bluuebunny/crossref_metadata_2025 huggingface dataset:
Structural analysis of the chromosome segregation protein Spo0J from Thermus thermophilus
Authors: Leonard Thomas A. , Butler P. Jonathan G. , Löwe Jan
Published: July 2004

Prokaryotic chromosomes and plasmids encode partitioning systems that are required for DNA segregation at cell division. The plasmid partitioning loci encode two proteins, ParA and ParB, and a cis‐acting centromere‐like site denoted parS. The chromosomally encoded homologues of ParA and ParB, Soj and Spo0J, play an active role in chromosome segregation during bacterial cell division and sporulation. Spo0J is a DNA‐binding protein that binds to parS sites in vivo. We have solved the X‐ray crystal structure of a C‐terminally truncated Spo0J (amino acids 1–222) from Thermus thermophilus to 2.3 Å resolution by multiwavelength anomalous dispersion. It is a DNA‐binding protein with structural similarity to the helix–turn–helix (HTH) motif of the lambda repressor DNA‐binding domain. The crystal structure is an antiparallel dimer with the recognition α‐helices of the HTH motifs of each monomer separated by a distance of 34 Å corresponding to the length of the helical repeat of B‐DNA. Sedimentation velocity and equilibrium ultracentrifugation studies show that full‐length Spo0J exists in a monomer–dimer equilibrium in solution and that Spo0J1–222 is exclusively monomeric. Sedimentation of the C‐terminal domain of Spo0J shows it to be exclusively dimeric, confirming that the C‐terminus is the primary dimerization domain. We hypothesize that the C‐terminus mediates dimerization of Spo0J, thereby effectively increasing the local concentration of the N‐termini, which most probably dimerize, as shown by our structure, upon binding to a cognate parS site.
Activation of the Bacillus subtilis global regulator CodY by direct interaction with branched‐chain amino acids
Authors: Shivers Robert P. , Sonenshein Abraham L.
Published: July 2004

CodY, a GTP‐activated global transcriptional regulator of early stationary phase genes, is conserved in many Gram‐positive bacterial species. Recently, a number of novel targets regulated by CodY have been identified, including three Bacillus subtilis operons involved in branched‐chain amino acid (BCAA) biosynthesis (Molle, V., et al., 2003, J Bacteriol 185: 1911–1922). The mechanism of involvement of CodY in regulating the ilvB operon was investigated here using in vivo transcriptional fusions, in vitro gel mobility shift assays and DNase I footprinting assays. CodY was found to mediate regulation of the ilvB operon by GTP and BCAAs and to bind to the ilvB promoter region. BCAAs increased the affinity of CodY for the ilvB promoter and for all other CodY targets tested. This effect of BCAAs in vitro was additive with the effect of GTP on CodY DNA‐binding activity.
Responsiveness to acidity via metal ion regulators mediates virulence in the gastric pathogen Helicobacter pylori
Authors: Bury‐Moné Stéphanie , Thiberge Jean‐Michel , Contreras Monica , Maitournam Aboubakar , Labigne Agnès , De Reuse Hilde
Published: July 2004

The virulence of pathogenic bacteria is dependent on their adaptation to and survival in the stressful conditions encountered in their hosts. Helicobacter pylori exclusively colonizes the acid stomach of primates, making it an ideal study model. Little is known about how H. pylori responds to the moderately acidic conditions encountered at its colonization site, the gastric mucus layer. Thus, we compared gene expression profiles of H. pylori 26695 grown at neutral and acidic pH, and validated the data for a selection of genes by real‐time polymerase chain reaction, dot‐blots or enzymatic assays. During growth in acidic conditions, 56 genes were upregulated and 45 genes downregulated. We found that acidity is a signal modulating the expression of several virulence factors. Regulation of genes related to metal ion homeostasis suggests protective mechanisms involving diminished transport and enhanced storage. Genes encoding subunits of the F0F1 ATPase and of a newly identified Na+/H+ antiporter (NhaC‐HP0946) were downregulated, revealing that this bacterium uses original mechanisms to control proton entry. Five of the upregulated genes encoded proteins controlling intracellular ammonia synthesis, including urease, amidase and formamidase, underlining the major role of this buffering compound in the protection against acidity in H. pylori. Regulatory networks and transcriptome analysis as well as enzymatic assays implicated two metal‐responsive transcriptional regulators (NikR and Fur) and an essential two‐component response regulator (HP0166, OmpR‐like) as effectors of the H. pylori acid response. Finally, a nikR‐fur mutant is attenuated in the mouse model, emphasizing the link between response to acidity, metal metabolism and virulence in this gastric pathogen.
FbpA, a novel multifunctional Listeria monocytogenes virulence factor
Authors: Dramsi S. , Bourdichon F. , Cabanes D. , Lecuit M. , Fsihi H. , Cossart P.
Published: July 2004

Listeria monocytogenes is a Gram‐positive intracellular bacterium responsible for severe opportunistic infections in humans and animals. Signature‐tagged mutagenesis (STM) was used to identify a gene named fbpA, required for efficient liver colonization of mice inoculated intravenously. FbpA was also shown to be required for intestinal and liver colonization after oral infection of transgenic mice expressing human E‐cadherin. fbpA encodes a 570‐amino‐acid polypeptide that has strong homologies to atypical fibronectin‐binding proteins. FbpA binds to immobilized human fibronectin in a dose‐dependent and saturable manner and increases adherence of wild‐type L. monocytogenes to HEp‐2 cells in the presence of exogenous fibronectin. Despite the lack of conventional secretion/anchoring signals, FbpA is detected using an antibody generated against the recombinant FbpA protein on the bacterial surface by immunofluorescence, and in the membrane compartment by Western blot analysis of cell extracts. Strikingly, FbpA expression affects the protein levels of two virulence factors, listeriolysin O (LLO) and InlB, but not that of InlA or ActA. FbpA co‐immunoprecipitates with LLO and InlB, but not with InlA or ActA. Thus, FbpA, in addition to being a fibronectin‐binding protein, behaves as a chaperone or an escort protein for two important virulence factors and appears as a novel multifunctional virulence factor of L. monocytogenes.
Inactivation of deoxyadenosine methyltransferase (dam) attenuates Haemophilus influenzae virulence
Authors: Watson Michael E. , Jarisch Justin , Smith Arnold L.
Published: July 2004

Mutants in deoxyadenosine methyltransferase (dam) from many Gram‐negative pathogens suggest multiple roles for Dam methylase: directing post‐replicative DNA mismatch repair to the correct strand, guiding the temporal control of DNA replication and regulating the expression of multiple genes (including virulence factors) by differential promoter methylation. Dam methylase (HI0209) in strain Rd KW20 was inactivated in Haemophilus influenzae strains Rd KW20, Strain 12 and INT‐1; restriction with Dam methylation‐sensitive enzymes DpnI and DpnII confirmed the absence of Dam methylation, which was restored by complementation with a single copy of dam ectopically expressed in cis. Despite the lack of increased mutation frequency, the dam mutants had a 2‐aminopurine‐susceptible phenotype that could be suppressed by secondary mutations in mutS, suggesting a role for Dam in H. influenzae DNA mismatch repair. Invasion of human brain microvascular endothelial cells (HBMECs) and human respiratory epithelial cells (NCI‐H292) by the dam mutants was significantly attenuated in all strains, suggesting the absence of a Dam‐regulated event necessary for uptake or invasion of host cells. Intracellular replication was inhibited only in the Strain 12 dam mutant, whereas in the infant rat model of infection, the INT‐1 dam mutant was less virulent. Dam activity appears to be necessary for both in vitro and in vivo virulence in a strain‐dependent fashion and may function as a regulator of gene expression including virulence factors.
The formation of the rodlet layer of streptomycetes is the result of the interplay between rodlins and chaplins
Authors: Claessen Dennis , Stokroos Ietse , Deelstra Heine J. , Penninga Nynke A. , Bormann Christiane , Salas José A. , Dijkhuizen Lubbert , Wösten Han A. B.
Published: July 2004

Streptomycetes form hydrophobic aerial hyphae that eventually septate into hydrophobic spores. Both aerial hyphae and spores possess a typical surface layer called the rodlet layer. We present here evidence that rodlet formation is conserved in the streptomycetes. The formation of the rodlet layer is the result of the interplay between rodlins and chaplins. A strain of Streptomyces coelicolor in which the rodlin genes rdlA and/or rdlB were deleted no longer formed the rodlet layer. Instead, these surfaces were decorated with fine fibrils. Deletion of all eight chaplin genes (strain ΔchpABCDEFGH) resulted in the absence of the rodlet layer as well as the fibrils at surfaces of aerial hyphae and spores. Apart from coating these surfaces, chaplins are involved in the escape of hyphae into the air, as was shown by the strong reduction in the number of aerial hyphae in the ΔchpABCDEFGH strain. The decrease in the number of aerial hyphae correlated with a lower expression of the rdl genes in the colony. Yet, expression per aerial hypha was similar to that in the wild‐type strain, indicating that expression of the rdl genes is initiated after the hypha has sensed that it has grown into the air.
IS231–MIC231 elements from Bacillus cereus sensu lato are modular
Authors: De Palmenaer Daniel , Vermeiren Céline , Mahillon Jacques
Published: July 2004

IS231A was originally discovered in Bacillus thuringiensis as a typical 1.6 kb insertion sequence (IS) displaying 20 bp inverted repeats (IR) flanking a transposase gene. A first major variation of this canonical organization was found in MIC231A1. This mobile insertion cassette (MIC), delineated by IS231A‐related extremities, contained an active d‐stereospecific endopeptidase (adp) gene instead of a transposase. Interestingly, it was shown that MIC231A1 can be mobilized in trans by the IS231A transposase. In this paper, we show that this family of IS231–MIC231 elements can be extended to a broad range of related entities displaying higher levels of structural complexity. Several IS231A‐like elements contained, upstream of their transposase gene, passenger genes coding for putative antibiotic resistances or regulatory factors. Furthermore, the diversity of the MIC231 elements ranged from empty cassettes to structures carrying up to three passenger genes. Among these, MIC231V carried, in addition to an adp gene, an active fosfomycin resistance determinant. In vivo transposition assays showed that MIC231V is also trans‐activated by the IS231A transposase. These results lend further support to the potential contribution of these modular mobile elements to the genome plasticity of the Bacillus cereus/B. thuringiensis group.
Activation of transcription initiation from a stable RNA promoter by a Fis protein‐mediated DNA structural transmission mechanism
Authors: Opel Michael L. , Aeling Kimberly A. , Holmes Walter M. , Johnson Reid C. , Benham Craig J. , Hatfield G. Wesley
Published: July 2004

The leuV operon of Escherichia coli encodes three of the four genes for the tRNA1Leu isoacceptors. Transcription from this and other stable RNA promoters is known to be affected by a cis‐acting UP element and by Fis protein interactions with the carboxyl‐terminal domain of the α‐subunits of RNA polymerase. In this report, we suggest that transcription from the leuV promoter also is activated by a Fis‐mediated, DNA supercoiling‐dependent mechanism similar to the IHF‐mediated mechanism described previously for the ilvPG promoter (S. D. Sheridan et al., 1998, J Biol Chem 273: 21298–21308). We present evidence that Fis binding results in the translocation of superhelical energy from the promoter‐distal portion of a supercoiling‐induced DNA duplex destabilized (SIDD) region to the promoter‐proximal portion of the leuV promoter that is unwound within the open complex. A mutant Fis protein, which is defective in contacting the carboxyl‐terminal domain of the α‐subunits of RNA polymerase, remains competent for stimulating open complex formation, suggesting that this DNA supercoiling‐dependent component of Fis‐mediated activation occurs in the absence of specific protein interactions between Fis and RNA polymerase. Fis‐mediated translocation of superhelical energy from upstream binding sites to the promoter region may be a general feature of Fis‐mediated activation of transcription at stable RNA promoters, which often contain A+T‐rich upstream sequences.
Dissection of septin actin interactions using actin overexpression in Saccharomyces cerevisiae
Authors: Norden Caren , Liakopoulos Dimitris , Barral Yves
Published: July 2004

Although many proteins can be overexpressed several fold without much effect on cell viability and morphology, some become toxic upon a slight increase in their intracellular level. This is particularly true for cytoskeletal proteins and has proven useful in the past for studying the cytoskeleton. In yeast, actin and tubulin are examples of proteins that cannot be overexpressed without affecting cell viability. Here, we have analysed the effect of actin overexpression in Saccharomyces cerevisiae. We show that actin overexpression interferes differently with distinct aspects of actin function. For example, two‐ to fourfold overexpression of actin did not affect the establishment of actin polarity, whereas it abrogated its maintenance. Also, actin structures that are barely visible in wild‐type cells could be observed upon actin overexpression. This allowed us to identify a new ring‐like actin structure genetically distinguishable from the actomyosin contractile ring. Formation of this actin structure upon actin overexpression was dependent on the septin cytoskeleton, the poorly understood cytokinetic protein Hof1 and the Arp2/3 complex. In contrast to the actomyosin ring, the ring formed upon actin overexpression required neither Myo1 nor formins for assembly. Therefore, we propose that Hof1 acts as a linker between actin and septins. Furthermore, we found that, in the absence of actin overexpression, a novel, Hof1‐dependent actin belt is formed at the bud neck of anaphase cells. The physiological role of this belt might be related to that of the similar structure observed in dividing fission yeast.
In vitro assembly of a complete, pentaglycine interpeptide bridge containing cell wall precursor (lipid II‐Gly5) of Staphylococcus aureus
Authors: Schneider Tanja , Senn Maria Magdalena , Berger‐Bächi Brigitte , Tossi Alessandro , Sahl Hans‐Georg , Wiedemann Imke
Published: July 2004

Staphylococcus aureus peptidoglycan is cross‐linked via a characteristic pentaglycine interpeptide bridge. Genetic analysis had identified three peptidyltransferases, FemA, FemB and FemX, to catalyse the formation of the interpeptide bridge, using glycyl t‐RNA as Gly donor. To analyse the pentaglycine bridge formation in vitro, we purified the potential substrates for FemA, FemB and FemX, UDP‐MurNAc‐pentapeptide, lipid I and lipid II and the staphylococcal t‐RNA pool, as well as His‐tagged Gly‐tRNA‐synthetase and His‐tagged FemA, FemB and FemX. We found that FemX used lipid II exclusively as acceptor for the first Gly residue. Addition of Gly 2,3 and of Gly 4,5 was catalysed by FemA and FemB, respectively, and both enzymes were specific for lipid II‐Gly1 and lipid II‐Gly3 as acceptors. None of the FemABX enzymes required the presence of one or two of the other Fem proteins for activity; rather, bridge formation was delayed in the in vitro system when all three enzymes were present. The in vitro assembly system described here will enable detailed analysis of late, membrane‐associated steps of S. aureus peptidoglycan biosynthesis.
Intragenic suppression of gain‐of‐function mutations in the Escherichia coli mechanosensitive channel, MscL
Authors: Li Yuezhou , Wray Robin , Blount Paul
Published: July 2004

Mechanosensitive channels play an important role in protecting bacterial cells from osmotic downshock by serving as biological ‘pressure release valves’. One of these channels, MscL, is found throughout the bacterial kingdom, but has been most studied in Escherichia coli. The E. coli MscL is a 136‐amino‐acid protein organized as a homopentamer with each subunit containing two transmembrane segments. Previous studies have shown that several residues, including V23 and G26, are essential for normal function of MscL; very severe gain‐of‐function phenotypes in which cell growth slows or is arrested can result from residue substitutions at these positions. Through random mutagenesis and growth selection, we have generated intragenic suppressors of the V23A and G26S mutations. The suppressor mutants have been characterized by growth phenotype, Western blot and patch clamp. Most of the mutations that render phenotypic suppression are located in the transmembrane domains with additional sites lying in the periplasmic loop. In contrast, only one mutation is found in the amino‐terminal S1 domain, and none is found within the carboxyl‐terminal domain. Not only have these findings revealed functional domains and subdomains critical for MscL function, but they also predict a pair of residues that interact directly during channel opening.
Trypanosomatid histones
Authors: Alsford Sam , Horn David
Published: July 2004

The histones are responsible for packaging and regulating access to eukaryotic genomes. Trypanosomatids are flagellated protists that diverged early from the eukaryotic lineage and include parasites that cause disease in humans and other mammals. Here, we review the properties of histones in parasitic trypanosomatids, from gene organization and sequence to expression, post‐translational modification and function within chromatin. Phylogenetic and experimental analysis indicates that certain specifically conserved histone sequence motifs, particularly within the N‐terminal ‘tail’ domains, possibly represent functionally important modification substrates conserved throughout the eukaryotic lineage. For example, histone H3 contains a highly conserved methylation substrate. Trypanosomatids also possess at least three variant histones. Among these is an orthologue of H2A.Z, a histone involved in protecting ‘active’ chromatin from silencing in yeast. Histones provide docking platforms for a variety of regulatory factors. The presence of histone modification and variant histones in trypanosomatids therefore represents evidence for a network that provides the discrimination required to regulate transcription, recombination, repair and chromosome replication and segregation.
DNA‐binding specificity of AdpA, a transcriptional activator in the A‐factor regulatory cascade in Streptomyces griseus
Authors: Yamazaki Haruka , Tomono Ayami , Ohnishi Yasuo , Horinouchi Sueharu
Published: July 2004

AdpA, belonging to the AraC/XylS family, is the key transcriptional activator for a number of genes of various functions in the A‐factor regulatory cascade in Streptomyces griseus. It consists of a ThiJ/PfpI/DJ‐1‐like dimerization domain at its N‐terminal portion and a DNA‐binding domain with two helix–turn–helix motifs at its C‐terminal portion, representing a large subgroup of the AraC/XylS family. Uracil interference assay and missing T and GA interference assays on several AdpA binding sites, followed by gel mobility shift assays on systematically mutated binding sites, revealed a consensus AdpA‐binding sequence, 5′‐TGGCSNGWWY‐3′ (S: G or C; W: A or T; Y: T or C; N: any nucleotide). A dimer of AdpA bound a site including the two consensus sequences, with a space of 13–14 bp, as an inverted repeat (type I) at various positions, for example more than 200 bp upstream (−200) and 25 bp downstream (+25) from the transcriptional start point of the target gene. In addition, AdpA also bound a site including the consensus sequence in a single copy (type II) at positions, in most cases, from −40 to −50 and from −50 to −60. For transcriptional activation, some genes required simultaneous binding of a dimer of AdpA to type I and II sites, but others required only a single type I or type II site. AdpA bound mutated type I sites with various distances between the two consensus sequences with significant affinities, although the optimal distances for AdpA to bind were 13–14 bp and 2 bp. The DNA‐binding domain is therefore connected to the ThiJ/PfpI/DJ‐1‐like dimerization domain with a flexible linker. The DNA‐binding specificity of AdpA in conjunction with that of other AraC/XylS family members is discussed.
Molecular analysis of rugosity in a Vibrio cholerae O1 El Tor phase variant
Authors: Yildiz Fitnat H. , Liu Xiaole S. , Heydorn Arne , Schoolnik Gary K.
Published: July 2004

Reversible phase variation between the rugose and smooth colony variants is predicted to be important for the survival of Vibrio cholerae in natural aquatic habitats. Microarray expression profiling studies of the  rugose  and  smooth  variants  of  the  same  strain led to the identification of 124 differentially regulated genes. Further expression profiling experiments showed how these genes are regulated by the VpsR and HapR transcription factors, which, respectively, positively and negatively regulate production of VPSEl Tor, a rugose‐associated extracellular polysaccharide. The study of mutants of rpoN and rpoS demonstrated the effects of these alternative sigma factors on phase variation‐specific gene expression. Bioinformatics analysis of these expression data shows that ‘rugosity’ and ‘smoothness’ are determined by a complex hierarchy of positive and negative regulators, which also affect the biofilm, surface hydrophobicity and motility phenotypes of the organism.
Ribosome recycling factor disassembles the post‐termination ribosomal complex independent of the ribosomal translocase activity of elongation factor G
Authors: Fujiwara Toshinobu , Ito Koichi , Yamami Tohru , Nakamura Yoshikazu
Published: July 2004

Ribosome recycling factor (RRF) disassembles post‐termination ribosomal complexes in concert with elongation factor EF‐G freeing the ribosome for a new round of polypeptide synthesis. How RRF interacts with EF‐G and disassembles post‐termination ribosomes is unknown. RRF is structurally similar to tRNA and is therefore thought to bind to the ribosomal A site and be translocated by EF‐G during ribosome disassembly as a mimic of tRNA. However, EF‐G variants that remain active in GTP hydrolysis but are defective in tRNA translocation fully activate RRF function in vivo and in vitro. Furthermore, RRF and the GTP form of EF‐G do not co‐occupy the terminating ribosome in vitro; RRF is ejected by EF‐G from the preformed complex. These findings suggest that RRF is not a functional mimic of tRNA and disassembles the post‐termination ribosomal complex independently of the translocation activity of EF‐G.
Yeast genome sequencing: the power of comparative genomics
Authors: Piškur Jure , Langkjær Rikke B.
Published: July 2004

For decades, unicellular yeasts have been general models to help understand the eukaryotic cell and also our own biology. Recently, over a dozen yeast genomes have been sequenced, providing the basis to resolve several complex biological questions. Analysis of the novel sequence data has shown that the minimum number of genes from each species that need to be compared to produce a reliable phylogeny is about 20. Yeast has also become an attractive model to study speciation in eukaryotes, especially to understand molecular mechanisms behind the establishment of reproductive isolation. Comparison of closely related species helps in gene annotation and to answer how many genes there really are within the genomes. Analysis of non‐coding regions among closely related species has provided an example of how to determine novel gene regulatory sequences, which were previously difficult to analyse because they are short and degenerate and occupy different positions. Comparative genomics helps to understand the origin of yeasts and points out crucial molecular events in yeast evolutionary history, such as whole‐genome duplication and horizontal gene transfer(s). In addition, the accumulating sequence data provide the background to use more yeast species in model studies, to combat pathogens and for efficient manipulation of industrial strains.
The SC15 protein of Schizophyllum commune mediates formation of aerial hyphae and attachment in the absence of the SC3 hydrophobin
Authors: Lugones L. G. , De Jong J. F. , De Vries O. M. H. , Jalving R. , Dijksterhuis J. , Wösten H. A. B.
Published: July 2004

Disruption of the SC3 gene in the basidiomycete Schizophyllum commune affected not only formation of aerial hyphae but also attachment to hydrophobic surfaces. However, these processes were not completely abolished, indicating involvement of other molecules. We here show that the SC15 protein mediates formation of aerial hyphae and attachment in the absence of SC3. SC15 is a secreted protein of 191 aa with a hydrophilic N‐terminal half and a highly hydrophobic C‐terminal half. It is not a hydrophobin as it lacks the eight conserved cysteine residues found in these proteins. Besides being secreted into the medium, SC15 was localized in the cell wall and the mucilage that binds aerial hyphae together. In a strain in which the SC15 gene was deleted (ΔSC15) formation of aerial hyphae and attachment were not affected. However, these processes were almost completely abolished when the SC15 gene was deleted in the ΔSC3 background. The absence of aerial hyphae in the ΔSC3ΔSC15 strain can be explained by the inability of the strain to lower the water surface tension and to make aerial hyphae hydrophobic.
Light‐to‐dark transitions trigger a transient increase in intracellular Ca2+ modulated by the redox state of the photosynthetic electron transport chain in the cyanobacterium Anabaena sp. PCC7120
Authors: TORRECILLA I. , LEGANÉS F. , BONILLA I. , FERNÁNDEZ‐PIÑAS F.
Published: July 2004

Light‐to‐dark transitions represent one of the most crucial environmental stresses that photosynthetic organisms must cope with, since substantial metabolism adaptations are required in order to utilize alternative energy and carbon sources. Although signal transduction systems for changing light regimes are not sufficiently understood, calcium has been implicated in plants as a second messenger in light‐on and light‐off events. Much less is known about light signalling in cyanobacteria, but it has been shown that calcium probably performs similar signalling roles in these organisms and other prokaryotes. Herein it is reported that light‐to‐dark transitions trigger a calcium transient in aequorin expressing Anabaena sp. PCC7120. The magnitude of this transient depends on the fluence rate previously irradiated and can reach a peak height over 2 µm free calcium when the fluence rate of light is around 400 µmol photons s−1 m−2. The use of increasing calcium concentration, ethylene glycol‐bis (β‐aminoethylether) N,N,N′,N′‐tetraacetic acid (EGTA), verapamil and trifluoperazine indicated that these transients are originated by a calcium influx probably through verapamil‐sensitive Ca2+ channels and are probably modulated by calcium‐binding proteins. Experiments with different light spectral qualities and the photosynthetic inhibitors 3‐(3,4 dichlorophenyl)1,1,dimelthylurea (DCMU) and 3,5‐dibromo‐3‐methyl‐b‐isopropyl‐p‐benzoquinone (DBMIB) indicate that the calcium transient triggered by the light‐to‐dark transition is not coupled to a specific photoreceptor but rather to changes in the redox state of photosynthetic electron transport chain components other than the plastoquinone pool.
Diurnal depression of leaf hydraulic conductance in a tropical tree species
Authors: BRODRIBB T. J. , HOLBROOK N. M.
Published: July 2004

Diurnal patterns of hydraulic conductance of the leaf lamina (Kleaf) were monitored in a field‐grown tropical tree species in an attempt to ascertain whether the dynamics of stomatal conductance (gs) and CO2 uptake (Aleaf) were associated with short‐term changes in Kleaf. On days of high evaporative demand mid‐day depression of Kleaf to between 40 and 50% of pre‐dawn values was followed by a rapid recovery after 1500 h. Leaf water potential during the recovery stage was less than −1 MPa implying a refilling mechanism, or that loss of Kleaf was not linked to cavitation. Laboratory measurement of the response of Kleaf to Ψleaf confirmed that leaves in the field were operating at water potentials within the depressed region of the leaf ‘vulnerability curve’. Diurnal courses of Kleaf and Ψleaf predicted from measured transpiration, xylem water potential and the Kleaf vulnerability function, yielded good agreement with observed trends in both leaf parameters. Close correlation between depression of Kleaf, gs and Aleaf suggests that xylem dysfunction in the leaf may lead to mid‐day depression of gas exchange in this species.
Reversible decreases in the bulk elastic modulus of mature leaves of deciduousQuercusspecies subjected to two drought treatments
Authors: SAITO T. , TERASHIMA I.
Published: July 2004

Changes in leaf water relations under water stress were examined. In experiment 1, water stress was imposed by withholding irrigation to potted seedlings of deciduous oak,Quercus crispulaandQ. serrata. Changes in the pressure–volume (P–V) curve in mature leaves were followed. The leaf water potential at turgor loss (Ψl,tlp) significantly decreased after 13 d of drought treatment. The bulk elastic modulus (ɛ) significantly decreased, which contributed to the maintenance of cell turgor together with the decrease in osmotic potential. In experiment 2, water stress was imposed by notching a branch of aQ. serratatree. After the notching, the daily minimum leaf water potential (Ψl) decreased, and a significant decrease in Ψl,tlpwas observed 15 d after notching. The osmotic potential at water saturation (Ψπ,sat) did not decrease significantly until 25 d after notching whereas,ɛhad already decreased significantly within 15 d after notching and increased promptly after substantial precipitation. It was confirmed thatɛof mature leaves decreased reversibly in water stress. This response ofɛwas more rapid than that of the osmotic potential and, thus, effectively maintained cell turgor when water stress was suddenly imposed on the leaves.
Constitutive and induced resistance to pathogens in Arabidopsis thaliana depends on nitrogen supply
Authors: DIETRICH R. , PLOß K. , HEIL M.
Published: July 2004

Knowledge about the induced pathogen resistance of plants is rapidly increasing, but little information exists on its dependence on abiotic growing conditions. Arabidopsis thaliana plants that had been cultivated under different nitrogen regimes were treated with BION®, a chemical resistance elicitor. The activities of three enzyme classes functionally involved in resistance (chitinase, chitosanase and peroxidase) were quantified over 8 d following treatment as resistance markers. Constitutive levels of three markers and the induced level of peroxidase and chitinase activity were significantly lower under limiting nitrogen supply. Under such conditions the increase of chitosanase activity after resistance induction was severely delayed, although the induced maximum activity of chitosanase was not significantly affected. Total soluble protein content decreased during the first 12 h after resistance elicitation. Thereafter, the induced plants cultivated under high N conditions reached higher protein contents than controls, whereas N‐limited induced plants continuously had reduced protein contents. A plant's investment in resistance‐related compounds can be severely constrained under limiting nitrogen supply.
Facies and basin architecture of the Late Carboniferous Salvan‐Dorénaz continental basin (Western Alps, Switzerland/France)
Authors: Capuzzo Nicola , Wetzel Andreas
Published: July 2004

The Salvan‐Dorénaz Basin formed during the Late Palaeozoic within the Aiguilles‐Rouges crystalline basement (Western Alps) as an asymmetric, intramontane graben elongated in a NE–SW direction and bounded by active faults. At least 1700 m of fluvial, alluvial fan and volcanic deposits provide evidence for a strong tectonic influence on deposition with long‐term, average subsidence rates of > 0·2 mm yr−1. The early basin fill was associated with coarse‐grained alluvial fans that were dominated by braided channels (unit I). These issued from the south‐western margin of the basin. The fans then retreated to a marginal position and were overlain by muddy floodplain deposits of an anastomosed fluvial system (unit II) that drained towards the NE. Deposition of thick muds resulted from a reduction in the axial fluvial gradient caused by accelerated tectonic subsidence. Overlying sand‐rich meandering river deposits (unit III) document a reversal in the drainage direction from the NE to the SW caused by synsedimentary tectonism, reflecting large‐scale topographic reorganization in this part of the Variscides with subsidence now preferentially in the W and SW and uplift in the E and NE. Coarse‐grained alluvial fan deposits (unit IV) repeatedly prograded into, and retreated from, the basin as documented by coarsening‐upward cycles tens of metres thick reflecting smaller scale tectonic cycles. Volcanism was active throughout the evolution of the basin, and U/Pb isotopic dating of the volcanic deposits restricts the time of basin development to the Late Carboniferous (308–295 Ma).40Ar/39Ar ages of detrital white mica indicate rapid tectonic movements and exhumation of the nearby basement. In unit I, youngest ages are close to that of the host sediment, but the age spectrum is wide. In unit II, high subsidence and/or sedimentation rates coincide with very narrow age spectra, indicating small, homogeneous catchment areas. In unit III, age spectra became wider again and indicate growing catchment areas.
Stratigraphic evolution of an aeolian erg margin system: the Permian Cedar Mesa Sandstone, SE Utah, USA
Authors: Mountney Nigel P. , Jagger Alison
Published: July 2004

The Permian Cedar Mesa Sandstone of south‐east Utah is a predominantly aeolian succession that exhibits a complex spatial variation in sedimentary architecture which, in terms of palaeogeographic setting, reflects a transition from a dry erg centre, through a water table‐controlled aeolian‐dominated erg margin, to an outer erg margin subject to periodic fluvial incursion. The erg margin succession represents a wet aeolian system, accumulation of which was controlled by progressive water table rise coupled with ongoing dune migration and associated changes in the supply and availability of sediment for aeolian transport. Variation in the level of the water table relative to the depositional surface determined the nature of interdune sedimentary processes, and a range of dry, damp and wet (flooded) interdune elements is recognized. Variations in the geometry of these units reflect the original morphology and the migratory behaviour of spatially isolated dry interdune hollows in the erg centre, locally interconnected damp and/or wet interdune ponds in the aeolian‐dominated erg margin and fully interconnected, fluvially flooded interdune corridors in the outer erg margin. Relationships between aeolian dune and interdune units indicate that dry, damp and wet interdune sedimentation occurred synchronously with aeolian bedform migration. Temporal variation in the rates of water‐table rise and bedform migration determined the angle of climb of the erg margin succession, such that accumulation rates increased during periods of rapidly rising water table, whereas sediment bypassing (zero angle of climb) occurred in the aftermath of flood events in response to periods of elevated but temporarily static water table. During these periods in the outer erg margin, the expansion of fluvially flooded interdunes in front of non‐climbing but migrating dunes resulted in the amalgamation of laterally adjacent interdunes and the generation of regionally extensive bypass (flood) supersurfaces. A spectrum of genetic depositional models is envisaged that accounts for the complex spatial and temporal evolution of the Cedar Mesa erg margin succession.
Depositional controls on Palaeoproterozoic iron formation accumulation, Gogebic Range, Lake Superior region, USA
Authors: Pufahl Peir K. , Fralick Philip W.
Published: July 2004

Shallowing‐upward, decametre‐scale, Palaeoproterozoic iron formation cycles in northern Wisconsin record the combined effects of tectonism and changing oceanographic conditions on a storm‐dominated shelf. Cycles consist of a lower unit of laminated, Fe‐ and Si‐rich chemical mudstone that is transitional into an upper unit dominated by trough cross‐stratified chert grainstone. Grainstone lenses become progressively thicker upwards in cycles with the largest at cycle tops, where they are sharply overlain by a unit of slumped chemical mudstone. The cycles developed through progradation when offshore‐directed storm currents transported chert sand intraclasts that were formed in nearshore settings into middle and distal shelf environments. Abrupt subsidence events, probably resulting from normal faulting associated with extensional tectonism, repeatedly terminated chert grainstone accumulation and may also have generated the slumped units at cycle boundaries. The episodic storm currents are also interpreted to have transported biologically oxygenated waters from the shallow‐water, inner shelf into otherwise anoxic bottom waters of the strongly stratified distal shelf. The consequence of such transport and mixing was rapid deposition of chemical mud, mainly as precipitated Fe‐oxide. In many cases, the resultant decrease in Fe2+ in the water column, together with pelagic inorganic precipitation of SiO2 and rainout of terrigenous clays, resulted in submillimetre‐ to millimetre‐thick, chemically graded laminae. The concomitant decreasing Fe2+/Mn2+ ratio also led to increasing Mn‐compound precipitation and enrichment in the upper portions of some chemically graded layers.
Differentiating the effect of episodic tectonism and eustatic sea‐level fluctuations in foreland basins filled by alluvial fans and axial deltaic systems: insights from a three‐dimensional stratigraphic forward model
Authors: Clevis Quintijn , De Boer Poppe L. , Nijman Wouter
Published: July 2004

Many studies of foreland basins have recognized a hierarchical organization in the stacking of sequences deposited by axial‐deltaic and alluvial fan systems. The hierarchy is often explained in terms of the competing control of eustasy and pulsed tectonic subsidence and the different frequencies at which these processes operate. Unravelling the relative contributions of tectonic and eustatic controls on the sequence stacking pattern is a fundamental question in foreland basin analysis, yet this is difficult because of the lack of independent stratigraphic evidence. In this study, a three‐dimensional numerical model is presented, which aids in the interpretation of alluvial successions in foreland basins filled by transverse and axial depositional systems, under conditions of variable tectonism and eustatic sea‐level change. The tectono‐sedimentary model is capable of simulating the hierarchical stratigraphic response to both eustatic and tectonic forcing, and is of higher resolution than previous models of foreland basin filling. Numerical results indicate that the onset of tectonic activity is reflected by rapid retrogradation of both depositional systems and by widespread flooding and onlap of carbonate sediments. Syntectonic fluvial patterns on the axial‐deltaic plain are dominated by bifurcating channels, swiftly relocating in response to the general rise in relative sea level induced by flexural subsidence. The resulting surface morphology of the axial delta is convex upwards. Syntectonic eustatic sea‐level fluctuations result in parasequence‐scale packages of retrograding and prograding fan and delta sediments bounded by minor flooding surfaces and type 2 sequence boundaries. Incised channels are rare within the syntectonic parasequences and are formed only during phases of tectonic quiescence when eustatic falls are no longer compensated by the subsidence component in the rise in relative sea level. Suites of amalgamating, axial channels corresponding to multiple eustatic falls delineate the resulting type 1 unconformities. Coarse‐grained, incised‐channel fills are found in the zone between the alluvial fan fringes and the convex‐upward body of the axial delta, as the axial streams tend to migrate towards this zone of maximum accommodation.
Shallow slides and pockmark swarms in the Eivissa Channel, western Mediterranean Sea
Authors: Lastras G. , Canals M. , Urgeles R. , Hughes‐Clarke J. E. , Acosta J.
Published: July 2004

Four slides, the Ana, Joan, Nuna and Jersi slides, have been imaged on the seafloor along the Balearic margin of the Eivissa Channel in the western Mediterranean. They have areas of up to 16 km2 and occur in water depths ranging between 600 and 900 m. Volumes range from 0·14 to 0·4 km3. Their headwall scarps, internal architecture and associated deposits are characterized using a combination of swath bathymetry data and very high‐resolution seismic reflection profiles. In general, they show horseshoe‐shaped headwall scarps and distinct depositional lobes with positive relief. Internally, the slide bodies are mostly composed of transparent seismic facies. Chaotic facies are observed at the toe of some of the slides, and blocks of coherent stratified facies embedded in the slide deposit have also been identified. The reflection profiles demonstrate that the four slides share the same slip horizon, which corresponds to a distinctive continuous, high‐amplitude reflector. Furthermore, the geometry of the headwall scars of the Nuna and Ana slides reveals evidence of pockmarks, and fluid escape features are also present further upslope. This indicates a possible link between fluid escape features and destabilization of the upper sediment layers. In addition, these well‐characterized slides demonstrate the pitfalls associated with calculating the volume of the slide masses using headwall scarp heights and the assumed preslide seafloor topography in the absence of seismic data. The internal structure also demonstrates that transport distances within the slides are generally low and poorly characterized by headwall scarp to slide toe lengths.
Implementing a rural programme of prevention of mother‐to‐child transmission of HIV in Zimbabwe: first 18 months of experience
Authors: Perez Freddy , Mukotekwa Tarisai , Miller Anna , Orne‐Gliemann Joanna , Glenshaw Monica , Chitsike Inam , Dabis François
Published: July 2004

Objective  To report on activities and lessons learned during the first 18 months of a rural programme of prevention of mother‐to‐child transmission of HIV (PMTCT) in Zimbabwe.

Methods  The PMTCT services were introduced in Murambinda Mission Hospital (120 beds), Buhera, in 2001. Programme strategies consisted in recruiting counselling staff, training health professionals, improving mother–child health (MCH) facilities and conducting information, education and communication activities within the community to address HIV/AIDS awareness and stigma. The following components were implemented within MCH services: voluntary counselling and testing of HIV using rapid testing, nevirapine short regimen proposed to all HIV‐infected mothers identified and their newborns, support to exclusive breastfeeding for 6‐ and 18‐month mother–child follow‐up. Routine monitoring data collected from August 2001 to February 2003 were used to estimate programme uptake.

Results  Of 2471 pregnant women using antenatal services, 2298 were pre‐test counselled, the acceptance of HIV testing reached 92.9%. Of the women who decided to take an HIV test, 1588 (74.3%) returned to collect their result. Overall HIV prevalence was 20.4% (n = 437); 326 of the HIV‐positive women were counselled and 104 (24%) received complete mother–child antiretroviral prophylaxis.

Conclusions  Acceptability of HIV testing after counselling has remained above 90% since the onset of the programme. Collection of test results and mother–child follow‐up are among the most challenging activities of the programme. A district approach and community participation are critical to develop PMTCT programmes in rural settings, even with reasonably good MCH services.
Epidemiology of community‐acquired and nosocomial bloodstream infections in tropical Australia: a 12‐month prospective study
Authors: Douglas Mark W. , Lum Gary , Roy Jhumur , Fisher Dale A. , Anstey Nicholas M. , Currie Bart J.
Published: July 2004

Objectives  To define the relative incidence of organisms causing blood stream infections in a tropical setting with a very low prevalence of human immunodeficiency virus infection (<1%).

Methods  A 12‐month prospective study of blood stream infections in 2000 at Royal Darwin Hospital in the tropical north of Australia.

Results  Significant isolates were grown from 257 sets of blood cultures. Staphylococcus aureus was the most common isolate overall (28%); 26% of these were methicillin‐resistant (MRSA). Escherichia coli was the most common cause of community‐acquired bacteraemia. Burkholderia pseudomallei caused 32% of community acquired, bacteraemic pneumonia; 6% of bacteraemias overall. Vancomycin‐resistant enterococci were not isolated. Crude mortality rates (13% overall; 9% attributable mortality) were lower than in most comparable studies.

Conclusions  The major difference between these findings and surveys performed elsewhere is the presence of B. pseudomallei as a significant cause of bacteraemic community‐acquired pneumonia. Our results demonstrate the effects of local environmental and patient characteristics on the range of organisms causing blood stream infections, and emphasize the important role of local microbiology laboratories in guiding empiric antibiotic therapy.
Spatial clustering of malaria and associated risk factors during an epidemic in a highland area of western Kenya
Authors: Brooker Simon , Clarke Siân , Njagi Joseph Kiambo , Polack Sarah , Mugo Benbolt , Estambale Benson , Muchiri Eric , Magnussen Pascal , Cox Jonathan
Published: July 2004

The epidemiology of malaria over small areas remains poorly understood, and this is particularly true for malaria during epidemics in highland areas of Africa, where transmission intensity is low and characterized by acute within and between year variations. We report an analysis of the spatial distribution of clinical malaria during an epidemic and investigate putative risk factors. Active case surveillance was undertaken in three schools in Nandi District, Western Kenya for 10 weeks during a malaria outbreak in May–July 2002. Household surveys of cases and age‐matched controls were conducted to collect information on household construction, exposure factors and socio‐economic status. Household geographical location and altitude were determined using a hand‐held geographical positioning system and landcover types were determined using high spatial resolution satellite sensor data. Among 129 cases identified during the surveillance, which were matched to 155 controls, we identified significant spatial clusters of malaria cases as determined using the spatial scan statistic. Conditional multiple logistic regression analysis showed that the risk of malaria was higher in children who were underweight, who lived at lower altitudes, and who lived in households where drugs were not kept at home.