Communications Biophysics

Contains research objectives and summary of research on five research projects, with ten sub-topics.National Institutes of Health (Grant 1 RO1 NS10916-01)National Institutes of Health (Grant 5 RO1 NS11000-03)National Institutes of Health (Grant 1 RO1 NS11153-01)Harvard-M.I.T. Rehabilitation Engineering CenterU. S. Department of Health, Education, and Welfare (Grant 23-P-55854)National Institutes of Health (Grant 1 RO1 NS11680-01)National Institutes of Health (Grant 5 ROI NS11080-02)M.I.T. Health Sciences FundNational Aeronautics and Space Administration (Grant NSG-2032)National Institutes of Health (Grant 5 TO1 GM01555-09)Massachusetts General Hospital Purchase Order F63853Boston City Hospital Purchase Order 4338-7543

Bayesian model-based inference of transcription factor activity

<b>Background:</b> In many approaches to the inference and modeling of regulatory interactions using microarray data, the expression of the gene coding for the transcription factor is considered to be an accurate surrogate for the true activity of the protein it produces. There are many instances where this is inaccurate due to post-translational modifications of the transcription factor protein. Inference of the activity of the transcription factor from the expression of its targets has predominantly involved linear models that do not reflect the nonlinear nature of transcription. We extend a recent approach to inferring the transcription factor activity based on nonlinear Michaelis-Menten kinetics of transcription from maximum likelihood to fully Bayesian inference and give an example of how the model can be further developed.<p></p> <b>Results:</b> We present results on synthetic and real microarray data. Additionally, we illustrate how gene and replicate specific delays can be incorporated into the model.<p></p> <b>Conclusion:</b> We demonstrate that full Bayesian inference is appropriate in this application and has several benefits over the maximum likelihood approach, especially when the volume of data is limited. We also show the benefits of using a non-linear model over a linear model, particularly in the case of repression.<p></p&gt

Communications Biophysics

Contains research objectives and summary of research on thirteen research projects split into four section.National Institutes of Health (Grant 1 RO1 NS10737-01)National Institutes of Health (Grant 1 ROI NS10916-01)National Institutes of Health (Grant 5 RO1 NS11000-02)National Institutes of Health (Grant 1 RO1 NS11153-01)Harvard M.I.T. Rehabilitation Engineering CenterU. S. Department of Health, Education, and Welfare, Grant 23-P-55854National Institutes of Health (Grant 1 RO1 NS11680-01)Norlin Music, Inc.Clarence J. LeBel FundNational Institutes of Health (Grant 1 RO1 NS11080-01A1)National Institutes of Health (Grant 5 TO1 GM01555-08)M.I.T. Health Sciences FundBoston City Hospital Purchase Order 1176-05-21335-C

Role for RACK1 Orthologue Cpc2 in the Modulation of Stress Response in Fission Yeast

The receptor of activated C kinase (RACK1) is a protein highly conserved among eukaryotes. In mammalian cells, RACK1 functions as an adaptor to favor protein kinase C (PKC)-mediated phosphorylation and subsequent activation of c-Jun NH2-terminal kinase mitogen-activated protein kinase. Cpc2, the RACK1 orthologue in the fission yeast Schizosaccharomyces pombe, is involved in the control of G2/M transition and interacts with Pck2, a PKC-type protein member of the cell integrity Pmk1 mitogen-activated protein kinase (MAPK) pathway. Both RACK1 and Cpc2 are structural components of the 40S ribosomal subunit, and recent data suggest that they might be involved in the control of translation. In this work, we present data supporting that Cpc2 negatively regulates the cell integrity transduction pathway by favoring translation of the tyrosine-phosphatases Pyp1 and Pyp2 that deactivate Pmk1. In addition, Cpc2 positively regulates the synthesis of the stress-responsive transcription factor Atf1 and the cytoplasmic catalase, a detoxificant enzyme induced by treatment with hydrogen peroxide. These results provide for the first time strong evidence that the RACK1-type Cpc2 protein controls from the ribosome the extent of the activation of MAPK cascades, the cellular defense against oxidative stress, and the progression of the cell cycle by regulating positively the translation of specific gene products involved in key biological processes

Postreplication Repair and PCNA Modification in Schizosaccharomyces pombe

Ubiquitination of proliferating cell nuclear antigen (PCNA) plays a crucial role in regulating replication past DNA damage in eukaryotes, but the detailed mechanisms appear to vary in different organisms. We have examined the modification of PCNA in Schizosaccharomyces pombe. We find that, in response to UV irradiation, PCNA is mono- and poly-ubiquitinated in a manner similar to that in Saccharomyces cerevisiae. However in undamaged Schizosaccharomyces pombe cells, PCNA is ubiquitinated in S phase, whereas in S. cerevisiae it is sumoylated. Furthermore we find that, unlike in S. cerevisiae, mutants defective in ubiquitination of PCNA are also sensitive to ionizing radiation, and PCNA is ubiquitinated after exposure of cells to ionizing radiation, in a manner similar to the response to UV-irradiation. We show that PCNA modification and cell cycle checkpoints represent two independent signals in response to DNA damage. Finally, we unexpectedly find that PCNA is ubiquitinated in response to DNA damage when cells are arrested in G

The Cell Surface Protein Gene ecm33+ Is a Target of the Two Transcription Factors Atf1 and Mbx1 and Negatively Regulates Pmk1 MAPK Cell Integrity Signaling in Fission Yeast

We identified and characterized ecm33+, which encodes a GPI-anchored cell surface protein as a transcriptional target of Atf1 and Mbx1. Here, we show that Ecm33 is involved in the negative regulation of Pmk1 MAPK signaling and demonstrates real-time monitoring of the activation of the cell integrity MAPK signaling pathway

Altered nuclear tRNA metabolism in La-deleted Schizosaccharomyces pombe is accompanied by a nutritional stress response involving Atf1p and Pcr1p that is suppressible by Xpo-t/Los1p

The La protein controls pre-tRNA metabolism in nuclei. Deletion of Schizosaccharomyces pombe La leads to altered pre-tRNA metabolism and up-regulation of amino acid genes and nutrient-sensitive growth defects, accompanied by apparently inefficient tRNA nuclear export. These sla1-Δ phenotypes are suppressed by modest overexpression of the tRNA nuclear export factor Los1p

Centromeric Localization of Dispersed Pol III Genes in Fission Yeast

The authors show that Pol III transcribed genes such as tRNA and 5S rRNA genes localize to centromeres in fission yeast. The centromeric localization of Pol III genes is mediated by condensin. This study suggests that there is a functional link between the centromeric localization of dispersed Pol III genes and mitotic chromosome condensation