NORMALITY OF GENE EXPRESSION REVISITED

Microarray data are a rich source of information, containing the collected expression values of thousands of genes for well defined states of a cell or tissue. Vast amounts of data (thousands of arrays) are publicly available and ready for analysis, e.g. to scrutinise correlations between genes at the level of gene expression. The large variety of arrays available makes it possible to combine different independent experiments to extract new knowledge. Starting with a large set of data, relevant information can be isolated for further analysis. To extract the required information from data sets of such size and complexity requires an appropriate and powerful analysis method. In this study, we chose to use an unsupervised hierarchical clustering algorithm, Chaotic Map Clustering (CMC), in a coupled two-way approach to analyse such data. However, the clustering approach is intrinsically difficult, both in terms of the unknown structure of the data and interpretation of the clustering results. It is therefore critical to evaluate the quality of any unsupervised procedure for such a complex set of data and to validate the clustering results, separating those clusters that are due simply to noise or statistical fluctuations. We used a resampling method to perform this validation. The resampling procedure applies the clustering algorithm to a large number of random sub-samples of the original data matrix and, consequently, the whole process becomes computationally intensive and time consuming. Using Grid technology, we show that we can drastically speed up this process by distributing the clustering of each matrix to a separate worker node, and thus retrieve resampling results within a few hours instead of several days. Further, we offer an online service to cluster large microarray data sets and conduct the subsequent validation described in this paper.

Gene expression analysis and classification of mode of toxicity of polycyclic aromatic hydrocarbons (PAHs) in Escherichia coli

Control of Splicing Efficiency by the Mouse Histone H2a Element in a Murine Leukemia Virus–based Retroviral Vector

Pleiotrophin is an important regulator of the renin–angiotensin system in mouse aorta

Differential gene expression activity among species-specific polypyrimidine/polypurine motifs in mu opioid receptor gene promoters

Control genes, commonly defined as genes that are ubiquitously expressed at stable levels in different biological contexts, have been used to standardize quantitative expression studies for more than 25 yr. We analyzed a group of large mammalian microarray datasets including the NCI60 cancer cell line panel, a leukemia tumor panel, and a phorbol ester induction time course as well as human and mouse tissue panels. Twelve housekeeping genes commonly used as controls in classical expression studies (including GAPD, ACTB, B2M, TUBA, G6PD, LDHA, and HPRT) show considerable variability of expression both within and across microarray datasets. Although we can identify genes with lower variability within individual datasets by heuristic filtering, such genes invariably show different expression levels when compared across other microarray datasets. We confirm these results with an analysis of variance in a controlled mouse dataset, showing the extent of variability in gene expression across tissues. The results show the problems inherent in the classical use of control genes in estimating gene expression levels in different mammalian cell contexts, and highlight the importance of controlled study design in the construction of microarray experiments.

The activation-dependent induction of APN-(CD13) in T-cells is controlled at different levels of gene expression

The purpose of this paper is to review the scientific results and summarise the emerging topic of the effects of statistic magnetic field on the structure, biochemical activity, and gene expression of plants. The literature on the subject reports a wide range of possibilities regarding the use of the magnetic field to modify the properties of plant cells. MFs have a significant impact on the photosynthesis efficiency of the biomass and vigour accumulation indexes. Treating plants with SMFs accelerates the formation and accumulation of reactive oxygen species. At the same time, the influence of MFs causes the high activity of antioxidant enzymes, which reduces oxidative stress. SMFs have a strong influence on the shape of the cell and the structure of the cell membrane, thus increasing their permeability and influencing the various activities of the metabolic pathways. The use of magnetic treatments on plants causes a higher content of proteins, carbohydrates, soluble and reducing sugars, and in some cases, lipids and fatty acid composition and influences the uptake of macro- and microelements and different levels of gene expression. In this study, the effect of MFs was considered as a combination of MF intensity and time exposure, for different varieties and plant species. The following article shows the wide-ranging possibilities of applying magnetic fields to the dynamics of changes in the life processes and structures of plants. Thus far, the magnetic field is not widely used in agricultural practice. The current knowledge about the influence of MFs on plant cells is still insufficient. It is, therefore, necessary to carry out detailed research for a more in-depth understanding of the possibilities of modifying the properties of plant cells and achieving the desired effects by means of a magnetic field.

The PsbS gene product (PSII-S) which is an integral subunit of photosystem II has recently been reported to be a new type of pigment-binding protein [11]. The chlorophylls of the PSII-S protein exhibit weak excitonic coupling and this protein is stable also in the absence of pigments. Here we investigated the expression of the PsbS gene in etiolated spinach seedlings grown either in complete darkness or exposed to light of various qualities. The results obtained reveal that the PsbS gene expression in etiolated spinach plants is subjected to endogenous control. This developmental control occurs at different levels of gene expression and results in transient accumulation of the PsbS transcripts with progressing etiolation. During the first two days after emerging of the cotyledons from the seed coat the steady-state level of the PsbS transcripts is regulated mainly through increased transcriptional activity of the PsbS gene. Prolonged growth of the seedlings in the dark resulted in additional post-transcriptional control of the PsbS transcript level. Translational activity of PsbS mRNA estimated by an integration of mRNA into polysomal complexes shows that the translation rate of PsbS mRNA is less influenced by seedling age. The maximal rate of translation is reached at the first day after cotyledons emergence but the translational activity of PsbS mRNA remains still high (50% of maximum) in 8-day old etiolated spinach plants. In addition to the light-independent developmental control, the PsbS gene expression is positively regulated by phytochrome in etiolated seedlings exposed to light. Red light, however, negatively influences the abundance of PsbS transcripts at post-transcriptional level. Studies on blue or far-red light effects reveal that the accumulation of PsbS transcripts exhibits the characteristics of very-low-fluence responses of the phytochrome receptor.

Control of gene expression is crucial for several biotechnological applications, especially for implementing predictable and controllable genetic circuits. Such circuits are often implemented with a transcriptional regulator activated by a specific signal. These regulators should work independently of the host machinery, with low gratuitous induction or crosstalk with host components. Moreover, the signal should also be orthogonal, recognized only by the regulator with minimal interference with the host operation. In this context, transcriptional regulators activated by plant metabolites as flavonoids emerge as candidates to control gene expression in bacteria. However, engineering novel circuits requires the characterization of the genetic parts (e.g., genes, promoters, ribosome binding sites, and terminators) in the host of interest. Therefore, we decomposed the QdoR regulatory system of B. subtilis, responsive to the flavonoid quercetin, and reassembled its parts into genetic circuits programmed to have different levels of gene expression and noise dependent on the concentration of quercetin. We showed that only one of the promoters regulated by QdoR worked well in E. coli, enabling the construction of other circuits induced by quercetin. The QdoR expression was modulated with constitutive promoters of different transcriptional strengths, leading to low expression levels when QdoR was highly expressed and vice versa. E. coli strains expressing high and low levels of QdoR were mixed and induced with the same quercetin concentration, resulting in two stable populations expressing different levels of their gene reporters. Besides, we demonstrated that the level of QdoR repression generated different noise levels in gene expression dependent on the concentration of quercetin. The circuits presented here can be exploited in applications requiring adjustment of gene expression and noise using a highly available and natural inducer as quercetin.

Scanning of bacterial genomes to identify essential genes is of biological interest, for understanding the basic functions required for life, and of practical interest, for the identification of novel targets for new antimicrobial therapies. In particular, the lack of efficacious antimicrobial treatments for infections caused by the Burkholderia cepacia complex is causing high morbidity and mortality of cystic fibrosis patients and of patients with nosocomial infections. Here, we present a method based on delivery of the tightly regulated rhamnose-inducible promoter P(rhaB) for identifying essential genes and operons in Burkholderia cenocepacia. We demonstrate that different levels of gene expression can be achieved by using two vectors that deliver P(rhaB) at two different distances from the site of insertion. One of these vectors places P(rhaB) at the site of transposon insertion, while the other incorporates the enhanced green fluorescent protein gene (e-gfp) downstream from P(rhaB). This system allows us to identify essential genes and operons in B. cenocepacia and provides a new tool for systematically identifying and functionally characterizing essential genes at the genomic level.

Soybean cyst nematode (SCN, Heterodera glycines Ichinohe) is a common disease of soybean (Glycine max (L.) Merr.) worldwide, seriously affecting yield. Kangxian 2 is a soybean variety with a high level of resistance to H. glycines (HG) Type 0 (SCN race 3) and a yellow seed coat. However, we know little about the mechanism of resistance to HG Type 0 in Kangxian 2. In this study, we used the Illumina HiSeq high-throughput sequencing platform to analyse the transcriptome of Kangxian 2 and obtained 65.74 Gb clean data. Transcriptional changes in Kangxian 2 caused by HG Type 0 stress after 0–10 days are described. Kangxian 2 showed different levels of gene expression after inoculation, and under HG Type 0 stress after different times. Overall, 6854 HG Type 0-induced genes and 5328 HG Type 0-repressed genes were found to be differentially regulated. The greatest number of differential genes annotated to cellular process, metabolic process, single-organism process, binding, catalytic activity and other pathways. In addition to findings of differentially expressed genes similar to other published work, such as the regulation of biosynthesis of many secondary metabolites, carbon sequestration of photosynthetic organisms, other types of O-polysaccharide biosynthesis, phenylpropane biosynthesis, pyruvate metabolism and other pathways, this study also revealed the differential regulation of genes related to the diarylheptanoid and gingerol biosynthesis pathway and found some metabolic pathways that were specifically expressed in the syncytial initiation and establishment stages. Gene expression analyses using real-time fluorescence quantitative PCR showed that the expression of GmMADS and GmTUB changed strongly after 7 days and 10 days of HG Type 0 stress compared with the control. We conclude that GmMADS and GmTUB transcription factor genes may play an important role in the resistance of Kangxian 2 to HG Type 0 stress.

KiSS-1 has been shown to function as a tumor metastasis suppressor gene and reduce the number of metastases in different cancers. The expression of KiSS-1 or KiSS1, like other tumor suppressor, is commonly reduced or completely ablated in a variety of cancers via an unknown mechanism. Here we show that the loss of KiSS-1 expression in highly metastatic breast cancer cell lines correlates directly with the expression levels of two transcription factors, activator protein-2alpha (AP-2alpha) and specificity protein 1 (Sp1), which synergistically activate the transcriptional regulation of KiSS-1 in breast cancer cells. Although the KiSS-1 promoter contains multiple AP-2alpha binding elements, AP-2alpha-mediated regulation occurs indirectly through Sp1 sites, as determined by deletion and mutation analysis. Overexpression of AP-2alpha into highly metastatic breast cell lines did not alter KiSS-1 promoter-driven luciferase gene activity. However, co-transfection of AP-2alpha wild-type or the dominant negative form of AP-2 lacking its C-terminal DNA-binding domain, AP-2B, together with Sp1, increased KiSS-1 promoter activity dramatically, suggesting that AP-2alpha regulation of KiSS-1 transcription does not require direct binding to the KiSS-1 promoter. Furthermore, we demonstrated that AP-2alpha directly interacted with Sp1 to form transcription complexes at two tandem Sp1-binding sites of the promoter to activate KiSS-1 transcription. Together, our results indicate that AP-2alpha and Sp1 are strong transcriptional regulators of KiSS-1 and that loss or decreased expression of AP-2alpha in breast cancer may account for the loss of tumor metastasis suppressor KiSS-1 expression and thus increased cancer metastasis.

ObjectivesThe miR-29 family have been demonstrated acting as vital tumor suppressor in multiple cancers as well as regulators in the adaptive immune system. Little is known about their role in leukemogenesis. The purpose of this study is to analyze the expression pattern of miR-29a/29b and its target genes Mcl-1 (myeloid cell leukemia sequence 1) and B-cell lymphoma 2 (Bcl-2) in myeloid leukemia.MethodsQuantitative real-time PCR was used for detecting genes expression level in peripheral blood mononuclear cells (PBMCs) from 10 cases with newly diagnosed, untreated acute myeloid leukemia (AML) and 14 cases with newly diagnosed, untreated chronic myeloid leukemia (CML) in chronic phase, and 14 healthy individual (HI) served as controls. Correlation between the relative expression levels of different genes have been analyzed.ResultsSignificant lower expression of miR-29a/29b and higher expression level of two potential target genes Bcl-2 and Mcl-1 were found in PBMCs from AML and CML patients compared with HI group. In addtion, miR-29a expression in AML was significantly lower than that in CML. Moreover, negative correlation between miR-29a/29b and its target genes have been found. While, positive correlation between relative expression level of miR-29a and miR-29b or Bcl-2 and Mcl-1 were presented in the total 38 research objects.ConclusionDown-regulated miR-29a and miR-29b, and accompanying up-regulated Bcl-2 and Mcl-1 are the common feature in myeloid leukemias. These data further support the role for miR-29a/29b dysregulation in myeloid leukemogenesis and the therapeutic promise of regulating miR-29a/29b expression for myeloid leukemia in the future.

Bladder cancer is the 7th most commonly diagnosed cancer in males worldwide and the 11th when both genders are considered. Seventy five per cent of bladder cancer cases are non-muscle invasive bladder cancer (NMIBC). Bacillus Calmette–Gu rin (BCG) immunotherapy remains the standard intravesical agent for NMIBC. The exact mechanism by which BCG prevents recurrence is unknown. The aim of this study was to evaluate NLR4 gene expression and IL-1β as possible prognostic indicators for NMIBC recurrence and BCG treatment failure, and to detect the difference in their levels among muscle invasive bladder cancer (MIBC) and NMIBC that may aid in primary differentiation between cases. This study was conducted in 30 patients who had NMIBC and 17 patients who had MIBC. Urine samples were obtained in sterile cups before operation. From NMIBC cases, four more samples were obtained as mentioned below. Evaluation of NLR4 gene expression was performed in pre-surgical sample for MIBC and in 4 samples for NMIBC: pre-surgical sample, sample collected 4 hours after the 3rd dose of BCG instillation, and samples collected during follow up (3 and 6 months post-surgically). There was statistical significant increase in NLRP4 expression levels in NMIBC (CT=0.87±1.48) compared to MIBC (CT=2.82±2.07). As far as we searched, no published results were found regarding comparative gene expression levels between NMIBC and MIBC cases. Gene expression in recurrent cases was higher in pre-surgical urine samples than in non-recurrent cases. The expression level further increased up to 21 fold than the pre-surgical level in the sample taken after injection of the 3rd dose of BCG. This level decreased distinctly to become 1-fold increase over pre-surgical level at the 3rd month follow up then to only 0.9-fold at the 6th month. In non- recurrent cases, gene expression level started pre-surgically in much lower levels than those encountered in recurrent cases. There were 11-fold increase in expression level after 3rd dose of BCG instillation and then decreased to be 5.6 folds higher in the sample taken at 3rd month follow up than in presurgical samples. Gene expression further decreased to become 4.1 fold higher in samples taken at 6 month follow up than the pre-surgical levels. IL-1β levels were estimated for NMIBC and MIBC cases in urine samples pre-surgically and during BCG therapy in case of NMIBC before and 4 hours after the 3rd dose and during 3rd month follow-up of those cases for searching its possible use of for primary differentiation between NMIBC and MIBC, and also as a prognostic factor for possible recurrence in case of NMIBC cases. The level of IL-1β was generally higher in pre-surgical samples (0.62±0.12 pg/ml) when compared to its level before the 3rd dose of BCG induction therapy (0.53±0.13 pg/ml). Its level was distinctly higher four hours after administration of the 3rd dose BCG (1.96±0.62 pg/ml) than both previous levels. Levels decreased bellow pre-surgical level at 3rd month follow up (0.57±0.099 pg/ml). The levels of IL-1β estimated in samples collected four hours after the 3rd dose BCG was higher in cases that showed recurrence later on than non-recurrent cases. The levels decreased in both cases and became higher in non-recurrent cases (0.64±0.05 pg/ml) than in cases already developed recurrence at the 3rd month diagnosed during follow-up (0.45±0.05 pg/ml). To conclude, on following NLRP4 gene expression and IL-1β levels during BCG administration among recurrent and non-recurrent cases of thirty NMIBC cases, there was a significant statistical difference in both levels for the samples collected after the third dose BCG, being higher in patients who showed subsequent recurrence at the 3rd and 6th month of follow-up. If these preliminary reported findings will be confirmed in upcoming larger cohort’s studies, it could be promising in prognosis of such cases, with the possibility of early manipulation of individualized treatment schedule, keeping patients most probably prone to encounter recurrence safe from possible side effects of BCG therapy. The assessment of NLRP4 expression and IL-1β levels could help predict failure of BCG therapy, playing an appreciable role in early deciding radical surgery. When comparing NLRP4 expression and IL-1β levels between MIBC and NMIBC cases, increased values were noted among non-invasive ones. This finding may serve as a possible diagnostic tool, which represents a challenging issue. Hence, cut-off values for gene expression and cytokine level are to be specified.