ISOLATION AND CHARACTERIZATION OF PHASE-SPECIFIC COMPLEMENTARY DNAs FROM SPOROPHYTES AND GAMETOPHYTES OF PORPHYRA PURPUREA (RHODOPHYTA) USING SUBTRACTED COMPLEMENTARY DNA LIBRARIES1

The red alga Porphyra purpurea (Roth) C. Agardh has a life cycle that alternates between shell-boring, filamentous sporophytes and free-living, foliose gametophytes. The significant morphological differences between these two phases suggest that many genes should be developmentally regulated and expressed in a phase-specific manner. In this study, we prepared and screened subtracted complementary DNA (cDNA) libraries specific for the sporophyte and gametophyte of P. purpurea. This involved the construction of cDNA libraries from each phase, followed by the removal of common clones through subtractive hybridization. Sampling of the subtracted libraries indicated that 8–10% of the recombinant colonies in each library were specific for the appropriate phase. Of 20 putative phase-specific cDNAs selected from each subtracted library, eight unique clones were obtained for the sporophyte and seven for the gametophyte. After confirming their phase-specificities by hybridization to gametophyte and sporophyte messenger RNA, these 15 phase-specific cDNAs were sequenced, and the deduced amino acid sequences were used to search protein databanks. Two proteins encoded by the sporophyte-specific cDNAs and two by the gametophyte-specific cDNAs were identified by their similarity to databank entries.     

A modified cDNA subtraction to identify differentially expressed genes from plants with universal application to other eukaryotes

We have designed a simple and efficient polymerase chain reaction (PCR)-based cDNA subtraction protocol for high-throughput cloning of differentially expressed genes from plants that can be applied to any experimental system and as an alternative to DNA chip technology. Sequence-independent PCR-amplifiable first-strand cDNA population was synthesized by priming oligo-dT primer with a defined 5' heel sequence and ligating another specified single-stranded oligonucleotide primer on the 3' ends of first-strand cDNAs by T4 RNA ligase. A biotin label was introduced into the sense strands of cDNA that must be subtracted by using 5' biotinylated forward primer during PCR amplification to immobilize the sense strand onto the streptavidin-linked paramagnetic beads. The unamplified first strand (antisense) of the interrogating cDNA population was hybridized with a large excess of amplified sense strands of control cDNA. We used magnetic bead technology for the efficient removal of common cDNA population after hybridization to reduce the complexity of the cDNA prior to PCR amplification for the enrichment and sequence abundance normalization of differentially expressed genes. Construction of a subtracted and normalized cDNA library efficiently eliminates common abundant cDNA messages and also increases the probability of identifying clones differentially expressed in low-abundance cDNA messages. We used this method to successfully isolate differentially expressed genes from Pennisetum seedlings in response to salinity stress. Sequence analysis of the selected clones showed homologies to genes that were reported previously and shown to be involved in plant stress adaptation.     

Ultrastructure of the early stages of carposporophyte development in the red algaChondria tenuissima (Rhodomelaceae,Ceramiales)

The ultrastructure of the early stages of carposporophyte development in the marine red algaChondria tenuissima has been studied. The diploid carposporophyte grows on the gametophyte. Apical gonimoblast cells develop into diploid carpospores. The basal gonimoblast cells cease to divide and undergo considerable cytoplasmic changes before they become incorporated into the expanding fusion cell. Nucleus and plastids degenerate gradually, while mitochondria remain intact. The smooth endoplasmic reticulum becomes prominent, it seems to produce small vesicles with electron dense contents. Simultaneously, numerous mucilage sacs are formed, presumably from dilating ER cisternae. The contents of the mucilage sacs are secreted by exocytosis. The pit connections between gonimoblast cells flare out. They remain as isolated bodies without connection to a wall after fusion. Secondary pit connections occur between vegetative gametophyte cells and sterile carposporophyte cells. There are three different morphological types of pit connections.     

Full-Length Normalization Subtractive Hybridization: A Novel Method for Generating Differentially Expressed cDNAs

Here we present a novel method termed full-length normalization subtractive hybridization (FNSH) for efficiently generating subtracted cDNA libraries with a high degree of productivity. This method has the ability to isolate full-length differentially expressed genes from target samples. Normalization and subtraction of FNSH are performed simultaneously with efficiency equal to or even higher than that of suppression subtractive hybridization. Using FNSH, we have isolated at least 40 unique cDNAs that are expressed in terminal ampullae but not in the ovaries of the prawn Macrobrachium rosenbergii from 120 randomly picked subtracted clones. Sequence analysis shows that 37 of the 40 cDNAs are full length.     

A Light Microscope Study of Carposporophyte Development in Gracilaria verrucosa (Hudson) Papenfuss

Gracilaria verrucosa is a very common marine red alga of Greekcoasts. The diploid carposporophyte which develops attachedto the female gametophyte of Gracilaria is described. The immaturecystocarps are very small while the mature ones are globose,ostiolate and are borne profusely all over the surface of thethallus. The earliest observed fusion cell is small and fusesprogressively with adjacent vegetative cells to form a largemultinucleate cell. From this fusion cell gonimoblast initialsoriginate, dividing further and giving rise to a large numberof gonimoblast cells. The resultant carposporophyte consistsof a basal-central, multinucleate cell surrounded by a conicalor hemispherical mass of gonimoblast cells. Chains or clustersof successively maturing carpospores are borne from the terminalgonimoblast cells. The liberation of mature carpospores takesplace through the ostiole of the cystocarp. The liberated carposporeslack cell walls and are naked in a mucilage mass. Gracilaria verrucosa (Hudson) Papenfuss, Gigartinales, Gracilariaceae, Rhodophyta, carposporophyte, development     

STRUCTURE AND DEVELOPMENT OF THE CARPOSPOROPHYTE OF NEMALION HELMINTHOIDES (NEMALIONALES,RHODOPHYTA)1

Following fertilization, the carposporophyte of Nemalion helminthoides (Velley in With.) Batters differentiates into four distinct regions: the fusion cell, the sterile gonimoblast cells, the carposporangial mother cells and the carposporangia. The gonimoblast is formed by apically dividing, monopodial filaments of limited growth which may later become pseudodichotomous. Upon differentiation of a terminal carposporangium, a gonimoblast filament may continue to grow sympodially. A single carposporangial mother cell may produce carposporangia in several different directions as well as proliferate successive carposporangia within the sporangial walls that remain after carpospore liberation. As the carposporophyte matures, the gonimoblast initial, the stalk cell, the hypogynous and subhypogynous cells fuse. Except for the fusion cell, all cells of the carposporophyte show organelle polarity and contain a distally located, lobed chloroplast and proximal nucleus.     

日本血吸虫期别差异表达基因文库的构建及分析

为从期别差异表达基因分析入手研究血吸虫的生长发育机制,应用抑制性消减杂交 (suppressed subtractive hybridization , SSH) 技术首次构建了日本血吸虫尾蚴、虫卵和成虫的期别差异表达基因文库 . 经消减效率分析和三种文库克隆的 EST 的期别差异性鉴定,表明所建文库质量较高,为在整个基因组水平分离血吸虫的差异表达基因提供了重要材料 . 由三个文库选择 257 个插入片段大于 500 bp 的克隆测定了 EST 序列 . 同源性分析结果表明 257 个 EST 代表 182 种血吸虫基因,其中有 22 种为血吸虫已知基因,有 128 种为血吸虫已知 EST ,有 32 种为新发现的血吸虫基因 . 对 EST 编码蛋白的功能预测结果显示：尾蚴消减文库的基因多与运动、能量代谢、转录调节及致病性相关;虫卵消减文库的基因可能参与信号转导、细胞粘附、蛋白质和碳水化合物的代谢以及抗氧化反应;成虫消减文库的基因多参与蛋白质的合成、转运及分解代谢,参与虫体的运动等 . 大规模分离、分析血吸虫期别差异表达基因将对从分子水平去解读血吸虫的生长发育机制,筛选高效疫苗候选抗原、药物靶标及诊断制剂有重要意义 .     

人细胞差异表达基因cDNA消减杂交体系的建立

为克隆肺腺癌分化相关基因, 采用诱导分化与消减杂交相结合的策略, 建立了全反式维甲酸(RA)诱导前后人肺腺癌细胞系的cDNA消减文库, 得到124个cDNA消减克隆. 经加减法杂交差异筛选、DNA和RNA印迹、cDNA全序列测定和生物学功能分析, 分离到3个在人肺腺癌细胞系分化过程中由RA激活而特异表达的新的cDNA序列这一策略和技术路线适用于分离细胞中呈过量表达或表达抑制基因的cDNA克隆, 并具有反映细胞分化过程中基因表达动态变化特征和相对简便适用的特点.     

Identification of over-expressed genes in human renal cell carcinoma by combining suppression subtractive hybridization and cDNA library array

To isolate the over-expressed genes in human renal cell carcinoma (RCC) and analyze its molecular basis of carcinogenesis, we used the mRNA from human RCC tissues as tester and that from the matched normal kidney tissues as driver to construct the suppression subtractive hybridization library. 379 of the subtracted clones were arrayed onto a nylon membrane and the over-expressed genes were then screened by hybridizing the filter with radioactively labeled cDNA from RCC and matched normal kidney tissues. 67 clones over-expressed in RCC by a factor of 6 or more were sequenced and its identities were analyzed in GenBank database. 4 clones were previously unknown fragments and 2 clones represent KIAA genes. The rest clones were the known genes and some of them were RCC-related, including vascular endothelial growth factor, vimentin and tissue factor. Most of the known genes were the RCC-related genes previously unknown, including zinc ribbon domain-containing 1 protein (ZNRD1), pituitary tumor transforming gene1 (PTTG1). Northern blot and semi-quantitative RT-PCR confirmed that the mRNA levels of the 3 novel fragments and 1 KIAA and 3 known genes were significantly higher in RCC than in the matched normal kidney tissues. Immunohistochemical and Western blot analysis for PTTG1 and ZNRD1 revealed increased protein level in RCC. The over-expressed genes in RCC are the potential molecular targets for diagnosis and therapy and it is very important to understand the molecular mechanism of RCC through the profile of over-expressed genes.     

Isolation and Identification of Submergence-induced Genes in Maize Seedlings by Suppression Subtractive Hybridization

To investigate the expression profile of maize genes induced by submergence, a subtracted cDNA library of maize seedling roots was constructed using suppression subtractive hybridization (SSH). The cDNA of maize seedling roots treated with submergence (ST) was used as tester and what from untreated roots (UT) as driver. Products of the secondary PCR from the forward subtraction were cloned into T/A vector and transferred into Escherichia coli strain JM10B by electroporation. Four hundred and eight randomly chosen transformants carrying cDNA fragments were screened with PCR-Select Deferential Screening Kit. One hundred and eighty-four cDNA clones were identified as submergence specifically induced or highly expressed. After sequencing and removing redundant cDNAs, we got 95 submergence-induced cDNA clones. Of the 95 cDNA clones, 68 contain the regions with 60%-90% identity to their homolog in GenBank, 21 are expected to be novel genes, only 6 correspond to the published maize sequences. Key words: maize; expression profile; suppression subtractive hybridization (SSH); submergence     

ULTRASTRUCTURE OF THE CARPOSPOROPHYTE AND CARPOSPOROGENESIS IN THE PARASITIC RED ALGA PLOCAMIOCOLAX PULVINATA SETCH, (GIGARTINALES,PLOCAMIACEAE) 1

The ultrastructure of the carposporophyte and carposporogenesis is described for the parasitic red alga Plocamiocolax pulvinata Setch. After presumed fertilization the zygote nucleus is apparently transferred to the auxiliary cell which initiates gonimoblast cell production. These gonimoblast cells differentiate into storage or generative cells. Storage gonimoblast cells (SGC) are large and multinucleate, contain large quantities of starch and are located nearest the auxiliary cell, when compared to the smaller uninucleate, devoid of starch, generative gonimoblast cells (GGC) that form terminal lobes of carpospores. In addition, compressed membrane bodies and annulate lamellae are common in these cells. During carposporophyte maturation the amount of starch in the SGC's decreases and eventually the auxiliary cell, as well as SGC's, degenerate. Generative gonimoblast cells (GGC's) cleave repeatedly to form carpospores which are interconnected by small pit connections. Stage one-carpospores are recognized by their elongated shape, the formation of small     

疫霉侵染下辣椒幼苗消减文库的构建与初步分析

为了分离和鉴定辣椒中疫霉诱导基因,以高抗疫霉病辣椒品种L11为材料,以接种辣椒疫霉菌的幼嫩叶片为处理（tester）,以未接种自然生长的幼嫩叶片为对照(driver),利用抑制性消减杂交技术(suppression subtractive hybridization,SSH)构建了疫霉侵染下辣椒幼苗的消减文库。从消减文库中随机挑取30个阳性克隆,提取质粒进行PCR鉴定,显示插入片段大小大部分集中在200～1 000 bp之间,文库质量良好。随机挑取40个克隆进行测序,共获得35个有效EST序列。经Blastx分析表明：有30个EST与GenBank中其他序列有同源性,5个EST为未知功能序列。已知功能的EST序列分别编码NAC转录因子、丝氨酸/苏氨酸蛋白激酶、P450单加氧酶、叶绿素a/b结合蛋白、谷胱甘肽转移酶、几丁质酶等,这些蛋白涉及抗病信号传递、抗氧化作用、转录调控及光合作用等多种生理过程。本研究为抗病基因克隆和系统研究疫霉侵染下辣椒基因的表达奠定了重要的理论基础。     

The "ups" and "downs" in Using Subtractive Cloning Techniques to Isolate Regulated Genes in Fish

Over the last decade, subtractive cloning approaches have beenused extensively to isolate genes that are up- or down-regulatedunder various conditions. These techniques have provided thefoundation for many subsequent studies concerning gene functionand regulation and, as such, have been valuable tools for manybiological fields. Over the past 10 years, we have used differentsubtractive cloning approaches to isolate genes in fish thatare regulated in relation to hormonal stimulation or the stageof ovarian maturation. These include conventional cDNA subtractionfollowed by library screening, differential display PCR, suppressionsubtraction hybridization, and more recently, iterative PCRsubtraction. We continue to use these techniques for the isolationof new genes involved in physiological processes in fish andbivalve molluscs. Examples that illustrate the use of thesedifferent subtractive cloning techniques are described, includingwhere possible the advantages and disadvantages of each. Inaddition, the use of ancillary methods (e.g., "Reverse Northerns")to facilitate the use of these subtractive approaches are discussed.     

一种用少量标本快速构建老年性白内障消减cDNA文库的方法

为从少量标本中获得含较多大片段的、高质量的老年性白内障消减cDNA文库,利用磁珠分离、生物素标记的改良消减杂交法获得差异cDNA,利用选择性PCR法扩增其中大片段差异cDNA,从而成功构建老年性白内障消减cDNA文库.在文库中随机挑取的22个克隆中,1 000 bp以上的片段有7个,占31.8%,750 bp以上有15个,占68.2%.所得cDNA片段较大,可以满足下一步研究需要.改良消减杂交法结合选择性PCR法可以从少量标本中快速有效地获得大片段高质量的消减cDNA文库.