LIVIVO - The Search Portal for Life Sciences

zur deutschen Oberfläche wechseln
Advanced search

Search results

Result 1 - 10 of total 241

Search options

  1. Article ; Online: Modelling speciation: Problems and implications.

    Bard, Jonathan B L

    In silico biology

    2022  Volume 15, Issue 1-2, Page(s) 23–42

    Abstract: Darwin's and Wallace's 1859 explanation that novel speciation resulted from natural variants that had been subjected to selection was refined over the next 150 years as genetic inheritance and the importance of mutation-induced change were discovered, ... ...

    Abstract Darwin's and Wallace's 1859 explanation that novel speciation resulted from natural variants that had been subjected to selection was refined over the next 150 years as genetic inheritance and the importance of mutation-induced change were discovered, the quantitative theory of evolutionary population genetics was produced, the speed of genetic change in small populations became apparent and the ramifications of the DNA revolution became clear. This paper first discusses the modern view of speciation in its historical context. It then uses systems-biology approaches to consider the many complex processes that underpin the production of a new species; these extend in scale from genes to populations with the processes of variation, selection and speciation being affected by factors that range from mutation to climate change. Here, events at a particular scale level (e.g. protein network activity) are activated by the output of the level immediately below (i.e. gene expression) and generate a new output that activates the layer above (e.g. embryological development), with this change often being modulated by feedback from higher and lower levels. The analysis shows that activity at each level in the evolution of a new species is marked by stochastic activity, with mutation of course being the key step for variation. The paper examines events at each of these scale levels and particularly considers how the pathway by which mutation leads to phenotypic variants and the wide range of factors that drive selection can be investigated computationally. It concludes that, such is the complexity of speciation, most steps in the process are currently difficult to model and that predictions about future speciation will, apart from a few special cases, be hard to make. The corollary is that opportunities for novel variants to form are maximised.
    MeSH term(s) Climate Change ; Embryonic Development ; Mutation ; Systems Biology
    Language English
    Publishing date 2022-12-01
    Publishing country Netherlands
    Document type Journal Article
    ZDB-ID 2084578-9
    ISSN 1434-3207 ; 1386-6338
    ISSN (online) 1434-3207
    ISSN 1386-6338
    DOI 10.3233/ISB-220253
    Database MEDical Literature Analysis and Retrieval System OnLINE

    More links

    Kategorien

  2. Article ; Online: Fungal endophytes can modulate plant invasion.

    Bard, Nicholas W / Cronk, Quentin C B / Davies, T Jonathan

    Biological reviews of the Cambridge Philosophical Society

    2024  

    Abstract: Symbiotic organisms may contribute to a host plant's success or failure to grow, its ability to maintain viable populations, and potentially, its probability of establishment and spread outside its native range. Intercellular and intracellular microbial ... ...

    Abstract Symbiotic organisms may contribute to a host plant's success or failure to grow, its ability to maintain viable populations, and potentially, its probability of establishment and spread outside its native range. Intercellular and intracellular microbial symbionts that are asymptomatic in their plant host during some or all of their life cycle - endophytes - can form mutualistic, commensal, or pathogenic relationships, and sometimes novel associations with alien plants. Fungal endophytes are likely the most common endosymbiont infecting plants, with life-history, morphological, physiological, and plant-symbiotic traits that are distinct from other endophytic guilds. Here, we review the community dynamics of fungal endophytes during the process of plant invasion, and how their functional role may shift during the different stages of invasion: transport, introduction (colonisation), establishment, and spread. Each invasion stage presents distinct ecological filters that an alien plant must overcome to advance to the subsequent stage of invasion. Endophytes can alternately aid the host in overcoming stage-specific filters, or contribute to the barriers imposed by filters (e.g. biotic resistance), thereby affecting invasion pathways. A few fungi can be transported as seed endophytes from their native range and be vertically transmitted to future generations in the non-native range, especially in graminoids. In other plant groups, alien plants mostly acquire endophytes via horizontal transmission from the invaded plant community, and the host endophyte community is shaped by host filtering and biogeographic factors (e.g. dispersal limitation, environmental filtering). Endophytes infecting alien plants (both those transported with their host and those accumulated in the non-native range) may influence invasion success by affecting plant growth, reproduction, environmental tolerance, and pathogen and herbivory defences; however, the direction and magnitude of these effects can be contingent upon the host identity, life stage, ecological conditions, and invasion stage. This context dependence may cause endophytic fungi to shift to a non-endophytic (e.g. pathogenic) functional life stage in the same or different hosts, which can modify alien-native plant community dynamics. We conclude by identifying paths in which alien hosts can exploit the context dependency of endophyte function in novel abiotic and biotic conditions and at the different stages of invasion.
    Language English
    Publishing date 2024-04-17
    Publishing country England
    Document type Journal Article
    ZDB-ID 1423558-4
    ISSN 1469-185X ; 0006-3231 ; 1464-7931
    ISSN (online) 1469-185X
    ISSN 0006-3231 ; 1464-7931
    DOI 10.1111/brv.13085
    Database MEDical Literature Analysis and Retrieval System OnLINE

    More links

    Kategorien

  3. Article: Inhibitory control of locomotor statistics in walking

    Gattuso, Hannah / Nuñez, Kavin / de la Rea, Beatriz / Ermentrout, Bard / Victor, Jonathan / Nagel, Katherine

    bioRxiv : the preprint server for biology

    2024  

    Abstract: In order to forage for food, many animals regulate not only specific limb movements but the statistics of locomotor behavior over time, for example switching between long-range dispersal behaviors and more localized search depending on the availability ... ...

    Abstract In order to forage for food, many animals regulate not only specific limb movements but the statistics of locomotor behavior over time, for example switching between long-range dispersal behaviors and more localized search depending on the availability of resources. How pre-motor circuits regulate such locomotor statistics is not clear. Here we took advantage of the robust changes in locomotor statistics evoked by attractive odors in walking
    Language English
    Publishing date 2024-04-16
    Publishing country United States
    Document type Preprint
    DOI 10.1101/2024.04.15.589655
    Database MEDical Literature Analysis and Retrieval System OnLINE

    More links

    Kategorien

  4. Article: Tinkering and the Origins of Heritable Anatomical Variation in Vertebrates.

    Bard, Jonathan B L

    Biology

    2018  Volume 7, Issue 1

    Abstract: Evolutionary change comes from natural and other forms of selection acting on existing anatomical and physiological variants. While much is known about selection, little is known about the details of how genetic mutation leads to the range of heritable ... ...

    Abstract Evolutionary change comes from natural and other forms of selection acting on existing anatomical and physiological variants. While much is known about selection, little is known about the details of how genetic mutation leads to the range of heritable anatomical variants that are present within any population. This paper takes a systems-based view to explore how genomic mutation in vertebrate genomes works its way upwards, though changes to proteins, protein networks, and cell phenotypes to produce variants in anatomical detail. The evidence used in this approach mainly derives from analysing anatomical change in adult vertebrates and the protein networks that drive tissue formation in embryos. The former indicate which processes drive variation-these are mainly patterning, timing, and growth-and the latter their molecular basis. The paper then examines the effects of mutation and genetic drift on these processes, the nature of the resulting heritable phenotypic variation within a population, and the experimental evidence on the speed with which new variants can appear under selection. The discussion considers whether this speed is adequate to explain the observed rate of evolutionary change or whether other non-canonical, adaptive mechanisms of heritable mutation are needed. The evidence to hand suggests that they are not, for vertebrate evolution at least.
    Language English
    Publishing date 2018-02-26
    Publishing country Switzerland
    Document type Journal Article ; Review
    ZDB-ID 2661517-4
    ISSN 2079-7737
    ISSN 2079-7737
    DOI 10.3390/biology7010020
    Database MEDical Literature Analysis and Retrieval System OnLINE

    More links

    Kategorien

  5. Article ; Online: Nuclear Factor I A and Nuclear Factor I B Are Jointly Required for Mouse Postnatal Neural Stem Cell Self-Renewal.

    Campbell, Christine E / Webber, Karstin / Bard, Jonathan E / Chaves, Lee D / Osinski, Jason M / Gronostajski, Richard M

    Stem cells and development

    2024  Volume 33, Issue 7-8, Page(s) 153–167

    Abstract: Mouse postnatal neural stem cells (pNSCs) can be expanded in vitro in the presence of epidermal growth factor and fibroblast growth factor 2 and upon removal of these factors cease proliferation and generate neurons, astrocytes, and oligodendrocytes. The ...

    Abstract Mouse postnatal neural stem cells (pNSCs) can be expanded in vitro in the presence of epidermal growth factor and fibroblast growth factor 2 and upon removal of these factors cease proliferation and generate neurons, astrocytes, and oligodendrocytes. The genetic requirements for self-renewal and lineage-commitment of pNSCs are incompletely understood. In this study, we show that the transcription factors NFIA and NFIB, previously shown individually, to be essential for the normal commitment of pNSCs to the astrocytic lineage in vivo, are jointly required for normal self-renewal of pNSCs in vitro and in vivo. Using conditional knockout alleles of
    MeSH term(s) Animals ; Mice ; Cell Differentiation/physiology ; Cell Self Renewal ; Neural Stem Cells/metabolism ; Neurons/metabolism ; NFI Transcription Factors/genetics ; NFI Transcription Factors/metabolism
    Chemical Substances NFI Transcription Factors ; Nfix protein, mouse ; NFIB protein, human ; Nfia protein, mouse
    Language English
    Publishing date 2024-03-21
    Publishing country United States
    Document type Journal Article
    ZDB-ID 2142214-X
    ISSN 1557-8534 ; 1547-3287
    ISSN (online) 1557-8534
    ISSN 1547-3287
    DOI 10.1089/scd.2022.0204
    Database MEDical Literature Analysis and Retrieval System OnLINE

    More links

    Kategorien

  6. Article ; Online: A model for the collective synchronization of flashing in

    McCrea, Madeline / Ermentrout, Bard / Rubin, Jonathan E

    Journal of the Royal Society, Interface

    2022  Volume 19, Issue 195, Page(s) 20220439

    Abstract: Recent empirical investigations have characterized the synchronized flashing behaviours of ... ...

    Abstract Recent empirical investigations have characterized the synchronized flashing behaviours of male
    MeSH term(s) Animals ; Male ; Fireflies ; Reproduction
    Language English
    Publishing date 2022-10-26
    Publishing country England
    Document type Journal Article ; Research Support, Non-U.S. Gov't
    ZDB-ID 2156283-0
    ISSN 1742-5662 ; 1742-5689
    ISSN (online) 1742-5662
    ISSN 1742-5689
    DOI 10.1098/rsif.2022.0439
    Database MEDical Literature Analysis and Retrieval System OnLINE

    More links

    Kategorien

  7. Article ; Online: Generating anatomical variation through mutations in networks - implications for evolution.

    Bard, Jonathan

    Journal of anatomy

    2014  Volume 225, Issue 2, Page(s) 123–131

    Abstract: Genetic mutation leads to anatomical variation only indirectly because many proteins involved in generating anatomical structures in embryos operate cooperatively within molecular networks. These include gene-regulatory or control networks (CNs) for ... ...

    Abstract Genetic mutation leads to anatomical variation only indirectly because many proteins involved in generating anatomical structures in embryos operate cooperatively within molecular networks. These include gene-regulatory or control networks (CNs) for timing, signaling and patterning together with the process networks (PNs) for proliferation, apoptosis, differentiation and morphogenesis that they control. This paper argues that anatomical variation is achieved through a two-stage process: mutation alters the outputs of CNs and perhaps the proliferation network, and such changed outputs alter the ways that PNs construct tissues. This systems-biology approach has several implications: first, because networks contain many cooperating proteins, they amplify the effects of genetic variation so enabling mutation to generate a wider range of phenotypes than a single changed protein acting alone could. Second, this amplification helps explain how novel phenotypes can be produced relatively rapidly. Third, because even organisms with novel anatomical phenotypes derive from variants in standard networks, there is no genetic barrier to their producing viable offspring. This approach also clarifies a terminological difficulty: classical evolutionary genetics views genes in terms of phenotype heritability rather than as DNA sequences. This paper suggests that the molecular phenotype of the classical concept of a gene is often a protein network, with a mutation leading to an alteration in that network's dynamics.
    MeSH term(s) Animals ; Biological Evolution ; Evolution, Molecular ; Genetic Variation ; Mutation ; Phenotype ; Systems Biology
    Language English
    Publishing date 2014-06-17
    Publishing country England
    Document type Journal Article
    ZDB-ID 2955-5
    ISSN 1469-7580 ; 0021-8782
    ISSN (online) 1469-7580
    ISSN 0021-8782
    DOI 10.1111/joa.12205
    Database MEDical Literature Analysis and Retrieval System OnLINE

    More links

    Kategorien

  8. Article: Multimodal Dimension Reduction and Subtype Classification of Head and Neck Squamous Cell Tumors.

    Bard, Jonathan E / Nowak, Norma J / Buck, Michael J / Sinha, Satrajit

    Frontiers in oncology

    2022  Volume 12, Page(s) 892207

    Abstract: Traditional analysis of genomic data from bulk sequencing experiments seek to group and compare sample cohorts into biologically meaningful groups. To accomplish this task, large scale databases of patient-derived samples, like that of TCGA, have been ... ...

    Abstract Traditional analysis of genomic data from bulk sequencing experiments seek to group and compare sample cohorts into biologically meaningful groups. To accomplish this task, large scale databases of patient-derived samples, like that of TCGA, have been established, giving the ability to interrogate multiple data modalities per tumor. We have developed a computational strategy employing multimodal integration paired with spectral clustering and modern dimension reduction techniques such as PHATE to provide a more robust method for cancer sub-type classification. Using this integrated approach, we have examined 514 Head and Neck Squamous Carcinoma (HNSC) tumor samples from TCGA across gene-expression, DNA-methylation, and microbiome data modalities. We show that these approaches, primarily developed for single-cell sequencing can be efficiently applied to bulk tumor sequencing data. Our multimodal analysis captures the dynamic heterogeneity, identifies new and refines subtypes of HNSC, and orders tumor samples along well-defined cellular trajectories. Collectively, these results showcase the inherent molecular complexity of tumors and offer insights into carcinogenesis and importance of targeted therapy. Computational techniques as highlighted in our study provide an organic and powerful approach to identify granular patterns in large and noisy datasets that may otherwise be overlooked.
    Language English
    Publishing date 2022-07-13
    Publishing country Switzerland
    Document type Journal Article
    ZDB-ID 2649216-7
    ISSN 2234-943X
    ISSN 2234-943X
    DOI 10.3389/fonc.2022.892207
    Database MEDical Literature Analysis and Retrieval System OnLINE

    More links

    Kategorien

  9. Article ; Online: A selection-based next generation sequencing approach to develop robust, genotype-specific mutation profiles in Saccharomyces cerevisiae.

    Lamb, Natalie A / Bard, Jonathan E / Buck, Michael J / Surtees, Jennifer A

    G3 (Bethesda, Md.)

    2022  Volume 11, Issue 6

    Abstract: Distinct mutation signatures arise from environmental exposures and/or from defects in metabolic pathways that promote genome stability. The presence of a particular mutation signature can therefore predict the underlying mechanism of mutagenesis. These ... ...

    Abstract Distinct mutation signatures arise from environmental exposures and/or from defects in metabolic pathways that promote genome stability. The presence of a particular mutation signature can therefore predict the underlying mechanism of mutagenesis. These insults to the genome often alter dNTP pools, which itself impacts replication fidelity. Therefore, the impact of altered dNTP pools should be considered when making mechanistic predictions based on mutation signatures. We developed a targeted deep-sequencing approach on the CAN1 gene in Saccharomyces cerevisiae to define information-rich mutational profiles associated with distinct rnr1 backgrounds. Mutations in the activity and selectivity sites of rnr1 lead to elevated and/or unbalanced dNTP levels, which compromises replication fidelity and increases mutation rates. The mutation spectra of rnr1Y285F and rnr1Y285A alleles were characterized previously; our analysis was consistent with this prior work but the sequencing depth achieved in our study allowed a significantly more robust and nuanced computational analysis of the variants observed, generating profiles that integrated information about mutation spectra, position effects, and sequence context. This approach revealed previously unidentified, genotype-specific mutation profiles in the presence of even modest changes in dNTP pools. Furthermore, we identified broader sequence contexts and nucleotide motifs that influenced variant profiles in different rnr1 backgrounds, which allowed specific mechanistic predictions about the impact of altered dNTP pools on replication fidelity.
    MeSH term(s) Saccharomyces cerevisiae/genetics ; Saccharomyces cerevisiae/metabolism ; High-Throughput Nucleotide Sequencing ; DNA Replication ; Mutation ; Saccharomyces cerevisiae Proteins/genetics ; Saccharomyces cerevisiae Proteins/metabolism ; Nucleotides/metabolism ; Genotype ; Ribonucleotide Reductases/genetics
    Chemical Substances Saccharomyces cerevisiae Proteins ; Nucleotides ; Rnr1 protein, S cerevisiae (EC 1.17.4.-) ; Ribonucleotide Reductases (EC 1.17.4.-)
    Language English
    Publishing date 2022-03-01
    Publishing country England
    Document type Journal Article ; Research Support, Non-U.S. Gov't
    ZDB-ID 2629978-1
    ISSN 2160-1836 ; 2160-1836
    ISSN (online) 2160-1836
    ISSN 2160-1836
    DOI 10.1093/g3journal/jkab099
    Database MEDical Literature Analysis and Retrieval System OnLINE

    More links

    Kategorien

  10. Book: Morphogenesis

    Bard, Jonathan

    the cellular and molecular processes of developmental anatomy

    (Developmental and cell biology series)

    1990  

    Author's details Jonathan Bard
    Series title Developmental and cell biology series
    Keywords Morphogenesis ; Zelldifferenzierung ; Tiere ; Morphogenese ; Embryonalentwicklung
    Subject Morphogenie ; Formbildung ; Embryo ; Embryogenese ; Keimesentwicklung ; Fauna ; Tier ; Tierwelt ; Animals ; Zelle
    Size XI, 303 S. : Ill., graph. Darst.
    Publisher Cambridge Univ. Pr
    Publishing place Cambridge u.a.
    Publishing country Great Britain
    Document type Book
    HBZ-ID HT003583067
    ISBN 0-521-36196-6 ; 978-0-521-36196-5
    Database Catalogue ZB MED Medicine, Health

    Kategorien

To top