bluuebunny/crossref_metadata_2025_split huggingface dataset:
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

Summary 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

SummaryRibonucleotide 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

SummarySingle 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

SummaryAs 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

SummaryThe 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

Summary 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

SummaryThe 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

SummaryIn 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

SummaryRisk 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

SummaryTo 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

SummaryArtificial 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

SummaryCongenital 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

SummaryFew 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.