Comparative analysis of vertebrate EIF2AK2 (PKR) genes and assignment of the equine gene to ECA15q24–q25 and the bovine gene to BTA11q12–q15

The structures of the canine, rabbit, bovine and equine EIF2AK2 genes were determined. Each of these genes has a 5'' non-coding exon as well as 15 coding exons. All of the canine, bovine and equine EIF2AK2 introns have consensus donor and acceptor splice sites. In the equine EIF2AK2 gene, a unique single nucleotide polymorphism that encoded a Tyr329Cys substitution was detected. Regulatory elements predicted in the promoter region were conserved in ungulates, primates, rodents, Afrotheria (elephant) and Insectifora (shrew). Western clawed frog and fugu EIF2AK2 gene sequences were detected in the USCS Genome Browser and compared to those of other vertebrate EIF2AK2 genes. A comparison of EIF2AK2 protein domains in vertebrates indicates that the kinase catalytic domains were evolutionarily more conserved than the nucleic acid-binding motifs. Nucleotide substitution rates were uniform among the vertebrate sequences with the exception of the zebrafish and goldfish EIF2AK2 genes, which showed substitution rates about 20% higher than those of other vertebrates. FISH was used to physically assign the horse and cattle genes to chromosome locations, ECA15q24–q25 and BTA11q12–15, respectively. Comparative mapping data confirmed conservation of synteny between ungulates, humans and rodents.     

Triplex gene dosage effect for β-glucronidase and possible assignment to band q22 in a partial duplication 7q

Summary A 2-year-old girl had a de novo duplication in the long arm of one chromosome 7 and an increased level of the enzyme -glucuronidase in cultured fibroblasts. The phenotype of the girl partly overlaps those of two presumptive syndromes due to secondary partial trisomies 7q. The ratio of the enzyme activity was 1.43 to the controls, and 1.37 to her parent's values. We could not define the abnormality but suggest two alternatives: either the patient is trisomic for region q112 to q22 or for the region q22 to q34. If the second alternative is correct the locus for -glucuronidase is possibly assigned to band 7q22.     

Regional assignment of the human C1-inhibitor gene to 11q11–q13.1

Summary In situ hybridisation using a biotinylated 1.8kb human cDNA clone in both normal and structurally abnormal chromosomes supports regional localisation of the gene for human C1-inhibitor to chromosome 11q11-q13.11.     

Localization of a novel locus for alopecia with mental retardation syndrome to chromosome 3q26.33–q27.3

Alopecia with mental retardation syndrome is a rare autosomal recessive disorder characterized clinically by total or partial alopecia and mental retardation. In an effort to understand the molecular bases of this form of alopecia syndrome, large Pakistani consanguineous kindred with multiple affected individuals has been ascertained from a remote region in Pakistan. Genome wide scan mapped the disease locus on chromosome 3q26.33–q27.3. A maximum two-point LOD score of 3.05 (θ=0.0) was obtained at marker D3S3583. Maximum multipoint LOD score exceeding 5.0, obtained with several markers, supported the linkage. Recombination events observed in affected individuals localized the disease locus between markers D3S1232 and D3S2436, spanning 11.49-cM region on chromosome 3q26.33–q27.3. Sequence analysis of a candidate gene ETS variant gene 5 from DNA samples of two affected individuals of the family revealed no mutation.     

Maternal origin of deletion 15q11–13 in 25/25 cases of Angelman syndrome

Summary About half of the cases of Angelman syndrome arise from deletions of chromosome band 15q12. In 25 cases we have been able to determine the parental origin of the deletion and, in line with other reported cases, we have found the deletion to be of maternal origin. There were no exceptions. The parental origin was determined using cytogenetic markers in 13 of the cases, in nine by using the pattern of inheritance of restriction fragment length polymorphisms, and in three using both techniques.     

Regional assignment of the gene coding for a human Graves' disease autoantigen to 10q21.3–q22.1

A cDNA coding for a human Graves' disease autoantigen (hGT) has been isolated from a thyroid expression library. Using this cDNA as a probe, the gene for hGT, previously assigned to chromosome 10, has been further localized to 10q21.3–q22.1 by non-isotopic in situ hybridization.     

Partial COL1A2 gene duplication produces features of osteogenesis imperfecta and Ehlers-Danlos syndrome type VII

Type I collagen is the most abundant structural protein in the mammalian body. It exists as a heterotrimer of two subunits in the form [alpha1(I)]2alpha2(I). Pathogenic mutations in COL1A1 and COL1A2, the genes that encode the two subunits, cause a range of phenotypes including mild to lethal forms of osteogenesis imperfecta and a restricted set of Ehlers-Danlos syndrome phenotypes. Lethal mutations usually result from missense mutations that disrupt the normal triple helical structure of the molecule. Multi-exon duplication or deletion in type I collagen genes has rarely been observed and has generally resulted in a lethal or severe phenotype. We report a partial duplication in the COLIA2 gene that causes a relatively mild phenotype, despite the addition of 477 amino acids to the triple helical domain of the proalpha2(I) chain. The abnormal molecule is synthesized and secreted by cultured dermal fibroblasts in a normal fashion. Electron microscopy of dermal tissue reveals small but otherwise near normal collagen fibrils. The gene duplication occurred by mitotic sister chromatid exchange in the mother who is mosaic for the duplication allele. Examination of the abnormal sequence suggests a means by which the duplicated molecule could be processed and properly incorporated into mature collagen fibrils.     

Paternal duplication of chromosome 5q11.2–5q14 in a male born with craniostenosis,ear tags,kidney dysplasia and several other anomalies

A de novo duplication of the proximal part of the long arms of chromosome 5 was found in a male born with craniostenosis, ear tags and kidney dysplasia. The nature of the chromosomal aberration was defined by fluorescence in situ hybridization and the orgin of the duplication was traced by polymorphic DNA markers. A comparison is made with the published cases showing similar duplications in the long arm of chromosome 5.     

An interstitial deletion of 8q23.3–q24.22 associated with Langer–Giedion syndrome,Cornelia de Lange syndrome and epilepsy

We present a 19-year-old male with laxity of skin and joints, sparse scalp hair, facial dysmorphism, epilepsy, multiple exostoses, scoliosis, gastroesophageal reflux, cardiovascular defects, and an 8q23.3–q24.22 deletion detected by array comparative genomic hybridization. The patient was previously misdiagnosed as having Ehlers–Danlos syndrome. However, his clinical findings are in fact correlated with trichorhinophalangeal syndrome type II/Langer–Giedion syndrome and Cornelia de Lange syndrome-4. We discuss the genotype–phenotype correlation and the consequence of haploinsufficiency of TRPS1, RAD21, EXT1 and KCNQ3 in this case.     

Regional assignment of the loci for adenylate kinase to 9q32 and for α1-acid glycoprotein to 9q31-q32

Summary Normal levels of adenylate kinase (AK-1) and of ₁-acid glycoprotein (ORM1) were found in a girl with a deletion 9q32-qter secondary to a maternal translocation (4q35; 9q32), thus excluding these loci from the deleted region. These results, and comparison with other informative data, map the locus for AK-1 to 9q32 and that for ORM1 to region 9q31-q32. The girl has several signs of the Goltz syndrome (focal dermal hypoplasia), which is listed in the McKusick catalog (no. 30560) as an X-linked dominant condition. Our finding indicates that the locus for Golz syndrome is autosomal and in region 9q32-qter or that there are two such conditions, one autosomal and one X-linked.     

Regional localization of human ecto-5′nucleotidase to chromosome 6q14–q21

Summary Human and mouse hybrids that contain fragments of human chromosome 6 as translocations were analysed for expression of ecto-5nucleotidase enzymic activity measured by the conversion of AMP to adenosine and for antigenicity recognized by a monoclonal antibody specific for the human isozyme. Both methods allow a regional assignment of ecto-5nucleotidase to 6q14–q21.     

Array CGH characterization of an unbalanced X-autosome translocation associated with Xq27.2–qter deletion, 11q24.3–qter duplication and Xq22.3–q27.1 duplication in a girl with primary amenorrhea and mental retardation

We present array comparative genomic hybridization (aCGH) characterization of an unbalanced X-autosome translocation with an Xq interstitial segmental duplication in a 16-year-old girl with primary ovarian failure, mental retardation, attention deficit disorder, learning difficulty and facial dysmorphism. aCGH analysis revealed an Xq27.2–q28 deletion, an 11q24.3–q25 duplication, and an inverted duplication of Xq22.3–q27.1. The karyotype was 46,X,der(X)t(X;11)(q27.2;q24.3) dup(X)(q27.1q22.3). We discuss the genotype–phenotype correlation in this case. Our case provides evidence for an association of primary amenorrhea and mental retardation with concomitant unbalanced X-autosome translocation and X chromosome rearrangement.     

Refinement of the hereditary neuralgic amyotrophy (HNA) locus to chromosome 17q24–q25

Hereditary neuralgic amyotrophy (HNA) is an autosomal dominant, recurrent focal neuropathy characterized by episodes of painful brachial plexus neuropathy with muscle weakness and atrophy, as well as sensory disturbances. Single episodes are commonly preceded by unspecific infections or immunization, or are associated with parturition. Minor facial dysmorphic features are present in some pedigrees but do not clearly segregate with the disease. To confirm the recently described HNA locus on distal chromosome 17q, we performed a genetic linkage study in an extended Turkish pedigree. We were able to refine the HNA locus on chromosome 17q24–q25 in a 16-cM region. Received: 21 October 1996     

Transformation of vitamin D3 to 1α,25-dihydroxyvitamin D3 via 25-hydroxyvitamin D3 using Amycolata sp. strains

To enzymatically synthesize active metabolites of vitamin D₃, we screened about 500 bacterial strains and 450 fungal strains, of which 12 strains were able to convert vitamin D₃ to 1,25-dihydroxyvitamin D₃ [1,25(OH)₂D₃] via 25-hyroxyvitamin D₃ [25(OH)D₃]. The conversion activity was only detected in strains belonging to the genus Amycolata among all the organisms tested. A preparative-scale conversion of vitamin D₃ to 25(OH)D₃ and 1,25(OH)₂D₃ in a 200-1 tank fermentor using A. autotrophica FERM BP-1573 was accomplished, yielding 8.3 mg 25(OH)D₃/l culture and 0.17 mg 1,25(OH)₂D₃/l culture. A related compound, vitamin D₂, could be also converted to 25-hydroxyvitamin D₂ and 1,25-dihydroxyvitamin D₂ using the same strain. The cytochrome P-450 of FERM BP-1573 was detected by reduced CO difference spectra in whole-cell suspensions. Vitamin D₃ in the culture induced cytochrome P-450 and the conversion activity simultaneously, suggesting that the hydroxylation at C-25 of vitamin D₃ and at C-1 of 25(OH)D₃ originates from cytochrome P-450.Correspondence to: J. Sasaki     

Partial trisomy of distal 8q derived from mother with mosaic 8q23.3→24.13 deletion,and relatively mild expression of trichorhinophalangeal syndrome I

Summary A 17-month-old girl with a partial trisomy of distal 8q derived from her mother, who has a mosaic 8q23.3q24.13 deletion, was studied. Both showed a relatively mild phenotype of trichorhinophalangeal syndrome I. The karyotype of the proposita was designated as: 46,XX,-8,+der(8),inv ins(8;8)(p23.1;q24.13q23.3)mat. Her phenotype was considered similar to that of her mother despite the trisomies of distal 8q. She seems to be the first example of a partial trisomy of distal 8q derived from a parent with an interstitial deletion of a distal 8q segment and trichorhinophalangeal syndrome I.     

A case of trisomy 3q21→qter syndrome

Summary An infant with karyotype 46,XY,der(8),t(3;8)(q21;p23) is presented. The presence of trisomy 3q21qter syndrome is suspected on the basis of comparison of the clinical and laboratory findings of this patient with those of cases that have been reported as partial 3q trisomy. The common phenotypic features of this syndrome include growth failure and mental or developmental retardation, hypotonia, persistent lanugo, distorted head, congenital glaucoma, short and upturned nose, prominent maxilla, micrognathia, short, webbed neck, short limbs, retroflexed third and fourth toes, cutaneous syndactyly of the second, third and fourth toes, and elevated galactose-1-phosphate uridyl transferase activity in the red blood cells.     

Chromosomal localization of 5S and 18S–5.8S–25S ribosomal DNA sites in five Asian pines using fluorescence in situ hybridization

Fluorescence in situ hybridization (FISH) was employed on mitotic metaphase chromosome preparations of five Asian Pinus species: Pinus tabuliformis, Pinus yunnanensis, Pinus densata, Pinus massoniana and Pinus merkusii, using simultaneously DNA probes of the 18S rRNA gene and the 5S rRNA gene including the non-transcribed spacer sequences. The number and location of 18S rDNA sites varied markedly (5-10 pairs of strong signals) among the five pines. A maximum of 20 major 18S rDNA sites was observed in the diploid genome (2n = 24) of P. massoniana. The 5S rDNA FISH pattern was less variable, with one major site and one minor site commonly observed in each species. The differentiation of rDNA sites on chromosomes among the five pines correlates well with their phylogenic positions in Pinus as reconstructed from other molecular data. P. densata, a species of hybrid origin, resembles its parents ( P. tabuliformis and P. yunnanensis), including some components characteristic of each parent in its pattern. However, the species is unique, showing new features resulting possibly from recombination and genome reorganization.     

Colocalization of the genes coding for the α3 and β3 subunits of soluble guanylyl cyclase to human chromosome 4 at q31.3–q33

We have determined the chromosomal location of the human genes coding for the ₃ and ₃ subunits of soluble guanylyl cyclase (GC-S). The study was performed by in situ hybridization of human metaphase spreads with two human cDNA probes, containing the coding sequences of the GC-S ₃ and ₃ subunits, respectively. Each probe gave a strong specific signal on chromosome 4 at the 4q31.3–4q33 region, with the maximal signal in the 4q32 band. The colocalization of both genes in 4q32 represents an interesting feature for the coordinated regulation of expression of both GC-S subunits.     

Positions of the cytoplasmic end of BK α S0 helix relative to S1–S6 and of β1 TM1 and TM2 relative to S0–S6

The large-conductance, voltage- and Ca²⁺-gated K⁺ (BK) channel consists of four α subunits, which form a voltage- and Ca²⁺-gated channel, and up to four modulatory β subunits. The β1 subunit is expressed in smooth muscle, where it slows BK channel kinetics and shifts the conductance–voltage (G-V) curve to the left at [Ca²⁺] > 2 µM. In addition to the six transmembrane (TM) helices, S1–S6, conserved in all voltage-dependent K⁺ channels, BK α has a unique seventh TM helix, S0, which may contribute to the unusual rightward shift in the G-V curve of BK α in the absence of β1 and to a leftward shift in its presence. Such a role is supported by the close proximity of S0 to S3 and S4 in the voltage-sensing domain. Furthermore, on the extracellular side of the membrane, one of the two TM helices of β1, TM2, is adjacent to S0. We have now analyzed induced disulfide bond formation between substituted Cys residues on the cytoplasmic side of the membrane. There, in contrast, S0 is closest to the S2–S3 loop, from which position it is displaced on the addition of β1. The cytoplasmic ends of β1 TM1 and TM2 are adjacent and are located between the S2–S3 loop of one α subunit and S1 of a neighboring α subunit and are not adjacent to S0; i.e., S0 and TM2 have different trajectories through the membrane. In the absence of β1, 70% of disulfide bonding of W43C (S0) and L175C (S2–S3) has no effect on V₅₀ for activation, implying that the cytoplasmic end of S0 and the S2–S3 loop move in concert, if at all, during activation. Otherwise, linking them together in one state would obstruct the transition to the other state, which would certainly change V₅₀.     

Use of the STR loci D18S53, D18S59, and D18S488 in the diagnosis of Edwards’ syndrome

The aim of this study was to investigate the feasibility of using short tandem repeats (STRs) to diagnose Edwards’ syndrome (ES). Quantitative fluorescence polymerase chain reaction (QF-PCR) was performed to amplify STR loci on chromosome 18, specifically D18S53, D18S59, and D18S488. The amplified products were subjected to a fluorescence signal analysis and their application to ES diagnosis was examined. Among the 807 cases that showed normal results in the karyotype analysis, 793 showed one or two fluorescence bands with a fluorescence intensity ratio of 1:1, and 14 cases showed 3 bands, which were false-positive results. ES was diagnosed in 9 samples. The sensitivities of D18S53, D18S59, and D18S488 for the diagnosis of ES were 77.78, 44.44, and 55.56 % and the specificities were 96.16, 96.03, and 96.28 %, respectively. The combined sensitivity of the three loci for diagnosing DS was 100 % (9/9), with a specificity of 98.27 % (793/807). QF-PCR amplification of STR loci had high sensitivity, strong specificity, and was simple and rapid. Thus, it might have wide clinical applications, and could be an ideal tool for large-scale genetic and prenatal diagnosis of ES.