Assessment of housekeeping genes for use in normalization of real time PCR in skeletal muscle with chronic degenerative changes.

The real time PCR technique requires the normalization of the gene of interest to reference genes that are accepted to be ubiquitously expressed. The choice of the reference gene(s) needs to be determined by researchers according to the particular tissue or model of interest. The best normalization gene is not easy to decide, particularly if the investigated tissue displays architectural changes and structural reorganization. We have investigated the expression of four housekeeping genes that are widely used for the normalization purposes (TATA binding protein, beta actin, hypoxanthine-guanine phosphorybosyl transferase and glyceraldehyde-3-phosphate dehydrogenase) in a skeletal muscle degeneration model applied by the release of the Achilles tendon which leads to a time-course degeneration of the soleus and gastrocnemius muscles. This study indicates that the TATA binding protein and the beta actin gene to be the least effected in the course of degeneration induced by tenotomy in rat soleus and gastrocnemius muscle.

Serial analysis of gene expression in the hippocampus of patients with mesial temporal lobe epilepsy.

Hippocampal sclerosis constitutes the most frequent neuropathological finding in patients with medically intractable mesial temporal lobe epilepsy. Serial analysis of gene expression was used to get a global view of the gene profile in human hippocampus in control condition and in epileptic condition associated with hippocampal sclerosis. Libraries were generated from control hippocampus, obtained by rapid autopsy, and from hippocampal surgical specimens of patients with mesial temporal lobe epilepsy and the classical pattern of hippocampal sclerosis. More than 50,000 tags were analyzed (28,282, control hippocampus; 25,953, hippocampal sclerosis) resulting in 9206 (control hippocampus) and 9599 (hippocampal sclerosis) unique tags (genes), each representing a specific mRNA transcript. Comparison of the two libraries resulted in the identification of 143 transcripts that were differentially expressed. These genes belong to a variety of functional classes, including basic metabolism, transcription regulation, protein synthesis and degradation, signal transduction, structural proteins, regeneration and synaptic plasticity and genes of unknown identity of function. The database generated by this study provides an extensive inventory of genes expressed in human control hippocampus, identifies new high-abundant genes associated with altered hippocampal morphology in patients with mesial temporal lobe epilepsy and serves as a reference for future studies aimed at detecting hippocampal transcriptional responses under various pathological conditions.

Effect of piracetam on sickle erythrocytes and sickle hemoglobin.

Piracetam, 2-oxo-1-pyrrolidine acetamide, inhibits sickling of red cells containing sickle hemoglobin (Hb S). The concentration required for 50% inhibition is about 300 mM. Addition of piracetam into the supersaturated Hb S solution in concentrated phosphate buffer prolongs the delay time prior to gelation. Piracetam shifts the oxygen equilibrium curves of blood toward the right, with a stronger effect at higher piracetam concentrations. Piracetam increases the viscosity of oxygenated cells but reduces the relative viscosity of deoxygenated sickle cells. The mechanism for the antisickling effect of piracetam will be discussed.

Mutation frequency of Familial Mediterranean Fever and evidence for a high carrier rate in the Turkish population.

Familial Mediterranean Fever (FMF) is a recessive disorder characterised by episodes of fever and neutrophil-mediated serozal inflammation. The FMF gene (MEFV) was recently identified and four common mutations characterised. The aim of this study was to determine the carrier rate in the Turkish population and the mutation frequency in the clinically diagnosed FMF patients. We found a high frequency of carriers in the healthy Turkish population (20%). The distribution of the five most common MEFV mutations among healthy individuals (M694V 3%, M680I 5%, V726A 2%, M694I 0% and E148Q 12%) was significantly different (P<0.005) from that found in patients (M694V 51.55%, M680I 9.22%, V726A 2.88%, M694I 0.44% and E148Q 3.55%).

Deletion analysis in Turkish patients with spinal muscular atrophy.

Childhood proximal spinal muscular atrophy (SMA) is an autosomal recessive disorder which presents as a severe, intermediate or mild condition. Here we present the molecular analysis of SMA candidate genes, the survival motor neuron gene (SMN), the neuronal apoptosis inhibitory protein gene (NAIP) and the p44 gene. Deletion frequency rate of these candidate genes is 93% in 106 Turkish SMA patients. Various deletion haplotypes by using genotypes of SMN, NAIP and p44 genes are constructed. Haplotype A, which is the deletion of all three involved genes, was found only in the most severe group with an early onset of usually less than 2 months of age.

Common deletion of mitochondrial DNA in a 5-year-old girl with failure to thrive, ptosis, ophthalmoplegia and ragged-red fibers.

A girl aged 4 years and 10 months presented with failure to thrive, ptosis, ragged-red fibers and the common 4.9 kb mitochondrial DNA deletion. She had elevated serum lactic and pyruvic acids. The onset was at around 18 months. There were no signs of retinitis, and abnormal renal, liver or pancreatic functions. She later developed mild ophthalmoplegia at 6 years of age. Additional features of chronic progressive external ophthalmoplegia (CPEO) or Kearns-Sayre syndrome (KSS) are the conditions that should be watched and investigated in the long-term follow-up of this girl.

Molecular deletion patterns in Turkish Duchenne and Becker muscular dystrophy patients.

The dystrophin gene deletion patterns of Duchenne/Becker dystrophy were investigated in 57 DMD, 7 BMD and 1 DMD-BMD intermediate muscular dystrophy patients. Deletions, analyzed by multiplex amplification of selected exons, were observed in 58% (38 cases) of the patients. It was found that exon 48 was the most frequently affected, while exon 44 was the least frequently affected. The number of deleted exons was variable, but single exon deletions were more frequent (41%) than larger deletions in our population and the great majority of deletions began distal to exon 44. The application of PCR to deletion analysis in D/BMD was found to be very useful in delineating the extent of the deletion in most of the cases (82%). It was seen that the frequency of deletion breakpoints in distal part of the dystrophin gene (exons 42-52) was detected in 64% of our cases. In our group, the frequency of deletion breakpoints in the same area of the dystrophin gene was between that of the French and the Finnish patients. The distribution of deletion breakpoints within the dystrophin gene of the Turkish population seems to have some differences from other populations. Deletion breakpoints were found to be clustered mainly in three separate regions covering introns 44, 45 and 50 within the central region of the dystrophin gene. Intron 44 was mostly 5' breakpoints but it was found not to be involved as 3' breakpoints. The correlation between phenotype and type of deletion agreed with the reading frame theory except for one DMD case.

mtDNA nt3243 mutation, external ophthalmoplegia, and hypogonadism in an adolescent girl.

A 14-year-old girl presented with a 3-month history of easy fatigue and exercise intolerance, especially when climbing stairs. She had a mild ptosis and mild limitation of upward gaze. Her puberty was delayed, and she manifested hypogonadotrophic hypogonadism. Serum lactic and pyruvic acids were elevated. Cranial magnetic resonance imaging was normal. Muscle biopsy documented typical ragged-red fibers. A point mutation at nucleotide 3243 in the tRNALeu(UUR) (typical mitochondrial encephalomyopathy, lactic acidosis, and stroke-like episodes (MELAS) mutation) was detected in mitochondrial DNA from both blood and muscle tissues, indicating that our patient was suffering from a mitochondrial myopathy. Hypogonadism may be a manifestation of the MELAS nucleotide 3243 mutation.

Allele distribution of D5S125, MAP1B5' and D5S679 microsatellite markers in Turkish spinal muscular atrophy families.

Spinal muscular atrophy (SMA) is an autosomal recessive disease and one of the most common genetic causes of death in childhood. The gene for SMA has been mapped to chromosome 5q11.2-13.3. Chromosomal distribution of the alleles of D5S125, MAP1B5' and D5S679 polymorphic microsatellite markers in 14 unrelated Turkish SMA families have been determined. It is observed that the A9 allele of D5S679 has a significant (chi 2: 3.41 p: 0.065) non-random association with mutant chromosomes.

Deletion analysis of Duchenne muscular dystrophy.

DNA of 15 patients with Duchenne muscular dystrophy (DMD) were analyzed for deletions within the DMD gene by using recombinant DNA technology. Deletion frequency was 47 percent and six of the deletions occurred in the region of probe 7 + 8. Only one of the deletions was observed in the region of probe 9-7, and no deletions were found in the region of probe 30-1, 30-2 and 47-4 (5b + 6). The frequency of deletions found in the Turkish DMD patients corresponds to frequencies reported for other populations.

Prenatal diagnosis of cystic fibrosis in a Turkish family.

Prenatal diagnosis of cystic fibrosis (CF) was made in a Turkish family whose first born child was diagnosed at necropsy as having CF. Two consecutive pregnancies followed. The fetus of the second pregnancy was diagnosed as having CF by the microvillar enzyme assay and was aborted. The diagnosis was verified by the DNA polymerase chain reaction analysis using chorionic villi from the abortus. In the third pregnancy, amniocentesis was performed in the 17th week, and KM19 polymorphism linked to CF was used to assess the status of the fetus. Since the fetus was determined to be a carrier, the family was advised to continue with the pregnancy.

Frequency of the IVS-10nt546 mutation in 44 Turkish phenylketonuria patients.

The newly identified point mutation in intron 10 of the phenylalanine hydroxylase gene activates a cryptic splice site and results in an in-frame insertion of nine nucleotides between exons 10 and 11 of the processed transcript. This mutation is observed in association with haplotype 6 of phenylketonuria chromosomes. Since in Turkey, haplotype 6 is observed in 40 percent of mutant phenylketonuria alleles, the aim of this study was to establish the incidence of this particular mutation. Forty-four classical phenylketonuria patients were studied and the frequency of the intron 10 splicing mutation was determined to be 31 percent.

Newborn PKU screening in Turkey: at present and organization for future.

At present, pkenylketonuria screening is a national child health program in Turkey which is carried out collaboratively by the Ministry of Health and three University Children's Hospitals in Ankara, Istanbul and Izmir. Since 1986 the number of cities included in the screening program has gradually increased, now and it covers all the metropolises the country. A total of 383 babies were found with persistent hyperphenylalaninemia (1:4,172) among 1,605,582 babies screened by the Guthrie test at the Hacettepe Screening Center in Ankara. By taking into account pretreatment phenylalanine levels and phenlyalanine tolerances at five years of age, the numbers of classical and mild-moderate phenylketonuria and mild hyperphenylalaninemia cases were 216, 102 and 58, respectively. The major problems encountered in the screening program and in management of the detected cases were unsatisfactory sample collection, early discharge from maternity hospitals, difficulties in reaching some detected cases, and noncompliance with dietary therapy due to illiterate parents or to lack of social insurance. To screen and treat all newborns for phenylketonuria and to include at least hypothyroidism in the screening program, there is a need for a more disciplinary intersectoral approach than exists at present.

Myogenic program induction in mature fat tissue (with MyoD expression).

MyoD exerts a master transcriptional control over the myogenic differentiation cascade. Here, we study different approaches to induce myogenic transdifferentiation in mature adipocytes utilizing MyoD gene transfer. Organotypic cultures of fat tissue and a long-term culture of in vitro differentiated adipocytes deduced that MyoD provoked morphological changes in mature adipocytes that can be summarized as loss of fat content, acquisition of a fusiform shape and eventual fusion with committed neighbor cells. In vivo, MyoD gene transfer into rat interscapular and inguinal fat pads demonstrated that while structural proteins of muscle lineage were expressed, they co-existed with specific adipocyte proteins. Expression of these proteins diminished over time likewise the fat content. The transdifferentiation process initiated by MyoD did not require cell cycle progression and was well tolerated by the fully differentiated and mature adipocytes.

Frequencies of TAP1 and TAP2 gene polymorphisms in the Anatolian population.

Anatolia has a long and complex record of immigration from various regions. Here, we have used TAP1 and TAP2 gene polymorphisms as genetic markers to study the relationship between the Anatolian population and other populations. A neighbour-joining tree was constructed indicating the relatedness of European populations and the Anatolian population with respect to TAP1 and TAP2 allele frequencies.

Mutation analysis in Turkish phenylketonuria patients.

Forty-four classical PKU patients have been screened for various mutations. The newly identified IVS 10 splicing mutation was found in 32% of the mutant alleles and comprises 74.5% of the mutations that could be typed: 261arg-gln (6.8%), 158arg-gly (2.3%), 252arg-trp (1.1%), 280glu-lys (-), and 272gly-stop (-) were the other mutations that were screened.

Sodium chloride deficiency in cystic fibrosis patients.

Sodium chloride deficiency (SCD) was observed within the 1st year of life in 12 of 46 cystic fibrosis (CF) patients between July 1989 and September 1992. All patients showed sweating, loss of appetite, fever, vomiting, irritation, dehydration, weakness, and cyanosis during an attack. Mean plasma sodium, potassium and chloride levels were 122.9 (range 106-135), 2.5 (range 1.6-3.5), and 73.3 (range 60-90) mEq/l respectively. Alkalosis and elevated plasma renin activity were detected in all patients. Of the patients, 50% showed microscopic haematuria, and hypercalciuria was detected in two out of four patients. Low urinary sodium and high urinary potassium were observed in the four examined patients. Increased creatinine, BUN and uric acid values returned to normal with treatment. All the patients were treated initially with intravenous fluids and electrolyte solutions. All patients were less than 7 months of age during the first attack, five received only breast milk and the others breast milk with formula milk. Their oral salt supplement was 2-4 mEq/kg per day, which is recommended for CF patients, but could be deficient in excessively sweating infants. The genotype of these patients might be cause of high salt losses. F508 is the most common mutation with the frequency of 38% in our CF patients with SCD, but the frequency of unknown mutations is high (54%).

Study of 12 mutations in Turkish cystic fibrosis patients.

67 unrelated cystic fibrosis (CF) patients were screened for some of the most common mutations of the CFTR gene. This analysis resulted in the identification of 34.6% of all CF alleles. The most common mutation is delta F508 (28.4%). Two other mutations account for a further 6.7% of the alleles (R347H: 3.0%; N1303K: 3.7%). 1677delTA, G542X, G551D, S549N/I, R553X, L558S, R334W, and R297Q were not detected.

Mitochondrial DNA analysis in the Turkish Leber's hereditary optic neuropathy population.

PURPOSE: To define the prevalence of a panel of mitochondrial DNA (mtDNA) mutations associated with Leber's hereditary optic neuropathy (LHON) in the Turkish LHON population. LHON-associated mtDNA mutations have been found in LHON patients from around the world, but the Turkish LHON population has not been studied. METHODS: Thirty-two Turkish patients were defined clinically as having LHON on the basis of painless, subacute, bilateral optic neuropathy and the exclusion of other causes of subacute optic neuropathy. mtDNA was extracted from blood of the 32 probands and assayed for a panel of primary and secondary LHON-associated mtDNA mutations by polymerase chain reaction (PCR)-based methods. We studied three well-known LHON-associated primary mutations (at nucleotide positions 11778, 3460 and 14484) and one common secondary mutation (at nucleotide 15257) in all 32 probands. In addition to these mutations, 18 of the 32 probands were tested for the Complex IV, COX III gene, LHON associated 9804 and 9438 mutations and secondary LHON mutations at nucleotide positions 3394, 4160, 4216, 4917, 5244, 7444, 7706, 13708, 13730 and 15812. RESULTS: Among the 32 probands tested for four common LHON mutations, 3 carried the 14484 mutation, 1 carried the 11778 mutation, 1 carried the 3460 mutation and 1 carried the 15257 mutation. Among the 18 LHON patients who tested for additional mutations, 1 proband harboured the 9804 mutation and 4 carried the secondary mutations at nucleotide positions 4216, 4917 and 13708. CONCLUSION: The results of mtDNA analysis of the Turkish LHON patients appear to be different from those of previous reports.