Prof. Jonas Tegenfeldt, PhD

Solid State Physics

Research

Nanotechnology spans a range of length scales that overlap with the length scales on which the most fundamental biological processes take place. Using nanotechnology we aim at investigating the basis for biology by making tools for measurements on the nanoscale and by creating artificial environments that mimic nature on a molecular level.

Currently, we focus on developing devices and tools for handling and analysis of biomolecules and cells using particle sorting and by stretching DNA in nanoscale channels.

If you would like to work in our group you will need access to one or more of the following lab facilities. The links are directed to information about contact persons and procedures to obtain training and access.

Lund Nano Lab - advanced micro and nanofabrication

BioPL Lab - two microscopy labs adapted to microfluidics and low light level imaging

PDMS Lab - soft lithography lab

Biochemistry lab - wet-lab for standard biochemistry

 

 

Separation science

Current junior team members:


Dr Jason Beech, Postdoc
Stefan Holm, PhD student
Trung Tran, PhD student
Kushagr Punyani, PhD student
Bao Ho Dang, PhD student

Key objectives: develop label-free sorting schemes based on physical properties of cells for parasitology and oncology.

We add further functionalities to a powerful microfluidic particle sorting approach based on deterministic lateral displacement (DLD) (originally developed at Princeton University: Huang et al in Science 2004). The feature size in the post array determines the scale of the particles to be separated. See Youtube video describing the basic idea. We use that fact that the effective size is dependent on the shear rate for deformable particles and of the orientation for non-spherical particles. The objective is to develop fractionation schemes based on inherent physical properties of cells as well as enrichment of rare molecules and particles with important relevance for the improving the sensitivity of bioanalytical assays and preparations.

We have added the following functionalities to deterministic lateral displacement: shape, deformability, dielectric properties, density and secretion.

Key publications

Jason P. Beech, Stefan Holm, Kalle Adolfsson, Jonas O. Tegenfeldt, “Sorting cells by size, shape and deformability”, Lab on a Chip, 12, 1048-1051 (2012) Abstract
Shear causes deformation of the particles passing through the device, thereby decreasing their effective size. Running a DLD at different flow speeds gives information on the deformability of the particles.

 

Stefan Holm*, Jason P. Beech*, Michael P. Barrett, and Jonas O. Tegenfeldt, “Separation of parasites from human blood using deterministic lateral displacement”, Lab Chip, 11, 1326-1332 (2011) Abstract
The morphological differences between the parasites and the red blood cells are accentuated through the shape sensitive sorting. The key to obtain a shape sensitive DLD is to control the orientation of the particles. Here the orientation is controlled through the variation of the depth of the device.
Collaboration with Prof Michael Barrett at Glasgow University.

 

Jason P. Beech, Peter Jönsson, and Jonas O. Tegenfeldt, “Tipping the balance with dielectrophoresis – electrical deterministic lateral displacement”, Lab Chip, 9, 2698 - 2706 (2009) Abstract
A dielectrophoretic force is applied to influence the trajectories of particles in a DLD device.

 

Brian R. Long, Martin Heller, Jason P. Beech, Heiner Linke, Henrik Bruus, Jonas O Tegenfeldt, “Diffusion and novel sorting modes in deterministic lateral displacement”, Physical Review E, 78(4), 046304 (2008) Abstract
Anomalous trajectories in DLD are demonstrated through simulation. Normally for DLD there are just two trajectories: one for particles with size greater than the critical size and one for particles with size smaller. However, here we show that for arrays with non-integer periodicities up to four different trajectories are possible.
Collaboration with Prof Henrik Bruus at the Technical University of Denmark. The concept was developed independently by the Tegenfeldt and the Bruus groups. Eventually we decided to copublish.

 

Jason P. Beech & Jonas O. Tegenfeldt, “Tuneable separation in elastomeric microfluidics devices”, Lab on a Chip, 8(5), 657-659 (2008) Abstract
Benefiting from the fact that PDMS is an elastic material we make an adjustable DLD device. As the device is stretched the critical size is increased accordingly.

 

DNA analysis with nanofluidics


Current junior team members:

Rebekah J Kim, PhD student

Dr Jason Beech, Postdoc

Alexandra Kühnlein, master student


Key objectives: develop simple techniques for coarse-grained labeling of DNA on the single-molecule and single-cell level with applications in bacterial identification and characterization of structural variations.

Direct visualization of DNA stretched in nanofluidic channels was pioneered a decade ago (Tegenfeldt et al. PNAS2004), opening up the possibility of directly reading out much of the information contained in the genomes of single cells. Using standard fluorescent probes for genetic variations and for regulatory modifications, we aim to complement conventional bioanalytical techniques for e.g. genetic mapping, SNP detection and epigenetic profiling with a technology that does not require any DNA amplification nor any cell culturing.

See our review paper in Chemical Society Reviews for an overview of the field.
 

Within the projects NanoDiaBac, funded through EuroNanoMed, and BeyondSeq, funded by Horizon2020 of "personalized healthcare" the main theme is genetically based diagnostics. Here we will work with the entire chain of clinical samples for analysis of DNA. The analysis takes place on single DNA molecules, which means no cell culture or DNA amplification is needed, which in turn opens up significantly faster diagnosis of infectious and genetic diseases than before, while obtaining unique information about the genetic variations between individual cells. We will work in close collaboration between academia, industry and clinics and develop advanced diagnostic tools of relevance in infectious medicine, hematology, oncology and genetic diseases.

 

 

Key publications


C. Freitag, C. Noble, J. Fritzsche, F. Persson, M. Reiter-Schad, A. N. Nilsson, A. Graneli, T. Ambjörnsson, K. U. Mir and Jonas O. Tegenfeldt, “Visualizing the entire DNA from a chromosome in a single frame”, Biomicrofluidics, 9, 044114 (2015) Abstract

A meandering channels allows a chromosomal length DNA to be fit within one single field of view.

Charleston Noble, Adam N. Nilsson, Camilla Freitag, Jason P. Beech, Jonas O. Tegenfeldt, Tobias Ambjörnsson, “A fast and scalable kymograph alignment algorithm for nanochannel-based optical DNA mappings”, PLoS ONE 10(4): e0121905 (2015) Abstract

A fast alignment algorithm for data analysis.

Mohammadreza Alizadehheidari, Erik Werner, Charleston Noble, Michaela Reiter-Schad, Lena K. Nyberg, Joachim Fritzsche, Bernhard Mehlig, Jonas O. Tegenfeldt, Tobias Ambjörnsson, Fredrik Persson and Fredrik Westerlund, “Nanoconfined circular and linear DNA – equilibrium conformations and unfolding kinetics”, Macromolecules, 48 (3), pp 871–878 (2015) Abstract

Experimental and theoretical comparison of biopysics of circular and linear DNA.

Erik Werner, Fredrik Westerlund, Jonas O. Tegenfeldt, Bernhard Mehlig "Density profile of DNA, Macromolecules 46(16), 6644–6650 (2013) Abstract
Collaboration with Prof Bernhard Mehlig at University of Gothenburg.

Eric Werner, Fredrik Persson, Fredrik Westerlund, Jonas O. Tegenfeldt, Bernhard Mehlig, “Orientational effects on confined DNA”, Physical Review E, 86(4), 041802 (2012) Abstract
The failure of using a powerlaw to describe the dependence of the extension as a function of channel diameter is explained by a model based on a biased random walk.
Collaboration with Prof Bernhard Mehlig at University of Gothenburg.

Fredrik Persson, Joachim Fritzsche, Kalim U Mir, Mauro Modesti, Fredrik Westerlund, Jonas O. Tegenfeldt, “Lipid-based passivation in nanofluidics”, Nano Letters, 12 (5), 2260-2265 (2012) Abstract
A passivation scheme based on a lipid bilayer opens up for studies of protein-DNA interactions with a minimum of non-specific adhesion to the nanochannels walls.

J. Lin, F. Persson, Joachim Fritzsche, J. O. Tegenfeldt, O. A. Saleh, “Bandpass filtering of DNA elastic modes using confinement and tension” Biophysical Journal, 102(1), 96-100 (2012) Abstract
First demonstration of tweezers combined with nanochannels. Lateral fluctuation modes are selectively suppressed by confinement
Collaboration with Prof Omar Saleh at UCSB.

Lena K Nyberg, Fredrik Persson, Johan Berg, Johanna Bergström, Emelie Fransson, Linnea Olsson, Moa Persson, Antti Stålnacke, Jens Wigenius, Jonas O Tegenfeldt, Fredrik Westerlund, “A single-step competitive binding assay for mapping of single DNA molecules” Biochemical and Biophysical Research Communications, 417, 404-408 (2012) Abstract
First demonstration of a labeling scheme based on competitive binding.
Collaboration with Prof Fredrik Westerlund at Chalmers Technical University.

 Fredrik Persson, Pit Bingen, Thorsten Staudt, Johann Engelhardt, Jonas O. Tegenfeldt, Stefan W. Hell “Fluorescence nanoscopy of single DNA molecules using STED”, Angewandte Chemie 50 (24), 5581-5583 (2011) Abstract
First demonstration of STED of DNA on a surface.
Collaboration with Prof Stefan Hell.

Walter W. Reisner, Niels B. Larsen, Asli Silahtaroglu, Anders Kristensen, Niels Tommerup, Jonas O. Tegenfeldt*, Henrik Flyvbjerg* “Single-Molecule Denaturation Mapping of Genomic DNA in Nanofluidic Channels”, Proceedings of the National Academy of Sciences USA 107 (30), 13294-13299 (2010) Abstract
Simple mapping scheme based on local melting of DNA. The resulting pattern is the result of the difference in binding and quantum yield of an intercalating dye along ds and ss DNA.
Collaboration with Technical University of Denmark (primarily Prof Henrik Flyvbjerg and Prof Anders Kristensen)

Fredrik Persson, Fredrik Westerlund, Jonas O. Tegenfeldt, Anders Kristensen, “Local Conformation of Confined DNA Studied Using Emission Polarization Anisotropy”, Small, 5(2), 190-193 (2009) Abstract
Direct monitoring of the local conformation of the DNA. The intercalating dye is such that the emitted light is polarized perpendicular to the backbone of the DNA.
Collaboration with Prof Anders Kristensen at the Technical University of Denmark.

Walter W. Reisner, Jason P. Beech, Niels B. Larsen, Henrik Flyvbjerg, Anders Kristensen, and Jonas O. Tegenfeldt, “Nanoconfinement-enhanced conformational response of single DNA molecules to changes in ionic environment”, Physical Review Letters, 99, 058302 (2007) Abstract
One of the first investigations of the effect of salt on the confirmation of confined DNA.
Collaboration with the Technical University of Denmark.

 

Nanoscale injection needles

 

Key objective: develop tools to directly access the cytosol of single cells.

To access the cytosol chemically in real time for perturbation and analysis, we develop arrays of hollow nanowires that can be used as nanoinjection needles for single cells. In this way we will be able to perturb large numbers of individual cells in parallel with a minimal variation in the perturbation and with a minimal mechanical disturbance to the cells. Any heterogeneity within the cell population will then be readily observable.

 

Key publications

 

Henrik Persson, Jason P. Beech, Lars Samuelson, Christelle N. Prinz, Jonas O. Tegenfeldt, “Vertical oxide nanotubes connected by subsurface microchannels”, Nano Research 5(3), 190–198 (2012) Abstract

Niklas Sköld, Waldemar Hällström, Henrik Persson, Lars Montelius, Martin Kanje, Lars Samuelson, Christelle N. Prinz, Jonas O. Tegenfeldt, “Nanofluidics in hollow nanowires” Nanotechnology 21(15), 155301 (2010) Abstract

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Contact information Lund:

 

Jonas Tegenfeldt


Office Q142
Division of Solid State Physics
Department of Physics
Lund University
Box 118
SE-221 00 Lund
Sweden

Visiting address:
Professorsgatan 1
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Office Phone: +46-(0)46-222 8063 (forwarded to mobile phone)
Fax: +46-(0)46-222 3637
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Optics and fluidics labs (Q129 and Q112)
Soft lithography (PDMS) lab (Q126)
Super resolution microscopy (STED) lab (Q115)

Short CV:


2014 - present Full Professor at Solid State Physics, Lund University

2008-2014 VR-financed "Rådsforskare" (Eng: Senior Research Fellowship Award)

2003-2008 VR-financed "Forskarassistent" (Eng: Assistant Professor)

2007 Docent (Associate Professor) in Solid State Physics

1998 - 2003 PostDoc at Princeton University

1997 PhD in Solid State Physics Lund University

1991 MSc in Engineering Physics / Materials Science Uppsala University

1986 Swedish Defense Institute of Language (Military Service)


Research interests

Micro and nanotechnology to address life science problems.

 

  • Separation science
  • Nanofluidics
  • Polymers in confined environments
  • Tools for single-cell biology
  • Super resolution microscopy (STED)