Genome wide screens in yeast to identify potential binding sites and target genes of DNA-binding proteins

Knowledge of all binding sites for transcriptional activators and repressors is essential for computationally aided identification of transcriptional networks. The techniques developed for defining the binding sites of transcription factors tend to be cumbersome and not adaptable to high throughput. We refined a versatile yeast strategy to rapidly and efficiently identify genomic targets of DNA-binding proteins. Yeast expressing a transcription factor is mated to yeast containing a library of genomic fragments cloned upstream of the reporter gene URA3. DNA fragments with target-binding sites are identified by growth of yeast clones in media lacking uracil. The experimental approach was validated with the tumor suppressor protein p53 and the forkhead protein FoxI1 using genomic libraries for zebrafish and mouse generated by shotgun cloning of short genomic fragments. Computational analysis of the genomic fragments recapitulated the published consensus-binding site for each protein. Identified fragments were mapped to identify the genomic context of each binding site. Our yeast screening strategy, combined with bioinformatics approaches, will allow both detailed and high-throughput characterization of transcription factors, scalable to the analysis of all putative DNA-binding proteins

Cdx4 and Menin Co-Regulate Hoxa9 Expression in Hematopoietic Cells

BACKGROUND: Transcription factor Cdx4 and transcriptional coregulator menin are essential for Hoxa9 expression and normal hematopoiesis. However, the precise mechanism underlying Hoxa9 regulation is not clear. METHODS AND FINDINGS: Here, we show that the expression level of Hoxa9 is correlated with the location of increased trimethylated histone 3 lysine 4 (H3K4M3). The active and repressive histone modifications co-exist along the Hoxa9 regulatory region. We further demonstrate that both Cdx4 and menin bind to the same regulatory region at the Hoxa9 locus in vivo, and co-activate the reporter gene driven by the Hoxa9 cis-elements that contain Cdx4 binding sites. Ablation of menin abrogates Cdx4 access to the chromatin target and significantly reduces both active and repressive histone H3 modifications in the Hoxa9 locus. CONCLUSION: These results suggest a functional link among Cdx4, menin and histone modifications in Hoxa9 regulation in hematopoietic cells

Investor's “capital” and “popularity” herd behavior in college students P2P platform

In this paper, using the data of "Su-Rong 360", we verified the existence of herd behavior in the college students peer to peer(P2P) platform by empirical study. We showed that herd behavior exists not only in "capital form", but also in "popularity form". In other words, the potential loan amount has significant positive correlation with characteristic variables of herd behavior. Besides that, after the rational test of herd behavior, the result shows that the investor's behavior in this platform was rational herd behavior. Generally, followers can study the borrower information, loan information and historical information to adjust their imitation level

Application of immunohistochemistry technique in hydrobiological studies

There is growing demand for biotechniques in oceanobiological and hydrobiological studies. Immunohistochemistry (IHC) combines anatomical, immunological and biochemical techniques to identify specific antigen-antibody interactions. Detecting the target antigen with labeled antibodies is a multi-step process that requires optimization at every level to maximize the signal detection. Here we use zebrafish samples and optimize each IHC step, particularly antigen retrieval, transgenic reporter double staining and background counterstaining. The resulting images with high signal intensity lead us to recommend the resulting protocols for experiments with fish

Combined effects of combustion chamber geometry and injection strategy on combustion and emissions of a diesel engine

For a certain type of direct injection diesel engine, a three-dimensional model of a single-cylinder complete combustion chamber and in-take/exhaust port was established. Three-dimensional Computational Fluid Dynamics (CFD) analysis software CONVERGE was used for simulation. The effects of fuel injection strategy and combustion chamber geometry on combustion emissions of diesel engine were studied while the combustion chamber volume, engine compression ratio, total fuel injection quantity and total injection duration were kept unchanged. The results show that the strategy of multiple injection and reasonable shape of combustion chamber can effectively increase the turbulent kinetic energy in cylinder, improve the uniformity of oil-gas mixing, reduce the emission of pollutants, and increase the quality of after injection can further reduce the emissions of NOx and soot

Dietary Safety Assessment of Flk1-Transgenic Fish

Genetic engineering, also called genetic modification, is facing with growing demands of aquaculture and aquatic products. Although various genetically modified (GM) aquatics have been generated, it is important to evaluate biosafety of GM organisms on the human health before entering into our food chain. For this purpose, we establish a zebrafish wild adult feeding Flk1-transgenic larvae model to examine the predatory fish's histology in multiple tissues, and the global gene expression profile in the liver. 180 days of feeding trial show that there are no significantly morphological changes in intestine, liver, kidney, and sex gonads between fish fed with Flk1 transgenic fish diet (TFD) and fish fed with regular food meal (RFM). However, a characteristic skin spot and autofluorescence increase in the theca of follicle are observed in F1 generation of TFD fish. Liver RNA-sequencing analyses demonstrate that 53 out of 56712 genes or isoforms are differentially transcribed, and mostly involved in proteolysis in extracellular region. According to GO enrichment terms these deregulated genes function in catalytic activity, steroid storing, lipid metabolic process and N-Glycan biosynthesis. These results suggest that a long term of Flk1-transgenic fish diet could alter certain metabolic pathways and possibly cause related tissue deformation. Compared to the previous reports, our feasible transgenic dietary assess system could evaluate subchronic and potential health impact of transgenic fish diet by combining multi-tissue histology and liver transcriptome analyses