bluuebunny/crossref_metadata_2025_split huggingface dataset:
The guanosine tetraphosphate (ppGpp) alarmone, DksA and promoter affinity for RNA polymerase in regulation of σ54‐dependent transcription
Authors: Bernardo Lisandro M. D. , Johansson Linda U. M. , Solera Dafne , Skärfstad Eleonore , Shingler Victoria 
Published: March 2006

SummaryThe RNA polymerase‐binding protein DksA is a cofactor required for guanosine tetraphosphate (ppGpp)‐responsive control of transcription from σ70 promoters. Here we present evidence: (i) that both DksA and ppGpp are required for in vivoσ54 transcription even though they do not have any major direct effects on σ54 transcription in reconstituted in vitro transcription and σ‐factor competition assays, (ii) that previously defined mutations rendering the housekeeping σ70 less effective at competing with σ54 for limiting amounts of core RNA polymerase similarly suppress the requirement for DksA and ppGpp in vivo and (iii) that the extent to which ppGpp and DksA affect transcription from σ54 promoters in vivo reflects the innate affinity of the promoters for σ54‐RNA polymerase holoenzyme in vitro. Based on these findings, we propose a passive model for ppGpp/DksA regulation of σ54‐dependent transcription that depends on the potent negative effects of these regulatory molecules on transcription from powerful stringently regulated σ70 promoters.
Lipid trafficking to the outer membrane of Gram‐negative bacteria
Authors: Doerrler William T. 
Published: March 2006

SummaryThe envelope of Gram‐negative bacteria is composed of two distinct lipid membranes: an inner membrane and outer membrane. The outer membrane is an asymmetric bilayer with an inner leaflet of phospholipids and an outer leaflet of lipopolysaccharide. Most of the steps of lipid synthesis occur within the cytoplasmic compartment of the cell. Lipids must then be transported across the inner membrane and delivered to the outer membrane. These topological features combined with the ability to apply the tools of biochemistry and genetics make the Gram‐negative envelope a fascinating model for the study of lipid trafficking. In addition, as lipopolysaccharide is essential for growth of most strains and is a potent inducer of the mammalian innate immune response via activation of Toll‐like receptors, Gram‐negative lipid transport is also a promising target for the development of novel antibacterial and anti‐inflammatory compounds. This review focuses on recent developments in our understanding of lipid transport across the inner membrane and to the outer membrane of Gram‐negative bacteria.
Identification of Bacillus subtilis	σW‐dependent genes that provide intrinsic resistance to antimicrobial compounds produced by Bacilli
Authors: Butcher Bronwyn G. , Helmann John D. 
Published: March 2006

Summary Bacillus subtilis produces many antibiotics of varying structures and specificity. Here we identify a prominent role for σW, an extracytoplasmic function (ECF) sigma factor, in providing intrinsic resistance to antimicrobial compounds produced by other Bacilli. By using a panel of B. subtilis mutants disrupted for each of the 30 known σW‐dependent operons we identified resistance genes for at least three different antimicrobial compounds. The ydbST and fosB genes contribute to resistance to antimicrobial compound(s) produced by B. amyloliquefaciens FZB42, the yqeZyqfAB operon provides resistance to the SPβ prophage‐encoded bacteriocin sublancin, and the yknWXYZ operon and yfhL provide resistance to the antimicrobial peptide SdpC. YfhL encodes a paralogue of SdpI, a membrane protein that provides immunity to SdpC. In competition experiments, we identify σW as a key factor in allowing B. subtilis to resist antibiotic killing and encroachment by competing strains. Together with the previous observation that σW provides inducible resistance against the Streptomyces antibiotic fosfomycin, these studies support the notion that σW controls an antibiosis regulon important in the microbial ecology of soil bacteria.
Oligonucleotide cleavage and rejoining by topoisomerase III from the hyperthermophilic archaeon Sulfolobus solfataricus: temperature dependence and strand annealing‐promoted DNA religation
Authors: Chen Liang , Huang Li 
Published: March 2006

SummaryTopoisomerase III from the hyperthermophilic archaeon Sulfolobus solfataricus (Sso topo III) is optimally active in DNA relaxation at 75°C. We report here that Sso topo III‐catalysed DNA cleavage and religation differed significantly in temperature dependence: the enzyme was most active in cleaving ssDNA containing a cleavage site at 25–50°C, but was efficient in rejoining the cleaved DNA strand only at higher temperatures (e.g. ≥ 45°C). The failure of Sso topo III to rejoin the cleaved DNA strand efficiently appeared to be responsible for the inability of the enzyme to relax negatively supercoiled DNA at low temperature (e.g. 25°C). Intriguingly, Sso topo III facilitated DNA annealing although it showed higher affinity for ssDNA than for dsDNA. Religation of the DNA strand cleaved by Sso topo III was drastically enhanced when the DNA was allowed to anneal to a complementary non‐cleaved oligonucleotide, presumably as a result of destabilization of the interaction between the enzyme and the cleaved strand through the formation of duplex DNA. A region in the non‐cleaved strand corresponding to a sequence containing six bases on the 5′ side and two bases on the 3′ side of the cleavage site in the cleaved strand was crucial to the annealing‐promoted religation. However, the annealing‐promoted religation was relatively insensitive to mismatches in this region and the region conserved for oligonucleotide cleavage, except for that at the 5′ end of the broken strand. These results suggest that Sso topo III is well suited for a role in DNA rewinding, whether it leads to homoduplex or heteroduplex formation.
Modification of intracellular levels of glutathione‐dependent formaldehyde dehydrogenase alters glutathione homeostasis and root development
Authors: ESPUNYA M. CARME , DÍAZ MAYKELIS , MORENO‐ROMERO JORDI , MARTÍNEZ M. CARMEN 
Published: March 2006

ABSTRACTGlutathione (GSH)‐dependent formaldehyde dehydrogenase (FALDH) is a highly conserved medium‐chain dehydrogenase reductase and the main enzyme that metabolizes intracellular formaldehyde in eukaryotes. It has been recently shown that it exhibits a strong S‐nitrosoglutathione (GSNO) reductase activity and could be a candidate to regulate NO‐signalling functions. However, there is a lack of knowledge about the tissue distribution of this enzyme in plants. Here, we have studied the localization and developmental expression of the enzyme using immunolocalization and histochemical activity assay methods. We conclude that FALDH is differentially expressed in the organs of Arabidopsis thaliana mature plants, with higher levels in roots and leaves from the first stages of development. Spatial distribution of FALDH in these two organs includes the main cell types [epidermis (Ep) and cortex (Cx) in roots, and mesophyll in leaves] and the vascular system. Arabidopsis thaliana mutants with modified levels of FALDH (both by over‐ and under‐expression of the FALDH‐encoding gene) show a significant reduction of root length, and this phenotype correlates with an overall decrease of intracellular GSH levels and alteration of spatial distribution of GSH in the root meristem. Transgenic roots are partially insensitive to exogenous GSH, suggesting an inability to detect reduction–oxidation (redox) changes of the GSH pool and/or maintain GSH homeostasis.
The Reduction of Serum B‐Lymphocyte Activating Factor levels following Quinacrine Add‐On Therapy in Systemic Lupus Erythematosus
Authors: Toubi E. , Kessel A. , Rosner I. , Rozenbaum M. , Paran D. , Shoenfeld Y. 
Published: March 2006

AbstractB‐Lymphocyte‐activating factor (BAFF/BLyS) is a survival factor for B cells, belonging to the tumor necrosis ligand super family. Serum BAFF levels have been found to be elevated in patients with systemic lupus erythematosus (SLE). Neutralization of BAFF activity was suggested as an additional therapeutic approach in SLE. To determine the effect of add‐on Quinacrine (Qn) treatment on serum BAFF levels and the effect of this treatment on SLE disease activity index (SLEDAI), antidsDNA and anticardiolipin (aCL) antibody levels, we treated 29 stable SLE patients, who were maintained on prednisolone and hydroxychloroquine and in some on azathioprine (AZT), with additional Qn (100 mg/d) with an aim to further reduce disease activity. SLEDAI, antidsDNA, aCL antibodies and serum BAFF levels were assessed before and 3 months after the addition of Qn. Three months following Qn initiation, a reduction in SLEDAI was noticed in 19/29 patients (mean 8.8 ± 2.3 to 3.3 ± 1.5,P = 0.009), followed by reduction or discontinuation of prednisolone in all patients and the discontinuation of AZT in five patients. Serum BAFF levels were significantly reduced in 8/12 patients (mean 6.3 ± 0.5 to 3.0 ± 0.56 ng/mlP = 0.0001). This reduction was found in correlation with a decrease in aCL titres. However, the decrease in SLEDAI scores and antidsDNA antibody titres was unrelated to the decrease in serum BAFF or aCL levels. We conclude that the addition of Qn to previous therapeutic regimens in active SLE is beneficial and seems to reduce SLEDAI scores, serum BAFF and aCL levels and therefore should be considered in many of our SLE patients before aggressive treatments are given.
Transient Appearance of Hepatic Natural Killer Cells with High Cytotoxicity and Unique Phenotype in Very Young Mice
Authors: Bai X. , Wang S. , Tomiyama‐Miyaji C. , Shen J. , Taniguchi T. , Izumi N. , Li C. , Bakir H. Y. , Nagura T. , Takahashi S. , Kawamura T. , Iiai T. , Okamoto H. , Hatakeyama K. , Abo T. 
Published: March 2006

AbstractThere were few natural killer (NK) cells in the liver in very young mice at the age of 1–2 weeks. This was because the cell yield from the liver of young mice was low. The percentage of NK cells in the liver of young mice, however, was almost comparable with that in the liver of adult mice. Lymphocytes were isolated from the liver and spleen of C57BL/6 (B6) mice, and NK cytotoxicity and phenotype were herein examined in this study. NK cytotoxicity was extremely high in the liver of very young mice. This phenomenon was seen in the liver of various normal mouse strains. In contrast, the appearance of high cytotoxicity was not seen in NK cells of the spleen, irrespective of mouse strains. The quality of NK cells in the liver of young mice was different from that in adult mice. NK cells in the liver of young mice were mainly CD69+Mac‐1– Fas ligand+, whereas those in the liver of adult mice were CD69–Mac‐1+ Fas ligand–. These results revealed that the quality of hepatic NK cells changes in the process of ageing. Namely, liver NK cells in very young mice temporarily show the highest NK cytotoxicity and a unique activated phenotype. Physiological meaning of the present phenomenon was discussed.
High‐Altitude Climate Therapy Reduces Local Airway Inflammation and Modulates Lymphocyte Activation
Authors: Karagiannidis C. , Hense G. , Rueckert B. , Mantel P. Y. , Ichters B. , Blaser K. , Menz G. , Schmidt‐Weber C. B. 
Published: March 2006

AbstractHigh‐altitude climate therapy is a well‐established therapeutic option, which improves clinical symptoms in asthma. However, little is known about the underlying immunological mechanisms. The study investigates the influence of high‐altitude climate therapy on airway inflammation and cellular components of specific and unspecific immune response. Exhaled NO significantly decreased within 3 weeks of therapy in patients with allergic and intrinsic, moderate and severe asthma. Interleukin‐10 (IL‐10)‐secreting peripheral blood mononuclear cells (PBMC) increased within 3 weeks of therapy in six of 11 patients, whereas transforming growth factor‐β1‐secreting PBMC remained stable. Furthermore, monocyte activation, assessed by CD80 expression significantly decreased during therapy. The frequency of CRTH2‐expressing T cells decreased, while regulatory T cells (Treg) remained stable. FOXP3 and GATA‐3 mRNA expression in CD4+ T cells did not change, while interferon‐γ and IL‐13 mRNA expression decreased in eight of 10 patients. The current data demonstrate that high‐altitude climate therapy reduces local airway inflammation. Furthermore, monocytes switch towards a tolerogenic phenotype under high‐altitude climate therapy. The Treg/Th2 ratio increases; however, because of the absence of antigens/allergens, no de novo differentiation of Th2 nor Treg cells is observed. The high‐altitude climate therapy therefore may form the immunological basis for the endogenous control of allergen‐driven diseases.
Human Cell Lines Used in a Micro Neutralization Test for Measuring Influenza‐Neutralizing Antibodies
Authors: Mittelholzer C. M. , Brokstad K. A. , Pauksens K. , Jonsson R. , Brytting M. , Linde A. 
Published: March 2006

AbstractAn in situ neutralization test (NT) including ELISA for the measurement of influenza antigen was developed and evaluated. Two human cell lines, fibroblasts (HS27) cells and salivary gland epithelial duct (HSG) cells, were compared with Madin‐Darby Canine Kidney (MDCK) cells. The viral production in the human cell lines was lower than that for MDCK cells, which influenced the results of the assay in the HSG and HS27 cells. However, when lowering the infectious dose, the NT using HS27 cells gave a sensitive and stable assay with low background in the ELISA. The NT titres were very low when using HSG cells compared to MDCK cells. The HS27 NT was used to analyze the humoral response after an influenza A infection in patients from a placebo‐controlled zanamivir study. We found no differences in NT titres between patients treated with zanamivir or placebo. The MDCK and HS27 NT gave higher titres and more pronounced titre differences than the gold standard haemagglutinin inhibition (HAI) assay. Compared to the HAI assay, the sensitive NT using HS27 cells also revealed heterologous NT‐titre rises after influenza infection in the patients.
Significance of Alterations in PBMC Immunophenotype of Children with Chronic Viral Hepatitis C – the Role of Dendritic Cells
Authors: Mozer‐Lisewska I. , Dworacki G. , Kaczmarek E. , Slużewski W. , Kaczmarek M. , Woźniak A. , Żeromski J. 
Published: March 2006

AbstractThere are differences in the clinical course of chronic viral hepatitis C between adults and children, but it is generally accepted that the disease has cell‐mediated immune background. The aim of this study was to evaluate PBMC subsets in children with chronic hepatitis C before treatment in order to find some predictive factors, useful for patients management. Several PBMC subsets, in particular lymphoid and dendritic cell (DC) ones, were tested by flow cytometry in HCV+ paediatric patients (n = 46) and in control children matched in terms of age and sex (n = 20). Data were subjected to extensive statistics. It was found that cells with cytotoxic potential such as CD8+CD28– T cells, NK and NKT cells as well as lineage–HLA‐DR+ DC were increased in per cent values, while CD4+ T cells and CD4:CD8 ratio were decreased in hepatitis C group. In HCV+ patients, CD4+ T cells were inversely correlated with alanine aminotransferase (ALT) levels and with viraemia. DC subset of myeloid origin (CD11c+) assessed both in per cent values and as mean fluorescence intensity (MFI) of HLA‐DR expression was shown to be downregulated in hepatitis patients, in spite of increased numbers. To conclude, PBMC subsets, and in particular DC, are affected by HCV chronic infection in children, reflected by the correlation with clinical parameters, such as ALT and viraemia.
Interplay between erosion and tectonics in the Western Alps
Authors: Malusà Marco G. , Vezzoli Giovanni 
Published: March 2006

AbstractBedrock fission‐track analysis, high‐resolution petrography and heavy mineral analyses of sediments are used to investigate the relationships between erosion and tectonics in the Western Alps. Along the Aosta Valley cross‐section, exhumation rates based on fission‐track data are higher in the fault‐bounded western block than in the eastern block (0.4–1.5 vs. 0.1–0.3 mm yr−1). Erosion rates based on the analysis of bed‐load in the Dora Baltea drainage display the same pattern and have similar magnitudes in the relative sub‐basins (0.4–0.7 vs. 0.04–0.08 mm yr−1). Results highlight that climate, relief and lithology are not the controlling factors of erosion in the Western Alps. The main driving force behind erosion is instead tectonics that causes the differential upward motion of crustal blocks.
Delamerian‐aged metamorphism in the southern Curnamona Province, Australia: implications for the evolution of the Mesoproterozoic Olarian Orogeny
Authors: Rutherford Lachlan , Hand Martin , Mawby Joanna 
Published: March 2006

AbstractMonazite electron microprobe U–Th–Pb and garnet Sm–Nd isotopic data from metapelitic assemblages in the Willyama Supergroup in the southern Curnamona Province, south‐central Australia, indicate that the terrain underwent regional greenschist to amphibolite‐grade metamorphism during the c. 500 Ma Delamerian Orogeny. The Delamerian‐aged mineral assemblages include prograde garnet–staurolite and kyanite‐bearing associations that overprint andalusite‐ and sillimanite‐bearing assemblages that are interpreted to have developed during the c. 1600 Ma Olarian Orogeny. Importantly, the development of secondary kyanite‐bearing assemblages in the southern Curnamona Province has been used previously to suggest that the Olarian Orogeny followed an anticlockwise P–T evolution. If such assemblages are the product of c. 500 Ma metamorphism, then the anticlockwise P–T path is an apparent path, due to the overprint of a distinct metamorphic cycle c. 1100 Ma later. Making such distinctions is therefore extremely important when using the textural and metamorphic evolution of polycyclic terrains to model the thermal behaviour of the crust during orogeny. This study highlights the utility of in situ geochronology, linking age data to petrologically important phases and assemblages.
50 Myr recovery from the largest negative δ13C excursion in the Ediacaran ocean
Authors: Le Guerroué Erwan , Allen Philip A. , Cozzi Andrea , Etienne James L. , Fanning Mark 
Published: March 2006

AbstractSedimentary rocks deposited during the Ediacaran period (∼630–542 Ma) contain carbonates whose carbon isotopic ratios show a marked negative excursion consisting of a precipitous drop from +5‰ to −12‰, followed by a sub‐linear recovery to positive δ13C values. Isotopic ages (U/Pb) and thermal subsidence modelling are combined to constrain the excursion in time and indicate an onset at ∼600 Ma, and duration of recovery of approximately 50 Myr. The excursion is widely recognized in Oman and has potential correlatives in Ediacaran strata elsewhere, and may thus represent a characteristic feature of the Ediacaran period. The amplitude of this carbon isotope excursion far exceeds those of other Neoproterozoic anomalies. The isotopic trend of negative excursion and long‐term recovery spanned at least one short‐lived glacial episode (at 580 Ma), but appears unrelated to glaciation, which indicates that negative anomalies in the Neoproterozoic marine carbon isotope record are not directly or uniquely linked to ice ages.
Simultaneous flux and current measurement from single plant protoplasts reveals a strong link between K+ fluxes and current, but no link between Ca2+ fluxes and current
Authors: Gilliham Matthew , Sullivan Wendy , Tester Mark , Tyerman Stephen D. 
Published: March 2006

SummaryWe present a thorough calibration and verification of a combined non‐invasive self‐referencing microelectrode‐based ion‐flux measurement and whole‐cell patch clamp system as a novel and powerful tool for the study of ion transport. The system is shown to be capable of revealing the movement of multiple ions across the plasma membrane of a single protoplast at multiple voltages and in complex physiologically relevant solutions. Wheat root protoplasts are patch clamped in the whole‐cell configuration and current–voltage relations obtained whilst monitoring net K+ and Ca2+ flux adjacent to the membrane with ion‐selective electrodes. At each voltage, net ion flux (nmol m−2 sec−1) is converted to an equivalent current density (mA m−2) taking into account geometry and electrode efficiency, and compared with the net current density measured with the patch clamp system. Using this technique, it is demonstrated that the K+‐permeable outwardly rectifying conductance (KORC) is responsible for net outward K+ movement across the plasma membrane [1:1 flux‐to‐current ratio (1.21 ± 0.14 SEM, n = 15)]. Variation in the K+ flux‐to‐current ratio among single protoplasts suggests a heterogeneous distribution of KORC channels on the membrane surface. As a demonstration of the power of the technique we show that despite a significant Ca2+ permeability being associated with KORC (analysis of tail current reversal potentials), there is no correlation between Ca2+ flux and KORC activity. A very significant observation is that large Ca2+ fluxes are electrically silent and probably tightly coupled to compensatory charge movements. This analysis demonstrates that it is mandatory to measure flux and currents simultaneously to investigate properly Ca2+ transport mechanisms and selectivity of ion channels in general.
Sequencing and characterization of telomere and subtelomere regions on rice chromosomes 1S, 2S, 2L, 6L, 7S, 7L and 8S
Authors: Mizuno Hiroshi , Wu Jianzhong , Kanamori Hiroyuki , Fujisawa Masaki , Namiki Nobukazu , Saji Shoko , Katagiri Satoshi , Katayose Yuichi , Sasaki Takuji , Matsumoto Takashi 
Published: March 2006

SummaryTelomeres, which are important for chromosome maintenance, are composed of long, repetitive DNA sequences associated with a variety of telomere‐binding proteins. We characterized the organization and structure of rice telomeres and adjacent subtelomere regions on the basis of cytogenetic and sequence analyses. The length of the rice telomeres ranged from 5.1 to 10.8 kb, as revealed by both fibre‐fluorescent in situ hybridization and terminal restriction‐fragment assay. Physical maps of the chromosomal ends were constructed from a fosmid library. This facilitated sequencing of the telomere regions of chromosomes 1S, 2S, 2L, 6L, 7S, 7L and 8S. The resulting sequences contained conserved TTTAGGG telomere repeats, which indicates that the physical maps partly covered the telomere regions of the respective chromosome arms. These repeats were organized in the order of 5′‐TTTAGGG‐3′ from the chromosome‐specific region, except in chromosome 7S, in which seven inverted copies also existed in tandem array. Analysis of the telomere‐flanking regions revealed the occurrence of deletions, insertions, or chromosome‐specific substitutions of single nucleotides within the repeat sequences at the junction between the telomere and subtelomere. The sequences of the 500‐kb regions of the seven chromosome ends were analysed in detail. A total of 598 genes were predicted in the telomeric regions. In addition, repetitive sequences derived from various kinds of retrotransposon were identified. No significant evidence for segmental duplication could be detected within or among the subtelomere regions. These results indicate that the rice chromosome ends are heterogeneous in both sequence and characterization.