A Dual-Mode Single-Molecule Fluorescence Assay for the Detection of Expanded CGG Repeats in Fragile X Syndrome

Fragile X syndrome is the leading cause of inherited mental impairment and is associated with expansions of CGG repeats within the FMR1 gene. To detect expanded CGG repeats, we developed a dual-mode single-molecule fluorescence assay that allows acquisition of two parallel, independent measures of repeat number based on (1) the number of Cy3-labeled probes bound to the repeat region and (2) the physical length of the electric field-linearized repeat region, obtained from the relative position of a single Cy5 dye near the end of the repeat region. Using target strands derived from cell-line DNA with defined numbers of CGG repeats, we show that this assay can rapidly and simultaneously measure the repeats of a collection of individual sample strands within a single field of view. With a low occurrence of false positives, the assay differentiated normal CGG repeat lengths (CGG _N , N = 23) and expanded CGG repeat lengths (CGG _N , N = 118), representing a premutation disease state. Further, mixtures of these DNAs gave results that correlated with their relative populations. This strategy may be useful for identifying heterozygosity or for screening collections of individuals, and it is readily adaptable for screening other repeat disorders.     

Sequestration of DROSHA and DGCR8 by Expanded CGG RNA Repeats Alters MicroRNA Processing in Fragile X-Associated Tremor/Ataxia Syndrome

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Highlights? DGCR8 binds to CGG RNA repeats, cause of the neurodegenerative FXTAS disease ? DGCR8 and its partner, DROSHA, are sequestered within CGG RNA aggregates ? DGCR8 rescues the neuronal cell death induced by expanded CGG RNA repeats ? MicroRNA processing is impaired in patients with FXTAS     

提高SCA2编码区CAG三核苷酸重复的PCR扩增效率

以遗传性脊髓小脑共济失调Ⅱ型基因（ｓｐｉｎｏｃｅｒｅｂｅｌｌａｒ ａｔａｘｉａ ｔｙｐｅⅡｇｅｎｅＳＣＡ２）编码区内的ＣＡＧ三核苷酸重复为研究对象（Ｇ＋Ｃ含量为６９．２％）,比较了热启动ＰＣＲ、碱基替代ＰＣＲ、添加增效剂（１％－１２．５％二甲亚砜、１％－２５％甘油、１％－１２．５％甲酰胺）与常规ＰＣＲ的扩增效率,发现热启动ＰＣＲ、碱基替代ＰＣＲ及添加增效剂（１％－１０％二甲亚砜、５％－２０％甘油、     

Cascade Screening for Fragile X Syndrome/CGG Repeat Expansions in Children Attending Special Education in Sri Lanka

Fragile X syndrome (FXS) is the commonest cause of inherited mental retardation and clinically presents with learning, emotional and behaviour problems. FXS is caused by expansion of cytosine-guanine-guanine (CGG) repeats present in the 5’ untranslated region of the FMR1 gene. The aim of this study was to screen children attending special education institutions in Sri Lanka to estimate the prevalence of CGG repeat expansions. The study population comprised a representative national sample of 850 children (540 males, 310 females) with 5 to 18 years of age from moderate to severe mental retardation of wide ranging aetiology. Screening for CGG repeat expansion was carried out on DNA extracted from buccal cells using 3’ direct triplet primed PCR followed by melting curve analysis. To identify the expanded status of screened positive samples, capillary electrophoresis, methylation specific PCR and Southern hybridization were carried out using venous blood samples. Prevalence of CGG repeat expansions was 2.2%. Further classification of the positive samples into FXS full mutation, pre-mutation and grey zone gave prevalence of 1.3%, 0.8% and 0.1% respectively. All positive cases were male. No females with FXS were detected in our study may have been due to the small sample size.     

PCR approach for detection of Fragile X syndrome and Huntington disease based on modified DNA: limits and utility

A group of mutations characterized by trinucleotide repeat expansion causes human diseases such as the Fragile X syndrome, Huntington disease (HD), and myotonic dystrophy. Methods based on PCR amplification of the CGG and CAG repeats region could facilitate the development of a rapid screening assay; unfortunately, amplification across CGG and CAG repeats can be inefficient and unreliable due to the G + C base composition. The utility of the PCR on modified DNA for amplification of the CGG and CAG repeats at the Fragile X syndrome and HD has been reported. In the present study, we analyzed the utility of PCR on modified DNA as a rapid screening method for diagnosis of patients with Fragile X syndrome and HD. A comparative analysis realized with 38 Fragile X and 29 HD patients showed that the molecular diagnosis by simple PCR on modified DNA has a sensitivity and specificity of 100% in Fragile X patients and 94.1% and 91.6% in HD patients. The results achieved from the statistical analysis allowed us to conclude that the amplification by simple PCR on modified DNA is a reliable and useful method for the molecular diagnosis of the Fragile X syndrome, but not for the HD.     

A PCR Detection Method for Rapid Identification of Paenibacillus larvae

American foulbrood is a disease of larval honeybees (Apis mellifera) caused by the bacterium Paenibacillus larvae. Over the years attempts have been made to develop a selective medium for the detection of P. larvae spores from honey samples. The most successful of these is a semiselective medium containing nalidixic acid and pipermedic acid. Although this medium allows the growth of P. larvae and prevents the growth of most other bacterial species, the false-positive colonies that grow on it prevent the rapid confirmation of the presence of P. larvae. Here we describe a PCR detection method which can be used on the colonies that grow on this semiselective medium and thereby allows the rapid confirmation of the presence of P. larvae. The PCR primers were designed on the basis of the 16S rRNA gene of P. larvae and selectively amplify a 973-bp amplicon. The PCR amplicon was confirmed as originating from P. larvae by sequencing in both directions. Detection was specific for P. larvae, and the primers did not hybridize with DNA from closely related bacterial species.     

Analysis of the Fragile X Trinucleotide Repeat in Basques: Association of Premutation and Intermediate Sizes,Anchoring AGGs and Linked Microsatellites with Unstable Alleles

Fragile X Syndrome (FXS) is associated with an unstable CGG repeat sequence in the 5’ untranslated region in the first exon of the FMR1 gene which resides at chromosome position Xq27.3 and is coincident with the fragile site FRAXA. The CGG sequence is polymorphic with respect to size and purity of the repeat. Interpopulation variation in the polymorphism of the FMR1 gene and consequently, in the predisposition to FXS due to the prevalence of certain unstable alleles has been observed. Spanish Basque population is distributed among narrow valleys in northeastern Spain with little migration between them until recently. This characteristic may have had an effect on allelic frequency distributions. We had previously reported preliminary data on the existence of FMR1 allele differences between two Basque valleys (Markina and Arratia). In the present work we extended the study to Uribe, Gernika, Durango, Goierri and Larraun, another five isolated valleys enclosing the whole area within the Spanish Basque region. We analyzed the prevalence of FMR1 premutated and intermediate/grey zone alleles. With the aim to complete the previous investigation about the stability of the Fragile X CGG repeat in Basque valleys, we also analyzed the existence of potentially unstable alleles, not only in relation with size and purity of CGG repeat but also in relation with DXS548 and FRAXAC1 haplotypes implicated in repeat instability. The data show that differences in allele frequencies as well as in the distribution of the mutational pathways previously identified are present among Basques. The data also suggest that compared with the analyzed Basque valleys, Gernika had increased frequency of susceptibility to instability alleles, although the prevalence of premutation and intermediate/grey zone alleles in all the analyzed valleys was lower than that reported in Caucasian populations.Key Words: Fragile X syndrome, FMR1 gene, CGG repeat, FRAXAC1, DXS548, basque country.     

Anticipation and Instability of IT-15 (CAG)N Repeats in Parent-Offspring Pairs with Huntington Disease

Huntington disease (HD) is an autosomal dominant degenerative disorder caused by an expanded and unstable trinucleotide repeat (CAG)n in a gene (IT-15) on chromosome 4. HD exhibits genetic anticipation—earlier onset in successive generations within a pedigree. From a population-based clinical sample, we ascertained parent-offspring pairs with expanded alleles, to examine the intergenerational behavior of the trinucleotide repeat and its relationship to anticipation. We find that the change in repeat length with paternal transmission is significantly correlated with the change in age at onset between the father and offspring. When expanded triplet repeats of affected parents are separated by median repeat length, we find that the longer paternal and maternal repeats are both more unstable on transmission. However, unlike in paternal transmission, in which longer expanded repeats display greater net expansion than do shorter expanded repeats, in maternal transmission there is no mean change in repeat length for either longer or shorter expanded repeats. We also confirmed the inverse relationship between repeat length and age at onset, the higher frequency of juvenile-onset cases arising from paternal transmission, anticipation as a phenomenon of paternal transmission, and greater expansion of the trinucleotide repeat with paternal transmission. Stepwise multiple regression indicates that, in addition to repeat length of offspring, age at onset of affected parent and sex of affected parent contribute significantly to the variance in age at onset of the offspring. Thus, in addition to triplet repeat length, other factors, which could act as environmental factors, genetic factors, or both, contribute to age at onset. Our data establish that further expansion of paternal repeats within the affected range provides a biological basis of anticipation in HD.     

CAG/CTG and CGG/GCC Repeats in Human Brain Reference cDNAs: Outcome in Searching for New Dynamic Mutations

CAG and CGG expansion is associated with 10 inherited neurological diseases and is thought to be involved in other human genetic diseases. To identify new candidate genes, we have undertaken a large-scale screening project for CAG/CTG ([CAG]n) and CGG/GCC ([CGG]n) repeats in human brain reference cDNAs. Here, we present the final classification for 597 cDNAs selected by CAG and CGG hybridization from two libraries (100,128 clones) and the updated characterization of [CAG]n- and [CGG]n-positive cDNAs (repeat polymorphism and cDNA localization). We have selected 124 CAG and 83 CGG hybridization-positive clones representing new genes, from which 49 CAG and 7 CGG repeats could be identified. New [CAG]nand [CGG]nwith more than seven to nine units were rare (1/2000), and perfect [CAG]n9 were more likely polymorphic. Overall, highly polymorphic to monomorphic new [CAG]n> 9 and [CGG]n> 7 were characterized. The comparison of our data with other [CAG]nand [CGG]nresources suggests that the screening of reference cDNAs leads to unique sources of new [CAG]nand [CGG]nand will enhance the study of enlarged triplet repeats in human genetic diseases.     

A PCR Detection Method for Rapid Identification of Melissococcus pluton in Honeybee Larvae

Melissococcus pluton is the causative agent of European foulbrood, a disease of honeybee larvae. This bacterium is particularly difficult to isolate because of its stringent growth requirements and competition from other bacteria. PCR was used selectively to amplify specific rRNA gene sequences of M. pluton from pure culture, from crude cell lysates, and directly from infected bee larvae. The PCR primers were designed from M. pluton 16S rRNA sequence data. The PCR products were visualized by agarose gel electrophoresis and confirmed as originating from M. pluton by sequencing in both directions. Detection was highly specific, and the probes did not hybridize with DNA from other bacterial species tested. This method enabled the rapid and specific detection and identification of M. pluton from pure cultures and infected bee larvae.     

秦巴山区儿童FRAXE脆性位点CGG重复多态性分布及与智力的相关性分析

采用PCR扩增技术和聚丙烯酰胺凝胶电泳技术, 并结合测序, 对秦巴山区随机抽样儿童及不同智力水平儿童的FRAXE脆性位点CGG重复序列进行检测。并把所得的CGG重复数与智测成绩(用韦氏儿童智力量表(C-WISC)进行智力测量)做关联分析。结果表明, FRAXE脆性位点CGG重复的等位基因分布范围在不同地域人群中有所差异, 同一地域人群中等位基因频率分布基本一致; 随机抽样儿童的CGG重复多态性与智力没有相关性(r=0.083, P>0.05), 男性和女性的CGG重复多态性分别与儿童智力也无相关性(r男＝0.225, r女＝-0.041, P>0.05); 在智力低下(MR)、边缘和正常儿童中, CGG重复数值之间也没有显著性差异(F=0.195, P>0.05)。因而认为, 秦巴山区儿童FRAXE脆性位点CGG的正常重复多态性(重复数为8-30)与其智力成绩亦无相关性。     

一种适于转基因水稻PCR检测的微量DNA快速提取法

对已报道的小麦基因组DNA快速提取方法的部分步骤进行了简化,在水稻上进行了尝试。结果表明,简化法提取的水稻基因组DNA完整性好,PCR扩增效果与试剂盒提取法无明显的差异,结果稳定可靠;而且整个提取过程操作简单、花费时间少,样品用量少,仅需5-10mg,适用于大规模转基因水稻的PCR检测。     

实时荧光定量PCR方法快速检测转基因大豆

针对转基因大豆中普遍含有的35S启动子进行引物设计,以双链DNA染料SYBR GreenⅠ为荧光标记物,利用实时荧光定量PCR方法对大豆样品进行检测。该法检测转基因大豆的检测低限为0.005 nmol/L的35S启动子,线性范围达3个数量级,可快速区分转基因大豆和非转基因大豆,具有快速、简便、灵敏、安全、高通量、低成本等优点,可推广用于转基因植物产品的快速定量检测。     

食源性致病菌多重PCR快速检测方法建立与应用

利用PCR技术,建立多组多重食源性致病菌PCR快速检测方法。设计受试菌特异性引物,反应体系中加入多对引物和多种DNA模板,采用正交试验优化PCR反应条件,进行特异性引物的PCR扩增。建立了多组多重食源性致病菌PCR快速检测方法,方法中所检测受试菌株和模拟样品均出现特异性扩增条带,结果与实际相符。所建立多组多重PCR快速检测体系符合设计要求,可以应用于食源性突发公共卫生事件的应急检测和日常样品检测工作。     

Normal CA1 Place Fields but Discoordinated Network Discharge in a Fmr1-Null Mouse Model of Fragile X Syndrome

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快速可靠的双链PCR产物直接测序法

利用T7DNA聚合酶在低温下仍具较高活性的特点,在热变性后低温下进行测序反应,使用该方法对多种PCR产物进行序列分析均取得较好的结果．