Avance 3 console

Manufactured by Bruker

Sourced in Germany, United Kingdom, United States

The Avance III console is an advanced NMR spectrometer system produced by Bruker. It serves as the central control and processing unit for nuclear magnetic resonance experiments. The Avance III console provides the necessary hardware and software to generate, receive, and analyze NMR signals. Its core function is to facilitate the operation and data management of NMR spectroscopy equipment.

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Lab products found in correlation

21.1 t magnet, by Bruker (3 mentions) Cptci probe, by Bruker (3 mentions) 7t horizontal bore magnet, by Agilent Technologies (2 mentions) Sodium phosphate, by Thermo Fisher Scientific (1 mentions) Dextran sulfate sodium (dss), by Merck Group (1 mentions) Ethylene diamine tetraacetic acid (edta), by Merck Group (1 mentions) L glutamine, by Thermo Fisher Scientific (1 mentions) Fetal bovine serum (fbs), by Thermo Fisher Scientific (1 mentions) 400 mhz spectrometer, by Bruker (1 mentions) Benzoyl peroxide, by Thermo Fisher Scientific (1 mentions) N butyllithium, by Merck Group (1 mentions) 1 3 dichlorobenzene, by Merck Group (1 mentions) 4 bromoaniline, by Merck Group (1 mentions) Vnmrs spectrometer, by Bruker (1 mentions) Avance 3 hd spectrometer, by Bruker (1 mentions) Warm water circulation system, by Thermo Fisher Scientific (1 mentions) Dotarem, by Guerbet (1 mentions) Cryogenic triple resonance probe, by Bruker (1 mentions) 600 mhz nmr instrument, by Bruker (1 mentions) Ascend 400 mhz, by Bruker (1 mentions)

34 protocols using avance 3 console

High-field NMR Spectroscopy Protocol

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NMR spectra were recorded at 298 K on a Bruker Avance III console (Bruker Biospin, Germany) combined with a 9.7 T Oxford Instruments magnet (¹H 500 MHz), equipped with a 5 mm inverse cryogenically cooled triple-resonance TCI (¹H, ¹³C, ¹⁵N, and ²H lock) cryoprobe with a z-axis magnetic field-gradient capability. The instrument also had a Bruker SampleXpress™ System for sample delivery and an ATMA unit (Bruker Biospin, Germany) for automated tuning and matching. The samples were run under automation by IconNMR and the acquired data were processed using Topspin 3.6

Raldúa D., Casado M., Prats E., Faria M., Puig-Castellví F., Pérez Y., Alfonso I., Hsu C.Y., Arick II M.A., Garcia-Reyero N., Ziv T., Ben-Lulu S., Admon A, & Piña B. (2020). Targeting redox metabolism: the perfect storm induced by acrylamide poisoning in the brain. Scientific Reports, 10, 312.

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NMR Structural Characterization of GluN1 LBD

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All protein samples were buffer exchanged with NMR buffer containing 20 mM sodium phosphate, 100 mM sodium chloride and 0.5 mM 4,4-dimethyl-4-silapentane-1-sufonic acid (DSS) in 100% D₂O, pH 7.4 using a 0.5 mL 10k Da molecular weight cutoff Amicon ultracentrifugal filter. All NMR spectra were collected at 25 °C using 4 mm Shigemi NMR tubes in an 800 MHz spectrometer equipped with cryogenically cooled probe and an Avance III console (Bruker). GluN1 LBD concentrations were between 0.25–0.65 mM with a sample volume of 150 μL. ¹H-¹³C HSQC NMR spectra were collected over 2048 (¹H) × 512 (¹³C) points with 64 scans using 256 dummy scans. The data collection time for each spectrum was approximately 15 hr. All NMR spectra were indirectly referenced to ¹H peak of DSS at 0.07 ppm.

Subedi G.P., Sinitskiy A.V., Roberts J.T., Patel K.R., Pande V.S, & Barb A.W. (2018). Intradomain interactions in an NMDA receptor fragment mediate N-glycan processing and conformational sampling. Structure (London, England : 1993), 27(1), 55-65.e3.

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NMR Characterization of PIRT and CaM

Cited 1 time

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¹⁵N-human PIRT (180 μL, 3 mm NMR tube) and ¹⁵N-human CaM (550 μL, 5 mm NMR tube) were measured in NMR buffer (4% D₂O (v/v, Sigma Aldrich), 20 mM sodium phosphate (Fisher Scientific), 500 µM DSS (Sodium trimethylsilylpropanesulfonate, Sigma Aldrich), and 0.5 mM EDTA (Sigma Aldrich) at pH 6.5) on a Bruker 850 MHz ¹H magnet with Avance III console. Two thousand forty-eight direct points and 128 indirect points were collected with 128 transients, processed in NMRpipe [47 (link)], and analyzed in CCPNMR [48 (link)]. Optimization of NMR conditions for PIRT was carried out previously [24 (link)], resulting in dodecylphosphocholine (DPC) as the most suitable detergent for investigations with PIRT and at a temperature of 40 °C. An HSQC of ¹⁵N-human CaM was measured with and without CaCl₂ to show that it was properly folded in the conditions we tested.
To validate the cholesterol-like and β-estradiol binding site, a saturating concentration of β-estradiol (3.82 mole %) was dissolved in DMSO before adding to a ¹⁵N-human PIRT sample. An HSQC of human PIRT was measured before and after adding β-estradiol, and the resonances with significant chemical shift perturbation identify the amino acids that comprise the binding site.

Sisco N.J., Luu D.D., Kim M, & Van Horn W.D. (2020). PIRT the TRP Channel Regulating Protein Binds Calmodulin and Cholesterol-Like Ligands. Biomolecules, 10(3), 478.

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C6 Glioma Tumor Induction in Wistar Rats

Cited 2 times

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C6 cells [8 (link), 10 (link)] from the American Type Culture Collection were grown in DMEM containing 25 mM glucose and 2 mM l-glutamine (product 31966-021 from Invitrogen, Cergy Pontoise, France) to which was added 10% FBS (Invitrogen) and antibiotics. The rat glioma model was prepared as described [58 (link)]: male Wistar rats (200–230 g) were anesthetized with isoflurane and 10⁵ C6 cells in DMEM were injected stereotaxically in the right caudate nucleus. The growth of the tumor was monitored by MRI under isofluorane anesthesia at 4.7 T (Avance III console; Bruker, Grenoble MRI Facility IRMaGe) using a T2-weighted sequence (TR/TE = 4,000/33 ms, with repetition time 4,000 ms, and echo time 33 ms [59 (link)]). When the tumor diameter was 5–7 mm (20–25 days after implantation), the rat was decapitated, the brain was rapidly removed and frozen in isopentane at −80°C, and 10 µm coronal cryosections were cut at −20°C.

Grillon E., Farion R., Reuveni M., Glidle A., Rémy C, & Coles J.A. (2015). Spatial profiles of markers of glycolysis, mitochondria, and proton pumps in a rat glioma suggest coordinated programming for proliferation. BMC Research Notes, 8, 207.

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NMR Characterization of PHD2-Nucleosome Interaction

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\sim 36

µ

mol/dm

^{3}

nucleosome with fractionally
deuterated,

^{13}

^{15}

N-labeled H3 in PK10 buffer with 10 % of
D

_{2}

O, 0.01 % NaN

_{3}

and protease inhibitors. PHD2 in either PK10 or
PK100 buffer was titrated to this sample and chemical shift and peak
intensity changes were monitored using 2D

^{15}

N–

^{1}

H TROSY HSQC spectra (

t_{1, \max}

122 ms,

t_{2, \max}

67 ms, total acquisition time per
spectrum

\sim 2

 h). The FID was apodized in both dimensions with a squared cosine bell function and extended once by linear prediction in the
indirect dimension before Fourier transform. Free nucleosome spectra were recorded in both low-salt PK10 buffer and high-salt PK100 buffer.

le Paige U.B., Xiang S., Hendrix M.M., Zhang Y., Folkers G.E., Weingarth M., Bonvin A.M., Kutateladze T.G., Voets I.K., Baldus M, & van Ingen H. (2021). Characterization of nucleosome sediments for protein interaction studies by solid-state NMR spectroscopy. Magnetic resonance, 2(1), 187-202.

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Solid-state 13C NMR Analysis of Samples

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For solid-state ¹³C NMR measurements,
beads were crushed and transferred into a 3.2 mm rotor for the magic-angle
spinning (MAS) solid-state NMR analysis. The analysis of the samples
was performed either on a Bruker 700 MHz wide-bore magnet with an
AVANCE-III console or on a Bruker 400 MHz spectrometer. The spectra
were recorded at RT (298 K) and using a MAS frequency between 10 and
14 kHz, chosen to minimize the overlap of the signal with spinning
sidebands. For the ¹³C direct excitation spectra, 30°
pulses were applied with field strengths of 55 kHz and 80 kHz SPINAL64.^{22 (link)}¹H decoupling was applied during
acquisition. The ¹³C T1 relaxation time for each sample
was determined using inverse recovery and used to establish the repetition
time for the different samples, set to 2*T1. Except
for the pVPE-Ox-(4) sample, which showed a very short relaxation time
of 1 s, for the other samples, the T1 varied from
40 to 80 s. Details for the specific experiments are given in the Supporting Information section 7. The NMR spectra
were processed with 200 Hz line-broadening and analyzed with Bruker
Topspin3.5.

Jong J.A., Guo Y., Veenhoven C., Moret M.E., van der Zwan J., Lucini Paioni A., Baldus M., Scheiner K.C., Dalebout R., van Steenbergen M.J., Verhaar M.C., Smakman R., Hennink W.E., Gerritsen K.G, & van Nostrum C.F. (2019). Phenylglyoxaldehyde-Functionalized Polymeric Sorbents for Urea Removal from Aqueous Solutions. ACS Applied Polymer Materials, 2(2), 515-527.

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Heteronuclear NMR Spectroscopy Protocol

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Spectra were recorded on a 600 MHz magnet with a Bruker DCH probe optimized for ¹³C detection and an Avance III Console or on a 900 MHz magnet with a Bruker TCO probe optimized for ¹⁵N/¹³C detection and an Avance III Console. J-Modulated HETCOR data were collected with 2048 x 32 points and spectral widths of 6 and 3 ppm in the direct and indirect dimensions, respectively. All spectra were processed identically using nmrPipe.^{16 (link)} In the direct dimension, data were zero-filled and apodized with a cosine-bell, while in the indirect dimension the number of points was increased to 64 using linear prediction, zero-filled and apodized with a cosine-squared-bell. Peak picking was performed in Sparky,¹⁷ and integrals were taken using nmrPipe with a footprint fixed in size and position that captured about 80% of modulated crosspeak intensity.

Williams R.V., Yang J.Y., Moremen K.W., Amster I.J, & Prestegard J.H. (2019). Measurement of Residual Dipolar Couplings in Methyl Groups via Carbon Detection. Journal of biomolecular NMR, 73(3-4), 191-198.

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Analyzing B. subtilis Colonies by MRI

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B. subtilis colonies (3610 and Δmatrix) were grown on LB media for 72 h. After that, colonies were covered with 1.5% agarose and subjected to analysis. All the MRI experiments were carried out on a 9.4 T Bruker Biospec system equipped with a 400 mT m⁻¹ gradients and an Avance III console (Bruker BioSpin, Ettlingen, Germany). High-resolution T2-weighted images were acquired using a turbo-RARE sequence (TE = 33 ms, TR = 500 ms, 2 averages, FOV = 3.2 cm, matrix size = 384 × 384, 78 mm in-plane resolution, and 1 mm slice thickness).

Molina-Santiago C., Pearson J.R., Navarro Y., Berlanga-Clavero M.V., Caraballo-Rodriguez A.M., Petras D., García-Martín M.L., Lamon G., Haberstein B., Cazorla F.M., de Vicente A., Loquet A., Dorrestein P.C, & Romero D. (2019). The extracellular matrix protects Bacillus subtilis colonies from Pseudomonas invasion and modulates plant co-colonization. Nature Communications, 10, 1919.

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Nucleosome Interaction Studied by NMR

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Solution-state NMR experiments for the interaction study of PHD2 and the nucleosome were performed on a Bruker 21.1 T magnet equipped with an Avance III console and a CPTCI probe, at a temperature of 298 K. NMR samples contained ~ 36 μmol/dm³ nucleosome with fractionally deuterated, ¹³C,¹⁵N-labeled H3 in PK10 buffer with 10 % of D₂O, 0.01 % NaN₃ and protease inhibitors. PHD2 in either PK10 or PK100 buffer was titrated to this sample and chemical shift and peak intensity changes were monitored using 2D ¹⁵N–¹H TROSY HSQC spectra (t_1,max 122 ms, t_2,max 67 ms, total acquisition time per spectrum ~ 2 h). The FID was apodized in both dimensions with a squared cosine bell function and extended once by linear prediction in the indirect dimension before Fourier transform. Free nucleosome spectra were recorded in both low-salt PK10 buffer and high-salt PK100 buffer.

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High-Field MRI Protocol for Functional Imaging

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All images were acquired with an 11.7 T/31cm and 14.1 T/26cm horizontal bore magnet (Magnex), interfaced to an AVANCE III console (Bruker) and equipped with a 12 cm gradient set, capable of providing 100 G/cm with a rise time of 150 μs (Resonance Research). For the 11.7 T scanner, a custom-built 9cm diameter quadrature transmitter coil was placed in the gradient. Surface receive-only coils were used during image acquisition. For the 14T scanner, a transceiver surface coil with 6mm diameter was used to acquire fMRI images.

Yu X., He Y., Wang M., Merkle H., Dodd S., Silva A.C, & Koretsky A.P. (2016). Sensory and optogenetically driven single-vessel fMRI. Nature methods, 13(4), 337-340.

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