bluuebunny/crossref_metadata_2025 huggingface dataset:
Phosphorylation of actin Tyr-53 inhibits filament nucleation and elongation and destabilizes filaments
Authors: Liu Xiong , Shu Shi , Hong Myoung-Soon S. , Levine Rodney L. , Korn Edward D.
Published: August 2006

Dictyostelium
actin was shown to become phosphorylated on Tyr-53 late in the developmental cycle and when cells in the amoeboid stage are subjected to stress but the phosphorylated actin had not been purified and characterized. We have separated phosphorylated and unphosphorylated actin and shown that Tyr-53 phosphorylation substantially reduces actin's ability to inactivate DNase I, increases actin's critical concentration, and greatly reduces its rate of polymerization. Tyr-53 phosphorylation substantially, if not completely, inhibits nucleation and elongation from the pointed end of actin filaments and reduces the rate of elongation from the barbed end. Negatively stained electron microscopic images of polymerized Tyr-53–phosphorylated actin show a variable mixture of small oligomers and filaments, which are converted to more typical, long filaments upon addition of myosin subfragment 1. Tyr-53–phosphorylated and unphosphorylated actin copolymerize
in vitro
, and phosphorylated and unphosphorylated actin colocalize in amoebae. Tyr-53 phosphorylation does not affect the ability of filamentous actin to activate myosin ATPase.
Phosphorylation of RhoGDI by Src Regulates Rho GTPase Binding and Cytosol-Membrane Cycling
Authors: DerMardirossian Céline , Rocklin Gabriel , Seo Ji-Yeon , Bokoch Gary M.
Published: August 2006

Rho GTPases (Rac, Rho, and Cdc42) play important roles in regulating cell function through their ability to coordinate the actin cytoskeleton, modulate the formation of signaling reactive oxidant species, and control gene transcription. Activation of Rho GTPase signaling pathways requires the regulated release of Rho GTPases from RhoGDI complexes, followed by their reuptake after membrane cycling. We show here that Src kinase binds and phosphorylates RhoGDI both in vitro and in vivo at Tyr156. Analysis of Rho GTPase–RhoGDI complexes using in vitro assays of complexation and in vivo by coimmunoprecipitation analysis indicates that Src-mediated phosphorylation of Tyr156 causes a dramatic decrease in the ability of RhoGDI to form a complex with RhoA, Rac1, or Cdc42. Phosphomimetic mutation of Tyr156→Glu results in the constitutive association of RhoGDIY156Ewith the plasma membrane and/or associated cortical actin. Substantial cortical localization of tyrosine-phosphorylated RhoGDI is also observed in fibroblasts expressing active Src, where it is most evident in podosomes and regions of membrane ruffling. Expression of membrane-localized RhoGDIY156Emutant is associated with enhanced cell spreading and membrane ruffling. These results suggest that Src-mediated RhoGDI phosphorylation is a novel physiological mechanism for regulating Rho GTPase cytosol membrane–cycling and activity.
Use of Magnetic Nanoparticles to Visualize Threadlike Structures inside Lymphatic Vessels of Rats
Authors: Johng Hyeon-Min , Yoo Jung Sun , Yoon Tae-Jong , Shin Hak-Soo , Lee Byung-Cheon , Lee Changhoon , Lee Jin-Kyu , Soh Kwang-Sup
Published: August 2006

A novel application of fluorescent magnetic nanoparticles was made to visualize a new tissue which had not been detectable by using simple stereomicroscopes. This unfamiliar threadlike structure inside the lymphatic vessels of rats was demonstrated in vivo by injecting nanoparticles into lymph nodes and applying magnetic fields on the collecting lymph vessels so that the nanoparticles were taken up by the threadlike structures. Confocal laser scanning microscope images of cryosectioned specimens exhibited that the nanoparticles were absorbed more strongly by the threadlike structure than by the lymphatic vessels. Further examination using a transmission electron microscope revealed that the nanoparticles had been captured between the reticular fibers in the extracellular matrix of the threadlike structures. The emerging technology of nanoparticles not only allows the extremely elusive threadlike structures to be visualized but also is expected to provide a magnetically controllable means to investigate their physiological functions.
Anaerobic and aerobic metabolism of glycogen-accumulating organisms selected with propionate as the sole carbon source
Authors: Oehmen Adrian , Zeng Raymond J. , Saunders Aaron M. , Blackall Linda L. , Keller Jürg , Yuan Zhiguo
Published: August 2006

In the microbial competition observed in enhanced biological phosphorus removal (EBPR) systems, an undesirable group of micro-organisms known as glycogen-accumulating organisms (GAOs) compete for carbon in the anaerobic period with the desired polyphosphate-accumulating organisms (PAOs). Some studies have suggested that a propionate carbon source provides PAOs with a competitive advantage over GAOs in EBPR systems; however, the metabolism of GAOs with this carbon source has not been previously investigated. In this study, GAOs were enriched in a laboratory-scale bioreactor with propionate as the sole carbon source, in an effort to better understand their biochemical processes. Based on comprehensive solid-, liquid- and gas-phase chemical analytical data from the bioreactor, a metabolic model was proposed for the metabolism of propionate by GAOs. The model adequately described the anaerobic stoichiometry observed through chemical analysis, and can be a valuable tool for further investigation of the competition between PAOs and GAOs, and for the optimization of the EBPR process. A group of Alphaproteobacteria dominated the biomass (96 % of Bacteria) from this bioreactor, while post-fluorescence in situ hybridization (FISH) chemical staining confirmed that these Alphaproteobacteria produced poly-β-hydroxyalkanoates (PHAs) anaerobically and utilized them aerobically, demonstrating that they were putative GAOs. Some of the Alphaproteobacteria were related to Defluvicoccus vanus (16 % of Bacteria), but the specific identity of many could not be determined by FISH. Further investigation into the identity of other GAOs is necessary.
Construction and characterization of a Lactococcus lactis strain deficient in intracellular ClpP and extracellular HtrA proteases
Authors: Cortes-Perez N. G. , Poquet I. , Oliveira M. , Gratadoux J. J. , Madsen S. M. , Miyoshi A. , Corthier G. , Azevedo V. , Langella P. , Bermúdez-Humarán L. G.
Published: August 2006

ALactococcus lactisstrain deficient in both its major proteases, intracellular (ClpP) and extracellular (HtrA), was constructed and characterized. This strain, hereafter calledclpP-htrA, could be obtained only by conjugation between aclpPdonor strain and anhtrArecipient strain in the NZ9000 context, allowing heterologous gene expression under the control of the NICE (nisin-controlled expression) system. TheclpP-htrAdouble mutant showed both higher stress tolerance (e.g. high temperature and ethanol resistance) and higher viability than singleclpPorhtrAmutant strains. In addition, the secretion rate of two heterologous proteins (staphylococcal nuclease Nuc and Nuc-E7) was also higher inclpP-htrAthan in the wild-type strain. This strain should be a useful host for high-level production and quality of stable heterologous proteins.
Laboratory and clinical Pseudomonas aeruginosa strains do not bind glycosphingolipids in vitro or during type IV pili-mediated initial host cell attachment
Authors: Emam Aufaugh , Yu Analyn R. , Park Hyun-Joo , Mahfoud Radhia , Kus Julianne , Burrows Lori L. , Lingwood Clifford A.
Published: August 2006

The glycosphingolipids (GSLs) gangliotriaosylceramide (Gg3) and gangliotetraosylceramide (Gg4) have been implicated as receptors for type IV pili (T4P)-mediatedPseudomonas aeruginosaepithelial cell attachment. SinceP. aeruginosaT4P are divided into five groups, the authors determined whether GSLs in general, and Gg3and Gg4in particular, are specifically bound and required for host epithelial cell attachment of clinical and laboratory strains within these groups. An enterohaemorrhagicEscherichia colistrain, CL56, known to bind to both Gg3and Gg4, provided a positive control. TLC overlay showed no binding of more than 12P. aeruginosastrains to either Gg3or Gg4(or other GSLs), while CL56 Gg3/Gg4binding was readily detectable. GSL ELISA similarly demonstrated no significantP. aeruginosabinding to Gg3or Gg4, compared with CL56. Using a selective chemical inhibitor, epithelial cell GSL synthesis was abrogated, and Gg3and Gg4expression deleted, butP. aeruginosaattachment was not impaired. Target cell attachment was mediated by T4P, since non-piliated, but flagellated, mutants were unable to bind to the target cells. CFTR (cystic fibrosis transmembrane conductance regulator) has also been implicated as a receptor; however, in this work, overexpression of CFTR had no effect onP. aeruginosabinding. It is concluded that neither Gg3nor Gg4are specifically recognized byP. aeruginosa, and that endogenous GSLs do not have a role in the attachment of live intactP. aeruginosato cultured lung epithelial cells. In contrast to whole piliatedP. aeruginosa, T4P sheared from such bacteria showed significant Gg3and Gg4binding, which may explain the results of other studies.
Regulation of the expression of whiB1 in Mycobacterium tuberculosis: role of cAMP receptor protein
Authors: Agarwal Nisheeth , Raghunand Tirumalai R. , Bishai William R.
Published: August 2006

The wbl (whiB-like) genes encode putative transcription factors unique to actinomycetes. This study characterized the promoter element of one of the seven wbl genes of Mycobacterium tuberculosis, whiB1 (Rv3219c). The results reveal that whiB1 is transcribed by a class I-type cAMP receptor protein (CRP)-dependent promoter, harbouring a CRP-binding site positioned at −58.5 with respect to its transcription start point. In vivo promoter activity analysis and electrophoretic mobility shift assays suggest that the expression of whiB1 is indeed regulated by cAMP-dependent binding of CRPM (encoded by the M. tuberculosis gene Rv3676) to the whiB1 5′ untranslated region (5′UTR). β-Galactosidase gene fusion analysis revealed induction of the whiB1 promoter in M. tuberculosis on addition of exogenous dibutyric cAMP (a diffusible cAMP analogue) only when an intact CRP-binding site was present. These results indicate that M. tuberculosis whiB1 transcription is regulated in part by cAMP levels via direct binding of cAMP-activated CRPM to a consensus CRP-binding site in the whiB1 5′UTR.
Identification of the Mycobacterium tuberculosis GlnE promoter and its response to nitrogen availability
Authors: Pashley Carey A. , Brown Amanda C. , Robertson Dina , Parish Tanya
Published: August 2006

Adenylyltransferase, GlnE, has a predicted role in controlling the enzymic activity of glutamine synthetase, the key enzyme in ammonia assimilation. It was previously demonstrated that glnE is an essential gene in Mycobacterium tuberculosis. glnE is located downstream of glnA2, one of four glutamine synthetases. The expression of GlnE under various conditions was determined. Although a co-transcript of glnA2 and glnE was detectable, the major transcript was monocistronic. A transcriptional start site immediately upstream of glnE was identified and it was shown by site-directed mutagenesis that the predicted −10 region is a functional promoter. It was demonstrated that in a Mycobacterium smegmatis background M. tuberculosis PglnE was up-regulated in ammonia- or glutamine-containing media.
Metabolic fingerprints of Mycobacterium bovis cluster with molecular type: implications for genotype–phenotype links
Authors: Winder Catherine L. , Gordon Stephen V. , Dale James , Hewinson R. Glyn , Goodacre Royston
Published: August 2006

Mycobacterium bovis is the causative agent of bovine tuberculosis. Various genetic typing techniques have been used to trace the reservoirs of infection; however, they have limited success in population genetics and outbreak studies. Fourier-transform infrared spectroscopy (FT-IR) is a rapid phenotypic typing technique, which may be used to generate a metabolic fingerprinting and is increasingly used to characterize bacteria. When coupled with multivariate cluster analysis, this powerful combination has sufficient resolving power to discriminate bacteria down to subspecies level; however, to date this method has not been used in the differentiation of mycobacteria. Multiple isolates of the ten major spoligotypes in the UK, recovered from different geographical locations, were analysed using FT-IR. Hierarchical cluster analysis of the spectra showed that the isolates could be differentiated according to their spoligotypes. Six of the spoligotype FT-IR clusters were very homogeneous and all isolates were recovered together. However, the remaining four groups displayed a more heterogeneous phenotype, which may reflect greater variation than previously suspected within these groups. Included in the ten spoligotypes are the two most dominant isolates in the UK, designated types 9 and 17. Whilst type 17 showed a highly conserved phenotype as judged by FT-IR, type 9 showed a very heterogeneous metabolic profile and isolates were recovered throughout the dendrogram. This variation in type 9 is reflected in the high degree of diversity observed by variable number tandem repeats (VNTR) analysis, underlining the exquisite resolving power of FT-IR.
Identification of a diacylglycerol acyltransferase gene involved in accumulation of triacylglycerol in Mycobacterium tuberculosis under stress
Authors: Sirakova Tatiana D. , Dubey Vinod S. , Deb Chirajyoti , Daniel Jaiyanth , Korotkova Tatiana A. , Abomoelak Bassam , Kolattukudy Pappachan E.
Published: August 2006

Mycobacterium tuberculosis under stress stores triacylglycerol (TG). There are 15 genes in M. tuberculosis that belong to a novel family of TG synthase genes (tgs), but it is not known which of them is responsible for this accumulation of TG. In this paper, it is reported that M. tuberculosis H37Rv accumulated TG under acidic, static or hypoxic growth conditions, or upon treatment with NO, whereas TG accumulation was drastically reduced in the tgs1 (Rv3130c) disrupted mutant. Complementation with tgs1 restored this TG accumulation. C26 was a major fatty acid in this TG, indicating that the TGS1 gene product uses C26 fatty acid, which is known to be produced by the mycobacterial fatty acid synthase. TGS1 expressed in Escherichia coli preferred C26 : 0-CoA for TG synthesis. If TG storage is needed for the long-term survival of M. tuberculosis under dormant conditions, the tgs1 product could be a suitable target for antilatency drugs.
Mechanisms of copper loading on the Schizosaccharomyces pombe copper amine oxidase 1 expressed in Saccharomyces cerevisiae
Authors: Laliberté Julie , Labbé Simon
Published: August 2006

Copper amine oxidases (CAOs) are found in almost every living kingdom. AlthoughSaccharomyces cerevisiaeis one of the few yeast species that lacks an endogenous CAO, heterologous gene expression of CAOs from other organisms produces a functional enzyme. To begin to characterize their function and mechanisms of copper acquisition, two putativecao+genes fromSchizosaccharomyces pombewere expressed inS. cerevisiae. Expression ofspao1+resulted in the production of an active enzyme capable of catalysing the oxidative deamination of primary amines. On the other hand, expression ofspao2+failed to produce an active CAO. Using a functionalspao1+–GFPfusion allele, the SPAO1 protein was localized in the cytosol. Under copper-limiting conditions, yeast cells harbouring deletions of theMAC1,CTR1andCTR3genes were defective in amine oxidase activity. Likewise,atx1Δ null cells exhibited no CAO activity, whileccc2Δ mutant cells exhibited decreased levels of amine oxidase activity, and mutations incox17Δ andccs1Δ did not cause any defects in this activity. Copper-deprivedS. cerevisiaecells expressingspao1+required a functionalatx1+gene for growth on minimal medium containing ethylamine as the sole nitrogen source. Under these conditions, the inability of theatx1Δ cells to utilize ethylamine correlated with the lack of SPAO1 activity, in spite of the efficient expression of the protein. Cells carrying a disruptedccc2Δ allele exhibited only weak growth on ethylamine medium containing a copper chelator. The results of these studies reveal that expression of the heterologousspao1+gene inS. cerevisiaeis required for its growth in medium containing ethylamine as the sole nitrogen source, and that expression of an activeSchiz. pombeSPAO1 protein inS. cerevisiaedepends on the acquisition of copper through the high-affinity copper transporters Ctr1 and Ctr3, and the copper chaperone Atx1.
In vivo monitoring of the potassium channel KcsA in Streptomyces lividans hyphae using immuno-electron microscopy and energy-filtering transmission electron microscopy
Authors: Hegermann Jan , Overbeck Jens , Schrempf Hildgund
Published: August 2006

The previous discovery of theStreptomyces lividans kcsAgene and its overexpression followed by the functional reconstitution of the purified gene product has resulted in new strategies to explore this channel proteinin vitro. KcsA has evolved as a general model to investigate the structure/function relationship of ion channel proteins. Using specific antibodies raised against a domain of KcsA lacking membrane-spanning regions, KcsA has now been localized within numerous separated clusters between the outer face of the cytoplasm and the cell envelope in substrate hyphae of theS. lividanswild-type strain but not in a designed chromosomal disruption mutant ΔK, lacking a functionalkcsAgene. Previous findings had revealed that caesium ions led to a block of KcsA channel activity withinS. lividansprotoplasts fused to giant vesicles. As caesium can be scored by electron energy loss spectroscopy better than potassium, this technique was applied to hyphae that had been briefly exposed to caesium instead of potassium ions. Caesium was found preferentially at the cell envelope. Compared to the ΔK mutant, the relative level of caesium was ≈30 % enhanced in the wild-type. This is attributed to the presence of KcsA channels. Additional visualization by electron spectroscopic imaging supported this conclusion. The data presented are believed to represent the first demonstration ofin vivomonitoring of KcsA in its original host.
Fermentation acids inhibit amino acid deamination by Clostridium sporogenes MD1 via a mechanism involving a decline in intracellular glutamate rather than protonmotive force
Authors: Flythe Michael D. , Russell James B.
Published: August 2006

Fermentation acids inhibited the growth and ammonia production of the amino-acid-fermenting bacteriumClostridium sporogenesMD1, but only when the pH was acidic. Such inhibition was traditionally explained by the ability of fermentation acids to act as uncouplers and decrease protonmotive force (Δp), butC. sporogenesMD1 grows even if the Δp is very low. Cell suspensions incubated with additional sodium chloride produced ammonia as rapidly at pH 5.0 as at pH 7.0, but cells incubated with additional sodium lactate were sensitive to even small decreases in extracellular pH. Similar results were obtained if the sodium lactate was replaced by sodium acetate or propionate. When extracellular pH declined, ΔpH increased even if sodium lactate was present. The cells accumulated intracellular lactate anion when the pH was acidic, and intracellular glutamate declined. Because amino acid deamination is linked to a transamination reaction involving glutamate dehydrogenase, the decrease in ammonia production could be explained by the decrease in intracellular glutamate. This latter hypothesis was consistent with the observation that extracellular glutamate addition restored amino acid deamination even though glutamate alone did not allow for the generation of ammonia.
Regulation of class D β-lactamase gene expression in Ralstonia pickettii
Authors: Girlich Delphine , Naas Thierry , Nordmann Patrice
Published: August 2006

Ralstonia pickettii, an environmental bacterium that may also be responsible for human infections, produces two unrelated, inducible and chromosomally encoded oxacillinases, OXA-22 and OXA-60. In order to study the molecular basis of the induction process of these oxacillinase genes, the induction kinetics, the promoter/operator regions necessary for expression and induction, and the role of several ORFs located upstream and downstream of theblaOXAgenes were investigated. Theβ-lactamase production reached a maximal level after 1 h induction, returned to its basal level within the following 3 h and was then again inducible. Using 5′RACE experiments, the promoter sequences of both oxacillinases were determined. These sequences showed weak promoter activities, which could, however, be increased approximately 200-fold by mutating the −35 promoter sequence. Deletion of the sequences located upstream of the promoter regions did not modify the basalβ-lactamase expression inR. pickettii, but resulted in the lack of induction. A minimum of 240 and 270 bp upstream of the transcription initiation sites was required for inducible expression of theblaOXA-22andblaOXA-60genes, respectively. Analysis of the genetic environment of bothblaOXAgenes revealed several ORFs that were inactivated by homologous recombination. Disruption of ORF-RP3, located 190 bp upstream ofblaOXA-60and divergently transcribed, abolished induction of bothβ-lactamases. ORF-RP3, which encoded a polypeptide of 532 aa with an estimated molecular mass of 58.7 kDa, displayed no obvious sequence homology with known regulatory proteins.Trans-complementation of ORF-RP3 restored the basal and inducible expression of both oxacillinase genes, indicating that the induction of both enzymes was related to the presence of ORF-RP3. In addition to the loss of induction, inactivation of the ORF-RP3 inR. pickettiiresulted in a complex pleiotropic phenotype, with increased lag phase and reduced survival after heat exposure, suggesting that ORF-RP3 might be a global regulator involved in unrelated regulatory pathways.
Microdiesel: Escherichia coli engineered for fuel production
Authors: Kalscheuer Rainer , Stölting Torsten , Steinbüchel Alexander
Published: August 2006

Biodiesel is an alternative energy source and a substitute for petroleum-based diesel fuel. It is produced from renewable biomass by transesterification of triacylglycerols from plant oils, yielding monoalkyl esters of long-chain fatty acids with short-chain alcohols such as fatty acid methyl esters and fatty acid ethyl esters (FAEEs). Despite numerous environmental benefits, a broader use of biodiesel is hampered by the extensive acreage required for sufficient production of oilseed crops. Therefore, processes are urgently needed to enable biodiesel production from more readily available bulk plant materials like sugars or cellulose. Toward this goal, the authors established biosynthesis of biodiesel-adequate FAEEs, referred to as Microdiesel, in metabolically engineeredEscherichia coli. This was achieved by heterologous expression inE. coliof theZymomonas mobilispyruvate decarboxylase and alcohol dehydrogenase and the unspecific acyltransferase fromAcinetobacter baylyistrain ADP1. By this approach, ethanol formation was combined with subsequent esterification of the ethanol with the acyl moieties of coenzyme A thioesters of fatty acids if the cells were cultivated under aerobic conditions in the presence of glucose and oleic acid. Ethyl oleate was the major constituent of these FAEEs, with minor amounts of ethyl palmitate and ethyl palmitoleate. FAEE concentrations of 1.28 g l−1and a FAEE content of the cells of 26 % of the cellular dry mass were achieved by fed-batch fermentation using renewable carbon sources. This novel approach might pave the way for industrial production of biodiesel equivalents from renewable resources by employing engineered micro-organisms, enabling a broader use of biodiesel-like fuels in the future.
A link in transcription between the native pbpB and the acquired mecA gene in a strain of Staphylococcus aureus
Authors: Gardete Susana , de Lencastre Hermínia , Tomasz Alexander
Published: August 2006

Conditional mutants ofpbpBwith an IPTG-inducible promoter were used to compare the effects of interrupted transcription of this gene in a meticillin-sensitive (MSSA) and a meticillin-resistant (MRSA) strain ofStaphylococcus aureus. After 3 h growth following the removal of IPTG, multiplication of the MSSA strain stopped abruptly, cells began to lyse, and membrane preparations showed greatly decreased quantities of penicillin-binding protein (PBP) 2. In contrast, the MRSA strain continued to grow for at least 20 h in the IPTG-free medium, but with gradually increasing doubling times, which eventually reached 180 min. The peptidoglycan produced during this period of extremely slow growth showed only minor alterations, but cells with abnormal morphology accumulated in the culture, the abundance ofmecAtranscript gradually declined, and the cellular amounts of PBP2A were significantly decreased. Adding back the IPTG inducer caused rapid resumption in the transcription ofpbpB, followed by an increase in the transcription ofmecA. No changes were detected in the transcription ofpbpA,CandD, the determinant of 16S rRNA or the housekeeping genepta. Promoter fusion experiments suggested that the transcription of the resistance genemecAmay respond to some regulatory signal generated in the bacteria during changes in the transcription ofpbpB.
Minimal diurnal change in foraging time in an Australian passerine, the white‐browed babbler Pomatostomus superciliosus
Authors: Taylor Sarah G. , Paul Warren L.
Published: August 2006

This paper describes the daily foraging pattern of the white‐browed babbler Pomatostomus superciliosus, a small passerine endemic to Australia. The percentage of time spent foraging as the day progressed increased by an average of only 9%. This contrasts markedly with studies of other passerines that have mostly shown a bimodal pattern, with a peak of foraging early in the day followed by a period of reduced activity and a second peak later in the day. The most likely explanation for the observed pattern of foraging time is that babblers experienced considerable diurnal certainty in their food supply mainly as a result of stable and predictable weather conditions. The lack of a marked increase in foraging towards the end of the day might also have resulted from an increase in predation risk at this time and a reduced need to build up food reserves at the end of the day because of the energetic advantages of communal roosting in an enclosed nest.
Relative importance of factors affecting nestling immune response differs between junior and senior nestlings within broods of hoopoesUpupa epops
Authors: Martín‐Vivaldi Manuel , Ruiz‐Rodríguez Magdalena , Méndez María , J. Soler Juan
Published: August 2006

Animals should invest in the immune system to protect themselves from parasites, but the cost of immune responses may limit investment depending on resource availability. In birds’ broods, senior and junior chicks in size hierarchies face different rearing conditions, and thus we predicted that factors affecting immune response should differ between them. In asynchronously hatched hoopoeUpupa epopsbroods, we found that the immune response of senior nestlings was not related to their body condition, but positively related to risk of parasitism (which was indirectly estimated by laying date). This suggests that their immunocompetence is not limited by access to resources, and they can differentially invest in immune response with increasing risk of parasitism. On the other hand, immune response of junior nestlings was related to their body condition, but secondarily also to risk of parasitism. Our results agree with previous studies that have found significant influence of nutritional status and risk of parasitism on nestlings immune defence, but show that the effects of these environmental factors on nestling immunocompetence differ between nestlings occupying high and low rank positions in size hierarchies. The possible influence of maternal effects on the results found is also discussed.
Molecular phylogeny and biogeographic history of the piculets (Piciformes: Picumninae)
Authors: Fuchs Jérôme , I. Ohlson Jan , G. P. Ericson Per , Pasquet Eric
Published: August 2006

The subfamily Picumninae (piculets) includes 3 genera and 30 species of tiny and short‐tailed woodpeckers with a pantropical distribution. Within the Picumninae, two cases of intercontinentally disrupted distributions at the genus level occur. The first one concerns the genus Sasia (one species in Africa and two in southeast Asia) while the second concerns Picumnus (one species in southeast Asia and 25 in South America). These disrupted distributions, as well as several morphological differences, have lead some authors to place the African representative of Sasia and the southeast Asian representative of Picumnus in their own monotypic genera (Verreauxia and Vivia, respectively). To address the taxonomic status and biogeographic history of the piculets, we sequenced 2676 bp of DNA from one mitochondrial (ND2) and two nuclear markers (myoglobin intron 2 and β‐fibrinogen intron 7). Monophyly of Picumninae could not be recovered with confidence, while monophyly of Sasia and Picumnus were always strongly supported. Molecular dating analyses revealed that the splits both between the African and Indo‐Malayan Sasia and between the New World and Old World Picumnus occurred at ca 7.9 Myr BP. This time corresponds to the beginning of the formation of the northern Hemisphere ice sheets and the accompanying expansion of grasslands throughout the world. The spread of open areas in the northern parts of Eurasia and America prevented gene flow between tropical forest birds, such as the piculets, in Africa, southeast Asia and South America, respectively.
Plasticity of brood patch development and its influence on incubation periods in the yellow‐eyed penguin Megadyptes antipodes: an experimental approach
Authors: Massaro Melanie , Davis Lloyd S. , Davidson R. Scott
Published: August 2006

In many bird species, eggs laid late in the laying period hatch after a shorter incubation period than early‐laid eggs. However, the mechanisms that explain these seasonal declines in incubation periods among clutches remain poorly understood. In this study we investigated the plasticity of brood patch development during incubation in yellow‐eyed penguins Megadyptes antipodes and established whether differences exist in brood patch formation among early, mean and late‐breeding penguins. We also examined whether brood patch development was influenced by sex and age of birds. We then placed an artificial egg in nests a few days prior to egg laying to investigate whether the presence of an egg influences brood patch development and whether an advanced brood patch development at the time of egg laying causes declines in incubation periods. Initial brood patch width on the day the first egg was laid was dependent on sex and age, while the development of brood patch width after first egg laying was slower in early‐laying birds than in mean‐ and late‐laying birds. Initial brood patch temperature as well as temperature throughout incubation was largely dependent upon sex, whereby males had higher brood patch surface temperatures than females. Placement of an artificial egg in nests stimulated successfully brood patch development in manipulated birds, so that by the time they laid their own first egg, their brood patches were wider and had higher temperatures than those of control birds. Moreover, incubation periods of first eggs from manipulated nests were significantly shorter (43.5 days) than were those from control nests (47.3 days). Thus, variation in brood patch development and related differences in incubation temperature during early incubation could contribute to seasonal declines in incubation periods.
Ruddy turnstones Arenaria interpres rapidly build pectoral muscle after raptor scares
Authors: J. van den Hout Piet , Piersma Theunis , Dekinga Anne , K. Lubbe Suzanne , Henk Visser G.
Published: August 2006

To cope with changes in the environment, organisms not only show behavioural but also phenotypic adjustments. This is well established for the digestive tract. Here we present a first case of birds adjusting their flight machinery in response to predation risk. In an indoor experiment, ruddy turnstones Arenaria interpres were subjected to an unpredictable daily appearance of either a raptor or a small gull (as a control). Ruddy turnstones experiencing threat induced by a flying raptor model, longer than after similar passage by the gull model, refrained from feeding after this disturbance. Pectoral muscle mass, but not lean mass, responded in a course of a few days to changes in the perceived threat of predation. Pectoral muscle mass increased after raptor scares. Taking the small increases in body mass into account, pectoral muscle mass was 3.6% higher than aerodynamically predicted for constant flight performance. This demonstrates that perceived risk factors may directly affect organ size.
Xanthomonas oryzae pathovars: model pathogens of a model crop
Authors: NIÑO‐LIU DAVID O. , RONALD PAMELA C. , BOGDANOVE ADAM J.
Published: August 2006

Xanthomonas oryzae pv. oryzae and Xanthomonas oryzae pv. oryzicola cause bacterial blight and bacterial leaf streak of rice (Oryza sativa), which constrain production of this staple crop in much of Asia and parts of Africa. Tremendous progress has been made in characterizing the diseases and breeding for resistance. X. oryzae pv. oryzae causes bacterial blight by invading the vascular tissue, while X. oryzae pv. oryzicola causes bacterial leaf streak by colonizing the parenchyma. In rice there are 29 major genes for resistance to bacterial blight, but so far only a few quantitative resistance loci for bacterial leaf streak. Over 30 races of X. oryzae pv. oryzae have been reported. Both pathogens exhibit genetic variation among isolates. Mechanisms of pathogenesis and resistance have begun to be elucidated. Members of the AvrBs3/PthA family of transcription activator‐like effectors play a major role in the virulence of X. oryzae pv. oryzae and possibly X. oryzae pv. oryzicola. Cloning of six rice resistance genes for bacterial blight and one from maize effective against bacterial leaf streak has uncovered a diversity of structure and function, some shared by genes involved in defence in animals. This article reviews research that spans a century. It also presents a perspective on challenges for sustainable control, and opportunities that interactions of X. oryzae pathovars with rice present as models for understanding fundamental aspects of bacterial pathogenesis of plants and plant disease resistance, as well as other aspects of plant and microbial biology, with implications also for animal innate immunity.
Review article: the role of bacteria in onset and perpetuation of inflammatory bowel disease
Authors: SEKSIK P. , SOKOL H. , LEPAGE P. , VASQUEZ N. , MANICHANH C. , MANGIN I. , POCHART P. , DORÉ J. , MARTEAU P.
Published: August 2006

We review the evidence that strongly suggests a role of the intestinal microbiota in the onset and perpetuation of inflammatory bowel disease (IBD).

Experimental studies consisted of suppressing micro‐organisms from the microbiota (using germ‐free or gnotoxenic animals or antibiotics), introducing new micro‐organisms or microbial components (e.g. probiotics, CpG‐DNA) or selectively increasing some endogenous bacteria (e.g. using prebiotics).

Intervention studies were performed in patients or animal models of spontaneous or chemically‐induced colitis.

Information was also obtained from observational studies that described the composition of the faecal and mucosal microbiota at various stages of the disease process and in controls. Many have used culture‐independent techniques that identify bacteria based on the nucleic acid sequence of ribosomal RNA molecules. Microbiota in patients with IBD seem to be characterized by high concentrations of bacteria in contact with the mucosa, instability, the presence of high numbers of unusual bacteria and sometimes a reduction in the biodiversity.

Studies searching for a generalized or localized dysbiosis in IBD are discussed, as well as those trying to identify bacterial molecules and receptors, which may be implicated in triggering the inflammatory process.
Review article: capsule endoscopy – are all small intestinal lesions Crohn's disease?
Authors: BAR‐MEIR S.
Published: August 2006

Capsule endoscopy is the gold‐standard examination for the diagnosis of Crohn's disease (CD) of the small intestine. Its incremental yield over other imaging modalities is above 30%.

It is important to keep in mind that over 10% of healthy subjects demonstrate mucosal breaks and erosions in their small intestinal mucosa. Thus, one should refrain from diagnosing CD based on the existence of a few erosions and ulcers of the small intestine. Such erosions and ulcers may in fact be the result of non‐steroidal anti‐inflammatory drug intake and other pathological conditions such as lymphoid hyperplasia, lymphoma and radiation enteritis. Non‐steroidal anti‐inflammatory drug intake should, therefore, be excluded as a cause prior to relating the presence of lesions to CD.

Misdiagnosis of CD may be harmful to the patient because if unresponsive, intensification of therapy may occur and occasionally an unnecessary operation may be performed. At the same time, the patient may also be deprived of the appropriate therapy for the treatment of their condition.
Review article: can post‐operative recurrence in Crohn's disease be prevented?
Authors: LÉMANN M.
Published: August 2006

The decision regarding prophylactic treatment after surgery in Crohn's disease (CD) requires a good estimation of the risk of recurrence. It is also important to consider the consequences of recurrence for the patient, and the risks and benefits of treatment, bearing in mind that it will be given over a long period.

Several drugs have been tried to decrease the risk of recurrence. Corticosteroids and budesonide have proved to be ineffective. Mesalazine has significant efficacy in some, but not all trials, and a meta‐analysis has established that it decreases the absolute risk by 10–15% after 1–2 years. Mercaptopurine seemed to be effective in a recent study. Metronidazole and ornidazole have significant efficacy, but cannot be tolerated for long periods. Probiotics represent a new approach, but evidence for their efficacy in CD is still lacking.

In the past, the strategy was to give no treatment until clinical recurrence. Another approach is to give no treatment, and then to treat the patient according to severity of endoscopic recurrence. Alternative strategies include treating all patients with mesalazine until either severe endoscopic or clinical recurrence occurs, and then to use azathioprine/mercaptopurine, or to give azathioprine/mercaptopurine immediately, especially in high‐risk patients.
Review article: recurrence of Crohn's disease after surgery – the need for treatment of new lesions
Authors: RUTGEERTS P.
Published: August 2006

Crohn's recurrence is the appearance of objective signs – defined radiologically, endoscopically or pathologically – of Crohn's disease in the bowel of a patient who has previously had a resection of all macroscopically diseased tissue.

New lesions can be visualized endoscopically within weeks to months after ileal resection and ileocolonic anastomosis in the neoterminal ileum. The evolution of these lesions mimics the natural history of ileal Crohn's disease at the onset. If we are able to prevent recurrence of early lesions, we will probably interrupt the natural course of the disease.

The drugs tested to date include different 5‐aminosalicylate formulations, nitro‐imidazole antibiotics, steroids and azathioprine. None of these therapies has convincingly been shown to prevent recurrent lesions. Metronidazole and ornidazole are effective, but cannot be used in the long‐term because of side effects.

Since there is a lag time of months to years between the development of recurrent lesions in the bowel and the recurrence of symptoms, we recommend performing imaging of the bowel 6 months after the operation to assess the severity of recurrence, and basing the further treatment strategy on this assessment.
Review article: should we treat symptoms or lesions in Crohn's disease? The case for treating symptoms
Authors: SCHÖLMERICH J.
Published: August 2006

Apart from treating symptoms, mucosal healing is a reasonable aim of therapy in Crohn's disease. In most patients, however, the disease takes a mild course and treating symptoms seems sufficient. Eliminating lesions may change the course of the disease long‐term but this has not yet been proven. Thus far we need to treat symptoms efficiently and may attempt to restore bacterial epithelial interaction.
Review article: aminosalicylates for distal colitis
Authors: GIONCHETTI P. , RIZZELLO F. , MORSELLI C. , TAMBASCO R. , CAMPIERI M.
Published: August 2006

About two‐thirds of patients with ulcerative colitis have an inflammatory involvement distal to the splenic flexure and therefore may be effectively treated with topical treatment. This allows the delivery of the active drug directly to the site of inflammation, limiting the systemic absorption and the potential side effects.

Topical aminosalicylate therapy is the most effective approach, provided that the formulation reaches the upper extent of the disease. Suppositories should be considered the treatment of choice for proctitis and distal sigmoiditis. A 1 g Pentasa‐suppository once daily induces a quicker clinical and endoscopic remission and was better tolerated than a 500‐mg suppository twice daily. Enemas, foams and gel, thanks to their proximal spread, should be the treatment of choice for proctosigmoiditis and left‐sided colitis.

Oral aminosalicylates are less effective than topical therapies for patients with active disease; however, a combination of oral and topical aminosalicylates can be successfully tried in refractory patients.

Topical aminosalicylates also play an important role in the maintenance of remission, and the combination of oral plus rectal 5‐aminosalicylate is superior to the single agent. Patients who prefer not to continue on long‐term rectal therapy can be treated with oral aminosalicylates.
Review article: how to control and improve adherence to therapy in inflammatory bowel disease
Authors: LÓPEZ‐SANROMÁN A. , BERMEJO F.
Published: August 2006

Any chronic disease is a risk situation for non‐adherence to treatment. This results in suboptimal medication, and poor disease control. Adherence and compliance are directly related to therapeutic success, which is further complicated in inflammatory bowel disease patients.

There is a wide array of circumstances that increase the likelihood of non‐compliance in a given patient: difficult‐to‐follow treatment schedules (multiple doses and multiple drugs), insufficient patient information, longer evolution of the disease and inactive disease. Depression, male gender, active employment and living alone are also associated with poorer adherence to therapy.

Monitoring drug intake is possible in many circumstances, directly or indirectly (urinary salicylate levels; erythrocyte metabolites and increased mean corpuscular volume and bilirubin in patients under azathioprine; blood levels of ciclosporin or tacrolimus). However, such measures are probably better utilized for dose adjustment and not for the identification of non‐compliant patients. High‐risk patients are a target group in which pre‐emptive intervention could ensure better compliance.

If the question of non‐adherence arises, for instance, as a possible cause of therapy failure, the patient should be carefully approached. This should take into consideration factors that may be corrected and, most importantly, should aim at building a better patient–doctor relationship.
Review article: what are the important endoscopic lesions for detection of dysplasia in inflammatory bowel disease?
Authors: GEBOES K.
Published: August 2006

It is recognized that inflammatory bowel diseases predispose to colorectal adenocarcinoma. Early detection of precursor lesions and subsequent treatment may prevent cancer development and this is possible with colonoscopy and biopsy.

Inflammatory bowel disease‐associated precursor lesions (dysplasia = intraepithelial neoplasia) must be distinguished from sporadic adenomas, occurring in non‐colitic mucosa.

Macroscopic lesions suspected of harbouring precursor lesions include irregular ‘polypoid or elevated’ lesions, which are usually broad‐based and ‘flat’ lesions. Flat lesions are more common than elevated lesions and they are usually smaller.

Chromoendoscopy increases the detection rate substantially as it allows targeted biopsies from suspicious lesions that increase the diagnostic yield of dysplasia.

Ultimately, the combination of chromoendoscopy, or more advanced endoscopic techniques, and targeted biopsies may become the standard approach, rather than random biopsy sampling.
Review article: saving the colon in severe colitis – the case for medical therapy
Authors: TRAVIS S.
Published: August 2006

The choice between ciclosporin (CsA), infliximab (IFX) and surgery for severe colitis not responding to intensive intravenous treatment, is challenging. With the advent of vislizumab and alternatives such as tacrolimus or leucocytapheresis, decisions will get harder.

This article reviews the evidence for each intervention, draws attention to disparities in the definition of severe colitis between different trials and gives practical guidance.

Early medical decision making is critical. Standard intensive treatment with intravenous steroids is still the first‐line approach. Progress should be monitored objectively using a simple predictive index. Rescue therapy with CsA (oral 5 mg/kg or 2 mg/kg iv) or IFX (5 mg/kg) should be started on the third day of intensive treatment if predictive factors are poor (e.g. C‐reactive protein > 45 mg/L).

Physicians should discuss with their patients that there is just one attempt at rescue therapy, because only one patient death, as a consequence of delayed colectomy, changes the balance of benefit between medicine and surgery.
Review article: colon‐saving medical therapy vs. colectomy in ulcerative colitis – the case for colectomy
Authors: ÖRESLAND T.
Published: August 2006

In the era of expanding medical therapy for ulcerative colitis, surgery is still a very valid option in those patients, where medicine is not able to control symptoms, both in the acute and chronic stages, and also for those at risk of developing a cancer.

The ileal pouch–anal anastomosis (IPAA) will, for the vast majority of patients, give a very acceptable functional outcome. There is a risk of surgical complications and pouchitis; however, mortality is very low and compares well with medical therapy. Reduced female fertility is a concern but compared with the preoperative state, overall sexual function is largely improved.

The ileorectal anastomosis is undergoing a revival and can be used especially in the case of female fertility concerns.

Either the continent ileostomy or a conventional ileostomy is an option for those 10–15% of patients who will eventually experience pouch failure, usually either because of septic complications or an unacceptable bowel function.

Quality of life following both these options, and IPAA, is excellent and does not differ from that of the matched background population.