Inference of Gene Regulation via miRNAs During ES Cell Differentiation Using MiRaGE Method

MicroRNA (miRNA) is a critical regulator of cell growth, differentiation, and development. To identify important miRNAs in a biological process, many bioinformatical tools have been developed. We have developed MiRaGE (MiRNA Ranking by Gene Expression) method to infer the regulation of gene expression by miRNAs from changes of gene expression profiles. The method does not require precedent array normalization. We applied the method to elucidate possibly important miRNAs during embryonic stem (ES) cell differentiation to neuronal cells and we infer that certain miRNAs, including miR-200 family, miR-429, miR-302 family, and miR-17-92 cluster members may be important to the maintenance of undifferentiated status in ES cells

Differences in brain transcriptomes of closely related baikal coregonid species

The aim of this work was to get deeper insight into genetic factors involved in the adaptive divergence of closely related species, specifically two representatives of Baikal coregonids—Baikal whitefish (Coregonus baicalensis Dybowski) and Baikal omul (Coregonus migratorius Georgi)—that diverged from a common ancestor as recently as 10–20 thousand years ago. Using the Serial Analysis of Gene Expression method, we obtained libraries of short representative cDNA sequences (tags) from the brains of Baikal whitefish and omul. A comparative analysis of the libraries revealed quantitative differences among ~4% tags of the fishes under study. Based on the similarity of these tags with cDNA of known organisms, we identified candidate genes taking part in adaptive divergence. The most important candidate genes related to the adaptation of Baikal whitefish and Baikal omul, identified in this work, belong to the genes of cell metabolism, nervous and immune systems, protein synthesis, and regulatory genes as well as to DTSsa4 Tc1-like transposons which are widespread among fishes

On-the-fly Uniformization of Time-Inhomogeneous Infinite Markov Population Models

This paper presents an on-the-fly uniformization technique for the analysis of time-inhomogeneous Markov population models. This technique is applicable to models with infinite state spaces and unbounded rates, which are, for instance, encountered in the realm of biochemical reaction networks. To deal with the infinite state space, we dynamically maintain a finite subset of the states where most of the probability mass is located. This approach yields an underapproximation of the original, infinite system. We present experimental results to show the applicability of our technique

Effects of antenatal betamethasone on preterm human and mouse ductus arteriosus: comparison with baboon data.

BackgroundAlthough studies involving preterm infants ≤34 weeks gestation report a decreased incidence of patent ductus arteriosus after antenatal betamethasone, studies involving younger gestation infants report conflicting results.MethodsWe used preterm baboons, mice, and humans (≤276/7 weeks gestation) to examine betamethasone's effects on ductus gene expression and constriction both in vitro and in vivo.ResultsIn mice, betamethasone increased the sensitivity of the premature ductus to the contractile effects of oxygen without altering the effects of other contractile or vasodilatory stimuli. Betamethasone's effects on oxygen sensitivity could be eliminated by inhibiting endogenous prostaglandin/nitric oxide signaling. In mice and baboons, betamethasone increased the expression of several developmentally regulated genes that mediate oxygen-induced constriction (K+ channels) and inhibit vasodilator signaling (phosphodiesterases). In human infants, betamethasone increased the rate of ductus constriction at all gestational ages. However, in infants born ≤256/7 weeks gestation, betamethasone's contractile effects were only apparent when prostaglandin signaling was inhibited, whereas at 26-27 weeks gestation, betamethasone's contractile effects were apparent even in the absence of prostaglandin inhibitors.ConclusionsWe speculate that betamethasone's contractile effects may be mediated through genes that are developmentally regulated. This could explain why betamethasone's effects vary according to the infant's developmental age at birth

A study of the traits associated with the biocontrol activity of Phlebiopsis gigantea

Phlebiopsis gigantea has routinely been used for the biocontrol of the conifer pathogen, Heterobasidion annosum s.l. but the mechanism for the biocontrol action has not been properly understood. In the present work, 64 isolates of P. gigantea were screened for traits important for the biocontrol of H. annosum. Growth rate and the interaction patterns of H. annosum s.l. and P.gigantea were studied in both carbon rich (Hagem) and low carbon media (Norkrans). Laccase assay and wood degradation capabilities were performed on the 64 isolates. Data was analyzed with multiple regression and principal component analysis. Results showed a significant effect of culture composition on the outcome of the interaction, 90 % of the isolates were able to displace H. annosum s.s. in sawdust media after 20 days, as compared with only 4% recorded in the glucose rich Hagem media. High growth rate on sawdust, a lignified carbon source, correlated with high growth rate in ferulic acid, a lignin precursor (P = 0.078), high growth rate in xylan, a hemicellulose (P = 0.001) and percentage weight loss in pine (P = 0.01). Interaction in sawdust correlated with high wood degradation capability in pine and spruce with P-values (P = 0.01, P = 0.03) respectively, high growth rate in xylan (P = 0.01), laccase production (P = 0.08), interaction in Hagem (P = 0.01) and mean growth rate at 10 °C (P = 0.001). Additionally, the role of hydrophobin in the competitive interaction was further investigated. The genomic sequence of Phlebiopsis gigantea hydrophobins 1 and 2 (Pgh1 and Pgh2) from a subset of isolates selected on the basis of geographical origins and antagonistic abilities was investigated. Similarly, the expression of Pgh1 and Pgh2 under different substrate conditions was also studied using quantitative PCR. Sequence analysis was performed with Clustal W and inspected with Megalign (DNA Star). Expression data was analyzed using the relative quantification method- 2-ΔΔCt and tested for effects of isolates, genes and culture conditions using the general linear model (GLM) procedure in SAS. There was a close sequence similarity between hydrophobin genes of isolates having different antagonistic capabilities and from different geographical sources. Higher transcript levels of Pgh1 and Pgh2 were recorded in submerged cultures compared with aerial conditions. The effect of substrate on the expression of the two genes (Pgh1 and Pgh2) was statistically significant (P = 0.0001). Differences in transcript levels of Pgh1 and Pgh2 were also observed among isolates belonging to different antagonistic categories. Overall, the results suggests that the antagonistic and competitive advantage of P. gigantea, hinged on the ability of the isolates to degrade the different structural components of wood. A significant correlation was also found between some high antagonistic isolates and the expression of hydrophobin genes (Pgh1 and Pgh2). The significance of these results in the biological control is discussed

Assessment of RNAi-induced silencing in banana (Musa spp.)

In plants, RNA- based gene silencing mediated by small RNAs functions at the transcriptional or post-transcriptional level to negatively regulate target genes, repetitive sequences, viral RNAs and/or transposon elements. Post-transcriptional gene silencing (PTGS) or the RNA interference (RNAi) approach has been achieved in a wide range of plant species for inhibiting the expression of target genes by generating double-stranded RNA (dsRNA). However, to our knowledge, successful RNAi-application to knock-down endogenous genes has not been reported in the important staple food crop banana

The Need and Potential of Biosensors to Detect Dioxins and Dioxin-Like Polychlorinated Biphenyls along the Milk, Eggs and Meat Food Chain

Dioxins and dioxin-like polychlorinated biphenyls (DL-PCBs) are hazardous toxic, ubiquitous and persistent chemical compounds, which can enter the food chain and accumulate up to higher trophic levels. Their determination requires sophisticated methods, expensive facilities and instruments, well-trained personnel and expensive chemical reagents. Ideally, real-time monitoring using rapid detection methods should be applied to detect possible contamination along the food chain in order to prevent human exposure. Sensor technology may be promising in this respect. This review gives the state of the art for detecting possible contamination with dioxins and DL-PCBs along the food chain of animal-source foods. The main detection methods applied (i.e., high resolution gas-chromatography combined with high resolution mass-spectrometry (HRGC/HRMS) and the chemical activated luciferase gene expression method (CALUX bioassay)), each have their limitations. Biosensors for detecting dioxins and related compounds, although still under development, show potential to overcome these limitations. Immunosensors and biomimetic-based biosensors potentially offer increased selectivity and sensitivity for dioxin and DL-PCB detection, while whole cell-based biosensors present interpretable biological results. The main shortcoming of current biosensors, however, is their detection level: this may be insufficient as limits for dioxins and DL-PCBs for food and feedstuffs are in pg per gram level. In addition, these contaminants are normally present in fat, a difficult matrix for biosensor detection. Therefore, simple and efficient extraction and clean-up procedures are required which may enable biosensors to detect dioxins and DL-PCBs contamination along the food chain

Heparanase Promotes Engraftment and Prevents Graft versus Host Disease in Stem Cell Transplantation

Heparanase, endoglycosidase that cleaves heparan sulfate side chains of heparan sulfate proteoglycans, plays important roles in cancer metastasis, angiogenesis and inflammation.Applying a mouse model of bone marrow transplantation and transgenic mice over-expressing heparanase, we evaluated the effect of heparanase on the engraftment process and the development of graft-versus-host disease.Analysis of F1 mice undergoing allogeneic bone marrow transplantation from C57BL/6 mice demonstrated a better and faster engraftment in mice receiving cells from donors that were pretreated with heparanase. Moreover, heparanase treated recipient F1 mice showed only a mild appearance of graft-versus-host disease and died 27 days post transplantation while control mice rapidly developed signs of graft-versus-host disease (i.e., weight loss, hair loss, diarrhea) and died after 12 days, indicating a protective effect of heparanase against graft-versus-host disease. Similarly, we applied transgenic mice over-expressing heparanase in most tissues as the recipients of BMT from C57BL/6 mice. Monitoring clinical parameters of graft-versus-host disease, the transgenic mice showed 100% survival on day 40 post transplantation, compared to only 50% survival on day 14, in the control group. In vitro and in vivo studies revealed that heparanase inhibited T cell function and activation through modulation of their cytokine repertoire, indicated by a marked increase in the levels of Interleukin-4, Interleukin-6 and Interleukin-10, and a parallel decrease in Interleukin-12, tumor necrosis factor-alfa and interferon-gamma. Using point mutated inactive enzyme, we found that the shift in cytokine profile was independent of heparanase enzymatic activity.Our results indicate a significant role of heparanase in bone marrow transplantation biology, facilitating engraftment and suppressing graft-versus-host disease, apparently through an effect on T cell activation and cytokine production pattern

A Microfluidic Platform for High-Throughput Screening of Aquaporin Performance

Aquaporins are a family of small integral membrane proteins that transport water across cell membranes in response to osmotic gradients. They facilitate fluid secretion and absorption across epithelial surfaces in kidney tubules, exocrine glands, and gastrointestinal tract. Here, we describe a novel microfluidic method to evaluate and screen for aquaporin-based transmembrane permeability in mammalian cells. A microfluidic device was designed and fabricated for the encapsulation of single mammalian and yeast cells in micron-sized droplets. For this purpose, Chinese Hamster Ovarian (CHO) cells were used. CHO cells express AQP1 (aquaporin-1) homologous to human kidney aquaporins. The cells were cultivated and exposed to different osmotic stresses to study the transmembrane water transport performance of aquaporins. Our microfluidic platform has the potential to screen for and isolate cells with best aquaporin water transport performance for a number of applications in bioengineering