High-density resolution synchrotron radiation based X-ray microtomography (SRμCT) for quantitative 3D-morphometrics in zoological sciences

in SPIE Optical Engineering+Application Conference, San Diego, California, USA, 10--14 August 2008 (2008)

best suitable methods like tomography allow for a direct representation of 3D-structures. In recent years, synchrotron radiation based x-ray microtomography (SR μCT) placed high resolutions to the ... [more ▼]

best suitable methods like tomography allow for a direct representation of 3D-structures. In recent years, synchrotron radiation based x-ray microtomography (SR μCT) placed high resolutions to the disposal of morphologists. With the development of highly brilliant and collimated third generation synchrotron sources, phase contrast SR μCT became widely available. A number of scientific contributions stressed the superiority of phase contrast over absorption contrast. However, here we demonstrate the power of high density resolution methods based on absorption-contrast SRμCT for quantitative 3D-measurements of tissues and other delicate bio-structures in zoological sciences. We used beamline BW2 at DORIS III (DESY, Hamburg, Germany) to perform microtomography on tissue and mineral skeletons of marine sponges (Porifera) which were shock frozen and/or fixed in a glutamate osmium tetroxide solution, followed by critical point drying. High density resolution tomographic reconstructions allowed running quantitative 3D-image analyses in Matlab and ImageJ. By applying contrast and shape rule based algorithms we semi-automatically extracted and measured sponge body structures like mineral spicules, elements of the canal system or tissue structures. This lead to a better understanding of sponge biology: from skeleton functional morphology and internal water flow regimes to body contractility. Our high density resolution based quantitative approach can be applied to a wide variety of biological structures. However, two prerequisites apply: (1) maximum density resolution is necessary; (2) edge effects as seen for example in phase outline contrast SR μCT must not be present. As a consequence, to allow biological sciences to fully exploit the power of SR μCT further increase of density resolution in absorption contrast methods is desirable. [less ▲]

The role of control and system theory in systems biology

in Annual Reviews in Control (2008), 32(1), 33-47

The use of new technology and mathematics to study the systems of nature is one of the most significant scientific trends of the century. Driven by the need for more precise scientific understanding ... [more ▼]

The use of new technology and mathematics to study the systems of nature is one of the most significant scientific trends of the century. Driven by the need for more precise scientific understanding, advances in automated measurement are providing rich new sources of biological and physiological data. These data provide information to create mathematical models of increasing sophistication and realism-models that can emulate biological and physiological systems with sufficient accuracy to advance our understanding of living systems and disease mechanisms. New measurement and modelling methods set the stage for control and systems theory to play their role in seeking out the mechanisms and principles that regulate life. It is of inestimable importance for the future of control as a discipline that this role is performed in the correct manner. If we handle the area wisely then living systems will present a seemingly boundless range of important new problems-just as physical and engineering systems have done in previous centuries. But there is a crucial difficulty. Faced with a bewildering array of choices in an unfamiliar area, how does a researcher select a worthwhile and fruitful problem? This article is an attempt to help by offering a control-oriented guide to the labyrinthine world of biology/physiology and its control research opportunities. (C) 2008 Elsevier Ltd. All rights reserved. [less ▲]

Parameter estimation in kinetic reaction models using nonlinear observers is facilitated by model extensions

in 17th IFAC World Congress, Seoul, Korea (2008)

Systembiologie: Integration von Modellierung und Experiment-Am Beispiel der Apoptosesignalwege

Scientific conference (2007, December 19)

A Systems Biology Perspective of Apoptosis Signalling

Scientific conference (2007, November 07)

Model Extension Facilitates Parameter Estimation for Kinetic Reaction Networks

Poster (2007, September)

Mathematical modelling of TNF- induced anti-apoptotic signalling pathways in mammalian cells based on dynamic and quantitative experiments

in Proc. 2nd Foundations of Systems Biology in Engineering FOSBE 2007 (2007, September)

2nd Foundations of Systems Biology in Engineering FOSBE 2007

A Systems Biology Perspective of Apoptosis Signalling

Scientific conference (2007, May 11)

Model Extension Facilitates Parameter Estimation for Kinetic Reaction Networks

Poster (2007)

An Observability Based Strategy for Parameter Identification in Systems Biology

in Proc. of the 2nd Foundations of Systems Biology in Engineering FOSBE 2007, 9–12 September, Stuttgart Germany (2007)