Rational primer design greatly improves differential display-PCR (DD-PCR)

Exploring the impact of nano-Se and nano-clay feed supplements on interleukin genes, immunity and growth rate in European Sea Bass (Dicentrarchus labrax)

This study aimed to investigate the effects of adding Nano-Selenium (NSe) and Nano-clay (NC) as feed supplements on European Sea Bass (Dicentrarchus labrax). Two separate experiments were conducted, one with NC and the other with NSe. Each experiment consisted of four sub-groups with varying concentrations of NC or NSe. The expression levels of five immune-related genes (TNF-α, TNF-β, IL-2, IL-6 and IL-12) were measured using Real-time Quantitative PCR (Rt-PCR) Assay. The results showed an increase in the expression of interleukins (IL-2, IL-6 and IL-12) and pro-inflammatory cytokines (TNF-α and TNF-β) after exposure to NC and NSe. TNF-α gene expression was significantly higher with both 1 mg and 10 mg concentrations of NC and NSe. TNF-β gene expression was highest with the 5 mg concentration of NC. The concentrations of 1 mg and 10 mg for NC, and 1 mg, 5 mg, and 10 mg for NSe, led to the highest (p < 0.05) levels of IL-2 expression compared to the control. Similar trends were observed for IL-6 and IL-12 gene expression. Understanding the impact of these concentrations on gene expression, growth rate, biochemical indices, and antioxidant status can provide valuable insights into the potential applications of NC and NSe supplements on European Sea Bass.

DDRT-PCR approaches applied for preeminent results in the isolation of DETs from fish brain tissues

Differential Display (DD) is a technique widely used in studies of differential expression. Most of these analyses, especially those involving fish species, are restricted to species from North America and Europe or to commercial species, as salmonids. Studies related to South American fish species are underexplored. Thus, the present work aimed to describe DD technique modifications in order to improve outcomes related to the isolation of DETs (Differentially Expressed Transcripts), using Leporinus macrocephalus, a large commercially exploited South American species, as a fish design. Different DDRT-PCR approaches were applied to brain samples and the products of the reactions were analyzed on 6% polyacrylamide gels stained with 0.17% Silver Nitrate (AgNO3). The use of PCR reactions under high stringency conditions and longer oligonucleotides based on VNTR (Variable Number of Tandem Repeats) core sequences led to better results when compared to low stringency PCR conditions and the use of decamer oligonucleotides. The improved approach led to the isolation of differentially expressed transcripts on adult males and females of L. macrocephalus. This study indicates that some modifications on the DDRT-PCR method can ensure isolation of DETs from different fish tissues and the development of robust data related to this approach.

Multi-targeted priming for genome-wide gene expression assays

BACKGROUND

Complementary approaches to assaying global gene expression are needed to assess gene expression in regions that are poorly assayed by current methodologies. A key component of nearly all gene expression assays is the reverse transcription of transcribed sequences that has traditionally been performed by priming the poly-A tails on many of the transcribed genes in eukaryotes with oligo-dT, or by priming RNA indiscriminately with random hexamers. We designed an algorithm to find common sequence motifs that were present within most protein-coding genes of Saccharomyces cerevisiae and of Neurospora crassa, but that were not present within their ribosomal RNA or transfer RNA genes. We then experimentally tested whether degenerately priming these motifs with multi-targeted primers improved the accuracy and completeness of transcriptomic assays.

RESULTS

We discovered two multi-targeted primers that would prime a preponderance of genes in the genomes of Saccharomyces cerevisiae and Neurospora crassa while avoiding priming ribosomal RNA or transfer RNA. Examining the response of Saccharomyces cerevisiae to nitrogen deficiency and profiling Neurospora crassa early sexual development, we demonstrated that using multi-targeted primers in reverse transcription led to superior performance of microarray profiling and next-generation RNA tag sequencing. Priming with multi-targeted primers in addition to oligo-dT resulted in higher sensitivity, a larger number of well-measured genes and greater power to detect differences in gene expression.

CONCLUSIONS

Our results provide the most complete and detailed expression profiles of the yeast nitrogen starvation response and N. crassa early sexual development to date. Furthermore, our multi-targeting priming methodology for genome-wide gene expression assays provides selective targeting of multiple sequences and counter-selection against undesirable sequences, facilitating a more complete and precise assay of the transcribed sequences within the genome.

LOX: inferring Level Of eXpression from diverse methods of census sequencing

SUMMARY

We present LOX (Level Of eXpression) that estimates the Level Of gene eXpression from high-throughput-expressed sequence datasets with multiple treatments or samples. Unlike most analyses, LOX incorporates a gene bias model that facilitates integration of diverse transcriptomic sequencing data that arises when transcriptomic data have been produced using diverse experimental methodologies. LOX integrates overall sequence count tallies normalized by total expressed sequence count to provide expression levels for each gene relative to all treatments as well as Bayesian credible intervals.

AVAILABILITY

http://www.yale.edu/townsend/software.html

Identification of sexually dimorphic gene expression in brain tissue of the fish Leporinus macrocephalus through mRNA differential display and real time PCR analyses

Differentially expressed genes in males and females of vertebrate species generally have been investigated in gonads and, to a lesser extent, in other tissues. Therefore, we attempted to identify sexually dimorphic gene expression in the brains of adult males and females of Leporinus macrocephalus, a gonochoristic fish species that presents a ZZ/ZW sex determination system, throughout a comparative analysis using differential display reverse transcriptase-PCR and real-time PCR. Four cDNA fragments were characterized, representing candidate genes with differential expression between the samples. Two of these fragments presented no significant identity with previously reported gene sequences. The other two fragments, isolated from male specimens, were associated to the gene that codes for the protein APBA2 (amyloid beta (A4) precursor protein-binding, family A, member 2) and to the Rab 37 gene, a member of the Ras oncogene family. The overexpression of these genes has been associated to a greater production of the beta-amyloid protein which, in turns, is the major factor that leads to Alzheimer's disease, and to the development of brain-tumors, respectively. Quantitative RT-PCR analyses revealed a higher Apba2 gene expression in males, thus validating the previous data on differential display. L. macrocephalus may represent an interesting animal model to the understanding of the function of several vertebrate genes, including those involved in neurodegenerative and cancer diseases.

The role of TGF-beta superfamily during T cell development: new insights

Members of the transforming growth factor beta (TGF-beta) superfamily are soluble factors that regulate a variety of functional responses including proliferation, differentiation, apoptosis and cell cycle, among others, depending not only on the cell type and its differentiation state, but also on the milieu of cytokines present. All three members of this superfamily: TGF-betas, bone morphogenetic proteins (BMPs) and Activins, have been shown to be expressed in the thymus suggesting their potential role as regulators of the T lymphocyte differentiation process. Although initial reports described the role of TGF-beta in controlling specific checkpoints during thymocyte development, recent data has provided new evidence on the role of BMPs and Activins in this process. This review provides new insights on the function of members of the TGF-beta superfamily at different stages of thymocyte development.

The application of differential display as a gene profiling tool

Differential display is an effective expression profiling tool which was first introduced in 1992. The original technique is discussed along with modifications that have been described over the last several years. A highly reproducible, semihigh-throughput differential display protocol used in our laboratories is described along with an example of its successful application using pancreatic cancer cells. In addition to the work performed in our laboratories, several examples of successful applications of differential display under a number of scenarios are reviewed. Differential display is one of several expression profiling technologies available and is compared with some of them. The future of differential display remains bright and is as applicable today as it was in 1992.

Differential display analysis of gene expression in two immunologically distinct strains of Eimeria maxima

Gene expression during sporulation and sporozoite excystation of two strains of Eimeria maxima was analyzed using the mRNA differential display technique. The two strains, the Guelph strain (GS) and a single sporocyst-derived strain (M6) from Florida, have been shown to be immunologically distinct. We isolated and cloned a 453-bp complimentary DNA (cDNA) fragment (GS-453) found only in GS sporozoites. In GS, this mRNA begins to be expressed during the earliest stages of oocyst sporulation and is continuously expressed up to and including in the excysted sporozoite. In all Northern blots, digoxigenin (DIG)-labeled GS-453 probe recognized an mRNA of approximately 1.6 kb from GS but not from RNA of M6. Southern blots using various endonucleases and probed with DIG-labeled GS-453 demonstrated that the genomes of both strains contained sufficiently similar sequences to permit hybridization with the probe, but the pattern of hybridization differed between the two strains. Extensive searches of the GenBank, European Molecular Biology Laboratory, and various apicomplexan expressed sequence tag databases using the DNA or inferred amino acid sequences of GS-453 cDNA clone did not identify similarity to any existing sequences.

FIGC, a novel FGF-induced ubiquitin-protein ligase in gastric cancers

We have previously shown that fibroblast growth factor receptor 2 (FGFR2) plays an important role in gastric carcinogenesis. In this study, we have used a differential display approach to identify basic fibroblast growth factor (bFGF)-inducible genes in gastric cancer cells. Here, we report that one of these genes is predicted to encode a RING finger protein, designated FIGC. The FIGC gene was found to encode a polypeptide of 381 amino acids with a novel RING finger module at the NH2-terminus and the COOH-terminal proline-rich region. Using an in vitro ubiquitination assay with recombinant protein, we demonstrate that FIGC has intrinsic E3 ubiquitin ligase activity and promotes ubiquitination. Our data indicate that FIGC upregulation in response to bFGF in gastric cancer might be implicated in carcinogenesis through dysregulation of growth modulator.

Identification of hypothalamic genes implicated in the development of obesity in Psammomys obesus using differential display PCR

The hypothalamus is a key central controller of energy homeostasis and is the source and/or site of action of many neuropeptides involved in this process. The aim of this study was to isolate hypothalamic genes differentially expressed between lean and obese Psammomys obesus, a polygenic animal model of obesity and type 2 diabetes. Differential display PCR was used to compare hypothalamic gene expression profiles of lean and healthy, obese and hyperinsulinemic, and obese, diabetic P. obesus in both the fed and fasted states. We conducted differential display with 180 separate primer combinations to amplify approximately 9,000 expressed transcripts. Sixty differentially expressed bands were excised. Taqman PCR was performed on 36 of these transcripts to confirm differential gene expression in a larger sample population. Of these 36 transcripts, 9 showed homology to known genes, and 27 were considered to be novel sequences. Gene expression profiles for two of these genes are presented here. In conclusion, differential display PCR was successfully used to isolate several transcripts that may be involved in the central regulation of energy balance. We are currently conducting numerous studies to further investigate the role of these genes in the development of obesity in P. obesus.

Optimization of differential display polymerase chain reaction as a bioindicator for the cladoceran Daphnia magna

Research on toxicant-responsive genes is providing new and important bioindicators for environmental biologists. Identifying genes whose expression is modulated by toxicant exposure provides important clues into the mechanisms underlying toxicity. In addition, toxicant-responsive genes can be developed as molecular end points that are likely to be sensitive tools for environmental assessment. Differential display polymerase chain reaction (ddPCR) is a useful approach for screening and analyzing the expression of genes. A ddPCR protocol was optimized to investigate gene expression in the cladoceran Daphnia magna. The modified protocol requires submicrogram quantities of total RNA (from <10 animals) and utilizes a sensitive fluorescent tagging system. By reverse-transcribing total RNA with arbitrary 18-nucleotide primers and PCR-amplifying the cDNA using the same arbitrary primers under low-stringency conditions, reproducible and consistent ddPCR profiles were generated. Minimal variability was introduced by reaction differences or biological variability. A trial stress (starvation) was found to generate modest differences in the ddPCR profiles. This technique promises to significantly advance knowledge regarding gene expression during toxicant insult. Furthermore, this represents the first step in the development of a novel gene fingerprinting technique that can be applied to any compound and organism of interest.

The developmentally regulated expression of Twisted gastrulation reveals a role for bone morphogenetic proteins in the control of T cell development

The evolutionarily conserved, secreted protein Twisted gastrulation (Tsg) modulates morphogenetic effects of decapentaplegic (dpp) and its orthologs, the bone morphogenetic proteins 2 and 4 (BMP2/4), in early Drosophila and vertebrate embryos. We have uncovered a role for Tsg at a much later stage of mammalian development, during T cell differentiation in the thymus. BMP4 is expressed by thymic stroma and inhibits the proliferation of CD4(-)CD8(-) double-negative (DN) thymocytes and their differentiation to the CD4(+)CD8(+) double-positive (DP) stage in vitro. Tsg is expressed by thymocytes and up-regulated after T cell receptor signaling at two developmental checkpoints, the transition from the DN to the DP and from the DP to the CD4(+) or CD8(+) single-positive stage. Tsg can synergize with the BMP inhibitor chordin to block the BMP4-mediated inhibition of thymocyte proliferation and differentiation. These data suggest that the developmentally regulated expression of Tsg may allow thymocytes to temporarily withdraw from inhibitory BMP signals.

New intra-renal graft genes associated with tolerance or rejection

BACKGROUND

Recipient type mononuclear cells infiltrating kidney allografts have different phenotypes and functions according to the fate of the graft. We hypothesized that different genetic programs were involved in rejected or accepted tissues and thus, transcripts that correlated with the clinical status could be identified by a differential expression strategy. This strategy was applied to miniature swine class II matched, class I disparate kidney grafts, which are accepted in recipient animals treated for 12 days with Cyclosporin A (CsA).

METHODS

The mRNA differential display RT-PCR technique (DDRT-PCR) was used to detect clinical status-specific transcripts. cDNA templates for this analysis were derived from biopsies of accepted (CsA treated) and rejected (untreated) kidney grafts 8 days post-transplantation.

RESULTS

A first screening procedure identified 23 PCR products differentially amplified in either tolerant or rejector samples. Nucleotide sequence of these partial transcripts showed that 11 out of 23 (48%) sequences had unknown open reading frames while 12 had substantial homology to known sequences. To validate the approach, rejection-associated (RA) cDNA 1 (RA-1) was characterized further. The results indicated that RA-1 is the porcine equivalent of secreted protein acidic and rich in cysteine (SPARC). Expression studies demonstrated that upregulation of SPARC gene transcription preceded other indicators of kidney dysfunction and correlated with the extent of graft infiltration.

CONCLUSION

DDRT-PCR appears to be a powerful technique to identify genes differentially expressed in grafted tissues that correlate with tolerance or rejection. One of the gene transcripts identified through this method, SPARC, may be a reliable marker of tissue injury consequent to cellular infiltration and rejection.

A critical evaluation of differential display as a tool to identify genes involved in legume nodulation: looking back and looking forward

Screening for differentially expressed genes is a straightforward approach to study the molecular basis of a biological system. In the last 10 years, differential screening technology has evolved rapidly and currently high-throughput tools for genome-wide transcript profiling, such as expressed sequence tags and microarray analysis, are becoming widely available. Here, an overview of this (r)evolution is given with emphasis on the differential display method, which for many years has been the preferred technique of scientists in diverse fields of research. Differential display has also been the method of choice for the identification of genes involved in the symbiotic interaction between Azorhizobium caulinodans and Sesbania rostrata. The advantages with respect to tissue specificity of this particular model system for legume nodulation and the results of a screening for early nodulation-related genes have been considered in the context of transcriptome analyses in other rhizobium-legume interactions.

Applications of differential-display reverse transcription-PCR to molecular pathogenesis and medical mycology

The host-fungus interaction is characterized by changes in gene expression in both host and pathogen. Differential-display reverse transcription PCR (DDRT-PCR) is a PCR-based method that allows extensive analysis of gene expression among several cell populations. Several limitations and drawbacks to this procedure have now been addressed, including the large number of false-positive results and the difficulty in confirming differential expression. Modifications that simplify the reaction time, allow the use of minute quantities of RNA, or address unusual species- or gene-specific sequences have been reported. DDRT-PCR has been used to address biological questions in mammalian systems, including cell differentiation, cell activation, cell stress, and identification of drug targets. In microbial pathogenesis and plant pathogenesis, DDRT-PCR has allowed the identification of virulence factors, genes involved in cell death, and signaling genes. In Candida albicans, DDRT-PCR studies identified TIF-2, which may play a role in the upregulation of phospholipases, and the stress-related genes, CIP1 and CIP2. In Histoplasma capsulatum and C. albicans, genes involved in the host-pathogen interaction, including a member of the 100-kDa family in Histoplasma and an ALS and 14-3-3 gene in Candida, were potentially identified by DDRT-PCR. Although very few reports have been published in medical mycology, studies in mammalian, nonfungal microbial, and plant pathogen systems are easily applied to basic questions in fungal pathogenesis and antifungal therapeutics.

Applications of differential-display reverse transcription-PCR to molecular pathogenesis and medical mycology

The host-fungus interaction is characterized by changes in gene expression in both host and pathogen. Differential-display reverse transcription PCR (DDRT-PCR) is a PCR-based method that allows extensive analysis of gene expression among several cell populations. Several limitations and drawbacks to this procedure have now been addressed, including the large number of false-positive results and the difficulty in confirming differential expression. Modifications that simplify the reaction time, allow the use of minute quantities of RNA, or address unusual species- or gene-specific sequences have been reported. DDRT-PCR has been used to address biological questions in mammalian systems, including cell differentiation, cell activation, cell stress, and identification of drug targets. In microbial pathogenesis and plant pathogenesis, DDRT-PCR has allowed the identification of virulence factors, genes involved in cell death, and signaling genes. In Candida albicans, DDRT-PCR studies identified TIF-2, which may play a role in the upregulation of phospholipases, and the stress-related genes, CIP1 and CIP2. In Histoplasma capsulatum and C. albicans, genes involved in the host-pathogen interaction, including a member of the 100-kDa family in Histoplasma and an ALS and 14-3-3 gene in Candida, were potentially identified by DDRT-PCR. Although very few reports have been published in medical mycology, studies in mammalian, nonfungal microbial, and plant pathogen systems are easily applied to basic questions in fungal pathogenesis and antifungal therapeutics.

Effect of primer purity on the banding patterns of differential display polymerase chain reaction

Differential display polymerase chain reaction (DD-PCR) is a novel method for identification of differentially expressed genes by comparative display of arbitrarily amplified cDNA subsets. The basic principle of the DD-PCR is to systematically amplify messenger RNAs and then distribute their 3' termini on a denaturing polyacrylamide gel. Although this technology has been successfully applied in a large number of studies, few novel genes of interest have been identified, suggesting that the method needs further improvement. We discovered that primer purity is crucial. We show that by purifying primers using reverse-phase high-performance liquid chromatography, sampling of differentially expressed genes can be greatly enhanced, and relevant genes can be isolated. Using these purified primers in DD-PCR, when compared with the unpurified primers, it should be possible to identify threefold to fourfold differences in expression or differential expression in a fraction of the cell population.

Limitations of differential display

Since its original description, differential display PCR (DD-PCR) has been extensively used in attempts to identify novel genes under a variety of circumstances. Despite its widespread use, however, few novel genes of interest have been identified. In the present study we describe a set of experiments examining reasons for failure of differential display. Evidence is presented that aberrant priming at both the 5' and 3' ends results in competition in the PCR, precluding detection of messages other than those which are abundantly expressed. Appropriate calculations are discussed which indicate this was predictable and unlikely to be overcome. While DD may be successfully applied in some settings, the evidence indicates that only abundantly expressed messages can be detected. This limitation is emphasized.

Differential display of mRNA

Differential display of mRNA (DD) is a technique in which mRNA species expressed by a cell population are reverse transcribed and then amplified by many separate polymerase chain reactions (PCR). PCR primers and conditions are chosen so that any given reaction yields a limited number of amplified cDNA fragments, permitting their visualization as discrete bands following gel electrophoresis. This robust and relatively simple procedure allows identification of genes that are differentially expressed in different cell populations. Here we review DD including some recent modifications, and compare it with other techniques for analyzing differential mRNA expression.

Efficient reamplification of differential display products by transient ligation and thermal asymmetric PCR

A new method for specific reamplification of DDRT-PCR products is presented. After transient ligation of the primary DDRT-PCR fragments into a T-vector, the cDNAs of interest were reamplified by hemi-nested PCR and thermally asymmetric cycles. In contrast to the originally described protocol, this method of reamplification is specific, sensitive, reproducibly gives a high yield of DNA and allows direct sequencing of the reamplified product without purification or cloning.