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J S Taylor

Publications and source records attributed to J S Taylor.

At least 19 recordsLinked to original sources
PubMed2006

A genomic view of the sea urchin nervous system.

The sequencing of the Strongylocentrotus purpuratus genome provides a unique opportunity to investigate the function and evolution of neural genes. The neurobiology of sea urchins is of particular interest because they have a close phylogenetic relationship with chordates, yet a distinctive pentaradiate body plan and unusual neural organization. Orthologues of transcription factors that regulate neurogenesis in other animals have been identified and several are expressed in neurogenic domains before gastrulation indicating that they may operate near the top of a conserved neural gene regulatory network. A family of genes encoding voltage-gated ion channels is present but, surprisingly, genes encoding gap junction proteins (connexins and pannexins) appear to be absent. Genes required for synapse formation and function have been identified and genes for synthesis and transport of neurotransmitters are present. There is a large family of G-protein-coupled receptors, including 874 rhodopsin-type receptors, 28 metabotropic glutamate-like receptors and a remarkably expanded group of 161 secretin receptor-like proteins. Absence of cannabinoid, lysophospholipid and melanocortin receptors indicates that this group may be unique to chordates. There are at least 37 putative G-protein-coupled peptide receptors and precursors for several neuropeptides and peptide hormones have been identified, including SALMFamides, NGFFFamide, a vasotocin-like peptide, glycoprotein hormones and insulin/insulin-like growth factors. Identification of a neurotrophin-like gene and Trk receptor in sea urchin indicates that this neural signaling system is not unique to chordates. Several hundred chemoreceptor genes have been predicted using several approaches, a number similar to that for other animals. Intriguingly, genes encoding homologues of rhodopsin, Pax6 and several other key mammalian retinal transcription factors are expressed in tube feet, suggesting tube feet function as photosensory organs. Analysis of the sea urchin genome presents a unique perspective on the evolutionary history of deuterostome nervous systems and reveals new approaches to investigate the development and neurobiology of sea urchins.

Animals↗
PubMed2006

Black markets, transplant kidneys and interpersonal coercion.

One of the most common arguments against legalising markets in human kidneys is that this would result in the widespread misuse that is present in the black market becoming more prevalent. In particular, it is argued that if such markets were to be legalised, this would lead to an increase in the number of people being coerced into selling their kidneys. Moreover, such coercion would occur even if markets in kidneys were regulated, for those subject to such coercion would not be able to avail themselves of the legal protections that regulation would afford them. Despite the initial plausibility of this argument, there are three reasons to reject it. Firstly, the advantages of legalising markets in human kidneys would probably outweigh its possible disadvantages. Secondly, if it is believed that no such coercion can ever be tolerated, markets in only those human kidneys that fail to do away with coercion should be condemned. Finally, if coercion is genuinely opposed, then legalising kidney markets should be supported rather than opposed, for more people would be coerced (ie, into not selling) were such markets to be prohibited.

Coercion↗
PubMed2003

Why primiparous mothers do not breastfeed in the United States: a national survey.

AIM: To investigate primiparous women's primary reason for not breastfeeding. METHODS: We used the 1995 National Survey of Family Growth to analyze the breastfeeding behaviors of a national probability sample of 6733 first-time US mothers, aged 15 to 44 y. Main outcome measures in this cross-sectional study were the reasons for never breastfeeding and reasons for stopping breastfeeding using closed-ended, multiple choice questions. RESULTS: Most commonly, women did not breastfeed because they "preferred to bottle feed" (66.3%). The most common reason for stopping breastfeeding was that the child was "old enough to wean" (35.7%), although 15%, 34%, 54%, and 78% of those women had stopped breastfeeding by 3, 6, 9, and 12 mo, respectively. "Physical or medical problem" was reported by 14.9% of women who did not breastfeed and 26.9% of women who had stopped breastfeeding, making it the second most common reason for not breastfeeding in each group. There were significant differences across racial and ethnic groups. CONCLUSION: Additional studies are needed to better understand why women "prefer to bottle feed", especially black women. Increasingly effective programs and policies to promote breastfeeding will logically follow. Since physical and medical problems are such common reasons both for never breastfeeding and for stopping breastfeeding, individual healthcare providers can have a significant impact on breastfeeding rates and duration.

Adolescent↗
PubMed2001

Comparative genomics provides evidence for an ancient genome duplication event in fish.

There are approximately 25 000 species in the division Teleostei and most are believed to have arisen during a relatively short period of time ca. 200 Myr ago. The discovery of 'extra' Hox gene clusters in zebrafish (Danio rerio), medaka (Oryzias latipes), and pufferfish (Fugu rubripes), has led to the hypothesis that genome duplication provided the genetic raw material necessary for the teleost radiation. We identified 27 groups of orthologous genes which included one gene from man, mouse and chicken, one or two genes from tetraploid Xenopus and two genes from zebrafish. A genome duplication in the ancestor of teleost fishes is the most parsimonious explanation for the observations that for 15 of these genes, the two zebrafish orthologues are sister sequences in phylogenies that otherwise match the expected organismal tree, the zebrafish gene pairs appear to have been formed at approximately the same time, and are unlinked. Phylogenies of nine genes differ a little from the tree predicted by the fish-specific genome duplication hypothesis: one tree shows a sister sequence relationship for the zebrafish genes but differs slightly from the expected organismal tree and in eight trees, one zebrafish gene is the sister sequence to a clade which includes the second zebrafish gene and orthologues from Xenopus, chicken, mouse and man. For these nine gene trees, deviations from the predictions of the fish-specific genome duplication hypothesis are poorly supported. The two zebrafish orthologues for each of the three remaining genes are tightly linked and are, therefore, unlikely to have been formed during a genome duplication event. We estimated that the unlinked duplicated zebrafish genes are between 300 and 450 Myr. Thus, genome duplication could have provided the genetic raw material for teleost radiation. Alternatively, the loss of different duplicates in different populations (i.e. 'divergent resolution') may have promoted speciation in ancient teleost populations.

Animals↗
PubMed2001

Use of a combined enzymatic digestion/ESI mass spectrometry assay to study the effect of TATA-binding protein on photoproduct formation in a TATA box.

Recently, it was reported that TATA-binding protein (TBP) enhances (6-4) photoproduct formation in a TATA box under UVC irradiation [Aboussekhra and Thoma (1999) EMBO J. 18, 433-443]. The conclusions of that study were based on an indirect enzymatic assay that was not specific for (6-4) photoproducts. Herein we report the use of a recently developed coupled enzymatic digestion/mass spectrometry assay [Wang et al. (1999) Chem. Res. Toxicol. 12, 1077-1082] to identify unambiguously and quantify the photoproducts formed in a TATA box-containing dodecamer duplex sequence in the presence or absence of TBP binding. Exposure of the adenovirus major late promoter TATA box to a high dose of UVC irradiation in the absence of the C-terminal domain of yeast TBP leads to predominant formation of the cis-syn dimer within the T(4) tract, whereas exposure in the presence of TBP leads to almost exclusive formation of the (6-4) photoproduct. In contrast, the (6-4) product is not detected at high doses of UVB irradiation in the absence of TBP but is detected in the presence of TBP, although the cis-syn product predominates. When the products of UVB irradiation were subsequently exposed to a high dose of UVC irradiation in the presence of TBP, the (6-4) photoproduct again becomes nearly the exclusive photoproduct, indicating that the cis-syn dimer is being reversed to TT by UVC light. Both cis-syn and (6-4) photoproducts are formed in approximately equal amounts upon irradiation with small doses of UVC in the presence of TBP, but the fraction of (6-4) photoproduct increases with dose. Through the use of a TATA box containing a site-specifically deuterated thymine, it was found that (6-4) photoproducts formed most selectively at the second and third positions of the T(4) tract upon either UVB or UVC irradiation in the presence of TBP. By using the same substrate, it was found that UVC-induced TA formation was inhibited by TBP binding and that TA formation was greatest at the 5' end of the TATA sequence.

Amino Acid Sequence↗
PubMed2001

Bacterial growth in distribution systems: effect of assimilable organic carbon and biodegradable dissolved organic carbon.

Two distribution systems, one treating water by ozonation and another treating water by nanofiltration in parallel with lime softening, were monitored for bacterial growth. Both systems kept disinfectant residuals such as chlorine and chloramine in their respective distribution systems. Bacterial growth was assessed by heterotrophic plate counts (HPC) on R2A agar. In the distribution systems fed by ozonated water, HPCs were correlated (R2 = 0.96) using an exponential model with the assimilable organic carbon (AOC) at each sampling site. Also, it was observed that ozonation caused a significant increase in the AOC concentration of the distribution system (over 100% increase) as well as a significant increase in the bacterial counts of the distribution system (average increase over 100%). The HPCs from the distribution systems fed by nanofiltration in parallel with lime-softening water also displayed an exponential correlation (R2 = 0.73) with an exponential model based on AOC. No significant correlation was found between bacteria growth on R2A agar and BDOC concentrations. Therefore, in agreement with previous work, bacterial growth in the distribution systems was found to correlate with AOC concentrations.

Bacteria↗
PubMed2001

Translesion synthesis by yeast DNA polymerase zeta from templates containing lesions of ultraviolet radiation and acetylaminofluorene.

In the yeast Saccharomyces cerevisiae, DNA polymerase zeta (Polzeta) is required in a major lesion bypass pathway. To help understand the role of Polzeta in lesion bypass, we have performed in vitro biochemical analyses of this polymerase in response to several DNA lesions. Purified yeast Polzeta performed limited translesion synthesis opposite a template TT (6-4) photoproduct, incorporating A or T with similar efficiencies (and less frequently G) opposite the 3' T, and predominantly A opposite the 5' T. Purified yeast Polzeta predominantly incorporated a G opposite an acetylaminofluorene (AAF)-adducted guanine. The lesion, however, significantly inhibited subsequent extension. Furthermore, yeast Polzeta catalyzed extension DNA synthesis from primers annealed opposite the AAF-guanine and the 3' T of the TT (6-4) photoproduct with varying efficiencies. Extension synthesis was more efficient when A or C was opposite the AAF-guanine, and when G was opposite the 3' T of the TT (6-4) photoproduct. In contrast, the 3' T of a cis-syn TT dimer completely blocked purified yeast Polzeta, whereas the 5' T was readily bypassed. These results support the following dual-function model of Polzeta. First, Polzeta catalyzes nucleotide incorporation opposite AAF-guanine and TT (6-4) photoproduct with a limited efficiency. Secondly, more efficient bypass of these lesions may require nucleotide incorporation by other DNA polymerases followed by extension DNA synthesis by Polzeta.

2-Acetylaminofluorene↗
PubMed2001

Response of human DNA polymerase iota to DNA lesions.

Lesion bypass is an important mechanism to overcome replication blockage by DNA damage. Translesion synthesis requires a DNA polymerase (Pol). Human Pol iota encoded by the RAD30B gene is a recently identified DNA polymerase that shares sequence similarity to Pol eta. To investigate whether human Pol iota plays a role in lesion bypass we examined the response of this polymerase to several types of DNA damage in vitro. Surprisingly, 8-oxoguanine significantly blocked human Pol iota. Nevertheless, translesion DNA synthesis opposite 8-oxoguanine was observed with increasing concentrations of purified human Pol iota, resulting in predominant C and less frequent A incorporation opposite the lesion. Opposite a template abasic site human Pol iota efficiently incorporated a G, less frequently a T and even less frequently an A. Opposite an AAF-adducted guanine, human Pol iota was able to incorporate predominantly a C. In both cases, however, further DNA synthesis was not observed. Purified human Pol iota responded to a template TT (6-4) photoproduct by inserting predominantly an A opposite the 3' T of the lesion before aborting DNA synthesis. In contrast, human Pol iota was largely unresponsive to a template TT cis-syn cyclobutane dimer. These results suggest a role for human Pol iota in DNA lesion bypass.

Acetoxyacetylaminofluorene↗
PubMed2001

The reaction mechanism of DNA glycosylase/AP lyases at abasic sites.

DNA glycosylase and glycosylase/abasic (AP) lyases are the enzymes responsible for initiating the base excision repair pathway by recognizing the damaged target base and catalyzing the breakage of the base-sugar glycosyl bond. The subset of glycosylases that have an associated AP lyase activity also catalyze DNA strand breakage at the resulting or preexisting AP site via a beta-elimination reaction, proceeding from an enzyme-DNA imino intermediate. Two distinct mechanisms have been proposed for the formation of this intermediate. These mechanisms essentially differ in the nature of the first bond broken and the timing of the opening of the deoxyribose ring. The data presented here demonstrate that the combined rate of sugar ring opening and reduction of the sugar is significantly slower than the rate of formation of a T4-pyrimidine dimer glycosylase (T4-pdg)-DNA intermediate. Using a methyl-deoxyribofuranose AP-site analogue that is incapable of undergoing sugar ring opening, it was demonstrated that the T4-pdg reaction can initiate at the ring-closed form, albeit at a drastically reduced rate. T4-pdg preferentially cleaved the beta-anomer of the methyl-deoxyribofuranose AP site analogue. This is consistent with a mechanism in which the methoxy group is backside-displaced by the amino group from the alpha-face of the deoxyribofuranose ring. In addition, studies examining rates of sugar-aldehyde reduction and the sodium borohydride concentration dependence of the rate of formation of the covalent imine intermediate suggest that the reduction of the intermediate is rate-limiting in the reaction.

Bacteriophage T4↗
PubMed2001

A method for quantification from composite spectra: application to the determination of isomeric DNA photoproducts by tandem mass spectrometry.

Quantification of mixture components from their composite optical or mass spectra is a common need in analytical chemistry. We encountered the need when applying a combination of enzymatic digestion with nuclease P1 and tandem mass spectrometry to a mixture of isomeric photomodified oligodeoxynucleotides. In the procedure, we collisionally activated the [M - H]- or [M + Na - 2H]- ion of trinucleotide triphosphates, which were extricated enzymatically from the larger, damaged oligodeoxynucleotides, and we measured the relative abundances of characteristic fragment ions. The results sometimes yield curved calibrations for plots of the relative fragment ion abundances in the product ion spectra of isomers versus their relative amounts. We developed a normalized linear model, which brings understanding to the nonlinear plots and allows quantification of the mixture components from their composite spectra. The outcome demonstrates a general quantification procedure and shows that different yields for generating fragment ions from different constituents of the mixture cause the curved calibration lines.

DNA↗
PubMed2001

Phototriggered formation and repair of DNA containing a site-specific single strand break of the type produced by ionizing radiation or AP lyase activity.

DNA strand breaks are produced by a variety of agents and processes such as ionizing radiation, xenobiotics, oxidative metabolism, and enzymatic processing of DNA base damage. One of the major types of strand breaks produced by these processes is a single nucleotide gap terminating in 5'- and 3'-phosphates. Previously, we had developed a method for sequence-specifically producing such phosphate-terminated strand breaks in an oligodeoxynucleotide by way of two photochemically activated (caged) building blocks placed in tandem. We now report the design and synthesis of a single caged building block consisting of 1,3-(2-nitrophenyl)-1,3-propanediol, for producing phosphate-terminated strand breaks, and its use producing such a break at a specific site in a double-stranded circular DNA vector. To produce the site-specific break in a duplex vector, a primer containing the caged single strand break was extended opposite the single strand form of a circular DNA vector followed by enzymatic ligation and purification. The single strand break could then be formed in quantitative yield by irradiation of the vector with 365 nm light. In contrast to a previous study, it was found that the strand break can be repaired by Escherichia coli DNA polymerase I and E. coli DNA ligase alone, though less efficiently than in the presence of the 3'-phosphate processing enzyme E. coli endonuclease IV. Repair in the absence of endonuclease IV could be attributed to hydrolysis of the 3'-phosphate in the presence of dNTP and to a lesser extent to exonucleolytic removal of the 3'-phosphate-bearing terminal nucleotide by way of the 3' --> 5' exonuclease activity of polymerase I. This work demonstrates that specialized 3'-end processing enzymes such as endonuclease IV or exonuclease III are not absolutely required for repair of phosphate-terminated gaps. In addition to preparing single strand breaks, the caged building block described should also be useful for preparing double strand breaks and multiply damaged sites that might otherwise be difficult to prepare by other methods due to their lability.

Bacteriophage T4↗
PubMed2001

Simplified analysis of contaminant rejection during ground- and surface water nanofiltration under the information collection rule.

A simple, closed-form analytical expression based on the homogenous solution diffusion model is derived for contaminant removal during nanofiltration (NF) of ground and surface water. Solute permeation and back-diffusion coefficients were used as fitting parameters to model rejection characteristics of four thin-film composite NF membranes under conditions typical of drinking water NF. Nonlinear fits of the model to experimental data suggests that the United States Environmental Protection Agency's (USEPA)'s Information Collection Rule protocol for bench-scale studies could be improved to obtain greater precision of the mass transfer coefficients. The model was found to fit rejection data for several water treatment contaminants including total organic carbon, precursors to total organic halide, four trihalomethanes and nine haloacetic acids containing chlorine and bromine, calcium and total hardness, alkalinity and conductivity. The simplified approach to mass transfer calculations from multisolute systems suggests that feed water recovery has a stronger influence on contaminant rejection than permeate flux. Evidence for coupled transport of divalent inorganic ions is also presented. Even though the model developed does not account for ion coupling and cannot be applied in a purely predictive mode, it can assist in the better design and interpretation of data obtained from site-specific pilot-scale water treatment NF studies conducted in support of plant design.

Acetates↗
PubMed2001

Genome duplication, divergent resolution and speciation.

What are the evolutionary consequences of gene duplication? One answer is speciation, according to a model initially called Reciprocal Silencing and recently expanded and renamed Divergent Resolution. This model shows how the loss of different copies of a duplicated gene in allopatric populations (divergent resolution) can promote speciation by genetically isolating these populations should they become reunited. Genome duplication events produce thousands of duplicated genes. Therefore, lineages with a history of genome duplication might have been especially prone to speciation via divergent resolution.

Animals↗
PubMed2001

2R or not 2R?

Explore the source record for details and available documents.

Animals↗
PubMed2001

Uranium decay products found on Mir space blanket mitt.

The space blanket mitt which covered the Trek detector on Mir during four years of orbital flight has been measured for gamma radiation with HPGe and multidimensional spectrometers. Difference spectra from very-long-period spectrometer runs on the mitt and on a similar non-deployed mitt from the same manufacturer show that the mitt has acquired small but significant amounts of gamma radioactivity during orbital flight. Twelve gamma-ray peaks have been measured in the difference spectra, including peaks identified as due to 214Bi and 214Pb from the uranium-radium alpha decay series, and others possibly due to the uranium-actinium series. This implies the presence of a sparse population of uranium decay products in lower orbital space which can only have come from nuclear explosions, burned-up satellite nuclear batteries, the solar wind, or supernova fragments in the local interstellar medium.

Gamma Rays↗
PubMed2001

Nucleic acid triggered catalytic drug and probe release: a new concept for the design of chemotherapeutic and diagnostic agents.

Recently, we described a new concept for the design of highly selective antiviral and anticancer chemotherapeutic agents that makes use of a disease-specific nucleic acid sequence to template the association of a prodrug with a catalyst which catalyzes the release of the drug. Herein, we report on the effect of mismatches, sterics, and electronics on the rate and specificity of drug and probe release in both two and three component model systems, and on the stability of the prodrug linker in human serum.

Antineoplastic Agents↗