High-throughput Gene and Protein Expression Analysis in Pulp Biologic Research: Review

Pääkkönen, Virve; Tjäderhane, Leo

doi:10.1016/j.joen.2009.10.016

Cited by 15 publications

(13 citation statements)

References 75 publications

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“…Tooth devolepment, nourishment,defence,sensitivity,regeneration and repair are main functions of pulp. [21]Pakkonen et.al [22] analysed the gene and protein expression of pulp tissues from sound and carious human 1073 teeth using c DNA microassay and 2-D gel electrophoresis to evaluate their usefulness in pulp biology .c DNA microarray reveals several differentiatally expressed genes with a high expression in both tissues.2-D electrophoresis followed by MS/MS technique helped in identifying 96 proteins. McLachalan et.al [23] analyzed oligonucleotide microarrays containing ~ 15000 human sequences using probe total RNA from both normal and healthy tooth.445 genes with 2-fold or greater difference in expression level with 85 genes abundant in health and 360 abundant in disease.…”

Section: Dental Soft Tissue Proteomics:-mentioning

confidence: 99%

Proteomics in Dentistry- A Review.

Alexander¹

2018

IJAR

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Section: Dental Soft Tissue Proteomics:-mentioning

confidence: 99%

Proteomics in Dentistry- A Review.

Alexander¹

2018

IJAR

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“…Several experimental techniques are available for molecular profiling studies such as DNA microarray, differential display, serial analysis of gene expression, massive parallel signature sequencing, and suppression subtractive hybridization [1]. Although useful, shortcomings with these systems are often encountered especially in input DNA, RNA, or proteins from pure population [2].…”

Section: Introductionmentioning

confidence: 99%

Laser Capture Microdissection in Dentistry

Chokechanachaisakul

Kaneko

Okiji

et al. 2010

International Journal of Dentistry

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Laser capture microdissection (LCM) allows for the microscopic procurement of specific cell types from tissue sections that can then be used for gene expression analysis. According to the recent development of the LCM technologies and methodologies, the LCM has been used in various kinds of tissue specimens in dental research. For example, the real-time polymerase-chain reaction (PCR) can be performed from the formaldehyde-fixed, paraffin-embedded, and immunostained sections. Thus, the advance of immuno-LCM method allows us to improve the validity of molecular biological analysis and to get more accurate diagnosis in pathological field in contrast to conventional LCM. This paper is focused on the presentation and discussion of the existing literature that covers the fields of RNA analysis following LCM in dentistry.

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“…The SSH procedure soon expanded to probe differences in prokaryotic chromosomal features (Agron et al 2002;Mokady et al 2005). Today SSH is commonly used in the basic science research of a diverse group of fields such as embryology (Luo et al 2009), botany (Hassan et al 2010), agricultural sciences (Stevens and van Elsas 2010;Oliver et al 2009), cancer biology (Sahin et al 2009), parasitology (Hao et al 2009;Ittiprasert et al 2010), neurology (Pottiez et al 2009), immunology (Feng et al 2009), microbiology (Gerrish et al 2010;Silveira et al 2010) and dentistry (Pääkkönen and Tjäderhane 2010).…”

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confidence: 99%

Tailed pooled suppression subtractive hybridization (PSSH) adaptors do not alter efficiency

Gerrish

Gill

2010

Antonie van Leeuwenhoek

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Suppression Subtractive Hybridization (SSH) and its derivative, Pooled Suppression Subtractive hybridization (PSSH), are powerful tools used to study variances larger than ~100 bp in prokaryotic genome structure. The initial steps involve ligating an oligonucleotide of known sequence (the "adaptor") to a fragmented genome to facilitate amplification, subtraction and downstream sequencing. SSH results in the creation of a library of unique DNA fragments which have been traditionally analyzed via Sanger sequencing. Numerous next generation sequencing technologies have entered the market yet SSH is incompatible with these platforms. This is due to the high level of sequence conservation of the oligonucleotide used for SSH. This rigid adherence is partly because it has yet to be determined if alteration of this oligonucleotide will have a deleterious impact on subtraction efficiency. The subtraction occurs when non-unique fragments are inhibited by a secondary self-pairing structure which requires exact nucleotide sequence. We determine if appending custom sequence to the 5' terminal ends of these oligonucleotides during the nested PCR stages of PSSH will reduce subtraction efficiency. We compare a pool of ten S. aureus clinical isolates with a standard PSSH and custom tailed-PSSH. We detected no statistically significant difference between their subtraction efficiencies. Our observations suggest that the adaptor's terminal ends may be labeled during the nested PCR step. This produces libraries labeled with custom sequence. This does not lead to loss of subtraction efficiency and would be invaluable for groups wishing to combine SSH or PSSH with their own downstream applications, such as a high throughput sequencing platform.

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High-throughput Gene and Protein Expression Analysis in Pulp Biologic Research: Review

Cited by 15 publications

References 75 publications

Proteomics in Dentistry- A Review.

Proteomics in Dentistry- A Review.

Laser Capture Microdissection in Dentistry

Tailed pooled suppression subtractive hybridization (PSSH) adaptors do not alter efficiency

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