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  • 1
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    The Pangenome (2021)
    Springer Nature | Springer
    Details
    Publication Date: 2024-04-05
    Description: This open access book offers the first comprehensive account of the pan-genome concept and its manifold implications. The realization that the genetic repertoire of a biological species always encompasses more than the genome of each individual is one of the earliest examples of big data in biology that opened biology to the unbounded. The study of genetic variation observed within a species challenges existing views and has profound consequences for our understanding of the fundamental mechanisms underpinning bacterial biology and evolution. The underlying rationale extends well beyond the initial prokaryotic focus to all kingdoms of life and evolves into similar concepts for metagenomes, phenomes and epigenomes. The book’s respective chapters address a range of topics, from the serendipitous emergence of the pan-genome concept and its impacts on the fields of microbiology, vaccinology and antimicrobial resistance, to the study of microbial communities, bioinformatic applications and mathematical models that tie in with complex systems and economic theory. Given its scope, the book will appeal to a broad readership interested in population dynamics, evolutionary biology and genomics.
    Keywords: Microbial Genetics and Genomics ; Evolutionary Biology ; Genetics and Population Dynamics ; Microbial Ecology ; Human Genetics ; Genetics and Genomics ; Comparative genomics ; Metagenomics ; Microbial Population Analysis ; Pangenome Profile ; Supra-Genome Analysis ; Adaptive Evolution ; Computational Tools ; Bioinformatic Genomics ; Core Dispensable Genome ; Selection, Recombination, Composition ; Acquired Resistance ; Bacterial Species Concept ; Genomic Diversity ; Bacterial Ecology, Microevolution ; Open Access ; Pan-metagenomics ; Pan-microbiomics ; Pan-epigenome ; Gene Transfer ; Pan-phenomes ; Microbiology (non-medical) ; Genetics (non-medical) ; Evolution ; Applied mathematics ; Ecological science, the Biosphere ; Medical genetics ; thema EDItEUR::P Mathematics and Science::PS Biology, life sciences::PSG Microbiology (non-medical) ; thema EDItEUR::P Mathematics and Science::PS Biology, life sciences::PSA Life sciences: general issues::PSAJ Evolution ; thema EDItEUR::P Mathematics and Science::PB Mathematics::PBW Applied mathematics ; thema EDItEUR::P Mathematics and Science::PS Biology, life sciences::PSA Life sciences: general issues::PSAF Ecological science, the Biosphere ; thema EDItEUR::M Medicine and Nursing::MF Pre-clinical medicine: basic sciences::MFN Medical genetics ; thema EDItEUR::P Mathematics and Science::PS Biology, life sciences::PSA Life sciences: general issues::PSAK Genetics (non-medical)
    Language: English
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  • 2
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    Everything Flows (2021)
    Oxford University Press
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    Publication Date: 2024-04-05
    Description: This collection of essays explores the metaphysical thesis that the living world is not ontologically made up of substantial particles or things, as has often been assumed, but is rather constituted by processes. The biological domain is organized as an interdependent hierarchy of processes, which are stabilized and actively maintained at different timescales. Even entities that intuitively appear to be paradigms of things, such as organisms, are actually better understood as processes. Unlike previous attempts to articulate processual views of biology, which have tended to use Alfred North Whitehead’s panpsychist metaphysics as a foundation, this book takes a naturalistic approach to metaphysics. It submits that the main motivations for replacing an ontology of substances with one of processes are to be looked for in the empirical findings of science. Biology provides compelling reasons for thinking that the living realm is fundamentally dynamic and that the existence of things is always conditional on the existence of processes. The phenomenon of life cries out for theories that prioritize processes over things, and it suggests that the central explanandum of biology is not change but rather stability—or, more precisely, stability attained through constant change. This multicontributor volume brings together philosophers of science and metaphysicians interested in exploring the consequences of a processual philosophy of biology. The contributors draw on an extremely wide range of biological case studies and employ a process perspective to cast new light on a number of traditional philosophical problems such as identity, persistence, and individuality.
    Keywords: explanation ; identity ; individuality ; metaphysics of science ; organism ; persistence ; philosophy of biology ; process ontology ; substance ontology ; symbiosis ; Evolution ; thema EDItEUR::P Mathematics and Science::PS Biology, life sciences
    Language: English
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  • 3
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    A-to-I RNA editing in the earliest-diverging Eumetazoan phyla (2017)
    Oxford University Press
    Details
    Publication Date: 2022-05-25
    Description: © The Author(s), 2017. This article is distributed under the terms of the Creative Commons Attribution License. The definitive version was published in Molecular Biology and Evolution 34 (2017): 1890-1901, doi:10.1093/molbev/msx125.
    Description: The highly conserved ADAR enzymes, found in all multicellular metazoans, catalyze the editing of mRNA transcripts by the deamination of adenosines to inosines. This type of editing has two general outcomes: site specific editing, which frequently leads to recoding, and clustered editing, which is usually found in transcribed genomic repeats. Here, for the first time, we looked for both editing of isolated sites and clustered, non-specific sites in a basal metazoan, the coral Acropora millepora during spawning event, in order to reveal its editing pattern. We found that the coral editome resembles the mammalian one: it contains more than 500,000 sites, virtually all of which are clustered in non-coding regions that are enriched for predicted dsRNA structures. RNA editing levels were increased during spawning and increased further still in newly released gametes. This may suggest that editing plays a role in introducing variability in coral gametes.
    Description: This work was supported by the Australian Research Council (to PK), the European Research Council (grant 311257), the I-CORE Program of the Planning and Budgeting Committee in Israel (grants 41/11 and 1796/12), and the Israel Science Foundation (1380/14).
    Keywords: RNA editing ; ADAR ; Evolution ; Coral
    Repository Name: Woods Hole Open Access Server
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  • 4
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    The reduced genome of the parasitic microsporidian Enterocytozoon bieneusi lacks genes for core carbon metabolism (2010)
    Oxford University Press
    Details
    Publication Date: 2022-05-25
    Description: © The Authors, 2010. This article is distributed under the terms of the Creative Commons Attribution-Noncommercial 2.5 License. The definitive version was published in Genome Biology and Evolution 2 (2010): 304, doi:10.1093/gbe/evq022.
    Description: Reduction of various biological processes is a hallmark of the parasitic lifestyle. Generally, the more intimate the association between parasites and hosts the stronger the parasite relies on its host's physiology for survival and reproduction. However, some systems have been held to be indispensable, for example, the core pathways of carbon metabolism that produce energy from sugars. Even the most hardened anaerobes that lack oxidative phosphorylation and the tricarboxylic acid cycle have retained glycolysis and some downstream means to generate ATP. Here we describe the deep-coverage genome resequencing of the pathogenic microsporidiian, Enterocytozoon bieneusi, which shows that this parasite has crossed this line and abandoned complete pathways for the most basic carbon metabolism. Comparing two genome sequence surveys of E. bieneusi to genomic data from four other microsporidia reveals a normal complement of 353 genes representing 30 functional pathways in E. bieneusi, except that only 2 out of 21 genes collectively involved in glycolysis, pentose phosphate, and trehalose metabolism are present. Similarly, no genes encoding proteins involved in the processing of spliceosomal introns were found. Altogether, E. bieneusi appears to have no fully functional pathway to generate ATP from glucose. Therefore, this intracellular parasite relies on transporters to import ATP from its host.
    Description: This work was supported by grants from the Canadian Institutes for Health Research (MOP-84265), the National Institutes of Health (NIH AI31788, R21 AI52792, and R21 AI064118), and the National Science Foundation (MCB- 0135272). N.C. is a Scholar of the Canadian Institute for Advanced Research and is supported by a fellowship from the Swiss National Science Foundation (NSF) (PA00P3- 124166). D.E. is supported by the Swiss NSF. P.J.K. is a Fellow of the Canadian Institute for Advanced Research and a Senior Scholar of the Michael Smith Foundation for Health Research.
    Keywords: Microsporidia ; Parasite ; Glycolysis ; Carbon metabolism ; Reduction ; Evolution
    Repository Name: Woods Hole Open Access Server
    Type: Article
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  • 5
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    Adaptive proteome diversification by nonsynonymous A-to-I RNA editing in coleoid cephalopods (2022)
    Oxford University Press
    Details
    Publication Date: 2022-10-27
    Description: © The Author(s), 2021. This article is distributed under the terms of the Creative Commons Attribution License. The definitive version was published in Shoshan, Y., Liscovitch-Brauer, N., Rosenthal, J. J. C., & Eisenberg, E. Adaptive proteome diversification by nonsynonymous A-to-I RNA editing in coleoid cephalopods. Molecular Biology and Evolution, 38(9), (2021): 3775–3788, https://doi.org/10.1093/molbev/msab154.
    Description: RNA editing by the ADAR enzymes converts selected adenosines into inosines, biological mimics for guanosines. By doing so, it alters protein-coding sequences, resulting in novel protein products that diversify the proteome beyond its genomic blueprint. Recoding is exceptionally abundant in the neural tissues of coleoid cephalopods (octopuses, squids, and cuttlefishes), with an over-representation of nonsynonymous edits suggesting positive selection. However, the extent to which proteome diversification by recoding provides an adaptive advantage is not known. It was recently suggested that the role of evolutionarily conserved edits is to compensate for harmful genomic substitutions, and that there is no added value in having an editable codon as compared with a restoration of the preferred genomic allele. Here, we show that this hypothesis fails to explain the evolutionary dynamics of recoding sites in coleoids. Instead, our results indicate that a large fraction of the shared, strongly recoded, sites in coleoids have been selected for proteome diversification, meaning that the fitness of an editable A is higher than an uneditable A or a genomically encoded G.
    Description: This research was supported by a grants from the United States–Israel Binational Science Foundation (BSF), Jerusalem, Israel (BSF2017262 to J.J.C.R. and E.E.), the Israel Science Foundation (3371/20 to E.E.) and the National Science Foundation (IOS 1827509 and 1557748 to J.J.C.R).
    Keywords: RNA editing ; Adaptation ; Evolution
    Repository Name: Woods Hole Open Access Server
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  • 6
    Electronic Resource
    Electronic Resource
    Response to insulin and the expression pattern of a gene encoding an insulin receptor homologue suggest a role for an insulin-like molecule in regulating growth and patterning in Hydra (1996)
    Springer
    Development genes and evolution 206 (1996), S. 247-259 
    Details
    ISSN: 1432-041X
    Keywords: Key words Hydra ; Insulin ; Development ; Receptor ; Evolution
    Source: Springer Online Journal Archives 1860-2000
    Topics: Biology
    Notes: Abstract  A gene encoding a receptor protein-tyrosine kinase closely related to the vertebrate insulin receptor has been identified in the Cnidarian Hydra vulgaris. The gene is expressed in both epithelial layers of the adult polyp. A particularly high level of expression is seen in the ectoderm of the proximal portions of the tentacles and in a ring of ectodermal cells at the border between the foot basal disk and body column. The expression pattern of the gene in asexual buds is dynamic; expression is high throughout the newly emerging bud but the area of high expression becomes restricted to the apex as the bud lengthens. When the bud begins hypostome and tentacle formation, a high level of expression appears at the bases of the emerging tentacles. Finally, a ring of high expression appears just above the foot of the bud, completing the pattern seen in the adult polyp. The presence of this receptor and its pattern of expression suggested that an endogenous molecule related to insulin plays a role in regulating cell division in the body column and in differentiation of the tentacle and foot cells in Hydra, with the switch between the two being determined by the level of the receptor. Treatment of Hydra polyps with mammalian insulin caused an increase in the number of ectodermal and endodermal cells undergoing DNA synthesis.
    Type of Medium: Electronic Resource
    URL: http://dx.doi.org/10.1007/s004270050050
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  • 7
    Electronic Resource
    Electronic Resource
    Rapid divergence in the course of Drosophila evolution reveals structural important domains of the Notch antagonist Hairless (1999)
    Springer
    Development genes and evolution 209 (1999), S. 155-164 
    Details
    ISSN: 1432-041X
    Keywords: Key words Notch pathway ; Antagonist ; Hairless ; Orthologue ; Evolution
    Source: Springer Online Journal Archives 1860-2000
    Topics: Biology
    Notes: Abstract  Hairless is a member of the Notch signalling pathway, where it acts as antagonist by binding to Suppressor of Hairless [Su(H)], thereby inhibiting Notch target gene activation. The pathway and its members are highly conserved in metazoans from worms to humans. However, a Hairless orthologue from another species has not yet been identified. The identification of Hairless in largely diverged species by cross-hybridization has failed so far probably due to a low degree of conservation. Therefore, we turned to D. hydei where a Hairless mutation has been described before. The D. hydei Hairless orthologue is reasonably well conserved with regard to gene structure and expression. The prospective Hairless protein orthologues share several highly conserved regions which are separated by quite diverged stretches. As to be expected, the largest region of high conservation corresponds to the Su(H) binding domain. This region is also functionally conserved, since this D. hydei protein domain binds very strongly to the D. melanogaster Su(H) protein. The other conserved regions support our earlier structure-function analysis since they nicely correspond to previously defined, functionally important protein domains. Most notably, the very C-terminal domain which is very sensitive to structural alterations, is nearly identical between the two species. In summary, this evolutionary study improves the knowledge on functionally significant domains of the Hairless protein, and may be helpful for the future identification of homologues in other animals, especially in vertebrates.
    Type of Medium: Electronic Resource
    URL: http://dx.doi.org/10.1007/s004270050239
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  • 8
    Electronic Resource
    Electronic Resource
    Association of developmental regulatory genes with the development of different molar tooth shapes in two species of rodents (1998)
    Springer
    Development genes and evolution 208 (1998), S. 477-486 
    Details
    ISSN: 1432-041X
    Keywords: Key words Tooth morphogenesis ; Evolution ; Mouse ; Microtus rossiaemeridionalis ; Enamel knot
    Source: Springer Online Journal Archives 1860-2000
    Topics: Biology
    Notes: Abstract  While the evolutionary history of mammalian tooth shapes is well documented in the fossil record, the developmental basis of their tooth shape evolution is unknown. We investigated the expression patterns of eight developmental regulatory genes in two species of rodents with different molar morphologies (mouse, Mus musculus and sibling vole, Microtus rossiaemeridionalis). The genes Bmp-2, Bmp-4, Fgf-4 and Shh encode signal molecules, Lef-1, Msx-1 and Msx-2, are transcription factors and p21 CIP1/WAF1 participates in the regulation of cell cycle. These genes are all known to be associated with developmental regulation in mouse molars. In this paper we show that the antisense mRNA probes made from mouse cDNA cross-hybridized with vole tissue. The comparisons of gene expression patterns and morphologies suggest that similar molecular cascades are used in the early budding of tooth germs, in the initiation of tooth crown base formation, and in the initiation of each cusp’s development. Furthermore, the co-localization of several genes indicate that epithelial signalling centres function at the three stages of morphogenesis. The earliest signalling centre in the early budding epithelium has not been reported before, but the latter signalling centres, the primary and the secondary enamel knots, have been studied in mouse. The appearance of species-specific tooth shapes was manifested by the regulatory molecules expressed in the secondary enamel knots at the areas of future cusp tips, whilst the mesenchymal gene expression patterns had a buccal bias without similar species-specific associations.
    Type of Medium: Electronic Resource
    URL: http://dx.doi.org/10.1007/s004270050206
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  • 9
    Electronic Resource
    Electronic Resource
    An amphioxus snail gene: Expression in paraxial mesoderm and neural plate suggests a conserved role in patterning the chordate embryo (1998)
    Springer
    Development genes and evolution 208 (1998), S. 569-577 
    Details
    ISSN: 1432-041X
    Keywords: Key words Amphioxus ; Snail ; Neural crest ; Evolution ; Chordate
    Source: Springer Online Journal Archives 1860-2000
    Topics: Biology
    Notes: Abstract  Homologs of the Drosophila snail gene have been characterized in several vertebrates. In addition to being expressed in mesoderm during gastrulation, vertebrate snail genes are also expressed in presumptive neural crest and/or its derivatives. Given that neural crest is unique to vertebrates and is considered to be of fundamental importance in their evolution, we have cloned and characterized the expression of a snail gene from amphioxus, a cephalochordate widely accepted as the sister group of the vertebrates. We show that, at the amino acid sequence level, the amphioxus snail gene is a clear phylogenetic outgroup to all the characterized vertebrate snail genes. During embryogenesis snail expression initially becomes restricted to the paraxial or presomitic mesoderm of amphioxus. Later, snail is expressed at high levels in the lateral neural plate, where it persists during neurulation. Our results indicate that an ancestral function of snail genes in the lineage leading to vertebrates is to define the paraxial mesoderm. Furthermore, our results indicate that a cell population homologous to the vertebrate neural crest may be present in amphioxus, thus providing an important link in the evolution of this key vertebrate tissue.
    Type of Medium: Electronic Resource
    URL: http://dx.doi.org/10.1007/s004270050216
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  • 10
    Electronic Resource
    Electronic Resource
    A role for Fringe in segment morphogenesis but not segment formation in the grasshopper, Schistocerca gregaria (2000)
    Springer
    Development genes and evolution 210 (2000), S. 329-336 
    Details
    ISSN: 1432-041X
    Keywords: Key words Development ; Evolution ; Notch ; Insect
    Source: Springer Online Journal Archives 1860-2000
    Topics: Biology
    Notes: Abstract  Studies of somitogenesis in vertebrates have identified a number of genes that are regulated by a periodic oscillator that patterns the pre-somitic mesoderm. One of these genes, hairy, is homologous to a Drosophila segmentation gene that also shows periodic spatial expression. This, and the periodic expression of a zebrafish homologue of hairy during somitogenesis, has suggested that insect segmentation and vertebrate somitogenesis may use similar molecular mechanisms and possibly share a common origin. In chicks and mice expression of the lunatic fringe gene also oscillates in the presomitic mesoderm. Fringe encodes an extracellular protein that regulates Notch signalling. This, and the finding that mutations in Notch or its ligands disrupt somite patterning, suggests that Notch signalling plays an important role in vertebrate somitogenesis. Although Notch signalling is not known to play a role in the formation of segments in Drosophila, we reasoned that it might do so in other insects such as the grasshopper, where segment boundaries form between cells, not between syncytial nuclei as they do in Drosophila. Here we report the cloning of a single fringe gene from the grasshopper Schistocerca. We show that it is not detectably expressed in the forming trunk segments of the embryo until after segment boundaries have formed. We conclude that fringe is not part of the mechanism that makes segments in Schistocerca. Thereafter it is expressed in a pattern which shows that it is a downstream target of the segmentation machinery and suggests that it may play a role in segment morphogenesis. Like its Drosophila counterpart, Schistocerca fringe is also expressed in the eye, in rings in the legs, and during oogenesis, in follicle cells.
    Type of Medium: Electronic Resource
    URL: http://dx.doi.org/10.1007/s004270000072
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