Identification and characterization of CACTA transposable elements capturing gene fragments in maize

Transposable elements (TEs)-mediated gene sequence movement is thought to play an important role in genome expansion and origin of genes with novel functions. In this study, a gene, HGGT, involved in vitamin E synthesis was used in a case study to discover and characterize transposons carrying gene fragments in maize. A total of 69 transposons that are distributed across the 10 chromosomes and have an average length of 3689 bp were identified from the maize sequence database by using the BLAST search algorithm. Three of these carry gene fragments from the progenitor HGGT gene, while the rest (66) contain gene fragments from other cellular genes. Nine of the 69 transposons contain fragments derived from two locations in the genome. By querying the maize Expressed Sequence Tag (EST) database, we found that at least thirteen out of the 69 TEs had corresponding transcripts. More interestingly, two transposons that carry gene fragments from two different chromosomal loci could be expressed as chimeric transcripts.

Genetic Variation in <i>Salamandra</i><i>infraimmaculata</i>from Different Habitats Using Amplified Fragment Length Polymorphism

The purpose of the present study was to examine the genetic variation in Salamandra infraimmaculata from different breeding site habitats using the Amplified Fragment Length Polymorphism (AFLP) method. The results of the dendogram from a hierarchical cluster analysis show that the grouping of S. infraimmaculata as cluster 5 differs from all the other clusters, including the St1 (Tel-Dan stream) population, which was the most predictable. Five Haplogroups (Hg) were characterized. The mean number of alleles per locus in each population (Ne) ranged from 10.566 (Sp1) to 2.720 (Po6). An average estimated heterozygosity (He) by population ranged from 0.100 (Po6) to 0.186 (St1). Population St1, a permanent breeding site where water was available all year round, exhibited the highest level of polymorphism, while population Po6, from the ephemeral breeding site, exhibited the lowest level of polymorphism. Gene flow between clusters showed that clusters 3 and 4 are sources of migrants and also receive gene flow, while clusters 1 and 2 may be a source of migrants but may not receive much gene flow. A phylogenetic analysis, based on clustering using Nei’s genetic distance, demonstrated that the Tel-Dan population is located on a separate branch within its sub-population. The conclusion of the present study shows that the genetic divergence among isolated populations is not correlated to distance but is affected by the variation of habitats.

Diversity of Microflora in Colonic Mucus from Severe Ulcerative Colitis Patients Analyzed by Terminal Restriction Fragment Length Polymorphism and Clone Libraries of Bacterial 16S rRNA Gene Sequences

Although the gut microflora is thought to be an essential factor in the development of ulcerative colitis (UC), the entire gut microflora occurring in UC remains unknown. Most studies use feces to represent the microflora distribution;however, here we analyzed the bacterial diversity in colonic mucus from UC patients receiving colectomy surgery and control patients. The diversity of microflora was investigated using a combination of terminal restriction fragment length polymorphism (T-RFLP) and clone library analyses of the 16S rRNA gene sequences. In the T-RFLP analysis, the number of terminal restriction fragments (T-RFs) decreased significantly in UC patients when compared to control samples. Also in the clone library analysis, the number of operational taxonomic units (OTU) and the Shannon diversity index were reduced significantly in UC patients. These molecular analyses reveal an overall dysbiosis in UC patients. No specific pathogen was found, and a strong negative correlation in relative abundance of bacterial populations was observed between the phyla Bacteroidetes and Firmicutes in the UC patients. This is the first report showing a significant correlation between these two phyla, which may be important characteristics in the pathogenesis of UC.

DGGE Analysis on Mitochondrial Cyt b Gene of Eriocheir sinensis and Eriocheir hepuensis

[Objective] The aim was to investigate the possibility to analyze the genetic diversity of Eriocheir sinensis and Eriocheir hepuensis by using the technique denaturing gradient gel electrophoresis（DGGE）.[Method] Mitochondrial cyt b gene fragment was amplified from 180 individuals of five populations of E.sinensis and a population of E.hepuensis and then analyzed by using DGGE.[Result] All PCR products showed two kinds of electrophoretic mobility on DGGE.The PCR products of all individuals from E.hepuensis showed the same mobility with that of the individuals from 46.7% of Jiangdu population,23.3% of Yizheng population and 20.0% of Wenzhou population of E.sinensis,while the rest of the individuals from the three populations of E.sinensis mentioned above as well as all the individuals of Nanjing and Panjin populations showed the same mobility,which was higher compared with that of E.hepuensis.The results indicated that there was the same genetic marker in E.sinensis populations as that of E.hepuensis population,which was consistent with previous studies.[Conclusion] DGGE technique could be used to analyze the genetic diversity of Chinese mitten crab.

Mapping of a New Gene Wbph6(t) Resistant to the Whitebacked Planthopper, Sogatella furcifera, in Rice

A rice population consisting of 90 TN1/Guiyigu F3 lines was employed to analyze the linkage between DNA markers and a new gene Wbph6(t) conferring resistance to whitebacked planthopper, Sogatella furcifera By using the mapping approach of bulked extremes and recessive class, Wbph6(t) was mapped onto the short arm of chromosome 11 with a genetic distance of 21.2 cM to SSLP marker RM167.

Establishment of a Gene Expression System in Rice Chloroplast and Obtainment of PPT-Resistant Rice Plants

In contrast to the situation of random integration of foreign genes in nuclear transformation, the introduction of genes via chloroplast genetic engineering is characterized by site-specific pattern via homologous recombination. To establish an expression system for alien genes in rice chloroplast, the intergenic region of ndhF and trnL was selected as target for sitespecific integration of PPT-resistant bar gene in this study. Two DNA fragments suitable for homologous recombination were cloned from rice chloroplast genome DNA using PCR technique, and the chloroplast-specific expression vector pRB was constructed by fusing a modified 16S rRNA gene promoter to bar gene together with terminator ofpsbA gene 3 sequence. Chloroplast transformation was carried out by biolistic bombardment of sterile rice calli with the pRB construct. Subsequently, the regenerated plantlets and seeds of progeny arising from reciprocal cross to the wild-type lines were obtained. Molecular analysis suggested that the bar gene has been integrated into rice chloroplast genome. Genetic analysis revealed that bar gene could be transmitted and expressed normally in chloroplast genome. Thus, the bar gene conferred not only selection pressure for the transformation of rice chloroplast genome, but PPT-resistant trait for rice plants as well. It is suggested that an efficient gene expression system in the rice chloroplast has been established by chloroplast transformation technique.

The relation between HLA-DQA1 genes and genetic susceptibility to duodenal ulcer in Wuhan Hans

AIM To study the genetic susceptibility of HLA-DQA1 alleles to duodenal ulcer in Wuhan Hans.METHODS Seventy patients with duodenalulcer and fifty healthy controls were examinedfor HLA-DQA1 genotypes.HLA-DQA1 typing wascarried out by digesting the locus specificpolymerase chain reaction amplified productswith alleles specific restriction enzymes(PCR-RFLP),i.e.,Apal Ⅰ,Bsaj Ⅰ,Hph Ⅰ,Fok Ⅰ,Mbo Ⅱ and Mnl Ⅰ.RESULTS The allele frequencies of DQA1 * 0301and DQA1 * 0102 in patients with duodenal ulcerwere significantly higher and lower respectivelythan those in healthy controls(0.40 vs 0.20,P = 0.003,mcorret = 0.024)and(0.05 vs 0.14,P = 0.012,but Pcorret】0.05),respectively.CONCLUSION DQA1 * 0301 is a susceptiblegene for duodenal ulcer in Wuhan Hans,andthere are immunogenetic differences in HLA-DQA1 locus between duodenal ulcer patients andhealthy controls.

APC gene mutations in Chinese familial adenomatous polyposis patients

AIM:To study the characteristics of APC(adenomatous polyposis coli)gene germline mutation in Chinese patients with familial adenomatous polyposis(FAP).METHODS:APC gene from 14 FAP families was amplified by polymerase chain reaction(PCR)and underwent direct sequencing to determine the micromutation type.For the samples without micromutation,the large fragment deletion of APC gene was examined by multiplex ligation-dependent probe amplification(MLPA).RESULTS:There were gene micromutations in 9 families with a micromutation detection rate of 64.3%(9/14),including 6 frameshift mutations(66.7%),1 nonsense mutation(11.1%)and 2 splicing mutations(22.2%).Large fragment deletions were detected by MLPA in 2 families.The total mutation detection rate of micromutations and large fragment deletions was 78.6%(11/14).CONCLUSION:The detection rate of APC gene germline mutation can be improved by direct sequencing combined with MLPA large fragment deletion detection.

The relationship of Imp2 and DR3 genes with susceptibility to type Ⅰ diabetes mellitus in south China Han population

AIN To study the relationship of Imp2 and DR3genes with type Ⅰ diabetes mellitus.NETHODS Imp2 genotypes and DR3 wereidentified in 68 patients with type Ⅰ diabetesmellitus(Ⅰ-DM)and 71 healthy controls.Then,Ⅰ-DM patients and controls were respectivelyallocated into DR3-positive and DR3-negativegroups.The frequencies of Imp2 and DR3 genein random subjects,and Imp2 genotypes in DR3-matched subjects were compared between Ⅰ-DMpatients and controls.At the same time,Ⅰ-DMpatients were divided into 3 groups based on theonset age of diabetics:group A≤14 years,group B 15-30 years and group C≥31 years.RESULTS The frequency of DR3 in Ⅰ-DMpatients was significantly higher than that incontrols(47% vs 21%,P【0.005),and it wassignificantly higher in group A than that in groupB+C(70% vs 36%,x^2=7.07,P【0.01).Therewas a significant difference among groups withdifferent onset age of diabetics(x^2=8.19,rp=0.33,P【0.05).In random subjects,thefrequency of Imp2.R/R in Ⅰ-DM patients waslower(43% vs 61%,P【0.05)and Imp2.R/Hhigher(53% vs 28%,P【0.05)than that incontrols,and there was no significant differenceamong groups with different onset age ofdiabetics.In DR3-positive subjects,thefrequency of Imp2.R/R in Ⅰ-DM patients waslower(47% vs 87%,P【0.05)and Imp2-R/H higher(47% vs 13%,P【0.05)than that incontrols.In DR3-negative subjects,thefrequency of Imp2.R/H in Ⅰ-DM patients washigher than that in controls(58% vs 32%,P【0.01),but the frequency of Imp2-R/R and Imp2H/H was not significantly different betweenthese two groups.CONCLUSION DR3 gene may be one of thesusceptible genes of Ⅰ-DM,and significantlyrelated to the onset age of diabetics,and thepersons with DR3 may have an younger onsetage of diabeteS.The Imp2-R/R may be theprotective genotype of Ⅰ-DM,and Imp2-R/H thesusceptible genotype.These were not affectedby DR3 gene.Imp-2 genotypes were not relatedwith the onset age of diabetics.

Analysis of parental strain DNA fragments existing in GEMs-Fhhh

There were 6 target DNA fragments of the three parental strains existing in the cell of GEMs(genetically engineered microorganism strain) Fhhh measured in this research by PCR(polymerase chain reaction). The determination showed that GEMs Fhhh contained all the 6 target DNA fragments, mnp 1, mnp 2、 lip 1、 lip 2, FLO 1 and 16S rDNA, and had the molecular genetic stability. Meanwhile the PCR production of each parental strain could only had its target DNA fragments and was different from each other. It may illustrate that the technique of the inter kingdom protoplast fusion for the construction of GEMs Fhhh through the process of intercellular gene recombination could be used as a reliable bioengineering technique to create the specific functional stain for the pollution control.

Analysis of Rb gene Xba Ⅰ polymorphism in Shaanxi aged atherosclerosis population

Objective:To investigate variable number tandem repeat (VNTR) polymorphism of the 17th intron of Rb gene in Shaanxi aged population and the relationship between the polymorphism of Rb gene and atherosclerosis(AS) genetic suscepti- bility. Methods: VNTR polymorphism of the 17th intron of Rb gene were examined in 100 Shaanxi aged AS patients and 100 Shaanxi aged control individuals by PCR-Rb-Xba Ⅰ-RFLP. Results::Two alleles were found both in AS group and control group, which were separately 945 bp(S1) and 630bp + 315bp(S2). S1S2 genotype was the most frequent one in the two populations. Significant difference in allele frequency was not found between AS group and control group, and allele frequency was no significant difference between Chinese and Caucasian. Conclusion: Xba Ⅰ enzyme site of Rb gene could have been certainly stable in AS population, and it was inferred that the polymorphism locus was not liable to cause mutation, which might not implicated in the formation of AS.

The Association between RASSF1 Gene Polymorphisms and Lung Cancer Susceptibility among People in Hubei Province of China

The relationship between Ala/Ser polymorphism in 133 codon of exon 3 region of the RASSF1 gene and genetic susceptibility of lung cancer in Hubei province Han population was investigated by a case-control study. Polymerase chain reaction-restriction fragment length polymorphism （PCR-RFLP） technique was adopted to analyze the polymorphism of codon 133 of exon 3 in the RASSF1 gene of 100 pathologically diagnosed lung cancer patients, and 100 healthy controls. The relationship between different genotypes and the susceptibility of lung cancer was analyzed. Among 200 blood samples from Han people in Hubei Province, including 100 from lung cancer patients and 100 from healthy controls, the frequencies of Ala/Ala, Ala/Ser, Ser/Ser genotype of the RASSF1 in lung cancer patients were 83%, 16%, 1%, and those in healthy controls was 93%, 7%, 0% respectively, with the difference being statistically significant between two groups （P〈0.05）. The individuals with Ala/Ser genotype had higher risk of suffering from lung cancer, with an OR of 2.341, and 95% CI of 1.009-6.393 respectively. It was concluded that RASSF1Ala133Ser was a susceptible genetic factor of lung cancer. Ala/Ser genotype increased the risk of lung cancer.

Molecular Cloning and Sequencing of a Specific cDNA Mapping to the Bam HI-I2 and -LFragments within the Inverted Repeats of Unique Long Region(IRL) from the Genom e of the Marek′s Disease Herpesvirus (MDV) Oncogenic Strain Beijing-1

Isolation and identification of a specific cDNA mapping to the BamHI I2 and L fragments from the inverted repeats of unique long region(IRL) in the genome of Marek′s disease herpesvirus (MDV) oncogenic strain Beijing 1 had been previously performed by us. In this study, the specific cDNA was cloned into phagemid vectors PUC118 and 119 on the basis of prefabricated two recognized sites in synthesized primers. Recombinants were further identified with restriction pattern, molecular hybridization, and DNA sequencing analysis. It was demonstrated that this cDNA with 720 base pair (bp) contained sequences including a potentially incomplete open reading frame (ORF) encoded a 238 amino acids (aa) predicted polypeptide which was significantly homologous not only to part of N terminus of meq, but also to that of XbaI ClaI subfragment of BamHI L. In accordance with these data, following results could be deduced:①the 720 bp cDNA represented a spliced transcript;②meq transcription could be extended from the right hand end of BamHI I2 to the adjacent BamHI L fragment;③the L region was transcribed in varying degrees\ in MDV induced lymphoblastoid tumors.

Preliminary Research on the p53 Gene Rearrangements in the Evolution of Chronic Myelogenous Leukemia to Blast Crisis

DNA from 36 patients with chronic myelogenous leukemia (CML) at various clinical stages and 6 cases of acute leukemia was investigated for alterations of the p53 gene by Southern blot analysis.Rearrangements of the p53 gene were seen in 3 of 12 (25.00%) cases of blast crisis and accelerated phase (AP) of CML and in only one of 18 chronic phrase (CP),just as has been reported previously. Meanwhile,by restriction fragment length polymorphism (RFLP) analysis the Bgl II site polymorphism in the p53 gene was also found. The frequency in Chinese people detected here was 0.392,which was strikingly higher than that in some other countries(P<0. 001).These results suggested that the alterations of the p53 gene, for example,p53 rearrangements,were probably responsible for the progression of BC in some CML patients, and that the frequency of Bgl II polymorphism in the p53 gene might be related to the population distribution.

基于高频组合片段-基因表达式编程算法的轨道交通地面沉降预测模型

[目的]地面沉降预测和控制是轨道交通盾构法隧道施工中最为关注的问题之一。为了解决现有地面沉降预测和控制中存在的模型表达过于复杂且缺乏解释性的问题,需要一种既简洁清晰,又能够描述复杂问题的可解释模型,GEP(基因表达式编程)算法提供了这种可能性,因此需对基于HFS(高频组合片段)-GEP算法的轨道交通地面沉降预测模型进行深入研究。[方法]以杭绍城际铁路某区段盾构隧道工程为依托,选取盾构施工过程中的土舱压力、刀盘扭矩、刀盘转速、推进速度、总推力、隧道埋深及盾尾注浆量等参数作为关键输入型施工参数,地面沉降作为输出型施工参数,通过备选公式集筛选以及HFS选取,建立基于HFS-GEP算法的轨道交通地面沉降预测模型。利用该模型对第180环—第210环区段的关键施工参数进行优化调整,分析盾构施工参数变化对地面最终沉降的影响效果。[结果及结论]基于HFS-GEP算法的地面沉降预测模型可以反映盾构施工参数与地面最终沉降的显式关系;相较于传统GEP算法的地面沉降预测模型,该模型准确度更高,结构更为简洁,且收敛速度更快。通过对盾构关键施工参数进行优化调整,该模型可将第180环—第210环区段的最终沉降量控制在10 mm以内。

Is type Ⅰ alpha 2 collagen gene responsible for intracranial aneurysm in Northeast China?

In this study, we investigated whether a single nucleotide polymorphism （rs42524 G 〉 C） in the type I alpha 2 collagen gene was associated with sporadic ruptured intracranial aneurysm or its clinical characteristics in patients from Northeast China. Genotyping of the rs42524 G 〉 C polymorphism was carried out using a polymerase chain reaction-restriction fragment length polymorphism assay. The data showed that the frequency of the rs42524 GC ＋ CC genotype was significantly higher than the GG genotype among intracranial aneurysm patients whose Hunt and Hess grading scale was 〉 3. In addition, the rs42524 G 〉 C genotype was found to have a statistically significant association with intracranial aneurysm risk. These findings indicate that the type I alpha 2 collagen gene gene may be involved in a predisposition to intracranial aneurysm in the Northeast Chinese population. Crucially, the rs42524 C allele may be an important risk factor for increased severity of the condition in patients with ruptured intracranial aneurysms.

利用CRISPR/Cas9基因编辑片段敲除技术创制玉米多样化等位变异

利用CRISPR/Cas9基因编辑技术创制等位变异已经成为众多植物中增加种质资源多样性的重要手段。提高玉米等谷物中类胡萝卜素含量是发展中国家解决维生素A缺乏症的一种经济方法。本研究以玉米中调控类胡萝卜素合成的基因crtRB1为研究对象,利用双靶标片段缺失性基因编辑技术,在原生质体中对crtRB1的启动子顺式元件进行片段敲除,获得了具有片段缺失和InDel(插入或缺失)的多样化等位变异,这为在玉米中实现稳定的crtRB1启动子元件的缺失突变奠定了基础,对启动子元件的功能研究和玉米的品质改良具有重要意义。

Identification of a gene engineering antibody against cystic echinococcosis in liver

OBJECTIVE: To identify a gene engineering antibody against cystic echinococcosis in liver. METHODS: A single chain of variable fragment of human antibodies (ScFvs) was selected from the library by using affinity selection technique with the recombinant antigen on solid surface. The positive clones were demonstrated by ELISA and their DNA sequences were also determined. RESULTS: The DNA sequence data showed that the antibody gene is composed of 768bp. In addition, a specific combination capacity with recombinant Echinococcus granulosus antigen B (r-EgB) was demonstrated by ELISA. CONCLUSION: The obtained gene engineering antibody against r-EgB may have potential implications in immunological treatment and drug targeting delivery.

猪流行性腹泻病毒Nsp6蛋白的分段表达及多克隆抗体制备

猪流行性腹泻病毒(PEDV)的非结构蛋白Nsp6在诱导宿主细胞自噬中起着重要作用。为进一步确定Nsp6蛋白诱导细胞自噬的关键功能域,本研究利用RT-PCR扩增技术获得了Nsp6及其3个分段基因。首先构建了重组原核表达质粒pSUMO-Nsp6,并转化至大肠杆菌Rosetta感受态中,经IPTG诱导并纯化后,所得蛋白用于小鼠免疫,制备抗Nsp6蛋白的多克隆抗体。再将Nsp6及其3个分段基因分别构建至真核表达载体pCMV-HA,并将其转染至IPEC-J2细胞进行真核表达,通过Western blot和双荧光标记法来确定蛋白表达情况。结果:Nsp6蛋白在Rosetta中成功表达,并通过免疫小鼠获得了效价为1∶10240的多克隆抗体,该抗体具有与PEDV和Nsp6蛋白特异性结合的能力;免疫荧光及Western blot结果表明,Nsp-6及其截短基因在IPEC-J2细胞中成功表达,且与制备的Nsp6多克隆抗体发生特异性结合。综上,本研究原核表达了Nsp6蛋白并制备了相应的特异性抗体,验证了Nsp6及其分段基因的在细胞中的真核表达,为进一步研究Nsp6蛋白的特性和功能奠定了基础。

青藏高原蕨麻的分子谱系地理学研究

青藏高原的隆升以及第四纪冰期气候的循环波动,对于青藏高原及其周边地区动植物的分布和遗传结构具有很大的影响。蕨麻是青藏高原极富营养、药用和生态价值的特有植物资源,蕨麻和鹅绒委陵菜的分类关系及分布在学术界存在争议,分子谱系地理学研究将为蕨麻遗传多样性形成机制及推断该物种迁移演化历史提供依据。以蕨麻为研究对象,对采集的30个居群的810个个体进行了叶绿体trnL-trnF序列和核基因ITS测序,揭示遗传变异在居群内和居群间的分布格局,结合群体遗传学和系统发生学,分析该物种的遗传结构与历史事件之间的关联,揭示物种及物种内不同种群形成现有分布格局的历史原因和演化过程。主要结论有:1)蕨麻具有较高水平的遗传多样性。cpDNA trnL-trnF片段共检测到40种单倍型,16个为共享单倍型,占比40%,24个为居群特有单倍型,占比60%,遗传多样性h=0.7078,单倍型多样性Hd=0.8217,核苷酸多样性π=0.010641,总遗传多样性HT=0.849;nrDNA ITS片段共检测到128种单倍型,共享单倍型42种,占比32.8%,居群特有单倍型86种,占比67.2%,遗传多样性h=0.7633,单倍型多样性Hd=0.8168,核苷酸多样性π=0.003584,总遗传多样性HT=0.844。2)居群内的遗传多样性大于居群间的遗传多样性。序列分析结果为居群内和居群间的遗传多样性都很高(cpDNA trnL-trnF:HT=0.849,居群内平均遗传多样性HS=0.640;nrDNA ITS序列:HT=0.844,HS=0.763,HT均大于HS)。蕨麻居群分为3个组:青海高原组、横断山脉组和藏南谷地组。蕨麻的遗传变异主要来源于居群内部。3)蕨麻种群具有明显的谱系地理结构。cpDNA trnL-trnF序列和nrDNA ITS遗传多态性分析及地理分布模式检验,cpDNA trnL-trnF序列:遗传分化系数G_(ST)=0.246,N_(ST)=0.417,nrDNA ITS序列:G_(ST)=0.096,N_(ST)=0.522,N_(ST)均显著大于G_(ST)(P<0.001),表明蕨麻所有居群单倍型存在显著的谱系地理结构,两种方法的结果高度一致。分子变异分析(AMOVA)表明,大部分遗传变异(59.69%)存在于居群内部,居群间分化水平很高(F_(ST)=0.40313)。4)共享单倍型和特有单倍型均由古老单倍型衍生而来。cpDNA trnL-trnF和nrDNA序列中央连接网状图呈以共享单倍型M4和H9位于中心,M_(1)、M_(3)和H_(2)、H_(10)、H_(11)、H_(12)位于主干位置的星状结构,其余共享单倍型和特有单倍型均由这些古老单倍型衍生而来,两者结果一致。5)蕨麻种群大小和范围发生过大规模扩张。利用cpDNA trnL-trnF和nrDNA序列进行歧点分析,前者歧点分布呈单峰曲线,表明近期群体大小和范围有大规模扩张发生;后者的歧点分布呈双峰曲线,反映基因谱系的高度复杂性,但Tajima’s D,Fu and Li’s D和Fu and Li’s F均为负值,且结果显著,且离差平方和(SSD)和扩张评估指数(H_(Rag))的统计检验不显著,表明蕨麻居群近期有扩张的可能。6)蕨麻存在3个冰期避难所,即东喜马拉雅区域、青藏高原东南边缘及横断山脉区域。