Placental expression of pituitary hormones is an ancestral feature of therian mammals

<p>Abstract</p> <p>Background</p> <p>The placenta is essential for supplying nutrients and gases to the developing mammalian young before birth. While all mammals have a functional placenta, only in therian mammals (marsupials and eutherians) does the placenta closely appose or invade the uterine endometrium. The eutherian placenta secretes hormones that are structurally and functionally similar to pituitary growth hormone (GH), prolactin (PRL) and luteinizing hormone (LH). Marsupial and eutherian mammals diverged from a common ancestor approximately 125 to 148 million years ago and developed distinct reproductive strategies. As in eutherians, marsupials rely on a short-lived but functional placenta for embryogenesis.</p> <p>Results</p> <p>We characterized pituitary GH, GH-R, IGF-2, PRL and LHβ in a macropodid marsupial, the tammar wallaby, <it>Macropus eugenii</it>. These genes were expressed in the tammar placenta during the last third of gestation when most fetal growth occurs and active organogenesis is initiated. The mRNA of key growth genes GH, GH-R, IGF-2 and PRL were expressed during late pregnancy. We found significant up-regulation of GH, GH-R and IGF-2 after the start of the rapid growth phase of organogenesis which suggests that the placental growth hormones regulate the rapid phase of fetal growth.</p> <p>Conclusions</p> <p>This is the first demonstration of the existence of pituitary hormones in the marsupial placenta. Placental expression of these pituitary hormones has clearly been conserved in marsupials as in eutherian mammals, suggesting an ancestral origin of the evolution of placental expression and a critical function of these hormones in growth and development of all therian mammals.</p

Comparative analysis of the mammalian WNT4 promoter

BACKGROUND: WNT4 is a critical signalling molecule in embryogenesis and homeostasis, but the elements that control its transcriptional regulation are largely unknown. This study uses comparative cross species sequence and functional analyses between humans and a marsupial (the tammar wallaby,Macropus eugenii) to refine the mammalian Wnt4 promoter. RESULTS: We have defined a highly conserved 89 bp minimal promoter region in human WNT4 by comparative analysis with the tammar wallaby. There are many conserved transcription factor binding sites in the proximal promoter region, including SP1, MyoD, NFkappaB and AP2, as well as highly conserved CpG islands within the human, mouse and marsupial promoters, suggesting that DNA methylation may play an important role in WNT4 transcriptional regulation. CONCLUSION: Using a marsupial model, we have been able to provide new information on the transcriptional regulators in the promoter of this essential mammalian developmental gene, WNT4. These transcription factor binding sites and CpG islands are highly conserved in two disparate mammals, and are likely key controlling elements in the regulation of this essential developmental gene

Soft and transferable pseudopotentials from multi-objective optimization

Ab initio pseudopotentials are a linchpin of modern molecular and condensed matter electronic structure calculations. In this work, we employ multi-objective optimization to maximize pseudopotential softness while maintaining high accuracy and transferability. To accomplish this, we develop a formulation in which softness and accuracy are simultaneously maximized, with accuracy determined by the ability to reproduce all-electron energy differences between Bravais lattice structures, whereupon the resulting Pareto frontier is scanned for the softest pseudopotential that provides the desired accuracy in established transferability tests. We employ an evolutionary algorithm to solve the multi-objective optimization problem and apply it to generate a comprehensive table of optimized norm-conserving Vanderbilt (ONCV) pseudopotentials (https://github.com/SPARC-X/SPMS-psps). We show that the resulting table is softer than existing tables of comparable accuracy, while more accurate than tables of comparable softness. The potentials thus afford the possibility to speed up calculations in a broad range of applications areas while maintaining high accuracy.Comment: 13 pages, 4 figure

Expression and protein localisation of IGF2 in the marsupial placenta

<p>Abstract</p> <p>Background</p> <p>In eutherian mammals, genomic imprinting is critical for normal placentation and embryo survival. <it>Insulin-like growth factor 2 </it>(<it>IGF2</it>) is imprinted in the placenta of both eutherians and marsupials, but its function, or that of any imprinted gene, has not been investigated in any marsupial. This study examines the role of <it>IGF2 </it>in the yolk sac placenta of the tammar wallaby, <it>Macropus eugenii</it>.</p> <p>Results</p> <p><it>IGF2 </it>mRNA and protein were produced in the marsupial placenta. Both IGF2 receptors were present in the placenta, and presumably mediate IGF2 mitogenic actions. <it>IGF2 </it>mRNA levels were highest in the vascular region of the yolk sac placenta. IGF2 increased <it>vascular endothelial growth factor </it>expression in placental explant cultures, suggesting that IGF2 promotes vascularisation of the yolk sac.</p> <p>Conclusion</p> <p>This is the first demonstration of a physiological role for any imprinted gene in marsupial placentation. The conserved imprinting of <it>IGF2</it> in this marsupial and in all eutherian species so far investigated, but not in monotremes, suggests that imprinting of this gene may have originated in the placenta of the therian ancestor.</p

ATRX has a critical and conserved role in mammalian sexual differentiation

BACKGROUND X-linked alpha thalassemia, mental retardation syndrome in humans is a rare recessive disorder caused by mutations in the ATRX gene. The disease is characterised by severe mental retardation, mild alpha-thalassemia, microcephaly, short stature, facial, skeletal, genital and gonadal abnormalities. RESULTS We examined the expression of ATRX and ATRY during early development and gonadogenesis in two distantly related mammals: the tammar wallaby (a marsupial) and the mouse (a eutherian). This is the first examination of ATRX and ATRY in the developing mammalian gonad and fetus. ATRX and ATRY were strongly expressed in the developing male and female gonad respectively, of both species. In testes, ATRY expression was detected in the Sertoli cells, germ cells and some interstitial cells. In the developing ovaries, ATRX was initially restricted to the germ cells, but was present in the granulosa cells of mature ovaries from the primary follicle stage onwards and in the corpus luteum. ATRX mRNA expression was also examined outside the gonad in both mouse and tammar wallaby whole embryos. ATRX was detected in the developing limbs, craniofacial elements, neural tissues, tail and phallus. These sites correspond with developmental deficiencies displayed by ATR-X patients. CONCLUSIONS There is a complex expression pattern throughout development in both mammals, consistent with many of the observed ATR-X syndrome phenotypes in humans. The distribution of ATRX mRNA and protein in the gonads was highly conserved between the tammar and the mouse. The expression profile within the germ cells and somatic cells strikingly overlaps with that of DMRT1, suggesting a possible link between these two genes in gonadal development. Taken together, these data suggest that ATRX has a critical and conserved role in normal development of the testis and ovary in both the somatic and germ cells, and that its broad roles in early mammalian development and gonadal function have remained unchanged for over 148 million years of mammalian evolution.This study was supported by a National Health and Medical Research Council R D Wright Fellowship to AJP the Australian Research Council Centre of Excellence in Kangaroo Genomics and a Federation Fellowship to MBR

Differential roles of TGIF family genes in mammalian reproduction

<p>Abstract</p> <p>Background</p> <p>TG-interacting factors (TGIFs) belong to a family of TALE-homeodomain proteins including TGIF1, TGIF2 and TGIFLX/Y in human. Both TGIF1 and TGIF2 act as transcription factors repressing TGF-β signalling. Human <it>TGIFLX </it>and its orthologue, <it>Tex1 </it>in the mouse, are X-linked genes that are only expressed in the adult testis. <it>TGIF2 </it>arose from <it>TGIF1 </it>by duplication, whereas <it>TGIFLX </it>arose by retrotransposition to the X-chromosome. These genes have not been characterised in any non-eutherian mammals. We therefore studied the TGIF family in the tammar wallaby (a marsupial mammal) to investigate their roles in reproduction and how and when these genes may have evolved their functions and chromosomal locations.</p> <p>Results</p> <p>Both <it>TGIF1 </it>and <it>TGIF2 </it>were present in the tammar genome on autosomes but <it>TGIFLX </it>was absent. Tammar <it>TGIF1 </it>shared a similar expression pattern during embryogenesis, sexual differentiation and in adult tissues to that of <it>TGIF1 </it>in eutherian mammals, suggesting it has been functionally conserved. Tammar <it>TGIF2 </it>was ubiquitously expressed throughout early development as in the human and mouse, but in the adult, it was expressed only in the gonads and spleen, more like the expression pattern of human <it>TGIFLX </it>and mouse <it>Tex1</it>. Tammar <it>TGIF2 </it>mRNA was specifically detected in round and elongated spermatids. There was no mRNA detected in mature spermatozoa. TGIF2 protein was specifically located in the cytoplasm of spermatids, and in the residual body and the mid-piece of the mature sperm tail. These data suggest that tammar <it>TGIF2 </it>may participate in spermiogenesis, like <it>TGIFLX </it>does in eutherians. <it>TGIF2 </it>was detected for the first time in the ovary with mRNA produced in the granulosa and theca cells, suggesting it may also play a role in folliculogenesis.</p> <p>Conclusions</p> <p>The restricted and very similar expression of tammar <it>TGIF2 </it>to X-linked paralogues in eutherians suggests that the evolution of <it>TGIF1</it>, <it>TGIF2 </it>and <it>TGIFLX </it>in eutherians was accompanied by a change from ubiquitous to tissue-specific expression. The distribution and localization of TGIF2 in tammar adult gonads suggest that there has been an ultra-conserved function for the TGIF family in fertility and that <it>TGIF2 </it>already functioned in spermatogenesis and potentially folliculogenesis long before its retrotransposition to the X-chromosome of eutherian mammals. These results also provide further evidence that the eutherian X-chromosome has actively recruited sex and reproductive-related genes during mammalian evolution.</p

Enhancing genome assemblies by integrating non-sequence based data

INTRODUCTION Many genome projects were underway before the advent of high-throughput sequencing and have thus been supported by a wealth of genome information from other technologies. Such information frequently takes the form of linkage and physical maps, both of which can provide a substantial amount of data useful in de novo sequencing projects. Furthermore, the recent abundance of genome resources enables the use of conserved synteny maps identified in related species to further enhance genome assemblies. METHODS The tammar wallaby (Macropus eugenii) is a model marsupial mammal with a low coverage genome. However, we have access to extensive comparative maps containing over 14,000 markers constructed through the physical mapping of conserved loci, chromosome painting and comprehensive linkage maps. Using a custom Bioperl pipeline, information from the maps was aligned to assembled tammar wallaby contigs using BLAT. This data was used to construct pseudo paired-end libraries with intervals ranging from 5-10 MB. We then used Bambus (a program designed to scaffold eukaryotic genomes by ordering and orienting contigs through the use of paired-end data) to scaffold our libraries. To determine how map data compares to sequence based approaches to enhance assemblies, we repeated the experiment using a 0.5× coverage of unique reads from 4 KB and 8 KB Illumina paired-end libraries. Finally, we combined both the sequence and non-sequence-based data to determine how a combined approach could further enhance the quality of the low coverage de novo reconstruction of the tammar wallaby genome. RESULTS Using the map data alone, we were able order 2.2% of the initial contigs into scaffolds, and increase the N50 scaffold size to 39 KB (36 KB in the original assembly). Using only the 0.5× paired-end sequence based data, 53% of the initial contigs were assigned to scaffolds. Combining both data sets resulted in a further 2% increase in the number of initial contigs integrated into a scaffold (55% total) but a 35% increase in N50 scaffold size over the use of sequence-based data alone. CONCLUSIONS We provide a relatively simple pipeline utilizing existing bioinformatics tools to integrate map data into a genome assembly which is available at http://www.mcb.uconn.edu/fac.php?name=paska. While the map data only contributed minimally to assigning the initial contigs to scaffolds in the new assembly, it greatly increased the N50 size. This process added structure to our low coverage assembly, greatly increasing its utility in further analyses

Kohn-Sham accuracy from orbital-free density functional theory via Δ\Delta-machine learning

We present a $\Delta$-machine learning model for obtaining Kohn-Sham accuracy from orbital-free density functional theory (DFT) calculations. In particular, we employ a machine learned force field (MLFF) scheme based on the kernel method to capture the difference between Kohn-Sham and orbital-free DFT energies/forces. We implement this model in the context of on-the-fly molecular dynamics simulations, and study its accuracy, performance, and sensitivity to parameters for representative systems. We find that the formalism not only improves the accuracy of Thomas-Fermi-von Weizs{\"a}cker (TFW) orbital-free energies and forces by more than two orders of magnitude, but is also more accurate than MLFFs based solely on Kohn-Sham DFT, while being more efficient and less sensitive to model parameters. We apply the framework to study the structure of molten Al$_{0.88}$Si$_{0.12}$, the results suggesting no aggregation of Si atoms, in agreement with a previous Kohn-Sham study performed at an order of magnitude smaller length and time scales.Comment: 10 pages, 7 figures, 2 table

HOXA13 and HOXD13 expression during development of the syndactylous digits in the marsupial Macropus eugenii

<p>Abstract</p> <p>Background</p> <p>Kangaroos and wallabies have specialised limbs that allow for their hopping mode of locomotion. The hindlimbs differentiate much later in development but become much larger than the forelimbs. The hindlimb autopod has only four digits, the fourth of which is greatly elongated, while digits two and three are syndactylous. We investigated the expression of two genes, <it>HOXA13 and HOXD13</it>, that are crucial for digit patterning in mice during formation of the limbs of the tammar wallaby.</p> <p>Results</p> <p>We describe the development of the tammar limbs at key stages before birth. There was marked heterochrony and the hindlimb developed more slowly than the forelimb. Both tammar <it>HOXA13 </it>and <it>HOXD13 </it>have two exons as in humans, mice and chickens. <it>HOXA13 </it>had an early and distal mRNA distribution in the tammar limb bud as in the mouse, but forelimb expression preceded that in the hindlimb. <it>HOXD13 </it>mRNA was expressed earlier in the forelimb than the hindlimb and was predominantly detected in the interdigital tissues of the forelimb. In contrast, the hindlimb had a more restricted expression pattern that appeared to be expressed at discrete points at both posterior and anterior margins of the limb bud, and was unlike expression seen in the mouse and the chicken.</p> <p>Conclusions</p> <p>This is the first examination of <it>HOXA </it>and <it>HOXD </it>gene expression in a marsupial. The gene structure and predicted proteins were highly conserved with their eutherian orthologues. Interestingly, despite the morphological differences in hindlimb patterning, there were no modifications to the polyalanine tract of either <it>HOXA13 </it>or <it>HOXD13 </it>when compared to those of the mouse and bat but there was a marked difference between the tammar and the other mammals in the region of the first polyserine tract of <it>HOXD13</it>. There were also altered expression domains for both genes in the developing tammar limbs compared to the chicken and mouse. Together these findings suggest that the timing of <it>HOX </it>gene expression may contribute to the heterochrony of the forelimb and hindlimb and that alteration to <it>HOX </it>domains may influence phenotypic differences that lead to the development of marsupial syndactylous digits.</p