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Article ; Online: Heterologous Expression, Engineering and Characterization of a Novel Laccase of

Aza, Pablo / Molpeceres, Gonzalo / Ruiz-Dueñas, Francisco Javier / Camarero, Susana

2021 Volume 7, Issue 5

Abstract: Agaricomycetes fungi responsible for decay of wood and other lignocellulosic substrates constitute a valuable source of lignin-degrading enzymes. Among these enzymes, laccases (multi-copper oxidases) present remarkable biotechnological potential as ... ...

Abstract	Agaricomycetes fungi responsible for decay of wood and other lignocellulosic substrates constitute a valuable source of lignin-degrading enzymes. Among these enzymes, laccases (multi-copper oxidases) present remarkable biotechnological potential as environmentally friendly biocatalysts able to oxidize a wide range of aromatic compounds using oxygen as the only requirement. Laccases from saprotrophic Agaricales species have been much less studied than laccases from Polyporales, despite the fact that the former fungi are excellent sources of laccases. Here, the gene of a novel laccase of
Language	English
Publishing date	2021-05-04
Publishing country	Switzerland
Document type	Journal Article
ZDB-ID	2784229-0
ISSN	2309-608X ; 2309-608X
ISSN (online)	2309-608X
ISSN	2309-608X
DOI	10.3390/jof7050359
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Article ; Online: Ancestral sequence reconstruction as a tool to study the evolution of wood decaying fungi.

Ayuso-Fernández, Iván / Molpeceres, Gonzalo / Camarero, Susana / Ruiz-Dueñas, Francisco Javier / Martínez, Angel T

Frontiers in fungal biology

2022 Volume 3, Page(s) 1003489

Abstract: The study of evolution is limited by the techniques available to do so. Aside from the use of the fossil record, molecular phylogenetics can provide a detailed characterization of evolutionary histories using genes, genomes and proteins. However, these ... ...

Abstract	The study of evolution is limited by the techniques available to do so. Aside from the use of the fossil record, molecular phylogenetics can provide a detailed characterization of evolutionary histories using genes, genomes and proteins. However, these tools provide scarce biochemical information of the organisms and systems of interest and are therefore very limited when they come to explain protein evolution. In the past decade, this limitation has been overcome by the development of ancestral sequence reconstruction (ASR) methods. ASR allows the subsequent resurrection in the laboratory of inferred proteins from now extinct organisms, becoming an outstanding tool to study enzyme evolution. Here we review the recent advances in ASR methods and their application to study fungal evolution, with special focus on wood-decay fungi as essential organisms in the global carbon cycling.
Language	English
Publishing date	2022-10-14
Publishing country	Switzerland
Document type	Journal Article ; Review
ISSN	2673-6128
ISSN (online)	2673-6128
DOI	10.3389/ffunb.2022.1003489
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Article: Efficacy of Rituximab in CANOMAD: A Systematic Review.

Aguirre, Alex S / Vivanco, Ricardo A / Ortiz, Juan Fernando / Rozen, Valery / InsuastI, Walter E / Fiallos, John / Gallegos, Camila / Villavicencio, Andrea / Salazar, Kevin / Duenas, Francisco / Singla, Ramit

Cureus

2023 Volume 15, Issue 5, Page(s) e39237

Abstract: CANOMAD, characterized by chronic ataxic neuropathy, ophthalmoplegia, immunoglobulin M (IgM) paraprotein, cold agglutinins, and disialosyl antibodies, encompasses a clinical, radiological, and laboratory diagnosis. CANOMAD is a rare condition, with fewer ...

Abstract	CANOMAD, characterized by chronic ataxic neuropathy, ophthalmoplegia, immunoglobulin M (IgM) paraprotein, cold agglutinins, and disialosyl antibodies, encompasses a clinical, radiological, and laboratory diagnosis. CANOMAD is a rare condition, with fewer than 100 cases reported in the literature. The understanding and diagnosis of the disease have improved in the last few years, but the treatment of CANOMAD is mainly unknown, and there is not a clear consensus about it. We conducted a systematic review regarding the efficacy of rituximab in CANOMAD's treatment to investigate the clinical and biological response of CANOMAD in patients treated with rituximab. We used the Preferred Reporting Items for Systematic Reviews and Meta-Analyses (PRISMA) and Meta-Analyses of Observational Studies in Epidemiology (MOOSE) reporting guidelines for this systematic review. To analyze the bias of the study, we used the Joanna Briggs Institute's (JBI) Critical Appraisal Checklist to analyze the bias of the case reports, and we used the Risk of Bias in Non-Randomized Studies of Interventions (ROBINS-I) tool for the observational studies. We only included case reports, case series, and observational studies written in English with patients formally diagnosed with CANOMAD and treated with rituximab. We excluded systematic reviews, literature reviews, and meta-analyses. We investigated the clinical and biological responses of the patients to rituximab. The clinical response was classified as complete recovery (CR), partial response (PR), stable disease (SD), and non-response (NR). We gathered 34 patients. The literature uses a modified Rankin score to define complete improvement (CR), partial response (PR), stable disease (SD), and progression. Clinically, there were three patients with CR, five with PR, 15 with SD, and 11 with progression. The biological response was assessed by measuring the decrease in antibody titers in 27 patients. Among those, six patients had CR, 12 had PR, eight had SD, and one had progression. Among 15 patients with neurological evaluation, 10 had ocular symptoms, and two presented with bulbar symptoms. Seven of the ten patients with ocular symptoms had SD, two had PR, and one had progression. Only 14 patients had a report of demyelinating features. Three had an axonal pattern, six had a demyelinating pattern, and five had a mixed pattern. Among patients with an axonal pattern, three had an SD. Among patients with a demyelinating pattern, three had a PR, two had an SD, and one had progression. Among patients with a mixed pattern, four had SD, and one had progression. We concluded that patients with CR have a shorter disease duration than patients with PR, SD, or progression. In addition, patients with CR had longer follow-ups than the other groups, suggesting that being treated early with rituximab improves the clinical outcome and has a sustained effect. There were no differences in the frequency of ocular and bulbar symptoms among patients with CANOMAD. The axonal pattern is more common in patients with SD, suggesting that axonal and mixed patterns could be markers of a bad prognosis.
Language	English
Publishing date	2023-05-19
Publishing country	United States
Document type	Journal Article ; Review
ZDB-ID	2747273-5
ISSN	2168-8184
ISSN	2168-8184
DOI	10.7759/cureus.39237
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Article: Different fungal peroxidases oxidize nitrophenols at a surface catalytic tryptophan

Linde, Dolores / Ayuso-Fernández, Iván / Martínez, Angel T / Ruiz-Dueñas, Francisco J

Archives of biochemistry and biophysics. 2019 June 15, v. 668

2019

Abstract: Dye-decolorizing peroxidase (DyP) from Auricularia auricula-judae and versatile peroxidase (VP) from Pleurotus eryngii oxidize the three mononitrophenol isomers. Both enzymes have been overexpressed in Escherichia coli and in vitro activated. Despite ... ...

Abstract	Dye-decolorizing peroxidase (DyP) from Auricularia auricula-judae and versatile peroxidase (VP) from Pleurotus eryngii oxidize the three mononitrophenol isomers. Both enzymes have been overexpressed in Escherichia coli and in vitro activated. Despite their very different three-dimensional structures, the nitrophenol oxidation site is located at a solvent-exposed aromatic residue in both DyP (Trp377) and VP (Trp164), as revealed by liquid chromatography coupled to mass spectrometry and kinetic analyses of nitrophenol oxidation by the native enzymes and their tryptophan-less variants (the latter showing 10–60 fold lower catalytic efficiencies).
Keywords	Auricularia auricula ; Escherichia coli ; fungi ; isomers ; liquid chromatography ; mass spectrometry ; nitrophenols ; oxidation ; peroxidase ; Pleurotus eryngii ; tryptophan
Language	English
Dates of publication	2019-0615
Size	p. 23-28.
Publishing place	Elsevier Inc.
Document type	Article
ZDB-ID	523-x
ISSN	1096-0384 ; 0003-9861
ISSN (online)	1096-0384
ISSN	0003-9861
DOI	10.1016/j.abb.2019.05.010
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Article ; Online: Evolutionary convergence in lignin-degrading enzymes.

Ayuso-Fernández, Iván / Ruiz-Dueñas, Francisco J / Martínez, Angel T

Proceedings of the National Academy of Sciences of the United States of America

2018 Volume 115, Issue 25, Page(s) 6428–6433

Abstract: The resurrection of ancestral enzymes of now-extinct organisms (paleogenetics) is a developing field that allows the study of evolutionary hypotheses otherwise impossible to be tested. In the present study, we target fungal peroxidases that play a key ... ...

Abstract	The resurrection of ancestral enzymes of now-extinct organisms (paleogenetics) is a developing field that allows the study of evolutionary hypotheses otherwise impossible to be tested. In the present study, we target fungal peroxidases that play a key role in lignin degradation, an essential process in the carbon cycle and often a limiting step in biobased industries. Ligninolytic peroxidases are secreted by wood-rotting fungi, the origin of which was recently established in the Carboniferous period associated with the appearance of these enzymes. These first peroxidases were not able to degrade lignin directly and used diffusible metal cations to attack its phenolic moiety. The phylogenetic analysis of the peroxidases of Polyporales, the order in which most extant wood-rotting fungi are included, suggests that later in evolution these enzymes would have acquired the ability to degrade nonphenolic lignin using a tryptophanyl radical interacting with the bulky polymer at the surface of the enzyme. Here, we track this powerful strategy for lignin degradation as a phenotypic trait in fungi and show that it is not an isolated event in the evolution of Polyporales. Using ancestral enzyme resurrection, we study the molecular changes that led to the appearance of the same surface oxidation site in two distant peroxidase lineages. By characterization of the resurrected enzymes, we demonstrate convergent evolution at the amino acid level during the evolution of these fungi and track the different changes leading to phylogenetically distant ligninolytic peroxidases from ancestors lacking the ability to degrade nonphenolic lignin.
MeSH term(s)	Biological Evolution ; Carbon Cycle/physiology ; Fungal Proteins/metabolism ; Fungi/metabolism ; Lignin/metabolism ; Oxidation-Reduction ; Peroxidases/metabolism ; Phylogeny ; Polymers/metabolism ; Polyporales/metabolism
Chemical Substances	Fungal Proteins ; Polymers ; Lignin (9005-53-2) ; Peroxidases (EC 1.11.1.-)
Language	English
Publishing date	2018-06-04
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.
ZDB-ID	209104-5
ISSN	1091-6490 ; 0027-8424
ISSN (online)	1091-6490
ISSN	0027-8424
DOI	10.1073/pnas.1802555115
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Article ; Online: Characterization of a Dye-Decolorizing Peroxidase from

de Eugenio, Laura Isabel / Peces-Pérez, Rosa / Linde, Dolores / Prieto, Alicia / Barriuso, Jorge / Ruiz-Dueñas, Francisco Javier / Martínez, María Jesús

Journal of fungi (Basel, Switzerland)

2021 Volume 7, Issue 5

Abstract: A dye-decolorizing peroxidase (DyP) ... ...

Abstract	A dye-decolorizing peroxidase (DyP) from
Language	English
Publishing date	2021-04-22
Publishing country	Switzerland
Document type	Journal Article
ZDB-ID	2784229-0
ISSN	2309-608X ; 2309-608X
ISSN (online)	2309-608X
ISSN	2309-608X
DOI	10.3390/jof7050325
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Article ; Online: Comparing Ligninolytic Capabilities of Bacterial and Fungal Dye-Decolorizing Peroxidases and Class-II Peroxidase-Catalases.

Linde, Dolores / Ayuso-Fernández, Iván / Laloux, Marcos / Aguiar-Cervera, José E / de Lacey, Antonio L / Ruiz-Dueñas, Francisco J / Martínez, Angel T

International journal of molecular sciences

2021 Volume 22, Issue 5

Abstract: We aim to clarify the ligninolytic capabilities of dye-decolorizing peroxidases (DyPs) from bacteria and fungi, compared to fungal lignin peroxidase (LiP) and versatile peroxidase (VP). With this purpose, DyPs ... ...

Abstract	We aim to clarify the ligninolytic capabilities of dye-decolorizing peroxidases (DyPs) from bacteria and fungi, compared to fungal lignin peroxidase (LiP) and versatile peroxidase (VP). With this purpose, DyPs from
MeSH term(s)	Catalase/chemistry ; Coloring Agents/chemistry ; Fungal Proteins/chemistry ; Fungi/enzymology ; Lignin/chemistry ; Peroxidase/chemistry
Chemical Substances	Coloring Agents ; Fungal Proteins ; Lignin (9005-53-2) ; Catalase (EC 1.11.1.6) ; Peroxidase (EC 1.11.1.7)
Language	English
Publishing date	2021-03-05
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/ijms22052629
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Article ; Online: Peroxidase evolution in white-rot fungi follows wood lignin evolution in plants.

Ayuso-Fernández, Iván / Rencoret, Jorge / Gutiérrez, Ana / Ruiz-Dueñas, Francisco Javier / Martínez, Angel T

Proceedings of the National Academy of Sciences of the United States of America

2019 Volume 116, Issue 36, Page(s) 17900–17905

Abstract: A comparison of sequenced Agaricomycotina genomes suggests that efficient degradation of wood lignin was associated with the appearance of secreted peroxidases with a solvent-exposed catalytic tryptophan. This hypothesis is experimentally demonstrated ... ...

Abstract	A comparison of sequenced Agaricomycotina genomes suggests that efficient degradation of wood lignin was associated with the appearance of secreted peroxidases with a solvent-exposed catalytic tryptophan. This hypothesis is experimentally demonstrated here by resurrecting ancestral fungal peroxidases, after sequence reconstruction from genomes of extant white-rot Polyporales, and evaluating their oxidative attack on the lignin polymer by state-of-the-art analytical techniques. Rapid stopped-flow estimation of the transient-state constants for the 2 successive one-electron transfers from lignin to the peroxide-activated enzyme (
MeSH term(s)	Biological Evolution ; Catalysis ; Fungi/enzymology ; Fungi/genetics ; Hydrolysis ; Kinetics ; Lignin/analysis ; Lignin/metabolism ; Oxidation-Reduction ; Peroxidase/genetics ; Peroxidase/metabolism ; Plants/genetics ; Plants/metabolism ; Plants/microbiology ; Wood/analysis ; Wood/metabolism ; Wood/microbiology
Chemical Substances	Lignin (9005-53-2) ; Peroxidase (EC 1.11.1.7)
Language	English
Publishing date	2019-08-19
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.
ZDB-ID	209104-5
ISSN	1091-6490 ; 0027-8424
ISSN (online)	1091-6490
ISSN	0027-8424
DOI	10.1073/pnas.1905040116
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Article ; Online: Different fungal peroxidases oxidize nitrophenols at a surface catalytic tryptophan.

Linde, Dolores / Ayuso-Fernández, Iván / Ruiz-Dueñas, Francisco J / Martínez, Angel T

Archives of biochemistry and biophysics

2019 Volume 668, Page(s) 23–28

Abstract	Dye-decolorizing peroxidase (DyP) from Auricularia auricula-judae and versatile peroxidase (VP) from Pleurotus eryngii oxidize the three mononitrophenol isomers. Both enzymes have been overexpressed in Escherichia coli and in vitro activated. Despite their very different three-dimensional structures, the nitrophenol oxidation site is located at a solvent-exposed aromatic residue in both DyP (Trp377) and VP (Trp164), as revealed by liquid chromatography coupled to mass spectrometry and kinetic analyses of nitrophenol oxidation by the native enzymes and their tryptophan-less variants (the latter showing 10-60 fold lower catalytic efficiencies).
MeSH term(s)	Basidiomycota/enzymology ; Catalytic Domain ; Escherichia coli/genetics ; Fungal Proteins/chemistry ; Fungal Proteins/genetics ; Fungal Proteins/metabolism ; Kinetics ; Mutagenesis, Site-Directed ; Nitrophenols/chemistry ; Nitrophenols/metabolism ; Oxidation-Reduction ; Peroxidases/chemistry ; Peroxidases/genetics ; Peroxidases/metabolism ; Pleurotus/enzymology ; Protein Binding ; Tryptophan/chemistry
Chemical Substances	Fungal Proteins ; Nitrophenols ; Tryptophan (8DUH1N11BX) ; Peroxidases (EC 1.11.1.-)
Language	English
Publishing date	2019-05-13
Publishing country	United States
Document type	Journal Article ; Research Support, Non-U.S. Gov't
ZDB-ID	523-x
ISSN	1096-0384 ; 0003-9861
ISSN (online)	1096-0384
ISSN	0003-9861
DOI	10.1016/j.abb.2019.05.010
Database	MEDical Literature Analysis and Retrieval System OnLINE

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Article: Experimental recreation of the evolution of lignin-degrading enzymes from the Jurassic to date.

Ayuso-Fernández, Iván / Martínez, Angel T / Ruiz-Dueñas, Francisco J

Biotechnology for biofuels

2017 Volume 10, Page(s) 67

Abstract: Background: Floudas et al. (: Results: With this purpose, we analyzed the evolutionary pathway leading to the most efficient lignin-degrading peroxidases characterizing Polyporales species. After sequence reconstruction from 113 genes of ten ... ...

Abstract	Background: Floudas et al. ( Results: With this purpose, we analyzed the evolutionary pathway leading to the most efficient lignin-degrading peroxidases characterizing Polyporales species. After sequence reconstruction from 113 genes of ten sequenced genomes, the main enzyme intermediates were resurrected and characterized. Biochemical changes were analyzed together with predicted sequences and structures, to understand how these enzymes acquired the ability to degrade lignin and how this ability changed with time. The most probable first peroxidase in Polyporales would be a manganese peroxidase (Mn Conclusions: We show how the change in peroxidase catalytic activities meant an evolutionary exploration for more efficient ways of lignin degradation by fungi, a key step for carbon recycling in land ecosystems. The study provides ancestral enzymes with a potential biotechnological interest for the sustainable production of fuels and chemicals in a biomass-based economy.
Language	English
Publishing date	2017-03-16
Publishing country	England
Document type	Journal Article
ZDB-ID	2421351-2
ISSN	1754-6834
ISSN	1754-6834
DOI	10.1186/s13068-017-0744-x
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