290 research outputs found
D. B. Stover
No full textCaptain D. B. Stover was serving at Fort Douglas during the era of General Patrick Edward Connor
Kinetics of methane production and hydrolysis in anaerobic digestion of corn stover
No full textIn order to develop a time-saving method for determination of ultimate methane production, obtain the hydrolysis kinetic constant, and identify a determination method for the nonbiodegradable organic fraction of substrate (VSNB) of green and air-dried corn stover, the kinetics of methane production and hydrolysis were studied using batch tests. The results showed that the conventional first-order hydrolysis kinetic model was not suitable for describing the entire hydrolysis process of corn stover, because there were two first-order decay periods for hydrolysis of corn stover. The hydrolysis kinetic constants k(H,1) and kH,2 of the first and second periods were 0.1701 and 0.04151/d for green stover and 0.1052 and 0.03601/d for air-dried stover. The value of VSNB could be obtained by the graphical method rather than by the hydrolysis kinetic model. The obtained VSNB contents were 12.9% and 24.7% of VS (volatile solid) for green and air-dried stover, respectively. The ultimate methane production and corresponding digestion time could be understood through the methane production kinetic model by digestion experiments within a short time. The ultimate methane productions were 347.1 and 319.4 mL/g based on VS and the corresponding digestion times were 69.2 and 1823 days for green and air-dried stover, respectively. (C) 2016 Elsevier Ltd. All rights reserved
Network analysis in systems nutrition
No full textNetwork analysis can be useful to put the results of genetics analyses into biological context. This chapter reviews approaches to network analysis and their usefulness in integrating different data types in the study of the impact of nutritional interventions on biological systems. It details some of the most common networks, such as metabolic networks, protein-protein interaction networks, gene co-expression networks, and regulatory networks. Metabolic networks can be found in the Kyoto Encyclopedia of Genes and Genomes (KEGG), HumanCyc, Edinburgh Human Metabolic Network (EHMN), and Human Metabolic Reconstruction (Recon2) databases. Metabolomic data were associated with each single-nucleotide polymorphism (SNP) in the genetic dataset using genome-wide association study (GWAS), then significant SNP results were used as input to the VEGAS algorithm to determine gene-level R-values from SNP-level data. The chapter describes different studies in which network analysis was useful in analyzing results from GWAS, expression quantitative trait loci (eQTL), transcriptomics data and multi-omics studies
Optimizing Harvest of Corn Stover Fractions Based on Overall Sugar Yields following AFEX Pretreatment and Enzymatic Hydrolysis
No full textBackground: Corn stover composition changes considerably throughout the growing season and also varies between the various fractions of the plant. These differences can impact optimal pretreatment conditions, enzymatic digestibility and maximum achievable sugar yields in the process of converting lignocellulosics to ethanol. The goal of this project was to determine which combination of corn stover fractions provides the most benefit to the biorefinery in terms of sugar yields and to determine the preferential order in which fractions should be harvested. Ammonia fiber expansion (AFEX) pretreatment, followed by enzymatic hydrolysis, was performed on early and late harvest corn stover fractions (stem, leaf, husk and cob). Sugar yields were used to optimize scenarios for the selective harvest of corn stover assuming 70% or 30% collection of the total available stover.
Results: The optimal AFEX conditions for all stover fractions, regardless of harvest period, were: 1.5 (g NH(3) g(-1) biomass); 60% moisture content (dry-weight basis; dwb), 90 degrees C and 5 min residence time. Enzymatic hydrolysis was conducted using cellulase, beta-glucosidase, and xylanase at 31.3, 41.3, and 3.1 mg g(-1) glucan, respectively. The optimal harvest order for selectively harvested corn stover (SHCS) was husk > leaf > stem > cob. This harvest scenario, combined with optimal AFEX pretreatment conditions, gave a theoretical ethanol yield of 2051 L ha(-1) and 912 L ha(-1) for 70% and 30% corn stover collection, respectively.
Conclusion: Changing the proportion of stover fractions collected had a smaller impact on theoretical ethanol yields (29 - 141 L ha(-1)) compared to the effect of altering pretreatment and enzymatic hydrolysis conditions (150 - 462 L ha(-1)) or harvesting less stover (852 - 1139 L ha(-1)). Resources may be more effectively spent on improving sustainable harvesting, thereby increasing potential ethanol yields per hectare harvested, and optimizing biomass processing rather than focusing on the selective harvest of specific corn stover fractions.Peer reviewed
The 5-formyltetrahydrofolate futile cycle reduces pathway stochasticity in an extended hybrid-stochastic model of folate-mediated one-carbon metabolism
No full textIn folate-mediated one-carbon metabolism (FOCM), 5-formyltetrahydrofolate (5fTHF), a one-carbon substituted tetrahydrofolate (THF) vitamer, acts as an intracellular storage form of folate and as an inhibitor of the folate-dependent enzymes phosphoribosylaminoimidazolecarboxamide formyltransferase (AICARFT) and serine hydroxymethyltransferase (SHMT). Cellular levels of 5fTHF are regulated by a futile cycle comprising the enzymes SHMT and 5,10-methenyltetrahydrofolate synthetase (MTHFS). MTHFS is an essential gene in mice; however, the roles of both 5fTHF and MTHFS in mammalian FOCM remain to be fully elucidated. We present an extension of our previously published hybrid-stochastic model of FOCM by including the 5fTHF futile-cycle to explore its effect on the FOCM network. Model simulations indicate that MTHFS plays an essential role in preventing 5fTHF accumulation, which consequently averts inhibition of all other reactions in the metabolic network. Moreover, in silico experiments show that 10-formylTHF inhibition of MTHFS is critical for regulating purine synthesis. Model simulations also provide evidence that 5-methylTHF (and not 5fTHF) is the predominant physiological binder/inhibitor of SHMT. Finally, the model simulations indicate that the 5fTHF futile cycle dampens the stochastic noise in FOCM that results from both folate deficiency and a common variant in the methylenetetrahydrofolate reductase (MTHFR) gene
A hybrid stochastic model of folate-mediated one-carbon metabolism: Effect of the common C677T MTHFR variant on de novo thymidylate biosynthesis
No full textFolate-mediated one-carbon metabolism (FOCM) is an interconnected network of metabolic pathways, including those required for the de novo synthesis of dTMP and purine nucleotides and for remethylation of homocysteine to methionine. Mouse models of folate-responsive neural tube defects (NTDs) indicate that impaired de novo thymidylate (dTMP) synthesis through changes in SHMT expression is causative in folate-responsive NTDs. We have created a hybrid computational model comprised of ordinary differential equations and stochastic simulation. We investigated whether the de novo dTMP synthesis pathway was sensitive to perturbations in FOCM that are known to be associated with human NTDs. This computational model shows that de novo dTMP synthesis is highly sensitive to the common MTHFR C677T polymorphism and that the effect of the polymorphism on FOCM is greater in folate deficiency. Computational simulations indicate that the MTHFR C677T polymorphism and folate deficiency interact to increase the stochastic behavior of the FOCM network, with the greatest instability observed for reactions catalyzed by serine hydroxymethyltransferase (SHMT). Furthermore, we show that de novo dTMP synthesis does not occur in the cytosol at rates sufficient for DNA replication, supporting empirical data indicating that impaired nuclear de novo dTMP synthesis results in uracil misincorporation into DNA
Stover management modifies soil organic carbon dynamics in the short-term under semiarid continuous maize
No full textIn croplands, the adoption of certain management practices may increase soil organic carbon (SOC) levels. In this study, we evaluated the short-term impact of crop stover management and the interaction between crop stover and irrigation method on SOC change in a continuous maize (Zea mays L.) system in Spain. Four years after the beginning of the experiment, total SOC and C fractions (particulate organic matter carbon, POM-C; and mineral-associated organic matter carbon, Min-C) contents, SOC stocks and SOC stock changes were measured in four different soil layers (0-5, 5-10, 10-25 and 25-50 cm) in an experiment with two irrigation methods (sprinkler and flood) and three stover management systems (conventional tillage with all the stover incorporated, CT; no-tillage maintaining the stover, NTr; and no-tillage removing the stover, NT). Stover management resulted in significant differences in SOC and POM-C but not in Min-C. In particular, NT reduced SOC and POM-C contents compared with CT and NTr (about 10 and 60 %, respectively). After 4 years, SOC change was not affected by the interaction between stover management and irrigation. Concurrently, both CT and NT showed SOC losses, reaching 0.11 and 1.22 Mg ha-1 yr-1 in CT and NT, respectively. However, NTr showed SOC gains at a rate of 0.09 Mg ha-1 yr-1. Consequently, the removal of crop stover has been demonstrated as a detrimental strategy to store SOC in the short-term in irrigated continuous maize systems. © 2021 The Author
Letter from Caleb Foote to A. J. Muste, April 1, 1942
No full textLetter to A. J. Muste, likely from Caleb Foote, regarding the possibility of Japanese American families resettle in the Midwestern states. Author describes a recent meeting between Joseph R. Goodman, himself, and Milton Stover Eisenhower, Director of the War Relocation Authority, and correspondence with the president of Antioch College. Author writes "I think the three main question the government will ask in any such plan are 1) are defense industries nearby? 2) what will public reaction be? 3) what are the employment opportunities for the Japanese?" Author also describes situation with curfew in San Francisco: "Typical of what is happening: the other night a Japanese doctor came to the YMCA secretary in San Francisco about 7 o'clock. He had a patient that he need to operate on immediately, but a) he couldn't get a hospital in the city to take the patient, and b) in an hour he had to be back in his house til 6 AM because of the curfew, not matter what happened to the patient during thPersonal correspondence, organizational records, government documents, publications, and other papers created or collected by Joseph R. Goodman documenting the forced removal and incarceration of Japanese Americans during World War II, as well as organized resistance to incarceration. Included in the collection are records of the Japanese Young Men's Christian Association and the Japanese American Citizens' League in San Francisco, including papers of the Japanese YMCA's executive secretary Lincoln Kanai; Sakai family papers; Goodman's correspondence to and from Japanese American incarcerees, organizations opposing forced removal and incarceration of Japanese Americans, the War Relocation Authority, and others; publications, photographs, and ephemera from the Topaz Relocation Center, where Goodman taught high school; War Relocation Authority records and publications; and newspaper clippings, pamphlets, and reports about forced removal and incarceration created by various government, religious, and civic organizations, in California and nationwide
INFLUENCE OF B-VITAMINS ON ONE-CARBON METABOLISM AND ASSOCIATIONS WITH CANCER RISK AND REPRODUCTIVE STATE
No full textFolate, choline and vitamin B12 are essential nutrients involved in one-carbon metabolism (OCM), a network of interconnected pathways necessary for the de novo synthesis of purines and thymidylate and for the remethylation of homocysteine to methionine. Disruptions in
OCM are associated with aberrant DNA synthesis and methylation and high risk for cancer. Thus, it is of particular importance to elucidate the role of these nutrients in the functioning of OCM. In addition, the status of these nutrients and their demand differ by reproductive and/or
pathological state, further addressing the need to better understand the effects of these nutrients. This dissertation research involves both human participant studies and laboratory-based molecular research to advance current knowledge of the role of these nutrients.
Study 1 examined the impact of mandatory folic acid fortification on DNA methylation status among postmenopausal women enrolled in the Women’s Health Initiative Observational Study (WHI-OS). As expected, given the role of folate in OCM, women with higher red blood
cell (RBC) folate concentration had higher DNA methylation in the pre-fortification period. However, this expected result was not observed in the post-fortification period during which women with higher (vs. lower) RBC folate status had lower DNA methylation. Overall, these
findings suggest an inverted U-shaped relationship between folate status and DNA methylation across fortification periods, and further investigation is warranted to clarify the health outcomes of the inverse relationship observed in the era of folic acid fortification.
Study 2 examined associations between biomarkers of choline metabolism and colorectal cancer risk in a case-control study nested within the WHI-OS. The main findings indicate 1) a positive association between plasma trimethylamine N-oxide (TMAO; a derivative of choline
produced by intestinal bacteria) and rectal cancer risk; and 2) an inverse relationship between plasma betaine and colorectal cancer risk. These findings demonstrate that alterations in choline metabolism associate with higher risk of colorectal cancer, suggesting the potential utilization of these biomarkers as predictors of increased colorectal cancer risk.
Study 3 assessed changes in status and functional biomarkers of vitamin B12 among pregnant, lactating and control (nonpregnant, nonlactating) women who consumed equivalent vitamin B12 intakes under controlled feeding conditions. Pregnant (vs. control) women had a higher ratio of plasma holotranscobalamin (bioactive form of vitamin B12) to total vitamin B12, indicating that greater amounts of vitamin B12 are partitioned toward the biologically active form in this reproductive state. Overall, the results of this study suggest that metabolic
adaptations transpire to enhance vitamin B12 supply during pregnancy.
Study 4 employed in vitro cell culture models to investigate the effect of folate-independent generation of formate, a primary source of one-carbons for folate-mediated OCM, on the synthesis of purines and thymidylate. The study findings demonstrate that in human
hepatocarcinoma (HepG2) cells, alcohol dehydrogenase 5 is a source of formate for de novo purine biosynthesis, especially during folate deficiency when folate-dependent formate production is limited.
Taken together, this dissertation research spans from in vitro molecular studies to epidemiological studies to address the role of folate, choline and vitamin B12. The findings of this research will help inform the development of nutrient intake recommendations and the use of
nutritional biomarkers for disease prediction
Dysregulation of Folate-Dependent Mitochondrial de novo Thymidylate Biosynthesis Affects Mitohcondrial DNA Integrity
No full textMitochondrial DNA (mtDNA) Depletion Syndrome (MDS) is a genetic disorder caused by mutations in nuclear-encoded mitochondrial proteins involved primarily in nucleotide or mtDNA synthesis. Folate-dependent one-carbon metabolism (FOCM) is a metabolic network compartmentalized in mitochondria, nucleus, and cytosol, where one-carbon units participate in the de novo synthesis of purines, thymidylate, and methionine metabolism. Either increase or decrease in mitochondrial dTTP pools reduces mtDNA content. However, FOCM has never been investigated as a pathway leading to loss of mtDNA integrity in MDS patients. Folate deficiency reduces de novo dTMP synthesis and increases uracil levels in nuclear DNA (nuDNA). Uracil misincorporation is not mutagenic but affects DNA integrity by inducing chromosome fragmentation and eventually apoptosis. Our knowledge of factors that contribute to uracil accumulation in mtDNA is limited but is expected to mirror uracil misincorporation in nuDNA. Enzymatic disruption of nuclear de novo dTMP synthesis due to lack of SHMT in mice and lack of mitochondrial SHMT2 in CHO cells results in reduced dTMP synthesis capacity. Similarly, mice deficient in MPV17, a protein of unknown function associated with hepatocerebral MDS, have reduced mitochondrial dTMP pools. This study investigates the role of genetic (MPV17 and SHMT2) and non-genetic factors (folate, glycine, and serine) on mtDNA integrity, in the context of mitochondrial de novo dTMP synthesis. These results reveal that mtDNA integrity is compromised in HeLa cells deficient in either MPV17 or SHMT2. MPV17-deficient cells exhibited reduced mitochondrial folate levels, suggesting it interacts with mitochondrial FOCM. Both, cells cultured in folate-depleted medium and MPV17-deficient cells, exhibit elevated uracil accumulation in mtDNA by at least 3-fold. Mitochondrial dTMP synthesis capacity and its incorporation into mtDNA were not affected in MPV17-deficient cells, but the elevated uracil levels imply that availability of dTMP for mtDNA synthesis is compromised. I propose that MPV17 is a mitochondrial dTMP transporter. SHMT2-deficient cells exhibited 164% more mtDNA content than control cells; glycine and serine in the culture medium did not have an effect, indicating that SHMT2 catalytic activity is fundamental for mitochondrial function. These data suggest that FOCM is involved in maintaining mtDNA integrity, which is highly susceptible to uracil misincorporation
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