TMT-Opsins differentially modulate medaka brain function in a context-dependent manner.

Vertebrate behavior is strongly influenced by light. Light receptors, encoded by functional opsin proteins, are present inside the vertebrate brain and peripheral tissues. This expression feature is present from fishes to human and appears to be particularly prominent in diurnal vertebrates. Despite their conserved widespread occurrence, the nonvisual functions of opsins are still largely enigmatic. This is even more apparent when considering the high number of opsins. Teleosts possess around 40 opsin genes, present from young developmental stages to adulthood. Many of these opsins have been shown to function as light receptors. This raises the question of whether this large number might mainly reflect functional redundancy or rather maximally enables teleosts to optimally use the complex light information present under water. We focus on tmt-opsin1b and tmt-opsin2, c-opsins with ancestral-type sequence features, conserved across several vertebrate phyla, expressed with partly similar expression in non-rod, non-cone, non-retinal-ganglion-cell brain tissues and with a similar spectral sensitivity. The characterization of the single mutants revealed age- and light-dependent behavioral changes, as well as an impact on the levels of the preprohormone sst1b and the voltage-gated sodium channel subunit scn12aa. The amount of daytime rest is affected independently of the eyes, pineal organ, and circadian clock in tmt-opsin1b mutants. We further focused on daytime behavior and the molecular changes in tmt-opsin1b/2 double mutants, and found that-despite their similar expression and spectral features-these opsins interact in part nonadditively. Specifically, double mutants complement molecular and behavioral phenotypes observed in single mutants in a partly age-dependent fashion. Our work provides a starting point to disentangle the highly complex interactions of vertebrate nonvisual opsins, suggesting that tmt-opsin-expressing cells together with other visual and nonvisual opsins provide detailed light information to the organism for behavioral fine-tuning. This work also provides a stepping stone to unravel how vertebrate species with conserved opsins, but living in different ecological niches, respond to similar light cues and how human-generated artificial light might impact on behavioral processes in natural environments.

Melanopsin elevates locomotor activity during the wake state of the diurnal zebrafish.

Mammalian and fish pineals play a key role in adapting behaviour to the ambient light conditions through the release of melatonin. In mice, light inhibits nocturnal locomotor activity via the non-visual photoreceptor Melanopsin. In contrast to the extensively studied function of Melanopsin in the indirect regulation of the rodent pineal, its role in the intrinsically photosensitive zebrafish pineal has not been elucidated. Therefore, it is not evident if the light signalling mechanism is conserved between distant vertebrates, and how Melanopsin could affect diurnal behaviour. A double knockout of melanopsins (opn4.1-opn4xb) was generated in the diurnal zebrafish, which manifests attenuated locomotor activity during the wake state. Transcriptome sequencing gave insight into pathways downstream of Melanopsin, implying that sustained repression of the melatonin pathway is required to elevate locomotor activity during the diurnal wake state. Moreover, we show that light induces locomotor activity during the diurnal wake state in an intensity-dependent manner. These observations suggest a common Melanopsin-driven mechanism between zebrafish and mammals, while the diurnal and nocturnal chronotypes are inversely regulated downstream of melatonin.

Addressing Global Inequities in Positron Emission Tomography-Computed Tomography (PET-CT) for Cancer Management: A Statistical Model to Guide Strategic Planning.

BACKGROUND According to the World Health Organization (WHO), non-communicable diseases are responsible for 71% of annual global mortality. National governments and international organizations are increasingly considering medical imaging and nuclear medicine access data in strategies to address epidemiologic priorities. Our objective here was to develop a statistical model to assist countries in estimating their needs for PET-CT systems for the management of specific cancer types. MATERIAL AND METHODS We introduce a patient-centered statistical model based on country-specific epidemiological data, PET-CT performance, and evidence-based clinical guidelines for PET-CT use for cancer. The output of the model was integrated into a Bayesian model to rank countries or world regions that would benefit the most from upscaling PET-CT scanners. RESULTS We applied our model to the IMAGINE database, recently developed by the International Atomic Energy Agency (IAEA). Our model indicates that at least 96 countries should upscale their PET-CT services and more than 200 additional PET-CT scanners would be required to fulfill their needs. The model also provides quantitative evidence indicating that low-income countries would benefit the most from increasing PET-CT provision. Finally, we discuss several cases in which the standard unit [number of scanners]/[million inhabitants] to guide strategic planning or address inequities is misleading. CONCLUSIONS Our model may help in the accurate delineation and further reduction of global inequities in access to PET-CT scanners. As a template, the model also has the potential to estimate the costs and socioeconomic impact of implementing any medical imaging modality for any clinical application.

Separable Roles for a Caenorhabditis elegans RMI1 Homolog in Promoting and Antagonizing Meiotic Crossovers Ensure Faithful Chromosome Inheritance.

During the first meiotic division, crossovers (COs) between homologous chromosomes ensure their correct segregation. COs are produced by homologous recombination (HR)-mediated repair of programmed DNA double strand breaks (DSBs). As more DSBs are induced than COs, mechanisms are required to establish a regulated number of COs and to repair remaining intermediates as non-crossovers (NCOs). We show that the Caenorhabditis elegans RMI1 homolog-1 (RMH-1) functions during meiosis to promote both CO and NCO HR at appropriate chromosomal sites. RMH-1 accumulates at CO sites, dependent on known pro-CO factors, and acts to promote CO designation and enforce the CO outcome of HR-intermediate resolution. RMH-1 also localizes at NCO sites and functions in parallel with SMC-5 to antagonize excess HR-based connections between chromosomes. Moreover, RMH-1 also has a major role in channeling DSBs into an NCO HR outcome near the centers of chromosomes, thereby ensuring that COs form predominantly at off-center positions.

Dosage Compensation and the Distribution of Sex-Biased Gene Expression in Drosophila: Considerations and Genomic Constraints.

Several studies in Drosophila have shown a paucity of male-biased genes (i.e., genes that express higher in males than in females) on the X chromosome. Dosage compensation (DC) is a regulatory mechanism of gene expression triggered in males that hypertranscribes the X-linked genes to the level of transcription in females. There are currently two different hypotheses about the effects of DC on the distribution of male-biased genes: (1) it might limit male-expression level, or (2) it might interfere with the male upregulation of gene expression. Here, we used previously published gene expression datasets to reevaluate both hypotheses and introduce a mutually exclusive prediction that helped us to reject the hypothesis that the paucity of male-biased genes in the X chromosome is due to a limit in the male-expression level. Our analysis also uncovers unanticipated details about how DC interferes with the genomic distribution of both, male-biased and female-biased genes. We suggest that DC actually interferes with female downregulation of gene expression and not male upregulation, as previously suggested.

Relocation facilitates the acquisition of short cis-regulatory regions that drive the expression of retrogenes during spermatogenesis in Drosophila.

Retrogenes are functional processed copies of genes that originate via the retrotranscription of an mRNA intermediate and often exhibit testis-specific expression. Although this expression pattern appears to be favored by selection, the origin of such expression bias remains unexplained. Here, we study the regulation of two young testis-specific Drosophila retrogenes, Dntf-2r and Pros28.1A, using genetic transformation and the enhanced green fluorescent protein reporter gene in Drosophila melanogaster. We show that two different short (<24 bp) regions upstream of the transcription start sites (TSSs) act as testis-specific regulatory motifs in these genes. The Dntf-2r regulatory region is similar to the known ß2 tubulin 14-bp testis motif (ß2-tubulin gene upstream element 1 [ß2-UE1]). Comparative sequence analyses reveal that this motif was already present before the Dntf-2r insertion and was likely driving the transcription of a noncoding RNA. We also show that the ß2-UE1 occurs in the regulatory regions of other testis-specific retrogenes, and is functional in either orientation. In contrast, the Pros28.1A testes regulatory region in D. melanogaster appears to be novel. Only Pros28.1B, an older paralog of the Pros28.1 gene family, seems to carry a similar regulatory sequence. It is unclear how the Pros28.1A regulatory region was acquired in D. melanogaster, but it might have evolved de novo from within a region that may have been preprimed for testes expression. We conclude that relocation is critical for the evolutionary origin of male germline-specific cis-regulatory regions of retrogenes because expression depends on either the site of the retrogene insertion or the sequence changes close to the TSS thereafter. As a consequence we infer that positive selection will play a role in the evolution of these regulatory regions and can often act from the moment of the retrocopy insertion.

1.688 g/cm(3) satellite-related repeats: a missing link to dosage compensation and speciation.

Despite the important progress that has been made on dosage compensation (DC), a critical link in our understanding of the X chromosome recognition mechanisms is still missing. Recent studies in Drosophila indicate that the missing link could be a family of DNA repeats populating the euchromatin of the X chromosome. In this opinion article, I discuss how these findings add a new fresh twist on the DC problem. In the following sections, I first summarize our understanding of DC in Drosophila and integrate these recent discoveries into our knowledge of the X chromosome recognition problem. Next, I introduce a model according to which, 1.688 g/cm(3) satellite-related (SR) repeats would be the primary recognition elements for the dosage compensation complex. Contrary to the current belief, I suggest that the DC system in Drosophila is not conserved and static, but it is continuously co-evolving with the target SR repeats. The potential role of the SR repeats in hybrid incompatibilities and speciation is also discussed.

A sequence motif enriched in regions bound by the Drosophila dosage compensation complex.

BACKGROUND: In Drosophila melanogaster, dosage compensation is mediated by the action of the dosage compensation complex (DCC). How the DCC recognizes the fly X chromosome is still poorly understood. Characteristic sequence signatures at all DCC binding sites have not hitherto been found. RESULTS: In this study, we compare the known binding sites of the DCC with oligonucleotide profiles that measure the specificity of the sequences of the D. melanogaster X chromosome. We show that the X chromosome regions bound by the DCC are enriched for a particular type of short, repetitive sequences. Their distribution suggests that these sequences contribute to chromosome recognition, the generation of DCC binding sites and/or the local spreading of the complex. Comparative data indicate that the same sequences may be involved in dosage compensation in other Drosophila species. CONCLUSIONS: These results offer an explanation for the wild-type binding of the DCC along the Drosophila X chromosome, contribute to delineate the forces leading to the establishment of dosage compensation and suggest new experimental approaches to understand the precise biochemical features of the dosage compensation system.

A-to-I RNA Editing Uncovers Hidden Signals of Adaptive Genome Evolution in Animals.

In animals, the most common type of RNA editing is the deamination of adenosines (A) into inosines (I). Because inosines basepair with cytosines (C), they are interpreted as guanosines (G) by the cellular machinery and genomically encoded G alleles at edited sites mimic the function of edited RNAs. The contribution of this hardwiring effect on genome evolution remains obscure. We looked for population genomics signatures of adaptive evolution associated with A-to-I RNA edited sites in humans and Drosophila melanogaster. We found that single nucleotide polymorphisms at edited sites occur 3 (humans) to 15 times (Drosophila) more often than at unedited sites, the nucleotide G is virtually the unique alternative allele at edited sites and G alleles segregate at higher frequency at edited sites than at unedited sites. Our study reveals that a significant fraction of coding synonymous and nonsynonymous as well as silent and intergenic A-to-I RNA editing sites are likely adaptive in the distantly related human and Drosophila lineages.

Global patterns of sequence evolution in Drosophila.

BACKGROUND: Sequencing of the genomes of several Drosophila allows for the first precise analyses of how global sequence patterns change among multiple, closely related animal species. A basic question is whether there are characteristic features that differentiate chromosomes within a species or between different species. RESULTS: We explored the euchromatin of the chromosomes of seven Drosophila species to establish their global patterns of DNA sequence diversity. Between species, differences in the types and amounts of simple sequence repeats were found. Within each species, the autosomes have almost identical oligonucleotide profiles. However, X chromosomes and autosomes have, in all species, a qualitatively different composition. The X chromosomes are less complex than the autosomes, containing both a higher amount of simple DNA sequences and, in several cases, chromosome-specific repetitive sequences. Moreover, we show that the right arm of the X chromosome of Drosophila pseudoobscura, which evolved from an autosome 10 - 18 millions of years ago, has a composition which is identical to that of the original, left arm of the X chromosome. CONCLUSION: The consistent differences among species, differences among X chromosomes and autosomes and the convergent evolution of X and neo-X chromosomes demonstrate that strong forces are acting on drosophilid genomes to generate peculiar chromosomal landscapes. We discuss the relationships of the patterns observed with differential recombination and mutation rates and with the process of dosage compensation.

UVPAR: fast detection of functional shifts in duplicate genes.

BACKGROUND: The imprint of natural selection on gene sequences is often difficult to detect. A plethora of methods have been devised to detect genetic changes due to selective processes. However, many of those methods depend heavily on underlying assumptions regarding the mode of change of DNA sequences and often require sophisticated mathematical treatments that made them computationally slow. The development of fast and effective methods to detect modifications in the selective constraints of genes is therefore of great interest. RESULTS: We describe UVPAR, a program designed to quickly test for changes in the functional constraints of duplicate genes. Starting with alignments of the proteins encoded by couples of duplicate genes in two different species, UVPAR detects the regions in which modifications of the functional constraints in the paralogs occurred since both species diverged. Sequences can be analyzed with UVPAR in just a few minutes on a standard PC computer. To demonstrate the power of the program, we first show how the results obtained with UVPAR compare to those based on other approaches, using data for vertebrate Hox genes. We then describe a comprehensive study of the RBR family of ubiquitin ligases in which we have performed 529 analyses involving 14 duplicate genes in seven model species. A significant increase in the number of functional shifts was observed for the species Danio rerio and for the gene Ariadne-2. CONCLUSION: These results show that UVPAR can be used to generate sensitive analyses to detect changes in the selection constraints acting on paralogs. The high speed of the program allows its application to genome-scale analyses.

Recurrent turnover of chromosome-specific satellites in Drosophila.

Repetitive DNA are DNA sequences that are repeated multiple times in the genome and normally considered nonfunctional. Several studies predict that the rapid evolution of chromosome-specific satellites led to hybrid incompatibilities and speciation. Interestingly, in Drosophila, the X and dot chromosomes share a unique and noteworthy property: They are identified by chromosome-specific binding proteins and they are particularly involved in genetic incompatibilities between closely related species. Here, I show that the X and dot chromosomes are overpopulated by certain repetitive elements that undergo recurrent turnover in Drosophila species. The portion of the X and dot chromosomes covered by such satellites is up to 52 times and 44 times higher than in other chromosomes, respectively. In addition, the newly evolved X chromosome in D. pseudoobscura (the chromosomal arm XR) has been invaded by the same satellite that colonized the ancestral X chromosome (chromosomal arm XL), whereas the autosomal homologs in other species remain mostly devoid of satellites. Contrarily, the Müller element F in D. ananassae, homolog to the dot chromosome in D. melanogaster, has no overrepresented DNA sequences compared with any other chromosome. The biology and evolutionary patterns of the characterized satellites suggest that they provide both chromosomes with some kind of structural identity and are exposed to natural selection. The rapid satellite turnover fits some speciation models and may explain why these two chromosomes are typically involved in hybrid incompatibilities.

SNP2GO: functional analysis of genome-wide association studies.

Genome-wide association studies (GWAS) are designed to identify the portion of single-nucleotide polymorphisms (SNPs) in genome sequences associated with a complex trait. Strategies based on the gene list enrichment concept are currently applied for the functional analysis of GWAS, according to which a significant overrepresentation of candidate genes associated with a biological pathway is used as a proxy to infer overrepresentation of candidate SNPs in the pathway. Here we show that such inference is not always valid and introduce the program SNP2GO, which implements a new method to properly test for the overrepresentation of candidate SNPs in biological pathways.

Intralocus sexual conflict resolved through gene duplication.

Gene duplication is mainly recognized by its primary role in the origin of new genes and functions. However, the idea that gene duplication can be a central player in resolving sexual genetic conflicts through its potential to generate sex-biased and sex-specifically expressed genes, has been almost entirely overlooked. We review recent data and theory that support gene duplication as a theoretically predicted and experimentally supported means of resolving intralocus sexual antagonism. We believe that this role is probably the consequence of sexual conflict for housekeeping genes that are required in males and females, and which are expressed in sexually dimorphic tissues (i.e. where sexually antagonistic selection is exerted). We think that these genes cannot evolve tissue-specific expression unless they duplicate.

Gene duplication and the genome distribution of sex-biased genes.

In species that have two sexes, a single genome encodes two morphs, as each sex can be thought of as a distinct morph. This means that the same set of genes are differentially expressed in the different sexes. Many questions emanate from this statement. What proportion of genes contributes to sexual dimorphism? How do they contribute to sexual dimorphism? How is sex-biased expression achieved? Which sex and what tissues contribute the most to sex-biased expression? Do sex-biased genes have the same evolutionary patterns as nonbiased genes? We review the current data on sex-biased expression in species with heteromorphic sex chromosomes and comment on the most important hypotheses suggested to explain the origin, evolution, and distribution patterns of sex-biased genes. In this perspective we emphasize how gene duplication serves as an important molecular mechanism to resolve genomic clashes and genetic conflicts by generating sex-biased genes, often sex-specific genes, and contributes greatly to the underlying genetic basis of sexual dimorphism.

Analyses of nuclearly encoded mitochondrial genes suggest gene duplication as a mechanism for resolving intralocus sexually antagonistic conflict in Drosophila.

Gene duplication is probably the most important mechanism for generating new gene functions. However, gene duplication has been overlooked as a potentially effective way to resolve genetic conflicts. Here, we analyze the entire set of Drosophila melanogaster nuclearly encoded mitochondrial duplicate genes and show that both RNA- and DNA-mediated mitochondrial gene duplications exhibit an unexpectedly high rate of relocation (change in location between parental and duplicated gene) as well as an extreme tendency to avoid the X chromosome. These trends are likely related to our observation that relocated genes tend to have testis-specific expression. We also infer that these trends hold across the entire Drosophila genus. Importantly, analyses of gene ontology and functional interaction networks show that there is an overrepresentation of energy production-related functions in these mitochondrial duplicates. We discuss different hypotheses to explain our results and conclude that our findings substantiate the hypothesis that gene duplication for male germline function is likely a mechanism to resolve intralocus sexually antagonistic conflicts that we propose are common in testis. In the case of nuclearly encoded mitochondrial duplicates, our hypothesis is that past sexually antagonistic conflict related to mitochondrial energy function in Drosophila was resolved by gene duplication.

Fast comparison of DNA sequences by oligonucleotide profiling.

BACKGROUND: The comparison of DNA sequences is a traditional problem in genomics and bioinformatics. Many new opportunities emerge due to the improvement of personal computers, allowing the implementation of novel strategies of analysis. FINDINGS: We describe a new program, called UVWORD, which determines the number of times that each DNA word present in a sequence (target) is found in a second sequence (source), a procedure that we have called oligonucleotide profiling. On a standard computer, the user may search for words of a size ranging from k = 1 to k = 14 nucleotides. Average counts for groups of contiguous words may also be established. The rate of analysis on standard computers is from 3.4 (k = 14) to 16 millions of words per second (1