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  1. Book ; Online: Genetic Variability in Conservation and Selection Programs in the Post-Genomics Era

    Saura, Maria / Bertolini, Francesca / Palaiokostas, Christos

    2020  

    Keywords Science: general issues ; Medical genetics ; Inbreeding ; Conservation ; Genetic diversity ; Effective population size ; Selection signature
    Size 1 electronic resource (170 pages)
    Publisher Frontiers Media SA
    Document type Book ; Online
    Note English ; Open Access
    HBZ-ID HT021230926
    ISBN 9782889662494 ; 2889662497
    Database ZB MED Catalogue: Medicine, Health, Nutrition, Environment, Agriculture

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  2. Article: Investigation of

    Bolner, Matteo / Bertolini, Francesca / Bovo, Samuele / Schiavo, Giuseppina / Fontanesi, Luca

    Animals : an open access journal from MDPI

    2023  Volume 14, Issue 1

    Abstract: Polymorphisms in the ... ...

    Abstract Polymorphisms in the human
    Language English
    Publishing date 2023-12-19
    Publishing country Switzerland
    Document type Journal Article
    ZDB-ID 2606558-7
    ISSN 2076-2615
    ISSN 2076-2615
    DOI 10.3390/ani14010005
    Database MEDical Literature Analysis and Retrieval System OnLINE

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  3. Article ; Online: Comparative genomics and signatures of selection in North Atlantic eels.

    Pujolar, Jose Martin / Jacobsen, Magnus Wulff / Bertolini, Francesca

    Marine genomics

    2022  Volume 62, Page(s) 100933

    Abstract: Comparative genomic approaches can identify putative private and shared signatures of selection. We performed a comparative genomic study of North Atlantic eels, European eel (Anguilla Anguilla) and American eel (A. rostrata). The two sister species are ... ...

    Abstract Comparative genomic approaches can identify putative private and shared signatures of selection. We performed a comparative genomic study of North Atlantic eels, European eel (Anguilla Anguilla) and American eel (A. rostrata). The two sister species are nearly undistinguishable at the phenotypic level and despite a wide non-overlapping continental distribution, they spawn in partial sympatry in the Sargasso Sea. Taking advantage of the newly assembled and annotated genome, we used genome wide RAD sequencing data of 359 individuals retrieved from Sequence Nucleotide Archive and state-of-the-art statistic tests to identify putative genomic signatures of selection in North Atlantic eels. First, using the F
    MeSH term(s) Anguilla/genetics ; Animals ; Atlantic Ocean ; Genomics/methods ; Humans ; Polymorphism, Single Nucleotide
    Language English
    Publishing date 2022-02-16
    Publishing country Netherlands
    Document type Journal Article
    ZDB-ID 2429626-0
    ISSN 1876-7478 ; 1874-7787
    ISSN (online) 1876-7478
    ISSN 1874-7787
    DOI 10.1016/j.margen.2022.100933
    Database MEDical Literature Analysis and Retrieval System OnLINE

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  4. Article: Comparative genomics and signatures of selection in North Atlantic eels

    Pujolar, Jose Martin / Jacobsen, Magnus Wulff / Bertolini, Francesca

    Marine genomics. 2022 Apr., v. 62

    2022  

    Abstract: Comparative genomic approaches can identify putative private and shared signatures of selection. We performed a comparative genomic study of North Atlantic eels, European eel (Anguilla Anguilla) and American eel (A. rostrata). The two sister species are ... ...

    Abstract Comparative genomic approaches can identify putative private and shared signatures of selection. We performed a comparative genomic study of North Atlantic eels, European eel (Anguilla Anguilla) and American eel (A. rostrata). The two sister species are nearly undistinguishable at the phenotypic level and despite a wide non-overlapping continental distribution, they spawn in partial sympatry in the Sargasso Sea. Taking advantage of the newly assembled and annotated genome, we used genome wide RAD sequencing data of 359 individuals retrieved from Sequence Nucleotide Archive and state-of-the-art statistic tests to identify putative genomic signatures of selection in North Atlantic eels. First, using the FST and XP-EHH methods, we detected apparent islands of divergence on a total of 7 chromosomes, particularly on chromosomes 6 and 10. Gene ontology analyses suggested candidate genes mainly related to energy production, development and regulation, which could reflect strong selection on traits related to eel migration and larval duration time. Gene effect prediction using SNPeff showed a high number of SNPs in noncoding regions, pointing to a possible regulatory role. Second, using the iHS method we detected shared regions under selection on a total of 11 chromosomes. Several hypotheses might account for the detection of shared islands of selection in North Atlantic eels, including parallel evolution due to adaptation to similar environments and introgression. Future comparative genomic studies will be needed to further clarify the causes and consequences of introgression, including the directionality of these introgression events.
    Keywords Anguilla anguilla ; Anguilla rostrata ; eel ; energy ; gene ontology ; genes ; genomics ; introgression ; larval development ; parallel evolution ; phenotype ; prediction ; sympatry ; Sargasso Sea
    Language English
    Dates of publication 2022-04
    Publishing place Elsevier B.V.
    Document type Article
    ZDB-ID 2429626-0
    ISSN 1876-7478 ; 1874-7787
    ISSN (online) 1876-7478
    ISSN 1874-7787
    DOI 10.1016/j.margen.2022.100933
    Database NAL-Catalogue (AGRICOLA)

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  5. Article ; Online: Footprints of Natural Selection in North Atlantic Eels: A Review

    Pujolar, José Martin / Bertolini, Francesca / Jacobsen, Magnus W.

    Fishes. 2022 Oct. 28, v. 7, no. 6

    2022  

    Abstract: The study of natural selection and local adaptation is a thriving field of research. Local adaptation is driven by environment components and results in locally adapted phenotypes with higher fitness relative to other phenotypes from other locations in ... ...

    Abstract The study of natural selection and local adaptation is a thriving field of research. Local adaptation is driven by environment components and results in locally adapted phenotypes with higher fitness relative to other phenotypes from other locations in the species range. Tests of local adaptations have traditionally been done using transplant experiments, but the advent of next-generation sequencing methods have allowed the study of local adaptation to move from a phenotypic to a genomic approach. By using genome scans and state-of-the-art statistical tests, researchers can identify genes putatively under selection and study the genomic architecture of local adaptation, which often includes the observation of clustering of adaptive genes concentrated in fewer genomic regions known as “genomic islands of divergence”. The two species of North Atlantic eels, the European and the American eel, are excellent species for studying selection since they are panmictic and present large population sizes, show a wide distribution range across extremely heterogenous environments, and are subject to high mortalities. We reviewed studies of natural selection and local adaptation in American eel, European eel, between life cycle stages, between European and American eel. Finally, we discussed genome architecture in relation to local adaptation in eels and the role of both genetic (i.e., local adaptation) and non-genetic (i.e., phenotypic plasticity) in the survival of eels across their distribution range.
    Keywords Anguilla anguilla ; Anguilla rostrata ; genome ; genomics ; natural selection ; phenotype ; phenotypic plasticity
    Language English
    Dates of publication 2022-1028
    Publishing place Multidisciplinary Digital Publishing Institute
    Document type Article ; Online
    ISSN 2410-3888
    DOI 10.3390/fishes7060311
    Database NAL-Catalogue (AGRICOLA)

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  6. Article ; Online: Population genomic structures and signatures of selection define the genetic uniqueness of several fancy and meat rabbit breeds.

    Ballan, Mohamad / Bovo, Samuele / Bertolini, Francesca / Schiavo, Giuseppina / Schiavitto, Michele / Negrini, Riccardo / Fontanesi, Luca

    Journal of animal breeding and genetics = Zeitschrift fur Tierzuchtung und Zuchtungsbiologie

    2023  Volume 140, Issue 6, Page(s) 663–678

    Abstract: Following the recent domestication process of the European rabbit (Oryctolagus cuniculus), many different breeds and lines, distinguished primarily by exterior traits such as coat colour, fur structure and body size and shape, have been constituted. In ... ...

    Abstract Following the recent domestication process of the European rabbit (Oryctolagus cuniculus), many different breeds and lines, distinguished primarily by exterior traits such as coat colour, fur structure and body size and shape, have been constituted. In this study, we genotyped, with a high-density single-nucleotide polymorphism panel, a total of 645 rabbits from 10 fancy breeds (Belgian Hare, Champagne d'Argent, Checkered Giant, Coloured Dwarf, Dwarf Lop, Ermine, Giant Grey, Giant White, Rex and Rhinelander) and three meat breeds (Italian White, Italian Spotted and Italian Silver). ADMIXTURE analysis indicated that breeds with similar phenotypic traits (e.g. coat colour and body size) shared common ancestries. Signatures of selection using two haplotype-based approaches (iHS and XP-EHH), combined with the results obtained with other methods previously reported that we applied to the same breeds, we identified a total of 5079 independent genomic regions with some signatures of selection, covering about 1777 Mb of the rabbit genome. These regions consistently encompassed many genes involved in pigmentation processes (ASIP, EDNRA, EDNRB, KIT, KITLG, MITF, OCA2, TYR and TYRP1), coat structure (LIPH) and body size, including two major genes (LCORL and HMGA2) among many others. This study revealed novel genomic regions under signatures of selection and further demonstrated that population structures and signatures of selection, left into the genome of these rabbit breeds, may contribute to understanding the genetic events that led to their constitution and the complex genetic mechanisms determining the broad phenotypic variability present in these untapped rabbit genetic resources.
    Language English
    Publishing date 2023-07-12
    Publishing country Germany
    Document type Journal Article
    ZDB-ID 631363-2
    ISSN 1439-0388 ; 0044-3581 ; 0931-2668 ; 1742-4488
    ISSN (online) 1439-0388
    ISSN 0044-3581 ; 0931-2668 ; 1742-4488
    DOI 10.1111/jbg.12818
    Database MEDical Literature Analysis and Retrieval System OnLINE

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  7. Article: The Role of Dupilumab in Severe Asthma.

    Ricciardolo, Fabio Luigi Massimo / Bertolini, Francesca / Carriero, Vitina

    Biomedicines

    2021  Volume 9, Issue 9

    Abstract: Dupilumab is a fully humanized monoclonal antibody, capable of inhibiting intracellular signaling of both interleukin (IL)-4 and IL-13. These are two molecules that, together with other proinflammatory cytokines such as IL-5 and eotaxins, play a pivotal ... ...

    Abstract Dupilumab is a fully humanized monoclonal antibody, capable of inhibiting intracellular signaling of both interleukin (IL)-4 and IL-13. These are two molecules that, together with other proinflammatory cytokines such as IL-5 and eotaxins, play a pivotal role in orchestrating the airway inflammatory response defined as Type 2 (T2) inflammation, driven by Th2 or Type 2 innate lymphoid cells, which is the major feature of the T2 high asthma phenotype. The dual inhibition of IL-4 and IL-13 activities is due to the blockade of type II IL-4 receptor through the binding of dupilumab with the subunit IL-4Rα. This results in the repression of STAT6 and in the suppression of subsequent de novo formation of several molecules involved in the T2 inflammatory signature. Several clinical trials tested the efficacy and safety of dupilumab in large populations of uncontrolled severe asthmatics, revealing significant improvements in lung function, asthma control, and exacerbation rate. Similar results were reported when dupilumab was employed in patients harboring pathogenetic processes related to T2 immune response, such as atopic dermatitis and chronic rhinosinusitis. In this review, we provide an overview of the recent research in the field of respiratory medicine about dupilumab mechanism of action and its effects.
    Language English
    Publishing date 2021-08-27
    Publishing country Switzerland
    Document type Journal Article ; Review
    ZDB-ID 2720867-9
    ISSN 2227-9059
    ISSN 2227-9059
    DOI 10.3390/biomedicines9091096
    Database MEDical Literature Analysis and Retrieval System OnLINE

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  8. Article: Which Therapy for Non-Type(T)2/T2-Low Asthma.

    Ricciardolo, Fabio L M / Carriero, Vitina / Bertolini, Francesca

    Journal of personalized medicine

    2021  Volume 12, Issue 1

    Abstract: Currently, the asthmatic population is divided into Type 2-high and non-Type 2/Type 2-low asthmatics, with 50% of patients belonging to one of the two groups. Differently from T2-high, T2-low asthma has not been clearly defined yet, and the T2-low ... ...

    Abstract Currently, the asthmatic population is divided into Type 2-high and non-Type 2/Type 2-low asthmatics, with 50% of patients belonging to one of the two groups. Differently from T2-high, T2-low asthma has not been clearly defined yet, and the T2-low patients are identified on the basis of the absence or non-predominant expression of T2-high biomarkers. The information about the molecular mechanisms underpinning T2-low asthma is scarce, but researchers have recognized as T2-low endotypes type 1 and type 3 immune response, and remodeling events occurring without inflammatory processes. In addition, the lack of agreed biomarkers reprents a challenge for the research of an effective therapy. The first-choice medication is represented by inhaled corticosteroids despite a low efficacy is reported for/in T2-low patients. However, macrolides and long-acting anti-muscarinic drugs have been recognized as efficacious. In recent years, clinical trials targeting biomarkers playing key roles in T3 and T1 immune pathways, alarmins, and molecules involved in neutrophil recruitment have provided conflicting results probably misleading (or biased) in patients' selection. However, further studies are warranted to achieve a precise characterization of T2-low asthma with the aim of defining a tailored therapy for each single asthmatic patient.
    Language English
    Publishing date 2021-12-23
    Publishing country Switzerland
    Document type Journal Article ; Review
    ZDB-ID 2662248-8
    ISSN 2075-4426
    ISSN 2075-4426
    DOI 10.3390/jpm12010010
    Database MEDical Literature Analysis and Retrieval System OnLINE

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  9. Article: Signatures of Admixture and Genetic Uniqueness in the Autochthonous Greek Black Pig Breed Deduced from Gene Polymorphisms Affecting Domestication-Derived Traits.

    Ribani, Anisa / Taurisano, Valeria / Karatosidi, Despoina / Schiavo, Giuseppina / Bovo, Samuele / Bertolini, Francesca / Fontanesi, Luca

    Animals : an open access journal from MDPI

    2023  Volume 13, Issue 11

    Abstract: The Greek Black Pig (or Greek Pig) is the only recognized autochthonous pig breed raised in Greece, usually in extensive or semi-extensive production systems. According to its name, the characteristic breed coat color is solid black. In this study, with ... ...

    Abstract The Greek Black Pig (or Greek Pig) is the only recognized autochthonous pig breed raised in Greece, usually in extensive or semi-extensive production systems. According to its name, the characteristic breed coat color is solid black. In this study, with the aim to start a systematic genetic characterization of the Greek Black Pig breed, we investigated polymorphisms in major genes well known to affect exterior and production traits (
    Language English
    Publishing date 2023-05-26
    Publishing country Switzerland
    Document type Journal Article
    ZDB-ID 2606558-7
    ISSN 2076-2615
    ISSN 2076-2615
    DOI 10.3390/ani13111763
    Database MEDical Literature Analysis and Retrieval System OnLINE

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  10. Article ; Online: Identification of population-informative markers from high-density genotyping data through combined feature selection and machine learning algorithms: Application to European autochthonous and cosmopolitan pig breeds.

    Schiavo, Giuseppina / Bertolini, Francesca / Bovo, Samuele / Galimberti, Giuliano / Muñoz, María / Bozzi, Riccardo / Čandek-Potokar, Marjeta / Óvilo, Cristina / Fontanesi, Luca

    Animal genetics

    2024  Volume 55, Issue 2, Page(s) 193–205

    Abstract: Large genotyping datasets, obtained from high-density single nucleotide polymorphism (SNP) arrays, developed for different livestock species, can be used to describe and differentiate breeds or populations. To identify the most discriminating genetic ... ...

    Abstract Large genotyping datasets, obtained from high-density single nucleotide polymorphism (SNP) arrays, developed for different livestock species, can be used to describe and differentiate breeds or populations. To identify the most discriminating genetic markers among thousands of genotyped SNPs, a few statistical approaches have been proposed. In this study, we applied the Boruta algorithm, a wrapper of the machine learning random forest algorithm, on a database of 23 European pig breeds (20 autochthonous and three cosmopolitan breeds) genotyped with a 70k SNP chip, to pre-select informative SNPs. To identify different sets of SNPs, these pre-selected markers were then ranked with random forest based on their mean decrease accuracy and mean decrease gene indexes. We evaluated the efficiency of these subsets for breed classification and the usefulness of this approach to detect candidate genes affecting breed-specific phenotypes and relevant production traits that might differ among breeds. The lowest overall classification error (2.3%) was reached with a subpanel including only 398 SNPs (ranked based on their mean decrease accuracy), with no classification error in seven breeds using up to 49 SNPs. Several SNPs of these selected subpanels were in genomic regions in which previous studies had identified signatures of selection or genes associated with morphological or production traits that distinguish the analysed breeds. Therefore, even if these approaches have not been originally designed to identify signatures of selection, the obtained results showed that they could potentially be useful for this purpose.
    MeSH term(s) Swine/genetics ; Animals ; Genotype ; Genome ; Phenotype ; Algorithms ; Polymorphism, Single Nucleotide ; Machine Learning
    Language English
    Publishing date 2024-01-08
    Publishing country England
    Document type Journal Article
    ZDB-ID 632766-7
    ISSN 1365-2052 ; 0268-9146 ; 0268-9154
    ISSN (online) 1365-2052
    ISSN 0268-9146 ; 0268-9154
    DOI 10.1111/age.13396
    Database MEDical Literature Analysis and Retrieval System OnLINE

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    In stock of ZB MED Cologne/Königswinter

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    bis Jg. 2021: Bestellungen von Artikeln über das Online-Bestellformular
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