Publications by authors named "William E Holmes"

25 Publications

  • Page 1 of 1

Synergistic adsorption and degradation of sulfamethoxazole from synthetic urine by hickory-sawdust-derived biochar: The critical role of the aromatic structure.

J Hazard Mater 2021 Jun 9;418:126366. Epub 2021 Jun 9.

Department of Civil Engineering, University of Louisiana at Lafayette, Lafayette, LA, 70504, USA; Energy Institute of Louisiana, University of Louisiana at Lafayette, Lafayette, LA, 70504, USA. Electronic address:

This study investigated the adsorptive removal and subsequent degradation of sulfamethoxazole (SMX) from a synthetic urine by biochar (BC). The BCs used in this study were prepared using two different feedstocks with different temperatures. Element analysis and Fourier transform infrared spectroscopy (FTIR) results suggested that the aromaticity of one of the BCs, 700HSBC was significantly different from the 700PSBC although both of them were prepared at the same temperature (700 °C) with similar pore size distributions and specific surface areas. Due to the presence of abundant aromatic structures, 700HSBC showed a higher SMX uptake than 700PSBC, suggesting that the π-π interaction was the main adsorption mechanism. The removal of SMX from the urine was significantly enhanced by adding hydrogen peroxide to the 700HSBC. The carbonate radicals degradation of SMX mechanism was proposed and verified. With 700HSBC having abundant aromatic structures acting as π-electron donors, it could be an efficient activator for peroxymonocarbonate (HCO) to generate carbonate radicals. Hence, it could be concluded that the aromatic structures on BCs play a key role in both of the adsorption and hydrogen peroxide degradation of the SMX resulting in its removal from urine.
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http://dx.doi.org/10.1016/j.jhazmat.2021.126366DOI Listing
June 2021

Evaluation of thioesterases from Acinetobacter baylyi for production of free fatty acids.

Can J Microbiol 2017 Apr 23;63(4):321-329. Epub 2017 Mar 23.

a Department of Biology, University of Louisiana at Lafayette, Lafayette, LA 70504, USA.

Acinetobacter baylyi is one of few Gram-negative bacteria capable of accumulating storage lipids in the form of triacylglycerides and wax esters, which makes it an attractive candidate for production of lipophilic products, including biofuel precursors. Thioesterases play a significant dual role in the triacylglyceride and wax ester biosynthesis by either providing or removing acyl-CoA from this pathway. Therefore, 4 different thioesterase genes were cloned from Acinetobacter baylyi ADP1 and expressed in Escherichia coli to investigate their contribution to free fatty acids (FFAs) accumulation. Overexpression of the genes tesA' (a leaderless form of the gene tesA) and tesC resulted in increased accumulation of FFAs when compared with the host E. coli strain. Overexpression of tesA' showed a 1.87-fold increase in production of long-chain fatty acids (C16 to C18) over the host strain. Unlike TesC and the other investigated thioesterases, the TesA' thioesterase also produced shorter chain FFAs (e.g., myristic acid) and unsaturated FFAs (e.g., cis-vaccenic acid (18:1Δ11)). A comparison of the remaining 3 A. baylyi ADP1 thioesterases (encoded by the tesB, tesC, and tesD genes) revealed that only the strain containing the tesC gene produced statistically higher levels of FFAs over the control, suggesting that it possesses the acyl-ACP thioesterase activity. Both E. coli strains containing the tesB and tesD genes produced levels of FFAs similar to those of the plasmid-free control E. coli strain, which indicates that TesB and TesD lack the acyl-ACP thioesterase activity.
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http://dx.doi.org/10.1139/cjm-2016-0458DOI Listing
April 2017

Circulating protein synthesis rates reveal skeletal muscle proteome dynamics.

J Clin Invest 2016 Jan 14;126(1):288-302. Epub 2015 Dec 14.

Here, we have described and validated a strategy for monitoring skeletal muscle protein synthesis rates in rodents and humans over days or weeks from blood samples. We based this approach on label incorporation into proteins that are synthesized specifically in skeletal muscle and escape into the circulation. Heavy water labeling combined with sensitive tandem mass spectrometric analysis allowed integrated synthesis rates of proteins in muscle tissue across the proteome to be measured over several weeks. Fractional synthesis rate (FSR) of plasma creatine kinase M-type (CK-M) and carbonic anhydrase 3 (CA-3) in the blood, more than 90% of which is derived from skeletal muscle, correlated closely with FSR of CK-M, CA-3, and other proteins of various ontologies in skeletal muscle tissue in both rodents and humans. Protein synthesis rates across the muscle proteome generally changed in a coordinate manner in response to a sprint interval exercise training regimen in humans and to denervation or clenbuterol treatment in rodents. FSR of plasma CK-M and CA-3 revealed changes and interindividual differences in muscle tissue proteome dynamics. In human subjects, sprint interval training primarily stimulated synthesis of structural and glycolytic proteins. Together, our results indicate that this approach provides a virtual biopsy, sensitively revealing individualized changes in proteome-wide synthesis rates in skeletal muscle without a muscle biopsy. Accordingly, this approach has potential applications for the diagnosis, management, and treatment of muscle disorders.
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http://dx.doi.org/10.1172/JCI79639DOI Listing
http://www.ncbi.nlm.nih.gov/pmc/articles/PMC4701543PMC
January 2016

Reduced in vivo hepatic proteome replacement rates but not cell proliferation rates predict maximum lifespan extension in mice.

Aging Cell 2016 Feb 6;15(1):118-27. Epub 2015 Nov 6.

Department of Nutritional Science and Toxicology, University of California at Berkeley, Berkeley, CA, 94720, USA.

Combating the social and economic consequences of a growing elderly population will require the identification of interventions that slow the development of age-related diseases. Preserved cellular homeostasis and delayed aging have been previously linked to reduced cell proliferation and protein synthesis rates. To determine whether changes in these processes may contribute to or predict delayed aging in mammals, we measured cell proliferation rates and the synthesis and replacement rates (RRs) of over a hundred hepatic proteins in vivo in three different mouse models of extended maximum lifespan (maxLS): Snell Dwarf, calorie-restricted (CR), and rapamycin (Rapa)-treated mice. Cell proliferation rates were not consistently reduced across the models. In contrast, reduced hepatic protein RRs (longer half-lives) were observed in all three models compared to controls. Intriguingly, the degree of mean hepatic protein RR reduction was significantly correlated with the degree of maxLS extension across the models and across different Rapa doses. Absolute rates of hepatic protein synthesis were reduced in Snell Dwarf and CR, but not Rapa-treated mice. Hepatic chaperone levels were unchanged or reduced and glutathione S-transferase synthesis was preserved or increased in all three models, suggesting a reduced demand for protein renewal, possibly due to reduced levels of unfolded or damaged proteins. These data demonstrate that maxLS extension in mammals is associated with improved hepatic proteome homeostasis, as reflected by a reduced demand for protein renewal, and that reduced hepatic protein RRs hold promise as an early biomarker and potential target for interventions that delay aging in mammals.
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http://dx.doi.org/10.1111/acel.12414DOI Listing
http://www.ncbi.nlm.nih.gov/pmc/articles/PMC4717272PMC
February 2016

Turnover rates of hepatic collagen and circulating collagen-associated proteins in humans with chronic liver disease.

PLoS One 2015 24;10(4):e0123311. Epub 2015 Apr 24.

Department of Fibrosis, KineMed Inc., Emeryville, California, United States of America; Department of Nutritional Science and Toxicology, University of California, Berkeley, California, United States of America.

Accumulation and degradation of scar tissue in fibrotic liver disease occur slowly, typically over many years. Direct measurement of fibrogenesis, the rate of scar tissue deposition, may provide valuable therapeutic and prognostic information. We describe here results from a pilot study utilizing in vivo metabolic labeling to measure the turnover rate of hepatic collagen and collagen-associated proteins in plasma for the first time in human subjects. Eight subjects with chronic liver disease were labeled with daily oral doses of 2H2O for up to 8 weeks prior to diagnostic liver biopsy and plasma collection. Tandem mass spectrometry was used to measure the abundance and fractional synthesis rate (FSR) of proteins in liver and blood. Relative protein abundance and FSR data in liver revealed marked differences among subjects. FSRs of hepatic type I and III collagen ranged from 0.2-0.6% per day (half-lives of 4 months to a year) and correlated significantly with worsening histologic fibrosis. Analysis of plasma protein turnover revealed two collagen-associated proteins, lumican and transforming growth factor beta-induced-protein (TGFBI), exhibiting FSRs that correlated significantly with FSRs of hepatic collagen. In summary, this is the first direct measurement of liver collagen turnover in vivo in humans and suggests a high rate of collagen remodeling in advanced fibrosis. In addition, the FSRs of collagen-associated proteins in plasma are measurable and may provide a novel strategy for monitoring hepatic fibrogenesis rates.
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http://journals.plos.org/plosone/article?id=10.1371/journal.pone.0123311PLOS
http://www.ncbi.nlm.nih.gov/pmc/articles/PMC4409311PMC
January 2016

Proteomic analysis of altered extracellular matrix turnover in bleomycin-induced pulmonary fibrosis.

Mol Cell Proteomics 2014 Jul 16;13(7):1741-52. Epub 2014 Apr 16.

From *KineMed Inc., 5980 Horton St., Suite 470, Emeryville California 94608;

Fibrotic disease is characterized by the pathological accumulation of extracellular matrix (ECM) proteins. Surprisingly, very little is known about the synthesis and degradation rates of the many proteins and proteoglycans that constitute healthy or pathological extracellular matrix. A comprehensive understanding of altered ECM protein synthesis and degradation during the onset and progression of fibrotic disease would be immensely valuable. We have developed a dynamic proteomics platform that quantifies the fractional synthesis rates of large numbers of proteins via stable isotope labeling and LC/MS-based mass isotopomer analysis. Here, we present the first broad analysis of ECM protein kinetics during the onset of experimental pulmonary fibrosis. Mice were labeled with heavy water for up to 21 days following the induction of lung fibrosis with bleomycin. Lung tissue was subjected to sequential protein extraction to fractionate cellular, guanidine-soluble ECM proteins and residual insoluble ECM proteins. Fractional synthesis rates were calculated for 34 ECM proteins or protein subunits, including collagens, proteoglycans, and microfibrillar proteins. Overall, fractional synthesis rates of guanidine-soluble ECM proteins were faster than those of insoluble ECM proteins, suggesting that the insoluble fraction reflected older, more mature matrix components. This was confirmed through the quantitation of pyridinoline cross-links in each protein fraction. In fibrotic lung tissue, there was a significant increase in the fractional synthesis of unique sets of matrix proteins during early (pre-1 week) and late (post-1 week) fibrotic response. Furthermore, we isolated fast turnover subpopulations of several ECM proteins (e.g. type I collagen) based on guanidine solubility, allowing for accelerated detection of increased synthesis of typically slow-turnover protein populations. This establishes the presence of multiple kinetic pools of pulmonary collagen in vivo with altered turnover rates during evolving fibrosis. These data demonstrate the utility of dynamic proteomics in analyzing changes in ECM protein turnover associated with the onset and progression of fibrotic disease.
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http://dx.doi.org/10.1074/mcp.M113.037267DOI Listing
http://www.ncbi.nlm.nih.gov/pmc/articles/PMC4083112PMC
July 2014

Greater muscle protein synthesis and mitochondrial biogenesis in males compared with females during sprint interval training.

FASEB J 2014 Jun 5;28(6):2705-14. Epub 2014 Mar 5.

Department of Health and Exercise Science, Colorado State University, Fort Collins, Colorado, USA;

Improved endurance exercise performance in adult humans after sprint interval training (SIT) has been attributed to mitochondrial biogenesis. However, muscle protein synthesis (MPS) and mitochondrial biogenesis during SIT have not been measured, nor have sex-specific differences. We hypothesized that males and females would have similar rates of MPS, mitochondrial biogenesis, and synthesis of individual proteins during SIT. Deuterium oxide (D2O) was orally administered to 21 adults [11 male, 10 female; mean age, 23±1 yr; body mass index (BMI), 22.8±0.6 kg/m(2); mean± SE] for 4 wk, to measure protein synthesis rates while completing 9 sessions of 4-8 bouts of 30 s duration on a cycle ergometer separated by 4 min of active recovery. Samples of the vastus lateralis were taken before and 48 h after SIT. SIT increased maximum oxygen uptake (VO(2max), males 43.4±2.1-44.0±2.3; females 39.5±0.9-42.5±1.3 ml/kg/min; P=0.002). MPS was greater in the males than in the females in the mixed (~150%; P < 0.001), cytosolic (~135%; P=0.038), and mitochondrial (~135%; P=0.056) fractions. The corresponding ontological clusters of individual proteins were significantly greater in the males than in the females (all P<0.00001). For the first time, we document greater MPS and mitochondrial biogenesis during SIT in males than in females and describe the synthetic response of individual proteins in humans during exercise training.
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http://dx.doi.org/10.1096/fj.13-246595DOI Listing
June 2014

Lipid-enhancement of activated sludges obtained from conventional activated sludge and oxidation ditch processes.

Bioresour Technol 2013 Nov 5;148:487-93. Epub 2013 Sep 5.

Renewable Fuels and Chemicals Laboratory, Dave C. Swalm School of Chemical Engineering, Mail Stop 9595, Mississippi State University, MS 39762, USA.

Lipid-enhancement of activated sludges was conducted to increase the amount of saponifiable lipids in the sludges. The sludges were obtained from a conventional activated sludge (CAS) and an oxidation ditch process (ODP). Results showed 59-222% and 150-250% increase in saponifiable lipid content of the sludges from CAS and ODP, respectively. The fatty acid methyl ester (FAMEs) obtained from triacylglycerides was 57-67% (of total FAMEs) for enhanced CAS and 55-73% for enhanced ODP, a very significant improvement from 6% to 10% (CAS) and 4% to 8% (ODP). Regardless of the source, the enhancement resulted in sludges with similar fatty acid profile indicating homogenization of the lipids in the sludges. This study provides a potential strategy to utilize existing wastewater treatment facilities as source of significant amount of lipids for biofuel applications.
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http://dx.doi.org/10.1016/j.biortech.2013.08.158DOI Listing
November 2013

Effect of different C/N ratios on carotenoid and lipid production by Rhodotorula glutinis.

Appl Microbiol Biotechnol 2013 Jul 1;97(14):6581-8. Epub 2013 Jun 1.

Institute of Crop Science, University of Hohenheim, Fruwirthstr. 23, 70599 Stuttgart, Germany.

Due to the increasing demand for sustainable biofuels, microbial oils as feedstock for the transesterification into biodiesel have gained scientific and commercial interest. Also, microbial carotenoids have a considerable market potential as natural colorants. The carbon to nitrogen (C/N) ratio of the respective cultivation media is one of the most important parameters that influence the production of microbial lipids and carotenoids. Thus, in the present experiment, the influence of different C/N ratios, initial glucose loadings, and ammonium concentrations of the cultivation medium on microbial cell growth and lipid and carotenoid production by the oleaginous red yeast Rhodotorula glutinis has been assessed. As a general trend, both lipid and carotenoid production increased at high C/N ratios. It was shown that not only the final C/N ratio but also the respectively applied initial carbon and nitrogen contents influenced the observed parameters. The lipid yield was not affected by different ammonium contents, while the carotenoid production significantly decreased both at low and high levels of ammonium supply. A glucose-based increase from C/N 70 to 120 did not lead to an increased lipid production, while carotenoid synthesis was positively affected. Generally, it can be asserted that lipid and carotenoid synthesis are stimulated at higher C/N ratios.
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http://dx.doi.org/10.1007/s00253-013-5005-8DOI Listing
July 2013

Biodegradation of clomazone in a California rice field soil: carbon allocation and community effects.

J Agric Food Chem 2013 Mar 6;61(11):2618-24. Epub 2013 Mar 6.

Department of Environmental Toxicology, University of California , Davis Department of Environmental Toxicology, One Shields Ave, Davis, California 95616, United States.

Degradation pathways for the herbicide clomazone in a California rice field soil were characterized via pulse-labeling of anaerobic (flooded) and aerobic (moist) soil microcosms. Clomazone-derived (13)C in the major C pools of a rice ecosystem and soil phospholipid fatty acid (PLFA) profiles were analyzed over time to determine if (1) the compound accumulates in the microbial biomass, (2) it affects temporal microbial population dynamics, and (3) it is either preferentially metabolized or cometabolized. In anaerobic microcosms, the compound was rapidly biotransformed to ring-open clomazone, upon which it persisted in the aqueous phase, whereas aerobic microcosms degraded it slower but a greater percentage was mineralized. Anaerobic biomass decreased after clomazone was added, and aerobic actinomycete abundance differed between treatments and controls. Additionally, PLFA and (13)C PLFA were statistically similar between treatment and controls. Thus, microbial cometabolism is likely to be the dominant degrading mechanism governing clomazone fate in California rice fields.
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http://dx.doi.org/10.1021/jf304692cDOI Listing
March 2013

The effect of long term calorie restriction on in vivo hepatic proteostatis: a novel combination of dynamic and quantitative proteomics.

Mol Cell Proteomics 2012 Dec 13;11(12):1801-14. Epub 2012 Sep 13.

Kinemed Inc., Emeryville, CA 94608, USA.

Calorie restriction (CR) promotes longevity. A prevalent mechanistic hypothesis explaining this effect suggests that protein degradation, including mitochondrial autophagy, is increased with CR, removing damaged proteins and improving cellular fitness. At steady state, increased catabolism must be balanced by increasing mitochondrial biogenesis and protein synthesis, resulting in faster protein replacement rates. To test this hypothesis, we measured replacement kinetics and relative concentrations of hundreds of proteins in vivo in long-term CR and ad libitum-fed mice using metabolic (2)H(2)O-labeling combined with the Stable Isotope Labeling in Mammals protocol and LC-MS/MS analysis of mass isotopomer abundances in tryptic peptides. CR reduced absolute synthesis and breakdown rates of almost all measured hepatic proteins and prolonged the half-lives of most (≈ 80%), particularly mitochondrial proteins (but not ribosomal subunits). Proteins with related functions exhibited coordinated changes in relative concentration and replacement rates. In silico expression pathway interrogation allowed the testing of potential regulators of altered network dynamics (e.g. peroxisome proliferator-activated receptor gamma coactivator 1-alpha). In summary, our combination of dynamic and quantitative proteomics suggests that long-term CR reduces mitochondrial biogenesis and mitophagy. Our findings contradict the theory that CR increases mitochondrial protein turnover and provide compelling evidence that cellular fitness is accompanied by reduced global protein synthetic burden.
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http://dx.doi.org/10.1074/mcp.M112.021204DOI Listing
http://www.ncbi.nlm.nih.gov/pmc/articles/PMC3518108PMC
December 2012

The pathology associated with visceral toxicosis of catfish.

J Vet Diagn Invest 2011 Nov;23(6):1217-21

Thad Cochran National Warmwater Aquaculture Center, College of Veterinary Medicine, Mississippi State University, PO Box 197, Stoneville, MS 38776, USA.

Visceral toxicosis of catfish (VTC) syndrome was recognized in the late 1990 s and recently has been associated with exposure to Clostridium botulinum type E neurotoxin. Tentative diagnosis is based on clinical presentation and gross findings, and is confirmed by bioassay. In April 2009, channel catfish (Ictalurus punctatus) from 2 different farms presented with abnormal swimming behavior and mortalities. Nine fish were submitted to the Aquatic Research and Diagnostic Laboratory (Stoneville, Mississippi) for evaluation. Bacterial cultures from these fish were negative. Necropsy findings included intestinal intussusceptions, ascites, pale proximal intestines with engorged serosal blood vessels, splenic congestion, and a reticular pattern to the liver. Significant histopathologic findings were limited to cerebral, splenic, and hepatic congestion, splenic lymphoid depletion and perivascular edema, vascular dilation and edema of the gastrointestinal tract, and perivascular edema in the anterior and posterior kidneys. Intoxication from C. botulinum type E neurotoxin was suspected based on the clinical signs and lack of gross and microbiological evidence of an infectious disease process. The toxicosis was confirmed with a positive bioassay using serum collected from the submitted fish.
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http://dx.doi.org/10.1177/1040638711425577DOI Listing
November 2011

Microbial community composition and carbon cycling within soil microenvironments of conventional, low-input, and organic cropping systems.

Soil Biol Biochem 2011 Jan;43(1):20-30

Department of Plant Sciences, University of California, Davis, One Shields Avenue, Davis, CA 95616, USA.

This study coupled stable isotope probing with phospholipid fatty acid analysis ((13)C-PLFA) to describe the role of microbial community composition in the short-term processing (i.e., C incorporation into microbial biomass and/or deposition or respiration of C) of root- versus residue-C and, ultimately, in long-term C sequestration in conventional (annual synthetic fertilizer applications), low-input (synthetic fertilizer and cover crop applied in alternating years), and organic (annual composted manure and cover crop additions) maize-tomato (Zea mays - Lycopersicum esculentum) cropping systems. During the maize growing season, we traced (13)C-labeled hairy vetch (Vicia dasycarpa) roots and residues into PLFAs extracted from soil microaggregates (53-250 μm) and silt-and-clay (<53 μm) particles. Total PLFA biomass was greatest in the organic (41.4 nmol g(-1) soil) and similar between the conventional and low-input systems (31.0 and 30.1 nmol g(-1) soil, respectively), with Gram-positive bacterial PLFA dominating the microbial communities in all systems. Although total PLFA-C derived from roots was over four times greater than from residues, relative distributions (mol%) of root- and residue-derived C into the microbial communities were not different among the three cropping systems. Additionally, neither the PLFA profiles nor the amount of root- and residue-C incorporation into the PLFAs of the microaggregates were consistently different when compared with the silt-and-clay particles. More fungal PLFA-C was measured, however, in microaggregates compared with silt-and-clay. The lack of differences between the mol% within the microbial communities of the cropping systems and between the PLFA-C in the microaggregates and the silt-and-clay may have been due to (i) insufficient differences in quality between roots and residues and/or (ii) the high N availability in these N-fertilized cropping systems that augmented the abilities of the microbial communities to process a wide range of substrate qualities. The main implications of this study are that (i) the greater short-term microbial processing of root- than residue-C can be a mechanistic explanation for the higher relative retention of root- over residue-C, but microbial community composition did not influence long-term C sequestration trends in the three cropping systems and (ii) in spite of the similarity between the microbial community profiles of the microaggregates and the silt-and-clay, more C was processed in the microaggregates by fungi, suggesting that the microaggregate is a relatively unique microenvironment for fungal activity.
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http://www.ncbi.nlm.nih.gov/pmc/articles/PMC3260532PMC
http://dx.doi.org/10.1016/j.soilbio.2010.09.005DOI Listing
January 2011

Measurement of human plasma proteome dynamics with (2)H(2)O and liquid chromatography tandem mass spectrometry.

Anal Biochem 2012 Jan 14;420(1):73-83. Epub 2011 Sep 14.

KineMed, Emeryville, CA 94608, USA.

Dysfunction of protein turnover is a feature of many human diseases, and proteins are substrates in important biological processes. Currently, no method exists for the measurement of global protein turnover (i.e., proteome dynamics) that can be applied in humans. Here we describe the use of metabolic labeling with deuterium ((2)H) from (2)H(2)O and liquid chromatography tandem mass spectrometry (LC-MS/MS) analysis of mass isotopomer patterns to measure protein turnover. We show that the positions available for (2)H label incorporation in vivo can be calculated using peptide sequence. The isotopic incorporation values calculated by combinatorial analysis of mass isotopomer patterns in peptides correlate very closely with values established for individual amino acids. Inpatient and outpatient heavy water labeling protocols resulted in (2)H label incorporation sufficient for reproducible quantitation in humans. Replacement rates were similar for peptides deriving from the same protein. Using a kinetic model to account for the time course of each individual's (2)H(2)O enrichment curves, dynamics of approximately 100 proteins with half-lives ranging from 0.4 to 40 days were measured using 8 μl of plasma. The measured rates were consistent with literature values. This method can be used to measure in vivo proteome homeostasis in humans in disease and during therapeutic interventions.
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http://dx.doi.org/10.1016/j.ab.2011.09.007DOI Listing
January 2012

Simulated atmospheric NO3- deposition increases soil organic matter by slowing decomposition.

Ecol Appl 2008 Dec;18(8):2016-27

School of Natural Resources and Environment, University of Michigan, Ann Arbor, Michigan 48109, USA.

Presently, there is uncertainty regarding the degree to which anthropogenic N deposition will foster C storage in the N-limited forests of the Northern Hemisphere, ecosystems which are globally important sinks for anthropogenic CO2. We constructed organic matter and N budgets for replicate northern hardwood stands (n = 4) that have received ambient (0.7-1.2 g N x m(-2) x yr(-1) and experimental NO3- deposition (ambient plus 3 g NO3(-)-N x m(-2) x yr(-1)) for a decade; we also traced the flow of a 15NO3- pulse over a six-year period. Experimental NO3- deposition had no effect on organic matter or N stored in the standing forest overstory, but it did significantly increase the N concentration (+19%) and N content (+24%) of canopy leaves. In contrast, a decade of experimental NO3- deposition significantly increased amounts of organic matter (+12%) and N (+9%) in forest floor and mineral soil, despite no increase in detritus production. A greater forest floor (Oe/a) mass under experimental NO3- deposition resulted from slower decomposition, which is consistent with previously reported declines in lignolytic activity by microbial communities exposed to experimental NO3- deposition. Tracing 15NO3- revealed that N accumulated in soil organic matter by first flowing through soil microorganisms and plants, and that the shedding of 15N-labeled leaf litter enriched soil organic matter over a six-year duration. Our results demonstrate that atmospheric NO3- deposition exerts a direct and negative effect on microbial activity in this forest ecosystem, slowing the decomposition of aboveground litter and leading to the accumulation of forest floor and soil organic matter. To the best of our knowledge, this mechanism is not represented in the majority of simulation models predicting the influence of anthropogenic N deposition on ecosystem C storage in northern forests.
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http://dx.doi.org/10.1890/07-1743.1DOI Listing
December 2008

Atmospheric CO2 and O3 alter the flow of 15N in developing forest ecosystems.

Ecology 2007 Oct;88(10):2630-9

School of Natural Resources & Environment, University of Michigan, Ann Arbor, Michigan 48109, USA.

Anthropogenic O3 and CO2-induced declines in soil N availability could counteract greater plant growth in a CO2-enriched atmosphere, thereby reducing net primary productivity (NPP) and the potential of terrestrial ecosystems to sequester anthropogenic CO2. Presently, it is uncertain how increasing atmospheric CO2 and O3 will alter plant N demand and the acquisition of soil N by plants as well as the microbial supply of N from soil organic matter. To address this uncertainty, we initiated an ecosystem-level 15N tracer experiment at the Rhinelander (Wisconsin, USA) free air CO2-O3 enrichment (FACE) facility to understand how projected increases in atmospheric CO2 and 03 alter the distribution and flow of N in developing northern temperate forests. Tracer amounts of 15NH4+ were applied to the forest floor of developing Populus tremuloides and P. tremuloides-Betula papyrifera communities that have been exposed to factorial CO2 and O3 treatments for seven years. One year after isotope addition, both forest communities exposed to elevated CO2 obtained greater amounts of 15N (29%) and N (40%) from soil, despite no change in soil N availability or plant N-use efficiency. As such, elevated CO2 increased the ability of plants to exploit soil for N, through the development of a larger root system. Conversely, elevated O3 decreased the amount of 15N (-15%) and N (-29%) in both communities, a response resulting from lower rates of photosynthesis, decreases in growth, and smaller root systems that acquired less soil N. Neither CO2 nor 03 altered the amount of N or 15N recovery in the forest floor, microbial biomass, or soil organic matter. Moreover, we observed no interaction between CO2 and 03 on the amount of N or 15N in any ecosystem pool, suggesting that 03 could exert a negative effect regardless of CO2 concentration. In a CO2-enriched atmosphere, greater belowground growth and a more thorough exploitation of soil for growth-limiting N is an important mechanism sustaining the enhancement of NPP in developing forests (0-8 years following establishment). However, as CO2 accumulates in the Earth's atmosphere, future O3 concentrations threaten to diminish the enhancement of plant growth, decrease plant N acquisition, and lessen the storage of anthropogenic C in temperate forests.
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http://dx.doi.org/10.1890/06-1819.1DOI Listing
October 2007

Development of a heterogeneous catalytic cracking reactor utilizing online mass spectrometry analysis.

J Chromatogr A 2007 Nov 2;1172(2):204-8. Epub 2007 Oct 2.

Renewable Fuels and Chemicals Laboratory, Chemical Engineering Department, Mail Stop 9595, Mississippi State University, MS 39762, USA.

A laboratory system has been designed, constructed, and validated that reduces the complexity, time required, and data variability associated with catalytic microreactors that require post reaction steps prior to product analysis. In this work, a Varian (Walnut Creek, CA, USA) 3600 GC (gas chromatography) system coupled with a Saturn quadrupole ion trap mass spectrometer was used to perform mass spectral analysis in real-time catalytic cracking reactions. As this was an integrated reactor/analyzer, the GC column was exposed to temperatures beyond the degradation point of the column, and so selective ion storage RF waveform was used to remove the siloxane masses from the spectra. This produced lower detection limits and full scan data for identification. Mass/charge segmentation of the mass spectrometer allowed the complete product identification for electron impact spectra. Hexane was reacted over H-ZSM-5 catalyst for instrument validation. This produced a series of alkanes, alkenes, and aromatics with distributions consistent with that reported for the cracking of hexane.
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http://dx.doi.org/10.1016/j.chroma.2007.09.061DOI Listing
November 2007

Increases in nitrogen uptake rather than nitrogen-use efficiency support higher rates of temperate forest productivity under elevated CO2.

Proc Natl Acad Sci U S A 2007 Aug 20;104(35):14014-9. Epub 2007 Aug 20.

Department of Biology, Boston University, Boston, MA 02215, USA.

Forest ecosystems are important sinks for rising concentrations of atmospheric CO(2). In previous research, we showed that net primary production (NPP) increased by 23 +/- 2% when four experimental forests were grown under atmospheric concentrations of CO(2) predicted for the latter half of this century. Because nitrogen (N) availability commonly limits forest productivity, some combination of increased N uptake from the soil and more efficient use of the N already assimilated by trees is necessary to sustain the high rates of forest NPP under free-air CO(2) enrichment (FACE). In this study, experimental evidence demonstrates that the uptake of N increased under elevated CO(2) at the Rhinelander, Duke, and Oak Ridge National Laboratory FACE sites, yet fertilization studies at the Duke and Oak Ridge National Laboratory FACE sites showed that tree growth and forest NPP were strongly limited by N availability. By contrast, nitrogen-use efficiency increased under elevated CO(2) at the POP-EUROFACE site, where fertilization studies showed that N was not limiting to tree growth. Some combination of increasing fine root production, increased rates of soil organic matter decomposition, and increased allocation of carbon (C) to mycorrhizal fungi is likely to account for greater N uptake under elevated CO(2). Regardless of the specific mechanism, this analysis shows that the larger quantities of C entering the below-ground system under elevated CO(2) result in greater N uptake, even in N-limited ecosystems. Biogeochemical models must be reformulated to allow C transfers below ground that result in additional N uptake under elevated CO(2).
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http://dx.doi.org/10.1073/pnas.0706518104DOI Listing
http://www.ncbi.nlm.nih.gov/pmc/articles/PMC1955801PMC
August 2007

Identification of (-)-beta-caryophyllene as a gender-specific terpene produced by the multicolored Asian lady beetle.

J Chem Ecol 2006 Nov;32(11):2489-99

Biological Control of Pests Research Unit, ARS, USDA, Stoneville, MS 38776, USA.

This work reports the development and use of techniques for characterizing volatile chemicals emitted by the multicolored Asian lady beetle, Harmonia axyridis (Pallas) (Coleoptera: Coccinellidae), in an effort to identify the semiochemicals involved in establishment and persistence of overwintering beetle aggregations. Volatiles emitted from live beetles were detected by using whole-air sampling and solid-phase microextraction (SPME). Adsorbed volatiles were thermally desorbed and identified with gas chromatography-mass spectrometry (GC/MS). By comparing the chromatograms of volatiles emitted from live male and female beetles, a sesquiterpene, (-)-beta-caryophyllene, was found only in the females. The identity of (-)-beta-caryophyllene was confirmed by using NIST Library searches, comparing retention times with those of known standards, and by using higher-resolution GC/MS above bench top capability. Although SPME trapping detected a wider array of compounds compared to whole-air sampling, the latter method is better suited for automation. Unattended automated sampling is required for the continuous measurement of targeted compounds under dynamically changing incubation conditions. These conditions, mimicking natural overwintering conditions, are essential to our long-term goal of using this technology to detect and identify the aggregation pheromone of H. axyridis.
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http://dx.doi.org/10.1007/s10886-006-9158-0DOI Listing
November 2006

Oral administration of sucrose solutions and measurement of serum sucrose concentrations to evaluate gastric permeability in adult bottlenose dolphins (Tursiops truncatus).

Am J Vet Res 2006 Jun;67(6):931-5

Department of Biological Sciences, College of Veterinary Medicine, Mississippi State University, Mississippi State, MS 39762, USA.

Objective: To measure concentrations of sucrose in the serum of captive dolphins after oral administration of a sucrose solution and determine the suitability of this method for use as a test to detect gastric ulcers.

Animals: 8 adult captive bottlenose dolphins (Tursiops truncatus).

Procedures: Blood samples were collected from the ventral fluke vein of dolphins before and 45 minutes after oral administration of 500 mL of solution containing 25 or 50 g of sucrose; oral administration was achieved by use of gastric intubation. Serum was separated, diluted in a solution of 90% acetonitrile-to 10% water that contained 10 ng of an internal standard (trichlormethiazide)/microL, mixed, and centrifuged. Supernatant was analyzed by use of liquid chromatography-mass spectrometry-mass spectrometry (LC-MS-MS).

Results: Serum sucrose concentrations of dolphins were at or less than the limits of detection before oral administration. Values after administration of sucrose solution varied among dolphins and were higher and more variable after administration of 50 g, compared with concentrations after administration of 25 g.

Conclusions And Clinical Relevance: Serum sucrose concentrations in samples collected during routine health evaluations of captive dolphins can be reliably measured by use of LC-MS-MS. Correlating serum sucrose concentrations with endoscopic observations of the gastric mucosa of dolphins will validate this approach for use in screening for the prevalence and severity of gastric ulcers and determining the efficacy of treatment regimens.
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http://dx.doi.org/10.2460/ajvr.67.6.931DOI Listing
June 2006

Determination of abamectin in soil samples using high-performance liquid chromatography with tandem mass spectrometry.

Rapid Commun Mass Spectrom 2004 ;18(15):1693-6

Department of Chemistry, Mississippi State University and Mississippi State Chemical Laboratory, Mississippi State, MS 39762, USA.

Abamectin, which is comprised of a mixture of avermectins B1a and B1b, is a natural pesticide used as an anti-parasitic agent in livestock, ornamental, and agricultural crops, which can potentially be transported to aquatic systems. These compounds are highly toxic to both aquatic vertebrates and invertebrates at low concentrations in water. This investigation developed high-performance liquid chromatography/tandem mass spectrometry (HPLC/MS/MS) techniques to support automated extraction by an accelerated solvent extraction (ASE) system and chromatographic techniques to measure residues of avermectins in complex soil samples. HPLC along with atmospheric pressure chemical ionization (APCI) MS/MS was used for separation and determination of avermectin isomers in soil samples. Average method recovery for abamectin by UV was 91%, while detection by MS/MS resulted in a 68% recovery for abamectin. Individual method recoveries by MS/MS were 53.6% for avermectin B1a and 36.8% for avermectin B1b. The use of tandem technology eliminated matrix interferences and resulted in an approximately eight-fold increase in sensitivity.
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http://dx.doi.org/10.1002/rcm.1537DOI Listing
November 2004

Follistatin-related protein and follistatin differentially neutralize endogenous vs. exogenous activin.

Endocrinology 2002 May;143(5):1613-24

Reproductive Endocrine Unit and National Center for Infertility Research, Massachusetts General Hospital, 55 Fruit Street, Boston, MA 02144, USA.

Follistatin-related protein (FSRP) is a new addition to the expanding follistatin (FS)-related gene family whose members contain at least one conserved 10-cysteine follistatin domain. In contrast to other members of this family, FSRP and follistatin also share a common exon/intron domain structure, substantial primary sequence homology, and an ability to irreversibly bind activin. In this study, we further explored the hypothesis that FSRP is a functional as well as structural homologue of FS. N-terminal sequencing of recombinant FSRP revealed that signal peptide cleavage occurs within exon 1, a significant structural difference from FS, in which cleavage occurs at the exon/intron boundary. Solid-phase radioligand competition assays revealed both FS and FSRP to preferentially bind activin with the next closest TGF-beta superfamily member, bone-morphogenic protein-7, being at least 500-fold less potent. Consistent with their similar activin-binding affinities, FSRP and FS both prevented exogenous (endocrine or paracrine) activin from accessing its receptor and inducing gene transcription in bioassays. However, FS was at least 100-fold more potent than FSRP in inhibiting gene transcription and FSH release mediated by endogenously produced (autocrine) activin-A or activin-B in multiple cell systems. Finally, FSRP lacks the heparin-binding sequence found in FS, and we found that it was also unable to bind cell surface heparin sulfated proteoglycans. These findings suggest that structural differences between FSRP and FS may underlie their different neutralizating capabilities with respect to exogenous vs. endogenous activin. Taken together with our previous studies showing that activin binding is essential for FS's biological activity, the differential activities of FSRP and FS further indicate that activin binding is necessary but not sufficient to account for all of FS's actions.
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http://dx.doi.org/10.1210/endo.143.5.8805DOI Listing
May 2002

Microbial community composition and function beneath temperate trees exposed to elevated atmospheric carbon dioxide and ozone.

Oecologia 2002 Apr 1;131(2):236-244. Epub 2002 Apr 1.

Center for Environmental Biotechnology, University of Tennessee, 10 515 Research Drive, Knoxville, TN, 37996, USA.

We hypothesized that changes in plant growth resulting from atmospheric CO and O enrichment would alter the flow of C through soil food webs and that this effect would vary with tree species. To test this idea, we traced the course of C through the soil microbial community using soils from the free-air CO and O enrichment site in Rhinelander, Wisconsin. We added either C-labeled cellobiose or C-labeled N-acetylglucosamine to soils collected beneath ecologically distinct temperate trees exposed for 3 years to factorial CO (ambient and 200 µl l above ambient) and O (ambient and 20 µl l above ambient) treatments. For both labeled substrates, recovery of C in microbial respiration increased beneath plants grown under elevated CO by 29% compared to ambient; elevated O eliminated this effect. Production of C-CO from soils beneath aspen (Populus tremuloides Michx.) and aspen-birch (Betula papyrifera Marsh.) was greater than that beneath aspen-maple (Acer saccharum Marsh.). Phospholipid fatty acid analyses (C-PLFAs) indicated that the microbial community beneath plants exposed to elevated CO metabolized more C-cellobiose, compared to the microbial community beneath plants exposed to the ambient condition. Recovery of C in PLFAs was an order of magnitude greater for N-acetylglucosamine-amended soil compared to cellobiose-amended soil, indicating that substrate type influenced microbial metabolism and soil C cycling. We found that elevated CO increased fungal activity and microbial metabolism of cellobiose, and that microbial processes under early-successional aspen and birch species were more strongly affected by CO and O enrichment than those under late-successional maple.
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http://dx.doi.org/10.1007/s00442-002-0868-xDOI Listing
April 2002

Novel genes regulated by the insulin sensitizer rosiglitazone during adipocyte differentiation.

Diabetes 2002 Apr;51(4):1042-51

Department of Molecular Genetics, Novo Nordisk, Bagsvaerd, Denmark.

Thiazolidinediones (TZDs) are a new class of compounds that improve insulin sensitivity in type 2 diabetic patients as well as in rodent models of this disease. These compounds act as ligands for a member of the nuclear hormone receptor superfamily, peroxisome proliferator-activated receptor-gamma (PPAR-gamma), which is highly expressed in adipose tissue and, moreover, has been shown to play an important role in adipocyte differentiation. The strong correlation between the antidiabetic activity of TZDs and their ability to activate PPAR-gamma suggests that PPAR-gamma, through downstream-regulated genes, mediates the effects of TZDs. In this report, we present the isolation and characterization of 81 genes, encoding proteins of known function, differentially expressed during TZD-stimulated differentiation of 3T3-L1 cells. By the use of different reverse- Northern blot techniques, the differential expression of 50 of these genes could be verified, and 21 genes were specifically regulated by a potent TZD during the course of adipocyte differentiation, whereas no effect of a PPAR-gamma antagonist could be observed in mature adipocytes. The differential expression of a large fraction of the isolated genes was also shown to occur in white adipose tissue of ob/ob mice treated with rosiglitazone; combined, our results suggest that an important effect of rosiglitazone in adipose tissue is based on activation of PPAR-gamma in preexisting preadipocytes found among the mature adipocytes, resulting in subsequent adipocyte differentiation.
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http://dx.doi.org/10.2337/diabetes.51.4.1042DOI Listing
April 2002
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