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  1. Article ; Online: pyPGCF: A Python Software for Phylogenomic Analysis, Species Demarcation, Identification of Core, and Fingerprint Proteins of Bacterial Genomes That Are Important for Plants.

    Nikolaidis, Marios / Oliver, Stephen G / Amoutzias, Grigorios D

    Methods in molecular biology (Clifton, N.J.)

    2024  Volume 2788, Page(s) 139–155

    Abstract: This computational protocol describes how to use pyPGCF, a python software package that runs in the linux environment, in order to analyze bacterial genomes and perform: (i) phylogenomic analysis, (ii) species demarcation, (iii) identification of the ... ...

    Abstract This computational protocol describes how to use pyPGCF, a python software package that runs in the linux environment, in order to analyze bacterial genomes and perform: (i) phylogenomic analysis, (ii) species demarcation, (iii) identification of the core proteins of a bacterial genus and its individual species, (iv) identification of species-specific fingerprint proteins that are found in all strains of a species and, at the same time, are absent from all other species of the genus, (v) functional annotation of the core and fingerprint proteins with eggNOG, and (vi) identification of secondary metabolite biosynthetic gene clusters (smBGCs) with antiSMASH. This software has already been implemented to analyze bacterial genera and species that are important for plants (e.g., Pseudomonas, Bacillus, Streptomyces). In addition, we provide a test dataset and example commands showing how to analyze 165 genomes from 55 species of the genus Bacillus. The main advantages of pyPGCF are that: (i) it uses adjustable orthology cut-offs, (ii) it identifies species-specific fingerprints, and (iii) its computational cost scales linearly with the number of genomes being analyzed. Therefore, pyPGCF is able to deal with a very large number of bacterial genomes, in reasonable timescales, using widely available levels of computing power.
    MeSH term(s) Software ; Genome, Bacterial ; Phylogeny ; Plants/genetics ; Plants/microbiology ; Bacterial Proteins/genetics ; Genomics/methods ; Computational Biology/methods ; Bacteria/genetics ; Bacteria/classification ; Multigene Family ; Species Specificity
    Chemical Substances Bacterial Proteins
    Language English
    Publishing date 2024-04-24
    Publishing country United States
    Document type Journal Article ; Research Support, Non-U.S. Gov't
    ISSN 1940-6029
    ISSN (online) 1940-6029
    DOI 10.1007/978-1-0716-3782-1_8
    Database MEDical Literature Analysis and Retrieval System OnLINE

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  2. Article: A comparative analysis of transcriptomics of newly diagnosed multiple myeloma: exploring drug repurposing.

    Giannakoulas, Angelos / Nikolaidis, Marios / Amoutzias, Grigorios D / Giannakoulas, Nikolaos

    Frontiers in oncology

    2024  Volume 14, Page(s) 1390105

    Abstract: Multiple myeloma (MM) is an incurable malignant plasma cell disorder characterized by the infiltration of clonal plasma cells in the bone marrow compartment. Gene Expression Profiling (GEP) has emerged as a powerful investigation tool in modern myeloma ... ...

    Abstract Multiple myeloma (MM) is an incurable malignant plasma cell disorder characterized by the infiltration of clonal plasma cells in the bone marrow compartment. Gene Expression Profiling (GEP) has emerged as a powerful investigation tool in modern myeloma research enabling the dissection of the molecular background of MM and allowing the identification of gene products that could potentially serve as targets for therapeutic intervention. In this study we investigated shared transcriptomic abnormalities across newly diagnosed multiple myeloma (NDMM) patient cohorts. In total, publicly available transcriptomic data of 7 studies from CD138+ cells from 281 NDMM patients and 44 healthy individuals were integrated and analyzed. Overall, we identified 28 genes that were consistently differentially expressed (DE) between NDMM patients and healthy donors (HD) across various studies. Of those, 9 genes were over/under-expressed in more than 75% of NDMM patients. In addition, we identified 4 genes (MT1F, PURPL, LINC01239 and LINC01480) that were not previously considered to participate in MM pathogenesis. Meanwhile, by mining three drug databases (ChEMBL, IUPHAR/BPS and DrugBank) we identified 31 FDA-approved and 144 experimental drugs that target 8 of these 28 over/under-expressed MM genes. Taken together, our study offers new insights in MM pathogenesis and importantly, it reveals potential new treatment options that need to be further investigated in future studies.
    Language English
    Publishing date 2024-04-16
    Publishing country Switzerland
    Document type Journal Article
    ZDB-ID 2649216-7
    ISSN 2234-943X
    ISSN 2234-943X
    DOI 10.3389/fonc.2024.1390105
    Database MEDical Literature Analysis and Retrieval System OnLINE

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  3. Article: The Notable Achievements and the Prospects of Bacterial Pathogen Genomics.

    Amoutzias, Grigorios D / Nikolaidis, Marios / Hesketh, Andrew

    Microorganisms

    2022  Volume 10, Issue 5

    Abstract: Throughout the entirety of human history, bacterial pathogens have played an important role and even shaped the fate of civilizations. The application of genomics within the last 27 years has radically changed the way we understand the biology and ... ...

    Abstract Throughout the entirety of human history, bacterial pathogens have played an important role and even shaped the fate of civilizations. The application of genomics within the last 27 years has radically changed the way we understand the biology and evolution of these pathogens. In this review, we discuss how the short- (Illumina) and long-read (PacBio, Oxford Nanopore) sequencing technologies have shaped the discipline of bacterial pathogen genomics, in terms of fundamental research (i.e., evolution of pathogenicity), forensics, food safety, and routine clinical microbiology. We have mined and discuss some of the most prominent data/bioinformatics resources such as NCBI pathogens, PATRIC, and Pathogenwatch. Based on this mining, we present some of the most popular sequencing technologies, hybrid approaches, assemblers, and annotation pipelines. A small number of bacterial pathogens are of very high importance, and we also present the wealth of the genomic data for these species (i.e., which ones they are, the number of antimicrobial resistance genes per genome, the number of virulence factors). Finally, we discuss how this discipline will probably be transformed in the near future, especially by transitioning into metagenome-assembled genomes (MAGs), thanks to long-read sequencing.
    Language English
    Publishing date 2022-05-17
    Publishing country Switzerland
    Document type Journal Article
    ZDB-ID 2720891-6
    ISSN 2076-2607
    ISSN 2076-2607
    DOI 10.3390/microorganisms10051040
    Database MEDical Literature Analysis and Retrieval System OnLINE

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  4. Article ; Online: The Notable Achievements and the Prospects of Bacterial Pathogen Genomics

    Grigorios D. Amoutzias / Marios Nikolaidis / Andrew Hesketh

    Microorganisms, Vol 10, Iss 1040, p

    2022  Volume 1040

    Abstract: Throughout the entirety of human history, bacterial pathogens have played an important role and even shaped the fate of civilizations. The application of genomics within the last 27 years has radically changed the way we understand the biology and ... ...

    Abstract Throughout the entirety of human history, bacterial pathogens have played an important role and even shaped the fate of civilizations. The application of genomics within the last 27 years has radically changed the way we understand the biology and evolution of these pathogens. In this review, we discuss how the short- (Illumina) and long-read (PacBio, Oxford Nanopore) sequencing technologies have shaped the discipline of bacterial pathogen genomics, in terms of fundamental research (i.e., evolution of pathogenicity), forensics, food safety, and routine clinical microbiology. We have mined and discuss some of the most prominent data/bioinformatics resources such as NCBI pathogens, PATRIC, and Pathogenwatch. Based on this mining, we present some of the most popular sequencing technologies, hybrid approaches, assemblers, and annotation pipelines. A small number of bacterial pathogens are of very high importance, and we also present the wealth of the genomic data for these species (i.e., which ones they are, the number of antimicrobial resistance genes per genome, the number of virulence factors). Finally, we discuss how this discipline will probably be transformed in the near future, especially by transitioning into metagenome-assembled genomes (MAGs), thanks to long-read sequencing.
    Keywords bacterial pathogen ; genomics ; Illumina ; Pacific Biosciences ; Oxford Nanopore ; evolution ; Biology (General) ; QH301-705.5
    Language English
    Publishing date 2022-05-01T00:00:00Z
    Publisher MDPI AG
    Document type Article ; Online
    Database BASE - Bielefeld Academic Search Engine (life sciences selection)

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  5. Article ; Online: A panoramic view of the genomic landscape of the genus

    Nikolaidis, Marios / Hesketh, Andrew / Frangou, Nikoletta / Mossialos, Dimitris / Van de Peer, Yves / Oliver, Stephen G / Amoutzias, Grigorios D

    Microbial genomics

    2023  Volume 9, Issue 6

    Abstract: We delineate the evolutionary plasticity of the ecologically and biotechnologically important ... ...

    Abstract We delineate the evolutionary plasticity of the ecologically and biotechnologically important genus
    MeSH term(s) Genomics ; Streptomyces/genetics ; Streptomyces/metabolism ; Codon ; Multigene Family
    Chemical Substances Codon
    Language English
    Publishing date 2023-06-02
    Publishing country England
    Document type Journal Article ; Research Support, Non-U.S. Gov't
    ZDB-ID 2835258-0
    ISSN 2057-5858 ; 2057-5858
    ISSN (online) 2057-5858
    ISSN 2057-5858
    DOI 10.1099/mgen.0.001028
    Database MEDical Literature Analysis and Retrieval System OnLINE

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  6. Article: Impact of Mt. Olympus Honeys on Virulence Factors Implicated in Pathogenesis Exerted by

    Tsavea, Eleni / Tzika, Paraskevi / Katsivelou, Eleni / Adamopoulou, Anna / Nikolaidis, Marios / Amoutzias, Grigorios D / Mossialos, Dimitris

    Antibiotics (Basel, Switzerland)

    2023  Volume 12, Issue 6

    Abstract: The aim of this study was to examine the impact of twenty honey samples, harvested in Mt. Olympus (Greece), on the virulence factors implicated ... ...

    Abstract The aim of this study was to examine the impact of twenty honey samples, harvested in Mt. Olympus (Greece), on the virulence factors implicated in
    Language English
    Publishing date 2023-06-01
    Publishing country Switzerland
    Document type Journal Article
    ZDB-ID 2681345-2
    ISSN 2079-6382
    ISSN 2079-6382
    DOI 10.3390/antibiotics12060998
    Database MEDical Literature Analysis and Retrieval System OnLINE

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  7. Article: A Comparative Analysis of the Core Proteomes within and among the

    Nikolaidis, Marios / Hesketh, Andrew / Mossialos, Dimitris / Iliopoulos, Ioannis / Oliver, Stephen G / Amoutzias, Grigorios D

    Microorganisms

    2022  Volume 10, Issue 9

    Abstract: By integrating phylogenomic and comparative analyses of 1104 high-quality genome sequences, we identify the core proteins and the lineage-specific fingerprint proteins of the various evolutionary clusters (clades/groups/species) of ... ...

    Abstract By integrating phylogenomic and comparative analyses of 1104 high-quality genome sequences, we identify the core proteins and the lineage-specific fingerprint proteins of the various evolutionary clusters (clades/groups/species) of the
    Language English
    Publishing date 2022-08-26
    Publishing country Switzerland
    Document type Journal Article
    ZDB-ID 2720891-6
    ISSN 2076-2607
    ISSN 2076-2607
    DOI 10.3390/microorganisms10091720
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  8. Article: A Comparative Analysis of the Core Proteomes within and among the Bacillus subtilis and Bacillus cereus Evolutionary Groups Reveals the Patterns of Lineage- and Species-Specific Adaptations

    Nikolaidis, Marios / Hesketh, Andrew / Mossialos, Dimitris / Iliopoulos, Ioannis / Oliver, Stephen G. / Amoutzias, Grigorios D.

    Microorganisms. 2022 Aug. 26, v. 10, no. 9

    2022  

    Abstract: By integrating phylogenomic and comparative analyses of 1104 high-quality genome sequences, we identify the core proteins and the lineage-specific fingerprint proteins of the various evolutionary clusters (clades/groups/species) of the Bacillus genus. As ...

    Abstract By integrating phylogenomic and comparative analyses of 1104 high-quality genome sequences, we identify the core proteins and the lineage-specific fingerprint proteins of the various evolutionary clusters (clades/groups/species) of the Bacillus genus. As fingerprints, we denote those core proteins of a certain lineage that are present only in that particular lineage and absent in any other Bacillus lineage. Thus, these lineage-specific fingerprints are expected to be involved in particular adaptations of that lineage. Intriguingly, with a few notable exceptions, the majority of the Bacillus species demonstrate a rather low number of species-specific fingerprints, with the majority of them being of unknown function. Therefore, species-specific adaptations are mostly attributed to highly unstable (in evolutionary terms) accessory proteomes and possibly to changes at the gene regulation level. A series of comparative analyses consistently demonstrated that the progenitor of the Cereus Clade underwent an extensive genomic expansion of chromosomal protein-coding genes. In addition, the majority (76–82%) of the B. subtilis proteins that are essential or play a significant role in sporulation have close homologs in most species of both the Subtilis and the Cereus Clades. Finally, the identification of lineage-specific fingerprints by this study may allow for the future development of highly specific vaccines, therapeutic molecules, or rapid and low-cost molecular tests for species identification.
    Keywords Bacillus cereus ; Bacillus subtilis ; Cereus ; genes ; genomics ; proteome ; species identification ; sporulation ; therapeutics
    Language English
    Dates of publication 2022-0826
    Publishing place Multidisciplinary Digital Publishing Institute
    Document type Article
    ZDB-ID 2720891-6
    ISSN 2076-2607
    ISSN 2076-2607
    DOI 10.3390/microorganisms10091720
    Database NAL-Catalogue (AGRICOLA)

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  9. Article ; Online: The Dynamic and Crucial Role of the Arginine Methylproteome in Myoblast Cell Differentiation.

    Papanikolaou, Nikolaos A / Nikolaidis, Marios / Amoutzias, Grigorios D / Fouza, Ariadni / Papaioannou, Maria / Pandey, Akhilesh / Papavassiliou, Athanasios G

    International journal of molecular sciences

    2023  Volume 24, Issue 3

    Abstract: Protein arginine methylation is an extensive and functionally significant post-translational modification. However, little is known about its role in differentiation at the systems level. Using stable isotope labeling by amino acids in cell culture ( ... ...

    Abstract Protein arginine methylation is an extensive and functionally significant post-translational modification. However, little is known about its role in differentiation at the systems level. Using stable isotope labeling by amino acids in cell culture (SILAC) proteomics of whole proteome analysis in proliferating or five-day differentiated mouse C2C12 myoblasts, followed by high-resolution mass spectrometry, biochemical assays, and specific immunoprecipitation of mono- or dimethylated arginine peptides, we identified several protein families that were differentially methylated on arginine. Our study is the first to reveal global changes in the arginine mono- or dimethylation of proteins in proliferating myoblasts and differentiated myocytes and to identify enriched protein domains and novel short linear motifs (SLiMs). Our data may be crucial for dissecting the links between differentiation and cancer growth.
    MeSH term(s) Mice ; Animals ; Arginine/metabolism ; Mass Spectrometry/methods ; Proteome/analysis ; Cell Differentiation ; Myoblasts/metabolism ; Isotope Labeling/methods
    Chemical Substances Arginine (94ZLA3W45F) ; Proteome
    Language English
    Publishing date 2023-01-20
    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/ijms24032124
    Database MEDical Literature Analysis and Retrieval System OnLINE

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  10. Article ; Online: The Remarkable Evolutionary Plasticity of Coronaviruses by Mutation and Recombination: Insights for the COVID-19 Pandemic and the Future Evolutionary Paths of SARS-CoV-2.

    Amoutzias, Grigorios D / Nikolaidis, Marios / Tryfonopoulou, Eleni / Chlichlia, Katerina / Markoulatos, Panayotis / Oliver, Stephen G

    Viruses

    2022  Volume 14, Issue 1

    Abstract: Coronaviruses (CoVs) constitute a large and diverse subfamily of positive-sense single-stranded RNA viruses. They are found in many mammals and birds and have great importance for the health of humans and farm animals. The current SARS-CoV-2 pandemic, as ...

    Abstract Coronaviruses (CoVs) constitute a large and diverse subfamily of positive-sense single-stranded RNA viruses. They are found in many mammals and birds and have great importance for the health of humans and farm animals. The current SARS-CoV-2 pandemic, as well as many previous epidemics in humans that were of zoonotic origin, highlights the importance of studying the evolution of the entire CoV subfamily in order to understand how novel strains emerge and which molecular processes affect their adaptation, transmissibility, host/tissue tropism, and patho non-homologous genicity. In this review, we focus on studies over the last two years that reveal the impact of point mutations, insertions/deletions, and intratypic/intertypic homologous and non-homologous recombination events on the evolution of CoVs. We discuss whether the next generations of CoV vaccines should be directed against other CoV proteins in addition to or instead of spike. Based on the observed patterns of molecular evolution for the entire subfamily, we discuss five scenarios for the future evolutionary path of SARS-CoV-2 and the COVID-19 pandemic. Finally, within this evolutionary context, we discuss the recently emerged Omicron (B.1.1.529) VoC.
    MeSH term(s) Animals ; Antiviral Agents/pharmacology ; COVID-19/epidemiology ; COVID-19/prevention & control ; COVID-19/virology ; Coronavirus/classification ; Coronavirus/genetics ; Coronavirus/immunology ; Drug Design ; Evolution, Molecular ; Genome, Viral/genetics ; Humans ; Mutation ; Recombination, Genetic ; SARS-CoV-2/classification ; SARS-CoV-2/drug effects ; SARS-CoV-2/genetics ; SARS-CoV-2/immunology ; Vaccination ; Viral Vaccines/immunology ; COVID-19 Drug Treatment
    Chemical Substances Antiviral Agents ; Viral Vaccines
    Language English
    Publishing date 2022-01-02
    Publishing country Switzerland
    Document type Journal Article ; Research Support, Non-U.S. Gov't ; Review
    ZDB-ID 2516098-9
    ISSN 1999-4915 ; 1999-4915
    ISSN (online) 1999-4915
    ISSN 1999-4915
    DOI 10.3390/v14010078
    Database MEDical Literature Analysis and Retrieval System OnLINE

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