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Biomedical subjects

Zachary Pincus

Publications and source records attributed to Zachary Pincus.

3 recordsLinked to original sources

Two independent spiral structures control cell shape in Caulobacter.

The actin homolog MreB contributes to bacterial cell shape. Here, we explore the role of the coexpressed MreC protein in Caulobacter and show that it forms a periplasmic spiral that is out of phase with the cytoplasmic MreB spiral. Both mreB and mreC are essential, and depletion of either protein results in a similar cell shape defect. MreB forms dynamic spirals in MreC-depleted cells, and MreC localizes helically in the presence of the MreB-inhibitor A22, indicating that each protein can form a spiral independently of the other. We show that the peptidoglycan transpeptidase Pbp2 also forms a helical pattern that partially colocalizes with MreC but not MreB. Perturbing either MreB (with A22) or MreC (with depletion) causes GFP-Pbp2 to mislocalize to the division plane, indicating that each is necessary but not sufficient to generate a helical Pbp2 pattern. We show that it is the division process that draws Pbp2 to midcell in the absence of MreB's regulation, because cells depleted of the tubulin homolog FtsZ maintain a helical Pbp2 localization in the presence of A22. By developing and employing a previously uncharacterized computational method for quantitating shape variance, we find that a FtsZ depletion can also partially rescue the A22-induced shape deformation. We conclude that MreB and MreC form spatially distinct and independently localized spirals and propose that MreB inhibits division plane localization of Pbp2, whereas MreC promotes lengthwise localization of Pbp2; together these two mechanism ensure a helical localization of Pbp2 and, thereby, the maintenance of proper cell morphology in Caulobacter.

Bacterial Proteins↗

Contextualizing heterogeneous data for integration and inference.

Systems that attempt to integrate and analyze data from multiple data sources are greatly aided by the addition of specific semantic and metadata "context" that explicitly describes what a data value means. In this paper, we describe a systematic approach to constructing models of data and their context. Our approach provides a generic "template" for constructing such models. For each data source, a developer creates a customized model by filling in the tem-plate with predefined attributes and value. This approach facilitates model construction and provides consistent syntax and semantics among models created with the template. Systems that can process the template structure and attribute values can reason about any model so described. We used the template to create a detailed knowledge base for syndromic surveillance data integration and analysis. The knowledge base provided support for data integration, translation, and analysis methods.

Database Management Systems↗

BioSTORM: a system for automated surveillance of diverse data sources.

Heightened concerns about bioterrorism are forcing changes to the traditional biosurveillance-model. Public health departments are under pressure to follow multiple, non-specific, pre-diagnostic indicators, often drawn from many data sources. As a result, there is a need for biosurveillance systems that can use a variety of analysis techniques to rapidly integrate and process multiple diverse data feeds using a variety of problem solving techniques to give timely analysis. To meet these requirements, we are developing a new system called BioSTORM (Biological Spatio-Temporal Outbreak Reasoning Module).

Bioterrorism↗