bluuebunny/crossref_metadata_2025 huggingface dataset:
Repairability of Underclad Cracks in the Main Vessel and of BMI Leakages Using Robots
Authors: Thauvin Damien , Tortolano Marcel , Guillet Jacques
Published: July 2008

The increase in the authorized lifetime of nuclear power plants and the subsequent ageing of the main primary system require a new maintenance strategy. The R&D division of the French electricity company EDF is working on robotized repairing feasibility. This approach can be more relevant than the replacement of components or the development of dedicated machines for costs, delays, dosimetry. EDF R&D has engaged two anticipating studies of feasibility demonstrations: repair of underclad cracks in the main vessel and repair of the Bottom Mounted Instrument penetration (BMI). The repair of underclad cracks in the main vessel is composed of different processes including machining and welding. The main work carried out in 2005 was on the welding procedure and on the mechanical and metallurgical substantiation of this repair. Robotized machining tests have also been done. A complete repair demonstration will be performed on a mock-up in 2006. The BMI leakages reparation consists of making a weld overlay between the penetration tube and the vessel external surface. The project aims at minimizing the number of adjoining guiding tubes that will have to be removed, and at using a robot and tools able to directly operate on all the BMI.
Corrosion Resistance of Iron-Based Amorphous Metal Coatings
Authors: Farmer J. C. , Haslam J. J. , Day S. D. , Lian T. , Rebak R. , Yang N. , Aprigliano L.
Published: July 2008

New amorphous-metal thermal-spray coatings have been developed recently that may provide a viable coating option for spent nuclear fuel & high-level waste repositories [Pang et al. 2002; Shinimiya et al. 2005; Ponnambalam et al. 2004; Branagan et al. 2000–2004]. Some Fe-based amorphous-metal formulations have been found to have corrosion resistance comparable to that of high-performance alloys such as Ni-based Alloy C-22 [Farmer et al. 2004–2006]. These materials rely on Cr, Mo and W for enhanced corrosion resistance, while B is added to promote glass formation and Y is added to lower the critical cooling rate (CCR). Materials discussed in this paper include yttrium-containing SAM1651 with CCR ∼ 80 K/s and yttrium-free Formula 2C with CCR ∼ 600 K/s. While nickel-based Alloy C-22 and Type 316L stainless steel lose their resistance to corrosion during thermal spraying, Fe-based SAM1651 and Formula 2C amorphous-metal coatings can be applied with thermal spray processes without any significant loss of corrosion resistance. In the future, such corrosion-resistant thermal-spray coatings may enable the development of less expensive containers for spent nuclear fuel (SNF) and high-level waste (HLW), including enhanced multipurpose containers (MPCs), protected closure welds, and shields to protect containers from drips and falling rocks. These materials are extremely hard and provide enhanced resistance to abrasion and gouges from backfill operations. For example, Type 316L stainless steel has a hardness of approximately 150 VHN, Alloy C-22 has a hardness of approximately 250 VHN, while the Fe-based amorphous metals typically have hardness values of 1100–1300 VHN. Both Formula 2C and SAM1651 have high boron content which allow them to absorb neutrons, and therefore be used for enhanced criticality control. Cost savings can also be realized through the substitution of Fe-based alloy for Ni-based materials. Applications are also envisioned in oil & gas industry.
Effect of Diaphragm Design on Gasket Contact Pressure
Authors: Idvorian Nick , Sun Nansheng
Published: July 2008

An improved diaphragm design for use with a gasket in a pressure vessel manway opening to prevent leakage of a pressurized fluid was developed by B&W Canada. The design was developed for high pressure typical of conditions in the primary side of a PWR steam generators. The sealing is achieved by a spiral-wound graphite filled gasket which is confined in a separate diaphragm groove. The diaphragm has an internal radial groove which uses strong spring back and the pressure of the fluid to increase and maintain the gasket seating load. As a result, this design provides a self-energizing joint which can accommodate changes in gasket contact pressure due to cover rotation, stud elongation and change in fluid pressure and temperature. Finite Element (FE) Analysis indicates that a more uniform distribution of gasket contact pressure along the radial gasket width is obtained and thus the sealing performance of the gasket is improved.
Establishing Integrity Operating Windows for Hydrocarbon Process Plants
Authors: Reynolds John T.
Published: July 2008

One of the more important uses of the “99 Diseases of Hydrocarbon Process Equipment”(1) is to determine how to safely operate process pressure equipment. Such a work process thereby minimizes the impact of any potential degradation mechanisms (the 99 Diseases), by establishing the appropriate boundaries for long and short-term safe process operation. Such boundaries are called Integrity Operating Windows (IOW’s)(1).
Comparison of Pressure Vessel Codes ASME Section VIII and EN13445
Authors: Antalffy Leslie P. , Hajovsky J. J. , Miller George A. , Millet Barry J. , Pfeifer Jeffrey A. , West George T.
Published: July 2008

This paper consists of a comparative study of the primary technical, commercial, and usage differences between the American Society of Mechanical Engineers (ASME) Boiler and Pressure Vessel Code Section VIII and the European Pressure Vessel Code EN13445 (EN). This study includes a review of “Comparative Study on Pressure Equipment Standards” (hereby referenced by the “EC Study”) [see REF-1] and provides technical comparisons between the code design requirements, material properties, fabrication, and contributing effects on overall cost. This study is intended to provide a broad viewpoint on the major differences and factors to consider when choosing the most appropriate vessel design code to use.
Benchmark Natural Convection/Radiation Simulations Within an Enclosed Array of Horizontal Heated Rods
Authors: Araya Go´mez Pablo E. , Greiner Miles
Published: July 2008

Experiments performed by others measured the temperature of an 8×8 array of horizontal heated rods in air within a constant temperature enclosure. That apparatus was a scaled-down model of a spent boiling water reactor fuel assembly in a transport package. In the current work, three-dimensional computational fluid dynamics simulations of natural convection and radiation heat transfer within this domain were conducted to determine appropriate boundary conditions and benchmark the results. Initial simulations employed nearly equal specified temperatures on the walls and endplates, and insulated rod ends. They accurately reproduced the shapes of the temperature profiles in the midplane between the rod ends, but over-predicted the temperature level at the highest heat load. Simulations that included conduction within the endplates and convection from their outside surfaces more accurately modeled heat losses. They brought the midplane temperatures at the highest heat load to the measured data once an appropriate convection coefficient was determined. The simulation technique will be used to design future experiments that model heat transfer from spent fuel assemblies to highly-non-isothermal support structures.
A Critical Analysis of the Plasticity Correction Factors Proposed in the EN13445 Standard for Fatigue Analysis of Unwelded Material
Authors: Pereira He´lder F. S. G. , De Jesus Abi´lio M. P. , Ribeiro Alfredo S. , Fernandes Anto´nio A.
Published: July 2008

This paper presents a preliminary investigation about the plasticity correction factor, Ke, proposed in the Part 3–Clause 18 of the EN13445 standard, for correction of the elastic stress ranges exceeding twice the yield stress, resulting from mechanical loading. The plasticity correction factors are re-analyzed using a calculation strategy based on a comparison between results from fully-elastic and elastoplastic analyses. Several materials, elastoplastic models and geometries are considered in the study. The analyses revealed, for an important number of the situations, non-conservative results for Ke calculated according to the standard, which suggests the need for improvements in the standard procedures. However, more intensive research will be carried out to support these preliminary results. Nevertheless, authors recommend that a greater emphasis should be dedicated in the standard to the elastoplastic analysis, since the fatigue resistance data presented in the standard is strain-life type data. The elastoplastic analysis should be the preferred approach for evaluation of the strains/stresses for fatigue analysis.
Design and Manufacturing of VVER-1500 Reactor Vessel Principal Problems and Ways of Their Solution
Authors: Bakaldin V. I. , Kashirin V. I. , Petrov V. V. , Fedosov V. G. , Fedosova G. V.
Published: July 2008

The principal design problems of VVER-1500 reactor vessel and its cover are reviewed in this report. A wide range of preliminary studies carried out permitting to solve principal design and manufacturing problems of the vessel and rector cover within the framework of the draft design: • minimization of overall dimensions, • sustentation of principle possibility to provide tightness of the reactor main seal, • process work-out of the vessel, reactor cover and bottom with provision of manufacturing, • design of the reactor vessel support structures. The main attention is payed to the aspects of manufacturability of the reactor vessel and its cover in design dimensions with provision of required mechanical properties and their transportability to the constructing site. It’s required to carry out experimental work to prove manufacturing technology and to ensure mechanical properties of the following: • cover; • nozzle zone shells; • supporting shell; • bottom. To confirm construction efficiency during design life-time (60 years) the principal design approaches should be worked out on a test bench. Taking into account the complexity of the construction and restrictions of full-scale simulation, experimental confirmation of reactor vessel and cover on photoelastic epoxide resin models should be performed. Moreover, strength and life-time of threaded connection parts of the reactor main seal shall be confirmed on full-scale models.
An Improved Method for Assessing Transient Thermal Stresses at a Pressure Vessel Nozzle
Authors: Nash David H.
Published: July 2008

An improved method for assessing the transient thermal stress distribution in a pressure vessel cylindrical nozzle to sphere intersection is presented. The main purpose of the work is to develop a new method that will give a more versatile solution than the existing simplified method used in Annex G of PD5500:2003. In the first instance, Heisler’s simplified approach is improved. Thereafter, three further methods are used for comparison, namely, an improved analytical method, a numerical method and the finite element method. This allows comparison of the three techniques in contrast with the existing classical solution. From this work, new improved charts are presented which extend the range of applicability of the curves in PD5500. The design curves have been verfied and extended to cover a wider range of applicability. In addition, the approach has been improved to included the step-type as opposed to the less severe ramp-type temperature variation in the fluid temperature from inside the shell to a final steady value. Finally, some case studies are presented which show the effects and improvements gained when using the new analysis method.
Observation of Fatigue Crack Initiation and Propagation for Carbon and Low-Alloy Steels in Oxygenated Water at Elevated Temperature
Authors: Higuchi Makoto , Sakaguchi Katsumi
Published: July 2008

Low cycle fatigue life of structural materials in LWR plants decreases remarkably in elevated temperature water depending on strain rate, temperature, water chemistry and material properties. The maximum reduction rate in fatigue life for carbon and low alloy steels is over 100 in severe conditions. Fatigue life is composed of fatigue crack initiation life and consequent propagation life. It is important to know the proportion of crack initiation life to propagation life in water environment when developing a model to estimate fatigue crack initiation life. The beachmark imprinting method was used to monitor fatigue crack initiation and consequent propagation. Environmental test conditions varied widely from severely accelerated conditions of high temperature and dissolved oxygen to mild conditions of lower temperature and oxygen. Fatigue crack initiation life could be determined using the beachmark imprinting method for all test conditions. Based on obtained test results, the susceptibility of each parameter in NWC and the relationships between NWC/NW and environmental fatigue life correction factor Fen under various conditions are discussed, but a good relationship could not be detected due to widely scattered data and a model to predict fatigue crack initiation life could not be proposed.
Development of a Three-Dimensional Green’s Function and Its Application to the Fatigue Evaluation of Reactor Pressure Vessel
Authors: Ahn M. Y. , Kim J. C. , Chang Y. S. , Choi J. B. , Kim Y. J. , Jhung M. J. , Choi Y. H.
Published: July 2008

The design of major nuclear components for the prevention of fatigue failure has been achieved on the basis of ASME codes, which are usually very conservative. However, it is necessary to make it more accurate for the continued operation beyond the design life. In this paper, 3-dimensional stress and fatigue analyses reflecting entire geometry have been carried out. The number of operating transient data obtained from a monitoring system were filtered and analyzed. Then, Green’s function which transfers temperature gradient into the corresponding thermal stress is proposed and applied to critical locations of a reactor pressure vessel. The validity of proposed Green’s function is approved by comparing the result with corresponding 3-D finite element analysis results. Also, the amount of conservatism included in design transients in comparison with real transients is analyzed. The results for 3-D finite element analysis are also compared with corresponding 2-D finite element analysis results, and a considerable amount of difference was observed in terms of fatigue life. Therefore, it is expected that the proposed evaluation scheme adopting real operating data and Green’s function can provide more accurate fatigue life evaluation for a reactor pressure vessel.
Fatigue Life Assessment of Boiler Components Under Cyclic Operating Conditions
Authors: Shi Jinhua , Bell William , Laird Alan M.
Published: July 2008

A fatigue life assessment application has been implemented using the methodology given in the European Standard EN 12952-3. The assessment application can use data from the Distributed Control System (DCS) of the plant or, to improve accuracy, use component metal temperatures if thermocouples have been fitted across the component of interest. Fatigue assessments have been carried out on typical high temperature components in Heat Recovery Steam Generators (HRSGs) and a large coal fired boiler which were subject to cyclic operation. The assessments carried out used recorded plant operating DCS and thermocouple data and examined main cyclic events, e.g. shutdown/cold start-up cycle, etc. Detailed finite element analyses have also been conducted on a typical superheater header using as input the plant operating data. Calculated fatigue damage levels for both methods are compared and it is shown that comparable values are obtained. In addition, further assessment has been performed on a component where the period of operation included several shutdown/cold start cycles and many sub-cycles. On completion of the above studies, Mitsui Babcock have implemented the fatigue assessment method into a simple plant life monitoring system.
A Quantitative Link Between Recycling and Osmium Isotopes
Authors: Sobolev Alexander V. , Hofmann Albrecht W. , Brügmann Gerhard , Batanova Valentina G. , Kuzmin Dmitry V.
Published: July 2008

Recycled subducted ocean crust has been traced by elevated 187Os/188Os in some studies and by high nickel and low manganese contents in others. Here, we show that these tracers are linked for Quaternary lavas of Iceland, strengthening the recycling model. An estimate of the osmium isotopic composition of both the recycled crust and the mantle peridotite implies that Icelandic Quaternary lavas are derived in part from an ancient crustal component with model ages between 1.1 × 10
9
and 1.8 × 10
9
years and from a peridotitic end-member close to present-day oceanic mantle.
ERdj5 Is Required as a Disulfide Reductase for Degradation of Misfolded Proteins in the ER
Authors: Ushioda Ryo , Hoseki Jun , Araki Kazutaka , Jansen Gregor , Thomas David Y. , Nagata Kazuhiro
Published: July 2008

Membrane and secretory proteins cotranslationally enter and are folded in the endoplasmic reticulum (ER). Misfolded or unassembled proteins are discarded by a process known as ER-associated degradation (ERAD), which involves their retrotranslocation into the cytosol. ERAD substrates frequently contain disulfide bonds that must be cleaved before their retrotranslocation. Here, we found that an ER-resident protein ERdj5 had a reductase activity, cleaved the disulfide bonds of misfolded proteins, and accelerated ERAD through its physical and functional associations with EDEM (ER degradation–enhancing α-mannosidase–like protein) and an ER-resident chaperone BiP. Thus, ERdj5 is a member of a supramolecular ERAD complex that recognizes and unfolds misfolded proteins for their efficient retrotranslocation.
Avoiding a Cliff Dive
Authors: Frischmann Brett M.
Published: July 2008

The Future of the Internet
. And How to Stop It.
By Jonathan L. Zittrain
. Yale University Press, New Haven, CT, 2008. 350 pp. $30. ISBN 9780300124873. ()

The author argues that the runaway success of the Internet has placed it on the road to a innovation-stifling and centrally monitored (and controlled) state.
Stable Integration Vector for Nutrient Broth-Based Selection of AttenuatedListeria monocytogenesStrains with Recombinant Antigen Expression
Authors: Lenz Laurel L. , Huang William A. , Zhou Chenghui , Li Zhongxia , Calendar Richard
Published: July 2008

RecombinantListeria monocytogenesstrains induce strong cellular immune responses and may prove useful for antigen delivery for the vaccination of humans. However, the genetic systems currently available for the stable expression of recombinant antigens byL. monocytogenesrely on the use of antibiotic resistance genes. We report on a derivative, pPL2dalGlnA, of theListeria monocytogenespPL2 integration vector that completely lacks drug resistance genes. The selectable markers in pPL2dalGlnA are glutamine synthetase (GlnA) and alanine racemase (Dal). This novel vector was stably maintained in auxotropicL. monocytogenesstrains that normally required-alanine. The pPL2dalGlnA vector also partially restored the ability of anL. monocytogenesΔdalΔdatstrain to colonize the spleens and livers of infected mice. A novel, highly attenuated strain ofL. monocytogeneswith quadruple deletions was also engineered by deleting theL. monocytogenes actAandplcBvirulence genes from a ΔdalΔdatstrain. Infection of mice with recombinants of this mutant strain that express the antigen from pPL2dalGlnA were shown to elicit CD8+T-cell responses to human immunodeficiency virus Tat. This vector system is thus useful for stable antigen expression and vaccination studies.
Neisseria meningitidis
Intermediately Resistant to Penicillin and Causing Invasive Disease in South Africa in 2001 to 2005
Authors: du Plessis Mignon , von Gottberg Anne , Cohen Cheryl , de Gouveia Linda , Klugman Keith P.
Published: July 2008

Neisseria meningitidis
strains (meningococci) with decreased susceptibility to penicillin (MICs, >0.06 μg/ml) have been reported in several parts of the world, but the prevalence of such isolates in Africa is poorly described. Data from an active national laboratory-based surveillance program from January 2001 through December 2005 were analyzed. A total of 1,897 cases of invasive meningococcal disease were reported, with an average annual incidence of 0.83/100,000 population. Of these cases, 1,381 (73%) had viable isolates available for further testing; 87 (6%) of these isolates tested intermediately resistant to penicillin (Pen
i
). Pen
i
meningococcal isolates were distributed throughout all provinces and age groups, and there was no association with outcome or human immunodeficiency virus infection. The prevalence of Pen
i
was lower in serogroup A (7/295; 2%) than in serogroup B (24/314; 8%), serogroup C (9/117; 8%), serogroup Y (22/248; 9%), or serogroup W135 (25/396; 6%) (
P
= 0.02). Pulsed-field gel electrophoresis grouped 63/82 Pen
i
isolates into nine clusters, mostly according to serogroup. The clustering of patterns from Pen
i
isolates was not different from that of penicillin-susceptible isolates. Twelve sequence types were identified among 18 isolates arbitrarily selected for multilocus sequence typing. DNA sequence analysis of the
penA
gene identified 26 different alleles among the Pen
i
isolates. Intermediate penicillin resistance is thus widespread among meningococcal serogroups, has been selected in a variety of lineages, and, to date, does not appear to be associated with increased mortality. This is the first report describing the prevalence and molecular epidemiology of Pen
i
meningococcal isolates from sub-Saharan Africa.
Intragenomic Variation in the Internal Transcribed Spacer 1 Region of
Dientamoeba fragilis
as a Molecular Epidemiological Marker
Authors: Bart Aldert , van der Heijden Harold M. , Greve Sophie , Speijer Dave , Landman Wil J. , van Gool Tom
Published: July 2008

Dientamoeba fragilis
is a parasite that has been recognized to be a causative agent of gastrointestinal symptoms. Because in most studies only some infected persons experience symptoms, it is possible that
D. fragilis
is a heterogeneous species with variants that display similar morphologies but different pathogenicities. The search for genetic variation in
D. fragilis
was based on the small-subunit rRNA gene, which was not found to be useful for molecular epidemiology. In this report, we describe the isolation and characterization of additional rRNA gene cluster sequences, the internal transcribed spacer 1 (ITS-1)-5.8S rRNA gene-ITS-2 region. For comparative purposes, we also isolated the ITS-1-5.8S rRNA gene-ITS-2 region of
Histomonas meleagridis
, a protozoan parasite of birds and a close relative of
D. fragilis
. This region was found to be highly variable, and 11 different alleles of the ITS-1 sequence could be identified. Variation in the ITS-1 region was found to be intragenomic, with up to four different alleles in a single isolate. So-called C profiles were produced from the ITS-1 repertoire of single isolates,. Analysis of the C profiles of isolates from nonrelated patients identified several clearly distinguishable strains of
D. fragilis
. Within families, it was shown that members can be infected with the same or different strains of
D. fragilis
. In conclusion, the ITS-1 region can serve as a molecular epidemiological tool for the subtyping of
D. fragilis
directly from feces. This may serve as a means of studying the transmission, geographical distribution, and relationships between strains and the pathogenicity of this parasite.
Novel Multiple-Locus Variable-Number Tandem-Repeat Analysis Method for Rapid Molecular Typing of Human
Staphylococcus aureus
Authors: Ikawaty Risma , Willems Rob J. L. , Box Adrienne T. A. , Verhoef Jan , Fluit Ad C.
Published: July 2008

We evaluated the use of a novel multiple-locus variable-number tandem-repeat analysis (MLVA) method for typing of human
Staphylococcus aureus
. For a total of 150 clinical isolates, MLVA demonstrated the highest discriminatory power. MLVA correctly assigned isolates to outbreaks or identified isolates as unlinked. MLVA is a rapid and simple method for the epidemiological typing of
S. aureus
.
Impact of Diversity of Colonizing Strains on Strategies for Sampling
Escherichia coli
from Fecal Specimens
Authors: Lautenbach Ebbing , Bilker Warren B. , Tolomeo Pam , Maslow Joel N.
Published: July 2008

Of 49 subjects, 21 were colonized with more than one strain of
Escherichia coli
and 12 subjects had at least one strain present in fewer than 20% of colonies. The ability to accurately characterize
E. coli
strain diversity is directly related to the number of colonies sampled and the underlying prevalence of the strain.
Detection of
Borrelia bissettii
in Cardiac Valve Tissue of a Patient with Endocarditis and Aortic Valve Stenosis in the Czech Republic
Authors: Rudenko Nataliia , Golovchenko Maryna , Mokráček Aleš , Piskunová Natalja , Růžek Daniel , Mallatová Nadja , Grubhoffer Libor
Published: July 2008

Molecular analysis of a clinical sample confirmed the presence of
Borrelia bissettii
DNA in cardiac valve tissue from a patient with endocarditis and aortic valve stenosis. This evidence strongly supports the involvement of
B. bissettii
in Lyme disease in Europe.
Characterization of
Clostridium difficile
Strains Isolated from Patients in Ontario, Canada, from 2004 to 2006
Authors: Martin H. , Willey B. , Low D. E. , Staempfli H. R. , McGeer A. , Boerlin P. , Mulvey M. , Weese J. S.
Published: July 2008

Clostridium difficile
is the bacterium most commonly surmised to cause antimicrobial- and hospital-associated diarrhea in developed countries worldwide, and such infections are thought to be increasing in frequency and severity. A laboratory-based study was carried out to characterize
C. difficile
strains isolated from persons in Ontario, Canada, during 2004 to 2006 according to toxin type (enterotoxin A, cytotoxin B, and binary toxin [CDT]),
tcdC
gene characterization, ribotyping, pulsed-field gel electrophoresis, and toxinotyping.
Clostridium difficile
was isolated from 1,080/1,152 (94%) samples from 21 diagnostic laboratories. Isolates with toxin profiles A
+
B
+
CDT
−
, A
+
B
+
CDT
+
, A
−
B
+
CDT
−
, and A
−
B
+
CDT
+
accounted for 63%, 34%, 2.4%, and 0.6% of isolates, respectively. Alterations in
tcdC
were detected in six different ribotypes, including ribotype 027. A total of 39 different ribotypes were identified, with ribotype 027/North American pulsotype 1 (NAP1), an internationally recognized outbreak strain associated with severe disease, being the second most common ribotype (19% of isolates). Transient resistance to metronidazole was identified in 19 (1.8%) isolates. While a large number of ribotypes were found, a few predominated across the province. The high prevalence and wide distribution of ribotype 027/NAP1 are disconcerting in view of the severity of disease associated with it.
Transcription of Subgenomic mRNA of Hepatitis Delta Virus Requires a Modified Hepatitis Delta Antigen That Is Distinct from Antigenomic RNA Synthesis
Authors: Tseng Chung-Hsin , Jeng King-Song , Lai Michael M. C.
Published: July 2008

Hepatitis delta virus (HDV) contains a viroid-like, 1.7-kb circular RNA genome, which replicates via a double-rolling-circle model. However, the exact mechanism involved in HDV genome RNA replication and subgenomic mRNA transcription is still unclear. Our previous studies have shown that the replications of genomic and antigenomic HDV RNA strands have different sensitivities to α-amanitin and are associated with different nuclear bodies, suggesting that these two strands are synthesized in different transcription machineries in the cells. In this study, we developed a unique quantitative reverse transcription-PCR (qRT-PCR) procedure for detection of various HDV RNA species from an RNA transfection system. Using this qRT-PCR procedure and a series of HDV mutants, we demonstrated that Arg-13 methylation, Lys-72 acetylation, and Ser-177 phosphorylation of small hepatitis delta antigen (S-HDAg) are important for HDV mRNA transcription. In addition, these three S-HDAg modifications are dispensable for antigenomic RNA synthesis but are required for genomic RNA synthesis. Furthermore, the three RNA species had different sensitivities to acetylation and deacetylation inhibitors, showing that the metabolic requirements for the synthesis of HDV antigenomic RNA are different from those for the synthesis of genomic RNA and mRNA. In sum, our data support the hypothesis that the cellular machinery involved in the synthesis of HDV antigenomic RNA is different from that of genomic RNA synthesis and mRNA transcription, even though the antigenomic RNA and the mRNA are made from the same RNA template. We propose that acetylation and deacetylation of HDAg may provide a molecular switch for the synthesis of the different HDV RNA species.
A Mobile Functional Region of Kaposi's Sarcoma-Associated Herpesvirus ORF50 Protein Independently Regulates DNA Binding and Protein Abundance
Authors: Chang Pey-Jium , Shedd Duane , Miller George
Published: July 2008

The protein encoded by open reading frame 50 (ORF50) of Kaposi's sarcoma-associated herpesvirus (KSHV) functions as a transcriptional activator and in lytic viral DNA replication to mediate the switch from latent viral infection to the lytic phase. Here we identify regulatory regions of ORF50 protein that independently control DNA binding and abundance of the protein. One region contains a DNA-binding inhibitory sequence (DBIS) located between amino acids (aa) 490 and 535 of ORF50. A cluster of basic amino acids in this sequence is important in inhibiting DNA binding. The DBIS can function at the N or C terminus or internally in the ORF50 protein. Since the DBIS is functional in ORF50 protein purified from
Escherichia coli
, it is likely to work through an intramolecular mechanism. The second regulatory region, a protein abundance regulatory signal (PARS), consists of two components. Component I of the PARS overlaps the DBIS but can be differentiated from the DBIS by specific substitution of basic amino acid residues. Component II of PARS is located between aa 590 and 650. Mutation or deletion of either component results in abundant expression of ORF50 protein. When the two-component PARS was fused to a heterologous protein, Glutathione
S
-transferase, the fusion protein was unstable. Mutations in the DBIS or PARS impair the capacity of ORF50 to activate direct and indirect target viral promoters. Since these overlapping regulatory motifs are located in the C-terminal transactivation domain, they are likely to be important in controlling many actions of ORF50 protein.
Aichi Virus 2A Protein Is Involved in Viral RNA Replication
Authors: Sasaki Jun , Taniguchi Koki
Published: July 2008

The Aichi virus 2A protein is not a protease, unlike many other picornavirus 2A proteins, and it is related to a cellular protein, H-rev107. Here, we examined the replication properties of two 2A mutants in Vero cells and a cell-free translation/replication system. In one mutant, amino acids 36 to 126 were replaced with an unrelated amino acid sequence. In the other mutant, the NC motif conserved in the H-rev107 family of proteins was changed to alanine residues. The two mutations abolished virus replication in cells. The mutations affected both negative- and positive-strand synthesis, the defect in positive-strand synthesis being more severe than that in negative-strand synthesis.
Regioselectivity of [2+3] Cycloaddition of Triphenylnitrone to Nitroethene - AM1/COSMO Computational Study
Authors: Jasiński Radomir , Barański Andrzej
Published: July 2008

Two isomeric pathways for the [2+3] cycloaddition of triphenylnitrone to nitroethene in a dielectric medium corresponding to the relative permittivity of toluene was evaluated in therms of AM1/COSMO calculations. It was found that reaction leading to 4-nitro-2,3,3-triphenylisoxazolidine (path A) occurs via a zwitterionic intermediate, whereas the reaction leading to 5-nitro-2,3,3-triphenylisoxazolidine (path B) takes place in concerted way. The activation parameters estimated for both reaction pathways indicate that A is favored (∆GTSA = 34.33 kcal/mol; ∆GTSB = 43.37 kcal/mol). The reaction regioselectivity is in good agreement with the experimental data.
Solid-Liquid Equilibrium in the Systems with an Ionic Liquid
Authors: Sedláková Zuzana , Sauton Hélène , Hynek Vladimír , Malijevská Ivona
Published: July 2008

An active interest in ionic liquids has grown over the last years. This relatively new class of solvents appears to be potentially useful as a "greener" alternative to volatile organic compounds. This work was aimed at studying the effect of addition of the ionic liquid 1-butyl-3-methylimidazolium chloride to two systems (acetic acid (1)-formamide (2) and propionic acid (1)-formamide (2)) on formation of a compound in the solid phase. In previous work, the presence of a solid compound with a formula (CH3COOH)2·HCONH2 was investigated in the binary system acetic acid (1)-formamide (2) and a stable solid compound with a different formula CH3CH2COOH·(HCONH2)2 was found in the binary system propionic acid (1)-formamide (2). In both cases the compound formation is attributed to a strong cross-association (O···H···N). Solid-liquid equilibrium of the systems measured in this work was determined from time-temperature warming curves. In both measured ternary systems with a small addition of the ionic liquid 1-butyl-3-methylimidazolium chloride (i.e. the systems acetic acid (1)-formamide (2)-1-butyl-3-methylimidazolium chloride (3) and propionic acid (1)-formamide (2)-1-butyl-3-methylimidazolium chloride (3)) the above mentioned stable solid compounds are formed and the corresponding melting temperature of these compounds decreased. Dissociation parameters were modelled thermodynamically for solid adducts.
A Novel Route for Waste Water Treatment: Photo-Assisted Fenton Degradation of Naphthol Green B
Authors: Kumar Anil , Paliwal Mukesh , Ameta Rameshwar , Ameta Suresh C.
Published: July 2008

This study was conducted to assess the removal of the Naphthol Green B dye from aqueous medium using the photo-Fenton process. The Fenton reagent, a mixture of hydrogen peroxide and Fe3+ions, was used to generate the hydroxyl radical (•OH) that degrades the dye. Experiments were conducted at laboratory temperature and atmospheric pressure to examine the effect of reaction conditions such as the concentration of Fe3+ions, the dye and hydrogen peroxide, pH, and light intensity on the reaction rate. The progress of the photochemical degradation was monitored spectrophotometrically. The optimum photochemical degradation conditions were determined. Naphthol Green B was completely degraded into CO2and H2O. A tentative mechanism for photochemical bleaching of the dye by the photo- Fenton reaction has been proposed.
Dispersal in a sterile lichen-forming fungus,Thamnolia subuliformis(Ascomycotina: Icmadophilaceae)This paper is one of a selection of papers published in the Special Issue on Systematics Research.
Authors: Cassie David M. , Piercey-Normore Michele D.
Published: July 2008

Thamnolia subuliformis (Ehrh.) Culb. is a sterile lichen-forming ascomycete with no known sexual or vegetative reproductive structures except fragments of thallus branches. The open tundra in northern Manitoba contains fragments of T. subuliformis randomly scattered over the landscape, giving the appearance that dispersal is common. This may provide a misleading impression of gene flow, but similar fragmentation is seen in seven other locally occurring species of lichen-forming fungi. The primary objective of this study was to examine the population structure of T. subuliformis using four multilocus markers (interspersed simple sequence repeats; ISSR) and a single locus marker (the presence/absence of a group I intron in the nuclear 18S rDNA locus). Significant population subdivision is reported for two different classifications of what constitutes a population. Thallus fragments of T. subuliformis may be intact and slow growing, having accumulated tissue over a long period of time, with low levels of gene flow occurring in localized areas. The presence of the group 1 intron in localized transects may suggest either that the intron was introduced recently and has not had sufficient time to disperse among populations, or that it has been lost in other locations.
Phylogenetic patterns and diversification in the caesalpinioid legumesThis paper is one of a selection of papers published in the Special Issue on Systematics Research.
Authors: Bruneau Anne , Mercure Marjorie , Lewis Gwilym P. , Herendeen Patrick S.
Published: July 2008

Subfamily Caesalpinioideae is a paraphyletic grade of 171 genera that comprises the first branches of the Leguminosae and from which are derived the monophyletic subfamilies Mimosoideae and Papilionoideae. We have sequenced the chloroplast matK gene, and the trnL and 3′-trnK introns for 153 genera of caesalpinioid legumes. Parsimony and Bayesian phylogenetic analyses of these data support the monophyly of several major groups within the caesalpinioid legumes: the Cercideae, Detarieae, Detarieae s. str., Prioria , Amherstieae, Dialiinae, Cassia , Caesalpinia , Peltophorum , and Tachigali clades. Relationships among the first branching lineages of the legumes are not well supported, with Cercideae, Detarieae, and the genus Duparquetia alternatively resolved as sister group to all of the legumes. The division of certain large genera (e.g., Caesalpinia s. l., Bauhinia s. l.) into segregate genera generally is supported by our molecular data. Using 18 well-documented fossils as calibration points, fixing the stem node of the legumes at 65 Ma, and using the Penalised Likelihood method, we estimate the crown node of the Leguminosae at 64 Ma and the crown age of each of the major caesalpinioid lineages varying from 34 to 56 Ma. Fossil cross-validation suggests that none of the 18 fossil calibrations is internally inconsistent. Analyses done without fossil calibrations yield much younger divergence times. The age estimates for the Detarieae clade are more sensitive to the presence of calibration points than other caesalpinioid clades, a situation which we attribute to the slow rate of chloroplast DNA evolution in this group.
Lower Cretaceous conifers from Apple Bay, Vancouver Island: Picea-like leaves, Midoriphyllum piceoides gen. et sp. nov. (Pinaceae)This paper is one of a selction of papers published on the Special Issue on Systematics Research.
Authors: Stockey Ruth A. , Wiebe Nicholas J.P.
Published: July 2008

A diverse assemblage of fossil conifer leaves was identified in calcareous marine concretions from the Lower Cretaceous (Valanginian–Hauterivian) Apple Bay locality, Vancouver Island. Of the hundreds of isolated leaf fragments, most show affinities to Pinaceae. Leaves with closest similarities to Picea (spruce) were studied using cellulose acetate peels. Picea-like leaves vary in cross-section from rhomboidal, pentagonal, triangular, to ovoid. One fused vascular bundle with a centrally located ray and abaxial sclerenchyma is surrounded by a circular endodermis and transfusion tissue. Mesophyll is plicate containing two lateral external resin canals surrounded by a sclerenchyma sheath. Hypodermal fibres are one to three layers thick, except in areas of stomata. Leaves are amphistomatic, with sunken guard cells. Vascular bundles are identical anatomically to Picea; however, plicate mesophyll is similar to that in leaves of Pinus. Extensive sclerenchyma in the hypodermis and surrounding resin canals differs from that in most extant Picea. The major difference between these leaves and those of Picea is leaf shape. These fossil leaves probably belong to an extinct pinaceous conifer, and are described as Midoriphyllum piceoides gen. et sp. nov. Similar evidence from Cretaceous seed cones suggests that like the angiosperms, the Pinaceae were undergoing rapid mosaic evolution during the Lower Cretaceous.
Inference of higher-order conifer relationships from a multi-locus plastid data setThis paper is one of a selection of papers published in the Special Issue on Systematics Research.
Authors: Rai Hardeep S. , Reeves Patrick A. , Peakall Rod , Olmstead Richard G. , Graham Sean W.
Published: July 2008

We reconstructed the broad backbone of conifer phylogeny from a survey of 15–17 plastid loci and associated noncoding regions from exemplar conifer species. Parsimony and likelihood analyses recover the same higher-order relationships, and we find strong support for most of the deep splits in conifer phylogeny, including those within our two most heavily sampled families, Araucariaceae and Cupressaceae. Our findings are broadly congruent with other recent studies, and are inferred with comparable or improved bootstrap support. The deepest phylogenetic split in conifers is inferred to be between Pinaceae and all other conifers (Cupressophyta). Our current gene and taxon sampling does not support a relationship between Pinaceae and Gnetales, observed in some published studies. Within the Cupressophyta clade, we infer well-supported relationships among Cephalotaxaceae, Cupressaceae, Sciadopityaceae, and Taxaceae. Our data support recent moves to recognize Cephalotaxus under Taxaceae, and we find strong support for a sister-group relationship between the two predominantly southern hemisphere conifer families, Araucariaceae and Podocarpaceae. A local hotspot of indel evolution shared by the latter two conifer families is identified in the coding portion of one of the plastid ribosomal protein genes. The removal of the most rapidly evolving plastid characters, as defined using a likelihood-based classification of substitution rates for the taxa considered here, is shown to have little to no effect on our inferences of higher-order conifer relationships.
Phylogenetic relationships in the monocot order Commelinales, with a focus on PhilydraceaeThis paper is one of a selection of papers published in the Special Issue on Systematics Research.
Authors: Saarela Jeffery M. , Prentis Peter J. , Rai Hardeep S. , Graham Sean W.
Published: July 2008

To characterize higher-order phylogenetic relationships among the five families of Commelinales, we surveyed multiple plastid loci from exemplar taxa sampled broadly from the order, and from other major monocot lineages. Phylogenetic inferences in Commelinales using parsimony and likelihood methods are congruent, and we find strong support for most aspects of higher-order relationship in the order. We obtain moderately strong support for the local placement of Philydraceae, a family whose position has proven particularly difficult to infer in previous studies. Commelinaceae and Hanguanaceae are sister taxa, and together they are the sister group of a clade consisting of Haemodoraceae, Philydraceae, and Pontederiaceae; Haemodoraceae and Pontederiaceae are also sister taxa. Our sampling of Philydraceae includes all three or four genera in the family; we identify Philydrella as the sister group of a Helmholtzia–Philydrum clade, a resolution that is potentially consistent with several aspects of morphology.
Differentiation-dependent regulation of the intestinal folate uptake process: studies with Caco-2 cells and native mouse intestine
Authors: Subramanian Veedamali S. , Reidling Jack C. , Said Hamid M.
Published: July 2008

Differentiation of intestinal epithelial cells is accompanied by alterations in levels of expression of many genes, including those involved in nutrient uptake. Effects of differentiation of intestinal epithelial cells on the physiological and molecular parameters of the intestinal folate uptake process are not well characterized. To address this issue, we used two models, Caco-2 cells and native mouse intestine. Studies with Caco-2 cells showed a significant increase in the initial rate of carrier-mediated folic acid uptake during differentiation (i.e., as the cells transitioned from preconfluent to confluent and then to postconfluent stages). This increase was associated with an increase in the level of expression of the human reduced folate carrier (hRFC) and the human proton-coupled folate transporter (hPCFT) both at the protein and mRNA levels with differentiation; it was also associated with a significant increase in activity of the hRFC and hPCFT promoters. Studies with native mouse intestine showed a significantly higher folate uptake in villus compared with crypt cells, which was again associated with a significantly higher level of expression of the mouse RFC and PCFT at the protein and mRNA levels. Together, these studies demonstrate that the intestinal folate uptake process undergoes differentiation-dependent regulation and that this regulation is mediated via changes in the level of expression of both the RFC and PCFT. In addition, the studies suggest the possible involvement (at least in part) of a transcriptional mechanism(s) in this type of regulation of the intestinal folate uptake process.
Protein Never in Mitosis Gene A Interacting-1 (PIN1) regulates degradation of inducible nitric oxide synthase in endothelial cells
Authors: Liu Tongzheng , Huang Yongcheng , Likhotvorik Rostislav I. , Keshvara Lakhu , Hoyt Dale G.
Published: July 2008

The peptidyl-proline isomerase Protein Never in Mitosis Gene A Interacting-1 (PIN1) increases the level or activity of several transcription factors that can induce the inducible nitric oxide (NO) synthase (iNOS). PIN1 can also regulate mRNA and protein turnover. Here, the effect of depletion of PIN1 on induction of iNOS by Escherichia coli endotoxin (LPS) and interferon-γ (IFNγ) in murine aortic endothelial cells (MAEC) was determined. Suppression of PIN1 by 85% with small hairpin RNA enhanced the induction of NO and iNOS protein by LPS-IFNγ. There was no effect on induction of iNOS mRNA, suggesting a posttranscriptional effect. The enhanced levels of iNOS protein were functionally significant since LPS-IFNγ was cytotoxic to MAEC lacking PIN1 but not MAEC harboring an inactive control construct, and because cytotoxicity was blocked by the NO synthase inhibitor Nω-nitro-l-arginine methyl ester. Consistent with posttranscriptional action, knockdown of PIN1 increased the stability of iNOS protein in cycloheximide-treated cells. Furthermore, loss of iNOS was blocked by the calpain inhibitor carbobenzoxy-valinyl-phenylalaninal but not by the selective proteasome inhibitor epoxomicin. Immunoprecipitation indicated that PIN1 can interact with iNOS. Pull down of iNOS with a wild-type glutathione- S-transferase-PIN1 fusion protein, but not with a mutant of the amino terminal phospho-(serine/threonine)-proline binding WW domain of PIN1, indicated that this domain mediates interaction. The results suggest that PIN1 associates with iNOS and can limit its induction by facilitating calpain-mediated degradation in MAEC.