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Article ; Online: An LIR motif in the Rift Valley fever virus NSs protein is critical for the interaction with LC3 family members and inhibition of autophagy.

Petraccione, Kaylee / Ali, Mohamed G H / Cyr, Normand / Wahba, Haytham M / Stocker, Timothy / Akhrymuk, Maryna / Akhrymuk, Ivan / Panny, Lauren / Bracci, Nicole / Cafaro, Raphaël / Sastre, Danuta / Silberfarb, Andrew / O'Maille, Paul / Omichinski, James / Kehn-Hall, Kylene

PLoS pathogens

2024 Volume 20, Issue 3, Page(s) e1012093

Abstract: Rift Valley fever virus (RVFV) is a viral zoonosis that causes severe disease in ruminants and humans. The nonstructural small (NSs) protein is the primary virulence factor of RVFV that suppresses the host's antiviral innate immune response. ... ...

Abstract	Rift Valley fever virus (RVFV) is a viral zoonosis that causes severe disease in ruminants and humans. The nonstructural small (NSs) protein is the primary virulence factor of RVFV that suppresses the host's antiviral innate immune response. Bioinformatic analysis and AlphaFold structural modeling identified four putative LC3-interacting regions (LIR) motifs (NSs 1-4) in the RVFV NSs protein, which suggest that NSs interacts with the host LC3-family proteins. Using, isothermal titration calorimetry, X-ray crystallography, co-immunoprecipitation, and co-localization experiments, the C-terminal LIR motif (NSs4) was confirmed to interact with all six human LC3 proteins. Phenylalanine at position 261 (F261) within NSs4 was found to be critical for the interaction of NSs with LC3, retention of LC3 in the nucleus, as well as the inhibition of autophagy in RVFV infected cells. These results provide mechanistic insights into the ability of RVFV to overcome antiviral autophagy through the interaction of NSs with LC3 proteins.
MeSH term(s)	Animals ; Humans ; Rift Valley fever virus/metabolism ; Viral Nonstructural Proteins/metabolism ; Rift Valley Fever ; Autophagy ; Antiviral Agents/metabolism
Chemical Substances	Viral Nonstructural Proteins ; Antiviral Agents
Language	English
Publishing date	2024-03-21
Publishing country	United States
Document type	Journal Article
ZDB-ID	2205412-1
ISSN	1553-7374 ; 1553-7374
ISSN (online)	1553-7374
ISSN	1553-7374
DOI	10.1371/journal.ppat.1012093
Database	MEDical Literature Analysis and Retrieval System OnLINE

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Article ; Online: Sindbis Virus Infection Causes Cell Death by nsP2-Induced Transcriptional Shutoff or by nsP3-Dependent Translational Shutoff.

Akhrymuk, Ivan / Frolov, Ilya / Frolova, Elena I

Journal of virology

2018 Volume 92, Issue 23

Abstract: Sindbis virus (SINV) is a representative member of ... ...

Abstract	Sindbis virus (SINV) is a representative member of the
MeSH term(s)	Alphavirus Infections/genetics ; Alphavirus Infections/metabolism ; Alphavirus Infections/pathology ; Alphavirus Infections/virology ; Animals ; Cysteine Endopeptidases/genetics ; Cysteine Endopeptidases/metabolism ; Cytopathogenic Effect, Viral ; Genome, Viral ; Mice ; NIH 3T3 Cells ; Protein Biosynthesis ; Sindbis Virus/physiology ; Transcription, Genetic ; Viral Nonstructural Proteins/genetics ; Viral Nonstructural Proteins/metabolism ; Virion ; Virus Replication
Chemical Substances	Viral Nonstructural Proteins ; nsp3 protein, alphavirus ; Cysteine Endopeptidases (EC 3.4.22.-) ; nsP2 proteinase (EC 3.4.22.-)
Language	English
Publishing date	2018-11-12
Publishing country	United States
Document type	Journal Article ; Research Support, N.I.H., Extramural
ZDB-ID	80174-4
ISSN	1098-5514 ; 0022-538X
ISSN (online)	1098-5514
ISSN	0022-538X
DOI	10.1128/JVI.01388-18
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Article: Dehydrated Human Amnion-Chorion Membrane Extracts Can Ameliorate Interstitial Cystitis in Rats by Down-Regulating Inflammatory Cytokines and Protein Coding Genes: A Preclinical Study.

Yang, Che-Hsueh / Tung, Min-Che / Lin, Yi-Sheng / Hsu, Chao-Yu / Akhrymuk, Ivan / Tan, Kok-Tong / Ou, Yen-Chuan / Lin, Chi-Chien

Life (Basel, Switzerland)

2022 Volume 12, Issue 11

Abstract: The study aimed to investigate the therapeutic impact of intravesical instillation of dehydrated human amnion-chorion membrane (HACM) extracts based on the primary pathological feature of interstitial cystitis (IC). We divided 15 female Sprague-Dawley ... ...

Abstract	The study aimed to investigate the therapeutic impact of intravesical instillation of dehydrated human amnion-chorion membrane (HACM) extracts based on the primary pathological feature of interstitial cystitis (IC). We divided 15 female Sprague-Dawley rats into three groups: sham control, IC, and treatment group. IC was induced by 400-µL lipopolysaccharide (1 µg/µL), and it was replaced with normal saline in the sham control group. After IC induction, 300 µL dehydrated HACM extracts (3 mg/kg) were instilled into rats’ urinary bladder weekly for 3 weeks. General histology, inflammatory cytokines, NF-κB, oxidative markers, and western blots results were examined. The urothelial denudation, mast-cell infiltration, and tissues fibrosis were all ameliorated. The elevated TNF-α, IL-1β, IL-6, IL-8, and NF-κB were all down-regulated by dehydrated HACM extracts (p < 0.05). For reactive oxygen species, increased malondialdehyde, decreased superoxide dismutase, and decreased glutathione peroxidase were all reversed (p < 0.05). In apoptosis of IC, elevated Bax and suppressed Bcl-2 were improved (p < 0.05) after instillation. In fibrosis, dysregulated TGFβ/R-Smads/Snail was corrected by the instillation of dehydrated HACM (p < 0.05). In conclusion, dehydrated HACM extracts could be a powerful remedy in treating IC by reconstructing the damaged urothelium, reducing mast-cell infiltration and inflammatory reactions, and ameliorating fibrotic changes.
Language	English
Publishing date	2022-10-25
Publishing country	Switzerland
Document type	Journal Article
ZDB-ID	2662250-6
ISSN	2075-1729
ISSN	2075-1729
DOI	10.3390/life12111693
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Article: RK-33, a small molecule inhibitor of host RNA helicase DDX3, suppresses multiple variants of SARS-CoV-2.

Vesuna, Farhad / Akhrymuk, Ivan / Smith, Amy / Winnard, Paul T / Lin, Shih-Chao / Panny, Lauren / Scharpf, Robert / Kehn-Hall, Kylene / Raman, Venu

Frontiers in microbiology

2022 Volume 13, Page(s) 959577

Abstract: SARS-CoV-2, the virus behind the deadly COVID-19 pandemic, continues to spread globally even as vaccine strategies are proving effective in preventing hospitalizations and deaths. However, evolving variants of the virus appear to be more transmissive and ...

Abstract	SARS-CoV-2, the virus behind the deadly COVID-19 pandemic, continues to spread globally even as vaccine strategies are proving effective in preventing hospitalizations and deaths. However, evolving variants of the virus appear to be more transmissive and vaccine efficacy toward them is waning. As a result, SARS-CoV-2 will continue to have a deadly impact on public health into the foreseeable future. One strategy to bypass the continuing problem of newer variants is to target host proteins required for viral replication. We have used this host-targeted antiviral (HTA) strategy that targets DDX3X (DDX3), a host DEAD-box RNA helicase that is usurped by SARS-CoV-2 for virus production. We demonstrated that targeting DDX3 with RK-33, a small molecule inhibitor, reduced the viral load in four isolates of SARS-CoV-2 (Lineage A, and Lineage B Alpha, Beta, and Delta variants) by one to three log orders in Calu-3 cells. Furthermore, proteomics and RNA-seq analyses indicated that most SARS-CoV-2 genes were downregulated by RK-33 treatment. Also, we show that the use of RK-33 decreases TMPRSS2 expression, which may be due to DDX3s ability to unwind G-quadraplex structures present in the TMPRSS2 promoter. The data presented support the use of RK-33 as an HTA strategy to control SARS-CoV-2 infection, irrespective of its mutational status, in humans.
Language	English
Publishing date	2022-08-25
Publishing country	Switzerland
Document type	Journal Article
ZDB-ID	2587354-4
ISSN	1664-302X
ISSN	1664-302X
DOI	10.3389/fmicb.2022.959577
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Article: RK-33, a small molecule inhibitor of host RNA helicase DDX3, suppresses multiple variants of SARS-CoV-2.

Vesuna, Farhad / Akhrymuk, Ivan / Smith, Amy / Winnard, Paul T / Lin, Shih-Chao / Scharpf, Robert / Kehn-Hall, Kylene / Raman, Venu

bioRxiv : the preprint server for biology

2022

Abstract	SARS-CoV-2, the virus behind the deadly COVID-19 pandemic, continues to spread globally even as vaccine strategies are proving effective in preventing hospitalizations and deaths. However, evolving variants of the virus appear to be more transmissive and vaccine efficacy towards them is waning. As a result, SARS-CoV-2 will continue to have a deadly impact on public health into the foreseeable future. One strategy to bypass the continuing problem of newer variants is to target host proteins required for viral replication. We have used this host-targeted antiviral (HTA) strategy that targets DDX3, a host DEAD-box RNA helicase that is usurped by SARS-CoV-2 for virus production. We demonstrated that targeting DDX3 with RK-33, a small molecule inhibitor, reduced the viral load in four isolates of SARS-CoV-2 (Lineage A, and Lineage B Alpha, Beta, and Delta variants) by one to three log orders in Calu-3 cells. Furthermore, proteomics and RNA-seq analyses indicated that most SARS-CoV-2 genes were downregulated by RK-33 treatment. Also, we show that the use of RK-33 decreases TMPRSS2 expression, which may be due to DDX3s ability to unwind G-quadraplex structures present in the TMPRSS2 promoter. The data presented supports the use of RK-33 as an HTA strategy to control SARS-CoV-2 infection, irrespective of its mutational status, in humans.
Language	English
Publishing date	2022-03-01
Publishing country	United States
Document type	Preprint
DOI	10.1101/2022.02.28.482334
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Article ; Online: Novel Mutations in nsP2 Abolish Chikungunya Virus-Induced Transcriptional Shutoff and Make the Virus Less Cytopathic without Affecting Its Replication Rates.

Akhrymuk, Ivan / Lukash, Tetyana / Frolov, Ilya / Frolova, Elena I

Journal of virology

2019 Volume 93, Issue 4

Abstract: Alphavirus infections are characterized by global inhibition of cellular transcription and rapid induction of a cytopathic effect (CPE) in cells of vertebrate origin. Transcriptional shutoff impedes the cellular response to alphavirus replication and ... ...

Abstract	Alphavirus infections are characterized by global inhibition of cellular transcription and rapid induction of a cytopathic effect (CPE) in cells of vertebrate origin. Transcriptional shutoff impedes the cellular response to alphavirus replication and prevents establishment of an antiviral state. Chikungunya virus (CHIKV) is a highly pathogenic alphavirus representative, and its nonstructural protein 2 (nsP2) plays critical roles in both inhibition of transcription and CPE development. Previously, we have identified a small peptide in Sindbis virus (SINV) nsP2 (VLoop) that determined the protein's transcriptional inhibition function. It is located in the surface-exposed loop of the carboxy-terminal domain of nsP2 and exhibits high variability between members of different alphavirus serocomplexes. In this study, we found that SINV-specific mutations could not be directly applied to CHIKV. However, by using a new selection approach, we identified a variety of new VLoop variants that made CHIKV and its replicons incapable of inhibiting cellular transcription and dramatically less cytopathic. Importantly, the mutations had no negative effect on RNA and viral replication rates. In contrast to parental CHIKV, the developed VLoop mutants were unable to block induction of type I interferon. Consequently, they were cleared from interferon (IFN)-competent cells without CPE development. Alternatively, in murine cells that have defects in type I IFN production or signaling, the VLoop mutants established persistent, noncytopathic replication. The mutations in nsP2 VLoop may be used for development of new vaccine candidates against alphavirus infections and vectors for expression of heterologous proteins.
MeSH term(s)	Animals ; Antiviral Agents ; Cell Line ; Chikungunya Fever/genetics ; Chikungunya Fever/metabolism ; Chikungunya virus/genetics ; Chikungunya virus/metabolism ; Chikungunya virus/physiology ; Cytopathogenic Effect, Viral/genetics ; DNA Viruses/genetics ; Humans ; Interferon Type I/genetics ; Mice ; Mutation ; NIH 3T3 Cells ; RNA, Viral/metabolism ; Replicon ; Signal Transduction ; Sindbis Virus/genetics ; Sindbis Virus/physiology ; Viral Nonstructural Proteins/genetics ; Viral Nonstructural Proteins/metabolism ; Virus Replication/genetics
Chemical Substances	Antiviral Agents ; Interferon Type I ; RNA, Viral ; Viral Nonstructural Proteins
Language	English
Publishing date	2019-02-05
Publishing country	United States
Document type	Journal Article ; Research Support, N.I.H., Extramural
ZDB-ID	80174-4
ISSN	1098-5514 ; 0022-538X
ISSN (online)	1098-5514
ISSN	0022-538X
DOI	10.1128/JVI.02062-18
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Article ; Online: Bioprospecting the American Alligator Peptidome for antiviral peptides against Venezuelan equine encephalitis virus.

Carfagno, Amy / Lin, Shih-Chao / Chafran, Liana / Akhrymuk, Ivan / Callahan, Victoria / Po, Marynet / Zhu, Yaling / Altalhi, Amaal / Durkin, David P / Russo, Paul / Vliet, Kent A / Webb-Robertson, Bobbie-Jo / Kehn-Hall, Kylene / Bishop, Barney

Proteomics

2023 Volume 23, Issue 5, Page(s) e2200237

Abstract: The innate immune protection provided by cationic antimicrobial peptides (CAMPs) has been shown to extend to antiviral activity, with putative mechanisms of action including direct interaction with host cells or pathogen membranes. The lack of ... ...

Abstract	The innate immune protection provided by cationic antimicrobial peptides (CAMPs) has been shown to extend to antiviral activity, with putative mechanisms of action including direct interaction with host cells or pathogen membranes. The lack of therapeutics available for the treatment of viruses such as Venezuelan equine encephalitis virus (VEEV) underscores the urgency of novel strategies for antiviral discovery. American alligator plasma has been shown to exhibit strong in vitro antibacterial activity, and functionalized hydrogel particles have been successfully employed for the identification of specific CAMPs from alligator plasma. Here, a novel bait strategy in which particles were encapsulated in membranes from either healthy or VEEV-infected cells was implemented to identify peptides preferentially targeting infected cells for subsequent evaluation of antiviral activity. Statistical analysis of peptide identification results was used to select five candidate peptides for testing, of which one exhibited a dose-dependent inhibition of VEEV and also significantly inhibited infectious titers. Results suggest our bioprospecting strategy provides a versatile platform that may be adapted for antiviral peptide identification from complex biological samples.
MeSH term(s)	Animals ; Horses ; Encephalitis Virus, Venezuelan Equine/physiology ; Antiviral Agents/pharmacology ; Antiviral Agents/therapeutic use ; Encephalomyelitis, Venezuelan Equine/drug therapy ; Encephalomyelitis, Venezuelan Equine/prevention & control ; Alligators and Crocodiles ; Bioprospecting ; Virus Replication ; Peptides
Chemical Substances	Antiviral Agents ; Peptides
Language	English
Publishing date	2023-01-03
Publishing country	Germany
Document type	Journal Article ; Research Support, U.S. Gov't, Non-P.H.S.
ZDB-ID	2032093-0
ISSN	1615-9861 ; 1615-9853
ISSN (online)	1615-9861
ISSN	1615-9853
DOI	10.1002/pmic.202200237
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Zs.A 5386: 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)
Zs.A 1868: Show issues			Location: Je nach Verfügbarkeit (siehe Angabe bei Bestand) bis Jg. 1994: Bestellungen von Artikeln über das Online-Bestellformular Jg. 1995 - 2021: Lesesall (1.OG) ab Jg. 2022: Lesesaal (EG)

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Article: Proteomic Discovery of VEEV E2-Host Partner Interactions Identifies GRP78 Inhibitor HA15 as a Potential Therapeutic for Alphavirus Infections.

Barrera, Michael D / Callahan, Victoria / Akhrymuk, Ivan / Bhalla, Nishank / Zhou, Weidong / Campbell, Catherine / Narayanan, Aarthi / Kehn-Hall, Kylene

Pathogens (Basel, Switzerland)

2021 Volume 10, Issue 3

Abstract: Alphaviruses are a genus of ... ...

Abstract	Alphaviruses are a genus of the
Language	English
Publishing date	2021-03-02
Publishing country	Switzerland
Document type	Journal Article
ZDB-ID	2695572-6
ISSN	2076-0817
ISSN	2076-0817
DOI	10.3390/pathogens10030283
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Article ; Online: Atractylodin Suppresses TGF-β-Mediated Epithelial-Mesenchymal Transition in Alveolar Epithelial Cells and Attenuates Bleomycin-Induced Pulmonary Fibrosis in Mice.

Chang, Kai-Wei / Zhang, Xiang / Lin, Shih-Chao / Lin, Yu-Chao / Li, Chia-Hsiang / Akhrymuk, Ivan / Lin, Sheng-Hao / Lin, Chi-Chien

International journal of molecular sciences

2021 Volume 22, Issue 20

Abstract: Idiopathic pulmonary fibrosis (IPF) is characterized by fibrotic change in alveolar epithelial cells and leads to the irreversible deterioration of pulmonary function. Transforming growth factor-beta 1 (TGF-β1)-induced epithelial-mesenchymal transition ( ... ...

Abstract	Idiopathic pulmonary fibrosis (IPF) is characterized by fibrotic change in alveolar epithelial cells and leads to the irreversible deterioration of pulmonary function. Transforming growth factor-beta 1 (TGF-β1)-induced epithelial-mesenchymal transition (EMT) in type 2 lung epithelial cells contributes to excessive collagen deposition and plays an important role in IPF. Atractylodin (ATL) is a kind of herbal medicine that has been proven to protect intestinal inflammation and attenuate acute lung injury. Our study aimed to determine whether EMT played a crucial role in the pathogenesis of pulmonary fibrosis and whether EMT can be utilized as a therapeutic target by ATL treatment to mitigate IPF. To address this topic, we took two steps to investigate: 1. Utilization of anin vitro EMT model by treating alveolar epithelial cells (A549 cells) with TGF-β1 followed by ATL treatment for elucidating the underlying pathways, including Smad2/3 hyperphosphorylation, mitogen-activated protein kinase (MAPK) pathway overexpression, Snail and Slug upregulation, and loss of E-cadherin. Utilization of an in vivo lung injury model by treating bleomycin on mice followed by ATL treatment to demonstrate the therapeutic effectiveness, such as, less collagen deposition and lower E-cadherin expression. In conclusion, ATL attenuates TGF-β1-induced EMT in A549 cells and bleomycin-induced pulmonary fibrosis in mice.
MeSH term(s)	A549 Cells ; Alveolar Epithelial Cells/drug effects ; Alveolar Epithelial Cells/physiology ; Animals ; Bleomycin/adverse effects ; Down-Regulation/drug effects ; Down-Regulation/genetics ; Epithelial-Mesenchymal Transition/drug effects ; Epithelial-Mesenchymal Transition/genetics ; Furans/pharmacology ; Furans/therapeutic use ; Humans ; Idiopathic Pulmonary Fibrosis/chemically induced ; Idiopathic Pulmonary Fibrosis/genetics ; Idiopathic Pulmonary Fibrosis/pathology ; Idiopathic Pulmonary Fibrosis/prevention & control ; Male ; Mice ; Mice, Inbred C57BL ; Signal Transduction/drug effects ; Signal Transduction/genetics ; Transforming Growth Factor beta/genetics ; Transforming Growth Factor beta/physiology
Chemical Substances	Furans ; Transforming Growth Factor beta ; Bleomycin (11056-06-7) ; atractylodin (55290-63-6)
Language	English
Publishing date	2021-10-15
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/ijms222011152
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Article ; Online: Both RIG-I and MDA5 detect alphavirus replication in concentration-dependent mode.

Akhrymuk, Ivan / Frolov, Ilya / Frolova, Elena I

Virology

2016 Volume 487, Page(s) 230–241

Abstract: Alphaviruses are a family of positive-strand RNA viruses that circulate on all continents between mosquito vectors and vertebrate hosts. Despite a significant public health threat, their biology is not sufficiently investigated, and the mechanisms of ... ...

Abstract	Alphaviruses are a family of positive-strand RNA viruses that circulate on all continents between mosquito vectors and vertebrate hosts. Despite a significant public health threat, their biology is not sufficiently investigated, and the mechanisms of alphavirus replication and virus-host interaction are insufficiently understood. In this study, we have applied a variety of experimental systems to further understand the mechanism by which infected cells detect replicating alphaviruses. Our new data strongly suggest that activation of the antiviral response by alphavirus-infected cells is determined by the integrity of viral genes encoding proteins with nuclear functions, and by the presence of two cellular pattern recognition receptors (PRRs), RIG-I and MDA5. No type I IFN response is induced in their absence. The presence of either of these PRRs is sufficient for detecting virus replication. However, type I IFN activation in response to pathogenic alphaviruses depends on the basal levels of RIG-I or MDA5.
MeSH term(s)	3T3 Cells ; Alphavirus/genetics ; Alphavirus/growth & development ; Alphavirus/immunology ; Animals ; Cell Line ; Cricetinae ; DEAD Box Protein 58 ; DEAD-box RNA Helicases/genetics ; DEAD-box RNA Helicases/metabolism ; Gene Knock-In Techniques ; Gene Knockdown Techniques ; Immunity, Innate/immunology ; Interferon-Induced Helicase, IFIH1 ; Interferon-beta/immunology ; Mice ; Receptors, Pattern Recognition/immunology ; Virus Replication
Chemical Substances	Receptors, Pattern Recognition ; Interferon-beta (77238-31-4) ; Ddx58 protein, mouse (EC 3.6.1.-) ; Ifih1 protein, mouse (EC 3.6.1.-) ; DEAD Box Protein 58 (EC 3.6.4.13) ; DEAD-box RNA Helicases (EC 3.6.4.13) ; Interferon-Induced Helicase, IFIH1 (EC 3.6.4.13)
Language	English
Publishing date	2016-01
Publishing country	United States
Document type	Journal Article ; Research Support, N.I.H., Extramural
ZDB-ID	200425-2
ISSN	1096-0341 ; 0042-6822
ISSN (online)	1096-0341
ISSN	0042-6822
DOI	10.1016/j.virol.2015.09.023
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