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Saunders AN, Gallant JR. A review of the reproductive biology of mormyroid fishes: An emerging model for biomedical research. JOURNAL OF EXPERIMENTAL ZOOLOGY. PART B, MOLECULAR AND DEVELOPMENTAL EVOLUTION 2024; 342:144-163. [PMID: 38361399 DOI: 10.1002/jez.b.23242] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Subscribe] [Scholar Register] [Received: 06/14/2023] [Revised: 12/13/2023] [Accepted: 01/17/2024] [Indexed: 02/17/2024]
Abstract
Mormyroidea is a superfamily of weakly electric African fishes with great potential as a model in a variety of biomedical research areas including systems neuroscience, muscle cell and craniofacial development, ion channel biophysics, and flagellar/ciliary biology. However, they are currently difficult to breed in the laboratory setting, which is essential for any tractable model organism. As such, there is a need to better understand the reproductive biology of mormyroids to breed them more reliably in the laboratory to effectively use them as a biomedical research model. This review seeks to (1) briefly highlight the biomedically relevant phenotypes of mormyroids and (2) compile information about mormyroid reproduction including sex differences, breeding season, sexual maturity, gonads, gametes, and courtship/spawning behaviors. We also highlight areas of mormyroid reproductive biology that are currently unexplored and/or have the potential for further investigation that may provide insights into more successful mormyroid laboratory breeding methods.
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Affiliation(s)
- Alyssa N Saunders
- Department of Integrative Biology, Michigan State University, East Lansing, Michigan, USA
- Ecology, Evolution, and Behavior Program, Michigan State University, East Lansing, Michigan, USA
| | - Jason R Gallant
- Department of Integrative Biology, Michigan State University, East Lansing, Michigan, USA
- Ecology, Evolution, and Behavior Program, Michigan State University, East Lansing, Michigan, USA
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2
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Schneider PN, Seemann F, Harris MP, Braasch I. Trawling aquatic life for new models in biomedical research and evolutionary developmental biology. JOURNAL OF EXPERIMENTAL ZOOLOGY. PART B, MOLECULAR AND DEVELOPMENTAL EVOLUTION 2024; 342:123-125. [PMID: 38686776 DOI: 10.1002/jez.b.23255] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [MESH Headings] [Grants] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 05/02/2024]
Affiliation(s)
- Patricia N Schneider
- Department of Biological Sciences, Division of Cellular, Developmental and Integrative Biology, Louisiana State University, Baton Rouge, Louisiana, USA
| | - Frauke Seemann
- Department of Life Sciences, Texas A&M University-Corpus Christi, Corpus Christi, Texas, USA
| | - Matthew P Harris
- Department of Genetics, Harvard Medical School, Boston, Massachusetts, USA
- Department of Orthopaedic Surgery, Boston Children's Hospital, Boston, Massachusetts, USA
| | - Ingo Braasch
- Department of Integrative Biology, Michigan State University, East Lansing, Michigan, USA
- Program in Ecology, Evolution, and Behavior, Michigan State University, East Lansing, Michigan, USA
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3
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Lukić M, Jovović L, Bedek J, Grgić M, Kuharić N, Rožman T, Čupić I, Weck B, Fong D, Bilandžija H. A practical guide for the husbandry of cave and surface invertebrates as the first step in establishing new model organisms. PLoS One 2024; 19:e0300962. [PMID: 38573919 PMCID: PMC10994295 DOI: 10.1371/journal.pone.0300962] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/02/2023] [Accepted: 03/07/2024] [Indexed: 04/06/2024] Open
Abstract
While extensive research on traditional model species has significantly advanced the biological sciences, the ongoing search for new model organisms is essential to tackle contemporary challenges such as human diseases or climate change, and fundamental phenomena including adaptation or speciation. Recent methodological advances such as next-generation sequencing, gene editing, and imaging are widely applicable and have simplified the selection of species with specific traits from the wild. However, a critical milestone in this endeavor remains the successful cultivation of selected species. A historically overlooked but increasingly recognized group of non-model organisms are cave dwellers. These unique animals offer invaluable insights into the genetic basis of human diseases like eye degeneration, metabolic and neurological disorders, and basic evolutionary principles and the origin of adaptive phenotypes. However, to take advantage of the beneficial traits of cave-dwelling animals, laboratory cultures must be established-a practice that remains extremely rare except for the cavefish Astyanax mexicanus. For most cave-dwelling organisms, there are no published culturing protocols. In this study, we present the results of our multi-year effort to establish laboratory cultures for a variety of invertebrate groups. We have developed comprehensive protocols for housing, feeding, and husbandry of cave dwellers and their surface relatives. Our recommendations are versatile and can be applied to a wide range of species. Hopefully our efforts will facilitate the establishment of new laboratory animal facilities for cave-dwelling organisms and encourage their greater use in experimental biology.
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Affiliation(s)
- Marko Lukić
- Department of Molecular Biology, Ruđer Bošković Institute, Zagreb, Croatia
- Croatian Natural History Museum, Zagreb, Croatia
| | - Lada Jovović
- Department of Molecular Biology, Ruđer Bošković Institute, Zagreb, Croatia
| | - Jana Bedek
- Department of Molecular Biology, Ruđer Bošković Institute, Zagreb, Croatia
- Croatian Biospeleological Society, Zagreb, Croatia
| | - Magdalena Grgić
- Department of Molecular Biology, Ruđer Bošković Institute, Zagreb, Croatia
| | | | - Tin Rožman
- Department of Molecular Biology, Ruđer Bošković Institute, Zagreb, Croatia
- Croatian Biospeleological Society, Zagreb, Croatia
| | - Iva Čupić
- Department of Molecular Biology, Ruđer Bošković Institute, Zagreb, Croatia
- Croatian Biospeleological Society, Zagreb, Croatia
| | - Bob Weck
- Department of Biology, Southwestern Illinois College, Belleville, Illinois, United States of America
| | - Daniel Fong
- Department of Biology, American University, Washington, DC, United States of America
| | - Helena Bilandžija
- Department of Molecular Biology, Ruđer Bošković Institute, Zagreb, Croatia
- Croatian Biospeleological Society, Zagreb, Croatia
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4
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Niotis A, Dimitroulis D, Spyropoulou D, Tsiambas E, Sarlanis H, Davris D, Falidas E, Kavantzas N, Peschos D, Manaios L, Konstantinidis KC. Comparative Expression Analysis of TP53 Tumor Suppressor and MDM2 Oncogene in Colorectal Adenocarcinoma. CANCER DIAGNOSIS & PROGNOSIS 2024; 4:129-134. [PMID: 38434910 PMCID: PMC10905287 DOI: 10.21873/cdp.10298] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Subscribe] [Scholar Register] [Received: 11/26/2023] [Accepted: 01/24/2024] [Indexed: 03/05/2024]
Abstract
Background/Aim The tumor protein 53 (TP53) tumor suppressor protein (17p13.1) acts as a significant regulator for the cell cycle normal function. The gene is frequently mutated in colorectal adenocarcinoma (CRC) patients and is associated to poor prognosis and low response rates to chemo-targeted therapy. Our purpose was to correlate TP53 expression with Mouse Double Minute 2 Homolog (MDM2), a proto-oncogene (12q14.3) and a major negative regulator in the TP53-MDM2 auto-regulatory pathway. Materials and Methods A total of forty (n=40) colorectal adenocarcinoma (CRC) cases were included in this study. An immunohistochemistry-based assay was implemented by using anti-TP53 and anti-MDM2 antibodies in the corresponding tissue sections. Additionally, a digital image analysis assay was implemented for objectively measuring TP53/MDM2 immunostaining intensity levels. Results TP53 protein overexpression was detected in 27/40 (67.5%), whereas MDM2 overexpression in 28/40 (70%) cases. Interestingly, in 21/40 (52.5%) cases, a combined TP53/MDM2 co-expression was detected, whereas in 6/40 (15%), a combined loss of expression was identified (overall co-expression: p=0.119). p53 overexpression was significantly correlated to grade of the examined cases (p=0.001), whereas MDM2 to stage and max diameter of the malignancies (p=0.001 and 0.024, respectively). Conclusion TP53/MDM2 over expression is a frequent and significant genetic event in CRCs associated with an aggressive biological behavior, as a result of increased dedifferentiation grade and advanced stage/elevated tumor volume, respectively. MDM2 oncogene overactivation combined with mutated and overexpressed TP53 is observed in sub-groups of patients leading to specific gene/protein signatures - targets for personalized chemotherapeutic approaches.
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Affiliation(s)
- Athanasios Niotis
- Second Department of Propaedeutic Surgery, 'Laiko' General Hospital, Medical School, National and Kapodistrian University, Athens, Greece
| | - Dimitrios Dimitroulis
- Second Department of Propaedeutic Surgery, 'Laiko' General Hospital, Medical School, National and Kapodistrian University, Athens, Greece
| | - Despoina Spyropoulou
- Department of Radiation Oncology, Medical School, University of Patras, Patras, Greece
| | - Evangelos Tsiambas
- First Department of Pathology, Medical School, National and Kapodistrian University, Athens, Greece
- Department of Cytopathology, 417 Army Equity Fund Hospital Cytology, Athens, Greece
| | - Helen Sarlanis
- First Department of Pathology, Medical School, National and Kapodistrian University, Athens, Greece
| | - Dimitrios Davris
- Department of Surgery, Halkida General Hospital, Halkida, Greece
| | | | - Nikolaos Kavantzas
- First Department of Pathology, Medical School, National and Kapodistrian University, Athens, Greece
| | - Dimitrios Peschos
- Department of Physiology, Medical School, University of Ioannina, Ioannina, Greece
| | - Loukas Manaios
- Department of Surgery, ''Bioclinic'' Hospital, Athens, Greece
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5
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Palominos MF, Muhl V, Richards EJ, Miller CT, Martin CH. Jaw size variation is associated with a novel craniofacial function for galanin receptor 2 in an adaptive radiation of pupfishes. Proc Biol Sci 2023; 290:20231686. [PMID: 37876194 PMCID: PMC10598438 DOI: 10.1098/rspb.2023.1686] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/28/2023] [Accepted: 10/02/2023] [Indexed: 10/26/2023] Open
Abstract
Understanding the genetic basis of novel adaptations in new species is a fundamental question in biology. Here we demonstrate a new role for galr2 in vertebrate craniofacial development using an adaptive radiation of trophic specialist pupfishes endemic to San Salvador Island, Bahamas. We confirmed the loss of a putative Sry transcription factor binding site upstream of galr2 in scale-eating pupfish and found significant spatial differences in galr2 expression among pupfish species in Meckel's cartilage using in situ hybridization chain reaction (HCR). We then experimentally demonstrated a novel role for Galr2 in craniofacial development by exposing embryos to Garl2-inhibiting drugs. Galr2-inhibition reduced Meckel's cartilage length and increased chondrocyte density in both trophic specialists but not in the generalist genetic background. We propose a mechanism for jaw elongation in scale-eaters based on the reduced expression of galr2 due to the loss of a putative Sry binding site. Fewer Galr2 receptors in the scale-eater Meckel's cartilage may result in their enlarged jaw lengths as adults by limiting opportunities for a circulating Galr2 agonist to bind to these receptors during development. Our findings illustrate the growing utility of linking candidate adaptive SNPs in non-model systems with highly divergent phenotypes to novel vertebrate gene functions.
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Affiliation(s)
- M. Fernanda Palominos
- Department of Integrative Biology, University of California, 3101 Valley Life Sciences Building, Berkeley, CA 94720, USA
- Museum of Vertebrate Zoology, University of California, Berkeley, CA 94720, USA
| | - Vanessa Muhl
- Department of Integrative Biology, University of California, 3101 Valley Life Sciences Building, Berkeley, CA 94720, USA
- Museum of Vertebrate Zoology, University of California, Berkeley, CA 94720, USA
| | - Emilie J. Richards
- Department of Ecology, Evolution, and Behavior, University of Minnesota, Minneapolis, MN, USA
| | - Craig T. Miller
- Department of Molecular & Cell Biology, University of California, Berkeley, CA, USA
| | - Christopher H. Martin
- Department of Integrative Biology, University of California, 3101 Valley Life Sciences Building, Berkeley, CA 94720, USA
- Museum of Vertebrate Zoology, University of California, Berkeley, CA 94720, USA
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Palominos MF, Muhl V, Richards EJ, Miller CT, Martin CH. Jaw size variation is associated with a novel craniofacial function for galanin receptor 2 in an adaptive radiation of pupfishes. BIORXIV : THE PREPRINT SERVER FOR BIOLOGY 2023:2023.06.02.543513. [PMID: 37333213 PMCID: PMC10274624 DOI: 10.1101/2023.06.02.543513] [Citation(s) in RCA: 2] [Impact Index Per Article: 2.0] [Reference Citation Analysis] [Abstract] [Key Words] [Grants] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 06/20/2023]
Abstract
Understanding the genetic basis of novel adaptations in new species is a fundamental question in biology that also provides an opportunity to uncover new genes and regulatory networks with potential clinical relevance. Here we demonstrate a new role for galr2 in vertebrate craniofacial development using an adaptive radiation of trophic specialist pupfishes endemic to San Salvador Island in the Bahamas. We confirmed the loss of a putative Sry transcription factor binding site in the upstream region of galr2 in scale-eating pupfish and found significant spatial differences in galr2 expression among pupfish species in Meckel's cartilage and premaxilla using in situ hybridization chain reaction (HCR). We then experimentally demonstrated a novel function for Galr2 in craniofacial development and jaw elongation by exposing embryos to drugs that inhibit Galr2 activity. Galr2-inhibition reduced Meckel's cartilage length and increased chondrocyte density in both trophic specialists but not in the generalist genetic background. We propose a mechanism for jaw elongation in scale-eaters based on the reduced expression of galr2 due to the loss of a putative Sry binding site. Fewer Galr2 receptors in the scale-eater Meckel's cartilage may result in their enlarged jaw lengths as adults by limiting opportunities for a postulated Galr2 agonist to bind to these receptors during development. Our findings illustrate the growing utility of linking candidate adaptive SNPs in non-model systems with highly divergent phenotypes to novel vertebrate gene functions.
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Affiliation(s)
- M Fernanda Palominos
- Department of Integrative Biology, University of California, Berkeley
- Museum of Vertebrate Zoology, University of California, Berkeley
| | - Vanessa Muhl
- Department of Integrative Biology, University of California, Berkeley
- Museum of Vertebrate Zoology, University of California, Berkeley
| | - Emilie J Richards
- Department of Ecology, Evolution, and Behavior, University of Minnesota
| | - Craig T Miller
- Department of Molecular & Cell Biology, University of California, Berkeley
| | - Christopher H Martin
- Department of Integrative Biology, University of California, Berkeley
- Museum of Vertebrate Zoology, University of California, Berkeley
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7
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Packard M, Gilbert MC, Tetrault E, Albertson RC. Zebrafish crocc2 mutants exhibit divergent craniofacial shape, misregulated variability, and aberrant cartilage morphogenesis. Dev Dyn 2023; 252:1026-1045. [PMID: 37032317 PMCID: PMC10524572 DOI: 10.1002/dvdy.591] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/07/2022] [Revised: 03/21/2023] [Accepted: 03/29/2023] [Indexed: 04/11/2023] Open
Abstract
BACKGROUND Phenotypic variation is of paramount importance in development, evolution, and human health; however, the molecular mechanisms that influence organ shape and shape variability are not well understood. During craniofacial development, the behavior of skeletal precursors is regulated by both biochemical and environmental inputs, and the primary cilia play critical roles in transducing both types of signals. Here, we examine a gene that encodes a key constituent of the ciliary rootlets, crocc2, and its role in cartilage morphogenesis in larval zebrafish. RESULTS Geometric morphometric analysis of crocc2 mutants revealed altered craniofacial shapes and expanded variation. At the cellular level, we observed altered chondrocyte shapes and planar cell polarity across multiple stages in crocc2 mutants. Notably, cellular defects were specific to areas that experience direct mechanical input. Cartilage cell number, apoptosis, and bone patterning were not affected in crocc2 mutants. CONCLUSIONS Whereas "regulatory" genes are widely implicated in patterning the craniofacial skeleton, genes that encode "structural" aspects of the cell are increasingly implicated in shaping the face. Our results add crocc2 to this list, and demonstrate that it affects craniofacial geometry and canalizes phenotypic variation. We propose that it does so via mechanosensing, possibly through the ciliary rootlet. If true, this would implicate a new organelle in skeletal development and evolution.
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Affiliation(s)
- Mary Packard
- Department of Biology, University of Massachusetts, Amherst, MA 01003, U.S.A
| | - Michelle C. Gilbert
- Organismic and Evolutionary Biology Graduate Program, University of Massachusetts, Amherst, MA 01003, U.S.A
- Current address, Department of Biology, Penn State University, University Park, PA 16802, U.S.A
| | - Emily Tetrault
- Molecular and Cellular Biology Graduate Program, University of Massachusetts, Amherst, MA 01003, U.S.A
| | - R. Craig Albertson
- Department of Biology, University of Massachusetts, Amherst, MA 01003, U.S.A
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Horani A, Gupta DK, Xu J, Xu H, del Carmen Puga-Molina L, Santi CM, Ramagiri S, Brennan SK, Pan J, Koenitzer JR, Huang T, Hyland RM, Gunsten SP, Tzeng SC, Strahle JM, Mill P, Mahjoub MR, Dutcher SK, Brody SL. The effect of Dnaaf5 gene dosage on primary ciliary dyskinesia phenotypes. JCI Insight 2023; 8:e168836. [PMID: 37104040 PMCID: PMC10393236 DOI: 10.1172/jci.insight.168836] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/13/2023] [Accepted: 04/20/2023] [Indexed: 04/28/2023] Open
Abstract
DNAAF5 is a dynein motor assembly factor associated with the autosomal heterogenic recessive condition of motile cilia, primary ciliary dyskinesia (PCD). The effects of allele heterozygosity on motile cilia function are unknown. We used CRISPR-Cas9 genome editing in mice to recreate a human missense variant identified in patients with mild PCD and a second, frameshift-null deletion in Dnaaf5. Litters with Dnaaf5 heteroallelic variants showed distinct missense and null gene dosage effects. Homozygosity for the null Dnaaf5 alleles was embryonic lethal. Compound heterozygous animals with the missense and null alleles showed severe disease manifesting as hydrocephalus and early lethality. However, animals homozygous for the missense mutation had improved survival, with partially preserved cilia function and motor assembly observed by ultrastructure analysis. Notably, the same variant alleles exhibited divergent cilia function across different multiciliated tissues. Proteomic analysis of isolated airway cilia from mutant mice revealed reduction in some axonemal regulatory and structural proteins not previously reported in DNAAF5 variants. Transcriptional analysis of mouse and human mutant cells showed increased expression of genes coding for axonemal proteins. These findings suggest allele-specific and tissue-specific molecular requirements for cilia motor assembly that may affect disease phenotypes and clinical trajectory in motile ciliopathies.
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Affiliation(s)
- Amjad Horani
- Department of Pediatrics
- Department of Cell Biology and Physiology
| | | | | | | | | | | | - Sruthi Ramagiri
- Department of Neurosurgery, Washington University School of Medicine, St. Louis, Missouri, USA
| | | | | | | | | | | | | | | | - Jennifer M. Strahle
- Department of Neurosurgery, Washington University School of Medicine, St. Louis, Missouri, USA
| | - Pleasantine Mill
- MRC Human Genetics Unit, University of Edinburgh, Edinburgh, United Kingdom
| | - Moe R. Mahjoub
- Department of Cell Biology and Physiology
- Department of Medicine
| | - Susan K. Dutcher
- Department of Cell Biology and Physiology
- Department of Genetics, Washington University School of Medicine, St. Louis, Missouri, USA
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9
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Minhas BF, Beck EA, Cheng CHC, Catchen J. Novel mitochondrial genome rearrangements including duplications and extensive heteroplasmy could underlie temperature adaptations in Antarctic notothenioid fishes. Sci Rep 2023; 13:6939. [PMID: 37117267 PMCID: PMC10147917 DOI: 10.1038/s41598-023-34237-1] [Citation(s) in RCA: 3] [Impact Index Per Article: 3.0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/06/2022] [Accepted: 04/25/2023] [Indexed: 04/30/2023] Open
Abstract
Mitochondrial genomes are known for their compact size and conserved gene order, however, recent studies employing long-read sequencing technologies have revealed the presence of atypical mitogenomes in some species. In this study, we assembled and annotated the mitogenomes of five Antarctic notothenioids, including four icefishes (Champsocephalus gunnari, C. esox, Chaenocephalus aceratus, and Pseudochaenichthys georgianus) and the cold-specialized Trematomus borchgrevinki. Antarctic notothenioids are known to harbor some rearrangements in their mt genomes, however the extensive duplications in icefishes observed in our study have never been reported before. In the icefishes, we observed duplications of the protein coding gene ND6, two transfer RNAs, and the control region with different copy number variants present within the same individuals and with some ND6 duplications appearing to follow the canonical Duplication-Degeneration-Complementation (DDC) model in C. esox and C. gunnari. In addition, using long-read sequencing and k-mer analysis, we were able to detect extensive heteroplasmy in C. aceratus and C. esox. We also observed a large inversion in the mitogenome of T. borchgrevinki, along with the presence of tandem repeats in its control region. This study is the first in using long-read sequencing to assemble and identify structural variants and heteroplasmy in notothenioid mitogenomes and signifies the importance of long-reads in resolving complex mitochondrial architectures. Identification of such wide-ranging structural variants in the mitogenomes of these fishes could provide insight into the genetic basis of the atypical icefish mitochondrial physiology and more generally may provide insights about their potential role in cold adaptation.
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Affiliation(s)
- Bushra Fazal Minhas
- Informatics Programs, University of Illinois at Urbana-Champaign, Urbana, USA
| | - Emily A Beck
- Data Science Initiative, University of Oregon, Eugene, USA
| | - C-H Christina Cheng
- Department of Evolution, Ecology, and Behavior, University of Illinois at Urbana-Champaign, Urbana, USA
| | - Julian Catchen
- Informatics Programs, University of Illinois at Urbana-Champaign, Urbana, USA.
- Department of Evolution, Ecology, and Behavior, University of Illinois at Urbana-Champaign, Urbana, USA.
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Lu Y, Rice E, Du K, Kneitz S, Naville M, Dechaud C, Volff JN, Boswell M, Boswell W, Hillier L, Tomlinson C, Milin K, Walter RB, Schartl M, Warren WC. High resolution genomes of multiple Xiphophorus species provide new insights into microevolution, hybrid incompatibility, and epistasis. Genome Res 2023; 33:557-571. [PMID: 37147111 PMCID: PMC10234306 DOI: 10.1101/gr.277434.122] [Citation(s) in RCA: 4] [Impact Index Per Article: 4.0] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/25/2022] [Accepted: 03/29/2023] [Indexed: 05/07/2023]
Abstract
Because of diverged adaptative phenotypes, fish species of the genus Xiphophorus have contributed to a wide range of research for a century. Existing Xiphophorus genome assemblies are not at the chromosomal level and are prone to sequence gaps, thus hindering advancement of the intra- and inter-species differences for evolutionary, comparative, and translational biomedical studies. Herein, we assembled high-quality chromosome-level genome assemblies for three distantly related Xiphophorus species, namely, X. maculatus, X. couchianus, and X. hellerii Our overall goal is to precisely assess microevolutionary processes in the clade to ascertain molecular events that led to the divergence of the Xiphophorus species and to progress understanding of genetic incompatibility to disease. In particular, we measured intra- and inter-species divergence and assessed gene expression dysregulation in reciprocal interspecies hybrids among the three species. We found expanded gene families and positively selected genes associated with live bearing, a special mode of reproduction. We also found positively selected gene families are significantly enriched in nonpolymorphic transposable elements, suggesting the dispersal of these nonpolymorphic transposable elements has accompanied the evolution of the genes, possibly by incorporating new regulatory elements in support of the Britten-Davidson hypothesis. We characterized inter-specific polymorphisms, structural variants, and polymorphic transposable element insertions and assessed their association to interspecies hybridization-induced gene expression dysregulation related to specific disease states in humans.
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Affiliation(s)
- Yuan Lu
- The Xiphophorus Genetic Stock Center, Texas State University, San Marcos, Texas 78666, USA;
| | - Edward Rice
- Department of Animal Sciences, Department of Surgery, Institute for Data Science and Informatics, University of Missouri, Bond Life Sciences Center, Columbia, Missouri 65201, USA
| | - Kang Du
- The Xiphophorus Genetic Stock Center, Texas State University, San Marcos, Texas 78666, USA
| | - Susanne Kneitz
- Biochemistry and Cell Biology, Biozentrum, University of Würzburg, 97074 Würzburg, Germany
| | - Magali Naville
- Institut de Génomique Fonctionnelle de Lyon, Ecole Normale Supérieure de Lyon, CNRS UMR 5242, Université Claude Bernard Lyon 1, F-69364 Lyon, France
| | - Corentin Dechaud
- Institut de Génomique Fonctionnelle de Lyon, Ecole Normale Supérieure de Lyon, CNRS UMR 5242, Université Claude Bernard Lyon 1, F-69364 Lyon, France
| | - Jean-Nicolas Volff
- Institut de Génomique Fonctionnelle de Lyon, Ecole Normale Supérieure de Lyon, CNRS UMR 5242, Université Claude Bernard Lyon 1, F-69364 Lyon, France
| | - Mikki Boswell
- The Xiphophorus Genetic Stock Center, Texas State University, San Marcos, Texas 78666, USA
| | - William Boswell
- The Xiphophorus Genetic Stock Center, Texas State University, San Marcos, Texas 78666, USA
| | - LaDeana Hillier
- Department of Genome Sciences, University of Washington, Seattle, Washington 98195, USA
| | - Chad Tomlinson
- McDonnell Genome Institute, Washington University, St. Louis, Missouri 63108, USA
| | - Kremitzki Milin
- McDonnell Genome Institute, Washington University, St. Louis, Missouri 63108, USA
| | - Ronald B Walter
- Department of Life Sciences, Texas A&M University, Corpus Christi, Texas 78412, USA
| | - Manfred Schartl
- The Xiphophorus Genetic Stock Center, Texas State University, San Marcos, Texas 78666, USA
- Developmental Biochemistry, Biozentrum, University of Würzburg, 97074 Würzburg, Germany
| | - Wesley C Warren
- Department of Animal Sciences, Department of Surgery, Institute for Data Science and Informatics, University of Missouri, Bond Life Sciences Center, Columbia, Missouri 65201, USA
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Papanikolaou V, Kyrodimos E, Mastronikolis N, Asimakopoulos AD, Papanastasiou G, Tsiambas E, Spyropoulou D, Katsinis S, Manoli A, Papouliakos S, Pantos P, Ragos V, Peschos D, Chrysovergis A. Anti-EGFR/BRAF-Tyrosine Kinase Inhibitors in Thyroid Carcinoma. CANCER DIAGNOSIS & PROGNOSIS 2023; 3:151-156. [PMID: 36875315 PMCID: PMC9949544 DOI: 10.21873/cdp.10194] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Subscribe] [Scholar Register] [Received: 12/11/2022] [Accepted: 02/06/2023] [Indexed: 03/07/2023]
Abstract
Alterations in significant genes located on chromosome 7 - including epidermal growth factor receptor (EGFR) and also v-Raf murine sarcoma viral oncogene homolog B (BRAF) as a mitogen-activated protein kinase (MAPK) - combined or not with numerical imbalances of the whole chromosome (aneuploidy-polysomy) are crucial genetic events involved in the development and progression of malignancies. Identification of EGFR/BRAF-dependent specific somatic mutations and other mechanisms of deregulation (i.e., amplification) is critical for applying targeted therapeutic approaches [tyrosine kinase inhibitors (TKIs] or monoclonal antibodies (mAbs). Thyroid carcinoma is a specific pathological entity characterized by a variety of histological sub-types. Follicular thyroid carcinoma (FTC), papillary thyroid carcinoma (PTC), medullary thyroid carcinoma (MTC), and anaplastic thyroid carcinoma (ATC) represent its main sub-types. In the current review, we explore the role of EGFR/BRAF alterations in thyroid carcinoma in conjunction with the corresponding anti-EGFR/BRAF TKI-based novel therapeutic strategies for patients with specific genetic signatures.
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Affiliation(s)
- Vasileios Papanikolaou
- 1st Department of Otorhinolaryngology, Hippocration Hospital, University of Athens, Athens, Greece
| | - Efthymios Kyrodimos
- 1st Department of Otorhinolaryngology, Hippocration Hospital, University of Athens, Athens, Greece
| | | | | | - George Papanastasiou
- Department of Maxillofacial, Medical School, University of Ioannina, Ioannina, Greece
| | - Evangelos Tsiambas
- Department of Cytology, 417 Veterans Army Hospital (NIMTS), Athens, Greece
| | - Despoina Spyropoulou
- Department of Radiation Oncology, Medical School, University of Patras, Patras, Greece
| | - Spyros Katsinis
- Department of Otorhinolaryngology, Pamakaristos General Hospital, Athens, Greece
| | - Arezina Manoli
- Department of Otorhinolaryngology, Thoracic Diseases General Hospital Sotiria, Athens, Greece
| | - Sotirios Papouliakos
- Department of Otorhinolaryngology, General Hospital "Gennimatas", Athens, Greece
| | - Pavlos Pantos
- 1st Department of Otorhinolaryngology, Hippocration Hospital, University of Athens, Athens, Greece
| | - Vasileios Ragos
- Department of Maxillofacial, Medical School, University of Ioannina, Ioannina, Greece
| | - Dimitrios Peschos
- Department of Physiology, Medical School, University of Ioannina, Ioannina, Greece
| | - Aristeidis Chrysovergis
- 1st Department of Otorhinolaryngology, Hippocration Hospital, University of Athens, Athens, Greece
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12
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Opazo JC, Vandewege MW, Hoffmann FG, Zavala K, Meléndez C, Luchsinger C, Cavieres VA, Vargas-Chacoff L, Morera FJ, Burgos PV, Tapia-Rojas C, Mardones GA. How Many Sirtuin Genes Are Out There? Evolution of Sirtuin Genes in Vertebrates With a Description of a New Family Member. Mol Biol Evol 2023; 40:6993039. [PMID: 36656997 PMCID: PMC9897032 DOI: 10.1093/molbev/msad014] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/07/2022] [Revised: 12/21/2022] [Accepted: 01/10/2023] [Indexed: 01/20/2023] Open
Abstract
Studying the evolutionary history of gene families is a challenging and exciting task with a wide range of implications. In addition to exploring fundamental questions about the origin and evolution of genes, disentangling their evolution is also critical to those who do functional/structural studies to allow a deeper and more precise interpretation of their results in an evolutionary context. The sirtuin gene family is a group of genes that are involved in a variety of biological functions mostly related to aging. Their duplicative history is an open question, as well as the definition of the repertoire of sirtuin genes among vertebrates. Our results show a well-resolved phylogeny that represents an improvement in our understanding of the duplicative history of the sirtuin gene family. We identified a new sirtuin gene family member (SIRT3.2) that was apparently lost in the last common ancestor of amniotes but retained in all other groups of jawed vertebrates. According to our experimental analyses, elephant shark SIRT3.2 protein is located in mitochondria, the overexpression of which leads to an increase in cellular levels of ATP. Moreover, in vitro analysis demonstrated that it has deacetylase activity being modulated in a similar way to mammalian SIRT3. Our results indicate that there are at least eight sirtuin paralogs among vertebrates and that all of them can be traced back to the last common ancestor of the group that existed between 676 and 615 millions of years ago.
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Affiliation(s)
| | - Michael W Vandewege
- College of Veterinary Medicine, North Carolina State University, Raleigh, NC
| | - Federico G Hoffmann
- Department of Biochemistry, Molecular Biology, Entomology, and Plant Pathology, Mississippi State University, Starkville, MS,Institute for Genomics, Biocomputing and Biotechnology, Mississippi State University, Starkville, MS
| | - Kattina Zavala
- Instituto de Ciencias Ambientales y Evolutivas, Facultad de Ciencias, Universidad Austral de Chile, Valdivia, Chile
| | - Catalina Meléndez
- Centro de Biología Celular y Biomedicina (CEBICEM), Facultad de Medicina y Ciencia, Universidad San Sebastián, Santiago, Chile
| | - Charlotte Luchsinger
- Department of Physiology, School of Medicine, Universidad Austral de Chile, Valdivia, Chile
| | - Viviana A Cavieres
- Centro de Biología Celular y Biomedicina (CEBICEM), Facultad de Medicina y Ciencia, Universidad San Sebastián, Santiago, Chile
| | - Luis Vargas-Chacoff
- Integrative Biology Group, Universidad Austral de Chile, Valdivia, Chile,Instituto de Ciencias Marinas y Limnológicas, Universidad Austral de Chile, Valdivia, Chile,Centro Fondap de Investigación de Altas Latitudes (IDEAL), Universidad Austral de Chile, Valdivia, Chile,Millennium Institute Biodiversity of Antarctic and Subantarctic Ecosystems, BASE, Universidad Austral de Chile, Valdivia, Chile
| | - Francisco J Morera
- Integrative Biology Group, Universidad Austral de Chile, Valdivia, Chile,Applied Biochemistry Laboratory, Facultad de Ciencias Veterinarias, Instituto de Farmacología y Morfofisiología, Universidad Austral de Chile, Valdivia, Chile
| | - Patricia V Burgos
- Centro de Biología Celular y Biomedicina (CEBICEM), Facultad de Medicina y Ciencia, Universidad San Sebastián, Santiago, Chile,Centro Ciencia & Vida, Fundación Ciencia & Vida, Santiago, Chile,Centro de Envejecimiento y Regeneración (CARE-UC), Facultad de Ciencias Biológicas, Pontificia Universidad Católica, Santiago, Chile
| | - Cheril Tapia-Rojas
- Centro de Biología Celular y Biomedicina (CEBICEM), Facultad de Medicina y Ciencia, Universidad San Sebastián, Santiago, Chile,Centro Ciencia & Vida, Fundación Ciencia & Vida, Santiago, Chile
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13
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Horani A, Gupta DK, Xu J, Xu H, Del Carmen Puga-Molina L, Santi CM, Ramagiri S, Brennen SK, Pan J, Huang T, Hyland RM, Gunsten SP, Tzeng SC, Strahle JM, Mill P, Mahjoub MR, Dutcher SK, Brody SL. The effect of Dnaaf5 gene dosage on primary ciliary dyskinesia phenotypes. BIORXIV : THE PREPRINT SERVER FOR BIOLOGY 2023:2023.01.13.523966. [PMID: 36712068 PMCID: PMC9882222 DOI: 10.1101/2023.01.13.523966] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 01/15/2023]
Abstract
DNAAF5 is a dynein motor assembly factor associated with the autosomal heterogenic recessive condition of motile cilia, primary ciliary dyskinesia (PCD). The effects of allele heterozygosity on motile cilia function are unknown. We used CRISPR-Cas9 genome editing in mice to recreate a human missense variant identified in patients with mild PCD and a second, frameshift null deletion in Dnaaf5 . Litters with Dnaaf5 heteroallelic variants showed distinct missense and null gene dosage effects. Homozygosity for the null Dnaaf5 alleles was embryonic lethal. Compound heterozygous animals with the missense and null alleles showed severe disease manifesting as hydrocephalus and early lethality. However, animals homozygous for the missense mutation had improved survival, with partial preserved cilia function and motor assembly observed by ultrastructure analysis. Notably, the same variant alleles exhibited divergent cilia function across different multiciliated tissues. Proteomic analysis of isolated airway cilia from mutant mice revealed reduction in some axonemal regulatory and structural proteins not previously reported in DNAAF5 variants. While transcriptional analysis of mouse and human mutant cells showed increased expression of genes coding for axonemal proteins. Together, these findings suggest allele-specific and tissue-specific molecular requirements for cilia motor assembly that may affect disease phenotypes and clinical trajectory in motile ciliopathies. Brief Summary A mouse model of human DNAAF5 primary ciliary dyskinesia variants reveals gene dosage effects of mutant alleles and tissue-specific molecular requirements for cilia motor assembly.
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14
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Beck EA, Bassham S, Cresko WA. Extreme intraspecific divergence in mitochondrial haplotypes makes the threespine stickleback fish an emerging evolutionary mutant model for mito-nuclear interactions. Front Genet 2022; 13:925786. [PMID: 36159975 PMCID: PMC9499175 DOI: 10.3389/fgene.2022.925786] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/21/2022] [Accepted: 08/09/2022] [Indexed: 11/13/2022] Open
Abstract
Mitochondrial DNA is primarily maternally inherited in most animals and evolves about 10 times faster than biparentally inherited nuclear DNA. Mitochondrial dysfunction (mt-dys) arises when interactions between the co-evolving mitochondrial and nuclear genomes are perturbed in essential processes like oxidative phosphorylation (OXPHOS). Over time mt-dys can lead to mitochondrial diseases (mt-diseases), which are surprisingly prevalent and include common diseases such as Alzheimer's, Parkinson's, and diabetes. Unfortunately, the strong impact that intraspecific mitochondrial and nuclear genetic variation has on mt-disease complicates its study and the development of effective treatments. Animal models have advanced our understanding of mt-disease but their relevance to human conditions is often limited by their relatively low nuclear genetic diversity. Many traditional laboratory models also typically have a single mitochondrial haplotype (mitotype), in stark contrast to over 5,000 mitotypes in humans worldwide. The threespine stickleback fish has an evolutionary history that has made it a favorable evolutionary mutant model (EMM) for studying mito-nuclear interactions and possibly mt-diseases. EMMs are species with naturally evolved states that mimic maladaptive human diseases. In threespine stickleback, a period of isolation followed by introgression of the mitochondrial genome from a sister species resulted in the maintenance of two distinct mitochondrial haplotypes which continue to segregate within many populations of wild stickleback. The existence of two mitogenomes segregating in numerous genetically diverse populations provides a unique system for exploring complex mito-nuclear dynamics. Here we provide the first complete coding region analysis of the two threespine stickleback mitotypes, whose mitogenomic divergence exceeds that of other mammalian models for mitochondrial disease and even that between ancient and modern humans. We find that divergence is not uniform across the mitogenome, but primarily impacts protein coding genes, and significantly impacts proteins in Complex I of OXPHOS. The full characterization of these highly divergent intraspecific mitotypes provides a foundation for the development of threespine stickleback as an EMM for mito-nuclear interactions.
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Affiliation(s)
- Emily A. Beck
- Institute of Ecology and Evolution, University of Oregon, Eugene, OR, United States
- Presidential Initiative in Data Science, University of Oregon, Eugene, OR, United States
| | - Susan Bassham
- Institute of Ecology and Evolution, University of Oregon, Eugene, OR, United States
| | - William A. Cresko
- Institute of Ecology and Evolution, University of Oregon, Eugene, OR, United States
- Presidential Initiative in Data Science, University of Oregon, Eugene, OR, United States
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15
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Anastasiadi D, Piferrer F, Wellenreuther M, Benítez Burraco A. Fish as Model Systems to Study Epigenetic Drivers in Human Self-Domestication and Neurodevelopmental Cognitive Disorders. Genes (Basel) 2022; 13:genes13060987. [PMID: 35741749 PMCID: PMC9222608 DOI: 10.3390/genes13060987] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.5] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 02/25/2022] [Revised: 04/28/2022] [Accepted: 05/11/2022] [Indexed: 12/24/2022] Open
Abstract
Modern humans exhibit phenotypic traits and molecular events shared with other domesticates that are thought to be by-products of selection for reduced aggression. This is the human self-domestication hypothesis. As one of the first types of responses to a novel environment, epigenetic changes may have also facilitated early self-domestication in humans. Here, we argue that fish species, which have been recently domesticated, can provide model systems to study epigenetic drivers in human self-domestication. To test this, we used in silico approaches to compare genes with epigenetic changes in early domesticates of European sea bass with genes exhibiting methylation changes in anatomically modern humans (comparison 1), and neurodevelopmental cognitive disorders considered to exhibit abnormal self-domestication traits, i.e., schizophrenia, Williams syndrome, and autism spectrum disorders (comparison 2). Overlapping genes in comparison 1 were involved in processes like limb morphogenesis and phenotypes like abnormal jaw morphology and hypopigmentation. Overlapping genes in comparison 2 affected paralogue genes involved in processes such as neural crest differentiation and ectoderm differentiation. These findings pave the way for future studies using fish species as models to investigate epigenetic changes as drivers of human self-domestication and as triggers of cognitive disorders.
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Affiliation(s)
- Dafni Anastasiadi
- Seafood Technologies, The New Zealand Institute for Plant and Food Research, Nelson 7010, New Zealand;
- Correspondence:
| | - Francesc Piferrer
- Institut de Ciències del Mar, Spanish National Research Council (CSIC), 08003 Barcelona, Spain;
| | - Maren Wellenreuther
- Seafood Technologies, The New Zealand Institute for Plant and Food Research, Nelson 7010, New Zealand;
- School of Biological Sciences, The University of Auckland, Auckland 1010, New Zealand
| | - Antonio Benítez Burraco
- Department of Spanish, Linguistics, and Theory of Literature (Linguistics), Faculty of Philology, University of Seville, 41004 Seville, Spain;
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16
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Beck EA, Healey HM, Small CM, Currey MC, Desvignes T, Cresko WA, Postlethwait JH. Advancing human disease research with fish evolutionary mutant models. Trends Genet 2022; 38:22-44. [PMID: 34334238 PMCID: PMC8678158 DOI: 10.1016/j.tig.2021.07.002] [Citation(s) in RCA: 17] [Impact Index Per Article: 8.5] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/07/2021] [Revised: 06/28/2021] [Accepted: 07/01/2021] [Indexed: 01/03/2023]
Abstract
Model organism research is essential to understand disease mechanisms. However, laboratory-induced genetic models can lack genetic variation and often fail to mimic the spectrum of disease severity. Evolutionary mutant models (EMMs) are species with evolved phenotypes that mimic human disease. EMMs complement traditional laboratory models by providing unique avenues to study gene-by-environment interactions, modular mutations in noncoding regions, and their evolved compensations. EMMs have improved our understanding of complex diseases, including cancer, diabetes, and aging, and illuminated mechanisms in many organs. Rapid advancements of sequencing and genome-editing technologies have catapulted the utility of EMMs, particularly in fish. Fish are the most diverse group of vertebrates, exhibiting a kaleidoscope of specialized phenotypes, many that would be pathogenic in humans but are adaptive in the species' specialized habitat. Importantly, evolved compensations can suggest avenues for novel disease therapies. This review summarizes current research using fish EMMs to advance our understanding of human disease.
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Affiliation(s)
- Emily A Beck
- Data Science, University of Oregon, Eugene, OR 97403, USA; Institute of Ecology and Evolution, University of Oregon, Eugene, OR 97403, USA.
| | - Hope M Healey
- Institute of Ecology and Evolution, University of Oregon, Eugene, OR 97403, USA
| | - Clayton M Small
- Data Science, University of Oregon, Eugene, OR 97403, USA; Institute of Ecology and Evolution, University of Oregon, Eugene, OR 97403, USA
| | - Mark C Currey
- Institute of Ecology and Evolution, University of Oregon, Eugene, OR 97403, USA
| | - Thomas Desvignes
- Institute of Neuroscience, University of Oregon, Eugene, OR 97403, USA
| | - William A Cresko
- Data Science, University of Oregon, Eugene, OR 97403, USA; Institute of Ecology and Evolution, University of Oregon, Eugene, OR 97403, USA
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17
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Opazo JC, Hoffmann FG, Zavala K, Edwards SV. Evolution of the DAN gene family in vertebrates. Dev Biol 2021; 482:34-43. [PMID: 34902310 DOI: 10.1016/j.ydbio.2021.12.002] [Citation(s) in RCA: 3] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/25/2021] [Revised: 12/07/2021] [Accepted: 12/08/2021] [Indexed: 11/26/2022]
Abstract
The DAN gene family (DAN, Differential screening-selected gene Aberrant in Neuroblastoma) is a group of genes that is expressed during development and plays fundamental roles in limb bud formation and digitation, kidney formation and morphogenesis and left-right axis specification. During adulthood the expression of these genes are associated with diseases, including cancer. Although most of the attention to this group of genes has been dedicated to understanding its role in physiology and development, its evolutionary history remains poorly understood. Thus, the goal of this study is to investigate the evolutionary history of the DAN gene family in vertebrates, with the objective of complementing the already abundant physiological information with an evolutionary context. Our results recovered the monophyly of all DAN gene family members and divide them into five main groups. In addition to the well-known DAN genes, our phylogenetic results revealed the presence of two new DAN gene lineages; one is only retained in cephalochordates, whereas the other one (GREM3) was only identified in cartilaginous fish, holostean fish, and coelacanth. According to the phyletic distribution of the genes, the ancestor of gnathostomes possessed a repertoire of eight DAN genes, and during the radiation of the group GREM1, GREM2, SOST, SOSTDC1, and NBL1 were retained in all major groups, whereas, GREM3, CER1, and DAND5 were differentially lost.
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Affiliation(s)
- Juan C Opazo
- Integrative Biology Group, Universidad Austral de Chile, Valdivia, Chile; Instituto de Ciencias Ambientales y Evolutivas, Facultad de Ciencias, Universidad Austral de Chile, Valdivia, Chile; David Rockefeller Center for Latin American Studies, Harvard University, Cambridge, MA, 02138, USA; Millennium Nucleus of Ion Channels-Associated Diseases (MiNICAD), Chile.
| | - Federico G Hoffmann
- Department of Biochemistry, Molecular Biology, Entomology, and Plant Pathology, Mississippi State University, Mississippi State, 39762, USA; Institute for Genomics, Biocomputing, and Biotechnology, Mississippi State University, Mississippi State, 39762, USA
| | - Kattina Zavala
- Instituto de Ciencias Ambientales y Evolutivas, Facultad de Ciencias, Universidad Austral de Chile, Valdivia, Chile
| | - Scott V Edwards
- Department of Organismic and Evolutionary Biology, Harvard University, Cambridge, MA, 02138, USA
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18
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Ashique AM, Atake OJ, Ovens K, Guo R, Pratt IV, Detrich HW, Cooper DML, Desvignes T, Postlethwait JH, Eames BF. Bone microstructure and bone mineral density are not systemically different in Antarctic icefishes and related Antarctic notothenioids. J Anat 2021; 240:34-49. [PMID: 34423431 PMCID: PMC8655173 DOI: 10.1111/joa.13537] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.3] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 02/05/2021] [Revised: 08/05/2021] [Accepted: 08/09/2021] [Indexed: 12/17/2022] Open
Abstract
Ancestors of the Antarctic icefishes (family Channichthyidae) were benthic and had no swim bladder, making it energetically expensive to rise from the ocean floor. To exploit the water column, benthopelagic icefishes were hypothesized to have evolved a skeleton with “reduced bone,” which gross anatomical data supported. Here, we tested the hypothesis that changes to icefish bones also occurred below the level of gross anatomy. Histology and micro‐CT imaging of representative craniofacial bones (i.e., ceratohyal, frontal, dentary, and articular) of extant Antarctic fish species specifically evaluated two features that might cause the appearance of “reduced bone”: bone microstructure (e.g., bone volume fraction and structure linear density) and bone mineral density (BMD, or mass of mineral per volume of bone). Measures of bone microstructure were not consistently different in bones from the icefishes Chaenocephalus aceratus and Champsocephalus gunnari, compared to the related benthic notothenioids Notothenia coriiceps and Gobionotothen gibberifrons. Some quantitative measures, such as bone volume fraction and structure linear density, were significantly increased in some icefish bones compared to homologous bones of non‐icefish. However, such differences were rare, and no microstructural measures were consistently different in icefishes across all bones and species analyzed. Furthermore, BMD was similar among homologous bones of icefish and non‐icefish Antarctic notothenioids. In summary, “reduced bone” in icefishes was not due to systemic changes in bone microstructure or BMD, raising the prospect that “reduced bone” in icefish occurs only at the gross anatomic level (i.e., smaller or fewer bones). Given that icefishes exhibit delayed skeletal development compared to non‐icefish Antarctic fishes, combining these phenotypic data with genomic data might clarify genetic changes driving skeletal heterochrony.
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Affiliation(s)
- Amir M Ashique
- Anatomy, Physiology, and Pharmacology, University of Saskatchewan, Saskatoon, Saskatchewan, Canada
| | - Oghenevwogaga J Atake
- Anatomy, Physiology, and Pharmacology, University of Saskatchewan, Saskatoon, Saskatchewan, Canada
| | - Katie Ovens
- Augmented Intelligence & Precision Health Laboratory (AIPHL), McGill University, Montreal, Quebec, Canada
| | - Ruiyi Guo
- Anatomy, Physiology, and Pharmacology, University of Saskatchewan, Saskatoon, Saskatchewan, Canada
| | - Isaac V Pratt
- Anatomy, Physiology, and Pharmacology, University of Saskatchewan, Saskatoon, Saskatchewan, Canada
| | - H William Detrich
- Marine and Environmental Sciences, Northeastern University Marine Science Center, Nahant, Massachusetts, USA
| | - David M L Cooper
- Anatomy, Physiology, and Pharmacology, University of Saskatchewan, Saskatoon, Saskatchewan, Canada
| | - Thomas Desvignes
- Institute of Neuroscience, University of Oregon, Eugene, Oregon, USA
| | | | - B Frank Eames
- Anatomy, Physiology, and Pharmacology, University of Saskatchewan, Saskatoon, Saskatchewan, Canada
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19
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Williams C, Kirby A, Marghoub A, Kéver L, Ostashevskaya-Gohstand S, Bertazzo S, Moazen M, Abzhanov A, Herrel A, Evans SE, Vickaryous M. A review of the osteoderms of lizards (Reptilia: Squamata). Biol Rev Camb Philos Soc 2021; 97:1-19. [PMID: 34397141 PMCID: PMC9292694 DOI: 10.1111/brv.12788] [Citation(s) in RCA: 6] [Impact Index Per Article: 2.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/28/2020] [Revised: 07/30/2021] [Accepted: 08/03/2021] [Indexed: 12/24/2022]
Abstract
Osteoderms are mineralised structures consisting mainly of calcium phosphate and collagen. They form directly within the skin, with or without physical contact with the skeleton. Osteoderms, in some form, may be primitive for tetrapods as a whole, and are found in representatives of most major living lineages including turtles, crocodilians, lizards, armadillos, and some frogs, as well as extinct taxa ranging from early tetrapods to dinosaurs. However, their distribution in time and space raises questions about their evolution and homology in individual groups. Among lizards and their relatives, osteoderms may be completely absent; present only on the head or dorsum; or present all over the body in one of several arrangements, including non-overlapping mineralised clusters, a continuous covering of overlapping plates, or as spicular mineralisations that thicken with age. This diversity makes lizards an excellent focal group in which to study osteoderm structure, function, development and evolution. In the past, the focus of researchers was primarily on the histological structure and/or the gross anatomy of individual osteoderms in a limited sample of taxa. Those studies demonstrated that lizard osteoderms are sometimes two-layered structures, with a vitreous, avascular layer just below the epidermis and a deeper internal layer with abundant collagen within the deep dermis. However, there is considerable variation on this model, in terms of the arrangement of collagen fibres, presence of extra tissues, and/or a cancellous bone core bordered by cortices. Moreover, there is a lack of consensus on the contribution, if any, of osteoblasts in osteoderm development, despite research describing patterns of resorption and replacement that would suggest both osteoclast and osteoblast involvement. Key to this is information on development, but our understanding of the genetic and skeletogenic processes involved in osteoderm development and patterning remains minimal. The most common proposition for the presence of osteoderms is that they provide a protective armour. However, the large morphological and distributional diversity in lizard osteoderms raises the possibility that they may have other roles such as biomechanical reinforcement in response to ecological or functional constraints. If lizard osteoderms are primarily for defence, whether against predators or conspecifics, then this 'bony armour' might be predicted to have different structural and/or mechanical properties compared to other hard tissues (generally intended for support and locomotion). The cellular and biomineralisation mechanisms by which osteoderms are formed could also be different from those of other hard tissues, as reflected in their material composition and nanostructure. Material properties, especially the combination of malleability and resistance to impact, are of interest to the biomimetics and bioinspired material communities in the development of protective clothing and body armour. Currently, the literature on osteoderms is patchy and is distributed across a wide range of journals. Herein we present a synthesis of current knowledge on lizard osteoderm evolution and distribution, micro- and macrostructure, development, and function, with a view to stimulating further work.
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Affiliation(s)
- Catherine Williams
- Department of Biomedical Sciences, University of Guelph, 50 Stone Road East, Guelph, ON, N1G 2W1, Canada.,Department of Biology, Aarhus University, Ny Munkegade 114-116, Aarhus C, DK-8000, Denmark
| | - Alexander Kirby
- Department of Medical Physics and Biomedical Engineering, University College London, London, WC1E 6BT, U.K.,Department of Cell and Developmental Biology, University College London, London, WC1E 6BT, U.K
| | - Arsalan Marghoub
- Department of Mechanical Engineering, University College London, London, WC1E 7JE, U.K
| | - Loïc Kéver
- Département Adaptations du Vivant, UMR 7179 MECADEV C.N.R.S/M.N.H.N., Bâtiment d'Anatomie Comparée, 55 rue Buffon, Paris, 75005, France
| | - Sonya Ostashevskaya-Gohstand
- Department of Life Sciences, Faculty of Natural Sciences, Imperial College London, Silwood Park Campus, Berkshire, SL5 7PY, U.K
| | - Sergio Bertazzo
- Department of Medical Physics and Biomedical Engineering, University College London, London, WC1E 6BT, U.K
| | - Mehran Moazen
- Department of Mechanical Engineering, University College London, London, WC1E 7JE, U.K
| | - Arkhat Abzhanov
- Department of Life Sciences, Faculty of Natural Sciences, Imperial College London, Silwood Park Campus, Berkshire, SL5 7PY, U.K
| | - Anthony Herrel
- Département Adaptations du Vivant, UMR 7179 MECADEV C.N.R.S/M.N.H.N., Bâtiment d'Anatomie Comparée, 55 rue Buffon, Paris, 75005, France
| | - Susan E Evans
- Department of Cell and Developmental Biology, University College London, London, WC1E 6BT, U.K
| | - Matt Vickaryous
- Department of Biomedical Sciences, University of Guelph, 50 Stone Road East, Guelph, ON, N1G 2W1, Canada
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20
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Toledo-Solís FJ, Hilerio-Ruiz AG, Delgadin T, Sirkin DP, Di Yorio MP, Vissio PG, Peña-Marín ES, Martínez-García R, Maytorena-Verdugo CI, Álvarez-González CA, de Rodrigáñez MAS. Changes in digestive enzyme activities during the early ontogeny of the South American cichlid (Cichlasoma dimerus). FISH PHYSIOLOGY AND BIOCHEMISTRY 2021; 47:1211-1227. [PMID: 34173183 DOI: 10.1007/s10695-021-00976-z] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.3] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Received: 09/23/2020] [Accepted: 06/14/2021] [Indexed: 06/13/2023]
Abstract
Cichlasoma dimerus is a neotropical cichlid that has been used as a biological model for neuroendocrinology studies. However, its culture is problematic in terms of larval feeding to allow having enough fry quantity and quality. Larviculture requires full knowledge about the digestive system and nutrition; therefore, this study was intended to assess the digestive enzymes' changes at different ages during the early ontogeny. Acid protease activity was detectable from the first day after hatching (dah), increasing to its maximum peaks on 9 dah. In contrast, alkaline proteases had low activity in the first days of life but reached their maximum activity on 17 dah. Chymotrypsin, L-aminopeptidase, and carboxypeptidase A activities increased at 6 dah, while trypsin activity was first detected on 13 dah and reached its maximum activity on 17 dah. Lipase and α-amylase activity were detectable at low levels in the first days of life, but the activity fluctuated and reaching its maximum activity at 21 dah. Alkaline phosphatase continued to oscillate and had two maximum activity peaks, the first at 6 dah and the second at 19 dah. Zymograms of alkaline proteases on day 6 dah six revealed four activity bands with molecular weights from 16.1 to 77.7 kDa. On 13 dah, two more activity bands of 24.4 and 121.9 kDa were detected, having a total of six proteases. The enzymatic activity analyzes indicate the digestive system shows the low activity of some enzymes in the first days after hatching, registering significant increases on 6 dah and the maximum peaks of activities around at 17 dah. Therefore, we recommend replacing live food with dry feed and only providing dry feed after day 17 dah.
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Affiliation(s)
- Francisco Javier Toledo-Solís
- Departamento de Biología y Geología, Universidad de Almería, 04120, Almería, Spain
- Consejo Nacional de Ciencia y Tecnología (CONACYT), Av. Insurgentes Sur 1582, Alcaldía Benito Juárez, C.P. 03940, Ciudad de México, Mexico
| | - Andrea Guadalupe Hilerio-Ruiz
- Laboratorio de Acuicultura Tropical, División Académica de Ciencias Biológicas, Universidad Juárez Autónoma de Tabasco, 0.5 km Carretera Villahermosa-Cárdenas, C.P. 86039, Villahermosa, TAB, Mexico
| | - Tomás Delgadin
- Departamento de Biodiversidad Y Biología Experimental, Facultad de Ciencias Exactas y Naturales, Universidad de Buenos Aires / Instituto de Biodiversidad y Biología Experimental Aplicada (IBBEA), CONICET-Universidad de Buenos Aires, Buenos Aires, Argentina
| | - Daniela Pérez Sirkin
- Departamento de Biodiversidad Y Biología Experimental, Facultad de Ciencias Exactas y Naturales, Universidad de Buenos Aires / Instituto de Biodiversidad y Biología Experimental Aplicada (IBBEA), CONICET-Universidad de Buenos Aires, Buenos Aires, Argentina
| | - María Paula Di Yorio
- Departamento de Biodiversidad Y Biología Experimental, Facultad de Ciencias Exactas y Naturales, Universidad de Buenos Aires / Instituto de Biodiversidad y Biología Experimental Aplicada (IBBEA), CONICET-Universidad de Buenos Aires, Buenos Aires, Argentina
| | - Paula Gabriela Vissio
- Departamento de Biodiversidad Y Biología Experimental, Facultad de Ciencias Exactas y Naturales, Universidad de Buenos Aires / Instituto de Biodiversidad y Biología Experimental Aplicada (IBBEA), CONICET-Universidad de Buenos Aires, Buenos Aires, Argentina
| | - Emyr Saul Peña-Marín
- Laboratorio de Acuicultura Tropical, División Académica de Ciencias Biológicas, Universidad Juárez Autónoma de Tabasco, 0.5 km Carretera Villahermosa-Cárdenas, C.P. 86039, Villahermosa, TAB, Mexico
- Cátedra CONACYT, Ciudad de México, Mexico
| | - Rafael Martínez-García
- Laboratorio de Acuicultura Tropical, División Académica de Ciencias Biológicas, Universidad Juárez Autónoma de Tabasco, 0.5 km Carretera Villahermosa-Cárdenas, C.P. 86039, Villahermosa, TAB, Mexico
| | - Claudia Ivette Maytorena-Verdugo
- Laboratorio de Acuicultura Tropical, División Académica de Ciencias Biológicas, Universidad Juárez Autónoma de Tabasco, 0.5 km Carretera Villahermosa-Cárdenas, C.P. 86039, Villahermosa, TAB, Mexico
| | - Carlos Alfonso Álvarez-González
- Laboratorio de Acuicultura Tropical, División Académica de Ciencias Biológicas, Universidad Juárez Autónoma de Tabasco, 0.5 km Carretera Villahermosa-Cárdenas, C.P. 86039, Villahermosa, TAB, Mexico.
| | - Miguel Angel Sáenz de Rodrigáñez
- Departamento de Fisiología, Facultad de Ciencias de La Salud, Universidad de Granada, Campus de Melilla, Calle Santander, 1, C.P. 52005, Melilla, Spain
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21
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Caccavo JA, Christiansen H, Constable AJ, Ghigliotti L, Trebilco R, Brooks CM, Cotte C, Desvignes T, Dornan T, Jones CD, Koubbi P, Saunders RA, Strobel A, Vacchi M, van de Putte AP, Walters A, Waluda CM, Woods BL, Xavier JC. Productivity and Change in Fish and Squid in the Southern Ocean. Front Ecol Evol 2021. [DOI: 10.3389/fevo.2021.624918] [Citation(s) in RCA: 9] [Impact Index Per Article: 3.0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/13/2022] Open
Abstract
Southern Ocean ecosystems are globally important and vulnerable to global drivers of change, yet they remain challenging to study. Fish and squid make up a significant portion of the biomass within the Southern Ocean, filling key roles in food webs from forage to mid-trophic species and top predators. They comprise a diverse array of species uniquely adapted to the extreme habitats of the region. Adaptations such as antifreeze glycoproteins, lipid-retention, extended larval phases, delayed senescence, and energy-conserving life strategies equip Antarctic fish and squid to withstand the dark winters and yearlong subzero temperatures experienced in much of the Southern Ocean. In addition to krill exploitation, the comparatively high commercial value of Antarctic fish, particularly the lucrative toothfish, drives fisheries interests, which has included illegal fishing. Uncertainty about the population dynamics of target species and ecosystem structure and function more broadly has necessitated a precautionary, ecosystem approach to managing these stocks and enabling the recovery of depleted species. Fisheries currently remain the major local driver of change in Southern Ocean fish productivity, but global climate change presents an even greater challenge to assessing future changes. Parts of the Southern Ocean are experiencing ocean-warming, such as the West Antarctic Peninsula, while other areas, such as the Ross Sea shelf, have undergone cooling in recent years. These trends are expected to result in a redistribution of species based on their tolerances to different temperature regimes. Climate variability may impair the migratory response of these species to environmental change, while imposing increased pressures on recruitment. Fisheries and climate change, coupled with related local and global drivers such as pollution and sea ice change, have the potential to produce synergistic impacts that compound the risks to Antarctic fish and squid species. The uncertainty surrounding how different species will respond to these challenges, given their varying life histories, environmental dependencies, and resiliencies, necessitates regular assessment to inform conservation and management decisions. Urgent attention is needed to determine whether the current management strategies are suitably precautionary to achieve conservation objectives in light of the impending changes to the ecosystem.
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22
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Independent duplications of the Golgi phosphoprotein 3 oncogene in birds. Sci Rep 2021; 11:12483. [PMID: 34127736 PMCID: PMC8203631 DOI: 10.1038/s41598-021-91909-6] [Citation(s) in RCA: 2] [Impact Index Per Article: 0.7] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/03/2021] [Accepted: 06/02/2021] [Indexed: 02/05/2023] Open
Abstract
Golgi phosphoprotein 3 (GOLPH3) was the first reported oncoprotein of the Golgi apparatus. It was identified as an evolutionarily conserved protein upon its discovery about 20 years ago, but its function remains puzzling in normal and cancer cells. The GOLPH3 gene is part of a group of genes that also includes the GOLPH3L gene. Because cancer has deep roots in multicellular evolution, studying the evolution of the GOLPH3 gene family in non-model species represents an opportunity to identify new model systems that could help better understand the biology behind this group of genes. The main goal of this study is to explore the evolution of the GOLPH3 gene family in birds as a starting point to understand the evolutionary history of this oncoprotein. We identified a repertoire of three GOLPH3 genes in birds. We found duplicated copies of the GOLPH3 gene in all main groups of birds other than paleognaths, and a single copy of the GOLPH3L gene. We suggest there were at least three independent origins for GOLPH3 duplicates. Amino acid divergence estimates show that most of the variation is located in the N-terminal region of the protein. Our transcript abundance estimations show that one paralog is highly and ubiquitously expressed, and the others were variable. Our results are an example of the significance of understanding the evolution of the GOLPH3 gene family, especially for unraveling its structural and functional attributes.
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23
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Rosa JT, Laizé V, Gavaia PJ, Cancela ML. Fish Models of Induced Osteoporosis. Front Cell Dev Biol 2021; 9:672424. [PMID: 34179000 PMCID: PMC8222987 DOI: 10.3389/fcell.2021.672424] [Citation(s) in RCA: 12] [Impact Index Per Article: 4.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 02/25/2021] [Accepted: 04/28/2021] [Indexed: 12/13/2022] Open
Abstract
Osteopenia and osteoporosis are bone disorders characterized by reduced bone mineral density (BMD), altered bone microarchitecture and increased bone fragility. Because of global aging, their incidence is rapidly increasing worldwide and novel treatments that would be more efficient at preventing disease progression and at reducing the risk of bone fractures are needed. Preclinical studies are today a major bottleneck to the collection of new data and the discovery of new drugs, since they are commonly based on rodent in vivo systems that are time consuming and expensive, or in vitro systems that do not exactly recapitulate the complexity of low BMD disorders. In this regard, teleost fish, in particular zebrafish and medaka, have recently emerged as suitable alternatives to study bone formation and mineralization and to model human bone disorders. In addition to the many technical advantages that allow faster and larger studies, the availability of several fish models that efficiently mimic human osteopenia and osteoporosis phenotypes has stimulated the interest of the academia and industry toward a better understanding of the mechanisms of pathogenesis but also toward the discovery of new bone anabolic or antiresorptive compounds. This mini review recapitulates the in vivo teleost fish systems available to study low BMD disorders and highlights their applications and the recent advances in the field.
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Affiliation(s)
- Joana T Rosa
- Centre of Marine Sciences, University of Algarve, Faro, Portugal
| | - Vincent Laizé
- Centre of Marine Sciences, University of Algarve, Faro, Portugal.,S2 AQUA - Sustainable and Smart Aquaculture Collaborative Laboratory, Olhão, Portugal
| | - Paulo J Gavaia
- Centre of Marine Sciences, University of Algarve, Faro, Portugal.,GreenCoLab - Associação Oceano Verde, Faro, Portugal.,Faculty of Medicine and Biomedical Sciences, University of Algarve, Faro, Portugal
| | - M Leonor Cancela
- Centre of Marine Sciences, University of Algarve, Faro, Portugal.,Faculty of Medicine and Biomedical Sciences, University of Algarve, Faro, Portugal.,Algarve Biomedical Center, University of Algarve, Faro, Portugal
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24
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Stegmann UE. Medical toolkit organisms and Covid-19. HISTORY AND PHILOSOPHY OF THE LIFE SCIENCES 2021; 43:14. [PMID: 33528761 PMCID: PMC7851655 DOI: 10.1007/s40656-021-00371-0] [Citation(s) in RCA: 2] [Impact Index Per Article: 0.7] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Received: 10/16/2020] [Accepted: 01/15/2021] [Indexed: 06/12/2023]
Abstract
The Covid-19 pandemic has intensified interest in animals with superior antiviral defences. I argue that the role of such animals in biomedical research contrasts with the role of disease models.
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Affiliation(s)
- Ulrich E Stegmann
- School of Divinity, History and Philosophy, University of Aberdeen, 50-52 College Bounds, Aberdeen, AB24 3DS, UK.
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25
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McGirr JA, Martin CH. Few Fixed Variants between Trophic Specialist Pupfish Species Reveal Candidate Cis-Regulatory Alleles Underlying Rapid Craniofacial Divergence. Mol Biol Evol 2021; 38:405-423. [PMID: 32877534 PMCID: PMC7826174 DOI: 10.1093/molbev/msaa218] [Citation(s) in RCA: 13] [Impact Index Per Article: 4.3] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 02/07/2023] Open
Abstract
Investigating closely related species that rapidly evolved divergent feeding morphology is a powerful approach to identify genetic variation underlying variation in complex traits. This can also lead to the discovery of novel candidate genes influencing natural and clinical variation in human craniofacial phenotypes. We combined whole-genome resequencing of 258 individuals with 50 transcriptomes to identify candidate cis-acting genetic variation underlying rapidly evolving craniofacial phenotypes within an adaptive radiation of Cyprinodon pupfishes. This radiation consists of a dietary generalist species and two derived trophic niche specialists-a molluscivore and a scale-eating species. Despite extensive morphological divergence, these species only diverged 10 kya and produce fertile hybrids in the laboratory. Out of 9.3 million genome-wide SNPs and 80,012 structural variants, we found very few alleles fixed between species-only 157 SNPs and 87 deletions. Comparing gene expression across 38 purebred F1 offspring sampled at three early developmental stages, we identified 17 fixed variants within 10 kb of 12 genes that were highly differentially expressed between species. By measuring allele-specific expression in F1 hybrids from multiple crosses, we found that the majority of expression divergence between species was explained by trans-regulatory mechanisms. We also found strong evidence for two cis-regulatory alleles affecting expression divergence of two genes with putative effects on skeletal development (dync2li1 and pycr3). These results suggest that SNPs and structural variants contribute to the evolution of novel traits and highlight the utility of the San Salvador Island pupfish system as an evolutionary model for craniofacial development.
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Affiliation(s)
- Joseph A McGirr
- Environmental Toxicology Department, University of California, Davis, CA
| | - Christopher H Martin
- Department of Integrative Biology and Museum of Vertebrate Zoology, University of California, Berkeley, CA
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26
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Unlocking the Secrets of the Regenerating Fish Heart: Comparing Regenerative Models to Shed Light on Successful Regeneration. J Cardiovasc Dev Dis 2021; 8:jcdd8010004. [PMID: 33467137 PMCID: PMC7830602 DOI: 10.3390/jcdd8010004] [Citation(s) in RCA: 5] [Impact Index Per Article: 1.7] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/02/2020] [Revised: 01/11/2021] [Accepted: 01/12/2021] [Indexed: 01/01/2023] Open
Abstract
The adult human heart cannot repair itself after injury and, instead, forms a permanent fibrotic scar that impairs cardiac function and can lead to incurable heart failure. The zebrafish, amongst other organisms, has been extensively studied for its innate capacity to repair its heart after injury. Understanding the signals that govern successful regeneration in models such as the zebrafish will lead to the development of effective therapies that can stimulate endogenous repair in humans. To date, many studies have investigated cardiac regeneration using a reverse genetics candidate gene approach. However, this approach is limited in its ability to unbiasedly identify novel genes and signalling pathways that are essential to successful regeneration. In contrast, drawing comparisons between different models of regeneration enables unbiased screens to be performed, identifying signals that have not previously been linked to regeneration. Here, we will review in detail what has been learnt from the comparative approach, highlighting the techniques used and how these studies have influenced the field. We will also discuss what further comparisons would enhance our knowledge of successful regeneration and scarring. Finally, we focus on the Astyanax mexicanus, an intraspecies comparative fish model that holds great promise for revealing the secrets of the regenerating heart.
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27
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Tao W, Conte MA, Wang D, Kocher TD. Network architecture and sex chromosome turnovers: Do epistatic interactions shape patterns of sex chromosome replacement? Bioessays 2020; 43:e2000161. [PMID: 33283342 DOI: 10.1002/bies.202000161] [Citation(s) in RCA: 3] [Impact Index Per Article: 0.8] [Reference Citation Analysis] [Abstract] [Key Words] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/26/2020] [Revised: 11/04/2020] [Accepted: 11/05/2020] [Indexed: 11/11/2022]
Abstract
Recent studies have revealed an astonishing diversity of sex chromosomes in many vertebrate lineages, prompting questions about the mechanisms of sex chromosome turnover. While there is considerable population genetic theory about the evolutionary forces promoting sex chromosome replacement, this theory has not yet been integrated with our understanding of the molecular and developmental genetics of sex determination. Here, we review recent data to examine four questions about how the structure of gene networks influences the evolution of sex determination. We argue that patterns of epistasis, arising from the structure of genetic networks, may play an important role in regulating the rates and patterns of sex chromosome replacement.
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Affiliation(s)
- Wenjing Tao
- Key Laboratory of Freshwater Fish Reproduction and Development (Ministry of Education), Key Laboratory of Aquatic Science of Chongqing, School of Life Sciences, Southwest University, Chongqing, China
| | - Matthew A Conte
- Department of Biology, University of Maryland, College Park, Maryland, USA
| | - Deshou Wang
- Key Laboratory of Freshwater Fish Reproduction and Development (Ministry of Education), Key Laboratory of Aquatic Science of Chongqing, School of Life Sciences, Southwest University, Chongqing, China
| | - Thomas D Kocher
- Department of Biology, University of Maryland, College Park, Maryland, USA
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28
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Abstract
The Bateson–Dobzhansky–Muller (BDM) model describes negative epistatic interactions that occur between genes with a different evolutionary history to account for hybrid incompatibility and is a central theory explaining genetic mechanisms underlying speciation. Since the early 1900 s when the BDM model was forwarded examples of BDM incompatibility have been described in only a few nonvertebrate cases. This study reports the only vertebrate system, with clearly defined interacting loci, that supports the BDM model. In addition, this study also poses that tumorigenesis serves as a novel mechanism that accounts for postzygotic isolation. Mixing genomes of different species by hybridization can disrupt species-specific genetic interactions that were adapted and fixed within each species population. Such disruption can predispose the hybrids to abnormalities and disease that decrease the overall fitness of the hybrids and is therefore named as hybrid incompatibility. Interspecies hybridization between southern platyfish and green swordtails leads to lethal melanocyte tumorigenesis. This occurs in hybrids with tumor incidence following progeny ratio that is consistent with two-locus interaction, suggesting melanoma development is a result of negative epistasis. Such observations make Xiphophorus one of the only two vertebrate hybrid incompatibility examples in which interacting genes have been identified. One of the two interacting loci has been characterized as a mutant epidermal growth factor receptor. However, the other locus has not been identified despite over five decades of active research. Here we report the localization of the melanoma regulatory locus to a single gene, rab3d, which shows all expected features of the long-sought oncogene interacting locus. Our findings provide insights into the role of egfr regulation in regard to cancer etiology. Finally, they provide a molecular explainable example of hybrid incompatibility.
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29
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Daane JM, Auvinet J, Stoebenau A, Yergeau D, Harris MP, Detrich HW. Developmental constraint shaped genome evolution and erythrocyte loss in Antarctic fishes following paleoclimate change. PLoS Genet 2020; 16:e1009173. [PMID: 33108368 PMCID: PMC7660546 DOI: 10.1371/journal.pgen.1009173] [Citation(s) in RCA: 10] [Impact Index Per Article: 2.5] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/09/2020] [Revised: 11/12/2020] [Accepted: 10/06/2020] [Indexed: 02/07/2023] Open
Abstract
In the frigid, oxygen-rich Southern Ocean (SO), Antarctic icefishes (Channichthyidae; Notothenioidei) evolved the ability to survive without producing erythrocytes and hemoglobin, the oxygen-transport system of virtually all vertebrates. Here, we integrate paleoclimate records with an extensive phylogenomic dataset of notothenioid fishes to understand the evolution of trait loss associated with climate change. In contrast to buoyancy adaptations in this clade, we find relaxed selection on the genetic regions controlling erythropoiesis evolved only after sustained cooling in the SO. This pattern is seen not only within icefishes but also occurred independently in other high-latitude notothenioids. We show that one species of the red-blooded dragonfish clade evolved a spherocytic anemia that phenocopies human patients with this disease via orthologous mutations. The genomic imprint of SO climate change is biased toward erythrocyte-associated conserved noncoding elements (CNEs) rather than to coding regions, which are largely preserved through pleiotropy. The drift in CNEs is specifically enriched near genes that are preferentially expressed late in erythropoiesis. Furthermore, we find that the hematopoietic marrow of icefish species retained proerythroblasts, which indicates that early erythroid development remains intact. Our results provide a framework for understanding the interactions between development and the genome in shaping the response of species to climate change. Our climate is rapidly changing. To better understand how species can adapt to major climate disturbance, we looked back into the past at a group of fishes that have encountered dramatic climate upheavals and thrived: Antarctic notothenioid fishes. In particular, we focus on the icefishes, which lost the ability to produce red blood cells in the frigid environment of the Southern Ocean. By integrating past climate records with a large genetic dataset of Antarctic fishes, we show that the loss of red blood cells occurred only after sustained cooling of the Southern Ocean. As cooling continued into the modern era, we discover that even some of the “red-blooded” relatives of the icefishes show early genetic and morphological signs of erythrocyte loss. This cooling event left a non-random imprint on the genome of icefishes. With few exceptions, the genetic toolkit underlying red cell development has remained intact in icefishes because many “erythroid” genes perform important functions in other tissues. Rather, mutations have accumulated in gene regulatory regions near genes that control terminal erythroid maturation, such that icefishes continue to produce red cell progenitors but not mature erythrocytes. These results show that the genetic constraints regulating embryonic development shaped the evolutionary response of this fish group to climate change.
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Affiliation(s)
- Jacob M. Daane
- Department of Marine and Environmental Sciences, Northeastern University Marine Science Center, Nahant, MA, United States of America
- Orthopaedic Research Laboratories, Department of Orthopaedic Surgery, Boston Children's Hospital, Boston, MA, United States of America
- Department of Genetics, Harvard Medical School, Boston, MA, United States of America
- * E-mail: (JMD); (HWD)
| | - Juliette Auvinet
- Department of Marine and Environmental Sciences, Northeastern University Marine Science Center, Nahant, MA, United States of America
| | - Alicia Stoebenau
- Department of Marine and Environmental Sciences, Northeastern University Marine Science Center, Nahant, MA, United States of America
| | - Donald Yergeau
- Department of Biology, Northeastern University, Boston, MA, United States of America
| | - Matthew P. Harris
- Orthopaedic Research Laboratories, Department of Orthopaedic Surgery, Boston Children's Hospital, Boston, MA, United States of America
- Department of Genetics, Harvard Medical School, Boston, MA, United States of America
| | - H. William Detrich
- Department of Marine and Environmental Sciences, Northeastern University Marine Science Center, Nahant, MA, United States of America
- Department of Biology, Northeastern University, Boston, MA, United States of America
- * E-mail: (JMD); (HWD)
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30
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Avelar RA, Ortega JG, Tacutu R, Tyler EJ, Bennett D, Binetti P, Budovsky A, Chatsirisupachai K, Johnson E, Murray A, Shields S, Tejada-Martinez D, Thornton D, Fraifeld VE, Bishop CL, de Magalhães JP. A multidimensional systems biology analysis of cellular senescence in aging and disease. Genome Biol 2020; 21:91. [PMID: 32264951 PMCID: PMC7333371 DOI: 10.1186/s13059-020-01990-9] [Citation(s) in RCA: 159] [Impact Index Per Article: 39.8] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/17/2019] [Accepted: 03/08/2020] [Indexed: 01/10/2023] Open
Abstract
BACKGROUND Cellular senescence, a permanent state of replicative arrest in otherwise proliferating cells, is a hallmark of aging and has been linked to aging-related diseases. Many genes play a role in cellular senescence, yet a comprehensive understanding of its pathways is still lacking. RESULTS We develop CellAge (http://genomics.senescence.info/cells), a manually curated database of 279 human genes driving cellular senescence, and perform various integrative analyses. Genes inducing cellular senescence tend to be overexpressed with age in human tissues and are significantly overrepresented in anti-longevity and tumor-suppressor genes, while genes inhibiting cellular senescence overlap with pro-longevity and oncogenes. Furthermore, cellular senescence genes are strongly conserved in mammals but not in invertebrates. We also build cellular senescence protein-protein interaction and co-expression networks. Clusters in the networks are enriched for cell cycle and immunological processes. Network topological parameters also reveal novel potential cellular senescence regulators. Using siRNAs, we observe that all 26 candidates tested induce at least one marker of senescence with 13 genes (C9orf40, CDC25A, CDCA4, CKAP2, GTF3C4, HAUS4, IMMT, MCM7, MTHFD2, MYBL2, NEK2, NIPA2, and TCEB3) decreasing cell number, activating p16/p21, and undergoing morphological changes that resemble cellular senescence. CONCLUSIONS Overall, our work provides a benchmark resource for researchers to study cellular senescence, and our systems biology analyses reveal new insights and gene regulators of cellular senescence.
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Affiliation(s)
- Roberto A Avelar
- Integrative Genomics of Ageing Group, Institute of Ageing and Chronic Disease, University of Liverpool, Liverpool, L7 8TX, UK
| | - Javier Gómez Ortega
- Integrative Genomics of Ageing Group, Institute of Ageing and Chronic Disease, University of Liverpool, Liverpool, L7 8TX, UK
- School of Biological Sciences, Monash University, Melbourne, VIC, 3800, Australia
| | - Robi Tacutu
- Integrative Genomics of Ageing Group, Institute of Ageing and Chronic Disease, University of Liverpool, Liverpool, L7 8TX, UK
- Computational Biology of Aging Group, Institute of Biochemistry, Romanian Academy, 060031, Bucharest, Romania
- Chronos Biosystems SRL, 060117, Bucharest, Romania
| | - Eleanor J Tyler
- Centre for Cell Biology and Cutaneous Research, Blizard Institute, Barts and The London School of Medicine and Dentistry, Queen Mary University of London, London, E1 2AT, UK
| | - Dominic Bennett
- Integrative Genomics of Ageing Group, Institute of Ageing and Chronic Disease, University of Liverpool, Liverpool, L7 8TX, UK
| | - Paolo Binetti
- Integrative Genomics of Ageing Group, Institute of Ageing and Chronic Disease, University of Liverpool, Liverpool, L7 8TX, UK
| | - Arie Budovsky
- Research and Development Authority, Barzilai Medical Center, Ashkelon, Israel
| | - Kasit Chatsirisupachai
- Integrative Genomics of Ageing Group, Institute of Ageing and Chronic Disease, University of Liverpool, Liverpool, L7 8TX, UK
| | - Emily Johnson
- Integrative Genomics of Ageing Group, Institute of Ageing and Chronic Disease, University of Liverpool, Liverpool, L7 8TX, UK
| | - Alex Murray
- Integrative Genomics of Ageing Group, Institute of Ageing and Chronic Disease, University of Liverpool, Liverpool, L7 8TX, UK
| | - Samuel Shields
- Integrative Genomics of Ageing Group, Institute of Ageing and Chronic Disease, University of Liverpool, Liverpool, L7 8TX, UK
| | - Daniela Tejada-Martinez
- Integrative Genomics of Ageing Group, Institute of Ageing and Chronic Disease, University of Liverpool, Liverpool, L7 8TX, UK
- Doctorado en Ciencias mención Ecología y Evolución, Instituto de Ciencias Ambientales y Evolutivas, Facultad de Ciencias, Universidad Austral de Chile, Independencia 631, Valdivia, Chile
| | - Daniel Thornton
- Integrative Genomics of Ageing Group, Institute of Ageing and Chronic Disease, University of Liverpool, Liverpool, L7 8TX, UK
| | - Vadim E Fraifeld
- The Shraga Segal Department of Microbiology, Immunology and Genetics, Faculty of Health Sciences, Center for Multidisciplinary Research on Aging, Ben-Gurion University of the Negev, 8410501, Beer Sheva, Israel
| | - Cleo L Bishop
- Centre for Cell Biology and Cutaneous Research, Blizard Institute, Barts and The London School of Medicine and Dentistry, Queen Mary University of London, London, E1 2AT, UK.
| | - João Pedro de Magalhães
- Integrative Genomics of Ageing Group, Institute of Ageing and Chronic Disease, University of Liverpool, Liverpool, L7 8TX, UK.
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31
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QTL Mapping of Intestinal Neutrophil Variation in Threespine Stickleback Reveals Possible Gene Targets Connecting Intestinal Inflammation and Systemic Health. G3-GENES GENOMES GENETICS 2020; 10:613-622. [PMID: 31843804 PMCID: PMC7003091 DOI: 10.1534/g3.119.400685] [Citation(s) in RCA: 5] [Impact Index Per Article: 1.3] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Subscribe] [Scholar Register] [Indexed: 02/07/2023]
Abstract
Selection, via host immunity, is often required to foster beneficial microbial symbionts and suppress deleterious pathogens. In animals, the host immune system is at the center of this relationship. Failed host immune system-microbial interactions can result in a persistent inflammatory response in which the immune system indiscriminately attacks resident microbes, and at times the host cells themselves, leading to diseases such as Ulcerative Colitis, Crohn’s Disease, and Psoriasis. Host genetic variation has been linked to both microbiome diversity and to severity of such inflammatory disease states in humans. However, the microbiome and inflammatory states manifest as quantitative traits, which encompass many genes interacting with one another and the environment. The mechanistic relationships among all of these interacting components are still not clear. Developing natural genetic models of host-microbe interactions is therefore fundamental to understanding the complex genetics of these and other diseases. Threespine stickleback (Gasterosteus aculeatus) fish are a tractable model for attacking this problem because of abundant population-level genetic and phenotypic variation in the gut inflammatory response. Previous work in our laboratory identified genetically divergent stickleback populations exhibiting differences in intestinal neutrophil activity. We took advantage of this diversity to genetically map variation in an emblematic element of gut inflammation - intestinal neutrophil recruitment - using an F2-intercross mapping framework. We identified two regions of the genome associated with increased intestinal inflammation containing several promising candidate genes. Within these regions we found candidates in the Coagulation/Complement System, NFkB and MAPK pathways along with several genes associated with intestinal diseases and neurological diseases commonly accompanying intestinal inflammation as a secondary symptom. These findings highlight the utility of using naturally genetically diverse ‘evolutionary mutant models’ such as threespine stickleback to better understand interactions among host genetic diversity and microbiome variation in health and disease states.
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32
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Kowalko J. Utilizing the blind cavefish Astyanax mexicanus to understand the genetic basis of behavioral evolution. J Exp Biol 2020; 223:223/Suppl_1/jeb208835. [DOI: 10.1242/jeb.208835] [Citation(s) in RCA: 17] [Impact Index Per Article: 4.3] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 01/01/2023]
Abstract
ABSTRACT
Colonization of novel habitats often results in the evolution of diverse behaviors. Comparisons between individuals from closely related populations that have evolved divergent behaviors in different environments can be used to investigate behavioral evolution. However, until recently, functionally connecting genotypes to behavioral phenotypes in these evolutionarily relevant organisms has been difficult. The development of gene editing tools will facilitate functional genetic analysis of genotype–phenotype connections in virtually any organism, and has the potential to significantly transform the field of behavioral genetics when applied to ecologically and evolutionarily relevant organisms. The blind cavefish Astyanax mexicanus provides a remarkable example of evolution associated with colonization of a novel habitat. These fish consist of a single species that includes sighted surface fish that inhabit the rivers of Mexico and southern Texas and at least 29 populations of blind cavefish from the Sierra Del Abra and Sierra de Guatemala regions of Northeast Mexico. Although eye loss and albinism have been studied extensively in A. mexicanus, derived behavioral traits including sleep loss, alterations in foraging and reduction in social behaviors are now also being investigated in this species to understand the genetic and neural basis of behavioral evolution. Astyanax mexicanus has emerged as a powerful model system for genotype–phenotype mapping because surface and cavefish are interfertile. Further, the molecular basis of repeated trait evolution can be examined in this species, as multiple cave populations have independently evolved the same traits. A sequenced genome and the implementation of gene editing in A. mexicanus provides a platform for gene discovery and identification of the contributions of naturally occurring variation to behaviors. This review describes the current knowledge of behavioral evolution in A. mexicanus with an emphasis on the molecular and genetic underpinnings of evolved behaviors. Multiple avenues of new research that can be pursued using gene editing tools are identified, and how these will enhance our understanding of behavioral evolution is discussed.
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Affiliation(s)
- Johanna Kowalko
- Harriet L. Wilkes Honors College, Florida Atlantic University, Jupiter, FL 33458, USA
- Program of Neurogenetics, Florida Atlantic University, Jupiter, FL 33458, USA
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Small CM, Currey M, Beck EA, Bassham S, Cresko WA. Highly Reproducible 16S Sequencing Facilitates Measurement of Host Genetic Influences on the Stickleback Gut Microbiome. mSystems 2019; 4:e00331-19. [PMID: 31409661 PMCID: PMC6697441 DOI: 10.1128/msystems.00331-19] [Citation(s) in RCA: 5] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Abstract] [Key Words] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/22/2019] [Accepted: 07/19/2019] [Indexed: 12/18/2022] Open
Abstract
Multicellular organisms interact with resident microbes in important ways, and a better understanding of host-microbe interactions is aided by tools such as high-throughput 16S sequencing. However, rigorous evaluation of the veracity of these tools in a different context from which they were developed has often lagged behind. Our goal was to perform one such critical test by examining how variation in tissue preparation and DNA isolation could affect inferences about gut microbiome variation between two genetically divergent lines of threespine stickleback fish maintained in the same laboratory environment. Using careful experimental design and intensive sampling of individuals, we addressed technical and biological sources of variation in 16S-based estimates of microbial diversity. After employing a two-tiered bead beating approach that comprised tissue homogenization followed by microbial lysis in subsamples, we found an extremely minor effect of DNA isolation protocol relative to among-host microbial diversity differences. Abundance estimates for rare operational taxonomic units (OTUs), however, showed much lower reproducibility. Gut microbiome composition was highly variable across fish-even among cohoused siblings-relative to technical replicates, but a subtle effect of host genotype (stickleback line) was nevertheless detected for some microbial taxa.IMPORTANCE Our findings demonstrate the importance of appropriately quantifying biological and technical variance components when attempting to understand major influences on high-throughput microbiome data. Our focus was on understanding among-host (biological) variance in community metrics and its magnitude in relation to within-host (technical) variance, because meaningful comparisons among individuals are necessary in addressing major questions in host-microbe ecology and evolution, such as heritability of the microbiome. Our study design and insights should provide a useful example for others desiring to quantify microbiome variation at biological levels in the face of various technical factors in a variety of systems.
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Affiliation(s)
- Clayton M Small
- Institute of Ecology and Evolution, University of Oregon, Eugene, Oregon, USA
| | - Mark Currey
- Institute of Ecology and Evolution, University of Oregon, Eugene, Oregon, USA
| | - Emily A Beck
- Institute of Ecology and Evolution, University of Oregon, Eugene, Oregon, USA
| | - Susan Bassham
- Institute of Ecology and Evolution, University of Oregon, Eugene, Oregon, USA
| | - William A Cresko
- Institute of Ecology and Evolution, University of Oregon, Eugene, Oregon, USA
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Pawluk RJ, Garcia de Leaniz C, Cable J, Tiddeman B, Consuegra S. Colour plasticity in response to social context and parasitic infection in a self-fertilizing fish. ROYAL SOCIETY OPEN SCIENCE 2019; 6:181418. [PMID: 31417688 PMCID: PMC6689574 DOI: 10.1098/rsos.181418] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.2] [Reference Citation Analysis] [Abstract] [Key Words] [Grants] [Track Full Text] [Figures] [Subscribe] [Scholar Register] [Received: 09/04/2018] [Accepted: 05/23/2019] [Indexed: 06/10/2023]
Abstract
Many animal species rely on changes in body coloration to signal social dominance, mating readiness and health status to conspecifics, which can in turn influence reproductive success, social dynamics and pathogen avoidance in natural populations. Such colour changes are thought to be controlled by genetic and environmental conditions, but their relative importance is difficult to measure in natural populations, where individual genetic variability complicates data interpretation. Here, we studied shifts in melanin-related body coloration in response to social context and parasitic infection in two naturally inbred lines of a self-fertilizing fish to disentangle the relative roles of genetic background and individual variation. We found that social context and parasitic infection had a significant effect on body coloration that varied between genetic lines, suggesting the existence of genotype by environment interactions. In addition, individual variation was also important for some of the colour attributes. We suggest that the genetic background drives colour plasticity and that this can maintain phenotypic variation in inbred lines, an adaptive mechanism that may be particularly important when genetic diversity is low.
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Affiliation(s)
| | | | - Joanne Cable
- School of Biosciences, Cardiff University, Cardiff CF10 3AX, UK
| | - Bernard Tiddeman
- Department of Computer Science, Aberystwyth University, Aberystwyth SY23 3FL, UK
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Demin KA, Lakstygal AM, Alekseeva PA, Sysoev M, de Abreu MS, Alpyshov ET, Serikuly N, Wang D, Wang M, Tang Z, Yan D, Strekalova TV, Volgin AD, Amstislavskaya TG, Wang J, Song C, Kalueff AV. The role of intraspecies variation in fish neurobehavioral and neuropharmacological phenotypes in aquatic models. AQUATIC TOXICOLOGY (AMSTERDAM, NETHERLANDS) 2019; 210:44-55. [PMID: 30822702 DOI: 10.1016/j.aquatox.2019.02.015] [Citation(s) in RCA: 20] [Impact Index Per Article: 4.0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Received: 11/28/2018] [Revised: 02/15/2019] [Accepted: 02/19/2019] [Indexed: 06/09/2023]
Abstract
Intraspecies variation is common in both clinical and animal research of various brain disorders. Relatively well-studied in mammals, intraspecies variation in aquatic fish models and its role in their behavioral and pharmacological responses remain poorly understood. Like humans and mammals, fishes show high variance of behavioral and drug-evoked responses, modulated both genetically and environmentally. The zebrafish (Danio rerio) has emerged as a particularly useful model organism tool to access neurobehavioral and drug-evoked responses. Here, we discuss recent findings and the role of the intraspecies variance in neurobehavioral, pharmacological and toxicological studies utilizing zebrafish and other fish models. We also critically evaluate common sources of intraspecies variation and outline potential strategies to improve data reproducibility and translatability.
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Affiliation(s)
- Konstantin A Demin
- Almazov National Medical Research Centre, Ministry of Healthcare of Russian Federation, St. Petersburg, Russia; Institute of Translational Biomedicine, St. Petersburg State University, St. Petersburg, Russia
| | - Anton M Lakstygal
- Institute of Translational Biomedicine, St. Petersburg State University, St. Petersburg, Russia; Granov Russian Research Centre of Radiology and Surgical Technologies, Ministry of Healthcare of Russian Federation, St. Petersburg, Russia
| | - Polina A Alekseeva
- Almazov National Medical Research Centre, Ministry of Healthcare of Russian Federation, St. Petersburg, Russia
| | - Maxim Sysoev
- Granov Russian Research Centre of Radiology and Surgical Technologies, Ministry of Healthcare of Russian Federation, St. Petersburg, Russia
| | - Murilo S de Abreu
- The International Zebrafish Neuroscience Research Consortium (ZNRC), Slidell, LA, USA; Bioscience Institute, University of Passo Fundo, Passo Fundo, RS, Brazil
| | | | - Nazar Serikuly
- School of Pharmacy, Southwest University, Chongqing, China
| | - DongMei Wang
- School of Pharmacy, Southwest University, Chongqing, China
| | - MengYao Wang
- School of Pharmacy, Southwest University, Chongqing, China
| | - ZhiChong Tang
- School of Pharmacy, Southwest University, Chongqing, China
| | - DongNi Yan
- School of Pharmacy, Southwest University, Chongqing, China
| | - Tatyana V Strekalova
- Department of Neuroscience, Maastricht University, Maastricht, Netherlands; Laboratory of Psychiatric Neurobiology and Department of Normal Physiology, Institute of Molecular Medicine, Sechenov First Moscow State Medical University, Moscow, Russia
| | - Andrey D Volgin
- Scientific Research Institute of Physiology and Basic Medicine, Novosibirsk, Russia
| | | | - JiaJia Wang
- Research Institute of Marine Drugs and Nutrition, Guangdong Ocean University, Zhanjiang, Guangdong, China
| | - Cai Song
- Research Institute of Marine Drugs and Nutrition, Guangdong Ocean University, Zhanjiang, Guangdong, China
| | - Allan V Kalueff
- School of Pharmacy, Southwest University, Chongqing, China; Scientific Research Institute of Physiology and Basic Medicine, Novosibirsk, Russia; The International Zebrafish Neuroscience Research Consortium (ZNRC), Slidell, LA, USA; Ural Federal University, Ekaterinburg, Russia; ZENEREI Research Center, Slidell, LA, USA; Laboratory of Biological Psychiatry, Institute of Translational Biomedicine, St. Petersburg State University, St. Petersburg, Russia; Institute of Experimental Medicine, Almazov National Medical Research Centre, Ministry of Healthcare of Russian Federation, St. Petersburg, Russia; Granov Russian Research Centre of Radiology and Surgical Technologies, Ministry of Healthcare of Russian Federation, St. Petersburg, Russia.
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Sarasamma S, Lai YH, Liang ST, Liu K, Hsiao CD. The Power of Fish Models to Elucidate Skin Cancer Pathogenesis and Impact the Discovery of New Therapeutic Opportunities. Int J Mol Sci 2018; 19:E3929. [PMID: 30544544 PMCID: PMC6321611 DOI: 10.3390/ijms19123929] [Citation(s) in RCA: 10] [Impact Index Per Article: 1.7] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/15/2018] [Revised: 11/30/2018] [Accepted: 12/05/2018] [Indexed: 01/21/2023] Open
Abstract
Animal models play important roles in investigating the pathobiology of cancer, identifying relevant pathways, and developing novel therapeutic tools. Despite rapid progress in the understanding of disease mechanisms and technological advancement in drug discovery, negative trial outcomes are the most frequent incidences during a Phase III trial. Skin cancer is a potential life-threatening disease in humans and might be medically futile when tumors metastasize. This explains the low success rate of melanoma therapy amongst other malignancies. In the past decades, a number of skin cancer models in fish that showed a parallel development to the disease in humans have provided important insights into the fundamental biology of skin cancer and future treatment methods. With the diversity and breadth of advanced molecular genetic tools available in fish biology, fish skin cancer models will continue to be refined and expanded to keep pace with the rapid development of skin cancer research. This review begins with a brief introduction of molecular characteristics of skin cancers, followed by an overview of teleost models that have been used in the last decades in melanoma research. Next, we will detail the importance of the zebrafish (Danio rerio) animal model and other emerging fish models including platyfish (Xiphophorus sp.), and medaka (Oryzias latipes) in future cutaneous malignancy studies. The last part of this review provides the recent development and genome editing applications of skin cancer models in zebrafish and the progress in small molecule screening.
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Affiliation(s)
- Sreeja Sarasamma
- Department of Chemistry, Chung Yuan Christian University, Chung-Li 32023, Taiwan.
- Department of Bioscience Technology, Chung Yuan Christian University, Chung-Li 32023, Taiwan.
| | - Yu-Heng Lai
- Department of Chemistry, Chinese Culture University, Taipei 11114, Taiwan.
| | - Sung-Tzu Liang
- Department of Bioscience Technology, Chung Yuan Christian University, Chung-Li 32023, Taiwan.
| | - Kechun Liu
- Biology Institute, Qilu University of Technology (Shandong Academy of Sciences), Jinan 250103, China.
| | - Chung-Der Hsiao
- Department of Chemistry, Chung Yuan Christian University, Chung-Li 32023, Taiwan.
- Department of Bioscience Technology, Chung Yuan Christian University, Chung-Li 32023, Taiwan.
- Taiwan Center for Biomedical Technology, Chung Yuan Christian University, Chung-Li 32023, Taiwan.
- Center for Nanotechnology, Chung Yuan Christian University, Chung-Li 32023, Taiwan.
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Gross JB, Powers AK. A Natural Animal Model System of Craniofacial Anomalies: The Blind Mexican Cavefish. Anat Rec (Hoboken) 2018; 303:24-29. [PMID: 30365238 DOI: 10.1002/ar.23998] [Citation(s) in RCA: 12] [Impact Index Per Article: 2.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/30/2017] [Revised: 03/26/2018] [Accepted: 04/19/2018] [Indexed: 12/27/2022]
Abstract
Natural model systems evolving under extreme environmental pressures provide the opportunity to advance our knowledge of how the craniofacial complex evolves in nature. Unlike traditional models, natural systems are less inbred, and, therefore, better model the complex variation of the human population. Owing to the nature of certain craniofacial aberrations in blind Mexican cavefish, we suggest that this organism can provide new insights to a variety of craniofacial changes. Diverse cranial features have evolved in natural cave-dwelling Astyanax fish, which have thrived in the unforgiving darkness and nutrient-poor environment of the cave for countless generations. While the genetic and environmental underpinnings of various cranial anomalies have been investigated for decades, a comprehensive characterization of their molecular and developmental origins remains incomplete. Cavefish provide numerous advantages given the availability of genomic resources, developmental and molecular tools, and the presence of a normative surface-dwelling "ancestral" surrogate for comparative studies. By leveraging the frequency of abnormal and asymmetric cranial features in cavefish, we anticipate advances in our knowledge of the etiologies of irregular cranial features. Extreme adaptations in cavefish are expected to offer new insights into the complex and multifactorial nature of craniofacial disorders and facial asymmetry. Anat Rec, 2018. © 2018 American Association for Anatomy.
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Affiliation(s)
- Joshua B Gross
- Department of Biological Sciences, University of Cincinnati, 312 Clifton Court, Rieveschl Hall Room 711B, Cincinnati, Ohio
| | - Amanda K Powers
- Department of Biological Sciences, University of Cincinnati, 312 Clifton Court, Rieveschl Hall Room 711B, Cincinnati, Ohio
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Atukorala ADS, Bhatia V, Ratnayake R. Craniofacial skeleton of MEXICAN tetra (Astyanax mexicanus): As a bone disease model. Dev Dyn 2018; 248:153-161. [PMID: 30450697 DOI: 10.1002/dvdy.4] [Citation(s) in RCA: 3] [Impact Index Per Article: 0.5] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/15/2018] [Revised: 11/12/2018] [Accepted: 11/12/2018] [Indexed: 12/16/2022] Open
Abstract
A small fresh water fish, the Mexican tetra (Astyanax mexicanus) is a novel animal model in evolutionary developmental biology. The existence of morphologically distinct surface and cave morphs of this species allows simultaneous comparative analysis of phenotypic changes at different life stages. The cavefish harbors many favorable constructive traits (i.e., large jaws with an increased number of teeth, neuromast cells, enlarged olfactory pits and excess storage of adipose tissues) and regressive traits (i.e., reduced eye structures and pigmentation) which are essential for cave adaptation. A wide spectrum of natural craniofacial morphologies can be observed among the different cave populations. Recently, the Mexican tetra has been identified as a human disease model. The fully sequenced genome along with modern genome editing tools has allowed researchers to generate transgenic and targeted gene knockouts with phenotypes that resemble human pathological conditions. This review will discuss the anatomy of the craniofacial skeleton of A. mexicanus with a focus on morphologically variable facial bones, jaws that house continuously replacing teeth and pharyngeal skeleton. Furthermore, the possible applications of this model animal in identifying human congenital and metabolic skeletal disorders is addressed. Developmental Dynamics 248:153-161, 2019. © 2018 Wiley Periodicals, Inc.
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Affiliation(s)
- Atukorallaya Devi Sewvandini Atukorala
- Department of Oral Biology, Dr. Gerald Niznick College of Dentistry, Rady Faculty of Health Sciences, University of Manitoba, Winnipeg, Manitoba, Canada
| | - Vikram Bhatia
- Department of Oral Biology, Dr. Gerald Niznick College of Dentistry, Rady Faculty of Health Sciences, University of Manitoba, Winnipeg, Manitoba, Canada
| | - Ravindra Ratnayake
- Department of Oral Biology, Dr. Gerald Niznick College of Dentistry, Rady Faculty of Health Sciences, University of Manitoba, Winnipeg, Manitoba, Canada
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Pawluk RJ, Uren Webster TM, Cable J, Garcia de Leaniz C, Consuegra S. Immune-Related Transcriptional Responses to Parasitic Infection in a Naturally Inbred Fish: Roles of Genotype and Individual Variation. Genome Biol Evol 2018; 10:319-327. [PMID: 29340582 PMCID: PMC5786212 DOI: 10.1093/gbe/evx274] [Citation(s) in RCA: 8] [Impact Index Per Article: 1.3] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Accepted: 12/20/2017] [Indexed: 12/15/2022] Open
Abstract
Parasites are strong drivers of evolutionary change and the genetic variation of both host and parasite populations can co-evolve as a function of parasite virulence and host resistance. The role of transcriptome variation in specific interactions between host and parasite genotypes has been less studied and can be confounded by differences in genetic variation. We employed two naturally inbred lines of a self-fertilizing fish to estimate the role of host genotype in the transcriptome response to parasite infection using RNA-seq. In addition, we targeted several differentially expressed immune-related genes to further investigate the relative role of individual variation in the immune response using RT-qPCR, taking advantage of the genomic uniformity of the self-fertilizing lines. We found significant differences in gene expression between lines in response to infection both in the transcriptome and in individual gene RT-qPCR analyses. Individual RT-qPCR analyses of gene expression identified significant variance differences between lines for six genes but only for three genes between infected and control fish. Our results indicate that although the genetic background plays an important role in the transcriptome response to parasites, it cannot fully explain individual differences within genetically homogeneous lines, which can be important for determining the response to parasites.
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Affiliation(s)
- Rebecca Jane Pawluk
- Department of Biosciences, College of Science, Swansea University, Singleton Park, Wales, United Kingdom
| | - Tamsyn M Uren Webster
- Department of Biosciences, College of Science, Swansea University, Singleton Park, Wales, United Kingdom
| | - Joanne Cable
- Cardiff University, School of Biosciences, Wales, United Kingdom
| | - Carlos Garcia de Leaniz
- Department of Biosciences, College of Science, Swansea University, Singleton Park, Wales, United Kingdom
| | - Sofia Consuegra
- Department of Biosciences, College of Science, Swansea University, Singleton Park, Wales, United Kingdom
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Cavefish as an evolutionary mutant model system for human disease. Dev Biol 2018; 441:355-357. [DOI: 10.1016/j.ydbio.2018.04.013] [Citation(s) in RCA: 13] [Impact Index Per Article: 2.2] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 02/13/2018] [Revised: 04/09/2018] [Accepted: 04/16/2018] [Indexed: 02/03/2023]
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Carlson BM, Klingler IB, Meyer BJ, Gross JB. Genetic analysis reveals candidate genes for activity QTL in the blind Mexican tetra, Astyanax mexicanus. PeerJ 2018; 6:e5189. [PMID: 30042884 PMCID: PMC6054784 DOI: 10.7717/peerj.5189] [Citation(s) in RCA: 9] [Impact Index Per Article: 1.5] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 02/27/2018] [Accepted: 06/15/2018] [Indexed: 12/30/2022] Open
Abstract
Animal models provide useful tools for exploring the genetic basis of morphological, physiological and behavioral phenotypes. Cave-adapted species are particularly powerful models for a broad array of phenotypic changes with evolutionary, developmental and clinical relevance. Here, we explored the genetic underpinnings of previously characterized differences in locomotor activity patterns between the surface-dwelling and Pachón cave-dwelling populations of Astyanax mexicanus. We identified multiple novel QTL underlying patterns in overall levels of activity (velocity), as well as spatial tank use (time spent near the top or bottom of the tank). Further, we demonstrated that different regions of the genome mediate distinct patterns in velocity and tank usage. We interrogated eight genomic intervals underlying these activity QTL distributed across six linkage groups. In addition, we employed transcriptomic data and draft genomic resources to generate and evaluate a list of 36 potential candidate genes. Interestingly, our data support the candidacy of a number of genes, but do not suggest that differences in the patterns of behavior observed here are the result of alterations to certain candidate genes described in other species (e.g., teleost multiple tissue opsins, melanopsins or members of the core circadian clockwork). This study expands our knowledge of the genetic architecture underlying activity differences in surface and cavefish. Future studies will help define the role of specific genes in shaping complex behavioral phenotypes in Astyanax and other vertebrate taxa.
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Affiliation(s)
- Brian M Carlson
- Department of Biology, The College of Wooster, Wooster, OH, United States of America
| | - Ian B Klingler
- Department of Biological Sciences, University of Cincinnati, Cincinnati, OH, United States of America
| | - Bradley J Meyer
- Department of Biological Sciences, University of Cincinnati, Cincinnati, OH, United States of America
| | - Joshua B Gross
- Department of Biological Sciences, University of Cincinnati, Cincinnati, OH, United States of America
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Genetic and developmental origins of a unique foraging adaptation in a Lake Malawi cichlid genus. Proc Natl Acad Sci U S A 2018; 115:7063-7068. [PMID: 29915062 PMCID: PMC6142203 DOI: 10.1073/pnas.1719798115] [Citation(s) in RCA: 25] [Impact Index Per Article: 4.2] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/03/2022] Open
Abstract
Biologists have long been captivated by novel traits because they provide insights into both the origin of and constraints on morphological variation. The iconic adaptive radiations of cichlid fishes have led to incredible diversity of form, including some species with an exaggerated snout. This novelty is mechanically integrated with the upper jaw, appears to be under directional selection, and is found in one of the most ecologically successful cichlid lineages. We used protein manipulation, gene expression, and genetic mapping to implicate the Tgfβ pathway in the development of this unusual trait. Given the functions of Tgfβ signaling in tissue proliferation, migration, invasion, and organ fibrosis, this represents an example of the cooption of existing pathways in the evolution of novelty. Phenotypic novelties are an important but poorly understood category of morphological diversity. They can provide insights into the origins of phenotypic variation, but we know relatively little about their genetic origins. Cichlid fishes display remarkable diversity in craniofacial anatomy, including several novelties. One aspect of this variation is a conspicuous, exaggerated snout that has evolved in a single Malawi cichlid lineage and is associated with foraging specialization and increased ecological success. We examined the developmental and genetic origins for this phenotype and found that the snout is composed of two hypertrophied tissues: the intermaxillary ligament (IML), which connects the right and left sides of the upper jaw, and the overlying loose connective tissue. The IML is present in all cichlids, but in its exaggerated form it interdigitates with the more superficial connective tissue and anchors to the epithelium, forming a unique ligament–epithelial complex. We examined the Transforming growth factor β (Tgfβ) → Scleraxis (Scx) candidate pathway and confirmed a role for these factors in snout development. We demonstrate further that experimental up-regulation of Tgfβ is sufficient to produce an expansion of scx expression and concomitant changes in snout morphology. Genetic and genomic mapping show that core members of canonical Tgfβ signaling segregate with quantitative trait loci (QTL) for snout variation. These data also implicate a candidate for ligament development, adam12, which we confirm using the zebrafish model. Collectively, these data provide insights into ligament morphogenesis, as well as how an ecologically relevant novelty can arise at the molecular level.
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Carlson BM, Gross JB. Characterization and comparison of activity profiles exhibited by the cave and surface morphotypes of the blind Mexican tetra, Astyanax mexicanus. Comp Biochem Physiol C Toxicol Pharmacol 2018; 208:114-129. [PMID: 28823830 PMCID: PMC5817046 DOI: 10.1016/j.cbpc.2017.08.002] [Citation(s) in RCA: 15] [Impact Index Per Article: 2.5] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Submit a Manuscript] [Subscribe] [Scholar Register] [Received: 05/31/2017] [Revised: 08/07/2017] [Accepted: 08/14/2017] [Indexed: 01/06/2023]
Abstract
Departure from normal circadian rhythmicity and exposure to atypical lighting cues has been shown to adversely affect human health and wellness in a variety of ways. In contrast, adaptation to extreme environments has led many species to alter or even entirely abandon their reliance upon cyclic environmental inputs, principally daily cycles of light and darkness. The extreme darkness, stability and isolation of cave ecosystems has made cave-adapted species particularly attractive systems in which to study the consequences of life without light and the strategies that allow species to survive and even thrive in such environments. In order to further explore these questions, we have assessed the rhythmicity of locomotion in the blind Mexican tetra, Astyanax mexicanus, under controlled laboratory conditions. Using high-resolution video tracking assays, we characterized patterns in locomotor activity and spatial tank usage for members of the surface and Pachón cave populations. Here we demonstrate that cavefish have a higher overall level of activity and use the space within the trial tank differently than surface fish. Further, Pachón cavefish show circadian rhythmicity in both activity and spatial tank usage under a 12:12 light/dark cycle. We provide further evidence that these cavefish retain a weakly light-entrainable, endogenous circadian oscillator with limited capability to sustain rhythms in activity, but not spatial tank usage, in the absence of photic cues. Finally, we demonstrate a putative behavioral "masking effect" contributing to behavioral rhythms and provide evidence that exposure to constant darkness during development may alter behavioral patterns later in life.
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Affiliation(s)
- Brian M Carlson
- Department of Biological Sciences, University of Cincinnati, Cincinnati, OH 45221, USA.
| | - Joshua B Gross
- Department of Biological Sciences, University of Cincinnati, Cincinnati, OH 45221, USA.
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Facial bone fragmentation in blind cavefish arises through two unusual ossification processes. Sci Rep 2018; 8:7015. [PMID: 29725043 PMCID: PMC5934472 DOI: 10.1038/s41598-018-25107-2] [Citation(s) in RCA: 11] [Impact Index Per Article: 1.8] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/08/2018] [Accepted: 04/13/2018] [Indexed: 01/04/2023] Open
Abstract
The precise mechanisms underlying cranial bone development, evolution and patterning remain incompletely characterised. This poses a challenge to understanding the etiologies of craniofacial malformations evolving in nature. Capitalising on natural variation, “evolutionary model systems” provide unique opportunities to identify underlying causes of aberrant phenotypes as a complement to studies in traditional systems. Mexican blind cavefish are a prime evolutionary model for cranial disorders since they frequently exhibit extreme alterations to the skull and lateral asymmetries. These aberrations occur in stark contrast to the normal cranial architectures of closely related surface-dwelling fish, providing a powerful comparative paradigm for understanding cranial bone formation. Using a longitudinal and in vivo analytical approach, we discovered two unusual ossification processes in cavefish that underlie the development of ‘fragmented’ and asymmetric cranial bones. The first mechanism involves the sporadic appearance of independent bony elements that fail to fuse together later in development. The second mechanism involves the “carving” of channels in the mature bone, a novel form of post-ossification remodeling. In the extreme cave environment, these novel mechanisms may have evolved to augment sensory input, and may indirectly result in a trade-off between sensory expansion and cranial bone development.
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Symonová R, Howell WM. Vertebrate Genome Evolution in the Light of Fish Cytogenomics and rDNAomics. Genes (Basel) 2018; 9:genes9020096. [PMID: 29443947 PMCID: PMC5852592 DOI: 10.3390/genes9020096] [Citation(s) in RCA: 20] [Impact Index Per Article: 3.3] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/30/2017] [Revised: 01/25/2018] [Accepted: 01/29/2018] [Indexed: 12/19/2022] Open
Abstract
To understand the cytogenomic evolution of vertebrates, we must first unravel the complex genomes of fishes, which were the first vertebrates to evolve and were ancestors to all other vertebrates. We must not forget the immense time span during which the fish genomes had to evolve. Fish cytogenomics is endowed with unique features which offer irreplaceable insights into the evolution of the vertebrate genome. Due to the general DNA base compositional homogeneity of fish genomes, fish cytogenomics is largely based on mapping DNA repeats that still represent serious obstacles in genome sequencing and assembling, even in model species. Localization of repeats on chromosomes of hundreds of fish species and populations originating from diversified environments have revealed the biological importance of this genomic fraction. Ribosomal genes (rDNA) belong to the most informative repeats and in fish, they are subject to a more relaxed regulation than in higher vertebrates. This can result in formation of a literal 'rDNAome' consisting of more than 20,000 copies with their high proportion employed in extra-coding functions. Because rDNA has high rates of transcription and recombination, it contributes to genome diversification and can form reproductive barrier. Our overall knowledge of fish cytogenomics grows rapidly by a continuously increasing number of fish genomes sequenced and by use of novel sequencing methods improving genome assembly. The recently revealed exceptional compositional heterogeneity in an ancient fish lineage (gars) sheds new light on the compositional genome evolution in vertebrates generally. We highlight the power of synergy of cytogenetics and genomics in fish cytogenomics, its potential to understand the complexity of genome evolution in vertebrates, which is also linked to clinical applications and the chromosomal backgrounds of speciation. We also summarize the current knowledge on fish cytogenomics and outline its main future avenues.
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Affiliation(s)
- Radka Symonová
- Faculty of Science, Department of Biology, University of Hradec Králové, 500 03 Hradec Králové, Czech Republic.
| | - W Mike Howell
- Department of Biological and Environmental Sciences, Samford University, Birmingham, AL 35229, USA.
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Currey MC, Bassham S, Perry S, Cresko WA. Developmental timing differences underlie armor loss across threespine stickleback populations. Evol Dev 2017; 19:231-243. [PMID: 29115024 DOI: 10.1111/ede.12242] [Citation(s) in RCA: 3] [Impact Index Per Article: 0.4] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/22/2022]
Abstract
Comparing ontogenetic patterns within a well-described evolutionary context aids in inferring mechanisms of change, including heterochronies or deletion of developmental pathways. Because selection acts on phenotypes throughout ontogeny, any within-taxon developmental variation has implications for evolvability. We compare ontogenetic order and timing of locomotion and defensive traits in three populations of threespine stickleback that have evolutionarily divergent adult forms. This analysis adds to the growing understanding of developmental genetic mechanisms of adaptive change in this evolutionary model species by delineating when chondrogenesis and osteogenesis in two derived populations begin to deviate from the developmental pattern in their immediate ancestors. We found that differences in adult defensive morphologies arise through abolished or delayed initiation of these traits rather than via an overall heterochronic shift, that intra-population ontogenetic variation is increased for some derived traits, and that altered armor developmental timing differentiates the derived populations from each other despite parallels in adult lateral plate armor phenotypes. We found that changes in ossified elements of the pelvic armor are linked to delayed and incomplete development of an early-forming pelvic cartilage, and that this disruption likely presages the variable pelvic vestiges documented in many derived populations.
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Affiliation(s)
- Mark C Currey
- Institute of Ecology and Evolution, University of Oregon, Eugene, Oregon
| | - Susan Bassham
- Institute of Ecology and Evolution, University of Oregon, Eugene, Oregon
| | - Stephen Perry
- Institute of Ecology and Evolution, University of Oregon, Eugene, Oregon
| | - William A Cresko
- Institute of Ecology and Evolution, University of Oregon, Eugene, Oregon
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Small CM, Milligan-Myhre K, Bassham S, Guillemin K, Cresko WA. Host Genotype and Microbiota Contribute Asymmetrically to Transcriptional Variation in the Threespine Stickleback Gut. Genome Biol Evol 2017; 9:504-520. [PMID: 28391321 PMCID: PMC5381569 DOI: 10.1093/gbe/evx014] [Citation(s) in RCA: 29] [Impact Index Per Article: 4.1] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Accepted: 02/26/2017] [Indexed: 02/07/2023] Open
Abstract
Recent studies of interactions between hosts and their resident microbes have revealed important ecological and evolutionary consequences that emerge from these complex interspecies relationships, including diseases that occur when the interactions go awry. Given the preponderance of these interactions, we hypothesized that effects of the microbiota on gene expression in the developing gut—an important aspect of host biology—would be pervasive, and that these effects would be both comparable in magnitude to and contingent on effects of the host genetic background. To evaluate the effects of the microbiota, host genotype, and their interaction on gene expression in the gut of a genetically diverse, gnotobiotic host model, the threespine stickleback (Gasterosteus aculeatus), we compared RNA-seq data among 84 larval fish. Surprisingly, we found that stickleback population and family differences explained substantially more gene expression variation than the presence of microbes. Expression levels of 72 genes, however, were affected by our microbiota treatment. These genes, including many associated with innate immunity, comprise a tractable subset of host genetic factors for precise, systems-level study of host–microbe interactions in the future. Importantly, our data also suggest subtle signatures of a statistical interaction between host genotype and the microbiota on expression patterns of genetic pathways associated with innate immunity, coagulation and complement cascades, focal adhesion, cancer, and peroxisomes. These genotype-by-environment interactions may prove to be important leads to the understanding of host genetic mechanisms commonly at the root of sometimes complex molecular relationships between hosts and their resident microbes.
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Affiliation(s)
- Clayton M Small
- Institute of Ecology and Evolution, University of Oregon, Eugene, OR
| | | | - Susan Bassham
- Institute of Ecology and Evolution, University of Oregon, Eugene, OR
| | - Karen Guillemin
- Institute of Molecular Biology, University of Oregon, Eugene, OR
| | - William A Cresko
- Institute of Ecology and Evolution, University of Oregon, Eugene, OR
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Malone L, Opazo JC, Ryan PL, Hoffmann FG. Progressive erosion of the Relaxin1 gene in bovids. Gen Comp Endocrinol 2017; 252:12-17. [PMID: 28733228 DOI: 10.1016/j.ygcen.2017.07.011] [Citation(s) in RCA: 8] [Impact Index Per Article: 1.1] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Journal Information] [Submit a Manuscript] [Subscribe] [Scholar Register] [Received: 04/12/2017] [Revised: 06/20/2017] [Accepted: 07/12/2017] [Indexed: 02/02/2023]
Abstract
The relaxin/insulin-like (RLN/INSL) gene family is a group of genes that encode peptide hormones involved in a variety of physiological functions related to reproduction. Previous studies have shown that relaxin plays a key role in widening of the pubic bone during labor and in gamete maturation. Because of these functions, studying the evolution of RLN1, the gene encoding for relaxin, is relevant in livestock species, most of which belong in the group Laurasiatheria, which includes cow, pig, horse, goat, and sheep in addition to bats, cetaceans and carnivores. Experimental evidence suggests that cows do not synthesize relaxin, but respond to it, and sheep apparently have a truncated RLN1 gene. Thus, we made use of genome sequence data to characterize the genomic locus of the RLN1 gene in Laurasiatherian mammals to better understand how cows lost the ability to synthesize this peptide. We found that all ruminants in our study (cow, giraffe, goat, sheep and Tibetan antelope) lack a functional RLN1 gene, and document the progressive loss of RLN1 in the lineage leading to cows. Our analyses indicate that 1 - all ruminants have lost all key regulatory elements upstream of the first exon, 2 - giraffe, goat, sheep and Tibetan antelope have multiple inactivating mutations in the RLN1 pseudogene, and 3 - the cow genome has lost all traces of RLN1. The 5' regulatory sequence plays a key role in activating expression, and the loss of this sequence would impair synthesis of mRNA. Our results suggest that changes in regulatory sequence preceded mutations in coding sequence and highlight the importance of these regions in maintaining proper gene function. In addition, we found that all bovids examined posses copies of the relaxin receptors, which explains why they are able to respond to relaxin despite their inability to produce it.
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Affiliation(s)
- Loggan Malone
- Department of Biochemistry, Molecular Biology, Entomology, and Plant Pathology, Mississippi State University, MS 39762, USA
| | - Juan C Opazo
- Instituto de Ciencias Ambientales y Evolutivas, Facultad de Ciencias, Universidad Austral de Chile, Valdivia, Chile
| | - Peter L Ryan
- Department of Animal and Dairy Sciences, Facility for Organismal and Cellular Imaging (FOCI), Mississippi State University, MS 39762, USA; Department of Pathobiology & Population Medicine, Mississippi State University, MS 39762, USA
| | - Federico G Hoffmann
- Department of Biochemistry, Molecular Biology, Entomology, and Plant Pathology, Mississippi State University, MS 39762, USA; Institute for Genomics, Biocomputing, and Biotechnology, Mississippi State University, MS 39762, USA.
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Dubansky BH, Dubansky BD. Natural development of dermal ectopic bone in the american alligator (Alligator mississippiensis
) resembles heterotopic ossification disorders in humans. Anat Rec (Hoboken) 2017; 301:56-76. [DOI: 10.1002/ar.23682] [Citation(s) in RCA: 19] [Impact Index Per Article: 2.7] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/07/2017] [Revised: 07/25/2017] [Accepted: 08/17/2017] [Indexed: 12/20/2022]
Affiliation(s)
- Brooke H. Dubansky
- Department of Medical Laboratory Sciences and Public Health; Tarleton State University; 1501 Enderly Place, Fort Worth Texas
| | - Benjamin D. Dubansky
- Department of Biological Sciences; University of North Texas, 1511 W. Sycamore St; Denton Texas
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Céspedes HA, Zavala K, Vandewege MW, Opazo JC. Evolution of the α 2-adrenoreceptors in vertebrates: ADRA2D is absent in mammals and crocodiles. Gen Comp Endocrinol 2017. [PMID: 28622977 DOI: 10.1016/j.ygcen.2017.06.006] [Citation(s) in RCA: 11] [Impact Index Per Article: 1.6] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Journal Information] [Submit a Manuscript] [Subscribe] [Scholar Register] [Indexed: 02/04/2023]
Abstract
Evolutionary studies of genes that have been functionally characterized and whose variation has been associated with pathological conditions represent an opportunity to understand the genetic basis of pathologies. α2-Adrenoreceptors (ADRA2) are a class of G protein-coupled receptors that regulate several physiological processes including blood pressure, platelet aggregation, insulin secretion, lipolysis, and neurotransmitter release. This gene family has been extensively studied from a molecular/physiological perspective, yet much less is known about its evolutionary history. Accordingly, the goal of this study was to investigate the evolutionary history of α2-adrenoreceptors (ADRA2) in vertebrates. Our results show that in addition to the three well-recognized α2-adrenoreceptor genes (ADRA2A, ADRA2B and ADRA2C), we recovered a clade that corresponds to the fourth member of the α2-adrenoreceptor gene family (ADRA2D). We also recovered a clade that possesses two ADRA2 sequences found in two lamprey species. Furthermore, our results show that mammals and crocodiles are characterized by possessing three α2-adrenoreceptor genes, whereas all other vertebrate groups possess the full repertoire of α2-adrenoreceptor genes. Among vertebrates ADRA2D seems to be a dispensable gene, as it was lost two independent times during the evolutionary history of the group. Additionally, we found that most examined species possess the most common alleles described for humans; however, there are cases in which non-human mammals possess the alternative variant. Finally, transcript abundance profiles revealed that during the early evolutionary history of gnathostomes, the expression of ADRA2D in different taxonomic groups became specialized to different tissues, but in the ancestor of sarcopterygians this specialization would have been lost.
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Affiliation(s)
- Héctor A Céspedes
- Instituto de Ciencias Ambientales y Evolutivas, Facultad de Ciencias, Universidad Austral de Chile, Valdivia, Chile
| | - Kattina Zavala
- Instituto de Ciencias Ambientales y Evolutivas, Facultad de Ciencias, Universidad Austral de Chile, Valdivia, Chile
| | - Michael W Vandewege
- Department of Biological Sciences, Texas Tech University, Lubbock, TX 79409, USA
| | - Juan C Opazo
- Instituto de Ciencias Ambientales y Evolutivas, Facultad de Ciencias, Universidad Austral de Chile, Valdivia, Chile; David Rockefeller Center For Latin American Studies, Harvard University, Cambridge, MA 02138, USA.
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