Endotoxin-induced cytokine gene transcription in monocytes and macrophages is regulated in part by NF-B. We have previously shown that the p38 mitogenactivated protein (MAP) kinase is necessary for endotoxin-induced cytokine gene transcription. Due to the fact that most cytokine promoter sequences have active NF-B sites, we hypothesized that the p38 MAP kinase was necessary for NF-B-dependent gene expression. We found that NF-B-dependent gene expression was reduced to near control levels with either SB 203580 or a dominant-negative p38 MAP kinase expression vector. Inhibition of the p38 MAP kinase did not alter NF-B activation at any level, but it significantly reduced the DNA binding of TATA-binding protein (TBP) to the TATA box. The dominant-negative p38 MAP kinase expression vector interfered with the direct interaction of native TFIID (TBP) with a co-transfected p65 fusion protein. Likewise, this dominant-negative plasmid also interfered with the direct interaction of a co-transfected TBP fusion protein with the native p65 subunit. The p38 kinase also phosphorylated TFIID (TBP) in vitro, and SB 203580 inhibited phosphorylation of TFIID (TBP) in vivo. Thus, the p38 MAP kinase regulates NF-B-dependent gene transcription, in part, by modulating activation of TFIID (TBP). Cytokine gene expression in endotoxin (LPS)1 -stimulated macrophages is regulated, at least in part, at the level of transcription. A transcription factor that is necessary for the transcription of many cytokine genes is nuclear factor B (NF-B) (1-4). In addition to others, we have previously shown that NF-B binds to specific cytokine promoter sequences (1-8). NF-B is composed of heterodimers (most commonly p50 and p65) of members of the Rel family of transcription factors. In quiescent cells the heterodimers are kept in the cytoplasm by an inhibitor protein, IB (9 -11). NF-B translocation and DNA binding is dependent on IB kinase (IKK), which phosphorylates IB on serines within the amino-terminal domain (12)(13)(14)(15)(16)(17). This phosphorylation results in IB degradation, thus allowing NF-B translocation to the nucleus. Other factors, however, have been shown to be essential for NF-B transcriptional activation, especially phosphorylation of the p65 subunit of NF-B in one of two of its transactivation domains (18). In addition, the association of the carboxyl terminus of p65 with basal transcription factors, such as transcription factor IIB (TFIIB) and TATA-binding protein (TBP), is known to be important for transcriptional regulation of .One family of kinases that is essential for transferring signals from the cell surface to the nucleus is the mitogen-activated protein (MAP) kinases. We and others have shown that the p38 MAP kinase is critical for LPS-induced cytokine gene expression (23)(24)(25)(26).Some of these studies showed that LPS, interleukin 1, and osmotic stress activate p38 MAP kinases, and inhibition with SB 203580, a competitive inhibitor of the p38 MAP kinases, reduced cytokine release but did not affect cytokine mRNA accumu...

Infertility and spontaneous pregnancy losses are an enduring problem to women's health. The establishment of pregnancy depends on successful implantation, where a complex series of interactions occurs between the heterogeneous cell types of the uterus and blastocyst. Although a number of genes are implicated in embryo-uterine interactions during implantation, genetic evidence suggests that only a small number of them are critical to this process. To obtain a global view and identify novel pathways of implantation, we used a dual screening strategy to analyze the expression of nearly 10,000 mouse genes by microarray analysis. Comparison of implantation and interimplantation sites by a conservative statistical approach revealed 36 up-regulated genes and 27 down-regulated genes at the implantation site. We also compared the uterine gene expression profile of progesterone-treated, delayed implanting mice to that of mice in which delayed implantation was terminated by estrogen. The results show up-regulation of 128 genes and down-regulation of 101 genes after termination of the delayed implantation. A combined analysis of these experiments showed specific up-regulation of 27 genes both at the implantation site and during uterine activation, representing a broad diversity of molecular functions. In contrast, the majority of genes that were decreased in the combined analysis were related to host immunity or the immune response, suggesting the importance of these genes in regulating the uterine environment for the implanting blastocyst. Collectively, we identified genes with recognized roles in implantation, genes with potential roles in this process, and genes whose functions have yet to be defined in this event. The identification of unique genetic markers for the onset of implantation signifies that genome-wide analysis coupled with functional assays is a promising approach to resolve the molecular pathways required for successful implantation.

We used expression quantitative trait locus mapping in the laboratory rat (Rattus norvegicus) to gain a broad perspective of gene regulation in the mammalian eye and to identify genetic variation relevant to human eye disease. Of >31,000 gene probes represented on an Affymetrix expression microarray, 18,976 exhibited sufficient signal for reliable analysis and at least 2-fold variation in expression among 120 F2 rats generated from an SR͞JrHsd ؋ SHRSP intercross. Genome-wide linkage analysis with 399 genetic markers revealed significant linkage with at least one marker for 1,300 probes (␣ ‫؍‬ 0.001; estimated empirical false discovery rate ‫؍‬ 2%). Both contiguous and noncontiguous loci were found to be important in regulating mammalian eye gene expression. We investigated one locus of each type in greater detail and identified putative transcription-altering variations in both cases. We found an inserted cREL binding sequence in the 5 flanking sequence of the Abca4 gene associated with an increased expression level of that gene, and we found a mutation of the gene encoding thyroid hormone receptor ␤2 associated with a decreased expression level of the gene encoding short-wavelength sensitive opsin (Opn1sw). In addition to these positional studies, we performed a pairwise analysis of gene expression to identify genes that are regulated in a coordinated manner and used this approach to validate two previously undescribed genes involved in the human disease Bardet-Biedl syndrome. These data and analytical approaches can be used to facilitate the discovery of additional genes and regulatory elements involved in human eye disease.bioinformatics ͉ expression quantitative trait locus analysis ͉ gene regulation ͉ ophthalmology

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Our studies suggest that the phase-on genotypes of licA and igaB are important for early human nasopharynx colonization. lex2A showed a trend from phase off to phase on, suggesting a potentially important role in the colonization process.