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Abstract
Paleoproteomics, the study of ancient proteins, is a rapidly growing field at the intersection of molecular biology, paleontology, archaeology, paleoecology, and history. Paleoproteomics research leverages the longevity and diversity of proteins to explore fundamental questions about the past. While its origins predate the characterization of DNA, it was only with the advent of soft ionization mass spectrometry that the study of ancient proteins became truly feasible. Technological gains over the past 20 years have allowed increasing opportunities to better understand preservation, degradation, and recovery of the rich bioarchive of ancient proteins found in the archaeological and paleontological records. Growing from a handful of studies in the 1990s on individual highly abundant ancient proteins, paleoproteomics today is an expanding field with diverse applications ranging from the taxonomic identification of highly fragmented bones and shells and the phylogenetic resolution of extinct species to the exploration of past cuisines from dental calculus and pottery food crusts and the characterization of past diseases. More broadly, these studies have opened new doors in understanding past human-animal interactions, the reconstruction of past environments and environmental changes, the expansion of the hominin fossil record through large scale screening of nondiagnostic bone fragments, and the phylogenetic resolution of the vertebrate fossil record. Even with these advances, much of the ancient proteomic record still remains unexplored. Here we provide an overview of the history of the field, a summary of the major methods and applications currently in use, and a critical evaluation of current challenges. We conclude by looking to the future, for which innovative solutions and emerging technology will play an important role in enabling us to access the still unexplored "dark" proteome, allowing for a fuller understanding of the role ancient proteins can play in the interpretation of the past.
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Affiliation(s)
- Christina Warinner
- Department
of Anthropology, Harvard University, Cambridge, Massachusetts 02138, United States
- Department of Archaeogenetics, Max Planck Institute for Evolutionary Anthropology, Leipzig 04103, Germany
| | - Kristine Korzow Richter
- Department
of Anthropology, Harvard University, Cambridge, Massachusetts 02138, United States
| | - Matthew J. Collins
- Department
of Archaeology, Cambridge University, Cambridge CB2 3DZ, United Kingdom
- Section
for Evolutionary Genomics, Globe Institute,
University of Copenhagen, Copenhagen 1350, Denmark
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2
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Abstract
Tooth enamel is the outer covering of tooth crowns, the hardest material in the mammalian body, yet fracture resistant. The extremely high content of 95 wt% calcium phosphate in healthy adult teeth is achieved through mineralization of a proteinaceous matrix that changes in abundance and composition. Enamel-specific proteins and proteases are known to be critical for proper enamel formation. Recent proteomics analyses revealed many other proteins with their roles in enamel formation yet to be unraveled. Although the exact protein composition of healthy tooth enamel is still unknown, it is apparent that compromised enamel deviates in amount and composition of its organic material. Why these differences affect both the mineralization process before tooth eruption and the properties of erupted teeth will become apparent as proteomics protocols are adjusted to the variability between species, tooth size, sample size and ephemeral organic content of forming teeth. This review summarizes the current knowledge and published proteomics data of healthy and diseased tooth enamel, including advancements in forensic applications and disease models in animals. A summary and discussion of the status quo highlights how recent proteomics findings advance our understating of the complexity and temporal changes of extracellular matrix composition during tooth enamel formation.
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Affiliation(s)
- Ana Gil-Bona
- The Forsyth Institute, Cambridge, MA 02142, USA
- Department of Developmental Biology, Harvard School of Dental Medicine, Boston, MA 02115, USA
- Correspondence: (A.G.-B.); (F.B.B.)
| | - Felicitas B. Bidlack
- The Forsyth Institute, Cambridge, MA 02142, USA
- Department of Developmental Biology, Harvard School of Dental Medicine, Boston, MA 02115, USA
- Correspondence: (A.G.-B.); (F.B.B.)
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3
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Simon R, Lischer HEL, Pieńkowska-Schelling A, Keller I, Häfliger IM, Letko A, Schelling C, Lühken G, Drögemüller C. New genomic features of the polled intersex syndrome variant in goats unraveled by long-read whole-genome sequencing. Anim Genet 2020; 51:439-448. [PMID: 32060960 DOI: 10.1111/age.12918] [Citation(s) in RCA: 12] [Impact Index Per Article: 3.0] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/03/2019] [Revised: 01/23/2020] [Accepted: 01/23/2020] [Indexed: 01/19/2023]
Abstract
In domestic goats, the polled intersex syndrome (PIS) refers to XX female-to-male sex reversal associated with the absence of horn growth (polled). The causal variant was previously reported as a 11.7 kb deletion at approximately 129 Mb on chromosome 1 that affects the transcription of both FOXL2 and several long non-coding RNAs. In the meantime the presence of different versions of the PIS deletion was postulated and trials to establish genetic testing with the existing molecular genetic information failed. Therefore, we revisited this variant by long-read whole-genome sequencing of two genetically female (XX) goats, a PIS-affected and a horned control. This revealed the presence of a more complex structural variant consisting of a deletion with a total length of 10 159 bp and an inversely inserted approximately 480 kb-sized duplicated segment of a region located approximately 21 Mb further downstream on chromosome 1 containing two genes, KCNJ15 and ERG. Publicly available short-read whole-genome sequencing data, Sanger sequencing of the breakpoints and FISH using BAC clones corresponding to both involved genome regions confirmed this structural variant. A diagnostic PCR was developed for simultaneous genotyping of carriers for this variant and determination of their genetic sex. We showed that the variant allele was present in all 334 genotyped polled goats of diverse breeds and that all analyzed 15 PIS-affected XX goats were homozygous. Our findings enable for the first time a precise genetic diagnosis for polledness and PIS in goats and add a further genomic feature to the complexity of the PIS phenomenon.
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Affiliation(s)
- R Simon
- Institute of Animal Breeding and Genetics, Justus Liebig University, Giessen, 35390, Germany
| | - H E L Lischer
- Interfaculty Bioinformatics Unit, University of Bern, Bern, 3001, Switzerland.,Swiss Institute of Bioinformatics, Lausanne, 1015, Switzerland
| | - A Pieńkowska-Schelling
- Institute of Genetics, University of Bern, Bern, 3001, Switzerland.,Clinic of Reproductive Medicine, Vetsuisse Faculty, University of Zürich, Zürich, 8057, Switzerland
| | - I Keller
- Swiss Institute of Bioinformatics, Lausanne, 1015, Switzerland.,Department for BioMedical Research, University of Bern, Bern, 3001, Switzerland
| | - I M Häfliger
- Institute of Genetics, University of Bern, Bern, 3001, Switzerland
| | - A Letko
- Institute of Genetics, University of Bern, Bern, 3001, Switzerland
| | - C Schelling
- Clinic of Reproductive Medicine, Vetsuisse Faculty, University of Zürich, Zürich, 8057, Switzerland
| | - G Lühken
- Institute of Animal Breeding and Genetics, Justus Liebig University, Giessen, 35390, Germany
| | - C Drögemüller
- Institute of Genetics, University of Bern, Bern, 3001, Switzerland
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4
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Strah R, Kunej T. Molecular sexing assays in 114 mammalian species: In silico sequence reanalysis and a unified graphical visualization of diagnostic tests. Ecol Evol 2019; 9:5018-5028. [PMID: 31031962 PMCID: PMC6476764 DOI: 10.1002/ece3.5093] [Citation(s) in RCA: 6] [Impact Index Per Article: 1.2] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/01/2018] [Revised: 01/29/2019] [Accepted: 03/05/2019] [Indexed: 11/11/2022] Open
Abstract
Molecular-based methods for identifying sex in mammals have a wide range of applications, from embryo manipulation to ecological studies. Various sex-specific or homologous genes can be used for this purpose, PCR amplification being a common method. Over the years, the number of reported tests and the range of tested species have increased greatly. The aim of the present analysis was to retrieve PCR-based sexing assays for a range of mammalian species, gathering the gene sequences from either the articles or online databases, and visualize the molecular design in a uniform manner. For nucleotide alignment and diagnostic test visualization, the following genomic databases and tools were used: NCBI, Ensembl Nucleotide BLAST, ClustalW2, and NEBcutter V2.0. In the 45 gathered articles, 59 different diagnostic tests based on eight different PCR-based methods were developed for 114 mammalian species. Most commonly used genes for the analysis were ZFX, ZFY, AMELX, and AMELY. The tests were most commonly based on sex-specific insertions and deletions (SSIndels) and sex-specific sequence polymorphisms (SSSP). This review provides an overview of PCR-based sexing methods developed for mammals. This information will facilitate more efficient development of novel molecular sexing assays and reuse of previously developed tests. Development of many novel and improvement of previously developed tests is also expected with the rapid increase in the quantity and quality of available genetic information.
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Affiliation(s)
- Rebeka Strah
- Biotechnical Faculty, Department of Animal ScienceUniversity of LjubljanaDomzaleSlovenia
| | - Tanja Kunej
- Biotechnical Faculty, Department of Animal ScienceUniversity of LjubljanaDomzaleSlovenia
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Hrovatin K, Kunej T. Genetic sex determination assays in 53 mammalian species: Literature analysis and guidelines for reporting standardization. Ecol Evol 2018; 8:1009-1018. [PMID: 29375774 PMCID: PMC5773321 DOI: 10.1002/ece3.3707] [Citation(s) in RCA: 13] [Impact Index Per Article: 2.2] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/31/2017] [Revised: 10/27/2017] [Accepted: 11/10/2017] [Indexed: 01/21/2023] Open
Abstract
Erstwhile, sex was determined by observation, which is not always feasible. Nowadays, genetic methods are prevailing due to their accuracy, simplicity, low costs, and time-efficiency. However, there is no comprehensive review enabling overview and development of the field. The studies are heterogeneous, lacking a standardized reporting strategy. Therefore, our aim was to collect genetic sexing assays for mammals and assemble them in a catalogue with unified terminology. Publications were extracted from online databases using key words such as sexing and molecular. The collected data were supplemented with species and gene IDs and the type of sex-specific sequence variant (SSSV). We developed a catalogue and graphic presentation of diagnostic tests for molecular sex determination of mammals, based on 58 papers published from 2/1991 to 10/2016. The catalogue consists of five categories: species, genes, SSSVs, methods, and references. Based on the analysis of published literature, we propose minimal requirements for reporting, consisting of: species scientific name and ID, genetic sequence with name and ID, SSSV, methodology, genomic coordinates (e.g., restriction sites, SSSVs), amplification system, and description of detected amplicon and controls. The present study summarizes vast knowledge that has up to now been scattered across databases, representing the first step toward standardization regarding molecular sexing, enabling a better overview of existing tests and facilitating planned designs of novel tests. The project is ongoing; collecting additional publications, optimizing field development, and standardizing data presentation are needed.
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Affiliation(s)
- Karin Hrovatin
- Department of Animal ScienceBiotechnical FacultyUniversity of LjubljanaDomzaleSlovenia
| | - Tanja Kunej
- Department of Animal ScienceBiotechnical FacultyUniversity of LjubljanaDomzaleSlovenia
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Abstract
A simple and fast method was established to identify the sex types of the rat-derived cell strains. The single copy X-chromosome-linked gene AR and the single copy Y-chromosome-linked gene Sry were both detected with qPCR for the rat genomic DNA sample and the AR/Sry ratio was calculated. According to the law of the AR/Sry ratio, a new method to identify the sex types of the rat-derived cell strains was developed. The new assay was proved effective. The new assay showed advantages over the traditional sex type identification PCR methods, which detected only the Sry gene. Moreover, the new method was used to identify the sex types of two rat-derived cell strains unknown for the sex types and the results were confirmed with the in situ hybridization. Finally, the problem of the cross contamination between the female and the male samples was addressed and discussed extensively.
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Affiliation(s)
- Junbei Xiang
- a Sichuan Nursing Vocational College , Chengdu , China
| | - Zhilin Li
- b Sichuan Cancer Hospital , Chengdu , China
| | - Qian Wan
- c Sichuan Cord Blood Bank/Sichuan Neo-life Stem Cell Biotech Inc. , Chengdu , China
| | - Qiang Chen
- c Sichuan Cord Blood Bank/Sichuan Neo-life Stem Cell Biotech Inc. , Chengdu , China
| | - Mianxue Liu
- d Department of Biotechnology , Sichuan Institute of Atomic Energy/Irradiation Preservation Key Laboratory of Sichuan Province , Chengdu , China
| | - Xiaohui Jiang
- e The Huaxi Second Affiliated Hosiptal , Sichuan University , Chengdu , China
| | - Linfeng Xie
- a Sichuan Nursing Vocational College , Chengdu , China
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7
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Lai CW, Chen HL, Tsai TC, Chu TW, Yang SH, Chong KY, Chen CM. Sexually Dimorphic Expression of eGFP Transgene in the Akr1A1 Locus of Mouse Liver Regulated by Sex Hormone-Related Epigenetic Remodeling. Sci Rep 2016; 6:24023. [PMID: 27087367 DOI: 10.1038/srep24023] [Citation(s) in RCA: 7] [Impact Index Per Article: 0.9] [Reference Citation Analysis] [What about the content of this article? (0)] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/06/2015] [Accepted: 03/14/2016] [Indexed: 12/19/2022] Open
Abstract
Sexually dimorphic gene expression is commonly found in the liver, and many of these genes are linked to different incidences of liver diseases between sexes. However, the mechanism of sexually dimorphic expression is still not fully understood. In this study, a pCAG-eGFP transgenic mouse strain with a specific transgene integration site in the Akr1A1 locus presented male-biased EGFP expression in the liver, and the expression was activated by testosterone during puberty. The integration of the pCAG-eGFP transgene altered the epigenetic regulation of the adjacent chromatin, including increased binding of STAT5b, a sexually dimorphic expression regulator, and the transformation of DNA methylation from hypermethylation into male-biased hypomethylation. Through this de novo sexually dimorphic expression of the transgene, the Akr1A1eGFP mouse provides a useful model to study the mechanisms and the dynamic changes of sexually dimorphic gene expression during either development or pathogenesis of the liver.
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Yan S, Bai C, Li Y, Li Y, Hou J, Zhao Z, Han W. Sex identification of dog by PCR based on the differences in theAMELXandAMELYgenes. Anim Genet 2013; 44:606. [DOI: 10.1111/age.12063] [Citation(s) in RCA: 10] [Impact Index Per Article: 0.9] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Accepted: 03/28/2013] [Indexed: 11/29/2022]
Affiliation(s)
- Shouqing Yan
- College of Animal Science; Jilin University; 5333 Xi'an Road; Changchun; 130062; China
| | - Chunyan Bai
- College of Animal Science; Jilin University; 5333 Xi'an Road; Changchun; 130062; China
| | - Yumei Li
- College of Animal Science; Jilin University; 5333 Xi'an Road; Changchun; 130062; China
| | - Ying Li
- College of Veterinary Medicine; Jilin University; 5333 Xi'an Road; Changchun; 130062; China
| | - Jiani Hou
- College of Animal Science; Jilin University; 5333 Xi'an Road; Changchun; 130062; China
| | - Zhihui Zhao
- College of Animal Science; Jilin University; 5333 Xi'an Road; Changchun; 130062; China
| | - Wenyu Han
- College of Veterinary Medicine; Jilin University; 5333 Xi'an Road; Changchun; 130062; China
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