TY - CONF TI - Effects of activated carbon surface chemistry and pore structure on the adsorption of MTBE from natural water AU - Li, L. AU - Quinlivan, P.A. AU - Knappe, D.R.U. C2 - 2001/// C3 - ACS Division of Environmental Chemistry, Preprints DA - 2001/// VL - 41 SP - 448-453 M1 - 2 UR - http://www.scopus.com/inward/record.url?eid=2-s2.0-23844487615&partnerID=MN8TOARS ER - TY - JOUR TI - Effectiveness of coagulants and coagulant aids for the removal of filter-clogging synedra AU - Jun, H.-B. AU - Lee, Y.-J. AU - Lee, B.-D. AU - Knappe, D.R.U. T2 - Journal of Water Supply: Research and Technology - AQUA DA - 2001/// PY - 2001/// VL - 50 IS - 3 SP - 135-148 UR - http://www.scopus.com/inward/record.url?eid=2-s2.0-0034986285&partnerID=MN8TOARS ER - TY - JOUR TI - Identification, characterization, and ontogeny of a second cytochrome P450 3A gene from the fresh water teleost medaka (Oryzias latipes) AU - Kullman, Seth W. AU - Hinton, David E. T2 - Molecular Reproduction and Development AB - Multiple copies of cytochrome P450 gene family 3 have been identified from numerous mammalian species. Often these genes exhibit differential catalytic activities and gene regulation. To date however, little information is available regarding multiple forms of this gene family in teleost fishes. In this study, a second isozyme of cytochrome P450 3A has been cloned from the teleost fish Oryzias latipes and designated CYP3A40. Screening of a cDNA library to medaka liver resulted in the identification of a full length cDNA clone containing a 2316 base pair (bp) insert with an open reading frame encoding a single peptide of 502 amino acids. Comparisons of the deduced amino acid sequence to other known cytochrome P450 sequences indicate that this gene product is most similar to the CYP3A gene family and shares a 90% identity to CYP3A38 previously identified from medaka liver. Consistent with Northern blot and Western blot analysis, Southern blots of medaka genomic DNA demonstrated the presence of two CYP3A genes. Gene expression studies demonstrated that CYP3A38 and CYP3A40 are differentially regulated according to embryonic development. Northern blot analysis, using a probe to a conserved region of both CYP3A genes, demonstrated the presence of a single CYP3A transcript for early and late embryonic stages and two CYP3A transcripts in larvae and adult liver. Similarly, Western blots show a single faint immunoreactive cytochrome P450 3A protein in microsomes from early and late embryos and two abundant protein bands in microsomes from larval and adult liver. To further examine the transcriptional differences in CYP3A expression, RT-PCR analysis was performed on embryonic stages 11–35, 1- and 14-day-old larvae, and adult liver using primer sets specific for CYP3A38 and CYP3A40. These results demonstrate that CYP3A40 is expressed early in embryonic development and continues throughout adult stages. CYP3A38, however, is tightly regulated during embryonic development and is only expressed post-hatch Mol. Reprod. Dev. 58:149–158, 2001. © 2001 Wiley-Liss, Inc. DA - 2001/2// PY - 2001/2// DO - 10.1002/1098-2795(200102)58:2<149::aid-mrd3>3.0.co;2-x VL - 58 IS - 2 SP - 149–158 SN - 1040-452X 1098-2795 UR - http://dx.doi.org/10.1002/1098-2795(200102)58:2<149::aid-mrd3>3.0.co;2-x KW - CYP3A KW - embryo KW - development ER - TY - JOUR TI - Differential biomarker gene and protein expressions in nonylphenol and estradiol-17β treated juvenile rainbow trout (Oncorhynchus mykiss) AU - Arukwe, A AU - Kullman, S.W. AU - Hinton, D.E. T2 - Comparative Biochemistry and Physiology Part C: Toxicology & Pharmacology AB - The time- and dose-dependent transcriptional and translational expression of biomarker genes in nonylphenol (NP) and estradiol-17beta (E(2)) treated juvenile rainbow trout is reported. Fish were exposed to NP (1, 5 and 25 mg/kg) and E(2) (5 mg/kg) and killed at 2, 6, 12, 24, 48 and 72 h after exposure. The estrogen receptor (ER), vitellogenin (Vtg) and eggshell zona radiata protein (Zr-protein) gene expressions were analyzed in total liver RNA using Northern and slot hybridization with specific cDNA probes. Plasma Vtg and Zr-protein levels were evaluated using indirect ELISA. While Zr-protein gene showed an induction only at 24 h post-exposure, the plasma protein levels showed a time-dependent increase in the 25-mg NP treated group. Vtg transcripts showed an apparent time-dependent increase without a concomitant increase in protein levels in the 25-mg NP treated fish. Time-dependent increases in Vtg and Zr-protein gene expressions without the corresponding increases in ER gene transcription was observed in E(2)-treated fish at 2, 6 and 12 h post-exposure. Induction of ER gene transcripts was observed from 24 h and did not change significantly at 48 and 72 h. In the E(2)-treated fish, induction of plasma Vtg levels was observed at 48 and 72 h, while plasma Zr-protein was induced at 24, 48 and 72 h, after exposure. We conclude that the E(2)- and NP-induced Vtg and Zr-protein gene expressions at the early time intervals after exposure are not dependent on increase in the transcriptional activity of the ER gene and that Vtg and Zr-protein gene transcriptions require only basal or minimal ER concentration, in addition to other mechanisms. DA - 2001/5// PY - 2001/5// DO - 10.1016/s1532-0456(01)00170-3 VL - 129 IS - 1 SP - 1–10 SN - 1532-0456 UR - http://dx.doi.org/10.1016/s1532-0456(01)00170-3 KW - estrogen-receptor KW - Zr-protein KW - vitellogenin KW - biomarkers KW - gene expression KW - xenoestrogen KW - rainbow trout ER - TY - BOOK TI - Introduction to Biochemical Toxicology DA - 2001/// PY - 2001/// ET - 3rd PB - J. Wiley and Sons ER - TY - JOUR TI - Method of treating alopecia AU - Smart, R. C. AU - Oh, H.-S. DA - 2001/// PY - 2001/// VL - 6,204,258 IS - 2001 Mar. 20 ER - TY - BOOK TI - Introduction to Biochemical Toxicology A3 - Hodgson, E. A3 - Smart, R.C. DA - 2001/// PY - 2001/// ET - 3rd PB - J. Wiley and Sons ER - TY - CHAP TI - Carcinogenesis AU - Smart, R.C. AU - Akunda, J.K. T2 - Introduction to Biochemical Toxicology A2 - Hodgson, E. A2 - Smart, R.C. PY - 2001/// ET - 3rd SP - 343–398 PB - J. Wiley and Sons ER - TY - CHAP TI - Molecular Techniques in Toxicology AU - Smart, R.C. T2 - Introduction to Biochemical Toxicology A2 - Hodgson, E. A2 - Smart, R.C. PY - 2001/// ET - 3rd SP - 11–32 PB - J. Wiley and Sons ER - TY - CHAP TI - Biochemical Toxicology: Definition and Scope AU - Hodgson, E. AU - Smart, R.C. T2 - Introduction to Biochemical Toxicology A2 - Hodgson, E. A2 - Smart, R.C. PY - 2001/// SP - 1–10 PB - J. Wiley and Sons ER - TY - CONF TI - Life Cycle Inventory Comparison of a Bioreactor Landfill and a Traditional MSW Landfill in Sainte Sophie, Quebec AU - Norstrom, J. AU - Barlaz, M.A. AU - Bourque, H. T2 - 6th Annual Solid Waste Association of North America (SWANA) Landfill Symposium C2 - 2001/// CY - San Diego, CA DA - 2001/// PY - 2001/6/18/ ER - TY - CONF TI - Closing Gaps in the Regulation of MSW Landfills: Defining the End of the Post-Closure Monitoring Period AU - Barlaz, M.A. T2 - WasteTech C2 - 2001/// CY - San Diego, CA DA - 2001/// PY - 2001/2/11/ ER - TY - CONF TI - Production of Non-Methane Organic Compounds During Refuse Decomposition in a Laboratory-Scale Landfill AU - Barlaz, M.A. T2 - WasteTech C2 - 2001/// CY - San Diego, CA DA - 2001/// PY - 2001/2/11/ ER - TY - RPRT TI - An Assessment of Price Volatility in Recyclables Markets and Market Mechanisms to Stabilize Prices AU - Kusa, J. AU - Barlaz, M.A. AU - Brill, E.D. AU - Green, B. AU - Knoeber, C.R. AU - Palmquist, R.B. A3 - Environmental Research and Education Foundation DA - 2001/// PY - 2001/// PB - Environmental Research and Education Foundation ER - TY - CONF TI - A Critical Evaluation of Factors Required to Terminate the Post-Closure Monitoring Period at Solid Waste Landfills AU - Barlaz, M.A. T2 - South African Institute of Civil Engineering C2 - 2001/// CY - Johannesburg, South Africa DA - 2001/// PY - 2001/9/5/ ER - TY - CHAP TI - Anaerobic Decomposition of Refuse in Landfills and Methane Oxidation in Landfill Cover Soils AU - Hilger, H.H. AU - Barlaz, M.A. T2 - Manual of Environmental Microbiology PY - 2001/// ET - 2nd Edition SP - 696 – 718 PB - American Society of Microbiology ER - TY - JOUR TI - Perspectives on the use of electrospray ionization Fourier transform ion cyclotron resonance mass spectrometry for short tandem repeat genotyping in the post‐genome era AU - Null, A.P. AU - Muddiman, D.C. T2 - Journal of Mass Spectrometry (Special Feature) AB - Abstract The recent completion of the first rough draft of the human genome has provided fundamental information regarding our genetic make‐up; however, the post‐genome era will certainly require a host of new technologies to address complex biological questions. In particular, a rapid and accurate approach to characterize genetic markers, including short tandem repeats (STRs) and single nucleotide polymorphisms (SNPs) is demanded. STRs are the most informative of the two polymorphisms owing to their remarkable variability and even dispersity throughout eukaryotic genomes. Mass spectrometry is rapidly becoming a significant method in DNA analysis and has high probability of revolutionizing the way in which scientists probe the human genome. It is our responsibility as biomolecular mass spectrometrists to understand the issues in genetic analysis and the capabilities of mass spectrometry so that we may fulfill our role in developing a rapid, reliable technology to answer specific biological questions. This perspective is intended to familiarize the mass spectrometry community with modern genomics and to report on the current state of mass spectrometry, specifically electrospray ionization Fourier transform ion cyclotron resonance mass spectrometry, for characterization of STRs. Copyright © 2001 John Wiley & Sons, Ltd. DA - 2001/6/21/ PY - 2001/6/21/ DO - 10.1002/jms.172 VL - 36 IS - 6 SP - 589–606 KW - electrospray ionization Fourier transform ion cyclotron resonance mass spectrometry KW - short tandem repeats KW - genotyping KW - DNA KW - human genome ER - TY - JOUR TI - Mutations of the Mouse Twist and sy (Fibrillin 2) Genes Induced by Chemical Mutagenesis of ES Cells AU - Browning, Victoria L. AU - Chaudhry, Shazia S. AU - Planchart, Antonio AU - Dixon, Michael J. AU - Schimenti, John C. T2 - Genomics AB - A prior phenotype-based screen of mice derived from ethylmethanesulfonate-mutagenized embryonic stem cells yielded two mouse limb defect mutants. Animals heterozygous for the polydactyly ems (Pde) mutation display preaxial polydactyly of the hindlimbs, and homozygous syndactyly ems (sne) animals are characterized by a fusion of the middle digits of their hindlimbs and sometimes forelimbs. We now report that Pde is a new allele of the basic helix-loop-helix protein gene Twist. Sequencing the full-length cDNA and several hundred basepairs of genomic DNA upstream of the coding region failed to reveal a mutation, suggesting that the lesion may be in a regulatory element of the gene. sne is a new fused phalanges (fp) allele of the shaker-with-syndactylism deletion complex (sy), and we show that the genomic lesion is a small deletion removing an entire exon, coincident with the insertion of the 3′ end of a LINE element belonging to the TF subfamily. DA - 2001/5// PY - 2001/5// DO - 10.1006/geno.2001.6523 VL - 73 IS - 3 SP - 291-298 J2 - Genomics LA - en OP - SN - 0888-7543 UR - http://dx.doi.org/10.1006/geno.2001.6523 DB - Crossref ER - TY - JOUR TI - Experimental and computational approaches yield a high-resolution, 1-Mb physical map of the region harboring the mouse t haplotype sterility factor, tcs1 AU - Planchart, Antonio AU - Schimenti, John C. T2 - Mammalian Genome DA - 2001/8// PY - 2001/8// DO - 10.1007/s00335-001-1002-9 VL - 12 IS - 8 SP - 668-670 J2 - Mammalian Genome LA - en OP - SN - 0938-8990 1432-1777 UR - http://dx.doi.org/10.1007/s00335-001-1002-9 DB - Crossref ER - TY - JOUR TI - Simplified serum- and steroid-free culture conditions for high-throughput viability analysis of primary cultures of cerebellar granule neurons AU - Wong, J.K. AU - Kennedy, P.R. AU - Belcher, S.M. T2 - Journal of Neuroscience Methods AB - A serum- and steroid-free primary culture system was developed for the maintenance and automated analysis of cerebellar granule cell viability. Conventional poly-lysine coated 96-well tissue culture plates serve as a platform for growth, experimental manipulation and subsequent automated analysis of these primary cultured neurons. Cerebellar granule neurons were seeded at densities ranging from 2 x 10(4) to 1.25 x 10(6) cells/cm(2) and maintained in serum- and steroid-free culture conditions for 7 days. Viability was subsequently determined by the reduction of [3-(4,5-dimethylthiazol-2-yl)-5-(3-carboxymethoxyphenyl)-2-(4-sulfophenyl)-2H-tetrazolium (MTS), and the degree of cell death occurring over that period was determined by the release of lactate dehydrogenase (LDH). At appropriate cell densities, the results of the MTS reduction and LDH release assays were directly proportional to the initial number of cerebellar granule cells plated. Those results indicate that an initial cell density of 0.5 - 1.0 x 10(5) cells per well (0.32 cm(2)) was appropriate for simultaneous analysis with the MTS reduction and LDH release assays. Both assays were then used to demonstrate the utility of this model system for analysis of tert-butyl-hydroperoxide and hydrogen peroxide induced oxidative stress. Additionally, the MTS reduction assay was used to demonstrate that the NMDA-receptor selective antagonist MK-801 was neuroprotective against glutamate-mediated excitotoxicity. This study defines a powerful and flexible primary culture system for cerebellar neurons that is useful for high-throughput analysis of factors that influence neuronal viability. DA - 2001/// PY - 2001/// DO - 10.1016/S0165-0270(01)00419-8 VL - 110 IS - 1-2 SP - 45-55 UR - http://www.scopus.com/inward/record.url?eid=2-s2.0-0035975671&partnerID=MN8TOARS KW - cell culture KW - cerebellum KW - excitotoxicity KW - glutamate KW - LDH release KW - MK-801 KW - MTT KW - neuron KW - neuroprotection KW - neurotoxicity KW - reactive oxygen ER - TY - JOUR TI - Identification of a developmental gradient of estrogen receptor expression and cellular localization in the developing and adult female rat primary somatosensory cortex AU - Zsarnovszky, A. AU - Belcher, S.M. T2 - Developmental Brain Research AB - Immunohistochemistry was used to investigate the spatiotemporal distribution of estrogen receptor alpha and beta (ER alpha, ER beta) in the posteromedial barrel subfield (PMBS) of the cerebral cortex in developing and adult female rats. Counting of immunopositive cells in predefined areas from each layer of the PMBS showed that at PN3, ER alpha immunoreactivity (IR) was present in every cell, whereas ER beta-IR was not detected. At PN6, about 59% of the cells were ER alpha immunopositive and low levels of ER beta-IR were observed in scattered cells. At PN18 the proportion of ER alpha-IR cells decreased to 49%; however, ER beta-IR became widespread and was detected in 39% of cells. By PN25 only faint ER alpha-IR was observed and in the adults ER alpha-IR was not detected. In contrast, at PN25 and in adults, ER beta-IR was detected in about half the cells of the PMBS. Regarding the cellular localization of ER-IR, at PN3 an outside-in gradient of cytoplasmic to nuclear localization of ER alpha-IR was observed. At PN18 and in adults ER beta-IR was preferentially localized to the nucleus of principal neurons, and to the cytoplasm of small, stellate-shaped interneurons. Together, these observations reveal a developmental transition of ER expression in the PMBS; ER alpha is expressed during early development, ER alpha and ER beta are co-expressed at later developmental times, and only ER beta is expressed in adults. These changes in ER expression and localization suggest that ER alpha and ER beta may play important, but different roles in the formation and function of the PMBS region of the primary somatosensory cortex. DA - 2001/// PY - 2001/// DO - 10.1016/S0165-3806(01)00180-8 VL - 129 IS - 1 SP - 39-46 UR - http://www.scopus.com/inward/record.url?eid=2-s2.0-0035939097&partnerID=MN8TOARS KW - barrel KW - cortex KW - development KW - estrogen KW - estrogen receptor KW - immunohistochemistry KW - posteromedial barrel subfield KW - somatosensory ER - TY - JOUR TI - Early postnatal ethanol exposure selectively decreases BDNF and truncated TrkB-T2 receptor mRNA expression in the rat cerebellum AU - Light, K.E. AU - Ge, Y. AU - Belcher, S.M. T2 - Molecular Brain Research AB - Binge-like ethanol exposure on postnatal day (PN) 4 induces a concentration dependent loss of Purkinje cells in the rat cerebellum. The mechanism of this ethanol-induced Purkinje cell vulnerability is not presently understood. Nevertheless, the specific timing of this vulnerability leads us to consider the neurotrophin system crucial to the regulation of neuronal development. Differentiation, maturation, and survival of Purkinje cells are shown to involve an intimate interaction between brain-derived nerve growth factor (BDNF) and neurotrophin-3 (NT3) acting primarily through their specific tyrosine-kinase (Trk) receptors. We believe that the specific ethanol vulnerability, and the timing of this vulnerability result from alterations in the BDNF-NT3 interplay. We hypothesize that disruption of TrkB and/or TrkC mediated neurotrophin communication is, in part, responsible for the ethanol-induced loss of Purkinje cells during development. The current study was undertaken to define the impact of ethanol exposure at the onset of ethanol vulnerability on the relative concentrations of mRNA encoding the neurotrophic factor receptors TrkB and TrkC. The reverse transcriptase (RT) polymerase chain reaction (PCR) amplification technique was used to identify the relative expression levels of mRNA specific to these receptors as well as the truncated TrkB receptor isoforms. We identify a specific decrease in overall TrkB receptor mRNA expression that is primarily a function of the TrkB-T2 receptor isoform. Concurrent decreases in mRNA specific to BDNF were also identified. No significant alterations to the expression of TrkC mRNA were found indicating that ethanol-exposure appears to act selectively on the BDNF communication system. DA - 2001/// PY - 2001/// DO - 10.1016/S0169-328X(01)00182-6 VL - 93 IS - 1 SP - 46-55 UR - http://www.scopus.com/inward/record.url?eid=2-s2.0-0035840303&partnerID=MN8TOARS KW - cerebellum KW - truncated TrkB KW - TrkC KW - ethanol-exposure KW - RT-PCR KW - mRNA ER - TY - JOUR TI - Estrogenic actions in the brain: Estrogen, phytoestrogens, and rapid intracellular signaling mechanisms AU - Belcher, S.M. AU - Zsarnovszky, A. T2 - Journal of Pharmacology and Experimental Therapeutics DA - 2001/// PY - 2001/// VL - 299 IS - 2 SP - 408-414 UR - http://www.scopus.com/inward/record.url?eid=2-s2.0-0034768705&partnerID=MN8TOARS ER - TY - JOUR TI - Estrogen receptor β immunoreactivity in differentiating cells of the developing rat cerebellum AU - Jakab, R.L. AU - Wong, J.K. AU - Belcher, S.M. T2 - Journal of Comparative Neurology AB - Estrogen receptors (ER) play a significant role in the development of some regions of the mammalian brain. Recently, ER-beta (ERβ) mRNA and protein were shown to be expressed in the rat cerebellum. In the present study, the ontogeny of ERβ protein expression was examined in the rat cerebellum during postnatal development. Western blot analysis indicated that a single ERβ-like immunoreactive species of ∼55 kDa was present in protein lysates prepared from the cerebella of female and male Sprague-Dawley rat pups. Immunocytochemical analysis of cerebellar sections from the midline vermis revealed that during development, the expression of ERβ varied with age and cell-type, but not sex. In the developing cerebellum, highest levels of ERβ-immunoreactivity (IR) were detected in neurons during neurite growth, and in some glia during migration. Throughout the first postnatal week, ERβ-IR was localized to differentiating granule cells in the external germinal layer and to migrating glia. Differentiating granule cells expressed detectable levels of ERβ throughout development. In Purkinje cells, ERβ-IR was first detected on postnatal day 6 (P6), with peak intensities of immunostaining coinciding with the initiation of axonal and dendritic growth that occurs between P7 and P8. Expression of ERβ-IR remained high during maturation of Purkinje cell dendrites, and then decreased to a lower level maintained in the adult. From the third postnatal week, ERβ-IR was also detected in the later developing Golgi, stellate, and basket neurons. These results suggest that ERβ may play a role in growth-related mechanisms during differentiation of cerebellar neurons and glia. J. Comp. Neurol. 430:396–409, 2001. © 2001 Wiley-Liss, Inc. DA - 2001/// PY - 2001/// DO - 10.1002/1096-9861(20010212)430:3<396::AID-CNE1039>3.0.CO;2-0 VL - 430 IS - 3 SP - 396-409 UR - http://www.scopus.com/inward/record.url?eid=2-s2.0-0035847559&partnerID=MN8TOARS KW - differentiation KW - development KW - glia KW - granule cells KW - growth KW - immunocytochemistry KW - migration KW - neurons KW - Purkinje cells ER - TY - JOUR TI - Homogeneous Preparations of 3′-Phosphoglycolate-Terminated Oligodeoxynucleotides from Bleomycin-Treated DNA as Verified by Electrospray Ionization Fourier Transform Ion Cyclotron Resonance Mass Spectrometry AU - Chen, Shuang AU - Hannis, James C. AU - Flora, Jason W. AU - Muddiman, David C. AU - Charles, Kwabena AU - Yu, Yin AU - Povirk, Lawrence F. T2 - Analytical Biochemistry AB - Single- and double-strand breaks bearing 3′-phosphoglycolate termini are among the most frequent lesions formed in DNA by ionizing radiation and other oxidative mutagens. In order to obtain homogeneous preparations of defined 3′-phosphoglycolate substrates for repair studies, 5′-32P-end-labeled partial duplex DNAs were treated with bleomycin, and individual cleavage products were isolated from polyacrylamide gels. The fragments were then treated with alkaline phosphatase and further purified by reverse-phase HPLC. Electrospray ionization Fourier transform ion cyclotron resonance (ESI-FTICR) mass spectrometry of the purified oligomers produced molecular ions of the expected masses, with no detectable contaminants. Gas-phase sequencing by tandem mass spectrometry of these single species yielded the expected sequence ions and confirmed the presence of phosphoglycolate on the 3′-terminal fragments only. The fragments could be relabeled with polynucleotide kinase to yield highly purified, high-specific-activity substrates for repair studies. DA - 2001/2// PY - 2001/2// DO - 10.1006/abio.2000.4936 VL - 289 IS - 2 SP - 274-280 J2 - Analytical Biochemistry LA - en OP - SN - 0003-2697 UR - http://dx.doi.org/10.1006/abio.2000.4936 DB - Crossref ER - TY - JOUR TI - Genotyping of Simple and Compound Short Tandem Repeat Loci Using Electrospray Ionization Fourier Transform Ion Cyclotron Resonance Mass Spectrometry AU - Null, Allison P. AU - Hannis, James C. AU - Muddiman, David C. T2 - Analytical Chemistry AB - The utility of electrospray ionization Fourier transform ion cyclotron resonance (ESI-FTICR) mass spectrometry as a new approach for genotyping short tandem repeats (STRs) is demonstrated. STRs are currently valued as a powerful source of genetic information with repeats that range in structure from simple to hypervariable. Two tetranucleotide STR loci were chosen to evaluate ESI-FTICR mass spectrometry as a tool for genotyping: HUMTH01, a simple STR with nonconsensus alleles, and vWA, a compound STR with nonconsensus alleles. For HUMTH01, the genotype (i.e., repeat number of each allele) was determined for each of 30 individuals using mass measurements of double-stranded amplicons. Low-intensity peaks observed in the spectra of amplicons derived from heterozygous individuals were identified by mass as heteroduplexes that had formed between nonhomologous strands. Mass measurement of the double-stranded vWA amplicon was not sufficient for determining whether the individual was homozygous for allele subtype 18 or 18‘ since the amplicons differ by only 0.99 Da. Therefore, single-stranded amplicons were generated by incorporating a phosphorylated primer, prepared using T4 polynucleotide kinase, into the PCR phase and subsequently digesting the bottom strand using λ-exonuclease. Accurate mass measurements were obtained for the single-stranded amplicons using internal calibration and the addition of a correction factor to adjust for the natural variation of isotopic abundances, confirming that the individual is homozygous for allele 18. Our results clearly demonstrate that ESI-FTICR mass spectrometry is a powerful approach to characterize both simple and compound STRs beyond the capabilities of electrophoretic technologies. DA - 2001/9// PY - 2001/9// DO - 10.1021/ac0103928 VL - 73 IS - 18 SP - 4514-4521 J2 - Anal. Chem. LA - en OP - SN - 0003-2700 1520-6882 UR - http://dx.doi.org/10.1021/ac0103928 DB - Crossref ER - TY - JOUR TI - Selective, Sensitive, and Rapid Phosphopeptide Identification in Enzymatic Digests Using ESI-FTICR-MS with Infrared Multiphoton Dissociation AU - Flora, Jason W. AU - Muddiman, David C. T2 - Analytical Chemistry AB - Rapid screening for phosphopeptides within complex proteolytic digests involving electrospray ionization Fourier transform ion cyclotron resonance mass spectrometry (ESI-FTICR-MS) in the negative ion mode with infrared multiphoton dissociation (IRMPD) accompanied by improved phosphopeptide sensitivity and selectivity is demonstrated with the tryptic digests of the naturally phosphorylated proteins bovine alpha- and beta-casein. All peptides in a complex proteolytic digest can be examined simultaneously for phosphorylation with a 4-s IR laser pulse at 7-11 W where phosphopeptide signature ions form upon irradiation, as the low energy of activation phosphate moiety cleavage transpires without the dissociation of the unphsophorylated peptide population. The tyrosine phosphorylated peptide HGLDN-pY-R, its nonphosphorylated analogue HGLDNYR, the kinase domain of insulin receptor unphosphorylated TRDIYETDYYRK, monophosphorylated TRDIYED-pY-YRK, and triphosphorylated TRDI-pY-ETD-pY-pY-RK were also used as model peptides in this research. The sensitivity and selectivity of phosphopeptides is shown to greatly improve when the volatile base piperidine is used to adjust the pH of th DA - 2001/7// PY - 2001/7// DO - 10.1021/ac010333u VL - 73 IS - 14 SP - 3305-3311 J2 - Anal. Chem. LA - en OP - SN - 0003-2700 1520-6882 UR - http://dx.doi.org/10.1021/ac010333u DB - Crossref ER - TY - JOUR TI - Complete sequencing of mono—deprotonated peptide nucleic acids by sustained off-resonance irradiation collision—induced dissociation AU - Flora, Jason W. AU - Muddiman, David C. T2 - Journal of the American Society for Mass Spectrometry AB - Complete peptide nucleic acids (PNAs) sequence information is obtained from the unimolecular decomposition of singly-charged PNA oligomers in the negative-ion mode using electrospray ionization coupled with Fourier transform ion cyclotron resonance mass spectrometry (ESI-FTICR-MS) and sustained off-resonance irradiation collision induced dissociation. The 4-mers, n-CATT-c, n-AGCT-c, n-AACT-c, and n-acetylated-AACT-c and two 6-mers, n-AAAAAA-c and n-CCCCCC-c, were investigated to explore the unimolecular decomposition of mixed-nucleobase and homopolymer PNAs representing purine and pyrimidine oligomers, respectively. PNA decomposition is explored using a product-ion appearance curve and double resonance experiments. A decomposition mechanism for sequence ion formation (PNA amide bond cleavage) is proposed. DA - 2001/7// PY - 2001/7// DO - 10.1016/s1044-0305(01)00259-8 VL - 12 IS - 7 SP - 805-809 J2 - J Am Soc Mass Spectrom LA - en OP - SN - 1044-0305 1879-1123 UR - http://dx.doi.org/10.1016/s1044-0305(01)00259-8 DB - Crossref ER - TY - JOUR TI - High-Mass Accuracy of Product Ions Produced by SORI-CID Using a Dual Electrospray Ionization Source Coupled with FTICR Mass Spectrometry AU - Flora, Jason W. AU - Hannis, James C. AU - Muddiman, David C. T2 - Analytical Chemistry AB - High-mass accuracy is demonstrated using internal calibration for product ions produced by sustained off-resonance irradiation collision-induced dissociation (SORI-CID) of a 15-mer oligonucleotide, 5'-(CTG)5-3'. Internal calibration for this tandem MS experiment was accomplished using a dual electrospray ionization (ESI) source coupled with Fourier transform ion cyclotron resonance mass spectrometry (FTICR-MS) utilizing hexapole accumulation and gated trapping. The pulse sequence entails injection, trapping, and gas-phase isolation of the precursor ion of interest followed by the SORI-CID of this ion and, subsequently, injection and trapping of the internal mass calibrant (i.e., poly(ethylene glycol) with a 1000 Da average mass). The product ions and the poly(ethylene glycol) ions are then simultaneously excited by a broadband frequency chirp excitation waveform and detected. This technique corrects for space-charge effects on the measurement of an ion's cyclotron frequency experienced when externally calibrated data are used. While external calibration for FTICR-MS can result in mass errors of greater than 100 ppm, this internal standardization method demonstrated significantly more consistent accurate mass measurements with average mass errors ranging from -1.2 to -3.2 ppm for the 15-mer oligonucleotide used in this study. This method requires limited modifications to ESI-FTICR mass spectrometers and is applicable for both positive and negative modes of ionization as well as other sample types (e.g., pharmaceuticals, proteins, etc.). DA - 2001/3// PY - 2001/3// DO - 10.1021/ac0011282 VL - 73 IS - 6 SP - 1247-1251 J2 - Anal. Chem. LA - en OP - SN - 0003-2700 1520-6882 UR - http://dx.doi.org/10.1021/ac0011282 DB - Crossref ER - TY - JOUR TI - Genotyping short tandem repeats using flow injection and electrospray ionization Fourier transform ion cyclotron resonance mass spectrometry AU - Hannis, James C. AU - Muddiman, David C. T2 - Rapid Communications in Mass Spectrometry AB - Characterizing polymerase chain reaction (PCR) amplicons has been accomplished for the first time using flow injection analysis coupled to electrospray ionization mass spectrometry (ESI-MS). The PCR amplicons were amplified at the human tyrosine hydroxylase short tandem repeat locus from an individual homozygotic for the 9.3 allele. One product was amplified using Pfu polymerase and yielded a blunt-ended amplicon of 82 base-pairs (bp) in length. The second PCR product was amplified using Taq polymerase that resulted in an amplicon with cohesive termini of 82 bp plus either mono- or diadenylation. The two PCR amplicons were alternatively injected using a 0.5-microL loop at 2 microM for the Pfu amplicon and 1 microM for the Taq amplicon with a flow rate of 200 nL/min during data acquisition. Both PCR amplicons were accurately identified using mass measurements illustrating the compatibility of ESI-MS for genotyping short tandem repeat sequences and the potential for high-throughput genotyping of large PCR amplicons. DA - 2001/// PY - 2001/// DO - 10.1002/rcm.234 VL - 15 IS - 5 SP - 348-350 J2 - Rapid Commun. Mass Spectrom. LA - en OP - SN - 0951-4198 1097-0231 UR - http://dx.doi.org/10.1002/rcm.234 DB - Crossref ER - TY - JOUR TI - Detection of double-stranded PCR amplicons at the attomole level electrosprayed from low nanomolar solutions using FT-ICR mass spectrometry AU - Hannis, James C. AU - Muddiman, David C. T2 - Fresenius' Journal of Analytical Chemistry DA - 2001/2/14/ PY - 2001/2/14/ DO - 10.1007/s002160000612 VL - 369 IS - 3-4 SP - 246-251 J2 - Fresenius' Journal of Analytical Chemistry OP - SN - 0937-0633 1432-1130 UR - http://dx.doi.org/10.1007/s002160000612 DB - Crossref ER - TY - JOUR TI - Impact of ion cloud densities on the measurement of relative ion abundances in Fourier transform ion cyclotron resonance mass spectrometry: experimental observations of coulombically induced cyclotron radius perturbations and ion cloud dephasing rates AU - Gordon, Eric F. AU - Muddiman, David C. T2 - Journal of Mass Spectrometry AB - Fundamental research into the quantitative properties of Fourier transform ion cyclotron resonance mass spectrometry (FTICR-MS) has yielded interesting observations, especially in terms of factors affecting the accuracy of relative ion abundances. However, most of the previous discussions have focused on theoretical systems, or systems of limited scope. In this paper, we document ion motion attributes of a 30 spectra (six samples, five replicates each) system previously established as linear over two orders of magnitude. Observed behaviors include the perturbation of one charged species (cyclosporin A, CsA) of low ion density to a cyclotron orbit of greater radius than that of an almost identical, but slightly mass-separated species (CsG) with a higher ion density. This radial perturbation is attributed to the coulombic repulsion between the two ion clouds as they interact during the excitation process, as previously proposed by Uechi and Dunbar. Magnitudes of the perturbation were confirmed by making cyclotron radii determinations utilizing the ratio of the third-to-first harmonics for the charged species of interest. It was found that these radial differences can account for as much as a 55% signal bias in favor of CsA for a single sample and a >20% positive bias in the slope of the regressed data set. A second behavior noted that also contributes to the potential inaccuracy of relative ion abundance measurements is the difference in signal decay rates for CsA and CsG. Damping constants and initial time domain signal amplitudes were evaluated using segmented Fourier transforms. Discrepancies in decay rates were not expected from two species that have essentially identical collisional cross-sections. However, it has been observed that the faster decay rates are observed by the species of lower ion cloud density. We have attributed this differential signal decay phenomenon to the rates of loss of phase coherence for the two ion clouds. Previously, others have reported that less dense ion clouds are more susceptible to shearing and other disruptive forces during the course of their excited cyclotron motion. Our experimental evidence supports that it is the loss of cloud coherence that accounts for the signal loss over time, with the less dense cloud de-phasing more quickly. As the ion populations of the two investigated species near equivalence, so do their time constants. DA - 2001/// PY - 2001/// DO - 10.1002/jms.121 VL - 36 IS - 2 SP - 195-203 J2 - J. Mass Spectrom. LA - en OP - SN - 1076-5174 1096-9888 UR - http://dx.doi.org/10.1002/jms.121 DB - Crossref KW - space-charge KW - ion cloud density KW - signal decay KW - proteomics KW - quantification ER - TY - JOUR TI - AGRICULTURAL EXPOSURE HISTORY AMONG AFRICAN-AMERICAN FARMERS IN GEORGIA AU - Hoppin, Jane A. AU - Guzman, J. David AU - Tolbert, Paige E. AU - Flagg, Elaine W. T2 - Journal of Toxicology and Environmental Health, Part A AB - Agricultural exposures differ across the United States by region, calendar time period, and agricultural practice, but most of the published literature focuses on white men in the Midwest. A pilot study was conducted to explore the breadth and diversity of farming practices over time among African-American farmers in Georgia whose exposures may differ in important ways. Using a comprehensive life events calendar questionnaire, 17 male African-American farmers aged 36 to 86 yr residing in southeastern Georgia were interviewed regarding their agricultural history in July 1997. Most men (15/17) reported working on multiple farms in their lifetime; 3 men worked on 5 different farms during their lifetime. These farmers reported using more chemicals during their lifetime than farmers in the Midwest. Used motor oil was the most frequently reported insecticide applied to animals; this apparently common practice has not been described in the literature and should be better understood since its use may result in dermal exposure to polyaromatic hydrocarbons. Better characterization of regionally specific farming history and individual farming practices will facilitate studies of the health effects of farming. DA - 2001/6/22/ PY - 2001/6/22/ DO - 10.1080/15287390151143631 VL - 63 IS - 4 SP - 237-241 J2 - Journal of Toxicology and Environmental Health, Part A LA - en OP - SN - 1528-7394 1087-2620 UR - http://dx.doi.org/10.1080/15287390151143631 DB - Crossref ER - TY - JOUR TI - Posttranscriptional silencing of cytochrome P4501A1 (CYP1A1) during zebrafish (Danio rerio) development AU - Mattingly, Carolyn J. AU - Toscano, William A. T2 - Developmental Dynamics AB - Abstract Induction patterns of cytochrome P4501A1 (CYP1A1), an early biochemical marker of exposure to the environmental toxicant 2,3,7,8‐tetrachlorodibenzo‐ p ‐dioxin (TCDD, or dioxin) were investigated during zebrafish ( Danio rerio ) development. A zebrafish CYP1A1 cDNA fragment was cloned and used to detect CYP1A1 mRNA in embryos exposed to TCDD (1 or 10 nM). Induction of CYP1A1 activity was dependent on age and state of hatch. CYP1A1 mRNA was observed by 15 hr postfertilization. CYP1A1 protein and monooxygenase activity were not detected until 3 days postfertilization and after hatch, as determined by Western immunoblot analysis and ethoxyresorufin O‐deethylase (EROD) activity, respectively. In contrast to embryos, concomitant induction of mRNA and activity was detected in juvenile zebrafish (3 days posthatch) after 6 hr of TCDD exposure. Asynchronous induction of CYP1A1 mRNA and activity during development may be a general regulatory mechanism, as similar ontogenetic expression of this gene was demonstrated in mouse embryos. To our knowledge, this is the first report of CYP1A1 posttranscriptional silencing during embryogenesis. Our data suggest that TCDD‐mediated induction of CYP1A1 activity is regulated differentially in developing and mature systems. © 2001 Wiley‐Liss, Inc. DA - 2001/// PY - 2001/// DO - 10.1002/dvdy.1215 VL - 222 IS - 4 SP - 645-654 J2 - Dev. Dyn. LA - en OP - SN - 1058-8388 1097-0177 UR - http://dx.doi.org/10.1002/dvdy.1215 DB - Crossref KW - cytochrome P450 KW - monooxygenase KW - zebrafish KW - Ah receptor KW - dioxin ER - TY - JOUR TI - Green fluorescent protein (GFP) as a marker of aryl hydrocarbon receptor (AhR) function in developing zebrafish (Danio rerio). AU - Mattingly, C J AU - McLachlan, J A AU - Toscano, W A, Jr T2 - Environmental Health Perspectives AB - We developed an inducible in vivo reporter system to examine expression of the aryl hydrocarbon receptor (AhR) during development in zebrafish (Danio rerio). AhR is a ligand-activated transcription factor that mediates the toxic actions of environmental contaminants such as 2,3,7,8-tetrachlorodibenzo-p-dioxin (TCDD). Induction of cytochrome P4501A1 (CYP1A1) is an early biomarker of AhR activation. A 1905 base pair region of the human CYP1A1 promoter/enhancer region was regulated by AhR in zebrafish liver cells after exposure to TCDD (10 nM) in a transient transfection assay. This regulatory region was fused to the cDNA sequence encoding green fluorescent protein (GFP) of jellyfish (Aequorea victoria). Transgenic zebrafish were generated to express this AhR-regulated GFP construct. Injected fish exposed to TCDD exhibited induction of GFP in the eye, nose, and vertebrae of zebrafish embryos (48 and 72 hr after fertilization) compared to vehicle controls (DMSO), which did not express GFP. To investigate whether AhR-regulated GFP expression correlated with sites of TCDD toxicity, we exposed wild-type zebrafish to DMSO or TCDD and examined them for morphologic abnormalities. By 5 days after fertilization, TCDD-exposed fish exhibited gross dysmorphogenesis in cranio-facial and vertebral development. DA - 2001/8// PY - 2001/8// DO - 10.1289/ehp.01109845 VL - 109 IS - 8 SP - 845-849 J2 - Environ Health Perspect LA - en OP - SN - 0091-6765 1552-9924 UR - http://dx.doi.org/10.1289/ehp.01109845 DB - Crossref ER - TY - JOUR TI - Corrigendum to: “The zebrafish fth1, slc3a2, men1, pc, fgf3 and cycd1 genes define two regions of conserved synteny between linkage group 7 and human chromosome 11q13” [Gene 261 (2000) 235–242] AU - Yoder, Jeffrey A AU - Litman, Gary W T2 - Gene DA - 2001/5// PY - 2001/5// DO - 10.1016/s0378-1119(01)00443-7 VL - 269 IS - 1-2 SP - 227 ER - TY - CONF TI - Closing gaps in the regulation of MSW landfills: Defining the end of the post-closure monitoring period and the future stability of leachate recirculation landfills AU - Barlaz, M. A. AU - Gabr, M. A. AU - Hossain, S. AU - Rooker, A. AU - Kjeldsen, P. C2 - 2001/// C3 - Waste Tech 2001 : February 11 - 14, 2001, Hyatt Islandia, San Diego, CA DA - 2001/// ER - TY - JOUR TI - Structure of human DNMT2, an enigmatic DNA methyltransferase homolog that displays denaturant-resistant binding to DNA AU - Dong, A. AU - Yoder, J.A. AU - Zhang, X. AU - Zhou, L. AU - Bestor, T.H. AU - Cheng, X. T2 - Nucleic Acids Research AB - DNMT2 is a human protein that displays strong sequence similarities to DNA (cytosine-5)-methyltransferases (m(5)C MTases) of both prokaryotes and eukaryotes. DNMT2 contains all 10 sequence motifs that are conserved among m(5)C MTases, including the consensus S:-adenosyl-L-methionine-binding motifs and the active site ProCys dipeptide. DNMT2 has close homologs in plants, insects and Schizosaccharomyces pombe, but no related sequence can be found in the genomes of Saccharomyces cerevisiae or Caenorhabditis elegans. The crystal structure of a deletion mutant of DNMT2 complexed with S-adenosyl-L-homocysteine (AdoHcy) has been determined at 1.8 A resolution. The structure of the large domain that contains the sequence motifs involved in catalysis is remarkably similar to that of M.HHAI, a confirmed bacterial m(5)C MTase, and the smaller target recognition domains of DNMT2 and M.HHAI are also closely related in overall structure. The small domain of DNMT2 contains three short helices that are not present in M.HHAI. DNMT2 binds AdoHcy in the same conformation as confirmed m(5)C MTases and, while DNMT2 shares all sequence and structural features with m(5)C MTases, it has failed to demonstrate detectable transmethylase activity. We show here that homologs of DNMT2, which are present in some organisms that are not known to methylate their genomes, contain a specific target-recognizing sequence motif including an invariant CysPheThr tripeptide. DNMT2 binds DNA to form a denaturant-resistant complex in vitro. While the biological function of DNMT2 is not yet known, the strong binding to DNA suggests that DNMT2 may mark specific sequences in the genome by binding to DNA through the specific target-recognizing motif. C2 - 29660 DA - 2001/1/15/ PY - 2001/1/15/ DO - 10.1093/nar/29.2.439 VL - 29 IS - 2 SP - 439-448 SN - 1362-4962 UR - http://dx.doi.org/10.1093/nar/29.2.439 ER - TY - JOUR TI - Novel immune-type receptor genes AU - Litman, GW AU - Hawke, NA AU - Yoder, JA T2 - IMMUNOLOGICAL REVIEWS AB - Novel immune-type receptor (NITR) genes, which initially were identified in the Southern pufferfish (Spheroides nephelus), encode products which consist of an extracellular variable (V) and V-like C2 (V/C2) domain, a transmembrane region, and a cytoplasmic tail, which typically possesses an immunoreceptor tyrosine-based inhibition motif (ITIM). Multiple NITR genes have been identified in close, contiguous chromosomal linkage. The V regions of NITRs resemble prototypic forms defined for immunoglobulin (Ig) and T-cell antigen receptor (TCR), are present in multiple families and exhibit regionalized variation in sequence, which also occurs in Ig and TCR. Comparisons of exons encoding transmembrane and cytoplasmic regions of multiple NITRs suggest that exon shuffling has factored in the diversification of the NITR gene complex. Zebrafish (Danio rerio) NITRs exhibit many of these characteristics. NITRs that have been identified in additional species of bony fish demonstrate additional variation in the number of extracellular domains as well as in the presence of intramembranous charged residues, cytoplasmic tails and ITIMs. The presence in NITRs of V regions that are related closely to those found in Ig and TCR, as well as regulatory motifs and other structural features that are characteristic of immune inhibitory receptors encoded at the leukocyte receptor cluster, suggests that the NITRs are representative of an integral stage in the evolution of innate and adaptive immune function. DA - 2001/6// PY - 2001/6// DO - 10.1034/j.1600-065X.2001.1810121.x VL - 181 IS - 1 SP - 250-259 SN - 0105-2896 ER - TY - JOUR TI - Immune-type receptor genes in zebrafish share genetic and functional properties with genes encoded by the mammalian leukocyte receptor cluster AU - Yoder, J. A. AU - Mueller, M. G. AU - Wei, S. AU - Corliss, B. C. AU - Prather, D. M. AU - Willis, T. AU - Litman, R. T. AU - Djeu, J. Y. AU - Litman, G. W. T2 - Proceedings of the National Academy of Sciences AB - An extensive, highly diversified multigene family of novel immune-type receptor (nitr) genes has been defined in Danio rerio (zebrafish). The genes are predicted to encode type I transmembrane glycoproteins consisting of extracellular variable (V) and V-like C2 (V/C2) domains, a transmembrane region and a cytoplasmic tail. All of the genes examined encode immunoreceptor tyrosine-based inhibition motifs in the cytoplasmic tail. Radiation hybrid panel mapping and analysis of a deletion mutant line (b240) indicate that a minimum of approximately 40 nitr genes are contiguous in the genome and span approximately 0.6 Mb near the top of zebrafish linkage group 7. One flanking region of the nitr gene complex shares conserved synteny with a region of mouse chromosome 7, which shares conserved synteny with human 19q13.3-q13.4 that encodes the leukocyte receptor cluster. Antibody-induced crosslinking of Nitrs that have been introduced into a human natural killer cell line inhibits the phosphorylation of mitogen-activated protein kinase that is triggered by natural killer-sensitive tumor target cells. Nitrs likely represent intermediates in the evolution of the leukocyte receptor cluster. DA - 2001/5/29/ PY - 2001/5/29/ DO - 10.1073/pnas.121101598 VL - 98 IS - 12 SP - 6771-6776 J2 - Proceedings of the National Academy of Sciences LA - en OP - SN - 0027-8424 1091-6490 UR - http://dx.doi.org/10.1073/pnas.121101598 DB - Crossref ER - TY - JOUR TI - Extraordinary variation in a diversified family of immune-type receptor genes AU - Hawke, N.A. AU - Yoder, Jeffrey AU - Haire, R.N. AU - Mueller, M.G. AU - Litman, R.T. AU - Miracle, A.L. AU - Stuge, T. AU - Shen, L. AU - Miller, N. AU - Litman, G.W. AU - al. T2 - Proceedings of the National Academy of Sciences AB - Immune inhibitory receptor genes that encode a variable (V) region, a unique V-like C2 (V/C2) domain, a transmembrane region, and a cytoplasmic tail containing immunoreceptor tyrosine-based inhibition motifs (ITIMs) have been described previously in two lineages of bony fish. In the present study, eleven related genes encoding distinct structural forms have been identified in Ictalurus punctatus (channel catfish), a well characterized immunological model system that represents a third independent bony fish lineage. Each of the different genes encodes an N-terminal V region but differs in the number of extracellular Ig domains, number and location of joining (J) region-like motifs, presence of transmembrane regions, presence of charged residues in transmembrane regions, presence of cytoplasmic tails, and/or distribution of ITIM(s) within the cytoplasmic tails. Variation in the numbers of genomic copies of the different gene types, their patterns of expression, and relative levels of expression in mixed leukocyte cultures (MLC) is reported. V region-containing immune-type genes constitute a far more complex family than recognized originally and include individual members that might function in inhibitory or, potentially activatory manners. DA - 2001/11/6/ PY - 2001/11/6/ DO - 10.1073/pnas.231418598 VL - 98 IS - 24 SP - 13832-13837 J2 - Proceedings of the National Academy of Sciences LA - en OP - SN - 0027-8424 1091-6490 UR - http://dx.doi.org/10.1073/pnas.231418598 DB - Crossref ER - TY - JOUR TI - Cloning and sequence analysis of a zebrafish cDNA encoding DNA (cytosine-5)-methyltransferase-1 AU - Mhanni, AA AU - Yoder, JA AU - Dubesky, C AU - McGowan, RA T2 - GENESIS AB - Abstract Summary: The zebrafish has become a well‐established animal model for the analysis of development and of several disease phenotypes. Several of the favorable traits that make it a popular model organism would also be beneficial for the study of normal and abnormal vertebrate development in which DNA methylation may play a role. We report the determination of the full‐length cDNA sequence corresponding to the zebrafish DNA (cytosine‐5‐) methyltransferase gene, Dnmt1 . It is 4,907 bases long and has an open reading frame predicted to encode a 1,499 amino acid protein that is similar in size and sequence to a number of other methyltransferases identified in other organisms. genesis 30:213–219, 2001. © 2001 Wiley‐Liss, Inc. DA - 2001/8// PY - 2001/8// DO - 10.1002/gene.1067 VL - 30 IS - 4 SP - 213-219 SN - 1526-968X UR - http://www.scopus.com/inward/record.url?eid=2-s2.0-0034861153&partnerID=MN8TOARS KW - DNA cytosine-5-methyltransferase KW - DNA mtase KW - Dnmt1 KW - zebrafish KW - methylation KW - development ER - TY - JOUR TI - Factors controlling alkylbenzene sorption to municipal solid waste AU - Wu, BY AU - Taylor, CM AU - Knappe, DRU AU - Nanny, MA AU - Barlaz, MA T2 - ENVIRONMENTAL SCIENCE & TECHNOLOGY AB - The sorption of toluene and o-xylene to individual municipal solid waste (MSW) constituents [office paper, newsprint, model food and yard waste, high density polyethylene, and poly(vinyl chloride) (PVC)] was evaluated. Effects of sorbent decomposition and solvent composition on alkylbenzene sorption were studied by evaluating biodegradable sorbents in both fresh and anaerobically decomposed form and by complementing single-solute isotherm tests with experiments conducted in acidogenic and methanogenic leachate. Alkylbenzene sorption to plastics was greaterthan to biopolymer composites, and differences in sorbate/sorbent solubility parameter compatibility explained this observation. Alkylbenzene sorption to biopolymer composites yielded linear isotherms, and sorption capacities [log(Koc/Kow)] decreased linearly with increasing sorbent polarity as expressed by the O-alkyl/alkyl ratio. Leachate composition had little effect on alkylbenzene sorption with one exception; volatile fatty acids in acidogenic leachate appeared to convert PVC from a glassy to a rubbery polymer. The results of this study showed that sorbent organic matter affinity for hydrophobic organic contaminants (HOCs) increases with increasing extent of MSW decomposition because of the recalcitrance of plastics and the preferential degradation of polar biopolymers. Furthermore, the plasticizing effect of volatile fatty acids in acidogenic leachate may enhance the bioavailability of HOCs sorbed to glassy organic matter in MSW or in soils contaminated with acidogenic leachate. DA - 2001/11/15/ PY - 2001/11/15/ DO - 10.1021/es010893a VL - 35 IS - 22 SP - 4569-4576 SN - 1520-5851 UR - http://www.scopus.com/inward/record.url?eid=2-s2.0-0035890552&partnerID=MN8TOARS ER - TY - JOUR TI - Genetic algorithm approaches for addressing unmodeled objectives in optimization problems AU - Loughlin, DH AU - Ranjithan, , SR AU - Brill, ED AU - Baugh, JW T2 - ENGINEERING OPTIMIZATION AB - Abstract Public sector decision-making typically involves complex problems that are often not completely understood. In these problems, there are invariably unmodeled issues that can greatly impact the acceptability of solutions. Modeling to Generate Alternatives (MGA) is an approach for addressing unmodeled issues in an optimization context. MGA techniques are used to generate a small number of good, yet very different, solutions to optimization problems. Because these solutions are different in decision space, they may differ considerably in performance when unmodeled objectives are considered. Many problems are sufficiently complex that traditional optimization solution procedures, and therefore traditional MGA techniques, are not readily applicable. Two techniques for performing MGA using genetic algorithms (GAs) are investigated and compared. One of these techniques, which uses specialized MGA operators, is shown to produce solutions that are both better in quality and more different. This technique is also demonstrated for a realistic air quality management problem. DA - 2001/// PY - 2001/// DO - 10.1080/03052150108940933 VL - 33 IS - 5 SP - 549-569 SN - 0305-215X KW - genetic algorithm KW - multimodal KW - modeling to generate alternatives KW - sharing KW - niching ER - TY - CHAP TI - Constraint method-based evolutionary algorithm (CMEA) for multiobjective optimization AU - Ranjithan, S. R. AU - Chetan, S. K. AU - Dakshina, H. K. T2 - Evolutionary multi-criterion optimization: First international conference, EMO 2001, Zurich, Switzerland, March 7-9, 2001: Proceedings AB - Evolutionary algorithms are becoming increasingly valuable in solving large-scale, realistic engineering multiobjective optimization (MO) problems, which typically require consideration of conflicting and competing design issues. The new procedure, Constraint Method-Based Evolutionary Algorithm (CMEA), presented in this paper is based upon underlying concepts in the constraint method described in the mathematical programming literature. Pareto optimality is achieved implicitly via a constraint approach, and convergence is enhanced by using beneficial seeding of the initial population. CMEA is evaluated by solving two test problems reported in the multiobjective evolutionary algorithm (MOEA) literature. Performance comparisons based on quantitative metrics for accuracy, coverage, and spread are presented. CMEA is relatively simple to implement and incorporate into existing implementations of evolutionary algorithm-based optimization procedures. CN - T57.95 .I57 2001 PY - 2001/// DO - 10.1007/3-540-44719-9_21 VL - 1993 SP - 299-313 PB - Berlin; New York: Springer SN - 3540417451 ER - TY - JOUR TI - Effects of subsurface heterogeneity on natural bioremediation at a gasoline spill site AU - Kao, CM AU - Kota, S AU - Ress, B AU - Barlaz, MA AU - Borden, RC T2 - WATER SCIENCE AND TECHNOLOGY AB - A test cell of 3-m by 6-m located at the mid-point of a gasoline spill site was selected to test the hypothesis that the rate of hydrocarbon biodegradation is influenced by the spatial distribution of the electron acceptors, aqueous geochemistry, and microbial population. Multilevel samplers (MLSs) were installed at four corners of the test cell for groundwater sampling. Sampling ports were placed at 0.3-m intervals from 1.5 to 4.8 m below land surface (bls). A 0.91-m by 12.7-cm sediment core (from 3.3 to 4.2 m bls) in the center of the MLSs was collected. The core was cut into 7 sections, and each was used for sediment extractions, microbial enumeration, grain size distribution, and microcosm studies. Groundwater analytical results indicate that iron reduction was the dominant biodegradation process within this test cell. Iron-reducing process caused the preferential removal of certain compounds. Microbial enumeration results show that the distribution of microbial population varied with depth and sediment materials. Lower microbial population was observed in those sections with higher portion of clayey materials. The less permeable materials would limit the bacterial transport, decrease the bioavailability of Fe(III) to iron-reducing bacteria, and thus cause the low biodegradation activity. Results suggest that using blended sediments for biodegradation rate measurements may provide misleading results. DA - 2001/// PY - 2001/// DO - 10.2166/wst.2001.0322 VL - 43 IS - 5 SP - 341-348 SN - 0273-1223 KW - natural bioremediation KW - multilevel sampler KW - heterogeneity KW - aqueous geochemistry ER - TY - JOUR TI - Decision support tool for life-cycle-based solid waste management AU - Harrison, K. W. AU - Dumas, R. D. AU - Solano, E. AU - Barlaz, Morton AU - Brill, E. D. AU - Ranjithan, S. R. T2 - Journal of Computing in Civil Engineering AB - Existing solid waste management (SWM) planning software provides only limited assistance to decision makers struggling to find strategies that address their multifarious concerns. The combinatorial nature (many waste items and many management options) and multiple objectives of the SWM problem severely constrain the effectiveness of a manual search process using these tools. Recognizing this, researchers have proposed several optimization-based search procedures. These methods, however, enjoy limited use due to the substantial expertise required for their application. This paper presents a new computer-based decision support framework that addresses these limitations. The new framework integrates process models that quantify the life-cycle inventory of a range of pollutants and costs for an extensive municipal solid waste system, an optimization search procedure that identifies strategies that meet cost and environmental objectives and site-specific restrictions, and a user-friendly interface that facilitates utilization of these components by practitioners. After describing the software design, the use and value of the tool in typical waste management scenarios is demonstrated through a hypothetical, but realistic, case study in which several alternative SWM strategies are generated and examined. DA - 2001/// PY - 2001/// DO - 10.1061/(ASCE)0887-3801(2001)15:1(44) VL - 15 IS - 1 SP - 44–58 ER - TY - JOUR TI - Protein kinase C-alpha coordinately regulates cytosolic phospholipase A(2) activity and the expression of cyclooxygenase-2 through different mechanisms in mouse keratinocytes AU - Wang, HQ AU - Kim, MP AU - Tiano, HF AU - Langenbach, R AU - Smart, RC T2 - MOLECULAR PHARMACOLOGY AB - Transgenic mice (K5-PKCα) in which the keratin 5 promoter directs the expression of protein kinase C-α (PKCα) to epidermal keratinocytes display a 10-fold increase in PKCα protein in their epidermis and alterations in phorbol ester-induced cutaneous inflammation [J Cell Science 1999;112:3497–3506]. In the current study, we have used these K5-PKCα mice to examine the role of PKCα in keratinocyte phospholipid metabolism/eicosanoid production and cutaneous inflammation. Primary keratinocytes from wild-type and transgenic mice were prelabeled in culture with [3H]arachidonic acid (AA) and subsequently treated with TPA. Compared with wild-type keratinocytes, K5-PKCα keratinocytes displayed a 2-fold increase in AA release. TPA treatment resulted in the phosphorylation of cPLA2. PKC inhibitors GF-109203X or H7, but not mitogen-activated protein/extracellular signal-regulated protein kinase (MEK) inhibitor PD 98059, could inhibit phosphorylation and AA release. Topical 12-O-tetradecanoylphorbol-13-acetate (TPA) treatment of K5-PKCα mice resulted in a 5-fold increase in epidermal COX-2 induction and a 2- to 3-fold increase in prostaglandin (PG) E2 levels above that observed in TPA-treated wild-type mice. PD 98059, GF-109203X, or H7 could block cyclooxygenase-2 (COX-2) induction by TPA. Because C/EBPβ, a basic leucine zipper transcription factor, can be activated via a PKCα/mitogen-activated protein kinase pathway and can influence COX-2 expression, we examined whether C/EBPβ is involved in TPA-induced epidermal COX-2 expression. TPA-induced COX-2 expression was similar in C/EBPβ nullizygous and wild-type mice. In summary, our results indicate that epidermal PKCα coordinately regulates cPLA2 activity and COX-2 expression resulting in increased levels of AA and PGE2. Furthermore, PKCα-induced AA release and cPLA2phosphorylation are independent of MEK, whereas PKCα-induced COX-2 expression and PGE2 production are MEK-dependent and C/EBPβ-independent events. DA - 2001/4// PY - 2001/4// DO - 10.1124/mol.59.4.860 VL - 59 IS - 4 SP - 860-866 SN - 0026-895X ER - TY - PAT TI - Method of treating alopecia AU - Smart, R. C. AU - Oh, H.-S. C2 - 2001/// DA - 2001/// PY - 2001/// ER - TY - JOUR TI - Effectiveness of coagulants and coagulant aids for the removal of filter-clogging Synedra AU - Jun, HB AU - Lee, YL AU - Lee, BD AU - Knappe, DRU T2 - JOURNAL OF WATER SUPPLY RESEARCH AND TECHNOLOGY-AQUA AB - Research Article| May 01 2001 Effectiveness of coagulants and coagulant aids for the removal of filter-clogging Synedra Hang-Bae Jun; Hang-Bae Jun 1Department of Environmental Engineering, Chungbuk National University, CheongJu, Korea Search for other works by this author on: This Site PubMed Google Scholar Young-Ju Lee; Young-Ju Lee 1Department of Environmental Engineering, Chungbuk National University, CheongJu, Korea Search for other works by this author on: This Site PubMed Google Scholar Byung-Du Lee; Byung-Du Lee 2Department of Water Supply Operation & Maintenance, KOWACO, Taejon, Korea Search for other works by this author on: This Site PubMed Google Scholar Detlef R. U. Knappe Detlef R. U. Knappe 3Department of Civil Engineering, North Carolina State University, Raleigh, NC 27695-7908, USA Phone: 919-515-8791 Fax: 919-515-7908; E-mail: knappe@eos.ncsu.edu Search for other works by this author on: This Site PubMed Google Scholar Journal of Water Supply: Research and Technology-Aqua (2001) 50 (3): 135–148. https://doi.org/10.2166/aqua.2001.0013 Views Icon Views Article contents Figures & tables Video Audio Supplementary Data Share Icon Share Twitter LinkedIn Tools Icon Tools Cite Icon Cite Permissions Search Site Search nav search search input Search input auto suggest search filter All ContentAll JournalsThis Journal Search Advanced Search Citation Hang-Bae Jun, Young-Ju Lee, Byung-Du Lee, Detlef R. U. Knappe; Effectiveness of coagulants and coagulant aids for the removal of filter-clogging Synedra. Journal of Water Supply: Research and Technology-Aqua 1 May 2001; 50 (3): 135–148. doi: https://doi.org/10.2166/aqua.2001.0013 Download citation file: Ris (Zotero) Reference Manager EasyBib Bookends Mendeley Papers EndNote RefWorks BibTex The occurrence of Synedra spp. in the source water of the CheongJu water treatment plant (South Korea) decreased filter run times of rapid sand filters to below 5 hours. During the filter-clogging episode, full-scale Synedra removal by coagulation with polyaluminium hydrogen chloride silicate (PAHCS), flocculation and sedimentation ranged from 20 to 70%. To reduce filter clogging, strategies needed to be developed to improve the coagulation of Synedra. Jar test results showed that alum was more effective for Synedra removal than polyaluminium chloride (PACl), PAHCS and ferric chloride. At the optimum alum dose, Synedra removal in jar tests reached 88%. The addition of flocculant aids (Na- and Mg-alginate; nonionic and anionic polymers) in conjunction with alum did not improve Synedra removal. In contrast, the addition of cationic polymer in conjunction with alum improved Synedra removal to 99%. Analysis of floc with scanning electron microscopy (SEM) and light microscopy showed that the cationic polymer addition led to the formation of larger, stronger, and denser floc. More effective charge neutralization and the formation of interparticle bridges as a result of the cationic polymer addition can explain the improved incorporation of Synedra cells into settleable floc. coagulation, diatoms, filter clogging, polymers, sedimentation This content is only available as a PDF. © IWA Publishing 2001 You do not currently have access to this content. DA - 2001/6// PY - 2001/6// DO - 10.2166/aqua.2001.0013 VL - 50 IS - 3 SP - 135-148 SN - 0003-7214 KW - coagulation KW - diatoms KW - filter clogging KW - polymers KW - sedimentation ER -