Biomedical subjects

Miriam L Gifford

Publications and source records attributed to Miriam L Gifford.

3 recordsLinked to original sources

PubMed2006

Sungear: interactive visualization and functional analysis of genomic datasets.

UNLABELLED: Sungear is a software system that supports a rapid, visually interactive and biologist-driven comparison of large datasets. The datasets can come from microarray experiments (e.g. genes induced in each experiment), from comparative genomics (e.g. genes present in each genome) or even from non-biological applications (e.g. demographics or baseball statistics). Sungear represents multiple datasets as vertices in a polygon. Each possible intersection among the sets is represented as a circle inside the polygon. The position of the circle is determined by the position of the vertices represented in the intersection and the area of the circle is determined by the number of elements in the intersection. Sungear shows which Gene Ontology terms are over-represented in a subset of circles or anchors. The intuitive Sungear interface has enabled biologists to determine quickly which dataset or groups of datasets play a role in a biological function of interest. AVAILABILITY: A live online version of Sungear can be found at http://virtualplant-prod.bio.nyu.edu/cgi-bin/sungear/index.cgi

Algorithms↗

PubMed2005

ARABIDOPSIS CRINKLY4 function, internalization, and turnover are dependent on the extracellular crinkly repeat domain.

The study of the regulation and cellular dynamics of receptor kinase signaling in plants is a rapidly evolving field that promises to give enormous insights into the molecular control of signal perception. In this study, we have analyzed the behavior of the L1-specific receptor kinase ARABIDOPSIS CRINKLY4 (ACR4) from Arabidopsis thaliana in planta and have shown it to be present in two distinct compartments within cells. These represent protein export bodies and a population of internalized vesicles. In parallel, deletion analysis has shown that a predicted beta-propeller-forming extracellular domain is necessary for ACR4 function. Nonfunctional ACR4 variants with deletions or point mutations in this domain behave differently to wild-type fusion protein in that they are not internalized to the same extent. In addition, in contrast with functional ACR4, which appears to be rapidly turned over, they are stabilized. Thus, for ACR4, internalization and turnover are linked and depend on functionality, suggesting that ACR4 signaling may be subject to damping down via internalization and degradation. The observed rapid turnover of ACR4 sets it apart from other recently studied plant receptor kinases. Finally, ACR4 kinase activity is not required for protein function, leading us to propose, by analogy to animal systems, that ACR4 may hetero-oligomerize with a kinase-active partner during signaling. Plant and animal receptor kinases have distinct evolutionary origins. However, with other recent work, our study suggests that there has been considerable convergent evolution between mechanisms used to regulate their activity.

Arabidopsis↗

PubMed2003

The Arabidopsis ACR4 gene plays a role in cell layer organisation during ovule integument and sepal margin development.

The mechanisms regulating cell layer organisation in developing plant organs are fundamental to plant growth, but remain largely uninvestigated. We have studied the receptor kinase-encoding ARABIDOPSIS CRINKLY4 gene and shown that its expression is restricted to the L1 cell layer of most meristems and organ primordia, including those of the ovule integuments. Insertion mutations show that ARABIDOPSIS CRINKLY4 is required for regulation of cellular organisation during the development of sepal margins and ovule integument outgrowth. We show that ARABIDOPSIS CRINKLY4 encodes a functional kinase that, in ovules and possibly other tissues, is abundant in anticlinal and the inner periclinal plasma membrane of 'outside' cells. We propose that ARABIDOPSIS CRINKLY4 may be involved in maintaining L1 cell layer integrity by receiving and transmitting signals from neighbouring L1 cells and/or from underlying cell layers.

Arabidopsis↗