of a qualitative change in dietary carbohydrate source on body weight and adiposity in a rodent model of diet-induced obesity. RESEARCH METHODS AND PROCEDURES We evaluated the effects of high-fat diets (basal) varying in carbohydrate source in aP2-agouti transgenic mice. In the ad libitum study, animals were given free access to the basal diet or one of four test diets for 6 weeks. In two of the diets, dietary carbohydrate was derived from a single source: mung bean noodles (MUNG) or rolled oats (ROLL). The remaining diets were designed to mimic commercially available instant oatmeal with added sugar (IO-S) or flavored instant oatmeal (IO-F). In the energy-restricted study, animals were given ad libitum access to the basal diet for 6 weeks. Subsequently, animals were assigned to one of six treatment groups for 6 weeks. One group was continued on the basal diet ad libitum. The remaining groups were maintained with energy restriction (70% ad libitum) on either the basal, MUNG, ROLL, IO-S, or IO-F diet. RESULTS Subcutaneous fat pad mass was significantly higher (p<0.05) in the energy-restricted basal and IO-S groups compared with the energy-restricted ROLL diet. Similarly, visceral fat pad mass was significantly lower with ROLL and MUNG diets (p<0.05 for both) compared with basal and IO-S diets, and the insulin:glucose ratio was reduced (by 23% to 34%, p<0.05) in these two diets compared with all others. In ad libitum-fed animals, liver fatty acid synthase expression was 43% to 62% lower (p<0.05) with ROLL and MUNG diets compared with all others. DISCUSSION These data suggest that a qualitative change in dietary carbohydrate source modulates body weight and adiposity.
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Affiliation(s)
- Kristin L Morris
- Department of Nutrition, University of Tennessee, Room 229 Jessie Harris Building, 1215 West Cumberland Avenue, Knoxville, TN 37996, USA
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Tenkanen M, Vršanská M, Siika-aho M, Wong DW, Puchart V, Penttilä M, Saloheimo M, Biely P. Xylanase XYN IV from Trichoderma reesei showing exo- and endo-xylanase activity. FEBS J 2012; 280:285-301. [PMID: 23167779 DOI: 10.1111/febs.12069] [Citation(s) in RCA: 58] [Impact Index Per Article: 4.8] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/14/2012] [Revised: 11/07/2012] [Accepted: 11/15/2012] [Indexed: 11/29/2022]
Abstract
A minor xylanase, named XYN IV, was purified from the cellulolytic system of the fungus Trichoderma reesei Rut C30. The enzyme was discovered on the basis of its ability to attack aldotetraohexenuronic acid (HexA-2Xyl-4Xyl-4Xyl, HexA(3)Xyl(3)), releasing the reducing-end xylose residue. XYN IV exhibited catalytic properties incompatible with previously described endo-β-1,4-xylanases of this fungus, XYN I, XYN II and XYN III, and the xylan-hydrolyzing endo-β-1,4-glucanase EG I. XYN IV was able to degrade several different β-1,4-xylans, but was inactive on β-1,4-mannans and β-1,4-glucans. It showed both exo-and endo-xylanase activity. Rhodymenan, a linear soluble β-1,3-β-1,4-xylan, was as the best substrate. Linear xylooligosaccharides were attacked exclusively at the first glycosidic linkage from the reducing end. The gene xyn4, encoding XYN IV, was also isolated. It showed clear homology with xylanases classified in glycoside hydrolase family 30, which also includes glucanases and mannanases. The xyn4 gene was expressed slightly when grown on xylose and xylitol, clearly on arabinose, arabitol, sophorose, xylobiose, xylan and cellulose, but not on glucose or sorbitol, resembling induction of other xylanolytic enzymes from T. reesei. A recombinant enzyme prepared in a Pichia pastoris expression system exhibited identical catalytic properties to the enzyme isolated from the T. reesei culture medium. The physiological role of this unique enzyme remains unknown, but it may involve liberation of xylose from the reducing end of branched oligosaccharides that are resistant toward β-xylosidase and other types of endoxylanases. In terms of its catalytic properties, XYN IV differs from bacterial GH family 30 glucuronoxylanases that recognize 4-O-methyl-D-glucuronic acid (MeGlcA) substituents as substrate specificity determinants.
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Affiliation(s)
- Maija Tenkanen
- VTT Technical Research Centre of Finland, Espoo, Finland
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195
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Isolation and biochemical, functional and structural characterization of a novel l-amino acid oxidase from Lachesis muta snake venom. Toxicon 2012; 60:1263-76. [DOI: 10.1016/j.toxicon.2012.08.008] [Citation(s) in RCA: 56] [Impact Index Per Article: 4.7] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/02/2012] [Revised: 08/06/2012] [Accepted: 08/09/2012] [Indexed: 11/20/2022]
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196
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Davis VL, Newbold RR, Couse JF, Rea SL, Gallagher KM, Hamilton KJ, Goulding EH, Jefferson W, Eddy EM, Bullock BC, Korach KS. Expression of a dominant negative estrogen receptor alpha variant in transgenic mice accelerates uterine cancer induced by the potent estrogen diethylstilbestrol. Reprod Toxicol 2012; 34:512-21. [PMID: 22989549 PMCID: PMC4164054 DOI: 10.1016/j.reprotox.2012.08.005] [Citation(s) in RCA: 8] [Impact Index Per Article: 0.7] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 02/21/2012] [Revised: 08/02/2012] [Accepted: 08/24/2012] [Indexed: 12/21/2022]
Abstract
ERΔ3 transgenic mice expressing a dominant negative estrogen receptor α (ERα) variant lacking the second zinc finger in the DNA binding domain were developed to examine its potential to inhibit estrogen action in vivo. To investigate if ERΔ3 expression influences uterine carcinogenesis, ERΔ3 transgenic mice were exposed to diethylstilbestrol (DES) on post-natal days 1-5. Neonatal DES treatment induced uterine adenocarcinomas in 81% of 8-month-old ERΔ3 mice compared to 49% of wild-type females (p<0.016). ERΔ3 did not inhibit the expression of the estrogen-responsive progesterone receptor and lactoferrin genes in the presence of ERα or modify their expression in ERα knockout (αERKO) mice. Higher circulating 17β-estradiol levels and non-classical signaling by ERΔ3 may be related to the earlier incidence of uterine cancer. These findings indicate that expression of this ERα variant can influence determining events in uterine cancer development and its natural occurrence in the human uterus would unlikely be protective.
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Affiliation(s)
- Vicki L Davis
- Receptor Biology Group, Laboratory of Reproductive and Developmental Toxicology, National Institute of Environmental Health Sciences, National Institutes of Health, Research Triangle Park, NC 27709, United States.
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197
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Li J, Yu L, Zhao Y, Fu G, Zhou B. Thymosin β4 reduces senescence of endothelial progenitor cells via the PI3K/Akt/eNOS signal transduction pathway. Mol Med Rep 2012; 7:598-602. [PMID: 23151623 DOI: 10.3892/mmr.2012.1180] [Citation(s) in RCA: 17] [Impact Index Per Article: 1.4] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/04/2012] [Accepted: 10/30/2012] [Indexed: 11/06/2022] Open
Abstract
We previously demonstrated that thymosin β4 (Tβ4) regulates a variety of endothelial progenitor cell (EPC) functions, including cell migration, proliferation, survival and angiogenesis. However, the effect of Tβ4 on the senescence of circulating EPCs remains unclear. In the present study, the effect of Tβ4 on EPC senescence and the signal transduction pathways involved in this process was investigated. Circulating EPCs isolated from healthy volunteers were cultured in the absence or presence of Tβ4 and various signal cascade inhibitors. Tβ4 inhibited EPC senescence in a concentration‑dependent manner. In addition, Tβ4 increased telomerase activity and expression of telomerase reverse transcriptase mRNA in EPCs. Tβ4 also regulated the expression of p21, p27 and cyclin D1. The effects of Tβ4 on EPC senescence were eliminated by the phosphoinositide 3'‑kinase (PI3K) inhibitor, wortmannin and the endothelial nitric oxide synthase inhibitor, L‑nitroarginine methyl ester hydrochloride (L‑NAME). In conclusion, the inhibitory effect on EPC senescence mediated by Tβ4 may be attributed, at least in part, to activation of the PI3K‑Akt‑eNOS signaling pathway.
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Affiliation(s)
- Juan Li
- Department of Cardiology, Biomedical Research (Therapy) Center, Sir Run Run Shaw Hospital, College of Medicine, Zhejiang University, Hangzhou 310016, Zhejiang, P.R. China
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198
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Southwood CM, Lipovich L, Gow A. Tissue-restricted transcription from a conserved intragenic CpG island in the Klf1 gene in mice. Biol Reprod 2012; 87:108. [PMID: 22933519 DOI: 10.1095/biolreprod.112.099879] [Citation(s) in RCA: 8] [Impact Index Per Article: 0.7] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/17/2022] Open
Abstract
Beyond Mendelian inheritance, an understanding of the complexities and consequences of the transfer of nonhereditary information to successive generations is at an early stage. Such epigenetic functionality is exemplified by DNA methylation and, as genome-wide high-throughput methodologies emerge, is increasingly being considered in the context of conserved intragenic and intergenic CpG islands that function as alternate sites of transcription initiation. Here we characterize an intragenic CpG island in exon 2 of the protein-coding mouse Klf1 gene, from which clustered transcription initiation sites yield positive-strand, severely truncated, capped and spliced RNAs. Expression from this CpG island in the testis begins between Postnatal Days 14-20, increases during development, and is temporally correlated with the maturation of secondary spermatocytes as they become the dominant cell population in the seminiferous epithelium. Only full-length KLF1-encoding mRNAs are detected in the hematopoietic tissue, spleen; thus, expression from the exon 2 CpG island is both developmentally regulated and tissue restricted. DNA methylation analysis indicates that spatiotemporal expression from the Klf1 CpG island is not associated with hypermethylation. Finally, our computational analysis from multiple species confirms intragenic transcription initiation and indicates that the KLF1 CpG island is evolutionarily conserved. Currently we have no evidence that these truncated RNAs can be translated via nonconventional mechanisms such as in-frame, conserved non-AUG-dependent Kozak consensus sequences; however, high-quality carboxyl-terminal antibodies will more effectively address this issue.
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Affiliation(s)
- Cherie M Southwood
- Center for Molecular Medicine and Genetics, Wayne State University School of Medicine, Detroit, Michigan 48201, USA
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199
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Mathieson W, Thomas GA. Simultaneously extracting DNA, RNA, and protein using kits: is sample quantity or quality prejudiced? Anal Biochem 2012; 433:10-8. [PMID: 23068038 DOI: 10.1016/j.ab.2012.10.006] [Citation(s) in RCA: 31] [Impact Index Per Article: 2.6] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/19/2012] [Revised: 10/01/2012] [Accepted: 10/04/2012] [Indexed: 11/17/2022]
Abstract
Interdisciplinary "omics" research and the stringent quality requirements of array-based technologies require the simultaneous yet efficient extraction of DNA, RNA, and protein from the same tissue block. However, the few commercially available simultaneous extraction kits have not been evaluated. We compare the TriplePrep (GE Healthcare) and AllPrep (Qiagen) kits using good, intermediate, and poor quality tissue with specialist single-extract methods: Puregene (DNA), RNeasy (RNA), and homogenizations into buffer (protein). The following parameters were evaluated: DNA-yield (total DNA and double-stranded), purity (260:280 and 260:230), and integrity (gel electrophoresis); RNA-yield, purity, and integrity (RNA integrity numbers [RINs] and quantitative reverse transcription polymerase chain reaction [Q-RT-PCR]); protein-yield and quality (two-dimensional difference gel electrophoresis [2D-DIGE]). Puregene DNA yields were 183% and 506% those of TriplePrep and AllPrep, respectively. For RNA, AllPrep and RNeasy were indistinguishable, but their yields were 412% to 588% those of TriplePrep (depending on block condition) and their between-sample variability was better. TriplePrep protein yields were 57% those of the control, and 6.9% of the gel spots were more than 2-fold altered. However, AllPrep yields were 20% of the control, with 11% of the gel spots being more than 2-fold altered. Therefore, TriplePrep outperformed AllPrep in DNA and protein extractions, the reverse was true for RNA, but neither kit achieved optimal efficiency because both yield and quality were compromised.
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Affiliation(s)
- William Mathieson
- Department of Surgery and Cancer, Imperial College London, London W12 0NN, UK.
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200
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Ewing JF, Maines MD. In situ hybridization and immunohistochemical localization of heme oxygenase-2 mRNA and protein in normal rat brain: Differential distribution of isozyme 1 and 2. Mol Cell Neurosci 2012; 3:559-70. [PMID: 19912899 DOI: 10.1016/1044-7431(92)90068-d] [Citation(s) in RCA: 162] [Impact Index Per Article: 13.5] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/29/1992] [Indexed: 11/27/2022] Open
Abstract
Heme oxygenase isozymes, HO-1 (HSP32) and HO-2, stereospecifically bind and degrade the potent prooxidant, the heme molecule, and convert it to the effective antioxidant, biliverdin, and the potential cellular messenger, carbon monoxide. In the present study we have examined the pattern of expression of the two HO-2 transcripts and protein in normal rat brain by in situ hybridization and immunochemical analysis, respectively. We have found by Northern blot analysis that HO-2 isozyme is by far the most prevalent form in the brain. Analysis of HO-2 1.3- and 1.9-kb mRNAs by in situ hybridization histochemistry showed that these transcripts are abundantly expressed in many neuronal and nonneuronal cell populations in forebrain, diencephalon, cerebellum, and brain stem regions. Furthermore, the pattern of expression of HO-2 transcripts, as detected by oligonucleotide probes, is in good agreement with that of immunoreactive protein detected by immunohistochemical analysis. Impressive levels of HO-2 transcripts and immunoreactive protein were observed in Purkinje cells of cerebellum, red nucleus, superior and inferior colliculus, nucleus of the trapezoid body, cochlear neurons, and facial nucleus of brain stem. Furthermore, in certain select brain cell populations the pattern of expression of HO-1- and HO-2-immunoreactive proteins overlapped. We suggest that the high levels of heme degradation activity and the localization of HO-2 transcripts and protein in the brain may reflect the functions of this enzyme in processes such as production of cellular messenger, regulation of the activity of heme-dependent enzymes catalyzing intracellular signaling molecule synthesis, and production of antioxidants.
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Affiliation(s)
- J F Ewing
- Department of Biophysics, University of Rochester Medical Center, Rochester, New York 14642, USA
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