The global gene expression profiles of industrial strains of <i>Saccharomyces cerevisiae</i> responding to nitrogen deficiency and very high sugar concentrations stresses were determined by oligonucleotide microarray analysis of ~ 6200 yeast open reading frames. Genomics analysis showed that 400 genes in S. cerevisiae was differentially expressed by more than 1.5-fold compared with controls at late-logarithmic phase of fermentation, as the yeast adapted to changing nutritional, environmental and physiological conditions. The genes of many pathways are regulated in a highly coordinated manner. The repressed expression of GDH1 and up-regulation of ARO10 within the contrast of Q270/Q10 indicated high energy demanding of yeast cells under high sugar stress. Activities of G3P shuttle indicated that under very high gravity environment, sufficient assimilatory nitrogen enhances yeasts ability of redox balancing, and therefore higher stress-tolerance and higher fermentation efficiency of yeast. Under contrast W270/Q270, the up-regulation of DUR1,2 responsible for urea degradation induces the glutamate biosynthesis and the consumption of -ketoglutarate. This may indicate that higher nitrogen level would enable higher activities in the TCA cycle, and therefore generate more energy for biosynthesis and yeast cell proliferation under very high gravity fermentation conditions. Nitrogen metabolism was also stimulated by high nitrogen level when yeast was grown in very high gravity environment.

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Cadmium (Cd) is one of the major contaminants in agricultural soil, threatening agricultural production and human health. The objectives of this research work were to understand the tolerance mechanism in rice (Oryza sativa L.) genotype with more Cd-tolerance, and the relation between changes of peroxidases activities and peroxidase gene expression profiles after Cd-treated. For more, we analysis about cis-acting elements in the rice peroxidase genes promoter sequences region, gene structure of rice peroxidase genes and phylogenic relation among 9 peroxidase genes which were blasted from 6 Arabidopsis thaliana Cd-induced based on the peroxidase genes protein sequences. We used 9 upland and 32 varieties rice seeds as materials for germination and the growth of seedlings test with 50 or 500 £gM CdCl2 application, respectively. Rice seeds germination is a complex physiological and biochemical process, and is highly affected by cadmium. The results showed that Cd inhibited both the growth of radicles and coleoptiles. At germination stage, Cd highly inhibited the growth of upland rice. Among these rice varieties, Japonica type cultivars are more tolerant to Cd, but Indica type are more sensitive to Cd. Upland rice cultivars are the most sensitive to Cd. At seedling stage, Cd highly inhibited the growth of roots, but slightly inhibited the growth of shoots. To cope with Cd-induced stresses, plants adopt different strategies and posses a variety of defense mechanisms to prevent themselves from Cd damage. Peroxidase (POXs) is an important antioxidative enzyme for defense responses against Cd oxidative stress. The results suggested that different rice variety has a specific peroxidase gene expression pattern by the pI focusing electrophoresis after Cd-treated, and the peroxidase activities are significant differences when these rice varieties faced Cd stress. In this study, we searched the rice databases (japonica type) and cloned the promoter sequences of the indica type of the rice peroxidase genes, pI 4.5 POX and pI 5.1 POX genes. According to the search results about cis-acting elements from PLACE and PlantCARE databases, these cis-acting elements can be divided into three classes, showing as follow¡G1. Transcriptional related; 2. Light regulated related, and 3. Plant hormones- and stress-related. Based on all reported cis-acting elements, there are many types of transcription factors (TFs) involved in regulation of rice pI 4.5 POX and pI 5.1 POX genes expression. These TFs, which can recognize the specific cis-acting elements to regulate the gene expression, and will be induced by stresses and defense-related plant hormones. We found a cis-acting element (CURECORECR) which response to copper in both rice peroxidase genes promoter regions. There is a number of difference between Japonica type and Indica type peroxidase genes, japonica type peroxidase has more cis-acting elements than indica type. Plant class III peroxidases are present in all land plants. All land plant peroxidase genes are with the same putative ancestor of peroxidase genes and are orthologous genes, but they have specific functions of individual perxidase genes owing to their promoter sequences are very divergent. We used 6 Arabidopsis Cd-related peroxidases protein sequences as a starting point for rice peroxidase datas mining. We found 9 rice peroxidase genes have a closely relation among them. For more details about these rice peroxidase genes, searching each one of these rice peroxidases its gene structure on the Rice Genome Annotation Project (RGAP), comparison and their relation. The expressions of these peroxidase genes are very different among them after Cd treatment, and we also found the same cis-acting element (CURECORECR) which response to copper in all 9 rice peroxidase genes promoter regions. There is a number of difference among them.

Differential gene expression of P. aeruginosa in a rhizosphere biofilm on poplar tree roots was examined in order to identify new virulence factors from this human pathogen. Changes in gene expression for poplar trees contacted with P. aeruginosa was examined as well to identify the response of poplar roots to P. aeruginosa infection. This is the first study of the whole-transcriptome analysis of P. aeruginosa on a plant tree root. The 20 most highly-induced genes of P. aeruginosa were examined for their role in biofilm formation, rhizosphere colonization, barley germination, and poplar tree killing assays. Seven previously uncharacterized virulence genes (PA1385, PA2146, PA2462, PA2463, PA2663, PA4150, and PA4295) were identified. The role of PA2663, a hypothetical protein discovered in the microarrays of P. aeruginosa while killing poplar trees, was examined in further detail. Expression of PA2663 protein increases biofilm formation in P. aeruginosa PAO1 drastically. By complementing the PA2663 mutation in trans and by studying with DNA microarrays and RT-PCR the PA2663 mutant vs. the wild-type strain, PA2663 was confirmed to be related to biofilm formation and was found that it is the first protein to control the psl operon in P. aeruginosa PAO1. Furthermore, PA2663 protein increases pyoverdine synthesis and quorum sensing (QS)- regulated phenotypes. A biofilm formation-related hypothetical protein, PA0939, was identified in this study. The effects of indole and 7-hydroxyindole on P. aeruginosa virulence factors were also examined for the first time. Indole and 7HI repressed expression of mexGHI-opmD multidrug efflux pump genes and genes involved in synthesis of QS-regulated virulence factors (pyocyanin, rhamnolipid, PQS, and pyoverdine production). In addition, the effects of an anti-cancer uracil analog, 5-fluorouracil (5-FU) on P. aeruginosa virulence factors and E. coli K-12 biofilm formation were examined. 5-FU repressed biofilm formation, abolished quorum-sensing phenotypes, and reduced virulence in P. aeruginosa. DNA microarray and biofilm studies with 5-FU in E. coli revealed that 5-FU controls biofilm formation through the AriR protein in E. coli K-12 strain. The effects of lsrR and lsrK mutations on E. coli biofilm formation were also examined by flow cell experiments.

Infectious agents such as bacteria or viruses can grow rapidly. If a microorganism invades a host, it must be recognized rapidly and destroyed before it overwhelms the immune system. Limiting infection to a minimum in the early stage is critical for the outcome and the recovery from infection. The innate immune system has evolved to recognize a few highly conserved, constitutive structures present only in microorganisms, such as bacterial lipopolysaccharide (LPS), called pathogen-associated molecular patterns (PAMP). Toll-like receptors are the host receptors that recognize PAMP, ultimately activating a variety of transcription factors to induce expression of a wide spectrum of immune related genes, e.g. defensins. Defensins are antimicrobial peptides that play an important role in innate defense against microorganisms in plants and animals. Beta-defensins are the largest family of antimicrobial peptides, which can directly kill microorganisms and have regulatory effects on the immune system. Thirteen beta-defensins have been identified; however, the regulation of these genes has not been well-investigated in the chicken. The objective of this research was to understand constitutive and inducible gene expression of beta-defensins in chicken white blood cells. Real-time RT-PCR was used to quantify gene expression level before and after LPS stimulation. Transcription factor binding sites in the genes were identified to understand the gene expression regulation. From the expression profile results, most chicken beta-defensins had induced gene expression by LPS stimulation in the early phase (0- to 3-hour) and reduced gene expression in the late phase (3- to 8-hour). As for the level of gene expression, the results show that the induced gene expression in the early phase corresponded to the higher levels of expression at 3-hours after LPS stimulation, and the reduced gene expression in the late phase corresponded to the lower levels of gene expression at 8-hours after LPS stimulation.

Prenatal mortality in the swine ranges from 30%~40%. Little is known about genes that involve in the preovulation events that the initiation of swine oocyte development. The main objective of this study was to utilize suppression subtractive hybridization¡]SSH¡^to delineate the differential gene expression between in vitro culture mature and antral-follicle oocytes of swine development. The knowledge of genes and their accumulated mRNA is essential to better understand the mechanisms involved in the oocyte maturation and the survival of the in vitro produced embryos. Porcine ovaries obtained from the slaughterhouse were used to collect oocytes from follicle with a diameter ≥ 3 mm. After in vitro mature for two days, oocytes with first polar body were subjected to as the testers and were lysed for mRNA extraction. Pools of 26 denuded oocytes without culture were submitted to suppressive subtraction hybridization (SSH) as the drivers. Forward and reverse subtractions were performed to identify candidate genes differentially expressed between in vitro culture mature and primordial-follicle oocytes. A total of one hundred and thirty-five differential expressed plasmid clones were sequenced, and each was analyzed by BLAST programs. Of these transcripts, 40 clones were subjected to differential screening by a dot blot cDNA array. We identified three genes like zona pellucida glycoprotein (ZP1), 1-aminocyclopropane-1-carboxylate synthase (ACS), and death associated protein 5¡]DAP 5¡^while other numerous clones remain novel. The in vivo functions of the genes remain further investigation.

The newly discovered oocyte-derived growth factor BMP15, like GDF9, is a member of the transforming growth factor-£] (TGF-£]) superfamily. To our knowledge, however, the expression and function of BMP15 in ovarian tissues has not yet been studied in the pig. We asked whether the relative abundance (RA) of BMP15 mRNA changes in oocytes and follicular cells during pre-ovulatory period or culture of cumulus-oocyte-complexs (COCs) in vitro. Denuded oocytes, cumulus cells and COCs were isolated from growing and pre-ovulatory follicles. Total RNA was extracted from the cells, and reverse transcriptase polymerase chain (RT-PCR) was carried out using specific oligo-nucleotide primers. Expansion of COCs was firstly observed at 18 h, when this period we found BMP15 mRNA expression obviously. But when we culture of denuded oocytes instead of COCs, BMP15 mRNA didn¡¦t express throughout the period. We also detected GDF9 and BMP15 mRNA in pig embryonic stage and in differentiation stage of pig stem cell. GDF9 mRNA level continued to express after fertilization, but BMP15 mRNA didn¡¦t appear. We also added BMP15 antibody against Expanding of COCs. The present results support the concept that BMP15 is a key mediator of oocyte-enabled cumulus expansion in pig.

The current knowledge concerning effects of polybrominated diphenyl ether (PBDEs) on benthic aquatic organisms is still very limited although they have been widely used as fire retardant additives for 3 decades. This study was conducted to evaluate the toxic effects of BDE-47 and BDE-183, the two common congeners of PBDEs in river sediments, on a benthic oligochaete worms, Monopylephorus limosus. The worms were exposed to BDE-47 or to BDE-183 for two or eight weeks. The survival rates of M. limosus decreased significantly when exposed to 700 ng/g dry soil of BDE-47 or BDE-183 for 8 weeks, but not in groups of 1-1000 ng/g BDE-47 for 2 weeks. A total of forty proteins of M. limosus has been expressed and determined by the two-dimensional gel electrophoresis (2-DE). Through the cluster analysis, it was found that the protein expression in the group of 100 ng/g BDE-47 was similar to 10 ng/g BDE-183. The results indicate that the toxicity of BDE-183 was greater than BDE-47 to M.limosus. Although the survival rate of M. limosus was not significantly affected when exposed to BDE-47 or BDE-183 at concentrations of 1 to 100 ng/g, significant differences in protein expression were found. Thus, the analysis of protein expression is more sensitive to detect the toxicological change in M. limosus than the survival test.

Gene of DC2 protein, a novel unknown gene, was identified previously in our laboratory while studying the death progression in the rat brain stem. According to the search results of bioinformatics database, both human DC2 and house mouse DC2 are 149 amino acids long and 16.8 kDa. The entire sequence of human DC2 differs from house mouse DC2 by only a single amino acid substitution. The bioinformatics revealed that human DC2 and house mouse DC2 had three predicted transmembrane regions. These results suggest human DC2 and house mouse are highly homologous. DC2 protein expresses differentially between organs. Human liver is the top fourth DC2-expressed organ, while house mouse liver is ranked 23rd DC2-expressed organ. Shibatani et al (Shibatani et al¡A2005) proposed DC2 protein as a potential subunit of mammalian Oligosaccharyltransferase (OST) after mass spectrometry analysis and suggested DC2 might involve in glycosylation. House mouse liver fibrosis was induced by giving 300mg/L thioacetamide (TAA) in the drinking water for different periods of time, and then gene expression of house mouse DC2 of liver was analyzed. mRNA expression was found in normal house mouse liver and mRNA expression increased gradually after TAA administration. DC2 protein also found in normal house mouse liver and DC2 protein of house mouse liver increased after TAA administration.

In tilapia , sex determination is controled by genetic and triggered by the environmental factors. Expressed sequence tags ( EST ) derived from the developing tilapia brain is cloned in our lab. The cDNA full length of the gene, F10A83 was cloned. In the present study, F10A83 is a gene with 1526 bp of cDNA sequence, and deduced 176 amino acids of protein sequence. F10A83 was overexpressed as a GFP fusion protein in mouse neuroblastoma Neuro-2a cells. F10A83 is abundantly distributed in the nucleus of Neuro-2a cell. The protein of F10A83 was expressed in the prokaryotic cell (BL21) and eukaryotic cell (neuro-2a), and purified using a simple purification process, inducing, isolation, and Ni-NTA affinity chromatography. The protein of F10A83 in both E. coli system and neuro-2a cell line expression has been established.