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Angewandte Chemie (International Ed. in... Oct 2021The template-directed synthesis of RNA played an important role in the transition from prebiotic chemistry to the beginnings of RNA based life, but the mechanism of RNA...
The template-directed synthesis of RNA played an important role in the transition from prebiotic chemistry to the beginnings of RNA based life, but the mechanism of RNA copying chemistry is incompletely understood. We measured the kinetics of template copying with a set of primers with modified 3'-nucleotides and determined the crystal structures of these modified nucleotides in the context of a primer/template/substrate-analog complex. pH-rate profiles and solvent isotope effects show that deprotonation of the primer 3'-hydroxyl occurs prior to the rate limiting step, the attack of the alkoxide on the activated phosphate of the incoming nucleotide. The analogs with a E ribose conformation show the fastest formation of 3'-5' phosphodiester bonds. Among those derivatives, the reaction rate is strongly correlated with the electronegativity of the 2'-substituent. We interpret our results in terms of differences in steric bulk and charge distribution in the ground vs. transition states.
Topics: Arabinose; Crystallography, X-Ray; DNA Primers; Deuterium Oxide; Imidazoles; Kinetics; Nucleic Acid Conformation; Nucleotides; RNA; Structure-Activity Relationship; Templates, Genetic; Water
PubMed: 34428345
DOI: 10.1002/anie.202109714 -
Royal Society Open Science Nov 2020African elephants, the largest land animal, face particular physiological challenges in captivity and the wild. Captive elephants can become over- or under-conditioned...
African elephants, the largest land animal, face particular physiological challenges in captivity and the wild. Captive elephants can become over- or under-conditioned with inadequate exercise and diet management. Few studies have quantified body composition or water turnover in elephants, and none to date have examined longitudinal responses to changes in diet or air temperature. Using the stable isotope deuterium oxide (HO), we investigated changes in body mass, estimated fat-free mass (FFM, including fat-free gut content) and body fat in response to a multi-year intervention that reduced dietary energy density for adult African elephants housed at the North Carolina Zoo. We also examined the relationship between air temperature and water turnover. Deuterium dilution and depletion rates were assayed via blood samples and used to calculate body composition and water turnover in two male and three female African elephants at six intervals over a 3-year period. Within the first year after the dietary intervention, there was an increase in overall body mass, a reduction in body fat percentage and an increase in FFM. However, final values of both body fat percentage and FFM were similar to initial values. Water turnover (males: 359 ± 9 l d; females: 241 ± 28 l d) was consistent with the allometric scaling of water use in other terrestrial mammals. Water turnover increased with outdoor air temperature. Our study highlights the physiological water dependence of elephants and shows that individuals have to drink every 2-3 days to avoid critical water loss of approximately 10% body mass in hot conditions.
PubMed: 33391799
DOI: 10.1098/rsos.201155 -
Analytical Chemistry Nov 2023In drug research and development, knowledge of the precise structure of an active ingredient is crucial. However, it is equally important to know the water content of...
In drug research and development, knowledge of the precise structure of an active ingredient is crucial. However, it is equally important to know the water content of the drug molecule, particularly the number of crystal waters present in its structure. Such knowledge ensures the avoidance of drug dosage and formulation errors since the number of water molecules affects the physicochemical and pharmaceutical properties of the molecule. Several methods have been used for crystal water measurements of organic compounds, of which thermogravimetry and crystallography may be the most common ones. To the best of our knowledge, solution-state NMR spectroscopy has not been used for crystal water determination in deuterium oxide. Quantitative NMR (qNMR) method will be presented in the paper with a comparison of single-crystal X-ray diffraction and thermogravimetric analysis results. The qNMR method for water content measurement is straightforward, reproducible, and accurate, including measurement of H NMR spectrum before and after the addition of the analyte compound, and the result can be calculated after integration of the reference compound, analyte, and HDO signals using the given equation. In practical terms, there is no need for weighing the samples under study, which makes it simple and is a clear advantage to the current determination methods. In addition, the crystal structures of two model bisphosphonates used herein are reported: that of monopotassium etidronate dihydrate and monosodium zoledronate trihydrate.
PubMed: 37923567
DOI: 10.1021/acs.analchem.3c03689 -
The Journal of Nutrition Feb 2023The medical body composition analyzer (mBCA) incorporates advances in multifrequency technology and has been validated using a 4-compartment (4C) model in adults but not...
Body Composition in Youths Aged 10‒17 Years by Deuterium Oxide Dilution, Air Displacement Plethysmography, and DXA: Validation of the Medical Body Composition Analyzer Bioimpedance Device by a 4-Compartment Model.
BACKGROUND
The medical body composition analyzer (mBCA) incorporates advances in multifrequency technology and has been validated using a 4-compartment (4C) model in adults but not in youths aged <18 y.
OBJECTIVES
This study aimed to formulate a 4C model based on 3 reference methods and develop and validate a body composition prediction equation for the mBCA in youths aged 10‒17 y.
METHODS
The body density of 60 female and male youths was measured by air displacement plethysmography, total body water by deuterium oxide dilution, and BMC by DXA. Data from the equation group (n = 30) were used to formulate a 4C model. The all-possible-regressions method was used to select variables. The model was validated in a second cohort (n = 30) in a random split design. The accuracy, precision, and potential bias were evaluated by the Bland and Altman procedure.
RESULTS
Mean age, weight (W), height (H), waist circumference, and z-score of BMI were 13.6 ± 2.3 y, 54.5 ± 15.5 kg, 156 ± 11.9 cm, 75.5 ± 10.9 cm, and 0.70 ± 1.32 z, respectively. The prediction equation was as follows: FFM in kg (FFM) = ([0.2081] ∗ [W] + [0.8814] ∗ [H/R] + [0.2055 ∗ Xc])-15.343; R = 0.96; standardized root-mean-square error (SRMSE) = 2.18 kg. FFM did not differ between the 4C method (38.9 ± 12.0 kg) and the mBCA (38.4 ± 11.4 kg) (P > 0.05). The relationship between these 2 variables did not deviate from the identity line, was not significantly different from 0, and the slope was not significantly different from 1.0. In the precision prediction model of mBCA, the R value was 0.98 and SRMSE was 2.1. No significant bias was found when regressing differences between methods and their means (P = 0.08).
CONCLUSIONS
The equation for the mBCA was accurate, precise, had no significant bias, had substantial strength of agreement and could be used in this age group when subjects were preferentially within the constraints of a specified body size.
Topics: Adult; Humans; Male; Female; Adolescent; Deuterium Oxide; Adipose Tissue; Body Composition; Plethysmography; Electric Impedance; Absorptiometry, Photon; Reproducibility of Results; Body Water
PubMed: 36894237
DOI: 10.1016/j.tjnut.2022.12.011 -
Molecules (Basel, Switzerland) May 2023An atmospheric pressure glow discharge ionisation source was constructed and utilized to study the dopamine (DA) oxidation process coupling with mass spectrometry....
An atmospheric pressure glow discharge ionisation source was constructed and utilized to study the dopamine (DA) oxidation process coupling with mass spectrometry. During the DA oxidation process catalysed by polyphenol oxidase (PPO), six cationic intermediates were directly detected by the atmospheric pressure glow discharge mass spectrometry (APGD-MS). Combined with tandem mass spectrometry, the structures of the dopamine semiquinone radical (DASQ) and leukodopaminochrome radical (LDAC) intermediates and structures of the isomers of dopaminochrome (DAC) and 5,6-dihydroxyindole (DHI) were further characterised with the introduction of 2,2,6,6-tetramethylpiperidine 1-oxyl (TEMPO) and deuterium oxide (DO) to APGD-MS. Meanwhile, UV-Vis studies confirmed the important role of PPO in catalyzing the DA oxidation reaction. Based on APGD-MS studies, a possible mechanism could be proposed for DA oxidation catalysed by PPO. Furthermore, APGD-MS could provide possibilities for the effective detection and characterisation of short-lived intermediates, even in complicated systems.
PubMed: 37175253
DOI: 10.3390/molecules28093844 -
Carbohydrate Polymers Jan 2022Previous researches suggested that polysaccharides from brown algae had anti-virus activity. We hypothesized that nature polysaccharide from marine plants might have the...
Previous researches suggested that polysaccharides from brown algae had anti-virus activity. We hypothesized that nature polysaccharide from marine plants might have the effect on anti-SARS-CoV-2 activity. By high throughput screening to target 3CLpro enzyme using polysaccharides library, we discover a crude polysaccharide 375 from seaweed Ecklonia kurome blocked 3CLpro enzymatic activity and shows good anti-SARS-CoV-2 infection activity in cell. Further, we show that homogeneous polysaccharide 37502 from the 375 may bind to 3CLpro well and disturb spike protein binding to ACE2 receptor. The structure characterization uncovers that 37502 is alginate. These results imply that the bioactivities of 375 on SARS-CoV-2 may target multiple key molecules implicated in the virus infection and replication. The above results suggest that 375 may be a potential drug candidate against SARS-CoV-2.
Topics: COVID-19; Humans; Molecular Docking Simulation; Polysaccharides; Seaweed; Virus Internalization
PubMed: 34742404
DOI: 10.1016/j.carbpol.2021.118779 -
Chemical & Pharmaceutical Bulletin 2015The current study used 3 types of carrageenan (denoted here as Car)-κ, ι, and λ-to prepare a jelly vehicle for acetaminophen (AAP), and then compared their usefulness...
The current study used 3 types of carrageenan (denoted here as Car)-κ, ι, and λ-to prepare a jelly vehicle for acetaminophen (AAP), and then compared their usefulness as jelly vehicles. The rheological characteristics of each preparation were assessed and then drug elution from the preparation was assessed using dissolution testing. The behavior of each preparation when immersed in water was also examined using magnetic resonance imaging (MRI) in order to better understand the drug elution behaviour of each preparation. Viscoelasticity measurements revealed that 0.75 w/v%-ι-Car and 1.25 w/v%-λ-Car had viscoelasticity values equivalent to that of 0.5 w/v%-κ-Car. Dissolution testing of these 3 preparations indicated that 100% drug elution took 45 min with 0.5 w/v%-κ-Car while it took only 5 min with 0.75 w/v%-ι-Car and 1.25 w/v%-λ-Car. When deuterium oxide was added to κ-Car 0.5%, the MRI images darkened overall starting immediately after addition. The images revealed that the sample and deuterium oxide quickly mixed. In contrast, images revealed that deuterium oxide gradually penetrated κ-Car 1.0%. MRI images had uniform contrast, and deuterium oxide took 6 h or longer to penetrate the samples overall. These findings suggest that water is less apt to penetrate a jelly with an increased car concentration and a denser 3-dimensional network structure. Differences in the structure of car are said to result in better gelling, with κ having the best gelling characteristics, followed by ι and then λ. Thus, this paper discusses the role that vehicle gelling strength plays in the elution of acetaminophen.
Topics: Acetaminophen; Carrageenan; Deuterium Oxide; Elasticity; Gels; Magnetic Resonance Imaging; Viscosity; Water
PubMed: 25877549
DOI: 10.1248/cpb.c15-00097 -
Journal of Cachexia, Sarcopenia and... Dec 2021Ageing and cachexia cause a loss of muscle mass over time, indicating that protein breakdown exceeds protein synthesis. Deuterium oxide (D O) is used for studies of...
BACKGROUND
Ageing and cachexia cause a loss of muscle mass over time, indicating that protein breakdown exceeds protein synthesis. Deuterium oxide (D O) is used for studies of protein turnover because of the advantages of long-term labelling, but these methods introduce considerations that have been largely overlooked when studying conditions of protein gain or loss. The purpose of this study was to demonstrate the importance of accounting for a change in protein mass, a non-steady state, during D O labelling studies while also exploring the contribution of protein synthesis and breakdown to denervation-induced muscle atrophy.
METHODS
Adult (6 months) male C57BL/6 mice (n = 14) were labelled with D O for a total of 7 days following unilateral sciatic nerve transection to induce denervation of hindlimb muscles. The contralateral sham limb and nonsurgical mice (n = 5) were used as two different controls to account for potential crossover effects of denervation. We calculated gastrocnemius myofibrillar and collagen protein synthesis and breakdown assuming steady-state or using non-steady-state modelling. We measured RNA synthesis rates to further understand ribosomal turnover during atrophy.
RESULTS
Gastrocnemius mass was less in denervated muscle (137 ± 9 mg) compared with sham (174 ± 15 mg; P < 0.0001) or nonsurgical control (162 ± 5 mg; P < 0.0001). With steady-state calculations, fractional synthesis and breakdown rates (FSR and FBR) were lower in the denervated muscle (1.49 ± 0.06%/day) compared with sham (1.81 ± 0.09%/day; P < 0.0001) or nonsurgical control (2.27 ± 0.04%/day; P < 0.0001). When adjusting for change in protein mass, FSR was 4.21 ± 0.19%/day in denervated limb, whereas FBR was 4.09 ± 0.22%/day. When considering change in protein mass (k ), myofibrillar synthesis was lower in denervated limb (2.44 ± 0.14 mg/day) compared with sham (3.43 ± 0.22 mg/day; P < 0.0001) and non-surgical control (3.74 ± 0.12 mg/day; P < 0.0001), whereas rate of protein breakdown (k 1/t) was greater in denervated limb (0.050 ± 0.003) compared with sham (0.019 ± 0.001; P < 0.0001) and nonsurgical control (0.023 ± 0.000; P < 0.0001). Muscle collagen breakdown was completely inhibited during denervation. There was a strong correlation (r = 0.83, P < 0.001) between RNA and myofibrillar protein synthesis in sham but not denervated muscle.
CONCLUSIONS
We show conflicting results between steady- and non-steady-state calculations on myofibrillar protein synthesis and breakdown during periods of muscle loss. We also found that collagen accumulation was largely from a decrease in collagen breakdown. Comparison between sham and non-surgical control demonstrated a crossover effect of denervation on myofibrillar protein synthesis and ribosomal biogenesis, which impacts study design for unilateral atrophy studies. These considerations are important because not accounting for them can mislead therapeutic attempts to maintain muscle mass.
Topics: Animals; Male; Mice; Mice, Inbred C57BL; Muscle Denervation; Muscle, Skeletal; Muscular Atrophy; Protein Biosynthesis
PubMed: 34418329
DOI: 10.1002/jcsm.12772 -
Journal of Cardiovascular Magnetic... Jun 2022Quantitative assessment of dynamic lung water accumulation is of interest to unmask latent heart failure. We develop and validate a free-breathing 3D ultrashort echo...
BACKGROUND
Quantitative assessment of dynamic lung water accumulation is of interest to unmask latent heart failure. We develop and validate a free-breathing 3D ultrashort echo time (UTE) sequence with automated inline image processing to image changes in lung water density (LWD) using high-performance 0.55 T cardiovascular magnetic resonance (CMR).
METHODS
Quantitative lung water CMR was performed on 15 healthy subjects using free-breathing 3D stack-of-spirals proton density weighted UTE at 0.55 T. Inline image reconstruction and automated image processing was performed using the Gadgetron framework. A gravity-induced redistribution of LWD was provoked by sequentially acquiring images in the supine, prone, and again supine position. Quantitative validation was performed in a phantom array of vials containing mixtures of water and deuterium oxide.
RESULTS
The phantom experiment validated the capability of the sequence in quantifying water density (bias ± SD 4.3 ± 4.8%, intraclass correlation coefficient, ICC = 0.97). The average global LWD was comparable between imaging positions (supine 24.7 ± 3.4%, prone 22.7 ± 3.1%, second supine 25.3 ± 3.6%), with small differences between imaging phases (first supine vs prone 2.0%, p < 0.001; first supine vs second supine - 0.6%, p = 0.001; prone vs second supine - 2.7%, p < 0.001). In vivo test-retest repeatability in LWD was excellent (- 0.17 ± 0.91%, ICC = 0.97). A regional LWD redistribution was observed in all subjects when repositioning, with a predominant posterior LWD accumulation when supine, and anterior accumulation when prone (difference in anterior-posterior LWD: supine - 11.6 ± 2.7%, prone 5.5 ± 2.7%, second supine - 11.4 ± 2.9%). Global LWD maps were calculated inline within 23.2 ± 0.3 s following the image reconstruction using the automated pipeline.
CONCLUSIONS
Redistribution of LWD due to gravitational forces can be depicted and quantified using a validated free-breathing 3D proton density weighted UTE sequence and inline automated image processing pipeline on a high-performance 0.55 T CMR system.
Topics: Humans; Imaging, Three-Dimensional; Lung; Magnetic Resonance Imaging; Magnetic Resonance Spectroscopy; Predictive Value of Tests; Protons
PubMed: 35668497
DOI: 10.1186/s12968-022-00862-4 -
Chemical Science Sep 2023Cucurbit[7]uril (CB[7]) encapsulates adamantyl and trimethylsilyl substituents of positively charged guests in dimethyl sulfoxide (DMSO). Unlike in water or deuterium...
Cucurbit[7]uril (CB[7]) encapsulates adamantyl and trimethylsilyl substituents of positively charged guests in dimethyl sulfoxide (DMSO). Unlike in water or deuterium oxide, addition of a selection of alkali and alkali-earth cations with van der Waals radii between 1.0 and 1.4 Å (Na, K, Ca, Sr, Ba and Eu) to the CB[7]/guest complexes triggers their cation-mediated trimerization, a process that is very slow on the nuclear magnetic resonance (NMR) time scale. Smaller (Li, Mg) or larger cations (Rb, Cs or NH) are inert. The trimers display extensive CH-O interactions between the equatorial and pseudo-equatorial hydrogens of CB[7] and the carbonyl rim of the neighboring CB[7] unit in the trimer, and a deeply nested cation between the three interacting carbonylated CB[7] rims; a counteranion is likely perched in the shallow cavity formed by the three outer walls of CB[7] in the trimer. Remarkably, a guest must occupy the cavity of CB[7] for trimerization to take place. Using a combination of semi-empirical and density functional theory techniques in conjunction with continuum solvation models, we showed that trimerization is favored in DMSO, and not in water, because the penalty for the partial desolvation of three of the six CB[7] portals upon aggregation into a trimer is less unfavorable in DMSO compared to water.
PubMed: 37712024
DOI: 10.1039/d3sc02032k