Construction and application of a bovine immune-endocrine cDNA microarray

A variety of commercial DNA arrays specific for humans and rodents are widely available; however, microarrays containing well-characterized genes to study pathway-specific gene expression are not as accessible for domestic animals, such as cattle, sheep and pigs. Therefore, a small-scale application-targeted bovine immune-endocrine cDNA array was developed to evaluate genetic pathways involved in the immune-endocrine axis of cattle during periods of altered homeostasis provoked by physiological or environmental stressors, such as infection, vaccination or disease. For this purpose, 167 cDNA sequences corresponding to immune, endocrine and inflammatory response genes were collected and categorized. Positive controls included 5 housekeeping genes (glyceraldehydes-3-phosphate dehydrogenase, hypoxanthine phosphoribosyltransferase, ribosomal protein L19, beta-actin, beta2-microglobulin) and bovine genomic DNA. Negative controls were a bacterial gene (Rhodococcus equi 17-kDa virulence-associated protein) and a partial sequence of the plasmid pACYC177. In addition, RNA extracted from un-stimulated, as well as superantigen (Staphylococcus aureus enterotoxin-A, S. aureus Cowan Pansorbin Cells) and mitogen-stimulated (LPS, ConA) bovine blood leukocytes was mixed, reverse transcribed and PCR amplified using gene-specific primers. The endocrine-associated genes were amplified from cDNA derived from un-stimulated bovine hypothalamus, pituitary, adrenal and thyroid gland tissues. The array was constructed in 4 repeating grids of 180 duplicated spots by coupling the PCR amplified 213-630 bp gene fragments onto poly-l-lysine coated glass slides. The bovine immune-endocrine arrays were standardized and preliminary gene expression profiles generated using Cy3 and Cy5 labelled cDNA from un-stimulated and ConA (5 microg/ml) stimulated PBMC of 4 healthy Holstein cows (2-4 replicate arrays/cow) in a time course study. Mononuclear cell-derived cytokine and chemokine (IL-2, IL-1alpha, TNFalpha, IFN-gamma, TGFbeta-1, MCP-1, MCP-2 and MIP-3alpha) mRNA exhibited a repeatable and consistently low expression in un-stimulated cells and at least a two-fold increased expression following 6 and 24 h ConA stimulation as compared to 0 h un-stimulated controls. In contrast, expression of antigen presenting molecules, MHC-DR, MHC-DQ and MHC-DY, were consistently at least two-fold lower following 6 and 24 h ConA stimulation. The only endocrine gene with differential expression following ConA stimulation was prolactin. Additionally, due to the high level of genetic homology between ovine, swine and bovine genes, RNA similarly acquired from sheep and pigs was evaluated and similar gene expression patterns were noted. These data demonstrate that this application-targeted array containing a set of well characterized genes can be used to determine the relative gene expression corresponding to immune-endocrine responses of cattle and related species, sheep and pigs.     

cDNA microarray gene expression analysis and toxicological phenotype for anticancer drug

Toxicogenomics, the subdiscipline that merges genomics with toxicology, hold the promise to contributing toward the goal of elucidating mechanism by studying genomic profiling related with various drugs. The application of gene expression profiling technology to examine multiple genes and signaling pathways promises a significant advance in understanding the toxic mechanisms of various drugs and prediction of new drug candidate. Toxicogenomics is emerging field combining genomics and bioinformatics to identify and characterize mechanisms of toxicity of drug and various compounds. The principal hypothesis underlying on this field is that chemical-specific pattern of altered gene expression is related with each chemicals properties, especially toxicological property, and it will be revealed using high-density microarray analysis of sample from exposed organisms. So, in this study we compare the gene expression pattern of two anticancer drugs paclitaxel and orally absorbable paclitaxel, using the cDNA microarray. And from the result of this study, it is possible to provide the new possibility for genome-wide insight into mechanism of their anticancer activity and toxicological phenotype.     

Cloning and expression of the cDNA for bovine granulocyte-macrophage colony-stimulating factor

A sequence encoding bovine granulocyte-macrophage colony-stimulating factor (GM-CSF) has been identified from a concanavalin A-stimulated bovine lymphocyte cDNA library. This sequence was isolated by hybridization with synthetic oligonucleotide probes based upon the human GM-CSF sequence. This bovine cDNA was engineered for expression and secretion of activity into the periplasmic space of E. coli. Periplasmic extracts contain a 14,500-dalton protein and stimulate colony formation of bovine bone marrow progenitor cells. The predicted protein is 70% homologous with human GM-CSF and 55% homologous with murine GM-CSF. Numerous structural features are conserved among these three proteins, such as location of cysteine residues, glycosylation sites, and overall change. The biological activity of bovine GM-CSF is species specific, since recombinant preparations do not cause proliferation of human or murine bone marrow cells. Similarly, murine GM-CSF does not exhibit activity on cells of bovine or human origin. However, human GM-CSF does stimulate colony formation of bovine bone marrow cells, although the specific activity appears reduced when compared to assays on human cells.     

牛抵抗素基因的cDNA克隆

<正>抵抗素是新近发现的一种由脂肪细胞分泌的富含半胱氨酸的多肽。人抵抗素基因定位于19p13.3,负责编码108个氨基酸残基组成的抵抗素蛋白。Tokushi确定了478bp的牛抵抗素序列,具有完整的开放阅读框架,负责编码109个氨基酸残基组成的牛抵抗素蛋白。这一序列同人的抵抗素cDNA序列具有83%的同源性。     

Cloning of bovine CD34 cDNA

CD34 is a leukocyte antigen that is expressed in various cell types including hematopoietic cells. Monoclonal antibodies against human, murine, and canine CD34 proteins have been used for the identification of lymphohematopoietic stem/progenitor cells. The cDNA encoding bovine CD34 was cloned, and its nucleotide sequence was determined. The identity of the deduced amino acid sequence of the encoded protein to those of human, murine. and canine CD34 proteins was 61.1%, 56.0%, and 66.1%, respectively. Northern blot hybridization with the cDNA as a probe detected CD34 RNA expression in the cerebrum, spleen, heart, and lung of a fetal calf.     

Generation and performance of an equine-specific large-scale gene expression microarray

OBJECTIVE: To create high-quality sequence data for the generation of an equine gene expression microarray and evaluate array performance by use of lipopolysaccharide (LPS) exposure of synoviocytes. SAMPLE POPULATION: Public nucleotide sequence database from Equus caballus and synoviocytes from clinically normal adult horses. PROCEDURE: Computer procurement of equine gene sequences, probe design, and manufacture of an oligomicroarray were performed. Array performance was evaluated by use of patterns for equine synoviocytes in response to LPS. RESULTS: Starting with 18,924 equine gene sequences, 3,098 equine 3' sequences were annotated and met the inclusion criteria for an expression microarray. An equine oligonucleotide expression microarray was created by use of 68,266 of the 25-oligomer probes to uniquely identify each gene. Most genes in the array (68%) were expressed in equine synoviocytes. Repeatability of the array was high (r, > 0.99), and LPS upregulated (> 5-fold change) 84 genes, many of which were inflammatory mediators, and downregulated (> 5-fold change) 14 genes. An initial pattern of gene expression for effects of LPS on synoviocytes consisted of 102 genes. CONCLUSIONS AND CLINICAL RELEVANCE: Use of a computer algorithm to curate an equine sequence database generated high-quality annotated species-specific gene sequences and probe sets for a gene expression oligomicroarray, which was used to document changes in gene expression associated with LPS exposure of equine synoviocytes. The equine public database was expanded from 290 annotated genes to > 3,000 provisionally annotated genes. Similar curation and annotation of public databases could be used to create other species-specific microarrays.     

Gene expression analysis of peroxisome proliferators- and phenytoin-induced hepatotoxicity using cDNA microarray

The recent DNA microarray technology enables us to understand a large number of gene expression profiling. The technology has potential possibility to comprehend mechanism of multiple genes were related to compounds which have toxicity in biological system. So, the toxicogenomics through this technology may be very powerful for understanding the effect of unknown toxic mechanisms in biological system. We have studied that the effect of compounds related to hepatotoxin in vivo system using DNA microarray and classified chemicals which have been well characterized. We have studied three compounds; 2 peroxisome proliferators: Clofibrate (ethyl-p-chlorophenoxyisobutyrate), gemfibrozil (5-2[2,5-dimethyl-phenoxy]2-2-dimethyl-pentanonic), and an antiepileptic drug: phenytoin (5,5-diphenylhydantoin). Male Sprague-Dawely VAF(+) albino rats of 5-6 weeks old were treated with each compound for 24 hr and 2 weeks. 4.8 K cDNA microarray in house has been used for gene expression profiling. We found that the clustering of gene expression had similarity like as the toxic phenotype of compounds.     

牛骨骼肌酵母双杂交cDNA文库构建

为构建应用于酵母双杂交系统的牛骨骼肌cDNA文库,利用Trizol法提取牛骨骼肌总RNA,采用SMART技术PCR扩增合成cDNA第二链片段,并与文库线性载体pGADT7-Rec共转化酵母菌Y187构建酵母双杂交文库。结果显示文库容量达到1．7×10^7cfu／mL,插入片段主要在0．5～3kb范围内,文库重组率为80％。以上结果表明该文库质量好,能够通过筛选文库得到与目的蛋白相互作用的蛋白质。     

Bovine intelectins: cDNA sequencing and expression in the bovine intestine

Intelectins (Itlns) are lectins with potential roles in innate immunity, capable of binding bacteria via galactofuranose residues. Itlns also function as intestinal receptors for the antimicrobial glycoprotein lactoferrin (Lf). Since Lf binds strongly to enterohemorrhagic Escherichia coli O157:H7 (EHEC), we aimed to determine the expression of Lf receptor in terminal rectum, the site of predilection of EHEC in cattle. We sequenced two bovine intelectins (Itln1 and Itln2) and showed that both were expressed in abomasum and rectum, but expression appeared minimal in the jejunum. There was significantly higher expression of Itln2 in terminal rather than proximal rectum. Lactoferrin was expressed in all samples examined. Thus, we have demonstrated two novel bovine Itlns and shown that they are expressed along with Lf in the gastrointestinal tract, where they may interact with microbial pathogens.     

家蚕黄茧近等基因系SSH文库的构建及部分EST序列分析

以家蚕黄茧品系KY(YYCC)和白茧品系C108(+Y+Y+C+C)组配黄茧(C)近等基因系。挑取回交11代的黄茧(C)近等基因系群体中的黄血个体的黄色和浅黄色中部丝腺作为实验材料,构建家蚕黄茧近等基因系抑制消减杂交(SSH)cDNA文库。通过对SSHcDNA文库中随机挑选的104个阳性克隆测序和聚类拼接,得到15个假定基因(contig)、25个已知功能基因(unigenes)和5个未知功能基因(unknown)。获得的表达序列标签(EST)经Blast比对和同源性分析,初步发现这些基因参与家蚕体内能量代谢、基因转录、信号传导、物质转运、细胞生长分裂、细胞结构形成、蛋白质合成与降解、核酸及蛋白质加工、机体防御等诸多生物学过程。分析结果可作为深入研究家蚕茧着色分子机制的基础信息。     

家蚕黄血近等基因系SSH文库的构建及部分EST的序列分析

以家蚕黄血品系KY和白血品系HB构建家蚕黄血近等基因系。用回交18代的家蚕黄血基因(Y)近等基因系群体中的黄血个体和白血个体中肠为材料,构建了家蚕黄血近等基因系抑制消减杂交(SSH)cDNA文库。从该抑制消减杂交cDNA文库随机挑选出46个阳性克隆进行测序,并用CAP3软件聚类拼接,得到4个假定基因(contig)和9个已知功能基因(unigenes)。通过BLAST比对和对所得表达序列标签(EST)的同源分析表明,这些基因主要涉及能量代谢因子、RNA分子水平相关调节因子、酶类、结构蛋白等,由此初步探明了参与黄血基因(Y)协同作用的相关基因表达蛋白的种类和数量,可为进一步研究蚕茧着色的分子机制及通过遗传选择培育天然有色茧品种提供基础信息。     

Cloning and sequencing of a cDNA encoding the bovine FcR gamma chain

Phagocytic cells of the immune system express specific receptors for the Fc region of immunoglobulins (FcRs). In humans, most FcRs for IgG (FcgammaR), IgA (FcalphaR) and IgE (FcvarepsilonR) consist of an immunoglobulin (Ig) -binding subunit associated with a specialized signaling molecule, the FcR gamma chain. The FcR gamma chain is crucial for the transmission of intracellular signals following receptor ligation. In cattle, however, although four distinct complimentary DNAs (cDNAs) encoding IgG-binding subunits have been described (corresponding to bovine FcgammaRI, FcgammaRII, FcgammaRIII, and Fcgamma2R), virtually, nothing is known about signal transduction via bovine FcRs. Therefore, in this study, a cDNA encoding the bovine FcR gamma chain was cloned. The cDNA is 258 base pairs long and encodes a protein of 85 amino-acids. The mature protein shows high homology with the FcR gamma chains from several other species. Interestingly, the cytoplasmic domain of the bovine FcR gamma chain is one amino-acid shorter than those previously described. Cloning of a cDNA encoding, the bovine FcR gamma chain will allow for a better understanding of signal transduction processes triggered by bovine FcRs.     

Generation and characterization of murine monoclonal antibodies specific for bovine immunoglobulin E

Monoclonal antibodies were produced against serum-derived bovine immunoglobulin E (IgE). Culture supernatants of hybridomas were initially screened by enzyme-linked immunosorbent assay (ELISA). Supernatant-derived antibodies were concentrated and further characterized using ELISA, reverse cutaneous anaphylaxis, immunohistochemical staining, and immunoblotting of IgE-containing samples separated by SDS-polyacrylamide gel electrophoresis (PAGE). Eight monoclonal antibodies showed specificity for bovine epsilon immunoglobulin heavy chain. Two antibodies (E2 and E32) reacted in immunoblots of SDS-PAGE of serum IgE under reducing conditions. Additionally, E2, E5, and E32 detected epsilon chain in serum separated by SDS-PAGE and then renatured. Antigen-specific IgE was detected in Western blots by E5 and E32. Immunoperoxidase staining of IgE-containing cells in mesenteric lymph node sections was detected with E5, E21 and E32. All eight antibodies produced positive reverse cutaneous anaphylaxis reactions in calf skin. All functioned well in ELISA as a plate-sensitizing reagent for quantitation of total IgE; E5 and E32 worked well as a primary antibody in antigen-specific IgE assays. These antibodies will be useful in research applications and in diagnostic assays.     

cDNA cloning, sequencing and characterization of bovine pim-1

The cDNA clone of bovine pim-1 has been isolated from phorbol-12-myristate-13-acetate (PMA) and concanavalin A (ConA)-activated peripheral blood lymphocytes (PBLs). The full-length cDNA contains a 411bp 5' untranslated region (5'-UTR), followed by a 939bp coding region and a 3' untranslated region (3'-UTR) that contains 1403bp. Comparison of the bovine pim-1 coding sequence with the human, rat, mouse, frog and zebrafish counterparts reveals 94, 90, 89, 67 and 40% homology at the nucleotide level, respectively. The predicted amino acid sequence of bovine Pim-1 shares 98.7, 97.1, 93.3, 68.8, and 52.4% similarity with the sequences of human, rat, mouse, frog, and zebrafish, respectively. The 5'-UTR of bovine pim-1 shares high sequence similarity to the human and mouse counterparts and is G/C-rich (75%) which may promote a high degree of secondary structure. The 3'-UTR of bovine pim-1 contains two potential polyadenylation sites and an A/T-rich motif which has been shown to decrease the stability of polyA mRNA molecules. Southern blot results indicate that a single copy of the gene exists in the bovine genome. Northern blot results show that PMA stimulation of PBLs increases the expression of the pim-1 mRNA. In addition, examination of Pim-1 protein expression in PBLs stimulated with a variety of mitogens including ConA, PMA, anti-CD3 and purified protein derivative (PPD) from Mycobacterium tuberculosis, reveals two different types of expression patterns during the course of a 24h period of stimulation. ConA and PPD gave a biphasic pattern of expression while PMA and anti-CD3 gave single transient pattern of expression suggesting that expression is controlled by more than one signaling pathway.     

重度感染家蚕微孢子虫的家蚕丝腺cDNA文库构建及EST测序分析

用家蚕微孢子虫(Nosema bombycis,Nb)感染家蚕品种大造的3龄幼虫,于感染后第10天选择有Nb重度感染特征的家蚕丝腺组织无菌操作提取RNA,构建Nb和家蚕丝腺混合样品cDNA文库(文库滴度≥1.6×106PFU/mL)。对文库进行测序,获得EST序列5 026条,其中家蚕丝腺EST3 901条、家蚕微孢子虫EST970条。拼接后,分别获得家蚕丝腺和Nb的单一EST(unique EST)563和383条。对EST和unique EST进行分析发现,感染后第10天家蚕丝腺中Nb的组蛋白、细胞分裂激酶等与孢子分裂增殖相关的基因表达水平较高,一些可能与Nb侵染或寄生适应相关的基因,如Nb孢壁蛋白、极丝蛋白、转运体蛋白等基因亦在此时期较高水平表达,尤其是此期间有相对高水平的组蛋白脱乙酰基酶基因表达,说明Nb基因的表达受到组蛋白去乙酰化方式的调控。对家蚕微孢子虫uniqueEST的序列特征分析发现,Nb mRNA UTR的长度和GC含量与其它微孢子虫差异较小,但ORF区的AT含量较高,即家蚕微孢子虫基因ORF序列较其它微孢子虫发生了高AT变化。Nb unique EST的功能注释及分类结果表明感染后第10天家蚕丝腺中的Nb孢子仍处于多形期,还未完全成熟化。     

Generation and purification of recombinant bovine pregnancy associated glycoprotein

Bovine pregnancy-associated glycoprotein-1 (bPAG-1) is predicted to play an essential role during pregnancy and is labelled as a potential biochemical marker of pregnancy in ungulates. We have compared the generation of the glycosylated form of recombinant bPAG-1 (rbPAG-1) by human embryonic kidney 293 (HEK 293) and Chinese hamster ovary (CHO) cells in attached cultures and evaluated the adaptation of the rbPAG-1 transfected cell line to suspension culture. The PAG cDNA was cloned from placental RNA obtained from a slaughtered cow on day 55 of pregnancy. The PAG-pRcRSV expression vector was transfected into HEK 293 and CHO cells. Western blot analysis showed that clonal HEK 293 cells expressed rbPAG-1 better than CHO cells in attached cultures. Transfected HEK 293 cells were adapted to suspension culture in spinner flasks and the rbPAG-1 purified to homogeneity using ion-exchange, pepstatin-sepharose affinity chromatographies and preparative SDS-PAGE. The expression of rbPAG-1 was immunocharacterised using a polyclonal antibody. Our findings indicated that 293 cells are suitable for production of glycosylated form of rbPAG-1 and that the availability of the recombinant glycoprotein will aid in further studies to elucidate the function and structure of the protein.