bluuebunny/crossref_metadata_2025 huggingface dataset:
Prevalence of dental caries and periodontal disease in patients with inflammatory bowel disease: a case–control study
Authors: Grössner‐Schreiber Birte , Fetter Thomas , Hedderich Jürgen , Kocher Thomas , Schreiber Stefan , Jepsen Søren
Published: June 2006

Aim: Previous reports suggest a higher incidence of dental caries in patients with inflammatory bowel disease (IBD) and similarities in the immunopathogenesis of IBD and periodontitis. This study assessed the prevalence of periodontal disease and caries in patients with IBD.

Methods: In the present case–control study, 62 patients seeking treatment of IBD and 59 matched healthy controls of a dental practice were clinically examined. Oral soft‐tissue alterations, the decayed, missing and filled tooth surface (DMF‐S) index, dentine caries, plaque index (PI), bleeding on probing (BOP), probing pocket depth (PPD) and clinical attachment loss (CAL) were evaluated in each patient and in the controls.

Results: Patients with IBD showed a significantly higher number of oral manifestations compared with controls. The DMF‐S index showed no significant differences, but there was a significantly higher number of subjects with dentine caries in patients with IBD. The mean PPD in patients with IBD was 2.08 versus 2.23 mm in controls (p=0.014). Compared with controls, patients with IBD had more sites with CAL of at least 4 mm (81%versus 64% in controls, p=0.07) and 5 mm (63%versus 46%, p=0.07), respectively.

Conclusions: The results of this case–control study demonstrate a higher frequency of dentine caries in patients with IBD but the periodontal findings showed no distinct differences between cases and controls.
Winter short‐distance migration of juvenile fish between two floodplain water bodies of the Lower River Rhine
Authors: Heermann L. , Borcherding J.
Published: June 2006

Abstract –  During winter, large numbers of juvenile fishes (mainly roach, Rutilus rutilus L.) were observed to migrate at dawn from a floodplain lake into a connected channel, whereas they migrated in the opposite direction at dusk. The diurnal migration pattern was strongly correlated to light intensity. The total number of migrating fish decreased from autumn to spring. Ice coverage and water temperature were the only abiotic factors that affected the seasonal migration pattern significantly. Moonlight, water level, current velocity, rainfall, insolation and wind velocity did not influence the observed migration of juvenile fish. The results are discussed in relation to food availability, predation risk and energy conservation.
Individual variability of diel vertical migrations in European vendace (Coregonus albula) explored by stationary vertical hydroacoustics
Authors: Mehner T.
Published: June 2006

Abstract –  Diel vertical migration (DVM) is a widespread behavioural pattern in populations of aquatic animals. Its adaptive value is explained by a trade‐off between the protection against visually feeding predators in the dark hypolimnion during daytime, and a higher food uptake in the upper food‐rich layers during the night. Whereas vertical migration patterns of entire populations have been frequently described, less is known with respect to individual variability of DVM within fish populations. Here, individual migration patterns of European vendace (Coregonus albula) are described, obtained by stationary vertical hydroacoustics in Lake Stechlin (Germany) during the dusk and dawn phases of 2 months in 2004. The variability of speeds of depth change was high, with only a few fish rising or falling faster than 1 cm s−1. Swimming activity was not dependent on fish size. There was some evidence that variability of echo strengths was highest in those fish which showed the greatest three‐dimensional swimming distances which might indicate a limited swimbladder compensation during vertical migrations. However, migration seems to be performed mainly in a saltatory mode with vertical swimming always interrupted by phases of constant depth. It is suggested that these phases are used for pressure compensation by fish with the consequence that overall the frequency distribution of target strengths deviates only slightly between the start and the end of the recordings. Stationary hydroacoustics proved to be a useful tool for studying individual fish swimming behaviour.
Effects of predator‐induced visual and olfactory cues on 0+ perch (Perca fluviatilis L.) foraging behaviour
Authors: Mikheev V. N. , Wanzenböck J. , Pasternak A. F.
Published: June 2006

Abstract –  Foraging juvenile fish with relatively high food demands are usually vulnerable to various aquatic and avian predators. To compromise between foraging and antipredator activity, they need exact and reliable information about current predation risk. Among direct predator‐induced cues, visual and olfactory signals are considered to be most important. Food intake rates and prey‐size selectivity of laboratory‐reared, naive young‐of‐the‐year (YOY) perch, Perca fluviatilis, were studied in experiments with Daphnia magna of two size classes: 2.8 and 1.3 mm as prey and northern pike, Esox lucius, as predator. Neither total intake rate nor prey‐size selectivity was modified by predator kairomones alone (water from an aquarium with a pike was pumped into the test aquaria) under daylight conditions. Visual presentation of pike reduced total food intake by perch. This effect was significantly more pronounced (synergistic) when visual and olfactory cues were presented simultaneously to foraging perch. Moreover, the combination of cues caused a significant shift in prey‐size selection, expressed as a reduced proportion of large prey in the diet. Our observations demonstrate that predator‐induced olfactory cues alone are less important modifiers of the feeding behaviour of naive YOY perch than visual cues under daylight conditions. However, pike odour acts as a modulatory stimulus enhancing the effects of visual cues, which trigger an innate response in perch.
Habitat distribution of fish in late summer: changes along a nutrient gradient in Danish lakes
Authors: Jeppesen E. , Pekcan‐Hekim Z. , Lauridsen T. L. , Søndergaard M. , Jensen J. P.
Published: June 2006

Abstract –  The horizontal distribution of fish in lakes varies with species, age, predation risk, vegetation coverage and water clarity. Although sporadic data are available for specific lakes, little is known about how habitat distribution generally changes along a gradient in nutrients and clarity. Here we analyse littoral and pelagic fish catch data for 34 Danish lakes (covering 94 lake years) with contrasting total phosphorus (TP) concentrations and mean depth levels (but mainly eutrophic and shallow). Electrofishing was conducted during day along the shore or along the edge of the reed belt if such existed. Gill nets were set overnight for 18 h in open water. We calculated a littoral proportion as: LITPRO = (100 × number caught by electrofishing in the near‐shore area)/(number caught by electrofishing in the near‐shore area and nets in the open water). At all summer TP concentrations LITPRO was high for several ‘littoral’ species such as gudgeon (Gobio gobio), rudd (Scardinius erythrophtalmus) and pike (Esox lucius) and low for more typical pelagic species like pikeperch (Sander lucioperca), ruffe (Gymnocephalus cernuus) and smelt (Osmerus eperlanus). However, for many of these species including the dominant roach (Rutilus rutilus) and perch (Perca fluviatilis) LITPRO increased with TP or lake water chlorophyll a (CHLA) for fish >10 cm, suggesting a more littoral distribution with increasing turbidity. Exceptions are pikeperch and bream (Abramis brama). For bream, LITPRO increased significantly with mean lake depth only. For fish ≤10 cm LITPRO showed only a weak relationship to TP, CHLA or depth. In accordance with the TP‐dependent distribution, major changes occurred in the fish community structure during the monitoring period following nutrient loading reduction. A comparison of LITPRO from the first part of the monitoring period (1989–1993) with a subsequent period (1997–2003) for four abundant species showed a significant decline in LITPRO over time for large‐ and small‐sized roach and perch and large rudd. This suggests a fast response in fish distribution to improved water quality. It further demonstrates that fish monitoring in lakes should cover both littoral and pelagic habitats to describe the recovery process.
Comparison of physiological smolt status in descending and nondescending wild brown trout (Salmo trutta) in a Danish stream
Authors: Nielsen C. , Aarestrup K. , Madsen S. S.
Published: June 2006

Abstract –  Downstream movement of a wild population of brown trout was examined in a small Danish stream in relation to morphological and physiological smolt status from March to May. Downstream movement was monitored in a Wolf‐type trap covering all possible passage routes in the stream. Trout caught in the trap were classified as parr, pre‐smolt or smolt based on morphological criteria and compared with trout randomly caught by electrofishing upstream of the trap. Representative gill samples from trap‐caught and electrofished trout were analysed for gill Na+, K+‐ATPase activity and used as a measure of physiological smolt status. Only a few parr occurred in the trap. Few pre‐smolts occurred in the trap evenly in March and early April. In late April, pre‐smolt movement peaked. By comparison, the main downstream movement of smolts occurred in distinct peaks through late March and April. The majority of fish caught in the trap were judged as pre‐smolts or smolts based on morphological criteria's and they were characterised by relatively high gill Na+, K+‐ATPase activity compared with trout judged as parr. Trout caught by electrofishing upstream the trap, were classified as parr, pre‐smolts and smolts early in the season (March). During and after the main smolt‐run in April the distribution of the remaining trout in the brook became skewed in favour of pre‐smolt and parr. The study suggests that smolting trout initiate downstream movement once having reached a certain physiological smolt condition (judged by increased gill Na+, K+‐ATPase activity).
Assessing the impact of hydropower and fisheries on downstream migrating silver eel, Anguilla anguilla, by telemetry in the River Meuse
Authors: Winter H. V. , Jansen H. M. , Bruijs M. C. M.
Published: June 2006

Abstract –  European eel Anguilla anguilla is in strong decline. We assessed the relative impact of fisheries and hydropower during the downstream migration of silver eel in the River Meuse in the Netherlands using radio‐telemetry. For this, 16 fixed detection stations (Nedap Trail‐System®) were used, each covering the entire river width, including all outlets to sea, and two covering the entrances of the two hydropower stations present. In September 2002, 150 silver eels were surgically implanted with Nedap‐transponders and released at the catch site. Of these, 121 started to migrate downstream of which 37% successfully reached the North Sea. Hydropower mortality was at least 9% and assessed to be 16–26%. Fisheries mortality was at least 16% (reported recaptures) and estimated to be 22–26%. A clear difference was found in passage behaviour at hydropower stations, where 40% showed recurrence, in contrast to the river stations where this hardly occurred, indicating a hesitation to pass the turbines. Also a difference was found in diurnal pattern; 63% of the eels that passed through the turbines did so during the first 5 h of the night, whereas for the stations on free‐flowing sections this was only 35%.
Classical reward conditioning in Drosophila melanogaster
Authors: Kim Y‐C. , Lee H‐G. , Han K‐A.
Published: June 2006

Negatively reinforced olfactory conditioning has been widely employed to identify learning and memory genes, signal transduction pathways and neural circuitry in Drosophila. To delineate the molecular and cellular processes underlying reward‐mediated learning and memory, we developed a novel assay system for positively reinforced olfactory conditioning. In this assay, flies were involuntarily exposed to the appetitive unconditioned stimulus sucrose along with a conditioned stimulus odour during training and their preference for the odour previously associated with sucrose was measured to assess learning and memory capacities. After one training session, wild‐type Canton S flies displayed reliable performance, which was enhanced after two training cycles with 1‐min or 15‐min inter‐training intervals. Higher performance scores were also obtained with increasing sucrose concentration. Memory in Canton S flies decayed slowly when measured at 30 min, 1 h and 3 h after training; whereas, it had declined significantly at 6 h and 12 h post‐training. When learning mutant t βh flies, which are deficient in octopamine, were challenged, they exhibited poor performance, validating the utility of this assay. As the Drosophila model offers vast genetic and transgenic resources, the new appetitive conditioning described here provides a useful tool with which to elucidate the molecular and cellular underpinnings of reward learning and memory. Similar to negatively reinforced conditioning, this reward conditioning represents classical olfactory conditioning. Thus, comparative analyses of learning and memory mutants in two assays may help identify the molecular and cellular components that are specific to the unconditioned stimulus information used in conditioning.
Glucocorticoid receptor polymorphisms and haplotypes associated with chronic fatigue syndrome
Authors: Rajeevan M. S. , Smith A. K. , Dimulescu I. , Unger E. R. , Vernon S. D. , Heim C. , Reeves W. C.
Published: June 2006

Chronic fatigue syndrome (CFS) is a significant public health problem of unknown etiology, the pathophysiology has not been elucidated, and there are no characteristic physical signs or laboratory abnormalities. Some studies have indicated an association of CFS with deregulation of immune functions and hypothalamic–pituitary–adrenal (HPA) axis activity. In this study, we examined the association of sequence variations in the glucocorticoid receptor gene (NR3C1) with CFS because NR3C1 is a major effector of the HPA axis. There were 137 study participants (40 with CFS, 55 with insufficient symptoms or fatigue, termed as ISF, and 42 non‐fatigued controls) who were clinically evaluated and identified from the general population of Wichita, KS. Nine single nucleotide polymorphisms (SNPs) in NR3C1 were tested for association of polymorphisms and haplotypes with CFS. We observed an association of multiple SNPs with chronic fatigue compared to non‐fatigued (NF) subjects (P < 0.05) and found similar associations with quantitative assessments of functional impairment (by the SF‐36), with fatigue (by the Multidimensional Fatigue Inventory) and with symptoms (assessed by the Centers for Disease Control Symptom Inventory). Subjects homozygous for the major allele of all associated SNPs were at increased risk for CFS with odds ratios ranging from 2.61 (CI 1.05–6.45) to 3.00 (CI 1.12–8.05). Five SNPs, covering a region of approximately 80 kb, demonstrated high linkage disequilibrium (LD) in CFS, but LD gradually declined in ISF to NF subjects. Furthermore, haplotype analysis of the region in LD identified two associated haplotypes with opposite alleles: one protective and the other conferring risk of CFS. These results demonstrate NR3C1 as a potential mediator of chronic fatigue, and implicate variations in the 5′ region of NR3C1 as a possible mechanism through which the alterations in HPA axis regulation and behavioural characteristics of CFS may manifest.
Exploring women’s views of breastfeeding: a focus group study within an area with high levels of socio‐economic deprivation
Authors: McFadden Alison , Toole Glenyce
Published: June 2006

There is ample evidence of the short‐ and long‐term health benefits of breastfeeding for mothers and infants, yet breastfeeding rates remain low in the UK, particularly in areas of high social deprivation. It is imperative that appropriate strategies are utilized to support more women to initiate and continue breastfeeding. This study used focus group methodology to explore women’s views in relation to breastfeeding. The study was conducted within an area with high levels of socio‐economic deprivation in the north‐east of England and aimed to identify local barriers to breastfeeding, influences on choice of infant‐feeding method and strategies which might improve breastfeeding rates. Focus group discussions were conducted with low‐income women, adolescent women and women from a minority ethnic group. The five key themes that emerged from the data were: society’s negative attitudes towards breastfeeding; the influence of family and friends and the experience on choice of method of infant feeding; lack of knowledge of some aspects of infant feeding; perceptions of professional support; and women’s positive and negative experiences of breastfeeding. Recommendations for promoting and supporting breastfeeding include improving facilities to breastfeed in public, enhancing the provision of information, addressing conflicting advice and poor professional practice and implementing support mechanisms. The findings and recommendations have been used to develop a breastfeeding strategy to meet local needs. This project was funded by the English Department of Health Infant Feeding Initiative.
Diet, physical inactivity and the prevalence of constipation throughout and after pregnancy
Authors: Derbyshire Emma , Davies Jill , Costarelli Vassiliki , Dettmar Peter
Published: June 2006

Few studies appear to have investigated the prevalence of constipation for all three trimesters of the gestative period, or indeed after birth. Using a prospective 4‐ to 7‐day weighed food diary, International Physical Activity Questionnaire and 7‐day bowel habit diary, dietary factors, physical activity levels and bowel habit parameters were assessed and examined concurrently at weeks 13, 25, 35 of pregnancy and 6 weeks post‐partum. Ninety‐four primiparous pregnant women were initially recruited, and 72, 59, 62 and 55 completed the first, second, third trimester and post‐partum study stages, respectively. Key dietary factors and physical activity levels were compared between the constipated and non‐constipated groups from each of the three trimesters and after parturition. Compared with non‐constipated mothers‐to‐be, constipated participants consumed statistically significantly less water in the first trimester (P = 0.04), more food in the second trimester (P = 0.04), and less iron (P = 0.02) and food (P = 0.04) in the third trimester and after birth, respectively. No statistically significant differences were identified between light, moderate and vigorous physical activity levels when groups were compared. This study demonstrates that dietary factors may play a role in terms of preventing, or alleviating, bowel habit perturbations both throughout and after pregnancy. Further research is required to investigate the interrelationship between physical activity and constipation during and after pregnancy.
Life cycle of Phacellophora camtschatica (Cnidaria: Scyphozoa)
Authors: Widmer Chad L.
Published: June 2006

Abstract. Gelatinous zooplankton play important roles in marine ecosystems and at times can have significant impacts on human activities. Many scyphozoans have enigmatic life cycles and the specific habitat for benthic life history stages is unknown. This is especially true for many of the large surface‐cruising scyphomedusae of the northeast Pacific Ocean. Phacellophora camtschatica belongs to the family Ulmaridae and is known to have scyphistomae in the life history. However, the life cycle of P. camtschatica has not been formally described. Here the life cycle of members of P. camtschatica is described based on laboratory observations and compared with early life history stages in the scyphomedusa Aurelia labiata.
Effects of Macrocycle Size and Rigidity on Melanocortin Receptor‐1 and ‐5 Selectivity in Cyclic Lactam α‐Melanocyte‐Stimulating Hormone Analogs
Authors: Mayorov Alexander V. , Han So‐Yeop , Cai Minying , Hammer Matthew R. , Trivedi Dev , Hruby Victor J.
Published: June 2006

The effects of the linker arm rigidity and size on melanocortin receptor selectivity were explored in a series of compounds using cyclic lactam α‐melanocyte‐stimulating hormone template. A variety of dicarboxylic acid linkers introduced between the α‐amino group of His6 and the ɛ‐amino group of Lys10 lead to high‐affinity, selective human melanocortin receptor‐1 and ‐5 (hMC1R and hMC5R) antagonists. The incorporation of hydrophilic functions into the linker arm was found to be unfavorable for both binding potency and receptor selectivity. Analogs 8 and 9 containing highly conformationally constrained hydrophobic linkers (m‐ and p‐phthalic acids) were found to be selective nanomolar range hMC1R antagonists (IC50 = 7 and 4 nm, respectively), whereas the employment of a small conformationally constrained linker (maleic acid) resulted in a high‐affinity (IC50 = 19 nm) and selective hMC5R antagonist (analog 12). These newly developed melanotropins will serve as critical biochemical tools for elucidating the full spectrum of functions performed by the physiologically important melanocortin‐1 and ‐5 receptors.
Rapid development of cleaning behaviour by Torresian crows Corvus orru on non‐native banteng Bos javanicus in northern Australia
Authors: J. A. Bradshaw Corey , W. White Warren
Published: June 2006

In this paper we report the observation of a rapidly developed vertebrate symbiosis involving ectoparasite cleaning by a native corvid of northern Australia, the Torresian crow Corvus orru, on a recently introduced bovid ungulate, the banteng Bos javanicus. Facultative symbioses benefiting both participants (mutualisms) between birds and mammals appear to be rare, despite the apparent advantages obtained by the participants (ecto‐parasite removal from the host and food provision to the cleaner). On three separate dates we observed a total of four C. orru individuals eliciting facilitation behaviours by a total of ten female banteng to assist in the removal of ectoparasites. Our observations document the first‐known incidence of facultative cleaning behaviour by a native bird species on a non‐native, wild vertebrate that has developed in approximately 150 years since the banteng's introduction to Australia.
RcsF Is an Outer Membrane Lipoprotein Involved in the RcsCDB Phosphorelay Signaling Pathway in
Escherichia coli
Authors: Castanié-Cornet Marie-Pierre , Cam Kaymeuang , Jacq Annick
Published: June 2006

The RcsCDB signal transduction system is an atypical His-Asp phosphorelay conserved in γ-proteobacteria. Besides the three proteins directly involved in the phosphorelay, two proteins modulate the activity of the system. One is RcsA, which can stimulate the activity of the response regulator RcsB independently of the phosphorelay to regulate a subset of RcsB targets. The other is RcsF, a putative outer membrane lipoprotein mediating the signaling to the sensor RcsC. How RcsF transduces the signal to RcsC is unknown. Although the molecular and physiological signals remain to be identified, the common feature among the reported Rcs-activating conditions is perturbation of the envelope. As an initial step to explore the RcsF-RcsC functional relationship, we demonstrate that RcsF is an outer membrane lipoprotein oriented towards the periplasm. We also report that a null mutation in
surA
, a gene required for correct folding of periplasmic proteins, activates the Rcs pathway through RcsF. In contrast, activation of this pathway by overproduction of the membrane chaperone-like protein DjlA does not require RcsF. Conversely, activation of the pathway by RcsF overproduction does not require DjlA either, indicating the existence of two independent signaling pathways toward RcsC.
Borrelia burgdorferiEbfC, a Novel, Chromosomally Encoded Protein, Binds Specific DNA Sequences Adjacent toerpLoci on the Spirochete's Resident cp32 Prophages
Authors: Babb Kelly , Bykowski Tomasz , Riley Sean P. , Miller M. Clarke , DeMoll Edward , Stevenson Brian
Published: June 2006

All examined isolates of the Lyme disease spirochete,Borrelia burgdorferi, naturally maintain numerous variants of a prophage family as circular cp32 episomes. Each cp32 carries a locus encoding one or two different Erp outer membrane, surface-exposed lipoproteins. Many of the Erp proteins bind a host complement regulator, factor H, which is hypothesized to protect the spirochete from complement-mediated killing. We now describe the isolation and characterization of a novel, chromosomally encoded protein, EbfC, that binds specific DNA sequences located immediately 5′ of allerploci. This is one of the first site-specific DNA-binding proteins to be identified in any spirochete. The location of theebfCgene on theB. burgdorferichromosome suggests that the cp32 prophages have evolved to use this bacterial host protein for their own benefit and that EbfC probably plays additional roles in the bacterium. A wide range of other bacteria encode homologs of EbfC, none of which have been well characterized, so demonstration thatB. burgdorferiEbfC is a site-specific DNA-binding protein has broad implications across the eubacterial kingdom.
Crystal Structure of Neurotropism-Associated Variable Surface Protein 1 (Vsp1) of
Borrelia turicatae
Authors: Lawson Catherine L. , Yung Brian H. , Barbour Alan G. , Zückert Wolfram R.
Published: June 2006

Vsp surface lipoproteins are serotype-defining antigens of relapsing fever spirochetes that undergo multiphasic antigenic variation to allow bacterial persistence in spite of an immune response. Two isogenic serotypes of
Borrelia turicatae
strain Oz1 differ in their Vsp sequences and in disease manifestations in infected mice: Vsp1 is associated with the selection of a neurological niche, while Vsp2 is associated with blood and skin infection. We report here crystal structures of the Vsp1 dimer at 2.7 and 2.2 Å. The structures confirm that relapsing fever Vsp proteins share a common helical fold with OspCs of Lyme disease-causing
Borrelia
. The fold features an inner stem formed by highly conserved N and C termini and an outer “dome” formed by the variable central residues. Both Vsp1 and OspC structures possess small water-filled cavities, or pockets, that are lined largely by variable residues and are thus highly variable in shape. These features appear to signify tolerance of the Vsp-OspC fold for imperfect packing of residues at its antigenic surface. Structural comparison of Vsp1 with a homology model for Vsp2 suggests that observed differences in disease manifestation may arise in part from distinct differences in electrostatic surface properties; additional predicted positively charged surface patches on Vsp2 compared to Vsp1 may be sufficient to explain the relative propensity of Vsp2 to bind to acidic glycosaminoglycans.
The Synchrony Phenotype Persists after Elimination of Multiple GATC Sites from the
dnaA
Promoter of
Escherichia coli
Authors: Wilkinson Terry G. , Kedar G. C. , Lee Chi , Guzmán Elena C. , Smith Douglas W. , Zyskind Judith W.
Published: June 2006

To examine whether methylation of the GATC sites present in the
dnaA
promoter region is responsible for the strict temporal coordination of initiation events at
oriC
as measured by the synchrony of initiation, we introduced point mutations eliminating three (TGW1) and five (TGW2) of the six GATC sites present in the
dnaA
promoter region. All of the strains containing these mutations, including the one with five GATC sites eliminated, initiated chromosomal replication synchronously.
Whole-Genome Transcription Profiling Reveals Genes Up-Regulated by Growth on Fucose in the Human Gut Bacterium “Roseburia inulinivorans”
Authors: Scott Karen P. , Martin Jennifer C. , Campbell Gillian , Mayer Claus-Dieter , Flint Harry J.
Published: June 2006

“Roseburia inulinivorans” is an anaerobic polysaccharide-utilizing firmicute bacterium from the human colon that was identified as a producer of butyric acid during growth on glucose, starch, or inulin.R. inulinivoransA2-194 is also able to grow on the host-derived sugar fucose, following a lag period, producing propionate and propanol as additional fermentation products. A shotgun genomic microarray was constructed and used to investigate the switch in gene expression that is involved in changing from glucose to fucose utilization. This revealed a set of genes coding for fucose utilization, propanediol utilization, and the formation of propionate and propanol that are up-regulated during growth on fucose. These include homologues of genes that are implicated in polyhedral body formation inSalmonella enterica. Dehydration of the intermediate 1,2-propanediol involves an enzyme belonging to the new B12-independent glycerol dehydratase family, in contrast toS. enterica, which relies on a B12-dependent enzyme. A typical gram-positiveagr-type quorum-sensing system was also up-regulated inR. inulinivoransduring growth on fucose. Despite the lack of genome sequence information for this commensal bacterium, microarray analysis has provided a powerful tool for obtaining new information on its metabolic capabilities.
The
rcsA
Promoter of
Pantoea stewartii
subsp.
stewartii
Features a Low-Level Constitutive Promoter and an EsaR Quorum-Sensing-Regulated Promoter
Authors: Carlier Aurelien L. , von Bodman S. B.
Published: June 2006

The upstream region of the
Pantoea stewartii rcsA
gene features two promoters, one for constitutive basal-level expression and a second autoregulated promoter for induced expression. The EsaR quorum-sensing repressor binds to a site centered between the two promoters, blocking transcription elongation from the regulated promoter under noninducing conditions.
Mutational Analysis of theBacillus subtilisRNA Polymerase α C-Terminal Domain Supports the Interference Model of Spx-Dependent Repression
Authors: Zhang Ying , Nakano Shunji , Choi Soon-Yong , Zuber Peter
Published: June 2006

The Spx protein ofBacillus subtilisexerts both positive and negative transcriptional control in response to oxidative stress by interacting with the C-terminal domain of the RNA polymerase (RNAP) alpha subunit (αCTD). Thus, transcription of thesrfoperon at the onset of competence development, which requires the ComA response regulator of the ComPA signal transduction system, is repressed by Spx-αCTD interaction. Previous genetic and structural analyses have determined that an Spx-binding surface resides in and around the α1 region of αCTD. Alanine-scanning mutagenesis ofB. subtilisαCTD uncovered residue positions required for Spx function and ComA-dependentsrftranscriptional activation. Analysis ofsrf-lacZfusion expression, DNase I footprinting, and solid-phase promoter retention experiments indicate that Spx interferes with ComA-αCTD interaction and that residues Y263, C265, and K267 of the α1 region lie within overlapping ComA- and Spx-binding sites for αCTD interaction. Evidence is also presented that oxidized Spx, while enhancing interference of activator-RNAP interaction, is not essential for negative control.
The
cbiS
Gene of the Archaeon
Methanopyrus kandleri
AV19 Encodes a Bifunctional Enzyme with Adenosylcobinamide Amidohydrolase and α-Ribazole-Phosphate Phosphatase Activities
Authors: Woodson Jesse D. , Escalante-Semerena Jorge C.
Published: June 2006

Here we report the initial biochemical characterization of the bifunctional α-ribazole-P (α-RP) phosphatase, adenosylcobinamide (AdoCbi) amidohydrolase CbiS enzyme from the hyperthermophilic methanogenic archaeon
Methanopyrus kandleri
AV19. The
cbiS
gene encodes a 39-kDa protein with two distinct segments, one of which is homologous to the AdoCbi amidohydrolase (CbiZ, EC 3.5.1.90) enzyme and the other of which is homologous to the recently discovered archaeal α-RP phosphatase (CobZ, EC 3.1.3.73) enzyme. CbiS function restored AdoCbi salvaging and α-RP phosphatase activity in strains of the bacterium
Salmonella enterica
where either step was blocked. The two halves of the
cbiS
genes retained their function in vivo when they were cloned separately. The CbiS enzyme was overproduced in
Escherichia coli
and was isolated to >95% homogeneity. High-performance liquid chromatography, UV-visible spectroscopy, and mass spectroscopy established α-ribazole and cobyric acid as the products of the phosphatase and amidohydrolase reactions, respectively. Reasons why the CbiZ and CobZ enzymes are fused in some archaea are discussed.
Transposon Mutations in the 5′ End ofglnD, the Gene for a Nitrogen Regulatory Sensor, That Suppress the Osmosensitive Phenotype Caused byotsBALesions inEscherichia coli
Authors: Tøndervik Anne , Torgersen Haakon R. , Botnmark Hans K. , Strøm Arne R.
Published: June 2006

GlnD ofEscherichia coliis a bifunctional signal-transducing enzyme (102.4 kDa) which uridylylates the allosteric regulatory protein PII and deuridylylates PII-UMP in response to growth with nitrogen excess or limitation, respectively. GlnD catalyzes these reactions in response to high or low levels of cytoplasmic glutamine, respectively, and indirectly directs the expression of nitrogen-regulated genes, e.g., theglnK-amtBoperon. We report that chromosomal mini-Tn10insertions situated after nucleotide number 997 or 1075 ofglnDpartially suppressed the osmosensitive phenotype of ΔotsBAorotsA::Tn10mutations (defective osmoregulatory trehalose synthesis). Strains carrying theseglnD::mini-Tn10mutations either completely repressed the expression oftrp::(glnKp-lacZ) or induced this reporter system to nearly 60% of the wild-typeglnDlevel in response to nitrogen availability, an essentially normal response. This was in contrast to the much-studiedglnD99::Tn10mutation, which carries its insertion in the 3′ end of the gene, causes a complete repression ofglnKp-lacZexpression under all growth conditions, and also confers leaky glutamine auxotrophy. When expressed from thePmpromoter in plasmid constructs, the presentglnDmutations produced proteins with an apparent mass of 39 or 42 kDa. These proteins were deduced to comprise 344 or 370 N-terminal residues, respectively, harboring the known nucleotidyltransferase domain of GlnD, plus a common C-terminal addition of 12 residues encoded by IS10. They lacked three other domains of GlnD. Apparently, the transferase domain by itself enabled the cells to catalyze the uridylylation reaction and direct nitrogen-regulated gene expression. Our data indicate that there exists a link between osmotic stress and the nitrogen response.
Role for Tandem Duplication and Lon Protease in AcrAB-TolC- Dependent Multiple Antibiotic Resistance (Mar) in an
Escherichia coli
Mutant without Mutations in
marRAB
or
acrRAB
Authors: Nicoloff Hervé , Perreten Vincent , McMurry Laura M. , Levy Stuart B.
Published: June 2006

A spontaneous mutant (M113) of
Escherichia coli
AG100 with an unstable multiple antibiotic resistance (Mar) phenotype was isolated in the presence of tetracycline. Two mutations were found: an insertion in the promoter of
lon
(
lon3
::IS
186
) that occurred first and a subsequent large tandem duplication, dupIS
186
, bearing the genes
acrAB
and extending from the
lon3
::IS
186
to another IS
186
present 149 kb away from
lon
. The decreased amount of Lon protease increased the amount of MarA by stabilization of the basal quantities of MarA produced, which in turn increased the amount of multidrug effux pump AcrAB-TolC. However, in a mutant carrying only a
lon
mutation, the overproduced pump mediated little, if any, increased multidrug resistance, indicating that the Lon protease was required for the function of the pump. This requirement was only partial since resistance was mediated when amounts of AcrAB in a
lon
mutant were further increased by a second mutation. In M113, amplification of
acrAB
on the duplication led to increased amounts of AcrAB and multidrug resistance. Spontaneous gene duplication represents a new mechanism for mediating multidrug resistance in
E. coli
through AcrAB-TolC.
Glycosylation of b-Type Flagellin of
Pseudomonas aeruginosa
: Structural and Genetic Basis
Authors: Verma Amrisha , Schirm Michael , Arora Shiwani K. , Thibault P. , Logan Susan M. , Ramphal Reuben
Published: June 2006

The flagellin of
Pseudomonas aeruginosa
can be classified into two major types—a-type or b-type—which can be distinguished on the basis of molecular weight and reactivity with type-specific antisera. Flagellin from the a-type strain PAK was shown to be glycosylated with a heterogeneous O-linked glycan attached to Thr189 and Ser260. Here we show that b-type flagellin from strain PAO1 is also posttranslationally modified with an excess mass of up to 700 Da, which cannot be explained through phosphorylation. Two serine residues at positions 191 and 195 were found to be modified. Each site had a deoxyhexose to which is linked a unique modification of 209 Da containing a phosphate moiety. In comparison to strain PAK, which has an extensive flagellar glycosylation island of 14 genes in its genome, the equivalent locus in PAO1 comprises of only four genes. PCR analysis and sequence information suggested that there are few or no polymorphisms among the islands of the b-type strains. Mutations were made in each of the genes, PA1088 to PA1091, and the flagellin from these isogenic mutants was examined by mass spectrometry to determine whether they were involved in posttranslational modification of the type-b flagellin. While mutation of PA1088, PA1089, and PA1090 genes altered the composition of the flagellin glycan, only unmodified flagellin was produced by the PA1091 mutant strain. There were no changes in motility or lipopolysaccharide banding in the mutants, implying a role that is limited to glycosylation.
Molecular Mechanism of Tryptophan-Dependent Transcriptional Regulation inChlamydia trachomatis
Authors: Akers Johnny C. , Tan Ming
Published: June 2006

Tryptophan is an essential amino acid that is required for normal development inChlamydiaspecies, and tryptophan metabolism has been implicated in chlamydial persistence and tissue tropism. The ability to synthesize tryptophan is not universal among theChlamydiaceae, but species that have a predicted tryptophan biosynthetic pathway also encode an ortholog of TrpR, a regulator of tryptophan metabolism in many gram-negative bacteria. We show that inChlamydia trachomatisserovar D, TrpR regulates its own gene andtrpBandtrpA, the genes for the two subunits of tryptophan synthase. These three genes form an operon that is transcribed by the major form of chlamydial RNA polymerase. TrpR acts as a tryptophan-dependent aporepressor that binds specifically to operator sequences upstream of thetrpRBAoperon. We also found that TrpR repressed in vitro transcription oftrpRBAin a promoter-specific manner, and the level of repression was dependent upon the concentrations of TrpR and tryptophan. Our findings provide a mechanism for chlamydiae to sense changes in tryptophan levels and to respond by modulating expression of the tryptophan biosynthesis genes, and we present a unified model that shows howC. trachomatiscan combine transcriptional repression and attenuation to regulate intrachlamydial tryptophan levels. In the face of host defense mechanisms that limit tryptophan availability from the infected cell, the ability to maintain homeostatic control of intrachlamydial tryptophan levels is likely to play an important role in chlamydial pathogenesis.
Novel Genetic Polymorphisms That Further Delineate the Phylogeny of the
Mycobacterium tuberculosis
Complex
Authors: Huard Richard C. , Fabre Michel , de Haas Petra , Claudio Oliveira Lazzarini Luiz , van Soolingen Dick , Cousins Debby , Ho John L.
Published: June 2006

In a previous report, we described a PCR protocol for the differentiation of the various species of the
Mycobacterium tuberculosis
complex (MTC) on the basis of genomic deletions (R. C. Huard, L. C. de Oliveira Lazzarini, W. R. Butler, D. van Soolingen, and J. L. Ho, J. Clin. Microbiol.
41:
1637-1650, 2003). That report also provided a broad cross-comparison of several previously identified, phylogenetically relevant, long-sequence and single-nucleotide polymorphisms (LSPs and SNPs, respectively). In the present companion report, we expand upon the previous work (i) by continuing the evaluation of known MTC phylogenetic markers in a larger collection of tubercle bacilli (
n
= 125), (ii) by evaluating additional recently reported MTC species-specific and interspecific polymorphisms, and (iii) by describing the identification and distribution of a number of novel LSPs and SNPs. Notably, new genomic deletions were found in various
Mycobacterium tuberculosis
strains, new species-specific SNPs were identified for “
Mycobacterium canettii
,”
Mycobacterium microti
, and
Mycobacterium pinnipedii
, and, for the first time, intraspecific single-nucleotide DNA differences were discovered for the dassie bacillus, the oryx bacillus, and the two
Mycobacterium africanum
subtype I variants. Surprisingly, coincident polymorphisms linked one
M. africanum
subtype I genotype with the dassie bacillus and
M. microti
with
M. pinnipedii
, thereby suggesting closer evolutionary ties within each pair of species than had been previously thought. Overall, the presented data add to the genetic definitions of several MTC organisms as well as fine-tune current models for the evolutionary history of the MTC.
Role of the Intramolecular Disulfide Bond in FlgI, the Flagellar P-Ring Component of
Escherichia coli
Authors: Hizukuri Yohei , Yakushi Toshiharu , Kawagishi Ikuro , Homma Michio
Published: June 2006

The P ring of the bacterial flagellar motor consists of multiple copies of FlgI, a periplasmic protein. The intramolecular disulfide bond in FlgI has previously been reported to be essential for P-ring assembly in
Escherichia coli
, because the P ring was not assembled in a
dsbB
strain that was defective for disulfide bond formation in periplasmic proteins. We, however, found that the two Cys residues of FlgI are not conserved in other bacterial species. We then assessed the role of this intramolecular disulfide bond in FlgI. A Cys-eliminated FlgI derivative formed a P ring that complemented the flagellation defect of our Δ
flgI
strain when it was overproduced, suggesting that disulfide bond formation in FlgI is not absolutely required for P-ring assembly. The levels of the mature forms of the FlgI derivatives were significantly lower than that of wild-type FlgI, although the precursor protein levels were unchanged. Moreover, the FlgI derivatives were more susceptible to degradation than wild-type FlgI. Overproduction of FlgI suppressed the motility defect of Δ
dsbB
cells. Additionally, the low level of FlgI observed in the Δ
dsbB
strain increased in the presence of
l
-cystine, an oxidative agent. We propose that intramolecular disulfide bond formation facilitates the rapid folding of the FlgI monomer to protect against degradation in the periplasmic space, thereby allowing its efficient self-assembly into the P ring.
Global Transcriptome Analysis of the Cold Shock Response of
Shewanellaoneidensis
MR-1 and Mutational Analysis of Its ClassicalCold ShockProteins
Authors: Gao Haichun , Yang Zamin K. , Wu Liyou , Thompson Dorothea K. , Zhou Jizhong
Published: June 2006

This
study presents a global transcriptional analysis of the cold shock
response of
Shewanella oneidensis
MR-1 after a temperature
downshift from 30°C to 8 or 15°C based on time series
microarray experiments. More than 700 genes were found to be
significantly affected (
P
≤ 0.05) upon cold shock
challenge, especially at 8°C. The temporal gene expression
patterns of the classical cold shock genes varied, and only some of
them, most notably so1648 and so2787, were differentially regulated in
response to a temperature downshift. The global response of
S.
oneidensis
to cold shock was also characterized by the
up-regulation of genes encoding membrane proteins, DNA metabolism and
translation apparatus components, metabolic proteins, regulatory
proteins, and hypothetical proteins. Most of the metabolic proteins
affected are involved in catalytic processes that generate NADH or
NADPH. Mutational analyses confirmed that the small cold shock
proteins, So1648 and So2787, are involved in the cold shock response of
S. oneidensis
. The analyses also indicated that So1648 may
function only at very low
temperatures.
Characterization of a Novel Partition System Encoded by the δ and ω Genes from the Streptococcal Plasmid pSM19035
Authors: Dmowski Michał , Sitkiewicz Izabela , Cegłowski Piotr
Published: June 2006

High segregational stability of the streptococcal plasmid pSM19035 is achieved by the concerted action of systems involved in plasmid copy number control, multimer resolution, and postsegregational killing. In this study, we demonstrate the role of two genes,δandω, in plasmid stabilization by a partition mechanism. We show that these two genes can stabilize the native pSM19035 replicon as well as other θ- and σ-type plasmids inBacillus subtilis. In contrast to other known partition systems, in this case the two genes are transcribed separately; however, they are coregulated by the product of theparB-like geneω. Analysis of mutants of theparA-like geneδshowed that the Walker A ATPase motif is necessary for plasmid stabilization. The ParB-like product of theωgene binds to three regions containing repeated WATCACW heptamers, localized in thecopS(regulation of plasmid copy number),δ, andωpromoter regions. We demonstrate that all three of these regions can cause partition-mediated incompatibility. Moreover, our data suggest that each of these could play the role of a centromere-like sequence. We conclude thatδandωconstitute a novel type of plasmid stabilization system.
CbrA Is a Stationary-Phase Regulator of Cell Surface Physiology and Legume Symbiosis in
Sinorhizobium meliloti
Authors: Gibson Katherine E. , Campbell Gordon R. , Lloret Javier , Walker Graham C.
Published: June 2006

Sinorhizobium meliloti
produces an exopolysaccharide called succinoglycan that plays a critical role in promoting symbiosis with its host legume, alfalfa (
Medicago sativa
). We performed a transposon mutagenesis and screened for mutants with altered succinoglycan production and a defect in symbiosis. In this way, we identified a putative two-component histidine kinase associated with a PAS sensory domain, now designated CbrA (
c
alcofluor-
b
right
r
egulator
A
). The
cbrA
::Tn
5
mutation causes overproduction of succinoglycan and results in increased accumulation of low-molecular-weight forms of this exopolysaccharide. Our results suggest the
cbrA
::Tn
5
allele leads to this succinoglycan phenotype through increased expression of
exo
genes required for succinoglycan biosynthesis and modification. Interestingly, CbrA-dependent regulation of
exo
and
exs
genes is observed almost exclusively during stationary-phase growth. The
cbrA
::Tn
5
mutant also has an apparent cell envelope defect, based on increased sensitivity to a number of toxic compounds, including the bile salt deoxycholate and the hydrophobic dye crystal violet. Growth of the
cbrA
mutant is also slowed under oxidative-stress conditions. The CbrA-regulated genes
exsA
and
exsE
encode putative inner membrane ABC transporters with a high degree of similarity to lipid exporters. ExsA is homologous to the
Escherichia coli
MsbA protein, which is required for lipopolysacharide transport, while ExsE is a member of the eukaryotic family of ABCD/hALD peroxisomal membrane proteins involved in transport of very long-chain fatty acids, which are a unique component of the lipopolysaccharides of alphaproteobacteria. Thus, CbrA could play a role in regulating the lipopolysaccharide or lipoprotein components of the cell envelope.