Unique spectrum of SPAST variants in Estonian HSP patients: presence of benign missense changes but lack of exonic rearrangements

Background

Hereditary spastic paraplegia (HSP) is a clinically and genetically heterogeneous disorder that can be an autosomal-dominant, autosomal-recessive, or X-linked disease. The most common autosomal-dominant form of the disease derives from mutations in the SPAST gene.

Methods

The aim of this study was to analyze 49 patients diagnosed with HSP from the Estonian population for sequence variants of the SPAST gene and to describe the associated phenotypes. Healthy control individuals (n = 100) with no family history of HSP were also analyzed. All patient samples were screened using denaturing high performance liquid chromatography (DHPLC) and multiplex ligation-dependent probe amplification (MLPA) assay. Samples with abnormal DHPLC and MLPA profiles were sequenced, with the same regions sequenced in control samples.

Results

Sequence variants of SPAST were identified in 19/49 HSP patients (38.8%), twelve among them had pathogenic mutations. Within the latter group there was one sporadic case. Eight patients had pure, and four - complex HSP. The twelve variants were identified: seven pathogenic (c.1174-1G>C, c.1185delA, c.1276C>T, c.1352_1356delGAGAA, c.1378C>A, c.1518_1519insTC, c.1841_1842insA) and five non-pathogenic (c.131C>T, c.484G>A, c.685A>G, c.1245+202delG, c.1245+215G>C). Only 2 of these mutations had previously been described (c.131C>T, c.1245+202delG). Three mutations, c.1174-1G>C, c.1276 C>T, c.1378C>A, showed intrafamilial segregation.

Conclusion

This study identified new variants of the SPAST gene which included benign missense variants and short insertions/deletions. No large rearrangements were found. Based on these data, 7 new pathogenic variants of HSP are associated with clinical phenotypes.

Splice variant IVS2-2A>G in the SLC26A5 (Prestin) gene in five Estonian families with hearing loss

OBJECTIVE

The aim of our study was to identify the IVS2-2A>G sequence change in the SLC26A5 (Prestin) gene in Estonian individuals with hearing loss and in their family members.

METHODS

In the years 2005-2007 we have screened 194 probands with early onset hearing loss and 68 family members with an arrayed primer extension (APEX) microarray, which covers 201 mutations in six nuclear genes (GJB2, GJB6, GJB3, GJA1, SLC26A4, SLC26A5) and two mitochondrial genes encoding 12S rRNA and tRNA-Ser (UCN).

RESULTS

In four probands with early onset hearing loss and in five unaffected family members from five families we identified the IVS2-2A>G change in one allele of the SLC26A5 gene. We did not find any homozygosity for this splice variant. IVS2-2A>G was identified in 2.1% of probands. One of these probands, however, is also homozygous for the 35delG mutation in the GJB2 gene and a second patient has Down syndrome, which is also associated with hearing impairment. Therefore, in those two cases the etiology of the hearing loss is probably not associated with the IVS2-2A>G sequence change in the SLC26A5 gene.

CONCLUSION

Our data support the hypothesis that heterozygosity for the mutation IVS2-2A>G in SLC26A5 gene may not, by itself, be sufficient to cause hearing loss.

Prevalence of the fragile X syndrome among Estonian mentally retarded and the entire children's population

The aim of this study is to establish the prevalence of fragile X syndrome among Estonian mentally retarded and also among the entire children's population born during the years 1984-2005. The study group consisted of 516 patients (448 boys and 68 girls) who were screened for full mutations in the FMR1 gene during the period 1997-2006. Fourteen boys (2.7%) were found with full mutations of the total mentally retarded individuals tested (3.1% of mentally retarded boys); the full mutation was not detected among girls. The live-birth prevalence of full mutation among boys was 1:13 947. The overall live-birth prevalence of fragile X syndrome was 1:27 115. It was found that the prevalence of fragile X syndrome among mentally retarded individuals in Estonia was the same as in previous studies, but the live-birth prevalence of fragile X syndrome among boys was significantly lower.

Mycoplasmas in semen of chronic prostatitis patients

OBJECTIVE

To evaluate the occurrence of mycoplasmas in the semen of chronic prostatitis patients.

MATERIAL AND METHODS

Genital mycoplasmas (Mycoplasma hominis, Mycoplasma genitalium, Ureaplasma urealyticum, Ureaplasma parvum) were sought in the semen of 121 chronic prostatitis patients [38 National Institutes of Health (NIH) category IIIa, 59 NIH category IIIb and 24 NIH category IV] and 40 controls. The commercially available kit Mycoplasma IST was applied to the semen samples of all 161 men, and polymerase chain reaction (PCR) to those of 60 randomly selected men.

RESULTS

Ureaplasmas were found in all study groups (at frequencies ranging from 12% to 25%) using the Mycoplasma IST test, but M. hominis was found only in one NIH category IIIb patient. Using PCR, most of the ureaplasmas appeared to be U. parvum, which was found in all prostatitis groups (18% of NIH category IIIa, 15% of NIH category IIIb and 25% of NIH category IV patients) but not in the controls. M. genitalium was found in 18% of the NIH category IIIa patients. All of the mycoplasmas occurred significantly more frequently in prostatitis patients than in controls and in NIH category IIIa patients than in controls.

CONCLUSION

Mycoplasmas occur more frequently in the semen of prostatitis patients than in that of healthy controls, with U. parvum being the most frequently occurring species.

Prevalence of Angelman syndrome and Prader–Willi syndrome in Estonian children: Sister syndromes not equally represented

In 2000-2004, we performed a focused search for individuals with Angelman syndrome (AS) and Prader-Willi syndrome (PWS) aiming to establish the prevalence data for the individuals born between 1984 and 2004 in Estonia. All persons with probable AS or PWS (n = 184) were studied using the DNA methylation test. Individuals with abnormal methylation were all further tested by chromosomal and FISH analysis, and if necessary for uniparental disomy and UBE3A gene mutation. Nineteen cases with abnormal methylation test result were identified. Seven of them had AS, including six (85.7%) due to 15q11-13 deletion and one paternal UPD15. Twelve subjects had PWS: 4 (33%) 15q11-13 deletions, 6 (50%) maternal UPD15, 1 unbalanced chromosome 14;15 translocation resulting in a chromosome 15pter-q13 deletion, and 1 Robertsonian 15q;15q translocation. The minimum livebirth prevalence in 1984-2004 for AS was 1:52,181 (95% CI 1:25,326-1:1,29,785) and for PWS 1:30,439 (95% CI 1:17,425-1:58,908). The livebirth prevalence of AS and PWS increased within this period, but the change was statistically significant only for PWS (P = 0.032), from expected 1:88,495 (95% CI 1:24,390-1:3,22,580) to expected 1:12,547 (95% CI 1:540-1:29,154). Six individuals with AS and 11 with PWS were alive on the prevalence day (January 1, 2005), indicating the point prevalence proportion of 1:56,112 (95% CI 1:25,780-1:1,52,899) and 1:30,606 (95% CI 1:17,105-1:61,311), respectively. Our results showing the birth prevalence of AS 1.7 times less than PWS challenge the opinion that both syndromes are equally represented, and are in line with the view that mutations in sperm and oocytes occur at different frequencies.

Atypical genital herpes: report of five cases

Manifestations of human genital herpes virus (HSV) infection are not limited to the typical cluster of genital lesions. Here we present 5 case histories suggestive to clinically atypical genital herpes (HSV detected with the polymerase chain reaction) collected in 2001 from a private outpatient clinic specializing in dermatological and venereal diseases. The clinical presentations included mucopurulent cervicitis, haemorrhagic cystitis, recurrent urethritis, and lower back pain.

Allergic sensitization among adults in Tallinn, Estonia

BACKGROUND

The prevalence of allergic sensitization has increased worldwide during recent years.

OBJECTIVE

The aim of the study was to estimate the prevalence of allergic sensitization and to evaluate the influence of age, gender, number of siblings, pet keeping in childhood, and residential area before the age of five on allergic sensitization among adolescents and adults aged 17-66 years in the capital of Estonia, Tallinn. A cross-sectional study was carried out between March 1997 and December 1998.

METHODS

The sensitization to 15 inhalant allergens was assessed. The associations between sensitization based on skin prick tests (SPTs), symptoms based on a structured interview, and possible risk factors were estimated. A random sample of 516 subjects was included in the study analysis.

RESULTS

The prevalence of allergic sensitization was 34.5%, while it was 39.3% in subjects aged 20-44 years. The most prevalent sensitization was against the German cockroach, 15.5%, and it was particularly high among adolescents. It was followed by mugwort, dog, two storage mites species, and cat dander. Subjects with wheezing during the last 12 months, attacks of shortness of breath, wheezing due to furred animals, and allergic rhinitis or conjunctivitis had a significantly higher prevalence of positive SPT.

CONCLUSION

We found a surprisingly high prevalence of allergic sensitization among adults in Tallinn. Our results suggest that the cockroach allergen should be included in the investigation panel in order to reach a true prevalence of allergic sensitization in Estonia. Further, the pattern of allergic sensitization in Estonia appears to be different from published data about allergic sensitization in Scandinavia.

Protonation of deoxycytidine residues in dC4 tetraloops: UV spectrophotometric study of dC10 and d(A14C4T14)

It is shown that component analysis could be applied to study the UV difference spectra of cytidine oligomers and hairpin oligonucleotides with cytidines in the loop region in order to account for the melting and titration results in terms of cytidine stacking and protonation. Upon acid titration, the dC(10) oligomer undergoes cooperative conformational transition at pH 6.3 accompanied by protonation and formation of the i-structure with half of the residues protonated. The stability of the hemiprotonated structure increases with decreasing pH, the i-structure persisting still in the region of pH<pK of cytidine. An UV difference spectrum that reflects the stacking/unstacking of hemiprotonated cytidine residues was acquired from the melting and titration experiments of the dC(10) oligomer and used to describe the behavior of the dC(4) loop of the hairpin oligonucleotide d(A(14)C(4)T(14)). It is shown that upon titration, the 50% level of protonation of the deoxycytidine tetraloop is attained at pH 5.0. Simultaneously, the stacking interactions of cytidine residues reach the maximum at this pH with two residues stacked, and thereafter decline again. Only marginal stabilization of the oligomer hairpin (DeltaT(m)=1.5 degrees C) is found to accompany the formation of this single hemiprotonated dC.dC(+) base pair. We propose that at pH 5 the cytidines of the dC(4) loop form a hemiprotonated dC.dC(+) pair stacked with the last dA.dT base pair of the hairpin stem.

Amniotic fluid microflora in asymptomatic women at mid-gestation

The presence and composition of amniotic fluid (AF) microflora, as well as AF glucose concentration and white blood cell (WBC) count, were investigated in 22 consecutive asymptomatic women with intact membranes at mid-gestation. AF was retrieved by trans-abdominal amniocentesis. Three of the 22 women (13.6%) had microorganisms in their AF: Chlamydia trachomatis in 2 and both Corynebacterium group absolute nonfermenter (ANF) group and Propionibacterium spp. in 1. No differences were found in clinical characteristics, glucose concentration or WBC count in patients with and without microorganisms in their AF.

Hepatitis C virus genotypes in Estonia

Distribution of hepatitis C virus (HCV) geno(sub)types among 215 Estonian patients hospitalized with acute or chronic hepatitis and with HCV RNA-positive sera was investigated. For genotyping, both multiplex PCR with subtype-specific primers of the core region and RFLP analysis of cDNA of the 5' NCR region were used. These two methods permitted a correct characterization of genotypes, a more truthful characterization of mixed infections, and combined use of single-tube performances. They revealed, respectively, 200 and 202 (93.0% and 93.9%) HCV-positive samples of sera, subtype 1a- 0.9% and 0.9%, 1b- 56.3% and 64.2%, 3a- 13.9% and 22.3%, 2a- 6.5% and 5.6%, type 4 0.5% and 0%, mixed infections- 13.5% and 0%, and unidentified- 1.4% and 0.9%. In the majority of cases (84.7%) both methods gave completely or partially concordant results; in mixed infections, as determined by subtype-specific PCR, only one subtype was revealed by the RFLP method. In the remaining 15.3% of the cases (Ohno- 7.0%, RFLP- 8.3%) only one of the methods was positive. The epidemiological analysis of the dynamics of the subtypes' relative participation may indicate increasing 3a and decreasing 1b subtype infection during recent years.

Distribution of Acinetobacter baumannii in a neurointensive care unit

In a 1-month prospective case-matched study we found Acinetobacter baumannii was a prevailing microbe simultaneously colonizing respiratory tract and skin of neurointensive care unit patients who stayed in our neurointensive care unit for more than 3 d. A. baumannii was not isolated from healthy case-matched controls. Based on their phenotypic properties and the results of amplified ribosomal DNA restriction analysis the 12 strains of Acinetobacter spp. isolated were identified as belonging to DNA group 2 (A. baumannii). For epidemiological typing, Biolog system results of 95-carbon source oxidation, antibiograms and restriction endonuclease analysis were used. One predominant A. baumannii strain was found in all colonized patients, skin and respiratory tract were found mainly to be colonized with the same strain. The starting point of A. baumannii colonization seemed to vary with the individual patient. Environmental strains were different from patients' strains: they were metabolically more active, more resistant and had a different restriction endonuclease analysis profile.

Are there molecules of nucleoprotamine?

A short critical review of the data related to protamine and nucleoprotamine (DNP) structure is given. A new model is proposed for DNP structure in which protamine molecules are located in channels between the DNA molecules. DNA molecules are arranged hexagonally in the x-y plane, whereas their relative positions with respect to the z-axis are shifted by 0, 1/3, and 2/3 of the pitch of the double helix. As a result, large cavities are formed in three out of six channels surrounding each DNA molecule where the large grooves are juxtaposed. Protamine molecules are also proposed to have some secondary/tertiary structure prior to complex formation. Inside the channels, a protamine molecule modifies its shape to fill the large grooves of all of the three surrounding DNA molecules simultaneously, and might possibly be in touch with other protamine molecules in neighbouring positions as well. This disposition allows the protamine molecules to be located between DNA molecules without a significant increase in the lattice parameters.

Free energy of the binding of uridylic acid oligomers with double stranded poly(A) · poly(U)

The binding parameters (K, omega) and the free energy (DeltaG(0)) of triple helix formation have been estimated for complexes of oligo(U)(n) (n = 5, 7-10) with poly(A) . poly(U) on the basis of hypochromicity measurements. The data were treated according to the formula of McGhee and von Hippel [J. Mol. Biol. 86 (1974) 469] by a computer program ALAU [H. Schütz et al., Stud. Biophys. 104 (1984) 23] which takes absorbancies and total concentrations as input. In 1 mM cacodylate buffer pH 7.0 with 10 mM NaCl and 10 mM MgCl(2) at 5 degrees C the free energy of contiguous binding was found to be a linear function of the oligomer length with a slope of DeltaG(c,U)(0) = -0.72 (+/-0.03) kcal x mol(-1) per nucleotide. The mean cooperativity coefficient (omega) was 24.5 (+/- 5.6), and the corresponding free energy of interaction between the neighbouring oligonucleotides in the third strand was DeltaG(0(omega)) = -1.74 (+/-0.13) kcal x mol(-1).

[Interaction specificity of violamycin BI and BII with DNA using the hyperchromic spectra method]

Interaction specificity of the anthracycline antibiotics violamycin BI and violamycin BII in respect to A.T and G.C pairs was investigated. For comparison denaturation of complexes with A.T and G.C specific ligands distamycin A and actinomycin D are presented. Making use of the least squares hyperchromic spectra measured in the course of thermal denaturation were partitioned into the components corresponding to the melting of A.T and G.C base pairs and dissociation of ligand. The mutual dependence of AT and GC denaturation allows one to draw conclusions about specificity of interaction. In case of both violamycins only slight preference of interaction with AT-rich regions was detected. The dissociation of violamycin BII in the latest stage of thermal denaturation was found to be cooperative.

Cooperative thermal denaturation of the assembly origin region of TMV RNA

The assembly origin (AO) region of the tobacco mosaic virus RNA melts in an usually narrow (2.5 degrees C) temperature range. In an 0.01 M phosphate buffer the melting temperature of AO was found to be 41.5 degrees C. This value corresponds to the regions with the most stable secondary/tertiary structure of the whole TMV RNA molecule. It is assumed that the AO region has a specific tertiary structure, which is maintained by the long-range interactions as well as by interactions of the pseudoknot type.

Nerve growth factor induces changes in (2'-5')oligo(A) synthetase and 2'-phosphodiesterase activities during differentiation of PC12 pheochromocytoma cells

Treatment of rat pheochromocytoma cell line PC12 with Vipera lebetina (snake) nerve growth factor (NGF) induces a rapid increase (from 5 to 25-fold) in the level of (2'-5')oligo(A) synthetase activity and a simultaneous decrease (from 2 to 5-fold) in the activity of 2'-5' A degrading enzymes--2'-phosphodiesterases (2'-PDE). These changes in the enzyme activities led to the significant increase in the intracellular concentration of 2'-5' A. We have found that the serum starvation of PC12 cells causes a 1.5 to 2.0-fold increase in the level of 2'-5' A-synthetase activity, but the activities of 2'-PDE and the intracellular concentration of 2'-5' A remain unaltered. These results show that NGF modulates the activity of (2'-5')oligo(A) enzymes and intracellular concentration of 2'-5' A during the neural differentiation of PC12 cells.

[Study of complexes of poly-L-histidine with DNA using hyperchromic spectra]

Complexes of DNA with poly-L-histidine in acidic media were investigated by the method of hyperchromic spectra. Making use of the least squares hyperchromic spectra were partitioned into the components corresponding to the melting of AT and GC base pairs and protonation of cytosine. The protonation of cytosine was found to be proportional to the fraction of broken GC base pairs and was not influenced by the presence of poly-L-histidine. Selectivity of poly-L-histidine towards the base pairs was found to be very weak or absent.

Thermal denaturation of distamycin A--DNA complexes as followed by hyperchromic spectra

Interaction of distamycin A with calf spleen DNA is investigated by the method of hyperchromic spectra. Hyperchromic spectra of complexes are partitioned into the components corresponding to the denaturation A . T and G . C base pairs and dissociation of the ligand, fractions of respective components are found as a function of temperature. A scheme of melting of successive regions of DNA with different G+C content together with the scheme of distamycin A redistribution in the course of thermal denaturation is presented.