Identification of Differentially Expressed Sequence Tags in Rapidly Elongating Phyllostachys pubescens Internodes by Suppressive Subtractive Hybridization

In vivo-derived bovine embryos are of higher quality than those derivedin vitro. Many of the differences in quality can be related to culture environment-induced changes in mRNA abundance. The aim of this study was to identify a range of mRNA transcripts that are differentially expressed between bovine blastocysts derived fromin vitroversusin vivoculture. Microarray (BOTL5) comparison betweenin vivo- andin vitro-cultured bovine blastocysts identified 384 genes and expressed sequence tags (ESTs) that were differentially expressed; 85% of these were down-regulated inin vitrocultured blastocysts, showing a much reduced overall level of mRNA expression inin vitro- compared within vivo-cultured blastocysts. Relative expression of 16 out of 23 (70%) differentially expressed genes (according toPvalue) were verified in new pools ofin vivo- andin vitro-cultured blastocysts, using quantitative real-time PCR. Most (10 out of 16) are involved in transcription and translation events, suggesting that the reason whyin vitro-derived embryos are of inferior quality compared within vivo-derived embryos is due to a deficiency of the machinery associated with transcription and translation.

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Screening of Differentially Expressed Microsporidia Genes from Nosema ceranae Infected Honey Bees by Suppression Subtractive Hybridization

Insects ◽

10.3390/insects11030199 ◽

2020 ◽

Vol 11 (3) ◽

pp. 199

Author(s):

Zih-Ting Chang ◽

Chong-Yu Ko ◽

Ming-Ren Yen ◽

Yue-Wen Chen ◽

Yu-Shin Nai

Keyword(s):

Gene Expression ◽

Real Time ◽

Differentially Expressed Genes ◽

Honey Bees ◽

Physiological Mechanism ◽

Subtractive Hybridization ◽

Infection Process ◽

Nosema Ceranae ◽

Differentially Expressed ◽

Suppressive Subtractive Hybridization

The microsporidium Nosema ceranae is a high prevalent parasite of the European honey bee (Apis mellifera). This parasite is spreading across the world into its novel host. The developmental process, and some mechanisms of N. ceranae-infected honey bees, has been studied thoroughly; however, few studies have been carried out in the mechanism of gene expression in N. ceranae during the infection process. We therefore performed the suppressive subtractive hybridization (SSH) approach to investigate the candidate genes of N. ceranae during its infection process. All 96 clones of infected (forward) and non-infected (reverse) library were dipped onto the membrane for hybridization. A total of 112 differentially expressed sequence tags (ESTs) had been sequenced. For the host responses, 20% of ESTs (13 ESTs, 10 genes, and 1 non-coding RNA) from the forward library and 93.6% of ESTs (44 ESTs, 28 genes) from the reverse library were identified as differentially expressed genes (DEGs) of the hosts. A high percentage of DEGs involved in catalytic activity and metabolic processes revealed that the host gene expression change after N. ceranae infection might lead to an unbalance of physiological mechanism. Among the ESTs from the forward library, 75.4% ESTs (49 ESTs belonged to 24 genes) were identified as N. ceranae genes. Out of 24 N. ceranae genes, nine DEGs were subject to real-time quantitative reverse transcription PCR (real-time qRT-PCR) for validation. The results indicated that these genes were highly expressed during N. ceranae infection. Among nine N. ceranae genes, one N. ceranae gene (AAJ76_1600052943) showed the highest expression level after infection. These identified differentially expressed genes from this SSH could provide information about the pathological effects of N. ceranae. Validation of nine up-regulated N. ceranae genes reveal high potential for the detection of early nosemosis in the field and provide insight for further applications.

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Microarray screening of suppression subtractive hybridization-PCR cDNA libraries identifies novel RNAs regulated by dehydration in the rat supraoptic nucleus

Physiological Genomics ◽

10.1152/physiolgenomics.00229.2005 ◽

2006 ◽

Vol 24 (2) ◽

pp. 163-172 ◽

Cited By ~ 17

Author(s):

Mohamed T. Ghorbel ◽

Greig Sharman ◽

Charles Hindmarch ◽

Kevin G. Becker ◽

Tanya Barrett ◽

...

Keyword(s):

General Circulation ◽

Supraoptic Nucleus ◽

Subtractive Hybridization ◽

Biologically Active ◽

Differentially Expressed ◽

Cdna Libraries ◽

Suppressive Subtractive Hybridization ◽

Cdna Clones ◽

Microarray Screening ◽

Mechanistic Basis

The magnocellular neurons (MCNs) of the supraoptic nucleus (SON) and paraventricular nucleus (PVN) of the hypothalamus are the principal site of biosynthesis of prepropeptide precursor of the antidiuretic hormone vasopressin (VP). This precursor is processed during anterograde axonal transportation to terminals in the posterior pituitary gland, where biologically active VP is stored until release into the general circulation in response to physiological activation of the SON by osmotic cues. By binding to V2-type receptors located in the kidney, VP decreases the amount of water lost in urine. Osmotic activation of the SON is accompanied by a dramatic morphological and functional remodeling. We have sought to understand the mechanistic basis of this plasticity in terms of the differential expression of genes. To identify such genes, we adopted an unbiased global approach based on suppressive subtractive hybridization-polymerase chain reaction (SSH-PCR) Using this method, we generated libraries of clones putatively differentially expressed in control vs. dehydrated SON. To rapidly screen these libraries, 1,152 clones were subjected to microarray analysis, resulting in the identification of 459 differentially expressed transcripts. cDNA clones corresponding to 56 of these RNAs were sequenced, revealing many of them to be novel expressed sequence tags (ESTs). Four transcripts were shown by in situ hybridization (ISH) to be significantly up- or downregulated in the SON after dehydration. These genes may represent novel effectors or mediators of SON physiological remodeling.

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Suppressive subtractive hybridization and differential screening identified genes differentially expressed in yeast and mycelial forms of

FEMS Microbiology Letters ◽

10.1016/j.femsle.2004.07.033 ◽

2004 ◽

Vol 238 (1) ◽

pp. 175-181 ◽

Cited By ~ 1

Author(s):

N DOGRA ◽

C BREUIL

Keyword(s):

Subtractive Hybridization ◽

Differential Screening ◽

Differentially Expressed ◽

Suppressive Subtractive Hybridization

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Isolation, identification and expression profile of fourteen differentially expressed sequence tags in the longissimus dorsi muscle tissues from Meishan, Meishan×Large White cross and Large White pigs

Chinese Journal of Agricultural Biotechnology ◽

10.1017/s1479236207001209 ◽

2007 ◽

Vol 4 (1) ◽

pp. 9-14

Author(s):

Liu Yong-Gang ◽

Xiong Yuan-Zhu ◽

Zuo Bo ◽

Jiang Si-Wen ◽

Deng Chang-Yan ◽

...

Keyword(s):

Expression Profile ◽

Differential Display ◽

Expressed Sequence Tags ◽

Differentially Expressed ◽

Longissimus Dorsi ◽

Large White ◽

Longissimus Dorsi Muscle ◽

Dorsi Muscle ◽

Muscle Tissues ◽

Expressed Sequence

AbstractIn order to detect the molecular mechanism of heterosis in pigs, an mRNA differential display (DD) technique was performed to investigate the differences in gene expression in the longissimus dorsi muscle tissues from Meishan, Meishan×Large White cross and Large White pigs. Fourteen expressed sequence tags (ESTs), differentially expressed between the hybrid and purebred pigs, were isolated and identified through semi-quantitative reverse transcriptase-polymerase chain reaction (RT-PCR). Nucleotide sequence analysis revealed that the 14 ESTs are not homologous to any of the known genes or ESTs. These novel ESTs were then deposited in the GenBank database. Tissue expression profile analysis showed that the ESTs were expressed in most tissues, including heart, spleen, liver, kidney, small intestine, ovary and lung, and this also implied that these genes must be important for the life process. Our results indicate the diversity of differential display of genes between the hybrids and purebreds in the Meishan×Large White cross combination. Results also suggest that heterosis in pigs might be derived from the differential expression of many indispensable genes in specific life phases.

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