AI algorithm combined with RNA editing-based blood biomarkers to discriminate bipolar from major depressive disorders in an external validation multicentric cohort

Bipolar disorder (BD) is a leading cause of disability worldwide, as it can lead to cognitive and functional impairment and premature mortality. The first episode of BD is usually a depressive episode and is often misdiagnosed as major depressive disorder (MDD). Growing evidence indicates that peripheral immune activation and inflammation are involved in the pathophysiology of BD and MDD. Recently, by developing a panel of RNA editing-based blood biomarkers able to discriminate MDD from depressive BD, we have provided clinicians a new tool to reduce the misdiagnosis delay observed in patients suffering from BD. The present study aimed at validating the diagnostic value of this panel in an external independent multicentric Switzerland-based cohort of 143 patients suffering from moderate to major depression. The RNA-editing based blood biomarker (BMK) algorithm developped allowed to accurately discriminate MDD from depressive BD in an external cohort, with high accuracy, sensitivity and specificity values (82.5 %, 86.4 % and 80.8 %, respectively). These findings further confirm the important role of RNA editing in the physiopathology of mental disorders and emphasize the possible clinical usefulness of the biomarker panel for optimization treatment delay in patients suffering from BD.

Illuminating the Function of the Orphan Transporter, SLC22A10 in Humans and Other Primates

SLC22A10 is classified as an orphan transporter with unknown substrates and function. Here we describe the discovery of the substrate specificity and functional characteristics of SLC22A10. The human SLC22A10 tagged with green fluorescent protein was found to be absent from the plasma membrane, in contrast to the SLC22A10 orthologs found in great apes. Estradiol-17β-glucuronide accumulated in cells expressing great ape SLC22A10 orthologs (over 4-fold, p<0.001). In contrast, human SLC22A10 displayed no uptake function. Sequence alignments revealed two amino acid differences including a proline at position 220 of the human SLC22A10 and a leucine at the same position of great ape orthologs. Site-directed mutagenesis yielding the human SLC22A10-P220L produced a protein with excellent plasma membrane localization and associated uptake function. Neanderthal and Denisovan genomes show human-like sequences at proline 220 position, corroborating that SLC22A10 were rendered nonfunctional during hominin evolution after the divergence from the pan lineage (chimpanzees and bonobos). These findings demonstrate that human SLC22A10 is a unitary pseudogene and was inactivated by a missense mutation that is fixed in humans, whereas orthologs in great apes transport sex steroid conjugates.

Illuminating the Function of the Orphan Transporter, SLC22A10 in Humans and Other Primates

SLC22A10 is classified as an orphan transporter with unknown substrates and function. Here we describe the discovery of the substrate specificity and functional characteristics of SLC22A10. The human SLC22A10 tagged with green fluorescent protein was found to be absent from the plasma membrane, in contrast to the SLC22A10 orthologs found in great apes. Estradiol-17β-glucuronide accumulated in cells expressing great ape SLC22A10 orthologs (over 4-fold, p<0.001). In contrast, human SLC22A10 displayed no uptake function. Sequence alignments revealed two amino acid differences including a proline at position 220 of the human SLC22A10 and a leucine at the same position of great ape orthologs. Site-directed mutagenesis yielding the human SLC22A10-P220L produced a protein with excellent plasma membrane localization and associated uptake function. Neanderthal and Denisovan genomes show human-like sequences at proline 220 position, corroborating that SLC22A10 were rendered nonfunctional during hominin evolution after the divergence from the pan lineage (chimpanzees and bonobos). These findings demonstrate that human SLC22A10 is a unitary pseudogene and was inactivated by a missense mutation that is fixed in humans, whereas orthologs in great apes transport sex steroid conjugates.

Genome assemblies of three closely related leaf beetle species (Galerucella spp.)

Galerucella (Coleoptera: Chrysomelidae) is a leaf beetle genus that has been extensively used for ecological and evolutionary studies. It has also been used as biological control agent against invading purple loosestrife in North America, with large effects on biodiversity. Here, we report genome assembly and annotation of three closely related Galerucella species: G. calmariensis, G. pusilla, and G. tenella. The three assemblies have a genome size ranging from 460 to 588 Mbp, with N50 from 31,588 to 79,674 kbp, containing 29,202 to 40,929 scaffolds. Using an ab initio evidence-driven approach, 30,302 to 33,794 protein-coding genes were identified and functionally annotated. These draft genomes will contribute to the understanding of host-parasitoid interactions, evolutionary comparisons of leaf beetle species and future population genomics studies.

Methods to Identify and Study the Evolution of Pseudogenes Using a Phylogenetic Approach

The discovery that pseudogenes are involved in important biological processes has excited enthusiasm and increased the research interest on them. An accurate detection and analysis of pseudogenes can be achieved using comparative methods, but only the use of phylogenetic tools can provide accurate information about their birth, their evolution and their death, hence about the impact that they have on genes and genomes. Here, phylogenetic methods that allow for studying pseudogene history are described.

Genome assembly of the basket willow, Salix viminalis, reveals earliest stages of sex chromosome expansion

BACKGROUND

Sex chromosomes have evolved independently multiple times in eukaryotes and are therefore considered a prime example of convergent genome evolution. Sex chromosomes are known to emerge after recombination is halted between a homologous pair of chromosomes, and this leads to a range of non-adaptive modifications causing gradual degeneration and gene loss on the sex-limited chromosome. However, the proximal causes of recombination suppression and the pace at which degeneration subsequently occurs remain unclear.

RESULTS

Here, we use long- and short-read single-molecule sequencing approaches to assemble and annotate a draft genome of the basket willow, Salix viminalis, a species with a female heterogametic system at the earliest stages of sex chromosome emergence. Our single-molecule approach allowed us to phase the emerging Z and W haplotypes in a female, and we detected very low levels of Z/W single-nucleotide divergence in the non-recombining region. Linked-read sequencing of the same female and an additional male (ZZ) revealed the presence of two evolutionary strata supported by both divergence between the Z and W haplotypes and by haplotype phylogenetic trees. Gene order is still largely conserved between the Z and W homologs, although the W-linked region contains genes involved in cytokinin signaling regulation that are not syntenic with the Z homolog. Furthermore, we find no support across multiple lines of evidence for inversions, which have long been assumed to halt recombination between the sex chromosomes.

CONCLUSIONS

Our data suggest that selection against recombination is a more gradual process at the earliest stages of sex chromosome formation than would be expected from an inversion and may result instead from the accumulation of transposable elements. Our results present a cohesive understanding of the earliest genomic consequences of recombination suppression as well as valuable insights into the initial stages of sex chromosome formation and regulation of sex differentiation.

Genome assembly of the basket willow, Salix viminalis, reveals earliest stages of sex chromosome expansion

BACKGROUND

Sex chromosomes have evolved independently multiple times in eukaryotes and are therefore considered a prime example of convergent genome evolution. Sex chromosomes are known to emerge after recombination is halted between a homologous pair of chromosomes, and this leads to a range of non-adaptive modifications causing gradual degeneration and gene loss on the sex-limited chromosome. However, the proximal causes of recombination suppression and the pace at which degeneration subsequently occurs remain unclear.

RESULTS

Here, we use long- and short-read single-molecule sequencing approaches to assemble and annotate a draft genome of the basket willow, Salix viminalis, a species with a female heterogametic system at the earliest stages of sex chromosome emergence. Our single-molecule approach allowed us to phase the emerging Z and W haplotypes in a female, and we detected very low levels of Z/W single-nucleotide divergence in the non-recombining region. Linked-read sequencing of the same female and an additional male (ZZ) revealed the presence of two evolutionary strata supported by both divergence between the Z and W haplotypes and by haplotype phylogenetic trees. Gene order is still largely conserved between the Z and W homologs, although the W-linked region contains genes involved in cytokinin signaling regulation that are not syntenic with the Z homolog. Furthermore, we find no support across multiple lines of evidence for inversions, which have long been assumed to halt recombination between the sex chromosomes.

CONCLUSIONS

Our data suggest that selection against recombination is a more gradual process at the earliest stages of sex chromosome formation than would be expected from an inversion and may result instead from the accumulation of transposable elements. Our results present a cohesive understanding of the earliest genomic consequences of recombination suppression as well as valuable insights into the initial stages of sex chromosome formation and regulation of sex differentiation.

The genomic footprint of sexual conflict

Genes with sex-biased expression show a number of unique properties and this has been seen as evidence for conflicting selection pressures in males and females, forming a genetic ‘tug-of-war’ between the sexes. However, we lack studies of taxa where an understanding of conflicting phenotypic selection in the sexes has been linked with studies of genomic signatures of sexual conflict. Here, we provide such a link. We used an insect where sexual conflict is unusually well understood, the seed beetle Callosobruchus maculatus, to test for molecular genetic signals of sexual conflict across genes with varying degrees of sex-bias in expression. We sequenced, assembled and annotated its genome and performed population resequencing of three divergent populations. Sex-biased genes showed increased levels of genetic diversity and bore a remarkably clear footprint of relaxed purifying selection. Yet, segregating genetic variation was also affected by balancing selection in weakly female-biased genes, while male-biased genes showed signs of overall purifying selection. Female-biased genes contributed disproportionally to shared polymorphism across populations, while male-biased genes, male seminal fluid protein genes and sex-linked genes did not. Genes showing genomic signatures consistent with sexual conflict generally matched life-history phenotypes known to experience sexually antagonistic selection in this species. Our results highlight metabolic and reproductive processes, confirming the key role of general life-history traits in sexual conflict.

Assembly and Analysis of the Genome Sequence of the Yeast Brettanomyces naardenensis CBS 7540

Brettanomyces naardenensis is a spoilage yeast with potential for biotechnological applications for production of innovative beverages with low alcohol content and high attenuation degree. Here, we present the first annotated genome of B. naardenensis CBS 7540. The genome of B. naardenensis CBS 7540 was assembled into 76 contigs, totaling 11,283,072 nucleotides. In total, 5168 protein-coding sequences were annotated. The study provides functional genome annotation, phylogenetic analysis, and discusses genetic determinants behind notable stress tolerance and biotechnological potential of B. naardenensis.

Chromosomal genome assembly of the ethanol production strain CBS 11270 indicates a highly dynamic genome structure in the yeast species Brettanomyces bruxellensis

Here, we present the genome of the industrial ethanol production strain Brettanomyces bruxellensis CBS 11270. The nuclear genome was found to be diploid, containing four chromosomes with sizes of ranging from 2.2 to 4.0 Mbp. A 75 Kbp mitochondrial genome was also identified. Comparing the homologous chromosomes, we detected that 0.32% of nucleotides were polymorphic, i.e. formed single nucleotide polymorphisms (SNPs), 40.6% of them were found in coding regions (i.e. 0.13% of all nucleotides formed SNPs and were in coding regions). In addition, 8,538 indels were found. The total number of protein coding genes was 4897, of them, 4,284 were annotated on chromosomes; and the mitochondrial genome contained 18 protein coding genes. Additionally, 595 genes, which were annotated, were on contigs not associated with chromosomes. A number of genes was duplicated, most of them as tandem repeats, including a six-gene cluster located on chromosome 3. There were also examples of interchromosomal gene duplications, including a duplication of a six-gene cluster, which was found on both chromosomes 1 and 4. Gene copy number analysis suggested loss of heterozygosity for 372 genes. This may reflect adaptation to relatively harsh but constant conditions of continuous fermentation. Analysis of gene topology showed that most of these losses occurred in clusters of more than one gene, the largest cluster comprising 33 genes. Comparative analysis against the wine isolate CBS 2499 revealed 88,534 SNPs and 8,133 indels. Moreover, when the scaffolds of the CBS 2499 genome assembly were aligned against the chromosomes of CBS 11270, many of them aligned completely, some have chunks aligned to different chromosomes, and some were in fact rearranged. Our findings indicate a highly dynamic genome within the species B. bruxellensis and a tendency towards reduction of gene number in long-term continuous cultivation.

Pervasive hybridizations in the history of wheat relatives

Cultivated wheats are derived from an intricate history of three genomes, A, B, and D, present in both diploid and polyploid species. It was recently proposed that the D genome originated from an ancient hybridization between the A and B lineages. However, this result has been questioned, and a robust phylogeny of wheat relatives is still lacking. Using transcriptome data from all diploid species and a new methodological approach, our comprehensive phylogenomic analysis revealed that more than half of the species descend from an ancient hybridization event but with a more complex scenario involving a different parent than previously thought-Aegilops mutica, an overlooked wild species-instead of the B genome. We also detected other extensive gene flow events that could explain long-standing controversies in the classification of wheat relatives.

EMBLmyGFF3: a converter facilitating genome annotation submission to European Nucleotide Archive

Objective

The state-of-the-art genome annotation tools output GFF3 format files, while this format is not accepted as submission format by the International Nucleotide Sequence Database Collaboration (INSDC) databases. Converting the GFF3 format to a format accepted by one of the three INSDC databases is a key step in the achievement of genome annotation projects. However, the flexibility existing in the GFF3 format makes this conversion task difficult to perform. Until now, no converter is able to handle any GFF3 flavour regardless of source.

Results

Here we present EMBLmyGFF3, a robust universal converter from GFF3 format to EMBL format compatible with genome annotation submission to the European Nucleotide Archive. The tool uses json parameter files, which can be easily tuned by the user, allowing the mapping of corresponding vocabulary between the GFF3 format and the EMBL format. We demonstrate the conversion of GFF3 annotation files from four different commonly used annotation tools: Maker, Prokka, Augustus and Eugene.

EMBLmyGFF3 is freely available at https://github.com/NBISweden/EMBLmyGFF3.

The genetic basis for ecological adaptation of the Atlantic herring revealed by genome sequencing

Ecological adaptation is of major relevance to speciation and sustainable population management, but the underlying genetic factors are typically hard to study in natural populations due to genetic differentiation caused by natural selection being confounded with genetic drift in subdivided populations. Here, we use whole genome population sequencing of Atlantic and Baltic herring to reveal the underlying genetic architecture at an unprecedented detailed resolution for both adaptation to a new niche environment and timing of reproduction. We identify almost 500 independent loci associated with a recent niche expansion from marine (Atlantic Ocean) to brackish waters (Baltic Sea), and more than 100 independent loci showing genetic differentiation between spring- and autumn-spawning populations irrespective of geographic origin. Our results show that both coding and non-coding changes contribute to adaptation. Haplotype blocks, often spanning multiple genes and maintained by selection, are associated with genetic differentiation.

The Bee Microbiome: Impact on Bee Health and Model for Evolution and Ecology of Host-Microbe Interactions

As pollinators, bees are cornerstones for terrestrial ecosystem stability and key components in agricultural productivity. All animals, including bees, are associated with a diverse community of microbes, commonly referred to as the microbiome. The bee microbiome is likely to be a crucial factor affecting host health. However, with the exception of a few pathogens, the impacts of most members of the bee microbiome on host health are poorly understood. Further, the evolutionary and ecological forces that shape and change the microbiome are unclear. Here, we discuss recent progress in our understanding of the bee microbiome, and we present challenges associated with its investigation. We conclude that global coordination of research efforts is needed to fully understand the complex and highly dynamic nature of the interplay between the bee microbiome, its host, and the environment. High-throughput sequencing technologies are ideal for exploring complex biological systems, including host-microbe interactions. To maximize their value and to improve assessment of the factors affecting bee health, sequence data should be archived, curated, and analyzed in ways that promote the synthesis of different studies. To this end, the BeeBiome consortium aims to develop an online database which would provide reference sequences, archive metadata, and host analytical resources. The goal would be to support applied and fundamental research on bees and their associated microbes and to provide a collaborative framework for sharing primary data from different research programs, thus furthering our understanding of the bee microbiome and its impact on pollinator health.

A universal genomic coordinate translator for comparative genomics

BACKGROUND

Genomic duplications constitute major events in the evolution of species, allowing paralogous copies of genes to take on fine-tuned biological roles. Unambiguously identifying the orthology relationship between copies across multiple genomes can be resolved by synteny, i.e. the conserved order of genomic sequences. However, a comprehensive analysis of duplication events and their contributions to evolution would require all-to-all genome alignments, which increases at N2 with the number of available genomes, N.

RESULTS

Here, we introduce Kraken, software that omits the all-to-all requirement by recursively traversing a graph of pairwise alignments and dynamically re-computing orthology. Kraken scales linearly with the number of targeted genomes, N, which allows for including large numbers of genomes in analyses. We first evaluated the method on the set of 12 Drosophila genomes, finding that orthologous correspondence computed indirectly through a graph of multiple synteny maps comes at minimal cost in terms of sensitivity, but reduces overall computational runtime by an order of magnitude. We then used the method on three well-annotated mammalian genomes, human, mouse, and rat, and show that up to 93% of protein coding transcripts have unambiguous pairwise orthologous relationships across the genomes. On a nucleotide level, 70 to 83% of exons match exactly at both splice junctions, and up to 97% on at least one junction. We last applied Kraken to an RNA-sequencing dataset from multiple vertebrates and diverse tissues, where we confirmed that brain-specific gene family members, i.e. one-to-many or many-to-many homologs, are more highly correlated across species than single-copy (i.e. one-to-one homologous) genes. Not limited to protein coding genes, Kraken also identifies thousands of newly identified transcribed loci, likely non-coding RNAs that are consistently transcribed in human, chimpanzee and gorilla, and maintain significant correlation of expression levels across species.

CONCLUSIONS

Kraken is a computational genome coordinate translator that facilitates cross-species comparisons, distinguishes orthologs from paralogs, and does not require costly all-to-all whole genome mappings. Kraken is freely available under LPGL from http://github.com/nedaz/kraken.

Impact of recurrent gene duplication on adaptation of plant genomes

BACKGROUND

Recurrent gene duplication and retention played an important role in angiosperm genome evolution. It has been hypothesized that these processes contribute significantly to plant adaptation but so far this hypothesis has not been tested at the genome scale.

RESULTS

We studied available sequenced angiosperm genomes to assess the frequency of positive selection footprints in lineage specific expanded (LSE) gene families compared to single-copy genes using a dN/dS-based test in a phylogenetic framework. We found 5.38% of alignments in LSE genes with codons under positive selection. In contrast, we found no evidence for codons under positive selection in the single-copy reference set. An analysis at the branch level shows that purifying selection acted more strongly on single-copy genes than on LSE gene clusters. Moreover we detect significantly more branches indicating evolution under positive selection and/or relaxed constraint in LSE genes than in single-copy genes.

CONCLUSIONS

In this - to our knowledge -first genome-scale study we provide strong empirical support for the hypothesis that LSE genes fuel adaptation in angiosperms. Our conservative approach for detecting selection footprints as well as our results can be of interest for further studies on (plant) gene family evolution.

Methods to study the occurrence and the evolution of pseudogenes through a phylogenetic approach

During the last few years, the study of pseudogenes has excited enthusiasm, because it has been proven that at least some of them are involved in important biological processes. An accurate detection and analysis of pseudogenes can be achieved using comparative methods, but only the use of phylogenetic tools can provide accurate information about their birth, their evolution and their death, hence about the impact that they have on genes and genomes. Here, phylogenetic methods that allow studying pseudogene history are described.

The chordate proteome history database

The chordate proteome history database (http://ioda.univ-provence.fr) comprises some 20,000 evolutionary analyses of proteins from chordate species. Our main objective was to characterize and study the evolutionary histories of the chordate proteome, and in particular to detect genomic events and automatic functional searches. Firstly, phylogenetic analyses based on high quality multiple sequence alignments and a robust phylogenetic pipeline were performed for the whole protein and for each individual domain. Novel approaches were developed to identify orthologs/paralogs, and predict gene duplication/gain/loss events and the occurrence of new protein architectures (domain gains, losses and shuffling). These important genetic events were localized on the phylogenetic trees and on the genomic sequence. Secondly, the phylogenetic trees were enhanced by the creation of phylogroups, whereby groups of orthologous sequences created using OrthoMCL were corrected based on the phylogenetic trees; gene family size and gene gain/loss in a given lineage could be deduced from the phylogroups. For each ortholog group obtained from the phylogenetic or the phylogroup analysis, functional information and expression data can be retrieved. Database searches can be performed easily using biological objects: protein identifier, keyword or domain, but can also be based on events, eg, domain exchange events can be retrieved. To our knowledge, this is the first database that links group clustering, phylogeny and automatic functional searches along with the detection of important events occurring during genome evolution, such as the appearance of a new domain architecture.

GLADX: an automated approach to analyze the lineage-specific loss and pseudogenization of genes

A well-established ancestral gene can usually be found, in one or multiple copies, in different descendant species. Sometimes during the course of evolution, all the representatives of a well-established ancestral gene disappear in specific lineages; such gene losses may occur in the genome by deletion of a DNA fragment or by pseudogenization. The loss of an entire gene family in a given lineage may reflect an important phenomenon, and could be due either to adaptation, or to a relaxation of selection that leads to neutral evolution. Therefore, the lineage-specific gene loss analyses are important to improve the understanding of the evolutionary history of genes and genomes. In order to perform this kind of study from the increasing number of complete genome sequences available, we developed a unique new software module called GLADX in the DAGOBAH framework, based on a comparative genomic approach. The software is able to automatically detect, for all the species of a phylum, the presence/absence of a representative of a well-established ancestral gene, and by systematic steps of re-annotation, confirm losses, detect and analyze pseudogenes and find novel genes. The approach is based on the use of highly reliable gene phylogenies, of protein predictions and on the analysis of genomic mutations. All the evidence associated to evolutionary approach provides accurate information for building an overall view of the evolution of a given gene in a selected phylum. The reliability of GLADX has been successfully tested on a benchmark analysis of 14 reported cases. It is the first tool that is able to fully automatically study the lineage-specific losses and pseudogenizations. GLADX is available at http://ioda.univ-provence.fr/IodaSite/gladx/.

SFRP2 expression in rabbit myogenic progenitor cells and in adult skeletal muscles

Satellite cells derived from fast- and slow-twitch muscles have different properties in culture. We have used the differential display technique to retrieve genes differentially expressed in fast- and slow-twitch muscle satellite cell cultures. Amongst these genes we have identified, cloned, sequenced and studied the expression in muscle of rabbit secreted frizzled related protein 2 (SFRP2) mRNA, whose importance in cell fate determination has been well documented. It has been shown that SFRP2 is widely expressed in the developing embryo but its expression in the adult is much more restricted. We show that primary cultures of satellite cells from adult rabbit fast- and slow-twitch muscles strongly and differentially express SFRP2 mRNA. Embryonic rabbit muscle cell primary cultures also strongly express SFRP2 mRNA whereas the myoblast C2.7 cell line shows little expression. We also studied SFRP2 mRNA expression in growing, regenerating and denervated muscles. Embryonic rabbit muscles express SFRP2 mRNA but this rapidly falls off after birth. In adult rabbit muscles SFRP2 mRNA is detected within 1 day of either muscle damage or denervation. Thereafter the SFRP2 mRNA expression profiles are different for fast- and slow-twitch muscle. The function of SFRP2 in muscle is unknown but its putative activity as a Wnt antagonist and its precocious expression after muscle damage suggest a role in satellite cell activation.

Effects of thyroid state alterations in ovo on the plasma levels of thyroid hormones and on the populations of fibers in the plantaris muscle of male and female chickens

Propylthiouracil (PTU), thyroxine (T4) or thyreoliberin (TRH) were injected in ovo to modify the thyroid state of chicken embryos. Significant sexual differences were observed in the effects of these treatments on the plasma concentrations of thyroid hormones and on plantaris muscle characteristics (DNA, RNA, populations of muscle fibers) in 3- and 35-day old male and female chickens. The T4 plasma concentration is lower in control males; it is decreased in PTU treated females and in the T4 treated females at 35 days. The T3 plasma concentration is lowered at 3 days in all treated chickens and also at 35 days in the TRH treated animals. The slow (STnO) and the fast (FTOG) fibers of the plantaris are always more numerous in males. In controls, the number of FTOG fibers remains steady between 3 and 35 days; at the same time, the number of STnO fibers rises in males only. Both PTU and T4 treatments increase the number of the FTOG and the STnO fibers respectively before and after the 3rd day. TRH treatment increases the number of STnO fibers at 3 and 35 days in males, but reduces it at 3 days in females. Thus changes in the number of FTOG fibers can be induced during in ovo myogenesis, whereas the number of STnO fibers may increase after hatching.

Postnatal changes in insulin binding in slow and fast-twitch rabbit skeletal muscles

Changes of insulin binding characteristics (number of receptors, Kd) were studied in the semimembranosus proprius (SMP) and psoas major (PM) muscle from birth to adult stage. The Kd was about 0.15 10(-9) M in both muscles and did not change with age. The numbers of receptors were similar in both muscles at birth and changed differently thereafter to reach 1.3 fmoles per mg of muscle in the PM and 5.6 in the SMP muscle.

Ontogenesis of triiodothyronine nuclear receptors in three skeletal muscles in male and female chicks

The ontogenesis of nuclear triiodothyronine receptors was determined in the pectoralis (alpha W fibers: fast contracting, glycolytic metabolism), adductor brevis (alpha R fibers: fast contracting, oxido-glycolytic metabolism) and adductor magnus (beta R fibers: slow contracting, oxidative metabolism), muscles of male and female chickens at 18 days in ovo and 0, 6, and 30 days ex ovo. In the fast muscles (adductor brevis and pectoralis major), the T3 receptor number decreases from the 18th day of incubation to hatching or the 6th day after hatching, respectively, and then increases. In the slow muscle (adductor magnus), the T3 receptor number increases from 18 days in ovo to hatching and then decreases. At 30 days after hatching, the number of T3 receptors was higher in the fast muscles than in the slow one. A comparison of the two fast muscles reveals that the number of T3 receptors was more elevated in the pectoralis (glycolytic) fibers than in the adductor brevis (oxido-glycolytic) fibers. An overall test of significance showed a higher number of T3 nuclear receptors in muscles from females than from males.

Perinatal age and sex variations of the triiodothyronine nuclear receptors in the chick pectoralis major muscle

The ontogenesis of the nuclear triiodothyronine receptors was determined in the pectoralis muscle of male and female chicken at 18 days in ovo and 0, 3, 6, 14 and 35 days ex ovo. Our results show the presence of putative T3 nuclear receptors with equilibrium dissociation constant values (Kd approximately 5.50 X 10(-10) M) in good agreement with these reported in other tissues. The T3 receptor numbers decrease from 18 days incubation to 6-day-old animals, then increase until 35 days of age. Compared to the already reported levels of thyroid hormone in plasma and tissues, the results seem to correspond to a down-regulation of the muscle T3 receptors. The nuclear binding capacity of T3 was higher in females than in males, which could be related to the known effects of various sex steroid hormones on the T4 to T3 tissue conversion.

Autoradiographic study of neurogenesis in the duck olfactory bulb

Neurogenesis was studied in the duck olfactory bulb by injection of tritiated thymidine into the eggs at 53 h and at the 3rd, 5th, 8th, 10th, 12th, 14th and 18th days of incubation. The large neurons appear before the small ones: the mitral cells arise between embryonic day 3 (E3) and E5, the tufted cells between E5 and E8 and the granular cells between E12 and E14. The periglomerular cells could be formed after E18. The order of appearance of this 4 main neurons of the duck olfactory bulb is the same as that in the mouse. All the neurons, except maybe for the periglomerular cells, are principally formed before the hatching of the duckling and the olfactory sense seems to have acquired most of its principal functional aptitudes at this moment.

Quantitative study of synapse formation in the duck olfactory bulb

Synaptic emergence and development in the duck olfactory bulb was quantitatively studied by electron microscopy from the 14th day of incubation (E 14) to the adult stage. Overall synaptic density in this bulb grew considerably during the last weeks of embryonic life and the first postnatal week. The pattern of synaptic density development was similar in the four main architectonic layers of the bulb. However, lower density values were observed in the mitral and inner granule cell layers. In the glomerular layer (GL), axodendritic synapse density was always higher than dendrodentritic synapse density. In the external plexiform layer, most synapses were dendrodendritic and were established between the gemmules of the granule cells (GC) and the dendrites of the mitral cells (MC) or tufted cells (TC). Synapses established by MC and TC on GC gemmules, or by GC on MC and TC dendrites had densities very similar to each other at all the stages studied. Reciprocal synapses already appeared at E 14; their density grew until a week after birth (P7) and thereafter remained stable. In the internal granular layer, the density of asymmetrical synapses was always higher than that of symmetrical synapses. Excitatory synapses formed earlier on MC and TC than inhibitory synapses. The ratio of inhibitory-to-excitatory synapses rose rapidly after birth, reaching 2.5 in the adult duck. The density of excitatory synapses received by granule cells was as high in the external plexiform layer as in the inner granule layer, at all stages of GC development. However, the ratio of received-to-formed synapses fell in these cells from 8.42 at E 14 to 2 after birth. These results are discussed as a function of the evolution of the different synaptic balances during olfactory bulb development. Synaptic development in the duck olfactory bulb at birth is relatively close to the adult state. It appears sufficiently advanced to enable the olfactory system to function in a way compatible with the relatively independent behavior displayed by the duckling.

Cerebellar tRNA methyltransferases: a developmental study

Developmental patterns of homologous and heterologous tRNA methylation by cerebellar tRNA methyltransferases are described. The study revealed that: (a) homologous tRNA methylation results in the predominant formation of N2-methylguanine and 1-methyladenine; (b) tRNA methyltransferase of bulk-isolated Purkinje and granule cells methylate E. coli tRNAglu2 in vitro in a characteristic manner, and (c) the methylation of 8-day-old cerebellar, cortical and hepatic tRNA in vivo yields tRNAs containing different proportions of methylated bases. The findings suggest that the presumably cell-specific populations of cerebellar tRNA methyltransferases continue to alter their substrate recognition characteristics up to and beyond the first month of post-natal life.

Age-dependent changes in the specificity of tRNA methyltransferases in the cerebellum of the icteric and nonicteric Gunn rat

The activity of tRNA methyltransferases present in the cerebellum of 6- and 21-day-old nonicteric and icteric Gunn rats was compared using purified E. coli tRNAs as substrates. At 6 days the tRNA methyltransferases of the icteric animals were significantly more effective in methylating tRNAGlu2 and tRNAPhe than were those of their nonicteric counterparts. This relationship reversed itself at 21 days. The action of the tRNA methyltransferases from the 6-day-old icteric animals led to higher proportions of 1-methyladenine in tRNAGlu2 and tRNAPhe than were obtained using the corresponding enzymes of the nonicteric animals. The proportion of N2-methylguanine was also higher, yet only in tRNAfMet and not in tRNAPhe. The study reveals much more extensive fluctuations in the activity and in the substrate recognition specificity among the cerebellar tRNA methyltransferases of the icteric than among those of the nonicteric controls during the crucial 6--21 day period of cerebellar development.

[Effects of thyroid hormones and heat value restriction of food intake on the glial surrounding and soma development of Purkinje cell (author's transl)]

Hyper- and hypothyroidism repercussions on soma, nucleus and cytoplasm increases were studied by electron microscopy on 7-, 14-, 21-, and 35-day-old rats. Adult normal animals were compared with adult ones made hypothyroid until they were 35 days old. Also heat value restriction of food intake effects were compared with hypothyroid ones at 14 and 35 days. Hyperthyroidism accelerated the soma and cytoplasm size increase as early as 14 days, and the nucleus size increase as early as 21 days. It did not change the nucleo-cytoplasmic ratio (N/P) markedly, except that maximal value of this ratio was reached earlier than in normal animals. Heat value restriction of food intake led to a transitory soma size decrease at 14 days and a high nucleus size increase. This diet did not change markedly either cytoplasm size or N/P ratio value. Hypothyroidism slackened the rate of the soma, nucleus and cytoplasm size increase during the third postnatal week especially. Beyond, these structures went on increasing and their size became greater than normal in adult hypothyroid animals. N/P ratio was always superior to normal. Hypothyroidism led to a high volumetric and linear density of Purkinje cell soma glial surrounding. Hyperthyroidism caused a slight increase of these parameters which were not greatly changed by heat value restriction of food intake.

Correction of the biochemical effects of neonatal hypothyroidism by daily low doses of thyroxine. Comparative effects of hyperthyroidism and these corrections

The purpose of the present communication was to study the corrective effects of low daily thyroxine doses, on the cerebellum biochemical maturation in propylthiouracile (PTU)-treated rats during the early postnatal life. The corrected hypothyroid animals were compared to the normal, hypo- and hyperthyroid ones. The protein, RNA and DNA cerebellar contents were evaluated at 6, 10, 14, 18 and 35 days old animals. At all ages hypothyroidism and hyperthyroidism decreased cerebellar protein, RNA and DNA contents, except in 35-day-old hyperthyroid animals, where DNA content returned to normal level. In these two experimental groups, protein/DNA and RNA/DNA ratios were higher than those of controls at 10 days and lower at 35 days. In hypothyroid animals treated by corrective doses of T4, cerebellar protein, RNA and DNA contents and DNA concentration were not different from hyperthyroid animal values at all stages, while protein/DNA and RNA/DNA ratios were higher than those of hyperthyroid animals. Administration of physiological doses of T4 to hypothyroid animals led to the same effects as higher doses in normal animals. Thus, neonatal hypothyroidism seems to lower the sensitivity threshold of the cerebellum to thyroid hormone effects.

Variations au cours de la journée de l'incorporation in vivo de la leucine tritiée dans les protéines du cervelet et du cerveau du jeune rat normal et hypothyroïdien. Daily variations of the in vivo [3H] leucine incorporation into the cerebellar and cerebral proteins of the normal and hypothyroid young rat [(author's transl)]

In the normal and hypothyroid 6-day-old rat, the specific radioactivity (RSA) and the relative RSA (ratio of the RSA to the [3H] lecine concentration of the acido soluble phase) of the cerebral and cerebellar proteins, changes during the day synchronally. They show a maximum at 15.00 h and a minimum at 0.300 h. At all stages studied, these values are significantly lower in the hyothyroid animals than in normal ones.

[Repercussions of hyperthyroidism on the total cerebellar DNA contents in the rat at 6 and 35 days of age. Comparative effects of LT3 and DLT4 (author's transl)]

The total cerebellar proteins RNA and DNA contents from DLT4-and LT3-treated rats was studied at 6 and 35 days of age. The effect of injections of 5 microng/j of DLT4 is comparable to that of 25 microng of LT3 at birth, followed by 0.5 microng every 2 days. On the other hand, injection of 0.5 microng of LT3 every 3 days does not induce any significant modification of the total DNA contents in the cerebellum.

[Quantitative ultrastructural study of the perikaryon of the Purkinje cell and of the adjacent area in normal and hypothyroid rats aged 21 days]

The effects of neonatal hypothyroidism on synaptic organization, glial surrounding and cytoplasmic structures of the Purkinje cell perikaryon of the 21 days old rat were studied by electron microscopy. Hypothyroidism decreases the size of the perikaryon but does not change the nucleo-cytoplasmic ratio of the cell. At 21 days the axonal endings that make synapse on the Purkinje cell perikaryon, already show the adult morphological features and hypothyroidism does not change these. The general synaptic density on the Purkinje perikaryon is not significantly altered, but the cells of hypothyroid animals still recieve 1/3 of their axo-somatic synapses on somatic spines, whereas euthyroid animals have practically no synapses on somatic spines. Hypothyroidism leads the disappearance of the synchronism which normally exists between the translocation or resorption of the Purkinje cell somatic spines and the establishment of the basket cell synapses. The basket cell axons of the normal animals form synapses only on the smooth surfaces of the Purkinje cell perikaryon while they also establish it on the somatic spines of the hypothyroid animals. The density of the axon terminals of basket cells is decreased, while that of the endings of Purkinje cell axon collaterals and of climbing fibers are increased. Hypothyroidism produces an increase in the size of the glial sheath around the Purkinje perikaryon. It does not alter the proportion of the cytoplasmic area occupied by mitochondria, but in thyroid deficiency there is an increase in the numbers of mitochondria which are reduced in average size. The Golgi apparatus is only slightly affected. Thyroid defiency does not alter the density of the cytoplasmic agreggates of free ribosomes but there is a decrease in density of the ergastoplasm and a disorganization of the Nissl bodies.

[Repercussions of hypothyroidism on the synaptogenesis of the rat cerebellar cortex: quantitative study of the thyroid hormone effect according to the age (author's transl)]

The corrective action of Thyroxine on the deficit of the synaptic density of the molecular layer of the cerebellar cortex was studed quantitatively, in the rat made hypothyroid by propylthiouracile (P.T.U.). In the normal as in the hypothyroid rat, the increase of the synaptic density does not extend over the fifth postnatal week. In the PTU treated animals, during the 2 first postnatal weeks, the administration of 0,25 mug/d during the third and 0.50 mug/d during the fourth postnatal week brings the synaptic density back to normal. In the PTU treated animals, during the 5 postnatal weeks, the administration during a week only of 0.50 mug/d of LT4 between 1 and 14 days or, of 1 mug/d between 15 and 28 days, increases, but does not return to normal the synaptic density. On the contrary, the administration of 1 mug/d of LT4 during 1 or even 2 consecutive weeks 28 days later, remains without effect on the synaptic density. After the end of the fourth postnatal week, the deficit of the synaptic density becomes irreversible.