Oliver Strbak

Quantitation of magnetic resonance spectroscopy signals: the jMRUI software package

The software package jMRUI with Java-based graphical user interface enables user-friendly time-domain analysis of magnetic resonance spectroscopy (MRS) and spectroscopic imaging (MRSI) and HRMAS-NMR signals. Version 3.x has been distributed in more than 1200 groups or hospitals worldwide. The new version 4.x is a plug-in platform enabling the users to add their own algorithms. Moreover, it offers new functionalities compared to versions 3.x. The quantum-mechanical simulator based on NMR-SCOPE, the quantitation algorithm QUEST and the main MRSI functionalities are described. Quantitation results of signals obtained in vivo from a mouse and a human brain are given.

Simulation of coupled-spin systems in the steady-state free-precession acquisition mode for fast magnetic resonance (MR) spectroscopic imaging

The steady-state free-precession (SSFP) acquisition mode may be found useful for fast in vivo proton magnetic resonance spectroscopic imaging in high-field MR systems because of the achievable signal-to-noise ratio and the avoidance of RF pulses with large flip angles. Detection of signals from metabolites with coupled-spin systems under SSFP has not yet been accomplished, but should be possible in high field, albeit with substantial signal truncation. It must be expected that the spin system evolution and the spectra will be affected by the steady-state conditions, which prevent the spin systems from returning to the Boltzmann equilibrium. Computer simulation is needed for the experiment design and spectrum quantification. This work outlines a suitable simulation method (QuaM-EPG), which combines and extends two pre-existing approaches: the density matrix calculation, used in high-resolution NMR, and the extended phase graph method, used to describe cyclic excitation in fast MRI of water protons. The method is illustrated by its application to model molecules and myo-inositol, which is one of the clinically relevant target molecules. It is shown that antiphase and multiple-quantum coherences may represent a considerable portion of the steady-state magnetization in a quantum-mechanical sense and that the spectral patterns are affected thereby.

jMRUI Version 4 : A plug-in platform

The software package jMRUI with Java-based graphical user interface enables user-friendly time-domain analysis of magnetic resonance spectroscopy (MRS) and spectroscopic imaging (MRSI), and HRMAS-NMR signals. The version 3.x has been distributed in more than 1000 groups or hospitals world-wide. The new version 4.x is a plug-in platform enabling the users to add their own algorithms. Moreover, it offers new functionalities compared to the versions 3.x.

Biogenic Magnetite in Humans and New Magnetic Resonance Hazard Questions

Biogenic Magnetite in Humans and New Magnetic Resonance Hazard Questions The widespread use of magnetic resonance (MR) techniques in clinical practice, and recent discovery of biogenic ferrimagnetic substances in human tissue, open new questions regarding health hazards and MR. Current studies are restricted just to the induction of Faraday currents and consequent thermal effects, or ‘inoffensive’ interaction with static magnetic field. We outlined that magnetic energies associated with interaction of ferrimagnetic particles and MR magnetic fields can be dangerous for sensitive tissues like the human brain is. To simulate the interaction mechanism we use our. ‘Cube’ model approach, which allows more realistic calculation of the particles magnetic moments. Biogenic magnetite nanoparticles face during MR examination three principal fields: (i) main B0 field, (ii) gradient field, and (iii) B1 field. Interaction energy of biogenic magnetite nanoparticle with static magnetic field B0 exceeds the covalent bond energy 5 times for particles from 4 nm up to 150 nm. Translation energy in gradient field exceeds biochemical bond energy for particles bigger than 50 nm. Biochemical bond disruption and particle release to the tissue environment, in the presence of all MR fields, are the most critical points of this interaction. And together with relaxation processes after application of RF pulses, they make biogenic magnetite nanoparticles a potential MR health hazard issue.

Single Biogenic Magnetite Nanoparticle Physical Characteristics—A Biological Impact Study (For MagMeet 2012 Participants)

Discovery of biogenic magnetite nanoparticles in living systems, including human brain tissue, raises new questions. Apart from the reasons answering the purpose of ferrimagnetic nanoparticle biomineralization there are also questions about the biophysical interactions. Since single domain magnetite nanoparticles are characteristic for their high magnetic moment, the basic unresolved problem is whether the nanoparticles are able to (directly by their own magnetic field or indirectly through interaction with external magnetic fields) affect biological processes. First, we have studied whether the magnetic gradient field of nanoparticles can affect the ion flow through the neuronal membrane during the transmission of action potential. This was not confirmed. Furthermore, we have studied the interaction energy of nanoparticles with an external magnetic field in comparison with the energy of biological bonds. Translational energy of magnetic gradient can be neglected. Simulation data, however, suggest that the rotational energy of interaction with the static magnetic field exceeds the energy of biological bonds. This confirms the idea of magnetoreception mechanism.

Proton Gradients as a Key Physical Factor in the Evolution of the Forced Transport Mechanism Across the Lipid Membrane

A critical phase in the transition from prebiotic chemistry to biological evolution was apparently an asymmetric ion flow across the lipid membrane. Due to imbalance in the ion flow, the early lipid vesicles could selectively take the necessary molecules from the environment, and release the side-products from the vesicle. Natural proton gradients played a definitively crucial role in this process, since they remain the basis of energy transfer in the present-day cells. On the basis of this supposition, and the premise of the early vesicle membrane’s impermeability to protons, we have shown that the emergence of the proton gradient in the lipid vesicle could be a key physical factor in the evolution of the forced transport mechanism (pore formation and active transport) across the lipid bilayer. This driven flow of protons across the membrane is the result of the electrochemical proton gradient and osmotic pressures on the integrity of the lipid vesicle. At a critical number of new lipid molecules incorporated into the vesicle, the energies associated with the creation of the proton gradient exceed the bending stiffness of the lipid membrane, and overlap the free energy of the lipid bilayer pore formation.

Exploring Fingerprints of the Extreme Thermoacidophile Metallosphaera sedula Grown on Synthetic Martian Regolith Materials as the Sole Energy Sources

The biology of metal transforming microorganisms is of a fundamental and applied importance for our understanding of past and present biogeochemical processes on Earth and in the Universe. The extreme thermoacidophile Metallosphaera sedula is a metal mobilizing archaeon, which thrives in hot acid environments (optimal growth at 74°C and pH 2.0) and utilizes energy from the oxidation of reduced metal inorganic sources. These characteristics of M. sedula make it an ideal organism to further our knowledge of the biogeochemical processes of possible life on extraterrestrial planetary bodies. Exploring the viability and metal extraction capacity of M. sedula living on and interacting with synthetic extraterrestrial minerals, we show that M. sedula utilizes metals trapped in the Martian regolith simulants (JSC Mars 1A; P-MRS; S-MRS; MRS07/52) as the sole energy sources. The obtained set of microbiological and mineralogical data suggests that M. sedula actively colonizes synthetic Martian regolith materials and releases free soluble metals. The surface of bioprocessed Martian regolith simulants is analyzed for specific mineralogical fingerprints left upon M. sedula growth. The obtained results provide insights of biomining of extraterrestrial material as well as of the detection of biosignatures implementing in life search missions.

Correction to: “Single Biogenic Magnetite Nanoparticle Physical Characteristics. A Biological Impact Study” [Jan 13 457-462]

Various errors in Section III are corrected for the above-named article [ibid., vol. 49, no. 1, pp. 457-462, Jan. 2013].

Simulation of steady state free precession acquisition mode in coupled spin systems for fast MR spectroscopic imaging

Steady state free precession (SSFP) is an acquisition mode that may be useful for fast magnetic resonance spectroscopic imaging in high field MR systems because of the high achievable SNR. In such systems, metabolites with coupled spin systems may be observed, but the knowledge of their behavior and the induced spectral changes is still limited. Such information is needed for both experiment design and spectrum quantification. This work presents computer simulations of model molecules and of myo-inositol, which is one of the clinically relevant target molecules and describes the algorithm used. It is shown that antiphase and multiple-quantum coherences may represent a considerable portion of the steady state. The effects in spectra are studied based on hypothesized relaxation parameters.