bluuebunny/crossref_metadata_2025 huggingface dataset:
Kinetic analysis of phenylalanine dehydrogenase mutants designed for aliphatic amino acid dehydrogenase activity with guidance from homology‐based modelling
Authors: Seah Stephen Y. K. , Britton K. Linda , Rice David W. , Asano Yasuhisa , Engel Paul C.
Published: November 2003

Through comparison with the high‐resolution structure of Clostridium symbiosum glutamate dehydrogenase, the different substrate specificities of the homologous enzymes phenylalanine dehydrogenase and leucine dehydrogenase were attributed to two residues, glycine 124 and leucine 307, in Bacillus sphaericus phenylalanine dehydrogenase, which are replaced with alanine and valine in leucine dehydrogenases [Britton, K.L., Baker, P.J., Engel, P.C., Rice, D.W. & Stillman, T.J. (1993) J. Mol. Biol.234, 938–945]. As predicted, making these substitutions in phenylalanine dehydrogenase decreased the specific activity towards aromatic substrates and enhanced the activity towards some aliphatic amino acids in standard assays with fixed concentrations of both substrates [Seah, S.Y.K., Britton, K.L., Baker, P.J., Rice, D.W., Asano, Y. & Engel, P.C. (1995) FEBS Lett.370, 93–96]. This study did not, however, distinguish effects on affinity from those on maximum catalytic rate. A fuller kinetic characterization of the single‐ and double‐mutant enzymes now reveals that the extent of the shift in specificity was underestimated in the earlier study. The maximum catalytic rates for aromatic substrates are reduced for all the mutants, but, in addition, the apparent Km values are higher for the single‐mutant G124A and double‐mutant G124A/L307V compared with the wild‐type enzyme. Conversely, specificity constants (kcat/Km) for the nonpolar aliphatic amino acids and the corresponding 2‐oxoacids for the mutants are all markedly higher than for the wild type, with up to a 40‐fold increase for l‐norvaline and a 100‐fold increase for its 2‐oxoacid in the double mutant. In some cases a favourable change in Km was found to outweigh a smaller negative change in kcat. These results emphasize the risk of misjudging the outcome of protein engineering experiments through too superficial an analysis. Overall, however, the success of the predictions from molecular modelling indicates the usefulness of this strategy for engineering new specificities, even in advance of more detailed 3D structural information.
Protein stabilization by compatible solutes
Authors: Lamosa Pedro , Turner David L. , Ventura Rita , Maycock Christopher , Santos Helena
Published: November 2003

Heteronuclear NMR relaxation measurements and hydrogen exchange data have been used to characterize protein dynamics in the presence or absence of stabilizing solutes from hyperthermophiles. Rubredoxin from Desulfovibrio gigas was selected as a model protein and the effect of diglycerol phosphate on its dynamic behaviour was studied. The presence of 100 mm diglycerol phosphate induces a fourfold increase in the half‐life for thermal denaturation of D. gigas rubredoxin [Lamosa, P., Burke, A., Peist, R., Huber, R., Liu, M.Y., Silva, G., Rodrigues‐Pousada, C., LeGall, J., Maycock, C. & Santos, H. (2000) Appl. Environ. Microbiol.66, 1974–1979]. A model‐free analysis of the protein backbone relaxation parameters shows an average increase of generalized order parameters of 0.015 reflecting a small overall reduction in mobility of fast‐scale motions. Hydrogen exchange data acquired over a temperature span of 20 °C yielded thermodynamic parameters for the structural opening reactions that allow for the exchange. This shows that the closed form of the protein is stabilized by an additional 1.6 kJ·mol−1 in the presence of the solute. The results seem to indicate that the stabilizing effect is due mainly to a reduction in mobility of the slower, larger‐scale motions within the protein structure with an associated increase in the enthalpy of interactions.
Reactions of gold(III) complexes with serum albumin
Authors: Marcon Giordana , Messori Luigi , Orioli Pierluigi , Cinellu Maria Agostina , Minghetti Giovanni
Published: November 2003

The reactions of a few representative gold(III) complexes –[Au(ethylenediamine)2]Cl3, [Au(diethylentriamine)Cl]Cl2, [Au(1,4,8,11‐tetraazacyclotetradecane)](ClO4)2Cl, [Au(2,2′,2′‐terpyridine)Cl]Cl2, [Au(2,2′‐bipyridine)(OH)2][PF6] and the organometallic compound [Au(6‐(1,1‐dimethylbenzyl)‐2,2′‐bipyridine‐H)(OH)][PF6]– with BSA were investigated by the joint use of various spectroscopic methods and separation techniques. Weak metal–protein interactions were revealed for the [Au(ethylenediamine)2]3+and [Au(1,4,8,11‐tetraazacyclotetradecane)]3+species, whereas progressive reduction of the gold(III) centre was observed in the cases of [Au(2,2′‐bipyridine)(OH)2]+and [Au(2,2′,2′‐terpyridine)Cl]2+. In contrast, tight metal–protein adducts are formed when BSA is reacted with either [Au(diethylentriamine)Cl]2+and [Au(6‐(1,1‐dimethylbenzyl)‐2,2′‐bipyridine‐H)(OH)]+. Notably, binding of the latter complex to serum albumin results in the appearance of characteristic CD bands in the visible spectrum. It is suggested that adduct formation for both of these gold(III) complexes occurs through coordination at the level of surface histidines. Stability of these gold(III) complexes/serum albumin adducts was tested under physiologically relevant conditions and found to be appreciable. Metal binding to the protein is tight; complete detachment of the metal from the protein has been achieved only after the addition of excess potassium cyanide. The implications of the present results for the pharmacological activity of these novel cytotoxic agents are discussed.
Role of the hinge peptide and the intersubunit interface in the swapping of N‐termini in dimeric bovine seminal RNase
Authors: Ercole Carmine , Avitabile Francesca , Del Vecchio Pompea , Crescenzi Orlando , Tancredi Teodorico , Picone Delia
Published: November 2003

Bovine seminal ribonuclease (BS‐RNase) is the only known dimeric enzyme characterized by an equilibrium between two different 3D structures: MxM, with exchange (or swapping) of the N‐terminal 1–20 residues, and M=M, without exchange. As a consequence, the hinge region 16–22 has a different tertiary structure in the two forms. In the native protein, the equilibrium ratio between MxM and M=M is about 7 : 3. Kinetic analysis of the swapping process for a recombinant sample shows that it folds mainly in the M=M form, then undergoes interconversion into the MxM form, reaching the same 7 : 3 equilibrium ratio. To investigate the role of the regions that are most affected structurally by the swapping, we expressed variant proteins by replacing two crucial residues with the corresponding ones from RNase A: Pro19, within the hinge peptide, and Leu28, located at the interface between subunits. We compared the structural properties of the monomeric forms of P19A‐BS‐RNase, L28Q‐BS‐RNase and P19A/L28Q‐BS‐RNase variants with those of the parent protein, and investigated the exchange kinetics of the corresponding dimers. The P19A mutation slightly increases the thermal stability of the monomer, but it does not alter the swapping tendency of the dimer. In contrast, the L28Q mutation significantly affects both the dimerization and swapping processes but not the thermal stability of the monomer. Overall, these results suggest that the structural determinants that control the exchange of N‐terminal arms in BS‐RNase may not be located within the hinge peptide, and point to a crucial role of the interface residues.
High thermal and chemical stability of Thermus thermophilus seven‐iron ferredoxin
Authors: Griffin Susanne , Higgins Catherine L. , Soulimane Tewfik , Wittung‐Stafshede Pernilla
Published: November 2003

To probe the stability of the seven‐iron ferredoxin from Thermus thermophilus (FdTt), we investigated its chemical and thermal denaturation processes in solution. As predicted from the crystal structure, FdTt is extremely resistant to perturbation. The guanidine hydrochloride‐induced unfolding transition shows a midpoint at 6.5 m (pH 7, 20 °C), and the thermal midpoint is above boiling, at 114 °C. The stability of FdTt is much lower at acidic pH, suggesting that electrostatic interactions are important for the high stability at higher pH. On FdTt unfolding at alkaline pH, new absorption bands at 520 nm and 610 nm appear transiently, resulting from rearrangement of the cubic clusters into linear three‐iron species. A range of iron–sulfur proteins has been found to accommodate these novel clusters in vitro, although no biological function has yet been assigned.
Giant keratoacanthoma arising in hypertrophic lichen planus
Authors: Giesecke Leah M , Reid Catherine M , James Craig L , Huilgol Shyamala C
Published: November 2003

A 45‐year‐old man presented with a rapidly enlarging tumour in an area of long‐standing hypertrophic lichen planus of the lower leg. Histological examination of the resected specimen showed it to be a giant keratoacanthoma measuring 37 × 57 mm. Neoplastic change is a rarely reported complication of chronic variants of cutaneous lichen planus. To date there have been only two reports of keratoacanthoma development in association with lichen planus.
Allergic contact dermatitis to an expired moisturiser
Authors: Lim Adrian C , Freeman Susanne
Published: November 2003

A 64‐year‐old man developed an allergic contact dermatitis while using an expired sorbolene cream. Patch tests to the product ingredients were all negative. Repeated open application test to the expired product produced a strong reaction while an identical‐brand non‐expired product did not elicit a reaction, suggesting the presence of an unidentified degradation product or compound, acting as an allergen in the expired product. This case is intriguing in that it contrasts the ubiquitous use of over‐the‐counter topical agents with the exceedingly low incidence of contact dermatitis to expired topical products.
Geographic Concentration and Increasing Returns
Authors: Surico Paolo
Published: November 2003

Abstract.  Economic activities are highly clustered. Why is geographic concentration becoming a predominant feature of industrialized economies? On the basis of the empirical models developed by the new theories of international trade, our answer is that increasing returns are the driving force of economic geography in the US as well as in Europe. In so doing, we review several econometric methods proposed in the literature to separate and to test alternative theoretical paradigms.
Shaping the Economic Landscapes of Postsocialism? Labour, Workplace and Community in Nowa Huta, Poland
Authors: Stenning Alison
Published: November 2003

For years, the countries of east central Europe and the former Soviet Union were described as workers' states. The formal commitment of the governing parties to the construction of states run by workers for workers was reflected materially and ideologically in the landscape. The end of communism in 1989 brought new challenges for workers and workers' organisations in the region as the processes of transformation led these countries towards neoliberal and globalising economic and political systems. This paper explores these transformations in the case of Nowa Huta in southern Poland, mapping the role of workers in the shaping of economic landscapes. After considering the importance of labour in the construction of Nowa Huta, the paper considers the place of workers and workers' organisations, especially Solidarity, in shaping political and economic issues at both the local and national scale as socialism in Poland began to falter. The latter half of the paper explores the role of labour in shaping the experience of reforms after 1989. This discussion is set in the context not only of wider literatures on postsocialist transformations, but also of the growing body of work in labour geography. The paper argues that the particular development of labour movements and institutions in Poland presents opportunities for a community‐based renaissance of worker influence, but that other historical and political factors—such as union support for marketisation and the divided nature of Polish labour politics—have, in practice, hindered the ability of Polish labour to shape the economic landscapes of postsocialism. The paper concludes on a note of optimism, recognising that the faltering of the Polish economy might open spaces for a successful labour intervention.
Ingroup Bias, Classic Ethnocentrism, and Non‐Ethnocentrism Among American Whites
Authors: Raden David
Published: November 2003

This study collapsed ingroup bias into two types: a classic Sumnerian type, in which favorable perceptions of the ingroup were linked to unfavorable perceptions of the outgroup, and a simple ingroup bias type that consisted of all other instances of ingroup superiority. Simple ingroup bias was the more common type among a General Social Survey (GSS) national probability sample of 1,119 non‐Jewish whites who rated Jews, blacks, Asians, and Hispanics on five traits. The two types appear to represent different points on an ethnocentrism continuum; thus, researchers who do not distinguish between them may underestimate the possible impact of ethnocentrism. The generally low levels of classic ethnocentrism did increase for people low in education or high in authoritarianism or social distance. The research also tested an ethnocentrism typology. Many respondents fell into two nonclassic ethnocentrism categories: positivity (where own‐group and other‐group ratings are both favorable) and neutral matching.
Women's Representation in an Australian Rural Context
Authors: Alston Margaret
Published: November 2003

Australian rural women are largely invisible in public areas of influence. This paper presents findings of research into Australian rural women 's public profile in powerful agricultural organisations. Using a survey of Chairs of influential Boards and follow up interviews, as well as a survey of women in influential positions it shows that the Australian agricultural agenda is largely framed around a masculinist position and that women remain shadowy presences of outraged silence. Few men in powerful positions express disquiet about the current situation, with most arguing that appointments are based on merit. This paper exposes the fallacy of such a position noting that merit‐based appointment is impossible under current selection processes. Disturbingly women who have gained access to positions of influence report overt and covert harassment from male colleagues. The paper concludes that changes to organisational culture are essential if women are to gain access to positions of influence.
Following the Leader? Mormon Voting on Ballot Propositions
Authors: Campbell David E. , Monson J. Quin
Published: November 2003

Why did Utah voters—most of whom are Mormons—vote in favor of repealing Prohibition in 1933, and against a modest relaxation of Utah's liquor laws in 1968? In answering this question, we illuminate some important facets of the political behavior of members of the Church of Jesus Christ of Latter‐day Saints. We hypothesize that Mormons are likely to “follow their leaders” on political questions when two conditions hold: (1) official endorsement of a position by LDS church leaders; and (2) internal agreement among those leaders. Each is necessary, but neither is sufficient alone. In 1933, only one of these two conditions held; in 1968 both did. Using ecological inference to generate estimates of individual‐level behavior of Mormon and non‐Mormon voters in Utah, we find that Mormon voters were significantly more likely to vote in accordance with the Mormon Church's official position in 1968 than in 1933. We further test our hypothesis by examining other referenda in states with a large Mormon population. We conclude with a discussion of when and how contemporary Mormon leaders get involved in political issues.
Staying on Track in School: Religious Influences in High‐ and Low‐Risk Settings
Authors: Regnerus Mark D. , Elder Glen H.
Published: November 2003

Religious communities are known to instill standards of achievement in their young people, but this observation may not apply as well to disadvantaged youth and their culture. In this study, we explore whether religious involvement enables youth in low‐income neighborhoods to stay on track in school, rather than falling behind. Using data from two waves of the National Longitudinal Study of Adolescent Health, we find that adolescents in low‐income neighborhoods do not differ in their church attendance patterns from their peers in higher‐income areas. However, their religious involvement is more likely to contribute to their academic progress than it is among youth in higher‐income neighborhoods, even with adjustments for key risk and protective factors. This cross‐level interaction involving youth church attendance shows a consistent relationship with several other measures of neighborhood disadvantage. We explore explanations for church attendance's uniquely positive effect in impoverished neighborhoods and its broader implications.
Nicotine‐induced neuroprotection against N‐methyl‐d‐aspartic acid or β‐amyloid peptide occur through independent mechanisms distinguished by pro‐inflammatory cytokines
Authors: Gahring Lorise C. , Meyer Erin L. , Rogers Scott W.
Published: November 2003

Nicotine, the causative agent of addiction to tobacco, can also be a neuroprotectant. Nicotine‐induced neuroprotection against different toxins is imparted through pharmacologically distinct neuronal nicotinic acetylcholine receptors (nAChR) where protection against chronic N‐methyl‐d‐aspartic acid (NMDA) exposure is through nAChRα7 but protection against the toxic peptide of amyloid precursor protein, Aβ25−35, is through nAChRα4β2. The inflammatory cytokine tumor necrosis factor alpha (TNFα) is also neuroprotective, however, in the presence of nicotine, neuroprotection against NMDA is abolished. The specificity of nicotine–TNFα antagonism was further refined using a mouse transgenic dominant negative of nAChRα7 in which nicotine failed to induce neuroprotection against NMDA and antagonism of TNFα was absent. However, nicotine‐mediated neuroprotection against Aβ25−35 was unaffected and, therefore, did not require the expression of functional nAChRα7s. The mechanism of TNFα‐mediated neuroprotection and antagonism by nicotine was independent of caspase 8 activation or nuclear factor kappa B translocation in neurons but C6‐ceramide addition to neuronal cultures subsequently exposed to NMDA mimicked the neuroprotective effect of TNFα and, like TNFα, it was antagonized by cotreatment with nicotine. Therefore, the neuroprotective effects of nicotine against differing toxic assaults requires distinct nAChR subtypes and proceeds through intracellular pathways that overlap with similarly different mechanisms initiated by pro‐inflammatory cytokines. These results provide insight into how nicotine imparts neuroprotection and modulates inflammatory responses.
Inhibition of excitatory neuronal cell death by cell‐permeable calcineurin autoinhibitory peptide
Authors: Terada Hiroaki , Matsushita Masayuki , Lu Yun‐Fei , Shirai Takeshi , Li Sheng‐Tian , Tomizawa Kazuhito , Moriwaki Akiyoshi , Nishio Shinsaku , Date Isao , Ohmoto Takashi , Matsui Hideki
Published: November 2003

In glutamate‐mediated excitatory neuronal cell death, immunosuppressants (FK506, Cys‐A) are powerful agents that protect neurons from apoptosis. Immunosuppressants inhibit two types of enzyme, calcium/calmodulin‐dependent protein phosphatase (calcineurin: CaN), and peptidyl‐prolylcis‐trans‐isomerase (PPIase) activity such as the FKBP family. In this study, we used a protein transduction approach to determine the functional role of CaN and to produce a potential therapeutic agent for glutamate‐mediated neuronal cell death. We created a novel cell‐permeable CaN autoinhibitory peptide using the 11 arginine protein transduction domain. This peptide was highly efficient at transducing into primary culture neurons, potently inhibited CaN phosphatase activities, and inhibited glutamate‐mediated neuronal cell death. These results showed that CaN plays an important role in excitatory neuronal cell death and cell‐permeable CaN autoinhibitory peptide could be a new drug to protect neurons from excitatory neuronal death.
Activation of Rho GTPases by synaptic transmission in the hippocampus
Authors: O'Kane E. M. , Stone T. W. , Morris B. J.
Published: November 2003

Ras‐related GTPases of the Rho family, such as RhoA and RhoB, are well‐characterised mediators of morphological change in peripheral tissues via their effects on the actin cytoskeleton. We tested the hypothesis that Rho family GTPases are involved in synaptic transmission in the CA1 region of the hippocampus. We show that GTPases are activated by synaptic transmission. RhoA and RhoB were activated by low frequency stimulation, while the induction of long‐term potentiation (LTP) by high frequency stimulation was associated with specific activation of RhoB via NMDA receptor stimulation. This illustrates that these GTPases are potential mediators of synaptic transmission in the hippocampus, and raises the possibility that RhoB may play a role in plasticity at hippocampal synapses during LTP.
Characterization of polymorphic microsatellite loci in a neotropical wood‐quail, Odontophorus leucolaemus
Authors: Hale Amanda M. , Hughes Colin R.
Published: November 2003

We developed a set of nine polymorphic microsatellite loci for black‐breasted wood‐quail, Odontophorus leucolaemus. We screened 50 individuals from Monteverde, Puntarenas Province, Costa Rica and found that locus‐specific allelic diversity ranges from two to 15 alleles (mean 10.2) and observed heterozygosity ranges from 0.24 to 0.96 (mean 0.78). These markers appear to be useful in other members of the Odontophorus genus.
Seven polymorphic microsatellite DNA loci from the red‐spotted newt (Notophthalmus viridescens)
Authors: Croshaw Dean A. , Glenn Travis C.
Published: November 2003

We describe polymerase chain reaction (PCR) primers and amplification conditions for seven microsatellite DNA loci isolated from the red‐spotted newt (Notophthalmus viridescens). Primers were tested on 16 individuals from two populations on the Savannah River Site in Aiken County, South Carolina. We detected six to 10 alleles per locus and an overall observed heterozygosity range of 0.31–0.81. Despite low heterozygosity at two of the seven loci, the high polymorphic information contents (from 0.54 to 0.85) of these markers render them useful for future studies of the behavioural and population ecology of this common salamander.
Novel polymorphic microsatellite markers for paternity analysis in the red‐capped robin (Petroica goodenovii: Aves)
Authors: Dowling D. K. , Adcock G. J. , Mulder R. A.
Published: November 2003

Seven microsatellite loci were isolated and characterized from the red‐capped robin Petroica goodenovii, using nonradioactive polymerase chain reaction (PCR)‐based techniques to screen an enriched genomic library. Five loci showed no evidence of null alleles and were variable [mean heterozygosity (HE) = 0.440, mean number of alleles = 8]. Cross‐amplification using primers for microsatellites in Phylloscopus occipitalis and Emberiza schoeniclus yielded another two polymorphic loci. The combined set of five red‐capped robin and two cross‐amplified loci are suitable for paternity assignment (exclusion probability for seven unlinked loci = 0.9760).
Polymorphic microsatellite DNA markers in the mangrove tree Avicennia alba
Authors: Teixeira S. , Arnaud‐Haond S. , Duarte C. M. , Serrão E.
Published: November 2003

Like most species of mangrove trees of the genus Avicennia, A. alba is widely distributed among tropical and subtropical coasts around the world. Mangroves play an essential role in ecosystem dynamics but are reported to be regressing as human pressure increases on coastal zones. Hypervariable genetic markers are useful for population genetics studies, to estimate the level of impact and the populations potential for recovery. Microsatellite markers for A. alba were obtained by screening a partial genomic library enriched for microsatellite dinucleotide repeats. Among 20 primer pairs defined, six amplified polymorphic microsatellites with a satisfying level of variability.
Polymorphic microsatellite loci for population studies of the bicolor damselfish, Stegastes partitus (Pomacentridae)
Authors: Williams D. A. , Purcell J. , Hughes C. R. , Cowen R. K.
Published: November 2003

The extent of dispersal between populations of Caribbean reef fish remains largely unknown. Resolution of this issue is critical for managing populations and designing marine reserves. As part of a larger study of reef fish dispersal, we developed and characterized 11 polymorphic microsatellite loci for the bicolor damselfish (Stegastes partitus), an abundant reef fish found throughout the Caribbean. These loci will be useful for population genetic and relatedness studies of this species and also appear to be useful in other Caribbean members of the Pomacentridae.
A simple method for isolation of microsatellites from the Japanese squirrel, Sciurus lis, without constructing a genomic library
Authors: Shibata K. , Bandoh K. , Yaekashiwa N. , Matsuzaka T. , Tamate H. B.
Published: November 2003

We developed a simple and easy method to isolate microsatellites without screening genomic libraries by hybridization. The method requires only three basic techniques: polymerase chain reaction, DNA cloning and sequencing. We applied this method to develop microsatellite markers for the Japanese squirrel and isolated 45 clones that contained repetitive sequences. Among the 22 clones that we tested further, we found 11 diagnostic microsatellite loci that are applicable to the molecular ecological study of Japanese squirrels.
A cheap, reliable and rapid method of extracting high‐quality DNA from plants
Authors: Mogg R. J. , Bond J. M.
Published: November 2003

Here we describe a rapid method for extracting DNA from plant material using a microtitre plate system. This extraction procedure has been tested using three species, Brassica napus, Brassica napus/rapa hybrids and Arum maculatum, stored frozen, in silica gel or used fresh. The length of storage was between 7 days and 2 years, and in all cases high molecular weight DNA was reliably purified. Polymerase chain reaction (PCR) testing, using multiplex and single product amplification, inter simple sequence repeats (ISSRs) and microsatellites, was always reliable. This method combines the speed of commercial 96‐well plate methods with the economies associated with readily available laboratory chemicals.
Summary: The Science of Genealogy by Genetics
Authors: Johnston Josephine , Thomas Mark
Published: November 2003

This summary lays out the basic science and methodology used in genetic testing that investigates historical population migrations and the ancestry of living individuals. The genetic markers used in this testing, and the distinction between Y‐chromosome, mitochrondial and autosomes analysis, are explained and the shortcomings of these methodologies are explored.
Diagnosis of Helicobacter pylori infection
Authors: Rautelin Hilpi , Lehours Philippe , Mégraud Francis
Published: November 2003

ABSTRACT Numerous studies are still published on diagnostic tests for Helicobacter pylori, essentially for noninvasive tests. The urea breath test is applied in different types of patients, and there are attempts to have quicker and simpler protocols. Stool tests using monoclonal antibodies are now evaluated while serology is still a subject of interest. The progress in PCR (multiplex PCR, real‐time PCR) has also stimulated the research in this area of invasive tests, in order to get insight into virulence factors, macrolide susceptibility and to detect H. pylori in nonconventional specimens.
Model for the Onset of Fibrillation Following Coronary Artery Occlusion
Authors: KEENER JAMES P.
Published: November 2003

Introduction: It is the hypothesis of this article that the onset of fibrillation following a coronary artery occlusion is a direct consequence of the spatial inhomogeneity of chemical processes that occur following the occlusion. In particular, the localized increase of extracellular potassium and decrease of ATP availability lead to an increase of resting potential in the affected cells. This difference in potential between affected cells and normal cells drives a current, the “current of injury,” which may drive oscillations in the border zone, a “border zone arrhythmia.” The border zone arrhythmia may drive a “breakup instability” (related to the action potential duration restitution instability) in the surrounding tissue, leading to self‐sustained fibrillation.

Methods and Results: In this article, we present a mathematical model demonstrating this transition from normal to fibrillatory dynamics, describing the general conditions under which this transition occurs and showing in a simple ionic model the way in which spatial inhomogeneity alone can initiate self‐sustained reentrant activity.

Conclusion: Using general arguments and numerical simulations with generic models of excitable media, we have demonstrated that a spatial region with an elevated resting potential surrounded by a spatial region wherein action potentials are foreshortened can drive a breakup instability, leading to the rapid initiation of a fibrillatory state. (J Cardiovasc Electrophysiol, Vol. 14, pp. 1225‐1232, November 2003)
Right Ventricular Outflow Versus Apical Pacing in Pacemaker Patients with Congestive Heart Failure and Atrial Fibrillation
Authors: STAMBLER BRUCE S. , ELLENBOGEN KENNETH A. , ZHANG XIAOZHENG , PORTER THOMAS R. , XIE FENG , MALIK RAJESH , SMALL ROY , BURKE MARTIN , KAPLAN ANDREW , NAIR LAWRENCE , BELZ MICHAEL , FUENZALIDA CHARLES , GOLD MICHAEL , LOVE CHARLES , SHARMA ARJUN , SILVERMAN RUSSELL , SOGADE FELIX , VAN NATTA BRUCE , WILKOFF BRUCE L. ,   ROVA Investigators
Published: November 2003

Introduction: Prior studies suggest that right ventricular apical (RVA) pacing has deleterious effects. Whether the right ventricular outflow tract (RVOT) is a more optimal site for permanent pacing in patients with congestive heart failure (CHF) has not been established.

Methods and Results: We conducted a randomized, cross‐over trial to determine whether quality of life (QOL) is better after 3 months of RVOT than RVA pacing in 103 pacemaker recipients with CHF, left ventricular (LV) systolic dysfunction (LV ejection fraction ≤ 40%), and chronic atrial fibrillation (AF). An additional aim was to compare dual‐site (RVOT + RVA, 31‐ms delay) with single‐site RVA and RVOT pacing. QRS duration was shorter during RVOT (167 ± 45 ms) and dual‐site (149 ± 19 ms) than RVA pacing (180 ± 58 ms, P < 0.0001). At 6 months, the RVOT group had higher (P = 0.01) role‐emotional QOL subscale scores than the RVA group. At 9 months, there were no significant differences in QOL scores between RVOT and RVA groups. Comparing RVOT to RVA pacing within the same patient, mental health subscale scores were better (P = 0.03) during RVOT pacing. After 9 months of follow‐up, LVEF was higher (P = 0.04) in those assigned to RVA rather than RVOT pacing between months 6 and 9. After 3 months of dual‐site RV pacing, physical functioning was worse (P = 0.04) than during RVA pacing, mental health was worse (P = 0.02) than during RVOT pacing, and New York Heart Association (NYHA) functional class was slightly better (P = 0.03) than during RVOT pacing. There were no other significant differences between RVA, RVOT and dual‐site RV pacing in QOL scores, NYHA class, distance walked in 6 minutes, LV ejection fraction, or mitral regurgitation.

Conclusion: In patients with CHF, LV dysfunction, and chronic AF, RVOT and dual‐site RV pacing shorten QRS duration but after 3 months do not consistently improve QOL or other clinical outcomes compared with RVA pacing. (J Cardiovasc Electrophysiol, Vol. 14, pp. 1180‐1186, November 2003)
Increase in Ventricular Tachycardia Frequency After Biventricular Implantable Cardioverter Defibrillator Upgrade
Authors: GUERRA JOSE M. , WU JIANYI , MILLER JOHN M. , GROH WILLIAM J.
Published: November 2003

We report the case of a patient in whom transvenous left ventricular pacing lead placement at the time of a biventricular upgrade led to an exacerbation of clinical monomorphic ventricular tachycardia (MVT). At implant, slow left ventricular pacing repeatedly induced sustained MVT. However, testing of the biventricular pacing showed no MVT inducibility, and the system was implanted. The patient was readmitted due to multiple episodes of the MVT observed at implant. The MVT was controlled with pharmacotherapy, allowing the patient to continue with biventricular pacing. (J Cardiovasc Electrophysiol, Vol. 14, pp. 1245‐1247, November 2003)
Techniques for trace element analysis: x‐ray fluorescence, x‐ray excitation with protons, and flame atomic absorption
Authors: Wheeler R. M. , Liebert R. B. , Zabel T. , Chaturvedi R. P. , Valković V. , Phillips G. C. , Ong P. S. , Cheng E. L. , Hrgovcić∥ M.
Published: November 2003

Trace element concentrations in human blood serum have been measured by x‐ray fluorescence and by x‐ray excitation with protons to test the current effectiveness of each technique for routine analysis of biological samples. Results are compared with those obtained from analysis by flame atomic absorption.
Effects of x‐ray tube current and voltage on effective focalspot size
Authors: Chaney Edward L. , Hendee William R.
Published: November 2003

In general, the dimensions of the effective focal spot of an x‐ray tube vary with tube current and voltage. This dependence on tube operating conditions has been noted in the literature but has not been investigated in detail. Star phantom measurements of seven focal spots for four x‐ray tubes operated at a variety of tube voltages and currents show that effective focal‐spot size varies as . This dependence may be suppressed for the focal‐spot dimension perpendicular to the tube axis, however, because of auxiliary electrostatic focusing. Experimental data are presented with a theoretical explanation of the relationship between effective focal‐spot size and tube operating conditions.
Bremsstrahlung radiators and beam filters for 25‐MeV cancer therapy
Authors: Sherman N. K. , Lokan K. H. , Hutcheon R. M. , Funk L. W. , Brown W. R. , Brown P.
Published: November 2003

Bremsstrahlung spectra and on‐axis depth‐dose distributions due to 25.5‐MeV electrons incident on seven different Ta and one Al radiator were studied, with and without beam‐hardening filters of Al and Pb. The photon spectra were measured with a gamma‐ray spectrometer consisting of a liquid deuterium target viewed by a time‐of‐flight detector of photoneutrons. A remote‐controlled, miniature ion chamber was used to measure depth‐dose profiles in a water phantom. The Ta radiators ranged in thickness from 0.012 radiation length up to 1.0 X0. The thinner the radiator, the harder was the measured spectrum. The maximum forward yield was obtained for a thickness of about 0.3 X0. The forward yield and spectral shape of the photon beam from 0.07 X0 of Al as radiator were very similar to those from 0.06 X0 of Ta. Beams produced in Ta radiators and filtered by 27.28 g/cm2 of Al gave a harder spectrum than those filtered by 15.06 g/cm2 of Pb. Total absorption cross sections of Al and Pb for photon energies between 4 and 24 MeV were obtained which agree with theoretical calculations, within measurement errors. The depths in water at which the dose fell to 0.5 of peak dose was greater when the Al filter was used than when the Pb filter was used. For end point energies greater than 10 MeV, beam‐hardening and field‐flattening filters should be made, if space permits, of low‐atomic‐number materials.
Deadtime of scintillation camera systems—definitions, measurement and applications
Authors: Adams Ralph , Jansen Carl , Grames George M. , Zimmerman C. Duane
Published: November 2003

Fast quantitative dynamic studies with scintillation camera systems require deadtime correction. Although such systems are semiparalyzable, they are most conveniently treated either as paralyzable or nonparalyzable. Paralyzing deadtime (τ) is that deadtime during which a system is unable to provide a second output pulse unless there is a time interval of at least τ between two successive events. Paralyzable systems are characterized by Poisson statistics, so that the “true” counting rate , where R is the observed counting rate. Nonparalyzing deadtime (T) is that deadtime during which a system is insensitive after each observed event. The period of insensitivity is not affected by any additional “true” events before full recovery occurs. For nonparalyzable systems the corrected counting rate . A two‐source method protocol is presented for deadtime measurement. The paralyzing deadtime is calculated by a 5‐dimension Newton–Raphson iteration. The nonparalyzing deadtime is calculated by a quadratic equation. Approximation equations are also presented not requiring a computer. Deadtimes are fitted to polynomial equations as dependent variables of measured counting rate. Algorithms incorporating the polynomials are presented for the deadtime correction of histogram curves. Using either the paralyzing or the nonparalyzing approach, precise deadtime corrections are demonstrated.
Calculation of the effects caused by bone present in phantoms irradiated by negatively charged pions
Authors: Santoro R. T. , Alsmiller R. G. , Chandler K. C.
Published: November 2003

The effects caused by bone present in phantoms irradiated by negatively charged pions on absorbed dose, cell survival, oxygen enhancement ratio, and relative biological effectiveness have been estimated using Monte Carlo methods. The influence of bone along the pion path and also the influence of a bone–tissue interface parallel to the direction of motion of the pions have been considered. Calculated results, as a function of spatial coordinates in a 30‐g/cm2‐thick tissue phantom with bone both included and excluded, are presented. All of the biological data reported here are for T‐1 human kidney cells. The extent to which the effects of bone in the path of the pion beam can be approximated by using results for tissue and measuring depth in the phantom in g/cm2 is considered and discussed.
An Arsenate Reductase from
Synechocystis
sp. Strain PCC 6803 Exhibits a Novel Combination of Catalytic Characteristics
Authors: Li Renhui , Haile January D. , Kennelly Peter J.
Published: November 2003

The deduced protein product of open reading frame
slr0946
from
Synechocystis
sp. strain PCC 6803, SynArsC, contains the conserved sequence features of the enzyme superfamily that includes the low-molecular-weight protein-tyrosine phosphatases and the
Staphylococcus aureus
pI258 ArsC arsenate reductase. The recombinant protein product of
slr0946
, rSynArsC, exhibited vigorous arsenate reductase activity (
V
max
= 3.1 μmol/min · mg), as well as weak phosphatase activity toward
p
-nitrophenyl phosphate (
V
max
= 0.08 μmol/min · mg) indicative of its phosphohydrolytic ancestry. pI258 ArsC from
S. aureus
is the prototype of one of three distinct families of detoxifying arsenate reductases. The prototypes of the others are Acr2p from
Saccharomyces cerevisiae
and R773 ArsC from
Escherichia coli.
All three have converged upon catalytic mechanisms involving an arsenocysteine intermediate. While SynArsC is homologous to pI258 ArsC, its catalytic mechanism exhibited a unique combination of features. rSynArsC employed glutathione and glutaredoxin as the source of reducing equivalents, like Acr2p and R773 ArsC, rather than thioredoxin, as does the
S. aureus
enzyme. As postulated for Acr2p and R773 ArsC, rSynArsC formed a covalent complex with glutathione in an arsenate-dependent manner. rSynArsC contains three essential cysteine residues like pI258 ArsC, whereas the yeast and
E. coli
enzymes require only one cysteine for catalysis. As in the
S. aureus
enzyme, these “extra” cysteines apparently shuttle a disulfide bond to the enzyme's surface to render it accessible for reduction. SynArsC and pI258 ArsC thus appear to represent alternative branches in the evolution of their shared phosphohydrolytic ancestor into an agent of arsenic detoxification.
Two Paralogous Families of a Two-Gene Subtilisin Operon Are Widely Distributed in Oral Treponemes
Authors: Correia Frederick F. , Plummer Alvin R. , Ellen Richard P. , Wyss Chris , Boches Susan K. , Galvin Jamie L. , Paster Bruce J. , Dewhirst Floyd E.
Published: November 2003

Certain oral treponemes express a highly proteolytic phenotype and have been associated with periodontal diseases. The periodontal pathogen
Treponema denticola
produces dentilisin, a serine protease of the subtilisin family. The two-gene operon
prcA-prtP
is required for expression of active dentilisin (PrtP), a putative lipoprotein attached to the treponeme's outer membrane or sheath. The purpose of this study was to examine the diversity and structure of treponemal subtilisin-like proteases in order to better understand their distribution and function. The complete sequences of five
prcA
-
prtP
operons were determined for
Treponema lecithinolyticum, “Treponema vincentii,”
and two canine species. Partial operon sequences were obtained for
T. socranskii
subsp. 04 as well as 450- to 1,000-base fragments of
prtP
genes from four additional treponeme strains. Phylogenetic analysis demonstrated that the sequences fall into two paralogous families. The first family includes the sequence from
T. denticola.
Treponemes possessing this operon family express chymotrypsin-like protease activity and can cleave the substrate
N
-succinyl-alanyl-alanyl-prolyl-phenylalanine-
p
-nitroanilide (SAAPFNA). Treponemes possessing the second paralog family do not possess chymotrypsin-like activity or cleave SAAPFNA. Despite examination of a range of protein and peptide substrates, the specificity of the second protease family remains unknown. Each of the fully sequenced
prcA
and
prtP
genes contains a 5′ hydrophobic leader sequence with a treponeme lipobox. The two paralogous families of treponeme subtilisins represent a new subgroup within the subtilisin family of proteases and are the only subtilisin lipoprotein family. The present study demonstrated that the subtilisin paralogs comprising a two-gene operon are widely distributed among treponemes.
Products Transcribed from Rearranged
rrn
Genes of
Escherichia coli
Can Assemble To Form Functional Ribosomes
Authors: Zaporojets Dmitry , French Sarah , Squires Catherine L.
Published: November 2003

To examine the flexibility of rRNA operons with respect to fundamental organization, transcription, processing, and assembly of ribosomes, operon variations were introduced by a plasmid into an
Escherichia coli
strain that has deletions of all chromosomal copies of rRNA genes. In the reconstructed operons, a
Salmonella
intervening sequence (IVS) from 23S helix 45 was introduced into the
E. coli
23S gene at the same position. Three different constructs of the
E. coli
16S gene were then placed wholly within the IVS sequence, and the 16S gene was deleted from its normal position. The resulting plasmids thus had the normal operon promoters and the leader region followed by the 5′ one-third of the 23S gene, the entire 16S gene within the IVS, the last two-thirds of the 23S gene, and the normal end of the operon. The three constructs differed in the amount of 16S leader and spacer regions they contained. Only two of the three constructs, those with redundant leader and spacer antiterminator signals, resulted in viable cultures of the
rrn
deletion strain. Electron micrographs of the variant operon suggest that the 23S rRNA is made in two separate parts which then must form subassemblies before assembling into a functional 50S subunit. Cells containing only the reshuffled genes were debilitated in their growth properties and ribosome contents. The fact that such out of the ordinary manipulation of rRNA sequences in
E. coli
is possible paves the way for detailed analysis of ribosome assembly and evolution.
Genomic Organization and Molecular Characterization of SM1, a Temperate Bacteriophage ofStreptococcus mitis
Authors: Siboo Ian R. , Bensing Barbara A. , Sullam Paul M.
Published: November 2003

The direct binding ofStreptococcus mitisto human platelets is mediated in part by two proteins (PblA and PblB) encoded by a lysogenic bacteriophage (SM1). Since SM1 is the first prophage ofS. mitisthat has been identified and because of the possible role of these phage-encoded proteins in virulence, we sought to characterize SM1 in greater detail. Sequencing of the SM1 genome revealed that it consisted of 34,692 bp, with an overall G+C content of 39 mol%. Fifty-six genes encoding proteins of 40 or more amino acids were identified. The genes of SM1 appear to be arranged in a modular, life cycle-specific organization. BLAST analysis also revealed that the proteins of SM1 have homologies to proteins from a wide variety of lambdoid phages. Bioinformatic analyses, in addition to N-terminal sequencing of the proteins, led to the assignment of possible functions to a number of proteins, including the integrase, the terminase, and two major structural proteins. Examination of the phage structural components indicates that the phage head may assemble using stable multimers of the major capsid protein, in a process similar to that of phage r1t. These findings indicate that SM1 may be part of a discrete subfamily of theSiphoviridaethat includes at least phages r1t ofLactococcus lactisand SF370.3 ofStreptococcus pyogenes.
Long-Term Survival After High-Dose Salvage Chemotherapy for Germ Cell Malignancies With Adverse Prognostic Variables
Authors: Vaena Daniel A. , Abonour Rafat , Einhorn Lawrence H.
Published: November 2003

Purpose: Independent prognostic variables for patients undergoing high-dose chemotherapy (HDCT) as salvage modality for germ cell tumors (GCT) were previously described, and a score was created. Patients with more than 2 points had a poor prognosis. However, these data were from patients treated from 1984 to 1993, and most received a single HDCT course. In this study, we evaluated outcomes at Indiana University and determined the applicability of the Beyer score to contemporary poor-risk patients.

Patients and Methods: We performed a retrospective analysis of patients who received salvage HDCT between 1988 and 2001 and had at least one of the following characteristics: platinum-refractory or absolutely platinum-refractory GCT, primary mediastinal nonseminomatous GCT (PMNSGCT), human chorionic gonadotropin (HCG) ≥ 1,000 mU/mL or alpha-fetoprotein (AFP) ≥ 1,000 ng/mL before HDCT. Primary end points were overall and 2-year failure-free survival (FFS).

Results: Eighty patients were identified. Fifty-six were platinum refractory, 23 had a Beyer score greater than 2, and 13 had PMNSGCT. Fifty-six patients received two HDCT courses. HDCT included carboplatin and etoposide. Forty-three patients received HDCT as first salvage modality. Median overall survival was 14.7 months. The 2-year FFS was 32%. No relapses have occurred after 2 years from HDCT. Patients with greater than 2 points in the Beyer score, platinum-refractory patients, and patients with HCG ≥ 1,000 mU/mL, AFP ≥ 1,000 ng/mL, and PMNSGCT had 2-year FFS of 30%, 37%, 26%, 18%, and 0%, respectively.

Conclusion: Results with PMNSGCT remained poor. However, other patients with poor prognosis should not be denied an attempt at curative salvage HDCT.