Origin and evolution of candidate mental retardation genes on the human X chromosome (MRX)

<p>Abstract</p> <p>Background</p> <p>The human X chromosome has a biased gene content. One group of genes that is over-represented on the human X are those expressed in the brain, explaining the large number of sex-linked mental retardation (MRX) syndromes.</p> <p>Results</p> <p>To determine if MRX genes were recruited to the X, or whether their brain-specific functions were acquired after relocation to the mammalian X chromosome, we examined the location and expression of their orthologues in marsupials, which diverged from human approximately 180 million years ago. We isolated and mapped nine tammar wallaby MRX homologues, finding that six were located on the tammar wallaby X (which represents the ancient conserved mammal X) and three on chromosome 5, representing the recently added region of the human X chromosome. The location of MRX genes within the same synteny groups in human and wallaby does not support the hypothesis that genes with an important function in the brain were recruited in multiple independent events from autosomes to the mammalian X chromosome. Most of the tammar wallaby MRX homologues were more widely expressed in tammar wallaby than in human. Only one, the tammar wallaby <it>ARX </it>homologue (located on tammar chromosome 5p), has a restricted expression pattern comparable to its pattern in human. The retention of the brain-specific expression of <it>ARX </it>over 180 million years suggests that this gene plays a fundamental role in mammalian brain development and function.</p> <p>Conclusion</p> <p>Our results suggest all the genes in this study may have originally had more general functions that became more specialised and important in brain function during evolution of humans and other placental mammals.</p

The evolution of imprinting: chromosomal mapping of orthologues of mammalian imprinted domains in monotreme and marsupial mammals.

BACKGROUND: The evolution of genomic imprinting, the parental-origin specific expression of genes, is the subject of much debate. There are several theories to account for how the mechanism evolved including the hypothesis that it was driven by the evolution of X-inactivation, or that it arose from an ancestrally imprinted chromosome. RESULTS: Here we demonstrate that mammalian orthologues of imprinted genes are dispersed amongst autosomes in both monotreme and marsupial karyotypes. CONCLUSION: These data, along with the similar distribution seen in birds, suggest that imprinted genes were not located on an ancestrally imprinted chromosome or associated with a sex chromosome. Our results suggest imprinting evolution was a stepwise, adaptive process, with each gene/cluster independently becoming imprinted as the need arose.RIGHTS : This article is licensed under the BioMed Central licence at http://www.biomedcentral.com/about/license which is similar to the 'Creative Commons Attribution Licence'. In brief you may : copy, distribute, and display the work; make derivative works; or make commercial use of the work - under the following conditions: the original author must be given credit; for any reuse or distribution, it must be made clear to others what the license terms of this work are

The Sloan Lens ACS Survey. IX. Colors, Lensing and Stellar Masses of Early-type Galaxies

We present the current photometric dataset for the Sloan Lens ACS (SLACS) Survey, including HST photometry from ACS, WFPC2, and NICMOS. These data have enabled the confirmation of an additional 15 grade `A' (certain) lens systems, bringing the number of SLACS grade `A' lenses to 85; including 13 grade `B' (likely) systems, SLACS has identified nearly 100 lenses and lens candidates. Approximately 80% of the grade `A' systems have elliptical morphologies while ~10% show spiral structure; the remaining lenses have lenticular morphologies. Spectroscopic redshifts for the lens and source are available for every system, making SLACS the largest homogeneous dataset of galaxy-scale lenses to date. We have developed a novel Bayesian stellar population analysis code to determine robust stellar masses with accurate error estimates. We apply this code to deep, high-resolution HST imaging and determine stellar masses with typical statistical errors of 0.1 dex; we find that these stellar masses are unbiased compared to estimates obtained using SDSS photometry, provided that informative priors are used. The stellar masses range from 10^10.5 to 10^11.8 M$_\odot$ and the typical stellar mass fraction within the Einstein radius is 0.4, assuming a Chabrier IMF. The ensemble properties of the SLACS lens galaxies, e.g. stellar masses and projected ellipticities, appear to be indistinguishable from other SDSS galaxies with similar stellar velocity dispersions. This further supports that SLACS lenses are representative of the overall population of massive early-type galaxies with M* >~ 10^11 M$_\odot$, and are therefore an ideal dataset to investigate the kpc-scale distribution of luminous and dark matter in galaxies out to z ~ 0.5.Comment: 20 pages, 18 figures, 5 tables, published in Ap

Sequence and gene content of a large fragment of a lizard sex chromosome and evaluation of candidate sex differentiating gene R-spondin 1

Background: Scant genomic information from non-avian reptile sex chromosomes is available, and for only a few lizards, several snakes and one turtle species, and it represents only a small fraction of the total sex chromosome sequences in these species. Results: We report a 352 kb of contiguous sequence from the sex chromosome of a squamate reptile, Pogona vitticeps, with a ZZ/ZW sex microchromosome system. This contig contains five protein coding genes (oprd1, rcc1, znf91, znf131, znf180), and major families of repetitive sequences with a high number of copies of LTR and non-LTR retrotransposons, including the CR1 and Bov-B LINEs. The two genes, oprd1 and rcc1 are part of a homologous syntenic block, which is conserved among amniotes. While oprd1 and rcc1 have no known function in sex determination or differentiation in amniotes, this homologous syntenic block in mammals and chicken also contains R-spondin 1 (rspo1), the ovarian differentiating gene in mammals. In order to explore the probability that rspo1 is sex determining in dragon lizards, genomic BAC and cDNA clones were mapped using fluorescence in situ hybridisation. Their location on an autosomal microchromosome pair, not on the ZW sex microchromosomes, eliminates rspo1 as a candidate sex determining gene in P. vitticeps. Conclusion: Our study has characterized the largest contiguous stretch of physically mapped sex chromosome sequence (352 kb) from a ZZ/ZW lizard species. Although this region represents only a small fraction of the sex chromosomes of P. vitticeps, it has revealed several features typically associated with sex chromosomes including the accumulation of large blocks of repetitive sequences

A second-generation anchored genetic linkage map of the tammar wallaby (Macropus eugenii)

Background: \ud The tammar wallaby, Macropus eugenii, a small kangaroo used for decades for studies of reproduction and metabolism, is the model Australian marsupial for genome sequencing and genetic investigations. The production of a more comprehensive cytogenetically-anchored genetic linkage map will significantly contribute to the deciphering of the tammar wallaby genome. It has great value as a resource to identify novel genes and for comparative studies, and is vital for the ongoing genome sequence assembly and gene ordering in this species.\ud \ud Results: \ud A second-generation anchored tammar wallaby genetic linkage map has been constructed based on a total of 148 loci. The linkage map contains the original 64 loci included in the first-generation map, plus an additional 84 microsatellite loci that were chosen specifically to increase coverage and assist with the anchoring and orientation of linkage groups to chromosomes. These additional loci were derived from (a) sequenced BAC clones that had been previously mapped to tammar wallaby chromosomes by fluorescence in situ hybridization (FISH), (b) End sequence from BACs subsequently FISH-mapped to tammar wallaby chromosomes, and (c) tammar wallaby genes orthologous to opossum genes predicted to fill gaps in the tammar wallaby linkage map as well as three X-linked markers from a published study. Based on these 148 loci, eight linkage groups were formed. These linkage groups were assigned (via FISH-mapped markers) to all seven autosomes and the X chromosome. The sex-pooled map size is 1402.4 cM, which is estimated to provide 82.6% total coverage of the genome, with an average interval distance of 10.9 cM between adjacent markers. The overall ratio of female/male map length is 0.84, which is comparable to the ratio of 0.78 obtained for the first-generation map.\ud \ud Conclusions: \ud Construction of this second-generation genetic linkage map is a significant step towards complete coverage of the tammar wallaby genome and considerably extends that of the first-generation map. It will be a valuable resource for ongoing tammar wallaby genetic research and assembling the genome sequence. The sex-pooled map is available online at http://compldb.angis.org.au/

Recent Assembly of an Imprinted Domain from Non-Imprinted Components

Genomic imprinting, representing parent-specific expression of alleles at a locus, raises many questions about how—and especially why—epigenetic silencing of mammalian genes evolved. We present the first in-depth study of how a human imprinted domain evolved, analyzing a domain containing several imprinted genes that are involved in human disease. Using comparisons of orthologous genes in humans, marsupials, and the platypus, we discovered that the Prader-Willi/Angelman syndrome region on human Chromosome 15q was assembled only recently (105–180 million years ago). This imprinted domain arose after a region bearing UBE3A (Angelman syndrome) fused with an unlinked region bearing SNRPN (Prader-Willi syndrome), which had duplicated from the non-imprinted SNRPB/B′. This region independently acquired several retroposed gene copies and arrays of small nucleolar RNAs from different parts of the genome. In their original configurations, SNRPN and UBE3A are expressed from both alleles, implying that acquisition of imprinting occurred after their rearrangement and required the evolution of a control locus. Thus, the evolution of imprinting in viviparous mammals is ongoing

Structure/Function Analysis of Nonwoven Cotton Topsheet Fabrics: Multi-Fiber Blending Effects on Fluid Handling and Fabric Handle Mechanics

Greige cotton (GC) has attracted interest in recent years as an eco-friendly, functional fiber for use in nonwoven topsheet materials. GC imparts favorable fluid management and sensorial properties associated with urinary liquid transport and indices related to comfort in wearable incontinence nonwovens. Nonwoven GC has material surface polarity, an ambient moisture content, and a lipid/polysaccharide matrix that imparts positive fluid mechanic properties applicable to incontinence management topsheet materials. However, a better understanding of the connection between functionality and compositional aspects of molecular, mechanical, and material property relations is still required to employ structure/function relations beyond a priori design. Thus, this study focuses on the relation of key indices of material fluid and sensorial functions to nonwoven topsheet composition. Greige cotton, polypropylene, bleached cotton, and polyester fiber blends were hydroentangled at 60, 80, and 100 bar. Greige cotton polypropylene and bleached cotton were blended at ratios to balance surface polarity, whereas low percentages of polyester were added to confer whiteness properties. Electrokinetic and contact angle measurements were obtained for the hydroentangled nonwovens to assess surface polarity in light of material composition. Notably, materials demonstrated a relation of hydrophobicity to swelling as determined electrokinetically by &#916;&#950;, &#950;plateau, and contact angles greater than 90&#176;. Subsequently, three blended nonwoven fabrics were selected to assess effects on fluid management properties including topsheet performance indices of rewet, strikethrough, and fluid handling (rate and efficiency of transport to the absorbent core). These materials aligned well with commercial topsheet fluid mechanics. Using the Leeds University Fabric Handle Evaluation System (LUFHES), the nonwovens were tested for total fabric hand. The results of the LUFHES measurements are discussed in light of fiber contributions. Fiber ratios were found to correlate well with improvement in softness, flexibility, and formability. This study provides insights that improves the understanding of the multifunctional properties accessible with greige cotton toward decisions valuable to selecting greige cotton as an environmentally friendly fiber for nonwoven topsheets

Retrotransposon Silencing by DNA Methylation Can Drive Mammalian Genomic Imprinting

Among mammals, only eutherians and marsupials are viviparous and have genomic imprinting that leads to parent-of-origin-specific differential gene expression. We used comparative analysis to investigate the origin of genomic imprinting in mammals. PEG10 (paternally expressed 10) is a retrotransposon-derived imprinted gene that has an essential role for the formation of the placenta of the mouse. Here, we show that an orthologue of PEG10 exists in another therian mammal, the marsupial tammar wallaby (Macropus eugenii), but not in a prototherian mammal, the egg-laying platypus (Ornithorhynchus anatinus), suggesting its close relationship to the origin of placentation in therian mammals. We have discovered a hitherto missing link of the imprinting mechanism between eutherians and marsupials because tammar PEG10 is the first example of a differentially methylated region (DMR) associated with genomic imprinting in marsupials. Surprisingly, the marsupial DMR was strictly limited to the 5′ region of PEG10, unlike the eutherian DMR, which covers the promoter regions of both PEG10 and the adjacent imprinted gene SGCE. These results not only demonstrate a common origin of the DMR-associated imprinting mechanism in therian mammals but provide the first demonstration that DMR-associated genomic imprinting in eutherians can originate from the repression of exogenous DNA sequences and/or retrotransposons by DNA methylation

The Sloan Lens ACS Survey. X. Stellar, Dynamical, and Total Mass Correlations of Massive Early-type Galaxies

We use stellar masses, photometry, lensing, and velocity dispersions to investigate empirical correlations for the final sample of 73 early-type lens galaxies (ETGs) from the SLACS survey. The traditional correlations (Fundamental Plane [FP] and its projections) are consistent with those found for non-lens galaxies, supporting the thesis that SLACS lens galaxies are representative of massive ETGs. The addition of strong lensing estimates of the total mass allows us to gain further insights into their internal structure: i) the mean slope of the total mass density profile is = 2.078+/-0.027 with an intrinsic scatter of 0.16+/-0.02; ii) gamma' correlates with effective radius and central mass density, in the sense that denser galaxies have steeper profiles; iii) the dark matter fraction within reff/2 is a monotonically increasing function of galaxy mass and size; iv) the dimensional mass M_dim is proportional to the total mass, and both increase more rapidly than stellar mass M*; v) the Mass Plane (MP), obtained by replacing surface brightness with surface mass density in the FP, is found to be tighter and closer to the virial relation than the FP and the M*P, indicating that the scatter of those relations is dominated by stellar population effects; vi) we construct the Fundamental Hyper-Plane by adding stellar masses to the MP and find the M* coefficient to be consistent with zero and no residual intrinsic scatter. Our results demonstrate that the dynamical structure of ETGs is not scale invariant and that it is fully specified by the total mass, r_eff, and sigma. Although the basic trends can be explained qualitatively in terms of varying star formation efficiency as a function of halo mass and as the result of dry and wet mergers, reproducing quantitatively the observed correlations and their tightness may be a significant challenge for galaxy formation models.Comment: 16 pages, 9 figures; submitted to ApJ after responding to the referee comment

Cone visual pigments of monotremes: Filling the phylogenetic gap

We have determined the sequence and genomic organization of the genes encoding the cone visual pigment of the platypus (Ornithorhynchus anatinus) and the echidna (Tachyglossus aculeatus), and inferred their spectral properties and evolutionary pathways. We prepared platypus and echidna retinal RNA and used primers of the middle-wave-sensitive (MWS), long-wave-sensitive (LWS), and short-wave sensitive (SWS1) pigments corresponding to coding sequences that are highly conserved among mammals; to PCR amplify the corresponding pigment sequences. Amplification from the retinal RNA revealed the expression of LWS pigment mRNA that is homologous in sequence and spectral properties to the primate LWS visual pigments. However, we were unable to amplify the mammalian SWS1 pigment from these two species, indicating this gene was lost prior to the echidna-platypus divergence ~21 MYA. Subsequently, when the platypus genome sequence became available, we found an LWS pigment gene in a conserved genomic arrangement that resembles the primate pigment, but, surprisingly we found an adjacent (~20 kb) SWS2 pigment gene within this conserved genomic arrangement. We obtained the same result after sequencing the echidna genes. The encoded SWS2 pigment is predicted to have a wavelength of maximal absorption of about 440 nm, and is paralogous to SWS pigments typically found in reptiles, birds, and fish but not in mammals. This study suggests the locus control region (LCR) has played an important role in the conservation of photo receptor gene arrays and the control of their spatial and temporal expression in the retina in all mammals. In conclusion, a duplication event of an ancestral cone visual pigment gene, followed by sequence divergence and selection gave rise to the LWS and SWS2 visual pigments. So far, the echidna and platypus are the only mammals that share the gene structure of the LWS-SWS2 pigment gene complex with reptiles, birds and fishes.Matthew J. Wakefield, Mark Anderson, Ellen Chang, Ke-Jun Wei, Rajinder Kaul, Jennifer A. Marshall Graves, Frank Grutzner and Samir S. Dee