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1.  Accounting for differences in the bioactivity and bioavailability of vitamers 
Food & Nutrition Research  2012;56:10.3402/fnr.v56i0.5809.
Essentially all vitamins exist with multiple nutritionally active chemical species often called vitamers. Our quantitative understanding of the bioactivity and bioavailability of the various members of each vitamin family has increased markedly, but many issues remain to be resolved concerning the reporting and use of analytical data. Modern methods of vitamin analysis rely heavily on chromatographic techniques that generally allow the measurement of the individual chemical forms of vitamins. Typical applications of food analysis include the evaluation of shelf life and storage stability, monitoring of nutrient retention during food processing, developing food composition databases and data needed for food labeling, assessing dietary adequacy and evaluating epidemiological relationships between diet and disease. Although the usage of analytical data varies depending on the situation, important issues regarding how best to present and interpret the data in light of the presence of multiple vitamers are common to all aspects of food analysis. In this review, we will evaluate the existence of vitamers that exhibit differences in bioactivity or bioavailability, consider when there is a need to address differences in bioactivity or bioavailability of vitamers, and then consider alternative approaches and possible ways to improve the reporting of data. Major examples are taken from literature and experience with vitamin B6 and folate.
doi:10.3402/fnr.v56i0.5809
PMCID: PMC3321260  PMID: 22489223
Vitamin; vitamers; bioactivity; bioavailability; analysis; databases
2.  Mathematical modeling of folate metabolism: Predicted effects of genetic polymorphisms on mechanisms and biomarkers relevant to carcinogenesis 
Low-folate status and genetic polymorphisms in folate metabolism have been linked to several cancers. Possible biologic mechanisms for this association include effects on purine and thymidine synthesis, DNA methylation, or homocysteine concentrations. The influence of genetic variation in folate metabolism on these putative mechanisms or biomarkers of cancer risk has been largely unexplored. We utilized a mathematical model simulating folate metabolism biochemistry to (a) predict the effects of polymorphisms with defined effects on enzyme function (MTHFR, TS), and (b) predict the effects of potential, as-of-yet-unidentified polymorphisms in a comprehensive set of folate-metabolizing enzymes on biomarkers and mechanisms related to cancer risk
The model suggests that there is substantial robustness in the pathway. Our predictions were consistent with measured effects of known polymorphisms in MTHFR and TS on biomarkers. Polymorphisms that alter enzyme function of FTD, FTS, and MTCH are expected to affect purine synthesis, FTS more so under a low-folate status. Also, MTCH polymorphisms are predicted to influence thymidine synthesis. Polymorphisms in methyltransferases should affect both methylation rates and thymidylate synthesis. Combinations of polymorphisms in MTHFR, TS and SHMT are expected to impact nucleotide synthesis in a non-linear fashion.
These investigations provide information on effects of genetic polymorphisms on biomarkers, including those that cannot be measured well, and highlights robustness and sensitivity in this complex biologic system in regards to genetic variability. While the proportional changes in biomarkers of risk with individual polymorphisms are frequently small, they may be quite relevant if present over an individual’s lifetime.
doi:10.1158/1055-9965.EPI-07-2937
PMCID: PMC3912564  PMID: 18628437
3.  Global hypothesis testing for high-dimensional repeated measures outcomes 
Statistics in medicine  2011;31(8):724-742.
High-throughput technology in metabolomics, genomics, and proteomics gives rise to high dimension, low sample size data when the number of metabolites, genes, or proteins exceeds the sample size. For a limited class of designs, the classic ‘univariate approach’ for Gaussian repeated measures can provide a reasonable global hypothesis test. We derive new tests that not only accurately allow more variables than subjects, but also give valid analyses for data with complex between-subject and within-subject designs. Our derivations capitalize on the dual of the error covariance matrix, which is nonsingular when the number of variables exceeds the sample size, to ensure correct statistical inference and enhance computational efficiency. Simulation studies demonstrate that the new tests accurately control Type I error rate and have reasonable power even with a handful of subjects and a thousand outcome variables. We apply the new methods to the study of metabolic consequences of vitamin B6 deficiency. Free software implementing the new methods applies to a wide range of designs, including one group pre-intervention and post-intervention comparisons, multiple parallel group comparisons with one-way or factorial designs, and the adjustment and evaluation of covariate effects.
doi:10.1002/sim.4435
PMCID: PMC3396026  PMID: 22161561
UNIREP; dual matrix; commensurate multivariate data; general linear multivariate model; MULTIREP; MANOVA
4.  S-ADENOSYLMETHIONINE TREATMENT OF ALCOHOLIC LIVER DISEASE: A DOUBLE-BLIND, RANDOMIZED, PLACEBO-CONTROLLED TRIAL 
Background
S-adenosyl-L-methionine (SAM) is the methyl donor for all methylation reactions and regulates the synthesis of glutathione (GSH), the main cellular antioxidant. Previous experimental studies suggested that SAM may benefit patients with established alcoholic liver diseases (ALD). The aim of this study was to determine the efficacy of SAM in treatment of ALD in a 24 week trial. The primary endpoints were changes in serum aminotransferase levels and liver histopathology scores, and the secondary endpoint was changes in serum levels of methionine metabolites.
Methods
We randomized 37 patients with ALD to receive 1.2 grams of SAM by mouth or placebo daily. Subjects were required to remain abstinent from alcohol drinking. A baseline liver biopsy was performed in 24 subjects and a post-treatment liver biopsy was performed in 14 subjects.
Results
Fasting serum SAM levels were increased over timed intervals in the SAM treatment group. The entire cohort showed an overall improvement of AST, ALT, and bilirubin levels after 24 weeks of treatment but there were no differences between the treatment groups in any clinical or biochemical parameters nor any intra- or intergroup differences or changes in liver histopathology scores for steatosis, inflammation, fibrosis, and Mallory-Denk hyaline bodies.
Conclusions
Whereas abstinence improved liver function, twenty-four weeks of therapy with SAM was no more effective than placebo in the treatment of ALD.
doi:10.1111/j.1530-0277.2011.01547.x
PMCID: PMC3315189  PMID: 22044287
S-adenosylmethionine; SAM; alcoholic liver disease
5.  MATHEMATICAL MODELING PREDICTS THE EFFECT OF FOLATE DEFICIENCY AND EXCESS ON CANCER RELATED BIOMARKERS 
Background
Folate is an essential B-vitamin that mediates one-carbon metabolism reactions, including nucleotide synthesis and others related to carcinogenesis. Both low and high folate status influences carcinogenesis.
Methods
We used a mathematical model of folate-mediated one-carbon metabolism to predict the effect of a range of intracellular epithelial folate concentrations (0.25 μmol/L–15.0 μmol/L) on methylation rate and purine and thymidylate synthesis. We also examined the interaction of these folate concentrations with polymorphisms in two enzymes [Methylene tetrahydrofolate reductase (MTHFR) and thymidylate synthase (TS)] in relation to the biochemical products.
Results
TS enzyme reaction rate increased markedly in response to the modeled higher intracellular folate concentrations. Changes in methylation rate were modest, while purine synthesis was only minimally related to increases in folate concentrations with an apparent threshold effect at 5.0–6.0 μmol/L. The relationship between folate concentrations and thymidylate synthesis was modified by genetic variation in TS, but less so by variation in MTHFR. These gene-folate interactions modestly influenced purine synthesis in a non-linear manner, but only affected methylation rate under conditions of very high MTHFR activity.
Conclusion
Thymidylate synthesis is very sensitive to changes in epithelial intracellular folate and increased nearly five-fold under conditions of high intracellular folate. Individuals with genetic variations causing reduced TS activity may present even greater susceptibility to excessive folate.
Impact
Our observation that thymidylate synthesis increases dramatically under conditions of very elevated intracellular folate provides biological support to observations that excessive folic acid intake increases risk of both precursor lesions (i.e., colorectal adenomas) and cancer.
doi:10.1158/1055-9965.EPI-10-1352
PMCID: PMC3169720  PMID: 21752986
6.  IMPAIRED HOMOCYSTEINE TRANSSULFURATION IS AN INDICATOR OF ALCOHOLIC LIVER DISEASE 
Journal of hepatology  2010;53(3):551-557.
Background & Aims
Although abnormal hepatic methionine metabolism plays a central role in the pathogenesis of experimental alcoholic liver disease (ALD), its relationship to the risk and severity of clinical ALD is not known. The aim of this clinical study was to determine the relationship between serum levels of methionine metabolites in chronic alcoholics and the risk and pathological severity of ALD.
Methods
Serum levels of liver function biochemical markers, vitamin B6, vitamin B12, folate, homocysteine, methionine, S-adenosylmethionine, S-adenosylhomocysteine, cystathionine, cysteine, α-aminobutyrate, glycine, serine, and dimethylglycine were measured in 40 ALD patients, of whom 24 had liver biopsies, 26 were active drinkers without liver disease, and 28 were healthy subjects.
Results
Serum homocysteine was elevated in all alcoholics, whereas ALD patients had low vitamin B6 with elevated cystathionine and decreased α-aminobutyrate/cystathionine ratios, consistent with decreased activity of vitamin B6 dependent cystathionase. The α-aminobutyrate/cystathionine ratio predicted the presence of ALD, while cystathionine correlated with the stage of fibrosis in all ALD patients.
Conclusions
The predictive role of the α- aminobutyrate/cystathionine ratio for the presence of ALD and the correlation between cystathionine serum levels with the severity of fibrosis point to the importance of the homocysteine transsulfuration pathway in ALD and may have important diagnostic and therapeutic implications.
doi:10.1016/j.jhep.2010.03.029
PMCID: PMC2923260  PMID: 20561703
alcohol; methionine; cystathionine; vitamin B6
7.  Biomarkers of folate status in NHANES: a roundtable summary123456 
A roundtable to discuss the measurement of folate status biomarkers in NHANES took place in July 2010. NHANES has measured serum folate since 1974 and red blood cell (RBC) folate since 1978 with the use of several different measurement procedures. Data on serum 5-methyltetrahydrofolate (5MTHF) and folic acid (FA) concentrations in persons aged ≥60 y are available in NHANES 1999–2002. The roundtable reviewed data that showed that folate concentrations from the Bio-Rad Quantaphase II procedure (Bio-Rad Laboratories, Hercules, CA; used in NHANES 1991–1994 and NHANES 1999–2006) were, on average, 29% lower for serum and 45% lower for RBC than were those from the microbiological assay (MA), which was used in NHANES 2007–2010. Roundtable experts agreed that these differences required a data adjustment for time-trend analyses. The roundtable reviewed the possible use of an isotope-dilution liquid chromatography–tandem mass spectrometry (LC-MS/MS) measurement procedure for future NHANES and agreed that the close agreement between the MA and LC-MS/MS results for serum folate supported conversion to the LC-MS/MS procedure. However, for RBC folate, the MA gave 25% higher concentrations than did the LC-MS/MS procedure. The roundtable agreed that the use of the LC-MS/MS procedure to measure RBC folate is premature at this time. The roundtable reviewed the reference materials available or under development at the National Institute of Standards and Technology and recognized the challenges related to, and the scientific need for, these materials. They noted the need for a commutability study for the available reference materials for serum 5MTHF and FA.
doi:10.3945/ajcn.111.013011
PMCID: PMC3127517  PMID: 21593502
8.  Biomarkers of vitamin B-12 status in NHANES: a roundtable summary123456 
A roundtable to discuss the measurement of vitamin B-12 (cobalamin) status biomarkers in NHANES took place in July 2010. NHANES stopped measuring vitamin B-12–related biomarkers after 2006. The roundtable reviewed 3 biomarkers of vitamin B-12 status used in past NHANES—serum vitamin B-12, methylmalonic acid (MMA), and total homocysteine (tHcy)—and discussed the potential utility of measuring holotranscobalamin (holoTC) for future NHANES. The roundtable focused on public health considerations and the quality of the measurement procedures and reference methods and materials that past NHANES used or that are available for future NHANES. Roundtable members supported reinstating vitamin B-12 status measures in NHANES. They noted evolving concerns and uncertainties regarding whether subclinical (mild, asymptomatic) vitamin B-12 deficiency is a public health concern. They identified the need for evidence from clinical trials to address causal relations between subclinical vitamin B-12 deficiency and adverse health outcomes as well as appropriate cutoffs for interpreting vitamin B-12–related biomarkers. They agreed that problems with sensitivity and specificity of individual biomarkers underscore the need for including at least one biomarker of circulating vitamin B-12 (serum vitamin B-12 or holoTC) and one functional biomarker (MMA or tHcy) in NHANES. The inclusion of both serum vitamin B-12 and plasma MMA, which have been associated with cognitive dysfunction and anemia in NHANES and in other population-based studies, was preferable to provide continuity with past NHANES. Reliable measurement procedures are available, and National Institute of Standards and Technology reference materials are available or in development for serum vitamin B-12 and MMA.
doi:10.3945/ajcn.111.013243
PMCID: PMC3127527  PMID: 21593512
9.  FolX and FolM Are Essential for Tetrahydromonapterin Synthesis in Escherichia coli and Pseudomonas aeruginosa▿ † 
Journal of Bacteriology  2009;192(2):475-482.
Tetrahydromonapterin is a major pterin in Escherichia coli and is hypothesized to be the cofactor for phenylalanine hydroxylase (PhhA) in Pseudomonas aeruginosa, but neither its biosynthetic origin nor its cofactor role has been clearly demonstrated. A comparative genomics analysis implicated the enigmatic folX and folM genes in tetrahydromonapterin synthesis via their phyletic distribution and chromosomal clustering patterns. folX encodes dihydroneopterin triphosphate epimerase, which interconverts dihydroneopterin triphosphate and dihydromonapterin triphosphate. folM encodes an unusual short-chain dehydrogenase/reductase known to have dihydrofolate and dihydrobiopterin reductase activity. The roles of FolX and FolM were tested experimentally first in E. coli, which lacks PhhA and in which the expression of P. aeruginosa PhhA plus the recycling enzyme pterin 4a-carbinolamine dehydratase, PhhB, rescues tyrosine auxotrophy. This rescue was abrogated by deleting folX or folM and restored by expressing the deleted gene from a plasmid. The folX deletion selectively eliminated tetrahydromonapterin production, which far exceeded folate production. Purified FolM showed high, NADPH-dependent dihydromonapterin reductase activity. These results were substantiated in P. aeruginosa by deleting tyrA (making PhhA the sole source of tyrosine) and folX. The ΔtyrA strain was, as expected, prototrophic for tyrosine, whereas the ΔtyrA ΔfolX strain was auxotrophic. As in E. coli, the folX deletant lacked tetrahydromonapterin. Collectively, these data establish that tetrahydromonapterin formation requires both FolX and FolM, that tetrahydromonapterin is the physiological cofactor for PhhA, and that tetrahydromonapterin can outrank folate as an end product of pterin biosynthesis.
doi:10.1128/JB.01198-09
PMCID: PMC2805310  PMID: 19897652
10.  DNA digestion to deoxyribonucleoside: A simplified one-step procedure 
Analytical biochemistry  2007;373(2):383-385.
We present a simple and inexpensive ‘one-step’ protocol for the hydrolysis of DNA to deoxyribonucleosides. Unlike the older DNA hydrolysis protocol which is cumbersome and labor intensive, thes new protocol is ideal for high-throughput assays and is suitable automation. Using this protocol we were able to hydrolyze several hundred samples within an 8-hour period. The new protocol is fully compatible with LC-MS/MS and gives similar recoveries for all five major deoxyribonucleosides when compared to the older protocol.
doi:10.1016/j.ab.2007.09.031
PMCID: PMC2239294  PMID: 18028864
11.  DNA methylation determination by liquid chromatography–tandem mass spectrometry using novel biosynthetic [U-15N]deoxycytidine and [U-15N]methyldeoxycytidine internal standards 
Nucleic Acids Research  2008;36(18):e119.
Methylation of the promoter CpG regions regulates gene transcription by inhibiting transcription factor binding. Deoxycytidine methylation may regulate cell differentiation, while aberrations in the process may be involved in cancer etiology and the development of birth defects (e.g. neural tube defects). Similarly, nutritional deficiency and certain nutragenomic interactions are associated with DNA hypomethylation. While LC-MS has been used previously to measure percentage genomic deoxycytidine methylation, a lack of a secure source of internal standards and the need for laborious and time-consuming DNA digestion protocols constitute distinct limitations. Here we report a simple and inexpensive protocol for the biosynthesis of internal standards from readily available precursors. Using these biosynthetic stable-isotopic [U-15N]-labeled internal standards, coupled with an improved DNA digestion protocol developed in our lab, we have developed a low-cost, high-throughput (>500 samples in 4 days) assay for measuring deoxycytidine methylation in genomic DNA. Inter- and intraassay variation for the assay (%RSD, n = 6) was <2.5%.
doi:10.1093/nar/gkn534
PMCID: PMC2566864  PMID: 18718928
12.  In silico experimentation with a model of hepatic mitochondrial folate metabolism 
Background
In eukaryotes, folate metabolism is compartmentalized and occurs in both the cytosol and the mitochondria. The function of this compartmentalization and the great changes that occur in the mitochondrial compartment during embryonic development and in rapidly growing cancer cells are gradually becoming understood, though many aspects remain puzzling and controversial.
Approach
We explore the properties of cytosolic and mitochondrial folate metabolism by experimenting with a mathematical model of hepatic one-carbon metabolism. The model is based on known biochemical properties of mitochondrial and cytosolic enzymes. We use the model to study questions about the relative roles of the cytosolic and mitochondrial folate cycles posed in the experimental literature. We investigate: the control of the direction of the mitochondrial and cytosolic serine hydroxymethyltransferase (SHMT) reactions, the role of the mitochondrial bifunctional enzyme, the role of the glycine cleavage system, the effects of variations in serine and glycine inputs, and the effects of methionine and protein loading.
Conclusion
The model reproduces many experimental findings and gives new insights into the underlying properties of mitochondrial folate metabolism. Particularly interesting is the remarkable stability of formate production in the mitochondria in the face of large changes in serine and glycine input. The model shows that in the presence of the bifunctional enzyme (as in embryonic tissues and cancer cells), the mitochondria primarily support cytosolic purine and pyrimidine synthesis via the export of formate, while in adult tissues the mitochondria produce serine for gluconeogenesis.
doi:10.1186/1742-4682-3-40
PMCID: PMC1713227  PMID: 17150100
13.  Metabolomic Analysis Reveals Extended Metabolic Consequences of Marginal Vitamin B-6 Deficiency in Healthy Human Subjects 
PLoS ONE  2013;8(6):e63544.
Marginal deficiency of vitamin B-6 is common among segments of the population worldwide. Because pyridoxal 5′-phosphate (PLP) serves as a coenzyme in the metabolism of amino acids, carbohydrates, organic acids, and neurotransmitters, as well as in aspects of one-carbon metabolism, vitamin B-6 deficiency could have many effects. Healthy men and women (age: 20-40 y; n = 23) were fed a 2-day controlled, nutritionally adequate diet followed by a 28-day low-vitamin B-6 diet (<0.5 mg/d) to induce marginal deficiency, as reflected by a decline of plasma PLP from 52.6±14.1 (mean ± SD) to 21.5±4.6 nmol/L (P<0.0001) and increased cystathionine from 131±65 to 199±56 nmol/L (P<0.001). Fasting plasma samples obtained before and after vitamin B6 restriction were analyzed by 1H-NMR with and without filtration and by targeted quantitative analysis by mass spectrometry (MS). Multilevel partial least squares-discriminant analysis and S-plots of NMR spectra showed that NMR is effective in classifying samples according to vitamin B-6 status and identified discriminating features. NMR spectral features of selected metabolites indicated that vitamin B-6 restriction significantly increased the ratios of glutamine/glutamate and 2-oxoglutarate/glutamate (P<0.001) and tended to increase concentrations of acetate, pyruvate, and trimethylamine-N-oxide (adjusted P<0.05). Tandem MS showed significantly greater plasma proline after vitamin B-6 restriction (adjusted P<0.05), but there were no effects on the profile of 14 other amino acids and 45 acylcarnitines. These findings demonstrate that marginal vitamin B-6 deficiency has widespread metabolic perturbations and illustrate the utility of metabolomics in evaluating complex effects of altered vitamin B-6 intake.
doi:10.1371/journal.pone.0063544
PMCID: PMC3679127  PMID: 23776431

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