Dissertations / Theses on the topic 'Eutherians'

Genomic imprinting is responsible for monoallelic gene expression that depends on the sex of the parent from which the alleles (one active, one silent) were inherited. X-chromosome inactivation is also a form of monoallelic gene expression. One of the two X chromosomes is transcriptionally silenced in the somatic cells of females, effectively equalising gene dosage with males who have only one X chromosome that is not complemented by a gene poor Y chromosome. X chromosome inactivation is random in eutherian mammals, but imprinted in marsupials, and in the extraembryonic membranes of some placentals. Imprinting and X inactivation have been studied in great detail in placental mammals (particularly humans and mice), and appear to occur also in marsupial mammals. However, both phenomena appear to have evolved specifically in mammals, since there is no evidence of imprinting or X inactivation in non-mammalian vertebrates, which do not show parent of origin effects and possess different sex chromosomes and dosage compensation mechanisms to mammals.¶ In order to understand how imprinting and X inactivation evolved, I have focused on the mammals most distantly related to human and mouse. I compared the sequence, location and expression of genes from major imprinted domains, and genes that regulate genomic imprinting and X-chromosome inactivation in the three extant mammalian groups and other vertebrates. Specifically, I studied the evolution of an autosomal region that is imprinted in humans and mouse, the evolution of the X-linked region thought to control X inactivation, and the evolution of the genes thought to establish and control differential expression of various imprinted loci. This thesis is presented as a collection of research papers that examines each of these topics, and a review and discussion that synthesizes my findings.¶ The first paper reports a study of the imprinted locus responsible for the human Prader-Willi and Angelman syndromes (PWS and AS). A search for kangaroo and platypus orthologues of PWS-AS genes identified only the putative AS gene UBE3A, and showed it was in a completely different genomic context to that of humans and mice. The only PWS gene found in marsupials (SNRPN) was located in tandem with its ancient paralogue SNRPB, on a different chromosome to UBE3A. Monotremes apparently have no orthologue of SNRPN. The several intronless genes of the PWS-AS domain also have no orthologues in marsupials or monotremes or non-mammal vertebrates, but all have close paralogues scattered about the genome from which they evidently retrotransposed. UBE3A in marsupials and monotremes, and SNRPN in marsupials were found to be expressed from both alleles, so are not imprinted. Thus, the PWA-AS imprinted domain was assembled from many non-imprinted components relatively recently, demonstrating that the evolution of imprinting has been an ongoing process during mammalian radiation.¶ In the second paper, I examine the evolution of the X-inactivation centre, the key regulatory region responsible for X-chromosome inactivation in humans and mice, which is imprinted in mouse extraembryonic membranes. By sequencing and aligning flanking regions across the three mammal groups and non-mammal vertebrates, I discovered that the region homologous to the X-inactivation centre, though intact in birds and frogs, was disrupted independently in marsupial and monotreme mammals. I showed that the key regulatory RNA of this locus (X-inactive specific transcript or XIST) is absent, explaining why a decade-long search for marsupial XIST was unsuccessful. Thus, XIST is eutherian-specific and is therefore not a basic requirement for X-chromosome inactivation in all mammals.¶ The broader significance of the findings reported in these two papers is explored with respect to other current work regarding the evolution and construction of imprinted loci in mammals in the form of a review. This comparison enabled me to conclude that like the PWS-AS domain and the X-inactivation centre, many domains show unexpected construction from disparate genomic elements that correlate with their acquisition of imprinting.¶ The fourth and last paper examines the evolution of CCCTC-binding Factor (CTCF) and its parologue Brother Of Regulator of Imprinted Sites (BORIS) which contribute to the establishment and interpretation of genomic imprinting at the Insulin-Like Growth Factor 2/H19 locus. In this paper I show that the duplication of CTCF giving rise to BORIS occurred much earlier than previously recognised, and demonstrate that a major change in BORIS expression (restriction to the germline) occurred in concert with the evolution of genomic imprinting. The papers that form the bulk of this thesis show that the evolution of epigenetic traits such as genomic imprinting and X-chromosome inactivation is labile and has apparently responded rapidly to different selective pressures during the independent evolution of the three mammal groups. I have introduced these papers, and discussed them generally in terms of current theories of how and why these forms of monoallelic expression have evolved in mammals.

After an initial chapter introducing the orbital region and surveying the literature, Chapter Two addresses the scope of the variation in orbital construction with a comprehensive description of the orbits of placental mammals, order by order. This information is used to score 23 morphological characters from the orbital region in representatives from as many eutherian families as possible. These character states are then plotted on to existing phylogenies of the Eutheria in order to study the evolution of orbital characters throughout the group. This elucidates which characters are more plastic than others, which orbital features are characteristic of particular placental groups, and which species are anomalous within their family or order with regard to the orbit. Chapter Three focuses on the muscles of mastication and the variation in their relative proportions throughout the Eutheria. The nature of the stresses and strains generated by these muscles across the skull, and particularly in the orbital region, is considered using dissection and the split-line technique. Drawing on this information, Chapter Four seeks to characterise the variation in orbital structure in a quantitative fashion. The surface areas of orbital bones along with various cranial dimensions in a wide sample of eutherians are measured using a 3-D digitiser. These data are then subjected to a number of statistical techniques such as principal components analysis, analysis of variance and cluster analysis, in order to assess whether orbital structure can be correlated with arrangement of the jaw closing musculature. Finally, all the evidence is drawn together to see if the construction of the orbit can be used as a predictor of masticatory musculature.

Reproduction is a complex phenomenon that is fundamental to all living things. There is a plethora of strategies that animals utilise to reproduce. The uterine epithelium of viviparous mammals undergoes vast remodelling to accommodate the developing embryo. There are several levels of placental invasion in mammals that develop a placenta, based on the number of cell layers that separate the developing fetus and maternal blood stream. This thesis investigated whether there are common molecular changes to the uterine surface during pregnancy in Theria. I compared uterine remodelling across several phylogenetic groups with independent origins of endotheliochorial placentae to determine how this placenta type evolved. I tested the generality of uterine remodelling during pregnancy in the marsupial, Sminthopsis crassicaudata (Dasyuridae; the fat-tailed dunnart) and the eutherian, Felis catus (Felidae; the domestic cat) and Dipodomys merriami (Heteromyidae; Merriam’s kangaroo rat). I used Transmission and Scanning Electron Microscopy to study the ultrastructural changes to the uterine epithelium during pregnancy. I used immunofluorescence microscopy and Western blotting to show that there are common changes to the distribution of key lateral adhesion molecules, desmoglein-2 and E-cadherin to facilitate the formation of the placenta. I confirmed that desmosomes and the adherens junction redistribute and break down at attachment during marsupial pregnancy. I also showed that the same ultrastructural and molecular changes to the uterine epithelium are seen in eutherian species which represent separate lineages of endotheliochorial placentation. I was the first to identify a plasma membrane transformation during pregnancy in Dipodomys merriami, a rodent species which represent a recent evolution of endotheliochorial placentation within Rodentia. I determined the effect of the reproductive hormones, progesterone and 17β-oestradiol on the reproductive tract of Sminthopsis crassicaudata, concluding that the plasma membrane transformation is regulated by the same hormonal mechanisms among therian species. The conclusions from this thesis support the theory that uterine remodelling and the plasma membrane transformation are crucial for successful pregnancy in viviparous mammals with commonalities in molecular and morphological changes among species.

Les modalités d'utilisation de l'espace et des ressources alimentaires ont été étudiées chez Caluromys philander (Marsupialia, Didelphidae) en forêt primaire de Guyane française, en comparaison avec Potos Flavus (Eutheria, Procyonidae). L'organisation du domaine vital est analysée chez C. Philander. On montre que cette espèce est opportuniste et qu'il existe une influence du sexe, du stade reproducteur des femelles, ainsi que de la disponibilité des ressources alimentaires, sur certains caractères du domaine vital et du comportement des individus. Les régimes alimentaires des deux mammifères, les caractères morphologiques et chimiques des fruits consommés ainsi que les stratégies d'exploitation des arbres en fleurs et en fruits sont considérés. L'efficacité des deux espèces pour la dissémination des graines est discutée en fonction de leur taille et de leurs modalités d'utilisation de l'espace et bdes ressources tropiques. Ces deux espèces présentent des particularités dont certaines augmentent et d'autres réduisent l'efficacité de la dissémination.

Genomic imprinting is responsible for monoallelic gene expression that depends on the sex of the parent from which the alleles (one active, one silent) were inherited. X-chromosome inactivation is also a form of monoallelic gene expression. One of the two X chromosomes is transcriptionally silenced in the somatic cells of females, effectively equalising gene dosage with males who have only one X chromosome that is not complemented by a gene poor Y chromosome. X chromosome inactivation is random in eutherian mammals, but imprinted in marsupials, and in the extraembryonic membranes of some placentals. Imprinting and X inactivation have been studied in great detail in placental mammals (particularly humans and mice), and appear to occur also in marsupial mammals. However, both phenomena appear to have evolved specifically in mammals, since there is no evidence of imprinting or X inactivation in non-mammalian vertebrates, which do not show parent of origin effects and possess different sex chromosomes and dosage compensation mechanisms to mammals.¶ In order to understand how imprinting and X inactivation evolved, I have focused on the mammals most distantly related to human and mouse. I compared the sequence, location and expression of genes from major imprinted domains, and genes that regulate genomic imprinting and X-chromosome inactivation in the three extant mammalian groups and other vertebrates. Specifically, I studied the evolution of an autosomal region that is imprinted in humans and mouse, the evolution of the X-linked region thought to control X inactivation, and the evolution of the genes thought to establish and control differential expression of various imprinted loci. This thesis is presented as a collection of research papers that examines each of these topics, and a review and discussion that synthesizes my findings.¶ ...

Marsupials and eutherians are mammals that differ in their physiological traits, predominately their reproductive and developmental strategies; eutherians give birth to well-developed young, while marsupials are born highly altricial after a much shorter gestation. These developmental traits result in differences in the development of the immune system of eutherian and marsupial species. B-cells are key to humoral immunity, are found in multiple lymphoid organs, and have the unique ability to mediate the production of antigen-specific antibodies in the presence of pathogens. Marsupial B-cell investigations have become increasingly important in understanding an adaptive immune system that develops primarily ex utero. In comparison to eutherians and monotremes, marsupial B-cells have four Immunoglobulin (Ig) heavy (H) chain isotypes (IgA, IgG, IgM and IgE) and two light (L) chain isotypes; lambda (Igλ) and kappa (Igκ). The gray short-tailed opossum (Monodelphis domestica) is a well-established model marsupial species, with a well annotated genome. The B-cell transcriptome of an individual opossum was investigated by Next Generation RNA-Seq techniques at the single-cell level. A total of 273 single-cells and 575,721 contigs were generated, annotation of the transcriptome identified 14,654 unique genes. The first study of this thesis analysed the IgH and IgL usage in the opossum B-cell repertoire. Not surprisingly, IgM had the highest expression in the repertoire, followed by IgA, IgG, and very few cells expressing IgE. Despite Igκ being the most complex IgL isotype, the ratio of Igκ to Igλ was 35:65. IgL isotypes have been identified to have a greater contribution to antibody diversification than IgH isotypes, due to the complexity and abundance of IgL variable (V) gene segments. The second study of this thesis examined the whole opossum B-cell transcriptome and analysed the most highly expressed genes. The most abundant gene transcripts were Sydnecan-4, making up 0.66% of the entire transcriptome. IgM and IgG cells produced significantly more transcripts of the golgi glycoprotein 1 and ELMO domain-containing protein genes in comparison to IgA. Since IgE expressing cells were very low in number, a definitive comparison could not be made between all IgH cells. Highly expressed genes associated with the marsupial immune system included MHC class II DRα chain and MHC class II DAβ chain. The diverse array of genes identified in the opossum single-cell transcriptome reveals the importance of marsupial B-cells in producing endogenous antibody responses, and has allowed for a comparative analysis with other mammalian lineages.

X chromosome inactivation has not been well studied in mammals other than humans and mice. In both species, the inactive X expresses the XIST/Xist (X-inactivation specific transcript) non-coding R N A that is crucial for dosage compensation in females. Although both species belong to the same mammalian subclass, Eutheria, they show significant differences in imprinting patterns, negative regulation of XIST/Xist, and extent of silencing on the inactive X chromosome. Furthermore, the mechanism by which the Xist transcript coats and silences the X in cis is unknown. This study focuses on X-inactivation in other eutherians, first to unravel domains within XIST/Xist of biological significance, and second to investigate whether incomplete silencing in humans is unique within the mammalian subclass. Comparative analysis to predict conserved secondary structures between seven eutherian orthologs revealed common stems in the sequence before the Xist A repeat, the A repeat, F repeat, and exon 4. Several complex secondary structures were also similar between rodents but were not conserved in other species. These included the D repeat; structures between the B and D, as well as A and F repeats; and the unique rodent exon 5. The significance of these conserved domains in the context of potential biological functions, and how the structural differences might account for some species-specific differences, is discussed in this thesis. To investigate the species variability in the extent of silencing, methylation analysis was performed on Zfic, JaridlC, Crsp2, Utx, Ubel, Ar, and Fmrl in the cow and coast mole, in addition to human and mouse. Results from this study suggest that mouse is distinct in its more complete inactivation at several loci - Zjx, Crsp2 - on the evolutionary newer part of the X , and Ubel on an evolutionary older part of the chromosome. In addition to evolutionary age, factors such as the position o f the centromere, distance from the X inactivation centre (XIC), and presence of Y homologs failed to consistently explain or predict whether the genes on the X chromosome would escape or be subject to inactivation. Further epigenetic analysis is necessary to understand the distinct mechanisms leading to escape versus inactivation amongst different mammals.
Medicine, Faculty of
Medical Genetics, Department of
Graduate

This thesis describes a comprehensive study of the cellular responses of a number of endangered marsupial species with a principal focus on the tammar wallaby (Macropus eugenii) as a model macropod species. The development of in vitro experimental assays for the assessment of immune responses in this model species are described, which provided a set of benchmarks for comparisons with other members of the Macropodidae and with eutherian mammals. Once this data was collected and protocols were established, the study was extended to include investigations of the immune responses in opportunistic samples obtained from the Rufous Hare-wallaby (Lagorchestes hirsutus), the Long-footed potoroo ( Potorous longipes) and the more common, but nonetheless still vulnerable, Long-nosed potoroo (Potorous tridactylus) with a view to investigating their apparent susceptibility to infection with intracellular pathogens, particularly mycobacterial species. The findings from the application of these assays suggest that the cellular immune responses of these species are relatively complex and involve a level of sophistication that rivals their eutherian counterparts. Specifically peripheral blood and tissue leukocytes were morphologically similar to those of other mammals, with the exception of tammar wallaby monocytes that appeared to contain few lysosomal granules, and the basophils of the Rufous Hare-wallaby that contained very large atypical granules. The overall findings of this study suggest that the immune systems of macropod species possess most of the sophistication associated with that of eutherian mammals. Whilst some differences were apparent in cells and their products in the test species, no single factor common to all macropods was identified as a cause for immune dysfunction. It appears likely that as yet undefined factors related to their confinement rather than an inherent defect in their immunocapacity is responsible for the apparent disease susceptibility of these animals.
Doctor of Philosophy (PhD)

This thesis describes a comprehensive study of the cellular responses of a number of endangered marsupial species with a principal focus on the tammar wallaby (Macropus eugenii) as a model macropod species. The development of in vitro experimental assays for the assessment of immune responses in this model species are described, which provided a set of benchmarks for comparisons with other members of the Macropodidae and with eutherian mammals. Once this data was collected and protocols were established, the study was extended to include investigations of the immune responses in opportunistic samples obtained from the Rufous Hare-wallaby (Lagorchestes hirsutus), the Long-footed potoroo ( Potorous longipes) and the more common, but nonetheless still vulnerable, Long-nosed potoroo (Potorous tridactylus) with a view to investigating their apparent susceptibility to infection with intracellular pathogens, particularly mycobacterial species. The findings from the application of these assays suggest that the cellular immune responses of these species are relatively complex and involve a level of sophistication that rivals their eutherian counterparts. Specifically peripheral blood and tissue leukocytes were morphologically similar to those of other mammals, with the exception of tammar wallaby monocytes that appeared to contain few lysosomal granules, and the basophils of the Rufous Hare-wallaby that contained very large atypical granules. The overall findings of this study suggest that the immune systems of macropod species possess most of the sophistication associated with that of eutherian mammals. Whilst some differences were apparent in cells and their products in the test species, no single factor common to all macropods was identified as a cause for immune dysfunction. It appears likely that as yet undefined factors related to their confinement rather than an inherent defect in their immunocapacity is responsible for the apparent disease susceptibility of these animals.

The morphological diversity of the external and internal surfaces of the petrosal bone, which contains the structures of the inner ear, across a broad range of therian mammals is documented, and patterns of variation across taxa are identified. One pattern of variation is the result of ontogenetic changes in the ear region, as described for the external surface morphology of a sample of isolated petrosal bones referred to Proboscidea from Pleistocene deposits in central Texas. The morphology of the aquaeductus Fallopii for passage of the greater petrosal branch of the facial nerve supports an ontogenetic explanation for some variation within the proboscidean sample, and a sequence of ossification surrounding the aquaeductus Fallopii is hypothesized. Further ontogenetic patterns are investigated using digital endocasts of the bony labyrinth (preserved on the internal surfaces of the petrosal) constructed from CT data across a growth series of the opossum Monodelphis domestica. Strong correlation between skull length and age is found, but from 27 days after birth onward, there is no correlation with age among most dimensions of the inner ear. Adult dimensions of several of the inner ear structures are achieved before the inner ear is functional in M. domestica. Morphological variation within the inner ear of several eutherian mammals from the Cretaceous of Asia, including zhelestids from the Bissekty Formation of Uzbekistan, is described. The variation within the fossil sample is compared to that observed within extant species of placental mammals, and it is determined that the amount of variation within the Bissekty zhelestid population is within the range of that measured for extant species. Additional evolutionary and physiological patterns preserved within the walls of the bony labyrinth are identified through a high level anatomical comparison of the inner ear cavities across Placentalia as a whole. In particular, features of the inner ear support monophyly of Cetacea, Carnivora, Primatomorpha, and caviomorph Rodentia. The volumetric percentage of the vestibular apparatus (vestibule plus semicircular canals) of aquatic mammals is smaller than that calculated for terrestrial relatives of comparable body size. Thus, aspects of the bony labyrinth are both phylogenetically and physiologically informative.
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No
The excavation at Cnip, Isle of Lewis, Scotland of the largest, and only known family cemetery from the early Norse period in the Hehrides, provided a unique opportunity to use Sr isotope analysis to examine the origins of people who may have been Norwegian Vikings. Sr isotope analysis permits direct investigation of a person's place of origin rather than indirectly through acquired cultural and artefactual affiliations. Sr isotope data suggest that the Norse group at Cnip was of mixed origins. The majority were consistent with indigenous origins but two individuals, of middle-age and different sex. were immigrants. They were, however, not from Norway but were raised separately, most probably on Tertiary volcanic rocks (e.g. the Inner Hebrides or NE Ireland) or, for the female, on marine carbonate rocks.

No
Traditional methods of dietary reconstruction do not allow the investigation of dietary variability within the lifetimes of individual hominins. However, laser ablation stable isotope analysis reveals that the ¿13C values of Paranthropus robustus individuals often changed seasonally and interannually. These data suggest that Paranthropus was not a dietary specialist and that by about 1.8 million years ago, savanna-based foods such as grasses or sedges or animals eating these foods made up an important but highly variable part of its diet.