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  1. Article ; Online: Review and perspective on bioinformatics tools using machine learning and deep learning for predicting antiviral peptides.

    Lefin, Nicolás / Herrera-Belén, Lisandra / Farias, Jorge G / Beltrán, Jorge F

    Molecular diversity

    2023  

    Abstract: Viruses constitute a constant threat to global health and have caused millions of human and animal deaths throughout human history. Despite advances in the discovery of antiviral compounds that help fight these pathogens, finding a solution to this ... ...

    Abstract Viruses constitute a constant threat to global health and have caused millions of human and animal deaths throughout human history. Despite advances in the discovery of antiviral compounds that help fight these pathogens, finding a solution to this problem continues to be a task that consumes time and financial resources. Currently, artificial intelligence (AI) has revolutionized many areas of the biological sciences, making it possible to decipher patterns in amino acid sequences that encode different functions and activities. Within the field of AI, machine learning, and deep learning algorithms have been used to discover antimicrobial peptides. Due to their effectiveness and specificity, antimicrobial peptides (AMPs) hold excellent promise for treating various infections caused by pathogens. Antiviral peptides (AVPs) are a specific type of AMPs that have activity against certain viruses. Unlike the research focused on the development of tools and methods for the prediction of antimicrobial peptides, those related to the prediction of AVPs are still scarce. Given the significance of AVPs as potential pharmaceutical options for human and animal health and the ongoing AI revolution, we have reviewed and summarized the current machine learning and deep learning-based tools and methods available for predicting these types of peptides.
    Language English
    Publishing date 2023-08-26
    Publishing country Netherlands
    Document type Journal Article ; Review
    ZDB-ID 1376507-3
    ISSN 1573-501X ; 1381-1991
    ISSN (online) 1573-501X
    ISSN 1381-1991
    DOI 10.1007/s11030-023-10718-3
    Database MEDical Literature Analysis and Retrieval System OnLINE

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    In stock of ZB MED Cologne/Königswinter

    Zs.A 4946: 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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  2. Article: Current Status of Omics in Biological Quality Elements for Freshwater Biomonitoring.

    Machuca-Sepúlveda, Jorge / Miranda, Javiera / Lefin, Nicolás / Pedroso, Alejandro / Beltrán, Jorge F / Farias, Jorge G

    Biology

    2023  Volume 12, Issue 7

    Abstract: Freshwater ecosystems have been experiencing various forms of threats, mainly since the last century. The severity of this adverse scenario presents unprecedented challenges to human health, water supply, agriculture, forestry, ecological systems, and ... ...

    Abstract Freshwater ecosystems have been experiencing various forms of threats, mainly since the last century. The severity of this adverse scenario presents unprecedented challenges to human health, water supply, agriculture, forestry, ecological systems, and biodiversity, among other areas. Despite the progress made in various biomonitoring techniques tailored to specific countries and biotic communities, significant constraints exist, particularly in assessing and quantifying biodiversity and its interplay with detrimental factors. Incorporating modern techniques into biomonitoring methodologies presents a challenging topic with multiple perspectives and assertions. This review aims to present a comprehensive overview of the contemporary advancements in freshwater biomonitoring, specifically by utilizing omics methodologies such as genomics, metagenomics, transcriptomics, proteomics, metabolomics, and multi-omics. The present study aims to elucidate the rationale behind the imperative need for modernization in this field. This will be achieved by presenting case studies, examining the diverse range of organisms that have been studied, and evaluating the potential benefits and drawbacks associated with the utilization of these methodologies. The utilization of advanced high-throughput bioinformatics techniques represents a sophisticated approach that necessitates a significant departure from the conventional practices of contemporary freshwater biomonitoring. The significant contributions of omics techniques in the context of biological quality elements (BQEs) and their interpretations in ecological problems are crucial for biomonitoring programs. Such contributions are primarily attributed to the previously overlooked identification of interactions between different levels of biological organization and their responses, isolated and combined, to specific critical conditions.
    Language English
    Publishing date 2023-06-28
    Publishing country Switzerland
    Document type Journal Article ; Review
    ZDB-ID 2661517-4
    ISSN 2079-7737
    ISSN 2079-7737
    DOI 10.3390/biology12070923
    Database MEDical Literature Analysis and Retrieval System OnLINE

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  3. Article ; Online: Current Status of Omics in Biological Quality Elements for Freshwater Biomonitoring

    Machuca-Sepúlveda, Jorge / Miranda, Javiera / Lefin, Nicolás / Pedroso, Alejandro / Beltrán, Jorge F. / Farias, Jorge G.

    Biology (Basel). 2023 June 28, v. 12, no. 7

    2023  

    Abstract: Freshwater ecosystems have been experiencing various forms of threats, mainly since the last century. The severity of this adverse scenario presents unprecedented challenges to human health, water supply, agriculture, forestry, ecological systems, and ... ...

    Abstract Freshwater ecosystems have been experiencing various forms of threats, mainly since the last century. The severity of this adverse scenario presents unprecedented challenges to human health, water supply, agriculture, forestry, ecological systems, and biodiversity, among other areas. Despite the progress made in various biomonitoring techniques tailored to specific countries and biotic communities, significant constraints exist, particularly in assessing and quantifying biodiversity and its interplay with detrimental factors. Incorporating modern techniques into biomonitoring methodologies presents a challenging topic with multiple perspectives and assertions. This review aims to present a comprehensive overview of the contemporary advancements in freshwater biomonitoring, specifically by utilizing omics methodologies such as genomics, metagenomics, transcriptomics, proteomics, metabolomics, and multi-omics. The present study aims to elucidate the rationale behind the imperative need for modernization in this field. This will be achieved by presenting case studies, examining the diverse range of organisms that have been studied, and evaluating the potential benefits and drawbacks associated with the utilization of these methodologies. The utilization of advanced high-throughput bioinformatics techniques represents a sophisticated approach that necessitates a significant departure from the conventional practices of contemporary freshwater biomonitoring. The significant contributions of omics techniques in the context of biological quality elements (BQEs) and their interpretations in ecological problems are crucial for biomonitoring programs. Such contributions are primarily attributed to the previously overlooked identification of interactions between different levels of biological organization and their responses, isolated and combined, to specific critical conditions.
    Keywords biodiversity ; environmental monitoring ; forestry ; freshwater ; human health ; metabolomics ; metagenomics ; modernization ; multiomics ; proteomics ; transcriptomics ; water supply
    Language English
    Dates of publication 2023-0628
    Publishing place Multidisciplinary Digital Publishing Institute
    Document type Article ; Online
    ZDB-ID 2661517-4
    ISSN 2079-7737
    ISSN 2079-7737
    DOI 10.3390/biology12070923
    Database NAL-Catalogue (AGRICOLA)

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  4. Article: Current state of molecular and metabolic strategies for the improvement of L-asparaginase expression in heterologous systems.

    Lefin, Nicolás / Miranda, Javiera / Beltrán, Jorge F / Belén, Lisandra Herrera / Effer, Brian / Pessoa, Adalberto / Farias, Jorge G / Zamorano, Mauricio

    Frontiers in pharmacology

    2023  Volume 14, Page(s) 1208277

    Abstract: Heterologous expression of L-asparaginase (L-ASNase) has become an important area of research due to its clinical and food industry applications. This review provides a comprehensive overview of the molecular and metabolic strategies that can be used to ... ...

    Abstract Heterologous expression of L-asparaginase (L-ASNase) has become an important area of research due to its clinical and food industry applications. This review provides a comprehensive overview of the molecular and metabolic strategies that can be used to optimize the expression of L-ASNase in heterologous systems. This article describes various approaches that have been employed to increase enzyme production, including the use of molecular tools, strain engineering, and
    Language English
    Publishing date 2023-06-22
    Publishing country Switzerland
    Document type Journal Article ; Review
    ZDB-ID 2587355-6
    ISSN 1663-9812
    ISSN 1663-9812
    DOI 10.3389/fphar.2023.1208277
    Database MEDical Literature Analysis and Retrieval System OnLINE

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  5. Article ; Online: VirusHound-I: prediction of viral proteins involved in the evasion of host adaptive immune response using the random forest algorithm and generative adversarial network for data augmentation.

    Beltrán, Jorge F / Belén, Lisandra Herrera / Farias, Jorge G / Zamorano, Mauricio / Lefin, Nicolás / Miranda, Javiera / Parraguez-Contreras, Fernanda

    Briefings in bioinformatics

    2023  Volume 25, Issue 1

    Abstract: Throughout evolution, pathogenic viruses have developed different strategies to evade the response of the adaptive immune system. To carry out successful replication, some pathogenic viruses encode different proteins that manipulate the molecular ... ...

    Abstract Throughout evolution, pathogenic viruses have developed different strategies to evade the response of the adaptive immune system. To carry out successful replication, some pathogenic viruses encode different proteins that manipulate the molecular mechanisms of host cells. Currently, there are different bioinformatics tools for virus research; however, none of them focus on predicting viral proteins that evade the adaptive system. In this work, we have developed a novel tool based on machine and deep learning for predicting this type of viral protein named VirusHound-I. This tool is based on a model developed with the multilayer perceptron algorithm using the dipeptide composition molecular descriptor. In this study, we have also demonstrated the robustness of our strategy for data augmentation of the positive dataset based on generative antagonistic networks. During the 10-fold cross-validation step in the training dataset, the predictive model showed 0.947 accuracy, 0.994 precision, 0.943 F1 score, 0.995 specificity, 0.896 sensitivity, 0.894 kappa, 0.898 Matthew's correlation coefficient and 0.989 AUC. On the other hand, during the testing step, the model showed 0.964 accuracy, 1.0 precision, 0.967 F1 score, 1.0 specificity, 0.936 sensitivity, 0.929 kappa, 0.931 Matthew's correlation coefficient and 1.0 AUC. Taking this model into account, we have developed a tool called VirusHound-I that makes it possible to predict viral proteins that evade the host's adaptive immune system. We believe that VirusHound-I can be very useful in accelerating studies on the molecular mechanisms of evasion of pathogenic viruses, as well as in the discovery of therapeutic targets.
    MeSH term(s) Viral Proteins/genetics ; Viral Proteins/chemistry ; Random Forest ; Neural Networks, Computer ; Algorithms ; Viruses/genetics
    Chemical Substances Viral Proteins
    Language English
    Publishing date 2023-12-29
    Publishing country England
    Document type Journal Article
    ZDB-ID 2068142-2
    ISSN 1477-4054 ; 1467-5463
    ISSN (online) 1477-4054
    ISSN 1467-5463
    DOI 10.1093/bib/bbad434
    Database MEDical Literature Analysis and Retrieval System OnLINE

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    In stock of ZB MED Cologne/Königswinter

    Zs.A 6262: Show issues Location:
    Je nach Verfügbarkeit (siehe Angabe bei Bestand)
    bis Jg. 2021: Bestellungen von Artikeln über das Online-Bestellformular
    ab Jg. 2022: Lesesaal (EG)

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  6. Article ; Online: Enzyme Engineering Strategies for the Bioenhancement of L-Asparaginase Used as a Biopharmaceutical.

    Miranda, Javiera / Lefin, Nicolás / Beltran, Jorge F / Belén, Lisandra Herrera / Tsipa, Argyro / Farias, Jorge G / Zamorano, Mauricio

    BioDrugs : clinical immunotherapeutics, biopharmaceuticals and gene therapy

    2023  Volume 37, Issue 6, Page(s) 793–811

    Abstract: Over the past few years, there has been a surge in the industrial production of recombinant enzymes from microorganisms due to their catalytic characteristics being highly efficient, selective, and biocompatible. L-asparaginase (L-ASNase) is an enzyme ... ...

    Abstract Over the past few years, there has been a surge in the industrial production of recombinant enzymes from microorganisms due to their catalytic characteristics being highly efficient, selective, and biocompatible. L-asparaginase (L-ASNase) is an enzyme belonging to the class of amidohydrolases that catalyzes the hydrolysis of L-asparagine into L-aspartic acid and ammonia. It has been widely investigated as a biologic agent for its antineoplastic properties in treating acute lymphoblastic leukemia. The demand for L-ASNase is mainly met by the production of recombinant type II L-ASNase from Escherichia coli and Erwinia chrysanthemi. However, the presence of immunogenic proteins in L-ASNase sourced from prokaryotes has been known to result in adverse reactions in patients undergoing treatment. As a result, efforts are being made to explore strategies that can help mitigate the immunogenicity of the drug. This review gives an overview of recent biotechnological breakthroughs in enzyme engineering techniques and technologies used to improve anti-leukemic L-ASNase, taking into account the pharmacological importance of L-ASNase.
    MeSH term(s) Humans ; Antineoplastic Agents/therapeutic use ; Asparaginase/therapeutic use ; Biological Factors ; Biological Products/therapeutic use ; Escherichia coli/metabolism ; Precursor Cell Lymphoblastic Leukemia-Lymphoma/drug therapy ; Protein Engineering/methods
    Chemical Substances Antineoplastic Agents ; Asparaginase (EC 3.5.1.1) ; Biological Factors ; Biological Products
    Language English
    Publishing date 2023-09-12
    Publishing country New Zealand
    Document type Journal Article ; Review
    ZDB-ID 1364202-9
    ISSN 1179-190X ; 1173-8804
    ISSN (online) 1179-190X
    ISSN 1173-8804
    DOI 10.1007/s40259-023-00622-5
    Database MEDical Literature Analysis and Retrieval System OnLINE

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    In stock of ZB MED Cologne/Königswinter

    Zs.A 4112: 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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