bluuebunny/crossref_metadata_2025 huggingface dataset:
2-Methylcitrate-dependent activation of the propionate catabolic operon (prpBCDE) of Salmonella enterica by the PrpR protein
Authors: Palacios Sergio , Escalante-Semerena Jorge C.
Published: November 2004

The function of the PrpR protein ofSalmonella entericaserovar Typhimurium LT2 was studiedin vitroandin vivo. The PrpR protein is a sensor of 2-methylcitrate (2-MC), an intermediate of the 2-methylcitric acid cycle used by this bacterium to convert propionate to pyruvate. PrpR was unresponsive to citrate (a close structural analogue of 2-MC) and to propionate, suggesting that 2-MC, not propionate, is the metabolite that signals the presence of propionate in the environment toS. enterica.prpRalleles encoding mutant proteins with various levels of 2-MC-independent activity were isolated. All lesions causing constitutive PrpR activity were mapped to the N-terminal domain of the protein. Removal of the entire sensing domain resulted in a protein (PrpRc) with the highest 2-MC-independent activity. Residue A162 is critical to 2-MC sensing, since the mutant PrpR protein PrpRA162Twas as active as the PrpRcprotein in the absence of 2-MC. DNA footprinting studies identified the site in the region betweenprpRand theprpBCDEoperon to which the PrpR protein binds. Analysis of the binding-site sequence revealed two sites with dyad symmetry. Results from DNase I footprinting assays suggested that the PrpR protein may have higher affinity for the site proximal to the PprpBCDEpromoter.
Reconstruction of the evolutionary history of the LexA-binding sequence
Authors: Mazón Gerard , Erill Ivan , Campoy Susana , Cortés Pilar , Forano Evelyne , Barbé Jordi
Published: November 2004

In recent years, the recognition sequence of the SOS repressor LexA protein has been identified for several bacterial clades, such as the Gram-positive, green non-sulfur bacteria and Cyanobacteria phyla, or the ‘Alphaproteobacteria’, ‘Deltaproteobacteria’ and ‘Gammaproteobacteria’ classes. Nevertheless, the evolutionary relationship among these sequences and the proteins that recognize them has not been analysed.Fibrobacter succinogenesis an anaerobic Gram-negative bacterium that branched from a common bacterial ancestor immediately before the Proteobacteria phylum. Taking advantage of its intermediate position in the phylogenetic tree, and in an effort to reconstruct the evolutionary history of LexA-binding sequences, theF. succinogenes lexAgene has been isolated and its product purified to identify its DNA recognition motif through electrophoretic mobility assays and footprinting experiments. After comparing the available LexA DNA-binding sequences with theF. succinogenesone, reported here, directed mutagenesis of theF. succinogenesLexA-binding sequence and phylogenetic analyses of LexA proteins have revealed the existence of two independent evolutionary lanes for the LexA recognition motif that emerged from the Gram-positive box: one generating the Cyanobacteria and ‘Alphaproteobacteria’ LexA-binding sequences, and the other giving rise to theF. succinogenesandMyxococcus xanthusones, in a transitional step towards the current ‘Gammaproteobacteria’ LexA box. The contrast between the results reported here and the phylogenetic data available in the literature suggests that, some time after its emergence as a distinct bacterial class, the ‘Alphaproteobacteria’ lost its vertically receivedlexAgene, but received later through lateral gene transfer a newlexAgene belonging to either a cyanobacterium or a bacterial species closely related to this phylum. This constitutes the first report based on experimental evidence of lateral gene transfer in the evolution of a gene governing such a complex regulatory network as the bacterial SOS system.
Identification and analysis of a siderophore biosynthetic gene cluster from Agrobacterium tumefaciens C58
Authors: Rondon Michelle R. , Ballering Katie S. , Thomas Michael G.
Published: November 2004

Using the complete genome sequence fromAgrobacterium tumefaciensC58, the authors identified a secondary metabolite gene cluster that encodes the biosynthesis of a metabolite with siderophore activity. Support for this conclusion came from genetic and regulatory analysis of the gene cluster, along with the purification of a metabolite fromA. tumefaciensC58 with iron-chelating activity. Genetic analysis of mutant strains disrupted in this gene cluster showed that these strains grew more slowly than the wild-type strain in medium lacking iron. Additionally, the mutant strains failed to produce a chrome-azurol-S-reactive material in liquid or solid medium, and failed to produce the metabolite with iron-chelating characteristics that was identified in the wild-type strain. Addition of this purified metabolite to the growth medium of a mutant strain restored its ability to grow in iron-deficient medium. Furthermore, expression of this gene cluster was induced by growth under iron-limiting conditions, suggesting that expression of this gene cluster occurs when iron is scarce. These data are all consistent with the proposal that the proteins encoded by this gene cluster are involved in the production of a siderophore. Interestingly, these proteins show the highest level of amino acid similarity to proteins from a gene cluster found in the filamentous cyanobacteriumNostocsp. PCC7120, rather than to known siderophore biosynthetic enzymes. Given these properties, it is proposed that the siderophore produced byA. tumefaciensC58 will have a unique chemical structure. Production of the siderophore was not required for virulence ofA. tumefacienswhen tested with a standard stem inoculation assay.
BLR-1 and BLR-2, key regulatory elements of photoconidiation and mycelial growth in Trichoderma atroviride
Authors: Casas-Flores Sergio , Rios-Momberg Mauricio , Bibbins Martha , Ponce-Noyola Patricia , Herrera-Estrella Alfredo
Published: November 2004

In fungi, phototropism, the induction of carotenogenesis and reproductive structures, and resetting of the circadian rhythm are controlled by blue light.Trichoderma atroviride, a fungus used in biological control, sporulates in a synchronized manner following a brief pulse of blue light. Due to its apparent simplicity, this response was chosen for pursuing photoreceptor isolation. Two genes were cloned, blue-light regulators 1 and 2 (blr-1andblr-2), similar to theNeurospora crassawhite-collar 1 and 2, respectively. The BLR-1 protein has all the characteristics of a blue-light photoreceptor, whereas the structure of the deduced BLR-2 protein suggests that it interacts with BLR-1 through PAS domains to form a complex. Disruption of the corresponding genes demonstrated that they are essential for blue-light-induced conidiation.blr-1andblr-2were also shown to be essential for the light-induced expression of the photolyase-encoding gene (phr-1). Mechanical injury of mycelia was found to trigger conidiation ofT. atroviride, a response not described previously. This response was not altered in the mutants. A novel effect of both red and blue light on mycelial growth was found involving another light receptor, which is compensated by the BLR proteins.
A calcium signal is involved in heterocyst differentiation in the cyanobacterium Anabaena sp. PCC7120
Authors: Torrecilla I. , Leganés F. , Bonilla I. , Fernández-Piñas F.
Published: November 2004

The impact of calcium signals in virtually all cells has led to the study of their role in prokaryotic organisms as stress response modulators. Cell differentiation in adverse conditions is a common Ca2+-requiring response. Nitrogen starvation induces the differentiation of N2-fixing heterocysts in the filamentous cyanobacterium Anabaena sp. PCC7120. This paper reports the use of a recombinant strain of this organism expressing the photoprotein aequorin to monitor the intracellular free-calcium concentration during the course of heterocyst differentiation. A specific calcium signature that is triggered exclusively when cells are deprived of combined nitrogen and generated by intracellular calcium stores was identified. The intracellular calcium signal was manipulated by treatment with specific calcium drugs, and the effect of such manipulation on the process of heterocyst differentiation was subsequently assessed. Suppression, magnification or poor regulation of this signal prevented the process of heterocyst differentiation, thereby suggesting that a calcium signal with a defined set of kinetic parameters may be required for differentiation. A hetR mutant of Anabaena sp. PCC7120 that cannot differentiate into heterocysts retains, however, the capacity to generate the calcium transient in response to nitrogen deprivation, strongly suggesting that Ca2+ may be involved in a very early step of the differentiation process.
Functional characterization of the BvgAS two-component system of Bordetella holmesii
Authors: Gerlach Gabriele , Janzen Simone , Beier Dagmar , Gross Roy
Published: November 2004

The BvgAS two-component system is the master regulator of virulence gene expression in the mammalian pathogens Bordetella pertussis, Bordetella parapertussis and Bordetella bronchiseptica. This paper reports the partial cloning and characterization of the bvgAS loci of the ‘new’ Bordetella species Bordetella holmesii, Bordetella trematum and Bordetella hinzii, which are increasingly recognized as opportunistic pathogens in humans. It is demonstrated that the cytoplasmic signalling domains of the BvgS histidine kinases of B. pertussis and B. holmesii are functionally interchangeable, while signal perception by the two sensor proteins seems to be different. Furthermore, it is shown that, despite the high similarity of the BvgA proteins of B. pertussis and B. holmesii, promoter recognition by the response regulator proteins differs substantially in these organisms.
Pathogenic and genetic variability among Colletotrichum lindemuthianum isolates of different geographic origins
Authors: Ansari K. I. , Palacios N. , Araya C. , Langin T. , Egan D. , Doohan F. M.
Published: November 2004

The pathogenic and genetic diversity of Colletotrichum lindemuthianum isolates collected from a total of 10 Central and South American, European and African countries were characterized using common bean differential cultivar pathogenicity tests and amplified fragment length polymorphism (AFLP) analysis. On the basis of pathogenicity tests, 74 isolates were attributed to 30 different pathogenic races using the CIAT‐defined binary race‐classification system. Twenty‐one races were restricted geographically, being exclusive to different countries. Race 9 was the most widespread, being detected in four different countries. Cluster analysis of consensus AFLP data generated using three selective AFLP primer combinations grouped 86 isolates (including the 74 subjected to pathogenicity tests) into three clusters (with one isolate as an outlier). This analysis showed that the majority of South and Central American isolates were divided among two clusters, and that the limited number of European and African isolates used in this study were genetically most similar to Central American isolates. Overall, the results of this research showed some associations between the genetic diversity of the isolates and their country of origin, but not between genetic diversity and race classification of isolates.
Biology of a new virus isolated from Lupinus nootkatensis plants in Alaska
Authors: Robertson N. L.
Published: November 2004

A new virus named Nootka lupine vein‐clearing virus (NLVCV) was isolated from Lupinus nootkatensis plants that were confined to a relatively small area in the Talkeetna mountains of south‐central Alaska. Annual surveys (2000–03) consistently found leaf symptoms of pronounced vein clearing and mosaic on 3‐ to 4‐week‐old plants in late June. Spherical particles ≈30 nm in diameter were isolated from these leaves. Virions contained a single‐stranded RNA of ≈4·0–4·2 kb and one species of capsid protein estimated to be ≈40 kDa. The double‐stranded RNA profile from naturally infected leaves consisted of three major bands ≈4·2, 1·9 and 1·5 kbp. Protein extractions from either sap or virions of diseased plants reacted to polyclonal antiserum made against the virions in Western blot assays. A predicted PCR product ≈500 bp was synthesized from virion RNA using primers specific to the carmovirus RNA‐dependent RNA polymerase (RDRP) gene. The nucleotide sequence of the amplified DNA did not match any known virus, but contained short regions of identity to several carmoviruses. Only species belonging to the Fabaceae were susceptible to NLVCV by mechanical inoculation. Based on dsRNA profile, size of virion RNA genome and capsid protein, and similarity of the RDRP gene to that of other carmoviruses, it is suggested that NLVCV is a member of the family Tombusviridae, and tentatively of the genus Carmovirus. As the host range, RDRP gene and dsRNA profile of NLVCV are different from those of known viruses, this is a newly described plant virus.
Phylogeny, evolutionary history and taxonomy of the Mustelidae based on sequences of the cytochrome b gene and a complex repetitive flanking region
Authors: Marmi Josep , López‐Giráldez Juan Francisco , Domingo‐Roura Xavier
Published: November 2004

The Mustelidae is a diverse family of carnivores which includes weasels, polecats, mink, tayra, martens, otters, badgers and, according to some authors, skunks. Evolutionary relationships within the family are under debate at a number of different taxonomic levels, and incongruencies between molecular and morphological results are important. We analysed a total of 241 cytochrome b (cyt b) gene sequences and 33 sequences of a complex repetitive flanking region from 33 different species to compile an extensive molecular phylogeny for the Mustelidae. We analysed these sequences and constructed phylogenetic trees using Bayesian and neighbor‐joining methods that are evaluated to propose changes to the taxonomy of the family. The peripheral position of skunks in phylogenetic trees based on both loci suggests that they should be considered a separate family, Mephitidae. The subfamily Melinae is the basal group within the Mustelidae and trees based on the cyt b gene suggest that the American badger, Taxidea taxus, should be considered a separate monotypic subfamily, Taxidiinae. Otters classified within the genera Lutra, Amblonyx and Aonyx are grouped within the same clade in cyt b and combined partial cyt b and flanking region trees and show reduced levels of inter specific divergence, suggesting that they could be classified together under a single genus, Lutra. The Bayesian tree based on combined data from both loci supports the idea that subfamily Mustelinae is paraphyletic, as otters (subfamily Lutrinae) are included in this subfamily. Low levels of genetic divergence among European polecat, Mustela putorius, steppe polecat, Mustela eversmannii, and European mink, Mustela lutreola, suggest that these species could be considered subspecies within a single species, Mustela putorius. Our results are consistent with a rapid diversification of mustelid lineages in six different radiation episodes identified since the Early Eocene, the oldest events being the separation of subfamilies and the split of marten (Martes, Gulo) and weasel (Mustela) lineages in the Early Middle Miocene. The separation of New World from Old World lineages and the split of the remaining genera are estimated to have occurred in Late Miocene. The most recent events have been the differentiation of species within genera and this probably occurred in four radiation episodes at the end of Late Miocene, Early Pliocene, Late Pliocene and Pleistocene epochs.
Characterization of XerC‐ and XerD‐dependent CTX phage integration in Vibrio cholerae
Authors: McLeod Sarah M. , Waldor Matthew K.
Published: November 2004

CTXφ is a filamentous bacteriophage that encodes cholera toxin and integrates site‐specifically into the larger of the two Vibrio cholerae chromosomes. The CTXφ genome lacks an integrase; instead, its integration depends on the chromosome‐encoded tyrosine recombinases XerC and XerD. During integration, recombination occurs between regions of homology in CTXφ and the V. cholerae chromosome. Here, we define the elements on the phage genome (attP ) and bacterial chromosome (attB) required for CTXφ integration. attB is a short sequence composed of one binding site for XerC and XerD spanning the site of recombination. Together, XerC and XerD bind to two sites within attP. While one XerC/D binding site in attP spans the core recombination region, the other site is ≈ 80 bp away. Although integration occurs at the core XerC/D binding site in attP, the second site is required for CTXφ integration, suggesting it performs an architectural role in the integration reaction. In vitro cleavage reactions showed that XerC and XerD are capable of cleaving attB and attP sequences; however, additional cellular processes such as DNA replication or Holliday junction resolution by a host resolvase may contribute to integration in vivo.
The Era‐like GTPase TrmE conditionally activates gadE and glutamate‐dependent acid resistance in Escherichia coli
Authors: Gong Shimei , Ma Zhuo , Foster John W.
Published: November 2004

Escherichia coli survives pH 2 acid stress at a level rivalling Helicobacter pylori. Of the three E. coli acid resistance systems involved, the one most efficient and most studied uses isozymes of glutamate decarboxylase (GadA/GadB) to consume intracellular protons, and a glutamate:γ‐amino butyric acid (GABA) anti‐porter (GadC) to expel GABA in exchange for extracellular glutamate. Because acid resistance is a critical factor in resisting stomach acidity, mechanisms that control this system are extremely important. Here we show that an Era‐like, molecular switch GTPase called TrmE regulates glutamate‐dependent acid resistance. Western blot analysis revealed a TrmE‐dependent, glucose‐induced system and a TrmE‐independent, glucose‐repressed pathway. Gene fusion studies indicated that the TrmE requirement for GadA/B production takes place at both the transcriptional and translational levels. TrmE controls GAD transcription by affecting the expression of GadE, the essential activator of the gadA and gadBC genes. TrmE most probably controls gadE expression indirectly by influencing the synthesis or activity of an unknown regulator that binds the gadE control region. Translational control of GAD production by TrmE appears to be more direct, affecting synthesis of the decarboxylase and the anti‐porter proteins. TrmE GTPase activity was critical for both the transcriptional and translational effects. Thus, TrmE is part of an increasingly complex control network designed to integrate diverse physiological signals and forecast future exposures to extreme acid. The significance of this network extends beyond acid resistance as the target of this control, GadE, regulates numerous genes in addition to gadA/BC.
Alternative oxygen‐dependent and oxygen‐independent ribonucleotide reductases in Streptomyces: cross‐regulation and physiological role in response to oxygen limitation
Authors: Borovok Ilya , Gorovitz Batia , Yanku Michaela , Schreiber Rachel , Gust Bertolf , Chater Keith , Aharonowitz Yair , Cohen Gerald
Published: November 2004

Ribonucleotide reductases (RNRs) catalyse the conversion of ribonucleotides to deoxyribonucleotides and are essential for de novo DNA synthesis and repair. Streptomyces spp. contain genes coding for two RNRs. We show here that the Streptomyces coelicolor M145 nrdAB genes encoding an oxygen‐dependent class I RNR are co‐transcribed with nrdS, which encodes an AraC‐like regulatory protein. Likewise, the class II oxygen‐independent RNR nrdJ gene forms an operon with a likely regulatory gene, nrdR, which encodes a protein possessing an ATP‐cone domain like those present in the allosteric activity site of many class Ia RNRs. Deletions in nrdB and nrdJ had no discernible effect on growth individually, but abolition of both RNR systems, using hydroxyurea to inactivate the class Ia RNR (NrdAB) in the nrdJ deletion mutant, was lethal, establishing that S. coelicolor possesses just two functional RNR systems. The class II RNR (NrdJ) may function to provide a pool of deoxyribonucleotide precursors for DNA repair during oxygen limitation and/or for immediate growth after restoration of oxygen, as the nrdJ mutant was slower in growth recovery than the nrdB mutant or the parent strain. The class Ia and class II RNR genes show complex regulation. The nrdRJ genes were transcribed some five‐ to sixfold higher than the nrdABS genes in vegetative growth, but when nrdJ was deleted, nrdABS transcription was upregulated by 13‐fold. In a reciprocal experiment, deletion of nrdB had little effect on nrdRJ transcription. Deletion of nrdR caused a dramatic increase in transcription of nrdJ and to a less extent nrdABS, whereas disruption of cobN, a gene required for synthesis of coenzyme B12 a cofactor for the class II RNR, caused similar upregulation of transcription of nrdRJ and nrdABS. In contrast, deletion of nrdS had no detectable effect on transcription of either set of RNR genes. These results establish the existence of control mechanisms that sense and regulate overall RNR gene expression.
A second‐site suppressor of a folding defect functions via interactions with a chaperone network to improve folding and assembly in vivo
Authors: Parent Kristin N. , Ranaghan Matthew J. , Teschke Carolyn M.
Published: November 2004

Single amino acid substitutions in a protein can cause misfolding and aggregation to occur. Protein misfolding can be rescued by second‐site amino acid substitutions called suppressor substitutions (su), commonly through stabilizing the native state of the protein or by increasing the rate of folding. Here we report evidence that su substitutions that rescue bacteriophage P22 temperature‐sensitive‐folding (tsf) coat protein variants function in a novel way. The ability of tsf:su coat proteins to fold and assemble under a variety of cellular conditions was determined by monitoring levels of phage production. The tsf:su coat proteins were found to more effectively utilize P22 scaffolding protein, an assembly chaperone, as compared with their tsf parents. Phage‐infected cells were radioactively labelled to quantify the associations between coat protein variants and folding and assembly chaperones. Phage carrying the tsf:su coat proteins induced more GroEL and GroES, and increased formation of protein:chaperone complexes as compared with their tsf parents. We propose that the su substitutions result in coat proteins that are more assembly competent in vivo because of a chaperone‐driven kinetic partitioning between aggregation‐prone intermediates and the final assembled state. Through more proficient use of this chaperone network, the su substitutions exhibit a novel means of suppression of a folding defect.
Genetic screening of Hrp type III‐related pathogenicity genes controlled by the HrpB transcriptional activator in Ralstonia solanacearum
Authors: Mukaihara Takafumi , Tamura Naoyuki , Murata Yukio , Iwabuchi Masaki
Published: November 2004

As in many other Gram‐negative phytopathogenic bacteria, the Hrp type III secretion system is essential for the pathogenicity of Ralstonia solanacearum on host plants. The expression of most of the type III effector genes previously isolated from R. solanacearum is co‐regulated with those of hrp genes by an AraC‐type transcriptional activator, HrpB. In order to isolate type III‐related pathogenicity genes, we screened hrpB‐regulated genes in R. solanacearum. Using a transposon‐based system, we isolated 30 novel hpx (hrpB‐dependent expression) genes outside the hrp gene cluster. Most of the hpx genes contain a PIP (plant‐inducible promoter) box‐like motif in their putative promoter regions. Seven hpx genes encoded homologues of known type III effectors and type III‐related proteins found in other animal and plant pathogens. Four encoded known enzymes, namely, glyoxalase I, Nudix hydrolase, spermidine synthase and transposase. Interestingly, six hpx genes encoded two types of leucine‐rich repeat (LRR) protein. Products of the remaining genes did not show any significant homology to known proteins. We also identified two novel hrpB‐regulated genes, hpaZ and hpaB, downstream of hrpY in the hrp cluster. The hpaB gene of R. solanacearum, but not hpaZ, was required for both the pathogenicity and ability to induce hypersensitive reaction on plants. We show that a hpaB null mutant still produces Hrp pili on the cell surface although it shows a typical Hrp‐defective phenotype on plants.
MicroCommentary: Smarter than the average phage
Authors: Blakely Garry W.
Published: November 2004

The seventh cholera pandemic emerged in the poorer nations of the world towards the end of the 20th century and continues to kill thousands of people per year. The causative agent of cholera, the Gram‐negative bacterium Vibrio cholera, is only pathogenic when it contains a lysogenic bacteriophage, CTXφ, that encodes the toxin responsible for inducing massive fluid loss from the human host. Site‐specific integration of CTXφ into chromosome I of V. cholera occurs at a site, dif, that is normally required for resolution of chromosome dimers generated by homologous recombination. An article in this issue of Molecular Microbiology reports the analysis of interactions between two host encoded recombinases, XerC and XerD, and the recombination sites involved in lysogeny. Surprisingly, recombination between the CTXφattP site and the chromosomal dif site requires additional recombinase binding sites, downstream from the positions of strand exchange, which might play an architectural role. The positions of strand cleavage also differ significantly between the two sites, suggesting a novel recombination mechanism that implicates additional host factors in resolution of the Holliday junction intermediate.
Quorum sensing and the LysR‐type transcriptional activator ToxR regulate toxoflavin biosynthesis and transport in Burkholderia glumae
Authors: Kim Jinwoo , Kim Jung‐Gun , Kang Yongsung , Jang Ji Youn , Jog Geetanjali J. , Lim Jae Yun , Kim Suhyun , Suga Hiroaki , Nagamatsu Tomohisa , Hwang Ingyu
Published: November 2004

Burkholderia glumae BGR1 produces a broad‐host range phytotoxin, called toxoflavin, which is a key pathogenicity factor in rice grain rot and wilt in many field crops. Our molecular and genetic analyses of toxoflavin‐deficient mutants demonstrated that gene clusters for toxoflavin production consist of four transcriptional units. The toxoflavin biosynthesis genes were composed of five genes, toxA to toxE, as Suzuki et al. (2004) reported previously. Genes toxF to toxI, which are responsible for toxoflavin transport, were polycistronic and similar to the genes for resistance‐nodulation‐division (RND) efflux systems. Using Tn3‐gusA reporter fusions, we found that ToxR, a LysR‐type regulator, regulates both the toxABCDE and toxFGHI operons in the presence of toxoflavin as a coinducer. In addition, the expression of both operons required a transcriptional activator, ToxJ, whose expression is regulated by quorum sensing. TofI, a LuxI homologue, was responsible for the biosynthesis of both N‐hexanoyl homoserine lactone and N‐octanoyl homoserine lactone (C8‐HSL). C8‐HSL and its cognate receptor TofR, a LuxR homologue, activated toxJ expression. This is the first report that quorum sensing is involved in pathogenicity by the regulation of phytotoxin biosynthesis and its transport in plant pathogenic bacteria.
MicroReview: Growth versus maintenance: a trade‐off dictated by RNA polymerase availability and sigma factor competition?
Authors: Nyström Thomas
Published: November 2004

The regulatory design of higher organisms is proposed to comprise a trade‐off between activities devoted to reproduction and those devoted to cellular maintenance and repair. Excessive reproduction will inevitably limit the organism's ability to resist stress whereas excessively devoted stress defence systems may increase lifespan but reduce Darwinian fitness. The trade‐off is arguably a consequence of limited resources in any one organism but the nature and identity of such limiting resources are ambiguous. Analysis of global control of gene expression in Escherichia coli suggests that reproduction and maintenance activities are also at odds in bacteria and that this antagonism may be a consequence of a battle between transcription factors for limiting RNA polymerase. The outcome of this battle is regulated and depends on the nutritional status of the environment, the levels of the alarmone ppGpp, and RNA polymerase availability. This paper reviews how the concentration of RNA polymerase available for transcription initiation may vary upon shifts between growth and growth‐arrest conditions and how this adjustment may differentially affect genes whose functions relate to reproduction and maintenance.
Residential mobility during pregnancy
Authors: Fell Deshayne B. , Dodds Linda , King Will D.
Published: November 2004

In epidemiological studies of environmental exposures and adverse pregnancy outcomes, maternal residence at delivery is often used to assign an exposure level, based on routinely collected data. In order to examine the potential for exposure misclassification due to residential mobility, we examined maternal mobility according to changes in residence overall, as well as changes in municipality and county. The potential for mobility to be related to pregnancy outcomes was considered by examining the relationship between mobility and risk factors commonly included in investigations of adverse pregnancy outcomes.

Previously collected data were studied from 398 population‐based control subjects from a case‐control study of stillbirths. We compared demographic, lifestyle, medical, pregnancy and environmental factors of women who moved during pregnancy with those who did not. Bivariable and multivariable log binomial regressions were used to identify risk factors that were associated with mobility during pregnancy.

Twelve per cent of subjects moved at least once during their pregnancy. Among women who moved, the majority (62%) moved within the same municipality. In bivariable analyses, we found that low family income, lower maternal age, unmarried status and tobacco use were associated with an increased likelihood of moving during pregnancy, whereas women who used folic acid before conception and who had a higher prepregnancy body mass index (BMI) were less likely to move during pregnancy. In multivariable analyses, only family income, age and prepregnancy BMI were independently predictive of mobility.

These results indicate that in studies using maternal residence at delivery to assign environmental exposures, mobility during pregnancy is likely to be prevalent enough to introduce exposure misclassification. The potential for differential exposure misclassification should be considered should any of the risk factors for moving identified by this study also be risk factors for the outcome under study.
Risk factors in term children for visual impairment without a known prenatal or postnatal cause
Authors: Tornqvist Kristina , Källén Bengt
Published: November 2004

Risk factors were studied for visual impairment in children without known pre‐ or postnatal cause, for a decrease of visual acuity. Children born at term 1979–98 and with a visual impairment were identified from the Swedish Register of Visually Impaired Children and data were linked with the Swedish Medical Birth Registry. Maternal characteristics such as maternal age, parity, maternal smoking habits in early pregnancy, maternal education, nationality, and subfertility were studied as well as maternal diagnoses such as pre‐eclampsia, prolonged second stage of labour, abruptio placentae, and placenta praevia. Mode of delivery was analysed as well as birthweight, and birthweight in relation to gestational age.

Abruptio placentae turned out to be the strongest risk factor (OR = 8.24 [95% CI 5.01, 13.51]). Smoking did not give a statistically significant increased risk. There is an increased risk with breech delivery (OR = 2.01 [95% CI 1.28, 3.17]). Pre‐eclampsia was associated with an increased risk (OR = 2.22 [95% CI 1.46, 3.38]). There is also an increase in risk at low birthweight and small‐for‐gestational‐age as well as birthweight > 4 kg and large‐for‐gestational‐age.

In this study we found that risk factors particularly worth noticing in term children with a presumed perinatal cause of visual impairment are abruptio placentae, pre‐eclampsia, excessively low as well as excessively high birthweight, and breech delivery, a fact worth noticing in current discussion on risks, advantages or excessive exploitation of caesarean section.
Methods for identifying pregnancy‐associated deaths: population‐based data from Finland 1987–2000
Authors: Gissler Mika , Berg Cynthia , Bouvier‐Colle Marie‐Hélène , Buekens Pierre
Published: November 2004

To find maternal and pregnancy‐related deaths, it is important that all pregnancy‐associated deaths are identified. This article examines the effect of data linkages between national health care registers and complete death certificate data on pregnancy‐associated deaths. All deaths among women of reproductive age (15–49 years) in Finland during the period 1987–2000 (n = 15 823) were identified from the Cause‐of‐Death Register and linked to the Medical Birth Register (n = 865 988 births), the Register on Induced Abortions (n = 156 789 induced abortions), and the Hospital Discharge Register (n = 118 490 spontaneous abortions) to determine whether women had been pregnant within 1 year before death. The death certificates of the 419 women thus identified were reviewed to find whether the pregnancy or its termination was coded or mentioned. In total, 405 deaths (96.7%) were identified in registers other than the Cause‐of‐Death Register. Without data linkages, 73% of all pregnancy‐associated deaths would have been missed; the percentage after induced and spontaneous abortions was even higher. Data linkages to national health care registers provide better information on maternal deaths and pregnancy‐associated deaths than death certificates alone. If possible, pregnancies not ending in a live birth should be included in the data linkages.
Artificial neural networks as statistical tools in epidemiological studies: analysis of risk factors for early infant wheeze
Authors: Sherriff Andrea , Ott Jurg ,   the ALSPAC Study Team
Published: November 2004

Artificial neural networks (ANNs) are being used increasingly for the prediction of clinical outcomes and classification of disease phenotypes. A lack of understanding of the statistical principles underlying ANNs has led to widespread misuse of these tools in the biomedical arena. In this paper, the authors compare the performance of ANNs with that of conventional linear logistic regression models in an epidemiological study of infant wheeze. Data on the putative risk factors for infant wheeze have been obtained from a sample of 7318 infants taking part in the Avon Longitudinal Study of Parents and Children (ALSPAC). The data were analysed using logistic regression models and ANNs, and performance based on misclassification rates of a validation data set were compared. Misclassification rates in the training data set decreased as the complexity of the ANN increased: h = 0: 17.9%; h = 2: 16.2%; h = 5: 14.9%, and h = 10: 9.2%. However, the more complex models did not generalise well to new data sets drawn from the same population: validation data set misclassification rates: h = 0: 17.9%; h = 2: 19.6%; h = 5: 20.2% and h = 10: 22.9%. There is no evidence from this study that ANNs outperform conventional methods of analysing epidemiological data. Increasing the complexity of the models serves only to overfit the model to the data. It is important that a validation or test data set is used to assess the performance of highly complex ANNs to avoid overfitting.
Descriptive epidemiology of selected congenital heart defects, Hawaii, 1986–1999
Authors: Forrester Mathias B. , Merz Ruth D.
Published: November 2004

Congenital heart defects are the most common type of birth defect and contribute the most to infant mortality due to birth defects. This study examined the relationship between several demographic factors and selected congenital heart defects among the unique multiethnic population in Hawaii during 1986–99, using data from a population‐based birth defects registry. Rates were significantly higher in 1993–99 than in 1986–92 for transposition of the great arteries and Ebstein's anomaly, and significantly lower for tetralogy of Fallot. Significantly elevated rates were found with maternal age of ≥35 years for ventricular septal defect, atrial septal defect, endocardial cushion defect, and hypoplastic left heart syndrome. When cases with a known chromosomal abnormality were excluded, elevated rates among the older maternal age group remained for ventricular septal defect, atrial septal defect, and hypoplastic left heart syndrome. Whites had significantly higher rates than one or more of the other racial/ethnic groups for Ebstein's anomaly and coarctation of aorta, and significantly lower rates for tetralogy of Fallot, atrial septal defect, pulmonary valve atresia/stenosis, tricuspid valve atresia/stenosis, and anomalous pulmonary venous return. Significantly higher rates were found among males for transposition of great arteries, aortic valve stenosis, and interrupted aortic arch and, among females, for ventricular septal defect, endocardial cushion defect, and anomalous pulmonary venous return. Some of these differences were consistent with the literature while others were not.
Leisure‐time physical activity among pregnant women in the US
Authors: Evenson Kelly R. ,   David, Savitz A. , Huston Sara L.
Published: November 2004

Few population‐based data exist that describe leisure‐time physical activity among pregnant women. The purpose of this study was to characterise the prevalence of leisure activity and to examine characteristics associated with participation in leisure activity during pregnancy. Using data collected from the year 2000 Behavioral Risk Factor Surveillance System, information on leisure activity was collected during telephone interviews from 1979 pregnant women and 44 657 non‐pregnant women 18–44 years of age, representative of the US population. The prevalence of any leisure activity in the past month was 65.6%, 95% confidence interval [95% CI] 62.0, 69.1, among pregnant women and 73.1%[95% CI 72.4, 73.9] among non‐pregnant women. The prevalence of recommended activity was also lower among pregnant women than non‐pregnant women (15.8% vs. 26.1%). The most common leisure activity for pregnant women was walking, followed by activities such as swimming laps, weight lifting, gardening, and aerobics. Among pregnant women, any leisure activity was significantly higher for those with higher education, younger age, and excellent or very good health than for those with fair or poor health. Pregnant women reported less leisure activity than non‐pregnant women of the same age. Studies to understand the enablers and barriers to participating in leisure activity during pregnancy are needed.
Association of early‐onset otitis media in infants and exposure to household mould
Authors: Pettigrew Melinda M. , Gent Janneane F. , Triche Elizabeth W. , Belanger Kathleen D. , Bracken Michael B. , Leaderer Brian P.
Published: November 2004

Otitis media is one of the most common infections of early childhood. Children who first experience acute otitis media at an early age (before 6 months) are at increased risk for recurrent otitis media. This prospective study investigated exposure to measured levels of airborne household mould and the risk of early otitis media in the first 6 months of life among a cohort of infants at high risk for asthma. Between September 1996 and December 1998, women were invited to participate if they had at least one other child with physician‐diagnosed asthma. Mothers were given a standardised questionnaire within 4 months of their infant's birth. Airborne mould samples were also taken at this time, and culturable fungi were categorised into four levels according to the report of the Commission of European Communities: 0 (undetectable), 1–499 colony forming units (CFU)/m3 (low), 500–999 CFU/m3 (medium), ≥1000 CFU/m3 (high). Infant respiratory symptoms were collected during quarterly telephone interviews at 6, 9 and 12 months of age.

 Of the 806 children in the study, 27.8% experienced otitis media before six months of age. Household levels of Penicillium and Cladosporium were modestly associated with the number of otitis media episodes (P = 0.056 and 0.081 respectively). After controlling for potential confounders, Penicillium and Cladosporium were not associated with early otitis media. High levels of ‘other’ mould (defined as total spore count minus counts for Penicillium, Cladosporium, and yeast) were associated with early otitis media (OR 3.49; 95% CI [1.38, 8.79]). We also found associations between day‐care outside of the home and birth during the summer or fall season with early otitis media. This study is suggestive of a relationship between otitis media and mould that warrants further study.
Real‐time PCR for detection and quantification of Erwinia amylovora, the causal agent of fireblight
Authors: Salm H. , Geider K.
Published: November 2004

Real‐time PCR was used for quantitative detection of Erwinia amylovora, the causative agent of fireblight. Specific primers were created from a DNA fragment of the common plasmid pEA29, successfully used for standard PCR identification of the pathogen. The primers amplified DNA from various E. amylovora strains, but not from other plant‐associated bacteria. DNA of E. amylovora was also amplified from field samples and from inoculated apple leaves or flowers. Neither the presence of other bacteria nor low amounts of tissue extracts from bark or leaves changed the signal threshold. Assays with SYBR Green I instead of the Taqman probe showed a similar sensitivity, detecting 50 cells per assay. Real‐time PCR could be especially useful for mass screening of commercial products and for resistance studies of transgenic host plants, in breeding experiments and after treatments to control fireblight.
Illite K–Ar dating and crystal growth processes in diagenetic environments: a critical review
Authors: Meunier Alain , Velde Bruce , Zalba Patricia
Published: November 2004

K–Ar dating of illitic minerals is commonly used in studies of diagenetic series applied to oil prospecting. In spite of a great number of specialized papers, some problems remain unresolved. These are mostly due to a misunderstanding of the argon accumulation process during illitization. Criteria for identifying detrital–authigenic mineral mixtures, crystal ripening, fast precipitation or continuous nucleation‐growth processes are discussed using K–Ar data available in the literature. Using different parameters, such as Δage (ageK–Ar − agestrati), Δcryst (diagenetic ageK–Ar − agestrati) or Δfrac (ageK–Arfraction −ageK–Arfinest), it is shown that the K–Ar age significance depends on the illite nucleation–growth processes. A ‘diagenetic age’ is obtained when these processes are rapid (the K2O accumulation period is shorter than 2σ). If lower than this value, the K–Ar ratio depends on the proportions of new and old particles, respectively, which are controlled by the relative rates of nucleation, crystal growth and ripening.
Antikörper‐Nachweis bei invasiver Aspergillose
Authors: Kappe R. , Rimek D.
Published: November 2004

Der Stellenwert von Aspergillus‐Antikörpertesten zur Diagnostik der invasiven Aspergillose (IA) ist unklar. In zwei Studien wurden drei verschiedene Antikörperteste an Patienten mit gesicherter IA evaluiert: (i) kommerzieller Hämagglutinationstest (HAT), (ii) kommerzieller Enzymimmunoassay (EIA) IgG, IgM, IgA und (iii) ein experimenteller Mitogillin EIA IgG, IgM, IgA. In der ersten Studie wurden 99 Serumproben von 26 Patienten mit IA und 22 Serumproben von 22 Kontrollpatienten mit allen drei Tests untersucht. 10 von 26 Patienten (38%) waren in mindestens einem Antikörpertest positiv. Die höchste Sensitivität wies der IgG‐Nachweis in beiden EIA‐Tests auf (22 bzw. 21%), der HAT erreichte eine Sensitivität von 8%. IgM‐Antikörper wurden nur bei zwei Patienten, IgA‐Antikörper bei keinem Patienten nachgewiesen. Die Spezifität des HAT betrug 85%, des IgG‐EIA 72%. Bei zwei Patienten mit gesicherter bzw. wahrscheinlicher IA war der Antikörpernachweis der einzig positive Labortest. In der zweiten Studie wurden retrospektiv die Ergebnisse von 60 Patienten mit gesicherter IA untersucht. 14 Patienten (23%) wiesen einen positiven Antikörpernachweis im EIA und/oder HAT auf. Die Untersuchung des zeitlichen Verlaufs der Antikörper zeigte, daß die IgG‐Antikörperbildung bei immunsupprimierten Patienten durchschnittlich 10,8 Tage nach der Diagnosestellung der IA einsetzte.

Schlußfolgerungen

Aspergillus‐Antikörper waren bei ca. 23% der Patienten mit invasiver Aspergillose nachweisbar. Die Antikörperbildung setzte bei erfolgreich therapierten immunsupprimierten Patienten durchschnittlich 10,8 Tage nach Beginn der Infektion ein. Insbesondere der IgG‐Antikörpernachweis im EIA‐Format kann hilfreich für die Diagnose‐Sicherung und Verlaufskontrolle sein.
Mykoserologische Untersuchungen an chirurgischen Intensivtherapie‐Patienten und bei Candida‐Ösophagitis
Authors: Bernhardt J. , Ludwig K.
Published: November 2004

Wir werteten retrospektiv die Ergebnisse eines serodiagnostischen Monitorings von 126 chirurgisch‐intensivmedizinischen Patienten hinsichtlich einer möglichen oberflächlichen und/oder invasiven Candida‐Infektion aus. Die Patienten waren zu einem hohen Prozentsatz mykoserologisch positiv (Candida‐Hämagglutinationstest 86,4%, Immunglobulin‐Subklassen 85,3%), was auf eine erhöhte Exposition hindeutet. Von den mikrobiologisch und kulturell untersuchten Patienten wiesen 43,7% einen Candida‐Befall auf. Dies war bei 83,9% mit einem erhöhten HAT‐Titer und in 74,2% mit erhöhten Immunglobulin‐ELISA‐Werten verbunden. Für diese letztgenannten Patienten wurde eine Candidose als möglich oder wahrscheinlich angesehen. Je invasiver die Infektion war wie bei einer positiven Blutkultur, einem invasiven Schleimhautbefall des Ösophagus oder einem positiven Urinbefund, desto häufiger fanden sich erhöhte Titerwerte.
Candida‐spezifische Antikörper bei Intensivtherapiepatienten und Nichtintensivtherapiepatienten
Authors: Knoke M. , Bernhardt H.
Published: November 2004

Die Titer des indirekten Anti‐Candida‐Hämagglutinationstests (C‐HAT) und der spezifischen Immunglobuline C‐IgM, C‐IgG und C‐IgA bei 328 Intensivtherapiepatienten (IT) und 166 Nichtintensivtherapiepatienten (NIT) wurden mit Hilfe verschiedener statistischer Prüfverfahren verglichen. Positive Korrelationen wurden zwischen den Werten des C‐HAT und denen aller drei Candida‐spezifischen Immunglobuline gesehen. Nur in der ersten Patientengruppe waren in der Verlaufsuntersuchung vor allem bei einem Abstand von ≤7 Tagen zwischen zwei Bestimmungen statistisch hochsignifikante Veränderungen zu sehen, die als kurzfristige Titeranstiege beim C‐IgM in Verbindung mit dem klinischen Bild im Sinne einer stattgefundenen mykotischen Infektion gedeutet werden können. So fanden wir innerhalb von sieben Tagen bei den IT‐Patienten einen durchschnittlichen Anstieg des C‐IgM um 259,3, des C‐IgG um 174,7 und des C‐IgA um 59,8 U ml−1 sowie des C‐HAT um drei Titerstufen. Nach unseren Erfahrungen sollte für die Diagnostik von mykotischen Infektionen in Intensivtherapiebereichen mit nichtneutropenischen Patienten in kurzfristigen Verlaufsuntersuchungen auf die Bestimmung der Anti‐Candida‐Immunglobulin‐Subklassen C‐IgM und C‐IgG sowie des C‐HAT als Screening‐Test nicht verzichtet werden.