Aplicación de la metodología ISA al análisis de la secuencia de pérdida del sistema de agua de refrigeración de componentes en una central nuclear con reactor de agua a presión

La metodología Integrated Safety Analysis (ISA), desarrollada en el área de Modelación y Simulación (MOSI) del Consejo de Seguridad Nuclear (CSN), es un método de Análisis Integrado de Seguridad que está siendo evaluado y analizado mediante diversas aplicaciones impulsadas por el CSN; el análisis integrado de seguridad, combina las técnicas evolucionadas de los análisis de seguridad al uso: deterministas y probabilistas. Se considera adecuado para sustentar la Regulación Informada por el Riesgo (RIR), actual enfoque dado a la seguridad nuclear y que está siendo desarrollado y aplicado en todo el mundo. En este contexto se enmarcan, los proyectos Safety Margin Action Plan (SMAP) y Safety Margin Assessment Application (SM2A), impulsados por el Comité para la Seguridad de las Instalaciones Nucleares (CSNI) de la Agencia de la Energía Nuclear (NEA) de la Organización para la Cooperación y el Desarrollo Económicos (OCDE) en el desarrollo del enfoque adecuado para el uso de las metodologías integradas en la evaluación del cambio en los márgenes de seguridad debidos a cambios en las condiciones de las centrales nucleares. El comité constituye un foro para el intercambio de información técnica y de colaboración entre las organizaciones miembro, que aportan sus propias ideas en investigación, desarrollo e ingeniería. La propuesta del CSN es la aplicación de la metodología ISA, especialmente adecuada para el análisis según el enfoque desarrollado en el proyecto SMAP que pretende obtener los valores best-estimate con incertidumbre de las variables de seguridad que son comparadas con los límites de seguridad, para obtener la frecuencia con la que éstos límites son superados. La ventaja que ofrece la ISA es que permite el análisis selectivo y discreto de los rangos de los parámetros inciertos que tienen mayor influencia en la superación de los límites de seguridad, o frecuencia de excedencia del límite, permitiendo así evaluar los cambios producidos por variaciones en el diseño u operación de la central que serían imperceptibles o complicados de cuantificar con otro tipo de metodologías. La ISA se engloba dentro de las metodologías de APS dinámico discreto que utilizan la generación de árboles de sucesos dinámicos (DET) y se basa en la Theory of Stimulated Dynamics (TSD), teoría de fiabilidad dinámica simplificada que permite la cuantificación del riesgo de cada una de las secuencias. Con la ISA se modelan y simulan todas las interacciones relevantes en una central: diseño, condiciones de operación, mantenimiento, actuaciones de los operadores, eventos estocásticos, etc. Por ello requiere la integración de códigos de: simulación termohidráulica y procedimientos de operación; delineación de árboles de sucesos; cuantificación de árboles de fallos y sucesos; tratamiento de incertidumbres e integración del riesgo. La tesis contiene la aplicación de la metodología ISA al análisis integrado del suceso iniciador de la pérdida del sistema de refrigeración de componentes (CCWS) que genera secuencias de pérdida de refrigerante del reactor a través de los sellos de las bombas principales del circuito de refrigerante del reactor (SLOCA). Se utiliza para probar el cambio en los márgenes, con respecto al límite de la máxima temperatura de pico de vaina (1477 K), que sería posible en virtud de un potencial aumento de potencia del 10 % en el reactor de agua a presión de la C.N. Zion. El trabajo realizado para la consecución de la tesis, fruto de la colaboración de la Escuela Técnica Superior de Ingenieros de Minas y Energía y la empresa de soluciones tecnológicas Ekergy Software S.L. (NFQ Solutions) con el área MOSI del CSN, ha sido la base para la contribución del CSN en el ejercicio SM2A. Este ejercicio ha sido utilizado como evaluación del desarrollo de algunas de las ideas, sugerencias, y los algoritmos detrás de la metodología ISA. Como resultado se ha obtenido un ligero aumento de la frecuencia de excedencia del daño (DEF) provocado por el aumento de potencia. Este resultado demuestra la viabilidad de la metodología ISA para obtener medidas de las variaciones en los márgenes de seguridad que han sido provocadas por modificaciones en la planta. También se ha mostrado que es especialmente adecuada en escenarios donde los eventos estocásticos o las actuaciones de recuperación o mitigación de los operadores pueden tener un papel relevante en el riesgo. Los resultados obtenidos no tienen validez más allá de la de mostrar la viabilidad de la metodología ISA. La central nuclear en la que se aplica el estudio está clausurada y la información relativa a sus análisis de seguridad es deficiente, por lo que han sido necesarias asunciones sin comprobación o aproximaciones basadas en estudios genéricos o de otras plantas. Se han establecido tres fases en el proceso de análisis: primero, obtención del árbol de sucesos dinámico de referencia; segundo, análisis de incertidumbres y obtención de los dominios de daño; y tercero, cuantificación del riesgo. Se han mostrado diversas aplicaciones de la metodología y ventajas que presenta frente al APS clásico. También se ha contribuido al desarrollo del prototipo de herramienta para la aplicación de la metodología ISA (SCAIS). ABSTRACT The Integrated Safety Analysis methodology (ISA), developed by the Consejo de Seguridad Nuclear (CSN), is being assessed in various applications encouraged by CSN. An Integrated Safety Analysis merges the evolved techniques of the usually applied safety analysis methodologies; deterministic and probabilistic. It is considered as a suitable tool for assessing risk in a Risk Informed Regulation framework, the approach under development that is being adopted on Nuclear Safety around the world. In this policy framework, the projects Safety Margin Action Plan (SMAP) and Safety Margin Assessment Application (SM2A), set up by the Committee on the Safety of Nuclear Installations (CSNI) of the Nuclear Energy Agency within the Organization for Economic Co-operation and Development (OECD), were aimed to obtain a methodology and its application for the integration of risk and safety margins in the assessment of the changes to the overall safety as a result of changes in the nuclear plant condition. The committee provides a forum for the exchange of technical information and cooperation among member organizations which contribute their respective approaches in research, development and engineering. The ISA methodology, proposed by CSN, specially fits with the SMAP approach that aims at obtaining Best Estimate Plus Uncertainty values of the safety variables to be compared with the safety limits. This makes it possible to obtain the exceedance frequencies of the safety limit. The ISA has the advantage over other methods of allowing the specific and discrete evaluation of the most influential uncertain parameters in the limit exceedance frequency. In this way the changes due to design or operation variation, imperceptibles or complicated to by quantified by other methods, are correctly evaluated. The ISA methodology is one of the discrete methodologies of the Dynamic PSA framework that uses the generation of dynamic event trees (DET). It is based on the Theory of Stimulated Dynamics (TSD), a simplified version of the theory of Probabilistic Dynamics that allows the risk quantification. The ISA models and simulates all the important interactions in a Nuclear Power Plant; design, operating conditions, maintenance, human actuations, stochastic events, etc. In order to that, it requires the integration of codes to obtain: Thermohydraulic and human actuations; Even trees delineation; Fault Trees and Event Trees quantification; Uncertainty analysis and risk assessment. This written dissertation narrates the application of the ISA methodology to the initiating event of the Loss of the Component Cooling System (CCWS) generating sequences of loss of reactor coolant through the seals of the reactor coolant pump (SLOCA). It is used to test the change in margins with respect to the maximum clad temperature limit (1477 K) that would be possible under a potential 10 % power up-rate effected in the pressurized water reactor of Zion NPP. The work done to achieve the thesis, fruit of the collaborative agreement of the School of Mining and Energy Engineering and the company of technological solutions Ekergy Software S.L. (NFQ Solutions) with de specialized modeling and simulation branch of the CSN, has been the basis for the contribution of the CSN in the exercise SM2A. This exercise has been used as an assessment of the development of some of the ideas, suggestions, and algorithms behind the ISA methodology. It has been obtained a slight increase in the Damage Exceedance Frequency (DEF) caused by the power up-rate. This result shows that ISA methodology allows quantifying the safety margin change when design modifications are performed in a NPP and is specially suitable for scenarios where stochastic events or human responses have an important role to prevent or mitigate the accidental consequences and the total risk. The results do not have any validity out of showing the viability of the methodology ISA. Zion NPP was retired and information of its safety analysis is scarce, so assumptions without verification or approximations based on generic studies have been required. Three phases are established in the analysis process: first, obtaining the reference dynamic event tree; second, uncertainty analysis and obtaining the damage domains; third, risk quantification. There have been shown various applications of the methodology and advantages over the classical PSA. It has also contributed to the development of the prototype tool for the implementation of the ISA methodology (SCAIS).

Caracterización teórica y experimental de un reactor de lecho fluidizado para operaciones de termoquímica solar

El objetivo del presente trabajo es la caracterización, tanto teórica como experimental, de un reactor de lecho fluidizado para operaciones de termoquímica solar. En el apartado experimental se emplea un reactor de lecho fluidizado cedido por el CIEMAT. Para la parte numérica, se realiza un análisis óptico-energético y un estudio termofluidodinámico (dinámica de fluidos computacional, DFC). Se llevan a cabo ensayos en frío y en caliente para la parte experimental. Los ensayos en frío tienen el objetivo de demostrar la teoría establecida de fluidización, usando partículas de alúmina y ferritas de níquel. Los ensayos en caliente se realizan para observar el comportamiento de un reactor de lecho fluidizado irradiado. Se emplean partículas de carburo de silicio (SiC) y ferritas de níquel. El análisis óptico-energético se realiza usando el software de trazado de rayos TracePro. La simulación se hace con partículas de α-SiC. Las propiedades del material se obtienen con un software adicional. Por otra parte, el estudio DFC se realiza con una licencia académica de Ansys Fluent. Se hacen 2 simulaciones de un modelo euleriano de 2 fases, sin condiciones de calor y con 2 paredes con una temperatura fijada.

Use of tomato and cucumber horticulture by-products in goat diets: effects o nrumen fermentation and microbial communities in batch and continuous cultures

Two in vitro experiments were conducted to analyse the effects of replacing dietary barley grain with wastes of tomato and cucumber fruits and a 1 : 1 tomato : cucumber mixture on rumen fermentation characteristics and microbial abundance. The control (CON) substrate contained 250 g/kg of barley grain on a dry matter (DM) basis, and another 15 substrates were formulated by replacing 50, 100, 150, 200 or 250 g of barley grain/kg with the same amount (DM basis) of tomato or cucumber fruits or 1 : 1 tomato : cucumber mixture. In Expt 1, all substrates were incubated in batch cultures with rumen micro-organisms from goats for 24 h. Increasing amounts of tomato, cucumber and the mixture of both fruits in the substrate increased final pH and gas production, without changes in final ammonia-nitrogen (NH3-N) concentrations, substrate degradability and total volatile fatty acid (VFA) production, indicating that there were no detrimental effects of any waste fruits on rumen fermentation. Therefore, in Expt 2 the substrates including 250 g of waste fruits (T250, C250 and M250 for tomato, cucumber and the mixture of both fruits, respectively) and the CON substrate were incubated in single-flow continuous-culture fermenters for 8 days. Total VFA production did not differ among substrates, but there were differences in VFA profile. Molar proportions of propionate, isobutyrate and isovalerate were lower and acetate : propionate ratio was greater for T250 compared with CON substrate. Fermentation of substrates containing cucumber (C250 and M250) resulted in lower proportions of acetate, isobutyrate and isovalerate and acetate : propionate ratio, but greater butyrate proportions than the CON substrate. Carbohydrate degradability and microbial N synthesis tended to be lower for substrates containing cucumber than for the CON substrate, but there were no differences between CON and T250 substrates. Abundance of total bacteria, Fibrobacter succinogenes and Ruminococcus flavefaciens, fungi, methanogenic archaea and protozoa were similar in fermenters fed T250 and CON substrates, but fermenters fed C250 and M250 substrates had lower abundances of R. flavefaciens, fungi and protozoa than those fed the CON substrate. Results indicated that tomato fruits could replace dietary barley grain up to 250 g/kg of substrate DM without noticeable effects on rumen fermentation and microbial populations, but the inclusion of cucumber fruits at 250 g/kg of substrate DM negatively affected some microbial populations as it tended to reduce microbial N synthesis and changed the VFA profile. More studies are needed to identify the dietary inclusion level of cucumber which produces no detrimental effects on rumen fermentation and microbial growth.

Comparison of fermentation characteristics and bacterial diversity in the rumen of sheep and batch cultures of rumen microorganisms

The objective of the current study was to assess how closely batch cultures (BC) of rumen microorganisms can mimic the dietary differences in fermentation characteristics found in the rumen, and to analyse changes in bacterial diversity over the in vitro incubation period. Four ruminally and duodenally cannulated sheep were fed four diets having forage : concentrate ratios (FCR) of 70 : 30 or 30 : 70, with either alfalfa hay or grass hay as forage. Rumen fluid from each sheep was used to inoculate BC containing the same diet fed to the donor sheep, and the main rumen fermentation parameters were determined after 24 h of incubation. There were differences between BC and sheep in the magnitude of most measured parameters, but BC detected differences among diets due to forage type similar to those found in sheep. In contrast, BC did not reproduce the dietary differences due to FCR found in sheep for pH, degradability of neutral detergent fibre and total volatile fatty acid (VFA) concentrations. There were differences between systems in the magnitude of most determined parameters and BC showed higher pH values and NH3–N concentrations, but lower fibre degradability and VFA and lactate concentrations compared with sheep. There were significant relationships between in vivo and in vitro values for molar proportions of acetate, propionate and butyrate, and the acetate : propionate ratio. The automated ribosomal intergenic spacer analysis (ARISA) of 16S ribosomal deoxyribonucleic acid showed that FCR had no effect on bacterial diversity either in the sheep rumen fluid used as inoculum (IN) or in BC samples. In contrast, bacterial diversity was greater with alfalfa hay diets than those with grass hay in the IN, but was unaffected by forage type in the BC. Similarity index between the bacterial communities in the inocula and those in the BC ranged from 67·2 to 74·7%, and was unaffected by diet characteristics. Bacterial diversity was lower in BC than in the inocula with 14 peaks out of a total of 181 detected in the ARISA electropherograms never appearing in BC samples, which suggests that incubation conditions in the BC may have caused a selection of some bacterial strains. However, each BC sample showed the highest similarity index with its corresponding rumen IN, which highlights the importance of using rumen fluid from donors fed a diet similar to that being incubated in BC when conducting in vitro experiments.

Complete sequencing of the Fugu WAGR region from WT1 to PAX6: Dramatic compaction and conservation of synteny with human chromosome 11p13

The pufferfish Fugu rubripes has a genome ≈7.5 times smaller than that of mammals but with a similar number of genes. Although conserved synteny has been demonstrated between pufferfish and mammals across some regions of the genome, there is some controversy as to what extent Fugu will be a useful model for the human genome, e.g., [Gilley, J., Armes, N. & Fried, M. (1997) Nature (London) 385, 305–306]. We report extensive conservation of synteny between a 1.5-Mb region of human chromosome 11 and <100 kb of the Fugu genome in three overlapping cosmids. Our findings support the idea that the majority of DNA in the region of human chromosome 11p13 is intergenic. Comparative analysis of three unrelated genes with quite different roles, WT1, RCN1, and PAX6, has revealed differences in their structural evolution. Whereas the human WT1 gene can generate 16 protein isoforms via a combination of alternative splicing, RNA editing, and alternative start site usage, our data predict that Fugu WT1 is capable of generating only two isoforms. This raises the question of the extent to which the evolution of WT1 isoforms is related to the evolution of the mammalian genitourinary system. In addition, this region of the Fugu genome shows a much greater overall compaction than usual but with significant noncoding homology observed at the PAX6 locus, implying that comparative genomics has identified regulatory elements associated with this gene.

Direct sequencing of bacterial and P1 artificial chromosome-nested deletions for identifying position-specific single-nucleotide polymorphisms

A loxP-transposon retrofitting strategy for generating large nested deletions from one end of the insert DNA in bacterial artificial chromosomes and P1 artificial chromosomes was described recently [Chatterjee, P. K. & Coren, J. S. (1997) Nucleic Acids Res. 25, 2205–2212]. In this report, we combine this procedure with direct sequencing of nested-deletion templates by using primers located in the transposon end to illustrate its value for position-specific single-nucleotide polymorphism (SNP) discovery from chosen regions of large insert clones. A simple ampicillin sensitivity screen was developed to facilitate identification and recovery of deletion clones free of transduced transposon plasmid. This directed approach requires minimal DNA sequencing, and no in vitro subclone library generation; positionally oriented SNPs are a consequence of the method. The procedure is used to discover new SNPs as well as physically map those identified from random subcloned libraries or sequence databases. The deletion templates, positioned SNPs, and markers are also used to orient large insert clones into a contig. The deletion clone can serve as a ready resource for future functional genomic studies because each carries a mammalian cell-specific antibiotic resistance gene from the transposon. Furthermore, the technique should be especially applicable to the analysis of genomes for which a full genome sequence or radiation hybrid cell lines are unavailable.

Evolution of paired domains: Isolation and sequencing of jellyfish and hydra Pax genes related to Pax-5 and Pax-6

Pax proteins are a family of transcription factors with a highly conserved paired domain; many members also contain a paired-type homeodomain and/or an octapeptide. Nine mammalian Pax genes are known and classified into four subgroups: Pax-1/9, Pax-2/5/8, Pax-3/7, and Pax-4/6. Most of these genes are involved in nervous system development. In particular, Pax-6 is a key regulator that controls eye development in vertebrates and Drosophila. Although the Pax-4/6 subgroup seems to be more closely related to Pax-2/5/8 than to Pax-3/7 or Pax-1/9, its evolutionary origin is unknown. We therefore searched for a Pax-6 homolog and related genes in Cnidaria, which is the lowest phylum of animals that possess a nervous system and eyes. A sea nettle (a jellyfish) genomic library was constructed and two pax genes (Pax-A and -B) were isolated and partially sequenced. Surprisingly, unlike most known Pax genes, the paired box in these two genes contains no intron. In addition, the complete cDNA sequences of hydra Pax-A and -B were obtained. Hydra Pax-B contains both the homeodomain and the octapeptide, whereas hydra Pax-A contains neither. DNA binding assays showed that sea nettle Pax-A and -B and hydra Pax-A paired domains bound to a Pax-5/6 site and a Pax-5 site, although hydra Pax-B paired domain bound neither. An alignment of all available paired domain sequences revealed two highly conserved regions, which cover the DNA binding contact positions. Phylogenetic analysis showed that Pax-A and especially Pax-B were more closely related to Pax-2/5/8 and Pax-4/6 than to Pax-1/9 or Pax-3/7 and that the Pax genes can be classified into two supergroups: Pax-A/Pax-B/Pax-2/5/8/4/6 and Pax-1/9/3/7. From this analysis and the gene structure, we propose that modern Pax-4/6 and Pax-2/5/8 genes evolved from an ancestral gene similar to cnidarian Pax-B, having both the homeodomain and the octapeptide.

Multiple-complete-digest restriction fragment mapping: Generating sequence-ready maps for large-scale DNA sequencing

Multiple-complete-digest mapping is a DNA mapping technique based on complete-restriction-digest fingerprints of a set of clones that provides highly redundant coverage of the mapping target. The maps assembled from these fingerprints order both the clones and the restriction fragments. Maps are coordinated across three enzymes in the examples presented. Starting with yeast artificial chromosome contigs from the 7q31.3 and 7p14 regions of the human genome, we have produced cosmid-based maps spanning more than one million base pairs. Each yeast artificial chromosome is first subcloned into cosmids at a redundancy of ×15–30. Complete-digest fragments are electrophoresed on agarose gels, poststained, and imaged on a fluorescent scanner. Aberrant clones that are not representative of the underlying genome are rejected in the map construction process. Almost every restriction fragment is ordered, allowing selection of minimal tiling paths with clone-to-clone overlaps of only a few thousand base pairs. These maps demonstrate the practicality of applying the experimental and software-based steps in multiple-complete-digest mapping to a target of significant size and complexity. We present evidence that the maps are sufficiently accurate to validate both the clones selected for sequencing and the sequence assemblies obtained once these clones have been sequenced by a “shotgun” method.

Cloning and Sequencing of a Protein Involved in Phagosomal Membrane Fusion in Paramecium

An mAb was raised to the C5 phagosomal antigen in Paramecium multimicronucleatum. To determine its function, the cDNA and genomic DNA encoding C5 were cloned. This antigen consisted of 315 amino acid residues with a predicted molecular weight of 36,594, a value similar to that determined by SDS-PAGE. Sequence comparisons uncovered a low but significant homology with a Schizosaccharomyces pombe protein and the C-terminal half of the β-fructofuranosidase protein of Zymomonas mobilis. Lacking an obvious transmembrane domain or a possible signal sequence at the N terminus, C5 was predicted to be a soluble protein, whereas immunofluorescence data showed that it was present on the membranes of vesicles and digestive vacuoles (DVs). In cells that were minimally permeabilized but with intact DVs, C5 was found to be located on the cytosolic surface of the DV membranes. Immunoblotting of proteins from the purified and KCl-washed DVs showed that C5 was tightly bound to the DV membranes. Cryoelectron microscopy also confirmed that C5 was on the cytosolic surface of the discoidal vesicles, acidosomes, and lysosomes, organelles known to fuse with the membranes of the cytopharynx, the DVs of stages I (DV-I) and II (DV-II), respectively. Although C5 was concentrated more on the mature than on the young DV membranes, the striking observation was that the cytopharyngeal membrane that is derived from the discoidal vesicles was almost devoid of C5. Approximately 80% of the C5 was lost from the discoidal vesicle-derived membrane after this membrane fused with the cytopharyngeal membrane. Microinjection of the mAb to C5 greatly inhibited the fusion of the discoidal vesicles with the cytopharyngeal membrane and thus the incorporation of the discoidal vesicle membranes into the DV membranes. Taken together, these results suggest that C5 is a membrane protein that is involved in binding and/or fusion of the discoidal vesicles with the cytopharyngeal membrane that leads to DV formation.

Automated parallel DNA sequencing on multiple channel microchips

We report automated DNA sequencing in 16-channel microchips. A microchip prefilled with sieving matrix is aligned on a heating plate affixed to a movable platform. Samples are loaded into sample reservoirs by using an eight-tip pipetting device, and the chip is docked with an array of electrodes in the focal plane of a four-color scanning detection system. Under computer control, high voltage is applied to the appropriate reservoirs in a programmed sequence that injects and separates the DNA samples. An integrated four-color confocal fluorescent detector automatically scans all 16 channels. The system routinely yields more than 450 bases in 15 min in all 16 channels. In the best case using an automated base-calling program, 543 bases have been called at an accuracy of >99%. Separations, including automated chip loading and sample injection, normally are completed in less than 18 min. The advantages of DNA sequencing on capillary electrophoresis chips include uniform signal intensity and tolerance of high DNA template concentration. To understand the fundamentals of these unique features we developed a theoretical treatment of cross-channel chip injection that we call the differential concentration effect. We present experimental evidence consistent with the predictions of the theory.

Automated de novo sequencing of proteins by tandem high-resolution mass spectrometry

A de novo sequencing program for proteins is described that uses tandem MS data from electron capture dissociation and collisionally activated dissociation of electrosprayed protein ions. Computer automation is used to convert the fragment ion mass values derived from these spectra into the most probable protein sequence, without distinguishing Leu/Ile. Minimum human input is necessary for the data reduction and interpretation. No extra chemistry is necessary to distinguish N- and C-terminal fragments in the mass spectra, as this is determined from the electron capture dissociation data. With parts-per-million mass accuracy (now available by using higher field Fourier transform MS instruments), the complete sequences of ubiquitin (8.6 kDa) and melittin (2.8 kDa) were predicted correctly by the program. The data available also provided 91% of the cytochrome c (12.4 kDa) sequence (essentially complete except for the tandem MS-resistant region K13–V20 that contains the cyclic heme). Uncorrected mass values from a 6-T instrument still gave 86% of the sequence for ubiquitin, except for distinguishing Gln/Lys. Extensive sequencing of larger proteins should be possible by applying the algorithm to pieces of ≈10-kDa size, such as products of limited proteolysis.

Sequencing of 3-O sulfate containing heparin decasaccharides with a partial antithrombin III binding site

Heparin- and heparan sulfate-like glycosaminoglycans (HLGAGs) represent an important class of molecules that interact with and modulate the activity of growth factors, enzymes, and morphogens. Of the many biological functions for this class of molecules, one of its most important functions is its interaction with antithrombin III (AT-III). AT-III binding to a specific heparin pentasaccharide sequence, containing an unusual 3-O sulfate on a N-sulfated, 6-O sulfated glucosamine, increases 1,000-fold AT-III's ability to inhibit specific proteases in the coagulation cascade. In this manner, HLGAGs play an important biological and pharmacological role in the modulation of blood clotting. Recently, a sequencing methodology was developed to further structure-function relationships of this important class of molecules. This methodology combines a property-encoded nomenclature scheme to handle the large information content (properties) of HLGAGs, with matrix-assisted laser desorption ionization MS and enzymatic and chemical degradation as experimental constraints to rapidly sequence picomole quantities of HLGAG oligosaccharides. Using the above property-encoded nomenclature-matrix-assisted laser desorption ionization approach, we found that the sequence of the decasaccharide used in this study is ΔU2SHNS,6SI2SHNS,6SI2SHNS,6SIHNAc,6SGHNS,3S,6S (±DDD4–7). We confirmed our results by using integral glycan sequencing and one-dimensional proton NMR. Furthermore, we show that this approach is flexible and is able to derive sequence information on an oligosaccharide mixture. Thus, this methodology will make possible both the analysis of other unusual sequences in HLGAGs with important biological activity as well as provide the basis for the structural analysis of these pharamacologically important group of heparin/heparan sulfates.

Isolation and sequencing of cDNAs for splice variants of growth hormone-releasing hormone receptors from human cancers

The proliferation of various tumors is inhibited by the antagonists of growth hormone-releasing hormone (GHRH) in vitro and in vivo, but the receptors mediating the effects of GHRH antagonists have not been identified so far. Using an approach based on PCR, we detected two major splice variants (SVs) of mRNA for human GHRH receptor (GHRH-R) in human cancer cell lines, including LNCaP prostatic, MiaPaCa-2 pancreatic, MDA-MB-468 breast, OV-1063 ovarian, and H-69 small-cell lung carcinomas. In addition, high-affinity, low-capacity binding sites for GHRH antagonists were found on the membranes of cancer cell lines such as MiaPaCa-2 that are negative for the vasoactive intestinal peptide/pituitary adenylate cyclase-activating polypeptide receptor (VPAC-R) or lines such as LNCaP that are positive for VPAC-R. Sequence analysis of cDNAs revealed that the first three exons in SV1 and SV2 are replaced by a fragment of retained intron 3 having a new putative in-frame start codon. The rest of the coding region of SV1 is identical to that of human pituitary GHRH-R, whereas in SV2 exon 7 is spliced out, resulting in a 1-nt upstream frameshift, which leads to a premature stop codon in exon 8. The intronic sequence may encode a distinct 25-aa fragment of the N-terminal extracellular domain, which could serve as a proposed signal peptide. The continuation of the deduced protein sequence coded by exons 4–13 in SV1 is identical to that of pituitary GHRH-R. SV2 may encode a GHRH-R isoform truncated after the second transmembrane domain. Thus SVs of GHRH-Rs have now been identified in human extrapituitary cells. The findings support the view that distinct receptors are expressed on human cancer cells, which may mediate the antiproliferative effect of GHRH antagonists.

Fluorescence-based directed termination PCR: direct mutation characterization without sequencing

We describe a fluorescence-based directed termination PCR (fluorescent DT–PCR) that allows accurate determination of actual sequence changes without dideoxy DNA sequencing. This is achieved using near infrared dye-labeled primers and performing two PCR reactions under low and unbalanced dNTP concentrations. Visualization of resulting termination fragments is accomplished with a dual dye Li-cor DNA sequencer. As each DT–PCR reaction generates two sets of terminating fragments, a pair of complementary reactions with limiting dATP and dCTP collectively provide information on the entire sequence of a target DNA, allowing an accurate determination of any base change. Blind analysis of 78 mutants of the supF reporter gene using fluorescent DT–PCR not only correctly determined the nature and position of all types of substitution mutations in the supF gene, but also allowed rapid scanning of the signature sequences among identical mutations. The method provides simplicity in the generation of terminating fragments and 100% accuracy in mutation characterization. Fluorescent DT–PCR was successfully used to generate a UV-induced spectrum of mutations in the supF gene following replication on a single plate of human DNA repair-deficient cells. We anticipate that the automated DT–PCR method will serve as a cost-effective alternative to dideoxy sequencing in studies involving large-scale analysis for nucleotide sequence changes.

The Comprehensive Microbial Resource

One challenge presented by large-scale genome sequencing efforts is effective display of uniform information to the scientific community. The Comprehensive Microbial Resource (CMR) contains robust annotation of all complete microbial genomes and allows for a wide variety of data retrievals. The bacterial information has been placed on the Web at http://www.tigr.org/CMR for retrieval using standard web browsing technology. Retrievals can be based on protein properties such as molecular weight or hydrophobicity, GC-content, functional role assignments and taxonomy. The CMR also has special web-based tools to allow data mining using pre-run homology searches, whole genome dot-plots, batch downloading and traversal across genomes using a variety of datatypes.