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  1. Article ; Online: An agent-based model of monocyte differentiation into tumour-associated macrophages in chronic lymphocytic leukemia.

    Verstraete, Nina / Marku, Malvina / Domagala, Marcin / Arduin, Hélène / Bordenave, Julie / Fournié, Jean-Jacques / Ysebaert, Loïc / Poupot, Mary / Pancaldi, Vera

    iScience

    2023  Volume 26, Issue 6, Page(s) 106897

    Abstract: Monocyte-derived macrophages help maintain tissue homeostasis and defend the organism against pathogens. In tumors, recent studies have uncovered complex macrophage populations, including tumor-associated macrophages, which support tumorigenesis through ... ...

    Abstract Monocyte-derived macrophages help maintain tissue homeostasis and defend the organism against pathogens. In tumors, recent studies have uncovered complex macrophage populations, including tumor-associated macrophages, which support tumorigenesis through cancer hallmarks such as immunosuppression, angiogenesis, or matrix remodeling. In the case of chronic lymphocytic leukemia, these macrophages are known as nurse-like cells (NLCs) and they protect leukemic cells from spontaneous apoptosis, contributing to their chemoresistance. We propose an agent-based model of monocyte differentiation into NLCs upon contact with leukemic B cells
    Language English
    Publishing date 2023-05-19
    Publishing country United States
    Document type Journal Article
    ISSN 2589-0042
    ISSN (online) 2589-0042
    DOI 10.1016/j.isci.2023.106897
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  2. Article ; Online: An agent-based model of monocyte differentiation into tumour-associated macrophages in chronic lymphocytic leukemia

    Nina Verstraete / Malvina Marku / Marcin Domagala / Hélène Arduin / Julie Bordenave / Jean-Jacques Fournié / Loïc Ysebaert / Mary Poupot / Vera Pancaldi

    iScience, Vol 26, Iss 6, Pp 106897- (2023)

    2023  

    Abstract: Summary: Monocyte-derived macrophages help maintain tissue homeostasis and defend the organism against pathogens. In tumors, recent studies have uncovered complex macrophage populations, including tumor-associated macrophages, which support tumorigenesis ...

    Abstract Summary: Monocyte-derived macrophages help maintain tissue homeostasis and defend the organism against pathogens. In tumors, recent studies have uncovered complex macrophage populations, including tumor-associated macrophages, which support tumorigenesis through cancer hallmarks such as immunosuppression, angiogenesis, or matrix remodeling. In the case of chronic lymphocytic leukemia, these macrophages are known as nurse-like cells (NLCs) and they protect leukemic cells from spontaneous apoptosis, contributing to their chemoresistance. We propose an agent-based model of monocyte differentiation into NLCs upon contact with leukemic B cells in vitro. We performed patient-specific model optimization using cultures of peripheral blood mononuclear cells from patients. Using our model, we were able to reproduce the temporal survival dynamics of cancer cells in a patient-specific manner and to identify patient groups related to distinct macrophage phenotypes. Our results show a potentially important role of phagocytosis in the polarization process of NLCs and in promoting cancer cells’ enhanced survival.
    Keywords Health sciences ; Immunology ; Computational bioinformatics ; Cancer ; Science ; Q
    Subject code 610
    Language English
    Publishing date 2023-06-01T00:00:00Z
    Publisher Elsevier
    Document type Article ; Online
    Database BASE - Bielefeld Academic Search Engine (life sciences selection)

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  3. Article ; Online: CovMulNet19, Integrating Proteins, Diseases, Drugs, and Symptoms: A Network Medicine Approach to COVID-19.

    Verstraete, Nina / Jurman, Giuseppe / Bertagnolli, Giulia / Ghavasieh, Arsham / Pancaldi, Vera / De Domenico, Manlio

    Network and systems medicine

    2020  Volume 3, Issue 1, Page(s) 130–141

    Abstract: Introduction: ...

    Abstract Introduction:
    Language English
    Publishing date 2020-11-17
    Publishing country United States
    Document type Journal Article
    ISSN 2690-5949
    ISSN (online) 2690-5949
    DOI 10.1089/nsm.2020.0011
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  4. Article ; Online: Non-nodulated bacterial leaf symbiosis promotes the evolutionary success of its host plants in the coffee family (Rubiaceae).

    Verstraete, Brecht / Janssens, Steven / Rønsted, Nina

    Molecular phylogenetics and evolution

    2017  Volume 113, Page(s) 161–168

    Abstract: Every plant species on Earth interacts in some way or another with microorganisms and it is well known that certain forms of symbiosis between different organisms can drive evolution. Within some clades of Rubiaceae (coffee family), a specific plant- ... ...

    Abstract Every plant species on Earth interacts in some way or another with microorganisms and it is well known that certain forms of symbiosis between different organisms can drive evolution. Within some clades of Rubiaceae (coffee family), a specific plant-bacteria interaction exists in which non-pathological endophytes are present in the leaves of their hosts. It is hypothesized that the bacterial endophytes, either alone or by interacting with the host, provide chemical protection against herbivory or pathogens by producing toxic or otherwise advantageous secondary metabolites. If the bacteria indeed have a direct beneficial influence on their hosts, it is reasonable to assume that the endophytes may increase the fitness of their hosts and therefore it is probable that their presence also has an influence on the long-term evolution of the particular plant lineages. In this study, the possible origin in time of non-nodulated bacterial leaf symbiosis in the Vanguerieae tribe of Rubiaceae is elucidated and dissimilarities in evolutionary dynamics between species with endophytes versus species without are investigated. Bacterial leaf symbiosis is shown to have most probably originated in the Late Miocene, a period when the savannah habitat is believed to have expanded on the African continent and herbivore pressure increased. The presence of bacterial leaf endophytes appears to be restricted to Old World lineages so far. Plant lineages with leaf endophytes show a significantly higher speciation rate than plant lineages without endophytes, while there is only a small difference in extinction rate. The transition rate shows that evolving towards having endophytes is twice as fast as evolving towards not having endophytes, suggesting that leaf symbiosis must be beneficial for the host plants. We conclude that the presence of bacterial leaf endophytes may also be an important driver for speciation of host plants.
    MeSH term(s) Bacteria/metabolism ; Biological Evolution ; Coffee ; Endophytes/classification ; Endophytes/physiology ; Phylogeny ; Plant Leaves/microbiology ; Rubiaceae/microbiology ; Symbiosis ; Time Factors
    Chemical Substances Coffee
    Language English
    Publishing date 2017-08
    Publishing country United States
    Document type Journal Article
    ZDB-ID 33610-5
    ISSN 1095-9513 ; 1055-7903
    ISSN (online) 1095-9513
    ISSN 1055-7903
    DOI 10.1016/j.ympev.2017.05.022
    Database MEDical Literature Analysis and Retrieval System OnLINE

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    In stock of ZB MED Cologne/Königswinter

    Zs.A 3644: 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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  5. Article: Non-nodulated bacterial leaf symbiosis promotes the evolutionary success of its host plants in the coffee family (Rubiaceae)

    Verstraete, Brecht / Nina Rønsted / Steven Janssens

    Molecular phylogenetics and evolution. 2017 Aug., v. 113

    2017  

    Abstract: Every plant species on Earth interacts in some way or another with microorganisms and it is well known that certain forms of symbiosis between different organisms can drive evolution. Within some clades of Rubiaceae (coffee family), a specific plant- ... ...

    Abstract Every plant species on Earth interacts in some way or another with microorganisms and it is well known that certain forms of symbiosis between different organisms can drive evolution. Within some clades of Rubiaceae (coffee family), a specific plant-bacteria interaction exists in which non-pathological endophytes are present in the leaves of their hosts. It is hypothesized that the bacterial endophytes, either alone or by interacting with the host, provide chemical protection against herbivory or pathogens by producing toxic or otherwise advantageous secondary metabolites. If the bacteria indeed have a direct beneficial influence on their hosts, it is reasonable to assume that the endophytes may increase the fitness of their hosts and therefore it is probable that their presence also has an influence on the long-term evolution of the particular plant lineages. In this study, the possible origin in time of non-nodulated bacterial leaf symbiosis in the Vanguerieae tribe of Rubiaceae is elucidated and dissimilarities in evolutionary dynamics between species with endophytes versus species without are investigated. Bacterial leaf symbiosis is shown to have most probably originated in the Late Miocene, a period when the savannah habitat is believed to have expanded on the African continent and herbivore pressure increased. The presence of bacterial leaf endophytes appears to be restricted to Old World lineages so far. Plant lineages with leaf endophytes show a significantly higher speciation rate than plant lineages without endophytes, while there is only a small difference in extinction rate. The transition rate shows that evolving towards having endophytes is twice as fast as evolving towards not having endophytes, suggesting that leaf symbiosis must be beneficial for the host plants. We conclude that the presence of bacterial leaf endophytes may also be an important driver for speciation of host plants.
    Keywords bacteria ; endophytes ; extinction ; habitats ; herbivores ; host plants ; leaves ; pathogens ; Rubiaceae ; savannas ; secondary metabolites ; symbiosis ; toxicity ; Africa
    Language English
    Dates of publication 2017-08
    Size p. 161-168.
    Publishing place Elsevier Inc.
    Document type Article
    ZDB-ID 33610-5
    ISSN 1095-9513 ; 1055-7903
    ISSN (online) 1095-9513
    ISSN 1055-7903
    DOI 10.1016/j.ympev.2017.05.022
    Database NAL-Catalogue (AGRICOLA)

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    In stock of ZB MED Cologne/Königswinter

    Zs.A 3644: 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)

    Order via subito

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  6. Article ; Online: CovMulNet19, Integrating Proteins, Diseases, Drugs, and Symptoms

    Verstraete, Nina / Jurman, Giuseppe / Bertagnolli, Giulia / Ghavasieh, Arsham / Pancaldi, Vera / De Domenico, Manlio

    A Network Medicine Approach to COVID-19

    2020  

    Keywords covid19
    Publishing country it
    Document type Article ; Online
    Database BASE - Bielefeld Academic Search Engine (life sciences selection)

    Full text online

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  7. Article: Insights on TAM Formation from a Boolean Model of Macrophage Polarization Based on In Vitro Studies.

    Marku, Malvina / Verstraete, Nina / Raynal, Flavien / Madrid-Mencía, Miguel / Domagala, Marcin / Fournié, Jean-Jacques / Ysebaert, Loïc / Poupot, Mary / Pancaldi, Vera

    Cancers

    2020  Volume 12, Issue 12

    Abstract: The tumour microenvironment is the surrounding of a tumour, including blood vessels, fibroblasts, signaling molecules, the extracellular matrix and immune cells, especially neutrophils and monocyte-derived macrophages. In a tumour setting, macrophages ... ...

    Abstract The tumour microenvironment is the surrounding of a tumour, including blood vessels, fibroblasts, signaling molecules, the extracellular matrix and immune cells, especially neutrophils and monocyte-derived macrophages. In a tumour setting, macrophages encompass a spectrum between a tumour-suppressive (M1) or tumour-promoting (M2) state. The biology of macrophages found in tumours (Tumour Associated Macrophages) remains unclear, but understanding their impact on tumour progression is highly important. In this paper, we perform a comprehensive analysis of a macrophage polarization network, following two lines of enquiry: (i) we reconstruct the macrophage polarization network based on literature, extending it to include important stimuli in a tumour setting, and (ii) we build a dynamical model able to reproduce macrophage polarization in the presence of different stimuli, including the contact with cancer cells. Our simulations recapitulate the documented macrophage phenotypes and their dependencies on specific receptors and transcription factors, while also unravelling the formation of a special type of tumour associated macrophages in an in vitro model of chronic lymphocytic leukaemia. This model constitutes the first step towards elucidating the cross-talk between immune and cancer cells inside tumours, with the ultimate goal of identifying new therapeutic targets that could control the formation of tumour associated macrophages in patients.
    Language English
    Publishing date 2020-12-07
    Publishing country Switzerland
    Document type Journal Article
    ZDB-ID 2527080-1
    ISSN 2072-6694
    ISSN 2072-6694
    DOI 10.3390/cancers12123664
    Database MEDical Literature Analysis and Retrieval System OnLINE

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  8. Article ; Online: Structural and Energetic Characterization of the Ankyrin Repeat Protein Family.

    Parra, R Gonzalo / Espada, Rocío / Verstraete, Nina / Ferreiro, Diego U

    PLoS computational biology

    2015  Volume 11, Issue 12, Page(s) e1004659

    Abstract: Ankyrin repeat containing proteins are one of the most abundant solenoid folds. Usually implicated in specific protein-protein interactions, these proteins are readily amenable for design, with promising biotechnological and biomedical applications. ... ...

    Abstract Ankyrin repeat containing proteins are one of the most abundant solenoid folds. Usually implicated in specific protein-protein interactions, these proteins are readily amenable for design, with promising biotechnological and biomedical applications. Studying repeat protein families presents technical challenges due to the high sequence divergence among the repeating units. We developed and applied a systematic method to consistently identify and annotate the structural repetitions over the members of the complete Ankyrin Repeat Protein Family, with increased sensitivity over previous studies. We statistically characterized the number of repeats, the folding of the repeat-arrays, their structural variations, insertions and deletions. An energetic analysis of the local frustration patterns reveal the basic features underlying fold stability and its relation to the functional binding regions. We found a strong linear correlation between the conservation of the energetic features in the repeat arrays and their sequence variations, and discuss new insights into the organization and function of these ubiquitous proteins.
    MeSH term(s) Amino Acid Sequence ; Ankyrin Repeat ; Ankyrins/chemistry ; Ankyrins/ultrastructure ; Computer Simulation ; Energy Transfer ; Models, Chemical ; Models, Molecular ; Molecular Sequence Data ; Sequence Analysis, Protein/methods
    Chemical Substances Ankyrins
    Language English
    Publishing date 2015-12-21
    Publishing country United States
    Document type Journal Article ; Research Support, Non-U.S. Gov't
    ZDB-ID 2193340-6
    ISSN 1553-7358 ; 1553-734X
    ISSN (online) 1553-7358
    ISSN 1553-734X
    DOI 10.1371/journal.pcbi.1004659
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  9. Article ; Online: Structural and Energetic Characterization of the Ankyrin Repeat Protein Family.

    R Gonzalo Parra / Rocío Espada / Nina Verstraete / Diego U Ferreiro

    PLoS Computational Biology, Vol 11, Iss 12, p e

    2015  Volume 1004659

    Abstract: Ankyrin repeat containing proteins are one of the most abundant solenoid folds. Usually implicated in specific protein-protein interactions, these proteins are readily amenable for design, with promising biotechnological and biomedical applications. ... ...

    Abstract Ankyrin repeat containing proteins are one of the most abundant solenoid folds. Usually implicated in specific protein-protein interactions, these proteins are readily amenable for design, with promising biotechnological and biomedical applications. Studying repeat protein families presents technical challenges due to the high sequence divergence among the repeating units. We developed and applied a systematic method to consistently identify and annotate the structural repetitions over the members of the complete Ankyrin Repeat Protein Family, with increased sensitivity over previous studies. We statistically characterized the number of repeats, the folding of the repeat-arrays, their structural variations, insertions and deletions. An energetic analysis of the local frustration patterns reveal the basic features underlying fold stability and its relation to the functional binding regions. We found a strong linear correlation between the conservation of the energetic features in the repeat arrays and their sequence variations, and discuss new insights into the organization and function of these ubiquitous proteins.
    Keywords Biology (General) ; QH301-705.5
    Subject code 612
    Language English
    Publishing date 2015-12-01T00:00:00Z
    Publisher Public Library of Science (PLoS)
    Document type Article ; Online
    Database BASE - Bielefeld Academic Search Engine (life sciences selection)

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  10. Article: Rush hour at the museum - Diversification patterns provide new clues for the success of figs (Ficus L., Moraceae)

    Bruun-Lund, Sam / Brecht Verstraete / Finn Kjellberg / Nina Rønsted

    Acta oecologica. 2017,

    2017  

    Abstract: Tropical rainforests harbour much of the earth's plant diversity but little is still known about how it evolved and why a small number of plant genera account for the majority. Whether this success is due to rapid turnover or constant evolution for these ...

    Abstract Tropical rainforests harbour much of the earth's plant diversity but little is still known about how it evolved and why a small number of plant genera account for the majority. Whether this success is due to rapid turnover or constant evolution for these hyper-diverse plant genera is here tested for the species-rich genus Ficus L. (figs). The pan-tropical distribution of figs makes it an ideal study group to investigate rainforest hyper-diversification patterns. Using a recently published, dated and comprehensive phylogenetic hypothesis, we infer that figs are an old lineage that gradually accumulated species and exhibits very low extinction rates, which corresponds to the ‘museum model’ of evolution. Overall, no major significant shifts in evolutionary dynamics are detected, yet two shifts with lower probability are found. Hemi-epiphytism, monoecy, and active pollination are traits that possibly are associated with the hyper-diversity found in figs, making it possible for the plants to occupy new niches followed by extensive radiation over evolutionary time scales. Figs possess unique diversification patterns compared to other typical rainforest genera.
    Keywords Ficus ; extinction ; figs ; models ; monoecy ; niches ; phylogeny ; pollination ; probability ; species diversity ; tropical rain forests
    Language English
    Size p. .
    Publishing place Elsevier Masson SAS
    Document type Article
    Note Pre-press version
    ZDB-ID 1033625-4
    ISSN 1146-609X
    ISSN 1146-609X
    DOI 10.1016/j.actao.2017.11.001
    Database NAL-Catalogue (AGRICOLA)

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    In stock of ZB MED Bonn / Germany

    Z 3406: Show issues

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