Molecular and Clinical Investigation of Iranian Patients with Friedreich Ataxia

Background: Friedreich ataxia (FRDA) is an autosomal recessive disorder caused by guanine-adenine-adenine (GAA) triplet expansions in the FXN gene. Its product, frataxin, which severely reduces in FRDA patients, leads to oxidative damage in mitochondria. The purpose of this study was to evaluate the triple nucleotide repeated expansions in Iranian FRDA patients and to elucidate distinguishable FRDA clinical differences in these patients. Methods: A number of 22 Iranian patients (8 females and 14 males) from 16 unrelated families were studied. DNA was extracted from the peripheral blood of patients. The frequency and length of (GAA)_n repeats in intron 1 of the FXN gene were analyzed using long-range PCR. In this study, the clinical criteria of FRDA in our patients and the variability in their clinical signs were also demonstrated. Results: An inverse relationship was observed between GAA repeat size and the age of onset. Although some distinguishable clinical features (such as limb ataxia and lower limb areflexia) were found in our patients, 90-95% of them had extensor plantar response and dysarthria. The results showed only one positive diabetes patient and also different effects on eye movement abnormality among our patients. Conclusion: The onset age of symptoms showed a significant inverse correlation with allele size in our patients (P>0.05). Based on comparisons of the clinical data of all patients, clinical presentation of FRDA in Iranian patients did not differ significantly from other FRDA patients previously reported. Key Words: Friedreich ataxia (FRDA), Frataxin, Mitochondria     

Exon Sequencing of PKD1 Gene in an Iranian Patient with Autosomal-Dominant Polycystic Kidney Disease

Introduction: Autosomal dominant polycystic kidney disease (ADPKD) is one of the most common genetic kidney disorders with the incidence of 1 in 1,000 births. ADPKD is genetically heterogeneous with two genes identified: PKD1 (16p13.3, 46 exons) and PKD2 (4q21, 15 exons). Eighty five percent of the patients with ADPKD have at least one mutation in the PKD1 gene. Genetic studies have demonstrated an important allelic variability among patients, but very few data are known about the genetic variation among Iranian populations. Methods: In this study, exon direct sequencing of PKD1 was performed in a seven-year old boy with ADPKD and in his parents. The patient’s father was ADPKD who was affected without any kidney dysfunction, and the patient’s mother was congenitally missing one kidney. Results: Molecular genetic testing found a mutation in all three members of this family. It was a missense mutation GTG>ATG at position 3057 in exon 25 of PKD1. On the other hand, two novel missense mutations were reported just in the 7-year-old boy: ACA>GCA found in exon 15 at codon 2241 and CAC>AAC found in exon 38 at codon 3710. For checking the pathogenicity of these mutations, exons 15, 25, and 38 of 50 unrelated normal cases were sequenced. Conclusion: our findings suggested that GTG>ATG is a polymorphism with high frequency (60%) as well as ACA>GCA and CAC>AAC are polymorphisms with frequencies of 14% and 22%, respectively in the population of Southwest Iran. Key Words: Autosomal dominant polycystic kidney disease (ADPKD), Polycystic kidney diseases (PKD), PKD1 gene, Iran     

Identification of a Novel Stop Loss Mutation in P2RX2 Gene in an Iranian Family with Autosomal Nonsyndromic Hearing Loss

Background:Hearing loss, a congenital genetic disorder in human, is difficult to diagnose. WES is a powerful approach for ethiological disgnosis of such disorders. Methods:One Iranian family with two patients were attented in the study. Sequencing of known NSHL genes was carried out to recognize the genetic causes of HL. Results:Molecular analyses identified a novel stop loss mutation, c.1048T>G (p.Term350Glu), whitin the P2RX2 gene, causing a termination-site modification.This event would lead to continued translation into the 3'' UTR of the gene, which in turn may result in a longer protein product. The mutation was segregating with the disease phenotype and predicted to be pathogenic by bioinformatic tools. Conclusion:This study is the first Iranian case report of a diagnosis of ADNSHL caused by P2RX2 mutation. The recognition of other causative mutations in P2RX2 gene more supports the probable function of this gene in causing ADNSHL. Key Words: Autosomal dominant 41, Deafness, Mutation, P2RX2, Whole exome sequencing     

Novel mutation in the EXT-1 gene in an Iranian family affected with hereditary multiple exostoses

Identification of casual mutations in Hereditary Multiple Exostoses (HME) is important because of similar conditions in which multiple exostoses occur. Therefore mutation analysis can help to confirm the clinical diagnosis and to improve the management of therapy. HME is an inherited disorder of bone growth. HME can be referred to by various names such as Heredity Multiple Exostoses, Hereditary Multiple Osteochondromata, Multiple Carthaginous Exostoses, etc. People who have HME grow exostoses, or bony bumps, on their bones which can vary in size, location and number depending on the individual. HME is inherited in an autosomal dominant manner with an estimated prevalence of 1/50,000 in western countries. At least three loci (EXT1, EXT2 and EXT3) thought to be involved in this skeletal disease. Approximately 90% of affected families possess mutations in the coding regions of EXT1 and EXT2 genes and the majority of these mutations cause loss of function. EXT1 and EXT2 genes encode related members of a putative tumor suppressor family. In this first report from Iran we identified a frame shift mutation (1100-1101 insA) in exon 3 of EXT1 gene in a family being suspicious of HME. This mutation leads to a premature stop codon and previously not described. Additionally, we have found an unreported silent mutation in the exon six of EXT1 gene with uncertain significance.     

The frequency of eight common point mutations in CYP21 gene in Iranian patients with congenital adrenal hyperplasia

BACKGROUND: Congenital Adrenal Hyperplasia (CAH, the inherited inability to synthesize cortisol) is one of the most common (1 in 10000 to 1 in 15000) autosomal recessive disorders. More than 95% of cases of CAH are caused by 21-hydroxylase deficiency (21-OHD). Females with severe, classic 21-OHD are exposed to excess androgens prenatally and are born with virilized external genitalia. Most patients cannot synthesize sufficient aldosterone to maintain sodium balance and may develop potentially fatal salt wasting crisis if not treated. METHODS: We applied allele specific PCR to detect the eight common mutations in the CYP21 gene in patients. Fifty unrelated patients with symptoms of classical CAH were studied. RESULTS AND CONCLUSION: Seventy percent of our subjects had these mutations. The most frequent mutations were found to be I2G and del-8 bp (28% and 13%, respectively). The frequencies of other alleles were as following: I172N, 9%; V281L, 3%; exon 6 cluster (I236N, V237E and M239K), 4%; Q318X, 9%; R356W, 5%; and P30L, 0%. The frequency of mutations did not differ substantially from other ethnics, however, a higher rate of del-8 bp (13%) was found in our population. The aim of this study was to detect common mutations for setting up a molecular method for prenatal diagnosis.     

Utilization of Whole Exome Sequencing in Non-Syndromic Premature Ovarian Failure: Ficolin-3 Gene Mutation in an Iranian Family

Background:Premature ovarian failure is a heterogeneous disorder, leading to early menopause. Several genes have been identified as the cause of non-syndromic POF. Our aim was to explore the genetic defects in Iranian patients with POF. Methods:We studied a family with three females exhibiting non-syndromic POF. WES was performed for one of the affected individuals after ruling out the presence of CGG repeat expansion at FMR1 gene in the family. Sanger sequencing was used to confirm the candidate sequence variants in the proband, and screening of the detected mutation was performed for the other affected and unaffected members of the family. Results:A homozygous frameshift mutation, c.349delC, was identified in FCN3 gene in the proband and two other patients. The parents and two healthy brothers were heterozygous for the mutation, and an unaffected sister was homozygous for wild type. Conclusion:This is the first report of a mutation in FCN3 gene in a family with POF. Our findings can lead to the enhancement of genetic databases of patients with POF, specifically for families with high-risk background. Key Words: Ficolin-3, Premature ovarian failure, Whole exome sequencing     

Screening of Human CYP1A2 and CYP3A4 Inhibitors from Seaweed In Silico and In Vitro

Phenolic compounds and carotenoids are potential inhibitors of cytochrome P450s. Sixteen known compounds, phenolic compounds and carotenoids from seaweed were examined for potential inhibitory capacity against CYP1A2 and CYP3A4 in silico and in vitro. Morin, quercetin, and fucoxanthin inhibited the enzyme activity of CYP1A2 and CYP3A4 in a dose-dependent manner. The IC₅₀ values of morin, quercetin, and fucoxanthin were 41.8, 22.5, and 30.3 μM for CYP1A2 and 86.6, 16.1, and 24.4 μM for CYP3A4, respectively. Siphonaxanthin and hesperidin did not show any significant effect on CYP1A2, but they slightly inhibited CYP3A4 activity at high concentrations. In silico modeling of CYP’s binding site revealed that the potential inhibitors bound in the cavity located above the distal surface of the heme prosthetic group through the 2a or 2f channel of CYPs. This study presents an approach for quickly predicting CYP inhibitory activity and shows the potential interactions of compounds and CYPs through in silico modeling.     

A Novel Mutation in the Aprataxin (APTX) Gene in an Iranian Individual Suffering Early-Onset Ataxia with Oculomotor Apraxia Type 1(AOA1) Disease

Background

Ataxia with oculomotor apraxia type 1 (AOA1) shows early onset with autosomal recessive inheritance and is caused by a mutation in the aprataxin (APTX) gene encoding for the APTX protein.

Methods

In this study, a 7-year-old girl born of a first-cousin consanguineous marriage was described with early-onset progressive ataxia and AOA, with increased cholesterol concentration and decreased albumin concentration in serum. PCR and direct DNA sequencing was performed after DNA extraction.

Results

Sequencing analysis revealed a novel homozygous deletion in c.643 and A>T single nucleotide polymorphism in c.641 in exon 6 of the APTX gene [ENST00000379825].

Conclusion

It seems that this region of exon 6 is probably a hot spot; however, no deletions have been reported in exon 6 yet. Key Words: Ataxia oculomotor apraxia 1 (AOA1), aprataxin (APTX), Iranian     

早熟水稻新品种龙粳27号的特征特性及栽培技术要点

龙粳27号是由黑龙江省农业科学院水稻研究所育成的早熟高产抗病耐寒水稻新品种,2009年1月通过黑龙江省农作物品种审定委员会审定。本文介绍了龙粳27号的选育经过、产量表现、特征特性及栽培要点。     

裸大麦突变体Ynbs-1的分枝穗特性及其遗传分析

为了解裸大麦突变体重要种质Ynbs株系的分枝穗特性及其遗传基础,在花后7d,调查了Ynbs-1突变体及其重组自交系(正常六棱穗)等材料的正、反杂交F1植株的穗分枝特性,分析了F2及其F3群体中正常穗与分枝穗植株的分离状况,检测了穗分枝基因连锁SSR标记和小穗轴短毛标记状况。结果表明,Ynbs-1的分枝穗长度、分枝穗数和分枝穗轴节数平均值分别为1.48±0.09cm、23.56±1.52个和1.32±0.63个,均极显著高于RIL。Ynbs-1与RIL-1正、反杂交F1及Ynbs-1(母本)与BDM-8的杂交F1植株均无分枝。Ynbs-1(母本)与RIL-1和BMD-8的杂交F2群体的分枝穗与正常穗植株的个体数之比均符合1∶3,纯合分枝穗、杂合正常穗和纯合正常穗的个体数之比均符合1∶2∶1。Ynbs-1的穗分枝基因与3个SSR标记(HVM40-190bp、Bmag0023-110bp、Bmag0508A-170bp)和小穗轴短毛基因均不连锁。Ynbs-1株系的分枝较多,其穗分枝遗传受1对隐性核基因控制,该基因与穗分枝突变体Prbs、F151和Foma的均不等位。     

穗上多叶玉米自交系LY-1的遗传特性研究

利用外引玉米杂交种通过多年连续自交获得1份穗上叶片数为7～10片的自交系LY-1。研究该材料穗上叶片数的遗传特性,分别将其与3个不同穗上叶片数材料L583、LS-1和昌7-2不同遗传背景的自交系杂交,获得3个衍生的后代分离群体。通过穗上叶片数、株高、穗位高和穗高系数的分析,结果表明,F_1的穗上叶片数介于双亲之间,偏高亲值,没有明显杂种优势,表现出不完全显性遗传特性。株高、穗位高以及穗高系数均表现超高值亲本,具有极强的杂种优势。相关分析结果表明,穗上叶片数与穗高系数呈极显著的负相关,株高与穗上叶片数、穗位高以及穗位高与穗高系数均呈极显著正相关。从各性状的遗传力来看,3个群体株高和穗位高的平均遗传力较高,均在75%以上;其次是穗高系数;穗上叶片数的遗传力仅为62.43%。因此,利用LY-1作为多叶资源进行种质改良和新品种选育,可降低穗位相对高度,提高植株的抗倒伏能力。     

Genetic Polymorphism of Wx Gene and Its Correlation with Main Grain Quality Characteristics in Rice

The allelic variation of the Wx gene in 50 non-glutinous rice varieties (lines) was analyzed by using the microsatellite marker RM190 [for (CT)n simple sequence repeat (SSR)] and cleaved amplified polymorphic sequence(CAPS) marker 484/W2R-ACCⅠ[for G/T single nucleotide polymorphism (SNP)]. Six homozygous (CT)n types, namely (CT)20, (CT)19, (CT)18, (CT)17, (CT)16, (CT)14, (CT)11 and (CT)10, and a heterozygous genotype (CT)11/(CT)18 were detected for RM190, of which (CT)11 and (CT)18 were predominant. Two homozygous Wx genotypes (G/G and T/T) and one heterozygous (G/T) were detected using 484/W2R-ACCⅠ . Most of the materials with a RM190 of (CT)11 were G/G for SNP of 484/W2R-ACC I, while T/T for SNP was predominantly appeared in materials with (CT)18. The materials tested could be grouped into 10 categories using the two markers together. Results indicated that 59.3% variance of amylose content was attributed to the polymorphism of Wx gene revealed by RM190, while 56.1% and 24.6% of the variances in amylose content and gel consistency were respectively to the polymorphism of Wx gene revealed by 484/W2R-ACC I. Furthermore, with both SSR and CAPS markers, 72.4% of the variance in amylose content could be explained. In addition, the application prospects of the two markers in breeding were also discussed.     

小麦白斑突变体I30的特征特性及遗传分析

类病斑突变体是研究植物程序性死亡和抗病性的理想材料。为了丰富小麦斑点突变体的研究,对叠氮化钠诱变小麦品种陕农33产生的稳定遗传的白斑突变体I30进行了特征特性研究和遗传分析。结果表明,突变体I30从三叶期开始表现白色块斑和长条纹。锥虫蓝染色和DAB染色显示,I30斑点处出现细胞死亡和H_2O_2积累现象。透射电子显微镜观察表明,I30的叶绿体形状发生改变,数目减少,基粒垛叠高度无序,部分甚至降解。农艺性状调查结果表明,I30的株高、单株有效穗数、穗粒数、穗长和结实率与野生型间无显著差异,但千粒重、穗粒重、单株产量、旗叶长度和宽度显著低于野生型。遗传分析表明,I30由1对隐性核基因控制。利用BSA+660K基因芯片技术,将该基因定位于小麦6D染色体上,位于SSR分子标记Xcfd190和6DS-5之间,遗传距离分别为6.4cM和9.1cM。     

植物miR172家族成员进化与分子特性分析

为了解植物miR172家族成员的进化与分子特性,对mi Rbase数据库中37个物种的161个miR172前体序列和196个miR172成熟体序列进行进化规律分析,并对植物miR172家族的保守基序、二级结构和靶基因进行预测分析。结果表明:miR172家族成员分布的37个物种都是被子植物,被子植物很可能是miR172家族进化来源的祖先。进化分析表明,植物miR172家族成员序列相似性是其聚类的首要影响因素,其次才是物种差异的影响。植物miR172家族成员成熟体序列分析表明,5p臂上形成的成熟体序列特异性较大,3p臂上形成的成熟体序列保守性较高。二级结构分析发现,植物miR172家族成员具有典型的茎环二级结构,且茎序列的保守性较环序列高。植物miR172前体序列包含1个UNCG环。靶基因预测分析发现,同一物种不同miR172成员的靶基因可能不同;不同物种miR172的靶基因也可能不同,AP2或AP2-like出现频率最高,其次还有arginine decarboxylase 1、Pathogenesis-related、MYB84等靶基因,表明其靶基因功能的多样性。     

Identification and Expression of Two Novel Cytochrome P450 Genes,CYP6CV1 and CYP9A38, in Cnaphalocrocis medinalis (Lepidoptera: Pyralidae)

Cnaphalocrocis medinalis Güenée can cause severe losses in rice. Cytochrome P450s play crucial roles in the metabolism of allelochemicals in herbivorous insects. Two novel P450 cDNAs, CYP6CV1 and CYP9A38, were cloned from the midgut of C. medinalis. CYP6CV1 encodes a protein of 500 amino acid residues, while CYP9A38-predicted protein has 531 amino acid residues. Both cDNA-predicted proteins contain the conserved functional domains for all P450s. Phylogenetic analyses showed that CYP6CV1 is grouped in the cluster containing CYP6B members, while CYP9A38 is in the cluster including CYP9 members. However, both clusters are contained in the same higher lineage. Homologous analysis revealed that CYP6CV1 is most similar to CYP6B8, CYP6B7, CYP6B6, CYP6B2, and CYP6B4 with the highest amino acid identity of 41%. CYP9A38 is closest to CYP9A17, CYP9A21, CYP9A20, and CYP9A19 with the highest amino acid identity of 66%. Studies of temporal expression profiles revealed that CYP9A38 showed a steady increase in mRNA level during the five instar stages, but a low-expression level in pupae, and then presented at a high-expression level again in adults. Similar expression patterns were obtained with CYP6CV1. In the fifth instar larvae, CYP6CV1 was mainly expressed in midgut and fat bodies, whereas CYP9A38 was mainly expressed in midgut. Expression studies also revealed a 3.20-fold over-expression of CYP6CV1 and 3.54-fold over-expression of CYP9A38 after larval exposure to host rice resistance. Our results suggest that both CYP6CV1 and CYP9A38 may be involved in detoxification of rice phytochemicals.     

中早熟籼型三系不育系泉5A生育特性的初步观察

通过对不育系泉5A生育特性的观察发现：泉5A在4月初播种,播始历期为76d,比珍汕97A长1d,属中早熟籼型三系不育系;主茎叶片数为14叶,与珍汕97A相同;泉5A有良好的不育特性,开花习性好,在繁殖和制种方面可以获得比较理想的产量。     

Antimutagenic Properties of Mangifera indica L. Stem Bark Extract and Evaluation of its Effects on Hepatic CYP1A1

Mangifera indica stem bark extract (MSBE) is a Cuban natural product which has shown strong antioxidant properties. In this work, the antimutagenic effect of MSBE was tested against 10 well-known mutagens/carcinogens in the Ames test in the absence or presence of metabolic fraction (S9). The chemical mutagens tested included: cyclophosphamide, mitomycin C, bleomycin, cisplatin, dimethylnitrosamine (DMNA), benzo[a]pyrene (BP), 2-acetylaminofluorene (2-AAF), sodium azide, 1-nitropyrene (1-NP) and picrolonic acid. Protective effects of the extract were also evaluated by comparing the efficiency of S9 fraction obtained from rats treated during 28?days with oral doses of MSBE (50?C500?mg/kg) with that obtained from rats treated with vehicle (control) to activate bleomycin and cyclophosphamide in the Ames test. MSBE concentrations between 50 and 500???g/plate significantly reduced the mutagenicity mediated by all the chemicals tested with the exception of sodium azide. Higher mutagenicity was found when bleomycin and cyclophosphamide (CP) were activated by control S9 than by MSBE S9. In addition, inhibition of CYP1A1 microsomal activity was observed in the presence of MSBE (10?C20???g/ml). We can conclude that besides its potent antioxidant activity previously reported, MSBE may also exert a chemoprotective effect due to its capacity to inhibit CYP activity.     

基于生物信息学分析的水稻无机焦磷酸化酶基因OsIP1的克隆及其遗传转化

 无机焦磷酸化酶在植物体内催化焦磷酸基团分解为磷酸基团的反应,而焦磷酸的及时降解,被认为是原初光合产物合成双糖特别是蔗糖,进而进行长距离运输的关键步骤之一。但是,蔗糖在维管束中的运输需要焦磷酸,因此,在叶肉细胞中特异性过表达焦磷酸化酶基因,被认为是拉动和促进光合作用的关键措施之一。对水稻中约30个无机焦磷酸化酶编码基因进行氨基酸序列比较、结构域特征、亚细胞定位预测以及上游顺式元件释义等生物信息学分析,进而克隆了1个预测为编码胞质型可溶性无机焦磷酸化酶的基因OsIP1（Os04g0687100）,并将其与叶肉细胞特异性启动子cyFBPase相连,构建成嵌合基因cyFBPase:OsIP1;通过农杆菌转化法将其转入2个水稻品种中,累计获得48个阳性转基因植株。     

优质水稻新品种新稻27号的特征特性及栽培要点

新稻27号是新疆伊犁哈萨克自治州农业科学研究所水稻研究室利用自育的优质品系90—6作母本,高产品系9704作父本进行人工杂交选育而成。该品种在种植过程中表现出生育期适宜,米质优,产量高,抗病抗倒性强,适应性广等特点,2009年3月经新疆维吾尔自治区农作物品种审定委员会审定并命名。