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Article ; Online: MMR Vaccine and COVID-19: Measles Protein Homology May Contribute to Cross-Reactivity or to Complement Activation Protection.

Marakasova, Ekaterina / Baranova, Ancha

2021 Volume 12, Issue 1

MeSH term(s)	COVID-19 ; Complement Activation ; Humans ; Measles/prevention & control ; Measles-Mumps-Rubella Vaccine ; Mumps ; Rubella ; SARS-CoV-2
Chemical Substances	Measles-Mumps-Rubella Vaccine
Language	English
Publishing date	2021-02-02
Publishing country	United States
Document type	Letter ; Comment
ZDB-ID	2557172-2
ISSN	2150-7511 ; 2161-2129
ISSN (online)	2150-7511
ISSN	2161-2129
DOI	10.1128/mBio.03447-20
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Article ; Online: Proteome Wide Profiling of

Marakasova, Ekaterina / Ii, Alexandra / Nelson, Kristina T / van Hoek, Monique L

Journal of proteome research

2020 Volume 19, Issue 4, Page(s) 1409–1422

Abstract: Francisella ... ...

Abstract	Francisella tularensis
MeSH term(s)	Acetylation ; Chitinases ; Francisella ; Lysine ; Protein Processing, Post-Translational ; Proteome/genetics ; Proteome/metabolism
Chemical Substances	Proteome ; Chitinases (EC 3.2.1.14) ; Lysine (K3Z4F929H6)
Language	English
Publishing date	2020-03-04
Publishing country	United States
Document type	Journal Article ; Research Support, Non-U.S. Gov't
ZDB-ID	2078618-9
ISSN	1535-3907 ; 1535-3893
ISSN (online)	1535-3907
ISSN	1535-3893
DOI	10.1021/acs.jproteome.9b00512
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Article ; Online: Characterization of protein unable to bind von Willebrand factor in recombinant factor VIII products.

Chun, Haarin / Pettersson, John R / Shestopal, Svetlana A / Wu, Wells W / Marakasova, Ekaterina S / Olivares, Philip / Surov, Stepan S / Ovanesov, Mikhail V / Shen, Rong-Fong / Sarafanov, Andrey G

Journal of thrombosis and haemostasis : JTH

2021 Volume 19, Issue 4, Page(s) 954–966

Abstract: Background: Therapeutic products with coagulation factor VIII (FVIII) have a wide range of specific activities, implying presence of protein with altered structure. Previous studies showed that recombinant FVIII products (rFVIII) contain a fraction ( ... ...

Abstract	Background: Therapeutic products with coagulation factor VIII (FVIII) have a wide range of specific activities, implying presence of protein with altered structure. Previous studies showed that recombinant FVIII products (rFVIII) contain a fraction (FVIII Objective: To isolate and characterize the FVIII Methods: Protein fractions unable (FVIII Results and conclusions: A robust IVAC methodology was developed and applied for analysis of 10 rFVIII products marketed in the United States. FVIII
MeSH term(s)	Animals ; Blood Coagulation Tests ; Factor VIII ; Hemophilia A/drug therapy ; Hemostatics ; Mice ; von Willebrand Factor
Chemical Substances	Hemostatics ; von Willebrand Factor ; Factor VIII (9001-27-8)
Language	English
Publishing date	2021-02-24
Publishing country	England
Document type	Journal Article ; Research Support, U.S. Gov't, P.H.S.
ZDB-ID	2112661-6
ISSN	1538-7836 ; 1538-7933
ISSN (online)	1538-7836
ISSN	1538-7933
DOI	10.1111/jth.15257
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Article ; Online: Characterization of interaction between blood coagulation factor VIII and LRP1 suggests dynamic binding by alternating complex contacts.

Chun, Haarin / Kurasawa, James H / Olivares, Philip / Marakasova, Ekaterina S / Shestopal, Svetlana A / Hassink, Gabriela U / Karnaukhova, Elena / Migliorini, Mary / Obi, Juliet O / Smith, Ally K / Wintrode, Patrick L / Durai, Prasannavenkatesh / Park, Keunwan / Deredge, Daniel / Strickland, Dudley K / Sarafanov, Andrey G

Journal of thrombosis and haemostasis : JTH

2022 Volume 20, Issue 10, Page(s) 2255–2269

Abstract: Background: Deficiency in blood coagulation factor VIII (FVIII) results in life-threating bleeding (hemophilia A) treated by infusions of FVIII concentrates. To improve disease treatment, FVIII has been modified to increase its plasma half-life, which ... ...

Abstract	Background: Deficiency in blood coagulation factor VIII (FVIII) results in life-threating bleeding (hemophilia A) treated by infusions of FVIII concentrates. To improve disease treatment, FVIII has been modified to increase its plasma half-life, which requires understanding mechanisms of FVIII catabolism. An important catabolic actor is hepatic low density lipoprotein receptor-related protein 1 (LRP1), which also regulates many other clinically significant processes. Previous studies showed complexity of FVIII site for binding LRP1. Objectives: To characterize binding sites between FVIII and LRP1 and suggest a model of the interaction. Methods: A series of recombinant ligand-binding complement-type repeat (CR) fragments of LRP1 including mutated variants was generated in a baculovirus system and tested for FVIII interaction using surface plasmon resonance, tissue culture model, hydrogen-deuterium exchange mass spectrometry, and in silico. Results: Multiple CR doublets within LRP1 clusters II and IV were identified as alternative FVIII-binding sites. These interactions follow the canonical binding mode providing major binding energy, and additional weak interactions are contributed by adjacent CR domains. A representative CR doublet was shown to have multiple contact sites on FVIII. Conclusions: FVIII and LRP1 interact via formation of multiple complex contacts involving both canonical and non-canonical binding combinations. We propose that FVIII-LRP1 interaction occurs via switching such alternative binding combinations in a dynamic mode, and that this mechanism is relevant to other ligand interactions of the low-density lipoprotein receptor family members including LRP1.
MeSH term(s)	Binding Sites ; Deuterium ; Factor VIII/metabolism ; Humans ; Ligands ; Lipoproteins, LDL/metabolism ; Low Density Lipoprotein Receptor-Related Protein-1/metabolism ; Protein Binding ; Receptors, LDL/genetics ; Receptors, LDL/metabolism
Chemical Substances	LRP1 protein, human ; Ligands ; Lipoproteins, LDL ; Low Density Lipoprotein Receptor-Related Protein-1 ; Receptors, LDL ; Factor VIII (9001-27-8) ; Deuterium (AR09D82C7G)
Language	English
Publishing date	2022-08-04
Publishing country	England
Document type	Journal Article ; Research Support, N.I.H., Extramural ; Research Support, U.S. Gov't, Non-P.H.S. ; Research Support, Non-U.S. Gov't
ZDB-ID	2112661-6
ISSN	1538-7836 ; 1538-7933
ISSN (online)	1538-7836
ISSN	1538-7933
DOI	10.1111/jth.15817
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Article: Prenylation of viral proteins by enzymes of the host: Virusâdriven rationale for therapy with statins and FT/GGT1 inhibitors

Marakasova, Ekaterina S / Ancha Baranova / Birgit Eisenhaber / Frank Eisenhaber / Sebastian MaurerâStroh

BioEssays. 2017 Oct., v. 39, no. 10

2017

Abstract: Intracellular bacteria were recently shown to employ eukaryotic prenylation system for modifying activity and ensuring proper intracellular localization of their own proteins. Following the same logic, the proteins of viruses may also serve as ... ...

Abstract	Intracellular bacteria were recently shown to employ eukaryotic prenylation system for modifying activity and ensuring proper intracellular localization of their own proteins. Following the same logic, the proteins of viruses may also serve as prenylation substrates. Using extensively validated highâconfidence prenylation predictions by PrePS with a cutâoff for experimentally confirmed farnesylation of hepatitis delta virus antigen, we compiled in silico evidence for several new prenylation candidates, including IRL9 (CMV) and few other proteins encoded by Herpesviridae, Nef (HIVâ1), E1A (human adenovirus 1), NS5A (HCV), PB2 (influenza), HN (human parainfluenza virus 3), L83L (African swine fever), MC155R (molluscum contagiosum virus), other Poxviridae proteins, and some bacteriophages of human associated bacteria. If confirmed experimentally, these findings may aid in dissection of molecular functions of uncharacterized viral proteins and provide a novel rationale for statin and FT/GGT1âbased inhibition of viral infections. Prenylation of bacteriophage proteins may aid in moderation of microbial infections.
Keywords	African swine fever ; bacteria ; bacteriophages ; enzymes ; Hepatitis delta virus ; Herpesviridae ; Human adenovirus C ; Human immunodeficiency virus 1 ; Human parainfluenza virus 3 ; humans ; influenza ; Molluscum contagiosum virus ; prediction ; therapeutics ; viral antigens ; viral proteins
Language	English
Dates of publication	2017-10
Size	p. .
Publishing place	John Wiley & Sons, Ltd
Document type	Article
Note	REVIEW
ZDB-ID	50140-2
ISSN	1521-1878 ; 0265-9247
ISSN (online)	1521-1878
ISSN	0265-9247
DOI	10.1002/bies.201700014
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Article ; Online: Molecular chaperone RAP interacts with LRP1 in a dynamic bivalent mode and enhances folding of ligand-binding regions of other LDLR family receptors.

Marakasova, Ekaterina / Olivares, Philip / Karnaukhova, Elena / Chun, Haarin / Hernandez, Nancy E / Kurasawa, James H / Hassink, Gabriela U / Shestopal, Svetlana A / Strickland, Dudley K / Sarafanov, Andrey G

The Journal of biological chemistry

2021 Volume 297, Issue 1, Page(s) 100842

Abstract: The low-density lipoprotein receptor (LDLR) family of receptors are cell-surface receptors that internalize numerous ligands and play crucial role in various processes, such as lipoprotein metabolism, hemostasis, fetal development, etc. Previously, ... ...

Abstract	The low-density lipoprotein receptor (LDLR) family of receptors are cell-surface receptors that internalize numerous ligands and play crucial role in various processes, such as lipoprotein metabolism, hemostasis, fetal development, etc. Previously, receptor-associated protein (RAP) was described as a molecular chaperone for LDLR-related protein 1 (LRP1), a prominent member of the LDLR family. We aimed to verify this role of RAP for LRP1 and two other LDLR family receptors, LDLR and vLDLR, and to investigate the mechanisms of respective interactions using a cell culture model system, purified system, and in silico modelling. Upon coexpression of RAP with clusters of the ligand-binding complement repeats (CRs) of the receptors in secreted form in insect cells culture, the isolated proteins had increased yield, enhanced folding, and improved binding properties compared with proteins expressed without RAP, as determined by circular dichroism and surface plasmon resonance. Within LRP1 CR-clusters II and IV, we identified multiple sites comprised of adjacent CR doublets, which provide alternative bivalent binding combinations with specific pairs of lysines on RAP. Mutational analysis of these lysines within each of isolated RAP D1/D2 and D3 domains having high affinity to LRP1 and of conserved tryptophans on selected CR-doublets of LRP1, as well as in silico docking of a model LRP1 CR-triplet with RAP, indicated a universal role for these residues in interaction of RAP and LRP1. Consequently, we propose a new model of RAP interaction with LDLR family receptors based on switching of the bivalent contacts between molecules over time in a dynamic mode.
MeSH term(s)	DNA Mutational Analysis ; Humans ; LDL-Receptor Related Protein-Associated Protein/metabolism ; Ligands ; Low Density Lipoprotein Receptor-Related Protein-1/chemistry ; Low Density Lipoprotein Receptor-Related Protein-1/metabolism ; Molecular Docking Simulation ; Protein Binding ; Protein Folding ; Receptors, LDL/metabolism ; Repetitive Sequences, Amino Acid
Chemical Substances	LDL-Receptor Related Protein-Associated Protein ; Ligands ; Low Density Lipoprotein Receptor-Related Protein-1 ; Receptors, LDL
Language	English
Publishing date	2021-05-29
Publishing country	United States
Document type	Journal Article ; Research Support, Non-U.S. Gov't
ZDB-ID	2997-x
ISSN	1083-351X ; 0021-9258
ISSN (online)	1083-351X
ISSN	0021-9258
DOI	10.1016/j.jbc.2021.100842
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Article ; Online: Prenylation of viral proteins by enzymes of the host: Virus-driven rationale for therapy with statins and FT/GGT1 inhibitors.

Marakasova, Ekaterina S / Eisenhaber, Birgit / Maurer-Stroh, Sebastian / Eisenhaber, Frank / Baranova, Ancha

BioEssays : news and reviews in molecular, cellular and developmental biology

2017 Volume 39, Issue 10

Abstract	Intracellular bacteria were recently shown to employ eukaryotic prenylation system for modifying activity and ensuring proper intracellular localization of their own proteins. Following the same logic, the proteins of viruses may also serve as prenylation substrates. Using extensively validated high-confidence prenylation predictions by PrePS with a cut-off for experimentally confirmed farnesylation of hepatitis delta virus antigen, we compiled in silico evidence for several new prenylation candidates, including IRL9 (CMV) and few other proteins encoded by Herpesviridae, Nef (HIV-1), E1A (human adenovirus 1), NS5A (HCV), PB2 (influenza), HN (human parainfluenza virus 3), L83L (African swine fever), MC155R (molluscum contagiosum virus), other Poxviridae proteins, and some bacteriophages of human associated bacteria. If confirmed experimentally, these findings may aid in dissection of molecular functions of uncharacterized viral proteins and provide a novel rationale for statin and FT/GGT1-based inhibition of viral infections. Prenylation of bacteriophage proteins may aid in moderation of microbial infections.
MeSH term(s)	Adenoviridae/metabolism ; Bacteriophages/metabolism ; Herpesviridae/metabolism ; Humans ; Prenylation ; Viral Proteins/metabolism
Chemical Substances	Viral Proteins
Language	English
Publishing date	2017-09-08
Publishing country	United States
Document type	Journal Article ; Review
ZDB-ID	50140-2
ISSN	1521-1878 ; 0265-9247
ISSN (online)	1521-1878
ISSN	0265-9247
DOI	10.1002/bies.201700014
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Article ; Online: Chitinases are negative regulators of Francisella novicida biofilms.

Chung, Myung-Chul / Dean, Scott / Marakasova, Ekaterina S / Nwabueze, Albert O / van Hoek, Monique L

PloS one

2014 Volume 9, Issue 3, Page(s) e93119

Abstract: Biofilms, multicellular communities of bacteria, may be an environmental survival and transmission mechanism of Francisella tularensis. Chitinases of F. tularensis ssp. novicida (Fn) have been suggested to regulate biofilm formation on chitin surfaces. ... ...

Abstract	Biofilms, multicellular communities of bacteria, may be an environmental survival and transmission mechanism of Francisella tularensis. Chitinases of F. tularensis ssp. novicida (Fn) have been suggested to regulate biofilm formation on chitin surfaces. However, the underlying mechanisms of how chitinases may regulate biofilm formation are not fully determined. We hypothesized that Fn chitinase modulates bacterial surface properties resulting in the alteration of biofilm formation. We analyzed biofilm formation under diverse conditions using chitinase mutants and their counterpart parental strain. Substratum surface charges affected biofilm formation and initial attachments. Biophysical analysis of bacterial surfaces confirmed that the chi mutants had a net negative-charge. Lectin binding assays suggest that chitinase cleavage of its substrates could have exposed the concanavalin A-binding epitope. Fn biofilm was sensitive to chitinase, proteinase and DNase, suggesting that Fn biofilm contains exopolysaccharides, proteins and extracellular DNA. Exogenous chitinase increased the drug susceptibility of Fn biofilms to gentamicin while decreasing the amount of biofilm. In addition, chitinase modulated bacterial adhesion and invasion of A549 and J774A.1 cells as well as intracellular bacterial replication. Our results support a key role of the chitinase(s) in biofilm formation through modulation of the bacterial surface properties. Our findings position chitinase as a potential anti-biofilm enzyme in Francisella species.
MeSH term(s)	Anti-Bacterial Agents/pharmacology ; Bacterial Adhesion/drug effects ; Bacterial Adhesion/physiology ; Bacterial Proteins/genetics ; Bacterial Proteins/metabolism ; Biofilms/drug effects ; Biofilms/growth & development ; Cell Line ; Chitinases/genetics ; Chitinases/metabolism ; Francisella/physiology ; Gentamicins/pharmacology ; Humans ; Mutation
Chemical Substances	Anti-Bacterial Agents ; Bacterial Proteins ; Gentamicins ; Chitinases (EC 3.2.1.14)
Language	English
Publishing date	2014-03-24
Publishing country	United States
Document type	Journal Article ; Research Support, Non-U.S. Gov't ; Research Support, U.S. Gov't, Non-P.H.S.
ISSN	1932-6203
ISSN (online)	1932-6203
DOI	10.1371/journal.pone.0093119
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Article ; Online: Protein partners of KCTD proteins provide insights about their functional roles in cell differentiation and vertebrate development.

Skoblov, Mikhail / Marakhonov, Andrey / Marakasova, Ekaterina / Guskova, Anna / Chandhoke, Vikas / Birerdinc, Aybike / Baranova, Ancha

BioEssays : news and reviews in molecular, cellular and developmental biology

2013 Volume 35, Issue 7, Page(s) 586–596

Abstract: The KCTD family includes tetramerization (T1) domain containing proteins with diverse biological effects. We identified a novel member of the KCTD family, BTBD10. A comprehensive analysis of protein-protein interactions (PPIs) allowed us to put forth a ... ...

Abstract	The KCTD family includes tetramerization (T1) domain containing proteins with diverse biological effects. We identified a novel member of the KCTD family, BTBD10. A comprehensive analysis of protein-protein interactions (PPIs) allowed us to put forth a number of testable hypotheses concerning the biological functions for individual KCTD proteins. In particular, we predict that KCTD20 participates in the AKT-mTOR-p70 S6k signaling cascade, KCTD5 plays a role in cytokinesis in a NEK6 and ch-TOG-dependent manner, KCTD10 regulates the RhoA/RhoB pathway. Developmental regulator KCTD15 represses AP-2α and contributes to energy homeostasis by suppressing early adipogenesis. TNFAIP1-like KCTD proteins may participate in post-replication DNA repair through PCNA ubiquitination. KCTD12 may suppress the proliferation of gastrointestinal cells through interference with GABAb signaling. KCTD9 deserves experimental attention as the only eukaryotic protein with a DNA-like pentapeptide repeat domain. The value of manual curation of PPIs and analysis of existing high-throughput data should not be underestimated.
MeSH term(s)	Animals ; Cell Differentiation/genetics ; DNA Replication ; Gene Expression Regulation, Developmental ; Humans ; NIMA-Related Kinases ; Nuclear Proteins/genetics ; Nuclear Proteins/physiology ; Potassium Channels/genetics ; Potassium Channels/physiology ; Potassium Channels, Voltage-Gated/genetics ; Potassium Channels, Voltage-Gated/physiology ; Proliferating Cell Nuclear Antigen/genetics ; Proliferating Cell Nuclear Antigen/physiology ; Protein-Serine-Threonine Kinases/genetics ; Protein-Serine-Threonine Kinases/physiology ; Repressor Proteins/genetics ; Repressor Proteins/physiology ; Ribosomal Protein S6 Kinases, 70-kDa/genetics ; Ribosomal Protein S6 Kinases, 70-kDa/physiology ; Signal Transduction ; TOR Serine-Threonine Kinases/genetics ; TOR Serine-Threonine Kinases/physiology ; Ubiquitination ; Vertebrates/genetics
Chemical Substances	BTBD10 protein, human ; KCTD10 protein, human ; KCTD15 protein, human ; KCTD5 protein, human ; KCTD9 protein, human ; Nuclear Proteins ; Potassium Channels ; Potassium Channels, Voltage-Gated ; Proliferating Cell Nuclear Antigen ; Repressor Proteins ; MTOR protein, human (EC 2.7.1.1) ; TOR Serine-Threonine Kinases (EC 2.7.1.1) ; NEK6 protein, human (EC 2.7.11.1) ; NIMA-Related Kinases (EC 2.7.11.1) ; Protein-Serine-Threonine Kinases (EC 2.7.11.1) ; Ribosomal Protein S6 Kinases, 70-kDa (EC 2.7.11.1)
Language	English
Publishing date	2013-07
Publishing country	United States
Document type	Journal Article
ZDB-ID	50140-2
ISSN	1521-1878 ; 0265-9247
ISSN (online)	1521-1878
ISSN	0265-9247
DOI	10.1002/bies.201300002
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Article ; Online: Chitinases are negative regulators of Francisella novicida biofilms.

Myung-Chul Chung / Scott Dean / Ekaterina S Marakasova / Albert O Nwabueze / Monique L van Hoek

PLoS ONE, Vol 9, Iss 3, p e

2014 Volume 93119

Abstract	Biofilms, multicellular communities of bacteria, may be an environmental survival and transmission mechanism of Francisella tularensis. Chitinases of F. tularensis ssp. novicida (Fn) have been suggested to regulate biofilm formation on chitin surfaces. However, the underlying mechanisms of how chitinases may regulate biofilm formation are not fully determined. We hypothesized that Fn chitinase modulates bacterial surface properties resulting in the alteration of biofilm formation. We analyzed biofilm formation under diverse conditions using chitinase mutants and their counterpart parental strain. Substratum surface charges affected biofilm formation and initial attachments. Biophysical analysis of bacterial surfaces confirmed that the chi mutants had a net negative-charge. Lectin binding assays suggest that chitinase cleavage of its substrates could have exposed the concanavalin A-binding epitope. Fn biofilm was sensitive to chitinase, proteinase and DNase, suggesting that Fn biofilm contains exopolysaccharides, proteins and extracellular DNA. Exogenous chitinase increased the drug susceptibility of Fn biofilms to gentamicin while decreasing the amount of biofilm. In addition, chitinase modulated bacterial adhesion and invasion of A549 and J774A.1 cells as well as intracellular bacterial replication. Our results support a key role of the chitinase(s) in biofilm formation through modulation of the bacterial surface properties. Our findings position chitinase as a potential anti-biofilm enzyme in Francisella species.
Keywords	Medicine ; R ; Science ; Q
Subject code	570
Language	English
Publishing date	2014-01-01T00:00:00Z
Publisher	Public Library of Science (PLoS)
Document type	Article ; Online
Database	BASE - Bielefeld Academic Search Engine (life sciences selection)

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