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  1. Article ; Online: Prebiotics and Probiotics: Healthy Biotools for Molecular Integrative and Modulation Approaches 2.0.

    Aguilera, Margarita / Daddaoua, Abdelali

    International journal of molecular sciences

    2024  Volume 25, Issue 9

    Abstract: The current version (2 [ ... ]. ...

    Abstract The current version (2 [...].
    MeSH term(s) Probiotics ; Prebiotics ; Humans ; Gastrointestinal Microbiome ; Animals
    Chemical Substances Prebiotics
    Language English
    Publishing date 2024-04-30
    Publishing country Switzerland
    Document type Editorial ; Introductory 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/ijms25094872
    Database MEDical Literature Analysis and Retrieval System OnLINE

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  2. Article ; Online: Prebiotics and Probiotics: Healthy Biotools for Molecular Integrative and Modulation Approaches.

    Aguilera, Margarita / Daddaoua, Abdelali

    International journal of molecular sciences

    2023  Volume 24, Issue 8

    Abstract: The scope of this Special Issue is to highlight and expand our knowledge on the molecular mechanisms of prebiotics and probiotics, as well as to offer a broad overview of current advancements and future directions in this research field [ ... ]. ...

    Abstract The scope of this Special Issue is to highlight and expand our knowledge on the molecular mechanisms of prebiotics and probiotics, as well as to offer a broad overview of current advancements and future directions in this research field [...].
    MeSH term(s) Prebiotics ; Probiotics
    Chemical Substances Prebiotics
    Language English
    Publishing date 2023-04-20
    Publishing country Switzerland
    Document type Editorial ; Introductory 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/ijms24087559
    Database MEDical Literature Analysis and Retrieval System OnLINE

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  3. Article: Corrigendum: A standardized extract of

    Tena-Garitaonaindia, Mireia / Ceacero-Heras, Diego / Montoro, María Del Mar Maldonado / de Medina, Fermín Sánchez / Martínez-Augustin, Olga / Daddaoua, Abdelali

    Frontiers in microbiology

    2023  Volume 14, Page(s) 1183760

    Abstract: This corrects the article DOI: 10.3389/fmicb.2022.814448.]. ...

    Abstract [This corrects the article DOI: 10.3389/fmicb.2022.814448.].
    Language English
    Publishing date 2023-03-28
    Publishing country Switzerland
    Document type Published Erratum
    ZDB-ID 2587354-4
    ISSN 1664-302X
    ISSN 1664-302X
    DOI 10.3389/fmicb.2023.1183760
    Database MEDical Literature Analysis and Retrieval System OnLINE

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  4. Article ; Online: Rio Tinto as a niche for acidophilus enzymes of industrial relevance.

    Daddaoua, Abdelali / Álvarez, Consolación / Oggerin, Monika / Rodriguez, Nuria / Duque, Estrella / Amils, Ricardo / Armengaud, Jean / Segura, Ana / Ramos, Juan Luis

    Microbial biotechnology

    2023  Volume 16, Issue 5, Page(s) 1069–1086

    Abstract: Lignocellulosic residues are amongst the most abundant waste products on Earth. Therefore, there is an increasing interest in the utilization of these residues for bioethanol production and for biorefineries to produce compounds of industrial interest. ... ...

    Abstract Lignocellulosic residues are amongst the most abundant waste products on Earth. Therefore, there is an increasing interest in the utilization of these residues for bioethanol production and for biorefineries to produce compounds of industrial interest. Enzymes that breakdown cellulose and hemicellulose into oligomers and monosaccharides are required in these processes and cellulolytic enzymes with optimum activity at a low pH area are desirable for industrial processes. Here, we explore the fungal biodiversity of Rıo Tinto, the largest acidic ecosystem on Earth, as far as the secretion of cellulolytic enzymes is concerned. Using colorimetric and industrial substrates, we show that a high proportion of the fungi present in this extremophilic environment secrete a wide range of enzymes that are able to hydrolyze cellulose and hemicellulose at acidic pH (4.5-5). Shotgun proteomic analysis of the secretomes of some of these fungi has identified different cellulases and hemicellulolytic enzymes as well as a number of auxiliary enzymes. Supplementation of pre-industrial cocktails from Myceliophtora with Rio Tinto secretomes increased the amount of monosaccharides released from corn stover or sugar cane straw. We conclude that the Rio Tinto fungi display a good variety of hydrolytic enzymes with high industrial potential.
    MeSH term(s) Ecosystem ; Proteomics ; Cellulose/metabolism ; Cellulases/metabolism ; Monosaccharides
    Chemical Substances Cellulose (9004-34-6) ; Cellulases (EC 3.2.1.-) ; Monosaccharides
    Language English
    Publishing date 2023-02-07
    Publishing country United States
    Document type Journal Article ; Research Support, Non-U.S. Gov't
    ZDB-ID 2406063-X
    ISSN 1751-7915 ; 1751-7915
    ISSN (online) 1751-7915
    ISSN 1751-7915
    DOI 10.1111/1751-7915.14192
    Database MEDical Literature Analysis and Retrieval System OnLINE

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  5. Article ; Online: A perspective current and past modes of inhalation therapy.

    Canto Mangana, José / Schilder, Kelsey Aguirre / Bretones-Pedrinaci, José Ignacio / Blesa, Ana Rosa Márquez / de Medina, Fermín Sánchez / Martínez-Augustin, Olga / Daddaoua, Abdelali

    Microbial biotechnology

    2024  Volume 17, Issue 2, Page(s) e14419

    Abstract: Inhalation is the preferred route of delivery for anti-asthma and chronic obstructive pulmonary disease (COPD) drugs. The use of this route has demonstrated efficacy in these and other conditions, it offers rapid onset of action, and is associated with ... ...

    Abstract Inhalation is the preferred route of delivery for anti-asthma and chronic obstructive pulmonary disease (COPD) drugs. The use of this route has demonstrated efficacy in these and other conditions, it offers rapid onset of action, and is associated with minimal systemic exposure, thereby reducing the risk of adverse effects. Therefore, the current brief covers an interesting collection of inhaler action modes, shedding light on their molecular mechanisms and clinical applications for anti-asthma, COPD and antibacterial inhalation therapy. Hence, not only enriches our understanding of inhalation therapy molecular intricacies but also provides a comprehensive overview of the evolving landscape in clinical and antibacterial inhalation therapy. In doing so, it underscores the pivotal role of microbiology and biotechnology in advancing therapeutic approaches that harness the power of inhalation.
    MeSH term(s) Humans ; Administration, Inhalation ; Anti-Bacterial Agents/administration & dosage ; Anti-Bacterial Agents/therapeutic use ; Nebulizers and Vaporizers ; Pulmonary Disease, Chronic Obstructive/drug therapy
    Chemical Substances Anti-Bacterial Agents
    Language English
    Publishing date 2024-02-21
    Publishing country United States
    Document type Journal Article ; Review ; Systematic Review
    ZDB-ID 2406063-X
    ISSN 1751-7915 ; 1751-7915
    ISSN (online) 1751-7915
    ISSN 1751-7915
    DOI 10.1111/1751-7915.14419
    Database MEDical Literature Analysis and Retrieval System OnLINE

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  6. Article ; Online: Characterization of an extremophile bacterial acid phosphatase derived from metagenomics analysis.

    Recio, Maria-Isabel / de la Torre, Jesús / Daddaoua, Abdelali / Udaondo, Zulema / Duque, Estrella / Gavira, José Antonio / López-Sánchez, Carmen / Ramos, Juan L

    Microbial biotechnology

    2024  Volume 17, Issue 4, Page(s) e14404

    Abstract: Acid phosphatases are enzymes that play a crucial role in the hydrolysis of various organophosphorous molecules. A putative acid phosphatase called FS6 was identified using genetic profiles and sequences from different environments. FS6 showed high ... ...

    Abstract Acid phosphatases are enzymes that play a crucial role in the hydrolysis of various organophosphorous molecules. A putative acid phosphatase called FS6 was identified using genetic profiles and sequences from different environments. FS6 showed high sequence similarity to type C acid phosphatases and retained more than 30% of consensus residues in its protein sequence. A histidine-tagged recombinant FS6 produced in Escherichia coli exhibited extremophile properties, functioning effectively in a broad pH range between 3.5 and 8.5. The enzyme demonstrated optimal activity at temperatures between 25 and 50°C, with a melting temperature of 51.6°C. Kinetic parameters were determined using various substrates, and the reaction catalysed by FS6 with physiological substrates was at least 100-fold more efficient than with p-nitrophenyl phosphate. Furthermore, FS6 was found to be a decamer in solution, unlike the dimeric forms of crystallized proteins in its family.
    MeSH term(s) Acid Phosphatase/metabolism ; Extremophiles/genetics ; Extremophiles/metabolism ; Hydrolysis ; Amino Acid Sequence ; Substrate Specificity ; Hydrogen-Ion Concentration
    Chemical Substances Acid Phosphatase (EC 3.1.3.2)
    Language English
    Publishing date 2024-02-07
    Publishing country United States
    Document type Journal Article
    ZDB-ID 2406063-X
    ISSN 1751-7915 ; 1751-7915
    ISSN (online) 1751-7915
    ISSN 1751-7915
    DOI 10.1111/1751-7915.14404
    Database MEDical Literature Analysis and Retrieval System OnLINE

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  7. Article: A Standardized Extract of

    Tena-Garitaonaindia, Mireia / Ceacero-Heras, Diego / Montoro, María Del Mar Maldonado / de Medina, Fermín Sánchez / Martínez-Augustin, Olga / Daddaoua, Abdelali

    Frontiers in microbiology

    2022  Volume 13, Page(s) 814448

    Abstract: The priority pathogen list of the World Health Organization ... ...

    Abstract The priority pathogen list of the World Health Organization classified
    Language English
    Publishing date 2022-03-16
    Publishing country Switzerland
    Document type Journal Article
    ZDB-ID 2587354-4
    ISSN 1664-302X
    ISSN 1664-302X
    DOI 10.3389/fmicb.2022.814448
    Database MEDical Literature Analysis and Retrieval System OnLINE

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  8. Article: Developing robust protein analysis profiles to identify bacterial acid phosphatases in genomes and metagenomic libraries

    Udaondo, Zulema / Duque, Estrella / Daddaoua, Abdelali / Caselles, Carlos / Roca, Amalia / Pizarro‐Tobias, Paloma / Ramos, Juan L

    Environmental microbiology. 2020 Aug., v. 22, no. 8

    2020  

    Abstract: Phylogenetic analysis of more than 4000 annotated bacterial acid phosphatases was carried out. Our analysis enabled us to sort these enzymes into the following three types: (1) class B acid phosphatases, which were distantly related to the other types, ( ... ...

    Abstract Phylogenetic analysis of more than 4000 annotated bacterial acid phosphatases was carried out. Our analysis enabled us to sort these enzymes into the following three types: (1) class B acid phosphatases, which were distantly related to the other types, (2) class C acid phosphatases and (3) generic acid phosphatases (GAP). Although class B phosphatases are found in a limited number of bacterial families, which include known pathogens, class C acid phosphatases and GAP proteins are found in a variety of microbes that inhabit soil, fresh water and marine environments. As part of our analysis, we developed three profiles, named Pfr‐B‐Phos, Pfr‐C‐Phos and Pfr‐GAP, to describe the three groups of acid phosphatases. These sequence‐based profiles were then used to scan genomes and metagenomes to identify a large number of formerly unknown acid phosphatases. A number of proteins in databases annotated as hypothetical proteins were also identified by these profiles as putative acid phosphatases. To validate these in silico results, we cloned genes encoding candidate acid phosphatases from genomic DNA or recovered from metagenomic libraries or genes synthesized in vitro based on protein sequences recovered from metagenomic data. Expression of a number of these genes, followed by enzymatic analysis of the proteins, further confirmed that sequence similarity searches using our profiles could successfully identify previously unknown acid phosphatases.
    Keywords DNA ; computer simulation ; freshwater ; metagenomics ; phylogeny ; sequence homology ; soil
    Language English
    Dates of publication 2020-08
    Size p. 3561-3571.
    Publishing place John Wiley & Sons, Inc.
    Document type Article
    Note NAL-AP-2-clean ; JOURNAL ARTICLE
    ZDB-ID 2020213-1
    ISSN 1462-2920 ; 1462-2912
    ISSN (online) 1462-2920
    ISSN 1462-2912
    DOI 10.1111/1462-2920.15138
    Database NAL-Catalogue (AGRICOLA)

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  9. Article: Full Transcriptomic Response of

    Rubio-Gómez, José Manuel / Santiago, Carlos Molina / Udaondo, Zulema / Garitaonaindia, Mireia Tena / Krell, Tino / Ramos, Juan-Luis / Daddaoua, Abdelali

    Frontiers in microbiology

    2020  Volume 11, Page(s) 202

    Abstract: Pseudomonas ... ...

    Abstract Pseudomonas aeruginosa
    Language English
    Publishing date 2020-02-20
    Publishing country Switzerland
    Document type Journal Article
    ZDB-ID 2587354-4
    ISSN 1664-302X
    ISSN 1664-302X
    DOI 10.3389/fmicb.2020.00202
    Database MEDical Literature Analysis and Retrieval System OnLINE

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  10. Article ; Online: Developing robust protein analysis profiles to identify bacterial acid phosphatases in genomes and metagenomic libraries.

    Udaondo, Zulema / Duque, Estrella / Daddaoua, Abdelali / Caselles, Carlos / Roca, Amalia / Pizarro-Tobias, Paloma / Ramos, Juan L

    Environmental microbiology

    2020  Volume 22, Issue 8, Page(s) 3561–3571

    Abstract: Phylogenetic analysis of more than 4000 annotated bacterial acid phosphatases was carried out. Our analysis enabled us to sort these enzymes into the following three types: (1) class B acid phosphatases, which were distantly related to the other types, ( ... ...

    Abstract Phylogenetic analysis of more than 4000 annotated bacterial acid phosphatases was carried out. Our analysis enabled us to sort these enzymes into the following three types: (1) class B acid phosphatases, which were distantly related to the other types, (2) class C acid phosphatases and (3) generic acid phosphatases (GAP). Although class B phosphatases are found in a limited number of bacterial families, which include known pathogens, class C acid phosphatases and GAP proteins are found in a variety of microbes that inhabit soil, fresh water and marine environments. As part of our analysis, we developed three profiles, named Pfr-B-Phos, Pfr-C-Phos and Pfr-GAP, to describe the three groups of acid phosphatases. These sequence-based profiles were then used to scan genomes and metagenomes to identify a large number of formerly unknown acid phosphatases. A number of proteins in databases annotated as hypothetical proteins were also identified by these profiles as putative acid phosphatases. To validate these in silico results, we cloned genes encoding candidate acid phosphatases from genomic DNA or recovered from metagenomic libraries or genes synthesized in vitro based on protein sequences recovered from metagenomic data. Expression of a number of these genes, followed by enzymatic analysis of the proteins, further confirmed that sequence similarity searches using our profiles could successfully identify previously unknown acid phosphatases.
    MeSH term(s) Acid Phosphatase/analysis ; Acid Phosphatase/classification ; Acid Phosphatase/genetics ; Amino Acid Sequence ; Bacteria/genetics ; Bacteria/metabolism ; Base Sequence ; Gene Expression Regulation, Bacterial/genetics ; Genome, Bacterial/genetics ; Metagenome/genetics ; Metagenomics ; Phylogeny
    Chemical Substances phosphoenolpyruvate phosphatase (EC 3.1.3.-) ; Acid Phosphatase (EC 3.1.3.2)
    Language English
    Publishing date 2020-07-16
    Publishing country England
    Document type Journal Article ; Research Support, Non-U.S. Gov't
    ZDB-ID 2020213-1
    ISSN 1462-2920 ; 1462-2912
    ISSN (online) 1462-2920
    ISSN 1462-2912
    DOI 10.1111/1462-2920.15138
    Database MEDical Literature Analysis and Retrieval System OnLINE

    Full text online

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