Paola Blasi

Disequilibrium of multiple DNA markers on the human Y chromosome.

We characterized four DNA polymorphisms on the Y chromosomes of 123 males from five Caucasian populations. Three markers on the male specific portion of the chromosome varied appreciably in frequency among the populations. When combined, these markers define a limited number of haplotypes compared with the maximum expected on the basis of random association. The associations found in the five groups are qualitatively similar and are thus considered to be relatively stable on an evolutionary time‐scale and possibly to predate the divergence of Caucasian populations. However, the haplotype frequencies varied markedly among populations, even between weakly isolated areas such as northern vs. southern Sardinia. This may indicate rapid progression towards fixation of alternative types of Y chromosomes.

Genetic structure of pastoral and farmer populations in the African Sahel

Traditional pastoralists survive in few places in the world. They can still be encountered in the African Sahel, where annual alternations of dry and wet seasons force them to continual mobility. Little is known about the genetic structure of these populations. We present here the population distribution of 312 hypervariable segment I mitochondrial DNA (mtDNA) and 364 Y-short tandem repeat haplotypes in both farmer and pastoralist groups from the Lake Chad Basin and the West African Sahel. We show that the majority of pastoral populations (represented in the African Sahel by the Fulani nomads) fail to show significant departure from neutrality for mtDNA as evidenced by Fus Fs statistics and exhibit lower levels of intrapopulation diversity measures for mtDNA when contrasted with farmers. These differences were not observed for the Y chromosome. Furthermore, analyses of molecular variance and population distributions of the mtDNA haplotypes show more heterogeneity in the sedentary groups than in the pastoralists. On the other hand, pastoralists retain a signature of a wide phylogenetic distance contributing to their male gene pool, whereas in at least some of the farmer populations, a founder effect and/or drift might have led to the presence of a single major lineage. Interestingly, these observations are in contrast with those recorded in Central Asia, where similar comparisons of farmer and pastoral groups have recently been carried out. We can conclude that in Africa, there have been no substantial mating exchanges between the Fulani pastoralists coming to the Lake Chad Basin from the West African Sahel and their farmer neighbors. At the same time, we suggest that the emergence of pastoralism might be an earlier and/or a demographically more important event than the introduction of sedentary agriculture, at least in this part of Africa.

SSADH Variation in Primates: Intra- and Interspecific Data on a Gene with a Potential Role in Human Cognitive Functions

In the present study we focus on the nucleotide and the inferred amino acid variation occurring in humans and other primate species for mitochondrial NAD+-dependent succinic semialdehyde dehydrogenase, a gene recently supposed to contribute to cognitive performance in humans. We determined 2527 bp of coding, intronic, and flanking sequences from chimpanzee, bonobo, gorilla, orangutan, gibbon, and macaque. We also resequenced the entire coding sequence on 39 independent chromosomes from Italian families. Four variable coding sites were genotyped in additional populations from Europe, Africa, and Asia. A test for constancy of the nonsynonymous vs. synonymous rates of nucleotide changes revealed that primates are characterized by largely variable dN/dS ratios. On a background of strong conservation, probably controlled by selective constraints, the lineage leading to humans showed a ratio increased to 0.42. Human polymorphic levels fall in the range reported for other genes, with a pattern of frequency and haplotype structure strongly suggestive of nonneutrality. The comparison with the primate sequences allowed inferring the ancestral state at all variable positions, suggesting that the c.538(C) allele and the associated functional variant is indeed a derived state that is proceeding to fixation. The unexpected pattern of human polymorphism compared to interspecific findings outlines the possibility of a recent positive selection on some variants relevant to new cognitive capabilities unique to humans.

A human derived SSADH coding variant is replacing the ancestral allele shared with primates.

Background: A growing number of reports describe markers with high frequencies of the ancestral alleles in Africa, contrasting with high frequencies and possibly fixation of derived variants out of Africa. Such a pattern can be explained by either neutral or non-neutral processes. Aim: The study examined worldwide frequencies of two non-synonymous variants in NAD+-dependent succinic semialdehyde dehydrogenase (SSADH), in a search for possible signatures of natural selection favouring the derived alleles. Subjects and methods: The typing of 1574 subjects were compiled, representing 60 populations from all continents. SSADH haplotype frequencies were correlated across 52 populations to those of 260 single nucleotide polymorphism (SNP) markers deposited in the CEPH database and of markers reported to be under positive Darwinian selection. Results: In the world population, the c.538C variant is proceeding to replace the ancestral c.538T, shared with primates. The overall population differentiation is within the normal range. A significant correlation was also found between the frequencies of the derived alleles in SSADH and Microcephalin (MCPH1), which showed concerted changes worldwide and, at least in Asian populations, also on a restricted geographical scale. Conclusion: The analysis of robust correlations based on a large panel of populations is potentially able to identify clusters of genomic regions or genes showing co-evolution of the frequencies of derived alleles.

Succinic semialdehyde dehydrogenase deficiency: clinical, biochemical and molecular characterization of a new patient with severe phenotype and a novel mutation.

To the Editor: 4-Hydroxybutyric aciduria (4-HBA, OMIM 271980) is a neurogenetic disorder due to deficiency of succinic semialdehyde dehydrogenase (SSADH; ALDH5A1; EC 1.2.1.24) (1), a mitochondrial NADþ-dependent enzyme that irreversibly catalyses the oxidation of succinic semialdehyde to succinate, the final step of GABA degradation. 4-HBA is inherited in an autosomal recessive fashion and results in the abnormal accumulation of g-hydroxybutyrate (GHB) and GABA in physiologic fluids (2–5). The clinical picture is highly heterogeneous and includes developmental delay, hypotonia, mental retardation, ataxia, hyperactivity and behavioural disturbances. Seizures occur in nearly half of all patients, including absences as well as tonic-clonic convulsions (1). Frequent abnormalities in MRI scanning involve the globus pallidus and the subcortical white matter (6). The SSADH gene is located in 6p22 (7); the ORF consists of 1605 bp (acc. n. Y11192), with 10 exons encoding 535 amino acids (8, 9).Mutation analyses in patients of different geographic origins (8, 10–12) revealed a wide spectrum of mutations. However, evidence for an immediate genotype– phenotype correlation is scanty (11). Here we present a novel SSADH mutation in an adopted 9-month-old girl, hospitalized because of psychomotor delay. Family history and parental biological samples were not available. Informed consent was obtained for all analytical procedures. Clinical examination revealed strabismus and generalized hypotonia. Routine laboratory examinations were in the normal range, except for intermittent hyperglycemia with associated glycosuria (up to 3 g/dl, corresponding to 20 g/day). Fundoscopy showed retinal hypopigmentation. EEG disclosed slowed and scarcely organized cerebral electrical activity, without epileptic discharges. Brain MRI showed mild cortical atrophy without abnormalities of brainstem nor of pallidi and dentate nuclei. Organic acids in urine and cerebrospinal fluid analysed by gas chromatography/mass spectrometry revealed the characteristic pattern of SSADH deficiency. Upon re-evaluation at the age of 26 months, she had never experienced epileptic seizures. Mild hypotonia persisted, and she was able to stand and walk with aid, but speech was absent. The Bayley’s Scale of Infant Development revealed mental retardation (DQ < 50). Intermittent hyperglycemia and glycosuria persisted. Nerve conduction velocity was normal. Enzymatic assay of SSADH was performed as described (13) in the patient’s fibroblasts and revealed a strongly reduced activity (0.12 nmol/min mgproteins , vs. 1.4 and 3.7 in controls).Mutation screeningwas performed by re-sequencing the entire coding region from either RT-PCR on lymphocyte RNA or from exon specific PCRs of genomic DNA (9). Since exon 7 could not be amplified, we investigated a possible deletion by examining the coding region by RT-PCR with primers located in exons 6 and 8. This yielded a single band shortened to 292 bp, instead of the expected 451 bp. Sequencing of this product revealed an in-frame exon skipping of exon 7, accounting for the missing 159 bp (Fig. 1a). In order to precisely identify the deletion in the genomic region, we performed a long-range PCR spanning from exon 6 to IVS7. We obtained a single band of approx. 1650 bp, instead of the expected 4156 bp. By sequencing this product, we identified the first 0.7 kb of IVS6 followed by 0.8 kb of IVS7 (Fig. 1b). Therefore, the patient displayed a single mRNA species encoding an exon-skipping deletion that Clin Genet 2006: 69: 294–296 # 2006 The Authors Printed in Singapore. All rights reserved Journal compilation # 2006 Blackwell Munksgaard

Linkage exclusion in Italian families with hereditary essential tremor

A. Novelletto, R. Gulli, P. Ciotti, C. Vitale, P. Malaspina, P. Blasi, T. Pippucci, M. Seri, A. Cozzolino, L. Bilo, G. Abbruzzese, P. Martinelli, E. Bellone, P. Barone and P. Mandich Department of Biology, University ‘‘Tor Vergata’’, Rome; Department of Neuroscience, Ophthalmology and Genetics – Section of Medical Genetics, University of Genoa, Genoa; University of Naples ‘‘Parthenope’’; IDC, Hermitage Capodimonte, Naples; Department of Gynaecologic, Medical Genetics Unit, Obstetric and Paediatric Sciences, University of Bologna, Bologna; Department of Neurological Sciences, University ‘‘Federico II’’, Naples; Department of Neuroscience, Ophthalmology and Genetics – Section of Neurology, University of Genoa, Genoa; and Department of Neurological Sciences, Neurology Clinic, University of Bologna, Bologna, Italy

Alcohol use disorder and GABAB receptor gene polymorphisms in an Italian sample: haplotype frequencies, linkage disequilibrium and association studies

Abstract Background: Alcohol use disorder (AUD) is a complex trait with genetic and environmental influences. Several gene variants have been associated with the risk for AUD, including genes encoding the sub-units of the γ-aminobutyric acid (GABA) receptors. Aim: This study evaluated whether specific single nucleotide polymorphisms (SNPs) in genes encoding GABAB receptor sub-units can be considered as candidates for the risk of AUD. Subjects and methods: Seventy-four AUD subjects and 128 Italian controls were genotyped for 10 SNPs in genes encoding GABA-B1 and GABA-B2 sub-units (GABBR1 and GABBR2). Allele, genotype, and haplotype frequencies were tested for the association with the AUD trait. Results: A significant difference between AUD individuals and controls was observed at genotype level for rs2900512 of GABBR2 gene. The homozygous T/T genotype was not found in the controls, whereas it was over-represented in the AUD individuals. Under the recessive model (T/T vs C/T + C/C) this result was statistically significant, as well as the Odds Ratio for the association with the AUD trait. Conclusions: The results provide preliminary data on the association between GABAB receptor gene variation and risk of AUD. To confirm this finding, studies with larger samples and additional characterisation of the phenotypic AUD trait are required.

Polymorphism in Mitochondrial Coding Regions of Mediterranean Loggerhead Turtles: Evolutionary Relevance and Structural Effects

We sequenced coding portions (1.6 kb) of the mtDNA in 170 loggerhead (Caretta caretta) turtles sampled in the central Mediterranean. The sequences spanned the entire ND1 and ND3 genes, the tRNAGly and tRNAArg, plus the 3′ and 5′ termini of COXIII and ND4L genes, respectively. Based on our sequencing results and published complete mitogenomes, we constructed a maximum parsimony phylogeny of C. caretta matrilines that sheds new light on the evolutionary relationships within the collection of lineages found in the Mediterranean and so far recognized by D-loop haplotypes only. We show that the new variants are useful to understand the ancestry of extant haplotypes, to improve genetically based studies on the philopatry and migratory behavior of the species, and for conservation purposes. In order to better understand the biological significance of the observed variation, we addressed intraspecific nonsynonymous substitutions in the context of the three-dimensional modeled structures of ND1 and ND3. The positions of variant amino acids within the folded subunits are consistent with a coadaptation with the restructuring of membrane thickness, fluidity, and lipid composition, a well-known response mechanism to thermal conditions. The pattern of amino acid substitutions departs from neutrality, suggesting local adaptation and/or polymorphism-based local selection.

The landscape of Y chromosome polymorphisms in Russia

Abstract Background: The pattern of diversity for the Y chromosome provides a view of male-driven processes of dispersal and settlement. By virtue of the broad geographic continuity, the genetic signature of movements from Asia to Europe can be detected in populations of north-eastern Europe. Aim: To directly test previous hypotheses on the peopling of Russia, by considering a broader spectrum of potential diversity. Subjects and methods: A total of 636 unrelated males (24 samples) from geographically and ethnically defined populations of Russia, Belarus, Azerbaijan and Georgia were analysed for 16 Y-STR loci. Some of the populations represent more or less distinct isolates. Results: Microsatellites alone can have the power of detecting Asian contributions to the gene pool of populations now residing in Europe. Within Europe, a greater heterogeneity among populations sharing the same language than between populations sharing the same ethnic affiliation was found. There was low diversity and marked population differentiation in some Altaic speakers. Sympatry eroded inter-ethnic differentiation. No regular decline in genetic similarity with geography was seen. Conclusion: Two layers of overall diversity represent a main feature of the genetic landscape of the population of the European portion of Russia.