Analysis of phosphate metabolites, the intracellular pH, and the state of adenosine triphosphate in intact muscle by phosphorus nuclear magnetic resonance

ATP, the 31P Spectral Modulus, and Metabolism

Adenosine triphosphate (ATP) has a high intracellular millimolar concentration (ca. 2.4 mM) throughout the phylogenetic spectrum of eukaryotes, archaea, and prokaryotes. In addition, the function of ATP as a hydrotrope in the prevention of protein aggregation and maintenance of protein solubilization is essential to cellular, tissue, and organ homeostasis. The 31P spectral modulus (PSM) is a measure of the health status of cell, tissue, and organ systems, as well as of ATP, and it is based on in vivo 31P nuclear magnetic resonance (31P NMR) spectra. The PSM is calculated by dividing the area of the 31P NMR integral curve representing the high-energy phosphates by that of the low-energy phosphates. Unlike the difficulties encountered in measuring organophosphates such as ATP or any other phosphorylated metabolites in a conventional 31P NMR spectrum or in processed tissue samples, in vivo PSM measurements are possible with NMR surface-coil technology. The PSM does not rely on the resolution of individual metabolite signals but uses the total area derived from each of the NMR integral curves of the above-described spectral regions. Calculation is based on a simple ratio of the high- and low-energy phosphate bands, which are conveniently arranged in the high- and low-field portions of the 31P NMR spectrum. In practice, there is essentially no signal overlap between these two regions, with the dividing point being ca. -3 δ. ATP is the principal contributor to the maintenance of an elevated PSM that is typically observed in healthy systems. The purpose of this study is to demonstrate that (1) in general, the higher the metabolic activity, the higher the 31P spectral modulus, and (2) the modulus calculation does not require highly resolved 31P spectral signals and thus can even be used with reduced signal-to-noise spectra such as those detected as a result of in vivo analyses or those that may be obtained during a clinical MRI examination. With increasing metabolic stress or maturation of metabolic disease in cells, tissues, or organ systems, the PSM index declines; alternatively, with decreasing stress or resolution of disease states, the PSM increases. The PSM can serve to monitor normal homeostasis as a diagnostic tool and may be used to monitor disease processes with and without interventional treatment.

Adenosine Triphosphate (ATP) and Protein Aggregation in Age-Related Vision-Threatening Ocular Diseases

Protein aggregation is the etiopathogenesis of the three most profound vision-threatening eye diseases: age-related cataract, presbyopia, and age-related macular degeneration. This perspective organizes known information on ATP and protein aggregation with a fundamental unrecognized function of ATP. With recognition that maintenance of protein solubility is related to the high intracellular concentration of ATP in cells, tissues, and organs, we hypothesize that (1) ATP serves a critical molecular function for organismal homeostasis of proteins and (2) the hydrotropic feature of ATP prevents pathological protein aggregation while assisting in the maintenance of protein solubility and cellular, tissue, and organismal function. As such, the metabolite ATP plays an extraordinarily important role in the prevention of protein aggregation in the leading causes of vision loss or blindness worldwide.

Messenger RNA in lipid nanoparticles rescues HEK 293 cells from lipid-induced mitochondrial dysfunction as studied by real time pulse chase NMR, RTPC-NMR, spectroscopy

Analytical tools to study cell physiology are critical for optimizing drug-host interactions. Real time pulse chase NMR spectroscopy, RTPC-NMR, was introduced to monitor the kinetics of metabolite production in HEK 293T cells treated with COVID-19 vaccine-like lipid nanoparticles, LNPs, with and without mRNA. Kinetic flux parameters were resolved for the incorporation of isotopic label into metabolites and clearance of labeled metabolites from the cells. Changes in the characteristic times for alanine production implicated mitochondrial dysfunction as a consequence of treating the cells with lipid nanoparticles, LNPs. Mitochondrial dysfunction was largely abated by inclusion of mRNA in the LNPs, the presence of which increased the size and uniformity of the LNPs. The methodology is applicable to all cultured cells.

In-cell NMR: Why and how?

NMR spectroscopy has been applied to cells and tissues analysis since its beginnings, as early as 1950. We have attempted to gather here in a didactic fashion the broad diversity of data and ideas that emerged from NMR investigations on living cells. Covering a large proportion of the periodic table, NMR spectroscopy permits scrutiny of a great variety of atomic nuclei in all living organisms non-invasively. It has thus provided quantitative information on cellular atoms and their chemical environment, dynamics, or interactions. We will show that NMR studies have generated valuable knowledge on a vast array of cellular molecules and events, from water, salts, metabolites, cell walls, proteins, nucleic acids, drugs and drug targets, to pH, redox equilibria and chemical reactions. The characterization of such a multitude of objects at the atomic scale has thus shaped our mental representation of cellular life at multiple levels, together with major techniques like mass-spectrometry or microscopies. NMR studies on cells has accompanied the developments of MRI and metabolomics, and various subfields have flourished, coined with appealing names: fluxomics, foodomics, MRI and MRS (i.e. imaging and localized spectroscopy of living tissues, respectively), whole-cell NMR, on-cell ligand-based NMR, systems NMR, cellular structural biology, in-cell NMR… All these have not grown separately, but rather by reinforcing each other like a braided trunk. Hence, we try here to provide an analytical account of a large ensemble of intricately linked approaches, whose integration has been and will be key to their success. We present extensive overviews, firstly on the various types of information provided by NMR in a cellular environment (the "why", oriented towards a broad readership), and secondly on the employed NMR techniques and setups (the "how", where we discuss the past, current and future methods). Each subsection is constructed as a historical anthology, showing how the intrinsic properties of NMR spectroscopy and its developments structured the accessible knowledge on cellular phenomena. Using this systematic approach, we sought i) to make this review accessible to the broadest audience and ii) to highlight some early techniques that may find renewed interest. Finally, we present a brief discussion on what may be potential and desirable developments in the context of integrative studies in biology.

Intracellular ATP Concentration and Implication for Cellular Evolution

Crystalline lens and striated muscle exist at opposite ends of the metabolic spectrum. Lens is a metabolically quiescent tissue, whereas striated muscle is a mechanically dynamic tissue with high-energy requirements, yet both tissues contain millimolar levels of ATP (>2.3 mM), far exceeding their underlying metabolic needs. We explored intracellular concentrations of ATP across multiple cells, tissues, species, and domains to provide context for interpreting lens/striated muscle data. Our database revealed that high intracellular ATP concentrations are ubiquitous across diverse life forms including species existing from the Precambrian Era, suggesting an ancient highly conserved role for ATP, independent of its widely accepted view as primarily "metabolic currency". Our findings reinforce suggestions that the primordial function of ATP was non-metabolic in nature, serving instead to prevent protein aggregation.

Corneal absorption of glycerylphosphorylcholine

This study documents the absorption of glycerylphosphorylcholine (GPC) into corneas ex vivo. Corneas in quadruplicate were incubated in preservation medium containing 30 mM GPC, which is used as a reference marker. The GPC reference marker is used to calibrate ³¹P nuclear magnetic resonance (NMR) spectral chemical-shift positions for identification of phosphatic metabolites and to calculate intracorneal pH in intact tissues ex vivo. Following baseline NMR ex vivo analysis, corneas were stored in eye bank chambers in preservation medium containing 30 mM GPC at 4 °C overnight for 8 h. After returning to room temperature, NMR analysis was repeated on the same corneas in fresh GPC-free preservation medium. NMR analysis also was performed on the 30 mM GPC preservation medium alone from the eye bank chambers for detection of the GPC signal. The elevated GPC signal unexpectedly persisted in corneas incubated at 4 °C overnight even though GPC was not present in the fresh GPC-free preservation medium. In fact, the concentration of GPC in the intact cornea was many times higher than that found in the cornea endogenously. The levels of phosphatic metabolites and the energy modulus, after subtracting the spectral contribution of the 30 mM exogenous GPC, as well as the intracorneal pH remained unchanged from pre-refrigeration analyses. Corneas also retained transparency through the time-course of this study irrespective of temperature or change in temperature. The GPC signal in the NMR analysis of the preservation medium from the eye bank chambers was nearly undetectable. GPC was unexpectedly absorbed into the corneal tissue without detectable metabolic or physical toxicity. The intracorneal uptake of GPC at reduced temperatures parallels the increase in GPC that occurs naturally in muscle tissue in animals during wintering periods and the very high concentration of GPC in sperm, a cryogenically compatible cell, suggestive of a potential role for GPC in cryopreservation.

Corneal Cryopreservation Using Glycerylphosphorylcholine-Enriched Medium

PURPOSE

To determine the effects of prolonged cryopreservation at subzero-degree temperatures on corneal transparency and histology after treatment with preservation medium containing the phosphodiester glycerylphosphorylcholine (GPC).

METHODS

Rabbit corneas (n = 30) were immersed for 3 hours in K-Sol preservation medium containing 30 mM GPC. Three groups with 6 corneas each were refrigerated at -8°C for 2 weeks and liquid nitrogen temperature for 2 and 6 weeks, respectively. Two groups with 6 corneas each immersed in K-Sol preservation medium only were refrigerated at -8°C for 2 weeks and liquid nitrogen temperature for 6 weeks, respectively. Postthawing corneal transparency was measured on a grading scale after which corneas were prepared for and analyzed by light and transmission electron microscopy.

RESULTS

All 3 groups of corneas preserved with GPC maintained a greater degree of corneal transparency compared with corneas preserved without GPC. The number of corneas retaining epithelial and endothelial layers increased in all groups where corneas were preserved in medium containing GPC, in contrast to corneas preserved in medium without GPC. Cytoplasmic vacuolization or nuclear damage was greater in corneas preserved without GPC. Similar findings were found in corneas stored at -8°C and liquid nitrogen temperatures.

CONCLUSIONS

This study demonstrates a cryoprotective effect of corneas preserved in K-Sol containing the phosphodiester GPC at subzero-degree temperatures. In corneas immersed in preservation medium containing GPC, a higher degree of transparency is maintained and a lesser degree of histopathologic changes is observed with storage at both -8°C and in liquid nitrogen.

Hydrotropic function of ATP in the crystalline lens

The hypothesis proposed herein is presented to explain the unexpectedly high concentration of ATP and provide evidence to support its hydrotropic function in the crystalline lens determined using ³¹P NMR. The lens, historically considered to be a metabolically quiescent organ, has the requisite machinery to synthesize ATP, such that the homeostatic level is maintained at about 3 mM. This relatively high concentration of ATP has been found to be consistent among multiple mammalian species including humans. This millimolar quantity is many times greater than the micromolar amounts required for the other known functions of ATP. The recent postulation that ATP at millimolar concentrations functions as a hydrotrope in various cell/tissue homogenates preventing protein aggregation coupled with observations presented herein, provide support for extending the hypothesis that ATP functions as a hydrotrope not only in homogenates but in an intact functioning organ, the crystalline lens. Concentrations of ATP of this magnitude are hypothesized to be required to maintain protein solubility and effectively prevent protein aggregation. This concept is important considering protein aggregation is the etiology for age-related cataractogenesis. ATP is a common ubiquitous intracellular molecule possessing the requisite hydrotropic properties for maintaining intracellular proteins in a fluid, non-aggregated state. It is proposed that the amphiphilic ATP molecule shields the hydrophobic regions on intralenticular fiber cell protein molecules and provides a hydrophilic interfacial surface comprised of the ATP negatively charged triphosphate side chain. Evidence is presented that this side chain is exposed to and has been reported to organize intracellular interstitial water to form an interfacial rheologically dynamic water layer. Such organization of water is substantiated with the effect of deuterium oxide (heavy water) on ATP line widths of the side chain phosphates measured ex vivo by ³¹P NMR. A novel model is presented to propose how this water layer separates adjacent lens fiber cell proteins, keeping them from aggregating. This hypothesis proposes that ATP can prevent protein aggregation in normal intact lenses, and with declining concentrations can be related to the disease process in age-related cataractogenesis, an affliction that affects every older human being.

Overview of NMR Spectroscopy-Based Metabolomics: Opportunities and Challenges

The fast-growing field of metabolomics is impacting numerous areas of basic and life sciences. In metabolomics, analytical methods play a pivotal role, and nuclear magnetic resonance (NMR) and mass spectrometry (MS) have proven to be the most suitable and powerful methods. Although NMR exhibits lower sensitivity and resolution compared to MS, NMR's numerous important characteristics far outweigh its limitations. Some of its characteristics include excellent reproducibility and quantitative accuracy, the capability to analyze intact biospecimens, an unparalleled ability to identify unknown metabolites, the ability to trace in-cell and in-organelle metabolism in real time, and the capacity to trace metabolic pathways atom by atom using ²H, ¹³C, or ¹⁵N isotopes. Each of these characteristics has been exploited extensively in numerous studies. In parallel, the field has witnessed significant progress in instrumentation, methods development, databases, and automation that are focused on higher throughput and alleviating the limitations of NMR, in particular, resolution and sensitivity. Despite the advances, however, the high complexity of biological mixtures combined with the limitations in sensitivity and resolution continues to pose major challenges. These challenges need to be dealt with effectively to better realize the potential of metabolomics, in general. As a result, multifaceted efforts continue to focus on addressing the challenges as well as reaping the benefits of NMR-based metabolomics. This chapter highlights the current status with emphasis on the opportunities and challenges in NMR-based metabolomics.

Systematic Evaluation of Amide Proton Chemical Exchange Saturation Transfer at 3 T: Effects of Protein Concentration, pH, and Acquisition Parameters

OBJECTIVE

The goal of this work was to systematically evaluate the reproducibility of amide proton transfer chemical exchange saturation transfer (APT-CEST) at 3 T and its signal dependence on pH, protein concentration, and acquisition parameters. An in vitro system based on bovine serum albumin (BSA) was used, and its limitations were tested by comparing it to in vivo measurements. The contribution of small endogenous metabolites on the APT-CEST signal at 3 T was also investigated. In addition, the reliability of different z-spectrum interpolations as well as the use of only a few frequency offset data points instead of a whole z-spectrum were tested.

MATERIALS AND METHODS

We created both a BSA phantom at different concentrations and pH values and a metabolite phantom with different small molecules. Chemical exchange saturation transfer data were acquired using a 2-dimensional fast spoiled gradient-echo sequence with pulsed CEST preparation at different saturation durations and power levels. Healthy volunteer measurements were taken for comparison. Z-spectra were interpolated using a 24th-order polynomial (Poly), an eighth-order Fourier series (Fourier), and a smoothing Spline (sSpline) algorithm. To evaluate reduced data sets, only 6 to 14 frequency offsets of the z-spectrum were used and interpolated via a cubic Spline. Region of interest (ROI) evaluations were used to investigate the reproducibility of amide magnetization transfer ratio asymmetry [MTRasym(3.5 ppm)] and to analyze the MTRasym and z-spectra.

RESULTS

Interscan standard deviations of MTRasym(3.5 ppm) were always below 0.3%. MTRasym(3.5 ppm) increased when the BSA concentrations increased and decreased when the pH increased. The amine MTRasym signal of small molecules was very small compared with BSA and was only detectable using short saturation times and higher power levels. The MTRasym(3.5 ppm) between BSA concentration steps and between nearly all pH steps was significantly different for all 3 fitting methods. The Fourier and sSpline methods showed no statistically significant differences; however, the results for the Poly method were significantly higher at some concentrations and pH values. Using only few frequency offsets resulted in less significant differences compared with fitting the complete z-spectrum. In general, MTRasym(3.5 ppm) of gray matter, white matter, and ventricle ROIs from volunteer scans increased with an increase in saturation power and partially decreased with an increase in saturation duration. Intra-ROI covariances of MTRasym(3.5 ppm) revealed the highest variations for Poly, whereas using reduced spectral data resulted in an increased signal variation.

CONCLUSIONS

Amide proton transfer-CEST imaging is a highly reproducible method in which absolute signal differences of approximately 0.5% are detectable in principle. For in vivo applications, Fourier or sSpline interpolations of z-spectra are preferable. Using reduced data sets delivers similar results but with increased variation and therefore decreased (pH/concentration) differentiation capability. Differentiation capability increases with increases in the saturation duration and power level. The results from the in vitro BSA system cannot be directly transferred to the in vivo situation due to different chemical environments resulting in, for example, higher asymmetric macromolecular cMT effects in vivo. Amine signals from small molecules are unlikely to contribute to APT-CEST at 3 T (except for creatine); however, signals can be enhanced by using short saturation times and higher power levels.

Transcriptome analysis illuminates the nature of the intracellular interaction in a vertebrate-algal symbiosis

During embryonic development, cells of the green alga Oophila amblystomatis enter cells of the salamander Ambystoma maculatum forming an endosymbiosis. Here, using de novo dual-RNA seq, we compared the host salamander cells that harbored intracellular algae to those without algae and the algae inside the animal cells to those in the egg capsule. This two-by-two-way analysis revealed that intracellular algae exhibit hallmarks of cellular stress and undergo a striking metabolic shift from oxidative metabolism to fermentation. Culturing experiments with the alga showed that host glutamine may be utilized by the algal endosymbiont as a primary nitrogen source. Transcriptional changes in salamander cells suggest an innate immune response to the alga, with potential attenuation of NF-κB, and metabolic alterations indicative of modulation of insulin sensitivity. In stark contrast to its algal endosymbiont, the salamander cells did not exhibit major stress responses, suggesting that the host cell experience is neutral or beneficial.

Use of in vivo magnetic resonance spectroscopy for studying metabolic diseases

Owing to the worldwide obesity epidemic and the sedentary lifestyle in industrialized countries, the number of people with metabolic diseases is explosively increasing. Magnetic resonance spectroscopy (MRS), which is fundamentally similar to magnetic resonance imaging, can detect metabolic changes in vivo noninvasively. With its noninvasive nature, (1)H, (13)C and (31)P MRS are being actively utilized in clinical and biomedical metabolic studies to detect lipids and important metabolites without ionizing radiation. (1)H MRS can quantify lipid content in liver and muscle and can detect other metabolites, such as 2-hydroxyglutarate, in vivo. Of interest, many studies have indicated that hepatic and intramyocellular lipid content is inversely correlated with insulin sensitivity in humans. Thus, lipid content can be utilized as an in vivo biomarker for detecting early insulin resistance. Employing (13)C MRS, hepatic glycogen synthesis and breakdown can be directly detected, whereas (31)P MRS provides in vivo adenosine triphosphate (ATP) synthesis rates by saturation transfer methods in addition to ATP content. These in vivo data can be very difficult to assess by other methods and offer a critical piece of metabolic information. To aid the reader in understanding these new methods, fundamentals of MRS are described in this review in addition to promising future applications of MRS and its limitations.

Modulation of 14-3-3/phosphotarget interaction by physiological concentrations of phosphate and glycerophosphates

Molecular mechanisms governing selective binding of a huge number of various phosphorylated protein partners to 14-3-3 remain obscure. Phosphate can bind to 14-3-3 and therefore being present at high intracellular concentration, which undergoes significant changes under physiological conditions, phosphate can theoretically regulate interaction of 14-3-3 with phosphorylated targets. In order to check this hypothesis we analyzed effect of phosphate and other natural abundant anions on interaction of 14-3-3 with phosphorylated human small heat shock protein HspB6 (Hsp20) participating in regulation of different intracellular processes. Inorganic phosphate, glycerol-1-phosphate and glycerol-2-phosphate at physiologically relevant concentrations (5-15 mM) significantly destabilized complexes formed by 14-3-3ζ and phosphorylated HspB6 (pHspB6), presumably, via direct interaction with the substrate-binding site of 14-3-3. Phosphate also destabilized complexes between pHspB6 and 14-3-3γ or the monomeric mutant form of 14-3-3ζ. Inorganic sulfate and pyrophosphate were less effective in modulation of 14-3-3 interaction with its target protein. The inhibitory effect of all anions on pHspB6/14-3-3 interaction was concentration-dependent. It is hypothesized that physiological changes in phosphate anions concentration can modulate affinity and specificity of interaction of 14-3-3 with its multiple targets and therefore the actual phosphointeractome of 14-3-3.

Chemical Exchange Saturation Transfer (CEST) Imaging: Description of Technique and Potential Clinical Applications

Chemical exchange saturation transfer (CEST) is a magnetic resonance imaging (MRI) contrast enhancement technique that enables indirect detection of metabolites with exchangeable protons. Endogenous metabolites with exchangeable protons including many endogenous proteins with amide protons, glycosaminoglycans (GAG), glycogen, myo-inositol (MI), glutamate (Glu), creatine (Cr) and several others have been identified as potential in vivo endogenous CEST agents. These endogenous CEST agents can be exploited as non-invasive and non-ionizing biomarkers of disease diagnosis and treatment monitoring. This review focuses on the recent technical developments in endogenous in vivo CEST MRI from various metabolites as well as their potential clinical applications. The basic underlying principles of CEST, its potential limitations and new techniques to mitigate them are discussed.

Method for high-resolution imaging of creatine in vivo using chemical exchange saturation transfer

PURPOSE

To develop a chemical exchange saturation transfer (CEST)-based technique to measure free creatine (Cr) and to validate the technique by measuring the distribution of Cr in muscle with high spatial resolution before and after exercise.

METHODS

Phantom studies were performed to determine contributions from other Cr kinase metabolites to the CEST effect from Cr (CrCEST). CEST, T2 , magnetization transfer ratio and (31) P magnetic resonance spectroscopy acquisitions of the lower leg were performed before and after plantar flexion exercise on a 7T whole-body magnetic resonance scanner on healthy volunteers.

RESULTS

Phantom studies demonstrated that while Cr exhibited significant CEST effect there were no appreciable contributions from other metabolites. In healthy human subjects, following mild plantar flexion exercise, increases in the CEST effect from Cr were observed, which recovered exponentially back to baseline. This technique exhibited good spatial resolution and was able to differentiate differences in muscle utilization among subjects. The CEST effect from Cr results were compared with (31) P magnetic resonance spectroscopy results showing good agreement in the Cr and phosphocreatine recovery kinetics.

CONCLUSION

Demonstrated a CEST-based technique to measure free Cr changes in in vivo muscle. The CEST effect from Cr imaging can spatially map changes in Cr concentration in muscle following mild exercise. This may serve as a tool for the diagnosis and treatment of various disorders affecting muscle.

Quantitative analysis in magnetic resonance spectroscopy: from metabolic profiling to in vivo biomarkers

Nuclear magnetic resonance spectroscopy (called NMR for ex vivo techniques and MRS for in vivo techniques) has become a useful analytical and diagnostic tool in biomedicine. In the past two decades, an MR-based spectroscopic approach for translational and clinical research has emerged that allows for biochemical characterization of the tissue of interest either ex vivo (NMR-based metabolomics) or in vivo (localized MRS-single voxel or multivoxel-spectroscopic imaging). The greatest advantages of MRS techniques are their ability to detect multiple tissue-specific metabolites in a single experiment, their quantitative nature and translational component (in vitro/ex vivo-discovered metabolic biomarkers can be translated into noninvasive spectroscopic imaging protocols). Disadvantages of MRS include low sensitivity and spectral resolution and, in case of NMR-metabolomics, metabolite degradation and incomplete recovery in processed samples. In vivo MRS has worse spectral resolution than ex vivo high-resolution NMR due to the inherently wider lines of metabolites in vivo and the difficulty of using traditional line-narrowing methods (e.g., sample spinning). It also suffers from poor time-resolution, therefore offering fewer metabolic biomarkers to be followed in vivo. In the present review article, we provide considerations for establishing reliable protocols (both in vivo and ex vivo) for metabolite detection, recovery and quantification from in vivo and ex vivo MR spectra.

Michael Bárány: a recollection

In this special edition of the Journal of Muscle Research and Cell Motility, we recall the lives and scientific contributions of Michael and Kate Bárány, who died in 2011. Michael and Kate were Holocaust survivors who went on to become leading researchers in muscle contraction. Their research topics included myosin isoforms, phosphorylation as a regulator of muscle contraction and the application of NMR to study muscle metabolism. They were deeply committed to science and to fostering the careers of young investigators.

Phosphate and R2D2 restrict the substrate specificity of Dicer-2, an ATP-driven ribonuclease

Drosophila Dicer-2 generates small interfering RNAs (siRNAs) from long double-stranded RNA (dsRNA), whereas Dicer-1 produces microRNAs (miRNAs) from pre-miRNA. What makes the two Dicers specific for their biological substrates? We find that purified Dicer-2 can efficiently cleave pre-miRNA, but that inorganic phosphate and the Dicer-2 partner protein R2D2 inhibit pre-miRNA cleavage. Dicer-2 contains C-terminal RNase III domains that mediate RNA cleavage and an N-terminal helicase motif, whose function is unclear. We show that Dicer-2 is a dsRNA-stimulated ATPase that hydrolyzes ATP to ADP; ATP hydrolysis is required for Dicer-2 to process long dsRNA, but not pre-miRNA. Wild-type Dicer-2, but not a mutant defective in ATP hydrolysis, can generate siRNAs faster than it can dissociate from a long dsRNA substrate. We propose that the Dicer-2 helicase domain uses ATP to generate many siRNAs from a single molecule of dsRNA before dissociating from its substrate.

Brain bioenergetics and response to triiodothyronine augmentation in major depressive disorder

BACKGROUND

Low cerebral bioenergetic metabolism has been reported in subjects with major depressive disorder (MDD). Thyroid hormones have been shown to increase brain bioenergetic metabolism. We assessed whether changes in brain bioenergetics measured with phosphorus magnetic resonance spectroscopy ((31)P MRS) correlate with treatment outcome during augmentation treatment with triiodothyronine (T3) in MDD.

METHODS

Nineteen subjects meeting DSM-IV criteria for MDD who had previously failed to respond to selective serotonin reuptake inhibitor (SSRI) antidepressant drugs received open label and prospective augmentation treatment with T3 for 4 weeks. We obtained (31)P MRS spectra before and after treatment from all MDD subjects and baseline (31)P MRS from nine normal control subjects matched for age and gender.

RESULTS

At baseline, depressed subjects had lower intracellular Mg(2+) compared with control subjects. Seven MDD subjects (38.9%) were treatment responders (>or= 50% improvement). Total nucleoside triphosphate (NTP), which primarily represents adenosine triphosphate (ATP), increased significantly in MDD subjects responding to T3 augmentation compared with treatment nonresponders. Phosphocreatine, which has a buffer role for ATP, decreased in treatment responders compared with nonresponders.

CONCLUSIONS

The antidepressant effect of thyroid hormone (T3) augmentation of SSRIs is correlated with significant changes in the brain bioenergetic metabolism. This seems to be a re-normalization of brain bioenergetics in treatment responders. Further studies will determine whether these findings can be generalized to other antidepressant treatments.

Energy metabolism and cellular pH in normal and pathological conditions. A new look through 31phosphorus nuclear magnetic resonance

Cellular energetics can be studied non-invasively using 31P nuclear magnetic resonance (NMR). Besides the concentration of the major phosphorus-containing metabolites, enzyme-catalysed fluxes and intracellular pH can be obtained from the NMR measurement. Metabolic acidosis in the ischaemic myocardium has been studied in the perfused rat heart. Comparison of the pH, measured from the position of the inorganic phosphate (Pi) resonance, with the pH obtained from the resonance of 2-deoxyglucose 6-phosphate (accumulated after perfusion with 2-deoxyglucose) demonstrates that cytoplasmic pH values are being obtained. The pH changes during ischaemia are quantitatively related to the glycogen leads to lactate conversion. Preperfusion with insulin enhanced the lactate production but resulted in the maintenance of ATP for a longer period during ischaemia, even though acidosis was enhanced. In acute renal acidosis, the decrease in intracellular pH is smaller than might have been expected, as demonstrated in the perfused rat kidney. The importance of acidosis in relation to renal preservation was examined in human kidneys prior to transplantation. 31P NMR studies on human forearm muscle have been done. The pH changes measured during aerobic and anaerobic exercise demonstrate the importance of glycogenolysis in providing energy for ATP production. In a patient with suspected McArdle's syndrome, 31P NMR was used to detect the lack of glycogenolysis since during both aerobic and anaerobic exercise a pH rise was observed together with the rapid breakdown of phosphocreatine.

Tourniquet-induced ischemia and reperfusion in human skeletal muscle

Microdialysis conceivably enables longitudinal and simultaneous investigation of several metabolites by repeated measurements in skeletal muscle. We used and evaluated microdialysis as an in vivo method to characterize the time-course and relative kinetics of pyruvate, glucose, lactate, glycerol, hypoxanthine, uric acid, and urea, in skeletal muscles, exposed to ischemia and reperfusion, in eight patients having arthroscopic-assisted anterior cruciate ligament reconstruction. A dialysis probe was implanted before surgery in the rectus femoris muscle. Dialysate samples were collected at 10-minute intervals at a flow rate of 1 microL/minute until 2 hours after tourniquet deflation. Ninety minutes of ischemia resulted in accumulation of lactate (234% +/- 38%), hypoxanthine (582% +/- 166%), and glycerol (146% +/- 46%), consumption of glucose (54% +/- 9%) and pyruvate (16% +/- 44%), and a slight decrease of urea (78% +/- 11%) compared with baseline (100%). Uric acid was unchanged (95% +/- 12%). Within 90 minutes after tourniquet deflation the concentrations were virtually normalized for all measured metabolites, suggesting that the duration of ischemia was well tolerated by the patients. The results indicate that the use of microdialysis for monitoring energy metabolic events during orthopaedic surgery that requires ischemia and reperfusion is feasible and safe.

Alpha-crystallin and ATP facilitate the in vitro renaturation of xylanase: enhancement of refolding by metal ions

Alpha-crystallin is a multimeric protein that functions as a molecular chaperone and shares extensive structural homology to small heat shock proteins. For the functional in vitro analysis of alpha-crystallin, the xylanase Xyl II from alkalophilic thermophilic Bacillus was used as a model system. The mechanism of chaperone action of alpha-crystallin is less investigated. Here we studied the refolding of Gdn HCl-denatured Xyl II in the presence and absence of alpha-crystallin to elucidate the molecular mechanism of chaperone-mediated in vitro folding. Our results, based on intrinsic tryptophan fluorescence and hydrophobic fluorophore 8-anilino-1-naphthalene sulfonate binding studies, suggest that alpha-crystallin formed a complex with a putative molten globule-like intermediate in the refolding pathway of Xyl II. The alpha-crystallin.Xyl II complex exhibited no functional activity. Addition of ATP to the complex initiated the renaturation of Xyl II with 30%-35% recovery of activity. The nonhydrolyzable analog 5'-adenylyl imidodiphosphate (AMP-PNP) was capable of reconstitution of active Xyl II to a lesser extent than ATP. Although the presence of Ca(2+) was not required for the in vitro refolding of Xyl II, the renaturation yield was enhanced in its presence. Experimental evidence indicated that the binding of ATP to the alpha-crystallin.Xyl II complex brought about conformational changes in alpha-crystallin facilitating the dissociation of xylanase molecules. This is the first report of the enhancement of alpha-crystallin chaperone functions by metal ions.

ATP causes small heat shock proteins to release denatured protein

Small heat-shock proteins (sHSPs) are a ubiquitous family of low molecular mass (15-30 kDa) stress proteins that have been found in all organisms. Under stress, sHSPs such as alpha-crystallin can act as chaperones binding partially denatured proteins and preventing further denaturation and aggregation. Recently, it has been proposed that the function of sHSPs is to stabilize stress-denatured protein and then act cooperatively with other HSPs to renature the partially denatured protein in an ATP-dependent manner. However, the process by which this occurs is obscure. As no significant phosphorylation of alpha-crystallin was observed during the renaturation, the role of ATP is not clear. It is now shown that ATP at normal physiological concentrations causes sHSPs to change their confirmation and release denatured protein, allowing other molecular chaperones such as HSP70 to renature the protein and renew its biological activity. In the absence of ATP, sHSPs such as alpha-crystallin are more efficient than HSP70 in preventing stress-induced protein aggregation. This work also indicates that in mammalian systems at normal cellular ATP concentrations, sHSPs are not effective chaperones.

Nuclear magnetic resonance spectroscopy and imaging in animal research

Nuclear magnetic resonance (NMR) spectroscopy and imaging can be used to investigate, noninvasively, a wide range of biological processes in systems as diverse as protein solutions, single cells, isolated perfused organs, and tissues in vivo. It is also possible to combine different NMR techniques enabling metabolic, anatomical, and physiological information to be obtained in the same experiment. This review provides a simple overview of the basic principles of NMR and outlines both the advantages and disadvantages of NMR spectroscopy and imaging. A few examples of potential applications of NMR spectroscopy and imaging are presented, which demonstrate the range of questions that can be asked using these techniques. The potential impact of using NMR techniques in a biomedical research program on the total number of animals required for specific investigations, as well as the number of animals used in research, are discussed. The article concludes with a personal perspective on the impact of continuing improvements in NMR technology for future applications in animal research.

Esophageal cancer phospholipids correlated with histopathologic findings: a 31P NMR study

We analyzed 36 esophageal tumor specimens for phospholipid content using phosphorus nuclear magnetic resonance spectroscopy (31P NMR) and correlated the individual phospholipid profiles with specific clinical and histopathologic features. Among the 18 phospholipids identified in the esophageal tumor specimens, the mean mole percentage concentration of dimethylphosphatidylethanolamine, lysoalkylacylphosphatidylcholine, lysophosphatidic acid, lysophosphatidylcholine (deacylated at the glycerol-1 carbon), and lysoethanolamine plasmalogen correlated with pathologic T stage, nuclear grade, or the presence of lymphatic invasion. 31P NMR produces well-dispersed phospholipid spectra and a precise determination of phospholipid relative mole percentages. These data provide a statistical correlation between histopathologic features and molecules known to play an important role in cellular activities and processes unique to malignant tissues.

Fibromyalgia is not a muscle disorder

Originally described as "fibrositis," fibromyalgia has long been considered a muscle disorder, and many studies have investigated the possible pathologic basis of the disorder by examining muscle tissue, using various methodologic approaches. Although initial studies suggested a possible pathologic basis in muscle, most had serious methodologic limitations. More recent studies, however, have avoided methodologic pitfalls and indicate that the muscles of patients with fibromyalgia are normal. When data from studies of tenderness are also taken into account, the weight of evidence suggests that fibromyalgia is a chronic pain syndrome which has a central rather than peripheral or muscular basis.

Post-ischemic 31P NMR determination of myocardial intracellular pH in vivo using ATP peak

31P NMR allows non-invasive measurement of intracellular pH, which drops during tissue hypoxia or ischemia. Determination is usually based on the chemical shift between the inorganic phosphate (P(i)) and phosphocreatine (PCr) peaks. During reperfusion, P(i) is taken up to form PCr and ATP, and in our model at least (an isolated, working rat heart perfused with an erythrocyte suspension), the level of P(i) reduces well below the pre-ischemic level, making pH determination difficult. The chemical shifts of the three ATP peaks also depend on pH, and the level of ATP remains high during reperfusion, so these might be used to determine pH. The results of one experiment are presented in detail, showing the time course of high energy phosphate levels before, during and after a 32 min ischemic insult, and close agreement between the pH determinations from the Pi and gamma-ATP peaks can be seen. The formula used to calculate pH from the ATP peak was: pH (ATP) = 0.59 delta 2-5.0 delta + 15.9 where delta is the shift in ppm between PCr and gamma-ATP. All pH readings by both methods from a series of seven experiments were compared and a 1:1 agreement demonstrated (correlation coefficient 0.63, p < 0.0001). Although the ATP shifts also depend on magnesium complexation which we have ignored, this appears to be justifiable within the errors of the method; the good agreement between the results of the two methods, and the ability to determine pH during reperfusion suggest that calculation of intracellular pH from the chemical shift of gamma-ATP is a useful technique.

ATP-enhanced molecular chaperone functions of the small heat shock protein human alphaB crystallin

We report direct experimental evidence that human alphaB-crystallin, a member of the small heat shock protein family, actively participates in the refolding of citrate synthase (CS) in vitro. In the presence of 3.5 mM ATP, CS reactivation by alphaB-crystallin was enhanced approximately twofold. Similarly, 3.5 mM ATP enhanced the chaperone activity of alphaB-crystallin on the unfolding and aggregation of CS at 45 degrees C. Consistent with these findings, cell viability at 50 degrees C was improved nearly five orders of magnitude in Escherichia coli expressing alphaB-crystallin. SDS/PAGE analysis of cell lysates suggested that alphaB-crystallin protects cells against physiological stress in vivo by maintaining cytosolic proteins in their native and functional conformations. This report confirms the action of alphaB-crystallin as a molecular chaperone both in vitro and in vivo and describes the enhancement of alphaB-crystallin chaperone functions by ATP.

Phospholipid profiling of sediments using phosphorus-31 nuclear magnetic resonance

A phosphorus-31 nuclear magnetic resonance method has been developed for the determination of aquatic sediment phospholipid profiles that may be generally applied to all soils and deposits containing viable cellular material. A method of scrubbing chloroform/methanol extracts with potassium acid phosphate overcomes adverse signal broadening from the mineral component, permitting eleven sediment phospholipids to be determined at the quantitative level.

31P-magnetic resonance spectroscopy of the rabbit masseter muscle

Dynamic biochemical changes in the masseter muscle were studied in 14 New Zealand adult male rabbits by 31P-nuclear magnetic resonance (NMR) spectroscopy. NMR spectra were obtained during rest and electrical stimulation of the muscle in the anaesthetized animal at 33 recording sessions. Electrical stimulation was applied by a pair of copper wires placed separately with hypodermic needles into the muscle. NMR spectra were acquired with a 2 x 3 cm, double-turn, copper transmit/receive coil. Sixteen spectra were averaged over 30 s to obtain averaged spectra continuously during a 30-min recording. The spectra were processed automatically using a non-linear 'least-squares' fitting program on the spectrometer. A Lorentzian line shape was assumed for the peaks, and values of peak height, area and chemical shifts were generated. Each averaged spectrum consisted of five peaks: inorganic phosphate (Pi), creatine phosphate (PCr), and three peaks related to ATP. Data were analysed as to absolute changes in Pi and PCr, in the ratio of Pi/PCr, and the shift of Pi to PCr to estimate pH. Several protocols were used in which ranges of frequency, intensity and duration of electrical stimulation were tested. The protocol for detailed studies involved stimulating the muscle twice at 5 Hz for 3 min separated by a 3-min rest period, then stimulating twice at 50 Hz for 3 min separated by a rest period. During contraction of the muscle, there was a significant increase in the Pi/PCr ratio (p < 0.05) as compared to the resting level. The ratio reached a plateau over a 3-min contraction using 5-Hz stimulation, then increased significantly more with the 50-Hz stimulation but decayed during the 3 min. Sustained stimulation with 50 Hz for 15-45 min evoked an initial sharp change in Pi/PCr, which then reached a steady plateau that remained over the entire stimulation. These findings indicate that the rabbit masseter muscle is relatively fatigue resistant in maintaining a steady-state equilibrium in the relation of Pi to PCr.

Glycerol phosphorylcholine (GPC) and serine ethanolamine phosphodiester (SEP): evolutionary mirrored metabolites and their potential metabolic roles

Water-soluble phosphodiesters (WSPDE) are a prominent feature of many 31P-NMR spectra; however, their role has remained somewhat of a mystery. What has been missed in almost all previous studies is the fact that two classes of WSPDE exist in vertebrates: those in mammals and those in the other (reptile-avian) line. The first is represented by glycerol phosphorylcholine and the second by serine ethanolamine phosphodiester. A further examination of the literature suggests a common role for all WSPDE as lysophospholipase inhibitors and therefore net sparers of phospholipids by decreasing phospholipid metabolic throughput.

In vivo 2D 1H NMR of mdx mouse muscle and myoblast cells during fusion: evidence for a characteristic signal of long chain fatty acids

We have previously demonstrated that 2D 1H NMR is suitable for studying cerebral metabolism. The same technique was used to study the hind leg muscle of normal (C57BL10) and dystrophic (mdx) mice. The results were compared to preliminary results for cultured muscle cells to determine the origin of fatty acid signals.

Effects of exercise training and anabolic steroids on plantaris and soleus phospholipids: a 31P nuclear magnetic resonance study

1. The purpose of this study was to examine the effect of exercise, anabolic steroid treatment, and a combination of both treatments on the phospholipid composition of predominantly fast twitch (plantaris) and slow twitch (soleus) skeletal muscles. The 4 experimental groups analyzed were sedentary control (C), steroid-treated (S), exercise-trained (E), and exercise plus steroid-treated (ES). 2. Among the 11 phospholipids quantitated, for the plantaris muscle, phosphatidylcholine was reduced in ES relative to C, while phosphatidylethanolamine and phosphatidylethanolamine plasmalogen were elevated in E and ES relative to C. For the soleus muscle, phosphatidylserine was reduced in S and E relative to C, and cardiolipin was elevated in E relative to C. 3. Of the 27 metabolic indices calculated for the plantaris, 15 changed significantly among E and ES relative to S and C, while for the soleus, only three indices changed among the four groups, two among E and ES relative to S and C and one between S and C. 4. For the plantaris muscle, the results are consistent with an exercise-induced alteration of membrane phospholipid composition that increases ion translocation activity. For the soleus muscle, this membrane alteration essentially does not take place. 5. Steroid treatment had little to no statistically significant effect on plantaris and soleus muscle phospholipid systems, regardless of the imposed regimen.

Effects of adenyl nucleotides and carbachol on cooperative interactions among G proteins

Muscarinic agonists and adenyl nucleotides are noncompetitive modulators of sites labeled by [35S]GTP gamma S in washed cardiac membranes from Syrian golden hamsters. Specific binding of the radioligand and its inhibition by either GTP gamma S or GDP reveals three states of affinity for guanyl nucleotides. In the absence of adenyl nucleotide, carbachol promotes an apparent interconversion of sites from higher to lower affinity for GDP; the effect recalls that of guanyl nucleotides on the binding of agonists to muscarinic receptors. In the presence of 0.1 mM ATP gamma S, the binding of [35S]GTP gamma S is increased at concentrations up to about 50 nM and decreased at higher concentrations. At a radioligand concentration of 160 pM, binding exhibits a bell-shaped dependence on the concentration of both ATP gamma S and AMP-PNP; with ADP and ATP, there is a second increase in bound [35S]GTP gamma S at the highest concentrations of adenyl nucleotide. ATP gamma S and AMP-PNP also modulate the effect of GDP, which itself emerges as a cooperative process: that is, binding of the radioligand in the presence of AMP-PNP exhibits a bell-shaped dependence on the concentration of GDP; moreover, the GDP-dependent increase in bound [35S]GTP gamma S is enhanced by carbachol. The interactions among GDP, GTP gamma S, and carbachol can be rationalized quantitatively in terms of a cooperative model involving two sites tentatively identified as G proteins. Both GTP gamma S and GDP exhibit negative homotropic cooperativity; carbachol enhances the homotropic cooperativity of GDP and induces or enhances positive heterotropic cooperativity between GDP and [35S]GTP gamma S. An analogous mechanism may underlie the guanyl nucleotide-dependent binding of agonists to muscarinic receptors. The data suggest that the binding properties of G proteins and their associated receptors reflect cooperative effects within heterooligomeric arrays; agonist-induced changes in cooperativity may facilitate the exchange of GTP for bound GDP and thereby constitute the mechanism of G protein activation in vivo.

31P NMR of Mg-ATP in dilute solutions: complexation and exchange

1. Monovalent-cation [(CH3)4N+, K(I), Na(I)] ATP, 1 mM in nucleotide, in aqueous solutions at pH 7.2, 24 degrees C, generates 2 different 31P NMR spectra, depending upon the salt content of the solution. At salt concentrations below 10 mM, the 31P NMR signals are chemically-shifted upfield (Na salt: alpha, -11.44 delta; beta, -22.91 delta; gamma, -8.36 delta) and the beta- and gamma-groups are broadened (at half-height: alpha, 3.5 Hz; beta, 9.6 Hz; gamma, 69 Hz). Above 10 mM salt, the signals are shifted downfield and are narrow (Na salt: alpha, -11.09 delta, 1.9 Hz; beta, -21.75 delta, 3.3 Hz; gamma, -6.30 delta, 3.9 Hz). 2. The Na-Mg-ATP complex, corresponding to the composition Na6Mg1ATP2, yields a single set of 31P resonances at concentrations of nucleotide of 100 mM, that upon dilution to 0.2 mM, resolve into 2 sets of ATP resonances characterized by low-field and high-field beta- and gamma-group resonance pairs. This set of ATP resonances, in contrast to the resonance set at 100 mM ATP, are broad (100 mM in ATP: alpha, -10.7 delta, 3.7 Hz; beta, -20.1 delta, 15 Hz; gamma, -5.7 delta, 7.3 Hz. 0.2 mM in ATP: alpha, -10.7 delta, 47 Hz; beta, -18.8 and -21.6 delta, 316 and 274 Hz; gamma, -5.5 and -8.7 delta, 460 and 374 Hz). 3. This new data, in combination with data derived from a survey of metal-ion-ATP studies, are interpreted in terms of ATP dimers, incorporating 2 molecules of ATP and 2 metal cations, that exist in water under the physiological conditions of neutral pH, high salt content [135 mM K(I)] and ATP concentrations in the range of 3 mM. 4. A compilation of 31P in vivo and ex vivo data compared to a reference Mg-ATP chemical shift vs Mg/ATP ratio plot indicates that ATP is not fully Mg-saturated in living systems and that 41% exists as the Mg(ATP)2 complex.

Improving data acquisition parameters of 31P in vivo spectra for signal analysis in the time domain

To obtain reliable NMR quantitation, experimental cautions concerning data acquisition must be taken when using automatic predictive calculations. For this study, 2000 31P in vitro and in vivo spectra were processed, using the enhancement procedure with linear prediction using singular value decomposition (EPLPSVD) method, and analyzed. The effects of quadrature detection modes (simultaneous or sequential), of the number of time-domain samples used are investigated and experimental conditions such as sample motions and spectral width are discussed.

31P NMR of tissue phospholipids: competition for Mg2+, Ca2+, Na+ and K+ cations

Phosphatidylcholine (PC), phosphatidylethanolamine (PE), ethanolamine plasmalogen (EPLAS), sphingomyelin (SPH), phosphatidylinositol (PI), phosphatidylserine (PS), cardiolipin (CL), phosphatidylglycerol (PG) and phosphatidic acid (PA) were dispersed together in Cs(ethylenedinitrilo)tetraacetic acid-scrubbed chloroform/methanol solution, and high resolution 31P nuclear magnetic resonance spectra were recorded. In separate titration experiments, Mg2+ and Ca2+ were added to the dispersed phospholipid mixture to determine the relative interaction potentials of each of the phospholipids for each of the added cations. The association of cations with individual phospholipids was indicated by 31P chemical-shift changes, signal broadening, signal quenching or a combination of these. The titrations revealed that CL had the highest, and PA the next highest, interaction potential for Mg2+ cations. In contrast, PS and PA had the highest, and CL the next highest, interaction potential for Ca2+. Considering only interactions with Ca2+ ions, the phospholipids can be divided into three distinct groups: PS and PA (high interaction potential); CL, PI and PG (intermediate interaction potential); and EPLAS, PE, SPH and PC (essentially no interaction potential). The two phospholipids with the least interaction potential for either of the alkaline-earth cations were PC and SPH. Na+ and K+ ion interactions with PA, CL, PI and PG were unique and resulted in positive chemical-shift changes relative to the chemical shifts in the presence of Cs+ ions. Relative to both Cs+ and K+ ions, chemical shifts in the presence of Na+ ions were deshielded delta greater than 0.1 ppm in the order PA greater than CL greater than PI greater than PG.

Temperature dependence of arginine kinase reaction in the tail muscle of live Sycionia ingentis as measured in vivo by 31P-NMR driven saturation transfer

We have employed the driven 31P-NMR saturation transfer method to measure in vivo the temperature dependence of the forward and reverse unidirectional fluxes of the arginine kinase reaction in the tail muscle of a live shrimp, Sycionia ingentis. Our results indicated that neither the forward nor the reverse rate constants of this reaction were significantly temperature-dependent between 8 and 16 degrees C, in contrast to the kinetic characteristics of isolated arginine kinases.