Quantitative RT-PCR Data Research Articles

In silico characterization and expression analysis of the multigene family encoding the Bowman–Birk protease inhibitor in soybean

The Bowman-Birk (BBI) protease inhibitors can be used as source of sulfur amino acids, can regulate endogenous protease activity during seed germination and during the defense response of plants to pathogens. In soybean this family has not been fully described. The goal of this work was to characterize in silico and analyze the expression of the members of this family in soybean. We identified 11 potential BBI genes in the soybean genome. In each one of them at least a characteristic BBI conserved domain was detected in addition to a potential signal peptide. The sequences have been positioned in the soybean physical map and the promoter regions were analyzed with respect to known regulatory elements. Elements related to seed-specific expression and also to response to biotic and abiotic stresses have been identified. Based on the in silico analysis and also on quantitative RT-PCR data it was concluded that BBI-A, BBI-CII and BBI-DII are expressed specifically in the seed. The expression profiles of these three genes are similar along seed development. Their expressions reach a maximum in the intermediate stages and decrease as the seed matures. The BBI-DII transcripts are the most abundant ones followed by those of BBI-A and BBI-CII.

Mechanisms regulating the chamber‐specific structure of cardiac ATP‐sensitive potassium (KATP) channels

KATP channels are widely expressed in cardiac myocytes where they act as key sensors of cell metabolism during metabolic stress. All KATP channels share the same architecture—a K+ channel pore (Kir6.1 or Kir6.2) combines with a sulfonylurea receptor (SUR1, SUR2A or SUR2B) to form a functional channel. We discovered that cardiac KATP structure is chamber-specific. Atrial KATP is made up of SUR1 and Kir6.2 while ventricular KATP contains SUR2A and Kir6.2. Quantitative RT-PCR data demonstrate that SUR1 subunit mRNA expression is greater in mouse atrium compared with ventricle, while SUR2 mRNA is greater in the ventricle. This observation suggests that the chamber-specific KATP composition is transcriptionally controlled. We have now identified two factors that regulate the expression of SURx subunits. Treatment of HL-1 cells with the HDAC inhibitor, trichostatin A, causes a decrease in SUR1 mRNA with a concomitant increase in SUR2 mRNA. Similarly, treatment with glycolytic inhibitor, 2-deoxyglucose, causes a coordinated decrease in SUR1 and increase in SUR2 expression. Taken together, the data show that the distribution of SURx transcripts correlates with chamber-specific KATP channel structure. Moreover, we have identified two factors that modulate SURx subunit expression and present data suggesting that SUR1 and SUR2 expression is coordinated such that only one isoform is dominant.

Loss of Skywalker Reveals Synaptic Endosomes as Sorting Stations for Synaptic Vesicle Proteins

Exchange of proteins at sorting endosomes is not only critical to numerous signaling pathways but also to receptor-mediated signaling and to pathogen entry into cells; however, how this process is regulated in synaptic vesicle cycling remains unexplored. In this work, we present evidence that loss of function of a single neuronally expressed GTPase activating protein (GAP), Skywalker (Sky) facilitates endosomal trafficking of synaptic vesicles at Drosophila neuromuscular junction boutons, chiefly by controlling Rab35 GTPase activity. Analyses of genetic interactions with the ESCRT machinery as well as chimeric ubiquitinated synaptic vesicle proteins indicate that endosomal trafficking facilitates the replacement of dysfunctional synaptic vesicle components. Consequently, sky mutants harbor a larger readily releasable pool of synaptic vesicles and show a dramatic increase in basal neurotransmitter release. Thus, the trafficking of vesicles via endosomes uncovered using sky mutants provides an elegant mechanism by which neurons may regulate synaptic vesicle rejuvenation and neurotransmitter release.

Molecular characterization, expression pattern, and functional analysis of the OsIRL gene family encoding intracellular Ras-group-related LRR proteins in rice

Leucine-rich repeat proteins constitute a large gene family and play important roles in plant growth and development. Among them, Arabidopsis PIRL is a plant-specific class of intracellular Ras-group-related leucine-rich repeat proteins. In this study, we identified eight homologues of PIRLs in rice and designated them as OsIRL proteins. We described the gene structures, chromosome localizations, protein motifs, and phylogenetic relationships of the OsIRL gene family. The expression profiles of OsIRL genes were analyzed throughout the entire rice life cycle, along with light and three hormone stress conditions, using quantitative RT-PCR and microarray data. All OsIRL genes were expressed in at least one experimental stage and exhibited divergent expression patterns, with several genes showing preferential expression at specific stages. OsIRL4 and OsIRL5 showed higher expression levels under light compared to dark. OsIRL4 and OsIRL7 exhibited significant differential expression in response to hormone treatments. Six T-DNA or Tos17 insertion lines for five individual OsIRL genes were identified and examined morphologically. The comprehensive expression profile elucidated in this investigation together with the characterized insertion lines will provide a solid foundation for in-depth dissection of OsIRL functions.

Human brain weight is correlated with expression of the ‘housekeeping genes’ beta-2-microglobulin (β2M) and TATA-binding protein (TBP)

Many variables affect mRNA measurements in post mortem human brain tissue. Brain weight has not hitherto been considered to be such a factor. This study examined whether there is any relationship between brain weight and mRNA abundance. We investigated quantitative real-time RT-PCR data for five 'housekeeping genes' using the 104 adult brains of the Stanley Microarray Consortium series. Eleven data sets were analysed, from cerebellum, hippocampus, and anterior cingulate cortex. We used a specified sequence of correlations, partial correlations and multiple regression analyses. Brain weight correlated with the 'raw' (i.e. non-normalized) data for two mRNAs, β2-microglobulin and TATA-binding protein, measured in cerebellum and hippocampus, respectively. In hippocampus, the geometric mean of three housekeeping gene transcripts also correlated with brain weight. The correlations were significant after adjusting for age, sex and other confounders, and the effect of brain weight was confirmed using multiple regression. No correlations with brain weight were seen in the anterior cingulate cortex, nor for the other mRNAs examined. The findings were not anticipated; they need replication in another brain series, and a more systematic survey is indicated. In the interim, we suggest that quantitative gene expression studies in human brain should inspect for a potential influence of brain weight, especially as the affected transcripts are commonly used as reference genes for normalization purposes in studies of neurological and psychiatric disorders. The relationship of brain weight with β2-microglobulin mRNA may reflect the roles of major histocompatibility complex class I genes in synapse formation and plasticity.

MicroRNA hsa-miR-135b Regulates Mineralization in Osteogenic Differentiation of Human Unrestricted Somatic Stem Cells

Unrestricted somatic stem cells (USSCs) have been recently identified in human umbilical cord blood and have been shown to differentiate into lineages representing all 3 germ layers. To characterize microRNAs that may regulate osteogenic differentiation of USSCs, we carried out expression analysis for 157 microRNAs using quantitative RT-PCR before and after osteogenic induction (t = 0.5, 24, 72, 168, 216 h). Three microRNAs, hsa-miR-135b, hsa-miR-224, and hsa-miR-31, were consistently down-regulated during osteogenesis of USSC line 1. Hsa-miR-135b was shown to be the most profoundly down-regulated in osteogenesis of USSC line 1 and further confirmed to be down-regulated in the osteogenic differentiation of 2 additional USSC lines. Function of hsa-miR-135b in osteogenesis of USSCs was examined by retroviral overexpression, which resulted in an evident decreased mineralization, indicating that hsa-miR-135b down-regulation is functionally important for full osteogenic differentiation of USSCs. MicroRNAs have been shown to regulate negatively expression of their target gene(s). To identify putative targets of hsa-miR-135b, we performed cDNA microarray expression analysis. We selected in total 10 transcripts that were down-regulated (>or=2-fold) in response to hsa-miR-135b overexpression at day 7 and day 9 of osteogenic differentiation. The function of most of these targets in human osteogenesis is unknown and requires further investigation. Markedly, quantitative RT-PCR data showed decreased expression of osteogenic markers IBSP and Osterix, both known to be involved in bone mineralization, in osteogenesis of USSCs that overexpress hsa-miR-135b. This finding suggests that hsa-miR-135b may control osteoblastic differentiation of USSCs by regulating expression of bone-related genes.

Identification and evaluation of new reference genes in Gossypium hirsutumfor accurate normalization of real-time quantitative RT-PCR data

BackgroundNormalizing through reference genes, or housekeeping genes, can make more accurate and reliable results from reverse transcription real-time quantitative polymerase chain reaction (qPCR). Recent studies have shown that no single housekeeping gene is universal for all experiments. Thus, suitable reference genes should be the first step of any qPCR analysis. Only a few studies on the identification of housekeeping gene have been carried on plants. Therefore qPCR studies on important crops such as cotton has been hampered by the lack of suitable reference genes.ResultsBy the use of two distinct algorithms, implemented by geNorm and NormFinder, we have assessed the gene expression of nine candidate reference genes in cotton: GhACT4, GhEF1α5, GhFBX6, GhPP2A1, GhMZA, GhPTB, GhGAPC2, GhβTUB3 and GhUBQ14. The candidate reference genes were evaluated in 23 experimental samples consisting of six distinct plant organs, eight stages of flower development, four stages of fruit development and in flower verticils. The expression of GhPP2A1 and GhUBQ14 genes were the most stable across all samples and also when distinct plants organs are examined. GhACT4 and GhUBQ14 present more stable expression during flower development, GhACT4 and GhFBX6 in the floral verticils and GhMZA and GhPTB during fruit development. Our analysis provided the most suitable combination of reference genes for each experimental set tested as internal control for reliable qPCR data normalization. In addition, to illustrate the use of cotton reference genes we checked the expression of two cotton MADS-box genes in distinct plant and floral organs and also during flower development.ConclusionWe have tested the expression stabilities of nine candidate genes in a set of 23 tissue samples from cotton plants divided into five different experimental sets. As a result of this evaluation, we recommend the use of GhUBQ14 and GhPP2A1 housekeeping genes as superior references for normalization of gene expression measures in different cotton plant organs; GhACT4 and GhUBQ14 for flower development, GhACT4 and GhFBX6 for the floral organs and GhMZA and GhPTB for fruit development. We also provide the primer sequences whose performance in qPCR experiments is demonstrated. These genes will enable more accurate and reliable normalization of qPCR results for gene expression studies in this important crop, the major source of natural fiber and also an important source of edible oil. The use of bona fide reference genes allowed a detailed and accurate characterization of the temporal and spatial expression pattern of two MADS-box genes in cotton.

Expression quantitative trait loci analysis of genes in porcine muscle by quantitative real-time RT-PCR compared to microarray data

Genetic analysis of transcriptional profiling is a promising approach for identifying biological pathways and dissecting the genetics of complex traits. Here, we report on expression quantitative trait loci (eQTL) that were estimated from the quantitative real-time RT-PCR data of 276 F(2) animals and compared with eQTL identified using 74 microarrays. In total, 13 genes were selected that showed trait-dependent expression in microarray experiments and exhibited 21 eQTL. Real-time RT-PCR and microarray data revealed seven cis eQTL in total, of which one was only detected by real-time RT-PCR, one was only detected by microarray analysis, three were consistently found in overlapping intervals and two were in neighbouring intervals on the same chromosome; whereas no trans eQTL was confirmed. We demonstrate that cis regulation is a stable characteristic of individual transcripts. Consequently, a global microarray eQTL analysis of a limited number of samples can be used for exploring functional and regulatory gene networks and scanning for cis eQTL, whereas the subsequent analysis of a subset of likely cis-regulated genes by real-time RT-PCR in a larger number of samples is relevant to narrow down a QTL region by targeting these positional candidate genes. In fact, when modelling SNPs of six genes as fixed effects in the eQTL analysis, eQTL peaks were shifted downwards, experimentally confirming the impact of the respective polymorphic genes, although these SNPs were not located in the regulatory sequence and these shifts occur as a result of linkage disequilibrium in the F(2) population.

Expressed Alu repeats as a novel, reliable tool for normalization of real-time quantitative RT-PCR data

Expressed Alu repeats are a reliable, accurate and universal reference for use in RT-qPCR normalization of human genes

Transgenic expression of prothymosin alpha on zebrafish epidermal cells promotes proliferation and attenuates UVB-induced apoptosis

This study generated a transgenic zebrafish line Tg(k18:Ptmaa-RFP) with overexpression of Prothymosin alpha type a (Ptmaa) in the skin epidermis. Red fluorescence first appears very weakly in the early stage, become stronger and mainly restricted in the nuclei of the epithelial cells from 3 dpf-larvae to adult fish. However, no evident morphological abnormalities were observed. Thus, overexpression of Ptmaa alone is not sufficient to cause disorganized growths or even cancer in zebrafish skin. Molecular and histological evidences showed that Tg(k18:Ptmaa-RFP) embryos have more proliferating cells in the pelvic fins [WT: 3.92 +/- 7.15; Tg(k18:Ptmaa-RFP): 38.00 +/- 10.87] and thicker skin [WT: 10.98 +/- 1.41 mum; Tg(k18:Ptmaa-RFP): 14.02 +/- 1.32 mum], indicating that overexpression of Ptmaa can promote proliferation. On the other hand, fewer apoptotic signals were found when Tg(k18:Ptmaa-RFP) embryos were exposed to UVB. Together with quantitative RT-PCR data, we suggest that UVB-induced epidermal cell apoptosis of zebrafish larvae can be attenuated by overexpression of Ptmaa through the enhancement of transcriptions of bcl2 mRNAs. Taken together, we conclude that overexpression of Ptmaa in zebrafish epidermal cells promotes proliferation and attenuates UVB-induced apoptosis but does not cause skin cancer.

233 DIFFERENTIAL GENE EXPRESSION IN BOVINE BLASTOCYSTS AND ELONGATING CONCEPTUSES DERIVED IN VIVO OR IN VITRO

The majority of embryonic mortality in cattle occurs before maternal recognition of pregnancy at Day 16 postconception. In vitro-derived embryos exhibit a greater incidence of loss than their in vivo-derived counterparts. To better understand the causes of such embryonic loss, the aim of the current study was to compare transcript profiles of Days 7 and 13 bovine embryos derived in vitro or in vivo using the bovine Affymetrix microarray. We wanted to answer 3 questions: (1) what genes differ on Day 7 between blastocysts derived in vivo or in vitro, (2) what genes differ between Day 13 embryos derived from in vitro or in vivo embryos, and (3) what genes change between the blastocyst stage (Day 7) and the initiation of elongation (Day 13) and how are these temporal changes affected by the origin of the embryo. Day 7 bovine blastocysts were produced either in vitro by maturation, fertilization, and culture or in vivo by superovulation, AI, and nonsurgical embryo recovery. Half of the Day 7 blastocysts were snap frozen in liquid nitrogen in pools of 25 (microarray) or 10 (quantitative RT-PCR), and the other half were transferred in groups of 10 to synchronized heifers (10 recipients per group) ipsilateral to the corpus luteum and recovered on Day 13 by flushing the uterus after slaughter. Day 13 conceptuses were snap frozen individually. Three replicate pools of 25 Day 7 blastocysts and 5 Day 13 conceptuses were used for microarray analysis. Of the 24 128 probe-sets on the array, approximately 9500 genes were actively expressed in Days 7 and 13 embryos, irrespective of source. In Day 7 blastocysts, 50 genes were found to be differentially expressed (≥ 1.5-fold; P ≤ 0.05), of which 19 were up-regulated and 31 down-regulated in the in vivo compared with in vitro embryos. In Day 13 conceptuses, 288 genes were found to be differentially expressed (≥1.5-fold; P ≤ 0.05), of which 133 were up-regulated and 155 down-regulated in the in vivo compared with in vitro embryos. The comparison between Days 7 and 13 embryos revealed significant temporal changes in transcript profile, with 1806 and 909 transcripts differentially expressed in in vitro and in vivo-derived embryos, respectively. Across the 3 array comparisons between Days 7 and 13 embryos, 444 genes were consistently exclusively present in in vivo embryos, whereas 1341 were exclusively present in in vitro embryos. Array validation was done by quantitative RT-PCR analysis of fatty acid desaturase 1 (FADS1), cytochrome P450, family 51, subfamily A, polypeptide I (CYP51), and hyaluronan binding protein 2 (HABP2) genes. In conclusion, these results indicate that the origin of the blastocyst can have a significant effect on the transcript profile of the conceptus at the initiation of elongation and might be associated with the likelihood of embryo survival/loss subsequently. Further hierarchical clustering analysis and quantitative RT-PCR data will address the functional roles for certain known genes and novel candidate genes related to embryonic mortality. This work was supported by a grant (AGL2006-05616) from the Spanish Ministry of Science and Technology.

Impact of titanium ions on osteoblast-, osteoclast- and gingival epithelial-like cells

To investigate the effects of titanium (Ti) ions on the cell viability, the cell differentiation and the gene expressions related to bone resorption including Receptor Activator of NF-kappaB Ligand (RANKL) and Osteoprotegerin (OPG) in the tissues around dental implants, the osteoblast-, osteoclast-, and gingival epithelial-like cells were exposed to Ti ions. An MTS assay was carried out to evaluate the viabilities of osteoblast-like MC3T3-E1, osteoclast-like RAW264.7 and epithelial cell-like GE-1 cells. The gene expressions in these cells were analyzed by the use of RT-PCR and real-time quantitative RT-PCR. Ti ions in the concentration range 1-9 ppm had little effect on the viabilities of MC3T3-E1, RAW264.7 and GE-1, whereas 20 ppm Ti ions significantly decreased the viabilities of all cells. Analyses of RT-PCR and real-time quantitative RT-PCR data revealed that Ti ions at 9 ppm remarkably inhibited the expressions of Runx2, Osterix and type I collagen in MC3T3-E1. In RAW264.7, Ti ions showed no effects on the levels of mRNAs for TRAP and cathepsin K enhanced by RANKL. Ti ions at the range of 1-9 ppm showed no effects on the levels of mRNAs for RANKL and OPG in GE-1, while Ti ions at 9 ppm enhanced the expression of these genes in MC3T3-E1. These results, taken together, suggested that Ti ions show the biological effects, both on the viabilities of osteoblast and osteoclast and on the differentiation of either the osteoblastic or osteoclastic cells, which may influence the prognosis of dental implants.

Translational Repression of Cyclin E Prevents Precocious Mitosis and Embryonic Gene Activation during C. elegans Meiosis

Germ cells, the cells that give rise to sperm and egg, maintain the potential to recreate all cell types in a new individual. This wide developmental potential, or totipotency, is manifested in unusual tumors called teratomas, in which germ cells undergo somatic differentiation. Although recent studies have implicated RNA regulation, the mechanism that normally prevents the loss of germ cell identity remains unexplained. In C. elegans, a teratoma is induced in the absence of the conserved RNA-binding protein GLD-1. Here, we demonstrate that GLD-1 represses translation of CYE-1/cyclin E during meiotic prophase, which prevents germ cells from re-entering mitosis and inducing embryonic-like transcription. We describe a mechanism that prevents precocious mitosis in germ cells undergoing meiosis, propose that this mechanism maintains germ cell identity by delaying the onset of embryonic gene activation until after fertilization, and provide a paradigm for the possible origin of human teratomas.

Validation of Candidate Reference Genes for the Accurate Normalization of Real-Time Quantitative RT-PCR Data in Rice During Seed Development

Rice seed, a natural storage organ for starch and protein, is also an ideal bioreactor for the production of valuable proteins. Increasingly, studies focused on rice have tried to determine the functions of its genes and also to improve its yield and quality. Real-time RT-PCR is the best available choice at present for gene expression analysis due to its accuracy, sensitivity, and reproducibility. The right choice of reference genes for normalization, however, is a critical precondition for reliable results. In this study, the expression stabilities of nine commonly used housekeeping genes in rice were carefully assessed using the software geNorm. Our results showed that eIF-4a and ACT1 were the most suitable reference genes among almost all the tested samples from two rice varieties, including different temporal and spatial-specific tissues, especially in seeds at different developmental stages. In contrast, 18S and 25S rRNAs, two common reference genes, were found to have the least stable expression. Moreover, it is necessary to use multiple suitable reference genes together for normalization to get a more reliable result in temporal and spatial expression analysis during rice seed development. The validated reference genes were further relied when used to quantify the expression of several genes of interest during rice seed development.

Immune- and stress-related transcriptomic responses of Solea senegalensis stimulated with lipopolysaccharide and copper sulphate using heterologous cDNA microarrays

The sole, Solea senegalensis, is a common flatfish of Atlantic and Mediterranean waters with a high potential for aquaculture. However, its cultivation is hampered by high sensitivity to different stresses and several infectious diseases. Improving protection from pathogens and stressors is thus a key step in reaching a standardized production. Fish were exposed to lipopolysaccharide (LPS), a mimetic of bacterial infections, and copper sulphate (CuSO 4), used in aquaculture to control algae and outbreaks of infectious diseases. We employed a European flounder cDNA microarray to determine the transcriptomic responses of Senegalese sole to these exposures. Microarray analyses showed that many genes were altered in expression following both LPS and copper treatments in comparison to vehicle controls. Gene ontology analysis highlighted copper-specific induction of genes related to cellular adhesion and cell signalling, LPS-specific induction of genes related to the immune response, and a common induction of genes related to unfolded protein binding, intracellular transport/secretion and proteasome. Additionally transcripts for glutathione- S-transferases were down-regulated by LPS, and those for digestive enzymes were down-regulated by both treatments. We selected nine changing genes for absolute quantification of transcript copy numbers by real-time RT-PCR to validate microarray differential expression and to assess inter-individual variability in individual fishes. The quantitative RT-PCR data correlated highly with the microarray results. Overall, data reported provide novel insights into the molecular pathways that could mediate the immune and heavy metal stress responses in Senegalese sole and thus might have biotechnological applications in the culture of this important fish species.

Adenosine receptors and second messenger signaling pathways in rat cardiac fibroblasts

The ability of adenosine (ADO) to inhibit proliferation and protein synthesis (in particular, collagen synthesis) in cardiac fibroblasts (CF) may ameliorate adverse cardiac remodeling and fibrosis seen in heart failure patients. However, little is known about the signaling pathways that ADO may modulate in CF to alter cell phenotype. Accordingly, this study was designed to identify ADO receptors (AR) and the signaling pathways linked to them in primary cultures of adult rat CF. Quantitative RT-PCR data indicate that the mRNAs for all four known ARs (A(1)R, A(2a)R, A(2b)R, and A(3)R) are present in rat CF, with a greater prevalence of A(2) receptor subtypes. No coupling of AR to the G(q)-phospholipase C signaling pathway or to mobilization of calcium is measurable. Studies using subtype specific agents imply that the A(2a)R and A(2b)R couple to G(s)-adenylyl cyclase and A(1)R couple weakly to G(i)-adenylyl cyclase. 2-Chloroadenosine, 5'-N-ethylcarboxamidoadensoine, and other agents that elevate cellular cAMP stimulate extracellular signal-regulated kinase 1/2 activity in a pertussis toxin-insensitive manner. We conclude that a combination of cAMP-dependent signals generated via A(2a) and A(2b) receptors likely mediate ADO signaling in adult rat CF.

Differential expression of Aedes aegypti salivary transcriptome upon blood feeding

Saliva of Aedes aegypti contains a complex array of proteins essential for both blood feeding and pathogen transmission. A large numbers of those proteins are classified as unknown in regard to their function(s). Understanding the dynamic interactions at the mosquito-host interface can be achieved in part by characterizing mosquito salivary gland gene expression relative to blood feeding. Towards this end, we developed an oligonucleotide microarray representing 463 transcripts to determine differential regulation of salivary gland genes. This microarray was used to investigate the temporal gene expression pattern of Ae. aegypti salivary gland transcriptome at different times post-blood feeding. Expression of the majority of salivary gland genes (77–87%) did not change significantly as a result of blood feeding, while 8 to 20% of genes were down-regulated and 2.8 to 11.6% genes were up-regulated. Up-regulated genes included defensins, mucins and other immune related proteins. Odorant-binding protein was significantly down-regulated. Among unknown function proteins, several were up-regulated during the first three hours post-blood feeding and one was significantly down-regulated. Quantitative real-time RT-PCR was used to substantiate differential expression patterns of five randomly selected genes. Linear regression analysis revealed a high degree of correlation (R2 > 0.89) between oligonucleotide microarray and quantitative RT-PCR data. To our knowledge, this is the first study to investigate differential expression of the Ae. aegypti salivary gland transcriptome upon blood feeding. A microarray provides a robust, sensitive way to investigate differential regulation of mosquito salivary gland genes.

Identification and validation of housekeeping genes in brains of the desert locust Schistocerca gregaria under different developmental conditions

BackgroundTo obtain reliable quantitative RT-PCR data, normalization relative to stable housekeeping genes is required. However, in practice, expression levels of 'typical' housekeeping genes have been found to vary between tissues and under different experimental conditions. To date, validation studies of reference genes in insects are extremely rare and have never been performed in locusts. In this study, putative housekeeping genes were identified in the desert locust, Schistocerca gregaria and two different software programs (geNorm and Normfinder) were applied to assess the stability of thesegenes.ResultsWe have identified seven orthologs of commonly used housekeeping genes in the desert locust. The selected genes were the orthologs of actin, EF1a, GAPDH, RP49, TubA1, Ubi, and CG13220. By employing real time RT-PCR we have analysed the expression of these housekeeping genes in brain tissue of fifth instar nymphs and adults. In the brain of fifth instar nymphs geNorm indicated Sg-EF1a, Sg-GAPDH and Sg-RP49 as most stable genes, while Normfinder ranked Sg-RP49, Sg-EF1a and Sg-ACT as most suitable candidates for normalization. The best normalization candidates for gene expression studies in the brains of adult locusts were Sg-EF1a, Sg-GAPDH and Sg-Ubi according to geNorm, while Normfinder determined Sg-GAPDH, Sg-Ubi and Sg-ACT as the most stable housekeeping genes.ConclusionTo perform transcript profiling studies on brains of the desert locust, the use of Sg-RP49, Sg-EF1a and Sg-ACT as reference genes is proposed for studies of fifth instar nymphs. In experiments with adult brains, however, the most preferred reference genes were Sg-GAPDH, Sg-Ubi and Sg-EF1a. These data will facilitate transcript profiling studies in desert locusts and provide a good starting point for the initial selection of genes for validation studies in other insects.

Selection of reference genes for quantitative RT-PCR studies in Rhipicephalus (Boophilus) microplus and Rhipicephalus appendiculatus ticks and determination of the expression profile of Bm86

BackgroundFor accurate and reliable gene expression analysis, normalization of gene expression data against reference genes is essential. In most studies on ticks where (semi-)quantitative RT-PCR is employed, normalization occurs with a single reference gene, usually β-actin, without validation of its presumed expression stability. The first goal of this study was to evaluate the expression stability of commonly used reference genes in Rhipicephalus appendiculatus and Rhipicephalus (Boophilus) microplus ticks. To demonstrate the usefulness of these results, an unresolved issue in tick vaccine development was examined. Commercial vaccines against R. microplus were developed based on the recombinant antigen Bm86, but despite a high degree of sequence homology, these vaccines are not effective against R. appendiculatus. In fact, Bm86-based vaccines give better protection against some tick species with lower Bm86 sequence homology. One possible explanation is the variation in Bm86 expression levels between R. microplus and R. appendiculatus. The most stable reference genes were therefore used for normalization of the Bm86 expression profile in all life stages of both species to examine whether antigen abundance plays a role in Bm86 vaccine susceptibility.ResultsThe transcription levels of nine potential reference genes: β-actin (ACTB), β-tubulin (BTUB), elongation factor 1α (ELF1A), glyceraldehyde 3-phosphate dehydrogenase (GAPDH), glutathione S-transferase (GST), H3 histone family 3A (H3F3A), cyclophilin (PPIA), ribosomal protein L4 (RPL4) and TATA box binding protein (TBP) were measured in all life stages of R. microplus and R. appendiculatus. ELF1A was found to be the most stable expressed gene in both species following analysis by both geNorm and Normfinder software applications, GST showed the least stability. The expression profile of Bm86 in R. appendiculatus and R. microplus revealed a more continuous Bm86 antigen abundance in R. microplus throughout its one-host life cycle compared to the three-host tick R. appendiculatus where large variations were observed between different life stages.ConclusionBased on these results, ELF1A can be proposed as an initial reference gene for normalization of quantitative RT-PCR data in whole R. microplus and R. appendiculatus ticks. The observed differences in Bm86 expression profile between the two species alone can not adequately explain the lack of a Bm86 vaccination effect in R. appendiculatus.

A supervised risk predictor of breast cancer based on biological subtypes

11008 Background: The biological subtypes of breast cancer designated as Luminal A (LumA), Luminal B (LumB), HER2, and Basal have shown prognostic significance. However, risk predictors based on these gene expression profiles have been difficult to clinically implement. Recognizing that there is a continuum in both the spectrum of breast cancer disease and the risk of survival, we sought to develop a supervised risk classier within the context of biological subtypes of breast cancer. Methods: Microarray and real-time quantitative RT-PCR data from 189 samples, procured as fresh frozen and formalin-fixed paraffin-embedded tissues, were used to statistically select prototypes for the biological subtypes of breast cancer. Classification algorithms were developed using 4 independent breast microarray studies consisting of 1,244 cases. A final test set prediction was done using real-time quantitative RT-PCR data generated on a cohort of 279 breast cancers archived for a median of 20.1 years. Results: The biological subtypes predicted on the combined training set showed prognostic significance in all stages of disease (1,244 subjects; p=7.1e-14), node negative disease with no adjuvant systemic therapy (733 subjects; p=6.2e-7), and in patients treated with endocrine therapy (404 subjects; p=1.3e-3). Basal tumors identified using the 50-gene breast classifier had a more complete response to chemotherapy as compared to the same cohort scored as triple negatives. An additional cohort of 279 heterogeneously treated samples was collected from formalin fixed paraffin embedded tissue. Our risk predictor based on distance to subtype centroids provided additional prognostic information and has a linear relationship to prognosis across diverse cohorts. Conclusions: We present an objective method to predict subtypes of breast cancer and generate a continuous risk score based on biological subtypes. The standardized assay can be performed on archived tissue blocks using real-time qRT-PCR, allowing retrospective cohorts and clinical samples to be tested within the framework of specimen processing. Author Disclosure Employment or Leadership Consultant or Advisory Role Stock Ownership Honoraria Research Expert Testimony Other Remuneration Universtiy Genomics