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  1. Article ; Online: Transposable Element Insertions Are Associated with Batesian Mimicry in the Pantropical Butterfly Hypolimnas misippus.

    Orteu, Anna / Kucka, Marek / Gordon, Ian J / Ng'iru, Ivy / van der Heijden, Eva S M / Talavera, Gerard / Warren, Ian A / Collins, Steve / Ffrench-Constant, Richard H / Martins, Dino J / Chan, Yingguang Frank / Jiggins, Chris D / Martin, Simon H

    Molecular biology and evolution

    2024  Volume 41, Issue 3

    Abstract: Hypolimnas misippus is a Batesian mimic of the toxic African Queen butterfly (Danaus chrysippus). Female H. misippus butterflies use two major wing patterning loci (M and A) to imitate three color morphs of D. chrysippus found in different regions of ... ...

    Abstract Hypolimnas misippus is a Batesian mimic of the toxic African Queen butterfly (Danaus chrysippus). Female H. misippus butterflies use two major wing patterning loci (M and A) to imitate three color morphs of D. chrysippus found in different regions of Africa. In this study, we examine the evolution of the M locus and identify it as an example of adaptive atavism. This phenomenon involves a morphological reversion to an ancestral character that results in an adaptive phenotype. We show that H. misippus has re-evolved an ancestral wing pattern present in other Hypolimnas species, repurposing it for Batesian mimicry of a D. chrysippus morph. Using haplotagging, a linked-read sequencing technology, and our new analytical tool, Wrath, we discover two large transposable element insertions located at the M locus and establish that these insertions are present in the dominant allele responsible for producing mimetic phenotype. By conducting a comparative analysis involving additional Hypolimnas species, we demonstrate that the dominant allele is derived. This suggests that, in the derived allele, the transposable elements disrupt a cis-regulatory element, leading to the reversion to an ancestral phenotype that is then utilized for Batesian mimicry of a distinct model, a different morph of D. chrysippus. Our findings present a compelling instance of convergent evolution and adaptive atavism, in which the same pattern element has independently evolved multiple times in Hypolimnas butterflies, repeatedly playing a role in Batesian mimicry of diverse model species.
    MeSH term(s) Animals ; Butterflies/genetics ; DNA Transposable Elements ; Biological Mimicry/genetics ; Phenotype ; Africa ; Wings, Animal/anatomy & histology
    Chemical Substances DNA Transposable Elements
    Language English
    Publishing date 2024-02-24
    Publishing country United States
    Document type Journal Article
    ZDB-ID 998579-7
    ISSN 1537-1719 ; 0737-4038
    ISSN (online) 1537-1719
    ISSN 0737-4038
    DOI 10.1093/molbev/msae041
    Database MEDical Literature Analysis and Retrieval System OnLINE

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  2. Article ; Online: Gradients in embolism resistance within stems driven by secondary growth in herbs.

    Haverroth, Eduardo J / Rimer, Ian M / Oliveira, Leonardo A / de Lima, Leydson G A / Cesarino, Igor / Martins, Samuel C V / McAdam, Scott A M / Cardoso, Amanda A

    Plant, cell & environment

    2024  

    Abstract: The stems of some herbaceous species can undergo basal secondary growth, leading to a continuum in the degree of woodiness along the stem. Whether the formation of secondary growth in the stem base results in differences in embolism resistance between ... ...

    Abstract The stems of some herbaceous species can undergo basal secondary growth, leading to a continuum in the degree of woodiness along the stem. Whether the formation of secondary growth in the stem base results in differences in embolism resistance between the base and the upper portions of stems is unknown. We assessed the embolism resistance of leaves and the basal and upper portions of stems simultaneously within the same individuals of two divergent herbaceous species that undergo secondary growth in the mature stem bases. The species were Solanum lycopersicum (tomato) and Senecio minimus (fireweed). Basal stem in mature plants of both species displayed advanced secondary growth and greater resistance to embolism than the upper stem. This also resulted in significant vulnerability segmentation between the basal stem and the leaves in both species. Greater embolism resistance in the woodier stem base was found alongside decreases in the pith-to-xylem ratio, increases in the proportion of secondary xylem, and increases in lignin content. We show that there can be considerable variation in embolism resistance across the stem in herbs and that this variation is linked to the degree of secondary growth present. A gradient in embolism resistance across the stem in herbaceous plants could be an adaptation to ensure reproduction or basal resprouting during episodes of drought late in the lifecycle.
    Language English
    Publishing date 2024-04-21
    Publishing country United States
    Document type Journal Article
    ZDB-ID 391893-2
    ISSN 1365-3040 ; 0140-7791
    ISSN (online) 1365-3040
    ISSN 0140-7791
    DOI 10.1111/pce.14921
    Database MEDical Literature Analysis and Retrieval System OnLINE

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  3. Article ; Online: Stepwise evolution of a butterfly supergene via duplication and inversion.

    Kim, Kang-Wook / De-Kayne, Rishi / Gordon, Ian J / Omufwoko, Kennedy Saitoti / Martins, Dino J / Ffrench-Constant, Richard / Martin, Simon H

    Philosophical transactions of the Royal Society of London. Series B, Biological sciences

    2022  Volume 377, Issue 1856, Page(s) 20210207

    Abstract: Supergenes maintain adaptive clusters of alleles in the face of genetic mixing. Although usually attributed to inversions, supergenes can be complex, and reconstructing the precise processes that led to recombination suppression and their timing is ... ...

    Abstract Supergenes maintain adaptive clusters of alleles in the face of genetic mixing. Although usually attributed to inversions, supergenes can be complex, and reconstructing the precise processes that led to recombination suppression and their timing is challenging. We investigated the origin of the BC supergene, which controls variation in warning coloration in the African monarch butterfly,
    MeSH term(s) Alleles ; Animals ; Butterflies/genetics ; Chromosome Inversion ; Evolution, Molecular ; Phylogeny ; Polymorphism, Genetic
    Language English
    Publishing date 2022-06-13
    Publishing country England
    Document type Journal Article ; Research Support, Non-U.S. Gov't
    ZDB-ID 208382-6
    ISSN 1471-2970 ; 0080-4622 ; 0264-3839 ; 0962-8436
    ISSN (online) 1471-2970
    ISSN 0080-4622 ; 0264-3839 ; 0962-8436
    DOI 10.1098/rstb.2021.0207
    Database MEDical Literature Analysis and Retrieval System OnLINE

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  4. Article ; Online: CD3

    de Almeida, Sergio M / Beltrame, Miriam Perlingeiro / Tang, Bin / Rotta, Indianara / Justus, Julie Lilian P / Schluga, Yara / da Rocha, Maria Tadeu / Martins, Edna / Liao, Antony / Abramson, Ian / Vaida, Florin / Schrier, Rachel / Ellis, Ronald J

    Journal of neuroimmunology

    2023  Volume 377, Page(s) 578067

    Abstract: The transactivator of transcription (Tat) is a HIV regulatory protein which promotes viral replication and chemotaxis. HIV-1 shows extensive genetic diversity, HIV-1 subtype C being the most dominant subtype in the world. Our hypothesis is the frequency ... ...

    Abstract The transactivator of transcription (Tat) is a HIV regulatory protein which promotes viral replication and chemotaxis. HIV-1 shows extensive genetic diversity, HIV-1 subtype C being the most dominant subtype in the world. Our hypothesis is the frequency of CSF CD3
    MeSH term(s) Humans ; HIV-1/metabolism ; Killer Cells, Natural/metabolism ; CD56 Antigen/metabolism ; Natural Killer T-Cells/metabolism ; HIV Infections/metabolism ; CD3 Complex ; Flow Cytometry
    Chemical Substances CD56 Antigen ; CD3 Complex
    Language English
    Publishing date 2023-03-17
    Publishing country Netherlands
    Document type Journal Article
    ZDB-ID 8335-5
    ISSN 1872-8421 ; 0165-5728
    ISSN (online) 1872-8421
    ISSN 0165-5728
    DOI 10.1016/j.jneuroim.2023.578067
    Database MEDical Literature Analysis and Retrieval System OnLINE

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  5. Article ; Online: Global biogeography of warning coloration in the butterfly

    Liu, Wanzhen / Smith, David A S / Raina, Gayatri / Stanforth, Rowan / Ng'Iru, Ivy / Ireri, Piera / Martins, Dino J / Gordon, Ian J / Martin, Simon H

    Biology letters

    2022  Volume 18, Issue 6, Page(s) 20210639

    Abstract: Warning coloration provides a textbook example of natural selection, but the frequent observation of polymorphism in aposematic species presents an evolutionary puzzle. We investigated biogeography and polymorphism of warning patterns in the widespread ... ...

    Abstract Warning coloration provides a textbook example of natural selection, but the frequent observation of polymorphism in aposematic species presents an evolutionary puzzle. We investigated biogeography and polymorphism of warning patterns in the widespread butterfly
    MeSH term(s) Adaptation, Biological ; Animals ; Biological Evolution ; Butterflies/genetics ; Citizen Science ; Gene Frequency ; Phenotype ; Pigmentation ; Predatory Behavior ; Selection, Genetic
    Language English
    Publishing date 2022-06-01
    Publishing country England
    Document type Journal Article ; Research Support, Non-U.S. Gov't
    ZDB-ID 2135022-X
    ISSN 1744-957X ; 1744-9561
    ISSN (online) 1744-957X
    ISSN 1744-9561
    DOI 10.1098/rsbl.2021.0639
    Database MEDical Literature Analysis and Retrieval System OnLINE

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  6. Article ; Online: Sodium Butyrate Reduces Brain Amyloid-β Levels and Improves Cognitive Memory Performance in an Alzheimer's Disease Transgenic Mouse Model at an Early Disease Stage.

    Fernando, W M A D Binosha / Martins, Ian J / Morici, Michael / Bharadwaj, Prashant / Rainey-Smith, Stephanie R / Lim, Wei Ling Florence / Martins, Ralph N

    Journal of Alzheimer's disease : JAD

    2020  Volume 74, Issue 1, Page(s) 91–99

    Abstract: Alzheimer's disease (AD) is a neurodegenerative disorder characterized by progressive cognitive decline and neuropathological features, including abnormal deposition of amyloid-β (Aβ) peptides, intracellular neurofibrillary tangles, and neuronal death. ... ...

    Abstract Alzheimer's disease (AD) is a neurodegenerative disorder characterized by progressive cognitive decline and neuropathological features, including abnormal deposition of amyloid-β (Aβ) peptides, intracellular neurofibrillary tangles, and neuronal death. Identifying therapeutics which can reduce memory deficits at an early stage of the disease has the advantage of slowing or even reversing disease progression before irreversible brain damage has occurred. Consequently, in this study, we investigated the ability of the histone deacetylase inhibitor sodium butyrate (NaB) to attenuate memory deficits in the 5xFAD mouse model of AD following a 12-week feeding regimen. 5xFAD mice demonstrate a unique time course of Aβ pathology, developing Aβ plaques as early as 2 months. Male mice were assigned to either a control diet or a NaB-supplemented diet which was administered at either 5 mg/kg/day, or 15 mg/kg/day for 12 weeks (each group, N = 15). Supplementation commenced at an early disease stage (8-10 weeks of age). Behavioral testing (contextual and cued fear conditioning) was undertaken, and brain Aβ levels measured, at the end of the 12-week intervention. NaB had profound effects on Aβ levels and on associative learning and cognitive functioning. A 40% reduction in brain Aβ levels and a 25% increase in fear response in both the cued and contextual testing was observed in the NaB-treated animals compared to the control group. These findings suggest that NaB warrants further investigation as a potential therapeutic agent in the treatment of cognitive deficits associated with early stages of AD.
    MeSH term(s) Alzheimer Disease/drug therapy ; Alzheimer Disease/genetics ; Amyloid beta-Peptides/metabolism ; Animals ; Brain Chemistry/drug effects ; Butyric Acid/pharmacology ; Cues ; Diet ; Fear/drug effects ; Humans ; Male ; Memory/drug effects ; Mice ; Mice, Transgenic ; Nootropic Agents/pharmacology
    Chemical Substances Amyloid beta-Peptides ; Nootropic Agents ; Butyric Acid (107-92-6)
    Language English
    Publishing date 2020-01-16
    Publishing country Netherlands
    Document type Journal Article ; Research Support, Non-U.S. Gov't
    ZDB-ID 1440127-7
    ISSN 1875-8908 ; 1387-2877
    ISSN (online) 1875-8908
    ISSN 1387-2877
    DOI 10.3233/JAD-190120
    Database MEDical Literature Analysis and Retrieval System OnLINE

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  7. Article ; Online: The Landscape of Potential Small and Drug Substance Related Nitrosamines in Pharmaceuticals.

    Schlingemann, Joerg / Burns, Michael J / Ponting, David J / Martins Avila, Carolina / Romero, Naiffer E / Jaywant, Mrunal A / Smith, Graham F / Ashworth, Ian W / Simon, Stephanie / Saal, Christoph / Wilk, Andrzej

    Journal of pharmaceutical sciences

    2022  Volume 112, Issue 5, Page(s) 1287–1304

    Abstract: This article reports the outcome of an in silico analysis of more than 12,000 small molecule drugs and drug impurities, identifying the nitrosatable structures, assessing their potential to form nitrosamines under relevant conditions and the challenges ... ...

    Abstract This article reports the outcome of an in silico analysis of more than 12,000 small molecule drugs and drug impurities, identifying the nitrosatable structures, assessing their potential to form nitrosamines under relevant conditions and the challenges to determine compound-specific AIs based on data available or read-across approaches for these nitrosamines and their acceptance by health authorities. Our data indicate that the presence of nitrosamines in pharmaceuticals is likely more prevalent than originally expected. In total, 40.4 % of the analyzed APIs and 29.6 % of the API impurities are potential nitrosamine precursors. Most structures identified through our workflow could form complex API-related nitrosamines, so-called nitrosamine drug substance related impurities (NDSRIs), although we also found structures that could release the well-known small and potent nitrosamines NDMA, NDEA, and others. Due to common structural motifs including secondary or tertiary amine moieties, whole essential drug classes such as beta blockers and ACE inhibitors are at risk. To avoid the risk of drug shortages or even the complete loss of therapeutic options, it will be essential that the well-established ICH M7 principles remain applicable for nitrosamines and that that the industry and regulatory authorities keep an open communication not only about the science but also to make sure there is a good balance between risk and benefit to patients.
    MeSH term(s) Humans ; Nitrosamines/chemistry ; Amines/chemistry ; Pharmaceutical Preparations
    Chemical Substances Nitrosamines ; Amines ; Pharmaceutical Preparations
    Language English
    Publishing date 2022-11-17
    Publishing country United States
    Document type Journal Article
    ZDB-ID 3151-3
    ISSN 1520-6017 ; 0022-3549
    ISSN (online) 1520-6017
    ISSN 0022-3549
    DOI 10.1016/j.xphs.2022.11.013
    Database MEDical Literature Analysis and Retrieval System OnLINE

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  8. Article ; Online: Taxonomic resolution of the ribosomal RNA operon in bacteria: implications for its use with long-read sequencing.

    de Oliveira Martins, Leonardo / Page, Andrew J / Mather, Alison E / Charles, Ian G

    NAR genomics and bioinformatics

    2019  Volume 2, Issue 1, Page(s) lqz016

    Abstract: DNA barcoding through the use of amplified regions of the ribosomal operon, such as the 16S gene, is a routine method to gain an overview of the microbial taxonomic diversity within a sample without the need to isolate and culture the microbes present. ... ...

    Abstract DNA barcoding through the use of amplified regions of the ribosomal operon, such as the 16S gene, is a routine method to gain an overview of the microbial taxonomic diversity within a sample without the need to isolate and culture the microbes present. However, bacterial cells usually have multiple copies of this ribosomal operon, and choosing the 'wrong' copy could provide a misleading species classification. While this presents less of a problem for well-characterized organisms with large sequence databases to interrogate, it is a significant challenge for lesser known organisms with unknown copy number and diversity. Using the entire length of the ribosomal operon, which encompasses the 16S, 23S, 5S and internal transcribed spacer regions, should provide greater taxonomic resolution but has not been well explored. Here, we use publicly available reference genomes and explore the theoretical boundaries when using concatenated genes and the full-length ribosomal operons, which has been made possible by the development and uptake of long-read sequencing technologies. We quantify the issues of both copy choice and operon length in a phylogenetic context to demonstrate that longer regions improve the phylogenetic signal while maintaining taxonomic accuracy.
    Language English
    Publishing date 2019-11-14
    Publishing country England
    Document type Journal Article
    ISSN 2631-9268
    ISSN (online) 2631-9268
    DOI 10.1093/nargab/lqz016
    Database MEDical Literature Analysis and Retrieval System OnLINE

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  9. Article ; Online: Applying an evolutionary mismatch framework to understand disease susceptibility.

    Lea, Amanda J / Clark, Andrew G / Dahl, Andrew W / Devinsky, Orrin / Garcia, Angela R / Golden, Christopher D / Kamau, Joseph / Kraft, Thomas S / Lim, Yvonne A L / Martins, Dino J / Mogoi, Donald / Pajukanta, Päivi / Perry, George H / Pontzer, Herman / Trumble, Benjamin C / Urlacher, Samuel S / Venkataraman, Vivek V / Wallace, Ian J / Gurven, Michael /
    Lieberman, Daniel E / Ayroles, Julien F

    PLoS biology

    2023  Volume 21, Issue 9, Page(s) e3002311

    Abstract: Noncommunicable diseases (NCDs) are on the rise worldwide. Obesity, cardiovascular disease, and type 2 diabetes are among a long list of "lifestyle" diseases that were rare throughout human history but are now common. The evolutionary mismatch hypothesis ...

    Abstract Noncommunicable diseases (NCDs) are on the rise worldwide. Obesity, cardiovascular disease, and type 2 diabetes are among a long list of "lifestyle" diseases that were rare throughout human history but are now common. The evolutionary mismatch hypothesis posits that humans evolved in environments that radically differ from those we currently experience; consequently, traits that were once advantageous may now be "mismatched" and disease causing. At the genetic level, this hypothesis predicts that loci with a history of selection will exhibit "genotype by environment" (GxE) interactions, with different health effects in "ancestral" versus "modern" environments. To identify such loci, we advocate for combining genomic tools in partnership with subsistence-level groups experiencing rapid lifestyle change. In these populations, comparisons of individuals falling on opposite extremes of the "matched" to "mismatched" spectrum are uniquely possible. More broadly, the work we propose will inform our understanding of environmental and genetic risk factors for NCDs across diverse ancestries and cultures.
    MeSH term(s) Humans ; Disease Susceptibility ; Diabetes Mellitus, Type 2/genetics ; Biological Evolution ; Cardiovascular Diseases ; Genomics
    Language English
    Publishing date 2023-09-11
    Publishing country United States
    Document type Journal Article ; Research Support, N.I.H., Extramural ; Research Support, Non-U.S. Gov't
    ZDB-ID 2126776-5
    ISSN 1545-7885 ; 1544-9173
    ISSN (online) 1545-7885
    ISSN 1544-9173
    DOI 10.1371/journal.pbio.3002311
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  10. Article ; Online: Evolutionary mismatch and the role of GxE interactions in human disease.

    Lea, Amanda J / Clark, Andrew G / Dahl, Andrew W / Devinsky, Orrin / Garcia, Angela R / Golden, Christopher D / Kamau, Joseph / Kraft, Thomas S / Lim, Yvonne A L / Martins, Dino / Mogoi, Donald / Pajukanta, Paivi / Perry, George / Pontzer, Herman / Trumble, Benjamin C / Urlacher, Samuel S / Venkataraman, Vivek V / Wallace, Ian J / Gurven, Michael /
    Lieberman, Daniel / Ayroles, Julien F

    ArXiv

    2023  

    Abstract: Globally, we are witnessing the rise of complex, non-communicable diseases (NCDs) related to changes in our daily environments. Obesity, asthma, cardiovascular disease, and type 2 diabetes are part of a long list of "lifestyle" diseases that were rare ... ...

    Abstract Globally, we are witnessing the rise of complex, non-communicable diseases (NCDs) related to changes in our daily environments. Obesity, asthma, cardiovascular disease, and type 2 diabetes are part of a long list of "lifestyle" diseases that were rare throughout human history but are now common. A key idea from anthropology and evolutionary biology-the evolutionary mismatch hypothesis-seeks to explain this phenomenon. It posits that humans evolved in environments that radically differ from the ones experienced by most people today, and thus traits that were advantageous in past environments may now be "mismatched" and disease-causing. This hypothesis is, at its core, a genetic one: it predicts that loci with a history of selection will exhibit "genotype by environment" (GxE) interactions and have differential health effects in ancestral versus modern environments. Here, we discuss how this concept could be leveraged to uncover the genetic architecture of NCDs in a principled way. Specifically, we advocate for partnering with small-scale, subsistence-level groups that are currently transitioning from environments that are arguably more "matched" with their recent evolutionary history to those that are more "mismatched". These populations provide diverse genetic backgrounds as well as the needed levels and types of environmental variation necessary for mapping GxE interactions in an explicit mismatch framework. Such work would make important contributions to our understanding of environmental and genetic risk factors for NCDs across diverse ancestries and sociocultural contexts.
    Language English
    Publishing date 2023-02-13
    Publishing country United States
    Document type Preprint
    ISSN 2331-8422
    ISSN (online) 2331-8422
    Database MEDical Literature Analysis and Retrieval System OnLINE

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