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Decellularization of intact tissue enables MALDI imaging mass spectrometry analysis of the extracellular matrix.
Gessel M, Spraggins JM, Voziyan P, Hudson BG, Caprioli RM
(2015) J Mass Spectrom 50: 1288-93
MeSH Terms: Amino Acid Sequence, Animals, Collagen, Extracellular Matrix, Extracellular Matrix Proteins, Freezing, Humans, Hydrolysis, Image Processing, Computer-Assisted, Mice, Molecular Sequence Data, Peptide Fragments, Rats, Sodium Dodecyl Sulfate, Spectrometry, Mass, Matrix-Assisted Laser Desorption-Ionization, Tandem Mass Spectrometry
Show Abstract · Added November 3, 2015
Matrix-assisted laser desorption/ionization imaging mass spectrometry (MALDI IMS) is a powerful molecular mapping technology that offers unbiased visualization of the spatial arrangement of biomolecules in tissue. Although there has been a significant increase in the number of applications employing this technology, the extracellular matrix (ECM) has received little attention, likely because ECM proteins are mostly large, insoluble and heavily cross-linked. We have developed a new sample preparation approach to enable MALDI IMS analysis of ECM proteins in tissue. Prior to freezing and sectioning, intact tissues are decellularized by incubation in sodium dodecyl sulfate. Decellularization removes the highly abundant, soluble species that dominate a MALDI IMS spectrum while preserving the structural integrity of the ECM. In situ tryptic hydrolysis and imaging of tryptic peptides are then carried out to accommodate the large sizes of ECM proteins. This new approach allows the use of MALDI IMS for identification of spatially specific changes in ECM protein expression and modification in tissue.
Copyright © 2015 John Wiley & Sons, Ltd.
1 Communities
4 Members
1 Resources
16 MeSH Terms
The effects of frozen tissue storage conditions on the integrity of RNA and protein.
Auer H, Mobley JA, Ayers LW, Bowen J, Chuaqui RF, Johnson LA, Livolsi VA, Lubensky IA, McGarvey D, Monovich LC, Moskaluk CA, Rumpel CA, Sexton KC, Washington MK, Wiles KR, Grizzle WE, Ramirez NC
(2014) Biotech Histochem 89: 518-28
MeSH Terms: Cold Temperature, Freezing, Gene Expression Profiling, Humans, Microarray Analysis, Neoplasms, Proteins, Proteomics, RNA, RNA, Messenger, Spectrometry, Mass, Matrix-Assisted Laser Desorption-Ionization, Tissue Preservation
Show Abstract · Added October 1, 2014
Unfixed tissue specimens most frequently are stored for long term research uses at either -80° C or in vapor phase liquid nitrogen (VPLN). There is little information concerning the effects such long term storage on tissue RNA or protein available for extraction. Aliquots of 49 specimens were stored for 5-12 years at -80° C or in VPLN. Twelve additional paired specimens were stored for 1 year under identical conditions. RNA was isolated from all tissues and assessed for RNA yield, total RNA integrity and mRNA integrity. Protein stability was analyzed by surface-enhanced or matrix-assisted laser desorption ionization time of flight mass spectrometry (SELDI-TOF-MS, MALDI-TOF-MS) and nano-liquid chromatography electrospray ionization tandem mass spectrometry (nLC-ESI-MS/MS). RNA yield and total RNA integrity showed significantly better results for -80° C storage compared to VPLN storage; the transcripts that were preferentially degraded during VPLN storage were these involved in antigen presentation and processing. No consistent differences were found in the SELDI-TOF-MS, MALDI-TOF-MS or nLC-ESI-MS/MS analyses of specimens stored for more than 8 years at -80° C compared to those stored in VPLN. Long term storage of human research tissues at -80° C provides at least the same quality of RNA and protein as storage in VPLN.
0 Communities
2 Members
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12 MeSH Terms
Urine stability studies for novel biomarkers of acute kidney injury.
Parikh CR, Butrymowicz I, Yu A, Chinchilli VM, Park M, Hsu CY, Reeves WB, Devarajan P, Kimmel PL, Siew ED, Liu KD, ASSESS-AKI Study Investigators
(2014) Am J Kidney Dis 63: 567-72
MeSH Terms: Acute Kidney Injury, Aged, Aged, 80 and over, Biomarkers, Centrifugation, Cross-Sectional Studies, Enzyme-Linked Immunosorbent Assay, Female, Freezing, Humans, Male, Prospective Studies, Urine Specimen Collection
Show Abstract · Added January 6, 2015
BACKGROUND - The study of novel urinary biomarkers of acute kidney injury has expanded exponentially. Effective interpretation of data and meaningful comparisons between studies require awareness of factors that can adversely affect measurement. We examined how variations in short-term storage and processing might affect the measurement of urine biomarkers.
STUDY DESIGN - Cross-sectional prospective.
SETTING & PARTICIPANTS - Hospitalized patients from 2 sites: Yale New Haven Hospital (n=50) and University of California, San Francisco Medical Center (n=36).
PREDICTORS - We tested the impact of 3 urine processing conditions on these biomarkers: (1) centrifugation and storage at 4°C for 48 hours before freezing at -80°C, (2) centrifugation and storage at 25°C for 48 hours before freezing at -80°C, and (3) uncentrifuged samples immediately frozen at -80°C.
OUTCOMES - Urine concentrations of 5 biomarkers: neutrophil gelatinase-associated lipocalin (NGAL), interleukin 18 (IL-18), kidney injury molecule 1 (KIM-1), liver-type fatty acid-binding protein (L-FABP), and cystatin C.
MEASUREMENTS - We measured urine biomarkers by established enzyme-linked immunosorbent assay methods. Biomarker values were log-transformed, and agreement with a reference standard of immediate centrifugation and storage at -80°C was compared using concordance correlation coefficients (CCCs).
RESULTS - Neither storing samples at 4°C for 48 hours nor centrifugation had a significant effect on measured levels, with CCCs higher than 0.9 for all biomarkers tested. For samples stored at 25°C for 48 hours, excellent CCC values (>0.9) also were noted between the test sample and the reference standard for NGAL, cystatin C, L-FABP and KIM-1. However, the CCC for IL-18 between samples stored at 25°C for 48 hours and the reference standard was 0.81 (95% CI, 0.66-0.96).
LIMITATIONS - No comparisons to fresh, unfrozen samples; no evaluation of the effect of protease inhibitors.
CONCLUSIONS - All candidate markers tested using the specified assays showed high stability with both short-term storage at 4°C and without centrifugation prior to freezing. For optimal fidelity, urine for IL-18 measurement should not be stored at 25°C before long-term storage or analysis.
Copyright © 2014 National Kidney Foundation, Inc. All rights reserved.
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1 Members
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13 MeSH Terms
Substrate-selective COX-2 inhibition decreases anxiety via endocannabinoid activation.
Hermanson DJ, Hartley ND, Gamble-George J, Brown N, Shonesy BC, Kingsley PJ, Colbran RJ, Reese J, Marnett LJ, Patel S
(2013) Nat Neurosci 16: 1291-8
MeSH Terms: Adaptation, Ocular, Amidohydrolases, Animals, Anxiety, Benzoxazines, Body Temperature, Calcium Channel Blockers, Cannabinoid Receptor Agonists, Cannabinoid Receptor Antagonists, Cyclooxygenase 2, Cyclooxygenase Inhibitors, Disease Models, Animal, Endocannabinoids, Exploratory Behavior, Freezing Reaction, Cataleptic, Humans, Indoles, Male, Maze Learning, Mice, Mice, Inbred ICR, Mice, Knockout, Morpholines, Naphthalenes, Receptor, Cannabinoid, CB1, Signal Transduction
Show Abstract · Added March 7, 2014
Augmentation of endogenous cannabinoid (eCB) signaling represents an emerging approach to the treatment of affective disorders. Cyclooxygenase-2 (COX-2) oxygenates arachidonic acid to form prostaglandins, but also inactivates eCBs in vitro. However, the viability of COX-2 as a therapeutic target for in vivo eCB augmentation has not been explored. Using medicinal chemistry and in vivo analytical and behavioral pharmacological approaches, we found that COX-2 is important for the regulation of eCB levels in vivo. We used a pharmacological strategy involving substrate-selective inhibition of COX-2 to augment eCB signaling without affecting related non-eCB lipids or prostaglandin synthesis. Behaviorally, substrate-selective inhibition of COX-2 reduced anxiety-like behaviors in mice via increased eCB signaling. Our data suggest a key role for COX-2 in the regulation of eCB signaling and indicate that substrate-selective pharmacology represents a viable approach for eCB augmentation with broad therapeutic potential.
0 Communities
4 Members
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26 MeSH Terms
Cumulative multiple freeze-thaw cycles and testing does not affect subsequent within-day variation in intervertebral flexibility of human cadaveric lumbosacral spine.
Tan JS, Uppuganti S
(2012) Spine (Phila Pa 1976) 37: E1238-42
MeSH Terms: Aged, Biomechanical Phenomena, Cadaver, Cryopreservation, Female, Freezing, Humans, Intervertebral Disc, Lumbar Vertebrae, Pliability, Range of Motion, Articular, Sacrum, Time Factors
Show Abstract · Added October 31, 2013
STUDY DESIGN - An in vitro biomechanical study on 3-dimensional flexibility of human lumbosacral motion segments after multiple freeze-thaw cycles and cumulative testing.
OBJECTIVE - To determine the significance of multiple freeze-thaw cycles and extended testing duration on between-day and within-day variations in motion segment flexibility.
SUMMARY OF BACKGROUND DATA - Previous studies have found no significant effect of single freeze-thaw cycle on creep behavior of human spinal motion segments. Up to 3 freeze-thaw cycles were found to not affect flexibility of porcine spines and viscoelastic properties of human tendons, but more than 5 freeze-thaw cycles resulted in declined structural properties of human tendons.
METHODS - Three lumbosacral motion segments were subjected to repeated flexibility tests to determine both the effects of within-day ambient exposure and between-day multiple freeze-thaw cycles on range of motion (ROM) and neutral zone (NZ). Repeated measures analysis of variance was carried out to evaluate within-day and between-day effects at α = .05.
RESULTS - Significant between-day effects were found for intervertebral ROM and NZ in flexion-extension (FE), lateral bending (LB), and axial rotation (AR) (all P < 0.001). Post hoc analysis indicated that significant differences from test day 1 become apparent after 4 freeze-thaw cycles with cumulative testing. There were no within-day variations from repeated testing on intervertebral FE ROM (P = 0.10), LB ROM (P = 0.36), AR ROM (P = 0.46), FE NZ (P = 0.83), LB NZ (P = 0.42), and AR NZ (P = 0.72).
CONCLUSION - The flexibility of the human cadaveric lumbosacral motion segments between test days was significantly affected after repeated freeze-thaw and cumulative testing cycles. Multiple freeze-thaw cycles and cumulative testing, however, does not affect flexibility data for tests carried out within a single test day.
0 Communities
1 Members
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13 MeSH Terms
Observational fear learning involves affective pain system and Cav1.2 Ca2+ channels in ACC.
Jeon D, Kim S, Chetana M, Jo D, Ruley HE, Lin SY, Rabah D, Kinet JP, Shin HS
(2010) Nat Neurosci 13: 482-8
MeSH Terms: Animals, Calcium Channels, L-Type, Cerebral Cortex, Conditioning, Classical, Fear, Female, Freezing Reaction, Cataleptic, Gyrus Cinguli, Learning, Male, Mice, Mice, Inbred C57BL, Mice, Knockout, Pain, Pain Measurement, Protein Subunits, Rats, Rats, Sprague-Dawley, Social Behavior
Show Abstract · Added May 29, 2014
Fear can be acquired vicariously through social observation of others suffering from aversive stimuli. We found that mice (observers) developed freezing behavior by observing other mice (demonstrators) receive repetitive foot shocks. Observers had higher fear responses when demonstrators were socially related to themselves, such as siblings or mating partners. Inactivation of anterior cingulate cortex (ACC) and parafascicular or mediodorsal thalamic nuclei, which comprise the medial pain system representing pain affection, substantially impaired this observational fear learning, whereas inactivation of sensory thalamic nuclei had no effect. The ACC neuronal activities were increased and synchronized with those of the lateral amygdala at theta rhythm frequency during this learning. Furthermore, an ACC-limited deletion of Ca(v)1.2 Ca(2+) channels in mice impaired observational fear learning and reduced behavioral pain responses. These results demonstrate the functional involvement of the affective pain system and Ca(v)1.2 channels of the ACC in observational social fear.
0 Communities
1 Members
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19 MeSH Terms
Performance of cryogenic probes as a function of ionic strength and sample tube geometry.
Voehler MW, Collier G, Young JK, Stone MP, Germann MW
(2006) J Magn Reson 183: 102-9
MeSH Terms: Equipment Design, Equipment Failure Analysis, Freezing, Ions, Magnetic Resonance Spectroscopy, Molecular Probe Techniques, Proteins, Reproducibility of Results, Sensitivity and Specificity, Transducers
Show Abstract · Added May 29, 2014
The pursuit for more sensitive NMR probes culminated with development of the cryogenic cooled NMR probe. A key factor for the sensitivity is the overall resistance of RF circuitry and sample. Lowering the coil temperature to approximately 25 K and the use of superconducting coil material has greatly reduced the resistance contribution of the hardware. However, the resistance of a salty sample remains the same and evolves as the major factor determining the signal-to-noise ratio. Several approaches have been proposed to reduce the resistance contribution of the sample. These range from encapsulating proteins in a water cavity formed by reverse micelles in low viscosity fluids to the optimal selection of low mobility, low conductivity buffer ions. Here we demonstrate that changing the sample diameter has a pronounced effect on the sample resistance and this results in dramatic improvements of the signal-to-noise ratio and shorter pi/2 pulses. We determined these parameters for common 5 mm NMR tubes under different experimental conditions and compared them to the 2, 3 and 4 mm tubes, in addition, 5mm Shigemi tubes were included since these are widely used. We demonstrate benefits and applicability of studying NMR samples with up to 4M salt concentrations in cryogenic probes. Under high salt conditions, best results in terms of short pi/2 pulses and high signal-to-noise ratios are obtained using 2 or 3mm NMR tubes, especially when limited sample is available. The 4 mm tube is preferred when sample amounts are abundant at intermediate salt conditions.
0 Communities
1 Members
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10 MeSH Terms
Mcg in 2030: new techniques for atomic position determination of immune complexes.
Hanson BL, Bunick GJ, Harp JM, Edmundson AB
(2002) J Mol Recognit 15: 297-305
MeSH Terms: Amyloidosis, Antigen-Antibody Complex, Bence Jones Protein, Crystallography, X-Ray, Dimerization, Freezing, Helium, Humans, Immunoglobulin lambda-Chains, Models, Molecular, Molecular Structure, Multiple Myeloma, Neutron Diffraction, Nitrogen, Static Electricity, Synchrotrons
Show Abstract · Added January 30, 2015
The lambda-type light chain dimer from a patient (Mcg) with multiple myeloma and amyloidosis was a pioneer protein for determining the three-dimensional structures of immunoglobulins, understanding the effects of ligand binding, and exploring the use of combinatorial methods to identify novel peptides complementary to protein active sites. Despite 30 years of intense study, there are still unanswered questions about the structure of the Mcg dimer, especially with respect to positions of hydrogen atoms and solvent molecules. In the present report, we describe two techniques that will help define the roles of solvent in ligand interactions and complex formation with this immunoglobulin fragment: (1) introduction of helium as a cryogenic agent during X-ray data collection; and (2) addition of neutron diffraction analyses. These techniques should provide improved resolution, and a more accurate structure of the Mcg dimer. Resolution enhancements of 0.5 A have been achieved in preliminary experiments with cryogenic helium, as compared with the best X-ray diffraction data obtained previously. In the near future, neutron diffraction studies should produce the first hydrogen structure for the Mcg dimer and help elucidate the ligand preferences and amyloidogenic properties of this eminently useful protein.
Copyright 2002 John Wiley & Sons, Ltd.
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1 Members
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16 MeSH Terms
Macromolecular crystal annealing: overcoming increased mosaicity associated with cryocrystallography.
Harp JM, Timm DE, Bunick GJ
(1998) Acta Crystallogr D Biol Crystallogr 54: 622-8
MeSH Terms: Crystallization, Crystallography, X-Ray, Freezing, Histones, Humans, Muramidase, Nucleosomes
Show Abstract · Added January 30, 2015
Although cryogenic data collection has become the method of choice for macromolecular crystallography, the flash-cooling step can dramatically increase the mosaicity of some crystals. Macromolecular crystal annealing significantly reduces the mosaicity of flash-cooled crystals without affecting molecular structure. The process, which cycles a flash-cooled crystal to ambient temperature and back to cryogenic temperature, is simple, quick and requires no special equipment. The annealing process has been applied to crystals of several different macromolecules grown from different precipitants and using a variety of cryoprotectants. The protocol for macromolecular crystal annealing also has been applied to restore diffraction from flash-cooled crystals that were mishandled during transfer to or from cryogenic storage. These results will be discussed in relation to crystal mosaicity and effects of radiation damage in flash-cooled crystals.
0 Communities
1 Members
0 Resources
7 MeSH Terms
A simple method for freezing and storing viable tissue fragments.
Hayward SW
(1998) In Vitro Cell Dev Biol Anim 34: 28-9
MeSH Terms: Cryopreservation, Freezing, Humans, Male, Prostate
Added December 10, 2013
0 Communities
1 Members
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5 MeSH Terms