Differential expression of allelic carboxylesterase-2 genes in oocytes of loach (Misgurnus fossilis L.) and heterogeneity of loach oocytes and eggs for the expression of allelic carboxylesterase-2 genes

Tissue and cell differences have been found in the expression of allelic carboxylesterase-2 (E-2) (carboxylic ester hydrolase, E.C. 3.1. 1.1) genes of the loach. The relative activity of two allozymes in the brain and muscles of heterozygotes is similar, whereas in oocytes and eggs of the same fish the activity of one of the allozymes is considerably greater than that of the other. Oocytes and eggs of some heterozygotes were shown to be heterogeneous for the expression of E-2 alleles. The phenomenon implies that roe produced by a heterozygous female can contain two or more egg types: in some the alleles are equally expressed, while in others one of the alleles is predominantly expressed.     

Prioritization of differentially expressed genes through integrating public expression data

Differentially expressed gene (DEG) analysis is a major approach for interpreting phenotype differences and produces a large number of candidate genes. Given that it is burdensome to validate too many genes through benchwork, an urgent need exists for DEG prioritization. Here, a novel method is proposed for prioritizing bona fide DEGs by constructing the normal range of gene expression through integrating public expression data. Prioritization was performed by ranking the differences in cumulative probability for genes in case and control groups. DEGs from a study on pig muscle tissue were used to evaluate the prioritization accuracy. The results showed that the method reached an area under the receiver operating characteristic curve of 96.42% and can effectively shorten the list of candidate genes from a differential expression experiment to find novel causal genes. Our method can be easily extended to other tissues or species to promote functional research in broad applications.     

Differential expression of two related organ-specific genes in pea

We have screened a pea genomic library using a cDNA probe derived from pea shoot RNA. From this screen, we isolated two closely related genes, designated as S2 and P4. An intriguing property of these two genes is the presence in their coding region of a repeated sequence that is conserved between them in sequence but not in the number of the repeating units. The predicted amino acid sequence suggests that these proteins could be exported and glycosylated. 3 S1 analysis reveals that one of the genes, S2, is expressed highly in stem, as expected from previous work. However, mRNA derived from the other gene, P4, is not detectable in stem tissue, but is present in tissue derived from pea pods. The 5 upstream sequence of S2 and P4 are 94% identical up to position -121, suggesting that sequences upstream of -121 are responsible for organ-specific expression of the two genes.     

A genome-wide survey of maize lipid-related genes: candidate genes mining,digital gene expression profiling and co-location with QTL for maize kernel oil

Lipids play an important role in plants due to their abundance and their extensive participation in many metabolic processes. Genes involved in lipid metabolism have been extensively studied in Arabidopsis and other plant species. In this study, a total of 1003 maize lipid-related genes were cloned and annotated, including 42 genes with experimental validation, 732 genes with full-length cDNA and protein sequences in public databases and 229 newly cloned genes. Ninety-seven maize lipid-related genes with tissue-preferential expression were discovered by in silico gene expression profiling based on 1984483 maize Expressed Sequence Tags collected from 182 cDNA libraries. Meanwhile, 70 QTL clusters for maize kernel oil were identified, covering 34.5% of the maize genome. Fifty-nine (84%) QTL clusters co-located with at least one lipid-related gene, and the total number of these genes amounted to 147. Interestingly, thirteen genes with kernel-preferential expression profiles fell within QTL clusters for maize kernel oil content. All the maize lipid-related genes identified here may provide good targets for maize kernel oil QTL cloning and thus help us to better understand the molecular mechanism of maize kernel oil accumulation.     

Genome‐wide expression quantitative trait locus studies facilitate isolation of causal genes controlling panicle structure

The morphology of rice (Oryza sativa L.) panicles is an important determinant of grain yield, and elucidation of the genetic control of panicle structure is very important for fulfilling the demand for high yield in breeding programs. In a quantitative trait locus (QTL) study using 82 backcross inbred lines (BILs) derived from Koshihikari and Habataki, 68 QTLs for 25 panicle morphological traits were identified. Gene expression profiling from inflorescence meristems of BILs was obtained. A combination of phenotypic QTL (pQTL) and expression QTL (eQTL) analysis revealed co‐localization between pQTLs and eQTLs, consistent with significant correlations between phenotypic traits and gene expression levels. By combining pQTL and eQTL data, two genes were identified as controlling panicle structure: OsMADS18 modulates the average length of the primary rachis and OsFTL1 has pleiotropic effects on the total number of secondary rachides, number of grains per panicle, plant height and the length of flag leaves. Phenotypes were confirmed in RNA interference knocked‐down plants and overexpressor lines. The combination of pQTL and eQTL analysis could facilitate identification of genes involved in rice panicle formation.     

Random allelic expression in the adult human body

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鼠疫耶尔森氏菌质粒上重要毒力相关基因的克隆与表达

鼠疫耶尔森氏菌含有3种质粒pMT1、pPCP1和pCD1,这3种质粒编码鼠疫耶尔森氏菌的多种重要毒力因子。首先通过生物信息学技术选定了18种可能重要的毒力相关基因作为拟克隆和表达的目的基因。通过：PCR技术、TA克隆技术、双酶切技术获得目的片段。这些目的片段再分别克隆入原核表达载体pET32a中,构建了一系列重组表达质粒,其中12个重要的毒力相关基因在原核表达载体pET32a中有稳定的高效表达,表达量占细菌总蛋白的20％～40％。实验结果为进一步研究质粒编码的毒力因子的结构与功能,及其作为新型疫苗选择的可能性奠定了基础。     

信息素信号通路基因在斑玉蕈生长发育过程中的差异表达

为了更清楚地了解斑玉蕈菌丝成熟、原基形成和子实体发育的过程,本研究对不同菌丝培养时期的栽培瓶进行出菇实验,并对其不同培养时期和生长发育关键时期的信息素通路基因进行差异表达分析,以期揭示信息素信号通路基因参与调节斑玉蕈菌丝的生长、子实体形成和发育的作用。研究结果表明：斑玉蕈菌丝培养40-80d过程中,子实体产量呈上升的趋势,说明菌丝的成熟程度对产量会产生重要影响。对斑玉蕈基因组中的信息素信号通路基因进行分析鉴定共获得了8个关键基因。信息素通路基因差异表达分析表明：在菌丝培养40-80d过程中,大部分信息素信号通路基因在第60天时表达量最高,其中ste20、cdc24和ste12上调了4-20倍,而在第80天出现下降。从菌丝恢复到扭结形成原基和子实体发育的过程中,大多数基因在原基时期表达量最高,其中ste20、cdc24、ste11和ste12表达量上调最为显著,在子实体成熟期这些基因表达量下降。因此,这说明在菌丝营养生长过程中,在第60天菌丝细胞增殖生长最为旺盛,而在第80天菌丝细胞基本停止生长,菌丝也逐渐达到成熟。同时,在菌丝生殖生长过程中,斑玉蕈持续地上调信息素通路基因表达使菌丝细胞不断地分裂增殖,从而使新生的菌丝扭结形成原基,其中ste3、ste20、cdc24、ste11和ste12基因可能对斑玉蕈菌丝细胞的分裂增殖和诱导子实体形成起到关键的作用。     

Interactions of the bovine placental lactogen and prolactin receptor genes are associated with fertility traits in cattle

Decline in fertility of high-producing dairy cattle has become a global challenge to the dairy industry. Because of low heritability and complexity, it is difficult to find genetic markers for fertility traits in cattle. Here, we report the use of an in vitro fertilization (IVF) system and candidate gene approach to test genetic associations of a single-nucleotide polymorphism (SNP) in bovine placental lactogen (bPL), and its interactions with SNPs in the prolactin receptor (PRLR) and growth hormone receptor genes with fertility traits in an IVF system. The associations suggest a possible involvement of genetic interactions between bPL and PRLR in the fertilization and embryonic development processes, and the potential for application in a marker-assisted selection program.     

Mapping candidate genes in Eucalyptus with emphasis on lignification genes

We used the single-strand conformation polymorphism (SSCP) technique to map eight genes on Eucalyptus urophylla and Eucalyptus grandis linkage maps. These included four genes involved in the common phenylpropanoid pathway (caffeic acid 3-0-methyltransferase, caffeoyl CoA 3-O-methyltransferase, 4-coumarate CoA ligase and phenylalanine ammonia-lyase), two genes involved in the `lignin specific' pathway (cinnamoyl CoA reductase and cinnamyl alcohol dehydrogenase), and two symbiosis regulated genes (EgHypar and EgTubA1). A novel source of variation which affects the SSCP pattern, i.e. the presence or absence of electrophoresis buffer upon loading the samples into the polyacrylamide gel, was found. The placement of these genes on the Eucalyptus maps was carried out using an interspecific hybrid mapping population. This will further facilitate the identification or exclusion of `positional' candidate genes for characterizing quantitative trait loci (QTL) for wood quality and vegetative propagation related traits.     

Differential expression of two barley SNF1-related protein kinase genes

We have amplified and cloned DNA sequences derived from a gene encoding a SNF1 (sucrose-non-fermenting 1)-related protein kinase which differs from that previously reported from barley. Northern blot and polymerase chain reaction (PCR) analysis of RNA populations, using specific probes and oligonucleotide primers, indicated that the two SNF1-related genes are differentially regulated. One is expressed in all tissues, whereas the other is expressed at high levels in the seed endosperm and aleurone, but at levels undetectable by northern blot analysis in other tissues. Comparisons with other plant SNF1-related protein kinase genes suggest that the form which is expressed at greatly enhanced levels in the seed is less similar to the other plant homologues which have been reported and may be unique to cereals.     

Differential expression of fungal genes at preinfection and mycorrhiza establishment between Terfezia boudieri isolates and Cistus incanus hairy root clones

Changes in gene expression by isolates of Terfezia boudieri during mycorrhization with Cistus incanus hairy roots were followed. Four fungus-hairy root clone combinations were cultivated under two sets of conditions, in which the root and the fungus were separated by a cellophane sheet or were allowed physical contact. One of the combinations produced endomycorrhizas, the other three solely ectomycorrhizas. Fragments isolated by cDNA-AFLP analysis from cellophane-separated cultures (preinfection) were used to identify differentially expressed genes by reverse Northern analysis. Genes showing no homology to known sequences constituted the largest group under both growth conditions. Some fungal genes were expressed transiently, while others exhibited altered expression patterns as conditions changed from individually growing through the preinfection stage to mycorrhizas. Genes expressed exclusively under combinations allowing either ectomycorrhiza or endomycorrhiza under a particular condition were detected. Our results point, for the first time, to some of the genes that might be involved in determining the type of association that will be formed: ecto- or endomycorrhiza.     

Codon usage of human hepatitis C virus clearance genes in relation to its expression

Hepatitis C virus (HCV) infection is among the leading causes of hepatocellular carcinoma and liver cirrhosis globally, with a high economic burden. The disease progression is well established, but less is known about the spontaneous HCV infection clearance. This study tries to establish the relationship between codon biasness and expression of HCV clearance candidate genes in normal and HCV infected liver tissues. A total of 112 coding sequences comprising 151 679 codons were subjected to the computation of codon indices, namely relative synonymous codon usage, an effective number of codon (Nc), frequency of optimal codon, codon adaptation index, codon bias index, and base compositions. Codon indices report of GC3s, GC12, hydropathicity, and aromaticity implicates both mutational and translational selection in the candidate gene set. This was further correlated with the differentially expressed genes among the selected genes using BioGPS. A significant correlation is observed between the gene expression of normal liver and cancerous liver tissues with codon bias (Nc). Gene expression is also correlated with relative codon bias values, indicating that CCL5, APOA2, CD28, IFITM1, and TNFSF4 genes have higher expression. These results are quite encouraging in selecting the high responsive genes in HCV clearance. However, there could be additional genes which could also orchestrate the clearance role with the above mentioned first line of defensive genes.     

应用DNA芯片技术对禽致病性大肠杆菌可能致病基因体外表达水平的研究

应用DNA芯片研究禽致病性大肠杆菌可能致病基因的表达.构建禽致病性大肠杆菌毒力基因、潜在毒力基因的DNA芯片,应用基因芯片技术对同属O2血清型的禽高致病性大肠杆菌E058株和低致病性大肠杆菌E526株在体外LB培养基和鸡血清培养状态下进行差异表达分析.结果:在体外LB静置培养状态下,低致病株E526与高致病株E058相比共有16个差异基因,均为下调基因.在鸡血清静置培养中,E526与E058相比共有15个差异基因,均为下调基因.应用基因芯片成功筛选了禽致病性大肠杆菌在体外不同条件下的毒力基因及可能毒力基因中差异表达基因,表明一些铁摄取系统相关基因对APEC的毒力较重要,同时也筛选出了一些新的可能致病基因aes-1,aes-2,aes-3,aes-4,aes-6,aes-8,aes-10,aes-13,aes-15,aes-31等.