Biomedical subjects

Maria J Schilstra

Publications and source records attributed to Maria J Schilstra.

6 recordsLinked to original sources

PubMed2006

An elastically tethered viscous load imposes a regular gait on the motion of myosin-V. Simulation of the effect of transient force relaxation on a stochastic process.

Myosin-V is a processive molecular motor that moves membrane vesicles along actin tracks. In the simple model for motor and cargo motion investigated here, an elastic connection between motor and cargo transiently absorbs the abrupt mechanical transitions of the motor, and allows smooth relaxation of the cargo to a new position. We use a stochastic description to model motor stepping, with kinetics that depends on the instantaneous force exerted on the motor through the elastic connection. Tether relaxation is modelled as a continuous process, in which the rate is determined by the viscous drag of the cargo and the stiffness profile of the connection. Quantitative combined stochastic-continuous simulation of the dynamics of this system shows that bulky loads can impose a highly regular gait on the motor. If the characteristics of the elastic connection are similar to those of the myosin-II coiled-coil domain, the myosin-V motor, tether and cargo form a true escapement, in which the motor only escapes from its current position after one or more force thresholds have been crossed. Multiple thresholds limit the variation in tether length to values below that of the total step size.

Actins↗

PubMed2006

CellML2SBML: conversion of CellML into SBML.

UNLABELLED: CellML and SBML are XML-based languages for storage and exchange of molecular biological and physiological reaction models. They use very similar subsets of MathML to specify the mathematical aspects of the models. CellML2SBML is implemented as a suite of XSLT stylesheets that, when applied consecutively, convert models expressed in CellML into SBML without significant loss of information. The converter is based on the most recent stable versions of the languages (CellML version 1.1; SBML Level 2 Version 1), and the XSLT used in the stylesheets adheres to the XSLT version 1.0 specification. Of all 306 models in the CellML repository in April 2005, CellML2SBML converted 91% automatically into SBML. Minor manual changes to the unit definitions in the originals raised the percentage of successful conversions to 96%. AVAILABILITY: http://sbml.org/software/cellml2sbml/. SUPPLEMENTARY INFORMATION: Instructions for use and further documentation available on http://sbml.org/software/cellml2sbml/

Cell Physiological Phenomena↗

PubMed2002

New computational approaches for analysis of cis-regulatory networks.

The investigation and modeling of gene regulatory networks requires computational tools specific to the task. We present several locally developed software tools that have been used in support of our ongoing research into the embryogenesis of the sea urchin. These tools are especially well suited to iterative refinement of models through experimental and computational investigation. They include: BioArray, a macroarray spot processing program; SUGAR, a system to display and correlate large-BAC sequence analyses; SeqComp and FamilyRelations, programs for comparative sequence analysis; and NetBuilder, an environment for creating and analyzing models of gene networks. We also present an overview of the process used to build our model of the Strongylocentrotus purpuratus endomesoderm gene network. Several of the tools discussed in this paper are still in active development and some are available as open source.

Chromosomes, Artificial, Bacterial↗

PubMed2002

A provisional regulatory gene network for specification of endomesoderm in the sea urchin embryo.

We present the current form of a provisional DNA sequence-based regulatory gene network that explains in outline how endomesodermal specification in the sea urchin embryo is controlled. The model of the network is in a continuous process of revision and growth as new genes are added and new experimental results become available; see http://www.its.caltech.edu/~mirsky/endomeso.htm (End-mes Gene Network Update) for the latest version. The network contains over 40 genes at present, many newly uncovered in the course of this work, and most encoding DNA-binding transcriptional regulatory factors. The architecture of the network was approached initially by construction of a logic model that integrated the extensive experimental evidence now available on endomesoderm specification. The internal linkages between genes in the network have been determined functionally, by measurement of the effects of regulatory perturbations on the expression of all relevant genes in the network. Five kinds of perturbation have been applied: (1) use of morpholino antisense oligonucleotides targeted to many of the key regulatory genes in the network; (2) transformation of other regulatory factors into dominant repressors by construction of Engrailed repressor domain fusions; (3) ectopic expression of given regulatory factors, from genetic expression constructs and from injected mRNAs; (4) blockade of the beta-catenin/Tcf pathway by introduction of mRNA encoding the intracellular domain of cadherin; and (5) blockade of the Notch signaling pathway by introduction of mRNA encoding the extracellular domain of the Notch receptor. The network model predicts the cis-regulatory inputs that link each gene into the network. Therefore, its architecture is testable by cis-regulatory analysis. Strongylocentrotus purpuratus and Lytechinus variegatus genomic BAC recombinants that include a large number of the genes in the network have been sequenced and annotated. Tests of the cis-regulatory predictions of the model are greatly facilitated by interspecific computational sequence comparison, which affords a rapid identification of likely cis-regulatory elements in advance of experimental analysis. The network specifies genomically encoded regulatory processes between early cleavage and gastrula stages. These control the specification of the micromere lineage and of the initial veg(2) endomesodermal domain; the blastula-stage separation of the central veg(2) mesodermal domain (i.e., the secondary mesenchyme progenitor field) from the peripheral veg(2) endodermal domain; the stabilization of specification state within these domains; and activation of some downstream differentiation genes. Each of the temporal-spatial phases of specification is represented in a subelement of the network model, that treats regulatory events within the relevant embryonic nuclei at particular stages.

Animals↗

PubMed2002

The temperature dependence of P680(+) reduction in oxygen-evolving photosystem II.

The temperature dependence for the reduction of the oxidized primary electron donor P680(+) by the redox active tyrosine Y(Z) has been studied in oxygen-evolving photosystem II preparations from spinach. The observed temperature dependence is found to vary markedly with the S-state of the manganese cluster. In the higher oxidation states, S(2) and S(3), sub-microsecond P680(+) reduction exhibits activation energies of about 260 meV. In contrast, there is only a small temperature dependence for the sub-microsecond reaction in the S(0) and S(1) states (an activation energy of approximately 50 meV). Slower microsecond components of P680(+) reduction show an activation energy of about 250 meV which, within experimental error, is independent of the oxidation state of the Mn cluster. By combining these values with measurements of DeltaG for electron transfer, the reorganization energies for each component of P680(+) reduction have been calculated. High activation and reorganization energies are found for sub-microsecond P680(+) reduction in S(2) and S(3), demonstrating that these electron transfers are coupled to significant reorganization events which do not occur in the presence of the lower S-states. One interpretation of these results is that there is an increase in the net charge on the manganese cluster on the S(1) to S(2) transition which acts as a barrier to electron transfer in the higher S-states. This argues against the electroneutrality requirement for some models of the function of the manganese cluster and hence against a role for Y(Z) as a hydrogen abstractor on all S-state transitions. An alternative or additional possibility is that there are proton (or other ion) motions in the sub-microsecond phases in S(2) and S(3) which contribute to the large reorganization energies observed, these motions being absent in the S(0) and S(1) states. Indeed charge accumulation may directly cause the increased reorganization energy.

Electron Transport↗

PubMed2002

A genomic regulatory network for development.

Development of the body plan is controlled by large networks of regulatory genes. A gene regulatory network that controls the specification of endoderm and mesoderm in the sea urchin embryo is summarized here. The network was derived from large-scale perturbation analyses, in combination with computational methodologies, genomic data, cis-regulatory analysis, and molecular embryology. The network contains over 40 genes at present, and each node can be directly verified at the DNA sequence level by cis-regulatory analysis. Its architecture reveals specific and general aspects of development, such as how given cells generate their ordained fates in the embryo and why the process moves inexorably forward in developmental time.

Animals↗