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Articles 1 - 4 of 4
Full-Text Articles in Physical Sciences and Mathematics
Principal Component Analysis For Predicting Transcription-Factor Binding Motifs From Array-Derived Data, Yunlong Liu, Matthew P Vincenti, Hiroki Yokota
Principal Component Analysis For Predicting Transcription-Factor Binding Motifs From Array-Derived Data, Yunlong Liu, Matthew P Vincenti, Hiroki Yokota
Dartmouth Scholarship
The responses to interleukin 1 (IL-1) in human chondrocytes constitute a complex regulatory mechanism, where multiple transcription factors interact combinatorially to transcription-factor binding motifs (TFBMs). In order to select a critical set of TFBMs from genomic DNA information and an array-derived data, an efficient algorithm to solve a combinatorial optimization problem is required. Although computational approaches based on evolutionary algorithms are commonly employed, an analytical algorithm would be useful to predict TFBMs at nearly no computational cost and evaluate varying modelling conditions. Singular value decomposition (SVD) is a powerful method to derive primary components of a given matrix. Applying SVD …
Integrated Recombinant Protein Expression And Purification Platform Based On Ralstonia Eutropha, Gavin C. Barnard, Jesse D. Mccool, David W. Wood, Tillman U. Gerngross
Integrated Recombinant Protein Expression And Purification Platform Based On Ralstonia Eutropha, Gavin C. Barnard, Jesse D. Mccool, David W. Wood, Tillman U. Gerngross
Dartmouth Scholarship
Protein purification of recombinant proteins constitutes a significant cost of biomanufacturing and various efforts have been directed at developing more efficient purification methods. We describe a protein purification scheme wherein Ralstonia eutropha is used to produce its own “affinity matrix,” thereby eliminating the need for external chromatographic purification steps. This approach is based on the specific interaction of phasin proteins with granules of the intracellular polymer poly
Knowing When To Draw The Line: Designing More Informative Ecological Experiments, Kathryn L. Cottingham, Jay T. Lennon, Bryan L. Brown
Knowing When To Draw The Line: Designing More Informative Ecological Experiments, Kathryn L. Cottingham, Jay T. Lennon, Bryan L. Brown
Dartmouth Scholarship
Linear regression and analysis of variance (ANOVA) are two of the most widely used statistical techniques in ecology. Regression quantitatively describes the relationship between a response variable and one or more continuous independent variables, while ANOVA determines whether a response variable differs among discrete values of the independent variable(s). Designing experiments with discrete factors is straightforward because ANOVA is the only option, but what is the best way to design experiments involving continuous factors? Should ecologists prefer experiments with few treatments and many replicates analyzed with ANOVA, or experiments with many treatments and few replicates per treatment analyzed with regression? …
Crystal Structure Of The Gtpase Domain Of Rat Dynamin 1, Thomas F. Reubold, Susanne Eschenburg, Andreas Becker, Marilyn Leonard, Sandra L. Schmid, Richard B. Vallee, F. Jon Kull, Dietmar J. Manstein
Crystal Structure Of The Gtpase Domain Of Rat Dynamin 1, Thomas F. Reubold, Susanne Eschenburg, Andreas Becker, Marilyn Leonard, Sandra L. Schmid, Richard B. Vallee, F. Jon Kull, Dietmar J. Manstein
Dartmouth Scholarship
Here, we present the 1.9-A crystal structure of the nucleotide-free GTPase domain of dynamin 1 from Rattus norvegicus. The structure corresponds to an extended form of the canonical GTPase fold observed in Ras proteins. Both nucleotide-binding switch motifs are well resolved, adopting conformations that closely resemble a GTP-bound state not previously observed for nucleotide-free GTPases. Two highly conserved arginines, Arg-66 and Arg-67, greatly restrict the mobility of switch I and are ideally positioned to relay information about the nucleotide state to other parts of the protein. Our results support a model in which switch I residue Arg-59 gates GTP binding …