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     

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     

木薯种质资源中醇腈裂解酶基因12G132600编码区终止突变及频率的研究

木薯是重要的粮食作物,但块根中含有的氰苷及其产生的氢氰酸严重影响木薯的食用品质,增加加工成本。α-醇腈裂解酶(alpha-hydroxynitrilelyase,HNL)是植物催化醇腈裂解产生氢氰酸的关键酶。重测序数据显示,‘华南8号’木薯品种中HNL编码基因家族的一个成员12G132600在编码区内部发生了终止突变,导致基因编码区变短。本研究对国内外251份木薯种质资源的重测序结果进行分析,共发现60份材料醇腈裂解酶基因12G132600存在相同的终止突变,该60份材料全部是终止突变与非终止突变的杂合基因型,且全部为栽培类型木薯。说明该突变是木薯由野生型驯化为栽培型以后发生的。通过对木薯品种‘华南9号’该基因的克隆测序以及与已发表的木薯品种‘TME3’基因组序列的比对分析,证实了该突变在木薯品种中真实存在。     

大豆Abhydrolase_3基因家族进化分析

异黄酮是大豆的重要次生代谢物,参与植物与微生物互作。2-羟基异黄酮脱水酶(hydroxyisoflavanone dehydratase,HID)催化2-羟基异黄酮形成稳定的异黄酮。HID属于Abhydrolase_3基因家族,该基因家族具有多种功能,但该基因家族在大豆中的进化模式尚待研究。为了研究Abhydrolase_3基因家族在大豆中的进化模式,本文在大豆基因组中鉴定了62个Abhydrolase_3基因,串联和片段复制是该基因家族主要扩增方式。根据系统进化关系,将大豆Abhydrolase_3基因家族划分为8个亚家族,其中HID所在的亚家族I基因数量最多,并发生多次基因扩增事件。对大豆Abhydrolase_3基因家族结构分析表明,不同亚家族具有不同的基序。多态性分析表明,亚家族Ⅰ、Ⅲ和Ⅴ具有较高的核苷酸差异,并受到放松的自然选择。基因表达分析表明,除了亚家族II和IV外,其它亚家族的基因在大豆不同组织中有较高表达;亚家族Ⅰ、Ⅲ、Ⅳ、Ⅴ和Ⅵ基因受病原菌诱导表达。结果说明HID所在的亚家族I存在基因扩增和功能分化,与病原菌互作相关的基因具有较高的遗传多样性并受病原菌诱导表达。     

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     

小麦OXS3基因家族的鉴定及表达模式分析

氧化应激3蛋白(OXS3)是一种植物特异性蛋白,在植物逆境耐受性中发挥重要作用。本研究利用生物信息学方法,在全基因组水平对小麦中的OXS3基因家族成员进行了鉴定,并对所有成员进行了高温胁迫下的表达模式分析以及4个小麦OXS3基因的酵母转化验证试验。结果表明,小麦具有9个OXS3基因,分布于8条染色体上,聚类为三个亚家族,主要定位于细胞核;小麦OXS3基因家族成员的启动子区具有多个激素响应和逆境响应顺式作用元件,暗示该家族成员在植物逆境响应中可能承担重要角色。共线性分析表明OXS3基因家族在单/双子叶植物间存在较大差异。qRT-PCR分析表明,小麦OXS3家族基因在高温胁迫下均上调表达。转化酵母的耐热功能验证表明,小麦基因TaOXS3-1D、TaOXS3-2A可以提高酵母的耐热性。本研究结果为系统研究OXS3的耐热功能奠定了基础。     

Clinical and Genetic Characteristics of Splicing Variant in CYP27A1 in an Iranian Family with Cerebrotendinous xanthomatosis

Background:CTX is a rare congenital lipid-storage disorder, leading to a progressive multisystem disease. CTX with autosomal recessive inheritance is caused by a defect in the CYP27A1 gene. Chronic diarrhea, tendon xanthomas, neurologic impairment, and bilateral cataracts are common symptoms of the disease. Methods:Three affected siblings with an initial diagnosis of non-syndromic intellectual disability were recruited for further molecular investigations. To identify the possible genetic cause(s), WES was performed on the proband. Sanger sequencing was applied to confirm the final variant. The clinical and molecular genetic features of the three siblings from the new CTX family and other patients with the same mutations, as previously reported, were analyzed. The CYP27A1 gene was also studied for the number of pathogenic variants and their location. Results:We found a homozygous splicing mutation, {"type":"entrez-nucleotide","attrs":{"text":"NM_000784","term_id":"1519312912"}}NM_000784: exon6: c.1184+1G>A, in CYP27A1 gene, which was confirmed by Sanger sequencing. Among the detected pathogenic variants, the splice site mutation had the highest prevalence, and the mutations were mostly found in exon 4. Conclusion:This study is the first to report the c.1184+1G>A mutation in Iran. Our findings highlight the other feature of the disease, which is the lack of relationship between phenotype and genotype. Due to nonspecific symptoms and delay in diagnosis, CYP27A1 genetic analysis should be the definitive method for CTX diagnosis. Key Words: Cerebrotendinous xanthomatosis, CYP27A1, Intellectual disability, Iran, Whole exome sequencing     

水稻转录因子基因OsPHR3在磷素利用过程中的作用

磷是植物体生长发育所必需的大量营养元素之一,广泛参与植物体多种生命活动。土壤中磷的有效性很低,是农业生产中限制作物产量的重要因素。OsPHR3(LOC_Os02g04640)属于MYB-CC家族,与水稻中磷信号途径中心调控因子OsPHR2是同源基因,且具有部分功能重叠。本研究利用转基因技术获得OsPHR3基因的突变体和超表达材料,通过水培实验、~(32)Pi同位素实验以及桶培实验来研究该基因在吸收利用磷素过程中的作用。水培实验表明,与野生型相比,突变体磷含量无明显差异,基因超表达能够提高水稻体内磷含量。~(32)Pi同位素实验显示,与野生型相比,缺磷时突变体吸收速率降低,而该基因超表达能够促进磷素的吸收与转运。桶培实验表明,该基因超表达能够增加水稻有效分蘖数,提高种子中磷含量,该基因缺失使得穗长变短。OsPHR3基因可能调控促进磷的吸收与向地上部转运。该研究将为以后分子育种提供依据。     

茶树Copine家族基因CsBON3的克隆与表达分析

Copine蛋白是一类包含2个C2(N端)和1个vWA(C端)保守域的Ca~(2+)依赖蛋白或磷脂结合蛋白,在胞内信号转导中发挥重要作用。基于序列相似性分析,从茶树转录组数据库中筛选出1条与Copine家族基因高度同源的EST序列。经测序验证该序列包含1 746 bp的完整ORF,编码581个氨基酸。同源比对显示该基因与拟南芥At BON3序列相似度最高(65%),将其命名为CsBON3(Gen Bank登录号为KY435900)。生物信息学分析显示,CsBON3蛋白分子量为63.66 k D,理论等电点为5.48;具有Copine家族蛋白特有的保守结构域;属亲水性蛋白,无信号肽位点,非分泌性蛋白,无跨膜结构域。表达分析表明,CsBON3在茶树花和根系中表达量最高,茎干和成熟叶中表达量最低。低温(4℃)处理茶树1 d后,其表达被显著上调;在生长阶段,该基因表达量高于休眠阶段;同时在接种炭疽菌的茶树叶片中,该基因也被快速上调,表明该基因可能与茶树低温、生长发育及抗病相关。     

瓜实蝇气味结合蛋白基因的克隆及表达谱分析

在气味识别过程中,气味结合蛋白(OBPs)对昆虫的行为反应有重要作用。通过转录组库和NCBI筛选获得瓜实蝇[Bactrocera cucurbitae(Coquillett)]OBPs基因序列,进而通过RT-PCR、克隆等方法获取c DNA全长序列,命名为BcucOBP19。结果表明:BcucOBP19基因开放阅读框全长471 bp,编码157个氨基酸,分子量17.5 ku,等电点5.14,具有昆虫OBPs典型的6个保守半胱氨酸位点。BcucOBP19在瓜实蝇各部位均有表达,以15日龄的雌虫触角中表达量最高,在头、腹、翅和前足中表达量较低,且没有显著性差异。     

Studies on samh seeds (Mesembryanthemum forsskalei Hochst) growing in Saudi Arabia: 3. Utilization of samh seeds in bakery products

Samh seeds obtained from Al-Jouf area were ground into flour analyzed and used as a replacement for wheat in the ratio of 10, 20 and 30% for bread and 30, 60 100% for cookies. The rheological effect of the Samh flour on Saudi wheat flour was also studied. The bread and cookies obtained were evaluated physically and by sensory evaluation. The results obtained indicated that samh flour has high protein content and could be used as a replacement for wheat flour upto 30% without adversely affecting the bread specific volume much. Samh flour has improved the cookies appearance specially the colour (chocolate colour) and spreading ratio. The results also revealed that it is possible to make cookies from 100% samh flour. Due to the high protein content of the samh seeds the nutritional value of the bread and cookies made with samh flour will be improved. The results of the sensory evaluation of the bread and cookies indicated that the bread made with samh flour upto 30% has similar characters except for the crumb color and the overall acceptability which were rated as significantly inferior. The sensory evaluation of the cookies showed that the cookies made with samh flour upto 100% were significantly superior (p<0.05) to the cookies made with 100% wheat flour (control).     

The beneficial effect of (-)-epigallocatechin-3-gallate in an experimental model of Alzheimer's disease in rat: a behavioral analysis

BACKGROUND: Progressive cognitive decline is one of the hallmark symptoms of Alzheimer's disease (AD) which can be modeled by beta-amyloid injection into specific regions of brain. Since epigallocatechin-3-gallate (EGCG) is a potent antioxidant agent which its role against oxidative stress and inflammation has been shown in prior studies, we tried to determine whether EGCG administration protects against beta-amyloid-induced memory and coordination impairment in rats. METHODS: Animals (male Wistar rats) were divided into four groups: sham operated, EGCG-pretreated sham operated (sham+EGCG), untreated lesion (lesion), and EGCG-pretreated lesion (lesion+EGCG). Animals in lesion, lesion+EGCG, and sham+EGCG groups received sterile saline or saline plus EGCG (10 mg/kg) intraperitoneally one day pre-surgery and every other day for three weeks. The lesion was induced one day after EGCG pretreatment by injection of 4 microl of sterile saline or water containing 2 nmol/microl beta-amyloid (1-40) into the hippocampal fissure. For behavioral analysis, psychomotor coordination (PMC) index and spontaneous alternation behavior were assessed using Rota-rod Treadmill and Y-maze, respectively at the third week post-lesion. RESULTS: We found that beta-amyloid (1-40) injection into hippocampus can decrease these behavioral indexes in lesion group in comparison with sham group which is similar to behavioral changes in AD. On the other hand, pretreatment with EGCG can improve the PMC index and spatial Y-maze alternation in the lesion+EGCG group in comparison with lesion group. CONCLUSION: We concluded that EGCG can be effective in restoring beta-amyloid-induced behavioral derangements in rats regarding coordination and memory abilities.     

Heritability of agronomic traits correlated with reduced stink bug damage in an F2:3 soybean population derived from IAC-100

In Brazil, some of the most important insect pests causing damage to soybean (Glycine max) are stink bugs. Soybean production would increase if varieties with enhanced resistance were developed. The aim of this work was to examine different traits associated with plant development, and yield-related traits, in an F_2:3 soybean population in a stink bug-infested field and to evaluate genetic parameters and correlations among those traits. The parents and progeny from 229 F₂ plants developed by crossing a resistant cultivar (IAC-100) with a susceptible cultivar (CD-215) were evaluated in three replications in a single environment. Seven agronomic traits and eight indicators of insect resistance were measured. Genotypes showed significant differences for all traits except lodging. The grain-filling period exhibited a positive genotypic correlation of 0.66 with hundred-seed weight, whereas a negative genotypic correlation of ?0.53 was found between pod damage index (%) and weight of healthy seeds. In general, a shorter pod-filling period, lower weight of hundred-seeds, lower indices of pod damage, and higher seed-yield per plant were phenotypic traits of genotypes resistant to these insects.     

Interspecific and Intraspecific Variation in Grain and Groat Characteristics of Wild Oat (Avena) Species: Very High Groat (1→3),(1→4)-β- -glucan in an Avena atlantica Genotype

Grain characteristics and groat composition have been evaluated in 35 genotypes from nine taxonomic species of Avena, including three species (A. agadiriana, A. atlantica, A. damascena) for which no previous data are available. There was substantial interspecific and intraspecific variation for all characteristics measured. The proportion of groat in the grain ranged from 32·7–62·1%, and mean groat weight from 2·4–37·4 mg. Groat protein concentrations ranged from 13·9–41·3%, and exceeded 32% in one A. atlantica, two A. damascena and one A. murphyi genotype. Groat β-glucan concentration showed very wide variation (2·2–11·3%) are there were substantial interspecific and intraspecific differences. The highest β-glucan concentrations were found in genotypes of A. atlantica. Although there were interspecific and intraspecific variations in groat oil concentration (4·2–10·6%), and in fatty acid composition, data were within previously reported ranges for A. sativa. Overall these data indicate that some of the genotypes of the wild species studied may be of value for breeding oats with improved levels of β-glucan and protein, and that further studies are warranted into both interspecific and intraspecific variations in grain quality factors in wild oat species.