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In situ dynamics and fluidics of biological matter

English title In situ dynamics and fluidics of biological matter
Applicant Pfohl Thomas
Number 141270
Funding scheme Project funding
Research institution Physikalische Chemie Departement Chemie Universität Basel
Institution of higher education University of Basel - BS
Main discipline Physical Chemistry
Start/End 01.04.2012 - 31.03.2015
Approved amount 365'377.00
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All Disciplines (2)

Discipline
Physical Chemistry
Biophysics

Keywords (11)

Self-assembly; X-ray photon correlation spectroscopy; low Reynolds number swimmers; in situ dynamics; Small angle X-ray scattering; Actin networks; cell motility; in-homogenous networks; DNA condensation/decondensation; Fibrin networks; microfluidics

Lay Summary (English)

Lead
Lay summary

Projekttitel

In situ dynamics and fluidics of biological matter

Hauptgesuchsteller

Prof. Dr. Thomas Pfohl, Chemie Departement, Universität Basel

Lead

Combining optical imaging and X-ray techniques with state of the art microfluidic technologies, we will be able to characterize the dynamics of hierarchical self-assembly and self-organization of protein networks and hybrid chromatin-like assemblies as well as the mobility and motility of biological microobjects in hydrodynamic flow.

 

Hintergrund

Understanding the fundamental principles of the dynamics, evolution and pattern formation in biological processes will facilitate control, manipulation and smart emulation of biological systems. As many biological processes consist of a series of transient steps in their reaction pathways that are undetectable in bulk measurements, microfluidics-based experiments provide an opportunity to study the complexity of hierarchical dynamic and structural assembly and to generate models, which reproduce biological processes in vitro.

 

Das Ziel

The mobility and motility of biological objects in microflow is of fundamental relevance in order to understand blood flow, intra- and extracellular transport, infection pathways and hydrodynamic “communication” of unicellular parasites and bacteria. We will mainly focus our hydrodynamic studies on the relationship between flow fields and biological objects at low Reynolds numbers.

The proposed experiments on cytoskeletal and extracellular matrix proteins follow a bottom-up approach to understand the fundamental mechanisms of bundling and network formation with increasing hierarchy and complexity. Studying these cellular principles in a physiological context, we will gain new insights into the underlying mechanisms. Owing to a better and easier in vitro manipulation, the study and formation of hybrid chromatin-like assemblies in variable experimental conditions advances an understanding of DNA properties from real chromatin. We expect to gain insights into the underlying mechanisms and aim to reveal the relationship between transcription and regulation of DNA with the compaction state in which it is found.

 

Bedeutung

The proposed research aims at a deeper fundamental understanding of the self-assembly and self-organization processes in biological systems. The innovative nature of the proposed experimental approaches will allow the monitoring of dynamic processes far from equilibrium, giving access to the detection of intermediate reaction states. Currently, these research approaches are starting to receive significant interest by the scientific community worldwide because of their potential use for studies of underlying fundamental mechanisms by emulating cell and tissue systems and for novel biotechnical and biomedical applications

Direct link to Lay Summary Last update: 21.02.2013

Responsible applicant and co-applicants

Employees

Publications

Publication
A self-filling microfluidic device for noninvasive and time-resolved single red blood cell experiments
Göllner Michael, Toma Adriana C., Strelnikova Natalja, Deshpande Siddharth, Pfohl Thomas (2016), A self-filling microfluidic device for noninvasive and time-resolved single red blood cell experiments, in Biomicrofluidics, 10, 054121.
Brownian and advective dynamics in microflow studied by coherent X-ray scattering experiments
Urbani Raphael, Westermeier Fabian, Banusch Benjamin, Sprung Michael, Pfohl Thomas (2016), Brownian and advective dynamics in microflow studied by coherent X-ray scattering experiments, in J. Synchrotron Rad., 23, 1401-1408.
Formation of actin networks in Microfluidic concentration gradients
Strelnikova Natalja, Herren Florian, Schoenenberger Cora-Ann, Pfohl Thomas (2016), Formation of actin networks in Microfluidic concentration gradients, in Frontiers in Materials, 3, 20.
Trapping, entrainment and synchronization of semiflexible polymers in narrow, asymmetric confinements
Swank Zoe, Deshpande Siddharth, Pfohl Thomas (2016), Trapping, entrainment and synchronization of semiflexible polymers in narrow, asymmetric confinements, in Soft Matter, 12(1), 87-92.
Microfluidics-based single cell analysis reveals drug-dependent motility changes in trypanosomes.
Hochstetter Axel, Stellamanns Eric, Deshpande Siddharth, Uppaluri Sravanti, Engstler Markus, Pfohl Thomas (2015), Microfluidics-based single cell analysis reveals drug-dependent motility changes in trypanosomes., in Lab on a chip, 15(8), 1961-8.
Real-time dynamics of emerging actin networks in cell-mimicking compartments.
Deshpande Siddharth, Pfohl Thomas (2015), Real-time dynamics of emerging actin networks in cell-mimicking compartments., in PloS one, 10(3), 0116521-0116521.
A chaperonin as protein nanoreactor for atom-transfer radical polymerization.
Renggli Kasper, Nussbaumer Martin G, Urbani Raphael, Pfohl Thomas, Bruns Nico (2014), A chaperonin as protein nanoreactor for atom-transfer radical polymerization., in Angewandte Chemie (International ed. in English), 53(5), 1443-7.
Optical trapping reveals propulsion forces, power generation and motility efficiency of the unicellular parasites Trypanosoma brucei brucei.
Stellamanns Eric, Uppaluri Sravanti, Hochstetter Axel, Heddergott Niko, Engstler Markus, Pfohl Thomas (2014), Optical trapping reveals propulsion forces, power generation and motility efficiency of the unicellular parasites Trypanosoma brucei brucei., in Scientific reports, 4, 6515-6515.
Analysis of complex fluids using microfluidics: the particular case of DNA/polycations assemblies
Toma Adriana C., Dootz Rolf, Pfohl Thomas (2013), Analysis of complex fluids using microfluidics: the particular case of DNA/polycations assemblies, in JOURNAL OF PHYSICS D-APPLIED PHYSICS, 46(11), 114001.
Understanding biorelevant drug release from a novel thermoplastic capsule by considering microstructural formulation changes during hydration
Misic Zdravka, Urbani Raphael, Pfohl Thomas, Muffler Katharina, Sydow Georg, Kuentz Martin Thomas (2013), Understanding biorelevant drug release from a novel thermoplastic capsule by considering microstructural formulation changes during hydration, in Pharmaceutical Research, 31(1), 194-203.
Hierarchical self-assembly of actin in micro-confinements using microfluidics
Deshpande Siddharth, Pfohl Thomas (2012), Hierarchical self-assembly of actin in micro-confinements using microfluidics, in BIOMICROFLUIDICS, 6(3), 541-545.
Mobility Gradient Induces Cross-Streamline Migration of Semiflexible Polymers
Steinhauser Dagmar, Koester Sarah, Pfohl Thomas (2012), Mobility Gradient Induces Cross-Streamline Migration of Semiflexible Polymers, in ACS MACRO LETTERS, 1(5), 541-545.
Monofunctionalized Gold Nanoparticles Stabilized by a Single Dendrimer Form Dumbbell Structures upon Homocoupling
Hermes Jens Peter, Sander Fabian, Fluch Ulrike, Peterle Torsten, Thompson Damien, Urbani Raphael, Pfohl Thomas, Mayor Marcel (2012), Monofunctionalized Gold Nanoparticles Stabilized by a Single Dendrimer Form Dumbbell Structures upon Homocoupling, in JOURNAL OF THE AMERICAN CHEMICAL SOCIETY, 134(36), 14674-14677.
X-RAY STUDIES OF BIOLOGICAL MATTER IN MICROFLUIDIC ENVIRONMENTS
Koester Sarah, Pfohl Thomas (2012), X-RAY STUDIES OF BIOLOGICAL MATTER IN MICROFLUIDIC ENVIRONMENTS, in MODERN PHYSICS LETTERS B, 26(26), 1230018.

Collaboration

Group / person Country
Types of collaboration
Prof. Dr. Martin Kuentz, FHNW Basel Switzerland (Europe)
- in-depth/constructive exchanges on approaches, methods or results
- Publication
- Research Infrastructure
Dr. Andreas Menzel, PSI Villigen Switzerland (Europe)
- in-depth/constructive exchanges on approaches, methods or results
- Research Infrastructure
Prof. Dr. Marcel Mayor, Chemie Departement, Universität Basel Switzerland (Europe)
- in-depth/constructive exchanges on approaches, methods or results
- Publication
- Research Infrastructure
- Exchange of personnel
Prof. Dr. Urs Jenal, Biozentrum, Universität Basel Switzerland (Europe)
- in-depth/constructive exchanges on approaches, methods or results
- Research Infrastructure
- Exchange of personnel
Prof. Dr. Nico Bruns, Universität Fribourg Switzerland (Europe)
- in-depth/constructive exchanges on approaches, methods or results
- Publication
- Research Infrastructure
Dr. Bernd Struth, HASYLAB, DESY, Hamburg Germany (Europe)
- in-depth/constructive exchanges on approaches, methods or results
- Publication
- Research Infrastructure
- Exchange of personnel

Scientific events

Active participation

Title Type of contribution Title of article or contribution Date Place Persons involved
DPG Frühjahrstagung 2015 Poster IN SITU NANOSCALE IMAGING OF CHROMOSOME OSCILLATIONS IN LIVING YEAST CELLS 16.03.2015 Berlin, Germany Strelnikova Natalja; Pfohl Thomas;
DPG Frühjahrstagung 2015 Talk given at a conference Dynamics of buckling transitions of freely diffusing single erythrocytes 16.03.2015 Berlin, Germany Pfohl Thomas; Göllner Michael;
SYSCHEM 2014 Talk given at a conference MICROFLUIDICS TOOLS FOR IN SITU REACTIONS: FROM SELF-ASSEMBLY TO DYNAMICS OF EMERGENT NETWORKS 09.06.2014 San Sebastian, Spain Pfohl Thomas;
SSD14 Talk given at a conference Analysis of single erythrocytes using whole human blood samples 06.06.2014 Basel, Switzerland Pfohl Thomas; Urbani Raphael;
Flow 2014 Talk given at a conference Cell motility of bloodstream parasites in flow and possible impact on host infections 19.05.2014 Twente, Netherlands Pfohl Thomas;
DPG Frühjahrstagung 2014 Poster Mechanical and spectroscopic analysis of single erythrocytes using whole human blood samples 31.03.2014 Dresden, Germany Göllner Michael; Pfohl Thomas;
DPG Frühjahrstagung 2014 Talk given at a conference In situ release of DNA from artificial gene carriers 31.03.2014 Dresden, Germany Strelnikova Natalja; Pfohl Thomas;
5th SAXS User-meeting Talk given at a conference Microfluidics 12.09.2013 Karlsruhe, Germany Pfohl Thomas;
DPG Frühjahrstagung 2013 Poster X-ray photon correlation spectroscopy (XPCS) study of nanospheres in parabolic microflow 11.03.2013 Regensburg, Germany, Germany Urbani Raphael; Pfohl Thomas;
Rheology-Workshop, HASYLAB, DESY Talk given at a conference Microfluidic application in rheology 24.01.2013 Hamburg, Germany, Germany Pfohl Thomas;
Molecular Assembly of Biomimetic Systems-MABS2012 Talk given at a conference Microfluidics tools for studies of the hierarchical self-assembly of biological materials 06.06.2012 Peking, China, China Pfohl Thomas;


Associated projects

Number Title Start Funding scheme
130171 In situ dynamics and fluidics of biological matter 01.04.2010 Project funding
128747 Dynamics of hierarchical self-assembly processes characterized by small angle X-ray scattering 01.12.2009 R'EQUIP

Abstract

The hierarchical self-organization of biological matter in cells, tissues, and organisms is one of the most fascinating phenomena in life science. Therefore, great efforts are devoted to elucidate the dynamics of these self-organization processes. Understanding the fundamental principles of the dynamics, evolution and pattern formation in biological processes will facilitate control, manipulation and smart emulation of biological systems. As many biological processes consist of a series of transient steps in their reaction pathways that are undetectable in bulk measurements, microfluidics-based experiments provide an opportunity to study the complexity of hierarchical dynamic and structural assembly and to generate models, which reproduce biological processes in vitro. The precise control of external parameters and the possibility to generate gradients on the nano- and micrometer length scale allows for investigations of intermediates and transitional states as well as dynamic and kinetic properties of the studied systems. The proposed studies will focus on in situ formation and design of protein fiber networks as cell and tissue mimics, the self-assembly, control and transcription of chromatin-like materials and mobility and motility of biological microobjects in flow.The proposed experiments on cytoskeletal and extracellular matrix proteins follow a bottom-up approach to understand the fundamental mechanisms of bundling and network formation with increasing hierarchy and complexity. Studying these cellular principles in a physiological context, we will gain new insights into the underlying mechanisms. Furthermore, we will not only be able to manipulate and test biological processes but also to emulate biological systems by developing artificial cell and microtissue systems.Owing to a better and easier in vitro manipulation, the study and formation of hybrid chromatin-like assemblies in variable experimental conditions advances an understanding of DNA properties from real chromatin. We expect to gain insights into the underlying mechanisms and aim to reveal the relationship between transcription and regulation of DNA with the compaction state in which it is found.The mobility and motility of biological objects in microflow is of fundamental relevance in order to understand blood flow, intra- and extracellular transport, infection pathways and hydrodynamic “communication” of unicellular parasites and bacteria. We will mainly focus our hydrodynamic studies on the relationship between flow fields and biological objects at low Reynolds numbers. Apart from analyzing unique phenomena, such as cross-streamline migration, tumbling, hydrodynamic interactions, hydrodynamic influence on cell metabolisms and behavior, these investigations may have an impact on biotechnical and biomedical applications.
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