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Journal of Proteome Research Feb 2023Retention time (RT) alignment has been important for robust protein identification and quantification in proteomics. In data-dependent acquisition mode, whereby the...
Retention time (RT) alignment has been important for robust protein identification and quantification in proteomics. In data-dependent acquisition mode, whereby the precursor ions are semistochastically chosen for fragmentation in MS/MS, the alignment is used in an approach termed matched between runs (MBR). MBR transfers peptides, which were fragmented and identified in one experiment, to a replicate experiment where they were not identified. Before the MBR transfer, the RTs of experiments are aligned to reduce the chance of erroneous transfers. Despite its widespread use in other areas of quantitative proteomics, RT alignment has not been applied in data analyses for protein turnover using an atom-based stable isotope-labeling agent such as metabolic labeling with deuterium oxide, DO. Deuterium incorporation changes isotope profiles of intact peptides in full scans and their fragment ions in tandem mass spectra. It reduces the peptide identification rates in current database search engines. Therefore, the MBR becomes more important. Here, we report on an approach to incorporate RT alignment with peptide quantification in studies of proteome turnover using heavy water metabolic labeling and LC-MS. The RT alignment uses correlation-optimized time warping. The alignment, followed by the MBR, improves labeling time point coverage, especially for long labeling durations.
Topics: Tandem Mass Spectrometry; Deuterium Oxide; Peptides; Proteome; Isotopes; Isotope Labeling
PubMed: 36692003
DOI: 10.1021/acs.jproteome.2c00592 -
Journal of Animal Science Jan 2023The digestibility of energy and nutrients in fiber-rich diets depends greatly on the fiber source but most data are from studies with growing pigs. The purpose of this...
The digestibility of energy and nutrients in fiber-rich diets depends greatly on the fiber source but most data are from studies with growing pigs. The purpose of this study was to investigate the apparent total tract digestibility (ATTD) of nutrients in different fiber-rich diets and to quantify whole-body metabolism and utilization of energy and nitrogen (N) in gestating sows. Four fiber-rich diets based on sugar beet pulp (SBP), soy hulls (SH), palm kernel expellers (PKE), or a mixed fiber (MF) were formulated, with an average daily intake of total fiber (TF) of 471, 507, 651, and 437 g/d, respectively. A total of 48 multiparous sows were stratified by body weight at mating (day 0) and assigned to one of the four diets throughout gestation. Body weight and backfat were measured, and body pools of fat and protein were estimated using the deuterium oxide dilution technique at days 0, 30, and 60. On days 30 and 60, urine and fecal grab samples were obtained. On days 15 and 45, heart rate was measured to estimate total heat production. The ATTD of nutrients differed across treatments (P < 0.001), while in vivo organic matter digestibility deviated with up to ±3.3% units from in vitro enzyme digestibility of organic matter. The ATTD of energy was highly negatively correlated with intake of lignin (P < 0.001), while ATTD of N was highest (negatively) correlated (P < 0.001) with intake of insoluble non-starch polysaccharides (NSP). The ATTD of all nutrients except NSP was lowest in PKE-fed sows and highest, except for N, in sows fed the SBP diet. The ATTD of N was highest in the MF-fed sows and ATTD of NSP was lowest in the MF-fed sows. Sows lost most energy as heat (53% to 72% of gross energy intake), followed by energy in feces (15% to 17%), urine (3% to 4%), and methane (0.5% to 0.9%). Energy for maintenance accounted for the majority of the heat production and the total energy retention was lowest and highest in the SBP- and PKE-fed sows, with a retention of 3.3 and 13.3 MJ/d, respectively (P < 0.001). Sows lost most N through urine, the lowest and highest N loss (relative to intake) was observed in SH- and SBP-fed sows (50% to 63%, respectively), while 14% to 26% was retained as body protein. In conclusion, the fiber-rich diets were utilized efficiently by gestating sows with respect to energy with ATTD values above 82% in all four fiber-rich diets, whereas the high TF content in the diets compromised the N utilization in gestating sows.
Topics: Swine; Animals; Female; Digestion; Nitrogen; Nutrients; Diet; Energy Intake; Animal Feed; Dietary Fiber; Animal Nutritional Physiological Phenomena
PubMed: 36637127
DOI: 10.1093/jas/skad007 -
Data in Brief Feb 2023The datasets presented in this article represent detailed NMR spectral analyses on red beet fiber, including the pomace, water-soluble and water-insoluble fractions, as...
The datasets presented in this article represent detailed NMR spectral analyses on red beet fiber, including the pomace, water-soluble and water-insoluble fractions, as well as the acid-extracted pectin. The samples were solvated in deuterium oxide and investigated by 1D-H, 1D-C NMR, and multiple 2D-NMR experiments, including gCOSY, zTOCSY, HSQC, HMBC, HSQCTOCSY, and H2BC. The NMR chemical shifts, coupling constants and spin-systems were identified for the major carbohydrate residues in each sample. This article provides additional data related to the research article "Structural characterization of red beet fiber and pectin" published in Food Hydrocolloids [1].
PubMed: 36624764
DOI: 10.1016/j.dib.2022.108845 -
BMC Nephrology Jan 2023Fluid overload is associated with morbidity and mortality in children receiving dialysis. Accurate clinical assessment is difficult, and using deuterium oxide (DO) to...
BACKGROUND
Fluid overload is associated with morbidity and mortality in children receiving dialysis. Accurate clinical assessment is difficult, and using deuterium oxide (DO) to measure total body water (TBW) is impractical. We investigated the use of ultrasound (US), bioimpedance spectroscopy (BIS), and anthropometry to assess fluid removal in children receiving maintenance hemodialysis (HD).
METHODS
Participants completed US, BIS, and anthropometry immediately before and 1-2 h after HD for up to five sessions. US measured inferior vena cava (IVC) diameter, lung B-lines, muscle elastography, and dermal thickness. BIS measured the volume of extracellular (ECF) and intracellular (ICF) fluid. Anthropometry included mid-upper arm, calf and ankle circumferences, and triceps skinfold thickness. DO was performed once pre-HD. We assessed the change in study measures pre- versus post-HD, and the correlation of change in study measures with percent change in body weight (%∆BW). We also assessed the agreement between TBW measured by BIS and DO.
RESULTS
Eight participants aged 3.4-18.5 years were enrolled. Comparison of pre- and post-HD measures showed significant decrease in IVC diameters, lung B-lines, dermal thickness, BIS %ECF, mid-upper arm circumference, ankle, and calf circumference. Repeated measures correlation showed significant relationships between %∆BW and changes in BIS ECF (r =0.51, 95% CI 0.04, 0.80) and calf circumference (r=0.80, 95% CI 0.51, 0.92). BIS TBW correlated with DO TBW but overestimated TBW by 2.2 L (95% LOA, -4.75 to 0.42).
CONCLUSION
BIS and calf circumference may be helpful to assess changes in fluid status in children receiving maintenance HD. IVC diameter, lung B-lines and dermal thickness are potential candidates for future studies.
Topics: Humans; Child; Renal Dialysis; Pilot Projects; Body Water; Anthropometry; Spectrum Analysis; Electric Impedance
PubMed: 36600202
DOI: 10.1186/s12882-022-03012-1 -
Function (Oxford, England) 2023The skeletal muscle research field generally accepts that nuclei in skeletal muscle fibers (ie, myonuclei) are post-mitotic and unable to proliferate. Because our...
The skeletal muscle research field generally accepts that nuclei in skeletal muscle fibers (ie, myonuclei) are post-mitotic and unable to proliferate. Because our deuterium oxide (DO) labeling studies showed DNA synthesis in skeletal muscle tissue, we hypothesized that resident myonuclei can replicate . To test this hypothesis, we used a mouse model that temporally labeled myonuclei with GFP followed by DO labeling during normal cage activity, functional overload, and with satellite cell ablation. During normal cage activity, we observed deuterium enrichment into myonuclear DNA in 7 out of 7 plantaris (PLA), 6 out of 6 tibialis anterior (TA), 5 out of 7 gastrocnemius (GAST), and 7 out of 7 quadriceps (QUAD). The average fractional synthesis rates (FSR) of DNA in myonuclei were: 0.0202 ± 0.0093 in PLA, 0.0239 ± 0.0040 in TA, 0.0076 ± 0. 0058 in GAST, and 0.0138 ± 0.0039 in QUAD, while there was no replication in myonuclei from EDL. These FSR values were largely reproduced in the overload and satellite cell ablation conditions, although there were higher synthesis rates in the overloaded PLA muscle. We further provided evidence that myonuclear replication is through endoreplication, which results in polyploidy. These novel findings contradict the dogma that skeletal muscle nuclei are post-mitotic and open potential avenues to harness the intrinsic replicative ability of myonuclei for muscle maintenance and growth.
Topics: Mice; Animals; Muscle, Skeletal; Muscle Fibers, Skeletal; Cell Nucleus; Quadriceps Muscle; Polyesters
PubMed: 36569816
DOI: 10.1093/function/zqac059 -
Metabolites Nov 2022Patients treated for traumatic brain injury (TBI) are in metabolic crises because of the trauma and underfeeding. We utilized fractional gluconeogenesis (fGNG) to assess...
Patients treated for traumatic brain injury (TBI) are in metabolic crises because of the trauma and underfeeding. We utilized fractional gluconeogenesis (fGNG) to assess nutritional adequacy in ad libitum-fed and calorically-restricted rats following TBI. Male Sprague-Dawley individually housed rats 49 days of age were randomly assigned into four groups: ad libitum (AL) fed control (AL-Con, sham), AL plus TBI (AL+TBI), caloric restriction (CR) control (CR-Con, sham), and CR plus TBI (CR+TBI). From days 1-7 animals were given AL access to food and water containing 6% deuterium oxide (DO). On day 8, a pre-intervention blood sample was drawn from each animal, and TBI, sham injury, and CR protocols were initiated. On day 22, the animals were euthanized, and blood was collected to measure fGNG. Pre-intervention, there was no significant difference in fGNG among groups ( ≥ 0.05). There was a significant increase in fGNG due to caloric restriction, independent of TBI ( ≤ 0.05). In addition, fGNG may provide a real-time, personalized biomarker for assessing patient dietary caloric needs.
PubMed: 36557201
DOI: 10.3390/metabo12121163 -
International Journal of Molecular... Nov 2022Metabolic stable isotope labeling followed by liquid chromatography coupled with mass spectrometry (LC-MS) is a powerful tool for in vivo protein turnover studies of...
Metabolic stable isotope labeling followed by liquid chromatography coupled with mass spectrometry (LC-MS) is a powerful tool for in vivo protein turnover studies of individual proteins on a large scale and with high throughput. Turnover rates of thousands of proteins from dozens of time course experiments are determined by data processing tools, which are essential components of the workflows for automated extraction of turnover rates. The development of sophisticated algorithms for estimating protein turnover has been emphasized. However, the visualization and annotation of the time series data are no less important. The visualization tools help to validate the quality of the model fits, their goodness-of-fit characteristics, mass spectral features of peptides, and consistency of peptide identifications, among others. Here, we describe a graphical user interface (GUI) to visualize the results from the protein turnover analysis tool, d2ome, which determines protein turnover rates from metabolic DO labeling followed by LC-MS. We emphasize the specific features of the time series data and their visualization in the GUI. The time series data visualized by the GUI can be saved in JPEG format for storage and further dissemination.
Topics: Chromatography, Liquid; Deuterium Oxide; Tandem Mass Spectrometry; Software; Isotope Labeling; Proteins; Peptides
PubMed: 36498948
DOI: 10.3390/ijms232314620 -
Journal of Labelled Compounds &... Jan 2023This paper describes the deuterium-labelling of alkylnitroaromatics by base-catalysed exchange with deuterium oxide. As the alkyl protons alpha to the aromatic ring are...
This paper describes the deuterium-labelling of alkylnitroaromatics by base-catalysed exchange with deuterium oxide. As the alkyl protons alpha to the aromatic ring are the most acidic sites in the molecule, regioselective hydrogen isotope exchange at this benzylic location leads to a regiospecifically deuterated product. The exchange labelling takes place in good yields and with high atom% abundance in the presence of an appropriate nitrogen base. Alkylated 2,4-dinitrobenzenes deuterate at room temperature under catalysis by triethylamine, whilst alkylated 2-nitro- or 4-nitrobenzenes and related mono-nitroaromatics require higher temperatures and catalysis by 1,5-diazobicyclo[4.3.0]non-5-ene (DBN). The labelling reactions require an inert gas atmosphere, but otherwise are simple and high yielding with no obvious byproducts. Those compounds in which the benzylic protons are in an ortho-orientation with respect to the nitro group label somewhat more slowly than the analogues where there is a para relationship. In addition, higher alkyl homologues undergo benzylic deuteration at slower rates than methyl.
Topics: Deuterium Oxide; Amines; Protons; Hydrogen; Catalysis
PubMed: 36453978
DOI: 10.1002/jlcr.4008 -
Chemistry (Weinheim An Der Bergstrasse,... Dec 2022A 3-amino-functionalized phosphabenzene (phosphinine) has been synthesized and structurally characterized. The pyramidalized nitrogen atom of the dimethylamino...
A 3-amino-functionalized phosphabenzene (phosphinine) has been synthesized and structurally characterized. The pyramidalized nitrogen atom of the dimethylamino substituent indicates only a weak interaction between the lone pair of the nitrogen atom and the aromatic phosphorus heterocycle, resulting in somewhat basic character. It turned out that the amino group can indeed be protonated by HCl. In contrast to pyridines, however, the phosphabenzene-ammonium salt undergoes a selective ring contraction to form a hydroxylphospholene oxide in the presence of additional water. Based on deuterium labeling experiments and quantum chemical calculations, a rational mechanism for this hitherto unknown conversion is proposed.
PubMed: 36383093
DOI: 10.1002/chem.202203406 -
Nutrients Oct 2022Sarcopenia is a multifactorial disease that limits autonomy for the growing elderly population. An optimal amount of dietary protein has shown to be important to... (Comparative Study)
Comparative Study Randomized Controlled Trial
Comparing Even with Skewed Dietary Protein Distribution Shows No Difference in Muscle Protein Synthesis or Amino Acid Utilization in Healthy Older Individuals: A Randomized Controlled Trial.
Sarcopenia is a multifactorial disease that limits autonomy for the growing elderly population. An optimal amount of dietary protein has shown to be important to maintain muscle mass during aging. Yet, the optimal distribution of that dietary protein has not been fully clarified. The aim of the present study was to examine whether an even, compared to a skewed, distribution of daily dietary protein leads to higher muscle protein synthesis and amino acid utilization. Twelve healthy males and twelve healthy females aged between 65 and 80 years were block randomized to either an even (EVEN, = 12) or skewed (SKEWED, = 12) dietary protein distribution for three daily main meals. Seven days of habituation were followed by three trial days, which were initiated by oral intake of deuterium oxide (DO). The dietary protein throughout all trial meals was intrinsically labelled with H-phenylalanine. Blood samples were drawn daily, and muscle biopsies were taken before and at the end of the trial to measure muscle protein synthesis (FSR) and muscle protein incorporation of the dietary-protein-derived tracer. Muscle protein FSR was no different between the two groups (EVEN 2.16 ± 0.13%/day and SKEWED 2.23 ± 0.09%/day, = 0.647), and the muscle protein incorporation of the intrinsically labeled H-phenylalanine tracer was not different between the two groups (EVEN 0.0049 ± 0.0004 MPE% and SKEWED 0.0054 ± 0.0003 MPE%, = 0.306). In conclusion, the daily distribution pattern of the dietary protein did not affect muscle protein synthesis or the utilization of dietary protein.
Topics: Aged; Aged, 80 and over; Female; Humans; Male; Amino Acids; Dietary Proteins; Muscle Proteins; Muscle, Skeletal; Phenylalanine
PubMed: 36364705
DOI: 10.3390/nu14214442