Wednesday, December 30, 2015

Characterization of Membrane Proteins in Isolated Native Cellular Membranes by Dynamic Nuclear Polarization Solid-State NMR Spectroscopy without Purification and Reconstitution


Jacso, T., et al., Characterization of Membrane Proteins in Isolated Native Cellular Membranes by Dynamic Nuclear Polarization Solid-State NMR Spectroscopy without Purification and Reconstitution. Angewandte Chemie, 2012. 124(2): p. 447-450.


Structural information is key for understanding biological processes. Insoluble proteins, like membrane proteins and amyloid fibrils, are a large class of proteins that are underrepresented in the protein data bank (PDB). As of today, only 7% of all entries in the PDB refer to either a membrane protein or an amyloid fibril structure (membrane protein: 4994 entries; amyloid fibril: 67 entries; total number of entries: 70,303; http://www.rcsb.org/pdb/home/home.do). Given the fact that many drugs target membrane proteins, involved in signal transduction, [1] structural information is highly desirable for a better understanding of the underlying biochemical mechanisms.

Monday, December 28, 2015

Metabolic imaging of patients with prostate cancer using hyperpolarized [1-(1)(3)C]pyruvate


Nelson, S.J., et al., Metabolic imaging of patients with prostate cancer using hyperpolarized [1-(1)(3)C]pyruvate. Sci Transl Med, 2013. 5(198): p. 198ra108.


This first-in-man imaging study evaluated the safety and feasibility of hyperpolarized [1-(1)(3)C]pyruvate as an agent for noninvasively characterizing alterations in tumor metabolism for patients with prostate cancer. Imaging living systems with hyperpolarized agents can result in more than 10,000-fold enhancement in signal relative to conventional magnetic resonance (MR) imaging. When combined with the rapid acquisition of in vivo (1)(3)C MR data, it is possible to evaluate the distribution of agents such as [1-(1)(3)C]pyruvate and its metabolic products lactate, alanine, and bicarbonate in a matter of seconds. Preclinical studies in cancer models have detected elevated levels of hyperpolarized [1-(1)(3)C]lactate in tumor, with the ratio of [1-(1)(3)C]lactate/[1-(1)(3)C]pyruvate being increased in high-grade tumors and decreased after successful treatment. Translation of this technology into humans was achieved by modifying the instrument that generates the hyperpolarized agent, constructing specialized radio frequency coils to detect (1)(3)C nuclei, and developing new pulse sequences to efficiently capture the signal. The study population comprised patients with biopsy-proven prostate cancer, with 31 subjects being injected with hyperpolarized [1-(1)(3)C]pyruvate. The median time to deliver the agent was 66 s, and uptake was observed about 20 s after injection. No dose-limiting toxicities were observed, and the highest dose (0.43 ml/kg of 230 mM agent) gave the best signal-to-noise ratio for hyperpolarized [1-(1)(3)C]pyruvate. The results were extremely promising in not only confirming the safety of the agent but also showing elevated [1-(1)(3)C]lactate/[1-(1)(3)C]pyruvate in regions of biopsy-proven cancer. These findings will be valuable for noninvasive cancer diagnosis and treatment monitoring in future clinical trials.

Wednesday, December 23, 2015

Coherent Control of Two Nuclear Spins Using the Anisotropic Hyperfine Interaction


Zhang, Y., C.A. Ryan, R. Laflamme, and J. Baugh, Phys. Rev. Lett., 107, (2011)


We demonstrate coherent control of two nuclear spins mediated by the magnetic resonance of a hyperfine-coupled electron spin. This control is used to create a double-nuclear coherence in one of the two electron spin manifolds, starting from an initial thermal state, in direct analogy to the creation of an entangled (Bell) state from an initially pure unentangled state. We identify challenges and potential solutions to obtaining experimental gate fidelities useful for quantum information processing in this type of system.

Monday, December 21, 2015

Detecting tumor response to treatment using hyperpolarized 13C magnetic resonance imaging and spectroscopy


Day, S.E., M.I. Kettunen, F.A. Gallagher, D.-E. Hu, M. Lerche, J. Wolber, K. Golman, J.H. Ardenkjaer-Larsen, and K.M. Brindle, Nat Med, 13, (2007)


Measurements of early tumor responses to therapy have been shown, in some cases, to predict treatment outcome. We show in lymphoma-bearing mice injected intravenously with hyperpolarized [1-13C]pyruvate that the lactate dehydrogenase–catalyzed flux of13C label between the carboxyl groups of pyruvate and lactate in the tumor can be measured using 13C magnetic resonance spectroscopy and spectroscopic imaging, and that this flux is inhibited within 24 h of chemotherapy. The reduction in the measured flux after drug treatment and the induction of tumor cell death can be explained by loss of the coenzyme NAD(H) and decreases in concentrations of lactate and enzyme in the tumors. The technique could provide a new way to assess tumor responses to treatment in the clinic.

Friday, December 18, 2015

Microwave frequency modulation to enhance Dissolution Dynamic Nuclear Polarization


Bornet, A., J. Milani, B. Vuichoud, A.J. Perez Linde, G. Bodenhausen, and S. Jannin, Chem. Phys. Lett., 602, (2014)


Hyperpolarization by Dissolution Dynamic Nuclear Polarization is usually achieved by monochromatic microwave irradiation of the ESR spectrum of free radicals embedded in glasses at 1.2 K and 3.35 T. Hovav et al. (2014) have recently shown that by using frequency-modulated (rather than monochromatic) microwave irradiation one can improve DNP at 3.35 T in the temperature range 10–50 K. We show in this Letter that this is also true under Dissolution-DNP conditions at 1.2 K and 6.7 T. We demonstrate the many virtues of using frequency-modulated microwave irradiation: higher polarizations, faster build-up rates, lower radical concentrations, less paramagnetic broadening, more efficient cross-polarization, and less critical frequency adjustments.

Wednesday, December 16, 2015

Production of hyperpolarized [1,4-13C2]malate from [1,4-13C2]fumarate is a marker of cell necrosis and treatment response in tumors


Gallagher, F.A., M.I. Kettunen, D.E. Hu, P.R. Jensen, R.I. Zandt, M. Karlsson, A. Gisselsson, S.K. Nelson, T.H. Witney, S.E. Bohndiek, G. Hansson, T. Peitersen, M.H. Lerche, and K.M. Brindle, Proc Natl Acad Sci U S A, 106, (2009)


Dynamic nuclear polarization of (13)C-labeled cell substrates has been shown to massively increase their sensitivity to detection in NMR experiments. The sensitivity gain is sufficiently large that if these polarized molecules are injected intravenously, their spatial distribution and subsequent conversion into other cell metabolites can be imaged. We have used this method to image the conversion of fumarate to malate in a murine lymphoma tumor in vivo after i.v. injection of hyperpolarized [1,4-(13)C(2)]fumarate. In isolated lymphoma cells, the rate of labeled malate production was unaffected by coadministration of succinate, which competes with fumarate for transport into the cell. There was, however, a correlation with the percentage of cells that had lost plasma membrane integrity, suggesting that the production of labeled malate from fumarate is a sensitive marker of cellular necrosis. Twenty-four hours after treating implanted lymphoma tumors with etoposide, at which point there were significant levels of tumor cell necrosis, there was a 2.4-fold increase in hyperpolarized [1,4-(13)C(2)]malate production compared with the untreated tumors. Therefore, the formation of hyperpolarized (13)C-labeled malate from [1,4-(13)C(2)]fumarate appears to be a sensitive marker of tumor cell death in vivo and could be used to detect the early response of tumors to treatment. Given that fumarate is an endogenous molecule, this technique has the potential to be used clinically.

Monday, December 14, 2015

Metabolic Imaging by Hyperpolarized 13C Magnetic Resonance Imaging for In vivo Tumor Diagnosis


Golman, K., R.I. Zandt, M. Lerche, R. Pehrson, and J.H. Ardenkjaer-Larsen, Cancer research, 66, (2006)


The "Warburg effect," an elevation in aerobic glycolysis, may be a fundamental property of cancer cells. For cancer diagnosis and treatment, it would be valuable if elevated glycolytic metabolism could be quantified in an image in animals and humans. The pyruvate molecule is at the metabolic crossroad for energy delivery inside the cell, and with a noninvasive measurement of the relative transformation of pyruvate into lactate and alanine within a biologically relevant time frame (seconds), it may be possible to quantify the glycolytic status of the cells. We have examined the metabolism after i.v. injection of hyperpolarized (13)C-pyruvate in rats with implanted P22 tumors. The strongly enhanced nuclear magnetic resonance signal generated by the hyperpolarization techniques allows mapping of pyruvate, lactate, and alanine in a 5 x 5 x 10 mm(3) imaging voxel using a 1.5 T magnetic resonance scanner. The magnetic resonance scanning (chemical shift imaging) was initiated 24 seconds after the pyruvate injection and had a duration of 14 seconds. All implanted tumors showed significantly higher lactate content than the normal tissue. The results indicate that noninvasive quantification of localized Warburg effect may be possible.

Friday, December 11, 2015

Rapid-melt Dynamic Nuclear Polarization


Sharma, M., et al., Rapid-melt Dynamic Nuclear Polarization. J Magn Reson, 2015. 258: p. 40-8.


In recent years, Dynamic Nuclear Polarization (DNP) has re-emerged as a means to ameliorate the inherent problem of low sensitivity in nuclear magnetic resonance (NMR). Here, we present a novel approach to DNP enhanced liquid-state NMR based on rapid melting of a solid hyperpolarized sample followed by 'in situ' NMR detection. This method is applicable to small (10nl to 1mul) sized samples in a microfluidic setup. The method combines generic DNP enhancement in the solid state with the high sensitivity of stripline (1)H NMR detection in the liquid state. Fast cycling facilitates options for signal averaging or 2D structural analysis. Preliminary tests show solid-state (1)H enhancement factors of up to 500 for H2O/D2O/d6-glycerol samples doped with TEMPOL radicals. Fast paramagnetic relaxation with nitroxide radicals, In nonpolar solvents such as toluene, we find proton enhancement factors up to 400 with negligible relaxation losses in the liquid state, using commercially available BDPA radicals. A total recycling delay (including sample freezing, DNP polarization and melting) of about 5s can be used. The present setup allows for a fast determination of the hyper-polarization as function of the microwave frequency and power. Even at the relatively low field of 3.4T, the method of rapid melting DNP can facilitate the detection of small quantities of molecules in the picomole regime.

Wednesday, December 9, 2015

PRESTO polarization transfer to quadrupolar nuclei: implications for dynamic nuclear polarization


Perras, F.A., T. Kobayashi, and M. Pruski, PRESTO polarization transfer to quadrupolar nuclei: implications for dynamic nuclear polarization. Phys Chem Chem Phys, 2015. 17(35): p. 22616-22.


We show both experimentally and numerically on a series of model systems that in experiments involving transfer of magnetization from (1)H to the quadrupolar nuclei under magic-angle-spinning (MAS), the PRESTO technique consistently outperforms traditionally used cross polarization (CP), affording more quantitative intensities, improved lineshapes, better overall sensitivity, and straightforward optimization. This advantage derives from the fact that PRESTO circumvents the convoluted and uncooperative spin dynamics during the CP transfer under MAS, by replacing the spin-locking of quadrupolar nuclei with a single central transition selective 90 degrees pulse and using a symmetry-based recoupling sequence in the (1)H channel. This is of particular importance in the context of dynamic nuclear polarization (DNP) NMR of quadrupolar nuclei, where the efficient transfer of enhanced (1)H polarization is desired to obtain the highest sensitivity.

Tuesday, December 8, 2015

[NMR] PhD position / Solid-State NMR / Utrecht / Bio-inspired Nanomaterials

From the Ampere Magnetic Resonance List


PhD position / Solid-State NMR / Utrecht / Bio-inspired Nanomaterials

We invite applications for a 4-years PhD position in the field of biomolecular solid-state NMR at the Bijvoet Center, Utrecht University, The Netherlands. The research deals with the atomic-level characterization of bio-inspired self-assembling nanomaterials for pharmaceutical and medical applications using a combined approach of modern solid-state NMR & MD simulation methods. Further information to the project is available by email (to m.h.weingarth@uu.nl).

The position is offered in the junior research group of by M. Weingarth, embedded in the NMR group of Prof. M. Baldus. We offer access to high-field NMR machines (950, 800, 700, 500, 400 MHz for solid-state NMR // 900 MHz magnet for solution NMR). A 1.2 GHz machine will be installed within the next years. The 950, 800 and 700 MHz machines are equipped with fast-spinning 1.3 mm probes. The 800 and 400 MHz magnetes are equipped for DNP. The candidate will have access to a powerful computational infrastructure and a well-equipped molecular biology lab. Research will also be carried out in collaboration with pharmaceutical groups.

Applicants should have a degree in biochemistry/biophysics or a related discipline. Cross-disciplinary applications are welcome. Strong experience in molecular biology techniques & protein/nucleic acid preparation is desirable. Experience in either MD simulations, NMR or programming is a plus, but not required. The starting date is March/April 2016 or later.

To apply, please send a (brief) cover letter, your CV as well as the names and the contact addresses of two references to:

Dr. Markus Weingarth / Phone: +31 30 253 2875 / Email : m.h.weingarth@uu.nl

See also here for further information: http://www.uu.nl/medewerkers/MHWeingarth

Project-relevant publications:

I.Rad Malekshahi, M., Visscher. K.M., Rodrigues J.P.G.L.M., de Vries, R., Hennink, W.E., Baldus, M., Bonvin A.M.J.J., Mastrobattista E., Weingarth. M. (2015) J. Am. Chem. Soc., 137, 7775, The supramolecular organization of a peptide based nanocarrier at high molecular detail

II. Mance, D., Sinnige., T., Kaplan, M., Daniels, M., Houben, K., Baldus, M., Weingarth, M. (2015) Angew. Chem., in press,A labeling approach to harness backbone and side chain protons in 1H-detected solid-state NMR

III. Sinnige, T., Daniels, M., Baldus, M., Weingarth, M. (2014) J. Am. Chem. Soc., 136, 4452. Proton clouds to measure nonexchangable sidechain protons in solid-state NMR. Cover article

The PhD position is funded by a NWO VIDI grant to M. Weingarth. The candidate is offered a full-time position for 4 years. The salary is supplemented with a holiday bonus of 8.0% and an end-of-year bonus of 8,3% per year. The salary starts at ca. € 2.100 and increases to € 2.700 gross per month in the fourth year.

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[NMR] Postdoctoral opportunity available – Nanometer-scale magnetic resonance

From the Ampere Magnetic Resonance List




The Karlsruhe Institute of Technology (KIT) is seeking an experienced postdoctoral researcher to initiate activities in the area of nanometer-scale magnetic resonance (nano-MR). Such activities may include, but are not limited to, techniques based on magnetic resonance force microscopy (MRFM), or nitrogen vacancy (NV) centers.

The ideal candidate will have a proven track record in nano-MR technology. She/he will be a highly motivated individual, and will be interested in building an independent research group. The candidate will be expected to build up nano-MR activities, with a focus on room temperature applications, within the highly collaborative environment available at KIT.

The candidate will formally join the Institute of Microstructure Technology (IMT), within the Science and Technology of Nanosystems (STN) framework, under the guidance of Prof. Jan G. Korvink. IMT features excellent infrastructure within which nano-MR activities would be expected to flourish. Specifically, IMT has a fully equipped RF characterization lab, a Bruker 500 MHz wide-bore NMR system, a Bruker 1 T ICON MRI system, e-beam lithography, 3D nanolithography, state-of-the art clean room facilities, as well as an in-house AFM competence centre led by Dr. Hendrik Hölscher. Prof. Korvink’s group specializes in micro-NMR detector design and implementation, has activities in hyperpolarisation techniques (para-H2 and DNP), and hence offers an excellent environment within which to build up new and exciting nano-MR techniques. The position is funded for two years. Interested applicants should send a motivation letter, their CV, and a copy of their most relevant publication(s) as a single pdf file to Prof. Jan G. Korvink (jan.korvink@kit.edu). The position will remain open until a suitable candidate is identified. We aim to balance the number of female and male employees at KIT. We therefore expressly encourage female applicants to apply for this job. Applicants with disabilities will be preferentially considered if equally qualified.

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Monday, December 7, 2015

Solid-State Dynamic Nuclear Polarization at 9.4 and 18.8 T from 100 K to Room Temperature


Lelli, M., et al., Solid-State Dynamic Nuclear Polarization at 9.4 and 18.8 T from 100 K to Room Temperature. J Am Chem Soc, 2015. 137(46): p. 14558-61.


Efficient dynamic nuclear polarization (DNP) in solids, which enables very high sensitivity NMR experiments, is currently limited to temperatures of around 100 K and below. Here we show how by choosing an adequate solvent, (1)H cross effect DNP enhancements of over 80 can be obtained at 240 K. To achieve this we use the biradical TEKPol dissolved in a glassy phase of ortho-terphenyl (OTP). We study the solvent DNP enhancement of both TEKPol and BDPA in OTP in the range from 100 to 300 K at 9.4 and 18.8 T. Surprisingly, we find that the DNP enhancement decreases only relatively slowly for temperatures below the glass transition of OTP (Tg = 243 K), and (1)H enhancements around 15-20 at ambient temperature can be observed. We use this to monitor molecular dynamic transitions in the pharmaceutically relevant solids Ambroxol and Ibuprofen.

Friday, December 4, 2015

Application of Good's buffers to pH imaging using hyperpolarized (13)C MRI


Flavell, R.R., et al., Application of Good's buffers to pH imaging using hyperpolarized (13)C MRI. Chem Commun (Camb), 2015. 51(74): p. 14119-22.


N-(2-Acetamido)-2-aminoethanesulfonic acid (ACES), one of Good's buffers, was applied to pH imaging using hyperpolarized (13)C magnetic resonance spectroscopy. Rapid NMR- and MRI-based pH measurements were obtained by exploiting the sensitive pH-dependence of its (13)C chemical shift within the physiologic range.

Wednesday, December 2, 2015

Hyperpolarized NMR of plant and cancer cell extracts at natural abundance


Dumez, J.N., et al., Hyperpolarized NMR of plant and cancer cell extracts at natural abundance. Analyst, 2015. 140(17): p. 5860-3.


Natural abundance (13)C NMR spectra of biological extracts are recorded in a single scan provided that the samples are hyperpolarized by dissolution dynamic nuclear polarization combined with cross polarization. Heteronuclear 2D correlation spectra of hyperpolarized breast cancer cell extracts can also be obtained in a single scan. Hyperpolarized NMR of extracts opens many perspectives for metabolomics.