调控通路内基因表达的相关性分析

本研究从基因表达调控通路的角度分析了基因功能与基因表达之间的关系,利用7套酿酒酵母基因芯片表达谱数据和通路数据库（KEGG和CYGD）所提供的信息,应用我们研制的Genehub软件分析研究了同一基因表达调控通路内的基因在mRNA表达水平上的相关性,共涉及16条通路,495个基因。通过Pearson相关系数和Spearman相关系数两种相似性测度的分析,我们发现有94%（15条）的基因表达调控通路内的基因在大于等于4套的表达谱数据中是共表达的,以上结果从基因表达调控通路的角度,证实了基因功能与基因表达之间存在着一定的相关性。     

MiRNA expression in the eye

MiRNAs are a newly discovered class of small noncoding RNAs that regulate gene expression by translational repression and mRNA degradation. It has become evident that miRNAs are involved in many important biological processes, including tissue differentiation and development. The role of miRNAs in the eye is beginning to be explored following their recent detection by miRNA expression analyses. Many of the target genes for these ocular miRNAs remain undefined. This review summarizes the current information about ocular miRNA expression. Future research should focus on the function of ocular miRNAs in eye development.     

Endothelin expression in the uterus

The endothelins (ETs) comprise a family of 21 amino acid peptides, ET-1, ET-2 and ET-3, first demonstrated as products of vascular endothelium. Subsequent work showed that they are also found in non-endothelial cells from a variety of tissues such as breast, parathyroid and adrenal gland. At first, the ETs were recognized for their pressor effects. However, ET administration in vivo initially caused hypotension at low concentrations by triggering the paracrine release of endothelial-derived vasodilators. The ETs exert powerful contractile actions on myometrium and other types of smooth muscle and are mitogenic, or co-mitogenic for fibroblasts, vascular smooth muscle and other cells. Demonstration of extravascular ET in endometrium has revealed a powerful vasoconstrictor which might act on the spiral arterioles to effect a powerful and sustained contraction of vascular smooth muscle. ETs might also contribute to the process of endometrial repair. In addition, the ETs appear to play a fundamental role in the control of uterine function in pregnancy. Effects on myometrial contractility have been implicated in the mechanisms governing the onset of normal and pre-term labour, and the peptides are likely to be key determinants of placental blood flow by binding to vascular smooth muscle receptors in the placenta.     

利用游离型表达质粒强化毕赤酵母表达木聚糖酶

巴斯德毕赤酵母是用途广泛的蛋白表达系统。目前用于毕赤酵母的质粒主要以整合型质粒为主,很少见到游离的质粒用于外源基因的表达。文中通过将来源于酵母自身的自主复制序列连接到酵母整合型表达载体pGAP中构成自主复制的游离型表达载体pGAPZαA-PARS,将该载体用于表达木聚糖酶基因。转化毕赤酵母后同传统的整合型表达菌株相比,以甘油为碳源时最高酶活达到343 U/mL,比整合型表达提高了45.9%。同时游离载体表达重组酶比活相对整合表达提高了81.2%。为了节约发酵成本,进一步研究了分别以甘油、葡萄糖、蔗糖、混合碳源(蔗糖︰甘油=1︰2)等不同碳源下游离型重组菌株的表达水平。发现甘油表达水平最高,蔗糖最低,但是以工业葡萄糖为碳源时产酶成本最低。由于pGAP载体不需要以甲醇为碳源,因而文中所构建的游离载体pGAPZαA-PARS极大促进了毕赤酵母在食品行业中的应用。同时,游离型载体可大幅度提高表达水平,为进一步研究提高GAP启动子的高效表达奠定了基础。     

Surface-based mapping of gene expression and probabilistic expression maps in the mouse cortex

The Allen Brain Atlas (ABA, www.brain-map.org) is a genome wide, spatially registered collection of cellular resolution in situ hybridization gene expression image data of the C57Bl/6J mouse brain. Derived from the ABA, the Anatomic Gene Expression Atlas (AGEA, http://mouse.brain-map.org/agea) has demonstrated both laminar and areal spatial gene expression correlations in the mouse cortex. While the mouse cortex is lissencephalic, its curvature and substantial bending in boundary areas renders it difficult to visualize and analyze laminar versus areal effects in a rectilinear coordinate framework. In context of human and non-human primate cortex, surface-based representation has proven useful for understanding relative locations of laminar, columnar, and areal features. In this paper, we describe a methodology for constructing surface-based flatmaps of the mouse cortex that enables mapping of gene expression data from individual genes in the ABA, or probabilistic expression maps from the AGEA, to identify and visualize genetic relationships between layers and areas.     

C-myc expression in the microvessels of medulloblastoma

The increased expression of c-myc is related to neoplastic transformation and angiogenesis. Therefore, the assessment of expression of c-myc in endothelial cells and neovascularization could help to determine the biological behavior of the tumor. We analyzed neovascularization and c-myc expression in 36 medulloblastoma specimens. The results were shown by determining immunohistochemical staining index (ISI), the sum of staining intensity (SI) and the percentage of positive cells (PPC) in the blood vessels endothelium of the tumor. We also performed the microvessel count (MVC) in 10 high-power fields (400X) with the most prominent vascularization and expressed it as microvessel density per mm2 (MVD). C-myc immunostaining intensity index in blood vessel endothelium is grouped into four groups, 0--no reaction, I-weak reaction (ISI = 1 or 2), II--moderate reaction (ISI = 3 or 4), III--strong reaction (ISI = 5 or 6). Statistically significant differences (p = 0.0214) have been found between groups 0 and 1 compared to groups 2 and 3. A higher percentage of positive cells has been found in male patients than in female ones (p = 0.0483). C-myc PPC 0 or 1 has on the average smaller density of blood vessels per mm2 than c-myc PPC 2 or 3, but the difference is not statistically significant. C-myc ISI 0 or 1 has, on the average, smaller density of blood vessels per mm2 than c-myc ISI 2 or 3, but the difference is not statistically significant. We concluded that c-myc staining intensity was associated with higher microvessels density.     

Chemokine expression in CF epithelia: implications for the role of CFTR in RANTES expression

To delineate themechanisms that facilitate leukocyte migration into the cystic fibrosis(CF) lung, expression of chemokines, including interleukin-8 (IL-8),monocyte chemoattractant protein-1 (MCP-1), andRANTES, was compared between CF and non-CF airway epithelia. Thefindings presented herein demonstrate that, under either basalconditions or tumor necrosis factor- (TNF-)- and/or interferon- (IFN-)-stimulated conditions, a consistent pattern ofdifferences in the secretion of IL-8 and MCP-1 between CF and non-CFepithelial cells was not observed. In contrast, CF epithelial cellsexpressed no detectable RANTES protein or mRNA under basal conditionsor when stimulated with TNF- and/or IFN-(P  0.05), unlike their non-CFcounterparts. Correction of the CF transmembrane conductance regulator(CFTR) defect in CF airway epithelial cells restored the induction ofRANTES protein and mRNA by TNF- in combination with IFN-(P  0.05) but had little effect onIL-8 or MCP-1 production compared with mock controls. Transfection studies utilizing RANTES promoter constructs suggested that CFTR activates the RANTES promoter via a nuclear factor-B-mediated pathway. Together, these results suggest that1) RANTES expression is altered inCF epithelia and 2) epithelialexpression of RANTES, but not IL-8 or MCP-1, is dependent on CFTR.     

Restricted expression pattern of vegf-d in the adult and fetal mouse: high expression in the embryonic lung

Endothelial growth factors have become the target of intense research since the initial discovery of vascular endothelial growth factor (VEGF/VPF). At present, VEGF is established as a major inducer of angiogenesis in normal and pathological conditions. Recently several new members in the VEGF family have been described; VEGF-B/VRF, VEGF-C and VEGF-D. VEGF-D is most closely related to VEGF-C by virtue of the presence of N- and C-terminal extensions that are not found in other VEGF family members. We have here examined the expression pattern of vegf-d mRNA with in situ hybridization in developing and adult mice. This shows a restricted expression pattern, with high levels mainly in lung tissue. The expression in embryonic lung is upregulated prior to birth. Expression of vegf-d in other tissues, as well as in lung tissue of the E14 embryo, was either low or absent. This suggests that VEGF-D may be of special relevance for the vascularization of lung tissue during the last trimester of fetal development.     

Construction of Rhodococcus expression vectors and expression of the aminoalcohol dehydrogenase gene in Rhodococcus erythropolis

NADP⁺-dependent aminoalcohol dehydrogenase (AADH) of Rhodococcus erythropolis MAK154 produces double chiral aminoalcohols, which are used as pharmaceuticals. However, the genetic manipulation of Rhodococcus strains to increase their production of such industrially important enzymes is not well studied. Therefore, I aimed to construct Rhodococcus expression vectors, derived from the Rhodococcus–Escherichia coli shuttle vector pRET1102, to express aadh. The plasmid pRET1102 could be transformed into many actinomycete strains, including R. erythropolis. The transformation ef?ciency for a species closely related to R. erythropolis was higher than that for other actinomycete strains. Promoters of various strengths, hsp, 1200rep, and TRR, were obtained from Gram-positive bacteria. The activity of TRR was stronger than that of hsp and 1200rep. The aadh-expressing plasmid pRET1172 with TRR could be transformed into many actinomycete strains to increase their AADH production. The Rhodococcus expression vector, pRET11100, constructed by removing aadh from the pRET1172 plasmid may be useful for bioconversion.     

Vasopressin receptor expression in the placenta

The arginine vasopressin (AVP) type 1a receptor (V1a) is well known to mediate vasoconstriction. In pregnancy, blood flow in the placenta is crucial for sustaining normal growth and development of the fetus. This is the first AVP receptor study in the placenta and fetal membranes. The aim was to compare, quantitatively, the level of V1a gene expression with that of a known marker for vascularization, aquaporin 1 (AQP1). V1a and AQP1 gene expression did not correlate; placental V1a mRNA levels were significantly upregulated at 45 and 66+/-1 compared with 27, 100+/-4, and 140 days (term approximately 150 days). V1a mRNA levels were much lower in fetal membranes in which no significant difference across gestation was observed. In situ hybridization histochemistry localized V1a gene expression in the maternal component of the placenta similar to the receptor-binding studies using 125I-labeled [d(CH2)5, sarcosine7] vasopressin. No AVP gene expression was observed in the placenta and fetal membranes, which eliminates local AVP production. This increase in V1a expression at 45 and 66+/-1 days of gestation correlates with the period of maximal placental growth in the sheep and suggests that AVP and V1a receptors may play a hitherto unrecognized role in placental growth, differentiation, and/or function, particularly in the deleterious effects of heat stress, early in pregnancy, on fetal growth.     

Autosomal monoallelic expression in the mouse

Background

Random monoallelic expression defines an unusual class of genes displaying random choice for expression between the maternal and paternal alleles. Once established, the allele-specific expression pattern is stably maintained and mitotically inherited. Examples of random monoallelic genes include those found on the X-chromosome and a subset of autosomal genes, which have been most extensively studied in humans. Here, we report a genome-wide analysis of random monoallelic expression in the mouse. We used high density mouse genome polymorphism mapping arrays to assess allele-specific expression in clonal cell lines derived from heterozygous mouse strains.

Results

Over 1,300 autosomal genes were assessed for allele-specific expression, and greater than 10% of them showed random monoallelic expression. When comparing mouse and human, the number of autosomal orthologs demonstrating random monoallelic expression in both organisms was greater than would be expected by chance. Random monoallelic expression on the mouse autosomes is broadly similar to that in human cells: it is widespread throughout the genome, lacks chromosome-wide coordination, and varies between cell types. However, for some mouse genes, there appears to be skewing, in some ways resembling skewed X-inactivation, wherein one allele is more frequently active.

Conclusions

These data suggest that autosomal random monoallelic expression was present at least as far back as the last common ancestor of rodents and primates. Random monoallelic expression can lead to phenotypic variation beyond the phenotypic variation dictated by genotypic variation. Thus, it is important to take into account random monoallelic expression when examining genotype-phenotype correlation.     

Chromogranin-A expression in the bovine testis

Chromogranin-A (CgA) is the most distributed member of the granin family. Chromogranins are soluble anionic glycoproteins, found in the majority of the neuroendocrine and neural cells, co-stored with other endocrine substances (like insulin, glucagon, FSH and LH or NPY) in secretory granules. Outside the cell, it has been suggested that this peptide or one of its fragments, obtained by proteolytic cleavage, could act in an autocrine or paracrine way, regulating either the cell function or the contractibility of vascular segments. The purpose of the present study is to determine the distribution of chromogranin-A in the structures of the bovine testis. Immunohistochemical analysis was performed employing the biotin-streptavidin-peroxidase immunostaining technique in tissue specimens obtained at a local abbatoir. A CgA expression was found in the germinal epithelium at several stages of differentiation. Generally the strongest positive reaction was consistently observed in the basal compartment of the seminiferous tubules, with spermatogonia presenting a dense granular immunostaining pattern; a less intense reaction was also consistently recorded in type II spermatocytes and in round spermatids, which showed a more scattered disposition of CgA-positive granules. Clusters of Leydig cells also displayed a faint and homogeneous cytoplasmatic immunoreactivity for chromogranin-A. These results demonstrate a widely distribution of CgA-positive cells in the organism, and its presence in the testis raises the possibility of its participation in the cohort of local factors involved in the regulation of spermatogenesis.     

MicroRNA-restricted transgene expression in the retina

Background

Gene transfer using adeno-associated viral (AAV) vectors has been successfully applied in the retina for the treatment of inherited retinal dystrophies. Recently, microRNAs have been exploited to fine-tune transgene expression improving therapeutic outcomes. Here we evaluated the ability of retinal-expressed microRNAs to restrict AAV-mediated transgene expression to specific retinal cell types that represent the main targets of common inherited blinding conditions.

Methodology/Principal Findings

To this end, we generated AAV2/5 vectors expressing EGFP and containing four tandem copies of miR-124 or miR-204 complementary sequences in the 3′UTR of the transgene expression cassette. These vectors were administered subretinally to adult C57BL/6 mice and Large White pigs. Our results demonstrate that miR-124 and miR-204 target sequences can efficiently restrict AAV2/5-mediated transgene expression to retinal pigment epithelium and photoreceptors, respectively, in mice and pigs. Interestingly, transgene restriction was observed at low vector doses relevant to therapy.

Conclusions

We conclude that microRNA-mediated regulation of transgene expression can be applied in the retina to either restrict to a specific cell type the robust expression obtained using ubiquitous promoters or to provide an additional layer of gene expression regulation when using cell-specific promoters.     

Region-specific gene expression in the epididymis

The epididymis is responsible for post-testicular sperm maturation, which consists in the acquisition of forward motility and fertilizing ability. This organ is composed of three main anatomical regions - the caput, corpus and cauda epididymidis - which possess distinct gene expression profiles, ensuring different epididymal functions essential to the different steps of sperm maturation. Since many genes display spatially restricted expression in the epididymis, this organ constitutes a model of choice to study the mechanisms that govern region-specific gene expression. Factors such as steroid hormones, lumicrine factors and temperature affect the pattern of gene expression in the epididymis. Recently, the contribution of small RNAs in epididymal gene regulation has been investigated and constitutes a promising avenue for clinical application with regard to male fertility.