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Article ; Online: Encounters with archaic hominins.

Mafessoni, Fabrizio

Nature ecology & evolution

2018 Volume 3, Issue 1, Page(s) 14–15

MeSH term(s)	Animals ; Fossils ; Hominidae ; Humans ; Neanderthals
Language	English
Publishing date	2018-11-23
Publishing country	England
Document type	Journal Article ; Comment
ISSN	2397-334X
ISSN (online)	2397-334X
DOI	10.1038/s41559-018-0729-6
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Article ; Online: On the fitness of informative cues in complex environments.

Mafessoni, Fabrizio / Lachmann, Michael / Gokhale, Chaitanya S

Journal of theoretical biology

2021 Volume 527, Page(s) 110819

Abstract: To be able to deal with uncertainty is of primary importance to most living organisms. When cues provide information about the state of the environment, organisms can use them to respond flexibly. Life forms have evolved complex adaptations and sensory ... ...

Abstract	To be able to deal with uncertainty is of primary importance to most living organisms. When cues provide information about the state of the environment, organisms can use them to respond flexibly. Life forms have evolved complex adaptations and sensory mechanisms to use these environmental cues and extract valuable information about the environment. Previous work has shown a theoretical limit to the amount of fitness benefit possible to be extracted from the cues. We show that the previously used information theoretical approaches can be generalised to scenarios involving any potential relationship between the number of possible phenotypes and environmental states. Such cases are relevant when physiological constraints or complex ecological scenarios lead to the number of environmental states exceeding potential phenotypes. We illustrate cases in which these scenarios can emerge: along environmental gradients, such as geographical transects or complex environments, where organisms adopt different bet-hedging strategies, switching stochastically between phenotypes or developing intermediate ones. In conclusion, we develop an information-theoretic extensible approach for investigating and quantifying fitness in ecological studies.
MeSH term(s)	Adaptation, Physiological ; Biological Evolution ; Cues ; Phenotype ; Uncertainty
Language	English
Publishing date	2021-06-26
Publishing country	England
Document type	Journal Article ; Research Support, Non-U.S. Gov't
ZDB-ID	2972-5
ISSN	1095-8541 ; 0022-5193
ISSN (online)	1095-8541
ISSN	0022-5193
DOI	10.1016/j.jtbi.2021.110819
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Article ; Online: The complexity of understanding others as the evolutionary origin of empathy and emotional contagion.

Mafessoni, Fabrizio / Lachmann, Michael

Scientific reports

2019 Volume 9, Issue 1, Page(s) 5794

Abstract: Contagious yawning, emotional contagion and empathy are characterized by the activation of similar neurophysiological states or responses in an observed individual and an observer. For example, it is hard to keep one's mouth closed when imagining someone ...

Abstract	Contagious yawning, emotional contagion and empathy are characterized by the activation of similar neurophysiological states or responses in an observed individual and an observer. For example, it is hard to keep one's mouth closed when imagining someone yawning, or not feeling distressed while observing other individuals perceiving pain. The evolutionary origin of these widespread phenomena is unclear, since a direct benefit is not always apparent. We explore a game theoretical model for the evolution of mind-reading strategies, used to predict and respond to others' behavior. In particular we explore the evolutionary scenarios favoring simulative strategies, which recruit overlapping neural circuits when performing as well as when observing a specific behavior. We show that these mechanisms are advantageous in complex environments, by allowing an observer to use information about its own behavior to interpret that of others. However, without inhibition of the recruited neural circuits, the observer would perform the corresponding downstream action, rather than produce the appropriate social response. We identify evolutionary trade-offs that could hinder this inhibition, leading to emotional contagion as a by-product of mind-reading. The interaction of this model with kinship is complex. We show that empathy likely evolved in a scenario where kin- and other indirect benefits co-opt strategies originally evolved for mind-reading, and that this model explains observed patterns of emotional contagion with kin or group members.
MeSH term(s)	Biological Evolution ; Brain/physiology ; Empathy ; Game Theory ; Humans ; Models, Neurological ; Models, Psychological
Language	English
Publishing date	2019-04-08
Publishing country	England
Document type	Journal Article ; Research Support, Non-U.S. Gov't
ZDB-ID	2615211-3
ISSN	2045-2322 ; 2045-2322
ISSN (online)	2045-2322
ISSN	2045-2322
DOI	10.1038/s41598-019-41835-5
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Article ; Online: Better support for a small effective population size of Neandertals and a long shared history of Neandertals and Denisovans.

Mafessoni, Fabrizio / Prüfer, Kay

Proceedings of the National Academy of Sciences of the United States of America

2017

Language	English
Publishing date	2017-11-14
Publishing country	United States
Document type	Letter
ZDB-ID	209104-5
ISSN	1091-6490 ; 0027-8424
ISSN (online)	1091-6490
ISSN	0027-8424
DOI	10.1073/pnas.1716918114
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Article ; Online: The complexity of understanding others as the evolutionary origin of empathy and emotional contagion

Fabrizio Mafessoni / Michael Lachmann

Scientific Reports, Vol 9, Iss 1, Pp 1-

2019 Volume 14

Abstract: Abstract Contagious yawning, emotional contagion and empathy are characterized by the activation of similar neurophysiological states or responses in an observed individual and an observer. For example, it is hard to keep one’s mouth closed when ... ...

Abstract	Abstract Contagious yawning, emotional contagion and empathy are characterized by the activation of similar neurophysiological states or responses in an observed individual and an observer. For example, it is hard to keep one’s mouth closed when imagining someone yawning, or not feeling distressed while observing other individuals perceiving pain. The evolutionary origin of these widespread phenomena is unclear, since a direct benefit is not always apparent. We explore a game theoretical model for the evolution of mind-reading strategies, used to predict and respond to others’ behavior. In particular we explore the evolutionary scenarios favoring simulative strategies, which recruit overlapping neural circuits when performing as well as when observing a specific behavior. We show that these mechanisms are advantageous in complex environments, by allowing an observer to use information about its own behavior to interpret that of others. However, without inhibition of the recruited neural circuits, the observer would perform the corresponding downstream action, rather than produce the appropriate social response. We identify evolutionary trade-offs that could hinder this inhibition, leading to emotional contagion as a by-product of mind-reading. The interaction of this model with kinship is complex. We show that empathy likely evolved in a scenario where kin- and other indirect benefits co-opt strategies originally evolved for mind-reading, and that this model explains observed patterns of emotional contagion with kin or group members.
Keywords	Medicine ; R ; Science ; Q
Subject code	120
Language	English
Publishing date	2019-04-01T00:00:00Z
Publisher	Nature Publishing Group
Document type	Article ; Online
Database	BASE - Bielefeld Academic Search Engine (life sciences selection)

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Article ; Online: Neandertal introgression and accumulation of hypomorphic mutations in the neuropeptide S (NPS) system promote attenuated functionality.

Reinscheid, Rainer K / Mafessoni, Fabrizio / Lüttjohann, Annika / Jüngling, Kay / Pape, Hans-Christian / Schulz, Stefan

Peptides

2021 Volume 138, Page(s) 170506

Abstract: The neuropeptide S (NPS) system plays an important role in fear and fear memory processing but has also been associated with allergic and inflammatory diseases. Genes for NPS and its receptor NPSR1 are found in all tetrapods. Compared to non-human ... ...

Abstract	The neuropeptide S (NPS) system plays an important role in fear and fear memory processing but has also been associated with allergic and inflammatory diseases. Genes for NPS and its receptor NPSR1 are found in all tetrapods. Compared to non-human primates, several non-synonymous single-nucleotide polymorphisms (SNPs) occur in both human genes that collectively result in functional attenuation, suggesting adaptive mechanisms in a human context. To investigate historic and geographic origins of these hypomorphic mutations and explore genetic signs of selection, we analyzed ancient genomes and worldwide genotype frequencies of four prototypic SNPs in the NPS system. Neandertal and Denisovan genomes contain exclusively ancestral alleles for NPSR1 while all derived alleles occur in ancient genomes of anatomically modern humans, indicating that they arose in modern Homo sapiens. Worldwide genotype frequencies for three hypomorphic NPSR1 SNPs show significant regional homogeneity but follow a gradient towards increasing derived allele frequencies that supports an out-of-Africa scenario. Increased density of high-frequency polymorphisms around the three NPSR1 loci suggests weak or possibly balancing selection. A hypomorphic mutation in the NPS precursor, however, was detected at high frequency in Eurasian Neandertal genomes and shows genetic signatures indicating that it was introgressed into the human gene pool, particularly in Southern Europe, by interbreeding with Neandertals. We discuss potential evolutionary scenarios including behavior and immune-based natural selection.
MeSH term(s)	Animals ; Biological Evolution ; Genetic Introgression/genetics ; Hominidae/genetics ; Humans ; Mutation/genetics ; Neanderthals/genetics ; Neuropeptides/genetics ; Polymorphism, Single Nucleotide/genetics ; Receptors, G-Protein-Coupled/genetics ; Selection, Genetic
Chemical Substances	NPSR1 protein, human ; Neuropeptides ; Receptors, G-Protein-Coupled ; neuropeptide S, human
Language	English
Publishing date	2021-02-05
Publishing country	United States
Document type	Journal Article
ZDB-ID	769028-9
ISSN	1873-5169 ; 0196-9781
ISSN (online)	1873-5169
ISSN	0196-9781
DOI	10.1016/j.peptides.2021.170506
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Article ; Online: Selective Strolls: Fixation and Extinction in Diploids Are Slower for Weakly Selected Mutations Than for Neutral Ones.

Mafessoni, Fabrizio / Lachmann, Michael

Genetics

2015 Volume 201, Issue 4, Page(s) 1581–1589

Abstract: In finite populations, an allele disappears or reaches fixation due to two main forces, selection and drift. Selection is generally thought to accelerate the process: a selected mutation will reach fixation faster than a neutral one, and a ... ...

Abstract	In finite populations, an allele disappears or reaches fixation due to two main forces, selection and drift. Selection is generally thought to accelerate the process: a selected mutation will reach fixation faster than a neutral one, and a disadvantageous one will quickly disappear from the population. We show that even in simple diploid populations, this is often not true. Dominance and recessivity unexpectedly slow down the evolutionary process for weakly selected alleles. In particular, slightly advantageous dominant and mildly deleterious recessive mutations reach fixation slightly more slowly than neutral ones (at most 5%). This phenomenon determines genetic signatures opposite to those expected under strong selection, such as increased instead of decreased genetic diversity around the selected site. Furthermore, we characterize a new phenomenon: mildly deleterious recessive alleles, thought to represent a wide fraction of newly arising mutations, on average survive in a population slightly longer than neutral ones, before getting lost. Consequently, these mutations are on average slightly older than neutral ones, in contrast with previous expectations. Furthermore, they slightly increase the amount of weakly deleterious polymorphisms, as a consequence of the longer unconditional sojourn times compared to neutral mutations.
MeSH term(s)	Alleles ; Diploidy ; Evolution, Molecular ; Genes, Dominant ; Genes, Recessive ; Genetic Variation ; Models, Biological ; Mutation ; Selection, Genetic
Language	English
Publishing date	2015-12
Publishing country	United States
Document type	Journal Article
ZDB-ID	2167-2
ISSN	1943-2631 ; 0016-6731
ISSN (online)	1943-2631
ISSN	0016-6731
DOI	10.1534/genetics.115.178160
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Zs.B 767: Show issues

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Article ; Online: CRISPR/Cas9-induced DNA breaks trigger crossover, chromosomal loss, and chromothripsis-like rearrangements.

Samach, Aviva / Mafessoni, Fabrizio / Gross, Or / Melamed-Bessudo, Cathy / Filler-Hayut, Shdema / Dahan-Meir, Tal / Amsellem, Ziva / Pawlowski, Wojciech P / Levy, Avraham A

The Plant cell

2023 Volume 35, Issue 11, Page(s) 3957–3972

Abstract: DNA double-stranded breaks (DSBs) generated by the Cas9 nuclease are commonly repaired via nonhomologous end-joining (NHEJ) or homologous recombination (HR). However, little is known about unrepaired DSBs and the type of damage they trigger in plants. We ...

Abstract	DNA double-stranded breaks (DSBs) generated by the Cas9 nuclease are commonly repaired via nonhomologous end-joining (NHEJ) or homologous recombination (HR). However, little is known about unrepaired DSBs and the type of damage they trigger in plants. We designed an assay that detects loss of heterozygosity (LOH) in somatic cells, enabling the study of a broad range of DSB-induced genomic events. The system relies on a mapped phenotypic marker which produces a light purple color (betalain pigment) in all plant tissues. Plants with sectors lacking the Betalain marker upon DSB induction between the marker and the centromere were tested for LOH events. Using this assay, we detected a tomato (Solanum lycopersicum) flower with a twin yellow and dark purple sector, corresponding to a germinally transmitted somatic crossover event. We also identified instances of small deletions of genomic regions spanning the T-DNA and whole chromosome loss. In addition, we show that major chromosomal rearrangements including loss of large fragments, inversions, and translocations were clearly associated with the CRISPR-induced DSB. Detailed characterization of complex rearrangements by whole-genome sequencing and molecular and cytological analyses supports a model in which a breakage-fusion-bridge cycle followed by chromothripsis-like rearrangements had been induced. Our LOH assay provides a tool for precise breeding via targeted crossover detection. It also uncovers CRISPR-mediated chromothripsis-like events in plants.
MeSH term(s)	Chromothripsis ; CRISPR-Cas Systems/genetics ; DNA Breaks, Double-Stranded ; DNA End-Joining Repair ; Homologous Recombination ; Solanum lycopersicum/genetics
Language	English
Publishing date	2023-07-27
Publishing country	England
Document type	Journal Article
ZDB-ID	623171-8
ISSN	1532-298X ; 1040-4651
ISSN (online)	1532-298X
ISSN	1040-4651
DOI	10.1093/plcell/koad209
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Article: Neandertal introgression and accumulation of hypomorphic mutations in the neuropeptide S (NPS) system promote attenuated functionality

Reinscheid, Rainer K / Mafessoni, Fabrizio / Lüttjohann, Annika / Jüngling, Kay / Pape, Hans-Christian / Schulz, Stefan

Peptides. 2021 Apr., v. 138

2021

Abstract	The neuropeptide S (NPS) system plays an important role in fear and fear memory processing but has also been associated with allergic and inflammatory diseases. Genes for NPS and its receptor NPSR1 are found in all tetrapods. Compared to non-human primates, several non-synonymous single-nucleotide polymorphisms (SNPs) occur in both human genes that collectively result in functional attenuation, suggesting adaptive mechanisms in a human context. To investigate historic and geographic origins of these hypomorphic mutations and explore genetic signs of selection, we analyzed ancient genomes and worldwide genotype frequencies of four prototypic SNPs in the NPS system. Neandertal and Denisovan genomes contain exclusively ancestral alleles for NPSR1 while all derived alleles occur in ancient genomes of anatomically modern humans, indicating that they arose in modern Homo sapiens. Worldwide genotype frequencies for three hypomorphic NPSR1 SNPs show significant regional homogeneity but follow a gradient towards increasing derived allele frequencies that supports an out-of-Africa scenario. Increased density of high-frequency polymorphisms around the three NPSR1 loci suggests weak or possibly balancing selection. A hypomorphic mutation in the NPS precursor, however, was detected at high frequency in Eurasian Neandertal genomes and shows genetic signatures indicating that it was introgressed into the human gene pool, particularly in Southern Europe, by interbreeding with Neandertals. We discuss potential evolutionary scenarios including behavior and immune-based natural selection.
Keywords	alleles ; fearfulness ; gene pool ; genotype ; humans ; introgression ; memory ; natural selection ; neuropeptides ; Southern European region
Language	English
Dates of publication	2021-04
Publishing place	Elsevier Inc.
Document type	Article
Note	NAL-AP-2-clean
ZDB-ID	769028-9
ISSN	1873-5169 ; 0196-9781
ISSN (online)	1873-5169
ISSN	0196-9781
DOI	10.1016/j.peptides.2021.170506
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Article ; Online: Genome sequences of five Sitopsis species of Aegilops and the origin of polyploid wheat B subgenome.

Li, Lin-Feng / Zhang, Zhi-Bin / Wang, Zhen-Hui / Li, Ning / Sha, Yan / Wang, Xin-Feng / Ding, Ning / Li, Yang / Zhao, Jing / Wu, Ying / Gong, Lei / Mafessoni, Fabrizio / Levy, Avraham A / Liu, Bao

Molecular plant

2022 Volume 15, Issue 3, Page(s) 488–503

Abstract: Common wheat (Triticum aestivum, BBAADD) is a major staple food crop worldwide. The diploid progenitors of the A and D subgenomes have been unequivocally identified; that of B, however, remains ambiguous and controversial but is suspected to be related ... ...

Abstract	Common wheat (Triticum aestivum, BBAADD) is a major staple food crop worldwide. The diploid progenitors of the A and D subgenomes have been unequivocally identified; that of B, however, remains ambiguous and controversial but is suspected to be related to species of Aegilops, section Sitopsis. Here, we report the assembly of chromosome-level genome sequences of all five Sitopsis species, namely Aegilops bicornis, Ae. longissima, Ae. searsii, Ae. sharonensis, and Ae. speltoides, as well as the partial assembly of the Amblyopyrum muticum (synonym Aegilops mutica) genome for phylogenetic analysis. Our results reveal that the donor of the common wheat B subgenome is a distinct, and most probably extinct, diploid species that diverged from an ancestral progenitor of the B lineage to which the still extant Ae. speltoides and Am. muticum belong. In addition, we identified interspecific genetic introgressions throughout the evolution of the Triticum/Aegilops species complex. The five Sitopsis species have various assembled genome sizes (4.11-5.89 Gb) with high proportions of repetitive sequences (85.99%-89.81%); nonetheless, they retain high collinearity with other genomes or subgenomes of species in the Triticum/Aegilops complex. Differences in genome size were primarily due to independent post-speciation amplification of transposons. We also identified a set of Sitopsis genes pertinent to important agronomic traits that can be harnessed for wheat breeding. These newly assembled genome resources provide a new roadmap for evolutionary and genetic studies of the Triticum/Aegilops complex, as well as for wheat improvement.
MeSH term(s)	Aegilops/genetics ; Genome, Plant/genetics ; Phylogeny ; Plant Breeding ; Polyploidy ; Triticum/genetics
Language	English
Publishing date	2022-01-01
Publishing country	England
Document type	Journal Article ; Research Support, Non-U.S. Gov't
ZDB-ID	2393618-6
ISSN	1752-9867 ; 1674-2052
ISSN (online)	1752-9867
ISSN	1674-2052
DOI	10.1016/j.molp.2021.12.019
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