Ectopic expression of NnPER1, a Nelumbo nucifera 1-cysteine peroxiredoxin antioxidant, enhances seed longevity and stress tolerance in Arabidopsis.

Seed longevity, the maintenance of viability during storage, is a major factor for conservation of genetic resources and biodiversity. Seed longevity is an important trait of agriculture crop and is impaired by reactive oxygen species (ROS) during seed desiccation, storage and germination (C. R. Biol., 331, 2008 and 796). Seeds possess a wide range of systems (protection, detoxification, repair) allowing them to survive during storage and to preserve a high germination ability. In many plants, 1-cys peroxiredoxin (1-Cys Prx, also named PER1) is a seed-specific antioxidant which eliminates ROS with cysteine residues. Here we identified and characterized a seed-specific PER1 protein from seeds of sacred lotus (Nelumbo nucifera Gaertn.). Purified NnPER1 protein protects DNA against the cleavage by ROS in the mixed-function oxidation system. The transcription and protein accumulation of NnPER1 increased during seed desiccation and imbibition and under abiotic stress treatment. Ectopic expression of NnPER1 in Arabidopsis enhanced the seed germination ability after controlled deterioration treatment (CDT), indicating that NnPER1 improves seed longevity of transgenic plants. Consistent with the function of NnPER1 on detoxifying ROS, we found that the level of ROS release and lipid peroxidation was strikingly lower in transgenic seeds compared to wild-type with or without CDT. Furthermore, transgenic Arabidopsis seeds ectopic-expressing NnPER1 displayed enhanced tolerance to high temperature and abscisic acid (ABA), indicating that NnPER1 may participate in the thermotolerance and ABA signaling pathway.

[Association study between candidate genes on transforming growth factor-ß signaling pathway and the risk of non-syndromic cleft lip with or without cleft palate in Chinese populations].

OBJECTIVE: To explore the association between 10 candidate genes on transforming growth factor-ß (TGFB) signaling pathway and non-syndromic cleft lip with or without cleft palate (NSCL/P) among Chinese populations, and to study the gene-environment interaction. METHODS: A total of 806 Chinese Han NSCL/P trios were ascertained from an international consortium, which conducted a genome-wide association study using a case-parent trio design to investigate the genes affecting risk to NSCL/P. The transmission disequilibrium test (TDT) was used to test for effects of 343 single nucleotide polymorphisms (SNPs) in 10 genes on TGFB signaling pathway including DCN, TGFB1, TGFB2, TGFB3, TGFBR1, TGFBR2, BAMBI, SMAD2, SMAD3 and SMAD4. The conditional regression models were used to test for gene-environment interaction. RESULTS: For TDT, although 19 SNPs showed nominal significant association with NSCL/P, no significant evidence of association was seen for all SNPs in 806 NSCL/P trios after Bonferroni correction. The interactions between genes and maternal smoking, environmental tobacco smoke, alcohol consumption and multi-vitamin supplementation during pregnancy did not attain statistical significance after correction for multiple comparisons. CONCLUSION: No evidence for SNP effect of genes on TGFB signaling pathway and significant gene-environment interaction was seen in our data.

[Association study for gene polymorphism of folic acid/homocysteine metabolic pathway and nonsyndromic cleft lip with or without cleft palate in Chinese populations].

OBJECTIVE: To explore the association between 18 candidate genes encoding enzymes on the folate/homocysteine metabolism pathway and non-syndromic cleft lip with or without cleft palate (NSCL/P) in Chinese populations. METHODS: A total of 806 NSCL/P trios were drawn by an international consortium, which conducted a genome-wide association study using a case-parent trio design to investigate genes affecting risks to NSCL/P. The transmission disequilibrium test (TDT) was used for deviation from Mendelian expectations for 257 SNPs in 18 folate/homocysteine metabolism-related genes. The interactions between markers in these gene and environmental risk factors were also tested using conditional Logistic regressions. RESULTS: Although four SNPs (rs6428977, rs12060264, rs7730643 and rs4920037) showed nominal significant association with NSCL/P in the TDT on 806 NSCL/P trios (P<0.05), no significant evidence of linkage and association remained in all the SNPs after Bonferroni correction. Similar tests for interactions between genes and maternal smoking, environmental tobacco smoke, alcohol consumption and multi-vitamin supplementation during pregnancy did not attain statistical significance after correction for multiple comparisons. CONCLUSION: Folate/homocysteine metabolism-related genes could not influence the risk of NSCL/P.

[Mutation analysis of PTPN11 gene in Noonan syndrome].

OBJECTIVE: To investigate the mutations in protein tyrosine phosphatase, nonreceptor-type 11 (PTPN11) gene in patients with Noonan syndrome (NS). METHODS: Three sporadic patients with NS were studied. Genomic DNAs were extracted from peripheral blood leukocytes. All 15 coding exons and their flanking intronic boundaries of the PTPN11 gene were amplified by polymerase chain reaction and followed by direct sequencing. DNAs from parents were sequenced in the corresponding region when the mutation was detected in their affected child. The identified mutation was screened in 100 healthy individuals for exclusion of polymorphism by restriction endonuclease digestion of the PCR products. Protein conservation analysis was performed among 10 species using an online ClustalW tool. RESULTS: Direct DNA sequence analysis identified a heterozygous 181G to A change in exon 3 of the PTPN11 gene in one patient, which resulted in the substitution of an aspartic acid residue by an asparagine at codon 61. The mutation was absent in his parents and 100 controls, and is located in a highly conserved amino acid site. No mutation in the coding region of PTPN11 gene was observed in the other two patients. CONCLUSION: The p.D61N mutation was reported previously in Caucasians and is a de-novo mutation in this patient. Our study further confirmed that the p.D61N is a pathogenic mutation for NS and consistent with the clinical diagnosis. Additional genes may be involved in the other two patients with NS, indicating high genetic heterogeneity of this disease.

[Clinical manifestations and mutation study in 16 Chinese patients with Fabry disease].

OBJECTIVE: To investigate the clinical manifestations and to characterize mutations of the GLA gene in Chinese patients with Fabry disease so to enhance the diagnosis of Fabry disease. METHODS: Sixteen Chinese affected males (from 16 unrelated families) with the classic phenotype of Fabry disease were investigated. The patients were diagnosed by a deficiency of alpha-galactosidase A (alpha-Gal A) activity. All seven exons and the neighboring intronic sequences of GLA gene were analyzed by PCR amplification and automated sequencing. RESULTS: A total of 14 mutations were identified including 12 single-base substitutions (11 missense and 1 nonsense mutations), 1 small deletion and 1 splicing mutation. Eight novel mutations (c.119 C > A, c.275 A > T, c.520T > C, c.547G > C, c.647A > G, c.929T > G, c.1045T > A, IVS1-1G > A) were identified. The novel mutations were not tested by RFLP on 100 GLA alleles in Chinese population, and were highly conservative in mammalian species. CONCLUSION: Fabry disease is often misdiagnosed in China. There is no hot spot for mutations in Chinese patients. GLA gene mutation analysis is a reliable method to diagnosis for Fabry disease.

[Novel CHST6 compound heterozygous mutations cause macular corneal dystrophy in a Chinese family].

OBJECTIVE: The aim of this study was to identify mutations of CHST6 gene in a Chinese family with macular corneal dystrophy (MCD) and to investigate the histopathological changes of MCD. METHODS: Corneal button of the proband was obtained from penetrating keratoplasty for the treatment of severe corneal dystrophy. The sections and ultrathin sections of this specimen were examined under light microscope and transmission electron microscope (TEM). Genomic DNA was extracted from leukocytes in peripheral blood from the family members. The coding region of CHST6 was amplified by polymerase chain reaction (PCR). The PCR products were analyzed by direct sequencing and restriction enzyme digestion. RESULTS: Histochemical study revealed positive results of colloidal iron stain. TEM revealed enlargement of smooth endoplasmic reticulum and the presence of intracytoplasmic vacuoles. Two mutations, Q298X Y358H, were identified in exon 3 of CHST6. Three patients were compound heterozygotes of these two mutations. The C892T transversion occurred at codon 298 turned the codon of glutamine to a stop codon; the T1072C transversion occurred at codon 358 caused a missense mutation, tyrosine to histidine. All six unaffected family members were heterozygotes. These two mutations were not detected in any of the 100 control subjects. CONCLUSIONS: The novel compound heterozygous mutation results in loss of CHST6 function and causes the occurrence of MCD. This is the first report of this gene mutation.

Clinical and genetic study of a novel mutation in the REEP1 gene.

OBJECTIVE: To examine the gene mutation associated with clinical phenotype from a Chinese kindred with autosomal dominant hereditary spastic paraplegia (ADHSP). METHOD: To perform linkage analysis and mutation detection. For two affected individual of the family, clinical analysis, electrophysiological examination, and MRI of brain and spinal cord were also performed. RESULT: A novel splice-site mutation (REEP1 c417+1g>a) was identified. Central motor conduction time to the first metatarsal interosseus and anterior tibial muscles were clearly prolonged. Thoracic cord atrophy was found from T1 to T10. CONCLUSION: Our study supports that mutations in REEP1 cause ADHSP and demonstrates genetic heterogeneity in ADHSP. Synapse

[Detection of microdeletion in Williams syndrome by multiplex ligation-dependent probe amplification].

OBJECTIVE: To establish a method of multiplex ligation-dependent probe amplification (MLPA) for clinical screening of Williams syndrome (WS) and for routine use in WS diagnosis. METHODS: Probes for MLPA were designed according to the frequent deletion regions, and used to screen the two patients suspected with Williams syndrome, and the density of the bands were analyzed with software. Linkage analysis using polymorphic markers was performed to confirm the positive result of MLPA. RESULTS: The MLPA data indicated that the two children had possible microdeletions in the WS critical region. The deletions were confirmed and both were maternal origin by polymorphism analysis. CONCLUSION: MLPA is a quick and convenient method for detecting deletion or duplication mutations. It can provide reliable and helpful information for clinical diagnose of Williams syndrome.

[Mutation analysis of the PAH gene in patients with phenylketonuria in Gansu province].

OBJECTIVE: To characterize the mutations of the phenylalanine hydroxylase (PAH) gene in patients with phenylketonuria in Gansu province. METHODS: Mutations of the PAH gene were detected in exons 3, 5, 6, 7, 11 and 12 with flaking introns of PAH gene by PCR and DNA sequencing. RESULTS: Mutations were identified in 45/58 alleles (detection rate: 96.4%), in total of 18 variants. Among them IVS12+5G>C was a novel mutation. The most frequent mutations were R243Q (22.7%), V399V (12.1%), EX6-96A>G (5.2%), R413P (5.2%) and IVS4-1G>A (5.2%), followed by Y356X (3.4%), R111X (3.4%) and INS7+2T>A (3.4%). CONCLUSION: The mutations of the phenylalanine hydroxylase gene in patients with phenylketonuria in Gansu province were similar to that in other areas of China, with obvious difference in mutation rate of some mutations.

[An analysis of mutations causing Gaucher disease in Chinese population].

OBJECTIVE: To review and investigate the relationship of genotype and phenotype in Chinese patients with Gaucher disease (GD). METHODS: The samples were first screened for known mutations as reported previously in Chinese population. Long chain PCR and nested PCR were employed to amplify the segments of glucocerebrosidase functional gene in patients with unknown mutant alleles. The products of nested-PCR were subjected to DNA sequencing to detect the new mutations. RESULTS: Forty kinds of mutations were detected in this panel of patients. The L444P mutation was the most common one accounting for 33.0% of mutant alleles. It was followed by F213I, N188S, V375L and M416V. CONCLUSION: There are at least 40 mutations in Chinese GD patients. The spectrum of mutation is significantly different from that in Caucasians. 70% of mutant alleles have been characterized. It becomes feasible to make clinical and prenatal diagnoses through gene analysis.

Array-MLPA: comprehensive detection of deletions and duplications and its application to DMD patients.

Multiplex ligation-dependent probe amplification (MLPA) is widely used to screen genes of interest for deletions and duplications. Since MLPA is usually based on size-separation of the amplification products, the maximum number of target sequences that can be screened in parallel is usually limited to approximately 40. We report the design of a robust array-based MLPA format that uses amplification products of essentially uniform size (100-120 bp) and distinguishes between them by virtue of incorporated tag sequences. We were thus able to increase probe complexity to 124, with very uniform product yields and signals that have a low coefficient of variance. The assay designed was used to screen the largest set studied so far (249 patients) of unrelated Duchenne muscular dystrophy (DMD) cases from the Chinese population. In a blind study we correctly assigned 98% of the genotypes and detected rearrangements in 181 cases (73%); i.e., 163 deletions (65%), 13 duplications (5%), and five complex rearrangements (2%). Although this value is significantly higher for Chinese patients than previously reported, it is similar to that found for other populations. The location of the rearrangements (76% in the major deletion hotspot) is also in agreement with other findings. The 96-well flow-through microarray system used in this research provides high-throughput and speed; hybridization can be completed in 5 to 30 minutes. Since array processing and data analysis are fully automated, array-MLPA should be easy to implement in a standard diagnostic laboratory. The universal array can be used to analyze any tag-modified MLPA probe set.

Nonsense mutation in the CRYBB2 gene causing autosomal dominant progressive polymorphic congenital coronary cataracts.

PURPOSE: We sought to identify the genetic defect in a large, five-generation Chinese family with autosomal dominant progressive polymorphic congenital coronary cataracts and to examine the clinical features in detail. METHODS: Clinical and ophthalmologic examinations were conducted on family members. All members were genotyped with microsatellite markers at loci previously associated with cataracts. Two-point LOD scores were calculated using a linkage package after genotyping. A mutation was detected by direct sequencing and verified by denaturing high-performance liquid chromatography (DHPLC). RESULTS: Clinical observations showed that all affected family members had progressive polymorphic coronary cataracts. Linkage analysis was obtained at markers, D22S303 (LOD score [Z]=2.11, recombination fraction [theta]=0.0) and D22S1167 (Z=1.20, theta=0.0). Haplotype analysis indicated that the cataract gene was closely linked with these two markers. Sequencing the betaB-crystallin gene (CRYBB2) revealed a C --> T transition in exon 6, which changed a codon from Gln to a stop codon (P.Q155X). This mutation cosegregated with all affected individuals and was not observed in any unaffected family member or 100 normal, unrelated individuals. CONCLUSIONS: This study identified a mutation in CRYBB2 in a large Chinese family with autosomal dominant progressive polymorphic congenital coronary cataracts. These results provide evidence that CRYBB2 is a pathogenic gene for congenital cataracts; at the same time, congenital cataracts are a clinically and genetically heterogeneous lens condition.

Clinical and genetic study of SPG6 mutation in a Chinese family with hereditary spastic paraplegia.

Mutations in the NIPA1 gene cause autosomal dominant hereditary spastic paraplegia (ADHSP). To date, little is known about the relationship between genotype-phenotype correlation. In order to examine the gene mutation associated with the genotype-phenotype of Chinese kindred with ADHSP, linkage analysis and mutation detection were performed. For affected family members, clinical analysis, electrophysiological examination and MRI of the brain and spinal cord were also performed. Every effected patient had a c316 (G106R) mutation in the NIPA1 gene. Neurophysiological examination revealed decreased amplitude of compound muscle action potentials (CMAP) from the tibial and peroneal motor nerves in most patients. Sensory nerve action potential (SNAP) from the tibialis nerve was not elicited in most patients. Central motor conduction time (CMCT) to the abductor pollicis brevis muscle (APB), first metatarsal interosseus muscle (FMI) and anterior tibial muscle (AT) were either absent or clearly prolonged in all patients. Spinal cord MRI showed different levels of atrophy in every affected individual. These lesions present an increased spot or patch signal on transverse axis T2WI and an intense signal of continual longitudinal strip on the anteroposterior axis. Our study supports that mutations in the NIPA1 gene cause ADHSP and further demonstrates genotype-phenotype correlations in SPG6.

[Quantitative analysis of SMN1 and SMN2 genes based on DHPLC: a reliable method for detection of non-homozygous patients with spinal muscular atrophy].

OBJECTIVE: To develop a rapid and reliable approach for testing the copy number of survival motor neuron (SMN) gene and analyze the compound heterozygous deletions of SMN1 gene. METHODS: Peripheral blood samples were collected from 38 non-homozygous deletion pediatric patients with SMA, 30 homozygous deletion patients with SMA, and 35 un-related healthy persons. SMN1 and SMN2 genes were amplified separately with allele-specific PCR (AS-PCR). Meanwhile, two irrelevant genes were amplified as internal quality control respectively. The copy numbers of SMN1 and SMN2 were determined by denaturing high-performance liquid chromatography (DHPLC). RESULTS: (1) A protocol combining multiplex allele-specific PCR and DHPLC was developed to separate SMN1 and SMN2 and to determine the copy numbers of them. The copy numbers of SMN1 and SMN2 varied from 1 to 4 and a clear-cut differentiation among the different copy number ranges could be observed for the two genes. (2) One single copy of SMN1 were detected in 20 of the 38 non-homozygous deletion patients with SMA (52.6%). Heterozygous deletions were determined in these 20 patients. Two copies of SMN2 were detected in 15 of the 20 patients with one copy of SMN1 (75.0%, 15/20). Other 5 of the 20 patients were with 3 copies of SMN2 (25.0%, 5/20). (3) One single copy of SMN1 was detected in 24 of the 30 (80%) parents of SMA patients with homozygous deletion. CONCLUSION: SMN copy number can be rapidly and reliably determined by the method of multiplex AS-PCR combined with DHPLC.

A novel mutation in the EXT2 gene identified in two unrelated Chinese families with hereditary multiple exostoses.

Hereditary multiple exostoses (HME) is an autosomal dominant disorder characterized by benign bone tumors. In this report, we describe two unrelated Chinese families with HME. Linkage analysis and mutation detection was performed. Clinical analysis was also performed for some affected individual in both families. Linkage with the EXT2 was established in both families. A novel mutation, c505 G > T, was identified in both families. Further allelic heterogeneity of EXT2 was demonstrated by the intrafamilial and interfamilial variability in clinical phenotype.

[The power of linkage analysis on PAH gene in prenatal gene diagnosis is improved with three additional short tandem repeat markers].

OBJECTIVE: To increase the success rate of prenatal diagnosis for classical phenylketonuria(PKU). METHODS: Three new short tandem repeat (STR) markers (PAH26, PAH32 and PAH9) within and surrounding phenylalanine hydroxylase(PAH) gene were selected for amplified fragment length polymorphism. The allele frequencies and polymorphism information contests (PIC) were determined in Chinese population. RESULTS: The PIC of these three new STR markers was 0.518 (PAH26), 0.413 (PAH32) and 0.362 (PAH9) respectively. There was linkage disequilibrium between PAH9 marker and PAH-STR marker (TCTA)n in the intron 3 of PAH gene. The linkage phase of the mutant genes and the markers was established using the combination of PAH-STR, PAH26 and PAH32 in 95% families. Prenatal diagnosis was performed successfully with these markers in four cases. CONCLUSION: By selecting or combining the three STR markers, the mutant genes could be distinguished from the normal allele in up to 95% of families with classical PKU.

[Rapid diagnosis of Down's syndrome by multiplex real-time fluorescence relative quantitative PCR].

To establish a multiplex real-time fluorescence relative quantitative PCR method for diagnosis of Down's syndrome. The fragment from Down's syndrome critical region gene 3 (DSCR3) on chromosome 21 was used as the target gene, and the glyceraldehyde-3-phosphate dehydrogenase (GAPDH) gene on chromosome 12 was used as the control gene. The two genes were amplified in the same tube. The relative quantitative index-CT value was used to differentiate trisomy 21 patient from normal person. The peripheral blood sample from a Down's syndrome patient was collected and the B-lymphocytes were transformed by Epstein-Barr virus to establish the immortalized cell lines as standard material. The reaction conditions were optimized to obtain an equal amplification efficiency from both the target and the control genes. The slopes of both genes were almost -3.32, indicating that the efficiencies of the two amplifications were approximately equal. Among a certain range from 3-300 ng/PCR, the variation of detected DeltaCT value were less than 15%, and amplification showed the highest reproducibility when the concentration of DNA template was 30 ng/microL. Then, the variation of DeltaCT value with inter- and intra-assay were 9.8% and 13.3% at this DNA concentration of the templates. Clinical samples, including 20 blood samples from patients and 30 blood samples from normal persons, were detected using the established method. The DeltaCT value from Down's syndrome group were dramatically different from normal group (P < 0.001). The trisomy 21 immortalized cell lines were established and the genetic integrity of the cell lines was stable as evaluated by karyotype and DNA analysis. The relative quantitative PCR with DeltaCT value could be used to rapidly diagnose Down's syndrome.

[TGFBI gene mutation analysis in a Chinese family with Thiel-Behnke corneal dystrophy].

OBJECTIVE: To identify the gene mutation in autosomal dominant Thiel-Behnke corneal dystrophy affecting a five-generation Chinese family. To study the TGFBI gene mutation in Chinese patients with Thiel-Behnke corneal dystrophy by molecular genetic analysis. METHODS: Ophthalmologic examinations were performed in 10 patients and two normal family members in an autosomal dominant Thiel-Behnke corneal dystrophy family. Five ml peripheral blood was collected and Genomic DNA was extracted using salt fractionation. The exons 4, 7, 8, 11 and 12 of the TGFBI gene were amplified by PCR and mutation analysis was performed by direct sequencing. RESULTS: Mutation analysis of the exons 4, 7, 8, 11 and 12 of the TGFBI gene identified a G-->A missense mutation in the exon 12 by bidirectional sequencing. This mutation resulted in a substitution of glutamine for arginine at amino acid 555 (R555Q) of the protein. This mutation existed in all of the patients, but not in unaffected individuals. CONCLUSION: Thiel-Behnke corneal dystrophy in this family is caused by R555Q mutation of the TGFBI gene, the phenotypes of this corneal dystrophy are closely correlated with TGFBI mutation.

A missense mutation in the gammaD-crystallin gene CRYGD associated with autosomal dominant congenital cataract in a Chinese family.

PURPOSE: To identify the genetic defect in autosomal dominant congenital cataracts in a six generation Chinese family. METHODS: Clinical and ophthalmological examinations were performed on the affected and unaffected family members. All the members were genotyped with microsatellite markers at loci which were considered to be associated with cataracts. A two-point LOD score was calculated using the Linkage package after genotyping. A mutation was detected by direct sequencing using gene specific primers. RESULTS: Clinical heterogeneity was observed within this family, three affected individuals showed nuclear cataract and others had coralliform cataracts. Significant evidence of linkage was obtained at markers D2S325 (LOD score [Z]=3.10, recombination fraction [theta]=0.0) and D2S1782 (Z=5.97, theta=0.0), respectively. Haplotype analysis indicated that the cataract gene was close to those two markers. Sequencing of the gammaD-crystallin gene (CRYGD) revealed a C>T transition in exon 2, that causes a conservative substitution of Arg to Cys at codon 14 (R14C). This mutation co-segregated with all affected individuals and was not observed in unaffected or 100 normal unrelated individuals. Bioinformatic analyses also showed that a highly conserved region was located at Arg14. CONCLUSIONS: This study is the first reported case with phenotype of coralliform/nuclear cataract that associated with the mutation of Arg14Cys (R14C) CRYGD.

Erectile dysfunction in Fragile X patients.

AIM: To report the clinical experience during collecting sperm samples in the Fragile X syndrome (FXS) male patients. METHODS: Two different polymerase chain reaction (PCR) based methods were used for the molecular diagnosis of FXS. Sperm collection was done mostly according to the laboratory manual of the World Health Organization. RESULTS: We failed to collect sperm samples from five Fragile X subjects aged 18-60 years as a result of an unexpected erectile dysfunction (ED). Multiple examinations of the same subject at different times, and of different subjects from different provinces examined by different physicians, showed the same result consistently in all the five subjects. CONCLUSION: Erectile reflex is an instinctive response in all healthy males. The absence of erection can be caused by hormonal, physical or neuronal malfunction. As hormonal profiles were reported to be generally normal in Fragile X men, we propose that an unknown physical factor or the neuronal circuit, or both, underlying the erection is compromised. The finding of this symptom in Fragile X patients may help better understand the clinical spectrum and pathogeneses of the disease.