Genomic screening of fish-specific genes in gnathostomes and their functions in fin development.

In this study, we comprehensively searched for fish-specific genes in gnathostomes that contribute to development of the fin, a fish-specific trait. Many previous reports suggested that animal group-specific genes are often important for group-specific traits. Clarifying the roles of fish-specific genes in fin development of gnathostomes, for example, can help elucidate the mechanisms underlying the formation of this trait. We first identified 91 fish-specific genes in gnathostomes by comparing the gene repertoire in 16 fish and 35 tetrapod species. RNA-seq analysis narrowed down the 91 candidates to 33 genes that were expressed in the developing pectoral fin. We analyzed the functions of approximately half of the candidate genes by loss-of-function analysis in zebrafish. We found that some of the fish-specific and fin development-related genes, including fgf24 and and1/and2, play roles in fin development. In particular, the newly identified fish-specific gene qkia is expressed in the developing fin muscle and contributes to muscle morphogenesis in the pectoral fin as well as body trunk. These results indicate that the strategy of identifying animal group-specific genes is functional and useful. The methods applied here could be used in future studies to identify trait-associated genes in other animal groups.

Open reading frame dominance indicates protein-coding potential of RNAs.

Recent studies have identified numerous RNAs with both coding and noncoding functions. However, the sequence characteristics that determine this bifunctionality remain largely unknown. In the present study, we develop and test the open reading frame (ORF) dominance score, which we define as the fraction of the longest ORF in the sum of all putative ORF lengths. This score correlates with translation efficiency in coding transcripts and with translation of noncoding RNAs. In bacteria and archaea, coding and noncoding transcripts have narrow distributions of high and low ORF dominance, respectively, whereas those of eukaryotes show relatively broader ORF dominance distributions, with considerable overlap between coding and noncoding transcripts. The extent of overlap positively and negatively correlates with the mutation rate of genomes and the effective population size of species, respectively. Tissue-specific transcripts show higher ORF dominance than ubiquitously expressed transcripts, and the majority of tissue-specific transcripts are expressed in mature testes. These data suggest that the decrease in population size and the emergence of testes in eukaryotic organisms allowed for the evolution of potentially bifunctional RNAs.

RNA-seq analysis to identify genes related to resting egg production of panarctic Daphnia pulex.

BACKGROUND: The genus Daphnia switches its reproductive mode from subitaneous egg production to resting egg production in response to environmental stimuli. Although this life history trait is essential for surviving unsuitable environments, the molecular mechanism of resting egg production is little understood. In this study, we examined genes related to induction of resting egg production using two genotypes of panarctic Daphnia pulex, the JPN1 and JPN2 lineages, which differ genetically in the frequency of resting egg production. We reared these genotypes under high and low food levels. At the high food level, individuals of both genotypes continually produced subitaneous eggs, whereas at the low food level, only the JPN2 genotype produced resting eggs. Then, we performed RNA-seq analysis on specimens of three instars, including before and after egg production. RESULTS: These results showed that expressed genes differed significantly between individuals grown under high and low food levels and among individuals of different instars and genotypes. Among these differentially expressed genes (DEGs), we found 16 that changed expression level before resting egg production. Some of these genes showed high-level expression only before resting egg production and one gene was an ortholog of bubblegum (bgm), which is reportedly up-regulated before diapause in bumblebees. According to gene ontology (GO) enrichment analysis, one GO term annotated as long-chain fatty acid biosynthetic process was enriched among these 16 genes. In addition, GO terms related to glycometabolism were enriched among down-regulated genes of individuals holding resting eggs, compared to those before resting egg production. CONCLUSIONS: We found candidate genes highly expressed only before resting egg production. Although functions of candidate genes found in this study have not been reported previously in Daphnia, catabolism of long-chain fatty acids and metabolism of glycerates are related to diapause in other organisms. Thus, it is highly probable that candidate genes identified in this study are related to the molecular mechanism regulating resting egg production in Daphnia.

Transcriptomic heterochrony and completely cleistogamous flower development in the mycoheterotrophic orchid Gastrodia.

Cleistogamy, in which plants can reproduce via self-fertilization within permanently closed flowers, has evolved in > 30 angiosperm lineages; however, consistent with Darwin's doubts about its existence, complete cleistogamy - the production of only cleistogamous flowers - has rarely been recognized. Thus far, the achlorophyllous orchid genus, Gastrodia, is the only known genus with several plausible completely cleistogamous species. Here, we analyzed the floral developmental transcriptomes of two recently evolved, completely cleistogamous Gastrodia species and their chasmogamous sister species to elucidate the possible changes involved in producing common cleistogamous traits. The ABBA-BABA test did not support introgression and protein sequence convergence as evolutionary mechanisms leading to cleistogamy, leaving convergence in gene expression as a plausible mechanism. Regarding transcriptomic differentiation, the two cleistogamous species had common modifications in the expression of developmental regulators, exhibiting a gene family-wide signature of convergent expression changes in MADS-box genes. Our transcriptomic pseudotime analysis revealed a prolonged juvenile state and eventual maturation, a heterochronic pattern consistent with partial neoteny, in cleistogamous flower development. These findings indicate that transcriptomic partial neoteny, arising from changes in the expression of conserved developmental regulators, might have contributed to the rapid and repeated evolution of cleistogamous flowers in Gastrodia.

Optimal pollen stickiness to pollinators for maximizing paternal fitness: Increased number of recipient flowers or increased pollen deposition on recipient flowers?

A plant can sire more seeds by increasing the number of pollen recipient flowers or the amount of pollen deposited on recipient flowers. We theoretically analyzed how pollen stickiness contributes to paternal fitness through changing the pattern of pollen dispersal including both the number of recipient flowers and overall pollen deposition (the overall amount of pollen deposited on recipient flowers) in animal-pollinated plants. We developed a numerical model in which pollen stickiness to pollinators increases with production of expensive materials on pollen surfaces, and a high level of stickiness diminishes the proportions of pollen lost from a pollinator body during a flight and pollen deposited on a stigma during a visit. We found that the number of recipient flowers monotonically increased with increasing pollen stickiness allocation while overall pollen deposition was maximized at a certain amount of stickiness allocation. We demonstrated that evolutionarily stable pollen stickiness attained many recipient flowers at the expense of overall pollen deposition in most cases while it merely favored maximization of overall pollen deposition in all other cases. Sticky pollen evolved if pollinators were highly likely to drop pollen during flights and did not diffuse well. In this situation, the evolutionarily stable pattern of pollen dispersal was acquisition of many pollen recipient flowers rather than maximization of overall pollen deposition. Sticky pollen also evolved if additional sticking elements were moderately effective in increasing the force of adhesion to pollinators. Pollen stickiness has a significant effect on the pattern of pollen dispersal via the extent of pollen carryover, and our results suggest that plants maximize paternal fitness by giving pollen the optimal stickiness, which varies with pollinating partners.

Invasive invertebrates associated with highly duplicated gene content.

Invasion of alien species has led to serious problems, including the destruction of native ecosystems. In general, invasive species adapt to new environments rapidly, suggesting that they have high genetic diversity that can directly influence environmental adaptability. However, it is not known how genomic architecture causes genetic diversity that leads to invasiveness. Recent studies have showed that the proportion of duplicated genes (PD ) in whole animal genomes correlate with environmental variability within a habitat. Here, we show that PD and propagule size significantly explain the differences in species categories (invasive species, noninvasive species, and parasites). PD correlated negatively with the propagule size. The residual values of regression of PD on propagule size revealed that the invasive species had higher PD values and larger propagule size than those of the noninvasive species, whereas the parasites had lower PD values and smaller propagule size than those of others. There were no correlations between the invasive species and other genomic factors including the genome size, number of genes, and certain gene families. Our results suggest that the PD values of a genome might be a potential genomic source causing genetic variations for adaptation to diverse environments. The results also showed that the invasiveness status of a species would be predicted by the residual values of regression of PD on propagule size. Our innovative approach provides a measure to estimate the environmental adaptability of organisms based on genomic data.

Inference of Causative Genes for Alzheimer's Disease Due to Dosage Imbalance.

Copy number variations (CNVs) have recently drawn attention as an important genetic factor for diseases, especially common neuropsychiatric disorders including Alzheimer's disease (AD). Because most of the pathogenic CNV regions overlap with multiple genes, it has been challenging to identify the true disease-causing genes amongst them. Notably, a recent study reported that CNV regions containing ohnologs, which are dosage-sensitive genes, are likely to be deleterious. Utilizing the unique feature of ohnologs could be useful for identifying causative genes with pathogenic CNVs, however its effectiveness is still unclear. Although it has been reported that AD is strongly affected by CNVs, most of AD-causing genes with pathogenic CNVs have not been identified yet. Here, we show that dosage-sensitive ohnologs within CNV regions reported in patients with AD are related to the nervous system and are highly expressed in the brain, similar to other known susceptible genes for AD. We found that CNV regions in patients with AD contained dosage-sensitive genes, which are ohnologs not overlapping with control CNV regions, frequently. Furthermore, these dosage-sensitive genes in pathogenic CNV regions had a strong enrichment in the nervous system for mouse knockout phenotype and high expression in the brain similar to the known susceptible genes for AD. Our results demonstrated that selecting dosage-sensitive ohnologs out of multiple genes with pathogenic CNVs is effective in identifying the causative genes for AD. This methodology can be applied to other diseases caused by dosage imbalance and might help to establish the medical diagnosis by analysis of CNVs.

Comparisons of behavioural and TRPA1 heat sensitivities in three sympatric Cuban Anolis lizards.

Thermal tolerances of organisms play a role in defining geographic ranges and occurrence of species. In Cuba, three sympatric species of Anolis lizards (Anolis allogus, Anolis homolechis and Anolis sagrei) inhabit different thermal microhabitats. A previous study found that these species showed distinct gene expression patterns in response to temperature stimuli, suggesting the genetically distinct thermal physiology among species. To investigate whether the Anolis species inhabiting locally distinct thermal habitats diverge their thermal tolerances, we first conducted behavioural experiments to analyse the temperatures at which the three Anolis species escape from heat source. Then, for each of the three species, we isolated cDNA encoding a putative molecular heat sensor, transient receptor potential ion channel ankyrin 1 (TRPA1), which has been suggested to play a role on eliciting behavioural responses to heat stimuli. We performed electrophysiological analysis to quantify activation temperature of Anolis TRPA1 to see whether the pattern of divergence in TRPA1 responses is congruent with that of divergence in behavioural responses. We found that temperatures triggering behavioural and TRPA1 responses were significantly lower for shade-dwelling species (A. allogus) than for sun-dwelling species (A. homolechis and A. sagrei). The ambient temperature of shade habitats where A. allogus occurs stays relatively cool compared to that of open habitats where A. homolechis and A. sagrei occur and bask. The high temperature thresholds of A. homolechis and A. sagrei may reflect their heat tolerances that would benefit these species to inhabit the open habitats.

Organ identity specification factor WGE localizes to the histone locus body and regulates histone expression to ensure genomic stability in Drosophila.

Over-expression of Winged-Eye (WGE) in the Drosophila eye imaginal disc induces an eye-to-wing transformation. Endogenous WGE is required for organ development, and wge-deficient mutants exhibit growth arrest at the larval stage, suggesting that WGE is critical for normal growth. The function of WGE, however, remains unclear. Here, we analyzed the subcellular localization of WGE to gain insight into its endogenous function. Immunostaining showed that WGE localized to specific nuclear foci called the histone locus body (HLB), an evolutionarily conserved nuclear body required for S phase-specific histone mRNA production. Histone mRNA levels and protein levels in cytosolic fractions were aberrantly up-regulated in wge mutant larva, suggesting a role for WGE in regulating histone gene expression. Genetic analyses showed that wge suppresses position-effect variegation, and that WGE and a HLB component Mute appears to be synergistically involved in heterochromatin formation. Further supporting a role in chromatin regulation, wge-deficient mutants showed derepression of retrotransposons and increased γH2Av signals, a DNA damage marker. These findings suggest that WGE is a component of HLB in Drosophila with a role in heterochromatin formation and transposon silencing. We propose that WGE at HLB contributes to genomic stability and development by regulating heterochromatin structure via histone gene regulation.

Genetic basis for variation in salinity tolerance between stickleback ecotypes.

Adaptation to different salinities can drive and maintain divergence between populations of aquatic organisms. Anadromous and stream ecotypes of threespine stickleback (Gasterosteus aculeatus) are an excellent model to explore the genetic mechanisms underlying osmoregulation divergence. Using a parapatric pair of anadromous and stream stickleback ecotypes, we employed an integrated genomic approach to identify candidate genes important for adaptation to different salinity environments. Quantitative trait loci (QTL) mapping of plasma sodium concentrations under a seawater challenge experiment identified a significant QTL on chromosome 16. To identify candidate genes within this QTL, we first conducted RNA-seq and microarray analysis on gill tissue to find ecotypic differences in gene expression that were associated with plasma Na+ levels. This resulted in the identification of ten candidate genes. Quantitative PCR analysis on gill tissue of additional Japanese stickleback populations revealed that the majority of the candidate genes showed parallel divergence in expression levels. Second, we conducted whole-genome sequencing and found five genes that are predicted to have functionally important amino acid substitutions. Finally, we conducted genome scan analysis and found that eight of these candidate genes were located in genomic islands of high differentiation, suggesting that they may be under divergent selection. The candidate genes included those involved in ATP synthesis and hormonal signalling, whose expression or amino acid changes may underlie the variation in salinity tolerance. Further functional molecular analysis of these genes will reveal the causative genetic and genomic changes underlying divergent adaptation.

Accumulation of Deleterious Mutations on the Neo-Y Chromosome of Japan Sea Stickleback (Gasterosteus nipponicus).

Degeneration of Y chromosomes is a common evolutionary path of XY sex chromosome systems. Recent genomic studies in flies and plants have revealed that even young neo-sex chromosomes with the age of a few million years show signs of Y degeneration, such as the accumulation of nonsense and frameshift mutations. However, it remains unclear whether neo-Y chromosomes also show rapid degeneration in fishes, which often have homomorphic sex chromosomes. Here, we investigated whether a neo-Y chromosome of Japan Sea stickleback (Gasterosteus nipponicus), which was formed by a Y-autosome fusion within the last 2 million years, accumulates deleterious mutations. Our previous genomic analyses did not detect excess nonsense and frameshift mutations on the Japan Sea stickleback neo-Y. In the present study, we found that the nonrecombining region of the neo-Y near the fusion end has accumulated nonsynonymous mutations altering amino acids of evolutionarily highly conserved residues. Enrichment of gene ontology terms related to protein phosphorylation and cellular protein modification process was found in the genes with potentially deleterious mutations on the neo-Y. These results suggest that the neo-Y of the Japan Sea stickleback has already accumulated mutations that may impair protein functions.

Ohnologs are overrepresented in pathogenic copy number mutations.

A number of rare copy number variants (CNVs), including both deletions and duplications, have been associated with developmental disorders, including schizophrenia, autism, intellectual disability, and epilepsy. Pathogenicity may derive from dosage sensitivity of one or more genes contained within the CNV locus. To understand pathophysiology, the specific disease-causing gene(s) within each CNV need to be identified. In the present study, we test the hypothesis that ohnologs (genes retained after ancestral whole-genome duplication events, which are frequently dosage sensitive) are overrepresented in pathogenic CNVs. We selected three sets of genes implicated in copy number pathogenicity: (i) genes mapping within rare disease-associated CNVs, (ii) genes within de novo CNVs under negative genetic selection, and (iii) genes identified by clinical array comparative genome hybridization studies as potentially pathogenic. We compared the proportion of ohnologs between these gene sets and control genes, mapping to CNVs not known to be disease associated. We found that ohnologs are significantly overrepresented in genes mapping to pathogenic CNVs, irrespective of how CNVs were identified, with over 90% containing an ohnolog, compared with control CNVs >100 kb, where only about 30% contained an ohnolog. In some CNVs, such as del15p11.2 (CYFIP1) and dup/del16p13.11 (NDE1), the most plausible prior candidate gene was also an ohnolog, as were the genes VIPR2 and NRXN1, each found in short CNVs containing no other genes. Our results support the hypothesis that ohnologs represent critical dosage-sensitive elements of the genome, possibly responsible for some of the deleterious phenotypes observed for pathogenic CNVs and as such are readily identifiable candidate genes for further study.

Sex chromosome turnover contributes to genomic divergence between incipient stickleback species.

Sex chromosomes turn over rapidly in some taxonomic groups, where closely related species have different sex chromosomes. Although there are many examples of sex chromosome turnover, we know little about the functional roles of sex chromosome turnover in phenotypic diversification and genomic evolution. The sympatric pair of Japanese threespine stickleback (Gasterosteus aculeatus) provides an excellent system to address these questions: the Japan Sea species has a neo-sex chromosome system resulting from a fusion between an ancestral Y chromosome and an autosome, while the sympatric Pacific Ocean species has a simple XY sex chromosome system. Furthermore, previous quantitative trait locus (QTL) mapping demonstrated that the Japan Sea neo-X chromosome contributes to phenotypic divergence and reproductive isolation between these sympatric species. To investigate the genomic basis for the accumulation of genes important for speciation on the neo-X chromosome, we conducted whole genome sequencing of males and females of both the Japan Sea and the Pacific Ocean species. No substantial degeneration has yet occurred on the neo-Y chromosome, but the nucleotide sequence of the neo-X and the neo-Y has started to diverge, particularly at regions near the fusion. The neo-sex chromosomes also harbor an excess of genes with sex-biased expression. Furthermore, genes on the neo-X chromosome showed higher non-synonymous substitution rates than autosomal genes in the Japan Sea lineage. Genomic regions of higher sequence divergence between species, genes with divergent expression between species, and QTL for inter-species phenotypic differences were found not only at the regions near the fusion site, but also at other regions along the neo-X chromosome. Neo-sex chromosomes can therefore accumulate substitutions causing species differences even in the absence of substantial neo-Y degeneration.

Natural selection in a population of Drosophila melanogaster explained by changes in gene expression caused by sequence variation in core promoter regions.

BACKGROUND: Understanding the evolutionary forces that influence variation in gene regulatory regions in natural populations is an important challenge for evolutionary biology because natural selection for such variations could promote adaptive phenotypic evolution. Recently, whole-genome sequence analyses have identified regulatory regions subject to natural selection. However, these studies could not identify the relationship between sequence variation in the detected regions and change in gene expression levels. We analyzed sequence variations in core promoter regions, which are critical regions for gene regulation in higher eukaryotes, in a natural population of Drosophila melanogaster, and identified core promoter sequence variations associated with differences in gene expression levels subjected to natural selection. RESULTS: Among the core promoter regions whose sequence variation could change transcription factor binding sites and explain differences in expression levels, three core promoter regions were detected as candidates associated with purifying selection or selective sweep and seven as candidates associated with balancing selection, excluding the possibility of linkage between these regions and core promoter regions. CHKov1, which confers resistance to the sigma virus and related insecticides, was identified as core promoter regions that has been subject to selective sweep, although it could not be denied that selection for variation in core promoter regions was due to linked single nucleotide polymorphisms in the regulatory region outside core promoter regions. Nucleotide changes in core promoter regions of CHKov1 caused the loss of two basal transcription factor binding sites and acquisition of one transcription factor binding site, resulting in decreased gene expression levels. Of nine core promoter regions regions associated with balancing selection, brat, and CG9044 are associated with neuromuscular junction development, and Nmda1 are associated with learning, behavioral plasticity, and memory. Diversity of neural and behavioral traits may have been maintained by balancing selection. CONCLUSIONS: Our results revealed the evolutionary process occurring by natural selection for differences in gene expression levels caused by sequence variation in core promoter regions in a natural population. The sequences of core promoter regions were diverse even within the population, possibly providing a source for natural selection.

Identification of dosage-sensitive genes in Saccharomyces cerevisiae using the genetic tug-of-war method.

Gene overexpression beyond a permissible limit causes defects in cellular functions. However, the permissible limits of most genes are unclear. Previously, we developed a genetic method designated genetic tug-of-war (gTOW) to measure the copy number limit of overexpression of a target gene. In the current study, we applied gTOW to the analysis of all protein-coding genes in the budding yeast Saccharomyces cerevisiae. We showed that the yeast cellular system was robust against an increase in the copy number by up to 100 copies in >80% of the genes. After frameshift and segmentation analyses, we isolated 115 dosage-sensitive genes (DSGs) with copy number limits of 10 or less. DSGs contained a significant number of genes involved in cytoskeletal organization and intracellular transport. DSGs tended to be highly expressed and to encode protein complex members. We demonstrated that the protein burden caused the dosage sensitivity of highly expressed genes using a gTOW experiment in which the open reading frame was replaced with GFP. Dosage sensitivities of some DSGs were rescued by the simultaneous increase in the copy numbers of partner genes, indicating that stoichiometric imbalances among complexes cause dosage sensitivity. The results obtained in this study will provide basic knowledge about the physiology of chromosomal abnormalities and the evolution of chromosomal composition.

Differentially expressed genes associated with adaptation to different thermal environments in three sympatric Cuban Anolis lizards.

How animals achieve evolutionary adaptation to different thermal environments is an important issue for evolutionary biology as well as for biodiversity conservation in the context of recent global warming. In Cuba, three sympatric species of Anolis lizards (Anolis allogus, A. homolechis and A. sagrei) inhabit different thermal microhabitats, thereby providing an excellent opportunity to examine how they have adapted to different environmental temperatures. Here, we performed RNA-seq on the brain, liver and skin tissues from these three species to analyse their transcriptional responses at two different temperatures. In total, we identified 400, 816 and 781 differentially expressed genes (DEGs) between the two temperatures in A. allogus, A. homolechis and A. sagrei, respectively. Only 62 of these DEGs were shared across the three species, indicating that global transcriptional responses have diverged among these species. Gene ontology (GO) analysis showed that large numbers of ribosomal protein genes were DEGs in the warm-adapted A. homolechis, suggesting that the upregulation of protein synthesis is an important physiological mechanism in the adaptation of this species to hotter environments. GO analysis also showed that GO terms associated with circadian regulation were enriched in all three species. A gene associated with circadian regulation, Nr1d1, was detected as a DEG with opposite expression patterns between the cool-adapted A. allogus and the hot-adapted A. sagrei. Because the environmental temperature fluctuates more widely in open habitats than in forests throughout the day, the circadian thermoregulation could also be important for adaptation to distinct thermal habitats.

Contribution of nonohnologous duplicated genes to high habitat variability in mammals.

The mechanism by which genetic systems affect environmental adaptation is a focus of considerable attention in the fields of ecology, evolution, and conservation. However, the genomic characteristics that constrain adaptive evolution have remained unknown. A recent study showed that the proportion of duplicated genes in whole Drosophila genomes correlated with environmental variability within habitat, but it remains unclear whether the correlation is observed even in vertebrates whose genomes including a large number of duplicated genes generated by whole-genome duplication (WGD). Here, we focus on fully sequenced mammalian genomes that experienced WGD in early vertebrate lineages and show that the proportion of small-scale duplication (SSD) genes in the genome, but not that of WGD genes, is significantly correlated with habitat variability. Moreover, species with low habitat variability have a higher proportion of lost duplicated genes, particularly SSD genes, than those with high habitat variability. These results indicate that species that inhabit variable environments may maintain more SSD genes in their genomes and suggest that SSD genes are important for adapting to novel environments and surviving environmental changes. These insights may be applied to predicting invasive and endangered species.

Positionally biased gene loss after whole genome duplication: evidence from human, yeast, and plant.

Whole genome duplication (WGD) has made a significant contribution to many eukaryotic genomes including yeast, plants, and vertebrates. Following WGD, some ohnologs (WGD paralogs) remain in the genome arranged in blocks of conserved gene order and content (paralogons). However, the most common outcome is loss of one of the ohnolog pair. It is unclear what factors, if any, govern gene loss from paralogons. Recent studies have reported physical clustering (genetic linkage) of functionally linked (interacting) genes in the human genome and propose a biological significance for the clustering of interacting genes such as coexpression or preservation of epistatic interactions. Here we conduct a novel test of a hypothesis that functionally linked genes in the same paralogon are preferentially retained in cis after WGD. We compare the number of protein-protein interactions (PPIs) between linked singletons within a paralogon (defined as cis-PPIs) with that of PPIs between singletons across paralogon pairs (defined as trans-PPIs). We find that paralogons in which the number of cis-PPIs is greater than that of trans-PPIs are significantly enriched in human and yeast. The trend is similar in plants, but it is difficult to assess statistical significance due to multiple, overlapping WGD events. Interestingly, human singletons participating in cis-PPIs tend to be classified into "response to stimulus." We uncover strong evidence of biased gene loss after WGD, which further supports the hypothesis of biologically significant gene clusters in eukaryotic genomes. These observations give us new insight for understanding the evolution of genome structure and of protein interaction networks.

Mammalian X chromosome inactivation evolved as a dosage-compensation mechanism for dosage-sensitive genes on the X chromosome.

How and why female somatic X-chromosome inactivation (XCI) evolved in mammals remains poorly understood. It has been proposed that XCI is a dosage-compensation mechanism that evolved to equalize expression levels of X-linked genes in females (2X) and males (1X), with a prior twofold increase in expression of X-linked genes in both sexes ("Ohno's hypothesis"). Whereas the parity of X chromosome expression between the sexes has been clearly demonstrated, tests for the doubling of expression levels globally along the X chromosome have returned contradictory results. However, changes in gene dosage during sex-chromosome evolution are not expected to impact on all genes equally, and should have greater consequences for dosage-sensitive genes. We show that, for genes encoding components of large protein complexes (≥ 7 members)--a class of genes that is expected to be dosage-sensitive--expression of X-linked genes is similar to that of autosomal genes within the complex. These data support Ohno's hypothesis that XCI acts as a dosage-compensation mechanism, and allow us to refine Ohno's model of XCI evolution. We also explore the contribution of dosage-sensitive genes to X aneuploidy phenotypes in humans, such as Turner (X0) and Klinefelter (XXY) syndromes. X aneuploidy in humans is common and is known to have mild effects because most of the supernumerary X genes are inactivated and not affected by aneuploidy. Only genes escaping XCI experience dosage changes in X-aneuploidy patients. We combined data on dosage sensitivity and XCI to compute a list of candidate genes for X-aneuploidy syndromes.

Viscosity scaling of the self-diffusion and velocity cross-correlation coefficients of two functionalised ionic liquids and of their non-functionalized analogues.

Ion self-diffusion coefficients have been measured for ionic liquids based on the cations N-acetoxyethyl-N,N-dimethyl-N-ethylammonium ([N(112,2OCO1)](+)) and its non-functionalised analogue, N,N-dimethyl-N-ethyl-N-pentylammonium ([N1125](+)), and N,N-dimethyl-N-ethyl-N-methoxyethoxyethylammonium ([N(112,2O2O1)](+)), and its analogue, N,N-dimethyl-N-ethyl-N-heptylammonium ([N1127](+)) and the bis(trifluoromethanesulfonyl)amide anion. The functionalised chain on an ammonium cation has the same length, in terms of the number of atoms, as the non-functionalised chain of the corresponding analogue. For [N(112,2OCO1)][Tf2N] and [N1127][Tf2N], the cation and anion self-diffusion coefficients are equal, within experimental error, whereas for [N1125][Tf2N], the cation diffuses more quickly, and for [N(112,2O2O1)][Tf2N], it is the anion that diffuses more quickly than the ether-functionalised cation. But these differences are relatively small, just beyond experimental error. The data are used to calculate velocity cross-correlation coefficients (VCC or f(ij)) and distinct diffusion coefficients (D(ij)(d)). Both the self-diffusion and distinct diffusion coefficients are analysed in terms of (fractional) Stokes-Einstein-Sutherland equations. Though the self-diffusion coefficients, as with the conductivity and viscosity, show marked differences in absolute terms between the functionalised and non-functionalised forms, being higher for the ethoxy-substituted IL and lower for the acetoxy-substituted IL, these are largely removed by scaling with the viscosity. Thus the transport properties are better understood as functions of the viscosity rather than the temperature and density, per se. The presence of the alkoxy-substituted side chains is known to change the local mesoscopic liquid structure, but it appears once this is done, the transport properties scale correspondingly. In the case of the acetoxy-substituted IL, this is also largely the case, but the Nernst-Einstein deviation parameter, Δ, which depends on the difference between the anion-cation VCC and the mean of the cation-cation and anion-anion VCCs, is smaller than that of its analogue salt, and also temperature dependent.