Gene Expression Profiles of Colonic Mucosa in Healthy Young Adult and Senior Dogs

Background

We have previously reported the effects of age and diet on nutrient digestibility, intestinal morphology, and large intestinal fermentation patterns in healthy young adult and senior dogs. However, a genome-wide molecular analysis of colonic mucosa as a function of age and diet has not yet been performed in dogs.

Methodology/Principal Findings

Colonic mucosa samples were collected from six senior (12-year old) and six young adult (1-year old) female beagles fed one of two diets (animal protein-based vs. plant protein-based) for 12 months. Total RNA in colonic mucosa was extracted and hybridized to Affymetrix GeneChip® Canine Genome Arrays. Results indicated that the majority of gene expression changes were due to age (212 genes) rather than diet (66 genes). In particular, the colonic mucosa of senior dogs had increased expression of genes associated with cell proliferation, inflammation, stress response, and cellular metabolism, whereas the expression of genes associated with apoptosis and defensive mechanisms were decreased in senior vs. young adult dogs. No consistent diet-induced alterations in gene expression existed in both age groups, with the effects of diet being more pronounced in senior dogs than in young adult dogs.

Conclusion

Our results provide molecular insight pertaining to the aged canine colon and its predisposition to dysfunction and disease. Therefore, our data may aid in future research pertaining to age-associated gastrointestinal physiological changes and highlight potential targets for dietary intervention to limit their progression.     

猪肌肉素基因的cDNA克隆与表达

从人肌肉素基因出发, 在dbEST数据库中进行同源性搜索, 找到七个有较高同源性的Expressed Sequence Tag(DY426490, CF787546, AJ660979, AJ664670, AJ663820, AJ680159, DN106254)。通过拼接和进一步RT-PCR实验验证, 获得猪肌肉素基因全长cDNA序列, 其全长651 bp, 开放阅读框为54~452 bp, 编码有132个氨基酸。同源性分析结果表明, 与人、小鼠和大鼠的肌肉素基因cDNA编码区(CDS)同源性分别为87.2%、77.6%和77.9%。利用克隆出的猪肌肉素cDNA, 构建表达载体pGEX-4T-1-musclin, 并在BL21大肠杆菌中成功表达和纯化了分子量为38.59 kD的融合蛋白GST-Musclin, 并运用蛋白印迹技术进行鉴定。     

猪脂肪及肌肉组织中基因表达信息分析

为探测猪脂肪及肌肉组织中基因表达概况,利用猪EST资源和人类基因序列开展计算机模拟研究,旨在为猪肉质改良的遗传基础分析提供候选信息。执行Blast比对程序以识别人类基因组基因与猪EST序列间的同源性并筛选出高度同源记录,同时编制4个Java程序进行序列检索收集、序列比对结果的过滤筛选以及分类处理。统计分析表明：至少有2002个基因在猪脂肪及肌肉组织中表达,其中1087个基因在脂肪组织表达,1205个基因在肌肉组织中表达,两组织共同表达的基因为290个;筛选出高同源基因,同时分类统计出了114个基础活性基因(脂肪和肌肉组织分别表达80和34个),并选取Top记录进行了描述分析和总结。     

猪骨骼肌快肌肌钙蛋白C2基因的cDNA克隆与表达分析

从人骨骼肌快肌肌钙蛋白C2（TNNC2）基因出发,在dbEST数据库中进行同源性搜索,找到一个有较高同源性且在猪背最长肌中表达EST（BM083186）。通过电子克隆和进一步RT-PCR实验验证,获得猪TNNC2基因全长cDNA序列,其全长843bp,开放阅读框为201～683bp,编码有160个氨基酸。同源性分析结果表明,与人、鼠的骨骼肌快肌肌钙蛋白C2基因cDNA编码区（CDS）同源性分别为93.6％、90.5％,蛋白序列同源性均为97.5%。多种组织的半定量RT-PCR研究表明,该基因在骨骼肌中表达,并且在杜洛克猪背最长肌中的表达比兰塘猪高。     

颊粘膜癌与舌癌差异基因表达的对比分析

目的:研究颊粘膜癌(Buccal Mucosa Cancer,BMC)与舌癌(Tongue Cancer,TC)的基因差异表达,探讨BMC与TC发生发展的基因学基础。方法:应用cDNA芯片技术对5例BMC和5例TC组织mRNA检测,通过芯片杂交、生物信息学处理,找出两者间差异表达基因。结果:BioStarH-40芯片发现差异表达基因503条,差异表达基因占12.9%,其中表达增强274条(显著增强69条),表达降低229条(显著降低54条)。结论:MBC与TC基因表达比较,差异有统计学意义,这些差异可能在两类肿瘤不同的生物学行为中起重要作用。     

DHPLC对猪肌肉组织差异表达EST的鉴定

采用DHPLC系统和Labwork4．0图像分析软件,对大白猪和广东地方品种蓝塘猪眼肌组织差异显示EST进行鉴定,两种方法均证实了差异显示条带的真实性。结果表明：用DHPLC系统能够准确而简捷的检测不同组织中mRNA表达的差异,是1种鉴定基因表达差异的有效方法,在研究基因表达,比较不同环境条件下动物组织的mRNA表达差异等方面具有广阔的应用前景。     

屯昌猪MYLPF基因序列分析及其组织表达量检测

为获得屯昌猪MYLPF基因的CDS区序列并分析其分子结构特征,研究屯昌猪、杜洛克猪以及其杂交F1代猪不同组织中的MYLPF mRNA表达水平,本研究以GenBank上公布的猪MYLPF基因序列(登录号:NM_001006592)为参考设计引物,通过RT-PCR扩增、测序获得屯昌猪MYLPF基因CDS区.结果显示:该基因...     

开放的差异基因表达技术研究进展

自 90年代早期发展以来 ,差异基因表达 (DGE)技术在许多领域得到了应用 .“开放”结构系统的DGE技术不需原始的生物学或序列信息 ,而且可应用于任何种群 .主要介绍 6项开放的DGE技术 :cDNA代表性差示分析 (cDNA RDA)、基因表达系统分析 (SAGE)、表达序列标签串联排列连接(TALEST) ,和早期的DGE技术差异显示 (DD)、随机引物聚合酶链反应 (AP PCR) ,以及一项受专利保护的技术———GeneCalling .通过几项重要的参数对这些技术进行了比较 ,认为DD虽然有其致命的弱点 ,但在目前仍然应用得非常广泛 .cDNA RDA能有效富增特异片段 ,扣除共有序列 ,如能和SAGE结合 ,将能进一步促进其发展 .TALEST和GeneCalling操作较简便 ,一次试验能获得大量的数据 ,但是分析这些数据比较麻烦 ,须借助另外的分析软件 .最后介绍了应用DGE技术取得的最新成果 .     

Differential Gene Expression in Synovium of Rheumatoid Arthritis and Osteoarthritis

Rheumatoid arthritis (RA) and osteoarthritis (OA) are the major types of arthritis. Although both diseases are characterized by joint destruction, their etiologies are different. To get insights into pathophysiological pathways, we used the suppression subtractive hybridization (SSH) method to identify differentially expressed genes in RA. DNA sequencing identified 12 gene products including cytoskeletal γ-actin and extracellular matrix components such as fibronectin, collagen IIIα₁, and superficial zone protein. Interferon γ-inducible genes such as a novel thiol reductase, two genes of unknown function (HSIFNIN4, RING3), and annexin II were also found. Two genes encoded proteins involved in proliferation such as elongation factor 1α and the granulin precursor. Furthermore, the protease cathepsin B and synovial phospholipase A2 group IIA were detected by SSH. To confirm the differential expression of the genes, we performed RT-PCR analyses of RA and OA synovial tissues. Compared to OA patients, 9 of the 12 genes were overexpressed in RA, suggesting that SSH is a powerful tool for the detection of differential gene expression in synovial tissues. Further characterization of the gene products may help to identify pathophysiological mechanisms in arthritic diseases.     

ABI 1700芯片分析系统在基因差异表达研究中的应用

应用化学发光法标记技术分别对正常和临床慢性髓细胞性白血病（chronic myelogenous leukemia,CML）病人骨髓单个核细胞的RNA进行标记,然后与ABI的人全基因组表达谱芯片杂交,对于杂交后所得到的荧光信号数据,应用1700芯片分析系统对其进行生物信息学分析.实验结果表明,ABI1700芯片分析系统可以对基因芯片杂交后得到的差异表达基因进行疾病学分类和生物功能分类分析,同时还发现与CML相关的差异表达基因75个,因此ABI1700芯片分析系统在芯片研究领域中具有重要的应用价值.     

The Gastrointestinal Mucosa in Young Milk-Fed Calves

Gastrointestinal segments from 4 healthy, 17-, 21-, 22- and 23-day-old calves fed on whole cow’s milk were examined. Scanning electron microscopy showed that the anterior duodenum had short villi varying in shape from leaf-shaped to nodular; the middle duodenum had broad, tongue-shaped villi and the anterior, middle, and parts of the posterior jejunum had slender, finger-shaped or leaf-shaped villi. The villi of the mucosa covering Peyer’s patches in the posterior jejunum were short and either conical or tongue-shaped; there were also small “pseudovilli” caused by bulges in the lymphoid tissue. Morphometry showed that the villi were longer in the anterior jejunum than in the duodenum and the posterior parts of the jejunum (P < 0.005). Morphologically fat absorption was most heavy in the anterior third of the small intestine. Moderate amounts of fat were also found in the epithelium of the posterior jejunum and of the abomasum. Large fat droplets were seen in apical duodenal enterocytes, in contrast to the small epithelial droplets in other areas with fat absorption. Nile blue staining indicated that the fat in the large droplets was esterified.     

Differential Expression of Programmed Cell Death on the Follicular Development in Normal and Miniature Pig Ovary

Follicles are important in oocyte maturation. Successful estrous cycle requires remodeling of follicular cells, and proper execution of programmed cell death is crucial for normal follicular development. The objectives of the present study were to understand programmed cell death during follicle development, to analyze the differential follicle development patterns, and to assess the patterns of apoptosis and autophagy expression during follicle development in normal and miniature pigs. Through the analysis of differential patterns of programmed cell death during follicular development in porcine, MAP1LC3A, B and other autophagy-associated genes (ATG5, mTOR, Beclin-1) were found to increase in normal pigs, while it decreased in miniature pigs. However, for the apoptosis-associated genes, progression of genes during follicular development increased in miniature pigs, while it decreased in normal pigs. Thus, results show that normal and miniature pigs showed distinct patterns of follicular remodeling manifesting that programmed cell death largely depends on the types of pathway during follicular development (Type II or autophagy for normal pigs and Type I or apoptosis for miniature pigs).     

猪早期孤雌激活胚不同发育阶段差异基因表达的研究

收集2细胞、4细胞、8-16细胞时期的猪孤雌激活胚,采用SPEDDRT-PCR方法挑选不同时期的差异表达产物,通过反向northern杂交去除假阳性的条带。将阳性条带克隆入T载体中,经过PCR鉴定后挑选其中的阳性克隆进行测序,筛选了8个代表不同时期表达差异的cDNA片段,编号为DD1-DD8。经过与GenBank中的数据进行同源性分析,发现其中DD1和DD2没有相似的数据, 提交数据库获得GenBank登录号(EU545158, EU545159);其余的DD3-DD8发现了相似性较高的数据,但除DD3外均无基因功能说明需要进行进一步的研究。     

Differential Patterns of Gene Expression and Gene Complement in Laboratory-Evolved Lines of E. coli

Laboratory selection experiments play a prominent role in understandingorganismal adaptation. Although bacteria are not yet commonlyused for such experiments, they are well suited for analysesof both the organismic and the genetic basis of adaptation.Bacteria can be maintained in large populations while occupyinglimited laboratory space, have short generation times, are wellcharacterized physiologically, biochemically, and genetically,and are readily frozen and revived from the freezer. In addition,the genomes of many species are completely sequenced and knowledgeof gene function is unparalleled. Here we review general aspectsof selection experiments, the history of using selection experimentsin combination with thermal biology and genomics, and highlightfindings from six lines of Escherichia coli adapted to hightemperature (41.5°C), including changes in organismal fitness,physiological performance, gene complement and gene expression.Our results are an example of the powerful insights that canbe discovered by combining the tools and analyses of many biologicaldisciplines including genomics, evolutionary biology, genetics,and evolutionary physiology.     

Differential Expression of Vitreous Proteins in Young and Mature New Zealand White Rabbits

Different anatomical regions have been defined in the vitreous humor including central vitreous, basal vitreous, vitreous cortex, vitreoretinal interface and zonule. In this study we sought to characterize changes in the proteome of vitreous humor (VH) related to compartments or age in New Zealand white rabbits (NZW). Vitreous humor was cryo-collected from young and mature New Zealand white rabbit eyes, and dissected into anterior and posterior compartments. All samples were divided into 4 groups: Young Anterior (YA), Young Posterior (YP), Mature Anterior (MA) and Mature Posterior (MP) vitreous. Tryptic digests of total proteins were analyzed by liquid chromatography followed by tandem mass spectrometry. Spectral count was used to determine the relative protein abundances and identify proteins with statistical differences between compartment and age groups. Western blotting was performed to validate some of the differentially expressed proteins. Our results showed that 231, 375, 273 and 353 proteins were identified in the YA, YP, MA and MP respectively. Fifteen proteins were significantly differentially expressed between YA and YP, and 11 between MA and MP. Carbonic anhydrase III, lambda crystallin, alpha crystallin A and B, beta crystallin B1 and B2 were more abundant in the anterior region, whereas vimentin was less abundant in the anterior region. For comparisons between age groups, 4 proteins were differentially expressed in both YA relative to MA and YP relative to MP. Western blotting confirmed the differential expression of carbonic anhydrase III, alpha crystallin B and beta crystallin B2. The protein profiles of the vitreous humor showed age- and compartment-related differences. This differential protein profile provides a baseline for understanding the vitreous compartmentalization in the rabbit and suggests that further studies profiling proteins in different compartments of the vitreous in other species may be warranted.