Genetic and morphological studies of Nothobranchius (Cyprinodontiformes) from Malawi with description of Nothobranchius wattersi sp. nov

Molecular and morphological data were used to explore evolutionary differentiation among populations of Nothobranchius in the Lake Malawi-upper Shire River and the Lakes Chilwa-Chiuta drainage systems in Malawi. The aim of the study was to test the hypothesis that Nothobranchius of the Malawi-Shire system constitute a separate evolutionary group from Nothobranchius kirki. Mitochondrial and nuclear sequence data show a strongly supported phylogenetic split into two monophyletic groups separating the Lake Malawi basin fish from N. kirki. Unlike N. kirki, Lake Malawi-Shire fish do not deviate from neutrality and express an excess of rare haplotypes and mutations in terminal branches, characteristic of recently expanded populations. Further, the two groups significantly differ in morphology. Two body characters (dorsal-fin base length and pre-pelvic-pre-anal distance) are significantly different between the two species in both sexes. Several other characters are significantly different in either male or female comparisons with respect to both standard and head lengths, and robust morphological differentiation is detected by multivariate analysis. The two groups are readily distinguished on the basis of male colouration, especially in scale centres and the caudal fin. On the basis of this differentiation at the molecular and morphological levels, in addition to colouration, the Lake Malawi-Shire fish are hereby formally recognized as constituting a new species, Nothobranchius wattersi. This distinction is in agreement with the geomorphologic and recent climatic history in the region.

No association of sequence variants in the neuropeptide Y2 receptor (NPY2R) gene with early onset obesity in Germans

The neuropeptide Y2 receptor (NPY2R) has been implicated in body weight regulation both in humans and rodents. We investigated if genetic variation in the NPY2R gene is associated with obesity in German extremely obese children and adolescents. The coding sequence and predicted promoter of the NPY2R were screened for variations. Subsequently, case-control (184 extremely obese children and adolescents: mean body mass index [BMI] 35.7+/-6.1 kg/m(2), 277 lean students: mean BMI 18.2+/-1.1 kg/m(2)) and family-based (770 parental pairs with a total of 1081 obese off-spring) association analyses were conducted in independent samples. We identified 14 sequence variants (seven novel variants including two coding variants c.369C >T and c.834G >A), five of which were detected once, each in the heterozygous state. In case-control analyses we did not detect association with obesity for seven common (minor allele frequency >1%) variants (all p >0.16); additional gender-stratified analyses employing several genetic models and haplotype analyses were also nonsignificant. Furthermore, in a family-based association study for coding synonymous SNP rs1047214 (Ile195) we found no evidence for a transmission disequilibrium in the total or in the gender-stratified PDT analyses (all p >0.50). In conclusion, we did not find evidence for an involvement of genetic variation in the NPY2R in early onset obesity in German samples.

Mutation screen of the brain derived neurotrophic factor gene (BDNF): identification of several genetic variants and association studies in patients with obesity, eating disorders, and attention-deficit/hyperactivity disorder

Several lines of evidence indicate an involvement of brain derived neurotrophic factor (BDNF) in body weight regulation and activity: heterozygous Bdnf knockout mice (Bdnf(+/-)) are hyperphagic, obese, and hyperactive; furthermore, central infusion of BDNF leads to severe, dose-dependent appetite suppression and weight loss in rats. We searched for the role of BDNF variants in obesity, eating disorders, and attention-deficit/hyperactivity disorder (ADHD). A mutation screen (SSCP and DHPLC) of the translated region of BDNF in 183 extremely obese children and adolescents and 187 underweight students was performed. Additionally, we genotyped two common polymorphisms (rs6265: p.V66M; c.-46C > T) in 118 patients with anorexia nervosa, 80 patients with bulimia nervosa, 88 patients with ADHD, and 96 normal weight controls. Three rare variants (c.5C > T: p.T2I; c.273G > A; c.*137A > G) and the known polymorphism (p.V66M) were identified. A role of the I2 allele in the etiology of obesity cannot be excluded. We found no association between p.V66M or the additionally genotyped variant c.-46C > T and obesity, ADHD or eating disorders. This article contains supplementary material, which may be viewed at the American Journal of Medical Genetics website at http://www.interscience.wiley.com/jpages/0148-7299:1/suppmat/index.html.

[Clinical and molecular genetic findings in four girls with Rett syndrome]

We report on four mental retarded girls with typical clinical signs of Rett syndrome. Rett syndrome is an X-linked neurodevelopment disorder which develops after a period of normal development at the age of 6 to 18 months, affecting 1/10 000 - 15 000 girls. Recently, the MeCP2-gene encoding the methyl-CpG-binding protein 2 has been shown to be mutated in 80 percent of girls with Rett Syndrome, studied so far. In our patients with Rett syndrome two common mutations of the MeCP2-gene, R168X (n=2) and T158M were found. In the 4th patient a novel "missense" mutation R294G was identified.

Deletion screening by fluorescence in situ hybridization in Rett syndrome patients

Mutations in the X-linked methyl-CpG-binding protein 2 (MECP2) gene have been found to be a cause of Rett syndrome (RTT). Mutation screening was based on various techniques including denaturing gradient gel electrophoresis, single-strand conformation polymorphism analysis, heteroduplex analysis, DNA sequencing and recently Southern Blot analysis. Mutation detection was achieved in 80% of typical RTT with a high prevalence of recurrent mutations. In order to provide further insights into the spectrum of MECP2 rearrangements in patients without any point mutation or small deletion/insertion in the coding region MECP2 gene, we screened 25 classical RTT females using fluorescence in situ hybridization analysis. No deletion were found in our group, suggesting that MECP2 gross rearrangements are a rare cause of Rett syndrome.

Identification and localization of a new human myotubularin-related protein gene, mtmr8, on 8p22-p23

Myotubularin and myotubularin-related proteins are dual-specificity phosphatases. Several myotubularin-related proteins have been identified in humans and mice. The members of the myotubularin protein family are highly conserved, from humans to yeast. Mutations in the human myotubularin gene (MTM1) lead to X-linked myotubular myopathy. Here we isolate and localize a novel putative myotubularin-related protein gene (MTMR8) on chromosome 8p22--p23,between the markers D8S550 and D8S265, by exon-trapping experiments and RT-PCR. Genomic sequencing revealed that the gene consists of 10 exons and spans approximately 43 kb. The corresponding cDNA is 7081 bp. The open reading frame predicts a protein of 549 amino acids and a calculated molecular mass of 63 kDa. Like myotubularin-related protein-5, MTMR8 has no dual-specificity phosphatase domain. It contains a double-helical motif similar to the SET interaction domain, which is thought to have a role in the control of cell proliferation.

[IRepeat sequences of genomes of Rhizobium and Sinorhizobium meliloti: a comparative analysis]

Amongst prokaryotic genomes, those of nitrogen-fixing members of the Rhizobiaceae family are relatively large (6-9 Mb), often include mega-plasmids of 1.5-2 Mb, and contain numerous families of repeated DNA sequences. Although most essential nodulation and nitrogen fixation genes are well characterized, these represent only a small fraction of the DNA content. Little is known about the detailed structure of rhizobial genomes. With the development of sequencing techniques and new bio-informatic tools such studies become possible, however. Using the 2275 shotgun sequences of ANU265 (a derivative of NGR234 cured of pNGR234a), we have identified numerous families of repeats. Amongst these, the 58-bp-long NGRREP-4 represents the third most abundant DNA sequence after the RIME1 and RIME2 repeats, all of which are also found in Sinorhizobium meliloti. Surprisingly, studies on the distribution of these elements showed that in proportion to its size, the chromosome of NGR234 carries many more RIME modules than pNGR234a or pNGR234b. Together with the presence in NGR234 and S. meliloti 1021 of an insertion sequence (IS) element more conserved than essential nodulation and nitrogen fixation genes, these results give new insights into the origin and evolution of rhizobial genomes.

Identification of a short cis-acting element in the human vasopressin type 2 receptor gene which confers high-level expression of a reporter gene specifically in collecting duct cells

In the kidney, water reabsorption is mainly regulated by the binding of arginine vasopressin to vasopressin type 2 (V2) receptors. These receptors are expressed selectively in principal cells of the collecting ducts. To identify molecular mechanisms responsible for the cell-specific expression of the V2 receptor, we have analyzed the proximal promoter of the corresponding gene. We report the identification of a 33-bp enhancer [collecting duct tissue-specific element 1 (CSE1)] that induced high levels of expression of the luciferase reporter gene in three collecting duct cell lines, but not in other renal cell lines. In gel shift assays, CSE1 bound a DNA-binding protein expressed selectively in collecting duct cell lines, and a 7-bp mutation, which abolished the activity of CSE1 in transient transfection experiments, also abolished the binding of this protein. Furthermore, decoy experiments performed using CSE1 showed that this sequence was involved not only in the expression of a construct containing 4.2 kb of the V2 receptor proximal promoter, but also in the expression of the endogenous V2 receptor gene. CSE1 appears to act mostly by counteracting the inhibitory effects of a strong ubiquitous repressor element that we called CIE1. Collectively, these results identify the first functional collecting duct-specific cis-acting element.

The DNA sequence of human chromosome 21

Chromosome 21 is the smallest human autosome. An extra copy of chromosome 21 causes Down syndrome, the most frequent genetic cause of significant mental retardation, which affects up to 1 in 700 live births. Several anonymous loci for monogenic disorders and predispositions for common complex disorders have also been mapped to this chromosome, and loss of heterozygosity has been observed in regions associated with solid tumours. Here we report the sequence and gene catalogue of the long arm of chromosome 21. We have sequenced 33,546,361 base pairs (bp) of DNA with very high accuracy, the largest contig being 25,491,867 bp. Only three small clone gaps and seven sequencing gaps remain, comprising about 100 kilobases. Thus, we achieved 99.7% coverage of 21q. We also sequenced 281,116 bp from the short arm. The structural features identified include duplications that are probably involved in chromosomal abnormalities and repeat structures in the telomeric and pericentromeric regions. Analysis of the chromosome revealed 127 known genes, 98 predicted genes and 59 pseudogenes.

Comparative sequence analysis of the MECP2-locus in human and mouse reveals new transcribed regions

Comparative sequence analysis facilitates the identification of evolutionarily conserved regions, that is, gene-regulatory elements, which can not be detected by analyzing one species only. Sequencing of a 152-kb region on human Chromosome (Chr) Xq28 and of the synthenic 123 kb on mouse Chr XC identified the MECP2/Mecp2 locus, which is flanked by the gene coding for Interleukin-1 receptor associated kinase (IRAK/Il1rak) and the red opsin gene (RCP/Rsvp). By comparative sequence analysis, we identified a previously unknown, non-coding 5' exon embedded in a CpG island associated with MECP2/Mecp2. Thus, the MECP2/Mecp2 gene is comprised of four exons instead of three. Furthermore, sequence comparison 3' to the previously reported polyadenylation signal revealed a highly conserved region of 8.5 kb terminating in an alternative polyadenylation signal. Northern blot analysis verified the existence of two main transcripts of 1.9 kb and approximately 10 kb, respectively. Both transcripts exhibit tissue-specific expression patterns and have almost identical short half-lifes. The approximately 10-kb transcript corresponds to a giant 3' UTR contained in the fourth exon of MECP2. The long 3' UTR and the newly identified first intron of MECP2/Mecp2 are highly conserved in human and mouse. Furthermore, the human MECP2 locus is heterogeneous with respect to its DNA composition. We postulate that it represents a boundary between two H3 isochores that has not been observed previously.

Human renin binding protein: complete genomic sequence and association of an intronic T/C polymorphism with the prorenin level in males

The role of renin binding protein (RnBP) in human (patho)physiology, despite its biochemical characterization, is as yet unclear. RnBP has been shown to bind and inactivate renin, a key player of the blood pressure regulating renin-angiotensin system. This renders the RnBP gene a promising candidate gene in human hypertension. Herein, a molecular genetic approach was employed to investigate if RnBP might affect renin, prorenin and/or blood pressure levels. Sequencing of the human Xq28 chromosomal region provided the precise chromosomal location and full genomic sequence of the RnBP gene. All 11 exons, adjacent intronic splice sites and the promoter region were sequenced in 20 patients with essential hypertension of early onset and possible X-linked inheritance and in four normotensive individuals. The only variant found was a single base exchange polymorphism 61 base pairs upstream of the intron 6/exon 7 boundary (T61C). Several cardiovascular parameters, the renin, and prorenin levels and the T61C allele status were determined in 505 Caucasian individuals. Male individuals without medication who were hemizygous for the C allele were characterized by lower prorenin levels (196 +/- 15 versus 256 +/- 12 mU/l, P = 0.05) and a significantly higher renin/prorenin ratio (10.7 +/- 1.5 versus 7.7 +/- 0.3%, P = 0.002), whereas no variations in circulating renin, blood pressure, heart rate and left ventricular mass index were associated with the C allele. No significant association was observed in women. The data do not exclude a role of RnBP in essential hypertension. The complete genomic structure of the RnBP gene, including the identified repetitive sequence elements, provides an essential tool for further studies of the RnBP gene in hypertensive patients with a different genetic background.

The genomic organization of a human creatine transporter (CRTR) gene located in Xq28

During the course of a large-scale sequencing project in Xq28, a human creatine transporter (CRTR) gene was discovered. The gene is located approximately 36 kb centromeric to ALD. The gene contains 13 exons and spans about 8.5 kb of genomic DNA. Since the creatine transporter has a prominent function in muscular physiology, it is a candidate gene for Barth syndrome and infantile cardiomyopathy mapped to Xq28.

Expression of the allatostatin gene in endocrine cells of the cockroach midgut

Cockroach allatostatins are neuropeptides that have been isolated from the brain of Diploptera punctata and shown to inhibit juvenile hormone production by the corpora allata. Enzyme-linked immunoassay and immunocytochemistry with antisera to two allatostatins, ASB2 (AYSYVSEYKRLPVYNFGL-NH2) and ASAL (APSGAQRLYGFGL-NH2), revealed that allatostatins were located not only in the insect brain but also in several peripheral tissues including the cockroach midgut and hindgut. Allatostatin-like immunoreactivity was found in nerve fibers of the stomatogastric nervous system as well as in intrinsic endocrine cells of the midgut. Midgut extracts were shown to be biologically active in an allatostatin bioassay and to contain several allatostatin-like peptides, including the octadecapeptide ASB2, which was identified by mass spectrometry following HPLC purification. Reverse transcription of brain mRNA followed by PCR with degenerate oligonucleotides for ASB2 and ASAL yielded a 338-bp fragment of the allatostatin gene that encoded six allatostatins. In situ hybridization with this probe confirmed that an allatostatin gene is expressed in intrinsic endocrine cells of the midgut. Reverse transcription of midgut mRNA followed by PCR and sequencing of the product revealed that the same gene is expressed in the midgut and in the brain. Allatostatins are thus an example of insect "brain-gut peptides" and we suggest that their function may not be restricted to the regulation of juvenile hormone production.