A preliminary genetic map in Solea senegalensis (Pleuronectiformes, Soleidae) using BAC-FISH and next-generation sequencing.

This article presents the first physical mapping carried out in the Senegalese sole (Solea senegalensis), an important marine fish species of Southern Europe. Eight probes were designated to pick up genes of interest in aquaculture (candidate genes) from a bacterial artificial chromosome (BAC) library using a method of rapid screening based on a 4-dimension PCR. Seven known and 3 unknown clones were isolated and labeled. The 10 BAC clones were used as probes to map the karyotype of the species by fluorescence in situ hybridization (FISH). Nine out of the 10 clones were localized in only 1 chromosome pair, whereas the remaining one hybridized on 2 chromosome pairs. The 2-color FISH experiments showed colocation of 4 probes in 2 chromosome pairs. In addition, 2-color FISH was carried out both with 5S rDNA and the BAC containing the lysozyme gene published previously. This first genetic map of the Senegalese sole represents a starting point for future studies of the sole genome. In addition, 7 out of the 10 BAC clones were sequenced using next-generation sequencing, and bioinformatic characterization of the sequences was carried out. Hence the anchoring of the sequences to specific chromosomes or chromosome arms is now possible, leading to an initial scaffold of the Senegalese sole genome.

High evolutionary dynamism in 5S rDNA of fish: state of the art.

The 5S ribosomal DNA (rDNA) consists of one transcriptional unit of about 120 base pairs, which is separated from the next unit by a non-transcribed spacer (NTS). The coding sequence and the NTS together form a repeat unit which can be found in hundreds to thousands of copies tandemly repeated in the genomes. The NTS regions seem to be subject to rapid evolution. The first general model of evolution of these multigene families was referred to as divergent evolution, based on studies using hemoglobin and myoglobin as model systems. Later studies showed that nucleotide sequences of different multigene family members are more closely related within species than between species. This observation led to a new model of multigene family evolution, termed concerted evolution. Another model of evolution, named the birth-and-death model, has been found to be more suitable to explain the long-term evolution of these multigene families. According to this model, new genes originate by successive duplications, and these new genes are either maintained for a long time or are lost, or else degenerate into pseudogenes. In this review we describe different sources of variability in the 5S rDNA genes observed in several distinct fish species. This variability is mainly referred to NTSs and includes the presence of other multigene families (mainly LINEs, SINEs, non-LTR retrotransposons, and U snRNA families). Different types of microsatellites have also been found to contribute to the increase of variability in this region. Our recent results suggest that horizontal transfer contributes to the increase of diversity in the NTSs of some species. Variability in the 5S rDNA coding region affecting the stability of the structure, but without effects on the function of the 5S rRNA, is also described. Retrotransposons seem to be responsible for the high dynamism of 5S rDNA, while microsatellites acting as recombination hot spots could stabilize a wide variety of unusual DNA structures, affecting DNA replication and enhancing or decreasing promoter activity in gene expression. The relationship between the high variability found at molecular level and the low variability found at chromosomal level is also discussed.

Comparative gene expression of gonadotropins (FSH and LH) and peptide levels of gonadotropin-releasing hormones (GnRHs) in the pituitary of wild and cultured Senegalese sole (Solea senegalensis) broodstocks.

The Senegalese sole (Solea senegalensis) is a valuable flatfish for aquaculture, but it presents important reproductive problems in captivity. Spawning is achieved by wild-caught breeders but cultured broodstocks fail to spawn spontaneously and, when they do, eggs are unfertilized. To gain knowledge on the physiological basis underlying this reproductive dysfunction, this study aimed at analyzing comparative hormone levels between wild and cultured broodstocks at the spawning season. The Senegalese sole gonadotropin (GTH) subunits, FSHbeta, LHbeta and GPalpha, were cloned and qualitative (in situ hybridization) and quantitative (real-time PCR) assays developed to analyze pituitary GTH gene expression. In females, FSHbeta and GPalpha mRNA levels were higher in wild than in cultured broodstocks, whereas in males all three subunits were highest in cultured. By ELISA, three GnRH forms were detected in the pituitary, displaying a relative abundance of GnRH2>GnRH1>GnRH3. All GnRHs were slightly more abundant in wild than cultured females, whereas no differences were observed in males. Plasma levels of vitellogenin and sex steroids were also analyzed. Results showed endocrine differences between wild and cultured broodstocks at the spawning period, which could be related to the endocrine failure of the reproductive axis in cultured breeders.

5S rDNA and U2 snRNA are linked in the genome of Crassostrea angulata and Crassostrea gigas oysters: does the (CT)n.(GA)n microsatellite stabilize this novel linkage of large tandem arrays?

The 5S rRNA genes from 2 species of the Ostreidae family, Crassostrea angulata and Crassostrea gigas, were molecularly characterized. The genes were amplified, cloned, and sequenced. The results revealed a 5S rDNA tandem array with a nucleotide sequence in an inverted position within the nontranscribed spacer region that corresponded to the U2 small nuclear RNA (snRNA) gene. The sequence analysis indicated that both genes could be functionally active. The presence of the microsatellite (CT)n x (GA)n at the 3' end of both genes and the possible involvement of concerted evolution are discussed.

Trisomy of the short stature homeobox-containing gene (SHOX), resulting from a duplication-deletion of the X chromosome.

The Turner syndrome (TS) is a complex disorder associated with almost invariant short stature and gonadal dysgenesis, as well as a variety of other major organ malformations. Recently, a homeobox-containing gene entitled short-stature homeobox-containing gene (SHOX), was isolated from a minimal short stature gene interval from the pseudoautosomal region of Xp (and Yp). Together with the demonstrable escape of SHOX from X-inactivation, this suggested SHOX to be a strong candidate gene for the short stature component of TS, and as SHOX haploinsufficiency appears to be the molecular basis of a mesomelic short statured skeletal dysplasia (Leri-Weill syndrome), this suggested that SHOX protein expression levels may confer a dosage effect on human stature. However, in this communication we report a normal statured female with gonadal dysgenesis, due to the inheritance of a recombinant duplication-deletion X-chromosome. The karyotype of the proband was 46,X,rec(X)dup(Xp)inv(X)(p11.22q21.2)mat and fluorescent in situ hybridization of her metaphases with a SHOX cosmid confirmed the proband to be trisomic for SHOX. This communication suggests the relationship between levels of SHOX expression and human stature to be more complex than envisaged previously. The presence of normal stature in our patient rather than tall stature is likely to represent the natural variation seen in patients with transcription factor disorders.

Music, cognition, culture, and evolution.

We seem able to define the biological foundations for our musicality within a clear and unitary framework, yet music itself does not appear so clearly definable. Music is different things and does different things in different cultures; the bundles of elements and functions that are music for any given culture may overlap minimally with those of another culture, even for those cultures where "music" constitutes a discrete and identifiable category of human activity in its own right. The dynamics of culture, of music as cultural praxis, are neither necessarily reducible, nor easily relatable, to the dynamics of our biologies. Yet music appears to be a universal human competence. Recent evolutionary theory, however, affords a means for exploring things biological and cultural within a framework in which they are at least commensurable. The adoption of this perspective shifts the focus of the search for the foundations of music away from the mature and particular expression of music within a specific culture or situation and on to the human capacity for musicality. This paper will survey recent research that examines that capacity and its evolutionary origins in the light of a definition of music that embraces music's multifariousness. It will be suggested that music, like speech, is a product of both our biologies and our social interactions; that music is a necessary and integral dimension of human development; and that music may have played a central role in the evolution of the modern human mind.

Neurofibromatosis pseudogene amplification underlies euchromatic cytogenetic duplications and triplications of proximal 15q.

Cytogenetically visible interstitial duplications of proximal 15q, which lack the Prader-Willi Angelman critical region (PWACR) frequently segregate in families without phenotypic effect, but the nature of the extra euchromatin has remained unclear. We used comparative genome hybridisation to confirm that the extra material in a cytogenetic triplication originated from proximal 15q. A PAC clone containing sequences specific for the type-1 neurofibromatosis (NF-1) pseudogenes, which map to 15q11.2, hybridised along the length of the enlarged region between the PWACR and the centromere. Computerised measurement of the fluorescent signal from the enlarged and normal chromosomes gave an average ratio of 9.85:1, consistent with amplification. In a second family, an amplified P1-4 signal co-segregated with a cytogenetic duplication and the average ratio between amplified and normal signals in the proband was 8.22:1. Ratios in noncarrier family members and control individuals were close to unity in most cases, but significantly greater than one in at least one instance. Our results provide a novel explanation for cytogenetic variation in 15q11.2. They also suggest that NF-1 pseudogene copy number may be polymorphic in the normal population, and that high copy numbers can produce G bands which do not reflect those of the normal constitutional karyotype.

A population study of chromosome 22q11 deletions in infancy.

AIMS: To determine the prevalence of submicroscopic deletions within chromosome band 22q11 in infants with significant heart disease and compare this with the prevalence of other chromosomal abnormalities causing significant heart disease. To determine a minimum prevalence of deletions within chromosome band 22q11 in infants in the general population. METHODS: Chromosome analysis was performed on samples from infants born in the former UK Northern Health Region in 1994 and 1995 who either had significant heart disease or who were suspected to have a chromosome band 22q11 deletion following referral to the Northern Genetics Service. Significant heart disease was defined as major structural malformation or cases where invasive investigation or intervention was required in infancy. RESULTS: Chromosome band 22q11 deletions were identified in nine infants in a population of 69,129 livebirths, giving a minimum prevalence of 13 per 100,000 (95% confidence interval 4.5 to 21.5). Six cases had significant heart disease, one of whom died before diagnosis. In the same population there were 53 cases of trisomy 21, 15 of whom had significant heart disease. CONCLUSION: The most common chromosomal cause of significant congenital heart disease remains trisomy 21, while the second most common chromosomal cause is deletion in chromosome band 22q11.

Renal abnormalities on obstetric ultrasound as a presentation of DiGeorge syndrome.

We describe three pregnancies that presented with renal anomalies on obstetric ultrasound as the main abnormality and were subsequently found to have interstitial deletions within chromosome 22q11. A cardiac defect, double-outlet right ventricle, was also seen in the first case. Amnio infusion was refused in the second pregnancy and the perimembranous ventricular septal defect was not identified prior to termination. In the third case, there was no cardiac defect. The genitourinary abnormalities were a right hydroureter and hydronephrosis with a ureterocele bulging into the bladder lumen, bilateral multicystic kidneys with associated oligohydramnios, and a left multicystic kidney with right renal agenesis and associated oligohydramnios. Absence of thymus at autopsy in all three cases led to fluorescent in situ hybridization studies looking for the submicroscopic deletion of chromosome 22q11 associated with DiGeorge syndrome.

FISH studies in a patient with sporadic aniridia and t(7;11) (q31.2;p13).

A 2 year old female presenting with bilateral sporadic aniridia was found to have an apparently balanced reciprocal translocation with a chromosome 11 breakpoint within band p13. Fluorescence in situ hybridisation (FISH) studies with distal 11p13 specific cosmids showed that the chromosome 11 breakpoint lay between the aniridia (PAX6) locus and a region approximately 100 kb distal to PAX6 defined by the cosmid FO2121. Although this patient did not have a detectable deletion within PAX6, her aniridia may have resulted from a disruption of the distal chromatin domain containing either enhancers or regulators for PAX6. This case may therefore be another example of aniridia caused by a position effect as recently described in two familial aniridia patients in which the phenotype cosegregated with chromosome abnormalities with 11p13 breakpoints.

Monozygotic twins with chromosome 22q11 deletion and discordant phenotype.

We report monozygotic twins concordant for 22q11.2 deletion but discordant for clinical phenotype. Both boys show the typical dysmorphic features with short palpebral fissures, square nasal tip, small mouth, and both have nasal speech, but only one twin had a heart defect. They show that the phenotypic variability seen in this microdeletion syndrome cannot be explained on the basis of genotypic differences alone.

Calibration and reliability of the Periotron 6000 for individual gingival crevicular fluid samples.

The Periotron 6000 fluid analyser has become widely used as a diagnostic tool for a variety of oral diseases and recent work has questioned its reliability. This paper investigates for the first time, the detailed calibration curves of 2 Periotron 6000 machines across a range of 23 different fluid volumes. Within and between machine reliability is analyzed and the shape of the calibration line determined. The measurement errors incurred by using a single fluid sample, as opposed to mean values of triplicate samples are also determined. We conclude that there are 3 sections to the calibration line, 2 linear and a quadrilateral zone, and that 2 separate regression equations should be used; from 0-0.1 microliter and from 0.1-1.0 microliter. Within machine calibration errors were only 3.2 +/- 7.5%, but values for volumes below 0.2 microliter were as high as 18.7%. Using a single fluid sample rather than mean values of multiple samples, incurred a further 4 +/- 4% error, which was as high as 7% for volumes lower than 0.12 microliter. Whilst significant differences in volume reading existed between different machines (p < 0.0004) and between the same volumes of different fluids (p < 0.00001), individual Periotron calibrations were extremely reproducible and reliable. We conclude that the Periotron 6000 is a reliable and convenient instrument for measuring fluid volumes greater than 0.2 microliter. For volumes lower than 0.2 microliter errors in measurement may be too high for some investigations, but this is likely to be due to problems with evaporation and with measurement technique, rather than errors directly due to the Periotron itself. Finally, for optimum accuracy, the digital display should be re-set to zero after each sample is measured.

Conotruncal anomaly face syndrome is associated with a deletion within chromosome 22q11.

The conotruncal anomaly face syndrome was described in a Japanese publication in 1976 and comprises dysmorphic facial appearance and outflow tract defects of the heart. The authors subsequently noted similarities to Shprintzen syndrome and DiGeorge syndrome. Chromosome analysis in five cases did not show a deletion at high resolution, but fluorescent in situ hybridisation using probe DO832 showed a deletion within chromosome 22q11 in all cases.

Confirmation that the velo-cardio-facial syndrome is associated with haplo-insufficiency of genes at chromosome 22q11.

The velo-cardio-facial syndrome (VCFS) and DiGeorge sequence (DGS) have many similar phenotypic characteristics, suggesting that in some cases they share a common cause. DGS is known to be associated with monosomy for a region of chromosome 22q11, and DNA probes have been shown to detect these deletions even in patients with apparently normal chromosomes. Twelve patients with VCFS were examined and monosomy for a region of 22q11 was found in all patients. The DNA probes used in this study could not distinguish the VCFS locus and the DGS locus, indicating that the genes involved in these haploinsufficiencies are closely linked, and may be identical. The phenotypic variation of expression in VCFS and DGS may indicate that patients without the full spectrum of VCFS abnormalities but with some manifestations of the disorder may also have 22q11 deletions.

Noonan's and DiGeorge syndromes with monosomy 22q11.

A boy with the dysmorphic features of Noonan's syndrome and pulmonary valve stenosis who had evidence of hypoparathyroidism and abnormal T lymphocyte numbers in the neonatal period is reported. He had a normal karyotype but molecular analysis revealed a submicroscopic deletion within chromosome 22q11, the region deleted in DiGeorge syndrome. Thus this child has both Noonan's syndrome and DiGeorge syndrome; 22q11 is a candidate region for a gene defective in Noonan's syndrome.

A prospective cytogenetic study of 36 cases of DiGeorge syndrome.

Cytogenetic analysis was carried out in a prospective series of 36 children with DiGeorge syndrome. High-resolution banding (> 850 bands/haploid set) was achieved in 30 cases. Monosomy 22q11.21-->q11.23 was found in 9 of these 30 cases. In each of these cases monosomy 22q11.21-->q11.23 resulted from an interstitial deletion and not from a translocation. No other chromosome abnormalities were seen.

Deletions within chromosome 22q11 in familial congenital heart disease.

Because a locus on chromosome 22q11 is deleted in most individuals with DiGeorge and Shprintzen syndromes--conditions in which heart abnormalities are an important feature--we have looked for deletions in nine families with recurrent outflow-tract heart defects. In five families, chromosome 22 deletions were detected in all the living affected individuals studied and also in the clinically normal father of three affected children. The deletion was transmitted from parents to offspring and was associated with an increase in the severity of cardiac defects. No deletions were found in four families in which the parents were normal and affected siblings had anatomically identical defects. We propose that deletions within band q11 of chromosome 22 are an important cause of familial heart defects.

VACTERL with hydrocephalus: one end of the Fanconi anemia spectrum of anomalies?

Two cases of Fanconi anemia presenting as hydrocephalus are discussed. Both infants had initially been considered to have features of VACTERL. Chromosomal breakage studies should be performed in all cases of VACTERL with hydrocephalus so that Fanconi anemia may be excluded.