Nischarin Is Differentially Expressed in Rat Brain and Regulates Neuronal Migration

Nischarin is a protein known to inhibit breast cancer cell motility by regulating the signaling of the Rho GTPase family. However, little is known about its location and function in the nervous system. The aim of the present study was to investigate the regional and cellular expression and functions of Nischarin in the adult rodent brain. As assessed by real-time PCR, Western blot analysis and immunostaining, we found that Nischarin was widely distributed throughout the brain, with a higher expression in the cerebral cortex and hippocampus. Double-labeling showed that Nischarin was expressed in neurons and was mainly located in the perinuclear region and F-actin-rich protrusions. The expression pattern of Nischarin in the brain was thought to be closely associated with its function. This was verified by our findings from cell migration assays that Nischarin regulated neuronal migration. These results provide a preliminary survey of the distribution of Nischarin in different regions and cell types in the rat brain. This might help to elucidate its physiological roles, and to evaluate its potential clinical implications.     

Differentially Expressed Genes in EEC and LMS Syndromes

Objectives

Ectrodactyly ectodermal dysplasia cleft lip/palate (EEC) syndrome and limb-mammary syndrome (LMS) share a similar phenotype and the same pathogenic gene, which complicates the ability to distinguish between these diagnoses. The current study aims to identify a potential and practical clinical biomarker to distinguish EEC from LMS.

Methods

Two EEC pedigrees and one LMS pedigree that have been previously reported were reanalyzed. After confirmation of the causative mutations for these new patients, whole-genome expression microarray analysis was performed to assess the molecular genetic changes in these families.

Results

Five new patients with classic symptoms were reported, and these individuals exhibited the same mutation as their relatives (c.812 G>C; c.611G>A; and c.680G>A). According to the whole genome expression results, the EEC patients exhibited different gene expression characteristics compared with the LMS patients. More than 5,000 genes were differentially expressed (changes >2 or <0.5-fold) among the EEC patients, LMS patients and healthy individuals. The top three altered pathways have been implicated in apoptosis, the hematopoietic cell lineage and the Toll-like receptor signaling pathway.

Conclusion

Our results provide additional clinical and molecular information regarding EEC and LMS and suggest that peripheral blood cytokines may represent a promising clinical biomarker for the diagnosis of these syndromes.     

基因差异表达分析技术进展

比较了目前几种主要的基因差异表达分析技术并简要地归纳了各种基因差异表达分析方法的特点,重点介绍了经典的基因差异表达分析技术———差异显示技术及其改进与完善,最后根据差异显示技术在高等植物方面已取得的成就乐观地展现了该技术在园艺植物研究上的应用前景.     

Localization of Cell Division Protein FtsQ by Immunofluorescence Microscopy in Dividing and Nondividing Cells of Escherichia coli

The localization of cell division protein FtsQ in Escherichia coli wild-type cells was studied by immunofluorescence microscopy with specific monoclonal antibodies. FtsQ could be localized to the division site in constricting cells. FtsQ could also localize to the division site in ftsQ1(Ts) cells grown at the permissive temperature. A hybrid protein in which the cytoplasmic domain and the transmembrane domain were derived from the γ form of penicillin-binding protein 1B and the periplasmic domain was derived from FtsQ was also able to localize to the division site. This result indicates that the periplasmic domain of FtsQ determines the localization of FtsQ, as has also been concluded by others for the periplasmic domain of FtsN. Noncentral FtsQ foci were found in the area of the cell where the nucleoid resides and were therefore assumed to represent sites where the FtsQ protein is synthesized and simultaneously inserted into the cytoplasmic membrane.     

水稻杂种与亲本间差异表达cDNA片段S 600的分离克隆

采用cDNA-AFLP技术分离克隆了水稻杂种与亲本间差异表达基因片段．S600,Northern杂交结果表明：在分蘖期和始穗期,S600在杂种和父本中表达丰度均较高,而在母本中表达丰度相对较低。S600在分蘖期和始穗期表达量不同,暗示了该基因的表达还受到发育时期的调节。同源搜索结果表明S600片段是水稻SBPase的部分编码序列。为了获得完整编码序列,以S600序列检索梗稻日本晴cDNA数据库,获得了两个高度同源(99％)且功能未知的全长cDNA克隆(AK062089和AK065773)。序列分析表明它们均包含一个相同的1179bp的开放阅读框,编码392个氨基酸组成的水稻SBPase前体,其中包含有与底物结合、氧化还原调节有关的保守氨基酸残基。检索发现该基因在水稻日本晴基因组中只有单个座位。     

Identifying Differentially Expressed Genes in Time Course Microarray Data

Identifying differentially expressed (DE) genes across conditions or treatments is a typical problem in microarray experiments. In time course microarray experiments (under two or more conditions/treatments), it is sometimes of interest to identify two classes of DE genes: those with no time-condition interactions (called parallel DE genes, or PDE), and those with time-condition interactions (nonparallel DE genes, NPDE). Although many methods have been proposed for identifying DE genes in time course experiments, methods for discerning NPDE genes from the general DE genes are still lacking. We propose a functional ANOVA mixed-effect model to model time course gene expression observations. The fixed effect of (the mean curve) of the model decomposes bivariate functions of time and treatments (or experimental conditions) as in the classic ANOVA method and provides the associated notions of main effects and interactions. Random effects capture time-dependent correlation structures. In this model, identifying NPDE genes is equivalent to testing the significance of the time-condition interaction, for which an approximate F-test is suggested. We examined the performance of the proposed method on simulated datasets in comparison with some existing methods, and applied the method to a study of human reaction to the endotoxin stimulation, as well as to a cell cycle expression data set.     

Differentially Expressed miRNAs Influence Metabolic Processes in Pituitary Oncocytoma

Neurochemical Research - Spindle cell oncocytomas (SCO) of the pituitary are rare tumors accounting for 0.1–0.4% of all sellar tumors. Due to their rarity, little information is available...     

High-Affinity Glucose Transport in Aspergillus nidulans Is Mediated by the Products of Two Related but Differentially Expressed Genes

Independent systems of high and low affinity effect glucose uptake in the filamentous fungus Aspergillus nidulans. Low-affinity uptake is known to be mediated by the product of the mstE gene. In the current work two genes, mstA and mstC, have been identified that encode high-affinity glucose transporter proteins. These proteins'' primary structures share over 90% similarity, indicating that the corresponding genes share a common origin. Whilst the function of the paralogous proteins is little changed, they differ notably in their patterns of expression. The mstC gene is expressed during the early phases of germination and is subject to CreA-mediated carbon catabolite repression whereas mstA is expressed as a culture tends toward carbon starvation. In addition, various pieces of genetic evidence strongly support allelism of mstC and the previously described locus sorA. Overall, our data define MstC/SorA as a high-affinity glucose transporter expressed in germinating conidia, and MstA as a high-affinity glucose transporter that operates in vegetative hyphae under conditions of carbon limitation.     

差异表达基因克隆技术的进展

分离并克隆差异表达基因,不仅有助于揭示生命的奥秘,而且还能为基因诊断与治疗提供重要的理论依据。基因差异表达的变化有两种,即新出现的基因表达与表达量差异的基因表达。以前,过多强调克隆新出现的表达基因,忽略表达量差异的基因。目前研究认为,表达量差异的基因...     

克隆差异表达基因的新策略

基因表达的变化有两种,即新出现的基因表达与表达量差异的基因表达.表达量差异的基因克隆技术主要有mRNA差异展示,此技术是目前筛选差异表达基因最有效的方法之一,但主要存在假阳性率高的不足,针对此缺点,近几年提出了新的策略与方法,如差异消减展示、基于PCR和减法杂交基础上的差异表达基因克隆技术,这些技术具有显著优势.     

Differentially Expressed MicroRNAs in Postpartum Breast Cancer in Hispanic Women

The risk of breast cancer transiently increases immediately following pregnancy; peaking between 3-7 years. The biology that underlies this risk window and the effect on the natural history of the disease is unknown. MicroRNAs (miRNAs) are small non-coding RNAs that have been shown to be dysregulated in breast cancer. We conducted miRNA profiling of 56 tumors from a case series of multiparous Hispanic women and assessed the pattern of expression by time since last full-term pregnancy. A data-driven splitting analysis on the pattern of 355 miRNAs separated the case series into two groups: a) an early group representing women diagnosed with breast cancer ≤ 5.2 years postpartum (n = 12), and b) a late group representing women diagnosed with breast cancer ≥ 5.3 years postpartum (n = 44). We identified 15 miRNAs with significant differential expression between the early and late postpartum groups; 60% of these miRNAs are encoded on the X chromosome. Ten miRNAs had a two-fold or higher difference in expression with miR-138, miR-660, miR-31, miR-135b, miR-17, miR-454, and miR-934 overexpressed in the early versus the late group; while miR-892a, miR-199a-5p, and miR-542-5p were underexpressed in the early versus the late postpartum group. The DNA methylation of three out of five tested miRNAs (miR-31, miR-135b, and miR-138) was lower in the early versus late postpartum group, and negatively correlated with miRNA expression. Here we show that miRNAs are differentially expressed and differentially methylated between tumors of the early versus late postpartum, suggesting that potential differences in epigenetic dysfunction may be operative in postpartum breast cancers.     

喉癌差异表达cDNA序列的分离与初步鉴定

分离和克隆人喉癌中新的相关基因将有助于提示喉癌的易感性与癌变机制。运用ｍＲＮＡ差异显示法对２例成人喉癌组织及配对癌旁正常组织的基因表达进行研究,分离到３５个差异显示片段;用反向Ｎｏｒｔｈｅｒｎ点杂交筛选到６个差异片段,经克隆、测序和匹配分析,得１２条不同ｃＤＮＡ序列,其中４条为新基因序列,另外８条与已知基因高度同源。将１２条ｃＤＮＡ序列固定在膜上,用来自喉癌和配对正常组织的总ｃＤＮＡ探针与其杂交和     

肝细胞癌相关差异基因的生物信息学及预后分析

肝细胞癌是全球癌症相关死亡的主要原因,目前对肝细胞癌的发病机制研究尚不完善,探索肝细胞癌发生、发展相关的分子标志物及其预后具有重要意义。从GEO数据库获得肝细胞癌组织和非癌组织的基因表达阵列数据GSE84402,利用GEO2R筛选差异表达基因;采用DAVID数据库对差异基因进行GO富集分析和KEGG通路分析;通过STRING数据库和Cytoscape软件构建差异表达基因对应的蛋白质相互作用网络,并从网络中筛选出核心基因(hub genes);结合KM plotter数据库的临床信息对hub genes进行预后分析。结果显示:共得到1 307个差异表达基因,其中上调基因741个,下调基因566个,这些差异表达基因主要涉及细胞分裂、细胞周期、DNA复制及物质代谢等生物学过程及生物通路。通过GO、KEGG及蛋白质相互作用网络筛选出BUB1、BUB1B、CCNA2、CCNB1、CCNB2、CDC20、CDK1、MAD2L1、PLK1等9个hub genes,进一步分析发现hub genes均与细胞周期的调控相关,表明细胞周期的调控失常在肝细胞癌的发生、发展过程中具有重要作用。生存分析显示9个hub genes在肝细胞癌患者中均为表达上调的基因,且与患者预后不良相关,这为寻找肝细胞癌患者预后相关生物标志物的研究提供了线索。     

Function and Chromosome Location of Differentially Expressed Genes in Gastric Cancer

Using Affymetrix U133A oligonucleotide microarrays, screening was done for genes that were differentially expressed in gastric cancer (T) and normal gastric mucosa (C), and their chromosome location was characterized by bioinformatics. A total of 270 genes were found to have a difference in expression levels of more than eight times. Of them 157 were up-regulated (Signal Log Ratio [SLR]≥3), and 113 were down-regulated (SLR≤-3). Except for, four genes with unknown localization, a vast majority of the genes were sporadically distributed over every chromosome. However, chromosome 1 contained the most differentially expressed genes (26 genes, or 9.8%), followed by chromosomes 11 and 19 (both 24 genes, or 9.1%). These genes were also more likely to be on the short-arm of the chromosome (q), which had 173 (65%). When these genes were classified according to their functions, it was found that most (67 genes, 24.8%) belonged to the enzymes and their regulators groups. The next group was the signal transduction genes group (43 genes, 15.9%). The rest of the top three groups were nucleic acid binding genes (17, 6.3%), transporter genes (15, 5.5%), and protein binding genes (12, 4.4%). These made up 56.9% of all the differentially expressed genes. There were also 50 genes of unknown function (18.5%). Therefore it was concluded that differentially expressed genes in gastric cancer seemed to be sporadically distributed across the genome, but most were found on chromosomes 1, 11 and 19. The five groups associated genes abnormality were important genes for further study on gastric cancer.     

胃癌差异表达基因在染色体上的定位及其功能分析

利用标准化的Affymetrix公司生产的U133A基因芯片检测胃癌（T）与切缘正常胃黏膜（C）基因表达谱差异,并利用生物信息学方法对检测结果进行差异基因在染色体定位和功能分析。结果表明：胃癌与正常胃黏膜比较差异8倍以上共有270个基因,其中表达上调[信号比的对数值（SLR）≥3]有157个,表达下调（SLR≤-3）有113个。从表达差异的基因在染色体定位分析,发现除4个基因未知其定位外,其余所有差异表达基因散在分布和各条染色体上,但以1号染色体为最多,有26个（占9．8％）,其次是11和19号染色体上分别有24个（各占9．1％）。而差异表达的基因发生在染色体短臂（q）上有173个（占65％）。从表达差异的基因功能分类看,属于酶和酶调控子基因最多（67个,24．8占％）,其次是信号传导基因（43个,占15．9％）,第3类是核酸结合基因（17个,占6．3％）,第4类是转运子基因（15个,占5．5％）,第5类是蛋白结合基因（12个,占4．4％）,还有功能未知的基因有50个,占18．5％。以上5大类共占基因总数56．9％。胃癌差异表达基因散在分布在各条染色体上,但以1、11、19号染色体差异表达基因居多。这5大类（酶和酶调控子、信号传导、核酸结合、转运子、蛋白结合）相关基因异常是今后研究胃癌的重要基因。     

4个棉花ADF基因的分子鉴定及其差异表达

肌动蛋白解聚合因子(actin-depolymerizing factor, ADF)是一种在真核生物中广泛存在的低分子量的肌动蛋白结合蛋白,它在调控细胞内肌动蛋白纤丝的解聚合和再聚合中起着关键作用。我们在棉纤维cDNA文库中分离克隆了4个ADF基因(cDNAs),分别命名为GhADF2,GhADF3,GhADF4,GhADF5。GhADF2 cDNA 长度为705 bp,编码139个氨基酸;GhADF3 cDNA长度为819 bp,编码139个氨基酸;GhADF4 cDNA长度为804 bp,编码143个氨基酸;GhADF5 cDNA长度为644 bp,编码141个氨基酸。分析表明,GhADF2与GhADF3的氨基酸序列同源性为99%。而且,GhADF2/3与矮牵牛PeADF2之间的氨基酸序列同源性也高达89%。GhADF4与拟南芥AtADF6的亲缘关系较近,二者的氨基酸序列同源性为78%。GhADF5与拟南芥AtADF5的亲缘关系较近,氨基酸序列的同源性为83%。上述结果表明植物ADF基因在进化中具有高度保守性。RT-PCR分析表明,GhADF2在纤维中优势表达,而GhADF5基因则在子叶中表达量最高。另一方面,GhADF3和GhADF4似乎不具有组织特异性或偏爱性表达。同一组织中不同GhADF基因表达量有较大的差异,表明它们可能涉及棉花不同组织生长发育过程的调节。而且,在进化过程中,各ADF同分异构体之间可能发展形成某种功能上的差异性。