金丝鲶体色基因组合的初步研究

通过胡子鲶、金丝鲶的交互繁殖，根据子代表现型，初步认定金丝鲶体色基因是隐性基因的纯合。

锦鲤基因组数据分析及体色相关基因的筛选

为了获得红白锦鲤的基因组信息,筛选与其肤色相关的基因,采用Illumina高通量测序技术对红白锦鲤皮肤组织的基因组进行测序,获得127.23 Gb clean data,Q20碱基比例在95.59%及以上,Q30碱基比例在90.81%及以上,GC含量为37.32%~42.38%,测序错误率为0.07。与鲤鱼基因组序列进行比对的结果显示,比对效率为96.35%。研究共鉴定了1048576个SNPs(单核苷酸多态性),其中3.12百万~5.40百万个SNPs位于短reads比对不到的区域,其中变异位点位于外显子区域的有579778个SNPs。SNP位点分布于锦鲤的50条染色体上,不包含scaffold(染色体骨架)。经ANNOVAR软件进行功能注释,纯合类型的SNPs数量是574310个,杂合类型的SNPs数量是474 265个。SNPs位于基因间的数量最多,SNPs位于基因内的外显子区域的多态性最高。通过对8个重要候选基因注释的理解,发现微管蛋白LOC109046532、LOC109049213这2个基因与色素颗粒运输有关。其中基因LOC109046532含有突变,而另1个基因LOC109049213则不含有任何突变。8个候选基因都含有外显子SNP位点,但是没有发现终止密码子突变。

鱼类体色相关功能基因的研究进展

鱼类表皮色素形成复杂,涉及一系列基因表达调控、基因编码酶催化及细胞因子等参与。为了解鱼类体色形成的相关机制,本文综述了色素合成通路中重要色素——黑色素形成的分子机制,并对鱼类体色相关基因中的酪氨酸酶相关蛋白1基因(tyrosinase-related protein gene 1,TYR1)、性别决定区基因(sex determining region Y-box 10,SOX10)、多巴素异构酶基因(dopachrome tautomerase,DCT)、黑皮质素受体-1基因(melanocortin 1 receptor,MC1R)和鼠灰色基因(Agouti)的研究进展概括。对于鱼类遗传、系统发育及分子进化等领域的研究具有重要意义,为体色形成机制提供理论参考和借鉴,并展望了今后对鱼类体色形成机制研究的新方向。

Chromosome Location of the Male-sterility and Yellow Seedling Gene in Line 1066A of Foxtail Millet

Using foxtail millet (Setaria italica (L.) Beauv.) male-sterile line 1066A as female parent and Yugu 1 primary trisomic series (1 - 7) and tetrasomics 8, 9 as male parents, chromosome location of gene for male-sterility and yellow seedling in line 1066A was studied by primary trisomic analysis. The plants of F-1 generation of trisomics 2 - 9 were obtained by crossing with a great many plants of 1066A. F-1 generation of trisomics was similar to their male parent in morphologic characters, the color of their seedling was green, and pollen was partially fertile. The segregation ratio of fertility to sterility is 3:1 in F-2 generation of trisomics 2, 3, 4, 5, 7, 8 and 9; and 14:1 only in F-2 generation of trisomic 6 (chi(0.05)(2) = 0.012). The segregation ratio of green seedling to yellow seedling is 12:1 only in F-2 generation of trisomic 7 (chi(0.05)(2) = 0.31), but in other cases, this ratio is 3:1. The results indicated that the male-sterility gene was located on chromosome 6, and the gene for yellow seedling was monogenic recessive and located on chromosome 7. The rate of trisomics transmission by pollen was tested, trisomics 8 and 9 were the highest in rates of trisomics transmission and followed by trisomics 6 and 4.

肾透明细胞癌3，7，8，9，17号染色体的杂合性缺失研究

肿瘤常在抑癌基因位点上出现染色体基因缺失，多表现为等位基因杂合性缺失（LOH）。我们通过检测肿瘤的LOH及其规律，旨在一定染色体范围内发现肿瘤相关的抑癌基因。

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.

Identification of sika deer and red deer using partial cytochrome b and 12s ribosomal RNA genes

A study was conducted on the identifications of the degraded samples of sika deer （Cervus nippon） and red deer （Cervus elaphus） by phylogenetic and nucleotide distance analysis of partial Cytb and 12s rRNA genes sequences. 402 bp Cytb genes were achieved by PCR-sequencing using DNA extracted from 8 case samples, and contrasted with 27 sequences of Cytb gene downloaded from GenBank database. The values of three nucleotide distance between three suspected samples and sika deer were identical （0.026±0.006）, which was smaller than the smallest nucleotide distance between eastern red deer and sika deer （0.036）. Furthermore, phylogenetic analysis of sika deer and red deer indicated that the evidences located within the same cluster as sika deer. The evidences were sika deer materials. As the same way, other three suspected samples were derived from red deer. The results were further confirmed by phylogenetic and nucleotide distance analysis of 387 bp 12s rRNA gene. The method was powerful and less time-consuming and helpful to reduce the related cases with wildlife.

Localization of Two GFP_tagged Tobacco Plastid Division Protein NtFtsZs in Escherichia coli

Two plastid division genes, NtFtsZ1 and NtFtsZ2 isolated from Nicotiana tabacum L. were fused with gfp and expressed in Escherichia coli . The regular localizations of full length NtFtsZs∶GFP along the filamentous bacteria indicated that the NtFtsZs could recognize the potential division sites in E. coli and be polymerized with heterogeneous FtsZ from bacteria. The overexpression of NtFtsZs ∶ gfp inhibited the division of host strain cells and resulted in the long filamentous bacterial morphology. These results suggested that eukaryotic ftsZs have similar function to their prokaryotic homologs. Meanwhile, the different deletions of motifs of NtFtsZs are also employed to investigate the functions of these proteins in E. coli . The results showed that the C_terminal domains of NtFtsZs were related to the correct localization of NtFtsZs in E. coli and the N_terminal domains of NtFtsZs were responsible for the polymerization of homogeneous and heterogeneous FtsZ proteins. The significance of these results in understanding the functions of NtFtsZs in plastid division were discussed.

Screening of the Metastasis-Associated Genes by Gene Chip in High Metastatic Human Ovarian Cancer Cell Lines

Affymetrix U133A oligonucleotide microarrays were used to study the differences of gene expressions between high （H） metastatic ovarian cancer cell line, HO-8910PM, and normal ovarian tissues （C）. Bioinformatics was used to identify their chromosomal localizations. A total of 1,237 genes were found to have a difference in expression levels more than eight times. Among them 597 were upregulated [Signal Log Ratio （SLR） ≥3], and 640 genes were downregulated （SLR≤-3）. Except one gene, whose location was unknown, all these genes were randomly distributed on all the chromosomes. However, chromosome 1 contained the most differentially expressed genes （115 genes, 9.3%）, followed by chromosome 2 （94 genes, 7.6%）, chromosome 12 （88 genes, 7.1%）, chromosome 11 （76 genes, 6.1%）, chromosomes X （71 genes, 5.7%）, and chromosomes l7 （69 genes, 5.6%）. These genes were localized on short-arm of chromosome （q）, which had 805 （65.1%） genes, and the short arms of No.13, 14, 15, 21, and 22 chromosomes were the only parts of the chromosomes where the differentially expressed genes were localized. Functional classification showed that most of the genes （306 genes, 24.7%） belonged to the enzymes and their regulator groups. The subsequent group was the nucleic acid binding genes （144 genes, 11.6%）. The rest of the top two groups were signal transduction genes （137 genes, 11.1%） and proteins binding genes （116 genes, 9.4%）. These comprised 56.8% of all the differentially expressed genes. There were also 207 genes whose functions were unknown （16.7 %）. Therefore it was concluded that differentially expressed genes in high metastatic ovarian cancer cell were supposed to be randomly distributed across the genome, but the majority were found on chromosomes 1, 2, 12, 11, 17, and X. Abnormality in four groups of genes, including in enzyme and its regulator, nucleic acid binding, signal transduction and protein binding associated genes, might play important roles in ovarian cancer metastasis. Those genes need to be further studied.

Isolation, Expression Characteristics and Chromosomal Locations of Three cDNA Fragments Under Salt Stress in Rice

cDNA libraries were constructed from the leaves of a rice (Oryza sativa L.) salt tolerancevariety Tesan抋i 2 growing in solutions with 150 mmol/L NaCl for 3 h or without salt stress. Three salt-responsive cDNA clones, Ts1, Ts2 and Ts3 were isolated by differential screening. Northern blottinganalysis showed that the transcription levels of Ts1 and Ts2 increased within 3 h salt stress and kept onincreasing within 24 h, while the transcription level of Ts3 reached its peak within 3 h. Sequence analysisindicated that there were no homologies between the three cDNA clones and any known gene. The threecDNA clones were mapped using a doubled haploid (DH) population derived from an indica variety ZYQ8,which was a salt tolerance parent of Tesan抋i 2, with a japonica variety JX17. Ts1, Ts2 and Ts3 werelocated on chromosomes 1, 3 and 7, respectively. It was noted that Ts1, Ts2, and Ts3 were in or near theregions of major or minor salt tolerance quantitative trait loci (QTLs), which were mapped in the same DHpopulation in a parallel study.

Research on the Construction of Bacterial Artificial Chromosome Vector DNA and the Potentials in Application

[ Objective] The aim of this study was to provide a method for solving the problems in preparing BAC vector with High-copy plasmid pUC119- Bluelox BAC. [ Method ] With selecting a proper single restriction site, sequences of a single copy BAC vector plasmid were inserted into proper site of High-copy plasmid pUC119 vector. [ Result] The gene sequence of BAC vector lost control function of single copy number in new plasmid pUC119-BAC and was copied through High-copy form. The gene sequence of BAC vector basic function was completely cutted off through single enzyme digestion and the control function of single copy could be recovered by auto-connection. [ Conclusion] The High-copy pUC119-BAC plasmid was used to copy and amplify high copy of basic function gene sequence in BAC vector, besides that it could be used to construct transfer vector of molecular cloned recombinant virus or BAC library.

Fine mapping and marker-assisted selection (MAS) of a low glutelin content gene in rice

Rice with low glutelin content is suitable as functional food for patients affected with diabetes and kidney failure. The fine mapping of the gene(s) responsible for low glutelin content will provide information regarding the distribution of glutelin related genes in rice genome and will generate markers for the selection of low glutelin rice varieties. Following an SDS-PAGE screen of rice germplasm from Taihu Valley of China, Japonica selection W3660 is identified to be a novel mutant characterized with low glutelin content. For fine mapping the mutant gene for low glutelin content, F2 and F3 populations were derived from a cross between W3660 and Jingrennuo. SDS-PAGE analysis of the total endosperm protein showed that the low glutelin content trait was controlled by a single dominant nuclear gene. Genetic mapping, using SSRs, located this gene to chromosome 2, in the region between SSR2-001/SSR2-004 and RM1358. The dis- tances of the two markers to the target gene were 1.1 cM and 3.8 cM respectively. By semi-quantitative RT-PCR analysis, the transcripts of GluB4/GluB5 genes located within the region do not change. However, GluB5 gene located proximal to SSR2-001/SSR2-004 was specifically reduced. SSR profiles of seven Japonica varieties were compared with that of W3660 for loci in the relevant genetic region. The markers SSR2-004 and RM1358 were used for marker- assisted selection. The selection efficiencies of SSR2-004 and RM1358 were 96.8% and 92.7% respectively. This provides a standard starting point for the breeding of low glutelin content rice varieties in China.

Frequent loss of heterozygosity at 8p22 chromosomal region in diffuse type of gastric cancer

AIM: To study the loss of heterozygosity (LOH) at 8p21-23 locus in diffuse gastric cancer.METHODS: To evaluate the involvement of this region in gastric cancer, we used eight microsatellite markers covering two Mb of mentioned region, to perform a high-resolution analysis of allele loss in 42 cases of late diffuse gastric adenocarcinoma.RESULTS: Six of these STS makers: D8S1149, D8S1645, D8S1643, D8S1508, D8S1591, and D8S1145 showed 36%, 28%, 37%, 41%, 44% and 53% LOH, respectively.CONCLUSION: A critical region of loss, close to the NAT2 locus and relatively far from FEZ1 gene currently postulated as tumor suppressor gene in this region.

Comparative Study on the Genomes Between Oryza alta and Oryza latifolia Based on C-Genome

[Objective] Genomic in situ hybridization (GISH) was used to study the relationship between the two CCDD genomes of Oryza alta and Oryza latifolia. [Method] Total DNA of Oryza officinalis (C-genome) was used as a probe for genomic in situ hybridization on metaphase chromosomes from Oryza alta and Oryza latifolia, respectively. [Result] Under certain post-hybridization washing stringencies, C- and D-genome could be distinguished in CCDD genome type; there were huge differences in some CC chromosomes of Oryza alta, Oryza latifolia, and Oryza officinalis. The genome of Oryza latifolia was more original. [Conclusion] Comparative analysis of the Oryza species with identical genome type may facilitate to elucidate the possible approaches to plant genome evolution and species evolution.

Characterization of a S-locus-related Receptor-like Kinase Cluster in Rice Chromosome 4

We have identified 14 S _locus glycoprotein (SLG)_related protein kinase genes in a 323 kb contig of rice (Oryza sativa L.) chromosome 4 and we detected the transcription pattern of this gene cluster by reverse transcription_polymerase reaction (RT_PCR). RT_PCR results revealed that nine putative genes were transcribed in rice and these genes had the different expression patterns: two genes are expressed predominantly in reproductive tissues while the other seven genes are expressed in both reproductive and vegetative tissues. Analysis of the predicted amino acid sequences demonstrated that the extracellular receptor domains are highly homologous to SLG of Brassica, whereas the cytoplasmic kinase domains contain conserved amino acids present in serine/threonine kinases.

Arabidopsis thaliana histone deacetylase1(AtHD1)is localized in euchromatic regions and demonstrates histone deacetylase activity in vitro

Arabidopsis thaliana histone deacetylase 1 （AtHD1 or AtHDA19）, a homolog ot yeast RPD3, is a global regulator ot many physiological and developmental processes in plants. In spite of the genetic evidence for a role of AtHD1 in plant gene regulation and development, the biochemical and cellular properties ofAtHD 1 are poorly understood. Here we report cellular localization patterns ofAtHD 1 in vivo and histone deacetylase activity in vitro. The transient and stable expression of a green fluorescent protein （GFP）-tagged AtHD1 in onion cells and in roots, seeds and leaves of the transgenic Arabidopsis, respectively, revealed that AtHD1 is localized in the nucleus presumably in the euchromatic regions and excluded from the nucleolus. The localization patterns ofAtHD 1 are different from those of AtHD2 and AtHDA6 that are involved in nucleolus formation and silencing of transgenes and repeated DNA elements, respectively. In addition, a histone deacetylase activity assay showed that the recombinant AtHD 1 produced in bacteria demonstrated a specific histone deacetylase activity in vitro. The data suggest that AtHD 1 is a nuclear protein and possesses histone deacetylase activities responsible for global transcriptional regulation important to plant growth and development.

Possible mechanism for hepatitis B virus X gene to induce apoptosis of hepatocytes

AIM： To investigate the possible mechanism for HBV X gene to induce apoptosis of hepatocyte HL-7702 cells.METHODS： HBV X gene eukaryon expression vector pcDNA3-X was established and transfected into HL-7702 cells by lipid-mediated transfection, including transient and stable transfection. Positive clones were screened by incubating in the selective medium with 600 μg/mL G418 and named HL-7702/HBV-encoded X protein （HBx） cells. The expressions of Fas/FasL, Bax/Bcl-2, and c-myc mRNA were measured by semi-quantitative RT-PCR in HL-7702/HBx and control group, respectively.RESULTS： RT-PCR analysis confirmed that HBV X gene was transfected into HL-7702 cells successfully. By semiquantitative RT-PCR analysis, Bax and c-myc mRNA levels in HL-7702/HBx cells of transient transfection were significantly higher than those in control, FasL and c-myc mRNA levels in HL-7702/HBx cells of stable transfection were significantly higher than those in control, whereas the Bcl-2 mRNA levels in HL-7702/HBx cells of transient and stable transfection were significantly lower than thosein control.CONCLUSION： HBV X gene may promote the apoptosis of hepatocytes by regulating the expressions of Fas/FasL, Bax/Bcl-2, and c-myc gene in a dose-dependent manner.

Approaches to functional genomics in filamentous fungi

The study of gene function in filamentous fungi is a field of research that has made great advances in very recent years. A number of transformation and gene manipulation strategies have been developed and applied to a diverse and rapidly expanding list of economically important filamentous fungi and oomycetes. With the significant number of fungal genomes now sequenced or being sequenced, functional genomics promises to uncover a great deal of new information in coming years. This review discusses recent advances that have been made in examining gene function in filamentous fungi and describes the advantages and limitations of the different approaches.

Yamanaka factors critically regulate the developmental signaling network in mouse embryonic stem cells

Yamanaka factors （Oct3/4, Sox2, Klf4, c-Myc） are highly expressed in embryonic stem （ES） cells, and their overexpression can induce pluripotency in both mouse and human somatic cells, indicating that these factors regulate the developmental signaling network necessary for ES cell pluripotency. However, systemic analysis of the signaling pathways regulated by Yamanaka factors has not yet been fully described. In this study, we identified the target promoters of endogenous Yamanaka factors on a whole genome scale using ChIP （chromatin immunoprecipitation）- on-chip in El4.1 mouse ES cells, and we found that these four factors co-occupied 58 promoters. Interestingly, when Oct4 and Sox2 were analyzed as core factors, Klf4 functioned to enhance the core factors for development regulation, whereas c-Myc seemed to play a distinct role in regulating metabolism. The pathway analysis revealed that Yamanaka factors collectively regulate a developmental signaling network composed of 16 developmental signaling pathways, nine of which represent earlier unknown pathways in ES cells, including apoptosis and cellcycle pathways. We further analyzed data from a recent study examining Yamanaka factors in mouse ES ceils. Interestingly, this analysis also revealed 16 developmental signaling pathways, of which 14 pathways overlap with the ones revealed by this study, despite that the target genes and the signaling pathways regulated by each individual Yamanaka factor differ significantly between these two datasets. We suggest that Yamanaka factors critically regulate a developmental signaling network composed of approximately a dozen crucial developmental signaling pathways to maintain the pluripotency of ES cells and probably also to induce pluripotent stem cells.