A simple characterization of special matchings in lower Bruhat intervals

We give a simple characterization of special matchings in lower Bruhat intervals (that is, intervals starting from the identity element) of a Coxeter group. As a byproduct, we obtain some results on the action of special matchings.Comment: accepted for publication on Discrete Mathematic

Motifs Q and I Are Required for ATP Hydrolysis but Not for ATP Binding in SWI2/SNF2 Proteins

Active DNA-dependent ATPase A Domain (ADAAD) is a SWI2/SNF2 protein that hydrolyzes ATP in the presence of stem–loop DNA that contains both double-stranded and single-stranded regions. ADAAD possesses the seven helicase motifs that are a characteristic feature of all the SWI2/SNF2 proteins present in yeast as well as mammalian cells. In addition, these proteins also possess the Q motif ∼17 nucleotides upstream of motif I. Using site-directed mutagenesis, we have sought to define the role of motifs Q and I in ATP hydrolysis mediated by ADAAD. We show that in ADAAD both motifs Q and I are required for ATP catalysis but not for ATP binding. In addition, the conserved glutamine present in motif Q also dictates the catalytic rate. The ability of the conserved glutamine present in motif Q to dictate the catalytic rate has not been observed in helicases. Further, the SWI2/SNF2 proteins contain a conserved glutamine, one amino acid residue downstream of motif I. This conserved glutamine, Q244 in ADAAD, also directs the rate of catalysis but is not required either for hydrolysis or for ligand binding. Finally, we show that the adenine moiety of ATP is sufficient for interaction with SWI2/SNF2 proteins. The γ-phosphate of ATP is required for inducing the conformational change that leads to ATPase activity. Thus, the SWI2/SNF2 proteins despite sequence conservation with helicases appear to behave in a manner distinct from that of the helicases

Unique motifs identify PIG-A proteins from glycosyltransferases of the GT4 family-8

appears to be closer to the archaeal proteins than to other eukaryotic PIG-A proteins.<p><b>Copyright information:</b></p><p>Taken from "Unique motifs identify PIG-A proteins from glycosyltransferases of the GT4 family"</p><p>http://www.biomedcentral.com/1471-2148/8/168</p><p>BMC Evolutionary Biology 2008;8():168-168.</p><p>Published online 4 Jun 2008</p><p>PMCID:PMC2446393.</p><p></p

Unique motifs identify PIG-A proteins from glycosyltransferases of the GT4 family-1

Rged away from other eukaroyotic PIG-A proteins.<p><b>Copyright information:</b></p><p>Taken from "Unique motifs identify PIG-A proteins from glycosyltransferases of the GT4 family"</p><p>http://www.biomedcentral.com/1471-2148/8/168</p><p>BMC Evolutionary Biology 2008;8():168-168.</p><p>Published online 4 Jun 2008</p><p>PMCID:PMC2446393.</p><p></p

Unique motifs identify PIG-A proteins from glycosyltransferases of the GT4 family-6

. Three of these motifs are absent in .<p><b>Copyright information:</b></p><p>Taken from "Unique motifs identify PIG-A proteins from glycosyltransferases of the GT4 family"</p><p>http://www.biomedcentral.com/1471-2148/8/168</p><p>BMC Evolutionary Biology 2008;8():168-168.</p><p>Published online 4 Jun 2008</p><p>PMCID:PMC2446393.</p><p></p

Unique motifs identify PIG-A proteins from glycosyltransferases of the GT4 family-7

Rged away from other eukaroyotic PIG-A proteins.<p><b>Copyright information:</b></p><p>Taken from "Unique motifs identify PIG-A proteins from glycosyltransferases of the GT4 family"</p><p>http://www.biomedcentral.com/1471-2148/8/168</p><p>BMC Evolutionary Biology 2008;8():168-168.</p><p>Published online 4 Jun 2008</p><p>PMCID:PMC2446393.</p><p></p

Unique motifs identify PIG-A proteins from glycosyltransferases of the GT4 family-4

Rom eukaryotes are evolutionarily a separate branch of proteins.<p><b>Copyright information:</b></p><p>Taken from "Unique motifs identify PIG-A proteins from glycosyltransferases of the GT4 family"</p><p>http://www.biomedcentral.com/1471-2148/8/168</p><p>BMC Evolutionary Biology 2008;8():168-168.</p><p>Published online 4 Jun 2008</p><p>PMCID:PMC2446393.</p><p></p

Global Epigenetic Changes Induced by SWI2/SNF2 Inhibitors Characterize Neomycin-Resistant Mammalian Cells

<div><h3>Background</h3><p>Previously, we showed that aminoglycoside phosphotransferases catalyze the formation of a specific inhibitor of the SWI2/SNF2 proteins. Aminoglycoside phosphotransferases, for example neomycin-resistant genes, are used extensively as selection markers in mammalian transfections as well as in transgenic studies. However, introduction of the neomycin-resistant gene is fraught with variability in gene expression. We hypothesized that the introduction of neomycin-resistant genes into mammalian cells results in inactivation of SWI2/SNF2 proteins thereby leading to global epigenetic changes.</p> <h3>Methodology</h3><p>Using fluorescence spectroscopy we have shown that the inhibitor, known as <u>A</u>ctive <u>D</u>NA-<u>d</u>ependent <u>A</u>TPase <u>A</u><u>D</u>omain inhibitor (ADAADi), binds to the SWI2/SNF2 proteins in the absence as well as presence of ATP and DNA. This binding occurs via a specific region known as Motif Ia leading to a conformational change in the SWI2/SNF2 proteins that precludes ATP hydrolysis. ADAADi is produced from a plethora of aminoglycosides including G418 and Streptomycin, two commonly used antibiotics in mammalian cell cultures. Mammalian cells are sensitive to ADAADi; however, cells stably transfected with neomycin-resistant genes are refractory to ADAADi. In resistant cells, endogenous SWI2/SNF2 proteins are inactivated which results in altered histone modifications. Microarray data shows that the changes in the epigenome are reflected in altered gene expression. The microarray data was validated using real-time PCR. Finally, we show that the epigenetic changes are quantized.</p> <h3>Significance</h3><p>The use of neomycin-resistant genes revolutionized mammalian transfections even though questions linger about efficacy. In this study, we have demonstrated that selection of neomycin-resistant cells results in survival of only those cells that have undergone epigenetic changes, and therefore, data obtained using these resistant genes as selection markers need to be cautiously evaluated.</p> </div

GST-Als5 specifically blocks binding of anti-Als5 antibody on Candida cell surface.

<p>Candida SC5314 cells were grown to an OD_600nm of 0.5. 500 µl of the cells after pelleting down were washed with PBS and then incubated with anti-Als5 antibody for 1 hour. This primary antibody was detected by a secondary antibody that was conjugated with TRITC and detected using flow cytometry as described in the text. The y-axis in the figure represents the percent fraction of fluorescently labelled cells. Unstained: Cells were incubated with the primary Ab buffer (instead of anti-Als5 Ab), washed thrice with PBS and then incubated with the fluorescently labelled secondary antibody before being detected using flow cytometry. Anti-Als5: Cells were incubated with anti-Als5 primary Ab, washed thrice with PBS and then incubated with the fluorescently labelled secondary antibody before being detected using flow cytometry. GST: Cells were incubated with GST, then with anti-Als5 Ab, washed thrice with PBS, and then incubated with the fluorescently labelled secondary antibody before being detected using flow cytometry. Als5: Cells were incubated with GST-Als5, then with anti-Als5 Ab, washed thrice with PBS, and then incubated with the fluorescently labelled secondary antibody before being detected using flow cytometry. All incubation steps were carried out at 37^oC for 1 hour. Concentrations of the GST as well as GST-Als5 used in the competition assays are as shown in the figure. The data presented is mean of 3 independent experiments done in duplicates. The anti-Als5 antibody generated in this study was able to recognize and bind to the adhesins on Candida cell surface, as exhibited by the fraction of fluorescent cells detected using TRITC labelled secondary Ab. The presence of GST-Als5, but not GST, inhibited the binding of anti-Als5 antibody to <i>C.albicans</i> cell surface in a concentration dependent manner, thus demonstrating the specificity of the interaction.</p

Cartoon representation of Rosetta models for Als5Nt complexes.

<p>(A) Low energy Rosetta model of Als5Nt. (B) Low energy Rosetta docked model of Als5Nt bound to peptide ligand (EHAHTPR) as well as to the eleven-residue long C-terminal peptide (KFISVALFFFL) from SS. The Als5Nt is colored in red, the peptide ligand is shown in green and the SS peptide is shown in blue. The figures were generated using the program PyMOL.</p