Length control of microtubules by depolymerizing motor proteins

In many intracellular processes, the length distribution of microtubules is controlled by depolymerizing motor proteins. Experiments have shown that, following non-specific binding to the surface of a microtubule, depolymerizers are transported to the microtubule tip(s) by diffusion or directed walk and, then, depolymerize the microtubule from the tip(s) after accumulating there. We develop a quantitative model to study the depolymerizing action of such a generic motor protein, and its possible effects on the length distribution of microtubules. We show that, when the motor protein concentration in solution exceeds a critical value, a steady state is reached where the length distribution is, in general, non-monotonic with a single peak. However, for highly processive motors and large motor densities, this distribution effectively becomes an exponential decay. Our findings suggest that such motor proteins may be selectively used by the cell to ensure precise control of MT lengths. The model is also used to analyze experimental observations of motor-induced depolymerization.Comment: Added section with figures and significantly expanded text, current version to appear in Europhys. Let

Raising Tc in charge density wave superconductor ZrTe3 by Ni intercalation

We report discovery of bulk superconductivity in Ni0.05ZrTe3 at Tc = 3.1 K, obtained through Ni intercalation. Superconductivity coexists with charge density wave (CDW) state with TCDW = 41 K. When compared to parent material ZrTe3, filamentary superconducting transition is substantially increased whereas TCDW was suppressed. The analysis of superconducting state indicates that Ni0.05ZrTe3 is an intermediately coupled superconductor.Comment: 5 pages, 5 figure

A comparison of maternal effects and current environment on vital rates of Aphis nerii , the milkweed–oleander aphid

Peer Reviewedhttp://deepblue.lib.umich.edu/bitstream/2027.42/72485/1/j.1365-2311.2007.00853.x.pd

Effects of nitrogen deposition on the interaction between an aphid and its host plant

Peer Reviewedhttp://deepblue.lib.umich.edu/bitstream/2027.42/71607/1/j.1365-2311.2007.00945.x.pd

Hierarchical Models for Independence Structures of Networks

We introduce a new family of network models, called hierarchical network models, that allow us to represent in an explicit manner the stochastic dependence among the dyads (random ties) of the network. In particular, each member of this family can be associated with a graphical model defining conditional independence clauses among the dyads of the network, called the dependency graph. Every network model with dyadic independence assumption can be generalized to construct members of this new family. Using this new framework, we generalize the Erd\"os-R\'enyi and beta-models to create hierarchical Erd\"os-R\'enyi and beta-models. We describe various methods for parameter estimation as well as simulation studies for models with sparse dependency graphs.Comment: 19 pages, 7 figure

The mwtab Python Library for RESTful Access and Enhanced Quality Control, Deposition, and Curation of the Metabolomics Workbench Data Repository

The Metabolomics Workbench (MW) is a public scientific data repository consisting of experimental data and metadata from metabolomics studies collected with mass spectroscopy (MS) and nuclear magnetic resonance (NMR) analyses. MW has been constantly evolving; updating its ‘mwTab’ text file format, adding a JavaScript Object Notation (JSON) file format, implementing a REpresentational State Transfer (REST) interface, and nearly quadrupling the number of datasets hosted on the repository within the last three years. In order to keep up with the quickly evolving state of the MW repository, the ‘mwtab’ Python library and package have been continuously updated to mirror the changes in the ‘mwTab’ and JSONized formats and contain many new enhancements including methods for interacting with the MW REST interface, enhanced format validation features, and advanced features for parsing and searching for specific metabolite data and metadata. We used the enhanced format validation features to evaluate all available datasets in MW to facilitate improved curation and FAIRness of the repository. The ‘mwtab’ Python package is now officially released as version 1.0.1 and is freely available on GitHub and the Python Package Index (PyPI) under a Clear Berkeley Software Distribution (BSD) license with documentation available on ReadTheDocs