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Article ; Online: Small molecule approaches to targeting RNA.

Kovachka, Sandra / Panosetti, Marc / Grimaldi, Benedetto / Azoulay, Stéphane / Di Giorgio, Audrey / Duca, Maria

Nature reviews. Chemistry

2024 Volume 8, Issue 2, Page(s) 120–135

Abstract: The development of innovative methodologies to identify RNA binders has attracted enormous attention in chemical biology and drug discovery. Although antibiotics targeting bacterial ribosomal RNA have been on the market for decades, the renewed interest ... ...

Abstract	The development of innovative methodologies to identify RNA binders has attracted enormous attention in chemical biology and drug discovery. Although antibiotics targeting bacterial ribosomal RNA have been on the market for decades, the renewed interest in RNA targeting reflects the need to better understand complex intracellular processes involving RNA. In this context, small molecules are privileged tools used to explore the biological functions of RNA and to validate RNAs as therapeutic targets, and they eventually are to become new drugs. Despite recent progress, the rational design of specific RNA binders requires a better understanding of the interactions which occur with the RNA target to reach the desired biological response. In this Review, we discuss the challenges to approaching this underexplored chemical space, together with recent strategies to bind, interact and affect biologically relevant RNAs.
MeSH term(s)	RNA, Ribosomal/genetics ; Drug Discovery/methods ; RNA, Bacterial/genetics ; Anti-Bacterial Agents/pharmacology
Chemical Substances	RNA, Ribosomal ; RNA, Bacterial ; Anti-Bacterial Agents
Language	English
Publishing date	2024-01-26
Publishing country	England
Document type	Journal Article ; Review ; Research Support, Non-U.S. Gov't
ISSN	2397-3358
ISSN (online)	2397-3358
DOI	10.1038/s41570-023-00569-9
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Article: Lysosomotropic REV-ERB antagonism: A metabolic connection between circadian rhythm and autophagy may tell cancer cells "it's time to die".

Grimaldi, Benedetto

Molecular & cellular oncology

2014 Volume 2, Issue 2, Page(s) e965626

Abstract: The discovery that inhibition of a circadian regulator enhances autophagy-dependent cancer cell death reveals potential avenues for the development of new multifunctional anticancer agents. Further studies may elucidate novel crosstalk between circadian ... ...

Abstract	The discovery that inhibition of a circadian regulator enhances autophagy-dependent cancer cell death reveals potential avenues for the development of new multifunctional anticancer agents. Further studies may elucidate novel crosstalk between circadian rhythm, metabolism, and autophagy that determines cancer cell viability.
Language	English
Publishing date	2014-10-30
Publishing country	United States
Document type	Journal Article
ISSN	2372-3556
ISSN	2372-3556
DOI	10.4161/23723548.2014.965626
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Article ; Online: Identification of a Dual Autophagy and REV-ERB Inhibitor with

Palomba, Martina / Vecchio, Donatella / Allavena, Giulia / Capaccio, Vito / De Mei, Claudia / Scarpelli, Rita / Grimaldi, Benedetto

Journal of medicinal chemistry

2023 Volume 67, Issue 1, Page(s) 349–379

Abstract: The autophagy process appears as a promising target for anticancer interventions. Chloroquine (CQ) and its derivative hydroxychloroquine (HCQ) are the only FDA-approved autophagy flux inhibitors. Although diverse anticancer clinical trials are providing ... ...

Abstract	The autophagy process appears as a promising target for anticancer interventions. Chloroquine (CQ) and its derivative hydroxychloroquine (HCQ) are the only FDA-approved autophagy flux inhibitors. Although diverse anticancer clinical trials are providing encouraging results, several limitations associated with the need of high dosage and long-term administration of these autophagy inhibitors are also emerging. We showed that the inhibition of REV-ERB, a nuclear receptor regulating circadian rhythm and metabolism, enhances CQ-mediated cancer cell death and identified a class of dual inhibitors of autophagy and REV-ERB displaying an
MeSH term(s)	Humans ; Animals ; Mice ; Antineoplastic Agents/pharmacology ; Antineoplastic Agents/therapeutic use ; Neoplasms/drug therapy ; Chloroquine/pharmacology ; Chloroquine/therapeutic use ; Autophagy ; Cell Death ; Cell Line, Tumor
Chemical Substances	Antineoplastic Agents ; Chloroquine (886U3H6UFF)
Language	English
Publishing date	2023-12-20
Publishing country	United States
Document type	Journal Article
ZDB-ID	218133-2
ISSN	1520-4804 ; 0022-2623
ISSN (online)	1520-4804
ISSN	0022-2623
DOI	10.1021/acs.jmedchem.3c01432
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Zs.MB 1: Show issues

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Article ; Online: MYC-Associated Factor MAX is a Regulator of the Circadian Clock.

Blaževitš, Olga / Bolshette, Nityanand / Vecchio, Donatella / Guijarro, Ana / Croci, Ottavio / Campaner, Stefano / Grimaldi, Benedetto

International journal of molecular sciences

2020 Volume 21, Issue 7

Abstract: The circadian transcriptional network is based on a competition between transcriptional activator and repressor complexes regulating the rhythmic expression of clock-controlled genes. We show here that the MYC-associated factor X, MAX, plays a repressive ...

Abstract	The circadian transcriptional network is based on a competition between transcriptional activator and repressor complexes regulating the rhythmic expression of clock-controlled genes. We show here that the MYC-associated factor X, MAX, plays a repressive role in this network and operates through a MYC-independent binding to E-box-containing regulatory regions within the promoters of circadian BMAL1 targets. We further show that this "clock" function of MAX is required for maintaining a proper circadian rhythm and that MAX and BMAL1 contribute to two temporally alternating transcriptional complexes on clock-regulated promoters. We also identified MAX network transcriptional repressor, MNT, as a fundamental partner of MAX-mediated circadian regulation. Collectively, our data indicate that MAX regulates clock gene expression and contributes to keeping the balance between positive and negative elements of the molecular clock machinery.
MeSH term(s)	ARNTL Transcription Factors/genetics ; ARNTL Transcription Factors/metabolism ; Basic Helix-Loop-Helix Leucine Zipper Transcription Factors/genetics ; Basic Helix-Loop-Helix Leucine Zipper Transcription Factors/metabolism ; Circadian Clocks/genetics ; Gene Regulatory Networks ; HEK293 Cells ; Hep G2 Cells ; Humans ; Promoter Regions, Genetic
Chemical Substances	ARNTL Transcription Factors ; BMAL1 protein, human ; Basic Helix-Loop-Helix Leucine Zipper Transcription Factors ; MAX protein, human
Language	English
Publishing date	2020-03-26
Publishing country	Switzerland
Document type	Journal Article
ZDB-ID	2019364-6
ISSN	1422-0067 ; 1422-0067 ; 1661-6596
ISSN (online)	1422-0067
ISSN	1422-0067 ; 1661-6596
DOI	10.3390/ijms21072294
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Article ; Online: Autophagy and cancer drug resistance in dialogue: Pre-clinical and clinical evidence.

Qin, Yi / Ashrafizadeh, Milad / Mongiardini, Vera / Grimaldi, Benedetto / Crea, Francesco / Rietdorf, Katja / Győrffy, Balázs / Klionsky, Daniel J / Ren, Jun / Zhang, Wei / Zhang, Xianbin

Cancer letters

2023 Volume 570, Page(s) 216307

Abstract: The emergence of drug resistance is a major challenge for oncologists. Resistance can be categorized as acquired or intrinsic; the alteration of several biological mechanisms contributes to both intrinsic and acquired resistance. Macroautophagy/autophagy ...

Abstract	The emergence of drug resistance is a major challenge for oncologists. Resistance can be categorized as acquired or intrinsic; the alteration of several biological mechanisms contributes to both intrinsic and acquired resistance. Macroautophagy/autophagy is the primary process in eukaryotes for the degradation of macromolecules and organelles. This process is critical in maintaining cellular homeostasis. Given its function as either a pro-survival or a pro-death phenomenon, autophagy has a complex physio-pathological role. In some circumstances, autophagy can confer chemoresistance and promote cell survival, whereas in others it can promote chemosensitivity and contribute to cell death. The role of autophagy in the modulation of cancer drug resistance reflects its impact on apoptosis and metastasis. The regulation of autophagy in cancer is mediated by various factors including AMP-activated protein kinase (AMPK), MAPK, phosphoinositide 3-kinase (PI3K)-AKT, BECN1 and ATG proteins. Non-coding RNAs are among the main regulators of autophagy, e.g., via the modulation of chemoresistance pathways. Due to the significant contribution of autophagy in cancer drug resistance, small molecule modulators and natural compounds targeting autophagy have been introduced to alter the response of cancer cells to chemotherapy. Furthermore, nanotherapeutic approaches based on autophagy regulation have been introduced in pre-clinical cancer therapy. In this review we consider the potential for using autophagy regulators for the clinical treatment of malignancies.
MeSH term(s)	Humans ; Drug Resistance, Neoplasm ; Phosphatidylinositol 3-Kinases/metabolism ; Apoptosis ; Phosphatidylinositol 3-Kinase ; Autophagy ; Neoplasms/drug therapy
Chemical Substances	Phosphatidylinositol 3-Kinases (EC 2.7.1.-) ; Phosphatidylinositol 3-Kinase (EC 2.7.1.137)
Language	English
Publishing date	2023-07-12
Publishing country	Ireland
Document type	Review ; Journal Article
ZDB-ID	195674-7
ISSN	1872-7980 ; 0304-3835
ISSN (online)	1872-7980
ISSN	0304-3835
DOI	10.1016/j.canlet.2023.216307
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Article: Disulfide-Mediated Bioconjugation: Disulfide Formation and Restructuring on the Surface of Nanomanufactured (Microfluidics) Nanoparticles

Geven, Mike / Donno, Roberto / Gennari, Arianna / Grimaldi, Benedetto / Koo, Donghun / Luo, Hanying / Marotta, Roberto / Panambur, Gangadhar / Tirelli, Nicola

ACS applied materials & interfaces. 2019 July 08, v. 11, no. 30

2019

Abstract: This study is about (1) nanomanufacturing (focusing on microfluidic-assisted nanoprecipitation), (2) advanced colloid characterization (focusing on field flow fractionation), and (3) the possible restructuring of surface disulfides. Disulfides are ... ...

Abstract	This study is about (1) nanomanufacturing (focusing on microfluidic-assisted nanoprecipitation), (2) advanced colloid characterization (focusing on field flow fractionation), and (3) the possible restructuring of surface disulfides. Disulfides are dynamic and exchangeable groups, and here we specifically focus, first, on their use to introduce biofunctional groups and, second, on their re-organization, which may lead to variable surface chemistries and uncontrolled cell interactions. The particles were obtained via microfluidic-assisted (flow-focused) nanoprecipitation of poly(ethylene glycol)-b-poly(ε-caprolactone) bearing or not a 2-pyridyl disulfide (PDS) terminal group, which quantitatively exchanges with thiols in solution. In this study, we have paid specific attention to size characterization, thereby also demonstrating the limitations of dynamic light scattering (DLS) as a stand-alone technique. By using asymmetric flow field flow fractionation coupled with DLS, static light scattering (SLS), and refractive index detectors, we show that relatively small amounts of >100 nm aggregates (cryogenic transmission electron microscopy and SLS/DLS comparison suggesting them to be wormlike micelles) dominated the stand-alone DLS results, whereas the “real” size distributions picked <50 nm. Our key result is that the kinetics of the conjugation based on PDS–thiol exchange was controlled by the thiol pKa, and this also determined the rate of the exchange between the resulting disulfides and glutathione (GSH). In particular, more acidic thiols (e.g., peptides, where a cysteine is flanked by cationic residues) react faster with PDS, but their disulfides hardly exchange with GSH; the reverse applies to thiols with a higher pKa. Disulfides that resist against restructuring via thiol–disulfide exchange allow for a stable bioconjugation, although they may be bad news for payload release under reducing conditions. However, experiments of both thiol release and nanoparticles uptake in cells (HCT116) show that also the disulfides formed from less-acidic and, therefore, less-reactive, and more exchangeable thiols were stable for at least a few hours even in a GSH-rich (10 mM) environment; this suggests a sufficiently long stability of surface groups to achieve, for example, a cell-targeting effect.
Keywords	chemical bonding ; cysteine ; detectors ; disulfides ; fractionation ; glutathione ; lactones ; light scattering ; micelles ; microfluidic technology ; nanoparticles ; polyethylene glycol ; refractive index ; thiols ; transmission electron microscopy
Language	English
Dates of publication	2019-0708
Size	p. 26607-26618.
Publishing place	American Chemical Society
Document type	Article
ISSN	1944-8252
DOI	10.1021/acsami.9b07972
Database	NAL-Catalogue (AGRICOLA)

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Article ; Online: A broad-spectrum antibiotic, DCAP, reduces uropathogenic Escherichia coli infection and enhances vorinostat anticancer activity by modulating autophagy.

Allavena, Giulia / Debellis, Doriana / Marotta, Roberto / Joshi, Chetanchandra S / Mysorekar, Indira U / Grimaldi, Benedetto

Cell death & disease

2018 Volume 9, Issue 7, Page(s) 780

Abstract: The cellular recycling pathway of autophagy plays a fundamental role in adaptive responses to nutrient deprivation and other forms of stress under physiological and pathological conditions. However, autophagy can also be a double-edge sword during ... ...

Abstract	The cellular recycling pathway of autophagy plays a fundamental role in adaptive responses to nutrient deprivation and other forms of stress under physiological and pathological conditions. However, autophagy can also be a double-edge sword during certain bacterial infections (such as urinary tract infections) and in cancer, where it can be hijacked by the pathogens and cancer cells, respectively, to promote their own survival. Thus, autophagy modulation can potentially have multiple effects in multiple contexts and this property can be leveraged to improve outcomes. In this report, we identify that a broad-spectrum antibiotic, 2-((3-(3, 6-dichloro-9H-carbazol-9-yl)-2-hydroxypropyl) amino)-2-(hydroxymethyl) propane-1, 3-diol (DCAP) modulates autophagy. We employed combined biochemical, fluorescence microscopy and correlative light electron microscopy approaches to demonstrate that DCAP treatment blocks autophagy at the late stages by preventing autophagolysosome maturation and interrupting the autophagic flux. We further show that, DCAP significantly reduces UPEC infection in urinary tract epithelial cells via inhibition of autophagy. Finally, we reveal that DCAP enhances the anticancer activity of the histone acetyltransferase (HDAC) inhibitor, vorinostat, which has been reported to increase susceptibility to bacterial infections as a common adverse effect. Collectively, our data support the concept that DCAP represents a valuable chemical scaffold for the development of an innovative class of bactericidal autophagy inhibitors for treatment of urinary tract infections and/or for adjuvant therapy in cancer treatment.
MeSH term(s)	Aminophenols/pharmacology ; Anti-Bacterial Agents/pharmacology ; Anti-Bacterial Agents/therapeutic use ; Antineoplastic Agents/pharmacology ; Autophagosomes/drug effects ; Autophagosomes/metabolism ; Autophagosomes/ultrastructure ; Autophagy/drug effects ; Cell Line, Tumor ; Escherichia coli Infections/drug therapy ; Escherichia coli Infections/microbiology ; Histone Deacetylase Inhibitors/pharmacology ; Humans ; Intracellular Membranes/drug effects ; Intracellular Membranes/metabolism ; Lysosomes/drug effects ; Lysosomes/metabolism ; Lysosomes/ultrastructure ; Mitochondria/drug effects ; Mitochondria/metabolism ; Urinary Tract Infections/drug therapy ; Urinary Tract Infections/microbiology ; Uropathogenic Escherichia coli/drug effects ; Uropathogenic Escherichia coli/physiology ; Vorinostat/pharmacology
Chemical Substances	Aminophenols ; Anti-Bacterial Agents ; Antineoplastic Agents ; Histone Deacetylase Inhibitors ; 3,5-dichloro-1,4-aminophenol (26271-75-0) ; Vorinostat (58IFB293JI)
Language	English
Publishing date	2018-07-13
Publishing country	England
Document type	Journal Article ; Research Support, N.I.H., Extramural ; Research Support, Non-U.S. Gov't
ZDB-ID	2541626-1
ISSN	2041-4889 ; 2041-4889
ISSN (online)	2041-4889
ISSN	2041-4889
DOI	10.1038/s41419-018-0786-4
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Article ; Online: Disulfide-Mediated Bioconjugation: Disulfide Formation and Restructuring on the Surface of Nanomanufactured (Microfluidics) Nanoparticles.

Geven, Mike / Luo, Hanying / Koo, Donghun / Panambur, Gangadhar / Donno, Roberto / Gennari, Arianna / Marotta, Roberto / Grimaldi, Benedetto / Tirelli, Nicola

ACS applied materials & interfaces

2019 Volume 11, Issue 30, Page(s) 26607–26618

Abstract	This study is about (1) nanomanufacturing (focusing on microfluidic-assisted nanoprecipitation), (2) advanced colloid characterization (focusing on field flow fractionation), and (3) the possible restructuring of surface disulfides. Disulfides are dynamic and exchangeable groups, and here we specifically focus, first, on their use to introduce biofunctional groups and, second, on their re-organization, which may lead to variable surface chemistries and uncontrolled cell interactions. The particles were obtained via microfluidic-assisted (flow-focused) nanoprecipitation of poly(ethylene glycol)-
MeSH term(s)	Cysteine/chemistry ; Disulfides/chemical synthesis ; Disulfides/chemistry ; Ethylene Glycols/chemistry ; Ethylene Glycols/pharmacology ; Glutathione/chemistry ; HCT116 Cells ; Humans ; Kinetics ; Microfluidics ; Nanoparticles/administration & dosage ; Nanoparticles/chemistry ; Peptides/chemistry ; Polyesters/chemistry ; Polyesters/pharmacology ; Sulfhydryl Compounds/chemistry ; Sulfhydryl Compounds/pharmacology ; Surface Properties
Chemical Substances	Disulfides ; Ethylene Glycols ; Peptides ; Polyesters ; Sulfhydryl Compounds ; poly(epsilon-caprolactone)-b-poly(ethylene glycol) ; Glutathione (GAN16C9B8O) ; Cysteine (K848JZ4886)
Language	English
Publishing date	2019-07-18
Publishing country	United States
Document type	Journal Article
ISSN	1944-8252
ISSN (online)	1944-8252
DOI	10.1021/acsami.9b07972
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Article ; Online: Physical association of the WC-1 photoreceptor and the histone acetyltransferase NGF-1 is required for blue light signal transduction in Neurospora crassa.

Brenna, Andrea / Grimaldi, Benedetto / Filetici, Patrizia / Ballario, Paola

Molecular biology of the cell

2012 Volume 23, Issue 19, Page(s) 3863–3872

Abstract: In Neurospora crassa and other filamentous fungi, light-dependent-specific phenomena are regulated by transcription factors WC-1 and WC-2. In addition to its transcriptional activity, WC-1 is able to directly sense light stimuli through a LOV sensor ... ...

Abstract	In Neurospora crassa and other filamentous fungi, light-dependent-specific phenomena are regulated by transcription factors WC-1 and WC-2. In addition to its transcriptional activity, WC-1 is able to directly sense light stimuli through a LOV sensor domain. Its location in the nucleus and heterodimerization with WC-2, together with the presence of a zinc-finger DNA-binding domain and an environmental sensor domain, all resemble the functional evolutionary architecture adopted by vertebrate nuclear receptors (NRs). Here we describe a scenario in which WC-1 represents a functional orthologue of NRs and acts through association with the chromatin-modifying coactivator NGF-1, which encodes a homologue of the yeast Gcn5p acetyltransferase. To support this view, we show a direct association between WC-1 and NGF-1 that depends on a WC-1 region containing a conserved functional LXXLL motif, a signature previously described as being an exclusive feature of NR/coactivator interaction. Our data suggest that a WC-1/NGF-1 complex is preassembled in the dark on light-inducible promoters and that, after exposure to light stimulation, NGF-1-associated HAT activity leads to histone H3 acetylation and transcriptional activation. Finally, we provide evidence for a NGF-1-independent acetylated form of WC-1. Overall our data indicate that Neurospora and higher eukaryotes share a common mechanism for the signal transduction of environmental stimuli.
MeSH term(s)	Acetylation ; Amino Acid Motifs ; Amino Acid Sequence ; DNA-Binding Proteins/chemistry ; DNA-Binding Proteins/metabolism ; Epigenesis, Genetic ; Fungal Proteins/chemistry ; Fungal Proteins/metabolism ; Gene Expression Regulation, Fungal ; Histone Acetyltransferases/chemistry ; Histone Acetyltransferases/metabolism ; Histones/metabolism ; Light ; Molecular Sequence Data ; Neurospora crassa/enzymology ; Neurospora crassa/metabolism ; Neurospora crassa/radiation effects ; Protein Binding ; Protein Interaction Domains and Motifs ; Protein Processing, Post-Translational ; Receptors, Cytoplasmic and Nuclear/chemistry ; Receptors, Cytoplasmic and Nuclear/metabolism ; Sequence Homology, Amino Acid ; Signal Transduction/radiation effects ; Transcription Factors/chemistry ; Transcription Factors/metabolism
Chemical Substances	DNA-Binding Proteins ; Fungal Proteins ; Histones ; Receptors, Cytoplasmic and Nuclear ; Transcription Factors ; wc-1 protein, Neurospora crassa ; Histone Acetyltransferases (EC 2.3.1.48)
Language	English
Publishing date	2012-08-08
Publishing country	United States
Document type	Journal Article
ZDB-ID	1098979-1
ISSN	1939-4586 ; 1059-1524
ISSN (online)	1939-4586
ISSN	1059-1524
DOI	10.1091/mbc.E12-02-0142
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Zs.A 2853: Show issues			Location: Je nach Verfügbarkeit (siehe Angabe bei Bestand) bis Jg. 1994: Bestellungen von Artikeln über das Online-Bestellformular Jg. 1995 - 2021: Lesesall (2.OG) ab Jg. 2022: Lesesaal (EG)
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Article ; Online: Circadian rhythms: metabolic clockwork.

Grimaldi, Benedetto / Sassone-Corsi, Paolo

Nature

2007 Volume 447, Issue 7143, Page(s) 386–387

MeSH term(s)	Animals ; Biological Clocks/genetics ; Circadian Rhythm/genetics ; Energy Metabolism/genetics ; Gene Expression Regulation/genetics ; Humans ; Mice ; Peroxisome Proliferator-Activated Receptor Gamma Coactivator 1-alpha ; Trans-Activators/genetics ; Trans-Activators/metabolism ; Transcription Factors
Chemical Substances	Peroxisome Proliferator-Activated Receptor Gamma Coactivator 1-alpha ; Ppargc1a protein, mouse ; Trans-Activators ; Transcription Factors
Language	English
Publishing date	2007-05-24
Publishing country	England
Document type	News ; Comment
ZDB-ID	120714-3
ISSN	1476-4687 ; 0028-0836
ISSN (online)	1476-4687
ISSN	0028-0836
DOI	10.1038/447386a
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