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Expression analysis, often encompassed in the term "functional genomics," is the link between physiology and molecular biology. Often, specific physiological changes in plant development are due to a limited number of genes, expressed exclusively in very few cells of an organ or organism. Compounding the situation, these physiological changes may also be transient. Therefore, searching for the responsible genes, though exciting and necessary to understand important processes, is hindered primarily by the scarcity of "precious" cells in the desired physiological state. Used judiciously, molecular methods such as reverse transcription polymerase chain reaction (RT-PCR), microarray analysis, or subtractive hybridization allow analysis of rare or special cells. Each of these methods has its advantages and pitfalls. Working with precious cells entails special biological strategies to avoid excessive work in obtaining the data and misinterpretation of it. To illustrate the logic and methods involved in working with precious cells-tissues, we describe how subtractive hybridization followed by expressed sequence tag (EST) sequencing can be used to search for a few genes specific to a few available cells.
Methods Mol Biol 2003
PMID:Precious cells contain precious information: strategies and pitfalls in expression analysis from a few cells. 1450 Oct 58

An expressed sequence tag (EST) library was established from the hypopharyngeal glands of Apis cerana. Sixty-six recombinant clones, possessing inserts > 500 bp, were randomly selected and unidirectional sequenced. Forty-two of these (63.6%) were identified as homologues of Major Royal Jelly Proteins families 1, 2, 3, and 4 of A. mellifera (AmMRJP) for which MRJP1 was the most abundant family. The open-reading frame of the MRJP1 homologue (AcMRJP1) was 1299 nucleotides that encoded 433 deduced amino acids with three predicted N-linked glycosylation sites. The AcMRJP1 sequence showed 93% and 90% homologies with nucleotide and deduced amino acid sequences of AmMRJP1, respectively. Two complete transcripts of apisimin, and one and two partial transcripts of alpha-glucosidase and glucose oxidase, were also isolated. In addition, the royal jelly proteins of A. cerana were purified and characterized using Q-Sepharose and Sephadex G-200 column chromatography. The native forms of protein peaks A1, A2, B1, and C1 were 115, 55, 50, and 300 kDa, respectively. SDS-PAGE analysis indicated that A1 and C1 were dimeric and oligomeric forms of the 80 kDa and 50 kDa subunits, respectively. The ratio of the total protein quantities of A1 : A2 : B1 : C1 were 2.52 : 4.72 : 1 : 12.21. Further characterization of each protein, using N-terminal and internal peptide sequencing, revealed that the respective proteins were homologues of MRJP3, MRJP2, MRJP1, and MRJP1 of A. mellifera.
J Biochem Mol Biol 2003 Nov 30
PMID:Isolation and characterization of major royal jelly cDNAs and proteins of the honey bee (Apis cerana). 1465 76

The main objective of this study was to identify mRNA transcripts associated with embryonic developmental competence. In cattle, mRNA transcripts, ribosomes, and proteins accumulated during the growth phase are drawn on to sustain maturation, fertilization, and the initial cell cycle divisions up to the 8- to 16-cell stage. Early cleaving mammalian zygotes are more likely to develop to the blastocyst stage than their later cleaving counterparts, thus reflecting the intrinsic quality of the oocytes from which they originated. We describe the combination of this well-established model for the retrospective determination of developmental competence in mammalian oocytes with a technique for wide screening of differential gene expression in different biological populations. Immature cumulus oocyte complexes were recovered from surface visible follicles on abattoir ovaries, washed, and submitted to routine in vitro maturation and fertilization. Two-cell embryos were removed from culture at 3-hr intervals from 24 to 42 hr post insemination (pi). Two populations of two-cell embryos were identified; those that cleaved early (before 27 hpi) and those that cleaved late (after 33 hpi). Suppressive subtractive hybridization was carried out on cDNA from the two populations, following which, differentially expressed amplicons were subcloned and sequenced. The sequences were submitted to the nonredundant and expressed sequence tag (EST) databases at NCBI using the BLAST algorithm. The differential expression of three selected candidate genes that were identified as putatively upregulated in the early cleaving zygotes were chosen for further investigations; histone H3, cyclin B1, and GDF-9B. Using quantitative real time PCR we have shown that histone H3A is significantly more abundant in embryos that cleave earliest.
Mol Reprod Dev 2004 Feb
PMID:Analysis of differential maternal mRNA expression in developmentally competent and incompetent bovine two-cell embryos. 1469 28

Magnaporthe grisea, the causal fungus of rice blast, forms a specialized infection structure called an appressorium that is crucial for host plant penetration. A cDNA clone of M. grisea, showing strong sequence homology to FEM1 of Fusarium oxysporum and encoding an extracellular matrix protein, was isolated during an expressed sequence tag (EST) analysis of an appressorium cDNA library and named extracellular matrix protein 1 (EMP1). Sequence analysis of the corresponding genomic clone revealed that EMP1 contains an open reading frame of 685 nucleotides encoding 207 amino acids. The estimated molecular weight of the protein product was 20.5 kDa with a pI of 7.84. It contains an 18 amino acid N-terminal secretion signal sequence, as well as four potential N-glycosylation sites. At its C-terminus, the protein contains a 16 amino acid sequence with the characteristics of a glycosylphosphatidylinositol (GPI) anchor addition signal. Northern blot analysis showed that EMP1 transcripts accumulate during appressorium formation but not during vegetative growth. An EMP1 null mutant, emp1, generated by targeted gene disruption, exhibited reduced levels of appressorium formation and pathogenicity but no effect on mycelial growth rate or conidiation ability. These data suggest that EMP1 plays important roles in appressorium formation and the pathogenicity of M. grisea.
Mol Cells 2004 Feb 29
PMID:Extracellular matrix protein gene, EMP1, is required for appressorium formation and pathogenicity of the rice blast fungus, Magnaporthe grisea. 1505 45

CPTF1, a transcription factor with significant homology to ATF/CREB bZIP factors, was identified during an expressed sequence tag (EST) analysis of in planta-expressed genes of the phytopathogen Claviceps purpurea. Using a gene-replacement approach, deletion mutants of cptf1 were created. Expression studies in axenic culture showed that the H2O2-inducible gene cpcat1 (encoding a secreted catalase) had a reduced basal expression level and no longer responded to oxidative stress in the delta cptf1 mutant. Biochemical analyses indicated that CPTF1 is a general regulator of catalase activity. Delta cptf1 mutants showed significantly reduced virulence on rye. Electron microscopical in situ localization revealed significant amounts of H2O2 in delta cptf1-infected rye epidermal tissues, indicating that the plant tissue displayed an oxidative burst-like reaction, an event not detected in wild-type infections. These data indicate that CPTF1 is involved not only in oxidative stress response in the fungus but also in modulation of the plant's defense reactions.
Mol Plant Microbe Interact 2004 Apr
PMID:CPTF1, a CREB-like transcription factor, is involved in the oxidative stress response in the phytopathogen Claviceps purpurea and modulates ROS level in its host Secale cereale. 1507 71

Virtually all testicular germ cell tumours originate from a common precursor, the carcinoma in situ (CIS) cell. The precise nature of the molecular mechanisms leading to CIS remains largely unknown. We performed the first systematic analysis of gene expression in testis with CIS compared to normal testis by the differential display (DDRT-PCR) method, with subsequent analysis by RT-PCR and in situ hybridization (ISH). In tissue containing CIS we identified overexpression of 28 mRNA, some previously reported in CIS and a number of genes not previously described in germ cell neoplasia, including the novel expressed sequence tag (EST) OIC1 (Overexpressed In CIS). The genes could be grouped functionally into genes involved in cell growth, proliferation, differentiation, immunological response, and genes with unknown biological function. Examples of overexpressed genes are SFRP1 that is involved in Wnt signalling and IGFBP6, which is of importance for fetal growth and inhibits cell growth through insulin-like growth factor-II. ISH analysis showed that both mRNA were localized to CIS cells. The results of our search for differentially expressed genes in CIS demonstrated a number of genes linked to testicular development (e.g. DCN, IGFBP6, SFRP1, SALL1), supporting our hypothesis that the origin of CIS is probably associated with disturbances of the fetal development of the testis.
Mol Hum Reprod 2004 Jun
PMID:Identification of genes differentially expressed in testes containing carcinoma in situ. 1512 80

Generating expressed sequence tags is a simple, cheap, and efficient way to sample the genome of a target organism. An expressed sequence tag (EST) is a single-pass sequence derived from a single complementary DNA (cDNA) clone, and the sequence serves to identify the gene from which it derives. We present a set of tested laboratory protocols for setting up and performing an EST analysis of any chosen species. These medium-throughput protocols do not require dedicated genomics equipment, such as robots, and focus on the use of microtiter plates and multichannels. Using these protocols, a single competent research worker should be able to generate 2000 ESTs in 1 mo. In a nonnormalized library, these 2000 ESTs should identify between 1000 and 1500 different genes, and thus possibly between 10 and 20% of the genes of any target parasite.
Methods Mol Biol 2004
PMID:Expressed sequence tags: medium-throughput protocols. 1515 23

Suppression of brassinosteroid (BR) biosynthesis in cotton ovules by treatment with brassinazole inhibits fiber formation, indicating that BR plays an important role in cotton fiber development. Plant responses to brassinosteroids (BR) are mediated through a plasma membrane-bound leucine-rich repeat (LRR) receptor-like protein kinase known as BRI1. Mutations in the BRI1 genes of several species result in dwarfed plants with reduced sensitivity to BR. A single expressed sequence tag (EST) from cotton with strong sequence similarity to Arabidopsis BRI1 ( AtBRI1 ) was identified in a search of publicly available databases. With this EST as a starting point, full-length cDNAs and genomic coding sequences from upland cotton ( Gossypium hirsutum ) BRI1 ( GhBRI1 ) were obtained and characterized. Ectopic expression of this coding sequence in BR-insensitive Arabidopsis plants resulted in recovery of normal growth indicating that GhBRI1 is a functional homologue of AtBRI1. G. hirsutum is an allotetraploid (AADD) derived from diploid ancestors. Analysis of several GhBRI1 cDNAs showed two distinct sequences indicating the presence of two GhBRI1 genes, denoted GhBRI1-1 and GhBRI1-2. Sequence comparisons between these GhBRI1 coding sequences and those from related A and D genome diploid Gossypium species ( G. arboreum and G. thurberi ) indicated that GhBRI1-1 is likely to the A sub-genome orthologue while GhBRI1-2 is from the D sub-genome.
Plant Mol Biol 2004 Jan
PMID:Characterization of the brassinosteroid insensitive 1 genes of cotton. 1515 24

In previous studies, we demonstrated that high corn oil diets promote the development of 7,12-dimethylbenz(alpha)anthracene (DMBA)-induced mammary tumors. In this study, we have investigated whether modulation of gene expression is one of the mechanisms by which this high-fat diet exerts such effects. Female Sprague-Dawley rats were induced with DMBA and fed normolipidic (3% corn oil) or high-fat (20% corn oil) diet. Screening of genes differentially expressed in adenocarcinomas from the high corn oil diet group compared to the control diet group was performed with cDNA microarrays. The resulting six upregulated and nine downregulated genes were validated by Northern blot and/or reverse transcription (RT)-polymerase chain reaction (PCR). Further investigation in a higher number of adenocarcinomas showed that in the high-fat n-6 diet group, where the tumor phenotype was verified to be more aggressive, the expression of submaxillary gland alpha-2u globulin, vitamin D(3)-upregulated protein 1 (VDUP1), H19, and the unknown function gene that codifies the expressed sequence tag (EST)-Rn.32385 was significantly decreased in comparison with the control group (C). These results, together with the fact that VDUP1, H19, and this globulin have been associated with cell proliferation and differentiation, open a new line of research about how the underexpression of these genes contributes to the stimulating effect of a high corn oil diet on experimental mammary carcinogenesis.
Mol Carcinog 2004 Jun
PMID:Identification of novel differentially expressed genes by the effect of a high-fat n-6 diet in experimental breast cancer. 1517 Aug 12

A new C-type lectin with putative mannose specificity was identified from the expressed sequence tag (EST) analysis of cDNA library from common carp head kidney (HK), stimulated with concanavalin A and lipopolysaccharide (LPS) during a routine EST analysis. The full sequence of 627 bp was identified by 5'-rapid amplification of cDNA ends. The gene is composed of 146 amino acid residues, including an 18-residue signal peptide for secretion and a single carbohydrate-recognition domain of approximately 118 residues typical of C-type lectins. Based on the predicted structure, this is a calcium dependent C-type lectin with putative mannose specificity suggested by the presence of an EPN motif. By hemagglutination assay, the mannose specificity of the Ca-CTL was determined. Reverse transcription (RT) PCR analysis demonstrated the expression of Ca-CTL mRNA in the hematopoietic organs and also the level of expression increased with LPS induction. Localization studies by in situ hybridization showed the presence of transcripts in the organs.
Mol Immunol 2004 Jul
PMID:Characterization of a new C-type lectin from common carp Cyprinus carpio. 1526 61


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