bluuebunny/crossref_metadata_2025_split huggingface dataset:
Comparative Genomics of Host-Specific Virulence in Pseudomonas syringae
Authors: Sarkar Sara F , Gordon Jeffrey S , Martin Gregory B , Guttman David S 
Published: September 2006

Abstract
While much study has gone into characterizing virulence factors that play a general role in disease, less work has been directed at identifying pathogen factors that act in a host-specific manner. Understanding these factors will help reveal the variety of mechanisms used by pathogens to suppress or avoid host defenses. We identified candidate Pseudomonas syringae host-specific virulence genes by searching for genes whose distribution among natural P. syringae isolates was statistically associated with hosts of isolation. We analyzed 91 strains isolated from 39 plant hosts by DNA microarray-based comparative genomic hybridization against an array containing 353 virulence-associated (VA) genes, including 53 type III secretion system effectors (T3SEs). We identified individual genes and gene profiles that were significantly associated with strains isolated from cauliflower, Chinese cabbage, soybean, rice, and tomato. We also identified specific horizontal gene acquisition events associated with host shifts by mapping the array data onto the core genome phylogeny of the species. This study provides the largest suite of candidate host-specificity factors from any pathogen, suggests that there are multiple ways in which P. syringae isolates can adapt to the same host, and provides insight into the evolutionary mechanisms underlying host adaptation.
Can Random Mutation Mimic Design?: A Guided Inquiry Laboratory for Undergraduate Students
Authors: Kalinowski Steven T , Taper Mark L , Metz Anneke M 
Published: September 2006

AbstractComplex biological structures, such as the human eye, have been interpreted as evidence for a creator for over three centuries. This raises the question of whether random mutation can create such adaptations. In this article, we present an inquiry-based laboratory experiment that explores this question using paper airplanes as a model organism. The main task for students in this investigation is to figure out how to simulate paper airplane evolution (including reproduction, inheritance, mutation, and selection). In addition, the lab requires students to practice analytic thinking and to carefully delineate the implications of their results.
Ribosomal DNA in the GrasshopperPodisma pedestris: Escape From Concerted Evolution
Authors: Keller Irene , Chintauan-Marquier Ioana C , Veltsos Paris , Nichols Richard A 
Published: September 2006

AbstractEukaryote nuclear ribosomal DNA (rDNA) typically exhibits strong concerted evolution: a pattern in which several hundred rDNA sequences within any one species show little or no genetic diversity, whereas the sequences of different species diverge. We report a markedly different pattern in the genome of the grasshopper Podisma pedestris. Single individuals contain several highly divergent ribosomal DNA groups. Analysis of the magnitude of divergence indicates that these groups have coexisted in the Podisma lineage for at least 11 million years. There are two putatively functional groups, each estimated to be at least 4 million years old, and several pseudogene groups, many of which are transcribed. Southern hybridization and real-time PCR experiments show that only one of the putatively functional types occurs at high copy number. However, this group is scarcely amplified under standard PCR conditions, which means that phylogenetic inference on the basis of standard PCR would be severely distorted. The analysis suggests that concerted evolution has been remarkably ineffective in P. pedestris. We propose that this outcome may be related to the species' exceptionally large genome and the associated low rate of deletion per base pair, which may allow pseudogenes to persist.
Statistical Tests for Detecting Positive Selection by Utilizing High-Frequency Variants
Authors: Zeng Kai , Fu Yun-Xin , Shi Suhua , Wu Chung-I 
Published: September 2006

Abstract
By comparing the low-, intermediate-, and high-frequency parts of the frequency spectrum, we gain information on the evolutionary forces that influence the pattern of polymorphism in population samples. We emphasize the high-frequency variants on which positive selection and negative (background) selection exhibit different effects. We propose a new estimator of θ (the product of effective population size and neutral mutation rate), θL, which is sensitive to the changes in high-frequency variants. The new θL allows us to revise Fay and Wu's H-test by normalization. To complement the existing statistics (the H-test and Tajima's D-test), we propose a new test, E, which relies on the difference between θL and Watterson's θW. We show that this test is most powerful in detecting the recovery phase after the loss of genetic diversity, which includes the postselective sweep phase. The sensitivities of these tests to (or robustness against) background selection and demographic changes are also considered. Overall, D and H in combination can be most effective in detecting positive selection while being insensitive to other perturbations. We thus propose a joint test, referred to as the DH test. Simulations indicate that DH is indeed sensitive primarily to directional selection and no other driving forces.
A Histone Methylation-Dependent DNA Methylation Pathway Is Uniquely Impaired by Deficiency in Arabidopsis S-Adenosylhomocysteine Hydrolase
Authors: Mull Lori , Ebbs Michelle L , Bender Judith 
Published: September 2006

Abstract
S-adenosylhomocysteine hydrolase (SAH) is a key enzyme in the maintenance of methylation homeostasis in eukaryotes because it is needed to metabolize the by-product of transmethylation reactions, S-adenosylhomocysteine (AdoHcy), which causes by-product inhibition of methyltransferases (MTase's). Complete loss of SAH function is lethal. Partial loss of SAH function causes pleiotropic effects including developmental abnormalities and reduced cytosine methylation. Here we describe a novel partial-function missense allele of the Arabidopsis SAH1 gene that causes loss of cytosine methylation specifically in non-CG contexts controlled by the CMT3 DNA MTase and transcriptional reactivation of a silenced reporter gene, without conferring developmental abnormalities. The CMT3 pathway depends on histone H3 lysine 9 methylation (H3 mK9) to guide DNA methylation. Our results suggest that this pathway is uniquely sensitive to SAH impairment because of its requirement for two transmethylation reactions that can both be inhibited by AdoHcy. Our results further suggest that gene silencing pathways involving an interplay between histone and DNA methylation in other eukaryotes can be selectively impaired by controlled SAH downregulation.
Ablation of Undifferentiated Human Embryonic Stem Cells: Exploiting Innate Immunity Against the Gal α1-3Galβ1-4GlcNAc-R (α-Gal) Epitope
Authors: Hewitt Zoe , Priddle Helen , Thomson Alison J. , Wojtacha Davina , McWhir Jim 
Published: September 2006

Abstract
Although undifferentiated human embryonic stem cells (hESCs) are tumorigenic, this capacity is lost after differentiation, and hESCs are being widely investigated for applications in regenerative medicine. To engineer protection against the unintentional transplantation of undifferentiated cells, we generated hESCs carrying a construct in which the α1,3-galactosyltransferase (GalT) open reading frame was transcribed from the hTERT promoter (pmGT). Because the endogenous GalT gene is inactive, GalT expression was limited to undifferentiated cells. A second chimeric construct (pmfGT) differed by replacement of the GalT leader sequence for that of the fucosyltransferase gene. Two subclones containing stable integrations of pmGT and pmfGT (M2 and F11, respectively) were assessed for their response to human serum containing antibodies to the Galα1-3Galβ1-4GlcNAc-R (α-gal) epitope. The low-variegation line, M2, and to a lesser extent the more variegated line F11, were sensitive to human serum when exposed in the undifferentiated state. However, M2 cells were largely insensitive after differentiation and retained both a normal karyotype and the ability to differentiate into derivatives of the three germ layers in severe combined immunodeficient mice. These data exemplify a method of protection against residual, undifferentiated hESCs prior to engraftment and may provide ongoing immune surveillance after engraftment against dedifferentiation or against de novo tumorigenesis involving hTERT reactivation. Untransfected H9 cells were not sensitive to the human serum used in this study. Hence, in our system, interactions of hESCs with other circulating antibodies, such as anti-Neu5Gc, were not observed.
In Vivo Distribution of Human Adipose-Derived Mesenchymal Stem Cells in Novel Xenotransplantation Models
Authors: Meyerrose Todd E. , De Ugarte Daniel A. , Hofling A. Alex , Herrbrich Phillip E. , Cordonnier Taylor D. , Shultz Leonard D. , Eagon J. Chris , Wirthlin Louisa , Sands Mark S. , Hedrick Marc A. , Nolta Jan A. 
Published: September 2006

AbstractThe potential for human adipose-derived mesenchymal stem cells (AMSC) to traffic into various tissue compartments was examined using three murine xenotransplantation models: nonobese diabetic/severe combined immunodeficient (NOD/SCID), nude/NOD/SCID, and NOD/SCID/MPSVII mice. Enhanced green fluorescent protein was introduced into purified AMSC via retroviral vectors to assist in identification of cells after transplantation. Transduced cells were administered to sublethally irradiated immune-deficient mice through i.v., intraperitoneal, or subcutaneous injection. Up to 75 days after transplantation, tissues were harvested and DNA polymerase chain reaction (PCR) was performed for specific vector sequences as well as for human Alu repeat sequences. Duplex quantitative PCR using human β-globin and murine rapsyn primers assessed the contribution of human cells to each tissue. The use of the novel NOD/SCID/MPSVII mouse as a recipient allowed rapid identification of human cells in the murine tissues, using an enzyme reaction that was independent of surface protein expression or transduction with an exogenous transgene. For up to 75 days after transplantation, donor-derived cells were observed in multiple tissues, consistently across the various administration routes and independent of transduction parameters. Tissue localization studies showed that the primary MSC did not proliferate extensively at the sites of lodgement. We conclude that human AMSC represent a population of stem cells with a ubiquitous pattern of tissue distribution after administration. AMSC are easily obtained and highly amenable to current transduction protocols for retroviral transduction, making them an excellent avenue for cell-based therapies that involve a wide range of end tissue targets.
The benefits of drinking water quality regulation – England and Wales
Authors: May A. 
Published: September 2006

This paper aims to demonstrate that the regulation of drinking water quality in England and Wales has been successful in securing the improvements to drinking water quality resulting in better performance against EU and national standards. The water industry in England and Wales went through a major change in 1989 when suppliers were privatised and the government set up a robust regulatory regime. The regime was necessary as the industry was, as a result of privatisation, a monopoly with customers having no choice of supplier, unlike what was later available with other utilities such as gas or electricity. The regime would protect the interests of the consumer, the environment and public health through the quality of the product. The Drinking Water Inspectorate (DWI), as established in 1990, had to ensure the implementation of the European Drinking Water Directive (DWD) that had been transposed into national legislation. The aim of the DWD is to ensure that all EU Member States provide drinking water of a prescribed quality. In England and Wales, a body was required to oversee the performance of the industry against those standards, reporting to the Government and the European Commission.
Through acts and legislation, the set up of the industry, the duties of the suppliers and regulators and the powers available to the regulators were established. The improvements to drinking water quality since privatisation were achieved by massive investment of the privatised water industry overseen by an independent regulator with clear duties and the powers to inspect, enforce and prosecute. The DWI's achievements show that to improve quality performance with the ability to report in detail how the improvements were made with extensive data evidence, a special regulator is required. The DWI advises policy departments and Ministers and when there are serious concerns regarding a threat to human health through drinking water, the highest level of regulatory power is the creation of new legislation, for example, the Cryptosporidium regulations that are unique to the UK. The DWI is more than what is traditionally thought of as a regulator because it has a single remit — drinking water quality — and its style of regulation has been key to improved drinking water quality in England and Wales.
Simulation of fast reactions in batch reactors under sub‐critical water condition
Authors: Abdelmoez Wael , Yoshida Hiroyuki 
Published: September 2006

AbstractIn this study the temperature profiles inside a tube batch reactor under the sub‐critical water condition were investigated under different operating conditions. The most important parameters that may affect the temperature profile, including salt bath mixing speed, reactor shaking, reactant viscosity, and reactor contents, were investigated both experimentally and theoretically. The results showed that both salt bath mixing and reactor shaking had a great effect in the rate of heating up. The study of the effect of reactant viscosity on the temperature profile revealed that the thermal conductivity rather than viscosity was found to affect the temperature profile in the case of comparing reactant with different viscosities. The reactant contents had the lowest pronounced effect on both heating up and cooling down rates among all tested parameters. Two different empirical equations were developed to describe the temperature profiles during both heating up and cooling down periods. Using these equations we developed a new mathematical model for describing the kinetic behavior of fast reactions that take place under the sub‐critical water condition. We assumed that the reaction was taking place under unsteady state conditions and following first order kinetics. Based on the simulation results, we developed a new strategy for finding out the correct values of activation energy and frequency factor involved in such fast reactions. © 2006 American Institute of Chemical Engineers AIChE J, 2006
Polypeptides and 100 Years of Chemistry of α‐Amino Acid N‐Carboxyanhydrides
Authors: Kricheldorf Hans R. 
Published: September 2006

AbstractSyntheses and polymerizations of α‐amino acid N‐carboxyanhydrides (NCAs) were reported for the first time by Hermann Leuchs in 1906. Since that time, these cyclic and highly reactive amino acid derivatives were used for stepwise peptide syntheses but mainly for the formation of polypeptides by ring‐opening polymerizations. This review summarizes the literature after 1985 and reports on new aspects of the polymerization processes, such as the formation of cyclic polypeptides or novel organometal catalysts. Polypeptides with various architectures, such as diblock, triblock, and multiblock sequences, and star‐shaped or dendritic structures are also mentioned. Furthermore, lyotropic and thermotropic liquid‐crystalline polypeptides will be discussed and the role of polypeptides as drugs or drug carriers are reviewed. Finally, the hypothetical role of NCAs in molecular evolution on the prebiotic Earth is discussed.
Synthesis of novel zirconium complexes bearing mono‐Cp and tridentate Schiff base [ONO] ligands and their catalytic activities for olefin polymerization
Authors: Chen Qihui , Huang Jiling 
Published: September 2006

AbstractA series of novel zirconium complexes {R2Cp[2‐R1‐6‐(2‐CH3OC6H4NCH)C6H3O]ZrCl2 (1, R1 = H, R2 = H, 2: R1 = CH3, R2 = H; 3, R1 = tBu, R2 = H; 4, R1 = H, R2 = CH3; 5, R1 = H, R2 = n‐Bu)} bearing mono‐Cp and tridentate Schiff base [ONO] ligands are prepared by the reaction of corresponding lithium salt of Schiff base ligands with R2CpZrCl3·DME. All complexes were well characterized by 1H NMR, MS, IR and elemental analysis. The molecular structure of complex 1 was further confirmed by X‐ray diffraction study, where the bond angle of ClZrCl is extremely wide [151.71(3)°]. A nine‐membered zirconoxacycle complex Cp(O2C6H4NCHC6H4‐2O)ZrCl2 (6) can be obtained by an intramolecular elimination of CH3Cl from complex 1 or by the reaction of CpZrCl3·DME with dilithium salt of ligand. When activated by excess methylaluminoxane (MAO), complexes 1–6 exhibit high catalytic activities for ethylene polymerization. The influence of polymerization temperature on the activities of ethylene polymerization is investigated, and these complexes show high thermal stability. Complex 6 is also active for the copolymerization of ethylene and 1‐hexene with low 1‐hexene incorporation ability (1.10%). Copyright © 2006 John Wiley & Sons, Ltd.
Heterogeneous postnatal transitions in myosin heavy chain isoforms within the rabbit temporalis muscle
Authors: Korfage Joannes A.M. , Van Wessel Tim , Langenbach Geerling E.J. , Van Eijden Theo M.G.J. 
Published: September 2006

AbstractPostnatal changes in the fiber type composition and fiber cross‐sectional area were investigated in the superficial (TEM1) and deep (TEM23) temporalis of male rabbits. It was hypothesized that, due to the transition from suckling to chewing during early postnatal development, the proportion of fast fiber types would decrease, while the proportion of fibers positive for myosin heavy chain (MyHC) cardiac α would increase, and that, due to the influence of testosterone during late postnatal development, the proportion of these α fibers would decrease again. Classification of the fibers types was performed by immunohistochemistry according to their MyHC content. The proportion of α fiber types significantly increased in both muscle portions from 2% and 8% for TEM1 and TEM23 at week 1 to 29% and 54% at week 8, respectively,. While in TEM1 the proportion of this fiber type did not change thereafter, it decreased again to 27% in TEM23 at week 20. The change for the fast fiber types was opposite to that of the α fiber types. Significantly more MyHC IIX fibers were found in TEM1 than in TEM23 in adult rabbits. In the first 8 weeks, the cross‐sectional areas of all fibers increased. After this period, only MyHC cardiac α + I fibers continued to increase significantly. It was concluded that there are developmental differences in the myosin heavy chain transitions of the two portions of the temporalis muscle. Anat Rec Part A, 288A:1095–1104, 2006. © 2006 Wiley‐Liss, Inc.
Long‐term effects of a midgestational asphyxial episode in the ovine fetus
Authors: O'Connell Amanda E. , Boyce Amanda C. , Kumarasamy Vasumathy , Douglas‐Denton Rebecca , Bertram John F. , Gibson Karen J. 
Published: September 2006

AbstractWe and others have shown previously that fetuses at midgestation can survive 30 min of complete umbilical cord occlusion, although hydrops fetalis (or gross fetal edema) results. To investigate whether this hydrops resolves by late gestation and if there are any long‐term consequences of the asphyxial insult on the heart and kidneys, eight fetuses were subjected to 30 min of complete umbilical cord occlusion at 0.6 gestation (90 days; term 150 days) and were compared to a sham group (n = 10). During the occlusion period, fetuses became severely hypoxemic, hypercapnemic, and acidotic, with both blood pressure and heart rate decreasing. Most variables had returned to normal by 2‐hr recovery. At 129 ± 1 days of gestation, approximately 40 days post occlusion, some fetuses were still slightly hydropic as skin fold measurements were increased (P < 0.01), although fetal body weight was not different from the sham group. The two groups had similar heart and kidney weights, ventricular cardiac myocyte nucleation, and glomerular number. By contrast, brain weight was reduced by 37% (P < 0.001) and the cerebral lateral ventricles were grossly dilated. Lungs were 50% smaller than in sham fetuses (P < 0.001). Thus, the hydrops that develops at midgestation as a result of a severe asphyxial episode can, but does not always, fully resolve by late gestation. Also, while fetuses at midgestation can survive this asphyxial episode with no long‐term impact in renal or cardiac size, nephron number, or cardiomyocyte nucleation, the brain and lungs are severely affected. Anat Rec Part A, 288A:1112–1120, 2006. © 2006 Wiley‐Liss, Inc.
Druckstrebentragfähigkeit torsionsbeanspruchter Stahlbetonbalken mit üblicher Betondeckung
Authors: Zedler Thomas , Mark Peter 
Published: September 2006

AbstractVergleichsrechnungen auf Basis einer Versuchsdatenbank zeigen, daß die Druckstrebentragfähigkeit unter Torsionsbelastung nach DIN 1045‐1 insbesondere im Falle einer großen Betondeckung deutlich überschätzt wird. Ein Vergleich gegenwärtiger internationaler Normenwerke läßt zudem erkennen, daß generell uneinheitliche Auffassungen über den Einfluß der Betondeckung auf den Bruchwiderstand von Stahlbetonbalken unter Torsionsbelastung bestehen.In diesem Beitrag werden experimentelle und begleitende theoretische Untersuchungen der Druckstrebentragfähigkeit von Stahlbetonbalken mit heutzutage baupraktischen Betondeckungen unter Torsionsbelastung vorgestellt. Die herausgestellten Versagenseinflüsse aufgreifend, wird ein auf DIN 1045‐1 basierender Bemessungsansatz entwickelt, der ein gleichmäßiges Sicherheitsniveau unabhängig von der vorhandenen Betondeckung sicherstellt.
Application of artificial neural network coupling particle swarm optimization algorithm to biocatalytic production of GABA
Authors: Huang Jun , Mei Le‐He , Xia Jiang 
Published: September 2006

AbstractThe biotransformation of L‐sodium glutamate (L‐MSG) to gamma‐aminobutyric acid (GABA) catalyzed by the cells of Lactobacillus brevis with higher glutamate decarboxylase activity was investigated. The results showed that pH, temperature, and FeSO4 · 7H2O concentration had significantly positive effect on GABA yield. The individual and interactive effects of pH, temperature, and FeSO4 · 7H2O concentration were further optimized in terms of GABA yield. In the present work, an artificial neural network (ANN) and response surface methodology (RSM) models were developed, which incorporated pH, temperature, and FeSO4 · 7H2O concentration as input variables, and GABA yield as output variable. The optimized ANN topology included four neurons in the hidden layer and the best network architecture was 3‐4‐1. The trained ANN gave total root‐mean square error (σ) equal to 1.84 for GABA yield while the RSM gave σ equal to 2.63. The results demonstrated a slightly higher prediction accuracy of ANN compared to RSM. The modeled maximum GABA yield was identified by applying particle swarm optimization algorithm to the ANN model developed. The modeled maximum GABA yield reached 91 mM under the following optimal conditions: 25 mL Na2HPO4‐citric acid buffer (100 mM, pH 4.23), 120 mM L‐MSG, 0.83 g/L FeSO4 · 7H2O, 10 µM PLP, the resting cells obtained from a 60‐h culture broth, 2.68 g dry cell weight (DCW)/L, and without agitation at 40°C for 5 h. The previous high value of GABA yield that was observed was 81.8 mM. The optimized conditions allowed GABA yield to be increased from 81.8 to 90.57 mM after verification experiments test. Biotechnol. Bioeng. 2007;96:924–931. © 2006 Wiley Periodicals, Inc.