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Biomedical subjects

G Dietler

Publications and source records attributed to G Dietler.

At least 19 recordsLinked to original sources
PubMed2006

Numerical simulation of gel electrophoresis of DNA knots in weak and strong electric fields.

Gel electrophoresis allows one to separate knotted DNA (nicked circular) of equal length according to the knot type. At low electric fields, complex knots, being more compact, drift faster than simpler knots. Recent experiments have shown that the drift velocity dependence on the knot type is inverted when changing from low to high electric fields. We present a computer simulation on a lattice of a closed, knotted, charged DNA chain drifting in an external electric field in a topologically restricted medium. Using a Monte Carlo algorithm, the dependence of the electrophoretic migration of the DNA molecules on the knot type and on the electric field intensity is investigated. The results are in qualitative and quantitative agreement with electrophoretic experiments done under conditions of low and high electric fields.

Algorithms↗
PubMed2005

Superficial and deep changes of cellular mechanical properties following cytoskeleton disassembly.

The cytoskeleton, composed of actin filaments, intermediate filaments, and microtubules, is a highly dynamic supramolecular network actively involved in many essential biological mechanisms such as cellular structure, transport, movements, differentiation, and signaling. As a first step to characterize the biophysical changes associated with cytoskeleton functions, we have developed finite elements models of the organization of the cell that has allowed us to interpret atomic force microscopy (AFM) data at a higher resolution than that in previous work. Thus, by assuming that living cells behave mechanically as multilayered structures, we have been able to identify superficial and deep effects that could be related to actin and microtubule disassembly, respectively. In Cos-7 cells, actin destabilization with Cytochalasin D induced a decrease of the visco-elasticity close to the membrane surface, while destabilizing microtubules with Nocodazole produced a stiffness decrease only in deeper parts of the cell. In both cases, these effects were reversible. Cell softening was measurable with AFM at concentrations of the destabilizing agents that did not induce detectable effects on the cytoskeleton network when viewing the cells with fluorescent confocal microscopy. All experimental results could be simulated by our models. This technology opens the door to the study of the biophysical properties of signaling domains extending from the cell surface to deeper parts of the cell.

Actins↗
PubMed2005

Interactive measurement and characterization of DNA molecules by analysis of AFM images.

BACKGROUND: In the past few years, computer-based analysis of atomic-force microscopic images has acquired increasing importance for studying biomolecules such as DNA. On the one hand, fully automated methods do not allow analysis of complex shapes; on the other hand, manual methods are usually time consuming and inaccurate. The semiautomated approach presented in this report overcomes the drawbacks of both methods. METHODS: Two kinds of images were analyzed: computer-generated filaments that modeled circular DNA molecules on a surface and real atomic-force microscopic images of DNA molecules adsorbed on an appropriate substrate surface. RESULTS: The algorithm was tested on a group of 140 simulated and 189 real plasmids with a nominal length of 913 nm. The accuracy of the length measurement was statistically evaluated on the ensemble of molecules, with particular attention to the influence of the noise. Mean contour lengths of 912 +/- 5 nm and 910 +/- 47 nm were found for simulated and real plasmids, respectively. The measured end-to-end distance of lambda-DNA molecules as a function of their contour length is reported, from which it is possible to estimate the stiffness of the DNA molecules adsorbed onto a surface; the value obtained for the DNA persistence length (42 +/- 5 nm) is consistent with values measured by other imaging techniques. CONCLUSIONS: An interactive algorithm for DNA molecule measurements based on the detection of the filament ridge line in a digitized image is presented. The simulation of artificial filaments combined with the experimental data demonstrates that the proposed method can be a valuable tool for the DNA contour length evaluation, especially in the case of complex shapes where the use of automatic methods is not possible.

Algorithms↗
PubMed2004

Oscillation modes of microtubules.

Microtubules are long, filamentous protein complexes which play a central role in several cellular physiological processes, such as cell division transport and locomotion. Their mechanical properties are extremely important since they determine the biological function. In a recently published experiment [Phys. Rev. Lett. 89 (2002) 248101], microtubule's Young's and shear moduli were simultaneously measured, proving that they are highly anisotropic. Together with the known structure, this finding opens the way to better understand and predict their mechanical behavior under a particular set of conditions. In the present study, we modeled microtubules by using the finite elements method and analyzed their oscillation modes. The analysis revealed that oscillation modes involving a change in the diameter of the microtubules strongly depend on the shear modulus. In these modes, the correlation times of the movements are just slightly shorter than diffusion times of free molecules surrounding the microtubule. It could be therefore speculated that the matching of the two timescales could play a role in facilitating the interactions between microtubules and MT associated proteins, and between microtubules and tubulins themselves.

Animals↗
PubMed2004

Shear force distance control in a scanning near-field optical microscope: in resonance excitation of the fiber probe versus out of resonance excitation.

The experimental results of the direct measurement of the absolute value of interaction force between the fiber probe of a scanning near-field optical microscope (SNOM) operated in shear force mode and a sample, which were performed using combined SNOM-atomic force microscope setup, are discussed for the out-of-resonance fiber probe excitation mode. We demonstrate that the value of the tapping component of the total force for this mode at typical dither amplitudes is of the order of 10 nN and thus is quite comparable with the value of this force for in resonance fiber probe excitation mode. It is also shown that for all modes this force component is essentially smaller than the usually neglected static attraction force, which is of the order of 200 nN. The true contact nature of the tip-sample interaction during the out of resonance mode is proven. From this, we conclude that such a detection mode is very promising for operation in liquids, where other modes encounter great difficulties.

Journal Article↗
PubMed2003

Interactions between synaptic vesicle fusion proteins explored by atomic force microscopy.

Measuring the biophysical properties of macromolecular complexes at work is a major challenge of modern biology. The protein complex composed of vesicle-associated membrane protein 2, synaptosomal-associated protein of 25 kDa, and syntaxin 1 [soluble N-ethyl-maleimide-sensitive factor attachment protein receptor (SNARE) complex] is essential for docking and fusion of neurotransmitter-filled synaptic vesicles with the presynaptic membrane. To better understand the fusion mechanisms, we reconstituted the synaptic SNARE complex in the imaging chamber of an atomic force microscope and measured the interaction forces between its components. Each protein was tested against the two others, taken either individually or as binary complexes. This approach allowed us to determine specific interaction forces and dissociation kinetics of the SNAREs and led us to propose a sequence of interactions. A theoretical model based on our measurements suggests that a minimum of four complexes is probably necessary for fusion to occur. We also showed that the regulatory protein neuronal Sec1 injected into the atomic force microscope chamber prevented the complex formation. Finally, we measured the effect of tetanus toxin protease on the SNARE complex and its activity by on-line registration during tetanus toxin injection. These experiments provide a basis for the functional study of protein microdomains and also suggest opportunities for sensitive screening of drugs that can modulate protein-protein interactions.

Antigens, Surface↗
PubMed2003

Scanning near-field optical microscopy using semiconductor nanocrystals as a local fluorescence and fluorescence resonance energy transfer source.

Local fluorescence probes based on CdSe semiconductor nanocrystals were prepared and tested by recording scanning near-field optical microscopy (SNOM) images of calibration samples and fluorescence resonance energy transfer SNOM (FRET SNOM) images of acceptor dye molecules inhomogeneously deposited onto a glass substrate. Thousands of nanocrystals contribute to the signal when this probe is used as a local fluorescence source while only tens of those (the most apical) are involved in imaging for the FRET SNOM operation mode. The dip-coating method used to make the probe enables diminishing the number of active fluorescent nanocrystals easily. Prospects to realize FRET SNOM based on a single fluorescence centre using such an approach are briefly described.

Journal Article↗
PubMed2003

Vitrification of cryoelectron microscopy specimens revealed by high-speed photographic imaging.

Cryoelectron microsopy is a widely used technique to observe biological material in an almost physiological, fully hydrated state. The sample is prepared for electron microsopy observation by quickly reducing its temperature to -180 degrees C. The high-speed cooling induces the formation of vitreous water, which preserves the sample conformation. However, the way vitrification occurs is still poorly understood. In order to better understand the phenomenon, we have used a stroboscopic device to visualize the interaction between the electron microscopy grid and the cryogen. By blocking the free fall of the plunger once the grid has penetrated the coolant by half its diameter, we have elucidated the way in which vitrification propagates. The findings were confirmed by numerical simulation. In addition, according to our observations, we now present an alternative way to prepare vitreous specimens. This new method, with the grid parallel to the liquid cryogen surface, decreases evaporation from the sample during its free fall towards the coolant and at the same time achieves a more uniform vitrification over the entire surface of the specimen.

Cryoelectron Microscopy↗
PubMed2002

AFM structural study of the molecular chaperone GroEL and its two-dimensional crystals: an ideal "living" calibration sample.

Supramolecular complexes, such as chaperonins, are suitable samples for atomic force microscope structural studies because they have a very well defined shape. High-resolution images can be made using tapping mode in liquid under native conditions. Details about the two-dimensional structures formed onto the surface upon adsorption and of the single protein can be observed. Dissection of the upper ring of the supramolecular complex as a result of the applied lateral force through scanning tip is observed. Finally, the combination of lateral convolution and tip penetration into the cavity of chaperonins offers a direct evaluation of the tip convolution effect on images of macromolecular samples.

Calibration↗
PubMed2001

Automatic classification of HITS into artifacts or solid or gaseous emboli by a wavelet representation combined with dual-gate TCD.

BACKGROUND AND PURPOSE: Transcranial Doppler (TCD) can detect high-intensity transient signals (HITS) in the cerebral circulation. HITS may correspond to artifacts or solid or gaseous emboli. The aim of this study was to develop an offline automated Doppler system allowing the classification of HITS. METHODS: We studied 600 HITS in vivo, including 200 artifacts from normal subjects, 200 solid emboli from patients with symptomatic internal carotid artery stenosis, and 200 gaseous emboli in stroke patients with patent foramen ovale. The study was 2-fold, each part involving 300 HITS (100 of each type). The first 300 HITS (learning set) were used to construct an automated classification algorithm. The remaining 300 HITS (validation set) were used to check the validity of this algorithm. To classify HITS, we combined dual-gate TCD with a wavelet representation and compared it with the current "gold standard," the human experts. RESULTS: A combination of the peak frequency of HITS and the time delay makes it possible to separate artifacts from emboli. On the validation set, we achieved a sensitivity of 97%, a specificity of 98%, a positive predictive value (PPV) of 99%, and a negative predictive value (NPV) of 94%. To distinguish between solid and gaseous emboli, where positive refers now to the solid emboli, we used the peak frequency, the relative power, and the envelope symmetry of HITS. On the validation set, we achieved a sensitivity of 89%, a specificity of 86%, a conditional PPV of 89%, and a conditional NPV of 89%. CONCLUSIONS: An automated wavelet representation combined with dual-gate TCD can reliably reject artifacts from emboli. From a clinical standpoint, however, this approach has only a fair accuracy in differentiating between solid and gaseous emboli.

Adult↗
PubMed2001

Single-molecule imaging by atomic force microscopy of the native chaperonin complex of the thermophilic archaeon Sulfolobus solfataricus.

The chaperonin of the extremely thermophilic archaeon Sulfolobus solfataricus has been imaged for the first time under native conditions using the atomic force microscope. This technique allows to visualize the structure of biomolecules in solution under physiological conditions providing a nanometer resolution topographic image of the sample. Single molecule studies can reveal fine structural details, providing a powerful insight into the active conformation of a macromolecule, and also allowing to detect different conformational states corresponding to functional changes.

Archaeal Proteins↗
PubMed2001

Examination of line crossings by atomic force microscopy.

Until now, the most widely used methods for the forensic examination of line crossings in documents were optical and electron microscopy. The combination of both techniques allows one in most cases to establish the sequence of lines. The recent development of scanning probe microscopy [1] gives an opportunity to complement or even replace the classical instruments used in this field. Scanning probe microscopes have been designed to study surfaces at high magnification. The aim of this study was to verify if their most popular member, the atomic force microscope (AFM) [2], can be applied to line crossing problems. The results show for the first time that AFM images present the same qualitative information obtained by scanning electron microscope (SEM) images and, consequently, allow the determination of the line crossing sequence under ambient conditions without vacuum and conductive coating of specimens.

Forensic Medicine↗
PubMed2001

Analysis of fiber probes of scanning near-field optical microscope by field emission microscopy.

It is shown that field emission microscopy and related methods can be used to analyze the metal coated fiber tips, which nowadays are the most frequently used sensor for the scanning near-field optical microscopy (SNOM). Metal free and thus non field-emitting aperture for the light transmission on the tip apex can be directly seen and its parameters can be measured, which is very important for the interpretation of SNOM data.

Journal Article↗
PubMed2001

Imaging the native structure of the chaperone protein GroEL without fixation using atomic force microscopy.

Most sample preparation methods for scanning probe or electron microscopy require that biomolecules, such as proteins, be fixed. Fixation destroys the molecular functionality and can possibly affect the true molecular structure. Here we report sample preparation conditions that allow the imaging of an unfixed protein, GroEL, under in-vivo conditions, by atomic force microscopy. Under these conditions, the protein should maintain its native structure and biological activity. The typical toroidal shape with pore of the GroEL complex was easily visible in the images. Images of a single complex show dimensions that agree well with crystallographic data. Under in-vivo conditions, it should be possible to study the biological activity and function of proteins.

Chaperonin 60↗
PubMed1996

Kinetics of cellular viability in warm versus cold ischemia conditions of kidney preservation. A biometric study.

We have determined the kinetics of the cellular viability ratio (CVR), defined as the number of living cells over the total cell count, in pig kidneys using propidium iodide and fluorescein diacetate staining, as a function of time and preservation conditions. The kidneys were preserved in warm or cold ischemia in order to mimic the conditions of transplantation from non-heart-beating donors or multiple removal with optimal preservation of the graft, respectively. To determine the CVR, the cells were obtained by a fine-needle aspiration biopsy, which minimizes the damage to the graft. A biometric analysis by regression enabled the determination of the time dependence for warm ischemia (CVR(t) = 80.0 x e(-0.733-t)(+2.7/-0.36)) and for cold ischemia (CVR(t) = 80.0 x e(-0.022-t)(+1.57/-0.64)) with a confidence interval of 95%. These master curves allow us to predict, under the described conditions, the CVR after a given ischemia time. The half-life of the cells can be deduced from the time-dependent CVR(t), and is 0.64 hr (38 min) for warm ischemia and 21.4 hr for cold ischemia. Further, the CVR for a given kidney can be used to assess its condition at removal: if the CVR is below 48% at 2 hr after removal, one can conclude that the organ has suffered a period of warm ischemia.

Animals↗